GapMind for catabolism of small carbon sources

 

Protein WP_011973239.1 in Methanococcus aeolicus Nankai-3

Annotation: NCBI__GCF_000017185.1:WP_011973239.1

Length: 225 amino acids

Source: GCF_000017185.1 in NCBI

Candidate for 45 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 45% 90% 165.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 45% 90% 165.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
L-glutamate catabolism gltL med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 45% 90% 165.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtM (characterized) 43% 90% 158.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 41% 84% 158.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 41% 84% 158.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
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) 41% 84% 156.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
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) 41% 84% 156.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
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) 41% 84% 156.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
L-histidine 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) 41% 84% 156.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
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) 41% 84% 156.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
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) 41% 84% 156.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
L-asparagine catabolism aatP med ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 41% 89% 154.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
L-aspartate catabolism aatP med ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 41% 89% 154.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
L-histidine catabolism hisP med histidine transport ATP-binding protein hisP (characterized) 41% 91% 149.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
L-lysine catabolism hisP med histidine transport ATP-binding protein hisP (characterized) 41% 91% 149.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
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) 40% 88% 150.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 62% 149.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 62% 149.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 62% 149.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 62% 149.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 62% 149.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 62% 149.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 62% 149.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 40% 62% 149.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 38% 67% 148.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 39% 85% 146.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 38% 82% 144.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 38% 82% 144.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 37% 85% 142.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-Glucosamine, putative ATPase component (characterized) 36% 86% 135.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
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) 35% 82% 135.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 36% 89% 132.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 38% 86% 131 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
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% 69% 126.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 38% 78% 124.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 91% 117.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
L-leucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 91% 117.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
L-valine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 91% 117.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 34% 78% 115.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 36% 64% 114.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
L-isoleucine catabolism livF lo high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) 31% 84% 90.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
L-leucine catabolism livF lo high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) 31% 84% 90.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
L-phenylalanine catabolism livF lo high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) 31% 84% 90.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5
L-valine catabolism livF lo high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) 31% 84% 90.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 50% 219.5

Sequence Analysis Tools

View WP_011973239.1 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

Fitness BLAST: loading...

Sequence

MIELKNVVKSYNLGGETIYALNNVSLKIDEGEFVAIMGPSGSGKSTLLNIIGCLDKPDEG
EVYIDNVKTNDLNDNQLTEIRRMKIGFVFQQFNLIPLLSALENVELPLIFKYRSEMSSEE
KQKRALECLKMAELDEQFANHRPNQLSGGQQQRVAIARALANNAPVLLCDEPTGALDSKT
GGKVMELLKKLNKSGKTVVVVTHDINVGKVADRIIDIRDGKIVEE

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