RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780676|ref|YP_003065089.1| lipoyl synthase [Candidatus Liberibacter asiaticus str. psy62] (329 letters) >gnl|CDD|30668 COG0320, LipA, Lipoate synthase [Coenzyme metabolism]. Length = 306 Score = 486 bits (1253), Expect = e-138 Identities = 179/302 (59%), Positives = 217/302 (71%) Query: 21 AERLRHPEKIHKPDTEKMQKPDWIRVRAPVSSGYKETYNILRSRNLTTVCEEAGCPNIGE 80 + R P K +P+ E ++KP+W++V+AP S Y+E ILR L TVCEEA CPNIGE Sbjct: 5 DKMARIPVKNVRPNEELLRKPEWLKVKAPTGSRYQEIKEILRKNGLHTVCEEASCPNIGE 64 Query: 81 CWNKNHATFMILGAICTRACTFCNVATGKPQPLDPQEPENISWAVRSMKLSHVVITSVDR 140 CW++ ATFMILG ICTR C FC+V TG+P PLDP EPE ++ AV+ M L +VVITSVDR Sbjct: 65 CWSRGTATFMILGDICTRRCRFCDVKTGRPNPLDPDEPERVAEAVKDMGLKYVVITSVDR 124 Query: 141 DDLDDGGAQHFAEVISAIRESAPSTTIEVLTPDFLRKPHALEKVVSAKPDVFNHNLETVA 200 DDL DGGAQHFAE I AIRE P TTIEVLTPDF ALE V A PDVFNHN+ETV Sbjct: 125 DDLPDGGAQHFAECIRAIRELNPQTTIEVLTPDFRGNDDALEIVADAGPDVFNHNVETVP 184 Query: 201 SNYLMVRPGARYFHSLRLLQRVKELDPLIFTKSGIMLGLGETRNEILQLMDDLRTADVDF 260 Y VRPGA Y SL LL+R KEL P I TKSG+M+GLGET E++++MDDLR+A VD Sbjct: 185 RLYPRVRPGATYERSLSLLERAKELGPDIPTKSGLMVGLGETDEEVIEVMDDLRSAGVDI 244 Query: 261 LTMGQYLQPTRKHHKVESFVTPQDFKSYETIAYSKGFLMVSASPLTRSSYHAGDDFLRLK 320 LT+GQYLQP+RKH V+ +VTP++F E +A GFL V++ PL RSSYHA + F + Sbjct: 245 LTIGQYLQPSRKHLPVQRYVTPEEFDELEEVAEEMGFLHVASGPLVRSSYHADEQFAEAE 304 Query: 321 NN 322 Sbjct: 305 VK 306 >gnl|CDD|37883 KOG2672, KOG2672, KOG2672, Lipoate synthase [Coenzyme transport and metabolism]. Length = 360 Score = 312 bits (800), Expect = 9e-86 Identities = 140/290 (48%), Positives = 185/290 (63%), Gaps = 7/290 (2%) Query: 36 EKMQKPDWIRVRAPVSSGYKETYNILRSRNLTTVCEEAGCPNIGECWN-----KNHATFM 90 E+++ P W++ + P+ Y + LR L TVCEEA CPNIGECW AT M Sbjct: 56 ERLRLPPWLKTKIPLGENYNKIKKDLRELKLHTVCEEARCPNIGECWGGGDKSTATATIM 115 Query: 91 ILGAICTRACTFCNVATGK-PQPLDPQEPENISWAVRSMKLSHVVITSVDRDDLDDGGAQ 149 ++G CTR C FC+V T + P PLDP EPEN + A+ S L ++V+TSVDRDDL DGGA Sbjct: 116 LMGDTCTRGCRFCSVKTSRNPPPLDPNEPENTAEAIASWGLDYIVLTSVDRDDLPDGGAN 175 Query: 150 HFAEVISAIRESAPSTTIEVLTPDFLRKPHALEKVVSAKPDVFNHNLETVASNYLMVR-P 208 H A+ + I+E AP +E LTPDF A+EKV + DV+ HN+ETV VR P Sbjct: 176 HIAKTVQKIKEKAPEILVECLTPDFRGDLKAVEKVAKSGLDVYAHNVETVEELTPFVRDP 235 Query: 209 GARYFHSLRLLQRVKELDPLIFTKSGIMLGLGETRNEILQLMDDLRTADVDFLTMGQYLQ 268 A Y SL +L+ KE+ P + TK+ IMLGLGET EI Q + DLR ADVD +T GQY+Q Sbjct: 236 RANYRQSLSVLKHAKEVKPGLITKTSIMLGLGETDEEIKQTLKDLRAADVDVVTFGQYMQ 295 Query: 269 