RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy16967
         (282 letters)



>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 = 48.8 bits (115), Expect = 4e-08
 Identities = 28/119 (23%), Positives = 49/119 (41%), Gaps = 8/119 (6%)

Query: 119 FTDGSKTENST--SCAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLV 176
           +TDGS    S      Y  ++  +  +     +   AEL A  + L +       K  ++
Sbjct: 11  YTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALTDSG----PKVNII 66

Query: 177 TDSMSSLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAK 235
            DS   +  + S+   +   SKI +  ++ +   + I   W P+H GI GN+ VD    
Sbjct: 67  VDSQYVMGIVASQPTESE--SKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVDHLVS 123


>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 = 43.0 bits (101), Expect = 3e-06
 Identities = 22/107 (20%), Positives = 43/107 (40%), Gaps = 12/107 (11%)

Query: 119 FTDGSKTENSTS--CAYTINKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLPSTKFLLV 176
           + DG+    +      Y  N+           +    EL AI L LQ+       +  +V
Sbjct: 12  YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSG----LEVNIV 67

Query: 177 TDSMSSLQAITS--KSCNNALLSKIYSTWLDLVACGKEISFMWCPSH 221
           TDS  +L  I +      + L+++I    ++ +   +++   W P+H
Sbjct: 68  TDSQYALGIIQAQPDQSESELVNQI----IEQLIKKEKVYLAWVPAH 110


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

 Score = 37.6 bits (86), Expect = 4e-04
 Identities = 29/139 (20%), Positives = 41/139 (29%), Gaps = 19/139 (13%)

Query: 115 RILCFTDGSKTENSTSCAYTI-----NKNVNSFRLNVVNSVFSAELMAILLCLQNLKYLP 169
           R+  FTDG+   N     +                    +    EL A +  L+ LK   
Sbjct: 3   RVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKE-- 60

Query: 170 STKFLLVTDSMSSLQAITSKSCNNAL----------LSKIYSTWLDLVACGKE--ISFMW 217
             +  L TDS    +A T                    K    W  L+       + F +
Sbjct: 61  PCEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHF 120

Query: 218 CPSHCGISGNEAVDVAAKN 236
              H G   NE VD  A+ 
Sbjct: 121 VKGHTGHPENERVDREARR 139


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

 Score = 31.9 bits (71), Expect = 0.043
 Identities = 13/40 (32%), Positives = 16/40 (40%), Gaps = 4/40 (10%)

Query: 203 WLDLVACGKEISFMWCPSHCGISGNEAVD----VAAKNPS 238
            LD      +I + W   H G   NE  D     AA NP+
Sbjct: 104 RLDAALGQHQIKWEWVKGHAGHPENERADELARAAAMNPT 143


>d1qk1a2 d.128.1.2 (A:103-379) Creatine kinase, C-terminal domain
           {Human (Homo sapiens), mitochondria [TaxId: 9606]}
          Length = 277

 Score = 25.6 bits (56), Expect = 6.9
 Identities = 18/99 (18%), Positives = 33/99 (33%), Gaps = 3/99 (3%)

Query: 70  DKHIPPWSSVVPSIDTSLHSGKKDNVSPSVF--QVQFLVNINTKYHDRILCFTDGSKTEN 127
           D H      V P +  +  +    +        +  FL+ +N + H R++    G   + 
Sbjct: 82  DDHFLFDKPVSPLLTAAGMARDWPDARGIWHNNEKSFLIWVNEEDHTRVISMEKGGNMKR 141

Query: 128 STSCAYTINKNV-NSFRLNVVNSVFSAELMAILLCLQNL 165
                    K V    +      +++  L  IL C  NL
Sbjct: 142 VFERFCRGLKEVERLIQERGWEFMWNERLGYILTCPSNL 180


  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
   0.318    0.131    0.403 

Gapped
Lambda     K      H
   0.267   0.0596    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 1,041,415
Number of extensions: 45932
Number of successful extensions: 101
Number of sequences better than 10.0: 1
Number of HSP's gapped: 101
Number of HSP's successfully gapped: 8
Length of query: 282
Length of database: 2,407,596
Length adjustment: 84
Effective length of query: 198
Effective length of database: 1,254,276
Effective search space: 248346648
Effective search space used: 248346648
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 (21.8 bits)
S2: 52 (24.1 bits)