Rv2609c Family assigned · medium auto-curated
H37Rv Rv2609c · MTBC0 mtbc0_002777 ·
351 aa · 2960363–2961418 (-) ·
RefSeq NP_217125.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | NUDIX domain-containing protein |
| Revised (this work) | NUDIX domain-containing protein. Pfam: NUDIX (PF00293.35). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YDV4
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | pfam nudix |
| Orthologous group | COG0494 |
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 | 0.375 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 |
|---|---|---|---|---|
NUDIX | PF00293.35 | 7.4e-20 | 177–316 | NUDIX domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pimA (alpha-(1-2)-phosphatidylinositol mannosyltransferase), high confidence from genomic context alone (score 968 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2610c pimA |
alpha-(1-2)-phosphatidylinositol mannosyltransferase | 982 | 968 ctx | neighborhood:781 cooccurence:506 coexpression:732 textmining:479 |
Rv3433c nnr |
bifunctional ADP-dependent (S)-NAD(P)H-hydrate dehydratase/NAD(P)H-hydrate epimerase | 941 | 933 | experimental:787 database:643 |
Rv2611c |
phosphatidylinositol mannoside acyltransferase | 951 | 893 ctx | neighborhood:798 cooccurence:490 textmining:566 |
Rv2613c |
AP-4-A phosphorylase | 934 | 831 ctx | neighborhood:798 textmining:631 |
Rv2614c thrS |
threonine--tRNA ligase | 877 | 819 ctx | neighborhood:798 |
Rv2612c pgsA1 |
CDP-diacylglycerol--inositol 3-phosphatidyltransferase | 884 | 814 ctx | neighborhood:798 textmining:402 |
Rv3211 rhlE |
ATP-dependent RNA helicase RhlE | 783 | 770 | experimental:403 database:615 |
Rv1253 deaD |
ATP-dependent RNA helicase DeaD | 782 | 769 | experimental:403 database:615 |
Rv2524c fas |
fatty acid synthase | 715 | 705 | database:406 |
Rv2418c octT hyp |
hypothetical protein | 703 | 704 ctx | cooccurence:680 |
Rv0556 |
transmembrane protein | 656 | 656 ctx | cooccurence:651 |
Rv1340 rphA |
ribonuclease PH | 683 | 652 | database:636 |
Rv1109c hyp |
hypothetical protein | 650 | 650 ctx | cooccurence:649 |
Rv3415c hyp |
hypothetical protein | 649 | 649 ctx | cooccurence:648 |
Rv3196 hyp |
hypothetical protein | 648 | 648 ctx | cooccurence:625 |
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: membrane protein
- MTBC0 PGAP product: NUDIX domain-containing protein
- Pfam (hmmscan --cut_ga): NUDIX PF00293.35 (E=7e-20)
- (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_217125.1)
- Domains: Pfam-A via hmmscan --cut_ga — NUDIX (PF00293.35)
- 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
COG0494 - Curated reference: UniProt I6YDV4 (TrEMBL, unreviewed; 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 —
152 functional partner(s); context anchor
pimA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002777|Rv2609c| MTWLVLAGAVLLVVLVAFGAWGYQTANRLNRLNVRYDLSWQSLDSALARRAVVARAVAIDAYGGAPQGSRLAALADAAEGAPRHARENAENELSAALAMVNPASLPAALIAELADAEARVLLARRFHNDAVRDTLALGERRLVRLLRLGGTAVLPTYFEIVERPHALVHGDQGASGRRTSARVVLLDDSGAVLLLCGSDPANPAFRDGAAPKWWFTVGGQVRPGERLAQAAARELAEETGLRVAPADMIGPIWRRDEVFEFNGSLIDSEEFYLVHRTRRFEPAVQGRTELERRYIRDARWCDANDIAQLVAAGERVYPLQLGELLPAANRLVDVALDNGAARDAGVPQPIR