RPS-BLAST 2.2.22 [Sep-27-2009]

Database: mmdb70 
           33,805 sequences; 4,956,049 total letters

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

Query= gi|254780250|ref|YP_003064663.1| 50S ribosomal protein L24
[Candidatus Liberibacter asiaticus str. psy62]
         (102 letters)



>2j01_Y 50S ribosomal protein L24; ribosome, tRNA, paromomycin,
          mRNA, translation; 2.8A {Thermus thermophilus} (Y:1-78)
          Length = 78

 Score = 76.6 bits (189), Expect = 1e-15
 Identities = 30/71 (42%), Positives = 42/71 (59%), Gaps = 1/71 (1%)

Query: 3  KIRTGDRVLVLAGKDKGKAGQVMGVVRKSGRAFVQGVNIVKRHQRQTP-NKEAGIISKEA 61
           ++ GD VLV +GK KG+ G+V  V+ K     V+GVNIVK+  R +P   + G I KEA
Sbjct: 6  HVKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIVEGVNIVKKAVRVSPKYPQGGFIEKEA 65

Query: 62 SIHLSNLSLID 72
           +H S +  I 
Sbjct: 66 PLHASKVRPIC 76


>2zjr_R 50S ribosomal protein L24; ribosome, large ribosomal
          subunit, ribonucleoprotein, RNA-binding, rRNA-binding,
          tRNA-binding, methylation; 2.91A {Deinococcus
          radiodurans} (R:1-87)
          Length = 87

 Score = 76.3 bits (188), Expect = 1e-15
 Identities = 22/73 (30%), Positives = 46/73 (63%), Gaps = 1/73 (1%)

Query: 3  KIRTGDRVLVLAGKDKGKAGQVMGVVRKSGRAFVQGVNIVKRHQRQTP-NKEAGIISKEA 61
            + GD V+VL+GK KG+ G+V+  + +  +  V+GVN++ ++ + +  N + G   +E 
Sbjct: 15 HFKKGDTVIVLSGKHKGQTGKVLLALPRDQKVVVEGVNVITKNVKPSMTNPQGGQEQREL 74

Query: 62 SIHLSNLSLIDKD 74
          ++H S ++L+D +
Sbjct: 75 ALHASKVALVDPE 87


>3bbo_W Ribosomal protein L24; large ribosomal subunit, spinach
           chloroplast ribosome, ribonucleoprotein particle,
           macromolecular complex; 9.40A {Spinacea oleracea}
           (W:1-140)
          Length = 140

 Score = 71.1 bits (174), Expect = 5e-14
 Identities = 22/73 (30%), Positives = 42/73 (57%), Gaps = 1/73 (1%)

Query: 3   KIRTGDRVLVLAGKDKGKAGQVMGVVRKSGRAFVQGVNIVKRHQRQTP-NKEAGIISKEA 61
            ++ GD V V++G +KGK G++  + + +    ++ +N   +H +     ++  II  EA
Sbjct: 68  HVKVGDTVKVISGGEKGKIGEISKIHKHNSTVIIKDLNFKTKHVKSKEEGEQGQIIKIEA 127

Query: 62  SIHLSNLSLIDKD 74
           +IH SN+ LI K+
Sbjct: 128 AIHSSNVMLILKE 140


>1vq8_T 50S ribosomal protein L24P; ribosome 50S, protein-protein
          complex, RNA-RNA complex, protein-RNA complex, peptidyl
          transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS;
          2.20A {Haloarcula marismortui} (T:20-120)
          Length = 101

 Score = 69.0 bits (169), Expect = 2e-13
 Identities = 17/87 (19%), Positives = 30/87 (34%), Gaps = 11/87 (12%)

Query: 3  KIRTGDRVLVLAGKDKGKAGQVMGVVRKSGRAFVQGVNIVKRHQRQTPNKEAGIISKEAS 62
          ++  GD V VL G   G+ G+V+ V        V+ V + K    +              
Sbjct: 23 RVNAGDTVEVLRGDFAGEEGEVINVDLDKAVIHVEDVTLEKTDGEE----------VPRP 72

Query: 63 IHLSNLSLID-KDGKQVRVGFSFVDGK 88
          +  SN+ + D     + R      +  
Sbjct: 73 LDTSNVRVTDLDLEDEKREARLESEDD 99


>3i1n_U 50S ribosomal protein L24; ribosome structure, protein-RNA
           complex, acetylation, ribonucleoprotein, ribosomal
           protein, RNA-binding, rRNA- binding, methylation; 3.19A
           {Escherichia coli k-12} PDB: 1vs8_U 1vs6_U 3i1p_U 3i1r_U
           3i1t_U 3i20_U 3i22_U 3e1b_O 3e1d_O 2qam_U* 1p85_S 1p86_S
           2awb_U 2aw4_U 2i2v_U 2i2t_U* 2qao_U* 2qba_U* 2qbc_U*
           2qbe_U ... (U:1-25,U:67-104)
          Length = 63

