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= 044606
(413 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 = 32.7 bits (73), Expect = 0.41, Method: Composition-based stats.
Identities = 13/23 (56%), Positives = 15/23 (65%)
Query: 277 YKCETCKKVFKSYQALGGHRASH 299
Y C CK+ F+S QALGGH H
Sbjct: 7 YTCSFCKREFRSAQALGGHMNVH 29
Score = 30.8 bits (68), Expect = 1.6, Method: Composition-based stats.
Identities = 15/31 (48%), Positives = 16/31 (51%), Gaps = 4/31 (12%)
Query: 327 PPLSVKKVHECPVCFRVFSSGQALGGHKRTH 357
PP S + C C R F S QALGGH H
Sbjct: 3 PPRS----YTCSFCKREFRSAQALGGHMNVH 29
Score = 28.9 bits (63), Expect = 5.1, Method: Composition-based stats.
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 41 HKCRLCFKNFSNGRALGGHMRSH 63
+ C C + F + +ALGGHM H
Sbjct: 7 YTCSFCKREFRSAQALGGHMNVH 29
>pdb|2I13|A Chain A, Aart, A Six Finger Zinc Finger Designed To Recognize Ann
Triplets
pdb|2I13|B Chain B, Aart, A Six Finger Zinc Finger Designed To Recognize Ann
Triplets
Length = 190
Score = 31.6 bits (70), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 37/83 (44%), Gaps = 4/83 (4%)
Query: 277 YKCETCKKVFKSYQALGGHRASHKKIKFY-TPVQETELDQENAGASINLASPPLSVKKVH 335
Y C C K F L H+ +H K Y P +E+ +++ + +K +
Sbjct: 106 YACPECGKSFSQLAHLRAHQRTHTGEKPYKCPECGKSFSRED---NLHTHQRTHTGEKPY 162
Query: 336 ECPVCFRVFSSGQALGGHKRTHV 358
+CP C + FS AL H+RTH
Sbjct: 163 KCPECGKSFSRRDALNVHQRTHT 185
Score = 30.8 bits (68), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 35/83 (42%), Gaps = 4/83 (4%)
Query: 277 YKCETCKKVFKSYQALGGHRASHKKIKFY-TPVQETELDQENAGASINLASPPLSVKKVH 335
YKC C K F + L H+ +H K Y P Q A++ + +K +
Sbjct: 50 YKCPECGKSFSDKKDLTRHQRTHTGEKPYKCPECGKSFSQR---ANLRAHQRTHTGEKPY 106
Query: 336 ECPVCFRVFSSGQALGGHKRTHV 358
CP C + FS L H+RTH
Sbjct: 107 ACPECGKSFSQLAHLRAHQRTHT 129
>pdb|2YT9|A Chain A, Solution Structure Of C2h2 Type Zinc Finger Domain 345 In
Zinc Finger Protein 278
Length = 95
Score = 31.2 bits (69), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 36/76 (47%), Gaps = 2/76 (2%)
Query: 279 CETCKKVFKSYQALGGHRASHKKIKFYT-PVQETELDQENAGASINLASPPLSVKKVHEC 337
CE C K+F+ L H+ SH K Y+ PV +++ S ++ S SV K + C
Sbjct: 10 CEICGKIFRDVYHLNRHKLSHSGEKPYSCPVCGLRFKRKDR-MSYHVRSHDGSVGKPYIC 68
Query: 338 PVCFRVFSSGQALGGH 353
C + FS L GH
Sbjct: 69 QSCGKGFSRPDHLNGH 84
>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 = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 42 KCRLCFKNFSNGRALGGHMRSHMLNLPIPQKI 73
+CR+C +NFS +L H+R+H P I
Sbjct: 36 QCRICMRNFSQQASLNAHIRTHTGEKPFACDI 67
>pdb|1MEY|C Chain C, Crystal Structure Of A Designed Zinc Finger Protein Bound
To Dna
pdb|1MEY|F Chain F, Crystal Structure Of A Designed Zinc Finger Protein Bound
To Dna
pdb|1MEY|G Chain G, Crystal Structure Of A Designed Zinc Finger Protein Bound
To Dna
Length = 87
Score = 31.2 bits (69), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 35/87 (40%), Gaps = 14/87 (16%)
Query: 277 YKCETCKKVFKSYQALGGHRASHKKIKFYTPVQETELDQENAGASINLASPPLSVKKVH- 335
YKC C K F L H+ +H K Y + G S + +S ++ H
Sbjct: 5 YKCPECGKSFSQSSNLQKHQRTHTGEKPYKCPE--------CGKSFSQSSDLQKHQRTHT 56
Query: 336 -----ECPVCFRVFSSGQALGGHKRTH 357
+CP C + FS L H+RTH
