RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780322|ref|YP_003064735.1| SAM-dependent methyltransferase protein [Candidatus Liberibacter asiaticus str. psy62] (273 letters) >gnl|CDD|38151 KOG2940, KOG2940, KOG2940, Predicted methyltransferase [General function prediction only]. Length = 325 Score = 153 bits (388), Expect = 5e-38 Identities = 82/270 (30%), Positives = 130/270 (48%), Gaps = 13/270 (4%) Query: 4 LFDMQLINRNRLRSFRQKDFSVYFLLDRVAKEIAFRLNMINQTFENALELHGITGIVG-- 61 +FD L R R+ D +L + + +A R+ ++F A ++ G V Sbjct: 30 IFDRDLKRIQRDRAAWLSDQKNDYLKEEIGDRLADRVFDCKKSFPTAFDIGCSLGAVKRH 89 Query: 62 --------YTCMETKKIHRMIRAEISTEFSTLKREVISCPLEEIPSISQSVDLILSPLNL 113 M+T + MI++ + +++ E + SVDLI+S L+L Sbjct: 90 LRGEGVEKLIMMDTS--YDMIKSCRDAQDPSIETSYFVGDEEFLDFKENSVDLIISSLSL 147 Query: 114 HIINDTLEMFSKINHMLKPGGMFLAAIPGIGTLHELRKALLKAETELTGGASPRVIPFMD 173 H ND + LKP G+F+A++ G TL+ELR +L AE E GG SP + PF Sbjct: 148 HWTNDLPGSMIQCKLALKPDGLFIASMLGGDTLYELRCSLQLAELEREGGISPHISPFTQ 207 Query: 174 IKSAGTLMEKSGFISPIIDQDTYTVYYKSMLHLMHDLRGMGMSNPLIRRSKTPPYKSLFK 233 ++ G L+ ++GF +D D V Y M LM DL+GMG SN + R+ +++ Sbjct: 208 VRDIGNLLTRAGFSMLTVDTDEIVVGYPRMFELMEDLQGMGESNAALNRNAILNRETMVA 267 Query: 234 RASTIYTEENSDLTGNVTASFSIIYVMGWK 263 A+ IY + G + A+F IIY++GWK Sbjct: 268 -AAAIYQSMYATEDGTIPATFQIIYMIGWK 296 >gnl|CDD|38255 KOG3045, KOG3045, KOG3045, Predicted RNA methylase involved in rRNA processing [RNA processing and modification]. Length = 325 Score = 32.3 bits (73), Expect = 0.15 Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 1/76 (1%) Query: 64 CMETKKIHRMIRAEISTEFSTLKREVISCPLEEIPSISQSVDLILSPLNLHIINDTLEMF 123 C E K S + + VI+C + +P +SVD+ + L+L + + + Sbjct: 189 CGEAKIASSERHKVHSFDLVAVNERVIACDMRNVPLEDESVDVAVFCLSL-MGTNLADFI 247 Query: 124 SKINHMLKPGGMFLAA 139 + N +LKPGG+ A Sbjct: 248 KEANRILKPGGLLYIA 263 >gnl|CDD|147365 pfam05148, Methyltransf_8, Hypothetical methyltransferase. This family consists of several uncharacterized eukaryotic proteins which are related to methyltransferases pfam01209. Length = 214 Score = 32.1 bits (73), Expect = 0.17 Identities = 25/93 (26%), Positives = 39/93 (41%), Gaps = 10/93 (10%) Query: 64 CMETKKIHRMIRAE--ISTEFSTLKREVISCPLEEIPSISQSVDLILSPLNLHIINDTLE 121 C E + R E S + + + VI C + +P +SVD+ + L+L N + Sbjct: 76 CGEARIAFRKREFENVHSFDLVAVNKRVIPCDMARVPLEDESVDVAVFCLSLMGTN--IA 133 Query: 122 MFSK-INHMLKPGGMFLAA-----IPGIGTLHE 148 F K N +LK GG+ A P +G Sbjct: 134 DFLKEANRILKNGGLLKIAEVRSRFPSVGLFER 166 >gnl|CDD|163681 cd07943, DRE_TIM_HOA, 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain. 4-hydroxy 2-ketovalerate aldolase (Also known as 4-hydroxy-2-ketovalerate aldolase and 4-hydroxy-2-oxopentanoate aldolase (HOA)) converts 4-hydroxy-2-oxopentanoate to acetaldehyde and pyruvate, the penultimate step in the meta-cleavage pathway for the degradation of phenols, cresols and catechol. This family includes the Escherichia coli MhpE aldolase, the Pseudomonas DmpG aldolase, and the Burkholderia xenovorans BphI pyruvate aldolase. In Pseudomonas, the DmpG aldolase tightly associates with a dehydrogenase (DmpF ) and is inactive without it. HOA has a canonical TIM-barrel fold with a C-terminal extension that forms a funnel leading to the active site. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name "DRE-TIM". Length = 263 Score = 31.7 bits (73), Expect = 0.20 Identities = 9/20 (45%), Positives = 14/20 (70%), Gaps = 2/20 (10%) Query: 134 GMFLAAIPGIGTLHELRKAL 153 G+ L +PGIGT+ +L+ A Sbjct: 78 GVLL--LPGIGTVDDLKMAA 95 >gnl|CDD|37932 KOG2721, KOG2721, KOG2721, Uncharacterized conserved protein [Function unknown]. Length = 260 Score = 29.6 bits (66), Expect = 0.85 Identities = 10/36 (27%), Positives = 20/36 (55%) Query: 228 YKSLFKRASTIYTEENSDLTGNVTASFSIIYVMGWK 263 Y +FK+++ ++ S + V + F+ +YV WK Sbjct: 72 YSFVFKKSTELFKRRASKILSLVASFFASVYVTKWK 107 >gnl|CDD|32408 COG2226, UbiE, Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]. Length = 238 Score = 29.1 bits (65), Expect = 1.4 Identities = 22/122 (18%), Positives = 44/122 (36%), Gaps = 12/122 (9%) Query: 27 FLLDRVAKEIAFRLNMINQTFENALELHGITGIVGYTCMETKKIHRMIRAEIST------ 80 F L R+ + A + + + L++ TG + ++ ++ +IS Sbjct: 33 FGLHRLWRR-ALISLLGIKPGDKVLDVACGTGDMALLLAKSVGTGEVVGLDISESMLEVA 91 Query: 81 -----EFSTLKREVISCPLEEIPSISQSVDLILSPLNLHIINDTLEMFSKINHMLKPGGM 135 + E + E +P S D + L + D + ++ +LKPGG Sbjct: 92 REKLKKKGVQNVEFVVGDAENLPFPDNSFDAVTISFGLRNVTDIDKALKEMYRVLKPGGR 151 Query: 136 FL 137 L Sbjct: 152 LL 153 >gnl|CDD|146872 pfam04446, Thg1, tRNAHis guanylyltransferase. The Thg1 protein from Saccharomyces cerevisiae is responsible for adding a GMP residue to the 5' end of tRNA His. Length = 181 Score = 29.2 bits (66), Expect = 1.5 Identities = 11/37 (29%), Positives = 19/37 (51%) Query: 228 YKSLFKRASTIYTEENSDLTGNVTASFSIIYVMGWKS 264 Y LF++++ ++ S L V + F+ YV WK Sbjct: 78 YSFLFRKSTKLFNRRLSKLLSLVVSLFTSSYVFLWKE 114 >gnl|CDD|33863 COG4106, Tam, Trans-aconitate methyltransferase [General function prediction only]. Length = 257 Score = 28.3 bits (63), Expect = 2.1 Identities = 11/42 (26%), Positives = 19/42 (45%) Query: 101 SQSVDLILSPLNLHIINDTLEMFSKINHMLKPGGMFLAAIPG 142 Q DL+ + L + D E+ ++ L PGG+ +P Sbjct: 90 EQPTDLLFANAVLQWLPDHPELLPRLVSQLAPGGVLAVQMPD 131 >gnl|CDD|38220 KOG3010, KOG3010, KOG3010, Methyltransferase [General function prediction only]. Length = 261 Score = 28.3 bits (63), Expect = 2.3 Identities = 10/51 (19%), Positives = 23/51 (45%), Gaps = 1/51 (1%) Query: 89 VISCPLEEIPSISQSVDLILSPLNLHIINDTLEMFSKINHMLKPGGMFLAA 139 + S + ++ +SVDLI + +H + + + +L+ G +A Sbjct: 86 MSSDEMVDLLGGEESVDLITAAQAVHWFDLE-RFYKEAYRVLRKDGGLIAV 135 >gnl|CDD|36315 KOG1099, KOG1099, KOG1099, SAM-dependent methyltransferase/cell division protein FtsJ [Cell cycle control, cell division, chromosome partitioning, General function prediction only]. Length = 294 Score = 28.0 bits (62), Expect = 3.0 Identities = 22/98 (22%), Positives = 38/98 (38%), Gaps = 20/98 (20%) Query: 50 ALELHGITGIVGYTCMETKKIHRMIRAEISTEFSTLKREVISCP-------LEEIPSISQ 102 A++L + I G ++ I F K +++ C L ++ Q Sbjct: 79 AVDLQPMAPIEGVIQLQGDITSASTAEAIIEHFGGEKADLVVCDGAPDVTGLHDLDEYVQ 138 Query: 103 SVDLILSPLNLHIINDTLEMFSKINHMLKPGGMFLAAI 140 + L+L+ LN+ +LKPGG F+A I Sbjct: 139 A-QLLLAALNI------------ATCVLKPGGSFVAKI 163 >gnl|CDD|119430 cd05170, PIKKc_SMG1, Suppressor of morphogenetic effect on genitalia-1 (SMG-1), catalytic domain; The SMG-1 catalytic domain subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. SMG-1 is a member of the phosphoinositide 3-kinase-related protein kinase (PIKK) subfamily. PIKKs have intrinsic serine/threonine kinase activity and are distinguished from other PKs by their unique catalytic domain, similar to that of lipid PI3K, and their large molecular weight (240-470 kDa). In addition to its catalytic domain, SMG-1 contains a FATC (FRAP, ATM and TRRAP, C-terminal) domain at the C-terminus. SMG-1 plays a critical role in the mRNA surveillance mechanism known as non-sense mediated mRNA decay (NMD). NMD protects the cells from the accumulation of aberrant mRNAs with premature termination codons (PTCs) generated by genome mutations and by errors during transcription and splicing. SMG-1 phosphorylates Upf1, another central component of NMD, at the C-terminus upon recognition of PTCs. The phosphorylation/dephosphorylation cycle of Upf1 is essential for promoting NMD.. Length = 307 Score = 27.8 bits (62), Expect = 3.1 Identities = 13/42 (30%), Positives = 22/42 (52%), Gaps = 3/42 (7%) Query: 31 RVAKEIAFRLNMINQTFENALELHGITGIVGYTCMETKKIHR 72 R+ +++ FR+ Q E AL L G+ G+ +C + I R Sbjct: 246 RIPEKVPFRMT---QNIETALGLTGVEGVFRLSCEQVLHIMR 284 >gnl|CDD|39501 KOG4300, KOG4300, KOG4300, Predicted methyltransferase [General function prediction only]. Length = 252 Score = 27.6 bits (61), Expect = 3.6 Identities = 11/46 (23%), Positives = 25/46 (54%), Gaps = 1/46 (2%) Query: 93 PLEEIPSISQ-SVDLILSPLNLHIINDTLEMFSKINHMLKPGGMFL 137 E +P ++ S D ++ L L + D ++ +++ +L+PGG + Sbjct: 134 DGENLPQLADGSYDTVVCTLVLCSVEDPVKQLNEVRRLLRPGGRII 179 >gnl|CDD|36312 KOG1096, KOG1096, KOG1096, Adenosine monophosphate deaminase [Nucleotide transport and metabolism]. Length = 768 Score = 27.6 bits (61), Expect = 3.7 Identities = 36/159 (22%), Positives = 64/159 (40%), Gaps = 27/159 (16%) Query: 12 RNRLRSFRQKDFSVYFLLDRVAKEIAFRLNMINQTFENALELHGITGIVGYTCMETKKIH 71 RL+ K F ++ LL+ KE+ + + ++ F N ++ T I CM K + Sbjct: 281 HRRLQYLESK-FQLHQLLNEK-KELLAQKKVPHRDFYNVRKVD--THIHASACMNQKHLL 336 Query: 72 RMIRAEISTEFSTLKREVISCPLEEIPSISQ--------SVDLILSPLNLHIINDTLEMF 123 R I+ ++ E R VI ++ ++ + + DL + L++H +T F