RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780137|ref|YP_003064550.1| malic enzyme [Candidatus Liberibacter asiaticus str. psy62] (779 letters) >gnl|CDD|30629 COG0281, SfcA, Malic enzyme [Energy production and conversion]. Length = 432 Score = 525 bits (1354), Expect = e-149 Identities = 217/433 (50%), Positives = 278/433 (64%), Gaps = 18/433 (4%) Query: 18 DSLFKQALLYHQYPSPGKLEVNATKMLNDQKDLSLAYSPGVAAPSMMIAEDPSKAAMYTN 77 + L +AL H+Y PGK+ + T L+ Q+DL LAY+PGVA I+EDP KA YT Sbjct: 15 EQLKTEALDKHEYLDPGKILIYPTVPLHTQEDLPLAYTPGVAEACKAISEDPRKAYSYTA 74 Query: 78 RSNLVAVVSNGSAVLGLGDIGPLASKPVMEGKAVLFKKFAGINVFDIEINAKDVDTMVST 137 R NLVAVV++G+AVLGLG+IGPLA KPVMEGKAVLFK FAGI+V IE++ + ++ Sbjct: 75 RGNLVAVVTDGTAVLGLGNIGPLAGKPVMEGKAVLFKAFAGIDVLPIELDVGTNNEIIEF 134 Query: 138 IVALEPTFGGINLEDIKAPECFEVERILSQKLKIPFLHDDQHGTAVTVTAATLNGMKLVG 197 + ALEPTFGGINLEDI AP CF +E L ++ IP HDDQ GTA+ AA LN +KL G Sbjct: 135 VKALEPTFGGINLEDIDAPRCFAIEERLRYRMNIPVFHDDQQGTAIVTLAALLNALKLTG 194 Query: 198 KKFSDIKIVTLGAGAAALACLNLLVTMGVRRENIWVYDLEGLVYEGREK-KFDKWKSVYA 256 KK D KIV GAGAA +A +LLV GV+ ENI+V D +GL+Y+GRE ++ K A Sbjct: 195 KKLKDQKIVINGAGAAGIAIADLLVAAGVKEENIFVVDRKGLLYDGREDLTMNQKKYAKA 254 Query: 257 Q-KSGPKPLSETMNNADVFLGLSVAGALDPAILKFMAEKPLIMVLANPNPEAMPDEIKKV 315 +G + L + ADV +G+S GA ++K MA+ P+I LANP PE P++ K+ Sbjct: 255 IEDTGERTLDLALAGADVLIGVSGVGAFTEEMVKEMAKHPIIFALANPTPEITPEDAKEW 314 Query: 316 RPD-AMICTGRSDFSNQVNNVLCFPYIFRGALDCGATAITEEMKVAAARAMAVLVRDVPP 374 A++ TGRSD+ NQVNNVL FP IFRGALD A IT+EMK+AAA A+A L R+ Sbjct: 315 GDGAAIVATGRSDYPNQVNNVLIFPGIFRGALDVRAKTITDEMKIAAAEAIADLAREEVL 374 Query: 375 DVVFDNFAKESPVFGPNYLIPSPFDPNLISYIAPAVAKAAEEAGVASSPIEDYEVYRDSL 434 Y+IP PFDP +IS +A AVAKAA E GVA PI+D E Y +L Sbjct: 375 ---------------EEYIIPPPFDPRVISRVAVAVAKAAMEEGVARRPIDDEEAYEQAL 419 Query: 435 KRFSFPGRSLMKK 447 + + MK+ Sbjct: 420 EARLWKPEYRMKR 432 >gnl|CDD|133453 cd05311, NAD_bind_2_malic_enz, NAD(P) binding domain of malic enzyme (ME), subgroup 2. Malic enzyme (ME), a member of the amino acid dehydrogenase (DH)-like domain family, catalyzes the oxidative decarboxylation of L-malate to pyruvate in the presence of cations (typically Mg++ or Mn++) with the concomitant reduction of cofactor NAD+ or NADP+. ME has been found in all organisms, and plays important roles in diverse metabolic pathways such as photosynthesis and lipogenesis. This enzyme generally forms homotetramers. The conversion of malate to pyruvate by ME typically involves oxidation of malate to produce oxaloacetate, followed by decarboxylation of oxaloacetate to produce pyruvate and CO2. This subfamily consists primarily of archaeal and bacterial ME. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts. Length = 226 Score = 289 bits (741), Expect = 2e-78 Identities = 116/241 (48%), Positives = 154/241 (63%), Gaps = 19/241 (7%) Query: 178 QHGTAVTVTAATLNGMKLVGKKFSDIKIVTLGAGAAALACLNLLVTMGVRRENIWVYDLE 237 QHGTA+ A LN +KLVGKK ++KIV GAGAA +A LL+ G + ENI V D + Sbjct: 1 QHGTAIVTLAGLLNALKLVGKKIEEVKIVINGAGAAGIAIARLLLAAGAKPENIVVVDSK 60 Query: 238 GLVYEGREKKFDKWKSVYAQKSGPKP----LSETMNNADVFLGLSVAGALDPAILKFMAE 293 G++YEGRE + K+ A+++ P+ L E + ADVF+G+S G + ++K MA+ Sbjct: 61 GVIYEGREDDLNPDKNEIAKETNPEKTGGTLKEALKGADVFIGVSRPGVVKKEMIKKMAK 120 Query: 294 KPLIMVLANPNPEAMPDEIKKVRPDAMICTGRSDFSNQVNNVLCFPYIFRGALDCGATAI 353 P++ LANP PE P+E K+ D ++ TGRSDF NQVNNVL FP IFRGALD AT I Sbjct: 121 DPIVFALANPVPEIWPEEAKEAGAD-IVATGRSDFPNQVNNVLGFPGIFRGALDVRATKI 179 Query: 354 TEEMKVAAARAMAVLVRDVPPDVVFDNFAKESPVFGPNYLIPSPFDPNLISYIAPAVAKA 413 TEEMK+AAA A+A + A+E V G Y+IP+PFDP ++ +A AVAKA Sbjct: 180 TEEMKLAAAEAIA-------------DLAEE-EVLGEEYIIPTPFDPRVVPRVATAVAKA 225 Query: 414 A 414 A Sbjct: 226 A 226 >gnl|CDD|146532 pfam03949, Malic_M, Malic enzyme, NAD binding domain. Length = 255 Score = 244 bits (625), Expect = 8e-65 Identities = 109/269 (40%), Positives = 138/269 (51%), Gaps = 47/269 (17%) Query: 178 QHGTAVTVTAATLNGMKLVGKKFSDIKIVTLGAGAAALACLNLLVTMGVR--------RE 229 GTA V A LN +K+ GK SD KIV GAGAA + LLV VR R+ Sbjct: 1 IQGTAAVVLAGLLNALKITGKPLSDQKIVFFGAGAAGIGIAELLVAAMVREGLSEEEARK 60 Query: 230 NIWVYDLEGLVYEGREKKFDKWKSVYAQK----SGPKPLSETMNNA--DVFLGLS-VAGA 282 NIW+ D +GL+ EGRE +K +A+K G L+E + A DV +G+S V G Sbjct: 61 NIWMVDRKGLLTEGREDLNP-FKKPFARKTNEVKGWGTLAEAVKGAKPDVLIGVSGVPGV 119 Query: 283 LDPAILKFMA---EKPLIMVLANPNP--EAMPDEIKKVRPD-AMICTG----------RS 326 I++ MA E+P+I L+NP P E P+E K A+ TG RS Sbjct: 120 FTEEIVRAMAEHTERPIIFALSNPTPKAEITPEEAYKWTAGRALFATGSPFPPVELNGRS 179 Query: 327 DFSNQVNNVLCFPYIFRGALDCGATAITEEMKVAAARAMAVLVRDVPPDVVFDNFAKESP 386 D+ NQVNNVL FP I GALD A IT+EM +AAA A+A LV + Sbjct: 180 DYPNQVNNVLIFPGIGLGALDVRARRITDEMFLAAAEALAELVTE--------------E 225 Query: 387 VFGPNYLIPSPFDPNLISY-IAPAVAKAA 414 G Y+IP FD +S +A AVAKAA Sbjct: 226 ELGEGYIIPPLFDIREVSPRVAVAVAKAA 254 >gnl|CDD|30628 COG0280, Pta, Phosphotransacetylase [Energy production and conversion]. Length = 327 Score = 218 bits (557), Expect = 4e-57 Identities = 97/324 (29%), Positives = 178/324 (54%), Gaps = 8/324 (2%) Query: 444 LMKKIFSIAKGTDSKRILFSAGEDERVLRATQILIKENIARPVLIGSLLTIQDNIRRHDL 503 + ++F A+ KRI+ GE+ERVLRA Q+L KE +A+P+L+G I++ + L Sbjct: 1 FLYRLFERARK-APKRIVLPEGEEERVLRAAQVLAKEGLAKPILVGRPEEIEEVAKALGL 59 Query: 504 QIIATKDFDVID-LNNKQSLKDYVDSYRSLSAEKGISLDSIYDLLRSNTTLLGSLALKRG 562 + ++I+ + + ++YVD L KG++ + +L+R + T+ ++ + G Sbjct: 60 DL---DGIEIINPELDPERFEEYVDRLYELRKRKGVTPEDAQELVREDPTVFAAMMVALG 116 Query: 563 EGDGMICMCDSESGYNSHLTDIHKIIGMGLGISHYSAMSMCIVRDNFLFFTDTHVSAEPS 622 E DG+ + + L +IIG G+S S++ + ++ D LFF D V+ +P+ Sbjct: 117 EADGL--VSGAVHTTADTLRPALQIIGTRPGVSLVSSVFIMLLPDGTLFFADCAVNPDPT 174 Query: 623 AMEIADSTILASQAICSLGMRPKVSVLFHSNSGSHCIKSSLKMRDSFEKICELS-KNLEV 681 A E+AD A++ G+ PKV++L +S GS S+ K+R++ + + E + +LEV Sbjct: 175 AEELADIAENAAETARRFGIEPKVALLSYSTFGSGKGPSTDKVREATKILRERAPPDLEV 234 Query: 682 DAIVQEEVCLSEIFCDKDVPNTSSSQDAQLLVFPNIDSANIALEMAKSVTNGLHIGTLLL 741 D +Q + L E K P++ + A +LVFP++++ NI ++ + + L +G +L Sbjct: 235 DGELQFDAALVEKVAAKKAPDSPLAGSANVLVFPDLEAGNIGYKLLQRLGGALAVGPILQ 294 Query: 742 GAALPVHIVPSSVSVREIIDMVAL 765 G A PV+ + SV +I++M AL Sbjct: 295 GLAKPVNDLSRGASVEDIVNMAAL 318 >gnl|CDD|144928 pfam01515, PTA_PTB, Phosphate acetyl/butaryl transferase. This family contains both phosphate acetyltransferase and phosphate butaryltransferase. These enzymes catalyse the transfer of an acetyl or butaryl group to orthophosphate. Length = 319 Score = 182 bits (463), Expect = 4e-46 Identities = 94/324 (29%), Positives = 178/324 (54%), Gaps = 8/324 (2%) Query: 443 SLMKKIFSIAKGTDSKRILFSAGEDERVLRATQILIKENIARPVLIGSLLTIQDNIRRHD 502 S +++IF AK KRI+F GEDERVL+A + L++E IA P+LIG+ + I+ Sbjct: 1 SFLERIFERAKS-AKKRIVFPEGEDERVLKAAKELLEEGIADPILIGNEIEIKAKALGLG 59 Query: 503 LQIIATKDFDVIDLNNKQSLKDYVDSYRSLSAEKGISLDSIYDLLRSNTTLLGSLALKRG 562 L + +++D ++Y D + L KG++ + +++R + T ++ +K G Sbjct: 60 LDLSG---IEIVDPETSPRDEEYADEFYELRKHKGMTPEIAREIVR-DPTYFAAMLVKLG 115 Query: 563 EGDGMICMCDSESGYNSHLTDIHKIIGMGLGISHYSAMSMCIVRDNFLFFTDTHVSAEPS 622 E DG+ + + + L +II G+ S++ + ++ D LFFTD V+ P+ Sbjct: 116 EADGL--VSGAVNTTADTLRPALQIIKTLPGVKIVSSVFIMLLPDRLLFFTDCAVNPNPT 173 Query: 623 AMEIADSTILASQAICSLG-MRPKVSVLFHSNSGSHCIKSSLKMRDSFEKICELSKNLEV 681 A E+A+ + A++ +LG + P+V++L +S GS +S K+R++ + E + +L V Sbjct: 174 AEELAEIALNAAKTAKALGNIEPRVAMLSYSTFGSGKGESVEKVREATKIAKEKAPDLVV 233 Query: 682 DAIVQEEVCLSEIFCDKDVPNTSSSQDAQLLVFPNIDSANIALEMAKSVTNGLHIGTLLL 741 D +Q + + E + P++ + A +LVFP++++ NI ++A+ + IG +L Sbjct: 234 DGELQLDAAIVEEVAAQKAPDSPVAGKANVLVFPDLEAGNIGYKIAQRLAGAEAIGPILQ 293 Query: 742 GAALPVHIVPSSVSVREIIDMVAL 765 G A PV+ + SV +I++ +A+ Sbjct: 294 GLAKPVNDLSRGASVEDIVNTIAI 317 >gnl|CDD|144108 pfam00390, malic, Malic enzyme, N-terminal