GapMind for catabolism of small carbon sources

 

Protein GFF3909 in Phaeobacter inhibens BS107

Annotation: FitnessBrowser__Phaeo:GFF3909

Length: 224 amino acids

Source: Phaeo in FitnessBrowser

Candidate for 23 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism Ac3H11_2554 lo ABC transporter for L-Histidine, permease component 1 (characterized) 37% 96% 134.8 Probable amino-acid permease protein YxeN 48% 206.1
L-asparagine catabolism natH lo Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale) 37% 55% 132.9 Probable amino-acid permease protein YxeN 48% 206.1
L-aspartate catabolism natH lo Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale) 37% 55% 132.9 Probable amino-acid permease protein YxeN 48% 206.1
L-lysine catabolism hisM lo ABC transporter for L-Lysine, permease component 2 (characterized) 36% 93% 122.5 Probable amino-acid permease protein YxeN 48% 206.1
L-arginine catabolism artM lo Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter membrane protein, 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) 34% 94% 117.5 Probable amino-acid permease protein YxeN 48% 206.1
L-asparagine catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 31% 79% 117.5 Probable amino-acid permease protein YxeN 48% 206.1
L-aspartate catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 31% 79% 117.5 Probable amino-acid permease protein YxeN 48% 206.1
L-glutamate catabolism peb1B lo PEP1B, component of Uptake system for glutamate and aspartate (characterized) 31% 79% 117.5 Probable amino-acid permease protein YxeN 48% 206.1
L-histidine catabolism hisM lo Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter membrane protein, 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) 34% 94% 117.5 Probable amino-acid permease protein YxeN 48% 206.1
L-asparagine catabolism aatM lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized) 32% 97% 115.5 Probable amino-acid permease protein YxeN 48% 206.1
L-aspartate catabolism aatM lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized) 32% 97% 115.5 Probable amino-acid permease protein YxeN 48% 206.1
L-glutamate catabolism gltK lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 1 (characterized) 32% 97% 115.5 Probable amino-acid permease protein YxeN 48% 206.1
L-asparagine catabolism aatQ lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 2 (characterized) 33% 82% 113.6 Probable amino-acid permease protein YxeN 48% 206.1
L-aspartate catabolism aatQ lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 2 (characterized) 33% 82% 113.6 Probable amino-acid permease protein YxeN 48% 206.1
L-glutamate catabolism gltJ lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, permease component 2 (characterized) 33% 82% 113.6 Probable amino-acid permease protein YxeN 48% 206.1
D-alanine catabolism Pf6N2E2_5404 lo ABC transporter for D-Alanine, permease component 1 (characterized) 32% 56% 113.2 Probable amino-acid permease protein YxeN 48% 206.1
L-citrulline catabolism AO353_03045 lo ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized) 33% 91% 109.8 Probable amino-acid permease protein YxeN 48% 206.1
L-histidine catabolism BPHYT_RS24010 lo Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale) 31% 91% 105.1 Probable amino-acid permease protein YxeN 48% 206.1
L-arginine catabolism artQ lo ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized) 32% 96% 102.4 Probable amino-acid permease protein YxeN 48% 206.1
L-citrulline catabolism AO353_03050 lo ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized) 32% 96% 102.4 Probable amino-acid permease protein YxeN 48% 206.1
L-glutamate catabolism gluC lo GluC aka CGL1952, component of Glutamate porter (characterized) 31% 94% 92 Probable amino-acid permease protein YxeN 48% 206.1
L-lysine catabolism hisQ lo Amino acid ABC transporter, membrane protein (characterized, see rationale) 30% 91% 83.2 Probable amino-acid permease protein YxeN 48% 206.1
L-histidine catabolism aapQ lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 (characterized) 30% 51% 72.4 Probable amino-acid permease protein YxeN 48% 206.1

Sequence Analysis Tools

View GFF3909 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

MQGLDIAYMLGLVPVLLSYVPLTLFMAVVAMVLALVLASLLAVERVLRIPVLDQLVVLFI
SFFRGTPLLVQLFLFYYGLPQVLSVLTQINGVSAAIMGLTLHFAAYMAESIRAAILGVDR
SQWEAAQSIGMTRGQMMRRIVLPQAARIAAPTLVNYFIDMIKGTSLAFTLGVTEMMGATQ
KEAAGSFLYFEAFLVVAVIYWILVEALSLVQRRLETHLNKAYAR

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