GapMind for catabolism of small carbon sources

 

Protein WP_004124101.1 in Rhizobium freirei PRF 81

Annotation: NCBI__GCF_000359745.1:WP_004124101.1

Length: 334 amino acids

Source: GCF_000359745.1 in NCBI

Candidate for 24 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
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) 54% 94% 334.3 Ribose import permease protein RbsC 50% 298.5
D-ribose catabolism rbsC med Ribose import permease protein RbsC (characterized) 50% 95% 298.5 RbsC, component of The probable autoinducer-2 (AI-2;, a furanosyl borate diester: 3aS,6S,6aR)-2,2,6,6a-tetrahydroxy-3a-methyltetrahydrofuro[3,2-d][1,3,2]dioxaborolan-2-uide) uptake porter (Shao et al., 2007) (50-70% identical to RbsABC of E. coli; TC# 3.A.1.2.1) 48% 291.2
myo-inositol catabolism PS417_11895 med Inositol transport system permease protein (characterized) 43% 98% 259.6 Ribose import permease protein RbsC 50% 298.5
myo-inositol catabolism iatP med 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) 46% 91% 255.4 Ribose import permease protein RbsC 50% 298.5
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% 96% 240.4 Ribose import permease protein RbsC 50% 298.5
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% 96% 240.4 Ribose import permease protein RbsC 50% 298.5
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% 96% 240.4 Ribose import permease protein RbsC 50% 298.5
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% 96% 240.4 Ribose import permease protein RbsC 50% 298.5
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% 96% 240.4 Ribose import permease protein RbsC 50% 298.5
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% 96% 240.4 Ribose import permease protein RbsC 50% 298.5
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% 96% 240.4 Ribose import permease protein RbsC 50% 298.5
D-fructose catabolism frcC med Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 45% 93% 238.8 Ribose import permease protein RbsC 50% 298.5
sucrose catabolism frcC med Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 45% 93% 238.8 Ribose import permease protein RbsC 50% 298.5
D-mannose catabolism HSERO_RS03645 med ABC-type sugar transport system, permease component protein (characterized, see rationale) 46% 86% 232.6 Ribose import permease protein RbsC 50% 298.5
L-fucose catabolism HSERO_RS05255 med ABC-type sugar transport system, permease component protein (characterized, see rationale) 41% 89% 228 Ribose import permease protein RbsC 50% 298.5
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% 98% 223 Ribose import permease protein RbsC 50% 298.5
D-galactose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 37% 95% 208.8 Ribose import permease protein RbsC 50% 298.5
L-rhamnose catabolism rhaP lo RhaP, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized) 38% 94% 198.7 Ribose import permease protein RbsC 50% 298.5
D-mannose catabolism frcC lo Fructose import permease protein FrcC (characterized) 37% 84% 192.2 Ribose import permease protein RbsC 50% 298.5
D-ribose catabolism frcC lo Fructose import permease protein FrcC (characterized) 37% 84% 192.2 Ribose import permease protein RbsC 50% 298.5
D-galactose catabolism yjtF lo Inner membrane ABC transporter permease protein YjfF (characterized) 36% 90% 173.7 Ribose import permease protein RbsC 50% 298.5
L-arabinose catabolism araZsh lo Inner-membrane translocator (characterized, see rationale) 32% 94% 161 Ribose import permease protein RbsC 50% 298.5
L-rhamnose catabolism rhaQ lo RhaQ (characterized, see rationale) 30% 91% 160.6 Ribose import permease protein RbsC 50% 298.5
L-arabinose catabolism xylHsa lo Xylose/arabinose import permease protein XylH (characterized, see rationale) 31% 84% 147.5 Ribose import permease protein RbsC 50% 298.5

Sequence Analysis Tools

View WP_004124101.1 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

MSATDNHQSNSWFGSDRRRLIIQEYGIFLAFLLLAIVLSFSNEYFLTAGNISNVLLQTSI
NGVLAIGMTFVILTRGIDLSVGSVVALTGIVSASFATTSATAGIVGAPYPPYVALAVGLL
VGVACGAVVGLIVSRFAVPAFVATLGMLSAARGMTLIYGGGKPVPALTPDFRWIGTGSVL
SIPMPVILLAIVFIVAWWVLNRTRFGRYIYAVGGNPHAATTSGIDVSKLRFLVYVISGGL
SGLAGMILAARTGSALPQAGIAYELDAIAAVVIGGTSLSGGVGRITGTLIGALIIGVMNN
GLDLMGIQSYYQQVLKGTLIVGAVMLDQKRNLGG

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