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:

- T0091 HI0442, H. influenzae
- gi|1074405|pir||G64152_13:121 hypothetical protein HI0442 - Haemophilus influenzae (strain Rd KW20) (Haemophilus influenzae)
- gi|1573418|gb|AAC22101.1| (U32727) conserved hypothetical protein [Haemophilus influenzae Rd] (Haemophilus influenzae Rd)
- gi|1175545|sp|P44711|YBAB_HAEIN_1:109 HYPOTHETICAL PROTEIN HI0442 (Haemophilus influenzae)
- gi|140249|sp|P17577|YBAB_ECOLI_1:109 HYPOTHETICAL 12.0 KD PROTEIN IN DNAX-RECR INTERGENIC REGION (Escherichia coli)
- gi|76266|pir||QQECZG ybaB protein - Escherichia coli (Escherichia coli)
- gi|145298|gb|AAA23458.1| (M38777) orf12 ORF [Escherichia coli] (Escherichia coli)
- gi|1786677|gb|AAC73573.1| (AE000153) orf, hypothetical protein [Escherichia coli] (Escherichia coli)
- gi|141372|sp|P24281|YAAK_BACSU_2:106 HYPOTHETICAL 11.8 KD PROTEIN IN DNAZ-RECR INTERGENIC REGION (Bacillus subtilis)
- gi|98365|pir||S13787 conserved hypothetical protein yaaK - Bacillus subtilis (Bacillus subtilis)
- gi|40073|emb|CAA34878.1| (X17014) ORF107 [Bacillus subtilis] (Bacillus subtilis)
- gi|467410|dbj|BAA05256.1| (D26185) unknown [Bacillus subtilis] (Bacillus subtilis)
- gi|2632287|emb|CAB11796.1| (Z99104) similar to hypothetical proteins [Bacillus subtilis] (Bacillus subtilis)
- gi|7380299|emb|CAB84885.1|_1:109 (AL162756) conserved hypothetical protein [Neisseria meningitidis] (Neisseria meningitidis)
- gi|7226685|gb|AAF41804.1|_1:109 (AE002494) conserved hypothetical protein [Neisseria meningitidis] (Neisseria meningitidis)
- gi|2644973|emb|CAA05823.1|_1:98 (AJ003049) hypothetical protein; similar to HP0035 from Helicobacter pylori [Wolinella succinogenes] (Wolinella succinogenes)
- gi|7007420|dbj|BAA90837.1|_1:102 (AB031210) YaaK [Bacillus halodurans] (Bacillus halodurans)
- gi|7444750|pir||B71649_2:107 hypothetical protein RP866 - Rickettsia prowazekii (Rickettsia prowazekii)
- gi|3861391|emb|CAA15290.1| (AJ235273) unknown [Rickettsia prowazekii] (Rickettsia prowazekii)
- gi|6969059|emb|CAB73630.1|_1:99 (AL139079) hypothetical protein Cj1642 [Campylobacter jejuni] (Campylobacter jejuni)
- gi|7477735|pir||E70795_1:102 hypothetical protein Rv3716c - Mycobacterium tuberculosis (strain H37RV) (Mycobacterium tuberculosis)
- gi|2960140|emb|CAA18038.1| (AL022121) hypothetical protein Rv3716c [Mycobacterium tuberculosis] (Mycobacterium tuberculosis)
- gi|7269963|emb|CAB79780.1|_71:176 (AL161577) putative protein [Arabidopsis thaliana] (Arabidopsis thaliana)
- gi|2496313|sp|P75502|Y134_MYCPN_1:99 HYPOTHETICAL PROTEIN MG134 HOMOLOG (Mycoplasma pneumoniae)
- gi|2146292|pir||S73886 hypothetical protein yaaK homolog A65_orf100 - Mycoplasma pneumoniae (strain ATCC 29342) (Mycoplasma pneumoniae)
- gi|1674259|gb|AAB96208.1| (AE000055) Mycoplasma pneumoniae, hypothetical protein (yaaK) homolog; similar to Swiss-Prot Accession Number P24281, from B. subtilis (Mycoplasma pneumoniae)
- gi|1723110|sp|P47380|Y134_MYCGE_1:99 HYPOTHETICAL PROTEIN MG134 (Mycoplasma genitalium)
- gi|1361565|pir||H64214 hypothetical protein homolog MG134 - Mycoplasma genitalium (Mycoplasma genitalium)
- gi|3844724|gb|AAC71351.1| (U39693) conserved hypothetical protein [Mycoplasma genitalium] (Mycoplasma genitalium)
