GapMind for catabolism of small carbon sources

 

Protein WP_017471434.1 in Amphibacillus jilinensis Y1

Annotation: NCBI__GCF_000306965.1:WP_017471434.1

Length: 463 amino acids

Source: GCF_000306965.1 in NCBI

Candidate for 12 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-fructose catabolism fruA hi Fructose phosphotransferase system, IIB/IIC components (characterized, see rationale) 47% 80% 425.6 The fructose porter, FruA (fructose-1-P forming IIABC) (Delobbe et al. 1975) FruA is 39% identical to 4.A.2.1.1). fructose can be metabolized to Fru-1-P via this system as well as Fru-6-P by another PTS system 46% 410.2
sucrose catabolism fruA hi Fructose phosphotransferase system, IIB/IIC components (characterized, see rationale) 47% 80% 425.6 The fructose porter, FruA (fructose-1-P forming IIABC) (Delobbe et al. 1975) FruA is 39% identical to 4.A.2.1.1). fructose can be metabolized to Fru-1-P via this system as well as Fru-6-P by another PTS system 46% 410.2
D-fructose catabolism fruII-ABC med The fructose porter, FruA (fructose-1-P forming IIABC) (Delobbe et al. 1975) FruA is 39% identical to 4.A.2.1.1). fructose can be metabolized to Fru-1-P via this system as well as Fru-6-P by another PTS system (characterized) 46% 73% 410.2 Fructose PTS Enzyme IIBC, FruA 48% 431.8
sucrose catabolism fruII-ABC med The fructose porter, FruA (fructose-1-P forming IIABC) (Delobbe et al. 1975) FruA is 39% identical to 4.A.2.1.1). fructose can be metabolized to Fru-1-P via this system as well as Fru-6-P by another PTS system (characterized) 46% 73% 410.2 Fructose PTS Enzyme IIBC, FruA 48% 431.8
D-fructose catabolism fruII-C med PTS system fructose-specific EIIC component; EIIC-Fru; Fructose permease IIC (characterized) 41% 96% 251.1 Fructose PTS Enzyme IIBC, FruA 48% 431.8
sucrose catabolism fruII-C med PTS system fructose-specific EIIC component; EIIC-Fru; Fructose permease IIC (characterized) 41% 96% 251.1 Fructose PTS Enzyme IIBC, FruA 48% 431.8
D-ribose catabolism fru2-IIB med PTS system, fructose-specific, IIB component, component of D-allose/D-ribose transporting Enzyme II complex (Fru2; IIA/IIB/IIC) (Patron et al. 2017). This system is similar to Frz of E. coli (TC#4.A.2.1.9) which is involved in environmental sensing, host adaptation and virulence (characterized) 54% 96% 97.4 Fructose PTS Enzyme IIBC, FruA 48% 431.8
D-fructose catabolism fruII-B med PTS system, fructose-specific, IIB subunnit, component of Fructose Enzyme II complex (IIAFru - IIBFru - IICFru) (based on homology) (characterized) 41% 80% 90.1 Fructose PTS Enzyme IIBC, FruA 48% 431.8
sucrose catabolism fruII-B med PTS system, fructose-specific, IIB subunnit, component of Fructose Enzyme II complex (IIAFru - IIBFru - IICFru) (based on homology) (characterized) 41% 80% 90.1 Fructose PTS Enzyme IIBC, FruA 48% 431.8
D-mannose catabolism manP lo protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized) 40% 71% 350.1 Fructose PTS Enzyme IIBC, FruA 48% 431.8
xylitol catabolism fruI lo The fructose inducible fructose/xylitol porter, FruI (characterized) 38% 74% 310.8 Fructose PTS Enzyme IIBC, FruA 48% 431.8
D-ribose catabolism fru2-IIC lo PTS system, fructose-specific, IIC component, component of D-allose/D-ribose transporting Enzyme II complex (Fru2; IIA/IIB/IIC) (Patron et al. 2017). This system is similar to Frz of E. coli (TC#4.A.2.1.9) which is involved in environmental sensing, host adaptation and virulence (characterized) 33% 93% 199.9 Fructose PTS Enzyme IIBC, FruA 48% 431.8

Sequence Analysis Tools

View WP_017471434.1 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

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Sequence

MKIIGVTACPTGIAHTYMAAEKLQKAAEAEGHQVKIETQGAKTENVLTEQEIKEADVVIL
AVDKGIDLSRFAGKTIKKVSTSKAIKDPITILEEAIRGEGTFQSSKDTEENSSVSSHKKG
LYSHFMNGVNYMLPFVIAGGILIAISFAFGIEASDPDSGKYNVIAGALSQIGGGTAFALM
VPALAAGIASSIAGRAGFAPGLIAGTLAAAGGSGFLGGMIGGILAGYVTDFTATKIHVKQ
SISAIFQLIVVPLISITIVGMAMVFLIDTPISWVLNGLTEFLNGLGETSGLMFGLLIGVM
MAADMGGPINKAISTFSIGLMSAGVNAPIAACMMAGMTPPLGLALATVIFKNKFTLEEKT
SGKSCWVLGASYITEGAIPFAVADPIRVIPSLMVGSAVAASISMAAGVTSMAPHGGVWVM
FIPNVINNLPMYLLALVVGTLVTAVMIGLLKKPIKQEALTNTI

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