a2m2html output for file 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, 1999.
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:

- T0105
- gi|6175041|sp|P23497|SP10_HUMAN_595:686 NUCLEAR AUTOANTIGEN SP-100 (SPECKLED 100 KDA) (Homo sapiens)
- gi|1173656|gb|AAC50743.1| (U36501) SP100-B [Homo sapiens] (Homo sapiens)
- gi|3252911|gb|AAC39790.1|_596:687 (AF056322) SP100-HMG nuclear autoantigen [Homo sapiens] (Homo sapiens)
- gi|2340123|gb|AAC53509.1|_360:449 (U83633) alternatively spliced; lacks nucleotides 1 to 91 and exon 11 [Mus caroli] (Mus caroli)
- gi|2340117|gb|AAC53506.1|_378:467 (U83629) Sp100 [Mus caroli] (Mus caroli)
- gi|2340152|gb|AAC12948.1| (U83654) Sp100 [Mus caroli] (Mus caroli)
- gi|7305513|ref|NP_038701.1|_378:467 nuclear antigen Sp100 (Mus musculus)
- gi|2340129|gb|AAC53512.1| (U83630) Sp100 [Mus musculus] (Mus musculus)
- gi|2340121|gb|AAC53508.1|_378:467 (U83632) alternatively spliced; lacks nucleotides 1 to 91 [Mus caroli] (Mus caroli)
- gi|2340131|gb|AAC53513.1|_360:449 (U83636) alternatively spliced; lacks exon 11 [Mus musculus] (Mus musculus)
- gi|6166538|sp|Q13342|LY10_HUMAN_580:669 LYSP100 PROTEIN (LYMPHOID-RESTRICTED HOMOLOG OF SP100) (Homo sapiens)
- gi|1173654|gb|AAB18617.1| (U36500) LYSP100-B [Homo sapiens] (Homo sapiens)
- gi|6005880|ref|NP_009168.1|_466:555 nuclear body protein Sp140 (Homo sapiens)
- gi|6094325|sp|Q92881|SP14_HUMAN NUCLEAR AUTOANTIGEN SP-140 (SPECKLED 140 KD) (Homo sapiens)
- gi|1669498|gb|AAC50817.1| (U63420) Sp140 protein [Homo sapiens] (Homo sapiens)
- gi|4758586|ref|NP_004500.1|_154:245 interferon-induced protein 41, 30kD (Homo sapiens)
- gi|1362889|pir||A49515 phosphoprotein 41 - human (Homo sapiens)
- gi|402205|gb|AAA18806.1| (L22342) phosphoprotein [Homo sapiens] (Homo sapiens)
- gi|7643905|gb|AAF65538.1|AF205779_1_82:163 (AF205779) GMEB-2a [Rattus norvegicus] (Rattus norvegicus)
- gi|6331220|dbj|BAA86583.1|_83:164 (AB033095) KIAA1269 protein [Homo sapiens] (Homo sapiens)
- gi|7643903|gb|AAF65537.1|AF205778_1_82:163 (AF205778) GMEB-2' [Rattus norvegicus] (Rattus norvegicus)
- gi|6912568|ref|NP_036516.1|_82:163 glucocorticoid modulatory element binding protein 2 (Homo sapiens)
- gi|5764634|gb|AAD51351.1|AF173867_1 (AF173867) DNA binding protein p79PIF [Homo sapiens] (Homo sapiens)
- gi|7643907|gb|AAF65539.1|AF205780_1_82:163 (AF205780) GMEB-2b [Rattus norvegicus] (Rattus norvegicus)
- gi|6599186|emb|CAB63765.1|_57:138 (AL133646) hypothetical protein [Homo sapiens] (Homo sapiens)
