GapMind for catabolism of small carbon sources

 

Protein WP_048081634.1 in Methanobacterium veterum MK4

Annotation: NCBI__GCF_000745485.1:WP_048081634.1

Length: 229 amino acids

Source: GCF_000745485.1 in NCBI

Candidate for 36 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) 44% 88% 167.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
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) 44% 88% 167.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-lysine catabolism hisP med Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 43% 85% 165.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 41% 84% 157.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 41% 84% 157.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-asparagine catabolism aatP med ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 42% 89% 156 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-aspartate catabolism aatP med ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 42% 89% 156 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 42% 90% 154.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 42% 90% 154.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-asparagine catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 40% 85% 153.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-aspartate catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 40% 85% 153.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 37% 59% 151.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
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) 40% 86% 149.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
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) 40% 86% 149.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
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) 40% 86% 149.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-histidine 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) 40% 86% 149.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
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) 40% 86% 149.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
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) 40% 86% 149.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 37% 89% 147.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-arginine catabolism artP lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 40% 89% 143.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 40% 89% 143.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-Glucosamine, putative ATPase component (characterized) 37% 88% 142.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
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) 37% 82% 136.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 35% 79% 132.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 37% 66% 123.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 34% 91% 116.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-arginine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 33% 88% 109.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-glutamate catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 33% 88% 109.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-histidine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 33% 88% 109.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-isoleucine catabolism livF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 33% 88% 109.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-leucine catabolism livF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 33% 88% 109.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
L-valine catabolism livF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 33% 88% 109.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
D-fructose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 88% 106.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 88% 106.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 88% 106.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7
sucrose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 88% 106.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 210.7

Sequence Analysis Tools

View WP_048081634.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

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Sequence

MNNENIIEIKGLKKSYDKGKIKALNGIDLEIRKGEFVSIIGPSGSGKSTLLNMIGALDTA
GEGSVEVAGIDLTKTKDLSKFRSQEIGFVFQLHNLIPNLTVLENVQIPMIGTSISGKDME
KRALKLLKSVDLEDRIDQRPTKLSGGERQRVAIARALVNNPSIILADEPTGALDSKTGDI
ILDLLKDLHKKENVTLVMVTHEPYVANMADRIITVRDGKILEEKTNNIT

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