GapMind for catabolism of small carbon sources

 

Protein WP_068223041.1 in Roseivirga spongicola UST030701-084

Annotation: NCBI__GCF_001592965.1:WP_068223041.1

Length: 317 amino acids

Source: GCF_001592965.1 in NCBI

Candidate for 88 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 PotG aka B0855, component of Putrescine porter (characterized) 41% 63% 182.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 39% 179.9
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 84% 175.6 PotG aka B0855, component of Putrescine porter 41% 182.6
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 84% 175.6 PotG aka B0855, component of Putrescine porter 41% 182.6
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 84% 175.6 PotG aka B0855, component of Putrescine porter 41% 182.6
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 84% 175.6 PotG aka B0855, component of Putrescine porter 41% 182.6
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 84% 175.6 PotG aka B0855, component of Putrescine porter 41% 182.6
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 84% 175.6 PotG aka B0855, component of Putrescine porter 41% 182.6
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 84% 175.6 PotG aka B0855, component of Putrescine porter 41% 182.6
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 34% 84% 175.6 PotG aka B0855, component of Putrescine porter 41% 182.6
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) 40% 63% 173.7 PotG aka B0855, component of Putrescine porter 41% 182.6
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 75% 168.3 PotG aka B0855, component of Putrescine porter 41% 182.6
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 75% 168.3 PotG aka B0855, component of Putrescine porter 41% 182.6
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 75% 168.3 PotG aka B0855, component of Putrescine porter 41% 182.6
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 75% 168.3 PotG aka B0855, component of Putrescine porter 41% 182.6
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 35% 72% 165.6 PotG aka B0855, component of Putrescine porter 41% 182.6
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 37% 77% 162.5 PotG aka B0855, component of Putrescine porter 41% 182.6
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 36% 69% 162.2 PotG aka B0855, component of Putrescine porter 41% 182.6
D-mannitol catabolism mtlK lo ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) 35% 74% 161 PotG aka B0855, component of Putrescine porter 41% 182.6
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) 35% 74% 161 PotG aka B0855, component of Putrescine porter 41% 182.6
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) 34% 75% 157.5 PotG aka B0855, component of Putrescine porter 41% 182.6
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 37% 70% 156.4 PotG aka B0855, component of Putrescine porter 41% 182.6
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 33% 77% 155.6 PotG aka B0855, component of Putrescine porter 41% 182.6
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 33% 77% 155.6 PotG aka B0855, component of Putrescine porter 41% 182.6
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 33% 87% 154.8 PotG aka B0855, component of Putrescine porter 41% 182.6
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 35% 100% 154.1 PotG aka B0855, component of Putrescine porter 41% 182.6
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 33% 87% 152.1 PotG aka B0855, component of Putrescine porter 41% 182.6
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 34% 78% 151.8 PotG aka B0855, component of Putrescine porter 41% 182.6
L-asparagine catabolism aatP lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 35% 98% 150.6 PotG aka B0855, component of Putrescine porter 41% 182.6
L-aspartate catabolism aatP lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 35% 98% 150.6 PotG aka B0855, component of Putrescine porter 41% 182.6
L-glutamate catabolism gltL lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 35% 98% 150.6 PotG aka B0855, component of Putrescine porter 41% 182.6
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 37% 82% 150.6 PotG aka B0855, component of Putrescine porter 41% 182.6
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 36% 64% 149.4 PotG aka B0855, component of Putrescine porter 41% 182.6
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 32% 73% 149.4 PotG aka B0855, component of Putrescine porter 41% 182.6
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 35% 65% 148.7 PotG aka B0855, component of Putrescine porter 41% 182.6
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) 30% 80% 146.7 PotG aka B0855, component of Putrescine porter 41% 182.6
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% 82% 146.7 PotG aka B0855, component of Putrescine porter 41% 182.6
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 32% 67% 146.4 PotG aka B0855, component of Putrescine porter 41% 182.6
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) 35% 63% 146 PotG aka B0855, component of Putrescine porter 41% 182.6
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 65% 144.1 PotG aka B0855, component of Putrescine porter 41% 182.6
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 65% 144.1 PotG aka B0855, component of Putrescine porter 41% 182.6
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 65% 144.1 PotG aka B0855, component of Putrescine porter 41% 182.6
D-maltose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 65% 144.1 PotG aka B0855, component of Putrescine porter 41% 182.6
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 65% 144.1 PotG aka B0855, component of Putrescine porter 41% 182.6
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 36% 61% 144.1 PotG aka B0855, component of Putrescine porter 41% 182.6
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) 36% 79% 144.1 PotG aka B0855, component of Putrescine porter 41% 182.6
sucrose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 65% 144.1 PotG aka B0855, component of Putrescine porter 41% 182.6
