GapMind for catabolism of small carbon sources

 

Protein WP_101588800.1 in Brevibacterium jeotgali SJ5-8

Annotation: NCBI__GCF_900169175.1:WP_101588800.1

Length: 440 amino acids

Source: GCF_900169175.1 in NCBI

Candidate for 17 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-proline catabolism proY hi GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized) 42% 93% 372.1 Aromatic amino acid permease, AroP 45% 359.4
L-histidine catabolism permease med Aromatic amino acid permease, AroP (characterized) 45% 95% 359.4 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 42% 372.1
L-phenylalanine catabolism aroP med Aromatic amino acid permease, AroP (characterized) 45% 95% 359.4 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 42% 372.1
L-tryptophan catabolism aroP med Aromatic amino acid permease, AroP (characterized) 45% 95% 359.4 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 42% 372.1
L-tyrosine catabolism aroP med Aromatic amino acid permease, AroP (characterized) 45% 95% 359.4 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 42% 372.1
D-alanine catabolism cycA lo L-alanine and D-alanine permease (characterized) 38% 94% 293.9 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 42% 372.1
L-alanine catabolism cycA lo L-alanine and D-alanine permease (characterized) 38% 94% 293.9 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 42% 372.1
L-threonine catabolism RR42_RS28305 lo D-serine/D-alanine/glycine transporter (characterized, see rationale) 37% 93% 292 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 42% 372.1
phenylacetate catabolism H281DRAFT_04042 lo Aromatic amino acid transporter AroP (characterized, see rationale) 35% 95% 286.2 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 42% 372.1
L-asparagine catabolism ansP lo L-asparagine permease; L-asparagine transport protein (characterized) 36% 88% 276.2 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 42% 372.1
L-arginine catabolism rocE lo Amino-acid permease RocE (characterized) 34% 96% 264.6 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 42% 372.1
D-serine catabolism cycA lo D-serine/L-alanine/D-alanine/glycine/D-cycloserine uptake porter of 556 aas, CycA (characterized) 34% 80% 247.7 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 42% 372.1
L-lysine catabolism lysP lo lysine-specific permease (characterized) 35% 82% 237.3 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 42% 372.1
L-isoleucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 32% 77% 214.5 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 42% 372.1
L-leucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 32% 77% 214.5 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 42% 372.1
L-valine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 32% 77% 214.5 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 42% 372.1
L-tryptophan catabolism TAT lo tryptophan permease (characterized) 32% 67% 204.9 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 42% 372.1

Sequence Analysis Tools

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

MRPRHLIMMSLGSAIGAGLFVGSGAGIAAAGPAVLVSYAIAGLIVIAVMRMLGEMVAADP
NPGAFSYYVGKALGPSAAFAVGWLWWITLCLVVAAEATAAAQIMAGVVPLFPQWGYALAF
MVLFTWINLWGVRSFGEFEFWFSFIKVAFVFLFLALGVAFLLGWTPADSPGLTHITETSF
MPNGMGGIAAGLLVVVFAFGGIEIVAVAAAETAEPQRSVRSATRTILWRILLFYMGSVSI
MVLALPWDDPSLLESPFVAVLNRAGLPVLAAIIGMIIVAALLSSLNANVYGASRMFYSLA
QRGMAPRGMGGVNERAVPSLGVWMSVAFGFVAVLLNYFWAEEVLGLLLNIVGSTLIVTWS
SAIIAHLVLRTRAEKAGEQLPLTMWLFPYLSWATLVGLVGIIVLGFTVPDVRTQLLLTFG
LFGALLVVGVITTRRDAQRA

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