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= 031251
         (163 letters)

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

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



>pdb|2A4H|A Chain A, Solution Structure Of Sep15 From Drosophila Melanogaster
          Length = 126

 Score = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 27/75 (36%), Positives = 44/75 (58%), Gaps = 1/75 (1%)

Query: 78  TYSGAILEACMRKLVFYPEIVGFIEEEKD-KFPTVRVQYVFNSPPKLIMLDEEGQHKETI 136
           TY+ AILE C  K   YP+I  FI+  +  KFP ++++YV    P + +LD  G+ +ET+
Sbjct: 19  TYAKAILEVCTCKFRAYPQIQAFIQSGRPAKFPNLQIKYVRGLDPVVKLLDASGKVQETL 78

Query: 137 RIDNWKREHMLQFLQ 151
            I  W  + + +F +
Sbjct: 79  SITKWNTDTVEEFFE 93


>pdb|2BA1|A Chain A, Archaeal Exosome Core
 pdb|2BA1|B Chain B, Archaeal Exosome Core
 pdb|2BA1|C Chain C, Archaeal Exosome Core
 pdb|3M7N|A Chain A, Archaeoglobus Fulgidus Exosome With Rna Bound To The
           Active Site
 pdb|3M7N|B Chain B, Archaeoglobus Fulgidus Exosome With Rna Bound To The
           Active Site
 pdb|3M7N|C Chain C, Archaeoglobus Fulgidus Exosome With Rna Bound To The
           Active Site
 pdb|3M85|A Chain A, Archaeoglobus Fulgidus Exosome Y70a With Rna Bound To The
           Active Site
 pdb|3M85|B Chain B, Archaeoglobus Fulgidus Exosome Y70a With Rna Bound To The
           Active Site
 pdb|3M85|C Chain C, Archaeoglobus Fulgidus Exosome Y70a With Rna Bound To The
           Active Site
          Length = 179

 Score = 32.3 bits (72), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 24/60 (40%), Positives = 35/60 (58%), Gaps = 8/60 (13%)

Query: 6   IYEAVLFIVIISAVAVTSKEQLSTRECEDLGFTGLALCSDCNTFAEYVKDQELVADCLKC 65
           I EAV ++ I+ A  +    +LST+E E++G    ALCS+C T  E V++     D LKC
Sbjct: 108 ISEAVGYLDILKARVIGDNLRLSTKE-EEMGVL-RALCSNCKT--EMVRE----GDILKC 159


>pdb|1GKU|B Chain B, Reverse Gyrase From Archaeoglobus Fulgidus
          Length = 1054

 Score = 27.7 bits (60), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 13/62 (20%)

Query: 37  FTGLALCSDCNTFAEYVKDQELVADCLKCCTEDSDDSMSKITYSGAILEACMRKLVFYPE 96
           +  +  C DC    ++ +D+E    C KC +E+ D+S S+I          +RKL    E
Sbjct: 578 YASIKRCRDCGY--QFTEDRE---SCPKCGSENVDNSRSRI--------EALRKLAHDAE 624

Query: 97  IV 98
            V
Sbjct: 625 FV 626


>pdb|1GL9|B Chain B, Archaeoglobus Fulgidus Reverse Gyrase Complexed With Adpnp
 pdb|1GL9|C Chain C, Archaeoglobus Fulgidus Reverse Gyrase Complexed With Adpnp
          Length = 1054

 Score = 27.7 bits (60), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 13/62 (20%)

Query: 37  FTGLALCSDCNTFAEYVKDQELVADCLKCCTEDSDDSMSKITYSGAILEACMRKLVFYPE 96
           +  +  C DC    ++ +D+E    C KC +E+ D+S S+I          +RKL    E
Sbjct: 578 YASIKRCRDCGY--QFTEDRE---SCPKCGSENVDNSRSRI--------EALRKLAHDAE 624

Query: 97  IV 98
            V
Sbjct: 625 FV 626


>pdb|3S4W|B Chain B, Structure Of The Fanci-Fancd2 Complex
          Length = 1323

 Score = 26.9 bits (58), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 16/63 (25%), Positives = 30/63 (47%), Gaps = 1/63 (1%)

Query: 47  NTFAEYVKDQELVADCLKCCTEDSDDSMSKIT-YSGAILEACMRKLVFYPEIVGFIEEEK 105
           N    Y +D E + +CL  C    D+  S  T YS ++++  +   +  P I+  + E+ 
Sbjct: 64  NGLESYTEDSESLRNCLLSCERLQDEEASMGTFYSKSLIKLLLGIDILQPAIIKMLFEKV 123

Query: 106 DKF 108
            +F
Sbjct: 124 PQF 126


  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
   0.320    0.134    0.392 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,495,474
Number of Sequences: 62578
Number of extensions: 167702
Number of successful extensions: 337
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 333
Number of HSP's gapped (non-prelim): 8
length of query: 163
length of database: 14,973,337
effective HSP length: 91
effective length of query: 72
effective length of database: 9,278,739
effective search space: 668069208
effective search space used: 668069208
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)