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= psy10246
         (287 letters)

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

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



>pdb|2E4L|A Chain A, Thermodynamic And Structural Analysis Of Thermolabile
           Rnase Hi From Shewanella Oneidensis Mr-1
          Length = 158

 Score = 31.2 bits (69), Expect = 0.63,   Method: Compositional matrix adjust.
 Identities = 18/46 (39%), Positives = 24/46 (52%), Gaps = 4/46 (8%)

Query: 216 VRNV----RAMKFARDINIKFLWIPSHCGIVENERVDQAAKNSIYA 257
           V+NV    R  K A+   I + W+  H G  ENER DQ A+ +  A
Sbjct: 100 VKNVDLWKRLDKAAQLHQIDWRWVKGHAGHAENERCDQLARAAAEA 145


>pdb|1JXB|A Chain A, I53a, A Point Mutant Of The Cysteine-Free Variant Of E.
           Coli Rnase Hi
          Length = 155

 Score = 30.0 bits (66), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 11/23 (47%), Positives = 15/23 (65%)

Query: 230 IKFLWIPSHCGIVENERVDQAAK 252
           IK+ W+  H G  ENER D+ A+
Sbjct: 116 IKWEWVKGHAGHPENERADELAR 138


>pdb|1G15|A Chain A, Co-Crystal Of E. Coli Rnase Hi With Two Mn2+ Ions Bound In
           The The Active Site
          Length = 155

 Score = 30.0 bits (66), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 11/23 (47%), Positives = 15/23 (65%)

Query: 230 IKFLWIPSHCGIVENERVDQAAK 252
           IK+ W+  H G  ENER D+ A+
Sbjct: 116 IKWEWVKGHAGHPENERADELAR 138


>pdb|1F21|A Chain A, Divalent Metal Cofactor Binding In The Kinetic Folding
           Trajectory Of E. Coli Ribonuclease Hi
          Length = 155

 Score = 30.0 bits (66), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 11/23 (47%), Positives = 15/23 (65%)

Query: 230 IKFLWIPSHCGIVENERVDQAAK 252
           IK+ W+  H G  ENER D+ A+
Sbjct: 116 IKWEWVKGHAGHPENERADELAR 138


>pdb|1JL1|A Chain A, D10a E. Coli Ribonuclease Hi
          Length = 155

 Score = 30.0 bits (66), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 11/23 (47%), Positives = 15/23 (65%)

Query: 230 IKFLWIPSHCGIVENERVDQAAK 252
           IK+ W+  H G  ENER D+ A+
Sbjct: 116 IKWEWVKGHAGHPENERADELAR 138


>pdb|1RIL|A Chain A, Crystal Structure Of Ribonuclease H From Thermus
           Thermophilus Hb8 Refined At 2.8 Angstroms Resolution
          Length = 166

 Score = 29.6 bits (65), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 11/29 (37%), Positives = 18/29 (62%)

Query: 230 IKFLWIPSHCGIVENERVDQAAKNSIYAQ 258
           ++F ++  H G  ENERVD+ A+    +Q
Sbjct: 121 VRFHFVKGHTGHPENERVDREARRQAQSQ 149


>pdb|1RBR|A Chain A, Structural Study Of Mutants Of Escherichia Coli
           Ribonuclease Hi With Enhanced Thermostability
          Length = 155

 Score = 29.3 bits (64), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 11/24 (45%), Positives = 15/24 (62%)

Query: 229 NIKFLWIPSHCGIVENERVDQAAK 252
            IK+ W+  H G  ENER D+ A+
Sbjct: 115 QIKWEWVKGHAGHPENERCDELAR 138


>pdb|1RBU|A Chain A, Structural Study Of Mutants Of Escherichia Coli
           Ribonuclease Hi With Enhanced Thermostability
          Length = 155

 Score = 29.3 bits (64), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 11/23 (47%), Positives = 15/23 (65%)

Query: 230 IKFLWIPSHCGIVENERVDQAAK 252
           IK+ W+  H G  ENER D+ A+
Sbjct: 116 IKWEWVKGHAGHPENERCDELAR 138


>pdb|1RBS|A Chain A, Structural Study Of Mutants Of Escherichia Coli
           Ribonuclease Hi With Enhanced Thermostability
          Length = 155

 Score = 29.3 bits (64), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 11/24 (45%), Positives = 15/24 (62%)

Query: 229 NIKFLWIPSHCGIVENERVDQAAK 252
            IK+ W+  H G  ENER D+ A+
Sbjct: 115 QIKWEWVKGHAGHPENERCDELAR 138


>pdb|1LAV|A Chain A, Stabilization Of Escherichia Coli Ribonuclease Hi By
           Cavity- Filling Mutations Within A Hydrophobic Core
          Length = 155

