GapMind for catabolism of small carbon sources

 

Protein 3607646 in Dinoroseobacter shibae DFL-12

Annotation: FitnessBrowser__Dino:3607646

Length: 366 amino acids

Source: Dino in FitnessBrowser

Candidate for 10 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA hi PotG aka B0855, component of Putrescine porter (characterized) 41% 95% 259.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 36% 237.7
L-histidine catabolism hutV med HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 43% 83% 180.3 PotG aka B0855, component of Putrescine porter 41% 259.2
L-proline catabolism hutV med HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 43% 83% 180.3 PotG aka B0855, component of Putrescine porter 41% 259.2
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 35% 93% 157.1 PotG aka B0855, component of Putrescine porter 41% 259.2
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 35% 93% 157.1 PotG aka B0855, component of Putrescine porter 41% 259.2
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 38% 98% 156.8 PotG aka B0855, component of Putrescine porter 41% 259.2
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 39% 91% 154.1 PotG aka B0855, component of Putrescine porter 41% 259.2
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 39% 91% 154.1 PotG aka B0855, component of Putrescine porter 41% 259.2
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 33% 98% 135.2 PotG aka B0855, component of Putrescine porter 41% 259.2
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 36% 77% 131 PotG aka B0855, component of Putrescine porter 41% 259.2

Sequence Analysis Tools

View 3607646 at FitnessBrowser

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

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Sequence

MRQTTPPAVEVKGLSKHYGPVKALRQVDLTIAAGEYFVLLGPSGGGKTTLLRTIGGFHRP
TEGQVLLHGRDMSHLPPDKRPTTMVFQAYALFPHMTVLQNVSYGLKVAGMDKATAQEKAA
AMMDVVGLAGFAERKPHELSGGQQQRVQLARALVLDRDILLLDEPLAALDAQLRKDMCLE
LKHLQEKVGITFIHVTHNQEEAMTVADRIALVADGQLVEQGAARDIYRAPIKKFTAGFVG
ENNLLSGTVSQVNGVSCMVEVAGAQLSVPKRGQEVTQGQAVDLSIRSELVQLSRVDASND
PGDGHSILGSYDEAVYLGLTTSHLVRLPNGVEMTSRTISDALGDLPTPGDPVRLSWQPDA
IRLHTS

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 (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