 Score = 51.9 bits (125), Expect = 3e-08
 Identities = 32/101 (31%), Positives = 41/101 (40%), Gaps = 41/101 (40%)

Query: 1   MEKIRTGDRVLVLAGKDKGKAGQVMGVVRKSGRAFVQGVNIVKRHQRQTPNKEAGIISKE 60
             KIR  D V+VL GKDKGK G+V                                    
Sbjct: 2   AAKIRRDDEVIVLTGKDKGKRGKV------------------------------------ 25

Query: 61  ASIHLSNLSLID-KDGKQVRVGFSFVDGKKIRIAKRSGEPI 100
               +SN+++ +   GK  RVGF F DGKK+R  K + E I
Sbjct: 26  ----VSNVAIFNAATGKADRVGFRFEDGKKVRFFKSNSETI 62


>3i1n_U 50S ribosomal protein L24; ribosome structure, protein-RNA
          complex, acetylation, ribonucleoprotein, ribosomal
          protein, RNA-binding, rRNA- binding, methylation; 3.19A
          {Escherichia coli k-12} PDB: 1vs8_U 1vs6_U 3i1p_U
          3i1r_U 3i1t_U 3i20_U 3i22_U 3e1b_O 3e1d_O 2qam_U*
          1p85_S 1p86_S 2awb_U 2aw4_U 2i2v_U 2i2t_U* 2qao_U*
          2qba_U* 2qbc_U* 2qbe_U ... (U:26-66)
          Length = 41

 Score = 48.4 bits (116), Expect = 3e-07
 Identities = 18/40 (45%), Positives = 27/40 (67%), Gaps = 2/40 (5%)

Query: 27 VVRKSGRAFVQGVNIVKRHQRQTP--NKEAGIISKEASIH 64
           V  SG+  V+G+N+VK+HQ+  P  N+  GI+ KEA+I 
Sbjct: 2  NVLSSGKVIVEGINLVKKHQKPVPALNQPGGIVEKEAAIQ 41


>1kwg_A Beta-galactosidase; TIM barrel, glycoside hydrolase family
           42, trimer; 1.60A {Thermus thermophilus} (A:1-394)
          Length = 394

 Score = 32.7 bits (72), Expect = 0.018
 Identities = 3/29 (10%), Positives = 7/29 (24%)

Query: 70  LIDKDGKQVRVGFSFVDGKKIRIAKRSGE 98
                 +Q+  G    D    +    +  
Sbjct: 354 QAPFAQEQMHAGLHRPDSAPDQGFFEAKR 382


>2ftc_N Mitochondrial ribosomal protein L24; mitochondrial
          ribosome, large ribosomal subunit, ribosomal RNA;
          12.10A {Bos taurus} PDB: 3iy9_N (N:1-31)
          Length = 31

 Score = 29.8 bits (67), Expect = 0.14
 Identities = 13/23 (56%), Positives = 17/23 (73%)

Query: 7  GDRVLVLAGKDKGKAGQVMGVVR 29
          GD V +L GKD GK G+V+ V+R
Sbjct: 1  GDTVEILEGKDAGKQGKVVQVIR 23


>1qd6_C Protein (outer membrane phospholipase (ompla));
           anti-parallel beta barrel dimer, membrane protein; HET:
           HDS; 2.10A {Escherichia coli} (C:)
          Length = 240

 Score = 25.8 bits (57), Expect = 2.1
 Identities = 9/20 (45%), Positives = 10/20 (50%), Gaps = 2/20 (10%)

Query: 69  SLIDKDGKQ--VRVGFSFVD 86
           SLID +  Q  V VG    D
Sbjct: 219 SLIDYNFNQTRVGVGVMLND 238


>1qd5_A Outer membrane phospholipase A; anti-parallel beta barrel,
           membrane protein; HET: BOG; 2.17A {Escherichia coli}
           (A:)
          Length = 275

 Score = 25.5 bits (56), Expect = 2.4
 Identities = 9/20 (45%), Positives = 10/20 (50%), Gaps = 2/20 (10%)

Query: 69  SLIDKDGKQ--VRVGFSFVD 86
           SLID +  Q  V VG    D
Sbjct: 254 SLIDYNFNQTRVGVGVMLND 273


>3gqh_A Preneck appendage protein; beta barrel, viral protein; 1.80A
           {Bacillus phage PHI29} PDB: 3gqk_A* (A:1-109)
          Length = 109

 Score = 25.5 bits (56), Expect = 2.7
 Identities = 7/28 (25%), Positives = 14/28 (50%), Gaps = 1/28 (3%)

Query: 74  DGKQVRVG-FSFVDGKKIRIAKRSGEPI 100
            G+ +  G    ++  KIR A++  + I
Sbjct: 10  GGQVIETGYLVTLEKGKIRKAEKGEKII 37


