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= 010863
(498 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 = 36/124 (29%), Positives = 57/124 (45%), Gaps = 22/124 (17%)
Query: 6 FVCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTSKEIRKKVYVCPEPNCVHHDPSRALGD 65
+ C C K F + NL+ H+R H +K Y CPE ++
Sbjct: 78 YKCPECGKSFSQRANLRAHQRTH-------------TGEKPYACPECG-------KSFSQ 117
Query: 66 LTGIKKHFCRKHGEKKWKCDKCSKRYAVQSDWKAHSKT-CGTREYRC-DCGTLFSRRDSF 123
L ++ H GEK +KC +C K ++ + + H +T G + Y+C +CG FSRRD+
Sbjct: 118 LAHLRAHQRTHTGEKPYKCPECGKSFSREDNLHTHQRTHTGEKPYKCPECGKSFSRRDAL 177
Query: 124 ITHR 127
H+
Sbjct: 178 NVHQ 181
Score = 46.2 bits (108), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 33/116 (28%), Positives = 53/116 (45%), Gaps = 22/116 (18%)
Query: 6 FVCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTSKEIRKKVYVCPEPNCVHHDPSRALGD 65
+ C C K F R +L H+R H +K Y CPE ++ D
Sbjct: 22 YACPECGKSFSRSDHLAEHQRTH-------------TGEKPYKCPECG-------KSFSD 61
Query: 66 LTGIKKHFCRKHGEKKWKCDKCSKRYAVQSDWKAHSKT-CGTREYRC-DCGTLFSR 119
+ +H GEK +KC +C K ++ +++ +AH +T G + Y C +CG FS+
Sbjct: 62 KKDLTRHQRTHTGEKPYKCPECGKSFSQRANLRAHQRTHTGEKPYACPECGKSFSQ 117
Score = 30.0 bits (66), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 2/52 (3%)
Query: 78 GEKKWKCDKCSKRYAVQSDWKAHSKT-CGTREYRC-DCGTLFSRRDSFITHR 127
GEK + C +C K ++ H +T G + Y+C +CG FS + H+
Sbjct: 18 GEKPYACPECGKSFSRSDHLAEHQRTHTGEKPYKCPECGKSFSDKKDLTRHQ 69
>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 = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 28/85 (32%), Positives = 43/85 (50%), Gaps = 9/85 (10%)
Query: 45 KVYVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKWKCDKCSKRYAVQSDWKAHSKT- 103
K Y CPE ++ + ++KH GEK +KC +C K ++ SD + H +T
Sbjct: 3 KPYKCPECG-------KSFSQSSNLQKHQRTHTGEKPYKCPECGKSFSQSSDLQKHQRTH 55
Query: 104 CGTREYRC-DCGTLFSRRDSFITHR 127
G + Y+C +CG FSR D H+
Sbjct: 56 TGEKPYKCPECGKSFSRSDHLSRHQ 80
Score = 35.0 bits (79), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 40/98 (40%), Gaps = 20/98 (20%)
Query: 6 FVCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTSKEIRKKVYVCPEPNCVHHDPSRALGD 65
+ C C K F + NLQ H+R H +K Y CPE ++
Sbjct: 5 YKCPECGKSFSQSSNLQKHQRTH-------------TGEKPYKCPECG-------KSFSQ 44
Query: 66 LTGIKKHFCRKHGEKKWKCDKCSKRYAVQSDWKAHSKT 103
+ ++KH GEK +KC +C K ++ H +T
Sbjct: 45 SSDLQKHQRTHTGEKPYKCPECGKSFSRSDHLSRHQRT 82
>pdb|2COT|A Chain A, Solution Structure Of The First And Second Zf-C2h2 Domain
Of Zinc Finger Protein 435
Length = 77
Score = 37.4 bits (85), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 29/49 (59%), Gaps = 2/49 (4%)
Query: 80 KKWKCDKCSKRYAVQSDWKAHSKT-CGTREYRCD-CGTLFSRRDSFITH 126
+++KCD+C K ++ SD H +T G + Y+CD CG F +R I H
Sbjct: 17 RRYKCDECGKSFSHSSDLSKHRRTHTGEKPYKCDECGKAFIQRSHLIGH 65
