GapMind for catabolism of small carbon sources

 

Protein WP_083529130.1 in Kocuria flava HO-9041

Annotation: NCBI__GCF_001482365.1:WP_083529130.1

Length: 482 amino acids

Source: GCF_001482365.1 in NCBI

Candidate for 17 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism permease med Aromatic amino acid permease, AroP (characterized) 45% 94% 380.6 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 42% 375.6
L-phenylalanine catabolism aroP med Aromatic amino acid permease, AroP (characterized) 45% 94% 380.6 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 42% 375.6
L-tryptophan catabolism aroP med Aromatic amino acid permease, AroP (characterized) 45% 94% 380.6 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 42% 375.6
L-tyrosine catabolism aroP med Aromatic amino acid permease, AroP (characterized) 45% 94% 380.6 GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP 42% 375.6
L-proline catabolism proY med GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized) 42% 96% 375.6 Aromatic amino acid permease, AroP 45% 380.6
L-lysine catabolism lysP med lysine-specific permease (characterized) 41% 87% 295.4 Aromatic amino acid permease, AroP 45% 380.6
L-threonine catabolism RR42_RS28305 lo D-serine/D-alanine/glycine transporter (characterized, see rationale) 38% 91% 315.8 Aromatic amino acid permease, AroP 45% 380.6
D-alanine catabolism cycA lo L-alanine and D-alanine permease (characterized) 38% 93% 313.9 Aromatic amino acid permease, AroP 45% 380.6
L-alanine catabolism cycA lo L-alanine and D-alanine permease (characterized) 38% 93% 313.9 Aromatic amino acid permease, AroP 45% 380.6
phenylacetate catabolism H281DRAFT_04042 lo Aromatic amino acid transporter AroP (characterized, see rationale) 38% 95% 308.5 Aromatic amino acid permease, AroP 45% 380.6
L-asparagine catabolism ansP lo Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized) 35% 92% 273.5 Aromatic amino acid permease, AroP 45% 380.6
D-serine catabolism cycA lo D-serine/D-alanine/glycine transporter (characterized) 34% 97% 270 Aromatic amino acid permease, AroP 45% 380.6
L-arginine catabolism rocE lo Amino-acid permease RocE (characterized) 34% 92% 269.6 Aromatic amino acid permease, AroP 45% 380.6
L-isoleucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 32% 77% 201.8 Aromatic amino acid permease, AroP 45% 380.6
L-leucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 32% 77% 201.8 Aromatic amino acid permease, AroP 45% 380.6
L-valine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 32% 77% 201.8 Aromatic amino acid permease, AroP 45% 380.6
L-tryptophan catabolism TAT lo tryptophan permease (characterized) 31% 65% 170.6 Aromatic amino acid permease, AroP 45% 380.6

Sequence Analysis Tools

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Sequence

MSSPSSWTAPGPEAPGAAPAAPGARLKARHLVMMALGSAIGTGLFIGSGAAVRTAGPAVL
LSFLVACVLLVLVMRALGEMAAADPSPGAFSTWAENAMGRTVGRTLGWLWWAQIVVVVAA
EATAAAQLLTELWPVTEQWVLALVFMVVFTVINLVKVRTLGETEFWFALMKVLAVLVFLA
VGVALLLGLLEVPSPGLRNLTAHGGFLPTGLTGVAAALLVVIFAFGGTELVTIAAAETED
PQHNVARAIRTILVRILVFYVGAVTVMVLVLPWNDEQLSVSPFVAVLEAAGVPGADVVMA
VIIILALLSALNANIYGSSRMLYSLARRGSAPRAFADLSDRGVPRTAVVVSVVFGFAAVV
LNYLWPETVLLWMLNTVGATCLVVWGLALVSQIVLRRRADRAGTVLPLRMWAFPWLSWFA
LALLAGIVLLGLLDDAVRVQLLLTAGLVALIALLARTLGRGRAAAQPPCPPASSASSSSS
RS

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