cpsY Family assigned · medium auto-curated
H37Rv Rv0806c · MTBC0 mtbc0_000855 ·
532 aa · 902799–904397 (-) ·
RefSeq NP_215321.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | exopolysaccharide phosphotransferase CpsY |
|---|---|
| MTBC0 PGAP re-annotation | stealth family protein |
| Revised (this work) | Stealth family protein. Pfam: Stealth_CR1 (PF17101.11), Stealth_CR2 (PF11380.14), Stealth_CR3 (PF17102.11), Stealth_CR4 (PF17103.11). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGD1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Exopolysaccharide phosphotransferase CpsY |
| EC (curated) |
EC 2.7.-.-
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | cpsY |
| eggNOG description | Thought to be involved in exopolysaccharide and or lipopolysaccharide biosynthetic pathway catalytic activity UDP-glucose UDP-galactose |
| Orthologous group | COG0438 |
| EC number |
EC 5.1.3.2
|
| KEGG orthology |
K01784
|
| KEGG pathways |
map00052, map00520, map01100
|
| KEGG modules |
M00361, M00362, M00632
|
| Gene Ontology (6) |
GO:0005575, GO:0005618, GO:0005623, 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)
| pN/pS | 0.389 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 6 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 |
|---|---|---|---|---|
Stealth_CR1 | PF17101.11 | 4.1e-09 | 201–221 | Stealth protein CR1, conserved region 1 |
Stealth_CR2 | PF11380.14 | 3.7e-40 | 239–343 | Stealth protein CR2, conserved region 2 |
Stealth_CR3 | PF17102.11 | 1.2e-18 | 389–435 | Stealth protein CR3, conserved region 3 |
Stealth_CR4 | PF17103.11 | 3.0e-16 | 465–518 | Stealth protein CR4, conserved region 4 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cpdA (3',5'-cyclic adenosine monophosphate phosphodiesterase CpdA), high confidence from genomic context alone (score 756 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1562c treZ |
malto-oligosyltrehalose trehalohydrolase | 792 | 782 | coexpression:411 database:572 |
Rv1326c glgB |
1,4-alpha-glucan branching protein | 792 | 782 | coexpression:411 database:572 |
Rv0805 cpdA |
3',5'-cyclic adenosine monophosphate phosphodiesterase CpdA | 764 | 756 ctx | cooccurence:750 |
Rv3809c glf |
UDP-galactopyranose mutase | 752 | 739 | coexpression:459 database:500 |
Rv2529 hyp |
hypothetical protein | 673 | 661 | database:516 |
Rv1510 hyp |
hypothetical protein | 553 | 531 | coexpression:414 |
Rv0619 galTb |
Rv0619, (MTCY19H5.02c), len: 181 aa (probable partial CDS). Probable galTb, second part of galactose-1-phosphate uridylyltransferase, highly | 527 | 509 | database:500 |
Rv0618 galTa |
Rv0618, (MTCY19H5.03c), len: 231 aa (probable partial CDS). Probable galTa, first part of galactose-1-phosphate uridylyltransferase, highly | 525 | 507 | database:500 |
Rv3630 |
integral membrane protein | 528 | 505 | coexpression:414 |
Rv3465 rmlC |
dTDP-4-dehydrorhamnose 3,5-epimerase | 514 | 485 | coexpression:455 |
Rv1328 glgP |
glycogen phosphorylase | 508 | 478 | |
Rv0322 udgA |
UDP-glucose 6-dehydrogenase UdgA | 493 | 463 | coexpression:441 |
Rv2627c hyp |
hypothetical protein | 482 | 458 | experimental:443 |
Rv0334 rmlA |
glucose-1-phosphate thymidylyltransferase | 487 | 456 | coexpression:422 |
Rv2307c hyp |
hypothetical protein | 479 | 455 | experimental:443 |
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: exopolysaccharide phosphotransferase CpsY
- MTBC0 PGAP product: stealth family protein
- Pfam (hmmscan --cut_ga): Stealth_CR1 PF17101.11 (E=4e-09), Stealth_CR2 PF11380.14 (E=4e-40), Stealth_CR3 PF17102.11 (E=1e-18), Stealth_CR4 PF17103.11 (E=3e-16)
- (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_215321.1)
- Domains: Pfam-A via hmmscan --cut_ga — Stealth_CR1 (PF17101.11), Stealth_CR2 (PF11380.14), Stealth_CR3 (PF17102.11), Stealth_CR4 (PF17103.11)
- 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
COG0438 - Curated reference: UniProt P9WGD1 (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
cpdA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000855|Rv0806c|cpsY MPKISSRDGGRPAQRTVNPIIVTRRGKIARLESGLTPQEAQIEDLVFLRKVLNRADIPYLLIRNHKNRPVLAINIELRAGLERALAAACATEPMYAKTIDEPGLSPVLVATDGLSQLVDPRVVRLYRRRIAPGGFRYGPAFGVELQFWVYEETVIRCPVENSLSRKVLPRNEITPTNVKLYGYKWPTLDGMFAPHASDVVFDIDMVFSWVDGSDPEFRARRMAQMSQYVVGEGDDAEARIRQIDELKYALRSVNMFAPWIRRIFIATDSTPPPWLAEHPKITIVRAEDHFSDRSALPTYNSHAVESQLHHIPGLSEHFLYSNDDMFFGRPLKASMFFSPGGVTRFIEAKTRIGLGANNPARSGFENAARVNRQLLFDRFGQVITRHLEHTAVPLRKSVLIEMEREFPEEFARTAASPFRSDTDISVTNSFYHYYALMTGRAVPQEKAKVLYVDTTSYAGLRLLPKLRKHRGYDFFCLNDGSFPEVPAAQRAERVVSFLERYFPIPAPWEKIAADVSRRDFAVPRTSAPSEGA