Rv3716c Family assigned · medium auto-curated
H37Rv Rv3716c · MTBC0 mtbc0_003939 ·
133 aa · 4184633–4185034 (-) ·
RefSeq NP_218233.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | YbaB/EbfC family nucleoid-associated protein |
| Revised (this work) | YbaB/EbfC family nucleoid-associated protein. Pfam: YbaB_DNA_bd (PF02575.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WNR9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Nucleoid-associated protein Rv3716c |
| Curated function | Binds to DNA and alters its conformation. May be involved in regulation of gene expression, nucleoid organization and DNA protection. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | ybaB |
| eggNOG description | Binds to DNA and alters its conformation. May be involved in regulation of gene expression, nucleoid organization and DNA protection |
| Orthologous group | COG0718 |
| KEGG orthology |
K09747
|
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, 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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 0 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 |
|---|---|---|---|---|
YbaB_DNA_bd | PF02575.22 | 1.2e-31 | 12–100 | YbaB/EbfC DNA-binding family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: recR (recombination protein RecR), high confidence from genomic context alone (score 973 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) |
|---|---|---|---|---|
Rv3715c recR |
recombination protein RecR | 983 | 973 ctx | neighborhood:876 coexpression:792 |
Rv2460c clpP2 |
ATP-dependent CLP protease proteolytic subunit 2 | 809 | 777 | coexpression:770 |
Rv3717 hyp |
hypothetical protein | 776 | 776 ctx | neighborhood:775 |
Rv3714c hyp |
hypothetical protein | 627 | 627 ctx | neighborhood:625 |
Rv3721c dnaZX |
DNA polymerase III subunit gamma/tau | 575 | 535 | coexpression:422 |
Rv2842c rimP |
ribosome maturation factor RimP | 514 | 515 | coexpression:410 |
Rv1307 atpH |
ATP synthase subunit b/delta | 463 | 464 | coexpression:448 |
Rv3443c rplM |
50S ribosomal protein L13 | 450 | 450 | coexpression:432 |
Rv3644c |
DNA polymerase | 487 | 439 | coexpression:420 |
Rv3709c ask |
aspartokinase | 434 | 435 | |
Rv0652 rplL |
50S ribosomal protein L7/L12 | 432 | 432 | coexpression:414 |
Rv2457c clpX |
ATP-dependent CLP protease ATP-binding subunit ClpX | 420 | 421 | |
Rv1901 cinA |
competence damage-inducible protein CinA | 416 | 415 | |
Rv0714 rplN |
50S ribosomal protein L14 | 403 | 403 | |
Rv2461c clpP1 |
ATP-dependent CLP protease proteolytic subunit 1 | 465 | 384 |
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: hypothetical protein
- MTBC0 PGAP product: YbaB/EbfC family nucleoid-associated protein
- Pfam (hmmscan --cut_ga): YbaB_DNA_bd PF02575.22 (E=1e-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_218233.1)
- Domains: Pfam-A via hmmscan --cut_ga — YbaB_DNA_bd (PF02575.22)
- 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
COG0718 - Curated reference: UniProt P9WNR9 (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 —
22 functional partner(s); context anchor
recR - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003939|Rv3716c| MQPGGDMSALLAQAQQMQQKLLEAQQQLANSEVHGQAGGGLVKVVVKGSGEVIGVTIDPKVVDPDDIETLQDLIVGAMRDASQQVTKMAQERLGALAGAMRPPAPPAAPPGAPGMPGMPGMPGAPGAPPVPGI