RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy5287
         (65 letters)



>3u5c_C Guanine nucleotide-binding protein subunit beta-L protein (ASC1,
          RACK1); translation, ribosome, ribosomal, ribosomal R
          ribosomal protein, eukaryotic ribosome, RNA-protein C;
          3.00A {Saccharomyces cerevisiae} PDB: 3izb_E 3o30_B
          3o2z_B 3u5g_C 3jyv_E* 1s1h_E
          Length = 254

 Score = 98.6 bits (246), Expect = 1e-29
 Identities = 6/62 (9%), Positives = 13/62 (20%)

Query: 4  QVVLARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESEREARR 63
               R        G   +      E  G    T +  +    +   I  +       + 
Sbjct: 6  AQQQKRGGFGGRNRGRPNRRGPRNTEEKGWVPVTKLGRLVKAGKITTIEEIFLHSLPVKE 65

Query: 64 LR 65
           +
Sbjct: 66 FQ 67


>2xzm_1 Ribosomal protein S28E containing protein; ribosome, translation;
          3.93A {Tetrahymena thermophila} PDB: 2xzn_1
          Length = 68

 Score = 95.2 bits (237), Expect = 2e-28
 Identities = 34/66 (51%), Positives = 46/66 (69%), Gaps = 2/66 (3%)

Query: 2  DKQVVLARVIKTLGRTGSQGQCTQVKVEFIG--DQNRTIIRNVKGPVREGDILTLLESER 59
           ++   AR++  LG+TGS+G  TQV+V  I   ++ R +IRNVKG  R GD+L L+E ER
Sbjct: 3  TEETTKARIMDVLGKTGSRGGITQVRVVLISGKEEGRQLIRNVKGACRVGDVLELMECER 62

Query: 60 EARRLR 65
          EARRLR
Sbjct: 63 EARRLR 68


>1ny4_A 30S ribosomal protein S28E; JR19, structure, autostructure,
          northeast structural genomics consortium, PSI, protein
          structure initiative; NMR {Pyrococcus horikoshii} SCOP:
          b.40.4.5
          Length = 82

 Score = 95.7 bits (238), Expect = 2e-28
 Identities = 34/66 (51%), Positives = 45/66 (68%), Gaps = 2/66 (3%)

Query: 2  DKQVVLARVIKTLGRTGSQGQCTQVKVEFIG--DQNRTIIRNVKGPVREGDILTLLESER 59
          + +   A VI+ +GRTG+ G  TQVKV  +   D+ R I RNV+GPVR GDIL L E+ER
Sbjct: 3  EDEGYPAEVIEIIGRTGTTGDVTQVKVRILEGRDKGRVIRRNVRGPVRVGDILILRETER 62

Query: 60 EARRLR 65
          EAR ++
Sbjct: 63 EAREIK 68


>1ne3_A 30S ribosomal protein S28E; beta protein, structural genomics,
          OCSP, NESG, protein structure initiative, PSI; NMR
          {Methanothermococcusthermolithotrophicus} SCOP:
          b.40.4.5
          Length = 68

 Score = 90.6 bits (225), Expect = 2e-26
 Identities = 30/64 (46%), Positives = 40/64 (62%), Gaps = 2/64 (3%)

Query: 4  QVVLARVIKTLGRTGSQGQCTQVKVEFIG--DQNRTIIRNVKGPVREGDILTLLESEREA 61
              A VI+ L RTG  G+  QVK   +   D+ R + RNV GP+REGDIL LL++ REA
Sbjct: 3  DATPAEVIEVLKRTGMTGEVMQVKCRILDGRDKGRILTRNVMGPIREGDILMLLDTIREA 62

Query: 62 RRLR 65
          + +R
Sbjct: 63 KEIR 66


>3dmo_A Cytidine deaminase; structural genomics, seattle structural
           genomics center for infectious disease, ssgcid,
           hydrolase; 1.60A {Burkholderia pseudomallei}
          Length = 138

 Score = 25.2 bits (55), Expect = 1.4
 Identities = 11/35 (31%), Positives = 16/35 (45%)

Query: 21  GQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLL 55
           G C QV +E        ++ N++G VR      LL
Sbjct: 97  GACRQVMIELGKPTLEVVLTNMQGDVRVTSAGDLL 131


>1w36_B RECB, exodeoxyribonuclease V beta chain; recombination, helicase,
           hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli}
           SCOP: c.37.1.19 c.37.1.19 c.52.1.24 PDB: 3k70_B*
          Length = 1180

 Score = 25.3 bits (55), Expect = 1.8
 Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 12/59 (20%)

Query: 7   LARVIKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVREGDILTLLESEREARRLR 65
            A  I+   + G +G+   +     GD  R        PVR  DI  L+ S +EA ++R
Sbjct: 522 CAAQIRDWLQAGQRGEALLMN----GDDAR--------PVRASDISVLVRSRQEAAQVR 568


>2qkd_A Zinc finger protein ZPR1; helical hairpins, beta helix,
          anti-parrallel beta sheet, double straded anti-parallel
          beta helix, metal binding protein; 2.00A {Mus musculus}
          Length = 404

 Score = 25.0 bits (54), Expect = 2.0
 Identities = 10/37 (27%), Positives = 16/37 (43%)

Query: 11 IKTLGRTGSQGQCTQVKVEFIGDQNRTIIRNVKGPVR 47
          I++ GR   QG    + V    D NR +++      R
Sbjct: 54 IQSAGRIQDQGVRYTLTVRSQEDMNREVVKTDSATTR 90


  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
   0.320    0.138    0.373 

Gapped
Lambda     K      H
   0.267   0.0678    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 924,169
Number of extensions: 41020
Number of successful extensions: 221
Number of sequences better than 10.0: 1
Number of HSP's gapped: 218
Number of HSP's successfully gapped: 23
Length of query: 65
Length of database: 6,701,793
Length adjustment: 36
Effective length of query: 29
Effective length of database: 5,696,637
Effective search space: 165202473
Effective search space used: 165202473
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 (21.8 bits)
S2: 51 (23.5 bits)