Rv3661 Family assigned · medium auto-curated
H37Rv Rv3661 · MTBC0 mtbc0_003879 ·
287 aa · 4123477–4124340 (+) ·
RefSeq NP_218178.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | HAD-IB family hydrolase |
| Revised (this work) | HAD-IB family hydrolase. Pfam: Hydrolase (PF00702.33), HAD (PF12710.14). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGJ1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable phosphatase Rv3661 |
| EC (curated) |
EC 3.1.3.-
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | serB |
| eggNOG description | HAD-superfamily subfamily IB hydrolase, TIGR01490 |
| Orthologous group | COG0560 |
| Gene Ontology (8) |
GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0044424, GO:0044444, GO:0044464
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 2 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 |
|---|---|---|---|---|
Hydrolase | PF00702.33 | 2.3e-07 | 27–216 | haloacid dehalogenase-like hydrolase |
HAD | PF12710.14 | 2.1e-34 | 28–213 | haloacid dehalogenase-like hydrolase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: dapD (2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase), medium confidence from genomic context alone (score 436 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) |
|---|---|---|---|---|
Rv1605 hisF |
imidazole glycerol phosphate synthase subunit HisF | 609 | 584 | coexpression:570 |
Rv1602 hisH |
imidazole glycerol phosphate synthase subunit HisH | 541 | 521 | coexpression:505 |
Rv1603 hisA |
1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase | 533 | 510 | coexpression:494 |
Rv1606 hisI |
phosphoribosyl-AMP cyclohydrolase | 526 | 494 | coexpression:477 |
Rv1601 hisB |
imidazole glycerol-phosphate dehydratase | 526 | 488 | coexpression:471 |
Rv0884c serC |
phosphoserine aminotransferase | 549 | 480 | |
Rv1416 ribH |
6,7-dimethyl-8-ribityllumazine synthase | 459 | 460 | |
Rv1599 hisD |
histidinol dehydrogenase | 484 | 447 | coexpression:429 |
Rv2122c hisE |
phosphoribosyl-ATP pyrophosphatase | 472 | 439 | coexpression:420 |
Rv1600 hisC1 |
histidinol-phosphate aminotransferase | 458 | 437 | coexpression:419 |
Rv1201c dapD |
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase | 435 | 436 ctx | cooccurence:407 |
Rv2231c cobC |
aminotransferase | 452 | 431 | coexpression:413 |
Rv3772 hisC2 |
histidinol-phosphate aminotransferase | 452 | 431 | coexpression:413 |
Rv2121c hisG |
ATP phosphoribosyltransferase | 449 | 415 | |
Rv1382 hyp |
hypothetical protein | 424 | 311 |
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: HAD-IB family hydrolase
- Pfam (hmmscan --cut_ga): Hydrolase PF00702.33 (E=2e-07), HAD PF12710.14 (E=2e-34)
- (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_218178.1)
- Domains: Pfam-A via hmmscan --cut_ga — Hydrolase (PF00702.33), HAD (PF12710.14)
- 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
COG0560 - Curated reference: UniProt P9WGJ1 (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 —
25 functional partner(s); context anchor
dapD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003879|Rv3661| MTVSDSPAQRQTPPQTPGGTAPRARTAAFFDLDKTIIAKSSTLAFSKPFFAQGLLNRRAVLKSSYAQFIFLLSGADHDQMDRMRTHLTNMCAGWDVAQVRSIVNETLHDIVTPLVFAEAADLIAAHKLCGRDVVVVSASGEEIVGPIARALGATHAMATRMIVEDGKYTGEVAFYCYGEGKAQAIRELAASEGYPLEHCYAYSDSITDLPMLEAVGHASVVNPDRGLRKEASVRGWPVLSFSRPVSLRDRIPAPSAAAIATTAAVGISALAAGAVTYALLRRFAFQP