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:

- T0405 lmo0819, listeria monocytogenes, 282 residues
- gi|47094827|ref|ZP_00232441.1|_1:282 conserved hypothetical protein [Listeria monocytogenes str. 1/2a F6854]
- gi|153185344|ref|ZP_01935931.1| conserved hypothetical protein [Listeria monocytogenes J0161]
- gi|153190221|ref|ZP_01937643.1| conserved hypothetical protein [Listeria monocytogenes J2818]
- gi|47016709|gb|EAL07628.1| conserved hypothetical protein [Listeria monocytogenes str. 1/2a F6854]
- gi|126941910|gb|EBA19782.1| conserved hypothetical protein [Listeria monocytogenes J0161]
- gi|127766153|gb|EBA26495.1| conserved hypothetical protein [Listeria monocytogenes J2818]
- gi|16802861|ref|NP_464346.1|_1:282 hypothetical protein lmo0819 [Listeria monocytogenes EGD-e]
- gi|153173736|ref|ZP_01929450.1| conserved hypothetical protein [Listeria monocytogenes FSL N3-165]
- gi|153197742|ref|ZP_01941954.1| conserved hypothetical protein [Listeria monocytogenes 10403S]
- gi|16410208|emb|CAC98897.1| lmo0819 [Listeria monocytogenes]
- gi|127632701|gb|EBA22143.1| conserved hypothetical protein [Listeria monocytogenes 10403S]
- gi|133730816|gb|EBA32514.1| conserved hypothetical protein [Listeria monocytogenes FSL N3-165]
- gi|46907052|ref|YP_013441.1|_1:282 hypothetical protein LMOf2365_0838 [Listeria monocytogenes str. 4b F2365]
- gi|47093898|ref|ZP_00231639.1| conserved hypothetical protein [Listeria monocytogenes str. 4b H7858]
- gi|167217042|ref|ZP_02286678.1| hypothetical protein LmonocFSL_06588 [Listeria monocytogenes FSL J1-175]
- gi|46880318|gb|AAT03618.1| conserved hypothetical protein [Listeria monocytogenes str. 4b F2365]
- gi|47017741|gb|EAL08533.1| conserved hypothetical protein [Listeria monocytogenes str. 4b H7858]
- gi|153166141|ref|ZP_01926760.1|_1:282 conserved hypothetical protein [Listeria monocytogenes FSL N1-017]
- gi|133727657|gb|EBA29355.1| conserved hypothetical protein [Listeria monocytogenes FSL N1-017]
- gi|16799889|ref|NP_470157.1|_1:282 hypothetical protein lin0815 [Listeria innocua Clip11262]
- gi|16413266|emb|CAC96047.1| lin0815 [Listeria innocua]
- gi|116872233|ref|YP_849014.1|_1:281 hypothetical protein lwe0813 [Listeria welshimeri serovar 6b str. SLCC5334]
- gi|116741111|emb|CAK20231.1| unnamed protein product [Listeria welshimeri serovar 6b str. SLCC5334]
- gi|153201526|ref|ZP_01943335.1|_7:255 conserved hypothetical protein [Listeria monocytogenes HPB2262]
- gi|133735834|gb|EBA37532.1| conserved hypothetical protein [Listeria monocytogenes HPB2262]
- gi|168265403|ref|ZP_02687368.1|_1:238 hypothetical protein LmonFSL_04399 [Listeria monocytogenes FSL J2-071]
- gi|167052963|ref|ZP_02279361.1|_4:41 hypothetical protein LmonF_08591 [Listeria monocytogenes FSL F2-515]
- gi|168265404|ref|ZP_02687369.1|_3:42 hypothetical protein LmonFSL_04404 [Listeria monocytogenes FSL J2-071]

              10        20        30        40        50        60     
              |         |         |         |         |         |     
   1 MNETEKLVAALLERNFGKNIGTRYPGNEAAQMRAEEVIGEIAIVIAPLVEKLGIENKTVKKTIPF
   2 MNETEKLVAALLERNFGKNIGTRYPGNEAAQMRAEEVIGEIAIVIAPLVEKLGIENKTVKKTIPF
   3 MNETEKLVAALLERNFGKNIGTRYPGNEAAQMRAEEVIGEIAIVIAPLVEKLGIENKTVKKTIPF
   4 MNETEKLVAALLERNFGKNIGTRYPDNEAAQMRAEEVIGEIAIVIAPLVEKLGIESKTVKKTIPF
   5 MNETEKLVAALLERNFGKNIGTRYPDNEAAQMRAEEVIGEIAIVIAPLVEKLGIESKTVKKTIPF
   6 MNETQKLVAASLERNFGKDIGARYEGNEEAQLRAEEVIEEIAIVIAPLVEKLGIESKTVKKTIPF
   7 MNETQKLVAASLERNFGKDIGTRYVGNEKAQLRAEEVIEEIAIVIAPLVEQLGIESKTVKKTIPF
   8 MNETEKLVAALLERNFGKNIGTRYPDNEAAQMRAEEVIGEIAIVIAPLVEKLGIESKTVKKTIPF
   9 MNETEKLVAASLERNFGKNIGTRYPGNEEAQMRAEEVIEEIAIVITPLVEKLGIESKTVKKTIPF
  10 -----------------------------------------------------------------
  11 -----------------------------------------------------------------


