GapMind for catabolism of small carbon sources

 

Protein Echvi_1582 in Echinicola vietnamensis KMM 6221, DSM 17526

Annotation: Echvi_1582 ABC-type antimicrobial peptide transport system, ATPase component

Length: 225 amino acids

Source: Cola in FitnessBrowser

Candidate for 29 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 40% 85% 150.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 200.3
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 36% 67% 147.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 200.3
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 39% 90% 147.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 200.3
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 39% 90% 147.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 200.3
L-glutamate catabolism gltL lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 39% 90% 147.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 200.3
L-lysine catabolism hisP lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 38% 84% 146.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 200.3
L-asparagine catabolism glnQ lo Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 38% 90% 145.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 200.3
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 39% 84% 145.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 200.3
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 39% 84% 145.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 200.3
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 38% 90% 142.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 200.3
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 38% 90% 142.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 200.3
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 38% 84% 141.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 200.3
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 40% 83% 140.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 200.3
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 40% 83% 140.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 200.3
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 38% 86% 139.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 200.3
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 39% 85% 138.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 200.3
L-asparagine catabolism aapP lo 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) 37% 85% 137.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 200.3
L-aspartate catabolism aapP lo 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) 37% 85% 137.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 200.3
L-glutamate catabolism aapP lo 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) 37% 85% 137.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 200.3
L-leucine catabolism aapP lo 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) 37% 85% 137.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 200.3
L-proline catabolism aapP lo 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) 37% 85% 137.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 200.3
L-arginine catabolism artP lo AotP aka PA0892, component of Arginine/ornithine (but not lysine) porter (characterized) 37% 89% 135.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 200.3
L-histidine catabolism hisP lo histidine transport ATP-binding protein hisP (characterized) 38% 83% 134 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 200.3
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 38% 86% 133.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 200.3
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) 36% 91% 126.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 200.3
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) 36% 91% 126.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 200.3
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) 36% 91% 126.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 200.3
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 33% 64% 117.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 200.3
D-cellobiose catabolism TM0027 lo TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 31% 89% 105.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 46% 200.3

Sequence Analysis Tools

View Echvi_1582 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: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MDILSIENVSKIYQSGSRTLTVLEDINLSVKAGDSIAIVGPSGSGKTTLLGLCAGLDSAS
SGSVALNGHRLEGLSEDQRAAVRSQEIGFIFQNFQLLPTLTALENVMVPLELKKRKDAKQ
KATELLQQVGLGDRMTHYPTQLSGGEQQRVSIARAFANEPKILFADEPTGNLDTETGELI
ETLIFDLNKALGTTLILVTHDTDLAAKTNRIIHIKGGKIQEEQHA

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, 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