RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780371|ref|YP_003064784.1| diaminopimelate decarboxylase protein [Candidatus Liberibacter asiaticus str. psy62] (431 letters) >gnl|CDD|143501 cd06828, PLPDE_III_DapDC, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase. Diaminopimelate decarboxylase (DapDC, EC 4.1.1.20) participates in the last step of lysine biosynthesis. It converts meso-2,6-diaminoheptanedioate to L-lysine. It is a fold type III PLP-dependent enzyme that contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. DapDC exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity. Length = 373 Score = 497 bits (1282), Expect = e-141 Identities = 176/374 (47%), Positives = 232/374 (62%), Gaps = 6/374 (1%) Query: 25 VQTPFYCYSTTAIEKNYLTFSNAFDGMDTMVCYALKANSNQAVIKTLAHLGSGLDIVSEG 84 TP Y Y I +NY AF G +CYA+KANSN A++K LA G G D+VS G Sbjct: 1 YGTPLYVYDEATIRENYRRLKEAFSGPGFKICYAVKANSNLAILKLLAEEGLGADVVSGG 60 Query: 85 ELRRALAAPVPAERIVFSGVGKTIDEIDLALQSGIYCFNVESESELKTLNQRAVSLGKKA 144 EL RAL A P ERIVF+G GK+ +E++LAL+ GI NV+S SEL+ L + A LGK A Sbjct: 61 ELYRALKAGFPPERIVFTGNGKSDEELELALELGILRINVDSLSELERLGEIAPELGKGA 120 Query: 145 PIAFRVNPDINANTHKKISTGKKEDKFGIPIHQIHSLYAYASTLPGVKISGVDMHIGSQI 204 P+A RVNP ++A TH ISTG K+ KFGIP+ Q Y A LPG+K+ G+ HIGSQI Sbjct: 121 PVALRVNPGVDAGTHPYISTGGKDSKFGIPLEQALEAYRRAKELPGLKLVGLHCHIGSQI 180 Query: 205 DQIESFHKAFKLLRDLTQQLRSNGHNIQHIDVGGGLGIAYHSDHRPPSSSDYASLIHQYF 264 +E F +A + L DL +LR G +++ +D+GGGLGI Y + P +YA I + Sbjct: 181 LDLEPFVEAAEKLLDLAAELRELGIDLEFLDLGGGLGIPYRDEDEPLDIEEYAEAIAEAL 240 Query: 265 GNLQ-----CKIILEPGRFLVADVGILVTKVISIKKSADKTFVILDVAMNDFMRPTLYDA 319 L K+I+EPGR++VA+ G+L+T+V +K++ KTFV +D MND +RP LY A Sbjct: 241 KELCEGGPDLKLIIEPGRYIVANAGVLLTRVGYVKETGGKTFVGVDAGMNDLIRPALYGA 300 Query: 320 YHEINYIVNPAGDRLHIHADIVGPICETGDFIALNRKIALPRPGDLLYIEKTGAYGAVQS 379 YHEI VN G+ D+VGPICE+GD A +R++ GDLL I GAYG S Sbjct: 301 YHEI-VPVNKPGEGETEKVDVVGPICESGDVFAKDRELPEVEEGDLLAIHDAGAYGYSMS 359 Query: 380 GTYNSRLLIPEIMV 393 YNSR E++V Sbjct: 360 SNYNSRPRPAEVLV 373 >gnl|CDD|30369 COG0019, LysA, Diaminopimelate decarboxylase [Amino acid transport and metabolism]. Length = 394 Score = 396 bits (1019), Expect = e-111 Identities = 164/397 (41%), Positives = 233/397 (58%), Gaps = 7/397 (1%) Query: 1 MSAFKYFEGSLHAENVSLEKLAHVVQTPFYCYSTTAIEKNYLTFSNAFDGMDTMVCYALK 60 + F+ +G L E V L LA TP Y Y + +N +AF G V YA+K Sbjct: 1 GTFFRNKDGELTIEGVDLPALAEEFGTPVYVYDEATLRRNARELKSAFPGSGAKVFYAVK 60 Query: 61 ANSNQAVIKTLAHLGSGLDIVSEGELRRALAAPVPAERIVFSGVGKTIDEIDLALQSGIY 120 ANSN A+++ LA GSG D+ S GEL ALAA P ERIVFSG K+ +EI AL+ GI Sbjct: 61 ANSNPAILRLLAEEGSGFDVASLGELELALAAGFPPERIVFSGPAKSEEEIAFALELGIK 120 Query: 121 CFNVESESELKTLNQRAVSLGKKAPIAFRVNPDINANTHKKISTGKKEDKFGIPIHQIHS 