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:

- T0300 MhR28B, 102 res
- gi|60373|emb|CAA45675.1|_1:100 unnamed protein product [Saimiriine herpesvirus 2]
- gi|9626008|ref|NP_040254.1| unnamed protein product [Saimiriine herpesvirus 2]
- gi|267333|sp|Q01050|VG52_SHV21 Hypothetical gene 52 protein [Taxonomy]
- gi|76685|pir||E36811 hypothetical protein ORF52 - saimiriine herpesvirus 1 (strain 11) [Taxonomy]
- gi|330981|gb|AAA46129.1| first methionine codon in the EDLF3 ORF [Taxonomy]
- gi|30348428|emb|CAC84999.1|_1:100 hypothetical protein [Saimiriine herpesvirus 2]
- gi|30348435|emb|CAC85005.1|_1:100 hypothetical protein [Saimiriine herpesvirus 2]
- gi|30348449|emb|CAC85011.1|_1:100 hypothetical protein [Saimiriine herpesvirus 2]
- gi|9631243|ref|NP_048024.1|_1:99 orf 52 [Ateline herpesvirus 3]
- gi|4019279|gb|AAC95577.1| orf 52 [Ateline herpesvirus 3]
- gi|30348442|emb|CAC84285.1|_1:100 hypothetical protein [Saimiriine herpesvirus 2]
- gi|30348556|emb|CAC84348.1|_1:99 hypothetical protein [Saimiriine herpesvirus 2]
- gi|30348463|emb|CAC84291.1| hypothetical protein [Saimiriine herpesvirus 2]
- gi|30348498|emb|CAC85047.1|_1:99 hypothetical protein [Saimiriine herpesvirus 2]
- gi|30348491|emb|CAC85041.1|_1:99 hypothetical protein [Saimiriine herpesvirus 2]
- gi|30348484|emb|CAC85035.1| hypothetical protein [Saimiriine herpesvirus 2]
- gi|30348477|emb|CAC85029.1| hypothetical protein [Saimiriine herpesvirus 2]
- gi|30348470|emb|CAC85023.1| hypothetical protein [Saimiriine herpesvirus 2]
- gi|30348456|emb|CAC85017.1| hypothetical protein [Saimiriine herpesvirus 2]
- gi|13095629|ref|NP_076544.1|_6:109 unknown [Bovine herpesvirus 4]
- gi|12802579|gb|AAK07971.1| unknown [Bovine herpesvirus 4]
- gi|18653858|ref|NP_570792.1|_8:110 unknown [Cercopithecine herpesvirus 17]
- gi|4494956|gb|AAD21378.1| unknown [Macaca mulatta rhadinovirus 17577]
- gi|7330041|gb|AAF60030.1| ORF52 [Macaca mulatta rhadinovirus 26-95]
- gi|66476638|ref|YP_238392.1|_8:110 JM89 [Macaca fuscata rhadinovirus]
- gi|46519418|gb|AAT00066.1| JM89 [Macaca fuscata rhadinovirus]
- gi|51518037|ref|YP_067962.1|_9:122 BLRF2 [Cercopithecine herpesvirus 15]
- gi|18025488|gb|AAK95432.1| BLRF2 [cercopithicine herpesvirus 15]
- gi|82703972|gb|ABB89241.1|_9:121 BLRF2 [Human herpesvirus 4]
- gi|82503222|ref|YP_401666.1| BLRF2 [Human herpesvirus 4]
- gi|1334866|emb|CAA24852.1| unnamed protein product [Human herpesvirus 4]
- gi|23893612|emb|CAD53416.1| putative BLRF2 protein [Human herpesvirus 4]
- gi|73974|pir||QQBE19 BLRF2 protein - human herpesvirus 4 (strain B95-8)
- gi|141002|sp|P03197|YLR2_EBV Hypothetical BLRF2 protein [Taxonomy]
- gi|64173265|gb|AAY41115.1|_9:121 unknown [Human herpesvirus 4]
- gi|2246538|gb|AAB62663.1|_5:104 ORF 52 [Human herpesvirus 8]
- gi|87196877|gb|ABD28903.1|_5:104 ORF52 [Human herpesvirus 8]
