fmu Resolved · high auto-curated
H37Rv Rv1407 · MTBC0 mtbc0_001508 ·
457 aa · 1592445–1593818 (+) ·
RefSeq NP_215923.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 16S rRNA m5C967 methyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | 16S rRNA m5C967 methyltransferase |
| Revised (this work) | 16S rRNA m5C967 methyltransferase. Pfam: NusB (PF01029.24), Methyltr_RsmB-F (PF01189.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGX3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative methyltransferase Rv1407 |
| EC (curated) |
EC 2.1.1.-
|
| Curated function | May act as RNA methyltransferase. |
UniProt still lists this protein as Putative methyltransferase Rv1407; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesisK Transcription
|
|---|---|
| Preferred name | fmu |
| eggNOG description | Belongs to the class I-like SAM-binding methyltransferase superfamily. RsmB NOP family |
| Orthologous group | COG0144 |
| EC number |
EC 2.1.1.176
|
| KEGG orthology |
K03500
|
| Gene Ontology (58) |
GO:0000154, GO:0001510, GO:0003674, GO:0003824, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0006139, GO:0006364 +46 more
|
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 | 0.298 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 3 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 |
|---|---|---|---|---|
NusB | PF01029.24 | 9.9e-26 | 15–137 | NusB family |
Methyltr_RsmB-F | PF01189.24 | 1.1e-66 | 260–454 | 16S rRNA methyltransferase RsmB/F |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fmt (methionyl-tRNA formyltransferase), high confidence from genomic context alone (score 997 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1406 fmt |
methionyl-tRNA formyltransferase | 998 | 997 ctx | neighborhood:881 coexpression:973 |
Rv3404c hyp |
hypothetical protein | 980 | 970 | coexpression:966 |
Rv0018c pstP |
phosphoserine/threonine phosphatase PstP | 942 | 934 | coexpression:906 |
Rv0651 rplJ |
50S ribosomal protein L10 | 923 | 915 | coexpression:400 experimental:835 |
Rv0700 rpsJ |
30S ribosomal protein S10 | 949 | 914 | experimental:890 textmining:437 |
Rv3014c ligA |
DNA ligase A | 913 | 908 | coexpression:893 |
Rv3443c rplM |
50S ribosomal protein L13 | 916 | 907 | experimental:837 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 957 | 901 ctx | neighborhood:544 coexpression:731 textmining:591 |
Rv0715 rplX |
50S ribosomal protein L24 | 909 | 893 | experimental:867 |
Rv1408 rpe |
ribulose-phosphate 3-epimerase | 896 | 892 ctx | neighborhood:846 |
Rv1409 ribG |
bifunctional riboflavin biosynthesis diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino) uracil reductas | 957 | 884 ctx | neighborhood:854 textmining:648 |
Rv2793c truB |
tRNA pseudouridine synthase B | 923 | 876 | coexpression:811 textmining:413 |
Rv0722 rpmD |
50S ribosomal protein L30 | 904 | 869 | experimental:814 |
Rv0701 rplC |
50S ribosomal protein L3 | 874 | 869 | experimental:848 |
Rv0706 rplV |
50S ribosomal protein L22 | 867 | 863 | experimental:843 |
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: 16S rRNA m5C967 methyltransferase
- MTBC0 PGAP product: 16S rRNA m5C967 methyltransferase
- Pfam (hmmscan --cut_ga): NusB PF01029.24 (E=1e-25), Methyltr_RsmB-F PF01189.24 (E=1e-66)
- (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_215923.1)
- Domains: Pfam-A via hmmscan --cut_ga — NusB (PF01029.24), Methyltr_RsmB-F (PF01189.24)
- 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
COG0144 - Curated reference: UniProt P9WGX3 (SwissProt, reviewed; 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 —
238 functional partner(s); context anchor
fmt - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001508|Rv1407|fmu MTPRSRGPRRRPLDPARRAAFETLRAVSARDAYANLVLPALLAQRGIGGRDAAFATELTYGTCRARGLLDAVIGAAAERSPQAIDPVLLDLLRLGTYQLLRTRVDAHAAVSTTVEQAGIEFDSARAGFVNGVLRTIAGRDERSWVGELAPDAQNDPIGHAAFVHAHPRWIAQAFADALGAAVGELEAVLASDDERPAVHLAARPGVLTAGELARAVRGTVGRYSPFAVYLPRGDPGRLAPVRDGQALVQDEGSQLVARALTLAPVDGDTGRWLDLCAGPGGKTALLAGLGLQCAARVTAVEPSPHRADLVAQNTRGLPVELLRVDGRHTDLDPGFDRVLVDAPCTGLGALRRRPEARWRRQPADVAALAKLQRELLSAAIALTRPGGVVLYATCSPHLAETVGAVADALRRHPVHALDTRPLFEPVLAGLGEGPHVQLWPHRHGTDAMFAAALRRLT