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= 030824
         (171 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|1WFP|A Chain A, Solution Structure Of The Zf-an1 Domain From Arabiopsis
           Thaliana F5o11.17 Protein
          Length = 74

 Score = 82.0 bits (201), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 35/47 (74%), Positives = 39/47 (82%)

Query: 103 EPQAKGPTRCLSCNKKVGLTGFKCKCGSTFCGIHRYPEKHDCTFDFK 149
           +P     TRCLSCNKKVG+TGFKC+CGSTFCG HRYPE H+C FDFK
Sbjct: 19  DPPKSTATRCLSCNKKVGVTGFKCRCGSTFCGTHRYPESHECQFDFK 65


>pdb|1WG2|A Chain A, Solution Structure Of Zf-An1 Domain From Arabidopsis
           Thaliana
          Length = 64

 Score = 79.3 bits (194), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 34/43 (79%), Positives = 37/43 (86%)

Query: 110 TRCLSCNKKVGLTGFKCKCGSTFCGIHRYPEKHDCTFDFKVTG 152
            RC SCNKKVG+ GFKCKCGSTFCG HRYPEKH+C+FDFK  G
Sbjct: 16  NRCFSCNKKVGVMGFKCKCGSTFCGSHRYPEKHECSFDFKEVG 58


>pdb|1WFH|A Chain A, Solution Structrue Of The Zf-An1 Domain From Arabidopsis
           Thaliana At2g36320 Protein
          Length = 64

 Score = 73.2 bits (178), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 31/44 (70%), Positives = 34/44 (77%)

Query: 109 PTRCLSCNKKVGLTGFKCKCGSTFCGIHRYPEKHDCTFDFKVTG 152
           P RC  C K+VGLTGF C+CG+TFCG HRYPE H CTFDFK  G
Sbjct: 15  PNRCTVCRKRVGLTGFMCRCGTTFCGSHRYPEVHGCTFDFKSAG 58


>pdb|1WFL|A Chain A, Solution Structure Of The Zf-An1 Domain From Mouse Zinc
           Finger Protein 216
          Length = 74

 Score = 67.0 bits (162), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 28/51 (54%), Positives = 37/51 (72%), Gaps = 3/51 (5%)

Query: 100 EQPEPQAKGPTRCLSCNKKVGLTGFKCKCGSTFCGIHRYPEKHDCTFDFKV 150
           E P+P+     RC  C KKVGLTGF C+CG+ FCG+HRY +KH+C +D+K 
Sbjct: 19  ELPKPKK---NRCFMCRKKVGLTGFDCRCGNLFCGLHRYSDKHNCPYDYKA 66


>pdb|1WFF|A Chain A, Solution Structure Of The Zf-An1 Domain From Mouse Riken
           Cdna 2810002d23 Protein
          Length = 85

 Score = 63.2 bits (152), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 27/53 (50%), Positives = 33/53 (62%), Gaps = 1/53 (1%)

Query: 111 RCLSCNKKVGL-TGFKCKCGSTFCGIHRYPEKHDCTFDFKVTGRDAIARANPV 162
            C  C KK GL T F+C+CG+ FC  HRY E H C +D+K  GR  +  ANPV
Sbjct: 27  HCFLCGKKTGLATSFECRCGNNFCASHRYAEAHGCNYDYKSAGRRYLEEANPV 79


>pdb|1X4W|A Chain A, Solution Structure Of The Zf-An1 Domain From Human
           Hypothetical Protein Flj13222
          Length = 67

 Score = 46.2 bits (108), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 22/49 (44%), Positives = 27/49 (55%), Gaps = 3/49 (6%)

Query: 107 KGPTRCLSCNKKVGLTGFK---CKCGSTFCGIHRYPEKHDCTFDFKVTG 152
           K   RC  C  K+ L   +   C+CG  FC +HR PE+HDCTFD    G
Sbjct: 13  KSRRRCFQCQTKLELVQQELGSCRCGYVFCMLHRLPEQHDCTFDHMGRG 61


>pdb|2KZY|A Chain A, Solution Nmr Structure Of The Znf216 A20 Zinc Finger
 pdb|2L00|A Chain A, Solution Structure Of The Non-Covalent Complex Of The
          Znf216 A20 Domain With Ubiquitin
          Length = 62

 Score = 36.2 bits (82), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 13 TSEPKLCVNGCAFFGTAANMGLCSKCYRDLRVKEDQAASAKAAMEKSLNLKSP 65
          T  P LC  GC F+G     G+CS CY++  ++  Q +   + M  +    SP
Sbjct: 10 TPGPMLCSTGCGFYGNPRTNGMCSVCYKE-HLQRQQNSGRMSPMGTASGSNSP 61


