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:

- T0358 NESG:ER397, Escherichia coli, 87 res
- gi|88770148|gb|ABD51585.1|_14:86 conserved hypothetical protein [Escherichia coli]
- gi|37962737|gb|AAR05684.1|_7:79 conserved hypothetical protein [Salmonella typhimurium]
- gi|58383258|ref|YP_194828.1| hypothetical protein pU302L_021 [Salmonella typhimurium]
- gi|83586571|ref|ZP_00925204.1|_5:77 hypothetical protein Ecol1_01002225 [Escherichia coli 101-1]
- gi|75259093|ref|ZP_00730461.1|_5:77 hypothetical protein EcolE2_01001358 [Escherichia coli E22]
- gi|45758187|gb|AAS76399.1|_5:77 YkfF [Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67]
- gi|60115629|ref|YP_209420.1| YkfF [Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67]
- gi|75512277|ref|ZP_00734839.1|_5:77 hypothetical protein Ecol5_01003544 [Escherichia coli 53638]
- gi|75208230|ref|ZP_00708597.1|_5:77 hypothetical protein EcolB_01004504 [Escherichia coli B171]
- gi|75230630|ref|ZP_00717105.1|_5:77 hypothetical protein EcolB7_01001278 [Escherichia coli B7A]
- gi|50346328|ref|NP_052923.2|_5:77 hypothetical protein R100p043 [Plasmid R100]
- gi|89033311|gb|ABD59989.1| hypothetical protein [Escherichia coli]
- gi|38606100|gb|AAR25064.1|_7:79 YdeA [Escherichia coli]
- gi|41056963|ref|NP_957583.1| YdeA [Escherichia coli]
- gi|5103191|dbj|BAA78827.1| 94% identical to gp:AF074613_85[hypothetical protein of plasmid pO157], 61% identical (1 gap) to 64 residues of 79 aa protein gp:ECAE000133_3[hypothetical protein of E. coli] [Plasmid R100]
- gi|75238464|ref|ZP_00722461.1|_5:77 hypothetical protein EcolF_01003511 [Escherichia coli F11]
- gi|91206338|ref|YP_538692.1|_7:79 hypothetical protein UTI89_P093 [Escherichia coli UTI89]
- gi|91075789|gb|ABE10669.1| hypothetical protein UTI89_P093 [Escherichia coli UTI89]
- gi|26110819|gb|AAN83003.1|_1:77 Hypothetical protein ykfF [Escherichia coli CFT073]
- gi|26250389|ref|NP_756429.1| Hypothetical protein ykfF [Escherichia coli CFT073]
- gi|24528054|emb|CAD33784.1| hypothetical protein [Escherichia coli]
- gi|70608383|gb|AAZ04455.1| conserved hypothetical protein [Escherichia coli]
- gi|73476837|gb|AAZ76452.1|_5:77 hypothetical protein LH0085 [Escherichia coli]
- gi|73853253|ref|YP_308749.1| hypothetical protein LH0085 [Escherichia coli]
- gi|5702179|gb|AAD47188.1|_5:77 unknown; orf77 [Escherichia coli]
- gi|75234993|ref|ZP_00719258.1| hypothetical protein EcolE1_01003133 [Escherichia coli E110019]
- gi|8918884|dbj|BAA97931.1|_7:79 yfjA [Plasmid F]
- gi|9507774|ref|NP_061440.1| hypothetical protein Fpla063 [Plasmid F]
- gi|91213937|ref|YP_543923.1|_1:77 hypothetical protein YkfF [Escherichia coli UTI89]
- gi|91075511|gb|ABE10392.1| hypothetical protein YkfF [Escherichia coli UTI89]
- gi|26111397|gb|AAN83579.1|_1:77 Hypothetical protein ykfF [Escherichia coli CFT073]
