RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780765|ref|YP_003065178.1| 3-deoxy-manno-octulosonate cytidylyltransferase [Candidatus Liberibacter asiaticus str. psy62] (268 letters) >gnl|CDD|133010 cd02517, CMP-KDO-Synthetase, CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide. CMP-KDO Synthetase: 3-Deoxy-D-manno-octulosonate cytidylyltransferase (CMP-KDO synthetase) catalyzes the conversion of CTP and 3-deoxy-D-manno-octulosonate into CMP-3-deoxy-D-manno-octulosonate (CMP-KDO) and pyrophosphate. KDO is an essential component of the lipopolysaccharide found in the outer surface of gram-negative eubacteria. It is also a constituent of the capsular polysaccharides of some gram-negative eubacteria. Its presence in the cell wall polysaccharides of green algae and plant were also discovered. However, they have not been found in yeast and animals. The absence of the enzyme in mammalian cells makes it an attractive target molecule for drug design. Length = 239 Score = 266 bits (683), Expect = 4e-72 Identities = 111/244 (45%), Positives = 148/244 (60%), Gaps = 14/244 (5%) Query: 9 KVLVIIPARLNSMRFPKKILADINGLPMILHTAIRARKAN-IGRVIVAVDDTKINEIVLQ 67 KV+V+IPAR S R P K LADI G PMI H RA+KA + V+VA DD +I + V Sbjct: 1 KVIVVIPARYASSRLPGKPLADIAGKPMIQHVYERAKKAKGLDEVVVATDDERIADAVES 60 Query: 68 AGFESVMTHTSHQSGSDRIFEALNIIDSDKKSQIIVNMQADIPNIEPEILASVLLPLQ-N 126 G + VMT H SG+DRI E +D+D I+VN+Q D P I PE++ V+ L+ + Sbjct: 61 FGGKVVMTSPDHPSGTDRIAEVAEKLDADDD--IVVNVQGDEPLIPPEMIDQVVAALKDD 118 Query: 127 PIVDIGTLGTRIHGSTDPDDPNIVKIVVASPSENGCFRALYFTRT-----KTPHGTGPFY 181 P VD+ TL T I + +PN+VK+V+ ++G ALYF+R+ + P+Y Sbjct: 119 PGVDMATLATPISDEEELFNPNVVKVVL---DKDG--YALYFSRSPIPYPRDSSEDFPYY 173 Query: 182 QHLGIYAYRREALKRFTQLSPSVLEQRESLEQLRALEARMRIDVKIVQSNAMSVDTTNDL 241 +H+GIYAYRR+ L RF L PS LEQ ESLEQLRALE +I V ++ VDT DL Sbjct: 174 KHIGIYAYRRDFLLRFAALPPSPLEQIESLEQLRALENGYKIKVVETDHESIGVDTPEDL 233 Query: 242 EKVR 245 E+V Sbjct: 234 ERVE 237 >gnl|CDD|31405 COG1212, KdsB, CMP-2-keto-3-deoxyoctulosonic acid synthetase [Cell envelope biogenesis, outer membrane]. Length = 247 Score = 259 bits (664), Expect = 4e-70 Identities = 113/246 (45%), Positives = 150/246 (60%), Gaps = 12/246 (4%) Query: 9 KVLVIIPARLNSMRFPKKILADINGLPMILHTAIRARKANIGRVIVAVDDTKINEIVLQA 68 K +VIIPARL S R P K LADI G PMI+ A RA K+ RV+VA DD +I E V Sbjct: 3 KFVVIIPARLASTRLPGKPLADIGGKPMIVRVAERALKSGADRVVVATDDERIAEAVQAF 62 Query: 69 GFESVMTHTSHQSGSDRIFEALNIIDSDKKSQIIVNMQADIPNIEPEILASVLLPLQNPI 128 G E+VMT HQSG+DR+ E + + +IIVN+Q D P IEPE++ +V L+N Sbjct: 63 GGEAVMTSKDHQSGTDRLAEVVEKLGLP-DDEIIVNVQGDEPFIEPEVIRAVAENLENSN 121 Query: 129 VDIGTLGTRIHGSTDPDDPNIVKIVVASPSENGCFRALYFTRTKTPH-----GTGPFYQH 183 D+ TL +I + +PN+VK+V + ALYF+R P+ G PF +H Sbjct: 122 ADMATLAVKITDEEEAFNPNVVKVV-----LDKEGYALYFSRAPIPYGRDNFGGTPFLRH 176 Query: 184 LGIYAYRREALKRFTQLSPSVLEQRESLEQLRALEARMRIDVKIVQSN-AMSVDTTNDLE 242 +GIYAYR L+RF L PS LE+ ESLEQLR LE +I V+IV+ ++ VDT DLE Sbjct: 177 IGIYAYRAGFLERFVALKPSPLEKIESLEQLRVLENGEKIHVEIVKEVPSIGVDTPEDLE 236 Query: 243 KVRTLI 248 +VR ++ Sbjct: 237 