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Selection summary: 5 segments, 4 strains, 3 species, 2 genera 
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Available tablesHMM Prediction of secretion system components
| Row | Organism
Click to show species | Sub-strain | Taxgroup | Segment
Click to show segment | %AT
| Size(bp)
| Number of
genes | Result Details | Distinct Secretion type I proteins | Distinct Secretion type II proteins | Distinct Secretion type III proteins | Distinct Secretion type IV proteins | Distinct Secretion type V proteins |
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| 1 | Deinococcus geothermalis
Strain: DSM11300 | DSM11300 | BDDD
Deinococcus-Thermus
Deinococci
NCBI: Tax 319795
| Main
cir | 33.4% | 2,467,205 bp | 2,335 genes | HMM Report
Fasta File | 2 | 13 | 0 | 0 | 1 |
| 2 | Deinococcus radiodurans
Strain: R1 | | BDDD
Deinococcus-Thermus
Deinococci
NCBI: Tax 243230
| Chr 1
cir | 33.0% | 2,648,638 bp | 2,579 genes | HMM Report
Fasta File | 2 | 13 | 0 | 0 | 1 |
BDDD
Deinococcus-Thermus
Deinococci
NCBI: Tax 243230
| Chr 2
cir | 33.3% | 412,348 bp | 357 genes | HMM Report
Fasta File | 2 | 0 | 0 | 0 | 0 |
| 3 | Thermus thermophilus
Strain: HB27 | | BDDT
Deinococcus-Thermus
Deinococci
NCBI: Tax 262724
| Main
cir | 30.6% | 1,894,877 bp | 1,982 genes | HMM Report
Fasta File | 2 | 13 | 0 | 0 | 1 |
| 4 | Thermus thermophilus
Strain: HB8 | | BDDT
Deinococcus-Thermus
Deinococci
NCBI: Tax 300852
| Main
cir | 30.5% | 1,849,742 bp | 1,973 genes | HMM Report
Fasta File | 2 | 12 | 0 | 0 | 1 |
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Background
HMMs have been build using HMMER version 2.3.2 compiled for Altix and Irix.
Training sets are created from homologs of 64 different proteins that have been aligned using ClustalX.
All 6 reading frames of complete genome sequences have been translated and searched through using these HMMs.
Only translations bigger than 25AA are used.
| InterPro ID | Assigned Type(s) | Description |
|---|
| IPR003995 | ,I, | Bacterial RTX cytolytic toxin, protein A |
| IPR003996 | ,I, | Bacterial RTX toxin-activating protein C |
| IPR003997 | ,I, | Gram-negative bacterial RTX secretion protein D |
| IPR010128 | ,I, | Type I secretion system ATPase, PrtD |
| IPR010132 | ,I, | Type I secretion system ATPase, HlyB |
| IPR010129 | ,I, | Type I secretion membrane fusion protein, HlyD |
| IPR006144 | ,I, | HlyD secretion protein, C-terminal |
| IPR010130 | ,I, | Type I secretion outer membrane protein, TolC |
| IPR010131 | ,I, | RND efflux system, outer membrane lipoprotein, NodT, related to type I |
| IPR005286 | ,I, | Wrong InterPro description. ABC transporter |
| IPR005897 | ,I, | ABC-type bacteriocin transporter |
| IPR000185 | ,II, | Receptor which binds SecB (ATPase) |
| IPR003708 | ,II, | Chaperone which bind the signal peptide |
| IPR004780 | ,II, | Signal recognition particle protein |
| IPR002208 | ,II, | part of membrane translocation machinery |
| IPR005807 | ,II, | part of membrane translocation machinery |
| IPR004692 | ,II, | part of membrane translocation machinery |
| IPR006312 | ,II, | Twin-arginine translocation protein |
| IPR003998 | ,II, | Twin-arginine translocation protein |
| IPR008277 | ,II, | Sec-independent periplasmic protein translocase |
| IPR000508 | ,II, | signal peptidase I, cleaves off Sec-signal peptides |
| IPR001872 | ,II, | signal peptidase II, cleaves off lipo-protein signal peptides |
| IPR000045 | ,II, | Prepilin peptidase, cleaves off signal peptides from type IV pilins |
| IPR001639 | ,II, | Bacterial type II secretion system protein C |
| IPR004845 | ,II, | Bacterial type II secretion system protein D |
| IPR001775 | ,II, | Bacterial general secretion pathway protein D |
| IPR001482 | ,II, | Bacterial type II secretion system protein E |
| IPR003004 | ,II, | Bacterial general secretion pathway protein F |
