BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 040864
(203 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2L1O|A Chain A, Zinc To Cadmium Replacement In The A. Thaliana Superman
Cys2his2 Zinc Finger Induces Structural Rearrangements
Of Typical Dna Base Determinant Positions
pdb|1NJQ|A Chain A, Nmr Structure Of The Single Qalggh Zinc Finger Domain
From Arabidopsis Thaliana Superman Protein
Length = 39
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 14/25 (56%), Positives = 20/25 (80%)
Query: 70 KVFSCNFCMRKFYSSQALGGHQNAH 94
+ ++C+FC R+F S+QALGGH N H
Sbjct: 5 RSYTCSFCKREFRSAQALGGHMNVH 29
>pdb|1F2I|G Chain G, Cocrystal Structure Of Selected Zinc Finger Dimer Bound
To Dna
pdb|1F2I|H Chain H, Cocrystal Structure Of Selected Zinc Finger Dimer Bound
To Dna
pdb|1F2I|I Chain I, Cocrystal Structure Of Selected Zinc Finger Dimer Bound
To Dna
pdb|1F2I|J Chain J, Cocrystal Structure Of Selected Zinc Finger Dimer Bound
To Dna
pdb|1F2I|K Chain K, Cocrystal Structure Of Selected Zinc Finger Dimer Bound
To Dna
pdb|1F2I|L Chain L, Cocrystal Structure Of Selected Zinc Finger Dimer Bound
To Dna
Length = 73
Score = 31.2 bits (69), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 16/39 (41%)
Query: 56 GDSTDRRSKPASGNKVFSCNFCMRKFYSSQALGGHQNAH 94
D R + +G K F C CMR F S L H H
Sbjct: 34 SDELTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTH 72
>pdb|1AAY|A Chain A, Zif268 Zinc Finger-Dna Complex
pdb|1A1L|A Chain A, Zif268 Zinc Finger-Dna Complex (Gcac Site)
Length = 90
Score = 30.0 bits (66), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 19/46 (41%)
Query: 56 GDSTDRRSKPASGNKVFSCNFCMRKFYSSQALGGHQNAHKRERGAA 101
D R + +G K F C CMR F S L H H E+ A
Sbjct: 19 SDELTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTHTGEKPFA 64
Score = 28.1 bits (61), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 67 SGNKVFSCNFCMRKFYSSQALGGHQNAHKRER 98
+G K F+C+ C RKF S H H R++
Sbjct: 58 TGEKPFACDICGRKFARSDERKRHTKIHLRQK 89
>pdb|1P47|A Chain A, Crystal Structure Of Tandem Zif268 Molecules Complexed
To Dna
pdb|1P47|B Chain B, Crystal Structure Of Tandem Zif268 Molecules Complexed
To Dna
Length = 87
Score = 30.0 bits (66), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 16/39 (41%)
Query: 56 GDSTDRRSKPASGNKVFSCNFCMRKFYSSQALGGHQNAH 94
D R + +G K F C CMR F S L H H
Sbjct: 18 SDELTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTH 56
Score = 27.3 bits (59), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 16/31 (51%)
Query: 67 SGNKVFSCNFCMRKFYSSQALGGHQNAHKRE 97
+G K F+C+ C RKF S H H R+
Sbjct: 57 TGEKPFACDICGRKFARSDERKRHTKIHLRQ 87
>pdb|1ZAA|C Chain C, Zinc Finger-Dna Recognition: Crystal Structure Of A
Zif268- Dna Complex At 2.1 Angstroms
Length = 87
Score = 30.0 bits (66), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 19/46 (41%)
Query: 56 GDSTDRRSKPASGNKVFSCNFCMRKFYSSQALGGHQNAHKRERGAA 101
D R + +G K F C CMR F S L H H E+ A
Sbjct: 19 SDELTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTHTGEKPFA 64
Score = 26.6 bits (57), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 15/30 (50%)
Query: 67 SGNKVFSCNFCMRKFYSSQALGGHQNAHKR 96
+G K F+C+ C RKF S H H R
Sbjct: 58 TGEKPFACDICGRKFARSDERKRHTKIHLR 87
>pdb|1G2F|C Chain C, Structure Of A Cys2his2 Zinc FingerTATA BOX COMPLEX
(Tatazf;clone #6)
pdb|1G2F|F Chain F, Structure Of A Cys2his2 Zinc FingerTATA BOX COMPLEX
(Tatazf;clone #6)
Length = 90
Score = 29.3 bits (64), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 16/35 (45%)
Query: 67 SGNKVFSCNFCMRKFYSSQALGGHQNAHKRERGAA 101
+G K F C CMR F +L H H E+ A
Sbjct: 30 TGQKPFQCRICMRNFSQQASLNAHIRTHTGEKPFA 64
Score = 26.9 bits (58), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 67 SGNKVFSCNFCMRKFYSSQALGGHQNAHKRER 98
+G K F+C+ C RKF + H H R++
Sbjct: 58 TGEKPFACDICGRKFATLHTRTRHTKIHLRQK 89
>pdb|1A1H|A Chain A, Qgsr (Zif268 Variant) Zinc Finger-Dna Complex (Gcac Site)
Length = 90
Score = 29.3 bits (64), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 19/44 (43%)
