GapMind for catabolism of small carbon sources

 

Protein WP_017867195.1 in Lactobacillus pobuzihii E100301

Annotation: NCBI__GCF_000349725.1:WP_017867195.1

Length: 464 amino acids

Source: GCF_000349725.1 in NCBI

Candidate for 16 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism rocE med Amino-acid permease RocE (characterized) 51% 97% 500 S-Methylmethionine permease, MmuP 56% 533.5
L-lysine catabolism lysP med Lysine permease LysP (characterized) 41% 91% 360.9 S-Methylmethionine permease, MmuP 56% 533.5
L-histidine catabolism permease lo Histidine permease HisP (characterized) 39% 97% 340.5 S-Methylmethionine permease, MmuP 56% 533.5
L-proline catabolism proY lo GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized) 37% 98% 328.9 S-Methylmethionine permease, MmuP 56% 533.5
D-alanine catabolism cycA lo L-alanine and D-alanine permease (characterized) 38% 95% 317.8 S-Methylmethionine permease, MmuP 56% 533.5
L-alanine catabolism cycA lo L-alanine and D-alanine permease (characterized) 38% 95% 317.8 S-Methylmethionine permease, MmuP 56% 533.5
L-tryptophan catabolism aroP lo Amino acid permease (characterized, see rationale) 37% 95% 317.8 S-Methylmethionine permease, MmuP 56% 533.5
L-threonine catabolism RR42_RS28305 lo D-serine/D-alanine/glycine transporter (characterized, see rationale) 38% 98% 311.6 S-Methylmethionine permease, MmuP 56% 533.5
L-phenylalanine catabolism aroP lo Phenylalanine:H+ symporter, PheP of 458 aas and 12 established TMSs (characterized) 37% 93% 293.1 S-Methylmethionine permease, MmuP 56% 533.5
D-serine catabolism cycA lo D-serine/D-alanine/glycine transporter (characterized) 35% 96% 285.4 S-Methylmethionine permease, MmuP 56% 533.5
L-asparagine catabolism ansP lo Asparagine permease (AnsP) of 497 aas and 12 TMSs (characterized) 35% 91% 283.5 S-Methylmethionine permease, MmuP 56% 533.5
L-tyrosine catabolism aroP lo L-tyrosine transporter (characterized) 36% 98% 273.1 S-Methylmethionine permease, MmuP 56% 533.5
L-isoleucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 30% 87% 231.1 S-Methylmethionine permease, MmuP 56% 533.5
L-leucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 30% 87% 231.1 S-Methylmethionine permease, MmuP 56% 533.5
L-valine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 30% 87% 231.1 S-Methylmethionine permease, MmuP 56% 533.5
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) 32% 83% 221.1 S-Methylmethionine permease, MmuP 56% 533.5

Sequence Analysis Tools

View WP_017867195.1 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

MEKPHYELKRRMEARHLLMISLGGVIGTGLFLSSGYTINQAGPIGTILAYTLGAIIVYLV
MLCLGELSVAMPQTGSFHVYADKYIGPGTGFTVAILYWLTWTVALGSEFTAAGLIMKTWF
PDTATWIWSLLFMVIIFTSNALSVKVFGETEFLFSSIKVIAIVLFIMLGLLAIFGILPIK
GYSHAPLFHNLVKDGVFPTGFKSVFTTMLTVNFAFSGTELIGVTAGETKDPEKNIPKAIH
TTLLRLAIFFIGSIVVMASLIPWQQAGVDQSPFVLVFNKIGLPFAGDLMNFVVLTAILSA
ANSGLYASTRMLWSLANEGMIPQKYAKTNSRGVPMIALILSMLGGILALLSSVVAASTIY
LVLVSISGLAVVIVWMAIAYAQINFRKQWLKDGHTTAELKFKTPWYPILPWSALILSFLS
CVLIVFDPTQRMALFYMIPFLIICYGVYYGKQKIHQKKQASRSK

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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