Rv2413c Family assigned · medium auto-curated
H37Rv Rv2413c · MTBC0 mtbc0_002569 ·
316 aa · 2734619–2735569 (-) ·
RefSeq NP_216929.3
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DNA polymerase III subunit delta |
| Revised (this work) | DNA polymerase III subunit delta. Pfam: DNA_pol3_delta_C (PF21694.3). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71730
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable DNA polymerase III subunit delta |
| EC (curated) |
EC 2.7.7.7
|
| Curated function | DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. Pol III also exhibits 3'-5' exonuclease activity. The delta subunit interacts with the gamma/tau subunit to load the beta sliding clamp (dnaN) onto the DNA (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | holA |
| eggNOG description | DNA polymerase III, delta |
| Orthologous group | COG1466 |
| EC number |
EC 2.7.7.7
|
| KEGG orthology |
K02340
|
| KEGG pathways |
map00230, map00240, map01100, map03030, map03430, map03440
|
| KEGG modules |
M00260
|
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 | 1.487 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 4 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 |
|---|---|---|---|---|
DNA_pol3_delta_C | PF21694.3 | 2.7e-08 | 193–304 | DNA polymerase III delta subunit, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3644c (DNA polymerase), high confidence from genomic context alone (score 995 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) |
|---|---|---|---|---|
Rv3644c |
DNA polymerase | 995 | 995 ctx | cooccurence:690 experimental:829 database:900 |
Rv0002 dnaN |
DNA polymerase III subunit beta | 989 | 988 | experimental:829 database:900 |
Rv3721c dnaZX |
DNA polymerase III subunit gamma/tau | 987 | 986 | experimental:829 database:900 |
Rv1547 dnaE1 |
DNA polymerase III subunit alpha | 988 | 985 | experimental:829 database:900 |
Rv2191 hyp |
hypothetical protein | 966 | 944 | experimental:442 database:900 textmining:413 |
Rv3711c dnaQ |
DNA polymerase III subunit epsilon | 948 | 942 | experimental:442 database:900 |
Rv2414c hyp |
hypothetical protein | 888 | 880 ctx | neighborhood:839 |
Rv3370c dnaE2 |
error-prone DNA polymerase | 895 | 857 | experimental:829 |
Rv2116 lppK |
lipoprotein LppK | 851 | 832 | experimental:829 |
Rv2415c hyp |
hypothetical protein | 836 | 830 ctx | neighborhood:829 |
Rv2050 rbpA |
RNA polymerase-binding protein RbpA | 769 | 769 ctx | cooccurence:769 |
Rv2708c hyp |
hypothetical protein | 760 | 761 ctx | cooccurence:759 |
Rv2680 hyp |
hypothetical protein | 738 | 739 ctx | cooccurence:738 |
Rv2146c |
transmembrane protein | 742 | 726 ctx | cooccurence:719 |
Rv2219 |
transmembrane protein | 725 | 726 ctx | cooccurence:725 |
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: DNA polymerase III subunit delta
- Pfam (hmmscan --cut_ga): DNA_pol3_delta_C PF21694.3 (E=3e-08)
- (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_216929.3)
- Domains: Pfam-A via hmmscan --cut_ga — DNA_pol3_delta_C (PF21694.3)
- 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
COG1466 - Curated reference: UniProt P71730 (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 —
82 functional partner(s); context anchor
Rv3644c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002569|Rv2413c| MHLVLGDEELLVERAVADVLRSARQRAGTADVPVSRMRAGDVGAYELAELLSPSLFAEERIVVLGAAAEAGKDAAAVIESAAADLPAGTVLVVVHSGGGRAKSLANQLRSMGAQVHPCARITKVSERADFIRSEFASLRVKVDDETVTALLDAVGSDVRELASACSQLVADTGGAVDAAAVRRYHSGKAEVRGFDIADKAVAGDVAGAAEALRWAMMRGEPLVVLADALAEAVHTIGRVGPQSGDPYRLAAQLGMPPWRVQKAQKQARRWSRDTVATAMRLVAELNANVKGAVADADYALESAVRQVAELVADRGR