Rv0140 Family assigned · medium
H37Rv Rv0140 · MTBC0 mtbc0_000151 ·
126 aa · 167256–167636 (+) ·
RefSeq NP_214654.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF427 domain-containing protein |
| Revised (this work) | Putative nucleotidyltransferase (Pfam NTP_transf_9 PF04248; the family formerly named DUF427). A minimal nucleotidyltransferase fold; the substrate is not established. |
Curated reference (UniProt)
| UniProt |
P96817
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Domain of unknown function (DUF427) |
| Orthologous group | COG2343 |
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 | 1.051 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 7 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 |
|---|---|---|---|---|
NTP_transf_9 | PF04248.20 | 5.5e-32 | 24–117 | Domain of unknown function (DUF427) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0139 (oxidoreductase), high confidence from genomic context alone (score 800 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) |
|---|---|---|---|---|
Rv0139 |
oxidoreductase | 800 | 800 ctx | neighborhood:800 |
Rv0138 hyp |
hypothetical protein | 800 | 800 ctx | neighborhood:800 |
Rv0137c msrA |
peptide methionine sulfoxide reductase MsrA | 584 | 583 ctx | neighborhood:582 |
Rv3701c egtD |
histidine-specific methyltransferase EtgD | 467 | 468 ctx | cooccurence:447 |
Rv2466c hyp |
hypothetical protein | 664 | 291 | textmining:546 |
Rv0569 hyp |
hypothetical protein | 446 | 55 | textmining:438 |
Rv0145 |
S-adenosylmethionine-dependent methyltransferase | 655 | 53 | textmining:651 |
Rv1337 |
integral membrane protein | 552 | 51 | textmining:548 |
Rv0274 hyp |
hypothetical protein | 532 | 50 | textmining:528 |
Rv0111 |
acyltransferase | 517 | 48 | textmining:514 |
Rv0711 atsA |
arylsulfatase AtsA | 656 | 47 | textmining:654 |
Rv1366 hyp |
hypothetical protein | 632 | 47 | textmining:630 |
Rv3001c ilvC |
ketol-acid reductoisomerase | 542 | 46 | textmining:540 |
Rv3407 vapB47 |
antitoxin VapB47 | 436 | 46 | textmining:434 |
Rv0110 |
integral membrane protein | 809 | 44 | textmining:809 |
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: 'DUF427 domain-containing protein'
- Pfam: NTP_transf_9 PF04248 (E=5.5e-32) -- putative nucleotidyltransferase (ex-DUF427)
ESM Atlas signal (exploratory)
Ancestral protein hash ece0212fdb78dd0ac92c0461699375d8 ·
10 ESM-space neighbours (max similarity 0.978).
SAE features are orienting indices, not validated domains.
| # | Index | Activation | Interpretation |
|---|---|---|---|
| 1 | 830 |
0.95 | Disordered hydrophobic terminal tails |
| 2 | 10740 |
0.78 | Small residue segment preference |
| 3 | 6702 |
0.54 | Glycine-rich N-terminal leaders |
| 4 | 7615 |
0.53 | TM-adjacent disordered tails and linkers |
| 5 | 1855 |
0.49 | Pro/Gly-rich disordered linkers |
| 6 | 5835 |
0.46 | Conserved functional core segments |
| 7 | 12482 |
0.46 | N-terminal anion-binding capping loops |
| 8 | 15589 |
0.43 | Mid-chain hydrophobic core |
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_214654.1)
- Domains: Pfam-A via hmmscan --cut_ga — NTP_transf_9 (PF04248.20)
- 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
COG2343 - Curated reference: UniProt P96817 (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 —
17 functional partner(s); context anchor
Rv0139 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000151|Rv0140| MSNRIVLEPSADHPITIEPTNRRVQVRVNGEVVADTAAALCLQEASYPAVQYIPLADVVQDRLIRTETSTYCPFKGEASYYSVTTDAGDIVDDVMWTYENPYPAVAAIAGHVACYPDKAEISIFPG