GapMind for catabolism of small carbon sources

 

Protein WP_088754101.1 in Herbaspirillum aquaticum IEH 4430

Annotation: NCBI__GCF_002213425.1:WP_088754101.1

Length: 373 amino acids

Source: GCF_002213425.1 in NCBI

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-alanine catabolism braC hi Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized) 60% 99% 461.5 Leu/Ile/Val-binding protein LivJ aka B3460 aka LIV-BP, component of Leucine; leucine/isoleucine/valine porter 52% 389.4
L-isoleucine catabolism livJ hi Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized) 60% 99% 461.5
L-leucine catabolism livJ hi Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized) 60% 99% 461.5
L-serine catabolism braC hi Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized) 60% 99% 461.5 Leu/Ile/Val-binding protein LivJ aka B3460 aka LIV-BP, component of Leucine; leucine/isoleucine/valine porter 52% 389.4
L-threonine catabolism braC hi Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized) 60% 99% 461.5 Leu/Ile/Val-binding protein LivJ aka B3460 aka LIV-BP, component of Leucine; leucine/isoleucine/valine porter 52% 389.4
L-valine catabolism livJ hi Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized) 60% 99% 461.5 leucine-specific-binding protein LivK 51% 384.0
L-phenylalanine catabolism livJ hi Leucine ABC transporter subunit substrate-binding protein LivK (characterized, see rationale) 63% 97% 449.1 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 43% 288.5
D-alanine catabolism AZOBR_RS08260 med Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale) 43% 97% 296.2 Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein 60% 461.5
L-proline catabolism AZOBR_RS08260 med Branched-chain amino acid ABC transporter,substrate-binding periplasmic component (characterized, see rationale) 43% 97% 296.2 Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein 60% 461.5
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) 43% 96% 288.5 Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein 60% 461.5
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) 43% 96% 288.5 Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein 60% 461.5
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) 43% 96% 288.5 Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein 60% 461.5

Sequence Analysis Tools

View WP_088754101.1 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

MKFASRLTKIALAAATFAAFAGVAHAETVKIAIAGPLTGAVAQYGDMVKAGALTAIEQIN
AAGGANGNKFEAVMMDDACEPKQAVAVANKIVSQGIKYVIGHVCSGSTIPASDIYENEGV
VMITPSATAPQLTEAKPHKFIFRTIGRDDQQGPAAARYVIEKLKPKKVAVLHDKQSYGQG
VASSVKSALDAAKVPVVVFEGINAGDSDYSAIVTKLKSQGVDFVYFGGYHPEMGLIMRQA
REQGVKAVFMGPEGVGNKDITAIAGPASEGMLVTLPADFAADPANAALVKAFAAAKRDAN
GPFQMPAYSAVKIIADAITGAKSTDPDKVAAYIHGNSFKTPIGNVEYDKKGDLKAFKFVV
FTWHKDATKTEAK

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