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= psy11070
         (148 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>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 = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 3/71 (4%)

Query: 54  QQLWSCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEHSN 113
           ++ ++CP+++C++RF+  SNL  H+  H       C    C R F      +TH++ H+ 
Sbjct: 2   ERPYACPVESCDRRFSDSSNLTRHIRIHTGQKPFQCR--ICMRNFSRSDHLTTHIRTHTG 59

Query: 114 VSAPYMCDYKG 124
              P+ CD  G
Sbjct: 60  -EKPFACDICG 69


>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 = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 28/90 (31%), Positives = 41/90 (45%), Gaps = 6/90 (6%)

Query: 36  GINKEYFISSTGGKNSKK---QQLWSCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEEL 92
           G NK YF  S    +S+K   ++ + C  K+C +RF+    LK H  RH       C+  
Sbjct: 13  GCNKRYFKLSHLQMHSRKHTGEKPYQCDFKDCERRFSRSDQLKRHQRRHTGVKPFQCK-- 70

Query: 93  GCGRKFQTMKQYSTHLKEHSNVSAPYMCDY 122
            C RKF       TH + H+    P+ C +
Sbjct: 71  TCQRKFSRSDHLKTHTRTHTG-EKPFSCRW 99



 Score = 40.4 bits (93), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 21/62 (33%), Positives = 30/62 (48%), Gaps = 1/62 (1%)

Query: 59  CPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEHSNVSAPY 118
           C    CNKR+  LS+L+MH  +H       C+   C R+F    Q   H + H+ V  P+
Sbjct: 9   CAYPGCNKRYFKLSHLQMHSRKHTGEKPYQCDFKDCERRFSRSDQLKRHQRRHTGV-KPF 67

Query: 119 MC 120
            C
Sbjct: 68  QC 69


>pdb|2GLI|A Chain A, Five-Finger GliDNA COMPLEX
          Length = 155

 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 26/82 (31%), Positives = 34/82 (41%), Gaps = 2/82 (2%)

Query: 59  CPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHL-KEHSNVSAP 117
           C  + C K ++ L NLK H+  H       CE  GC + F      + H  + HSN   P
Sbjct: 70  CTFEGCRKSYSRLENLKTHLRSHTGEKPYMCEHEGCSKAFSNASDRAKHQNRTHSN-EKP 128

Query: 118 YMCDYKGVCMSLTLKISFVKAV 139
           Y+C   G     T   S  K V
Sbjct: 129 YVCKLPGCTKRYTDPSSLRKHV 150



 Score = 33.9 bits (76), Expect = 0.037,   Method: Compositional matrix adjust.
 Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 1/57 (1%)

Query: 68  FTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEHSNVSAPYMCDYKG 124
           F     L +HM RH       C   GC + +  ++   THL+ H+    PYMC+++G
Sbjct: 49  FKAQYMLVVHMRRHTGEKPHKCTFEGCRKSYSRLENLKTHLRSHTG-EKPYMCEHEG 104


>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 = 39.7 bits (91), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 3/71 (4%)

Query: 54  QQLWSCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEHSN 113
           ++ ++CP+++C++RF+  ++L  H+  H       C    C R F      +TH++ H+ 
Sbjct: 2   ERPYACPVESCDRRFSRSADLTRHIRIHTGQKPFQCR--ICMRNFSRSDHLTTHIRTHTG 59

Query: 114 VSAPYMCDYKG 124
              P+ CD  G
Sbjct: 60  -EKPFACDICG 69


>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 = 39.3 bits (90), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 29/106 (27%), Positives = 45/106 (42%), Gaps = 9/106 (8%)

Query: 43  ISSTGGKNSKKQQLWSCPIKNCNKRFTTLSNLKMHMVRHG--KPLTLCCEELGCGRKFQT 100
           ++ TG KN      ++C    C+ RFTT +N+K H  R    K     C    CG+ F+ 
Sbjct: 65  LTHTGEKN------FTCDSDGCDLRFTTKANMKKHFNRFHNIKICVYVCHFENCGKAFKK 118

