GapMind for catabolism of small carbon sources

 

Protein Echvi_1282 in Echinicola vietnamensis KMM 6221, DSM 17526

Annotation: Echvi_1282 ABC-type sugar transport system, ATPase component

Length: 502 amino acids

Source: Cola in FitnessBrowser

Candidate for 34 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-ribose catabolism rbsA hi Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized) 51% 96% 488.4 Inositol transport system ATP-binding protein 45% 431.4
myo-inositol catabolism PS417_11890 med Inositol transport system ATP-binding protein (characterized) 45% 94% 431.4 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
D-xylose catabolism xylG med Xylose import ATP-binding protein XylG; EC 7.5.2.10 (characterized) 46% 97% 429.9 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
L-fucose catabolism HSERO_RS05250 med Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 46% 95% 424.5 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
D-cellobiose catabolism mglA med Monosaccharide-transporting ATPase, 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) 45% 99% 409.8 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
D-glucose catabolism mglA med Monosaccharide-transporting ATPase, 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) 45% 99% 409.8 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
lactose catabolism mglA med Monosaccharide-transporting ATPase, 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) 45% 99% 409.8 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
D-maltose catabolism mglA med Monosaccharide-transporting ATPase, 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) 45% 99% 409.8 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
sucrose catabolism mglA med Monosaccharide-transporting ATPase, 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) 45% 99% 409.8 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
trehalose catabolism mglA med Monosaccharide-transporting ATPase, 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) 45% 99% 409.8 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
D-galactose catabolism mglA med Galactose/methyl galactoside import ATP-binding protein MglA aka B2149, component of Galactose/glucose (methyl galactoside) porter (characterized) 43% 97% 406.8 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
L-arabinose catabolism gguA med GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 44% 98% 398.7 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
D-galactose catabolism gguA med GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 44% 98% 398.7 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
myo-inositol catabolism iatA med Inositol transport ATP-binding protein IatA, 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) 42% 97% 390.6 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
D-xylose catabolism xylK_Tm med Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale) 44% 97% 388.3 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
L-rhamnose catabolism rhaT' med RhaT, 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) 43% 96% 384.8 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
L-arabinose catabolism araG med L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized) 41% 97% 384 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
D-galactose catabolism BPHYT_RS16930 med Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) 41% 96% 380.6 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
D-mannose catabolism HSERO_RS03640 med Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 42% 94% 380.2 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
xylitol catabolism PS417_12065 med D-ribose transporter ATP-binding protein; SubName: Full=Putative xylitol transport system ATP-binding protein; SubName: Full=Sugar ABC transporter ATP-binding protein (characterized, see rationale) 43% 99% 376.3 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
D-fructose catabolism frcA med ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 41% 93% 345.9 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
sucrose catabolism frcA med ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 41% 93% 345.9 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
L-arabinose catabolism araVsh lo ABC transporter related (characterized, see rationale) 40% 99% 370.5 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
D-galactose catabolism ytfR lo galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized) 39% 98% 364 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
D-fructose catabolism fruK lo Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 38% 96% 340.5 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
sucrose catabolism fruK lo Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 38% 96% 340.5 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
2'-deoxyinosine catabolism H281DRAFT_01113 lo deoxynucleoside transporter, ATPase component (characterized) 36% 97% 317 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
2'-deoxyinosine catabolism nupA lo Purine/cytidine ABC transporter ATP-binding protein, component of General nucleoside uptake porter, NupABC/BmpA (transports all common nucleosides as well as 5-fluorocytidine, inosine, deoxyuridine and xanthosine) (Martinussen et al., 2010) (Most similar to 3.A.1.2.12). NupA is 506aas with two ABC (C) domains. NupB has 8 predicted TMSs, NupC has 9 or 10 predicted TMSs in a 4 + 1 (or 2) + 4 arrangement (characterized) 36% 97% 301.2 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
L-fucose catabolism BPHYT_RS34245 lo ABC transporter related; Flags: Precursor (characterized, see rationale) 35% 95% 276.2 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
L-rhamnose catabolism BPHYT_RS34245 lo ABC transporter related; Flags: Precursor (characterized, see rationale) 35% 95% 276.2 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 38% 94% 159.5 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 34% 97% 152.9 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 39% 87% 143.3 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 39% 87% 143.3 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 51% 488.4

Sequence Analysis Tools

View Echvi_1282 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

MLTVKNITKEFVGVKALDDVSLELQAGRVTAILGENGAGKSTLMKILSGVYPDYKGTIYY
NGDPVKFQNTRDAQEKGINIIHQELNLIPYLSIRENIFLGREPETPMGLLDVAKMHKEAA
QLLHRLKLNVDPETPVSQLKVGQQQLVEIAKALSLESQVIIMDEPTSAISDQEVEILFGI
IRALRAEGKAIAYISHKLDELFAIADRYVVLRDGKMIESGEMEGMTEEALIQKMVGREIV
IERSCSGRQFDETVLSVKHLTVKHPKIADKFLLQDINFELGKGEVLGIFGLMGAGRTELM
EALFGVLPHQGAEITLAGKVHEFQKPQEAMDAGLALVPEDRKQDGLVLCMDLCTNSSLTV
VDSILSGGLLDDKKEKGLAQKYMGELKIKASSHRQLVEKLSGGNQQKVVLAKWLATRPKV
LMLDEPTRGIDINAKNEIYKLIRQLANEGLGLIVVSSELPEILAVSDRVLVMAEGRLTAN
IPIDAQTSEDEILQAAIPKKKD

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