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= 011807
(477 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 = 53.9 bits (128), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 41/152 (26%), Positives = 69/152 (45%), Gaps = 23/152 (15%)
Query: 68 IALSPKTLLATNRFVCEVCNKGFQRDQNLQLHRRGH--NLPWK-------LKQRSN---- 114
+A +T + C C K F ++L H+R H P+K QR+N
Sbjct: 37 LAEHQRTHTGEKPYKCPECGKSFSDKKDLTRHQRTHTGEKPYKCPECGKSFSQRANLRAH 96
Query: 115 -KDIIKKKAYVCPEPSCVHHHPSRALGDLTGIKKHFCRKHGERKWKCEKCSKVYAVQSDW 173
+ +K Y CPE C ++ L ++ H GE+ +KC +C K ++ + +
Sbjct: 97 QRTHTGEKPYACPE--C-----GKSFSQLAHLRAHQRTHTGEKPYKCPECGKSFSREDNL 149
Query: 174 KAHSKT-CGTREYRC-DCGTLFSRKDSFITHR 203
H +T G + Y+C +CG FSR+D+ H+
Sbjct: 150 HTHQRTHTGEKPYKCPECGKSFSRRDALNVHQ 181
Score = 45.8 bits (107), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 33/117 (28%), Positives = 54/117 (46%), Gaps = 23/117 (19%)
Query: 81 FVCEVCNKGFQRDQNLQLHRRGHNLPWKLKQRSNKDIIKKKAYVCPEPSCVHHHPSRALG 140
+ C C K F R +L H+R H +K Y CPE C ++
Sbjct: 22 YACPECGKSFSRSDHLAEHQRTH--------------TGEKPYKCPE--C-----GKSFS 60
Query: 141 DLTGIKKHFCRKHGERKWKCEKCSKVYAVQSDWKAHSKT-CGTREYRC-DCGTLFSR 195
D + +H GE+ +KC +C K ++ +++ +AH +T G + Y C +CG FS+
Sbjct: 61 DKKDLTRHQRTHTGEKPYKCPECGKSFSQRANLRAHQRTHTGEKPYACPECGKSFSQ 117
Score = 30.4 bits (67), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 2/52 (3%)
Query: 154 GERKWKCEKCSKVYAVQSDWKAHSKT-CGTREYRC-DCGTLFSRKDSFITHR 203
GE+ + C +C K ++ H +T G + Y+C +CG FS K H+
Sbjct: 18 GEKPYACPECGKSFSRSDHLAEHQRTHTGEKPYKCPECGKSFSDKKDLTRHQ 69
Score = 30.0 bits (66), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 29/133 (21%), Positives = 51/133 (38%), Gaps = 27/133 (20%)
Query: 64 DAEVIALSPKTLLATNRFVCEVCNKGFQRDQNLQLHRRGH--NLPW-------------- 107
D + + +T + C C K F + NL+ H+R H P+
Sbjct: 61 DKKDLTRHQRTHTGEKPYKCPECGKSFSQRANLRAHQRTHTGEKPYACPECGKSFSQLAH 120
Query: 108 -KLKQRSNKDIIKKKAYVCPEPSCVHHHPSRALGDLTGIKKHFCRKHGERKWKCEKCSKV 166
+ QR++ +K Y CPE C ++ + H GE+ +KC +C K
Sbjct: 121 LRAHQRTH---TGEKPYKCPE--C-----GKSFSREDNLHTHQRTHTGEKPYKCPECGKS 170
Query: 167 YAVQSDWKAHSKT 179
++ + H +T
Sbjct: 171 FSRRDALNVHQRT 183
>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 = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 28/85 (32%), Positives = 44/85 (51%), Gaps = 9/85 (10%)
Query: 121 KAYVCPEPSCVHHHPSRALGDLTGIKKHFCRKHGERKWKCEKCSKVYAVQSDWKAHSKT- 179
K Y CPE C ++ + ++KH GE+ +KC +C K ++ SD + H +T
Sbjct: 3 KPYKCPE--C-----GKSFSQSSNLQKHQRTHTGEKPYKCPECGKSFSQSSDLQKHQRTH 55
Query: 180 CGTREYRC-DCGTLFSRKDSFITHR 203
G + Y+C +CG FSR D H+
Sbjct: 56 TGEKPYKCPECGKSFSRSDHLSRHQ 80
>pdb|2COT|A Chain A, Solution Structure Of The First And Second Zf-C2h2 Domain
Of Zinc Finger Protein 435
Length = 77
Score = 36.2 bits (82), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 29/49 (59%), Gaps = 2/49 (4%)
Query: 156 RKWKCEKCSKVYAVQSDWKAHSKT-CGTREYRCD-CGTLFSRKDSFITH 202
R++KC++C K ++ SD H +T G + Y+CD CG F ++ I H
Sbjct: 17 RRYKCDECGKSFSHSSDLSKHRRTHTGEKPYKCDECGKAFIQRSHLIGH 65
>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 = 34.7 bits (78), Expect = 0.12, Method: Composition-based stats.
