a2m2html output for tmp.a2m

Citations (SAM, SAM-T99, HMMs)

R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: Extension and analysis of the basic method, CABIOS 12:95-107, 1996.
K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting remote protein homologies, Bioinformatics 14(10):846-856, 1998.
A. Krogh et al., Hidden Markov models in computational biology: Applications to protein modeling, JMB 235:1501-1531, Feb 1994.

Sequence numbers correspond to the following labels:

- T0500
- gi|18079216|ref|NP_065815.1|_1203:1402 CASK interacting protein 1 [Homo sapiens]
- gi|61213003|sp|Q8WXD9|CSKI1_HUMAN Caskin-1 (CASK-interacting protein 1) [Taxonomy]
- gi|17940758|gb|AAL49758.1|AF451977_1 cask-interacting protein 1 [Homo sapiens]
- gi|119605949|gb|EAW85543.1|_1121:1320 CASK interacting protein 1, isoform CRA_a [Homo sapiens]
- gi|119605951|gb|EAW85545.1| CASK interacting protein 1, isoform CRA_a [Homo sapiens]
- gi|7242967|dbj|BAA92544.1|_926:1125 KIAA1306 protein [Homo sapiens]
- gi|119605950|gb|EAW85544.1|_888:1087 CASK interacting protein 1, isoform CRA_b [Homo sapiens]
- gi|37360318|dbj|BAC98137.1|_1121:1317 mKIAA1306 protein [Mus musculus]
- gi|161168996|ref|NP_082213.2|_1205:1401 CASK interacting protein 1 [Mus musculus]
- gi|61212969|sp|Q6P9K8|CSKI1_MOUSE Caskin-1 (CASK-interacting protein 1) [Taxonomy]
- gi|26339338|dbj|BAC33340.1|_427:623 unnamed protein product [Mus musculus]
- gi|26340714|dbj|BAC34019.1|_539:735 unnamed protein product [Mus musculus]
- gi|109127251|ref|XP_001084114.1|_1224:1420 PREDICTED: similar to CASK interacting protein 1 [Macaca mulatta]
- gi|61212441|sp|Q8VHK2|CSKI1_RAT_1204:1400 Caskin-1 (CASK-interacting protein 1) [Taxonomy]
- gi|17940754|gb|AAL49756.1|AF451975_1 cask-interacting protein 1 [Rattus norvegicus]
- gi|158138557|ref|NP_542421.2|_1204:1400 CASK interacting protein 1 [Rattus norvegicus]
- gi|119916513|ref|XP_871198.2|_1072:1270 PREDICTED: similar to mKIAA1306 protein [Bos taurus]
- gi|118097927|ref|XP_414857.2|_1230:1419 PREDICTED: similar to cask-interacting protein 1 [Gallus gallus]
- gi|189514414|ref|XP_682906.3|_1188:1416 PREDICTED: similar to CASK interacting protein 1 [Danio rerio]
- gi|189514420|ref|XP_001919695.1|_796:1024 PREDICTED: similar to CASK interacting protein 1 [Danio rerio]
- gi|189517204|ref|XP_692129.3|_1272:1498 PREDICTED: CASK interacting protein 1 [Danio rerio]
- gi|47216277|emb|CAG05973.1|_1225:1460 unnamed protein product [Tetraodon nigroviridis]
- gi|148690385|gb|EDL22332.1|_1219:1370 CASK interacting protein 1, isoform CRA_a [Mus musculus]
- gi|73959509|ref|XP_853631.1|_1189:1315 PREDICTED: similar to CASK interacting protein 1 [Canis familiaris]
- gi|38511409|gb|AAH60720.1|_1188:1325 Caskin1 protein [Mus musculus]

