SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing WP_011912926.1 NCBI__GCF_000013785.1:WP_011912926.1 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 16 hits to proteins with known functional sites (download)

O14289 3-isopropylmalate dehydratase; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase; EC 4.2.1.33 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
56% identity, 96% coverage: 4:210/215 of query aligns to 540:734/758 of O14289

query
sites
O14289

F

F

T

T

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V

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V

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E

G

G

L

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A

C

A

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M

Sites not aligning to the query:

486 modified: Phosphoserine
488 modified: Phosphoserine

P9WK95 3-isopropylmalate dehydratase small subunit; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase; EC 4.2.1.33 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see paper)
43% identity, 93% coverage: 1:200/215 of query aligns to 1:184/198 of P9WK95

query
sites
P9WK95

M

M

K

E

A

A

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E

K154 (≠ E170) modified: Isoglutamyl lysine isopeptide (Lys-Gln) (interchain with Q-Cter in protein Pup)

Q58667 Methanogen homoaconitase small subunit; HACN; Homoaconitate hydratase; EC 4.2.1.114 from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii) (see paper)
39% identity, 56% coverage: 18:137/215 of query aligns to 13:112/170 of Q58667

query
sites
Q58667

N

D

V

V

D

D

T

T

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D

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A

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R26 (≠ D50) mutation R->K,V: Allows the recognition of substrates of IPMI enzymes since it becomes able to efficiently catalyze citraconate hydration and 3-isopropylmalate dehydration. Largely decreases substrate affinity for cis-homo(1-3)-aconitate.
T27 (≠ V51) mutation to A: Largely decreases substrate affinity for cis-homo(1-3)-aconitate while slightly increases activity on these substrates, and also decreases substrate affinity for maleate. Gains the ability to hydrate citraconate, an IPMI substrate.

2pkpA Crystal structure of 3-isopropylmalate dehydratase (leud)from methhanocaldococcus jannaschii dsm2661 (mj1271) (see paper)
39% identity, 56% coverage: 18:137/215 of query aligns to 13:112/167 of 2pkpA

query
sites
2pkpA

N
x
D

V

V

D

D

T

T

D

D

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A

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binding zinc ion: D13 (≠ N18), C63 (= C88)

P20004 Aconitate hydratase, mitochondrial; Aconitase; Citrate hydro-lyase; EC 4.2.1.3 from Bos taurus (Bovine) (see 2 papers)
48% identity, 25% coverage: 79:132/215 of query aligns to 658:711/780 of P20004

query
sites
P20004

V

V

L

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E

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SR 670:671 (= SR 91:92) binding substrate

Sites not aligning to the query:

99 binding substrate
192:194 binding substrate
385 binding [4Fe-4S] cluster
448 binding [4Fe-4S] cluster
451 binding [4Fe-4S] cluster
474 binding substrate
479 binding substrate
607 binding substrate

5acnA Structure of activated aconitase. Formation of the (4fe-4s) cluster in the crystal (see paper)
46% identity, 25% coverage: 79:132/215 of query aligns to 631:684/754 of 5acnA

query
sites
5acnA

V

V

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active site: S642 (= S90), R644 (= R92)
binding tricarballylic acid: R666 (≠ D114)

Sites not aligning to the query:

active site: 100, 101, 165, 447
binding fe3-s4 cluster: 145, 147, 167, 358, 421, 424, 446
binding tricarballylic acid: 198, 235

P16276 Aconitate hydratase, mitochondrial; Aconitase; Citrate hydro-lyase; EC 4.2.1.3 from Sus scrofa (Pig) (see 3 papers)
46% identity, 25% coverage: 79:132/215 of query aligns to 658:711/781 of P16276

query
sites
P16276

V

V

L

V

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E

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SR 670:671 (= SR 91:92) binding substrate

Sites not aligning to the query:

28 modified: Pyrrolidone carboxylic acid
99 binding substrate
192:194 binding substrate
385 binding [4Fe-4S] cluster
448 binding [4Fe-4S] cluster
451 binding [4Fe-4S] cluster
474 binding substrate
479 binding substrate
607 binding substrate

1b0kA S642a:fluorocitrate complex of aconitase (see paper)
44% identity, 25% coverage: 79:132/215 of query aligns to 630:683/753 of 1b0kA

query
sites
1b0kA

V

V

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active site: A641 (≠ S90), R643 (= R92)
binding citrate anion: A641 (≠ S90), S642 (= S91), R643 (= R92)

