GapMind for catabolism of small carbon sources

 

Protein WP_037448405.1 in Skermanella stibiiresistens SB22

Annotation: NCBI__GCF_000576635.1:WP_037448405.1

Length: 258 amino acids

Source: GCF_000576635.1 in NCBI

Candidate for 25 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-alanine catabolism Pf6N2E2_5405 med ABC transporter for D-Alanine, ATPase component (characterized) 77% 100% 416 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component 78% 415.2
L-histidine catabolism aapP med ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 78% 98% 415.2 ABC transporter for D-Alanine, ATPase component 77% 416.0
L-asparagine catabolism aapP med 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) 82% 94% 414.1 ABC transporter for D-Alanine, ATPase component 77% 416.0
L-aspartate catabolism aapP med 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) 82% 94% 414.1 ABC transporter for D-Alanine, ATPase component 77% 416.0
L-glutamate catabolism aapP med 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) 82% 94% 414.1 ABC transporter for D-Alanine, ATPase component 77% 416.0
L-leucine catabolism aapP med 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) 82% 94% 414.1 ABC transporter for D-Alanine, ATPase component 77% 416.0
L-proline catabolism aapP med 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) 82% 94% 414.1 ABC transporter for D-Alanine, ATPase component 77% 416.0
L-asparagine catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 80% 94% 411.4 ABC transporter for D-Alanine, ATPase component 77% 416.0
L-aspartate catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 80% 94% 411.4 ABC transporter for D-Alanine, ATPase component 77% 416.0
L-glutamate catabolism gltL med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 80% 94% 411.4 ABC transporter for D-Alanine, ATPase component 77% 416.0
L-lysine catabolism hisP med Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 62% 97% 317.8 ABC transporter for D-Alanine, ATPase component 77% 416.0
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 61% 93% 299.7 ABC transporter for D-Alanine, ATPase component 77% 416.0
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 61% 93% 299.7 ABC transporter for D-Alanine, ATPase component 77% 416.0
L-asparagine catabolism aatP med ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 59% 100% 292.4 ABC transporter for D-Alanine, ATPase component 77% 416.0
L-aspartate catabolism aatP med ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 59% 100% 292.4 ABC transporter for D-Alanine, ATPase component 77% 416.0
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 58% 100% 276.6 ABC transporter for D-Alanine, ATPase component 77% 416.0
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 58% 100% 276.6 ABC transporter for D-Alanine, ATPase component 77% 416.0
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) 55% 99% 266.9 ABC transporter for D-Alanine, ATPase component 77% 416.0
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtM (characterized) 54% 100% 256.9 ABC transporter for D-Alanine, ATPase component 77% 416.0
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-glucosamine, ATPase component (characterized) 51% 97% 255 ABC transporter for D-Alanine, ATPase component 77% 416.0
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 53% 96% 247.7 ABC transporter for D-Alanine, ATPase component 77% 416.0
L-histidine catabolism hisP med Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 51% 97% 239.2 ABC transporter for D-Alanine, ATPase component 77% 416.0
L-citrulline catabolism AO353_03040 med ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 48% 98% 233.4 ABC transporter for D-Alanine, ATPase component 77% 416.0
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 48% 95% 230.7 ABC transporter for D-Alanine, ATPase component 77% 416.0
L-citrulline catabolism PS417_17605 med ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) 48% 95% 229.9 ABC transporter for D-Alanine, ATPase component 77% 416.0

Sequence Analysis Tools

View WP_037448405.1 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

MSDVRQTVAPQVGDDIAVQLSDVHKWYGEFHVLKGINLTVSRGERIVICGPSGSGKSTLI
RCINRLEEHQRGNIVVDGVELTNNLKNIDQVRRDVGMVFQHFNLFPHLTVLENCTLAPIW
VRKMPKDQAEAVAMKYLERVRIPDQARKYPGQLSGGQQQRVAIARSLCMNPKVMLFDEPT
SALDPEMIKEVLDVMIGLAREGMTMLCVTHEMGFAKTVANRVIFMDRGEIVEQNAPNEFF
NNPQSERTKLFLSQILAH

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