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= psy5092
         (291 letters)

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

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



>pdb|3BD0|A Chain A, Crystal Structure Of Memo, Form Ii
 pdb|3BD0|B Chain B, Crystal Structure Of Memo, Form Ii
 pdb|3BD0|C Chain C, Crystal Structure Of Memo, Form Ii
 pdb|3BD0|D Chain D, Crystal Structure Of Memo, Form Ii
          Length = 293

 Score =  261 bits (668), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 116/196 (59%), Positives = 150/196 (76%)

Query: 51  ELDKQLGNWLNNAELSHGPARAIISPHAGYRYCGECAAFAYRQISPASVQRIFILGPSHY 110
           +L+ QL  WL+  + +  PARAII+PHAGY YCG CAA AY+Q+ P+  +RIFILGPSH+
Sbjct: 19  QLNAQLEGWLSQVQSTKRPARAIIAPHAGYTYCGSCAAHAYKQVDPSITRRIFILGPSHH 78

Query: 111 YQLGGCALSGAKKYSTPLYDLKIDSQIYSELEATNKFETISMDVDEEEHSLEMQIPYIAK 170
             L  CALS    Y TPLYDL+ID +IY EL  T  FE +S+  DE+EHS+EM +PY AK
Sbjct: 79  VPLSRCALSSVDIYRTPLYDLRIDQKIYGELWKTGMFERMSLQTDEDEHSIEMHLPYTAK 138

Query: 171 VMEDFKNEFTIVPVMVGSLSTGREAEYGRIFAPYLADPRNLFVISSDFCHWGDRFRFTYY 230
            ME  K+EFTI+PV+VG+LS  +E E+G++F+ YLADP NLFV+SSDFCHWG RFR++YY
Sbjct: 139 AMESHKDEFTIIPVLVGALSESKEQEFGKLFSKYLADPSNLFVVSSDFCHWGQRFRYSYY 198

Query: 231 DSAYGEIHQSIEALDR 246
           D + GEI++SIE LD+
Sbjct: 199 DESQGEIYRSIEHLDK 214


>pdb|3BCZ|A Chain A, Crystal Structure Of Memo
 pdb|3BCZ|B Chain B, Crystal Structure Of Memo
 pdb|3BCZ|C Chain C, Crystal Structure Of Memo
 pdb|3BCZ|D Chain D, Crystal Structure Of Memo
          Length = 293

 Score =  256 bits (653), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 115/200 (57%), Positives = 148/200 (74%)

Query: 51  ELDKQLGNWLNNAELSHGPARAIISPHAGYRYCGECAAFAYRQISPASVQRIFILGPSHY 110
           +L+ QL  WL+  + +  PARAII+PHAGY YCG CAA AY+Q+ P+  +RIFILGPSH+
Sbjct: 19  QLNAQLEGWLSQVQSTKRPARAIIAPHAGYTYCGSCAAHAYKQVDPSITRRIFILGPSHH 78

Query: 111 YQLGGCALSGAKKYSTPLYDLKIDSQIYSELEATNKFETISMDVDEEEHSLEMQIPYIAK 170
             L  CALS    Y TPLYDL+ID +IY EL  T  FE  S+  DE+EHS+E  +PY AK
Sbjct: 79  VPLSRCALSSVDIYRTPLYDLRIDQKIYGELWKTGXFERXSLQTDEDEHSIEXHLPYTAK 138

Query: 171 VMEDFKNEFTIVPVMVGSLSTGREAEYGRIFAPYLADPRNLFVISSDFCHWGDRFRFTYY 230
             E  K+EFTI+PV+VG+LS  +E E+G++F+ YLADP NLFV+SSDFCHWG RFR++YY
Sbjct: 139 AXESHKDEFTIIPVLVGALSESKEQEFGKLFSKYLADPSNLFVVSSDFCHWGQRFRYSYY 198

Query: 231 DSAYGEIHQSIEALDRKSPS 250
           D + GEI++SIE LD+   S
Sbjct: 199 DESQGEIYRSIEHLDKXGXS 218


>pdb|1O65|A Chain A, Crystal Structure Of An Hypothetical Protein
 pdb|1O65|B Chain B, Crystal Structure Of An Hypothetical Protein
 pdb|1O65|C Chain C, Crystal Structure Of An Hypothetical Protein
          Length = 246

 Score = 30.8 bits (68), Expect = 0.82,   Method: Compositional matrix adjust.
 Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 6/59 (10%)

Query: 2   LSMVGIWMGNCFSQGPEYALVTLCTVLLPRPPCYKLSNHLRFKCSKQTKELDKQLGNWL 60
           L+   ++MG+ F  G       L  V  PR PCYKL+ H       Q  +   ++G WL
Sbjct: 105 LTESNVYMGDIFRWGE-----ALIQVSQPRSPCYKLNYHFDISDIAQLMQNTGKVG-WL 157


>pdb|3GSZ|A Chain A, Structure Of The Genotype 2b Hcv Polymerase
 pdb|3GSZ|B Chain B, Structure Of The Genotype 2b Hcv Polymerase
 pdb|3HVO|A Chain A, Structure Of The Genotype 2b Hcv Polymerase Bound To A Nni
 pdb|3HVO|B Chain B, Structure Of The Genotype 2b Hcv Polymerase Bound To A Nni
          Length = 563

 Score = 29.3 bits (64), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 5/44 (11%)

Query: 69  PARAIISPHAGYRYCGECAAFAYRQISPASVQRIFILGPSHYYQ 112
           PAR I+ P  G R C + A +   Q  P +     I+GPS+ +Q
Sbjct: 156 PARLIVYPDLGVRVCEKMALYDIAQKLPKA-----IMGPSYGFQ 194


  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
   0.321    0.137    0.423 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,760,711
Number of Sequences: 62578
Number of extensions: 344250
Number of successful extensions: 716
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 714
Number of HSP's gapped (non-prelim): 5
length of query: 291
length of database: 14,973,337
effective HSP length: 98
effective length of query: 193
effective length of database: 8,840,693
effective search space: 1706253749
effective search space used: 1706253749
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)