SitesBLAST – Find functional sites

 

SitesBLAST

Comparing RR42_RS27210 FitnessBrowser__Cup4G11:RR42_RS27210 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 3 hits to proteins with known functional sites (download)

3nojA The structure of hmg/cha aldolase from the protocatechuate degradation pathway of pseudomonas putida (see paper)
63% identity, 95% coverage: 4:229/237 of query aligns to 9:234/235 of 3nojA

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3nojA
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D

A5W059 4-hydroxy-4-methyl-2-oxoglutarate aldolase/4-carboxy-4-hydroxy-2-oxoadipate aldolase; HMG/CHA aldolase; Oxaloacetate decarboxylase; OAA decarboxylase; EC 4.1.3.17; EC 4.1.1.112 from Pseudomonas putida (strain ATCC 700007 / DSM 6899 / BCRC 17059 / F1) (see paper)
63% identity, 95% coverage: 4:229/237 of query aligns to 10:235/238 of A5W059

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A5W059
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D

1nxjA Structure of rv3853 from mycobacterium tuberculosis (see paper)
27% identity, 56% coverage: 42:174/237 of query aligns to 25:156/156 of 1nxjA

query
sites
1nxjA
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V

Sites not aligning to the query:

Query Sequence

>RR42_RS27210 FitnessBrowser__Cup4G11:RR42_RS27210
MKTIAYRNILRAAAADIDALGAAGVATVHEAQRRTGLMKPYMRPVQSRAAMAGSAVTVLM
HPGDNWMIHVAVEMVQPGDVLVVALVSDCTDGLFGDLLATSLKARGARGLVIDAGVRDVS
TLNAMGFPVWSRAVSAQGAVKETVGAVNVPVVCAGAHVRPGDVIVADDDGVVVVPRPLAA
ETARRAAERGAMEEGKRATLAAGVLGLDMYQMREALAAKGLAYAEQTVDWYSGFDEA

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