RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy5074
         (204 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 = 35.6 bits (81), Expect = 0.010
 Identities = 19/128 (14%), Positives = 41/128 (32%), Gaps = 39/128 (30%)

Query: 45  VVSLLSSLLIDRLGR--RFLL-----LTSEITMAFCQLLLVAYFVFKNQGYDMQDYSWIP 97
            +S+++  + D L     +       LT+ I  +   L          +  + +      
Sbjct: 329 RLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVL----------EPAEYRKM---- 374

Query: 98  IFSVCTIVAIFRIGIGPIP-------WFMMAEIIPLE--AKLWSSSLLMCYSWSCLFLVS 148
            F      ++F      IP       WF + +   +    KL   SL+          +S
Sbjct: 375 -FDRL---SVFPPSA-HIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEK--QPKESTIS 427

Query: 149 --KVFMDL 154
              ++++L
Sbjct: 428 IPSIYLEL 435


>3fvc_A GP115, glycoprotein GP110; viral fusion protein, PH domains, fusion
           loops, glycoprotein protein, membrane, transmembrane,
           viral protein; HET: NAG; 3.20A {Human herpesvirus 4}
          Length = 663

 Score = 28.4 bits (63), Expect = 1.9
 Identities = 12/46 (26%), Positives = 20/46 (43%), Gaps = 4/46 (8%)

Query: 62  LLLTSEITMAFCQLLLVAYFVFKNQGYDMQDY---SWIPIFSVCTI 104
           + LT ++T   CQ     YF   N+ +   DY     I +  + T+
Sbjct: 556 IFLTKKMTEV-CQATSQYYFQSGNEIHVYNDYHHFKTIELDGIATL 600


>3nwa_A GB, GB-1, GB1, envelope glycoprotein B; coiled-coil, membrane
           fusion, viral P glycoprotein B, HSV-1, membrane; HET:
           NAG; 2.26A {Human herpesvirus 1} PDB: 3nwf_A* 3nw8_A*
           3nwd_A*
          Length = 703

 Score = 27.2 bits (60), Expect = 4.9
 Identities = 9/46 (19%), Positives = 18/46 (39%), Gaps = 4/46 (8%)

Query: 62  LLLTSEITMAFCQLLLVAYFVFKNQGYDMQDYSW---IPIFSVCTI 104
           L LT +     C +    YF F       ++Y++   +    + T+
Sbjct: 596 LRLTRDAIEP-CTVGHRRYFTFGGGYVYFEEYAYSHQLSRADITTV 640


>3vp7_A Vacuolar protein sorting-associated protein 30; targeting,
           PI3-kinase complex I, PRE-autophagosomal structur
           protein transport; 2.30A {Saccharomyces cerevisiae}
          Length = 220

 Score = 26.6 bits (58), Expect = 4.9
 Identities = 13/40 (32%), Positives = 19/40 (47%)

Query: 66  SEITMAFCQLLLVAYFVFKNQGYDMQDYSWIPIFSVCTIV 105
            EI  A  QL+L+   + KN   ++ DY   P+ S   I 
Sbjct: 35  KEINAALGQLILLLATINKNLKINLVDYELQPMGSFSKIK 74


>2gum_A Glycoprotein B; envelope glycoprotein, membrane fusion, viral
           protein; 2.10A {Human herpesvirus 1} SCOP: e.76.1.1
          Length = 628

 Score = 26.8 bits (59), Expect = 6.0
 Identities = 9/46 (19%), Positives = 18/46 (39%), Gaps = 4/46 (8%)

Query: 62  LLLTSEITMAFCQLLLVAYFVFKNQGYDMQDYSW---IPIFSVCTI 104
           L LT +     C +    YF F       ++Y++   +    + T+
Sbjct: 521 LRLTRDAIEP-CTVGHRRYFTFGGGYVYFEEYAYSHQLSRADITTV 565


>3p9z_A Uroporphyrinogen III cosynthase (HEMD); MCSG, PSI2, structural
           genomics, protein structure initiativ midwest center for
           structural genomics; HET: MSE; 2.10A {Helicobacter
           pylori}
          Length = 229

 Score = 26.2 bits (58), Expect = 7.7
 Identities = 7/42 (16%), Positives = 18/42 (42%), Gaps = 1/42 (2%)

Query: 59  RRFLLLTSEITMAFCQLLLVAYFVFKNQGYDMQDYSWIPIFS 100
            R ++      +A  + L++  F +     D   ++ + IF+
Sbjct: 4   MREIVWVHSQRIAPYKTLILNEFCYYPLELDPTPFNAL-IFT 44


>1g5c_A Beta-carbonic anhydrase; zinc, hepes, lyase; HET: EPE; 2.10A
          {Methanothermobacterthermautotrophicus} SCOP: c.53.2.1
          Length = 170

 Score = 25.8 bits (57), Expect = 9.2
 Identities = 4/23 (17%), Positives = 8/23 (34%)

Query: 22 IFRNAGTRIAPSTASIIVGAVQV 44
          + +NAG  +          A+  
Sbjct: 54 VIKNAGNIVDDGVIRSAAVAIYA 76


  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
   0.330    0.141    0.430 

Gapped
Lambda     K      H
   0.267   0.0675    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,102,958
Number of extensions: 177210
Number of successful extensions: 415
Number of sequences better than 10.0: 1
Number of HSP's gapped: 414
Number of HSP's successfully gapped: 15
Length of query: 204
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 115
Effective length of database: 4,216,824
Effective search space: 484934760
Effective search space used: 484934760
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 55 (25.1 bits)