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= psy6931
         (81 letters)

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

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



>pdb|3D45|A Chain A, Crystal Structure Of Mouse Parn In Complex With M7gpppg
 pdb|3D45|B Chain B, Crystal Structure Of Mouse Parn In Complex With M7gpppg
          Length = 507

 Score = 77.0 bits (188), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 35/66 (53%), Positives = 50/66 (75%), Gaps = 4/66 (6%)

Query: 20 KAIKSALFVTIDGEFTGLNNGPN----TTPYDTPAQYYDKIRQGSMDFLLIQFGLCAFKY 75
          +AI+ A F  IDGEF+G+++GP+    T+ +DTP + Y K+++ SMDFLL QFGLCAFKY
Sbjct: 19 QAIEEADFFAIDGEFSGISDGPSVTALTSGFDTPEERYQKLKKHSMDFLLFQFGLCAFKY 78

Query: 76 DNTTKR 81
          D+T  +
Sbjct: 79 DHTDSK 84


>pdb|2A1R|A Chain A, Crystal Structure Of Parn Nuclease Domain
 pdb|2A1R|B Chain B, Crystal Structure Of Parn Nuclease Domain
 pdb|2A1S|A Chain A, Crystal Structure Of Native Parn Nuclease Domain
 pdb|2A1S|B Chain B, Crystal Structure Of Native Parn Nuclease Domain
 pdb|2A1S|C Chain C, Crystal Structure Of Native Parn Nuclease Domain
 pdb|2A1S|D Chain D, Crystal Structure Of Native Parn Nuclease Domain
          Length = 430

 Score = 73.6 bits (179), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 34/66 (51%), Positives = 47/66 (71%), Gaps = 4/66 (6%)

Query: 20 KAIKSALFVTIDGEFTGLNNGPN----TTPYDTPAQYYDKIRQGSMDFLLIQFGLCAFKY 75
          +AI+ A F  IDGEF+G+++GP+    T  +DTP + Y K+++ SMDFLL QFGLC FKY
Sbjct: 17 QAIEEADFFAIDGEFSGISDGPSVSALTNGFDTPEERYQKLKKHSMDFLLFQFGLCTFKY 76

Query: 76 DNTTKR 81
          D T  +
Sbjct: 77 DYTDSK 82


>pdb|1UUM|A Chain A, Rat Dihydroorotate Dehydrogenase (Dhod)in Complex With
           Atovaquone
 pdb|1UUM|B Chain B, Rat Dihydroorotate Dehydrogenase (Dhod)in Complex With
           Atovaquone
 pdb|1UUO|A Chain A, Rat Dihydroorotate Dehydrogenase (Dhod)in Complex With
           Brequinar
          Length = 372

 Score = 27.7 bits (60), Expect = 1.8,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 4/49 (8%)

Query: 9   ILQHNITTRYAKAIKSALFVTIDGEFTGLNNGPNTTPYDTPAQYYDKIR 57
           +++H +  R  K  +    +T DG   G+N G N T  D  A Y + +R
Sbjct: 132 VVEHRLRARQQKQAQ----LTADGLPLGINLGKNKTSEDAAADYAEGVR 176


>pdb|3H8S|A Chain A, Structure Of D19n T4 Rnase H In The Presence Of Divalent
           Mag
          Length = 305

 Score = 27.3 bits (59), Expect = 1.9,   Method: Composition-based stats.
 Identities = 16/52 (30%), Positives = 26/52 (50%)

Query: 26  LFVTIDGEFTGLNNGPNTTPYDTPAQYYDKIRQGSMDFLLIQFGLCAFKYDN 77
           L ++ DG+FT L+  PN   +    + + KI+ GS +   +   L   K DN
Sbjct: 150 LIISSDGDFTQLHKYPNVKQWSPMHKKWVKIKSGSAEIDCMTKILKGDKKDN 201


>pdb|2IHN|A Chain A, Co-Crystal Of Bacteriophage T4 Rnase H With A Fork Dna
           Substrate
 pdb|3H7I|A Chain A, Structure Of The Metal-Free D132n T4 Rnase H
 pdb|3H8W|A Chain A, Structure Of D132n T4 Rnase H In The Presence Of Divalent
           Ma
          Length = 305

 Score = 27.3 bits (59), Expect = 1.9,   Method: Composition-based stats.
 Identities = 16/52 (30%), Positives = 26/52 (50%)

Query: 26  LFVTIDGEFTGLNNGPNTTPYDTPAQYYDKIRQGSMDFLLIQFGLCAFKYDN 77
           L ++ DG+FT L+  PN   +    + + KI+ GS +   +   L   K DN
Sbjct: 150 LIISSDGDFTQLHKYPNVKQWSPMHKKWVKIKSGSAEIDCMTKILKGDKKDN 201


