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:

- T0214 Hypothetical protein, Pyrococcus furiosus
- gi|18976827|ref|NP_578184.1|_1:110 hypothetical protein PF0455 [Pyrococcus furiosus DSM 3638]
- gi|18892426|gb|AAL80579.1| hypothetical protein [Pyrococcus furiosus DSM 3638]
- gi|14590265|ref|NP_142331.1|_1:108 hypothetical protein PH0355 [Pyrococcus horikoshii OT3]
- gi|7518597|pir||H71142 hypothetical protein PH0355 - Pyrococcus horikoshii [Taxonomy]
- gi|3256746|dbj|BAA29429.1| 109aa long hypothetical protein [Pyrococcus horikoshii OT3]
- gi|14521811|ref|NP_127287.1|_1:108 hypothetical protein PAB1060 [Pyrococcus abyssi GE5]
- gi|7518025|pir||G75009 hypothetical protein PAB1060 - Pyrococcus abyssi (strain Orsay) [Taxonomy]
- gi|5459031|emb|CAB50517.1| Hypothetical protein [Pyrococcus abyssi]
- gi|42782608|ref|NP_979855.1|_1:111 conserved hypothetical protein [Bacillus cereus ATCC 10987]
- gi|42738534|gb|AAS42463.1| conserved hypothetical protein [Bacillus cereus ATCC 10987]
- gi|30021646|ref|NP_833277.1|_1:111 hypothetical Cytosolic Protein [Bacillus cereus ATCC 14579]
- gi|29897201|gb|AAP10478.1| hypothetical Cytosolic Protein [Bacillus cereus ATCC 14579]
- gi|20093930|ref|NP_613777.1|_237:341 Archaea-specific enzyme related to ProFAR isomerase (HisA) and containing an additional uncharacterized domain [Methanopyrus kandleri AV19]
- gi|19886880|gb|AAM01707.1| Archaea-specific enzyme related to ProFAR isomerase (HisA) and containing an additional uncharacterized domain [Methanopyrus kandleri AV19]
- gi|14521785|ref|NP_127261.1|_3:109 hypothetical protein PAB1310 [Pyrococcus abyssi GE5]
- gi|7518092|pir||E75006 hypothetical protein PAB1310 - Pyrococcus abyssi (strain Orsay) [Taxonomy]
- gi|5459005|emb|CAB50491.1| Hypothetical protein [Pyrococcus abyssi]
- gi|18976842|ref|NP_578199.1|_3:109 hypothetical protein PF0470 [Pyrococcus furiosus DSM 3638]
- gi|18892443|gb|AAL80594.1| hypothetical protein [Pyrococcus furiosus DSM 3638]
- gi|14590361|ref|NP_142427.1|_4:110 hypothetical protein PH0447 [Pyrococcus horikoshii OT3]
- gi|7518651|pir||H71155 hypothetical protein PH0447 - Pyrococcus horikoshii [Taxonomy]
- gi|3256850|dbj|BAA29533.1| 114aa long hypothetical protein [Pyrococcus horikoshii OT3]
- gi|21401466|ref|NP_657451.1|_1:111 hypothetical protein predicted by GeneMark [Bacillus anthracis A2012]
- gi|30263492|ref|NP_845869.1| conserved hypothetical protein [Bacillus anthracis str. Ames]
- gi|47528885|ref|YP_020234.1| conserved hypothetical protein [Bacillus anthracis str. Ames 0581]
- gi|30258127|gb|AAP27355.1| conserved hypothetical protein [Bacillus anthracis str. Ames]
- gi|47504033|gb|AAT32709.1| conserved hypothetical protein [Bacillus anthracis str. Ames 0581]
- gi|47568902|ref|ZP_00239594.1|_1:111 hypothetical protein cytosolic protein [Bacillus cereus G9241]
- gi|47554386|gb|EAL12745.1| hypothetical protein cytosolic protein [Bacillus cereus G9241]
- gi|18396513|ref|NP_566202.1|_107:208 expressed protein [Arabidopsis thaliana]
- gi|6017115|gb|AAF01598.1| unknown protein [Arabidopsis thaliana]
- gi|22655129|gb|AAM98155.1| expressed protein [Arabidopsis thaliana]
- gi|32189307|gb|AAP75808.1| At3g03320 [Arabidopsis thaliana]
- gi|21536491|gb|AAM60823.1|_107:208 unknown [Arabidopsis thaliana]
- gi|15613379|ref|NP_241682.1|_1:110 BH0816~unknown conserved protein in others [Bacillus halodurans C-125]
- gi|25489507|pir||H83751 hypothetical protein BH0816 [imported] - Bacillus halodurans (strain C-125) [Taxonomy]
- gi|10173430|dbj|BAB04535.1| BH0816 [Bacillus halodurans C-125]
- gi|23038239|ref|ZP_00070409.1|_3:110 COG4043: Uncharacterized conserved protein [Oenococcus oeni MCW]
- gi|23023726|ref|ZP_00062958.1|_10:116 COG4043: Uncharacterized conserved protein [Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293]
- gi|25408874|pir||E84866_244:338 hypothetical protein At2g43470 [imported] - Arabidopsis thaliana [Taxonomy]
- gi|2289012|gb|AAB64341.1| hypothetical protein [Arabidopsis thaliana]
- gi|30689388|ref|NP_181875.2|_244:338 expressed protein [Arabidopsis thaliana]
- gi|28379445|ref|NP_786337.1|_4:112 unknown [Lactobacillus plantarum WCFS1]
- gi|28272284|emb|CAD65197.1| unknown [Lactobacillus plantarum WCFS1]

