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= 044902
         (389 letters)

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

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



>pdb|3LFU|A Chain A, Crystal Structure Of E. Coli Uvrd
          Length = 647

 Score = 31.2 bits (69), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 22/54 (40%), Positives = 30/54 (55%), Gaps = 3/54 (5%)

Query: 223 GFKQG-FPSGMRLGKDFKGRVKEWQRLPYVGPYEEMGESKKTKAGVKRLEKRAV 275
           G ++G FPS M L  D  GR++E +RL YVG    M +   T A  +RL  + V
Sbjct: 574 GMEEGMFPSQMSL--DEGGRLEEERRLAYVGVTRAMQKLTLTYAETRRLYGKEV 625


>pdb|2IS1|A Chain A, Crystal Structure Of Uvrd-Dna-So4 Complex
 pdb|2IS1|B Chain B, Crystal Structure Of Uvrd-Dna-So4 Complex
 pdb|2IS2|A Chain A, Crystal Structure Of Uvrd-Dna Binary Complex
 pdb|2IS2|B Chain B, Crystal Structure Of Uvrd-Dna Binary Complex
 pdb|2IS4|A Chain A, Crystal Structure Of Uvrd-Dna-Adpnp Ternary Complex
 pdb|2IS4|B Chain B, Crystal Structure Of Uvrd-Dna-Adpnp Ternary Complex
 pdb|2IS6|A Chain A, Crystal Structure Of Uvrd-Dna-Adpmgf3 Ternary Complex
 pdb|2IS6|B Chain B, Crystal Structure Of Uvrd-Dna-Adpmgf3 Ternary Complex
          Length = 680

 Score = 31.2 bits (69), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 22/54 (40%), Positives = 30/54 (55%), Gaps = 3/54 (5%)

Query: 223 GFKQG-FPSGMRLGKDFKGRVKEWQRLPYVGPYEEMGESKKTKAGVKRLEKRAV 275
           G ++G FPS M L  D  GR++E +RL YVG    M +   T A  +RL  + V
Sbjct: 574 GMEEGMFPSQMSL--DEGGRLEEERRLAYVGVTRAMQKLTLTYAETRRLYGKEV 625


>pdb|2IUS|A Chain A, E. Coli Ftsk Motor Domain
 pdb|2IUS|B Chain B, E. Coli Ftsk Motor Domain
 pdb|2IUS|C Chain C, E. Coli Ftsk Motor Domain
 pdb|2IUS|D Chain D, E. Coli Ftsk Motor Domain
 pdb|2IUS|E Chain E, E. Coli Ftsk Motor Domain
 pdb|2IUS|F Chain F, E. Coli Ftsk Motor Domain
          Length = 512

 Score = 30.8 bits (68), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 28/96 (29%), Positives = 44/96 (45%), Gaps = 8/96 (8%)

Query: 215 VERMELRYGFKQGFPSGMRLGKDFKGRVKEWQRL--PYVGPYEEMGESKKTKAGVKRLEK 272
           V  ME RY        G+R    +  ++ E  R+  P   PY + G+S   +  V + E 
Sbjct: 240 VNEMERRYKLMSAL--GVRNLAGYNEKIAEADRMMRPIPDPYWKPGDSMDAQHPVLKKEP 297

Query: 273 RAVAIVHEF--LSLTVEKMVE--VEKISHFRKWFGI 304
             V +V EF  L +TV K VE  + +++   +  GI
Sbjct: 298 YIVVLVDEFADLMMTVGKKVEELIARLAQKARAAGI 333


  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    0.406 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,188,791
Number of Sequences: 62578
Number of extensions: 452459
Number of successful extensions: 886
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 886
Number of HSP's gapped (non-prelim): 4
length of query: 389
length of database: 14,973,337
effective HSP length: 101
effective length of query: 288
effective length of database: 8,652,959
effective search space: 2492052192
effective search space used: 2492052192
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: 52 (24.6 bits)