RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780569|ref|YP_003064982.1| phosphoribosylaminoimidazole synthetase [Candidatus Liberibacter asiaticus str. psy62] (357 letters) >gnl|CDD|100032 cd02196, PurM, PurM (Aminoimidazole Ribonucleotide [AIR] synthetase), one of eleven enzymes required for purine biosynthesis, catalyzes the conversion of formylglycinamide ribonucleotide (FGAM) and ATP to AIR, ADP, and Pi, the fifth step in de novo purine biosynthesis. The N-terminal domain of PurM is related to the ATP-binding domains of hydrogen expression/formation protein HypE, the AIR synthases, selenophosphate synthetase (SelD), and FGAM synthase and is thought to bind ATP.. Length = 297 Score = 470 bits (1212), Expect = e-133 Identities = 174/299 (58%), Positives = 222/299 (74%), Gaps = 2/299 (0%) Query: 42 GEIGGFGGLFDLKKAGFVDPILVSSSDGVGTKLKIAIETGKNDTIGIDLVAMCVNDILTH 101 G IGGF GLFDL G+ DP+LVS +DGVGTKLK+A E GK+DTIGIDLVAMCVNDIL Sbjct: 1 GGIGGFAGLFDLGLGGYKDPVLVSGTDGVGTKLKLAQEMGKHDTIGIDLVAMCVNDILCQ 60 Query: 102 GAEPLFFLDYLATSQLNPDQATSIIKGIAAGCCQAGCALIGGETAEMPGLYHDRDYDLAG 161 GAEPLFFLDY+AT +L+P+ A I+KGIA GC QAGCAL+GGETAEMPG+Y + +YDLAG Sbjct: 61 GAEPLFFLDYIATGKLDPEVAAEIVKGIAEGCRQAGCALLGGETAEMPGVYAEGEYDLAG 120 Query: 162 FAVGAVERKELLSPENVCAGDLILGLPSSGLHSNGFALVRKIISLSQLSWKDPSPISSEH 221 FAVG VE+ +++ + GD+++GLPSSGLHSNG++LVRKI+ L + DP P + Sbjct: 121 FAVGVVEKDKIIDGSKIKPGDVLIGLPSSGLHSNGYSLVRKILFEEGLDYDDPEPGLGK- 179 Query: 222 SLGETLLTPTRIYVSPLLKILRKTGKIKALAHITGGGLTENIPRAIPAHLTASINLNSVE 281 +LGE LLTPTRIYV P+L +L K +K +AHITGGGL EN+PR +P L A I+L S E Sbjct: 180 TLGEELLTPTRIYVKPILPLLEK-VLVKGMAHITGGGLPENLPRVLPEGLGAVIDLGSWE 238 Query: 282 VPQIISWLSKKAHVKPAEVLRTFNCGIGMVIIVHPDNKDCIIKKFQENNENIILIGEVT 340 +P I W+ K +V E+ RTFN GIGMV+IV ++ D +++ ++ E +IGEV Sbjct: 239 IPPIFKWIQKAGNVSEEEMYRTFNMGIGMVLIVSEEDADEVLEILEKLGEKAYVIGEVV 297 >gnl|CDD|30499 COG0150, PurM, Phosphoribosylaminoimidazole (AIR) synthetase [Nucleotide transport and metabolism]. Length = 345 Score = 447 bits (1151), Expect = e-126 Identities = 185/342 (54%), Positives = 237/342 (69%), Gaps = 2/342 (0%) Query: 6 KRGLTYGQAGVNIEAGNRTVTQIKSAVKSTKRAGTIGEIGGFGGLFDLKKAGFVDPILVS 65 LTY AGV+I+AGN V +IK AVK T+R +G +GGF GLFDL +A + P+LVS Sbjct: 1 MTSLTYADAGVDIDAGNEAVERIKPAVKRTRRPEVMGGLGGFAGLFDLGQAYY-KPVLVS 59 Query: 66 SSDGVGTKLKIAIETGKNDTIGIDLVAMCVNDILTHGAEPLFFLDYLATSQLNPDQATSI 125 +DGVGTKL +A + GK+DTIGIDLVAMCVND++ GAEPLFFLDYLAT +L+P+ A I Sbjct: 60 GTDGVGTKLLLAEDAGKHDTIGIDLVAMCVNDLVVQGAEPLFFLDYLATGKLDPEVAAQI 119 Query: 126 IKGIAAGCCQAGCALIGGETAEMPGLYHDRDYDLAGFAVGAVERKELLSPENVCAGDLIL 185 +KGIA GC QAGCAL+GGETAEMPG+Y DYDLAGFAVG VE+ E++ V GD+I+ Sbjct: 120 VKGIAEGCKQAGCALVGGETAEMPGMYRGGDYDLAGFAVGVVEKDEIIDGSKVKEGDVII 179 Query: 186 GLPSSGLHSNGFALVRKIISLSQLSWKDPSPISSEHSLGETLLTPTRIYVSPLLKILRKT 245 GL SSGLHSNG++LVRKII S L + D P +LGE LL PTRIYV P+L ++++ Sbjct: 180 GLASSGLHSNGYSLVRKIIEESGLDYDDELPEELGKTLGEELLEPTRIYVKPVLALIKE- 