GapMind for catabolism of small carbon sources

 

Protein Echvi_2204 in Echinicola vietnamensis KMM 6221, DSM 17526

Annotation: Echvi_2204 ABC-type antimicrobial peptide transport system, ATPase component

Length: 240 amino acids

Source: Cola in FitnessBrowser

Candidate for 19 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 39% 95% 148.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 56% 254.6
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 39% 95% 148.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 56% 254.6
L-glutamate catabolism gltL lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 39% 95% 148.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 56% 254.6
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 38% 91% 146.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 56% 254.6
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 35% 72% 146.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 56% 254.6
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 36% 94% 144.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 56% 254.6
L-lysine catabolism hisP lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 38% 89% 143.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 56% 254.6
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 35% 87% 140.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 56% 254.6
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 35% 87% 140.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 56% 254.6
L-histidine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 35% 91% 137.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 56% 254.6
L-asparagine catabolism aatP lo ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 36% 89% 135.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 56% 254.6
L-aspartate catabolism aatP lo ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 36% 89% 135.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 56% 254.6
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 34% 92% 132.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 56% 254.6
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 39% 75% 128.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 56% 254.6
D-mannose catabolism TM1749 lo TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 32% 73% 103.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 56% 254.6
D-fructose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 83% 86.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 56% 254.6
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 83% 86.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 56% 254.6
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 83% 86.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 56% 254.6
sucrose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 83% 86.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 56% 254.6

Sequence Analysis Tools

View Echvi_2204 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

MGKIIETKEIKKTYVMGAEKVQALKSVTIDIIKGEYVAFMGPSGSGKSTLMNIIGCLDTP
TAGNYILNNKDVSHMTENELAEIRNKEIGFVFQTFNLLPRATCLENVALPLIYAGYSKSD
REDKAFLALKSVGLEDRIHHKPNELSGGQRQRVAIARALVNDPSIILADEPTGNLDTKTS
YDIMNLFDELHQKGNTIIMVTHEDDIAHYAHRIVRLRDGLVETDQNNPNPTRNNFQPVSE

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