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= 012504
         (462 letters)

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

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



>pdb|2X7K|A Chain A, The Crystal Structure Of Ppil1 In Complex With
           Cyclosporine A Suggests A Binding Mode For Skip
          Length = 166

 Score = 34.3 bits (77), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 32/133 (24%), Positives = 55/133 (41%), Gaps = 13/133 (9%)

Query: 235 LDVALGTALVEMYSKCGHVEKAFKVFNLMREKNLQSWT--------IMISGLADNGRGNY 286
           L+ ++G  ++E+Y K  H  K  K F  +  +   + T         MI G    G G  
Sbjct: 16  LETSMGIIVLELYWK--HAPKTCKNFAELARRGYYNGTKFHRIIKDFMIQGGDPTGTGRG 73

Query: 287 AISLFAKMIQTGLKPDSISFSAILSACSHLGLVDEGKNYFDEMARVYNIKPTMEHYG--C 344
             S++ K  +  L PD     A + A ++ G    G  +F  +A    +      +G  C
Sbjct: 74  GASIYGKQFEDELHPDLKFTGAGILAMANAGPDTNGSQFFVTLAPTQWLDGKHTIFGRVC 133

Query: 345 M-VDMLGRAGLIE 356
             + M+ R G++E
Sbjct: 134 QGIGMVNRVGMVE 146


>pdb|1XWN|A Chain A, Solution Structure Of Cyclophilin Like 1(Ppil1) And
           Insights Into Its Interaction With Skip
          Length = 174

 Score = 34.3 bits (77), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 32/133 (24%), Positives = 55/133 (41%), Gaps = 13/133 (9%)

Query: 235 LDVALGTALVEMYSKCGHVEKAFKVFNLMREKNLQSWT--------IMISGLADNGRGNY 286
           L+ ++G  ++E+Y K  H  K  K F  +  +   + T         MI G    G G  
Sbjct: 16  LETSMGIIVLELYWK--HAPKTCKNFAELARRGYYNGTKFHRIIKDFMIQGGDPTGTGRG 73

Query: 287 AISLFAKMIQTGLKPDSISFSAILSACSHLGLVDEGKNYFDEMARVYNIKPTMEHYG--C 344
             S++ K  +  L PD     A + A ++ G    G  +F  +A    +      +G  C
Sbjct: 74  GASIYGKQFEDELHPDLKFTGAGILAMANAGPDTNGSQFFVTLAPTQWLDGKHTIFGRVC 133

Query: 345 M-VDMLGRAGLIE 356
             + M+ R G++E
Sbjct: 134 QGIGMVNRVGMVE 146


>pdb|2K7N|A Chain A, Solution Structure Of The Ppil1 Bound To A Fragment Of
           Skip
          Length = 203

 Score = 34.3 bits (77), Expect = 0.16,   Method: Compositional matrix adjust.
 Identities = 32/133 (24%), Positives = 55/133 (41%), Gaps = 13/133 (9%)

Query: 235 LDVALGTALVEMYSKCGHVEKAFKVFNLMREKNLQSWT--------IMISGLADNGRGNY 286
           L+ ++G  ++E+Y K  H  K  K F  +  +   + T         MI G    G G  
Sbjct: 16  LETSMGIIVLELYWK--HAPKTCKNFAELARRGYYNGTKFHRIIKDFMIQGGDPTGTGRG 73

Query: 287 AISLFAKMIQTGLKPDSISFSAILSACSHLGLVDEGKNYFDEMARVYNIKPTMEHYG--C 344
             S++ K  +  L PD     A + A ++ G    G  +F  +A    +      +G  C
Sbjct: 74  GASIYGKQFEDELHPDLKFTGAGILAMANAGPDTNGSQFFVTLAPTQWLDGKHTIFGRVC 133

Query: 345 M-VDMLGRAGLIE 356
             + M+ R G++E
Sbjct: 134 QGIGMVNRVGMVE 146


>pdb|3CTD|A Chain A, Crystal Structure Of A Putative Aaa Family Atpase From
           Prochlorococcus Marinus Subsp. Pastoris
 pdb|3CTD|B Chain B, Crystal Structure Of A Putative Aaa Family Atpase From
           Prochlorococcus Marinus Subsp. Pastoris
          Length = 213

 Score = 32.3 bits (72), Expect = 0.55,   Method: Compositional matrix adjust.
 Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 3/70 (4%)

Query: 254 EKAFKVFNLMREKNLQSWTIMISGLADNGRG---NYAISLFAKMIQTGLKPDSISFSAIL 310
           E + +  N++ +KN Q+   +IS    + RG   +  +   A M++ G  P+ I    ++
Sbjct: 18  EDSIQKKNIVYDKNGQNHFDVISAFIKSIRGSDPDATLYWLANMVEAGEDPNFIFRRLLI 77

Query: 311 SACSHLGLVD 320
           SAC  +GL D
Sbjct: 78  SACEDIGLAD 87


  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
   0.322    0.134    0.396 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,458,181
Number of Sequences: 62578
Number of extensions: 461689
Number of successful extensions: 954
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 953
Number of HSP's gapped (non-prelim): 8
length of query: 462
length of database: 14,973,337
effective HSP length: 102
effective length of query: 360
effective length of database: 8,590,381
effective search space: 3092537160
effective search space used: 3092537160
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 bits)