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= 007853
         (587 letters)

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

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



>pdb|4FM2|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase (Triple Mutant)
           Bound To A Dsdna, In Edition Mode
          Length = 793

 Score = 30.4 bits (67), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 12/35 (34%), Positives = 21/35 (60%)

Query: 226 ATLSDGNIEEATTIINELRQMVSIQGDPPQRIAAY 260
           A L  GN++EA  I+ E+ + +S    PP+++  Y
Sbjct: 651 AILKHGNVDEAVKIVKEVTEKLSKYEIPPEKLVIY 685


>pdb|4FLT|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
           Dsdna, In Edition Mode
 pdb|4FLU|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
           Dsdna, In Edition Mode
 pdb|4FLV|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
           Dsdna, In Edition Mode
 pdb|4FLW|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
           Dsdna, In Edition Mode
 pdb|4FLX|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
           Dsdna, In Edition Mode
 pdb|4FLY|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
           Dsdna, In Edition Mode
 pdb|4FLZ|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
           Dsdna, In Edition Mode
 pdb|4FM0|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
           Dsdna, In Edition Mode
 pdb|4FM1|A Chain A, Pyrococcus Abyssi B Family Dna Polymerase Bound To A
           Dsdna, In Edition Mode
          Length = 793

 Score = 30.4 bits (67), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 12/35 (34%), Positives = 21/35 (60%)

Query: 226 ATLSDGNIEEATTIINELRQMVSIQGDPPQRIAAY 260
           A L  GN++EA  I+ E+ + +S    PP+++  Y
Sbjct: 651 AILKHGNVDEAVKIVKEVTEKLSKYEIPPEKLVIY 685


>pdb|1D5A|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase
           D.Tok. Deposition Of Second Native Structure At 2.4
           Angstrom
          Length = 733

 Score = 30.0 bits (66), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 12/35 (34%), Positives = 21/35 (60%)

Query: 226 ATLSDGNIEEATTIINELRQMVSIQGDPPQRIAAY 260
           A L  G++EEA  I+ E+ + +S    PP+++  Y
Sbjct: 629 AILKHGDVEEAVRIVKEVTEKLSRHEVPPEKLVIY 663


>pdb|1QQC|A Chain A, Crystal Structure Of An Archaebacterial Dna Polymerase
           D.Tok
          Length = 773

 Score = 30.0 bits (66), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 12/35 (34%), Positives = 21/35 (60%)

Query: 226 ATLSDGNIEEATTIINELRQMVSIQGDPPQRIAAY 260
           A L  G++EEA  I+ E+ + +S    PP+++  Y
Sbjct: 629 AILKHGDVEEAVRIVKEVTEKLSRHEVPPEKLVIY 663


>pdb|2I6Y|A Chain A, Structure And Mechanism Of Mycobacterium Tuberculosis
           Salicylate Synthase, Mbti
          Length = 470

 Score = 29.6 bits (65), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 18/66 (27%), Positives = 37/66 (56%), Gaps = 4/66 (6%)

Query: 233 IEEATTIINELRQMVSIQGDPPQRIAAYMVEGLAARMAASGKFLYKALKCKEPPSSDRLA 292
           +E A ++ + L ++  I  +P    +A +++ +  R   S + L   ++ +  PSSDR+A
Sbjct: 316 VEHAISVRSSLEEITDI-AEPG---SAAVIDFMTVRERGSVQHLGSTIRARLDPSSDRMA 371

Query: 293 AMQILF 298
           A++ LF
Sbjct: 372 ALEALF 377


>pdb|3RV8|A Chain A, Structure Of A M. Tuberculosis Salicylate Synthase, Mbti,
           In Complex With An Inhibitor With Cyclopropyl R-Group
 pdb|3RV8|B Chain B, Structure Of A M. Tuberculosis Salicylate Synthase, Mbti,
           In Complex With An Inhibitor With Cyclopropyl R-Group
 pdb|3RV8|C Chain C, Structure Of A M. Tuberculosis Salicylate Synthase, Mbti,
           In Complex With An Inhibitor With Cyclopropyl R-Group
 pdb|3RV8|D Chain D, Structure Of A M. Tuberculosis Salicylate Synthase, Mbti,
           In Complex With An Inhibitor With Cyclopropyl R-Group
 pdb|3ST6|A Chain A, Structure Of A M. Tuberculosis Synthase, Mbti, In Complex
           With An Isochorismate Analogue Inhibitor
 pdb|3ST6|B Chain B, Structure Of A M. Tuberculosis Synthase, Mbti, In Complex
           With An Isochorismate Analogue Inhibitor
 pdb|3ST6|C Chain C, Structure Of A M. Tuberculosis Synthase, Mbti, In Complex
           With An Isochorismate Analogue Inhibitor
 pdb|3ST6|D Chain D, Structure Of A M. Tuberculosis Synthase, Mbti, In Complex
           With An Isochorismate Analogue Inhibitor
          Length = 450

 Score = 29.6 bits (65), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 18/66 (27%), Positives = 37/66 (56%), Gaps = 4/66 (6%)

