Rv0038 Family assigned · low
H37Rv Rv0038 · MTBC0 mtbc0_000043 ·
202 aa · 41403–42011 (+) ·
RefSeq NP_214552.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | YqgE/AlgH family protein |
| Revised (this work) | UPF0301 / YqgE/AlgH family protein (Pfam DUF179, PF02622). A widely conserved bacterial family of unknown precise molecular function; the AlgH homolog has been linked to alginate regulation in Pseudomonas, but the activity is uncharacterised. Role in M. tuberculosis unknown. |
Curated reference (UniProt)
| UniProt |
P9WFK5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | UPF0301 protein Rv0038 |
UniProt still lists this protein as UPF0301 protein Rv0038; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Belongs to the UPF0301 (AlgH) family |
| Orthologous group | COG1678 |
| KEGG orthology |
K07735
|
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, GO:0044464, GO:0071944
|
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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 0 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 |
|---|---|---|---|---|
DUF179 | PF02622.22 | 1.1e-33 | 31–184 | AlgH-like |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0037c (MFS-type transporter), high confidence from genomic context alone (score 765 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) |
|---|---|---|---|---|
Rv3051c nrdE |
ribonucleoside-diphosphate reductase subunit alpha | 969 | 966 | coexpression:560 experimental:789 database:662 |
Rv0570 nrdZ |
vitamin B12-dependent ribonucleoside-diphosphate reductase | 969 | 965 | coexpression:548 experimental:789 database:662 |
Rv1019 |
transcriptional regulator | 841 | 841 | coexpression:841 |
Rv1359 |
transcriptional regulator | 823 | 823 | coexpression:802 |
Rv1488 hyp |
hypothetical protein | 805 | 806 | coexpression:804 |
Rv0691c mftR |
mycofactocin biosynthesis transcriptional regulator MftR | 798 | 798 | coexpression:798 |
Rv3263 |
DNA methylase | 797 | 797 | coexpression:797 |
Rv1776c |
transcriptional regulator | 797 | 797 | coexpression:797 |
Rv0212c nadR |
transcriptional regulator NadR | 794 | 795 | coexpression:767 |
Rv2788 sirR |
transcriptional repressor SirR | 793 | 793 | coexpression:793 |
Rv1152 |
transcriptional regulator | 781 | 781 | coexpression:780 |
Rv0894 |
transcriptional regulator | 772 | 772 | coexpression:772 |
Rv1674c |
transcriptional regulator | 765 | 766 | coexpression:758 |
Rv0037c |
MFS-type transporter | 765 | 765 ctx | neighborhood:762 |
Rv1100 hyp |
hypothetical protein | 763 | 764 | coexpression:730 |
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: 'YqgE/AlgH family protein'
- Pfam: DUF179 PF02622 (E=1.1e-33) -- UPF0301 / YqgE/AlgH family, conserved but functionally uncharacterised
- No Mtb-specific functional study found in tbmonitor (2021-2026)
ESM Atlas signal (exploratory)
Ancestral protein hash 0cce37a4c66121ebb2d0e82af00406ec ·
10 ESM-space neighbours (max similarity 0.944).
SAE features are orienting indices, not validated domains.
| # | Index | Activation | Interpretation |
|---|---|---|---|
| 1 | 16204 |
0.95 | Aromatic-anchored disulfide loop motif |
| 2 | 3864 |
0.77 | NTase ligase/GTase catalytic cores |
| 3 | 13483 |
0.76 | Phosphoryl group binding pocket |
| 4 | 198 |
0.65 | N-terminal gating loops |
| 5 | 7714 |
0.54 | C-terminal cofactor-binding tails |
| 6 | 5122 |
0.53 | Basic histidine polyanion binding loops |
| 7 | 8075 |
0.53 | Amphipathic C-terminal helix-loop linker |
| 8 | 3114 |
0.51 | Active-site rim β-loop elements |
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_214552.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF179 (PF02622.22)
- 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
COG1678 - Curated reference: UniProt P9WFK5 (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 —
70 functional partner(s); context anchor
Rv0037c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000043|Rv0038| MVAPHEDPEDHVAPAAQRVRAGTLLLANTDLLEPTFRRSVIYIVEHNDGGTLGVVLNRPSETAVYNVLPQWAKLAAKPKTMFIGGPVKRDAALCLAVLRVGADPEGVPGLRHVAGRLVMVDLDADPEVLAAAVEGVRIYAGYSGWTIGQLEGEIERDDWIVLSALPSDVLVGPRADLWGQVLRRQPLPLSLLATHPIDLSRN