otsB1 Resolved · high auto-curated
H37Rv Rv2006 · MTBC0 - ·
1327 aa · 2252002–2255985 (+) ·
RefSeq YP_177855.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | trehalose-6-phosphate phosphatase OtsB |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Trehalose-6-phosphate phosphatase OtsB. Pfam: Hydrolase (PF00702.33), Trehalose_PPase (PF02358.23), Glyco_hydro_65N (PF03636.22), Glyco_hydro_65m (PF03632.22), Glyco_hydro_65C (PF03633.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WN15
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized glycosyl hydrolase Rv2006 |
| EC (curated) |
EC 3.2.1.-
|
UniProt still lists this protein as Uncharacterized glycosyl hydrolase Rv2006; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | otsB1 |
| eggNOG description | hydrolase, family 65, central catalytic |
| Orthologous group | COG0561 |
| EC number |
EC 3.1.3.12, EC 3.2.1.28
|
| KEGG orthology |
K01087, K01194
|
| KEGG pathways |
map00500, map01100
|
| CAZy family |
GH37
|
| Gene Ontology (12) |
GO:0003674, GO:0003824, GO:0005575, GO:0005576, GO:0005618, GO:0005623, GO:0005886, GO:0016020, GO:0016787, GO:0030312, 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) pseudogene candidate
| pN/pS | 0.593 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 14 synonymous, 24 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 2.39% of strains (3466) · 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 |
|---|---|---|---|---|
Hydrolase | PF00702.33 | 9.6e-12 | 22–220 | haloacid dehalogenase-like hydrolase |
Trehalose_PPase | PF02358.23 | 1.1e-70 | 285–511 | Trehalose-phosphatase |
Glyco_hydro_65N | PF03636.22 | 3.9e-72 | 540–793 | Glycosyl hydrolase family 65, N-terminal domain |
Glyco_hydro_65m | PF03632.22 | 1.1e-146 | 847–1242 | Glycosyl hydrolase family 65 central catalytic domain |
Glyco_hydro_65C | PF03633.21 | 6.6e-13 | 1252–1313 | Glycosyl hydrolase family 65, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: otsB2 (trehalose 6-phosphate phosphatase), high confidence from genomic context alone (score 973 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3372 otsB2 |
trehalose 6-phosphate phosphatase | 987 | 973 ctx | neighborhood:544 database:900 textmining:561 |
Rv0126 treS |
trehalose synthase/amylase TreS | 993 | 968 | coexpression:408 database:900 textmining:794 |
Rv1562c treZ |
malto-oligosyltrehalose trehalohydrolase | 992 | 968 | coexpression:496 database:900 textmining:773 |
Rv3401 |
glycosyl hydrolase | 971 | 962 | database:900 |
Rv2004c hyp |
hypothetical protein | 953 | 953 ctx | neighborhood:762 coexpression:811 |
Rv2402 |
trehalase | 973 | 935 | database:900 textmining:618 |
Rv2003c hyp |
hypothetical protein | 897 | 898 ctx | neighborhood:420 coexpression:831 |
Rv2029c pfkB |