238 Query: 246 GKIKALAHITGGGLTENIPRAIPAHLTASINLNSVEVPQIISWLSKKAHVKPAEVLRTFN 305 G +K +AHITGGG EN+PR +P L A I+ S P I WL K +V+ E+ RTFN Sbjct: 239 GDVKGMAHITGGGFVENLPRVLPEGLGAVIDKPSWPPPPIFKWLQKAGNVEREEMYRTFN 298 Query: 306 CGIGMVIIVHPDNKDCIIKKFQENNENIILIGEVTQRSEKSP 347 G+GMV+IV ++ + + +E E +IG V + Sbjct: 299 MGVGMVLIVPEEDAEKALALLKEQGETAYVIGRVEAGEGEVV 340 >gnl|CDD|35458 KOG0237, KOG0237, KOG0237, Glycinamide ribonucleotide synthetase (GARS)/Aminoimidazole ribonucleotide synthetase (AIRS) [Nucleotide transport and metabolism]. Length = 788 Score = 443 bits (1142), Expect = e-125 Identities = 202/348 (58%), Positives = 256/348 (73%), Gaps = 2/348 (0%) Query: 6 KRGLTYGQAGVNIEAGNRTVTQIKSAVKSTKRAGTIGEIGGFGGLFDLKKAGFVDPILVS 65 LTY +GV+I+AGN V +IK VK T+R G +IGGFGGLFDLK+AGF DP+LVS Sbjct: 434 TPSLTYKDSGVDIDAGNELVQRIKPLVKGTRRPGADADIGGFGGLFDLKQAGFKDPLLVS 493 Query: 66 SSDGVGTKLKIAIETGKNDTIGIDLVAMCVNDILTHGAEPLFFLDYLATSQLNPDQATSI 125 +DGVGTKLKIA ET +DT+GIDLVAM VNDI+ GAEPLFFLDY AT +L+ A + Sbjct: 494 GTDGVGTKLKIAQETNIHDTVGIDLVAMNVNDIIVQGAEPLFFLDYFATGKLDVSVAEQV 553 Query: 126 IKGIAAGCCQAGCALIGGETAEMPGLYHDRDYDLAGFAVGAVERKELLS-PENVCAGDLI 184 +KGIA GC QAGCAL+GGETAEMPG+Y +YDLAGFAVGAVER ++L + AGD++ Sbjct: 554 VKGIAEGCRQAGCALVGGETAEMPGMYAPGEYDLAGFAVGAVERTDILPKLNEIVAGDVL 613 Query: 185 LGLPSSGLHSNGFALVRKIISLSQLSWKDPSPISSEHSLGETLLTPTRIYVSPLLKILRK 244 LGLPSSG+HSNGF+LVRKI++ S LS+KDP P S +LG+ LL PT+IYV LL ++RK Sbjct: 614 LGLPSSGVHSNGFSLVRKILARSGLSYKDPLPWDSSKTLGDELLAPTKIYVKQLLPLIRK 673 Query: 245 TGKIKALAHITGGGLTENIPRAIPAHLTASINLNSVEVPQIISWLSKKAHVKPAEVLRTF 304 G +K LAHITGGGLTENIPR +P HL A I+ ++ E+P + WL + +V +E+ RTF Sbjct: 674 -GGVKGLAHITGGGLTENIPRVLPDHLGAVIDADTWELPPVFKWLQQAGNVPDSEMARTF 732 Query: 305 NCGIGMVIIVHPDNKDCIIKKFQENNENIILIGEVTQRSEKSPPILYQ 352 NCGIGMV++V P+N + ++K+ + E IGEV R SP + Sbjct: 733 NCGIGMVLVVSPENVERVLKELTNHGEEAYRIGEVVNREGVSPQCVVV 780 >gnl|CDD|145754 pfam02769, AIRS_C, AIR synthase related protein, C-terminal domain. This family includes Hydrogen expression/formation protein HypE, AIR synthases EC:6.3.3.1, FGAM synthase EC:6.3.5.3 and selenide, water dikinase EC:2.7.9.3. The function of the C-terminal domain of AIR synthase is unclear, but the cleft formed between N and C domains is postulated as a sulphate binding site. Length = 150 Score = 104 bits (261), Expect = 4e-23 Identities = 56/166 (33%), Positives = 83/166 (50%), Gaps = 24/166 (14%) Query: 180 AGDLILGLPSSGLHSNGFALVRKIISLSQLSWKDPSPISSEHSLGETLLTPTRIYVSPLL 239 GD+++ L SSGL +G +LVRK + +D + LG+ LL PT IYV LL Sbjct: 2 PGDVLILLGSSGLGGSGLSLVRKGL------EEDGAVP-----LGDPLLEPTLIYVVLLL 50 Query: 240 KILRKTGKIKALAHITGGGLTENIPR-AIPAHLTASINLNSVEVPQIISWLSKKAHVKPA 298 L G +KA ITGGGL + A + + A I+L+ V I L + P Sbjct: 51 AAL---GLVKAAHDITGGGLAGALAEMAPASGVGAEIDLDKVP---IFDEL-----LLPL 99 Query: 299 EVLRTFNCGIGMVIIVHPDNKDCIIKKFQENNENIILIGEVTQRSE 344 E+L + N G G+V++V P+ + ++ +E +IGEVT Sbjct: 100 