GapMind for catabolism of small carbon sources

 

Protein WP_017177976.1 in Actinomyces timonensis 7400942

Annotation: NCBI__GCF_000295095.1:WP_017177976.1

Length: 375 amino acids

Source: GCF_000295095.1 in NCBI

Candidate for 34 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism PA5503 med Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 42% 99% 242.3 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 42% 88% 171.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 42% 88% 171.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 41% 95% 166.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 41% 95% 166.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
L-glutamate catabolism gltL med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 41% 95% 166.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
L-arginine catabolism artP med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 42% 85% 166 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 42% 85% 166 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
L-lysine catabolism hisP med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 42% 85% 166 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
L-asparagine catabolism aatP lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 40% 94% 162.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
L-asparagine catabolism glnQ lo Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 39% 91% 162.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
L-aspartate catabolism aatP lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 40% 94% 162.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
L-histidine catabolism hisP lo Probable ATP-binding component of ABC transporter, 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) 38% 93% 161 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 38% 97% 159.1 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 36% 93% 157.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 38% 92% 152.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
D-mannose catabolism TM1750 lo TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 33% 80% 151.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 35% 92% 149.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 35% 92% 149.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 35% 96% 149.8 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
L-asparagine catabolism aapP lo AapP, 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% 91% 149.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
L-aspartate catabolism aapP lo AapP, 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% 91% 149.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
L-glutamate catabolism aapP lo AapP, 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% 91% 149.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
L-leucine catabolism aapP lo AapP, 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% 91% 149.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
L-proline catabolism aapP lo AapP, 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% 91% 149.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
L-citrulline catabolism PS417_17605 lo ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) 38% 85% 149.1 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 37% 92% 146.7 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
D-mannose catabolism TM1749 lo TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 33% 85% 137.5 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 36% 84% 134.4 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
D-lactate catabolism PGA1_c12640 lo D-lactate transporter, ATP-binding component (characterized) 31% 87% 106.7 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
D-fructose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 31% 87% 96.7 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 31% 87% 96.7 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 31% 87% 96.7 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4
sucrose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 31% 87% 96.7 Methionine import ATP-binding protein MetN; EC 7.4.2.11 53% 255.4

Sequence Analysis Tools

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Sequence

MSDPIPGAEPIEADGAVADEPTDLTDAELSTAEAAQAGAPEAADDSMISLRDVVKVYTLR
DGTEVRALDGLTLTVPAGSIHGIVGTSGAGKSTLIRCLTALEPVTAGEVRVAGQDMTALS
ARELREARRRIGMVFQHANLLDSRTTAQNIAYPLALAGVAKGERHETVAEMLDLVGLADR
GGSYPSQLSGGQKQRVGIARALADQPAVLLCDEPTSALDPETTRSILDLIKDVRDRLGVT
VVIITHEMSVVRQVCDSVSLLEAGRIVESGPIEDVASDVDSRLSHELVPVPAIPEGSLAE
GDAVIDVALTAHPGQPAAAHVLALASEHGADVAGGVFETLGQAQVGRLALTIPADKAPGV
VDALAAAGATAEVRS

This GapMind analysis is from Sep 24 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