RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy5480
         (446 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 = 46.1 bits (108), Expect = 7e-07
 Identities = 27/122 (22%), Positives = 47/122 (38%), Gaps = 13/122 (10%)

Query: 155 FTDGSKTANNT--SCAYIIDKTLISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKFVV 212
           +TDGS    +      Y+ D+       L    +   +EL A  + L         K  +
Sbjct: 11  YTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQT-TNQQAELEAFAMALTD----SGPKVNI 65

Query: 213 ISDSKSTLLALSN--PSNTNPIVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRA 270
           I DS+  +  +++    + + IV+ I           + +   W P+H GI GN+ VD  
Sbjct: 66  IVDSQYVMGIVASQPTESESKIVNQIIEEM----IKKEAIYVAWVPAHKGIGGNQEVDHL 121

Query: 271 AR 272
             
Sbjct: 122 VS 123


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

 Score = 38.0 bits (87), Expect = 6e-04
 Identities = 28/135 (20%), Positives = 42/135 (31%), Gaps = 18/135 (13%)

Query: 155 FTDGSKTANNTSCAY----IIDKTLISSFVLNNVNSVYTSELIAVLLCLKHLKFLPKEKF 210
           FTDG+   N     +                    +    EL A +  LK LK     + 
Sbjct: 7   FTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKE--PCEV 64

Query: 211 VVISDSKSTLLALSNP------------SNTNPIVSLIHSCWTDLLCYGKQLAFLWCPSH 258
            + +DS     A +              +   P+ +        L     ++ F +   H
Sbjct: 65  DLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFVKGH 124

Query: 259 TGIQGNEAVDRAARN 273
           TG   NE VDR AR 
Sbjct: 125 TGHPENERVDREARR 139


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

 Score = 36.1 bits (82), Expect = 0.003
 Identities = 14/57 (24%), Positives = 23/57 (40%), Gaps = 1/57 (1%)

Query: 226 PSNTNPIVSLIHSCWTDLLCYGKQLAFLWCPSHTGIQGNEAVDRAARNPSASLPPLK 282
            ++  P+ ++      D      Q+ + W   H G   NE  D  AR  +A  P L+
Sbjct: 90  TADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERADELARA-AAMNPTLE 145


>d1whna_ d.50.1.1 (A:) tRNA-dihydrouridine synthase 2-like, Dus2l
           (2310016k04Rik) {Mouse (Mus musculus) [TaxId: 10090]}
          Length = 128

 Score = 30.1 bits (67), Expect = 0.19
 Identities = 7/61 (11%), Positives = 18/61 (29%)

Query: 118 VIDNALSFDKKENVSSVVFQQRFHELVQSKYQDFTLCFTDGSKTANNTSCAYIIDKTLIS 177
           +I  A+ FD++     +  +    E  + +     +  T              + +    
Sbjct: 10  IIKMAIRFDRRAYPPQITPKMCLLEWCRREKLPQPVYETVQRTIDRMFCSVVTVAEQKYQ 69

Query: 178 S 178
           S
Sbjct: 70  S 70


>d1epua_ e.25.1.1 (A:) Neuronal Sec1, NSec1 {Longfin inshore squid
           (Loligo pealei) [TaxId: 6621]}
          Length = 590

 Score = 27.4 bits (60), Expect = 4.8
 Identities = 25/145 (17%), Positives = 46/145 (31%), Gaps = 22/145 (15%)

Query: 128 KENVSSVVFQQRFHELVQSKYQDFTLCFTDGSKTANNTSCAYIIDKTLISSFVLNNVNSV 187
           +E+V  ++    F      +Y+   + FT+        +C   + K L  S     + ++
Sbjct: 77  EESVKCLM--ADFQNPDNPQYRGAHIFFTE--------ACPEELFKELCKSTTARFIKTL 126

Query: 188 YTSELIAVLLCLKHLKFLPKEKFVVISDSKSTLLALSNPSNTNPIVSLIHSCWTDLLCYG 247
              E+        ++ FLP E  +   DS  T     NPS     +     C   +    
Sbjct: 127 K--EI--------NIAFLPYESQIFSLDSPDTFQVYYNPSRAQGGIPNKERCAEQIATL- 175

Query: 248 KQLAFLWCPSHTGIQGNEAVDRAAR 272
                   PS       +     A+
Sbjct: 176 -CATLGEYPSVRYRSDFDENASFAQ 199


>d1ng7a_ a.178.1.1 (A:) Soluble domain of poliovirus core protein 3a
           {Poliovirus type 1, strain Mahoney [TaxId: 12080]}
          Length = 60

 Score = 24.4 bits (53), Expect = 6.2
 Identities = 8/24 (33%), Positives = 14/24 (58%), Gaps = 2/24 (8%)

Query: 418 PAPPALTDDVESVDS--MLKYLKK 439
           P P  + D +++VDS  +  Y +K
Sbjct: 17  PPPECINDLLQAVDSQEVRDYCEK 40


>d1u59a_ d.144.1.7 (A:) Tyrosine-protein kinase ZAP-70 {Human (Homo
           sapiens) [TaxId: 9606]}
          Length = 285

 Score = 26.6 bits (58), Expect = 6.5
 Identities = 20/92 (21%), Positives = 34/92 (36%), Gaps = 10/92 (10%)

Query: 237 HSCWTDLLCYGKQLAFLWC---PSHTGIQGNEAVDRAARNPSASLPPLKLCSPEDFKPFI 293
            S  +D+  YG  +          +  ++G E +    +      PP   C PE     +
Sbjct: 189 FSSRSDVWSYGVTMWEALSYGQKPYKKMKGPEVMAFIEQGKRMECPPE--CPPE-----L 241

Query: 294 CKLIKDLWQNSWSNIPNSEAVDRAARNPSASL 325
             L+ D W   W + P+   V++  R    SL
Sbjct: 242 YALMSDCWIYKWEDRPDFLTVEQRMRACYYSL 273


  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    0.418 

Gapped
Lambda     K      H
   0.267   0.0571    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 1,659,250
Number of extensions: 75895
Number of successful extensions: 147
Number of sequences better than 10.0: 1
Number of HSP's gapped: 147
Number of HSP's successfully gapped: 8
Length of query: 446
Length of database: 2,407,596
Length adjustment: 88
Effective length of query: 358
Effective length of database: 1,199,356
Effective search space: 429369448
Effective search space used: 429369448
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: 54 (24.9 bits)