;  SAM: /projects/compbio/experiments/protein-predict/SAM_T08test/bin_freeze/sam/prettyalign v3.5 (July 15, 2005) compiled 04/12/08_09:06:02
;  (c) 1992-2001 Regents of the University of California, Santa Cruz
;
;          Sequence Alignment and Modeling Software System
;         http://www.cse.ucsc.edu/research/compbio/sam.html
;
; ----------------- Citations (SAM, SAM-T2K, 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, et al., What is the value added by human intervention in protein
;  structure prediction, Proteins: Stucture, Function, Genetics 45(S5):86--91, 2001.
; A. Krogh et al., Hidden Markov models in computational biology:
;  Applications to protein modeling, JMB 235:1501-1531, Feb 1994.
; ---------------------------------------------------------------------
; Sequences correspond to the following labels:
; 1 T0405 lmo0819, listeria  monocytogenes, 282 residues
; 2 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]
; 3 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]
; 4 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]
; 5 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]
; 6 gi|116872233|ref|YP_849014.1|_1:282 hypothetical protein lwe0813 [Listeria welshimeri serovar 6b str. SLCC5334] >gi|116741111|emb|CAK20231.1| unnamed protein product [Listeria welshimeri serovar 6b str. SLCC5334]
; 7 gi|16799889|ref|NP_470157.1|_1:282 hypothetical protein lin0815 [Listeria innocua Clip11262] >gi|16413266|emb|CAC96047.1| lin0815 [Listeria innocua]
; 8 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]
; 9 gi|168265403|ref|ZP_02687368.1|_1:241 hypothetical protein LmonFSL_04399 [Listeria monocytogenes FSL J2-071]
; 10 gi|167052963|ref|ZP_02279361.1|_1:47 hypothetical protein LmonF_08591 [Listeria monocytogenes FSL F2-515]
; 11 gi|168265404|ref|ZP_02687369.1|_1:43 hypothetical protein LmonFSL_04404 [Listeria monocytogenes FSL J2-071]
                 10        20        30        40        50        60  
                 |         |         |         |         |         |  
   1 ...MNETEKLVAALLERNFGKNIGTRYPGNEAAQMRAEEVIGEIAIVIAPLVEKLGIENKTVKKT
   2 ...MNETEKLVAALLERNFGKNIGTRYPGNEAAQMRAEEVIGEIAIVIAPLVEKLGIENKTVKKT
   3 ...MNETEKLVAALLERNFGKNIGTRYPGNEAAQMRAEEVIGEIAIVIAPLVEKLGIENKTVKKT
   4 ...MNETEKLVAALLERNFGKNIGTRYPDNEAAQMRAEEVIGEIAIVIAPLVEKLGIESKTVKKT
   5 ...MNETEKLVAALLERNFGKNIGTRYPDNEAAQMRAEEVIGEIAIVIAPLVEKLGIESKTVKKT
   6 ...MNETQKLVAASLERNFGKDIGTRYVGNEKAQLRAEEVIEEIAIVIAPLVEQLGIESKTVKKT
   7 ...MNETQKLVAASLERNFGKDIGARYEGNEEAQLRAEEVIEEIAIVIAPLVEKLGIESKTVKKT
   8 gnyMNETEKLVAALLERNFGKNIGTRYPDNEAAQMRAEEVIGEIAIVIAPLVEKLGIESKTVKKT
   9 ...MNETEKLVAASLERNFGKNIGTRYPGNEEAQMRAEEVIEEIAIVITPLVEKLGIESKTVKKT
  10 ...--------------------------------------------------------------
  11 ...--------------------------------------------------------------


            70        80        90       100       110       120       
            |         |         |         |         |         |       
   1 IPFLYELQKNQFCDMSAYPYPLLLVNGTSTDTEKYWRDLPTYWTDDANKIVLPYVLEHIKNNKVR
   2 IPFLYELQKNQFCDMSAYPYPLLLVNGTSADTEKYWRDLPTYWTDDANKIVLPYVLEHIKNNKVR
   3 IPFLYELQKNQFCDMSAYPYPLLLVNGTSTDTEKYWRDLPTYWTDDANKIVLPYVLEHIKNNKVR
   4 IPFLYELQKNQFCDMSAYPYPLLLVNGTSADTEKYWRDLPTYWTDDANKIVLPYVLEHIKNNKVR
   5 IPFLYELQKNQFCDMSAYPYPLLLVNGTSADTEKYWRDLPTYWTDDANKIVLPYVLEHIKNNKVR
   6 IPFLYELQKNQFCDMSAYPYPLLLVNGTSADTEKYWRDLPTYWTDDANKIVLPYVLEHMKNNKVR
   7 IPFLYELQKNQFCDMSAYPYPLLLVNGTSADTEKYWRDLPTYWTDEANKIVLPYVLEHIKNNKVR
   8 IPFLYELQKNQFCDMSAYPYPLLLVNGTSADTEKYWRDLPTYWTDDANKIVLPYVLEHIKNNKVR
   9 IPFLYELQKNQFCDMSAYPYPLLLVNGTSADTEKYWRDLPTYWTDDANKIVLPYVLEHIKNNKVR
  10 -----------------------------------------------------------------
  11 -----------------------------------------------------------------