EMLFSENQGRGLVVVV-PEEAEAVLAILEEEGLPAAVIGEVTAGGG 144 >gnl|CDD|100027 cd00396, PurM-like, AIR (aminoimidazole ribonucleotide) synthase related protein. This family includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM (formylglycinamidine ribonucleotide) synthase and Selenophosphate synthetase (SelD). The N-terminal domain of AIR synthase forms the dimer interface of the protein, and is suggested as a putative ATP binding domain.. Length = 222 Score = 99.4 bits (248), Expect = 1e-21 Identities = 69/278 (24%), Positives = 101/278 (36%), Gaps = 59/278 (21%) Query: 63 LVSSSDGVGTKLKIAIETGKNDTIGIDLVAMCVNDILTHGAEPLFFLDYLATSQ-LNPDQ 121 L S+DG+ L I G V VNDI GA P+ L L+ S L D Sbjct: 2 LAMSTDGINPPLAI-----NPWAGGRLAVGGAVNDIAAMGARPIALLASLSLSNGLEVDI 56 Query: 122 ATSIIKGIAAGCCQAGCALIGGETAEMPGLYHDRDYDLAGFAVGAVERKELLSPENVCAG 181 ++ G+A C Q G ++GG T+ PG LA FA+G VE Sbjct: 57 LEDVVDGVAEACNQLGVPIVGGHTSVSPG-TMGHKLSLAVFAIGVVE------------- 102 Query: 182 DLILGLPSSGLHSNGFALVRKIISLSQLSWKDPSPISSEHSLGETLLTPTRIYVSPLLKI 241 KD SS G+ L+ V Sbjct: 103 ------------------------------KDRVIDSSGARPGDVLILTGVDAV----LE 128 Query: 242 LRKTGKIKALAHITGGGLTENIPRAIPA-HLTASINLNSVEVPQIISWLSKKAHVKPAEV 300 L G + A+ IT GGL +P A + A I+L ++ + +++ WL + E Sbjct: 129 LVAAGDVHAMHDITDGGLLGTLPELAQASGVGAEIDLEAIPLDEVVRWLCVEHI----EE 184 Query: 301 LRTFNCGIGMVIIVHPDNKDCIIKKFQENNENIILIGE 338 FN G++I V + D ++ N + +IG Sbjct: 185 ALLFNSSGGLLIAVPAEEADAVLLLLNGNGIDAAVIGR 222 >gnl|CDD|144251 pfam00586, AIRS, AIR synthase related protein, N-terminal domain. This family includes Hydrogen expression/formation protein HypE, AIR synthases EC:6.3.3.1, FGAM synthase EC:6.3.5.3 and selenide, water dikinase EC:2.7.9.3. The N-terminal domain of AIR synthase forms the dimer interface of the protein, and is suggested as a putative ATP binding domain. Length = 95 Score = 98.0 bits (245), Expect = 4e-21 Identities = 34/102 (33%), Positives = 52/102 (50%), Gaps = 8/102 (7%) Query: 45 GGFGGLFDLKKAGFVDPILVSSSDGVGTKLKIAIETGKNDTIGIDLVAMCVNDILTHGAE 104 G + L + P LV ++DGV T + A + G VA ++D+ GA+ Sbjct: 1 GDDAAVIRLGE----GPALVVTTDGVVTHVHFAADP---YDGGATAVAGNLSDLAAMGAK 53 Query: 105 PLFFLDYLATSQ-LNPDQATSIIKGIAAGCCQAGCALIGGET 145 PL FLD LA + L+P+ I++GIA + G L+GG+T Sbjct: 54 PLAFLDGLALGEGLDPEWLEEIVRGIAEAANEFGVPLVGGDT 95 >gnl|CDD|30657 COG0309, HypE, Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]. Length = 339 Score = 51.4 bits (123), Expect = 4e-07 Identities = 55/272 (20%), Positives = 108/272 (39%), Gaps = 27/272 (9%) Query: 81 GKNDTIGIDLVAMCVNDILTHGAEPLFF-LDYLATSQLNPDQATSIIKGIAAGCCQAGCA 139 IG V ND+ GA+P + + + L + I+K I +AG + Sbjct: 65 FPGGDIGKLAVHGTANDVAVSGAKPRYLSVGLILPEGLPIEDLERILKSIDEEAEEAGVS 124 Query: 140 LIGGETAEMPGLYHDRDYDLAGF-AVGAVERKELLSPENVCAGDLILGLPSSGLHSNGFA 198 ++ G+T +PG +D + +G ++++ L+SP GD ++ + G+H Sbjct: 125 IVTGDTKVVPGG---KDPIVINTTGIGIIDKEILVSPSGARPGDAVIVTGTIGIHGASIL 181 Query: 199 