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:

- T0487
- gi|81300343|ref|YP_400551.1|_355:498 hypothetical protein Synpcc7942_1534 [Synechococcus elongatus PCC 7942]
- gi|81169224|gb|ABB57564.1| conserved hypothetical protein [Synechococcus elongatus PCC 7942]
- gi|56752529|ref|YP_173230.1|_355:498 hypothetical protein syc2520_d [Synechococcus elongatus PCC 6301]
- gi|56687488|dbj|BAD80710.1| hypothetical protein [Synechococcus elongatus PCC 6301]
- gi|22298491|ref|NP_681738.1|_372:515 hypothetical protein tll0948 [Thermosynechococcus elongatus BP-1]
- gi|22294671|dbj|BAC08500.1| tll0948 [Thermosynechococcus elongatus BP-1]
- gi|86606806|ref|YP_475569.1|_351:492 Piwi domain protein [Synechococcus sp. JA-3-3Ab]
- gi|86555348|gb|ABD00306.1| Piwi domain protein [Synechococcus sp. JA-3-3Ab]
- gi|86610170|ref|YP_478932.1|_367:508 Piwi domain protein [Synechococcus sp. JA-2-3B'a(2-13)]
- gi|86558712|gb|ABD03669.1| Piwi domain protein [Synechococcus sp. JA-2-3B'a(2-13)]
- gi|55978251|ref|YP_145307.1|_323:463 hypothetical protein TTHB068 [Thermus thermophilus HB8]
- gi|55773424|dbj|BAD71864.1| conserved hypothetical protein [Thermus thermophilus HB8]
- gi|46255097|ref|YP_006009.1|_323:463 hypothetical protein TT_P0026 [Thermus thermophilus HB27]
- gi|46197946|gb|AAS82356.1| hypothetical protein TT_P0026 [Thermus thermophilus HB27]
- gi|170077638|ref|YP_001734276.1|_221:383 conserved hypothetical protein containing Piwi domain [Synechococcus sp. PCC 7002]
- gi|169885307|gb|ACA99020.1| conserved hypothetical protein containing Piwi domain [Synechococcus sp. PCC 7002]

              10        20          30         40        50            
              |         |           |          |         |            
   1 GRRAVSKPADALRVGFYRAQETALALLRL..DGAQ.GWPEFLRRALLRAFGASGASLRLH...TL
   2 NKQPVSKTADIRNKGCAKIGETSFGYLNL..YNNQlQYPLEVHKCLLEIANKNNLQLSLDqrrVL
   3 NKQPVSKTADIRNKGCAKIGETSFGYLNL..YNNQlQYPLEVHKCLLEIANKNNLQLSLDqrrVL
   4 NNKEVNQTARIKSFGCAKIGETKFGCLNLf.DNKP.EYPEEVHKCLLAIARSSGVQIKID...SY
   5 GRRPVENPARVRYRGCAKVGETKFACLNLy.DDKR.EYPSEVLNCLLEVAQKSGAEIEVD...FY
   6 GHRQVQNPARVRYQGCARVGETKFGLLNLd.DNKR.EYPTEVRKCLLEVAKKSGARVEID...FY
   7 GRRAVSKPADALRVGFYRAQETALALLRL..DGAQ.GWPEFLRRALLRAFGASGASLRLH...TL
   8 GRRAVSKPADALRVGFYRAQETALALLRL..DGAQ.GWPEFLRRALLRAFGASGASLRLH...TL
   9 -SKRIDKVFKSLDQGCFRVGEIKFGCINLldKNQD.GWSKFILQKLQKLATIHNINIDAN...LV


        60        70        80        90       100       110           
        |         |         |         |         |         |           
   1 ...HAHPSQGLAFREALRKAKEEGVQAVLVLTPPMAWEDRNRLKALLLREGLPSQILN.....VP
   2 ...SDYPQDDLDQQMFWQTWSSQGIKTVLVVMPWDSHHDKQKIRIQAIQAGIATQFM-.....VP
   3 ...SDYPQDDLDQQMFWQTWSSQGIKTVLVVMPWDSHHDKQKIRIQAIQAGIATQFM-.....VP
   4 ftgSDYPKDDLAQQRFWQQWAAQGIKTVLVVMPWSPHEEKTRLRIQALKAGIATQFM-.....IP
   5 atqQDLPKGDLARKRFWQTWAEQGIKTVLVVMPWSPNERKQRIRMEALEAGIATQFM-.....--
   6 atrQDLPEGDLAQQRFWQSWADKGIKTVLVVMPLSPNEHKQKIRLQALRAGIATQFM-.....--
   7 ...HAHPSQGLAFREALRKAKEEGVQAVLVLTPPMAWEDRNRLKALLLREGLPSQILN.....VP
   8 ...HAHPSQGLAFREALRKAKEEGVQAVLVLTPPMAWEDRNRLKALLLREGLPSQILN.....VP
   9 kaaVDIPEKDFEIDQFWESWVEQDIKTILVISEWLDNKYKTKLTRDALEHGITLQFMLp18skIT


       120       130       140 
        |         |         | 
   1 LREEERHRWENALLGLLAKAGLQVV
   2 LPKADKYKALNVTLGLLCKAGWQPI
   3 LPKADKYKALNVTLGLLCKAGWQPI
   4 TPQDNPYKALNVALGLLCKAKWQPV
   5 IPGADPYKALNVVLGLLCKAAWQPV
   6 IPGADPYKALNVVLGLLCKAAWQPV
   7 LREEERHRWENALLGLLAKAGLQVV
   8 LREEERHRWENALLGLLAKAGLQVV
   9 CFTSDQYRANNILLGLLAKAGWQAV