RVRKIL 242 >gnl|CDD|145475 pfam02348, CTP_transf_3, Cytidylyltransferase. This family consists of two main Cytidylyltransferase activities: 1) 3-deoxy-manno-octulosonate cytidylyltransferase,, EC:2.7.7.38 catalysing the reaction:- CTP + 3-deoxy-D-manno-octulosonate <=> diphosphate + CMP-3-deoxy-D-manno-octulosonate, 2) acylneuraminate cytidylyltransferase EC:2.7.7.43,, catalysing the reaction:- CTP + N-acylneuraminate <=> diphosphate + CMP-N-acylneuraminate. NeuAc cytydilyltransferase of Mannheimia haemolytica has been characterized describing kinetics and regulation by substrate charge, energetic charge and amino-sugar demand. Length = 197 Score = 130 bits (328), Expect = 5e-31 Identities = 66/204 (32%), Positives = 102/204 (50%), Gaps = 15/204 (7%) Query: 11 LVIIPARLNSMRFPKKILADINGLPMILHTAIRARK-ANIGRVIVAVDDTKINEIVLQAG 69 + IIPAR S R P K L + G P+I A + +V+VA D +I +I + G Sbjct: 1 IAIIPARSGSKRLPGKNLLKLGGKPLIARVIEAALQSKLFDKVVVATDSEEIADIAEKFG 60 Query: 70 FESVMTHTSHQSGSDRIFEALNIIDSDKKSQIIVNMQADIPNIEPE-ILASVLLPLQNPI 128 V+ S SG+DR EA+ +D +IIVN+Q D P ++P IL ++ + Sbjct: 61 GGVVVRRGSLASGTDRFIEAVKAFLAD--EEIIVNLQGDEPLLQPTSILRAIEHLREAGE 118 Query: 129 VDIGTLGTRIHGSTDPDDPNIVKIVVASPSENGCFRALYFTRTKTPHGT------GPFYQ 182 + TL + S + +PN +K+V+ ALYF+R+ P+ + + Sbjct: 119 DYVSTLVKPVVSSEEILNPNPLKVVLDDAG-----YALYFSRSPIPYIRDHPAPLQLYLR 173 Query: 183 HLGIYAYRREALKRFTQLSPSVLE 206 H GIYA+R+E L R+ +PS LE Sbjct: 174 HKGIYAFRKEHLIRYVIDTPSDLE 197 >gnl|CDD|133011 cd02518, GT2_SpsF, SpsF is a glycosyltrnasferase implicated in the synthesis of the spore coat. Spore coat polysaccharide biosynthesis protein F (spsF) is a glycosyltransferase implicated in the synthesis of the spore coat in a variety of bacteria challenged by stress as starvation. The spsF gene is expressed in the late stage of coat development responsible for a terminal step in coat formation that involves the glycosylation of the coat. SpsF gene mutation resulted in spores that appeared normal. But, the spores tended to aggregate and had abnormal adsorption properties, indicating a surface alteration. Length = 233 Score = 60.3 bits (147), Expect = 6e-10 Identities = 31/132 (23%), Positives = 59/132 (44%), Gaps = 25/132 (18%) Query: 11 LVIIPARLNSMRFPKKILADINGLPMILHTAIRARKAN-IGRVIVA----VDDTKINEIV 65 + II AR+ S R P K+L + G P++ H R +++ I +++A +D + + Sbjct: 1 VAIIQARMGSTRLPGKVLKPLGGKPLLEHLLDRLKRSKLIDEIVIATSTNEEDDPLEALA 60 Query: 66 LQAGF-------ESVMTHTSHQSGSDRIFEALNIIDSDKKSQIIVNMQADIPNIEPEILA 118 + G E V+ R ++A ++D ++V + D P I+PEI+ Sbjct: 61 KKLGVKVFRGSEEDVL---------GRYYQAAEEYNAD----VVVRITGDCPLIDPEIID 107 Query: 119 SVLLPLQNPIVD 130 +V+ D Sbjct: 108 AVIRLFLKSGAD 119 >gnl|CDD|133006 cd02513, CMP-NeuAc_Synthase, CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety. CMP-N-acetylneuraminic acid synthetase (CMP-NeuAc synthetase) or acylneuraminate cytidylyltransferase catalyzes the transfer the CMP moiety of CTP to the anomeric hydroxyl group of NeuAc in the presence of Mg++. It is the second to last step in the sialylation of the oligosaccharide