GapMind for catabolism of small carbon sources

 

Protein WP_003943879.1 in Rhodococcus qingshengii djl-6-2

Annotation: NCBI__GCF_002893965.1:WP_003943879.1

Length: 469 amino acids

Source: GCF_002893965.1 in NCBI

Candidate for 14 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) 56% 99% 526.9 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 53% 468.8
L-histidine catabolism permease med Aromatic amino acid permease, AroP (characterized) 44% 91% 376.7 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 56% 526.9
L-phenylalanine catabolism aroP med Aromatic amino acid permease, AroP (characterized) 44% 91% 376.7 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 56% 526.9
L-tryptophan catabolism aroP med Aromatic amino acid permease, AroP (characterized) 44% 91% 376.7 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 56% 526.9
L-tyrosine catabolism aroP med Aromatic amino acid permease, AroP (characterized) 44% 91% 376.7 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 56% 526.9
D-alanine catabolism cycA lo L-alanine and D-alanine permease (characterized) 38% 96% 347.4 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 56% 526.9
L-alanine catabolism cycA lo L-alanine and D-alanine permease (characterized) 38% 96% 347.4 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 56% 526.9
L-threonine catabolism RR42_RS28305 lo D-serine/D-alanine/glycine transporter (characterized, see rationale) 38% 95% 329.3 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 56% 526.9
phenylacetate catabolism H281DRAFT_04042 lo Aromatic amino acid transporter AroP (characterized, see rationale) 38% 97% 319.3 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 56% 526.9
L-lysine catabolism lysP lo lysine-specific permease (characterized) 37% 93% 312 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 56% 526.9
L-arginine catabolism rocE lo Amino-acid permease RocE (characterized) 38% 89% 308.1 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 56% 526.9
D-serine catabolism cycA lo D-serine/D-alanine/glycine transporter (characterized) 34% 95% 278.5 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 56% 526.9
L-tryptophan catabolism TAT lo tryptophan permease (characterized) 33% 78% 231.9 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 56% 526.9
L-valine catabolism Bap2 lo Valine amino-acid permease; Branched-chain amino-acid permease 3 (characterized) 30% 66% 191.4 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 56% 526.9

Sequence Analysis Tools

View WP_003943879.1 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

MSSTDQPALQHTLKKRHLSMIAIAGVIGAGLFVGSGVAIQETGPGVLISYALAGVVVILV
MRMLGEMSAASPETGSFSSYADKAIGRWAGFSIGWLYAWFWIIVLGIEATAGALIMNRWV
PGVPQWTWALILMIVLTLTNIISVKSFGEFEFWFASIKVVAIIAFLGMGIVAICGWMPGV
EAPGMTNLTGHGGFLPNGTGAMLAAVLVVVFSFFGAEIATIAAGESANPLEAVRAAVKSV
VWRILIFYIGSIAVVVTLLPWDSASVALSPYVAVMDSYGIPAAGNIMDVVVLTSVLSCLN
SGLYTASRMIFSLAGRGDAPKSLSRIEKTGVPMRAVLVSTIVGFLTVGMNYLSPDKVFLF
LVNSSGAIALFVWLVISVSQLRTRRKLEASGQELELKMWFFPYLTYATIAAIIALCIGML
TLDSTRSQMIVSLGLAAILVGIGLYRYRNHKDTDTDAEVVPVAESAPTP

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