GapMind for catabolism of small carbon sources

 

Protein WP_047007399.1 in Erythrobacter gangjinensis K7-2

Annotation: NCBI__GCF_001010925.1:WP_047007399.1

Length: 255 amino acids

Source: GCF_001010925.1 in NCBI

Candidate for 55 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism artP med AotP aka PA0892, component of Arginine/ornithine (but not lysine) porter (characterized) 40% 89% 152.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
L-asparagine catabolism glnQ med Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 40% 86% 147.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
L-glutamate catabolism gltL med Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 40% 86% 147.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
L-histidine catabolism hisP med Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 40% 88% 147.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
L-lysine catabolism hisP med Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 40% 88% 147.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
D-maltose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 40% 63% 147.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 40% 63% 147.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
trehalose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 40% 63% 147.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 40% 90% 146.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 40% 90% 146.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 37% 90% 144.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 40% 86% 144.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 38% 88% 142.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 38% 88% 142.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 38% 84% 141.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 38% 84% 141.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 37% 89% 141.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 40% 87% 138.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 40% 87% 138.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 37% 85% 137.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 38% 88% 137.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 37% 61% 135.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
L-asparagine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 38% 84% 133.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
L-aspartate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 38% 84% 133.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
L-glutamate catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 38% 84% 133.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
L-histidine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 38% 84% 133.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
L-leucine catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 38% 84% 133.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
L-proline catabolism aapP lo AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 38% 84% 133.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 38% 59% 131.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 34% 66% 129.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 34% 66% 129.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 56% 127.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 56% 127.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 56% 127.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 56% 127.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 56% 127.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 56% 127.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 56% 127.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 38% 56% 127.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 37% 83% 126.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 38% 59% 125.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 35% 56% 121.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 34% 57% 121.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 36% 64% 120.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 34% 58% 120.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 34% 58% 120.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 34% 58% 120.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
D-cellobiose catabolism msiK lo MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) 34% 53% 120.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
D-maltose catabolism malK1 lo MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) 33% 58% 117.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
L-histidine catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 34% 89% 116.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
L-proline catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 34% 89% 116.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
trehalose catabolism malK lo MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized) 32% 54% 109 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 31% 54% 105.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
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% 54% 104.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 30% 62% 92 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 49% 225.7

Sequence Analysis Tools

View WP_047007399.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MNTQPLTPEASADRGRSDSALIELRDITKTFGTGAAAFQALKGVDMTIERGDFVAVMGPS
GSGKSTTMNILGCLDVPTSGTFRFRGVEVQDLSRDQRSLLRRRYLGFVFQGFNLLARTSA
LENVELPLLYRGETKKQRREAAERSLDLVGLLPWADHTPAELSGGQQQRVAIARALVTDP
DVLLADEPTGNLDTERSVEIMELLTELNQRGITVLMVTHEDEMAQFAKTIVHFRDGLVER
VDRGMRSAAAMTETV

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