GapMind for catabolism of small carbon sources

 

Protein 16031 in Escherichia coli BW25113

Annotation: b1917 predicted transporter subunit: ATP-binding component of ABC superfamily (NCBI)

Length: 250 amino acids

Source: Keio in FitnessBrowser

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-arginine catabolism artP med Arginine transport ATP-binding protein ArtM (characterized) 56% 100% 264.2 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 100% 481.1
L-histidine catabolism hisP med Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 53% 97% 255 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 100% 481.1
L-lysine catabolism hisP med Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 53% 97% 255 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 100% 481.1
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 51% 95% 241.9 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 100% 481.1
L-citrulline catabolism AO353_03040 med ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 50% 100% 238.4 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 100% 481.1
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-Glucosamine, putative ATPase component (characterized) 51% 94% 235.3 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 100% 481.1
L-citrulline catabolism PS417_17605 med 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) 51% 90% 231.5 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 100% 481.1
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 51% 90% 229.6 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 100% 481.1
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 51% 90% 229.6 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 100% 481.1
L-glutamate catabolism gltL med GluA aka CGL1950, component of Glutamate porter (characterized) 51% 97% 226.1 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 100% 481.1
L-asparagine catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 50% 99% 225.3 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 100% 481.1
L-aspartate catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 50% 99% 225.3 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 100% 481.1
L-tryptophan catabolism ecfA2 med Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 41% 80% 141.7 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 100% 481.1
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 46% 65% 184.9 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 100% 481.1
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% 98% 137.5 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 100% 481.1
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% 98% 137.5 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 100% 481.1
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% 98% 137.5 L-cystine transport system ATP-binding protein YecC; EC 7.4.2.- 100% 481.1

Sequence Analysis Tools

View 16031 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MSAIEVKNLVKKFHGQTVLHGIDLEVKPGEVVAIIGPSGSGKTTLLRSINLLEQPEAGTI
TVGDITIDTARSLSQQKSLIRQLRQHVGFVFQNFNLFPHRTVLENIIEGPVIVKGEPKEE
ATARARELLAKVGLAGKETSYPRRLSGGQQQRVAIARALAMRPEVILFDEPTSALDPELV
GEVLNTIRQLAQEKRTMVIVTHEMSFARDVADRAIFMDQGRIVEQGAAKALFADPEQPRT
RQFLEKFLLQ

This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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