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= 018719
         (351 letters)

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

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



>pdb|3GG2|A Chain A, Crystal Structure Of Udp-Glucose 6-Dehydrogenase From
           Porphyromonas Gingivalis Bound To Product
           Udp-Glucuronate
 pdb|3GG2|B Chain B, Crystal Structure Of Udp-Glucose 6-Dehydrogenase From
           Porphyromonas Gingivalis Bound To Product
           Udp-Glucuronate
 pdb|3GG2|C Chain C, Crystal Structure Of Udp-Glucose 6-Dehydrogenase From
           Porphyromonas Gingivalis Bound To Product
           Udp-Glucuronate
 pdb|3GG2|D Chain D, Crystal Structure Of Udp-Glucose 6-Dehydrogenase From
           Porphyromonas Gingivalis Bound To Product
           Udp-Glucuronate
          Length = 450

 Score = 32.7 bits (73), Expect = 0.31,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 19/75 (25%)

Query: 268 SLYYTKFKHYCKPNMEGRNCYA-----------DEHYLPTLFHLE--LQIGLS---HMPI 311
           S+ + KF  Y K N++GR C A           D    P+L  +E  L++G     + P+
Sbjct: 302 SILFDKFSTYYKGNVQGR-CVAIWGLSFKPGTDDMREAPSLVLIEKLLEVGCRVRVYDPV 360

Query: 312 GLKESGIQKRIGHKI 326
            +KE+  QKR+G K+
Sbjct: 361 AMKEA--QKRLGDKV 373


>pdb|2VWK|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
           X-Ray Crystallography. V93q Polymerase Variant
          Length = 773

 Score = 30.4 bits (67), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 4/54 (7%)

Query: 258 RQHAMIIMADSLY----YTKFKHYCKPNMEGRNCYADEHYLPTLFHLELQIGLS 307
           RQ A+ I+A+S Y    Y K + YCK   E    +  ++   T+  +E + G  
Sbjct: 482 RQRAIKILANSFYGYYGYAKARWYCKECAESVTAWGRQYIETTIREIEEKFGFK 535


>pdb|2XHB|A Chain A, Crystal Structure Of Dna Polymerase From Thermococcus
           Gorgonarius In Complex With Hypoxanthine-Containing Dna
          Length = 773

 Score = 30.4 bits (67), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 4/54 (7%)

Query: 258 RQHAMIIMADSLY----YTKFKHYCKPNMEGRNCYADEHYLPTLFHLELQIGLS 307
           RQ A+ I+A+S Y    Y K + YCK   E    +  ++   T+  +E + G  
Sbjct: 482 RQRAIKILANSFYGYYGYAKARWYCKECAESVTAWGRQYIETTIREIEEKFGFK 535


>pdb|2VWJ|A Chain A, Uracil Recognition In Archaeal Dna Polymerases Captured By
           X-Ray Crystallography
          Length = 773

 Score = 30.4 bits (67), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 4/54 (7%)

Query: 258 RQHAMIIMADSLY----YTKFKHYCKPNMEGRNCYADEHYLPTLFHLELQIGLS 307
           RQ A+ I+A+S Y    Y K + YCK   E    +  ++   T+  +E + G  
Sbjct: 482 RQRAIKILANSFYGYYGYAKARWYCKECAESVTAWGRQYIETTIREIEEKFGFK 535


>pdb|1TGO|A Chain A, Thermostable B Type Dna Polymerase From Thermococcus
           Gorgonarius
          Length = 773

 Score = 30.4 bits (67), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 4/54 (7%)

Query: 258 RQHAMIIMADSLY----YTKFKHYCKPNMEGRNCYADEHYLPTLFHLELQIGLS 307
           RQ A+ I+A+S Y    Y K + YCK   E    +  ++   T+  +E + G  
Sbjct: 482 RQRAIKILANSFYGYYGYAKARWYCKECAESVTAWGRQYIETTIREIEEKFGFK 535


>pdb|1QHT|A Chain A, Dna Polymerase From Thermococcus Sp. 9on-7 Archaeon
          Length = 775

 Score = 30.0 bits (66), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 4/54 (7%)

Query: 258 RQHAMIIMADSLY----YTKFKHYCKPNMEGRNCYADEHYLPTLFHLELQIGLS 307
           RQ A+ I+A+S Y    Y K + YCK   E    +  E+    +  LE + G  
Sbjct: 482 RQRAIKILANSFYGYYGYAKARWYCKECAESVTAWGREYIEMVIRELEEKFGFK 535


>pdb|3IHW|A Chain A, Crystal Structure Of The Ras-Like Domain Of Centg3
          Length = 184

 Score = 28.5 bits (62), Expect = 6.4,   Method: Compositional matrix adjust.
 Identities = 28/101 (27%), Positives = 42/101 (41%), Gaps = 13/101 (12%)

Query: 123 ENLWEKFFHGHEDRFSVYVHASSEKPMHVSRYFVGRDIRSEKVAWGRIS---MLDAEK-R 178
           ENL+   F G E +  +  + SS K   V RY  G  ++ E    GR     ++D +   
Sbjct: 12  ENLY---FQGPELKVGIVGNLSSGKSALVHRYLTGTYVQEESPEGGRFKKEIVVDGQSYL 68

Query: 179 LLAHALLDPDNQQFVLLSDSCIPLH------NFDYVYNYLM 213
           LL      P   QF    D+ + +       +F  VYNY +
Sbjct: 69  LLIRDEGGPPELQFAAWVDAVVFVFSLEDEISFQTVYNYFL 109


  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
   0.325    0.140    0.442 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,261,823
Number of Sequences: 62578
Number of extensions: 491835
Number of successful extensions: 1047
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 1047
Number of HSP's gapped (non-prelim): 8
length of query: 351
length of database: 14,973,337
effective HSP length: 100
effective length of query: 251
effective length of database: 8,715,537
effective search space: 2187599787
effective search space used: 2187599787
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 bits)