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|83586571|ref|ZP_00925204.1|_1:77 hypothetical protein Ecol1_01002225 [Escherichia coli 101-1]
- gi|75259093|ref|ZP_00730461.1|_1:77 hypothetical protein EcolE2_01001358 [Escherichia coli E22]
- gi|75512277|ref|ZP_00734839.1|_1:77 hypothetical protein Ecol5_01003544 [Escherichia coli 53638]
- gi|75208230|ref|ZP_00708597.1|_1:77 hypothetical protein EcolB_01004504 [Escherichia coli B171]
- gi|37962737|gb|AAR05684.1|_3:79 conserved hypothetical protein [Salmonella typhimurium]
- gi|58383258|ref|YP_194828.1| hypothetical protein pU302L_021 [Salmonella typhimurium]
- gi|45758187|gb|AAS76399.1|_1:77 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|50346328|ref|NP_052923.2|_1:77 hypothetical protein R100p043 [Plasmid R100]
- gi|89033311|gb|ABD59989.1| hypothetical protein [Escherichia coli]
- gi|75230630|ref|ZP_00717105.1|_1:77 hypothetical protein EcolB7_01001278 [Escherichia coli B7A]
- 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|75238464|ref|ZP_00722461.1|_1:77 hypothetical protein EcolF_01003511 [Escherichia coli F11]
- gi|88770148|gb|ABD51585.1|_10:86 conserved hypothetical protein [Escherichia coli]
- gi|73476837|gb|AAZ76452.1|_1:77 hypothetical protein LH0085 [Escherichia coli]
- gi|73853253|ref|YP_308749.1| hypothetical protein LH0085 [Escherichia coli]
- gi|38606100|gb|AAR25064.1|_3:79 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|5702179|gb|AAD47188.1|_1:77 unknown; orf77 [Escherichia coli]
- gi|75234993|ref|ZP_00719258.1| hypothetical protein EcolE1_01003133 [Escherichia coli E110019]
- gi|91206338|ref|YP_538692.1|_3:79 hypothetical protein UTI89_P093 [Escherichia coli UTI89]
- gi|91075789|gb|ABE10669.1| hypothetical protein UTI89_P093 [Escherichia coli UTI89]
- 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|8918884|dbj|BAA97931.1|_3:79 yfjA [Plasmid F]
- gi|9507774|ref|NP_061440.1| hypothetical protein Fpla063 [Plasmid F]
- gi|75234748|ref|ZP_00719058.1|_1:77 hypothetical protein EcolE1_01003386 [Escherichia coli E110019]
- gi|41223299|ref|NP_958724.1|_1:77 hypothetical protein ECp054 [Escherichia coli O157:H7 str. Sakai]
- gi|75226917|ref|ZP_00713803.1|_1:77 hypothetical protein EcolB7_01004569 [Escherichia coli B7A]
- gi|57903248|gb|AAW58878.1|_18:94 YkfF [Escherichia coli]
- gi|58000348|ref|YP_190158.1| YkfF [Escherichia coli]
- gi|3822199|gb|AAC70153.1|_10:86 hypothetical protein [Escherichia coli O157:H7]
- gi|75994531|ref|YP_325645.1| hypothetical protein L7085 [Escherichia coli O157:H7 EDL933]
- gi|47154999|emb|CAE85198.1|_13:89 YkfF protein [Escherichia coli]
- gi|71559064|ref|YP_271791.1|_1:75 hypothetical protein pOU1113_67 [Salmonella enterica]
