Rv0142 Resolved · medium
H37Rv Rv0142 · MTBC0 mtbc0_000153 ·
308 aa · 168057–168983 (+) ·
RefSeq NP_214656.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DNA-3-methyladenine glycosylase |
| Revised (this work) | DNA-3-methyladenine glycosylase: a base-excision-repair enzyme that removes alkylated bases (e.g. 3-methyladenine) from DNA, initiating their repair. Assigned by RefSeq/PGAP homology (no Pfam domain above the gathering threshold). |
Curated reference (UniProt)
| UniProt |
P96819
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | DNA-3-methyladenine glycosylase II |
| EC (curated) |
EC 3.2.2.21
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | DNA glycosylase |
| Orthologous group | COG0122 |
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 | 0.162 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 3 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rslA (anti-sigma-L factor RslA), medium confidence from genomic context alone (score 535 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) |
|---|---|---|---|---|
Rv0427c xthA |
exodeoxyribonuclease III protein XthA | 757 | 725 | database:651 |
Rv0141c hyp |
hypothetical protein | 618 | 617 ctx | neighborhood:615 |
Rv0736 rslA |
anti-sigma-L factor RslA | 535 | 535 ctx | cooccurence:521 |
Rv3731 ligC |
DNA ligase C | 544 | 515 ctx | cooccurence:485 |
Rv3202c adnA |
ATP-dependent DNA helicase | 502 | 475 | |
Rv3062 ligB |
DNA ligase | 479 | 446 ctx | cooccurence:404 |
Rv0786c hyp |
hypothetical protein | 442 | 443 ctx | cooccurence:425 |
Rv0670 end |
endonuclease IV | 503 | 436 | |
Rv1171 hyp |
hypothetical protein | 424 | 425 ctx | cooccurence:407 |
Rv1635c |
mannosyltransferase | 422 | 422 ctx | cooccurence:404 |
Rv2090 |
5'-3' exonuclease | 409 | 354 | |
Rv1629 polA |
DNA polymerase I | 480 | 265 | |
Rv3197A whiB7 |
transcriptional regulator WhiB7 | 555 | 54 | textmining:549 |
Rv0102 |
integral membrane protein | 871 | 53 | textmining:870 |
Rv1911c lppC |
lipoprotein LppC | 519 | 50 | textmining:515 |
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
- MTBC0 PGAP product: 'DNA-3-methyladenine glycosylase'
- Pfam: no domain above cut_ga; assignment from RefSeq/PGAP homology
ESM Atlas signal (exploratory)
Ancestral protein hash 02cf801cc7770368a4456da256100aec ·
10 ESM-space neighbours (max similarity 0.879).
SAE features are orienting indices, not validated domains.
| # | Index | Activation | Interpretation |
|---|---|---|---|
| 1 | 9583 |
1.43 | HhH-GPD DNA glycosylase core |
| 2 | 9822 |
1.23 | HhH glycosylase DNA-binding helix |
| 3 | 8366 |
1.16 | DNA glycosylase catalytic cores |
| 4 | 12414 |
1.03 | N-terminal DNA entry module |
| 5 | 6660 |
0.93 | Glycosylase C-terminal lesion-recognition |
| 6 | 14043 |
0.87 | Terminal IDRs in DNA repair |
| 7 | 6006 |
0.79 | Small-residue hinge detector |
| 8 | 15399 |
0.78 | DNA glycosylase catalytic helix-loop |
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_214656.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG0122 - Curated reference: UniProt P96819 (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 —
16 functional partner(s); context anchor
rslA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000153|Rv0142| MRSIDVVVEAVVTFAGAAGFAHTLAPLRRGQQDPCFRVPGDGTIWRTSLLPTGPVTARISRAGRDAARCVAWGSGAEEFVDMAPAMLGAADDASDFVPLHPAVAAAHRRLPNLRLGRTGQVLEALIPAVIEQRVPGADAFRSWRLLVSKYGTQAPGPAPPGMRVPPSAEVWRHIPSWEFHRANVDPGRARAVVGCAQRAASLERLVSLPAARAAEALTSLPGVGVWTAAETTQRVFGDADAVSVGDYHIPKMIGWTLVGRPVDDAGMLELLEPMRPHRHRVVRLLEASGLAREPRRGPRLPVQNIRAL