                 10          20        30           40         50      
                 |           |         |            |          |      
   1 ...TDLAHLPPLPPP..EGEARKPAKPPVSPKPVLTQPVPKLQG...SPTPTSKK.VPLPGP.GS
   2 pppTDLAHLPPLPPP..EGEARKPAKPPVSPKPVLTQPVPKLQG...SPTPTSKK.VPLPGP.GS
   3 pppTDLAHLPPLPPP..EGEARKPAKPPVSPKPVLTQPVPKLQG...SPTPTSKK.VPLPGP.GS
   4 pppTDLAHLPPLPPP..EGEARKPAKPPVSPKPVLTQPVPKLQG...SPTPTSKK.VPLPGP.GS
   5 pppTDLAHLPPLPPP..EGEARKPAKPPVSPKPVLTQPVPKLQG...SPTPTSKK.VPLPGP.GS
   6 pppADLMQLPPLPLP..DGNARKPVKPPVSPKPILAQPVSKIQG...SPTPASKK.VPLPGP.GS
   7 pppADLMQLPPLPLP..DGNARKPVKPPVSPKPILSQPVSKIQG...SPTPASKK.VPLPGP.GS
   8 pppADLMQLPPLPLP..DGNARKPVKPPVSPKPILSQPVSKIQG...SPTPASKK.VPLPGP.GS
   9 pppADLMQLPPLPLP..DGNARKPVKPPVSPKPILSQPVSKIQG...SPTPASKK.VPLPGP.GS
  10 pppTDLAHLPPLPPP..EGEARKPAKPPVSPKPVLTQPMPKIQG...SPTPTSKK.VPLPGP.GS
  11 pppTDLMPLPPLPLP..DGSARKPVKPPVSPKPILAQPVSKIQG...SPTPASKK.VPLPGP.GS
  12 pppTDLMPLPPLPLP..DGSARKPVKPPVSPKPILAQPVSKIQG...SPTPASKK.VPLPGP.GS
  13 pppSDLMHLPPLPPP..DSDARKLAKPPVSPKPILAQPVPKIQG...SPTPASKK.VPLPGP.SS
  14 pppATRPDGPDFTPP..SAEPKKPFKPPVSPKPVLTQPAQKVPG...PPVPIPKK.MPVPSP.GS
  15 acvGDGGRDEELHHDgfGSLPRQILKPPVSPKPAMA--LRKFD-...PPTP-TRR.VPLPGPeGQ
  16 acvGDGGRDEELHHDgfGSLPRQILKPPVSPKPAMA--LRKFD-...PPTP-TRR.VPLPGPeGQ
  17 sprRDSADLEG-HVT..ESTPRKSVKPPVSPKPVLAQHMKK-QG...PTAAITKK.APFPGPaGA
  18 rrrNSVEQAAPGSTD..GGPARKP-KPPVSPKPIVAQ-IKRQGGpqtPPHPASNKsIPLPGP.GT
  19 pppADLMQLPPLPLP..DGNARKPVKPPVSPKPILAQPVSKIQG...SPTPASKK.VPLPGP.G-
  20 pppTDLLHLPPLPPP..DTDTRKPAKPPVSPKPVLAQPVPKIQG...SPTPASKK.VPLPGP.GS
  21 pppADLMQLPPLPLP..DGNARKPVKPPVSPKPILSQPVSKIQG...SPTPASKK.VPLPGP.GS


