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:

- T0205 At2g34160, Arabidopsis
- gi|18403464|ref|NP_565781.1|_1:130 expressed protein [Arabidopsis thaliana]
- gi|25370772|pir||B84753 hypothetical protein At2g34160 [imported] - Arabidopsis thaliana [Taxonomy]
- gi|2342735|gb|AAB67633.1| expressed protein [Arabidopsis thaliana]
- gi|21536653|gb|AAM60985.1| unknown [Arabidopsis thaliana]
- gi|26450089|dbj|BAC42164.1| unknown protein [Arabidopsis thaliana]
- gi|18397011|ref|NP_564325.1|_1:130 expressed protein [Arabidopsis thaliana]
- gi|25370773|pir||A86415 hypothetical protein F28N24.7 - Arabidopsis thaliana [Taxonomy]
- gi|9502415|gb|AAF88114.1| Unknown protein [Arabidopsis thaliana]
- gi|15529270|gb|AAK97729.1| At1g29250/F28N24_8 [Arabidopsis thaliana]
- gi|16974409|gb|AAL31130.1| At1g29250/F28N24_8 [Arabidopsis thaliana]
- gi|21553922|gb|AAM63005.1| unknown [Arabidopsis thaliana]
- gi|46390081|dbj|BAD15498.1|_2:139 unknown protein [Oryza sativa (japonica cultivar-group)]
- gi|34910240|ref|NP_916467.1|_4:150 OSJNBa0089K24.4 [Oryza sativa (japonica cultivar-group)]
- gi|15128221|dbj|BAB62549.1| OSJNBa0089K24.4 [Oryza sativa (japonica cultivar-group)]
- gi|15229322|ref|NP_187113.1|_32:141 expressed protein [Arabidopsis thaliana]
- gi|6175166|gb|AAF04892.1| unknown protein [Arabidopsis thaliana]
- gi|38454036|gb|AAR20712.1| At3g04620 [Arabidopsis thaliana]
- gi|38604012|gb|AAR24749.1| At3g04620 [Arabidopsis thaliana]
- gi|15029401|gb|AAK81869.1|_3:114 unknown [Leishmania infantum]
- gi|8745040|emb|CAB95258.1|_3:114 conserved hypothetical protein L6293.01 [Leishmania major]
- gi|13751124|emb|CAC37138.1| conserved hypothetical protein [Leishmania major]
- gi|15679480|ref|NP_276597.1|_5:91 conserved protein [Methanothermobacter thermautotrophicus]
- gi|7482138|pir||F69064 conserved hypothetical protein MTH1483 - Methanobacterium thermoautotrophicum (strain Delta H) [Taxonomy]
- gi|2622599|gb|AAB85958.1| conserved protein [Methanothermobacter thermautotrophicus str. Delta H]
- gi|46397799|sp|O27527|ALBA_METTH_4:90 DNA/RNA-binding protein Alba [Taxonomy]
- gi|15921554|ref|NP_377223.1|_6:97 99aa long hypothetical reverse gyrase [Sulfolobus tokodaii str. 7]
- gi|34582331|sp|Q971T8|ALB1_SULTO DNA/RNA-binding protein Alba 1 [Taxonomy]
- gi|15622340|dbj|BAB66332.1| 99aa long hypothetical reverse gyrase [Sulfolobus tokodaii str. 7]
- gi|18978253|ref|NP_579610.1|_4:90 hypothetical protein PF1881 [Pyrococcus furiosus DSM 3638]
- gi|34582318|sp|Q8TZV1|ALBA_PYRFU DNA/RNA-binding protein Alba [Taxonomy]
- gi|18894072|gb|AAL82005.1| hypothetical protein [Pyrococcus furiosus DSM 3638]
