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= psy3492
(85 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DMD|A Chain A, Solution Structure Of The N-Terminal C2h2 Type
Zinc-Binding Domain Of The Zinc Finger Protein 64,
Isoforms 1 And 2
Length = 96
Score = 34.7 bits (78), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 32/66 (48%), Gaps = 6/66 (9%)
Query: 14 LKRHLNTH--IKPFNCALCEYKAARPERLATHVIKVHNKR---ICSKCSFLADDQETLNE 68
LK H+ H +KP+ C C+Y AA L H +++H+ C C + + + L
Sbjct: 24 LKTHMRCHTGVKPYKCKTCDYAAADSSSLNKH-LRIHSDERPFKCQICPYASRNSSQLTV 82
Query: 69 HLQQHI 74
HL+ H
Sbjct: 83 HLRSHT 88
>pdb|3UK3|C Chain C, Crystal Structure Of Znf217 Bound To Dna
pdb|3UK3|D Chain D, Crystal Structure Of Znf217 Bound To Dna
pdb|4F2J|C Chain C, Crystal Structure Of Znf217 Bound To Dna, P6522 Crystal
Form
pdb|4IS1|C Chain C, Crystal Structure Of Znf217 Bound To Dna
pdb|4IS1|D Chain D, Crystal Structure Of Znf217 Bound To Dna
Length = 57
Score = 32.7 bits (73), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 17/40 (42%), Positives = 22/40 (55%), Gaps = 2/40 (5%)
Query: 11 NWCLKRHLNTHI--KPFNCALCEYKAARPERLATHVIKVH 48
N+ L HL TH KP+ C CEY AA+ L H+ + H
Sbjct: 17 NYYLNIHLRTHTGEKPYKCEFCEYAAAQKTSLRYHLERHH 56
>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 = 31.2 bits (69), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 19/33 (57%), Gaps = 2/33 (6%)
Query: 14 LKRHLNTH--IKPFNCALCEYKAARPERLATHV 44
LKRH H +KPF C C+ K +R + L TH
Sbjct: 54 LKRHQRRHTGVKPFQCKTCQRKFSRSDHLKTHT 86
>pdb|2ADR|A Chain A, Adr1 Dna-Binding Domain From Saccharomyces Cerevisiae,
Nmr, 25 Structures
Length = 60
Score = 29.6 bits (65), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 14 LKRHLNTHI--KPFNCALCEYKAARPERLATHVIKVHNKRI 52
LKRH +H KP+ C LC R + L H K+H+ +
Sbjct: 18 LKRHYRSHTNEKPYPCGLCNRAFTRRDLLIRHAQKIHSGNL 58
>pdb|1A1H|A Chain A, Qgsr (Zif268 Variant) Zinc Finger-Dna Complex (Gcac
Site)
Length = 90
Score = 29.3 bits (64), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 8 ISYNWCLKRHLNTHI--KPFNCALCEYKAARPERLATHV 44
S + L RH+ H KPF C +C +R + L TH+
Sbjct: 16 FSQSGSLTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHI 54
>pdb|5ZNF|A Chain A, Alternating Zinc Fingers In The Human Male Associated
Protein Zfy: 2d Nmr Structure Of An Even Finger And
Implications For "jumping-Linker" Dna Recognition
Length = 30
Score = 28.5 bits (62), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 23 KPFNCALCEYKAARPERLATHVIKVHNK 50
K + C CEY++A L TH+ H+K
Sbjct: 1 KTYQCQYCEYRSADSSNLKTHIKTKHSK 28
>pdb|1U85|A Chain A, Arg326-Trp Mutant Of The Third Zinc Finger Of Bklf
Length = 33
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 19 NTHIKPFNCALCEYKAARPERLATH 43
+T IKPF C C++ +R + LA H
Sbjct: 2 STGIKPFQCPDCDWSFSRSDHLALH 26
>pdb|2LCE|A Chain A, Chemical Shift Assignment Of Hr4436b From Homo Sapiens,
Northeast Structural Genomics Consortium
Length = 74
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 18/44 (40%), Gaps = 2/44 (4%)
Query: 3 RLQVLISYNWCLKRHLNTHI--KPFNCALCEYKAARPERLATHV 44
R Q Y L H H KP+ C +C + RP L TH
Sbjct: 22 RCQASFRYKGNLASHKTVHTGEKPYRCNICGAQFNRPANLKTHT 65
>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 = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 14 LKRHLNTHI--KPFNCALCEYKAARPERLATHV 44