          60        70        80        90         100             110 
          |         |         |         |           |               | 
   1 PE.VKRAHGTPPPVSPKPPPPPTAPKPVKAVAGLPSGSAG.PSP.APSPARQ.....PPAAL.AK
   2 PE.VKRAHGTPPPVSPKPPPPPTAPKPVKAVAGLPSGSAG.PSP.APSPARQ.....PPAAL.AK
   3 PE.VKRAHGTPPPVSPKPPPPPTAPKPVKAVAGLPSGSAG.PSP.APSPARQ.....PPAAL.AK
   4 PE.VKRAHGTPPPVSPKPPPPPTAPKPVKAVAGLPSGSAG.PSP.APSPARQ.....PPAAL.AK
   5 PE.VKRAHGTPPPVSPKPPPPPTAPKPVKAVAGLPSGSAG.PSP.APSPARQ.....PPAAL.AK
   6 PE.VKRAHGTPPPVSPKPPPPPTAPKPAKALAGLQSSSAT.PSP.VPSPARQ.....PPAAL.IK
   7 PE.VKRAHGTPPPVSPKPPPPPTAPKPAKALAGLQSSSAT.PSP.VPSPARQ.....PPAAL.IK
   8 PE.VKRAHGTPPPVSPKPPPPPTAPKPAKALAGLQSSSAT.PSP.VPSPARQ.....PPAAL.IK
   9 PE.VKRAHGTPPPVSPKPPPPPTAPKPAKALAGLQSSSAT.PSP.VPSPARQ.....PPAAL.IK
  10 PE.VKRAHGTPPPVSPKPPPPPTAPKPAKVAAGLPSGSAG.PSP.APSPARQ.....PPAAL.AK
  11 PE.VKRAHGTPPPVSPKPPPPPTAPKPAKALAGLQSSSAT.PSP.VPSPARQ.....PPAAL.IK
  12 PE.VKRAHGTPPPVSPKPPPPPTAPKPAKALAGLQSSSAT.PSP.VPSPARQ.....PPAAL.IK
  13 PE.VKRAHGTPPPVSPKPPPPPTAPKPAKAAAGLQSGSSS.PSP.APSPARQ.....QPAAL.AK
  14 PE.VKRVHGTPPPVSPKPTPPPTAPKPPKPHATIQSVSAG.STP.TPSPARQ.....LGAA-.AK
  15 HS.PVEVRKIPPPVSPKPSPPPTLPKPVKIKPIHTIGTPGsPQPdVVSPFSAs25pmEGNMLsPR
  16 HS.PVEVRKIPPPVSPKPSPPPTLPKPVKIKPIHTIGTPGsPQPdVVSPFSAs25pmEGSMLsPR
  17 PGsPVEGKKVPPPISPKPTPPPTAPKPSKNVLQSLNATPN.PTP.TPSPAKQt21ttPPALI.VQ
  18 PGsPVEGKKIPPPVSPKPAPPPTAPKPAKLVHSMTSPSCH.STTtAPAPVRQh14glPPTNI.PS
  19 --.-------------------------------------.---.--SPARQ.....PPAAL.IK
  20 PE.VKRAHGTPPPVSPKPPPPPTAPKPAKAAAGLQSGSAS.PSP.APSPARQ.....PPAAL.AK
  21 PE.VKRAHGTPPPVSPKPPPPPTAP---------------.---.-------.....-----.--


                        120       130            140       150         
                         |         |              |         |         
   1 PPG....TP.....PSL...GASPAKPPSPGAP....ALH.VPAKPPRAAAAAAAAA.AAPP...
   2 PPG....TP.....PSL...GASPAKPPSPGAP....ALH.VPAKPPRAAAAAAAAA.AAPP...
   3 PPG....TP.....PSL...GASPAKPPSPGAP....ALH.VPAKPPRAAAAAAAAA.AAPP...
   4 PPG....TP.....PSL...GASPAKPPSPGAP....ALH.VPAKPPRAAAAAAAAA.AAPP...
   5 PPG....TP.....PSL...GASPAKPPSPGAP....ALH.VPAKPPRAAAAAAAAA.AAPP...
   6 PAS....SP.....PSQ...SASPVKPPSPGTP....ALH.VPAKPPR---AAASVV.SGPP...
   7 PAS....SP.....PSQ...SASPVKPPSPGTP....ALH.VPAKPPR---AAASVV.SGPP...
   8 PAS....SP.....PSQ...SASPVKPPSPGTP....ALH.VPAKPPR---AAASVV.SGPP...
   9 PAS....SP.....PSQ...SASPVKPPSPGTP....ALH.VPAKPPR---AAASVV.SGPP...
  10 PPG....TP.....PSL...GTSPVKPPSPGAP....ALH.VPAKPPRAAAAAAA--.-APP...
  11 PAS....SP.....PSQ...SASPAKPPSPGAP....ALQ.VPTKPPR---AAASVV.SGPP...
  12 PAS....SP.....PSQ...SASPAKPPSPGAP....ALQ.VPTKPPR---AAASVV.SGPP...
  13 PAS....TP.....PALsasPASPARPPSPGAP....ALH.VPAKPPRAAAAA----.TGPP...
  14 PSS....TP.....PSL...CSSPAKPLSPGTQ....PQQ.VPVKPPRSAIAGPSVD.SASP...
  15 PAT....SPaqs..PQT...PQTPQTPQTPSTP....GSGsAPVKPPRSSMAGLSVD.IPSP...
  16 PAT....SPaqs..PQT...PQTPQTPQTPSTP....GSGsAPVKPPRSSMAGLSVD.IPSP...
  17 TPH....TPqsphtPQT...PQTPQTPQTPPTPt...PTP.PPVKPPRSSISGVSMDsSTGS...
  18 PPNakplSPs....PQS...PHTPQTPPTPQTPatpsPTP.PPVKPPRSSIGGVSVD.SGTPggg
  19 PAS....SP.....PSQ...SASPVKPPSPGTP....ALH.VPAKPPR---AAASVV.SGPP...
  20 PAS....TR.....PSL...SASTAKPP-PSS-....---.----------------.----...
  21 ---....--.....---...-------------....---.---KPPR---AAASVV.SGPP...


