RPS-BLAST 2.2.22 [Sep-27-2009] Database: mmdb70 33,805 sequences; 4,956,049 total letters Searching..................................................done Query= gi|254780261|ref|YP_003064674.1| 50S ribosomal protein L3 [Candidatus Liberibacter asiaticus str. psy62] (221 letters) >3bbo_F Ribosomal protein L3; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Nicotiana tabacum} (F:) Length = 259 Score = 205 bits (522), Expect = 4e-54 Identities = 83/218 (38%), Positives = 117/218 (53%), Gaps = 3/218 (1%) Query: 1 MRSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVV-VHRTLDKNGYMAVQVGAGEAKVK 59 GV+A KLGM + G +PVTV+ +V +T +GY AVQVG + + Sbjct: 42 AGVGVMATKLGMMSFFEESGTVVPVTVVGFREGNIVTQIKTEATDGYNAVQVGYRRVRDR 101 Query: 60 NVSKPMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKG 119 ++KP G + P + L EFR+Q D + F G LVDV+G TIGKG Sbjct: 102 KLTKPEMGHLEKSGIIPLRHLQEFRLQSIDGFEVTQKLDFGELFKEGDLVDVSGTTIGKG 161 Query: 120 FSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEV 179 F G +KRHNF + THG S SHR GS G PGRV+K KKM GRMGG + ++ L++ Sbjct: 162 FQGGIKRHNFKRGQMTHG-SKSHRQLGSIGAGTTPGRVYKGKKMPGRMGGTKRKIRKLKI 220 Query: 180 VSVDDKRGLILVKGCVPGAKKNSWILVRDSFKSAVNCK 217 V +DD+ +I++KG +PG + + + + N Sbjct: 221 VKIDDQLNIIMIKGALPGK-PGNLLRIAPAKIVGKNIP 257 >2j01_E 50S ribosomal protein L3; ribosome, tRNA, paromomycin, mRNA, translation; 2.8A {Thermus thermophilus} (E:) Length = 206 Score = 196 bits (500), Expect = 2e-51 Identities = 91/211 (43%), Positives = 124/211 (58%), Gaps = 7/211 (3%) Query: 3 SGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKNVS 62 G++ K+GMT ++ + R +PVTV+ C VV RT +K+GY AVQ+G K V+ Sbjct: 2 KGILGVKVGMTRIFR-DDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLGFLPQNPKRVN 60 Query: 63 KPMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSG 122 +P++G F+ V P + L E R + G + F G+ VDVTG + G+GF+G Sbjct: 61 RPLKGHFAKAGVEPVRILREIRDFNPE-----GDTVTVEIFKPGERVDVTGTSKGRGFAG 115 Query: 123 AMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVVSV 182 MKR NF G +HG HR GS G R+ PGRV+K KKMAG G RVTV NLEVV V Sbjct: 116 VMKRWNFAGGPDSHGAHKIHRHPGSIGNRKTPGRVYKGKKMAGHYGAERVTVMNLEVVDV 175 Query: 183 DDKRGLILVKGCVPGAKKNSWILVRDSFKSA 213 + L+LVKG VPG ++VR++ K+A Sbjct: 176 IPEENLLLVKGAVPGP-NGGLVIVRETKKAA 205 >1vq8_B 50S ribosomal protein L3P; ribosome 50S, protein-protein complex, RNA-RNA complex, protein-RNA complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} (B:) Length = 338 Score = 157 bits (398), Expect = 1e-39 Identities = 45/282 (15%), Positives = 72/282 (25%), Gaps = 73/282 (25%) Query: 1 MRSGVVARKLGMTCVYNIEGR----------RIPVTVLHLDNCQVVVHRTLDKNGYMAVQ 50 G K GMT V + +PVTV+ + V R + Y Sbjct: 38 GVQGFAGYKAGMTHVVLVNDEPNSPREGMEETVPVTVIETPPMRAVALRAYEDTPYGQRP 97 Query: 51 VGAGEA------KVKNVSKPMRGFFSSVNVSPKKKLFEFRVQK----------------- 87 + + + P + + + Sbjct: 98 LTEVWTDEFHSELDRTLDVPEDHDPDAAEEQIRDAHEAGDLGDLRLITHTVPDAVPSVPK 157 Query: 88 ----------------------DDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGAMK 125 D + G F G+ DV G+T GKG G +K Sbjct: 158 KKPDVMETRVGGGSVSDRLDHALDIVEDGGEHAMNDIFRAGEYADVAGVTKGKGTQGPVK 217 Query: 126 RHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVVSVDD- 184 R + H R +P RV G+ G ++ T N ++ + + Sbjct: 218 RWGVQKRKGKHARQGWRR-RIGNLGPWNPSRVRSTVPQQGQTGYHQRTELNKRLIDIGEG 276 Query: 185 ---------------KRGLILVKGCVPGAKKNSWILVRDSFK 211 LVKG VPG + R + + Sbjct: 277 DEPTVDGGFVNYGEVDGPYTLVKGSVPGP-DKRLVRFRPAVR 317 >2zjr_B 50S ribosomal protein L3; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} (B:1-29,B:91-211) Length = 150 Score = 141 bits (356), Expect = 9e-35 Identities = 63/144 (43%), Positives = 85/144 (59%), Gaps = 4/144 (2%) Query: 79 KLFEFRVQKDDDLLPVGSV---FSPSYFTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRAT 135 K+ ++ K+D +PV V + F G+ +D TG + GKG G MKR NF G A+ Sbjct: 8 KIGMTQIWKNDRAIPVTVVLAGVNVDIFAEGEKIDATGTSKGKGTQGVMKRWNFAGGPAS 67 Query: 136 HGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVVSVDDKRGLILVKGCV 195 HG HR GS G R+ PGRV+K K+MAG MG RVTV+NLEVV + LILVKG + Sbjct: 68 HGSKKWHRRPGSIGQRKTPGRVYKGKRMAGHMGMERVTVQNLEVVEIRAGENLILVKGAI 127 Query: 196 PGAKKNSWILVRDSFKSAVNCKGK 219 PGA +++R + K++ GK Sbjct: 128 PGA-NGGLVVLRSAAKASAAKGGK 150 >3i1n_D 50S ribosomal protein L3; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1p85_B 1p86_B 1vs8_D 2aw4_D 2awb_D 2gya_B 2gyc_B 1vs6_D 2i2v_D 2j28_D 2i2t_D* 2qao_D* 2qba_D* 2qbc_D* 2qbe_D 2qbg_D 2qbi_D* 2qbk_D* 2qov_D 2qox_D ... (D:1-30,D:102-209) Length = 138 Score = 136 bits (344), Expect = 3e-33 Identities = 60/108 (55%), Positives = 77/108 (71%), Gaps = 1/108 (0%) Query: 105 VGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMA 164 + VDVTG + GKGF+G +KR NF ATHG S+SHR GS G Q PG+VFK KKMA Sbjct: 32 DVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMA 91 Query: 165 GRMGGNRVTVKNLEVVSVDDKRGLILVKGCVPGAKKNSWILVRDSFKS 212 G+MG RVTV++L+VV VD +R L+LVKG VPGA S ++V+ + K+ Sbjct: 92 GQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGA-TGSDLIVKPAVKA 138 Score = 35.4 bits (82), Expect = 0.006 Identities = 12/30 (40%), Positives = 21/30 (70%) Query: 3 SGVVARKLGMTCVYNIEGRRIPVTVLHLDN 32 G+V +K+GMT ++ +G IPVTV+ ++ Sbjct: 2 IGLVGKKVGMTRIFTEDGVSIPVTVIEVEA 31 >2ftc_C L3MT, MRP-L3, mitochondrial 39S ribosomal protein L3; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} (C:1-29,C:104-211) Length = 137 Score = 127 bits (322), Expect = 8e-31 Identities = 50/110 (45%), Positives = 61/110 (55%), Gaps = 2/110 (1%) Query: 104 TVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKM 163 GQ VDVT TIGKGF G MKR F G ATHG + +HR G+ D GRV+ KM Sbjct: 30 RPGQYVDVTAKTIGKGFQGVMKRWGFKGQPATHGQTKTHRRPGAVAT-GDIGRVWPGTKM 