GapMind for catabolism of small carbon sources

 

Protein Echvi_2909 in Echinicola vietnamensis KMM 6221, DSM 17526

Annotation: Echvi_2909 ABC-type antimicrobial peptide transport system, ATPase component

Length: 218 amino acids

Source: Cola in FitnessBrowser

Candidate for 15 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 lo GluA aka CGL1950, component of Glutamate porter (characterized) 39% 90% 154.1 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 45% 195.7
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) 34% 81% 126.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 45% 195.7
L-alanine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 32% 91% 111.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 45% 195.7
L-isoleucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 32% 91% 111.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 45% 195.7
L-leucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 32% 91% 111.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 45% 195.7
L-serine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 32% 91% 111.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 45% 195.7
L-threonine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 32% 91% 111.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 45% 195.7
L-valine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 32% 91% 111.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 45% 195.7
L-phenylalanine catabolism livF lo high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) 30% 91% 105.1 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 45% 195.7
L-arginine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 30% 86% 100.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 45% 195.7
L-glutamate catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 30% 86% 100.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 45% 195.7
L-histidine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 30% 86% 100.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 45% 195.7
L-proline catabolism HSERO_RS00900 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 88% 99.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 45% 195.7
L-serine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 88% 99.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 45% 195.7
L-tyrosine catabolism Ac3H11_1692 lo ABC transporter ATP-binding protein (characterized, see rationale) 32% 88% 99.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 45% 195.7

Sequence Analysis Tools

View Echvi_2909 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

MLRAKGIHKYYGDLHVLKGVDVEIAAGEIVSIVGASGAGKSTLLHILGTLDDADKGLVSI
DDKSLTALKGDKLAAYRNQEVGFIFQFHNLLPEFTAEENIIIPGLIAKKDEKYLTEKAKE
LARLLGIMDRLGHKPSELSGGEQQRVAVARALINDPKIIFADEPSGNLDTQSAESLHELF
FTLRDRFGQSFVIVTHNQQLAQMADRMLTMQDGVIVSE

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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