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:

- T0108 Family 17 carbohydrate binding module, C. cellulovorans
- gi|7459698|pir||JC5467_377:572 cellulase (EC 3.2.1.4) - Bacillus sp (Bacillus sp.)
- gi|1339852|dbj|BAA12744.1|_377:572 (D85236) endo-1,4-beta-glucanase [Bacillus sp.] (Bacillus sp.)
- gi|1345369|dbj|BAA12826.1|_359:556 (D85526) beta-1,4-endoglucanase [Clostridium josui] (Clostridium josui)
- gi|121795|sp|P19570|GUN3_BACS4_407:605 ENDOGLUCANASE C PRECURSOR (ENDO-1,4-BETA-GLUCANASE) (CELLULASE) (Bacillus sp. N-4)
- gi|80145|pir||JS0174 cellulase (EC 3.2.1.4) C precursor - Bacillus sp (Bacillus sp.)
- gi|142669|gb|AAA22306.1| (M25500) endoglucanase [Bacillus sp.] (Bacillus sp.)
- gi|7475991|pir||JC5487_352:557 cellulase (EC 3.2.1.4) precursor - Clostridium cellulovorans (Clostridium cellulovorans)
- gi|1778709|gb|AAB40891.1| (U37056) endo-1,4-beta glucanase EngF [Clostridium cellulovorans] (Clostridium cellulovorans)
- gi|121837|sp|P06564|GUN_BACS1_571:758 ENDOGLUCANASE PRECURSOR (ENDO-1,4-BETA-GLUCANASE) (ALKALINE CELLULASE) (Bacillus sp. 1139)
- gi|80146|pir||A29003 cellulase (EC 3.2.1.4), alkaline - Bacillus sp (Bacillus sp.)
- gi|142667|gb|AAA22305.1| (M15743) cellulase (EC 3.2.1.4) [Bacillus sp.] (Bacillus sp.)
- gi|216224|dbj|BAA00045.1| (D00066) alkaline cellulase [Bacillus sp.] (Bacillus sp.)
- gi|80147|pir||JT0611_571:758 cellulase (EC 3.2.1.4), alkaline - Bacillus sp. (strain KSM-64) (Bacillus sp.)
- gi|289266|gb|AAA73189.1|_570:757 (M84963) endo-1,4-beta-glucanase [Bacillus sp.] (Bacillus sp.)
- gi|7459698|pir||JC5467_573:760 cellulase (EC 3.2.1.4) - Bacillus sp (Bacillus sp.)
- gi|1339852|dbj|BAA12744.1|_573:760 (D85236) endo-1,4-beta-glucanase [Bacillus sp.] (Bacillus sp.)
- gi|121838|sp|P19424|GUN_BACS6_557:750 ENDOGLUCANASE PRECURSOR (ENDO-1,4-BETA-GLUCANASE) (ALKALINE CELLULASE) (Bacillus sp. KSM-635)
- gi|322158|pir||S29043 cellulase (EC 3.2.1.4) - Bacillus sp (Bacillus sp.)
- gi|142665|gb|AAA22304.1| (M27420) endo-beta-1,4-glucanase [Bacillus sp.] (Bacillus sp.)
- gi|1483210|emb|CAB01405.1|_358:572 (Z77855) endoglucanase [Anaerocellum thermophilum] (Anaerocellum thermophilum)
- gi|80147|pir||JT0611_377:569 cellulase (EC 3.2.1.4), alkaline - Bacillus sp. (strain KSM-64) (Bacillus sp.)
- gi|289266|gb|AAA73189.1|_376:568 (M84963) endo-1,4-beta-glucanase [Bacillus sp.] (Bacillus sp.)
- gi|121837|sp|P06564|GUN_BACS1_377:569 ENDOGLUCANASE PRECURSOR (ENDO-1,4-BETA-GLUCANASE) (ALKALINE CELLULASE) (Bacillus sp. 1139)
- gi|80146|pir||A29003 cellulase (EC 3.2.1.4), alkaline - Bacillus sp (Bacillus sp.)
