GapMind for catabolism of small carbon sources

 

Protein WP_007664885.1 in Cronobacter condimenti 1330

Annotation: NCBI__GCF_000319285.1:WP_007664885.1

Length: 283 amino acids

Source: GCF_000319285.1 in NCBI

Candidate for 17 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-maltose catabolism malG_Bb lo ABC-type Maltose/ Maltodextrin permease (characterized, see rationale) 38% 100% 204.5 Putative arabinogalactan oligomer transport system permease protein ganQ, component of The galactooligosaccharide (transports the di, tri and tetrasaccharides) uptake porter GanOPQ (GanSPQ; MalEFG) functioning with the energizing ATPase MsmX (see 3.A.1.1.26) 66% 382.9
D-maltose catabolism malG_Aa lo Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) 36% 93% 200.7 Putative arabinogalactan oligomer transport system permease protein ganQ, component of The galactooligosaccharide (transports the di, tri and tetrasaccharides) uptake porter GanOPQ (GanSPQ; MalEFG) functioning with the energizing ATPase MsmX (see 3.A.1.1.26) 66% 382.9
D-maltose catabolism malG_Sm lo MalG, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 39% 100% 194.5 Putative arabinogalactan oligomer transport system permease protein ganQ, component of The galactooligosaccharide (transports the di, tri and tetrasaccharides) uptake porter GanOPQ (GanSPQ; MalEFG) functioning with the energizing ATPase MsmX (see 3.A.1.1.26) 66% 382.9
trehalose catabolism malG lo MalG, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 39% 100% 194.5 Putative arabinogalactan oligomer transport system permease protein ganQ, component of The galactooligosaccharide (transports the di, tri and tetrasaccharides) uptake porter GanOPQ (GanSPQ; MalEFG) functioning with the energizing ATPase MsmX (see 3.A.1.1.26) 66% 382.9
D-maltose catabolism malG lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 33% 100% 168.7 Putative arabinogalactan oligomer transport system permease protein ganQ, component of The galactooligosaccharide (transports the di, tri and tetrasaccharides) uptake porter GanOPQ (GanSPQ; MalEFG) functioning with the energizing ATPase MsmX (see 3.A.1.1.26) 66% 382.9
D-maltose catabolism thuG lo Putative maltose permease, component of MalEFG (K unknown), involved in maltose and maltodextrin uptake (characterized) 33% 86% 165.6 Putative arabinogalactan oligomer transport system permease protein ganQ, component of The galactooligosaccharide (transports the di, tri and tetrasaccharides) uptake porter GanOPQ (GanSPQ; MalEFG) functioning with the energizing ATPase MsmX (see 3.A.1.1.26) 66% 382.9
L-fucose catabolism SM_b21105 lo ABC transporter for L-Fucose, permease component 2 (characterized) 32% 95% 146 Putative arabinogalactan oligomer transport system permease protein ganQ, component of The galactooligosaccharide (transports the di, tri and tetrasaccharides) uptake porter GanOPQ (GanSPQ; MalEFG) functioning with the energizing ATPase MsmX (see 3.A.1.1.26) 66% 382.9
D-cellobiose catabolism gtsC lo ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized) 31% 95% 125.6 Putative arabinogalactan oligomer transport system permease protein ganQ, component of The galactooligosaccharide (transports the di, tri and tetrasaccharides) uptake porter GanOPQ (GanSPQ; MalEFG) functioning with the energizing ATPase MsmX (see 3.A.1.1.26) 66% 382.9
D-galactose catabolism PfGW456L13_1896 lo ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized) 31% 95% 125.6 Putative arabinogalactan oligomer transport system permease protein ganQ, component of The galactooligosaccharide (transports the di, tri and tetrasaccharides) uptake porter GanOPQ (GanSPQ; MalEFG) functioning with the energizing ATPase MsmX (see 3.A.1.1.26) 66% 382.9
