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= 010257
         (514 letters)

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

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



>pdb|3B39|A Chain A, Structure Of The Dnag Primase Catalytic Domain Bound To
           Ssdna
 pdb|3B39|B Chain B, Structure Of The Dnag Primase Catalytic Domain Bound To
           Ssdna
          Length = 322

 Score = 33.5 bits (75), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 1/44 (2%)

Query: 12  PKSRFFFTPLRPSINLKPPDSFPRIQPLPFPRISGKIPGSRVLV 55
           P S F F  L P ++L  PD   R+  L  P IS ++PG  + +
Sbjct: 260 PLSAFLFNSLMPQVDLSTPDGRARLSTLALPLIS-QVPGETLRI 302


>pdb|1EQN|A Chain A, E.Coli Primase Catalytic Core
 pdb|1EQN|B Chain B, E.Coli Primase Catalytic Core
 pdb|1EQN|C Chain C, E.Coli Primase Catalytic Core
 pdb|1EQN|D Chain D, E.Coli Primase Catalytic Core
 pdb|1EQN|E Chain E, E.Coli Primase Catalytic Core
          Length = 321

 Score = 33.1 bits (74), Expect = 0.34,   Method: Compositional matrix adjust.
 Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 1/44 (2%)

Query: 12  PKSRFFFTPLRPSINLKPPDSFPRIQPLPFPRISGKIPGSRVLV 55
           P S F F  L P ++L  PD   R+  L  P IS ++PG  + +
Sbjct: 259 PLSAFLFNSLXPQVDLSTPDGRARLSTLALPLIS-QVPGETLRI 301


>pdb|1DD9|A Chain A, Structure Of The Dnag Catalytic Core
 pdb|1DDE|A Chain A, Structure Of The Dnag Catalytic Core
          Length = 338

 Score = 33.1 bits (74), Expect = 0.39,   Method: Compositional matrix adjust.
 Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 1/44 (2%)

Query: 12  PKSRFFFTPLRPSINLKPPDSFPRIQPLPFPRISGKIPGSRVLV 55
           P S F F  L P ++L  PD   R+  L  P IS ++PG  + +
Sbjct: 272 PLSAFLFNSLMPQVDLSTPDGRARLSTLALPLIS-QVPGETLRI 314


>pdb|1YGY|A Chain A, Crystal Structure Of D-3-Phosphoglycerate Dehydrogenase
           From Mycobacterium Tuberculosis
 pdb|1YGY|B Chain B, Crystal Structure Of D-3-Phosphoglycerate Dehydrogenase
           From Mycobacterium Tuberculosis
 pdb|3DC2|A Chain A, Crystal Structure Of Serine Bound D-3-Phosphoglycerate
           Dehydrogenase From Mycobacterium Tuberculosis
 pdb|3DC2|B Chain B, Crystal Structure Of Serine Bound D-3-Phosphoglycerate
           Dehydrogenase From Mycobacterium Tuberculosis
          Length = 529

 Score = 30.8 bits (68), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 38/77 (49%), Gaps = 13/77 (16%)

Query: 269 EEKRWKLIGEYI--ASN-GGVVTAEELAPYLDIDR-------TMSDESYVLPVLLRFDGQ 318
           E  R  L GE++  A N GG V  EE+AP+LD+ R        +SDE   LPV L    +
Sbjct: 298 ESVRLALAGEFVPDAVNVGGGVVNEEVAPWLDLVRKLGVLAGVLSDE---LPVSLSVQVR 354

Query: 319 PEIDEEGNILYRFPSFQ 335
            E+  E   + R  + +
Sbjct: 355 GELAAEEVEVLRLSALR 371


>pdb|3DDN|A Chain A, Crystal Structure Of Hydroxypyruvic Acid Phosphate Bound
           D-3- Phosphoglycerate Dehydrogenase In Mycobacterium
           Tuberculosis
 pdb|3DDN|B Chain B, Crystal Structure Of Hydroxypyruvic Acid Phosphate Bound
           D-3- Phosphoglycerate Dehydrogenase In Mycobacterium
           Tuberculosis
          Length = 528

 Score = 30.8 bits (68), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 38/77 (49%), Gaps = 13/77 (16%)

Query: 269 EEKRWKLIGEYI--ASN-GGVVTAEELAPYLDIDR-------TMSDESYVLPVLLRFDGQ 318
           E  R  L GE++  A N GG V  EE+AP+LD+ R        +SDE   LPV L    +
Sbjct: 297 ESVRLALAGEFVPDAVNVGGGVVNEEVAPWLDLVRKLGVLAGVLSDE---LPVSLSVQVR 353

Query: 319 PEIDEEGNILYRFPSFQ 335
            E+  E   + R  + +
Sbjct: 354 GELAAEEVEVLRLSALR 370


  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
   0.322    0.139    0.408 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,946,224
Number of Sequences: 62578
Number of extensions: 561327
Number of successful extensions: 1243
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1234
Number of HSP's gapped (non-prelim): 11
length of query: 514
length of database: 14,973,337
effective HSP length: 103
effective length of query: 411
effective length of database: 8,527,803
effective search space: 3504927033
effective search space used: 3504927033
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: 54 (25.4 bits)