GapMind for catabolism of small carbon sources

 

Protein 351439 in Bacteroides thetaiotaomicron VPI-5482

Annotation: BT1911 7-alpha-hydroxysteroid dehydrogenase (NCBI ptt file)

Length: 259 amino acids

Source: Btheta in FitnessBrowser

Candidate for 23 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
ethanol catabolism etoh-dh-nad lo alcohol dehydrogenase (EC 1.1.1.1) (characterized) 36% 98% 150.6 7α-hydroxysteroid dehydrogenase subunit (EC 1.1.1.159) 85% 448.0
L-rhamnose catabolism LRA1 lo NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized) 35% 98% 137.9 7α-hydroxysteroid dehydrogenase subunit (EC 1.1.1.159) 85% 448.0
D-sorbitol (glucitol) catabolism sdh lo sorbitol dehydrogenase, D-fructose forming (EC 1.1.1.14) (characterized) 36% 97% 133.7 7α-hydroxysteroid dehydrogenase subunit (EC 1.1.1.159) 85% 448.0
L-fucose catabolism fucDH lo Short-chain alcohol dehydrogenase protein (characterized, see rationale) 35% 96% 132.1 7α-hydroxysteroid dehydrogenase subunit (EC 1.1.1.159) 85% 448.0
L-arabinose catabolism xacB lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 32% 93% 130.2 7α-hydroxysteroid dehydrogenase subunit (EC 1.1.1.159) 85% 448.0
D-galactose catabolism galdh lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 32% 93% 130.2 7α-hydroxysteroid dehydrogenase subunit (EC 1.1.1.159) 85% 448.0
lactose catabolism galdh lo L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized) 32% 93% 130.2 7α-hydroxysteroid dehydrogenase subunit (EC 1.1.1.159) 85% 448.0
D-xylose catabolism DKDP-dehydrog lo SDR family oxidoreductase (characterized, see rationale) 34% 96% 127.9 7α-hydroxysteroid dehydrogenase subunit (EC 1.1.1.159) 85% 448.0
L-rhamnose catabolism LRA5 lo 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; L-KDR 4-dehydrogenase; EC 1.1.1.401 (characterized) 31% 97% 124.4 7α-hydroxysteroid dehydrogenase subunit (EC 1.1.1.159) 85% 448.0
D-xylose catabolism xdh lo D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized) 33% 93% 124 7α-hydroxysteroid dehydrogenase subunit (EC 1.1.1.159) 85% 448.0
xylitol catabolism xdhA lo D-xylulose reductase (EC 1.1.1.9) (characterized) 32% 72% 109 7α-hydroxysteroid dehydrogenase subunit (EC 1.1.1.159) 85% 448.0
D-xylose catabolism xdhA lo D-xylulose reductase (EC 1.1.1.9) (characterized) 32% 72% 109 7α-hydroxysteroid dehydrogenase subunit (EC 1.1.1.159) 85% 448.0
4-hydroxybenzoate catabolism fadB lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 31% 95% 104 7α-hydroxysteroid dehydrogenase subunit (EC 1.1.1.159) 85% 448.0
4-hydroxybenzoate catabolism paaH lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 31% 95% 104 7α-hydroxysteroid dehydrogenase subunit (EC 1.1.1.159) 85% 448.0
L-arginine catabolism fadB lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 31% 95% 104 7α-hydroxysteroid dehydrogenase subunit (EC 1.1.1.159) 85% 448.0
L-citrulline catabolism fadB lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 31% 95% 104 7α-hydroxysteroid dehydrogenase subunit (EC 1.1.1.159) 85% 448.0
L-isoleucine catabolism ivdG lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 31% 95% 104 7α-hydroxysteroid dehydrogenase subunit (EC 1.1.1.159) 85% 448.0
L-lysine catabolism fadB lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 31% 95% 104 7α-hydroxysteroid dehydrogenase subunit (EC 1.1.1.159) 85% 448.0
phenylacetate catabolism fadB lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 31% 95% 104 7α-hydroxysteroid dehydrogenase subunit (EC 1.1.1.159) 85% 448.0
phenylacetate catabolism paaH lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 31% 95% 104 7α-hydroxysteroid dehydrogenase subunit (EC 1.1.1.159) 85% 448.0
L-phenylalanine catabolism fadB lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 31% 95% 104 7α-hydroxysteroid dehydrogenase subunit (EC 1.1.1.159) 85% 448.0
L-phenylalanine catabolism paaH lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 31% 95% 104 7α-hydroxysteroid dehydrogenase subunit (EC 1.1.1.159) 85% 448.0
L-proline catabolism fadB lo GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized) 31% 95% 104 7α-hydroxysteroid dehydrogenase subunit (EC 1.1.1.159) 85% 448.0

Sequence Analysis Tools

View 351439 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

MKRFENKVVVITGAAGGIGEATTRRIVSEGGKVVIADLSQERADKLAAELTQAGADVRPI
YFSATELQSCKELVDFAMKEYGQIDVLINNVGGTDPKRDLNIEKLDIDYFDEVFHLNLCC
TMYLSQQVIPIMTTHGGGNIVNVASISGLTADANGTLYGASKAGVINLTKYIATQMGKKN
IRCNAVAPGLVLTPAALDNLNEEVRNIFLGQCATPYLGEPEDVAATIAFLASNDARYITG
QTIVVDGGLTIHNPTVELS

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