Query: 233 IEEATTIINELRQMVSIQGDPPQRIAAYMVEGLAARMAASGKFLYKALKCKEPPSSDRLA 292
           +E A ++ + L ++  I  +P    +A +++ +  R   S + L   ++ +  PSSDR+A
Sbjct: 296 VEHAISVRSSLEEITDI-AEPG---SAAVIDFMTVRERGSVQHLGSTIRARLDPSSDRMA 351

Query: 293 AMQILF 298
           A++ LF
Sbjct: 352 ALEALF 357


>pdb|2G5F|A Chain A, The Structure Of Mbti From Mycobacterium Tuberculosis, The
           First Enzyme In The Synthesis Of Mycobactin, Reveals It
           To Be A Salicylate Synthase
 pdb|2G5F|B Chain B, The Structure Of Mbti From Mycobacterium Tuberculosis, The
           First Enzyme In The Synthesis Of Mycobactin, Reveals It
           To Be A Salicylate Synthase
 pdb|2G5F|C Chain C, The Structure Of Mbti From Mycobacterium Tuberculosis, The
           First Enzyme In The Synthesis Of Mycobactin, Reveals It
           To Be A Salicylate Synthase
 pdb|2G5F|D Chain D, The Structure Of Mbti From Mycobacterium Tuberculosis, The
           First Enzyme In The Synthesis Of Mycobactin, Reveals It
           To Be A Salicylate Synthase
 pdb|3RV6|A Chain A, Structure Of A M. Tuberculosis Salicylate Synthase, Mbti,
           In Complex With An Inhibitor With Phenyl R-Group
 pdb|3RV6|B Chain B, Structure Of A M. Tuberculosis Salicylate Synthase, Mbti,
           In Complex With An Inhibitor With Phenyl R-Group
 pdb|3RV7|A Chain A, Structure Of A M. Tuberculosis Salicylate Synthase, Mbti,
           In Complex With An Inhibitor With Isopropyl R-Group
 pdb|3RV7|B Chain B, Structure Of A M. Tuberculosis Salicylate Synthase, Mbti,
           In Complex With An Inhibitor With Isopropyl R-Group
 pdb|3RV7|C Chain C, Structure Of A M. Tuberculosis Salicylate Synthase, Mbti,
           In Complex With An Inhibitor With Isopropyl R-Group
 pdb|3RV7|D Chain D, Structure Of A M. Tuberculosis Salicylate Synthase, Mbti,
           In Complex With An Inhibitor With Isopropyl R-Group
 pdb|3RV9|A Chain A, Structure Of A M. Tuberculosis Salicylate Synthase, Mbti,
           In Complex With An Inhibitor With Ethyl R-Group
 pdb|3RV9|B Chain B, Structure Of A M. Tuberculosis Salicylate Synthase, Mbti,
           In Complex With An Inhibitor With Ethyl R-Group
 pdb|3RV9|C Chain C, Structure Of A M. Tuberculosis Salicylate Synthase, Mbti,
           In Complex With An Inhibitor With Ethyl R-Group
 pdb|3RV9|D Chain D, Structure Of A M. Tuberculosis Salicylate Synthase, Mbti,
           In Complex With An Inhibitor With Ethyl R-Group
          Length = 450

 Score = 29.6 bits (65), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 18/66 (27%), Positives = 37/66 (56%), Gaps = 4/66 (6%)

Query: 233 IEEATTIINELRQMVSIQGDPPQRIAAYMVEGLAARMAASGKFLYKALKCKEPPSSDRLA 292
           +E A ++ + L ++  I  +P    +A +++ +  R   S + L   ++ +  PSSDR+A
Sbjct: 296 VEHAISVRSSLEEITDI-AEPG---SAAVIDFMTVRERGSVQHLGSTIRARLDPSSDRMA 351

Query: 293 AMQILF 298
           A++ LF
Sbjct: 352 ALEALF 357


>pdb|3LOG|A Chain A, Crystal Structure Of Mbti From Mycobacterium Tuberculosis
 pdb|3LOG|B Chain B, Crystal Structure Of Mbti From Mycobacterium Tuberculosis
 pdb|3LOG|C Chain C, Crystal Structure Of Mbti From Mycobacterium Tuberculosis
 pdb|3LOG|D Chain D, Crystal Structure Of Mbti From Mycobacterium Tuberculosis
 pdb|3VEH|A Chain A, Structure Of A M. Tuberculosis Salicylate Synthase, Mbti,
           In Complex With An Inhibitor Methylamt
 pdb|3VEH|B Chain B, Structure Of A M. Tuberculosis Salicylate Synthase, Mbti,
           In Complex With An Inhibitor Methylamt
 pdb|3VEH|C Chain C, Structure Of A M. Tuberculosis Salicylate Synthase, Mbti,
           In Complex With An Inhibitor Methylamt
 pdb|3VEH|D Chain D, Structure Of A M. Tuberculosis Salicylate Synthase, Mbti,
           In Complex With An Inhibitor Methylamt
          Length = 451

