GapMind for catabolism of small carbon sources

 

Protein WP_007514889.1 in Rhodanobacter denitrificans 2APBS1

Annotation: NCBI__GCF_000230695.2:WP_007514889.1

Length: 243 amino acids

Source: GCF_000230695.2 in NCBI

Candidate for 25 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 43% 89% 172.2 Uncharacterized ABC transporter ATP-binding protein Rv0986 43% 189.5
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 43% 89% 172.2 Uncharacterized ABC transporter ATP-binding protein Rv0986 43% 189.5
L-glutamate catabolism gltL med GluA aka CGL1950, component of Glutamate porter (characterized) 44% 86% 151.8 Uncharacterized ABC transporter ATP-binding protein Rv0986 43% 189.5
L-histidine catabolism aapP med ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 42% 81% 146.7 Uncharacterized ABC transporter ATP-binding protein Rv0986 43% 189.5
L-asparagine catabolism aapP med 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) 40% 81% 145.2 Uncharacterized ABC transporter ATP-binding protein Rv0986 43% 189.5
L-aspartate catabolism aapP med 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) 40% 81% 145.2 Uncharacterized ABC transporter ATP-binding protein Rv0986 43% 189.5
L-glutamate catabolism aapP med 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) 40% 81% 145.2 Uncharacterized ABC transporter ATP-binding protein Rv0986 43% 189.5
L-leucine catabolism aapP med 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) 40% 81% 145.2 Uncharacterized ABC transporter ATP-binding protein Rv0986 43% 189.5
L-proline catabolism aapP med 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) 40% 81% 145.2 Uncharacterized ABC transporter ATP-binding protein Rv0986 43% 189.5
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-Glucosamine, putative ATPase component (characterized) 40% 87% 142.9 Uncharacterized ABC transporter ATP-binding protein Rv0986 43% 189.5
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized) 42% 86% 142.1 Uncharacterized ABC transporter ATP-binding protein Rv0986 43% 189.5
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 41% 83% 137.5 Uncharacterized ABC transporter ATP-binding protein Rv0986 43% 189.5
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 43% 64% 161.4 Uncharacterized ABC transporter ATP-binding protein Rv0986 43% 189.5
L-lysine catabolism hisP lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 39% 90% 146 Uncharacterized ABC transporter ATP-binding protein Rv0986 43% 189.5
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 35% 60% 137.9 Uncharacterized ABC transporter ATP-binding protein Rv0986 43% 189.5
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 36% 61% 137.5 Uncharacterized ABC transporter ATP-binding protein Rv0986 43% 189.5
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 38% 66% 136.7 Uncharacterized ABC transporter ATP-binding protein Rv0986 43% 189.5
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 35% 57% 136.7 Uncharacterized ABC transporter ATP-binding protein Rv0986 43% 189.5
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 38% 66% 136.7 Uncharacterized ABC transporter ATP-binding protein Rv0986 43% 189.5
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 36% 56% 133.7 Uncharacterized ABC transporter ATP-binding protein Rv0986 43% 189.5
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 36% 58% 131.3 Uncharacterized ABC transporter ATP-binding protein Rv0986 43% 189.5
D-fructose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 31% 96% 95.1 Uncharacterized ABC transporter ATP-binding protein Rv0986 43% 189.5
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 31% 96% 95.1 Uncharacterized ABC transporter ATP-binding protein Rv0986 43% 189.5
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 31% 96% 95.1 Uncharacterized ABC transporter ATP-binding protein Rv0986 43% 189.5
sucrose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 31% 96% 95.1 Uncharacterized ABC transporter ATP-binding protein Rv0986 43% 189.5

Sequence Analysis Tools

View WP_007514889.1 at NCBI

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

Fitness BLAST: loading...

Sequence

MAVVAPLPVGEAVFRARGLTKTYRMGEVEVHALRGIDLDLFRGEFVVLLGPSGSGKSTLL
NILGGLDAPTAGEVWYEGHHLTGASERELTLFRREHVGFVFQFYNLIPSLTARENVAIVT
EIAEQPMTPEEALARVDLADRMDHFPAQLSGGQQQRVAIARAIAKRPAVLLCDEPTGALD
SATGVRVLEALERVNAELGTTTVVITHNADIARMAHRVLYLGDGRIVREERPAQRTPAKE
LRW

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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