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, 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:

- YGR023W MTL1 SGDID:S0003255, Chr VII from 529258-530913
- gi|6321459|ref|NP_011537.1|_1:551 Mid-Two Like 1; Mtl1p [Saccharomyces cerevisiae]
- gi|1723652 sp|P53214|YG1F_YEAST HYPOTHETICAL 57.5 KD PROTEIN IN VMA7-RPS25A INTERGENIC REGION
- gi|2132585|pir||S64314 probable membrane protein YGR023w - yeast (Saccharomyces cerevisiae)
- gi|1322994|emb|CAA97006.1| ORF YGR023w [Saccharomyces cerevisiae]
- gi|6323363|ref|NP_013436.1|_51:376 Protein required for mating; Mid2p [Saccharomyces cerevisiae]
- gi|547907 sp|P36027|MID2_YEAST MATING PROCESS PROTEIN MID2 (SERINE-RICH PROTEIN SMS1) (PROTEIN KINASE A INTERFERENCE PROTEIN)
- gi|1078113|pir||S52137 MID2 protein - yeast (Saccharomyces cerevisiae)
- gi|479041|dbj|BAA06220.1| Mid2p [Saccharomyces cerevisiae]
- gi|662143|gb|AAB64527.1| Mid2p: Mating process protein [Saccharomyces cerevisiae]
- gi|676885|dbj|BAA06230.1| serine-rich transmembrane protein [Saccharomyces cerevisiae]
- gi|1093610|prf||2104276A integral membrane protein
- gi|1093947|prf||2105188A Ser-rich transmembrane protein

              10        20        30        40        50        60     
              |         |         |         |         |         |     
   1 MASCNPTRKKSSASSLSMWRTILMALTTLPLSVLSQELVPANSTTSSTAPSITSLSAVESFTSST
   2 MASCNPTRKKSSASSLSMWRTILMALTTLPLSVLSQELVPANSTTSSTAPSITSLSAVESFTSST
   3 -----------------------------------------------------------------


         70        80        90       100       110       120       130
         |         |         |         |         |         |         |
   1 DATSSASLSTPSIASVSFTSFPQSSSLLTLSSTLSSELSSSSMQVSSSSTSSSSSEVTSSSSSSS
   2 DATSSASLSTPSIASVSFTSFPQSSSLLTLSSTLSSELSSSSMQVSSSSTSSSSSEVTSSSSSSS
   3 -----------------------------------------------------------------


             140       150       160       170       180       190     
              |         |         |         |         |         |     
   1 ISPSSSSSTIISSSSSLPTFTVASTSSTVASSTLSTSSSLVISTSSSTFTFSSESSSSLISSSI.
   2 ISPSSSSSTIISSSSSLPTFTVASTSSTVASSTLSTSSSLVISTSSSTFTFSSESSSSLISSSI.
   3 ------------------------------------------------------SSSSILSSSMv


          200       210       220       230       240       250       2
           |         |         |         |         |         |        
   1 .STSVSTSSVYVPSSSTSSPPSSSSELTSSSYSSSSSSSTLFSYSSSFSSSSSSSSSSSSSSSSS
   2 .STSVSTSSVYVPSSSTSSPPSSSSELTSSSYSSSSSSSTLFSYSSSFSSSSSSSSSSSSSSSSS
   3 sSSSADSSSL---TSSTSS--RSLVSHTSSSTSIASISFTSFSFSSDSSTSSSSSASSDSSSSSS


      60       270       280       290        300       310       320  
      |         |         |         |          |         |         |  
   1 SSSSSSYFTLSTSSSSSIYSSSSYPSFSSSSSS.NPTSSITSTSASSSITPASEYSNLAKTITSI
   2 SSSSSSYFTLSTSSSSSIYSSSSYPSFSSSSSS.NPTSSITSTSASSSITPASEYSNLAKTITSI
   3 FSISSTSATSESSTSSTQTSTSSSSSLSSTPSSsSSPSTITSAPSTSS-TPSTTAYNQGSTITSI


           330       340       350       360       370       380       
            |         |         |         |         |         |       
   1 IEGQTILSNYYTTITYSPTASASSGKNSHHSGLSKKNRNIIIGCVVGIGAPLILILLILIYMFCV
   2 IEGQTILSNYYTTITYSPTASASSGKNSHHSGLSKKNRNIIIGCVVGIGAPLILILLILIYMFCV
   3 INGKTILSNHYTTVTYTPSATADSSNKSKSSGLSKKNRNIVIGCVVGIGVPLILVILALIYMFCI


      390       400       410       420       430       440       450  
       |         |         |         |         |         |         |  
   1 QPKKTDFIDSDGKIVTAYRSNIFTKIWYFLLGKKIGETERFSSDSPIGSNNIQNFGDIDPEDILN
   2 QPKKTDFIDSDGKIVTAYRSNIFTKIWYFLLGKKIGETERFSSDSPIGSNNIQNFGDIDPEDILN
   3 QSSRTDFIDSDGKVVTAYRANKFTKWWYMLLGKKV--SDEYHSDSPLGGS---------------


           460       470       480       490       500       510       
            |         |         |         |         |         |       
   1 NDNPYTPKHTNVEGYDDDDDDDANDENLSSNFHNRGIDDQYSPTKSASYSMSNSNSQDYNDADEV
   2 NDNPYTPKHTNVEGYDDDDDDDANDENLSSNFHNRGIDDQYSPTKSASYSMSNSNSQDYNDADEV
   3 --------ASSAGGLDLDEADDVMEQ--SSLFDVRIRD--------SDSVLPNANTADHNNTNS-


      520       530       540       550 
       |         |         |         | 
   1 MHDENIHRVYDDSEASIDENYYTKPNNGLNITNY
   2 MHDENIHRVYDDSEASIDENYYTKPNNGLNITNY
   3 -GGEPINSSV-ASNDIIEEKFYDEQGNELSPRNY