GapMind for catabolism of small carbon sources

 

Protein 5210164 in Shewanella loihica PV-4

Annotation: Shew_2608 inner-membrane translocator (RefSeq)

Length: 357 amino acids

Source: PV4 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
L-isoleucine catabolism livM med ABC transporter ATP-binding protein (characterized, see rationale) 30% 96% 164.1 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 34% 141.7
L-leucine catabolism livM med ABC transporter ATP-binding protein (characterized, see rationale) 30% 96% 164.1 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 34% 141.7
L-phenylalanine catabolism livM med ABC transporter ATP-binding protein (characterized, see rationale) 30% 96% 164.1 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 31% 150.6
L-proline catabolism HSERO_RS00890 med ABC transporter ATP-binding protein (characterized, see rationale) 30% 96% 164.1 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 31% 150.6
L-serine catabolism Ac3H11_1694 med ABC transporter ATP-binding protein (characterized, see rationale) 30% 96% 164.1 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 31% 150.6
L-tyrosine catabolism Ac3H11_1694 med ABC transporter ATP-binding protein (characterized, see rationale) 30% 96% 164.1 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 31% 150.6
L-valine catabolism livM med ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 86% 152.1 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 34% 141.7
L-arginine catabolism braE lo Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 30% 70% 134.4 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 31% 150.6
L-glutamate catabolism braE lo Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 30% 70% 134.4 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 31% 150.6
L-histidine catabolism braE lo Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 30% 70% 134.4 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 31% 150.6
L-alanine catabolism braE lo High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 30% 69% 129 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 31% 150.6
L-serine catabolism braE lo High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 30% 69% 129 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 31% 150.6
L-threonine catabolism braE lo High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 30% 69% 129 ABC transporter membrane-spanning permease-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 31% 150.6

Sequence Analysis Tools

View 5210164 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

MSSLAMRPCGDFRTSYKADNTIFETKTIRLVTCLVIALACAAPLVLDGYFLTLFIQISYL
GIAALGLNILVGFTGQISLGHGAFFGFGAFASAWLNTSFNIPVVFCIPLAGFLTMGVGMM
FGMPAARIKGLYLAIATLAAQFIIQDFFGRAEWFSGGSSGAMAAPVSLFGFDFDTDMSFY
FIALFALVFMYIWGCNLMRSRDGRAFVAVRDHYLSAEIMGVKLNKYRLLSFGISSFYAGI
GGALYAHYLGYVSSEGFTILMSIQFLAMVIIGGLGSIKGTLMGVVFMVLLPEVLEGMVGL
MKYTDYGNLPMVTDGLAYIKEMAIGLVIILFLIFEPEGLAHRWGQIKNYWKCYPFAY

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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