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, 1999.
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:

- T0097 C-terminal domain of ERp29, rat
- gi|2507015|sp|P52555|ER29_RAT_156:260 ENDOPLASMIC RETICULUM PROTEIN ERP29 PRECURSOR (ERP31) (Rattus norvegicus)
- gi|1772594|emb|CAA71313.1| (Y10264) ERp29 precursor [Rattus norvegicus] (Rattus norvegicus)
- gi|2317800|gb|AAC15239.1| (U36482) endoplasmic reticulum protein ERp29 precursor [Rattus norvegicus] (Rattus norvegicus)
- gi|5803013|ref|NP_006808.1|_156:261 endoplasmic reticulum lumenal protein (Homo sapiens)
- gi|6015110|sp|P30040|ER29_HUMAN ENDOPLASMIC RETICULUM PROTEIN ERP29 PRECURSOR (ERP31) (ERP28) (Homo sapiens)
- gi|7512406|pir||T09549 endoplasmic-reticulum-lumenal protein 28 - human (Homo sapiens)
- gi|3413293|emb|CAA64397.1| (X94910) ERp28 [Homo sapiens] (Homo sapiens)
- gi|7488158|pir||T00437_264:357 probable protein disulfide-isomerase (EC 5.3.4.1) precursor - Arabidopsis thaliana (Arabidopsis thaliana)
- gi|2529680|gb|AAC62863.1| (AC002535) putative protein disulfide-isomerase [Arabidopsis thaliana] (Arabidopsis thaliana)
- gi|7489183|pir||T03644_265:358 probable protein disulfide-isomerase (EC 5.3.4.1) precursor - common tobacco (Nicotiana tabacum)
- gi|1848212|emb|CAA72092.1| (Y11209) protein disulfide-isomerase precursor [Nicotiana tabacum] (Nicotiana tabacum)
- gi|2895202|gb|AAC02944.1|_148:257 (AF025408) Windbeutel [Drosophila melanogaster] (Drosophila melanogaster)
- gi|7302506|gb|AAF57590.1| (AE003796) wbl gene product [Drosophila melanogaster] (Drosophila melanogaster)
- gi|729442|sp|P38661|ERP5_MEDSA_270:362 PROBABLE PROTEIN DISULFIDE ISOMERASE P5 PRECURSOR (Medicago sativa)
- gi|7488740|pir||T09614 gluprotein disulfide-isomerase precursor homolog - alfalfa (Medicago sativa)
- gi|166380|gb|AAB46930.1| (M80235) glucose-regulated endoplasmic reticular protein precursor [Medicago sativa] (Medicago sativa)
- gi|3928886|gb|AAC79709.1|_119:213 (AF093614) putative protein disulfide isomerase [Acetabularia acetabulum] (Acetabularia acetabulum)
- gi|2627440|gb|AAB86685.1|_267:361 (AF019112) protein disulfide isomerase; PDI; P5-like [Dictyostelium discoideum] (Dictyostelium discoideum)
- gi|3287888|sp|O13811|PDI2_SCHPO_264:354 PUTATIVE PROTEIN DISULFIDE ISOMERASE C17H9.14C PRECURSOR (Schizosaccharomyces pombe)
- gi|7492860|pir||T37880 probable protein disulfide-isomerase (EC 5.3.4.1) - fission yeast (Schizosaccharomyces pombe) (Schizosaccharomyces pombe)
- gi|2330721|emb|CAB11223.1| (Z98597) putative protein disulfide isomerase (EC 5.3.4.1) [Schizosaccharomyces pombe] (Schizosaccharomyces pombe)
- gi|2501209|sp|Q92249|ER38_NEUCR_265:364 PUTATIVE DISULFIDE ISOMERASE ERP38 PRECURSOR (Neurospora crassa)
- gi|1504103|emb|CAA68847.1| (Y07562) ERp38 [Neurospora crassa] (Neurospora crassa)
- gi|2501210|sp|Q00216|TIGA_ASPNG_264:354 PUTATIVE DISULFIDE ISOMERASE TIGA PRECURSOR (Aspergillus niger)
- gi|1419383|emb|CAA67299.1| (X98748) tigA [Aspergillus niger] (Aspergillus niger)
- gi|4650854|dbj|BAA77026.1|_6:46 (AB026252) disulfide-isomerase precursor [Lithospermum erythrorhizon] (Lithospermum erythrorhizon)