- gi|142667|gb|AAA22305.1| (M15743) cellulase (EC 3.2.1.4) [Bacillus sp.] (Bacillus sp.)
- gi|216224|dbj|BAA00045.1| (D00066) alkaline cellulase [Bacillus sp.] (Bacillus sp.)
- gi|121838|sp|P19424|GUN_BACS6_752:940 ENDOGLUCANASE PRECURSOR (ENDO-1,4-BETA-GLUCANASE) (ALKALINE CELLULASE) (Bacillus sp. KSM-635)
- gi|322158|pir||S29043 cellulase (EC 3.2.1.4) - Bacillus sp (Bacillus sp.)
- gi|142665|gb|AAA22304.1| (M27420) endo-beta-1,4-glucanase [Bacillus sp.] (Bacillus sp.)
- gi|121795|sp|P19570|GUN3_BACS4_611:795 ENDOGLUCANASE C PRECURSOR (ENDO-1,4-BETA-GLUCANASE) (CELLULASE) (Bacillus sp. N-4)
- gi|80145|pir||JS0174 cellulase (EC 3.2.1.4) C precursor - Bacillus sp (Bacillus sp.)
- gi|142669|gb|AAA22306.1| (M25500) endoglucanase [Bacillus sp.] (Bacillus sp.)
- gi|1345369|dbj|BAA12826.1|_562:751 (D85526) beta-1,4-endoglucanase [Clostridium josui] (Clostridium josui)

              10        20           30        40        50          60
              |         |            |         |         |           |
   1 MGASGQYVRARIKGAYYATPVDPVTNQ...PTAPKDFSSGFWDFNDGTTQGFGVNPDSPIT..AI
   2 LSLSGEYVRARIKGAKY-EPIDRT---...-----RYTKVLWDFNDGTKQGFGVNSDSPNKe.AI
   3 LSLSGEYVRARIKGAKY-EPIDRT---...-----RYTKVLWDFNDGTKQGFGVNSDSPNKe.AI
   4 LSVSGEYARARIKGIKY-EPIERS---...--EKEEFTTNVWDFNDGTTQGFGINGDSPIKadSI
   5 LSVSGEYVRSRILGEEY-QPIDRT---...--PREEFSEVIWDFNDGTTQGFVQNSDSPL-..DV
   6 LTTSGQYVRARIKGAYYATPVDPVTNQ...PTAPKDFSSGFWDFNDGTTQGFGVNPDSPIT..AI
   7 -------------GTEVEIPVVHD---...---PKGEAVLPSVFEDGTRQGWDWAGESGVKt.AL
   8 -------------GTEVEIPVVHD---...---PKGEAVLPSVFEDGTRQGWDWAGESGVKt.AL
   9 -------------GTEVEIPVVHD---...---PKGEAVLPSVFEDGTRQGWDWAGESGVKt.AL
  10 -------------GKIVEIPVVHS---...---PKGDAALPSNFEYGTRQGWDWAGESGVKt.AL
  11 -------------GKIVEIPVVHS---...---PKGDAALPSNFEYGTRQGWDWAGESGVKt.AL
  12 LSLSGEYVRARIKGIEY-TPIDRT---...-----KFTKLVWDFNDGTTQGFQVNGDSPNKe.SI
  13 LSISGEYVRARIKGIAY-QPIKRDNKIkegENAPLGEKVLPSTFEDDTRQGWDWDGPSGVKg.PI
  14 LSLSGEYVRARIKGVNY-EPIDRT---...-----KYTKVLWDFNDGTKQGFGVNGDSPVE..DV
  15 LSLSGEYVRARIKGVNY-EPIDRT---...-----KYTKVLWDFNDGTKQGFGVNGDSPVE..DV
