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:

- T0277 1wj8, Thermus thermophilus
- gi|16272048|ref|NP_438247.1|_8:141 nucleotidyltransferase [Haemophilus influenzae Rd KW20]
- gi|1175098|sp|P43934|Y074_HAEIN Hypothetical protein HI0074 [Taxonomy]
- gi|1074246|pir||F64000 hypothetical protein HI0074 - Haemophilus influenzae (strain Rd KW20) [Taxonomy]
- gi|1573031|gb|AAC21759.1| H. influenzae predicted coding region HI0074 [Haemophilus influenzae Rd KW20]
- gi|46133694|ref|ZP_00157581.2|_8:141 hypothetical protein Hflu2021262 [Haemophilus influenzae R2866]
- gi|20808390|ref|NP_623561.1|_11:127 conserved hypothetical protein [Thermoanaerobacter tengcongensis]
- gi|20517003|gb|AAM25165.1| conserved hypothetical protein [Thermoanaerobacter tengcongensis MB4]
- gi|15892084|ref|NP_359798.1|_81:198 unknown [Rickettsia conorii str. Malish 7]
- gi|25501935|pir||A97720 hypothetical protein RC0161 [imported] - Rickettsia conorii (strain Malish 7) [Taxonomy]
- gi|15619206|gb|AAL02699.1| unknown [Rickettsia conorii str. Malish 7]
- gi|46200260|ref|YP_005927.1|_3:118 probable nucleotidyltransferase [Thermus thermophilus HB27]
- gi|46197888|gb|AAS82300.1| probable nucleotidyltransferase [Thermus thermophilus HB27]
- gi|27573673|pdb|1JOG|A_8:141 Chain A, Structure Of Hi0074 From Heamophilus Influenzae Reveals The Fold Of A Substrate Binding Domain Of A Nucleotidyltransferase [Taxonomy]
- gi|27573674|pdb|1JOG|B Chain B, Structure Of Hi0074 From Heamophilus Influenzae Reveals The Fold Of A Substrate Binding Domain Of A Nucleotidyltransferase [Taxonomy]
- gi|27573675|pdb|1JOG|C Chain C, Structure Of Hi0074 From Heamophilus Influenzae Reveals The Fold Of A Substrate Binding Domain Of A Nucleotidyltransferase [Taxonomy]
- gi|27573676|pdb|1JOG|D Chain D, Structure Of Hi0074 From Heamophilus Influenzae Reveals The Fold Of A Substrate Binding Domain Of A Nucleotidyltransferase [Taxonomy]
- gi|34580885|ref|ZP_00142365.1|_78:195 hypothetical protein [Rickettsia sibirica]
- gi|28262270|gb|EAA25774.1| unknown [Rickettsia sibirica 246]
- gi|22974147|ref|ZP_00020500.1|_13:132 hypothetical protein [Chloroflexus aurantiacus]
- gi|23113807|ref|ZP_00099152.1|_12:132 hypothetical protein [Desulfitobacterium hafniense]
- gi|28211093|ref|NP_782037.1|_14:131 nucleotidyltransferase [Clostridium tetani E88]
- gi|28203533|gb|AAO35974.1| nucleotidyltransferase [Clostridium tetani E88]
- gi|29654335|ref|NP_820027.1|_25:144 conserved hypothetical protein [Coxiella burnetii RSA 493]
- gi|29541602|gb|AAO90541.1| conserved hypothetical protein [Coxiella burnetii RSA 493]
- gi|23335528|ref|ZP_00120763.1|_5:122 COG0365: Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Bifidobacterium longum DJO10A]
- gi|46914268|emb|CAG21048.1|_31:151 conserved hypothetical protein [Photobacterium profundum]
