GapMind for catabolism of small carbon sources

 

Protein WP_017867705.1 in Lactobacillus pobuzihii E100301

Annotation: NCBI__GCF_000349725.1:WP_017867705.1

Length: 461 amino acids

Source: GCF_000349725.1 in NCBI

Candidate for 24 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arabinose catabolism araE hi Arabinose/xylose transporter, AraE (characterized) 68% 95% 619.4 D-xylose transporter; D-xylose-proton symporter 41% 342.0
D-xylose catabolism xylT hi Arabinose/xylose transporter, AraE (characterized) 68% 95% 619.4 Probable metabolite transport protein CsbC 40% 330.1
D-cellobiose catabolism MFS-glucose lo The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) (characterized) 37% 86% 310.1 Arabinose/xylose transporter, AraE 68% 619.4
D-glucose catabolism MFS-glucose lo The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) (characterized) 37% 86% 310.1 Arabinose/xylose transporter, AraE 68% 619.4
lactose catabolism MFS-glucose lo The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) (characterized) 37% 86% 310.1 Arabinose/xylose transporter, AraE 68% 619.4
D-maltose catabolism MFS-glucose lo The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) (characterized) 37% 86% 310.1 Arabinose/xylose transporter, AraE 68% 619.4
sucrose catabolism MFS-glucose lo The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) (characterized) 37% 86% 310.1 Arabinose/xylose transporter, AraE 68% 619.4
trehalose catabolism MFS-glucose lo The D-glucose:H+ symporter, GlcP (glucose uptake is inhibited by 2-deoxyglucose, mannose and galactose) (characterized) 37% 86% 310.1 Arabinose/xylose transporter, AraE 68% 619.4
myo-inositol catabolism iolT lo Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized) 35% 90% 283.1 Arabinose/xylose transporter, AraE 68% 619.4
D-galactose catabolism galP lo Galactose-proton symporter; Galactose transporter (characterized) 34% 98% 251.9 Arabinose/xylose transporter, AraE 68% 619.4
D-fructose catabolism glcP lo D-fructose transporter, sugar porter family (characterized) 31% 93% 239.6 Arabinose/xylose transporter, AraE 68% 619.4
sucrose catabolism glcP lo D-fructose transporter, sugar porter family (characterized) 31% 93% 239.6 Arabinose/xylose transporter, AraE 68% 619.4
glycerol catabolism PLT5 lo polyol transporter 5 (characterized) 31% 85% 225.3 Arabinose/xylose transporter, AraE 68% 619.4
D-mannitol catabolism PLT5 lo polyol transporter 5 (characterized) 31% 85% 225.3 Arabinose/xylose transporter, AraE 68% 619.4
D-ribose catabolism PLT5 lo polyol transporter 5 (characterized) 31% 85% 225.3 Arabinose/xylose transporter, AraE 68% 619.4
D-sorbitol (glucitol) catabolism SOT lo polyol transporter 5 (characterized) 31% 85% 225.3 Arabinose/xylose transporter, AraE 68% 619.4
xylitol catabolism PLT5 lo polyol transporter 5 (characterized) 31% 85% 225.3 Arabinose/xylose transporter, AraE 68% 619.4
D-fructose catabolism Slc2a5 lo The fructose/xylose:H+ symporter, PMT1 (polyol monosaccharide transporter-1). Also transports other substrates at lower rates. PMT2 is largely of the same sequence and function. Both are present in pollen and young xylem cells (Klepek et al., 2005). A similar ortholog has been identifed in pollen grains of Petunia hybrida (characterized) 31% 91% 217.2 Arabinose/xylose transporter, AraE 68% 619.4
sucrose catabolism Slc2a5 lo The fructose/xylose:H+ symporter, PMT1 (polyol monosaccharide transporter-1). Also transports other substrates at lower rates. PMT2 is largely of the same sequence and function. Both are present in pollen and young xylem cells (Klepek et al., 2005). A similar ortholog has been identifed in pollen grains of Petunia hybrida (characterized) 31% 91% 217.2 Arabinose/xylose transporter, AraE 68% 619.4
D-mannose catabolism STP6 lo The high affinity sugar:H+ symporter (sugar uptake) porter of 514 aas and 12 TMSs, STP10. It transports glucose, galactose and mannose, and is therefore a hexose transporter (Rottmann et al. 2016). The 2.4 (characterized) 31% 90% 216.5 Arabinose/xylose transporter, AraE 68% 619.4
D-galacturonate catabolism gatA lo The galacturonic acid (galacturonate) uptake porter, GatA, of 518 aas and 12 TMSs (characterized) 30% 88% 207.6 Arabinose/xylose transporter, AraE 68% 619.4
D-fructose catabolism STP6 lo sugar transport protein 6 (characterized) 30% 93% 203.8 Arabinose/xylose transporter, AraE 68% 619.4
sucrose catabolism STP6 lo sugar transport protein 6 (characterized) 30% 93% 203.8 Arabinose/xylose transporter, AraE 68% 619.4
myo-inositol catabolism HMIT lo Probable inositol transporter 2 (characterized) 33% 58% 189.9 Arabinose/xylose transporter, AraE 68% 619.4

Sequence Analysis Tools

View WP_017867705.1 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

MAQEKKISSKFIYFFGSFGGILFGYDIGVMTGALPFLKNDWNLTNASVIGWITSAVMFGA
IFGGAFAGQLSDKYGRRKMILVSAVIFAIFSLLSMVSPENGSTYLIIIRMLLGLAVGAAS
ALVPAYMSEMAPANARGSLSGLNQTMITLGMLLSYVMDFVLKDLPQAWGWRVMLGCAAIP
AVILLAGVMKLPESPRFLINHGKPDEARKVLSYIRKDKSEIDSEMQSIRDTSKQESSAAK
KTSWGTLFTGKYRYLVMAGVGVATFQQFQGANAIFYYIPLIIEDVTGKAADSALVWPVIQ
GVILVLGSLLYIAIAEKVKRRTLLLMGGTVMGLSFILPAILNAMIDNLNPFTTVVFLFIY
VAFYSFTWAPLTWVIVGEMFPLAIRGRASGLASSMNWVGSWAVGLIFPIMTAAMSQEIVF
AIFGVICLAGVLFVRYCVPETKGRTLEEIEEAGMNHSKNKD

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