RPS-BLAST 2.2.16 [Mar-25-2007]

Database: 40scop73nmM 
           9549 sequences; 1,678,726 total letters

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

Query= ACD31158.1 ftul2 rnd GIB00719CH01 "ribonuclease D"
         (364 letters)



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

1yt3A3 [c.55.3.5] RIBONUCLEASE D A:1 -- 193                           114   2e-28
2hbjA2 [c.55.3.5] EXOSOME COMPLEX EXONUCLEASE RRP6 A:129 -- 420        98   2e-23
1l3sA1 [c.55.3.5] DNA POLYMERASE I A:297 -- 468                        92   9e-22
1d8yA1 [c.55.3.5] DNA POLYMERASE I A:324 -- 518                        88   1e-20
1vk0A [c.55.3.5] HYPOTHETICAL PROTEIN                                  65   1e-13
1yt3A1 [a.60.8.3] RIBONUCLEASE D A:194 -- 294                          50   4e-09
1skrA1 [c.55.3.5] DNA POLYMERASE A:1 -- 210                            50   6e-09
2cprA1 [a.60.8.4] EXOSOME COMPONENT 10 A:483 -- 595                    48   1e-08
1yt3A2 [a.60.8.3] RIBONUCLEASE D A:295 -- 375                          48   1e-08
2e1eA1 [a.60.8.1] WERNER SYNDROME ATP-DEPENDENT HELICASE A:1142 ...    44   3e-07
2hbjA1 [a.60.8.4] EXOSOME COMPLEX EXONUCLEASE RRP6 A:421 -- 516        44   4e-07
1d8bA [a.60.8.1] SGS1 RECQ HELICASE                                    41   3e-06
1wudA1 [a.60.8.1] ATP-DEPENDENT DNA HELICASE RECQ A:530 -- 606         33   5e-04

>1yt3A3 [c.55.3.5] RIBONUCLEASE D A:1 -- 193
          Length = 193

 Score =  114 bits (285), Expect = 2e-28
 Identities = 54/179 (30%), Positives = 79/179 (44%)

Query: 2   IINTNKQLNNVIEILKNTSQIAVDTEFYWMRTYYPELCLVQLATENEIFLIDTLKDLEFK 61
           +I T+  L ++ E ++    IA+DTEF   RTYYP+L L+QL     + LID L   ++ 
Sbjct: 5   MITTDDALASLCEAVRAFPAIALDTEFVRTRTYYPQLGLIQLFDGEHLALIDPLGITDWS 64

Query: 62  KLKEIFEDKDILKIIHSATNDIPIIKRFFNCEVNNIFDTQLAATFLGFQTQSSXXXXXXX 121
            LK I  D  I K +H+ + D+ +    F      + DTQ+ A F G             
Sbjct: 65  PLKAILRDPSITKFLHAGSEDLEVFLNVFGELPQPLIDTQILAAFCGRPMSWGFASMVEE 124

Query: 122 XXXXXXXXXSQFSDWRNRPLTQNQLNYAIKDVEYLIQLKEYLQQQLAKSEYQDFFEQEL 180
                       +DW  RPLT+ Q  YA  DV YL+ +   L  +   S +      E 
Sbjct: 125 YSGVTLDKSESRTDWLARPLTERQCEYAAADVWYLLPITAKLMVETEASGWLPAALDEC 183


>2hbjA2 [c.55.3.5] EXOSOME COMPLEX EXONUCLEASE RRP6 A:129 -- 420
          Length = 292

 Score = 97.8 bits (242), Expect = 2e-23
 Identities = 57/186 (30%), Positives = 94/186 (50%), Gaps = 2/186 (1%)

Query: 1   MIINTNKQLNNVIEILKNTSQIAVDTEFYWMRTYYPELCLVQLATENEIFLIDTLK-DLE 59
           + ++T+ +L +++E LKNT +IAVD E +  R+YY  +CL+Q++T    +L+DTLK    
Sbjct: 86  IWVDTSTELESMLEDLKNTKEIAVDLEHHDYRSYYGIVCLMQISTRERDYLVDTLKLREN 145

