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= psy5512
         (245 letters)

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

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



>pdb|1PEM|A Chain A, Ribonucleotide Reductase Protein R1e From Salmonella
           Typhimurium
 pdb|1PEO|A Chain A, Ribonucleotide Reductase Protein R1e From Salmonella
           Typhimurium
 pdb|1PEQ|A Chain A, Ribonucleotide Reductase Protein R1e From Salmonella
           Typhimurium
 pdb|1PEU|A Chain A, Ribonucleotide Reductase Protein R1e From Salmonella
           Typhimurium
 pdb|2BQ1|E Chain E, Ribonucleotide Reductase Class 1b Holocomplex R1e,R2f From
           Salmonella Typhimurium
 pdb|2BQ1|F Chain F, Ribonucleotide Reductase Class 1b Holocomplex R1e,R2f From
           Salmonella Typhimurium
          Length = 714

 Score = 28.5 bits (62), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 19/83 (22%), Positives = 38/83 (45%), Gaps = 5/83 (6%)

Query: 17  IGGDVNTRNIGGDVKTTNIGGD----VNTPNIGGDVKTHVSTPNIGGDVNTPNIGGDVKT 72
           I G +N  N+  ++   N        ++  +IG D+  ++ + NI   +++P+IG  V+T
Sbjct: 378 IAGRINMSNLCSEILQVNSASRYDDNLDYTHIGHDISCNLGSLNIAHVMDSPDIGRTVET 437

Query: 73  PNIGGDVKTPNIGGDVKTPNIGG 95
             I G     ++      P+I  
Sbjct: 438 A-IRGLTAVSDMSHIRSVPSIAA 459


>pdb|4GER|A Chain A, Crystal Structure Of Gentlyase, The Neutral
           Metalloprotease Of Paenibacillus Polymyxa
 pdb|4GER|B Chain B, Crystal Structure Of Gentlyase, The Neutral
           Metalloprotease Of Paenibacillus Polymyxa
 pdb|4B52|A Chain A, Crystal Structure Of Gentlyase, The Neutral
           Metalloprotease Of Paenibacillus Polymyxa
 pdb|4B52|B Chain B, Crystal Structure Of Gentlyase, The Neutral
           Metalloprotease Of Paenibacillus Polymyxa
          Length = 304

 Score = 27.7 bits (60), Expect = 6.8,   Method: Compositional matrix adjust.
 Identities = 14/34 (41%), Positives = 20/34 (58%), Gaps = 2/34 (5%)

Query: 26  IGGDVKTTN--IGGDVNTPNIGGDVKTHVSTPNI 57
           IG D++  N  +G D+ TPNI GD    +S P +
Sbjct: 165 IGNDIQRKNWLVGDDIYTPNIAGDALRSMSNPTL 198


  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
   0.308    0.140    0.417 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,485,564
Number of Sequences: 62578
Number of extensions: 512930
Number of successful extensions: 646
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: 577
Number of HSP's gapped (non-prelim): 38
length of query: 245
length of database: 14,973,337
effective HSP length: 96
effective length of query: 149
effective length of database: 8,965,849
effective search space: 1335911501
effective search space used: 1335911501
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (22.0 bits)
S2: 50 (23.9 bits)