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= psy11328
         (410 letters)

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

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



>pdb|1J22|A Chain A, Crystal Structure Of Archaeal XpfMUS81 HOMOLOG, HEF FROM
           PYROCOCCUS Furiosus, Nuclease Domain, Selenomet
           Derivative
 pdb|1J23|A Chain A, Crystal Structure Of Archaeal XpfMUS81 HOMOLOG, HEF FROM
           PYROCOCCUS Furiosus, Nuclease Domain
 pdb|1J24|A Chain A, Crystal Structure Of Archaeal XpfMUS81 HOMOLOG, HEF FROM
           PYROCOCCUS Furiosus, Nuclease Domain, Ca Cocrystal
 pdb|1J25|A Chain A, Crystal Structure Of Archaeal XpfMUS81 HOMOLOG, HEF FROM
           PYROCOCCUS Furiosus, Nuclease Domain, Mn Cocrystal
          Length = 143

 Score = 73.2 bits (178), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 52/160 (32%), Positives = 81/160 (50%), Gaps = 39/160 (24%)

Query: 99  RVIVDMREFRSELPVLLHKRGLYIEPVTISVGDYILSPDICVERKSISDLIGSLQSGRLY 158
           +V+VD RE RSE+   L   G+ +E  T+ VGDYI+S D+ +ERKS +DLI S+  G L+
Sbjct: 6   KVVVDSRELRSEVVKRLKLLGVKLEVKTLDVGDYIISEDVAIERKSANDLIQSIIDGGLF 65

Query: 159 TQVQQMCRHYAKPLLLIEFDHNKPFELQGNYYLSRDIAAKFLIEFDHNKPFELQGNYYLS 218
            QV+++   Y++P++++E          G+ Y  R++            P  ++G     
Sbjct: 66  DQVKRLKEAYSRPIMIVE----------GSLYGIRNV-----------HPNAIRGA---- 100

Query: 219 RDIAAKSSDITAKLQLLTLHFPKLRLIWSSGPYNTAQLFF 258
             IAA + D            P   +I+SS P  TAQ  F
Sbjct: 101 --IAAVTVD---------FGVP---IIFSSTPEETAQYIF 126


>pdb|2BGW|A Chain A, Xpf From Aeropyrum Pernix, Complex With Dna
 pdb|2BGW|B Chain B, Xpf From Aeropyrum Pernix, Complex With Dna
          Length = 219

 Score = 65.9 bits (159), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 32/78 (41%), Positives = 48/78 (61%)

Query: 99  RVIVDMREFRSELPVLLHKRGLYIEPVTISVGDYILSPDICVERKSISDLIGSLQSGRLY 158
           RV VD+RE RS +P +L   G+ + P  + +GDY++S  I VERK+ SD   SL  GRL+
Sbjct: 10  RVYVDVREERSPVPSILESLGVQVIPKQLPMGDYLVSDSIIVERKTSSDFAKSLFDGRLF 69

Query: 159 TQVQQMCRHYAKPLLLIE 176
            Q  ++  HY    +++E
Sbjct: 70  EQASRLAEHYETVFIIVE 87


>pdb|2BHN|A Chain A, Xpf From Aeropyrum Pernix
 pdb|2BHN|B Chain B, Xpf From Aeropyrum Pernix
 pdb|2BHN|C Chain C, Xpf From Aeropyrum Pernix
 pdb|2BHN|D Chain D, Xpf From Aeropyrum Pernix
          Length = 214

 Score = 65.5 bits (158), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 32/78 (41%), Positives = 48/78 (61%)

Query: 99  RVIVDMREFRSELPVLLHKRGLYIEPVTISVGDYILSPDICVERKSISDLIGSLQSGRLY 158
           RV VD+RE RS +P +L   G+ + P  + +GDY++S  I VERK+ SD   SL  GRL+
Sbjct: 3   RVYVDVREERSPVPSILESLGVQVIPKQLPMGDYLVSDSIIVERKTSSDFAKSLFDGRLF 62

