GapMind for catabolism of small carbon sources

 

Protein Ga0059261_3874 in Sphingomonas koreensis DSMZ 15582

Annotation: Ga0059261_3874 ABC-type antimicrobial peptide transport system, ATPase component

Length: 243 amino acids

Source: Korea in FitnessBrowser

Candidate for 40 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 41% 86% 140.2 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 41% 86% 140.2 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
L-glutamate catabolism gltL lo GluA aka CGL1950, component of Glutamate porter (characterized) 38% 85% 136.7 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 38% 91% 130.2 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 38% 91% 130.2 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 33% 63% 127.1 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 33% 63% 127.1 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 33% 63% 127.1 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 33% 63% 127.1 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 33% 63% 127.1 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 33% 63% 127.1 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 63% 124.4 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 63% 124.4 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 63% 124.4 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 63% 124.4 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 63% 124.4 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 63% 124.4 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 63% 124.4 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 63% 124.4 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 37% 53% 122.9 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
D-maltose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 34% 62% 119.4 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 34% 62% 119.4 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
trehalose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 34% 62% 119.4 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 33% 62% 119 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 33% 61% 115.9 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
D-mannitol catabolism mtlK lo ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 33% 53% 115.5 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 31% 61% 110.2 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
D-maltose catabolism malK_Sm lo MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 32% 53% 105.1 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
trehalose catabolism malK lo MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 32% 53% 105.1 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
D-mannose catabolism TM1749 lo TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 36% 66% 104.4 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
D-cellobiose catabolism TM0027 lo TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 31% 91% 102.1 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 30% 56% 97.1 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 31% 67% 96.3 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
D-cellobiose catabolism TM0028 lo TM0028, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 31% 76% 94.7 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 32% 69% 94.7 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
D-fructose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 87% 91.3 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 87% 91.3 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 87% 91.3 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
sucrose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 87% 91.3 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 31% 84% 84.7 DevA, component of Glycolipid exporter (under nitrogen control in heterocysts), DevABC-HgdD (Moslavac et al., 2007). Heterocyst envelope glycolipids (HGLs) function as an O2 40% 173.7

Sequence Analysis Tools

View Ga0059261_3874 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 and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MMIKADAAIDAREVSKSYTVGQVRTQILFGVSVSVMPGELTLVVGPSGCGKSTLLAILSG
LTLPDQGEVDALGNPICRMKAGARDAFRLANTGFVFQGFNLFNALTAEEQVAYVLQCMKV
KPAEARQRARAALEAVGLGPRMRLRPFELSGGEKQRVAIARALAKQPRILFADEPTSALD
SHNGHAVIALLRDIAHNQGAAVLCVTHDPRLLSFADRIIHMEDGRIIRDERPDPTSAVQR
ETH

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