polA Resolved · high auto-curated
H37Rv Rv1629 · MTBC0 mtbc0_001737 ·
904 aa · 1842629–1845343 (+) ·
RefSeq NP_216145.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | DNA polymerase I |
|---|---|
| MTBC0 PGAP re-annotation | DNA polymerase I |
| Revised (this work) | DNA polymerase I. Pfam: 5_3_exonuc_N (PF02739.23), 5_3_exonuc (PF01367.26), DNA_polI_exo1 (PF22619.3), DNA_pol_A (PF00476.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WNU5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | DNA polymerase I |
| EC (curated) |
EC 2.7.7.7
|
| Curated function | In addition to polymerase activity, this DNA polymerase exhibits 3'-5' and 5'-3' exonuclease activity. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | polA |
| eggNOG description | In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity |
| Orthologous group | COG0258 |
| EC number |
EC 2.7.7.7
|
| KEGG orthology |
K02335
|
| KEGG pathways |
map00230, map00240, map01100, map03030, map03410, map03420, map03440
|
| Gene Ontology (61) |
GO:0003674, GO:0003824, GO:0003887, GO:0004518, GO:0004527, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005886, GO:0006139 +49 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 | 0.279 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 15 synonymous, 12 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 |
|---|---|---|---|---|
5_3_exonuc_N | PF02739.23 | 3.7e-59 | 16–184 | 5'-3' exonuclease, N-terminal resolvase-like domain |
5_3_exonuc | PF01367.26 | 2.6e-29 | 186–279 | 5'-3' exonuclease, C-terminal SAM fold |
DNA_polI_exo1 | PF22619.3 | 1.4e-08 | 356–443 | DNA polymerase I, ribonuclease H-like domain |
DNA_pol_A | PF00476.27 | 1.2e-151 | 526–900 | DNA polymerase family A |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: coaE (dephospho-CoA kinase CoaE), high confidence from genomic context alone (score 856 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0002 dnaN |
DNA polymerase III subunit beta | 997 | 995 | coexpression:414 experimental:970 database:630 textmining:508 |
Rv2116 lppK |
lipoprotein LppK | 995 | 993 | coexpression:414 experimental:970 database:630 |
Rv2737c recA |
recombinase A | 996 | 987 | coexpression:460 experimental:898 database:585 textmining:750 |
Rv1277 hyp |
hypothetical protein | 989 | 980 | experimental:836 database:844 textmining:494 |
Rv2529 hyp |
hypothetical protein | 969 | 951 | experimental:662 database:844 textmining:412 |
Rv1278 hyp |
hypothetical protein | 952 | 919 | experimental:432 database:844 textmining:430 |
Rv1329c dinG |
ATP-dependent helicase DinG | 955 | 897 | experimental:721 database:621 textmining:580 |
Rv2101 helZ |
helicase HelZ | 930 | 863 | experimental:538 database:660 textmining:513 |
Rv1252c lprE |
lipoprotein LprE | 878 | 861 | database:844 |
Rv1631 coaE |
dephospho-CoA kinase CoaE | 922 | 856 ctx | neighborhood:726 coexpression:405 textmining:488 |
Rv0938 ligD |
multifunctional non-homologous end joining DNA repair protein/ATP dependent DNA ligase LigD | 949 | 850 | experimental:454 database:569 textmining:680 |
Rv1630 rpsA |
30S ribosomal protein S1 | 891 | 844 ctx | neighborhood:710 |
Rv3062 ligB |
DNA ligase | 901 | 842 | experimental:454 database:569 textmining:405 |
Rv3731 ligC |
DNA ligase C | 906 | 840 | experimental:454 database:569 textmining:439 |
Rv2464c nei1 |
DNA glycosylase | 865 | 816 | coexpression:791 |
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 I
- MTBC0 PGAP product: DNA polymerase I
- Pfam (hmmscan --cut_ga): 5_3_exonuc_N PF02739.23 (E=4e-59), 5_3_exonuc PF01367.26 (E=3e-29), DNA_polI_exo1 PF22619.3 (E=1e-08), DNA_pol_A PF00476.27 (E=1e-151)
- (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_216145.1)
- Domains: Pfam-A via hmmscan --cut_ga — 5_3_exonuc_N (PF02739.23), 5_3_exonuc (PF01367.26), DNA_polI_exo1 (PF22619.3), DNA_pol_A (PF00476.27)
- 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
COG0258 - Curated reference: UniProt P9WNU5 (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 —
338 functional partner(s); context anchor
coaE - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001737|Rv1629|polA MVTTASAPSEDRAKPTLMLLDGNSLAFRAFYALPAENFKTRGGLTTNAVYGFTAMLINLLRDEAPTHIAAAFDVSRQTFRLQRYPEYKANRSSTPDEFAGQIDITKEVLGALGITVLSEPGFEADDLIATLATQAENEGYRVLVVTGDRDALQLVSDDVTVLYPRKGVSELTRFTPEAVVEKYGLTPRQYPDFAALRGDPSDNLPGIPGVGEKTAAKWIAEYGSLRSLVDNVDAVRGKVGDALRANLASVVRNRELTDLVRDVPLAQTPDTLRLQPWDRDHIHRLFDDLEFRVLRDRLFDTLAAAGGPEVDEGFDVRGGALAPGTVRQWLAEHAGDGRRAGLTVVGTHLPHGGDATAMAVAAADGEGAYLDTATLTPDDDAALAAWLADPAKPKALHEAKAAVHDLAGRGWTLEGVTSDTALAAYLVRPGQRSFTLDDLSLRYLRRELRAETPQQQQLSLLDDDDTDAETIQTTILRARAVIDLADALDAELARIDSTALLGEMELPVQRVLAKMESAGIAVDLPMLTELQSQFGDQIRDAAEAAYGVIGKQINLGSPKQLQVVLFDELGMPKTKRTKTGYTTDADALQSLFDKTGHPFLQHLLAHRDVTRLKVTVDGLLQAVAADGRIHTTFNQTIAATGRLSSTEPNLQNIPIRTDAGRRIRDAFVVGDGYAELMTADYSQIEMRIMAHLSGDEGLIEAFNTGEDLHSFVASRAFGVPIDEVTGELRRRVKAMSYGLAYGLSAYGLSQQLKISTEEANEQMDAYFARFGGVRDYLRAVVERARKDGYTSTVLGRRRYLPELDSSNRQVREAAERAALNAPIQGSAADIIKVAMIQVDKALNEAQLASRMLLQVHDELLFEIAPGERERVEALVRDKMGGAYPLDVPLEVSVGYGRSWDAAAH