GapMind for catabolism of small carbon sources

 

Protein WP_102106217.1 in Halioglobus japonicus S1-36

Annotation: NCBI__GCF_002869505.1:WP_102106217.1

Length: 322 amino acids

Source: GCF_002869505.1 in NCBI

Candidate for 28 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-ribose catabolism rbsC hi ABC-type sugar transport system, permease component protein (characterized, see rationale) 58% 91% 346.7 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 36% 198.7
xylitol catabolism PS417_12060 hi ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale) 43% 94% 221.1 ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 40% 206.8
L-fucose catabolism HSERO_RS05255 med ABC-type sugar transport system, permease component protein (characterized, see rationale) 38% 87% 227.3 ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 40% 206.8
D-fructose catabolism frcC med Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 44% 91% 210.3 ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 40% 206.8
sucrose catabolism frcC med Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 44% 91% 210.3 ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 40% 206.8
D-mannose catabolism HSERO_RS03645 med ABC-type sugar transport system, permease component protein (characterized, see rationale) 42% 90% 190.7 ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 40% 206.8
D-cellobiose catabolism mglC lo 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) 36% 98% 198.7 ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 40% 206.8
D-glucose catabolism mglC lo 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) 36% 98% 198.7 ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 40% 206.8
lactose catabolism mglC lo 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) 36% 98% 198.7 ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 40% 206.8
D-maltose catabolism mglC lo 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) 36% 98% 198.7 ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 40% 206.8
sucrose catabolism mglC lo 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) 36% 98% 198.7 ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 40% 206.8
trehalose catabolism mglC lo 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) 36% 98% 198.7 ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 40% 206.8
D-xylose catabolism xylH lo 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) 36% 98% 198.7 ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 40% 206.8
myo-inositol catabolism PS417_11895 lo Inositol transport system permease protein (characterized) 37% 93% 183.7 ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 40% 206.8
D-mannose catabolism frcC lo Fructose import permease protein FrcC (characterized) 33% 85% 183.3 ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 40% 206.8
D-ribose catabolism frcC lo Fructose import permease protein FrcC (characterized) 33% 85% 183.3 ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 40% 206.8
myo-inositol catabolism iatP lo Inositol ABC transport system, permease protein IatP, component of The myoinositol (high affinity)/ D-ribose (low affinity) transporter IatP/IatA/IbpA. The structure of IbpA with myoinositol bound has been solved (characterized) 37% 90% 179.1 ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 40% 206.8
L-arabinose catabolism araH lo L-arabinose ABC transporter, permease protein AraH (characterized) 32% 92% 173.3 ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 40% 206.8
D-xylose catabolism xylF_Tm lo ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized) 34% 98% 170.6 ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 40% 206.8
D-galactose catabolism BPHYT_RS16925 lo Monosaccharide-transporting ATPase; EC 3.6.3.17 (characterized, see rationale) 32% 90% 163.7 ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 40% 206.8
D-fructose catabolism fruF lo Fructose import permease protein FruF (characterized) 33% 92% 157.5 ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 40% 206.8
sucrose catabolism fruF lo Fructose import permease protein FruF (characterized) 33% 92% 157.5 ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 40% 206.8
D-galactose catabolism ytfT lo Galactofuranose transporter permease protein YtfT (characterized) 34% 91% 152.9 ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 40% 206.8
L-arabinose catabolism araWsh lo Inner-membrane translocator (characterized, see rationale) 33% 77% 149.4 ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 40% 206.8
D-galactose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 31% 94% 148.3 ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 40% 206.8
D-galactose catabolism yjtF lo Inner membrane ABC transporter permease protein YjfF (characterized) 36% 85% 140.6 ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 40% 206.8
2'-deoxyinosine catabolism H281DRAFT_01112 lo deoxynucleoside transporter, permease component 2 (characterized) 31% 84% 135.2 ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 40% 206.8
L-arabinose catabolism araZsh lo Inner-membrane translocator (characterized, see rationale) 32% 93% 134.4 ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 40% 206.8

Sequence Analysis Tools

View WP_102106217.1 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

MLKIKLPWNSLGLIAVLLALVLFFSLASEYFFTGVTFRTLVNQIPTLTVIAVGMTYVLLI
AGIDLSVGSVMALCSAVMGIVIADMGMPLPVAIAAALASGLMAGLVNGLISARWAIPSFV
VTLGMLEIARGGAYLVTNSETRYLGSSVEIIGSPLAGLGVSPALIFAVVVVVVAQFVLSK
TVFGRYMIAIGTNEEAVRLTGINPVPWKILVFALCGLLAGLGGVFQLGYLQTADPNAGIG
LELSAIAAVVIGGTSLTGGRGSVVNTFIGVLIIAVIQTGLAQMGVSEPSKRIITGAVIIA
AVLFDQFRDPMSHRLRTILLRR

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