LVRKIISLSQLSWKDPSPISSEHSLGETLLTPTRIYVSPLLKILRKT--GKIKALAHITG 256 R L + S+ P V LL ++ + + A+ T Sbjct: 182 AHRFGEELET-------ELGSD-------CAPLAKLVKALLSVVGEALAAAVTAMHDATR 227 Query: 257 GGLTENIPR-AIPAHLTASINLNSVEVPQIISWLSKKAHVKPAEVLRTFNCGIGMVIIVH 315 GGL + A + + SI + V + + + + + P L N G +VI V Sbjct: 228 GGLAGALNEMAEASGVGISIEEEKIPVREEVRGVCELLGLDP---LELANEGK-LVIAVP 283 Query: 316 PDNKDCIIKKFQENNE-NIILIGEVTQRSEKS 346 P++ + +++ + + + +IGEV + Sbjct: 284 PEHAEEVLEALRSHGLKDAAIIGEVVEEKGGV 315 >gnl|CDD|30956 COG0611, ThiL, Thiamine monophosphate kinase [Coenzyme metabolism]. Length = 317 Score = 51.1 bits (122), Expect = 5e-07 Identities = 52/262 (19%), Positives = 94/262 (35%), Gaps = 36/262 (13%) Query: 86 IGIDLVAMCVNDILTHGAEPLFFLDYLA-TSQLNPDQATSIIKGIAAGCCQAGCALIGGE 144 +G +A+ ++D+ GA P FL L L+ + ++ GI + G LIGG+ Sbjct: 62 LGWKALAVNLSDLAAMGARPKAFLLSLGLPPDLDEEWLEALADGIFEAAKKYGVKLIGGD 121 Query: 145 TAEMPGLYHDRDYDLAGFAVGAVERKELLSPENVCAGDLILGLPSSGLHSNGFALVRKII 204 T P ++ A+G + + L GDL+ + G + G L Sbjct: 122 TNRGP-------LSISVTAIGVLPKGRALLRSGAKPGDLVAVTGTLGRSAAGLEL----- 169 Query: 205 SLSQLSWKDPSPISSEHSLGETLLTPT-RIYVSPLLKILRKTGKIKALAHITGGGLTENI 263 + E L E L PT R+ + L L A I+ G + Sbjct: 170 ------LLNVLGPEDEEELIERHLRPTPRVELGLALAKL-----ASAAMDISDGLAAD-- 216 Query: 264 PRAIPAHLTASINLNSVEVPQIISWLSKKAHVKPAEVLRTFNCGIG----MVIIVHPDNK 319 I I ++ +P + L + + G +V V +N+ Sbjct: 217 LGHIARASGVGIVIDEDLLPLSDAVLE---ALDELGDPLEWALSGGEDYELVFTVPEENR 273 Query: 320 DCIIKKFQENNENIILIGEVTQ 341 + ++ + + + +IG VT+ Sbjct: 274 EALLDALR--SLGVTIIGRVTE 293 >gnl|CDD|100030 cd02194, ThiL, ThiL (Thiamine-monophosphate kinase) plays a dual role in de novo biosynthesis and in salvage of exogenous thiamine. Thiamine salvage occurs in two steps, with thiamine kinase catalyzing the formation of thiamine phosphate, and ThiL catalyzing the conversion of this intermediate to thiamine pyrophosphate. The N-terminal domain of ThiL binds ATP and is related to the ATP-binding domains of hydrogen expression/formation protein HypE, the AIR synthases, FGAM synthase and selenophosphate synthetase (SelD).. Length = 291 Score = 49.1 bits (118), Expect = 2e-06 Identities = 31/111 (27%), Positives = 46/111 (41%), Gaps = 20/111 (18%) Query: 89 DLVAMCVNDILTHGAEPLFFLDYLATSQ-LNPDQATSIIKGIAAGCCQAGCALIGGETAE 147 DL AM GA PL FL L + + +G+A + G L+GG+T Sbjct: 70 DLAAM--------GARPLGFLLSLGLPPDTDEEWLEEFYRGLAEAADRYGVPLVGGDTTS 121 Query: 148 MPGLYHDRDYDLAGFAVGAVERKELLSPENVCAGDLI-----LGLPSSGLH 193 L ++ A+G VE+ + L GDL+ LG ++GL Sbjct: 122 GSELV------ISVTALGEVEKGKPLRRSGAKPGDLLYVTGTLGDAAAGLA 166 >gnl|CDD|32327 COG2144, COG2144, Selenophosphate synthetase-related proteins [General function prediction only]. Length = 324 Score = 46.4 bits (110), Expect = 1e-05 Identities = 62/285 (21%), Positives = 116/285 (40%), Gaps = 47/285 (16%) Query: 60 DPILVSSSDGVGTKLKIAIETGKNDTIGIDLVAMCVNDILTHGAEPLFFLDYLATSQLNP 119 D L+ ++DG+ KL A G V + VND+ G EP+ +D ++ + Sbjct: 