Identities = 23/79 (29%), Positives = 34/79 (43%), Gaps = 18/79 (22%)
Query: 117 IIKKKAYVCPEPSCVHHHPSRALGDLTGIKKHFCRKHGERKWKCEKCSKVYAVQSDWKAH 176
I+ K++YVC LT +++HF E+K+ C C KV+ + H
Sbjct: 26 IVCKRSYVC----------------LTSLRRHFNIHSWEKKYPCRYCEKVFPLAEYRTKH 69
Query: 177 S-KTCGTREYRC-DCGTLF 193
G R Y+C CG F
Sbjct: 70 EIHHTGERRYQCLACGKSF 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 = 34.3 bits (77), Expect = 0.15, Method: Composition-based stats.
Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 4/55 (7%)
Query: 152 KHGERKWKCEKCSKVYAVQSDWKAHSKTCGTRE---YRCD-CGTLFSRKDSFITH 202
K GE ++C+ CS+VY S++ H T R Y C C F+RKD+ H
Sbjct: 5 KEGEHTYRCKVCSRVYTHISNFCRHYVTSHKRNVKVYPCPFCFKEFTRKDNMTAH 59
>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 = 33.1 bits (74), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 7/77 (9%)
Query: 120 KKAYVCPEPSCVHHHPSRALGDLTGIKKHFCRKHGERKWKCEKCSKVYAVQSDWKAHSKT 179
++ Y CP SC R T + H G++ ++C C + ++ Q+ AH +T
Sbjct: 2 ERPYACPVESC-----DRRFSQKTNLDTHIRIHTGQKPFQCRICMRNFSQQASLNAHIRT 56
Query: 180 -CGTREYRCD-CGTLFS 194
G + + CD CG F+
Sbjct: 57 HTGEKPFACDICGRKFA 73
>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 = 32.7 bits (73), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 31/128 (24%), Positives = 52/128 (40%), Gaps = 25/128 (19%)
Query: 81 FVCEV--CNKGFQRDQNLQLHRRGHNLPWKLKQRSNKDIIKKKAYVCPEPSCVHHHPSRA 138
F+C CNK + + +LQ+H R H +K Y C C R
Sbjct: 7 FMCAYPGCNKRYFKLSHLQMHSRKH--------------TGEKPYQCDFKDC-----ERR 47
Query: 139 LGDLTGIKKHFCRKHGERKWKCEKCSKVYAVQSDWKAHSKT-CGTREYRC---DCGTLFS 194
+K+H R G + ++C+ C + ++ K H++T G + + C C F+
Sbjct: 48 FSRSDQLKRHQRRHTGVKPFQCKTCQRKFSRSDHLKTHTRTHTGEKPFSCRWPSCQKKFA 107
Query: 195 RKDSFITH 202
R D + H
Sbjct: 108 RSDELVRH 115
>pdb|2ADR|A Chain A, Adr1 Dna-Binding Domain From Saccharomyces Cerevisiae,
Nmr, 25 Structures
Length = 60
Score = 32.0 bits (71), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 81 FVCEVCNKGFQRDQNLQLHRRGH 103
FVCEVC + F R ++L+ H R H
Sbjct: 3 FVCEVCTRAFARQEHLKRHYRSH 25
Score = 28.5 bits (62), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 2/47 (4%)
Query: 158 WKCEKCSKVYAVQSDWKAHSKT-CGTREYRCD-CGTLFSRKDSFITH 202
+ CE C++ +A Q K H ++ + Y C C F+R+D I H
Sbjct: 3 FVCEVCTRAFARQEHLKRHYRSHTNEKPYPCGLCNRAFTRRDLLIRH 49
>pdb|1ARD|A Chain A, Structures Of Dna-Binding Mutant Zinc Finger Domains:
Implications For Dna Binding
Length = 29
Score = 31.6 bits (70), Expect = 0.94, Method: Composition-based stats.
