RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781160|ref|YP_003065573.1| 16S rRNA m3U1498 methyltransferase [Candidatus Liberibacter asiaticus str. psy62] (245 letters) >gnl|CDD|146878 pfam04452, Methyltrans_RNA, RNA methyltransferase. RNA methyltransferases modify nucleotides during ribosomal RNA maturation in a site-specific manner. The Escherichia coli member is specific for U1498 methylation. Length = 225 Score = 188 bits (480), Expect = 1e-48 Identities = 77/222 (34%), Positives = 124/222 (55%), Gaps = 9/222 (4%) Query: 26 GDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVG-KSIRFKVEYQSRSQTKQSD-VQ 83 ++ H+L VLR+KEGD I LF+G GE+L++I + KS+ K+ + + + Sbjct: 5 DEEAHHLVRVLRLKEGDEIKLFDGDGGEYLAEIEEISKKSVLVKILEKLEVNKELPLKIT 64 Query: 84 YIFSPIKTNRLDYMIQKSVEMGMGAIRPVITRYTQNTHY------NMDRVRTYTISAAEQ 137 + K +RL+ ++QK+ E+G+ I P+I+ + ++R + I AAEQ Sbjct: 65 LAQALPKGDRLELILQKATELGVDRIVPLISERSVVKLDGKRADKKLERWQKIAIEAAEQ 124 Query: 138 CDILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPE 197 LP + PP +L+ LL+ D +++ +E S L +L A V ++IGPE Sbjct: 125 SGRTRLPEVLPPISLKELLEELDDADKLILHEEAAKSLGELSELLASLKGGKVLLIIGPE 184 Query: 198 GGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAAMALVQA 239 GG+ EE E L TP+SLGPRILR++TAA+AA++ +QA Sbjct: 185 GGFSPEEIELLKEA-GFTPVSLGPRILRTETAALAALSALQA 225 >gnl|CDD|31575 COG1385, COG1385, Uncharacterized protein conserved in bacteria [Function unknown]. Length = 246 Score = 184 bits (468), Expect = 2e-47 Identities = 90/245 (36%), Positives = 132/245 (53%), Gaps = 9/245 (3%) Query: 7 LKRLFVDFPLCIKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGEWLSKISYVGK-SI 65 + RLFVD L +GD+ H+L VLR+KEGD + LF+G GE+L++I+ +GK Sbjct: 3 MPRLFVDEELAEGATVILTGDEAHHLKRVLRLKEGDELRLFDGSGGEFLAEITKIGKKEA 62 Query: 66 RFKVEYQSRSQTKQSDVQYIFSPI-KTNRLDYMIQKSVEMGMGAIRPVITRYTQ-----N 119 K+ Q + + I K ++L+ +IQK+ E+G+ I P+IT + Sbjct: 63 LLKIVEQLEPNPELPLKITLAQAIPKGDKLELIIQKATELGVSKIIPLITERSVVKLDGK 122 Query: 120 THYNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWDHNCQIVFADETCGSENSLE 179 ++R + I AAEQ +P I PP +L+ LLK D + E E L Sbjct: 123 KAAKLERWQKIAIEAAEQSGRNVVPEIKPPESLKELLKEIDDEDALKLIYEEKAKEGLLA 182 Query: 180 KLHAIAHIP-NVAILIGPEGGYHSEEKETLHSLPFVTPLSLGPRILRSDTAAVAAMALVQ 238 A V ++IGPEGG+ +E E L F TP+SLGPRILR++TAA+AA+A +Q Sbjct: 183 LPLLEALPEGKVLLIIGPEGGFSEDEIELLREAGF-TPVSLGPRILRTETAALAALAALQ 241 Query: 239 AICGD 243 A+ GD Sbjct: 242 ALLGD 246 >gnl|CDD|35259 KOG0036, KOG0036, KOG0036, Predicted mitochondrial carrier protein [Nucleotide transport and metabolism]. Length = 463 Score = 29.9 bits (67), Expect = 0.69 Identities = 15/44 (34%), Positives = 18/44 (40%), Gaps = 3/44 (6%) Query: 124 MDRVRTYTISAAEQCDILTLPFIYPPTTLEFLLKNWDHNCQIVF 167 MD+ TI E D L L YP + LE + W H I Sbjct: 127 MDKDGKATIDLEEWRDHLLL---YPESDLEDIYDFWRHVLLIDI 167 >gnl|CDD|39880 KOG4682, KOG4682, KOG4682, Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only]. Length = 488 Score = 28.8 bits (64), Expect = 1.3 Identities = 17/74 (22%), Positives = 31/74 (41%), Gaps = 2/74 (2%) Query: 58 ISYVGKSIRFKVEYQSRSQTKQSDVQYIFSPIKTNRLDYMIQKSVEMGMGAIRP--VITR 115 I V + F Y+ + K SDV + + +LD +IQ+ E+ + + P Sbjct: 119 IDVVALQVAFGSLYRDEVEIKLSDVVGVLAAACLLQLDGLIQRCGEVMIETLSPKTACGY 178 Query: 116 YTQNTHYNMDRVRT 129 Y Y ++ V+ Sbjct: 179 YEAACKYGLESVKK 192 >gnl|CDD|39719 KOG4519, KOG4519, KOG4519, Phosphomevalonate kinase [Lipid transport and metabolism]. Length = 459 Score = 27.4 bits (60), Expect = 3.4 Identities = 13/46 (28%), Positives = 20/46 (43%) Query: 50 KDGEWLSKISYVGKSIRFKVEYQSRSQTKQSDVQYIFSPIKTNRLD 