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:

- T0369 PC05163A, EXIGUOBACTERIUM SP. 255-15, 148 res
- gi|47502519|gb|AAT31195.1|_2:153 hypothetical protein GBAA2078 [Bacillus anthracis str. 'Ames Ancestor']
- gi|49178869|gb|AAT54245.1| hypothetical protein BAS1931 [Bacillus anthracis str. Sterne]
- gi|47527371|ref|YP_018720.1| hypothetical protein GBAA2078 [Bacillus anthracis str. 'Ames Ancestor']
- gi|49184942|ref|YP_028194.1| hypothetical protein BAS1931 [Bacillus anthracis str. Sterne]
- gi|30256727|gb|AAP25964.1| hypothetical protein BA_2078 [Bacillus anthracis str. Ames]
- gi|30262101|ref|NP_844478.1| hypothetical protein BA2078 [Bacillus anthracis str. Ames]
- gi|65319385|ref|ZP_00392344.1|_2:153 hypothetical protein Bant_01002692 [Bacillus anthracis str. A2012]
- gi|42781228|ref|NP_978475.1|_2:153 hypothetical protein BCE2162 [Bacillus cereus ATCC 10987]
- gi|42737150|gb|AAS41083.1| hypothetical protein BCE_2162 [Bacillus cereus ATCC 10987]
- gi|49332142|gb|AAT62788.1|_2:153 hypothetical protein BT9727_1893 [Bacillus thuringiensis serovar konkukian str. 97-27]
- gi|49480586|ref|YP_036224.1| hypothetical protein BT9727_1893 [Bacillus thuringiensis serovar konkukian str. 97-27]
- gi|47566848|ref|ZP_00237566.1|_2:153 conserved hypothetical protein protein [Bacillus cereus G9241]
- gi|47556477|gb|EAL14810.1| conserved hypothetical protein protein [Bacillus cereus G9241]
- gi|29895749|gb|AAP09031.1|_2:153 hypothetical protein BC_2062 [Bacillus cereus ATCC 14579]
- gi|30020199|ref|NP_831830.1| hypothetical protein BC2062 [Bacillus cereus ATCC 14579]
- gi|89206809|ref|ZP_01185362.1|_2:153 conserved hypothetical protein [Bacillus weihenstephanensis KBAB4]
- gi|89155319|gb|EAR75334.1| conserved hypothetical protein [Bacillus weihenstephanensis KBAB4]
- gi|89202744|ref|ZP_01181456.1|_2:153 conserved hypothetical protein [Bacillus cereus subsp. cytotoxis NVH 391-98]
- gi|89149248|gb|EAR69779.1| conserved hypothetical protein [Bacillus cereus subsp. cytotoxis NVH 391-98]
- gi|68053564|ref|ZP_00537729.1|_1:148 conserved hypothetical protein; RBL00553 [Exiguobacterium sibiricum 255-15]
- gi|68009342|gb|EAM88552.1| conserved hypothetical protein; RBL00553 [Exiguobacterium sibiricum 255-15]
- gi|52002905|gb|AAU22847.1|_5:157 conserved hypothetical protein [Bacillus licheniformis ATCC 14580]
- gi|52347559|gb|AAU40193.1| hypothetical protein BLi01287 [Bacillus licheniformis DSM 13]
- gi|52079694|ref|YP_078485.1| hypothetical protein BL02656 [Bacillus licheniformis ATCC 14580]
- gi|52785057|ref|YP_090886.1| hypothetical protein BLi01287 [Bacillus licheniformis ATCC 14580]
- gi|94969339|ref|YP_591387.1|_1:154 DinB [Acidobacteria bacterium Ellin345]
- gi|94551389|gb|ABF41313.1| DinB [Acidobacteria bacterium Ellin345]
- gi|51855763|dbj|BAD39921.1|_64:195 conserved domain protein [Symbiobacterium thermophilum IAM 14863]
- gi|51892074|ref|YP_074765.1| hypothetical protein STH936 [Symbiobacterium thermophilum IAM 14863]
