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= 018790
         (350 letters)

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

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



>pdb|1CF7|A Chain A, Structural Basis Of Dna Recognition By The Heterodimeric
          Cell Cycle Transcription Factor E2f-Dp
          Length = 76

 Score = 62.0 bits (149), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 34/70 (48%), Positives = 48/70 (68%), Gaps = 5/70 (7%)

Query: 23 SRKEKSLGLLCSKFLKLYN--RDGVESIGLDDAASRLGV-ERRRIYDVVNILESIGVVAR 79
          SR EKSLGLL +KF+ L    +DGV  + L  AA  L V ++RRIYD+ N+LE IG++ +
Sbjct: 6  SRHEKSLGLLTTKFVSLLQEAKDGVLDLKL--AADTLAVRQKRRIYDITNVLEGIGLIEK 63

Query: 80 QAKNLYSWQG 89
          ++KN   W+G
Sbjct: 64 KSKNSIQWKG 73


>pdb|1KMY|A Chain A, Crystal Structure Of 2,3-Dihydroxybiphenyl 1,2-Dioxygenase
           Complexed With 2,3-Dihydroxybiphenyl Under Anaerobic
           Condition
 pdb|1KND|A Chain A, Crystal Structure Of 2,3-Dihydroxybiphenyl 1,2-Dioxygenase
           Complexed With Catechol Under Anaerobic Condition
 pdb|1KNF|A Chain A, Crystal Structure Of 2,3-Dihydroxybiphenyl 1,2-Dioxygenase
           Complexed With 3-Methyl Catechol Under Anaerobic
           Condition
 pdb|1LGT|A Chain A, Crystal Structure Of 2,3-Dihydroxybiphenyl 1,2-Dioxygenase
           (Dhbd) Complexed With 2'-Cl Dihydroxybiphenyl (Dhb)
 pdb|1LKD|A Chain A, Crystal Structure Of 2,3-Dihydroxybiphenyl 1,2-Dioxygenase
           (Dhbd) Complexed With 2',6'-Dicl Dihydroxybiphenyl (Dhb)
 pdb|1HAN|A Chain A, Crystal Structure Of The Biphenyl-Cleaving Extradiol
           Dioxygenase From A Pcb-Degrading Pseudomonad
          Length = 297

 Score = 34.3 bits (77), Expect = 0.10,   Method: Compositional matrix adjust.
 Identities = 15/45 (33%), Positives = 21/45 (46%), Gaps = 5/45 (11%)

Query: 221 KKRVFGTDITNLRLKKNKVDSLTEKKSNPKLNVPKYFKHCNEESN 265
           K   F TD+   +L       + + K  P + VP YF HCNE  +
Sbjct: 155 KALAFYTDVLGFQLSD-----VIDMKMGPDVTVPAYFLHCNERHH 194


>pdb|1CF7|B Chain B, Structural Basis Of Dna Recognition By The Heterodimeric
          Cell Cycle Transcription Factor E2f-Dp
          Length = 95

 Score = 30.4 bits (67), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 10/30 (33%), Positives = 21/30 (70%), Gaps = 1/30 (3%)

Query: 61 RRRIYDVVNILESIGVVARQAKNLYSWQGF 90
          RRR+YD +N+L ++ +++++ K +  W G 
Sbjct: 61 RRRVYDALNVLMAMNIISKEKKEI-KWIGL 89


  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
   0.315    0.133    0.397 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,513,968
Number of Sequences: 62578
Number of extensions: 422399
Number of successful extensions: 1144
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1140
Number of HSP's gapped (non-prelim): 5
length of query: 350
length of database: 14,973,337
effective HSP length: 100
effective length of query: 250
effective length of database: 8,715,537
effective search space: 2178884250
effective search space used: 2178884250
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: 52 (24.6 bits)