Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | molybdopterin biosynthesis protein MoeW |
|---|
| MTBC0 PGAP re-annotation | ThiF family adenylyltransferase |
|---|
| Revised (this work) | ThiF family adenylyltransferase. Pfam: ThiF (PF00899.28). |
|---|
Auto-curated: this verdict and function were generated by rules from
PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P95234
TrEMBL · unreviewed
· Evidence at protein level
|
|---|
| UniProt name | Possible molybdopterin biosynthesis protein MoeW |
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|
| Preferred name | moeW |
|---|
| eggNOG description | ThiF family |
|---|
| Orthologous group | COG0476 |
|---|
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 |
1.957 · diversifying/relaxed
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
1 synonymous, 6 missense, 0 nonsense, 1 frameshift
|
|---|
| Disruption |
1 distinct premature-stop/frameshift site(s); most common in
0.11% of strains
(162) · 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 |
|---|
ThiF | PF00899.28 |
9.3e-55 | 26–286 |
ThiF family |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv3323c moaX |
MoaD-MoaE fusion protein MoaX |
838 |
815 |
coexpression:446 experimental:473 |
Rv2337c hyp |
hypothetical protein |
813 |
813 ctx |
neighborhood:505 cooccurence:443 |
Rv0417 thiG |
thiazole synthase |
776 |
759 |
coexpression:647 |
Rv0416 thiS |
sulfur carrier protein ThiS |
725 |
708 |
coexpression:461 experimental:463 |
Rv3119 moaE1 |
molybdopterin synthase catalytic subunit 1 |
695 |
679 |
coexpression:436 |
Rv0866 moaE2 |
molybdopterin synthase catalytic subunit 2 |
694 |
678 |
coexpression:434 |
Rv3025c iscS |
cysteine desulfurase |
691 |
672 |
database:615 |
Rv0434 hyp |
hypothetical protein |
657 |
645 |
database:595 |
Rv2555c alaS |
alanine--tRNA ligase |
589 |
584 |
database:517 |
Rv3529c hyp |
hypothetical protein |
569 |
551 |
database:416 |
Rv1691 hyp |
hypothetical protein |
569 |
551 |
database:416 |
Rv2267c stf3 hyp |
hypothetical protein |
568 |
551 |
database:416 |
Rv0422c thiD |
hydroxymethylpyrimidine/phosphomethylpyrimidine kinase |
584 |
550 |
coexpression:428 |
Rv3492c |
Mce associated protein |
562 |
547 |
database:466 |
Rv1363c |
membrane protein |
562 |
546 |
database:466 |
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: molybdopterin biosynthesis protein MoeW
- MTBC0 PGAP product: ThiF family adenylyltransferase
- Pfam (hmmscan --cut_ga): ThiF PF00899.28 (E=9e-55)
- (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_216854.1)
- Domains: Pfam-A via hmmscan --cut_ga — ThiF (PF00899.28)
- 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
COG0476
- Curated reference: UniProt
P95234
(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 —
60 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002488|Rv2338c|moeW
MRAGADAPDSGRVKESAPWSYDEAFCRNLGLISPTEQQRLRNSRVAIAGMGGVGGIDMVALARMGIGKFTIADPDVFEIRNSNRQYGAMRSTNGQAKAEVMRNIVHDINPEAEIRAFCEPIGKENAATFLEGADVLVDGIDAFEIDLRRLLYREAQQRGIYALGAGPLGFSTAWVVFDPKGMTFDRYFDLSDAMNTVDKFVAFIAGIAPSATHRRSIDLSYVDIENRTGPSVGLACHLASGVVAAEVLKILLGHGRVYAAPYFHQFDAYRSIYVRKRLRCGNRHPLQRVKRRLLARYINRRSAGVIPGLRYHRTEPSY
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