Rv3920c Family assigned · medium auto-curated
H37Rv Rv3920c · MTBC0 mtbc0_004154 ·
187 aa · 4432585–4433148 (-) ·
RefSeq NP_218437.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | R3H domain-containing nucleic acid-binding protein |
| Revised (this work) | R3H domain-containing nucleic acid-binding protein. Pfam: R3H (PF01424.29). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53598
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein similar to jag protein |
UniProt still lists this protein as Conserved protein similar to jag protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | jag |
| eggNOG description | RNA-binding protein |
| Orthologous group | COG1847 |
| KEGG orthology |
K06346
|
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 | 1.296 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 8 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 |
|---|---|---|---|---|
R3H | PF01424.29 | 4.1e-18 | 126–185 | R3H domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: yidC (membrane protein insertase YidC), high confidence from genomic context alone (score 986 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) |
|---|---|---|---|---|
Rv3921c yidC |
membrane protein insertase YidC | 987 | 986 ctx | neighborhood:792 coexpression:909 |
Rv3923c rnpA |
ribonuclease P protein component | 961 | 960 ctx | neighborhood:792 coexpression:814 |
Rv3922c yidD |
membrane protein insertion efficiency factor | 955 | 955 ctx | neighborhood:792 coexpression:794 |
Rv3919c gid |
16S rRNA (guanine(527)-N(7))-methyltransferase RsmG | 947 | 938 ctx | neighborhood:727 coexpression:783 |
Rv2908c hyp |
hypothetical protein | 992 | 931 | experimental:891 textmining:889 |
Rv3917c parB |
chromosome partitioning protein ParB | 842 | 833 ctx | neighborhood:758 |
Rv1297 rho |
transcription termination factor Rho | 817 | 806 | coexpression:805 |
Rv0708 rplP |
50S ribosomal protein L16 | 804 | 804 | coexpression:804 |
Rv1613 trpA |
tryptophan synthase subunit alpha | 804 | 804 | coexpression:804 |
Rv0706 rplV |
50S ribosomal protein L22 | 803 | 803 | coexpression:803 |
Rv0721 rpsE |
30S ribosomal protein S5 | 802 | 802 | coexpression:802 |
Rv0705 rpsS |
30S ribosomal protein S19 | 801 | 801 | coexpression:801 |
Rv0723 rplO |
50S ribosomal protein L15 | 800 | 800 | coexpression:800 |
Rv0710 rpsQ |
30S ribosomal protein S17 | 799 | 799 | coexpression:799 |
Rv0704 rplB |
50S ribosomal protein L2 | 794 | 795 | coexpression:795 |
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: R3H domain-containing nucleic acid-binding protein
- Pfam (hmmscan --cut_ga): R3H PF01424.29 (E=4e-18)
- (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_218437.1)
- Domains: Pfam-A via hmmscan --cut_ga — R3H (PF01424.29)
- 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
COG1847 - Curated reference: UniProt O53598 (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 —
46 functional partner(s); context anchor
yidC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004154|Rv3920c| MADADTTDFDVDAEAPGGGVREDTATDADEADDQEERLVAEGEIAGDYLEELLDVLDFDGDIDLDVEGNRAVVSIDGSDDLNKLVGRGGEVLDALQELTRLAVHQKTGVRSRLMLDIARWRRRRREELAALADEVARRVAETGDREELVPMTPFERKIVHDAVAAVPGVHSESEGVEPERRVVVLRD