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= psy4019
(109 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2GLI|A Chain A, Five-Finger GliDNA COMPLEX
Length = 155
Score = 55.8 bits (133), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 25/32 (78%), Positives = 28/32 (87%)
Query: 11 SSQKPYVCGEENCTKRYTDPSSLRKHIKTVHG 42
S++KPYVC CTKRYTDPSSLRKH+KTVHG
Sbjct: 124 SNEKPYVCKLPGCTKRYTDPSSLRKHVKTVHG 155
Score = 25.8 bits (55), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 20/33 (60%)
Query: 11 SSQKPYVCGEENCTKRYTDPSSLRKHIKTVHGE 43
+ +KP+ C E C K Y+ +L+ H+++ GE
Sbjct: 63 TGEKPHKCTFEGCRKSYSRLENLKTHLRSHTGE 95
>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 = 33.5 bits (75), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 22/31 (70%)
Query: 13 QKPYVCGEENCTKRYTDPSSLRKHIKTVHGE 43
++PY C E+C +R++D S+L +HI+ G+
Sbjct: 2 ERPYACPVESCDRRFSDSSNLTRHIRIHTGQ 32
>pdb|2J7J|A Chain A, Invariance Of The Zinc Finger Module: A Comparison Of
The Free Structure With Those In Nucleic-Acid Complexes
Length = 85
Score = 32.3 bits (72), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 23/50 (46%), Gaps = 11/50 (22%)
Query: 11 SSQKPYVCGEENCTKRYTDPSSLRKHIKTVHGEHCYANKKHKGMPSKDKD 60
+ Q PY C E C KR++ PS L++H K H G P K D
Sbjct: 27 TQQLPYECPHEGCDKRFSLPSRLKRHEKV-----------HAGYPCKKDD 65
>pdb|1UN6|B Chain B, The Crystal Structure Of A Zinc Finger - Rna Complex
Reveals Two Modes Of Molecular Recognition
pdb|1UN6|C Chain C, The Crystal Structure Of A Zinc Finger - Rna Complex
Reveals Two Modes Of Molecular Recognition
pdb|1UN6|D Chain D, The Crystal Structure Of A Zinc Finger - Rna Complex
Reveals Two Modes Of Molecular Recognition
pdb|2HGH|A Chain A, Transcription Factor Iiia Zinc Fingers 4-6 Bound To 5s
Rrna 55mer (Nmr Structure)
Length = 87
Score = 32.3 bits (72), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 23/50 (46%), Gaps = 11/50 (22%)
Query: 11 SSQKPYVCGEENCTKRYTDPSSLRKHIKTVHGEHCYANKKHKGMPSKDKD 60
+ Q PY C E C KR++ PS L++H K H G P K D
Sbjct: 27 TQQLPYECPHEGCDKRFSLPSRLKRHEKV-----------HAGYPCKKDD 65
>pdb|1TF6|A Chain A, Co-crystal Structure Of Xenopus Tfiiia Zinc Finger Domain
Bound To The 5s Ribosomal Rna Gene Internal Control
Region
pdb|1TF6|D Chain D, Co-crystal Structure Of Xenopus Tfiiia Zinc Finger Domain
Bound To The 5s Ribosomal Rna Gene Internal Control
Region
Length = 190
Score = 32.0 bits (71), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 23/50 (46%), Gaps = 11/50 (22%)
Query: 11 SSQKPYVCGEENCTKRYTDPSSLRKHIKTVHGEHCYANKKHKGMPSKDKD 60
+ Q PY C E C KR++ PS L++H K H G P K D
Sbjct: 130 TQQLPYECPHEGCDKRFSLPSRLKRHEKV-----------HAGYPCKKDD 168
Score = 26.9 bits (58), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 18/33 (54%)
Query: 11 SSQKPYVCGEENCTKRYTDPSSLRKHIKTVHGE 43
+ +KP+ C EE C K +T L +H T GE
Sbjct: 38 TGEKPFPCKEEGCEKGFTSLHHLTRHSLTHTGE 70