- gi|14520610|ref|NP_126085.1|_4:90 conserved hypothetical protein [Pyrococcus abyssi GE5]
- gi|34582344|sp|Q9V1N3|ALBA_PYRAB DNA/RNA-binding protein Alba [Taxonomy]
- gi|7514537|pir||E75154 conserved hypothetical protein PAB7094 - Pyrococcus abyssi (strain Orsay) [Taxonomy]
- gi|5457826|emb|CAB49316.1| Conserved hypothetical protein, DUF78 family [Pyrococcus abyssi]
- gi|14591589|ref|NP_143671.1|_4:90 hypothetical protein PHS053 [Pyrococcus horikoshii OT3]
- gi|34582290|sp|O74101|ALBA_PYRHO DNA/RNA-binding protein Alba [Taxonomy]
- gi|7519402|pir||A71196 hypothetical protein PHS053 - Pyrococcus horikoshii [Taxonomy]
- gi|46397339|sp|P60848|ALB1_SULSH_6:96 DNA/RNA-binding protein Alba 1 (Ssh10b) [Taxonomy]
- gi|46397340|sp|P60849|ALB1_SULSO DNA/RNA-binding protein Alba 1 (Sso10b) [Taxonomy]
- gi|7484125|pir||T29101 hypothetical protein - Sulfolobus shibatae [Taxonomy]
- gi|1679874|emb|CAA67066.1| unknown [Sulfolobus shibatae]
- gi|10697160|emb|CAC12668.1| putative histone-like protein [Sulfolobus solfataricus]
- gi|20094152|ref|NP_613999.1|_5:91 Archaea-specific DNA-binding protein [Methanopyrus kandleri AV19]
- gi|34582317|sp|Q8TXF9|ALB1_METKA DNA/RNA-binding protein Alba 1 [Taxonomy]
- gi|19887165|gb|AAM01929.1| Archaea-specific DNA-binding protein [Methanopyrus kandleri AV19]
- gi|11499538|ref|NP_070780.1|_4:88 conserved hypothetical protein [Archaeoglobus fulgidus DSM 4304]
- gi|34582288|sp|O28323|ALB2_ARCFU DNA/RNA-binding protein Alba 2 (Af1) [Taxonomy]
- gi|7483187|pir||C69494 conserved hypothetical protein AF1956 - Archaeoglobus fulgidus [Taxonomy]
- gi|34810782|pdb|1NFH|A Chain A, Structure Of A Sir2 Substrate, Alba, Reveals A Mechanism For Deactylation-Induced Enhancement Of Dna-Binding [Taxonomy]
- gi|34810783|pdb|1NFH|B Chain B, Structure Of A Sir2 Substrate, Alba, Reveals A Mechanism For Deactylation-Induced Enhancement Of Dna-Binding [Taxonomy]
- gi|34810784|pdb|1NFJ|A Chain A, Structure Of A Sir2 Substrate, Alba, Reveals A Mechanism For Deactylation-Induced Enhancement Of Dna-Binding [Taxonomy]
- gi|2648586|gb|AAB89299.1| conserved hypothetical protein [Archaeoglobus fulgidus DSM 4304]
- gi|15897841|ref|NP_342446.1|_9:99 DNA binding protein SSO10b [Sulfolobus solfataricus P2]
- gi|25366651|pir||E90247 DNA binding protein SSO10b [imported] - Sulfolobus solfataricus [Taxonomy]
- gi|24158634|pdb|1H0X|A Chain A, Structure Of Alba: An Archaeal Chromatin Protein Modulated By Acetylation [Taxonomy]
- gi|24158635|pdb|1H0X|B Chain B, Structure Of Alba: An Archaeal Chromatin Protein Modulated By Acetylation [Taxonomy]
- gi|24158636|pdb|1H0Y|A Chain A, Structure Of Alba: An Archaeal Chromatin Protein Modulated By Acetylation [Taxonomy]
