GapMind for catabolism of small carbon sources

 

Protein 8501226 in Desulfovibrio vulgaris Miyazaki F

Annotation: DvMF_1960 putrescine/spermidine ABC transporter ATPase protein (RefSeq)

Length: 399 amino acids

Source: Miya in FitnessBrowser

Candidate for 68 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 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 53% 89% 319.7 Uncharacterized ABC transporter ATP-binding protein YdcT 44% 267.3
D-maltose catabolism malK1 med 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) 51% 71% 263.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
trehalose catabolism thuK med 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) 51% 71% 263.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 46% 82% 253.1 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 46% 84% 251.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 46% 84% 251.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 50% 72% 249.6 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
D-mannitol catabolism mtlK med SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 49% 73% 247.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
lactose catabolism lacK med LacK, component of Lactose porter (characterized) 43% 82% 245.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 44% 82% 243 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
D-maltose catabolism thuK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 44% 82% 243 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 44% 82% 243 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 44% 82% 243 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
D-maltose catabolism malK med Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 42% 78% 239.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 46% 73% 236.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 43% 79% 235.7 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 43% 71% 233 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 43% 78% 231.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
sucrose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 46% 72% 228 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 44% 75% 227.6 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
D-cellobiose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 41% 83% 223.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
D-glucose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 41% 83% 223.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
lactose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 41% 83% 223.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
D-maltose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 41% 83% 223.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
sucrose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 41% 83% 223.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
trehalose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 41% 83% 223.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
D-cellobiose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 70% 213.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
D-galactose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 70% 213.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
D-glucose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 70% 213.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
lactose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 70% 213.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
D-maltose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 70% 213.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
D-mannose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 70% 213.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
sucrose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 70% 213.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
trehalose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 70% 213.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 43% 83% 166 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 49% 63% 245.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
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) 40% 96% 245 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
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% 88% 239.6 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 47% 68% 236.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 49% 63% 234.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 51% 57% 234.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
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) 46% 65% 231.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 65% 226.1 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 65% 226.1 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 65% 226.1 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 65% 226.1 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 65% 226.1 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 47% 65% 226.1 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 37% 95% 223.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 45% 64% 221.1 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
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) 42% 69% 220.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 35% 99% 205.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 90% 201.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 90% 201.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 90% 201.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 90% 201.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 36% 82% 194.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
L-proline catabolism opuBA lo BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) 41% 60% 189.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 38% 70% 188 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 38% 82% 172.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
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) 40% 82% 171 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 34% 75% 167.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 37% 82% 146 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
D-fructose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 90% 124.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 90% 124.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 90% 124.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
sucrose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 90% 124.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7
L-arabinose catabolism araG lo L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized) 31% 55% 117.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 53% 319.7

Sequence Analysis Tools

View 8501226 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

MAEQDHIIELRGVTKTFEDTVALDSIDLTIRNGEFLTLLGPSGCGKTTILRLVSGFEQPT
SGEVRINGQVVNRVPPEQRQVNTVFQNYALFPHMTVRDNVAFGLKMQGVAADETARRVLD
ALRMVHLENFADRKPRQLSGGQQQRVAIARAVINNPLVLLLDEPFSALDFKLRKQMQLEI
KHLQRQLGITFVFVTHDQEEAFAMSDRVVVMNEGRIEQIGAPKEIYEEPANMYVARFVGD
INALPGRIDAVRLDWSAAPGTPLAPPAPGTPEHAALPPDLKPGEHLYDATVGGTVFPVRS
RRRLAPGDGVQVLLRPEDLRIDRIAVAETPDWPHLWGRIEESVYKGATVDLVITLDDGQR
LMAAEFFNEDDEDINYNPGERVAVSWVDGWEVLLPDDAA

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