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= 043322
(187 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2L1O|A Chain A, Zinc To Cadmium Replacement In The A. Thaliana Superman
Cys2his2 Zinc Finger Induces Structural Rearrangements
Of Typical Dna Base Determinant Positions
pdb|1NJQ|A Chain A, Nmr Structure Of The Single Qalggh Zinc Finger Domain
From Arabidopsis Thaliana Superman Protein
Length = 39
Score = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 14/25 (56%), Positives = 20/25 (80%)
Query: 60 KVFSCNFCMRKFFSSQALGGHQNAH 84
+ ++C+FC R+F S+QALGGH N H
Sbjct: 5 RSYTCSFCKREFRSAQALGGHMNVH 29
>pdb|2EN9|A Chain A, Solution Structure Of The C2h2 Type Zinc Finger (Region
415- 447) Of Human Zinc Finger Protein 28 Homolog
Length = 46
Score = 28.9 bits (63), Expect = 1.8, Method: Composition-based stats.
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 60 KVFSCNFCMRKFFSSQALGGHQNAHKRER 88
K+F CN C + F S +L HQ H E+
Sbjct: 11 KLFKCNECKKTFTQSSSLTVHQRIHTGEK 39
>pdb|1ZNF|A Chain A, Three-Dimensional Solution Structure Of A Single Zinc
Finger Dna-Binding Domain
Length = 27
Score = 28.1 bits (61), Expect = 2.7, Method: Composition-based stats.
Identities = 10/24 (41%), Positives = 11/24 (45%)
Query: 62 FSCNFCMRKFFSSQALGGHQNAHK 85
+ C C R F AL HQ HK
Sbjct: 2 YKCGLCERSFVEKSALSRHQRVHK 25
>pdb|2ELS|A Chain A, Solution Structure Of The 2nd C2h2 Zinc Finger Of Human
Zinc Finger Protein 406
Length = 36
Score = 27.7 bits (60), Expect = 3.4, Method: Composition-based stats.
Identities = 9/32 (28%), Positives = 17/32 (53%)
Query: 57 TTAKVFSCNFCMRKFFSSQALGGHQNAHKRER 88
++ K+F+C +C + F +L H H E+
Sbjct: 5 SSGKIFTCEYCNKVFKFKHSLQAHLRIHTNEK 36
>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 = 27.7 bits (60), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 22/55 (40%)
Query: 57 TTAKVFSCNFCMRKFFSSQALGGHQNAHKRERGAAKRYQSQRMMTMMGLPVHTNM 111
T K F C CMR F +L H H E+ A ++ T+ HT +
Sbjct: 30 TGQKPFQCRICMRNFSQQASLNAHIRTHTGEKPFACDICGRKFATLHTRTRHTKI 84
>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 = 27.3 bits (59), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 35/87 (40%), Gaps = 10/87 (11%)
Query: 60 KVFSCNFCMRKFFSSQALGGHQNAHKRE---------RGAAKRYQSQRMMTMMG-LPVHT 109
K F C CMR F S L H H E R A+ + +R + LP+
Sbjct: 2 KPFQCRICMRNFSRSDHLTTHIRTHTGEKPFACDICGRKFARSDERKRHRDIQHILPILE 61
Query: 110 NMVRSLGVRAHSLVHKPSRDGAGVGAR 136
+ V L + + L ++ +R VG R
Sbjct: 62 DKVEELLSKNYHLENEVARLKKLVGER 88
>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 = 27.3 bits (59), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 15/31 (48%)
Query: 58 TAKVFSCNFCMRKFFSSQALGGHQNAHKRER 88
T K F C FC R F S L H+ H ER
Sbjct: 14 TKKEFICKFCGRHFTKSYNLLIHERTHTDER 44
>pdb|2LV2|A Chain A, Solution Nmr Structure Of C2h2-Type Zinc-Fingers 4 And 5
From Human Insulinoma-Associated Protein 1 (Fragment
424-497), Northeast Structural Genomics Consortium
Target Hr7614b
Length = 85
Score = 26.6 bits (57), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 58 TAKVFSCNFCMRKFFSSQALGGHQN 82
A+VF C +C F+SS L H N
Sbjct: 53 AAQVFPCKYCPATFYSSPGLTRHIN 77
>pdb|2EOY|A Chain A, Solution Structure Of The C2h2 Type Zinc Finger (Region
557- 589) Of Human Zinc Finger Protein 473
Length = 46
Score = 26.6 bits (57), Expect = 9.5, Method: Composition-based stats.
Identities = 11/27 (40%), Positives = 14/27 (51%)
Query: 60 KVFSCNFCMRKFFSSQALGGHQNAHKR 86
K F CN C + F S+ L H+ H R
Sbjct: 11 KCFKCNKCEKTFSCSKYLTQHERIHTR 37
>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 = 26.6 bits (57), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 12/28 (42%)
Query: 57 TTAKVFSCNFCMRKFFSSQALGGHQNAH 84
T K F C CMR F S L H H
Sbjct: 45 TGQKPFQCRICMRNFSRSDHLTTHIRTH 72
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
0.320 0.132 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,423,855
Number of Sequences: 62578
Number of extensions: 154573
Number of successful extensions: 355
Number of sequences better than 100.0: 29
Number of HSP's better than 100.0 without gapping: 28
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 314
Number of HSP's gapped (non-prelim): 42
length of query: 187
length of database: 14,973,337
effective HSP length: 93
effective length of query: 94
effective length of database: 9,153,583
effective search space: 860436802
effective search space used: 860436802
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)