component of glycoconjugates by providing the activated sugar-nucleotide cytidine 5'-monophosphate N-acetylneuraminic acid (CMP-Neu5Ac), the substrate for sialyltransferases. Eukaryotic CMP-NeuAc synthetases are predominantly located in the nucleus. The activated CMP-Neu5Ac diffuses from the nucleus into the cytoplasm. Length = 223 Score = 54.5 bits (132), Expect = 3e-08 Identities = 34/108 (31%), Positives = 52/108 (48%), Gaps = 11/108 (10%) Query: 9 KVLVIIPARLNSMRFPKKILADINGLPMILHTAIRARKAN-IGRVIVAVDDTKINEIVLQ 67 K+L IIPAR S P K + + G P+I T A ++ RV+V+ DD +I E+ + Sbjct: 1 KILAIIPARGGSKGIPGKNIRPLGGKPLIAWTIEAALESKLFDRVVVSTDDEEIAEVARK 60 Query: 68 AGFESVM-------THTSHQSGSDRIFEALNIIDS-DKKSQIIVNMQA 107 G E T T+ S D I AL+ ++ + I+V +Q Sbjct: 61 YGAEVPFLRPAELATDTA--SSIDVILHALDQLEELGRDFDIVVLLQP 106 >gnl|CDD|32046 COG1861, SpsF, Spore coat polysaccharide biosynthesis protein F, CMP-KDO synthetase homolog [Cell envelope biogenesis, outer membrane]. Length = 241 Score = 50.3 bits (120), Expect = 6e-07 Identities = 27/117 (23%), Positives = 56/117 (47%), Gaps = 3/117 (2%) Query: 7 KEKVLVIIPARLNSMRFPKKILADINGLPMILHTAIRARKA-NIGRVIVAVDDTKINEIV 65 +LVII AR+ S R P K+L + G PMI + R RK+ ++ +++VA D + ++ + Sbjct: 1 MSMILVIIQARMGSTRLPGKVLLPLGGEPMIEYQLERVRKSKDLDKIVVATSDKEEDDAL 60 Query: 66 LQAGFESVMTHTSHQSGSDRIFEALNIIDSDKKSQIIVNMQADIPNIEPEILASVLL 122 + + + + I + ++V + D P ++PE++ + + Sbjct: 61 --EEVCRSHGFYVFRGSEEDVLQRFIIAIKAYSADVVVRVTGDNPFLDPELVDAAVD 115 >gnl|CDD|31280 COG1083, NeuA, CMP-N-acetylneuraminic acid synthetase [Cell envelope biogenesis, outer membrane]. Length = 228 Score = 41.0 bits (96), Expect = 3e-04 Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 1/62 (1%) Query: 9 KVLVIIPARLNSMRFPKKILADINGLPMILHTAIRARKAN-IGRVIVAVDDTKINEIVLQ 67 K + IIPAR S K + G P+I +T A + +V+++ D +I E + Sbjct: 3 KNIAIIPARGGSKGIKNKNIRKFGGKPLIGYTIEAALNSKLFDKVVISSDSEEILEEAKK 62 Query: 68 AG 69 G Sbjct: 63 YG 64 >gnl|CDD|32447 COG2266, COG2266, GTP:adenosylcobinamide-phosphate guanylyltransferase [Coenzyme metabolism]. Length = 177 Score = 35.6 bits (82), Expect = 0.013 Identities = 28/116 (24%), Positives = 53/116 (45%), Gaps = 10/116 (8%) Query: 21 MRFPKKILADINGLPMILHTAIRARKANIGRVIVAVDD--TKINEIVLQAGFESVMTHTS 78 M P+K L ++ G P+I + A + + +IVA+ K E + G + + T Sbjct: 14 MGRPEKPLLEVCGKPLIDRV-LEALRKIVDEIIVAISPHTPKTKEYLESVGVKVIET--- 69 Query: 79 HQSGSDRIFEALNIIDSDKKSQIIVNMQADIPNIEPEILASVLLPLQNPIVDIGTL 134 G + + ++S ++V+ AD+P + P I+ SV+ + V I T+ Sbjct: 70 --PGEGYVEDLRFALESLGTPILVVS--ADLPFLNPSIIDSVIDAAASVEVPIVTV 121 >gnl|CDD|32251 COG2068, COG2068, Uncharacterized MobA-related protein [General function prediction only]. Length = 199 Score = 35.6 bits (82), Expect = 0.013 Identities = 27/116 (23%), Positives = 52/116 (44%), Gaps = 4/116 (3%) Query: 9 KVLVIIPARLNSMRF-PKKILADINGLPMILHTAIRARKANIGRVIVAV--DDTKINEIV 65 V ++ A S R K+LA ++G P++ +A A A + RVIV + E + Sbjct: 5 TVAAVVLAAGRSSRMGQPKLLAPLDGKPLVRASAETALSAGLDRVIVVTGHRVAEAVEAL 64 Query: 66 LQAGFESVMTHTSHQSGSDRIFEALNIIDSDKKSQIIVNMQADIPNIEPEILASVL 121 L +V+ + + G +A + +D + +V M D+P + P + ++ Sbjct: 65 LAQLGVTVVVNPDYAQGLSTSLKAG-LRAADAEGDGVVLMLGDMPQVTPATVRRLI 119 >gnl|CDD|31400 COG1207, GlmU, N-acetylglucosamine-1-phosphate uridyltransferase (contains nucleotidyltransferase and I-patch acetyltransferase domains) [Cell envelope biogenesis, outer membrane]. Length = 460 Score = 34.4 bits (79), Expect = 0.038 Identities = 30/141 (21%), Positives = 47/141 (33%), Gaps = 19/141 (13%) Query: 26 KILADINGLPMILHTAIRARKANIGRVIVAVDDTKINEIVLQAGFESVMTHTSHQS---- 81 K+L + G PM+ H AR ++V V E V +A E Q Sbjct: 22 KVLHPVAGKPMLEHVIDAARALGPDDIVVVVGHGA--EQVREALAERDDVEFVLQEEQLG 79 Query: 82 GSDRIFEALNIIDSDKKSQIIVNMQADIPNIEPEILASVLLPLQNPIVDIGTLGTRIHGS 141 + +AL + D ++V + D+P I E L +L L + Sbjct: 80 TGHAVLQALPALADDYDGDVLV-LYGDVPLITAETLEELLAAHPAHGAAATVLTAEL--- 135 Query: 142 TDP---------DDPNIVKIV 153 DP + + IV Sbjct: 136 DDPTGYGRIVRDGNGEVTAIV 156 >gnl|CDD|133025 cd04182, GT_2_like_f, GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function. GT-2 includes diverse families of glycosyltransferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. Glycosyltransferases have been classified into more than 90 distinct sequence based families. Length = 186 Score = 34.1 bits (79), Expect = 0.045 Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 1/48 (2%) Query: 10 VLVIIPARLNSMRFPK-KILADINGLPMILHTAIRARKANIGRVIVAV 56 + II A S R K+L ++G P++ H A A + RVIV + Sbjct: 1 IAAIILAAGRSSRMGGNKLLLPLDGKPLLRHALDAALAAGLSRVIVVL 48 >gnl|CDD|31089 COG0746, MobA, Molybdopterin-guanine dinucleotide biosynthesis protein A [Coenzyme metabolism]. Length = 192 Score = 31.8 bits (72), Expect = 0.20 Identities = 14/39 (35%), Positives = 17/39 (43%) Query: 20 SMRFPKKILADINGLPMILHTAIRARKANIGRVIVAVDD 58 S R K L +NG P+I H R R VI A + Sbjct: 15 SRRMRDKALLPLNGRPLIEHVIDRLRPQVDVVVISANRN 53 >gnl|CDD|32634 COG2802, COG2802, Uncharacterized protein, similar to the N-terminal domain of Lon protease [General function prediction only]. Length = 221 Score = 30.7 bits (69), Expect = 0.42 Identities = 23/144 (15%), Positives = 38/144 (26%), Gaps = 19/144 (13%) Query: 85 RIFEA--LNIIDSDKKSQIIVNMQADIPNIEPEILASVLLPLQNPIVDIGTLGTRIHGST 142 IFE L ++ + + + + V L + D+G L Sbjct: 31 NIFEPRYLAMVRTCLAEGRRFGV------VLIDRGREVGGGLPPELSDVGCLARITEFEE 84 Query: 143 DPDDPNIVKIVVASPSENGCFRALYFTRTKTPH--GTGPFYQHLGIYAYRREALKR---- 196 D ++ + FR L P+ PF+ L E + R Sbjct: 85 LGDGRYLILVRGGQ-----RFRVLEELADDDPYRRARVPFWPDLPSDPDGAEEVDRRLDA 139 Query: 197 FTQLSPSVLEQRESLEQLRALEAR 220 + QR L R Sbjct: 140 LLMRAARAYLQRLELLADWESYER 163 >gnl|CDD|133009 cd02516, CDP-ME_synthetase, CDP-ME synthetase is involved in mevalonate-independent isoprenoid production. 