- gi|13814144|gb|AAK41236.1| DNA binding protein SSO10b [Sulfolobus solfataricus P2]
- gi|11498672|ref|NP_069900.1|_3:88 conserved hypothetical protein [Archaeoglobus fulgidus DSM 4304]
- gi|34582289|sp|O29195|ALB1_ARCFU DNA/RNA-binding protein Alba 1 (Af2) [Taxonomy]
- gi|7483085|pir||C69383 conserved hypothetical protein AF1067 - Archaeoglobus fulgidus [Taxonomy]
- gi|2649521|gb|AAB90173.1| conserved hypothetical protein [Archaeoglobus fulgidus DSM 4304]
- gi|15668385|ref|NP_247181.1|_3:86 conserved hypothetical protein [Methanocaldococcus jannaschii DSM 2661]
- gi|2495857|sp|Q57665|ALBA_METJA DNA/RNA-binding protein Alba [Taxonomy]
- gi|2128181|pir||E64326 hypothetical protein MJ0212 - Methanococcus jannaschii [Taxonomy]
- gi|40889143|pdb|1NH9|A Chain A, Crystal Structure Of A Dna Binding Protein Mja10b From The Hyperthermophile Methanococcus Jannaschii [Taxonomy]
- gi|1498988|gb|AAB98197.1| conserved hypothetical protein [Methanocaldococcus jannaschii DSM 2661]
- gi|20094525|ref|NP_614372.1|_4:90 Archaea-specific DNA-binding protein [Methanopyrus kandleri AV19]
- gi|34582316|sp|Q8TWE6|ALB2_METKA DNA/RNA-binding protein Alba 2 [Taxonomy]
- gi|19887640|gb|AAM02302.1| Archaea-specific DNA-binding protein [Methanopyrus kandleri AV19]
- gi|41615153|ref|NP_963651.1|_4:89 NEQ363 [Nanoarchaeum equitans Kin4-M]
- gi|46395650|sp|P60851|ALBA_NANEQ DNA/RNA-binding protein Alba [Taxonomy]
- gi|40068877|gb|AAR39212.1| NEQ363 [Nanoarchaeum equitans Kin4-M]
- gi|6729010|gb|AAF27007.1|_15:116 unknown protein [Arabidopsis thaliana]
- gi|32526671|dbj|BAC79194.1|_505:605 chloroplast nucleoid DNA-binding protein -like protein [Oryza sativa (japonica cultivar-group)]
- gi|14601649|ref|NP_148190.1|_7:97 hypothetical protein APE1823 [Aeropyrum pernix K1]
- gi|34582348|sp|Q9YAX2|ALB2_AERPE DNA/RNA-binding protein Alba 2 [Taxonomy]
- gi|7516755|pir||E72567 hypothetical protein APE1823 - Aeropyrum pernix (strain K1) [Taxonomy]
- gi|5105513|dbj|BAA80826.1| 102aa long hypothetical protein [Aeropyrum pernix K1]
- gi|45502131|emb|CAF74922.1|_3:89 DNA-binding protein AlbA [Methanococcus voltae]
- gi|14601658|ref|NP_148199.1|_6:96 hypothetical protein APES060 [Aeropyrum pernix K1]
- gi|34582347|sp|Q9YAW1|ALB1_AERPE DNA/RNA-binding protein Alba 1 [Taxonomy]
- gi|7517335|pir||H72568 hypothetical protein APES060 - Aeropyrum pernix (strain K1) [Taxonomy]
- gi|5105524|dbj|BAA80837.1| 98aa long hypothetical protein [Aeropyrum pernix K1]
- gi|22405840|ref|ZP_00000705.1|_4:89 COG1581: Archaeal DNA-binding protein [Ferroplasma acidarmanus]
- gi|23619387|ref|NP_705349.1|_9:68 hypothetical protein [Plasmodium falciparum 3D7]