- gi|68166363|gb|AAY88124.1| hypothetical protein [Salmonella enterica]
- 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|_1:77 hypothetical protein [Escherichia coli]
- gi|57545662|gb|AAW51753.1| Aec70 [Escherichia coli]
- gi|26109909|gb|AAN82114.1|_1:77 Hypothetical protein ykfF [Escherichia coli CFT073]
- gi|26249501|ref|NP_755541.1| Hypothetical protein ykfF [Escherichia coli CFT073]
- gi|26106581|gb|AAN78767.1|_1:77 Hypothetical protein ykfF [Escherichia coli CFT073]
- gi|26246184|ref|NP_752223.1| Hypothetical protein ykfF [Escherichia coli CFT073]
- gi|14195539|sp|P58095|YPJI_ECOLI_10:90 Hypothetical protein ypjI [Taxonomy]
- gi|18265878|gb|AAL67351.1|_1:69 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|_1:52 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          
                          |          |         |           |          
   1 ...MTQS..V.L....L..PPGPFTRRQA.QAVTTTYSNITLEDDQ..GSHFRLVVRD...TEGR
   2 ...MSEY..F.RifqgL..PDGSFTREQA.EAVAAQYRNVFIEDDQ..GTHFRLVVRQ...-DGT
   3 ...MSEY..F.RilqgL..PDGPFTRKHA.EAVAAQYRNVFIEDDH..GEHFRLVVRN...-NGT
   4 ...MSEY..F.RifqgL..PDGSFTREQA.EAVAAQYRNVFIEDDQ..GTHFRLVVRQ...-DGT
   5 ...MSEY..F.RifqgL..PDGSFTREQA.EAVAAQYQNVFIEDDQ..GTHFRLVVRQ...-DGT
   6 mr.MSEY..F.RilqgL..PDGPFTRKQA.EAVAAQYRNVFIEDDQ..GTHFRLVVRQ...-DGT
   7 ...MSEY..F.RilqgL..PDGSFTREQA.EAVAAQYRNVFIEDDQ..GTHFRLVVRQ...-DGT
   8 ...MSEY..F.RilqgL..PDGPFTRKQA.EAVAAQYRNVFIEDDH..GEQFRLVVRN...-NGT
   9 ...MSEY..F.RilqgL..PDGSFTREQA.EAVAAQYRNVFIEDDQ..GTHFRLVVRN...NNG-
  10 ...MSDChpV.L....L..PEGPFSREQA.VAVTTAYRNVLIEDDQ..GTHFRLVIRN...AEGQ
  11 ...MSEY..F.RilqgL..PDGSFTREQA.EAVAAQYRNVFIEDDQ..GTHFRLVVRN...NSG-
  12 emrMSEY..F.RilqgL..PDGPFTRKQA.EAVAAQYRNVFIEDDQ..GTHFRLVVRQ...-DGT
  13 ...MSEY..F.RilqgL..PDGSFTREQA.EAVAAQYRNVFIEDEQ..GTHFRLVVRN...NSG-
  14 mr.MSEY..F.RilqgL..PDGPFTRKQA.EAVAAQYRNVFIEDDH..GEQFRLVVRN...-NGT
  15 ...MSEY..F.RilqgL..PDGPFTRKHA.EAVAAQYRNVFIEDDH..GEQFRLVVRN...-NGA
  16 mr.MSEY..F.RilqgL..PDGSFTREQA.EAVAAQYRNVFIEDDQ..GTHFRLVVRN...NSG-
  17 ...MSDChpV.L....L..PEGPFSREQA.VAVTTAYRNVLIEDDQ..GTHFRLVIRN...AGGQ
  18 ...MSDChpV.L....L..PEGPFSREQA.MAVTTAYRNVLIEDDQ..GTHFRLVIHN...AEGQ
  19 mr.MSEY..F.RilqgL..PDGPFTRKHA.EAVAAQYRNVFIEDDH..GEQFRLVVRN...-NGA
  20 ...MSEY..F.RilqgL..PDGPFTRKHA.EAVAAQYRNVFIEDDH..GEQFRLVVRN...NE-T
  21 ...MSEY..F.RilqgL..PDGPFTRKHA.EAVAAQYRNVFIENDH..GEQFRLVVRN...-NGA
  22 ...MSEY..F.RilqgL..PDGPFTRKQA.EAVAAQYRNVFIGDDH..GEQFRLVVRN...-NGA
  23 emrMSEY..F.RilqgL..PDGSFTREQA.EAVAVQYRNVFIEDDH..GEQFRLVVRN...-NGA
  24 emrMSEY..F.RilqgL..PDGPFTRKHA.EAVAAQYRNVFIENDH..GEQFRLVVRN...-NGA
  25 atdMPGC..T.Srl..L..PEGPFSRNQA.LAVTTAYLNVLIEDDQ..GTHFRLVIRN...AEGQ
