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= psy3509
         (157 letters)

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

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



>pdb|3S84|A Chain A, Dimeric Apoa-Iv
 pdb|3S84|B Chain B, Dimeric Apoa-Iv
          Length = 273

 Score = 32.0 bits (71), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 25/116 (21%), Positives = 62/116 (53%), Gaps = 4/116 (3%)

Query: 33  EIERRLKEFQVEIERRLKEFQVEIERRLKEFQVEIERRLKEFQVEIERRLKEFQVEIERR 92
           E+  RL     E+ +++ +   E+++RL+ +  ++  ++     ++ R+L  +   +ER 
Sbjct: 26  ELRARLLPHANEVSQKIGDNLRELQQRLEPYADQLRTQVNTQAEQLRRQLTPYAQRMERV 85

Query: 93  LKE----FQVEIERRLKEFQVEIERRLKEFQVEIERRLKEFQVEIERRLKELRSSI 144
           L+E     Q  +     E + +I++ ++E +  +     EF+V+I++ ++ELR S+
Sbjct: 86  LRENADSLQASLRPHADELKAKIDQNVEELKGRLTPYADEFKVKIDQTVEELRRSL 141



 Score = 27.7 bits (60), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 25/134 (18%), Positives = 69/134 (51%), Gaps = 4/134 (2%)

Query: 11  EIERRLKEFQVEIERRLKEFQVEIERRLKEFQVEIERRLKEFQVEIERRLKEFQVEIERR 70
           E+  RL     E+ +++ +   E+++RL+ +  ++  ++     ++ R+L  +   +ER 
Sbjct: 26  ELRARLLPHANEVSQKIGDNLRELQQRLEPYADQLRTQVNTQAEQLRRQLTPYAQRMERV 85

Query: 71  LKE----FQVEIERRLKEFQVEIERRLKEFQVEIERRLKEFQVEIERRLKEFQVEIERRL 126
           L+E     Q  +     E + +I++ ++E +  +     EF+V+I++ ++E +  +    
Sbjct: 86  LRENADSLQASLRPHADELKAKIDQNVEELKGRLTPYADEFKVKIDQTVEELRRSLAPYA 145

Query: 127 KEFQVEIERRLKEL 140
           ++ Q ++  +L+ L
Sbjct: 146 QDTQEKLNHQLEGL 159



 Score = 26.2 bits (56), Expect = 8.5,   Method: Compositional matrix adjust.
 Identities = 27/150 (18%), Positives = 71/150 (47%), Gaps = 12/150 (8%)

Query: 7   HCQVE-IERRLKEFQVEIERRLKE----FQVEIERRLKEFQVEIERRLKEFQVEIERRLK 61
           + Q E + R+L  +   +ER L+E     Q  +     E + +I++ ++E +  +     
Sbjct: 65  NTQAEQLRRQLTPYAQRMERVLRENADSLQASLRPHADELKAKIDQNVEELKGRLTPYAD 124

Query: 62  EFQVEIERRLKEFQVEIERRLKEFQVEIERRLKEFQVEIERRLKEFQV-------EIERR 114
           EF+V+I++ ++E +  +    ++ Q ++  +L+    ++++  +E +        E+ +R
Sbjct: 125 EFKVKIDQTVEELRRSLAPYAQDTQEKLNHQLEGLTFQMKKNAEELKARISASAEELRQR 184

Query: 115 LKEFQVEIERRLKEFQVEIERRLKELRSSI 144
           L     ++   L+     +++ L EL   +
Sbjct: 185 LAPLAEDVRGNLRGNTEGLQKSLAELGGHL 214


>pdb|2AQ4|A Chain A, Ternary Complex Of The Catalytic Core Of Rev1 With Dna And
           Dctp.
 pdb|3BJY|A Chain A, Catalytic Core Of Rev1 In Complex With Dna (Modified
           Template Guanine) And Incoming Nucleotide
 pdb|3OSP|A Chain A, Structure Of Rev1
          Length = 434

 Score = 30.0 bits (66), Expect = 0.56,   Method: Compositional matrix adjust.
 Identities = 13/46 (28%), Positives = 24/46 (52%)

Query: 110 EIERRLKEFQVEIERRLKEFQVEIERRLKELRSSIFSRHEKLGMQT 155
           EI +   +  +++ RR K+  +E  + +   R   FSR  +LG+ T
Sbjct: 352 EINKTTSQITLKLMRRCKDAPIEPPKYMGMGRCDSFSRSSRLGIPT 397


  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
   0.324    0.140    0.369 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,767,986
Number of Sequences: 62578
Number of extensions: 150490
Number of successful extensions: 1293
Number of sequences better than 100.0: 55
Number of HSP's better than 100.0 without gapping: 32
Number of HSP's successfully gapped in prelim test: 23
Number of HSP's that attempted gapping in prelim test: 924
Number of HSP's gapped (non-prelim): 234
length of query: 157
length of database: 14,973,337
effective HSP length: 91
effective length of query: 66
effective length of database: 9,278,739
effective search space: 612396774
effective search space used: 612396774
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 47 (22.7 bits)