RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780147|ref|YP_003064560.1| 50S ribosomal protein L11
[Candidatus Liberibacter asiaticus str. psy62]
         (142 letters)



>gnl|CDD|100101 cd00349, Ribosomal_L11, Ribosomal protein L11. Ribosomal protein
           L11, together with proteins L10 and L7/L12, and 23S
           rRNA, form the L7/L12 stalk on the surface of the large
           subunit of the ribosome. The homologous eukaryotic
           cytoplasmic protein is also called 60S ribosomal protein
           L12, which is distinct from the L12 involved in the
           formation of the L7/L12 stalk. The C-terminal domain
           (CTD) of L11 is essential for binding 23S rRNA, while
           the N-terminal domain (NTD) contains the binding site
           for the antibiotics thiostrepton and micrococcin. L11
           and 23S rRNA form an essential part of the
           GTPase-associated region (GAR). Based on differences in
           the relative positions of the L11 NTD and CTD during the
           translational cycle, L11 is proposed to play a
           significant role in the binding of initiation factors,
           elongation factors, and release factors to the ribosome.
           Several factors, including the class I release factors
           RF1 and RF2, are known to interact directly with L11. In
           eukaryotes, L11 has been implicated in regulating the
           levels of ubiquinated p53 and MDM2 in the MDM2-p53
           feedback loop, which is responsible for apoptosis in
           response to DNA damage. In bacteria, the "stringent
           response" to harsh conditions allows bacteria to
           survive, and ribosomes that lack L11 are deficient in
           stringent factor stimulation..
          Length = 131

 Score =  178 bits (454), Expect = 5e-46
 Identities = 64/132 (48%), Positives = 93/132 (70%), Gaps = 1/132 (0%)

Query: 9   VKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVTCYKDKSFT 68
           +KLQ+ +G A P+PP+GPA+GQ G+ IM FCK FNA T+   KG+P+P  +T Y D+SFT
Sbjct: 1   IKLQVPAGKASPAPPLGPALGQLGVNIMKFCKEFNARTKDY-KGLPVPVKITVYNDRSFT 59

Query: 69  FTMSQPPVSFFLKKEVGIKSGSKLPGKESCGSITRENIRKIAQLKMQDMGAIDIEGAMRM 128
           F +  PP S  LKK  GI+ GSK P KE  G+IT + + +IA++K+ D+ A  ++ A++ 
Sbjct: 60  FEVKTPPASALLKKAAGIEKGSKKPNKEKVGNITLDQVYEIAKIKLPDLNAKTLKSAVKE 119

Query: 129 VEGSACSMGISV 140
           + G+A SMGI+V
Sbjct: 120 ILGTARSMGITV 131


>gnl|CDD|30429 COG0080, RplK, Ribosomal protein L11 [Translation, ribosomal
           structure and biogenesis].
          Length = 141

 Score =  165 bits (420), Expect = 3e-42
 Identities = 72/141 (51%), Positives = 98/141 (69%), Gaps = 1/141 (0%)

Query: 2   AKVVSRIVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVTC 61
           AK V +I+KLQ+ +G A PSPPVGPA+GQ G+ IM FCK FNAAT+  EKG+P+P  +T 
Sbjct: 1   AKKVVKIIKLQVPAGKANPSPPVGPALGQLGVNIMEFCKEFNAATKD-EKGLPVPVVITV 59

Query: 62  YKDKSFTFTMSQPPVSFFLKKEVGIKSGSKLPGKESCGSITRENIRKIAQLKMQDMGAID 121
           Y+D+SFTF +  PP S  LKK  GI+ GS  P K   G +T   +R+IA+ KM D+ A D
Sbjct: 60  YEDRSFTFIVKTPPASALLKKAAGIEKGSGKPNKNKVGKLTLAQVREIAKTKMPDLNAKD 119

Query: 122 IEGAMRMVEGSACSMGISVVD 142
           +E A++ + G+A SMG++V  
Sbjct: 120 LEAAVKEILGTARSMGVTVEG 140


>gnl|CDD|177049 CHL00127, rpl11, ribosomal protein L11; Validated.
          Length = 140

