| Accession | GenProp0310 |
| Name | CRISPR system, I-F/Ypest subtype |
| Type | SYSTEM |
| Description | CRISPR repeats are by definition Clustered Regularly Interspaced Short Palindromic Repeats, described by Jansen [1]. Certain proteins, including Cas1 to Cas4, are found only in genomes with CRISPR repeats, and are near these repeats. Jansen, et al. describe CRISPR loci as having direct repeats, varying in size from 21 to 37 bp, interspaced by similarly sized non-repetitive sequences. Variants of CRISP/Cas loci (subtypes) have been described (Haft, Selengut, et al., submitted) in which certain groups of subtype-specific genes are found in addition to characteristic sets of the more widely distributed cas genes. The Ypest subtype, so named because this subtype is the only one found in the genome of Yersinia pestis, consists of cas1, cas3 and the subtype specific genes csy1-4. The cas3 gene of this subtype is sufficiently diverged from the cas3 gene of other CRISPR subtypes that the construction of a separate HMM was warranted. The spacers of these CRISPRs have been analyzed and some have been shown to have been captured from extrachromosomal sources [2]. The repeats associated with this subtype tend to have a periodicity of 60 nucleotides. This subtype is found only in the Proteobacteria. |
| JCVI Role | Other |
| Parent Property | GenProp0021: CRISPR region
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| Literature References | [ 1 ]Saunders NF, Goodchild A, Raftery M, Guilhaus M, Curmi PM, Cavicchioli R Predicted roles for hypothetical proteins in the low-temperature expressed proteome of the Antarctic archaeon Methanococcoides burtonii. J Proteome Res 2005 Mar-Apr;4(2):464-72. PMID 15822923
[ 2 ]Pourcel C, Salvignol G, Vergnaud G CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology 2005 Mar;151(Pt 3):653-63. PMID 15758212
[ 3 ]Haft DH, Selengut J, Mo ngodin EF, Nelson KE A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput Biol. 2005 Nov;1(6):e60. PMID 16292354
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| Step Name | Step Num | Required | Evidence (Method) | Evidence Go Terms |
|---|
| Cas1, Ypest region | Cas1 | YES | TIGR03637 (HMM): CRISPR-associated endonuclease Cas1, subtype I-F/YPEST | |
| Cas3, Ypest subtype variant | Cas3 | YES | TIGR02562 (HMM): CRISPR-associated helicase Cas3, subtype I-F/YPEST | |
| Csy1 | Csy1 | YES | TIGR02564 (HMM): CRISPR type I-F/YPEST-associated protein Csy1 | |
| Csy2 | Csy2 | YES | TIGR02565 (HMM): CRISPR type I-F/YPEST-associated protein Csy2 | |
| Csy3 | Csy3 | YES | TIGR02566 (HMM): CRISPR type I-F/YPEST-associated protein Csy3 | |
| CRISPR-derived RNA endonuclease Csy4 | Csy4 | YES | TIGR02563 (HMM): CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST | |
| Accession | Name |
|---|
| GenProp0313 | CRISPR system, I-C/Dvulg subtype |
| GenProp0314 | CRISPR system, II/Nmeni subtype |
| GenProp0315 | CRISPR system, I-E/Ecoli subtype |
| GenProp0316 | CRISPR system, III-B/RAMP module subtype |
| GenProp0317 | CRISPR system, I-B subtype, Tneap branch |
| GenProp0318 | CRISPR system, III-A/Mtube subtype |
| GenProp0319 | CRISPR system, I-A/Apern subtype |
| GenProp0320 | CRISPR system, I-B subtype, Hmari branch |
| GenProp0469 | CRISPR system, Dpsyc subtype |
| GenProp0670 | CRISPR system, Aferr subtype |
| GenProp0685 | CRISPR system, I-D/Cyano subtype |
| GenProp0768 | CRISPR system, Pging subtype |
| GenProp0922 | CRISPR system, Myxan subtype |
| GenProp1061 | CRISPR system, PreFran subtype |
