GapMind for catabolism of small carbon sources

 

Protein 7024900 in Shewanella sp. ANA-3

Annotation: Shewana3_2074 ABC transporter related (RefSeq)

Length: 499 amino acids

Source: ANA3 in FitnessBrowser

Candidate for 36 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arabinose catabolism araVsh hi ABC transporter related (characterized, see rationale) 100% 100% 954.1 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
D-galactose catabolism ytfR hi galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized) 53% 98% 501.1 Fructose import ATP-binding protein FruK; EC 7.5.2.- 47% 452.6
D-fructose catabolism fruK med Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 47% 97% 452.6 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
sucrose catabolism fruK med Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized) 47% 97% 452.6 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
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) 42% 100% 389.8 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
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) 42% 100% 389.8 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
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) 42% 100% 389.8 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
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) 42% 100% 389.8 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
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) 42% 100% 389.8 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
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) 42% 100% 389.8 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
D-xylose catabolism xylG 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) 42% 100% 389.8 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
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) 39% 97% 378.3 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
L-fucose catabolism HSERO_RS05250 lo Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 38% 95% 372.9 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
myo-inositol catabolism PS417_11890 lo Inositol transport system ATP-binding protein (characterized) 39% 95% 367.1 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
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) 38% 95% 367.1 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
D-xylose catabolism xylK_Tm lo Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale) 38% 95% 359.8 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
D-mannose catabolism HSERO_RS03640 lo Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale) 38% 95% 352.4 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
D-galactose catabolism mglA lo Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized) 38% 97% 348.2 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
L-arabinose catabolism araG lo L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized) 37% 99% 345.5 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
D-fructose catabolism frcA lo ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 39% 93% 340.5 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
sucrose catabolism frcA lo ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale) 39% 93% 340.5 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
L-rhamnose catabolism rhaT' lo 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) 38% 95% 339 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
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% 99% 333.6 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
D-galactose catabolism BPHYT_RS16930 lo Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale) 37% 95% 324.3 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
L-arabinose catabolism gguA lo GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 36% 98% 311.6 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
D-galactose catabolism gguA lo GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized) 36% 98% 311.6 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
2'-deoxyinosine catabolism H281DRAFT_01113 lo deoxynucleoside transporter, ATPase component (characterized) 36% 96% 310.8 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
L-fucose catabolism BPHYT_RS34245 lo ABC transporter related; Flags: Precursor (characterized, see rationale) 35% 96% 301.6 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
L-rhamnose catabolism BPHYT_RS34245 lo ABC transporter related; Flags: Precursor (characterized, see rationale) 35% 96% 301.6 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
2'-deoxyinosine catabolism nupA lo RnsB, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases (characterized) 33% 97% 274.2 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 38% 96% 174.5 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 39% 92% 173.3 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 37% 86% 149.4 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 37% 86% 149.4 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
L-isoleucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) 32% 100% 105.5 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1
L-phenylalanine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) 32% 100% 105.5 galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) 52% 501.1

Sequence Analysis Tools

View 7024900 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

MSLILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGD
ILFLGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYAD
ARAVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLF
GILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRS
LQEQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEV
CNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILA
LQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPI
LLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVR
ELSGAELTSQHVMQAIAEG

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