 Score =  143 bits (362), Expect = 2e-35
 Identities = 64/141 (45%), Positives = 93/141 (65%), Gaps = 1/141 (0%)

Query: 1   MAKVVSRIVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVT 60
           MAK    I+KL + +G A P+PPVGPA+GQ G+ I  FCK +NA T+    G+ IP  ++
Sbjct: 1   MAKKKLAIIKLALPAGKATPAPPVGPALGQHGVNINLFCKEYNARTKDKI-GLIIPVEIS 59

Query: 61  CYKDKSFTFTMSQPPVSFFLKKEVGIKSGSKLPGKESCGSITRENIRKIAQLKMQDMGAI 120
            Y+DKS+TF +  PP S  L K  GIK GS  P K+  GSIT + + +IAQ+K+ D+  I
Sbjct: 60  VYEDKSYTFILKTPPASVLLAKAAGIKKGSGEPNKKKVGSITIKQLEEIAQIKLPDLNTI 119

Query: 121 DIEGAMRMVEGSACSMGISVV 141
            +  A++++EG+A +MGIS+ 
Sbjct: 120 SLSKAIKIIEGTAKNMGISIK 140


>gnl|CDD|38467 KOG3257, KOG3257, KOG3257, Mitochondrial/chloroplast ribosomal
           protein L11 [Translation, ribosomal structure and
           biogenesis].
          Length = 168

 Score =  129 bits (326), Expect = 2e-31
 Identities = 60/143 (41%), Positives = 94/143 (65%), Gaps = 2/143 (1%)

Query: 1   MAKVVSRIVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVT 60
                S  +KL +++G A P+PP+GPA+GQ G+ ++AFCK FNA T+ ++ G+P+P  +T
Sbjct: 14  SKLSHSASIKLIVKAGLAAPAPPLGPALGQRGLNVIAFCKEFNARTKKVKPGVPLPGKIT 73

Query: 61  CYKDKSFTFTMSQPPVSFFLKKEVGIKSGSKLPGKESCGSITRENIRKIAQLKMQD--MG 118
              D+SFTF +  PP S+ LKK  G++ GSK PG+E  G +T +++ +IA++K+ D  + 
Sbjct: 74  VKPDRSFTFIIKTPPTSWLLKKAAGVEKGSKDPGQEKVGMLTLKHVYEIAKIKLPDPNLQ 133

Query: 119 AIDIEGAMRMVEGSACSMGISVV 141
              +E   R + G+A SMGI VV
Sbjct: 134 CTTLESICRSIIGTARSMGIKVV 156


>gnl|CDD|144037 pfam00298, Ribosomal_L11, Ribosomal protein L11, RNA binding
           domain. 
          Length = 69

 Score = 97.9 bits (245), Expect = 9e-22
 Identities = 33/68 (48%), Positives = 47/68 (69%)

Query: 73  QPPVSFFLKKEVGIKSGSKLPGKESCGSITRENIRKIAQLKMQDMGAIDIEGAMRMVEGS 132
            PP S+ LKK  GI+ GS  PGKE  G IT + + +IA++KM D+ A D+E A++++ G+
Sbjct: 2   TPPASYLLKKAAGIEKGSGKPGKEKVGKITLKQVYEIAKIKMPDLNANDLEAAVKIIIGT 61

Query: 133 ACSMGISV 140
           A SMGI V
Sbjct: 62  ARSMGIEV 69


>gnl|CDD|146529 pfam03946, Ribosomal_L11_N, Ribosomal protein L11, N-terminal
          domain.  The N-terminal domain of Ribosomal protein L11
          adopts an alpha/beta fold and is followed by the RNA
          binding C-terminal domain.
          Length = 59

 Score = 88.7 bits (221), Expect = 6e-19
 Identities = 33/60 (55%), Positives = 46/60 (76%), Gaps = 1/60 (1%)

