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Results from PredictProtein for predict_h23874

TOC for file /home/phd/server/work/predict_h23874

The following information has been received by the server (TOC)
PROSITE motif search (A Bairoch; P Bucher and K Hofmann) (TOC)
MAXHOM alignment header (TOC)
MAXHOM alignment (TOC)
CYSPRED prediction(P Fariselli,P Riccobelli & R Casadio) (TOC)
PHD information about accuracy (TOC)
PHD predictions (TOC)
GLOBE prediction of globularity (TOC)
TOPITS (threading) header (TOC)
TOPITS (threading) results in MSF format (TOC)
TOPITS (threading) results in HSSP format (TOC)
TOPITS (threading) results in STRIP format (TOC)
Threading results in TOPITS format (TOC)

END of TOC

BEG of results for file /home/phd/server/work/predict_h23874

The following information has been received by the server

reference predict_h23874 (Jan 23, 2001 04:42:55)
reference pred_h23874 (Jan 23, 2001 04:43:05)
PPhdr from: pagomez@cnb.uam.es
PPhdr resp: MAIL
PPhdr orig: HTML
PPhdr want: HTML
PPhdr password(###)
prediction of: - threading             (TOPITS)-
return msf format
ret topits hssp
ret topits strip
ret topits own
ret html
ret html detail
ret html perline=60
ret html detail perline=60
# default: single protein sequence description=curso3
MINRTDCNENSYLEIHNNEGRDTLCFANAGTMPVAIYGVNWVESGNNVVT
LQFQRNLSDPRLETITLQKWGSWNPGHIHEILSIRIY

PROSITE motif search (A Bairoch; P Bucher and K Hofmann)

TOP - BOTTOM - ProSite

-------------------------------------------------------------
Pattern-ID: ASN_GLYCOSYLATION PS00001 PDOC00001
Pattern-DE: N-glycosylation site
Pattern:    N[^P][ST][^P]
   3        NRTD
   56       NLSD

Pattern-ID: PKC_PHOSPHO_SITE PS00005 PDOC00005
Pattern-DE: Protein kinase C phosphorylation site
Pattern:    [ST].[RK]
   83       SIR

Pattern-ID: CK2_PHOSPHO_SITE PS00006 PDOC00006
Pattern-DE: Casein kinase II phosphorylation site
Pattern:    [ST].{2}[DE]
   11       SYLE

MAXHOM alignment header

--- ------------------------------------------------------------
--- MAXHOM multiple sequence alignment
--- ------------------------------------------------------------
--- 
--- MAXHOM ALIGNMENT HEADER: ABBREVIATIONS FOR SUMMARY
--- ID           : identifier of aligned (homologous) protein
--- STRID        : PDB identifier (only for known structures)
--- IDE          : percentage of pairwise sequence identity
--- WSIM         : percentage of weighted similarity
--- LALI         : number of residues aligned
--- NGAP         : number of insertions and deletions (indels)
--- LGAP         : number of residues in all indels
--- LSEQ2        : length of aligned sequence
--- ACCNUM       : SwissProt accession number
--- OMIM         : OMIM (Online Mendelian Inheritance in Man) ID
--- NAME         : one-line description of aligned protein
--- 
--- MAXHOM ALIGNMENT HEADER: SUMMARY
ID         STRID  IDE WSIM LALI NGAP LGAP LSEQ2 ACCNUM NAME                     
xyn_triha  1XND    27   16   78    2   28   190 P48793 XYLANOHYDROLASE).        
--- 
--- MAXHOM ALIGNMENT: IN MSF FORMAT

--- ------------------------------------------------------------
--- 3D homologue: the known structure that appeared to have sig-
--- 3D homologue: nificant sequence identity to your protein is:
--- 3D homologue: 1XND, 
.
--- 3D homologue: Note: we do  NOT  check whether the similarity
--- 3D homologue:       is in the region for which structure has
--- 3D homologue:       been determined.  Thus, please verify!  
--- ------------------------------------------------------------

--- 
--- Version of database searched for alignment:
--- SWISS-PROT release 39.0 (5/00) with 85 249 proteins
---

MAXHOM alignment

TOP - BOTTOM - MaxHom - MView

Identities computed with respect to: (1) predict_h2380
Colored by: consensus/70% and property

                  1 [        .         .         .         .         :         . 60
1 predict_h2380     MINRTDCNENSYLEIHNNEGRDTLCFANAGTMPVAIYGVNWVESGNNVVTLQFQRNLSDP   
2 xyn_triha         -IGPGTGYSNGYYYSYWNDGHAGVTYTNGGG---GSFTVNWSNSGNFVAGKGWQPGtrNP   
  consensus/100%    .Is.sss.pNuYh..a.N-G+sslsasNuGs...u.asVNWspSGN.VsshtaQ.shpsP   
  consensus/90%     .Is.sss.pNuYh..a.N-G+sslsasNuGs...u.asVNWspSGN.VsshtaQ.shpsP   
  consensus/80%     .Is.sss.pNuYh..a.N-G+sslsasNuGs...u.asVNWspSGN.VsshtaQ.shpsP   
  consensus/70%     .Is.sss.pNuYh..a.N-G+sslsasNuGs...u.asVNWspSGN.VsshtaQ.shpsP   

                 61          .         .      ] 87
1 predict_h2380     RLETITLQKWGSWNPGHIHEILSIRIY   
2 xyn_triha         LIEYYIVENFGTYNPSTGATKL-----   
  consensus/100%    hlEhhhlppaGoaNPuphtphL.....   
  consensus/90%     hlEhhhlppaGoaNPuphtphL.....   
  consensus/80%     hlEhhhlppaGoaNPuphtphL.....   
  consensus/70%     hlEhhhlppaGoaNPuphtphL.....

CYSPRED prediction(P Fariselli,P Riccobelli & R Casadio)

TOP - BOTTOM - CYSPRED

PREDICTION OF BONDING STATE OF CYSTEINES
Network N. 1  Conservation+ Entropy
N.cys	Prob.SS		Prob.SH
7	0.049275	0.950725
25	0.049275	0.950725
###################
Network N. 2  Conservation+ Entropy + Charges
N.cys	Prob.SS		Prob.SH
7	0.988365	0.010245
25	0.053160	0.939948
###################
Network N. 3  Charge
N.cys	Prob.SS		Prob.SH
7	0.002449	0.997551
###################
Network N. 4   Conservation+ Entropy+Hydrophobicity
N.cys	Prob.SS		Prob.SH
7	0.971578	0.028427
25	0.051110	0.948892
###################
Network N. 5   Conservation+ Entropy + Charges + Hydrophobicity
N.cys	Prob.SS		Prob.SH
7	0.910539	0.089446
25	0.107506	0.892495
###################
JURY AMONG THE DIFFERENT NETWORKS
	Prob.SS	Prob.SH
N.cys	BONDED	NON-BONDED	DISULFIDE
7	0.584	0.415		YES
25	0.052	0.746		NO 
#==============================================#

PHD information about accuracy

****************************************************************************
*                                                                          *
*    PHD: Profile fed neural network systems from HeiDelberg               *
*    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~               *
*                                                                          *
*    Prediction of:			                                   *
* 	secondary structure,   			   by PHDsec		   *
* 	solvent accessibility, 			   by PHDacc		   *
* 	and helical transmembrane regions, 	   by PHDhtm		   *
*                                                                          *
*    Author:             						   *
*	Burkhard Rost							   *
*       EMBL, 69012 Heidelberg, Germany					   *
*       Internet: Rost@EMBL-Heidelberg.DE				   *
*                                                                          *
*    All rights reserved.                                                  *
*                                                                          *
****************************************************************************
*                                                                          *
*    The network systems are described in:   	                     	   *
*                                                                          *
*    PHDsec:    B Rost & C Sander: JMB, 1993, 232, 584-599.		   *
*    		B Rost & C Sander: Proteins, 1994, 19, 55-72.		   *
*    PHDacc:  	B Rost & C Sander: Proteins, 1994, 20, 216-226.		   *
*    PHDhtm:  	B Rost et al.: 	   Prot. Science, 1995, 4, 521-533.	   *
*                                                                          *
****************************************************************************

PHD predictions for predict_h23874

Different levels of data:

PHD brief
PHD normal
PHD detail

PHDsec summary overall your protein can be classified as:
mixed given the following classes:
- 'all-alpha': %H > 45% AND %E < 5%
- 'all-beta': %H < 5% AND %E > 45%
- 'alpha-beta': %H > 30% AND %E > 20%
- 'mixed': all others

Predicted secondary structure composition for your protein:

%H: 0.0 %E: 47.1 %L: 52.9

Residue composition for your protein:

%A: 3.5 %C: 2.3 %D: 3.5 %E: 6.9 %F: 2.3

%G: 6.9 %H: 3.5 %I: 9.2 %K: 1.1 %L: 8.1

%M: 2.3 %N: 12.6 %P: 3.5 %Q: 3.5 %R: 5.8

%S: 5.8 %T: 6.9 %V: 5.8 %W: 3.5 %Y: 3.5

AA : amino acid sequence

PHD_sec: PHD predicted secondary structure: H=helix, E=extended (sheet), blank=other (loop)
PHD = PHD: Profile network prediction HeiDelberg

Rel_sec: reliability index for PHDsec prediction (0=low to 9=high)
Note: for the brief presentation strong predictions marked by '*'

SUB_sec: subset of the PHDsec prediction, for all residues with an expected average accuracy > 82% (tables in header)
NOTE: for this subset the following symbols are used:
L: is loop (for which above ' ' is used)
.: means that no prediction is made for this residue, as the reliability is: Rel < 5

pH_sec: 'probability' for assigning helix (1=high, 0=low)

pE_sec: 'probability' for assigning strand (1=high, 0=low)

pL_sec: 'probability' for assigning neither helix, nor strand (1=high, 0=low)

P_3_acc: PHD predicted relative solvent accessibility (acc) in 3 states: b = 0-9%, i = 9-36%, e = 36-100%.

Rel_acc: reliability index for PHDacc prediction (0=low to 9=high)
Note: for the brief presentation strong predictions marked by '*'

SUB_acc: subset of the PHDacc prediction, for all residues with an expected average correlation > 0.69 (tables in header)
NOTE: for this subset the following symbols are used:
I: is intermediate (for which above ' ' is used)
.: means that no prediction is made for this residue, as the reliability is: Rel < 4

PHD_acc: PHD predicted relative solvent accessibility (acc) in 10 states: a value of n (=0-9) corresponds to a relative acc. of between n*n % and (n+1)*(n+1) % (e.g. for n=5: 16-25%).

PHD results (brief)

....,....1....,....2....,....3....,....4....,....5....,....6 AA MINRTDCNENSYLEIHNNEGRDTLCFANAGTMPVAIYGVNWVESGNNVVTLQFQRNLSDP PHD_sec EEEEE EEEEEE EEEEEEEEE EEEEEEE Rel_sec ***** ***** **** **** ***** **** ****** **** ** ****** P_3_acc ebeeeee ebbbb bbebeb ebbbbbbbbebbbbbbbbbbbebbb bbbeeb ee eeb Rel_acc * * ****** * * ** ....,....7....,....8....,....9 AA RLETITLQKWGSWNPGHIHEILSIRIY PHD_sec EEEEEE EEEEEEEE Rel_sec ***** ******* ******* P_3_acc ebbbbbbeebbe bbeebeeebbbebe Rel_acc * * *** *

PHD results (normal)

....,....1....,....2....,....3....,....4....,....5....,....6 AA MINRTDCNENSYLEIHNNEGRDTLCFANAGTMPVAIYGVNWVESGNNVVTLQFQRNLSDP PHD_sec EEEEE EEEEEE EEEEEEEEE EEEEEEE Rel_sec 999972888884898527885259999399974236987770689726634431599999 SUB_sec LLLLL.LLLLL.EEEE.LLLL.EEEEE.LLLL...EEEEEE.LLLL.EE.....LLLLLL P_3_acc ebeeeee ebbbb bbebeb ebbbbbbbbebbbbbbbbbbbebbb bbbeeb ee eeb Rel_acc 111211001121103000111006172100110464747260151118621220321211 SUB_acc .......................b.b.......bbbbbb.b..b...bb........... ....,....7....,....8....,....9 AA RLETITLQKWGSWNPGHIHEILSIRIY PHD_sec EEEEEE EEEEEEEE Rel_sec 288885131377699972326888879 SUB_sec .EEEEE....LLLLLLL...EEEEEEL P_3_acc ebbbbbbeebbe bbeebeeebbbebe Rel_acc 051003621231011220020755150 SUB_acc .b....b..............bbb.b.

