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= psy3485
(304 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3UK3|C Chain C, Crystal Structure Of Znf217 Bound To Dna
pdb|3UK3|D Chain D, Crystal Structure Of Znf217 Bound To Dna
pdb|4F2J|C Chain C, Crystal Structure Of Znf217 Bound To Dna, P6522 Crystal
Form
pdb|4IS1|C Chain C, Crystal Structure Of Znf217 Bound To Dna
pdb|4IS1|D Chain D, Crystal Structure Of Znf217 Bound To Dna
Length = 57
Score = 47.8 bits (112), Expect = 8e-06, Method: Composition-based stats.
Identities = 22/50 (44%), Positives = 28/50 (56%)
Query: 188 CFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMRTTH 237
C C + R + IHLRTHT EKP+ CE C Y AA K ++ H+ H
Sbjct: 7 CSYCGKFFRSNYYLNIHLRTHTGEKPYKCEFCEYAAAQKTSLRYHLERHH 56
>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 = 47.0 bits (110), Expect = 1e-05, Method: Composition-based stats.
Identities = 26/91 (28%), Positives = 41/91 (45%), Gaps = 7/91 (7%)
Query: 188 CFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMRTTHIMPDTSEERR 247
C C + H+R HT KP+ C+ C+Y AA ++ H+R S+ER
Sbjct: 11 CEVCGKCFSRKDKLKTHMRCHTGVKPYKCKTCDYAAADSSSLNKHLRI------HSDERP 64
Query: 248 YHCAFCNFTSPTQWAINRHTKYTHMNTSGPT 278
+ C C + S + H + +H SGP+
Sbjct: 65 FKCQICPYASRNSSQLTVHLR-SHTGDSGPS 94
Score = 44.3 bits (103), Expect = 9e-05, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 36/73 (49%), Gaps = 7/73 (9%)
Query: 170 CKLCLRRKRK--NPMR-----RNFMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYR 222
C C RK K MR + + C C Y SS+ HLR H+ E+PF C++C Y
Sbjct: 14 CGKCFSRKDKLKTHMRCHTGVKPYKCKTCDYAAADSSSLNKHLRIHSDERPFKCQICPYA 73
Query: 223 AASKIAIYAHMRT 235
+ + + H+R+
Sbjct: 74 SRNSSQLTVHLRS 86
Score = 32.7 bits (73), Expect = 0.29, Method: Composition-based stats.
Identities = 13/26 (50%), Positives = 16/26 (61%)
Query: 184 RNFMCFACPYYCRYGSSMAIHLRTHT 209
R F C CPY R S + +HLR+HT
Sbjct: 63 RPFKCQICPYASRNSSQLTVHLRSHT 88
>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 = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 26/55 (47%)
Query: 186 FMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMRTTHIMP 240
F C C + H+RTHT EKPFAC++C + A H HI+P
Sbjct: 4 FQCRICMRNFSRSDHLTTHIRTHTGEKPFACDICGRKFARSDERKRHRDIQHILP 58
>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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 28/52 (53%), Gaps = 5/52 (9%)
Query: 186 FMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMRTTH 237
F C C +S+ H+RTHT EKPFAC++C + A+ H RT H
Sbjct: 35 FQCRICMRNFSQQASLNAHIRTHTGEKPFACDICGRKFAT-----LHTRTRH 81
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 6/70 (8%)
Query: 199 SSMAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCNFTSP 258
+++ H+R HT +KPF C +C + + ++ AH+RT + E+ + C C
Sbjct: 20 TNLDTHIRIHTGQKPFQCRICMRNFSQQASLNAHIRT------HTGEKPFACDICGRKFA 73
Query: 259 TQWAINRHTK 268
T RHTK
Sbjct: 74 TLHTRTRHTK 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 = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 26/92 (28%), Positives = 39/92 (42%), Gaps = 7/92 (7%)