- gi|51976821|gb|AAU18371.1|_2:85 group-specific protein [Bacillus cereus E33L]
- gi|52143352|ref|YP_083476.1| group-specific protein [Bacillus cereus E33L]
- gi|94967112|ref|YP_589160.1|_5:153 DinB [Acidobacteria bacterium Ellin345]
- gi|94549162|gb|ABF39086.1| DinB [Acidobacteria bacterium Ellin345]
- gi|67928342|ref|ZP_00521531.1|_50:196 DinB [Solibacter usitatus Ellin6076]
- gi|67864642|gb|EAM59647.1| DinB [Solibacter usitatus Ellin6076]
- gi|51857853|dbj|BAD42011.1|_20:148 conserved hypothetical protein [Symbiobacterium thermophilum IAM 14863]
- gi|51894164|ref|YP_076855.1| hypothetical protein STH3028 [Symbiobacterium thermophilum IAM 14863]
- gi|86141066|ref|ZP_01059625.1|_44:163 hypothetical protein MED217_17980 [Flavobacterium sp. MED217]
- gi|85833008|gb|EAQ51457.1| hypothetical protein MED217_17980 [Flavobacterium sp. MED217]
- gi|48856107|ref|ZP_00310265.1|_6:152 hypothetical protein Chut02001345 [Cytophaga hutchinsonii]
- gi|89096900|ref|ZP_01169791.1|_19:142 hypothetical protein B14911_18385 [Bacillus sp. NRRL B-14911]
- gi|89088280|gb|EAR67390.1| hypothetical protein B14911_18385 [Bacillus sp. NRRL B-14911]
- gi|67931363|ref|ZP_00524525.1|_33:163 DinB [Solibacter usitatus Ellin6076]
- gi|67861365|gb|EAM56397.1| DinB [Solibacter usitatus Ellin6076]
- gi|94971571|ref|YP_593619.1|_10:153 DinB [Acidobacteria bacterium Ellin345]
- gi|94553621|gb|ABF43545.1| DinB [Acidobacteria bacterium Ellin345]
- gi|67931469|ref|ZP_00524630.1|_23:153 DinB [Solibacter usitatus Ellin6076]
- gi|67861313|gb|EAM56346.1| DinB [Solibacter usitatus Ellin6076]
- gi|10176309|dbj|BAB07404.1|_21:150 BH3685 [Bacillus halodurans C-125]
- gi|15616247|ref|NP_244552.1| hypothetical protein BH3685 [Bacillus halodurans C-125]
- gi|67933163|ref|ZP_00526288.1|_9:158 hypothetical protein AcidDRAFT_0639 [Solibacter usitatus Ellin6076]
- gi|67859568|gb|EAM54637.1| hypothetical protein AcidDRAFT_0639 [Solibacter usitatus Ellin6076]
- gi|67932457|ref|ZP_00525600.1|_20:154 DinB [Solibacter usitatus Ellin6076]
- gi|67860306|gb|EAM55357.1| DinB [Solibacter usitatus Ellin6076]

              10        20        30         40        50              
              |         |         |          |         |              
   1 MTDWQQALDRHVGVGVRTTRDLIRLIQPEDWDKRP.ISGKRSVYEVAVHLAV.....LLEADL..
   2 ---FVQSALHQLKVAVDTSIQMLDQYTEIDLKIAP.IQSKRSLFEMCAHLSL.....ICHADL..
   3 ---FVQSALHQLKVAVDTSIQMLDQYTEIDLKIAP.XQSKRSLFEMCAHLSL.....ICHADL..
   4 ---FVQSALHQLKVAVDTSIQMLDQYTEIDLKIAP.IQSKRSLFEMYAHLSL.....ICHADL..
   5 ---FVQSALHQLKVAVDTSIQMLDQYTEIDLKIAP.IQSKRSLFEMCAHLSL.....ICHADL..
   6 ---FVESALHQLKVAVDTSIQMFNQYNEADLKTQP.IHAKRSVFEMCAHLSL.....ICHADL..
   7 ---FVQSALHQLKVAIDTSIDMLNQYSENDLKIQP.IHSKRSLFEMCAHLSL.....ICHADL..
   8 ---FVPSALNQVKIAIDTSIQILNQYTESDLKIKS.IESKRALFEMCTHLSL.....ICHADL..
   9 ---FVQAALHQLKIAIHTSIKMLNQLTESDLNIKP.IQHKRSLFEMYAHLAL.....ICHADL..
  10 MTDWQQALDRHVGVGVRTTRDLIRLIQPEDWDKRP.ISGKRSVYEVAVHLAV.....LLEADL..
  11 -QALRGDLFHELETGIRSTCHLLKKVKESDWSYRP.ADRMRSLKELASHLTA.....IPEADL..
