RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780146|ref|YP_003064559.1| 50S ribosomal protein L1 [Candidatus Liberibacter asiaticus str. psy62] (232 letters) >gnl|CDD|180071 PRK05424, rplA, 50S ribosomal protein L1; Validated. Length = 230 Score = 379 bits (975), Expect = e-106 Identities = 142/229 (62%), Positives = 185/229 (80%) Query: 3 SKISKRMQQISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMVRG 62 +K+SKR + ++ +DR+ LY L +A+ ++KE ATA+FDETV++A+NLG+DPR A+Q VRG Sbjct: 1 AKLSKRYRAAAEKVDRTKLYSLEEAIALVKETATAKFDETVDVAVNLGVDPRKADQQVRG 60 Query: 63 VVTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRCIATPDMM 122 V +P+GTG VRVAVFA KA+EA+ AGADIVGGEDL E +KGG +DFD IATPDMM Sbjct: 61 AVVLPHGTGKTVRVAVFAKGEKAEEAKAAGADIVGGEDLIEKIKGGWLDFDVVIATPDMM 120 Query: 123 PLVGRLGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFE 182 VG+LGRILGPRG+MPN + GTVT DVA AV+E+K+G V+FR +KAGIIHA IGKVSF+ Sbjct: 121 GKVGKLGRILGPRGLMPNPKTGTVTMDVAKAVKEAKAGKVEFRVDKAGIIHAPIGKVSFD 180 Query: 183 NKKIEENVLAFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKVDLSSFS 231 +K++EN+ A + A+ KAKP+ AKG Y+K V+LSSTMG G+KVD SS + Sbjct: 181 AEKLKENLKALIDAIKKAKPATAKGTYIKSVSLSSTMGPGVKVDPSSLA 229 >gnl|CDD|162232 TIGR01169, rplA_bact, ribosomal protein L1, bacterial/chloroplast. This model describes bacterial (and chloroplast) ribosomal protein L1. The apparent mitochondrial L1 is sufficiently diverged to be the subject of a separate model. Length = 227 Score = 335 bits (860), Expect = 8e-93 Identities = 139/227 (61%), Positives = 178/227 (78%) Query: 4 KISKRMQQISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMVRGV 63 K+SKR + + +DR+ LY L +A+ +LKE ATA+FDETVE+A+ LGIDPR ++Q VRG Sbjct: 1 KLSKRYRAAREKVDRNKLYSLDEAIALLKETATAKFDETVEVAIRLGIDPRKSDQQVRGT 60 Query: 64 VTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRCIATPDMMP 123 V +P+GTG VRVAVFA KA+EA+ AGAD VG +DL E +K G +DFD IATPDMM Sbjct: 61 VVLPHGTGKTVRVAVFAKGEKAEEAKAAGADYVGSDDLIEKIKKGWLDFDVVIATPDMMR 120 Query: 124 LVGRLGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFEN 183 +VG+LGRILGPRG+MPN + GTVT DVA AV+ +K G V+FR++KAG IHA IGKVSF++ Sbjct: 121 VVGKLGRILGPRGLMPNPKTGTVTADVAKAVKNAKKGQVEFRADKAGNIHASIGKVSFDS 180 Query: 184 KKIEENVLAFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKVDLSSF 230 +K++EN+ A + A+ KAKPS AKG Y+K + LSSTMG GIKVDLSS Sbjct: 181 EKLKENLEALLDAIKKAKPSGAKGQYIKNIALSSTMGPGIKVDLSSL 227 >gnl|CDD|179783 PRK04203, rpl1P, 50S ribosomal protein L1P; Reviewed. Length = 215 Score = 109 bits (274), Expect = 8e-25 Identities = 66/214 (30%), Positives = 104/214 (48%), Gaps = 19/214 (8%) Query: 24 LSDAVVMLKERATAR-FDETVEIAMNL-GIDPRHANQMVRGVVTMPNGTGVNVRVAVFAT 