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= 018123
         (360 letters)

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

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



>pdb|2O19|A Chain A, Structure Of E. Coli Topoisomersae Iii In Complex With An
           8- Base Single Stranded Oligonucleotide. Frozen In
           Glycerol At Ph 5.5
 pdb|2O19|B Chain B, Structure Of E. Coli Topoisomersae Iii In Complex With An
           8- Base Single Stranded Oligonucleotide. Frozen In
           Glycerol At Ph 5.5
 pdb|2O54|A Chain A, Structure Of E. Coli Topoisomerase Iii In Complex With An
           8- Base Single Stranded Oligonucleotide. Frozen In
           Glycerol At Ph 7.0
 pdb|2O54|B Chain B, Structure Of E. Coli Topoisomerase Iii In Complex With An
           8- Base Single Stranded Oligonucleotide. Frozen In
           Glycerol At Ph 7.0
 pdb|2O59|A Chain A, Structure Of E. Coli Topoisomerase Iii In Complex With An
           8- Base Single Stranded Oligonucleotide. Frozen In
           Glycerol Ph 8.0
 pdb|2O59|B Chain B, Structure Of E. Coli Topoisomerase Iii In Complex With An
           8- Base Single Stranded Oligonucleotide. Frozen In
           Glycerol Ph 8.0
 pdb|2O5C|A Chain A, Structure Of E. Coli Topoisomerase Iii In Complex With An
           8- Base Single Stranded Oligonucleotide. Frozen In
           Glucose Ph 5.5
 pdb|2O5C|B Chain B, Structure Of E. Coli Topoisomerase Iii In Complex With An
           8- Base Single Stranded Oligonucleotide. Frozen In
           Glucose Ph 5.5
 pdb|2O5E|A Chain A, Structure Of E. Coli Topoisomerase Iii In Complex With An
           8- Base Single Stranded Oligonucleotide. Frozen In
           Glucose Ph 7.0
 pdb|2O5E|B Chain B, Structure Of E. Coli Topoisomerase Iii In Complex With An
           8- Base Single Stranded Oligonucleotide. Frozen In
           Glucose Ph 7.0
          Length = 659

 Score = 33.5 bits (75), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 18/71 (25%), Positives = 37/71 (52%)

Query: 35  NTSSPLSLVIGSLCIKHPNLFGGSEKLDVSWDKGLYDSNVLVAYRRPRPEWLSQQCFVIQ 94
           + S+PL   + +L I+    FG S +  +   + LY+++ L+ Y R    +L ++ F  +
Sbjct: 285 SESAPLPFSLSALQIEAAKRFGLSAQNVLDICQKLYETHKLITYPRSDCRYLPEEHFAGR 344

Query: 95  HSLSPEVGVHG 105
           H++   + VH 
Sbjct: 345 HAVMNAISVHA 355


>pdb|1D6M|A Chain A, Crystal Structure Of E. Coli Dna Topoisomerase Iii
          Length = 653

 Score = 33.5 bits (75), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 18/71 (25%), Positives = 37/71 (52%)

Query: 35  NTSSPLSLVIGSLCIKHPNLFGGSEKLDVSWDKGLYDSNVLVAYRRPRPEWLSQQCFVIQ 94
           + S+PL   + +L I+    FG S +  +   + LY+++ L+ Y R    +L ++ F  +
Sbjct: 285 SESAPLPFSLSALQIEAAKRFGLSAQNVLDICQKLYETHKLITYPRSDCRYLPEEHFAGR 344

Query: 95  HSLSPEVGVHG 105
           H++   + VH 
Sbjct: 345 HAVMNAISVHA 355


>pdb|3I4K|A Chain A, Crystal Structure Of Muconate Lactonizing Enzyme From
           Corynebacterium Glutamicum
 pdb|3I4K|B Chain B, Crystal Structure Of Muconate Lactonizing Enzyme From
           Corynebacterium Glutamicum
 pdb|3I4K|C Chain C, Crystal Structure Of Muconate Lactonizing Enzyme From
           Corynebacterium Glutamicum
 pdb|3I4K|D Chain D, Crystal Structure Of Muconate Lactonizing Enzyme From
           Corynebacterium Glutamicum
 pdb|3I4K|E Chain E, Crystal Structure Of Muconate Lactonizing Enzyme From
           Corynebacterium Glutamicum
 pdb|3I4K|F Chain F, Crystal Structure Of Muconate Lactonizing Enzyme From
           Corynebacterium Glutamicum
 pdb|3I4K|G Chain G, Crystal Structure Of Muconate Lactonizing Enzyme From
           Corynebacterium Glutamicum
 pdb|3I4K|H Chain H, Crystal Structure Of Muconate Lactonizing Enzyme From
           Corynebacterium Glutamicum
          Length = 383