Query: 101 MKQYSTHLKEHSNVSAPYMCDYKGVCMSLTLKISFVKAVANNSKYP 146
             Q   H   H+    PY C ++G     +L     +    ++ YP
Sbjct: 119 HNQLKVHQFSHTQ-QLPYECPHEGCDKRFSLPSRLKRHEKVHAGYP 163



 Score = 38.1 bits (87), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 22/71 (30%), Positives = 31/71 (43%), Gaps = 4/71 (5%)

Query: 56  LWSCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEHSNVS 115
           ++ C  +NC K F   + LK+H   H + L   C   GC ++F       + LK H  V 
Sbjct: 104 VYVCHFENCGKAFKKHNQLKVHQFSHTQQLPYECPHEGCDKRFSL----PSRLKRHEKVH 159

Query: 116 APYMCDYKGVC 126
           A Y C     C
Sbjct: 160 AGYPCKKDDSC 170



 Score = 33.1 bits (74), Expect = 0.055,   Method: Compositional matrix adjust.
 Identities = 18/71 (25%), Positives = 31/71 (43%), Gaps = 1/71 (1%)

Query: 54  QQLWSCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEHSN 113
           ++ + C  + C K FT+L +L  H + H       C+  GC  +F T      H     N
Sbjct: 40  EKPFPCKEEGCEKGFTSLHHLTRHSLTHTGEKNFTCDSDGCDLRFTTKANMKKHFNRFHN 99

Query: 114 VS-APYMCDYK 123
           +    Y+C ++
Sbjct: 100 IKICVYVCHFE 110



 Score = 30.4 bits (67), Expect = 0.35,   Method: Compositional matrix adjust.
 Identities = 18/81 (22%), Positives = 33/81 (40%), Gaps = 1/81 (1%)

Query: 57  WSCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEHSNVSA 116
           + C   +C   +     L+ H+ +H       C+E GC + F ++   + H   H+    
Sbjct: 13  YICSFADCGAAYNKNWKLQAHLCKHTGEKPFPCKEEGCEKGFTSLHHLTRHSLTHTG-EK 71

Query: 117 PYMCDYKGVCMSLTLKISFVK 137
            + CD  G  +  T K +  K
Sbjct: 72  NFTCDSDGCDLRFTTKANMKK 92



 Score = 28.9 bits (63), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 23/62 (37%), Positives = 31/62 (50%), Gaps = 5/62 (8%)

Query: 51  SKKQQL-WSCPIKNCNKRFTTLSNLKMHMVRH-GKPLTLCCEELGCGRKFQTMKQYSTHL 108
           S  QQL + CP + C+KRF+  S LK H   H G P   C ++  C    +T   Y  H+
Sbjct: 128 SHTQQLPYECPHEGCDKRFSLPSRLKRHEKVHAGYP---CKKDDSCSFVGKTWTLYLKHV 184

Query: 109 KE 110
            E
Sbjct: 185 AE 186


>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 = 38.9 bits (89), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 3/71 (4%)

Query: 54  QQLWSCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEHSN 113
           ++ ++CP+++C++RF+  +NL  H+  H       C    C R F      + H++ H+ 
Sbjct: 2   ERPYACPVESCDRRFSQKTNLDTHIRIHTGQKPFQCR--ICMRNFSQQASLNAHIRTHTG 59

Query: 114 VSAPYMCDYKG 124
              P+ CD  G
Sbjct: 60  -EKPFACDICG 69


>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 = 38.9 bits (89), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 22/71 (30%), Positives = 31/71 (43%), Gaps = 4/71 (5%)

Query: 56  LWSCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEHSNVS 115
           ++ C  +NC K F   + LK+H   H + L   C   GC ++F       + LK H  V 
Sbjct: 1   MYVCHFENCGKAFKKHNQLKVHQFSHTQQLPYECPHEGCDKRFSL----PSRLKRHEKVH 56