>pdb|1TFR|A Chain A, Rnase H From Bacteriophage T4
 pdb|3H8J|A Chain A, Native T4 Rnase H In The Absence Of Divalent Metal Ions
          Length = 305

 Score = 27.3 bits (59), Expect = 2.0,   Method: Composition-based stats.
 Identities = 16/52 (30%), Positives = 26/52 (50%)

Query: 26  LFVTIDGEFTGLNNGPNTTPYDTPAQYYDKIRQGSMDFLLIQFGLCAFKYDN 77
           L ++ DG+FT L+  PN   +    + + KI+ GS +   +   L   K DN
Sbjct: 150 LIISSDGDFTQLHKYPNVKQWSPMHKKWVKIKSGSAEIDCMTKILKGDKKDN 201


>pdb|4GXP|A Chain A, Chimeric Family 1 Beta-Glucosidase Made With
           Non-Contiguous Schema
 pdb|4GXP|B Chain B, Chimeric Family 1 Beta-Glucosidase Made With
           Non-Contiguous Schema
 pdb|4GXP|C Chain C, Chimeric Family 1 Beta-Glucosidase Made With
           Non-Contiguous Schema
          Length = 467

 Score = 27.3 bits (59), Expect = 2.0,   Method: Composition-based stats.
 Identities = 14/44 (31%), Positives = 21/44 (47%)

Query: 4   TQHPMILQHNITTRYAKAIKSALFVTIDGEFTGLNNGPNTTPYD 47
           T  P  + HNI   + +A+K       DG+   + NG  T P+D
Sbjct: 194 TSEPWTVGHNILVAHGRAVKVFRETVKDGKIGIVLNGDFTYPWD 237


>pdb|2EOB|A Chain A, Solution Structure Of The Second Sh2 Domain From Rat Plc
          Gamma-2
          Length = 124

 Score = 26.6 bits (57), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 8/28 (28%), Positives = 18/28 (64%)

Query: 41 PNTTPYDTPAQYYDKIRQGSMDFLLIQF 68
          PN  P+++   YYD++ +G  + +L++ 
Sbjct: 11 PNPNPHESKPWYYDRLSRGEAEDMLMRI 38


>pdb|2B0M|A Chain A, Human Dihydroorotate Dehydrogenase Bound To A Novel
           Inhibitor
          Length = 393

 Score = 26.6 bits (57), Expect = 3.8,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 4/49 (8%)

Query: 9   ILQHNITTRYAKAIKSALFVTIDGEFTGLNNGPNTTPYDTPAQYYDKIR 57
           +++H +  R  K  K    +T DG   G+N G N T  D    Y + +R
Sbjct: 153 VVEHRLRARQQKQAK----LTEDGLPLGVNLGKNKTSVDAAEDYAEGVR 197


>pdb|3U2O|A Chain A, Dihydroorotate Dehydrogenase (Dhodh) Crystal Structure In
           Complex With Small Molecule Inhibitor
          Length = 395

 Score = 26.6 bits (57), Expect = 3.8,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 4/49 (8%)

Query: 9   ILQHNITTRYAKAIKSALFVTIDGEFTGLNNGPNTTPYDTPAQYYDKIR 57
           +++H +  R  K  K    +T DG   G+N G N T  D    Y + +R
Sbjct: 155 VVEHRLRARQQKQAK----LTEDGLPLGVNLGKNKTSVDAAEDYAEGVR 199


>pdb|1D3G|A Chain A, Human Dihydroorotate Dehydrogenase Complexed With
           Brequinar Analog
 pdb|1D3H|A Chain A, Human Dihydroorotate Dehydrogenase Complexed With
           Antiproliferative Agent A771726
 pdb|2BXV|A Chain A, Dual Binding Mode Of A Novel Series Of Dhodh Inhibitors
 pdb|2PRH|A Chain A, The Structures Of Apo- And Inhibitor Bound Human
           Dihydroorotate Dehydrogenase Reveal Conformational
           Flexibility Within The Inhibitor Binding Site
 pdb|2PRL|A Chain A, The Structures Of Apo- And Inhibitor Bound Human
           Dihydroorotate Dehydrogenase Reveal Conformational
           Flexibility Within The Inhibitor Binding Site
 pdb|2PRM|A Chain A, The Structures Of Apo- And Inhibitor Bound Human
           Dihydroorotate Dehydrogenase Reveal Conformational
           Flexibility Within The Inhibitor Binding Site
 pdb|3F1Q|A Chain A, Human Dihydroorotate Dehydrogenase In Complex With A
           Leflunomide Derivative Inhibitor 1
 pdb|3FJ6|A Chain A, Human Dihydroorotate Dehydrogenase In Complex With A
           Leflunomide Derivative Inhibitor 2
 pdb|3FJL|A Chain A, Human Dihydroorotate Dehydrogenase In Complex With A
           Leflunomide Derivative Inhibitor 3
 pdb|3G0U|A Chain A, Human Dihydroorotate Dehydrogenase In Complex With A
           Leflunomide Derivative Inhibitor 4
 pdb|3G0X|A Chain A, Human Dihydroorotate Dehydrogenase In Complex With A
           Leflunomide Derivative Inhibitor 5
 pdb|3ZWS|A Chain A, Structure Of Human Dihydroorotate Dehydrogenase With A
           Bound Inhibitor
 pdb|3ZWT|A Chain A, Structure Of Human Dihydroorotate Dehydrogenase With A
           Bound Inhibitor
          Length = 367

