Sites on a Tree

 

Searching for up to 100 curated homologs for RR42_RS25930 FitnessBrowser__Cup4G11:RR42_RS25930 (422 a.a.)

Found high-coverage hits (≥70%) to 16 curated proteins.

Removed hits that are identical to the query, leaving 15

You can add additional sequences or change the %identity threshold for inclusion. Once you have selected sequences, you can build an alignment and a tree.

Hits with ≥ 30% identity

AZOBR_RS08020 D-alanine dehydrogenase (EC 1.4.99.-) from Azospirillum brasilense Sp245
    35% identity, 94% coverage of query (224 bits)

Ac3H11_4848 D-alanine dehydrogenase (EC 1.4.99.-) from Acidovorax sp. GW101-3H11
    34% identity, 95% coverage of query (223 bits)

DadR / b1189 D-amino acid dehydrogenase (EC 1.4.5.1) from Escherichia coli K-12 substr. MG1655 (see 3 papers)
dadA / P0A6J5 D-amino acid dehydrogenase (EC 1.4.5.1) from Escherichia coli (strain K12) (see 22 papers)
DADA_ECOLI / P0A6J5 D-amino acid dehydrogenase; D-alanine dehydrogenase; EC 1.4.99.- from Escherichia coli (strain K12) (see 4 papers)
dadA / AAC36880.1 D-amino acid dehydrogenase from Escherichia coli (see paper)
    32% identity, 94% coverage of query (206 bits)

DADA_KLEAE / O30745 D-amino acid dehydrogenase; D-alanine dehydrogenase; EC 1.4.99.- from Klebsiella aerogenes (Enterobacter aerogenes) (see paper)
    32% identity, 94% coverage of query (196 bits)

Psest_3793 D-alanine dehydrogenase (EC 1.4.99.-) from Pseudomonas stutzeri RCH2
    31% identity, 94% coverage of query (191 bits)

DADA1_PSEAE / Q9HTQ0 D-amino acid dehydrogenase 1; D-alanine dehydrogenase 1; EC 1.4.99.- from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see paper)
Q9HTQ0 D-arginine dehydrogenase (EC 1.4.99.6) from Pseudomonas aeruginosa (see paper)
    30% identity, 95% coverage of query (189 bits)

Build an alignment

Build an alignment for RR42_RS25930 and 6 homologs with ≥ 30% identity

Select sequences

Add sequences from UniProt, PDB, RefSeq, or MicrobesOnline (separate identifiers with commas or spaces):

Or download the sequences

Change minimum %identity:

Additional hits (identity < 30%)

lhpB / Q88NF6 D-hydroxyproline dehydrogenase subunit from Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440) (see 2 papers)
    25% identity, 96% coverage of query (92.0 bits)

dadA / A3KEZ1 D-amino acid dehydrogenase (EC 1.4.5.1) from Helicobacter pylori (see paper)
DADA_HELPX / A3KEZ1 D-amino acid dehydrogenase; DAD; EC 1.4.5.1 from Helicobacter pylori (Campylobacter pylori) (see paper)
A3KEZ1 D-amino acid dehydrogenase (quinone) (EC 1.4.5.1); D-arginine dehydrogenase (EC 1.4.99.6) from Helicobacter pylori (see 2 papers)
    23% identity, 94% coverage of query (90.1 bits)

amaD / Q88GX1 D-lysine oxidase (EC 1.4.3.3) from Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440) (see paper)
    25% identity, 94% coverage of query (80.1 bits)

L7T8Y9 glycine oxidase (EC 1.4.3.19) from Bacillus cereus (see 2 papers)
    21% identity, 95% coverage of query (67.4 bits)

6j38A / X5IYZ1 Crystal structure of cmis2 (see paper)
    24% identity, 81% coverage of query (67.0 bits)

6j39A Crystal structure of cmis2 with inhibitor
    24% identity, 81% coverage of query (67.0 bits)

7cyxA / Q81HQ7 Crystal strcuture of glycine oxidase from bacillus cereus atcc 14579 (see paper)
    21% identity, 95% coverage of query (64.3 bits)

HCNC_PSEAE / G3XD12 Hydrogen cyanide synthase subunit HcnC; HcnC; Glycine dehydrogenase (cyanide-forming); EC 1.4.99.5 from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (see 6 papers)
    22% identity, 95% coverage of query (54.3 bits)

C7E717 glycine dehydrogenase (cyanide-forming) (subunit 1/3) (EC 1.4.99.5) from Pseudomonas fluorescens (see paper)
    21% identity, 95% coverage of query (50.8 bits)

Or start over

by Morgan Price, Arkin group
Lawrence Berkeley National Laboratory