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:

- T0307 PG_1108, Porphyromonas gingivalis, 133 res
- gi|34540841|ref|NP_905320.1|_1:133 hypothetical protein PG1108 [Porphyromonas gingivalis W83]
- gi|34397155|gb|AAQ66219.1| hypothetical protein PG_1108 [Porphyromonas gingivalis W83]
- gi|88713297|ref|ZP_01107380.1|_1:104 hypothetical protein FB2170_08064 [Flavobacteriales bacterium HTCC2170]
- gi|88708207|gb|EAR00444.1| hypothetical protein FB2170_08064 [Flavobacteriales bacterium HTCC2170]
- gi|88711303|ref|ZP_01105391.1|_1:104 hypothetical protein FB2170_04295 [Flavobacteriales bacterium HTCC2170]
- gi|88710244|gb|EAR02476.1| hypothetical protein FB2170_04295 [Flavobacteriales bacterium HTCC2170]
- gi|14022014|dbj|BAB48625.1|_46:158 mll1192 [Mesorhizobium loti MAFF303099]
- gi|13471270|ref|NP_102839.1| hypothetical protein mll1192 [Mesorhizobium loti MAFF303099]
- gi|88804076|ref|ZP_01119596.1|_1:101 hypothetical protein RB2501_04480 [Robiginitalea biformata HTCC2501]
- gi|88784955|gb|EAR16124.1| hypothetical protein RB2501_04480 [Robiginitalea biformata HTCC2501]
- gi|88804074|ref|ZP_01119594.1|_2:99 hypothetical protein RB2501_04470 [Robiginitalea biformata HTCC2501]
- gi|88784953|gb|EAR16122.1| hypothetical protein RB2501_04470 [Robiginitalea biformata HTCC2501]
- gi|62196338|gb|AAX74638.1|_34:135 conserved hypothetical protein [Brucella abortus biovar 1 str. 9-941]
- gi|82700128|ref|YP_414702.1| hypothetical protein BAB1_1322 [Brucella melitensis biovar Abortus 2308]
- gi|62290206|ref|YP_221999.1| hypothetical protein BruAb1_1303 [Brucella abortus biovar 1 str. 9-941]
- gi|82616229|emb|CAJ11278.1| conserved hypothetical protein [Brucella melitensis biovar Abortus]
- gi|23348144|gb|AAN30220.1|_34:135 conserved hypothetical protein [Brucella suis 1330]
- gi|23502178|ref|NP_698305.1| hypothetical protein BR1302 [Brucella suis 1330]
- gi|17982632|gb|AAL51880.1|_151:252 Hypothetical Protein [Brucella melitensis 16M]
- gi|17986982|ref|NP_539616.1| hypothetical protein BMEI0699 [Brucella melitensis 16M]
- gi|32444146|emb|CAD73589.1|_130:227 hypothetical protein-transmembrane prediction [Rhodopirellula baltica SH 1]
- gi|32472909|ref|NP_865903.1| hypothetical protein-transmembrane prediction [Rhodopirellula baltica SH 1]
- gi|90416110|ref|ZP_01224043.1|_24:132 hypothetical protein GB2207_02717 [marine gamma proteobacterium HTCC2207]
- gi|90332484|gb|EAS47681.1| hypothetical protein GB2207_02717 [marine gamma proteobacterium HTCC2207]
- gi|83592297|ref|YP_426049.1|_70:176 hypothetical protein Rru_A0961 [Rhodospirillum rubrum ATCC 11170]
- gi|83575211|gb|ABC21762.1| conserved hypothetical protein [Rhodospirillum rubrum ATCC 11170]

