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= psy7463
(319 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 60.1 bits (144), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 54/206 (26%), Positives = 79/206 (38%), Gaps = 33/206 (16%)
Query: 5 ESDLKDKVVPQKCPLCERLYKSVYRMKEHMKKQHKGQLYECDCCTEYFIDRIAYEEHVRL 64
++ L+ P CP C + + + EH + + Y+C C + F D+ H R
Sbjct: 12 QAALEPGEKPYACPECGKSFSRSDHLAEHQRTHTGEKPYKCPECGKSFSDKKDLTRHQRT 71
Query: 65 HEG--GIICRLCGEKF-EKSLMRDHLVTHIPPEHRGKVSDAFFNKKQTALLTHYLKRNGI 121
H G C CG+ F +++ +R H TH +K A
Sbjct: 72 HTGEKPYKCPECGKSFSQRANLRAHQRTHT-------------GEKPYA----------- 107
Query: 122 KLQCNLCADTFCPRSNMLRHYLLKHRGDKVFYACDRCDKRFSLLQNLKRHLAIHE-RIAY 180
C C +F ++ LR + H G+K Y C C K FS NL H H Y
Sbjct: 108 ---CPECGKSFSQLAH-LRAHQRTHTGEKP-YKCPECGKSFSREDNLHTHQRTHTGEKPY 162
Query: 181 QCNVCDKKYSRLSDYKIHMNMHNGFK 206
+C C K +SR +H H G K
Sbjct: 163 KCPECGKSFSRRDALNVHQRTHTGKK 188
Score = 56.6 bits (135), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 40/118 (33%), Positives = 54/118 (45%), Gaps = 5/118 (4%)
Query: 111 LLTHYLKRNGIK-LQCNLCADTFCPRSNMLRHYLLKHRGDKVFYACDRCDKRFSLLQNLK 169
L H G K +C C +F + ++ RH H G+K Y C C K FS NL+
Sbjct: 37 LAEHQRTHTGEKPYKCPECGKSFSDKKDLTRHQRT-HTGEKP-YKCPECGKSFSQRANLR 94
Query: 170 RHLAIHE-RIAYQCNVCDKKYSRLSDYKIHMNMHNGFK-YQCHICLKCTSRKNYLKRH 225
H H Y C C K +S+L+ + H H G K Y+C C K SR++ L H
Sbjct: 95 AHQRTHTGEKPYACPECGKSFSQLAHLRAHQRTHTGEKPYKCPECGKSFSREDNLHTH 152
>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 = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 153 YACDRCDKRFSLLQNLKRHLAIHE-RIAYQCNVCDKKYSRLSDYKIHMNMHNGFK-YQCH 210
Y C C K FS NL++H H Y+C C K +S+ SD + H H G K Y+C
Sbjct: 5 YKCPECGKSFSQSSNLQKHQRTHTGEKPYKCPECGKSFSQSSDLQKHQRTHTGEKPYKCP 64
Query: 211 ICLKCTSRKNYLKRH 225
C K SR ++L RH
Sbjct: 65 ECGKSFSRSDHLSRH 79
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 37/84 (44%), Gaps = 3/84 (3%)
Query: 124 QCNLCADTFCPRSNMLRHYLLKHRGDKVFYACDRCDKRFSLLQNLKRHLAIHE-RIAYQC 182
+C C +F SN+ +H H G+K Y C C K FS +L++H H Y+C
Sbjct: 6 KCPECGKSFSQSSNLQKHQRT-HTGEKP-YKCPECGKSFSQSSDLQKHQRTHTGEKPYKC 63
Query: 183 NVCDKKYSRLSDYKIHMNMHNGFK 206
C K +SR H H K
Sbjct: 64 PECGKSFSRSDHLSRHQRTHQNKK 87
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 5/79 (6%)
Query: 14 PQKCPLCERLYKSVYRMKEHMKKQHKGQLYECDCCTEYFIDRIAYEEHVRLHEG--GIIC 71
P KCP C + + +++H + + Y+C C + F ++H R H G C
Sbjct: 4 PYKCPECGKSFSQSSNLQKHQRTHTGEKPYKCPECGKSFSQSSDLQKHQRTHTGEKPYKC 63
Query: 72 RLCGEKFEKSLMRDHLVTH 90
CG+ F +S DHL H
Sbjct: 64 PECGKSFSRS---DHLSRH 79
>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 = 51.6 bits (122), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 30/78 (38%), Positives = 43/78 (55%), Gaps = 4/78 (5%)
Query: 153 YAC--DRCDKRFSLLQNLKRHLAIHE-RIAYQCNVCDKKYSRLSDYKIHMNMHNGFK-YQ 208
YAC + CD+RFS NL RH+ IH + +QC +C + +SR H+ H G K +
Sbjct: 5 YACPVESCDRRFSDSSNLTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTHTGEKPFA 64
Query: 209 CHICLKCTSRKNYLKRHI 226
C IC + +R + KRH
Sbjct: 65 CDICGRKFARSDERKRHT 82
Score = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 30/55 (54%), Gaps = 2/55 (3%)
Query: 123 LQCNLCADTFCPRSNMLRHYLLKHRGDKVFYACDRCDKRFSLLQNLKRHLAIHER 177
QC +C F RS+ L ++ H G+K F ACD C ++F+ KRH IH R
Sbjct: 35 FQCRICMRNF-SRSDHLTTHIRTHTGEKPF-ACDICGRKFARSDERKRHTKIHLR 87
Score = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 3/76 (3%)
Query: 128 CADTFCPRSNMLRHYLLKHRGDKVFYACDRCDKRFSLLQNLKRHLAIHE-RIAYQCNVCD 186
C F SN+ RH + H G K F C C + FS +L H+ H + C++C
Sbjct: 12 CDRRFSDSSNLTRHIRI-HTGQKPF-QCRICMRNFSRSDHLTTHIRTHTGEKPFACDICG 69
Query: 187 KKYSRLSDYKIHMNMH 202
+K++R + K H +H
Sbjct: 70 RKFARSDERKRHTKIH 85
Score = 35.8 bits (81), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 32/75 (42%), Gaps = 4/75 (5%)
Query: 14 PQKCPL--CERLYKSVYRMKEHMKKQHKGQLYECDCCTEYFIDRIAYEEHVRLHEG--GI 69
P CP+ C+R + + H++ + ++C C F H+R H G
Sbjct: 4 PYACPVESCDRRFSDSSNLTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTHTGEKPF 63
Query: 70 ICRLCGEKFEKSLMR 84
C +CG KF +S R
Sbjct: 64 ACDICGRKFARSDER 78
>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 = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 43/78 (55%), Gaps = 4/78 (5%)
Query: 153 YAC--DRCDKRFSLLQNLKRHLAIHE-RIAYQCNVCDKKYSRLSDYKIHMNMHNGFK-YQ 208
YAC + CD+RFS +L RH+ IH + +QC +C + +SR H+ H G K +
Sbjct: 5 YACPVESCDRRFSRSADLTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTHTGEKPFA 64
Query: 209 CHICLKCTSRKNYLKRHI 226
C IC + +R + KRH
Sbjct: 65 CDICGRKFARSDERKRHT 82
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 27/72 (37%), Positives = 40/72 (55%), Gaps = 4/72 (5%)
Query: 108 QTALLTHYLK-RNGIK-LQCNLCADTFCPRSNMLRHYLLKHRGDKVFYACDRCDKRFSLL 165
++A LT +++ G K QC +C F RS+ L ++ H G+K F ACD C ++F+
Sbjct: 18 RSADLTRHIRIHTGQKPFQCRICMRNF-SRSDHLTTHIRTHTGEKPF-ACDICGRKFARS 75
Query: 166 QNLKRHLAIHER 177
KRH IH R
Sbjct: 76 DERKRHTKIHLR 87
Score = 35.0 bits (79), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 31/72 (43%), Gaps = 4/72 (5%)
Query: 14 PQKCPL--CERLYKSVYRMKEHMKKQHKGQLYECDCCTEYFIDRIAYEEHVRLHEG--GI 69
P CP+ C+R + + H++ + ++C C F H+R H G
Sbjct: 4 PYACPVESCDRRFSRSADLTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTHTGEKPF 63
Query: 70 ICRLCGEKFEKS 81
C +CG KF +S
Sbjct: 64 ACDICGRKFARS 75
Score = 34.3 bits (77), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 3/76 (3%)
Query: 128 CADTFCPRSNMLRHYLLKHRGDKVFYACDRCDKRFSLLQNLKRHLAIHE-RIAYQCNVCD 186
C F +++ RH + H G K F C C + FS +L H+ H + C++C