- gi|23466304|ref|NP_696907.1|_5:121 hypothetical protein possibly involved in exopolysaccharide production [Bifidobacterium longum NCC2705]
- gi|23327057|gb|AAN25543.1| hypothetical protein possibly involved in exopolysaccharide production [Bifidobacterium longum NCC2705]
- gi|22973025|ref|ZP_00019871.1|_13:138 hypothetical protein [Chloroflexus aurantiacus]
- gi|23102674|ref|ZP_00089176.1|_44:161 hypothetical protein [Azotobacter vinelandii]
- gi|46198578|ref|YP_004245.1|_10:127 probable nucleotidyltransferase [Thermus thermophilus HB27]
- gi|46196200|gb|AAS80618.1| probable nucleotidyltransferase [Thermus thermophilus HB27]
- gi|23104511|ref|ZP_00090975.1|_15:137 hypothetical protein [Azotobacter vinelandii]
- gi|22971527|ref|ZP_00018476.1|_15:139 hypothetical protein [Chloroflexus aurantiacus]
- gi|33865009|ref|NP_896568.1|_12:99 conserved hypothetical protein [Synechococcus sp. WH 8102]
- gi|33638693|emb|CAE06988.1| conserved hypothetical protein [Synechococcus sp. WH 8102]
- gi|33865110|ref|NP_896669.1|_5:99 conserved hypothetical protein [Synechococcus sp. WH 8102]
- gi|33638794|emb|CAE07089.1| conserved hypothetical protein [Synechococcus sp. WH 8102]
- gi|42453316|ref|ZP_00153223.1|_2:57 hypothetical protein Rick015401 [Rickettsia rickettsii]
- gi|48867357|ref|ZP_00320897.1|_8:83 hypothetical protein Hinf801001676 [Haemophilus influenzae 86-028NP]

              10                   20        30        40             5
              |                    |         |         |              
   1 MASLARAVERLKAALE....RP.....K..DEFIRDSAIQRFEFTFELAWKTLKTFLEL.....Q
   2 LNVLDAAFYSLEQTVV....QIs12siV..QDTLIAGAIQKFEFVYELSLKMMKRQLQQdaintD
   3 LNVLDAAFYSLEQTVV....QIs12siV..QDTLIAGAIQKFEFVYELSLKMMKRQLQQdaintN
   4 -KDFENALMRLKEALAi...EV.....T..NEIIIDGVIQRFEFTFELAWKIMKDYLAY.....E
   5 LEKFRKAFMTLEDIYL....KP.....TteDRAYIDATIQRFEFTFELAWKFLKEYFSQ.....K
   6 --SLARAVERLKAALE....QP.....K..DEFIRDSAIQRFEFTFELAWKTLKTFLEL.....Q
   7 LNVLDAAFYSLEQTVV....QIs12siV..QDTLIAGAIQKFEFVYELSLKXXKRQLQQdaintD
   8 LEKFRKAFMKLEDIYL....KP.....TteDRAYIDATIQRFEFTFELAWKFLKEYFSQ.....K
   9 -KHFTKALWQLEQAIElsrtRA.....L..SELETLGLIQAFEYTHELAWKTLKDFLED.....K
  10 LDNFEKAYARLKEGSN....RYdg...N..DDLMRDGLIQRFEFTFELAWKTLQAVFED.....E
  11 -SDFANAFSRLQEAFK....KDi....D..DDIIIDGIIQRFEFTFEQSWKVMKLYLED.....Q
  12 -KSFEEAVDYSNNLPE....NI.....A..ADIVRDSVIQRFEYTYELGWKLLQRWIKLnigp.E
  13 -ENYVSALKSLRKAPE....QD.....Ls.NDFIQSGIIDKFELQFELGWKLFKALLAY.....E
  14 LENYQKANQRLQNACQ....QDs....Y..TELERAGLIQMFEFTYELSWKTLKDILNF.....E
  15 -ENYVSALNSLRKAPE....QD.....Lg.NDFIQSGIIDKFGLQFELGWKLFKALLAY.....E
  16 -QALDAALRIVNDRSW....FDaqsaeV..QQTIMAGVVQNFEFVYELCIKMIRRRLELdaafpE
  17 LNNFRKALLQLDEAMElmsrRP.....L..SKLERQGAFHVFECSYELAWNTLKDFLVW.....Q
  18 --VAEKALATLKELAFl...ED.....P..SPVERDAAIQRFEYTFEAFWKALQAYLREk....E
  19 ---LEQALLALEKTPSse..DI.....L..FDLYRNAAIKSFELSLETAGKLLRKALKLyvgspR