4-diphosphocytidyl-2-methyl-D-erythritol synthase (CDP-ME), also called 2C-methyl-d-erythritol 4-phosphate cytidylyltransferase catalyzes the third step in the alternative (non-mevalonate) pathway of Isopentenyl diphosphate (IPP) biosynthesis: the formation of 4-diphosphocytidyl-2C-methyl-D-erythritol from CTP and 2C-methyl-D-erythritol 4-phosphate. This mevalonate independent pathway that utilizes pyruvate and glyceraldehydes 3-phosphate as starting materials for production of IPP occurs in a variety of bacteria, archaea and plant cells, but is absent in mammals. Thus, CDP-ME synthetase is an attractive targets for the structure-based design of selective antibacterial, herbicidal and antimalarial drugs. Length = 218 Score = 30.6 bits (70), Expect = 0.45 Identities = 24/124 (19%), Positives = 51/124 (41%), Gaps = 22/124 (17%) Query: 12 VIIPA-----RLNSMRFPKKILADINGLPMILHTAIRA--RKANIGRVIVAV--DDTKIN 62 II A R+ + K ++ G P++ HT + A I ++V V DD + Sbjct: 3 AIILAAGSGSRMGADI--PKQFLELGGKPVLEHT-LEAFLAHPAIDEIVVVVPPDDIDLA 59 Query: 63 EIVLQAGFESVMTHTSHQSGSDR---IFEALNIIDSDKKSQIIVNMQADI--PNIEPEIL 117 + + + G V+ + G+ R + L + ++++ D P + PE++ Sbjct: 60 KELAKYGLSKVVKIV--EGGATRQDSVLNGLKALPDADPDIVLIH---DAARPFVSPELI 114 Query: 118 ASVL 121 ++ Sbjct: 115 DRLI 118 >gnl|CDD|31401 COG1208, GCD1, Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis/translation initiation factor 2B, gamma/epsilon subunits (eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis, outer membrane / Translation, ribosomal structure and biogenesis]. Length = 358 Score = 28.8 bits (64), Expect = 1.6 Identities = 39/227 (17%), Positives = 68/227 (29%), Gaps = 20/227 (8%) Query: 26 KILADINGLPMILHTAIRARKANIGRVIVAVD--DTKINEIVLQAGFESVMTHTSHQSGS 83 K L I G P+I + A + +++ V +I E V + Sbjct: 24 KPLLPIAGKPLIEYVLEALAAAGVEEIVLVVGYLGEQIEEYFGDGEGLGVRITYVVEKEP 83 Query: 84 DRIFEALNIIDSDKKSQIIVNMQADIPNIEPEILASVLLPLQNPIVDIGTLGTRIHGSTD 143 AL + + D+ L+ +L + TR+ D Sbjct: 84 LGTAGALKNALDLLGGDDFLVLNGDVLTDLD--LSELLEFHKKKGALATIALTRV---LD 138 Query: 144 PDDPNIVKIVVASPSENGCFRALYFTRTKTPHGTGPFYQHLGIYAYRREALKRFTQLSPS 203 P + +V+ ++G R + F P + GIY + E + Sbjct: 139 PSEFGVVET------DDGDGRVVEFREKPGPEEPPSNLINAGIYIFDPEVFDYIEKGERF 192 Query: 204 VLEQRESLEQLRALEARMRIDVKIVQSNA--MSVDTTNDLEKVRTLI 248 E E+L A DV + + T DL + L+ Sbjct: 193 DFE-----EELLPALAAKGEDVYGYVFEGYWLDIGTPEDLLEANELL 234 >gnl|CDD|133014 cd02523, PC_cytidylyltransferase, Phosphocholine cytidylyltransferases catalyze the synthesis of CDP-choline. This family contains proteins similar to prokaryotic phosphocholine (P-cho) cytidylyltransferases. Phosphocholine (PC) cytidylyltransferases catalyze the transfer of a cytidine monophosphate from CTP to phosphocholine to form CDP-choline. PC is the most abundant phospholipid in eukaryotic membranes and it is also important in prokaryotic membranes. For pathogenic prokaryotes, the cell surface PC facilitates the interaction with host surface and induces attachment and invasion. In addition cell wall PC serves as scaffold for a group of choline-binding proteins that are secreted from the cells. Phosphocholine (PC) cytidylyltransferase is a key enzyme in the prokaryotic choline metabolism pathway. It has been hypothesized to consist of a choline transport system, a choline kinase, CTP:phosphocholine cytidylyltransferase, and a choline phosphotransferase that transfers P-Cho from CDP-Cho to either lipoteichoic acid or lipopolysaccharide. Length = 