Sbjct: 12 CDRRFSRSADLTRHIRI-HTGQKPF-QCRICMRNFSRSDHLTTHIRTHTGEKPFACDICG 69
Query: 187 KKYSRLSDYKIHMNMH 202
+K++R + K H +H
Sbjct: 70 RKFARSDERKRHTKIH 85
>pdb|1A1H|A Chain A, Qgsr (Zif268 Variant) Zinc Finger-Dna Complex (Gcac Site)
Length = 90
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 43/78 (55%), Gaps = 4/78 (5%)
Query: 153 YAC--DRCDKRFSLLQNLKRHLAIHE-RIAYQCNVCDKKYSRLSDYKIHMNMHNGFK-YQ 208
YAC + CD+RFS +L RH+ IH + +QC +C + +SR H+ H G K +
Sbjct: 5 YACPVESCDRRFSQSGSLTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTHTGEKPFA 64
Query: 209 CHICLKCTSRKNYLKRHI 226
C IC + +R + KRH
Sbjct: 65 CDICGRKFARSDERKRHT 82
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 27/72 (37%), Positives = 39/72 (54%), Gaps = 4/72 (5%)
Query: 108 QTALLTHYLK-RNGIK-LQCNLCADTFCPRSNMLRHYLLKHRGDKVFYACDRCDKRFSLL 165
Q+ LT +++ G K QC +C F RS+ L ++ H G+K F ACD C ++F+
Sbjct: 18 QSGSLTRHIRIHTGQKPFQCRICMRNF-SRSDHLTTHIRTHTGEKPF-ACDICGRKFARS 75
Query: 166 QNLKRHLAIHER 177
KRH IH R
Sbjct: 76 DERKRHTKIHLR 87
Score = 35.0 bits (79), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 31/72 (43%), Gaps = 4/72 (5%)
Query: 14 PQKCPL--CERLYKSVYRMKEHMKKQHKGQLYECDCCTEYFIDRIAYEEHVRLHEG--GI 69
P CP+ C+R + + H++ + ++C C F H+R H G
Sbjct: 4 PYACPVESCDRRFSQSGSLTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTHTGEKPF 63
Query: 70 ICRLCGEKFEKS 81
C +CG KF +S
Sbjct: 64 ACDICGRKFARS 75
Score = 34.3 bits (77), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 3/76 (3%)
Query: 128 CADTFCPRSNMLRHYLLKHRGDKVFYACDRCDKRFSLLQNLKRHLAIHE-RIAYQCNVCD 186
C F ++ RH + H G K F C C + FS +L H+ H + C++C
Sbjct: 12 CDRRFSQSGSLTRHIRI-HTGQKPF-QCRICMRNFSRSDHLTTHIRTHTGEKPFACDICG 69
Query: 187 KKYSRLSDYKIHMNMH 202
+K++R + K H +H
Sbjct: 70 RKFARSDERKRHTKIH 85
>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 = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 42/78 (53%), Gaps = 4/78 (5%)
Query: 153 YAC--DRCDKRFSLLQNLKRHLAIHE-RIAYQCNVCDKKYSRLSDYKIHMNMHNGFK-YQ 208
YAC + CD+RFS L RH+ IH + +QC +C + +SR H+ H G K +
Sbjct: 5 YACPVESCDRRFSRSAELTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTHTGEKPFA 64
Query: 209 CHICLKCTSRKNYLKRHI 226
C IC + +R + KRH
Sbjct: 65 CDICGRKFARSDERKRHT 82
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 27/72 (37%), Positives = 40/72 (55%), Gaps = 4/72 (5%)
Query: 108 QTALLTHYLK-RNGIK-LQCNLCADTFCPRSNMLRHYLLKHRGDKVFYACDRCDKRFSLL 165
++A LT +++ G K QC +C F RS+ L ++ H G+K F ACD C ++F+
Sbjct: 18 RSAELTRHIRIHTGQKPFQCRICMRNF-SRSDHLTTHIRTHTGEKPF-ACDICGRKFARS 75
Query: 166 QNLKRHLAIHER 177
KRH IH R
Sbjct: 76 DERKRHTKIHLR 87
Score = 35.0 bits (79), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 31/72 (43%), Gaps = 4/72 (5%)
Query: 14 PQKCPL--CERLYKSVYRMKEHMKKQHKGQLYECDCCTEYFIDRIAYEEHVRLHEG--GI 69
P CP+ C+R + + H++ + ++C C F H+R H G
Sbjct: 4 PYACPVESCDRRFSRSAELTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTHTGEKPF 63
Query: 70 ICRLCGEKFEKS 81
C +CG KF +S
Sbjct: 64 ACDICGRKFARS 75
Score = 34.3 bits (77), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 2/69 (2%)
Query: 135 RSNMLRHYLLKHRGDKVFYACDRCDKRFSLLQNLKRHLAIHE-RIAYQCNVCDKKYSRLS 193
RS L ++ H G K F C C + FS +L H+ H + C++C +K++R
Sbjct: 18 RSAELTRHIRIHTGQKPF-QCRICMRNFSRSDHLTTHIRTHTGEKPFACDICGRKFARSD 76
Query: 194 DYKIHMNMH 202
+ K H +H
Sbjct: 77 ERKRHTKIH 85
>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 = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 42/78 (53%), Gaps = 4/78 (5%)
Query: 153 YAC--DRCDKRFSLLQNLKRHLAIHE-RIAYQCNVCDKKYSRLSDYKIHMNMHNGFK-YQ 208
YAC + CD+RFS L RH+ IH + +QC +C + +SR H+ H G K +
Sbjct: 4 YACPVESCDRRFSRSDELTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTHTGEKPFA 63
Query: 209 CHICLKCTSRKNYLKRHI 226
C IC + +R + KRH
Sbjct: 64 CDICGRKFARSDERKRHT 81
Score = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 30/55 (54%), Gaps = 2/55 (3%)
Query: 123 LQCNLCADTFCPRSNMLRHYLLKHRGDKVFYACDRCDKRFSLLQNLKRHLAIHER 177
QC +C F RS+ L ++ H G+K F ACD C ++F+ KRH IH R
Sbjct: 34 FQCRICMRNF-SRSDHLTTHIRTHTGEKPF-ACDICGRKFARSDERKRHTKIHLR 86
Score = 35.4 bits (80), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 2/69 (2%)
Query: 135 RSNMLRHYLLKHRGDKVFYACDRCDKRFSLLQNLKRHLAIHE-RIAYQCNVCDKKYSRLS 193
RS+ L ++ H G K F C C + FS +L H+ H + C++C +K++R
Sbjct: 17 RSDELTRHIRIHTGQKPF-QCRICMRNFSRSDHLTTHIRTHTGEKPFACDICGRKFARSD 75
Query: 194 DYKIHMNMH 202
+ K H +H
Sbjct: 76 ERKRHTKIH 84
Score = 34.3 bits (77), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 32/75 (42%), Gaps = 4/75 (5%)
Query: 14 PQKCPL--CERLYKSVYRMKEHMKKQHKGQLYECDCCTEYFIDRIAYEEHVRLHEG--GI 69
P CP+ C+R + + H++ + ++C C F H+R H G
Sbjct: 3 PYACPVESCDRRFSRSDELTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTHTGEKPF 62
Query: 70 ICRLCGEKFEKSLMR 84
C +CG KF +S R
Sbjct: 63 ACDICGRKFARSDER 77
>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 = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 42/78 (53%), Gaps = 4/78 (5%)
Query: 153 YAC--DRCDKRFSLLQNLKRHLAIHE-RIAYQCNVCDKKYSRLSDYKIHMNMHNGFK-YQ 208
YAC + CD+RFS L RH+ IH + +QC +C + +SR H+ H G K +
Sbjct: 5 YACPVESCDRRFSRSDELTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTHTGEKPFA 64
Query: 209 CHICLKCTSRKNYLKRHI 226
C IC + +R + KRH
Sbjct: 65 CDICGRKFARSDERKRHT 82
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 30/55 (54%), Gaps = 2/55 (3%)
Query: 123 LQCNLCADTFCPRSNMLRHYLLKHRGDKVFYACDRCDKRFSLLQNLKRHLAIHER 177
QC +C F RS+ L ++ H G+K F ACD C ++F+ KRH IH R
Sbjct: 35 FQCRICMRNF-SRSDHLTTHIRTHTGEKPF-ACDICGRKFARSDERKRHTKIHLR 87
Score = 35.0 bits (79), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 2/69 (2%)