Query: 58 STDRRSKPASGNKVFSCNFCMRKFYSSQALGGHQNAHKRERGAA 101
S R + +G K F C CMR F S L H H E+ A
Sbjct: 21 SLTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTHTGEKPFA 64
Score = 27.7 bits (60), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 67 SGNKVFSCNFCMRKFYSSQALGGHQNAHKRER 98
+G K F+C+ C RKF S H H R++
Sbjct: 58 TGEKPFACDICGRKFARSDERKRHTKIHLRQK 89
>pdb|1A1F|A Chain A, Dsnr (Zif268 Variant) Zinc Finger-Dna Complex (Gacc Site)
pdb|1A1G|A Chain A, Dsnr (Zif268 Variant) Zinc Finger-Dna Complex (Gcgt Site)
Length = 90
Score = 28.9 bits (63), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 16/35 (45%)
Query: 67 SGNKVFSCNFCMRKFYSSQALGGHQNAHKRERGAA 101
+G K F C CMR F S L H H E+ A
Sbjct: 30 TGQKPFQCRICMRNFSRSDHLTTHIRTHTGEKPFA 64
Score = 27.7 bits (60), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 67 SGNKVFSCNFCMRKFYSSQALGGHQNAHKRER 98
+G K F+C+ C RKF S H H R++
Sbjct: 58 TGEKPFACDICGRKFARSDERKRHTKIHLRQK 89
>pdb|1JK1|A Chain A, Zif268 D20a Mutant Bound To Wt Dna Site
pdb|1JK2|A Chain A, Zif268 D20a Mutant Bound To The Gct Dna Site
Length = 90
Score = 28.9 bits (63), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 13/28 (46%)
Query: 67 SGNKVFSCNFCMRKFYSSQALGGHQNAH 94
+G K F C CMR F S L H H
Sbjct: 30 TGQKPFQCRICMRNFSRSDHLTTHIRTH 57
Score = 27.7 bits (60), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 67 SGNKVFSCNFCMRKFYSSQALGGHQNAHKRER 98
+G K F+C+ C RKF S H H R++
Sbjct: 58 TGEKPFACDICGRKFARSDERKRHTKIHLRQK 89
>pdb|1A1I|A Chain A, Radr (Zif268 Variant) Zinc Finger-Dna Complex (Gcac Site)
pdb|1A1J|A Chain A, Radr (Zif268 Variant) Zinc Finger-Dna Complex (Gcgt Site)
pdb|1A1K|A Chain A, Radr (Zif268 Variant) Zinc Finger-Dna Complex (Gacc Site)
Length = 90
Score = 28.9 bits (63), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 16/35 (45%)
Query: 67 SGNKVFSCNFCMRKFYSSQALGGHQNAHKRERGAA 101
+G K F C CMR F S L H H E+ A
Sbjct: 30 TGQKPFQCRICMRNFSRSDHLTTHIRTHTGEKPFA 64
Score = 27.7 bits (60), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 67 SGNKVFSCNFCMRKFYSSQALGGHQNAHKRER 98
+G K F+C+ C RKF S H H R++
Sbjct: 58 TGEKPFACDICGRKFARSDERKRHTKIHLRQK 89
>pdb|2EE8|A Chain A, Solution Structure Of Three Zf-C2h2 Domains From Mouse
Protein Odd-Skipped-Related 2 Splicing Isoform 2
Length = 106
Score = 28.9 bits (63), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 16/34 (47%)
Query: 65 PASGNKVFSCNFCMRKFYSSQALGGHQNAHKRER 98
P+ K F C FC R F S L H+ H ER
Sbjct: 11 PSKTKKEFICKFCGRHFTKSYNLLIHERTHTDER 44
>pdb|2JP9|A Chain A, Structure Of The Wilms Tumor Suppressor Protein Zinc
Finger Domain Bound To Dna
pdb|2JPA|A Chain A, Structure Of The Wilms Tumor Suppressor Protein Zinc
Finger Domain Bound To Dna
pdb|2PRT|A Chain A, Structure Of The Wilms Tumor Suppressor Protein Zinc
Finger Domain Bound To Dna
Length = 119
Score = 28.5 bits (62), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 16/39 (41%)
Query: 56 GDSTDRRSKPASGNKVFSCNFCMRKFYSSQALGGHQNAH 94
D R + +G K F C C RKF S L H H
Sbjct: 51 SDQLKRHQRRHTGVKPFQCKTCQRKFSRSDHLKTHTRTH 89
>pdb|2EMX|A Chain A, Solution Structure Of The C2h2 Type Zinc Finger (Region
273- 303) Of Human Zinc Finger Protein 268
Length = 44
Score = 28.5 bits (62), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 17/33 (51%)
Query: 66 ASGNKVFSCNFCMRKFYSSQALGGHQNAHKRER 98
+SG K F C+ C + F S L HQ H E+
Sbjct: 5 SSGEKPFGCSCCEKAFSSKSYLLVHQQTHAEEK 37
>pdb|2YRH|A Chain A, Solution Structure Of The C2h2-Type Zinc Finger Domain
(699- 729) From Zinc Finger Protein 473
Length = 44
Score = 28.1 bits (61), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 16/33 (48%)
Query: 66 ASGNKVFSCNFCMRKFYSSQALGGHQNAHKRER 98
+SG K CN C + F S L HQ H E+
Sbjct: 5 SSGKKPLVCNECGKTFRQSSCLSKHQRIHSGEK 37
>pdb|2EN9|A Chain A, Solution Structure Of The C2h2 Type Zinc Finger (Region
415- 447) Of Human Zinc Finger Protein 28 Homolog
Length = 46
Score = 28.1 bits (61), Expect = 3.4, Method: Composition-based stats.