 Score = 29.3 bits (64), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 11/23 (47%), Positives = 15/23 (65%)

Query: 230 IKFLWIPSHCGIVENERVDQAAK 252
           IK+ W+  H G  ENER D+ A+
Sbjct: 116 IKWEWVKGHAGHPENERCDELAR 138


>pdb|1GOA|A Chain A, Cooperative Stabilization Of Escherichia Coli Ribonuclease
           Hi By Insertion Of Gly-80b And Gly-77-> Ala Substitution
          Length = 156

 Score = 29.3 bits (64), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 11/23 (47%), Positives = 15/23 (65%)

Query: 230 IKFLWIPSHCGIVENERVDQAAK 252
           IK+ W+  H G  ENER D+ A+
Sbjct: 117 IKWEWVKGHAGHPENERCDELAR 139


>pdb|1RDA|A Chain A, Crystal Structures Of Ribonuclease Hi Active Site Mutants
           From Escherichia Coli
          Length = 155

 Score = 29.3 bits (64), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 11/23 (47%), Positives = 15/23 (65%)

Query: 230 IKFLWIPSHCGIVENERVDQAAK 252
           IK+ W+  H G  ENER D+ A+
Sbjct: 116 IKWEWVKGHAGHPENERCDELAR 138


>pdb|1RDC|A Chain A, Crystal Structures Of Ribonuclease Hi Active Site Mutants
           From Escherichia Coli
          Length = 155

 Score = 29.3 bits (64), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 11/23 (47%), Positives = 15/23 (65%)

Query: 230 IKFLWIPSHCGIVENERVDQAAK 252
           IK+ W+  H G  ENER D+ A+
Sbjct: 116 IKWEWVKGHAGHPENERCDELAR 138


>pdb|1WSH|A Chain A, Crystal Structure Of E.Coli Rnase Hi Active Site Mutant
           (E48aK87A)
 pdb|1WSH|B Chain B, Crystal Structure Of E.Coli Rnase Hi Active Site Mutant
           (E48aK87A)
 pdb|1WSH|C Chain C, Crystal Structure Of E.Coli Rnase Hi Active Site Mutant
           (E48aK87A)
 pdb|1WSH|D Chain D, Crystal Structure Of E.Coli Rnase Hi Active Site Mutant
           (E48aK87A)
 pdb|1WSE|A Chain A, Co-Crystal Structure Of E.Coli Rnase Hi Active Site Mutant
           (E48a) With Mn2+
 pdb|1WSE|B Chain B, Co-Crystal Structure Of E.Coli Rnase Hi Active Site Mutant
           (E48a) With Mn2+
          Length = 155

 Score = 29.3 bits (64), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 11/23 (47%), Positives = 15/23 (65%)

Query: 230 IKFLWIPSHCGIVENERVDQAAK 252
           IK+ W+  H G  ENER D+ A+
Sbjct: 116 IKWEWVKGHAGHPENERCDELAR 138


>pdb|1RBT|A Chain A, Structural Study Of Mutants Of Escherichia Coli
           Ribonuclease Hi With Enhanced Thermostability
          Length = 155

 Score = 29.3 bits (64), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 11/23 (47%), Positives = 15/23 (65%)

Query: 230 IKFLWIPSHCGIVENERVDQAAK 252
           IK+ W+  H G  ENER D+ A+
Sbjct: 116 IKWEWVKGHAGHPENERCDELAR 138


>pdb|1RDB|A Chain A, Crystal Structures Of Ribonuclease Hi Active Site Mutants
           From Escherichia Coli
          Length = 155

 Score = 29.3 bits (64), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 11/24 (45%), Positives = 15/24 (62%)

Query: 229 NIKFLWIPSHCGIVENERVDQAAK 252
            IK+ W+  H G  ENER D+ A+
Sbjct: 115 QIKWEWVKGHAGHPENERCDELAR 138


>pdb|1GOB|A Chain A, Cooperative Stabilization Of Escherichia Coli Ribonuclease
           Hi By Insertion Of Gly-80b And Gly-77-> Ala Substitution
          Length = 155

 Score = 29.3 bits (64), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 11/24 (45%), Positives = 15/24 (62%)

Query: 229 NIKFLWIPSHCGIVENERVDQAAK 252
            IK+ W+  H G  ENER D+ A+
Sbjct: 115 QIKWEWVKGHAGHPENERCDELAR 138


>pdb|1RBV|A Chain A, Structural Study Of Mutants Of Escherichia Coli
           Ribonuclease Hi With Enhanced Thermostability
          Length = 155