- gi|23615594|emb|CAD52586.1| hypothetical protein [Plasmodium falciparum 3D7]
- gi|15921556|ref|NP_377225.1|_5:87 90aa long conserved hypothetical protein [Sulfolobus tokodaii str. 7]
- gi|34582330|sp|Q971T6|ALB2_SULTO DNA/RNA-binding protein Alba 2 [Taxonomy]
- gi|15622342|dbj|BAB66334.1| 90aa long conserved hypothetical protein [Sulfolobus tokodaii str. 7]

              10             20        30        40           50       
              |              |         |         |            |       
   1 SEEITDGVNNMNLATDS.....QKKNRIQVSNTKKPLFFYVNLAK.RYMQ..QYNDVELSALGMA
   2 MEEITDGVNNMNLATDS.....QKKNRIQVSNTKKPLFFYVNLAK.RYMQ..QYNDVELSALGMA
   3 MEEITEGVNNMNLAVDT.....QKKNRIQVSNTKKPLFFYVNLAK.RYMQ..QYTDVELSALGMA
   4 -EEVTEAVGNLTIAAGEa11eaHKKNRIQVSNTKKPLFFYVNLAK.RYMQ..LHNEVELSALGMA
   5 -EEITEGVRNLAVEGEPa20agSSSNRIQVSNTKKPLFFYVNLAK.RYMQ..QHGDVELSALGMA
   6 --------------VET.....HKKNRIQVSNTKKPLFFYVNLAK.RYIQ..QHNEVELSALGMA
   7 --------------AEN.....GGNAIVRVSS-NKRKFGYVDYTKhRLHE..GYPEVIISALGTA
   8 --------------AEN.....GGNAIVRVSS-NKRKFGYVDYTKhRLHE..GYPEVIVSALGTA
   9 -----------------.....--ENVVYIG--NKPVMNYVLAVV.TQMNg.GTSEVILKARGIA
  10 -----------------.....--ENVVYIG--NKPVMNYVLAVV.TQMNg.GTSEVILKARGIA
  11 ---------------TP.....TPSNVVLVG--KKPVMNYVLAALtLLNQ..GVSEIIIKARGRA
  12 -----------------.....--EHVVYIG--KKPVMNYVLAVItQFNE..GAKEVSIKARGRA
  13 -----------------.....--EHVVYIG--KKPVMNYVLAVItQFHE..GAKEVSIKARGRA
  14 -----------------.....--EHVVYIG--KKPVMNYVLAVItQFHE..GAKEVSIKARGRA
  15 ----------------P.....TPSNVVLIG--KKPVMNYVLAALtLLNQ..GVSEIVIKARGRA
  16 -----------------.....--ENVVYVG--SKPVMNYVLACItQFNE..GANEVRIKARGRA
  17 -----------------.....---HVVYVG--NKPVMNYVLATLtQLNE..GADEVVIKARGRA
  18 ----------------P.....TPSNVVLIG--KKPVMNYVLAALtLLNQ..GVSEIVIKARGRA
  19 -----------------.....--ENSVFVG--NKPVMNYVLAVLtQFNS..GATEVSIKARGRA
  20 -----------------.....---NVVLIG--KKPVMNYVVAVL.TQLT..SNDEVIIKARGKA
  21 -----------------.....--ENVIYVG--NKPVTNYVLAVMtQFSE..GADEVKLVARGRA
  22 -----------------.....-----VFIG--KKPLTNYVMAVVmQFMQ..GANEVVIKARGRN
  23 ----------------P.....INENEIRITS-KGLIRNYISYAT.SLLQekSVKDIVLKAMGQA
  24 ----------------P.....IKENEIRIT-TQGRMRNYITYAT.TLLQdkGSDEVVFKAMGRA
  25 -----------------.....---PEVRIG--RKPVMNYVLAILtTLMEq.GTNQVVVKARGRN
  26 -----------------.....---NSIYVG--DKGVMNYVTAVM.TLFDkpDINEVILKARGKS
  27 -------------SIEP.....QKPNTILVG--RKPTINYVMAAL.KLLNeeGAPEVVIKARGRN
  28 -----------------.....--ENIIFVG--KKPTMNYVLAIV.TQFNnsDMPRIVIKARGKA
  29 ----------------T.....KLENEIRISY-KSDALDYVYKAI.VLFE..TYDEIILSGVGKA
  30 -----------------.....-KPNEILISR-TKRVEDYVLDVIvMFNQ..GYDEVELKGVGNS


