ssb Family assigned · medium auto-curated
H37Rv Rv0054 · MTBC0 mtbc0_000059 ·
164 aa · 58694–59188 (+) ·
RefSeq NP_214568.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | single-strand DNA-binding protein |
|---|---|
| MTBC0 PGAP re-annotation | single-stranded DNA-binding protein |
| Revised (this work) | Single-stranded DNA-binding protein. Pfam: SSB (PF00436.32). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGD5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Single-stranded DNA-binding protein |
| Curated function | Binds single-stranded (ss)DNA. At low concentrations (0.02 to 0.16 uM), stimulates the 5'-3' helicase activity of DnaB. At higher concentrtions eventually totally inhibits DnaB helicase. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | ssb |
| eggNOG description | Single-stranded DNA-binding protein |
| Orthologous group | COG0629 |
| KEGG orthology |
K03111
|
| KEGG pathways |
map03030, map03430, map03440
|
| Gene Ontology (23) |
GO:0003674, GO:0003676, GO:0003677, GO:0003697, GO:0005488, GO:0005575, GO:0005576, GO:0005623, GO:0005886, GO:0006950, GO:0006974, GO:0008150 +11 more
|
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 | 0.232 · 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
SSB | PF00436.32 | 7.7e-31 | 6–106 | Single-strand binding protein family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rplI (50S ribosomal protein L9), high confidence from genomic context alone (score 957 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0056 rplI |
50S ribosomal protein L9 | 959 | 957 ctx | neighborhood:783 coexpression:809 |
Rv0053 rpsF |
30S ribosomal protein S6 | 955 | 949 ctx | neighborhood:770 coexpression:733 |
Rv2478c hyp |
hypothetical protein | 913 | 910 | database:900 |
Rv0055 rpsR1 |
30S ribosomal protein S18 | 866 | 858 ctx | neighborhood:821 |
Rv0058 dnaB |
replicative DNA helicase | 893 | 856 ctx | neighborhood:554 experimental:621 |
Rv3644c |
DNA polymerase | 843 | 829 | experimental:773 |
Rv1547 dnaE1 |
DNA polymerase III subunit alpha | 843 | 829 | experimental:773 |
Rv2228c |
multifunctional RNASE H/alpha-ribazole phosphatase/acid phosphatase | 839 | 823 | experimental:775 |
Rv1402 priA |
primosomal protein N' | 865 | 818 | experimental:787 |
Rv3370c dnaE2 |
error-prone DNA polymerase | 826 | 810 | experimental:773 |
Rv3721c dnaZX |
DNA polymerase III subunit gamma/tau | 809 | 780 | experimental:773 |
Rv0700 rpsJ |
30S ribosomal protein S10 | 784 | 759 | coexpression:671 |
Rv0640 rplK |
50S ribosomal protein L11 | 763 | 755 | coexpression:661 |
Rv0651 rplJ |
50S ribosomal protein L10 | 750 | 751 | coexpression:688 |
Rv0683 rpsG |
30S ribosomal protein S7 | 728 | 728 | coexpression:682 |
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: single-strand DNA-binding protein
- MTBC0 PGAP product: single-stranded DNA-binding protein
- Pfam (hmmscan --cut_ga): SSB PF00436.32 (E=8e-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_214568.1)
- 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 P9WGD5 (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 —
93 functional partner(s); context anchor
rplI - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000059|Rv0054|ssb MAGDTTITIVGNLTADPELRFTPSGAAVANFTVASTPRIYDRQTGEWKDGEALFLRCNIWREAAENVAESLTRGARVIVSGRLKQRSFETREGEKRTVIEVEVDEIGPSLRYATAKVNKASRSGGFGSGSRPAPAQTSSASGDDPWGSAPASGSFGGGDDEPPF