Query: 182 MRRNFMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMRTTHIMPD 241
M + + C C S++ H RTHT EKP+ C C + + H RT
Sbjct: 1 MEKPYKCPECGKSFSQSSNLQKHQRTHTGEKPYKCPECGKSFSQSSDLQKHQRT------ 54
Query: 242 TSEERRYHCAFCNFTSPTQWAINRHTKYTHMN 273
+ E+ Y C C + ++RH + TH N
Sbjct: 55 HTGEKPYKCPECGKSFSRSDHLSRHQR-THQN 85
Score = 32.3 bits (72), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 26/61 (42%)
Query: 175 RRKRKNPMRRNFMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMR 234
+ +R + + + C C S + H RTHT EKP+ C C + + H R
Sbjct: 22 KHQRTHTGEKPYKCPECGKSFSQSSDLQKHQRTHTGEKPYKCPECGKSFSRSDHLSRHQR 81
Query: 235 T 235
T
Sbjct: 82 T 82
>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 = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 33/108 (30%), Positives = 43/108 (39%), Gaps = 8/108 (7%)
Query: 180 NPMRRNFMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMRTTHIM 239
P + + C C +A H RTHT EKP+ C C + K + H RT
Sbjct: 16 EPGEKPYACPECGKSFSRSDHLAEHQRTHTGEKPYKCPECGKSFSDKKDLTRHQRT---- 71
Query: 240 PDTSEERRYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKIL 287
+ E+ Y C C S +Q A R + TH P PEC K
Sbjct: 72 --HTGEKPYKCPECG-KSFSQRANLRAHQRTHTGEK-PYACPECGKSF 115
Score = 38.1 bits (87), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 31/113 (27%), Positives = 48/113 (42%), Gaps = 8/113 (7%)
Query: 175 RRKRKNPMRRNFMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMR 234
R +R + + + C C +++ H RTHT EKP+AC C + + AH R
Sbjct: 67 RHQRTHTGEKPYKCPECGKSFSQRANLRAHQRTHTGEKPYACPECGKSFSQLAHLRAHQR 126
Query: 235 TTHIMPDTSEERRYHCAFCNFTSPTQWAINRHTKYTHMNTSGPTIQPECIKIL 287
T + E+ Y C C + + ++ H + TH P PEC K
Sbjct: 127 T------HTGEKPYKCPECGKSFSREDNLHTHQR-THTGEK-PYKCPECGKSF 171
Score = 33.1 bits (74), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 19/35 (54%)
Query: 201 MAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMRT 235
+ H RTHT EKP+ C C + + A+ H RT
Sbjct: 149 LHTHQRTHTGEKPYKCPECGKSFSRRDALNVHQRT 183
>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 = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 29/98 (29%), Positives = 47/98 (47%), Gaps = 11/98 (11%)
Query: 183 RRNFMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMRTTHIMPDT 242
++ F+C C + ++ IH RTHT E+P+ C++C+ + + H R H
Sbjct: 15 KKEFICKFCGRHFTKSYNLLIHERTHTDERPYTCDICHKAFRRQDHLRDH-RYIH----- 68
Query: 243 SEERRYHCAFC--NFTSPTQWAINRHTKYTHMNTSGPT 278
S+E+ + C C F A++ K HM TS PT
Sbjct: 69 SKEKPFKCQECGKGFCQSRTLAVH---KTLHMQTSSPT 103
>pdb|2YT9|A Chain A, Solution Structure Of C2h2 Type Zinc Finger Domain 345 In
Zinc Finger Protein 278
Length = 95
Score = 37.7 bits (86), Expect = 0.008, Method: Composition-based stats.
Identities = 25/77 (32%), Positives = 37/77 (48%), Gaps = 11/77 (14%)
Query: 204 HLRTHTKEKPFACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFC--NFTSPTQW 261
H +H+ EKP++C +C R K + H+R+ D S + Y C C F+ P
Sbjct: 26 HKLSHSGEKPYSCPVCGLRFKRKDRMSYHVRSH----DGSVGKPYICQSCGKGFSRPDH- 80
Query: 262 AINRHTKYTHMNTSGPT 278
+N H K H SGP+
Sbjct: 81 -LNGHIKQVH---SGPS 93
Score = 29.6 bits (65), Expect = 2.2, Method: Composition-based stats.
