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= 012778
         (456 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 =  104 bits (260), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 52/73 (71%), Positives = 61/73 (83%), Gaps = 1/73 (1%)

Query: 129 PTGPCRYDSSLGLLTKKFINLIKHAEDGILDLNKAADTLEV-QKRRIYDITNVLEGIGLI 187
           P  P R++ SLGLLT KF++L++ A+DG+LDL  AADTL V QKRRIYDITNVLEGIGLI
Sbjct: 2   PGTPSRHEKSLGLLTTKFVSLLQEAKDGVLDLKLAADTLAVRQKRRIYDITNVLEGIGLI 61

Query: 188 EKKLKNRIQWKGL 200
           EKK KN IQWKG+
Sbjct: 62  EKKSKNSIQWKGV 74


>pdb|2AZE|B Chain B, Structure Of The Rb C-Terminal Domain Bound To An E2f1-Dp1
           Heterodimer
          Length = 106

 Score = 54.7 bits (130), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 32/89 (35%), Positives = 51/89 (57%), Gaps = 7/89 (7%)

Query: 226 ERRLDEQIRIMQERLRDLSEDENNQKWLFVTEDDIKSLPCFQNETLIAIKAPHGTTLEVP 285
           E++LD  + I   +LR LSED ++Q+  +VT  D++S+     + ++ IKAP  T L+  
Sbjct: 22  EQQLDHLMNICTTQLRLLSEDTDSQRLAYVTCQDLRSIADPAEQMVMVIKAPPETQLQAV 81

Query: 286 DPDEAVDYPQRRYRIVLRSTMGPIDVYLV 314
           D  E        ++I L+S  GPIDV+L 
Sbjct: 82  DSSE-------NFQISLKSKQGPIDVFLC 103


>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 = 2.0,   Method: Composition-based stats.
 Identities = 19/41 (46%), Positives = 25/41 (60%), Gaps = 4/41 (9%)

Query: 163 AADTLEVQK---RRIYDITNVLEGIGLIEKKLKNRIQWKGL 200
           AAD+   QK   RR+YD  NVL  + +I K+ K  I+W GL
Sbjct: 50  AADSAYDQKNIRRRVYDALNVLMAMNIISKE-KKEIKWIGL 89


>pdb|3GAA|A Chain A, The Crystal Structure Of The Protein With Unknown Function
           From Thermoplasma Acidophilum
 pdb|3GAA|B Chain B, The Crystal Structure Of The Protein With Unknown Function
           From Thermoplasma Acidophilum
 pdb|3GAA|C Chain C, The Crystal Structure Of The Protein With Unknown Function
           From Thermoplasma Acidophilum
 pdb|3GAA|D Chain D, The Crystal Structure Of The Protein With Unknown Function
           From Thermoplasma Acidophilum
 pdb|3GAA|E Chain E, The Crystal Structure Of The Protein With Unknown Function
           From Thermoplasma Acidophilum
          Length = 252

 Score = 29.3 bits (64), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 17/61 (27%), Positives = 34/61 (55%), Gaps = 6/61 (9%)

Query: 200 LDVSRPG------EADENASSLQAEVESLTIQERRLDEQIRIMQERLRDLSEDENNQKWL 253
           +D+  PG      EA   A +L+ + + L  Q + LDEQI+ ++E+ ++L E +   + +
Sbjct: 191 VDIPDPGAVLSIIEAINKAYNLKIKTDLLEEQVKALDEQIKKIEEQYKELQEKQKEPQSM 250

Query: 254 F 254
           +
Sbjct: 251 Y 251


  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
   0.311    0.131    0.372 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,185,777
Number of Sequences: 62578
Number of extensions: 553189
Number of successful extensions: 1004
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 989
Number of HSP's gapped (non-prelim): 20
length of query: 456
length of database: 14,973,337
effective HSP length: 102
effective length of query: 354
effective length of database: 8,590,381
effective search space: 3040994874
effective search space used: 3040994874
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 53 (25.0 bits)