Query: 60  FKKLKEIFEDKDILKIIHSATNDIPIIKRFFNCEVNNIFDTQLAATFLGFQTQSSXXXXX 119
              L E+F +  I+K+ H A  DI  ++R     V  +FDT  A+  +G   + S     
Sbjct: 146 LHILNEVFTNPSIVKVFHGAFMDIIWLQRDLGLYVVGLFDTYHASKAIGL-PRHSLAYLL 204

Query: 120 XXXXXXXXXXXSQFSDWRNRPLTQNQLNYAIKDVEYLIQLKEYLQQQLAKSEYQDFFEQE 179
                       Q +DWR RPL++     A  D  +L+ + + L+ +L +S        E
Sbjct: 205 ENFANFKTSKKYQLADWRIRPLSKPMTAAARADTHFLLNIYDQLRNKLIESNKLAGVLYE 264

Query: 180 LIEVQK 185
              V K
Sbjct: 265 SRNVAK 270


>1l3sA1 [c.55.3.5] DNA POLYMERASE I A:297 -- 468
          Length = 172

 Score = 92.2 bits (228), Expect = 9e-22
 Identities = 20/171 (11%), Positives = 43/171 (25%), Gaps = 5/171 (2%)

Query: 3   INTNKQLNNVIEILKNTSQIAVDTEFYWMRTYYPELCLVQLATENEIFLIDTLKDLEFKK 62
                  + V E +      A+  E      +   +  + +  E+  F +     L   +
Sbjct: 2   KMAFTLADRVTEEMLADK-AALVVEVVEENYHDAPIVGIAVVNEHGRFFLRPETALADPQ 60

Query: 63  LKEIFEDKDILKIIHSATNDIPIIKRFFNCEVNNIFDTQLAATFLGFQTQS----SXXXX 118
                 D+   K +  +      +K          FD  LAA  L          +    
Sbjct: 61  FVAWLGDETKKKSMFDSKRAAVALKWKGIELCGVSFDLLLAAYLLDPAQGVDDVAAAAKM 120

Query: 119 XXXXXXXXXXXXSQFSDWRNRPLTQNQLNYAIKDVEYLIQLKEYLQQQLAK 169
                             R  P       + ++    + +L+     +L +
Sbjct: 121 KQYEAVRPDEAVYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRR 171


>1d8yA1 [c.55.3.5] DNA POLYMERASE I A:324 -- 518
          Length = 195

 Score = 88.3 bits (218), Expect = 1e-20
 Identities = 33/187 (17%), Positives = 55/187 (29%), Gaps = 19/187 (10%)

Query: 2   IINTNKQLNNVIEILKNTSQIAVDTEFYWMRTYYPELCLVQLATENEIFLIDTL------ 55
            I   + L   I  L+     A  T    +      L  +  A E  +     +      
Sbjct: 9   TILDEETLKAWIAKLEKAPVFAFATATDSLDNISANLVGLSFAIEPGVAAYIPVAHDYLD 68

Query: 56  ------KDLEFKKLKEIFEDKDILKIIHSATNDIPIIKRFFNCEVNNIFDTQLAATFLGF 109
                 ++   + LK + ED+  LK+  +   D  I+  +        FDT L +  L  
Sbjct: 69  APDQISRERALELLKPLLEDEKALKVGQNLKYDRGILANYGIELRGIAFDTMLESYILNS 128

Query: 110 QTQS-SXXXXXXXXXXXXXXXXSQFSDWRNRPLTQNQ------LNYAIKDVEYLIQLKEY 162
                                  + +      LT NQ        YA +D +  +QL   
Sbjct: 129 VAGRHDMDSLAERWLKHKTITFEEIAGKGKNQLTFNQIALEEAGRYAAEDADVTLQLHLK 188

Query: 163 LQQQLAK 169
           +   L K
Sbjct: 189 MWPDLQK 195


>1vk0A [c.55.3.5] HYPOTHETICAL PROTEIN
          Length = 200

 Score = 65.0 bits (157), Expect = 1e-13
 Identities = 22/170 (12%), Positives = 48/170 (28%), Gaps = 9/170 (5%)

