GapMind for catabolism of small carbon sources

 

Protein GFF196 in Phaeobacter inhibens BS107

Annotation: FitnessBrowser__Phaeo:GFF196

Length: 432 amino acids

Source: Phaeo in FitnessBrowser

Candidate for 15 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism bztC hi BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 51% 100% 417.2 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 51% 236.9
L-aspartate catabolism bztC hi BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 51% 100% 417.2 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 51% 236.9
L-glutamate catabolism bztC hi BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 51% 100% 417.2 ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 51% 236.9
D-alanine catabolism Pf6N2E2_5404 med ABC transporter for D-Alanine, permease component 1 (characterized) 45% 76% 227.6 BztC, component of Glutamate/glutamine/aspartate/asparagine porter 51% 417.2
L-histidine catabolism aapM lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 2 (characterized) 51% 62% 236.9 BztC, component of Glutamate/glutamine/aspartate/asparagine porter 51% 417.2
L-asparagine catabolism aapM lo AapM, 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) 48% 64% 227.6 BztC, component of Glutamate/glutamine/aspartate/asparagine porter 51% 417.2
L-aspartate catabolism aapM lo AapM, 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) 48% 64% 227.6 BztC, component of Glutamate/glutamine/aspartate/asparagine porter 51% 417.2
L-glutamate catabolism aapM lo AapM, 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) 48% 64% 227.6 BztC, component of Glutamate/glutamine/aspartate/asparagine porter 51% 417.2
L-leucine catabolism aapM lo AapM, 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) 48% 64% 227.6 BztC, component of Glutamate/glutamine/aspartate/asparagine porter 51% 417.2
L-proline catabolism aapM lo AapM, 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) 48% 64% 227.6 BztC, component of Glutamate/glutamine/aspartate/asparagine porter 51% 417.2
L-asparagine catabolism natH lo Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale) 35% 95% 223 BztC, component of Glutamate/glutamine/aspartate/asparagine porter 51% 417.2
L-aspartate catabolism natH lo Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale) 35% 95% 223 BztC, component of Glutamate/glutamine/aspartate/asparagine porter 51% 417.2
L-glutamate catabolism gltK lo Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida (characterized) 32% 98% 116.7 BztC, component of Glutamate/glutamine/aspartate/asparagine porter 51% 417.2
D-glucosamine (chitosamine) catabolism AO353_21720 lo ABC transporter for D-glucosamine, permease component 2 (characterized) 32% 93% 107.1 BztC, component of Glutamate/glutamine/aspartate/asparagine porter 51% 417.2
L-glutamate catabolism gluD lo GluD aka CGL1953, component of Glutamate porter (characterized) 32% 74% 106.3 BztC, component of Glutamate/glutamine/aspartate/asparagine porter 51% 417.2

Sequence Analysis Tools

View GFF196 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

Fitness BLAST: loading...

Sequence

MSDTHAQTVAFVRETQIPPAPPPGRETGVYKWIRENLFSSVPNSILTLAALALIYALLSS
TLPWLLNGVWTTNSLAECREVLDGKLGACFSVLTERWNQLLYGFKYPGTEYWRPNLALVL
LLVALAPVLFFDLPRKLLAFTAIYPFLAFWLIWGGSILVPIVALLGFVAAGFVFQKFGKG
SFALGFFGAIVAAVVVWNIGGFLIPEGASDNAMLSAVPSRDLGGFMLNMMLGVTCVSLSV
PLGIALALGRQSNMPLIKWICVVFIEFVRGVPLITLLFVASVMLSYFFPPDATVDLFLRV
VIMITLFSAAYIAEVIRGGLAALPKGQYEAADSLGLDYPQAMRLIILPQALKISIPGIVN
VAVGLFKDTTLVSVISMFDLVGMIRGPILASTEWNGVYWELLGFAAFLFFIVCYGISQYS
QWLERRLATDHH

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