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= 008471
         (564 letters)

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

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



>pdb|1YVP|A Chain A, Ro Autoantigen Complexed With Rnas
 pdb|1YVP|B Chain B, Ro Autoantigen Complexed With Rnas
 pdb|1YVR|A Chain A, Ro Autoantigen
 pdb|2I91|A Chain A, 60kda Ro Autoantigen In Complex With A Fragment Of
           Misfolded Rna
 pdb|2I91|B Chain B, 60kda Ro Autoantigen In Complex With A Fragment Of
           Misfolded Rna
          Length = 538

 Score = 30.8 bits (68), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 29/117 (24%), Positives = 51/117 (43%), Gaps = 20/117 (17%)

Query: 62  TSFLTSQSNATFKSDDTVVKTGEDFM-------ALNQTVVATFINATDVEYKEESV---T 111
           TS + +  NA +KS   V  TG+ F+       ++NQ V+ + +NA+ V      +   T
Sbjct: 347 TSIVEALDNAFYKSFKLVEPTGKRFLLAIDVSASMNQRVLGSILNASVVAAAMCMLVART 406

Query: 112 ETVPNCEGNVDSPIDCTDPEVFHLLMSKAIDQFKDIHFYRFGKAVRGDSDNACDMAW 168
           E   +     D  + C  P   ++L+ + +++  DI          G +D A  M W
Sbjct: 407 EKDSHMVAFSDEMLPC--PITVNMLLHEVVEKMSDITM--------GSTDCALPMLW 453


>pdb|3VM8|A Chain A, Crystal Structure Of The Human Apobec3c Having Hiv-1
           Vif-Binding Interface
 pdb|3VM8|B Chain B, Crystal Structure Of The Human Apobec3c Having Hiv-1
           Vif-Binding Interface
 pdb|3VOW|A Chain A, Crystal Structure Of The Human Apobec3c Having Hiv-1
           Vif-Binding Interface
 pdb|3VOW|B Chain B, Crystal Structure Of The Human Apobec3c Having Hiv-1
           Vif-Binding Interface
          Length = 190

 Score = 28.9 bits (63), Expect = 7.2,   Method: Compositional matrix adjust.
 Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 5/63 (7%)

Query: 483 NPLKDKYSTHFLDEYKDLW---DENSEWYSETMK-LNKGAAVEFD-GYMRASVDTEVFLR 537
           NP+K  Y   F  ++K+LW   D N  W   T++ + + + V +  G  R  VD+E    
Sbjct: 7   NPMKAMYPGTFYFQFKNLWEANDRNETWLCFTVEGIKRRSVVSWKTGVFRNQVDSETHCH 66

Query: 538 GKK 540
            ++
Sbjct: 67  AER 69


>pdb|1JYO|E Chain E, Structure Of The Salmonella Virulence Effector Sptp In
           Complex With Its Secretion Chaperone Sicp
 pdb|1JYO|F Chain F, Structure Of The Salmonella Virulence Effector Sptp In
           Complex With Its Secretion Chaperone Sicp
          Length = 105

 Score = 28.9 bits (63), Expect = 7.3,   Method: Compositional matrix adjust.
 Identities = 14/53 (26%), Positives = 29/53 (54%)

Query: 73  FKSDDTVVKTGEDFMALNQTVVATFINATDVEYKEESVTETVPNCEGNVDSPI 125
           FK+ + V K  E+    +Q ++ TF++A   +Y E +V + +     N++ P+
Sbjct: 25  FKNTEVVQKHTENIRVQDQKILQTFLHALTEKYGETAVNDALLMSRINMNKPL 77


  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    0.134    0.407 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,255,484
Number of Sequences: 62578
Number of extensions: 747001
Number of successful extensions: 1923
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1919
Number of HSP's gapped (non-prelim): 7
length of query: 564
length of database: 14,973,337
effective HSP length: 104
effective length of query: 460
effective length of database: 8,465,225
effective search space: 3894003500
effective search space used: 3894003500
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)