Score = 25.4 bits (54), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 8/31 (25%), Positives = 17/31 (54%)
Query: 11 SSQKPYVCGEENCTKRYTDPSSLRKHIKTVH 41
+ +K + C + C R+T ++++KH H
Sbjct: 68 TGEKNFTCDSDGCDLRFTTKANMKKHFNRFH 98
>pdb|1A1H|A Chain A, Qgsr (Zif268 Variant) Zinc Finger-Dna Complex (Gcac
Site)
Length = 90
Score = 30.8 bits (68), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 20/31 (64%)
Query: 13 QKPYVCGEENCTKRYTDPSSLRKHIKTVHGE 43
++PY C E+C +R++ SL +HI+ G+
Sbjct: 2 ERPYACPVESCDRRFSQSGSLTRHIRIHTGQ 32
>pdb|2YT9|A Chain A, Solution Structure Of C2h2 Type Zinc Finger Domain 345
In Zinc Finger Protein 278
Length = 95
Score = 30.4 bits (67), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 19/31 (61%), Gaps = 2/31 (6%)
Query: 11 SSQKPYVCGEENCTKRYTDPSSLRKHIKTVH 41
S KPY+C ++C K ++ P L HIK VH
Sbjct: 61 SVGKPYIC--QSCGKGFSRPDHLNGHIKQVH 89
>pdb|2LVR|A Chain A, Solution Structure Of Miz-1 Zinc Finger 8
Length = 30
Score = 30.0 bits (66), Expect = 0.31, Method: Composition-based stats.
Identities = 12/30 (40%), Positives = 21/30 (70%), Gaps = 2/30 (6%)
Query: 14 KPYVCGEENCTKRYTDPSSLRKHIKTVHGE 43
KPYVC +C +++ DP +L++H++ GE
Sbjct: 2 KPYVC--IHCQRQFADPGALQRHVRIHTGE 29
>pdb|2EPS|A Chain A, Solution Structure Of The 4th Zinc Finger Domain Of Zinc
Finger Protein 278
Length = 54
Score = 30.0 bits (66), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 18/28 (64%), Gaps = 2/28 (7%)
Query: 14 KPYVCGEENCTKRYTDPSSLRKHIKTVH 41
KPY+C ++C K ++ P L HIK VH
Sbjct: 11 KPYIC--QSCGKGFSRPDHLNGHIKQVH 36
>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 = 30.0 bits (66), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 22/40 (55%)
Query: 4 NLAYPLLSSQKPYVCGEENCTKRYTDPSSLRKHIKTVHGE 43
NL ++ +PY C E+C +R++ L +HI+ G+
Sbjct: 8 NLLNYVVPKMRPYACPVESCDRRFSRSDELTRHIRIHTGQ 47
>pdb|7ZNF|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 = 29.6 bits (65), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 14/30 (46%), Positives = 19/30 (63%), Gaps = 2/30 (6%)
Query: 14 KPYVCGEENCTKRYTDPSSLRKHIKTVHGE 43
K Y C + C KR+ D S+L+ HIKT H +
Sbjct: 1 KTYQC--QYCEKRFADSSNLKTHIKTKHSK 28
>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 = 29.3 bits (64), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 10/31 (32%), Positives = 20/31 (64%)
Query: 13 QKPYVCGEENCTKRYTDPSSLRKHIKTVHGE 43
++PY C E+C +R++ + L +HI+ G+
Sbjct: 2 ERPYACPVESCDRRFSRSAELTRHIRIHTGQ 32
>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 = 29.3 bits (64), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 10/31 (32%), Positives = 20/31 (64%)
Query: 13 QKPYVCGEENCTKRYTDPSSLRKHIKTVHGE 43
++PY C E+C +R++ + L +HI+ G+
Sbjct: 2 ERPYACPVESCDRRFSRSADLTRHIRIHTGQ 32
>pdb|2EBT|A Chain A, Solution Structure Of Three Tandem Repeats Of Zf-C2h2
Domains From Human Kruppel-Like Factor 5
Length = 100
Score = 28.9 bits (63), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 8 PLLSSQKPYVCGEENCTKRYTDPSSLRKHIKTVHGE 43
