Rv2566 Family assigned · medium auto-curated
H37Rv Rv2566 · MTBC0 - ·
1140 aa · 2886373–2889795 (+) ·
RefSeq NP_217082.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains Bact_transglu_N (PF08379.16), Transglut_core (PF01841.26), DUF2126 (PF09899.15) domain(s); putative function inferred from the domain architecture. |
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 |
Q50732
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Long conserved protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| eggNOG description | transglutaminase |
| Orthologous group | COG1305 |
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 | 0.898 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 10 synonymous, 24 missense, 1 nonsense, 3 frameshift |
| Disruption | 4 distinct premature-stop/frameshift site(s); most common in 9.67% of strains (14039) · convergent |
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 |
|---|---|---|---|---|
Bact_transglu_N | PF08379.16 | 1.1e-22 | 33–109 | Bacterial transglutaminase-like N-terminal region |
Transglut_core | PF01841.26 | 8.2e-16 | 166–284 | Transglutaminase-like superfamily |
DUF2126 | PF09899.15 | 0.0e+00 | 314–1133 | Putative amidoligase enzyme (DUF2126) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2565 (NTE family protein), high confidence from genomic context alone (score 773 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) |
|---|---|---|---|---|
Rv2567 hyp |
hypothetical protein | 979 | 977 ctx | neighborhood:892 cooccurence:767 |
Rv2411c hyp |
hypothetical protein | 852 | 847 ctx | neighborhood:526 cooccurence:660 |
Rv2568c hyp |
hypothetical protein | 846 | 846 ctx | neighborhood:544 cooccurence:675 |
Rv2565 |
NTE family protein | 773 | 773 ctx | neighborhood:770 |
Rv2410c hyp |
hypothetical protein | 772 | 763 ctx | neighborhood:526 cooccurence:501 |
Rv2409c hyp |
hypothetical protein | 676 | 677 ctx | cooccurence:629 |
Rv1673c hyp |
hypothetical protein | 658 | 658 ctx | cooccurence:610 |
Rv2560 hyp |
hypothetical protein | 610 | 610 ctx | neighborhood:609 |
Rv2559c hyp |
hypothetical protein | 600 | 600 ctx | neighborhood:599 |
Rv2572c aspS |
aspartate--tRNA ligase | 544 | 544 ctx | neighborhood:544 |
Rv2569c hyp |
hypothetical protein | 504 | 505 | |
Rv2564 glnQ |
glutamine ABC transporter ATP-binding protein | 438 | 438 ctx | neighborhood:437 |
Rv2563 |
glutamine ABC transporter permease | 425 | 425 ctx | neighborhood:423 |
Rv3163c hyp |
hypothetical protein | 406 | 396 | |
Rv2703 sigA |
RNA polymerase sigma factor SigA | 459 | 71 | textmining:442 |
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): hypothetical protein
- Pfam (hmmscan --cut_ga): Bact_transglu_N PF08379.16 (E=1e-22), Transglut_core PF01841.26 (E=8e-16), DUF2126 PF09899.15 (E=0e+00)
- (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_217082.1)
- Domains: Pfam-A via hmmscan --cut_ga — Bact_transglu_N (PF08379.16), Transglut_core (PF01841.26), DUF2126 (PF09899.15)
- 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
COG1305 - Curated reference: UniProt Q50732 (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 —
25 functional partner(s); context anchor
Rv2565 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2566| MPLRPTQVSGTGRTRCAGRSGVISSAAMSIKVALEHRTSYTFDRLVRVYPHIVRLRPAPHSRTSIEAYSLRIEPADHFINWQQDALGNFLARLVFPNPMRQLRITVGLIADLKVINPFDFFIEDWAEIWPCAGMAYPKALADDLRPYLRPVDEDGDGSGPGELTQAWVRNFTVPDGTRTIDFLVALNRAINADVGYCVRMEPGVQTPDFTLRTGVGSCRDSAWLLVSILRQFGLAARFVSGYLVQLASDIEALDGPSGPAADFTDLHAWAEAYIPGAGWIGLDPTSGLLAGEGHIPLAATPHPASAAPISGGTDVCDTVLEFSNTVTRVHEDPRVTLPYTDESWKTICEVGQRVDERLAAADVRLTVGGEPTFVSVDNQVAEEWRTAADGPHKRERASDLAARLKAVWAPQGLIHRGQGRWYPGEPLPRWQIALYWRTDGRPLWTNDALLADPWGAPPADPVDDDAAYRVLAGIADGLGLPISQVRPAYEDPLSRLAAAVRMPAGDPVESGDDLGCDTNPDTPTGRAALLARLDEAITSPAAYVLPLHRRDDGQGWASANWRLRRGRIVLLEGDSPAGLRLPLDSISWRPPRASFDADPVAVRSTLPAELHTDRAVVEDPETAPTTALVAEVRGGLVHIFLPPTDALEHFIDLVARVEAAATTANCPVVIEGYGPPPDPRLTSTTITPDPGVIEVNIAPTASFAEQRQQLETLYQQARLARLTTEAFDVDGTHGGTGGGNHITLGGVTPADSPLLRRPDLLVSLLTYWQRHPSLSYLFAGRFVGTTSQAPRVDEGRAEALYELEIAFAEILRLSPSSGGGRPQPWVTDRALRHLLTDITGNTHRAEFCIDKLYSPDSARGRLGLLELRGFEMPPHLHMAMVQSLLVRSLVAWFWDQPLRAPLIRHGANLHGRYLLPHFLIHDIADVAADLRAHGIAFETSWLDPFTEFRFPRIGTAVFDGIEIELRGAIEPWHTLGEEATAAGTARYVDSSVERIQVRIIGADRHRYVVTCNGYPMPLLATDNPDIHVGGVRFKAWQPPSALHPTITVDGPLRFELIDIATATSCGGCTYHVAHPGGRAYDEPPVNAVEAEARRARRFEATGFTPGKLDLSDIREKQARISTDIGAPGILDLRRVRTVQQ