Sites not aligning to the query:

active site: 99, 100, 164, 446
binding citrate anion: 71, 100, 164, 165, 446, 451, 579
binding oxygen atom: 164, 166
binding iron/sulfur cluster: 100, 164, 166, 356, 357, 420, 423

8acnA Crystal structures of aconitase with isocitrate and nitroisocitrate bound (see paper)
46% identity, 25% coverage: 79:132/215 of query aligns to 630:683/753 of 8acnA

query
sites
8acnA

V

V

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active site: S641 (= S90), R643 (= R92)
binding nitroisocitric acid: S641 (= S90), S642 (= S91), R643 (= R92)

Sites not aligning to the query:

active site: 99, 100, 164, 446
binding nitroisocitric acid: 71, 74, 100, 164, 165, 446, 451, 579
binding iron/sulfur cluster: 100, 164, 166, 356, 357, 420, 423, 424

1fghA Complex with 4-hydroxy-trans-aconitate (see paper)
46% identity, 25% coverage: 79:132/215 of query aligns to 630:683/753 of 1fghA

query
sites
1fghA

V

V

L

V

L

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E

N

N

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active site: S641 (= S90), R643 (= R92)
binding 4-hydroxy-aconitate ion: S641 (= S90), S642 (= S91), R643 (= R92)

Sites not aligning to the query:

active site: 99, 100, 164, 446
binding 4-hydroxy-aconitate ion: 71, 74, 100, 164, 165, 446, 451, 579
binding iron/sulfur cluster: 100, 164, 166, 356, 357, 420, 423, 424, 451

1amjA Steric and conformational features of the aconitase mechanism (see paper)
46% identity, 25% coverage: 79:132/215 of query aligns to 630:683/753 of 1amjA

query
sites
1amjA

V

V

L

V

L

I

A

G

R

D

E

E

N

N

F

Y

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active site: S641 (= S90), R643 (= R92)
binding sulfate ion: R643 (= R92)

Sites not aligning to the query:

active site: 99, 100, 164, 446
binding iron/sulfur cluster: 144, 166, 357, 420, 423
binding sulfate ion: 71, 579

1amiA Steric and conformational features of the aconitase mechanism (see paper)
46% identity, 25% coverage: 79:132/215 of query aligns to 630:683/753 of 1amiA

query
sites
1amiA

V

V

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V

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E

N

N

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Y

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R
|
R

E

E

H

H

A

S

P

A

W

L

A

E

L

P

E

R

E

F

Y

L

G

G

F

G

R

R

A

A

I

I

A

T

P

K

S

S

F

F

A

A

D

R

I

I

F

H

Y

E

N

T

N

N

S

L

F

K

K

K

N

Q

G

G

L

L

P

P

I

L

V

T

L

F

K

A

E

D

active site: S641 (= S90), R643 (= R92)
binding alpha-methylisocitric acid: S641 (= S90), S642 (= S91), R643 (= R92)

Sites not aligning to the query:

active site: 99, 100, 164, 446
binding alpha-methylisocitric acid: 71, 74, 100, 164, 165, 446, 451, 579
binding iron/sulfur cluster: 100, 144, 164, 166, 356, 357, 420, 423, 445

1acoA Crystal structure of aconitase with transaconitate bound (see paper)
46% identity, 25% coverage: 79:132/215 of query aligns to 630:683/753 of 1acoA

query
sites
1acoA

V

V

L

V

L

I

A

G

R

D

E

E

N

N

F

Y

G

G

C

E

G

G

S
|
S

R
|
R

E

E

H

H

A

S

P

A

W

L

A

E

L

P

E

R

E

F

Y

L

G

G

F

G

R

R

A

A

I

I

A

T

P

K

S

S

F

F

A

A

D

R

I

I

F

H

Y

E

N

T

N

N

S

L

F

K

K

K

N

Q

G

G

L

L

P

P

I

L

V

T

L

F

K

A

E

D

active site: S641 (= S90), R643 (= R92)
binding aconitate ion: S641 (= S90), S642 (= S91), R643 (= R92)

Sites not aligning to the query:

active site: 99, 100, 164, 446
binding iron/sulfur cluster: 100, 144, 164, 166, 356, 357, 420, 423, 445
binding aconitate ion: 71, 164, 165, 446, 451, 579

