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22 avril 2013
Zoom sur la bioinformatique structurale
Priorité est donnée à la bioinformatique appliquée à la biologie structurale à l'ère post-génomique.
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short, <25% identity
1aboA SH3 1idy myb dna-binding domain 1r69 repressor 1tvxA pertussis toxin 1ubi ubiquitin 1wit twitchin 2trx thioredoxinshort, 20%=40% identity
1aab high mobility group protein 1fjlA homeodomain 1hfh factor h 1hpi high-potential iron-sulfur protein 1csy SH2 1pfc immunoglobulin PFc fragment 1tgxA cardiotoxin 1ycc cytochrome e 3cyr cytochrome c3 451c cytochrome cshort, >35% identity
1aho toxin II 1csp cold shock protein 1dox ferredoxin [2fe-2s] 1fkj immunophilin 1fmb hiv-1 protease 1krn serine protease 1plc plastocyanin 2fxb ferredoxin 2mhr hemerythrin 9rnt ribonucleasemedium, <25% identity
1bbt3 foot-and-mouth disease virus 1sbp sulfate binding protein 1havA hepatitis proteinase 1uky uridylate kinase 2hsdA 3 Alpha, 20 beta-hydroxysteroid dehydrogenase 2pia phtalate reductase 3grs glutathione reductase kinase protein kinasemedium, 20-40% identity
1ad2 ribosomal protein l1 1aym3 rhinovirus 16 coat protein 1gdoA glucosamine 6-phosphate synthase 1ldg lactate dehydrogenase 1mrj alpha tricosanthin 1pgtA glutathione 1pii anthranilate isomerase 1ton tonin 2cba anhydrasemedium, >35% identity
1amk triose phosphate isomerase 1ar5A superoxide dismutase 1ezm elastase 1led lectin 1ppn papain 1pysA phenylalanyl-trna synthetase 1thm serine protease 1tis thymidylate sythase 1zin adenylate kinase 5ptp serine proteaselong, <25% identity
1ajsA aminotransferase 1cpt cytochrome p450 1lvl dihydrolipoamide dehydrogenase 1pamA cyclodextrin 1ped alcohol dehydrogenase 2myr myrosinase 4enl enolase gal4 gal4long, 20%<40% identity
1ac5 carboxypeptidase 1adj histidyl-trna synthetase 1bgl b-galactoxidase 1dlc endotoxin 1eft eftu 1fieA coagulation factor xiii 1gowA beta_glycosidase 1pkm pyruvate kinase 1sesA seryl-tRNA synthetase 2ack acetylcholinesterase arp actin glg glutamyl-trna synthetaselong, >35% identity
1ad3 aldehyde dehydrogenase 1gpb glycogen phosphorylase b 1gtr glutaminyl-tRNA synthetase 1lcf lactoferrin 1rthA reverse transcriptase 1taq taq DNA polymerase 3pmg phosphoglucomutase actin actinBack to Top
Reference 2
short
1aboA SH3 1csy SH2 1idy myb dna-binding domain 1r69 repressor 1tgxA cardiotoxin 1tvxA pertussis toxin 1ubi ubiquitin 1wit twitchin 2trx thioredoxinmedium
1sbp sulfate binding protein 1havA hepatitis proteinase 1uky uridylate kinase 2hsdA 3 Alpha, 20 beta-hydroxysteroid dehydrogenase 2pia phtalate reductase 3grs glutathione reductase kinase protein kinaselong
1ajsA aminotransferase 1cpt cytochrome p450 1lvl dihydrolipoamide dehydrogenase 1pamA cyclodextrin 1ped alcohol dehydrogenase 2myr myrosinase 4enl enolaseBack to Top
Reference 3
short
1idy myb dna-binding domain 1r69 repressor 1ubi ubiquitin 1wit twitchinmedium
1uky uridylate kinase 2pia phtalate reductase kinase protein kinaselong
1ajsA aminotransferase 1pamA cyclodextrin 1ped alcohol dehydrogenase 2myr myrosinase 4enl enolaseBack to Top
Reference 4 - Extensions
1ckaA SH3 1csp major cold shock protein 1dynA pleckstrin homology domain 1lkl SH2 1mfa immunoglobulin fab fragment 1pfc immunoglobulin PFc fragment 1pysA glycyl-tRNA synthetase 1vln concanavalin a 1ycc cytochrome e 2abk endonuclease iii kinase1 protein kinase kinase2 protein kinaseBack to Top
Reference 5 - Insertions