PHD results (detail)

....,....1....,....2....,....3....,....4....,....5....,....6 AA MINRTDCNENSYLEIHNNEGRDTLCFANAGTMPVAIYGVNWVESGNNVVTLQFQRNLSDP pH_sec 1.0 pH_sec 0.9 pH_sec 0.8 pH_sec 0.7 pH_sec 0.6 pH_sec 0.5 pH_sec 0.4 pH_sec 0.3 pH_sec . 0.2 ------------------------------------------------------------ pE_sec . .... . 1.0 pE_sec ... .... ..... 0.9 pE_sec ... ..... ...... .. 0.8 pE_sec ..... ...... ...... ..... 0.7 pE_sec ..... ...... ........ ....... 0.6 pE_sec . ..... ....... ......... ........ 0.5 pE_sec . ...... ....... .......... ........ 0.4 pE_sec . ...... ........ ........... ......... 0.3 pE_sec ..... ....... ........ ............ ........... 0.2 ------------------------------------------------------------ pL_sec .... ... . ..... 1.0 pL_sec ..... ..... .. .... ... ..... 0.9 pL_sec ..... ..... .... .... .... ...... 0.8 pL_sec ..... ..... .... ..... .... ...... 0.7 pL_sec ........... ...... ..... .... ....... 0.6 pL_sec ........... ...... ..... ..... ....... 0.5 pL_sec ............ ...... ........ ...... . ......... 0.4 pL_sec ............ ........ ......... ...... ............ 0.3 pL_sec ............. ........ ......... ....................... 0.2 ------------------------------------------------------------ P_3_acc ebeeeee ebbbb bbebeb ebbbbbbbbebbbbbbbbbbbebbb bbbeeb ee eeb PHD_acc . . . 100% PHD_acc . . . . 81% PHD_acc . ..... . . . . .. .. . 64% PHD_acc . ..... . . . . . . .. .. .. 49% PHD_acc . ....... . . . .. . . . .. ...... 36% PHD_acc . ....... . . . .. . . . .. ...... 25% PHD_acc . ....... . . . .. . . . .. ...... 16% PHD_acc . ....... . ... .. . . . .. ...... 9% PHD_acc . ....... . ... .. . . . .. ...... 4% ------------------------------------------------------------ ....,....7....,....8....,....9 AA RLETITLQKWGSWNPGHIHEILSIRIY pH_sec 1.0 pH_sec 0.9 pH_sec 0.8 pH_sec 0.7 pH_sec . 0.6 pH_sec ... 0.5 pH_sec .... 0.4 pH_sec .... 0.3 pH_sec ..... . 0.2 --------------------------- pE_sec 1.0 pE_sec .... ..... 0.9 pE_sec ..... ...... 0.8 pE_sec ..... . ...... 0.7 pE_sec ...... ........ 0.6 pE_sec ...... ......... 0.5 pE_sec ...... ......... 0.4 pE_sec ....... ......... 0.3 pE_sec ....... ... .......... 0.2 --------------------------- pL_sec ... . 1.0 pL_sec ..... . 0.9 pL_sec ....... . 0.8 pL_sec ........ . 0.7 pL_sec .......... . 0.6 pL_sec .......... . 0.5 pL_sec . .............. . 0.4 pL_sec . ............... . 0.3 pL_sec .. . ................. ... 0.2 --------------------------- P_3_acc ebbbbbbeebbe bbeebeeebbbebe PHD_acc . . 100% PHD_acc . . 81% PHD_acc . . . . . 64% PHD_acc . .. . .. ... . . 49% PHD_acc . .. . .. ... . . 36% PHD_acc . .. . .. ... . . 25% PHD_acc . .. .. .. ... . . 16% PHD_acc . .. .. .. ... . . 9% PHD_acc . .. .. .. ... . . 4% ---------------------------

GLOBE prediction of globularity

--- 
--- GLOBE: prediction of protein globularity
--- 
--- nexp =    35    (number of predicted exposed residues)
--- nfit =    45    (number of expected exposed residues
--- diff =   -10.00 (difference nexp-nfit)
--- =====> your protein appears not to be globular
--- 
--- 
--- GLOBE: further explanations preliminaryily in:
---        http://www.columbia.edu/~rost/Papers/98globe.html
--- 
--- END of GLOBE

TOPITS (threading) header

--- 
--- ------------------------------------------------------------
--- TOPITS prediction-based threading 
--- ------------------------------------------------------------
--- 
--- TOPITS ALIGNMENTS HEADER: PARAMETERS
--- str:seq=  50 : structure (sec str, acc)= 50%, sequence= 50%
--- str:seq = 50 : weight structure/sequence,i.e. str= 50%, seq= 50%
--- smin = -1.00 : minimal value of alignment metric
--- smax = 2.00  : maximal value of alignment metric
--- go   = 2     : gap open penalty
--- ge   = 0.2   : gap elongation penalty
--- len1 = 87    : length of search sequence, i.e., your protein
--- 
--- TOPITS ALIGNMENTS HEADER: ABBREVIATIONS
--- RANK         : rank in alignment list, sorted according to z-score
--- EALI         : alignment score
--- LALI         : length of alignment
--- IDEL         : number of residues inserted
--- NDEL         : number of insertions
--- ZALI         : alignment zcore;  note: hits with z>3 more reliable 
--- PIDE         : percentage of pairwise sequence identity
--- LEN2         : length of aligned protein structure
--- ID2          : PDB identifier of aligned structure
--- NAME2        : name of aligned protein structure
--- IFIR         : position of first residue of search sequence
--- ILAS         : position of last residue of search sequence
--- JFIR         : PDB position of first residue of remote homologue
--- JLAS         : PDB position of last residue of remote homologue
--- 
--- TOPITS ALIGNMENTS HEADER: ACCURACY
---              : Tested on 80 proteins, TOPITS found the
---              : correct remote homologue in about 30% of
---              : the cases, detection accuracy was higher
---              : for higher z-scores (ZALI):
--- ZALI>0       : 1st hit correct in 33% of cases
--- ZALI>3       : 1st hit correct in 50% of cases
--- ZALI>3.5     : 1st hit correct in 60% of cases
--- 
--- TOPITS ALIGNMENTS HEADER: SUMMARY
 RANK   EALI LALI IDEL NDEL   ZALI PIDE LEN2  ID2 NAME2                     
    1  35.53   83   16    7   2.21   28  270 1ybv_A OL_ID: 1;                 
    2  34.40   77   38   10   2.04   40  435 1csh RATE SYNTHASE (E.C.4.1.3. 
    3  34.20   83   17    8   2.01   31  184 1cax_B ANAVALIN (JACK BEAN 7S VI 
    4  33.80   85   44    8   1.95   36  326 1qor_A UINONE OXIDOREDUCTASE COM 
    5  33.80   79   14    8   1.95   33  432 1bif _ID: 1;                   
    6  33.60   74   25    8   1.92   34  484 1cwv_A OL_ID: 1;                 
    7  32.87   68   13    4   1.81   32  358 1ece_A OL_ID: 1;                 
    8  32.47   83   24    8   1.75   33  530 1gtr_A LUTAMINYL-TRNA SYNTHETASE 
    9  32.47   73   18    7   1.75   32  471 1pfo _ID: 1;                   
   10  32.47   75   25    9   1.75   36  305 2reb CA PROTEIN (E.C.3.4.99.37 
   11  32.13   83   16    5   1.70   27  103 3chb_D MOL_ID: 1;                
   12  32.13   78   25    9   1.70   31  150 1amx L_ID: 1;                  
   13  32.13   85   23    7   1.70   26  273 6prc_L MOL_ID: 1;                
   14  31.93   71   18    6   1.67   31  397 2tys_B MOL_ID: 1;                
   15  31.87   74   16    7   1.66   35  534 1b8b_A MOL_ID: 1;                
   16  31.73   80   20    7   1.64   31  150 1bj7 L_ID: 1;                  
   17  31.53   83   25    6   1.61   28  196 1smv_A MOL_ID: 1;                
   18  31.53   84   15    6   1.61   30  195 1qhv_A MOL_ID: 1;                
   19  31.53   81   33    9   1.61   32  393 1axk_A MOL_ID: 1;                
   20  31.53   81   33    9   1.61   32  434 1cel_A 1,4-BETA-D-GLUCAN CELLOBI 
--- 
--- TOPITS ALIGNMENTS HEADER: PDB_POSITIONS FOR ALIGNED PAIR
 RANK PIDE IFIR ILAS JFIR JLAS LALI LEN2 ID2   
--- 
--- TOPITS ALIGNMENTS: SYMBOLS AND EXPLANATIONS
--- BLOCK 1      : your protein and its predicted 1D structure,
---              : i.e., secondary structure and solvent accessibility
--- line 1       : amino acid sequence (one-letter-code)
--- line 2       : predicted secondary structure:
--- H            : helix
--- E            : strand (extended)
--- L            : other (no regular secondary structure)
--- line 3       : predicted residue relative solvent accessibility
--- B            : buried, i.e., relative accessibility < 15%
--- O            : exposed (outside), i.e., relative accessibility >= 15%
---              : 
--- BLOCKS 1-20  : 20 best hits of the prediction-based threading 
---    ATTENTION : We chose to include all first 20 hit.  However,
---    ATTENTION : most of them will not constitute true remote
---    ATTENTION : homologues.  Instead, all hits with a zscore 
---    ATTENTION : (ZALI) < 3.5 are, at best, rather speculative!
---              : for each aligned protein:
--- line 1       : amino acids conserved between guide (yours) and the
---              : aligned protein (putative homologue)
--- line 1       : sequence of aligned protein
--- line 3       : secondary structure, taken from DSSP (assignment
---              : of secondary structure based on experimental coordinates)
--- line 4       : relative solvent accessibility, taken from DSSP
--- 
--- TOPITS ALIGNMENTS
   1 -  51               ....:....1....:....2....:....3....:....4....:....5
      pred               MINRTDCNENSYLEIHNNEGRDTLCFANAGTMPVAIYGVNWVESGNNVVTL
                                    EEEEE      EEEEEE     EEEEEEEEE    EEEEE
                         OBOOOOOOOBBBBOBBOBOBOOBBBBBBBBOBBBBBBBBBBBOBBBOBBBO

