RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy3878
         (299 letters)



>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 = 31.4 bits (70), Expect = 0.47
 Identities = 19/134 (14%), Positives = 37/134 (27%), Gaps = 40/134 (29%)

Query: 195 MHAQMAANYAASSDYSLSHSIAS-------NHLLTSGQHLLNDTYKSMLPAQ--SSFS-- 243
           +H  +  +Y     +     I         +H+   G HL     K++   +  + F   
Sbjct: 445 LHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHI---GHHL-----KNIEHPERMTLFRMV 496

Query: 244 ----------IPHPTPPTPAPTTPTP---RTRLYMKLINYFVSRYGVYSMTLYK-TSFVF 289
                     I H +    A  +      + + Y     Y       Y   +     F+ 
Sbjct: 497 FLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKP---YICDNDPKYERLVNAILDFLP 553

Query: 290 -PGRD---SKTCNL 299
               +   SK  +L
Sbjct: 554 KIEENLICSKYTDL 567


>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 = 30.8 bits (69), Expect = 0.71
 Identities = 17/69 (24%), Positives = 26/69 (37%), Gaps = 15/69 (21%)

Query: 210 SLSHSI---ASNHLLTSGQHLLNDTYKSMLPAQSSFSIPHPTPPTPAPTTPTPRTRLYMK 266
           SL H +    ++  + S Q  L + +  +LP         PT    A   PT    L  K
Sbjct: 15  SLEHVLLVPTASFFIAS-Q--LQEQFNKILPE--------PTEGFAADDEPTTPAELVGK 63

Query: 267 LINYFVSRY 275
            +  +VS  
Sbjct: 64  FLG-YVSSL 71


>4agy_A VP1 protein; picornavirus, enterovirus, HEV-A; 6.09A {Human
           coxsackievirus A7} PDB: 4agx_A
          Length = 181

 Score = 29.6 bits (66), Expect = 0.94
 Identities = 15/100 (15%), Positives = 33/100 (33%), Gaps = 3/100 (3%)

Query: 73  GSLSPTSQRNTNSSTPNNTSTSSNNNNNTSYTSRVITSSCAATPTYSTSGDIYFSGSQND 132
           G+  PT + +    T  N S  S   +  +   +V     +    Y    D Y +  ++ 
Sbjct: 82  GAPLPTRRDSYEWQTSTNPSIISKMADPPA---QVSVPFLSPASAYQWFYDGYPTFGKHP 138

Query: 133 NSHQLLGKAVESHHLGSMYSRHPYESWPFNTMTSSSHHKP 172
                      ++ +G+   R      P  ++T   + + 
Sbjct: 139 IDQDFQYGMCPNNMMGTFCVRMIGGGKPTQSVTIRIYMRL 178


>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
            multi-protein complex, DNA- binding, magnesium; 3.65A
            {Schizosaccharomyces pombe}
          Length = 1752

 Score = 27.7 bits (61), Expect = 5.5
 Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 5/81 (6%)

Query: 53   HPWKKSPQSAGGNSTTPAQLGSLSPTSQRNTNSSTPNNTSTSSNNNNNTSYTSRVITSSC 112
                 SP S   + T+P    S SPTS   + +S   + ++ S +  + SY+    + S 
Sbjct: 1658 TSPSYSPTSPSYSPTSP----SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS- 1712

Query: 113  AATPTYSTSGDIYFSGSQNDN 133
              +P+YS +   Y   S + +
Sbjct: 1713 PTSPSYSPTSPSYSPTSPSYS 1733


>3k2k_A Putative carboxypeptidase; structural genomics, joint center
           structural genomics, JCSG, protein structure initiative;
           2.49A {Burkholderia mallei atcc 23344}
          Length = 403

 Score = 27.5 bits (60), Expect = 6.0
 Identities = 16/95 (16%), Positives = 25/95 (26%), Gaps = 13/95 (13%)

Query: 189 LDMSGGMHAQMAANYAASSDYSLSHSIASNHLLTSGQHLLNDTYKSMLPAQS-SFSIPHP 247
            D+   +H      Y  ++   +          T  Q +    +       S  F   H 
Sbjct: 280 CDLFFDIHGDEDLPYVFAAGSEMLPG------FTEQQRVEQSAFIDSFKRASPDFQDEHG 333

Query: 248 TPPTPAPTTPTPRTRLYMKLINYFVSRYGVYSMTL 282
            PP                   Y   R+G  S+TL
Sbjct: 334 YPPGKYREDAFKLAS------KYIGHRFGCLSLTL 362


>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription,
            mRNA, multiprotein complex; HET: UTP; 2.30A
            {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A
            1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A*
            1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A*
            1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
          Length = 1733

 Score = 27.4 bits (60), Expect = 7.3
 Identities = 19/79 (24%), Positives = 35/79 (44%), Gaps = 11/79 (13%)

Query: 58   SPQSAGGNSTTPAQLGS---LSPTSQRNTNSSTPNNTSTSSNNNNNTSYTSRVITSSCAA 114
            SP S   + T+P+   +    SPTS   + +S   + ++ S +  + SY+          
Sbjct: 1627 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSP--------T 1678

Query: 115  TPTYSTSGDIYFSGSQNDN 133
            +P+YS +   Y   S N +
Sbjct: 1679 SPSYSPTSPSYSPTSPNYS 1697


  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
   0.311    0.124    0.382 

Gapped
Lambda     K      H
   0.267   0.0534    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,353,281
Number of extensions: 234834
Number of successful extensions: 489
Number of sequences better than 10.0: 1
Number of HSP's gapped: 488
Number of HSP's successfully gapped: 19
Length of query: 299
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 206
Effective length of database: 4,105,140
Effective search space: 845658840
Effective search space used: 845658840
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 57 (26.2 bits)