81 + +AV E A R F ++V++ +NL ID + + V +P+G G V++AV A Sbjct: 7 IEEAVKEALEEAPKRNFTQSVDLIVNLKDIDLKKPENRIDEEVVLPHGRGKEVKIAVIAK 66 Query: 82 SSKADEAREAGADIV-GGEDLFEIVK--------GGQIDFDRCIATPDMMPLVGR-LGRI 131 A +A+EAGAD V E+L E+ + DF IA D+MPL+GR LG + Sbjct: 67 GELALQAKEAGADYVITREELEELGGDKRAAKKLANEYDF--FIAEADLMPLIGRYLGPV 124 Query: 132 LGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFENKKIEENVL 191 LGPRG MP D+ V K+ V R++ H +G +++ EN+ Sbjct: 125 LGPRGKMP--TPLPPNADIKPLVERLKN-TVRIRTKDQPTFHVRVGTEDMSPEELAENID 181 Query: 192 AFVSAVVKAKPSVAKGDYVKRVTLSSTMGCGIKV 225 A ++ + + +K V + +TMG +KV Sbjct: 182 AVLNRIESKLEKGRQ--NIKSVYVKTTMGPAVKV 213 >gnl|CDD|162233 TIGR01170, rplA_mito, ribosomal protein L1, mitochondrial. This model represents the mitochondrial homolog of bacterial ribosomal protein L1. Unlike chloroplast L1, this form was not sufficiently similar to bacterial forms to include in a single bacterial/organellar L1. Length = 141 Score = 91.0 bits (226), Expect = 2e-19 Identities = 49/141 (34%), Positives = 87/141 (61%), Gaps = 2/141 (1%) Query: 22 YGLSDAVVMLKERATARFDETVEIAMNLGIDPRHANQMVRGVVTMPNGTGVNVRVAVFAT 81 Y + A V LK ++ + + + +++G+ + V+G+ + P+ G ++AVF Sbjct: 1 YKVIKAFVYLKTKSISMYVPKQSVNLDIGLLMELGKESVQGMFSFPHPFGKEPKIAVFTK 60 Query: 82 -SSKADEAREAGADIVGGEDLFEIVKGGQID-FDRCIATPDMMPLVGRLGRILGPRGIMP 139 +S+ +EAREAGAD VGG+DL + ++ G+I FD IA PD++P + +L R+LGP+G+MP Sbjct: 61 GASEVEEAREAGADYVGGDDLIKKIEDGEIKPFDYLIAHPDIVPELAQLRRLLGPKGLMP 120 Query: 140 NLRVGTVTTDVATAVRESKSG 160 + + GTV ++ + + K G Sbjct: 121 SPKRGTVGDNLLSMIETFKKG 141 >gnl|CDD|185405 PTZ00029, PTZ00029, 60S ribosomal protein L10a; Provisional. Length = 216 Score = 53.6 bits (129), Expect = 4e-08 Identities = 56/227 (24%), Positives = 107/227 (47%), Gaps = 22/227 (9%) Query: 9 MQQISQGIDRSALYGLSDAVVMLKERATARFDETVEIAMNL-GIDPRHANQMVRGVVTMP 67 M ++S R A+ ++ E +F ETVE+ + L D + ++ G V +P Sbjct: 1 MSKLSSEALRKAI----AEILEGSEEKKRKFVETVELQIGLKDYDTQK-DKRFSGSVKLP 55 Query: 68 NGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQI------DFDRCIATPDM 121 N N++V V + DEA++ G D + E L + K ++ +D +A+ + Sbjct: 56 NVPKPNLKVCVLGDAVHCDEAKKLGLDFMDIEGLKKFNKNKKLVKKLAKKYDAFLASQSL 115 Query: 122 MPLVGR-LGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVS 180 +P + R LG L G P L T D+ + E KS +V F+ +K + +G V Sbjct: 116 LPQIPRLLGPGLNKAGKFPTLI--THNDDIEDKINELKS-SVKFQLKKVLCLGVAVGNVE 172 Query: 181 FENKKIEENVLAFVSAVVKAKPSVAKGDY--VKRVTLSSTMGCGIKV 225 +++ +N++ ++ +V S+ K ++ +K + + STMG ++ Sbjct: 173 MTEEQLRQNIVLSINFLV----SLLKKNWQNIKTLHIKSTMGKPQRI 215 >gnl|CDD|140252 PTZ00225, PTZ00225, 60S ribosomal protein L10a; Provisional. Length = 