   1. 1ybv_A       35.53   NSTESAEEVVAAIKKN.GSDAACvaNVGVVevKIFglDIVCSNSGVVSF
                           LLHHHHHHHHHHHHHL.LLLEEEELLLLLHHHHHHLLLEEEELLLLLLL
                         M   TD  E  YL IH  EG   L FA A        G       N  V L
   2. 1csh         34.40 MLGYTDPqerLYLTIHSdeGGNvlSFAAanGLAGPLHGL.....ANQEVLl
                         HHLLLLHHHHHHHHHLLLLLLLHHHHHHHHHHLLLLLLL.....HHHHHHH
                            R     N Y EI N   RD LC  N G   V  Y V  V  G   V L
   3. 1cax_B       34.20 LRSRDPIYSNNyyEikNSQLrdIlclmNEGALFVPHYnvILVAngRAEVEL
                         ELLLLLLEEELLEEELLHHHHLEEEEELLLEEEEEEEEEEEEEELLEEEEE
                          INR         EI    GRDT C    G M  A  GVN    G   VTL
   4. 1qor_A       33.80 VInrEEDLVERLKEItdSVGRDTwcLQRRGLmsGAVTGVNLgqKGSLYVtl
                         EEELLLLHHHHHHHHLELLLHHHHLEEEEEEELLLLLLELLHHLLLLEEEH
                            R  C ENSY        RD L       M V  Y VN V      V  
   5. 1bif         33.80 FMRRIECYENSYESLDEEQDRD.LSYIK..IMDvqSYVVNRVAdqSRIVYY
                         HHHHHHHHHLLLLLLLLLLLLL.LLEEE..EELLLEEEEELLLLHHHHHHH
                             T     S      N G   L F   G  PV I        GN VVT 
   6. 1cwv_A       33.60 LADGTMSSTLSFVPVDKnsGMQGLSFTQNG.VPVSISPisYTAtgNSvvTI
                         ELLLLLLEEEEEELELLLLLLLLEEEEEEE.LLLEELLLLEEEELLLLEEE
                                            GR  L    A   PV I G NW E  N VV  
   7. 1ece_A       32.87                 HTSGREIL...DANNVPVRIAGINwfETCNYVVHG
                                         EEELLEEE...LLLLLEELLEEEELELLLLLLLLL
                         M   T C     LE   N         N  T PV     N V S N  VT 
   8. 1gtr_A       32.47 MYDFTHCISDAllEFQDNRRLYDWVLDNI.TIPveFSRLNlvMSknLLVTD
                         LHHHHHHHHHHHHHHLLLHHHHHHHHHHL.LLLLEELLLLELLLHHHHHHL
                           N TD     Y E    EG   L    A    VA   V     GN V T 
   9. 1pfo         32.47 VHNKTD.....YIETTSTegKINLDHSGaaQFEVAWDEVSYDKEGNEVLTH
                         LLEEEE.....EEEEEEEEEEEEEEELLLEEEEEEEEEEEELLLLLEEEEE
                          I R    E          G   L  A AG  PV IYG     SG    TL
  10. 2reb         32.47  IMRL..GEDRSMDvtISTGSLSLDIagAGGLpvEIYGPE..SSGKTTLTL
                          LLLL..LLLLLLLLEELLLLHHHHHHLLLLEEEEEELLL..LLLHHHHHH
                           N TDC E     IHN  G     F N  T  V   G     S       
  11. 3chb_D       32.13   NITdcAEYHNTQIhndaGkaIITFKNGATFQVEVPGSQHIDSQKKAIE.
                           LHHHHLLLLLEEEEEELLLEEEELLLLLEEEELLLLLLLLHHHHHHHH.
                          IN    NE SY  I    G   L      T      G N   SG    T 
  12. 1amx         32.13  IN....NEKSyiTIKDqqGGQQL...DLSTLNINVTGtnYY.SGQSAIT.
                          EL....LLLLLEEEEEELLLEEE...EEEEEEEEEEELEEE.LLLLHHH.
                              D   N YL  H N G     F NA  M     G   V  G  V T 
  13. 6prc_L       32.13 ILSHLDWVNnqYLNWHYNPGHmsFLFVNA..MALGLHgiLSVAngDKVKTa
                         LLHHHHHHHHHLLLHHHLHHHHHHHHHHH..HHHHHHHHHHHHLLLLLLLH
                          I R D     Y  I   E   TLC    G  P         ES      L
  14. 2tys_B       31.93  IGRAD.....YVSITDDEALetLC.RHEGIIPA.......LESSHALAhl
                          LLLLE.....EEEEEHHHHHHHHH.HHHLLLEL.......HHHHHHHHHH
                             T  NE    E  N   R  LCF         I     V     V   
  15. 1b8b_A       31.87     TQFNEQKFVELFNE..RMDLCFE...ALMCRISSLKGVKA..TVAPI
                             LLELHHHHHHHHHH..HHHHHHH...HHHHHHHHLLLLEH..HHLHH
                            R  CN    L I    G   L    A       YG N  ES N  VT 
  16. 1bj7         31.73    RIEcnDCESLSItkDQGTCLLLTEVAKRQelEFYGTNTLesENMLVT.
                            EEEELLLLEEEEEEELLEEEEEEEEEEEEEEELLLEEEEELLLEEEE.
                           N    N   Y       G   LCF N  T  V   G  W       V  
  17. 1smv_A       31.53  VNKLS.NLRGYVSGQVWSGSAGLCFInsTTLDVSELGKKWYPYKTSavDV
                          HHHHH.LLEEEEEEELLLLHHHHHHHLEEELLLLLLLLLLEELLLHHHLH
                            R D NENS L  HN          NAG MP A          NN V  
  18. 1qhv_A       31.53 IFLRFDQneNSSLKKhnGNSTNANPYTNagFMplAYPKTQSQTAKNNIVSQ
                         EEEEELLLLLLLELLLELLEELLLLLLLLHHLELLLLLLLLLLHHHEEEEE
                           N TD          N  G       N G   V IYGV W   GN   TL
  19. 1axk_A       31.53   NWTD..GGGIVNAVNGSGGnsVNWSNTGNFVvtiygV.WAPNGNGYLTl
                           EEEL..LLLEEEEEELLLLEEEEEELLLLEEEEEEEE.EEEEEEEEEEE
                             T    N Y     N    TLC  N G      YGV    SGN  VT 
  20. 1cel_A       31.53   HATNSSTNCY...DGNTWSSTLCPDNegAAYASTYGV..TTSGNSlvTQ
                           EELLLLLELE...ELLEELLLLLLLHHLLLHHHHHLE..EEELLEEEEE
--- 
--- TOPITS ALIGNMENTS CONTINUED 
--- 
   1. 1ybv_A       35.53 FGHVKDVTPEEFDRvtINTRGQFFVAraYKHLEirL
                         LLLHHHLLHHHHHHHHHHLHHHHHHHHHHHHLLLEE
                         LQ Q  LSD  L   TL   G   PG  H  L 
   2. 1csh         34.40 lqLQKDlsDEKLRDytL.NSGRVVPGYGHAVLR
                         HHHHHHLLHHHHHHHHH.HLLLLLLLELLLLLL
                         L          LE   L        G I  I S
   3. 1cax_B       34.20 LVGLEQQQQQGLESMQLRRyaTLSEGDIIVIPS
                         EEEELLLLLLLLLLLLEEEEEEELLLLEEEELL
                         LQ    L     E   LQK         HEIL  R
   4. 1qor_A       33.80 lqtREELTEASNELFSlqKYPLKDAQRAHEILESR
                         HHLHHHHHHHHHHHHHHHEEEHHHHHHHHHHHHLL
                                  PR   I L   G    G I   LS R
   5. 1bif         33.80 YLMNIHVT.PR..SIYLCRHGESekGRidPGLSPR
                         HHLLLLLL.LL..LEEEEELLLEHHLELLLLELHH
                                  P   T TLQK  S  P     IL
   6. 1cwv_A       33.60 I.......TPQVDTltLQKKISLFppTLTGIL
                         E.......EEEELLEHHLEEEEEELLLEEEEE
                             R      L  I               ILSI  Y
   7. 1ece_A       32.87 GLWSRDYR.SMLDQIKSLGYNTIRLPYSDDIlsINFY
                         LLLLLLHH.HHHHHHHHLLLLEEEEEEEHHHHLLLLL
                                 DPR  TI L   G      I E    RI
   8. 1gtr_A       32.47 DKHVEGWDDPRMPTIslRRRG.YTAASIRE.FCKRI
                         LLLLLLLLLLLLLEHHHHHHL.LLHHHHHH.HHHHH
                              N  D    TI L      N   I 
   9. 1pfo         32.47 HkwDGNYQdaHYStiPLEA....NARNIR
                         EELLLLLLLLLEEEEEELL....LEEEEE
                         LQ QR   D  L  I   K G      I   L
  10. 2reb         32.47 LQvqRefIDAelDPIYARKLG....VDIDNLL
                         HHHHHLEEELLLLHHHHHHLL....LLHHHLE
                               L    L      K   WN      I  I  
  11. 3chb_D       32.13 .RMKDTLRIAYLTEAKVEKLCVWNNKTPRAIAAISM
                         .HHHHHHHHHHHHLLLEEEEEEELLLLLEEEEEEEE
                           F          TI  Q  GS N   I     I
  12. 1amx         32.13 .DFEKAFPGSKinTIDvqGYGSYNSFSINYKTKI
                         .HHHHHLLLLEELEEEEHHHHLLEEEEEEEEEEE
                          Q  R               G      I  I S    
  13. 6prc_L       32.13 aqYFRDVVGYSIGALSIHRLGLFLASNIftIASGPFW
                         HHHHHHHHLLLLLHHHHHHHHHHHHHHHHHHHELLLE
                         L   R      L    L   G       H IL  R
  14. 2tys_B       31.93 lKMMREQPeeQLLVVNLSGRGDKDIFTVHDILKAR
                         HHHHHHLLLLEEEEEEELEELHHHHHHHHHHHHLL
                            Q      RL  I L K GS   G IHE L I  
  15. 1b8b_A       31.87 ILYQEGAFGVRldIIELFKNgsVSLGyiHE.LNILV
                         HHHLLLLLLLLLELHHHHLLLEEEEEEHHH.HHHHH
                              N    R    TL K  S  P       S R
  16. 1bj7         31.73 ..YVENYDGERITKMtlAKGTSFTpeKYQQLNSER
                         ..EEEEELLLLEEEEEEELLLLLLHHHHHHHHHHH
                               L   RL  I L   GS   G I     I  
  17. 1smv_A       31.53 VNIATDLVPARL.VIALLD.GSSsaGRIYDTYTIQM
                         HHHHLLLLLLEE.EEEEEL.LLLLEEEEEEEEEEEE
                                  P   TITL   G        E      
  18. 1qhv_A       31.53 QVYLhdKTKPMILTITLN..GTSESTETSEVSTYSM
                         EEEHHLLLLEEEEEEEEL..HHHLLLLLLLLLLEEE
                         L   R    P  E      WG   PG    I     Y
  19. 1axk_A       31.53 lgWTRS...PLIEYYVVDSWGTYRpgGTYDIYTTTRY
                         EEEEEL...LLEEEEEEEEELLLLLLEEEEEEEEEEE
                            Q N SD      TL    S         L    Y
  20. 1cel_A       31.53 QSAQKNvsDTTYQEFTlnEF.SFD.VDVSQllNGALY
                         ELLLEEEELLEELEEELEEE.EEE.EELLLLEEEEEE
--- 
--- TOPITS ALIGNMENTS END
---

TOPITS (threading) results in MSF format

TOP - BOTTOM - TOPITS

Identities computed with respect to: (1) predict_h2380
Colored by: consensus/70% and property


                   1 [        .         .         .         .         :         . 60
 1 predict_h2380     MINRTDCNENSYLEIHNNEGRDTLCFANAGTMPVAIYGVNWVESGNNVVTLQFQRNLSDP   
 2 1ybv_A            --NSTESAEEVVAAIKKN-GSDAACvaNVGVVevKIFglDIVCSNSGVVSFGHVKDVTPE   
 3 1csh              MLGYTDPqerLYLTIHSdeGGNvlSFAAanGLAGPLHGL-----ANQEVLlqLQKDlsDE   
 4 1cax_B            LRSRDPIYSNNyyEikNSQLrdIlclmNEGALFVPHYnvILVAngRAEVELVGLEQQQQQ   
 5 1qor_A            VInrEEDLVERLKEItdSVGRDTwcLQRRGLmsGAVTGVNLgqKGSLYVtlqtREELTEA   
 6 1bif              FMRRIECYENSYESLDEEQDRD-LSYIK--IMDvqSYVVNRVAdqSRIVYYLMNIHVT-P   
 7 1cwv_A            LADGTMSSTLSFVPVDKnsGMQGLSFTQNG-VPVSISPisYTAtgNSvvTI-------TP   
 8 1ece_A            ----------------HTSGREIL---DANNVPVRIAGINwfETCNYVVHGLWSRDYR-S   
 9 1gtr_A            MYDFTHCISDAllEFQDNRRLYDWVLDNI-TIPveFSRLNlvMSknLLVTDKHVEGWDDP   
10 1pfo              VHNKTD-----YIETTSTegKINLDHSGaaQFEVAWDEVSYDKEGNEVLTHkwDGNYQda   
11 2reb              -IMRL--GEDRSMDvtISTGSLSLDIagAGGLpvEIYGPE--SSGKTTLTLQvqRefIDA   
12 3chb_D            --NITdcAEYHNTQIhndaGkaIITFKNGATFQVEVPGSQHIDSQKKAIE-RMKDTLRIA   
13 1amx              -IN----NEKSyiTIKDqqGGQQL---DLSTLNINVTGtnYY-SGQSAIT-DFEKAFPGS   
14 6prc_L            ILSHLDWVNnqYLNWHYNPGHmsFLFVNA--MALGLHgiLSVAngDKVKTaqYFRDVVGY   
15 2tys_B            -IGRAD-----YVSITDDEALetLC-RHEGIIPA-------LESSHALAhlKMMREQPee   
16 1b8b_A            ----TQFNEQKFVELFNE--RMDLCFE---ALMCRISSLKGVKA--TVAPILYQEGAFGV   
17 1bj7              ---RIEcnDCESLSItkDQGTCLLLTEVAKRQelEFYGTNTLesENMLVT--YVENYDGE   
18 1smv_A            -VNKLS-NLRGYVSGQVWSGSAGLCFInsTTLDVSELGKKWYPYKTSavDVNIATDLVPA   
19 1qhv_A            IFLRFDQneNSSLKKhnGNSTNANPYTNagFMplAYPKTQSQTAKNNIVSQVYLhdKTKP   
20 1axk_A            --NWTD--GGGIVNAVNGSGGnsVNWSNTGNFVvtiygV-WAPNGNGYLTlgWTRS---P   
21 1cel_A            --HATNSSTNCY---DGNTWSSTLCPDNegAAYASTYGV--TTSGNSlvTQSAQKNvsDT   
   consensus/100%    .................................h..............h...........   
   consensus/90%     ..............h..t.....h...t...h.h.........ttp.hh...h.tt....   
   consensus/80%     ...hh.......hphppstst..hsh.t.t.h.sth.sh..h.stpthlp..h.cph...   
   consensus/70%     ..thhp..ppthhphppspuptslshtstshh.lth.shphhtststhlsh.h.csh.ts   

                  61          .         .      ] 87
 1 predict_h2380     RLETITLQKWGSWNPGHIHEILSIRIY   
 2 1ybv_A            EFDRvtINTRGQFFVAraYKHLEirL-   
 3 1csh              KLRDytL-NSGRVVPGYGHAVLR----   
 4 1cax_B            GLESMQLRRyaTLSEGDIIVIPS----   
 5 1qor_A            SNELFSlqKYPLKDAQRAHEILESR--   
 6 1bif              R--SIYLCRHGESekGRidPGLSPR--   
 7 1cwv_A            QVDTltLQKKISLFppTLTGIL-----   
 8 1ece_A            MLDQIKSLGYNTIRLPYSDDIlsINFY   
 9 1gtr_A            RMPTIslRRRG-YTAASIRE-FCKRI-   
10 1pfo              HYStiPLEA----NARNIR--------   
11 2reb              elDPIYARKLG----VDIDNLL-----   
12 3chb_D            YLTEAKVEKLCVWNNKTPRAIAAISM-   
13 1amx              KinTIDvqGYGSYNSFSINYKTKI---   
14 6prc_L            SIGALSIHRLGLFLASNIftIASGPFW   
15 2tys_B            QLLVVNLSGRGDKDIFTVHDILKAR--   
16 1b8b_A            RldIIELFKNgsVSLGyiHE-LNILV-   
17 1bj7              RITKMtlAKGTSFTpeKYQQLNSER--   
18 1smv_A            RL-VIALLD-GSSsaGRIYDTYTIQM-   
19 1qhv_A            MILTITLN--GTSESTETSEVSTYSM-   
20 1axk_A            LIEYYVVDSWGTYRpgGTYDIYTTTRY   
21 1cel_A            TYQEFTlnEF-SFD-VDVSQllNGALY   
   consensus/100%    ....h......................   
   consensus/90%     .h..h.l.t........h.........   
   consensus/80%     th..htltt.s.....ph.thhp....   
   consensus/70%     plpthslpphsphp.sphpthhp...

