GapMind for catabolism of small carbon sources

 

Protein 5210164 in Shewanella loihica PV-4

Annotation: FitnessBrowser__PV4:5210164

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

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

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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 (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