Query: 135 RSNMLRHYLLKHRGDKVFYACDRCDKRFSLLQNLKRHLAIHE-RIAYQCNVCDKKYSRLS 193
RS+ L ++ H G K F C C + FS +L H+ H + C++C +K++R
Sbjct: 18 RSDELTRHIRIHTGQKPF-QCRICMRNFSRSDHLTTHIRTHTGEKPFACDICGRKFARSD 76
Query: 194 DYKIHMNMH 202
+ K H +H
Sbjct: 77 ERKRHTKIH 85
Score = 34.3 bits (77), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 31/72 (43%), Gaps = 4/72 (5%)
Query: 14 PQKCPL--CERLYKSVYRMKEHMKKQHKGQLYECDCCTEYFIDRIAYEEHVRLHEG--GI 69
P CP+ C+R + + H++ + ++C C F H+R H G
Sbjct: 4 PYACPVESCDRRFSRSDELTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTHTGEKPF 63
Query: 70 ICRLCGEKFEKS 81
C +CG KF +S
Sbjct: 64 ACDICGRKFARS 75
>pdb|1ZAA|C Chain C, Zinc Finger-Dna Recognition: Crystal Structure Of A
Zif268- Dna Complex At 2.1 Angstroms
Length = 87
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 42/78 (53%), Gaps = 4/78 (5%)
Query: 153 YAC--DRCDKRFSLLQNLKRHLAIHE-RIAYQCNVCDKKYSRLSDYKIHMNMHNGFK-YQ 208
YAC + CD+RFS L RH+ IH + +QC +C + +SR H+ H G K +
Sbjct: 5 YACPVESCDRRFSRSDELTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTHTGEKPFA 64
Query: 209 CHICLKCTSRKNYLKRHI 226
C IC + +R + KRH
Sbjct: 65 CDICGRKFARSDERKRHT 82
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/55 (41%), Positives = 34/55 (61%), Gaps = 4/55 (7%)
Query: 175 HERIAYQCNV--CDKKYSRLSDYKIHMNMHNGFK-YQCHICLKCTSRKNYLKRHI 226
HER Y C V CD+++SR + H+ +H G K +QC IC++ SR ++L HI
Sbjct: 1 HER-PYACPVESCDRRFSRSDELTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHI 54
Score = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 30/55 (54%), Gaps = 2/55 (3%)
Query: 123 LQCNLCADTFCPRSNMLRHYLLKHRGDKVFYACDRCDKRFSLLQNLKRHLAIHER 177
QC +C F RS+ L ++ H G+K F ACD C ++F+ KRH IH R
Sbjct: 35 FQCRICMRNF-SRSDHLTTHIRTHTGEKPF-ACDICGRKFARSDERKRHTKIHLR 87
Score = 35.0 bits (79), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 2/69 (2%)
Query: 135 RSNMLRHYLLKHRGDKVFYACDRCDKRFSLLQNLKRHLAIHE-RIAYQCNVCDKKYSRLS 193
RS+ L ++ H G K F C C + FS +L H+ H + C++C +K++R
Sbjct: 18 RSDELTRHIRIHTGQKPF-QCRICMRNFSRSDHLTTHIRTHTGEKPFACDICGRKFARSD 76
Query: 194 DYKIHMNMH 202
+ K H +H
Sbjct: 77 ERKRHTKIH 85
Score = 34.7 bits (78), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 32/75 (42%), Gaps = 4/75 (5%)
Query: 14 PQKCPL--CERLYKSVYRMKEHMKKQHKGQLYECDCCTEYFIDRIAYEEHVRLHEG--GI 69
P CP+ C+R + + H++ + ++C C F H+R H G
Sbjct: 4 PYACPVESCDRRFSRSDELTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTHTGEKPF 63
Query: 70 ICRLCGEKFEKSLMR 84
C +CG KF +S R
Sbjct: 64 ACDICGRKFARSDER 78
>pdb|2KMK|A Chain A, Gfi-1 Zinc Fingers 3-5 Complexed With Dna
Length = 82
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 41/83 (49%), Gaps = 3/83 (3%)
Query: 123 LQCNLCADTFCPRSNMLRHYLLKHRGDKVFYACDRCDKRFSLLQNLKRHLAIHE-RIAYQ 181
C +C +F RS+ L +LL H D Y C C KRF ++K+H IH ++
Sbjct: 2 FDCKICGKSF-KRSSTLSTHLLIH-SDTRPYPCQYCGKRFHQKSDMKKHTFIHTGEKPHK 59
Query: 182 CNVCDKKYSRLSDYKIHMNMHNG 204
C VC K +S+ S+ H H G
Sbjct: 60 CQVCGKAFSQSSNLITHSRKHTG 82
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 36/75 (48%), Gaps = 2/75 (2%)
Query: 153 YACDRCDKRFSLLQNLKRHLAIHERI-AYQCNVCDKKYSRLSDYKIHMNMHNGFK-YQCH 210
+ C C K F L HL IH Y C C K++ + SD K H +H G K ++C
Sbjct: 2 FDCKICGKSFKRSSTLSTHLLIHSDTRPYPCQYCGKRFHQKSDMKKHTFIHTGEKPHKCQ 61
Query: 211 ICLKCTSRKNYLKRH 225
+C K S+ + L H
Sbjct: 62 VCGKAFSQSSNLITH 76
Score = 31.6 bits (70), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 5/76 (6%)
Query: 17 CPLCERLYKSVYRMKEHMKKQHKGQLYECDCCTEYFIDRIAYEEHVRLHEGGII--CRLC 74
C +C + +K + H+ + Y C C + F + ++H +H G C++C
Sbjct: 4 CKICGKSFKRSSTLSTHLLIHSDTRPYPCQYCGKRFHQKSDMKKHTFIHTGEKPHKCQVC 63
Query: 75 GEKFEKSLMRDHLVTH 90
G+ F +S +L+TH
Sbjct: 64 GKAFSQS---SNLITH 76
Score = 28.9 bits (63), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 179 AYQCNVCDKKYSRLSDYKIHMNMHNGFK-YQCHICLKCTSRKNYLKRHIIM 228
++ C +C K + R S H+ +H+ + Y C C K +K+ +K+H +
Sbjct: 1 SFDCKICGKSFKRSSTLSTHLLIHSDTRPYPCQYCGKRFHQKSDMKKHTFI 51
>pdb|2YT9|A Chain A, Solution Structure Of C2h2 Type Zinc Finger Domain 345 In
Zinc Finger Protein 278
Length = 95
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 33/91 (36%), Positives = 47/91 (51%), Gaps = 13/91 (14%)
Query: 17 CPLCERLYKSVYRMKEHMKKQHKGQ-LYECDCCTEYFI--DRIAYEEHVRLHEGGI---- 69
C +C ++++ VY + H K H G+ Y C C F DR++Y HVR H+G +
Sbjct: 10 CEICGKIFRDVYHLNRH-KLSHSGEKPYSCPVCGLRFKRKDRMSY--HVRSHDGSVGKPY 66
Query: 70 ICRLCGEKFEKSLMRDHLVTHIPPEHRGKVS 100
IC+ CG+ F + DHL HI H G S
Sbjct: 67 ICQSCGKGFSRP---DHLNGHIKQVHSGPSS 94
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 27/82 (32%), Positives = 38/82 (46%), Gaps = 4/82 (4%)
Query: 154 ACDRCDKRFSLLQNLKRHLAIHE-RIAYQCNVCDKKYSRLSDYKIHMNMHNGF---KYQC 209
AC+ C K F + +L RH H Y C VC ++ R H+ H+G Y C
Sbjct: 9 ACEICGKIFRDVYHLNRHKLSHSGEKPYSCPVCGLRFKRKDRMSYHVRSHDGSVGKPYIC 68
Query: 210 HICLKCTSRKNYLKRHIIMMHT 231
C K SR ++L HI +H+
Sbjct: 69 QSCGKGFSRPDHLNGHIKQVHS 90
Score = 32.3 bits (72), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 36/83 (43%), Gaps = 9/83 (10%)
Query: 123 LQCNLCADTFCPRSNMLRHYLLKHRGDKVFYACDRCDKRFSLLQNLKRHLAIHERIA--- 179
+ C +C F ++ RH L H G+K Y+C C RF + H+ H+
Sbjct: 8 VACEICGKIFRDVYHLNRH-KLSHSGEKP-YSCPVCGLRFKRKDRMSYHVRSHDGSVGKP 65
Query: 180 YQCNVCDKKYSRLSDYKIHMNMH 202
Y C C K +SR H+N H
Sbjct: 66 YICQSCGKGFSRPD----HLNGH 84
>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 = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 36/96 (37%), Positives = 48/96 (50%), Gaps = 7/96 (7%)
Query: 139 LRHYLLKHRGDKVFYACD--RCDKRFSLLQNLKRHLAIHERI-AYQCNVCDKKYSRLSDY 195