88 Query: 164 AGRMGGNRVTVKNLEVVSVDDKRGLILVKGCVPGAKKNSWILVRDSFKSA 213 G+MG T L+V ++ K +I V G VPG KN + V+DS A Sbjct: 89 PGKMGNIYRTEYGLKVWRINTKHNIIYVNGSVPGH-KNCLVKVKDSKLPA 137 Score = 28.9 bits (65), Expect = 0.50 Identities = 13/35 (37%), Positives = 22/35 (62%) Query: 2 RSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVV 36 R G++A KLGM ++ +G++ VT+L + Q V Sbjct: 1 RVGLIALKLGMMPLWTKDGQKHVVTLLQVRPGQYV 35 >2zkr_b 60S ribosomal protein L3; protein-RNA complex, 60S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} (b:1-82,b:209-403) Length = 277 Score = 116 bits (291), Expect = 3e-27 Identities = 26/107 (24%), Positives = 40/107 (37%), Gaps = 3/107 (2%) Query: 93 PVGSVFSPSYFTVGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQ 152 V V +P F +++DV G+T GKG+ G R + L R G Sbjct: 75 AVTIVETPQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKL--PRKTHRGLRKVACIGA-W 131 Query: 153 DPGRVFKNKKMAGRMGGNRVTVKNLEVVSVDDKRGLILVKGCVPGAK 199 P RV + AG+ G + T N ++ + + K A Sbjct: 132 HPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIKNNAS 178 >3jyw_C 60S ribosomal protein L3; eukaryotic ribosome, RACK1 protein, flexible fitting; 8.90A {Thermomyces lanuginosus} PDB: 1s1i_C (C:40-78,C:206-362) Length = 196 Score = 100 bits (251), Expect = 1e-22 Identities = 29/137 (21%), Positives = 43/137 (31%), Gaps = 34/137 (24%) Query: 105 VGQLVDVTGMTIGKGFSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMA 164 +++D +T G GF G R L R G P V + A Sbjct: 41 QNEMIDAIAVTKGHGFEGVTHRWGTKKLPRKT--HRGLRKVACIGAW-HPAHVMWSVARA 97 Query: 165 GRMGGNRVTVKNLEVVSVDD------------------------------KRGLILVKGC 194 G+ G + T N ++ V K I+VKGC Sbjct: 98 GQRGYHSRTSINHKIYRVGKGDDEANGATSFDRTKKTITPMGGFVHYGEIKNDFIMVKGC 157 Query: 195 VPGAKKNSWILVRDSFK 211 +PG +K + +R S Sbjct: 158 IPGNRK-RIVTLRKSLY 173 >3i1n_D 50S ribosomal protein L3; ribosome structure, protein-RNA complex, acetylation, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA- binding, methylation; 3.19A {Escherichia coli k-12} PDB: 1p85_B 1p86_B 1vs8_D 2aw4_D 2awb_D 2gya_B 2gyc_B 1vs6_D 2i2v_D 2j28_D 2i2t_D* 2qao_D* 2qba_D* 2qbc_D* 2qbe_D 2qbg_D 2qbi_D* 2qbk_D* 2qov_D 2qox_D ... (D:31-101) Length = 71 Score = 87.0 bits (216), Expect = 2e-18 Identities = 23/71 (32%), Positives = 34/71 (47%), Gaps = 1/71 (1%) Query: 33 CQVVVHRTLDKNGYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKKLFEFRVQKDDDLL 92 +V + L +GY A+QV G K V+KP G F+ V + L+EFR+ + + Sbjct: 2 NRVTQVKDLANDGYRAIQVTTGAKKANRVTKPEAGHFAKAGVEAGRGLWEFRL-AEGEEF 60 Query: 93 PVGSVFSPSYF 103 VG S F Sbjct: 61 TVGQSISVELF 71 >2ftc_C L3MT, MRP-L3, mitochondrial 39S ribosomal protein L3; mitochondrial ribosome, large ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus} (C:30-103) Length = 74 Score = 83.6 bits (207), Expect = 2e-17 Identities = 