RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780775|ref|YP_003065188.1| undecaprenyl diphosphate synthase [Candidatus Liberibacter asiaticus str. psy62] (243 letters) >gnl|CDD|144739 pfam01255, Prenyltransf, Putative undecaprenyl diphosphate synthase. Previously known as uncharacterized protein family UPF0015, a single member of this family has been identified as an undecaprenyl diphosphate synthase. Length = 222 Score = 304 bits (782), Expect = 1e-83 Identities = 111/222 (50%), Positives = 149/222 (67%) Query: 17 IMDGNGRWAAARGLPRCAGHRKGIEVFNEIVAAAAEVGIKNLTIFAFSINNWRRPVSEIS 76 IMDGN RWA RGLPR GHR G E EI+ E+GIK LT++AFS NW+RP E+ Sbjct: 1 IMDGNRRWAKKRGLPRTEGHRAGAEALREILEWCLELGIKYLTLYAFSTENWKRPKEEVD 60 Query: 77 ELVKLIKSFLKKGFYSLKKNNIKVRVIGNRLSLDDDILCVLKEAEDQTRLNTGLNLFIAF 136 L++L++ L++ L KN ++VRVIG+ L +D+ +++AE+ T+ NTGL L IA Sbjct: 61 FLMELLEEKLRRLLEDLHKNGVRVRVIGDLSLLPEDLRKAIEDAEEATKNNTGLTLNIAL 120 Query: 137 NYSSRDEISRAIKNIFQDIESGSVCSHDVDSSLIAKYLDTSDVPDPDLIIRTGGEKRLSD 196 NY RDEI A+K + +D++ G + D+D +I KYL TSD+PDPDL+IRT GEKRLS+ Sbjct: 121 NYGGRDEIVDAVKRLAEDVKDGKLSPEDIDEEVIEKYLYTSDLPDPDLLIRTSGEKRLSN 180 Query: 197 FLLWQVAYSEFVFIPEYWPDFSRELFFHALNQYNLRDRRFGG 238 FLLWQ AY+E F WPDF++E A+ Y R+RRFG Sbjct: 181 FLLWQSAYAELYFTDTLWPDFTKEDLLRAIRDYQSRERRFGK 222 >gnl|CDD|30370 COG0020, UppS, Undecaprenyl pyrophosphate synthase [Lipid metabolism]. Length = 245 Score = 285 bits (730), Expect = 1e-77 Identities = 109/237 (45%), Positives = 155/237 (65%) Query: 3 ASMMSSSPPDHIGIIMDGNGRWAAARGLPRCAGHRKGIEVFNEIVAAAAEVGIKNLTIFA 62 + + P H+ IIMDGN RWA RGLPR GH+ G + EI+ E+GIK LT++A Sbjct: 9 KRELPARLPRHVAIIMDGNRRWAKKRGLPRIEGHKAGAKALREILEWCLELGIKYLTLYA 68 Query: 63 FSINNWRRPVSEISELVKLIKSFLKKGFYSLKKNNIKVRVIGNRLSLDDDILCVLKEAED 122 FS NW+RP E+S L++L + L++ L KN +++R+IG+ L +++ +++AE+ Sbjct: 69 FSTENWKRPKEEVSFLMELFEKALREELKKLHKNGVRIRIIGDLSRLPEEVREAIEKAEE 128 Query: 123 QTRLNTGLNLFIAFNYSSRDEISRAIKNIFQDIESGSVCSHDVDSSLIAKYLDTSDVPDP 182 +T+ NTGL L IA NY RDEI A++ I +D+ +G + D+D LI+ +L TS +PDP Sbjct: 129 KTKNNTGLTLNIAVNYGGRDEIVDAVRKIAEDVAAGKLSPEDIDEELISSHLYTSGLPDP 188 Query: 183 DLIIRTGGEKRLSDFLLWQVAYSEFVFIPEYWPDFSRELFFHALNQYNLRDRRFGGL 239 DL+IRT GE+RLS+FLLWQ AYSE F WPDF RE A+ Y R+RRFG + Sbjct: 189 DLLIRTSGEQRLSNFLLWQSAYSELYFTDVLWPDFRREDLLRAIRDYQKRERRFGRV 245 >gnl|CDD|29593 cd00475, CIS_IPPS, Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl diphosphates. A few can also catalyze the condensation of IPP to trans-geranyl diphosphate to form the short-chain cis,trans- FPP. In prokaryotes, the cis-IPPS, undecaprenyl diphosphate synthase (UPP synthase) catalyzes the formation of the carrier lipid UPP in bacterial cell wall peptidooglycan biosynthesis. Similarly, in eukaryotes, the cis-IPPS, dehydrodolichyl diphosphate (dedol-PP) synthase catalyzes the formation of the polyisoprenoid glycosyl carrier lipid dolichyl monophosphate. cis-IPPS are mechanistically and