GapMind for catabolism of small carbon sources

 

Protein Ac3H11_1841 in Acidovorax sp. GW101-3H11

Annotation: Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Length: 892 amino acids

Source: acidovorax_3H11 in FitnessBrowser

Candidate for 27 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-ribose catabolism rbsC hi ABC transporter permease (characterized, see rationale) 66% 94% 401.4
D-fructose catabolism frcC hi Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 41% 97% 206.5
sucrose catabolism frcC hi Ribose ABC transport system, permease protein RbsC (characterized, see rationale) 41% 97% 206.5
D-ribose catabolism rbsA med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 52% 79% 418.3 Inositol transport system ATP-binding protein 35% 249.6
D-mannose catabolism HSERO_RS03645 med ABC-type sugar transport system, permease component protein (characterized, see rationale) 38% 99% 206.5
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) 38% 100% 204.9
L-fucose catabolism HSERO_RS05255 med ABC-type sugar transport system, permease component protein (characterized, see rationale) 33% 99% 199.9
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) 37% 98% 186
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) 33% 96% 179.1
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) 33% 96% 179.1
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) 33% 96% 179.1
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) 33% 96% 179.1
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) 33% 96% 179.1
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) 33% 96% 179.1
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) 33% 96% 179.1
myo-inositol catabolism PS417_11895 med Inositol transport system permease protein (characterized) 35% 99% 178.3
D-galactose catabolism BPHYT_RS16925 med Monosaccharide-transporting ATPase; EC 3.6.3.17 (characterized, see rationale) 33% 96% 172.2
D-mannose catabolism frcC med Fructose import permease protein FrcC (characterized) 31% 86% 167.2
D-ribose catabolism frcC med Fructose import permease protein FrcC (characterized) 31% 86% 167.2
D-fructose catabolism fruF med Fructose import permease protein FruF (characterized) 36% 81% 164.5
sucrose catabolism fruF med Fructose import permease protein FruF (characterized) 36% 81% 164.5
L-arabinose catabolism araH med L-arabinose ABC transporter, permease protein AraH (characterized) 31% 98% 162.9
D-galactose catabolism ytfT med Galactofuranose transporter permease protein YtfT (characterized) 33% 94% 160.6
L-rhamnose catabolism rhaQ med RhaQ (characterized, see rationale) 31% 89% 151.8
L-fucose catabolism BPHYT_RS34240 med Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) 32% 95% 131.3
L-rhamnose catabolism BPHYT_RS34240 med Monosaccharide-transporting ATPase; EC 3.6.3.17; Flags: Precursor (characterized, see rationale) 32% 95% 131.3
D-galactose catabolism yjtF lo Inner membrane ABC transporter permease protein YjfF (characterized) 36% 76% 138.7

Sequence Analysis Tools

View Ac3H11_1841 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

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

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MPSDAREQPMTPKPPTNTSPPLLAIQAIGKDYTATVLDGVNVELFAGEVLALTGENGAGK
STLSKILCGLEQPTRGGMLLAGQAYAPTSRRDAERHGVRMVMQELGLVPTLTVAENLLMG
RLPHRLGWLQRDVLHAAARAQLAKIGLDSIDPATPVSQLGIGQQQMVEIARNLQDDTRIL
VLDEPTAMLTPRETNYLFEQIAHLTARGVAIIYVSHRLEELRRIADRVAVLRDGRLVDVR
PMAGMSEDDLVQRMVGRVVSDLDHRPRRPVGPVVMSAEGLGRGTAVQGVSLELRAGEIFG
IAGLVGSGRTELVRLLFGADRADRGSVTLHPEFEQKQALPRDGQAQAAIQKIANTPNPAT
AAPRTWQRGFASPLQAIAAGVGLVTEDRKSQGLLLSQPIRINATLSDLSAVSRGGWLQRG
FENRLVQGFVRTLGIRCRSPEQPVGQLSGGNQQKGGVRPLAAPRRPRAAARRTHARRGRG
RPRRAVWRAGPHGPGRPRAAHGVVRPARTHGHGRPHRRDECGPPGGRVRARRVVRAIAAG
GCVLRARRAHQHHTFNFFSCDRMNAPTAPAAPAATPSSASVWRSQLGTYLGLLAVLAGMV
ALFSSLSEYFWSAETFITIANEIPALAVMAVGMTFVLIIAGIDLSVGSVMALAAATSAAA
ILQWGWTVPAAAALALATGLVCGTITGAISVAWRLPSFIVSLGMLEAVRGSAYVVTDSRT
QYVGDAISWLSAPFFGGISFAFLLAVVLVVVAQLVLSRTVFGRCVVGIGTNEEAMRLAGV
DPRPIRVIVFAMTGLLAGLAGLMQSARLEAADPNAGTGMELQVIAAVVIGGTSLMGGRGS
VVNTAFGVLIIAVLEAGLAQVGASEPSKRIITGFVIVAAVIVDTLRQRRAKV

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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