Query: 6   NKQLNNVIEI--LKNTSQIAVDTEFY--WMRTYYPELCLVQLATENEIFLIDTLKDLE-- 59
           +  L+ + E   L     +  D  +   + +T    L  V+L+T N    +   K     
Sbjct: 31  SPYLSLIREDSILNGNRAVIFDVYWDVGFTKTSGWSLSSVKLSTRNLCLFLRLPKPFHDN 90

Query: 60  FKKLKEIFEDKDILKIIHSATNDIPIIKRFFNCEVNNIFDTQLAATFL---GFQTQSSXX 116
            K L   F  K +  +      D+ +++      + N  +    A               
Sbjct: 91  LKDLYRFFASKFVTFVGVQIEEDLDLLRENHGLVIRNAINVGKLAAEARGTLVLEFLGTR 150

Query: 117 XXXXXXXXXXXXXXSQFSDWRNRPLTQNQLNYAIKDVEYLIQLKEYLQQQ 166
                                 +   + QL  A  +   ++ + + L  +
Sbjct: 151 ELAHRVLWSDLGQLDSIEAKWEKAGPEEQLEAAAIEGWLIVNVWDQLSDE 200


>1yt3A1 [a.60.8.3] RIBONUCLEASE D A:194 -- 294
          Length = 101

 Score = 50.2 bits (120), Expect = 4e-09
 Identities = 16/63 (25%), Positives = 30/63 (47%)

Query: 192 ENIHAKIGNIQKFDEKTQRNAILIAQWRETIAQEKNIPVRFIFNNKILYTIAHINPKSLN 251
           E+    I N  +   +      L+A WR   A+E+++ V F+   + L+++A   P SL 
Sbjct: 4   EDAWRDITNAWQLRTRQLACLQLLADWRLRKARERDLAVNFVVREEHLWSVARYMPGSLG 63

Query: 252 SFE 254
             +
Sbjct: 64  ELD 66


>1skrA1 [c.55.3.5] DNA POLYMERASE A:1 -- 210
          Length = 204

 Score = 49.6 bits (117), Expect = 6e-09
 Identities = 17/185 (9%), Positives = 38/185 (20%), Gaps = 38/185 (20%)

Query: 22  IAVDTEFYWMRTYYPELCLVQLA----TENEIFLIDTLKDLEFKKLKEIFEDKDILKIIH 77
           I  D E   +     +     +      E   +            L+       ++   +
Sbjct: 2   IVSDIEANALLESVTKFHCGVIYDYSTAEYVSYRPSDFGAY-LDALEAEVARGGLIVFHN 60

Query: 78  SATNDIPIIKR--------FFNCEVNNIFDTQLAATFLGFQTQS---------------- 113
               D+P + +         F+    N  DT + +  +    +                 
Sbjct: 61  GHKYDVPALTKLAKLQLNREFHLPRENCIDTLVLSRLIHSNLKDTDMGLLRSGKLPGALE 120

Query: 114 ---------SXXXXXXXXXXXXXXXXSQFSDWRNRPLTQNQLNYAIKDVEYLIQLKEYLQ 164
                                                 +  ++Y ++DV     L E L 
Sbjct: 121 AWGYRLGEMKGEYKDDFKRMLEEQGEEYVDGMEWWNFNEEMMDYNVQDVVVTKALLEKLL 180

Query: 165 QQLAK 169
                
Sbjct: 181 SDKHY 185


>2cprA1 [a.60.8.4] EXOSOME COMPONENT 10 A:483 -- 595
          Length = 113

 Score = 48.4 bits (115), Expect = 1e-08
 Identities = 17/107 (15%), Positives = 42/107 (39%), Gaps = 14/107 (13%)

Query: 197 KIGNIQKFDEKTQRNAIL--IAQWRETIAQEKNIPVRFIFNNKILYTIAHINPKSLNSFE 254
           ++   QK    TQ+      +  WR+  A+ ++    ++  N ++  IA   PK      
Sbjct: 11  ELYRKQKKHLNTQQLTAFQLLFAWRDKTARREDESYGYVLPNHMMLKIAEELPKEP---- 66