 Score = 29.3 bits (64), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 11/23 (47%), Positives = 15/23 (65%)

Query: 230 IKFLWIPSHCGIVENERVDQAAK 252
           IK+ W+  H G  ENER D+ A+
Sbjct: 116 IKWEWVKGHAGHPENERCDELAR 138


>pdb|1RCH|A Chain A, Solution Nmr Structure Of Ribonuclease Hi From Escherichia
           Coli, 8 Structures
 pdb|1RDD|A Chain A, Crystal Structure Of Escherichia Coli Rnase Hi In Complex
           With Mg2+ At 2.8 Angstroms Resolution: Proof For A
           Single Mg2+ Site
 pdb|2RN2|A Chain A, Structural Details Of Ribonuclease H From Escherichia Coli
           As Refined To An Atomic Resolution
          Length = 155

 Score = 29.3 bits (64), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 11/23 (47%), Positives = 15/23 (65%)

Query: 230 IKFLWIPSHCGIVENERVDQAAK 252
           IK+ W+  H G  ENER D+ A+
Sbjct: 116 IKWEWVKGHAGHPENERCDELAR 138


>pdb|1LAW|A Chain A, Stabilization Of Escherichia Coli Ribonuclease Hi By
           Cavity- Filling Mutations Within A Hydrophobic Core
          Length = 155

 Score = 29.3 bits (64), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 11/23 (47%), Positives = 15/23 (65%)

Query: 230 IKFLWIPSHCGIVENERVDQAAK 252
           IK+ W+  H G  ENER D+ A+
Sbjct: 116 IKWEWVKGHAGHPENERCDELAR 138


>pdb|3AA3|A Chain A, A52l E. Coli Rnase Hi
          Length = 155

 Score = 29.3 bits (64), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 11/24 (45%), Positives = 15/24 (62%)

Query: 229 NIKFLWIPSHCGIVENERVDQAAK 252
            IK+ W+  H G  ENER D+ A+
Sbjct: 115 QIKWEWVKGHAGHPENERCDELAR 138


>pdb|1GOC|A Chain A, Cooperative Stabilization Of Escherichia Coli Ribonuclease
           Hi By Insertion Of Gly-80b And Gly-77-> Ala Substitution
          Length = 156

 Score = 29.3 bits (64), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 11/24 (45%), Positives = 15/24 (62%)

Query: 229 NIKFLWIPSHCGIVENERVDQAAK 252
            IK+ W+  H G  ENER D+ A+
Sbjct: 116 QIKWEWVKGHAGHPENERCDELAR 139


>pdb|3AA4|A Chain A, A52v E.Coli Rnase Hi
          Length = 155

 Score = 29.3 bits (64), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 11/23 (47%), Positives = 15/23 (65%)

Query: 230 IKFLWIPSHCGIVENERVDQAAK 252
           IK+ W+  H G  ENER D+ A+
Sbjct: 116 IKWEWVKGHAGHPENERCDELAR 138


>pdb|2Z1H|A Chain A, Crystal Structure Of E.Coli Rnase Hi Surface Charged
           Mutant(Q4rT92KQ105KQ113RQ115KN143KT145K)
          Length = 155

 Score = 29.3 bits (64), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 11/23 (47%), Positives = 15/23 (65%)

Query: 230 IKFLWIPSHCGIVENERVDQAAK 252
           IK+ W+  H G  ENER D+ A+
Sbjct: 116 IKWEWVKGHAGHPENERCDELAR 138


>pdb|1RNH|A Chain A, Structure Of Ribonuclease H Phased At 2 Angstroms
           Resolution By Mad Analysis Of The Selenomethionyl
           Protein
          Length = 155

 Score = 28.9 bits (63), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 11/23 (47%), Positives = 15/23 (65%)

Query: 230 IKFLWIPSHCGIVENERVDQAAK 252
           IK+ W+  H G  ENER D+ A+
Sbjct: 116 IKWEWVKGHAGHPENERCDELAR 138


>pdb|3AA5|X Chain X, A52f E.Coli Rnase Hi
          Length = 155

 Score = 28.9 bits (63), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 11/23 (47%), Positives = 15/23 (65%)

Query: 230 IKFLWIPSHCGIVENERVDQAAK 252
           IK+ W+  H G  ENER D+ A+
Sbjct: 116 IKWEWVKGHAGHPENERCDELAR 138


>pdb|3AA2|A Chain A, A52i E. Coli Rnase Hi
          Length = 155

 Score = 28.9 bits (63), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 11/24 (45%), Positives = 15/24 (62%)

