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= 035901
         (415 letters)

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

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



>pdb|3FW7|A Chain A, Structure Of Berberine Bridge Enzyme, H104a Variant
          Length = 498

 Score = 30.8 bits (68), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 27/98 (27%), Positives = 43/98 (43%), Gaps = 17/98 (17%)

Query: 215 NSEFDNACVSE---VIGPPDTSEIENKI-------------SNESVSEGFYNYSNDAPTL 258
           N  F N+ +S+   +I P    E+ N I             S  +  EG  +Y++D P +
Sbjct: 38  NPLFQNSLISKPSAIILPGSKEELSNTIRCIRKGSWTIRLRSGGASYEGL-SYTSDTPFI 96

Query: 259 LTDYNNIDASSRSGQSEAEFYESRTEPSNLYDQIVEGT 296
           L D  N++  S   +SE  + ES +    LY  I E +
Sbjct: 97  LIDLMNLNRVSIDLESETAWVESGSTLGELYYAITESS 134


>pdb|3FW8|A Chain A, Structure Of Berberine Bridge Enzyme, C166a Variant
          Length = 495

 Score = 30.0 bits (66), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 27/98 (27%), Positives = 42/98 (42%), Gaps = 17/98 (17%)

Query: 215 NSEFDNACVSE---VIGPPDTSEIENKI-------------SNESVSEGFYNYSNDAPTL 258
           N  F N+ +S+   +I P    E+ N I             S     EG  +Y++D P +
Sbjct: 35  NPLFQNSLISKPSAIILPGSKEELSNTIRCIRKGSWTIRLRSGGHSYEGL-SYTSDTPFI 93

Query: 259 LTDYNNIDASSRSGQSEAEFYESRTEPSNLYDQIVEGT 296
           L D  N++  S   +SE  + ES +    LY  I E +
Sbjct: 94  LIDLMNLNRVSIDLESETAWVESGSTLGELYYAITESS 131


>pdb|3FW9|A Chain A, Structure Of Berberine Bridge Enzyme In Complex With
           (S)-Scoulerine
          Length = 495

 Score = 30.0 bits (66), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 27/98 (27%), Positives = 42/98 (42%), Gaps = 17/98 (17%)

Query: 215 NSEFDNACVSE---VIGPPDTSEIENKI-------------SNESVSEGFYNYSNDAPTL 258
           N  F N+ +S+   +I P    E+ N I             S     EG  +Y++D P +
Sbjct: 35  NPLFQNSLISKPSAIILPGSKEELSNTIRCIRKGSWTIRLRSGGHSYEGL-SYTSDTPFI 93

Query: 259 LTDYNNIDASSRSGQSEAEFYESRTEPSNLYDQIVEGT 296
           L D  N++  S   +SE  + ES +    LY  I E +
Sbjct: 94  LIDLMNLNRVSIDLESETAWVESGSTLGELYYAITESS 131


>pdb|3FWA|A Chain A, Structure Of Berberine Bridge Enzyme, C166a Variant In
           Complex With (S)-Reticuline
          Length = 497

 Score = 30.0 bits (66), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 27/98 (27%), Positives = 42/98 (42%), Gaps = 17/98 (17%)

Query: 215 NSEFDNACVSE---VIGPPDTSEIENKI-------------SNESVSEGFYNYSNDAPTL 258
           N  F N+ +S+   +I P    E+ N I             S     EG  +Y++D P +
Sbjct: 35  NPLFQNSLISKPSAIILPGSKEELSNTIRCIRKGSWTIRLRSGGHSYEGL-SYTSDTPFI 93

Query: 259 LTDYNNIDASSRSGQSEAEFYESRTEPSNLYDQIVEGT 296
           L D  N++  S   +SE  + ES +    LY  I E +
Sbjct: 94  LIDLMNLNRVSIDLESETAWVESGSTLGELYYAITESS 131


>pdb|3D2D|A Chain A, Structure Of Berberine Bridge Enzyme In Complex With
           (S)-Reticuline
 pdb|3D2H|A Chain A, Structure Of Berberine Bridge Enzyme From Eschscholzia
           Californica, Monoclinic Crystal Form
 pdb|3D2J|A Chain A, Structure Of Berberine Bridge Enzyme From Eschscholzia
           Californica, Tetragonal Crystal Form
          Length = 538

