RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy5946
         (63 letters)



>2ftc_D Mitochondrial ribosomal protein L4 isoform A, mitochondrial 39S
           ribosomal protein L3; mitochondrial ribosome, large
           ribosomal subunit, ribosomal R ribosome; 12.10A {Bos
           taurus} PDB: 3iy9_D
          Length = 175

 Score = 46.1 bits (110), Expect = 3e-08
 Identities = 21/39 (53%), Positives = 25/39 (64%)

Query: 5   LGLTSTLSIKLMQDDLHIVKDLVLPVDDPKYLENLVEER 43
           LGL   L++KL QDDLHI+  L LP  DP+YL  L   R
Sbjct: 76  LGLKVALTVKLAQDDLHIMDSLELPTGDPQYLTELAHYR 114


>2zjr_C 50S ribosomal protein L4; ribosome, large ribosomal subunit,
           ribonucleoprotein, RNA-binding, rRNA-binding,
           tRNA-binding, methylation; 2.91A {Deinococcus
           radiodurans} SCOP: c.22.1.1 PDB: 1j5a_K* 1jzy_K* 1jzz_K*
           1k01_K* 1nkw_C 1sm1_C* 2zjp_C* 2zjq_C 1jzx_K 3cf5_C*
           3dll_C* 3pio_C* 3pip_C* 1nwy_C* 1nwx_C* 1xbp_C* 1pnu_C
           1pny_C 1vor_F 1vou_F ...
          Length = 205

 Score = 38.0 bits (89), Expect = 3e-05
 Identities = 6/39 (15%), Positives = 13/39 (33%)

Query: 5   LGLTSTLSIKLMQDDLHIVKDLVLPVDDPKYLENLVEER 43
           LGL   ++ +     L  V    +     K   +  ++ 
Sbjct: 102 LGLAMAIASRQEGGKLVAVDGFDIADAKTKNFISWAKQN 140


>1dmg_A Ribosomal protein L4; alpha-beta, ribosome, RNA, S10 operon, gene
           regulation; HET: CIT; 1.70A {Thermotoga maritima} SCOP:
           c.22.1.1
          Length = 225

 Score = 36.6 bits (85), Expect = 1e-04
 Identities = 12/39 (30%), Positives = 21/39 (53%)

Query: 5   LGLTSTLSIKLMQDDLHIVKDLVLPVDDPKYLENLVEER 43
           L L S LS+K  ++ L ++ DL L     K L+ +++  
Sbjct: 107 LALRSALSVKYRENKLLVLDDLKLERPKTKSLKEILQNL 145


>3v2d_F 50S ribosomal protein L4; ribosome associated inhibitor A, RAIA,
           protein Y, stress RES stationary phase, ribosome
           hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
           2hgq_F 2hgj_F 2hgu_F 2j03_F 2jl6_F 2jl8_F 2v47_F 2v49_F
           2wdi_F 2wdj_F 2wdl_F 2wdn_F 2wh2_F 2wh4_F 2wrj_F 2wrl_F
           2wro_F 2wrr_F 2x9s_F 2x9u_F ...
          Length = 210

 Score = 34.6 bits (80), Expect = 6e-04
 Identities = 6/39 (15%), Positives = 13/39 (33%)

Query: 5   LGLTSTLSIKLMQDDLHIVKDLVLPVDDPKYLENLVEER 43
            GL   ++ +  +  L +V+         K      +E 
Sbjct: 108 KGLAMAVADRAREGKLLLVEAFAGVNGKTKEFLAWAKEA 146


>3r8s_E 50S ribosomal protein L4; protein biosynthesis, RNA, tRNA, transfer
           RNA, 23S ribosomal subunit, ribosome recycling factor,
           RRF, ribosome; 3.00A {Escherichia coli} PDB: 1p85_C
           1p86_C 1vs8_E 1vs6_E 2aw4_E 2awb_E 1vt2_E 2i2v_E 2j28_E
           2i2t_E* 2qao_E* 2qba_E* 2qbc_E* 2qbe_E 2qbg_E 2qbi_E*
           2qbk_E* 2qov_E 2qox_E 2qoz_E* ...
          Length = 201

 Score = 31.4 bits (72), Expect = 0.007
 Identities = 10/38 (26%), Positives = 17/38 (44%)

Query: 5   LGLTSTLSIKLMQDDLHIVKDLVLPVDDPKYLENLVEE 42
             L S LS  + QD L +V+   +     K L   +++
Sbjct: 103 GALKSILSELVRQDRLIVVEKFSVEAPKTKLLAQKLKD 140


>3bbo_G Ribosomal protein L4; large ribosomal subunit, spinach chloroplast
           ribosome, ribonucleoprotein particle, macromolecular
           complex; 9.40A {Spinacea oleracea}
          Length = 293

 Score = 27.9 bits (62), Expect = 0.15
 Identities = 4/30 (13%), Positives = 11/30 (36%), Gaps = 2/30 (6%)

Query: 5   LGLTSTLSIKLMQDDLHIVKDLVLPVDDPK 34
           L L++ ++  +    +          + PK
Sbjct: 159 LALSTAIASAVGNSFVVEEFA--ENFEKPK 186


  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
   0.319    0.138    0.374 

Gapped
Lambda     K      H
   0.267   0.0744    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 902,909
Number of extensions: 38157
Number of successful extensions: 44
Number of sequences better than 10.0: 1
Number of HSP's gapped: 44
Number of HSP's successfully gapped: 6
Length of query: 63
Length of database: 6,701,793
Length adjustment: 34
Effective length of query: 29
Effective length of database: 5,752,479
Effective search space: 166821891
Effective search space used: 166821891
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: 51 (23.4 bits)