GapMind for catabolism of small carbon sources

 

Protein GFF3114 in Marinobacter adhaerens HP15

Annotation: HP15_3057 leucine/isoleucine/valine transporter permease subunit

Length: 423 amino acids

Source: Marino in FitnessBrowser

Candidate for 19 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-alanine catabolism braE hi High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 60% 100% 510.4 High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M 57% 451.1
L-isoleucine catabolism livM hi High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 60% 100% 510.4 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% 166.4
L-leucine catabolism livM hi High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 60% 100% 510.4 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% 166.4
L-serine catabolism braE hi High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 60% 100% 510.4 High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M 57% 451.1
L-threonine catabolism braE hi High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 60% 100% 510.4 High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M 57% 451.1
L-valine catabolism livM hi High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 60% 100% 510.4 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% 166.4
L-phenylalanine catabolism livM hi High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale) 59% 100% 500 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% 166.4
D-alanine catabolism AZOBR_RS08240 med Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale) 49% 90% 401.4 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 60% 510.4
L-proline catabolism AZOBR_RS08240 med Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale) 49% 90% 401.4 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 60% 510.4
L-arginine catabolism braE med Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 55% 71% 335.1 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 60% 510.4
L-glutamate catabolism braE med Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 55% 71% 335.1 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 60% 510.4
L-histidine catabolism braE med Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 55% 71% 335.1 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 60% 510.4
L-proline catabolism HSERO_RS00890 med ABC transporter ATP-binding protein (characterized, see rationale) 44% 95% 274.2 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 60% 510.4
L-serine catabolism Ac3H11_1694 med ABC transporter ATP-binding protein (characterized, see rationale) 44% 95% 274.2 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 60% 510.4
L-tyrosine catabolism Ac3H11_1694 med ABC transporter ATP-binding protein (characterized, see rationale) 44% 95% 274.2 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 60% 510.4
L-isoleucine catabolism natC lo NatC, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 58% 104.8 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 60% 510.4
L-leucine catabolism natC lo NatC, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 58% 104.8 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 60% 510.4
L-proline catabolism natC lo NatC, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 58% 104.8 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 60% 510.4
L-valine catabolism natC lo NatC, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 31% 58% 104.8 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 60% 510.4

Sequence Analysis Tools

View GFF3114 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

MAANNFRHALFCAFITLIISYPIIGFNLEAQGINVTLTGADASTIVMVLFAAVIVFLFQM
FREQIMGGLKSIPHPLPQSNKEPMAENRRAKIESWVLTGIVVLALFWPFFVSRGAVDLAT
LVLIYIMLALGLNVVVGLAGLLDLGYVAFYAVGAYTFALLSQYTGISFWLALPIGALLAA
LFGLVLGFPVLRLRGDYLAIVTLGFGEIIRILLNNWTTLTGGPNGIGGIPDPTLFGMEFG
RRVKEEGNTSFHETFGIAYSGEHKVIFLYLIALVLAVFTALVIRRFMRMPVGRAWEALRE
DEIAARSLGLSRTAVKLSAFTIGAFFAGFAGTVFASKQGFISPESFVFLESAIILAIVVL
GGMGSQIGVVLAAIAVTILPELAREFSEYRMLIFGAAMVLMMVWRPQGLMPMRRIHIELK
RQE

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