GapMind for catabolism of small carbon sources

 

Protein CCNA_01507 in Caulobacter crescentus NA1000

Annotation: CCNA_01507 cystine transport system permease protein

Length: 219 amino acids

Source: Caulo in FitnessBrowser

Candidate for 37 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism Ac3H11_2554 lo ABC transporter for L-Histidine, permease component 1 (characterized) 39% 94% 156.8 L-cystine transport system permease protein YecS 63% 275.8
L-lysine catabolism hisM lo ABC transporter for L-Lysine, permease component 2 (characterized) 39% 99% 138.7 L-cystine transport system permease protein YecS 63% 275.8
D-glucosamine (chitosamine) catabolism AO353_21715 lo ABC transporter for D-Glucosamine, permease component 2 (characterized) 38% 93% 135.6 L-cystine transport system permease protein YecS 63% 275.8
L-arginine catabolism artM lo Arginine ABC transporter permease protein ArtM (characterized) 36% 97% 133.7 L-cystine transport system permease protein YecS 63% 275.8
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) 37% 98% 131.7 L-cystine transport system permease protein YecS 63% 275.8
L-lysine catabolism hisQ lo ABC transporter for L-Lysine, permease component 1 (characterized) 36% 92% 126.7 L-cystine transport system permease protein YecS 63% 275.8
L-citrulline catabolism AO353_03045 lo ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized) 34% 94% 124.4 L-cystine transport system permease protein YecS 63% 275.8
L-asparagine catabolism aatM lo Glutamate/aspartate import permease protein GltK (characterized) 37% 95% 120.9 L-cystine transport system permease protein YecS 63% 275.8
L-aspartate catabolism aatM lo Glutamate/aspartate import permease protein GltK (characterized) 37% 95% 120.9 L-cystine transport system permease protein YecS 63% 275.8
L-glutamate catabolism gltK lo Glutamate/aspartate import permease protein GltK (characterized) 37% 95% 120.9 L-cystine transport system permease protein YecS 63% 275.8
L-arginine catabolism artQ lo ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized) 34% 98% 119.8 L-cystine transport system permease protein YecS 63% 275.8
L-citrulline catabolism AO353_03050 lo ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized) 34% 98% 119.8 L-cystine transport system permease protein YecS 63% 275.8
L-histidine catabolism BPHYT_RS24005 lo Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale) 33% 90% 117.5 L-cystine transport system permease protein YecS 63% 275.8
L-histidine catabolism BPHYT_RS24010 lo Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale) 34% 92% 117.1 L-cystine transport system permease protein YecS 63% 275.8
L-glutamate catabolism gltJ lo Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida (characterized) 34% 86% 112.8 L-cystine transport system permease protein YecS 63% 275.8
L-asparagine catabolism aatQ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 34% 86% 111.3 L-cystine transport system permease protein YecS 63% 275.8
L-aspartate catabolism aatQ lo PP1070, component of Acidic amino acid uptake porter, AatJMQP (characterized) 34% 86% 111.3 L-cystine transport system permease protein YecS 63% 275.8
L-asparagine catabolism natH lo NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 34% 56% 108.2 L-cystine transport system permease protein YecS 63% 275.8
L-aspartate catabolism natH lo NatH, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 34% 56% 108.2 L-cystine transport system permease protein YecS 63% 275.8
L-citrulline catabolism PS417_17600 lo ABC transporter permease; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine ABC transporter permease HisM; SubName: Full=Histidine transport system permease protein; SubName: Full=Histidine/lysine/arginine/ornithine ABC transporter permease HisM (characterized, see rationale) 35% 88% 108.2 L-cystine transport system permease protein YecS 63% 275.8
L-asparagine catabolism aapM lo AapM, 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) 32% 58% 107.5 L-cystine transport system permease protein YecS 63% 275.8
L-aspartate catabolism aapM lo AapM, 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) 32% 58% 107.5 L-cystine transport system permease protein YecS 63% 275.8
L-glutamate catabolism aapM lo AapM, 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) 32% 58% 107.5 L-cystine transport system permease protein YecS 63% 275.8
L-histidine catabolism aapM lo AapM, 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) 32% 58% 107.5 L-cystine transport system permease protein YecS 63% 275.8
L-leucine catabolism aapM lo AapM, 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) 32% 58% 107.5 L-cystine transport system permease protein YecS 63% 275.8
L-proline catabolism aapM lo AapM, 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) 32% 58% 107.5 L-cystine transport system permease protein YecS 63% 275.8
D-alanine catabolism Pf6N2E2_5404 lo ABC transporter for D-Alanine, permease component 1 (characterized) 32% 60% 105.5 L-cystine transport system permease protein YecS 63% 275.8
D-glucosamine (chitosamine) catabolism AO353_21720 lo ABC transporter for D-glucosamine, permease component 2 (characterized) 30% 91% 104.4 L-cystine transport system permease protein YecS 63% 275.8
L-asparagine catabolism natG lo NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 31% 70% 101.7 L-cystine transport system permease protein YecS 63% 275.8
L-aspartate catabolism natG lo NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized) 31% 70% 101.7 L-cystine transport system permease protein YecS 63% 275.8
L-glutamate catabolism gluC lo GluC aka CGL1952, component of Glutamate porter (characterized) 34% 95% 97.8 L-cystine transport system permease protein YecS 63% 275.8
L-glutamate catabolism gluD lo GluD aka CGL1953, component of Glutamate porter (characterized) 32% 76% 96.7 L-cystine transport system permease protein YecS 63% 275.8
L-asparagine catabolism peb1D lo Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale) 31% 90% 95.9 L-cystine transport system permease protein YecS 63% 275.8
L-aspartate catabolism peb1D lo Amino acid ABC transporter, permease protein PEB1 (characterized, see rationale) 31% 90% 95.9 L-cystine transport system permease protein YecS 63% 275.8
L-asparagine catabolism bztC lo BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 30% 52% 89.4 L-cystine transport system permease protein YecS 63% 275.8
L-aspartate catabolism bztC lo BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 30% 52% 89.4 L-cystine transport system permease protein YecS 63% 275.8
L-glutamate catabolism bztC lo BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 30% 52% 89.4 L-cystine transport system permease protein YecS 63% 275.8

Sequence Analysis Tools

View CCNA_01507 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

MDTGLDLLRQSAPLLLKGAGYTIVLSVIGMSIGVVLGFLLALMRLSRSALLRWPAGVYVS
AFRGTPLLVQLFLIYYGLPQFGLEMPPLVAAGIGFSLNVAAYSCEILRSAIAAVDKGQWE
AASVLGMSRGQTLRRVILPQAARTAVAPLSNSFISLVKDTSLAATIQVPELFRQAQLITA
RTYEIFTLYLAAAAIYWILSTILAAAQTRLERRAAEGRR

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, 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