GapMind for catabolism of small carbon sources

 

Protein WP_011385004.1 in Magnetospirillum magneticum AMB-1

Annotation: AMB_RS13205 polyamine ABC transporter ATP-binding protein

Length: 379 amino acids

Source: GCF_000009985.1 in NCBI

Candidate for 69 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA hi PotG aka B0855, component of Putrescine porter (characterized) 56% 98% 394.4 Uncharacterized ABC transporter ATP-binding protein YdcT 54% 263.1
sucrose catabolism thuK med ABC transporter (characterized, see rationale) 40% 88% 248.8 PotG aka B0855, component of Putrescine porter 56% 394.4
D-maltose catabolism malK med Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 41% 95% 246.5 PotG aka B0855, component of Putrescine porter 56% 394.4
D-mannitol catabolism mtlK med SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 42% 94% 244.2 PotG aka B0855, component of Putrescine porter 56% 394.4
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 92% 241.5 PotG aka B0855, component of Putrescine porter 56% 394.4
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 92% 241.5 PotG aka B0855, component of Putrescine porter 56% 394.4
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 92% 241.5 PotG aka B0855, component of Putrescine porter 56% 394.4
D-maltose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 92% 241.5 PotG aka B0855, component of Putrescine porter 56% 394.4
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 92% 241.5 PotG aka B0855, component of Putrescine porter 56% 394.4
sucrose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 92% 241.5 PotG aka B0855, component of Putrescine porter 56% 394.4
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 92% 241.5 PotG aka B0855, component of Putrescine porter 56% 394.4
trehalose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 92% 241.5 PotG aka B0855, component of Putrescine porter 56% 394.4
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 41% 92% 241.5 PotG aka B0855, component of Putrescine porter 56% 394.4
D-maltose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 42% 92% 240.7 PotG aka B0855, component of Putrescine porter 56% 394.4
trehalose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 42% 92% 240.7 PotG aka B0855, component of Putrescine porter 56% 394.4
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 44% 89% 239.2 PotG aka B0855, component of Putrescine porter 56% 394.4
D-cellobiose catabolism msiK med 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) 42% 90% 237.7 PotG aka B0855, component of Putrescine porter 56% 394.4
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 82% 233.4 PotG aka B0855, component of Putrescine porter 56% 394.4
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 82% 233.4 PotG aka B0855, component of Putrescine porter 56% 394.4
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 41% 94% 233.4 PotG aka B0855, component of Putrescine porter 56% 394.4
D-cellobiose catabolism gtsD med 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) 44% 76% 228.8 PotG aka B0855, component of Putrescine porter 56% 394.4
D-glucose catabolism gtsD med 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) 44% 76% 228.8 PotG aka B0855, component of Putrescine porter 56% 394.4
lactose catabolism gtsD med 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) 44% 76% 228.8 PotG aka B0855, component of Putrescine porter 56% 394.4
D-maltose catabolism gtsD med 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) 44% 76% 228.8 PotG aka B0855, component of Putrescine porter 56% 394.4
D-mannose catabolism TT_C0211 med 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) 44% 76% 228.8 PotG aka B0855, component of Putrescine porter 56% 394.4
sucrose catabolism gtsD med 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) 44% 76% 228.8 PotG aka B0855, component of Putrescine porter 56% 394.4
trehalose catabolism gtsD med 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) 44% 76% 228.8 PotG aka B0855, component of Putrescine porter 56% 394.4
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 40% 80% 227.6 PotG aka B0855, component of Putrescine porter 56% 394.4
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 44% 77% 223.4 PotG aka B0855, component of Putrescine porter 56% 394.4
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 47% 70% 220.7 PotG aka B0855, component of Putrescine porter 56% 394.4
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 42% 84% 217.6 PotG aka B0855, component of Putrescine porter 56% 394.4
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 43% 74% 216.9 PotG aka B0855, component of Putrescine porter 56% 394.4
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 41% 77% 213.4 PotG aka B0855, component of Putrescine porter 56% 394.4
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 42% 75% 213 PotG aka B0855, component of Putrescine porter 56% 394.4
