GapMind for catabolism of small carbon sources

 

Protein GFF1277 in Pseudomonas stutzeri RCH2

Annotation: FitnessBrowser__psRCH2:GFF1277

Length: 418 amino acids

Source: psRCH2 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-isoleucine catabolism livM hi High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale) 81% 100% 680.2 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% 169.1
L-phenylalanine catabolism livM hi High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale) 81% 100% 680.2 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% 169.1
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) 78% 100% 647.5 High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M 63% 496.1
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) 78% 100% 647.5 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% 169.1
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) 78% 100% 647.5 High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M 63% 496.1
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) 78% 100% 647.5 High-affinity branched-chain amino acid transport system permease protein LivM; LIV-I protein M 63% 496.1
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) 78% 100% 647.5 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% 169.1
L-arginine catabolism braE med Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 50% 93% 360.1 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 78% 647.5
L-glutamate catabolism braE med Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 50% 93% 360.1 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 78% 647.5
L-histidine catabolism braE med Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale) 50% 93% 360.1 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 78% 647.5
L-proline catabolism HSERO_RS00890 med ABC transporter ATP-binding protein (characterized, see rationale) 44% 98% 271.9 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 78% 647.5
L-serine catabolism Ac3H11_1694 med ABC transporter ATP-binding protein (characterized, see rationale) 44% 98% 271.9 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 78% 647.5
L-tyrosine catabolism Ac3H11_1694 med ABC transporter ATP-binding protein (characterized, see rationale) 44% 98% 271.9 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 78% 647.5
D-alanine catabolism AZOBR_RS08240 lo Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale) 62% 65% 406.8 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 78% 647.5
L-proline catabolism AZOBR_RS08240 lo Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale) 62% 65% 406.8 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 78% 647.5
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% 51% 87.8 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 78% 647.5
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% 51% 87.8 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 78% 647.5
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% 51% 87.8 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 78% 647.5
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% 51% 87.8 High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine 78% 647.5

Sequence Analysis Tools

View GFF1277 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

Fitness BLAST: loading...

Sequence

MSGNLRTAFFSALLVIAVAVPVFGLKLTTVGIRVEVHGAEIGTFWIIAACAVAMFVWQLF
RTHLAAGWAASPSLPTVPAGAGNFLTLPSTQRWIILALVLVALVWPFYGSRGAVDIATLI
LIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYTYALLSHYYGVGFWTALPIAGAMAALF
GFLLGFPVLRLRGDYLAIVTLGFGEIIRILLRNMTSVTGGPNGISGIDKPTLFGLSFDRR
AAEGMQTFHEYFGVAYNSVNKVIFLYLIALLLVLLTLFVINRLLRMPIGRAWEALREDEI
ACRALGMNPTVIKLSAFTLGATFAGFAGSFFAARQGLVSPESFTFIESAIILAIVVLGGM
GSQLGVILAAIVMILLPELMREFSEYRMLMFGALMVLMMIWRPQGLLPMQRPHLELKQ

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