RPS-BLAST 2.2.26 [Sep-21-2011]

Database: scop70_1_75 
           13,730 sequences; 2,407,596 total letters

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

Query= psy874
         (191 letters)



>d1s1ta1 c.55.3.1 (A:430-539) HIV RNase H (Domain of reverse
          transcriptase) {Human immunodeficiency virus type 1
          [TaxId: 11676]}
          Length = 110

 Score = 43.8 bits (103), Expect = 7e-07
 Identities = 16/60 (26%), Positives = 21/60 (35%), Gaps = 6/60 (10%)

Query: 7  VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
             + DGA  R  K+G  AGY    G               TN   E+Q    AL+ +  
Sbjct: 9  ETFYVDGAANRETKLGK-AGYVTNRGRQKV-----VTLTDTTNQKTELQAIYLALQDSGL 62


>d1zbfa1 c.55.3.1 (A:62-193) BH0863-like Ribonuclease H {Bacillus
          halodurans [TaxId: 86665]}
          Length = 132

 Score = 43.0 bits (101), Expect = 2e-06
 Identities = 13/72 (18%), Positives = 23/72 (31%), Gaps = 4/72 (5%)

Query: 9  VFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSAN 68
          +  D     N  +     Y     +   +    +     TNN  E    +H L+  K  N
Sbjct: 7  LSVDVGSQGNPGIV---EYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERN 63

Query: 69 EKVKLKRSYNDT 80
           +  +  S + T
Sbjct: 64 SRKPI-YSNSQT 74


>d1rila_ c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermophilus
          [TaxId: 274]}
          Length = 147

 Score = 43.4 bits (101), Expect = 2e-06
 Identities = 20/61 (32%), Positives = 25/61 (40%), Gaps = 3/61 (4%)

Query: 5  NHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQA 64
            V +FTDGAC  N   G  A    +      L+         TNN  E++ AI  LK  
Sbjct: 2  KRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGE---ACTTNNRMELKAAIEGLKAL 58

Query: 65 K 65
          K
Sbjct: 59 K 59


>d1mu2a1 c.55.3.1 (A:430-555) HIV RNase H (Domain of reverse
          transcriptase) {Human immunodeficiency virus type 2
          [TaxId: 11709]}
          Length = 126

 Score = 39.5 bits (91), Expect = 3e-05
 Identities = 18/63 (28%), Positives = 26/63 (41%), Gaps = 6/63 (9%)

Query: 7  VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
             +TDG+C R  K G  AGY    G++       K   + TN  AE++    AL  +  
Sbjct: 8  ETFYTDGSCNRQSKEGK-AGYVTDRGKDKV-----KKLEQTTNQQAELEAFAMALTDSGP 61

Query: 67 ANE 69
             
Sbjct: 62 KVN 64


>d1jl1a_ c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli
          [TaxId: 562]}
          Length = 152

 Score = 37.7 bits (86), Expect = 2e-04
 Identities = 17/55 (30%), Positives = 20/55 (36%), Gaps = 3/55 (5%)

Query: 6  HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHA 60
           V +FT G+   N   G   GYG                 R TNN  E+  AI A
Sbjct: 2  QVEIFTAGSALGNPGPG---GYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVA 53


  Database: scop70_1_75
    Posted date:  Mar 27, 2010  6:21 PM
  Number of letters in database: 2,407,596
  Number of sequences in database:  13,730
  
Lambda     K      H
   0.314    0.130    0.366 

Gapped
Lambda     K      H
   0.267   0.0601    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 675,300
Number of extensions: 28818
Number of successful extensions: 46
Number of sequences better than 10.0: 1
Number of HSP's gapped: 42
Number of HSP's successfully gapped: 5
Length of query: 191
Length of database: 2,407,596
Length adjustment: 80
Effective length of query: 111
Effective length of database: 1,309,196
Effective search space: 145320756
Effective search space used: 145320756
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 50 (23.3 bits)