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= psy15595
         (221 letters)

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

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



>pdb|2QK9|A Chain A, Human Rnase H Catalytic Domain Mutant D210n In Complex
           With 18-Mer RnaDNA HYBRID
 pdb|2QKK|A Chain A, Human Rnase H Catalytic Domain Mutant D210n In Complex
           With 14-Mer RnaDNA HYBRID
 pdb|2QKK|B Chain B, Human Rnase H Catalytic Domain Mutant D210n In Complex
           With 14-Mer RnaDNA HYBRID
 pdb|2QKK|E Chain E, Human Rnase H Catalytic Domain Mutant D210n In Complex
           With 14-Mer RnaDNA HYBRID
 pdb|2QKK|F Chain F, Human Rnase H Catalytic Domain Mutant D210n In Complex
           With 14-Mer RnaDNA HYBRID
 pdb|2QKK|I Chain I, Human Rnase H Catalytic Domain Mutant D210n In Complex
           With 14-Mer RnaDNA HYBRID
 pdb|2QKK|J Chain J, Human Rnase H Catalytic Domain Mutant D210n In Complex
           With 14-Mer RnaDNA HYBRID
 pdb|2QKK|M Chain M, Human Rnase H Catalytic Domain Mutant D210n In Complex
           With 14-Mer RnaDNA HYBRID
 pdb|2QKK|N Chain N, Human Rnase H Catalytic Domain Mutant D210n In Complex
           With 14-Mer RnaDNA HYBRID
 pdb|2QKK|R Chain R, Human Rnase H Catalytic Domain Mutant D210n In Complex
           With 14-Mer RnaDNA HYBRID
 pdb|2QKK|S Chain S, Human Rnase H Catalytic Domain Mutant D210n In Complex
           With 14-Mer RnaDNA HYBRID
 pdb|2QKK|W Chain W, Human Rnase H Catalytic Domain Mutant D210n In Complex
           With 14-Mer RnaDNA HYBRID
          Length = 154

 Score = 30.0 bits (66), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 23/85 (27%), Positives = 39/85 (45%), Gaps = 6/85 (7%)

Query: 95  GDFVQVYTDGSKSDSS-----VGCAFVIPQLHIVKKQTLNP-KSSIFHAELLAISDAVST 148
           GDFV VYTDG  S +       G        H +      P + +   AE+ A   A+  
Sbjct: 5   GDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQ 64

Query: 149 IKSQSIGEAVIISDSLSALQAISSM 173
            K+Q+I + V+ ++S+  +  I++ 
Sbjct: 65  AKTQNINKLVLYTNSMFTINGITNW 89


>pdb|3MIS|A Chain A, I-Msoi Re-Designed For Altered Dna Cleavage Specificity
           (-8g)
 pdb|3MIS|B Chain B, I-Msoi Re-Designed For Altered Dna Cleavage Specificity
           (-8g)
          Length = 161

 Score = 29.3 bits (64), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 21/79 (26%), Positives = 40/79 (50%), Gaps = 4/79 (5%)

Query: 53  EPKESWLHKKPSCNLSLT-LYKKDGMPH--QVFQQEFQR-NMNENYGDFVQVYTDGSKSD 108
           EP+  +   K    L+++ + +KD  P+   ++ Q  +R N+ ++ GD +  YT    + 
Sbjct: 25  EPRPDYKDIKYQVRLAISFIQRKDKFPYLQDIYDQLGKRGNLRKDRGDGIADYTIYGSTH 84

Query: 109 SSVGCAFVIPQLHIVKKQT 127
            S+    ++P L I KKQ 
Sbjct: 85  LSIILPDLVPYLRIKKKQA 103


>pdb|2QKB|A Chain A, Human Rnase H Catalytic Domain Mutant D210n In Complex
           With 20-Mer RnaDNA HYBRID
 pdb|2QKB|B Chain B, Human Rnase H Catalytic Domain Mutant D210n In Complex
           With 20-Mer RnaDNA HYBRID
          Length = 154

 Score = 28.5 bits (62), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 23/85 (27%), Positives = 38/85 (44%), Gaps = 6/85 (7%)

Query: 95  GDFVQVYTDGSKSDSS-----VGCAFVIPQLHIVKKQTLNP-KSSIFHAELLAISDAVST 148
           GDFV VYTDG  S +       G        H +      P + +   AE+ A   A+  
Sbjct: 5   GDFVVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQ 64

Query: 149 IKSQSIGEAVIISDSLSALQAISSM 173
            K+Q+I + V+ ++S   +  I++ 
Sbjct: 65  AKTQNINKLVLYTNSXFTINGITNW 89


>pdb|3B43|A Chain A, I-band Fragment I65-i70 From Titin
          Length = 570

 Score = 28.1 bits (61), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 18/50 (36%), Positives = 24/50 (48%)

Query: 165 SALQAISSMSHSNPLVQSIHEEISTGDLKNVSLNLHEVERNRIICHIFGS 214
           SA   + + S S  L  S HE     DLK VS++L   E     CH+ G+
Sbjct: 175 SASNPLGTASSSAKLTLSEHEVPPFFDLKPVSVDLALGESGTFKCHVTGT 224


  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
   0.317    0.131    0.380 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,373,267
Number of Sequences: 62578
Number of extensions: 233413
Number of successful extensions: 630
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 627
Number of HSP's gapped (non-prelim): 4
length of query: 221
length of database: 14,973,337
effective HSP length: 95
effective length of query: 126
effective length of database: 9,028,427
effective search space: 1137581802
effective search space used: 1137581802
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)