P L ++ + C CTK YT S L+ H++T GE
Sbjct: 8 PDLEKRRIHYCDYPGCTKVYTKSSHLKAHLRTHTGE 43
Score = 26.2 bits (56), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 28/68 (41%), Gaps = 12/68 (17%)
Query: 11 SSQKPYVCGEENCTKRYTDPSSLRKHIKTVHGEHCYANKKHKGMPSKDKDGLGGASPSRS 70
+ +KPY C E C R+ L +H +KH G + G+ S SRS
Sbjct: 41 TGEKPYKCTWEGCDWRFARSDELTRHY-----------RKHTGAKP-FQCGVCNRSFSRS 88
Query: 71 DDMPLSAK 78
D + L K
Sbjct: 89 DHLALHMK 96
>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 = 28.9 bits (63), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 10/31 (32%), Positives = 20/31 (64%)
Query: 13 QKPYVCGEENCTKRYTDPSSLRKHIKTVHGE 43
++PY C E+C +R++ ++L HI+ G+
Sbjct: 2 ERPYACPVESCDRRFSQKTNLDTHIRIHTGQ 32
>pdb|1UBD|C Chain C, Co-Crystal Structure Of Human Yy1 Zinc Finger Domain
Bound To The Adeno-Associated Virus P5 Initiator
Element
Length = 124
Score = 28.9 bits (63), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 11 SSQKPYVCGEENCTKRYTDPSSLRKHIKTVHGEHCYA 47
+ +KP+ C E C KR++ +LR H++ G+ Y
Sbjct: 58 TGEKPFQCTFEGCGKRFSLDFNLRTHVRIHTGDRPYV 94
Score = 28.5 bits (62), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 10/31 (32%), Positives = 19/31 (61%)
Query: 9 LLSSQKPYVCGEENCTKRYTDPSSLRKHIKT 39
+ + +PYVC + C K++ ++L+ HI T
Sbjct: 86 IHTGDRPYVCPFDGCNKKFAQSTNLKSHILT 116
Score = 26.6 bits (57), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 14 KPYVCGEENCTKRYTDPSSLRKHIKTVHG 42
+ C + CTK + D S++RKH+ T HG
Sbjct: 4 RTIACPHKGCTKMFRDNSAMRKHLHT-HG 31
>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 = 28.5 bits (62), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 10/31 (32%), Positives = 19/31 (61%)
Query: 13 QKPYVCGEENCTKRYTDPSSLRKHIKTVHGE 43
++PY C E+C +R++ L +HI+ G+
Sbjct: 2 ERPYACPVESCDRRFSRSDELTRHIRIHTGQ 32
>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 = 28.5 bits (62), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 10/31 (32%), Positives = 19/31 (61%)
Query: 13 QKPYVCGEENCTKRYTDPSSLRKHIKTVHGE 43
++PY C E+C +R++ L +HI+ G+
Sbjct: 1 ERPYACPVESCDRRFSRSDELTRHIRIHTGQ 31
>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 = 28.5 bits (62), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 10/31 (32%), Positives = 20/31 (64%)
Query: 13 QKPYVCGEENCTKRYTDPSSLRKHIKTVHGE 43
++PY C E+C +R++ ++L HI+ G+
Sbjct: 2 ERPYACPVESCDRRFSQKTNLDTHIRIHTGQ 32
>pdb|3U5C|G Chain G, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome A
pdb|3U5G|G Chain G, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 40s
Subunit, Ribosome B
pdb|3J16|C Chain C, Models Of Ribosome-Bound Dom34p And Rli1p And Their
Ribosomal Binding Partners
Length = 236
Score = 28.5 bits (62), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 19/29 (65%)
Query: 1 MKLNLAYPLLSSQKPYVCGEENCTKRYTD 29
MKLN++YP+ SQK + +E+ + + D
Sbjct: 1 MKLNISYPVNGSQKTFEIDDEHRIRVFFD 29
