GapMind for catabolism of small carbon sources

 

Protein AO356_28510 in Pseudomonas fluorescens FW300-N2C3

Annotation: FitnessBrowser__pseudo5_N2C3_1:AO356_28510

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

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

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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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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