GapMind for catabolism of small carbon sources

 

Protein Pf1N1B4_409 in Pseudomonas fluorescens FW300-N1B4

Annotation: FitnessBrowser__pseudo1_N1B4:Pf1N1B4_409

Length: 322 amino acids

Source: pseudo1_N1B4 in FitnessBrowser

Candidate for 23 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-galactose catabolism BPHYT_RS16925 hi Arabinose ABC transporter permease (characterized, see rationale) 97% 100% 605.9 L-arabinose ABC transporter, permease protein AraH 59% 382.5
L-arabinose catabolism araH hi L-arabinose ABC transporter, permease protein AraH (characterized) 59% 98% 382.5 Ribose import permease protein RbsC 36% 211.8
D-ribose catabolism rbsC lo Ribose import permease protein RbsC (characterized) 36% 97% 211.8 L-arabinose ABC transporter, permease protein AraH 59% 382.5
xylitol catabolism PS417_12060 lo ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale) 34% 100% 199.9 L-arabinose ABC transporter, permease protein AraH 59% 382.5
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) 35% 94% 194.1 L-arabinose ABC transporter, permease protein AraH 59% 382.5
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) 35% 98% 191.8 L-arabinose ABC transporter, permease protein AraH 59% 382.5
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) 35% 98% 191.8 L-arabinose ABC transporter, permease protein AraH 59% 382.5
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) 35% 98% 191.8 L-arabinose ABC transporter, permease protein AraH 59% 382.5
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) 35% 98% 191.8 L-arabinose ABC transporter, permease protein AraH 59% 382.5
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) 35% 98% 191.8 L-arabinose ABC transporter, permease protein AraH 59% 382.5
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) 35% 98% 191.8 L-arabinose ABC transporter, permease protein AraH 59% 382.5
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) 35% 98% 191.8 L-arabinose ABC transporter, permease protein AraH 59% 382.5
myo-inositol catabolism PS417_11895 lo m-Inositol ABC transporter, permease component (iatP) (characterized) 32% 97% 179.5 L-arabinose ABC transporter, permease protein AraH 59% 382.5
D-fructose catabolism frcC lo Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 33% 88% 175.3 L-arabinose ABC transporter, permease protein AraH 59% 382.5
sucrose catabolism frcC lo Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 33% 88% 175.3 L-arabinose ABC transporter, permease protein AraH 59% 382.5
D-mannose catabolism HSERO_RS03645 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 33% 82% 172.6 L-arabinose ABC transporter, permease protein AraH 59% 382.5
D-galactose catabolism mglC lo MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized) 35% 94% 167.9 L-arabinose ABC transporter, permease protein AraH 59% 382.5
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) 32% 93% 161 L-arabinose ABC transporter, permease protein AraH 59% 382.5
L-rhamnose catabolism rhaQ lo RhaQ (characterized, see rationale) 30% 96% 159.1 L-arabinose ABC transporter, permease protein AraH 59% 382.5
L-fucose catabolism BPHYT_RS34240 lo Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) 30% 92% 154.5 L-arabinose ABC transporter, permease protein AraH 59% 382.5
L-rhamnose catabolism BPHYT_RS34240 lo Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) 30% 92% 154.5 L-arabinose ABC transporter, permease protein AraH 59% 382.5
D-mannose catabolism frcC lo Fructose import permease protein FrcC (characterized) 31% 85% 139.8 L-arabinose ABC transporter, permease protein AraH 59% 382.5
D-ribose catabolism frcC lo Fructose import permease protein FrcC (characterized) 31% 85% 139.8 L-arabinose ABC transporter, permease protein AraH 59% 382.5

Sequence Analysis Tools

View Pf1N1B4_409 at FitnessBrowser

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

MTVQNKALPTPRKPLDLRRFLDDWVMLLAAVGIFVLCTLLIDNFLSPLNMRGLGLAISTT
GIAACTMLYCLASGHFDLSVGSVIACAGVVAAVVMRDTDSVFLGVSAALVMGLIVGLING
IVIAKLRVNALITTLATMQIVRGLAYIFANGKAVGVSQEQFFVFGNGQLFGVPVPILITI
VCFLFFGWLLNYTTYGRNTMAIGGNQEAALLAGVNVDRTKTLIFAVHGVIGALAGVILAS
RMTSGQPMIGQGFELTVISACVLGGVSLSGGIGMIRHVIAGVLILAIIENAMNLKNIDTF
YQYVIRGSILLLAVVIDRLKQR

This GapMind analysis is from Sep 17 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