GapMind for catabolism of small carbon sources

 

Protein WP_254914263.1 in Billgrantia desiderata SP1

Annotation: NCBI__GCF_002151265.1:WP_254914263.1

Length: 255 amino acids

Source: GCF_002151265.1 in NCBI

Candidate for 18 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-alanine catabolism braF med High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 40% 100% 177.2 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 41% 183.3
L-isoleucine catabolism livG med High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 40% 100% 177.2 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 41% 183.3
L-leucine catabolism livG med High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 40% 100% 177.2 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 41% 183.3
L-serine catabolism braF med High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 40% 100% 177.2 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 41% 183.3
L-threonine catabolism braF med High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 40% 100% 177.2 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 41% 183.3
L-valine catabolism livG med High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 40% 100% 177.2 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 41% 183.3
L-phenylalanine catabolism livG med High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale) 40% 100% 173.3 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 41% 183.3
L-proline catabolism HSERO_RS00895 lo ABC transporter ATP-binding protein (characterized, see rationale) 39% 97% 180.6 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 41% 183.3
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 39% 97% 180.6 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 41% 183.3
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 39% 97% 180.6 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 41% 183.3
D-lactate catabolism PGA1_c12640 lo D-lactate transporter, ATP-binding component (characterized) 37% 100% 178.3 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 41% 183.3
L-histidine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 39% 94% 175.6 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 41% 183.3
L-leucine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 39% 94% 175.6 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 41% 183.3
L-proline catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 39% 94% 175.6 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 41% 183.3
L-isoleucine catabolism natA lo NatA, 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) 37% 96% 173.3 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 41% 183.3
L-valine catabolism natA lo NatA, 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) 37% 96% 173.3 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 41% 183.3
D-alanine catabolism AZOBR_RS08245 lo Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 36% 90% 154.1 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 41% 183.3
L-proline catabolism AZOBR_RS08245 lo Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 36% 90% 154.1 ABC transporter, ATP-binding protein, component of The protocatechuate (3,4-dihydroxybenzoate) uptake porter, PcaMNVWX 41% 183.3

Sequence Analysis Tools

View WP_254914263.1 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

MGSAILEVRNLTKEFRGFTAVDDVNLQVQEGHIHALIGPNGAGKTTVFNLLTKFLPPTRG
EILYRGKPITGMKANEIARLGLVRSFQISAVFGHMTAMENVRVALQRPMGTSFHFWKSER
SLDHLNDRAIELLEEVGLREYADVLTVEMPYGRKRALEVATTLAMDPTMMLLDEPTQGMG
AEDVDRIVELVRRVAKGRTVLMVEHNLSVVSRLCDRITVLARGAVLAEGDYATVSADPRV
KEAYMGSDAEEEASA

This GapMind analysis is from Apr 09 2024. 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