Query: 229 NIKFLWIPSHCGIVENERVDQAAK 252
            IK+ W+  H G  ENER D+ A+
Sbjct: 115 QIKWEWVKGHAGHPENERCDELAR 138


>pdb|2Z1I|A Chain A, Crystal Structure Of E.Coli Rnase Hi Surface Charged
           Mutant(Q4rT40EQ72HQ76KQ80ET92KQ105KQ113RQ115K)
 pdb|2Z1I|B Chain B, Crystal Structure Of E.Coli Rnase Hi Surface Charged
           Mutant(Q4rT40EQ72HQ76KQ80ET92KQ105KQ113RQ115K)
          Length = 155

 Score = 28.9 bits (63), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 11/23 (47%), Positives = 15/23 (65%)

Query: 230 IKFLWIPSHCGIVENERVDQAAK 252
           IK+ W+  H G  ENER D+ A+
Sbjct: 116 IKWEWVKGHAGHPENERCDELAR 138


>pdb|2Z1G|A Chain A, Crystal Structure Of E.Coli Rnase Hi Surface Charged
           Mutant(Q4rT40EQ72HQ76KQ80ET92KQ105K)
          Length = 155

 Score = 28.9 bits (63), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 11/23 (47%), Positives = 15/23 (65%)

Query: 230 IKFLWIPSHCGIVENERVDQAAK 252
           IK+ W+  H G  ENER D+ A+
Sbjct: 116 IKWEWVKGHAGHPENERCDELAR 138


>pdb|2Z1J|A Chain A, Crystal Structure Of E.Coli Rnase Hi Surface Charged
           Mutant(Q4rT40EQ72HQ76KQ80ET92KQ105KQ113RQ115KN143K
           T145K)
          Length = 155

 Score = 28.9 bits (63), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 11/23 (47%), Positives = 15/23 (65%)

Query: 230 IKFLWIPSHCGIVENERVDQAAK 252
           IK+ W+  H G  ENER D+ A+
Sbjct: 116 IKWEWVKGHAGHPENERCDELAR 138


>pdb|4AI6|A Chain A, Dynein Motor Domain - Adp Complex
 pdb|4AI6|B Chain B, Dynein Motor Domain - Adp Complex
 pdb|4AKG|A Chain A, Dynein Motor Domain - Atp Complex
 pdb|4AKG|B Chain B, Dynein Motor Domain - Atp Complex
 pdb|4AKH|A Chain A, Dynein Motor Domain - Amppnp Complex
 pdb|4AKH|B Chain B, Dynein Motor Domain - Amppnp Complex
 pdb|4AKI|A Chain A, Dynein Motor Domain - Luac Derivative
 pdb|4AKI|B Chain B, Dynein Motor Domain - Luac Derivative
          Length = 2695

 Score = 28.1 bits (61), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 11/26 (42%), Positives = 18/26 (69%)

Query: 55  ILEKDSPVSAHRILFLLLNPDCNDPS 80
           +LE+++P+S H  +F+ LNP  N  S
Sbjct: 737 LLEEETPLSPHTAVFITLNPGYNGRS 762


>pdb|3QMZ|A Chain A, Crystal Structure Of The Cytoplasmic Dynein Heavy Chain
           Motor Domain
 pdb|3QMZ|B Chain B, Crystal Structure Of The Cytoplasmic Dynein Heavy Chain
           Motor Domain
          Length = 2486

 Score = 28.1 bits (61), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 11/26 (42%), Positives = 18/26 (69%)

Query: 55  ILEKDSPVSAHRILFLLLNPDCNDPS 80
           +LE+++P+S H  +F+ LNP  N  S
Sbjct: 518 LLEEETPLSPHTAVFITLNPGYNGRS 543


>pdb|1G0D|A Chain A, Crystal Structure Of Red Sea Bream Transglutaminase
          Length = 695

 Score = 27.7 bits (60), Expect = 6.8,   Method: Compositional matrix adjust.
 Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 6/52 (11%)

Query: 42  GHSRSACQFQ--NNEILEKDSPVSAHRILFLLLNPDCNDPSFFLPDPGSFEK 91
           GH R A      +  I+E+   +S H    +L NP C D   +LPD    ++
Sbjct: 106 GHYRLAVLVMSPDGHIVERADKISFH----MLFNPWCRDDMVYLPDESKLQE 153


  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    0.133    0.402 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,136,807
Number of Sequences: 62578
Number of extensions: 304713
Number of successful extensions: 848
Number of sequences better than 100.0: 33
Number of HSP's better than 100.0 without gapping: 32
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 816
Number of HSP's gapped (non-prelim): 33
length of query: 287
length of database: 14,973,337
effective HSP length: 98
effective length of query: 189
effective length of database: 8,840,693
effective search space: 1670890977
effective search space used: 1670890977
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: 51 (24.3 bits)