GapMind for catabolism of small carbon sources

 

Protein CA265_RS04175 in Pedobacter sp. GW460-11-11-14-LB5

Annotation: CA265_RS04175 phosphonate ABC transporter ATP-binding protein

Length: 232 amino acids

Source: Pedo557 in FitnessBrowser

Candidate for 32 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-glutamate catabolism gltL lo GluA aka CGL1950, component of Glutamate porter (characterized) 39% 90% 152.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 38% 86% 146.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 38% 84% 146.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 37% 84% 145.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 37% 84% 145.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8
L-asparagine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 38% 84% 144.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8
L-aspartate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 38% 84% 144.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8
L-glutamate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 38% 84% 144.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8
L-leucine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 38% 84% 144.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8
L-proline catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 38% 84% 144.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 38% 83% 143.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 38% 83% 143.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 37% 85% 142.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 62% 142.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 62% 142.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 62% 142.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 62% 142.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 62% 142.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 62% 142.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 62% 142.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 62% 142.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 60% 137.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 60% 137.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 60% 137.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 34% 60% 137.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 37% 58% 134.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8
L-arginine catabolism artP lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 35% 90% 131 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 35% 90% 131 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 35% 63% 119 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8
D-mannose catabolism TM1749 lo TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 33% 72% 118.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8
citrate catabolism fecE lo iron(III) dicitrate transport ATP-binding protein FecE (characterized) 31% 85% 105.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 31% 59% 91.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 44% 203.8

Sequence Analysis Tools

View CA265_RS04175 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

MIKIENLEKVYKTEEVETTALNGINLHVAAGEFVSIMGPSGCGKSTLLNVMGLLDKPENG
SYKFIDTELLTLNDRERSNFRKRNMGFVFQNFNLIDELTVFENIELPLIYNKIPAGERKK
LVNEIIERMNIVNRSGHFPQQLSGGQQQRVAVARALVTKPKLVLADEPTGNLDSSHGNEV
MELLCELNETGTTIVMVTHSSHDASFSNRIINLKDGHVISEKINKSRNEELI

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