 Score = 30.0 bits (66), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 27/98 (27%), Positives = 42/98 (42%), Gaps = 17/98 (17%)

Query: 215 NSEFDNACVSE---VIGPPDTSEIENKI-------------SNESVSEGFYNYSNDAPTL 258
           N  F N+ +S+   +I P    E+ N I             S     EG  +Y++D P +
Sbjct: 60  NPLFQNSLISKPSAIILPGSKEELSNTIRCIRKGSWTIRLRSGGHSYEGL-SYTSDTPFI 118

Query: 259 LTDYNNIDASSRSGQSEAEFYESRTEPSNLYDQIVEGT 296
           L D  N++  S   +SE  + ES +    LY  I E +
Sbjct: 119 LIDLMNLNRVSIDLESETAWVESGSTLGELYYAITESS 156


>pdb|4EC3|A Chain A, Structure Of Berberine Bridge Enzyme, H174a Variant In
           Complex With (S)-Reticuline
          Length = 519

 Score = 29.6 bits (65), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 27/98 (27%), Positives = 42/98 (42%), Gaps = 17/98 (17%)

Query: 215 NSEFDNACVSE---VIGPPDTSEIENKI-------------SNESVSEGFYNYSNDAPTL 258
           N  F N+ +S+   +I P    E+ N I             S     EG  +Y++D P +
Sbjct: 41  NPLFQNSLISKPSAIILPGSKEELSNTIRCIRKGSWTIRLRSGGHSYEGL-SYTSDTPFI 99

Query: 259 LTDYNNIDASSRSGQSEAEFYESRTEPSNLYDQIVEGT 296
           L D  N++  S   +SE  + ES +    LY  I E +
Sbjct: 100 LIDLMNLNRVSIDLESETAWVESGSTLGELYYAITESS 137


>pdb|3GSY|A Chain A, Structure Of Berberine Bridge Enzyme In Complex With
           Dehydroscoulerine
          Length = 519

 Score = 29.6 bits (65), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 27/98 (27%), Positives = 42/98 (42%), Gaps = 17/98 (17%)

Query: 215 NSEFDNACVSE---VIGPPDTSEIENKI-------------SNESVSEGFYNYSNDAPTL 258
           N  F N+ +S+   +I P    E+ N I             S     EG  +Y++D P +
Sbjct: 41  NPLFQNSLISKPSAIILPGSKEELSNTIRCIRKGSWTIRLRSGGHSYEGL-SYTSDTPFI 99

Query: 259 LTDYNNIDASSRSGQSEAEFYESRTEPSNLYDQIVEGT 296
           L D  N++  S   +SE  + ES +    LY  I E +
Sbjct: 100 LIDLMNLNRVSIDLESETAWVESGSTLGELYYAITESS 137