PTRKHHKVESFVTPQDFKSYETIAYSKGFLMVSASPLTRSSYHAGDDFLR 318 PT++H KV+ +VTP+ F ++ GFL V++ PL RSSY AG+ F++ Sbjct: 296 PTKRHLKVKEYVTPEKFDYWKEYGEELGFLYVASGPLVRSSYKAGEYFIK 345 >gnl|CDD|146602 pfam04055, Radical_SAM, Radical SAM superfamily. Radical SAM proteins catalyse diverse reactions, including unusual methylations, isomerisation, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation. Length = 165 Score = 79.1 bits (195), Expect = 1e-15 Identities = 33/169 (19%), Positives = 65/169 (38%), Gaps = 9/169 (5%) Query: 90 MILGAICTRACTFCNV----ATGKPQPLDPQEPENISWAVRSMKLSHVVITSVDRDDLDD 145 +I+ C CT+C A GK + L P+E + + + + V++T + L D Sbjct: 1 IIITPGCNLRCTYCAFPSIRARGKGRELSPEEILEEAKELARLGVEVVILTGGEPLLLPD 60 Query: 146 GGAQHFAEVISAIRESAPSTTIEVLTPDFLRKPHALEKVVSAKPDVFNHNLETVASNYL- 204 E I + T L LE++ A D + +L++ L Sbjct: 61 LVELLERL---LKLEELEGIRITLETNGTLLDEELLEELKEAGLDRVSISLQSGDDEVLK 117 Query: 205 MVRPGARYFHSLRLLQRVKELDPLIFTKSGIMLGLGETRNEILQLMDDL 253 ++ G + L L+ ++E + I+ GE ++ + ++ L Sbjct: 118 IINRGHTFEEVLEALELLREAG-IPVVVDNIVGLPGENDEDLEETLELL 165 >gnl|CDD|30848 COG0502, BioB, Biotin synthase and related enzymes [Coenzyme metabolism]. Length = 335 Score = 57.6 bits (139), Expect = 5e-09 Identities = 42/168 (25%), Positives = 66/168 (39%), Gaps = 13/168 (7%) Query: 96 CTRACTFCNVATGKPQPLDPQ---EPENISWAVRSMK---LSHVVITSVDRDDLDDGGAQ 149 C C +C+ + + + E E I A + K + + + R D Sbjct: 61 CPEDCAYCSQSARYKTGVKARKLMEVEEILEAAKKAKAAGATRFCMGAAGRGPGRD---- 116 Query: 150 HFAEVISAIRESAPSTTIEVLTPDFLRKPHALEKVVSAKPDVFNHNLETVASNYLMVRPG 209 EV+ AI+ +EV + EK+ A D +NHNLET Y + Sbjct: 117 -MEEVVEAIKAVKEELGLEVCASLGMLTEEQAEKLADAGVDRYNHNLETSPEFYENIITT 175 Query: 210 ARYFHSLRLLQRVKELDPLIFTKSGIMLGLGETRNEILQLMDDLRTAD 257 Y L L+ V+E I SG ++GLGET + +L+ +L Sbjct: 176 RTYEDRLNTLENVREAG--IEVCSGGIVGLGETVEDRAELLLELANLP 221 >gnl|CDD|100105 cd01335, Radical_SAM, Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and MoaA, an enzyme of the biosynthesis of molybdopterin.. Length = 204 Score = 56.2 bits (135), Expect = 1e-08 Identities = 32/186 (17%), Positives = 72/186 (38%), Gaps = 15/186 (8%) Query: 90 MILGAICTRACTFCNVATGK----PQPLDPQEPENISWAVRSMKLSHVVITSVDRDDLDD 145 + L C C FC+ K P + +E +I + + V++T + Sbjct: 1 LELTRGCNLNCGFCSNPASKGRGPESPPEIEEILDIVLEAKERGVEVVILTGGEPLLYP- 59 Query: 146 GGAQHFAEVISAIRESAPSTTIEVLTPDFLRKPHALEKVVSAKPDVFNHNLETV--ASNY 203 AE++ +++ P I + T L L+++ D +L++ Sbjct: 60 ----ELAELLRRLKKELPGFEISIETNGTLLTEELLKELKELGLDGVGVSLDSGDEEVAD 115 Query: 204 