GapMind for catabolism of small carbon sources

 

Protein 3610344 in Dinoroseobacter shibae DFL-12

Annotation: FitnessBrowser__Dino:3610344

Length: 294 amino acids

Source: Dino in FitnessBrowser

Candidate for 13 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-alanine catabolism AZOBR_RS08235 lo L-proline and D-alanine ABC transporter, permease component 1 (characterized) 33% 96% 159.1 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 37% 176.0
L-proline catabolism AZOBR_RS08235 lo L-proline and D-alanine ABC transporter, permease component 1 (characterized) 33% 96% 159.1 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 37% 176.0
L-isoleucine catabolism livH lo ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 97% 153.3 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 37% 176.0
L-leucine catabolism livH lo ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 97% 153.3 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 37% 176.0
L-valine catabolism livH lo ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 97% 153.3 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 37% 176.0
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) 31% 98% 146 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 37% 176.0
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) 31% 98% 146 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 37% 176.0
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) 31% 98% 146 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 37% 176.0
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) 31% 98% 144.4 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 37% 176.0
L-arginine catabolism braD lo Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 97% 138.7 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 37% 176.0
L-glutamate catabolism braD lo Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 97% 138.7 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 37% 176.0
L-histidine catabolism braD lo Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 97% 138.7 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 37% 176.0
D-lactate catabolism PGA1_c12660 lo D-lactate transporter, permease component 2 (characterized) 34% 71% 134 UrtA, component of The high affinity urea/thiourea/hydroxyurea porter 37% 176.0

Sequence Analysis Tools

View 3610344 at FitnessBrowser

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

MAEYLHFVLAPQMLNGLALGVSVILVALGLTIIFGLLDVINMSHGEFYAVGAYGALALAA
FGVNYWVLMAMVPLMMIPLGIVTERYLIRRVYDGADRHVSTLLLTFGLGLIAEDVLKIIF
GPNTQRPENPLPGATDLMGIFIPTYRLFLIAISAAVILAVAFVVYRTRLGAIVRAASFDR
NMAASLGVRVGWVYSGAFAFGVALAGLAGVLLAPIYSVFPTMGRDFILIAFTVVIVGGMG
SIWGAVVAGIVLTQIQAISSLVISPVWSEPIVFGVMVLVLMFRPQGLFGRIGHA

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 (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