RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= 048067
         (75 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 = 38.7 bits (91), Expect = 1e-05
 Identities = 17/41 (41%), Positives = 25/41 (60%)

Query: 34 KLYGLEIEKVRTLNKQGMKKRREGCLVTGPNYKKAYRTLKK 74
          KL+ +E+E V TL  +G  KR    +    ++KKAY TLK+
Sbjct: 49 KLFEVEVEVVNTLVVKGKVKRHGQRIGRRSDWKKAYVTLKE 89


>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 = 36.7 bits (86), Expect = 6e-05
 Identities = 13/41 (31%), Positives = 21/41 (51%)

Query: 34 KLYGLEIEKVRTLNKQGMKKRREGCLVTGPNYKKAYRTLKK 74
            + +++ KV TL+ +G KKR    L   P+ KKA   +  
Sbjct: 43 TAFKVKVVKVNTLHVRGKKKRLGRYLGKRPDRKKAIVQVAP 83


>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 = 36.0 bits (84), Expect = 1e-04
 Identities = 10/41 (24%), Positives = 20/41 (48%)

Query: 34 KLYGLEIEKVRTLNKQGMKKRREGCLVTGPNYKKAYRTLKK 74
          + +G+ +  + T+N  G +KR    +    + KKA   L +
Sbjct: 44 QAFGVRVIGISTMNVPGKRKRVGRFIGQRNDRKKAIVRLAE 84


>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
           vesicle, membrane, Ca structural protein; 7.94A {Bos
           taurus}
          Length = 190

 Score = 25.5 bits (55), Expect = 1.6
 Identities = 6/31 (19%), Positives = 15/31 (48%)

Query: 19  ENIKEIAFKTMHAASKLYGLEIEKVRTLNKQ 49
           +  +E A K +   ++    ++EK +  N+ 
Sbjct: 110 QEWREKAKKDLEEWNQRQSEQVEKNKINNRI 140


>1vq8_S 50S ribosomal protein L23P; ribosome 50S, protein-protein
          complex, RNA-RNA complex, PROT complex, peptidyl
          transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS;
          2.20A {Haloarcula marismortui} SCOP: d.12.1.1 PDB:
          1vq4_S* 1vq5_S* 1vq6_S* 1vq7_S* 1s72_S* 1vq9_S* 1vqk_S*
          1vql_S* 1vqm_S* 1vqn_S* 1vqo_S* 1vqp_S* 1yhq_S* 1yi2_S*
          1yij_S* 1yit_S* 1yj9_S* 1yjn_S* 1yjw_S* 2otj_S* ...
          Length = 85

 Score = 24.5 bits (54), Expect = 2.0
 Identities = 7/24 (29%), Positives = 13/24 (54%)

Query: 31 AASKLYGLEIEKVRTLNKQGMKKR 54
          A  + Y + +E+V T N    +K+
Sbjct: 41 AVEEQYDVTVEQVNTQNTMDGEKK 64


>4a17_R RPL23A, 60S ribosomal protein L21; eukaryotic ribosome, ribosome,
           eukaryotic initiation factor 60S, translation, large
           ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
           4a1a_R 4a1c_R 4a1e_R
          Length = 150

 Score = 24.8 bits (54), Expect = 2.8
 Identities = 9/24 (37%), Positives = 13/24 (54%)

Query: 31  AASKLYGLEIEKVRTLNKQGMKKR 54
           A  KLY +++  V TLN     K+
Sbjct: 106 AFEKLYNVKVRSVNTLNTITGNKK 129


>3tac_B Liprin-alpha-2; transferase-protein binding complex; 2.20A {Homo
           sapiens} PDB: 3tad_A
          Length = 334

 Score = 24.9 bits (53), Expect = 2.8
 Identities = 8/35 (22%), Positives = 16/35 (45%)

Query: 30  HAASKLYGLEIEKVRTLNKQGMKKRREGCLVTGPN 64
           H  S  YG+   K    +++ +++RRE       +
Sbjct: 211 HRTSLQYGIMCLKRLNYDRKELERRREASQHEIKD 245


>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB,
           proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR
           binding; 3.65A {Bacillus subtilis}
          Length = 468

 Score = 24.5 bits (54), Expect = 3.5
 Identities = 9/39 (23%), Positives = 12/39 (30%)

Query: 36  YGLEIEKVRTLNKQGMKKRREGCLVTGPNYKKAYRTLKK 74
            G+ + K R    Q +     G    G N      TL  
Sbjct: 127 LGVSLNKARQQVLQLLGSNETGSSAAGTNSNANTPTLDS 165


>3bbo_V Ribosomal protein L23; large ribosomal subunit, spinach chloroplast
           ribosome, ribonucleoprotein particle, macromolecular
           complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.1
          Length = 198

 Score = 24.2 bits (52), Expect = 4.7
 Identities = 8/24 (33%), Positives = 14/24 (58%)

Query: 31  AASKLYGLEIEKVRTLNKQGMKKR 54
           A S  +G+++ KV TL +    K+
Sbjct: 150 AISNFFGVKVRKVNTLIRPDGTKK 173


>1yco_A Branched-chain phosphotransacylase; structural genomics, protein
           structure initiative, PSI, nysgxrc; 2.40A {Enterococcus
           faecalis}
          Length = 279

 Score = 23.7 bits (52), Expect = 6.1
 Identities = 3/23 (13%), Positives = 7/23 (30%), Gaps = 2/23 (8%)

Query: 41  EKVRTLNKQGMKKRREGCLVTGP 63
              + +        ++   V GP
Sbjct: 168 VLAKEVTA--HFNDQQEATVFGP 188


>1zco_A 2-dehydro-3-deoxyphosphoheptonate aldolase;
          arabino-heptulosonate, synthase, shikimate, DAHP,
          DAH7P, DAH DAH7PS, lyase; HET: PEP; 2.25A {Pyrococcus
          furiosus}
          Length = 262

 Score = 23.7 bits (52), Expect = 6.7
 Identities = 10/26 (38%), Positives = 13/26 (50%)

Query: 15 PSSFENIKEIAFKTMHAASKLYGLEI 40
          P SF+   E A + M  A+  YGL  
Sbjct: 65 PYSFQGYGEKALRWMREAADEYGLVT 90


>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 = 23.8 bits (50), Expect = 7.5
 Identities = 8/28 (28%), Positives = 10/28 (35%), Gaps = 8/28 (28%)

Query: 48 KQGMKKRREGCLVTGPNYKKAYRTLKKP 75
          KQ +KK  +  L       K Y     P
Sbjct: 19 KQALKK-LQASL-------KLYADDSAP 38



 Score = 23.8 bits (50), Expect = 7.7
 Identities = 7/15 (46%), Positives = 10/15 (66%), Gaps = 1/15 (6%)

Query: 22 KEIAFKTMHAASKLY 36
          K+ A K + A+ KLY
Sbjct: 19 KQ-ALKKLQASLKLY 32


  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
   0.320    0.135    0.386 

Gapped
Lambda     K      H
   0.267   0.0619    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,090,553
Number of extensions: 51370
Number of successful extensions: 122
Number of sequences better than 10.0: 1
Number of HSP's gapped: 122
Number of HSP's successfully gapped: 16
Length of query: 75
Length of database: 6,701,793
Length adjustment: 44
Effective length of query: 31
Effective length of database: 5,473,269
Effective search space: 169671339
Effective search space used: 169671339
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 (21.8 bits)
S2: 51 (23.7 bits)