LMVRPGARYFHSLRLLQRVKELDPLIFTKSGIMLGLG-ETRNEILQLMDDLRTAD-VDFL 261 + G + L L+ ++E + + +++GLG E + L+ ++ L D + Sbjct: 116 KIRGSGESFKERLEALKELREAG--LGLSTTLLVGLGDEDEEDDLEELELLAEFRSPDRV 173 Query: 262 TMGQYL 267 ++ + L Sbjct: 174 SLFRLL 179 >gnl|CDD|31260 COG1060, ThiH, Thiamine biosynthesis enzyme ThiH and related uncharacterized enzymes [Coenzyme metabolism / General function prediction only]. Length = 370 Score = 41.0 bits (96), Expect = 4e-04 Identities = 44/221 (19%), Positives = 80/221 (36%), Gaps = 39/221 (17%) Query: 95 ICTRACTFCNVATGKPQP----LDPQEPENISWAVRSMKLSHVVITSVDRDDLDDGGAQH 150 IC CTFC P L P+E ++ V+I + +L ++ Sbjct: 68 ICVNDCTFCAFYRKPGDPKAYTLSPEEILEEVREAVKRGITEVLIVGGEHPELS---LEY 124 Query: 151 FAEVISAIRESAPSTTIEVLTPDFLRKPHALEKVVSAKPDVF----NHNLETV---ASNY 203 + E+ I+E P I L+ + A E +S + +V L+++ + Sbjct: 125 YEELFRTIKEEFPDLHIHALSAGEIL-FLAREGGLSYE-EVLKRLKEAGLDSMPGGGAEI 182 Query: 204 LM--VR-----PGARYFHSLRLLQRVKELDPLIFTKSGIMLGLGETRNEILQLMDDLRTA 256 L VR P L + +R L I T + ++LG ETR + + ++ +R Sbjct: 183 LSEEVRKIHCPPKKSPEEWLEIHERAHRLG--IPTTATMLLGHVETREDRIDHLEHIR-- 238 Query: 257 DVDFLTMGQYLQPTRKHHKVESFVTPQDFKSYETIAYSKGF 297 LQ + + F+ P F+ ++ Sbjct: 239 ---------DLQ--DETGGFQEFI-PLRFRPENGPLPAEVV 267 >gnl|CDD|35762 KOG0542, KOG0542, KOG0542, Predicted exonuclease [Replication, recombination and repair]. Length = 280 Score = 30.3 bits (68), Expect = 0.85 Identities = 10/43 (23%), Positives = 16/43 (37%) Query: 37 KMQKPDWIRVRAPVSSGYKETYNILRSRNLTTVCEEAGCPNIG 79 ++ P + + YK YN N+T + E G G Sbjct: 177 NIRIPAFFNQWINIRKIYKNFYNRPAPTNITGMLEHYGLQFEG 219 >gnl|CDD|30966 COG0621, MiaB, 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]. Length = 437 Score = 29.4 bits (66), Expect = 1.4 Identities = 40/186 (21%), Positives = 78/186 (41%), Gaps = 20/186 (10%) Query: 96 CTRACTFCNV--ATGKPQPLDPQEPENISWAVRSMKLS---HVVITSVD----RDDLDDG 146 C + CTFC + A GK + PE+I V+ + +V+T D DL G Sbjct: 154 CNKFCTFCIIPYARGK---ERSRPPEDILKEVKRLVAQGVKEIVLTGQDVNAYGKDLGGG 210 Query: 147 GAQHFAEVISAIRESAPSTTIEVLTPDFLRKPHALEKVVSAKPDVFNH---NLETVASNY 203 + A+++ + + I + L L + ++ P V H +++ + Sbjct: 211 KP-NLADLLRELSKIPGIERIRFGSSHPLEFTDDLIEAIAETPKVCPHLHLPVQSGSDRI 269 Query: 204 L--MVRPGARYFHSLRLLQRVKELDPLIFTKSGIMLGL-GETRNEILQLMDDLRTADVDF 260 L M R + L ++++++ P I + I++G GET + + +D + D Sbjct: 270 LKRMKRGYTVEEY-LEIIEKLRAARPDIAISTDIIVGFPGETEEDFEETLDLVEEVRFDR 328 Query: 261 LTMGQY 266 L + +Y Sbjct: 329 LHVFKY 334 >gnl|CDD|73367 cd00564, TMP_TenI, Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5- (beta-hydroxyethyl) thiazole