Identities = 15/70 (21%), Positives = 29/70 (41%), Gaps = 2/70 (2%)
Query: 175 RRKRKNPMRRNFMCFACPYYCRYGSSMAIHLRTHTKE--KPFACEMCNYRAASKIAIYAH 232
R K + + + C C + M+ H+R+H KP+ C+ C + + H
Sbjct: 25 RHKLSHSGEKPYSCPVCGLRFKRKDRMSYHVRSHDGSVGKPYICQSCGKGFSRPDHLNGH 84
Query: 233 MRTTHIMPDT 242
++ H P +
Sbjct: 85 IKQVHSGPSS 94
>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 = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 6/70 (8%)
Query: 199 SSMAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCNFTSP 258
+++ H+R HT +KPF C +C + + H+RT + E+ + C C
Sbjct: 20 TNLDTHIRIHTGQKPFQCRICMRNFSQHTGLNQHIRT------HTGEKPFACDICGRKFA 73
Query: 259 TQWAINRHTK 268
T +RHTK
Sbjct: 74 TLHTRDRHTK 83
Score = 37.0 bits (84), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 23/40 (57%)
Query: 186 FMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAAS 225
F C C + + H+RTHT EKPFAC++C + A+
Sbjct: 35 FQCRICMRNFSQHTGLNQHIRTHTGEKPFACDICGRKFAT 74
>pdb|2CT1|A Chain A, Solution Structure Of The Zinc Finger Domain Of
Transcriptional Repressor Ctcf Protein
Length = 77
Score = 37.4 bits (85), Expect = 0.009, Method: Composition-based stats.
Identities = 20/73 (27%), Positives = 34/73 (46%), Gaps = 5/73 (6%)
Query: 206 RTHTKEKPFACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCNFTSPTQWAINR 265
RTH+ EKP+ C +C+ R + H+ H T ++HC C+ + +
Sbjct: 8 RTHSGEKPYECYICHARFTQSGTMKMHILQKH----TENVAKFHCPHCDTVIARKSDLGV 63
Query: 266 HTKYTHMNTSGPT 278
H + H + SGP+
Sbjct: 64 HLRKQH-SYSGPS 75
>pdb|2COT|A Chain A, Solution Structure Of The First And Second Zf-C2h2 Domain
Of Zinc Finger Protein 435
Length = 77
Score = 37.0 bits (84), Expect = 0.013, Method: Composition-based stats.
Identities = 17/52 (32%), Positives = 25/52 (48%)
Query: 183 RRNFMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMR 234
RR + C C + S ++ H RTHT EKP+ C+ C + + H R
Sbjct: 16 RRRYKCDECGKSFSHSSDLSKHRRTHTGEKPYKCDECGKAFIQRSHLIGHHR 67
>pdb|1A1F|A Chain A, Dsnr (Zif268 Variant) Zinc Finger-Dna Complex (Gacc Site)
pdb|1A1G|A Chain A, Dsnr (Zif268 Variant) Zinc Finger-Dna Complex (Gcgt Site)
Length = 90
Score = 37.0 bits (84), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 21/39 (53%)
Query: 186 FMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAA 224
F C C + H+RTHT EKPFAC++C + A
Sbjct: 35 FQCRICMRNFSRSDHLTTHIRTHTGEKPFACDICGRKFA 73
Score = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 31/71 (43%), Gaps = 6/71 (8%)
Query: 198 GSSMAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCNFTS 257
S++ H+R HT +KPF C +C + + H+RT + E+ + C C
Sbjct: 19 SSNLTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRT------HTGEKPFACDICGRKF 72
Query: 258 PTQWAINRHTK 268
RHTK
Sbjct: 73 ARSDERKRHTK 83
>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 = 37.0 bits (84), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 21/39 (53%)
Query: 186 FMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAA 224
F C C + H+RTHT EKPFAC++C + A
Sbjct: 35 FQCRICMRNFSRSDHLTTHIRTHTGEKPFACDICGRKFA 73
Score = 32.7 bits (73), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 38/87 (43%), Gaps = 15/87 (17%)
Query: 189 FACPYYC---RYGSS--MAIHLRTHTKEKPFACEMC--NYRAASKIAIYAHMRTTHIMPD 241
