GapMind for catabolism of small carbon sources

 

Protein WP_011372556.1 in Sulfurimonas denitrificans DSM 1251

Annotation: NCBI__GCF_000012965.1:WP_011372556.1

Length: 290 amino acids

Source: GCF_000012965.1 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
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 42% 59% 173.7 Chloroplast ATP-binding protein, component of The chloroplast sulfate transporter, SulP/SulP2/Sabc/Sbp 39% 172.2
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 39% 63% 170.6 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 39% 60% 169.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 39% 60% 169.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 41% 58% 168.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 41% 58% 168.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 41% 58% 168.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 41% 58% 168.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 41% 58% 168.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 41% 58% 168.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 78% 163.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 78% 163.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 78% 163.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 78% 163.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 78% 163.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 78% 163.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 78% 163.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 78% 163.3 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 77% 161.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 77% 161.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 41% 62% 161.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 77% 161.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 36% 77% 161.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
D-mannitol catabolism mtlK lo MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 42% 58% 159.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
D-sorbitol (glucitol) catabolism mtlK lo MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 42% 58% 159.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
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) 41% 56% 159.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
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) 39% 55% 157.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
sucrose catabolism thuK 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) 39% 55% 157.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 39% 60% 157.1 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 42% 53% 156.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
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) 38% 62% 155.6 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 37% 66% 152.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 37% 59% 152.1 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 36% 57% 151.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 40% 55% 151 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 36% 66% 150.6 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 36% 66% 150.6 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
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) 36% 65% 149.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 32% 85% 149.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 37% 56% 147.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 37% 55% 147.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 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) 38% 59% 146 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 36% 60% 145.6 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 38% 67% 145.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 35% 60% 144.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 35% 60% 144.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 35% 60% 144.4 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 40% 59% 144.1 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
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) 37% 92% 140.6 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
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) 37% 92% 140.6 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 58% 137.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 58% 137.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 58% 137.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 58% 137.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 58% 137.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 58% 137.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
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) 35% 51% 136 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
L-lysine catabolism hisP lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 37% 91% 132.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
L-asparagine catabolism aatP lo PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) 35% 88% 127.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
L-aspartate catabolism aatP lo PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) 35% 88% 127.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 36% 80% 125.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 37% 87% 124.8 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized) 36% 88% 122.5 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 32% 92% 120.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 31% 73% 111.7 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
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) 34% 66% 110.9 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 32% 61% 110.2 spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 42% 173.7

Sequence Analysis Tools

View WP_011372556.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

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Sequence

MIEINIIKPLNTADGEINLAVDKKIEDGEFLTLFGKSGSGKTTLLRIIAGLEVPESGYIK
VDNEVWFDSKRGINIPPQRRNVGFVFQDYALFPNMSVEDNLKFALQDKNKFKKVDDILKI
MEIQNLSKMKPQHLSGGQKQRVAVARALMREPKILLLDEPLSALDSTMRQKLQDELFFIH
QKFGIISLLVSHDIGEIFRLSSRVFKISSGEITHDGSPSEVFANQNISGKFKILGEVLSI
KKSDILYIVEVLAHNEIIKVTAIKDEIKELLVGDKILLSSKAFNPILTKI

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