- gi|7463957|pir||C64524_1:94 conserved hypothetical protein HP0035 - Helicobacter pylori (strain 26695) (Helicobacter pylori)
- gi|2313110|gb|AAD07104.1| (AE000525) conserved hypothetical protein [Helicobacter pylori 26695] (Helicobacter pylori 26695)
- gi|3150108|emb|CAA19160.1|_1:101 (AL023596) hypothetical protein MLCB2407.20 [Mycobacterium leprae] (Mycobacterium leprae)
- gi|3738329|gb|AAC63670.1|_69:174 (AC005170) unknown protein [Arabidopsis thaliana] (Arabidopsis thaliana)
- gi|7464580|pir||E71983_3:97 hypothetical protein jhp0031 - Helicobacter pylori (strain J99) (Helicobacter pylori)
- gi|4154536|gb|AAD05615.1| (AE001442) putative [Helicobacter pylori J99] (Helicobacter pylori J99)
- gi|7444751|pir||S75165_11:113 hypothetical protein slr1847 - Synechocystis sp. (strain PCC 6803) (Synechocystis sp.)
- gi|1652155|dbj|BAA17079.1| (D90903) hypothetical protein [Synechocystis sp.] (Synechocystis sp.)
- gi|7479647|pir||T35387_5:105 hypothetical protein SC66T3.30c - Streptomyces coelicolor (Streptomyces coelicolor)
- gi|5123894|emb|CAB45486.1| (AL079348) hypothetical protein [Streptomyces coelicolor A3(2)] (Streptomyces coelicolor A3(2))
- gi|5748804|gb|AAD34031.2|AF151381_1 (AF151381) unknown [Streptomyces coelicolor] (Streptomyces coelicolor)
- gi|7471319|pir||A75548_1:91 conserved hypothetical protein - Deinococcus radiodurans (strain R1) (Deinococcus radiodurans)
- gi|6457869|gb|AAF09786.1|AE001882_4 (AE001882) conserved hypothetical protein [Deinococcus radiodurans] (Deinococcus radiodurans)
- gi|7463079|pir||E70157_14:105 conserved hypothetical protein BB0462 - Lyme disease spirochete (Borrelia burgdorferi)
- gi|2688378|gb|AAC66830.1| (AE001151) conserved hypothetical protein [Borrelia burgdorferi] (Borrelia burgdorferi)
- gi|7444752|pir||E72344_21:116 conserved hypothetical protein - Thermotoga maritima (strain MSB8) (Thermotoga maritima)
- gi|4981210|gb|AAD35769.1|AE001741_2 (AE001741) conserved hypothetical protein [Thermotoga maritima] (Thermotoga maritima)
- gi|3925824|dbj|BAA34649.1|_1:86 (AB020241) dnaX-recR junction region; orf-12 [Deinococcus radiodurans] (Deinococcus radiodurans)
- gi|6899040|gb|AAF30493.1|AE002108_6_1:89 (AE002108) conserved hypothetical [Ureaplasma urealyticum] (Ureaplasma urealyticum)
- gi|43322|emb|CAA28176.1|_1:73 (X04487) open reading frame 2 (75AA) (2775 is 1st base in codon) [Escherichia coli] (Escherichia coli)
- gi|7190651|gb|AAF39443.1|_7:95 (AE002330) conserved hypothetical protein [Chlamydia muridarum] (Chlamydia muridarum)
- gi|7468586|pir||B72127_7:94 ybab family hypothetical protein - Chlamydia pneumoniae (strain CWL029) (Chlamydophila pneumoniae)
- gi|4376293|gb|AAD18192.1| (AE001589) YbaB family hypothetical protein [Chlamydophila pneumoniae] (Chlamydophila pneumoniae)
- gi|7189651|gb|AAF38541.1| (AE002232) conserved hypothetical protein [Chlamydophila pneumoniae AR39] (Chlamydophila pneumoniae AR39)
- gi|7468701|pir||B71528_7:95 hypothetical protein CT335 - Chlamydia trachomatis (serotype D, strain UW3/Cx) (Chlamydia trachomatis)
- gi|3328754|gb|AAC67930.1| (AE001306) hypothetical protein [Chlamydia trachomatis] (Chlamydia trachomatis)