domain. Length = 182 Score = 142 bits (361), Expect = 3e-34 Identities = 56/180 (31%), Positives = 77/180 (42%), Gaps = 50/180 (27%) Query: 33 PGKLEVNATKMLNDQ--KDLSLAYSPGVAAPSMMIAEDPSKA-AMYTNRSNL-------- 81 GK EV K+L+ +DL + Y+P V I+E + +YT+ NL Sbjct: 1 QGKNEVLFYKLLSTHIEEDLPIVYTPTVGEACQAISEIYRRPRGLYTSIGNLGKIKDILK 60 Query: 82 --------VAVVSNGSAVLGLGDIGPLASKPVMEGKAVLFKKFAGIN---VFDIEINAK- 129 V VV++G +LGLGD+G +A P+MEGK L+ FAGI+ V I ++ Sbjct: 61 NWPEEDVRVIVVTDGERILGLGDLG-VAGMPIMEGKLALYTAFAGIDPSRVLPIVLDVGT 119 Query: 130 --------------------------DVDTMVSTIVALEPTFGGINLEDIKAPECFEVER 163 VD V + AL P FGGI ED AP FE+ Sbjct: 120 NNEKLLNDPLYLGLRHKRVRGEEYDEFVDEFVEAVKALFPPFGGIQFEDFGAPNAFEILE 179 >gnl|CDD|36471 KOG1257, KOG1257, KOG1257, NADP+-dependent malic enzyme [Energy production and conversion]. Length = 582 Score = 135 bits (341), Expect = 5e-32 Identities = 113/398 (28%), Positives = 164/398 (41%), Gaps = 78/398 (19%) Query: 84 VVSNGSAVLGLGDIGPLASKPVMEGKAVLFKKFAGIN-------VFDIEIN--------- 127 VV++G +LGLGD+G + + GK L+ GI D+ N Sbjct: 165 VVTDGERILGLGDLG-VNGMGIPVGKLALYTALGGIRPSRCLPVCLDVGTNNEKLLNDPL 223 Query: 128 ----------AKDVDTMVST-IVALEPTFGG---INLEDIKAPECFEVERILSQ-KLKIP 172 K+ D + + A+ +G I ED F R+L + + K Sbjct: 224 YIGLRQRRVRGKEYDEFLDEFMEAVVQRYGPNTLIQFEDFANHNAF---RLLEKYRNKYC 280 Query: 173 FLHDDQHGTAVTVTAATLNGMKLVGKKFSDIKIVTLGAGAAAL----ACLNLLVTMGV-- 226 +DD GTA A L +++ GK SD I+ LGAG AAL + +V G+ Sbjct: 281 MFNDDIQGTAAVALAGLLAALRITGKPLSDHVILFLGAGEAALGIANLIVMAMVKEGLSE 340 Query: 227 --RRENIWVYDLEGLVYEGREKKFDKWKSVYAQKSGP-KPLSETMNNA--DVFLGLS-VA 280 R+ IW+ D +GL+ +GR+ + K +A+ K L E + V +G S V Sbjct: 341 EEARKKIWLVDSKGLITKGRKASLTEEKKPFAKDHEEIKDLEEAVKEVKPTVLIGASGVG 400 Query: 281 GALDPAILKFMA---EKPLIMVLANP--NPEAMPDEIKKVRPDAMICTGRSDFSN----- 330 GA +L+ MA E+P+I L+NP E ++ K I S F Sbjct: 401 GAFTEEVLRAMAKSNERPIIFALSNPTSKAECTAEQAYKWTKGRAIFASGSPFPPVEYNG 460 Query: 331 ------QVNNVLCFPYIFRGALDCGATAITEEMKVAAARAMAVLVRDVPPDVVFDNFAKE 384 Q NN FP I G + GA I +EM +AAA A+A V + + K Sbjct: 461 KVYVPGQGNNAYIFPGIGLGVVLSGARRIPDEMFLAAAEALAEQVSE-------EELEKG 513 Query: 385 SPVFGPNYLIPSPFDPNLISY-IAPAVAKAAEEAGVAS 421 L P + IS IA AV K A E G+A+ Sbjct: 514 R-------LYPPLSNIREISANIAAAVLKYAYEEGLAT 544 >gnl|CDD|133454 cd05312, NAD_bind_1_malic_enz, NAD(P) binding domain of malic enzyme (ME), subgroup 1. Malic enzyme (ME), a member of the amino acid dehydrogenase (DH)-like domain family, catalyzes the oxidative decarboxylation of L-malate to pyruvate in the presence of cations (typically Mg++ or Mn++) with the