- gi|3746541|gb|AAC64001.1|_81:162 (AF059273) glucocorticoid modulatory element binding protein 2 [Rattus norvegicus] (Rattus norvegicus)
- gi|3309569|gb|AAC79679.1|_193:273 (AF055884) nuclear DEAF-1 related transcriptional regulator [Rattus norvegicus] (Rattus norvegicus)
- gi|3309567|gb|AAC79678.1|_193:273 (AF049461) nuclear DEAF-1 related transcriptional regulator protein [Pan troglodytes] (Pan troglodytes)
- gi|5764636|gb|AAD51352.1|AF173868_1_76:156 (AF173868) DNA binding protein p96PIF [Homo sapiens] (Homo sapiens)
- gi|7021843|dbj|BAA91410.1|_76:156 (AK000892) unnamed protein product [Homo sapiens] (Homo sapiens)
- gi|3309565|gb|AAC79677.1|_179:259 (AF049460) nuclear DEAF-1 related transcriptional regulator protein 8 [Homo sapiens] (Homo sapiens)
- gi|5729846|ref|NP_006573.1|_86:166 glucocorticoid modulatory element binding protein 1 (Homo sapiens)
- gi|5081374|gb|AAD39355.1|AF099013_1 (AF099013) glucocorticoid modulatory element binding protein-1 [Homo sapiens] (Homo sapiens)
- gi|3309563|gb|AAC79676.1|_193:273 (AF049459) nuclear DEAF-1 related transcriptional regulator protein [Homo sapiens] (Homo sapiens)
- gi|8393248|ref|NP_058570.1|_194:274 deformed epidermal autoregulatory factor 1 (Drosophila) (Mus musculus)
- gi|4063898|gb|AAC98511.1| (AF102818) deformed epidermal autoregulatory factor 1 [Mus musculus] (Mus musculus)
- gi|1389895|gb|AAC35994.1|_125:205 (U59659) suppressin [Rattus norvegicus] (Rattus norvegicus)
- gi|3293446|gb|AAC25717.1|_125:205 (AF068895) suppressin [Homo sapiens] (Homo sapiens)
- gi|8118043|gb|AAF72874.1|AF210433_1_77:156 (AF210433) glucocorticoid modulatory element binding protein 1; GMEB-1 [Mus musculus] (Mus musculus)
- gi|2246694|gb|AAB62704.1|_125:205 (AF007165) suppressin [Homo sapiens] (Homo sapiens)
- gi|3293444|gb|AAC25716.1|_125:205 (AF068894) suppressin [Homo sapiens] (Homo sapiens)
- gi|3293440|gb|AAC25714.1|_125:205 (AF068892) truncated suppressin [Homo sapiens] (Homo sapiens)
- gi|3293442|gb|AAC25715.1|_125:205 (AF068893) suppressin [Homo sapiens] (Homo sapiens)
- gi|3293448|gb|AAC25718.1|_125:205 (AF068896) suppressin [Homo sapiens] (Homo sapiens)
- gi|3293450|gb|AAC25719.1|_125:205 (AF068897) suppressin [Homo sapiens] (Homo sapiens)
- gi|1362890|pir||B49515_215:291 phosphoprotein 75 - human (Homo sapiens)
- gi|4758588|ref|NP_004501.1|_252:328 interferon-induced protein 75, 52kD (Homo sapiens)