structurally distinct from trans-IPPS, lacking the DDXXD motifs, yet requiring Mg2+ for activity.. Length = 221 Score = 250 bits (641), Expect = 2e-67 Identities = 95/219 (43%), Positives = 139/219 (63%) Query: 11 PDHIGIIMDGNGRWAAARGLPRCAGHRKGIEVFNEIVAAAAEVGIKNLTIFAFSINNWRR 70 P H+ IMDGN RWA RG+ R GH+ G E +I+ E+G+K +T++AFS NW+R Sbjct: 1 PKHVAFIMDGNRRWAKQRGMDRIEGHKAGAEKLRDILRWCLELGVKEVTLYAFSTENWKR 60 Query: 71 PVSEISELVKLIKSFLKKGFYSLKKNNIKVRVIGNRLSLDDDILCVLKEAEDQTRLNTGL 130 P E+ L++L + L++ L+K +++R+IG+ L + + +K+AE+ T+ NTG Sbjct: 61 PKEEVDFLMELFRDVLRRILKELEKLGVRIRIIGDLSLLPESLQKEIKKAEEATKNNTGF 120 Query: 131 NLFIAFNYSSRDEISRAIKNIFQDIESGSVCSHDVDSSLIAKYLDTSDVPDPDLIIRTGG 190 L +AFNY R EI A++ I + +++G + D+D S + K+L T D PDPDL+IRT G Sbjct: 121 TLNVAFNYGGRQEIIHAVREIAEKVKAGKLTPEDIDESTLNKHLYTHDSPDPDLLIRTSG 180 Query: 191 EKRLSDFLLWQVAYSEFVFIPEYWPDFSRELFFHALNQY 229 E+RLS+FLLWQ AYSE F WPDF+ F AL Y Sbjct: 181 EQRLSNFLLWQSAYSELYFSDVLWPDFTFWDFLRALLDY 219 >gnl|CDD|36815 KOG1602, KOG1602, KOG1602, Cis-prenyltransferase [Lipid transport and metabolism]. Length = 271 Score = 215 bits (548), Expect = 1e-56 Identities = 91/234 (38%), Positives = 133/234 (56%), Gaps = 4/234 (1%) Query: 11 PDHIGIIMDGNGRWAAARGLPRCAGHRKGIEVFNEIVAAAAEVGIKNLTIFAFSINNWRR 70 P H+ IMDGN R+A RGL GH G E EI+ E+GIK +T+FAFSI N++R Sbjct: 37 PRHVAFIMDGNRRYAKKRGLETSEGHEAGFEALKEILELCKELGIKEVTVFAFSIENFKR 96 Query: 71 PVSEISELVKLIKSFLKKGF---YSLKKNNIKVRVIGNRLSLDDDILCVLKEAEDQTRLN 127 E+ L+ L +++ L K +++RVIG+ L + + +K+ E+ T+ N Sbjct: 97 SPEEVDGLMDLALEKIERLLEQGEKLDKYGVRIRVIGDLSLLPESLRKAIKKIEEATKNN 156 Query: 128 TGLNLFIAFNYSSRDEISRAIKNIFQDIESGSVCSHDVDSSLIAKYLDTSDVPDPDLIIR 187 T L L + F Y+SRDEI A++ I + ++ G + D++ S I + L TSDVP PDL+IR Sbjct: 157 TRLILNVCFAYTSRDEILHAVRGIVKRVKDGDIDV-DINLSDIEECLYTSDVPHPDLLIR 215 Query: 188 TGGEKRLSDFLLWQVAYSEFVFIPEYWPDFSRELFFHALNQYNLRDRRFGGLSK 241 T GE RLS+FLLWQ + +E F WP+F F A+ ++ G K Sbjct: 216 TSGEDRLSNFLLWQTSETELFFADALWPEFGLWHLFWAILKFQRNQSYLGKRKK 269 >gnl|CDD|38029 KOG2818, KOG2818, KOG2818, Predicted undecaprenyl diphosphate synthase [Lipid transport and metabolism]. Length = 263 Score = 48.4 bits (115), Expect = 2e-06 Identities = 47/195 (24%), Positives = 71/195 (36%), Gaps = 21/195 (10%) Query: 45 EIVAAAAEVGIKNLTIFAFSINNWRRPVSEISELVKLIKSFLKKGFYSLKKNNIKVRVIG 104 IV A VGIK L+++ R + I S L F L + + V Sbjct: 87 SIVFWAVTVGIKYLSLYDRVGIKKRNM----PVVRDEIISHLANYF-GLDEPTLAVT--- 138 Query: 105 NRLSLDDDILCVLKEAEDQTRLNTGLNLFIAFNYSSRDEISRAIKNIFQDIESGSVC--S 162 +LS D+ ED+ +L T R I + I + + Sbjct: 139 IKLSNDEP------NQEDKCKLGTHAIS----LEDGRMIIIDLTRLIQELCYLYELYRSE 188 Query: 163 HDVDSSLIAKYLDTSDVPDPDLIIRTGGEKRLSDFLLWQVAYSEFVFIPEYWPDFSRELF 222 D+ + L P+PDL++ G L F W + +EF P + S E F Sbjct: 189 TDITVETVDSELKEFVEPEPDLLLFFGPVLVLQGFPPWHIRLTEFTRKPSHLC-TSYETF 247 Query: 223 FHALNQYNLRDRRFG 237 F AL +Y ++R G Sbjct: 248 FRALRKYADCEQRVG 262 >gnl|CDD|32865 COG3051, CitF, Citrate lyase, alpha subunit [Energy production and conversion]. Length = 513 Score = 32.2 bits (73), Expect = 0.12 Identities = 13/38 (34%), Positives = 23/38 (60%) Query: 37 RKGIEVFNEIVAAAAEVGIKNLTIFAFSINNWRRPVSE 74 R G V N ++ A++G KNLT+ + S+++ P+ E Sbjct: 75 RGGDLVVNMVMDVIAKMGFKNLTLASSSLSDCHAPLVE 112 >gnl|CDD|113013 pfam04223, CitF, Citrate lyase, alpha subunit (CitF). In citrate-utilising prokaryotes, citrate lyase EC:4.1.3.6 cleaves intracellular citrate into acetate and oxaloacetate, and is organized as a functional complex consisting of alpha, beta, and gamma subunits. The gamma subunit serves as an acyl carrier protein (ACP), and has a 2'-(5''-phosphoribosyl)-3'-dephospho-CoA prosthetic group. The citrate lyase is active only if this prosthetic group is acetylated; this acetylation is catalysed by an acetate:SH-citrate lyase ligase. The alpha subunit substitutes citryl for the acetyl group to form citryl-S-ACP. The beta subunit completes the reaction by cleaving the citryl to yield oxaloacetate and (regenerated) acetyl-S-ACP. This family represents the alpha subunit EC:2.8.3.10. Length = 466 Score = 30.9 bits (70), Expect = 0.31 Identities = 15/38 (39%), Positives = 22/38 (57%) Query: 37 RKGIEVFNEIVAAAAEVGIKNLTIFAFSINNWRRPVSE 74 R+G V N ++ A++G KNLTI S+ N P+ E Sbjct: 30 REGDYVVNMVMEVIAKMGFKNLTIAPSSLTNVHEPLVE 67 >gnl|CDD|146124 pfam03328, HpcH_HpaI, HpcH/HpaI aldolase/citrate lyase family. This family includes 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase and 4-hydroxy-2-oxovalerate aldolase. Length = 221 Score = 28.1 bits (63), Expect = 2.0 Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 1/54 (1%) Query: 14 IGIIMDGNGRWAAARGLPRCAGHRKGIEVFNEIVAAAAEVGIKNLTIFAFSINN 67 G+ + G +A G R G + + I+AAA GI A I++ Sbjct: 145 DGVFL-GPEDLSADLGTLRSPGGPEVLFARTRILAAARAAGIAAFDTVASDIDD 197 >gnl|CDD|37375 KOG2164, KOG2164, KOG2164, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]. Length = 513 Score = 28.1 bits (62), Expect = 2.5 Identities = 23/119 (19%), Positives = 40/119 (33%), Gaps = 26/119 (21%) Query: 70 RPVSEISELVKLIKSFLKKGF-----YSLKKNNIKVRVIGNRLSLDDDILCVLKEAEDQT 124 P + + +K SFL + S L DDD+L V +A Sbjct: 323 LPRRMVPQAIKGRISFLDECTNDQLILSEMSRIDNEYNASRGLGRDDDLLSVSGDAYYFY 382 Query: 125 RLNTGLNLFI----------AFNYSSRDEISRAIKNIFQDIESGSVCSHDVDSSLIAKY 173 + G ++++ ++Y DEI I+N+ VD L ++ Sbjct: 383 QSVDGQHIYLHPLDVKILLACYSYDLFDEIEAQIENM-----------EQVDEELRRRF 430 >gnl|CDD|39545 KOG4344, KOG4344, KOG4344, Uncharacterized conserved protein [Function unknown]. Length = 1121 Score = 27.5 bits (60), Expect = 3.2 Identities = 25/120 (20%), Positives = 46/120 (38%), Gaps = 4/120 (3%) Query: 15 GIIMDGNGRWAAARGLPRCAGHRKGIEVFNEIVAAAAEVGIKNLTIFAFSINNWRRPVSE 74 G + DG + AR R HR ++ +A A + +N + + Sbjct: 511 GHLDDGAAEFIIARLKNRLVKHRDFQYAPHQKLATAEKF--ENEEKMCDIADASSGRAAG 568 Query: 75 ISELVKLIKSFLKKGFYSLKKNNIKVRVIGNRLSLDDDILCVLKEAEDQTRLNTGLNLFI 134 L + I F K+ ++ + +++GN +DD+ L