SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing WP_038065550.1 NCBI__GCF_000715505.1:WP_038065550.1 to proteins with known functional sites using BLASTp with E ≤ 0.001.

Or try Sites on a Tree, PaperBLAST, Conserved Domains, or compare to all protein structures

Found 6 hits to proteins with known functional sites (download)

2wdrB E. Coli succinate:quinone oxidoreductase (sqr) with pentachlorophenol bound (see paper)
27% identity, 22% coverage: 8:103/430 of query aligns to 132:233/238 of 2wdrB

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2wdrB

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binding fe3-s4 cluster: C159 (= C35), P172 (= P48), C206 (= C76), S208 (= S78), I209 (≠ C79), M210 (≠ L80), N211 (≠ A81), C212 (= C82), T223 (≠ M93)
binding pentachlorophenol: P160 (= P36), W164 (≠ V40), I209 (≠ C79)
binding iron/sulfur cluster: C149 (= C25), I150 (≠ V26), L151 (≠ H27), C152 (= C28), C155 (= C31), A173 (≠ R49), C216 (= C86), P217 (= P87)

Sites not aligning to the query:

binding fe2/s2 (inorganic) cluster: 55, 56, 60, 61, 63, 75

2wdqB E. Coli succinate:quinone oxidoreductase (sqr) with carboxin bound (see paper)
27% identity, 22% coverage: 8:103/430 of query aligns to 132:233/238 of 2wdqB

query
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2wdqB

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binding 2-methyl-n-phenyl-5,6-dihydro-1,4-oxathiine-3-carboxamide: P160 (= P36), W164 (≠ V40), H207 (≠ L77)
binding fe3-s4 cluster: C159 (= C35), P172 (= P48), C206 (= C76), H207 (≠ L77), S208 (= S78), I209 (≠ C79), M210 (≠ L80), N211 (≠ A81), C212 (= C82), T223 (≠ M93)
binding iron/sulfur cluster: C149 (= C25), I150 (≠ V26), L151 (≠ H27), C152 (= C28), A153 (≠ G29), C155 (= C31), A173 (≠ R49), C216 (= C86), P217 (= P87)

Sites not aligning to the query:

binding fe2/s2 (inorganic) cluster: 55, 56, 58, 60, 61, 63, 75

2aczB Complex ii (succinate dehydrogenase) from e. Coli with atpenin a5 inhibitor co-crystallized at the ubiquinone binding site (see paper)
27% identity, 22% coverage: 8:103/430 of query aligns to 132:233/238 of 2aczB

query
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2aczB

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binding 3-[(2s,4s,5r)-5,6-dichloro-2,4-dimethyl-1-oxohexyl]-4-hydroxy-5,6-dimethoxy-2(1h)-pyridinone: P160 (= P36), W164 (≠ V40), H207 (≠ L77), I209 (≠ C79)
binding fe3-s4 cluster: C159 (= C35), P172 (= P48), C206 (= C76), S208 (= S78), M210 (≠ L80), C212 (= C82), T223 (≠ M93)
binding iron/sulfur cluster: C149 (= C25), I150 (≠ V26), C152 (= C28), A153 (≠ G29), C155 (= C31), C216 (= C86), L220 (≠ V90)

Sites not aligning to the query:

binding fe2/s2 (inorganic) cluster: 53, 54, 55, 56, 58, 59, 60, 63, 75

1nenB Complex ii (succinate dehydrogenase) from e. Coli with dinitrophenol-17 inhibitor co-crystallized at the ubiquinone binding site (see paper)
27% identity, 22% coverage: 8:103/430 of query aligns to 132:233/238 of 1nenB

query
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1nenB

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binding calcium ion: D187 (= D66), T190 (= T69)
binding 2-[1-methylhexyl]-4,6-dinitrophenol: P160 (= P36), W164 (≠ V40), I209 (≠ C79)
binding fe3-s4 cluster: C159 (= C35), P172 (= P48), C206 (= C76), S208 (= S78), I209 (≠ C79), M210 (≠ L80), C212 (= C82), T223 (≠ M93)
binding iron/sulfur cluster: C149 (= C25), I150 (≠ V26), L151 (≠ H27), C152 (= C28), A153 (≠ G29), C155 (= C31), C216 (= C86), L220 (≠ V90)

Sites not aligning to the query:

binding fe2/s2 (inorganic) cluster: 54, 55, 56, 58, 59, 60, 61, 63, 75

1nekB Complex ii (succinate dehydrogenase) from e. Coli with ubiquinone bound (see paper)
27% identity, 22% coverage: 8:103/430 of query aligns to 132:233/238 of 1nekB

query
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1nekB

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binding calcium ion: D187 (= D66), T190 (= T69)
binding fe3-s4 cluster: C159 (= C35), P172 (= P48), C206 (= C76), S208 (= S78), I209 (≠ C79), M210 (≠ L80), C212 (= C82), T223 (≠ M93)
binding iron/sulfur cluster: C149 (= C25), I150 (≠ V26), C152 (= C28), A153 (≠ G29), C154 (≠ F30), C155 (= C31), A173 (≠ R49), C216 (= C86), L220 (≠ V90)
binding ubiquinone-2: P160 (= P36), W164 (≠ V40), I209 (≠ C79)

Sites not aligning to the query:

binding fe2/s2 (inorganic) cluster: 54, 55, 56, 58, 59, 60, 61, 63, 75

P07014 Succinate dehydrogenase iron-sulfur subunit; EC 1.3.5.1 from Escherichia coli (strain K12) (see paper)
27% identity, 22% coverage: 8:103/430 of query aligns to 132:233/238 of P07014

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P07014

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W164 (≠ V40) binding a ubiquinone

Query Sequence

>WP_038065550.1 NCBI__GCF_000715505.1:WP_038065550.1
MQTNFTPEQLEDPGIARSNSILRACVHCGFCTATCPSYQVLGDELDSPRGRIYLIKDMLE
NDRPADAKTVKHLDRCLSCLACVSTCPSGVDYMHLIDHARAHVEKTYKRPLMDRLLRATL
ARILPYPGRFRLAMGGAKLARPFARFLPDRRLRAMLEMAPKVIPPVSRNDDPQVFAPEGR
KRYRVALQTGCAQRALNTDINDATIRLLRRLGCEVVIPKGLGCCGALAHHMGREGESHAQ
ALANIRAYLAEPELDAVIINTSGCGTTVKDYGEMLRHGPHAQEAAKVAELACDISEFVAR
IGLPERQNPKAEPGALRVAYHAACSLQHGQQIKAAPKDLLRQAGFEVVEPADSHLCCGSA
GTYNLLQPEIAQELRKRKVATLEAKAPQVIAAGNIGCMMQIAGGTGIPVVHSVELLDWAT
GGPKPRALSA

Or try a new SitesBLAST search

SitesBLAST's Database

SitesBLAST's database includes (1) SwissProt entries with experimentally-supported functional features; and (2) protein structures with bound ligands, from the BioLip database.

by Morgan Price, Arkin group
Lawrence Berkeley National Laboratory