 Score = 32.7 bits (73), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 35/133 (26%), Positives = 56/133 (42%), Gaps = 28/133 (21%)

Query: 46  SLCIKHPNLFGGS--EKLDVSWDKGLYDSNVLVAYRRPRPEWLSQQCFVIQHSLSPEVGV 103
           SL +   +L GG+  +K+DV+W  G+   +V VA    R E    + F ++         
Sbjct: 121 SLNVPVRDLLGGTVRDKVDVTWALGVLPLDVAVAEIEERIEEFGNRSFKLKXG------- 173

Query: 104 HGLPIDNFSRSGSGGVNL-SRLSLGLDISEPISSKWSNTTSLK------------FEHVR 150
            G P ++  R       +  R+SL +D    I+++W   T+L             FE   
Sbjct: 174 AGDPAEDTRRVAELAREVGDRVSLRID----INARWDRRTALHYLPILAEAGVELFEQPT 229

Query: 151 PVND--DWRSITR 161
           P +D    R ITR
Sbjct: 230 PADDLETLREITR 242


>pdb|1I7D|A Chain A, Noncovalent Complex Of E.Coli Dna Topoisomerase Iii With
           An 8-Base Single-Stranded Dna Oligonucleotide
          Length = 659

 Score = 32.0 bits (71), Expect = 0.53,   Method: Compositional matrix adjust.
 Identities = 17/71 (23%), Positives = 37/71 (52%)

Query: 35  NTSSPLSLVIGSLCIKHPNLFGGSEKLDVSWDKGLYDSNVLVAYRRPRPEWLSQQCFVIQ 94
           + S+PL   + +L I+    FG S +  +   + LY+++ L+ + R    +L ++ F  +
Sbjct: 285 SESAPLPFSLSALQIEAAKRFGLSAQNVLDICQKLYETHKLITFPRSDCRYLPEEHFAGR 344

Query: 95  HSLSPEVGVHG 105
           H++   + VH 
Sbjct: 345 HAVMNAISVHA 355


>pdb|1RJM|A Chain A, Crystal Structure Of Menb (rv0548c) From Mycobacterium
           Tuberculosis
 pdb|1RJM|B Chain B, Crystal Structure Of Menb (rv0548c) From Mycobacterium
           Tuberculosis
 pdb|1RJM|C Chain C, Crystal Structure Of Menb (rv0548c) From Mycobacterium
           Tuberculosis
 pdb|1RJN|A Chain A, The Crystal Structure Of Menb (Rv0548c) From Mycobacterium
           Tuberculosis In Complex With The Coa Portion Of
           Naphthoyl Coa
 pdb|1RJN|B Chain B, The Crystal Structure Of Menb (Rv0548c) From Mycobacterium
           Tuberculosis In Complex With The Coa Portion Of
           Naphthoyl Coa
 pdb|1RJN|C Chain C, The Crystal Structure Of Menb (Rv0548c) From Mycobacterium
           Tuberculosis In Complex With The Coa Portion Of
           Naphthoyl Coa
          Length = 339

 Score = 31.2 bits (69), Expect = 0.91,   Method: Compositional matrix adjust.
 Identities = 23/85 (27%), Positives = 41/85 (48%), Gaps = 8/85 (9%)

Query: 27  SLMLPPPRNTSSPLSLVIGSLCIKHPNLFGGSEKL-DVSWDKGLYDSNVLVAYRRP---- 81
           +++ P      S  +L       K   L  G + L D+++ + + D+ V VA+ RP    
Sbjct: 25  AMVAPAGEQGRSSTALSDNPFDAKAWRLVDGFDDLTDITYHRHVDDATVRVAFNRPEVRN 84