              10        20        30        40         50        60    
              |         |         |         |          |         |    
   1 GCLPAYDALAGQFIEASSREARQAILKQGQDGLSGVKETDK.KWASQYLKIMGKILDQGEDFPAS
   2 GCLPAYDALAGQFIEASSREARQAILKQGQDGLSGVKETDK.KWASQYLKIMGKILDQGEDFPAS
   3 GCLPVYDALAGEFIRASGVEARQALLKQGQDNLSSVKETQK.KWAEQYLKIMGKILDQGEDFPAS
   4 GIVESLDALVKELVAASE-DEKKAVLSRIEEEASTLKGSTT.RYGKLYLKLAKSYIEKGSDYASK
   5 GIVESLDTLVNEFVSATN-EEKKAVFSKMEDEAGKLNGFAA.RYGKIYLKAAKSSMEKGADYAKN
   6 GCIKEFNEVLKNYANIPDAEQLKLIEKLQAKQEQLTDPEQQ.QNARAYLIYMRKIHEVGYDFLEE
   7 GIVEDLDELVKEFVAAND-EEKKAVFARIEEEVKKLEGSAS.RYGKIYLKVSKKYLEKGSDYAKN
   8 -TVKALMPIVEQFVKSS--EGREALVVEAEAIVPTLKPSEA.RVAKWYVKTMSSMQKKGENYLEK
   9 GRVEQLDTIATEFIAAAA-EVRKELVKKAQTVVDSLPEELR.IEGSYYVKVMKTIAEKSIDFVTT
  10 GRIPTFDEFAAEFLDMSN-AAKEVVLEKVKQLA---LEDSS.RWTKYYKKVFEKILN-DENWVHK
  11 GTIAALDEIVAKYTGGAS---LAEVAEEAKEAVKSLKNSAElKYADYYLRVLDK-LSKSEGYATK
  12 GTIASLDEL----IASTSAADLAAAVKKAATEL------KD.KYAQYYVKVADK-LSQNAEYAAK
  13 -----------------------------------------.-------------MEKGADYAKN


          70         80           90            100     
          |          |            |              |     
   1 ELARISKLI.ENKMSEGKKE...ELQRSLNILTAFR.....KKGAEKEEL
   2 ELARISKLI.ENKMSEGKKE...ELQRSLNILTAFR.....KKGAEKEEL
   3 EMTRIARLIeKNKMSDGKKE...ELQKSLNILTAFQ.....KKGAEKEEL
   4 ETERLGRVL.GKSISPVKAD...ELTLKRNILTTF-.....---------
   5 EIQRLERML.AKSISPAKSD...EFTLKKNILATF-.....---------
   6 ETKRLLRLK.AGKVTEAKKE...ELLRKLNILEVFRvhkvtKTAPEKEEL
   7 EIQRLERLL.EKSISPAKAD...ELTLKKNILST--.....---------
   8 EYERLNRML.QNQADSLKAEkltEFHDRLGVLQVF-.....---------
   9 EIARITKLV.SGSMSGKKAD...EFAKKLNILESFK.....---------
  10 EAKRLSKLLrQKSIALASAD...DFKTRLNILNSF-.....---------
  11 EFARLEGILkKGGLAPAKVD...ELTVKVNVLRKFV.....EKAAEE---
  12 ELARLEKILaKGGSAPEKVD...DLISRSNILRKF-.....-VGEEKE--
  13 EIQRLDRIL.SKAVSPAKAD...EFTLKKNILSTF-.....---------