TOPITS (threading) results in HSSP format

TOP - BOTTOM - TOPITS

HSSP       HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 1.0 1991
PDBID      predict_h23874
DATE       file generated on 23-Jan-01
SEQBASE    RELEASE 38.0 OF EMBL/SWISS-PROT WITH  80000 SEQUENCES
PARAMETER  SMIN: -1.0  SMAX:  2.0
PARAMETER  gap-open:  2.0 gap-elongation:  0.2
PARAMETER  conservation weights: NO
PARAMETER  InDels in secondary structure allowed: YES
PARAMETER  alignments sorted according to :ZSCORE
THRESHOLD  according to: ALL
REFERENCE  Sander C., Schneider R. : Database of homology-derived protein structures. Proteins, 9:56-68 (1991).
CONTACT    e-mail (INTERNET) Schneider@EMBL-Heidelberg.DE or Sander@EMBL-Heidelberg.DE / fax +49-6221-387306
AVAILABLE  Free academic use. Commercial users must apply for license.
AVAILABLE  No inclusion in other databanks without permission.
HEADER      predict_h23874.phdRdb
COMPND     
SOURCE     
AUTHOR     
SEQLENGTH    87
NCHAIN        1 chain(s) in predict_h23874 data set
KCHAIN        1 chain(s) used here ; chain(s) :  A
NALIGN       20
NOTATION : ID: EMBL/SWISSPROT identifier of the aligned (homologous) protein
NOTATION : STRID: if the 3-D structure of the aligned protein is known, then STRID is the Protein Data Bank identifier as taken
NOTATION : from the database reference or DR-line of the EMBL/SWISSPROT entry
NOTATION : %IDE: percentage of residue identity of the alignment
NOTATION : %SIM (%WSIM):  (weighted) similarity of the alignment
NOTATION : IFIR/ILAS: first and last residue of the alignment in the test sequence
NOTATION : JFIR/JLAS: first and last residue of the alignment in the alignend protein
NOTATION : LALI: length of the alignment excluding insertions and deletions
NOTATION : NGAP: number of insertions and deletions in the alignment
NOTATION : LGAP: total length of all insertions and deletions
NOTATION : LSEQ2: length of the entire sequence of the aligned protein
NOTATION : ACCESSION: SwissProt accession number
NOTATION : PROTEIN: one-line description of aligned protein
NOTATION : SeqNo,PDBNo,AA,STRUCTURE,BP1,BP2,ACC: sequential and PDB residue numbers, amino acid (lower case = Cys), secondary
NOTATION : structure, bridge partners, solvent exposure as in DSSP (Kabsch and Sander, Biopolymers 22, 2577-2637(1983)
NOTATION : VAR: sequence variability on a scale of 0-100 as derived from the NALIGN alignments
NOTATION : pair of lower case characters (AvaK) in the alignend sequence bracket a point of INSERTION IN THIS sequence
NOTATION : dots (....) in the alignend SEQUENCE INDICATE POINTS of deletion in this sequence
NOTATION : SEQUENCE PROFILE: relative frequency of an amino acid type at each position. Asx and Glx are in their
NOTATION : acid/amide form in proportion to their database frequencies
NOTATION : NOCC: number of aligned sequences spanning this position (including the test sequence)
NOTATION : NDEL: number of sequences with a deletion in the test protein at this position
NOTATION : NINS: number of sequences with an insertion in the test protein at this position
NOTATION : ENTROPY: entropy measure of sequence variability at this position
NOTATION : RELENT: relative entropy, i.e.  entropy normalized to the range 0-100
NOTATION : WEIGHT: conservation weight