L RH+ H KPF C +C +R + L TH+
Sbjct: 22 LTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHI 54
>pdb|2EBT|A Chain A, Solution Structure Of Three Tandem Repeats Of Zf-C2h2
Domains From Human Kruppel-Like Factor 5
Length = 100
Score = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 14 LKRHLNTHI--KPFNCALCEYKAARPERLATHVIKVHN 49
L RH H KPF C +C +R + LA H+ + N
Sbjct: 63 LTRHYRKHTGAKPFQCGVCNRSFSRSDHLALHMKRHQN 100
>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 = 28.1 bits (61), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 14 LKRHLNTHI--KPFNCALCEYKAARPERLATHV 44
L RH+ H KPF C +C +R + L TH+
Sbjct: 22 LTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHI 54
>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 = 28.1 bits (61), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 8 ISYNWCLKRHLNTHI--KPFNCALCEYKAARPERLATHV 44
S + L RH+ H KPF C +C +R + L TH+
Sbjct: 16 FSRSADLTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHI 54
>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 = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 14 LKRHLNTHI--KPFNCALCEYKAARPERLATHV 44
L RH+ H KPF C +C +R + L TH+
Sbjct: 21 LTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHI 53
>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 = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 14 LKRHLNTHI--KPFNCALCEYKAARPERLATHV 44
L RH+ H KPF C +C +R + L TH+
Sbjct: 22 LTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHI 54
>pdb|2YT9|A Chain A, Solution Structure Of C2h2 Type Zinc Finger Domain 345
In Zinc Finger Protein 278
Length = 95
Score = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 11/39 (28%), Positives = 22/39 (56%)
Query: 11 NWCLKRHLNTHIKPFNCALCEYKAARPERLATHVIKVHN 49
++ ++ H + KP+ C C +RP+ L H+ +VH+
Sbjct: 52 SYHVRSHDGSVGKPYICQSCGKGFSRPDHLNGHIKQVHS 90
>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 = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 14 LKRHLNTHI--KPFNCALCEYKAARPERLATHV 44
L RH+ H KPF C +C +R + L TH+
Sbjct: 37 LTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHI 69
>pdb|1ZAA|C Chain C, Zinc Finger-Dna Recognition: Crystal Structure Of A
Zif268- Dna Complex At 2.1 Angstroms
Length = 87
Score = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 14 LKRHLNTHI--KPFNCALCEYKAARPERLATHV 44
L RH+ H KPF C +C +R + L TH+
Sbjct: 22 LTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHI 54
>pdb|1X5W|A Chain A, Solution Structure Of The C2h2 Type Zinc-Binding Domain
Of Human Zinc Finger Protein 64, Isoforms 1 And 2
Length = 70
Score = 27.3 bits (59), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 23 KPFNCALCEYKAARPERLATHVIKVHN 49
+PF C C + +P L+ H+ K H
Sbjct: 36 RPFKCNYCSFDTKQPSNLSKHMKKFHG 62
>pdb|2EPS|A Chain A, Solution Structure Of The 4th Zinc Finger Domain Of Zinc
Finger Protein 278
Length = 54
Score = 27.3 bits (59), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 23 KPFNCALCEYKAARPERLATHVIKVHNKRICSKC 56
KP+ C C +RP+ L H+ +VH KC
Sbjct: 11 KPYICQSCGKGFSRPDHLNGHIKQVHTSERPHKC 44
>pdb|1KLR|A Chain A, Nmr Structure Of The Zfy-6t[y10f] Zinc Finger
Length = 30
Score = 26.9 bits (58), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 23 KPFNCALCEYKAARPERLATHVIKVHNK 50
K + C CE+++A L TH+ H+K
Sbjct: 1 KTYQCQYCEFRSADSSNLKTHIKTKHSK 28
