GapMind for catabolism of small carbon sources

 

Protein 3607124 in Dinoroseobacter shibae DFL-12

Annotation: Dshi_0546 ABC transporter related (RefSeq)

Length: 338 amino acids

Source: Dino in FitnessBrowser

Candidate for 39 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
xylitol catabolism Dshi_0546 hi ABC transporter for Xylitol, ATPase component (characterized) 100% 100% 666.8 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 54% 361.3
D-mannitol catabolism mtlK med ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) 54% 98% 361.3 ABC transporter for Xylitol, ATPase component 100% 666.8
D-sorbitol (glucitol) catabolism mtlK med MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 53% 98% 359 ABC transporter for Xylitol, ATPase component 100% 666.8
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 54% 100% 350.1 ABC transporter for Xylitol, ATPase component 100% 666.8
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 54% 100% 350.1 ABC transporter for Xylitol, ATPase component 100% 666.8
lactose catabolism lacK med LacK, component of Lactose porter (characterized) 50% 100% 331.6 ABC transporter for Xylitol, ATPase component 100% 666.8
D-maltose catabolism malK med Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 50% 97% 318.9 ABC transporter for Xylitol, ATPase component 100% 666.8
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 50% 99% 318.5 ABC transporter for Xylitol, ATPase component 100% 666.8
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 50% 99% 318.5 ABC transporter for Xylitol, ATPase component 100% 666.8
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 50% 99% 318.5 ABC transporter for Xylitol, ATPase component 100% 666.8
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 49% 99% 313.9 ABC transporter for Xylitol, ATPase component 100% 666.8
trehalose catabolism malK med 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) 48% 100% 308.1 ABC transporter for Xylitol, ATPase component 100% 666.8
D-maltose catabolism malK_Sm med 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) 47% 98% 307.4 ABC transporter for Xylitol, ATPase component 100% 666.8
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 47% 96% 307 ABC transporter for Xylitol, ATPase component 100% 666.8
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) 49% 95% 306.6 ABC transporter for Xylitol, ATPase component 100% 666.8
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 49% 94% 300.8 ABC transporter for Xylitol, ATPase component 100% 666.8
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 48% 98% 300.1 ABC transporter for Xylitol, ATPase component 100% 666.8
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 45% 93% 298.9 ABC transporter for Xylitol, ATPase component 100% 666.8
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 46% 98% 297.7 ABC transporter for Xylitol, ATPase component 100% 666.8
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 48% 96% 297 ABC transporter for Xylitol, ATPase component 100% 666.8
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 46% 99% 295 ABC transporter for Xylitol, ATPase component 100% 666.8
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 44% 93% 292 ABC transporter for Xylitol, ATPase component 100% 666.8
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 47% 95% 291.2 ABC transporter for Xylitol, ATPase component 100% 666.8
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 45% 89% 283.1 ABC transporter for Xylitol, ATPase component 100% 666.8
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 41% 97% 248.4 ABC transporter for Xylitol, ATPase component 100% 666.8
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized) 42% 92% 154.1 ABC transporter for Xylitol, ATPase component 100% 666.8
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 96% 196.4 ABC transporter for Xylitol, ATPase component 100% 666.8
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 96% 196.4 ABC transporter for Xylitol, ATPase component 100% 666.8
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 96% 196.4 ABC transporter for Xylitol, ATPase component 100% 666.8
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 96% 196.4 ABC transporter for Xylitol, ATPase component 100% 666.8
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 96% 196.4 ABC transporter for Xylitol, ATPase component 100% 666.8
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 96% 196.4 ABC transporter for Xylitol, ATPase component 100% 666.8
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 96% 196.4 ABC transporter for Xylitol, ATPase component 100% 666.8
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 96% 196.4 ABC transporter for Xylitol, ATPase component 100% 666.8
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 32% 95% 191 ABC transporter for Xylitol, ATPase component 100% 666.8
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 38% 62% 172.6 ABC transporter for Xylitol, ATPase component 100% 666.8
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 37% 94% 154.5 ABC transporter for Xylitol, ATPase component 100% 666.8
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 38% 94% 154.1 ABC transporter for Xylitol, ATPase component 100% 666.8
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% 77% 129 ABC transporter for Xylitol, ATPase component 100% 666.8

Sequence Analysis Tools

View 3607124 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 and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MAGIKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRI
EIGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARV
LQLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLH
KQLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMN
VFSSDVGLQDISLDASAAFVGCRPEHIEIVPDGDGHIAATVHVKERLGGESLLYLGLKGG
GQIVARVGGDDETKVGAAVSLRFSRHRLHQFDEAGRAI

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, the preprint on GapMind for carbon sources, 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