RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780713|ref|YP_003065126.1| 16S rRNA-processing protein [Candidatus Liberibacter asiaticus str. psy62] (190 letters) >gnl|CDD|178881 PRK00122, rimM, 16S rRNA-processing protein RimM; Provisional. Length = 172 Score = 127 bits (322), Expect = 2e-30 Identities = 47/170 (27%), Positives = 83/170 (48%), Gaps = 6/170 (3%) Query: 1 MVKLDKLVLMATIGTTHGLNGEVYIDSYANNPIDL----NRYVLYSNDNRELRILKMYRK 56 M K + L+++ I + HG+ GEV + S+ + P + + + +E+ I Sbjct: 1 MSKPEDLLVVGKIVSAHGIKGEVKVKSFTDFPERIFDYGPWLLGKGGEWQEVEIESGRFH 60 Query: 57 NKRFIATFSGIDNIHSASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYW 116 I F G+D+ ++A L+ +L+ R ELEEDE++ DL +E D G+ Sbjct: 61 KGFLIVKFEGVDDRNAAEALKGCELFVPRSQL--PELEEDEYYWHDLIGLEVVDEDGEEL 118 Query: 117 GQVCGVYNFGAGSILEIKNTMEKTFLIPFTKFAVLEVNLQENKILIDPIA 166 G+V + GA +L + ++ LIPF + V EV+L+ +I +D Sbjct: 119 GKVTDILETGANDVLVVLKDKKEERLIPFVEEVVKEVDLEAKRITVDWPE 168 >gnl|CDD|162792 TIGR02273, 16S_RimM, 16S rRNA processing protein RimM. This family consists of the bacterial protein RimM (YfjA, 21K), a 30S ribosomal subunit-binding protein implicated in 16S ribsomal RNA processing. It has been partially characterized in Escherichia coli, is found with other translation-associated genes such as trmD. It is broadly distributed among bacteria, including some minimal genomes such the aphid endosymbiont Buchnera aphidicola. The protein contains a PRC-barrel domain that it shares with other protein families (pfam05239) and a unique domain (pfam01782). This model describes the full-length protein. A member from Arabidopsis (plant) has additional N-terminal sequence likely to represent a chloroplast transit peptide. Length = 165 Score = 122 bits (309), Expect = 5e-29 Identities = 52/166 (31%), Positives = 90/166 (54%), Gaps = 8/166 (4%) Query: 7 LVLMATIGTTHGLNGEVYIDSYANNPIDLNRY--VLYSNDNRELRILKMYRK---NKRFI 61 L+++ IG HG+ GEV + S+ + P L Y L +++ + +K+ R N + I Sbjct: 1 LLVVGKIGGPHGIKGEVKVKSFTDFPESLFDYGPWLILKGSKQWQTVKVARVRKQNNKLI 60 Query: 62 ATFSGIDNIHSASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVCG 121 F GID+ +A L+ L+L+ R+ ELEEDE++ TDL +E +G+ G+V Sbjct: 61 VKFEGIDDREAAEALKGLELFVPREAL--PELEEDEYYWTDLIGLEVVTEEGEELGKVVE 118 Query: 122 VYNFGAGSILEIKN-TMEKTFLIPFTKFAVLEVNLQENKILIDPIA 166 + GA +L +++ +K LIPF + V E++L++ I +D Sbjct: 119 ILETGANDVLVVRSKKGKKEVLIPFVEEIVKEIDLEKKIITVDWPE 164 >gnl|CDD|184351 PRK13828, rimM, 16S rRNA-processing protein RimM; Provisional. Length = 161 Score = 102 bits (256), Expect = 6e-23 Identities = 51/148 (34%), Positives = 75/148 (50%), Gaps = 7/148 (4%) Query: 21 GEVYIDSYANNPIDLNRY-VLYSND-NRELRILKMYRKNK-RFIATFSGIDNIHSASELR 77 GEV + S+ +P+ + Y L + D R + R K +A G+ +A LR Sbjct: 3 GEVRLKSFTEDPLAIADYGPLTTEDGARSFTVALA-RPAKDGLVARLKGVATREAAEALR 