  20 -RALETAYSMYQRAVE....EQept..T..QEVLRMAIIKGFELAQEVSFRLIRRRLRD.....F
  21 -SNYCSALEQLETFFE....PPa....L..NEREQQGLIKAFEYTFELSWNTLRDLLRS.....Q
  22 ----------------....--.....-..----ELGLIQAFEFTHELSWLLIRDFLVD.....Q
  23 ----------------....--.....-..-----------------------------.....-
  24 LNVLDAAFYSLEQTVV....QIs12siV..QDTLIAGAIQKFEFVYELSLKMMKRQLQQdaintD


      0               60          70          80         90       100  
     |                |           |           |          |         |  
   1 GL..EAR.....SPRAAIRGAFQVGLL..PEDP..FWLEMLELR.NLTNHTYDEALAERIYAELP
   2 DI..GAY.....GFKDILREALRFGLI..GDMS..KWVAYRDMR.NITSHTYDQEKAMAVYAQID
   3 DI..GAY.....GFKDILREALRFGLI..EDMS..KWVVYRDMR.NITSHTYDQEKAMAVYAQID
   4 GI..EVN.....SPRSAIKAAYSAGLI..QDGE..MWIDMLMDR.NRTTHIYNSKMALEIYENIK
   5 GT..FLH.....YPKEVIKEAFVAGII..NDES..LWIYMLTDRsNMISYTYDKKLADEIYNRIR
   6 GL..EAR.....SPRAAIRGAFQVGLL..PEDP..FWLEMLELR.NLTNHTYDEALAERIYAELP
   7 DI..GAY.....GFKDILREALRFGLI..GDXS..KWVAYRDXR.NITSHTYDQEKAXAVYAQID
   8 GT..FLH.....YPKEVIKEAFVAGII..NDES..LWIYMLTDRsNMISYTYDKKLADEIYNRIR
   9 GVy.NLY.....GSRDSTREAFKRGLI..DDGE..VWMDMIKSR.NLSSHTYNQEIADAIAGRIV
  10 GLi.GLN.....SPKRILREAFATEVI..GNEE..LWLSMLDDR.NATVHIYNEMTAVRICQDIK
  11 GIldEAL.....SPRSTIRLAFKYKII..SDGD..IWIQMMLDR.NRTSHMYDETIAKNIVKRIK
  12 EA..EPR.....TKKDLFRLAAKKNLI..DDPS..PWFEFSEAR.NQVARTYNEKNAKYVYDVAI
  13 GD..PVSasg..SPRDVLKTAFQYYDF..MDES..LWLRMLRDR.NDSAHIYDEERARRLVDAII
  14 GY..DAA.....SPRAVIRTSLEAGLVnsDECE..QLLTALGKR.NLLAHTYDENTSLEAERLIL
  15 GD..PVSasg..SPRDVLKTAFQYYDF..MDES..LWLRMLRDR.NDSAHIYDEERARRLVDAII
  16 EV..DVS.....NFRNFIRTAAEKGLI..TDVE..AWFRYRLLR.NMTSHTYDSAKALMVCQHAG
  17 GIe.GIV.....GSRDTIREAFSAGLI..ADGQ..GWMRMLTDR.GRTLHTCNEETAEAI---LL
  18 GL..EGA.....SPKGVIRLAREVGLL..RDEEarLALGMVDDR.SLTVHTYNEPLARAILRRLP
  19 SV..DAL.....VFNDLLRHAGKHGLLdaDGVE..RWLAYRANR.NNTAHDYGEGFANDTLKLLP
  20 GY..GIRrleatPVRELLRLAAQHSLLsiPEVE..RWFTYRDNR.NSTAHDYGDAFVQQTLTLLP
  21 GNa.NLL.....GSSDTLREAFQLGLI..SDGE..TWMLMIQDR.NLTSH---------------
  22 GVa.GIS.....GSRDAVREAVVRQLLpqGDET..VWMAMIRSR.NLTSHPYNPAVAREIADLIV
  23 --..---.....-----IKEAFVAGII..NDES..LWIYMLTDR.NMISYTYDKKLADEIYNRIR
  24 DI..GAY.....GFKDI----------..----..---------.--------------------


            110         
             |         
   1 .KALERFQELLRRLEEPA
   2 .DFLIESSFLLEQLRQ--
   3 .DFLIESRFLLEQLRQ--
   4 rRYVSCFEELSEKIR---
   5 .NYVPELKKLLNII----
   6 .KVLERFQELLRRLEEP-
   7 .DFLIESSFLLEQLRQ--
   8 .TYVPELKKLLNII----
   9 eRYVTAFQQLLNRL----
  10 gKYVPAFGELVERIRE--
  11 dTYMKEFTKLQDFL----
  12 .KFLPAVKVLLKELEQ--
  13 vDYIPEFERVNQG-----
  14 kEYAPLLHTIYTRLKE--
  15 aDYIPEFERANQ------
  16 .ELLAEAQVVLKALDR--
  17 .DIRQQHHPLLEALE---
  18 .DYARLMEQVLGRLR---
  19 .GYLADVRALAGKLQE--
  20 .DFIRDAYALAERLR---
  21 .-----------------
  22 hRYGLAFQQLSGV-----
  23 .NYVPELKKLLNII----
  24 .-----------------