RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy17738
         (316 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 = 35.3 bits (81), Expect = 0.002
 Identities = 18/80 (22%), Positives = 26/80 (32%), Gaps = 7/80 (8%)

Query: 203 IYTDGSKDEENAGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALEYLHHPNNNTVEN 262
            Y DG+ + E              +       ++    EL AIY AL+            
Sbjct: 11  FYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQDSGLE------- 63

Query: 263 YVIISDSQAALQAISNIYTI 282
             I++DSQ AL  I      
Sbjct: 64  VNIVTDSQYALGIIQAQPDQ 83


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

 Score = 30.0 bits (66), Expect = 0.20
 Identities = 17/64 (26%), Positives = 25/64 (39%), Gaps = 3/64 (4%)

Query: 200 HVRIYTDGS--KDEENAGCAFVIPDRNITKMFSL-DPKSSIFACELYAIYAALEYLHHPN 256
            V I+T GS   +    G   ++  R   K FS    +++    EL A   ALE L    
Sbjct: 2   QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHA 61

Query: 257 NNTV 260
              +
Sbjct: 62  EVIL 65


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

 Score = 29.9 bits (66), Expect = 0.21
 Identities = 17/89 (19%), Positives = 33/89 (37%), Gaps = 8/89 (8%)

Query: 200 HVRIYTDGSKDEE--NAGCAFVIPDRNITKMFS-LDPKSSIFACELYAIYAALEYLHHPN 256
            V ++TDG+        G A ++      K+ S  +  ++    EL A    L+ L  P 
Sbjct: 3   RVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKEPC 62

Query: 257 NNTVENYVIISDSQAALQAISNIYTIQNQ 285
                   + +DS    +A +  +    +
Sbjct: 63  EVD-----LYTDSHYLKKAFTEGWLEGWR 86


>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 = 26.4 bits (57), Expect = 2.9
 Identities = 21/77 (27%), Positives = 31/77 (40%), Gaps = 9/77 (11%)

Query: 203 IYTDGS-KDEENAGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALEYLHHPNNNTVE 261
            YTDGS   +   G A  + DR   K+  L  +++    EL A   AL            
Sbjct: 10  FYTDGSCNRQSKEGKAGYVTDRGKDKVKKL-EQTTNQQAELEAFAMALTDSGP------- 61

Query: 262 NYVIISDSQAALQAISN 278
              II DSQ  +  +++
Sbjct: 62  KVNIIVDSQYVMGIVAS 78


>d2c1wa1 d.294.1.1 (A:6-289) EndoU {African clawed frog (Xenopus
           laevis) [TaxId: 8355]}
          Length = 284

 Score = 26.0 bits (57), Expect = 5.5
 Identities = 9/43 (20%), Positives = 19/43 (44%), Gaps = 1/43 (2%)

Query: 177 TKKITSSPIIKSNFLAILQNYETHVRIYTDGSKDEENAGCAFV 219
            +K+ S     + F+++L NYE    +    + +E      F+
Sbjct: 60  EEKLKSRKTFAT-FISLLDNYEMDTGVAEVVTPEEIAENNNFL 101


>d1gx5a_ e.8.1.4 (A:) Viral RNA polymerase {Hepatitis C virus
           [TaxId: 11103]}
          Length = 530

 Score = 26.3 bits (58), Expect = 6.0
 Identities = 23/111 (20%), Positives = 36/111 (32%), Gaps = 27/111 (24%)

Query: 49  LNPDASENNLKILNPIQNQCLRLATGAFCTTPIQALHLETNEPPLEIRRKILTFNYAAKV 108
           + P A+E +   +N + N  LR     + TT   A           +R+K +TF+   ++
Sbjct: 11  ITPCAAEESKLPINALSNSLLRHHNMVYATTSRSA----------GLRQKKVTFD---RL 57

Query: 109 TSVPQHPCYKLLMFPKYVQNYKNKKINTINVFLEEKFPLFKKIHTLTHPPP 159
             +  H          Y    K  K     V    K  L          PP
Sbjct: 58  QVLDDH----------YRDVLKEMKAKASTV----KAKLLSVEEACKLTPP 94


  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
   0.321    0.135    0.405 

Gapped
Lambda     K      H
   0.267   0.0597    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 1,174,040
Number of extensions: 54621
Number of successful extensions: 113
Number of sequences better than 10.0: 1
Number of HSP's gapped: 113
Number of HSP's successfully gapped: 9
Length of query: 316
Length of database: 2,407,596
Length adjustment: 85
Effective length of query: 231
Effective length of database: 1,240,546
Effective search space: 286566126
Effective search space used: 286566126
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.5 bits)