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|7242967|dbj|BAA92544.1|_1028:1154 KIAA1306 protein [Homo sapiens]
- gi|18079216|ref|NP_065815.1|_1305:1431 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|_1223:1349 CASK interacting protein 1, isoform CRA_a [Homo sapiens]
- gi|119605951|gb|EAW85545.1| CASK interacting protein 1, isoform CRA_a [Homo sapiens]
- gi|119605950|gb|EAW85544.1|_990:1116 CASK interacting protein 1, isoform CRA_b [Homo sapiens]
- gi|109127251|ref|XP_001084114.1|_1326:1449 PREDICTED: similar to CASK interacting protein 1 [Macaca mulatta]
- gi|37360318|dbj|BAC98137.1|_1223:1347 mKIAA1306 protein [Mus musculus]
- gi|148690385|gb|EDL22332.1|_1276:1400 CASK interacting protein 1, isoform CRA_a [Mus musculus]
- gi|158138557|ref|NP_542421.2|_1306:1430 CASK interacting protein 1 [Rattus norvegicus]
- gi|161168996|ref|NP_082213.2|_1307:1431 CASK interacting protein 1 [Mus musculus]
- gi|61212969|sp|Q6P9K8|CSKI1_MOUSE Caskin-1 (CASK-interacting protein 1) [Taxonomy]
- gi|61212441|sp|Q8VHK2|CSKI1_RAT_1306:1430 Caskin-1 (CASK-interacting protein 1) [Taxonomy]
- gi|17940754|gb|AAL49756.1|AF451975_1 cask-interacting protein 1 [Rattus norvegicus]
- gi|31981530|ref|NP_542374.2|_1078:1201 cask-interacting protein 2 [Mus musculus]
- gi|31418584|gb|AAH53083.1| Cask-interacting protein 2 [Mus musculus]
- gi|123267559|emb|CAM21977.1| cask-interacting protein 2 [Mus musculus]
- gi|37360258|dbj|BAC98107.1|_1101:1224 mKIAA1139 protein [Mus musculus]
- gi|61213002|sp|Q8VHK1|CSKI2_MOUSE_1078:1201 Caskin-2 [Taxonomy]
- gi|17940760|gb|AAL49759.1|AF451978_1_1078:1201 cask-interacting protein 2 [Mus musculus]
- gi|148702574|gb|EDL34521.1|_1078:1201 cask-interacting protein 2 [Mus musculus]
- gi|157818437|ref|NP_001100535.1|_1077:1200 cask-interacting protein 2 [Rattus norvegicus]
- gi|149054796|gb|EDM06613.1| cask-interacting protein 2 (predicted) [Rattus norvegicus]
- gi|24638431|ref|NP_065804.1|_1078:1202 cask-interacting protein 2 [Homo sapiens]
- gi|61213006|sp|Q8WXE0|CSKI2_HUMAN Caskin-2 [Taxonomy]
- gi|17940756|gb|AAL49757.1|AF451976_1 cask-interacting protein 2 [Homo sapiens]
- gi|45219847|gb|AAH66643.1| CASK interacting protein 2 [Homo sapiens]
- gi|119609684|gb|EAW89278.1| CASK interacting protein 2 [Homo sapiens]
- gi|149723299|ref|XP_001495695.1|_1079:1201 PREDICTED: similar to cask-interacting protein 2 [Equus caballus]
- gi|109118200|ref|XP_001097098.1|_1080:1204 PREDICTED: similar to cask-interacting protein 2 [Macaca mulatta]
