Rv3644c Family assigned · medium auto-curated
H37Rv Rv3644c · MTBC0 mtbc0_003861 ·
401 aa · 4105221–4106426 (-) ·
RefSeq NP_218161.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | DNA polymerase |
|---|---|
| MTBC0 PGAP re-annotation | DNA polymerase III subunit delta' |
| Revised (this work) | DNA polymerase III subunit delta'. Pfam: DNA_pol3_delta2 (PF13177.13), AAA (PF00004.36), DNApol3-delta_C (PF09115.16). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06363
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | DNA polymerase III subunit delta' |
| EC (curated) |
EC 2.7.7.7
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | holB |
| eggNOG description | DNA polymerase III |
| Orthologous group | COG0470 |
| EC number |
EC 2.7.7.7
|
| KEGG orthology |
K02341
|
| KEGG pathways |
map00230, map00240, map01100, map03030, map03430, map03440
|
| KEGG modules |
M00260
|
| Gene Ontology (34) |
GO:0005575, GO:0005622, GO:0005623, GO:0006139, GO:0006259, GO:0006260, GO:0006261, GO:0006725, GO:0006807, GO:0008150, GO:0008152, GO:0009058 +22 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 | 0.192 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 8 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_delta2 | PF13177.13 | 5.2e-36 | 37–179 | DNA polymerase III, delta subunit |
AAA | PF00004.36 | 3.4e-04 | 44–178 | ATPase family associated with various cellular activities (AAA) |
DNApol3-delta_C | PF09115.16 | 7.1e-05 | 325–380 | DNA polymerase III, delta subunit, C terminal |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: dnaN (DNA polymerase III subunit beta), high confidence from genomic context alone (score 987 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2413c hyp |
hypothetical protein | 995 | 995 ctx | cooccurence:690 experimental:829 database:900 |
Rv0002 dnaN |
DNA polymerase III subunit beta | 988 | 987 ctx | cooccurence:454 experimental:773 database:900 |
Rv1547 dnaE1 |
DNA polymerase III subunit alpha | 983 | 982 | experimental:773 database:900 |
Rv2191 hyp |
hypothetical protein | 971 | 961 | experimental:474 database:900 |
Rv3711c dnaQ |
DNA polymerase III subunit epsilon | 951 | 947 | experimental:474 database:900 |
Rv3721c dnaZX |
DNA polymerase III subunit gamma/tau | 924 | 925 | database:900 |
Rv0054 ssb |
single-strand DNA-binding protein | 843 | 829 | experimental:773 |
Rv2478c hyp |
hypothetical protein | 823 | 806 | experimental:773 |
Rv3370c dnaE2 |
error-prone DNA polymerase | 805 | 787 | experimental:773 |
Rv2116 lppK |
lipoprotein LppK | 799 | 780 | experimental:773 |
Rv2977c thiL |
thiamine-monophosphate kinase | 733 | 734 | coexpression:733 |
Rv3195 hyp |
hypothetical protein | 623 | 623 ctx | cooccurence:622 |
Rv2343c dnaG |
DNA primase | 661 | 616 ctx | cooccurence:595 |
Rv2362c recO |
DNA repair protein RecO | 649 | 602 ctx | cooccurence:424 |
Rv1830 |
HTH-type transcriptional regulator | 584 | 585 |
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: DNA polymerase
- MTBC0 PGAP product: DNA polymerase III subunit delta'
- Pfam (hmmscan --cut_ga): DNA_pol3_delta2 PF13177.13 (E=5e-36), AAA PF00004.36 (E=3e-04), DNApol3-delta_C PF09115.16 (E=7e-05)
- (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_218161.1)
- Domains: Pfam-A via hmmscan --cut_ga — DNA_pol3_delta2 (PF13177.13), AAA (PF00004.36), DNApol3-delta_C (PF09115.16)
- 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
COG0470 - Curated reference: UniProt O06363 (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 —
47 functional partner(s); context anchor
dnaN - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003861|Rv3644c| MSGVFTRLVGQQAVEAELLATAKAARRDSAHSAGGGGTMTHAWLLTGPPGSGRSVAALCFAAALQCTSGGEPGCGRCRACTTTLAGTHADVRRVIPEGLSIGVDEMRAIVQIAARRPTTGHWQIVVIEDADRLTEGAANALLKVVEEPPPSTVFLLCAPSVDPEDIAVTLRSRCRHVALVTPSTHAIAQVLSDGDGLDPDTANWAASVSGGHVGRARRLATDPQARQRRERALGLARDAATPSRAYAAAEELVAGAEAEALALTAQRIEAETEELRTALGAGGTGKGTGAALRGATGAMKDLERRQKSRQTRASRDALDRALIDLATYFRDALLVAAHAGGVRANHPDMADRVAALAAHAPPERLLRCIEAVLACREALAVNVKPKFAVDAMVATIGQELR