- gi|18846019|ref|NP_572105.1| ORF 52; EBV BLRF2 homolog [Human herpesvirus 8]
- gi|1718305|gb|AAC57134.1| ORF 52; EBV BLRF2 homolog [Human herpesvirus 8]
- gi|1850851|emb|CAA70267.1|_1:102 hypothetical protein [Murid herpesvirus 4]
- gi|9629617|ref|NP_044889.1| unknown [Murid herpesvirus 4]
- gi|6625615|gb|AAF19316.1| 52 [murid herpesvirus 4]
- gi|2317987|gb|AAB66445.1| unknown [murid herpesvirus 4]
- gi|24943138|ref|NP_733900.1|_7:124 ORF46 [Callitrichine herpesvirus 3]
- gi|13676689|gb|AAK38255.1| ORF46 [callitrichine herpesvirus 3]
- gi|20453842|gb|AAM22154.1|_6:110 unknown [porcine lymphotropic herpesvirus 1]
- gi|2338015|gb|AAC58099.1|_1:104 ORF52 [Alcelaphine herpesvirus 1]
- gi|10140974|ref|NP_065551.1| ORF52 [Alcelaphine herpesvirus 1]
- gi|83642889|ref|YP_438176.1|_8:117 ORF52 [Ovine herpesvirus 2]
- gi|61971003|gb|AAX58088.1| ORF52 [Ovine herpesvirus 2]
- gi|9628055|ref|NP_042649.1|_10:109 ORF 52 [Equid herpesvirus 2]
- gi|695225|gb|AAC13840.1| ORF 52 [Taxonomy]

                           10        20        30                      
                           |         |         |                      
   1 ...MA...SKKP..D.....KTYEEMVKEVERLKLENKTLKQKVKS....S..GA..V..S....
   2 ...MA...SRRS..C.....ADVEELEKELQKLKIENKALKKKLVQ....-..-H..T..S....
   3 ...MA...SRRS..C.....ADVEELEKELQKLKIENKALKKKLVQ....-..-H..T..S....
   4 ...MA...SRRS..C.....ADVEELEKELQKLKIENKALKKKLVQ....-..-H..T..S....
   5 ...MA...SKRP..C.....AGVEELEKELQKLKLENKTLKKQLIQ....-..-Q..A..G....
   6 ...MA...SGRA..S.....SDVEELQKELQKLKLENKALKKKMLQ....G..N-..-..-....
   7 ...MA...SRRS..C.....ADVEELEKELQKLKIENKALKKKLVQ....-..-H..T..S....
   8 ...MA...SKKP..S.....VDVDELQKELQRLKLENKTLKKKMQQ....-..--..V..S....
   9 ...MA...SKKP..S.....VDVDELQKELQKLKLENKALKKKMQQ....-..--..V..S....
  10 ...MA...SKKP..S.....VDVDELQKELQKLKLENKALKKKMQQ....-..--..V..S....
  11 sgsRK...NPKA..Q.....PTMEDLEAKIAQLQLENKQLKKRIKH....GtdPQ..P..L....
  12 ...RPktrAPKK..E.....LTMEELAAQVQKLSVENKQLKKLINS....G..DP..Tr.S....
  13 ...RPktrAPKK..E.....LTMEELAAQVQKLSVENKQLKKLINS....G..DP..Tr.S....
  14 ktrVP...SGKGmaE.....MSVEDMAARLARLESENKALKQQVRR....G..GT..C..As10p
  15 kvrLP...SVKAv.D.....MSMEDMAARLARLESENKALKQQVLR....G..GA..C..As10p
  16 kvrLP...SVKAv.D.....MSMEDMAARLARLESENKALKQQVLR....G..GA..C..As10p
  17 aapRG...RPKK..D.....LTMEDLTAKISQLTVENRELRKAL--....G..ST..A..D....
  18 aapRG...RPKK..D.....LTMEDLTAKISQLTVENRELRKAL--....G..ST..A..D....
  19 ...MA...SKKP..D.....KTYEEMVKEVERLKLENKTLKQKVKS....S..GA..V..S....
  20 ipaMA...SSKK..Skg6egMSMEELVTRLTRLEMENKTLKNQVKSksqsA..DP..Iq.S....
  21 qstKG...APGQ..G.....QTMAQLAAQLAQLQMENRNLKRQIRK....Sv.GH..P..E....
  22 ...M-...-DPK..N.....LTVEQLAAELTKLQMENSHLKRKLRRsv..G..GP..PkeP....
  23 gkpQA...GGPA..D.....NSVEKLAAELTRLQMENSKLRRKLRQst..G..GAscL..L....
  24 ggsKR...CPKK..Q.....PTPEELAEELVKLRMENKALKSKLKE....-..-H..V..G....


