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= 010444
(510 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 = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 37/138 (26%), Positives = 56/138 (40%), Gaps = 24/138 (17%)
Query: 6 FVCEICNKGFQRDQNLQLHRRGH--NLPWK-------------LRQRTTTEVRKRVYICP 50
+ C C K F ++L H+R H P+K LR T ++ Y CP
Sbjct: 50 YKCPECGKSFSDKKDLTRHQRTHTGEKPYKCPECGKSFSQRANLRAHQRTHTGEKPYACP 109
Query: 51 EPSCVHHNPARALGDLTGIKKHFSRKHGEXXXXXXXXXXXYAVQSDWKAHQKT-CGTREY 109
E C ++ L ++ H GE ++ + + HQ+T G + Y
Sbjct: 110 E--C-----GKSFSQLAHLRAHQRTHTGEKPYKCPECGKSFSREDNLHTHQRTHTGEKPY 162
Query: 110 KC-DCGTIFSRRDSFITH 126
KC +CG FSRRD+ H
Sbjct: 163 KCPECGKSFSRRDALNVH 180
Score = 42.7 bits (99), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 37/138 (26%), Positives = 56/138 (40%), Gaps = 24/138 (17%)
Query: 6 FVCEICNKGFQRDQNLQLHRRGH--NLPWK-------------LRQRTTTEVRKRVYICP 50
+ C C K F R +L H+R H P+K L + T ++ Y CP
Sbjct: 22 YACPECGKSFSRSDHLAEHQRTHTGEKPYKCPECGKSFSDKKDLTRHQRTHTGEKPYKCP 81
Query: 51 EPSCVHHNPARALGDLTGIKKHFSRKHGEXXXXXXXXXXXYAVQSDWKAHQKT-CGTREY 109
E C ++ ++ H GE ++ + +AHQ+T G + Y
Sbjct: 82 E--C-----GKSFSQRANLRAHQRTHTGEKPYACPECGKSFSQLAHLRAHQRTHTGEKPY 134
Query: 110 KC-DCGTIFSRRDSFITH 126
KC +CG FSR D+ TH
Sbjct: 135 KCPECGKSFSREDNLHTH 152
>pdb|2ADR|A Chain A, Adr1 Dna-Binding Domain From Saccharomyces Cerevisiae,
Nmr, 25 Structures
Length = 60
Score = 32.7 bits (73), Expect = 0.55, 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|1ARD|A Chain A, Structures Of Dna-Binding Mutant Zinc Finger Domains:
Implications For Dna Binding
Length = 29
Score = 32.0 bits (71), Expect = 0.79, 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|1ARF|A Chain A, Structures Of Dna-Binding Mutant Zinc Finger Domains:
Implications For Dna Binding
Length = 29
Score = 32.0 bits (71), Expect = 0.86, 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|1ARE|A Chain A, Structures Of Dna-Binding Mutant Zinc Finger Domains:
Implications For Dna Binding
Length = 29
Score = 31.6 bits (70), Expect = 0.98, 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|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 = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 30/123 (24%), Positives = 41/123 (33%), Gaps = 50/123 (40%)
Query: 6 FVCEICNKGFQRDQNLQLHRRGHNLPWKLRQRTTTEVRKRVYICPEPSCVHHNPARALGD 65
+ C C K F + NLQ H+R H ++ Y CPE
Sbjct: 5 YKCPECGKSFSQSSNLQKHQRTH-------------TGEKPYKCPE-------------- 37
Query: 66 LTGIKKHFSRKHGEXXXXXXXXXXXYAVQSDWKAHQKT-CGTREYKC-DCGTIFSRRDSF 123
++ SD + HQ+T G + YKC +CG FSR D
Sbjct: 38 ---------------------CGKSFSQSSDLQKHQRTHTGEKPYKCPECGKSFSRSDHL 76
Query: 124 ITH 126
H
Sbjct: 77 SRH 79
>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 = 3.7, Method: Compositional matrix adjust.
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|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 = 4.1, Method: Compositional matrix adjust.
Identities = 8/17 (47%), Positives = 14/17 (82%)
Query: 111 CDCGTIFSRRDSFITHR 127
C+CG +FSR+D ++H+
Sbjct: 16 CECGKVFSRKDQLVSHQ 32
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
0.315 0.127 0.380
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,917,833
Number of Sequences: 62578
Number of extensions: 431891
Number of successful extensions: 1026
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 998
Number of HSP's gapped (non-prelim): 26
length of query: 510
length of database: 14,973,337
effective HSP length: 103
effective length of query: 407
effective length of database: 8,527,803
effective search space: 3470815821
effective search space used: 3470815821
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 bits)