RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

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



>gnl|CDD|30547 COG0198, RplX, Ribosomal protein L24 [Translation, ribosomal
           structure and biogenesis].
          Length = 104

 Score = 77.3 bits (190), Expect = 8e-16
 Identities = 55/105 (52%), Positives = 75/105 (71%), Gaps = 6/105 (5%)

Query: 1   MEKIRTGDRVLVLAGKDKGKAGQVMGVVRKSGRAFVQGVNIVKRHQR-QTPNKEAGIISK 59
             K++ GD V V+AGKDKGK G+V+ V+ K  +  V+GVN+VK+H +    N E GII+K
Sbjct: 2   KMKVKKGDTVKVIAGKDKGKEGKVLKVLPK--KVVVEGVNVVKKHIKPSQENPEGGIINK 59

Query: 60  EASIHLSNLSLID--KDGKQVRVGFSFV-DGKKIRIAKRSGEPID 101
           EA IH+SN+++ID  K GK  RVG+    DGKK+R+AK+SGE ID
Sbjct: 60  EAPIHISNVAIIDPNKTGKPTRVGYKVEEDGKKVRVAKKSGEVID 104


>gnl|CDD|36920 KOG1708, KOG1708, KOG1708, Mitochondrial/chloroplast ribosomal
           protein L24 [Translation, ribosomal structure and
           biogenesis].
          Length = 236

 Score = 66.2 bits (161), Expect = 2e-12
 Identities = 41/99 (41%), Positives = 55/99 (55%), Gaps = 4/99 (4%)

Query: 7   GDRVLVLAGKDKGKAGQVMGVVRKSGRAFVQGVNIVKRHQRQTPNKEAGIISK-EASIHL 65
           GD V VL GKDKGK G+V  V+R      V+G+N   RH       E G I K EA +H+
Sbjct: 76  GDTVEVLVGKDKGKQGEVTQVIRHRSWVVVKGLNTKYRHMGSEKEGEPGTIVKSEAPLHV 135

Query: 66  SN-LSLIDKDGKQV-RVGFSFV-DGKKIRIAKRSGEPID 101
           S  + L+D +  Q   V + F  DG+K+R++ RSG  I 
Sbjct: 136 SKQVMLVDPEDDQPTEVEWRFTEDGEKVRVSTRSGRIIP 174


>gnl|CDD|177063 CHL00141, rpl24, ribosomal protein L24; Validated.
          Length = 83

 Score = 56.2 bits (136), Expect = 2e-09
 Identities = 27/73 (36%), Positives = 46/73 (63%), Gaps = 1/73 (1%)

Query: 3  KIRTGDRVLVLAGKDKGKAGQVMGVVRKSGRAFVQGVNIVKRHQRQTPNKEAG-IISKEA 61
           ++ GD V +++G DKGK G+V+ +++KS +  V+G+NI  +H +     E G I   EA
Sbjct: 8  HVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVKGINIKFKHIKPNKENEVGEIKQFEA 67

Query: 62 SIHLSNLSLIDKD 74
           IH SN+ L +++
Sbjct: 68 PIHSSNVMLYNEE 80


>gnl|CDD|144165 pfam00467, KOW, KOW motif.  This family has been extended to
          coincide with ref. The KOW (Kyprides, Ouzounis, Woese)
          motif is found in a variety of ribosomal proteins and
          NusG.
          Length = 32

 Score = 28.6 bits (65), Expect = 0.44
 Identities = 13/30 (43%), Positives = 17/30 (56%)

Query: 7  GDRVLVLAGKDKGKAGQVMGVVRKSGRAFV 36
          GD V V++G  KGK G+V+ V     R  V
Sbjct: 2  GDVVRVISGPFKGKKGKVVEVDDSKARVHV 31


>gnl|CDD|173771 cd08529, STKc_FA2-like, Catalytic domain of the Protein
          Serine/Threonine Kinase, Chlamydomonas reinhardtii FA2
          and similar domains.  Serine/Threonine Kinases (STKs),
          Chlamydomonas reinhardtii FA2-like subfamily, catalytic
          (c) domain. STKs catalyze the transfer of the
          gamma-phosphoryl group from ATP to serine/threonine
          residues on protein substrates. The Chlamydomonas
          reinhardtii FA2-like subfamily belongs to the
          (NIMA)-related kinase (Nek) family. The Nek family
          includes seven different Chlamydomonas Neks (CNKs 1-6
          and Fa2). This subfamily includes FA2 and CNK4.  The
          Nek family is part of a larger superfamily that
          includes the catalytic domains of other protein STKs,
          protein tyrosine kinases, RIO kinases, aminoglycoside
          phosphotransferase, choline kinase, and
          phosphoinositide 3-kinase.  Chlamydomonas reinhardtii
          FA2 was discovered in a genetic screen for
          deflagellation-defective mutants. It is essential for
          basal-body/centriole-associated microtubule severing,
          and plays a role in cell cycle progression. No cellular
          function has yet been ascribed to CNK4.
          Length = 256

