GapMind for catabolism of small carbon sources

 

Protein 8500415 in Desulfovibrio vulgaris Miyazaki F

Annotation: DvMF_1165 inner-membrane translocator (RefSeq)

Length: 306 amino acids

Source: Miya in FitnessBrowser

Candidate for 16 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 hi ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 45% 100% 246.9 L-proline and D-alanine ABC transporter, permease component 1 41% 223.4
L-leucine catabolism livH hi ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 45% 100% 246.9 L-proline and D-alanine ABC transporter, permease component 1 41% 223.4
L-valine catabolism livH hi ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 45% 100% 246.9 L-proline and D-alanine ABC transporter, permease component 1 41% 223.4
D-alanine catabolism AZOBR_RS08235 med L-proline and D-alanine ABC transporter, permease component 1 (characterized) 41% 100% 223.4 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 45% 246.9
L-proline catabolism AZOBR_RS08235 med L-proline and D-alanine ABC transporter, permease component 1 (characterized) 41% 100% 223.4 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 45% 246.9
L-proline catabolism HSERO_RS00885 med ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale) 40% 98% 207.2 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 45% 246.9
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) 37% 98% 214.5 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 45% 246.9
L-phenylalanine catabolism livH lo branched chain amino acid/phenylalanine ABC transporter membrane subunit LivH (EC 7.4.2.2) (characterized) 36% 98% 214.5 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 45% 246.9
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) 37% 98% 214.5 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 45% 246.9
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) 37% 98% 214.5 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 45% 246.9
L-arginine catabolism braD lo Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 39% 100% 214.2 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 45% 246.9
L-glutamate catabolism braD lo Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 39% 100% 214.2 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 45% 246.9
L-histidine catabolism braD lo Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 39% 100% 214.2 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 45% 246.9
L-serine catabolism Ac3H11_1695 lo ABC transporter permease (characterized, see rationale) 36% 98% 204.9 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 45% 246.9
L-tyrosine catabolism Ac3H11_1695 lo ABC transporter permease (characterized, see rationale) 36% 98% 204.9 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 45% 246.9
D-lactate catabolism PGA1_c12660 lo D-lactate transporter, permease component 2 (characterized) 30% 98% 127.9 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 45% 246.9

Sequence Analysis Tools

View 8500415 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

MEIFIQNLFNALQWGSFYALIALGYTLVYGVLLLINFAHGDIFMVGAYIAFFVSSLLLGD
LLGVFNLPGWAALALTVPLTMLLTAGVGVTLERIAYRPLRRKGAHRLYVVITALMCGLIL
ENGNLALLGASRRKLPDMVDKVVYTFGSVSVTNLKVWVIITAFLVFFLLQFIVTRTRIGM
AMRAVAWDKFALPLMGIPLDSIIVFTFVLGSGFAGLAGLLFAMSYPILDPYMGAMVGWKA
FIAAVVGGIGDIRGAFIGGFLLAFIEIMVAAFLPSTFRDLFAFTILLMILWQRPTGLFGV
AKTTKI

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 preprint 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