SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing Synpcc7942_2129 FitnessBrowser__SynE:Synpcc7942_2129 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)

8a6tB Cryo-em structure of the electron bifurcating fe-fe hydrogenase hydabc complex from thermoanaerobacter kivui in the reduced state (see paper)
38% identity, 39% coverage: 79:130/134 of query aligns to 577:627/630 of 8a6tB

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binding iron/sulfur cluster: I577 (= I79), C582 (= C84), I583 (≠ V85), C585 (= C87), C588 (= C90), C592 (= C94), A596 (= A98), I597 (≠ L99), I607 (≠ F110), C612 (= C115), C618 (= C121), C622 (= C125), K624 (≠ V127), A626 (= A129), I627 (= I130)

Sites not aligning to the query:

binding fe2/s2 (inorganic) cluster: 31, 33, 36, 82, 85, 86
binding flavin mononucleotide: 201, 227, 230, 355, 535, 536
binding nadp nicotinamide-adenine-dinucleotide phosphate: 320, 337, 340, 341, 342, 433
binding iron/sulfur cluster: 487, 488, 489, 491, 494, 534, 536, 537, 575
binding zinc ion: 471, 558, 564

5t61L Tungsten formylmethanofuran dehydrogenase subunit fwdF (see paper)
35% identity, 44% coverage: 72:130/134 of query aligns to 141:208/348 of 5t61L

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binding iron/sulfur cluster: I146 (= I77), C153 (= C84), C156 (= C87), C159 (= C90), C163 (= C94), P164 (= P95), I168 (≠ L99), I186 (≠ L108), C193 (= C115), H195 (≠ V117), C196 (= C118), G197 (≠ E119), C199 (= C121), C203 (= C125), P204 (= P126), I208 (= I130)

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binding iron/sulfur cluster: 30, 31, 32, 33, 34, 36, 40, 41, 70, 71, 72, 73, 74, 76, 80, 85, 114, 117, 118, 120, 124, 129, 212, 215, 238, 239, 240, 241, 242, 244, 248, 249, 270, 272, 273, 274, 276, 280, 281, 284, 307, 308, 309, 310, 311, 313, 317

6cfwN Cryoem structure of a respiratory membrane-bound hydrogenase (see paper)
34% identity, 42% coverage: 75:130/134 of query aligns to 36:91/121 of 6cfwN

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binding iron/sulfur cluster: C45 (= C84), G47 (≠ D86), C48 (= C87), M50 (≠ L89), C51 (= C90), C55 (= C94), C76 (= C115), M78 (≠ V117), C79 (= C118), C82 (= C121), C86 (= C125)

8a8oD Paps reductase from methanothermococcus thermolithotrophicus refined to 1.45 a (see paper)
45% identity, 38% coverage: 84:134/134 of query aligns to 9:59/102 of 8a8oD

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binding iron/sulfur cluster: C9 (= C84), I10 (≠ V85), G11 (≠ D86), C12 (= C87), G13 (= G88), C15 (= C90), C19 (= C94), P20 (= P95), S32 (= S105), C40 (= C115), W41 (≠ S116), D42 (≠ V117), C43 (= C118), A44 (≠ E119), C46 (= C121), C50 (= C125), I55 (= I130)

Sites not aligning to the query:

binding iron/sulfur cluster: 2

7q4vB Electron bifurcating hydrogenase - hydabc from a. Woodii (see paper)
34% identity, 40% coverage: 79:131/134 of query aligns to 546:597/599 of 7q4vB

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binding iron/sulfur cluster: C551 (= C84), K552 (≠ V85), G553 (≠ D86), C554 (= C87), G555 (= G88), I556 (≠ L89), C557 (= C90), C561 (= C94), P562 (= P95), Y574 (≠ L108), C581 (= C115), K583 (≠ V117), C584 (= C118), G585 (≠ E119), A586 (≠ Q120), C587 (= C121), C591 (= C125), F593 (≠ V127), S595 (≠ A129)

Sites not aligning to the query:

binding fe2/s2 (inorganic) cluster: 11, 16, 48, 49, 51, 52
binding flavin mononucleotide: 166, 168, 196, 198, 284, 287, 288, 289, 324
binding iron/sulfur cluster: 457, 458, 459, 460, 463, 503, 506, 544
binding zinc ion: 440, 527, 533

7q4vF Electron bifurcating hydrogenase - hydabc from a. Woodii (see paper)
34% identity, 40% coverage: 79:131/134 of query aligns to 417:468/470 of 7q4vF

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binding iron/sulfur cluster: I417 (= I79), C422 (= C84), G424 (≠ D86), C425 (= C87), G426 (= G88), I427 (≠ L89), C428 (= C90), C432 (= C94), P433 (= P95), I437 (≠ L99), Y445 (≠ L108), C452 (= C115), K454 (≠ V117), C455 (= C118), G456 (≠ E119), A457 (≠ Q120), C458 (= C121), C462 (= C125), P463 (= P126), I467 (= I130)

Sites not aligning to the query:

binding flavin mononucleotide: 37, 39, 67, 158, 159, 160, 375
binding nicotinamide-adenine-dinucleotide: 40, 43, 48, 177, 180, 297
binding iron/sulfur cluster: 327, 328, 329, 330, 331, 334, 373, 374, 415
binding zinc ion: 311, 398, 404, 409

Query Sequence

>Synpcc7942_2129 FitnessBrowser__SynE:Synpcc7942_2129
MKKRVTLTFPRRIVQMPITYRLATEFNVAANIIRAQITPNQSGKLVVELSGDIDALEAAI
DWMGMQDINVSLTTAEIVIDRDRCVDCGLCTGVCPTGALRLDPKSFQLQFDRPRCSVCEQ
CIPTCPVQAIATNL

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