L+ + KH G+K Y CD C++RFS LKRH H + +QC C +K+SR
Sbjct: 24 LQMHSRKHTGEKP-YQCDFKDCERRFSRSDQLKRHQRRHTGVKPFQCKTCQRKFSRSDHL 82
Query: 196 KIHMNMHNGFK-YQCHI--CLKCTSRKNYLKRHIIM 228
K H H G K + C C K +R + L RH M
Sbjct: 83 KTHTRTHTGEKPFSCRWPSCQKKFARSDELVRHHNM 118
Score = 37.0 bits (84), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 34/102 (33%), Positives = 47/102 (46%), Gaps = 8/102 (7%)
Query: 107 KQTALLTHYLKRNGIK-LQCNL--CADTFCPRSNMLRHYLLKHRGDKVFYACDRCDKRFS 163
K + L H K G K QC+ C F RS+ L+ + +H G K F C C ++FS
Sbjct: 20 KLSHLQMHSRKHTGEKPYQCDFKDCERRF-SRSDQLKRHQRRHTGVKPF-QCKTCQRKFS 77
Query: 164 LLQNLKRHLAIHE-RIAYQCN--VCDKKYSRLSDYKIHMNMH 202
+LK H H + C C KK++R + H NMH
Sbjct: 78 RSDHLKTHTRTHTGEKPFSCRWPSCQKKFARSDELVRHHNMH 119
Score = 33.1 bits (74), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 34/78 (43%), Gaps = 7/78 (8%)
Query: 18 PLCERLYKSVYRMKEHMKKQHKGQLYECDC--CTEYFIDRIAYEEHVRLHEG--GIICRL 73
P C + Y + ++ H +K + Y+CD C F + H R H G C+
Sbjct: 12 PGCNKRYFKLSHLQMHSRKHTGEKPYQCDFKDCERRFSRSDQLKRHQRRHTGVKPFQCKT 71
Query: 74 CGEKFEKSLMRDHLVTHI 91
C KF +S DHL TH
Sbjct: 72 CQRKFSRS---DHLKTHT 86
Score = 32.7 bits (73), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 26/91 (28%), Positives = 38/91 (41%), Gaps = 16/91 (17%)
Query: 4 YESDLKDKVVPQKCPLCERLYKSVYRMKEHMKKQHKGQLYECDCCTEYFIDRIAYEEHVR 63
Y+ D KD CER + ++K H ++ + ++C C F + H R
Sbjct: 37 YQCDFKD---------CERRFSRSDQLKRHQRRHTGVKPFQCKTCQRKFSRSDHLKTHTR 87
Query: 64 LHEG--GIICRL--CGEKFEKSLMRDHLVTH 90
H G CR C +KF +S D LV H
Sbjct: 88 THTGEKPFSCRWPSCQKKFARS---DELVRH 115
Score = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 19/44 (43%), Positives = 26/44 (59%), Gaps = 3/44 (6%)
Query: 185 CDKKYSRLSDYKIHMNMHNGFK-YQCHI--CLKCTSRKNYLKRH 225
C+K+Y +LS ++H H G K YQC C + SR + LKRH
Sbjct: 14 CNKRYFKLSHLQMHSRKHTGEKPYQCDFKDCERRFSRSDQLKRH 57
>pdb|2CSH|A Chain A, Solution Structure Of Tandem Repeat Of The Zf-C2h2 Domains
Of Human Zinc Finger Protein 297b
Length = 110
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 31/94 (32%), Positives = 46/94 (48%), Gaps = 4/94 (4%)
Query: 148 GDKVFYACDRCDKRFSLLQNLKRHLAIHERI-AYQCNVCDKKYSRLSDYKIHMNMHNGFK 206
GDK+ Y C +C K F+ RH+++H + Y C VC KK+ HM +H G K
Sbjct: 7 GDKL-YPC-QCGKSFTHKSQRDRHMSMHLGLRPYGCGVCGKKFKMKHHLVGHMKIHTGIK 64
Query: 207 -YQCHICLKCTSRKNYLKRHIIMMHTKFEGQIGE 239
Y+C+IC K ++ RH+ +E E
Sbjct: 65 PYECNICAKRFMWRDSFHRHVTSCTKSYEAAKAE 98
Score = 32.7 bits (73), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 26/49 (53%)
Query: 14 PQKCPLCERLYKSVYRMKEHMKKQHKGQLYECDCCTEYFIDRIAYEEHV 62
P C +C + +K + + HMK + YEC+ C + F+ R ++ HV
Sbjct: 37 PYGCGVCGKKFKMKHHLVGHMKIHTGIKPYECNICAKRFMWRDSFHRHV 85
Score = 32.0 bits (71), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 30/104 (28%), Positives = 45/104 (43%), Gaps = 31/104 (29%)
Query: 41 QLYECDCCTEYFIDRIAYEEHVRLHEG--GIICRLCGEKFEKSLMRDHLVTHIPPEHRGK 98
+LY C C + F + + H+ +H G C +CG+KF+ M+ HLV H+ K
Sbjct: 9 KLYPCQC-GKSFTHKSQRDRHMSMHLGLRPYGCGVCGKKFK---MKHHLVGHM------K 58
Query: 99 VSDAFFNKKQTALLTHYLKRNGIK-LQCNLCADTFCPRSNMLRH 141
+ GIK +CN+CA F R + RH
Sbjct: 59 I------------------HTGIKPYECNICAKRFMWRDSFHRH 84
>pdb|2LCE|A Chain A, Chemical Shift Assignment Of Hr4436b From Homo Sapiens,
Northeast Structural Genomics Consortium
Length = 74
Score = 45.1 bits (105), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 153 YACDRCDKRFSLLQNLKRHLAIHE-RIAYQCNVCDKKYSRLSDYKIHMNMHNGFK 206
Y CDRC F NL H +H Y+CN+C +++R ++ K H +H+G K
Sbjct: 18 YKCDRCQASFRYKGNLASHKTVHTGEKPYRCNICGAQFNRPANLKTHTRIHSGEK 72
>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 = 44.7 bits (104), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 36/64 (56%), Gaps = 4/64 (6%)
Query: 153 YAC--DRCDKRFSLLQNLKRHLAIHE-RIAYQCNVCDKKYSRLSDYKIHMNMHNGFK-YQ 208
YAC + CD+RFS NL H+ IH + +QC +C + +S+ + H+ H G K +
Sbjct: 5 YACPVESCDRRFSQKTNLDTHIRIHTGQKPFQCRICMRNFSQQASLNAHIRTHTGEKPFA 64
Query: 209 CHIC 212
C IC
Sbjct: 65 CDIC 68
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 41/78 (52%), Gaps = 4/78 (5%)
Query: 101 DAFFNKKQTALLTHYLKRNGIK-LQCNLCADTFCPRSNMLRHYLLKHRGDKVFYACDRCD 159
D F++K T L TH G K QC +C F ++++ H + H G+K F ACD C
Sbjct: 13 DRRFSQK-TNLDTHIRIHTGQKPFQCRICMRNFSQQASLNAH-IRTHTGEKPF-ACDICG 69
Query: 160 KRFSLLQNLKRHLAIHER 177
++F+ L RH IH R
Sbjct: 70 RKFATLHTRTRHTKIHLR 87
Score = 37.0 bits (84), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 31/69 (44%), Gaps = 4/69 (5%)
Query: 14 PQKCPL--CERLYKSVYRMKEHMKKQHKGQLYECDCCTEYFIDRIAYEEHVRLHEG--GI 69
P CP+ C+R + + H++ + ++C C F + + H+R H G
Sbjct: 4 PYACPVESCDRRFSQKTNLDTHIRIHTGQKPFQCRICMRNFSQQASLNAHIRTHTGEKPF 63
Query: 70 ICRLCGEKF 78
C +CG KF
Sbjct: 64 ACDICGRKF 72
Score = 31.6 bits (70), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 3/76 (3%)
Query: 128 CADTFCPRSNMLRHYLLKHRGDKVFYACDRCDKRFSLLQNLKRHLAIHE-RIAYQCNVCD 186
C F ++N+ H + H G K F C C + FS +L H+ H + C++C
Sbjct: 12 CDRRFSQKTNLDTHIRI-HTGQKPF-QCRICMRNFSQQASLNAHIRTHTGEKPFACDICG 69
Query: 187 KKYSRLSDYKIHMNMH 202
+K++ L H +H
Sbjct: 70 RKFATLHTRTRHTKIH 85
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 36/64 (56%), Gaps = 4/64 (6%)
Query: 153 YAC--DRCDKRFSLLQNLKRHLAIHE-RIAYQCNVCDKKYSRLSDYKIHMNMHNGFK-YQ 208
YAC + CD+RFS NL H+ IH + +QC +C + +S+ + H+ H G K +
Sbjct: 5 YACPVESCDRRFSQKTNLDTHIRIHTGQKPFQCRICMRNFSQHTGLNQHIRTHTGEKPFA 64
Query: 209 CHIC 212
C IC
Sbjct: 65 CDIC 68
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 40/78 (51%), Gaps = 4/78 (5%)
Query: 101 DAFFNKKQTALLTHYLKRNGIK-LQCNLCADTFCPRSNMLRHYLLKHRGDKVFYACDRCD 159
