RPS-BLAST 2.2.26 [Sep-21-2011]

Database: pdb70 
           27,921 sequences; 6,701,793 total letters

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

Query= psy11389
         (73 letters)



>2kq2_A Ribonuclease H-related protein; PSI, NESG, protein structure, APO
           enzyme, structural genomics, protein structure
           initiative; NMR {Desulfitobacterium hafniense dcb-2}
           PDB: 2kw4_A
          Length = 147

 Score = 25.8 bits (57), Expect = 0.97
 Identities = 6/15 (40%), Positives = 10/15 (66%)

Query: 20  HCGIKGNEIVDVAAR 34
           H G + N+ VD+ A+
Sbjct: 118 HSGNEFNDYVDMKAK 132


>1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus
           thermophilus} SCOP: c.55.3.1 PDB: 2rpi_A
          Length = 166

 Score = 26.0 bits (58), Expect = 0.98
 Identities = 11/34 (32%), Positives = 12/34 (35%)

Query: 20  HCGIKGNEIVDVAARNPTNATPLNLCTPEDFKPF 53
           H G   NE VD  AR    +     C P     F
Sbjct: 129 HTGHPENERVDREARRQAQSQAKTPCPPRAPTLF 162


>1rrv_A Glycosyltransferase GTFD; GT-B, glycosyltransferase, rossmann
          fold, glycopeptide, VACO antibiotic,
          transferase-antibiotic complex; HET: OMZ GHP OMY 3FG
          TYD BGC; 2.00A {Amycolatopsis orientalis} SCOP:
          c.87.1.5
          Length = 416

 Score = 26.0 bits (57), Expect = 1.0
 Identities = 3/13 (23%), Positives = 6/13 (46%)

Query: 44 LCTPEDFKPFVAS 56
          +C P   +  +A 
Sbjct: 33 MCAPPAAEERLAE 45


>3qio_A GAG-POL polyprotein; RNAse H, inhibitor, nuclease, transferase,
           hydrolase- complex; HET: QID; 1.40A {Hiv-1 M} PDB:
           3qin_A* 3hyf_A* 1o1w_A 3lp3_A* 1hrh_A 3k2p_A* 1rdh_A
          Length = 150

 Score = 25.6 bits (57), Expect = 1.1
 Identities = 8/16 (50%), Positives = 8/16 (50%)

Query: 20  HCGIKGNEIVDVAARN 35
           H GI GNE VD     
Sbjct: 128 HKGIGGNEQVDKLVSA 143


>2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo
           sapiens} PDB: 2qk9_A 2qkk_A*
          Length = 154

 Score = 25.2 bits (56), Expect = 1.6
 Identities = 8/16 (50%), Positives = 8/16 (50%)

Query: 20  HCGIKGNEIVDVAARN 35
           H G  GNE  D  AR 
Sbjct: 132 HSGFIGNEEADRLARE 147


>1iir_A Glycosyltransferase GTFB; rossmann fold; 1.80A {Amycolatopsis
          orientalis} SCOP: c.87.1.5
          Length = 415

 Score = 25.2 bits (55), Expect = 1.9
 Identities = 4/13 (30%), Positives = 6/13 (46%)

Query: 44 LCTPEDFKPFVAS 56
          +C P D    +A 
Sbjct: 33 MCAPPDCAERLAE 45


>2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A
           {Shewanella oneidensis} PDB: 2zqb_A
          Length = 158

 Score = 24.0 bits (53), Expect = 4.1
 Identities = 9/23 (39%), Positives = 9/23 (39%)

Query: 20  HCGIKGNEIVDVAARNPTNATPL 42
           H G   NE  D  AR    A P 
Sbjct: 126 HAGHAENERCDQLARAAAEANPT 148


>1lvm_A Catalytic domain of the nuclear inclusion protein A (NIA); beta
           barrel, chymotrypsin-type cystein protease, enzyme-
           peptide complex; 1.80A {Tobacco etch virus} SCOP:
           b.47.1.3 PDB: 1lvb_A 1q31_A
          Length = 229

 Score = 23.7 bits (51), Expect = 7.2
 Identities = 5/20 (25%), Positives = 10/20 (50%)

Query: 47  PEDFKPFVASLMNSEWQSQW 66
           P++F   + +    +W S W
Sbjct: 191 PKNFMELLTNQEAQQWVSGW 210


>1jl1_A Ribonuclease HI; RNAse HI, protein stability, thermostability,
           hydrogen exchange, cooperativity, hydrolase; 1.30A
           {Escherichia coli} SCOP: c.55.3.1 PDB: 1f21_A 1jxb_A
           1g15_A 1rch_A 1rdd_A 1rnh_A* 2rn2_A 1rda_A 1law_A 1rdb_A
           1lav_A 3aa4_A 1rbu_A 1gob_A 1rdc_A 1kvc_A 3aa3_A 3aa2_A
           3aa5_X 1rbv_A ...
          Length = 155

 Score = 23.2 bits (51), Expect = 9.8
 Identities = 7/16 (43%), Positives = 7/16 (43%)

Query: 20  HCGIKGNEIVDVAARN 35
           H G   NE  D  AR 
Sbjct: 124 HAGHPENERADELARA 139


  Database: pdb70
    Posted date:  Sep 4, 2012  3:40 AM
  Number of letters in database: 6,701,793
  Number of sequences in database:  27,921
  
Lambda     K      H
   0.317    0.133    0.432 

Gapped
Lambda     K      H
   0.267   0.0802    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,145,761
Number of extensions: 50707
Number of successful extensions: 120
Number of sequences better than 10.0: 1
Number of HSP's gapped: 120
Number of HSP's successfully gapped: 10
Length of query: 73
Length of database: 6,701,793
Length adjustment: 43
Effective length of query: 30
Effective length of database: 5,501,190
Effective search space: 165035700
Effective search space used: 165035700
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (23.3 bits)