GapMind for catabolism of small carbon sources

 

Protein WP_047215506.1 in Pandoraea thiooxydans ATSB16

Annotation: NCBI__GCF_001931675.1:WP_047215506.1

Length: 241 amino acids

Source: GCF_001931675.1 in NCBI

Candidate for 17 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism aatP hi Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 77% 100% 364.8 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 62% 297.0
L-aspartate catabolism aatP hi Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 77% 100% 364.8 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 62% 297.0
L-glutamate catabolism gltL hi Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 77% 100% 364.8 uncharacterized amino-acid ABC transporter ATP-binding protein yhdZ 62% 297.0
D-alanine catabolism Pf6N2E2_5405 med ABC transporter for D-Alanine, ATPase component (characterized) 61% 95% 285.4 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 77% 364.8
L-histidine catabolism aapP med ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 60% 93% 281.2 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 77% 364.8
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) 60% 94% 279.3 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 77% 364.8
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) 60% 94% 279.3 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 77% 364.8
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) 60% 94% 279.3 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 77% 364.8
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) 60% 94% 279.3 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 77% 364.8
L-lysine catabolism hisP med Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 58% 93% 279.3 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 77% 364.8
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) 60% 94% 279.3 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 77% 364.8
L-asparagine catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 59% 91% 277.3 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 77% 364.8
L-aspartate catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 59% 91% 277.3 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 77% 364.8
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 57% 92% 261.2 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 77% 364.8
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 57% 92% 261.2 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 77% 364.8
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 53% 99% 238 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 77% 364.8
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 53% 99% 238 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 77% 364.8

Sequence Analysis Tools

View WP_047215506.1 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

MIAMENVSKWYGQFKVLDNCTAQVGKGEVVVVCGPSGSGKSTLIKTVNGLEQYQQGRITV
DGVELGAPSIKLTQLRARVGMVFQHFELFPHLSILDNLTLAQIKVLKRGKEEARLKGLAL
LERVGLREHAPKYPAQLSGGQQQRVAIARALSMDPIAMLFDEPTSALDPEMINEVLDVMV
ELAREGMTMICVTHEMGFAKKVAHRVIFMDGGAIVEDACKDAFFGTPNSPRAREFLAKIL
H

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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