       60        70             80           90            100       11
       |         |              |            |              |         
   1 IATVVTVTEILKNNGF.....AVEKKIMTSIVDIK...DDARGRP.....VQKAKIEITLVKSEK
   2 IATVVTVTEILKNNGF.....AVEKKIMTSTVDIK...DDARGRP.....VQKAKIEITLVKSEK
   3 IATVVTVAEILKNNGF.....AVEKKIMTSTVDIK...DDSRGRP.....VQKAKIEITLAKSEK
   4 IATVVTVAEILKNNGL.....AVEKKIMTSTVDVK...DDSRSRP.....MQKAKIEIVLGKTDK
   5 IATVVTVAEILKNNGF.....AVEKKIRTSTVEIN...DESRVRP.....LQKAKIEIVLEKSEK
   6 ITTVVTISEILKNNGL.....ATEKKVLTSTVGMK...DETKGKM.....VQKAKIEIVLGKSDK
   7 IADAVSVVELLKNQGV.....VEVKKICTSRAQFD...D---VRS.....TTTDKIEVVVVKSPE
   8 IADAVSVVELLKNQGV.....VEVKKICTSRAQFD...D---VRS.....TTTDKIEVVVVKSPE
   9 ISRAVDVAEIVRNRFIpdiq.IENIDICTEEIIGN...E---GTA.....TNVSAIEIQLRK---
  10 ISRAVDVAEIVRNRFIpdiq.IENIDICTEEIIGN...E---GTA.....TNVSAIEIQLRK---
  11 ISKAVDTVEIVRNRFLpdkieVKEIRIGSQVVTSQ...D---GRQ.....SRVSTIEIAIRK---
  12 ISRAVDVAEIVRNRFLkdtvdIKEIKIGTEELPTA...D---GRT.....TNTSTIEIVLE----
  13 ISRAVDVAEIVRNRFLkddvdVKEIKIGTEELPTA...D---GRT.....TNTSTIEIVLA----
  14 ISRAVDVAEIVRNRFLkddvdVKEIKIGTEELPTA...D---GRT.....TNTSTIEIVLA----
  15 ISKAVDTVEIVRNRFLpdkieIKEIRVGSQVVTSQ...D---GRQ.....SRVSTIEIAIRK---
  16 ISRAVDVAEIVRNRFMpeve.VKDIKIGTEELETE...E---GDT.....VNVSTIEIVLEK---
  17 ISRAVDVAEIVRNRFMpgvk.VKEIKIDTEELESE...Q---GRR.....SNVSTIEIVLA----
  18 ISKAVDTVEIVRNRFLpdkieIKEIRVGSQVVTSQ...D---GRQ.....SRVSTIEIAIRK---
  19 ISRAVDVAEIVRKRFLpdvd.VKDIKISTEQIDSE...Q----GT.....ANVSAIEIILAK---
  20 INKAVDVAEMIRNRFIkdik.IKKIEIGTDKVKNP...D---GRE.....VNVSTIEIVLA----
  21 ISRAVDVAEFIRNNVMpeve.VKDIEIGTEEIETE...E---GDT.....ISVSTIAITLAK---
  22 ISRAVDVAERVRKRFL.....AGQVDVGDIKIDSEevvDPATGQK.....RTVSTIEIKLVK---
  23 ISKTVAISEILKNKIP.....GLHQDIAISSISIT...DVWEPTEeg9ltRHVSMISITLSLSE-
  24 INKTVMIAELIKRRIV.....GLHQNTTTGSTDIT...DMWEPLEeg9ttRHVSMITITLSKK--
  25 INRAVDAVEIVRKRFAknie.IKDIKIDSQEIEVQt..PEGQTRT.....RRVSSIEICLEK---
  26 IVKAVDVEEVLKNRVMksvn.IKNIALGTEILKSN...T---GKE.....INVSTIEITISK---
  27 ICNAVDTVEMLKNLFIknlv.IKKVNIYSESLDSE...G-----K.....KKVSAIEIVVA----
  28 ISKAVDIAEITKHKFIqtak.YESIKLDTETLEGE...N----GP.....SNVSSIEIILA----
  29 ISSVVNVAEMVKRRAK.....GLHQ----------...-------.....---------------
  30 IYKAVEVYNQLKDR--.....-LGDGIILEKADIG...SEVKDR-.....RRISYISIKLK----


      0       120       130
     |         |         |
   1 FDELMAAANEEKEDAETQVQN
   2 FDELMAAANEEKEDAEAQVQN
   3 FDELMAAANEEKEAAEAQEQN
   4 FDELMAAAAEEREAAAAEA--
   5 FDELMAAAAEEREAAEAEE--
   6 FDSLVPPVTNGKTPE------
   7 FDAIYEQQQKDREIAKARAE-
   8 FDAIYEQQQKDREIAKARAE-
   9 ---------------------
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