Rv1868 Family assigned · medium auto-curated
H37Rv Rv1868 · MTBC0 mtbc0_001981 ·
699 aa · 2135386–2137485 (+) ·
RefSeq NP_216384.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | NAD(P)H-binding protein |
| Revised (this work) | NAD(P)H-binding protein. Pfam: Rph_4th (PF27448.1). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P95147
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein |
UniProt still lists this protein as Uncharacterized protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolismM Cell wall / membrane / envelope biogenesis
|
|---|---|
| eggNOG description | epimerase |
| Orthologous group | COG0702 |
| EC number |
EC 2.7.9.2
|
| KEGG orthology |
K01007
|
| KEGG pathways |
map00620, map00680, map00720, map01100, map01120, map01200
|
| KEGG modules |
M00173, M00374
|
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) pseudogene candidate
| pN/pS | 0.765 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 12 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 6.18% of strains (8967) · clonal |
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 |
|---|---|---|---|---|
Rph_4th | PF27448.1 | 4.6e-08 | 509–621 | Rifampicin phosphotransferase fourth domain |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0705 rpsS |
30S ribosomal protein S19 | 816 | 816 | experimental:463 database:574 |
Rv0682 rpsL |
30S ribosomal protein S12 | 813 | 805 | experimental:463 database:573 |
Rv0710 rpsQ |
30S ribosomal protein S17 | 803 | 797 | experimental:463 database:578 |
Rv0707 rpsC |
30S ribosomal protein S3 | 802 | 795 | experimental:463 database:578 |
Rv0721 rpsE |
30S ribosomal protein S5 | 796 | 789 | experimental:463 database:575 |
Rv2056c rpsN2 |
30S ribosomal protein S14 | 787 | 788 | experimental:436 database:548 |
Rv0717 rpsN1 |
30S ribosomal protein S14 | 787 | 788 | experimental:436 database:548 |
Rv0718 rpsH |
30S ribosomal protein S8 | 793 | 786 | experimental:463 database:578 |
Rv0700 rpsJ |
30S ribosomal protein S10 | 788 | 785 | experimental:463 database:557 |
Rv0702 rplD |
50S ribosomal protein L4 | 786 | 780 | experimental:463 database:575 |
Rv2785c rpsO |
30S ribosomal protein S15 | 782 | 779 | experimental:463 database:573 |
Rv1006 hyp |
hypothetical protein | 774 | 774 ctx | cooccurence:774 |
Rv1435c hyp |
hypothetical protein | 773 | 773 ctx | cooccurence:773 |
Rv2890c rpsB |
30S ribosomal protein S2 | 778 | 770 | experimental:463 database:573 |
Rv3459c rpsK |
30S ribosomal protein S11 | 775 | 767 | experimental:463 database:558 |
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: NAD(P)H-binding protein
- Pfam (hmmscan --cut_ga): Rph_4th PF27448.1 (E=5e-08)
- (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_216384.1)
- Domains: Pfam-A via hmmscan --cut_ga — Rph_4th (PF27448.1)
- 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
COG0702 - Curated reference: UniProt P95147 (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 — 148 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001981|Rv1868| MQILVTDATGAVGRSVTRQLIAAGHTVSGIAQHPHDALDPRVDYVCASLRNPVLQELAGEADAVIHLAPVDTSAPGGVGITGLAHVANAAARAGARLLFVSQAAGRPELYRQAETLVSTGWAPSLVIRIAPPVGRQLDWMVCRTVATLLRSKVSARPIRVLHLDDLVRFLVLALNTDRNGVVDLATPDTTNVVTAWRLLRSVDPHLRTRRVRSWEQLIPEVDIAAVQEDWNFEFGWQATEAIVDTGRGLVGRRLHPAGATNGSGQLALPVEAPPRSVPSHGEPLGSAAPEGLEGEFDDRIDERFPVFSSASLAEALPGPLTPMTLDVQLSGLRAAGRAMGRVLALGGVVADEWERRAIAVFGHRPYIGVSANIVAAAQLPGWDAQAVARRALGEQPQVTELLPFGRPQLAGGPLGSVAKVVVTARSLALLRHLRSDTHHYVAAADAEHLAAGQLASLPDAGLEVRIRLLRDRIHQGWILTVLWVIDTGVTAATLEHTRAGSAVSGGGMIMESGRIGAEIAPLAAVLRADPPLCALANDGNLASIRALSAPAAAAVDAVIARIGHRGLGEAELANLTFADDPALLLKTAAEIAARPAGPAHPATLIQRLAAGTRSARELAHDTTIRFTHELRMTLRELGSRRVAADVIDVVDDVFYLTCDELITTPADARLRIKRRRAERERLQAQRPPDVIDHAWVPVE