              10        20        30        40         50             6
              |         |         |         |          |              
   1 MGLGRQSLNIMTFSGQELTAIIKMAKSMVMADGKIKPAEIAVMTR.EFMRFGILQDQ.....VDL
   2 MGLGRQSLNIMTFSGQELTAIIKMAKSMVMADGKIKPAEIAVMTR.EFMRFGILQDQ.....VDL
   3 ----------MEFSIAEKLALVKAVDEVIYVDGNVDVEEMVFMSQ.LMDTLNFDR--.....--I
   4 ----------MEFNLAEKLAIVRVLESVIIADGIVHKNELNTLSD.LMKRLDFDSN-.....---
   5 ------------------SAELLMLFRMILADGTVSESEMVAFRR.ICKDAFGIQETsidavIEY
   6 ----------MKYNLVEQLAVIKALDEVILVDKLVYEEEASFIAH.LAKVLGFKMD-.....---
   7 ----------------EKLAVLKTIDEVIQMDEEIKDGEIDFMNR.LSDTLDVGPD-.....---
   8 -----------------------LLLHVVVADGNQHPAEIAAFKE.IAANNFGIPPEelpevAEY
   9 -----------------------LLLHVVVADGNQHPAEIAAFKE.IAANNFGIPPEelpevAEY
  10 -----------------------LLLHVVVADGNQHPAEIAAFKE.IAANNFGIPPEelpevAEY
  11 ------------------------AASMILADGEVDEAEVLAAEK.SGDEVFEGFDEar...LRM
  12 ----------------EQLATAALLIEVMVIDGNLAEDELQSISAtLAQMLELSSEQ.....VDE
  13 -------------------AVVALSAKMAKADGAVTREEISAFKR.AFRIPPQDMAA.....VGR


      0          70               80        90          100       110  
     |           |                |         |            |         |  
   1 LLKASD.S.IEASQAVA..LI.....ARMDEERKKYVASYLG...VIMASDGDIDDNELALWTLI
   2 LLKASD.S.IEASQAVA..LI.....ARMDEERKKYVASYLG...VIMASDGDIDDNELALWTLI
   3 LVEEAR.G.ISAKESLS..IL.....KNMTFEKKQSLSKVLN...EMASVDGELNKKEYRLIFNI
   4 FLVQAR.A.VATNQAIL..IL.....NEMPDDKKKALASILD...EMAMSDGFLHEKEVEVIIKT
   5 LNEFGY.E.TNGSQAIA..LF.....RDLDVERRKQLAQHMA...EIAKADSQLAESEVRLLRRT
   6 LIRKAR.N.VEAAQAMA..VL.....KLMSENKKHALSVLLR...EAAGADGRITDAELELIQGI
   7 LILEAR.N.TEPAEALA..VL.....RAMPDEQKQLLARLLN...EAANSDGEVDEREIQFIYRV
   8 LKDFGY.E.TTTKQAAN..ML.....AEMAPERRLALLSDLM...KIACSDHRLDRSETTMIQRI
   9 LKDFGY.E.TTTKQAAN..ML.....AEMAPERRLALLSDLM...KIACSDHRLDRSETTMIQRI
  10 LKDFGY.E.TTTKQAAN..ML.....AEMAPERRLALLSDLM...KIACSDHRLDRSETTMIQRI
  11 ILQHGK.D.LPSADDLAgmLR.....DVLDQESKAKVMEFLS...EIAMADGRVAKEEREMLQRV
  12 LVLLSR.DeVSDATSLY..QFtkeinAHFDHEKKLKLMTAMW...RVAFADGHLDKHEESIIRRV
  13 IFDEAKkS.PDGYEAYAr.QI.....ARMFADSPQILEELLGalfVIAQADGRLHPSEIAFLHKV


           120       130   
            |         |   
   1 STLCGLPTMTVMEAINNMKNL
   2 STLCGLPTMTVMEAINNMKNL
   3 LHEVGI---------------
   4 CTGMGI---------------
   5 LDLLDISPVDVVKP-------
   6 LRE------------------
   7 LTAAGI---------------
   8 ANTLGIKP-------------
   9 ANTLGIKP-------------
  10 ANTLGIKP-------------
  11 AAGLGV---------------
  12 ADLLHL---------------
  13 ADLFGLPPR------------