RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy6045
         (105 letters)



>4a18_C 60S ribosomal protein L36A; ribosome, eukaryotic initiation factor
           6, EIF6, transla large ribosomal subunit, rRNA; 3.52A
           {Tetrahymena thermophila} PDB: 4a19_C 4a1b_C 4a1d_C
          Length = 109

 Score = 92.3 bits (229), Expect = 4e-26
 Identities = 59/99 (59%), Positives = 72/99 (72%)

Query: 4   VNVPKQRRTFCKKCKIHKVHKVTQYKKSKERKACQGRRRYDRKQAGYGGQTKPIFRKKAK 63
           V VPK R+T+CKKC  H  HKV+QYKKSKE    QGRRRYD KQ+G+GGQTKPIFRKKAK
Sbjct: 2   VQVPKTRKTYCKKCNSHTNHKVSQYKKSKESTHAQGRRRYDMKQSGFGGQTKPIFRKKAK 61

Query: 64  TTKKIVLRMECTECKYRKQLPLKRCKHFELGGDKKRKVQ 102
           TTKK+ L+ +CT CK ++ +P+KRCK        + K  
Sbjct: 62  TTKKVALKFDCTTCKTKRVIPIKRCKTIVFMDITQIKKA 100


>1vq8_3 50S ribosomal protein L44E; ribosome 50S, protein-protein
          complex, RNA-RNA complex, PROT complex, peptidyl
          transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS;
          2.20A {Haloarcula marismortui} SCOP: g.41.8.3 PDB:
          1jj2_2 1k73_4* 1k8a_4* 1k9m_4* 1kc8_4* 1kd1_4* 1kqs_2*
          1m1k_4* 1m90_4* 1n8r_4* 1nji_4* 1q7y_4* 1q81_4* 1q82_4*
          1q86_4* 1qvf_2 1qvg_2 1s72_3* 1vq4_3* 1vq5_3* ...
          Length = 92

 Score = 89.4 bits (222), Expect = 4e-25
 Identities = 19/90 (21%), Positives = 33/90 (36%)

Query: 4  VNVPKQRRTFCKKCKIHKVHKVTQYKKSKERKACQGRRRYDRKQAGYGGQTKPIFRKKAK 63
          + +P++  T+C  C  H+ H+V + +  ++       R+ +R                 K
Sbjct: 1  MQMPRRFNTYCPHCNEHQEHEVEKVRSGRQTGMKWIDRQRERNSGIGNDGKFSKVPGGDK 60

Query: 64 TTKKIVLRMECTECKYRKQLPLKRCKHFEL 93
           TKK  L+  C EC         R    E 
Sbjct: 61 PTKKTDLKYRCGECGKAHLREGWRAGRLEF 90


>3iz5_R 60S ribosomal protein L18 (L18E); eukaryotic ribosome,homology
           modeling,de novo modeling,ribos proteins,novel ribosomal
           proteins, ribosome; 5.50A {Triticum aestivum} PDB:
           3izr_R
          Length = 188

 Score = 87.7 bits (217), Expect = 3e-24
 Identities = 3/101 (2%), Positives = 11/101 (10%), Gaps = 2/101 (1%)

Query: 4   VNVPKQRRTFCK--KCKIHKVHKVTQYKKSKERKACQGRRRYDRKQAGYGGQTKPIFRKK 61
                      +  +          +      R   +  +                 R  
Sbjct: 2   GIDLVAGGRNKRTKRVAPKSDDVYLKLLVKLYRFLVRRTKSKFNAVILKRLFMSKTNRPP 61

Query: 62  AKTTKKIVLRMECTECKYRKQLPLKRCKHFELGGDKKRKVQ 102
               +         E      +               +   
Sbjct: 62  LSMRRLSNFMKGKEEKNIAVVVGTITDDMRIQEVPAMKVTA 102


>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 = 25.6 bits (55), Expect = 4.6
 Identities = 14/97 (14%), Positives = 26/97 (26%), Gaps = 22/97 (22%)

Query: 1   MSHVNVPKQRRTFCKKCKI---HKVHKVTQYKKSKERKACQGRRRYDRKQAGYG-GQTKP 56
           + +V   K    F   CKI    +  +VT +  +            D         + K 
Sbjct: 250 LLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTT----HISLDHHSMTLTPDEVKS 305

Query: 57  IFRKKAKTTKKIVLRMECTECKYRKQLPLKRCKHFEL 93
           +  K               +C+  + LP +       
Sbjct: 306 LLLK-------------YLDCRP-QDLPREVLTTNPR 328


>3avx_A Elongation factor TS, elongation factor TU, linke replicase; RNA
           polymerase, translation, transferase-RNA complex; HET:
           GH3; 2.41A {Escherichia coli O157} PDB: 3agq_A 3agp_A*
           3avu_A 3avv_A 3avt_A* 3avw_A* 3avy_A* 3mmp_A* 3mmp_G*
           1efu_B
          Length = 1289

 Score = 24.5 bits (53), Expect = 9.0
 Identities = 12/49 (24%), Positives = 17/49 (34%)

Query: 51  GGQTKPIFRKKAKTTKKIVLRMECTECKYRKQLPLKRCKHFELGGDKKR 99
           GG T    R     + K  L   CT    +  L L+   HF++      
Sbjct: 850 GGATTTNNRSYGHPSFKFALPQACTPRALKYVLALRASTHFDIRISDIS 898


  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
   0.322    0.134    0.410 

Gapped
Lambda     K      H
   0.267   0.0577    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,491,473
Number of extensions: 72129
Number of successful extensions: 144
Number of sequences better than 10.0: 1
Number of HSP's gapped: 140
Number of HSP's successfully gapped: 18
Length of query: 105
Length of database: 6,701,793
Length adjustment: 70
Effective length of query: 35
Effective length of database: 4,747,323
Effective search space: 166156305
Effective search space used: 166156305
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (23.8 bits)