GapMind for catabolism of small carbon sources

 

Protein WP_011767548.1 in Azoarcus olearius BH72

Annotation: NCBI__GCF_000061505.1:WP_011767548.1

Length: 335 amino acids

Source: GCF_000061505.1 in NCBI

Candidate for 67 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 43% 95% 250.4 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
putrescine catabolism potA med PotG aka B0855, component of Putrescine porter (characterized) 42% 91% 244.2 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 45% 81% 236.1 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 45% 80% 233.4 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 45% 80% 233.4 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
trehalose catabolism thuK med Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized) 41% 76% 224.9 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
D-mannitol catabolism mtlK med MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 43% 80% 223.4 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
D-maltose catabolism malK med Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 41% 82% 216.9 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 42% 81% 211.5 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
D-cellobiose catabolism gtsD med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 42% 77% 211.1 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 42% 77% 211.1 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
D-glucose catabolism gtsD med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 42% 77% 211.1 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
lactose catabolism gtsD med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 42% 77% 211.1 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
D-maltose catabolism gtsD med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 42% 77% 211.1 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
sucrose catabolism gtsD med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 42% 77% 211.1 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
trehalose catabolism gtsD med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 42% 77% 211.1 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 41% 77% 206.1 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-glucosamine, ATPase component (characterized) 41% 92% 164.9 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 49% 75% 164.1 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
L-lysine catabolism hisP med Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 40% 91% 156 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 39% 88% 227.3 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 38% 93% 218 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 39% 86% 216.1 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 40% 82% 214.2 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 94% 212.2 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
D-maltose catabolism thuK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 94% 212.2 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 94% 212.2 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 94% 212.2 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
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) 39% 80% 211.1 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 48% 58% 211.1 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
D-mannose catabolism TT_C0211 lo Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) 37% 91% 210.7 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 41% 70% 209.9 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
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) 42% 65% 208.8 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 45% 61% 208 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 37% 94% 206.5 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 36% 91% 206.5 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
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) 43% 65% 204.9 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 38% 90% 202.2 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 36% 94% 201.1 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
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) 44% 63% 197.2 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 83% 194.5 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 83% 194.5 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 83% 194.5 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 83% 194.5 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 83% 194.5 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 83% 194.5 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 35% 66% 170.6 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
L-proline catabolism opuBA lo BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) 37% 73% 166.8 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 36% 87% 164.1 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
L-asparagine catabolism glnQ lo 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) 39% 96% 161.4 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
L-glutamate catabolism gltL lo 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) 39% 96% 161.4 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 38% 79% 160.6 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
L-arginine catabolism artP lo 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) 38% 96% 156 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
L-histidine catabolism hisP lo 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) 38% 96% 156 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
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) 37% 81% 155.2 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 38% 95% 150.2 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 39% 85% 149.8 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 39% 85% 149.8 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 33% 88% 148.7 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 37% 93% 144.8 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
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) 36% 94% 142.9 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
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) 36% 94% 142.9 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
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) 36% 94% 142.9 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
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) 36% 94% 142.9 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
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) 36% 94% 142.9 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 36% 94% 140.2 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 33% 99% 139.8 CP4-6 prophage; ABC transporter ATP-binding protein AfuC 45% 267.7

Sequence Analysis Tools

View WP_011767548.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

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Sequence

MSLEIRNLHKSFAGHAALERIDLTLGGAEFVCLLGPSGCGKTTLLRIIAGLLAADRGDIR
LNGRDLAAVPTRERGFGIVFQSYSLFPHMTVAQNVGYGLGIRGVAPARIAERVAGLLATV
KLADFGERYPGQLSGGQQQRVAIARALAVDPALLLLDEPLSALDARVRAELRGELREVQR
KLGIPTLMVTHDQDEAMVLADRVVCMNHGRIEQIGTPQELYEQPRTRFVAEFMGHGNLLP
PDWLQDAAPALLAGMPVGLGQQGAACVRPERIVLTRTPEGDGRVIEVAFMGNFKRVRLDW
RGRELLAEVSAAAVLVAGDAVWVDITAQDCAWVAA

This GapMind analysis is from Apr 09 2024. 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