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 65% 144.1 PotG aka B0855, component of Putrescine porter 41% 182.6
trehalose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 65% 144.1 PotG aka B0855, component of Putrescine porter 41% 182.6
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 35% 65% 144.1 PotG aka B0855, component of Putrescine porter 41% 182.6
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) 34% 97% 142.9 PotG aka B0855, component of Putrescine porter 41% 182.6
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 33% 75% 142.1 PotG aka B0855, component of Putrescine porter 41% 182.6
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 31% 83% 141.7 PotG aka B0855, component of Putrescine porter 41% 182.6
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 31% 83% 141.7 PotG aka B0855, component of Putrescine porter 41% 182.6
D-cellobiose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 34% 61% 141.4 PotG aka B0855, component of Putrescine porter 41% 182.6
D-glucose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 34% 61% 141.4 PotG aka B0855, component of Putrescine porter 41% 182.6
lactose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 34% 61% 141.4 PotG aka B0855, component of Putrescine porter 41% 182.6
D-maltose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 34% 61% 141.4 PotG aka B0855, component of Putrescine porter 41% 182.6
sucrose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 34% 61% 141.4 PotG aka B0855, component of Putrescine porter 41% 182.6
trehalose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 34% 61% 141.4 PotG aka B0855, component of Putrescine porter 41% 182.6
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) 33% 60% 139 PotG aka B0855, component of Putrescine porter 41% 182.6
L-citrulline catabolism PS417_17605 lo ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) 34% 89% 137.9 PotG aka B0855, component of Putrescine porter 41% 182.6
L-lysine catabolism hisP lo ABC transporter for L-Lysine, ATPase component (characterized) 34% 97% 137.5 PotG aka B0855, component of Putrescine porter 41% 182.6
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 34% 61% 137.5 PotG aka B0855, component of Putrescine porter 41% 182.6
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 34% 56% 136.7 PotG aka B0855, component of Putrescine porter 41% 182.6
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 32% 93% 136 PotG aka B0855, component of Putrescine porter 41% 182.6
L-histidine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 34% 96% 134.8 PotG aka B0855, component of Putrescine porter 41% 182.6
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 33% 64% 134.4 PotG aka B0855, component of Putrescine porter 41% 182.6
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 32% 69% 132.9 PotG aka B0855, component of Putrescine porter 41% 182.6
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 34% 64% 130.2 PotG aka B0855, component of Putrescine porter 41% 182.6
L-isoleucine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 34% 94% 127.5 PotG aka B0855, component of Putrescine porter 41% 182.6
L-leucine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 34% 94% 127.5 PotG aka B0855, component of Putrescine porter 41% 182.6
L-valine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 34% 94% 127.5 PotG aka B0855, component of Putrescine porter 41% 182.6
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 94% 126.3 PotG aka B0855, component of Putrescine porter 41% 182.6
L-leucine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 94% 126.3 PotG aka B0855, component of Putrescine porter 41% 182.6
L-phenylalanine catabolism livG lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 94% 126.3 PotG aka B0855, component of Putrescine porter 41% 182.6
L-proline catabolism HSERO_RS00895 lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 94% 126.3 PotG aka B0855, component of Putrescine porter 41% 182.6
L-serine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 94% 126.3 PotG aka B0855, component of Putrescine porter 41% 182.6
L-tyrosine catabolism Ac3H11_1693 lo ABC transporter ATP-binding protein (characterized, see rationale) 31% 94% 126.3 PotG aka B0855, component of Putrescine porter 41% 182.6
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 30% 97% 118.2 PotG aka B0855, component of Putrescine porter 41% 182.6
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 33% 69% 118.2 PotG aka B0855, component of Putrescine porter 41% 182.6
D-cellobiose catabolism TM0027 lo TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 31% 91% 116.3 PotG aka B0855, component of Putrescine porter 41% 182.6
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 31% 67% 112.8 PotG aka B0855, component of Putrescine porter 41% 182.6
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 31% 63% 112.1 PotG aka B0855, component of Putrescine porter 41% 182.6
L-alanine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 32% 94% 107.5 PotG aka B0855, component of Putrescine porter 41% 182.6
L-serine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 32% 94% 107.5 PotG aka B0855, component of Putrescine porter 41% 182.6
L-threonine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 32% 94% 107.5 PotG aka B0855, component of Putrescine porter 41% 182.6
D-lactate catabolism PGA1_c12640 lo D-lactate transporter, ATP-binding component (characterized) 30% 97% 106.7 PotG aka B0855, component of Putrescine porter 41% 182.6
L-arabinose catabolism araVsh lo ABC transporter related (characterized, see rationale) 30% 55% 106.3 PotG aka B0855, component of Putrescine porter 41% 182.6

Sequence Analysis Tools

View WP_068223041.1 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

MLKVKNLHKKYSGESLSAVVDISFSLKECEVLAVVGKSGSGKSTLLRMLAGLMKPDAGVV
EFDGKPLKNPEEQLIAGHDKIKMVFQDFQVKPNMTVAENVKYKLLHFNKEYQAERCEELL
DTCGLSTLAEKMPHELSGGQQQRLSLARALADDPKLLLMDEPFSNLDPIIKEDLLLELTE
IVKKERLSLILVSHDTRDALLIADRIAYVEEGRLVQIGDNETVYKQPKTLEVAQFFGRVN
EISLDGQKHFIRAEDLTPQLEENKFEVTVSSSTFMGGVYLNRARYSGRKLVVFYSSEKLS
ENSNMVLGFKGRCQLHF

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