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= 033983
         (106 letters)

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

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



>pdb|1PCF|A Chain A, Human Transcriptional Coactivator Pc4 C-Terminal Domain
 pdb|1PCF|B Chain B, Human Transcriptional Coactivator Pc4 C-Terminal Domain
 pdb|1PCF|C Chain C, Human Transcriptional Coactivator Pc4 C-Terminal Domain
 pdb|1PCF|D Chain D, Human Transcriptional Coactivator Pc4 C-Terminal Domain
 pdb|1PCF|E Chain E, Human Transcriptional Coactivator Pc4 C-Terminal Domain
 pdb|1PCF|F Chain F, Human Transcriptional Coactivator Pc4 C-Terminal Domain
 pdb|1PCF|G Chain G, Human Transcriptional Coactivator Pc4 C-Terminal Domain
 pdb|1PCF|H Chain H, Human Transcriptional Coactivator Pc4 C-Terminal Domain
 pdb|2C62|A Chain A, Crystal Structure Of The Human Transcription Cofactor Pc4
           In Complex With Single-Stranded Dna
 pdb|2C62|B Chain B, Crystal Structure Of The Human Transcription Cofactor Pc4
           In Complex With Single-Stranded Dna
 pdb|2PHE|A Chain A, Model For Vp16 Binding To Pc4
 pdb|2PHE|B Chain B, Model For Vp16 Binding To Pc4
          Length = 66

 Score = 59.3 bits (142), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 28/62 (45%), Positives = 48/62 (77%), Gaps = 1/62 (1%)

Query: 42  VCEISKNRRVSVRNWQGKVWVDIREFYV-KEGKKFPGKKGISLSVDQWNTLRDHVEEINK 100
           + +I K R VSVR+++GKV +DIRE+++  EG+  PG+KGISL+ +QW+ L++ + +I+ 
Sbjct: 2   MFQIGKMRYVSVRDFKGKVLIDIREYWMDPEGEMKPGRKGISLNPEQWSQLKEQISDIDD 61

Query: 101 AL 102
           A+
Sbjct: 62  AV 63


>pdb|4AGH|A Chain A, Structural Features Of Ssdna Binding Protein Mosub1 From
           Magnaporthe Oryzae
          Length = 158

 Score = 52.8 bits (125), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 36/104 (34%), Positives = 50/104 (48%), Gaps = 7/104 (6%)

Query: 6   KRKEEEEYDSDGSVDGHAP-PKKASKTXXXXXXXXIVVCE------ISKNRRVSVRNWQG 58
           KR  +EE  S GS     P P K +K+         V  E      IS  RRV +  ++ 
Sbjct: 5   KRARDEEAQSGGSEAETKPAPVKKAKSKASNPGGSQVDAEGNPFWEISDKRRVGISQFKK 64

Query: 59  KVWVDIREFYVKEGKKFPGKKGISLSVDQWNTLRDHVEEINKAL 102
             +++IRE+Y   G+  PGKKGI L+VDQ+      +  IN  L
Sbjct: 65  MDFINIREYYEAGGEMKPGKKGIGLTVDQYTAFLKAIPAINAEL 108


>pdb|3OMW|A Chain A, Crystal Structure Of Ssu72, An Essential Eukaryotic
          Phosphatase Specific For The C-Terminal Domain Of Rna
          Polymerase Ii
 pdb|3OMW|B Chain B, Crystal Structure Of Ssu72, An Essential Eukaryotic
          Phosphatase Specific For The C-Terminal Domain Of Rna
          Polymerase Ii
 pdb|3OMW|C Chain C, Crystal Structure Of Ssu72, An Essential Eukaryotic
          Phosphatase Specific For The C-Terminal Domain Of Rna
          Polymerase Ii
 pdb|3OMW|D Chain D, Crystal Structure Of Ssu72, An Essential Eukaryotic
          Phosphatase Specific For The C-Terminal Domain Of Rna
          Polymerase Ii
 pdb|3OMX|A Chain A, Crystal Structure Of Ssu72 With Vanadate Complex
 pdb|3OMX|B Chain B, Crystal Structure Of Ssu72 With Vanadate Complex
 pdb|3OMX|C Chain C, Crystal Structure Of Ssu72 With Vanadate Complex
 pdb|3OMX|D Chain D, Crystal Structure Of Ssu72 With Vanadate Complex
          Length = 190

 Score = 25.4 bits (54), Expect = 7.4,   Method: Compositional matrix adjust.
 Identities = 12/37 (32%), Positives = 18/37 (48%)

Query: 41 VVCEISKNRRVSVRNWQGKVWVDIREFYVKEGKKFPG 77
          VVC  + NR +   N+  K   ++R +   E  K PG
Sbjct: 6  VVCSSNMNRSMEAHNFLAKKGFNVRSYGTGERVKLPG 42


  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
   0.310    0.131    0.389 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,267,257
Number of Sequences: 62578
Number of extensions: 102094
Number of successful extensions: 169
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 164
Number of HSP's gapped (non-prelim): 4
length of query: 106
length of database: 14,973,337
effective HSP length: 71
effective length of query: 35
effective length of database: 10,530,299
effective search space: 368560465
effective search space used: 368560465
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 45 (21.9 bits)