Query: 116 APYMCDYKGVC 126
           A Y C     C
Sbjct: 57  AGYPCKKDDSC 67



 Score = 28.9 bits (63), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 23/62 (37%), Positives = 31/62 (50%), Gaps = 5/62 (8%)

Query: 51  SKKQQL-WSCPIKNCNKRFTTLSNLKMHMVRH-GKPLTLCCEELGCGRKFQTMKQYSTHL 108
           S  QQL + CP + C+KRF+  S LK H   H G P   C ++  C    +T   Y  H+
Sbjct: 25  SHTQQLPYECPHEGCDKRFSLPSRLKRHEKVHAGYP---CKKDDSCSFVGKTWTLYLKHV 81

Query: 109 KE 110
            E
Sbjct: 82  AE 83


>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 = 38.9 bits (89), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 3/71 (4%)

Query: 54  QQLWSCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEHSN 113
           ++ ++CP+++C++RF+  + L  H+  H       C    C R F      +TH++ H+ 
Sbjct: 2   ERPYACPVESCDRRFSRSAELTRHIRIHTGQKPFQCR--ICMRNFSRSDHLTTHIRTHTG 59

Query: 114 VSAPYMCDYKG 124
              P+ CD  G
Sbjct: 60  -EKPFACDICG 69


>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 = 38.5 bits (88), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 22/71 (30%), Positives = 31/71 (43%), Gaps = 4/71 (5%)

Query: 56  LWSCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEHSNVS 115
           ++ C  +NC K F   + LK+H   H + L   C   GC ++F       + LK H  V 
Sbjct: 1   MYVCHFENCGKAFKKHNQLKVHQFSHTQQLPYECPHEGCDKRFSL----PSRLKRHEKVH 56

Query: 116 APYMCDYKGVC 126
           A Y C     C
Sbjct: 57  AGYPCKKDDSC 67



 Score = 28.9 bits (63), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 23/62 (37%), Positives = 31/62 (50%), Gaps = 5/62 (8%)

Query: 51  SKKQQL-WSCPIKNCNKRFTTLSNLKMHMVRH-GKPLTLCCEELGCGRKFQTMKQYSTHL 108
           S  QQL + CP + C+KRF+  S LK H   H G P   C ++  C    +T   Y  H+
Sbjct: 25  SHTQQLPYECPHEGCDKRFSLPSRLKRHEKVHAGYP---CKKDDSCSFVGKTWTLYLKHV 81

Query: 109 KE 110
            E
Sbjct: 82  AE 83


>pdb|2EBT|A Chain A, Solution Structure Of Three Tandem Repeats Of Zf-C2h2
           Domains From Human Kruppel-Like Factor 5
          Length = 100

 Score = 38.5 bits (88), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 23/83 (27%), Positives = 39/83 (46%), Gaps = 4/83 (4%)

Query: 44  SSTGGKNSKKQQLWSCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQ 103
           S + G + +K+++  C    C K +T  S+LK H+  H       C   GC  +F    +
Sbjct: 3   SGSSGPDLEKRRIHYCDYPGCTKVYTKSSHLKAHLRTHTGEKPYKCTWEGCDWRFARSDE 62

Query: 104 YSTHLKEHSNVSAPYMCDYKGVC 126
            + H ++H+    P+ C   GVC
Sbjct: 63  LTRHYRKHTGAK-PFQC---GVC 81



 Score = 26.9 bits (58), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 15/60 (25%), Positives = 23/60 (38%), Gaps = 2/60 (3%)

Query: 54  QQLWSCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEHSN 113
           ++ + C  + C+ RF     L  H  +H       C    C R F      + H+K H N
Sbjct: 43  EKPYKCTWEGCDWRFARSDELTRHYRKHTGAKPFQCGV--CNRSFSRSDHLALHMKRHQN 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 = 38.5 bits (88), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 3/71 (4%)

Query: 54  QQLWSCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEHSN 113
           ++ ++CP+++C++RF+    L  H+  H       C    C R F      +TH++ H+ 
Sbjct: 2   ERPYACPVESCDRRFSRSDELTRHIRIHTGQKPFQCR--ICMRNFSRSDHLTTHIRTHTG 59