Query: 8  IVKLQIESGSAKPSPPVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVTCYKDKSF 67
          ++KLQ+ +G A P+PP+GPA+GQ G+ IM FCK FNAAT+   KG+P+P  +T Y D+SF
Sbjct: 1  VIKLQVPAGKANPAPPLGPALGQLGVNIMEFCKEFNAATKDY-KGLPVPVKITVYNDRSF 59


>gnl|CDD|112637 pfam03833, PolC_DP2, DNA polymerase II large subunit DP2. 
          Length = 852

 Score = 32.0 bits (73), Expect = 0.062
 Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 3/73 (4%)

Query: 47  EGMEKGI-PIPTTVTCYKDKSFTFTMSQPPVSFFLKKEVGIKSG--SKLPGKESCGSITR 103
           E +EKGI      V  +KD +  F M+  P++ F   E+G+      +L           
Sbjct: 698 EPLEKGILRAKHDVYVFKDGTIRFDMTDLPITHFRPAEIGVSVEKLRELGYTRDIYGDEL 757

Query: 104 ENIRKIAQLKMQD 116
           ++  +I +LK QD
Sbjct: 758 KDEDQIVELKPQD 770


>gnl|CDD|32204 COG2021, MET2, Homoserine acetyltransferase [Amino acid transport
          and metabolism].
          Length = 368

 Score = 28.7 bits (64), Expect = 0.60
 Identities = 10/32 (31%), Positives = 14/32 (43%)

Query: 63 KDKSFTFTMSQPPVSFFLKKEVGIKSGSKLPG 94
           D SF   M+  PV  F    + ++SG  L  
Sbjct: 4  VDPSFASLMAVGPVGLFAIGPLTLESGGVLSD 35


>gnl|CDD|99834 cd06130, DNA_pol_III_epsilon_like, an uncharacterized bacterial
           subgroup of the DEDDh 3'-5' exonuclease domain family
           with similarity to the epsilon subunit of DNA polymerase
           III.  This subfamily is composed of uncharacterized
           bacterial proteins with similarity to the epsilon
           subunit of DNA polymerase III (Pol III), a multisubunit
           polymerase which is the main DNA replicating enzyme in
           bacteria, functioning as the chromosomal replicase. The
           Pol III holoenzyme is a complex of ten different
           subunits, three of which (alpha, epsilon, and theta)
           compose the catalytic core. The Pol III epsilon subunit,
           encoded by the dnaQ gene, is a DEDDh-type 3'-5'
           exonuclease which is responsible for the proofreading
           activity of the polymerase, increasing the fidelity of
           DNA synthesis. It contains three conserved sequence
           motifs termed ExoI, ExoII and ExoIII, with a specific
           Hx(4)D conserved pattern at ExoIII. These motifs are
           clustered around the active site and contain four
           conserved acidic residues that serve as ligands for the
           two metal ions required for catalysis. The epsilon
           subunit of Pol III also functions as a stabilizer of the
           holoenzyme complex.
          Length = 156

 Score = 28.2 bits (64), Expect = 0.78
 Identities = 11/23 (47%), Positives = 13/23 (56%), Gaps = 1/23 (4%)

Query: 119 AIDIEGAMRMVEGSACSMGISVV 141
           AID E A      SACS+G+  V
Sbjct: 3   AIDFETANADR-ASACSIGLVKV 24


>gnl|CDD|31936 COG1750, COG1750, Archaeal serine proteases [General function
          prediction only].
          Length = 579

 Score = 27.3 bits (60), Expect = 1.6
 Identities = 12/52 (23%), Positives = 20/52 (38%)

Query: 23 PVGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVTCYKDKSFTFTMSQP 74
             PA  Q    + A   A +  ++G   G+PI  +VT        +  + P
Sbjct: 20 LASPAFAQCYRTVKAKAPAVSVTSQGQGVGVPINISVTVTPGDGRVYVATFP 71


>gnl|CDD|32254 COG2071, COG2071, Predicted glutamine amidotransferases [General
           function prediction only].
          Length = 243