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 70 KVFSCNFCMRKFYSSQALGGHQNAHKRER 98
K+F CN C + F S +L HQ H E+
Sbjct: 11 KLFKCNECKKTFTQSSSLTVHQRIHTGEK 39
>pdb|1G2D|C Chain C, Structure Of A Cys2his2 Zinc FingerTATA BOX COMPLEX (CLONE
#2)
pdb|1G2D|F Chain F, Structure Of A Cys2his2 Zinc FingerTATA BOX COMPLEX (CLONE
#2)
Length = 90
Score = 28.1 bits (61), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 15/35 (42%)
Query: 67 SGNKVFSCNFCMRKFYSSQALGGHQNAHKRERGAA 101
+G K F C CMR F L H H E+ A
Sbjct: 30 TGQKPFQCRICMRNFSQHTGLNQHIRTHTGEKPFA 64
Score = 26.9 bits (58), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 67 SGNKVFSCNFCMRKFYSSQALGGHQNAHKRER 98
+G K F+C+ C RKF + H H R++
Sbjct: 58 TGEKPFACDICGRKFATLHTRDRHTKIHLRQK 89
>pdb|2ELS|A Chain A, Solution Structure Of The 2nd C2h2 Zinc Finger Of Human
Zinc Finger Protein 406
Length = 36
Score = 27.7 bits (60), Expect = 4.4, Method: Composition-based stats.
Identities = 10/33 (30%), Positives = 16/33 (48%)
Query: 66 ASGNKVFSCNFCMRKFYSSQALGGHQNAHKRER 98
S K+F+C +C + F +L H H E+
Sbjct: 4 GSSGKIFTCEYCNKVFKFKHSLQAHLRIHTNEK 36
>pdb|1ZNF|A Chain A, Three-Dimensional Solution Structure Of A Single Zinc
Finger Dna-Binding Domain
Length = 27
Score = 27.7 bits (60), Expect = 4.6, Method: Composition-based stats.
Identities = 10/24 (41%), Positives = 11/24 (45%)
Query: 72 FSCNFCMRKFYSSQALGGHQNAHK 95
+ C C R F AL HQ HK
Sbjct: 2 YKCGLCERSFVEKSALSRHQRVHK 25
>pdb|2EMW|A Chain A, Solution Structure Of The C2h2 Type Zinc Finger (Region
301- 331) Of Human Zinc Finger Protein 268
Length = 44
Score = 26.9 bits (58), Expect = 6.7, Method: Composition-based stats.
Identities = 14/36 (38%), Positives = 18/36 (50%)
Query: 63 SKPASGNKVFSCNFCMRKFYSSQALGGHQNAHKRER 98
S +SG K + CN C + F S L HQ H E+
Sbjct: 2 SSGSSGEKPYGCNECGKDFSSKSYLIVHQRIHTGEK 37
>pdb|2LV2|A Chain A, Solution Nmr Structure Of C2h2-Type Zinc-Fingers 4 And 5
From Human Insulinoma-Associated Protein 1 (Fragment
424-497), Northeast Structural Genomics Consortium
Target Hr7614b
Length = 85
Score = 26.6 bits (57), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 58 STDRRSKPASGNKVFSCNFCMRKFYSSQALGGHQN 92
+ +R + +VF C +C FYSS L H N
Sbjct: 43 AQERHLRLLHAAQVFPCKYCPATFYSSPGLTRHIN 77
>pdb|1LLM|C Chain C, Crystal Structure Of A Zif23-Gcn4 Chimera Bound To Dna
pdb|1LLM|D Chain D, Crystal Structure Of A Zif23-Gcn4 Chimera Bound To Dna
Length = 88
Score = 26.6 bits (57), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 14/32 (43%)
Query: 70 KVFSCNFCMRKFYSSQALGGHQNAHKRERGAA 101
K F C CMR F S L H H E+ A
Sbjct: 2 KPFQCRICMRNFSRSDHLTTHIRTHTGEKPFA 33
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.316 0.131 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,316,342
Number of Sequences: 62578
Number of extensions: 191319
Number of successful extensions: 413
Number of sequences better than 100.0: 57
Number of HSP's better than 100.0 without gapping: 57
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 338
Number of HSP's gapped (non-prelim): 75
length of query: 203
length of database: 14,973,337
effective HSP length: 94
effective length of query: 109
effective length of database: 9,091,005
effective search space: 990919545
effective search space used: 990919545
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)