>pdb|1ZAA|C Chain C, Zinc Finger-Dna Recognition: Crystal Structure Of A
Zif268- Dna Complex At 2.1 Angstroms
Length = 87
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 10/31 (32%), Positives = 19/31 (61%)
Query: 13 QKPYVCGEENCTKRYTDPSSLRKHIKTVHGE 43
++PY C E+C +R++ L +HI+ G+
Sbjct: 2 ERPYACPVESCDRRFSRSDELTRHIRIHTGQ 32
>pdb|1SP2|A Chain A, Nmr Structure Of A Zinc Finger Domain From Transcription
Factor Sp1f2, Minimized Average Structure
pdb|1VA2|A Chain A, Solution Structure Of Transcription Factor Sp1 Dna
Binding Domain (Zinc Finger 2)
Length = 31
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 14 KPYVCGEENCTKRYTDPSSLRKHIKTVHGE 43
+P++C C KR+T L++H +T GE
Sbjct: 1 RPFMCTWSYCGKRFTRSDELQRHKRTHTGE 30
>pdb|1TF3|A Chain A, Tfiiia Finger 1-3 Bound To Dna, Nmr, 22 Structures
Length = 92
Score = 27.3 bits (59), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 18/33 (54%)
Query: 11 SSQKPYVCGEENCTKRYTDPSSLRKHIKTVHGE 43
+ +KP+ C EE C K +T L +H T GE
Sbjct: 29 TGEKPFPCKEEGCEKGFTSLHHLTRHSLTHTGE 61
Score = 26.2 bits (56), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 8/31 (25%), Positives = 17/31 (54%)
Query: 11 SSQKPYVCGEENCTKRYTDPSSLRKHIKTVH 41
+ +K + C + C R+T ++++KH H
Sbjct: 59 TGEKNFTCDSDGCDLRFTTKANMKKHFNRFH 89
>pdb|2EP3|A Chain A, Solution Structure Of The C2h2 Type Zinc Finger (Region
631- 663) Of Human Zinc Finger Protein 484
Length = 46
Score = 26.9 bits (58), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 13 QKPYVCGEENCTKRYTDPSSLRKHIKTVHGE 43
+KPY C E C K +TD S+L H K GE
Sbjct: 10 EKPYRCAE--CGKAFTDRSNLFTHQKIHTGE 38
>pdb|2EMH|A Chain A, Solution Structure Of The C2h2 Type Zinc Finger (Region
491- 523) Of Human Zinc Finger Protein 484
Length = 46
Score = 26.9 bits (58), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 19/31 (61%), Gaps = 2/31 (6%)
Query: 13 QKPYVCGEENCTKRYTDPSSLRKHIKTVHGE 43
++PY+C C K +TD S+L KH K GE
Sbjct: 10 ERPYIC--TVCGKAFTDRSNLIKHQKIHTGE 38
>pdb|3BD2|A Chain A, Crystal Structure Of Staphylococcus Aureus Dsba E96q
Length = 186
Score = 26.9 bits (58), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 24/61 (39%)
Query: 9 LLSSQKPYVCGEENCTKRYTDPSSLRKHIKTVHGEHCYANKKHKGMPSKDKDGLGGASPS 68
L QK +++ K + L KHIK +H + NK K +KD A
Sbjct: 79 FLDFQKQLFAAQQDQNKEWLTKELLDKHIKQLHLDKETENKIIKDYKTKDSKSWKAAEKD 138
Query: 69 R 69
+
Sbjct: 139 K 139
>pdb|4A4Z|A Chain A, Crystal Structure Of The S. Cerevisiae Dexh Helicase Ski2
Bound To Amppnp
Length = 997
Score = 26.9 bits (58), Expect = 3.2, Method: Composition-based stats.
Identities = 13/36 (36%), Positives = 21/36 (58%), Gaps = 6/36 (16%)
Query: 31 SSLRKHIKTVHGEHCYANKKHKGMPSKDKDGLGGAS 66
++ RKH + ++GE KG PSK +G GG++
Sbjct: 241 ANFRKHKEILNGESA------KGAPSKTDNGRGGST 270
>pdb|2LVU|A Chain A, Solution Structure Of Miz-1 Zinc Finger 10
Length = 26
Score = 26.6 bits (57), Expect = 4.0, Method: Composition-based stats.