phosphate to yield thiamine phosphate. TenI is a enzymatically inactive regulatory protein involved in the regulation of several extracellular enzymes. This superfamily also contains other enzymatically inactive proteins with unknown functions.. Length = 196 Score = 29.4 bits (66), Expect = 1.6 Identities = 14/53 (26%), Positives = 22/53 (41%), Gaps = 4/53 (7%) Query: 109 KPQPLDPQEPENISWAVRSMKLSHVVITSVDRDDLDD---GGAQHFAEVISAI 158 KP P E + +++ V I + ++ + GA A VISAI Sbjct: 130 KPGAGPPLGLELLREIAELVEIPVVAIGGITPENAAEVLAAGADGVA-VISAI 181 >gnl|CDD|32379 COG2197, CitB, Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]. Length = 211 Score = 29.2 bits (65), Expect = 1.9 Identities = 19/102 (18%), Positives = 38/102 (37%), Gaps = 6/102 (5%) Query: 152 AEVISAIRESAPSTTIEVLTPDFLRKPHALEKVVSAKPDVFNH---NLETVASNYLMVRP 208 E + +R P + VLT P + + + A D + + E + V Sbjct: 62 LEALKQLRARGPDIKVVVLTAHD--DPAYVIRALRAGADGYLLKDASPEELVEAIRAVAA 119 Query: 209 GARYFHSLRLLQRVKELDPLIFTKSGIMLGLGETRNEILQLM 250 G Y + +++ L P ++ + L E+L+L+ Sbjct: 120 GGTYLPP-DIARKLAGLLPSSSAEAPLAELLTPRELEVLRLL 160 >gnl|CDD|38111 KOG2900, KOG2900, KOG2900, Biotin synthase [Coenzyme transport and metabolism]. Length = 380 Score = 28.5 bits (63), Expect = 2.8 Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 2/64 (3%) Query: 192 FNHNLETVASNYLMVRPGARYFHSLRLLQRVKELDPLIFTKSGIMLGLGETRNEILQLMD 251 +NHNL+T Y V Y L+ ++ V+E I SG +LGLGE+ ++ + L+ Sbjct: 193 YNHNLDTSREYYSKVITTRTYDDRLQTIKNVREAG--IKVCSGGILGLGESEDDRIGLIH 250 Query: 252 DLRT 255 L T Sbjct: 251 TLAT 254 >gnl|CDD|176152 cd08463, PBP2_DntR_like_4, The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. 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 = 203 Score = 27.7 bits (62), Expect = 4.3 Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 3/38 (7%) Query: 147 GAQHFAEVISAIRESAPSTTIEV--LTPDFLRKPHALE 182 A E+++ R AP +E+ L PDF AL Sbjct: 11 NALFLPELVARFRREAPGARLEIHPLGPDF-DYERALA 47 >gnl|CDD|39700 KOG4500, KOG4500, KOG4500, Rho/Rac GTPase guanine nucleotide exchange factor smgGDS/Vimar [Signal transduction mechanisms]. Length = 604 Score = 27.4 bits (60), Expect = 5.8 Identities = 16/49 (32%), Positives = 23/49 (46%) Query: 216 LRLLQRVKELDPLIFTKSGIMLGLGETRNEILQLMDDLRTADVDFLTMG 264 L L +R+ ELD L+ T M L + L R+ D + +TMG Sbjct: 287 LNLFKRIAELDVLLLTGDESMQKLHADPQFLDFLESWFRSDDSNLITMG 335 >gnl|CDD|30911 COG0565, LasT, rRNA methylase [Translation, ribosomal structure and