 Score = 29.6 bits (65), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 18/66 (27%), Positives = 37/66 (56%), Gaps = 4/66 (6%)

Query: 233 IEEATTIINELRQMVSIQGDPPQRIAAYMVEGLAARMAASGKFLYKALKCKEPPSSDRLA 292
           +E A ++ + L ++  I  +P    +A +++ +  R   S + L   ++ +  PSSDR+A
Sbjct: 298 VEHAISVRSSLEEITDI-AEPG---SAAVIDFMTVRERGSVQHLGSTIRARLDPSSDRMA 353

Query: 293 AMQILF 298
           A++ LF
Sbjct: 354 ALEALF 359


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

 Score = 29.6 bits (65), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 12/35 (34%), Positives = 21/35 (60%)

Query: 226 ATLSDGNIEEATTIINELRQMVSIQGDPPQRIAAY 260
           A L  G++EEA  I+ E+ + +S    PP+++  Y
Sbjct: 629 AILKHGDVEEAVRIVKEVTEKLSKYEVPPEKLVIY 663


>pdb|3A2F|A Chain A, Crystal Structure Of Pyrococcus Furiosus Dna
           PolymerasePCNA Monomer Mutant Complex
          Length = 775

 Score = 29.6 bits (65), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 8/64 (12%)

Query: 228 LSDGNIEEATTIINELRQMVSIQGDPPQRIAAY--------MVEGLAARMAASGKFLYKA 279
           L  G++EEA  I+ E+ Q ++    PP+++A Y          + +   +A + K   K 
Sbjct: 632 LKHGDVEEAVRIVKEVIQKLANYEIPPEKLAIYEQITRPLHEYKAIGPHVAVAKKLAAKG 691

Query: 280 LKCK 283
           +K K
Sbjct: 692 VKIK 695


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

 Score = 29.6 bits (65), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 12/35 (34%), Positives = 21/35 (60%)

Query: 226 ATLSDGNIEEATTIINELRQMVSIQGDPPQRIAAY 260
           A L  G++EEA  I+ E+ + +S    PP+++  Y
Sbjct: 629 AILKHGDVEEAVRIVKEVTEKLSKYEVPPEKLVIY 663


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

 Score = 29.6 bits (65), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 12/35 (34%), Positives = 21/35 (60%)

Query: 226 ATLSDGNIEEATTIINELRQMVSIQGDPPQRIAAY 260
           A L  G++EEA  I+ E+ + +S    PP+++  Y
Sbjct: 629 AILKHGDVEEAVRIVKEVTEKLSKYEVPPEKLVIY 663


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

 Score = 29.6 bits (65), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 12/35 (34%), Positives = 21/35 (60%)

Query: 226 ATLSDGNIEEATTIINELRQMVSIQGDPPQRIAAY 260
           A L  G++EEA  I+ E+ + +S    PP+++  Y
Sbjct: 629 AILKHGDVEEAVRIVKEVTEKLSKYEVPPEKLVIY 663


>pdb|4AHC|A Chain A, Crystal Structure Of An Evolved Replicating Dna Polymerase
 pdb|4AHC|B Chain B, Crystal Structure Of An Evolved Replicating Dna Polymerase
 pdb|4AIL|C Chain C, Crystal Structure Of An Evolved Replicating Dna Polymerase
          Length = 775

 Score = 29.6 bits (65), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 8/64 (12%)

Query: 228 LSDGNIEEATTIINELRQMVSIQGDPPQRIAAY--------MVEGLAARMAASGKFLYKA 279
           L  G++EEA  I+ E+ Q ++    PP+++A Y          + +   +A + K   K 
Sbjct: 632 LKHGDVEEAVRIVKEVIQKLANYEIPPEKLAIYEQITRPLHEYKAIGPHVAVAKKLAAKG 691

Query: 280 LKCK 283
           +K K
Sbjct: 692 VKIK 695


>pdb|2JGU|A Chain A, Crystal Structure Of Dna-directed Dna Polymerase
          Length = 775

 Score = 29.6 bits (65), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 8/64 (12%)

Query: 228 LSDGNIEEATTIINELRQMVSIQGDPPQRIAAY--------MVEGLAARMAASGKFLYKA 279
           L  G++EEA  I+ E+ Q ++    PP+++A Y          + +   +A + K   K 
Sbjct: 632 LKHGDVEEAVRIVKEVIQKLANYEIPPEKLAIYEQITRPLHEYKAIGPHVAVAKKLAAKG 691

Query: 280 LKCK 283
           +K K
Sbjct: 692 VKIK 695


  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
   0.318    0.133    0.389 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,827,330
Number of Sequences: 62578
Number of extensions: 598474
Number of successful extensions: 1308
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 1292
Number of HSP's gapped (non-prelim): 16
length of query: 587
length of database: 14,973,337
effective HSP length: 104
effective length of query: 483
effective length of database: 8,465,225
effective search space: 4088703675
effective search space used: 4088703675
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: 54 (25.4 bits)