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:

- T0283 BH3980, Bacillus halodurans, 112 res
- gi|89209513|ref|ZP_01187915.1|_1:108 conserved hypothetical protein [Bacillus weihenstephanensis KBAB4]
- gi|89152556|gb|EAR72723.1| conserved hypothetical protein [Bacillus weihenstephanensis KBAB4]
- gi|47564563|ref|ZP_00235608.1|_1:108 hypothetical protein cytosolic protein [Bacillus cereus G9241]
- gi|47558715|gb|EAL17038.1| hypothetical protein cytosolic protein [Bacillus cereus G9241]
- gi|42782501|ref|NP_979748.1|_1:108 hypothetical protein BCE3448 [Bacillus cereus ATCC 10987]
- gi|42738427|gb|AAS42356.1| conserved hypothetical protein [Bacillus cereus ATCC 10987]
- gi|29897095|gb|AAP10372.1|_1:108 hypothetical Cytosolic Protein [Bacillus cereus ATCC 14579]
- gi|30021540|ref|NP_833171.1| hypothetical Cytosolic Protein [Bacillus cereus ATCC 14579]
- gi|49329787|gb|AAT60433.1|_1:108 conserved hypothetical protein [Bacillus thuringiensis serovar konkukian str. 97-27]
- gi|49478231|ref|YP_037537.1| hypothetical protein BT9727_3214 [Bacillus thuringiensis serovar konkukian str. 97-27]
- gi|51975558|gb|AAU17108.1|_1:108 conserved hypothetical protein [Bacillus cereus E33L]
- gi|52142089|ref|YP_084738.1| hypothetical protein BCZK3151 [Bacillus cereus E33L]
- gi|10176605|dbj|BAB07699.1|_2:111 BH3980 [Bacillus halodurans C-125]
- gi|15616542|ref|NP_244848.1| hypothetical protein BH3980 [Bacillus halodurans C-125]
- gi|47503929|gb|AAT32605.1|_1:108 conserved hypothetical protein [Bacillus anthracis str. 'Ames Ancestor']
- gi|49180173|gb|AAT55549.1| conserved hypothetical protein [Bacillus anthracis str. Sterne]
- gi|47528781|ref|YP_020130.1| hypothetical protein GBAA3494 [Bacillus anthracis str. 'Ames Ancestor']
- gi|49186246|ref|YP_029498.1| hypothetical protein BAS3241 [Bacillus anthracis str. Sterne]
- gi|30258032|gb|AAP27260.1| conserved hypothetical protein [Bacillus anthracis str. Ames]
- gi|30263397|ref|NP_845774.1| hypothetical protein BA3494 [Bacillus anthracis str. Ames]
- gi|65320729|ref|ZP_00393688.1| COG4817: Uncharacterized protein conserved in bacteria [Bacillus anthracis str. A2012]
- gi|89096657|ref|ZP_01169549.1|_2:112 hypothetical protein B14911_13492 [Bacillus sp. NRRL B-14911]
- gi|89088672|gb|EAR67781.1| hypothetical protein B14911_13492 [Bacillus sp. NRRL B-14911]
- gi|10176601|dbj|BAB07695.1|_4:104 BH3976 [Bacillus halodurans C-125]
- gi|15616538|ref|NP_244844.1| hypothetical protein BH3976 [Bacillus halodurans C-125]
- gi|62462434|ref|ZP_00381844.1|_3:103 COG4817: Uncharacterized protein conserved in bacteria [Lactococcus lactis subsp. cremoris SK11]
- gi|12725109|gb|AAK06155.1|_3:103 UNKNOWN PROTEIN [Lactococcus lactis subsp. lactis Il1403]
- gi|15674039|ref|NP_268214.1| hypothetical protein L127611 [Lactococcus lactis subsp. lactis Il1403]
- gi|68205464|ref|ZP_00557666.1|_4:106 conserved hypothetical conserved protein [Desulfitobacterium hafniense DCB-2]
- gi|68170615|gb|EAM98499.1| conserved hypothetical conserved protein [Desulfitobacterium hafniense DCB-2]
- gi|22779009|dbj|BAC15276.1|_4:104 hypothetical conserved protein [Oceanobacillus iheyensis HTE831]
