GapMind for catabolism of small carbon sources

 

Protein Ga0059261_3668 in Sphingomonas koreensis DSMZ 15582

Annotation: Ga0059261_3668 ABC transporter

Length: 201 amino acids

Source: Korea 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
D-maltose catabolism malK lo Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 41% 52% 137.5 ABC-type molybdate transporter (EC 7.3.2.5) 46% 169.1
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 40% 58% 137.1 ABC-type molybdate transporter (EC 7.3.2.5) 46% 169.1
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 40% 58% 137.1 ABC-type molybdate transporter (EC 7.3.2.5) 46% 169.1
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 40% 58% 137.1 ABC-type molybdate transporter (EC 7.3.2.5) 46% 169.1
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 40% 58% 137.1 ABC-type molybdate transporter (EC 7.3.2.5) 46% 169.1
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 40% 58% 137.1 ABC-type molybdate transporter (EC 7.3.2.5) 46% 169.1
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 40% 58% 137.1 ABC-type molybdate transporter (EC 7.3.2.5) 46% 169.1
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 38% 51% 131.7 ABC-type molybdate transporter (EC 7.3.2.5) 46% 169.1
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 38% 51% 131.7 ABC-type molybdate transporter (EC 7.3.2.5) 46% 169.1
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 37% 56% 128.3 ABC-type molybdate transporter (EC 7.3.2.5) 46% 169.1
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 37% 56% 128.3 ABC-type molybdate transporter (EC 7.3.2.5) 46% 169.1
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 39% 51% 127.5 ABC-type molybdate transporter (EC 7.3.2.5) 46% 169.1
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 40% 51% 126.7 ABC-type molybdate transporter (EC 7.3.2.5) 46% 169.1
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 38% 54% 126.3 ABC-type molybdate transporter (EC 7.3.2.5) 46% 169.1
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 54% 125.2 ABC-type molybdate transporter (EC 7.3.2.5) 46% 169.1
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 54% 125.2 ABC-type molybdate transporter (EC 7.3.2.5) 46% 169.1
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 54% 125.2 ABC-type molybdate transporter (EC 7.3.2.5) 46% 169.1
D-maltose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 54% 125.2 ABC-type molybdate transporter (EC 7.3.2.5) 46% 169.1
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 54% 125.2 ABC-type molybdate transporter (EC 7.3.2.5) 46% 169.1
sucrose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 54% 125.2 ABC-type molybdate transporter (EC 7.3.2.5) 46% 169.1
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 54% 125.2 ABC-type molybdate transporter (EC 7.3.2.5) 46% 169.1
trehalose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 54% 125.2 ABC-type molybdate transporter (EC 7.3.2.5) 46% 169.1
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 54% 125.2 ABC-type molybdate transporter (EC 7.3.2.5) 46% 169.1
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 37% 56% 124.8 ABC-type molybdate transporter (EC 7.3.2.5) 46% 169.1
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 38% 52% 124 ABC-type molybdate transporter (EC 7.3.2.5) 46% 169.1
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 39% 51% 123.2 ABC-type molybdate transporter (EC 7.3.2.5) 46% 169.1
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 35% 60% 120.9 ABC-type molybdate transporter (EC 7.3.2.5) 46% 169.1
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 35% 56% 109 ABC-type molybdate transporter (EC 7.3.2.5) 46% 169.1
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 37% 51% 104.4 ABC-type molybdate transporter (EC 7.3.2.5) 46% 169.1

Sequence Analysis Tools

View Ga0059261_3668 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

MSFDIAIEKRRGDAQISCRIEGGEGIIVLFGPSGVGKTSVLDMVAGLLEPDTGHVRVGGE
TLFDAAIGEDVPPERRRAGYVFQDARLFPHLSVRANLLYGAGGDPSGLGDLAARFDIAHL
LDRWPRSLSGGEARRVAIGRALLAKPRFLLLDEPLSSLDRARREEVTRVIERLRDEAALP
ILMVTHDPVEAERLGQRIIEI

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