GapMind for catabolism of small carbon sources

 

Protein WP_082697561.1 in Novosphingobium fuchskuhlense FNE08-7

Annotation: NCBI__GCF_001519075.1:WP_082697561.1

Length: 469 amino acids

Source: GCF_001519075.1 in NCBI

Candidate for 18 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) 44% 94% 383.3 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 40% 345.9
L-phenylalanine catabolism aroP lo Aromatic amino acid transport protein AroP (characterized, see rationale) 37% 98% 292.7 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 44% 383.3
phenylacetate catabolism H281DRAFT_04042 lo Aromatic amino acid transporter AroP (characterized, see rationale) 36% 94% 276.9 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 44% 383.3
D-alanine catabolism cycA lo L-alanine and D-alanine permease (characterized) 36% 96% 273.1 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 44% 383.3
L-alanine catabolism cycA lo L-alanine and D-alanine permease (characterized) 36% 96% 273.1 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 44% 383.3
L-histidine catabolism permease lo Aromatic amino acid permease, AroP (characterized) 36% 94% 272.3 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 44% 383.3
L-tryptophan catabolism aroP lo Aromatic amino acid permease, AroP (characterized) 36% 94% 272.3 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 44% 383.3
L-tyrosine catabolism aroP lo Aromatic amino acid permease, AroP (characterized) 36% 94% 272.3 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 44% 383.3
L-threonine catabolism RR42_RS28305 lo D-serine/D-alanine/glycine transporter (characterized, see rationale) 36% 93% 270 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 44% 383.3
D-serine catabolism cycA lo D-serine/D-alanine/glycine transporter (characterized) 32% 97% 262.3 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 44% 383.3
L-asparagine catabolism ansP lo Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized) 33% 88% 241.5 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 44% 383.3
L-arginine catabolism rocE lo Amino-acid permease RocE (characterized) 32% 93% 239.2 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 44% 383.3
L-lysine catabolism lysP lo The lysine specific transporter, LysP of 488 aas and 12 TMSs (characterized) 33% 94% 236.1 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 44% 383.3
L-serine catabolism serP lo Serine transporter, SerP2 or YdgB, of 459 aas and 12 TMSs (Trip et al. 2013). Transports L-alanine (Km = 20 μM), D-alanine (Km = 38 μM), L-serine, D-serine (Km = 356 μM) and glycine (Noens and Lolkema 2015). The encoding gene is adjacent to the one encoding SerP1 (TC# 2.A.3.1.21) (characterized) 31% 95% 189.1 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 44% 383.3
L-tryptophan catabolism TAT lo tryptophan permease (characterized) 31% 67% 176.8 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 44% 383.3
L-isoleucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 32% 77% 167.5 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 44% 383.3
L-leucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 32% 77% 167.5 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 44% 383.3
L-valine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 32% 77% 167.5 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 44% 383.3

Sequence Analysis Tools

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Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MAGQAKGNGVGAVGVAEAGGAGSVELSRTLLPRHVSMIAIGGIIGAGLFVGSSTTIALTG
PAAVISYLIAGLLILLVMRMIAEMAIVLEGVRTFPDFARAGLGHLAGFLSGWLYWYFWVV
VVAVEAIAGAKIIGGWLPGVPEWAIGAGLTALMTGVNLMSTRSYGEFEFWFSSIKVAAIL
VFSLICALWVFGITAPQGFSIGNLTAHGGFAPHGWGPVLAGVASTIFSLCGAEIATIAAA
ESPDPAKVIARMTVSVALRIVIFYVLAIGLIVAVVPWTQIVPGHSPFATTLAAMHIPGGE
TIMSAVVLVAVLSCLNSGLYVTSRALFGLARFGDAPDWLVHVNARGVPARAIIAASLFAY
GALAAQWLSPGTVFSFLVNSSGVTMILLYALVGIAQLKERTRMEREAPERLTLKMWFHPF
GTLTALAAMLAVLVFMGLQPDLASQLWMSLLVAGLFAGAFWLLRTGKRA

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