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= psy15598
         (258 letters)

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

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



>pdb|1K78|A Chain A, Pax5(1-149)+ets-1(331-440)+dna
 pdb|1K78|E Chain E, Pax5(1-149)+ets-1(331-440)+dna
 pdb|1K78|I Chain I, Pax5(1-149)+ets-1(331-440)+dna
 pdb|1MDM|A Chain A, Inhibited Fragment Of Ets-1 And Paired Domain Of Pax5
           Bound To Dna
          Length = 149

 Score =  195 bits (495), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 94/127 (74%), Positives = 108/127 (85%)

Query: 32  YGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETG 91
           +G VNQLGGVFVNGRPLP+ VR RIVELA  G+RPCDISRQLRVSHGCVSKIL RY+ETG
Sbjct: 17  HGGVNQLGGVFVNGRPLPDVVRQRIVELAHQGVRPCDISRQLRVSHGCVSKILGRYYETG 76

Query: 92  SILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSIS 151
           SI PG IGGSKP+V TPKVV  I E K+++P +FAWEIRDRLL++ VCD   VPSVSSI+
Sbjct: 77  SIKPGVIGGSKPKVATPKVVEKIAEYKRQNPTMFAWEIRDRLLAERVCDNDTVPSVSSIN 136

Query: 152 RILRNKI 158
           RI+R K+
Sbjct: 137 RIIRTKV 143


>pdb|2K27|A Chain A, Solution Structure Of Human Pax8 Paired Box Domain
          Length = 159

 Score =  191 bits (485), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 91/127 (71%), Positives = 107/127 (84%)

Query: 32  YGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETG 91
           +G +NQLGG FVNGRPLP  VR RIV+LA  G+RPCDISRQLRVSHGCVSKIL RY+ETG
Sbjct: 10  HGGLNQLGGAFVNGRPLPEVVRQRIVDLAHQGVRPCDISRQLRVSHGCVSKILGRYYETG 69

Query: 92  SILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSIS 151
           SI PG IGGSKP+V TPKVV  I + K+++P +FAWEIRDRLL++GVCD   VPSVSSI+
Sbjct: 70  SIRPGVIGGSKPKVATPKVVEKIGDYKRQNPTMFAWEIRDRLLAEGVCDNDTVPSVSSIN 129

Query: 152 RILRNKI 158
           RI+R K+
Sbjct: 130 RIIRTKV 136


>pdb|6PAX|A Chain A, Crystal Structure Of The Human Pax-6 Paired Domain-Dna
           Complex Reveals A General Model For Pax Protein-Dna
           Interactions
          Length = 133

 Score =  186 bits (471), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 92/122 (75%), Positives = 103/122 (84%)

Query: 35  VNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSIL 94
           VNQLGGVFVNGRPLP+S R RIVELA  G RPCDISR L+VS+GCVSKIL RY+ TGSI 
Sbjct: 5   VNQLGGVFVNGRPLPDSTRQRIVELAHSGARPCDISRILQVSNGCVSKILGRYYATGSIR 64

Query: 95  PGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRIL 154
           P AIGGSKPRV TP+VVS I + KQ+ P IFAWEIRDRLLS+GVC   N+PSVSSI+R+L
Sbjct: 65  PRAIGGSKPRVATPEVVSKIAQYKQECPSIFAWEIRDRLLSEGVCTNDNIPSVSSINRVL 124

Query: 155 RN 156
           RN
Sbjct: 125 RN 126


>pdb|1PDN|C Chain C, Crystal Structure Of A Paired Domain-Dna Complex At 2.5
           Angstroms Resolution Reveals Structural Basis For Pax
           Developmental Mutations
          Length = 128

 Score =  183 bits (464), Expect = 8e-47,   Method: Compositional matrix adjust.
 Identities = 83/125 (66%), Positives = 106/125 (84%)

Query: 33  GEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGS 92
           G VNQLGGVF+NGRPLPN++R++IVE+A  GIRPC ISRQLRVSHGCVSKIL RY ETGS
Sbjct: 3   GRVNQLGGVFINGRPLPNNIRLKIVEMAADGIRPCVISRQLRVSHGCVSKILNRYQETGS 62

Query: 93  ILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISR 152
           I PG IGGSKPR+ TP++ + I+E K+  PG+F+WEIR++L+ +GVCD+   PSVS+ISR
Sbjct: 63  IRPGVIGGSKPRIATPEIENRIEEYKRSSPGMFSWEIREKLIREGVCDRSTAPSVSAISR 122

Query: 153 ILRNK 157
           ++R +
Sbjct: 123 LVRGR 127


  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
   0.318    0.135    0.425 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,948,946
Number of Sequences: 62578
Number of extensions: 329992
Number of successful extensions: 4201
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 4180
Number of HSP's gapped (non-prelim): 41
length of query: 258
length of database: 14,973,337
effective HSP length: 97
effective length of query: 161
effective length of database: 8,903,271
effective search space: 1433426631
effective search space used: 1433426631
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: 50 (23.9 bits)