RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy11109
         (93 letters)



>2au3_A DNA primase; zinc ribbon, toprim, RNA polymerase, DNA replication,
           transf; HET: DNA; 2.00A {Aquifex aeolicus}
          Length = 407

 Score = 26.7 bits (60), Expect = 0.96
 Identities = 6/26 (23%), Positives = 9/26 (34%)

Query: 44  LRGGFRLLQTPRILKVLFDPHPEDPD 69
                 LL     +  ++ P   DPD
Sbjct: 305 KSAIPLLLSAGVEVYPVYLPEGYDPD 330


>4edg_A DNA primase; catalytic domain, nucleoside triphosphate, nucleoside
           polyph protein-ligand complex, transferase; HET: DNA
           ATP; 2.00A {Staphylococcus aureus} PDB: 4edk_A* 4edr_A*
           4edt_A* 4edv_A* 4ee1_A*
          Length = 329

 Score = 26.5 bits (59), Expect = 1.2
 Identities = 10/26 (38%), Positives = 13/26 (50%)

Query: 44  LRGGFRLLQTPRILKVLFDPHPEDPD 69
           L+ G  LLQ    + V+  P   DPD
Sbjct: 213 LKTGQHLLQQGLNVFVIQLPSGMDPD 238


>3htx_A HEN1; HEN1, small RNA methyltransferase, protein-RNA complex; HET:
           SAH; 3.10A {Arabidopsis thaliana}
          Length = 950

 Score = 25.6 bits (55), Expect = 3.0
 Identities = 7/47 (14%), Positives = 12/47 (25%), Gaps = 1/47 (2%)

Query: 36  FIEDVFPNLRGGFRLLQTP-RILKVLFDPHPEDPDYSPLPEDRPGGF 81
           F E V         ++ TP      +      +       E +   F
Sbjct: 817 FGEKVLSLFHPKLLIVSTPNYEFNTILQRSTPETQEENNSEPQLPKF 863


>1f0y_A HCDH, L-3-hydroxyacyl-COA dehydrogenase; abortive ternary complex,
           oxidoreductase; HET: CAA NAD; 1.80A {Homo sapiens} SCOP:
           a.100.1.3 c.2.1.6 PDB: 3rqs_A 1lsj_A* 1il0_A* 1lso_A*
           1m76_A* 1m75_A* 1f14_A 1f12_A 1f17_A* 3had_A* 2hdh_A*
           3hdh_A*
          Length = 302

 Score = 25.2 bits (56), Expect = 3.4
 Identities = 5/19 (26%), Positives = 9/19 (47%)

Query: 56  ILKVLFDPHPEDPDYSPLP 74
           I+    +   E+P + P P
Sbjct: 261 IVDGWHEMDAENPLHQPSP 279


>2qr4_A Peptidase M3B, oligoendopeptidase F; structural genomics, PSI-2,
           protein ST initiative; 2.50A {Enterococcus faecium}
          Length = 587

 Score = 25.0 bits (55), Expect = 4.1
 Identities = 7/24 (29%), Positives = 9/24 (37%)

Query: 69  DYSPLPEDRPGGFDWGERPNNPFI 92
           D       R G +  G    NP+I
Sbjct: 330 DVVENKGKRSGAYSSGSYDTNPYI 353


>3ce2_A Putative peptidase; structural genomics, unknown function, P
           protein structure initiative; 2.60A {Chlamydophila
           abortus}
          Length = 618

 Score = 25.0 bits (55), Expect = 4.6
 Identities = 5/24 (20%), Positives = 10/24 (41%)

Query: 69  DYSPLPEDRPGGFDWGERPNNPFI 92
           D       R G +  G   ++P++
Sbjct: 363 DKYENLNKRSGAYSSGCYDSHPYV 386


>4ej6_A Putative zinc-binding dehydrogenase; structural genomics, nysgrc,
           PSI-biology, NEW YORK structura genomics research
           consortium; 1.89A {Sinorhizobium meliloti} PDB: 4ejm_A*
          Length = 370

 Score = 24.5 bits (54), Expect = 6.0
 Identities = 6/36 (16%), Positives = 7/36 (19%), Gaps = 2/36 (5%)

Query: 36  FIEDVFP--NLRGGFRLLQTPRILKVLFDPHPEDPD 69
            I                     +KVL  P  E   
Sbjct: 333 MISRRISLDEAPDVISNPAAAGEVKVLVIPSAERVA 368


>1orq_C Potassium channel; voltage-dependent, KVAP, FAB complex, MEM
           protein; 3.20A {Aeropyrum pernix} SCOP: f.14.1.1 PDB:
           2a0l_A
          Length = 223

 Score = 24.5 bits (54), Expect = 6.7
 Identities = 5/39 (12%), Positives = 13/39 (33%), Gaps = 4/39 (10%)

Query: 22  WVDLLGIAVGHMYYFIEDVFPNLRGGFRLLQTPRILKVL 60
             ++  +        +  +      G  L +  R+L+ L
Sbjct: 74  LYEIPALVP----AGLLALIEGHLAGLGLFRLVRLLRFL 108


  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
   0.324    0.152    0.522 

Gapped
Lambda     K      H
   0.267   0.0774    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,716,954
Number of extensions: 97574
Number of successful extensions: 191
Number of sequences better than 10.0: 1
Number of HSP's gapped: 191
Number of HSP's successfully gapped: 25
Length of query: 93
Length of database: 6,701,793
Length adjustment: 60
Effective length of query: 33
Effective length of database: 5,026,533
Effective search space: 165875589
Effective search space used: 165875589
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (23.3 bits)