RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy7584
         (67 letters)



>1twf_B DNA-directed RNA polymerase II 140 kDa polypeptid; transcription,
           mRNA, multiprotein complex; HET: UTP; 2.30A
           {Saccharomyces cerevisiae} SCOP: e.29.1.1 PDB: 1i3q_B
           1i6h_B 1k83_B* 1nik_B 1nt9_B 1pqv_B 1r5u_B 1r9s_B*
           1r9t_B* 1sfo_B* 1twa_B* 1twc_B* 1i50_B* 1twg_B* 1twh_B*
           1wcm_B 1y1v_B 1y1w_B 1y1y_B 1y77_B* ...
          Length = 1224

 Score =  107 bits (269), Expect = 1e-29
 Identities = 44/65 (67%), Positives = 51/65 (78%)

Query: 3   LEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRH 62
           L   T   SKRD ST LR++E GIVDQV++T N DG KF K+RVR+ +IPQIGDKFASRH
Sbjct: 925 LGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRH 984

Query: 63  GQKGT 67
           GQKGT
Sbjct: 985 GQKGT 989


>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription,
           multi-protein complex, DNA- binding, magnesium; 3.65A
           {Schizosaccharomyces pombe}
          Length = 1210

 Score =  107 bits (269), Expect = 2e-29
 Identities = 44/65 (67%), Positives = 53/65 (81%)

Query: 3   LEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFASRH 62
           L   T+  +KRD ST LR++E+GIVDQVM+T N +G KF K+R+RS RIPQIGDKFASRH
Sbjct: 914 LGQRTQLHAKRDVSTPLRSTESGIVDQVMVTTNQEGLKFVKVRMRSTRIPQIGDKFASRH 973

Query: 63  GQKGT 67
           GQKGT
Sbjct: 974 GQKGT 978


>4ayb_B DNA-directed RNA polymerase; transferase, multi-subunit,
           transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_B
           2y0s_B 2waq_B 4b1o_B 4b1p_R 2pmz_B 3hkz_B
          Length = 1131

 Score =  105 bits (263), Expect = 8e-29
 Identities = 34/67 (50%), Positives = 43/67 (64%)

Query: 1   MHLEGTTKRFSKRDGSTFLRNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKFAS 60
              +  +   +KRD S   R+ E GIVD V++T   +G K  K+RVR +RIP IGDKFAS
Sbjct: 824 QEFKELSPEQAKRDTSIVTRHGEMGIVDLVLITETAEGNKLVKVRVRDLRIPSIGDKFAS 883

Query: 61  RHGQKGT 67
           RHGQKG 
Sbjct: 884 RHGQKGV 890


>2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme,
           streptolydigin, antibiotic, transcription regulation;
           HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1
           PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C*
           2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3aoh_C* 3aoi_C*
           3dxj_C* 3eql_C* 1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C ...
          Length = 1119

 Score = 30.3 bits (69), Expect = 0.028
 Identities = 21/62 (33%), Positives = 28/62 (45%), Gaps = 8/62 (12%)

Query: 13  RDGSTFLRNSETGIV-DQVMLTLNVDGY-------KFCKIRVRSVRIPQIGDKFASRHGQ 64
           +D S  +   E GIV   V L     G        +  ++ V   R  Q+GDK A+RHG 
Sbjct: 786 KDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQKRKLQVGDKLANRHGN 845

Query: 65  KG 66
           KG
Sbjct: 846 KG 847


>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase,
            nucleotidyltransferase, transcription, transferase;
            11.20A {Escherichia coli} PDB: 3iyd_C*
          Length = 1342

 Score = 28.1 bits (63), Expect = 0.16
 Identities = 13/28 (46%), Positives = 15/28 (53%)

Query: 40   KFCKIRVRSVRIPQIGDKFASRHGQKGT 67
            K  K+ +   R  Q GDK A RHG KG 
Sbjct: 1048 KIVKVYLAVKRRIQPGDKMAGRHGNKGV 1075


>2izv_A Suppressor of cytokine signaling 4; signal transduction
          inhibitor, growth regulation, signal transduction, SH2
          domain, nuclear protein; 2.55A {Homo sapiens} SCOP:
          a.271.1.1 d.93.1.1
          Length = 187

 Score = 25.2 bits (55), Expect = 1.7
 Identities = 12/49 (24%), Positives = 16/49 (32%), Gaps = 9/49 (18%)

Query: 11 SKRDGSTFL-RNSETGIVDQVMLTLNVDGYKFCKIRVRSVRIPQIGDKF 58
           K +G TFL R+S         ++           R    RI Q    F
Sbjct: 52 GKPEG-TFLLRDSAQEDYLFS-VSFRRYS------RSLHARIEQWNHNF 92


  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    0.137    0.398 

Gapped
Lambda     K      H
   0.267   0.0620    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 955,352
Number of extensions: 42773
Number of successful extensions: 68
Number of sequences better than 10.0: 1
Number of HSP's gapped: 68
Number of HSP's successfully gapped: 6
Length of query: 67
Length of database: 6,701,793
Length adjustment: 38
Effective length of query: 29
Effective length of database: 5,640,795
Effective search space: 163583055
Effective search space used: 163583055
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 (23.7 bits)