cas1 Resolved · high auto-curated
H37Rv Rv2817c · MTBC0 mtbc0_002995 ·
338 aa · 3144624–3145640 (-) ·
RefSeq NP_217333.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | CRISPR-associated endonuclease Cas1 |
|---|---|
| MTBC0 PGAP re-annotation | CRISPR-associated endonuclease Cas1 |
| Revised (this work) | CRISPR-associated endonuclease Cas1. Pfam: Cas_Cas1 (PF01867.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPJ5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | CRISPR-associated endonuclease Cas1 |
| EC (curated) |
EC 3.1.-.-
|
| Curated function | CRISPR (clustered regularly interspaced short palindromic repeat) is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). The type III-A Csm effector complex binds crRNA and acts as a crRNA-guided RNase, DNase and cyclic oligoadenylate synthase; binding of target RNA cognate to the crRNA is required for all activiti. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | cas1 |
| eggNOG description | CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Acts as a dsDNA endonuclease. Involved in the integration of spacer DNA into the CRISPR cassette |
| Orthologous group | COG1518 |
| KEGG orthology |
K15342
|
| Gene Ontology (8) |
GO:0005575, GO:0005618, GO:0005623, GO:0008150, GO:0030312, GO:0040007, GO:0044464, GO:0071944
|
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 5 missense, 0 nonsense, 0 frameshift |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
Cas_Cas1 | PF01867.22 | 1.3e-75 | 4–283 | CRISPR associated protein Cas1 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cas2 (CRISPR-associated endoribonuclease Cas2), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2816c cas2 |
CRISPR-associated endoribonuclease Cas2 | 999 | 1000 ctx | neighborhood:882 cooccurence:646 coexpression:865 experimental:928 |
Rv2821c csm3 |
CRISPR type III-associated RAMP protein Csm3 | 859 | 859 ctx | neighborhood:559 cooccurence:692 |
Rv2823c cas10 |
CRISPR-associated protein Cas10/Csm1 | 863 | 843 ctx | neighborhood:559 cooccurence:647 |
Rv2818c csm6 |
CRISPR-associated protein Csm6 | 777 | 777 ctx | neighborhood:775 |
Rv2820c csm4 |
CRISPR type III-associated RAMP protein Csm4 | 777 | 777 ctx | neighborhood:559 cooccurence:512 |
Rv2824c cas6 |
CRISPR-associated endoribonuclease Cas6 | 795 | 757 ctx | neighborhood:559 cooccurence:447 |
Rv2819c csm5 |
CRISPR type III-associated RAMP protein Csm5 | 731 | 731 ctx | neighborhood:559 cooccurence:411 |
Rv2822c csm2 |
CRISPR type III-associated protein Csm2 | 719 | 719 ctx | neighborhood:559 |
Rv1752 hyp |
hypothetical protein | 557 | 518 | coexpression:408 |
Rv2986c hupB |
DNA-binding protein HU | 470 | 471 | experimental:465 |
Rv1343c lprD |
lipoprotein LprD | 404 | 404 | coexpression:404 |
Rv1213 glgC |
glucose-1-phosphate adenylyltransferase | 404 | 404 | coexpression:404 |
Rv1525 wbbL2 |
rhamnosyl transferase WbbL | 400 | 401 | |
Rv2515c hyp |
hypothetical protein | 504 | 193 | textmining:411 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Legacy H37Rv annotation: CRISPR-associated endonuclease Cas1
- MTBC0 PGAP product: CRISPR-associated endonuclease Cas1
- Pfam (hmmscan --cut_ga): Cas_Cas1 PF01867.22 (E=1e-75)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_217333.1)
- Domains: Pfam-A via hmmscan --cut_ga — Cas_Cas1 (PF01867.22)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG1518 - Curated reference: UniProt P9WPJ5 (SwissProt, reviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
14 functional partner(s); context anchor
cas2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002995|Rv2817c|cas1 MVQLYVSDSVSRISFADGRVIVWSEELGESQYPIETLDGITLFGRPTMTTPFIVEMLKRERDIQLFTTDGHYQGRISTPDVSYAPRLRQQVHRTDDPAFCLSLSKRIVSRKILNQQALIRAHTSGQDVAESIRTMKHSLAWVDRSGSLAELNGFEGNAAKAYFTALGHLVPQEFAFQGRSTRPPLDAFNSMVSLGYSLLYKNIIGAIERHSLNAYIGFLHQDSRGHATLASDLMEVWRAPIIDDTVLRLIADGVVDTRAFSKNSDTGAVFATREATRSIARAFGNRIARTATYIKGDPHRYTFQYALDLQLQSLVRVIEAGHPSRLVDIDITSEPSGA