RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy15450
         (659 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 = 46.8 bits (110), Expect = 6e-07
 Identities = 20/92 (21%), Positives = 31/92 (33%), Gaps = 10/92 (10%)

Query: 291 TIFTAEAFAILQALKYVSSIKENEVIIITDSKSCLEKLKNTSKSNGNPSHLILDIFKALS 350
           T   AE  A   AL            II DS+  +  + +    + +           + 
Sbjct: 43  TNQQAELEAFAMALTDSGPKV----NIIVDSQYVMGIVASQPTESESKIV------NQII 92

Query: 351 HLQEWNISVRFIWVRGHAGIAGNEAVDRLAKE 382
                  ++   WV  H GI GN+ VD L  +
Sbjct: 93  EEMIKKEAIYVAWVPAHKGIGGNQEVDHLVSQ 124


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

 Score = 42.3 bits (98), Expect = 3e-05
 Identities = 19/90 (21%), Positives = 37/90 (41%), Gaps = 1/90 (1%)

Query: 297 AFAILQALKYVSSIKENEVIIITDSKSCLEKLKNTSKSNGNPSHLILDIFKALSHLQEWN 356
           A   L+    V    +++ +    ++      K   K+        +D+++ L      +
Sbjct: 53  ALEALKEHAEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQH 112

Query: 357 ISVRFIWVRGHAGIAGNEAVDRLAKETARG 386
             +++ WV+GHAG   NE  D LA+  A  
Sbjct: 113 Q-IKWEWVKGHAGHPENERADELARAAAMN 141


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

 Score = 41.9 bits (97), Expect = 4e-05
 Identities = 15/36 (41%), Positives = 19/36 (52%)

Query: 351 HLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARG 386
            L      VRF +V+GH G   NE VDR A+  A+ 
Sbjct: 108 LLAMAPHRVRFHFVKGHTGHPENERVDREARRQAQS 143


>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 = 39.6 bits (92), Expect = 1e-04
 Identities = 21/79 (26%), Positives = 33/79 (41%), Gaps = 10/79 (12%)

Query: 289 FATIFTAEAFAILQALKYVSSIKENEVIIITDSKSCLEKLKNTSKSNGNPSHLILDIFKA 348
             T    E  AI  AL+        EV I+TDS+  L  +   ++ + + S L+  I + 
Sbjct: 42  DTTNQKTELQAIYLALQDSGL----EVNIVTDSQYALGII--QAQPDQSESELVNQIIEQ 95

Query: 349 LSHLQEWNISVRFIWVRGH 367
           L   ++    V   WV  H
Sbjct: 96  LIKKEK----VYLAWVPAH 110



 Score = 31.1 bits (70), Expect = 0.12
 Identities = 14/75 (18%), Positives = 22/75 (29%), Gaps = 9/75 (12%)

Query: 194 KDKWPNAYLIFTDGSKTSESVASAFYDTQNKNSGTFKLQNFATIFTAEAFAILQALKYAS 253
           K+    A   + DG+   E+         N+           T    E  AI  AL    
Sbjct: 2   KEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLAL---- 57

Query: 254 SIKEKEAGYCKVSIR 268
                +    +V+I 
Sbjct: 58  -----QDSGLEVNIV 67


>d1nmla1 a.3.1.5 (A:1-166) Di-heme cytochrome c peroxidase
           {Pseudomonas nautica [TaxId: 2743]}
          Length = 166

 Score = 28.2 bits (62), Expect = 2.2
 Identities = 16/111 (14%), Positives = 29/111 (26%), Gaps = 12/111 (10%)

Query: 348 ALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETARGTDALNPYPIPVQ--DVRAVTD 405
              H              GH    G      +           N      Q  D RA   
Sbjct: 52  NTCHNVGLGGDDELPTSIGHGWQKGPRNSPTVF----------NAVFNAAQFWDGRAADL 101

Query: 406 MQHEIQWRENVMSQNNNKGLFYKNLFTITDKKPWFAKAIPLRKFIVTFNRL 456
            +      +  +  ++        L ++ +    F  A P ++  VTF+ +
Sbjct: 102 AEQAKGPVQAGVEMSSTPDRVVATLKSMPEYIERFEDAFPGQENPVTFDNM 152


>d3c7ba1 d.58.1.5 (A:239-304) DsrA insert domain {Archaeoglobus
           fulgidus [TaxId: 2234]}
          Length = 66

 Score = 26.1 bits (58), Expect = 2.8
 Identities = 12/57 (21%), Positives = 24/57 (42%), Gaps = 6/57 (10%)

Query: 70  DKI-ITEDCKKKYKNLSVAWIDLLKA-YDNCPHEWMVKVIQMYKIDLKSATFCVFCV 124
           D I + ++  K+Y     +W+D+       CP   +    +   ID +    C+ C+
Sbjct: 2   DDIKVDQEAVKEY----ASWMDIENEVVKLCPTGAIKWDGKELTIDNRECVRCMHCI 54


>d1ry2a_ e.23.1.1 (A:) Acetyl-CoA synthetase {Baker's yeast
           (Saccharomyces cerevisiae) [TaxId: 4932]}
          Length = 640

 Score = 27.5 bits (60), Expect = 7.1
 Identities = 8/62 (12%), Positives = 18/62 (29%)

Query: 147 MSGDCPRDKRGIPPDPGKGSGNATQDDGDQYESAPEYAKQNCFLNEVKDKWPNAYLIFTD 206
              + P  +  +          A     D   +  +   +  +     D     +L++T 
Sbjct: 189 ALRETPGVRHVLVYRKTNNPSVAFHAPRDLDWATEKKKYKTYYPCTPVDSEDPLFLLYTS 248

Query: 207 GS 208
           GS
Sbjct: 249 GS 250


  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    0.416 

Gapped
Lambda     K      H
   0.267   0.0742    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 2,477,320
Number of extensions: 118285
Number of successful extensions: 247
Number of sequences better than 10.0: 1
Number of HSP's gapped: 246
Number of HSP's successfully gapped: 13
Length of query: 659
Length of database: 2,407,596
Length adjustment: 91
Effective length of query: 568
Effective length of database: 1,158,166
Effective search space: 657838288
Effective search space used: 657838288
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: 56 (25.3 bits)