>pdb|3M9B|A Chain A, Crystal Structure Of The Amino Terminal Coiled Coil Domain
           And The Inter Domain Of The Mycobacterium Tuberculosis
           Proteasomal Atpase Mpa
 pdb|3M9B|B Chain B, Crystal Structure Of The Amino Terminal Coiled Coil Domain
           And The Inter Domain Of The Mycobacterium Tuberculosis
           Proteasomal Atpase Mpa
 pdb|3M9B|C Chain C, Crystal Structure Of The Amino Terminal Coiled Coil Domain
           And The Inter Domain Of The Mycobacterium Tuberculosis
           Proteasomal Atpase Mpa
 pdb|3M9B|D Chain D, Crystal Structure Of The Amino Terminal Coiled Coil Domain
           And The Inter Domain Of The Mycobacterium Tuberculosis
           Proteasomal Atpase Mpa
 pdb|3M9B|E Chain E, Crystal Structure Of The Amino Terminal Coiled Coil Domain
           And The Inter Domain Of The Mycobacterium Tuberculosis
           Proteasomal Atpase Mpa
 pdb|3M9B|F Chain F, Crystal Structure Of The Amino Terminal Coiled Coil Domain
           And The Inter Domain Of The Mycobacterium Tuberculosis
           Proteasomal Atpase Mpa
 pdb|3M9B|G Chain G, Crystal Structure Of The Amino Terminal Coiled Coil Domain
           And The Inter Domain Of The Mycobacterium Tuberculosis
           Proteasomal Atpase Mpa
 pdb|3M9B|H Chain H, Crystal Structure Of The Amino Terminal Coiled Coil Domain
           And The Inter Domain Of The Mycobacterium Tuberculosis
           Proteasomal Atpase Mpa
 pdb|3M9B|I Chain I, Crystal Structure Of The Amino Terminal Coiled Coil Domain
           And The Inter Domain Of The Mycobacterium Tuberculosis
           Proteasomal Atpase Mpa
 pdb|3M9B|J Chain J, Crystal Structure Of The Amino Terminal Coiled Coil Domain
           And The Inter Domain Of The Mycobacterium Tuberculosis
           Proteasomal Atpase Mpa
 pdb|3M9B|K Chain K, Crystal Structure Of The Amino Terminal Coiled Coil Domain
           And The Inter Domain Of The Mycobacterium Tuberculosis
           Proteasomal Atpase Mpa
 pdb|3M9B|L Chain L, Crystal Structure Of The Amino Terminal Coiled Coil Domain
           And The Inter Domain Of The Mycobacterium Tuberculosis
           Proteasomal Atpase Mpa
 pdb|3M9D|A Chain A, Crystal Structure Of The Prokaryotic Ubiquintin-Like
           Protein Pup Complexed With The Hexameric Proteasomal
           Atpase Mpa Which Includes The Amino Terminal Coiled Coil
           Domain And The Inter Domain
 pdb|3M9D|B Chain B, Crystal Structure Of The Prokaryotic Ubiquintin-Like
           Protein Pup Complexed With The Hexameric Proteasomal
           Atpase Mpa Which Includes The Amino Terminal Coiled Coil
           Domain And The Inter Domain
 pdb|3M9D|C Chain C, Crystal Structure Of The Prokaryotic Ubiquintin-Like
           Protein Pup Complexed With The Hexameric Proteasomal
           Atpase Mpa Which Includes The Amino Terminal Coiled Coil
           Domain And The Inter Domain
 pdb|3M9D|D Chain D, Crystal Structure Of The Prokaryotic Ubiquintin-Like
           Protein Pup Complexed With The Hexameric Proteasomal
           Atpase Mpa Which Includes The Amino Terminal Coiled Coil
           Domain And The Inter Domain
 pdb|3M9D|E Chain E, Crystal Structure Of The Prokaryotic Ubiquintin-Like
           Protein Pup Complexed With The Hexameric Proteasomal
           Atpase Mpa Which Includes The Amino Terminal Coiled Coil
           Domain And The Inter Domain
 pdb|3M9D|F Chain F, Crystal Structure Of The Prokaryotic Ubiquintin-Like
           Protein Pup Complexed With The Hexameric Proteasomal
           Atpase Mpa Which Includes The Amino Terminal Coiled Coil
           Domain And The Inter Domain
 pdb|3M9D|J Chain J, Crystal Structure Of The Prokaryotic Ubiquintin-Like
           Protein Pup Complexed With The Hexameric Proteasomal
           Atpase Mpa Which Includes The Amino Terminal Coiled Coil
           Domain And The Inter Domain
 pdb|3M9D|K Chain K, Crystal Structure Of The Prokaryotic Ubiquintin-Like
           Protein Pup Complexed With The Hexameric Proteasomal
           Atpase Mpa Which Includes The Amino Terminal Coiled Coil
           Domain And The Inter Domain
 pdb|3M9D|L Chain L, Crystal Structure Of The Prokaryotic Ubiquintin-Like
           Protein Pup Complexed With The Hexameric Proteasomal
           Atpase Mpa Which Includes The Amino Terminal Coiled Coil
           Domain And The Inter Domain
 pdb|3M9D|M Chain M, Crystal Structure Of The Prokaryotic Ubiquintin-Like
           Protein Pup Complexed With The Hexameric Proteasomal
           Atpase Mpa Which Includes The Amino Terminal Coiled Coil
           Domain And The Inter Domain
 pdb|3M9D|N Chain N, Crystal Structure Of The Prokaryotic Ubiquintin-Like
           Protein Pup Complexed With The Hexameric Proteasomal
           Atpase Mpa Which Includes The Amino Terminal Coiled Coil
           Domain And The Inter Domain
 pdb|3M9D|O Chain O, Crystal Structure Of The Prokaryotic Ubiquintin-Like
           Protein Pup Complexed With The Hexameric Proteasomal
           Atpase Mpa Which Includes The Amino Terminal Coiled Coil
           Domain And The Inter Domain
          Length = 251