  26 ...MIPL..K.S....L..PDGTFTHEQA.EAVAAQYQNVAIEDDQ..GTHLRLVVRK...-DGE
  27 ...MTQS..V.L....L..PPGPFTRRQA.QAVTTTYSNITLEDDQ..GSHFRLVVRD...TEGR
  28 dniMSPL..K.S....L..PDGTFTHEQA.EAVAAQYQNVAIEDDQ..GTHLRLVVRK...-DGE
  29 ...MSEA..LaV....L..PDDTFTREQA.EVVAAQYTNVAIEDDQ..GAHFRLVVRQ...-NGE
  30 ...MPGYteY.V....L..AEGSFSYGQA.VAVITAYRNVFIQDDP..GMHFRRVIRN...AEGQ
  31 ...MPGYteY.V....L..AEGSFSYGQA.VAVITAYRNVFIQDDP..GMHFRRVIRN...AEGQ
  32 ...MRGC..T.L....LlfSEAPFLREQE.VAVITAYRNVFIQDDP..GMHFRWVIRN...AEGQ
  33 wxsFXQT..L.Sg...L..PQWASADCVAgPLVSAGITDINIEDDQ..GIHVRLIVRD...AEGR
  34 ...MRGC..T.L....LlfSEAPFLREQE.VAVITAYRNVFIQDDP..GMHFRWVIRN...AEGQ
  35 ...MSDL..F.S....-..SESPVTLAQA.RTVAAGYQNVFIENLQpaG-HFQIVIRDhrdHDSQ
  36 ...MPGC..T.Srl..L..PEGPFSREQA.VAVKTAYRNVFTEDDQ..GTYSRLVIRN...AEGQ
  37 atdMPGC..T.Srl..L..PEGPFSREQA.VAVKTAYRNVFTEDDQ..GTYSRLVIRN...AEGQ


       50        60        70        80       
       |         |         |         |       
   1 MVWRAWNFEPDAGEGLNRYIRTSGIRTDTATRLEHHHHHH
   2 LIWRSWNFEDCAGYWMNRYIRDFGIRK-------------
   3 MVWRTWNFEDGAGYWMNHAIRDFGILK-------------
   4 LIWRSWNFEDCAGYWMNRYIRDFGILK-------------
   5 LIWRSWNFEDCAGYWMNQYIRDFGIRK-------------
   6 LIWRSWNFEDCAGYWMNRYIRDFGILK-------------
   7 LIWRSWNFEDCAGYWMNQYIRDFGILK-------------
   8 MVWRTWNFEDGAGYWMNHVIRDFGILK-------------
   9 LVWRTWNFEDGAGYWMNHVIRNFGILK-------------
  10 LRWRCWNFEPDAGKQLNSYLASEGILRQ------------
  11 LVWRTWNFEDGAGYWMNHVIRNFGILK-------------
  12 LIWRSWNFEDCAGYWMNRYIRDFGILK-------------
  13 LVWRTWNFEDGAGYWMNHVIRDFGILK-------------
  14 MVWRTWNFEDGAGYWMNHVIRDFGILK-------------
  15 MVWRTWNFEDGAGYWMNHVIRDFGILK-------------
  16 LVWRTWNFEDGAGYWMNHVIRNFGILK-------------
  17 LRWRCWNFEPDAGKQLNSYLASEGILRQ------------
  18 LRWRCWNFEPDAGKQLNPYLASEGILRQ------------
  19 MVWRTWNFEDGAGYWMNHVIRDFGILK-------------
  20 MVWRTWNFEDGAGYWMNHVIRDFGILK-------------
  21 MVWRTWNFEDGAGYWMNHVIRDFGIIK-------------
  22 MVWRTWNFEDGAGYWMNRYIRDFGILK-------------
  23 MVWRTWNFEDGAGYWMNHVIRDFGILK-------------
  24 MVWRTWNFEDGAGYWMNHVIRDFGIIK-------------
  25 LRWRCWNFEPDAGKQLNPYLASEGILRQ------------
  26 MVWRGWNFEPGGEYWLNRCIESHGIRKTQ-----------
  27 MVWRAWNFEPDAGEGLNRYIRTSGIRTDTATR--------
  28 MVWRGWNFEPGGEYWLNRCIESHGIRKTQ-----------
  29 MVWRTWNFEPGGTYWLNRYIADYGIRKPQ-----------
  30 RRWRCRNSEPDAGKVLNTRLASDGLLRQ------------
  31 RRWRCRNSEADAGKQLNAWLASGGLLRQ------------
  32 RRWRCRNSEPDAGKVLNTRLASDGPLRQ------------
  33 MVWRAWNFEPDAGEGFNRYIHRSGIRTDTFPR--------
  34 RRWRCRNSPLILNPMPERCLIR-G----------------
  35 LVWRNWNYESGANDALNSYLQSHGLKAS------------
  36 LRW-------------------------------------
  37 LRW-------------------------------------