Query: 114 VSAPYMCDYKG 124
              P+ CD  G
Sbjct: 60  -EKPFACDICG 69


>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 = 38.5 bits (88), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 3/71 (4%)

Query: 54  QQLWSCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEHSN 113
           ++ ++CP+++C++RF+    L  H+  H       C    C R F      +TH++ H+ 
Sbjct: 1   ERPYACPVESCDRRFSRSDELTRHIRIHTGQKPFQCR--ICMRNFSRSDHLTTHIRTHTG 58

Query: 114 VSAPYMCDYKG 124
              P+ CD  G
Sbjct: 59  -EKPFACDICG 68


>pdb|2RPC|A Chain A, Solution Structure Of The Tandem Zf-C2h2 Domains From The
           Human Zinc Finger Protein Zic 3
          Length = 155

 Score = 38.5 bits (88), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 21/65 (32%), Positives = 28/65 (43%), Gaps = 1/65 (1%)

Query: 54  QQLWSCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEH-S 112
           ++ + CP   C K F    NLK+H   H       CE  GC R+F        H+  H S
Sbjct: 88  EKPFPCPFPGCGKIFARSENLKIHKRTHTGEKPFKCEFEGCDRRFANSSDRKKHMHVHTS 147

Query: 113 NVSAP 117
           + S P
Sbjct: 148 DKSGP 152


>pdb|1A1H|A Chain A, Qgsr (Zif268 Variant) Zinc Finger-Dna Complex (Gcac Site)
          Length = 90

 Score = 38.1 bits (87), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 3/71 (4%)

Query: 54  QQLWSCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEHSN 113
           ++ ++CP+++C++RF+   +L  H+  H       C    C R F      +TH++ H+ 
Sbjct: 2   ERPYACPVESCDRRFSQSGSLTRHIRIHTGQKPFQCR--ICMRNFSRSDHLTTHIRTHTG 59

Query: 114 VSAPYMCDYKG 124
              P+ CD  G
Sbjct: 60  -EKPFACDICG 69


>pdb|1ZAA|C Chain C, Zinc Finger-Dna Recognition: Crystal Structure Of A
           Zif268- Dna Complex At 2.1 Angstroms
          Length = 87

 Score = 38.1 bits (87), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 3/71 (4%)

Query: 54  QQLWSCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEHSN 113
           ++ ++CP+++C++RF+    L  H+  H       C    C R F      +TH++ H+ 
Sbjct: 2   ERPYACPVESCDRRFSRSDELTRHIRIHTGQKPFQCR--ICMRNFSRSDHLTTHIRTHTG 59

Query: 114 VSAPYMCDYKG 124
              P+ CD  G
Sbjct: 60  -EKPFACDICG 69


>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 = 37.4 bits (85), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 19/71 (26%), Positives = 36/71 (50%), Gaps = 3/71 (4%)

Query: 54  QQLWSCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEHSN 113
           ++ ++CP+++C++RF+  +NL  H+  H       C    C R F      + H++ H+ 
Sbjct: 2   ERPYACPVESCDRRFSQKTNLDTHIRIHTGQKPFQCR--ICMRNFSQHTGLNQHIRTHTG 59

Query: 114 VSAPYMCDYKG 124
              P+ CD  G
Sbjct: 60  -EKPFACDICG 69


>pdb|2WBU|A Chain A, Crystal Structure Of The Zinc Finger Domain Of Klf4 Bound
           To Its Target Dna
          Length = 90

 Score = 37.4 bits (85), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 1/63 (1%)

Query: 58  SCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEHSNVSAP 117
           +C    C K +T  S+LK H+  H       C+  GCG KF    + + H ++H+    P
Sbjct: 8   TCDYAGCGKTYTKSSHLKAHLRTHTGEKPYHCDWDGCGWKFARSDELTRHYRKHTG-HRP 66