+ACP R+ S + H+R HT +KPF C +C N+ + + TTHI
Sbjct: 5 YACPVESCDRRFSRSDELTRHIRIHTGQKPFQCRICMRNFSRSDHL-------TTHIRTH 57
Query: 242 TSEERRYHCAFCNFTSPTQWAINRHTK 268
T E+ + C C RHTK
Sbjct: 58 TG-EKPFACDICGRKFARSDERKRHTK 83
>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 = 37.0 bits (84), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 21/39 (53%)
Query: 186 FMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAA 224
F C C + H+RTHT EKPFAC++C + A
Sbjct: 35 FQCRICMRNFSRSDHLTTHIRTHTGEKPFACDICGRKFA 73
Score = 32.7 bits (73), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 38/87 (43%), Gaps = 15/87 (17%)
Query: 189 FACPYYC---RYGSSMAI--HLRTHTKEKPFACEMC--NYRAASKIAIYAHMRTTHIMPD 241
+ACP R+ S + H+R HT +KPF C +C N+ + + TTHI
Sbjct: 5 YACPVESCDRRFSRSADLTRHIRIHTGQKPFQCRICMRNFSRSDHL-------TTHIRTH 57
Query: 242 TSEERRYHCAFCNFTSPTQWAINRHTK 268
T E+ + C C RHTK
Sbjct: 58 TG-EKPFACDICGRKFARSDERKRHTK 83
>pdb|1A1H|A Chain A, Qgsr (Zif268 Variant) Zinc Finger-Dna Complex (Gcac Site)
Length = 90
Score = 36.6 bits (83), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 21/39 (53%)
Query: 186 FMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAA 224
F C C + H+RTHT EKPFAC++C + A
Sbjct: 35 FQCRICMRNFSRSDHLTTHIRTHTGEKPFACDICGRKFA 73
Score = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 39/87 (44%), Gaps = 15/87 (17%)
Query: 189 FACPYYC---RYGSSMAI--HLRTHTKEKPFACEMC--NYRAASKIAIYAHMRTTHIMPD 241
+ACP R+ S ++ H+R HT +KPF C +C N+ + + TTHI
Sbjct: 5 YACPVESCDRRFSQSGSLTRHIRIHTGQKPFQCRICMRNFSRSDHL-------TTHIRTH 57
Query: 242 TSEERRYHCAFCNFTSPTQWAINRHTK 268
T E+ + C C RHTK
Sbjct: 58 TG-EKPFACDICGRKFARSDERKRHTK 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 = 36.6 bits (83), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 21/39 (53%)
Query: 186 FMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAA 224
F C C + H+RTHT EKPFAC++C + A
Sbjct: 35 FQCRICMRNFSRSDHLTTHIRTHTGEKPFACDICGRKFA 73
Score = 32.7 bits (73), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 38/87 (43%), Gaps = 15/87 (17%)
Query: 189 FACPYYC---RYGSSMAI--HLRTHTKEKPFACEMC--NYRAASKIAIYAHMRTTHIMPD 241
+ACP R+ S + H+R HT +KPF C +C N+ + + TTHI
Sbjct: 5 YACPVESCDRRFSRSAELTRHIRIHTGQKPFQCRICMRNFSRSDHL-------TTHIRTH 57
Query: 242 TSEERRYHCAFCNFTSPTQWAINRHTK 268
T E+ + C C RHTK
Sbjct: 58 TG-EKPFACDICGRKFARSDERKRHTK 83
>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 = 36.6 bits (83), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 21/39 (53%)
Query: 186 FMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAA 224
F C C + H+RTHT EKPFAC++C + A
Sbjct: 34 FQCRICMRNFSRSDHLTTHIRTHTGEKPFACDICGRKFA 72
Score = 32.0 bits (71), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 38/87 (43%), Gaps = 15/87 (17%)
Query: 189 FACPYYC---RYGSS--MAIHLRTHTKEKPFACEMC--NYRAASKIAIYAHMRTTHIMPD 241
+ACP R+ S + H+R HT +KPF C +C N+ + + TTHI
Sbjct: 4 YACPVESCDRRFSRSDELTRHIRIHTGQKPFQCRICMRNFSRSDHL-------TTHIRTH 56
Query: 242 TSEERRYHCAFCNFTSPTQWAINRHTK 268
T E+ + C C RHTK
Sbjct: 57 TG-EKPFACDICGRKFARSDERKRHTK 82
>pdb|1ZAA|C Chain C, Zinc Finger-Dna Recognition: Crystal Structure Of A
Zif268- Dna Complex At 2.1 Angstroms
Length = 87