  16 LSLSGEYVRARIKGVNY-EPIDRT---...-----KYTKVLWDFNDGTKQGFGVNGDSPVE..DV
  17 -------------GTEIEIEVIHD---...---EKGTATLPSTFEDGTRQGWDWHTESGVKt.AL
  18 ----------------VPEPVEHD---...---TKGDSALPSDFEDGTRQGWEWDSESAVRt.AL
  19 ---------------VVEAPVEHA---...---PIGKATLPSTFEDSTRQDWAWDATSGVQs.AL


              70        80        90          100       110         120
              |         |         |            |         |           |
   1 NVENANNALKISNLNSKGSNDLSEGNFWAN...VRISADIWGQSINIYGDTKLTMDVI..APTPV
   2 EVENENGTLRISGLNV--SNDLSDGNFWAN...FRLSANGWGKSVDILGAEKLTMDVI..VDEPT
   3 EVENENGTLRISGLNV--SNDLSDGNFWAN...VRLSANGWGKSVDILGAEKLTMDVI..VDEPT
   4 TLANEKNALKITGLNN--SNDLTEGNYWAN...VRLSADGTSNKPNIFGAEKLTMDVI..TAAPA
   5 TIENVNDALQITGLDESNAIAGEEEDYWSN...VRISADEWEETFDILGAEELSMDVV..VDDPT
   6 NVENANNALKISNLNSKGSNDLSEGNFWAN...VRISADIWGQSINIYGDTKLTMDVI..APTPV
   7 TIEEANGSNALSW--EFGYPEVKPSDNWATaprLDFWKSDLVRGENDYVTFDFYLDPV..RATEG
   8 TIEEANGSNALSW--EFGYPEVKPSDNWATaprLDFWKSDLVRGENDYVTFDFYLDPV..RATEG
   9 TIEEANGSNALSW--EFGYPEVKPSDNWATaprLDFWKSDLVRGENDYVTFDFYLDPV..RATEG
  10 TIEEANGSQALSW--EFGYPEVKPSDNWASaprLDFHKDNLVRGENDYVAFDFYIDPA..RATEG
  11 TIEEANGSQALSW--EFGYPEVKPSDNWASaprLDFHKDNLVRGENDYVAFDFYIDPA..RATEG
  12 TLSNNNDALQIEGLNV--SNDISEGNYWDN...VRLSADGWSENVDILGATELTIDVI..VEEPT
  13 TIESANGSKALSF--NVEYPEKKPQDGWATaarLILKDINVERGNNKYLAFDFYLKPD..RASKG
  14 VIENEAGALKLSGLDA--SNDVSEGNYWAN...ARLSADGWGKSVDILGAEKLTMDVI..VDEPT
  15 VIENEAGALKLSGLDA--SNDVSEGNYWAN...ARLSADGWGKSVDILGAEKLTMDVI..VDEPT
  16 VIENEAGALKLSGLDA--SNDVSEGNYWAN...ARLSADGWGKSVDILGAEKLTMDVI..VDEPT
  17 TIEEANGSNALSW--EYAYPEVKPSDGWATaprLDFWKDELVRGTSDYISFDFYIDAV..RASEG
  18 TIEEANGSNALSW--EYAYPEVKPSDDWATaprLTLYKDDLVRGDYEFVAFDFYIDPIedRATEG
  19 TIKDANESKAISW--EVKYPEVKPVDGWASaprIMLGNVNTTRGNNKYLTFDFYLKPT..QASKG


             130        140       150           160       170       180
              |          |         |             |         |         |
   1 NVSIAAIPQSSTHG.WGNPTRARIVWTNNFVA....QTDGTYKATLTISTNDSPNFNTIATDAAD
