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:

- T0094 CPDase, A. thaliana
- gi|7484882|pir||T05030_1:181 cyclic phosphodiesterase (EC 3.1.4.-) - Arabidopsis thaliana (Arabidopsis thaliana)
- gi|2065013|emb|CAA72363.1| (Y11650) cyclic phosphodiesterase [Arabidopsis thaliana] (Arabidopsis thaliana)
- gi|2832621|emb|CAA16750.1| (AL021711) putative protein [Arabidopsis thaliana] (Arabidopsis thaliana)
- gi|7268687|emb|CAB78895.1| (AL161549) putative protein [Arabidopsis thaliana] (Arabidopsis thaliana)
- gi|7484883|pir||T05031_17:189 cyclic phosphodiesterase homolog F13C5.110 - Arabidopsis thaliana (Arabidopsis thaliana)
- gi|2832622|emb|CAA16751.1| (AL021711) hypothetical protein [Arabidopsis thaliana] (Arabidopsis thaliana)
- gi|7268688|emb|CAB78896.1| (AL161549) hypothetical protein [Arabidopsis thaliana] (Arabidopsis thaliana)
- gi|7484882|pir||T05030_1:181 cyclic phosphodiesterase (EC 3.1.4.-) - Arabidopsis thaliana (Arabidopsis thaliana)
- gi|2065013|emb|CAA72363.1| (Y11650) cyclic phosphodiesterase [Arabidopsis thaliana] (Arabidopsis thaliana)
- gi|2832621|emb|CAA16750.1| (AL021711) putative protein [Arabidopsis thaliana] (Arabidopsis thaliana)
- gi|7268687|emb|CAB78895.1| (AL161549) putative protein [Arabidopsis thaliana] (Arabidopsis thaliana)
- gi|7484883|pir||T05031_17:189 cyclic phosphodiesterase homolog F13C5.110 - Arabidopsis thaliana (Arabidopsis thaliana)
- gi|2832622|emb|CAA16751.1| (AL021711) hypothetical protein [Arabidopsis thaliana] (Arabidopsis thaliana)
- gi|7268688|emb|CAB78896.1| (AL161549) hypothetical protein [Arabidopsis thaliana] (Arabidopsis thaliana)
- gi|540075|gb|AAA73459.1|_44:91 (U13207) large subunit ribosomal protein 29 [Euplotes crassus] (Euplotes crassus)
- gi|1093613|prf||2104279A ribosomal protein L29 [Euplotes crassus] (Euplotes crassus)
- gi|1350705|sp|P48161|RL2A_EUPCR_44:91 60S RIBOSOMAL PROTEIN L27A (L29) (Euplotes crassus)
- gi|6686226|sp|Q9X2H4|YI60_THEMA_95:164 HYPOTHETICAL PROTEIN TM1860 (Thermotoga maritima)
- gi|7446644|pir||E72201 conserved hypothetical protein - Thermotoga maritima (strain MSB8) (Thermotoga maritima)
- gi|4982445|gb|AAD36922.1|AE001823_4 (AE001823) conserved hypothetical protein [Thermotoga maritima] (Thermotoga maritima)
- gi|7959355|dbj|BAA96068.1|_47:90 (AB042856) 60S ribosomal protein L27a [Panax ginseng] (Panax ginseng)

              10        20        30             40         50         
              |         |         |              |          |         
   1 MEEVKKDVYSVWALPDEESEPRFKKLMEALRSEFTGP.....RFVPHVT.VAVSAY.LTADEAKK
   2 MEEVKKDVYSVWALPDEESEPRFKKLMEALRSEFTGP.....RFVPHVT.VAVSAY.LTADEAKK
   3 DDEEEKAMYAIWAVPEDDVEDRLQRLMEGLRSEFGGP.....AFDPHLTlVGPFPYkLTASEAKR
   4 MEEVKKDVYSVWALPDEESEPRFKKLMEALRSEFTGP.....RFVPHVT.VAVSAY.LTADEAKK
   5 DDEEEKAMYAIWAVPEDDVEDRLQRLMEGLRSEFGGP.....AFDPHLTlVGPFPYkLTASEAKR
   6 -------------------------------------.....-------.------.--------
   7 -------------------------------------.....-------.------.--------
   8 -----------------ENTDRLMKLYEELRNELSHHgf6eeKFVPHIT.IGRVKY.Y-PDKWEK
   9 -------------------------------------.....-------.------.--------


      60             70        80        90       100       110        
      |              |         |         |         |         |        
   1 MFE.....SACDGLKAYTATVDRVSTGTFFFQCVFLLLQTTPEVMEAGEHCKNHFNCSTTTPYMP
   2 MFE.....SACDGLKAYTATVDRVSTGTFFFQCVFLLLQTTPEVMEAGEHCKNHFNCSTTTPYMP
   3 MFK.....SACEGFKVYPATVDQVSAGTSYFQCLYVSLRHTVEVMNAAGHFMAHFKPFTGKFYVP
   4 MFE.....SACDGLKAYTATVDRVSTGTFFFQCVFLLLQTTPEVMEAGEHCKNHFNCSTTTPYMP
   5 MFK.....SACEGFKVYPATVDQVSAGTSYFQCLYVSLRHTVEVMNAAGHFMAHFKPFTGKFYVP
   6 ---.....---NVFKYHPGHI--------------------------GKHGMRHFHLMRNQYYCP
   7 ---.....---NVFKYHPGHI--------------------------GKHGMRHFHLMRNQYYCP
   8 LIEdi8ieVAVDRFKIYSSTL--------------------------------------------
   9 ---.....------KYHPGYF--------------------------GKVGMRYFHRLRNKFYCP


       120       130       140       150       160       170       180 
        |         |         |         |         |         |         | 
   1 ..HLSLLYAELTEEEKKNAQEKAYTLDSSLDGLSFRLNRLALCKTDTEDKTLETWETVAVCNLNP
   2 ..HLSLLYAELTEEEKKNAQEKAYTLDSSLDGLSFRLNRLALCKTDTEDKTLETWETVAVCNLNP
   3 ..HMSILYGDLTEREKKKALEKAYTLDSSLDGLNFKINRVALWITDAD---VGSWVKV-------
   4 ..HLSLLYAELTEEEKKNAQEKAYTLDSSLDGLSFRLNRLALCKTDTEDKTLETWETVAVCNLNP
   5 ..HMSILYGDLTEREKKKALEKAYTLDSSLDGLNFKINRVALWITDAD---VGSWVKV-------
   6 siNLSKLWSLVTEEERQKAQ---------------------------------------------
   7 siNLSKLWSLVTEEERQKAQ---------------------------------------------
   8 ..---------------------------------------------------------------
   9 vvNIDKLWSLLPQEAKEKA----------------------------------------------