GapMind for catabolism of small carbon sources

 

Protein WP_013402619.1 in Caldicellulosiruptor hydrothermalis 108

Annotation: NCBI__GCF_000166355.1:WP_013402619.1

Length: 328 amino acids

Source: GCF_000166355.1 in NCBI

Candidate for 27 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-fucose catabolism HSERO_RS05255 hi ABC-type sugar transport system, permease component protein (characterized, see rationale) 62% 93% 398.7 Ribose import permease protein RbsC 39% 236.1
xylitol catabolism PS417_12060 med ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale) 41% 90% 240 Ribose import permease protein RbsC 39% 236.1
D-fructose catabolism frcC med Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 42% 91% 237.7 Ribose import permease protein RbsC 39% 236.1
sucrose catabolism frcC med Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 42% 91% 237.7 Ribose import permease protein RbsC 39% 236.1
D-ribose catabolism rbsC med Ribose import permease protein RbsC (characterized) 39% 98% 236.1 Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR 41% 235.3
D-cellobiose catabolism mglC med Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 41% 97% 235.3 Ribose import permease protein RbsC 39% 236.1
D-glucose catabolism mglC med Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 41% 97% 235.3 Ribose import permease protein RbsC 39% 236.1
lactose catabolism mglC med Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 41% 97% 235.3 Ribose import permease protein RbsC 39% 236.1
D-maltose catabolism mglC med Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 41% 97% 235.3 Ribose import permease protein RbsC 39% 236.1
sucrose catabolism mglC med Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 41% 97% 235.3 Ribose import permease protein RbsC 39% 236.1
trehalose catabolism mglC med Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 41% 97% 235.3 Ribose import permease protein RbsC 39% 236.1
D-xylose catabolism xylH med Putative beta-xyloside ABC transporter, permease component, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized) 41% 97% 235.3 Ribose import permease protein RbsC 39% 236.1
D-xylose catabolism xylF_Tm med ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized) 41% 97% 229.2 Ribose import permease protein RbsC 39% 236.1
myo-inositol catabolism PS417_11895 med Inositol transport system permease protein (characterized) 40% 90% 226.5 Ribose import permease protein RbsC 39% 236.1
D-mannose catabolism HSERO_RS03645 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 40% 87% 218 Ribose import permease protein RbsC 39% 236.1
L-arabinose catabolism araH lo L-arabinose ABC transporter, permease protein AraH (characterized) 39% 91% 205.3 Ribose import permease protein RbsC 39% 236.1
D-mannose catabolism frcC lo Fructose import permease protein FrcC (characterized) 35% 88% 194.9 Ribose import permease protein RbsC 39% 236.1
D-ribose catabolism frcC lo Fructose import permease protein FrcC (characterized) 35% 88% 194.9 Ribose import permease protein RbsC 39% 236.1
D-galactose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 37% 94% 184.1 Ribose import permease protein RbsC 39% 236.1
L-rhamnose catabolism rhaQ lo RhaQ (characterized, see rationale) 33% 91% 177.6 Ribose import permease protein RbsC 39% 236.1
D-galactose catabolism ytfT lo Galactofuranose transporter permease protein YtfT (characterized) 34% 91% 164.1 Ribose import permease protein RbsC 39% 236.1
D-fructose catabolism fruG lo Fructose import permease protein FruG (characterized) 31% 93% 156.8 Ribose import permease protein RbsC 39% 236.1
sucrose catabolism fruG lo Fructose import permease protein FruG (characterized) 31% 93% 156.8 Ribose import permease protein RbsC 39% 236.1
L-arabinose catabolism araZsh lo Inner-membrane translocator (characterized, see rationale) 36% 94% 156.4 Ribose import permease protein RbsC 39% 236.1
D-fructose catabolism fruF lo Fructose import permease protein FruF (characterized) 34% 74% 146 Ribose import permease protein RbsC 39% 236.1
sucrose catabolism fruF lo Fructose import permease protein FruF (characterized) 34% 74% 146 Ribose import permease protein RbsC 39% 236.1
D-galactose catabolism yjtF lo Inner membrane ABC transporter permease protein YjfF (characterized) 31% 91% 136.3 Ribose import permease protein RbsC 39% 236.1

Sequence Analysis Tools

View WP_013402619.1 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

METTQKFRGFRKEALRQLLMFGSLFLLFVFFSLASPNFCTFENIISIILATCVNGMLALG
VTFVIITSGIDLSIGTVMTLSAVMSGVFITYWHLPVWLGVLGGIGTGMLCGFVNGIVISK
MKLPPFIATLGMMMIAKGLALVISGATPIYYTDAPSFSDIAMGSIIGKIIPGADIPNAIL
IFILFAIIANIILTKTAIGRYDFAIGSNEEAARLSGLNVDRWKIIIYMLCGFFVGIGGIL
MASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGEGSIIGTVIGALIMSTLTNGLRILSV
PQEWQIVISGIIVIGAVYLDIIRRRRTK

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