 Score = 26.6 bits (57), Expect = 3.8,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 4/49 (8%)

Query: 9   ILQHNITTRYAKAIKSALFVTIDGEFTGLNNGPNTTPYDTPAQYYDKIR 57
           +++H +  R  K  K    +T DG   G+N G N T  D    Y + +R
Sbjct: 127 VVEHRLRARQQKQAK----LTEDGLPLGVNLGKNKTSVDAAEDYAEGVR 171


>pdb|2WV8|A Chain A, Complex Of Human Dihydroorotate Dehydrogenase With The
           Inhibitor 221290
          Length = 365

 Score = 26.6 bits (57), Expect = 3.8,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 4/49 (8%)

Query: 9   ILQHNITTRYAKAIKSALFVTIDGEFTGLNNGPNTTPYDTPAQYYDKIR 57
           +++H +  R  K  K    +T DG   G+N G N T  D    Y + +R
Sbjct: 125 VVEHRLRARQQKQAK----LTEDGLPLGVNLGKNKTSVDAAEDYAEGVR 169


>pdb|3KVJ|A Chain A, Crystal Structure Of Human Dihydroorotate Dehydrogenase
           (Dhodh) With Amino-Benzoic Acid Inhibitor 105 At 1.94a
           Resolution
 pdb|3KVK|A Chain A, Crystal Structure Of Human Dihydroorotate Dehydrogenase
           (Dhodh) With Amino-Benzoic Acid Inhibitor 641 At 2.05a
           Resolution
 pdb|3KVL|A Chain A, Crystal Structure Of Human Dihydroorotate Dehydrogenase
           (Dhodh) With Amino-Benzoic Acid Inhibitor 715 At 1.85a
           Resolution
 pdb|3KVM|A Chain A, Crystal Structure Of Human Dihydroorotate Dehydrogenase
           (Dhodh) With Amino-Benzoic Acid Inhibitor 951 At 2.00a
           Resolution
          Length = 390

 Score = 26.6 bits (57), Expect = 3.8,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 4/49 (8%)

Query: 9   ILQHNITTRYAKAIKSALFVTIDGEFTGLNNGPNTTPYDTPAQYYDKIR 57
           +++H +  R  K  K    +T DG   G+N G N T  D    Y + +R
Sbjct: 150 VVEHRLRARQQKQAK----LTEDGLPLGVNLGKNKTSVDAAEDYAEGVR 194


>pdb|2FPT|A Chain A, Dual Binding Mode Of A Novel Series Of Dhodh Inhibitors
 pdb|2FPV|A Chain A, Dual Binding Mode Of A Novel Series Of Dhodh Inhibitors
 pdb|2FPY|A Chain A, Dual Binding Mode Of A Novel Series Of Dhodh Inhibitors
 pdb|2FQI|A Chain A, Dual Binding Modes Of A Novel Series Of Dhodh Inhibitors
          Length = 395

 Score = 26.6 bits (57), Expect = 3.8,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 4/49 (8%)

Query: 9   ILQHNITTRYAKAIKSALFVTIDGEFTGLNNGPNTTPYDTPAQYYDKIR 57
           +++H +  R  K  K    +T DG   G+N G N T  D    Y + +R
Sbjct: 155 VVEHRLRARQQKQAK----LTEDGLPLGVNLGKNKTSVDAAEDYAEGVR 199


  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    0.136    0.413 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,607,583
Number of Sequences: 62578
Number of extensions: 96594
Number of successful extensions: 244
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 234
Number of HSP's gapped (non-prelim): 21
length of query: 81
length of database: 14,973,337
effective HSP length: 50
effective length of query: 31
effective length of database: 11,844,437
effective search space: 367177547
effective search space used: 367177547
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: 45 (21.9 bits)