Sbjct: 57 GEKPYKCPECGKSFSRSDHLSRHQRTH 83
>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 = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 38 MEKHKCRLCFKNFSNGRALGGHMRSHMLNLPIPQKI 73
M+ +CR+C +NFS L H+R+H P I
Sbjct: 1 MKPFQCRICMRNFSRSDHLTTHIRTHTGEKPFACDI 36
>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 = 30.0 bits (66), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 42 KCRLCFKNFSNGRALGGHMRSHMLNLPIPQKI 73
+CR+C +NFS L H+R+H P I
Sbjct: 36 QCRICMRNFSQHTGLNQHIRTHTGEKPFACDI 67
>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 = 29.6 bits (65), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 42 KCRLCFKNFSNGRALGGHMRSHMLNLPIPQKI 73
+CR+C +NFS L H+R+H P I
Sbjct: 35 QCRICMRNFSRSDHLTTHIRTHTGEKPFACDI 66
>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 = 29.6 bits (65), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 42 KCRLCFKNFSNGRALGGHMRSHMLNLPIPQKI 73
+CR+C +NFS L H+R+H P I
Sbjct: 36 QCRICMRNFSRSDHLTTHIRTHTGEKPFACDI 67
>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 = 29.6 bits (65), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 42 KCRLCFKNFSNGRALGGHMRSHMLNLPIPQKI 73
+CR+C +NFS L H+R+H P I
Sbjct: 36 QCRICMRNFSRSDHLTTHIRTHTGEKPFACDI 67
>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 = 29.6 bits (65), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 42 KCRLCFKNFSNGRALGGHMRSHMLNLPIPQKI 73
+CR+C +NFS L H+R+H P I
Sbjct: 36 QCRICMRNFSRSDHLTTHIRTHTGEKPFACDI 67
>pdb|1ZAA|C Chain C, Zinc Finger-Dna Recognition: Crystal Structure Of A
Zif268- Dna Complex At 2.1 Angstroms
Length = 87
Score = 29.6 bits (65), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 42 KCRLCFKNFSNGRALGGHMRSHMLNLPIPQKI 73
+CR+C +NFS L H+R+H P I
Sbjct: 36 QCRICMRNFSRSDHLTTHIRTHTGEKPFACDI 67
>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 = 29.3 bits (64), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 42 KCRLCFKNFSNGRALGGHMRSHMLNLPIPQKI 73
+CR+C +NFS L H+R+H P I
Sbjct: 36 QCRICMRNFSRSDHLTTHIRTHTGEKPFACDI 67
>pdb|1A1H|A Chain A, Qgsr (Zif268 Variant) Zinc Finger-Dna Complex (Gcac
Site)
Length = 90
Score = 29.3 bits (64), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 42 KCRLCFKNFSNGRALGGHMRSHMLNLPIPQKI 73
+CR+C +NFS L H+R+H P I
Sbjct: 36 QCRICMRNFSRSDHLTTHIRTHTGEKPFACDI 67
>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 = 29.3 bits (64), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 42 KCRLCFKNFSNGRALGGHMRSH 63
+CR+C +NFS L H+R+H
Sbjct: 51 QCRICMRNFSRSDHLTTHIRTH 72
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
0.319 0.134 0.394
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,108,340
Number of Sequences: 62578
Number of extensions: 268270
Number of successful extensions: 833
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 20
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 752
Number of HSP's gapped (non-prelim): 71
length of query: 413
length of database: 14,973,337
effective HSP length: 101
effective length of query: 312
effective length of database: 8,652,959
effective search space: 2699723208
effective search space used: 2699723208
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)