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:

- T0320
- gi|6320159|ref|NP_010239.1|_210:306 Flavin adenine dinucleotide (FAD) synthetase, performs the second step in synthesis of FAD from riboflavin; Fad1p [Saccharomyces cerevisiae]
- gi|45270204|gb|AAS56483.1| YDL045C [Saccharomyces cerevisiae]
- gi|1279671|emb|CAA96444.1| FAD synthetase [Saccharomyces cerevisiae]
- gi|1431034|emb|CAA98604.1| FAD1 [Saccharomyces cerevisiae]
- gi|729461|sp|P38913|FAD1_YEAST FAD synthetase (FMN adenylyltransferase) (FAD pyrophosphorylase) (Flavin adenine dinucleotide synthetase) [Taxonomy]
- gi|520745|gb|AAA65730.1| FAD synthetase [Taxonomy]
- gi|50291705|ref|XP_448285.1|_209:303 unnamed protein product [Candida glabrata]
- gi|49527597|emb|CAG61246.1| unnamed protein product [Candida glabrata CBS138]
- gi|50309093|ref|XP_454552.1|_213:310 unnamed protein product [Kluyveromyces lactis]
- gi|49643687|emb|CAG99639.1| unnamed protein product [Kluyveromyces lactis NRRL Y-1140]
- gi|44983843|gb|AAS52879.1|_210:312 AER198Wp [Ashbya gossypii ATCC 10895]
- gi|45190801|ref|NP_985055.1| AER198Wp [Eremothecium gossypii]
- gi|24641632|ref|NP_727648.1|_226:291 CG4407-PB, isoform B [Drosophila melanogaster]
- gi|22832170|gb|AAN09317.1| CG4407-PB, isoform B [Drosophila melanogaster]
- gi|18859847|ref|NP_572837.1|_254:319 CG4407-PA, isoform A [Drosophila melanogaster]
- gi|15291793|gb|AAK93165.1| LD26737p [Drosophila melanogaster]
- gi|22832169|gb|AAF48210.2| CG4407-PA, isoform A [Drosophila melanogaster]
- gi|20148293|gb|AAM10037.1|_183:235 putative protein [Arabidopsis thaliana]
- gi|14423558|gb|AAK62461.1| putative protein [Arabidopsis thaliana]
- gi|18414227|ref|NP_568117.1|_183:235 transferase [Arabidopsis thaliana]
- gi|7378626|emb|CAB83302.1| putative protein [Arabidopsis thaliana]
- gi|71755811|ref|XP_828820.1|_272:320 phosphoadenosine phosphosulfate reductase-like protein [Trypanosoma brucei TREU927]
- gi|70834206|gb|EAN79708.1| phosphoadenosine phosphosulfate reductase-like protein [Trypanosoma brucei]
- gi|90305238|gb|EAS34869.1|_288:351 hypothetical protein CIMG_00223 [Coccidioides immitis RS]
- gi|71019763|ref|XP_760112.1|_320:389 hypothetical protein UM03965.1 [Ustilago maydis 521]
- gi|46099726|gb|EAK84959.1| hypothetical protein UM03965.1 [Ustilago maydis 521]
- gi|67516619|ref|XP_658195.1|_231:277 hypothetical protein AN0591.2 [Aspergillus nidulans FGSC A4]
- gi|40747534|gb|EAA66690.1| hypothetical protein AN0591.2 [Aspergillus nidulans FGSC A4]
- gi|50551609|ref|XP_503279.1|_195:244 hypothetical protein [Yarrowia lipolytica]
- gi|49649147|emb|CAG81483.1| unnamed protein product [Yarrowia lipolytica CLIB122]
- gi|3668151|emb|CAA21108.1|_191:237 SPCC1235.04c [Schizosaccharomyces pombe]
