GapMind for catabolism of small carbon sources

 

Protein WP_047007739.1 in Erythrobacter gangjinensis K7-2

Annotation: NCBI__GCF_001010925.1:WP_047007739.1

Length: 239 amino acids

Source: GCF_001010925.1 in NCBI

Candidate for 29 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-lysine catabolism hisP lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 38% 88% 146.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 41% 182.6
L-proline catabolism opuBA lo BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) 34% 50% 135.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 41% 182.6
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 37% 85% 134.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 41% 182.6
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 37% 85% 134.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 41% 182.6
L-glutamate catabolism gltL lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 37% 85% 134.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 41% 182.6
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 63% 131.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 41% 182.6
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 63% 131.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 41% 182.6
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 63% 131.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 41% 182.6
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 63% 131.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 41% 182.6
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 63% 131.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 41% 182.6
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 63% 131.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 41% 182.6
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 63% 131.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 41% 182.6
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 63% 131.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 41% 182.6
D-cellobiose catabolism TM0027 lo TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 33% 88% 121.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 41% 182.6
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 36% 64% 119.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 41% 182.6
D-mannose catabolism TM1750 lo TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 33% 67% 118.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 41% 182.6
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 33% 58% 109.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 41% 182.6
D-cellobiose catabolism mglA lo glucose transporter, ATPase component (characterized) 33% 87% 105.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 41% 182.6
D-glucose catabolism mglA lo glucose transporter, ATPase component (characterized) 33% 87% 105.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 41% 182.6
lactose catabolism mglA lo glucose transporter, ATPase component (characterized) 33% 87% 105.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 41% 182.6
D-maltose catabolism mglA lo glucose transporter, ATPase component (characterized) 33% 87% 105.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 41% 182.6
sucrose catabolism mglA lo glucose transporter, ATPase component (characterized) 33% 87% 105.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 41% 182.6
trehalose catabolism mglA lo glucose transporter, ATPase component (characterized) 33% 87% 105.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 41% 182.6
D-fructose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 85% 101.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 41% 182.6
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 32% 56% 101.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 41% 182.6
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 85% 101.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 41% 182.6
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 85% 101.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 41% 182.6
sucrose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 85% 101.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 41% 182.6
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 31% 62% 101.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 41% 182.6

Sequence Analysis Tools

View WP_047007739.1 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

MSPTPDNNAAISVRGITRDFEAGQQTITVLHGIDTDIRAGELTYVVGESGSGKTTLISIM
CGILWPTEGEVQVFGTDIYSLSDTDLVEFRLNNIGFIFQQYNLIPSIDAASNASVPLIAQ
GMDRDEARERAVAIMDKLNIRDQAGKLPSQLSGGQQQRVAIARALVHEPRLVVCDEPTAA
LDASSGRRVMDLLREVAVAEDRACIIVTHDNRVFDLADRILVLEDGKITHDGKEMPEDH

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