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= 035700
         (179 letters)

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

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



>pdb|3KT4|A Chain A, Crystal Structure Of Tpa1 From Saccharomyces Cerevisiae, A
           Component Of The Messenger Ribonucleoprotein Complex
          Length = 633

 Score = 27.7 bits (60), Expect = 3.8,   Method: Composition-based stats.
 Identities = 10/24 (41%), Positives = 18/24 (75%)

Query: 130 SEMDGSVSAYSETCHVLTYEDKEG 153
           S+ D S++ Y++ CH+LT++D  G
Sbjct: 122 SKTDXSINTYTKGCHLLTHDDVIG 145


>pdb|3MGU|A Chain A, Saccharomyces Cerevisiae Tpa1
          Length = 644

 Score = 27.3 bits (59), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 9/21 (42%), Positives = 17/21 (80%)

Query: 130 SEMDGSVSAYSETCHVLTYED 150
           S+ D S++ Y++ CH+LT++D
Sbjct: 141 SKTDMSINTYTKGCHLLTHDD 161


>pdb|3KT7|A Chain A, Crystal Structure Of Tpa1 From Saccharomyces Cerevisiae, A
           Component Of The Messenger Ribonucleoprotein Complex
          Length = 633

 Score = 27.3 bits (59), Expect = 5.1,   Method: Compositional matrix adjust.
 Identities = 9/21 (42%), Positives = 17/21 (80%)

Query: 130 SEMDGSVSAYSETCHVLTYED 150
           S+ D S++ Y++ CH+LT++D
Sbjct: 122 SKTDMSINTYTKGCHLLTHDD 142


>pdb|3KT1|A Chain A, Crystal Structure Of Tpa1 From Saccharomyces Cerevisiae, A
           Component Of The Messenger Ribonucleoprotein Complex
          Length = 633

 Score = 27.3 bits (59), Expect = 5.1,   Method: Compositional matrix adjust.
 Identities = 9/21 (42%), Positives = 17/21 (80%)

Query: 130 SEMDGSVSAYSETCHVLTYED 150
           S+ D S++ Y++ CH+LT++D
Sbjct: 122 SKTDMSINTYTKGCHLLTHDD 142


>pdb|4F91|B Chain B, Brr2 Helicase Region
          Length = 1724

 Score = 27.3 bits (59), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 13/36 (36%), Positives = 18/36 (50%)

Query: 83   EGSSATFFVKVYMEGIPIGRKLDLLAHDGYHDLIRT 118
            +GS   FF K   E +P+   LD   HD ++  I T
Sbjct: 1306 QGSKKDFFKKFLYEPLPVESHLDHCMHDHFNAEIVT 1341


>pdb|4F92|B Chain B, Brr2 Helicase Region S1087l
 pdb|4F93|B Chain B, Brr2 Helicase Region S1087l, Mg-Atp
          Length = 1724

 Score = 26.9 bits (58), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 13/36 (36%), Positives = 18/36 (50%)

Query: 83   EGSSATFFVKVYMEGIPIGRKLDLLAHDGYHDLIRT 118
            +GS   FF K   E +P+   LD   HD ++  I T
Sbjct: 1306 QGSKKDFFKKFLYEPLPVESHLDHCMHDHFNAEIVT 1341


  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
   0.320    0.135    0.408 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,951,601
Number of Sequences: 62578
Number of extensions: 198869
Number of successful extensions: 422
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 418
Number of HSP's gapped (non-prelim): 9
length of query: 179
length of database: 14,973,337
effective HSP length: 93
effective length of query: 86
effective length of database: 9,153,583
effective search space: 787208138
effective search space used: 787208138
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)