Query: 255 HSELKSL----KPWIKK---GVVTALNSSKSLDQVTLEQTSGSKLST 294
              + +      P +++    +   +  ++ +  +  E  +G K S+
Sbjct: 67  -QGIIACCNPVPPLVRQQINEMHLLIQQAREMPLLKSEVAAGVKKSS 112


>1yt3A2 [a.60.8.3] RIBONUCLEASE D A:295 -- 375
          Length = 81

 Score = 48.3 bits (115), Expect = 1e-08
 Identities = 13/63 (20%), Positives = 29/63 (46%), Gaps = 1/63 (1%)

Query: 298 DKIIDFFDTYTKQLKFDSSIIASRKDIRSL-AYNLNIDTNYKNNKLLNGWRYEIVGKKLK 356
             I       ++  K  + ++ASR+ I  L  ++  +       +L++GWR E++ + L 
Sbjct: 14  KAIKSLITDVSETHKISAELLASRRQINQLLNWHWKLKPQNNLPELISGWRGELMAEALH 73

Query: 357 EYI 359
             +
Sbjct: 74  NLL 76


>2e1eA1 [a.60.8.1] WERNER SYNDROME ATP-DEPENDENT HELICASE A:1142 --
           1235
          Length = 94

 Score = 44.1 bits (104), Expect = 3e-07
 Identities = 10/52 (19%), Positives = 25/52 (48%), Gaps = 3/52 (5%)

Query: 202 QKFDEKTQRNAIL---IAQWRETIAQEKNIPVRFIFNNKILYTIAHINPKSL 250
               ++ +   +L   + + R+  A + ++P   +  NKIL  +A + P ++
Sbjct: 3   VISAQEQETQIVLYGKLVEARQKHANKMDVPPAILATNKILVDMAKMRPTTV 54


>2hbjA1 [a.60.8.4] EXOSOME COMPLEX EXONUCLEASE RRP6 A:421 -- 516
          Length = 96

 Score = 43.7 bits (103), Expect = 4e-07
 Identities = 10/54 (18%), Positives = 22/54 (40%)

Query: 197 KIGNIQKFDEKTQRNAILIAQWRETIAQEKNIPVRFIFNNKILYTIAHINPKSL 250
            +        + +     + QWR+ IA+  +   RF+  N++L  +    P  +
Sbjct: 7   ILMYQYNIPPEREVLVRELYQWRDLIARRDDESPRFVMPNQLLAALVAYTPTDV 60


>1d8bA [a.60.8.1] SGS1 RECQ HELICASE
          Length = 81

 Score = 40.6 bits (95), Expect = 3e-06
 Identities = 7/36 (19%), Positives = 13/36 (36%)

Query: 215 IAQWRETIAQEKNIPVRFIFNNKILYTIAHINPKSL 250
           + +    +      PV     + IL  +A I P + 
Sbjct: 12  LRELSLNLGNRMVPPVGNFMPDSILKKMAAILPMND 47


>1wudA1 [a.60.8.1] ATP-DEPENDENT DNA HELICASE RECQ A:530 -- 606
          Length = 77

 Score = 33.1 bits (76), Expect = 5e-04
 Identities = 11/32 (34%), Positives = 17/32 (53%)

Query: 219 RETIAQEKNIPVRFIFNNKILYTIAHINPKSL 250
           R++IA E N+P   +FN+  L   A   P + 
Sbjct: 14  RKSIADESNVPPYVVFNDATLIEXAEQXPITA 45


  Database: 40scop73nmM
    Posted date:  Nov 2, 2009 11:39 AM
  Number of letters in database: 1,678,726
  Number of sequences in database:  9549
  
Lambda     K      H
   0.318    0.136    0.375 

Gapped
Lambda     K      H
   0.267   0.0699    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 9549
Number of Hits to DB: 14,384,956
Number of extensions: 1021483
Number of successful extensions: 4319
Number of sequences better than 1.0e-03: 7
Number of HSP's gapped: 4220
Number of HSP's successfully gapped: 117
Length of database: 100,000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 6.9 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.2 bits)