GapMind for catabolism of small carbon sources

 

Protein WP_015446964.1 in Rhodanobacter denitrificans 2APBS1

Annotation: NCBI__GCF_000230695.2:WP_015446964.1

Length: 238 amino acids

Source: GCF_000230695.2 in NCBI

Candidate for 22 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) 40% 96% 172.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 205.3
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 40% 90% 160.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 205.3
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 40% 90% 160.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 205.3
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 39% 86% 156 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 205.3
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 38% 86% 155.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 205.3
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 38% 86% 155.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 205.3
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 39% 70% 155.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 205.3
L-lysine catabolism hisP lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 37% 89% 155.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 205.3
L-asparagine catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 36% 95% 154.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 205.3
L-aspartate catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 36% 95% 154.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 205.3
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) 36% 86% 149.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 205.3
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) 36% 86% 149.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 205.3
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) 36% 86% 149.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 205.3
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) 36% 86% 149.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 205.3
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) 36% 86% 149.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 205.3
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 39% 93% 147.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 205.3
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 37% 85% 146.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 205.3
putrescine catabolism potA lo Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) 38% 60% 144.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 205.3
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 35% 83% 141.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 205.3
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 38% 85% 139.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 205.3
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 37% 88% 137.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 205.3
trehalose catabolism malK lo MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized) 36% 54% 129.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 45% 205.3

Sequence Analysis Tools

View WP_015446964.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MLKMTHLSKVYRTEVVETYALRDFNIDVKEGEFVAVTGPSGSGKTTFLTIAGLLETFSGG
EYHLDGIEVSNLNDNARSKIRNEKIGFIFQAFNLIPDLNVFDNIEVPLRYRGMKAAERKQ
RIMDSLERVGLASRAKHYPAELSGGQQQRVAIARALAGSPRLLLADEPTGNLDTQMARGV
MELLEDIHREGATIVMVTHDPELAARAQRNVHIIDGQVVDLSEDPRFHTVHAAEEAHG

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