180 NV+SE EL+ L+ A G A ++ R+NP ++A TH+ I+TG K KFGI + Sbjct: 121 LINVDSEEELERLSAIAP--GLVARVSLRINPGVSAGTHEYIATGGKSSKFGISPEEALD 178 Query: 181 LYAYASTLPGVKISGVDMHIGSQIDQIESFHKAFKLLRDLTQQL-RSNGHNIQHIDVGGG 239 + A+ L G+++ G+ HIGSQI ++ F +A + +L +L G ++ +++GGG Sbjct: 179 VLERAAKLLGLELVGLHFHIGSQITDLDPFEEALAKVEELFGRLAEELGIQLEWLNLGGG 238 Query: 240 LGIAYHSDHRPPSSSDYASLIHQYFGN--LQCKIILEPGRFLVADVGILVTKVISIKKSA 297 LGI Y ++ PP + YA + + FG ++ILEPGR +VA+ G+LVT+V+ +K++ Sbjct: 239 LGITYEDEYDPPDLAAYAKALKEAFGEYAEDVELILEPGRAIVANAGVLVTEVLDVKENG 298 Query: 298 DKTFVILDVAMNDFMRPTLYDAYHEINYIVNPAGDRLHIHADIVGPICETGDFIALNRKI 357 ++ FVI+D MND MRP LY AYH I + D D+VGP CE+GD +A +R + Sbjct: 299 ERNFVIVDGGMNDLMRPALYGAYHHI-RLNRTDEDAEREEYDVVGPTCESGDVLARDRAL 357 Query: 358 ALP-RPGDLLYIEKTGAYGAVQSGTYNSRLLIPEIMV 393 P + GDLL I GAYGA S YN R E++V Sbjct: 358 PEPLKVGDLLVILDAGAYGASMSSNYNGRPRPAEVLV 394 >gnl|CDD|143485 cd06810, PLPDE_III_ODC_DapDC_like, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Ornithine and Diaminopimelate Decarboxylases, and Related Enzymes. This family includes eukaryotic ornithine decarboxylase (ODC, EC 4.1.1.17), diaminopimelate decarboxylase (DapDC, EC 4.1.1.20), plant and prokaryotic biosynthetic arginine decarboxylase (ADC, EC 4.1.1.19), carboxynorspermidine decarboxylase (CANSDC), and ODC-like enzymes from diverse bacterial species. These proteins are fold type III PLP-dependent enzymes that catalyze essential steps in the biosynthesis of polyamine and lysine. ODC and ADC participate in alternative pathways of the biosynthesis of putrescine, which is the precursor of aliphatic polyamines in many organisms. ODC catalyzes the direct synthesis of putrescine from L-ornithine, while ADC converts L-arginine to agmatine, which is hydrolysed to putrescine by agmatinase in a pathway that exists only in plants and bacteria. DapDC converts meso-2,6-diaminoheptanedioate to L-lysine, which is the final step of lysine biosynthesis. CANSDC catalyzes the decarboxylation of carboxynorspermidine, which is the last step in the synthesis of norspermidine. The PLP-dependent decarboxylases in this family contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Prokaryotic ornithine, lysine and biodegradative arginine decarboxylases are fold type I PLP-dependent enzymes and are not included in this family. Length = 368 Score = 310 bits (797), Expect = 4e-85 Identities = 147/365 (40%), Positives = 211/365 (57%), Gaps = 11/365 (3%) Query: 27 TPFYCYSTTAIEKNYLTFSNAFDGMDTMVCYALKANSNQAVIKTLAHLGSGLDIVSEGEL 86 TPFY Y I +Y A + YA+KAN N V++TLA G+G D+ S+GEL Sbjct: 1 TPFYVYDLDIIRAHYAALKEALPS-GVKLFYAVKANPNPHVLRTLAEAGTGFDVASKGEL 59 Query: 87 RRALAAPVPAERIVFSGVGKTIDEIDLALQSGIYCFNVESESELKTLNQRAVSLGKKAPI 