D F++K T L TH G K QC +C F + + +H + H G+K F ACD C
Sbjct: 13 DRRFSQK-TNLDTHIRIHTGQKPFQCRICMRNFSQHTGLNQH-IRTHTGEKPF-ACDICG 69
Query: 160 KRFSLLQNLKRHLAIHER 177
++F+ L RH IH R
Sbjct: 70 RKFATLHTRDRHTKIHLR 87
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 32/76 (42%), Gaps = 4/76 (5%)
Query: 14 PQKCPL--CERLYKSVYRMKEHMKKQHKGQLYECDCCTEYFIDRIAYEEHVRLHEG--GI 69
P CP+ C+R + + H++ + ++C C F +H+R H G
Sbjct: 4 PYACPVESCDRRFSQKTNLDTHIRIHTGQKPFQCRICMRNFSQHTGLNQHIRTHTGEKPF 63
Query: 70 ICRLCGEKFEKSLMRD 85
C +CG KF RD
Sbjct: 64 ACDICGRKFATLHTRD 79
Score = 31.2 bits (69), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 3/76 (3%)
Query: 128 CADTFCPRSNMLRHYLLKHRGDKVFYACDRCDKRFSLLQNLKRHLAIHE-RIAYQCNVCD 186
C F ++N+ H + H G K F C C + FS L +H+ H + C++C
Sbjct: 12 CDRRFSQKTNLDTHIRI-HTGQKPF-QCRICMRNFSQHTGLNQHIRTHTGEKPFACDICG 69
Query: 187 KKYSRLSDYKIHMNMH 202
+K++ L H +H
Sbjct: 70 RKFATLHTRDRHTKIH 85
>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 = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 30/82 (36%), Positives = 44/82 (53%), Gaps = 5/82 (6%)
Query: 125 CNLCADTFCPRSNMLRHYLLKHRGDKVFYAC-DRCDKRFSLLQNLKRHLAIHERI-AYQC 182
C C F S + RH L+ H G+K F + C KRFSL NL+ H+ IH Y C
Sbjct: 37 CAECGKAFVESSKLKRHQLV-HTGEKPFQCTFEGCGKRFSLDFNLRTHVRIHTGDRPYVC 95
Query: 183 --NVCDKKYSRLSDYKIHMNMH 202
+ C+KK+++ ++ K H+ H
Sbjct: 96 PFDGCNKKFAQSTNLKSHILTH 117
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 37/105 (35%), Positives = 49/105 (46%), Gaps = 10/105 (9%)
Query: 79 EKSLMRDHLVTHIPPEHR-GKVSDAFFNKKQTALLTHYLKRNGIK-LQCNL--CADTFCP 134
+ S MR HL TH P H + AF + + L H L G K QC C F
Sbjct: 19 DNSAMRKHLHTHGPRVHVCAECGKAFV--ESSKLKRHQLVHTGEKPFQCTFEGCGKRFSL 76
Query: 135 RSNMLRHYLLKHRGDKVFYAC--DRCDKRFSLLQNLKRHLAIHER 177
N LR ++ H GD+ Y C D C+K+F+ NLK H+ H +
Sbjct: 77 DFN-LRTHVRIHTGDRP-YVCPFDGCNKKFAQSTNLKSHILTHAK 119
Score = 27.7 bits (60), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 158 CDKRFSLLQNLKRHLAIHERIAYQCNVCDKKYSRLSDYKIHMNMHNGFK-YQC 209
C K F +++HL H + C C K + S K H +H G K +QC
Sbjct: 13 CTKMFRDNSAMRKHLHTHGPRVHVCAECGKAFVESSKLKRHQLVHTGEKPFQC 65
>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 = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 28/92 (30%), Positives = 47/92 (51%), Gaps = 6/92 (6%)
Query: 145 KHRGDKVFYACDRCDKRFSLLQNLKRHLAIH----ERIAYQCNVCDKKYSRLSDYKIHMN 200
KH G+K F C +C K + +NL H A + + C+VC + + R + ++HM
Sbjct: 29 KHTGEKPF-ECPKCGKCYFRKENLLEHEARNCMNRSEQVFTCSVCQETFRRRMELRLHMV 87
Query: 201 MHNG-FKYQCHICLKCTSRKNYLKRHIIMMHT 231
H G Y+C C + +K L+ H+I +H+
Sbjct: 88 SHTGEMPYKCSSCSQQFMQKKDLQSHMIKLHS 119
Score = 34.7 bits (78), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 30/110 (27%), Positives = 49/110 (44%), Gaps = 10/110 (9%)
Query: 16 KCPLCERLYKSVYRMKEHMKKQHKGQLYECDCCTEYFIDRIAYEEH-----VRLHEGGII 70
+CP C + + S Y +K H +K + +EC C + + + EH + E
Sbjct: 9 ECPTCHKKFLSKYYLKVHNRKHTGEKPFECPKCGKCYFRKENLLEHEARNCMNRSEQVFT 68
Query: 71 CRLCGEKFEKSL-MRDHLVTHIP--PEHRGKVSDAFFNKKQTALLTHYLK 117
C +C E F + + +R H+V+H P S F KK L +H +K
Sbjct: 69 CSVCQETFRRRMELRLHMVSHTGEMPYKCSSCSQQFMQKKD--LQSHMIK 116
>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 = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 7/72 (9%)
Query: 134 PRSNMLRHYLLKHRGDKVFYAC--DRCDKRFSLLQNLKRHLAIHE-RIAYQCNVCDKKYS 190
P +N+L + + K R YAC + CD+RFS L RH+ IH + +QC +C + +S
Sbjct: 5 PMNNLLNYVVPKMRP----YACPVESCDRRFSRSDELTRHIRIHTGQKPFQCRICMRNFS 60
Query: 191 RLSDYKIHMNMH 202
R H+ H
Sbjct: 61 RSDHLTTHIRTH 72
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 31/51 (60%), Gaps = 3/51 (5%)
Query: 179 AYQCNV--CDKKYSRLSDYKIHMNMHNGFK-YQCHICLKCTSRKNYLKRHI 226
Y C V CD+++SR + H+ +H G K +QC IC++ SR ++L HI
Sbjct: 19 PYACPVESCDRRFSRSDELTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHI 69
>pdb|2EBT|A Chain A, Solution Structure Of Three Tandem Repeats Of Zf-C2h2
Domains From Human Kruppel-Like Factor 5
Length = 100
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 37/71 (52%), Gaps = 4/71 (5%)
Query: 135 RSNMLRHYLLKHRGDKVFYAC--DRCDKRFSLLQNLKRHLAIHERI-AYQCNVCDKKYSR 191
+S+ L+ +L H G+K Y C + CD RF+ L RH H +QC VC++ +SR
Sbjct: 29 KSSHLKAHLRTHTGEKP-YKCTWEGCDWRFARSDELTRHYRKHTGAKPFQCGVCNRSFSR 87
Query: 192 LSDYKIHMNMH 202
+HM H
Sbjct: 88 SDHLALHMKRH 98
Score = 35.8 bits (81), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 4/73 (5%)
Query: 158 CDKRFSLLQNLKRHLAIHE-RIAYQCNV--CDKKYSRLSDYKIHMNMHNGFK-YQCHICL 213
C K ++ +LK HL H Y+C CD +++R + H H G K +QC +C
Sbjct: 23 CTKVYTKSSHLKAHLRTHTGEKPYKCTWEGCDWRFARSDELTRHYRKHTGAKPFQCGVCN 82
Query: 214 KCTSRKNYLKRHI 226
+ SR ++L H+
Sbjct: 83 RSFSRSDHLALHM 95
Score = 31.2 bits (69), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 32/78 (41%), Gaps = 7/78 (8%)
Query: 18 PLCERLYKSVYRMKEHMKKQHKGQLYEC--DCCTEYFIDRIAYEEHVRLHEGG--IICRL 73
P C ++Y +K H++ + Y+C + C F H R H G C +
Sbjct: 21 PGCTKVYTKSSHLKAHLRTHTGEKPYKCTWEGCDWRFARSDELTRHYRKHTGAKPFQCGV 80
Query: 74 CGEKFEKSLMRDHLVTHI 91
C F +S DHL H+
Sbjct: 81 CNRSFSRS---DHLALHM 95
>pdb|2LT7|A Chain A, Solution Nmr Structure Of Kaiso Zinc Finger Dna Binding
Domain In Complex With Kaiso Binding Site Dna
pdb|4F6M|A Chain A, Crystal Structure Of Kaiso Zinc Finger Dna Binding Domain
In Complex With Kaiso Binding Site Dna
pdb|4F6N|A Chain A, Crystal Structure Of Kaiso Zinc Finger Dna Binding Protein
In Complex With Methylated Cpg Site Dna
Length = 133
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 29/95 (30%), Positives = 48/95 (50%), Gaps = 5/95 (5%)
Query: 141 HYLLKHRGDKVFYACDRCDKRFSLLQNLKRHLAIHE-RIAYQCNVCDKKYSRLSDYKIHM 199