EA D + LF+ Sbjct: 569 EDHLQEFIVEFCKEEDANIIMAGKRKQLLGNLQCAEDDLC--LAEAFDAEQSCPLYQLFL 626 >gnl|CDD|32142 COG1959, COG1959, Predicted transcriptional regulator [Transcription]. Length = 150 Score = 27.2 bits (60), Expect = 3.7 Identities = 11/48 (22%), Positives = 20/48 (41%) Query: 51 AEVGIKNLTIFAFSINNWRRPVSEISELVKLIKSFLKKGFYSLKKNNI 98 E ++ L A +EI+E + S+L+K L+K + Sbjct: 7 GEYALRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKAGL 54 >gnl|CDD|31056 COG0712, AtpH, F0F1-type ATP synthase, delta subunit (mitochondrial oligomycin sensitivity protein) [Energy production and conversion]. Length = 178 Score = 26.4 bits (58), Expect = 8.1 Identities = 31/160 (19%), Positives = 63/160 (39%), Gaps = 32/160 (20%) Query: 40 IEVFNEIVAAAAEVGIKNLTIFAFSINNWRRPVSEISELVKLIKSFLKKGFYSLKKNNIK 99 +E E + AE+ +KN +++ P + +L+ S KK L +N ++ Sbjct: 25 LEEVEEELTFLAEI-LKNSPKLKQLLSS---PAVSAEDKKELLISIFKKIGDPLLQNFLR 80 Query: 100 VRVIGNRLSLDDDILCVLKEAEDQTRLNTGLNLFIAFNYSS-------RDEISRAIKNIF 152 + RL+L +IL + ++R + A S+ ++ ++ F Sbjct: 81 LLAENKRLNLLPEILEEFLKLAAESR-----GIVEAEVTSAFELSDEQLTKLEAKLEKKF 135 Query: 153 -QDIESGSVCSHDVDSSLIAKYLDTSDVPDPDLIIRTGGE 191 + ++ ++ +D SLI LII+ G E Sbjct: 136 GKKVK----LNNKIDPSLIGG-----------LIIKVGDE 160 >gnl|CDD|29636 cd01424, MGS_CPS_II, Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways responsible for the synthesis of pyrimidine nucleotides or arginine. The MGS-like domain is the C-terminal domain of CarB and appears to play a regulatory role in CPS function by binding allosteric effector molecules, including UMP and ornithine.. Length = 110 Score = 26.2 bits (58), Expect = 9.4 Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 9/61 (14%) Query: 77 ELVKLIKSFLKKGF---------YSLKKNNIKVRVIGNRLSLDDDILCVLKEAEDQTRLN 127 E V++ K + GF L++ I V V+ +I+ ++K E Q +N Sbjct: 14 EAVEIAKRLAELGFKLVATEGTAKYLQEAGIPVEVVNKVSEGRPNIVDLIKNGEIQLVIN 73 Query: 128 T 128 T Sbjct: 74 T 74 >gnl|CDD|30504 COG0155, CysI, Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]. Length = 510 Score = 26.0 bits (57), Expect = 9.9 Identities = 12/52 (23%), Positives = 20/52 (38%), Gaps = 3/52 (5%) Query: 9 SPPDHIGIIMDGNGRWAAARGLPRCAGHRKGIEVFNEIVAAAAEVGIKNLTI 60 DHIG + +G W +P G K + + A E+G + + Sbjct: 292 GNGDHIGWVPQKDGLWHLGLAVP--NGRLKAEGLI-PLATEAEEIGFGEIRL 340 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 0.139 0.413 Gapped Lambda K H 0.267 0.0643 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 3,080,616 Number of extensions: 165520 Number of successful extensions: 426 Number of sequences better than 10.0: 1 Number of HSP's gapped: 424 Number of HSP's successfully gapped: 19 Length of query: 243 Length of database: 6,263,737 Length adjustment: 91 Effective length of query: 152 Effective length of database: 4,297,318 Effective search space: 653192336 Effective search space used: 653192336 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 (25.5 bits)