- gi|19075230|ref|NP_587730.1| hypothetical protein SPCC1235.04c [Schizosaccharomyces pombe 972h-]
- gi|7387648|sp|O74841|FAD1_SCHPO Probable FAD synthetase (FMN adenylyltransferase) (FAD pyrophosphorylase) (Flavin adenine dinucleotide synthetase) [Taxonomy]
- gi|7492571|pir||T40878 probable FAD synthetase - fission yeast (Schizosaccharomyces pombe) [Taxonomy]
- gi|54642749|gb|EAL31494.1|_316:372 GA18164-PA [Drosophila pseudoobscura]
- gi|21627810|emb|CAD37142.1|_206:268 probable FAD synthetase [Aspergillus fumigatus]
- gi|70992283|ref|XP_750990.1|_261:321 FAD synthetase [Aspergillus fumigatus Af293]
- gi|66848623|gb|EAL88952.1| FAD synthetase, putative [Aspergillus fumigatus Af293]
- gi|56783975|dbj|BAD81430.1|_26:75 unknown protein [Oryza sativa (japonica cultivar-group)]
- gi|56783972|dbj|BAD81409.1| unknown protein [Oryza sativa (japonica cultivar-group)]
- gi|50422645|ref|XP_459898.1|_227:256 hypothetical protein DEHA0E14204 [Debaryomyces hansenii CBS767]
- gi|49655566|emb|CAG88139.1| unnamed protein product [Debaryomyces hansenii CBS767]
- gi|68464665|ref|XP_723410.1|_139:165 flavin adenine dinucleotide synthetase [Candida albicans SC5314]
- gi|68465042|ref|XP_723220.1| flavin adenine dinucleotide synthetase [Candida albicans SC5314]
- gi|46445443|gb|EAL04711.1| hypothetical protein CaO19.4723 [Candida albicans SC5314]
- gi|46445246|gb|EAL04515.1| hypothetical protein CaO19.12186 [Candida albicans SC5314]
- gi|85111171|ref|XP_963810.1|_267:305 hypothetical protein [Neurospora crassa OR74A]
- gi|32422363|ref|XP_331625.1| hypothetical protein [Neurospora crassa OR74A]
- gi|38566980|emb|CAE76280.1| conserved hypothetical protein [Neurospora crassa]
- gi|28925547|gb|EAA34574.1| hypothetical protein [Neurospora crassa]
- gi|66811140|ref|XP_639278.1|_225:257 hypothetical protein DDB0185283 [Dictyostelium discoideum]
- gi|60467908|gb|EAL65921.1| hypothetical protein DDBDRAFT_0185283 [Dictyostelium discoideum AX4]
- gi|55242026|gb|EAA07691.3|_146:170 ENSANGP00000010849 [Anopheles gambiae str. PEST]
- gi|58382797|ref|XP_312180.2| ENSANGP00000010849 [Anopheles gambiae str. PEST]
- gi|47937753|gb|AAH72314.1|_445:475 MGC82686 protein [Xenopus laevis]
- gi|83768917|dbj|BAE59054.1|_246:276 unnamed protein product [Aspergillus oryzae]

              10        20        30             40        50        60
              |         |         |              |         |         |
   1 NEPICGLYGKGFTSIGGINNSLPNPHLRKDS.....NNPALHFEWEIIHAFGKDAEGERSSAINT
   2 NEPICGLYGKGFTSIGGINNSLPNPHLRKDS.....NNPALHFEWEIIHAFGKDAEGERSSAINT
   3 NEPICELYRYGFTSLGNVEETLPNPHLRKDK.....NSTPLKLNFEW--EIENRYKHNEVTKAEP
   4 GEEVCGLYEMGFTSLGSVNNTLRNPYLRIPE.....PIGSMTKAETEHSDFQWEIENNYRGDSNM
   5 GEEICGLYQVGFTSIGGINSTTRNPYLLATKaa9vsNEERINNHFTWEISNAYGLEQADDKPHCS