HY L G +V+Y C C + + L +L+RH IH Y C C+K + L++Y+
Sbjct: 12 HYELIVDG-RVYYICIVCKRSYVCLTSLRRHFNIHSWEKKYPCRYCEKVFP-LAEYRTKH 69
Query: 200 NMHNGF--KYQCHICLKCTSRKNYLKRHIIMMHTK 232
+H+ +YQC C K ++ HI +H++
Sbjct: 70 EIHHTGERRYQCLACGKSFINYQFMSSHIKSVHSQ 104
Score = 30.8 bits (68), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 32/70 (45%), Gaps = 1/70 (1%)
Query: 159 DKRFSLLQNLKRHLAIHERIAYQCNVCDKKYSRLSDYKIHMNMHNGF-KYQCHICLKCTS 217
+KR + + L + R+ Y C VC + Y L+ + H N+H+ KY C C K
Sbjct: 2 NKRMKVKHDDHYELIVDGRVYYICIVCKRSYVCLTSLRRHFNIHSWEKKYPCRYCEKVFP 61
Query: 218 RKNYLKRHII 227
Y +H I
Sbjct: 62 LAEYRTKHEI 71
>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 = 0.011, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 3/77 (3%)
Query: 128 CADTFCPRSNMLRHYLLKHRGDKVFYA-CDRCDKRFSLLQNLKRHLAIHE-RIAYQCNVC 185
C T+ +S+ L+ +L H G+K ++ D C +F+ L RH H +QC C
Sbjct: 14 CGKTY-TKSSHLKAHLRTHTGEKPYHCDWDGCGWKFARSDELTRHYRKHTGHRPFQCQKC 72
Query: 186 DKKYSRLSDYKIHMNMH 202
D+ +SR +HM H
Sbjct: 73 DRAFSRSDHLALHMKRH 89
>pdb|2WBS|A Chain A, Crystal Structure Of The Zinc Finger Domain Of Klf4 Bound
To Its Target Dna
Length = 89
Score = 37.4 bits (85), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 3/77 (3%)
Query: 128 CADTFCPRSNMLRHYLLKHRGDKVFYA-CDRCDKRFSLLQNLKRHLAIHE-RIAYQCNVC 185
C T+ +S+ L+ +L H G+K ++ D C +F+ L RH H +QC C
Sbjct: 13 CGKTY-TKSSHLKAHLRTHTGEKPYHCDWDGCGWKFARSDELTRHYRKHTGHRPFQCQKC 71
Query: 186 DKKYSRLSDYKIHMNMH 202
D+ +SR +HM H
Sbjct: 72 DRAFSRSDHLALHMKRH 88
>pdb|2DRP|A Chain A, The Crystal Structure Of A Two Zinc-Finger Peptide Reveals
An Extension To The Rules For Zinc-FingerDNA RECOGNITION
pdb|2DRP|D Chain D, The Crystal Structure Of A Two Zinc-Finger Peptide Reveals
An Extension To The Rules For Zinc-FingerDNA RECOGNITION
Length = 66
Score = 37.4 bits (85), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 28/55 (50%)
Query: 124 QCNLCADTFCPRSNMLRHYLLKHRGDKVFYACDRCDKRFSLLQNLKRHLAIHERI 178
+C +C+ + SN RHY+ H+ + Y C C K F+ N+ H+ I +I
Sbjct: 12 RCKVCSRVYTHISNFCRHYVTSHKRNVKVYPCPFCFKEFTRKDNMTAHVKIIHKI 66
Score = 29.3 bits (64), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 3/55 (5%)
Query: 179 AYQCNVCDKKYSRLSDYKIHM---NMHNGFKYQCHICLKCTSRKNYLKRHIIMMH 230
Y+C VC + Y+ +S++ H + N Y C C K +RK+ + H+ ++H
Sbjct: 10 TYRCKVCSRVYTHISNFCRHYVTSHKRNVKVYPCPFCFKEFTRKDNMTAHVKIIH 64
>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 = 36.6 bits (83), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 6/68 (8%)
Query: 180 YQCNVCDKKYSRLSDYKIHMNMHNGFK-YQCHICLKCTSRKNYLKRHIIMMHTKFEGQIG 238
+QC +C + +SR H+ H G K + C IC + +R + KRH + H +
Sbjct: 4 FQCRICMRNFSRSDHLTTHIRTHTGEKPFACDICGRKFARSDERKRHRDIQHI-----LP 58
Query: 239 EMEDKVGE 246
+EDKV E
Sbjct: 59 ILEDKVEE 66
Score = 33.9 bits (76), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 123 LQCNLCADTFCPRSNMLRHYLLKHRGDKVFYACDRCDKRFSLLQNLKRHLAI 174
QC +C F RS+ L ++ H G+K F ACD C ++F+ KRH I
Sbjct: 4 FQCRICMRNF-SRSDHLTTHIRTHTGEKPF-ACDICGRKFARSDERKRHRDI 53
>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 = 35.8 bits (81), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 38/82 (46%), Gaps = 3/82 (3%)
Query: 124 QCNLCADTFCPRSNMLRHYLLKHRGDKVFYACDRCDKRFSLLQNLKRHLAIH-ERIAYQC 182
+C +C F R + L+ ++ H G K Y C CD + +L +HL IH + ++C
Sbjct: 10 KCEVCGKCF-SRKDKLKTHMRCHTGVKP-YKCKTCDYAAADSSSLNKHLRIHSDERPFKC 67
Query: 183 NVCDKKYSRLSDYKIHMNMHNG 204
+C S +H+ H G
Sbjct: 68 QICPYASRNSSQLTVHLRSHTG 89
Score = 35.4 bits (80), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 40/90 (44%), Gaps = 3/90 (3%)
Query: 148 GDKVFYACDRCDKRFSLLQNLKRHLAIHERI-AYQCNVCDKKYSRLSDYKIHMNMHNGFK 206
G + C+ C K FS LK H+ H + Y+C CD + S H+ +H+ +
Sbjct: 4 GSSGPHKCEVCGKCFSRKDKLKTHMRCHTGVKPYKCKTCDYAAADSSSLNKHLRIHSDER 63
Query: 207 -YQCHICLKCTSRKNYLKRHIIMMHTKFEG 235
++C IC + + L H + HT G
Sbjct: 64 PFKCQICPYASRNSSQLTVH-LRSHTGDSG 92
Score = 33.1 bits (74), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 37/81 (45%), Gaps = 3/81 (3%)
Query: 14 PQKCPLCERLYKSVYRMKEHMKKQHKGQLYECDCCTEYFIDRIAYEEHVRLH--EGGIIC 71
P KC +C + + ++K HM+ + Y+C C D + +H+R+H E C
Sbjct: 8 PHKCEVCGKCFSRKDKLKTHMRCHTGVKPYKCKTCDYAAADSSSLNKHLRIHSDERPFKC 67
Query: 72 RLCG-EKFEKSLMRDHLVTHI 91
++C S + HL +H
Sbjct: 68 QICPYASRNSSQLTVHLRSHT 88
>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 = 35.8 bits (81), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 30/99 (30%), Positives = 46/99 (46%), Gaps = 6/99 (6%)
Query: 112 LTHYLKRNGIKLQCNLCADTFCPRSNMLRHYLLKHRGDKVFYAC--DRCDKRFSLLQNLK 169
LTH ++N + C F ++NM +H+ H Y C + C K F LK
Sbjct: 65 LTHTGEKN-FTCDSDGCDLRFTTKANMKKHFNRFHNIKICVYVCHFENCGKAFKKHNQLK 123
Query: 170 RHLAIH-ERIAYQC--NVCDKKYSRLSDYKIHMNMHNGF 205
H H +++ Y+C CDK++S S K H +H G+
Sbjct: 124 VHQFSHTQQLPYECPHEGCDKRFSLPSRLKRHEKVHAGY 162
Score = 34.7 bits (78), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 31/97 (31%), Positives = 47/97 (48%), Gaps = 11/97 (11%)
Query: 139 LRHYLLKHRGDKVFYAC--DRCDKRFSLLQNLKRHLAIH---ERIAYQCNVCDKKYSRLS 193
L+ +L KH G+K F C + C+K F+ L +L RH H + + CD +++ +
Sbjct: 30 LQAHLCKHTGEKPF-PCKEEGCEKGFTSLHHLTRHSLTHTGEKNFTCDSDGCDLRFTTKA 88
Query: 194 DYKIHMNMHNGFK---YQCHI--CLKCTSRKNYLKRH 225
+ K H N + K Y CH C K + N LK H
Sbjct: 89 NMKKHFNRFHNIKICVYVCHFENCGKAFKKHNQLKVH 125
Score = 28.9 bits (63), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 9/75 (12%)
Query: 114 HYLKRNGIKLQCNLCADTFCPRS----NMLRHYLLKHRGDKVFYAC--DRCDKRFSLLQN 167
H+ + + IK+ +C C ++ N L+ + H ++ Y C + CDKRFSL
Sbjct: 93 HFNRFHNIKICVYVCHFENCGKAFKKHNQLKVHQFSHT-QQLPYECPHEGCDKRFSLPSR 151