## PROTEINS : EMBL/SWISSPROT identifier and alignment statistics
  NR.    ID         STRID   %IDE  %SIM IFIR ILAS JFIR JLAS LALI NGAP LGAP LSEQ2 ACCESSION     PROTEIN
    1 : 1ybv_A              0.28  0.00    3   86   49  146   83    7   16  270             MOL_ID: 1;
    2 : 1csh                0.40  0.00    1   83  214  322   77   10   38  435             CITRATE SYNTHASE (E.C.4.1.3.7) COMPLEXED
    3 : 1cax_B              0.31  0.00    1   83   11  110   83    8   17  184             CANAVALIN (JACK BEAN 7S VICILIN)
    4 : 1qor_A              0.36  0.00    1   85  188  316   85    8   44  326             QUINONE OXIDOREDUCTASE COMPLEXED WITH NAD
    5 : 1bif                0.33  0.00    1   85  154  240   79    8   14  432             MOL_ID: 1;
    6 : 1cwv_A              0.34  0.00    1   82  210  300   74    8   25  484             MOL_ID: 1;
    7 : 1ece_A              0.32  0.00   17   87    7   82   68    4   13  358             MOL_ID: 1;
    8 : 1gtr_A              0.33  0.00    1   86  203  306   83    8   24  530             GLUTAMINYL-TRNA SYNTHETASE (E.C.6.1.1.18)
    9 : 1pfo                0.32  0.00    1   79  346  424   73    7   18  471             MOL_ID: 1;
   10 : 2reb                0.36  0.00    2   82   24  113   75    9   25  305             RECA PROTEIN (E.C.3.4.99.37)
   11 : 3chb_D              0.27  0.00    3   86    4  101   83    5   16  103             MOL_ID: 1;
   12 : 1amx                0.31  0.00    2   84   26  115   78    9   25  150             MOL_ID: 1;
   13 : 6prc_L              0.26  0.00    1   87  150  255   85    7   23  273             MOL_ID: 1;
   14 : 2tys_B              0.31  0.00    2   85  317  392   71    6   18  397             MOL_ID: 1;
   15 : 1b8b_A              0.35  0.00    5   86  304  385   74    7   16  534             MOL_ID: 1;
   16 : 1bj7                0.31  0.00    4   85   35  132   80    7   20  150             MOL_ID: 1;
   17 : 1smv_A              0.28  0.00    2   86   83  186   83    6   25  196             MOL_ID: 1;
   18 : 1qhv_A              0.30  0.00    1   86   70  166   84    6   15  195             MOL_ID: 1;
   19 : 1axk_A              0.32  0.00    3   87  164  269   81    9   33  393             MOL_ID: 1;
   20 : 1cel_A              0.32  0.00    3   87   42  145   81    9   33  434             1,4-BETA-D-GLUCAN CELLOBIOHYDROLASE I (CE
## ALIGNMENTS    1 -   20
 SeqNo  PDBNo AA STRUCTURE BP1 BP2  ACC NOCC  VAR  ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
     1    1   M              0   0  152   10   22   MLVFL MV   I    I
     2    2   I              0   0    0   14   40   LRIMA YHI ILI  VF
     3    3   N              0   0   76   18   39  NGSnRD DNMNNSG  NLNH
     4    4   R              0   0  121   18   43  SYRrRG FKRI.HR RKRWA
     5    5   T              0   0  115   19   37  TTDEIT TTLT.LATILFTT
     6    6   D              0   0   79   18   30  EDPEEM HD.d.DDQESDDN
     7    7   C              0   0   66   14   49  SPIDCS C..c.W.Fc.Q.S
     8    8   N              0   0   39   17   48  AqYLYS I.GANV.NnNn.S
     9    9   E              0   0   95   18   36  EeSVET S.EEEN.EDLeGT
    10   10   N              0   0    0   18   45  ErNENL D.DYKn.QCRNGN
    11   11   S              0   0    0   18   48  VLNRSS A.RHSq.KEGSGC
    12   12   Y  E           0   0    0   20   36  VYyLYF lYSNyYYFSYSIY
    13   13   L  E           0   0    0   19   36  ALyKEV lIMTiLVVLVLV.
    14   14   E  E           0   0   48   19   38  ATEESP EEDQTNSESSKN.
    15   15   I  E           0   0    0   19   36  IIiILV FTvIIWILIGKA.
    16   16   H  E           0   0    0   20   45  KHktDD QTthKHTFtQhVD
    17   17   N              0   0   56   21   42  KSNdEKHDSInDYDNkVnNG
    18   18   N              0   0    6   21   38  NdSSEnTNTSdqNDEDWGGN
    19   19   E              0   0  157   19   43  .eQVQsSReTaqPE.QSNST
    20   20   G              0   0    0   20   29  GGLGDGGRgGGGGA.GGSGW
    21   21   R              0   0   62   21   47  SGrRRMRLKSkGHLRTSTGS
    22   22   D              0   0   79   21   47  DNdDDQEYILaQmeMCANnS
    23   23   T  E           0   0    0   20   45  AvIT.GIDNSIQstDLGAsT
    24   24   L  E           0   0    0   21   24  AllwLLLWLLILFLLLLNVL
    25   25   C  E           0   0    0   19   45  CSccSS.VDDT.LCCLCPNC
    26   26   F  E           0   0    0   18   33  vFlLYF.LHIF.F.FTFYWP
    27   27   A  E           0   0    0   19   47  aAmQIT.DSaK.VREEITSD
    28   28   N  E           0   0    0   20   33  NANRKQDNGgNDNH.VnNNN
    29   29   A              0   0    0   19   41  VaER.NAIaAGLAE.AsaTe
    30   30   G              0   0    0   17   27  GnGG.GN.aGAS.G.KTgGg
    31   31   T              0   0   69   19   47  VGALI.NTQGTT.IARTFNA
    32   32   M              0   0    0   21   27  VLLmMVVIFLFLMILQLMFA
    33   33   P              0   0    0   21   47  eAFsDPPPEpQNAPMeDpVY
    34   34   V  E           0   0    0   21   28  vGVGvVVvVvVILAClVlvA
    35   35   A  E           0   0    0   20   42  KPPAqSReAEENG.RESAtS
    36   36   I  E           0   0    0   20   39  ILHVSIIFWIVVL.IFEYiT
    37   37   Y  E           0   0    0   20   50  FHYTYSASDYPTH.SYLPyY
    38   38   G  E           0   0    0   20   28  gGnGVPGREGGGg.SGGKgG
    39   39   V  E           0   0    0   20   35  lLvVViILVPSti.LTKTVV
    40   40   N  E           0   0    0   17   40  D.INNsNNSEQnL.KNKQ..
    41   41   W  E           0   0    0   17   47  I.LLRYwlY.HYS.GTWSW.
    42   42   V  E           0   0    0   19   43  V.VgVTfvD.IYVLVLYQAT
    43   43   E              0   0   69   19   44  C.AqAAEMKSD.AEKePTPT
    44   44   S              0   0    0   20   38  S.nKdtTSESSSnSAsYANS
    45   45   G              0   0    0   20   35  NAgGqgCkGGQGgS.EKKGG
    46   46   N              0   0    0   20   33  SNRSSNNnNKKQDH.NTNNN
    47   47   N  E           0   0   39   21   49  GQALRSYLETKSKATMSNGS
    48   48   V  E           0   0    0   21   39  VEEYIvVLVTAAVLVLaIYl
    49   49   V  E           0   0    0   21   22  VVVVVvVVLLIIKAAVvVLv
    50   50   T  E           0   0    0   21   38  SLEtYTHTTTETThPTDSTT
    51   51   L  E           0   0   80   18   43  FlLlYIGDHL..alI.VQlQ
    52   52   Q  E           0   0   97   19   47  GqVqL.LKkQRDqKL.NVgS
    53   53   F  E           0   0    0   20   47  HLGtM.WHwvMFYMYYIYWA
    54   54   Q              0   0   49   20   49  VQLRN.SVDqKEFMQVALTQ
    55   55   R              0   0  121   20   40  KKEEI.REGRDKRREEThRK
    56   56   N              0   0   76   20   32  DDQEH.DGNeTADEGNDdSN
    57   57   L              0   0   41   19   43  VlQLV.YWYfLFVQAYLK.v
    58   58   S              0   0   83   19   49  TsQTT.RDQIRPVPFDVT.s
    59   59   D              0   0   58   18   36  PDQE.T.DdDIGGeGGPK.D
    60   60   P              0   0    0   21   41  EEQAPPSPaAASYeVEAPPT
    61   61   R  E           0   0   89   21   48  EKGSRQMRHeYKSQRRRMLT
    62   62   L  E           0   0    0   20   26  FLLN.VLMYlLiILlILIIY
    63   63   E  E           0   0    0   19   42  DREE.DDPSDTnGLdT.LEQ
    64   64   T  E           0   0    0   21   48  RDSLSTQTtPETAVIKVTYE
    65   65   I  E           0   0    0   21   27  vyMFIlIIiIAILVIMIIYF
    66   66   T  E           0   0    0   21   46  ttQSYtKsPYKDSNEtATVT
    67   67   L              0   0    0   21   21  ILLlLLSlLAVvILLlLLVl
    68   68   Q              0   0   71   20   49  N.RqCQLREREqHSFALNDn
    69   69   K              0   0  100   20   39  TNRKRKGRAKKGRGKKD.SE
    70   70   W              0   0    0   18   48  RSyYHKYR.LLYLRNG..WF
    71   71   G              0   0    0   19   25  GGaPGING.GCGGGgTGGG.
    72   72   S              0   0   63   18   44  QRTLEST...VSLDsSSTTS
    73   73   W              0   0   20   19   43  FVLKSLIY..WYFKVFSSYF
    74   74   N              0   0    0   20   49  FVSDeFRTN.NNLDSTsERD
    75   75   P              0   0    0   19   44  VPEAkpLAA.NSAILpaSp.
    76   76   G              0   0   68   21   46  AGGQGpPARVKFSFGeGTgV
    77   77   H              0   0   66   21   49  rYDRRTYSNDTSNTyKREGD
    78   78   I              0   0    0   21   37  aGIAiLSIIIPIIViYITTV
    79   79   H  E           0   0   66   21   49  YHIHdTDRRDRNfHHQYSYS
    80   80   E  E           0   0   95   20   40  KAVEPGDE NAYtDEQDEDQ
    81   81   I  E           0   0   60   18   32  HVIIGII. LIKII.LTVIl
    82   82   L  E           0   0    0   20   39  LLPLLLlF LATALLNYSYl
    83   83   S  E           0   0    0   18   41  ERSES sC  AKSKNSTTTN
    84   84   I  E           0   0    0   16   47  i  SP IK  IIGAIEIYTG
    85   85   R  E           0   0   89   15   43  r  RR NR  S PRLRQSTA
    86   86   I  E           0   0    0   11   30  L     FI  M F V MMRL
    87   87   Y              0   0  179    5    6        Y     W     YY
## SEQUENCE PROFILE AND ENTROPY
 SeqNo PDBNo   V   L   I   M   F   W   Y   G   A   P   S   T   C   H   R   K   Q   E   N   D  NOCC NDEL NINS ENTROPY RELENT WEIGHT
    1    1    20  20  20  30  10   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0    10    0    0   1.557     68  1.33
    2    2     7  14  36   7   7   0   7   0   7   0   0   0   0   7   7   0   0   0   0   0    14    0    0   1.965     74  1.00
    3    3     0   6   0   6   0   0   0  11   0   0  11   0   0   6   6   0   0   0  44  11    18    0    1   1.735     60  1.01
    4    4     0   0   6   0   6   6   6   6   6   0   6   0   0   6  44  11   0   0   0   0    18    1    0   1.889     65  0.94
    5    5     0  16  11   0   5   0   0   0   5   0   0  53   0   0   0   0   0   5   0   5    19    1    0   1.486     50  1.04
    6    6     0   0   0   6   0   0   0   0   0   6   6   0   0   6   0   0   6  22   6  44    18    2    1   1.658     57  1.18
    7    7     0   0   7   0   7   7   0   0   0   7  21   0  36   0   0   0   7   0   0   7    14    6    1   1.829     69  0.82
    8    8     6   6   6   0   0   0  12   6  12   0  12   0   0   0   0   0   6   0  35   0    17    3    2   1.956     69  0.84
    9    9     6   6   0   0   0   0   0   6   0   0  11  11   0   0   0   0   0  50   6   6    18    2    0   1.638     57  1.07
   10   10     0   6   0   0   0   0   6   6   0   0   0   0   6   0  11   6   6  11  33  11    18    2    2   2.062     71  0.90
   11   11     6   6   0   0   0   0   0  11   6   0  28   0   6   6  11   6   6   6   6   0    18    2    0   2.289     79  0.84
   12   12     5  10   5   0  10   0  50   0   0   0  15   0   0   0   0   0   0   0   5   0    20    0    3   1.541     51  1.06
   13   13    26  32  11   5   0   0   5   0   5   0   0   5   0   0   0   5   0   5   0   0    19    1    0   1.882     64  1.06
   14   14     0   0   0   0   0   0   0   0   5   5  21  11   0   0   0   5   5  32  11   5    19    1    0   1.941     66  1.02
   15   15    11  11  47   0   5   5   0   5   5   0   0   5   0   0   0   5   0   0   0   0    19    1    2   1.758     60  1.07
   16   16     5   0   0   0   5   0   0   0   0   0   0  25   0  25   0  15  10   0   0  15    20    0    4   1.792     60  0.90
   17   17     5   0   5   0   0   0   5   5   0   0  10   0   0   5   0  14   0   5  29  19    21    0    0   2.046     68  0.95
   18   18     0   0   0   0   0   5   0  10   0   0  14  10   0   0   0   0   5  10  29  19    21    0    4   1.914     64  1.03
   19   19     5   0   0   0   0   0   0   0   5   5  21  11   0   0   5   0  21  21   5   0    19    2    1   1.996     68  0.93
   20   20     0   5   0   0   0   5   0  70   5   0   5   0   0   0   5   0   0   0   0   5    20    1    0   1.148     38  1.20
   21   21     0  10   0   5   0   0   0  14   0   0  19  10   0   5  29  10   0   0   0   0    21    0    2   1.914     64  0.86
   22   22     0   5   5  10   0   0   5   0  10   0   5   0   5   0   0   0  10  10  14  24    21    0    3   2.240     75  0.85
