GapMind for catabolism of small carbon sources

 

Protein GFF1279 in Pseudomonas stutzeri RCH2

Annotation: Psest_1312 ABC-type branched-chain amino acid transport systems, periplasmic component

Length: 372 amino acids

Source: psRCH2 in FitnessBrowser

Candidate for 15 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-alanine catabolism braC hi Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized) 75% 99% 577.4 leucine-specific-binding protein LivK 58% 448.4
L-isoleucine catabolism livJ hi Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized) 75% 99% 577.4
L-leucine catabolism livJ hi Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized) 75% 99% 577.4
L-serine catabolism braC hi Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized) 75% 99% 577.4 leucine-specific-binding protein LivK 58% 448.4
L-threonine catabolism braC hi Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized) 75% 99% 577.4 leucine-specific-binding protein LivK 58% 448.4
L-valine catabolism livJ hi Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized) 75% 99% 577.4 leucine-specific-binding protein LivK 58% 448.4
L-phenylalanine catabolism livJ hi Leucine ABC transporter subunit substrate-binding protein LivK (characterized, see rationale) 74% 99% 564.7 BraC, component of General L- (and D-)amino acid uptake porter (transports acidic, basic, polar, semipolar and hydrophobic amino acids). The amino and carboxyl groups do not need to be α since γ-aminobutyric acid (GABA) is a substrate. The system may function with additional binding proteins since L-alanine uptake is not dependent on BraC 42% 285.4
D-alanine catabolism AZOBR_RS08260 med Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale) 43% 99% 298.5 Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein 75% 577.4
L-proline catabolism AZOBR_RS08260 med Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale) 43% 99% 298.5 Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein 75% 577.4
L-arginine catabolism braC med BraC, component of General L- (and D-)amino acid uptake porter (transports acidic, basic, polar, semipolar and hydrophobic amino acids). The amino and carboxyl groups do not need to be α since γ-aminobutyric acid (GABA) is a substrate. The system may function with additional binding proteins since L-alanine uptake is not dependent on BraC (characterized) 42% 96% 285.4 Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein 75% 577.4
L-glutamate catabolism braC med BraC, component of General L- (and D-)amino acid uptake porter (transports acidic, basic, polar, semipolar and hydrophobic amino acids). The amino and carboxyl groups do not need to be α since γ-aminobutyric acid (GABA) is a substrate. The system may function with additional binding proteins since L-alanine uptake is not dependent on BraC (characterized) 42% 96% 285.4 Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein 75% 577.4
L-histidine catabolism braC med BraC, component of General L- (and D-)amino acid uptake porter (transports acidic, basic, polar, semipolar and hydrophobic amino acids). The amino and carboxyl groups do not need to be α since γ-aminobutyric acid (GABA) is a substrate. The system may function with additional binding proteins since L-alanine uptake is not dependent on BraC (characterized) 42% 96% 285.4 Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein 75% 577.4
L-proline catabolism HSERO_RS00870 lo Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale) 33% 99% 190.7 Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein 75% 577.4
L-serine catabolism Ac3H11_2396 lo Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale) 33% 99% 190.7 Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein 75% 577.4
L-tyrosine catabolism Ac3H11_2396 lo Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale) 33% 99% 190.7 Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein 75% 577.4

Sequence Analysis Tools

View GFF1279 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

MKTKQRLSKIFLAMALTGAASYTLAADTIRIGLAGPVTGPVAQYGDMQFIGAEMAIEQIN
KAGGVNGAQLKGVRYDDACDPKQAVAVANKIVNDNVKFVVGHLCSSSTQPASDIYEDEGI
LMITAASTSPDITSRGYELIFRTIGLDSLQGPTAGNFIADHVKPKNVAVIHDKQQYGEGI
ATAVKQTLEGKNIKVGLFEGINAGDKDFSSLIAKLKREGVDFVYYGGYHPELGLLLRQSK
EKGLNVRFMGPEGVGNSEISAIAGPASEGMYVTLPKSFDQDPRNKELVDGFKAKKQDPSG
PFVFPAYAAVQVIAEGIEKAGSTDTDKVAEALRSNTFDTPTGMLSFDEKGDLKDFNFVVY
EWHQDGTKTEAK

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