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= 004820
         (728 letters)

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

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



>pdb|1WID|A Chain A, Solution Structure Of The B3 Dna-Binding Domain Of Rav1
          Length = 130

 Score = 52.8 bits (125), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 30/87 (34%), Positives = 43/87 (49%)

Query: 44  FCKTLTASDTSTHGGFSVPRRAAEKVFPSLDFSLQPPAQELIARDLHDVEWKFRHIFRGQ 103
           F K +T SD        +P+  AEK FP    ++      L   D++   W+FR+ +   
Sbjct: 14  FEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYWNS 73

Query: 104 PKRHLLTTGWSVFVSAKRLVAGDSVLF 130
            + ++LT GWS FV  K L AGD V F
Sbjct: 74  SQSYVLTKGWSRFVKEKNLRAGDVVSF 100


>pdb|4B0T|A Chain A, Structure Of The Pup Ligase Pafa Of The Prokaryotic
           Ubiquitin-Like Modification Pathway In Complex With Adp
 pdb|4B0T|B Chain B, Structure Of The Pup Ligase Pafa Of The Prokaryotic
           Ubiquitin-Like Modification Pathway In Complex With Adp
          Length = 493

 Score = 30.0 bits (66), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 32/122 (26%), Positives = 49/122 (40%), Gaps = 25/122 (20%)

Query: 261 AGERQPRVSLWEIEPLTTFPMYPSLFPLRLKRPWHPSTSSFND-------NRDETASGLN 313
           A   +P ++L     L    M  + F L       PS    ND       +RD T S L 
Sbjct: 227 ANMAEPSIALKVGSTLLVLEMIEADFGL-------PSLELANDIASIREISRDATGSTLL 279

Query: 314 WLRGGTGEQGLTTLNFQSL---GMFPWMQQRVEPSFLGNDHNQQYQAM-----LAAGMQS 365
            L+ GT    +T L  Q +       W++QR EP F G  + +  + +     +   ++S
Sbjct: 280 SLKDGTT---MTALQIQQVVFEHASKWLEQRPEPEFSGTSNTEMARVLDLWGRMLKAIES 336

Query: 366 GD 367
           GD
Sbjct: 337 GD 338


>pdb|1Z81|A Chain A, Crystal Structure Of Cyclophilin From Plasmodium Yoelii
          Length = 229

 Score = 29.3 bits (64), Expect = 8.9,   Method: Composition-based stats.
 Identities = 22/89 (24%), Positives = 45/89 (50%), Gaps = 4/89 (4%)

Query: 478 GNLLNFSGAGP-SMLRQQFPQQSLGSKYEPSQVRDFVHSMSLPSSYNGKDAAVGTENCNT 536
           G+ +N +G+G  S+  ++F  ++   K++   +    +S   P++ NG    + T+ C  
Sbjct: 126 GDFINHNGSGSLSIYGEKFDDENFDIKHDKEGLLSMANSG--PNT-NGCQFFITTKKCEW 182

Query: 537 DSQNSVVFGVHIDSSGLLLPTTVSSFTTS 565
               +VVFG  ID+  LLL   + + + +
Sbjct: 183 LDGKNVVFGRIIDNDSLLLLKKIENVSVT 211


  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    0.132    0.399 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,487,824
Number of Sequences: 62578
Number of extensions: 847756
Number of successful extensions: 1609
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1608
Number of HSP's gapped (non-prelim): 4
length of query: 728
length of database: 14,973,337
effective HSP length: 106
effective length of query: 622
effective length of database: 8,340,069
effective search space: 5187522918
effective search space used: 5187522918
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)