RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy17574
         (143 letters)



>3tuo_A DNA-binding protein SATB1; 1.70A {Homo sapiens}
          Length = 105

 Score =  128 bits (322), Expect = 1e-39
 Identities = 33/109 (30%), Positives = 55/109 (50%), Gaps = 7/109 (6%)

Query: 1   PGKSLPVHCVVEAVYSVHHWKSAKNSRKAILETDTYVITPTNTNFQDLVPVALQRLGYSK 60
            G  LPV CVVE   +   +   +       E   +V+   +  F  L+ +AL  LGYS 
Sbjct: 4   SGTMLPVFCVVEHYENAIEYDCKE-------EHAEFVLVRKDMLFNQLIEMALLSLGYSH 56

Query: 61  ENFYSAKGYVGIKNWKPISISKISENPATTVGDILGELTTVATLRIKIF 109
            +   AKG + +  W P+ +S +++ P  TV D+L ++  V TL+I++ 
Sbjct: 57  SSAAQAKGLIQVGKWNPVPLSYVTDAPDATVADMLQDVYHVVTLKIQLH 105


>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
           acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
           synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
          Length = 2006

 Score = 29.6 bits (66), Expect = 0.33
 Identities = 32/162 (19%), Positives = 61/162 (37%), Gaps = 35/162 (21%)

Query: 4   SLPVHCVVEAV-YSVHHWKSAKNSRKAILETDTYVITPTNTNFQDLVPVALQRLGYSKEN 62
           S P+  V++   Y V    +AK       E  +Y+   T  + Q LV         S E+
Sbjct: 237 SCPLIGVIQLAHYVV----TAKLLGFTPGELRSYLKGAT-GHSQGLVTAVAIAETDSWES 291

Query: 63  FYSA--KG-----YVGIKNWK-------PISISKISEN-------PATTVGDILGELTTV 101
           F+ +  K      ++G++ ++       P SI + S         P  ++ ++     T 
Sbjct: 292 FFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNL-----TQ 346

Query: 102 ATLRIKIFRTRPCILAEMKDKLLRLLLVQSQTQIIASGCPLD 143
             ++  + +T    L     K + + LV     ++ SG P  
Sbjct: 347 EQVQDYVNKTN-SHLPA--GKQVEISLVNGAKNLVVSGPPQS 385


>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
           programmed cell death; HET: DTP; 6.90A {Drosophila
           melanogaster} PDB: 3iz8_A*
          Length = 1221

 Score = 27.9 bits (61), Expect = 1.3
 Identities = 18/129 (13%), Positives = 38/129 (29%), Gaps = 17/129 (13%)

Query: 21  KSAKNSRKAIL---ETDTYVITPTNTNFQDLVPVALQRLGYSK-ENFYS---AKGYVGIK 73
           K  ++  K+IL   E D  +++    +    +   L        + F        Y    
Sbjct: 36  KDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINY---- 91

Query: 74  NWKPISISKISENPA---TTVGDILGELTTVATLRIKIFRTRPCILAEMKDKLLRLLLVQ 130
            +    I      P+       +    L     +  K   +R     +++  LL L   +
Sbjct: 92  KFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLEL---R 148

Query: 131 SQTQIIASG 139
               ++  G
Sbjct: 149 PAKNVLIDG 157


>3izc_R 60S ribosomal protein RPL18 (L18E); eukaryotic ribosome,homology
           modeling,de novo modeling,ribos proteins,novel ribosomal
           proteins; NMR {Saccharomyces cerevisiae} PDB: 3izs_R
           3o58_R 3o5h_R 3u5e_Q 3u5i_Q
          Length = 186

 Score = 25.4 bits (55), Expect = 7.8
 Identities = 18/115 (15%), Positives = 31/115 (26%), Gaps = 36/115 (31%)

Query: 17  VHHWKSAKNSRKAILETDTYVIT----------PTNTNFQDLVPVALQRLGYSKENFYSA 66
                     R A    + Y+             T+  F  +V   L+ L  SK      
Sbjct: 6   TSKQHKRSGHRTAPKSDNVYLKLLVKLYTFLARRTDAPFNKVV---LKALFLSK------ 56

Query: 67  KGYVGIKNWKPISISKIS---------ENPATTVGDILGE--LTTVATLRIKIFR 110
                  N  P+S+S+I+               VG +  +  +       +   R
Sbjct: 57  ------INRPPVSVSRIARALKQEGAANKTVVVVGTVTDDARIFEFPKTTVAALR 105


>2w5q_A Processed glycerol phosphate lipoteichoic acid synthase;
           transmembrane, cell WALL biogenesis/degradation, LTAS,
           membrane, secreted; 1.20A {Staphylococcus aureus} PDB:
           2w5s_A* 2w5t_A* 2w5r_A*
          Length = 424

 Score = 25.2 bits (55), Expect = 9.1
 Identities = 5/35 (14%), Positives = 12/35 (34%)

Query: 35  TYVITPTNTNFQDLVPVALQRLGYSKENFYSAKGY 69
           +      +  +Q L  +  Q+ GY  +  +     
Sbjct: 101 SAFSLKGDNTYQSLPAILDQKQGYKSDVMHGDYKT 135


>2nyu_A Putative ribosomal RNA methyltransferase 2; SAM, structural
           genomics, structural genomics consortium, SGC; HET: SAM;
           1.76A {Homo sapiens}
          Length = 196

 Score = 24.8 bits (55), Expect = 9.9
 Identities = 6/19 (31%), Positives = 8/19 (42%)

Query: 59  SKENFYSAKGYVGIKNWKP 77
           S E ++ A  Y G K    
Sbjct: 177 SSEVYFLATQYHGRKGTVK 195


  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
   0.318    0.134    0.394 

Gapped
Lambda     K      H
   0.267   0.0549    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,086,515
Number of extensions: 109697
Number of successful extensions: 174
Number of sequences better than 10.0: 1
Number of HSP's gapped: 171
Number of HSP's successfully gapped: 12
Length of query: 143
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 59
Effective length of database: 4,356,429
Effective search space: 257029311
Effective search space used: 257029311
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 (21.7 bits)
S2: 52 (24.2 bits)