Query: 118 YMC 120
           + C
Sbjct: 67  FQC 69



 Score = 30.4 bits (67), Expect = 0.37,   Method: Compositional matrix adjust.
 Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 1/42 (2%)

Query: 83  KPLTLCCEELGCGRKFQTMKQYSTHLKEHSNVSAPYMCDYKG 124
           +  T  C+  GCG+ +        HL+ H+    PY CD+ G
Sbjct: 3   RTATHTCDYAGCGKTYTKSSHLKAHLRTHTG-EKPYHCDWDG 43


>pdb|2WBS|A Chain A, Crystal Structure Of The Zinc Finger Domain Of Klf4 Bound
           To Its Target Dna
          Length = 89

 Score = 37.0 bits (84), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 1/63 (1%)

Query: 58  SCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEHSNVSAP 117
           +C    C K +T  S+LK H+  H       C+  GCG KF    + + H ++H+    P
Sbjct: 7   TCDYAGCGKTYTKSSHLKAHLRTHTGEKPYHCDWDGCGWKFARSDELTRHYRKHTG-HRP 65

Query: 118 YMC 120
           + C
Sbjct: 66  FQC 68


>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 = 37.0 bits (84), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 1/61 (1%)

Query: 64  CNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEHSNVSAPYMCDYK 123
           C K F   S LK H + H       C   GCG++F       TH++ H+    PY+C + 
Sbjct: 40  CGKAFVESSKLKRHQLVHTGEKPFQCTFEGCGKRFSLDFNLRTHVRIHTG-DRPYVCPFD 98

Query: 124 G 124
           G
Sbjct: 99  G 99



 Score = 37.0 bits (84), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 22/82 (26%), Positives = 36/82 (43%), Gaps = 4/82 (4%)

Query: 58  SCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEHSNVSAP 117
           +CP K C K F   S ++ H+  HG  + +C E   CG+ F    +   H   H+    P
Sbjct: 7   ACPHKGCTKMFRDNSAMRKHLHTHGPRVHVCAE---CGKAFVESSKLKRHQLVHTG-EKP 62

Query: 118 YMCDYKGVCMSLTLKISFVKAV 139
           + C ++G     +L  +    V
Sbjct: 63  FQCTFEGCGKRFSLDFNLRTHV 84



 Score = 32.7 bits (73), Expect = 0.079,   Method: Compositional matrix adjust.
 Identities = 16/59 (27%), Positives = 27/59 (45%)

Query: 54  QQLWSCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEHS 112
           ++ + C  + C KRF+   NL+ H+  H       C   GC +KF       +H+  H+
Sbjct: 60  EKPFQCTFEGCGKRFSLDFNLRTHVRIHTGDRPYVCPFDGCNKKFAQSTNLKSHILTHA 118



 Score = 32.3 bits (72), Expect = 0.10,   Method: Compositional matrix adjust.
 Identities = 12/27 (44%), Positives = 17/27 (62%)

Query: 57  WSCPIKNCNKRFTTLSNLKMHMVRHGK 83
           + CP   CNK+F   +NLK H++ H K
Sbjct: 93  YVCPFDGCNKKFAQSTNLKSHILTHAK 119


>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 = 34.3 bits (77), Expect = 0.028,   Method: Compositional matrix adjust.
 Identities = 16/60 (26%), Positives = 30/60 (50%), Gaps = 2/60 (3%)

Query: 53  KQQLWSCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEHS 112
           K + ++CP+++C++RF+    L  H+  H       C    C R F      +TH++ H+
Sbjct: 16  KMRPYACPVESCDRRFSRSDELTRHIRIHTGQKPFQCR--ICMRNFSRSDHLTTHIRTHT 73


>pdb|2DLK|A Chain A, Solution Structure Of The First And The Second Zf-C2h2
           Domains Of Zinc Finger Protein 692
          Length = 79

 Score = 33.9 bits (76), Expect = 0.032,   Method: Compositional matrix adjust.
 Identities = 19/67 (28%), Positives = 29/67 (43%), Gaps = 2/67 (2%)

