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= 008078
         (578 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 = 69.3 bits (168), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 40/115 (34%), Positives = 63/115 (54%), Gaps = 4/115 (3%)

Query: 122 FAKILTPSDANNGGGFSVPRFCADSIFPPLNYQVDPPVQNISVTDIHGAVWEFRHIYRGT 181
           F K +TPSD        +P+  A+  FP  +  V      ++  D++G VW FR+ Y  +
Sbjct: 14  FEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYWNS 73

Query: 182 PRRHLLTTGWSKFVNRKKLIAGDSVVFMRDS--RGKMYIGLRRSVRYGNNGDSAG 234
            + ++LT GWS+FV  K L AGD V F R +    ++YIG +   R G++ D++G
Sbjct: 74  SQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQDQQLYIGWKS--RSGSDLDASG 126


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

 Score = 32.0 bits (71), Expect = 0.92,   Method: Compositional matrix adjust.
 Identities = 20/68 (29%), Positives = 28/68 (41%), Gaps = 7/68 (10%)

Query: 162 ISVTDIHGAVWEFRHIYRGTPRRHLLTTGWSKFVNRKKLIAGDSVVFMRDSRGKMYIGLR 221
           + + D  G  W  R   RG   +  LT GW  FV    L  G  + F+ D     Y+   
Sbjct: 42  VDLLDYSGRSWTVRMKKRG--EKVFLTVGWENFVKDNNLEDGKYLQFIYDRDRTFYV--- 96

Query: 222 RSVRYGNN 229
             + YG+N
Sbjct: 97  --IIYGHN 102


>pdb|4IWH|A Chain A, Crystal Structure Of A 3-isopropylmalate Dehydrogenase
           From Burkholderia Pseudomallei
 pdb|4IWH|B Chain B, Crystal Structure Of A 3-isopropylmalate Dehydrogenase
           From Burkholderia Pseudomallei
          Length = 363

 Score = 29.6 bits (65), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 14/40 (35%), Positives = 23/40 (57%)

Query: 197 RKKLIAGDSVVFMRDSRGKMYIGLRRSVRYGNNGDSAGAR 236
           + +L+AG  ++ +R+  G +Y G  R VR   +G  AG R
Sbjct: 123 KPELVAGLDILIVRELNGDIYFGQPRGVRAAPDGPFAGER 162


>pdb|3K1I|C Chain C, Crystal Strcture Of Flis-Hp1076 Complex In H. Pylori
 pdb|3K1I|D Chain D, Crystal Strcture Of Flis-Hp1076 Complex In H. Pylori
          Length = 178

 Score = 28.5 bits (62), Expect = 9.8,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 32/63 (50%), Gaps = 9/63 (14%)

Query: 51  SITLSVTKPFIPCLITHVEFLADP---------VTDQVFAKVVLNPITALEPSRNFLEQQ 101
           ++  S+ K  +  ++ + +FLA P         + D++F+ +V+NP+  LE    F    
Sbjct: 76  ALQASIIKQELREIVENCQFLASPLFDTQLNIAINDEIFSMIVVNPLDLLENVGEFQAYL 135

Query: 102 QEQ 104
           +E+
Sbjct: 136 EEK 138


>pdb|3K1H|A Chain A, Crystal Structure Of Hp1076 From H.Pylori
          Length = 158

 Score = 28.5 bits (62), Expect = 9.8,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 32/63 (50%), Gaps = 9/63 (14%)

Query: 51  SITLSVTKPFIPCLITHVEFLADP---------VTDQVFAKVVLNPITALEPSRNFLEQQ 101
           ++  S+ K  +  ++ + +FLA P         + D++F+ +V+NP+  LE    F    
Sbjct: 56  ALQASIIKQELREIVENCQFLASPLFDTQLNIAINDEIFSMIVVNPLDLLENVGEFQAYL 115

Query: 102 QEQ 104
           +E+
Sbjct: 116 EEK 118


  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    0.135    0.415 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,680,638
Number of Sequences: 62578
Number of extensions: 749608
Number of successful extensions: 1182
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1178
Number of HSP's gapped (non-prelim): 9
length of query: 578
length of database: 14,973,337
effective HSP length: 104
effective length of query: 474
effective length of database: 8,465,225
effective search space: 4012516650
effective search space used: 4012516650
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: 54 (25.4 bits)