RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy8376
         (328 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 = 49.9 bits (118), Expect = 2e-08
 Identities = 29/127 (22%), Positives = 49/127 (38%), Gaps = 13/127 (10%)

Query: 62  YTDGS-KTNTFTGGA-YLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFK 119
           YTDGS    +  G A Y+ +   ++ +  +  +   AEL A           +       
Sbjct: 11  YTDGSCNRQSKEGKAGYVTDRGKDKVKKLEQTTNQQAELEA---------FAMALTDSGP 61

Query: 120 DFVICSDSKSSLQALKFNLNDSILISKILLKIKEISSFGSQVSFLWIPSHVGIRENEMVD 179
              I  DS+  +  +     +S   SKI+ +I E       +   W+P+H GI  N+ VD
Sbjct: 62  KVNIIVDSQYVMGIVASQPTESE--SKIVNQIIEEMIKKEAIYVAWVPAHKGIGGNQEVD 119

Query: 180 RAARNAV 186
                 +
Sbjct: 120 HLVSQGI 126


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

 Score = 44.9 bits (105), Expect = 2e-06
 Identities = 26/144 (18%), Positives = 52/144 (36%), Gaps = 10/144 (6%)

Query: 56  KDKILCYTDGS-KTNTFTGG-AYLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQ 113
           + ++  +TDG+   N   GG A LL     +  L+   +  T   M +   +  +    +
Sbjct: 1   RKRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKE 60

Query: 114 NNF--CFKDFVICSDSKSSLQALKFNLNDSILISKILLKIKEI------SSFGSQVSFLW 165
                 + D      + +      +            +K +++      +    +V F +
Sbjct: 61  PCEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHF 120

Query: 166 IPSHVGIRENEMVDRAARNAVNAR 189
           +  H G  ENE VDR AR    ++
Sbjct: 121 VKGHTGHPENERVDREARRQAQSQ 144


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

 Score = 37.3 bits (85), Expect = 6e-04
 Identities = 25/138 (18%), Positives = 39/138 (28%), Gaps = 9/138 (6%)

Query: 58  KILCYTDGS-KTNTFTGG--AYLL--NETVEQFQLNQIASIYTAELMAID--LCLNSILM 110
           ++  +T GS   N   GG  A L                +    ELMA    L       
Sbjct: 2   QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHA 61

Query: 111 YIQNNFCFKDFVICSDSKSSLQALKFNLNDSILISKILLKIKEIS--SFGSQVSFLWIPS 168
            +  +   +               +          K +   + +       Q+ + W+  
Sbjct: 62  EVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKG 121

Query: 169 HVGIRENEMVDRAARNAV 186
           H G  ENE  D  AR A 
Sbjct: 122 HAGHPENERADELARAAA 139


>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 = 34.2 bits (78), Expect = 0.005
 Identities = 26/110 (23%), Positives = 45/110 (40%), Gaps = 13/110 (11%)

Query: 62  YTDGS-KTNTFTGGA-YLLNETVEQFQLNQIASIYTAELMAIDLCLNSILMYIQNNFCFK 119
           Y DG+    T  G A Y+ N   ++       +    EL AI L L              
Sbjct: 12  YVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLALQD---------SGL 62

Query: 120 DFVICSDSKSSLQALKFNLNDSILISKILLKIKEISSFGSQVSFLWIPSH 169
           +  I +DS+ +L  ++   + S   S+++ +I E      +V   W+P+H
Sbjct: 63  EVNIVTDSQYALGIIQAQPDQSE--SELVNQIIEQLIKKEKVYLAWVPAH 110


>d1wb9a4 d.75.2.1 (A:2-116) DNA repair protein MutS, domain I
          {Escherichia coli [TaxId: 562]}
          Length = 115

 Score = 26.0 bits (57), Expect = 2.9
 Identities = 8/39 (20%), Positives = 18/39 (46%)

Query: 33 SSKKDEELPSEINNKYLEFKKDNKDKILCYTDGSKTNTF 71
          S+ ++ +  + +  +YL  K  + + +L Y  G     F
Sbjct: 1  SAIENFDAHTPMMQQYLRLKAQHPEILLFYRMGDFYTLF 39


>d1d6za1 b.30.2.1 (A:301-724) Copper amine oxidase, domain 3
           {Escherichia coli [TaxId: 562]}
          Length = 424

 Score = 26.1 bits (57), Expect = 6.4
 Identities = 3/20 (15%), Positives = 10/20 (50%)

Query: 230 TDVRKWKSSNRNIRQEEVVL 249
           T + ++   N ++   + V+
Sbjct: 362 TGLGQYSKDNESLDNTDAVV 381


>d1w2za1 b.30.2.1 (A:207-647) Copper amine oxidase, domain 3 {Pea
           seedling (Pisum sativum) [TaxId: 3888]}
          Length = 441

 Score = 26.1 bits (57), Expect = 6.4
 Identities = 5/18 (27%), Positives = 10/18 (55%)

Query: 232 VRKWKSSNRNIRQEEVVL 249
           +  W   NR I  +++V+
Sbjct: 372 LAVWTKQNREIVNKDIVM 389


  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    0.135    0.409 

Gapped
Lambda     K      H
   0.267   0.0577    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 1,201,819
Number of extensions: 54570
Number of successful extensions: 134
Number of sequences better than 10.0: 1
Number of HSP's gapped: 133
Number of HSP's successfully gapped: 14
Length of query: 328
Length of database: 2,407,596
Length adjustment: 86
Effective length of query: 242
Effective length of database: 1,226,816
Effective search space: 296889472
Effective search space used: 296889472
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)