RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy13055
         (97 letters)



>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 = 33.9 bits (77), Expect = 0.004
 Identities = 13/89 (14%), Positives = 26/89 (29%), Gaps = 31/89 (34%)

Query: 17  DEFIRRFLRGT-WHNLFLS-----EIIIKRQHNIIRI----GGIVERAIHPR-------- 58
            EF   +L G   H L        +  + +   +I+       + +R    +        
Sbjct: 89  TEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRA 148

Query: 59  ------KIYFLIG-------YTEELLSFW 74
                 ++  + G       Y EEL   +
Sbjct: 149 VGEGNAQLVAIFGGQGNTDDYFEELRDLY 177


>2vqe_C 30S ribosomal protein S3; tRNA-binding, rRNA-binding,
          metal-binding, zinc-finger, translation; HET: TM2 PAR;
          2.5A {Thermus thermophilus} PDB: 1gix_F* 1hnw_C*
          1hnx_C* 1hnz_C* 1hr0_C 1ibk_C* 1ibl_C* 1ibm_C 1j5e_C
          1jgo_F* 1jgp_F* 1jgq_F* 1ml5_F* 1n32_C* 1n33_C* 1n34_C
          1n36_C 1xmo_C* 1xmq_C* 1xnq_C* ...
          Length = 239

 Score = 32.2 bits (74), Expect = 0.013
 Identities = 12/55 (21%), Positives = 24/55 (43%), Gaps = 6/55 (10%)

Query: 11 SETAVEDEFIRRFLRGTWHNLFLSEIIIKRQHNIIRIGGIVERAIHPRKIYFLIG 65
              +ED+ IR  L    ++  L+ + I+R  + + +       +H  K   +IG
Sbjct: 30 RHLLLEDQRIRGLLEKELYSAGLARVDIERAADNVAV------TVHVAKPGVVIG 78


>3i1m_C 30S ribosomal protein S3; ribosome structure, protein-RNA
          complex, ribonucleoprotein, ribosomal protein,
          RNA-binding, rRNA-binding, antibiotic resistance; 3.19A
          {Escherichia coli k-12} PDB: 1vs7_C* 3e1a_O 3e1c_O
          1vs5_C 3i1o_C 3i1q_C 3i1s_C 3i1z_C 3i21_C 3izv_G*
          3izw_G* 3kc4_C 3or9_C 3ora_C 3sfs_C* 3uoq_C* 2qal_C*
          1p6g_C 1p87_C 2aw7_C ...
          Length = 233

 Score = 31.8 bits (73), Expect = 0.017
 Identities = 13/55 (23%), Positives = 24/55 (43%), Gaps = 6/55 (10%)

Query: 11 SETAVEDEFIRRFLRGTWHNLFLSEIIIKRQHNIIRIGGIVERAIHPRKIYFLIG 65
          ++    D  +R++L        +S I+I+R    IR+       IH  +   +IG
Sbjct: 30 ADNLDSDFKVRQYLTKELAKASVSRIVIERPAKSIRV------TIHTARPGIVIG 78


>3r8n_C 30S ribosomal protein S3; protein biosynthesis, RNA, tRNA,
          transfer RNA, 16S ribosomal subunit, RRF; 3.00A
          {Escherichia coli} PDB: 2gyb_C 2gy9_C* 2ykr_C 3fih_C*
          2wwl_C 3oar_C 3oaq_C 3ofb_C 3ofa_C 3ofp_C 3ofx_C 3ofy_C
          3ofo_C 3r8o_C 4a2i_C
          Length = 206

 Score = 31.7 bits (73), Expect = 0.017
 Identities = 9/37 (24%), Positives = 18/37 (48%)

Query: 11 SETAVEDEFIRRFLRGTWHNLFLSEIIIKRQHNIIRI 47
          ++    D  +R++L        +S I+I+R    IR+
Sbjct: 29 ADNLDSDFKVRQYLTKELAKASVSRIVIERPAKSIRV 65


>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 = 29.4 bits (65), Expect = 0.17
 Identities = 12/94 (12%), Positives = 21/94 (22%), Gaps = 24/94 (25%)

Query: 10  PSETAVEDEFIRRFLRGTWHN---LFLSEI----IIK------------RQHNIIRIGGI 50
                     +RR L+   +    L L  +                   R   +      
Sbjct: 224 KLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLS- 282

Query: 51  VERAIHPRKIYFLIGYTE----ELLSFWLQCPVK 80
                H    +  +  T      LL  +L C  +
Sbjct: 283 AATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQ 316



 Score = 24.4 bits (52), Expect = 8.8
 Identities = 17/110 (15%), Positives = 33/110 (30%), Gaps = 50/110 (45%)

Query: 15  VEDEFIRRFL------RGTW--HNLFLSEIIIKRQ-----HNIIRIGGIVERAIHPRK-- 59
           V ++  +  L        T    +++L E+ +K +     H  I     V+    P+   
Sbjct: 407 VVNKLHKYSLVEKQPKESTISIPSIYL-ELKVKLENEYALHRSI-----VDHYNIPKTFD 460

Query: 60  ------------IYFLIGY-------TEELLSF--------WLQCPVKLE 82
                        Y  IG+        E +  F        +L+   K+ 
Sbjct: 461 SDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLE--QKIR 508


>3bbn_C Ribosomal protein S3; small ribosomal subunit, spinach
          chloroplast ribosome, ribonucleoprotein particle,
          macromolecular complex; 9.40A {Spinacea oleracea}
          Length = 218

 Score = 26.4 bits (59), Expect = 1.4
 Identities = 8/45 (17%), Positives = 21/45 (46%), Gaps = 8/45 (17%)

Query: 11 SETAVEDEFIRRFLRGTWHNLF--------LSEIIIKRQHNIIRI 47
          +E   ED+ IR  ++               ++ I I+++ ++I++
Sbjct: 30 AEGLQEDQKIRDCIKNYVQKNTKTSSGVEGIARIEIQKRIDLIQV 74


>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA
           helicase, acetyltransferase, GCN5 acetyltransferase;
           HET: ACO ADP; 2.35A {Escherichia coli K12}
          Length = 671

 Score = 25.4 bits (55), Expect = 3.3
 Identities = 9/20 (45%), Positives = 12/20 (60%), Gaps = 3/20 (15%)

Query: 65  GYTEELLSFWLQC---PVKL 81
           GYT EL  FW +C    V++
Sbjct: 495 GYTGELWRFWQRCGFVLVRM 514


  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
   0.328    0.146    0.445 

Gapped
Lambda     K      H
   0.267   0.0820    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,605,787
Number of extensions: 88485
Number of successful extensions: 179
Number of sequences better than 10.0: 1
Number of HSP's gapped: 178
Number of HSP's successfully gapped: 19
Length of query: 97
Length of database: 6,701,793
Length adjustment: 63
Effective length of query: 34
Effective length of database: 4,942,770
Effective search space: 168054180
Effective search space used: 168054180
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 (21.7 bits)
S2: 51 (23.3 bits)