Query: 168 LKRHLAIHERIAYQC 182
LKRH +H Y C
Sbjct: 152 LKRHEKVH--AGYPC 164
>pdb|2RPC|A Chain A, Solution Structure Of The Tandem Zf-C2h2 Domains From The
Human Zinc Finger Protein Zic 3
Length = 155
Score = 34.7 bits (78), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 31/109 (28%), Positives = 49/109 (44%), Gaps = 13/109 (11%)
Query: 111 LLTHYLKR--NGIKLQCNLCADTFCPRSNM-------LRHYLLKHRGDKVFY-ACDRCDK 160
L+TH G + ++C CPR L +++ H G+K F C K
Sbjct: 41 LVTHVTMEHVGGPEQNNHVCYWEECPREGKSFKAKYKLVNHIRVHTGEKPFPCPFPGCGK 100
Query: 161 RFSLLQNLKRHLAIHE-RIAYQCNV--CDKKYSRLSDYKIHMNMHNGFK 206
F+ +NLK H H ++C CD++++ SD K HM++H K
Sbjct: 101 IFARSENLKIHKRTHTGEKPFKCEFEGCDRRFANSSDRKKHMHVHTSDK 149
>pdb|2ADR|A Chain A, Adr1 Dna-Binding Domain From Saccharomyces Cerevisiae,
Nmr, 25 Structures
Length = 60
Score = 34.3 bits (77), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 179 AYQCNVCDKKYSRLSDYKIHMNMHNGFK-YQCHICLKCTSRKNYLKRHIIMMHTKFEGQI 237
++ C VC + ++R K H H K Y C +C + +R++ L RH +H+ G +
Sbjct: 2 SFVCEVCTRAFARQEHLKRHYRSHTNEKPYPCGLCNRAFTRRDLLIRHAQKIHS---GNL 58
Query: 238 GE 239
GE
Sbjct: 59 GE 60
Score = 28.5 bits (62), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 12/40 (30%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 153 YACDRCDKRFSLLQNLKRHLAIH-ERIAYQCNVCDKKYSR 191
+ C+ C + F+ ++LKRH H Y C +C++ ++R
Sbjct: 3 FVCEVCTRAFARQEHLKRHYRSHTNEKPYPCGLCNRAFTR 42
>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 = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 34/79 (43%), Gaps = 3/79 (3%)
Query: 125 CNLCADTFCPRSNMLRHYLLKHRGDKVFYACDRCDKRFSLLQNLKRHLAIHER-IAYQCN 183
C C F N+L H + D+ Y CD C K F +L+ H IH + ++C
Sbjct: 20 CKFCGRHFTKSYNLLIHE--RTHTDERPYTCDICHKAFRRQDHLRDHRYIHSKEKPFKCQ 77
Query: 184 VCDKKYSRLSDYKIHMNMH 202
C K + + +H +H
Sbjct: 78 ECGKGFCQSRTLAVHKTLH 96
Score = 27.7 bits (60), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 34/74 (45%), Gaps = 12/74 (16%)
Query: 153 YACDRCDKRFSLLQNLKRHLAIHERI-----AYQCNVCDKKYSRLSDYKIHMNMHNGFK- 206
+ C C + F+ NL IHER Y C++C K + R + H +H+ K
Sbjct: 18 FICKFCGRHFTKSYNL----LIHERTHTDERPYTCDICHKAFRRQDHLRDHRYIHSKEKP 73
Query: 207 YQCHICLK--CTSR 218
++C C K C SR
Sbjct: 74 FKCQECGKGFCQSR 87
>pdb|2COT|A Chain A, Solution Structure Of The First And Second Zf-C2h2 Domain
Of Zinc Finger Protein 435
Length = 77
Score = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 153 YACDRCDKRFSLLQNLKRHLAIHE-RIAYQCNVCDKKYSRLSDYKIHMNMHNG 204
Y CD C K FS +L +H H Y+C+ C K + + S H +H G
Sbjct: 19 YKCDECGKSFSHSSDLSKHRRTHTGEKPYKCDECGKAFIQRSHLIGHHRVHTG 71
Score = 32.7 bits (73), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 176 ERIAYQCNVCDKKYSRLSDYKIHMNMHNGFK-YQCHICLKCTSRKNYLKRH 225
ER Y+C+ C K +S SD H H G K Y+C C K ++++L H
Sbjct: 15 ERRRYKCDECGKSFSHSSDLSKHRRTHTGEKPYKCDECGKAFIQRSHLIGH 65
Score = 28.1 bits (61), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 24/52 (46%)
Query: 16 KCPLCERLYKSVYRMKEHMKKQHKGQLYECDCCTEYFIDRIAYEEHVRLHEG 67
KC C + + + +H + + Y+CD C + FI R H R+H G
Sbjct: 20 KCDECGKSFSHSSDLSKHRRTHTGEKPYKCDECGKAFIQRSHLIGHHRVHTG 71
Score = 27.7 bits (60), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 5/57 (8%)
Query: 36 KQHKGQLYECDCCTEYFIDRIAYEEHVRLHEG--GIICRLCGEKFEKSLMRDHLVTH 90
+Q + + Y+CD C + F +H R H G C CG+ F + R HL+ H
Sbjct: 12 QQRERRRYKCDECGKSFSHSSDLSKHRRTHTGEKPYKCDECGKAF---IQRSHLIGH 65
>pdb|1TF3|A Chain A, Tfiiia Finger 1-3 Bound To Dna, Nmr, 22 Structures
Length = 92
Score = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 37/71 (52%), Gaps = 7/71 (9%)
Query: 139 LRHYLLKHRGDKVFYAC--DRCDKRFSLLQNLKRHLAIH---ERIAYQCNVCDKKYSRLS 193
L+ +L KH G+K F C + C+K F+ L +L RH H + + CD +++ +
Sbjct: 21 LQAHLSKHTGEKPF-PCKEEGCEKGFTSLHHLTRHSLTHTGEKNFTCDSDGCDLRFTTKA 79
Query: 194 DYKIHMN-MHN 203
+ K H N HN
Sbjct: 80 NMKKHFNRFHN 90
Score = 27.7 bits (60), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 23/46 (50%), Gaps = 2/46 (4%)
Query: 128 CADTFCPRSNMLRHYLLKHRGDKVFYA-CDRCDKRFSLLQNLKRHL 172
C F ++ RH L H G+K F D CD RF+ N+K+H
Sbjct: 41 CEKGFTSLHHLTRHSLT-HTGEKNFTCDSDGCDLRFTTKANMKKHF 85
>pdb|2EOS|A Chain A, Solution Structure Of The C2h2 Type Zinc Finger (Region
626- 654) Of Human B-Cell Lymphoma 6 Protein
Length = 42
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 13/23 (56%), Positives = 14/23 (60%)
Query: 153 YACDRCDKRFSLLQNLKRHLAIH 175
Y C+ C RF LQ LK HL IH
Sbjct: 12 YPCEICGTRFRHLQTLKSHLRIH 34
>pdb|2M0E|A Chain A, Solution Structure Of Miz-1 Zinc Finger 6
Length = 29
Score = 29.6 bits (65), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 153 YACDRCDKRFSLLQNLKRHLAIH 175
+ C CDK+F+ + NLK HL IH
Sbjct: 3 HKCPHCDKKFNQVGNLKAHLKIH 25
>pdb|1X6E|A Chain A, Solution Structures Of The C2h2 Type Zinc Finger Domain Of
Human Zinc Finger Protein 24
Length = 72
Score = 29.3 bits (64), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 153 YACDRCDKRFSLLQNLKRHLAIHE-RIAYQCNVCDKKYSRLSDYKIHMNMHN 203
Y C C K FS L +H +H Y+C C K +S+ S H +H
Sbjct: 15 YGCVECGKAFSRSSILVQHQRVHTGEKPYKCLECGKAFSQNSGLINHQRIHT 66
Score = 27.7 bits (60), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 180 YQCNVCDKKYSRLSDYKIHMNMHNGFK-YQCHICLKCTSRKNYLKRH 225
Y C C K +SR S H +H G K Y+C C K S+ + L H
Sbjct: 15 YGCVECGKAFSRSSILVQHQRVHTGEKPYKCLECGKAFSQNSGLINH 61
>pdb|1X6H|A Chain A, Solution Structures Of The C2h2 Type Zinc Finger Domain Of
Human Transcriptional Repressor Ctcf
Length = 86
Score = 29.3 bits (64), Expect = 2.8, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 27/60 (45%), Gaps = 6/60 (10%)