        160            170       180        190       200   
         |              |         |          |         |   
   1 APPEGASPGD.....SARQKLEETSACLAAALQAVEEKI.RQEDAQGPRDS...
   2 APPEGASPGD.....SARQKLEETSACLAAALQAVEEKI.RQEDAQGPRDSaae
   3 APPEGASPGD.....SARQKLEETSACLAAALQAVEEKI.RQEDAQGPRDSaae
   4 APPEGASPGD.....SARQKLEETSACLAAALQAVEEKI.RQEDAQGPRDSaae
   5 APPEGASPGD.....SARQKLEETSACLAAALQAVEEKI.RQEDAQGPRDSaae
   6 VASDCASPGD.....SARQKLEETSACLAAALQAVEEKI.RQEDGQGPRPSsie
   7 VASDCASPGD.....SARQKLEETSACLAAALQAVEEKI.RQEDGQGPRPSsie
   8 VASDCASPGD.....SARQKLEETSACLAAALQAVEEKI.RQEDGQGPRPSsie
   9 VASDCASPGD.....SARQKLEETSACLAAALQAVEEKI.RQEDGQGPRPSsie
  10 APTEGASPGD.....SARQKLEETSACLAAALQAVEEKI.RQEDAQGPRDSaae
  11 VASDCASPGD.....SARQKLEETSACLAAALQAVEEKI.RQEDGQGPRPSsie
  12 VASDCASPGD.....SARQKLEETSACLAAALQAVEEKI.RQEDGQGPRPSsie
  13 AAPDGASPGD.....SARQKLEETSACLAAALQAVEEKI.RQEDAQGSRPSaae
  14 ---------E.....LVQQKLEETSASLAAALQAVEEKI.KQEDSQAADSTaea
  15 LEVD--VPGL.....DVQKRLRESDKQREDDDMRKQERV.DEVGFAKMERTgli
  16 LEVD--VPGL.....DVQKRLRESDKQREDDDMRKQERV.DEVGFAKMERTgli
  17 ALVAGVVTAD.....AVHQKIEETSASLAAALQAVEQKI.K-EDGQKDSIAenk
  18 VTTPTPTTTDfsvdfLVQQKLEETSASLAAALQAVEDKIlHQEDSVAEQKTtvs
  19 VASDCASPGD.....SARQKLEETSACLAAALQAVEEKI.RQEDGQGPRPSsie
  20 ----------.....------------------------.-----------...
  21 VASDCASPGD.....SARQKLEETSACLAAALQAVEEKI.RQEDGQGPRPSsie