RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

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

Query= gi|254780243|ref|YP_003064656.1| 50S ribosomal protein L30
[Candidatus Liberibacter asiaticus str. psy62]
         (64 letters)



>gnl|CDD|180163 PRK05611, rpmD, 50S ribosomal protein L30; Reviewed.
          Length = 59

 Score = 82.8 bits (206), Expect = 2e-17
 Identities = 26/58 (44%), Positives = 37/58 (63%)

Query: 7  MQKITVQQIGSPIRRPSVQRKVLIGLGLNKMNRCRVLDDTPSVRGMISTVHHLVRIVE 64
          M+ + +  + S I R   QR  L GLGL K+N    L+DTP++RGMI+ V HLV++ E
Sbjct: 1  MKTLKITLVKSLIGRKPKQRATLRGLGLRKINSTVELEDTPAIRGMINKVSHLVKVEE 58


>gnl|CDD|130375 TIGR01308, rpmD_bact, ribosomal protein L30, bacterial/organelle.
           This model describes bacterial (and organellar) 50S
          ribosomal protein L30. Homologous ribosomal proteins of
          the eukaryotic cytosol and of the archaea differ
          substantially in architecture, from bacterial L30 and
          also from each other, and are described by separate
          models.
          Length = 55

 Score = 63.9 bits (156), Expect = 8e-12
 Identities = 27/55 (49%), Positives = 36/55 (65%)

Query: 10 ITVQQIGSPIRRPSVQRKVLIGLGLNKMNRCRVLDDTPSVRGMISTVHHLVRIVE 64
          I V  + S I RP  QRK L  LGL K+ R  VL+D P++RGM++ V HLV++ E
Sbjct: 1  IKVTLVRSLIGRPKKQRKTLKALGLRKIGRQVVLEDNPAIRGMVNKVKHLVKVEE 55


>gnl|CDD|180369 PRK06049, rpl30p, 50S ribosomal protein L30P; Reviewed.
          Length = 154

 Score = 35.2 bits (82), Expect = 0.003
 Identities = 11/29 (37%), Positives = 19/29 (65%)

Query: 32 LGLNKMNRCRVLDDTPSVRGMISTVHHLV 60
          L L+++N C ++ +TPS +GM+  V   V
Sbjct: 25 LRLHRVNHCVLVPETPSYKGMLQKVKDYV 53


>gnl|CDD|130376 TIGR01309, L30P_arch, 50S ribosomal protein L30P, archaeal.  This
          model represents the archaeal ribosomal protein similar
          to longer (~ 250 residue) eukaryotic 60S ribosomal
          protein L7 and to the much shorter (~ 60 residue)
          bacterial 50S ribosomal protein L30. Protein naming
          follows the SwissProt designation as L30P, while the
          gene symbol rpmD follows TIGR usage.
          Length = 152

 Score = 29.7 bits (67), Expect = 0.17
 Identities = 9/25 (36%), Positives = 16/25 (64%)

Query: 32 LGLNKMNRCRVLDDTPSVRGMISTV 56
          L L+++N C +  +TP+  GM+  V
Sbjct: 23 LRLHRVNHCVLYPETPTYLGMLQKV 47


>gnl|CDD|132218 TIGR03174, cas_Csc3, CRISPR-associated protein Csc3.  CRISPR
          (Clustered Regularly Interspaced Short Palindromic
          Repeats) is a widespread family of prokaryotic direct
          repeats with spacers of unique sequence between
          consecutive repeats. This protein family is a
          CRISPR-associated (Cas) family strictly associated with
          the Cyano subtype of CRISPR/Cas locus, found in several
          species of Cyanobacteria and several archaeal species.
          This family is designated Csc3 for CRISPR/Cas Subtype
          Cyano protein 3, as it is often the third gene upstream
          of the core cas genes, cas3-cas4-cas1-cas2.
          Length = 953

 Score = 24.5 bits (53), Expect = 6.8
 Identities = 11/38 (28%), Positives = 21/38 (55%), Gaps = 1/38 (2%)

Query: 11 TVQQIGSPIRRPSVQRKVLI-GLGLNKMNRCRVLDDTP 47
           +QQ+  P+R    +R+++I G  L+  ++    DD P
Sbjct: 23 RLQQLDFPVRLNVKERRLVIAGFTLHDYHKHCHADDMP 60


>gnl|CDD|184920 PRK14956, PRK14956, DNA polymerase III subunits gamma and tau;
           Provisional.
          Length = 484

 Score = 24.1 bits (52), Expect = 7.5
 Identities = 13/45 (28%), Positives = 26/45 (57%), Gaps = 5/45 (11%)

Query: 21  RPSVQRKVLIGLGLNKMNRCRVLDDT-PSVRGMISTVHHLVRIVE 64
           R S + KV   + + K+    V + T PS+ G++  ++HL+ +V+
Sbjct: 350 RNSFEIKVFTEIQIKKL----VEELTYPSLAGLLDKINHLILMVQ 390


>gnl|CDD|162552 TIGR01833, HMG-CoA-S_euk,
          3-hydroxy-3-methylglutaryl-CoA-synthase, eukaryotic
          clade.  Hydroxymethylglutaryl(HMG)-CoA synthase is the
          first step of isopentenyl pyrophosphate (IPP)
          biosynthesis via the mevalonate pathway. This pathway
          is found mainly in eukaryotes, but also in archaea and
          some bacteria. This model is specific for eukaryotes.
          Length = 454

 Score = 24.0 bits (52), Expect = 9.9
 Identities = 10/22 (45%), Positives = 11/22 (50%)

Query: 27 KVLIGLGLNKMNRCRVLDDTPS 48
          K  IGLG  KM  C   +D  S
Sbjct: 31 KYTIGLGQTKMGFCTDREDINS 52


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.323    0.136    0.377 

Gapped
Lambda     K      H
   0.267   0.0592    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 983,922
Number of extensions: 45173
Number of successful extensions: 79
Number of sequences better than 10.0: 1
Number of HSP's gapped: 79
Number of HSP's successfully gapped: 8
Length of query: 64
Length of database: 5,994,473
Length adjustment: 35
Effective length of query: 29
Effective length of database: 5,238,193
Effective search space: 151907597
Effective search space used: 151907597
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 50 (23.3 bits)