concomitant reduction of cofactor NAD+ or NADP+. ME has been found in all organisms, and plays important roles in diverse metabolic pathways such as photosynthesis and lipogenesis. This enzyme generally forms homotetramers. The conversion of malate to pyruvate by ME typically involves oxidation of malate to produce oxaloacetate, followed by decarboxylation of oxaloacetate to produce pyruvate and CO2. This subfamily consists of eukaryotic and bacterial ME. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts. Length = 279 Score = 124 bits (315), Expect = 7e-29 Identities = 93/284 (32%), Positives = 132/284 (46%), Gaps = 48/284 (16%) Query: 180 GTAVTVTAATLNGMKLVGKKFSDIKIVTLGAGAAALACLNLLVTMGVR--------RENI 231 GTA A L +++ GK SD +I+ LGAG+A + +L+V+ VR R+ I Sbjct: 3 GTAAVALAGLLAALRITGKPLSDQRILFLGAGSAGIGIADLIVSAMVREGLSEEEARKKI 62 Query: 232 WVYDLEGLVYEGREKKFDKWKSVYAQK---SGPKPLSETMNNA--DVFLGLS-VAGALDP 285 W+ D +GL+ + R+ +K +A+K K L E + V +GLS V GA Sbjct: 63 WLVDSKGLLTKDRKDL-TPFKKPFARKDEEKEGKSLLEVVKAVKPTVLIGLSGVGGAFTE 121 Query: 286 AILKFMA---EKPLIMVLANP--NPEAMPDEIKKVRPDAMICTGRSDFS----------- 329 +++ MA E+P+I L+NP E ++ K + S F Sbjct: 122 EVVRAMAKSNERPIIFALSNPTSKAECTAEDAYKWTDGRALFASGSPFPPVEYNGKTYVP 181 Query: 330 NQVNNVLCFPYIFRGALDCGATAITEEMKVAAARAMAVLVRDVPPDVVFDNFAKESPVFG 389 Q NN FP I GA+ GA IT+EM +AAA A+A LV D + A+ Sbjct: 182 GQGNNAYIFPGIGLGAILSGARHITDEMFLAAAEALASLVTD-------EELARGR---- 230 Query: 390 PNYLIPSPFDPNLISY-IAPAVAKAAEEAGVASS--PIEDYEVY 430 L P + IS IA AVAK A E G+A+ P ED E Y Sbjct: 231 ---LYPPLSNIREISAQIAVAVAKYAYEEGLATRYPPPEDLEEY 271 >gnl|CDD|133442 cd00762, NAD_bind_malic_enz, NAD(P) binding domain of malic enzyme. Malic enzyme (ME), a member of the amino acid dehydrogenase (DH)-like domain family, catalyzes the oxidative decarboxylation of L-malate to pyruvate in the presence of cations (typically Mg++ or Mn++) with the concomitant reduction of cofactor NAD+ or NADP+. ME has been found in all organisms and plays important roles in diverse metabolic pathways such as photosynthesis and lipogenesis. This enzyme generally forms homotetramers. The conversion of malate to pyruvate by ME typically involves oxidation of malate to produce oxaloacetate, followed by decarboxylation of oxaloacetate to produce pyruvate and CO2. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts. Length = 254 Score = 110 bits (276), Expect = 2e-24 Identities = 76/269 (28%), Positives = 119/269 (44%), Gaps = 47/269 (17%) Query: 178 QHGTAVTVTAATLNGMKLVGKKFSDIKIVTLGAGAAALACLNLLVTMGVRR--------E 229 GTA A L +K+ KK S+ K++ GAGAAAL NL+V + V+ + Sbjct: 1 IQGTASVAVAGLLAALKVTKKKISEHKVLFNGAGAAALGIANLIVXLXVKEGISKEEACK 60 Query: 230 NIWVYDLEGLVYEGREKKFDKWKSVYAQKSGPKPLSETMNNA------DVFLGLS-VAGA 282 IW D +GL+ + R++ + A+ + P+ S + +A D +G+S V GA Sbjct: 61 RIWXVDRKGLLVKNRKETCPN-EYHLARFANPERESGDLEDAVEAAKPDFLIGVSRVGGA 119 Query: 283 LDPAILKFMA---EKPLIMVLANPNPEA--MPDEIKKVRPDAMI-CTGRSDFSN------ 330 P +++ A E+P+I L+NP +A +E I +G Sbjct: 120 FTPEVIRAXAEINERPVIFALSNPTSKAECTAEEAYTATEGRAIFASGSPFHPVELNGGT 179 Query: 331 ----QVNNVLCFPYIFRGALDCGATAITEEMKVAAARAMAVLVRDVPPDVVFDNFAKESP 386 Q NN+ FP + G + C IT+++ ++AA A+A V + + Sbjct: 180 YKPGQGNNLYIFPGVALGVILCRIRHITDDVFLSAAEAIA---SSVTEESL--------- 227 Query: 387 VFGPNYLIPSPFDPNLISY-IAPAVAKAA 414 P L P FD +S IA AVAK A Sbjct: 228 --KPGRLYPPLFDIQEVSLNIAVAVAKYA 254 >gnl|CDD|133449 cd05191, NAD_bind_amino_acid_DH, NAD(P) binding domain of amino acid dehydrogenase-like proteins. Amino acid dehydrogenase(DH)-like NAD(P)-binding domains are members of the Rossmann fold superfamily and are found in glutamate, leucine, and phenylalanine DHs (DHs), methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts. Length = 86 Score = 36.2 bits (84), Expect = 0.033 Identities = 14/56 (25%), Positives = 20/56 (35%), Gaps = 2/56 (3%) Query: 180 GTAVTVTAATLNGMKLVGKKFSDIKIVTLGAGAAALACLNLLVTMGVRRENIWVYD 235 TA A K+ K +V LGAG LL G ++ + + D Sbjct: 1 ATAAGAVALLKAAGKVTNKSLKGKTVVVLGAGEVGKGIAKLLADEGGKK--VVLCD 54 >gnl|CDD|31690 COG1501, COG1501, Alpha-glucosidases, family 31 of glycosyl hydrolases [Carbohydrate transport and metabolism]. Length = 772 Score = 33.5 bits (76), Expect = 0.22 Identities = 32/157 (20%), Positives = 54/157 (34%), Gaps = 22/157 (14%) Query: 401 NLISYIAPAVAKAAEEAGVASSPI-----EDYEVYRDSLKRFSFPGRSLM-KKIFSIAKG 454 L+ YI A+A+E P+ ED Y +L G L+ + +G Sbjct: 568 RLLPYIYTLAAEASETGLPMMRPLFLEFPEDETTY--NLDDQYMFGDDLLVAPVVE--EG 623 Query: 455 TDSKRILFSAGE------DERVLRATQILIKENIAR-PVLI--GSLLTIQDNIRRHDLQI 505 S+ + G E I ++ + PV + GS++ + +N Sbjct: 624 QTSREVYLPEGTWYDFWTGEEYEGGQTITVEAPLETIPVFVRAGSIIPLLENELYVGESY 683 Query: 506 IATKDFDVIDLNNKQSLKDYVD---SYRSLSAEKGIS 539 + FDV + S + Y D S+ E S Sbjct: 684 VEDVAFDVFPGQDGASGELYDDDGESFAYEKGEYTDS 720 >gnl|CDD|36108 KOG0890, KOG0890, KOG0890, Protein kinase of the PI-3 kinase family involved in mitotic growth, DNA repair and meiotic recombination [Signal transduction mechanisms, Chromatin structure and dynamics, Replication, recombination and repair, Cell cycle control, cell division, chromosome partitioning]. Length = 2382 Score = 30.4 