Score = 36.6 bits (83), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 21/39 (53%)
Query: 186 FMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAA 224
F C C + H+RTHT EKPFAC++C + A
Sbjct: 35 FQCRICMRNFSRSDHLTTHIRTHTGEKPFACDICGRKFA 73
Score = 32.0 bits (71), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 38/87 (43%), Gaps = 15/87 (17%)
Query: 189 FACPYYC---RYGSS--MAIHLRTHTKEKPFACEMC--NYRAASKIAIYAHMRTTHIMPD 241
+ACP R+ S + H+R HT +KPF C +C N+ + + TTHI
Sbjct: 5 YACPVESCDRRFSRSDELTRHIRIHTGQKPFQCRICMRNFSRSDHL-------TTHIRTH 57
Query: 242 TSEERRYHCAFCNFTSPTQWAINRHTK 268
T E+ + C C RHTK
Sbjct: 58 TG-EKPFACDICGRKFARSDERKRHTK 83
>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 = 35.8 bits (81), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 26/96 (27%), Positives = 41/96 (42%), Gaps = 11/96 (11%)
Query: 152 FFCIHCNGCVLYAD-LLDHCKLCLRRKRKNPMRRN---FMCFACPYYCRYGSSMAIHLRT 207
F C C C + LL+H + +N M R+ F C C R + +H+ +
Sbjct: 36 FECPKCGKCYFRKENLLEH-------EARNCMNRSEQVFTCSVCQETFRRRMELRLHMVS 88
Query: 208 HTKEKPFACEMCNYRAASKIAIYAHMRTTHIMPDTS 243
HT E P+ C C+ + K + +HM H P +
Sbjct: 89 HTGEMPYKCSSCSQQFMQKKDLQSHMIKLHSGPSSG 124
>pdb|2EBT|A Chain A, Solution Structure Of Three Tandem Repeats Of Zf-C2h2
Domains From Human Kruppel-Like Factor 5
Length = 100
Score = 35.0 bits (79), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 28/58 (48%), Gaps = 8/58 (13%)
Query: 199 SSMAIHLRTHTKEKPFAC--EMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCN 254
S + HLRTHT EKP+ C E C++R A + H R + + + C CN
Sbjct: 31 SHLKAHLRTHTGEKPYKCTWEGCDWRFARSDELTRHYR------KHTGAKPFQCGVCN 82
Score = 28.5 bits (62), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 201 MAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMR 234
+ H R HT KPF C +CN + + HM+
Sbjct: 63 LTRHYRKHTGAKPFQCGVCNRSFSRSDHLALHMK 96
>pdb|1BBO|A Chain A, High-Resolution Solution Structure Of The Double Cys2His2
Zinc Finger From The Human Enhancer Binding Protein
Mbp-1
Length = 57
Score = 34.7 bits (78), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 6/55 (10%)
Query: 214 FACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCNFTSPTQWAINRHTK 268
+ CE C R + H+RT ++ R YHC +CNF+ T+ + +H K
Sbjct: 2 YICEECGIRXKKPSMLKKHIRTH------TDVRPYHCTYCNFSFKTKGNLTKHMK 50
Score = 34.3 bits (77), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 27/50 (54%)
Query: 186 FMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMRT 235
++C C + S + H+RTHT +P+ C CN+ +K + HM++
Sbjct: 2 YICEECGIRXKKPSMLKKHIRTHTDVRPYHCTYCNFSFKTKGNLTKHMKS 51
>pdb|2ADR|A Chain A, Adr1 Dna-Binding Domain From Saccharomyces Cerevisiae,
Nmr, 25 Structures
Length = 60
Score = 33.5 bits (75), Expect = 0.14, Method: Composition-based stats.
Identities = 15/53 (28%), Positives = 24/53 (45%)
Query: 185 NFMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMRTTH 237
+F+C C + H R+HT EKP+ C +CN + + H + H
Sbjct: 2 SFVCEVCTRAFARQEHLKRHYRSHTNEKPYPCGLCNRAFTRRDLLIRHAQKIH 54
>pdb|2EP0|A Chain A, Solution Structure Of The C2h2 Type Zinc Finger (Region
528- 560) Of Human Zinc Finger Protein 28 Homolog
Length = 46
Score = 33.5 bits (75), Expect = 0.15, Method: Composition-based stats.