  12 MQELIDSIHDEFHDEIPATRRVLERVTDENLSWKP.HPKSRSLGELAFHVAN.....IPGMAA..
  13 ------------------TVNALRRMTPEQLAWKP.PGWHSSAFELAEHMALcewvwIYRNAL..
  14 ---FVQSALHQLKVAVDTSIQMLDQYTEIDLKIAP.IQSKRSLFEMCAHLSL.....ICHADL..
  15 -----QSMTGELEHEMANTRRVLERVPYEKADWKP.HVKSGTLKWLAGHCAI.....MPGWGA..
  16 -------LVKHWKTTGELTMAVAEAMPAESYNFRP.NPEEMSFGQLMAHIGL.....ADRNAC..
  17 -------------------LAFIQAIPEDRMDFAP.QPGKFTFGDLIRHIAA.....TERMF-..
  18 -----------------------EKMPDSLYGYKP.TEREMSFGEQLEHINQn....MEWLST..
  19 ------VFLKEFDAEAQTTRNMLSRIPDDKYDWQP.HPKSMTIRSLATHIAE.....LSTWVS..
  20 -------------------IELLGTFEEGQQDFKA.WEQGMSVSELTAHITG.....SMEMFV..
  21 ----------EFKMAGRQIITLAEAIPTEKFEWRP.APGVRSVSEVLMHTAS.....GNYFFL..
  22 ----------DIERDAEATRKVLERVPMGHEKYKP.HEKSMELGPLVYMVTT.....MVEWTD..
  23 ----------------RLTKSVIEAIPHDKGDYRP.DEFAKSAMELAWHIV-.....--ATEM..
  24 -----------------------EKLSADEWTAQN.GYGLQSVRDTLVHMAD.....CYHAWLgs
  25 ------ALLAKIHEQIEGTVHLISAVPADRLNWTPaIPGAWPVDILLGHLLE.....CLAGFC..
  26 ------------------TLKLAEDVPEDKYDFRP.APDCRSIRETLVHIAV.....APRLQE..


              60        70                  80        90       100     
              |         |                   |         |         |     
   1 ...RI....ATGATADEMAQF.....Y.....AVPVLPEQLVDRLDQSWQYYQDRLMADFSTE..
   2 ...LI....LNGSTEKELRTF.....Yle...HTPETITYMQQIMLEGFTLLSKTFLSYSQEEla
   3 ...LI....LNGSTEKELRTF.....Yle...HTPETITYMQQIMLEGFTLLSKTFLSYSQEEla
   4 ...LI....LNGSTEKELHTF.....Yke...QTPETIAQMQKTMIQGYDLLSKTFLSYSNEQla
   5 ...LI....LNGSTEKELRTF.....Yle...HTPETITYMQQIMLEGFTLLSKTFLSYSQEElv
   6 ...LI....LNGITEKQLHTF.....Yke...QTPETITQMQQTMIQGYDLLSKTFLSYSNEQla
   7 ...LI....LNGIPEKELHTF.....Yie...RTPVTVAHMQQTMIEGYNLLSKTFLSYSQIEla
   8 ...LI....LNGITEKDLHTF.....Yie...QTPETITQIQQTMIQGYDLLSKTFLSYSNEEla
   9 ...LI....LNETPQEELHTF.....Yrk...HTPKTIHEIQQTMLQGYDLLSETFLSYSHEEla
  10 ...RI....ATGATADEMAQF.....Y.....AVPVLPEQLVDRLDQSWQYYQDRLMADFSTE..
  11 ...AI....MQEKEEDVIARIekk..Y.....GALQSADQMAAAMQKGFDAFQTYMTSLSDEDfl
  12 ...KI....IENDEYAAGAGT.....P.....TQVTSADQIRQAFEKSVFDADRAFSTLTPEKa1
  13 ...KV....VPWEARWESGRF.....P.....DLDSLLQYWDEIHRVTVQWLKDTPISQLGRKlp
  14 ...LI....LNGHTEKELRTF.....Yle...HTPETITYMQQIM------------------..
  15 ...NV....LTSDELNVHGVG.....Sai...PDFATKEDMIAHFEAELAKYRGALMEASDDYil
  16 ...AN....ASGMTAPALPDA.....Iaa7daTLEVDKASAVAFDKQIFDFCNTAVASVTLEKld
  17 ...--....VEGAIEGRWAYP.....Ghg7gsTKDEALGYLMGAHEEAMARLRAADPGVLQEKr.
