RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy16098
         (99 letters)



>3r8s_T 50S ribosomal protein L23; protein biosynthesis, RNA, tRNA,
          transfer RNA, 23S ribosomal subunit, ribosome recycling
          factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
          3fik_T 2wwq_T 3oat_T* 3oas_T* 3ofd_T 3ofc_T 3ofr_T*
          3ofz_T* 3og0_T 3ofq_T 3r8t_T 2j28_T 3e1b_M 3e1d_M
          3iy9_T 3i1n_T 1p85_R 1p86_R 1vs8_T 1vs6_T ...
          Length = 93

 Score = 25.6 bits (57), Expect = 2.0
 Identities = 11/29 (37%), Positives = 13/29 (44%), Gaps = 5/29 (17%)

Query: 17 AVPVLNEKGEVTMKKVKVHRYVSGKRPDY 45
           V  L  KG     KVK H    G+R D+
Sbjct: 57 VVNTLVVKG-----KVKRHGQRIGRRSDW 80


>2k2q_B Surfactin synthetase thioesterase subunit; A/B-hydrolase, NRPS,
           non-ribosomal peptide synthetase, type II thioesterase,
           antibiotic biosynthesis; NMR {Bacillus subtilis} PDB:
           2ron_A
          Length = 242

 Score = 25.9 bits (57), Expect = 2.6
 Identities = 8/50 (16%), Positives = 18/50 (36%)

Query: 33  KVHRYVSGKRPDYAQGSSDSEDDDDEVVNRKSEFTSIPHIPFEDPRLRRL 82
                +S  +P + Q    S   DD+ ++   +   +P    E+  +   
Sbjct: 106 PQAVIISAIQPPHIQRKKVSHLPDDQFLDHIIQLGGMPAELVENKEVMSF 155


>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 = 26.0 bits (56), Expect = 2.9
 Identities = 10/43 (23%), Positives = 15/43 (34%), Gaps = 4/43 (9%)

Query: 51 DSEDDDDEVVNRKSEFTSIPHIPFEDPRLRRL---TSRKQEDA 90
          D +D    +++ K E   I           RL      KQE+ 
Sbjct: 37 DVQDMPKSILS-KEEIDHIIMSKDAVSGTLRLFWTLLSKQEEM 78


>3bkp_A Cyclophilin; malaria, isomerase, structural GENO structural
           genomics consortium, SGC; 1.80A {Toxoplasma gondii}
          Length = 232

 Score = 25.1 bits (55), Expect = 4.1
 Identities = 10/25 (40%), Positives = 13/25 (52%)

Query: 73  PFEDPRLRRLTSRKQEDAEEDRRSR 97
           PFED   RRL        +E +R+R
Sbjct: 195 PFEDLVPRRLPDAPPAQKDERKRAR 219


>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
          photosynthetic reaction center, peripheral antenna;
          HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
          Length = 154

 Score = 24.9 bits (53), Expect = 4.1
 Identities = 7/26 (26%), Positives = 11/26 (42%), Gaps = 4/26 (15%)

Query: 23 EKGEVTMKKVK--VHRYVSGKRPDYA 46
          EK  +  KK++  +  Y     P  A
Sbjct: 18 EKQAL--KKLQASLKLYADDSAPALA 41


>4a82_A Cystic fibrosis transmembrane conductance regulat; CFTR, ION
           channel, transport protein, casse protein; 2.00A {Homo
           sapiens} PDB: 2onj_A* 2hyd_A
          Length = 578

 Score = 25.2 bits (56), Expect = 4.9
 Identities = 7/33 (21%), Positives = 17/33 (51%), Gaps = 1/33 (3%)

Query: 11  VQSTAGAVPVLNEKGEVTMKKVKVHRYVSGKRP 43
           +++  GA P+  ++G + +  V   +Y   + P
Sbjct: 324 IKNGVGAQPIEIKQGRIDIDHVS-FQYNDNEAP 355


>2wa0_A Melanoma-associated antigen 4; immune system, multiple anomalous
           dispersion, cancer/testis 1.4, melanoma antigen family A
           4, CT1.4, MAGE-41; 2.30A {Homo sapiens}
          Length = 240

 Score = 24.8 bits (54), Expect = 5.7
 Identities = 8/34 (23%), Positives = 15/34 (44%)

Query: 45  YAQGSSDSEDDDDEVVNRKSEFTSIPHIPFEDPR 78
             +G S SE++  E +     +    H  + +PR
Sbjct: 134 AMEGDSASEEEIWEELGVMGVYDGREHTVYGEPR 167


>2zjr_Q 50S ribosomal protein L23; ribosome, large ribosomal subunit,
          ribonucleoprotein, RNA-binding, rRNA-binding,
          tRNA-binding, methylation; 2.91A {Deinococcus
          radiodurans} SCOP: d.12.1.1 PDB: 1sm1_R* 2aar_R 2d3o_R
          2zjp_Q* 2zjq_Q 1nkw_R 3cf5_Q* 3dll_Q* 3pio_Q* 3pip_Q*
          1nwy_R* 1nwx_R* 1xbp_R* 1pnu_R 1pny_R 1vor_U 1vou_U
          1vow_U 1voy_U 1vp0_U
          Length = 95

 Score = 24.0 bits (53), Expect = 6.5
 Identities = 7/29 (24%), Positives = 10/29 (34%), Gaps = 5/29 (17%)

Query: 17 AVPVLNEKGEVTMKKVKVHRYVSGKRPDY 45
           +  +N  G     K K      G+R D 
Sbjct: 52 GISTMNVPG-----KRKRVGRFIGQRNDR 75


>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 = 24.6 bits (53), Expect = 7.3
 Identities = 8/36 (22%), Positives = 17/36 (47%), Gaps = 5/36 (13%)

Query: 62  RKSEFTS--IPHI--PFEDPRLRRLTSRKQEDAEED 93
           RK +F++  +P +  PF    L   +    +D  ++
Sbjct: 412 RKLKFSNRFLP-VASPFHSHLLVPASDLINKDLVKN 446


>3tve_T 50S ribosomal protein L23; RNA, ribosome, tRNA, translation,
          mRNA; 3.10A {Thermus thermophilus} PDB: 3pyr_T 3pyo_T
          3pyv_T 3pyt_T 3tvh_T 1n88_A 1vsa_R 1vsp_R 2hgj_W 2hgq_W
          2hgu_W 2j01_X 2j03_X 2jl6_X 2jl8_X 2v47_X 2v49_X 2wdi_X
          2wdj_X 2wdl_X ...
          Length = 92

 Score = 24.0 bits (53), Expect = 7.3
 Identities = 10/29 (34%), Positives = 12/29 (41%), Gaps = 5/29 (17%)

Query: 17 AVPVLNEKGEVTMKKVKVHRYVSGKRPDY 45
           V  L+ +G     K K      GKRPD 
Sbjct: 51 KVNTLHVRG-----KKKRLGRYLGKRPDR 74


  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
   0.309    0.127    0.350 

Gapped
Lambda     K      H
   0.267   0.0792    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,487,646
Number of extensions: 78141
Number of successful extensions: 160
Number of sequences better than 10.0: 1
Number of HSP's gapped: 160
Number of HSP's successfully gapped: 14
Length of query: 99
Length of database: 6,701,793
Length adjustment: 65
Effective length of query: 34
Effective length of database: 4,886,928
Effective search space: 166155552
Effective search space used: 166155552
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 51 (23.3 bits)