>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 = 34.7 bits (78), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 32/127 (25%), Positives = 53/127 (41%), Gaps = 24/127 (18%)
Query: 6 FVCEI--CNKGFQRDQNLQLHRRGHNLPWKLKQRTSKEIRKKVYVCPEPNCVHHDPSRAL 63
F+C CNK + + +LQ+H R H +K Y C +C R
Sbjct: 7 FMCAYPGCNKRYFKLSHLQMHSRKHTG-------------EKPYQCDFKDC-----ERRF 48
Query: 64 GDLTGIKKHFCRKHGEKKWKCDKCSKRYAVQSDWKAHSKT-CGTREYRC---DCGTLFSR 119
+K+H R G K ++C C ++++ K H++T G + + C C F+R
Sbjct: 49 SRSDQLKRHQRRHTGVKPFQCKTCQRKFSRSDHLKTHTRTHTGEKPFSCRWPSCQKKFAR 108
Query: 120 RDSFITH 126
D + H
Sbjct: 109 SDELVRH 115
>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 = 32.3 bits (72), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 7/74 (9%)
Query: 47 YVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKWKCDKCSKRYAVQSDWKAHSKT-CG 105
Y CP +C R T + H G+K ++C C + ++ Q+ AH +T G
Sbjct: 5 YACPVESC-----DRRFSQKTNLDTHIRIHTGQKPFQCRICMRNFSQQASLNAHIRTHTG 59
Query: 106 TREYRCD-CGTLFS 118
+ + CD CG F+
Sbjct: 60 EKPFACDICGRKFA 73
>pdb|2LCE|A Chain A, Chemical Shift Assignment Of Hr4436b From Homo Sapiens,
Northeast Structural Genomics Consortium
Length = 74
Score = 32.3 bits (72), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 2/50 (4%)
Query: 79 EKKWKCDKCSKRYAVQSDWKAHSKT-CGTREYRCD-CGTLFSRRDSFITH 126
+K +KCD+C + + + +H G + YRC+ CG F+R + TH
Sbjct: 15 DKPYKCDRCQASFRYKGNLASHKTVHTGEKPYRCNICGAQFNRPANLKTH 64
>pdb|1TF3|A Chain A, Tfiiia Finger 1-3 Bound To Dna, Nmr, 22 Structures
Length = 92
Score = 32.0 bits (71), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 24/98 (24%), Positives = 40/98 (40%), Gaps = 18/98 (18%)
Query: 5 RFVCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTSKEIRKKVYVCPEPNCVHHDPSRALG 64
R++C + G ++N WKL+ SK +K + C E C +
Sbjct: 3 RYICSFADCGAAYNKN-----------WKLQAHLSKHTGEKPFPCKEEGC-----EKGFT 46
Query: 65 DLTGIKKHFCRKHGEKKWKCDK--CSKRYAVQSDWKAH 100
L + +H GEK + CD C R+ +++ K H
Sbjct: 47 SLHHLTRHSLTHTGEKNFTCDSDGCDLRFTTKANMKKH 84
>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 = 31.6 bits (70), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 36/82 (43%), Gaps = 7/82 (8%)
Query: 47 YVCPEPNCVHHDPSRALGDLTGIKKHFCRKHGEKKWKCDKCSKRYAVQSDWKAHSKT-CG 105
Y CP +C R D + + +H G+K ++C C + ++ H +T G
Sbjct: 5 YACPVESC-----DRRFSDSSNLTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTHTG 59
Query: 106 TREYRCD-CGTLFSRRDSFITH 126
+ + CD CG F+R D H
Sbjct: 60 EKPFACDICGRKFARSDERKRH 81
>pdb|2ADR|A Chain A, Adr1 Dna-Binding Domain From Saccharomyces Cerevisiae,
Nmr, 25 Structures
Length = 60
Score = 31.6 bits (70), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 6 FVCEICNKGFQRDQNLQLHRRGH 28
FVCE+C + F R ++L+ H R H
Sbjct: 3 FVCEVCTRAFARQEHLKRHYRSH 25
>pdb|2GLI|A Chain A, Five-Finger GliDNA COMPLEX
Length = 155