Identities = 13/25 (52%), Positives = 15/25 (60%), Gaps = 2/25 (8%)
Query: 14 KPYVCGEENCTKRYTDPSSLRKHIK 38
KPYVC E C KR+ S L HI+
Sbjct: 1 KPYVC--ERCGKRFVQSSQLANHIR 23
>pdb|2ELX|A Chain A, Solution Structure Of The 8th C2h2 Zinc Finger Of Mouse
Zinc Finger Protein 406
Length = 35
Score = 26.6 bits (57), Expect = 4.2, Method: Composition-based stats.
Identities = 13/32 (40%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 11 SSQKPYVCGEENCTKRYTDPSSLRKHIKTVHG 42
S YVC C K++ LR HI+ VHG
Sbjct: 3 SGSSGYVCAL--CLKKFVSSIRLRSHIREVHG 32
>pdb|2RPC|A Chain A, Solution Structure Of The Tandem Zf-C2h2 Domains From The
Human Zinc Finger Protein Zic 3
Length = 155
Score = 26.2 bits (56), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 9/27 (33%), Positives = 17/27 (62%)
Query: 11 SSQKPYVCGEENCTKRYTDPSSLRKHI 37
+ +KP+ C E C +R+ + S +KH+
Sbjct: 116 TGEKPFKCEFEGCDRRFANSSDRKKHM 142
>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 = 26.2 bits (56), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 20/31 (64%), Gaps = 2/31 (6%)
Query: 13 QKPYVCGEENCTKRYTDPSSLRKHIKTVHGE 43
+KPY C E C K ++ S+L+KH +T GE
Sbjct: 2 EKPYKCPE--CGKSFSQSSNLQKHQRTHTGE 30
Score = 25.8 bits (55), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 2/33 (6%)
Query: 11 SSQKPYVCGEENCTKRYTDPSSLRKHIKTVHGE 43
+ +KPY C E C K ++ S L+KH +T GE
Sbjct: 28 TGEKPYKCPE--CGKSFSQSSDLQKHQRTHTGE 58
>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 = 26.2 bits (56), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 11 SSQKPYVCGEENCTKRYTDPSSLRKHIKTVHGE 43
S ++P++C C KRY S L+ H + GE
Sbjct: 2 SEKRPFMCAYPGCNKRYFKLSHLQMHSRKHTGE 34
>pdb|2WBU|A Chain A, Crystal Structure Of The Zinc Finger Domain Of Klf4
Bound To Its Target Dna
Length = 90
Score = 26.2 bits (56), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 28/66 (42%), Gaps = 16/66 (24%)
Query: 11 SSQKPYVCGEENCTKRYTDPSSLRKHIKTVHGE---HCYANKKHKGMPSKDKDGLGGASP 67
S + C C K YT S L+ H++T GE HC D DG G
Sbjct: 2 SRTATHTCDYAGCGKTYTKSSHLKAHLRTHTGEKPYHC------------DWDGC-GWKF 48
Query: 68 SRSDDM 73
+RSD++
Sbjct: 49 ARSDEL 54
>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 = 26.2 bits (56), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 22/37 (59%), Gaps = 2/37 (5%)
Query: 11 SSQKPYVCGEENCTKRYTDPSSLRKHIKTVHGEHCYA 47
+ +KPY C E C K ++ ++LR H +T GE YA
Sbjct: 73 TGEKPYKCPE--CGKSFSQRANLRAHQRTHTGEKPYA 107
>pdb|2EN1|A Chain A, Solution Structure Of The C2h2 Type Zinc Finger (Region
563- 595) Of Human Zinc Finger Protein 224
Length = 46
Score = 26.2 bits (56), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 13 QKPYVCGEENCTKRYTDPSSLRKHIKTVHGE 43
+KP+ C E C KR+T S L H + GE
Sbjct: 10 EKPFKC--EECGKRFTQNSQLHSHQRVHTGE 38
>pdb|2YTH|A Chain A, Solution Structure Of The C2h2 Type Zinc Finger (Region
479- 511) Of Human Zinc Finger Protein 224
Length = 46
Score = 26.2 bits (56), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 13 QKPYVCGEENCTKRYTDPSSLRKHIKTVHGE 43