 Score = 26.4 bits (58), Expect = 2.9
 Identities = 23/90 (25%), Positives = 33/90 (36%), Gaps = 16/90 (17%)

Query: 30  QAGIPIMAFCKAF---NAATEGMEKGIPIPTTVTCYKDKSFTFTMSQPPVSFFLKKEVGI 86
           + GIPI+  C+     N A  G        T      ++       QP        EV I
Sbjct: 105 ERGIPILGICRGLQLLNVALGG--------TLYQDISEQPGHIDHRQPNPVHIESHEVHI 156

Query: 87  KSGSKL---PGKES--CGSITRENIRKIAQ 111
           + GSKL    G+      S   + I+K+A 
Sbjct: 157 EPGSKLAKILGESEFMVNSFHHQAIKKLAP 186


>gnl|CDD|36374 KOG1159, KOG1159, KOG1159, NADP-dependent flavoprotein reductase
           [Energy production and conversion].
          Length = 574

 Score = 25.7 bits (56), Expect = 4.4
 Identities = 31/141 (21%), Positives = 45/141 (31%), Gaps = 27/141 (19%)

Query: 9   VKLQIESGS-AKPSPP------VGPAIGQAGIPIMAFCKAFNAATEGMEKGIPIPTTVTC 61
           + +++  G+   PS        VGP  G A  P  A  +         +          C
Sbjct: 416 IPIKVRPGTLYFPSDLNKPLIMVGPGTGVA--PFRALIQERIY-----QGDKENVLFFGC 468

Query: 62  -YKDKSFTFTMSQPPVSFFLKKEVGIKSGSK-LPGKESCGSITRENIRKIAQLKMQDMGA 119
             KDK F +          L K     + S+    K       REN  ++  L       
Sbjct: 469 RNKDKDFLY----EDEWTELNKRAFHTAFSRDQEQKVYVQHKIRENGEEVWDL------- 517

Query: 120 IDIEGAMRMVEGSACSMGISV 140
           +D  GA   V GS+  M   V
Sbjct: 518 LDNLGAYFFVAGSSGKMPKDV 538


>gnl|CDD|37135 KOG1924, KOG1924, KOG1924, RhoA GTPase effector DIA/Diaphanous
           [Signal transduction mechanisms, Cytoskeleton].
          Length = 1102

 Score = 24.6 bits (53), Expect = 9.4
 Identities = 14/46 (30%), Positives = 14/46 (30%), Gaps = 5/46 (10%)

Query: 16  GSAKPSPPVGPAIGQAGIP-----IMAFCKAFNAATEGMEKGIPIP 56
           G A P PP  P  G AG P                  G   G P P
Sbjct: 552 GGAGPPPPPPPLPGIAGGPPPPPPPPGGGGPPPPPPPGGFLGGPPP 597


>gnl|CDD|32505 COG2358, Imp, TRAP-type uncharacterized transport system,
           periplasmic component [General function prediction
           only].
          Length = 321

 Score = 24.9 bits (54), Expect = 9.5
 Identities = 13/54 (24%), Positives = 21/54 (38%), Gaps = 4/54 (7%)

Query: 60  TCYKDKSFTFTMSQPPVSFFLKKEVGIKSGSKLPGKE----SCGSITRENIRKI 109
              ++      +   P     +K+ GIK+ + L GK       GS T    R+I
Sbjct: 103 GKDENLRAVAALYPEPFHVVTRKDAGIKTIADLKGKRVAIGPPGSGTEATARQI 156


  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    0.133    0.379 

Gapped
Lambda     K      H
   0.267   0.0834    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,606,356
Number of extensions: 75048
Number of successful extensions: 164
Number of sequences better than 10.0: 1
Number of HSP's gapped: 157
Number of HSP's successfully gapped: 18
Length of query: 142
Length of database: 6,263,737
Length adjustment: 84
Effective length of query: 58
Effective length of database: 4,448,581
Effective search space: 258017698
Effective search space used: 258017698
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 (21.7 bits)
S2: 52 (23.6 bits)