GapMind for catabolism of small carbon sources

 

Protein WP_084703851.1 in Streptacidiphilus oryzae TH49

Annotation: NCBI__GCF_000744815.1:WP_084703851.1

Length: 559 amino acids

Source: GCF_000744815.1 in NCBI

Candidate for 18 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-mannose catabolism HSERO_RS03640 med Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 39% 95% 338.6 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 40% 330.1
D-galactose catabolism ytfR med galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized) 40% 98% 330.1 Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose 37% 328.9
D-ribose catabolism rbsA lo Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized) 37% 97% 328.9 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 40% 330.1
D-cellobiose catabolism mglA lo 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) 37% 99% 328.6 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 40% 330.1
D-glucose catabolism mglA lo 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) 37% 99% 328.6 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 40% 330.1
lactose catabolism mglA lo 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) 37% 99% 328.6 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 40% 330.1
D-maltose catabolism mglA lo 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) 37% 99% 328.6 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 40% 330.1
sucrose catabolism mglA lo 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) 37% 99% 328.6 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 40% 330.1
trehalose catabolism mglA lo 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) 37% 99% 328.6 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 40% 330.1
D-xylose catabolism xylG lo 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) 37% 99% 328.6 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 40% 330.1
L-fucose catabolism HSERO_RS05250 lo Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 37% 94% 324.7 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 40% 330.1
D-xylose catabolism xylK_Tm lo Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale) 38% 98% 321.2 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 40% 330.1
L-arabinose catabolism araG lo L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized) 37% 98% 318.5 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 40% 330.1
myo-inositol catabolism iatA lo 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) 38% 97% 314.3 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 40% 330.1
xylitol catabolism PS417_12065 lo 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) 36% 98% 298.5 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 40% 330.1
D-galactose catabolism BPHYT_RS16930 lo Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) 38% 96% 297 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 40% 330.1
L-arabinose catabolism gguA lo GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 37% 99% 294.7 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 40% 330.1
D-galactose catabolism gguA lo GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 37% 99% 294.7 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 40% 330.1

Sequence Analysis Tools

View WP_084703851.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MADENGPRNDGAVAVSLRGISKSYGPVKVLDLPELELRHGQIVGVVGENGAGKSTLMGVL
SGTVTPTTGEITVSGRRLHAGRPDHAQQLGVALVAQEFPLVGRMSVAENLLLGRRPQREA
AEQREDGAEARTGGLRRWLFDRAGTRREARRLLGDVGVTGVDVDRPVERLSVPLRQMVEI
AKAWGRSPLVLILDEPTSSLGPVEAERVLALARRHAADGGAVLFIGHRLDEVQAISDRVL
VLRSGRLVADLTPEEATEERLIREMVGSELAAVDISPPPSVAEDGTDGAVLQVRGLTADG
LGPVDLDVRAGEIVGVAGLMGSGRSRLLHTVFGAQPRTGGRIRLAGREFTPGHPAEAVAA
GVGLVPEDRKLQSLLPDHPVRWNATLATLRRISPRGVLTPRADRAHARRIVGDLGVRLHS
AEQPISGLSGGNQQKVVFGRWLAARPRLLLLDEPTRGVDVGAKAEIYRLIDEAAKDGLAV
LAASSELEELLWICHRIVVMAGGRVVADIPRERFSKELIMTAAAGSAVRAEQDGHGDGNG
NGSGRAPEPGYAKSGRNGG

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