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:

- T0120-1-115 DNA repair protein XRCC4, human
- gi|5706612|gb|AAD47298.1|_1:115 (AF055285) DNA repair protein XRCC4 [Homo sapiens] (Homo sapiens)
- gi|4507945|ref|NP_003392.1|_1:115 X-ray repair complementing defective repair in Chinese hamster cells 4 (Homo sapiens)
- gi|1151115|gb|AAC50339.1| (U40622) XRCC4 [Homo sapiens] (Homo sapiens)
- gi|5706611|gb|AAD47297.1| (AF055285) DNA repair protein XRCC4 [Homo sapiens] (Homo sapiens)
- gi|1586944|prf||2205251A XRCC4 gene [Homo sapiens] (Homo sapiens)
- gi|4507945|ref|NP_003392.1|_1:115 X-ray repair complementing defective repair in Chinese hamster cells 4 (Homo sapiens)
- gi|1151115|gb|AAC50339.1| (U40622) XRCC4 [Homo sapiens] (Homo sapiens)
- gi|5706611|gb|AAD47297.1| (AF055285) DNA repair protein XRCC4 [Homo sapiens] (Homo sapiens)
- gi|1586944|prf||2205251A XRCC4 gene [Homo sapiens] (Homo sapiens)
- gi|5706612|gb|AAD47298.1|_1:115 (AF055285) DNA repair protein XRCC4 [Homo sapiens] (Homo sapiens)
- gi|6572958|gb|AAF17484.1|AF189776_1_124:199 (AF189776) NLI-interacting factor isoform R5; NLI/Ldb1/CLIM interacting factor [Gallus gallus] (Gallus gallus)
- gi|6572952|gb|AAF17481.1|AF189773_1_135:210 (AF189773) NLI-interacting factor isoform T1; NLI/Ldb1/CLIM interacting factor [Gallus gallus] (Gallus gallus)
- gi|6572954|gb|AAF17482.1|AF189774_1_124:199 (AF189774) NLI-interacting factor isoform T2; NLI/Ldb1/CLIM interacting factor [Gallus gallus] (Gallus gallus)
- gi|5031775|ref|NP_005799.1|_200:275 HYA22 protein (Homo sapiens)
- gi|2289786|dbj|BAA21667.1| (D88153) HYA22 [Homo sapiens] (Homo sapiens)
- gi|7294201|gb|AAF49553.1|_92:167 (AE003529) CG5830 gene product [Drosophila melanogaster] (Drosophila melanogaster)
- gi|4731912|gb|AAD28548.1|AF111941_1_166:241 (AF111941) development protein DG1148 [Dictyostelium discoideum] (Dictyostelium discoideum)
- gi|9972366|gb|AAG10616.1|AC008030_16_106:178 (AC008030) Hypothetical protein [Arabidopsis thaliana] (Arabidopsis thaliana)
- gi|6754010|ref|NP_034434.1|_5:58 guanine nucleotide binding protein, alpha 15 (Mus musculus)
- gi|232138|sp|P30678|GB15_MOUSE GUANINE NUCLEOTIDE-BINDING PROTEIN, ALPHA-15 SUBUNIT (Mus musculus)
- gi|109929|pir||B41534 GTP-binding protein alpha-15 chain - mouse (Mus musculus)
- gi|193571|gb|AAA37713.1| (M80632) G protein alpha subunit [Mus musculus] (Mus musculus)
- gi|1051246|gb|AAB36840.1| (U37419) guanine nucleotide-binding protein [Mus musculus] (Mus musculus)
- gi|9296971|sp|O88302|GB15_RAT_5:58 GUANINE NUCLEOTIDE-BINDING PROTEIN, ALPHA-15 SUBUNIT (Rattus norvegicus)
- gi|3219265|dbj|BAA28827.1| (AB015308) GTP binding protein alpha 15 [Rattus norvegicus] (Rattus norvegicus)
- gi|6323587|ref|NP_013658.1|_101:142 Cytochrome b2 [L--lactate cytochrome-c oxidoreductase]; Cyb2p (Saccharomyces cerevisiae)
- gi|117804|sp|P00175|CYB2_YEAST CYTOCHROME B2 PRECURSOR (L-LACTATE DEHYDROGENASE (CYTOCHROME)) (L-LACTATE FERRICYTOCHROME C OXIDOREDUCTASE) (L-LCR) (Saccharomyces cerevisiae)
- gi|279439|pir||CBBY2 L-lactate dehydrogenase (cytochrome) (EC 1.1.2.3) precursor - yeast (Saccharomyces cerevisiae) (Saccharomyces cerevisiae)
- gi|3633|emb|CAA26959.1| (X03215) cytochrome b2 precursor [Saccharomyces cerevisiae] (Saccharomyces cerevisiae)