P19414 Aconitate hydratase, mitochondrial; Aconitase; Citrate hydro-lyase; EC 4.2.1.3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 2 papers)
50% identity, 27% coverage: 73:131/215 of query aligns to 648:707/778 of P19414

query
sites
P19414

R

R

Y

D

Q

Q

G

G

A

I

S

K

-

W

V

V

L

V

L

I

A

G

R

D

E

E

N

N

F

F

G

G

C

E

G

G

S

S

R

R

E

E

H

H

A

A

P

A

W

L

A

E

L

P

E

R

E

F

Y

L

G

G

F

G

R

F

A

A

I

I

A

T

P

K

S

S

F

F

A

A

D

R

I

I

F

H

Y

E

N

T

N

N

S

L

F

K

K

K

N

Q

G

G

L

L

P

P

I

L

V

N

L

F

K

K

Sites not aligning to the query:

1:16 modified: transit peptide, Mitochondrion
604 R→K: Strongly diminishes the catalytic activity towards both known substrates, aconitate and homoaconitate.

1nisA Crystal structure of aconitase with trans-aconitate and nitrocitrate bound (see paper)
46% identity, 25% coverage: 79:132/215 of query aligns to 630:683/753 of 1nisA

query
sites
1nisA

V

V

L

V

L

I

A

G

R

D

E

E

N

N

F

Y

G

G

C

E

G

G

S
|
S

R
|
R

E

E

H

H

A

R

P

A

W

L

A

E

L

P

E

R

E

F

Y

L

G

G

F

G

R

R

A

A

I

I

A

T

P

K

S

S

F

F

A

A

D

R

I

I

F

H

Y

E

N

T

N

N

S

L

F

K

K

K

N

Q

G

G

L

L

P

P

I

L

V

T

L

F

K

A

E

D

active site: S641 (= S90), R643 (= R92)
binding 2-hydroxy-2-nitromethyl succinic acid: S641 (= S90), S642 (= S91)

Sites not aligning to the query:

active site: 99, 100, 164, 446
binding 2-hydroxy-2-nitromethyl succinic acid: 71, 100, 164, 165, 446, 451, 579
binding iron/sulfur cluster: 100, 144, 166, 356, 357, 420, 423

P39533 Homocitrate dehydratase, mitochondrial; Aconitase 2; EC 4.2.1.- from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see paper)
25% identity, 50% coverage: 79:186/215 of query aligns to 660:785/789 of P39533

query
sites
P39533

V

T

L

V

L

I

A

A

R

E

E

H

N

N

F

Y

G

G

C

E

G

G

S

S

S

A

R

R

E

E

H

H

A

A

P

A

W

L

A

S

L

P

E

R

E

F

Y

L

G

G

F

G

R

E

A

I

I

L

A

V

P

K

S

S

F

F

A

A

D

R

I

I

F

H

Y

E

N

T

N

N

S

L

F

K

K

K

N

Q

G

G

L

V

L

L

P

P

I

L

V

T

L

F

K

A

E

N

E

E

E

S

V

D

D

Y

E

D

L

K

F

I

Q

S

A

G

E

D

A

V

T

L

E

E

G

T

Y

L

Q

N

L

L

T

-

V

V

D

D

L

M

A

I

A

A

Q

K

-

D

-

G

-

N

-

G

-

E

-

I

-

D

-

V

T

K

V

I

T

T

R

K

P

P

D

N

G

G

K

E

Q

S

Y

F

G

T

F

I

-

K

-

A

-

K

-

H

-

T

-

M

-

S

-

K

-

D

E

Q

V

I

D

D

A

F

F

F

R

K

K

A

H

G

C

S

L

A

L

I

N

N

G

Y

L

I

D

G

D

N

I

I

Sites not aligning to the query:

610 K→R: Reduces catalytic activity towards homoaconitate by 45% and increases the activity towards aconitate by a factor 116.

Query Sequence

>WP_011912926.1 NCBI__GCF_000013785.1:WP_011912926.1
MKAFTQHTGLVCPLDRANVDTDQIIPKQFLKSIKRTGFGPNLFDEWRYLDVGQPNQDCSQ
RPLNKDFVLNFPRYQGASVLLARENFGCGSSREHAPWALEEYGFRAIIAPSFADIFYNNS
FKNGLLPIVLKEEEVDELFQQAEATEGYQLTVDLAAQTVTRPDGKQYGFEVDAFRKHCLL
NGLDDIGLTLQDAEAIKAFEVRHQQSQPWLFGAIK

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