>3gqn_A Preneck appendage protein; coiled coil, beta helix, beta
           barrel, ATP binding, viral protein; HET: ATP; 2.15A
           {Bacillus phage PHI29} (A:605-772)
          Length = 168

 Score = 25.2 bits (55), Expect = 3.1
 Identities = 7/28 (25%), Positives = 14/28 (50%), Gaps = 1/28 (3%)

Query: 74  DGKQVRVG-FSFVDGKKIRIAKRSGEPI 100
            G+ +  G    ++  KIR A++  + I
Sbjct: 15  GGQVIETGYLVTLEKGKIRKAEKGEKII 42


>2wwb_L 60S ribosomal protein L26-A; ribosome, protein EXIT
          tunnel, cotranslational protein translocation, protein
          conducting channel; 6.48A {Triticum aestivum} PDB:
          2wwa_L 2ww9_L 1s1i_U (L:26-70,L:100-112)
          Length = 58

 Score = 24.7 bits (54), Expect = 5.0
 Identities = 10/21 (47%), Positives = 14/21 (66%)

Query: 4  IRTGDRVLVLAGKDKGKAGQV 24
          IR  D VLV+ G  KG+ G++
Sbjct: 25 IRRDDEVLVVRGSKKGQEGKI 45


>1xdn_A RNA editing ligase MP52; HET: MSE ATP; 1.20A {Trypanosoma
          brucei} (A:43-194)
          Length = 152

 Score = 24.5 bits (53), Expect = 5.1
 Identities = 8/21 (38%), Positives = 10/21 (47%), Gaps = 5/21 (23%)

Query: 82 FSFV-----DGKKIRIAKRSG 97
          F        D + +R AKRSG
Sbjct: 4  FGIYLINQGDHEVVRFAKRSG 24


>1ygy_A PGDH, D-3-phosphoglycerate dehydrogenase; oxidoreductase,
           serine biosynthesis, structural genomics, PSI, protein
           structure initiative; HET: TAR; 2.30A {Mycobacterium
           tuberculosis} (A:323-452)
          Length = 130

 Score = 23.9 bits (52), Expect = 7.3
 Identities = 13/69 (18%), Positives = 24/69 (34%), Gaps = 11/69 (15%)

Query: 34  AFVQGVNIVKRHQRQTPNKEAGIISKEASIHLSNLSLIDKDGKQVRV-GFSFVDGKKIRI 92
           A  +GV        ++PN  + +           +  +  DG  V V G  +      +I
Sbjct: 69  AAERGVTAEICKASESPNHRSVVD----------VRAVGADGSVVTVSGTLYGPQLSQKI 118

Query: 93  AKRSGEPID 101
            + +G   D
Sbjct: 119 VQINGRHFD 127


>1lkf_A LUKF, HLGB, leukocidin F subunit; leukotoxin, hemolysin,
          pore-forming toxin; 1.90A {Staphylococcus aureus} (A:)
          Length = 299

 Score = 23.7 bits (51), Expect = 8.5
 Identities = 5/55 (9%), Positives = 17/55 (30%), Gaps = 8/55 (14%)

Query: 48 QTPNKEAGIISKEASIHLSNLSLIDKDG--------KQVRVGFSFVDGKKIRIAK 94
          ++ +K+  ++    +I+   +     D          +  V  S      + +  
Sbjct: 44 KSYDKDTLVLKATGNINSGFVKPNPNDYDFSKLYWGAKYNVSISSQSNDSVNVVD 98


>1lpl_A Hypothetical 25.4 kDa protein F53F4.3 in chromosome V;
          structural genomics, CAP-Gly domain, cytoskeleton,
          tubulin, PSI; 1.77A {Caenorhabditis elegans} (A:)
          Length = 95

 Score = 23.6 bits (51), Expect = 9.0
 Identities = 8/27 (29%), Positives = 12/27 (44%)

Query: 1  MEKIRTGDRVLVLAGKDKGKAGQVMGV 27
           + I  G+R  V  G    + G+V  V
Sbjct: 9  AKNIMVGNRCEVTVGAQMARRGEVAYV 35


  Database: mmdb70
    Posted date:  Jun 20, 2010  3:12 AM
  Number of letters in database: 4,956,049
  Number of sequences in database:  33,805
  
Lambda     K      H
   0.317    0.137    0.373 

Gapped
Lambda     K      H
   0.267   0.0623    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 739,785
Number of extensions: 29773
Number of successful extensions: 175
Number of sequences better than 10.0: 1
Number of HSP's gapped: 169
Number of HSP's successfully gapped: 36
Length of query: 102
Length of database: 4,956,049
Length adjustment: 60
Effective length of query: 42
Effective length of database: 2,927,749
Effective search space: 122965458
Effective search space used: 122965458
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.3 bits)