Identities = 14/30 (46%), Positives = 18/30 (60%)
Query: 184 RNFMCFACPYYCRYGSSMAIHLRTHTKEKP 213
+ + C C RYGSS+ +H R HT EKP
Sbjct: 11 KPYKCDVCHKSFRYGSSLTVHQRIHTGEKP 40
>pdb|2RPC|A Chain A, Solution Structure Of The Tandem Zf-C2h2 Domains From The
Human Zinc Finger Protein Zic 3
Length = 155
Score = 33.5 bits (75), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 27/53 (50%), Gaps = 9/53 (16%)
Query: 189 FACPY------YCRYGSSMAIHLRTHTKEKPFACEM--CNYRAASKIAIYAHM 233
F CP+ + R ++ IH RTHT EKPF CE C+ R A+ HM
Sbjct: 91 FPCPFPGCGKIFARS-ENLKIHKRTHTGEKPFKCEFEGCDRRFANSSDRKKHM 142
Score = 28.9 bits (63), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 34/83 (40%), Gaps = 19/83 (22%)
Query: 180 NPMRRNFMCF--ACPYYCRYGSS------MAIHLRTHTKEKPFACEM--CNYRAASKIAI 229
P + N +C+ CP R G S + H+R HT EKPF C C A +
Sbjct: 52 GPEQNNHVCYWEECP---REGKSFKAKYKLVNHIRVHTGEKPFPCPFPGCGKIFARSENL 108
Query: 230 YAHMRTTHIMPDTSEERRYHCAF 252
H RT + E+ + C F
Sbjct: 109 KIHKRT------HTGEKPFKCEF 125
>pdb|2GLI|A Chain A, Five-Finger GliDNA COMPLEX
Length = 155
Score = 33.5 bits (75), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 35/76 (46%), Gaps = 9/76 (11%)
Query: 200 SMAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMRTTHIMPDTSEERRYHCAFCN----F 255
++ HLR+HT EKP+ MC + SK A R H S E+ Y C +
Sbjct: 84 NLKTHLRSHTGEKPY---MCEHEGCSKAFSNASDRAKHQNRTHSNEKPYVCKLPGCTKRY 140
Query: 256 TSPTQWAINRHTKYTH 271
T P+ ++ +H K H
Sbjct: 141 TDPS--SLRKHVKTVH 154
>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 = 32.7 bits (73), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 29/99 (29%), Positives = 42/99 (42%), Gaps = 11/99 (11%)
Query: 183 RRNFMCFAC--PYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMRTTHIMP 240
R ++C C Y C +S+ H H+ EK + C C K+ A RT H +
Sbjct: 20 RVYYICIVCKRSYVCL--TSLRRHFNIHSWEKKYPCRYCE-----KVFPLAEYRTKHEIH 72
Query: 241 DTSEERRYHCAFCNFTSPTQWAINRHTKYTH-MNTSGPT 278
T E RRY C C + ++ H K H + SG +
Sbjct: 73 HTGE-RRYQCLACGKSFINYQFMSSHIKSVHSQDPSGDS 110
>pdb|2D9H|A Chain A, Solution Structure Of The Forth And Fifth Zf-C2h2 Domains
Of Zinc Finger Protein 692
Length = 78
Score = 32.3 bits (72), Expect = 0.36, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 23/53 (43%), Gaps = 3/53 (5%)
Query: 188 CFACPYYCRYGSSMAIHLRTHTKEKP---FACEMCNYRAASKIAIYAHMRTTH 237
C C + CR +S+ H R H + F CE C R ++ AH +H
Sbjct: 10 CEICGFTCRQKASLNWHQRKHAETVAALRFPCEFCGKRFEKPDSVAAHRSKSH 62
>pdb|1X6H|A Chain A, Solution Structures Of The C2h2 Type Zinc Finger Domain Of
Human Transcriptional Repressor Ctcf
Length = 86
Score = 32.0 bits (71), Expect = 0.48, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 32/75 (42%), Gaps = 12/75 (16%)
Query: 206 RTHTKEKPFACEMCNYRAASKIAIYAHMRTTH---IMPDTSEERRYHCAFCNFTSPTQWA 262
