GapMind for catabolism of small carbon sources

 

Protein WP_110751348.1 in Phyllobacterium leguminum ORS 1419

Annotation: NCBI__GCF_003217235.1:WP_110751348.1

Length: 458 amino acids

Source: GCF_003217235.1 in NCBI

Candidate for 18 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism braE hi Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 77% 96% 677.2 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 57% 348.2
L-glutamate catabolism braE hi Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 77% 96% 677.2 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 57% 348.2
L-histidine catabolism braE hi Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 77% 96% 677.2 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 57% 348.2
L-isoleucine catabolism livM hi Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 77% 96% 677.2 BraE aka Bra2E, 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 32% 160.6
L-leucine catabolism livM hi Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 77% 96% 677.2 BraE aka Bra2E, 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 32% 160.6
L-valine catabolism livM hi Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 77% 96% 677.2 BraE aka Bra2E, 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 32% 160.6
L-phenylalanine catabolism livM hi High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale) 49% 98% 364.8 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 34% 179.5
L-alanine catabolism braE med High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 57% 76% 348.2 High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M 45% 323.2
L-serine catabolism braE med High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 57% 76% 348.2 High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M 45% 323.2
L-threonine catabolism braE med High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 57% 76% 348.2 High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M 45% 323.2
L-proline catabolism HSERO_RS00890 med ABC transporter ATP-binding protein (characterized, see rationale) 43% 96% 251.9 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 57% 348.2
L-serine catabolism Ac3H11_1694 med ABC transporter ATP-binding protein (characterized, see rationale) 43% 96% 251.9 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 57% 348.2
L-tyrosine catabolism Ac3H11_1694 med ABC transporter ATP-binding protein (characterized, see rationale) 43% 96% 251.9 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 57% 348.2
D-alanine catabolism AZOBR_RS08240 lo Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale) 60% 64% 383.3 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 57% 348.2
L-proline catabolism AZOBR_RS08240 lo Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale) 60% 64% 383.3 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 57% 348.2
L-histidine catabolism natC lo NatC aka SLL0146, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 57% 89 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 57% 348.2
L-leucine catabolism natC lo NatC aka SLL0146, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 57% 89 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 57% 348.2
L-proline catabolism natC lo NatC aka SLL0146, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 57% 89 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 57% 348.2

Sequence Analysis Tools

View WP_110751348.1 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

MAELSKPGTQSVFIPAIREGIMAGIIAFGLFVLIVGFRADANISNELVLEQRWGLLFTMV
GIAAVGRFLFKAFLSPWMAARKAHASAKTEIAGEPSFFRRHFSQIAIGFLVVYPVLIVSM
VGMQGSLKWVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYYG
LSFWILLPMAGIFAATWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTAVTKGTFG
ISGIAKATLFGIPFTAGPNGFAAIFGLPPSSAYYKIFLYYLILCLALLTAWVTIRLRRMP
VGRAWEALREDEIACRSLGINTTTTKLTAFATGAMFGGFAGSFFAARQGFVSPESFVFLE
SAVILAIVVLGGMGSLVGIAIAAVAMIGGTEILREMSFLKLIFGESFTPELYRMLIFGLA
MVVVMVWKPRGFVGSREPSAFLHKRKLVSGSFTKEGHG

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