bits (68), Expect = 2.3 Identities = 33/184 (17%), Positives = 57/184 (30%), Gaps = 31/184 (16%) Query: 277 LSVAGALDPAILKFMAEKPLIMVLANPNPEAMPDEIKKVRPDAMICTGRSDFSNQVNNVL 336 L GA+DP+ +F ++ + +L E IK DF+ Sbjct: 1108 LGELGAIDPSCHRFKEQETIPSILQVLPIECSDLPIK-----------FIDFAWDTLVKA 1156 Query: 337 CFPYIFRGALDCGATAITEEMKVAAARAMAVLVRDVPPDVVFDNFAKES-PVFGPNYLIP 395 + D A AI E + + + + L R + +++ F E P + Sbjct: 1157 FLCEPDQLKQDVVAYAIQEVLVLGGSSNIEPLDRGMCE--LWERFPNEVKEEMEP--TLT 1212 Query: 396 SPFDPNLISYIAPAVAKAAEEAGVASSPIEDYEVYRDSLKRFS-----FPGRSLMKKIFS 450 S + K G + YR+ L R+S S +FS Sbjct: 1213 SRYASQ----------KPEPSVGEKKPIYKSSLGYREWLSRWSLKLIAKAESSEASPLFS 1262 Query: 451 IAKG 454 + Sbjct: 1263 LCSI 1266 >gnl|CDD|144968 pfam01568, Molydop_binding, Molydopterin dinucleotide binding domain. This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entire subunit. The formylmethanofuran dehydrogenase catalyses the first step in methane formation from CO2 in methanogenic archaea and has a molybdopterin dinucleotide cofactor. This domain corresponds to the C-terminal domain IV in dimethyl sulfoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules. Length = 110 Score = 29.5 bits (67), Expect = 4.0 Identities = 10/42 (23%), Positives = 13/42 (30%), Gaps = 2/42 (4%) Query: 361 AARAMAVLVRDVPPDVVF--DNFAKESPVFGPNYLIPSPFDP 400 + A + V P VVF + N L DP Sbjct: 58 SVVVRAKVTDRVRPGVVFMPFGWWAAPKGGNANVLTSDGTDP 99 >gnl|CDD|133443 cd01065, NAD_bind_Shikimate_DH, NAD(P) binding domain of Shikimate dehydrogenase. Shikimate dehydrogenase (DH) is an amino acid DH family member. Shikimate pathway links metabolism of carbohydrates to de novo biosynthesis of aromatic amino acids, quinones and folate. It is essential in plants, bacteria, and fungi but absent in mammals, thus making enzymes involved in this pathway ideal targets for broad spectrum antibiotics and herbicides. Shikimate DH catalyzes the reduction of 3-hydroshikimate to shikimate using the cofactor NADH. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DHs, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts. Length = 155 Score = 29.2 bits (66), Expect = 4.6 Identities = 11/32 (34%), Positives = 16/32 (50%), Gaps = 2/32 (6%) Query: 204 KIVTLGAGAAALACLNLLVTMGVRRENIWVYD 235 K++ LGAG AA A L +G I + + Sbjct: 21 KVLILGAGGAARAVAYALAELGA--AKIVIVN 50 >gnl|CDD|35591 KOG0370, KOG0370, KOG0370, Multifunctional pyrimidine synthesis protein CAD (includes carbamoyl-phophate synthetase, aspartate transcarbamylase, and glutamine amidotransferase) [General function