   2 TVAIAAIPQSTKHG.WANPERSVKVTEADFVK....QDDGKYKALLTITGDDAPNLKNIGFDDEN
   3 TVAIAAIPQSTKHG.WANPERSVKVTEADFVK....QDDGKYKALLTITGDDAPNLKNIGKDDEN
   4 TVSIAAIPQSSTHG.WANPTRAIAVKPADFVK....QEDGTYKAVLTITPADSPNFDSIAKDSKD
   5 TVAIAAIPQSSAHE.WANASNSVLITEDDFEE....QEDGTYKALLTITGEDAPNLTNIAEDPEG
   6 NVSIAAIPQSSTHG.WGNPTRAIRVWTNNFVA....QTDGTYKATLTISTNDSPNFNTIATDAAD
   7 AMNINLVFQPPTNGyWVQAPKTYTINFDELEEpn..QVNGLYHYEVKI------NVRDITNIQDD
   8 AMNINLVFQPPTNGyWVQAPKTYTINFDELEEan..QVNGLYHYEVKI------NVRDITNIQDD
   9 AMNINLVFQPPTNGyWVQAPKTYTINFDELEEan..QVNGLYHYEVKI------NVRDITNIQDD
  10 AMNINLVFQPPANGyWVQAPKTFTINFEELEEan..QVNGLYHYEVKI------NVRDIANIQDD
  11 AMNINLVFQPPANGyWVQAPKTFTINFEELEEan..QVNGLYHYEVKI------NVRDIANIQDD
  12 TVSIAAIPQGPAAG.WANPTRAIKVTEDDFES....FGDG-YKALVTITSEDSPSLETIATSPED
  13 MIQMFLAFSPPSLGyWAQVQDSFNIDLGKTVKckkdRRTEVYKFNVFF---DLDKIQDNKVLSPD
  14 TVSIAAIPQGPSAN.WVNPNRAIKVEPTNFVP....LGDK-FKAELTITSADSPSLEAIAMHAEN
  15 TVSIAAIPQGPSAN.WVNPNRAIKVEPTNFVP....LGDK-FKAELTITSADSPSLEAIAMHAEN
  16 TVSIAAIPQGPSAN.WVNPNRAIKVEPTNFVP....LEDK-FKAELTITSADSPSLEAIAMHAEN
  17 AISINAVFQPPANGyWQEVPTTFEIDLTELDSatv.TSDELYHYEVKI------NIRDIEAITDD
  18 AIDINLIFQPPAAGyWAQASETFEIDLEELDSatv.TDDGLYHYEVEI---------NIEDIEND
  19 SLTISLAFAPPSLGfWAQATGDVNIPLSSLSKmkk.TTDGLYHFQVKY---DLDKINDGKVLTAN


               190           200      
                |             |      
   1 SVVTNM.IL.FVGSN.SDN...ISLDNIKFTK
   2 NNMNNI.IL.FVGTEaADV...IYLDNIKVT-
   3 NNMNNI.IL.FVGTEaADV...IYLDNIKVT-
   4 STMTNI.IL.FVGAD.TDV...ISLDNITV--
   5 SELNNI.IL.FVGTEnADV...ISLDNITVT-
   6 SVVTNM.IL.FVGSN.SDN...ISLDNIKFTK
   7 TLLRNMmII.FADVE.SDFagrVFVDNVRF--
   8 TLLRNMmII.FADVE.SDFagrVFVDNVRF--
   9 TLLRNMmII.FADVE.SDFagrVFVDNVRF--
  10 TVLRNM.ILiFADVQ.SDFagrVFVDNVRF--
  11 TVLRNM.ILiFADVQ.SDFagrVFVDNVRF--
  12 NTMSNI.IL.FVGTEdADV...ISLDNITV--
  13 TLLRDI.IVvIADGN.SDFkgkMYIDNVRFT-
  14 NNINNI.IL.FVGTEgADV...IYLDNIKV--
  15 NNINNI.IL.FVGTEgADV...IYLDNIKV--
  16 NNINNI.IL.FVGTEgADV...IYLDNIKV--
  17 TELRNL.LLiFADED.SDFagrVFVDNVRF--
  18 IELRNL.MLiFADDE.SDFagrVFLDNVRM--
  19 TVLRDItIV.VADGN.SDFpgtMYLDNIRF--