              10        20        30        40             50        60
              |         |         |         |              |         |
   1 MEWEMGLQEEFLELIKLRKKKIEGRLYDEKRRQIKPGDVISFEG.....GKLKVRVKAIRVYNSF
   2 MEWEMGLQEEFLELIKLRKKKIEGRLYDEKRRQIKPGDVISFEG.....GKLKVRVKAIRVYNSF
   3 MKWEMGLQEEYIELIKAGKKKIEGRLYDEKRRQIKPGDIIIFEG.....GKLKVKVKGIRVYSSF
   4 MEWEMGLQEEYIELIKRGLKKIEGRLYDEKRRKIKPGDIIVFEG.....GKLKVRVKALRVYKSF
   5 MRYEMGLYNKPFQSIKLGKKVYEVRLYDKKRQLIKQGDHIIFTNltta.ATMAVKVTEIKRYENF
   6 MRYEMGLYNKPFQSIRSGKKVYEVRLYDKKRQLINKDDEIVFTNlktt.EMMTVKVTEIKRYESF
   7 --HHMGLEEEYLNLIKEGKKTVEGRVKDDKRARIKPGDKILFNR.....-RLLVKVIDVREYDSF
   8 -VYRLYLRDEYLEMVKSGKKKIEVRVAYPQLRGIKKGDKIIFND.....-MIPAEVIDVKRYETF
   9 -VYRLYLKDEYLEMVKSGKKRIEVRVAYPQLKDIKRGDKIIFND.....-LIPAEVVEVKKYETF
  10 -VYRLYLRDEYLEMVKSGKKRIEVRVAYPQLKGMKRGDKIIFND.....-EVPAEVIEVKHYETF
  11 MRYEMGLYNKPFQSIQSGKKVYEVRLYDKKRQLINKGDEIVFTNlttk.EMMAVKVTEIKRYESF
  12 MRYEMGLYNKPFQSIQSGKKVYEVRLYDKKRQLINKGDEIVFTNlttk.EMMAVKVTEIKRYENF
  13 --FELHVQEPYFTQLKDGLKTVEGRCAVGDYMRISSGDFLLFNK.....-CLLLEVQDVHRYTSF
  14 --FELHVQEPYFTQLKDGLKTVEGRCAVGDYMRISSGAFLLFNK.....-CLLLEVQDVHRYTSF
  15 MKHAMGLFKVPFESIKAGRKTVEVRLNDAKRRQVAVGDTIEFTKlpekeETLKVVVTKLRSYDTF
  16 ----MGLNHSQFLLMQQGDKSVEIRLNDRKRSFLKEGSLITFIDlktd.KKIEVIVKKIYKFKTF
  17 --MLMGLNHDQFVLVQRGTKTIEIGLYDEKRAQLKIGHKILFTDlenn.NQIMVSVKQLYKFTTF
  18 --IDSGSFCGTFEKISLGKEVIRLKEKEDEWSKL--------IN.....QKGSELVNELHQYASF
  19 --IDSGSFCGTFEKISLGKEVIRLKEKEDEWSKL--------IN.....QKGSELVNELHQYASF
  20 ----MQLIHPQWLLIKSGLKTIEIRLNDAKRQALQVGDIVNFIDlttg.QQLTTQLIDITRFASF


              70         80        90       100       110
              |          |         |         |         |
   1 REMLEKEGLENVLPG.VKSIEEGIQVYRRFYDEEKEKKYGVVAIEIEPLEY
   2 REMLEKEGLENVLPG.VKSIEEGIQVYRRFYDEEKEKKYGVVAIEIEPLEY
   3 KEMLEKEGIENVLPG.VKSIEEGVKVYRQFYDEEREKKYGVVAIEIEPI--
   4 KEMLEKEGIENVLPG.VNSVEEGVKIYRKFYDEEREKKYGVVAIEIEPI--
   5 QAMYEQIDKKLLDCE.NDSLEEMLESTYKIYTKEQEKKWGTVAIGIKV---
   6 KAIYEQIDKKLLDCE.NDSLEEMLESTYKIYTKEQEKEWGTVAIRIEV---
   7 EEMLREEGLENVLPN.VDSIEEGVEIYRRFYSSGKEKMFGVLAIEIEPI--
   8 RQVLREEPIEKIFPD.EPSFERALRRFHNMYPKWKEYRYGVIAIKFRILG-
   9 RQVLREEPIDKIFPD.KPSFEKALKRFHNMYPKWKEYRYGVLAIKFRVLG-
  10 RQVLREEPIDKIFPD.EPSFERALRRFHNLYPKWKENRYGVIAIKFKLLG-
  11 KVMYEQIDKKLMDCE.NDSLEEMLESTYKIYTKEQEKEWGTVAIGIEV---
  12 QAMYEQIDKKLLDCE.NDRLEEMLESTYKIYTKEQEKKWGTVAIGIEV---
  13 SEMLKVEGLAKVLPG.VESIEEGVQVYRNFYSEEKERMNGVVAIRV-----
  14 SEMLKVEGLSKVLPG.VESIEEGVQVYRNFYSEEKERMNGVVAIRV-----
  15 EAMYKEIPFEAFDCE.GWTMDEMLDGTYEIYTSEQENEWGALPIYV-----
  16 CELYKSFTSTEVGSAtNDSLEKMVNDTYKIYSPAQERNFGVLAIRIRL---
  17 ADLYAQFNGAKVGSNsTDNIEKIVNDTYEIYTPEQERHYGVLAIE------
  18 YELLKAESSEKVFPG.TKTVEEGMQMFRKLYDTDQENFNGVVAIHL-----
  19 YELLKAESSEKVFPG.TKTVEEGMQMFRKLYDTDQENFNGVVAIHL-----
  20 ESLLSEYTAVQVGSApGTPVTQMVQEMLTLYSPVQVAQSGVVALQVRPL--