         40                 50        60        70        80        90 
         |                  |         |         |         |         | 
   1 .S..DD.....SI....LTAAKRESIIVSSSRALGAVAMRKIEAKVRSRAAKAVTEQELTSLLQS
   2 .P..ED.....EL....LTPAQKDAIINSTVNKLTKKAEEKIRERVLKDVLPLVSKNQCMEAIAH
   3 .P..ED.....EM....LTSAQKDAIINSTVNKLTKKAEEKIRERVLKDLLPLVSKNQCMGAIAR
   4 .P..ED.....EM....LTSAQKDAIINSTVNKLTKKAEEKIRERVLKDLLPLVSKNQCMEAIAR
   5 .P..DD.....EI....LTPSQKDALITSVVNKLTKQADEKIRIKVTKDLLPLVTKKQCMEAITI
   6 .P..EE.....EM....LTPPQKEILINSLVSKLTKQAELKIRERVTKDLLPLVTKNQCMEAIAD
   7 .S..ED.....EM....LTSAQKDAIINSTVNKLTKKAEEKIRERVLKDLLPLVSKNQCMEAIAR
   8 .P..ND.....EM....LTPSQKESIINSVVNSLTKNAEKKIRLRVSNDLLPLVTKQQCVDAIAN
   9 .P..ND.....EI....LTPSQKETIINSVVNSLTKNAEKKIRLRVSNDLLPLVTKHQCMEAIAN
  10 .P..ND.....EI....LTPSQKETIINSVVNSLTKNAEKKIRLRVSNDLLPLVTKQQCMEAIPN
  11 .P..GD.....PI....VTPAQREAMIGAATAALTSQASKKIEAKVRHHTSRAVTKEELEAAIAN
  12 .G..SD.....PV....ISNTEKEAKIAAAVSALCNVATRKIEAKVRAATAKAVTRGQMEDALAG
  13 .G..SD.....PV....ISNSEKEAKIAAAVSALCNVATRKIEAKVRAVTAKAVTRGQVEEALAG
  14 lP..PP.....EP....LTPRQREVMITQATGRLVSLAMQKIEDKVRKAVDGVNTRPEMEDILKN
  15 vP..PP.....EP....LTARQREVMITQATGRLASQAMKKIEDKVRKSVDGVTTRNEMENILQN
  16 vP..PP.....EP....LTARQREVMITQATGRLASQAMKKIEDKVRKSVDGVTTRNEMENILQN
  17 .P..RD.....RH....LTPTEKEAQLTATVGALSAAAAKKIEARVRTIFSKVVTQKQVDDALKG
  18 .P..RD.....RP....LTATEKEAQLTATVGALSAAAAKKIEARVRTIFSKVVTQKQVDDALKG
  19 .S..DD.....SI....LTAAKRESIIVSSSRALGAVAMRKIEAKVRSRAAKAVTEQELTSLLQS
  20 .P..PGggrtrEV....LTARQKQVLITQAISRLSSQAMQKIEQRVVAEMEDVRTRDEAEQKIQS
  21 .DisQP.....KS....LNPRQKQALISSYLTKFSSLATKKLEFKLATLTAPLQTKEEIEAVLEG
  22 .P..KP.....RE....LTEPERQLVLARWHNRFSSRSSELLRRQLDKLTATLVTEEDIDEVLKN
  23 .P..GE.....ETkpgkLSPEDKNILLAAWHTKFAAKASEKLYRKIKALTAEEDDEEGINKVLAS
  24 .D..DD.....VV....LTQAAKEAMVGSVVSGLTRSAAKQIEERIRKETLKATTKNEFEEVIKT


            100     
             |     
   1 LTLRVDVSMEE...
   2 IKYRIDVSIDEtyn
   3 IKYRIDVSVDEtcd
   4 IKYRIDVSVDEtcd
   5 LKYRIDVSTDEpqd
   6 IKYRIDVSTKEsqd
   7 IRYRIDVSVDEtcd
   8 IKYRIEVSPEEpqd
   9 IKYRIEVFPEEpqd
  10 IKYRIEVSPEEpqd
  11 IRIRVDLSMEDvtl
  12 ISIRVDVSMDEttr
  13 INIRVDVSMDEttr
  14 LTVRLQVSMSGakg
  15 LTLRIQVSMLGakg
  16 LTLRIQVSMLGakg
  17 LSLRIDVCMSDggt
  18 LSLRIDVCMSDggt
  19 LTLRVDVSMEEttv
  20 LTIRIQVSMSCskc
  21 TTIRLHLTLQDlvp
  22 ADFRLHFRPDPsen
  23 STIRVHASVDPedr
  24 LSFRVSLSYADlgg