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= 034727
         (86 letters)

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

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



>pdb|3HST|B Chain B, N-Terminal Rnase H Domain Of Rv2228c From Mycobacterium
           Tuberculosis As A Fusion Protein With Maltose Binding
           Protein
 pdb|3HST|D Chain D, N-Terminal Rnase H Domain Of Rv2228c From Mycobacterium
           Tuberculosis As A Fusion Protein With Maltose Binding
           Protein
          Length = 141

 Score = 37.0 bits (84), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 28/79 (35%), Positives = 41/79 (51%), Gaps = 3/79 (3%)

Query: 9   LIYNHNGVGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCC-WLMEDQTP 67
           L  +   +G  TNNVA+Y  LI GL  A++ G     V  DSKLV  Q+   W ++   P
Sbjct: 34  LAESKQAIGRATNNVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQMSGRWKVKH--P 91

Query: 68  GMAELCGEAKRLKDKFLSI 86
            + +L  +A+ L  +F  I
Sbjct: 92  DLLKLYVQAQALASQFRRI 110


>pdb|2EHG|A Chain A, Crystal Structure Of Hyperthermophilic Archaeal Rnase Hi
          Length = 149

 Score = 31.6 bits (70), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 16/39 (41%), Positives = 26/39 (66%)

Query: 19 TTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQV 57
          +TNNVA+Y  LI  ++  L+ G  +  ++GDS+LV  Q+
Sbjct: 46 STNNVAEYSGLICLMETMLRLGISSPIIKGDSQLVIKQM 84


>pdb|3ALY|A Chain A, Crystal Structure Of Rnase Hi From Sulfolobus Tokodaii
          With C-Terminal Deletion
 pdb|3ALY|B Chain B, Crystal Structure Of Rnase Hi From Sulfolobus Tokodaii
          With C-Terminal Deletion
          Length = 143

 Score = 31.2 bits (69), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 16/39 (41%), Positives = 26/39 (66%)

Query: 19 TTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQV 57
          +TNNVA+Y  LI  ++  L+ G  +  ++GDS+LV  Q+
Sbjct: 46 STNNVAEYSGLICLMETMLRLGISSPIIKGDSQLVIKQM 84


>pdb|3U3G|D Chain D, Structure Of Lc11-Rnase H1 Isolated From Compost By
           Metagenomic Approach: Insight Into The Structural Bases
           For Unusual Enzymatic Properties Of Sto-Rnase H1
 pdb|3U3G|B Chain B, Structure Of Lc11-Rnase H1 Isolated From Compost By
           Metagenomic Approach: Insight Into The Structural Bases
           For Unusual Enzymatic Properties Of Sto-Rnase H1
 pdb|3U3G|C Chain C, Structure Of Lc11-Rnase H1 Isolated From Compost By
           Metagenomic Approach: Insight Into The Structural Bases
           For Unusual Enzymatic Properties Of Sto-Rnase H1
 pdb|3U3G|A Chain A, Structure Of Lc11-Rnase H1 Isolated From Compost By
           Metagenomic Approach: Insight Into The Structural Bases
           For Unusual Enzymatic Properties Of Sto-Rnase H1
          Length = 140

 Score = 28.1 bits (61), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 26/75 (34%), Positives = 40/75 (53%), Gaps = 15/75 (20%)

Query: 16  VGITTNNVAKYGSLILGLKYALQKGFFNFRVRGDSKLVHMQVCC----WLMEDQTPGMAE 71
           +G TTNNVA+Y +LI  L+        + ++ GD KLV M+V       L+  Q  G+ +
Sbjct: 40  IGETTNNVAEYEALIRALE--------DLQMFGD-KLVDMEVEVRMDSELIVRQMQGVYK 90

Query: 72  LCGEAKRLKDKFLSI 86
           +  +   LK+KF  I
Sbjct: 91  V--KEPTLKEKFAKI 103


  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
   0.324    0.140    0.433 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,627,518
Number of Sequences: 62578
Number of extensions: 89050
Number of successful extensions: 186
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 174
Number of HSP's gapped (non-prelim): 16
length of query: 86
length of database: 14,973,337
effective HSP length: 54
effective length of query: 32
effective length of database: 11,594,125
effective search space: 371012000
effective search space used: 371012000
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 45 (21.9 bits)