GapMind for catabolism of small carbon sources

 

Protein WP_048081629.1 in Methanobacterium veterum MK4

Annotation: NCBI__GCF_000745485.1:WP_048081629.1

Length: 222 amino acids

Source: GCF_000745485.1 in NCBI

Candidate for 39 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-glutamate catabolism gltL med GluA aka CGL1950, component of Glutamate porter (characterized) 41% 88% 156 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
L-lysine catabolism hisP med Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 41% 82% 148.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
L-asparagine catabolism aatP med ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 40% 88% 145.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 41% 88% 145.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
L-aspartate catabolism aatP med ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 40% 88% 145.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 41% 88% 145.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 61% 159.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 61% 159.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 61% 159.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 61% 159.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 61% 159.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 61% 159.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 61% 159.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 61% 159.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 37% 56% 150.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
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% 83% 144.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
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% 83% 144.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
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% 83% 144.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
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% 83% 144.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
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% 83% 144.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
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% 83% 144.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 37% 59% 144.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 39% 83% 143.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 39% 83% 143.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 38% 85% 141.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 37% 84% 138.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 37% 77% 134.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
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) 36% 66% 125.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
D-fructose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 83% 108.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 83% 108.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 83% 108.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
sucrose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 83% 108.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
L-proline catabolism HSERO_RS00900 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 32% 84% 95.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
L-alanine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 30% 90% 94.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
L-histidine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 30% 90% 94.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
L-leucine catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 30% 90% 94.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
L-proline catabolism natE lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 30% 90% 94.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
L-serine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 30% 90% 94.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1
L-threonine catabolism braG lo NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 30% 90% 94.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 199.1

Sequence Analysis Tools

View WP_048081629.1 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

MNDINVIEIKGLKKSYEEGQITALNGIDLEIKEGEFVSIIGPSGSGKSTLLNMIGALDNP
DEGSISVAGTDLTRSEDLSKFRSDEIGFVFQLHNLIPNLTVFENVQIPLIETPLSDEQME
KRALELLKSVNLENKINQKPTKLSGGERQRVAIARALVNHPSIILADEPTGSLDSKTQEI
ILDLLKDIHKKENVTLIIVTHSPDVATMADRIITVLDGEIKG

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