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= 002390
         (928 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 = 9e-07,   Method: Compositional matrix adjust.
 Identities = 30/87 (34%), Positives = 43/87 (49%)

Query: 158 FCKTLTASDTSTHGGFSVPRRAAEKVFPPLDYSQTPPAQELIARDLHDNEWKFRHIFRGQ 217
           F K +T SD        +P+  AEK FP    + +     L   D++   W+FR+ +   
Sbjct: 14  FEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYWNS 73

Query: 218 PKRHLLTTGWSVFVSAKRLVAGDSVLF 244
            + ++LT GWS FV  K L AGD V F
Sbjct: 74  SQSYVLTKGWSRFVKEKNLRAGDVVSF 100


>pdb|1YEL|A Chain A, Structure Of The Hypothetical Arabidopsis Thaliana Protein
           At1g16640.1
          Length = 104

 Score = 32.3 bits (72), Expect = 1.3,   Method: Composition-based stats.
 Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 5/76 (6%)

Query: 175 VPRRAAEKVFPPLDYSQTPPAQELIARDLHD---NEWKFRHIFRGQPKRHLLTTGWSVFV 231
           +  ++++ +  PL +++  PA   I  DL D     W  R   RG+  +  LT GW  FV
Sbjct: 16  ISEKSSKSLEIPLGFNEYFPAPFPITVDLLDYSGRSWTVRMKKRGE--KVFLTVGWENFV 73

Query: 232 SAKRLVAGDSVLFIWN 247
               L  G  + FI++
Sbjct: 74  KDNNLEDGKYLQFIYD 89


>pdb|2AU3|A Chain A, Crystal Structure Of The Aquifex Aeolicus Primase (Zinc
           Binding And Rna Polymerase Domains)
          Length = 407

 Score = 31.2 bits (69), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 43/184 (23%), Positives = 70/184 (38%), Gaps = 30/184 (16%)

Query: 743 NESLSLPYAASNFTNNVGTDFPLNSDMTTSSCVDESGFLQSSENVDQVNPPTRTFVKVHK 802
           +E L+L    SN+  N     P + D T S  V                 P++   K   
Sbjct: 21  SEYLNLEKVGSNYRTNC----PFHPDDTPSFYV----------------SPSKQIFKCFG 60

Query: 803 SGSFGRSLDISKFS---SYDELRSELARMFGLEGQLEDPQRSGWQLVFVDRENDVL---L 856
            G  G ++         SY E   ELA+ +G +  LE   +     V +DR  D     L
Sbjct: 61  CGVGGDAIKFVSLYEDISYFEAALELAKRYGKKLDLEKISKDEKVYVALDRVCDFYRESL 120

Query: 857 LGDDPWQEFVNNVGYIKILSPLEVQQMGKGLSPVTSGPGQRLSSNNNFDDYVSRQELRSS 916
           L +    E+V + G    + P   ++   G +P +    + L  N+  + Y+  + L S 
Sbjct: 121 LKNREASEYVKSRG----IDPKVARKFDLGYAPSSEALVKVLKENDLLEAYLETKNLLSP 176

Query: 917 SNGV 920
           + GV
Sbjct: 177 TKGV 180


>pdb|3IBG|A Chain A, Crystal Structure Of Aspergillus Fumigatus Get3 With Bound
           Adp
 pdb|3IBG|B Chain B, Crystal Structure Of Aspergillus Fumigatus Get3 With Bound
           Adp
 pdb|3IBG|C Chain C, Crystal Structure Of Aspergillus Fumigatus Get3 With Bound
           Adp
 pdb|3IBG|D Chain D, Crystal Structure Of Aspergillus Fumigatus Get3 With Bound
           Adp
 pdb|3IBG|E Chain E, Crystal Structure Of Aspergillus Fumigatus Get3 With Bound
           Adp
 pdb|3IBG|F Chain F, Crystal Structure Of Aspergillus Fumigatus Get3 With Bound
           Adp
          Length = 348

 Score = 30.8 bits (68), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 26/83 (31%), Positives = 36/83 (43%), Gaps = 4/83 (4%)

Query: 719 FGVSIDSSLMGQNGLPNLKNISSENESLSLPYAASNFTNNVGTDFPLNSDMTTSSCVDES 778
           FG  ++S L  + GLP  +NI   +E L    +     + V T F  N DMTT  CV  +
Sbjct: 189 FGPMLNSILGARGGLPGGQNI---DELLQKMESLRETISEVNTQFK-NPDMTTFVCVCIA 244

Query: 779 GFLQSSENVDQVNPPTRTFVKVH 801
            FL   E    +   T   +  H
Sbjct: 245 EFLSLYETERMIQELTSYGIDTH 267


  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
   0.316    0.132    0.396 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,686,788
Number of Sequences: 62578
Number of extensions: 1014812
Number of successful extensions: 1858
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1856
Number of HSP's gapped (non-prelim): 5
length of query: 928
length of database: 14,973,337
effective HSP length: 108
effective length of query: 820
effective length of database: 8,214,913
effective search space: 6736228660
effective search space used: 6736228660
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (26.2 bits)