gcvT Resolved · high auto-curated
H37Rv Rv2211c · MTBC0 - ·
379 aa · 2476042–2477181 (-) ·
RefSeq NP_216727.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | aminomethyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Aminomethyltransferase. Pfam: GCV_T (PF01571.27), GCV_T_C (PF08669.18). |
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 |
P9WN51
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Aminomethyltransferase |
| EC (curated) |
EC 2.1.2.10
|
| Curated function | The glycine cleavage system catalyzes the degradation of glycine. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | gcvT |
| eggNOG description | The glycine cleavage system catalyzes the degradation of glycine |
| Orthologous group | COG0404 |
| EC number |
EC 2.1.2.10
|
| KEGG orthology |
K00605
|
| KEGG pathways |
map00260, map00630, map00670, map01100, map01110, map01130, map01200
|
| KEGG modules |
M00532
|
| Gene Ontology (8) |
GO:0005575, GO:0005618, GO:0005623, GO:0008150, GO:0030312, GO:0040007, 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 | 0.242 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
GCV_T | PF01571.27 | 5.7e-75 | 25–277 | GCVT N-terminal domain |
GCV_T_C | PF08669.18 | 1.8e-16 | 296–374 | Glycine cleavage T-protein C-terminal barrel domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: gcvH (glycine cleavage system protein H), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1826 gcvH |
glycine cleavage system protein H | 999 | 1000 ctx | cooccurence:774 coexpression:859 experimental:790 database:984 textmining:625 |
Rv1832 gcvB |
glycine dehydrogenase | 999 | 1000 ctx | fusion:679 cooccurence:743 coexpression:999 database:900 textmining:625 |
Rv0070c glyA2 |
serine hydroxymethyltransferase | 994 | 991 ctx | fusion:792 coexpression:469 database:900 textmining:450 |
Rv1093 glyA1 |
serine hydroxymethyltransferase | 994 | 990 ctx | fusion:784 coexpression:475 database:900 textmining:450 |
Rv0462 lpdC |
dihydrolipoamide dehydrogenase | 976 | 974 | database:955 |
Rv3356c folD |
bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase | 960 | 948 | coexpression:460 database:900 |
Rv0957 purH |
bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/inosinemonophosphate cyclohydrolase | 963 | 938 | coexpression:401 database:900 textmining:434 |
Rv2124c metH |
methionine synthase | 966 | 935 | database:900 textmining:516 |
Rv0956 purN |
phosphoribosylglycinamide formyltransferase PurN | 955 | 913 | database:900 textmining:510 |
Rv0389 purT |
phosphoribosylglycinamide formyltransferase PurT | 913 | 913 | database:900 |
Rv2964 purU |
formyltetrahydrofolate deformylase | 930 | 909 | database:900 |
Rv1406 fmt |
methionyl-tRNA formyltransferase | 933 | 906 | database:900 |
Rv2764c thyA |
thymidylate synthase ThyA | 928 | 905 | database:900 |
Rv2763c dfrA |
dihydrofolate reductase | 925 | 905 | database:900 |
Rv1248c kgd |
multifunctional 2-oxoglutarate dehydrogenase E1 component /2-oxoglutarate dehydrogenase dihydrolipoyllysine-residue succinyltransferase | 931 | 903 | coexpression:769 database:585 |
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): aminomethyltransferase
- Pfam (hmmscan --cut_ga): GCV_T PF01571.27 (E=6e-75), GCV_T_C PF08669.18 (E=2e-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_216727.1)
- Domains: Pfam-A via hmmscan --cut_ga — GCV_T (PF01571.27), GCV_T_C (PF08669.18)
- 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
COG0404 - Curated reference: UniProt P9WN51 (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 —
85 functional partner(s); context anchor
gcvH - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2211c|gcvT MCQQGRPLGWDAVSDVPELIHGPLEDRHRELGASFAEFGGWLMPVSYAGTVSEHNATRTAVGLFDVSHLGKALVRGPGAAQFVNSALTNDLGRIGPGKAQYTLCCTESGGVIDDLIAYYVSDDEIFLVPNAANTAAVVGALQAAAPGGLSITNLHRSYAVLAVQGPCSTDVLTALGLPTEMDYMGYADASYSGVPVRVCRTGYTGEHGYELLPPWESAGVVFDALLAAVSAAGGEPAGLGARDTLRTEMGYPLHGHELSLDISPLQARCGWAVGWRKDAFFGRAALLAEKAAGPRRLLRGLRMVGRGVLRPGLAVLVGDETVGVTTSGTFSPTLQVGIGLALIDSDAGIEDGQQINVDVRGRAVECQVVCPPFVAVKTR