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= psy2180
         (129 letters)

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

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



>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 = 84.3 bits (207), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 37/41 (90%), Positives = 40/41 (97%)

Query: 15 HSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRT 55
          HSG+NQLGGV+VNGRPLPDSTRQ+IVELAHSGARPCDISR 
Sbjct: 2  HSGVNQLGGVFVNGRPLPDSTRQRIVELAHSGARPCDISRI 42


>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 = 79.3 bits (194), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 34/44 (77%), Positives = 37/44 (84%)

Query: 11 SAAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR 54
          S  GH G+NQLGGV+VNGRPLPD  RQ+IVELAH G RPCDISR
Sbjct: 13 SRTGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHQGVRPCDISR 56


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

 Score = 72.8 bits (177), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 30/42 (71%), Positives = 36/42 (85%)

Query: 13 AGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR 54
          +GH G+NQLGG +VNGRPLP+  RQ+IV+LAH G RPCDISR
Sbjct: 8  SGHGGLNQLGGAFVNGRPLPEVVRQRIVDLAHQGVRPCDISR 49


>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 = 60.5 bits (145), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 26/41 (63%), Positives = 32/41 (78%)

Query: 14 GHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISR 54
          G   +NQLGGV++NGRPLP++ R KIVE+A  G RPC ISR
Sbjct: 1  GQGRVNQLGGVFINGRPLPNNIRLKIVEMAADGIRPCVISR 41


>pdb|1UEP|A Chain A, Solution Structure Of The Third Pdz Domain Of Human
           Atrophin-1 Interacting Protein 1 (Kiaa0705 Protein)
          Length = 103

 Score = 30.0 bits (66), Expect = 0.31,   Method: Compositional matrix adjust.
 Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 3/46 (6%)

Query: 24  VYVNGRPLPDSTRQKIVELAHSGARPCDISRTCSAVRRPATRGSTS 69
           VYV+G P+   T + +++L H  AR   ++ T   VRR    G +S
Sbjct: 60  VYVDGIPVAGKTHRYVIDLMHHAARNGQVNLT---VRRKVLSGPSS 102


>pdb|3V65|B Chain B, Crystal Structure Of Agrin And Lrp4 Complex
 pdb|3V65|D Chain D, Crystal Structure Of Agrin And Lrp4 Complex
          Length = 386

 Score = 25.8 bits (55), Expect = 5.9,   Method: Compositional matrix adjust.
 Identities = 22/68 (32%), Positives = 29/68 (42%), Gaps = 9/68 (13%)

Query: 44  HSGARPCDISRTCSAVRRPATRGSTSWAAFTSTG-------APYRTQRDRRSWNWRTLAR 96
           H+G R  +  RTC  V   A  G  S     S G       A Y  + DRRS   + L  
Sbjct: 29  HTGYRLTEDGRTCQDVNECAEEGYCSQGCTNSEGAFQCWCEAGYELRPDRRS--CKALGP 86

Query: 97  DPVISRAS 104
           +PV+  A+
Sbjct: 87  EPVLLFAN 94


>pdb|2W1V|A Chain A, Crystal Structure Of Mouse Nitrilase-2 At 1.4a
          Resolution
 pdb|2W1V|B Chain B, Crystal Structure Of Mouse Nitrilase-2 At 1.4a
          Resolution
          Length = 276

 Score = 25.4 bits (54), Expect = 8.2,   Method: Compositional matrix adjust.
 Identities = 13/47 (27%), Positives = 24/47 (51%)

Query: 36 RQKIVELAHSGARPCDISRTCSAVRRPATRGSTSWAAFTSTGAPYRT 82
          R  +++L  S  +  +++R CS VR  A +G+   +      +PY T
Sbjct: 5  RLALIQLQVSSIKSDNLTRACSLVREAAKQGANIVSLPECFNSPYGT 51


  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    0.129    0.408 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,761,426
Number of Sequences: 62578
Number of extensions: 136452
Number of successful extensions: 294
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 288
Number of HSP's gapped (non-prelim): 8
length of query: 129
length of database: 14,973,337
effective HSP length: 88
effective length of query: 41
effective length of database: 9,466,473
effective search space: 388125393
effective search space used: 388125393
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)