- gi|577142|emb|CAA86721.1| (Z46729) cytochrome b2 precursor [Saccharomyces cerevisiae] (Saccharomyces cerevisiae)
- gi|229531|prf||751845B_23:64 cytochrome b5 [Saccharomycetales] (Saccharomycetales)
- gi|229530|prf||751845A_21:62 cytochrome b2 1-103 [Saccharomycetales] (Saccharomycetales)
- gi|640259|pdb|1LTD|A_16:57 Chain A, Flavocytochrome B2 (E.C.1.1.2.3) Complexed With Sulfite (Saccharomyces cerevisiae)
- gi|640260|pdb|1LTD|B Chain B, Flavocytochrome B2 (E.C.1.1.2.3) Complexed With Sulfite (Saccharomyces cerevisiae)
- gi|1127122|pdb|1LCO|A_21:62 Chain A, Mol_id: 1; Molecule: L-Lactate Dehydrogenase; Chain: A, B; Synonym: Cytochrome C Oxidoreductase, Flavocytochrome B2; Ec: 1.1.2.3; Engineered: Yes; Mutation: Tyr 143 Phe; Heterogen: Phenyl-Pyruvate (Saccharomyces cerevisiae)
- gi|1065320|pdb|1LDC|A Chain A, L-Lactate Dehydrogenase: Cytochrome C Oxidoreductase (Flavocytochrome B2) (E.C.1.1.2.3) Mutant With Tyr 143 Replaced By Phe (Y143f) Complexed With Pyruvate (Saccharomyces cerevisiae)
- gi|1127123|pdb|1LCO|B Chain B, Mol_id: 1; Molecule: L-Lactate Dehydrogenase; Chain: A, B; Synonym: Cytochrome C Oxidoreductase, Flavocytochrome B2; Ec: 1.1.2.3; Engineered: Yes; Mutation: Tyr 143 Phe; Heterogen: Phenyl-Pyruvate (Saccharomyces cerevisiae)
- gi|1065321|pdb|1LDC|B Chain B, L-Lactate Dehydrogenase: Cytochrome C Oxidoreductase (Flavocytochrome B2) (E.C.1.1.2.3) Mutant With Tyr 143 Replaced By Phe (Y143f) Complexed With Pyruvate (Saccharomyces cerevisiae)
- gi|229909|pdb|1FCB|A_21:62 Chain A, Flavocytochrome b2 (E.C.1.1.2.3) (Saccharomyces cerevisiae)
- gi|229910|pdb|1FCB|B Chain B, Flavocytochrome b2 (E.C.1.1.2.3) (Saccharomyces cerevisiae)
- gi|9107994|gb|AAF85537.1|AE004081_9_100:140 (AE004081) hypothetical protein [Xylella fastidiosa] (Xylella fastidiosa)
- gi|5729848|ref|NP_006563.1|_20:64 guanine nucleotide binding protein (G protein), alpha 13 (Homo sapiens)
- gi|2494886|sp|Q14344|GB13_HUMAN GUANINE NUCLEOTIDE-BINDING PROTEIN, ALPHA-13 SUBUNIT (G ALPHA 13) (Homo sapiens)
- gi|2135318|pir||I57490 guanine nucleotide regulatory protein - human (Homo sapiens)
- gi|404722|gb|AAA74235.1| (L22075) guanine nucleotide regulatory protein [Homo sapiens] (Homo sapiens)
- gi|6754008|ref|NP_034433.1|_19:64 guanine nucleotide binding protein, alpha 13 (Mus musculus)
- gi|120984|sp|P27601|GB13_MOUSE GUANINE NUCLEOTIDE-BINDING PROTEIN, ALPHA-13 SUBUNIT (G ALPHA 13) (Mus musculus)
- gi|109932|pir||B41095 GTP-binding regulatory protein alpha-13 chain - mouse (Mus musculus)
- gi|193379|gb|AAA37649.1| (M63660) G-alpha-13 protein [Mus musculus] (Mus musculus)
- gi|6288792|gb|AAF06740.1|AF169627_1_6:58 (AF169627) Galpha16 [Oryctolagus cuniculus] (Oryctolagus cuniculus)
- gi|4156172|gb|AAD05026.1|_37:73 (AC004933) guanine nucleotide-binding protein alpha subunit [Homo sapiens] (Homo sapiens)

              10        20        30        40             50          
              |         |         |         |              |          
   1 MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSE.....SEISQEA..DD
   2 MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSE.....SEISQEA..DD
   3 MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSE.....SEISQEA..DD