- gi|6382016|dbj|BAA86453.1|_1000:1124 KIAA1139 protein [Homo sapiens]
- gi|114670443|ref|XP_001137464.1|_984:1108 PREDICTED: cask-interacting protein 2 [Pan troglodytes]
- gi|57099343|ref|XP_540433.1|_1080:1202 PREDICTED: similar to cask-interacting protein 2 [Canis familiaris]
- gi|119912755|ref|XP_001255913.1|_1071:1193 PREDICTED: similar to cask-interacting protein 2 [Bos taurus]
- gi|119916513|ref|XP_871198.2|_1188:1299 PREDICTED: similar to mKIAA1306 protein [Bos taurus]
- gi|189532899|ref|XP_692620.3|_1169:1293 PREDICTED: similar to cask-interacting protein 2 [Danio rerio]
- gi|26339338|dbj|BAC33340.1|_529:653 unnamed protein product [Mus musculus]
- gi|55962741|emb|CAI11563.1|_648:772 novel protein similar to human and mouse CASK interacting protein 2 (CASKIN2) [Danio rerio]
- gi|26340714|dbj|BAC34019.1|_641:765 unnamed protein product [Mus musculus]
- gi|189514414|ref|XP_682906.3|_1437:1557 PREDICTED: similar to CASK interacting protein 1 [Danio rerio]
- gi|189514420|ref|XP_001919695.1|_1045:1165 PREDICTED: similar to CASK interacting protein 1 [Danio rerio]
- gi|118097927|ref|XP_414857.2|_1340:1448 PREDICTED: similar to cask-interacting protein 1 [Gallus gallus]
- gi|189529310|ref|XP_001919376.1|_629:751 PREDICTED: similar to cask-interacting protein 2, partial [Danio rerio]
- gi|47213676|emb|CAF95629.1|_229:344 unnamed protein product [Tetraodon nigroviridis]
- gi|47213675|emb|CAF95628.1|_270:391 unnamed protein product [Tetraodon nigroviridis]
- gi|189517204|ref|XP_692129.3|_1406:1526 PREDICTED: CASK interacting protein 1 [Danio rerio]
- gi|47216277|emb|CAG05973.1|_1367:1484 unnamed protein product [Tetraodon nigroviridis]
- gi|47210421|emb|CAF90109.1|_987:1105 unnamed protein product [Tetraodon nigroviridis]
- gi|38511409|gb|AAH60720.1|_1238:1355 Caskin1 protein [Mus musculus]
- gi|47210928|emb|CAF92727.1|_39:159 unnamed protein product [Tetraodon nigroviridis]
- gi|114660493|ref|XP_523265.2|_1344:1472 PREDICTED: CASK interacting protein 1 [Pan troglodytes]
- gi|73959509|ref|XP_853631.1|_1224:1347 PREDICTED: similar to CASK interacting protein 1 [Canis familiaris]
- gi|118099945|ref|XP_420128.2|_1418:1488 PREDICTED: similar to cask-interacting protein 2 [Gallus gallus]
- gi|148226138|ref|NP_001086927.1|_1170:1205 CASK interacting protein 2 [Xenopus laevis]
- gi|61212962|sp|Q6DD51|CSKI2_XENLA Caskin-2 [Taxonomy]
- gi|50417662|gb|AAH77777.1| Caskin2-prov protein [Xenopus laevis]
- gi|47213675|emb|CAF95628.1|_195:265 unnamed protein product [Tetraodon nigroviridis]
