Rv3394c Family assigned · medium auto-curated
H37Rv Rv3394c · MTBC0 mtbc0_003606 ·
527 aa · 3834881–3836464 (-) ·
RefSeq NP_217911.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DNA polymerase Y family protein |
| Revised (this work) | DNA polymerase Y family protein. Pfam: IMS (PF00817.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O50419
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | UmuC domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | dinB_2 |
| eggNOG description | DNA polymerase |
| Orthologous group | COG0389 |
| KEGG orthology |
K14161
|
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 | 0.777 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 |
|---|---|---|---|---|
IMS | PF00817.26 | 3.8e-11 | 25–148 | impB/mucB/samB family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: dnaE2 (error-prone DNA polymerase), high confidence from genomic context alone (score 889 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) |
|---|---|---|---|---|
Rv3395c hyp |
hypothetical protein | 999 | 998 ctx | neighborhood:882 cooccurence:772 coexpression:936 textmining:661 |
Rv3370c dnaE2 |
error-prone DNA polymerase | 917 | 889 ctx | cooccurence:773 coexpression:450 |
Rv0002 dnaN |
DNA polymerase III subunit beta | 861 | 853 | experimental:627 database:612 |
Rv2116 lppK |
lipoprotein LppK | 861 | 852 | experimental:627 database:612 |
Rv2737c recA |
recombinase A | 826 | 808 | experimental:439 database:523 |
Rv1629 polA |
DNA polymerase I | 770 | 678 | database:553 |
Rv2101 helZ |
helicase HelZ | 687 | 667 | database:452 |
Rv1278 hyp |
hypothetical protein | 668 | 635 | database:548 |
Rv2090 |
5'-3' exonuclease | 656 | 635 | database:553 |
Rv0938 ligD |
multifunctional non-homologous end joining DNA repair protein/ATP dependent DNA ligase LigD | 678 | 632 | database:521 |
Rv3395A |
membrane protein | 610 | 611 ctx | neighborhood:609 |
Rv3731 ligC |
DNA ligase C | 632 | 610 | database:521 |
Rv1329c dinG |
ATP-dependent helicase DinG | 645 | 607 | database:577 |
Rv2720 lexA |
repressor LexA | 629 | 589 | experimental:463 |
Rv3646c topA |
DNA topoisomerase I | 645 | 587 | database:548 |
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 Y family protein
- Pfam (hmmscan --cut_ga): IMS PF00817.26 (E=4e-11)
- (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_217911.1)
- Domains: Pfam-A via hmmscan --cut_ga — IMS (PF00817.26)
- 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
COG0389 - Curated reference: UniProt O50419 (TrEMBL, unreviewed; Predicted)
- 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 —
63 functional partner(s); context anchor
dnaE2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003606|Rv3394c| MMASARVLAIWCMDWPAVAAAAAAGLSATAPVAVTLANRVIACSATARAAGVRRGLRRREAAARCPQLFIATADADRDARLFEGVIAAVDDLVPRAELLRPGLLVLPVRGPARFFGSEQMAAERLIDAVAAAGAECQVGIADRLSTAVFAARAGRIVEPGGDARFLSLLSIRQLATEPSLSGPGRDDLTDLLWRMGIRTIGQFAALSRTDVASRFGADAVAAHRFARGEPERAPCGREPPPDLAAELACDPPIDRVDAAAFAGRSLAAELHRALMAAGVGCTRLAIHAVTANGEERSRVWRCAEPLTEDATADRVRWQLDGWLNNRNARDRPTAAVTLLRLQAVETVSASEGLQLPLWGGLGEQDRLRARRALVRVQGLLGPEAVRVPVLSGGHGPAERITLTVLGLVAPEPVPQADPGQPWPGRLPDPSPAVLFDDPVDLLDAQGNPIRVTSRGMFSADPARLRVRGRDDRLRWWAGPWPDDERWWDPDRASGRTARAQVLLDGDPGTALLLCYRQRRWYLEGSYE