Rv2000 Family assigned · medium auto-curated
H37Rv Rv2000 · MTBC0 mtbc0_002127 ·
537 aa · 2268822–2270435 (+) ·
RefSeq NP_216516.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | FAD/NAD(P)-binding protein |
| Revised (this work) | FAD/NAD(P)-binding protein. Pfam: NAD_binding_8 (PF13450.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WLN7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv2000 |
UniProt still lists this protein as Uncharacterized protein Rv2000; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| eggNOG description | flavoprotein involved in K transport |
| Orthologous group | COG0121 |
| Gene Ontology (13) |
GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0016020, GO:0030312, GO:0044424, GO:0044444, GO:0044464 +1 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 | 0.255 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 8 synonymous, 6 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.11% of strains (156) · clonal |
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 |
|---|---|---|---|---|
NAD_binding_8 | PF13450.13 | 7.1e-05 | 79–117 | NAD(P)-binding Rossmann-like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fabG3 (3-alpha(or 20-beta)-hydroxysteroid dehydrogenase), medium confidence from genomic context alone (score 650 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) |
|---|---|---|---|---|
Rv2001 hyp |
hypothetical protein | 972 | 973 ctx | neighborhood:867 coexpression:804 |
Rv2002 fabG3 |
3-alpha(or 20-beta)-hydroxysteroid dehydrogenase | 650 | 650 ctx | neighborhood:605 |
Rv1999c |
transporter | 556 | 555 ctx | neighborhood:554 |
Rv3633 hyp |
hypothetical protein | 532 | 513 ctx | cooccurence:509 |
Rv1730c |
penicillin-binding protein | 466 | 466 ctx | cooccurence:462 |
Rv1311 atpC |
ATP synthase subunit epsilon | 462 | 462 | |
Rv1308 atpA |
ATP synthase subunit alpha | 435 | 436 | experimental:427 |
Rv1998c hyp |
hypothetical protein | 452 | 430 | |
Rv1507c hyp |
hypothetical protein | 412 | 413 | |
Rv1309 atpG |
ATP synthase subunit gamma | 412 | 413 | |
Rv3456c rplQ |
50S ribosomal protein L17 | 407 | 407 | |
Rv1310 atpD |
ATP synthase subunit beta | 403 | 404 | |
Rv3846 sodA |
superoxide dismutase | 412 | 403 | |
Rv3461c rpmJ |
50S ribosomal protein L36 | 400 | 401 | |
Rv0363c fba |
fructose-bisphosphate aldolase | 410 | 388 |
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: FAD/NAD(P)-binding protein
- Pfam (hmmscan --cut_ga): NAD_binding_8 PF13450.13 (E=7e-05)
- (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_216516.1)
- Domains: Pfam-A via hmmscan --cut_ga — NAD_binding_8 (PF13450.13)
- 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
COG0121 - Curated reference: UniProt P9WLN7 (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 —
21 functional partner(s); context anchor
fabG3 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002127|Rv2000| MRPGFVGLGFGQWPVYVVRWPKLHLTPRQRKRVLHRRRLLTDRPISLSQIPIRTGGPMNDPWPRPTQGPAKTIETDYLVIGAGAMGMAFTDTLITESGARVVMIDRACQPGGHWTTAYPFVRLHQPSAYYGVNSRALGNNTIDLVGWNQGLNELAPVGEICAYFDAVLQQQLLPTGRVDYFPMSEYLGDGRFRTLAGTEYVVTVNRRIVDATYLRAVVPSMRPAPYSVAPGVDCVAPNELPKLGTRDRYVVVGAGKTGMDVCLWLLRNDVCPDKLTWIMPRDSWLIDRATLQPGPTFVRQFRESYGATLEAIGAATSTDDLFDRLETAGTLLRIDPSVRPSMYRCATVSHLELEQLRRIRDIVRMGHVQRIEPTTIVLDGGSVPATPTALYIDCTADGAPQRPAKPVFDADHLTLQAVRGCQQVFSAAFIAHVEFAYEDDAVKNELCTPIPHPDCDLDWMRLMHSDLGNFQRWLNDPDLTDWLSSARLNLLADLLPPLSHKPRVRERVVSMFQKRLGTAGDQLAKLLDAATATTEQR