- gi|62132930|gb|AAH92148.1|_1176:1205 Unknown (protein for MGC:98998) [Xenopus laevis]

              10        20        30        40        50        60     
              |         |         |         |         |         |     
   1 PARQPPAALAKPPGTPPSLGASPAKPPSPGAPALHVPAKPPRAAAAAAAAAAAPPAPPEGA.SPG
   2 --RQPPAALAKPPGTPPSLGASPAKPPSPGAPALHVPAKPPRAAAAAAAAAAAPPAPPEGA.SPG
   3 --RQPPAALAKPPGTPPSLGASPAKPPSPGAPALHVPAKPPRAAAAAAAAAAAPPAPPEGA.SPG
   4 --RQPPAALAKPPGTPPSLGASPAKPPSPGAPALHVPAKPPRAAAAAAAAAAAPPAPPEGA.SPG
   5 --RQPPAALAKPPGTPPSLGASPAKPPSPGAPALHVPAKPPRAAAAAAAAAAAPPAPPEGA.SPG
   6 --RQPPAALAKPPGTPPSLGTSPVKPPSPGAPALHVPAKPPRAAAAAAA---APPAPTEGA.SPG
   7 --RQPPAALIKPASSPPSQSASPVKPPSPGTPALHVPAKPPRAAASVVS---GPPVASDCA.SPG
   8 --RQPPAALIKPASSPPSQSASPVKPPSPGTPALHVPAKPPRAAASVVS---GPPVASDCA.SPG
   9 --RQPPAALIKPASSPPSQSASPAKPPSPGAPALQVPTKPPRAAASVVS---GPPVASDCA.SPG
  10 --RQPPAALIKPASSPPSQSASPVKPPSPGTPALHVPAKPPRAAASVVS---GPPVASDCA.SPG
  11 --RQPPAALIKPASSPPSQSASPAKPPSPGAPALQVPTKPPRAAASVVS---GPPVASDCA.SPG
  12 --PNVETEPPAPPAALLKVPGAGTAPKPVSVACTQLAFSGPKLAPRLGPRPVPPPRPENTGpVCP
  13 --PNVETEPPAPPAALLKVPGAGTAPKPVSVACTQLAFSGPKLAPRLGPRPVPPPRPENTGpVCP
  14 --PNVETEPPAPPAALLKVPGAGTAPKPVSVACTQLAFSGPKLAPRLGPRPVPPPRPENTGpVCP
  15 --PNVETEPPAPPAALLKVPGAGTAPKPVSVACTQLAFSGPKLAPRLGPRPVPPPRPENTGpVCP
  16 --PNVETEPPAPPAALLKVPGAGTAPKPVSVACTQLAFSGPKLAPRLGPRPVPPPRPENTGpVCP
  17 --QNVDTEPPAPPAALLKVPGAGTAPKPVSVACTQLAFSGPKLAPRLGPRPVPPPRPENTGpVCP
  18 -RWNGETEPPAAPAALLKVPGAGTAPKPVSVACTQLAFSGPKLAPRLGPRPVPPPRPESTG.TVG
  19 ---HGETETPTPPAALIKVPGAGTAPKPVSVACTQLAFSGPKLAPRPGPRPVPPPRPESTG.ATG
  20 -RWNGETEPPAAPAALLKVPGAGTAPKPVSVACTQLAFSGPKLASRLGPRPVPPPRPESTG.TVG
  21 -RWNGETEPPAAPAALLKVPGAGTAPKPVSVACTQLAFSGPKLAPRLGPRPVPPPRPESTG.TVG
  22 -RWNGETEPPTAPAALLKVPGAGTAPKPVSVACTQLAFSGPKLAPRLGPRPVPPPRPESTG.TVG
  23 ---HGETEPPASPAALIKVPGAGTAPKPVSVACTQLAFSGPKLAPRLGPRPVPPPRPESTG.AVG
  24 ---PGETEPPAAPATLIKVPGAGTAPKPVSVACTQLAFSGPKLAPRLGPRPVPPPRPESTG.AAG
  25 -------------PALSASPASPARPPSPGAPALHVPAKPPRAAA----AATGPPAAPDGA.SPG
  26 ---PHKPPTPSKPIRHSAAATSGVSMSVVQSVAFAVSPPCSPLACCPPNATPQGQSALTAE.GQN
  27 --RQPPAALIKPASSPPSQSASPVKPPSPGTPALHVPAKPPRAAASVVS---GPPVASDCA.SPG
  28 ---PHKPPTPSKPIRHSAAATSGVSMSVVQSVAFAVSPPCSPLACCPPNATPQGQSALTAE.GQN
  29 --RQPPAALIKPASSPPSQSASPVKPPSPGTPALHVPAKPPRAAASVVS---GPPVASDCA.SPG
  30 ----VGSHLIEAGDGAGPVVMRRRKVGVARQTQVEGESQEGEGKTEMEGQGLLKIAETGGS.SCG
  31 ----VGSHLIEAGDGAGPVVMRRRKVGVARQTQVEGESQEGEGKTEMEGQGLLKIAETGGS.SCG
  32 --------------------PSSTPPSLCSSPAKPLSPGTQPQQVPVKPPRSAIAGPSVDS.ASP