>pdb|1P7A|A Chain A, Solution Stucture Of The Third Zinc Finger From Bklf
Length = 37
Score = 26.6 bits (57), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 19 NTHIKPFNCALCEYKAARPERLATH 43
+T IKPF C C+ +R + LA H
Sbjct: 6 STGIKPFQCPDCDRSFSRSDHLALH 30
>pdb|2ELQ|A Chain A, Solution Structure Of The 14th C2h2 Zinc Finger Of Human
Zinc Finger Protein 406
Length = 36
Score = 26.6 bits (57), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 10/22 (45%), Positives = 12/22 (54%)
Query: 23 KPFNCALCEYKAARPERLATHV 44
KPF C+LCEY L H+
Sbjct: 8 KPFKCSLCEYATRSKSNLKAHM 29
>pdb|1XF7|A Chain A, High Resolution Nmr Structure Of The Wilms' Tumor
Suppressor Protein (Wt1) Finger 3
Length = 29
Score = 26.6 bits (57), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 23 KPFNCALCEYKAARPERLATHV 44
KPF C C+ K +R + L TH
Sbjct: 1 KPFQCKTCQRKFSRSDHLKTHT 22
>pdb|1BBO|A Chain A, High-Resolution Solution Structure Of The Double
Cys2His2 Zinc Finger From The Human Enhancer Binding
Protein Mbp-1
Length = 57
Score = 26.2 bits (56), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 3/41 (7%)
Query: 14 LKRHLNTH--IKPFNCALCEYKAARPERLATHV-IKVHNKR 51
LK+H+ TH ++P++C C + L H+ K H+K+
Sbjct: 17 LKKHIRTHTDVRPYHCTYCNFSFKTKGNLTKHMKSKAHSKK 57
>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 = 25.4 bits (54), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 22 IKPFNCALCEYKAARPERLATHV 44
+KPF C +C +R + L TH+
Sbjct: 1 MKPFQCRICMRNFSRSDHLTTHI 23
>pdb|2CT1|A Chain A, Solution Structure Of The Zinc Finger Domain Of
Transcriptional Repressor Ctcf Protein
Length = 77
Score = 25.4 bits (54), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 13/58 (22%), Positives = 27/58 (46%), Gaps = 5/58 (8%)
Query: 23 KPFNCALCEYKAARPERLATHVIKVHNKRI----CSKCSFLADDQETLNEHL-QQHIF 75
KP+ C +C + + + H+++ H + + C C + + L HL +QH +
Sbjct: 14 KPYECYICHARFTQSGTMKMHILQKHTENVAKFHCPHCDTVIARKSDLGVHLRKQHSY 71
>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 = 25.4 bits (54), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 2/52 (3%)
Query: 2 PRLQVLISYNWCLKRHLNTHI--KPFNCALCEYKAARPERLATHVIKVHNKR 51
P S + L++H TH KP+ C C +R + L+ H NK+
Sbjct: 36 PECGKSFSQSSDLQKHQRTHTGEKPYKCPECGKSFSRSDHLSRHQRTHQNKK 87
>pdb|1XRZ|A Chain A, Nmr Structure Of A Zinc Finger With Cyclohexanylalanine
Substituted For The Central Aromatic Residue
Length = 30
Score = 25.4 bits (54), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 10/28 (35%), Positives = 15/28 (53%)
Query: 23 KPFNCALCEYKAARPERLATHVIKVHNK 50
K + C CE ++A L TH+ H+K
Sbjct: 1 KTYQCQYCEXRSADSSNLKTHIKTKHSK 28
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
0.327 0.135 0.456
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,488,478
Number of Sequences: 62578
Number of extensions: 77861
Number of successful extensions: 216
Number of sequences better than 100.0: 41
Number of HSP's better than 100.0 without gapping: 30
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 173
Number of HSP's gapped (non-prelim): 52
length of query: 85
length of database: 14,973,337
effective HSP length: 53
effective length of query: 32
effective length of database: 11,656,703
effective search space: 373014496
effective search space used: 373014496
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 45 (21.9 bits)