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 42% 73% 211.5 PotG aka B0855, component of Putrescine porter 56% 394.4
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 40% 81% 208.4 PotG aka B0855, component of Putrescine porter 56% 394.4
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 46% 71% 207.2 PotG aka B0855, component of Putrescine porter 56% 394.4
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 39% 92% 233 PotG aka B0855, component of Putrescine porter 56% 394.4
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) 39% 95% 226.9 PotG aka B0855, component of Putrescine porter 56% 394.4
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) 39% 95% 226.9 PotG aka B0855, component of Putrescine porter 56% 394.4
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) 40% 93% 223 PotG aka B0855, component of Putrescine porter 56% 394.4
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 39% 88% 222.6 PotG aka B0855, component of Putrescine porter 56% 394.4
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 39% 88% 210.3 PotG aka B0855, component of Putrescine porter 56% 394.4
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 95% 201.4 PotG aka B0855, component of Putrescine porter 56% 394.4
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 95% 201.4 PotG aka B0855, component of Putrescine porter 56% 394.4
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 95% 201.4 PotG aka B0855, component of Putrescine porter 56% 394.4
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 95% 201.4 PotG aka B0855, component of Putrescine porter 56% 394.4
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 95% 201.4 PotG aka B0855, component of Putrescine porter 56% 394.4
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 95% 201.4 PotG aka B0855, component of Putrescine porter 56% 394.4
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 95% 201.4 PotG aka B0855, component of Putrescine porter 56% 394.4
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 95% 201.4 PotG aka B0855, component of Putrescine porter 56% 394.4
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 40% 70% 184.5 PotG aka B0855, component of Putrescine porter 56% 394.4
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 40% 70% 184.5 PotG aka B0855, component of Putrescine porter 56% 394.4
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 40% 70% 184.5 PotG aka B0855, component of Putrescine porter 56% 394.4
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 40% 70% 184.5 PotG aka B0855, component of Putrescine porter 56% 394.4
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 39% 60% 171.8 PotG aka B0855, component of Putrescine porter 56% 394.4
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) 34% 98% 169.9 PotG aka B0855, component of Putrescine porter 56% 394.4
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 32% 92% 165.2 PotG aka B0855, component of Putrescine porter 56% 394.4
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 37% 89% 164.1 PotG aka B0855, component of Putrescine porter 56% 394.4
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 35% 89% 159.8 PotG aka B0855, component of Putrescine porter 56% 394.4
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) 36% 84% 156 PotG aka B0855, component of Putrescine porter 56% 394.4
D-mannose catabolism TM1750 lo TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 33% 72% 120.2 PotG aka B0855, component of Putrescine porter 56% 394.4
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 32% 65% 119.8 PotG aka B0855, component of Putrescine porter 56% 394.4
D-cellobiose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 87% 103.6 PotG aka B0855, component of Putrescine porter 56% 394.4
D-glucose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 87% 103.6 PotG aka B0855, component of Putrescine porter 56% 394.4
lactose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 87% 103.6 PotG aka B0855, component of Putrescine porter 56% 394.4
D-maltose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 87% 103.6 PotG aka B0855, component of Putrescine porter 56% 394.4
sucrose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 87% 103.6 PotG aka B0855, component of Putrescine porter 56% 394.4
trehalose catabolism mglA lo glucose transporter, ATPase component (characterized) 32% 87% 103.6 PotG aka B0855, component of Putrescine porter 56% 394.4

Sequence Analysis Tools

View WP_011385004.1 at NCBI

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

MAQAAVKREVTAPWNDPQAVPLIRFEGISKRFGDFTAVEHVDLAIHKGEFFSLLGASGCG
KTTLLRMLAGFEIPTTGRILIDGQDVTEVPPYERPVNMMFQSYALFPHMSVADNIAFGLK
QDGLAKPVIKDKVAAALELVQMGRFSGRKPHQLSGGQRQRVALARCLAKEPKVVLLDEPL
AALDKKLREATQLELVNIQDRVGITFVMVTHDQGEAMTMSSRIGVMNAGCIEQVGSPVDI
YEYPGTRFVADFIGAANMFQGSVRGGEGALAIACPELEHDLSVTEAGAVAAGTPVTVMVR
PEKVMIARDKPASGLNWAEGVVSDIAYLGDVSIYHVRLASGRKIQALRTNLHHGEESRLT
WEDPVFLAWHPADSLVLTK

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