146 ALAA VP ERI+F+G K++ EI+ AL SG+ V+S EL+ LN+ A LG KA I Sbjct: 60 ALALAAGVPPERIIFTGPAKSVSEIEAALASGVDHIVVDSLDELERLNELAKKLGPKARI 119 Query: 147 AFRVNPDINANTHKKISTGKKEDKFGIPIHQIHSLYAYASTLPGVKISGVDMHIGSQIDQ 206 RVNPD++A TH KISTG + KFG+ + + + A L +++ G+ H+GSQI Sbjct: 120 LLRVNPDVSAGTH-KISTGGLKSKFGLSLSEARAALERAKEL-DLRLVGLHFHVGSQILD 177 Query: 207 IESFHKAFKLLRDLTQQLRSNGHNIQHIDVGGGLGIAYHSDHRPPSSSDYASLIHQYFGN 266 +E+ +A R+L ++L G ++ +D+GGGLGI Y P +YA+LI+ Sbjct: 178 LETIVQALSDARELIEELVEMGFPLEMLDLGGGLGIPYDEQ--PLDFEEYAALINPLLKK 235 Query: 267 LQC-----KIILEPGRFLVADVGILVTKVISIKKSADKTFVILDVAMNDFMRPTL-YDAY 320 +ILEPGR++VA G+LVT+V+++K + + F ++D MN RP L YDAY Sbjct: 236 YFPNDPGVTLILEPGRYIVAQAGVLVTRVVAVKVNGGRFFAVVDGGMNHSFRPALAYDAY 295 Query: 321 HEINYIVNPAGDRLHIHADIVGPICETGDFIALNRKIALPRPGDLLYIEKTGAYGAVQSG 380 H I + P D + A + GP+C++GD I +R + GDLL E GAYG +S Sbjct: 296 HPITPLKAPGPDEPLVPATLAGPLCDSGDVIGRDRLLPELEVGDLLVFEDMGAYGFSESS 355 Query: 381 TYNSR 385 +NS Sbjct: 356 NFNSH 360 >gnl|CDD|143506 cd06839, PLPDE_III_Btrk_like, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Btrk Decarboxylase. This subfamily is composed of Bacillus circulans BtrK decarboxylase and similar proteins. These proteins are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases, eukaryotic ornithine decarboxylases and diaminopimelate decarboxylases. BtrK is presumed to function as a PLP-dependent decarboxylase involved in the biosynthesis of the aminoglycoside antibiotic butirosin. Homodimer formation and the presence of the PLP cofactor may be required for catalytic activity. Length = 382 Score = 254 bits (652), Expect = 3e-68 Identities = 117/377 (31%), Positives = 186/377 (49%), Gaps = 28/377 (7%) Query: 21 LAHVVQTPFYCYSTTAIEKNYLTFSNAF-DGMDTMVCYALKANSNQAVIKTLAHLGSGLD 79 LA TPFY Y + + Y A ++ + Y+LKAN N A++ L LG G + Sbjct: 1 LADAYGTPFYVYDRDRVRERYAALRAALPPAIE--IYYSLKANPNPALVAHLRQLGDGAE 58 Query: 80 IVSEGELRRALAAPVPAERIVFSGVGKTIDEIDLALQSGIYCFNVESESELKTLNQRAVS 139 + S GEL AL A VP E+I+F+G GK+ E+ A+++GI NVES EL+ ++ A Sbjct: 59 VASAGELALALEAGVPPEKILFAGPGKSDAELRRAIEAGIGTINVESLEELERIDALAEE 118 Query: 140 LGKKAPIAFRVNPDINANTHKKISTGKKEDKFGIPIHQIHSLYAYASTLPGVKISGVDMH 199 G A +A R+NPD + G +FGI + ++ ++ A + LP ++ G +H Sbjct: 119 HGVVARVALRINPDFELK-GSGMKMGGGPSQFGIDVEELPAVLARIAALPNLRFVG--LH 175 Query: 200 I--GSQIDQ----IESFHKAFKLLRDLTQQLRSNGHNIQHIDVGGGLGIAYHSDHRPPSS 253 I G+QI IE+F + L L ++L G ++ +D+GGG GI Y P Sbjct: 176 IYPGTQILDADALIEAFRQTLALALRLAEEL---GLPLEFLDLGGGFGIPYFPGETPLDL 232 Query: 254 SDYASLIHQYFGNL-----QCKIILEPGRFLVADVGILVTKVISIKKSADKTFVILDVAM 308 + + L +++LE GR+LV + G+ VT+V+ K S +TF++ D M Sbjct: 233 EALGAALAALLAELGDRLPGTRVVLELGRYLVGEAGVYVTRVLDRKVSRGETFLVTDGGM 292 Query: 309 