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= 041864
         (300 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 = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 40/113 (35%), Positives = 63/113 (55%), Gaps = 8/113 (7%)

Query: 110 LFQKELKNSDVSSLRRMILPKKAAEAHLPVLESK---EGIFISMEDLDGLHVWTFKYRFW 166
           LF+K +  SDV  L R+++PK  AE H P+  S    +G+ ++ ED++G  VW F+Y +W
Sbjct: 13  LFEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNG-KVWRFRYSYW 71

Query: 167 PNNNSRMYVL-ENTGDFVNAHGLQLGDFIIVYKDD-QNQNYVIQAKKASDQDV 217
             N+S+ YVL +    FV    L+ GD +   + + Q+Q   I  K  S  D+
Sbjct: 72  --NSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQDQQLYIGWKSRSGSDL 122


>pdb|2DBY|A Chain A, Crystal Structure Of The Gtp-Binding Protein Ychf In
           Complexed With Gdp
          Length = 368

 Score = 28.5 bits (62), Expect = 5.1,   Method: Compositional matrix adjust.
 Identities = 17/55 (30%), Positives = 34/55 (61%), Gaps = 4/55 (7%)

Query: 102 IDPGRLRFLFQKELKNSDVSSL-RRMILPKKAAEA---HLPVLESKEGIFISMED 152
           +DP     + + EL  +D+++L RR+   +K A A    LP+LE+ EG+++ +++
Sbjct: 122 VDPLEDAEVVETELLLADLATLERRLERLRKEARADRERLPLLEAAEGLYVHLQE 176


>pdb|2DWQ|A Chain A, Thermus Thermophilus Ychf Gtp-Binding Protein
 pdb|2DWQ|B Chain B, Thermus Thermophilus Ychf Gtp-Binding Protein
          Length = 368

 Score = 28.1 bits (61), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 17/55 (30%), Positives = 34/55 (61%), Gaps = 4/55 (7%)

Query: 102 IDPGRLRFLFQKELKNSDVSSL-RRMILPKKAAEA---HLPVLESKEGIFISMED 152
           +DP     + + EL  +D+++L RR+   +K A A    LP+LE+ EG+++ +++
Sbjct: 122 VDPLEDAEVVETELLLADLATLERRLERLRKEARADRERLPLLEAAEGLYVHLQE 176


>pdb|4B9G|A Chain A, Structure Of Cssb Subunit Complemented With Donor Strand
           From Cssa Subunit Of Enterotoxigenic Escherichia Coli
           Colonization Factor Cs6
 pdb|4B9G|B Chain B, Structure Of Cssb Subunit Complemented With Donor Strand
           From Cssa Subunit Of Enterotoxigenic Escherichia Coli
           Colonization Factor Cs6
          Length = 161

 Score = 27.7 bits (60), Expect = 8.1,   Method: Compositional matrix adjust.
 Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 13/72 (18%)

Query: 150 MEDLD-GLHVWTFKYRFWPNNNSRMYVLENT------------GDFVNAHGLQLGDFIIV 196
           + D+D  + +    Y   P  NS++Y +E T             D + + G Q+G  + V
Sbjct: 14  IPDIDSAVRIIPVNYDSDPKLNSQLYTVEMTIPAGVSAVKIVPTDSLTSSGQQIGKLVNV 73

Query: 197 YKDDQNQNYVIQ 208
              DQN NY I+
Sbjct: 74  NNPDQNMNYYIR 85


  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    0.134    0.381 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,728,312
Number of Sequences: 62578
Number of extensions: 300048
Number of successful extensions: 640
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 636
Number of HSP's gapped (non-prelim): 6
length of query: 300
length of database: 14,973,337
effective HSP length: 98
effective length of query: 202
effective length of database: 8,840,693
effective search space: 1785819986
effective search space used: 1785819986
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: 51 (24.3 bits)