GapMind for catabolism of small carbon sources

 

Protein 6938761 in Shewanella amazonensis SB2B

Annotation: Sama_2864 ABC transporter related (RefSeq)

Length: 230 amino acids

Source: SB2B in FitnessBrowser

Candidate for 17 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-lysine catabolism hisP med Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 41% 83% 153.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 214.2
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 40% 83% 155.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 214.2
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 40% 83% 155.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 214.2
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 39% 65% 155.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 214.2
L-asparagine catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 37% 89% 146.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 214.2
L-aspartate catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 37% 89% 146.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 214.2
L-glutamate catabolism gltL lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 37% 89% 146.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 214.2
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 38% 85% 146 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 214.2
L-arginine catabolism artP lo Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 37% 84% 142.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 214.2
L-histidine catabolism hisP lo Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 37% 84% 142.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 214.2
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 37% 83% 139.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 214.2
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) 36% 82% 137.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 214.2
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) 36% 82% 137.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 214.2
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) 36% 82% 137.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 214.2
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 39% 74% 137.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 214.2
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) 36% 82% 137.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 214.2
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) 36% 82% 137.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 214.2

Sequence Analysis Tools

View 6938761 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

MLTMKNINKLFRTDLVETHALRDFNLEVAEGEFVAVTGPSGSGKTTFLNIAGLLENASGG
EYWLDGENVANLSDSAAARVRNQKIGFIFQGFNLIPDLNLAENVELPLRYRGFGSSERKR
RVEQALSQVGLAARQKHLPSQLSGGQQQRVAIARALAGEPRFLLADEPTGNLDSLMARQV
MELLEDINRQGTTIIMVTHDGELARRAERNIQIVDGQVCDFLTSRAVVNG

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