11/74 (14%), Positives = 30/74 (40%), Gaps = 3/74 (4%) Query: 32 NCQVVVHRTLDK--NGYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKKLFEFRVQKDD 89 +C V+ + + + + VG + + F+ + + PK+ + F + D+ Sbjct: 2 DCHVLKYTSKENCNGKMATLSVGGKTVSRFRKATSILEFYRELGLPPKQTVKIFNI-TDN 60 Query: 90 DLLPVGSVFSPSYF 103 + G+ ++F Sbjct: 61 AAIKPGTPLYAAHF 74 >2zjr_B 50S ribosomal protein L3; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} (B:30-90) Length = 61 Score = 78.5 bits (194), Expect = 6e-16 Identities = 22/58 (37%), Positives = 32/58 (55%) Query: 33 CQVVVHRTLDKNGYMAVQVGAGEAKVKNVSKPMRGFFSSVNVSPKKKLFEFRVQKDDD 90 C +V +T +GY AVQ+G + V+KPM+G F+ V+P + L EFR D Sbjct: 2 CPIVQRKTAQTDGYEAVQIGYAPKAERKVNKPMQGHFAKAGVAPTRILREFRGFAPDG 59 >2pff_B Fatty acid synthase subunit beta; fatty acid synthase, acyl-carrier-protein, beta-ketoacyl reductase, beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces cerevisiae} (B:1772-1800,B:1916-2006) Length = 120 Score = 27.4 bits (61), Expect = 1.5 Identities = 10/36 (27%), Positives = 15/36 (41%), Gaps = 12/36 (33%) Query: 94 VGSVFSPSYFTVGQLVDVT---GMTIGKGFSGAMKR 126 + V S + LV+V GMT+ A+ R Sbjct: 2 LADVMS-----IESLVEVVFYRGMTM----QVAVPR 28 >2qmm_A UPF0217 protein AF_1056; alpha/beta knot, SAM, structural genomics, PSI-2, protein structure initiative; HET: SAM; 1.85A {Archaeoglobus fulgidus dsm 4304} (A:) Length = 197 Score = 27.1 bits (60), Expect = 2.2 Identities = 6/19 (31%), Positives = 10/19 (52%) Query: 28 LHLDNCQVVVHRTLDKNGY 46 L + C V+ H LD+ + Sbjct: 179 LLAEQCVVIAHHHLDRLQF 197 >2pcr_A Inositol-1-monophosphatase; bipolar disorder, structural genomics, NPPSFA, national project on protein structural and functional analyses; 2.60A {Aquifex aeolicus VF5} (A:) Length = 264 Score = 26.4 bits (57), Expect = 2.8 Identities = 10/70 (14%), Positives = 18/70 (25%) Query: 125 KRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVVSVDD 184 N+ VS+ F + G V K ++V + Sbjct: 90 GTKNYINGFPIFAVSVGLVKGEEPIVGAVYLPYFDKLYWGAKGLGAYVNGKRIKVKDNES 149 Query: 185 KRGLILVKGC 194 + +V G Sbjct: 150 LKHAGVVYGF 159 Database: mmdb70 Posted date: Jun 20, 2010 3:12 AM Number of letters in database: 4,956,049 Number of sequences in database: 33,805 Lambda K H 0.321 0.137 0.405 Gapped Lambda K H 0.267 0.0647 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 33805 Number of Hits to DB: 1,682,163 Number of extensions: 74558 Number of successful extensions: 182 Number of sequences better than 10.0: 1 Number of HSP's gapped: 159 Number of HSP's successfully gapped: 20 Length of query: 221 Length of database: 4,956,049 Length adjustment: 85 Effective length of query: 136 Effective length of database: 2,082,624 Effective search space: 283236864 Effective search space used: 283236864 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 53 (24.4 bits)