              10         20        30        40        50        60    
              |          |         |         |         |         |    
   1 MFGKGGLGGLMKQAQQ.MQEKMQKMQEEIAQLEVTGESGAGLVKITINGAHNCRRIDIDPSLME.
   2 MFGKGGLGGLMKQAQQ.MQEKMQKMQEEIAQLEVTGESGAGLVKITINGAHNCRRIDIDPSLME.
   3 MFGKGGLGGLMKQAQQ.MQEKMQKMQEEIAQLEVTGESGAGLVKITINGAHNCRRIDIDPSLME.
   4 MFGKGGLGNLMKQAQQ.MQEKMQKMQEEIAQLEVTGESGAGLVKVTINGAHNCRRVEIDPSLLE.
   5 RGGMGNMQKMMKQMQK.MQKDMAKAQEELAEKVVEGTAGGGMVTVKANGQKEILDVIIKEEVVDp
   6 MFGKAGLGGLMKQAQQ.MQENMKKAQAKLAETEIEGEAGNGLVKITMTCAHEVRKIDISPDLIQe
   7 MFGKAGLGGLMKQAQQ.MQENMKKAQAKLAETEIEGEAGNGLVKITMTCAHEVRKIDISPDLIQe
   8 ---MFDPSKLSEMLTQ.FQDKAKEMEEKSHNTSFTAKSGGGLVSVSMSGAGELLDVSIDDSLLE.
   9 ---MKNMGQMMKQMQK.MQKQMMKAQEELKEKTVEATAGGGMVTVVASGDKRILDVRISEDVVDp
  10 ----VNFNQFLKQAQS.MQKKMQEAQEQMANTRYTGKAGGMLVEIIITGKGEVEKISIDESLLKt
  11 MFENMDFSKMGELLNQ.VQEKAKNIELELANREFSAKSGAGLVKVSANGKGEIIDVSIDDSLLE.
  12 MQPGGDMSALLAQAQQ.MQQKLLEAQQQLANSEVHGQAGGGLVKVVVKGSGEVIGVTIDPKVVDp
  13 LGNMQNLYETVKKAQMvVQVEAVRVQKELAVAEFDGYCQGELVKVTLSGNQQPIRTDITDAAME.
  14 ----MSFKKITEMMRQ.AERQSKQKALDFEQKLFEYSYKNAAIKIIIFGNLTIKSITIDPALIDp
  15 ----MSFKKIAEMMRQ.AERETKKKTLAFEQQAFEYNYKNGAIKITILGDLTLKSINIDPVLIDa
  16 ----MDFSQLGGLLDG.MKKEFSQLEEKNKDTIHTSKSGGGMVSVSFNGLGELVDLQIDDSLLE.
  17 MQPGGDMSALLAQAQQ.MQQKLLETQQQLANAQVHGQGGGGLVEVVVKGSGEVVSVAIDPKVVDp
  18 FGNMQNMYETVKKAQMvVQVEAVRVQKELAAAEFDGYCAGELVKVTLSGNQQPIRTDITEAAME.
  19 ---FSQLGGLSGLLDG.VKKEFSQLEEKNKDTIHTSKSGGGMVSVSFNGLGELVDLQIDDSLLE.
  20 LGKIKELQEAFQKAQQ.VQEGAKVLQEELERMEIPGKSADGLVTVLMSGNQEPLSIEIDPSALE.
  21 -GGQPNMQQLLQQAQK.MQQDLAKAQEELARTEVDGQAGGGLVKATVTGSGELRGLVIDPKAVDp
  22 ----MDMKKLMKQMQQ.AQVAAGKIQDELAAQSVEGTA-SGLVTVQMNGHGKVTSLKIKPEAVDg
  23 ----VNPLDFLKNMSS.VKNNIDNIKKEISKITVCGKAGSNIVTIEMDGEFNVKKVSINKEFFDd
  24 ------LKDFARMQEE.LQKKIQELEESFSQIEVEASVGGGAVRIVATCDRRVKDIEIDEDLKE.