- gi|26250965|ref|NP_757005.1| Hypothetical protein ykfF [Escherichia coli CFT073]
- gi|57903248|gb|AAW58878.1|_22:94 YkfF [Escherichia coli]
- gi|58000348|ref|YP_190158.1| YkfF [Escherichia coli]
- gi|75234748|ref|ZP_00719058.1|_5:77 hypothetical protein EcolE1_01003386 [Escherichia coli E110019]
- gi|3822199|gb|AAC70153.1|_14:86 hypothetical protein [Escherichia coli O157:H7]
- gi|75994531|ref|YP_325645.1| hypothetical protein L7085 [Escherichia coli O157:H7 EDL933]
- gi|41223299|ref|NP_958724.1|_5:77 hypothetical protein ECp054 [Escherichia coli O157:H7 str. Sakai]
- gi|75226917|ref|ZP_00713803.1|_5:77 hypothetical protein EcolB7_01004569 [Escherichia coli B7A]
- gi|71559064|ref|YP_271791.1|_1:75 hypothetical protein pOU1113_67 [Salmonella enterica]
- gi|68166363|gb|AAY88124.1| hypothetical protein [Salmonella enterica]
- gi|47154999|emb|CAE85198.1|_13:89 YkfF protein [Escherichia coli]
- gi|16128234|ref|NP_414783.1|_1:79 CP4-6 prophage; predicted protein [Escherichia coli K12]
- gi|1786443|gb|AAC73352.1| CP4-6 prophage; predicted protein [Escherichia coli K12]
- gi|89107122|ref|AP_000902.1| hypothetical protein [Escherichia coli W3110]
- gi|85674398|dbj|BAA77918.2| hypothetical protein [Escherichia coli W3110]
- gi|3025208|sp|P75677|YKFF_ECOLI Hypothetical protein ykfF [Taxonomy]
- gi|16445257|gb|AAL23475.1|_6:80 putative cytoplasmic protein [Salmonella typhimurium LT2]
- gi|17233436|ref|NP_490555.1| putative cytoplasmic protein [Salmonella typhimurium LT2]
- gi|45357335|gb|AAS58729.1|_1:76 hypothetical protein pMT098 [Yersinia pestis biovar Medievalis str. 91001]
- gi|108793825|ref|YP_636672.1| hypothetical protein YPN_MT0093 [Yersinia pestis Nepal516]
- gi|108793621|ref|YP_636780.1| hypothetical protein YPA_MT0089 [Yersinia pestis Antiqua]
- gi|108782168|gb|ABG16225.1| hypothetical protein YPA_MT0089 [Yersinia pestis Antiqua]
- gi|108777889|gb|ABG20407.1| hypothetical protein YPN_MT0093 [Yersinia pestis Nepal516]
- gi|3883089|gb|AAC82749.1| unknown [Yersinia pestis KIM]
- gi|2996363|gb|AAC13243.1| unknown [Yersinia pestis KIM]
- gi|31795419|ref|NP_857872.1| hypothetical protein Y1091 [Yersinia pestis KIM]
- gi|31795259|ref|NP_857714.1| hypothetical protein YPKMT101 [Yersinia pestis KIM]
- gi|52788195|ref|YP_094023.1| hypothetical protein pG8786_144 [Yersinia pestis]
- gi|5834744|emb|CAB55242.1| hypothetical protein YPMT1.60c [Yersinia pestis CO92]
- gi|52538124|emb|CAG27550.1| hypothetical protein [Yersinia pestis]
- gi|16082850|ref|NP_395404.1| hypothetical protein YPMT1.60c [Yersinia pestis CO92]
- gi|89103272|ref|ZP_01175857.1| hypothetical protein Ypesb_01002735 [Yersinia pestis biovar Orientalis str. IP275]
- gi|45478682|ref|NP_995538.1| hypothetical protein pMT098 [Yersinia pestis biovar Medievalis str. 91001]
- gi|57434425|emb|CAI43842.1|_4:77 hypothetical protein [Escherichia coli]