Query: 159 TQVQQMCRHYAKPLLLIE 176
            Q  ++  HY    +++E
Sbjct: 63  EQASRLAEHYETVFIIVE 80


>pdb|4AFL|A Chain A, The Crystal Structure Of The Ing4 Dimerization Domain
           Reveals The Functional Organization Of The Ing Family Of
           Chromatin Binding Proteins.
 pdb|4AFL|B Chain B, The Crystal Structure Of The Ing4 Dimerization Domain
           Reveals The Functional Organization Of The Ing Family Of
           Chromatin Binding Proteins.
 pdb|4AFL|C Chain C, The Crystal Structure Of The Ing4 Dimerization Domain
           Reveals The Functional Organization Of The Ing Family Of
           Chromatin Binding Proteins.
 pdb|4AFL|D Chain D, The Crystal Structure Of The Ing4 Dimerization Domain
           Reveals The Functional Organization Of The Ing Family Of
           Chromatin Binding Proteins.
 pdb|4AFL|E Chain E, The Crystal Structure Of The Ing4 Dimerization Domain
           Reveals The Functional Organization Of The Ing Family Of
           Chromatin Binding Proteins.
 pdb|4AFL|F Chain F, The Crystal Structure Of The Ing4 Dimerization Domain
           Reveals The Functional Organization Of The Ing Family Of
           Chromatin Binding Proteins
          Length = 104

 Score = 32.0 bits (71), Expect = 0.70,   Method: Compositional matrix adjust.
 Identities = 13/34 (38%), Positives = 21/34 (61%)

Query: 206 NKPFELQGNYYLSRDIAAKSSDITAKLQLLTLHF 239
           N PFELQ N+ L RD+  ++ D+ A++  L   +
Sbjct: 15  NLPFELQRNFQLXRDLDQRTEDLKAEIDKLATEY 48


>pdb|1KOH|A Chain A, The Crystal Structure And Mutational Analysis Of A Novel
           Rna-Binding Domain Found In The Human Tap Nuclear Mrna
           Export Factor
 pdb|1KOH|B Chain B, The Crystal Structure And Mutational Analysis Of A Novel
           Rna-Binding Domain Found In The Human Tap Nuclear Mrna
           Export Factor
 pdb|1KOH|C Chain C, The Crystal Structure And Mutational Analysis Of A Novel
           Rna-Binding Domain Found In The Human Tap Nuclear Mrna
           Export Factor
 pdb|1KOH|D Chain D, The Crystal Structure And Mutational Analysis Of A Novel
           Rna-Binding Domain Found In The Human Tap Nuclear Mrna
           Export Factor
          Length = 277

 Score = 28.1 bits (61), Expect = 9.4,   Method: Compositional matrix adjust.
 Identities = 14/44 (31%), Positives = 24/44 (54%)

Query: 354 PRVTSKNKAAVLNRGSSLPALCKLSEQELCSLVENTTLGNALYK 397
           P + ++N   VLNR SS+ A  ++ E+ +  L+      N LY+
Sbjct: 141 PDLVAQNIDVVLNRRSSMAATLRIIEENIPELLSLNLSNNRLYR 184


>pdb|2ZIU|A Chain A, Crystal Structure Of The Mus81-Eme1 Complex
 pdb|2ZIV|A Chain A, Crystal Structure Of The Mus81-Eme1 Complex
          Length = 311

 Score = 28.1 bits (61), Expect = 9.5,   Method: Compositional matrix adjust.
 Identities = 16/41 (39%), Positives = 23/41 (56%), Gaps = 1/41 (2%)

Query: 137 DICVERKSISDLIGSLQSGRLYTQVQQMCR-HYAKPLLLIE 176
           D  +ERK + DL GS+  GR   Q  ++ R    KP+ L+E
Sbjct: 87  DYIIERKRMDDLCGSIIDGRFREQKFRLKRCGLRKPIYLVE 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
   0.317    0.133    0.381 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,526,410
Number of Sequences: 62578
Number of extensions: 455266
Number of successful extensions: 1024
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1016
Number of HSP's gapped (non-prelim): 10
length of query: 410
length of database: 14,973,337
effective HSP length: 101
effective length of query: 309
effective length of database: 8,652,959
effective search space: 2673764331
effective search space used: 2673764331
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)