GapMind for catabolism of small carbon sources

 

Protein WP_017221498.1 in Moritella dasanensis ArB 0140

Annotation: NCBI__GCF_000276805.1:WP_017221498.1

Length: 251 amino acids

Source: GCF_000276805.1 in NCBI

Candidate for 33 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism glnQ med 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) 58% 98% 289.3 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
L-glutamate catabolism gltL med 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) 58% 98% 289.3 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 60% 93% 275.4 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 60% 93% 275.4 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
L-histidine catabolism aapP med ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 54% 94% 261.9 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtM (characterized) 57% 100% 261.2 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
L-asparagine catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 55% 93% 260.8 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
L-aspartate catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 55% 93% 260.8 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
L-asparagine catabolism aapP med 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) 55% 96% 260 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
L-aspartate catabolism aapP med 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) 55% 96% 260 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
L-glutamate catabolism aapP med 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) 55% 96% 260 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
L-leucine catabolism aapP med 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) 55% 96% 260 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
L-proline catabolism aapP med 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) 55% 96% 260 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
L-asparagine catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 56% 100% 258.1 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
L-aspartate catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 56% 100% 258.1 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
D-alanine catabolism Pf6N2E2_5405 med ABC transporter for D-Alanine, ATPase component (characterized) 55% 92% 255.4 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
L-lysine catabolism hisP med Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 55% 87% 249.2 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 50% 99% 241.5 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 50% 99% 241.5 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 52% 94% 232.3 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 49% 95% 228.4 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-glucosamine, ATPase component (characterized) 52% 92% 226.9 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
L-histidine catabolism hisP med histidine transport ATP-binding protein hisP (characterized) 50% 96% 226.9 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
L-citrulline catabolism PS417_17605 med 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) 49% 86% 216.1 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
L-citrulline catabolism AO353_03040 med ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 47% 97% 212.6 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
L-alanine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 35% 95% 126.7 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
L-isoleucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 35% 95% 126.7 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
L-leucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 35% 95% 126.7 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
L-serine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 35% 95% 126.7 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
L-threonine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 35% 95% 126.7 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
L-valine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 35% 95% 126.7 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
L-phenylalanine catabolism livF lo high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) 31% 92% 108.6 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 31% 79% 99.8 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 59% 290.8

Sequence Analysis Tools

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Sequence

MTRANYNGDDMVIATDVDKIYPNKCHALKKVSVTVKRGEVVVIIGPSGSGKSTFLRTLNQ
LETVTEGDITIDGINMYDSSTNINTLRENVGMVFQSFNLFPHLSVKENVKLAPLKVSNLG
KEQVEKDAISLLTRVGLAEKVDVYPSQLSGGQQQRVAIARALAMKPDLMLFDEPTSALDP
EMVGEVLEVMKSLAEEGMTMVVVTHEMGFANEVADRVLFMEDGQLLVDDVPANFFENPSH
PRLKKFLSSIL

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