Rv2133c Family assigned · low auto-curated
H37Rv Rv2133c · MTBC0 mtbc0_002266 ·
262 aa · 2421114–2421902 (-) ·
RefSeq NP_216649.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | SCO1664 family protein |
| Revised (this work) | SCO1664 family protein. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06242
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Protein Rv2133c |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
B Chromatin structure and dynamicsD Cell cycle control, cell division, chromosome partitioningL Replication, recombination and repairT Signal transduction mechanismsU Intracellular trafficking, secretion and vesicular transport
|
|---|---|
| eggNOG description | Phosphatidylinositol |
| Orthologous group | COG5032 |
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 | 1.062 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 2 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.32% of strains (465) · 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: uppP (undecaprenyl-diphosphatase), high confidence from genomic context alone (score 801 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) |
|---|---|---|---|---|
Rv2134c hyp |
hypothetical protein | 975 | 975 ctx | neighborhood:879 cooccurence:773 |
Rv2135c hyp |
hypothetical protein | 950 | 951 ctx | neighborhood:798 cooccurence:760 |
Rv2101 helZ |
helicase HelZ | 922 | 915 | experimental:832 database:485 |
Rv3036c TB22.2 hyp |
hypothetical protein | 871 | 863 | experimental:772 database:425 |
Rv2328 PE23 |
PE family protein PE23 | 871 | 863 | experimental:772 database:425 |
Rv3812 PE_PGRS62 |
PE-PGRS family protein PE_PGRS62 | 871 | 863 | experimental:772 database:425 |
Rv0832 PE_PGRS12 |
PE-PGRS family protein PE_PGRS12 | 871 | 863 | experimental:772 database:425 |
Rv2136c uppP |
undecaprenyl-diphosphatase | 801 | 801 ctx | neighborhood:798 |
Rv3834c serS |
serine--tRNA ligase | 771 | 771 | experimental:771 |
Rv2137c hyp |
hypothetical protein | 741 | 742 ctx | neighborhood:740 |
Rv2130c mshC |
cysteine:1D-myo-inosityl 2-amino-2-deoxy--D-glucopyranoside ligase | 748 | 738 ctx | neighborhood:544 cooccurence:416 |
Rv1170 mshB |
1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside deacetylase | 641 | 642 ctx | cooccurence:640 |
Rv0959 hyp |
hypothetical protein | 579 | 579 ctx | cooccurence:451 |
Rv1082 mca |
mycothiol S-conjugate amidase | 571 | 571 ctx | cooccurence:569 |
Rv2131c cysQ |
3'(2'),5'-bisphosphate nucleotidase CysQ | 550 | 550 ctx | neighborhood:544 |
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: SCO1664 family protein
- (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_216649.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG5032 - Curated reference: UniProt O06242 (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 —
22 functional partner(s); context anchor
uppP - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002266|Rv2133c| MLADGELTVLGRIRSASNATFLCESTLGLRSLHCVYKPVSGERPLWDFPDGTLAGRELSAYLVSTQLGWNLVPHTIIRDGPAGIGMLQLWVQQPGDAVDSDPLPGPDLVDLFPAHRPRPGYLPVLRAYDYAGDEVVLMHADDIRLRRMAVFDVLINNADRKGGHILCGIDGQVYGVDHGLCLHVENKLRTVLWGWAGKPIDDQILQAVAGLADALGGPLAEALAGRIAAAEIGALRRRAQSLLDQPVMPGPNGHRPIPWPAF