 Score = 29.6 bits (65), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 19/48 (39%), Positives = 25/48 (52%), Gaps = 3/48 (6%)

Query: 17  DIDTDRLLEKDSVTLDEALKTANNAVFLAVNAISTLS---SDMHRKLI 61
           +ID   L +  +V L+EAL       F AV  ISTL    +D HR L+
Sbjct: 129 NIDAASLKKGQTVRLNEALTVVEAGTFEAVGEISTLREILADGHRALV 176


>pdb|3FP9|A Chain A, Crystal Structure Of Intern Domain Of
          Proteasome-Associated Atpase, Mycobacterium
          Tuberculosis
 pdb|3FP9|B Chain B, Crystal Structure Of Intern Domain Of
          Proteasome-Associated Atpase, Mycobacterium
          Tuberculosis
 pdb|3FP9|C Chain C, Crystal Structure Of Intern Domain Of
          Proteasome-Associated Atpase, Mycobacterium
          Tuberculosis
 pdb|3FP9|D Chain D, Crystal Structure Of Intern Domain Of
          Proteasome-Associated Atpase, Mycobacterium
          Tuberculosis
 pdb|3FP9|E Chain E, Crystal Structure Of Intern Domain Of
          Proteasome-Associated Atpase, Mycobacterium
          Tuberculosis
 pdb|3FP9|F Chain F, Crystal Structure Of Intern Domain Of
          Proteasome-Associated Atpase, Mycobacterium
          Tuberculosis
 pdb|3FP9|G Chain G, Crystal Structure Of Intern Domain Of
          Proteasome-Associated Atpase, Mycobacterium
          Tuberculosis
 pdb|3FP9|H Chain H, Crystal Structure Of Intern Domain Of
          Proteasome-Associated Atpase, Mycobacterium
          Tuberculosis
 pdb|3FP9|I Chain I, Crystal Structure Of Intern Domain Of
          Proteasome-Associated Atpase, Mycobacterium
          Tuberculosis
 pdb|3FP9|J Chain J, Crystal Structure Of Intern Domain Of
          Proteasome-Associated Atpase, Mycobacterium
          Tuberculosis
 pdb|3FP9|K Chain K, Crystal Structure Of Intern Domain Of
          Proteasome-Associated Atpase, Mycobacterium
          Tuberculosis
 pdb|3FP9|L Chain L, Crystal Structure Of Intern Domain Of
          Proteasome-Associated Atpase, Mycobacterium
          Tuberculosis
          Length = 153

 Score = 28.9 bits (63), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 24/47 (51%), Gaps = 3/47 (6%)

Query: 18 IDTDRLLEKDSVTLDEALKTANNAVFLAVNAISTLS---SDMHRKLI 61
          ID   L +  +V L+EAL       F AV  ISTL    +D HR L+
Sbjct: 34 IDAASLKKGQTVRLNEALTVVEAGTFEAVGEISTLREILADGHRALV 80


>pdb|3UJH|A Chain A, Crystal Structure Of Substrate-Bound Glucose-6-Phosphate
           Isomerase From Toxoplasma Gondii
 pdb|3UJH|B Chain B, Crystal Structure Of Substrate-Bound Glucose-6-Phosphate
           Isomerase From Toxoplasma Gondii
          Length = 567

 Score = 28.1 bits (61), Expect = 9.2,   Method: Compositional matrix adjust.
 Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 4/50 (8%)

Query: 353 FCSQQQEPKTENDVKEPPTGASFDVMRDFYSTAATLLKGKTADVRKKQGV 402
           FC  Q+  K    +KE P     ++M +F++    L  GKT +  +K+G+
Sbjct: 417 FCKSQRAIK----LKEEPVSNHDELMSNFFAQPDALAFGKTPEELRKEGI 462


  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
   0.315    0.131    0.372 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,458,694
Number of Sequences: 62578
Number of extensions: 449514
Number of successful extensions: 1113
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 1104
Number of HSP's gapped (non-prelim): 16
length of query: 415
length of database: 14,973,337
effective HSP length: 101
effective length of query: 314
effective length of database: 8,652,959
effective search space: 2717029126
effective search space used: 2717029126
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)