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= 003731
         (799 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 = 7e-07,   Method: Compositional matrix adjust.
 Identities = 30/87 (34%), Positives = 43/87 (49%)

Query: 115 FCKTLTASDTSTHGGFSVPRRAAEKVFPSLDFSLQPPAQELIARDLHDVEWKFRHIFRGQ 174
           F K +T SD        +P+  AEK FP    ++      L   D++   W+FR+ +   
Sbjct: 14  FEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYWNS 73

Query: 175 PKRHLLTTGWSVFVSAKRLVAGDSVLF 201
            + ++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 = 30.4 bits (67), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 32/119 (26%), Positives = 50/119 (42%), Gaps = 27/119 (22%)

Query: 336 QPRVSLWEIEPLTTFPMYPSLFPLRLKRPWHPSTSSFND-------NRDETASGLNWLRG 388
           +P ++L     L    M  + F L       PS    ND       +RD T S L  L+ 
Sbjct: 231 EPSIALKVGSTLLVLEMIEADFGL-------PSLELANDIASIREISRDATGSTLLSLKD 283

Query: 389 GTGEQGLTTLNFQSLGMF----PWMQQRVEPSFLGNDHNQQYQAM-----LAAGMQSGD 438
           GT    +T L  Q + +F     W++QR EP F G  + +  + +     +   ++SGD
Sbjct: 284 GTT---MTALQIQQV-VFEHASKWLEQRPEPEFSGTSNTEMARVLDLWGRMLKAIESGD 338


>pdb|3NHM|A Chain A, Crystal Structure Of A Response Regulator From Myxococcus
           Xanthus
 pdb|3NHM|B Chain B, Crystal Structure Of A Response Regulator From Myxococcus
           Xanthus
          Length = 133

 Score = 29.3 bits (64), Expect = 8.3,   Method: Composition-based stats.
 Identities = 19/64 (29%), Positives = 28/64 (43%)

Query: 14  HACAGPLVSLPTVGTRVVYFPQGHSEQVAATTNKEVDSHIPNYPNLPPQLICQLHNVTMH 73
           +A  G   S PT+    V F  G++ +     ++ V       P  PP LI QLH +   
Sbjct: 63  YALCGHFRSEPTLKHIPVIFVSGYAPRTEGPADQPVPDAYLVKPVKPPVLIAQLHALLAR 122

Query: 74  ADVE 77
           A+ E
Sbjct: 123 AEAE 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
   0.317    0.133    0.403 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,883,698
Number of Sequences: 62578
Number of extensions: 957894
Number of successful extensions: 1761
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1759
Number of HSP's gapped (non-prelim): 5
length of query: 799
length of database: 14,973,337
effective HSP length: 107
effective length of query: 692
effective length of database: 8,277,491
effective search space: 5728023772
effective search space used: 5728023772
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)