a2m2html output for file 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, 1999.
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:

- T0087-181-end
- gi|7674163|sp|O68579|PPAC_STRMU_181:310 PROBABLE MANGANESE-DEPENDENT INORGANIC PYROPHOSPHATASE (PYROPHOSPHATE PHOSPHO-HYDROLASE) (PPASE) (Streptococcus mutans)
- gi|2952533|gb|AAC05778.1| (AF051356) putative exopolyphosphatase [Streptococcus mutans] (Streptococcus mutans)
- gi|3403205|gb|AAC29042.1| (AF050517) unknown [Streptococcus mutans] (Streptococcus mutans)
- gi|8134646|sp|Q9WZ56|PPAC_THEMA_417:544 PROBABLE MANGANESE-DEPENDENT INORGANIC PYROPHOSPHATASE (PYROPHOSPHATE PHOSPHO-HYDROLASE) (PPASE) (Thermotoga maritima)
- gi|7462213|pir||D72359_436:563 conserved hypothetical protein - Thermotoga maritima (strain MSB8) (Thermotoga maritima)
- gi|4981105|gb|AAD35672.1|AE001733_9 (AE001733) conserved hypothetical protein [Thermotoga maritima] (Thermotoga maritima)
- gi|8134643|sp|P95765|PPAC_STRGC_182:310 PROBABLE MANGANESE-DEPENDENT INORGANIC PYROPHOSPHATASE (PYROPHOSPHATE PHOSPHO-HYDROLASE) (PPASE) (Streptococcus gordonii challis)
- gi|1743856|gb|AAB39104.1| (U57759) intrageneric coaggregation-relevant adhesin [Streptococcus gordonii] (Streptococcus gordonii)
- gi|8134641|sp|O29502|PPAC_ARCFU_192:319 PROBABLE MANGANESE-DEPENDENT INORGANIC PYROPHOSPHATASE (PYROPHOSPHATE PHOSPHO-HYDROLASE) (PPASE) (Archaeoglobus fulgidus)
- gi|7447473|pir||D69344 exopolyphosphatase (ppx1) homolog - Archaeoglobus fulgidus (Archaeoglobus fulgidus)
- gi|2649851|gb|AAB90480.1| (AE001052) exopolyphosphatase (ppx1) [Archaeoglobus fulgidus] (Archaeoglobus fulgidus)
- gi|2496072|sp|Q58025|PPAC_METJA_179:307 PROBABLE MANGANESE-DEPENDENT INORGANIC PYROPHOSPHATASE (PYROPHOSPHATE PHOSPHO-HYDROLASE) (PPASE) (Methanococcus jannaschii)
- gi|2128021|pir||H64375 hypothetical protein homolog MJ0608 - Methanococcus jannaschii (Methanococcus jannaschii)
- gi|1591318|gb|AAB98601.1| (U67509) exopolyphosphatase (ppx1) [Methanococcus jannaschii] (Methanococcus jannaschii)
- gi|8134645|sp|Q9RRB7|PPAC_DEIRA_178:310 PROBABLE MANGANESE-DEPENDENT INORGANIC PYROPHOSPHATASE (PYROPHOSPHATE PHOSPHO-HYDROLASE) (PPASE) (Deinococcus radiodurans)
- gi|7471265|pir||A75258 conserved hypothetical protein - Deinococcus radiodurans (strain R1) (Deinococcus radiodurans)
- gi|6460400|gb|AAF12113.1|AE002086_5 (AE002086) conserved hypothetical protein [Deinococcus radiodurans] (Deinococcus radiodurans)
- gi|586817|sp|P37487|PPAC_BACSU_180:306 MANGANESE-DEPENDENT INORGANIC PYROPHOSPHATASE (PYROPHOSPHATE PHOSPHO-HYDROLASE) (PPASE) (Bacillus subtilis)
- gi|2126990|pir||S65980 conserved hypothetical protein yybQ - Bacillus subtilis (Bacillus subtilis)
- gi|467340|dbj|BAA05186.1| (D26185) unknown [Bacillus subtilis] (Bacillus subtilis)
- gi|2636602|emb|CAB16092.1| (Z99124) similar to hypothetical proteins [Bacillus subtilis] (Bacillus subtilis)
- gi|9656203|gb|AAF94837.1|_177:296 (AE004246) conserved hypothetical protein [Vibrio cholerae] (Vibrio cholerae)