| IPR000983 | ,II, | Bacterial general secretion pathway protein G |
| IPR010054 | ,II, | General secretion pathway protein G |
| IPR002416 | ,II, | Bacterial general secretion pathway protein H |
| IPR010053 | ,II, | General secretion pathway protein H |
| IPR010052 | ,II, | Bacterial type II secretion system protein I |
| IPR003413 | ,II, | Bacterial type II secretion system protein I/J |
| IPR010055 | ,II, | Bacterial type II secretion system protein J |
| IPR005628 | ,II, | General secretion pathway protein K |
| IPR007812 | ,II, | General secretion pathway L |
| IPR007690 | ,II, | General secretion pathway M protein |
| IPR000645 | ,II, | Bacterial type II secretion system protein N |
| IPR001992 | ,II, | Bacterial type II secretion system protein |
| IPR004846 | ,II,III, | Bacterial type II and III secretion system protein (Secretin C) |
| IPR001712 | ,III, | Bacterial type III secretion FHIPEP |
| IPR002010 | ,III, | Type III secretion system inner membrane R protein |
| IPR010737 | ,III, | Type III effector Hrp-dependent outers |
| IPR010812 | ,III, | Hypersensitivity response secretion HrpJ |
| IPR008108 | ,III, | Type III secretion system outer membrane, B protein |
| IPR003282 | ,III, | Type III secretion system outer membrane K protein |
| IPR003283 | ,III, | Type III secretion system outer membrane O protein |
| IPR003522 | ,III, | Type III secretion system outer membrane G protein |
| IPR005415 | ,III, | Gram-negative bacterial type III secretion SycD chaperon |
| IPR005416 | ,III, | Gram-negative bacterial type III secretion SycE chaperon |
| IPR005838 | ,III, | Type III secretion system inner membrane P protein |
| IPR006135 | ,III, | Type III secretion exporter |
| IPR006302 | ,III, | Type III secretion protein HrcV |
| IPR006304 | ,III, | Type III secretion protein SpaR/YscT. FliR like |
| IPR006306 | ,III, | Type III secretion protein HrpO. FliQ like |
| IPR006307 | ,III, | Type III secretion protein HrpY/HrcU |
| IPR006303 | ,III, | Flagellar biosynthesis protein FliR |
| IPR006305 | ,III, | Flagellar biosynthesis protein FliQ |
| IPR004346 | ,IV, | CagE, TrbE, VirB component of type IV transporter system |
| IPR004355 | ,IV, | Type IV secretion system CagA exotoxin |
| IPR009691 | ,IV, | VIRB2 type IV secretion |
| IPR007792 | ,IV, | Type IV secretory pathway, VirB3-like |
| IPR006584 | ,IV, | Cellulose binding |
| IPR007430 | ,IV, | VirB8 |
| IPR010258 | ,IV, | Conjugal transfer protein TrbG/VirB9/CagX |
| IPR007688 | ,IV, | TrbL/VirB6 plasmid conjugal transfer protein |
| IPR003518 | ,IV, | Salmonella virulence plasmid 28.1 kDa A protein |
| IPR003519 | ,IV, | Salmonella virulence-associated 28 kDa protein |
| IPR009868 | ,IV, | VirE2 |
| IPR009933 | ,IV, | T-DNA border endonuclease VirD1 |
| IPR010834 | ,IV, | VirB7 |
| IPR005546 | ,V, | Autotransporter beta-domain |
| IPR006315 | ,V, | Outer membrane autotransporter barrel |
| IPR007157 | ,V, | PspA/IM30 |
| IPR003842 | ,V, | Vacuolating cytotoxin |
| IPR007488 | ,V, | Protein of unknown function DUF535 |
| IPR003991 | ,V, | Pertactin virulence factor, C-terminal |
| IPR003992 | ,V, | Pertactin virulence factor, N-terminal |
| IPR004899 | ,V, | Pertactin |
| IPR008126 | ,V, | Yersinia outer membrane adhesion |
| IPR007985 | ,V, | Haemolysin expression modulating |
| IPR005594 | ,V, | YadA-like, C-terminal |
| IPR011050 | ,V, | Pectin lyase-like |
CORRESPONDENCE:
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This file is last modified Thursday 1st of June 2006 16:58:48 GMTGenome Atlas Database Tables has been accessed 1,935,136 times since 2004-03-23 14:56:50Genome Atlas Database Tables (Secretion Systems Overview) has been accessed 106,023 times since 2004-12-23 12:35:59Total hits for all Bacteria related pages has been accessed 58,827,383 times since 2004-03-23 14:47:10 |
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