RPS-BLAST 2.2.22 [Sep-27-2009]

Database: pdb70 
           24,244 sequences; 5,693,230 total letters

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

Query= gi|254780584|ref|YP_003064997.1| 50S ribosomal protein L28
[Candidatus Liberibacter asiaticus str. psy62]
         (97 letters)



>3bbo_Y Ribosomal protein L28; large ribosomal subunit, spinach chloroplast
           ribosome, ribonucleoprotein particle, macromolecular
           complex; 9.40A {Nicotiana tabacum}
          Length = 151

 Score = 80.3 bits (198), Expect = 9e-17
 Identities = 24/80 (30%), Positives = 42/80 (52%), Gaps = 2/80 (2%)

Query: 1   MSRVCELTKKTVMSGNKVSHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVE 60
             R+C  T K     NKVSH+N+KT++    NL    +  +  ++  +LR+S  A++++E
Sbjct: 74  ARRICPFTGKKSNRANKVSHSNHKTKKLQFVNLQYKRIWWEAGKRYVKLRLSTKAIKTIE 133

Query: 61  RQGGLDRFLSNSKKENLSAR 80
           +  GLD         +LS +
Sbjct: 134 K-NGLDAVA-KKAGIDLSKK 151


>3ofq_X 50S ribosomal protein L28; protein biosynthesis, ribosomes, RNA,
          tRNA, transfer, antibi EXIT, peptidyl, ribosomal
          subunit, large; 3.10A {Escherichia coli} PDB: 2i2v_X
          2wwq_0* 3fik_X 2i2t_X 3ofr_X* 3i1n_X 1vt2_X* 2qao_Z*
          2qba_Z* 2qbc_Z* 2qbe_Z 2qbg_Z 2qbi_Z* 2qbk_Z* 2qov_Z
          2qox_Z 2qoz_Z* 2qp1_Z* 2z4l_Z* 2z4n_Z* ...
          Length = 77

 Score = 77.3 bits (191), Expect = 7e-16
 Identities = 27/72 (37%), Positives = 43/72 (59%), Gaps = 1/72 (1%)

Query: 2  SRVCELTKKTVMSGNKVSHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVER 61
          SRVC++T K  ++GN  SHA N T+RRFLPNL       +  ++   LR+S   +R +++
Sbjct: 1  SRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVIDK 60

Query: 62 QGGLDRFLSNSK 73
            G+D  L+  +
Sbjct: 61 -KGIDTVLAELR 71


>3i1n_X 50S ribosomal protein L28; ribosome structure, protein-RNA
          complex, acetylation, ribonucleoprotein, ribosomal
          protein, RNA-binding, rRNA- binding, methylation; 3.19A
          {Escherichia coli k-12} PDB: 2qao_Z* 2qba_Z* 2qbc_Z*
          2qbe_Z 2qbg_Z 2qbi_Z* 2qbk_Z* 2qov_Z 2qox_Z 2qoz_Z*
          2qp1_Z* 2z4l_Z* 2z4n_Z* 3df2_Z 3df4_Z 2qam_Z 3i1p_X
          3i1r_X 3i1t_X 3i20_X ...
          Length = 78

 Score = 77.0 bits (190), Expect = 8e-16
 Identities = 28/76 (36%), Positives = 44/76 (57%), Gaps = 1/76 (1%)

Query: 1  MSRVCELTKKTVMSGNKVSHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVE 60
          MSRVC++T K  ++GN  SHA N T+RRFLPNL       +  ++   LR+S   +R ++
Sbjct: 1  MSRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVID 60

Query: 61 RQGGLDRFLSNSKKEN 76
          +  G+D  L+  +   
Sbjct: 61 K-KGIDTVLAELRARG 75


>2jz6_A 50S ribosomal protein L28; structure, NESG, ribonucleoprotein,
          structural genomics, PSI-2, protein structure
          initiative; NMR {Thermotoga maritima MSB8} SCOP:
          d.325.1.1
          Length = 77

 Score = 70.4 bits (173), Expect = 8e-14
 Identities = 20/74 (27%), Positives = 39/74 (52%), Gaps = 5/74 (6%)

Query: 1  MSRVCELTKKTVMSGNKVSHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVE 60
          M++ CE+  K   SGN VSH++ K+ R F PNL ++ ++        ++R+    L+S  
Sbjct: 6  MAKRCEVCGKAPRSGNTVSHSDKKSERWFRPNLQKVRVVLPD-GTIKRMRVCTSCLKS-- 62

Query: 61 RQGGLDRFLSNSKK 74
            G + +++    +
Sbjct: 63 --GKVKKYVGQVSE 74


>2jl6_1 50S ribosomal protein L28, 50S ribosomal protein L25;
          methylation, translation, paromomycin, tRNA-binding,
          tRNA, zinc, mRNA, ribosome, repressor, RNA-binding;
          3.45A {Thermus thermophilus} PDB: 2jl8_1
          Length = 89

 Score = 59.5 bits (144), Expect = 2e-10
 Identities = 15/74 (20%), Positives = 29/74 (39%), Gaps = 15/74 (20%)

Query: 1  MSRVCELTKKTVMSGNKVSH-------------ANNKTRRRFLPNLCRITLISDIMEQKY 47
          MS+VCE++ K  +  N +                   ++RR  PNL ++ +      Q+ 
Sbjct: 1  MSKVCEISGKRPIVANSIQRRGKAKREGGVGKKTTGISKRRQYPNLQKVRVRVA--GQEI 58