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 81 FVCEVCNKGFQRDQNLQLHRRGH 103
FVCEVC + F R ++L+ H R H
Sbjct: 3 FVCEVCTRAFARQEHLKRHYRSH 25
>pdb|1ARF|A Chain A, Structures Of Dna-Binding Mutant Zinc Finger Domains:
Implications For Dna Binding
Length = 29
Score = 31.6 bits (70), Expect = 1.0, Method: Composition-based stats.
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 81 FVCEVCNKGFQRDQNLQLHRRGH 103
FVCEVC + F R + L+ H R H
Sbjct: 3 FVCEVCTRAFARQEYLKRHYRSH 25
>pdb|1ARE|A Chain A, Structures Of Dna-Binding Mutant Zinc Finger Domains:
Implications For Dna Binding
Length = 29
Score = 31.2 bits (69), Expect = 1.2, Method: Composition-based stats.
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 81 FVCEVCNKGFQRDQNLQLHRRGH 103
FVCEVC + F R + L+ H R H
Sbjct: 3 FVCEVCTRAFARQEALKRHYRSH 25
>pdb|1X6E|A Chain A, Solution Structures Of The C2h2 Type Zinc Finger Domain Of
Human Zinc Finger Protein 24
Length = 72
Score = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 2/51 (3%)
Query: 155 ERKWKCEKCSKVYAVQSDWKAHSKT-CGTREYRC-DCGTLFSRKDSFITHR 203
E+ + C +C K ++ S H + G + Y+C +CG FS+ I H+
Sbjct: 12 EKPYGCVECGKAFSRSSILVQHQRVHTGEKPYKCLECGKAFSQNSGLINHQ 62
>pdb|2LCE|A Chain A, Chemical Shift Assignment Of Hr4436b From Homo Sapiens,
Northeast Structural Genomics Consortium
Length = 74
Score = 30.4 bits (67), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 2/50 (4%)
Query: 155 ERKWKCEKCSKVYAVQSDWKAHSKT-CGTREYRCD-CGTLFSRKDSFITH 202
++ +KC++C + + + +H G + YRC+ CG F+R + TH
Sbjct: 15 DKPYKCDRCQASFRYKGNLASHKTVHTGEKPYRCNICGAQFNRPANLKTH 64
>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 = 30.4 bits (67), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 23/89 (25%), Positives = 37/89 (41%), Gaps = 10/89 (11%)
Query: 118 IKKKAYVCPEPSCVHHHPSRALGDLTGIKKHFCRKHGERKWKCEKCSKVYAVQSDWKAHS 177
++ + CP C ++ D + ++KH HG R C +C K + S K H
Sbjct: 1 MEPRTIACPHKGC-----TKMFRDNSAMRKHL-HTHGPRVHVCAECGKAFVESSKLKRHQ 54
Query: 178 KT-CGTREYRC---DCGTLFSRKDSFITH 202
G + ++C CG FS + TH
Sbjct: 55 LVHTGEKPFQCTFEGCGKRFSLDFNLRTH 83
>pdb|2KMK|A Chain A, Gfi-1 Zinc Fingers 3-5 Complexed With Dna
Length = 82
Score = 30.0 bits (66), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 27/49 (55%), Gaps = 2/49 (4%)
Query: 156 RKWKCEKCSKVYAVQSDWKAHSKT-CGTREYRCD-CGTLFSRKDSFITH 202
R + C+ C K + +SD K H+ G + ++C CG FS+ + ITH
Sbjct: 28 RPYPCQYCGKRFHQKSDMKKHTFIHTGEKPHKCQVCGKAFSQSSNLITH 76
>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 = 30.0 bits (66), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 14/30 (46%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 83 CEVCNKGFQRDQNLQLHRRGHN--LPWKLK 110
CEVC K F R L+ H R H P+K K
Sbjct: 11 CEVCGKCFSRKDKLKTHMRCHTGVKPYKCK 40
>pdb|2EOJ|A Chain A, Solution Structure Of The C2h2 Type Zinc Finger (Region
355- 385) Of Human Zinc Finger Protein 268
Length = 44
Score = 29.6 bits (65), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 9/17 (52%), Positives = 14/17 (82%)
Query: 187 CDCGTLFSRKDSFITHR 203
C+CG +FSRKD ++H+
Sbjct: 16 CECGKVFSRKDQLVSHQ 32
>pdb|2ELZ|A Chain A, Solution Structure Of The 17th Zf-C2h2 Domain From Human
Zinc Finger Protein 224
Length = 46
Score = 29.6 bits (65), Expect = 3.6, Method: Composition-based stats.