- gi|57545662|gb|AAW51753.1| Aec70 [Escherichia coli]
- gi|26109909|gb|AAN82114.1|_4:77 Hypothetical protein ykfF [Escherichia coli CFT073]
- gi|26249501|ref|NP_755541.1| Hypothetical protein ykfF [Escherichia coli CFT073]
- gi|26106581|gb|AAN78767.1|_4:77 Hypothetical protein ykfF [Escherichia coli CFT073]
- gi|26246184|ref|NP_752223.1| Hypothetical protein ykfF [Escherichia coli CFT073]
- gi|14195539|sp|P58095|YPJI_ECOLI_11:90 Hypothetical protein ypjI [Taxonomy]
- gi|18265878|gb|AAL67351.1|_4:69 intergenic-region protein [Escherichia coli]
- gi|18466655|ref|NP_569463.1|_1:76 hypothetical protein HCM1.279bc [Salmonella enterica subsp. enterica serovar Typhi str. CT18]
- gi|10957300|ref|NP_058324.1| hypothetical protein [Salmonella typhi]
- gi|7800353|gb|AAF69949.1| orf; hypothetical protein [Salmonella typhi]
- gi|16505971|emb|CAD09857.1| hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi str. CT18]
- gi|75259064|ref|ZP_00730432.1|_4:52 hypothetical protein EcolE2_01001328 [Escherichia coli E22]
- gi|75212146|ref|ZP_00712186.1| hypothetical protein EcolB_01000748 [Escherichia coli B171]
- gi|75208370|ref|ZP_00708708.1| hypothetical protein EcolB_01004372 [Escherichia coli B171]
- gi|75189020|ref|ZP_00702287.1|_13:64 hypothetical protein EcolE_01002298 [Escherichia coli E24377A]

                    10         20        30          40           50   
                    |          |         |           |            |   
   1 ...M..TQ.SVLLPPGPFTRRQA.QAVTTTYSNITLEDDQ..GSHFRLVVRD...TEGRMVWRAW
   2 seyF..RI.LQGLPDGPFTRKQA.EAVAAQYRNVFIEDDQ..GTHFRLVVRQ...-DGTLIWRSW
   3 seyF..RI.LQGLPDGPFTRKQA.EAVAAQYRNVFIEDDQ..GTHFRLVVRQ...-DGTLIWRSW
   4 seyF..RI.FQGLPDGSFTREQA.EAVAAQYRNVFIEDDQ..GTHFRLVVRQ...-DGTLIWRSW
   5 seyF..RI.LQGLPDGPFTRKHA.EAVAAQYRNVFIEDDH..GEHFRLVVRN...-NGTMVWRTW
   6 seyF..RI.LQGLPDGSFTREQA.EAVAAQYRNVFIEDDQ..GTHFRLVVRQ...-DGTLIWRSW
   7 seyF..RI.FQGLPDGSFTREQA.EAVAAQYRNVFIEDDQ..GTHFRLVVRQ...-DGTLIWRSW
   8 seyF..RI.FQGLPDGSFTREQA.EAVAAQYQNVFIEDDQ..GTHFRLVVRQ...-DGTLIWRSW
   9 seyF..RI.LQGLPDGSFTREQA.EAVAAQYRNVFIEDDQ..GTHFRLVVRN...NNG-LVWRTW
  10 seyF..RI.LQGLPDGPFTRKQA.EAVAAQYRNVFIEDDH..GEQFRLVVRN...-NGTMVWRTW
  11 seyF..RI.LQGLPDGPFTRKQA.EAVAAQYRNVFIEDDH..GEQFRLVVRN...-NGTMVWRTW
  12 seyF..RI.LQGLPDGSFTREQA.EAVAAQYRNVFIEDDQ..GTHFRLVVRN...NSG-LVWRTW
  13 seyF..RI.LQGLPDGSFTREQA.EAVAAQYRNVFIEDDQ..GTHFRLVVRN...NSG-LVWRTW
  14 ...MsdCH.PVLLPEGPFSREQA.VAVTTAYRNVLIEDDQ..GTHFRLVIRN...AEGQLRWRCW
  15 seyF..RI.LQGLPDGSFTREQA.EAVAAQYRNVFIEDEQ..GTHFRLVVRN...NSG-LVWRTW
  16 seyF..RI.LQGLPDGPFTRKHA.EAVAAQYRNVFIEDDH..GEQFRLVVRN...-NGAMVWRTW
  17 seyF..RI.LQGLPDGPFTRKHA.EAVAAQYRNVFIEDDH..GEQFRLVVRN...-NGAMVWRTW
  18 ...MsdCH.PVLLPEGPFSREQA.VAVTTAYRNVLIEDDQ..GTHFRLVIRN...AGGQLRWRCW
  19 ...MsdCH.PVLLPEGPFSREQA.MAVTTAYRNVLIEDDQ..GTHFRLVIHN...AEGQLRWRCW
