GapMind for catabolism of small carbon sources

 

Protein WP_110753407.1 in Phyllobacterium leguminum ORS 1419

Annotation: NCBI__GCF_003217235.1:WP_110753407.1

Length: 442 amino acids

Source: GCF_003217235.1 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) 52% 95% 472.6 Probable GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease 45% 382.1
L-histidine catabolism permease lo Aromatic amino acid permease, AroP (characterized) 40% 94% 329.7 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 52% 472.6
L-phenylalanine catabolism aroP lo Aromatic amino acid permease, AroP (characterized) 40% 94% 329.7 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 52% 472.6
L-tryptophan catabolism aroP lo Aromatic amino acid permease, AroP (characterized) 40% 94% 329.7 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 52% 472.6
L-tyrosine catabolism aroP lo Aromatic amino acid permease, AroP (characterized) 40% 94% 329.7 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 52% 472.6
D-alanine catabolism cycA lo L-alanine and D-alanine permease (characterized) 38% 91% 308.9 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 52% 472.6
L-alanine catabolism cycA lo L-alanine and D-alanine permease (characterized) 38% 91% 308.9 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 52% 472.6
L-threonine catabolism RR42_RS28305 lo D-serine/D-alanine/glycine transporter (characterized, see rationale) 37% 92% 303.9 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 52% 472.6
D-serine catabolism cycA lo D-serine/D-alanine/glycine transporter (characterized) 37% 90% 293.5 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 52% 472.6
phenylacetate catabolism H281DRAFT_04042 lo Aromatic amino acid transporter AroP (characterized, see rationale) 37% 90% 282 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 52% 472.6
L-asparagine catabolism ansP lo Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized) 37% 90% 281.6 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 52% 472.6
L-arginine catabolism rocE lo Amino-acid permease RocE (characterized) 33% 88% 258.5 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 52% 472.6
L-lysine catabolism lysP lo lysine-specific permease (characterized) 39% 76% 255.4 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 52% 472.6
L-serine catabolism serP lo Serine uptake transporter, SerP1, of 259 aas and 12 TMSs (Trip et al. 2013). L-serine is the highest affinity substrate (Km = 18 μM), but SerP1 also transports L-threonine and L-cysteine (Km values = 20 - 40 μM) (characterized) 32% 81% 200.3 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 52% 472.6
L-threonine catabolism serP1 lo Serine uptake transporter, SerP1, of 259 aas and 12 TMSs (Trip et al. 2013). L-serine is the highest affinity substrate (Km = 18 μM), but SerP1 also transports L-threonine and L-cysteine (Km values = 20 - 40 μM) (characterized) 32% 81% 200.3 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 52% 472.6
L-isoleucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 33% 69% 183 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 52% 472.6
L-leucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 33% 69% 183 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 52% 472.6
L-valine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 33% 69% 183 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 52% 472.6

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

MIAMGGVIGAGLFVGSGAVIRSVGPAAFITYALTGLMIVMVMRMLGEMAIANSVEGSFSR
YARLALGDWAGFTVAWLYWYFWVIVVGAEAVAGAGILQKWMPDVPLWAAALGLIVVMTAT
NLYSVRSFGEFEYWFSSIKVAAIVAFLALGVSYVFGLWPGEPMSFLNIDPAGGFLPHGPG
AIFTGIAIVVFSMVGVEIATVAAAEAKDPERAVVQATRSVVIRILIFYVGSILLLTTILP
WNSLAPNTSPFVAALDKMNIPFGGDAMNFVVLTAVLSCLNSGLYTASRMLFVLAKRGDAP
AWLAKTSAKGVPIRTILASTLVGYVAVIAAYLAPDTIFLFLLNSSGAIMLFVYMFITVSQ
LILRPRTPPERLKVKMWFHPWLSLATFAGMAAIIVMMLLEQGTRSQVTLSLLSAAAIIAI
WFVRSKLIGVNASNVKPRNRPV

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