RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy5071
         (366 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 = 43.4 bits (101), Expect = 5e-06
 Identities = 24/124 (19%), Positives = 44/124 (35%), Gaps = 8/124 (6%)

Query: 104 DSVLCFTDGSKTVNST--SCAYSIGNQVHAFKLNKVNSVLSSELMAILLCVKNLIFLPST 161
            +   +TDGS    S      Y         K  +  +   +EL A  + + +       
Sbjct: 6   GAETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEAFAMALTD----SGP 61

Query: 162 NFTLISDSMSALLAISNCKNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVD 221
              +I DS   +  +++   +    S +    +E     + +   W P+H GI GN+ VD
Sbjct: 62  KVNIIVDSQYVMGIVASQPTESE--SKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVD 119

Query: 222 IAAR 225
               
Sbjct: 120 HLVS 123


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

 Score = 36.1 bits (82), Expect = 0.002
 Identities = 25/138 (18%), Positives = 38/138 (27%), Gaps = 19/138 (13%)

Query: 106 VLCFTDGSKTVNSTSCAYSI-----GNQVHAFKLNKVNSVLSSELMAILLCVKNLIFLPS 160
           V  FTDG+   N     ++       ++          +    EL A +  +K       
Sbjct: 4   VALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLK--ALKEP 61

Query: 161 TNFTLISDSMSALLAISNCKNDHPLVSLVYT----------TWLEAKDCGKN--LNFVWC 208
               L +DS     A +    +        T           W           + F + 
Sbjct: 62  CEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFV 121

Query: 209 PSHCGITGNELVDIAARN 226
             H G   NE VD  AR 
Sbjct: 122 KGHTGHPENERVDREARR 139


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

 Score = 32.3 bits (72), Expect = 0.043
 Identities = 14/57 (24%), Positives = 23/57 (40%)

Query: 179 CKNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSHCGITGNELVDIAARNPITNITLKN 235
             +  P+ ++     L+A      + + W   H G   NE  D  AR    N TL++
Sbjct: 90  TADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERADELARAAAMNPTLED 146


>d1dvoa_ a.136.1.1 (A:) Repressor of bacterial conjugation FinO
          {Escherichia coli [TaxId: 562]}
          Length = 152

 Score = 27.5 bits (61), Expect = 1.8
 Identities = 4/22 (18%), Positives = 9/22 (40%), Gaps = 1/22 (4%)

Query: 29 FPPNKPKPLCVRI-KDMSDFLP 49
          F  + P+ L   I   + + + 
Sbjct: 56 FDGDTPRLLACGIRDVLLEDVA 77


>d1bhea_ b.80.1.3 (A:) Polygalacturonase {Erwinia carotovora, subsp.
           carotovora [TaxId: 554]}
          Length = 376

 Score = 26.3 bits (57), Expect = 5.9
 Identities = 22/141 (15%), Positives = 42/141 (29%), Gaps = 9/141 (6%)

Query: 137 VNSVLSSELMAILLCVKNLIFLPSTNFTLISDSMSALLAISNCKNDHPLVSLVYTTWLEA 196
           V         A    +K      +T+      S +  +A SN       V++        
Sbjct: 177 VVFSDGDGFTAWKTTIKTPSTARNTDGIDPMSSKNITIAYSNIATGDDNVAIKAYKGRAE 236

Query: 197 KDCGKNLNFVWCPSHCGITGNELVDIAARNPITNITLKNCTSFDFRPVISSIIHKQWQIS 256
                 L+  +   H    G+E         + N+T+ +         +     K     
Sbjct: 237 TRNISILHNDFGTGHGMSIGSE------TMGVYNVTVDDLKMNGTTNGLRIKSDKSAAGV 290

Query: 257 WDNVI--NNKLKRVK-PLIVD 274
            + V   N  +K V  P+++D
Sbjct: 291 VNGVRYSNVVMKNVAKPIVID 311


>d1w77a1 c.68.1.13 (A:75-300)
           4-diphosphocytidyl-2C-methyl-D-erythritol (CDP-me)
           synthase (IspD, YgbP) {Thale cress (Arabidopsis
           thaliana), chloroplast [TaxId: 3702]}
          Length = 226

 Score = 25.8 bits (55), Expect = 7.4
 Identities = 11/161 (6%), Positives = 39/161 (24%), Gaps = 5/161 (3%)

Query: 157 FLPSTNFTLISDSMSALLAISN-----CKNDHPLVSLVYTTWLEAKDCGKNLNFVWCPSH 211
           ++P     +   S      +          D     +            +          
Sbjct: 26  YIPLLGQPIALYSFFTFSRMPEVKEIVVVCDPFFRDIFEEYEESIDVDLRFAIPGKERQD 85

Query: 212 CGITGNELVDIAARNPITNITLKNCTSFDFRPVISSIIHKQWQISWDNVINNKLKRVKPL 271
              +G + +D+ +     + + +   + +    +                   +K V   
Sbjct: 86  SVYSGLQEIDVNSELVCIHDSARPLVNTEDVEKVLKDGSAVGAAVLGVPAKATIKEVNSD 145

Query: 272 IVDWETSNRNSRYEEVVITRLRIGHTRVTHDHLFKRDPRPT 312
            +  +T +R + +E      ++    +   + +       T
Sbjct: 146 SLVVKTLDRKTLWEMQTPQVIKPELLKKGFELVKSEGLEVT 186


  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
   0.322    0.136    0.432 

Gapped
Lambda     K      H
   0.267   0.0412    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 1,405,404
Number of extensions: 65251
Number of successful extensions: 145
Number of sequences better than 10.0: 1
Number of HSP's gapped: 144
Number of HSP's successfully gapped: 10
Length of query: 366
Length of database: 2,407,596
Length adjustment: 87
Effective length of query: 279
Effective length of database: 1,213,086
Effective search space: 338450994
Effective search space used: 338450994
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 (25.0 bits)