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= 005475
         (695 letters)

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

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



>pdb|2EQN|A Chain A, Solution Structure Of The Naf1 Domain Of Hypothetical
           Protein Bc008207 [homo Sapiens]
          Length = 103

 Score = 42.0 bits (97), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 21/55 (38%), Positives = 39/55 (70%), Gaps = 2/55 (3%)

Query: 327 PLNEGSILWITESRVPLGLIDEIFGPVKNPYYVVRYNSENEIPAE-IRVGTSISF 380
           P+NE ++++ ++ R   G I EIFGPV +P+YV+R+NS + I ++ I++  ++ F
Sbjct: 49  PVNEETVIFKSD-RQAAGKIFEIFGPVAHPFYVLRFNSSDHIESKGIKIKETMYF 102


>pdb|2V3M|A Chain A, Structure Of The Gar1 Domain Of Naf1
 pdb|2V3M|B Chain B, Structure Of The Gar1 Domain Of Naf1
 pdb|2V3M|C Chain C, Structure Of The Gar1 Domain Of Naf1
 pdb|2V3M|D Chain D, Structure Of The Gar1 Domain Of Naf1
 pdb|2V3M|E Chain E, Structure Of The Gar1 Domain Of Naf1
 pdb|2V3M|F Chain F, Structure Of The Gar1 Domain Of Naf1
          Length = 131

 Score = 36.6 bits (83), Expect = 0.047,   Method: Composition-based stats.
 Identities = 18/48 (37%), Positives = 32/48 (66%), Gaps = 2/48 (4%)

Query: 328 LNEGSILWITESRVPLGLIDEIFGPVKNPYYVVRY-NSENEIPAEIRV 374
           L EGSI  + E R  +G + E+FGP++NP+Y ++  +S+  +  E++V
Sbjct: 57  LKEGSIFCL-EDRTLIGXLTEVFGPLQNPFYRIKLPDSKKNLFDELKV 103


>pdb|3PEH|A Chain A, Crystal Structure Of The N-Terminal Domain Of An Hsp90
           From Plasmodium Falciparum, Pfl1070c In The Presence Of
           A Thienopyrimidine Derivative
 pdb|3PEH|B Chain B, Crystal Structure Of The N-Terminal Domain Of An Hsp90
           From Plasmodium Falciparum, Pfl1070c In The Presence Of
           A Thienopyrimidine Derivative
 pdb|3PEJ|A Chain A, Crystal Structure Of The N-Terminal Domain Of An Hsp90
           From Plasmodium Falciparum, Pfl1070c In The Presence Of
           Macbecin
 pdb|3PEJ|B Chain B, Crystal Structure Of The N-Terminal Domain Of An Hsp90
           From Plasmodium Falciparum, Pfl1070c In The Presence Of
           Macbecin
          Length = 281

 Score = 29.6 bits (65), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 28/87 (32%), Positives = 40/87 (45%), Gaps = 17/87 (19%)

Query: 83  QEENFHFGNLVSDGSDCVVKVE-----EALVGGKEKNLSCCIEEDMGKVSLVDAKSGIAS 137
           Q+E F    L+S+ +D + K+      +  V G+EK L   I  +  K  L      I  
Sbjct: 46  QKEVF-LRELISNAADALEKIRFLSLSDESVLGEEKKLEIRISANKEKNIL-----SITD 99

Query: 138 DGDGSKKVDLVGNMGSFPADKDGAKSG 164
            G G  KVDL+ N+G+       AKSG
Sbjct: 100 TGIGMTKVDLINNLGTI------AKSG 120


>pdb|3MQK|C Chain C, Cbf5-Nop10-Gar1 Complex Binding With 17mer Rna Containing
           Aca Trinucleotide
          Length = 75

 Score = 29.6 bits (65), Expect = 6.4,   Method: Composition-based stats.
 Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 3/33 (9%)

Query: 343 LGLIDEIFGPVKNPYYVVRYNSENEIPAEIRVG 375
           +G++ ++FGPVK PY  ++    N    EI VG
Sbjct: 38  VGIVKDVFGPVKMPYVAIKPKVSN---PEIYVG 67


>pdb|2RFK|C Chain C, Substrate Rna Positioning In The Archaeal HACA
           Ribonucleoprotein Complex
          Length = 74

 Score = 29.6 bits (65), Expect = 6.5,   Method: Composition-based stats.
 Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 3/33 (9%)

Query: 343 LGLIDEIFGPVKNPYYVVRYNSENEIPAEIRVG 375
           +G++ ++FGPVK PY  ++    N    EI VG
Sbjct: 38  VGIVKDVFGPVKMPYVAIKPKVSN---PEIYVG 67


>pdb|2EY4|C Chain C, Crystal Structure Of A Cbf5-Nop10-Gar1 Complex
 pdb|2EY4|D Chain D, Crystal Structure Of A Cbf5-Nop10-Gar1 Complex
          Length = 82

 Score = 28.9 bits (63), Expect = 8.8,   Method: Composition-based stats.
 Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 3/33 (9%)

Query: 343 LGLIDEIFGPVKNPYYVVRYNSENEIPAEIRVG 375
           +G++ ++FGPVK PY  ++    N    EI VG
Sbjct: 45  VGIVKDVFGPVKMPYVAIKPKVSN---PEIYVG 74


  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
   0.312    0.133    0.398 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,278,087
Number of Sequences: 62578
Number of extensions: 701521
Number of successful extensions: 1150
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1148
Number of HSP's gapped (non-prelim): 11
length of query: 695
length of database: 14,973,337
effective HSP length: 106
effective length of query: 589
effective length of database: 8,340,069
effective search space: 4912300641
effective search space used: 4912300641
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 55 (25.8 bits)