D-glucose catabolism gtsC lo ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized) 31% 95% 125.6 Putative arabinogalactan oligomer transport system permease protein ganQ, component of The galactooligosaccharide (transports the di, tri and tetrasaccharides) uptake porter GanOPQ (GanSPQ; MalEFG) functioning with the energizing ATPase MsmX (see 3.A.1.1.26) 66% 382.9
lactose catabolism gtsC lo ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized) 31% 95% 125.6 Putative arabinogalactan oligomer transport system permease protein ganQ, component of The galactooligosaccharide (transports the di, tri and tetrasaccharides) uptake porter GanOPQ (GanSPQ; MalEFG) functioning with the energizing ATPase MsmX (see 3.A.1.1.26) 66% 382.9
D-maltose catabolism gtsC lo ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized) 31% 95% 125.6 Putative arabinogalactan oligomer transport system permease protein ganQ, component of The galactooligosaccharide (transports the di, tri and tetrasaccharides) uptake porter GanOPQ (GanSPQ; MalEFG) functioning with the energizing ATPase MsmX (see 3.A.1.1.26) 66% 382.9
sucrose catabolism gtsC lo ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized) 31% 95% 125.6 Putative arabinogalactan oligomer transport system permease protein ganQ, component of The galactooligosaccharide (transports the di, tri and tetrasaccharides) uptake porter GanOPQ (GanSPQ; MalEFG) functioning with the energizing ATPase MsmX (see 3.A.1.1.26) 66% 382.9
trehalose catabolism gtsC lo ABC transporter for D-Galactose and D-Glucose, permease component 2 (characterized) 31% 95% 125.6 Putative arabinogalactan oligomer transport system permease protein ganQ, component of The galactooligosaccharide (transports the di, tri and tetrasaccharides) uptake porter GanOPQ (GanSPQ; MalEFG) functioning with the energizing ATPase MsmX (see 3.A.1.1.26) 66% 382.9
D-mannose catabolism TT_C0326 lo Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized) 34% 77% 123.6 Putative arabinogalactan oligomer transport system permease protein ganQ, component of The galactooligosaccharide (transports the di, tri and tetrasaccharides) uptake porter GanOPQ (GanSPQ; MalEFG) functioning with the energizing ATPase MsmX (see 3.A.1.1.26) 66% 382.9
D-xylose catabolism gtsC lo ABC transporter for D-Glucose-6-Phosphate, permease component 1 (characterized) 31% 97% 120.6 Putative arabinogalactan oligomer transport system permease protein ganQ, component of The galactooligosaccharide (transports the di, tri and tetrasaccharides) uptake porter GanOPQ (GanSPQ; MalEFG) functioning with the energizing ATPase MsmX (see 3.A.1.1.26) 66% 382.9
xylitol catabolism Dshi_0549 lo ABC transporter for Xylitol, permease component 2 (characterized) 31% 96% 119.4 Putative arabinogalactan oligomer transport system permease protein ganQ, component of The galactooligosaccharide (transports the di, tri and tetrasaccharides) uptake porter GanOPQ (GanSPQ; MalEFG) functioning with the energizing ATPase MsmX (see 3.A.1.1.26) 66% 382.9

Sequence Analysis Tools

View WP_007664885.1 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

MAKRQSMKQEKWLRLSLSWLVILTVSVIIIYPLIWTIGASLNAGNSLLSSSIIPENLSFQ
HYADLFNGQVNYVTWYWNSMKISFMTMVLTLISVSFTAYAFSRFRFKGRQNGLMLFLLLQ
MIPQFSALIAIFVLSQLLGLINSHLALVLIYVAGMIPMNTYLMKGYLDAIPKDLDESARM
DGASNFRIFIEIIMPLSKPIVAVVALFSFTGPLGDFILSSTILRTPDKYTLPIGLYNLVA
QKMGASYTTYAAGAVLIAVPVAILYLALQKYFVSGLTSGSTKG

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