214 Score = 37.7 bits (87), Expect = 0.003 Identities = 49/212 (23%), Positives = 97/212 (45%), Gaps = 27/212 (12%) Query: 24 LSDAV-VMLKERATARFDETVEIAMNL-GIDPRHANQMVRGVVTMPNGTGVNVRVAVFAT 81 LS+A+ +LK +F E++++ +NL DP+ ++ G + +PN + V + Sbjct: 9 LSEAIQAVLKVDKERKFKESIDLQVNLKNYDPQK-DKRFSGSLKLPNVCRPRMTVCLLCD 67 Query: 82 SSKADEAREAGADIVGGEDLFEIVKGGQI------DFDRCIATPDMMPLVGRLGRILGPR 135 D A++ G + E+L ++ K ++ +D + + ++ V RL +GP Sbjct: 68 LVHEDIAKKEGVPTMNQEELKKLNKNKKLVKKMCNQYDAFLCSESIIKTVPRL---VGPH 124 Query: 136 ----GIMPNLRVGTVTTDVATAVRESKSGAVDFRSEKAGIIHAGIGKVSFENKKIEENV- 190 G P V + + + V E +S V F+ +K + +G V +++ +NV Sbjct: 125 MHRMGKFPT--VCSPSESLPDKVVELRS-TVKFQLKKVLCLGTCVGHVEMTEEQLRQNVV 181 Query: 191 --LAFVSAVVKAKPSVAKGDYVKRVTLSSTMG 220 + F+ +++K K Y+K STMG Sbjct: 182 MAINFLVSLLKKNWQNLKSAYIK-----STMG 208 >gnl|CDD|161874 TIGR00425, CBF5, rRNA pseudouridine synthase, putative. This family, found in archaea and eukaryotes, includes the only archaeal proteins markedly similar to bacterial TruB, the tRNA pseudouridine 55 synthase. However, among two related yeast proteins, the archaeal set matches yeast YLR175w far better than YNL292w. The first, termed centromere/microtubule binding protein 5 (CBF5), is an apparent rRNA pseudouridine synthase, while the second is the exclusive tRNA pseudouridine 55 synthase for both cytosolic and mitochondrial compartments. It is unclear whether archaeal proteins found by this model modify tRNA, rRNA, or both. Length = 322 Score = 30.1 bits (68), Expect = 0.52 Identities = 19/68 (27%), Positives = 26/68 (38%), Gaps = 3/68 (4%) Query: 56 ANQMVRGVVTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRC 115 A+ MVRG+ + G VAV EA G ++ +D+ KG D R Sbjct: 254 ADLMVRGIARLEKGIEKGDTVAVITLKG---EAVAVGIALMSTKDIANADKGVVADVKRV 310 Query: 116 IATPDMMP 123 I P Sbjct: 311 IMERGTYP 318 >gnl|CDD|106159 PRK13190, PRK13190, putative peroxiredoxin; Provisional. Length = 202 Score = 29.4 bits (66), Expect = 0.73 Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 14/77 (18%) Query: 44 EIAMNLGIDPRHANQMVRGVVTM-PNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLF 102 E+A + ++ VRGV + PN VR ++ + E G +I +++ Sbjct: 101 ELAREYNLIDENSGATVRGVFIIDPNQI---VRWMIYYPA-------ETGRNI---DEII 147 Query: 103 EIVKGGQIDFDRCIATP 119 I K Q+++ R +ATP Sbjct: 148 RITKALQVNWKRKVATP 164 >gnl|CDD|183509 PRK12409, PRK12409, D-amino acid dehydrogenase small subunit; Provisional. Length = 410 Score = 27.7 bits (62), Expect = 2.8 Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 6/61 (9%) Query: 138 MPNLRVGTV-TTDVATAVRE-----SKSGAVDFRSEKAGIIHAGIGKVSFENKKIEENVL 191 +PN R T+ T +A A R+ ++ +DF E+ GI+H