95 D EWL KIS +I+ SR+ + +QY+ + L Sbjct: 61 SDREWLYKISLNHLTIQVVSASDSRNPFVEHAIQYVIAYFHLATLH 106 >gnl|CDD|38182 KOG2971, KOG2971, KOG2971, RNA-binding protein required for biogenesis of the ribosomal 60S subunit [Translation, ribosomal structure and biogenesis]. Length = 299 Score = 27.7 bits (61), Expect = 3.6 Identities = 14/72 (19%), Positives = 25/72 (34%), Gaps = 6/72 (8%) Query: 4 HSHLKRLFVDF-PLCIKTQGKASGDQYHYLAHVLRMKEGDNILLFNGKDGE----WLSKI 58 HL + P K + L + +K ++ L F + + W+S Sbjct: 64 TRHLMKDISSLLPHSKKDSKLDRKKKLGVLNELAELKNCNSCLFFESRKRKDLYLWMSNS 123 Query: 59 SYVGKSIRFKVE 70 G S++F V Sbjct: 124 PN-GPSVKFLVH 134 >gnl|CDD|119356 cd02877, GH18_hevamine_XipI_class_III, This conserved domain family includes xylanase inhibitor Xip-I, and the class III plant chitinases such as hevamine, concanavalin B, and PPL2, all of which have a glycosyl hydrolase family 18 (GH18) domain. Hevamine is a class III endochitinase that hydrolyzes the linear polysaccharide chains of chitin and peptidoglycan and is important for defense against pathogenic bacteria and fungi. PPL2 (Parkia platycephala lectin 2) is a class III chitinase from Parkia platycephala seeds that hydrolyzes beta(1-4) glycosidic bonds linking 2-acetoamido-2-deoxy-beta-D-glucopyranose units in chitin.. Length = 280 Score = 26.8 bits (60), Expect = 5.7 Identities = 6/18 (33%), Positives = 10/18 (55%) Query: 121 HYNMDRVRTYTISAAEQC 138 + D + Y ++AA QC Sbjct: 147 LFASDPSKKYYLTAAPQC 164 >gnl|CDD|143602 cd07578, nitrilase_1_R1, First nitrilase domain of an uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases). Members of this subgroup have two nitrilase domains. This is the first of those two domains. The nitrilase superfamily is comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13). Class 13 represents proteins that at the time were difficult to place in a distinct similarity group; this subgroup represents either a new class or one that was included previously in class 13. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. Length = 258 Score = 26.7 bits (59), Expect = 6.8 Identities = 33/119 (27%), Positives = 44/119 (36%), Gaps = 29/119 (24%) Query: 144 PFIYP---PTTLEFLLKNWDHNCQIVFADETCGSENSLEKLHAIAHIPNVAILIGPEG-- 198 PF+ P PTT F +H+C IV S + + N A+LIGP G Sbjct: 57 PFVEPIPGPTTARFAELAREHDCYIVVGLPEVDSRSGI--------YYNSAVLIGPSGVI 108 Query: 199 GYH-------SEEKET----LHSLPFVTPLSLGPRILRSD-----TAAVAAMALVQAIC 241 G H SE K L F T + ++ D TA + A+ IC Sbjct: 109 GRHRKTHPYISEPKWAADGDLGHQVFDTEIGRIALLICMDIHFFETARLLALGGADVIC 167 >gnl|CDD|33901 COG4149, ModC, ABC-type molybdate transport system, permease component [Inorganic ion transport and metabolism]. Length = 225 Score = 25.9 bits (57), Expect = 9.5 Identities = 13/35 (37%), Positives = 17/35 (48%), Gaps = 2/35 (5%) Query: 122 YNMDRVRTYTISAAEQCDILTLPFIYPPTTLEFLL 156 Y + R R S E ++ LP + PP L FLL Sbjct: 32 YLLARRRFRGKSLLES--LVLLPLVLPPVVLGFLL 64 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 0.136 0.414 Gapped Lambda K H 0.267 0.0776 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,972,896 Number of extensions: 149223 Number of successful extensions: 315 Number of sequences better than 10.0: 1 Number of HSP's gapped: 308 Number of HSP's successfully gapped: 12 Length of query: 245 Length of database: 6,263,737 Length adjustment: 91 Effective length of query: 154 Effective length of database: 4,297,318 Effective search space: 661786972 Effective search space used: 661786972 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 (21.9 bits) S2: 56 (25.3 bits)