   6 --PYCSLYDRGYTSIGNRANTVPNPHLRRTD.....AECECGSNSD-------------------
   7 --PYCSLYDRGYTSIGNRANTVPNPHLRRTD.....AECECGSNSD-------------------
   8 ----CSLYDQGYTSIGSIHDTVPNSLLSVND.....T----------------------------
   9 ----CSLYDQGYTSIGSIHDTVPNSLLSVND.....T----------------------------
  10 --PFCELYEKGYTSLGGANSTIPNSHLSRED.....-----------------------------
  11 --EYCQLYDQGYTSLGGTNDTHPNPKLQINK.....ASP--------------------------
  12 -VPYCLLYDQGYTSLGSTHNTLPNPKLRMDD.....EQQTSSTEQPV------------------
  13 ----CSLYDQGYTSLGGLSNTHQNPSLWDP-.....-----------------------------
  14 ----CCLYDKGYTSLGGTDSTVPNPKLLKKG.....-----------------------------
  15 ---YCSLYDRGYTSLGGVSDTSPNPALKNPD.....-----------------------------
  16 ----CPLYNKGYTSIGYRSNTVPNPHLKRLD.....L----------------------------
  17 ---YCSLYDRGYTSLGGTSDTHPNPKLRVEH.....SADP-------------------------
  18 ---YCSLYDRGYTSLGGTSDTHPNPKLRVEH.....SADP-------------------------
  19 ----CSLYDQGYTSIGSIYDTVPNALLCD--.....-----------------------------
  20 ----CEMYDLGYTSLGGINTTTPNPYLKIEG.....DEV--------------------------
  21 ----CEMYDQGYTSLGGINSTVPNPLLKLPN.....-----------------------------
  22 --PFCSLYSQGFSSLGGTKDTRPNPALALNA.....EGNKFRPAYE-------------------
  23 --PYCELYDQGYTSIGQQHDTIPNPDLLIPS.....TLDQ-------------------------
  24 --PYCALYDRGYTSIGDRTNTIPNPHL----.....-----------------------------
  25 ---YCILYDKGYTSLGSMENTVKNPALRFTT.....PAG--------------------------
  26 --EYCPLYDQGYTSLGGQTDTHPNPKLRVDT.....TA---------------------------


                 70        80        90       
                 |         |         |       
   1 SPISVVD...KERFSKYHDNYYPGWYLVDDTLERAGRIKN
   2 SPISVVD...KERFSKYHDNYYPGWYLVDDTLERAGRIKN
   3 IPIADED...LVKIENLHEDYYPGWYLVDDKLERAGRIKK
   4 HCNEINEndlNTIKQHDSSEFHPGWYLTKDEWERAGRL--
   5 ALTDDDL...RLIASHSQQDYLPGWFLINDRWERAGR---
   6 -------...-AVCSCDLGGYRPAWELQDATMERAGRL--
   7 -------...-AVCSCDLGGYRPAWELQDATMERAGRL--
   8 -------...-----SSKEKFKPAYLLSDGRLERAGRVKK
   9 -------...-----SSKEKFKPAYLLSDGRLERAGRVKK
  10 -------...--------GTFRPAWELANGRSERCGRL--
  11 --VEASK...PSNAGQETPKFRPAYELVEDEEERLGR---
  12 -------...LVGDGTAKGRWRPAYMLKDASFERAGRVQ-
  13 -------...------VKEEYRPAYELTDDSLERSGR---
  14 -------...------TCAEFLPAYALVKDEEERLGRFR-
  15 -------...--------GTYSPAYLLSDGSLERAGR---
  16 -------...TSPCSGAEGDYRPAWELADPTQERDGRLQ-
  17 -----GQ...GVADGTQSQHYRPAYELTEDQEERLGRIL-
  18 -----GQ...GVADGTQSQHYRPAYELTEDQEERLGR---
  19 -------...----STTGKSFRPAYMLSDGRLERAGRTK-
  20 -------...------------------------------
  21 -------...------------------------------
  22 -------...------------------------------
  23 -------...------------------------------
  24 -------...------------------------------
  25 -------...------------------------------
  26 -------...------------------------------