GapMind for catabolism of small carbon sources

 

Protein WP_076583239.1 in Haloterrigena daqingensis JX313

Annotation: NCBI__GCF_001971705.1:WP_076583239.1

Length: 253 amino acids

Source: GCF_001971705.1 in NCBI

Candidate for 27 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) 43% 90% 164.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 53% 241.5
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 41% 87% 160.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 53% 241.5
L-arginine catabolism artP med histidine transport ATP-binding protein hisP (characterized) 40% 92% 154.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 53% 241.5
L-histidine catabolism hisP med histidine transport ATP-binding protein hisP (characterized) 40% 92% 154.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 53% 241.5
L-lysine catabolism hisP med histidine transport ATP-binding protein hisP (characterized) 40% 92% 154.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 53% 241.5
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 41% 87% 152.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 53% 241.5
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 41% 87% 152.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 53% 241.5
L-asparagine catabolism aatP med ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 41% 87% 147.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 53% 241.5
L-aspartate catabolism aatP med ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 41% 87% 147.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 53% 241.5
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 43% 64% 158.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 53% 241.5
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 40% 81% 149.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 53% 241.5
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 40% 81% 149.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 53% 241.5
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) 39% 83% 147.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 53% 241.5
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) 38% 88% 142.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 53% 241.5
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) 38% 88% 142.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 53% 241.5
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 37% 89% 142.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 53% 241.5
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) 38% 88% 142.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 53% 241.5
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) 38% 88% 142.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 53% 241.5
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) 38% 88% 142.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 53% 241.5
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) 38% 88% 142.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 53% 241.5
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) 32% 85% 104.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 53% 241.5
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) 32% 85% 104.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 53% 241.5
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) 32% 85% 104.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 53% 241.5
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) 32% 85% 104.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 53% 241.5
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) 32% 85% 104.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 53% 241.5
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) 32% 85% 104.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 53% 241.5
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) 32% 85% 104.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 53% 241.5

Sequence Analysis Tools

View WP_076583239.1 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

MATSDPATTGDSGSAVSLENVHKTYHLGEPVHALDGVSLEIPRGSYTAIMGPSGSGKSTL
MNLVGCLDTPTSGTVVVDGRDVGGLSDAERTTLRGTTVGFVFQTFNLMPRLSALENVAMP
QLFRNVGRAERRERASTLLERVGLADRADHHPNELSGGQRQRVALARALVNEPELVLADE
PTGNLDTETGANVLELFAEFHEAGTTMVVVTHERHVATHAERIVHLLDGTLERVESVDGT
DGADERGDAYGGH

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