 Score = 27.5 bits (61), Expect = 0.74
 Identities = 22/80 (27%), Positives = 38/80 (47%), Gaps = 16/80 (20%)

Query: 17 DKGKAGQVMGVVRKS-GRAFV-QGVNIVK--RHQRQTPNKEAGIISKEASIHLSNLSLID 72
           KG  G V  VVRK+  R +  + +++ K  R +R+    EA +++K  S ++       
Sbjct: 9  GKGSFGVVFKVVRKADKRVYAMKQIDLSKMNRREREEAIDEARVLAKLDSSYI------- 61

Query: 73 KDGKQVRVGFSFVDGKKIRI 92
               +R   SF+D  K+ I
Sbjct: 62 -----IRYYESFLDKGKLNI 76


>gnl|CDD|36641 KOG1428, KOG1428, KOG1428, Inhibitor of type V adenylyl
           cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1
           [Signal transduction mechanisms].
          Length = 3738

 Score = 26.2 bits (57), Expect = 1.9
 Identities = 11/43 (25%), Positives = 18/43 (41%), Gaps = 2/43 (4%)

Query: 34  AFVQGVNIVKRHQRQTPNKEAGIISKEASIHLSNLSLIDKDGK 76
           A V       R +R  P+    I+   AS H+     + ++GK
Sbjct: 549 ASVDDKKRNGRLRRLVPSNRRKIVHVCASGHV--YGYVSENGK 589


>gnl|CDD|36124 KOG0906, KOG0906, KOG0906, Phosphatidylinositol 3-kinase VPS34,
           involved in signal transduction [Signal transduction
           mechanisms, Intracellular trafficking, secretion, and
           vesicular transport].
          Length = 843

 Score = 25.0 bits (54), Expect = 4.6
 Identities = 11/25 (44%), Positives = 16/25 (64%), Gaps = 1/25 (4%)

Query: 64  HLSNLSLIDKDGKQVRVGFSFVDGK 88
           HL NL L+ KDGK   + F ++ G+
Sbjct: 702 HLDNL-LLTKDGKLFHIDFGYILGR 725


>gnl|CDD|39516 KOG4315, KOG4315, KOG4315, G-patch nucleic acid binding protein
           [General function prediction only].
          Length = 455

 Score = 24.3 bits (52), Expect = 7.7
 Identities = 10/33 (30%), Positives = 18/33 (54%)

Query: 5   RTGDRVLVLAGKDKGKAGQVMGVVRKSGRAFVQ 37
           R G++V+V++GK KG  G ++          V+
Sbjct: 395 RGGEKVMVVSGKHKGVYGSLLSKDLDKETGVVR 427


>gnl|CDD|146721 pfam04234, CopC, Copper resistance protein CopC.  CopC is a
          bacterial blue copper protein that binds 1 atom of
          copper per protein molecule. Along with CopA, CopC
          mediates copper resistance by sequestration of copper
          in the periplasm.
          Length = 120

 Score = 23.7 bits (52), Expect = 10.0
 Identities = 11/25 (44%), Positives = 16/25 (64%)

Query: 65 LSNLSLIDKDGKQVRVGFSFVDGKK 89
           S+++L D DGK V +G + VDG  
Sbjct: 57 FSSVTLTDADGKGVALGKATVDGDP 81


  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
   0.317    0.137    0.373 

Gapped
Lambda     K      H
   0.267   0.0762    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,122,274
Number of extensions: 49959
Number of successful extensions: 176
Number of sequences better than 10.0: 1
Number of HSP's gapped: 171
Number of HSP's successfully gapped: 20
Length of query: 102
Length of database: 6,263,737
Length adjustment: 69
Effective length of query: 33
Effective length of database: 4,772,716
Effective search space: 157499628
Effective search space used: 157499628
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: 51 (23.4 bits)