GapMind for catabolism of small carbon sources

 

Protein GFF3104 in Pseudomonas stutzeri RCH2

Annotation: Psest_3163 ABC-type amino acid transport/signal transduction systems, periplasmic component/domain

Length: 342 amino acids

Source: psRCH2 in FitnessBrowser

Candidate for 12 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-alanine catabolism Pf6N2E2_5402 hi ABC transporter for D-Alanine, periplasmic substrate-binding component (characterized) 79% 100% 549.7 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, periplasmic substrate-binding component 63% 447.2
L-histidine catabolism aapJ med ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, periplasmic substrate-binding component (characterized) 63% 100% 447.2 ABC transporter for D-Alanine, periplasmic substrate-binding component 79% 549.7
L-asparagine catabolism aapJ med AapJ, 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) 60% 100% 432.6 ABC transporter for D-Alanine, periplasmic substrate-binding component 79% 549.7
L-aspartate catabolism aapJ med AapJ, 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) 60% 100% 432.6 ABC transporter for D-Alanine, periplasmic substrate-binding component 79% 549.7
L-glutamate catabolism aapJ med AapJ, 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) 60% 100% 432.6 ABC transporter for D-Alanine, periplasmic substrate-binding component 79% 549.7
L-leucine catabolism aapJ med AapJ, 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) 60% 100% 432.6 ABC transporter for D-Alanine, periplasmic substrate-binding component 79% 549.7
L-proline catabolism aapJ med AapJ, 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) 60% 100% 432.6 ABC transporter for D-Alanine, periplasmic substrate-binding component 79% 549.7
L-asparagine catabolism bztA med BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 55% 98% 382.1 ABC transporter for D-Alanine, periplasmic substrate-binding component 79% 549.7
L-aspartate catabolism bztA med BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 55% 98% 382.1 ABC transporter for D-Alanine, periplasmic substrate-binding component 79% 549.7
L-glutamate catabolism bztA med BztA, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 55% 98% 382.1 ABC transporter for D-Alanine, periplasmic substrate-binding component 79% 549.7
L-asparagine catabolism natF med Extracellular solute-binding protein, family 3 (characterized, see rationale) 49% 92% 329.3 ABC transporter for D-Alanine, periplasmic substrate-binding component 79% 549.7
L-aspartate catabolism natF med Extracellular solute-binding protein, family 3 (characterized, see rationale) 49% 92% 329.3 ABC transporter for D-Alanine, periplasmic substrate-binding component 79% 549.7

Sequence Analysis Tools

View GFF3104 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

MIRVKSTLAVLGAASLLGISGLAQAGATLDAVQKKGFVQCGISDGLPGFSFADAKGKYQG
IDVDICRAVAAAVFGDASKVKYSPLTAKERFTALQSGEVDVLSRNTTWTSSRDAAMGLNF
TGVTYYDGQGFLVNKELGVSSAKELDGATVCIQAGTTTELNLSDYFRANGHKYTPITYDT
SDESAKSLESGRCDVLTSDQSQLYAQRIKLAKPADYVVLPEVISKEPLGPAVRQGDEEWF
DIVRWTLFAMLNAEELGVTSANVEEMAKSTKNPDVARLLGAEGEYGKDLKLPKDWAVQIV
KQVGNYGEIFDRNVGAGSELKIERGLNALWNNGGLQYAPPVR

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