   23   23     5   5  15   0   0   0   0  10  10   0  15  20   0   0   0   0   5   0   5  10    20    1    1   2.181     73  0.89
   24   24     5  67   5   0   5  10   0   0   5   0   0   0   0   0   0   0   0   0   5   0    21    0    2   1.219     41  1.30
   25   25     5  11   0   0   0   0   0   0   0   5  16   5  42   0   0   0   0   0   5  11    19    2    0   1.749     59  0.88
   26   26     6  17   6   0  39   6  11   0   0   6   0   6   0   6   0   0   0   0   0   0    18    3    2   1.874     65  1.13
   27   27     5   0  11   5   0   0   0   0  21   0  11  11   0   0   5   5   5  11   0  11    19    2    1   2.288     78  0.86
   28   28     5   0   0   0   0   0   0  10   5   0   0   0   0   5   5   5   5   0  50  10    20    1    1   1.706     57  1.12
   29   29     5   5   5   0   0   0   0   5  42   0   5   5   0   0   5   0   0  16   5   0    19    2    4   1.895     64  0.97
   30   30     0   0   0   0   0   0   0  59  12   0   6   6   0   0   0   6   0   0  12   0    17    4    0   1.316     46  1.24
   31   31     5   5  11   0   5   0   0  11  16   0   0  26   0   0   5   0   5   0  11   0    19    2    0   2.129     72  0.85
   32   32    14  29  10  24  14   0   0   0   5   0   0   0   0   0   0   0   5   0   0   0    21    0    1   1.769     59  1.23
   33   33     5   0   0   5   5   0   5   0  10  33   5   0   0   0   0   0   5  14   5  10    21    0    4   2.107     70  0.86
   34   34    57  14   5   0   0   0   0  10  10   0   0   0   5   0   0   0   0   0   0   0    21    0    3   1.336     45  1.23
   35   35     0   0   0   0   0   0   0   5  20  10  15   5   0   0  10   5   5  20   5   0    20    1    0   2.138     71  0.95
   36   36    15  10  35   0  10   5   5   0   0   0   5   5   0   5   0   0   0   5   0   0    20    1    1   2.011     67  1.01
   37   37     0   5   0   0   5   0  35   0   5  10  15  10   0  10   0   0   0   0   0   5    20    1    0   1.942     65  0.80
   38   38     5   0   0   0   0   0   0  65   0   5   5   0   0   0   5   5   0   5   5   0    20    1    4   1.329     44  1.21
   39   39    35  20  15   0   0   0   0   0   0   5   5  15   0   0   0   5   0   0   0   0    20    1    2   1.708     57  1.08
   40   40     0   6   6   0   0   0   0   0   0   0  12   0   0   0   0  12  12   6  41   6    17    4    0   1.787     63  0.99
   41   41     0  18   6   0   0  24  18   6   0   0  12   6   0   6   6   0   0   0   0   0    17    4    2   2.038     72  0.85
   42   42    37  11   5   0   5   0  11   5   5   0   0  11   0   0   0   0   5   0   0   5    19    2    1   2.009     68  0.93
   43   43     0   0   0   5   0   0   0   0  21  11   5  11   5   0   0  11   5  21   0   5    19    2    1   2.142     73  0.91
   44   44     0   0   0   0   0   0   5   0  10   0  45  10   0   0   0   5   0   5  15   5    20    1    4   1.704     57  1.04
   45   45     0   0   0   0   0   0   0  50   5   0   5   0   5   0   0  15  10   5   5   0    20    1    1   1.610     54  1.08
   46   46     0   0   0   0   0   0   0   0   0   0  15   5   0   5   5  10   5   0  50   5    20    1    0   1.610     54  1.12
   47   47     0  10   0   5   0   0   5  10  10   0  19  10   0   0   5  10   5   5  10   0    21    0    0   2.384     80  0.81
   48   48    33  19  10   0   0   0  10   0  14   0   0   5   0   0   0   0   0  10   0   0    21    0    3   1.777     59  1.00
   49   49    62  14  10   0   0   0   0   0  10   0   0   0   0   0   0   5   0   0   0   0    21    0    0   1.168     39  1.33
   50   50     0   5   0   0   0   0   5   0   0   5  10  52   0  10   0   0   0  10   0   5    21    0    2   1.590     53  1.02
   51   51     6  39  11   0   6   0   6   6   6   0   0   0   0   6   0   0  11   0   0   6    18    3    3   1.980     68  0.93
   52   52    11  16   0   0   0   0   0  11   0   0   5   0   0   0   5  16  26   0   5   5    19    2    2   2.028     69  0.84
   53   53     5   5   5  15  10  15  20   5   5   0   0   5   0  10   0   0   0   0   0   0    20    1    1   2.250     75  0.86
   54   54    15  10   0   5   5   0   0   0   5   0   5   5   0   0   5   5  25   5   5   5    20    1    0   2.359     79  0.81
   55   55     0   0   5   0   0   0   0   5   0   0   0   5   0   5  30  20   0  25   0   5    20    1    1   1.779     59  0.99
   56   56     0   0   0   0   0   0   0  10   5   0   5   5   0   5   0   0   5  15  20  30    20    1    1   1.947     65  1.14
   57   57    21  26   0   0  11   5  16   0   5   0   0   0   0   0   0   5  11   0   0   0    19    2    2   1.910     65  0.94
   58   58    11   0   5   0   5   0   0   0   0  11  16  21   0   0  11   0  11   0   0  11    19    2    0   2.114     72  0.81
   59   59     0   0   6   0   0   0   0  22   0  11   0   6   0   0   0   6   6  11   0  33    18    3    2   1.831     63  1.06
   60   60     5   0   0   0   0   0   5   0  24  29  10   5   0   0   0   0   5  19   0   0    21    0    0   1.819     61  0.97
   61   61     0   5   0  10   0   0   5   5   0   0  10   5   0   5  29  10  10  10   0   0    21    0    1   2.203     74  0.84
   62   62     5  45  25   5   5   0  10   0   0   0   0   0   0   0   0   0   0   0   5   0    20    1    2   1.535     51  1.25
   63   63     0  11   0   0   0   0   0   5   0   5   5  11   0   0   5   0   5  21   5  26    19    2    0   2.083     71  0.95
   64   64    10   5   5   0   0   0   5   0   5   5  10  29   0   0   5   5   5  10   0   5    21    0    1   2.335     78  0.84
   65   65    10  10  48  10  10   0  10   0   5   0   0   0   0   0   0   0   0   0   0   0    21    0    3   1.618     54  1.24
   66   66     5   0   0   0   0   0  10   0   5   5  14  33   0   0   0  10   5   5   5   5    21    0    2   2.107     70  0.88
   67   67    14  67  10   0   0   0   0   0   5   0   5   0   0   0   0   0   0   0   0   0    21    0    3   1.062     35  1.36
   68   68     0  10   0   0   5   0   0   0   5   0   5   0   5   5  15   0  20  10  15   5    20    1    0   2.250     75  0.81
   69   69     0   0   0   0   0   0   0  15   5   0   5   5   0   0  20  35   0   5   5   5    20    1    0   1.873     63  1.01
   70   70     0  17   0   0   6  11  22   6   0   0   6   0   0   6  17   6   0   0   6   0    18    3    1   2.139     74  0.84
   71   71     0   0   5   0   0   0   0  68   5   5   0   5   5   0   0   0   0   0   5   0    19    2    1   1.189     40  1.27
   72   72     6  11   0   0   0   0   0   0   0   0  39  22   0   0   6   0   6   6   0   6    18    3    0   1.749     60  0.91
   73   73    11  11   5   0  21  11  16   0   0   0  16   0   0   0   0  11   0   0   0   0    19    2    0   2.014     68  0.93
   74   74     5   5   0   0  10   0   0   0   0   0  15  10   0   0  10   0   0  10  20  15    20    1    2   2.112     70  0.81
   75   75     5  11   5   0   0   0   0   0  26  26  11   0   0   0   0   5   0   5   5   0    19    2    3   1.951     66  0.92
   76   76    10   0   0   0  10   0   0  33  10  10   5   5   0   0   5   5   5   5   0   0    21    0    0   2.132     71  0.87
   77   77     0   0   0   0   0   0  14   5   0   0  10  14   0   5  19   5   0   5  10  14    21    0    2   2.178     73  0.81
   78   78    10   5  48   0   0   0   5   5  10   5   5  10   0   0   0   0   0   0   0   0    21    0    1   1.750     58  1.05
   79   79     0   0   5   0   5   0  14   0   0   0  10   5   0  24  14   0   5   0   5  14    21    0    1   2.124     71  0.82
   80   80     5   0   0   0   0   0   5   5  10   5   0   5   0   0   0   5  10  25   5  20    20    0    0   2.177     73  0.98
   81   81    11  17  50   0   0   0   0   6   0   0   0   6   0   6   0   6   0   0   0   0    18    2    1   1.532     53  1.14
   82   82     0  55   0   0   5   0  10   0  10   5   5   5   0   0   0   0   0   0   5   0    20    0    1   1.538     51  1.01
   83   83     0   0   0   0   0   0   0   0   6   0  33  17   6   0   6  11   0  11  11   0    18    0    0   1.879     65  0.97
   84   84     0   0  44   0   0   0   6  13   6   6   6   6   0   0   0   6   0   6   0   0    16    0    1   1.835     66  0.86
   85   85     0   7   0   0   0   0   0   0   7   7  13   7   0   0  47   0   7   0   7   0    15    0    0   1.708     63  0.93
   86   86     9  18  18  27  18   0   0   0   0   0   0   0   0   0   9   0   0   0   0   0    11    0    0   1.720     72  1.18
   87   87     0   0   0   0   0  20  80   0   0   0   0   0   0   0   0   0   0   0   0   0     5    0    0   0.500     31  1.64
## INSERTION LIST
 AliNo  IPOS  JPOS   Len Sequence
     1    26    72     1 vKa
     1    33    80     9 eDIVRMFEEAv
     1    38    94     1 gKl
     1    65   122     1 vFt
     1    77   135     1 rEa
     1    84   143     2 iGGr
     2     8   222     2 qFTe
     2     9   225     2 eLMr
     2    18   236     1 dHe
     2    23   242    16 vSAHTSHLVGSALSDPYl
     2    29   264     1 aMn
     2    51   282     3 lWLSq
     2    57   291     4 lGADAs
     2    65   303     3 yIWNt
     3    12    23     3 yGKLy
     3    15    29     3 iTPEk
     3    21    38     2 rDLd
     3    24    43     2 lLNc
     3    26    47     1 lQm
     3    38    60     4 nSRATv
     3    44    70     1 nEg
     3    70    97     1 yAa
     4     3   191     1 nYr
     4    16   205     9 tGGKKVRVVYd
     4    24   222     5 wERSLDc
     4    32   235     6 mVSFGNSs
     4    42   251     3 gILNq
     4    50   262     3 tRPSl
     4    52   267     4 qGYITt
     4    67   286    13 lIASGVIKVDVAEQq
     5    34   185     1 vGq
     5    44   196     2 dHIq
     5    74   225     3 eLNLk
     5    78   232     2 iGGd
     6    18   228     4 nGHFIs
     6    39   252     5 iTEQPDs
     6    44   262     2 tVVg
     6    48   268     2 vGDv
     6    65   280     3 lILSt
     6    75   293     1 pVp
     7    41    29     2 wFGf
     7    82    71     7 lKPGTMPNs
     8    12   215     9 lEGITHSLCTl
     8    34   245     5 vHPRQYe
     8    41   257     3 lEYTv
     8    45   264     3 kRKLn
     8    66   288     1 sGl
     9    19   360     3 eYSKg
     9    29   373     2 aYVa
     9    52   398     1 kTw
     9    59   406     2 dKTa
     9    64   413     1 tVi
    10    15    36     1 vEt
    10    27    49     1 aLg
    10    33    56     4 pMGRIv
    10    53    78     4 vIAAAq
    10    56    85     5 eGKTCAf
    10    61    95     2 eHAl
    11     6     8     1 dLc
    11    16    19     2 hTLn
    11    18    23     9 dKIFSYTESLa
    11    21    35     3 kREMa
    12    12    33     4 yVSKDi
    12    18    43     1 qIq
    12    39    62     2 tHSn
    12    62    85     6 iTVDNTKn
    12    67    96     3 vTIPq
    13    10   160     3 nFGYq
    13    22   175     3 mSSVs
    13    38   192     2 gGLi
    13    44   200     3 nPGDg
    13    51   210     4 aEHENq
    13    79   242     6 fLTGAFGt
    14    22   333     3 eAFKt
    14    50   356     1 hAl
    14    59   366     1 eKe
    15    62   355     4 lKPDDd
    15    71   368     2 gRSs
    15    77   376     2 yIGi
    16     7    39     1 cIn
    16    16    49     3 tFYLk
    16    33    69     5 eGYVYVl
    16    43    84     4 eVIHVs
    16    66   109     2 tEGl
    16    75   120     3 pEELe
    17    28   109    11 nNSRCSDTSTAIs
    17    48   140     7 aDYATAVGv
    17    74   171     4 sTAVAa
    18     8    78     4 nGVLMe
    18    16    90     5 hYWNFRn
    18    29   108     1 aVg
    18    33   113     2 pNLl
    18    55   137     1 hGd
    19    22   182     1 nYs
    19    34   195    11 vGKGWTTGSPFRt
    19    36   208     1 iNy
    19    37   210     2 yNAg
    19    51   225     1 lYg
    19    75   247    11 pTGTYKGTVKSDg
    20    29    66     9 eTCAKNCCLDg
    20    48    92     4 lSIGFv
    20    57   105     8 vGARLYLMAs
    20    67   123     2 lLGn
    20    81   137     3 lPCGl
//

