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= psy8797
         (122 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 = 93.6 bits (231), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 49/77 (63%), Positives = 61/77 (79%), Gaps = 6/77 (7%)

Query: 46  PPTTPAKEKGTRYDTSLGLLTKKFVKLLQSSPQGVVDLNVASESLDV-QKRRIYDITNVL 104
           PP TP     +R++ SLGLLT KFV LLQ +  GV+DL +A+++L V QKRRIYDITNVL
Sbjct: 1   PPGTP-----SRHEKSLGLLTTKFVSLLQEAKDGVLDLKLAADTLAVRQKRRIYDITNVL 55

Query: 105 EGIGILEKKSKNNIQCK 121
           EGIG++EKKSKN+IQ K
Sbjct: 56  EGIGLIEKKSKNSIQWK 72


>pdb|1ZBA|1 Chain 1, Foot-And-Mouth Disease Virus Serotype A1061 Complexed
          With Oligosaccharide Receptor.
 pdb|1ZBE|1 Chain 1, Foot-And Mouth Disease Virus Serotype A1061
          Length = 212

 Score = 27.3 bits (59), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 11/27 (40%), Positives = 17/27 (62%)

Query: 57 RYDTSLGLLTKKFVKLLQSSPQGVVDL 83
          R+ T +G +  +FVK+   SP  V+DL
Sbjct: 27 RHHTDVGFIMDRFVKINSLSPTHVIDL 53


>pdb|3JWH|A Chain A, Crystal Structure Analysis Of The Methyltransferase
          Domain Of Bacterial-Avhen1-C
 pdb|3JWH|B Chain B, Crystal Structure Analysis Of The Methyltransferase
          Domain Of Bacterial-Avhen1-C
          Length = 217

 Score = 26.9 bits (58), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 17/72 (23%), Positives = 35/72 (48%), Gaps = 2/72 (2%)

Query: 28 DEESPFKTPKSVKKMRVNPPTTPAKEKGTRYDTSLGLLTKKFVKLL--QSSPQGVVDLNV 85
          +EE+  + P S+ + R+N      K+   R    LG      +K+L   S  + +  ++V
Sbjct: 2  EEEAAVEKPISLNQQRMNGVVAALKQSNARRVIDLGCGQGNLLKILLKDSFFEQITGVDV 61

Query: 86 ASESLDVQKRRI 97
          +  SL++ + R+
Sbjct: 62 SYRSLEIAQERL 73


>pdb|2RCC|A Chain A, Crystal Structure Of Putative Class I Ribonucleotide
           Reductase (Np_241368.1) From Bacillus Halodurans At 1.90
           A Resolution
 pdb|2RCC|B Chain B, Crystal Structure Of Putative Class I Ribonucleotide
           Reductase (Np_241368.1) From Bacillus Halodurans At 1.90
           A Resolution
 pdb|2RCC|C Chain C, Crystal Structure Of Putative Class I Ribonucleotide
           Reductase (Np_241368.1) From Bacillus Halodurans At 1.90
           A Resolution
          Length = 346

 Score = 26.6 bits (57), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 13/25 (52%), Positives = 15/25 (60%)

Query: 92  VQKRRIYDITNVLEGIGILEKKSKN 116
           +QKR+IYD T      GIL  KS N
Sbjct: 5   LQKRKIYDTTASNASTGILNGKSSN 29


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

 Score = 25.4 bits (54), Expect = 9.1,   Method: Compositional matrix adjust.
 Identities = 14/35 (40%), Positives = 22/35 (62%), Gaps = 3/35 (8%)

Query: 84  NVASESLDVQK---RRIYDITNVLEGIGILEKKSK 115
           ++A++S   QK   RR+YD  NVL  + I+ K+ K
Sbjct: 48  HLAADSAYDQKNIRRRVYDALNVLMAMNIISKEKK 82


  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
   0.314    0.132    0.361 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,363,746
Number of Sequences: 62578
Number of extensions: 120098
Number of successful extensions: 187
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 182
Number of HSP's gapped (non-prelim): 7
length of query: 122
length of database: 14,973,337
effective HSP length: 84
effective length of query: 38
effective length of database: 9,716,785
effective search space: 369237830
effective search space used: 369237830
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 45 (21.9 bits)