RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy9580
         (71 letters)



>3r8s_3 50S ribosomal protein L35; protein biosynthesis, RNA, tRNA,
          transfer RNA, 23S ribosomal subunit, ribosome recycling
          factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
          2awb_3 2aw4_3 2i2v_3 2j28_3 2i2t_3* 2qao_3* 2qba_3*
          2qbc_3* 2qbe_3 2qbg_3 2qbi_3* 2qbk_3* 2qov_3 2qox_3
          2qoz_3* 2qp1_3* 2rdo_3 2vhm_3 2vhn_3 2wwq_7* ...
          Length = 64

 Score = 66.5 bits (163), Expect = 6e-17
 Identities = 30/61 (49%), Positives = 34/61 (55%)

Query: 9  KIKTKSSAKKRFFIRTGGVIKRGQAFKRHILTKKSTKVKRKLRGLASVHKSNIASVRAMM 68
          KIKT   A KRF     G  K   A  RHILTKK+TK KR LR  A V K ++  V A +
Sbjct: 2  KIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIACL 61

Query: 69 P 69
          P
Sbjct: 62 P 62


>3v2d_8 50S ribosomal protein L35; ribosome associated inhibitor A, RAIA,
          protein Y, stress RES stationary phase, ribosome
          hibernation, ribosome; 2.70A {Thermus thermophilus}
          PDB: 1vsp_a 2hgj_7 2hgq_7 2hgu_7 1vsa_a 2j03_8 2jl6_8
          2jl8_8 2v47_8 2v49_8 2wdi_8 2wdj_8 2wdl_8 2wdn_8 2wh2_8
          2wh4_8 2wrj_8 2wrl_8 2wro_8 2wrr_8 ...
          Length = 65

 Score = 64.6 bits (158), Expect = 3e-16
 Identities = 18/61 (29%), Positives = 29/61 (47%)

Query: 9  KIKTKSSAKKRFFIRTGGVIKRGQAFKRHILTKKSTKVKRKLRGLASVHKSNIASVRAMM 68
          K+KT   AKKR  I   G +   +  KRH+  +KS K  R+      + K     ++ ++
Sbjct: 3  KMKTHKGAKKRVKITASGKVVAMKTGKRHLNWQKSGKEIRQKGRKFVLAKPEAERIKLLL 62

Query: 69 P 69
          P
Sbjct: 63 P 63


>3bbo_5 Ribosomal protein L35; large ribosomal subunit, spinach chloroplast
           ribosome, ribonucleoprotein particle, macromolecular
           complex; 9.40A {Spinacea oleracea}
          Length = 159

 Score = 65.9 bits (160), Expect = 9e-16
 Identities = 24/62 (38%), Positives = 37/62 (59%)

Query: 9   KIKTKSSAKKRFFIRTGGVIKRGQAFKRHILTKKSTKVKRKLRGLASVHKSNIASVRAMM 68
           K+KT  ++ KRF +   G I R +A K+H+L KK+TK K +L  L  V +S+  +V   +
Sbjct: 91  KMKTHKASAKRFRVTGKGKIVRRRAGKQHLLAKKNTKRKNRLSKLIQVDRSDYDNVIGAL 150

Query: 69  PN 70
           P 
Sbjct: 151 PY 152


>2zjr_3 50S ribosomal protein L35; ribosome, large ribosomal subunit,
          ribonucleoprotein, RNA-binding, rRNA-binding,
          tRNA-binding, methylation; 2.91A {Deinococcus
          radiodurans} SCOP: d.301.1.1 PDB: 2zjp_3* 1sm1_3 2zjq_3
          3cf5_3* 3dll_3* 3pio_3* 3pip_3* 1nwy_3* 1nwx_3* 1xbp_3*
          1nkw_3 1yl3_8 2b66_8 2b9n_8 2b9p_8 1pnu_3 1pny_3 1vor_5
          1vou_5 1vow_5 ...
          Length = 66

 Score = 40.7 bits (95), Expect = 9e-07
 Identities = 19/62 (30%), Positives = 29/62 (46%)

Query: 9  KIKTKSSAKKRFFIRTGGVIKRGQAFKRHILTKKSTKVKRKLRGLASVHKSNIASVRAMM 68
          K+KT   AK+R  I   G +   ++ KRH  T KS    R       + K+  A ++ M+
Sbjct: 3  KMKTHKMAKRRIKITGTGKVMAFKSGKRHQNTGKSGDEIRGKGKGFVLAKAEWARMKLML 62

Query: 69 PN 70
          P 
Sbjct: 63 PR 64


>3e59_A Pyoverdine biosynthesis protein PVCA; isonitrIle, paerucumarin,
           2-isocyano-6,7-dihydroxycoum transferase; HET: PGE;
           2.10A {Pseudomonas aeruginosa}
          Length = 330

 Score = 28.0 bits (62), Expect = 0.22
 Identities = 7/38 (18%), Positives = 18/38 (47%)

Query: 1   MKELFSVFKIKTKSSAKKRFFIRTGGVIKRGQAFKRHI 38
            ++  +     +K++ ++    R  GVI+R  A+   +
Sbjct: 207 YEDGLTPDYQGSKTALQRDAKERAYGVIQRSWAWGALL 244


>3ty4_A Probable homoisocitrate dehydrogenase; B-hydroxyacid oxidative
           decarboxylase, amino-acid biosynthes lysine
           biosynthesis; 1.55A {Schizosaccharomyces pombe} PDB:
           3ty3_A
          Length = 366

 Score = 25.3 bits (56), Expect = 1.9
 Identities = 8/29 (27%), Positives = 13/29 (44%)

Query: 33  AFKRHILTKKSTKVKRKLRGLASVHKSNI 61
           A  R  + +  T    K   +  +HKSN+
Sbjct: 175 AKSRQKIRESGTYSIHKKPLVTIIHKSNV 203


>1y9l_A Lipoprotein MXIM; cracked beta barrel, mixed alpha/beta, lipid
           binding protein; HET: UND; 1.50A {Shigella flexneri}
           PDB: 1y9t_A* 2jw1_A
          Length = 115

 Score = 23.5 bits (50), Expect = 6.2
 Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 1/54 (1%)

Query: 1   MKELFSVFKIKTKSSAKKRFFIRTGGVIKRGQAFKRHILTKKSTKVKRKL-RGL 53
           +KE+   F    K +  K F +   GV+ +G      IL +K  +VK KL RG+
Sbjct: 62  VKEVDGCFMDAQKIAIDKLFSMLKDGVVLKGNKINDTILIEKDGEVKLKLIRGI 115


>1x0l_A Homoisocitrate dehydrogenase; oxidoreductase, decarboxylating
           dehydrogenase, lysine biosyn; 1.85A {Thermus
           thermophilus} PDB: 3asj_A* 3ah3_A
          Length = 333

 Score = 23.6 bits (52), Expect = 7.2
 Identities = 5/15 (33%), Positives = 8/15 (53%)

Query: 47  KRKLRGLASVHKSNI 61
            R  + L   HK+N+
Sbjct: 159 GRPRKTLHIAHKANV 173


  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
   0.322    0.131    0.348 

Gapped
Lambda     K      H
   0.267   0.0769    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 950,993
Number of extensions: 42100
Number of successful extensions: 168
Number of sequences better than 10.0: 1
Number of HSP's gapped: 168
Number of HSP's successfully gapped: 11
Length of query: 71
Length of database: 6,701,793
Length adjustment: 41
Effective length of query: 30
Effective length of database: 5,557,032
Effective search space: 166710960
Effective search space used: 166710960
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: 40 (21.5 bits)
S2: 51 (23.3 bits)