GapMind for catabolism of small carbon sources

 

Protein Echvi_3653 in Echinicola vietnamensis KMM 6221, DSM 17526

Annotation: Echvi_3653 ABC-type sulfate/molybdate transport systems, ATPase component

Length: 290 amino acids

Source: Cola in FitnessBrowser

Candidate for 42 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism glnQ med 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) 41% 89% 159.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
L-glutamate catabolism gltL med 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) 41% 89% 159.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 42% 59% 164.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 38% 73% 163.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 38% 73% 163.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 40% 60% 160.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 40% 68% 159.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 36% 72% 156.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 38% 68% 152.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 38% 68% 152.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
L-proline catabolism opuBA lo BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) 35% 83% 152.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 38% 68% 152.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 38% 68% 152.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 37% 67% 152.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 32% 66% 149.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 39% 55% 147.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
L-asparagine catabolism aatP lo ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 38% 85% 145.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
L-aspartate catabolism aatP lo ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 38% 85% 145.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 35% 87% 141.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 35% 85% 139.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 35% 85% 139.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 36% 53% 138.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 38% 80% 137.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized) 39% 84% 136.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-Glucosamine, putative ATPase component (characterized) 36% 89% 134.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 36% 75% 127.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
glycerol catabolism glpT lo ABC transporter for Glycerol, ATPase component 2 (characterized) 33% 61% 114.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 35% 58% 110.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
L-alanine catabolism braG lo NatE, 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) 31% 81% 96.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
L-isoleucine catabolism natE lo NatE, 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) 31% 81% 96.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
L-leucine catabolism natE lo NatE, 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) 31% 81% 96.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
L-proline catabolism natE lo NatE, 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) 31% 81% 96.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
L-serine catabolism braG lo NatE, 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) 31% 81% 96.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
L-threonine catabolism braG lo NatE, 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) 31% 81% 96.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
L-valine catabolism natE lo NatE, 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) 31% 81% 96.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
L-alanine catabolism braF 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) 32% 53% 73.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
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) 32% 53% 73.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
L-leucine 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) 32% 53% 73.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
L-proline 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) 32% 53% 73.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
L-serine catabolism braF 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) 32% 53% 73.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
L-threonine catabolism braF 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) 32% 53% 73.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2
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) 32% 53% 73.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 41% 170.2

Sequence Analysis Tools

View Echvi_3653 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

MINIDLQKSLKANGPAMDLDIKLTISQGEFITLFGPSGSGKTSTLRMISGLLTPDKGHLS
VNGEQWFDASFGKNVSPGRRKLGYLFQDYSLFPNMTVKENIAFALKNAKDKAYLMELLES
MGLLHLQDTLPKHLSGGQQQRVALARALALKPDILLLDEPLSALDPSMREKLQEYILAIH
RKYALTTILVSHDAGEIIKLSDRIIELDHGKVLRQCTPKEFFGTGLTSAKFQFQGEIMDI
LEDDVVHIVHVKTGNDLVKVVCDMDETKELGVGDKVLVGSKAFNPLIKKL

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