- gi|4239654|gb|AAD13402.1| (L22343) nuclear phosphoprotein [Homo sapiens] (Homo sapiens)
- gi|2133648|pir||S69214_211:291 deformed epidermal autoregulatory factor-1 - fruit fly (Drosophila melanogaster) (Drosophila melanogaster)
- gi|1209883|gb|AAC47040.1| (U46686) DEAF-1 [Drosophila melanogaster] (Drosophila melanogaster)
- gi|7293736|gb|AAF49105.1| (AE003515) Deaf1 gene product [Drosophila melanogaster] (Drosophila melanogaster)
- gi|1589475|prf||2211283A DEAF-1 protein [Drosophila melanogaster] (Drosophila melanogaster)
- gi|7497426|pir||T19932_76:151 hypothetical protein C44F1.2 - Caenorhabditis elegans (Caenorhabditis elegans)
- gi|3874918|emb|CAA88849.1| (Z49067) weak similarity to the human high mobility group protein I-C (PIR accession number S43153) [Caenorhabditis elegans] (Caenorhabditis elegans)
- gi|7496508|pir||T19470_72:150 hypothetical protein C25G4.4 - Caenorhabditis elegans (Caenorhabditis elegans)
- gi|3874418|emb|CAA94573.1| (Z70680) similar to SAND domain [Caenorhabditis elegans] (Caenorhabditis elegans)
- gi|7504108|pir||T22598_6:84 hypothetical protein F53H4.5 - Caenorhabditis elegans (Caenorhabditis elegans)
- gi|3877542|emb|CAB03138.1| (Z81089) similar to SAND domain [Caenorhabditis elegans] (Caenorhabditis elegans)
- gi|7239187|gb|AAF43110.1|AF169948_1_2:61 (AF169948) SP100-HMG nuclear autoantigen [Hylobates lar] (Hylobates lar)
- gi|7495061|pir||T32370_91:158 hypothetical protein C01B12.2 - Caenorhabditis elegans (Caenorhabditis elegans)
- gi|2429436|gb|AAB70975.1| (AF025458) C01B12.2 gene product [Caenorhabditis elegans] (Caenorhabditis elegans)
- gi|7108534|gb|AAF36461.1|AF128116_1_190:247 (AF128116) autoimmune regulator [Mus musculus] (Mus musculus)
- gi|7108546|gb|AAF36467.1|AF128122_1_190:247 (AF128122) autoimmune regulator [Mus musculus] (Mus musculus)
- gi|7108536|gb|AAF36462.1|AF128117_1_190:247 (AF128117) autoimmune regulator [Mus musculus] (Mus musculus)
- gi|7108548|gb|AAF36468.1|AF128123_1_190:247 (AF128123) autoimmune regulator [Mus musculus] (Mus musculus)
- gi|7108538|gb|AAF36463.1|AF128118_1_190:247 (AF128118) autoimmune regulator [Mus musculus] (Mus musculus)
- gi|7108550|gb|AAF36469.1|AF128124_1_190:247 (AF128124) autoimmune regulator [Mus musculus] (Mus musculus)
- gi|7108540|gb|AAF36464.1|AF128119_1_190:247 (AF128119) autoimmune regulator [Mus musculus] (Mus musculus)
- gi|6753020|ref|NP_033776.1|_190:247 autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy) (Mus musculus)