      130       140       150       160       170       180       190  
       |         |         |         |         |         |         |  
   1 QKLLAFHAWLLGEVVEMNEALGADFRVKLVFESDMRIRLRVYEVEQIAIEVHFLDNHDTEQQHLG
   2 QKLLAFHAWLLGEVVEMNEALGADFRVKLVFESDMRIRLRVYEVEQIAIEVHFLDNHDTEQQHLG
   3 QKLLAFHAWLLGEVVEMNEALGADFRVKLVFESDMRIRLRVYEVEQIAIEVHFLDNHDTEQQHLG
   4 QKLLAFHAWLIGEVVEMNEELGADFRIKLVFESDMRIRLRVYDVEQIAIEVHFLDNHDTEQQHLG
   5 QKLLAFHAWLIGEVVEMNEELGADFRIKLVFESDMRIRLRVYDVEQIAIEVHFLDNHDTEQQHLG
   6 QKLLAFHAWLLGEVAEMNEELGAAFRVKLVFESDMRIRLRVYEVEQIAVEVHFLDNHDTEQQHLG
   7 QKLLSFHAWLLGEVAEMNTELGAQFRVKLVFESDMRIRLRIYEVEQIAIEVHFLDNHDTEQQHLG
   8 QKLLAFHAWLIGEVVEMNEELGADFRIKLVFESDMRIRLRVYDVEQIAIEVHFLDNHDTEQQHLG
   9 QKLLAFHAWLLGEVAEMNGVLGADFRVKLVFESDMRIRLRVYEVEQIAIEVHFLDNHDTEQQHLG
  10 -----------------------------------------------------------------
  11 -----------------------------------------------------------------


           200       210       220       230       240       250       
            |         |         |         |         |         |       
   1 YDVSLDADFTEKARLLLRQGILTENLGLEALKAYMKSVLPIAHSLKNLEHLTFEETKKLTKLLTQ
   2 YDVSLDADFTEKARLLLRQGILTENLGLEALKAYMKSVLPIAHSLKNLEHLTFEETKKLTKLLTQ
   3 YDVSLDADFTEKARLLLRQGILTENLGLEALKAYMKSVLPIAHSLKNLEHLTFEETKKLTKLLTQ
   4 YDVSLDVDITDKARLLLRQGILTENLGLEALKAYMKSVLPIAHSLKNLEYLTVEDTKKLTKLLTQ
   5 YDVSLDVDITDKARLLLRQGILTENLGLEALKAYMKSVLPIAHSLKNLEYLTVKDTKKLTKLLTQ
   6 YDVSLDAELEVKARLLLRQGILTENLGLEALKAYIKSVLPIAHNLETLKQLTGEETKKLTKLLMQ
   7 YDVSLDAELEVKARLLLRQGILTENLGLVALKAYIRSVLPIAHSLKKLEKLTDEEAKKLTKWLTH
   8 YDVSLDVDITDKARLLLRQGILTENLGLEALKAYMKSVLPIAHSLKNLEYLTVEDTKN-------
   9 YDVSLDADFTEKARLLLRQGILTENLGLEALKAYMKSVLPIAHSLKIWNS---------------
  10 --------------------FVQENLGLEALKAYMKSVLPIAHSLKNLEHLTFEETKKLDQIINA
  11 -----------------------------------------------MEQLTEEETKKLTKLLTQ


      260       270       280   
       |         |         |   
   1 EEPKIMEDTDLTSKALDFLQKAAQQ.
   2 EEPKIMEDTDLTSKALDFLQKAAQQ.
   3 EEPKIMEDTDLTSKALDFLQKAAQQ.
   4 EEPKIMEDTDLTSKALDFLQKAAQQ.
   5 EEPKIMEDTDLTSKALDFLQKAAQQ.
   6 EEPKIMEDTDLTSKALDFLQKLAPKk
   7 EEPKIMEDTDLTSKALDFLQKVAQQ.
   8 -------------------------.
   9 -------------------------.
  10 RRT----------------------.
  11 EEPKIMEDTDLTSKALDFLQNAALQ.