GapMind for catabolism of small carbon sources

 

Protein WP_052717993.1 in Oleispira antarctica

Annotation: NCBI__GCF_000967895.1:WP_052717993.1

Length: 362 amino acids

Source: GCF_000967895.1 in NCBI

Candidate for 63 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 40% 71% 181.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 40% 71% 181.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 36% 88% 194.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 45% 60% 192.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 45% 60% 192.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 39% 72% 188.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 40% 60% 188 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 32% 91% 184.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 32% 91% 184.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 32% 91% 184.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 32% 91% 184.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 32% 91% 184.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 32% 91% 184.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
D-mannitol catabolism mtlK lo MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 38% 65% 179.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
D-sorbitol (glucitol) catabolism mtlK lo MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 38% 65% 179.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 39% 57% 175.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 40% 56% 175.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 37% 64% 174.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 41% 62% 174.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 41% 62% 174.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 41% 62% 174.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 41% 62% 174.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 39% 65% 173.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
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% 61% 173.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
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) 37% 61% 173.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
D-maltose catabolism malK lo Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 31% 88% 172.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
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) 39% 62% 171.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 39% 63% 171.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 37% 66% 169.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 37% 59% 169.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
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% 58% 166.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 39% 53% 166.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 67% 166.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 67% 166.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 67% 166.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 67% 166.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 67% 166.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 67% 166.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 67% 166.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 67% 166.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 36% 72% 166 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 36% 65% 165.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 36% 65% 165.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 36% 65% 165.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
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% 61% 162.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
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) 35% 65% 161.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 31% 85% 161 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 38% 56% 158.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 64% 155.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 64% 155.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 64% 155.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 64% 155.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 64% 155.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 64% 155.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
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) 39% 70% 154.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 32% 65% 152.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized) 37% 99% 146.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 38% 84% 142.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
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) 32% 97% 136 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 34% 62% 131.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 31% 95% 131.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 32% 63% 129.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 36% 77% 124 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 43% 256.5

Sequence Analysis Tools

View WP_052717993.1 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

MKDKNISNERYTQKKTTALELFNIQLAIDNHAILQALTFDLTEGEILCLLGPSGCGKTTA
LKTIAGLSIPQQGHISLFGDTVFSDNIINQPPEQRSIGFIFQDYALFPHMTVSQNIAYGL
SHLGKQERQQRIKESLELVELSDLEQRYPHELSGGQQQRIAVARALAPKPKLLLMDEPFS
NIDGQVKRRMMADLRRLLKEHNISCIFVTHAKEEAFAFADKTAVMINGHIEQLDIPAKVF
NQPNTFAVAEFMEAGNLATLKHSQQVLDKIPHQWPRDIDNSGYWLFKPQHLILSHSLQNT
GIELIDSTYIGRGYQHDIAIRLTKSNHAPTVIWKAETETPLGIAIGENIALEYDQQPHWL
QD

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