GapMind for catabolism of small carbon sources

 

Protein 3607559 in Dinoroseobacter shibae DFL-12

Annotation: Dshi_0971 ABC transporter related (RefSeq)

Length: 334 amino acids

Source: Dino in FitnessBrowser

Candidate for 24 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-sorbitol (glucitol) catabolism mtlK hi ABC transporter for D-Sorbitol, ATPase component (characterized) 80% 100% 537.3 N-Acetyl-D-glucosamine ABC transport system, ATPase component 59% 387.1
D-mannitol catabolism mtlK med SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 76% 99% 500.4 ABC transporter for D-Sorbitol, ATPase component 80% 537.3
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 59% 93% 387.1 ABC transporter for D-Sorbitol, ATPase component 80% 537.3
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 59% 93% 387.1 ABC transporter for D-Sorbitol, ATPase component 80% 537.3
D-maltose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 57% 96% 369.8 ABC transporter for D-Sorbitol, ATPase component 80% 537.3
sucrose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 57% 96% 369.8 ABC transporter for D-Sorbitol, ATPase component 80% 537.3
trehalose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 57% 96% 369.8 ABC transporter for D-Sorbitol, ATPase component 80% 537.3
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 56% 100% 351.7 ABC transporter for D-Sorbitol, ATPase component 80% 537.3
lactose catabolism lacK med ABC transporter for Lactose, ATPase component (characterized) 54% 99% 351.3 ABC transporter for D-Sorbitol, ATPase component 80% 537.3
D-maltose catabolism malK med Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 60% 70% 319.3 ABC transporter for D-Sorbitol, ATPase component 80% 537.3
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 58% 74% 317 ABC transporter for D-Sorbitol, ATPase component 80% 537.3
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 58% 74% 317 ABC transporter for D-Sorbitol, ATPase component 80% 537.3
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 58% 74% 317 ABC transporter for D-Sorbitol, ATPase component 80% 537.3
D-maltose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 58% 74% 317 ABC transporter for D-Sorbitol, ATPase component 80% 537.3
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 58% 74% 317 ABC transporter for D-Sorbitol, ATPase component 80% 537.3
sucrose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 58% 74% 317 ABC transporter for D-Sorbitol, ATPase component 80% 537.3
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 58% 74% 317 ABC transporter for D-Sorbitol, ATPase component 80% 537.3
trehalose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 58% 74% 317 ABC transporter for D-Sorbitol, ATPase component 80% 537.3
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 58% 74% 317 ABC transporter for D-Sorbitol, ATPase component 80% 537.3
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) 45% 100% 307.8 ABC transporter for D-Sorbitol, ATPase component 80% 537.3
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 47% 99% 293.9 ABC transporter for D-Sorbitol, ATPase component 80% 537.3
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 48% 87% 255 ABC transporter for D-Sorbitol, ATPase component 80% 537.3
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 52% 62% 239.6 ABC transporter for D-Sorbitol, ATPase component 80% 537.3
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 34% 95% 195.3 ABC transporter for D-Sorbitol, ATPase component 80% 537.3

Sequence Analysis Tools

View 3607559 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

MGQIKLNQVTKSFGDVEVIPPLDLTIEDGEFAVFVGPSGCGKSTLLRLIAGLEDITSGHI
EIDGKDATNVPPAKRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIDEAEQQRRIDAAAKA
LNLTDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEISELH
KRLETTMIYVTHDQVEAMTMADKIVVLRAGHIEQVGSPLELYHSPRNEFVAGFIGSPKMN
LIKGAEAAKHGVATIGIRPEHTDVSTTEGLWEGRVGVAEHLGSDTFLHIHGVPDCDPMTV
RVDGELPVKHGDKIFLTPQLDKLHKFDAQGLRVS

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