>pdb|2C7M|A Chain A, Human Rabex-5 Residues 1-74 In Complex With Ubiquitin
 pdb|2C7N|A Chain A, Human Rabex-5 Residues 1-74 In Complex With Ubiquitin
 pdb|2C7N|C Chain C, Human Rabex-5 Residues 1-74 In Complex With Ubiquitin
 pdb|2C7N|E Chain E, Human Rabex-5 Residues 1-74 In Complex With Ubiquitin
 pdb|2C7N|G Chain G, Human Rabex-5 Residues 1-74 In Complex With Ubiquitin
 pdb|2C7N|I Chain I, Human Rabex-5 Residues 1-74 In Complex With Ubiquitin
 pdb|2C7N|K Chain K, Human Rabex-5 Residues 1-74 In Complex With Ubiquitin
          Length = 74

 Score = 35.8 bits (81), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 12/24 (50%), Positives = 16/24 (66%)

Query: 18 LCVNGCAFFGTAANMGLCSKCYRD 41
          LC  GC ++G  A  G CSKC+R+
Sbjct: 18 LCKKGCGYYGNPAWQGFCSKCWRE 41


>pdb|2FID|B Chain B, Crystal Structure Of A Bovine Rabex-5 Fragment Complexed
          With Ubiquitin
 pdb|2FIF|B Chain B, Crystal Structure Of A Bovine Rabex-5 Fragment Complexed
          With Ubiquitin
 pdb|2FIF|D Chain D, Crystal Structure Of A Bovine Rabex-5 Fragment Complexed
          With Ubiquitin
 pdb|2FIF|F Chain F, Crystal Structure Of A Bovine Rabex-5 Fragment Complexed
          With Ubiquitin
          Length = 70

 Score = 35.4 bits (80), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 12/24 (50%), Positives = 16/24 (66%)

Query: 18 LCVNGCAFFGTAANMGLCSKCYRD 41
          LC  GC ++G  A  G CSKC+R+
Sbjct: 15 LCKKGCGYYGNPAWQGFCSKCWRE 38


>pdb|3OJ3|I Chain I, Crystal Structure Of The A20 Znf4 And Ubiquitin Complex
 pdb|3OJ3|J Chain J, Crystal Structure Of The A20 Znf4 And Ubiquitin Complex
 pdb|3OJ3|K Chain K, Crystal Structure Of The A20 Znf4 And Ubiquitin Complex
 pdb|3OJ3|L Chain L, Crystal Structure Of The A20 Znf4 And Ubiquitin Complex
 pdb|3OJ3|M Chain M, Crystal Structure Of The A20 Znf4 And Ubiquitin Complex
 pdb|3OJ3|N Chain N, Crystal Structure Of The A20 Znf4 And Ubiquitin Complex
 pdb|3OJ3|O Chain O, Crystal Structure Of The A20 Znf4 And Ubiquitin Complex
 pdb|3OJ3|P Chain P, Crystal Structure Of The A20 Znf4 And Ubiquitin Complex
 pdb|3OJ4|C Chain C, Crystal Structure Of The A20 Znf4, Ubiquitin And Ubch5a
          Complex
 pdb|3OJ4|F Chain F, Crystal Structure Of The A20 Znf4, Ubiquitin And Ubch5a
          Complex
          Length = 49

 Score = 28.9 bits (63), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 10/22 (45%), Positives = 14/22 (63%)

Query: 22 GCAFFGTAANMGLCSKCYRDLR 43
          GC +FGT  N G C+ C+ + R
Sbjct: 25 GCVYFGTPENKGFCTLCFIEYR 46


>pdb|2EQE|A Chain A, Solution Structure Of The Fourth A20-Type Zinc Finger
          Domain From Human Tumor Necrosis Factor, Alpha-Induced
          Protein3
          Length = 48

 Score = 26.6 bits (57), Expect = 7.7,   Method: Compositional matrix adjust.
 Identities = 9/18 (50%), Positives = 12/18 (66%)

Query: 22 GCAFFGTAANMGLCSKCY 39
          GC +FGT  N G C+ C+
Sbjct: 22 GCVYFGTPENKGFCTLCF 39


  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    0.131    0.402 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,733,673
Number of Sequences: 62578
Number of extensions: 164687
Number of successful extensions: 248
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 235
Number of HSP's gapped (non-prelim): 13
length of query: 171
length of database: 14,973,337
effective HSP length: 92
effective length of query: 79
effective length of database: 9,216,161
effective search space: 728076719
effective search space used: 728076719
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: 48 (23.1 bits)