- gi|3550508|emb|CAA07620.1| (AJ007715) autoimmune regulator [Mus musculus] (Mus musculus)
- gi|4426599|gb|AAD20444.1| (AF079536) autoimmune regulator [Mus musculus] (Mus musculus)
- gi|4456675|emb|CAB36909.1| (AJ132243) Aire protein [Mus musculus] (Mus musculus)
- gi|5669676|gb|AAD46421.1|AF105002_1 (AF105002) autoimmune regulator [Mus musculus] (Mus musculus)
- gi|6706793|emb|CAB66141.1| (AJ243821) APECED protein [Mus musculus] (Mus musculus)
- gi|7108573|gb|AAF36481.1|AF128772_1 (AF128772) autoimmune regulator [Mus musculus] (Mus musculus)
- gi|7108575|gb|AAF36482.1|AF128773_1 (AF128773) autoimmune regulator [Mus musculus] (Mus musculus)
- gi|7108552|gb|AAF36470.1|AF128125_1_190:247 (AF128125) autoimmune regulator [Mus musculus] (Mus musculus)
- gi|7108542|gb|AAF36465.1|AF128120_1_190:247 (AF128120) autoimmune regulator [Mus musculus] (Mus musculus)
- gi|7108532|gb|AAF36460.1|AF128115_1_190:247 (AF128115) autoimmune regulator [Mus musculus] (Mus musculus)
- gi|7108544|gb|AAF36466.1|AF128121_1_190:247 (AF128121) autoimmune regulator [Mus musculus] (Mus musculus)

              10        20         30        40          50        60  
              |         |          |         |           |         |  
   1 DENINFKQSELPVTCGEVKGTLYKERF.KQGTSKKCIQSED..KKWFTPREFEIEGDRGASKNWK
   2 DENINFKQSELPVTCGEVKGTLYKERF.KQGTSKKCIQSED..KKWFTPREFEIEGDRGASKNWK
   3 -ENINFKQSELPVTCGEVKGTLYKERF.KQGTSKKCIQSED..KKWFTPREFEIEGDRGASKNWK
   4 EENADFGGAELPVVCGNVQGFLNKEKF.KQGIYVRSIRSET..GRLFTPMDFEIEGNCEKAKNWR
   5 EENADFGGAELPVVCGNVQGFLNKEKF.KQGIYSRSIRSET..GRLFTPMDFEIEGNCEKAKNWR
   6 EENADFGGAELPVVCGNAQGFLDKEKF.KQGIYVRSIRGKT..GRLFTPMDFEIEGNCEKAKNWR
   7 EENADFGGAELPAVCGNVQGFLNKEKF.KQGIYVRSIRSET..GRLFTPMDFEIEGNCEKAKNWR
   8 EENADFGGAELPVVCGNAQGFLDKEKF.KQGIYVRSIRGKT..GRLFTPMDFEIEGNCEKAKNWR
   9 DETVDFKAPLLPVTCGGVKGILHKKKL.QQGILVKCIQTED..GKWFTPTEFEIKGGHARSKNWR
  10 DETVDFKAPLLPVTCGGVKGILHKKKL.QQGILVKCIQTED..GKWFTPTEFEIKGGHARSKNWR
  11 -DTVDFHCSKSPVTCGEAKGILYKKKM.KHGSSVKCIRNED..GTWLTPNEFEVEGKGRNAKNWK
  12 EGENLEAEIVYPITCGDSRANLIWRKFvCPGINVKCVQYDE..-HVISPKEFVHLAGKSTLKDWK
  13 EGENLEAEIVYPITCGDSRANLIWRKFvCPGINVKCVQYDE..-HVISPKEFVHLAGKSTLKDWK
  14 EGENLEAEIVYPITCGDSRANLIWRKFvCPGINVKCVQYDE..-HVISPKEFVHLAGKSTLKDWK
  15 EGENLEAEIVYPITCGDSRANLIWRKFvCPGINVKCVQYDE..-HVISPKEFVHLAGKSTLKDWK
  16 EGENLEAEIVYPITCGDSRANLIWRKFvCPGINVKCVQYDE..-HVISPKEFVHLAGKSTLKDWK
  17 EGENLEAEIVYPITCGDSRANLIWRKFvCPGINVKCVQYDE..-HVISPKEFVHLAGKSTLKDWK
