RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy3498
         (81 letters)



>1wii_A Hypothetical UPF0222 protein MGC4549; domain of unknown function,
          zinc finger, metal-binding protein, structural
          genomics; NMR {Mus musculus} SCOP: g.41.3.4
          Length = 85

 Score =  106 bits (265), Expect = 3e-32
 Identities = 47/75 (62%), Positives = 58/75 (77%)

Query: 3  RRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVCLEDFQTTIN 62
             S RKPPPK+K    L+ QF CPFCNHEKSC+VKMD+ RN+  I+C VCLE+FQT I 
Sbjct: 3  SGSSGRKPPPKKKMTGTLETQFTCPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQTPIT 62

Query: 63 FLSEAIDVYNDWVDA 77
          +LSE +DVY+DW+DA
Sbjct: 63 YLSEPVDVYSDWIDA 77


>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
          transcription factor, DNA-binding, DNA-directed RNA
          polymerase; 4.30A {Saccharomyces cerevisiae}
          Length = 197

 Score = 29.2 bits (65), Expect = 0.10
 Identities = 14/59 (23%), Positives = 21/59 (35%), Gaps = 8/59 (13%)

Query: 1  MGRRKSKRKPPPKRKNIEPLDIQFNCPFCNHEKSCEVKMDKGRNSARIACRVC---LED 56
          M  R+S  K   +R     L+I   CP C      ++          + C +C   L D
Sbjct: 1  MMTRESIDKRAGRRG--PNLNIVLTCPECKVYPP-KIVERFSE--GDVVCALCGLVLSD 54


>3ak8_A DNA protection during starvation protein; DPS-like protein,
           dodecamer, iron-binding protein, metal BIN protein,
           oxidoreductase; HET: DNA; 1.25A {Salmonella enterica
           subsp} PDB: 3ak9_A* 1f33_A* 1f30_A* 1dps_A 1jts_A*
           1jre_A* 1l8h_A* 1l8i_A* 4dyu_A*
          Length = 167

 Score = 25.8 bits (57), Expect = 1.6
 Identities = 5/39 (12%), Positives = 13/39 (33%)

Query: 40  DKGRNSARIACRVCLEDFQTTINFLSEAIDVYNDWVDAS 78
               ++ +   +   + +    N + +AI    D   A 
Sbjct: 108 PLDIHNVQDHLKELADRYAVVANDVRKAIGEAKDEDTAD 146


>2q3x_A Regulating synaptic membrane exocytosis protein 1; C2 domain dimer,
           neurotransmitter release, transport protein; HET: MSE;
           1.73A {Rattus norvegicus}
          Length = 171

 Score = 25.1 bits (55), Expect = 2.3
 Identities = 12/45 (26%), Positives = 18/45 (40%), Gaps = 3/45 (6%)

Query: 2   GRRKSKRKPPPKRKNIEPL---DIQFNCPFCNHEKSCEVKMDKGR 43
           G   +K+K    RK ++PL    + F+           V  D GR
Sbjct: 64  GACIAKKKTRIARKTLDPLYQQSLVFDESPQGKVLQVIVWGDYGR 108


>1juv_A DHFR, dihydrofolate reductase; complexed with NADPH,
          oxidoreductase; HET: NDP; 1.70A {Enterobacteria phage
          T4} SCOP: c.71.1.1
          Length = 193

 Score = 23.5 bits (51), Expect = 8.6
 Identities = 6/19 (31%), Positives = 9/19 (47%), Gaps = 2/19 (10%)

Query: 1  MGRR--KSKRKPPPKRKNI 17
          MG +  +S     P R +I
Sbjct: 51 MGAKTFQSLPTLLPGRSHI 69


  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
   0.321    0.135    0.431 

Gapped
Lambda     K      H
   0.267   0.0492    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,225,034
Number of extensions: 55009
Number of successful extensions: 245
Number of sequences better than 10.0: 1
Number of HSP's gapped: 244
Number of HSP's successfully gapped: 12
Length of query: 81
Length of database: 6,701,793
Length adjustment: 50
Effective length of query: 31
Effective length of database: 5,305,743
Effective search space: 164478033
Effective search space used: 164478033
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 (21.9 bits)
S2: 51 (24.0 bits)