RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= 029248
         (196 letters)



>2ogh_A Eukaryotic translation initiation factor EIF-1; alpha-beta protein;
           NMR {Saccharomyces cerevisiae}
          Length = 108

 Score = 80.3 bits (198), Expect = 4e-20
 Identities = 25/88 (28%), Positives = 36/88 (40%), Gaps = 1/88 (1%)

Query: 95  GKIKKKERQEVVIEKVVRNKRKCITIVKGLDLFGVKLSDASKKLGKKFATGASVVKGPTE 154
           G  +      + I    RN RK +T V+G+      L    K L K FA   ++VK P  
Sbjct: 16  GDDETATSNYIHIRIQQRNGRKTLTTVQGVPE-EYDLKRILKVLKKDFACNGNIVKDPEM 74

Query: 155 KEQIDVQGDISYDIVEFITDTWPAVPET 182
            E I +QGD    + EF+        + 
Sbjct: 75  GEIIQLQGDQRAKVCEFMISQLGLQKKN 102


>2if1_A EIF1, SUI1; translation initiation factor; NMR {Homo sapiens} SCOP:
           d.64.1.1
          Length = 126

 Score = 78.4 bits (193), Expect = 3e-19
 Identities = 23/90 (25%), Positives = 37/90 (41%), Gaps = 1/90 (1%)

Query: 93  PGGKIKKKERQEVVIEKVVRNKRKCITIVKGLDLFGVKLSDASKKLGKKFATGASVVKGP 152
               +       + I    RN RK +T V+G+           K   KKFA   +V++ P
Sbjct: 32  GDDLLPAGTEDYIHIRIQQRNGRKTLTTVQGIA-DDYDKKKLVKAFKKKFACNGTVIEHP 90

Query: 153 TEKEQIDVQGDISYDIVEFITDTWPAVPET 182
              E I +QGD   +I +F+ +   A  + 
Sbjct: 91  EYGEVIQLQGDQRKNICQFLVEIGLAKDDQ 120


>2xzm_F EIF1; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
           2xzn_F
          Length = 101

 Score = 74.9 bits (184), Expect = 4e-18
 Identities = 19/83 (22%), Positives = 34/83 (40%), Gaps = 1/83 (1%)

Query: 100 KERQEVVIEKVVRNKRKCITIVKGLDLFGVKLSDASKKLGKKFATGASVVKGPTEKEQID 159
             +  + I    R  RKC T V+G+           K   K  +  A++V+    K+ I 
Sbjct: 14  DFQTHIHIRVEQRRGRKCFTTVEGIPP-EFDYEKIMKYWKKWLSCNATIVEEDEGKKVIK 72

Query: 160 VQGDISYDIVEFITDTWPAVPET 182
           + GD    I +F+++   A  + 
Sbjct: 73  LNGDHRNQIQQFLSEEGIAAVDN 95


>1d1r_A Hypothetical 11.4 KD protein YCIH in PYRF-OSMB intergenic region;
           alpha-beta plait, open-faced beta sandwich,
           ferredoxin-like fold; NMR {Escherichia coli} SCOP:
           d.64.1.1
          Length = 116

 Score = 56.4 bits (136), Expect = 5e-11
 Identities = 19/93 (20%), Positives = 41/93 (44%), Gaps = 6/93 (6%)

Query: 83  SSKQEEVKRLPGGKIKKKERQEVVIEKVVRNKR-KCITIVKGLDLFGVKLSDASKKLGKK 141
           S++   +       ++ K    V I++    ++ K + ++ G+DL   +L+  + +L KK
Sbjct: 11  STETGRIDEPKAAPVRPKGDGVVRIQRQTSGRKGKGVCLITGVDLDDAELTKLAAELKKK 70

Query: 142 FATGASVVKGPTEKEQIDVQGDISYDIVEFITD 174
              G +V  G      I++QGD    +   +  
Sbjct: 71  CGCGGAVKDG-----VIEIQGDKRDLLKSLLEA 98


>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 = 30.0 bits (67), Expect = 0.54
 Identities = 19/108 (17%), Positives = 38/108 (35%), Gaps = 27/108 (25%)

Query: 107  IEKVVRNKRKCITIVKGLDLFGVKLSDASKKLGKKFA--TGASVVKGPTEKEQIDVQGDI 164
            I  +V N    +TI      FG +     K++ + ++     ++V G  + E+I  + + 
Sbjct: 1661 ILDIVINNPVNLTI-----HFGGE---KGKRIRENYSAMIFETIVDGKLKTEKIFKEINE 1712

Query: 165  SYDIVEF------ITDTW---PA--VPETAIY------FIEDGKKVAA 195
                  F      ++ T    PA  + E A +       +       A
Sbjct: 1713 HSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKGLIPADATFA 1760


>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
          photosynthetic reaction center, peripheral antenna;
          HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
          Length = 154

 Score = 28.4 bits (62), Expect = 1.1
 Identities = 8/22 (36%), Positives = 13/22 (59%), Gaps = 1/22 (4%)

Query: 53 EKEA-EKVSGQLQLFGLSSGGA 73
          EK+A +K+   L+L+   S  A
Sbjct: 18 EKQALKKLQASLKLYADDSAPA 39


>3l8k_A Dihydrolipoyl dehydrogenase; redox-active center, structural
           genomics, PSI-2, protein structure initiative; HET: ADP;
           2.50A {Sulfolobus solfataricus}
          Length = 466

 Score = 27.5 bits (62), Expect = 3.3
 Identities = 8/49 (16%), Positives = 14/49 (28%), Gaps = 6/49 (12%)

Query: 118 ITIVKGLDLFGVKLSD------ASKKLGKKFATGASVVKGPTEKEQIDV 160
             I++ LD   + L D          L       + V +    K+    
Sbjct: 198 THIIEMLDRALITLEDQDIVNTLLSILKLNIKFNSPVTEVKKIKDDEYE 246


>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 = 26.7 bits (58), Expect = 6.7
 Identities = 8/38 (21%), Positives = 10/38 (26%), Gaps = 7/38 (18%)

Query: 9   RVLYCSICSLPAEYCEFGPDFEKCKPWLIKNAPELYPD 46
           + L C    LP E            P  +    E   D
Sbjct: 309 KYLDCRPQDLPREVL-------TTNPRRLSIIAESIRD 339


  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
   0.313    0.133    0.383 

Gapped
Lambda     K      H
   0.267   0.0807    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,999,289
Number of extensions: 173672
Number of successful extensions: 277
Number of sequences better than 10.0: 1
Number of HSP's gapped: 274
Number of HSP's successfully gapped: 12
Length of query: 196
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 107
Effective length of database: 4,216,824
Effective search space: 451200168
Effective search space used: 451200168
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: 55 (24.8 bits)