GapMind for catabolism of small carbon sources

 

Protein 209035 in Desulfovibrio vulgaris Hildenborough

Annotation: DVU0105 glutamine ABC transporter, ATP-binding protein

Length: 244 amino acids

Source: 882 in MicrobesOnline

Candidate for 51 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) 60% 99% 298.1 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
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) 60% 99% 298.1 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
L-histidine catabolism aapP med ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 60% 93% 289.7 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtM (characterized) 58% 100% 282 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
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) 57% 93% 282 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
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) 57% 93% 282 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
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) 57% 93% 282 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
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) 57% 93% 282 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
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) 57% 93% 282 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
L-asparagine catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 57% 91% 281.6 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
L-aspartate catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 57% 91% 281.6 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
D-alanine catabolism Pf6N2E2_5405 med ABC transporter for D-Alanine, ATPase component (characterized) 55% 95% 280 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
L-asparagine catabolism aatP med ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 58% 100% 279.3 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
L-aspartate catabolism aatP med ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 58% 100% 279.3 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 59% 97% 279.3 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
L-lysine catabolism hisP med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 59% 97% 279.3 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-Glucosamine, putative ATPase component (characterized) 55% 94% 271.6 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
L-histidine catabolism hisP med 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) 54% 98% 270 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 55% 99% 269.6 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 55% 99% 269.6 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 56% 92% 268.1 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 56% 92% 268.1 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 53% 94% 265 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
L-citrulline catabolism AO353_03040 med ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 50% 97% 250 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
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) 50% 89% 240 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
L-histidine catabolism PA5503 med Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 42% 72% 183 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 40% 70% 166 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 37% 67% 175.6 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
D-mannitol catabolism mtlK lo ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 40% 63% 167.2 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 40% 65% 166.8 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
D-maltose catabolism thuK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 40% 65% 166.8 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 40% 65% 166.8 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 40% 65% 166.8 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 39% 66% 166.4 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 39% 66% 166.4 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 63% 166 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 63% 166 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 63% 166 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 63% 166 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 63% 166 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 63% 166 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 41% 63% 162.9 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 39% 65% 161.8 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 39% 68% 161.4 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
L-alanine catabolism braG lo NatE, 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) 35% 96% 136 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
L-isoleucine catabolism natE lo NatE, 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) 35% 96% 136 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
L-leucine catabolism natE lo NatE, 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) 35% 96% 136 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
L-proline catabolism natE lo NatE, 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) 35% 96% 136 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
L-serine catabolism braG lo NatE, 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) 35% 96% 136 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
L-threonine catabolism braG lo NatE, 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) 35% 96% 136 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1
L-valine catabolism natE lo NatE, 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) 35% 96% 136 Glutamine transport ATP-binding protein GlnQ; EC 7.4.2.- 63% 310.1

Sequence Analysis Tools

View 209035 at MicrobesOnline

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

MTPMIEIRNLHKSYGDHHVLRGIDLTVRTGEVVVVIGPSGSGKSTALRCINRLEEITSGT
IIVDGYDLYDPKTDINHVRTEAGMVFQQFNLFPHMSVLENVTIGPVKVRRMARQEAQALG
LALLEKVGLADKAHAYPDQLSGGQKQRVAIARSLAMQPKVLLFDEPTSALDPELVGEVLE
VMKQLAREGMTMVVVTHEMGFAREVADRVIFIDYGKIQEEGPPNELFADPKNPRLREFLG
KVIH

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