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= 008017
(581 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 = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 32/124 (25%), Positives = 50/124 (40%), Gaps = 22/124 (17%)
Query: 108 FLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKVERKKVYVCPEPTCVHHDPSRALGD 167
+ C C K F + NL+ H+R H +K Y CPE C ++
Sbjct: 78 YKCPECGKSFSQRANLRAHQRTHTG-------------EKPYACPE--C-----GKSFSQ 117
Query: 168 LTGIKKHFSRKHGXXXXXXXXXXXXYAVQSDWKAHSKI-CGTREYKC-DCGKLFSRRDSF 225
L ++ H G ++ + + H + G + YKC +CGK FSRRD+
Sbjct: 118 LAHLRAHQRTHTGEKPYKCPECGKSFSREDNLHTHQRTHTGEKPYKCPECGKSFSRRDAL 177
Query: 226 ITHR 229
H+
Sbjct: 178 NVHQ 181
Score = 38.5 bits (88), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 38/141 (26%), Positives = 56/141 (39%), Gaps = 28/141 (19%)
Query: 108 FLCEICNKGFQRDQNLQLHRRGH--NLPWKL---------------KQRTNKVERKKVYV 150
+ C C K F R +L H+R H P+K QRT+ E K Y
Sbjct: 22 YACPECGKSFSRSDHLAEHQRTHTGEKPYKCPECGKSFSDKKDLTRHQRTHTGE--KPYK 79
Query: 151 CPEPTCVHHDPSRALGDLTGIKKHFSRKHGXXXXXXXXXXXXYAVQSDWKAHSKI-CGTR 209
CPE C ++ ++ H G ++ + +AH + G +
Sbjct: 80 CPE--C-----GKSFSQRANLRAHQRTHTGEKPYACPECGKSFSQLAHLRAHQRTHTGEK 132
Query: 210 EYKC-DCGKLFSRRDSFITHR 229
YKC +CGK FSR D+ TH+
Sbjct: 133 PYKCPECGKSFSREDNLHTHQ 153
>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 = 30.8 bits (68), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 9/17 (52%), Positives = 15/17 (88%)
Query: 213 CDCGKLFSRRDSFITHR 229
C+CGK+FSR+D ++H+
Sbjct: 16 CECGKVFSRKDQLVSHQ 32
>pdb|2ADR|A Chain A, Adr1 Dna-Binding Domain From Saccharomyces Cerevisiae,
Nmr, 25 Structures
Length = 60
Score = 30.4 bits (67), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 108 FLCEICNKGFQRDQNLQLHRRGH 130
F+CE+C + F R ++L+ H R H
Sbjct: 3 FVCEVCTRAFARQEHLKRHYRSH 25
>pdb|1ARD|A Chain A, Structures Of Dna-Binding Mutant Zinc Finger Domains:
Implications For Dna Binding
Length = 29
Score = 30.0 bits (66), Expect = 3.5, Method: Composition-based stats.
Identities = 10/23 (43%), Positives = 16/23 (69%)
Query: 108 FLCEICNKGFQRDQNLQLHRRGH 130
F+CE+C + F R ++L+ H R H
Sbjct: 3 FVCEVCTRAFARQEHLKRHYRSH 25
>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 = 30.0 bits (66), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 33/124 (26%), Positives = 43/124 (34%), Gaps = 50/124 (40%)
Query: 108 FLCEICNKGFQRDQNLQLHRRGHNLPWKLKQRTNKVERKKVYVCPEPTCVHHDPSRALGD 167
+ C C K F + NLQ H+R H +K Y CPE
Sbjct: 5 YKCPECGKSFSQSSNLQKHQRTHTG-------------EKPYKCPE-------------- 37
Query: 168 LTGIKKHFSRKHGXXXXXXXXXXXXYAVQSDWKAHSKI-CGTREYKC-DCGKLFSRRDSF 225
K FS+ SD + H + G + YKC +CGK FSR D
Sbjct: 38 ---CGKSFSQ------------------SSDLQKHQRTHTGEKPYKCPECGKSFSRSDHL 76
Query: 226 ITHR 229
H+
Sbjct: 77 SRHQ 80
>pdb|1ARF|A Chain A, Structures Of Dna-Binding Mutant Zinc Finger Domains:
Implications For Dna Binding
Length = 29
Score = 30.0 bits (66), Expect = 3.8, Method: Composition-based stats.
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 108 FLCEICNKGFQRDQNLQLHRRGH 130
F+CE+C + 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 = 30.0 bits (66), Expect = 3.9, Method: Composition-based stats.
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 108 FLCEICNKGFQRDQNLQLHRRGH 130
F+CE+C + F R + L+ H R H
Sbjct: 3 FVCEVCTRAFARQEALKRHYRSH 25
>pdb|2ELZ|A Chain A, Solution Structure Of The 17th Zf-C2h2 Domain From Human
Zinc Finger Protein 224
Length = 46
Score = 29.3 bits (64), Expect = 7.1, Method: Composition-based stats.
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 108 FLCEICNKGFQRDQNLQLHRRGH 130
+ CE C KG+ R NL +H+R H
Sbjct: 13 YKCEDCGKGYNRRLNLDMHQRVH 35
>pdb|2EL5|A Chain A, Solution Structure Of The 18th Zf-C2h2 Domain From Human
Zinc Finger Protein 268
Length = 42
Score = 28.9 bits (63), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 11/24 (45%), Positives = 17/24 (70%), Gaps = 1/24 (4%)
Query: 207 GTREYKC-DCGKLFSRRDSFITHR 229
G Y+C +CGK F+R+D I+H+
Sbjct: 7 GENPYECSECGKAFNRKDQLISHQ 30
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 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,286,980
Number of Sequences: 62578
Number of extensions: 390720
Number of successful extensions: 801
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 773
Number of HSP's gapped (non-prelim): 35
length of query: 581
length of database: 14,973,337
effective HSP length: 104
effective length of query: 477
effective length of database: 8,465,225
effective search space: 4037912325
effective search space used: 4037912325
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: 54 (25.4 bits)