GapMind for catabolism of small carbon sources

 

Protein Pf1N1B4_409 in Pseudomonas fluorescens FW300-N1B4

Annotation: L-arabinose transport system permease protein (TC 3.A.1.2.2)

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

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices: TMHMM

Check the SEED with FIGfam search

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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