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= 045498
         (207 letters)

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

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



>pdb|3ZT9|A Chain A, The Bacterial Stressosome: A Modular System That Has Been
           Adapted To Control Secondary Messenger Signaling
          Length = 193

 Score = 28.1 bits (61), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 23/76 (30%), Positives = 33/76 (43%), Gaps = 14/76 (18%)

Query: 117 IDGLCRVGR----WEEA---RKKLDQLSEKGLV-----PGVVTYNILINGLCKKGMIMEA 164
           +  LCRV R    W+ A      +  LS KG++     PG++ YN     L  KG   E 
Sbjct: 83  VAALCRVDRRQGLWQAAIVGNIHVKILSAKGIITPLATPGILGYNYPHQLLIAKGSYQEG 142

Query: 165 DKLLVQMK--EKGCFP 178
           D  L+     ++G  P
Sbjct: 143 DLFLIHSDGIQEGAVP 158


>pdb|1GL9|B Chain B, Archaeoglobus Fulgidus Reverse Gyrase Complexed With Adpnp
 pdb|1GL9|C Chain C, Archaeoglobus Fulgidus Reverse Gyrase Complexed With Adpnp
          Length = 1054

 Score = 27.7 bits (60), Expect = 5.1,   Method: Compositional matrix adjust.
 Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 8/80 (10%)

Query: 48  NGLCTFNRLKEAVELFDKMVAQGITAELVTYNPLIHDNWEKQGRFSAMALLQTLERDKYE 107
           NGL T++R  ++  + D  V Q I  E +  +  +   W + G    +   + L RD  +
Sbjct: 804 NGLITYHR-TDSTRVSD--VGQRIAKEYLG-DDFVGREWGESGAHECIRPTRPLTRDDVQ 859

Query: 108 LNIEVYSLVIDGLCRVGRWE 127
             I+   LV++GL    RWE
Sbjct: 860 RLIQEGVLVVEGL----RWE 875


>pdb|1GKU|B Chain B, Reverse Gyrase From Archaeoglobus Fulgidus
          Length = 1054

 Score = 27.3 bits (59), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 8/80 (10%)

Query: 48  NGLCTFNRLKEAVELFDKMVAQGITAELVTYNPLIHDNWEKQGRFSAMALLQTLERDKYE 107
           NGL T++R  ++  + D  V Q I  E +  +  +   W + G    +   + L RD  +
Sbjct: 804 NGLITYHR-TDSTRVSD--VGQRIAKEYLG-DDFVGREWGESGAHECIRPTRPLTRDDVQ 859

Query: 108 LNIEVYSLVIDGLCRVGRWE 127
             I+   LV++GL    RWE
Sbjct: 860 RLIQEGVLVVEGL----RWE 875


  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
   0.323    0.139    0.410 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,784,455
Number of Sequences: 62578
Number of extensions: 221084
Number of successful extensions: 616
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 615
Number of HSP's gapped (non-prelim): 7
length of query: 207
length of database: 14,973,337
effective HSP length: 94
effective length of query: 113
effective length of database: 9,091,005
effective search space: 1027283565
effective search space used: 1027283565
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 bits)