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:

- T0213 Hypothetical protein, E. coli
- gi|16766351|ref|NP_461966.1|_1:103 putative cytoplasmic protein [Salmonella typhimurium LT2]
- gi|33112550|sp|Q8ZM79|YQFB_SALTY Hypothetical UPF0267 protein yqfB [Taxonomy]
- gi|16421601|gb|AAL21925.1| putative cytoplasmic protein [Salmonella typhimurium LT2]
- gi|15803436|ref|NP_289469.1|_1:103 orf, hypothetical protein [Escherichia coli O157:H7 EDL933]
- gi|15833026|ref|NP_311799.1| hypothetical protein ECs3772 [Escherichia coli O157:H7]
- gi|16130802|ref|NP_417376.1| hypothetical protein b2900 [Escherichia coli K12]
- gi|2495660|sp|Q46828|YQFB_ECOLI Hypothetical UPF0267 protein yqfB [Taxonomy]
- gi|7466479|pir||D65074 hypothetical protein b2900 - Escherichia coli (strain K-12) [Taxonomy]
- gi|25367943|pir||D91100 hypothetical protein ECs3772 [imported] - Escherichia coli (strain O157:H7, substrain RIMD 0509952) [Taxonomy]
- gi|25367945|pir||H85945 hypothetical protein yqfB [imported] - Escherichia coli (strain O157:H7, substrain EDL933) [Taxonomy]
- gi|887850|gb|AAA83081.1| ORF_f103 [Taxonomy]
- gi|1789267|gb|AAC75938.1| orf, hypothetical protein [Escherichia coli K12]
- gi|12517428|gb|AAG58028.1| orf, hypothetical protein [Escherichia coli O157:H7 EDL933]
- gi|13363244|dbj|BAB37195.1| hypothetical protein [Escherichia coli O157:H7]
- gi|26249316|ref|NP_755356.1|_1:103 Hypothetical protein yqfB [Escherichia coli CFT073]
- gi|33112545|sp|Q8FE69|YQFB_ECOL6 Hypothetical UPF0267 protein yqfB [Taxonomy]
- gi|26109724|gb|AAN81929.1| Hypothetical protein yqfB [Escherichia coli CFT073]
- gi|16761831|ref|NP_457448.1|_1:103 conserved hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi str. CT18]
- gi|29143318|ref|NP_806660.1| conserved hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi Ty2]
- gi|33112548|sp|Q8Z3X3|YQFB_SALTI Hypothetical UPF0267 protein yqfB [Taxonomy]
- gi|25367949|pir||AH0872 conserved hypothetical protein STY3206 [imported] - Salmonella enterica subsp. enterica serovar Typhi (strain CT18) [Taxonomy]
- gi|16504133|emb|CAD02880.1| conserved hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi]
- gi|29138952|gb|AAO70520.1| conserved hypothetical protein [Salmonella enterica subsp. enterica serovar Typhi Ty2]
- gi|42629312|ref|ZP_00154859.1|_1:103 COG3097: Uncharacterized protein conserved in bacteria [Haemophilus influenzae R2846]
- gi|37676214|ref|NP_936610.1|_22:123 uncharacterized protein conserved in bacteria [Vibrio vulnificus YJ016]
- gi|37200755|dbj|BAC96580.1| uncharacterized protein conserved in bacteria [Vibrio vulnificus YJ016]
- gi|39932467|sp|Q7MEW6|Y9F4_VIBVY_3:104 Hypothetical UPF0267 protein VVA0554 [Taxonomy]
- gi|33112482|sp|Q8D7V1|Y4E7_VIBVU_3:104 Hypothetical UPF0267 protein VV20047 [Taxonomy]
- gi|27366507|ref|NP_762034.1|_15:116 Uncharacterized protein conserved in bacteria [Vibrio vulnificus CMCP6]
