GapMind for catabolism of small carbon sources

 

Protein WP_097070282.1 in Rhodobacter maris JA276

Annotation: NCBI__GCF_900217815.1:WP_097070282.1

Length: 289 amino acids

Source: GCF_900217815.1 in NCBI

Candidate for 13 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-isoleucine catabolism livH med ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 36% 97% 175.6 L-proline and D-alanine ABC transporter, permease component 1 32% 157.1
L-leucine catabolism livH med ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 36% 97% 175.6 L-proline and D-alanine ABC transporter, permease component 1 32% 157.1
L-valine catabolism livH med ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 36% 97% 175.6 L-proline and D-alanine ABC transporter, permease component 1 32% 157.1
L-phenylalanine catabolism livH lo Branched-chain amino acid ABC transporter permease LivH; SubName: Full=Branched-chain amino acid transporter permease subunit LivH; SubName: Full=L-leucine ABC transporter membrane protein /L-isoleucine ABC transporter membrane protein /L-valine ABC transporter membrane protein (characterized, see rationale) 32% 96% 162.2 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 36% 175.6
L-alanine catabolism braD lo High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 96% 161.8 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 36% 175.6
L-serine catabolism braD lo High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 96% 161.8 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 36% 175.6
L-threonine catabolism braD lo High-affinity branched-chain amino acid transport system permease protein BraD, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 33% 96% 161.8 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 36% 175.6
D-alanine catabolism AZOBR_RS08235 lo L-proline and D-alanine ABC transporter, permease component 1 (characterized) 32% 97% 157.1 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 36% 175.6
L-proline catabolism AZOBR_RS08235 lo L-proline and D-alanine ABC transporter, permease component 1 (characterized) 32% 97% 157.1 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 36% 175.6
L-proline catabolism HSERO_RS00885 lo ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale) 33% 96% 152.5 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 36% 175.6
L-arginine catabolism braD lo Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 97% 148.3 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 36% 175.6
L-glutamate catabolism braD lo Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 97% 148.3 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 36% 175.6
L-histidine catabolism braD lo Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 97% 148.3 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 36% 175.6

Sequence Analysis Tools

View WP_097070282.1 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

MEQIIVNGLFLGASYALIALGLTLIFSLMNVLNFAHGQMYVLGGFITYTVVAQFHLPFVV
GLICSAVALAALGAFAERFLFAPVIRRSKREESTMLLAAGIAFFLDAVTLLVFGEKQRGI
PKIVQGVFNWDFRIVMPYDRILIGCLAVALIAAFILFMRLSRTGRAMRALAQDRMAAELM
GVDVGRYSMIGFALGAMLAGLVGGLLVSIVGVNLGMGGPTSIKAFMMIMIGGAGVISGAI
AGGFILGMLESVGLSLLAAYGDITYLVIFVSLLIFLAFRPQGLMGKPWG

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