RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy2244
         (73 letters)



>1twf_L ABC10-alpha, DNA-directed RNA polymerases I, II, and III 7.7 K
          polypeptide; transcription, mRNA, multiprotein complex;
          HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP:
          g.41.9.2 PDB: 1i3q_L 1i6h_L 1k83_L* 1nik_L 1nt9_L
          1pqv_L 1r5u_L 1r9s_L* 1r9t_L* 1sfo_L* 1twa_L* 1twc_L*
          1i50_L* 1twg_L* 1twh_L* 1wcm_L 1y1v_L 1y1w_L 1y1y_L
          1y77_L* ...
          Length = 70

 Score = 65.7 bits (160), Expect = 2e-16
 Identities = 14/35 (40%), Positives = 23/35 (65%)

Query: 22 ECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILY 56
          EC  +  +   D +RC++CG+RI+ K RTKR + +
Sbjct: 33 ECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQF 67


>3h0g_L DNA-directed RNA polymerases I, II, and III subunit rpabc4;
          transcription, multi-protein complex, DNA- binding,
          magnesium; 3.65A {Schizosaccharomyces pombe}
          Length = 63

 Score = 64.9 bits (158), Expect = 3e-16
 Identities = 18/35 (51%), Positives = 26/35 (74%)

Query: 22 ECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILY 56
          +C   N I+ ++ IRCRECG+R+MYK RTKR + +
Sbjct: 26 DCGARNTIQAKEVIRCRECGHRVMYKMRTKRMVQF 60


>1s5p_A NAD-dependent deacetylase; protein deacetylase, SIR2 homologue,
           hydrolase; HET: ALY; 1.96A {Escherichia coli} SCOP:
           c.31.1.5
          Length = 235

 Score = 24.5 bits (54), Expect = 3.3
 Identities = 5/36 (13%), Positives = 13/36 (36%), Gaps = 5/36 (13%)

Query: 14  GDIEKYY-LECH----FENEIRPRDPIRCRECGYRI 44
           G++ K    +      +  ++ P D   C +    +
Sbjct: 109 GELLKVRCSQSGQVLDWTGDVTPEDKCHCCQFPAPL 144


>4f3l_A Mclock, circadian locomoter output cycles protein kaput; BHLH, PAS,
           circadian rhythm proteins, transcription-activato; 2.27A
           {Mus musculus}
          Length = 361

 Score = 24.5 bits (53), Expect = 4.3
 Identities = 13/74 (17%), Positives = 23/74 (31%), Gaps = 14/74 (18%)

Query: 1   MGYS-QVLVGKCLPGDIEKYYLECHFENEIRPRDPIRCRECGYRIMYKKRTKRCILYFKP 59
           +GY    ++G          Y   H        D     +C   +M   + K C   F  
Sbjct: 274 IGYLPFEVLGTSG-------YDYYH------VDDLENLAKCHEHLMQYGKGKSCYYRFLT 320

Query: 60  QTGGFPKLKTTVTV 73
           +   +  L+T   +
Sbjct: 321 KGQQWIWLQTHYYI 334


>4ayb_P DNA-directed RNA polymerase; transferase, multi-subunit,
          transcription; 3.20A {Sulfolobus shibatae} PDB: 2pmz_P
          2wb1_P 2y0s_P 3hkz_P 2waq_P 4b1o_P 4b1p_X
          Length = 48

 Score = 22.7 bits (48), Expect = 6.1
 Identities = 7/15 (46%), Positives = 11/15 (73%)

Query: 35 IRCRECGYRIMYKKR 49
          +RC  CGY+I++  R
Sbjct: 24 VRCPYCGYKIIFMVR 38


>2i4l_A Proline-tRNA ligase; alpha beta; 2.00A {Rhodopseudomonas palustris}
           PDB: 2i4m_A* 2i4n_A* 2i4o_A*
          Length = 458

 Score = 23.8 bits (52), Expect = 6.8
 Identities = 15/56 (26%), Positives = 18/56 (32%), Gaps = 21/56 (37%)

Query: 25  FENEIRPRDPI-RCRE-----------------CGYRIMYK--KRT-KRCILYFKP 59
           F +E RPR  + R RE                   Y  M+    RT  R  L   P
Sbjct: 159 FRDEQRPRFGVMRGREFLMKDAYSFDVDEAGARKSYNKMFVAYLRTFARMGLKAIP 214


  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
   0.327    0.146    0.479 

Gapped
Lambda     K      H
   0.267   0.0579    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,158,441
Number of extensions: 54612
Number of successful extensions: 272
Number of sequences better than 10.0: 1
Number of HSP's gapped: 272
Number of HSP's successfully gapped: 14
Length of query: 73
Length of database: 6,701,793
Length adjustment: 43
Effective length of query: 30
Effective length of database: 5,501,190
Effective search space: 165035700
Effective search space used: 165035700
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 (21.6 bits)
S2: 51 (23.8 bits)