GapMind for catabolism of small carbon sources

 

Protein WP_043920798.1 in Jannaschia aquimarina GSW-M26

Annotation: NCBI__GCF_000877395.1:WP_043920798.1

Length: 351 amino acids

Source: GCF_000877395.1 in NCBI

Candidate for 15 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-cellobiose catabolism gtsD hi Sugar ABC transporter ATP-binding protein (characterized, see rationale) 55% 97% 360.1 ABC transporter for D-Glucosamine, ATPase component 51% 327.0
D-glucose catabolism gtsD hi Sugar ABC transporter ATP-binding protein (characterized, see rationale) 55% 97% 360.1 ABC transporter for D-Glucosamine, ATPase component 51% 327.0
lactose catabolism gtsD hi Sugar ABC transporter ATP-binding protein (characterized, see rationale) 55% 97% 360.1 ABC transporter for D-Glucosamine, ATPase component 51% 327.0
D-maltose catabolism gtsD hi Sugar ABC transporter ATP-binding protein (characterized, see rationale) 55% 97% 360.1 ABC transporter for D-Glucosamine, ATPase component 51% 327.0
sucrose catabolism gtsD hi Sugar ABC transporter ATP-binding protein (characterized, see rationale) 55% 97% 360.1 ABC transporter for D-Glucosamine, ATPase component 51% 327.0
trehalose catabolism gtsD hi Sugar ABC transporter ATP-binding protein (characterized, see rationale) 55% 97% 360.1 ABC transporter for D-Glucosamine, ATPase component 51% 327.0
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 52% 94% 333.2 ABC transporter for D-Glucosamine, ATPase component 51% 327.0
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 51% 99% 327 ABC transporter for D-Glucose-6-Phosphate, ATPase component 52% 333.2
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 50% 94% 320.9 ABC transporter for D-Glucosamine, ATPase component 51% 327.0
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 48% 98% 311.6 ABC transporter for D-Glucose-6-Phosphate, ATPase component 52% 333.2
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 48% 99% 304.7 ABC transporter for D-Glucose-6-Phosphate, ATPase component 52% 333.2
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 37% 97% 225.3 ABC transporter for D-Glucose-6-Phosphate, ATPase component 52% 333.2
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% 96% 164.5 ABC transporter for D-Glucose-6-Phosphate, ATPase component 52% 333.2
L-glutamate catabolism gltL 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% 96% 164.5 ABC transporter for D-Glucose-6-Phosphate, ATPase component 52% 333.2
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 38% 98% 155.2 ABC transporter for D-Glucose-6-Phosphate, ATPase component 52% 333.2

Sequence Analysis Tools

View WP_043920798.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MTDALKVTALRKSYGAVDVLRGIDASIAQGEFLVLVGPSGCGKSTMLNCIAGLEETTSGT
IEIAGRDVTNLPPRERDIAMVFQSYALYPTMSVRENIAFGMKVRGIDRDVQRAKVEEVAG
LLQIGPLLDRRPGQLSGGQRQRVAMGRALVRDPALFLFDEPLSNLDAKLRVEMRAEIRRL
HQTTGASIVYVTHDQIEAMTLASRIVVLDGGVVQQAGTPAEIYDAPANTFVADFMGSPSM
NLVPARLGEGRLEFGDGRSIALSAPPAGAAPGAEVIAGIRPEAFGPGGDLPVRPDMIENT
GSDLYLRFDLAGKPVTARLPARAGLGAEPALAVDTSRICFFDPGEGGRRLG

This GapMind analysis is from Sep 24 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 (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). 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. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. 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:

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