| Accession | GenProp0317 |
| Name | CRISPR system, I-B subtype, Tneap branch |
| 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 Tneap subtype, so named because this subtype is the only one found in the genome of Thermotoga neapolitana DSM4359, consists of cas1-5 and the subtype specific genes cst1-2. The repeats associated with this subtype tend to have a periodicity of 66 nucleotides. This subtype is found both in Archaea and Bacteria (with the notable exclusion of the Proteobacteria). |
| JCVI Role | Other |
| Parent Property | GenProp0021: CRISPR region
|
| 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 ]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, Tneap region | Cas1 | YES | TIGR00287 (HMM-CLUST): CRISPR-associated endonuclease Cas1 | |
| Cas2, Tneap region | Cas2 | YES | TIGR01573 (HMM-CLUST): CRISPR-associated endonuclease Cas2 | |
| Cas3, Tneap region | Cas3 | YES | TIGR01596 (HMM-CLUST): CRISPR-associated endonuclease Cas3-HD
TIGR01587 (HMM-CLUST): CRISPR-associated helicase Cas3 | |
| Cas4, Tneap region | Cas4 | YES | TIGR00372 (HMM-CLUST): CRISPR-associated protein Cas4 | |
| Cas5, Tneap specific variant | Cas5t | YES | TIGR01895 (HMM): CRISPR-associated protein Cas5, subtype I-B/TNEAP | |
| Cas6, Tneap region | Cas6 | YES | TIGR01877 (HMM-CLUST): CRISPR-associated endoribonuclease Cas6 | |
| Cst1 | Cst1 | YES | TIGR01908 (HMM): CRISPR-associated protein Cas8b1/Cst1, subtype I-B/TNEAP | |
| Cst2, DevR family regulator | Cst2 | YES | TIGR02585 (HMM-CLUST): CRISPR-associated protein Cas7/Cst2/DevR, subtype I-B/TNEAP | |
| Accession | Name |
|---|
| GenProp0310 | CRISPR system, I-F/Ypest subtype |
| 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 |
| 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 |
