MTBC Gene Atlas

cspA Resolved · high auto-curated

H37Rv Rv3648c · MTBC0 mtbc0_003865 · 67 aa · 4112033–4112236 (-) · RefSeq NP_218165.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)cold shock protein A
MTBC0 PGAP re-annotationcold shock protein CspA
Revised (this work)Cold shock protein CspA. Pfam: CSD (PF00313.29).

Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.

Curated reference (UniProt)

UniProt P9WP75 SwissProt · reviewed · Evidence at protein level
UniProt nameProbable cold shock protein A

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category K Transcription
Preferred namecspA_1
eggNOG descriptioncold-shock protein
Orthologous groupCOG1278
KEGG orthology K03704
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 0.189 · strong purifying
Polymorphic sites (≥ 0.1% of strains) 3 synonymous, 2 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)

PfamAccessioni-EvalueResiduesDescription
CSDPF00313.29 1.6e-313–65 'Cold-shock' DNA-binding domain

Functional interaction network (STRING v12, guilt-by-association)

PartnerProductScoreNo text-miningChannels (≥400)
Rv0682 rpsL 30S ribosomal protein S12 864 858 coexpression:756 experimental:441
Rv0723 rplO 50S ribosomal protein L15 849 846 coexpression:743 experimental:424
Rv0685 tuf elongation factor Tu 862 844 coexpression:844
Rv3461c rpmJ 50S ribosomal protein L36 842 832 coexpression:757
Rv1038c esxJ ESAT-6 like protein EsxJ 826 826 coexpression:824
Rv1298 rpmE 50S ribosomal protein L31 839 820 coexpression:734
Rv2346c esxO ESAT-6 like protein EsxO 841 808 coexpression:806
Rv2347c esxP ESAT-6 like protein EsxP 807 807 coexpression:805
Rv0641 rplA 50S ribosomal protein L1 807 807 coexpression:773
Rv3620c esxW ESAT-6 like protein EsxW 839 806 coexpression:804
Rv1793 esxN ESAT-6 like protein EsxN 804 804 coexpression:802
Rv1197 esxK ESAT-6 like protein EsxK 802 803 coexpression:800
Rv1198 esxL ESAT-6 like protein EsxL 802 803 coexpression:800
Rv1037c esxI ESAT-6 like protein EsxI 801 802 coexpression:799
Rv3456c rplQ 50S ribosomal protein L17 773 773 coexpression:620 experimental:428

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: cold shock protein A
  • MTBC0 PGAP product: cold shock protein CspA
  • Pfam (hmmscan --cut_ga): CSD PF00313.29 (E=2e-31)
  • (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_218165.1)
  • Domains: Pfam-A via hmmscan --cut_ga — CSD (PF00313.29)
  • 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 COG1278
  • Curated reference: UniProt P9WP75 (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 — 104 functional partner(s)
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_003865|Rv3648c|cspA
MPQGTVKWFNAEKGFGFIAPEDGSADVFVHYTEIQGTGFRTLEENQKVEFEIGHSPKGPQATGVRSL