GapMind for catabolism of small carbon sources

 

Protein GFF3462 in Pseudomonas simiae WCS417

Annotation: PS417_17725 ribose ABC transporter permease

Length: 330 amino acids

Source: WCS417 in FitnessBrowser

Candidate for 26 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 med ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale) 47% 98% 277.3 Ribose import permease protein RbsC 47% 275.0
D-ribose catabolism rbsC med Ribose import permease protein RbsC (characterized) 47% 93% 275 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) 49% 273.5
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) 42% 95% 238.8 Ribose import permease protein RbsC 47% 275.0
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) 42% 95% 238.8 Ribose import permease protein RbsC 47% 275.0
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) 42% 95% 238.8 Ribose import permease protein RbsC 47% 275.0
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) 42% 95% 238.8 Ribose import permease protein RbsC 47% 275.0
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) 42% 95% 238.8 Ribose import permease protein RbsC 47% 275.0
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) 42% 95% 238.8 Ribose import permease protein RbsC 47% 275.0
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) 42% 95% 238.8 Ribose import permease protein RbsC 47% 275.0
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) 43% 94% 228 Ribose import permease protein RbsC 47% 275.0
myo-inositol catabolism PS417_11895 med m-Inositol ABC transporter, permease component (iatP) (characterized) 41% 89% 227.6 Ribose import permease protein RbsC 47% 275.0
D-fructose catabolism frcC med Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 42% 92% 224.9 Ribose import permease protein RbsC 47% 275.0
D-mannose catabolism HSERO_RS03645 med ABC-type sugar transport system, permease component protein (characterized, see rationale) 44% 86% 224.9 Ribose import permease protein RbsC 47% 275.0
sucrose catabolism frcC med Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 42% 92% 224.9 Ribose import permease protein RbsC 47% 275.0
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) 39% 94% 221.5 Ribose import permease protein RbsC 47% 275.0
L-fucose catabolism HSERO_RS05255 lo ABC-type sugar transport system, permease component protein (characterized, see rationale) 38% 96% 220.7 Ribose import permease protein RbsC 47% 275.0
L-arabinose catabolism araH lo L-arabinose ABC transporter, permease protein AraH (characterized) 39% 91% 209.1 Ribose import permease protein RbsC 47% 275.0
D-galactose catabolism BPHYT_RS16925 lo Arabinose ABC transporter permease (characterized, see rationale) 38% 91% 207.2 Ribose import permease protein RbsC 47% 275.0
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) 36% 94% 185.7 Ribose import permease protein RbsC 47% 275.0
D-galactose catabolism ytfT lo Galactofuranose transporter permease protein YtfT (characterized) 35% 92% 183.7 Ribose import permease protein RbsC 47% 275.0
D-fructose catabolism fruG lo Fructose import permease protein FruG (characterized) 33% 90% 169.1 Ribose import permease protein RbsC 47% 275.0
L-rhamnose catabolism rhaQ lo RhaQ (characterized, see rationale) 35% 96% 169.1 Ribose import permease protein RbsC 47% 275.0
sucrose catabolism fruG lo Fructose import permease protein FruG (characterized) 33% 90% 169.1 Ribose import permease protein RbsC 47% 275.0
L-arabinose catabolism araZsh lo Inner-membrane translocator (characterized, see rationale) 35% 92% 162.9 Ribose import permease protein RbsC 47% 275.0
D-galactose catabolism yjtF lo Inner membrane ABC transporter permease protein YjfF (characterized) 36% 90% 158.3 Ribose import permease protein RbsC 47% 275.0
2'-deoxyinosine catabolism H281DRAFT_01112 lo deoxynucleoside transporter, permease component 2 (characterized) 35% 88% 154.1 Ribose import permease protein RbsC 47% 275.0

Sequence Analysis Tools

View GFF3462 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

MQQGAQVNTSISTGDSSRLRLNLARLVRSPAFYPFVGLVVVTLVMILASDTFLTASNLSN
IARQVSINAIIAVGMTCVILTGGIDLSVGPVMALSGTLTAGLMVAGLPPGLAIGAGMLIG
VAFGIGNGLFVAYLHMPPIIVTLATMGIARGLGLMYTDGYPISGLPDWFAFFGRESLFGI
QVPILIMLLTYLVAYVLLQHTRIGRYIYAIGGNEEAVRLSGVRAARFKLLVYGISGLTAA
IAGLVLTSRLMSGQPNAGVSFELDAIAAVVLGGASIAGGRGVIVGTLLGAMLLGVLNNGL
NMLGVSPYVQSVIKGGIILLAIFISRQRHK

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