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:

- YGL228W SHE10 SGDID:S0003197, Chr VII from 67597-69330
- gi|6321209|ref|NP_011286.1|_1:577 (NC_001139) Mrna (identified by a library screen) that causes growth arrest when overexpressed; She10p [Saccharomyces cerevisiae]
- gi|1723969 sp|P53075|YGX8_YEAST HYPOTHETICAL 66.9 KD PROTEIN IN SAP4-OST5 INTERGENIC REGION
- gi|2132570|pir||S64250 probable membrane protein YGL228w - yeast (Saccharomyces cerevisiae)
- gi|1322883|emb|CAA96945.1| (Z72750) ORF YGL228w [Saccharomyces cerevisiae]
- gi|14318564|ref|NP_116697.1|_1:504 (NC_001138) Hypothetical ORF; Yfr039cp [Saccharomyces cerevisiae]
- gi|1176016 sp|P43611|YFK9_YEAST Hypothetical 59.4 kDa protein in CDC26-SAP155 intergenic region
- gi|1084753|pir||S56294 probable membrane protein YFR039c - yeast (Saccharomyces cerevisiae)
- gi|836794|dbj|BAA09278.1| (D50617) YFR039C [Saccharomyces cerevisiae]

              10        20         30        40        50        60    
              |         |          |         |         |         |    
   1 MGKLIKLITTLTVLVSLLQY.CCEFNSGSISCERTQTLCHYTNPRVWNTYFSRNCELYKNKVSPG
   2 MGKLIKLITTLTVLVSLLQY.CCEFNSGSISCERTQTLCHYTNPRVWNTYFSRNCELYKNKVSPG
   3 MKAVFKVTTALLACVFIARYlVCQQNGLGSFATDLQPICRHTEFSVGSLFDSKLVEG-----SAV


          70        80        90       100       110       120       13
          |         |         |         |         |         |         
   1 FDIVARKYDTAVKPVIDDATVKVNKVAIQPAFKVIHSQCKKWNCGKYYQLVRSPMVKTRRFFFAK
   2 FDIVARKYDTAVKPVIDDATVKVNKVAIQPAFKVIHSQCKKWNCGKYYQLVRSPMVKTRRFFFAK
   3 SDYLVGKYSQSIKPLIERYPNSSLKR----------------IMGY--------------FYRFW


      0       140       150       160       170       180        190   
     |         |         |         |         |         |          |   
   1 YNAFVKPNLDKFFTAEFRSHLKERILKYKNIGHYYFTITSRCIKSKYDFIVGNTEEKL.MGKFKN
   2 YNAFVKPNLDKFFTAEFRSHLKERILKYKNIGHYYFTITSRCIKSKYDFIVGNTEEKL.MGKFKN
   3 YNIFSFLRLNELCCS-LHSKL-GPLLNHLRIAWYYLKPYTDNVKNVLENPFNSSTDWMkYGSFSA


          200       210       220       230       240       250       2
           |         |         |         |         |         |        
   1 KDTHGIHGSVTREPSSEDMVLTVSTMESDEEELTTTSTQTVVETITLDQEEASAVANHAHDDEAS
   2 KDTHGIHGSVTREPSSEDMVLTVSTMESDEEELTTTSTQTVVETITLDQEEASAVANHAHDDEAS
   3 DGTL---TKPIFETDSETE-----DYEDDENENEDEDEDEDEDDVGIEDENKEYEFDGVQDGHGN


      60               270       280       290       300       310     
      |                 |         |         |         |         |     
   1 TDV.....EGS...TDVNVNEQALLQEDFDMWSETILQKTQDVIQLFEKDVSKYINGKLVEEANH
   2 TDV.....EGS...TDVNVNEQALLQEDFDMWSETILQKTQDVIQLFEKDVSKYINGKLVEEANH
   3 SQLv13iiIGSnshAELETYEAESLKMEYEAWIKAIDSKIHSAMALLDSEIQSVFEAEVQNKSIE


        320       330       340       350       360       370       380
         |         |         |         |         |         |         |
   1 FKAKFQSLDDKSKKFFSKISLAINDIECVEGIDSETGKKIFFDKSGSTEISQYITRELVREYFNE
   2 FKAKFQSLDDKSKKFFSKISLAINDIECVEGIDSETGKKIFFDKSGSTEISQYITRELVREYFNE
   3 ITRNLDDLNTTVNEQLVFLDSKIKDINCTSKFDPVQNKIKYFDESGQVELEAYITKSSITSILKN


             390       400       410       420       430       440     
              |         |         |         |         |         |     
   1 TRSTLDELTNAMEKDLSEITDEIEKKVNAIREENVEVFEEWGDIIVNEWSKRMAYVDVINAHMGA
   2 TRSTLDELTNAMEKDLSEITDEIEKKVNAIREENVEVFEEWGDIIVNEWSKRMAYVDVINAHMGA
   3 YKIHLLDFEKSLFHSLDSFLTEMAKLAESIRLENVEVYEEWGDVMISQWSQRMAYMDVRGLHLED


        450       460       470       480       490       500       510
         |         |         |         |         |         |         |
   1 DDDTTLDEEKAKSSVNWKKFLKGKKQIIESRDKLAHHSADLSRVNAFRQKVQKKILSFTQESGEF
   2 DDDTTLDEEKAKSSVNWKKFLKGKKQIIESRDKLAHHSADLSRVNAFRQKVQKKILSFTQESGEF
   3 QYDPAYIEENH---SNWLRFMELKKKVISERNRLVKHDLDMTLILEWITKLKAD-----------


             520       530       540       550       560       570     
              |         |         |         |         |         |     
   1 LYILRSKANLQFQERERKERERKEREKAAAEEFQRQQELLRQQEEEDEEDVSYTSTSTITTTITM
   2 LYILRSKANLQFQERERKERERKEREKAAAEEFQRQQELLRQQEEEDEEDVSYTSTSTITTTITM
   3 --FQNTKNNIQDT--------FLQRMNT-ADTLFKNRELKEQLEEE-------------------


        
       
   1 TL
   2 TL
   3 --