- gi|27358073|gb|AAO07024.1| Uncharacterized protein conserved in bacteria [Vibrio vulnificus CMCP6]
- gi|16273304|ref|NP_439548.1|_1:101 unknown protein [Haemophilus influenzae Rd KW20]
- gi|1175747|sp|P44172|YD94_HAEIN UPF0267 protein HI1394 [Taxonomy]
- gi|1074751|pir||B64027 hypothetical protein HI1394 - Haemophilus influenzae (strain Rd KW20) [Taxonomy]
- gi|1574227|gb|AAC23041.1| conserved hypothetical protein [Haemophilus influenzae Rd KW20]
- gi|15603312|ref|NP_246386.1|_2:103 Tex [Pasteurella multocida Pm70]
- gi|33112537|sp|Q9CL02|YE47_PASMU Hypothetical UPF0267 protein PM1447 [Taxonomy]
- gi|12721826|gb|AAK03531.1| Tex [Pasteurella multocida]
- gi|46913783|emb|CAG20565.1|_9:110 conserved hypothetical protein [Photobacterium profundum]
- gi|32033862|ref|ZP_00134133.1|_3:101 COG3097: Uncharacterized protein conserved in bacteria [Actinobacillus pleuropneumoniae serovar 1 str. 4074]
- gi|16122032|ref|NP_405345.1|_3:99 conserved hypothetical protein [Yersinia pestis]
- gi|33112530|sp|Q8ZFD6|YH78_YERPE Hypothetical UPF0267 protein YPO1778/Y2529/YP1615 [Taxonomy]
- gi|25367947|pir||AH0216 conserved hypothetical protein YPO1778 [imported] - Yersinia pestis (strain CO92) [Taxonomy]
- gi|15979803|emb|CAC90596.1| conserved hypothetical protein [Yersinia pestis CO92]
- gi|22126411|ref|NP_669834.1|_8:105 hypothetical protein y2529 [Yersinia pestis KIM]
- gi|45441432|ref|NP_992971.1| conserved hypothetical protein [Yersinia pestis biovar Medievalis str. 91001]
- gi|21959399|gb|AAM86085.1| hypothetical protein [Yersinia pestis KIM]
- gi|45436293|gb|AAS61848.1| conserved hypothetical protein [Yersinia pestis biovar Medievalis str. 91001]
- gi|28901269|ref|NP_800924.1|_4:105 conserved hypothetical protein [Vibrio parahaemolyticus RIMD 2210633]
- gi|33112510|sp|Q87GA3|YIB4_VIBPA Hypothetical UPF0267 protein VPA1414 [Taxonomy]
- gi|28809782|dbj|BAC62757.1| conserved hypothetical protein [Vibrio parahaemolyticus]
- gi|33151635|ref|NP_872988.1|_3:101 conserved hypothetical protein [Haemophilus ducreyi 35000HP]
- gi|33147856|gb|AAP95377.1| conserved hypothetical protein [Haemophilus ducreyi 35000HP]
- gi|24373486|ref|NP_717529.1|_4:102 conserved hypothetical protein [Shewanella oneidensis MR-1]
- gi|33112518|sp|Q8EFP8|YJ22_SHEON Hypothetical UPF0267 protein SO1922 [Taxonomy]
- gi|24347783|gb|AAN54973.1| conserved hypothetical protein [Shewanella oneidensis MR-1]
- gi|15641584|ref|NP_231216.1|_4:103 conserved hypothetical protein [Vibrio cholerae O1 biovar eltor str. N16961]
- gi|33112539|sp|Q9KRR0|YF76_VIBCH Hypothetical UPF0267 protein VC1576 [Taxonomy]
- gi|11345548|pir||B82182 conserved hypothetical protein VC1576 [imported] - Vibrio cholerae (strain N16961 serogroup O1) [Taxonomy]
- gi|9656085|gb|AAF94730.1| conserved hypothetical protein [Vibrio cholerae O1 biovar eltor str. N16961]
- gi|33112505|sp|Q9RA13|Y267_VIBMA_5:103 Hypothetical UPF0267 protein ORF16 [Taxonomy]
- gi|6691662|dbj|BAA89390.1| ORF16 [Moritella marina]