61 Query: 78 DLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVCGVYNFGAGSILEIKNTM 137 L+LY R EL++DEF++ DL + D G G+V V+NFGAG ILEI Sbjct: 62 GLELYVPRDRLP--ELDDDEFYHADLIGLAAVDTGGALLGRVKAVHNFGAGDILEIAPPG 119 Query: 138 EK-TFLIPFTKFAVLEVNLQENKILIDP 164 T L+PFT+ V V+L +++ DP Sbjct: 120 GGPTLLLPFTRAVVPTVDLAAGRVVADP 147 >gnl|CDD|173056 PRK14592, rimM, 16S rRNA-processing protein RimM; Provisional. Length = 165 Score = 80.5 bits (199), Expect = 2e-16 Identities = 50/161 (31%), Positives = 88/161 (54%), Gaps = 6/161 (3%) Query: 7 LVLMATIGTTHGLNGEVYIDSYANNPIDLNRY--VLYSNDNRELRILKMYRKNKRFIATF 64 L+ + I + HG+ G V I ++ +P +++ Y + ++ ++ ++ + N IA Sbjct: 2 LICLGVITSPHGIKGHVKIKTFTEDPENISAYGKLTDGSNTYKISVVSVIGANL-VIAKI 60 Query: 65 SGIDNIHSASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVCGVYN 124 SGI++ A LR+ KLY +R K L EDEF+ +DL ME +G + +YN Sbjct: 61 SGINSRTEAELLRNKKLYVERS--KLPNLNEDEFYQSDLIGMEVKLEDNTIYGYIKKIYN 118 Query: 125 FGAGSILEIKNT-MEKTFLIPFTKFAVLEVNLQENKILIDP 164 FG+ I+EI T +K+ ++PFTK +N++E I++ P Sbjct: 119 FGSCDIIEISLTSTKKSTMLPFTKEIFPHINVKERYIILVP 159 >gnl|CDD|173054 PRK14590, rimM, 16S rRNA-processing protein RimM; Provisional. Length = 171 Score = 44.5 bits (105), Expect = 2e-05 Identities = 32/121 (26%), Positives = 56/121 (46%), Gaps = 5/121 (4%) Query: 47 ELRILKMYRKNKRFIATFSGIDNIHSASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEM 106 E+ +L++ +F+ F G D A + R L+ ++ E + EF++ DL + Sbjct: 47 EIALLEIRPHGGKFLVRFEGYDTPEEAVKWRGGSLFLPQELLPKIE-TKGEFYSEDLIGL 105 Query: 107 ETFDRQGKY--WGQVCGVYNFGAGSILEIKNTMEKTFLIPFTKFAVLEVNLQENKI-LID 163 + D GK W ++ V + A IL + LIPF V +++L++ I LI Sbjct: 106 QAIDETGKPLNW-KLTDVQDNPAHPILVFIKGEGEEILIPFLNVFVGDLDLEKQTIVLIQ 164 Query: 164 P 164 P Sbjct: 165 P 165 >gnl|CDD|184352 PRK13829, rimM, 16S rRNA-processing protein RimM; Provisional. Length = 162 Score = 42.8 bits (101), Expect = 5e-05 Identities = 37/164 (22%), Positives = 66/164 (40%), Gaps = 19/164 (11%) Query: 13 IGTTHGLNGEVYIDSYANNP--IDLNRYVLYSNDNRELRILKMYRKNKRFIATFSGIDNI 70 G +G+ G + + P +DL R +Y I + R + +G+ + Sbjct: 9 FGGPYGVQGGL---KFRGEPVVLDLPR--VYVEGLGWRAIERAERVGPELVLHLAGVTSR 63 Query: 71 HSASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVCGVYNFGAGSI 130 A L L++YA D LEE ++ +L + + G+ G+V V + GA + Sbjct: 64 EGAEALVGLRVYADDADLPP--LEEGSYYYHELRGLPVYV-DGEPLGEVVDVEDAGAQDL 120 Query: 131 LEIKN-----TMEKTFLIPFTKFAVLEVNLQENKILIDPIAAGL 169 L I++ T+ +P V ++ + I D I GL Sbjct: 121 LVIRHVGGSLRARATYFVPLQAPYVR---VELDGITADAI-PGL 160 >gnl|CDD|173055 PRK14591, rimM, 16S rRNA-processing protein RimM; Provisional. Length = 169 Score = 38.1 bits (88), Expect = 0.002 Identities = 38/163 (23%), Positives = 74/163 (45%), Gaps = 9/163 (5%) Query: 7 LVLMATIGTTHGLNGEVYIDSYANNPIDLNRY------VLYSNDNRELRILKMYRKNKRF 60 V +A IG T+ LNGE+ + AN+ L Y + +N ++L+ + ++ + Sbjct: 5 FVEIAKIGATYKLNGELNLYPLANSIETLLSYGDWYIQLPATNVWQQLKGESVLKRADKV 64 Query: 61 IATFSGIDNIHSASELRDLKLYAKRQDFKDEELEEDEFFNTDLEEMETFDRQGKYWGQVC 120 + I+N +A + + + ++ +L EDE + DL + +G V Sbjct: 65 YIKLANINNADTAKKYVNALIGVPKRALP--QLAEDEVYFKDLIGCSVKNINNDSFGVVV 122 Query: 121 GVYNFGAGSILEIKNTMEKTFLIPFTKFAVLEVNLQENKILID 163 + GA +L K + +LIP+ K ++ +L KI++D Sbjct: 123 DIIETGANEVLVCKEDNSE-YLIPYVKQYIVSEDLNSKKIVVD 164 >gnl|CDD|173057 PRK14593, rimM, 16S rRNA-processing protein RimM; Provisional. Length = 184 Score = 34.2 bits (78), Expect = 0.020 Identities = 48/185 (25%), Positives = 76/185 (41%), Gaps = 23/185 (12%) Query: 7 LVLMATIGTTHGLNGEVYIDSYANNPIDLNRYVLYS----NDNRELRILKMY-------R 55 ++L+ IG + GLNG + + ++ P L + V S N K Y Sbjct: 4 MLLVGRIGKSVGLNGGLKLHLESDFPECLKKGVKVSVAPLNAFSCASSFKDYVIHSYEHA 63 Query: 56 KNKRFIATFSGIDNIHSASELRDLKLYAKRQDFKDE-ELEEDEFFNTDLEEMETFDRQGK 114 KN F+ T I A EL +L L+ + K L+E EFF DL + + + + Sbjct: 64 KNLLFLET---IHTPEKAKELTNLGLFMSEAESKKLCVLKEGEFFYCDLVGLSVVE-ENE 119 Query: 115 YWGQVCGVYNFGAGSILEIKNT-------MEKTFLIPFTKFAVLEVNLQENKILIDPIAA 167 G+V + ++ T + K FLIP+ F + E+ LQ+ KI Sbjct: 120 ILGKVIEIQRISQTDYFMVETTLSLVEKGLAKIFLIPYRDFYIQEILLQDKKITTHNAKT 179 Query: 168 GLNNT 172 L N+ Sbjct: 180 LLENS 184 >gnl|CDD|178669 PLN03122, PLN03122, Poly [ADP-ribose] polymerase; Provisional. Length = 815 Score = 27.1 bits (60), Expect = 3.3 Identities = 10/19 (52%), Positives = 15/19 (78%) Query: 78 DLKLYAKRQDFKDEELEED 96 +LKLY KR +KD +L+E+ Sbjct: 306 ELKLYGKRGVYKDSKLQEE 324 >gnl|CDD|182821 PRK10899, PRK10899, hypothetical protein; Provisional. Length = 1022 Score = 26.4 bits (59), Expect = 4.3 Identities = 9/25 (36%), Positives = 15/25 (60%), Gaps = 5/25 (20%) Query: 152 EVNLQENKILIDPIAAGLNNTTMKN 176 EV L+ N + I P+ ++T+KN Sbjct: 436 EVTLRNNSLFIKPL-----DSTLKN 455 >gnl|CDD|179087 PRK00685, PRK00685, metal-dependent hydrolase; Provisional. Length = 228 Score = 25.5 bits (57), Expect = 7.5 Identities = 10/39 (25%), Positives = 13/39 (33%), Gaps = 7/39 (17%) Query: 149 AVLEVNLQENKILIDPIAAGLNNTTMKNPQYDCPLDSAG 187 + + KILIDP G NP D + Sbjct: 9 SAFLIETGGKKILIDPFITG-------NPLADLKPEDVK 40 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 0.137 0.392 Gapped Lambda K H 0.267 0.0660 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 3,126,740 Number of extensions: 196188 Number of successful extensions: 358 Number of sequences better than 10.0: 1 Number of HSP's gapped: 344 Number of HSP's successfully gapped: 25 Length of query: 190 Length of database: 5,994,473 Length adjustment: 88 Effective length of query: 102 Effective length of database: 4,092,969 Effective search space: 417482838 Effective search space used: 417482838 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: 54 (24.7 bits)