GapMind for catabolism of small carbon sources

 

Protein AO356_28510 in Pseudomonas fluorescens FW300-N2C3

Annotation: AO356_28510 xylose transporter

Length: 518 amino acids

Source: pseudo5_N2C3_1 in FitnessBrowser

Candidate for 26 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-xylose catabolism xylG hi Xylose import ATP-binding protein XylG; EC 7.5.2.10 (characterized) 56% 97% 553.1 RbsA, component of The probable autoinducer-2 (AI-2;, a furanosyl borate diester: 3aS,6S,6aR)-2,2,6,6a-tetrahydroxy-3a-methyltetrahydrofuro[3,2-d][1,3,2]dioxaborolan-2-uide) uptake porter (Shao et al., 2007) (50-70% identical to RbsABC of E. coli; TC# 3.A.1.2.1) 45% 411.8
L-arabinose catabolism gguA med GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 43% 100% 411.8 Xylose import ATP-binding protein XylG; EC 7.5.2.10 56% 553.1
D-cellobiose catabolism mglA med GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 43% 100% 411.8 Xylose import ATP-binding protein XylG; EC 7.5.2.10 56% 553.1
D-galactose catabolism gguA med GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 43% 100% 411.8 Xylose import ATP-binding protein XylG; EC 7.5.2.10 56% 553.1
D-glucose catabolism mglA med GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 43% 100% 411.8 Xylose import ATP-binding protein XylG; EC 7.5.2.10 56% 553.1
lactose catabolism mglA med GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 43% 100% 411.8 Xylose import ATP-binding protein XylG; EC 7.5.2.10 56% 553.1
D-maltose catabolism mglA med GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 43% 100% 411.8 Xylose import ATP-binding protein XylG; EC 7.5.2.10 56% 553.1
sucrose catabolism mglA med GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 43% 100% 411.8 Xylose import ATP-binding protein XylG; EC 7.5.2.10 56% 553.1
trehalose catabolism mglA med GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 43% 100% 411.8 Xylose import ATP-binding protein XylG; EC 7.5.2.10 56% 553.1
D-ribose catabolism rbsA med Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized) 43% 96% 411 Xylose import ATP-binding protein XylG; EC 7.5.2.10 56% 553.1
D-mannose catabolism HSERO_RS03640 med Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 42% 94% 384.4 Xylose import ATP-binding protein XylG; EC 7.5.2.10 56% 553.1
myo-inositol catabolism PS417_11890 med Inositol transport system ATP-binding protein (characterized) 44% 95% 381.7 Xylose import ATP-binding protein XylG; EC 7.5.2.10 56% 553.1
D-galactose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized) 41% 98% 372.5 Xylose import ATP-binding protein XylG; EC 7.5.2.10 56% 553.1
L-fucose catabolism HSERO_RS05250 med Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 42% 94% 365.2 Xylose import ATP-binding protein XylG; EC 7.5.2.10 56% 553.1
D-galactose catabolism BPHYT_RS16930 med Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) 41% 96% 358.2 Xylose import ATP-binding protein XylG; EC 7.5.2.10 56% 553.1
L-rhamnose catabolism rhaT' med RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized) 41% 96% 355.9 Xylose import ATP-binding protein XylG; EC 7.5.2.10 56% 553.1
L-arabinose catabolism araG med L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized) 40% 97% 349.7 Xylose import ATP-binding protein XylG; EC 7.5.2.10 56% 553.1
D-xylose catabolism xylK_Tm med Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale) 40% 95% 349 Xylose import ATP-binding protein XylG; EC 7.5.2.10 56% 553.1
D-fructose catabolism frcA med ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 41% 93% 330.9 Xylose import ATP-binding protein XylG; EC 7.5.2.10 56% 553.1
sucrose catabolism frcA med ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 41% 93% 330.9 Xylose import ATP-binding protein XylG; EC 7.5.2.10 56% 553.1
myo-inositol catabolism iatA lo Inositol transport ATP-binding protein IatA, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized) 39% 97% 339 Xylose import ATP-binding protein XylG; EC 7.5.2.10 56% 553.1
xylitol catabolism PS417_12065 lo D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale) 38% 99% 317.8 Xylose import ATP-binding protein XylG; EC 7.5.2.10 56% 553.1
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 38% 96% 156 Xylose import ATP-binding protein XylG; EC 7.5.2.10 56% 553.1
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 34% 95% 147.5 Xylose import ATP-binding protein XylG; EC 7.5.2.10 56% 553.1
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 35% 95% 143.3 Xylose import ATP-binding protein XylG; EC 7.5.2.10 56% 553.1
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 35% 95% 143.3 Xylose import ATP-binding protein XylG; EC 7.5.2.10 56% 553.1

Sequence Analysis Tools

View AO356_28510 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MSDYLLQMNGIVKTFGGVKALNGIDIKVRPGECVGLCGENGAGKSTLMKVLSAVYPHGTW
EGEIIWDGQPLKAQSISETEAAGIVIIHQELTLVPDLSVAENIFMGHELTLPGGRMNYPA
MIHRAEALMRELKVPDMNVSLPVSQYGGGYQQLVEIAKALNKQARLLILDEPSSALTRSE
IEVLLDIIRDLKAKGVACVYISHKLDEVAAVCDTISVIRDGKHIATTAMTDMDIPKIITQ
MVGREMSNLYPTEPHDIGEVIFEARHVTCYDVDNPRRKRVDDISFVLKRGEILGIAGLVG
AGRTELVSALFGAYPGRYEGEVWLNGQQIDTRTPLKSIRAGLCMVPEDRKRQGIIPDLGV
GQNITLAVLDNYSKLTRIDAEAELGSIDKEIARMHLKTASPFLPITSLSGGNQQKAVLAK
MLLTKPRVLILDEPTRGVDVGAKYEIYKLMGALAAEGVSIIMVSSELAEVLGVSDRVLVI
GDGQLRGDFINHELTQEQVLAAALSHPDGHNNNDRKSA

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory