GapMind for catabolism of small carbon sources

 

Protein BPHYT_RS31715 in Burkholderia phytofirmans PsJN

Annotation: BPHYT_RS31715 branched-chain amino acid ABC transporter substrate-binding protein

Length: 380 amino acids

Source: BFirm 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
L-isoleucine catabolism livJ hi Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale) 47% 98% 344.4
L-leucine catabolism livJ hi Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale) 47% 98% 344.4
L-phenylalanine catabolism livJ hi Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale) 47% 98% 344.4 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 36% 211.1
L-proline catabolism HSERO_RS00870 hi Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale) 47% 98% 344.4 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 36% 211.1
L-serine catabolism Ac3H11_2396 hi Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale) 47% 98% 344.4 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 36% 211.1
L-tyrosine catabolism Ac3H11_2396 hi Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale) 47% 98% 344.4 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 36% 211.1
D-alanine catabolism AZOBR_RS08260 med Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale) 37% 98% 232.3 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 36% 211.1
L-proline catabolism AZOBR_RS08260 med Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale) 37% 98% 232.3 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 36% 211.1
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) 36% 93% 211.1 Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein 33% 205.7
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) 36% 93% 211.1 Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein 33% 205.7
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) 36% 93% 211.1 Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein 33% 205.7
L-valine catabolism livJ 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) 36% 93% 211.1 leucine-specific-binding protein LivK 31% 184.9

Sequence Analysis Tools

View BPHYT_RS31715 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

MNSYMKHGFAVAALSAACNAAFAADDITVIKIGSAAPTTGAIANLGKENENGARLAVEDV
NRRGLVINGKKIKLELDAVDDQADPRQGTQVAQRLVDDGVVAVVGHLNSGVSIAASRIYH
DAQILQISPDSTNPKFTQQGFNTTYRLVATDAQQSPVLAHYALETLKAKKVAIVDDSTAY
GQGLADQFSSAVKSGGATVVAREATNDKTIDFKGVITKIKGQSPDVIFYGGMDATAGPFI
KQVAQLGLNAKVLGGDGTCSDEVIALAGPAVDRLVCSIAGLPLSRMKAGPAFEKEYQQRF
GMPVQIYAPYAYDAVMVIVDAMKKSGSTDHAKILAAASATDYQGLTGQIQFDDKGDVRSP
RLTLYGYKDGKKTLLTTMTP

This GapMind analysis is from Sep 17 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 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