Score = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 30/98 (30%), Positives = 41/98 (41%), Gaps = 21/98 (21%)
Query: 9 EICNKGFQRDQNLQLHRRGHNLPWKLKQRTSKEIRKKVYVCPEPNCVHHDPSRALGDLTG 68
E C K + R +NL+ H R H +K Y+C C S+A + +
Sbjct: 73 EGCRKSYSRLENLKTHLRSH-------------TGEKPYMCEHEGC-----SKAFSNASD 114
Query: 69 IKKHFCRKH-GEKKWKCD--KCSKRYAVQSDWKAHSKT 103
KH R H EK + C C+KRY S + H KT
Sbjct: 115 RAKHQNRTHSNEKPYVCKLPGCTKRYTDPSSLRKHVKT 152
>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 = 1.6, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 2/51 (3%)
Query: 79 EKKWKCDKCSKRYAVQSDWKAHSKT-CGTREYRC-DCGTLFSRRDSFITHR 127
EK + C +C K ++ S H + G + Y+C +CG FS+ I H+
Sbjct: 12 EKPYGCVECGKAFSRSSILVQHQRVHTGEKPYKCLECGKAFSQNSGLINHQ 62
>pdb|1ARF|A Chain A, Structures Of Dna-Binding Mutant Zinc Finger Domains:
Implications For Dna Binding
Length = 29
Score = 30.8 bits (68), Expect = 1.9, Method: Composition-based stats.
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 6 FVCEICNKGFQRDQNLQLHRRGH 28
FVCE+C + F R + L+ H R H
Sbjct: 3 FVCEVCTRAFARQEYLKRHYRSH 25
>pdb|1ARD|A Chain A, Structures Of Dna-Binding Mutant Zinc Finger Domains:
Implications For Dna Binding
Length = 29
Score = 30.8 bits (68), Expect = 1.9, Method: Composition-based stats.
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 6 FVCEICNKGFQRDQNLQLHRRGH 28
FVCE+C + F R ++L+ H R H
Sbjct: 3 FVCEVCTRAFARQEHLKRHYRSH 25
>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 = 30.8 bits (68), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 29/135 (21%), Positives = 51/135 (37%), Gaps = 24/135 (17%)
Query: 1 MATNRFVCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTSKEIRKKVYVCPEPNCVHHDPS 60
+ R++C + G ++N WKL+ K +K + C E C
Sbjct: 8 VVYKRYICSFADCGAAYNKN-----------WKLQAHLCKHTGEKPFPCKEEGC-----E 51
Query: 61 RALGDLTGIKKHFCRKHGEKKWKCDK--CSKRYAVQSDWKAH------SKTCGTREYRCD 112
+ L + +H GEK + CD C R+ +++ K H K C + +
Sbjct: 52 KGFTSLHHLTRHSLTHTGEKNFTCDSDGCDLRFTTKANMKKHFNRFHNIKICVYVCHFEN 111
Query: 113 CGTLFSRRDSFITHR 127
CG F + + H+
Sbjct: 112 CGKAFKKHNQLKVHQ 126
>pdb|1ARE|A Chain A, Structures Of Dna-Binding Mutant Zinc Finger Domains:
Implications For Dna Binding
Length = 29
Score = 30.4 bits (67), Expect = 2.1, Method: Composition-based stats.
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 6 FVCEICNKGFQRDQNLQLHRRGH 28
FVCE+C + F R + L+ H R H
Sbjct: 3 FVCEVCTRAFARQEALKRHYRSH 25
>pdb|2KMK|A Chain A, Gfi-1 Zinc Fingers 3-5 Complexed With Dna
Length = 82
Score = 30.4 bits (67), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 26/47 (55%), Gaps = 2/47 (4%)
Query: 82 WKCDKCSKRYAVQSDWKAHSKT-CGTREYRCD-CGTLFSRRDSFITH 126
+ C C KR+ +SD K H+ G + ++C CG FS+ + ITH
Sbjct: 30 YPCQYCGKRFHQKSDMKKHTFIHTGEKPHKCQVCGKAFSQSSNLITH 76
>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 = 30.0 bits (66), Expect = 2.7, Method: Composition-based stats.
Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 2/54 (3%)
Query: 66 LTGIKKHFCRKHGEKKWKCDKCSKRYAVQSDWKAHS-KTCGTREYRC-DCGTLF 117
LT +++HF EKK+ C C K + + H G R Y+C CG F
Sbjct: 35 LTSLRRHFNIHSWEKKYPCRYCEKVFPLAEYRTKHEIHHTGERRYQCLACGKSF 88
>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 = 29.6 bits (65), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 8 CEICNKGFQRDQNLQLHRRGHN--LPWKLK 35
CE+C K F R L+ H R H P+K K
Sbjct: 11 CEVCGKCFSRKDKLKTHMRCHTGVKPYKCK 40
>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 = 29.6 bits (65), Expect = 4.2, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 76 KHGEKKWKCDKCSKRYAVQSDWKAHSKTCGTRE---YRCD-CGTLFSRRDSFITH 126
K GE ++C CS+ Y S++ H T R Y C C F+R+D+ H
Sbjct: 5 KEGEHTYRCKVCSRVYTHISNFCRHYVTSHKRNVKVYPCPFCFKEFTRKDNMTAH 59
>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 = 28.9 bits (63), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 8/17 (47%), Positives = 14/17 (82%)
Query: 111 CDCGTLFSRRDSFITHR 127
C+CG +FSR+D ++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 = 28.9 bits (63), Expect = 7.4, Method: Composition-based stats.
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 6 FVCEICNKGFQRDQNLQLHRRGH 28
+ CE C KG+ R NL +H+R H
Sbjct: 13 YKCEDCGKGYNRRLNLDMHQRVH 35
>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 = 7.6, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 14/23 (60%)
Query: 6 FVCEICNKGFQRDQNLQLHRRGH 28
F CE CNK F+ +LQ H R H
Sbjct: 10 FTCEYCNKVFKFKHSLQAHLRIH 32
>pdb|3IYN|Q Chain Q, 3.6-Angstrom Cryoem Structure Of Human Adenovirus Type 5
pdb|3IYN|R Chain R, 3.6-Angstrom Cryoem Structure Of Human Adenovirus Type 5
pdb|3IYN|S Chain S, 3.6-Angstrom Cryoem Structure Of Human Adenovirus Type 5
pdb|3IYN|T Chain T, 3.6-Angstrom Cryoem Structure Of Human Adenovirus Type 5
Length = 140
Score = 28.9 bits (63), Expect = 7.8, Method: Composition-based stats.
Identities = 14/39 (35%), Positives = 24/39 (61%), Gaps = 1/39 (2%)
Query: 189 SYSLRQEMPPWLGSQQPSILGSAVPGLGQPPSSSHTVDH 227
S L MPPW G +Q +++GS++ G P++S T+ +
Sbjct: 12 SSYLTTRMPPWAGVRQ-NVMGSSIDGRPVLPANSTTLTY 49
>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 = 28.5 bits (62), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 6 FVCEICNKGFQRDQNLQLHRRGH--NLPWKLKQRTSKEIRKK 45
F C +C + F+R L+LH H +P+K + + ++KK
Sbjct: 67 FTCSVCQETFRRRMELRLHMVSHTGEMPYKCSSCSQQFMQKK 108
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: 13,138,291
Number of Sequences: 62578
Number of extensions: 465603
Number of successful extensions: 1413
Number of sequences better than 100.0: 48
Number of HSP's better than 100.0 without gapping: 28
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 1303
Number of HSP's gapped (non-prelim): 113
length of query: 498
length of database: 14,973,337
effective HSP length: 103
effective length of query: 395
effective length of database: 8,527,803
effective search space: 3368482185
effective search space used: 3368482185
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)