GapMind for catabolism of small carbon sources

 

Protein WP_007692562.1 in Halococcus hamelinensis 100A6

Annotation: NCBI__GCF_000336675.1:WP_007692562.1

Length: 290 amino acids

Source: GCF_000336675.1 in NCBI

Candidate for 21 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
xylitol catabolism Dshi_0549 lo ABC transporter for Xylitol, permease component 2 (characterized) 32% 97% 155.2 Diacetylchitobiose uptake system permease protein NgcG 32% 163.3
trehalose catabolism thuG lo ABC-type transporter, integral membrane subunit, component of Trehalose porter. Also binds sucrose (Boucher and Noll, 2011). Induced by glucose and trehalose. Directly regulated by trehalose-responsive regulator TreR (characterized) 32% 95% 152.9 Diacetylchitobiose uptake system permease protein NgcG 32% 163.3
N-acetyl-D-glucosamine catabolism ngcG lo NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) 33% 85% 147.1 Diacetylchitobiose uptake system permease protein NgcG 32% 163.3
D-glucosamine (chitosamine) catabolism ngcG lo NgcG, component of N-Acetylglucosamine/N,N'-diacetyl chitobiose porter (NgcK (C) not identified) (characterized) 33% 85% 147.1 Diacetylchitobiose uptake system permease protein NgcG 32% 163.3
D-cellobiose catabolism msdB2 lo Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) 32% 91% 146.4 Diacetylchitobiose uptake system permease protein NgcG 32% 163.3
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) 32% 96% 143.7 Diacetylchitobiose uptake system permease protein NgcG 32% 163.3
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) 32% 96% 143.7 Diacetylchitobiose uptake system permease protein NgcG 32% 163.3
D-maltose catabolism thuG lo ABC transporter for D-Trehalose, permease component 2 (characterized) 33% 97% 143.3 Diacetylchitobiose uptake system permease protein NgcG 32% 163.3
sucrose catabolism thuG lo ABC transporter for D-Trehalose, permease component 2 (characterized) 33% 97% 143.3 Diacetylchitobiose uptake system permease protein NgcG 32% 163.3
N-acetyl-D-glucosamine catabolism SMc02871 lo N-Acetyl-D-glucosamine ABC transport system, permease component 2 (characterized) 30% 93% 125.9 Diacetylchitobiose uptake system permease protein NgcG 32% 163.3
D-glucosamine (chitosamine) catabolism SMc02871 lo N-Acetyl-D-glucosamine ABC transport system, permease component 2 (characterized) 30% 93% 125.9 Diacetylchitobiose uptake system permease protein NgcG 32% 163.3
D-cellobiose catabolism msdC2 lo Binding-protein-dependent transport systems inner membrane component (characterized, see rationale) 31% 91% 116.3 Diacetylchitobiose uptake system permease protein NgcG 32% 163.3
D-cellobiose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 33% 57% 111.3 Diacetylchitobiose uptake system permease protein NgcG 32% 163.3
D-glucose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 33% 57% 111.3 Diacetylchitobiose uptake system permease protein NgcG 32% 163.3
lactose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 33% 57% 111.3 Diacetylchitobiose uptake system permease protein NgcG 32% 163.3
D-maltose catabolism aglG lo Inner membrane ABC transporter permease protein (characterized, see rationale) 33% 57% 111.3 Diacetylchitobiose uptake system permease protein NgcG 32% 163.3
D-maltose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 33% 57% 111.3 Diacetylchitobiose uptake system permease protein NgcG 32% 163.3
sucrose catabolism aglG lo Inner membrane ABC transporter permease protein (characterized, see rationale) 33% 57% 111.3 Diacetylchitobiose uptake system permease protein NgcG 32% 163.3
sucrose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 33% 57% 111.3 Diacetylchitobiose uptake system permease protein NgcG 32% 163.3
trehalose catabolism aglG lo Inner membrane ABC transporter permease protein (characterized, see rationale) 33% 57% 111.3 Diacetylchitobiose uptake system permease protein NgcG 32% 163.3
trehalose catabolism aglG' lo Inner membrane ABC transporter permease protein (characterized, see rationale) 33% 57% 111.3 Diacetylchitobiose uptake system permease protein NgcG 32% 163.3

Sequence Analysis Tools

View WP_007692562.1 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

MATETETGGESNGWRGRLDADLAARYTILLVTSALVAFPLLWMVSTALKTGSDLTAFPPT
LVPENPSLEPTIEALTTGPWAQWFLNTFLVVIGAVILELVVAVPAAYALARREFLGDRLV
YVSIVAFLMIPPQILVLPIFIQFAQLQLLETFVGLIVAYTLLFSAFVTFLLSGFFQTLPS
DVEDAARIAGIPEWKIFVRIVLPLAKPAIGIAAIFVFIFAWNEFFWALVFLNEQEMYTIS
IGLTIFEGTQGQIAMNRLMAMSVLTTIPVLVLFALTQERFIQGITTGYEF

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