              10         20        30            40        50        60
              |          |         |             |         |         |
   1 YGLAMLKAGTNL.ASKTAAQLVDIDAKTFELNG....SQVRVAQVNTVDINEVLERQNEIEEAIK
   2 YGLAMLKAGTNL.ASKTAAQLVDIDAKTFELNG....SQVRVAQVNTVDINEVLERQNEIEEAIK
   3 FAKKLLKEGMKIpEDVDPAELLKRDVKVYEMGE....ESFAVSQIMTSDFSTLLKEKERFMNTLK
   4 FAKKLLKEGMKIpEDVDPAELLKRDVKVYEMGE....ESFAVSQIMTSDFSTLLKEKERFMNTLK
   5 YGLAMLKAGTNL.ASKSAEELIDIDAKTFELNG....NNVRVAQVNTVDIAEVLERQAEIEAAIE
   6 FGVEIKAKLSAV.DDLTAMDIIKRDYKDFDMSG....KKVGVGQIELVDLSLIESRIDEIYEAMK
   7 FGMEILKAKSVV.GKLKPEEIINMDFKNFDFNG....KKVGIGQVEVIDVSEVESKKEDIYKLLE
   8 YALAMFAAKSDL.GNTPAETLLRMDYKVFPFGDpvqpQNWGIGVIETTNPAYVFGRQQELLAAMD
   9 YGLNMLKAGADL.SKKTVEELISLDAKEFTLGS....KKVEIAQVNTVDIEDVKKRQAELEAVIS
  10 FIKALLIAKTDI.EGLSAAQLVEKDLKAYPFNG....RELVVGQVELATLEQVADMIDALEADLQ


              70        80        90        100       110       120    
              |         |         |          |         |         |    
   1 ASQAANGYSDFVLMITDILNSNSEILALGNNTDKV.EAAFNFTLKNNHAFLAGAVSRKKQVVPQL
   2 ASQAANGYSDFVLMITDILNSNSEILALGNNTDKV.EAAFNFTLKNNHAFLAGAVSRKKQVVPQL
   3 TLKGEFGVKHFFVLFTNPVEEAS-LLMMDGDQKLV.EKAFNAEKKDGLFLLKGVMSRKKDFVPKI
   4 TLKGEFGVKHFFVLFTNPVEEAS-LLMMDGDQKLV.EKAFNAEKKDGLFLLKGVMSRKKDFVPKI
   5 KAIADNGYSDFVLMITDIINSNSEILAIGSNMDKV.EAAFNFVLENNHAFLAGAVSRKKQVVPQL
   6 KMKEEGGYAGIFLMLTDIMKEGTELLVVTDYPEVV.EKAFGKKLEGKSVWLDGVMSRKKQVVPPL
   7 EKLKNEGYDLIVFLITDIMKEGSEALVVGN-KEMF.EKAFNVKVEGNSVFLEGVMSRKKQVVPPL
   8 QVKAEDTLSGMLLSVVDILNETNRTLVLGATEAKVlREAFGAEAEGQVADLGNRISRKKQIVPTL
   9 KVVAEKNLDLFLLVITDILENDSLALAIGNEAAKV.EKAFNVTLENNTALLKGVVSRKKQVVPVL
  10 RRCDEESLALAALMLTDITTAQTRLLFKGEWSEKL.AKH----AKDGVLMMENTLSRKKQGWPWL


         130
          |
   1 TESFNG
   2 TESFNG
   3 GEVL--
   4 GEVL--
   5 TESFN-
   6 EKAF--
   7 ERAYNG
   8 EKYF--
   9 TDA---
  10 ------