1eft eftu 1ivy human protective protein 1pysA glycyl-tRNA synthetase 1qpg 3-Phosphoglycerate kinase 1thm1 thermitase 1thm2 thermitase 2cba carbonic anhydrase ii S51 nuclear receptor S52 nuclear receptor kinase1 protein kinase kinase2 protein kinase kinase3 protein kinaseBack to Top
Reference 6 - Repeats
sh3 SH3 zf Zinc Finger apo Apolipoprotein sushi Sushi myb Myb dna-binding domain ank Ankyrin kringle KRINGLE dead DEAD/DEAH box helicase trk TrkA potassium uptake protein ktn+trk KTN NAD-binding domain, plus TrkA potassium uptake protein faa Fumarylacetoacetate hydrolase lrr Leucine-rich repeat ion IONBack to Top
Reference 7 - Transmembrane Sequences
ion ION acr ACR dtd DTD ptga PTGA Nat Nat photo PHOTO msl MSL 7tm 7 TMBack to Top
Reference 8 - Circular Permutations
sh3/sh2 SH3 / SH2 gsh glutathione synthetase lectin Lectin1 / Lectin2 ptga PTSEIIB / PTGA cellulase Cellulase / CBD_1Back to Top
Reference 6 (C1-C4) - Repeat Subsets
Back to TopC1-A - Same number of repeats of unique subtype
sh3 SH3 zf Zinc Finger sushi Sushi dead DEAD/DEAH box helicase ktn+trk KTN NAD-binding domain, plus TrkA potassium uptake proteinC1-B - Variable number of repeats of unique subtype
sh3_1 SH3 sh3_2 SH3 zf Zinc Finger sushi Sushi dead DEAD/DEAH box helicaseC2-A - Same number of repeats of variable subtypes in the same order
sh3 SH3 apo_1 Apolipoprotein apo_2 Apolipoprotein apo_3 Apolipoprotein sushi Sushi myb_1 Myb DNA-binding domain myb_2 Myb DNA-binding domain kringle_1 KRINGLE kringle_2 KRINGLE lrr_1 Leucine-rich repeat lrr_2 Leucine-rich repeat lrr_3 Leucine-rich repeatC2-b - Same number of repeats of variable subtypes in any order
sh3_1 SH3 sh3_2 SH3 zf_1 Zinc Finger zf_2 Zinc Finger apo_1 Apolipoprotein apo_2 Apolipoprotein apo_3 Apolipoprotein sushi_1 Sushi sushi_2 Sushi sushi_3 Sushi sushi_4 Sushi sushi_5 Sushi sushi_6 Sushi myb Myb DNA-binding domain ank_1 Ankyrin ank_2 Ankyrin ank_3 Ankyrin ank_4 Ankyrin trk TrkA potassium uptake protein kringle_1 KRINGLE kringle_2 KRINGLE lrr_1 Leucine-rich repeat lrr_2 Leucine-rich repeatC2-c - Variable number of repeats of variable subtypes
sh3_1 SH3 sh3_2 SH3 sh3_3 SH3 zf_1 Zinc Finger zf_2 Zinc Finger apo_1 Apolipoprotein apo_2 Apolipoprotein sushi_1 Sushi sushi_2 Sushi sushi_3 Sushi myb_1 Myb dna-binding domain myb_2 Myb dna-binding domain ank_1 Ankyrin ank_2 Ankyrin kringle_1 KRINGLE kringle_2 KRINGLE dead DEAD/DEAH box helicase trk TrkA potassium uptake protein ktn+trk_1 KTN NAD-binding domain, plus TrkA potassium uptake protein ktn+trk_2 KTN NAD-binding domain, plus TrkA potassium uptake protein faa_1 Fumarylacetoacetate hydrolase faa_2 Fumarylacetoacetate hydrolase faa_3 Fumarylacetoacetate hydrolase lrr_1 Leucine-rich repeat lrr_2 Leucine-rich repeat ion IONC3 - Repeats with an additional conserved domain
sh3 SH3 with a conserved SH2 domain sushi_1 Sushi with a conserved trypsin domain sushi_2 Sushi with a conserved lectin domain ank_1 Ankyrin with a conserved DEATH domain ank_2 Ankyrin with a conserved protein kinase domain kringle_1 Kringle with a conserved trypsin domain kringle_2 Kringle with a conserved PAN domain dead DEAD/DEAH box helicase with a conserved C-terminal domain lrr Leucine-rich repeat with associated N-terminal domainC4 - several different repeats
sh3 SH3 with EF-hand repeats zf Zinc Finger with homeobox repeats sushi SUSHI with CUB repeats ank Ankyrin with BTB/POZ repeats lrr Leucine-rich repeat with associated N- and C- terminal domains