  33 ------PAPAHPTVVGSSVTLSVVQSVAFAAPPSPIPYCPSAENTTQGVTSGNVQTPTEGG.QGA
  34 ----------SVTISGVQTLAFTAPSSPVHGPPAPGPGWVSAPQSPCLTSARSQVHLQGRG.LGT
  35 ----WTLGSLRDHQRGSRPLAFTAPSSPVHGPPAPGPGWVSAPQSPCLTSARSQVHLQGRG.LGT
  36 ------HTPQSPHTPQTPQTPQTPQTPPTPTPTPPPVKPPRSSISGVSMDSSTGSALVAGV.VTA
  37 -------PHTPQTPPTPQTPATPSPTPPPVKPPRSSIGGVSVDSGTPGGGVTTPTPTTTDF.SVD
  38 ------MPPVEKCTALSDLMESQSCSTIGKGKFKRIQDGPAAASFPQGPGSPPGLPLMNAA.QLE
  39 ------------PGPGSPEVKRAHGTPPPVSPKPPPPPTAPKPPRAAASVVSGPPVASDCA.SPG
  40 -----AIGVMKPGHRKKLMSEVSKLPATDWLPDHKPANLADWLAHLGLSQYYQVLVQNGYE.NID
  41 ----TDLAHLPPLPPPEGEARKPAKPPVSPKPVLTQPVPKLQGSPTPTSKKVPLPGPGSPG.RCM
  42 -----KIQGSPTPASKKVPLPGPGSPEVKRAHGTPPPVSPKPPPPPTAPKPAKAAAGLQSG.SAS
  43 -----------------------------------------------------FVKPLASA.PGA
  44 -------------------------------------------------------------.---
  45 -----------------------FHPNLRPLPQNQFATACWQRRSPCLTSARSQVHLQGRG.LGT
  46 -------------------------------------------------------------.---


           70            80        90        100       110       120   
           |             |         |          |         |         |   
   1 .DSARQKLE....ETSACLAAALQAVEEKIRQEDAQGPR.DSAAEKSTGSILDDIGSMFDDLADQ
   2 .DSARQKLE....ETSACLAAALQAVEEKIRQEDAQGPR.DSAAEKSTGSILDDIGSMFDDLADQ
   3 .DSARQKLE....ETSACLAAALQAVEEKIRQEDAQGPR.DSAAEKSTGSILDDIGSMFDDLADQ
   4 .DSARQKLE....ETSACLAAALQAVEEKIRQEDAQGPR.DSAAEKSTGSILDDIGSMFDDLADQ
   5 .DSARQKLE....ETSACLAAALQAVEEKIRQEDAQGPR.DSAAEKSTGSILDDIGSMFDDLADQ
   6 .DSARQKLE....ETSACLAAALQAVEEKIRQEDAQGPR.DSAAEKSTGSILDDIGSMFDDLADQ
   7 .DSARQKLE....ETSACLAAALQAVEEKIRQEDGQGPRpSSIEEKSTGSILEDIGSMFDDLADQ
   8 .DSARQKLE....ETSACLAAALQAVEEKIRQEDGQGPRpSSIEEKSTGSILEDIGSMFDDLADQ
   9 .DSARQKLE....ETSACLAAALQAVEEKIRQEDGQGPRpSSIEEKSTGSILEDIGSMFDDLADQ
  10 .DSARQKLE....ETSACLAAALQAVEEKIRQEDGQGPRpSSIEEKSTGSILEDIGSMFDDLADQ
  11 .DSARQKLE....ETSACLAAALQAVEEKIRQEDGQGPRpSSIEEKSTGSILEDIGSMFDDLADQ
  12 .GRAQQRLE....QTSSSLEAALRAAEKSIGTEERDGPT.G----TSTKHILDDISTMFDALADQ
  13 .SRAQQRLE....QTSSSLEAALRAAEKSIGTEERDGPT.G----TSTKHILDDISTMFDALADQ
  14 .SRAQQRLE....QTSSSLEAALRAAEKSIGTEERDGPT.G----TSTKHILDDISTMFDALADQ
  15 .SRAQQRLE....QTSSSLEAALRAAEKSIGTEERDGPT.G----TSTKHILDDISTMFDALADQ
  16 .SRAQQRLE....QTSSSLEAALRAAEKSIGTEERDGPT.G----TSTKHILDDISTMFDALADQ
  17 .GRAQQRLE....QTSSSLEAALRAAEKNIGSEEQDGPT.G----PSTKHILDDISTMFDALADQ
  18 pGQAQQRLE....QTSSSLAAALRAAEKSIGTKEQEGTP.S----ASTKHILDDISTMFDALADQ
  19 sGRAQQRLE....QTSSSLAAALRAAEKSIGTEEREGPP.G----TSTKHILDDISTMFDALADQ