- gi|42631695|ref|ZP_00157233.1|_3:74 COG3097: Uncharacterized protein conserved in bacteria [Haemophilus influenzae R2866]

              10        20        30        40        50        60     
              |         |         |         |         |         |     
   1 MQPNDITFFQRFQDDILAGRKTITIRDESESHFKTGDVLRVGRFEDDGYFCTIEVTATSTVTLDT
   2 MQPNDITFFQRFQNDILAGRKTITIRDASESHFKAGDVLRVGRFEDDGYFCTIEVTGTSTVTLDT
   3 MQPNDITFFQRFQDDILAGRKTITIRDESESHFKTGDVLRVGRFEDDGYFCTIEVTATSTVTLDT
   4 MQPNDITFFQRFQDDILAGRKTITIRDESESHFKTGDVLRVGRFEDDGYFCTIEVTATSTVTLDT
   5 MQPNDITFFQRFQNDILAGRKTITIRDASESHFKAGDALRVGRFEDDGYFCTIEVTGTSTVTLDT
   6 MQPNDITFYQRFEADILAGRKTITIRDKSESYFKAGDILRVGRFEDNQYFCTIEVLSVSPITLDE
   7 -APTKMTFFSRFEADILAGKKTITIRDESEKDYQPGTTVEVSTLEEGRVFCQLKILSVEPIAFSE
   8 -APTKMTFFSRFEADILAGKKTITIRDESEKDYQPGTTVEVSTLEEGRVFCQLKILSVEPIAFSE
   9 -APTKMTFFSRFEADILAGKKTITIRDESEKDYQPGTTVEVSTLEEGRVFCQLKILSVEPIAFSA
  10 -APTKMTFFSRFEADILAGKKTITIRDESEKDYQPGTTVEVSTLEEGRVFCQLKILSVEPIAFSA
  11 MQPNDITFYQRFEADILAGHKTISIRDDSESHFKAGDILRVGRFEDNQYFCNIEVLSVSPITLDE
  12 -DSNKITFFTRFEQDILAGRKTITIRDKSESSFQPNQILAVYTNETDRFFANIKVLSVTPIHFEA
  13 -IPTEMTFFARFEHDILSSKKTITIRDESERYYVPGTTVKVSTLEEGREFCNLEIVSVEPILFDE
  14 ----NITFFSRFEADILAGKKNITIRDKSEAYFQPQQELKVFTNETNLFFADIRVISVTPIRFEQ
  15 ---REITFFGRFEADILADRKTITIRDSSESDFRSGEVLRVCRNEDGVFFCHIKVKSVTPVTLDG
  16 --NREITFFGRFEADILADRKTITIRDSSESDFRSGEVLRVCRNEDGVFFCHIKVKSVTPVTLDG
  17 -HPTKITFFEFLTPLITSGQKTITIRDESESHYVPNTEVEVFTLETDRKVCDIKILSVEPLNFDE
  18 ----KITFFSRFEADILGGKKTITIRDKSESYFQPQQQLNVFTHETDRLFAQIRVLSVVAIDFDD
  19 ----EITFFERFEHDILMGKKTITLRNEAESHVIPGQILPVSTFETHRWFCDIQVLEVTPITLSG
  20 --STQITFFEFLTPLVASGQKTITIRDKSESHYVPGTRVEVFTLETQRKVCEIDILAVEPLKFDE
  21 -----ITFFQRLERSILSGNKTATIRDKSDSHYLVGQMLDACTHEDNRKMCQIEILSIEYVTFSE
  22 ----DITFYQRFEADILAGRKTITIRDKSESHFKAGDILRVGRFEDNQYFCTIEILSVSPITLDE


         70         80        90       100   
         |          |         |         |   
   1 LTEKHAEQENMT.LTELKKVIADIYPGQTQFYVIEFKCL
   2 LNEKHAQQENMS.LDELKRVIAEIYPNQTQFYVIDFKCL
   3 LTEKHAEQENMT.LTELKKVIADIYPGQTQFYVIEFKCL
   4 LTEKHAEQENMT.LTELKKVIADIYPDQTQFYVIEFKCL
   5 LNEKHAQQENMS.LDELKRVIAEIYPNQTQFYVIDFKCL
   6 LTEQHAKQENMG.LAELREVIKTIYPNESEFWVIEIRLV
   7 LNEFHAEQENMT.LATLKEVIQEIYPGIEQLYVIQYQRV
   8 LNEFHAEQENMT.LATLKEVIQEIYPGIEQLYVIQYQRV
   9 LNEFHAEQENMT.LETLKEVIQEIYPGIEQLYVIQYQRV
  10 LNEFHAEQENMT.LETLKEVIQEIYPGIEQLYVIQYQRV
  11 LTQPHAKQENMG.LDELKEVIRGIYPNEIIFWVIQFS--
  12 LSEAHAQQENMT.LPELRQVIKEIYPQEDCFWVIAFELV
  13 LTQYHADQENMT.LPVLKDVIQDIYPGITQLYVVSYKLV
  14 LNEQHAKQENMS.LAELKQVIREIYPNDNDFFVIEFELI
  15 LSERHAEQENMS.LDELKKVIKAIYPGLDRFYVIEF---
  16 LSERHAEQENMS.LDELKKVIKAIYPGLDRFYVIEF---
  17 INEFHAEQEAIE.LPKLKQLIREIYPNIDKLFVIEYELI
  18 LNEQHAQQENMS.LAELRQVIREIYPNEQKFFVIKFALI
  19 LTTLHAQQENMT.LAELRLVIAEIYPDLEQLYMIRFKVL
  20 INEFHAEQEAIE.LPKLKALIQEIYPNIDELYVITYQL-
  21 LNRAHANAEGLPfLFMLKWIVRKIYPTSNDLFFISFRVV
  22 LTELHAKEENM-.--------------------------