229 Score = 28.7 bits (65), Expect = 1.6 Identities = 8/31 (25%), Positives = 16/31 (51%) Query: 26 KILADINGLPMILHTAIRARKANIGRVIVAV 56 K L +ING P++ ++A I +++ Sbjct: 21 KCLLEINGKPLLERQIETLKEAGIDDIVIVT 51 >gnl|CDD|37300 KOG2089, KOG2089, KOG2089, Metalloendopeptidase family - saccharolysin & thimet oligopeptidase [Posttranslational modification, protein turnover, chaperones]. Length = 718 Score = 28.8 bits (64), Expect = 1.7 Identities = 19/91 (20%), Positives = 34/91 (37%), Gaps = 14/91 (15%) Query: 171 TKTPHGTGPFYQHLGIYAYRREALKRFTQLSPS-VLEQRESLEQLRALEAR--------- 220 T P +H I R+ + + + LE +EQL L Sbjct: 243 TLKYPHYFPVMKHCKIRQTRKTVWRAYNSRASEGDLENSAIIEQLLKLRLELAKLLGYST 302 Query: 221 ---MRIDVKIVQSNAMSVDTTNDL-EKVRTL 247 + +K+ +S+ V+ +DL +K+R L Sbjct: 303 YADYSLAMKMAKSSETVVEFLDDLSQKLRPL 333 >gnl|CDD|133044 cd06422, NTP_transferase_like_1, NTP_transferase_like_1 is a member of the nucleotidyl transferase family. This is a subfamily of nucleotidyl transferases. Nucleotidyl transferases transfer nucleotides onto phosphosugars. The activated sugars are precursors for synthesis of lipopolysaccharide, glycolipids and polysaccharides. Other subfamilies of nucleotidyl transferases include Alpha-D-Glucose-1-Phosphate Cytidylyltransferase, Mannose-1-phosphate guanyltransferase, and Glucose-1-phosphate thymidylyltransferase. Length = 221 Score = 28.7 bits (65), Expect = 1.9 Identities = 11/29 (37%), Positives = 15/29 (51%) Query: 26 KILADINGLPMILHTAIRARKANIGRVIV 54 K L + G P+I H R A I R++V Sbjct: 22 KPLVPVAGKPLIDHALDRLAAAGIRRIVV 50 >gnl|CDD|99743 cd06450, DOPA_deC_like, DOPA decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to DOPA/tyrosine decarboxylase (DDC), histidine decarboxylase (HDC), and glutamate decarboxylase (GDC). DDC is active as a dimer and catalyzes the decarboxylation of tyrosine. GDC catalyzes the decarboxylation of glutamate and HDC catalyzes the decarboxylation of histidine.. Length = 345 Score = 28.7 bits (65), Expect = 1.9 Identities = 17/73 (23%), Positives = 30/73 (41%), Gaps = 7/73 (9%) Query: 72 SVMTHTSHQSGSDRIFEALNIIDSDKKSQIIVNMQADIPNIEPEILASVLLPLQNPIVDI 131 S H S + + + + ++ D+ ++ D +E I L NPI+ + Sbjct: 101 SDQAHVSVEKAAAYLDVKVRLVPVDEDGRM------DPEALEAAIDEDKAEGL-NPIMVV 153 Query: 132 GTLGTRIHGSTDP 144 T GT G+ DP Sbjct: 154 ATAGTTDTGAIDP 166 >gnl|CDD|133065 cd06915, NTP_transferase_WcbM_like, WcbM_like is a subfamily of nucleotidyl transferases. WcbM protein of Burkholderia mallei is involved in the biosynthesis, export or translocation of capsule. It is a subfamily of nucleotidyl transferases that transfer nucleotides onto phosphosugars. Length = 223 Score = 28.3 bits (64), Expect = 2.1 Identities = 13/51 (25%), Positives = 19/51 (37%), Gaps = 5/51 (9%) Query: 185 GIYAYRREALKRFTQLSPS----VLEQRESLEQLRALEARMR-IDVKIVQS 230 G+Y R+E L + S VL +L E ID+ I + Sbjct: 168 GVYLLRKEILAEIPADAFSLEADVLPALVKRGRLYGFEVDGYFIDIGIPED 218 >gnl|CDD|176140 cd08449, PBP2_XapR, The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold. In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Length = 197 Score = 27.6 bits (62), Expect = 3.7 Identities = 21/76 (27%), Positives = 31/76 (40%), Gaps = 19/76 (25%) Query: 191 REALKRFTQLSPSV----LEQRESLEQLRALEARMRIDVKIVQSNAMSVDTTNDL----- 241 AL+RF + P+V E Q AL ++ RID+ V+ DT ND Sbjct: 16 GPALRRFKRQYPNVTVRFHELSPE-AQKAALLSK-RIDLGFVR----FADTLNDPPLASE 69 Query: 242 ----EKVRTLIPHDHH 253 E + +P +H Sbjct: 70 LLWREPMVVALPEEHP 85 >gnl|CDD|31406 COG1213, COG1213, Predicted sugar nucleotidyltransferases [Cell envelope biogenesis, outer membrane]. Length = 239 Score = 27.5 bits (61), Expect = 3.9 Identities = 18/84 (21%), Positives = 30/84 (35%), Gaps = 10/84 (11%) Query: 177 TGPFYQHLGIYAYRREALKRFTQLSPSVLEQRESLEQLRALEARMRI-----DVKIVQSN 231 T + +GI+ + +L S R +E + D+ + Sbjct: 157 TEYDGEDIGIFILSDSIFEDTYELL-----VERSEYDYREVEKEAGLPFTEVDIHVDGLF 211 Query: 232 AMSVDTTNDLEKVRTLIPHDHHKG 255 M VDT DLE+ R + + KG Sbjct: 212 WMEVDTPEDLERARKYLVPNIKKG 235 >gnl|CDD|146356 pfam03678, Adeno_hexon_C, Hexon, adenovirus major coat protein, C-terminal domain. Hexon is the major coat protein from adenovirus type 2. Hexon forms a homo-trimer. The 240 copies of the hexon trimer are organized so that 12 lie on each of the 20 facets. The central 9 hexons in a facet are cemented together by 12 copies of polypeptide IX. The penton complex, formed by the peripentonal hexons and base hexon (holding in place a fibre), lie at each of the 12 vertices. The N and C-terminal domains adopt the same PNGase F-like fold although they are significantly different in length. Length = 236 Score = 27.3 bits (61), Expect = 4.7 Identities = 10/28 (35%), Positives = 12/28 (42%), Gaps = 1/28 (3%) Query: 147 PNIVKIVVASPSEN-GCFRALYFTRTKT 173 N + + PS N FR FTR K Sbjct: 23 ANSTNVPINIPSRNWAAFRGWSFTRLKA 50 >gnl|CDD|32265 COG2082, CobH, Precorrin isomerase [Coenzyme metabolism]. Length = 210 Score = 27.1 bits (60), Expect = 5.0 Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 3/56 (5%) Query: 14 IPARLNSMRFPKKILADINGLPMILHTAIRARKANIGRVIVAVDDTKINEIVLQAG 69 I A +++ I+ D+N M+ R R + VI VDD ++ E+ + G Sbjct: 59 IEAGREALKAGCPIVVDVN---MVAAGITRRRLPALNPVICYVDDPRVAELAKEEG 111 >gnl|CDD|30496 COG0147, TrpE, Anthranilate/para-aminobenzoate synthases component I [Amino acid transport and metabolism / Coenzyme metabolism]. Length = 462 Score = 26.9 bits (59), Expect = 5.7 Identities = 14/34 (41%), Positives = 18/34 (52%), Gaps = 1/34 (2%) Query: 212 EQLRALEARMRIDVKIVQSNAMSVDTT-NDLEKV 244 E+ ALEA + D K + M VD NDL +V Sbjct: 287 EEDEALEAELLNDEKERAEHLMLVDLARNDLGRV 320 >gnl|CDD|133020 cd02540, GT2_GlmU_N_bac, N-terminal domain of bacterial GlmU. The N-terminal domain of N-Acetylglucosamine-1-phosphate uridyltransferase (GlmU). GlmU is an essential bacterial enzyme with both an acetyltransferase and an uridyltransferase activity which have been mapped to the C-terminal and N-terminal domains, respectively. This family represents the N-terminal uridyltransferase. GlmU performs the last two steps in the synthesis of UDP-N-acetylglucosamine (UDP-GlcNAc), which is an essential precursor in both the