Query: 48 QLRISKCALRSVER 61
            R++   +  V  
Sbjct: 59 TFRVAASHIPKVYE 72


>2j01_1 50S ribosomal protein L28; ribosome, tRNA, paromomycin, mRNA,
          translation; 2.8A {Thermus thermophilus} SCOP:
          d.325.1.1 PDB: 2j03_1 2v47_1 2v49_1 2wdi_1 2wdj_1
          2wdl_1 2wdn_1 2wh2_1 2wh4_1 3hux_1 3huz_1 3f1f_1 1vsp_V
          1vsa_V 3d5d_1 3d5b_1 3f1h_1 3fin_1
          Length = 98

 Score = 57.5 bits (139), Expect = 6e-10
 Identities = 19/104 (18%), Positives = 40/104 (38%), Gaps = 22/104 (21%)

Query: 1  MSRVCELTKKTVMSGNKVSH-------------ANNKTRRRFLPNLCRITLISDIMEQKY 47
          MS+VCE++ K  +  N +                   ++RR  PNL ++ +      Q+ 
Sbjct: 1  MSKVCEISGKRPIVANSIQRRGKAKREGGVGKKTTGISKRRQYPNLQKVRVRVA--GQEI 58

Query: 48 QLRISKCALRSVERQGGLDRFLSNSKKENLSA-RMRTLRSQILK 90
            R++   +  V         +  +K   L     + ++ ++LK
Sbjct: 59 TFRVAASHIPKV------YELVERAKGLKLEGLSPKEIKKELLK 96


>2zjr_U 50S ribosomal protein L28; ribosome, large ribosomal subunit,
          ribonucleoprotein, RNA-binding, rRNA-binding,
          tRNA-binding, methylation; 2.91A {Deinococcus
          radiodurans} SCOP: d.325.1.1 PDB: 2zjp_U 2zjq_U 3cf5_U*
          3dll_U*
          Length = 81

 Score = 54.8 bits (132), Expect = 4e-09
 Identities = 18/76 (23%), Positives = 28/76 (36%), Gaps = 15/76 (19%)

Query: 1  MSRVCELTKKTVMSGNKV-------------SHANNKTRRRFLPNLCRITLISDIMEQKY 47
          MSR C LT K  +  N V                   T+R    NL +  +  +   Q  
Sbjct: 1  MSRECYLTGKKNLVVNSVIRRGKARADGGVGRKTTGITKRVQRANLHKKAIREN--GQVK 58

Query: 48 QLRISKCALRSVERQG 63
           + +S  ALR++ +  
Sbjct: 59 TVWLSANALRTLSKGP 74


>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
           acyl-carrier-protein, beta-ketoacyl reductase,
           beta-ketoacyl synthase, dehydratase; 4.00A
           {Saccharomyces cerevisiae}
          Length = 2006

 Score = 27.6 bits (61), Expect = 0.80
 Identities = 19/101 (18%), Positives = 35/101 (34%), Gaps = 29/101 (28%)

Query: 7   LTKKTVMSG---NKVSHANNKTR--RRFLPNLCRIT------LISD----IMEQ--KYQL 49
           L K    SG   +++  +  K +   RFLP    +       L+      I +   K  +
Sbjct: 393 LRKAKAPSGLDQSRIPFSERKLKFSNRFLP----VASPFHSHLLVPASDLINKDLVKNNV 448

Query: 50  RISKCALR-SV-ERQGGLDRFLSNSKKENLSARMRTLRSQI 88
             +   ++  V +   G D  L      ++S R   +   I
Sbjct: 449 SFNAKDIQIPVYDTFDGSD--LRVL-SGSISER---IVDCI 483


>1u04_A Argonaute, hypothetical protein PF0537; RNAI, silencing, PIWI, PAZ,
           RISC, slicer, RNAse H, hydrolase/gene regulation
           complex; 2.25A {Pyrococcus furiosus dsm 3638} SCOP:
           b.34.14.1 c.55.3.10 PDB: 1z25_A 1z26_A
          Length = 771

 Score = 26.2 bits (57), Expect = 1.8
 Identities = 13/75 (17%), Positives = 29/75 (38%), Gaps = 2/75 (2%)

Query: 12  VMSGNKVSHANNKTRRRFL-PNLCRITLISDIMEQKYQLRISKCA-LRSVERQGGLDRFL 69
           +++        NK  + +L P L   T  ++ +E      I +   L   ER+  L+  L
Sbjct: 246 ILAKFASKIKKNKNYKIYLLPQLVVPTYNAEQLESDVAKEILEYTKLMPEERKELLENIL 305

Query: 70  SNSKKENLSARMRTL 84
           +    + +   +  +
Sbjct: 306 AEVDSDIIDKSLSEI 320


>1vh4_A SUFD protein; structural genomics, protein binding protein; 1.75A
          {Escherichia coli} SCOP: b.80.6.1 PDB: 2zu0_A*
          Length = 435

 Score = 24.6 bits (52), Expect = 5.2
 Identities = 8/30 (26%), Positives = 16/30 (53%)

Query: 40 SDIMEQKYQLRISKCALRSVERQGGLDRFL 69
          S+ ++Q + L  ++   RS + Q  L + L
Sbjct: 10 SNALQQWHHLFEAEGTKRSPQAQQHLQQLL 39


  Database: pdb70
    Posted date:  Jan 26, 2011 11:21 AM
  Number of letters in database: 5,693,230
  Number of sequences in database:  24,244
  
Lambda     K      H
   0.319    0.128    0.342 

Gapped
Lambda     K      H
   0.267   0.0730    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 699,669
Number of extensions: 26007
Number of successful extensions: 78
Number of sequences better than 10.0: 1
Number of HSP's gapped: 71
Number of HSP's successfully gapped: 13
Length of query: 97
Length of database: 5,693,230
Length adjustment: 63
Effective length of query: 34
Effective length of database: 4,165,858
Effective search space: 141639172
Effective search space used: 141639172
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: 50 (23.0 bits)