RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780261|ref|YP_003064674.1| 50S ribosomal protein L3 [Candidatus Liberibacter asiaticus str. psy62] (221 letters) >gnl|CDD|30436 COG0087, RplC, Ribosomal protein L3 [Translation, ribosomal structure and biogenesis]. Length = 218 Score = 243 bits (621), Expect = 4e-65 Identities = 111/214 (51%), Positives = 138/214 (64%), Gaps = 3/214 (1%) Query: 2 RSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKNV 61 G + K+GMT V++ G +PVTV+ + VV +T + +GY AVQVGAG+ K K V Sbjct: 1 MLGFLGYKVGMTHVFDERGISVPVTVIEVPPNVVVQVKTYETDGYRAVQVGAGDRKAKRV 60 Query: 62 SKPMRGFFSSVNVSPKKKLFEFRVQKDD--DLLPVGSVFSPSYFTVGQLVDVTGMTIGKG 119 +KP+ G F+ V PK+ L EFRV D + VG + F G+LVDVTG+T GKG Sbjct: 61 NKPLVGHFAKAGVKPKRHLAEFRVGGGDVAEKFEVGQEITVDVFKEGELVDVTGVTKGKG 120 Query: 120 FSGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEV 179 F G MKR F G A+HG S+SHR GS G RQ PGRVFK KKMAG MG RVTV+NLEV Sbjct: 121 FQGVMKRWGFKGGPASHGSSLSHRRPGSIGQRQTPGRVFKGKKMAGHMGNERVTVQNLEV 180 Query: 180 VSVDDKRGLILVKGCVPGAKKNSWILVRDSFKSA 213 V VD + LILVKG VPGAKK ++VR + K+ Sbjct: 181 VKVDVENNLILVKGAVPGAKK-RLVVVRPAVKAK 213 >gnl|CDD|38351 KOG3141, KOG3141, KOG3141, Mitochondrial/chloroplast ribosomal protein L3 [Translation, ribosomal structure and biogenesis]. Length = 310 Score = 229 bits (584), Expect = 6e-61 Identities = 101/215 (46%), Positives = 132/215 (61%), Gaps = 3/215 (1%) Query: 2 RSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRT-LDKNGYMAVQVGAGEAKVKN 60 R GV+ARKLGM +++ +G RIPVT+L +D+ V+ + T K GY AVQVG G K K Sbjct: 62 RVGVIARKLGMMPLWDKDGERIPVTILQVDDNHVIKYITPEAKGGYFAVQVGYGTVKPKK 121 Query: 61 VSKPMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGF 120 ++K G F S V PK+ L EFRV ++ LLP G+ +F GQ VDVTG TIGKGF Sbjct: 122 LTKAELGHFRSAGVPPKRHLREFRV-TEEALLPPGTPLFARHFKPGQYVDVTGKTIGKGF 180 Query: 121 SGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVV 180 G MKRH F G A+HG S SHR GS G PGRV+ +KM G MG T+K L+V Sbjct: 181 QGVMKRHGFKGGPASHGTSKSHRRPGSIGQGTTPGRVWPGRKMPGHMGNEWRTIKGLKVW 240 Query: 181 SVDDKRGLILVKGCVPGAKKNSWILVRDSFKSAVN 215 +D + +I VKG VPG K + + ++D+ V+ Sbjct: 241 KIDTELNVIWVKGSVPG-PKGNLVKIKDAILPTVD 274 >gnl|CDD|177065 CHL00143, rpl3, ribosomal protein L3; Validated. Length = 207 Score = 190 bits (484), Expect = 3e-49 Identities = 88/201 (43%), Positives = 126/201 (62%), Gaps = 2/201 (0%) Query: 1 MRSGVVARKLGMTCVYNIEGRRIPVTVLHLDNCQVVVHRTLDKNGYMAVQVGAGEAKVKN 60 M G++ K+GMT +++ G IPVT+L + C + +TL +GY A+Q+G + K Sbjct: 1 MSIGLLGTKIGMTQIFDETGNAIPVTILKVGPCVITQIKTLTTDGYNAIQIGYKQVSTKK 60 Query: 61 VSKPMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGF 120 ++KP G NV P K L EFRV+ ++ VG + F+VGQLV+V+G +IGKGF Sbjct: 61 LTKPQLGHLQKSNVPPLKYLKEFRVKSSEEF-EVGQPLTVDAFSVGQLVNVSGKSIGKGF 119 Query: 121 SGAMKRHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVV 180 +G KRHNF THG S +HR+ GS G PGRV+ KKMAGR+G +VT+KNL+++ Sbjct: 120 AGLQKRHNFSRGPMTHG-SKNHRAPGSIGAGTTPGRVYPGKKMAGRLGNKKVTIKNLKIL 178 Query: 181 SVDDKRGLILVKGCVPGAKKN 201 VD + L+++KG VPG N Sbjct: 179 KVDSENNLLVLKGSVPGKPGN 199 >gnl|CDD|144036 pfam00297, Ribosomal_L3, Ribosomal protein L3. Length = 199 Score = 175 bits (445), Expect = 9e-45 Identities = 79/195 (40%), Positives = 105/195 (53%), Gaps = 5/195 (2%) Query: 9 KLGMTCVY-NIEGRRIPVTVLHLDNCQVVVHRTLDK--NGYMAVQVGAGEAKVKNVSKPM 65 K GMT ++ +G PVTV+ + VV +T ++ +GY A+QVG K V K + Sbjct: 1 KAGMTHIFTEKKGVLEPVTVIEVPPMVVVQVKTYEETNDGYKAIQVGLESIKKYRVVKRV 