RTHT EKP+AC C+ K + H + H +P + C+ C T +
Sbjct: 8 RTHTGEKPYACSHCDKTFRQKQLLDMHFKRYHDPNFVPAA-----FVCSKCGKTFTRRNT 62
Query: 263 INRHTKYTHMNTSGP 277
+ RH N +GP
Sbjct: 63 MARHAD----NCAGP 73
>pdb|2LCE|A Chain A, Chemical Shift Assignment Of Hr4436b From Homo Sapiens,
Northeast Structural Genomics Consortium
Length = 74
Score = 31.6 bits (70), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 22/49 (44%)
Query: 186 FMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMR 234
+ C C RY ++A H HT EKP+ C +C + + H R
Sbjct: 18 YKCDRCQASFRYKGNLASHKTVHTGEKPYRCNICGAQFNRPANLKTHTR 66
>pdb|2EPA|A Chain A, Solution Structure Of The First And Second Zf-C2h2 Domains
From Human Krueppel-Like Factor 10
Length = 72
Score = 31.6 bits (70), Expect = 0.52, Method: Composition-based stats.
Identities = 17/39 (43%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 199 SSMAIHLRTHTKEKPFACEM--CNYRAASKIAIYAHMRT 235
S + H RTHT EKPF+C C R A + H RT
Sbjct: 33 SHLKAHTRTHTGEKPFSCSWKGCERRFARSDELSRHRRT 71
>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 = 31.2 bits (69), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 5/52 (9%)
Query: 189 FACPYYC---RYGSS--MAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMRT 235
+ACP R+ S + H+R HT +KPF C +C + + H+RT
Sbjct: 20 YACPVESCDRRFSRSDELTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRT 71
>pdb|2WBU|A Chain A, Crystal Structure Of The Zinc Finger Domain Of Klf4 Bound
To Its Target Dna
Length = 90
Score = 30.8 bits (68), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 199 SSMAIHLRTHTKEKPFAC--EMCNYRAASKIAIYAHMR 234
S + HLRTHT EKP+ C + C ++ A + H R
Sbjct: 22 SHLKAHLRTHTGEKPYHCDWDGCGWKFARSDELTRHYR 59
>pdb|2WBS|A Chain A, Crystal Structure Of The Zinc Finger Domain Of Klf4 Bound
To Its Target Dna
Length = 89
Score = 30.8 bits (68), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 199 SSMAIHLRTHTKEKPFAC--EMCNYRAASKIAIYAHMR 234
S + HLRTHT EKP+ C + C ++ A + H R
Sbjct: 21 SHLKAHLRTHTGEKPYHCDWDGCGWKFARSDELTRHYR 58
>pdb|2EOG|A Chain A, Solution Structure Of The C2h2 Type Zinc Finger (Region
693- 723) Of Human Zinc Finger Protein 268
Length = 44
Score = 30.8 bits (68), Expect = 1.0, Method: Composition-based stats.
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 184 RNFMCFACPYYCRYGSSMAIHLRTHTKEKP 213
+ + C C R S + IH+RTHT EKP
Sbjct: 9 KPYGCSECGKAFRSKSYLIIHMRTHTGEKP 38
>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 = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 21/42 (50%)
Query: 175 RRKRKNPMRRNFMCFACPYYCRYGSSMAIHLRTHTKEKPFAC 216
R +R++ + F C C + H RTHT EKPF+C
Sbjct: 56 RHQRRHTGVKPFQCKTCQRKFSRSDHLKTHTRTHTGEKPFSC 97
>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 = 2.6, Method: Composition-based stats.
