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= psy9645
         (98 letters)

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

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



>pdb|3F9V|A Chain A, Crystal Structure Of A Near Full-Length Archaeal Mcm:
           Functional Insights For An Aaa+ Hexameric Helicase
          Length = 595

 Score = 80.1 bits (196), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 34/65 (52%), Positives = 51/65 (78%)

Query: 32  EKHRVRGDINVLLCGDPGTAKSQFLKYMEKIGPRAIFTTGQGASAVGLTAYVGKHPTTKE 91
           E  R+RGDI++L+ GDPGTAKSQ L+++ ++ PRA++TTG+G++A GLTA V +   T E
Sbjct: 320 EDTRIRGDIHILIIGDPGTAKSQMLQFISRVAPRAVYTTGKGSTAAGLTAAVVREKGTGE 379

Query: 92  WTVEA 96
           + +EA
Sbjct: 380 YYLEA 384


>pdb|3H0K|A Chain A, Crystal Structure Of An Adenylated Kinase Related
          Protein From Sulfolobus Solfataricus To 3.25a
 pdb|3H0K|B Chain B, Crystal Structure Of An Adenylated Kinase Related
          Protein From Sulfolobus Solfataricus To 3.25a
          Length = 178

 Score = 26.9 bits (58), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 10/29 (34%), Positives = 19/29 (65%)

Query: 42 VLLCGDPGTAKSQFLKYMEKIGPRAIFTT 70
          +L+ G PG+ KS+F K +++ G + I  +
Sbjct: 3  ILITGMPGSGKSEFAKLLKERGAKVIVMS 31


>pdb|3LW7|A Chain A, The Crystal Structure Of An Adenylate Kinase-Related
          Protein Bound To Amp From Sulfolobus Solfataricus To
          2.3a
 pdb|3LW7|B Chain B, The Crystal Structure Of An Adenylate Kinase-Related
          Protein Bound To Amp From Sulfolobus Solfataricus To
          2.3a
          Length = 179

 Score = 26.9 bits (58), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 10/29 (34%), Positives = 19/29 (65%)

Query: 42 VLLCGDPGTAKSQFLKYMEKIGPRAIFTT 70
          +L+ G PG+ KS+F K +++ G + I  +
Sbjct: 4  ILITGMPGSGKSEFAKLLKERGAKVIVMS 32


>pdb|2XR1|A Chain A, Dimeric Archaeal Cleavage And Polyadenylation Specificity
           Factor With N-Terminal Kh Domains (Kh-Cpsf) From
           Methanosarcina Mazei
 pdb|2XR1|B Chain B, Dimeric Archaeal Cleavage And Polyadenylation Specificity
           Factor With N-Terminal Kh Domains (Kh-Cpsf) From
           Methanosarcina Mazei
          Length = 640

 Score = 26.6 bits (57), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 18/72 (25%), Positives = 37/72 (51%), Gaps = 3/72 (4%)

Query: 17  KEWTNIPGNQQAGASEKHRVRGDINVLLCGDPGTAKSQFLKYMEKIGPRA--IFTT-GQG 73
           K W  IP   + G++E  ++  ++ V+      + + Q ++Y++++ PR   +FT  G  
Sbjct: 551 KGWKEIPMTGKNGSTEMLKMNMEVQVVDGFSGHSDRRQLMEYVKRMQPRPERVFTEHGDE 610

Query: 74  ASAVGLTAYVGK 85
            + V L + V K
Sbjct: 611 KACVDLASSVYK 622


>pdb|1G6O|A Chain A, Crystal Structure Of The Helicobacter Pylori Atpase,
           Hp0525, In Complex With Adp
 pdb|1G6O|B Chain B, Crystal Structure Of The Helicobacter Pylori Atpase,
           Hp0525, In Complex With Adp
 pdb|1NLY|A Chain A, Crystal Structure Of The Traffic Atpase Of The
           Helicobacter Pylori Type Iv Secretion System In Complex
           With Atpgammas
 pdb|1NLY|B Chain B, Crystal Structure Of The Traffic Atpase Of The
           Helicobacter Pylori Type Iv Secretion System In Complex
           With Atpgammas
 pdb|1NLZ|A Chain A, Crystal Structure Of Unliganded Traffic Atpase Of The Type
           Iv Secretion System Of Helicobacter Pylori
 pdb|1NLZ|B Chain B, Crystal Structure Of Unliganded Traffic Atpase Of The Type
           Iv Secretion System Of Helicobacter Pylori
 pdb|1NLZ|C Chain C, Crystal Structure Of Unliganded Traffic Atpase Of The Type
           Iv Secretion System Of Helicobacter Pylori
 pdb|1NLZ|D Chain D, Crystal Structure Of Unliganded Traffic Atpase Of The Type
           Iv Secretion System Of Helicobacter Pylori
 pdb|1NLZ|E Chain E, Crystal Structure Of Unliganded Traffic Atpase Of The Type
           Iv Secretion System Of Helicobacter Pylori
 pdb|1NLZ|F Chain F, Crystal Structure Of Unliganded Traffic Atpase Of The Type
           Iv Secretion System Of Helicobacter Pylori
 pdb|1OPX|A Chain A, Crystal Structure Of The Traffic Atpase (Hp0525) Of The
           Helicobacter Pylori Type Iv Secretion System Bound By
           Sulfate
 pdb|1OPX|B Chain B, Crystal Structure Of The Traffic Atpase (Hp0525) Of The
           Helicobacter Pylori Type Iv Secretion System Bound By
           Sulfate
          Length = 330