Query: 59  CPIKNCNKRFTTLSNLKMHM-VRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEHSNVSAP 117
           C    C + F+    L  H   +H    +  C E  CG+ F   K    H+K HS+    
Sbjct: 10  CDFPGCGRIFSNRQYLNHHKKYQHIHQKSFSCPEPACGKSFNFKKHLKEHMKLHSDTRD- 68

Query: 118 YMCDYKG 124
           Y+C++ G
Sbjct: 69  YICEFSG 75



 Score = 28.5 bits (62), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 15/40 (37%), Positives = 18/40 (45%)

Query: 54 QQLWSCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELG 93
          Q+ +SCP   C K F    +LK HM  H       CE  G
Sbjct: 36 QKSFSCPEPACGKSFNFKKHLKEHMKLHSDTRDYICEFSG 75


>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 = 33.1 bits (74), Expect = 0.056,   Method: Compositional matrix adjust.
 Identities = 19/67 (28%), Positives = 29/67 (43%), Gaps = 5/67 (7%)

Query: 54  QQLWSCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEHSN 113
           ++ + CP   C K F+  +NL+ H   H       C E  CG+ F  +     H + H+ 
Sbjct: 75  EKPYKCP--ECGKSFSQRANLRAHQRTHTGEKPYACPE--CGKSFSQLAHLRAHQRTHTG 130

Query: 114 VSAPYMC 120
              PY C
Sbjct: 131 -EKPYKC 136


>pdb|1TF3|A Chain A, Tfiiia Finger 1-3 Bound To Dna, Nmr, 22 Structures
          Length = 92

 Score = 32.7 bits (73), Expect = 0.068,   Method: Compositional matrix adjust.
 Identities = 16/61 (26%), Positives = 26/61 (42%)

Query: 54  QQLWSCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEHSN 113
           ++ + C  + C K FT+L +L  H + H       C+  GC  +F T      H     N
Sbjct: 31  EKPFPCKEEGCEKGFTSLHHLTRHSLTHTGEKNFTCDSDGCDLRFTTKANMKKHFNRFHN 90

Query: 114 V 114
           +
Sbjct: 91  I 91



 Score = 31.2 bits (69), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 18/79 (22%), Positives = 32/79 (40%), Gaps = 1/79 (1%)

Query: 59  CPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEHSNVSAPY 118
           C   +C   +     L+ H+ +H       C+E GC + F ++   + H   H+     +
Sbjct: 6   CSFADCGAAYNKNWKLQAHLSKHTGEKPFPCKEEGCEKGFTSLHHLTRHSLTHTG-EKNF 64

Query: 119 MCDYKGVCMSLTLKISFVK 137
            CD  G  +  T K +  K
Sbjct: 65  TCDSDGCDLRFTTKANMKK 83


>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 = 32.3 bits (72), Expect = 0.088,   Method: Compositional matrix adjust.
 Identities = 25/91 (27%), Positives = 36/91 (39%), Gaps = 5/91 (5%)

Query: 54  QQLWSCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEHSN 113
           ++ + CP   C K F+  SNL+ H   H       C E  CG+ F        H + H+ 
Sbjct: 2   EKPYKCP--ECGKSFSQSSNLQKHQRTHTGEKPYKCPE--CGKSFSQSSDLQKHQRTHTG 57

Query: 114 VSAPYMCDYKGVCMSLTLKISFVKAVANNSK 144
              PY C   G   S +  +S  +    N K
Sbjct: 58  -EKPYKCPECGKSFSRSDHLSRHQRTHQNKK 87


>pdb|2CSH|A Chain A, Solution Structure Of Tandem Repeat Of The Zf-C2h2 Domains
           Of Human Zinc Finger Protein 297b
          Length = 110

 Score = 30.4 bits (67), Expect = 0.41,   Method: Compositional matrix adjust.
 Identities = 28/99 (28%), Positives = 41/99 (41%), Gaps = 10/99 (10%)

Query: 47  GGKNSKKQQLWSCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYST 106
           G   S   +L+ C    C K FT  S    HM  H       C    CG+KF+       
Sbjct: 1   GSSGSSGDKLYPC---QCGKSFTHKSQRDRHMSMHLGLRPYGCGV--CGKKFKMKHHLVG 55

Query: 107 HLKEHSNVSAPYMCDYKGVCM-SLTLKISFVKAVANNSK 144
           H+K H+ +  PY C+   +C      + SF + V + +K
Sbjct: 56  HMKIHTGIK-PYECN---ICAKRFMWRDSFHRHVTSCTK 90


>pdb|2EPA|A Chain A, Solution Structure Of The First And Second Zf-C2h2 Domains
           From Human Krueppel-Like Factor 10
          Length = 72

 Score = 30.0 bits (66), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 16/53 (30%), Positives = 21/53 (39%)

Query: 59  CPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEH 111
           C    C K +   S+LK H   H       C   GC R+F    + S H + H
Sbjct: 20  CSHPGCGKTYFKSSHLKAHTRTHTGEKPFSCSWKGCERRFARSDELSRHRRTH 72


>pdb|2DLQ|A Chain A, Solution Structure Of The Tandem Four Zf-C2h2 Domain
           Repeats Of Murine Gli-Kruppel Family Member Hkr3
          Length = 124

 Score = 27.7 bits (60), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 5/66 (7%)

Query: 52  KKQQLWSCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHL-KE 110
           + +Q+++C +  C + F     L++HMV H   +   C    C ++F   K   +H+ K 
Sbjct: 62  RSEQVFTCSV--CQETFRRRMELRLHMVSHTGEMPYKCS--SCSQQFMQKKDLQSHMIKL 117

Query: 111 HSNVSA 116
           HS  S+
Sbjct: 118 HSGPSS 123


>pdb|1AKO|A Chain A, Exonuclease Iii From Escherichia Coli
          Length = 268

 Score = 27.7 bits (60), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 12/43 (27%), Positives = 23/43 (53%)

Query: 65  NKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTH 107
           +K F     L++ ++   +PL  CC E G   + ++M++ S H
Sbjct: 217 SKGFDDNRGLRIDLLLASQPLAECCVETGIDYEIRSMEKPSDH 259


>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 = 27.3 bits (59), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 18/64 (28%), Positives = 30/64 (46%), Gaps = 4/64 (6%)

Query: 54  QQLWSCPIKNCNKRFTTLSNLKMHMVRHGKPLTLCCEELGCGRKFQTMKQYSTHLKEHSN 113
           ++ ++C I  C+K F    +L+ H   H K     C+E  CG+ F   +  + H   H  
Sbjct: 43  ERPYTCDI--CHKAFRRQDHLRDHRYIHSKEKPFKCQE--CGKGFCQSRTLAVHKTLHMQ 98

Query: 114 VSAP 117
            S+P
Sbjct: 99  TSSP 102


>pdb|2KMK|A Chain A, Gfi-1 Zinc Fingers 3-5 Complexed With Dna
          Length = 82

 Score = 26.9 bits (58), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 14/31 (45%), Positives = 18/31 (58%), Gaps = 1/31 (3%)

Query: 94  CGRKFQTMKQYSTHLKEHSNVSAPYMCDYKG 124
           CG+ F+     STHL  HS+ + PY C Y G
Sbjct: 7   CGKSFKRSSTLSTHLLIHSD-TRPYPCQYCG 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
   0.316    0.128    0.384 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,788,929
Number of Sequences: 62578
Number of extensions: 128142
Number of successful extensions: 349
Number of sequences better than 100.0: 39
Number of HSP's better than 100.0 without gapping: 25
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 275
Number of HSP's gapped (non-prelim): 78
length of query: 148
length of database: 14,973,337
effective HSP length: 90
effective length of query: 58
effective length of database: 9,341,317
effective search space: 541796386
effective search space used: 541796386
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)