Sbjct: 337 RFIKKKLRKE---PDRVVIQRDGRKL-TLREVFKSLGLTAYDLSVDTLDVHADRNTFHRF 392 Query: 124 SKINHMLKPGGMFLAAIPGIGTLHELRKALLKAETELTG 162 K N P G LR+ LK + + G Sbjct: 393 DKFNAKYNPVGE-----------SRLREIFLKTDNYING 420 >gnl|CDD|36109 KOG0891, KOG0891, KOG0891, DNA-dependent protein kinase [Replication, recombination and repair]. Length = 2341 Score = 27.2 bits (60), Expect = 5.0 Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 3/50 (6%) Query: 23 FSVYFLLDRVAKEIAFRLNMINQTFENALELHGITGIVGYTCMETKKIHR 72 F V L ++ +++ FRL + NA+E+ GI G TC ++ R Sbjct: 2168 FEVAMLREKFPEKVPFRLT---RMLINAMEVTGIEGTYRITCEHVMRVLR 2214 >gnl|CDD|37572 KOG2361, KOG2361, KOG2361, Predicted methyltransferase [General function prediction only]. Length = 264 Score = 26.9 bits (59), Expect = 5.8 Identities = 23/89 (25%), Positives = 32/89 (35%), Gaps = 4/89 (4%) Query: 123 FSKINHMLKPGGMFLAAIPGIGTLHELR--KALLKAETELTGGASPRVIPFMDIKSAGTL 180 + +LKPGG L G L +LR K +E G R F + L Sbjct: 166 IKNLRTLLKPGGSLLFRDYGRYDLAQLRFKKGQCISENFYVRGDGTRAYFF-TEEELDEL 224 Query: 181 MEKSGFISPIIDQD-TYTVYYKSMLHLMH 208 K+GF ++ D V K L + Sbjct: 225 FTKAGFEEVQLEVDCRLLVNRKKQLKMYR 253 >gnl|CDD|30790 COG0441, ThrS, Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Length = 589 Score = 26.8 bits (59), Expect = 7.6 Identities = 9/35 (25%), Positives = 18/35 (51%) Query: 14 RLRSFRQKDFSVYFLLDRVAKEIAFRLNMINQTFE 48 R+R F Q D ++ D++ E L +I + ++ Sbjct: 324 RVRGFTQDDAHIFCTPDQIKDEFKGILELILEVYK 358 >gnl|CDD|112099 pfam03269, DUF268, Caenorhabditis protein of unknown function, DUF268. Length = 177 Score = 26.3 bits (58), Expect = 8.2 Identities = 10/26 (38%), Positives = 14/26 (53%), Gaps = 1/26 (3%) Query: 120 LEMFSKINHMLKPGGMFLAAIPGIGT 145 L KI +LK GG+ +P +GT Sbjct: 91 LREMLKIKCVLKKGGLLFLGLP-LGT 115 >gnl|CDD|37186 KOG1975, KOG1975, KOG1975, mRNA cap methyltransferase [RNA processing and modification]. Length = 389 Score = 26.5 bits (58), Expect = 9.4 Identities = 16/69 (23%), Positives = 25/69 (36%), Gaps = 7/69 (10%) Query: 95 EEIPSISQSVDLILSPLNLHIINDTLE----MFSKINHMLKPGGMFLAAIPGIGTLHELR 150 + + D++ H +T E + LKPGG+F+ IP + Sbjct: 188 DLLEFKDPRFDIVSCQFAFHYAFETEESARIALRNVAKCLKPGGVFIGTIP---DSDVII 244 Query: 151 KALLKAETE 159 K L E E Sbjct: 245 KRLRAGEVE 253 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 0.322 0.136 0.389 Gapped Lambda K H 0.267 0.0636 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,238,728 Number of extensions: 168736 Number of successful extensions: 396 Number of sequences better than 10.0: 1 Number of HSP's gapped: 395 Number of HSP's successfully gapped: 23 Length of query: 273 Length of database: 6,263,737 Length adjustment: 92 Effective length of query: 181 Effective length of database: 4,275,709 Effective search space: 773903329 Effective search space used: 773903329 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: 57 (25.9 bits)