 Score = 25.8 bits (55), Expect = 5.8,   Method: Composition-based stats.
 Identities = 11/40 (27%), Positives = 24/40 (60%)

Query: 26  QQAGASEKHRVRGDINVLLCGDPGTAKSQFLKYMEKIGPR 65
           +QA ++ K  +    NV++CG  G+ K+ ++K + +  P+
Sbjct: 158 EQAISAIKDGIAIGKNVIVCGGTGSGKTTYIKSIXEFIPK 197


>pdb|2PT7|A Chain A, Crystal Structure Of Cag Virb11 (Hp0525) And An Inhibitory
           Protein (Hp1451)
 pdb|2PT7|B Chain B, Crystal Structure Of Cag Virb11 (Hp0525) And An Inhibitory
           Protein (Hp1451)
 pdb|2PT7|C Chain C, Crystal Structure Of Cag Virb11 (Hp0525) And An Inhibitory
           Protein (Hp1451)
 pdb|2PT7|D Chain D, Crystal Structure Of Cag Virb11 (Hp0525) And An Inhibitory
           Protein (Hp1451)
 pdb|2PT7|E Chain E, Crystal Structure Of Cag Virb11 (Hp0525) And An Inhibitory
           Protein (Hp1451)
 pdb|2PT7|F Chain F, Crystal Structure Of Cag Virb11 (Hp0525) And An Inhibitory
           Protein (Hp1451)
          Length = 330

 Score = 25.4 bits (54), Expect = 8.5,   Method: Composition-based stats.
 Identities = 11/40 (27%), Positives = 24/40 (60%)

Query: 26  QQAGASEKHRVRGDINVLLCGDPGTAKSQFLKYMEKIGPR 65
           +QA ++ K  +    NV++CG  G+ K+ ++K + +  P+
Sbjct: 158 EQAISAIKDGIAIGKNVIVCGGTGSGKTTYIKSIMEFIPK 197


>pdb|3K7T|A Chain A, Crystal Structure Of Apo-Form 6-Hydroxy-L-Nicotine
          Oxidase, Crystal Form P3121
 pdb|3K7T|B Chain B, Crystal Structure Of Apo-Form 6-Hydroxy-L-Nicotine
          Oxidase, Crystal Form P3121
          Length = 425

 Score = 25.4 bits (54), Expect = 8.6,   Method: Composition-based stats.
 Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 4/55 (7%)

Query: 17 KEWTNIPGNQ-QAGAS---EKHRVRGDINVLLCGDPGTAKSQFLKYMEKIGPRAI 67
          +E  N+PG + + G +    KH  R    +   G P  A S+F  +  ++GP A+
Sbjct: 43 RESRNVPGLRVEIGGAYLHRKHHPRLAAELDRYGIPTAAASEFTSFRHRLGPTAV 97


>pdb|3K7M|X Chain X, Crystal Structure Of 6-Hydroxy-L-Nicotine Oxidase From
          Arthrobacter Nicotinovorans
 pdb|3K7Q|X Chain X, Crystal Structure Of Substrate-Bound
          6-Hydroxy-L-Nicotine Oxidase From Arthrobacter
          Nicotinovorans
 pdb|3NG7|X Chain X, Complex Of Dithionite-Reduced 6-Hydroxy-L-Nicotine
          Oxidase With Substrate Bound At Active Site And
          Inhibitor At Exit Cavity
 pdb|3NGC|X Chain X, Complex Of 6-Hydroxy-L-Nicotine Oxidase With
          Intermediate Methylmyosmine Product Formed During
          Catalytic Turnover
 pdb|3NH3|X Chain X, Complex Of 6-Hydroxy-L-Nicotine Oxidase With Final
          Ketone Product Formed During Catalytic Turnover
 pdb|3NHO|X Chain X, Complex Of 6-Hydroxy-L-Nicotine Oxidase With Product
          Bound At Active Site
 pdb|3NK0|X Chain X, Complex Of 6-Hydroxy-L-Nicotine Oxidase With Inhibitor
          Bound At Active Site And Turnover Product At Exit
          Cavity
 pdb|3NK1|X Chain X, Complex Of 6-Hydroxy-L-Nicotine Oxidase With Serotonin
 pdb|3NK2|X Chain X, Complex Of 6-Hydroxy-L-Nicotine Oxidase With Dopamine
 pdb|3NN6|X Chain X, Crystal Structure Of Inhibitor-Bound In Active Centre
          6-Hydroxy-L- Nicotine Oxidase From Arthrobacter
          Nicotinovorans
 pdb|3NN0|X Chain X, Complex Of 6-Hydroxy-L-Nicotine Oxidase With
          Nicotinamide
          Length = 431

 Score = 25.4 bits (54), Expect = 8.7,   Method: Composition-based stats.
 Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 4/55 (7%)

Query: 17 KEWTNIPGNQ-QAGAS---EKHRVRGDINVLLCGDPGTAKSQFLKYMEKIGPRAI 67
          +E  N+PG + + G +    KH  R    +   G P  A S+F  +  ++GP A+
Sbjct: 43 RESRNVPGLRVEIGGAYLHRKHHPRLAAELDRYGIPTAAASEFTSFRHRLGPTAV 97


  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
   0.316    0.133    0.411 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,260,673
Number of Sequences: 62578
Number of extensions: 118426
Number of successful extensions: 302
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 295
Number of HSP's gapped (non-prelim): 12
length of query: 98
length of database: 14,973,337
effective HSP length: 64
effective length of query: 34
effective length of database: 10,968,345
effective search space: 372923730
effective search space used: 372923730
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: 45 (21.9 bits)