+KP+ C E C KR+T S L H + GE
Sbjct: 10 EKPFQC--EECGKRFTQNSHLHSHQRVHTGE 38
>pdb|1BHI|A Chain A, Structure Of Transactivation Domain Of Cre-Bp1ATF-2,
Nmr, 20 Structures
Length = 38
Score = 26.2 bits (56), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 9/27 (33%), Positives = 15/27 (55%)
Query: 10 LSSQKPYVCGEENCTKRYTDPSSLRKH 36
+S KP++C C +R+T+ L H
Sbjct: 1 MSDDKPFLCTAPGCGQRFTNEDHLAVH 27
>pdb|2WBS|A Chain A, Crystal Structure Of The Zinc Finger Domain Of Klf4
Bound To Its Target Dna
Length = 89
Score = 25.8 bits (55), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 27/61 (44%), Gaps = 16/61 (26%)
Query: 16 YVCGEENCTKRYTDPSSLRKHIKTVHGE---HCYANKKHKGMPSKDKDGLGGASPSRSDD 72
+ C C K YT S L+ H++T GE HC D DG G +RSD+
Sbjct: 6 HTCDYAGCGKTYTKSSHLKAHLRTHTGEKPYHC------------DWDGCGW-KFARSDE 52
Query: 73 M 73
+
Sbjct: 53 L 53
>pdb|3AX1|A Chain A, Molecular Insights Into Mirna Processing By Arabidopsis
Serrate
Length = 358
Score = 25.4 bits (54), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 15/28 (53%)
Query: 16 YVCGEENCTKRYTDPSSLRKHIKTVHGE 43
Y CG + CTK + + KH+K H E
Sbjct: 305 YGCGAKGCTKLFHAAEFVYKHLKLKHTE 332
>pdb|2JJD|A Chain A, Protein Tyrosine Phosphatase, Receptor Type, E Isoform
pdb|2JJD|B Chain B, Protein Tyrosine Phosphatase, Receptor Type, E Isoform
pdb|2JJD|C Chain C, Protein Tyrosine Phosphatase, Receptor Type, E Isoform
pdb|2JJD|D Chain D, Protein Tyrosine Phosphatase, Receptor Type, E Isoform
pdb|2JJD|E Chain E, Protein Tyrosine Phosphatase, Receptor Type, E Isoform
pdb|2JJD|F Chain F, Protein Tyrosine Phosphatase, Receptor Type, E Isoform
Length = 599
Score = 25.4 bits (54), Expect = 8.3, Method: Composition-based stats.
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 29 DPSSLRKHIKTVHGEHCYANK 49
D SSL KH++T+HG + +K
Sbjct: 298 DVSSLEKHLQTMHGTTTHFDK 318
>pdb|1VA1|A Chain A, Solution Structure Of Transcription Factor Sp1 Dna
Binding Domain (Zinc Finger 1)
Length = 37
Score = 25.4 bits (54), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 13 QKPYVCGEENCTKRYTDPSSLRKHIKTVHGE 43
+K ++C + C K Y S LR H++ GE
Sbjct: 6 KKQHICHIQGCGKVYGKTSHLRAHLRWHTGE 36
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
0.311 0.128 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,596,576
Number of Sequences: 62578
Number of extensions: 88993
Number of successful extensions: 177
Number of sequences better than 100.0: 55
Number of HSP's better than 100.0 without gapping: 38
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 122
Number of HSP's gapped (non-prelim): 72
length of query: 109
length of database: 14,973,337
effective HSP length: 73
effective length of query: 36
effective length of database: 10,405,143
effective search space: 374585148
effective search space used: 374585148
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 45 (21.9 bits)