Rv2478c Family assigned · medium auto-curated
H37Rv Rv2478c · MTBC0 - ·
161 aa · 2784123–2784608 (-) ·
RefSeq NP_216994.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains SSB (PF00436.32) domain(s); putative function inferred from the domain architecture. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
O53205
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Single-stranded DNA-binding protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | ssb2 |
| eggNOG description | Single-stranded DNA-binding protein |
| Orthologous group | COG0629 |
| KEGG orthology |
K03111
|
| KEGG pathways |
map03030, map03430, map03440
|
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, 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 |
|---|---|---|---|---|
SSB | PF00436.32 | 7.2e-15 | 1–96 | Single-strand binding protein family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ettA (macrolide ABC transporter ATP-binding protein), high confidence from genomic context alone (score 796 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0054 ssb |
single-strand DNA-binding protein | 913 | 910 | database:900 |
Rv3370c dnaE2 |
error-prone DNA polymerase | 824 | 809 | experimental:773 |
Rv3644c |
DNA polymerase | 823 | 806 | experimental:773 |
Rv2228c |
multifunctional RNASE H/alpha-ribazole phosphatase/acid phosphatase | 816 | 797 | experimental:775 |
Rv2477c ettA |
macrolide ABC transporter ATP-binding protein | 796 | 796 ctx | neighborhood:786 |
Rv1402 priA |
primosomal protein N' | 812 | 792 | experimental:787 |
Rv1547 dnaE1 |
DNA polymerase III subunit alpha | 799 | 781 | experimental:773 |
Rv3721c dnaZX |
DNA polymerase III subunit gamma/tau | 809 | 780 | experimental:773 |
Rv0053 rpsF |
30S ribosomal protein S6 | 765 | 736 | coexpression:721 |
Rv0651 rplJ |
50S ribosomal protein L10 | 717 | 717 | coexpression:680 |
Rv2476c gdh |
NAD-dependent glutamate dehydrogenase | 713 | 713 ctx | neighborhood:710 |
Rv0683 rpsG |
30S ribosomal protein S7 | 713 | 713 | coexpression:665 |
Rv0700 rpsJ |
30S ribosomal protein S10 | 733 | 703 | coexpression:664 |
Rv0640 rplK |
50S ribosomal protein L11 | 713 | 703 | coexpression:650 |
Rv2474c hyp |
hypothetical protein | 701 | 701 ctx | neighborhood:699 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): hypothetical protein
- Pfam (hmmscan --cut_ga): SSB PF00436.32 (E=7e-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_216994.1)
- Domains: Pfam-A via hmmscan --cut_ga — SSB (PF00436.32)
- 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
COG0629 - Curated reference: UniProt O53205 (TrEMBL, unreviewed; Predicted)
- 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 —
95 functional partner(s); context anchor
ettA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2478c| MVGHIVNDLQRRKVGDQEVVKFRVASNSRRRTSDGGWEPGNSLFITVNCWGRLVTGVGAALGKGAPVIVVGHVYTSEYEDRDGIRRSSLEMRATSVGPDLSRVIVRIEKPAYTGPSAGDLPAATGTGAAGAADAPASAADSVSDVVVDDAITGHNPLPISA