  18 EGENLEAEIVYPITCGDSRANLIWRKFvCPGINVKCVQYDE..-HVISPKEFVHLAGKSTLKDWK
  19 NWDPSVYDSELPVRCRNISGTLYKSRL.GSGGRGRCIKQGE..-NWYSPTEFEAMAGRASSKDWK
  20 NWDPSVYDSELPVRCRNISGTLYKNRL.GSGGRGRCIKQGE..-NWYSPTEFEAMAGRASSKDWK
  21 -EANEDMEIAYPITCGESKAILLWKKFvCPGINVKCVKFND..-QLISPKHFVHLAGKSTLKDWK
  22 -EANEDMEIAYPITCGESKAILLWKKFvCPGINVKCVKFND..-QLISPKHFVHLAGKSTLKDWK
  23 NWDPSVYDSELPVRCRNISGTLYKNRL.GSGGRGRCIKQGE..-NWYSPTEFEAMAGRASSKDWK
  24 -EANEDMEIAYPITCGESKAILLWKKFvCPGINVKCVKFND..-QLISPKHFVHLAGKSTLKDWK
  25 NWDPSVYDSELPVRCRNISGTLYKNRL.GSGGRGRCIKQGE..-NWYSPTEFEAMAGRASSKDWK
  26 NWDPSVYDSELPVRCRNISGTLYKSRL.GSGGRGRCIKQGE..-NWYSPTEFEAMAGRASSKDWK
  27 NWDPSVYDSELPVRCRNISGTLYKSRL.GSGGRGRCIKQGE..-NWYSPTEFEAMAGRASSKDWK
  28 NWDPSVYDSELPVRCRNISGTLYKNKL.GSGGRGRCIKQGE..-NWYSPTEFEAMAGRASSKDWK
  29 --GNEDMEIAYPITCGESKAVLLWKKFvCPGINVKCVKFND..-QLISPKHFVHLAGKSTLKDWK
  30 NWDPSVYDSELPVRCRNISGTLYKNRL.GSGGRGRCIKQGE..-NWYSPTEFEAMAGRTSSKDWK
  31 NWDPSVYDSELPVRCRNISGTLYKNKL.GSGGRGRCIKQGE..-NWYSPTEFEAMAGRASSKDWK
  32 NWDPSVYDSDLPVRCRNISGTLYKNRL.GSGGRGRCIKQGE..-NWYSPTEFEAMAGRASSKDWK
  33 NWDPSVCDNDLPVRCRNISGTLYKNKL.GSGGRGRCIKQGE..-NWYSPTEFEAMAGRASSKDWK
  34 NWDPSVYDSELPVRCRNISGTLYKNRL.GSAAGDGASSRGR..-TGTCPTEFEAMAGRASSKDWK
  35 NWDPSVYDSELPVRCRNISGTLYKNRL.GSAAGDGASSRGR..-TGTCPTEFEAMAGRASSKDWK
  36 -DTVDFHCSKLPVTCGEAKGILYKKKM.KHGSSVKCIRNED..GTWLTPNEFEVEGKGRNAKNWK
  37 -DTVDFHCSKLPVTCGEAKGILYKKKM.KHGSSVKCIRNED..GTWLTPNEFEVEGKGRNAKNWK
  38 ENPSTQHNEVFQIRCKTTCAELYRSKL.GSGGRGRCVKYKD..-KWHTPSEFEHVCGRGSSKDWK
  39 ------NATTVPVTCGYVKGIMHLKLFrCPGIRQACIEYES..-QYLTPKQFTELGGKGRQKDWK
  40 ---EGDASPTVPVSCGVVNGKMHLNLFmCPGIHQPCIEVGN..-DLLSPKQFTIRGDKERQKDWK
  41 -----LLKIIFQVKCGTLTAKMVTKLFtCPGIHQNCILIDGe.TEYISPKEFTVRANKDKQKDWK
  42 ---------------------------.------KCIQSED..KKWFTPREFEIEGDRRASKNWK
  43 --------KYMELKCGALVARLHTELFiCPGIREKCIEVLDcpGELLTPVEFTIKAEKSKQKDWK
  44 QRAVTVASGDVPGTRGAVEGILIQQVF.ESGRSKKCIQVGG..-EFYTPNKFEDPSGNLKNK---
  45 QRAVTVASGDVPGTRGAVEGILIQQVF.ESGRSKKCIQVGG..-EFYTPNKFEDPSGNLKNK---
  46 QRAVTVASGDVPGTRGAVEGILIQQVF.ESGRSKKCIQVGG..-EFYTPNKFEDPSGNLKNK---
  47 QRAVTVASGDVPGTRGAVEGILIQQVF.ESGRSKKCIQVGG..-EFYTPNKFEDPSGNLKNK---
  48 QRAVTVASGDVPGTRGAVEGILIQQVF.ESGRSKKCIQVGG..-EFYTPNKFEDPSGNLKNK---
  49 QRAVTVASGDVPGTRGAVEGILIQQVF.ESGRSKKCIQVGG..-EFYTPNKFEDPSGNLKNK---
  50 QRAVTVASGDVPGTRGAVEGILIQQVF.ESGRSKKCIQVGG..-EFYTPNKFEDPSGNLKNK---
  51 QRAVTVASGDVPGTRGAVEGILIQQVF.ESGRSKKCIQVGG..-EFYTPNKFEDPSGNLKNK---
