GapMind for catabolism of small carbon sources

 

Protein Ga0059261_0562 in Sphingomonas koreensis DSMZ 15582

Annotation: Ga0059261_0562 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component

Length: 232 amino acids

Source: Korea in FitnessBrowser

Candidate for 33 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 med GluA aka CGL1950, component of Glutamate porter (characterized) 40% 83% 136 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 41% 63% 147.1 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-Glucosamine, putative ATPase component (characterized) 38% 83% 132.1 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
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) 39% 83% 131 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
L-arginine catabolism artP lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 40% 81% 129.4 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 40% 81% 129.4 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
L-lysine catabolism hisP lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 40% 81% 129.4 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 36% 90% 127.1 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 36% 90% 127.1 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 36% 56% 126.7 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 38% 61% 123.6 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 38% 61% 123.6 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 35% 55% 123.2 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
D-cellobiose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 55% 119.8 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
D-glucose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 55% 119.8 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
lactose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 55% 119.8 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
D-maltose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 55% 119.8 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
sucrose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 55% 119.8 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
trehalose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 55% 119.8 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 55% 119.8 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 40% 68% 118.2 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 37% 55% 116.3 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 33% 55% 116.3 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
D-maltose catabolism thuK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 33% 55% 116.3 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 33% 55% 116.3 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 33% 55% 116.3 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
D-maltose catabolism malK lo Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 32% 56% 112.8 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 53% 112.5 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 53% 112.5 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 53% 112.5 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 53% 112.5 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 53% 112.5 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 53% 112.5 Uncharacterized ABC transporter ATP-binding protein Rv0986 41% 170.6

Sequence Analysis Tools

View Ga0059261_0562 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

MSIDPAADIAIRARNVTLTLGTREAPTEILKGIDVDIARGSSVAILGPSGSGKSSLMAIL
SGLERASGGEVSVAGIAYGTLDEDGLARARRGRVGIVLQAFHLLPTMTAHENVAVPLELA
GAPDAFARAGAELDAVGLGHRLTHYPVQLSGGEQQRVAIARAVAGRPEILFADEPTGNLD
GATSGAIVDLLFDRQRAADATLLIITHDPALAERCDRVLTMRDGLIVADSAA

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