  20 pGQAQQRLE....QTSSSLAAALRAAEKSIGTEEQEGAP.S----ASTKHILDDISTMFDALADQ
  21 pGQAQQRLE....QTSSSLAAALRAAEKSIGTKEQEGTP.S----ASTKHILDDISTMFDALADQ
  22 pGQAQQRLE....QTSSSLAAALRAAEKSIGTKEQEGTP.S----ASTKHILDDISTMFDALADQ
  23 sGRAQQRLE....QTSSSLAAALRAAEKSIGAEEREGPP.S----TSAKHILDDISTMFDALADQ
  24 pGRAQQRLE....QTSSSLAAALRAAEKSIGAEEREGAP.G----ASTKHILDDISTMFDALADQ
  25 .DSARQKLE....ETSACLAAALQAVEEKIRQEDAQGSR.PSAAEKSTGSILDDIGSMFDDLADQ
  26 .VLVHKRLE....QTSTSLQAALQVVERKLAQDDPAS-R.GINTVKSAGNILDDIGNMFDDLADQ
  27 .DSARQKLE....ETSACLAAALQAVEEKIRQEDGQGPRpSSIEEKSTGSILEDIGSMFDDLADQ
  28 .VLVHKRLE....QTSTSLQAALQVVERKLAQDDPAS-R.GINTVKSAGNILDDIGNMFDDLADQ
  29 .DSARQKLE....ETSACLAAALQAVEEKIRQEDGQGPRpSSIEEKSTGSILEDIGSMFDDLADQ
  30 .DVMQLRLD....ETSASLAAALEVVEEKIKKDD----S.STVDNKSTVNILDDIGSMFDDLADQ
  31 .DVMQLRLD....ETSASLAAALEVVEEKIKKDD----S.STVDNKSTVNILDDIGSMFDDLADQ
  32 .ELVQQKLE....ETSASLAAALQAVEEKIKQEDSQAAD.STAEAKSTGSILDDIGSMFDDLADQ
  33 .TLKHQRLE....KTSSTLEEALKAVERKLTLKNNNNVG.VSHAVKSAGNILDDIGNMFDDLADQ
  34 .EVVQQRLD....QTSWSLAAALKAVESKLSQEEDSSRN.---AVTSARTILDDIGNMFDDLADQ
  35 .EVVQQRLD....QTSWSLAAALKAVESKLSQEEDSSRN.---AVTSARTILDDIGNMFDDLADQ
  36 .DAVHQKIE....ETSASLAAALQAVEQKIKEDGQKD--.SIAENKSTVSILDDIGSMFDDLADQ
  37 .FLVQQKLE....ETSASLAAALQAVEDKILHQE----D.SVAEQKTTVSILDDIGSMFDDLADQ
  38 .ALAQRRLE....QTSTSLEAALRVVENKLSQDSLDRS-.---TVKAAGNILDDIGSMFDDLADQ
  39 .DSARQKLE....ETSACLAAALQAVEEKIRQEDGQGPRpSSIEEKSTGSILEDIGSMFDDLADQ
  40 .FISDISLEdl..QEIGITKLAVEAVEHKIKEEDAEN--.---EKKTTVSILDDIGSMFDDLADQ
  41 .GPARAEADgdagRGRVLVEVGVARPAPPTHAPCPAPRS.DSAAEKSTGSILDDIGSMFDDLADQ
  42 .PSPAPSPA....RQPPAALAKPASTRPSLSASTAKPPP.SSAEEKSTGSILDDIGSMFDDLADQ
  43 .ALVQQQLE....HTSII---TLQAAEKKITVEEVQSPP.R--ATHSAKNILEDISNMFDDLADQ
  44 .--------....---------------------TRGKS.CRETVQLTKNILDDISTMFDDLAEQ
  45 .EVVQQRLD....QTSWSLAAALKAVESKLSQEED----.-------------------------
  46 .--------....--------------------------.-RETVQLTKNILDDISTMFDDLAEQ


            
           
   1 LDAMLE
   2 LDAMLE
   3 LDAMLE
   4 LDAMLE
   5 LDAMLE
   6 LDAMLE
   7 LDAMLE
   8 LDAMLE
   9 LDAMLE
  10 LDAMLE
  11 LDAMLE
  12 LDAMLD
  13 LDAMLD
  14 LDAMLD
  15 LDAMLD
  16 LDAMLD
  17 LDAMLD
  18 LDAMLD
  19 LDAMLD
  20 LDAMLD
  21 LDAMLD
  22 LDAMLD
  23 LDAMLD
  24 LDAMLD
  25 LDAMLE
  26 LDAMLD
  27 LDAMLE
  28 LDAMLD
  29 LDAMLE
  30 LDAMLD
  31 LDAMLD
  32 LDAMLE
  33 LDAMLD
  34 LDAMLD
  35 LDAMLD
  36 LDAMLE
  37 LDAMLE
  38 LDAMLE
  39 LDAMLE
  40 LDAMLD
  41 LDAMLE
  42 LDAMLE
  43 LDAMLD
  44 LEAMLD
  45 ------
  46 LEAMLD