  25 ----MDMKKLMKQMQQ.AQVAAGKIQDELAAQSVEGTA-SGLVTVQMNGHGKVTSLKIKPEAVDg
  26 ----MDFQKLAQELKK.MQNTLSKKQKEFEEKVFDFDYK-GYVLVKIKGDLNIEAIEIKTEIVDp
  27 MFGKGGLGNLMKQAQQ.MQEKMQKMQEEIAQLEVTGESGAGLVKVTINGAHNCRRVEIDPSLLE.
  28 --------KKKKEAKL.MERQFMEMEASLEQKRFSGEAGNGLVSVTINGKCNLVDVKIKPDCLDp
  29 --------KKKKEAKI.MEQQFLEMEASLLEKRYEGQAGNGLVSVVINGKCDLISVKVQPTCLDp
  30 --------KKKKEAKL.MERQFMEMEASLEQKRFSGEAGNGLVSVTINGKCDLVDVRIKPDCLDp


             70        80        90       100         
             |         |         |         |         
   1 ..DDKEMLEDLIAAAFNDAVRRAEELQKEKMASVTAGMPLPPGMKFPF
   2 ..DDKEMLEDLIAAAFNDAVRRAEELQKEKMASVTAGMPLPPGMKFPF
   3 ..DDKEMLEDLIAAAFNDAVRRAEELQKEKMASVTAGMPLPPGMKFPF
   4 ..DDKEMLEDLVAAAFNDAARRIEETQKEKMASVSSGMQLPPGFKMPF
   5 ..EDIDMLQDLVLAATNEALKKVDEITNETMGQFTKGMNM-PGL----
   6 aaDDKEMLEDLILAALKSARDKAEETANKTMGAFTQGL--PPGVGDF-
   7 aaDDKEMLEDLILAALKSARGKAEETANKTMGAFTQGL--PPGVGDF-
   8 ..-DKESLQILLISAINDVYKSVEENKKSMTLGMLGGMAPF-------
   9 ..DDVEMLQDLILAATNEALKKVDELVEQDMGKFTKGLNM-PGM----
  10 ..EEKEMLEDLIKVAFNDAKQKCDEDSQNSLSGALNGMSLPPGFKIPF
  11 ..-DKESLQILLISAINDVLAMVAQNRSSMANDVLGGFG---------
  12 ..DDIETLQDLIVGAMRDASQQVTKMAQERLGALAGAMRP--------
  13 ..LGSEKLSLLVTEAYKDAHSKSVLAMKERMSDLAQSLGMPPGL----
  14 ..EDKVTLEEMITEAVNEAVGDVKAKYDQLMEE---AMPQMPGL----
  15 ..SDKVILEEMIIEATNEAVSDVKTKYDNLVEK---TMPKVPGL----
  16 ..-DKEAMQIYLMSALNDGYKAVEENRKNLAFNMLGNF----------
  17 ..GDIETLQDLIVGAMADASKQVTKLAQERLGALTSAMR---------
  18 ..LGSEKLSQLVTEAYKDAHAKSVVAMKERMSDLAQSLGMPPGL----
  19 ..-DKEAMQIYLMSALNDGYKAVEENRKNLAFNMLGNF----------
  20 ..KGAEGLSASVTEAMKAAYAESTETMRSKMEELTSGLNL-PG-----
  21 ..EDTETLADLVVAAVQAANENAQNLQQQKLGPLAQGMGG--------
  22 ..DDVEALEDLILAAINDAAEKAEGLQREATAGL--------------
  23 ..LDNDAFEQMIKSALNDAVSKVKEEIKLKTMGV--------------
  24 ..-DFDTLKDLLIAGMNEVMEKIEKRREEEMSKITQQFGI-PG-----
  25 ..DDVEALEDLILAAINDAAEKAEGLQRE-------------------
  26 ..EDKETLQDILRAAINEAISITCKERDAIMN----------------
  27 ..DDKEMLEDLV------------------------------------
  28 ..EDPEVVADLFRAAFKAA----KAALDSEMSAMHMGMP---------
  29 ..EDPEVIEDLFRAAFKLA----KEQMDQEMSLMRSTM----------
  30 ..EDPEVVADLFRAAFKAA----KAALDSEMSAMQMGMP---------