RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

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

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



>gnl|CDD|100100 cd01658, Ribosomal_L30, Ribosomal protein L30, which is found in
          eukaryotes and prokaryotes but not in archaea, is one
          of the smallest ribosomal proteins with a molecular
          mass of about 7kDa. L30 binds the 23SrRNA as well as
          the 5S rRNA and is one of five ribosomal proteins that
          mediate the interactions 5S rRNA makes with the
          ribosome.  The eukaryotic L30 members have N- and/or
          C-terminal extensions not found in their prokaryotic
          orthologs.  L30 is closely related to the ribosomal L7
          protein found in eukaryotes and archaea..
          Length = 54

 Score = 66.3 bits (163), Expect = 2e-12
 Identities = 25/54 (46%), Positives = 34/54 (62%)

Query: 10 ITVQQIGSPIRRPSVQRKVLIGLGLNKMNRCRVLDDTPSVRGMISTVHHLVRIV 63
          + +  + S I RP  QR  L  LGL K+N+  V  DTPS+RGMI+ V HLV++ 
Sbjct: 1  LKITLVKSLIGRPKKQRATLKALGLKKINQTVVHKDTPSIRGMINKVKHLVKVE 54


>gnl|CDD|32026 COG1841, RpmD, Ribosomal protein L30/L7E [Translation, ribosomal
          structure and biogenesis].
          Length = 55

 Score = 60.1 bits (146), Expect = 1e-10
 Identities = 27/55 (49%), Positives = 36/55 (65%)

Query: 10 ITVQQIGSPIRRPSVQRKVLIGLGLNKMNRCRVLDDTPSVRGMISTVHHLVRIVE 64
          + V  I SPI RP   RK L  LGL K+N   +++DTP+VRGM++ V HLV + E
Sbjct: 1  LKVTLIRSPIGRPPKIRKTLRLLGLRKINHTVIVEDTPAVRGMLNKVKHLVTVGE 55


>gnl|CDD|100098 cd00355, Ribosomal_L30_like, Ribosomal protein L30, which is
          found in eukaryotes and prokaryotes but not in archaea,
          is one of the smallest ribosomal proteins with a
          molecular mass of about 7kDa. L30 binds the 23SrRNA as
          well as the 5S rRNA and is one of five ribosomal
          proteins that mediate the interactions 5S rRNA makes
          with the ribosome.  The eukaryotic L30 members have N-
          and/or C-terminal extensions not found in their
          prokaryotic orthologs.  L30 is closely related to the
          ribosomal L7 protein found in eukaryotes and archaea..
          Length = 53

 Score = 58.2 bits (142), Expect = 5e-10
 Identities = 25/51 (49%), Positives = 33/51 (64%)

Query: 12 VQQIGSPIRRPSVQRKVLIGLGLNKMNRCRVLDDTPSVRGMISTVHHLVRI 62
          V ++ S I RP  QRK L  LGL K+N+   + DTPS+RGM+  V HLV +
Sbjct: 2  VTRVRSLIGRPPKQRKTLKALGLRKINQTVFVKDTPSIRGMLRKVKHLVTV 52


>gnl|CDD|144060 pfam00327, Ribosomal_L30, Ribosomal protein L30p/L7e.  This
          family includes prokaryotic L30 and eukaryotic L7.
          Length = 52

 Score = 57.5 bits (140), Expect = 7e-10
 Identities = 23/52 (44%), Positives = 33/52 (63%)

Query: 9  KITVQQIGSPIRRPSVQRKVLIGLGLNKMNRCRVLDDTPSVRGMISTVHHLV 60
           + + +I S I RP  Q+K L  LGL K+N+   + DTP++RGM+  V HLV
Sbjct: 1  LLKITRIRSIIGRPPKQKKTLKLLGLRKINQTVFVKDTPAIRGMLRKVKHLV 52


>gnl|CDD|100099 cd01657, Ribosomal_L7_archeal_euk, Ribosomal protein L7, which is
          found in archaea and eukaryotes but not in prokaryotes,
          binds domain II of the 23S rRNA as well as the 5S rRNA
          and is one of five ribosomal proteins that mediate the
          interactions 5S rRNA makes with the ribosome.  The
          eukaryotic L7 members have an N-terminal extension not
          found in the archeal L7 orthologs.  L7 is closely
          related to the ribosomal L30 protein found in
          eukaryotes and prokaryotes..
          Length = 159

 Score = 31.3 bits (72), Expect = 0.051
 Identities = 11/35 (31%), Positives = 16/35 (45%)

Query: 26 RKVLIGLGLNKMNRCRVLDDTPSVRGMISTVHHLV 60
          RK L  L L ++N    +  T +  GM+  V   V
Sbjct: 18 RKTLQLLRLRRINNAVFVKLTKATIGMLKKVEPYV 52


>gnl|CDD|39996 KOG4799, KOG4799, KOG4799, Mitochondrial ribosomal protein L30
           [Translation, ribosomal structure and biogenesis].
          Length = 182

 Score = 30.1 bits (67), Expect = 0.13
 Identities = 18/53 (33%), Positives = 30/53 (56%), Gaps = 1/53 (1%)

Query: 12  VQQIGSPIRRPSVQRKVLIGLGLN-KMNRCRVLDDTPSVRGMISTVHHLVRIV 63
           V +I S  RRP  ++ ++  LGL+ K  R +V  + PSV   +  + HL+R+ 
Sbjct: 62  VTRIKSTRRRPYWEKDIIKMLGLDKKHTRPQVHKNIPSVNAKLWKIKHLIRLR 114


>gnl|CDD|37701 KOG2490, KOG2490, KOG2490, Predicted membrane protein [Function
           unknown].
          Length = 601

 Score = 25.7 bits (56), Expect = 2.9
 Identities = 7/26 (26%), Positives = 15/26 (57%)

Query: 1   MSSSLKMQKITVQQIGSPIRRPSVQR 26
           +SSS+ ++KI   ++   I+  S  +
Sbjct: 158 VSSSILLRKIDTSRLYHIIKSQSFIK 183


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.323    0.136    0.377 

Gapped
Lambda     K      H
   0.267   0.0869    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 706,182
Number of extensions: 26503
Number of successful extensions: 57
Number of sequences better than 10.0: 1
Number of HSP's gapped: 57
Number of HSP's successfully gapped: 7
Length of query: 64
Length of database: 6,263,737
Length adjustment: 36
Effective length of query: 28
Effective length of database: 5,485,813
Effective search space: 153602764
Effective search space used: 153602764
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: 51 (23.2 bits)