GapMind for catabolism of small carbon sources

 

Protein 3607949 in Dinoroseobacter shibae DFL-12

Annotation: Dshi_1357 ABC transporter related (RefSeq)

Length: 349 amino acids

Source: Dino in FitnessBrowser

Candidate for 34 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) 57% 95% 372.9 SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter 58% 372.1
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 57% 95% 372.9 SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter 58% 372.1
D-mannitol catabolism mtlK med SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 58% 100% 372.1 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 57% 100% 365.2 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9
lactose catabolism lacK med ABC transporter for Lactose, ATPase component (characterized) 55% 100% 355.9 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 54% 100% 346.3 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9
D-maltose catabolism thuK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 54% 100% 346.3 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 54% 100% 346.3 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 54% 100% 346.3 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 54% 100% 339.7 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 54% 97% 337 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 54% 97% 337 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 54% 97% 337 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 54% 97% 337 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 54% 97% 337 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 54% 97% 337 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9
sucrose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 54% 97% 335.9 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9
trehalose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 54% 97% 335.9 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 51% 99% 331.6 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9
D-maltose catabolism malK med Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 52% 98% 327.8 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9
D-cellobiose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 47% 98% 306.6 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9
D-glucose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 47% 98% 306.6 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9
lactose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 47% 98% 306.6 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9
D-maltose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 47% 98% 306.6 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9
sucrose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 47% 98% 306.6 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9
trehalose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 47% 98% 306.6 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 47% 86% 305.1 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 46% 93% 299.7 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 48% 99% 294.3 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 45% 88% 246.9 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9
glycerol catabolism glpT lo ABC transporter for Glycerol, ATPase component 2 (characterized) 38% 92% 212.6 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 39% 65% 172.2 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9
L-asparagine catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 35% 91% 146.4 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9
L-aspartate catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 35% 91% 146.4 N-Acetyl-D-glucosamine ABC transport system, ATPase component 57% 372.9

Sequence Analysis Tools

View 3607949 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

MGAITLSKVEKWFGDVQVIKGVDLEIRDGEFVVFVGPSGCGKSTLLRMIGGLEDTSRGAM
LIDGVDVTDHPPAKRGLTMVFQSYALYPHMSVRENMGFSLKTAGAPAAEIAEKVEAAAAV
LKLEPYLDRRPKDLSGGQRQRVAIGRSIVRAPTAFLFDEPLSNLDAALRVEMRYEIAKLH
QSLDTTMIYVTHDQVEAMTLADRIVVLEFGKIAQVGTPRELYETPANLFVAQFIGSPKMN
VMPCTTDAGRYRLSAGRGGVFSGDRPAVQLGIRPEHITPGAPGTGACDGRVDVVEYLGAD
TLLVLDCGPEGRVTVRVIGDTDLTPGDAVGLSFNPDRLSFFDTDGLAIR

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