Query: 82  --RPEWLSQQCFVIQHS-LSPEVGV 103
             RP  + +   V+ H+ +SP+VGV
Sbjct: 85  AFRPHTVDELYRVLDHARMSPDVGV 109


>pdb|1Q51|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Menb In
           Complex With Acetoacetyl-Coenzyme A, A Key Enzyme In
           Vitamin K2 Biosynthesis
 pdb|1Q51|B Chain B, Crystal Structure Of Mycobacterium Tuberculosis Menb In
           Complex With Acetoacetyl-Coenzyme A, A Key Enzyme In
           Vitamin K2 Biosynthesis
 pdb|1Q51|C Chain C, Crystal Structure Of Mycobacterium Tuberculosis Menb In
           Complex With Acetoacetyl-Coenzyme A, A Key Enzyme In
           Vitamin K2 Biosynthesis
 pdb|1Q51|D Chain D, Crystal Structure Of Mycobacterium Tuberculosis Menb In
           Complex With Acetoacetyl-Coenzyme A, A Key Enzyme In
           Vitamin K2 Biosynthesis
 pdb|1Q51|E Chain E, Crystal Structure Of Mycobacterium Tuberculosis Menb In
           Complex With Acetoacetyl-Coenzyme A, A Key Enzyme In
           Vitamin K2 Biosynthesis
 pdb|1Q51|F Chain F, Crystal Structure Of Mycobacterium Tuberculosis Menb In
           Complex With Acetoacetyl-Coenzyme A, A Key Enzyme In
           Vitamin K2 Biosynthesis
 pdb|1Q51|G Chain G, Crystal Structure Of Mycobacterium Tuberculosis Menb In
           Complex With Acetoacetyl-Coenzyme A, A Key Enzyme In
           Vitamin K2 Biosynthesis
 pdb|1Q51|H Chain H, Crystal Structure Of Mycobacterium Tuberculosis Menb In
           Complex With Acetoacetyl-Coenzyme A, A Key Enzyme In
           Vitamin K2 Biosynthesis
 pdb|1Q51|I Chain I, Crystal Structure Of Mycobacterium Tuberculosis Menb In
           Complex With Acetoacetyl-Coenzyme A, A Key Enzyme In
           Vitamin K2 Biosynthesis
 pdb|1Q51|J Chain J, Crystal Structure Of Mycobacterium Tuberculosis Menb In
           Complex With Acetoacetyl-Coenzyme A, A Key Enzyme In
           Vitamin K2 Biosynthesis
 pdb|1Q51|K Chain K, Crystal Structure Of Mycobacterium Tuberculosis Menb In
           Complex With Acetoacetyl-Coenzyme A, A Key Enzyme In
           Vitamin K2 Biosynthesis
 pdb|1Q51|L Chain L, Crystal Structure Of Mycobacterium Tuberculosis Menb In
           Complex With Acetoacetyl-Coenzyme A, A Key Enzyme In
           Vitamin K2 Biosynthesis
 pdb|1Q52|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Menb, A
           Key Enzyme In Vitamin K2 Biosynthesis
 pdb|1Q52|B Chain B, Crystal Structure Of Mycobacterium Tuberculosis Menb, A
           Key Enzyme In Vitamin K2 Biosynthesis
 pdb|1Q52|C Chain C, Crystal Structure Of Mycobacterium Tuberculosis Menb, A
           Key Enzyme In Vitamin K2 Biosynthesis
 pdb|1Q52|D Chain D, Crystal Structure Of Mycobacterium Tuberculosis Menb, A
           Key Enzyme In Vitamin K2 Biosynthesis
 pdb|1Q52|E Chain E, Crystal Structure Of Mycobacterium Tuberculosis Menb, A
           Key Enzyme In Vitamin K2 Biosynthesis
 pdb|1Q52|F Chain F, Crystal Structure Of Mycobacterium Tuberculosis Menb, A
           Key Enzyme In Vitamin K2 Biosynthesis
 pdb|1Q52|G Chain G, Crystal Structure Of Mycobacterium Tuberculosis Menb, A
           Key Enzyme In Vitamin K2 Biosynthesis
 pdb|1Q52|H Chain H, Crystal Structure Of Mycobacterium Tuberculosis Menb, A
           Key Enzyme In Vitamin K2 Biosynthesis
 pdb|1Q52|I Chain I, Crystal Structure Of Mycobacterium Tuberculosis Menb, A
           Key Enzyme In Vitamin K2 Biosynthesis
 pdb|1Q52|J Chain J, Crystal Structure Of Mycobacterium Tuberculosis Menb, A
           Key Enzyme In Vitamin K2 Biosynthesis
 pdb|1Q52|K Chain K, Crystal Structure Of Mycobacterium Tuberculosis Menb, A
           Key Enzyme In Vitamin K2 Biosynthesis
 pdb|1Q52|L Chain L, Crystal Structure Of Mycobacterium Tuberculosis Menb, A
           Key Enzyme In Vitamin K2 Biosynthesis
          Length = 314