   4 MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSE.....SEISQEA..DD
   5 MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSE.....SEISQEA..DD
   6 IDGTIHQVYVLKRPHVDEFL----QRMGELFECVLFTASLAKYADPVADlldrwGVFRARLfrES
   7 IDGTIHQVYVLKRPHVDEFL----QRMGELFECVLFTASLAKYADPVADlldrwGVFRARLfrES
   8 IDGTIHQVYVLKRPHVDEFL----QRMGELFECVLFTASLAKYADPVADlldrwGVFRARLfrES
   9 IDGTIHQVYVLKRPHVDEFL----QRMGQLFECVLFTASLAKYADPVADlldrwGVFRARLfrES
  10 IDGTVHQVYVLKRPHVDEFL----QKMGELYECVLFTASLAKYADPVADlldkwNVFRARLfrES
  11 IEGTIHQVYVVKRPFVDDFL----RAIAEKFEIVVFTASLAKYADPVLDfldtgRVIHYRLfrES
  12 MEREIMPIFVVKRPGVTEFL----ERLGENYKVVVFTAGLEEYASQVLDkldknGVISQRLyrDS
  13 -----------------------------------LTWGCCPWCLTEEEkta..ARIDQEI..NR
  14 -----------------------------------LTWGCCPWCLTEEEkta..ARIDQEI..NK
  15 -------------------------------------------------.....-----KP..DD
  16 -------------------------------------------------.....-----KP..DD
  17 -------------------------------------------------.....-----KP..DD
  18 -------------------------------------------------.....-----KP..DD
  19 -------------------------------------------------.....-----KP..DD
  20 -------------------------------------------------.....-----KP..DD
  21 -------------------------------------------------.....-------..-K
  22 -----------------------------------LTSG-------EAEq....QRKSKEI..DK
  23 ----------------------------------VLTNG-------EAEq....QRKSKEI..DK
  24 ------------------------------------AWRCCPWCLSEDEkaa..ARVDQEI..TR
  25 -------------------------------------------------.....RRRSRDI..DA


      60        70        80        90       100       110     
      |         |         |         |         |         |     
   1 MAMEKGKYVGELRKALLSGAGPADVYTFNFSKESCYFFFEKNLKDVSFRLGSFNLEK
   2 MAMEKGKYVGELRKALLSGAGPADVYTFNFSKESCYFFFEKNLKDVSFRLGSFNLEK
   3 MAMEKGKYVGELRKALLSGAGPADVYTFNFSKESCYFFFEKNLKDVSFRLGSFNLEK
   4 MAMEKGKYVGELRKALLSGAGPADVYTFNFSKESCYFFFEKNLKDVSFRLGSFNLEK
   5 MAMEKGKYVGELRKALLSGAGPADVYTFNFSKESCYFFFEKNLKDVSFRLGSFNLEK
   6 CVFHRGNYVKDLSRL------------------------------------------
   7 CVFHRGNYVKDLSRL------------------------------------------
   8 CVFHRGNYVKDLSRL------------------------------------------
   9 CVFHRGNYVKDLSRL------------------------------------------
  10 CVYYRGNYIKDLNRL------------------------------------------
  11 CHNHKGNYVKDLSRL------------------------------------------
  12 CTEVNGKYVKDL---------------------------------------------
  13 ILLEQKKQEREELKLLLLGPGESGKSTF-----------------------------
  14 ILLEQKKQERGELKLLLLGPGESGKSTF-----------------------------
  15 CWVVINGYVYDLTRFLPNHPGGQDVIKFNAGKDVTAIF-------------------
  16 CWVVINGYVYDLTRFLPNHPGGQDVIKFNAGKDVTAIF-------------------
  17 CWVVINGYVYDLTRFLPNHPGGQDVIKFNAGKDVTAIF-------------------
  18 CWVVINGYVYDLTRFLPNHPGGQDVIKFNAGKDVTAIF-------------------
  19 CWVVINGYVYDLTRFLPNHPGGQDVIKFNAGKDVTAIF-------------------
  20 CWVVINGYVYDLTRFLPNHPGGQDVIKFNAGKDVTAIF-------------------
  21 MLEVRQRYVNENRKAILIKPNTDDVTVYEFVKDGCWHLWS-----------------
  22 CLSREKTYVKRLVKILLLGAGESGKSTF-----------------------------
  23 CLSREKTYVKRLVKILLLGAGESGKSTF-----------------------------
  24 LLLEHRRQVRGELKLLLLGTGESGKSTF-----------------------------
  25 LLARERRAVRRLVKILLLGAGESGKSTF-----------------------------