GapMind for catabolism of small carbon sources

 

Protein WP_089137183.1 in Lactobacillus silagei IWT126

Annotation: NCBI__GCF_002217945.1:WP_089137183.1

Length: 462 amino acids

Source: GCF_002217945.1 in NCBI

Candidate for 13 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-alanine catabolism cycA hi L-alanine and D-alanine permease (characterized) 44% 93% 386.7 ProY of 457 aas and 12 TMSs 42% 372.9
L-alanine catabolism cycA hi L-alanine and D-alanine permease (characterized) 44% 93% 386.7 ProY of 457 aas and 12 TMSs 42% 372.9
L-proline catabolism proY med ProY of 457 aas and 12 TMSs (characterized) 42% 97% 372.9 L-alanine and D-alanine permease 44% 386.7
L-tryptophan catabolism aroP med Aromatic amino acid transport protein AroP (characterized, see rationale) 43% 98% 351.7 L-alanine and D-alanine permease 44% 386.7
L-phenylalanine catabolism aroP med Aromatic amino acid transport protein AroP (characterized, see rationale) 40% 96% 342 L-alanine and D-alanine permease 44% 386.7
L-threonine catabolism RR42_RS28305 lo D-serine/D-alanine/glycine transporter (characterized, see rationale) 39% 96% 357.1 L-alanine and D-alanine permease 44% 386.7
phenylacetate catabolism H281DRAFT_04042 lo Aromatic amino acid transporter AroP (characterized, see rationale) 40% 97% 334.7 L-alanine and D-alanine permease 44% 386.7
L-histidine catabolism permease lo histidine permease (characterized) 36% 95% 332 L-alanine and D-alanine permease 44% 386.7
L-lysine catabolism lysP lo lysine-specific permease (characterized) 36% 88% 268.9 L-alanine and D-alanine permease 44% 386.7
L-arginine catabolism rocE lo arginine permease (characterized) 31% 78% 208 L-alanine and D-alanine permease 44% 386.7
L-isoleucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 31% 79% 193 L-alanine and D-alanine permease 44% 386.7
L-leucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 31% 79% 193 L-alanine and D-alanine permease 44% 386.7
L-valine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 31% 79% 193 L-alanine and D-alanine permease 44% 386.7

Sequence Analysis Tools

View WP_089137183.1 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

MKRKVKKSPALRRSMTAGQMEMISLGGAIGVGLFMGSTSTIKWTGPSVLLAYMFVGLILY
IVMRALGEMIYVNPGTGSFADYATEYVHPLAGYLAKWANVFEYIVVGMSEVVAATQYLQY
WWPHINTFTVGVIIIAFLVAANLASAKAYGSLEFWFAMIKVITIIMMIILGLLVIFFGLG
NGGHPVGFSNLWSHGGFFTGGVKGFFFSMSIIVGSYEGIELLGITAGEVANPQKAIVKSV
KSVLFRILIFYVGAIFVIVTIYPWNRLSAIGSPFVSTFAKVGITAAASVINFVVLTAALS
SANSGIYSSSRMLFKLAHESDAPKIFGRLSKRVVPDAAILGISSGIFLGFLLDIIFSAYN
KSTSDLFVVVFSSSVLPGMIPWFVILLAELRFRKNNAIVMKDHPFKLPLYPFSNYFAMFV
LVVIVGFMFVNPDTRVSVIVGAAVLVVATLFYVVRHRKGRLD

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