GapMind for catabolism of small carbon sources

 

Protein 3610344 in Dinoroseobacter shibae DFL-12

Annotation: Dshi_3725 inner-membrane translocator (RefSeq)

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

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 and signal peptides: Phobius

Check the SEED with FIGfam search

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.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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