  52 QRAVTVASGDVPGTRGAVEGILIQQVF.ESGRSKKCIQVGG..-EFYTPNKFEDPSGNLKNK---
  53 QRAVTVASGDVPGTRGAVEGILIQQVF.ESGRSKKCIQVGG..-EFYTPNKFEDPSGNLKNK---
  54 QRAVTVASGDVPGTRGAVEGILIQQVF.ESGRSKKCIQVGG..-EFYTPNKFEDPSGNLKNK---
  55 QRAVTVASGDVPGTRGAVEGILIQQVF.ESGRSKKCIQVGG..-EFYTPNKFEDPSGNLKNK---


            70        80        90    
            |         |         |    
   1 LSIRCGGYTLKVLMENKFLPEPPSTRKKVTIK
   2 LSIRCGGYTLKVLMENKFLPEPPSTRKKVT--
   3 LSIRCGGYTLKVLMENKFLPEPPSTRKKRIL-
   4 QTIRCKGWTLRELIQKGVLQDPPRKKKE----
   5 QTIRCKGWTLRELIQQGVLQDPPRKKKE----
   6 QTIRCKGWTLRELIQKGVLQDPPRKKKE----
   7 QTIRCKGWTLRELIQKGVLQDPPRKKKE----
   8 QTIRCKGWTLRELIQKGVLQDPPRKKKE----
   9 LSVRCGGWPLRWLMENGFLPDPPRIRYR----
  10 LSVRCGGWPLRWLMENGFLPDPPRIRYR----
  11 RNIRCEGMTLGELLKSGLLLCPPRINLKREL-
  12 RAIRMNGIMLRKIMDSGELD------------
  13 RAIRMNGIMLRKIMDSGELD------------
  14 RAIRMNGIMLRKIMDSGELD------------
  15 RAIRMNGIMLRKIMDSGELD------------
  16 RAIRMNGIMLRKIMDSGELD------------
  17 RAIRMNGIMLRKIMDSGELD------------
  18 RAIRMNGIMLRKIMDSGELD------------
  19 RSIRYAGRPLQCLIQDGILN------------
  20 RSIRYAGRPLQCLIQDGILN------------
  21 RAIRLGGIMLRKMMDSGQID------------
  22 RAIRLGGIMLRKMMDSGQID------------
  23 RSIRYAGRPLQCLIQDGILN------------
  24 RAIRLGGIMLRKMMDSGQID------------
  25 RSIRYAGRPLQCLIQDGILN------------
  26 RSIRYAGRPLQCLIQDGILN------------
  27 RSIRYAGRPLQCLIQDGILN------------
  28 RSIRYAGRPLQCLIQDGILN------------
  29 RAIRLGGIMLRKMMDSGQID------------
  30 RSIRYAGRPLQCLIQDGILN------------
  31 RSIRYAGRPLQCLIQDGILN------------
  32 RSIRYAGRPLQCLIQDGILN------------
  33 RSIRYAGRPLQCLIQDGILN------------
  34 RSIRYAGRPLQCLIQDGILN------------
  35 RSIRYAGRPLQCLIQDGILN------------
  36 RNIRCEGMTLGELLKR----------------
  37 RNIRCEGMTLGELLKR----------------
  38 RSIKYGGKSLQSLIDEGTLT------------
  39 ACIRVENVSLRTLLENKTID------------
  40 ASIRVGRSSLRTHMEAMTID------------
  41 GSIRIGKSNLRTLMEMRSLD------------
  42 LSIRCGGYTLKFLMENKLLPEPPSTRKKRIL-
  43 GAIKHNGRMLR---------------------
  44 --------------------------------
  45 --------------------------------
  46 --------------------------------
  47 --------------------------------
  48 --------------------------------
  49 --------------------------------
  50 --------------------------------
  51 --------------------------------
  52 --------------------------------
  53 --------------------------------
  54 --------------------------------
  55 --------------------------------