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= 044892
         (152 letters)

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

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



>pdb|1ECR|A Chain A, Escherichia Coli Replication Terminator Protein (Tus)
           Complexed With Dna
 pdb|2EWJ|A Chain A, Escherichia Coli Replication Terminator Protein (Tus)
           Complexed With Dna- Locked Form
 pdb|2I05|A Chain A, Escherichia Coli Replication Terminator Protein (Tus)
           Complexed With Tera Dna
 pdb|2I06|A Chain A, Escherichia Coli Replication Terminator Protein (tus)
           Complexed With Dna- Locked Form
          Length = 309

 Score = 27.3 bits (59), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 19/80 (23%), Positives = 37/80 (46%), Gaps = 2/80 (2%)

Query: 71  VNRLELVDILSNDSRAAVRVNVPAIFLNSSSKRTSNIAKSVNLSGTPFCFSTDNKFAAIG 130
           +NR+E+   L ND+++    +   +F+   S+  S+ A +V L G   C+  DN   A  
Sbjct: 53  LNRIEVKQHLGNDAQSLALRHFRHLFIQQQSENRSSKA-AVRLPGV-LCYQVDNLSQAAL 110

Query: 131 CKMRYHQGNGSSLFDGCLSI 150
                H     + F+  +++
Sbjct: 111 VSHIQHINKLKTTFEHIVTV 130


>pdb|3K1H|A Chain A, Crystal Structure Of Hp1076 From H.Pylori
          Length = 158

 Score = 26.9 bits (58), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 12/28 (42%), Positives = 17/28 (60%)

Query: 59  HSSGTPKAFLPGVNRLELVDILSNDSRA 86
            S   PKAF+P  +   L D+LS++ RA
Sbjct: 131 ESLSNPKAFMPSFSNQSLKDLLSDNLRA 158


>pdb|3K1I|C Chain C, Crystal Strcture Of Flis-Hp1076 Complex In H. Pylori
 pdb|3K1I|D Chain D, Crystal Strcture Of Flis-Hp1076 Complex In H. Pylori
          Length = 178

 Score = 26.9 bits (58), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 12/28 (42%), Positives = 17/28 (60%)

Query: 59  HSSGTPKAFLPGVNRLELVDILSNDSRA 86
            S   PKAF+P  +   L D+LS++ RA
Sbjct: 151 ESLSNPKAFMPSFSNQSLKDLLSDNLRA 178


>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation
           Initiation Factor 4a-2
          Length = 237

 Score = 26.2 bits (56), Expect = 7.7,   Method: Compositional matrix adjust.
 Identities = 13/38 (34%), Positives = 22/38 (57%)

Query: 51  KGYEVICDHSSGTPKAFLPGVNRLELVDILSNDSRAAV 88
           KGY+VI    SGT K     ++ L+ ++I   +++A V
Sbjct: 66  KGYDVIAQAQSGTGKTATFAISILQQLEIEFKETQALV 103


  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    0.139    0.434 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,475,347
Number of Sequences: 62578
Number of extensions: 171589
Number of successful extensions: 454
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 451
Number of HSP's gapped (non-prelim): 8
length of query: 152
length of database: 14,973,337
effective HSP length: 90
effective length of query: 62
effective length of database: 9,341,317
effective search space: 579161654
effective search space used: 579161654
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 47 (22.7 bits)