RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy10187
         (78 letters)



>1xpp_A TA1416, DNA-directed RNA polymerase subunit L; structural
          genomics, protein structure initiative, MCSG; 1.60A
          {Thermoplasma acidophilum} SCOP: d.74.3.2
          Length = 115

 Score = 27.2 bits (60), Expect = 0.40
 Identities = 6/20 (30%), Positives = 10/20 (50%), Gaps = 1/20 (5%)

Query: 49 YVAYHVNHPLFSPPNF-VQV 67
             Y++ HP+   P   V+V
Sbjct: 50 EARYYIKHPVIDNPQIYVRV 69


>3eeq_A Putative cobalamin biosynthesis protein G homolog; structural
           genomics, unknown function, PSI-2, protein structure
           initiative; 2.30A {Sulfolobus solfataricus} SCOP:
           c.151.1.1 c.152.1.1
          Length = 336

 Score = 26.7 bits (58), Expect = 0.68
 Identities = 8/33 (24%), Positives = 13/33 (39%)

Query: 46  FTAYVAYHVNHPLFSPPNFVQVFVGLAAFAEFC 78
                  +  +P  +PP+   + VGL   AE  
Sbjct: 267 VNEEEINNFMNPCLTPPSKTLIEVGLKGVAEIS 299


>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 = 26.4 bits (57), Expect = 0.91
 Identities = 7/47 (14%), Positives = 18/47 (38%), Gaps = 11/47 (23%)

Query: 9   YIVHYTKRVLETLFVHR-FSHATMPIMNLFKNCGY-YWGFTAYVAYH 53
           Y +H  + +++   + + F    +    L     Y Y     ++ +H
Sbjct: 443 YALH--RSIVDHYNIPKTFDSDDLIPPYLD---QYFYS----HIGHH 480


>3s98_A Interferon alpha/beta receptor 1; human, type I interferons,
           receptor chain, ifnar1, fibronect III, type I interferon
           receptor chain; HET: NAG; 1.90A {Homo sapiens}
          Length = 306

 Score = 26.0 bits (56), Expect = 1.2
 Identities = 8/60 (13%), Positives = 17/60 (28%)

Query: 7   LCYIVHYTKRVLETLFVHRFSHATMPIMNLFKNCGYYWGFTAYVAYHVNHPLFSPPNFVQ 66
             Y +   K            ++   I  L     Y     A +       ++SP + ++
Sbjct: 137 FTYSLVIWKNSSGVEERIENIYSRHKIYKLSPETTYCLKVKAALLTSWKIGVYSPVHCIK 196


>4a2w_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2
           RNA helicase, ATP and dsRNA binding antiviral signalling
           pathway; 3.70A {Anas platyrhynchos}
          Length = 936

 Score = 25.7 bits (55), Expect = 1.7
 Identities = 9/28 (32%), Positives = 12/28 (42%)

Query: 38  KNCGYYWGFTAYVAYHVNHPLFSPPNFV 65
            NC + WG T       N P+    +FV
Sbjct: 872 NNCQHDWGITVKYLTFDNLPVIKIKSFV 899


>3h0g_K DNA-directed RNA polymerase II subunit RPB11; transcription,
          multi-protein complex, DNA- binding, magnesium; 3.65A
          {Schizosaccharomyces pombe}
          Length = 123

 Score = 25.3 bits (55), Expect = 2.1
 Identities = 7/32 (21%), Positives = 10/32 (31%)

Query: 33 IMNLFKNCGYYWGFTAYVAYHVNHPLFSPPNF 64
          + N+  N         +  Y V HPL      
Sbjct: 41 LANMLANQLLSDERVLFAGYKVPHPLNHNFIL 72


>1twf_K B13.6, DNA-directed RNA polymerase II 13.6 kDa polypepti;
          transcription, mRNA, multiprotein complex; HET: UTP;
          2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.2 PDB:
          1i3q_K 1i6h_K 1k83_K* 1nik_K 1nt9_K 1pqv_K 1r5u_K
          1r9s_K* 1r9t_K* 1sfo_K* 1twa_K* 1twc_K* 1i50_K* 1twg_K*
          1twh_K* 1wcm_K 1y1v_K 1y1w_K 1y1y_K 1y77_K* ...
          Length = 120

 Score = 24.9 bits (54), Expect = 2.8
 Identities = 8/32 (25%), Positives = 12/32 (37%)

Query: 33 IMNLFKNCGYYWGFTAYVAYHVNHPLFSPPNF 64
          + NL +          + AY V HP F+    
Sbjct: 42 LGNLIRAELLNDRKVLFAAYKVEHPFFARFKL 73


>3eqt_A ATP-dependent RNA helicase DHX58; innate immunity, RIG-I-like
          helicases, viral RNA detection, LGP2/dsRNA complex,
          ATP-binding, coiled coil; 2.00A {Homo sapiens} PDB:
          2w4r_A 2rqa_A
          Length = 145

 Score = 24.7 bits (53), Expect = 3.3
 Identities = 7/28 (25%), Positives = 12/28 (42%), Gaps = 1/28 (3%)

Query: 38 KNCGYYWGFTAYVAYHVNHPLFSPPNFV 65
          +NCG  WG    +   V  P+    + +
Sbjct: 73 RNCGEVWG-LQMIYKSVKLPVLKVRSML 99


  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
   0.335    0.143    0.489 

Gapped
Lambda     K      H
   0.267   0.0443    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,252,808
Number of extensions: 57975
Number of successful extensions: 200
Number of sequences better than 10.0: 1
Number of HSP's gapped: 200
Number of HSP's successfully gapped: 9
Length of query: 78
Length of database: 6,701,793
Length adjustment: 47
Effective length of query: 31
Effective length of database: 5,389,506
Effective search space: 167074686
Effective search space used: 167074686
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.7 bits)
S2: 51 (24.1 bits)