  18 ...TY....FDKQEAEVSTNV.....N.....EKKRIIANLQNAFDLIYETIQSYPESRLTEK..
  19 ...LA....LTTDELDFAAAP.....Ynp6vnNTKELLRLFEKSLIEGRTELIPENEAKLSENwt
  20 ...QT....VKKGEFTPPPE-.....Y.....PAIETLEQLKALVQEETSKTKSALEELTQDQlg
  21 ...QS....MGVKAGEDLPKN.....Pe....KSVTAKADVVRWLKASFEAAQENYPKIDKQKa.
  22 ...FM....INRDELDVAPKGggnw.PkvdvsSREKLLEAHSAAVKKAVAALQKTNEEHLQTHwk
  23 ...RF....LEAVETGAFDFT.....Pkpkp.DSVKTSADMGAWYAENFAPHVAKLEKLSAGQle
  24 7lk--tkspITSKEARQKMTI.....H.....DCIERFNQADIYVEEVFRLLGDQLDQPIERTip
  25 ...AV....LSAVEPKRLAHFs11ha-cspg.DAIRRIALYRTRIDEGFALLVDASLCKS-VS..
  26 ...QI....HFTEHLSSLNGFd15ka-pr...TKAEILELLRTEGEKYASKLEGTSESFLAE-iv


             110        120       130       140        
              |          |         |         |        
   1 ...TTYWGVTDSTTGWLL.EAAVHLYHHRSQLLDYLNLLGYDIKLDLFE
   2 eikTAYWGVSYSRFEWLL.EIVAHFYHHRGQIHILLCEHIKDPNVPLFQ
   3 eikTAYWGVSYSRFEWLL.EIVAHFYHHRGQIHILLCEHIKDPNVPLFQ
   4 emkTAYWGISYSRFEWLL.EIVAHFYHHRGQIHILLCEHMKDPNIPLFQ
   5 eikTSYWGVSYSRFEWLL.EIVAHFYHHRGQIHILLCEHIKDPNVPFFQ
   6 eikTAYWGISYSCFEWLL.EIVAHFYHHRGQIHILLCEHMKDPNIPLFQ
   7 evmTAYWGISYSRFEWLL.EIVAHFYHHRGQIHILLCEHMNDPRIPLFE
   8 eimTAYWGISYSRFEWLL.EIVAHFYHHRGQIHILLVEHIKDPCIRLFE
   9 hitTAYWGVSYSRFEWLL.EIIAHVYHHRAQIHMLVTEHIQDPSVALFE
  10 ...TTYWGVTDSTTGWLL.EAAVHLYHHRSQLLDYLNLLGYDIKLDLFE
  11 7tkPFYLDEGMTQSRWLT.ETLTHIFHHRAQLFNYLKQLGYDVNM----
  12 0frDKEIFRKKRTAALRT.NMLNHLYHHRGQLSVYLRLLEIPVPM----
  13 ...MPYPDMPWATMDWVIyHVMEHEIHHRGQIFMLMRMQGIDP------
  14 ...---------------.------------------------------
  15 9rdNEQVIFTMSRIAVLRgMVMNHMIHHRAELIVYLRLLDVPV------
  16 ki.AGPPARNLTGYEWLW.SYFTHTAHHRGQAEVYLRVKGIKPP-----
  17 ...TTPLGATVSAWRLLM.MMTEHEIHHRSQIGQYLVALGLEPP-----
  18 ...VDFFAGEKSKLQILN.LLQDHLTHHRGQLIVYLNLNGLEP------
  19 6ng-DIIYSVQTKAETIR.HAFSQIIHHRAQLGVNLRLLNVPI------
  20 kt.IDFYGMTMPGIVLLE.NAKDHEIHHKGQLFTYARLAGI--------
  21 ...VKFLGHDATCDGVLL.RALAHANEHLGQMIAYARMNG---------
  22 6akGKVMSEGPRHVMIRD.TVLNHLAHHRGQLTVYLRLLS---------
  23 kvvDFRGMFQLPAVMYLG.FLMHHSVHHRGQLSVYLRPMGGK-------
  24 wr.EGGDPISMTPRKLLT.HTMTHEFHHKGQIVVMLRQLGH--------
  25 ...TVFVREGEPLLTLLL.GNLEHLVNHKHQLFTYLRQLGVDV------
  26 eypQGMVPPTKSRFEMLM.APKEHEMHHRGQLMV---------------