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 81 FVCEVCNKGFQRDQNLQLHRRGH 103
+ CE C KG+ R NL +H+R H
Sbjct: 13 YKCEDCGKGYNRRLNLDMHQRVH 35
>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 = 29.3 bits (64), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 81 FVCEVCNKGFQRDQNLQLHRRGH--NLPWKLKQRSNKDIIKK 120
F C VC + F+R L+LH H +P+K S + + KK
Sbjct: 67 FTCSVCQETFRRRMELRLHMVSHTGEMPYKCSSCSQQFMQKK 108
>pdb|2GLI|A Chain A, Five-Finger GliDNA COMPLEX
Length = 155
Score = 29.3 bits (64), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 30/116 (25%), Positives = 47/116 (40%), Gaps = 22/116 (18%)
Query: 67 VIALSPKTLLATNRFVCEVCNKGFQRDQNLQLHRRGHNLPWKLKQRSNKDIIKKKAYVCP 126
V+ + T ++ E C K + R +NL+ H R H +K Y+C
Sbjct: 56 VVHMRRHTGEKPHKCTFEGCRKSYSRLENLKTHLRSH--------------TGEKPYMCE 101
Query: 127 EPSCVHHHPSRALGDLTGIKKHFCRKH-GERKWKCE--KCSKVYAVQSDWKAHSKT 179
C S+A + + KH R H E+ + C+ C+K Y S + H KT
Sbjct: 102 HEGC-----SKAFSNASDRAKHQNRTHSNEKPYVCKLPGCTKRYTDPSSLRKHVKT 152
>pdb|2WBU|A Chain A, Crystal Structure Of The Zinc Finger Domain Of Klf4 Bound
To Its Target Dna
Length = 90
Score = 28.9 bits (63), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 21/44 (47%), Gaps = 4/44 (9%)
Query: 163 CSKVYAVQSDWKAHSKT-CGTREYRCD---CGTLFSRKDSFITH 202
C K Y S KAH +T G + Y CD CG F+R D H
Sbjct: 14 CGKTYTKSSHLKAHLRTHTGEKPYHCDWDGCGWKFARSDELTRH 57
>pdb|2ELS|A Chain A, Solution Structure Of The 2nd C2h2 Zinc Finger Of Human
Zinc Finger Protein 406
Length = 36
Score = 28.9 bits (63), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 14/23 (60%)
Query: 81 FVCEVCNKGFQRDQNLQLHRRGH 103
F CE CNK F+ +LQ H R H
Sbjct: 10 FTCEYCNKVFKFKHSLQAHLRIH 32
>pdb|2WBS|A Chain A, Crystal Structure Of The Zinc Finger Domain Of Klf4 Bound
To Its Target Dna
Length = 89
Score = 28.5 bits (62), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 21/44 (47%), Gaps = 4/44 (9%)
Query: 163 CSKVYAVQSDWKAHSKT-CGTREYRCD---CGTLFSRKDSFITH 202
C K Y S KAH +T G + Y CD CG F+R D H
Sbjct: 13 CGKTYTKSSHLKAHLRTHTGEKPYHCDWDGCGWKFARSDELTRH 56
>pdb|2YSV|A Chain A, Solution Structure Of C2h2 Type Zinc Finger Domain 17 In
Zinc Finger Protein 473
Length = 42
Score = 28.5 bits (62), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 81 FVCEVCNKGFQRDQNLQLHRRGH 103
+VC+ C K F + L +HRR H
Sbjct: 11 YVCQECGKAFTQSSCLSIHRRVH 33
>pdb|2EBT|A Chain A, Solution Structure Of Three Tandem Repeats Of Zf-C2h2
Domains From Human Kruppel-Like Factor 5
Length = 100
Score = 28.1 bits (61), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 29/66 (43%), Gaps = 12/66 (18%)
Query: 141 DLTGIKKHFCRKHGERKWKCEKCSKVYAVQSDWKAHSKT-CGTREYRC---DCGTLFSRK 196
DL + H+C G C+KVY S KAH +T G + Y+C C F+R
Sbjct: 9 DLEKRRIHYCDYPG--------CTKVYTKSSHLKAHLRTHTGEKPYKCTWEGCDWRFARS 60
Query: 197 DSFITH 202
D H
Sbjct: 61 DELTRH 66
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
0.317 0.130 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,778,297
Number of Sequences: 62578
Number of extensions: 444963
Number of successful extensions: 1377
Number of sequences better than 100.0: 35
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 1292
Number of HSP's gapped (non-prelim): 92
length of query: 477
length of database: 14,973,337
effective HSP length: 102
effective length of query: 375
effective length of database: 8,590,381
effective search space: 3221392875
effective search space used: 3221392875
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: 53 (25.0 bits)