- gi|23100775|ref|NP_694242.1| hypothetical protein OB3320 [Oceanobacillus iheyensis HTE831]
- gi|62462433|ref|ZP_00381843.1|_7:100 COG4817: Uncharacterized protein conserved in bacteria [Lactococcus lactis subsp. cremoris SK11]
- gi|68205463|ref|ZP_00557665.1|_8:102 Uncharacterised conserved protein UCP029876 [Desulfitobacterium hafniense DCB-2]
- gi|68170614|gb|EAM98498.1| Uncharacterised conserved protein UCP029876 [Desulfitobacterium hafniense DCB-2]
- gi|10176602|dbj|BAB07696.1|_8:102 BH3977 [Bacillus halodurans C-125]
- gi|15616539|ref|NP_244845.1| hypothetical protein BH3977 [Bacillus halodurans C-125]
- gi|29343328|gb|AAO81090.1|_5:104 conserved hypothetical protein [Enterococcus faecalis V583]
- gi|29375866|ref|NP_815020.1| hypothetical protein EF1298 [Enterococcus faecalis V583]
- gi|12725110|gb|AAK06156.1|_6:103 UNKNOWN PROTEIN [Lactococcus lactis subsp. lactis Il1403]
- gi|15674040|ref|NP_268215.1| hypothetical protein L127921 [Lactococcus lactis subsp. lactis Il1403]
- gi|46906971|ref|YP_013360.1|_2:99 hypothetical protein LMOf2365_0756 [Listeria monocytogenes str. 4b F2365]
- gi|47095286|ref|ZP_00232897.1| conserved hypothetical protein [Listeria monocytogenes str. 1/2a F6854]
- gi|47091683|ref|ZP_00229479.1| conserved hypothetical protein [Listeria monocytogenes str. 4b H7858]
- gi|47020002|gb|EAL10739.1| conserved hypothetical protein [Listeria monocytogenes str. 4b H7858]
- gi|47016357|gb|EAL07279.1| conserved hypothetical protein [Listeria monocytogenes str. 1/2a F6854]
- gi|16410109|emb|CAC98798.1| lmo0720 [Listeria monocytogenes]
- gi|46880237|gb|AAT03537.1| conserved hypothetical protein [Listeria monocytogenes str. 4b F2365]
- gi|16802762|ref|NP_464247.1| hypothetical protein lmo0720 [Listeria monocytogenes EGD-e]
- gi|16413180|emb|CAC95960.1|_2:98 lin0728 [Listeria innocua]
- gi|16799803|ref|NP_470071.1| hypothetical protein lin0728 [Listeria innocua Clip11262]
- gi|15004857|ref|NP_149317.1|_26:86 Membrane protein [Clostridium acetobutylicum ATCC 824]
- gi|14994469|gb|AAK76899.1| Membrane protein [Clostridium acetobutylicum ATCC 824]
- gi|29897847|gb|AAP11122.1|_26:89 hypothetical protein BC_4207 [Bacillus cereus ATCC 14579]
- gi|30022290|ref|NP_833921.1| hypothetical protein BC4207 [Bacillus cereus ATCC 14579]
- gi|49330136|gb|AAT60782.1|_24:81 conserved hypothetical protein [Bacillus thuringiensis serovar konkukian str. 97-27]
- gi|49478580|ref|YP_038269.1| hypothetical protein BT9727_3950 [Bacillus thuringiensis serovar konkukian str. 97-27]
- gi|42783327|ref|NP_980574.1|_24:81 hypothetical protein BCE4281 [Bacillus cereus ATCC 10987]
- gi|42739255|gb|AAS43182.1| conserved hypothetical protein [Bacillus cereus ATCC 10987]

              10        20        30        40         50        60    
              |         |         |         |          |         |    
   1 MSFIEKMIGSLNDKREWKAMEARAKALPKEYHHAYKAIQKYMWTSGG.PTDWQDTKRIFGGILDL
   2 --MLEMFKKLIGDKKEYKMMMARVGALPEDYQFVFKKIQNYMWNFSA.GNGM-DMLHIQYELIDL
   3 --MLEMFKKLIGDKKEYKMMMARVEALPEDYQFVFKKIQNYMWNFSA.GNGM-DMLHIQYELIDL