NDFMRPT-LYDAYHEINYIVNPAGDRLHIH---ADIVGPICETGDFIALNRKIALPR--P 362 + + + + NY + +VGP+C D + R + LP P Sbjct: 293 HHHLAASGNFGQVLRRNYPLAILNRMGGEERETVTVVGPLCTPLDLLG--RNVELPPLEP 350 Query: 363 GDLLYIEKTGAYGAVQS 379 GDL+ + ++GAYG S Sbjct: 351 GDLVAVLQSGAYGLSAS 367 >gnl|CDD|111657 pfam02784, Orn_Arg_deC_N, Pyridoxal-dependent decarboxylase, pyridoxal binding domain. These pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates This domain has a TIM barrel fold. Length = 245 Score = 220 bits (564), Expect = 5e-58 Identities = 86/249 (34%), Positives = 133/249 (53%), Gaps = 9/249 (3%) Query: 36 AIEKNYLTFSNAFDGMDTMVCYALKANSNQAVIKTLAHLGSGLDIVSEGELRRALAAPVP 95 I + AF YA+KANS+ AV++ LA LG G D S+GEL R LAA VP Sbjct: 4 RIIERAHALWQAFLPRIQ-PFYAVKANSDPAVLRLLAELGLGFDCASKGELERVLAAGVP 62 Query: 96 AERIVFSGVGKTIDEIDLALQSGIYCFNVESESELKTLNQRAVSLGKKAPIAFRVNPDIN 155 ERI+F+ K+ E+ AL+ G+ C V++ EL+ L + L +A + RV PD++ Sbjct: 63 PERIIFANPCKSRSELRYALEHGVVCVTVDNVEELEKLAR----LAPEARLLLRVKPDVD 118 Query: 156 ANTHKKISTGKKEDKFGIPIHQIHSLYAYASTLPGVKISGVDMHIGSQIDQIESFHKAFK 215 A+ H +STG ++ KFG + + +L A L G+ + GV H+GS E+F KA + Sbjct: 119 AHAHCYLSTG-QDSKFGADLEEAEALLKAAKEL-GLNVVGVHFHVGSGCTDAEAFVKAAR 176 Query: 216 LLRDLTQQLRSNGHNIQHIDVGGGLGIAYHSDHRPPSSSDYAS-LIHQYFGNLQ-CKIIL 273 R++ Q G ++ +D+GGG G+ Y ++ + + + F + II Sbjct: 177 DARNVFDQGAELGFELKILDLGGGFGVDYTGAEDFEEYAEVINAALEEVFPHDPHPTIIA 236 Query: 274 EPGRFLVAD 282 EPGR++VA Sbjct: 237 EPGRYIVAP 245 >gnl|CDD|143507 cd06840, PLPDE_III_Bif_AspK_DapDC, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Bifunctional Aspartate Kinase/Diaminopimelate Decarboxylase. Bifunctional aspartate kinase/diaminopimelate decarboxylase (AspK/DapDC, EC 4.1.1.20/EC 2.7.2.4) typically exists in bacteria. These proteins contain an N-terminal AspK region and a C-terminal DapDC region, which contains a PLP-binding TIM-barrel domain followed by beta-sandwich domain, characteristic of fold type III PLP-dependent enzymes. Members of this subfamily have not been fully characterized. Based on their sequence, these proteins may catalyze both reactions catalyzed by AspK and DapDC. AspK catalyzes the phosphorylation of L-aspartate to produce 4-phospho-L-aspartate while DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine. Length = 368 Score = 206 bits (526), Expect = 9e-54 Identities = 107/347 (30%), Positives = 170/347 (48%), Gaps = 28/347 (8%) Query: 57 YALKANSNQAVIKTLAHLGSGLDIVSEGELRRALAA-P-VPAERIVFSGVGKTIDEIDLA 114 YA+KAN + V++TL G G + VS GEL L P + R++F+ E + A Sbjct: 40 YAIKANPHPDVLRTLEEAGLGFECVSIGELDLVLKLFPDLDPRRVLFTPNFAARSEYEQA 99 Query: 115 LQSGIYCFNVESESELKTLNQRAVSLGKKAPIAFRVNPDINANTHKKISTGKKEDKFGIP 174 L+ G+ V++ L+ + L + + R++P HK + TG E KFG+ Sbjct: 100 