 Score = 30.8 bits (68), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 23/84 (27%), Positives = 40/84 (47%), Gaps = 8/84 (9%)

Query: 28  LMLPPPRNTSSPLSLVIGSLCIKHPNLFGGSEKL-DVSWDKGLYDSNVLVAYRRP----- 81
           ++ P      S  +L       K   L  G + L D+++ + + D+ V VA+ RP     
Sbjct: 1   MVAPAGEQGRSSTALSDNPFDAKAWRLVDGFDDLTDITYHRHVDDATVRVAFNRPEVRNA 60

Query: 82  -RPEWLSQQCFVIQHS-LSPEVGV 103
            RP  + +   V+ H+ +SP+VGV
Sbjct: 61  FRPHTVDELYRVLDHARMSPDVGV 84


>pdb|3T8A|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Menb In
           Complex With Substrate Analogue, Osb-Ncoa
 pdb|3T8A|B Chain B, Crystal Structure Of Mycobacterium Tuberculosis Menb In
           Complex With Substrate Analogue, Osb-Ncoa
 pdb|3T8A|C Chain C, Crystal Structure Of Mycobacterium Tuberculosis Menb In
           Complex With Substrate Analogue, Osb-Ncoa
 pdb|3T8B|A Chain A, Crystal Structure Of Mycobacterium Tuberculosis Menb With
           Altered Hexameric Assembly
 pdb|3T8B|B Chain B, Crystal Structure Of Mycobacterium Tuberculosis Menb With
           Altered Hexameric Assembly
          Length = 334

 Score = 30.8 bits (68), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 23/84 (27%), Positives = 40/84 (47%), Gaps = 8/84 (9%)

Query: 28  LMLPPPRNTSSPLSLVIGSLCIKHPNLFGGSEKL-DVSWDKGLYDSNVLVAYRRP----- 81
           ++ P      S  +L       K   L  G + L D+++ + + D+ V VA+ RP     
Sbjct: 21  MVAPAGEQGRSSTALSDNPFDAKAWRLVDGFDDLTDITYHRHVDDATVRVAFNRPEVRNA 80

Query: 82  -RPEWLSQQCFVIQHS-LSPEVGV 103
            RP  + +   V+ H+ +SP+VGV
Sbjct: 81  FRPHTVDELYRVLDHARMSPDVGV 104


>pdb|2WJQ|A Chain A, Nanc Porin Structure In Hexagonal Crystal Form
          Length = 215

 Score = 28.1 bits (61), Expect = 8.5,   Method: Compositional matrix adjust.
 Identities = 18/70 (25%), Positives = 34/70 (48%), Gaps = 4/70 (5%)

Query: 64  SWDKGLYDSNVLVAYRRPRPEWLSQQCFVIQHSLSPEVGVHGLPIDNFSRSG--SGGVNL 121
           +W   LY       Y   + +W ++  FV+Q+ ++P++  + +  D   R G  +G  NL
Sbjct: 145 AWQTTLYSKQNDYRYANHK-KWATENAFVLQYHMTPDITPY-IEYDYLDRQGVYNGRDNL 202

Query: 122 SRLSLGLDIS 131
           S  S  + +S
Sbjct: 203 SENSYRIGVS 212


>pdb|2WJR|A Chain A, Nanc Porin Structure In Rhombohedral Crystal Form
          Length = 214

 Score = 28.1 bits (61), Expect = 8.8,   Method: Compositional matrix adjust.
 Identities = 18/70 (25%), Positives = 34/70 (48%), Gaps = 4/70 (5%)

Query: 64  SWDKGLYDSNVLVAYRRPRPEWLSQQCFVIQHSLSPEVGVHGLPIDNFSRSG--SGGVNL 121
           +W   LY       Y   + +W ++  FV+Q+ ++P++  + +  D   R G  +G  NL
Sbjct: 144 AWQTTLYSKQNDYRYANHK-KWATENAFVLQYHMTPDITPY-IEYDYLDRQGVYNGRDNL 201

Query: 122 SRLSLGLDIS 131
           S  S  + +S
Sbjct: 202 SENSYRIGVS 211


  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
   0.319    0.137    0.417 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,534,012
Number of Sequences: 62578
Number of extensions: 512930
Number of successful extensions: 1154
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1151
Number of HSP's gapped (non-prelim): 10
length of query: 360
length of database: 14,973,337
effective HSP length: 100
effective length of query: 260
effective length of database: 8,715,537
effective search space: 2266039620
effective search space used: 2266039620
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)