RPS-BLAST 2.2.26 [Sep-21-2011]

Database: pdb70 
           27,921 sequences; 6,701,793 total letters

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

Query= psy14229
         (119 letters)



>2xau_A PRE-mRNA-splicing factor ATP-dependent RNA helica; hydrolase,
           ribosome biogenesis, ATPase, ATP-binding, OB-fold; HET:
           ADP; 1.90A {Saccharomyces cerevisiae} PDB: 3kx2_B*
          Length = 773

 Score = 62.3 bits (152), Expect = 9e-13
 Identities = 25/102 (24%), Positives = 46/102 (45%), Gaps = 16/102 (15%)

Query: 17  CLDANDELTPLGKILARLPLEPRLGKMLLLGSIFNCGD-ALNIVAASASGSNEIFVTERR 75
           CLD    LTPLG++ ++ PL+P L  ML+    F C    L IVA  +  +  +F+    
Sbjct: 503 CLDDEGNLTPLGRLASQFPLDPMLAVMLIGSFEFQCSQEILTIVAMLSVPN--VFI---- 556

Query: 76  LSYAQRSNEIFVTERRLSYAQRAFAGSRYSDFVAVINAFNMF 117
                R  +    +++ +   +        D + ++N ++ F
Sbjct: 557 -----RPTK----DKKRADDAKNIFAHPDGDHITLLNVYHAF 589


>3i4u_A ATP-dependent RNA helicase DHX8; splicing, ATP-binding, hydrolase,
           mRNA processing, splicing, nucleotide-binding, nucleus,
           phosphoprotein, SPLI; 2.10A {Homo sapiens}
          Length = 270

 Score = 54.6 bits (132), Expect = 3e-10
 Identities = 25/102 (24%), Positives = 45/102 (44%), Gaps = 16/102 (15%)

Query: 17  CLDANDELTPLGKILARLPLEPRLGKMLLLGSIFNCGD-ALNIVAASASGSNEIFVTERR 75
            LD    LT LG+ +A  PLEP L KML++     C +  L IV+  +  +  +F     
Sbjct: 32  ALDDEGLLTRLGRRMAEFPLEPMLCKMLIMSVHLGCSEEMLTIVSMLSVQN--VFY---- 85

Query: 76  LSYAQRSNEIFVTERRLSYAQRAFAGSRYSDFVAVINAFNMF 117
                R  +    ++ L+  ++A       D + ++  +N +
Sbjct: 86  -----RPKD----KQALADQKKAKFHQTEGDHLTLLAVYNSW 118


>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
           acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
           synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
          Length = 2006

 Score = 29.6 bits (66), Expect = 0.22
 Identities = 6/46 (13%), Positives = 16/46 (34%), Gaps = 8/46 (17%)

Query: 74  RRLSYAQRSNEIFVTERRLSYAQRAFAGSRYSDFVAVINAFNMFIV 119
             L+  Q  + +  T   L   ++          ++++N     +V
Sbjct: 342 SNLTQEQVQDYVNKTNSHLPAGKQVE--------ISLVNGAKNLVV 379


>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold,
           winged-helix-turn-helix, antiparallel-coiled-COI domain,
           ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces
           cerevisiae}
          Length = 1108

 Score = 27.5 bits (60), Expect = 1.2
 Identities = 12/72 (16%), Positives = 20/72 (27%), Gaps = 6/72 (8%)

Query: 14  EMKCLDANDELTPLGKILARLPLE-PRLGKMLLLGSIFNCGDALNIVAASASGSNEIFVT 72
            +     ND +   G++   +      L   L+    FN        A  +      F  
Sbjct: 926 RLGFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSC-----FAF 980

Query: 73  ERRLSYAQRSNE 84
           + R   A R   
Sbjct: 981 QERCKEAPRLKP 992


>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase,
           tramp, exosome, DEAD, nucleotide-binding; HET: ADP;
           2.90A {Saccharomyces cerevisiae}
          Length = 1010

 Score = 27.4 bits (60), Expect = 1.2
 Identities = 10/65 (15%), Positives = 18/65 (27%), Gaps = 6/65 (9%)

Query: 14  EMKCLDANDELTPLGKILARLPLE-PRLGKMLLLGSIFNCGDALNIVAASASGSNEIFVT 72
            +     ND +   G++   +      L   L+    FN        A  +      F  
Sbjct: 828 RLGFCTPNDIIELKGRVACEISSGDELLLTELIFNGNFNELKPEQAAALLSC-----FAF 882

Query: 73  ERRLS 77
           + R  
Sbjct: 883 QERCK 887


>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
           programmed cell death; HET: DTP; 6.90A {Drosophila
           melanogaster} PDB: 3iz8_A*
          Length = 1221

 Score = 26.0 bits (56), Expect = 3.9
 Identities = 12/45 (26%), Positives = 14/45 (31%), Gaps = 4/45 (8%)

Query: 5   DANDELTPLEMKCLDANDELTPLGKILARLPLEPRLGKMLLLGSI 49
             +  LTP E+K L        L      LP E        L  I
Sbjct: 293 HHSMTLTPDEVKSLLLK----YLDCRPQDLPREVLTTNPRRLSII 333


>2hd0_A Protease NS2-3 (P23); cysteine protease, dimer, composite active
           site, hydrolase; HET: DMU BOG; 2.28A {Hepatitis c virus}
          Length = 128

 Score = 24.5 bits (53), Expect = 7.1
 Identities = 11/38 (28%), Positives = 19/38 (50%)

Query: 10  LTPLEMKCLDANDELTPLGKILARLPLEPRLGKMLLLG 47
            + +E K +    +    G I+  LP+  R G+ +LLG
Sbjct: 78  FSRMETKLITWGADTAACGDIINGLPVSARRGQEILLG 115


  Database: pdb70
    Posted date:  Sep 4, 2012  3:40 AM
  Number of letters in database: 6,701,793
  Number of sequences in database:  27,921
  
Lambda     K      H
   0.323    0.137    0.389 

Gapped
Lambda     K      H
   0.267   0.0686    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,742,616
Number of extensions: 93107
Number of successful extensions: 107
Number of sequences better than 10.0: 1
Number of HSP's gapped: 107
Number of HSP's successfully gapped: 9
Length of query: 119
Length of database: 6,701,793
Length adjustment: 81
Effective length of query: 38
Effective length of database: 4,440,192
Effective search space: 168727296
Effective search space used: 168727296
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (23.5 bits)