Rv2721c Family assigned · medium auto-curated
H37Rv Rv2721c · MTBC0 mtbc0_002895 ·
699 aa · 3054935–3057034 (-) ·
RefSeq NP_217237.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | LGFP repeat-containing protein |
| Revised (this work) | LGFP repeat-containing protein. Pfam: LGFP (PF08310.18), ArfC (PF27542.1). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6XF52
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible conserved transmembrane alanine and glycine rich protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| eggNOG description | protein potentially involved in peptidoglycan biosynthesis |
| Orthologous group | COG5479 |
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 | 0.55 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 8 synonymous, 13 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 |
|---|---|---|---|---|
LGFP | PF08310.18 | 2.7e-11 | 240–289 | LGFP repeat |
ArfC | PF27542.1 | 7.1e-11 | 642–696 | ArfC |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pirG (cell surface protein), high confidence from genomic context alone (score 918 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) |
|---|---|---|---|---|
Rv3810 pirG |
cell surface protein | 918 | 918 ctx | cooccurence:709 coexpression:730 |
Rv0312 hyp |
hypothetical protein | 851 | 850 | coexpression:827 |
Rv1477 ripA |
peptidoglycan endopeptidase RipA | 837 | 831 | coexpression:804 |
Rv0040c mtc28 hyp |
hypothetical protein | 803 | 803 | coexpression:803 |
Rv1157c hyp |
hypothetical protein | 798 | 799 | coexpression:730 |
Rv1478 ripB |
peptidoglycan endopeptidase RipB | 803 | 796 | coexpression:796 |
Rv3414c sigD |
ECF RNA polymerase sigma factor SigD | 785 | 785 | coexpression:785 |
Rv2145c wag31 |
cell wall synthesis protein Wag31 | 751 | 751 | coexpression:751 |
Rv0479c |
membrane protein | 745 | 746 ctx | cooccurence:742 |
Rv1566c ripD hyp |
hypothetical protein | 747 | 738 | coexpression:738 |
Rv2015c hyp |
hypothetical protein | 728 | 729 ctx | cooccurence:727 |
Rv1765c hyp |
hypothetical protein | 704 | 705 ctx | cooccurence:703 |
Rv0941c hyp |
hypothetical protein | 686 | 686 ctx | cooccurence:685 |
Rv0320 hyp |
hypothetical protein | 681 | 681 ctx | cooccurence:677 |
Rv0441c hyp |
hypothetical protein | 679 | 680 ctx | cooccurence:679 |
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: LGFP repeat-containing protein
- Pfam (hmmscan --cut_ga): LGFP PF08310.18 (E=3e-11), ArfC PF27542.1 (E=7e-11)
- (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_217237.1)
- Domains: Pfam-A via hmmscan --cut_ga — LGFP (PF08310.18), ArfC (PF27542.1)
- 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
COG5479 - Curated reference: UniProt I6XF52 (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 —
88 functional partner(s); context anchor
pirG - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002895|Rv2721c| MNGQRGQLSTLIGRTLLGLAATAVTAVLLAPTVAASPMGDAEDAMMAAWEKAGGDTSTLGVRKGDVYPIGDGFALDFAGGKMFFTPATGAKYLYGPLLDKYESLGGAADSDLGFPTINEVPGLAGPDSRVSTFSAADNPVIFWTPEHGAFVVRGALNAAWDKLGSSGGVLGAPVGDETYDGEVTAQKFSGGEVSWNRATKEFTTVPAVLAEQLKGLQVAIDPSAAINMAWRAAGGAAGPLGAKKGGQYPIGGDGIAQDFVGGKVFFSPATGANAVEGEILAKYESLGGPVSSDLGFPIANETDGGFGPSSRIVRFSAADKPVIFWTPDHGAFVVRGAMVAAWDKLRGPNGKLGAPVGDQTVDGDVVSQKFTGGMISWNRAKNTFTTDPANLAPLLSGLQVSGQNQPSTSAMPPPGKKFTWHWWWLGAAALGVLLVVMVALVVFGLRRRRRGYDAAAYDDDRAGDVEYGTAADGDWPPDEDFGSEHFGFGDQFPPEPVAPDAGSTPRVSWPRGAGAAVGDAEHLPGEEGYGSDLLSGPSNVGVEEEDTDAVDTTPTPVVSQADLSEVGPDLIVPERVVPETFVPQAFVPEAVAPEAVPPDVHAADLADTGLPAAAVSAAEDRGGRHAAAEPPEPPSAGVRPAIHLPLEDPYQMPNGYPVKASVSFGLYYPPGSALYHDTLAELWFASEEVAQVNGFIRAD