GapMind for catabolism of small carbon sources

 

Protein Pf1N1B4_3974 in Pseudomonas fluorescens FW300-N1B4

Annotation: FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3974

Length: 341 amino acids

Source: pseudo1_N1B4 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-cellobiose catabolism gtsD med Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) 43% 96% 270.4 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 47% 273.5
D-glucose catabolism gtsD med Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) 43% 96% 270.4 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 47% 273.5
lactose catabolism gtsD med Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) 43% 96% 270.4 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 47% 273.5
D-maltose catabolism gtsD med Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) 43% 96% 270.4 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 47% 273.5
D-maltose catabolism thuK med Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) 43% 96% 270.4 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 47% 273.5
D-mannose catabolism TT_C0211 med Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) 43% 96% 270.4 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 47% 273.5
sucrose catabolism gtsD med Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) 43% 96% 270.4 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 47% 273.5
sucrose catabolism thuK med Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) 43% 96% 270.4 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 47% 273.5
trehalose catabolism gtsD med Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) 43% 96% 270.4 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 47% 273.5
trehalose catabolism thuK med Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) 43% 96% 270.4 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 47% 273.5
D-mannitol catabolism mtlK med SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 44% 95% 268.5 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 47% 273.5
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 42% 95% 261.5 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 47% 273.5
lactose catabolism lacK med LacK, component of Lactose porter (characterized) 45% 73% 248.4 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 47% 273.5
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 40% 95% 246.5 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 47% 273.5
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 84% 245.7 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 47% 273.5
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 84% 245.7 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 47% 273.5
D-cellobiose catabolism msiK med MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) 44% 77% 244.6 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 47% 273.5
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 42% 84% 229.2 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 47% 273.5
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 38% 99% 233 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 47% 273.5
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 38% 97% 231.5 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 47% 273.5
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 39% 83% 213.4 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 47% 273.5
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 39% 83% 213.4 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 47% 273.5
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 39% 83% 213.4 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 47% 273.5
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 39% 83% 213.4 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 47% 273.5
L-isoleucine catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 32% 85% 115.2 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 47% 273.5
L-valine catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 32% 85% 115.2 Fe(3+) ions import ATP-binding protein FbpC, component of Hexose-phosphate transporter 47% 273.5

Sequence Analysis Tools

View Pf1N1B4_3974 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MAFVQLENLGKRYGEIDAVVATNLSVEKGEFVSLLGPSGCGKTTTLQMIAGFVEVSSGRI
VLDGRDITHAKPASRGLGVVFQSYALFPHMTVRDNVAFGLRMRKVPNDELQQRVDRVLKL
VRLNQHAERYPRELSGGQRQRVALARALVIEPPVLLLDEPLSNLDANLREEMQFEIRRIQ
REVGITTLMVTHDQSEALSISDRVVVMQAGRITQIDAPYTLYEHPRTEFISGFVGKANLL
PGERDSAGVVQVCNRDNGELTLSLRPEKIDLRDVGLGRLQGKIVSRFFLGSQWLYGVSTS
LGELSVVRRNDGSAPLIEGTAVGLDWDTALLRVLSVDEVSA

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