53 DGKLLIAADGIWGKLIDADPW----WAGYCSVLVNVNDVAAMGGEPVGAVDAISAK--SE 106 Query: 120 DQATSIIKGIAAGCCQAGCALIGGETAEMPGLYHDRDYDLAGFAVGAVERKE-LLSPENV 178 DQA I++G+ G + G ++GG T D Y + +G + +E +++ Sbjct: 107 DQAREILEGLRKGARKFGVPIVGGHTHP------DTPYCVLDVVIGGLIAEEPIITSGTA 160 Query: 179 CAGDLILGLPSSGLHSNGFALVRKIISLSQLSWKDPSPISSEHSLGETLLTPTRIYVSPL 238 GDL++ + L K L+W +T + Sbjct: 161 KPGDLLIFV---------GDLDGKPYPNFPLNW-------------DTTTMKAKEKFRAQ 198 Query: 239 LKILRKTGK-IKALAHITGGGLTENIPRA-IPAHLTASINLNSVEVPQIISWLSKKAHVK 296 L++LR+ K +KA ++ GGL + + + A ++L+S+ P + + Sbjct: 199 LELLREGAKLVKAGKDVSNGGLLGTLLMLLEKSRVGAGVDLDSIPYPADVDFRQ------ 252 Query: 297 PAEVLRTFNCGIGMVIIVHPDNKDCIIKKFQENNENIILIGEVTQ 341 G G V+ V P++ + ++ F+E +IGEV + Sbjct: 253 ----WLKRYPGSGFVLTVDPEDVEEVVDVFEEEGCPATVIGEVIE 293 >gnl|CDD|30395 COG0046, PurL, Phosphoribosylformylglycinamidine (FGAM) synthase, synthetase domain [Nucleotide transport and metabolism]. Length = 743 Score = 44.4 bits (105), Expect = 5e-05 Identities = 60/280 (21%), Positives = 112/280 (40%), Gaps = 50/280 (17%) Query: 95 VNDILTHGAEPLFFLDYLATSQLNPDQATSIIKGIAAGCC----QAGCALIGGETAEMPG 150 + D+L+ GA P+ LD L + ++ I+KG+ AG + G +GGE Sbjct: 124 IRDVLSMGARPIALLDSLRFGIPDIEKTRYIMKGVVAGIAAYGNEIGVPTVGGEFRFDES 183 Query: 151 LYHDRDYDLAGFAVGAVERKELLSPENVCAGDLI--LGLPS--SGLHSNGFA---LVRKI 203 + + VG + ++ ++ E + GD + LG + G+ FA L + Sbjct: 184 YVGNP--LVNAGCVGLIRKEHIVKGEAIGPGDKLILLGGKTGRDGIGGATFASMELGEES 241 Query: 204 ISLSQLSWKDPSPISSEHSLGETLLTPTRIYVSPLLKILRKTGKIKALAHITGGGLTENI 263 + S + P E L E +L +TG IK + + GGL+ I Sbjct: 242 EEEDRPSVQVGDPF-MEKRLQEAILE------------CVQTGLIKGIQDLGAGGLSCAI 288 Query: 264 PR-AIPAHLTASINLNSVEVPQIISWLSKKAHVKPAEVL------RTFNCGIGMVIIVHP 316 A L A I+L+ V ++ + P E+ R M+++V P Sbjct: 289 SELAAKGGLGAEIDLDKV--------PLREPGMSPYEIWLSESQER-------MLLVVAP 333 Query: 317 DNKDCIIKKFQENNENIILIGEVTQRSEKSPPILYQGSLI 356 ++ + ++ ++ ++GEVT E + ++G + Sbjct: 334 EDVEEFLEICEKERLPAAVVGEVTD--EPRLVVDWKGEPV 371 >gnl|CDD|100037 cd06061, PurM-like1, AIR synthase (PurM) related protein, subgroup 1 of unknown function. The family of PurM related proteins includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM synthase and Selenophosphate synthetase (SelD). They all contain two conserved domains and seem to dimerize. The N-terminal domain forms the dimer interface and is a putative ATP binding domain.. Length = 298 Score = 43.0 bits (102), Expect = 1e-04 Identities = 28/101 (27%), Positives = 45/101 (44%), Gaps = 14/101 (13%) Query: 91 VAMCVNDILTHGAEPLFFLDYLATSQLNPDQAT-----SIIKGIAAGCCQAGCALIGGET 145 V + NDI T GA P + L L L P +I++ I + G +++GG T Sbjct: 64 VHIAANDIATSGARPRWLLVTL----LLPPGTDEEELKAIMREINEAAKELGVSIVGGHT 119 Query: 146 AEMPGLYHDRDYDLAG-FAVGAVERKELLSPENVCAGDLIL 185 PG+ + A+G E+ +L++P GD I+ Sbjct: 120 EVTPGV----TRPIISVTAIGKGEKDKLVTPSGAKPGDDIV 156 >gnl|CDD|100031 cd02195, SelD, Selenophosphate synthetase (SelD) catalyzes the conversion