TOPITS (threading) results in STRIP format

==================================================  MAXHOM-STRIP  =====================================================
 test sequence    : /home/phd/server/work/predict_h23874.phdDssp
 list name        : /home/phd/server/work/TOPITS_DB.list              
 last name was    : /data/dssp/1lst.dssp
 seq_length       :     87
 alignments       : 2697
 sort-mode        : ZSCORE              
 weights 1        : NO                                      
 weights 2        : NO                                      
 smin             : -1.00
 smax             :  2.00
 maplow           :  0.00
 maphigh          :  0.00
 epsilon          :  0.00
 gamma            :  0.00
 gap_open         : 2                                       
 gap_elongation   : 0.2                                     
 INDEL in sec-struc of SEQ 1: YES                                     
 INDEL in sec-struc of SEQ 2: YES                                     
 NBEST alignments   :    1
 secondary structure alignment: NO                                      
=================================================== SUMMARY ===========================================================
 IAL    VAL   LEN IDEL NDEL  ZSCORE   %IDEN  STRHOM  LEN2   RMS SIGMA NAME
   1   35.53   83   16    7    2.21    0.28    0.26   270 -1.00 0.000 1ybv_A                                   MOL_ID: 1;                                                                                                           .
   2   34.40   77   38   10    2.04    0.40    0.25   435 -1.00 0.000 1csh                                     CITRATE SYNTHASE (E.C.4.1.3.7) COMPLEXED WITH OXALOACETATE                                                           .
   3   34.20   83   17    8    2.01    0.31    0.60   184 -1.00 0.000 1cax_B                                   CANAVALIN (JACK BEAN 7S VICILIN)                                                                                     .
   4   33.80   85   44    8    1.95    0.36    0.21   326 -1.00 0.000 1qor_A                                   QUINONE OXIDOREDUCTASE COMPLEXED WITH NADPH                                                                          .
   5   33.80   79   14    8    1.95    0.33    0.39   432 -1.00 0.000 1bif                                     MOL_ID: 1;                                                                                                           .
   6   33.60   74   25    8    1.92    0.34    0.51   484 -1.00 0.000 1cwv_A                                   MOL_ID: 1;                                                                                                           .
   7   32.87   68   13    4    1.81    0.32    0.37   358 -1.00 0.000 1ece_A                                   MOL_ID: 1;                                                                                                           .
   8   32.47   83   24    8    1.75    0.33    0.27   530 -1.00 0.000 1gtr_A                                   GLUTAMINYL-TRNA SYNTHETASE (E.C.6.1.1.18) COMPLEXED WITH                                                             .
   9   32.47   73   18    7    1.75    0.32    0.58   471 -1.00 0.000 1pfo                                     MOL_ID: 1;                                                                                                           .
  10   32.47   75   25    9    1.75    0.36    0.37   305 -1.00 0.000 2reb                                     RECA PROTEIN (E.C.3.4.99.37)                                                                                         .
  11   32.13   83   16    5    1.70    0.27    0.37   103 -1.00 0.000 3chb_D                                   MOL_ID: 1;                                                                                                           .
  12   32.13   78   25    9    1.70    0.31    0.52   150 -1.00 0.000 1amx                                     MOL_ID: 1;                                                                                                           .
  13   32.13   85   23    7    1.70    0.26    0.10   273 -1.00 0.000 6prc_L                                   MOL_ID: 1;                                                                                                           .
  14   31.93   71   18    6    1.67    0.31    0.29   397 -1.00 0.000 2tys_B                                   MOL_ID: 1;                                                                                                           .
  15   31.87   74   16    7    1.66    0.35    0.17   534 -1.00 0.000 1b8b_A                                   MOL_ID: 1;                                                                                                           .
  16   31.73   80   20    7    1.64    0.31    0.55   150 -1.00 0.000 1bj7                                     MOL_ID: 1;                                                                                                           .
  17   31.53   83   25    6    1.61    0.28    0.48   196 -1.00 0.000 1smv_A                                   MOL_ID: 1;                                                                                                           .
  18   31.53   84   15    6    1.61    0.30    0.45   195 -1.00 0.000 1qhv_A                                   MOL_ID: 1;                                                                                                           .
  19   31.53   81   33    9    1.61    0.32    0.67   393 -1.00 0.000 1axk_A                                   MOL_ID: 1;                                                                                                           .
  20   31.53   81   33    9    1.61    0.32    0.46   434 -1.00 0.000 1cel_A                                   1,4-BETA-D-GLUCAN CELLOBIOHYDROLASE I (CELLULASE)                                                                    .
==================================== ALIGNMENTS ===================================
   1 -  51               ....:....1....:....2....:....3....:....4....:....5
      pred               MINRTDCNENSYLEIHNNEGRDTLCFANAGTMPVAIYGVNWVESGNNVVTL
                                    EEEEE      EEEEEE     EEEEEEEEE    EEEEE
                         OBOOOOOOOBBBBOBBOBOBOOBBBBBBBBOBBBBBBBBBBBOBBBOBBBO
                         HELLLLLLLLLHHHHLLLLLLLHHEHLLLLLLLHHHHLLLHHLLLLLHHHH
                           N T   E     I  N G D  C AN G   V I G   V S   VV  
   1. 1ybv_A       35.53   NSTESAEEVVAAIKKN.GSDAACvaNVGVVevKIFglDIVCSNSGVVSF
                           LLHHHHHHHHHHHHHL.LLLEEEELLLLLHHHHHHLLLEEEELLLLLLL
                         M   TD  E  YL IH  EG   L FA A        G       N  V L
   2. 1csh         34.40 MLGYTDPqerLYLTIHSdeGGNvlSFAAanGLAGPLHGL.....ANQEVLl
                         HHLLLLHHHHHHHHHLLLLLLLHHHHHHHHHHLLLLLLL.....HHHHHHH
                            R     N Y EI N   RD LC  N G   V  Y V  V  G   V L
   3. 1cax_B       34.20 LRSRDPIYSNNyyEikNSQLrdIlclmNEGALFVPHYnvILVAngRAEVEL
                         ELLLLLLEEELLEEELLHHHHLEEEEELLLEEEEEEEEEEEEEELLEEEEE
                          INR         EI    GRDT C    G M  A  GVN    G   VTL
   4. 1qor_A       33.80 VInrEEDLVERLKEItdSVGRDTwcLQRRGLmsGAVTGVNLgqKGSLYVtl
                         EEELLLLHHHHHHHHLELLLHHHHLEEEEEEELLLLLLELLHHLLLLEEEH
                            R  C ENSY        RD L       M V  Y VN V      V  
   5. 1bif         33.80 FMRRIECYENSYESLDEEQDRD.LSYIK..IMDvqSYVVNRVAdqSRIVYY
                         HHHHHHHHHLLLLLLLLLLLLL.LLEEE..EELLLEEEEELLLLHHHHHHH
                             T     S      N G   L F   G  PV I        GN VVT 
   6. 1cwv_A       33.60 LADGTMSSTLSFVPVDKnsGMQGLSFTQNG.VPVSISPisYTAtgNSvvTI
                         ELLLLLLEEEEEELELLLLLLLLEEEEEEE.LLLEELLLLEEEELLLLEEE
                                            GR  L    A   PV I G NW E  N VV  
   7. 1ece_A       32.87                 HTSGREIL...DANNVPVRIAGINwfETCNYVVHG
                                         EEELLEEE...LLLLLEELLEEEELELLLLLLLLL
                         M   T C     LE   N         N  T PV     N V S N  VT 
   8. 1gtr_A       32.47 MYDFTHCISDAllEFQDNRRLYDWVLDNI.TIPveFSRLNlvMSknLLVTD
                         LHHHHHHHHHHHHHHLLLHHHHHHHHHHL.LLLLEELLLLELLLHHHHHHL
                           N TD     Y E    EG   L    A    VA   V     GN V T 
   9. 1pfo         32.47 VHNKTD.....YIETTSTegKINLDHSGaaQFEVAWDEVSYDKEGNEVLTH
                         LLEEEE.....EEEEEEEEEEEEEEELLLEEEEEEEEEEEELLLLLEEEEE
                          I R    E          G   L  A AG  PV IYG     SG    TL
  10. 2reb         32.47  IMRL..GEDRSMDvtISTGSLSLDIagAGGLpvEIYGPE..SSGKTTLTL
                          LLLL..LLLLLLLLEELLLLHHHHHHLLLLEEEEEELLL..LLLHHHHHH
                           N TDC E     IHN  G     F N  T  V   G     S       
  11. 3chb_D       32.13   NITdcAEYHNTQIhndaGkaIITFKNGATFQVEVPGSQHIDSQKKAIE.
                           LHHHHLLLLLEEEEEELLLEEEELLLLLEEEELLLLLLLLHHHHHHHH.
                          IN    NE SY  I    G   L      T      G N   SG    T 
  12. 1amx         32.13  IN....NEKSyiTIKDqqGGQQL...DLSTLNINVTGtnYY.SGQSAIT.
                          EL....LLLLLEEEEEELLLEEE...EEEEEEEEEEELEEE.LLLLHHH.
                              D   N YL  H N G     F NA  M     G   V  G  V T 
  13. 6prc_L       32.13 ILSHLDWVNnqYLNWHYNPGHmsFLFVNA..MALGLHgiLSVAngDKVKTa
                         LLHHHHHHHHHLLLHHHLHHHHHHHHHHH..HHHHHHHHHHHHLLLLLLLH
                          I R D     Y  I   E   TLC    G  P         ES      L
  14. 2tys_B       31.93  IGRAD.....YVSITDDEALetLC.RHEGIIPA.......LESSHALAhl
                          LLLLE.....EEEEEHHHHHHHHH.HHHLLLEL.......HHHHHHHHHH
                             T  NE    E  N   R  LCF         I     V     V   
  15. 1b8b_A       31.87     TQFNEQKFVELFNE..RMDLCFE...ALMCRISSLKGVKA..TVAPI
                             LLELHHHHHHHHHH..HHHHHHH...HHHHHHHHLLLLEH..HHLHH
                            R  CN    L I    G   L    A       YG N  ES N  VT 
  16. 1bj7         31.73    RIEcnDCESLSItkDQGTCLLLTEVAKRQelEFYGTNTLesENMLVT.
                            EEEELLLLEEEEEEELLEEEEEEEEEEEEEEELLLEEEEELLLEEEE.
                           N    N   Y       G   LCF N  T  V   G  W       V  
  17. 1smv_A       31.53  VNKLS.NLRGYVSGQVWSGSAGLCFInsTTLDVSELGKKWYPYKTSavDV
                          HHHHH.LLEEEEEEELLLLHHHHHHHLEEELLLLLLLLLLEELLLHHHLH
                            R D NENS L  HN          NAG MP A          NN V  
  18. 1qhv_A       31.53 IFLRFDQneNSSLKKhnGNSTNANPYTNagFMplAYPKTQSQTAKNNIVSQ
                         EEEEELLLLLLLELLLELLEELLLLLLLLHHLELLLLLLLLLLHHHEEEEE
                           N TD          N  G       N G   V IYGV W   GN   TL
  19. 1axk_A       31.53   NWTD..GGGIVNAVNGSGGnsVNWSNTGNFVvtiygV.WAPNGNGYLTl
                           EEEL..LLLEEEEEELLLLEEEEEELLLLEEEEEEEE.EEEEEEEEEEE
                             T    N Y     N    TLC  N G      YGV    SGN  VT 
  20. 1cel_A       31.53   HATNSSTNCY...DGNTWSSTLCPDNegAAYASTYGV..TTSGNSlvTQ
                           EELLLLLELE...ELLEELLLLLLLHHLLLHHHHHLE..EEELLEEEEE
================================== ALIGNMENTS ==================================
  51 -  87               ....:....1....:....2....:....3....:....4....:....5
      pred               LQFQRNLSDPRLETITLQKWGSWNPGHIHEILSIRIY
                         EEE       EEEEEE            EEEEEEEE 
                         OOBOOOOOOBOBBBBBBOOBBOBBBOOBOOOBBBOBO
                         HHHHHLLLLLLHHHHHHHHLLLLLLLLHHHHHHHHHH
                                        T    G          L IR 
   1. 1ybv_A       35.53 FGHVKDVTPEEFDRvtINTRGQFFVAraYKHLEirL
                         LLLHHHLLHHHHHHHHHHLHHHHHHHHHHHHLLLEE
                         LQ Q  LSD  L   TL   G   PG  H  L 
   2. 1csh         34.40 lqLQKDlsDEKLRDytL.NSGRVVPGYGHAVLR
                         HHHHHHLLHHHHHHHHH.HLLLLLLLELLLLLL
                         L          LE   L        G I  I S
   3. 1cax_B       34.20 LVGLEQQQQQGLESMQLRRyaTLSEGDIIVIPS
                         EEEELLLLLLLLLLLLEEEEEEELLLLEEEELL
                         LQ    L     E   LQK         HEIL  R
   4. 1qor_A       33.80 lqtREELTEASNELFSlqKYPLKDAQRAHEILESR
                         HHLHHHHHHHHHHHHHHHEEEHHHHHHHHHHHHLL
                                  PR   I L   G    G I   LS R
   5. 1bif         33.80 YLMNIHVT.PR..SIYLCRHGESekGRidPGLSPR
                         HHLLLLLL.LL..LEEEEELLLEHHLELLLLELHH
                                  P   T TLQK  S  P     IL
   6. 1cwv_A       33.60 I.......TPQVDTltLQKKISLFppTLTGIL
                         E.......EEEELLEHHLEEEEEELLLEEEEE
                             R      L  I               ILSI  Y
   7. 1ece_A       32.87 GLWSRDYR.SMLDQIKSLGYNTIRLPYSDDIlsINFY
                         LLLLLLHH.HHHHHHHHLLLLEEEEEEEHHHHLLLLL
                                 DPR  TI L   G      I E    RI
   8. 1gtr_A       32.47 DKHVEGWDDPRMPTIslRRRG.YTAASIRE.FCKRI
                         LLLLLLLLLLLLLEHHHHHHL.LLHHHHHH.HHHHH
                              N  D    TI L      N   I 
   9. 1pfo         32.47 HkwDGNYQdaHYStiPLEA....NARNIR
                         EELLLLLLLLLEEEEEELL....LEEEEE
                         LQ QR   D  L  I   K G      I   L
  10. 2reb         32.47 LQvqRefIDAelDPIYARKLG....VDIDNLL
                         HHHHHLEEELLLLHHHHHHLL....LLHHHLE
                               L    L      K   WN      I  I  
  11. 3chb_D       32.13 .RMKDTLRIAYLTEAKVEKLCVWNNKTPRAIAAISM
                         .HHHHHHHHHHHHLLLEEEEEEELLLLLEEEEEEEE
                           F          TI  Q  GS N   I     I
  12. 1amx         32.13 .DFEKAFPGSKinTIDvqGYGSYNSFSINYKTKI
                         .HHHHHLLLLEELEEEEHHHHLLEEEEEEEEEEE
                          Q  R               G      I  I S    
  13. 6prc_L       32.13 aqYFRDVVGYSIGALSIHRLGLFLASNIftIASGPFW
                         HHHHHHHHLLLLLHHHHHHHHHHHHHHHHHHHELLLE
                         L   R      L    L   G       H IL  R
  14. 2tys_B       31.93 lKMMREQPeeQLLVVNLSGRGDKDIFTVHDILKAR
                         HHHHHHLLLLEEEEEEELEELHHHHHHHHHHHHLL
                            Q      RL  I L K GS   G IHE L I  
  15. 1b8b_A       31.87 ILYQEGAFGVRldIIELFKNgsVSLGyiHE.LNILV
                         HHHLLLLLLLLLELHHHHLLLEEEEEEHHH.HHHHH
                              N    R    TL K  S  P       S R
  16. 1bj7         31.73 ..YVENYDGERITKMtlAKGTSFTpeKYQQLNSER
                         ..EEEEELLLLEEEEEEELLLLLLHHHHHHHHHHH
                               L   RL  I L   GS   G I     I  
  17. 1smv_A       31.53 VNIATDLVPARL.VIALLD.GSSsaGRIYDTYTIQM
                         HHHHLLLLLLEE.EEEEEL.LLLLEEEEEEEEEEEE
                                  P   TITL   G        E      
  18. 1qhv_A       31.53 QVYLhdKTKPMILTITLN..GTSESTETSEVSTYSM
                         EEEHHLLLLEEEEEEEEL..HHHLLLLLLLLLLEEE
                         L   R    P  E      WG   PG    I     Y
  19. 1axk_A       31.53 lgWTRS...PLIEYYVVDSWGTYRpgGTYDIYTTTRY
                         EEEEEL...LLEEEEEEEEELLLLLLEEEEEEEEEEE
                            Q N SD      TL    S         L    Y
  20. 1cel_A       31.53 QSAQKNvsDTTYQEFTlnEF.SFD.VDVSQllNGALY
                         ELLLEEEELLEELEEELEEE.EEE.EELLLLEEEEEE
 2    45    40