  20 seyF..RI.LQGLPDGSFTREQA.EAVAVQYRNVFIEDDH..GEQFRLVVRN...-NGAMVWRTW
  21 seyF..RI.LQGLPDGPFTRKHA.EAVAAQYRNVFIEDDH..GEQFRLVVRN...NE-TMVWRTW
  22 seyF..RI.LQGLPDGPFTRKHA.EAVAAQYRNVFIENDH..GEQFRLVVRN...-NGAMVWRTW
  23 seyF..RI.LQGLPDGPFTRKHA.EAVAAQYRNVFIENDH..GEQFRLVVRN...-NGAMVWRTW
  24 seyF..RI.LQGLPDGPFTRKQA.EAVAAQYRNVFIGDDH..GEQFRLVVRN...-NGAMVWRTW
  25 ...M..IP.LKSLPDGTFTHEQA.EAVAAQYQNVAIEDDQ..GTHLRLVVRK...-DGEMVWRGW
  26 atdMpgCT.SRLLPEGPFSRNQA.LAVTTAYLNVLIEDDQ..GTHFRLVIRN...AEGQLRWRCW
  27 ...M..TQ.SVLLPPGPFTRRQA.QAVTTTYSNITLEDDQ..GSHFRLVVRD...TEGRMVWRAW
  28 dniM..SP.LKSLPDGTFTHEQA.EAVAAQYQNVAIEDDQ..GTHLRLVVRK...-DGEMVWRGW
  29 ...M..SEaLAVLPDDTFTREQA.EVVAAQYTNVAIEDDQ..GAHFRLVVRQ...-NGEMVWRTW
  30 ...MpgYT.EYVLAEGSFSYGQA.VAVITAYRNVFIQDDP..GMHFRRVIRN...AEGQRRWRCR
  31 ...MpgYT.EYVLAEGSFSYGQA.VAVITAYRNVFIQDDP..GMHFRRVIRN...AEGQRRWRCR
  32 ...MrgCT.LLLFSEAPFLREQE.VAVITAYRNVFIQDDP..GMHFRWVIRN...AEGQRRWRCR
  33 xs.Fx.QT.LSGLPQWASADCVAgPLVSAGITDINIEDDQ..GIHVRLIVRD...AEGRMVWRAW
  34 ...MrgCT.LLLFSEAPFLREQE.VAVITAYRNVFIQDDP..GMHFRWVIRN...AEGQRRWRCR
  35 ...M..SD.LFS-SESPVTLAQA.RTVAAGYQNVFIENLQpaG-HFQIVIRDhrdHDSQLVWRNW
  36 ...MpgCT.SRLLPEGPFSREQA.VAVKTAYRNVFTEDDQ..GTYSRLVIRN...AEGQLRW---
  37 atdMpgCT.SRLLPEGPFSREQA.VAVKTAYRNVFTEDDQ..GTYSRLVIRN...AEGQLRW---


           60        70        80       
           |         |         |       
   1 NFEPDAGEGLNRYIRTSGIRTDTATRLEHHHHHH
   2 NFEDCAGYWMNRYIRDFGILK-------------
   3 NFEDCAGYWMNRYIRDFGILK-------------
   4 NFEDCAGYWMNRYIRDFGIRK-------------
   5 NFEDGAGYWMNHAIRDFGILK-------------
   6 NFEDCAGYWMNQYIRDFGILK-------------
   7 NFEDCAGYWMNRYIRDFGILK-------------
   8 NFEDCAGYWMNQYIRDFGIRK-------------
   9 NFEDGAGYWMNHVIRNFGILK-------------
  10 NFEDGAGYWMNHVIRDFGILK-------------
  11 NFEDGAGYWMNHVIRDFGILK-------------
  12 NFEDGAGYWMNHVIRNFGILK-------------
  13 NFEDGAGYWMNHVIRNFGILK-------------
  14 NFEPDAGKQLNSYLASEGILRQ------------
  15 NFEDGAGYWMNHVIRDFGILK-------------
  16 NFEDGAGYWMNHVIRDFGILK-------------
  17 NFEDGAGYWMNHVIRDFGILK-------------
  18 NFEPDAGKQLNSYLASEGILRQ------------
  19 NFEPDAGKQLNPYLASEGILRQ------------
  20 NFEDGAGYWMNHVIRDFGILK-------------
  21 NFEDGAGYWMNHVIRDFGILK-------------
  22 NFEDGAGYWMNHVIRDFGIIK-------------
  23 NFEDGAGYWMNHVIRDFGIIK-------------
  24 NFEDGAGYWMNRYIRDFGILK-------------
  25 NFEPGGEYWLNRCIESHGIRKTQ-----------
  26 NFEPDAGKQLNPYLASEGILRQ------------
  27 NFEPDAGEGLNRYIRTSGIRTDTATR--------
  28 NFEPGGEYWLNRCIESHGIRKTQ-----------
  29 NFEPGGTYWLNRYIADYGIRKPQ-----------
  30 NSEPDAGKVLNTRLASDGLLRQ------------
  31 NSEADAGKQLNAWLASGGLLRQ------------
  32 NSEPDAGKVLNTRLASDGPLRQ------------
  33 NFEPDAGEGFNRYIHRSGIRTDTFPR--------
  34 NSPLILNPMPERCLIR-G----------------
  35 NYESGANDALNSYLQSHGLKAS------------
  36 ----------------------------------
  37 ----------------------------------