of selenium to selenophosphate which is required by a number of bacterial, archaeal and eukaryotic organisms for synthesis of Secys-tRNA, the precursor of selenocysteine in selenoenzymes. The N-terminal domain of SelD is related to the ATP-binding domains of hydrogen expression/formation protein HypE, the AIR synthases, and FGAM synthase and is thought to bind ATP.. Length = 287 Score = 40.2 bits (95), Expect = 0.001 Identities = 29/103 (28%), Positives = 39/103 (37%), Gaps = 21/103 (20%) Query: 89 DLVAMCVNDILTHGAEPLFFLDYLA----TSQLNPDQATSIIKGIAAGCCQAGCALIGGE 144 D+ AM GA+PL L + L + I+ G +AG L+GG Sbjct: 83 DIYAM--------GAKPLSALAIVTLPRKLPALQEEVLREILAGGKDKLREAGAVLVGGH 134 Query: 145 TAEMPGLYHDRDYDLAGFAV-GAVERKELLSPENVCAGD-LIL 185 T E P G +V G V ++L GD LIL Sbjct: 135 TIEGPEP-------KYGLSVTGLVHPNKILRNSGAKPGDVLIL 170 >gnl|CDD|100028 cd02192, PurM-like3, AIR synthase (PurM) related protein, subgroup 3 of unknown function. The family of PurM related proteins includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM synthase and Selenophosphate synthetase (SelD). They all contain two conserved domains and seem to dimerize. The N-terminal domain forms the dimer interface and is a putative ATP binding domain.. Length = 283 Score = 36.4 bits (85), Expect = 0.012 Identities = 23/91 (25%), Positives = 41/91 (45%), Gaps = 8/91 (8%) Query: 95 VNDILTHGAEPLFFLDYLATSQLNPDQATSIIKGIAAGCCQAGCALIGGETAEMPGLYHD 154 V+DI G PL +D L + + + A +++G+ + G ++GG T + D Sbjct: 76 VSDIAAMGGRPLAMVDALWSP--SAEAAAQVLEGMRDAAEKFGVPIVGGHT------HPD 127 Query: 155 RDYDLAGFAVGAVERKELLSPENVCAGDLIL 185 Y+ A+ RK+LL GD ++ Sbjct: 128 SPYNALSVAILGRARKDLLISFGAKPGDRLI 158 >gnl|CDD|100033 cd02197, HypE, HypE (Hydrogenase expression/formation protein). HypE is involved in Ni-Fe hydrogenase biosynthesis. HypE dehydrates its own carbamoyl moiety in an ATP-dependent process to yield the enzyme thiocyanate. The N-terminal domain of HypE is related to the ATP-binding domains of the AIR synthases, selenophosphate synthetase (SelD), and FGAM synthase and is thought to bind ATP.. Length = 293 Score = 31.7 bits (73), Expect = 0.30 Identities = 25/102 (24%), Positives = 44/102 (43%), Gaps = 22/102 (21%) Query: 95 VNDILTHGAEPLFFLDY------LATSQLNPDQATSIIKGIAAGCCQAGCALIGGETAEM 148 VND+ GA+PL+ L I+K +A +AG ++ G+T + Sbjct: 67 VNDLAMMGAKPLYLSLGFILEEGFPLEDL-----ERIVKSMAEAAREAGVKIVTGDTKVV 121 Query: 149 P-----GLYHDRDYDLAGFAVGAVERKELLSPENVCAGDLIL 185 P G++ + +G + R ++SP N+ GD I+ Sbjct: 122 PKGKADGIF------INTTGIGVIPRGVIISPSNIRPGDKII 157 >gnl|CDD|176245 cd08285, NADP_ADH, NADP(H)-dependent alcohol dehydrogenases. This group is predominated by atypical alcohol dehydrogenases; they exist as tetramers and exhibit specificity for NADP(H) as a cofactor in the interconversion of alcohols and aldehydes, or ketones. Like other zinc-dependent alcohol dehydrogenases (ADH) of the medium chain alcohol dehydrogenase/reductase family (MDR), tetrameric ADHs have a catalytic zinc that resides between the catalytic and NAD(H)binding domains; however, they do not have and a structural zinc in a lobe of the catalytic domain. The medium chain alcohol dehydrogenase family (MDR) has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The N-terminal region typically has an all-beta catalytic domain. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit. Length = 351 Score = 30.3 bits (69), Expect = 0.89 Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 4/43 (9%) Query: 9 LTYGQAGVN--IEAGNRTVTQIKSAVKSTKRAGTIGEIGGFGG 49 LT G+ GV+ I AG T + A+K K GTI + +G Sbjct: 230 LTGGK-GVDAVIIAGGGQDT-FEQALKVLKPGGTISNVNYYGE 270 >gnl|CDD|100034 cd02203, PurL_repeat1, PurL subunit of the formylglycinamide ribonucleotide amidotransferase (FGAR-AT), first repeat. FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP, phosphate, and glutamate in the fourth step of the purine biosynthetic pathway. In eukaryotes and Gram-negative bacteria, FGAR-AT is encoded by the purL gene as a multidomain protein with a molecular mass of about 140 kDa. In Gram-positive bacteria and archaea FGAR-AT is a complex of three proteins: PurS, PurL, and PurQ. PurL itself contains two tandem N- and C-terminal domains (four domains altogether). The N-terminal domains bind ATP and are related to the ATP-binding domains of HypE, ThiL, SelD and PurM.. Length = 313 Score = 30.1 bits (69), Expect = 0.97 Identities = 24/105 (22%), Positives = 37/105 (35%), Gaps = 22/105 (20%) Query: 97 DILTHGAEPLFFLDYLATSQLNPDQATS------------IIKGIAAGCCQAGCALIGGE 144 DIL+ GA P+ LD L L+ ++ GI+ G +GGE Sbjct: 57 DILSMGARPIALLDGLRFGDLDIPGYEPKGKLSPRRILDGVVAGISDYGNCIGIPTVGGE 116 Query: 145 TAEMPGLYHDRDYDL----AGFAVGAVERKELLSPENVCAGDLIL 185 D Y VG V + ++ + GDL++ Sbjct: 117 V------RFDPSYYGNPLVNVGCVGIVPKDHIVKSKAPGPGDLVV 155 >gnl|CDD|143893 pfam00118, Cpn60_TCP1, TCP-1/cpn60 chaperonin family. This family includes members from the HSP60 chaperone family and the TCP-1 (T-complex protein) family. Length = 481 Score = 29.9 bits (68), Expect = 1.2 Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 11/67 (16%) Query: 14 AGVNIEAGNRTVTQIKSAVKSTKRAGTIGEIGGFGGLFDLKKAGFVDPILVSSSDGVGTK 73 AG++ + ++K+A K G + G G D+K+AG +DP+ V S Sbjct: 411 AGLD---PIEVLAKLKAAHKKGNNLGIDADTGEIG---DMKEAGIIDPLKVKRSA----- 459 Query: 74 LKIAIET 80 LK A+E Sbjct: 460 LKSAVEV 466 >gnl|CDD|176243 cd08283, FDH_like_1, Glutathione-dependent formaldehyde dehydrogenase related proteins, child 1. Members identified as glutathione-dependent formaldehyde dehydrogenase(FDH), a member of the zinc-dependent/medium chain alcohol dehydrogenase family. FDH converts formaldehyde and NAD(P) to formate and NAD(P)H. The initial step in this process the spontaneous formation of a S-(hydroxymethyl)glutathione adduct from formaldehyde and glutathione, followed by FDH-mediated oxidation (and