K F++ K +L Sbjct: 97 IPNYRANTIETVRLAIAARKHLFDIAEREGIDFDLERRGILHIYHDKAGFDHAKRVNALL 156 Query: 192 A 192 A Sbjct: 157 A 157 >gnl|CDD|180244 PRK05764, PRK05764, aspartate aminotransferase; Provisional. Length = 393 Score = 27.0 bits (61), Expect = 4.6 Identities = 13/44 (29%), Positives = 20/44 (45%), Gaps = 11/44 (25%) Query: 77 AVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDFDRCIATPD 120 A A ++KA E + G D++ G+ DFD TP+ Sbjct: 15 ATLAVTAKAKELKAQGRDVIS----LGA---GEPDFD----TPE 47 >gnl|CDD|178209 PLN02599, PLN02599, dihydroorotase. Length = 364 Score = 26.6 bits (59), Expect = 5.6 Identities = 19/58 (32%), Positives = 22/58 (37%), Gaps = 11/58 (18%) Query: 116 IATPDMMPLVGRLG-----------RILGPRGIMPNLRVGTVTTDVATAVRESKSGAV 162 I PD L R G R G +MPNL+ TT A A RE A+ Sbjct: 25 ITRPDDWHLHLRDGAKLAAVVPHSARHFGRAIVMPNLKPPVTTTARALAYRERIMKAL 82 >gnl|CDD|181815 PRK09390, fixJ, response regulator FixJ; Provisional. Length = 202 Score = 26.1 bits (58), Expect = 7.5 Identities = 20/56 (35%), Positives = 25/56 (44%), Gaps = 10/56 (17%) Query: 115 CIAT----PDM--MPLVGRLGRILGPRGIMPNLRVGTVTTDVATAVRESKSGAVDF 164 C+ T P + + L+ RL RG + V T DV AV K GAVDF Sbjct: 50 CVVTDVRMPGIDGIELLRRLKA----RGSPLPVIVMTGHGDVPLAVEAMKLGAVDF 101 >gnl|CDD|180850 PRK07116, PRK07116, flavodoxin; Provisional. Length = 160 Score = 26.2 bits (58), Expect = 8.2 Identities = 11/30 (36%), Positives = 16/30 (53%), Gaps = 1/30 (3%) Query: 76 VAVFATSSKADEAREAGADIVGGEDLFEIV 105 VA F+ + + E A++ G DLFEI Sbjct: 7 VAYFSATGTTKKVAEKLAEVTGA-DLFEIK 35 >gnl|CDD|132281 TIGR03237, dnd_assoc_2, dnd system-associated protein 2. cereus E33L, Hahella chejuensis KCTC 2396, and Pseudoalteromonas haloplanktis TAC12. Length = 1256 Score = 26.0 bits (57), Expect = 8.9 Identities = 10/62 (16%), Positives = 24/62 (38%) Query: 53 PRHANQMVRGVVTMPNGTGVNVRVAVFATSSKADEAREAGADIVGGEDLFEIVKGGQIDF 112 P H N +V+ + + + ++ ++ E G E+L+ + G ++F Sbjct: 125 PWHPNSIVKLLRQEIDSSMLDKTASICLLDMIKQEQAHDQVTFFGFEELYSTIADGDLEF 184 Query: 113 DR 114 Sbjct: 185 QE 186 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.318 0.134 0.367 Gapped Lambda K H 0.267 0.0822 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 3,686,153 Number of extensions: 240626 Number of successful extensions: 559 Number of sequences better than 10.0: 1 Number of HSP's gapped: 553 Number of HSP's successfully gapped: 40 Length of query: 232 Length of database: 5,994,473 Length adjustment: 90 Effective length of query: 142 Effective length of database: 4,049,753 Effective search space: 575064926 Effective search space used: 575064926 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: 55 (24.8 bits)