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Output form the CPH ModelsWorld Wide Web Prediction ServerCenter for Biological Sequence Analysis |
Query sequence: >rk MDFGSLETVVANSAFIAARGSFDGSSSQPSRDKKYLAKLKLPPLSKCESLRDSLSLEFES VCLEQPIGKKLFQQFLQSAEKHLPALELWKDIEDYDTADNDLQPQKAQTILAQYLDPQAK LFCSFLDEGIVAKFKEGPVEIQDGLFQPLLQATLAHLGQAPFQEYLGSLYFLRFLQWKWL EAQPMGEDWFLDFRVLGKGGFGEVSACQMKATGKLYACKKLNKKRLKKRKGYQGAMVEKK ILMKVHSRFIVSLAYAFETKADLCLVMTIMNGGDIRYHIYNVNEENPGFPEPRALFYTAQ IICGLEHLHQRRIVYRDLKPENVLLDNDGNVRISDLGLAVELLDGQSKTKGYAGTPGFMA PELLQGEEYDFSVDYFALGVTLYEMIAARGPFRARGEKVENKELKHRIISEPVKYPDKFS QASKDFCEALLEKDPEKRLGFRDETCDKLRAHPLFKDLNWRQLEAGMLMPPFIPDSKTVY AKDIQDVGAFSTVKGVAFDKTDTEFFQEFATGNCPIPWQEEMIETGIFGELNVWRSDGQM PDDMKGISGGSSSSSKSGMCLVS Finding template for your sequence Output from fasta: opt: 514 z-sco: 657.1 E: 1.2e-30 Template: /usr/cbs/databases/pdb/allpdb/pdb1cdk.ent chain A Template sequence: >1CDK.A (null) KGSEQESVKEFLAKAKEDFLKKWENPAQNTAHLDQFERIKTLGTGSFGRVMLVKHKETGN HFAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEYSFKDNSNLYMVMEYVPGGE MFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGF AKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFADQPIQIY EKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKDGVNDIKNHKWFATTDWIAIYQ RKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF Using alignment with position specific gap penalties: >1CDK.A rk 1CDK.A ------------------------------------------------------------ rk MDFGSLETVVANSAFIAARGSFDGSSSQPSRDKKYLAKLKLPPLSKCESLRDSLSLEFES 1CDK.A ------------------------------------------------------------ rk VCLEQPIGKKLFQQFLQSAEKHLPALELWKDIEDYDTADNDLQPQKAQTILAQYLDPQAK 1CDK.A ------------------------------------KGSEQESVKEFLAKAKEDFLKKWE rk LFCSFLDEGIVAKFKEGPVEIQDGLFQPLLQATLAHLG--QAPFQEYLGSLYFLRFLQWK 1CDK.A N-PAQNTAHLDQFERIKTLGTGSFGRVMLVKHKETGNHFAMKILDKQKVVKLKQIEHTLN rk WLEAQPMGE-DWFLDFRVLGKGGFGEVSACQMKATGKLYACKKLNKKRLKKRKGYQGAMV 1CDK.A EKRILQAVNFPFLVKLEYSFKDNSNLYMVMEYVPGGEMFSHLRRIGR----FSEPHARFY rk EKKILMKVHSRFIVSLAYAFETKADLCLVMTIMNGGDIRYHIYNVNEENPGFPEPRALFY 1CDK.A AAQIVLTFEYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFA-KRVKGRTWT--LCGTPE rk TAQIICGLEHLHQRRIVYRDLKPENVLLDNDGNVRISDLGLAVELLDGQSKTKGYAGTPG 1CDK.A YLAPEIILSKGYNKAVDWWALGVLIYEMAAGYPPFFAD----QPIQIYEKIVSGKVRFPS rk FMAPELLQGEEYDFSVDYFALGVTLYEMIAARGPFRARGEKVENKELKHRIISEPVKYPD 1CDK.A HFSSDLKDLLRNLLQVDLTKRFGNLKDGVNDIKNHKWFATTDWIAIYQRKVEA-----PF rk KFSQASKDFCEALLEKDPEKRLGFRDETCDKLRAHPLFKDLNW-----RQLEAGMLMPPF 1CDK.A IPKFKGPGDTSNFDDYEEEEIRVSIN----EKCGKEF-SEF------------------- rk IPDSK----TVYAKDIQDVGAFSTVKGVAFDKTDTEFFQEFATGNCPIPWQEEMIETGIF 1CDK.A ----------------------------------- rk GELNVWRSDGQMPDDMKGISGGSSSSSKSGMCLVS Making distance prediction for sequence gawk: cmd. line:2: (FILENAME=- FNR=852) warning: error writing standard output (Broken pipe).Figure: Upper triangle is the predicted sistance constraints using a neural network. The predicted probability of a contact is shown below the distance matrix.Lower triangle is a combination of constraints from the alignment and from the neural networks. Red is predicted contact blue is predicted non contact. PostScript Graphics removing unaligned ends Folding Calpha-Calpha distances outside 3.6-4.0AA range res_1 Res_2 Calpha-Calpha distance 494 495 4.008 - - -
PDB3D
is a high speed 3D molecule rendering applet written by Scott Legrand at
UCLA.
Controls:
Download pdb file with the CPH Model