Threading results in TOPITS format

TOP - BOTTOM - TOPITS

# TOPITS (Threading One-D Predictions Into Three-D Structures)
# --------------------------------------------------------------------------------
# FORMAT   begin
# FORMAT   general:    - lines starting with hashes contain comments or PARAMETERS
# FORMAT   general:    - columns are delimited by tabs
# FORMAT   general:    - the data are given in BLOCKS, each introduced by a line
# FORMAT   general:      beginning with a hash and a keyword
# FORMAT   parameters: '# PARA:tab     keyword =tab value tab (further-information)'
# FORMAT   notation:   '# NOTATION:tab keyword tab explanation'
# FORMAT   info:       '# INFO:tab     text'
# FORMAT   blocks 0:   '# BLOCK        keyword'
# FORMAT   blocks 1:    column names (tab delimited)
# FORMAT   blocks n>1:  column data  (tab delimited)
# FORMAT   file end:   '//' marks the end of a complete file
# FORMAT   end
# --------------------------------------------------------------------------------
# PARA     begin
# PARA     TOPITS HEADER: PARAMETERS
# PARA:	len1       =	87    
# PARA:	nali       =	2697  
# PARA:	listName   =	/home/phd/server/work/TOPITS_DB.list
# PARA:	sortMode   =	ZSCORE
# PARA:	weight1    =	NO    
# PARA:	weight2    =	NO    
# PARA:	smin       =	-1.00 
# PARA:	smax       =	2.00  
# PARA:	gapOpen    =	2     
# PARA:	gapElon    =	0.2   
# PARA:	indel1     =	YES   
# PARA:	indel2     =	YES   
# PARA:	threshold  =	ALL   
# PARA:	str:seq    =	50    	(i.e. str= 50%, seq= 50%)
# PARA     end
# --------------------------------------------------------------------------------
# NOTATION begin
# NOTATION TOPITS HEADER: ABBREVIATIONS PARAMETERS
# NOTATION:	len1        :	length of search sequence, i.e., your protein
# NOTATION:	nali        :	number of alignments in file
# NOTATION:	listName    :	fold library used for threading
# NOTATION:	sortMode    :	mode of ranking the hits
# NOTATION:	weight1     :	YES if guide sequence weighted by residue conservation
# NOTATION:	weight2     :	YES if aligned sequence weighted by residue conservation
# NOTATION:	smin        :	minimal value of alignment metric
# NOTATION:	smax        :	maximal value of alignment metric
# NOTATION:	gapOpen     :	gap open penalty
# NOTATION:	gapElon     :	gap elongation penalty
# NOTATION:	indel1      :	YES if insertions in sec str regions allowed for guide seq
# NOTATION:	indel2      :	YES if insertions in sec str regions allowed for aligned seq
# NOTATION:	threshold   :	hits above this threshold included (ALL means no threshold)
# NOTATION:	str:seq     :	weight structure:sequence
# NOTATION TOPITS HEADER: ABBREVIATIONS SUMMARY
# NOTATION:	id2         :	PDB identifier of aligned structure (1pdbC -> C = chain id)
# NOTATION:	pide        :	percentage of pairwise sequence identity
# NOTATION:	lali        :	length of alignment
# NOTATION:	ngap        :	number of insertions
# NOTATION:	lgap        :	number of residues inserted
# NOTATION:	len2        :	length of aligned protein structure
# NOTATION:	Eali        :	alignment score
# NOTATION:	Zali        :	alignment zcore;  note: hits with z>3 more reliable
# NOTATION:	strh        :	secondary str identity between guide and aligned protein
# NOTATION:	ifir        :	position of first residue of search sequence
# NOTATION:	ilas        :	position of last residue of search sequence
# NOTATION:	jfir        :	pos of first res of remote homologue (e.g. DSSP number)
# NOTATION:	jlas        :	pos of last res of remote homologue  (e.g. DSSP number)
# NOTATION:	name        :	name of aligned protein structure
# NOTATION end
# --------------------------------------------------------------------------------
# INFO     begin
# INFO     TOPITS HEADER: ACCURACY
# INFO:	 Tested on 80 proteins, TOPITS found the correct remote homologue in about
# INFO:	 30%of the cases.  Detection accuracy was higher for higher z-scores:
# INFO:	 ZALI>0   => 1st hit correct in 33% of cases
# INFO:	 ZALI>3   => 1st hit correct in 50% of cases
# INFO:	 ZALI>3.5 => 1st hit correct in 60% of cases
# INFO     end
# --------------------------------------------------------------------------------
# BLOCK    TOPITS HEADER: SUMMARY
rank	id2	pide	lali	ngap	lgap	len2	Eali	Zali	strh	ifir	ilas	jfir	jlas	name
1	1ybvA	28	83	7	16	270	35.53	2.21	26	3	86	49	146	1ybv_A MOL_ID: 1; .
2	1csh	40	77	10	38	435	34.40	2.04	25	1	83	214	322	1csh CITRATE SYNTHASE (E.C.4.1.3.7) COMPLEXED WITH OXALOACETATE .
3	1caxB	31	83	8	17	184	34.20	2.01	60	1	83	11	110	1cax_B CANAVALIN (JACK BEAN 7S VICILIN) .
4	1qorA	36	85	8	44	326	33.80	1.95	21	1	85	188	316	1qor_A QUINONE OXIDOREDUCTASE COMPLEXED WITH NADPH .
5	1bif	33	79	8	14	432	33.80	1.95	39	1	85	154	240	1bif MOL_ID: 1; .
6	1cwvA	34	74	8	25	484	33.60	1.92	51	1	82	210	300	1cwv_A MOL_ID: 1; .
7	1eceA	32	68	4	13	358	32.87	1.81	37	17	87	7	82	1ece_A MOL_ID: 1; .
8	1gtrA	33	83	8	24	530	32.47	1.75	27	1	86	203	306	1gtr_A GLUTAMINYL-TRNA SYNTHETASE (E.C.6.1.1.18) COMPLEXED WITH .
9	1pfo	32	73	7	18	471	32.47	1.75	58	1	79	346	424	1pfo MOL_ID: 1; .
10	2reb	36	75	9	25	305	32.47	1.75	37	2	82	24	113	2reb RECA PROTEIN (E.C.3.4.99.37) .
11	3chbD	27	83	5	16	103	32.13	1.70	37	3	86	4	101	3chb_D MOL_ID: 1; .
12	1amx	31	78	9	25	150	32.13	1.70	52	2	84	26	115	1amx MOL_ID: 1; .
13	6prcL	26	85	7	23	273	32.13	1.70	10	1	87	150	255	6prc_L MOL_ID: 1; .
14	2tysB	31	71	6	18	397	31.93	1.67	29	2	85	317	392	2tys_B MOL_ID: 1; .
15	1b8bA	35	74	7	16	534	31.87	1.66	17	5	86	304	385	1b8b_A MOL_ID: 1; .
16	1bj7	31	80	7	20	150	31.73	1.64	55	4	85	35	132	1bj7 MOL_ID: 1; .
17	1smvA	28	83	6	25	196	31.53	1.61	48	2	86	83	186	1smv_A MOL_ID: 1; .
18	1qhvA	30	84	6	15	195	31.53	1.61	45	1	86	70	166	1qhv_A MOL_ID: 1; .
19	1axkA	32	81	9	33	393	31.53	1.61	67	3	87	164	269	1axk_A MOL_ID: 1; .
20	1celA	32	81	9	33	434	31.53	1.61	46	3	87	42	145	1cel_A 1,4-BETA-D-GLUCAN CELLOBIOHYDROLASE I (CELLULASE) .
//

END of results for file predict_h23874

Quotes for methods

PredictProtein: PredicProtein: B Rost (1996) Methods in Enzymology, 266:525-539
- Author: B Rost
- Contact: liu@cubic.bioc.columbia.edu
- Url: http://cubic.bioc.columbia.edu
- Version: 1.99.08
- Description: PredictProtein is the acronym for all prediction programs run.
ProSite: K Hofmann , P Bucher, L Falquet, A Bairoch:: The PROSITE database, its status in 1999. Nucleic Acids Res, 27, 215-219, 1999
- Author: Kay Hofmann, Philip Bucher, and Amos Bairoch (SIB, Geneva, Switzerland)
- Contact: Christian.Sigrist\@isb-sib.ch
- Url: http://www.expasy.ch/prosite/
- Version: 99.07
- Description: PROSITE is a database of functional motifs. ScanProsite, finds all functional motifs in your sequence that are annotated in the ProSite db
MaxHom: C Sander, and R Schneider::Database of Homology-Derived Structures and the Structural Meaning of Sequence Alignment. Proteins, 9, 56-68, 1991
- Author: Reinhard Schneider (LION, Boston) and Chris Sander (Millenium, Boston)
- Contact: rost\@columbia.edu
- Url: local
- Version: 1.99.04
- Description: MaxHom is a dynamic multiple sequence alignment program which finds similar sequences in a database.
MView: N P Brown, C Leroy, and C Sander:: MView: A Web compatible database search or multiple alignment viewer. Bioinformatics, 14, 380-381, 1998
- Author: Nigel Brown
- Contact: nbrown\@nimr.mrc.ac.uk
- Url: http://mathbio.nimr.mrc.ac.uk/~nbrown/mview/
- Copyright: Copyright (C) Nigel P. Brown, 1997-1998. All rights reserved.
- Version: 1.40.2
- Description: MView is a program converting multiple sequence alignments into fancy HTML formatted output
PHD: B Rost:: PHD: predicting one-dimensional protein structure by profile based neural networks. Methods in Enzymology, 266, 525-539, 1996
- Author: Burkhard Rost (CUBIC, Columbia Univ, New York)
- Contact: rost\@columbia.edu
- Url: http://cubic.bioc.columbia.edu/predictprotein
- Version: 1.96
- Description: PHD is a suite of programs predicting 1D structure (secondary structure, solvent accessibility) from multiple sequence alignments
PHDsec: B Rost & C Sander (1993) J. of Molecular Biology, 232:584-599
- Author: B Rost
- Url: http://cubic.bioc.columbia.edu
- Version: 1.96
- Description: PHDsec predicts secondary structure from multiple sequence alignments.
PHDacc: B Rost & C Sander (1994) Proteins, 20:216-226
- Url: rost@columbia.edu
- Version: 1.96
- Description: PHDacc predicts per residue solvent accessibility from multiple sequence alignments.
GLOBE: B Rost::Short yeast ORFs: expressed protein or not? unpublished, 2000
- Author: Burkhard Rost (CUBIC, Columbia Univ, New York)
- Contact: rost\@columbia.edu
- Url: http://cubic.bioc.columbia.edu/predictprotein
- Version: 1.98.05
- Description: GLOBE predicts the globularity of a protein
TOPITS: B Rost:: TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures. In: C Rawlings, D Clark, R Altman, L Hunter, T Lengauer, and S Wodak (eds.) The third international conference on Intelligent Systems for Molecular Biology (ISMB), Cambridge, England, Menlo Park, CA: AAAI Press, 314-321, 1995. \n B Rost, R Schneider, and C Sander:: Protein fold recognition by prediction-based threading. J of Molecular Biology, 270, 471-480, 1997
- Author: Burkhard Rost (CUBIC, Columbia Univ, New York)
- Contact: rost\@columbia.edu
- Url: http://cubic.bioc.columbia.edu/predictprotein
- Version: 1.97
- Description: TOPITS is a prediction-based threading program, that finds remote structural homologues in the DSSP database
CYSPRED: P Fariselli, P Riccobelli, and R Casadio:: Role of evolutionary information in predicting the disulfide-bonding state of cysteine in proteins. Proteins, 36, 340-346, 1999
- Author: Piero Fariselli and Rita Casadio (Bologna Univ, Bologna)
- Contact: farisel\@kaiser.alma.unibo.it
- Url: http://prion.biocomp.unibo.it/cyspred.html
- Description: CYSPRED finds whether the cys residue in your protein forms disulfide bridge

Links:

TOP

%A: 3.5	%C: 2.3	%D: 3.5	%E: 6.9	%F: 2.3
%G: 6.9	%H: 3.5	%I: 9.2	%K: 1.1	%L: 8.1
%M: 2.3	%N: 12.6	%P: 3.5	%Q: 3.5	%R: 5.8
%S: 5.8	%T: 6.9	%V: 5.8	%W: 3.5	%Y: 3.5

AA :	amino acid sequence
PHD_sec:	PHD predicted secondary structure: H=helix, E=extended (sheet), blank=other (loop) PHD = PHD: Profile network prediction HeiDelberg
Rel_sec:	reliability index for PHDsec prediction (0=low to 9=high) Note: for the brief presentation strong predictions marked by '*'
SUB_sec:	subset of the PHDsec prediction, for all residues with an expected average accuracy > 82% (tables in header) NOTE: for this subset the following symbols are used: L: is loop (for which above ' ' is used) .: means that no prediction is made for this residue, as the reliability is: Rel < 5

pH_sec:	'probability' for assigning helix (1=high, 0=low)
pE_sec:	'probability' for assigning strand (1=high, 0=low)
pL_sec:	'probability' for assigning neither helix, nor strand (1=high, 0=low)
P_3_acc:	PHD predicted relative solvent accessibility (acc) in 3 states: b = 0-9%, i = 9-36%, e = 36-100%.
Rel_acc:	reliability index for PHDacc prediction (0=low to 9=high) Note: for the brief presentation strong predictions marked by '*'
SUB_acc:	subset of the PHDacc prediction, for all residues with an expected average correlation > 0.69 (tables in header) NOTE: for this subset the following symbols are used: I: is intermediate (for which above ' ' is used) .: means that no prediction is made for this residue, as the reliability is: Rel < 4

PHD_acc:	PHD predicted relative solvent accessibility (acc) in 10 states: a value of n (=0-9) corresponds to a relative acc. of between nn % and (n+1)(n+1) % (e.g. for n=5: 16-25%).