60 Query: 66 RGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFSGAMK 125 G PK + EFRV ++ P ++ F G+ VDVTG+T GKGF G MK Sbjct: 61 LGHTQKRGTPPKAHVMEFRVNGGEEFEPGQTIAVSDVFREGEYVDVTGVTKGKGFQGVMK 120 Query: 126 RHNFGGLRATHGVSISHRSHGSTGCRQDPGRVFKNKKMAGRMGGNRVTVKNLEVVSVDDK 185 R F L HG HR GS G PGRVF KMAG+MG + T +NL++ +D + Sbjct: 121 RWGFKRLPRKHGRGY-HRKPGSIG-AWHPGRVFPGVKMAGQMGNHHRTEQNLKIYRIDQE 178 Query: 186 RGLILVKGCVPGAKK 200 L+LVKG VPG KK Sbjct: 179 NNLLLVKGSVPGPKK 193 >gnl|CDD|40019 KOG4822, KOG4822, KOG4822, Predicted nuclear membrane protein involved in mRNA transport and sex determination via splicing modulation [RNA processing and modification, Signal transduction mechanisms]. Length = 1906 Score = 28.2 bits (62), Expect = 2.1 Identities = 15/61 (24%), Positives = 22/61 (36%), Gaps = 6/61 (9%) Query: 54 GEAKVKNVSKPMRGFFSSVNVSPKKKLFEFRVQKDDDLLPVGSVFSPSYFTVGQLVDVTG 113 GE+K K + P ++ P E + L+ GS S S G +V G Sbjct: 24 GESKFKRLCNPF--LYTPSAPYP----LEVEAVVTNHLVVRGSYRSLSLIVYGNIVKDLG 77 Query: 114 M 114 Sbjct: 78 Q 78 >gnl|CDD|110448 pfam01446, Rep_1, Replication protein. Replication proteins (rep) are involved in plasmid replication. The Rep protein binds to the plasmid DNA and nicks it at the double strand origin (dso) of replication. The 3'-hydroxyl end created is extended by the host DNA replicase, and the 5' end is displaced during synthesis. At the end of one replication round, Rep introduces a second single stranded break at the dso and ligates the ssDNA extremities generating one double-stranded plasmid and one circular ssDNA form. Complementary strand synthesis of the circular ssDNA is usually initiated at the single-stranded origin by the host RNA polymerase. Length = 232 Score = 26.9 bits (60), Expect = 4.9 Identities = 16/55 (29%), Positives = 20/55 (36%), Gaps = 19/55 (34%) Query: 57 KVKNVSKPMRGFFSSVNVSPKKKLFEFRVQKDDD-------LLPVGSVFSPSYFT 104 + K V K + G+ S V+ K D LL V PSYFT Sbjct: 54 QYKKVKKNLLGYIRSTEVTVNK--------DDGSYHPHFHVLLMV----KPSYFT 96 >gnl|CDD|38005 KOG2794, KOG2794, KOG2794, Delta-aminolevulinic acid dehydratase [Coenzyme transport and metabolism]. Length = 340 Score = 26.1 bits (57), Expect = 9.2 Identities = 13/58 (22%), Positives = 25/58 (43%), Gaps = 1/58 (1%) Query: 65 MRGFFSSVNVSPKKKLFE-FRVQKDDDLLPVGSVFSPSYFTVGQLVDVTGMTIGKGFS 121 +R + N+SP ++ F + +DD P+ S+ V +L + + KG Sbjct: 27 LRAWQQETNISPANLIYPLFIHEGEDDFTPIDSMPGIYRLGVNRLKEELAPLVAKGLR 84 >gnl|CDD|36142 KOG0924, KOG0924, KOG0924, mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]. Length = 1042 Score = 25.8 bits (56), Expect = 9.2 Identities = 7/41 (17%), Positives = 17/41 (41%), Gaps = 1/41 (2%) Query: 16 YNIEGRRIPVTVLHL-DNCQVVVHRTLDKNGYMAVQVGAGE 55 + I GR PV +++ + V + + + + G+ Sbjct: 525 FTIPGRTYPVEIMYTKTPVEDYVEAAVKQAVQIHLSGPPGD 565 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 0.321 0.137 0.405 Gapped Lambda K H 0.267 0.0732 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,581,360 Number of extensions: 129431 Number of successful extensions: 267 Number of sequences better than 10.0: 1 Number of HSP's gapped: 256 Number of HSP's successfully gapped: 12 Length of query: 221 Length of database: 6,263,737 Length adjustment: 90 Effective length of query: 131 Effective length of database: 4,318,927 Effective search space: 565779437 Effective search space used: 565779437 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: 55 (25.0 bits)