GapMind for catabolism of small carbon sources

 

Protein Pf1N1B4_3974 in Pseudomonas fluorescens FW300-N1B4

Annotation: ABC transporter, ATP-binding protein

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

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: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

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 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, 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