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)