xylB Resolved · high auto-curated
H37Rv Rv0729 · MTBC0 mtbc0_000771 ·
448 aa · 825700–827046 (+) ·
RefSeq NP_215243.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | D-xylulose kinase XylB |
|---|---|
| MTBC0 PGAP re-annotation | FGGY-family carbohydrate kinase |
| Revised (this work) | FGGY-family carbohydrate kinase. Pfam: FGGY_N (PF00370.28), FGGY_C (PF02782.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6Y4K0
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible D-xylulose kinase XylB |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | xylB |
| eggNOG description | Belongs to the FGGY kinase family |
| Orthologous group | COG1070 |
| EC number |
EC 2.7.1.17
|
| KEGG orthology |
K00854
|
| KEGG pathways |
map00040, map01100
|
| KEGG modules |
M00014
|
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 | 0.574 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 6 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 |
|---|---|---|---|---|
FGGY_N | PF00370.28 | 9.4e-09 | 7–112 | FGGY family of carbohydrate kinases, N-terminal domain |
FGGY_C | PF02782.23 | 1.7e-23 | 291–402 | FGGY family of carbohydrate kinases, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fucA (L-fuculose phosphate aldolase FucA), high confidence from genomic context alone (score 916 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1408 rpe |
ribulose-phosphate 3-epimerase | 938 | 920 | database:900 |
Rv0727c fucA |
L-fuculose phosphate aldolase FucA | 936 | 916 ctx | neighborhood:790 coexpression:445 |
Rv0728c serA2 |
D-3-phosphoglycerate dehydrogenase SerA | 903 | 899 ctx | neighborhood:790 cooccurence:467 |
Rv0730 |
GCN5-like N-acetyltransferase | 981 | 858 ctx | neighborhood:858 textmining:875 |
Rv3575c |
LacI family transcriptional regulator | 754 | 679 ctx | cooccurence:489 |
Rv1006 hyp |
hypothetical protein | 604 | 604 ctx | cooccurence:604 |
Rv1868 hyp |
hypothetical protein | 601 | 581 ctx | cooccurence:580 |
Rv2298 |
oxidoreductase | 571 | 532 ctx | cooccurence:483 |
Rv1435c hyp |
hypothetical protein | 527 | 527 ctx | cooccurence:527 |
Rv2436 rbsK |
ribokinase RbsK | 537 | 475 | |
Rv0186 bglS |
beta-glucosidase BglS | 504 | 473 ctx | cooccurence:409 |
Rv1448c tal |
transaldolase | 655 | 443 | textmining:406 |
Rv3033 hyp |
hypothetical protein | 420 | 420 ctx | cooccurence:419 |
Rv3788 hyp |
hypothetical protein | 419 | 420 | |
Rv3138 pflA |
pyruvate formate lyase activating protein PflA | 413 | 414 | coexpression:414 |
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: D-xylulose kinase XylB
- MTBC0 PGAP product: FGGY-family carbohydrate kinase
- Pfam (hmmscan --cut_ga): FGGY_N PF00370.28 (E=9e-09), FGGY_C PF02782.23 (E=2e-23)
- (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_215243.1)
- Domains: Pfam-A via hmmscan --cut_ga — FGGY_N (PF00370.28), FGGY_C (PF02782.23)
- 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
COG1070 - Curated reference: UniProt I6Y4K0 (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 —
35 functional partner(s); context anchor
fucA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000771|Rv0729|xylB MSRDDVTIGIDIGTTAVKAVAADDNGRVTARVRIGHQLAVPAPDRLEHDADEAWRRGPLAALDRLVGPDTRALAVAAMVPSLTAVDPAGRPITPGLLYGDARGRVPNASVARAQSVPSVGETAEFLRWTAGQAPDASGYWPAPAVANYALSGEAVIDYATAVTTLPLFDGTGWNATACADCGVTVDRMPRVETFGVGVGQVRGTGAVLAVGAVDALCEQIVAGADRDGDVLVLCGATLIVWTTISAARQVPGLWTIPHTAPGKSQIGGASNAGGLFLNWVDRVIGPGDPALADPRRVPVWLPYIRGERTPFHEPDRRAVLDGVDLSQDAASVRRAAYEASGFVVRQLIELSGAPVARIVAAGGGTRIQPWMQAIADATGRPVEVSRVAEGAALGAAFLGRLAAGLESSIADAARWASTDRIVEPSADWAGPTKERYRRFLALSGSKLA