GapMind for catabolism of small carbon sources

 

Protein RR42_RS33780 in Cupriavidus basilensis 4G11

Annotation: FitnessBrowser__Cup4G11:RR42_RS33780

Length: 474 amino acids

Source: Cup4G11 in FitnessBrowser

Candidate for 11 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) 53% 99% 493.4 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 46% 403.7
L-histidine catabolism permease med Aromatic amino acid permease, AroP (characterized) 41% 91% 333.2 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 53% 493.4
L-phenylalanine catabolism aroP med Aromatic amino acid permease, AroP (characterized) 41% 91% 333.2 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 53% 493.4
L-tryptophan catabolism aroP med Aromatic amino acid permease, AroP (characterized) 41% 91% 333.2 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 53% 493.4
L-tyrosine catabolism aroP med Aromatic amino acid permease, AroP (characterized) 41% 91% 333.2 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 53% 493.4
D-alanine catabolism cycA lo L-alanine and D-alanine permease (characterized) 39% 98% 349 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 53% 493.4
L-alanine catabolism cycA lo L-alanine and D-alanine permease (characterized) 39% 98% 349 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 53% 493.4
phenylacetate catabolism H281DRAFT_04042 lo Aromatic amino acid transporter AroP (characterized, see rationale) 38% 99% 327 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 53% 493.4
D-serine catabolism cycA lo D-serine/D-alanine/glycine transporter (characterized) 36% 99% 303.1 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 53% 493.4
L-lysine catabolism lysP lo lysine-specific permease (characterized) 38% 81% 278.9 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 53% 493.4
L-arginine catabolism rocE lo arginine permease (characterized) 37% 75% 259.2 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 53% 493.4

Sequence Analysis Tools

View RR42_RS33780 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

MIHHQQQQQSSGLKHGLKQRHMTMIALGGVIGAGLFVGSGVVIKSAGPAAVISFLITGLL
VVLVMRMLGEMACALPTVGSFYEYAREAWSDRPAMGELAGFLTGWMYWYFWVIVVALEAV
AGASLVQFWLPGVPAWSISLVLLVMLTLTNLISVKSFGEFEFWFASIKVAAIVVFLFLAG
LFVLGMWPGATASVAHLTVHGGFAPNGIMPVLTGAVAATGFYFGAEIVTIAAAETAEPQK
AVARATSSVITRVLVFYVGSVLLVVCLVPWNSAGIATPYVSALNAMRIPAAAQIMNAVVL
TAVLSALNSGLYASSRMLFALTKRGDAPKALARLSRNGVPVRAILFATLFGYGAVVMSYV
SPDKVFAFLVNSYGTVAIFVYILIAISQLRLRARLEREAPHRLKVRMWAFPYLTWVAIAG
MVGIVVAMAFIPDQRTPLLLGVASLGILVVAYAVRQQLRKHAAAAPLGEVRRAD

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