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= 034697
         (86 letters)

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

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



>pdb|2CJJ|A Chain A, Crystal Structure Of The Myb Domain Of The Rad
          Transcription Factor From Antirrhinum Majus
          Length = 93

 Score = 98.6 bits (244), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 45/66 (68%), Positives = 54/66 (81%)

Query: 18 VKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGRYPHPN 77
           K+NK FE ALA YDKDTPDRW NVA+AV G+T E+VKKHYE+LV+DI  IE+G+ P PN
Sbjct: 13 AKENKAFERALAVYDKDTPDRWANVARAVEGRTPEEVKKHYEILVEDIKYIESGKVPFPN 72

Query: 78 YRSTTG 83
          YR+T G
Sbjct: 73 YRTTGG 78


>pdb|4EEF|G Chain G, Crystal Structure Of The Designed Inhibitor Protein
          F-Hb80.4 In Complex With The 1918 Influenza Virus
          Hemagglutinin.
 pdb|4EEF|H Chain H, Crystal Structure Of The Designed Inhibitor Protein
          F-Hb80.4 In Complex With The 1918 Influenza Virus
          Hemagglutinin.
 pdb|4EEF|I Chain I, Crystal Structure Of The Designed Inhibitor Protein
          F-Hb80.4 In Complex With The 1918 Influenza Virus
          Hemagglutinin
          Length = 74

 Score = 57.0 bits (136), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 26/41 (63%), Positives = 32/41 (78%)

Query: 20 QNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYEL 60
          +N  FE AL+F +KDTPDRW  VA+ V G+T E+VKKHYEL
Sbjct: 27 ENIAFEIALSFTNKDTPDRWKKVAQYVKGRTPEEVKKHYEL 67


>pdb|2M2E|A Chain A, Solution Nmr Structure Of The Sant Domain Of Human
          Dnajc2, Northeast Structural Genomics Consortium Target
          Hr8254a
          Length = 73

 Score = 43.1 bits (100), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 20/53 (37%), Positives = 32/53 (60%)

Query: 20 QNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAGR 72
          + K  E AL  Y  +TP+RW  +A+AV G+T +D  K Y+ LV+ +   +A +
Sbjct: 10 EQKLLEQALKTYPVNTPERWKKIAEAVPGRTKKDCMKRYKELVEMVKAKKAAQ 62


>pdb|2CQR|A Chain A, Solution Structure Of Rsgi Ruh-043, A Myb Dna-Binding
          Domain In Human Cdna
          Length = 73

 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 18/43 (41%), Positives = 24/43 (55%)

Query: 20 QNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLV 62
          Q K  E AL  Y + + D WD +A+ V  K+ ED    Y+LLV
Sbjct: 25 QQKLLELALQQYPRGSSDCWDKIARCVPSKSKEDCIARYKLLV 67


>pdb|1N8Y|C Chain C, Crystal Structure Of The Extracellular Region Of Rat Her2
          Length = 608

 Score = 27.3 bits (59), Expect = 2.3,   Method: Composition-based stats.
 Identities = 17/54 (31%), Positives = 27/54 (50%), Gaps = 3/54 (5%)

Query: 18  VKQNKQFETALAFYDKDTPDRWDNVAKAVSGKTVEDVKKHYELLVKDINDIEAG 71
           V+  + FE   A    D  D  DNVA +  G+T E ++   EL ++ + +I  G
Sbjct: 80  VRGTQLFEDKYALAVLDNRDPQDNVAASTPGRTPEGLR---ELQLRSLTEILKG 130


>pdb|3EI4|B Chain B, Structure Of The Hsddb1-Hsddb2 Complex
 pdb|3EI4|D Chain D, Structure Of The Hsddb1-Hsddb2 Complex
 pdb|3EI4|F Chain F, Structure Of The Hsddb1-Hsddb2 Complex
          Length = 436

 Score = 26.6 bits (57), Expect = 3.7,   Method: Composition-based stats.
 Identities = 10/17 (58%), Positives = 12/17 (70%)

Query: 66  NDIEAGRYPHPNYRSTT 82
           N I  GRYP PN++S T
Sbjct: 358 NLIVVGRYPDPNFKSCT 374


>pdb|4E54|B Chain B, Damaged Dna Induced Uv-Damaged Dna-Binding Protein
           (Uv-Ddb) Dimerization And Its Roles In Chromatinized Dna
           Repair
          Length = 435

 Score = 26.6 bits (57), Expect = 3.7,   Method: Composition-based stats.
 Identities = 10/17 (58%), Positives = 12/17 (70%)

Query: 66  NDIEAGRYPHPNYRSTT 82
           N I  GRYP PN++S T
Sbjct: 357 NLIVVGRYPDPNFKSCT 373


>pdb|4E5Z|B Chain B, Damaged Dna Induced Uv-Damaged Dna-Binding Protein
           (Uv-Ddb) Dimerization And Its Roles In Chromatinized Dna
           Repair
          Length = 436

 Score = 26.6 bits (57), Expect = 3.9,   Method: Composition-based stats.
 Identities = 10/17 (58%), Positives = 12/17 (70%)

Query: 66  NDIEAGRYPHPNYRSTT 82
           N I  GRYP PN++S T
Sbjct: 357 NLIVVGRYPDPNFKSCT 373


  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
   0.312    0.130    0.382 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,373,353
Number of Sequences: 62578
Number of extensions: 81029
Number of successful extensions: 213
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 202
Number of HSP's gapped (non-prelim): 14
length of query: 86
length of database: 14,973,337
effective HSP length: 54
effective length of query: 32
effective length of database: 11,594,125
effective search space: 371012000
effective search space used: 371012000
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 45 (21.9 bits)