GapMind for catabolism of small carbon sources

 

Protein WP_039103680.1 in Frischella perrara PEB0191

Annotation: NCBI__GCF_000807275.1:WP_039103680.1

Length: 484 amino acids

Source: GCF_000807275.1 in NCBI

Candidate for 19 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-lysine catabolism lysP hi lysine-specific permease (characterized) 75% 98% 748 Histidine permease HisP 53% 520.8
L-histidine catabolism permease med Histidine permease HisP (characterized) 53% 99% 520.8 lysine-specific permease 75% 748.0
L-arginine catabolism rocE med Amino-acid permease RocE (characterized) 41% 96% 377.9 lysine-specific permease 75% 748.0
L-alanine catabolism cycA med General amino-acid permease GAP2 (characterized) 41% 81% 375.9 lysine-specific permease 75% 748.0
L-proline catabolism proY lo GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized) 38% 95% 332.8 lysine-specific permease 75% 748.0
L-threonine catabolism RR42_RS28305 lo D-serine/D-alanine/glycine transporter (characterized, see rationale) 38% 94% 315.8 lysine-specific permease 75% 748.0
L-isoleucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 35% 89% 313.9 lysine-specific permease 75% 748.0
L-leucine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 35% 89% 313.9 lysine-specific permease 75% 748.0
L-phenylalanine catabolism aroP lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 35% 89% 313.9 lysine-specific permease 75% 748.0
L-tryptophan catabolism aroP lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 35% 89% 313.9 lysine-specific permease 75% 748.0
L-valine catabolism Bap2 lo Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized) 35% 89% 313.9 lysine-specific permease 75% 748.0
D-alanine catabolism cycA lo L-alanine and D-alanine permease (characterized) 35% 94% 301.6 lysine-specific permease 75% 748.0
L-tryptophan catabolism TAT lo tryptophan permease (characterized) 35% 82% 300.4 lysine-specific permease 75% 748.0
L-asparagine catabolism AGP1 lo general amino acid permease AGP1 (characterized) 31% 77% 288.1 lysine-specific permease 75% 748.0
phenylacetate catabolism H281DRAFT_04042 lo Aromatic amino acid transporter AroP (characterized, see rationale) 34% 94% 278.1 lysine-specific permease 75% 748.0
L-tyrosine catabolism aroP lo L-tyrosine transporter (characterized) 37% 89% 274.6 lysine-specific permease 75% 748.0
L-tyrosine catabolism TAT1 lo valine/tyrosine/tryptophan amino-acid permease (characterized) 30% 78% 269.2 lysine-specific permease 75% 748.0
D-serine catabolism cycA lo D-serine/D-alanine/glycine transporter (characterized) 34% 95% 265.8 lysine-specific permease 75% 748.0
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% 98% 221.1 lysine-specific permease 75% 748.0

Sequence Analysis Tools

View WP_039103680.1 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

MQNKLKRDLKARHLTMIAIGGSIGTGLFVASGATIAQAGPAGSLLSYAIIGVMVYFLMTS
LGELAAYLPVSGTFATYGSKYVDESFGFAIGWNYWYNWAITVAVDLVAAQLVISYWFDFG
AYSWLWSLLFLVIIFFLNVISVKGFGEAEFWFSLIKVITVVVFIAVGLLMIVGILHGGSD
TAIGWHNWNIGDAPFVGGFSSMIGVAMIVGFSFQGTELIGIAAGESKDPEKNIPKSMRQV
FWRILLFYIFAIFVISLIIPYTDPRLLRNDEADISVSPFTLVFEHAGLLSAAAIMNAVVL
TSVLSAGNSGLYASTRMLYALAKEGKAPKIFGRLSKSGIPTMSLIATTIVAMLCFLTSMF
KDQQVYLWLLNLSGMTGFIAWLGIAISHYRFRKGYIKQGYDVNKLPYRSSFFPFGPIFAF
ILCLLITLGQNYEAFLQDNIDWYGVLATYIGLPLFFFIMIIYKFIKKTKWVKYQDMDFSR
IDEN

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