         70        80        90       100       110       120       130
         |         |         |         |         |         |         |
   1 LYELQKNQFCDMSAYPYPLLLVNGTSTDTEKYWRDLPTYWTDDANKIVLPYVLEHIKNNKVRQKL
   2 LYELQKNQFCDMSAYPYPLLLVNGTSADTEKYWRDLPTYWTDDANKIVLPYVLEHIKNNKVRQKL
   3 LYELQKNQFCDMSAYPYPLLLVNGTSTDTEKYWRDLPTYWTDDANKIVLPYVLEHIKNNKVRQKL
   4 LYELQKNQFCDMSAYPYPLLLVNGTSADTEKYWRDLPTYWTDDANKIVLPYVLEHIKNNKVRQKL
   5 LYELQKNQFCDMSAYPYPLLLVNGTSADTEKYWRDLPTYWTDDANKIVLPYVLEHIKNNKVRQKL
   6 LYELQKNQFCDMSAYPYPLLLVNGTSADTEKYWRDLPTYWTDEANKIVLPYVLEHIKNNKVRQKL
   7 LYELQKNQFCDMSAYPYPLLLVNGTSADTEKYWRDLPTYWTDDANKIVLPYVLEHMKNNKVRQKL
   8 LYELQKNQFCDMSAYPYPLLLVNGTSADTEKYWRDLPTYWTDDANKIVLPYVLEHIKNNKVRQKL
   9 LYELQKNQFCDMSAYPYPLLLVNGTSADTEKYWRDLPTYWTDDANKIVLPYVLEHIKNNKVRQKL
  10 -----------------------------------------------------------------
  11 -----------------------------------------------------------------


             140       150       160       170       180       190     
              |         |         |         |         |         |     
   1 LAFHAWLLGEVVEMNEALGADFRVKLVFESDMRIRLRVYEVEQIAIEVHFLDNHDTEQQHLGYDV
   2 LAFHAWLLGEVVEMNEALGADFRVKLVFESDMRIRLRVYEVEQIAIEVHFLDNHDTEQQHLGYDV
   3 LAFHAWLLGEVVEMNEALGADFRVKLVFESDMRIRLRVYEVEQIAIEVHFLDNHDTEQQHLGYDV
   4 LAFHAWLIGEVVEMNEELGADFRIKLVFESDMRIRLRVYDVEQIAIEVHFLDNHDTEQQHLGYDV
   5 LAFHAWLIGEVVEMNEELGADFRIKLVFESDMRIRLRVYDVEQIAIEVHFLDNHDTEQQHLGYDV
   6 LSFHAWLLGEVAEMNTELGAQFRVKLVFESDMRIRLRIYEVEQIAIEVHFLDNHDTEQQHLGYDV
   7 LAFHAWLLGEVAEMNEELGAAFRVKLVFESDMRIRLRVYEVEQIAVEVHFLDNHDTEQQHLGYDV
   8 LAFHAWLIGEVVEMNEELGADFRIKLVFESDMRIRLRVYDVEQIAIEVHFLDNHDTEQQHLGYDV
   9 LAFHAWLLGEVAEMNGVLGADFRVKLVFESDMRIRLRVYEVEQIAIEVHFLDNHDTEQQHLGYDV
  10 -----------------------------------------------------------------
  11 -----------------------------------------------------------------


        200       210       220       230       240       250       260
         |         |         |         |         |         |         |
   1 SLDADFTEKARLLLRQGILTENLGLEALKAYMKSVLPIAHSLKNLEHLTFEETKKLTKLLTQEEP
   2 SLDADFTEKARLLLRQGILTENLGLEALKAYMKSVLPIAHSLKNLEHLTFEETKKLTKLLTQEEP
   3 SLDADFTEKARLLLRQGILTENLGLEALKAYMKSVLPIAHSLKNLEHLTFEETKKLTKLLTQEEP
   4 SLDVDITDKARLLLRQGILTENLGLEALKAYMKSVLPIAHSLKNLEYLTVEDTKKLTKLLTQEEP
   5 SLDVDITDKARLLLRQGILTENLGLEALKAYMKSVLPIAHSLKNLEYLTVKDTKKLTKLLTQEEP
   6 SLDAELEVKARLLLRQGILTENLGLVALKAYIRSVLPIAHSLKKLEKLTDEEAKKLTKWLTHEEP
   7 SLDAELEVKARLLLRQGILTENLGLEALKAYIKSVLPIAHNLETLKQLTGEETKKLTKLLMQEEP
   8 SLDVDITDKARLLLRQGILTENLGLEALKAYMKSVLPIAHSLKNLEYLTVEDTK-----------
   9 SLDADFTEKARLLLRQGILTENLGLEALKAYMKSVLPIAHSLK----------------------
  10 --------------------ENLGLEALKAYMKSVLPIAHSLKNLEHLTFEETKKLDQ-------
  11 ----------------------------------------------QLTEEETKKLTKLLTQEEP


             270       280  
              |         |  
   1 KIMEDTDLTSKALDFLQKAAQQ
   2 KIMEDTDLTSKALDFLQKAAQQ
   3 KIMEDTDLTSKALDFLQKAAQQ
   4 KIMEDTDLTSKALDFLQKAAQQ
   5 KIMEDTDLTSKALDFLQKAAQQ
   6 KIMEDTDLTSKALDFLQKVAQQ
   7 KIMEDTDLTSKALDFLQKLAP-
   8 ----------------------
   9 ----------------------
  10 ----------------------
  11 KIMEDTDLTSKALDFLQNAAL-