prediction only]. Length = 1435 Score = 29.1 bits (65), Expect = 4.8 Identities = 43/214 (20%), Positives = 65/214 (30%), Gaps = 76/214 (35%) Query: 276 GLSV--AGALDPAI---LKFMAEKPLIMVLANPN--------------------PEAMPD 310 GLS+ AG D + +K + E+ + +L NPN PE + Sbjct: 387 GLSIGQAGEFDYSGSQAIKALKEENIFTILINPNIATVQTSKGLADKVYFLPVTPEYVTK 446 Query: 311 EIKKVRPDAMICTGRSDFSNQVNNVLCFPYIFRGALDCG--------------------- 349 IK RPD ++ T F Q AL+CG Sbjct: 447 VIKAERPDGILLT----FGGQ------------TALNCGVELDKAGVFAQYGVKVLGTPI 490 Query: 350 ATAITEEMKVAAARAMAVLVRDVPPDVVFDNFAKESPVFGPNYLIPSPFDPNLISYIAPA 409 T IT E + ARA+ + + P S + + + Y P Sbjct: 491 QTIITTEDRDLFARALNEINEKIAP------SEAVSTIEE------ALEAAERLGY--PV 536 Query: 410 VAKAAEEAGVASSPIEDYEVYRDSLKRFSFPGRS 443 + +AA G S + E L + Sbjct: 537 IVRAAYALGGLGSGFANNEEELQDLAAQALALSP 570 >gnl|CDD|133101 cd06243, Peptidase_M14-like_1_6, Peptidase M14-like domain of a functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavages. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others. Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism. Length = 236 Score = 28.7 bits (64), Expect = 6.3 Identities = 21/62 (33%), Positives = 29/62 (46%), Gaps = 4/62 (6%) Query: 356 EMKVAAARAMAVLVRDVPPDVVFDNFAKESPVFGPNYLIPSPFDPNLISYIAPAVAKAAE 415 + A+A+A ++RD PDVV D A E P NY I + NL I + K + Sbjct: 103 LLNTPEAQALASVLRDYRPDVVVD--AHEYPGASQNYDILLLWPRNL--NIDEFLTKLNQ 158 Query: 416 EA 417 A Sbjct: 159 AA 160 >gnl|CDD|145900 pfam02994, Transposase_22, L1 transposable element. Length = 370 Score = 28.1 bits (62), Expect = 9.0 Identities = 19/85 (22%), Positives = 38/85 (44%), Gaps = 5/85 (5%) Query: 463 SAGEDERVLRATQILIKENIAR-PVLIGSLLTIQDNIRRHDLQIIATKDFDVIDLNNKQS 521 S ED + + K N R L ++ IQD +RR +L+II + + L ++ Sbjct: 154 SGAEDS--IEEIKRTGKFNEKRKKRLEQNIQEIQDYVRRPNLRIIGVPESEDEQLKGPEN 211 Query: 522 LKDYV--DSYRSLSAEKGISLDSIY 544 + + +++ +L E + + Y Sbjct: 212 IFQKIIEENFPNLKREANVQIQEAY 236 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 0.133 0.376 Gapped Lambda K H 0.267 0.0801 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 8,953,215 Number of extensions: 482257 Number of successful extensions: 1249 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1215 Number of HSP's successfully gapped: 28 Length of query: 779 Length of database: 6,263,737 Length adjustment: 101 Effective length of query: 678 Effective length of database: 4,081,228 Effective search space: 2767072584 Effective search space used: 2767072584 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: 61 (27.1 bits)