GapMind for catabolism of small carbon sources

 

Protein Synpcc7942_0247 in Synechococcus elongatus PCC 7942

Annotation: Synpcc7942_0247 ABC-type permease for basic amino acids and glutamine

Length: 377 amino acids

Source: SynE in FitnessBrowser

Candidate for 27 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism bgtB' hi ABC-type permease for basic amino acids and glutamine (characterized, see rationale) 100% 100% 750.4 ABC transporter for D-Alanine, permease component 2 42% 263.1
L-aspartate catabolism bgtB' hi ABC-type permease for basic amino acids and glutamine (characterized, see rationale) 100% 100% 750.4 ABC transporter for D-Alanine, permease component 2 42% 263.1
D-alanine catabolism Pf6N2E2_5403 hi ABC transporter for D-Alanine, permease component 2 (characterized) 42% 98% 263.1 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 36% 235.0
L-histidine catabolism aapQ lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 (characterized) 36% 97% 235 ABC transporter for D-Alanine, permease component 2 42% 263.1
L-asparagine catabolism aapQ lo AapQ, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 37% 95% 233 ABC transporter for D-Alanine, permease component 2 42% 263.1
L-aspartate catabolism aapQ lo AapQ, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 37% 95% 233 ABC transporter for D-Alanine, permease component 2 42% 263.1
L-glutamate catabolism aapQ lo AapQ, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 37% 95% 233 ABC transporter for D-Alanine, permease component 2 42% 263.1
L-leucine catabolism aapQ lo AapQ, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 37% 95% 233 ABC transporter for D-Alanine, permease component 2 42% 263.1
L-proline catabolism aapQ lo AapQ, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 37% 95% 233 ABC transporter for D-Alanine, permease component 2 42% 263.1
L-asparagine catabolism bztB lo glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized) 36% 95% 219.2 ABC transporter for D-Alanine, permease component 2 42% 263.1
L-aspartate catabolism bztB lo glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized) 36% 95% 219.2 ABC transporter for D-Alanine, permease component 2 42% 263.1
L-glutamate catabolism bztB lo glutamate/glutamine/aspartate/asparagine transport system permease protein BztB (characterized) 36% 95% 219.2 ABC transporter for D-Alanine, permease component 2 42% 263.1
L-asparagine catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 34% 54% 89 ABC transporter for D-Alanine, permease component 2 42% 263.1
L-aspartate catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 34% 54% 89 ABC transporter for D-Alanine, permease component 2 42% 263.1
L-glutamate catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 34% 54% 89 ABC transporter for D-Alanine, permease component 2 42% 263.1
D-glucosamine (chitosamine) catabolism AO353_21715 lo ABC transporter for D-glucosamine, permease component 1 (characterized) 31% 85% 87 ABC transporter for D-Alanine, permease component 2 42% 263.1
L-arginine catabolism artM lo Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter membrane protein, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 33% 55% 81.6 ABC transporter for D-Alanine, permease component 2 42% 263.1
L-histidine catabolism hisM lo Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter membrane protein, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 33% 55% 81.6 ABC transporter for D-Alanine, permease component 2 42% 263.1
L-lysine catabolism hisM lo Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter membrane protein, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 33% 55% 81.6 ABC transporter for D-Alanine, permease component 2 42% 263.1
L-asparagine catabolism aatM lo Glutamate/aspartate import permease protein GltK (characterized) 30% 91% 81.3 ABC transporter for D-Alanine, permease component 2 42% 263.1
L-aspartate catabolism aatM lo Glutamate/aspartate import permease protein GltK (characterized) 30% 91% 81.3 ABC transporter for D-Alanine, permease component 2 42% 263.1
L-glutamate catabolism gltK lo Glutamate/aspartate import permease protein GltK (characterized) 30% 91% 81.3 ABC transporter for D-Alanine, permease component 2 42% 263.1
L-histidine catabolism BPHYT_RS24010 lo Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale) 33% 54% 79.3 ABC transporter for D-Alanine, permease component 2 42% 263.1
D-glucosamine (chitosamine) catabolism AO353_21720 lo ABC transporter for D-Glucosamine, permease component 1 (characterized) 32% 58% 75.1 ABC transporter for D-Alanine, permease component 2 42% 263.1
L-arginine catabolism artQ lo ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized) 30% 56% 73.9 ABC transporter for D-Alanine, permease component 2 42% 263.1
L-citrulline catabolism AO353_03050 lo ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized) 30% 56% 73.9 ABC transporter for D-Alanine, permease component 2 42% 263.1
L-lysine catabolism hisQ lo ABC transporter for L-Lysine, permease component 1 (characterized) 34% 52% 69.7 ABC transporter for D-Alanine, permease component 2 42% 263.1

Sequence Analysis Tools

View Synpcc7942_0247 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

MPFRLKLQGPFWRDERLWRWVWQLLVLLVVGLGAIWLVDNLVYNLSQRGLSLSFDWLDQS
AGFNIGESAIAYRTADSYARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQ
LSRGYVAVVRNTPLLLQLIVWYFPILLSLPAAQQPWHWLGSLYLSKQGIYLPWPQTPGWL
VVILAIALVLFVSWLAQRQRSPRDWRWLYGAIAVVTVLMLLTQLSWPQQLQPGQIRGGLR
LSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQALR
VIVPSLNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILMLTYLAINAVI
SAGMNGLQQRLQRWGVR

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