   4 --MLEMFKKLIGDKKEYKMMMARVAALPEDYQFVFKKIQNYMWNFSA.GNGM-DMLHIQYELIDL
   5 --MLEMFKKLIGDKKEYKMMMARVEALPEDYQFVFKKIQNYMWNFSA.GNGM-DMLHIQYELIDL
   6 --MLEIFKKLIGDKKEYRMMMARVAALPEDYQFVFKKIQNYMWNFST.GNGM-DMLHIQYELIDL
   7 --MLEIFKKIIGDKKEYRMMMARVAALPEDYQFVFKKIQNYMWNFST.GNGM-DMLHIQYELIDL
   8 -SFIEKMIGSLNDKREWKAMEARAKALPKEYHHAYKAIQKYMWTSGG.PTDWQDTKRIFGGILDL
   9 --MLEIFKKLIGDKKEYRMMMARVAALSEDYQFVFKKIQNYMWNFST.GNGM-DMLHIQYELIDL
  10 -SIFEKIIGSLDDKREWKAMEARAKALPSEYSAAYKAIQKYMWTAGGgPTDWKGTNRIFTGILDL
  11 -------KKIIEGKREWRAHVSRVEKLPKDYQIVYKEIQKYLFKVGP.VE-LNEGIGLLSEILGF
  12 ---LEKISDVLKEKREWQAMENRAKNLPKDFYLAYKAIQKYMFNMGE.TD-----WHIFTDIIEL
  13 ---LDKISDLLAEKKDWQEMQNRAKKLPKDFYQAYRSIQKYMFKMGA.TD-----WHIFNDIIEL
  14 -------QDIIEGKKEWRGHMARVKALPRDYQIVYKELQKYLFKVGP.VE-LTDGMGLLSGIIDL
  15 -------QDIIEGKKEWRAHKARVKALPKDYQIVYKEIQKYLFKVGP.VE-LTDGIGLLSGIIDL
  16 --NIVDRMIGLEEKREFREFEERAKNLGPDYYKDYCELKRYVWISGA.SK-WSDFKFIFNQLLDL
  17 --------TGSDMTKEWKAFESRVQKLPADYQAAWEKISLNLWPHSD.FTG-RNLMPILDGVLGL
  18 --------TGSDMTKEMKGFETRAKVLPAEYRAAWEEITSNLWLHSD.FTG-RNLMPILDSALEL
  19 ---KALIKKVVGDKKEYKEYKRRIAALPVEYRQVFQEIEKYAWHFSD.HSG-ANMFNALTDLLDL
  20 --NIVDRMIGLEEKREFHEFENRAQKLGENYYEDYKELKKYIWHSG-.VTKWADFKFIFGQVLDL
  21 ---FNWYKKYREEKRDYKQYKKRIAALPEDYKTAMKAIETYLWNFAK.GA---GMFEILKNVLEM
  22 ---FKWYTKYREEKRDYKQYKKRIDALPEDYKTAMKAIETYLWNFAK.GA---GMFEILKNVLEM
  23 ---------------------------------VYTNILCYIRVSSL.DA--KEKEEIISDILEM
  24 --------------------------------VAYSDMLVYLRLSNV.PE--QQMEELLLEILDH
  25 ---------------------------------AYGDMLIYLRLTSV.PQ--KQMEELLLEILDH
  26 ---------------------------------AYGDMLIYLRLTSV.PQ--KQMEELLLEILDH


          70        80        90       100       110  
          |         |         |         |         |  
   1 FEEGAAEGKKVTDLTGEDVAAFCDELMKDTKTWMDKYRTKLNDSIGRD
   2 FEAGAAEGRQVLEITGEDVASFADELVANAKTYVSKYREDLNESIMK-
   3 FEAGAAEGRQVLDITGEDVASFADELVANAKTYVSKYREDLNESIMK-
   4 FEAGAAEGRQVLDITGEDVASFADELVANAKTYVSKYREDLNESIMK-
   5 FEAGAAEGRQVLDITGDDVASFADELVANAKTYVSKYREDLNESIMK-
   6 FEAGAAEGRQVLDITGEDVASFADELVANAKTYVSKYREDLNESIMK-
   7 FEAGAAEGRQVLDITGEDVASFADELVANAKTYVSKYREDLNESIMK-
   8 FEEGAAEGKKVTDLTGEDVAAFCDELMKDTKTWMDKYRTKLNDSIGR-
   9 FEAGAAEGRQVLDITGEDVASFADELVANAKTYVSKYREDLNESIMK-
  10 FEEGAAEGKKVTDLTGEDVAAFCDELVKDEKTWNDKYRKKLNDTIGR-
  11 FEEGAAAGKGVLDVTGTDVAAFCDALIGDSKTYADLYQESIQQHV---
  12 FELAVIDGRTLAEVLGEDSSAFADELLSENKQDWRETYRQELNDY---
  13 FELAVVDGRSPAEVLGDDVATFADKLLSDNKEDWRNKYRQALNDY---
  14 FEEGAALGKGVLEVTGRDVAAFCDDLIKDSKTYADIYQESADQEVCK-
  15 FEKGAHMGKDVLEVTGEDVAAFCDELIKDSKTYADLYQESVNQTV---
  16 LEEAKGQKRKLTDLIGTDVAAFIDEMIDDKGWE---------------
  17 LEETAAEGQRVQEVLGDDIKGFCAALAGEEGAKTYRDKWR--------
  18 LEVASADGQSVEEVLGDDIEGFCAALVGDQGAKTFRDKWR--------
  19 FEEGAANGTPIKNITGEKVGDFAETIVNEVAGKWTDKQKE--------
  20 LEEAKIQDKELTDLIGPDVATFIDEMMDDNSWGKKQK-----------
  21 FENAAADNLELKAVVGDDLAEFADNLLSEFPEETWMDKQR--------
  22 FENAAADQLELKAVVGDDLAEFADSLLNEYPEETWMDKQ---------
  23 FLRCQAEEKSIDELIGNDYKSFCDSIIESAGE----------------
  24 LIEAQAENKNAYDIFGDNLQSYCDELISALPTQT--------------
  25 LLEAQEDGKTAHDIFGEDLKAYCDELIKS-------------------
  26 LLEAQEDGKTAHDIFGEDLKAYCDELIKS-------------------