cspB Resolved · high auto-curated
H37Rv Rv0871 · MTBC0 mtbc0_000926 ·
135 aa · 971101–971508 (+) ·
RefSeq NP_215386.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | cold shock-like protein CspB |
|---|---|
| MTBC0 PGAP re-annotation | cold-shock protein |
| Revised (this work) | Cold-shock protein. 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 |
I6WZM9
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable cold shock-like protein B CspB |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | cspB |
| eggNOG description | Cold-shock' |
| Orthologous group | COG1278 |
| KEGG orthology |
K03704
|
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 | 0.057 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 1 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 |
|---|---|---|---|---|
CSD | PF00313.29 | 4.3e-15 | 3–62 | 'Cold-shock' DNA-binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: moaA2 (molybdenum cofactor biosynthesis protein MoaA), high confidence from genomic context alone (score 776 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0869c moaA2 |
molybdenum cofactor biosynthesis protein MoaA | 787 | 776 ctx | neighborhood:768 |
Rv0870c |
integral membrane protein | 770 | 770 ctx | neighborhood:768 |
Rv0868c moaD2 |
cyclic pyranopterin monophosphate synthase | 768 | 769 ctx | neighborhood:768 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 732 | 705 | database:638 |
Rv3754 tyrA |
prephenate dehydrogenase TyrA | 686 | 687 | coexpression:686 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 673 | 655 | database:634 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 681 | 651 | database:638 |
Rv2442c rplU |
50S ribosomal protein L21 | 610 | 610 | experimental:421 |
Rv0427c xthA |
exodeoxyribonuclease III protein XthA | 626 | 608 | database:542 |
Rv0701 rplC |
50S ribosomal protein L3 | 613 | 599 | experimental:453 |
Rv3211 rhlE |
ATP-dependent RNA helicase RhlE | 808 | 589 | experimental:419 textmining:553 |
Rv1253 deaD |
ATP-dependent RNA helicase DeaD | 922 | 584 | experimental:419 textmining:821 |
Rv2412 rpsT |
30S ribosomal protein S20 | 616 | 577 | |
Rv1643 rplT |
50S ribosomal protein L20 | 565 | 563 | experimental:459 |
Rv0683 rpsG |
30S ribosomal protein S7 | 575 | 559 | experimental:451 |
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-like protein CspB
- MTBC0 PGAP product: cold-shock protein
- Pfam (hmmscan --cut_ga): CSD PF00313.29 (E=4e-15)
- (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_215386.1)
- 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 I6WZM9 (TrEMBL, unreviewed; 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 —
76 functional partner(s); context anchor
moaA2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000926|Rv0871|cspB MPTGKVKWYDPDKGFGFLSQEGGEDVYVRSSALPTGVEALKAGQRVEFGIASGRRGPQALSLRLIEPPPSLSRPRREPAAEHKHSPDELHGMVEDMITLLESTVQPELRKGRYPDRKTARRVAEVVRAVAREFES