RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780481|ref|YP_003064894.1| 50S ribosomal protein L34
[Candidatus Liberibacter asiaticus str. psy62]
         (44 letters)



>3i1n_2 50S ribosomal protein L34; ribosome structure, protein-RNA
          complex, acetylation, ribonucleoprotein, ribosomal
          protein, RNA-binding, rRNA- binding, methylation; 3.19A
          {Escherichia coli k-12} PDB: 1vs8_2 2aw4_2 2awb_2
          1vs6_2 2i2v_2 2j28_2 2i2t_2* 2qao_2* 2qba_2* 2qbc_2*
          2qbe_2 2qbg_2 2qbi_2* 2qbk_2* 2qov_2 2qox_2 2qoz_2*
          2qp1_2* 2rdo_2 2vhm_2 ... (2:)
          Length = 46

 Score = 42.3 bits (100), Expect = 3e-05
 Identities = 24/44 (54%), Positives = 33/44 (75%)

Query: 1  MKRTYNPSNIVRKRRCGFLARMSTRSGIRILNRRRSKGRKRLSA 44
          MKRT+ PS + R R  GF ARM+T++G ++L RRR+KGR RL+ 
Sbjct: 1  MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTV 44


>2j01_7 50S ribosomal protein L34; ribosome, tRNA, paromomycin,
          mRNA, translation; 2.8A {Thermus thermophilus} (7:)
          Length = 49

 Score = 41.5 bits (98), Expect = 4e-05
 Identities = 22/44 (50%), Positives = 28/44 (63%)

Query: 1  MKRTYNPSNIVRKRRCGFLARMSTRSGIRILNRRRSKGRKRLSA 44
          MKRT+ P+   R +  GF ARM T  G ++L RRR KGR RL+ 
Sbjct: 1  MKRTWQPNRRKRAKTHGFRARMRTPGGRKVLKRRRQKGRWRLTP 44


>3bbo_4 Ribosomal protein L34; large ribosomal subunit, spinach
           chloroplast ribosome, ribonucleoprotein particle,
           macromolecular complex; 9.40A {Spinacea oleracea} (4:)
          Length = 152

 Score = 35.8 bits (82), Expect = 0.002
 Identities = 20/44 (45%), Positives = 23/44 (52%), Gaps = 1/44 (2%)

Query: 1   MKRTYNP-SNIVRKRRCGFLARMSTRSGIRILNRRRSKGRKRLS 43
           +  T    S     R  GF  RMST SG  +L RRR+KGRK L 
Sbjct: 96  LCLTKRSRSRKSLARTHGFRLRMSTTSGRALLKRRRAKGRKILC 139


>2ftc_Q L34MT, MRP-L34, 39S ribosomal protein L34, mitochondrial;
          mitochondrial ribosome, large ribosomal subunit,
          ribosomal RNA; 12.10A {Bos taurus} (Q:)
          Length = 38

 Score = 31.9 bits (73), Expect = 0.032
 Identities = 19/38 (50%), Positives = 28/38 (73%)

Query: 5  YNPSNIVRKRRCGFLARMSTRSGIRILNRRRSKGRKRL 42
          Y PSNI RK + G++ R+ST +G++++ RR  KGRK L
Sbjct: 1  YQPSNIKRKNKHGWVRRLSTPAGVQVILRRMLKGRKSL 38


>3hid_A Adenylosuccinate synthetase; niaid structural genomics,
           virulence associated factor, PURA, purine ribonucleotide
           biosynthesis, cytoplasm; 1.60A {Yersinia pestis CO92}
           PDB: 1kjx_A* 1kkb_A* 1kkf_A* 1ade_A 1adi_A 1cg0_A*
           1ch8_A* 1cib_A* 1gim_A* 1gin_A* 1hon_A* 1hoo_A* 1hop_A*
           1juy_A* 1ksz_A* 1nht_A* 1qf4_A* 1qf5_A* 1son_A* 1soo_A*
           ... (A:1-71,A:217-432)
          Length = 287

 Score = 25.2 bits (55), Expect = 3.4
 Identities = 7/19 (36%), Positives = 12/19 (63%)

Query: 12  RKRRCGFLARMSTRSGIRI 30
           R RR G+L  ++ R  ++I
Sbjct: 159 RSRRTGWLDIVAVRRAVQI 177


>2fi9_A Outer membrane protein; PSI, protein structure initiative,
           midwest center for structural genomics, MCSG; 1.80A
           {Bartonella henselae str} (A:)
          Length = 128

 Score = 24.4 bits (53), Expect = 6.0
 Identities = 7/29 (24%), Positives = 13/29 (44%), Gaps = 1/29 (3%)

Query: 12  RKRRCGFLARMSTRSGIRILNRRRSKGRK 40
            ++R      MST + +R  N   ++ R 
Sbjct: 92  WEKRISSDT-MSTGAAVRTFNVLLAEDRA 119


>1p9b_A Adenylosuccinate synthetase; ligase; HET: IMO GDP; 2.00A
           {Plasmodium falciparum} (A:)
          Length = 442

 Score = 24.1 bits (52), Expect = 6.5
 Identities = 7/19 (36%), Positives = 8/19 (42%)

Query: 12  RKRRCGFLARMSTRSGIRI 30
           R RRCG+L          I
Sbjct: 311 RPRRCGWLDIPMLLYVKCI 329


>2gm2_A Conserved hypothetical protein; MTH938-like fold, structural
           genomics, PSI, protein structure initiative; NMR
           {Xanthomonas campestris PV} (A:)
          Length = 132

 Score = 24.0 bits (52), Expect = 7.5
 Identities = 9/29 (31%), Positives = 13/29 (44%), Gaps = 1/29 (3%)

Query: 12  RKRRCGFLARMSTRSGIRILNRRRSKGRK 40
             R  G  A M+  +  R  N   S+GR+
Sbjct: 88  LTRGIGLEA-MTNAAAARTYNVLASEGRR 115


>2ab1_A Hypothetical protein; HS.95870, DUF498, structural genomics,
           protein structure initiative, PSI, center for eukaryotic
           structural genomics, CESG; 2.59A {Homo sapiens} (A:)
          Length = 122

 Score = 23.6 bits (51), Expect = 9.6
 Identities = 4/30 (13%), Positives = 12/30 (40%), Gaps = 1/30 (3%)

Query: 11  VRKRRCGFLARMSTRSGIRILNRRRSKGRK 40
           ++K        + T   ++  N   ++G +
Sbjct: 85  LKKHGIDVRV-LQTEQAVKEYNALVAQGVR 113


  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
   0.329    0.136    0.388 

Gapped
Lambda     K      H
   0.267   0.0733    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 332,675
Number of extensions: 9577
Number of successful extensions: 24
Number of sequences better than 10.0: 1
Number of HSP's gapped: 23
Number of HSP's successfully gapped: 9
Length of query: 44
Length of database: 4,956,049
Length adjustment: 16
Effective length of query: 28
Effective length of database: 4,415,169
Effective search space: 123624732
Effective search space used: 123624732
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 50 (23.0 bits)