Query: 146 HRGDKVFYACDRCDKRFSLLQNLKRHLAIHER-----IAYQCNVCDKKYSRLSDYKIHMN 200
H G+K YAC CDK F Q L H + A+ C+ C K ++R + H +
Sbjct: 10 HTGEKP-YACSHCDKTFRQKQLLDMHFKRYHDPNFVPAAFVCSKCGKTFTRRNTMARHAD 68
>pdb|2EP2|A Chain A, Solution Structure Of The C2h2 Type Zinc Finger (Region
603- 635) Of Human Zinc Finger Protein 484
Length = 46
Score = 28.9 bits (63), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 9/28 (32%), Positives = 17/28 (60%)
Query: 179 AYQCNVCDKKYSRLSDYKIHMNMHNGFK 206
Y+C++C K +++ S +H +H G K
Sbjct: 12 PYECSICGKSFTKKSQLHVHQQIHTGEK 39
>pdb|2EQ2|A Chain A, Solution Structure Of The 16th C2h2 Type Zinc Finger
Domain Of Zinc Finger Protein 347
Length = 46
Score = 28.9 bits (63), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 15/27 (55%)
Query: 180 YQCNVCDKKYSRLSDYKIHMNMHNGFK 206
YQCN C K +S+ S H +H G K
Sbjct: 13 YQCNECGKAFSQTSKLARHQRVHTGEK 39
>pdb|2EM6|A Chain A, Solution Structure Of The C2h2 Type Zinc Finger (Region
199- 231) Of Human Zinc Finger Protein 224
Length = 46
Score = 28.9 bits (63), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 18/27 (66%)
Query: 180 YQCNVCDKKYSRLSDYKIHMNMHNGFK 206
Y+C+VC K++S+ S + H +H G K
Sbjct: 13 YKCDVCGKEFSQSSHLQTHQRVHTGEK 39
>pdb|1XF7|A Chain A, High Resolution Nmr Structure Of The Wilms' Tumor
Suppressor Protein (Wt1) Finger 3
Length = 29
Score = 28.5 bits (62), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 14/27 (51%)
Query: 180 YQCNVCDKKYSRLSDYKIHMNMHNGFK 206
+QC C +K+SR K H H G K
Sbjct: 3 FQCKTCQRKFSRSDHLKTHTRTHTGEK 29
>pdb|2M0F|A Chain A, Solution Structure Of Miz-1 Zinc Finger 7
Length = 29
Score = 28.5 bits (62), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 155 CDRCDKRFSLLQNLKRHLAIH 175
C C K+F+ NLKRHL IH
Sbjct: 5 CRECGKQFTTSGNLKRHLRIH 25
>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 = 28.5 bits (62), Expect = 5.4, Method: Composition-based stats.
Identities = 11/46 (23%), Positives = 19/46 (41%)
Query: 17 CPLCERLYKSVYRMKEHMKKQHKGQLYECDCCTEYFIDRIAYEEHV 62
CP+C + S + H++ H Q++ C C F H+
Sbjct: 31 CPVCGESFASKGAQERHLRLLHAAQVFPCKYCPATFYSSPGLTRHI 76
>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 = 28.1 bits (61), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 5/58 (8%)
Query: 153 YAC--DRCDKRFSLLQNLKRHLAIH-ERIAYQC--NVCDKKYSRLSDYKIHMNMHNGF 205
Y C + C K F LK H H +++ Y+C CDK++S S K H +H G+
Sbjct: 2 YVCHFENCGKAFKKHNQLKVHQFSHTQQLPYECPHEGCDKRFSLPSRLKRHEKVHAGY 59
Score = 28.1 bits (61), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 28/57 (49%), Gaps = 6/57 (10%)
Query: 128 CADTFCPRSNMLRHYLLKHRGDKVFYAC--DRCDKRFSLLQNLKRHLAIHERIAYQC 182
C F + N L+ + H ++ Y C + CDKRFSL LKRH +H Y C
Sbjct: 9 CGKAF-KKHNQLKVHQFSHT-QQLPYECPHEGCDKRFSLPSRLKRHEKVH--AGYPC 61
>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 = 28.1 bits (61), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 5/58 (8%)
Query: 153 YAC--DRCDKRFSLLQNLKRHLAIH-ERIAYQC--NVCDKKYSRLSDYKIHMNMHNGF 205
Y C + C K F LK H H +++ Y+C CDK++S S K H +H G+
Sbjct: 2 YVCHFENCGKAFKKHNQLKVHQFSHTQQLPYECPHEGCDKRFSLPSRLKRHEKVHAGY 59
Score = 28.1 bits (61), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 28/57 (49%), Gaps = 6/57 (10%)
Query: 128 CADTFCPRSNMLRHYLLKHRGDKVFYAC--DRCDKRFSLLQNLKRHLAIHERIAYQC 182
C F + N L+ + H ++ Y C + CDKRFSL LKRH +H Y C
Sbjct: 9 CGKAF-KKHNQLKVHQFSHT-QQLPYECPHEGCDKRFSLPSRLKRHEKVH--AGYPC 61
>pdb|2EML|A Chain A, Solution Structure Of The C2h2 Type Zinc Finger (Region
752- 784) Of Human Zinc Finger Protein 28 Homolog
Length = 46
Score = 28.1 bits (61), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 10/27 (37%), Positives = 16/27 (59%)
Query: 180 YQCNVCDKKYSRLSDYKIHMNMHNGFK 206
Y+C+VC K +S +H +H+G K
Sbjct: 13 YECSVCGKAFSHRQSLSVHQRIHSGKK 39
>pdb|4GZN|C Chain C, Mouse Zfp57 Zinc Fingers In Complex With Methylated Dna
Length = 60
Score = 28.1 bits (61), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 1/52 (1%)
Query: 182 CNVCDKKYSRLSDYKIHMNMHNGFKYQ-CHICLKCTSRKNYLKRHIIMMHTK 232
CN C K Y S H H G++ + C C KC ++ + RH+ + K
Sbjct: 7 CNFCGKTYRDASGLSRHRRAHLGYRPRSCPECGKCFRDQSEVNRHLKVHQNK 58
>pdb|2CT1|A Chain A, Solution Structure Of The Zinc Finger Domain Of
Transcriptional Repressor Ctcf Protein
Length = 77
Score = 28.1 bits (61), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 29/57 (50%), Gaps = 4/57 (7%)
Query: 146 HRGDKVFYACDRCDKRFSLLQNLKRH-LAIH-ERIA-YQCNVCDKKYSRLSDYKIHM 199
H G+K Y C C RF+ +K H L H E +A + C CD +R SD +H+
Sbjct: 10 HSGEKP-YECYICHARFTQSGTMKMHILQKHTENVAKFHCPHCDTVIARKSDLGVHL 65
>pdb|2EME|A Chain A, Solution Structure Of The C2h2 Type Zinc Finger (Region
725- 757) Of Human Zinc Finger Protein 473
Length = 46
Score = 28.1 bits (61), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 12/23 (52%)
Query: 153 YACDRCDKRFSLLQNLKRHLAIH 175
Y CD C K F L L RH IH
Sbjct: 13 YVCDYCGKAFGLSAELVRHQRIH 35
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
0.324 0.138 0.438
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,428,962
Number of Sequences: 62578
Number of extensions: 363460
Number of successful extensions: 1603
Number of sequences better than 100.0: 75
Number of HSP's better than 100.0 without gapping: 64
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 1233
Number of HSP's gapped (non-prelim): 278
length of query: 319
length of database: 14,973,337
effective HSP length: 99
effective length of query: 220
effective length of database: 8,778,115
effective search space: 1931185300
effective search space used: 1931185300
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.3 bits)