GapMind for catabolism of small carbon sources

 

Protein WP_076475776.1 in Williamsia sterculiae CPCC 203464

Annotation: NCBI__GCF_900156495.1:WP_076475776.1

Length: 480 amino acids

Source: GCF_900156495.1 in NCBI

Candidate for 16 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 med GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized) 50% 97% 450.3 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 58% 520.0
L-histidine catabolism permease med Aromatic amino acid permease, AroP (characterized) 43% 97% 367.5 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 58% 520.0
L-phenylalanine catabolism aroP med Aromatic amino acid permease, AroP (characterized) 43% 97% 367.5 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 58% 520.0
L-tryptophan catabolism aroP med Aromatic amino acid permease, AroP (characterized) 43% 97% 367.5 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 58% 520.0
L-tyrosine catabolism aroP med Aromatic amino acid permease, AroP (characterized) 43% 97% 367.5 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 58% 520.0
D-alanine catabolism cycA lo L-alanine and D-alanine permease (characterized) 40% 94% 324.7 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 58% 520.0
L-alanine catabolism cycA lo L-alanine and D-alanine permease (characterized) 40% 94% 324.7 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 58% 520.0
L-threonine catabolism RR42_RS28305 lo D-serine/D-alanine/glycine transporter (characterized, see rationale) 38% 94% 317 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 58% 520.0
L-arginine catabolism rocE lo Amino-acid permease RocE (characterized) 33% 98% 274.6 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 58% 520.0
L-asparagine catabolism ansP lo L-asparagine permease; L-asparagine transport protein (characterized) 35% 90% 273.1 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 58% 520.0
L-isoleucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 34% 84% 216.5 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 58% 520.0
L-leucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 34% 84% 216.5 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 58% 520.0
L-valine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 34% 84% 216.5 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 58% 520.0
L-lysine catabolism lysP lo uncharacterized amino-acid permease C869.11 (characterized) 33% 76% 214.9 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 58% 520.0
L-serine catabolism serP lo Serine permease SerP1 (characterized) 32% 82% 194.9 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 58% 520.0
L-tryptophan catabolism TAT lo tryptophan permease (characterized) 33% 70% 192.2 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 58% 520.0

Sequence Analysis Tools

View WP_076475776.1 at NCBI

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

MSTDTPASTPPPSSDPTAPASAPGGHGPALGTSLKPRHITMISIAGVIGAGLFVGSANAI
EKAGPAVLISYLLAGTLVVLVMRMLGEMATANPDTGSFSVYSDRALGRWAGFSVGWLYWW
FWVLVIPVEATAAASILSDLIGGAQWIWALAVTVLLTVTNLISVGNYGEFEFWFALIKVV
AIVAFIVVGALAIFGVFPGSDVSGISNLWKPDGFLPNGFGAVIAGMLVTMFSFMGTEIVT
IAAAESPNPEAGISKAVNSVIWRISLFYIGSIFVVVALLPYDKLDDGSYQSVLEAIGIPH
AKQIMDVVILTAVASCLNSALYTASRMLFSLGERRDAPRVVRKLTGNGVPWVAVLASMVI
GFLAVVGNYVLPDKIFAYLLATSGAVALFVYLAIATSQLVLGRKMRATGGRSAVRMWLFP
YLTGVVIVFIIAVLILMAFDPNQQQAIGFSIISAVIIVGLGVYRQRTDRAGREKVSAGTV

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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