biogenesis]. Length = 242 Score = 26.7 bits (59), Expect = 7.9 Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 7/52 (13%) Query: 114 DPQEPENISWAVRSMK---LSHVVITSVDRDDLDD---GGAQHFAEVISAIR 159 +P P NI R+MK LS + + + R LD+ A +++ + Sbjct: 11 EPSHPGNIGSVARAMKNFGLSELRLVN-PRAGLDEEARALAAGARDILENAK 61 >gnl|CDD|30059 cd01316, CAD_DHOase, The eukaryotic CAD protein is a trifunctional enzyme of carbamoylphosphate synthetase-aspartate transcarbamoylase-dihydroorotase, which catalyzes the first three steps of de novo pyrimidine nucleotide biosynthesis. Dihydroorotase (DHOase) catalyzes the third step, the reversible interconversion of carbamoyl aspartate to dihydroorotate.. Length = 344 Score = 26.8 bits (59), Expect = 8.2 Identities = 12/48 (25%), Positives = 18/48 (37%) Query: 281 TPQDFKSYETIAYSKGFLMVSASPLTRSSYHAGDDFLRLKNNRRQHLH 328 +DF S A + GF MV A P T S +++ + Sbjct: 22 HKEDFASGTKAALAGGFTMVRAMPNTNPSIVDVASLKLVQSLAQAKAR 69 >gnl|CDD|30955 COG0610, COG0610, Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]. Length = 962 Score = 26.9 bits (59), Expect = 8.3 Identities = 11/48 (22%), Positives = 16/48 (33%), Gaps = 1/48 (2%) Query: 123 WAVRSMKLSHVVITSVDRDDLDDGGAQHFAEVISAIRESAPSTTIEVL 170 + K V+ VDR DLDD + F + + L Sbjct: 296 LLLELPKNPKVLFV-VDRKDLDDQTSDEFQSFGKVAFNDPKAESTSEL 342 >gnl|CDD|36773 KOG1560, KOG1560, KOG1560, Translation initiation factor 3, subunit h (eIF-3h) [Translation, ribosomal structure and biogenesis]. Length = 339 Score = 26.5 bits (58), Expect = 9.8 Identities = 20/81 (24%), Positives = 32/81 (39%), Gaps = 20/81 (24%) Query: 241 ETRNEILQLMDDLRTADVDFLTMGQYLQPTRKHHKVESFVTPQDFKS------------- 287 + L ++ LR ++D L +G Y V SF++P +S Sbjct: 79 ARQAYQLAMLRRLRYVNIDHLHVGWYQS-----AYVGSFLSPALVESQYAYQKAIPESVV 133 Query: 288 --YETIAYSKGFLMVSASPLT 306 Y+ I S+G L + A LT Sbjct: 134 LIYDPIKSSQGTLSLRAYRLT 154 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 0.134 0.402 Gapped Lambda K H 0.267 0.0623 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 4,063,824 Number of extensions: 211833 Number of successful extensions: 458 Number of sequences better than 10.0: 1 Number of HSP's gapped: 453 Number of HSP's successfully gapped: 23 Length of query: 329 Length of database: 6,263,737 Length adjustment: 94 Effective length of query: 235 Effective length of database: 4,232,491 Effective search space: 994635385 Effective search space used: 994635385 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: 58 (26.3 bits)