detoxification) of the adduct to S-formylglutathione. MDH family uses NAD(H) as a cofactor in the interconversion of alcohols and aldehydes, or ketones. Like many zinc-dependent alcohol dehydrogenases (ADH) of the medium chain alcohol dehydrogenase/reductase family (MDR), these FDHs form dimers, with 4 zinc ions per dimer. The medium chain alcohol dehydrogenase family (MDR) has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The N-terminal region typically has an all-beta catalytic domain. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit. Length = 386 Score = 27.9 bits (63), Expect = 4.8 Identities = 7/25 (28%), Positives = 17/25 (68%) Query: 28 IKSAVKSTKRAGTIGEIGGFGGLFD 52 ++ A+++ ++ GT+ IG +GG + Sbjct: 289 LREAIQAVRKGGTVSIIGVYGGTVN 313 >gnl|CDD|144458 pfam00871, Acetate_kinase, Acetokinase family. This family includes acetate kinase, butyrate kinase and 2-methylpropanoate kinase. Length = 387 Score = 27.7 bits (62), Expect = 5.2 Identities = 12/51 (23%), Positives = 26/51 (50%), Gaps = 3/51 (5%) Query: 283 PQIISWLSKKAHVKPAEVLRTFNCGIGMVII--VHPDNKDCIIKKFQENNE 331 P I+ +L++ + EV+ T N G++ + + D +D + +E +E Sbjct: 244 PAIVFYLAETEGMSADEVVNTLNKKSGLLGLSGLSSDLRD-VEDAMEEGDE 293 >gnl|CDD|38891 KOG3687, KOG3687, KOG3687, Tuberin - Rap/ran-GTPase-activating protein [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]. Length = 1697 Score = 27.4 bits (60), Expect = 6.6 Identities = 29/135 (21%), Positives = 43/135 (31%), Gaps = 23/135 (17%) Query: 109 LDYLATSQLNPDQATSIIKGIAAGCCQAGCALIGG------ETAEMPGLYHDRDYDLAGF 162 + L T + T + G+ +G Q+G +T E P + AG Sbjct: 965 GNKLVTITTSVGTGTRSLLGLDSGELQSGPESSASPGVPVRQTKEAPAKLESQ----AGQ 1020 Query: 163 AVGAVERKELLSPENVCAGDLILGLPSSGLHSNGFALVRKIISLSQLSWKDPSPISSEHS 222 V + S G GL L S LS P P ++ + Sbjct: 1021 QVSRGAEDRVRSMSF--GG---HGLRVGALDVP--------ASQFLLSATSPGPRTAPAA 1067 Query: 223 LGETLLTPTRIYVSP 237 L E T +R+ V P Sbjct: 1068 LPEKASTGSRVPVQP 1082 >gnl|CDD|31541 COG1350, COG1350, Predicted alternative tryptophan synthase beta-subunit (paralog of TrpB) [General function prediction only]. Length = 432 Score = 26.8 bits (59), Expect = 9.2 Identities = 11/26 (42%), Positives = 14/26 (53%) Query: 209 LSWKDPSPISSEHSLGETLLTPTRIY 234 L P+P+ +L E L TP RIY Sbjct: 73 LQIGRPTPLIRAKNLEEALGTPARIY 98 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 0.318 0.137 0.398 Gapped Lambda K H 0.267 0.0710 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 4,228,630 Number of extensions: 224021 Number of successful extensions: 504 Number of sequences better than 10.0: 1 Number of HSP's gapped: 480 Number of HSP's successfully gapped: 31 Length of query: 357 Length of database: 6,263,737 Length adjustment: 95 Effective length of query: 262 Effective length of database: 4,210,882 Effective search space: 1103251084 Effective search space used: 1103251084 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 58 (26.2 bits)