peptidoglycan and the lipopolysaccharide metabolic pathways in Gram-positive and Gram-negative bacteria, respectively. Length = 229 Score = 26.3 bits (59), Expect = 8.2 Identities = 33/156 (21%), Positives = 60/156 (38%), Gaps = 40/156 (25%) Query: 21 MRFPK-KILADINGLPMILHTAIR-ARKANIGRVIV-----------AVDDTKINEIVLQ 67 M+ K+L + G PM+ H + AR R++V A+ + + E VLQ Sbjct: 12 MKSDLPKVLHPLAGKPMLEH-VLDAARALGPDRIVVVVGHGAEQVKKALANPNV-EFVLQ 69 Query: 68 AGFESVMTHTSHQSGS-DRIFEALNIIDSDKKSQIIVNMQADIPNIEPEILASVLLPLQN 126 Q G+ + +AL + + +++ D+P I PE L +L + Sbjct: 70 ----------EEQLGTGHAVKQALPALKDFEGDVLVLY--GDVPLITPETLQRLLEAHRE 117 Query: 127 PIVDIGTLGTRIHGSTDP---------DDPNIVKIV 153 D+ L + DP + +++IV Sbjct: 118 AGADVTVLTAEL---EDPTGYGRIIRDGNGKVLRIV 150 >gnl|CDD|144176 pfam00483, NTP_transferase, Nucleotidyl transferase. This family includes a wide range of enzymes which transfer nucleotides onto phosphosugars. Length = 247 Score = 26.4 bits (59), Expect = 8.5 Identities = 10/37 (27%), Positives = 16/37 (43%) Query: 20 SMRFPKKILADINGLPMILHTAIRARKANIGRVIVAV 56 + K ++ ++ PMI +T R A I IV Sbjct: 17 TRTLAKPLVPVLDKYPMIQYTLSRLMNAGIREPIVIC 53 >gnl|CDD|38856 KOG3651, KOG3651, KOG3651, Protein kinase C, alpha binding protein [Signal transduction mechanisms]. Length = 429 Score = 26.6 bits (58), Expect = 8.6 Identities = 13/33 (39%), Positives = 20/33 (60%) Query: 181 YQHLGIYAYRREALKRFTQLSPSVLEQRESLEQ 213 Y++ I R+EA RF ++ VLE+ E L+Q Sbjct: 277 YEYRLILRCRQEARARFMKMRDDVLEKMELLDQ 309 >gnl|CDD|153378 cd07366, 3MGA_Dioxygenase, Subunit B of the Class III Extradiol ring-cleavage dioxygenase, 3-O-Methylgallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 3-O-Methylgallate. 3-O-Methylgallate Dioxygenase catalyzes the oxidization and subsequent ring-opening of 3-O-Methylgallate (3MGA) between carbons 2 and 3. 3-O-Methylgallate Dioxygenase is a key enzyme in the syringate degradation pathway, in which the syringate is first converted to 3-O-Methylgallate by O-demethylase. This enzyme is a member of the class III extradiol dioxygenase family, a group of enzymes which uses a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents the catalytic subunit, B. Length = 328 Score = 26.2 bits (58), Expect = 9.3 Identities = 9/38 (23%), Positives = 18/38 (47%), Gaps = 5/38 (13%) Query: 199 QLSPSVLEQRE-----SLEQLRALEARMRIDVKIVQSN 231 Q++P + R +L++L RIDV ++ + Sbjct: 58 QITPEEMAARYARCQAALDRLADFIRAARIDVAVIVGD 95 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 0.320 0.136 0.383 Gapped Lambda K H 0.267 0.0782 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,165,666 Number of extensions: 166292 Number of successful extensions: 474 Number of sequences better than 10.0: 1 Number of HSP's gapped: 458 Number of HSP's successfully gapped: 42 Length of query: 268 Length of database: 6,263,737 Length adjustment: 92 Effective length of query: 176 Effective length of database: 4,275,709 Effective search space: 752524784 Effective search space used: 752524784 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: 56 (25.2 bits)