Identities = 14/51 (27%), Positives = 20/51 (39%)
Query: 184 RNFMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMR 234
+ + C C S + H R HT EKP+ C C + + H R
Sbjct: 13 KPYGCVECGKAFSRSSILVQHQRVHTGEKPYKCLECGKAFSQNSGLINHQR 63
>pdb|1X5W|A Chain A, Solution Structure Of The C2h2 Type Zinc-Binding Domain Of
Human Zinc Finger Protein 64, Isoforms 1 And 2
Length = 70
Score = 28.5 bits (62), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 11/39 (28%), Positives = 20/39 (51%)
Query: 199 SSMAIHLRTHTKEKPFACEMCNYRAASKIAIYAHMRTTH 237
+++ IH R H ++PF C C++ + HM+ H
Sbjct: 23 AALRIHERIHCTDRPFKCNYCSFDTKQPSNLSKHMKKFH 61
>pdb|3ZNF|A Chain A, High-Resolution Three-Dimensional Structure Of A Single
Zinc Finger From A Human Enhancer Binding Protein In
Solution
pdb|4ZNF|A Chain A, High-Resolution Three-Dimensional Structure Of A Single
Zinc Finger From A Human Enhancer Binding Protein In
Solution
Length = 30
Score = 28.5 bits (62), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 246 RRYHCAFCNFTSPTQWAINRHTK 268
R YHC++CNF+ T+ + +H K
Sbjct: 1 RPYHCSYCNFSFKTKGNLTKHMK 23
>pdb|3IUF|A Chain A, Crystal Structure Of The C2h2-Type Zinc Finger Domain Of
Human Ubi-D4
Length = 48
Score = 28.5 bits (62), Expect = 5.4, Method: Composition-based stats.
Identities = 9/37 (24%), Positives = 22/37 (59%)
Query: 210 KEKPFACEMCNYRAASKIAIYAHMRTTHIMPDTSEER 246
++KP+AC++C R ++ + H +H+ + E++
Sbjct: 4 RDKPYACDICGKRYKNRPGLSYHYAHSHLAEEEGEDK 40
>pdb|2KVH|A Chain A, Structure Of The Three-Cys2his2 Domain Of Mouse Testis
Zinc Finger Protein
Length = 27
Score = 28.1 bits (61), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 211 EKPFACEMCNYRAASKIAIYAHMRT 235
EKPF+C +C R+ A+ H+RT
Sbjct: 1 EKPFSCSLCPQRSRDFSAMTKHLRT 25
>pdb|2KMK|A Chain A, Gfi-1 Zinc Fingers 3-5 Complexed With Dna
Length = 82
Score = 28.1 bits (61), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 33/75 (44%), Gaps = 10/75 (13%)
Query: 170 CKLCLRR-KRKNPMRRNFMCFAC--PYYCRY-------GSSMAIHLRTHTKEKPFACEMC 219
CK+C + KR + + + + + PY C+Y S M H HT EKP C++C
Sbjct: 4 CKICGKSFKRSSTLSTHLLIHSDTRPYPCQYCGKRFHQKSDMKKHTFIHTGEKPHKCQVC 63
Query: 220 NYRAASKIAIYAHMR 234
+ + H R
Sbjct: 64 GKAFSQSSNLITHSR 78
Score = 27.3 bits (59), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 23/48 (47%)
Query: 185 NFMCFACPYYCRYGSSMAIHLRTHTKEKPFACEMCNYRAASKIAIYAH 232
+F C C + S+++ HL H+ +P+ C+ C R K + H
Sbjct: 1 SFDCKICGKSFKRSSTLSTHLLIHSDTRPYPCQYCGKRFHQKSDMKKH 48
>pdb|2EOW|A Chain A, Solution Structure Of The C2h2 Type Zinc Finger (Region
368- 400) Of Human Zinc Finger Protein 347
Length = 46
Score = 27.3 bits (59), Expect = 9.8, Method: Composition-based stats.
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 184 RNFMCFACPYYCRYGSSMAIHLRTHTKEKP 213
+ + C C R SS+AIH TH+ EKP
Sbjct: 11 KPYKCNECGKAFRARSSLAIHQATHSGEKP 40
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 0.134 0.431
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,293,094
Number of Sequences: 62578
Number of extensions: 291400
Number of successful extensions: 1011
Number of sequences better than 100.0: 54
Number of HSP's better than 100.0 without gapping: 48
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 896
Number of HSP's gapped (non-prelim): 111
length of query: 304
length of database: 14,973,337
effective HSP length: 98
effective length of query: 206
effective length of database: 8,840,693
effective search space: 1821182758
effective search space used: 1821182758
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)