6-phosphofructokinase PfkB | 898 | 896 ctx | neighborhood:460 coexpression:781 |
Rv2005c |
universal stress protein | 893 | 894 ctx | neighborhood:553 coexpression:772 |
Rv1997 ctpF |
cation transporter ATPase F | 892 | 852 | coexpression:814 |
Rv0571c hyp |
hypothetical protein | 847 | 847 | coexpression:802 |
Rv3490 otsA |
trehalose-phosphate synthase | 973 | 816 | coexpression:650 textmining:861 |
Rv2028c |
universal stress protein | 809 | 810 | coexpression:803 |
Rv2624c |
universal stress protein | 803 | 804 | coexpression:797 |
Rv3132c devS |
two component sensor histidine kinase DevS | 782 | 756 | coexpression:740 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): trehalose-6-phosphate phosphatase OtsB
- Pfam (hmmscan --cut_ga): Hydrolase PF00702.33 (E=1e-11), Trehalose_PPase PF02358.23 (E=1e-70), Glyco_hydro_65N PF03636.22 (E=4e-72), Glyco_hydro_65m PF03632.22 (E=1e-146), Glyco_hydro_65C PF03633.21 (E=7e-13)
- (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 YP_177855.1)
- Domains: Pfam-A via hmmscan --cut_ga — Hydrolase (PF00702.33), Trehalose_PPase (PF02358.23), Glyco_hydro_65N (PF03636.22), Glyco_hydro_65m (PF03632.22), Glyco_hydro_65C (PF03633.21)
- 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
COG0561 - Curated reference: UniProt P9WN15 (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 —
139 functional partner(s); context anchor
otsB2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2006|otsB1 MRCGIVVNVTGPPPTIDRRYHDAVIVGLDNVVDKATRVHAAAWTKFLDDYLTRRPQRTGEDHCPLTHDDYRRFLAGKPDGVADFLAARGIRLPPGSPTDLTDDTVYGLQNLERQTFLQLLNTGVPEGKSIASFARRLQVAGVRVAAHTSHRNYGHTLDATGLAEVFAVFVDGAVTAELGLPAEPNPAGLIETAKRLGANPGRCVVIDSCQTGLRAGRNGGFALVIAVDAHGDAENLLSSGADAVVADLAAVTVGSGDAAISTIPDALQVYSQLKRLLTGRRPAVFLDFDGTLSDIVERPEAATLVDGAAEALRALAAQCPVAVISGRDLADVRNRVKVDGLWLAGSHGFELVAPDGSHHQNAAATAAIDGLAEAAAQLADALREIAGAVVEHKRFAVAVHYRNVADDSVDNLIAAVRRLGHAAGLRVTTGRKVVELRPDIAWDKGKALDWIGERLGPAEVGPDLRLPIYIGDDLTDEDAFDAVRFTGVGIVVRHNEHGDRRSAATFRLECPYTVCQFLSQLACDLQEAVQHDDPWTLVFHGYDPGQERLREALCAVGNGYLGSRGCAPESAESEAHYPGTYVAGVYNQLTDHIEGCTVDNESLVNLPNWLSLTFRIDGGAWFNVDTVELLSYRQTFDLRRATLTRSLRFRDAGGRVTTMTQERFASMNRPNLVALQTRIESENWSGTVDFRSLVDGGVHNTLVDRYRQLSSQHLTTAEIEVLADSVLLRTQTSQSGIAIAVAARSTLWRDGQRVDAQYRVARDTNRGGHDIQVTLSAGQSVTLEKVATIFTSRDAATLTAAISAQRCLGEAGRYAELCQQHVRAWARLWERCAIDLTGNTEELRLVRLHLLHLLQTISPHTAELDAGVPARGLNGEAYRGHVFWDALFVAPVLSLRMPKVARSLLDYRYRRLPAARRAAHRAGHLGAMYPWQSGSDGSEVSQQLHLNPRSGRWTPDPSDRAHHVGLAVAYNAWHYYQVTGDRQYLVDCGAELLVEIARFWVGLAKLDDSRGRYLIRGVIGPDEFHSGYPGNEYDGIDNNAYTNVMAVWVILRAMEALDLLPLTDRRHLIEKLGLTTQERDQWDDVSRRMFVPFHDGVISQFEGYSELAELDWDHYRHRYGNIQRLDRILEAEGDSVNNYQASKQADALMLLYLLSSDELIGLLARLGYRFAPTQIPGTVDYYLARTSDGSTLSAVVHAWVLARANRSNAMEYFRQVLRSDIADVQGGTTQEGIHLAAMAGSIDLLQRCYSGLELRDDRLVLSPQWPEALGPLEFPFVYRRHQLSLRISGRSATLTAESGDAEPIEVECRGHVQRLRCGHTIEVGCSR