LELGVN-VTVDNLHPLREWPE----LFRGREVILRIDPGQGEGHHKHVRTGGPESKFGLD 154 Query: 175 IHQIHSLYAYASTLPGVKISGVDMHIGSQIDQIESFHKAFKLLRDLTQQLRSNGHNIQHI 234 + ++ A G+ + G+ H GS ++ + + + L L + + ++ + Sbjct: 155 VDELDEARDLAKKA-GIIVIGLHAHSGSGVEDTDHWARHGDYLASLARHFPA----VRIL 209 Query: 235 DVGGGLGIAYHSDHRPPSSSDYASL------IHQYFGNLQCKIILEPGRFLVADVGILVT 288 +VGGGLGI RP D +L Q + +EPGRF+VA+ G+L+ Sbjct: 210 NVGGGLGIPEAPGGRP---IDLDALDAALAAAKAAHPQYQ--LWMEPGRFIVAESGVLLA 264 Query: 289 KVISIKKSADKTFVILDVAMNDFMRPTLYDAYHEINYIVNPA--GDRLHIHADIVGPICE 346 +V IK FV L+ MN +RP LY AYHE IVN + + +AD+VGPICE Sbjct: 265 RVTQIKHKDGVRFVGLETGMNSLIRPALYGAYHE---IVNLSRLDEPPAGNADVVGPICE 321 Query: 347 TGDFIALNRKIALPRPGDLLYIEKTGAYGAVQSGTYNSRLLIPEIMV 393 +GD + +R + GD++ I GAYG + TYN R E+++ Sbjct: 322 SGDVLGRDRLLPETEEGDVILIANAGAYGFCMASTYNLREPAEEVVL 368 >gnl|CDD|143482 cd00622, PLPDE_III_ODC, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase. This subfamily is composed mainly of eukaryotic ornithine decarboxylases (ODC, EC 4.1.1.17) and ODC-like enzymes from prokaryotes represented by Vibrio vulnificus LysineOrnithine decarboxylase. These are fold type III PLP-dependent enzymes that differ from most bacterial ODCs which are fold type I PLP-dependent enzymes. ODC participates in the formation of putrescine by catalyzing the decarboxylation of ornithine, the first step in polyamine biosynthesis. Members of this subfamily contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity. Also members of this subfamily are proteins with homology to ODC but do not possess any catalytic activity, the Antizyme inhibitor (AZI) and ODC-paralogue (ODC-p). AZI binds to the regulatory protein Antizyme with a higher affinity than ODC and prevents ODC degradation. ODC-p is a novel ODC-like protein, present only in mammals, that is specifically exressed in the brain and testes. ODC-p may function as a tissue-specific antizyme inhibitory protein. Length = 362 Score = 194 bits (495), Expect = 4e-50 Identities = 102/372 (27%), Positives = 167/372 (44%), Gaps = 36/372 (9%) Query: 27 TPFYCYSTTAIEKNYLTFSNAFDGMDTMVCYALKANSNQAVIKTLAHLGSGLDIVSEGEL 86 TPF + + Y + A YA+K N + AV++TLA LG+G D S+GE+ Sbjct: 2 TPFLVVDLGDVVRKYRRWKKALP--RVRPFYAVKCNPDPAVLRTLAALGAGFDCASKGEI 59 Query: 87 RRALAAPVPAERIVFSGVGKTIDEIDLALQSGIYCFNVESESELKTLNQRAVSLGKKAPI 146 L V ERI+F+ K+I +I A + G+ F +SE EL+ + + A A + Sbjct: 60 ELVLGLGVSPERIIFANPCKSISDIRYAAELGVRLFTFDSEDELEKIAKHA----PGAKL 115 Query: 147 AFRVNPDINANTHKKISTGKKEDKFGIPIHQIHSLYAYASTLPGVKISGVDMHIGSQIDQ 206 R+ D ++ + KFG + L A L G+ + GV H+GSQ Sbjct: 116 LLRIATD---DSGALCPLSR---KFGADPEEARELLRRAKEL-GLNVVGVSFHVGSQCTD 168 Query: 207 IESFHKAFKLLRDLTQQLRSNGHNIQHIDVGGGLGIAYHSDHRPPSSSDYASLIHQ---- 262 ++ A R++ + G ++ +D+GGG +Y PS + A++I++ Sbjct: 169 PSAYVDAIADAREVFDEAAELGFKLKLLDIGGGFPGSYDGV--VPSFEEIAAVINRALDE 226 Query: 263 YFGNLQCKIILEPGRFLVADVGILVTKVISIKK---SADKTFVILDV----AMNDFMRPT 315 YF + +II EPGR+LVA L VI+ +K + + L+ + N+ Sbjct: 227 YFPDEGVRIIAEPGRYLVASAFTLAVNVIAKRKRGDDDRERWYYLNDGVYGSFNE----I 282 Query: 316 LYDAYHEINYIVNPAGDRLHIHADIV-GPICETGDFIALNRKIALP---RPGDLLYIEKT 371 L+D ++ G ++ + GP C++ D I + LP GD L E Sbjct: 283 LFDHIRYPPRVLKDGGRDGELYPSSLWGPTCDSLDVIY--EDVLLPEDLAVGDWLLFENM 340 Query: 372 GAYGAVQSGTYN 383 GAY + T+N Sbjct: 341 GAYTTAYASTFN 352 >gnl|CDD|35841 KOG0622, KOG0622, KOG0622, Ornithine decarboxylase [Amino acid transport and metabolism]. Length = 448 Score = 185 bits (470), Expect = 3e-47 Identities = 96/370 (25%), Positives = 154/370 (41%), Gaps = 27/370 (7%) Query: 28 PFYCYSTTAIEKNYLTFSNAFDGMDTMVCYALKANSNQAVIKTLAHLGSGLDIVSEGELR 87 F+ AIE+ + A + YA+K NS+ V++ LA LG G D S+ EL Sbjct: 57 AFFVADLGAIERKLEAWKKALPRVRPF--YAVKCNSDPKVLRLLASLGCGFDCASKNELD 114 Query: 88 RALAAPVPAERIVFSGVGKTIDEIDLALQSGIYCFNVESESELKTLNQRAVSLGKKAPIA 147 L+ V ERI+++ K + +I A + G+ ++E EL+ + + A + Sbjct: 115 LVLSLGVSPERIIYANPCKQVSQIKYAAKHGVSVMTFDNEEELEKVAK----SHPNANLL 170 Query: 148 FRVNPDINANTHKKISTGKKEDKFGIPIHQIHSLYAYASTLPGVKISGVDMHIGSQIDQI 207 R+ D + +T + KFG + L A L + + GV H+GS + Sbjct: 171 LRIATDDS------TATCRLNLKFGCSLDNCRHLLDMAKEL-ELNVVGVSFHVGSGCTDL 223 Query: 208 ESFHKAFKLLRDLTQQLRSNGHNIQHIDVGGGLGIAYHSDHRPPSSSD-YASLIHQYFGN 266 +++ A R++ G + +D+GGG +D + + YF + Sbjct: 224 QAYRDAISDARNVFDMGAELGFEMDILDIGGGFPGDEGHAVVFEEIADVINTALDLYFPS 283 Query: 267 LQCKIILEPGRFLVADVGILVTKVISIKKSADKTFVILDVA--------MND----FMRP 314 II EPGRF VA L VI+ K+ K D +ND Sbjct: 284 GGVDIIAEPGRFFVASAFTLAVNVIAKKEVDAKKITSDDEDDEVTFMYYVNDGVYGSFNC 343 Query: 315 TLYDAYHEINYIV-NPAGDRLHIHADIVGPICETGDFIALNRKIALPRPGDLLYIEKTGA 373 L+D H I +V +P+ + + I GP C+ D IA + + GD L E GA Sbjct: 344 ILFDHQHPIPLVVKDPSEEEPLYKSSIWGPTCDGLDVIAEDCLLPQLNVGDWLVFENMGA 403 Query: 374 YGAVQSGTYN 383 Y + T+N Sbjct: 404 YTMSAASTFN 413 >gnl|CDD|143510 cd06843, PLPDE_III_PvsE_like, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme PvsE. This subfamily is composed of PvsE from Vibrio parahaemolyticus and similar proteins. PvsE is a vibrioferrin biosynthesis protein which is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. It has been suggested that PvsE may be involved in the biosynthesis of the polycarboxylate siderophore vibrioferrin. It may catalyze the decarboxylation of serine to yield ethanolamine. PvsE may require homodimer formation and the presence of the PLP cofactor for activity. Length = 377 Score = 175 bits (445), Expect = 3e-44 Identities = 94/336 (27%), Positives = 150/336 (44%), Gaps = 25/336 (7%) Query: 57 YALKANSNQAVIKTLAHLGSGLDIVSEGELRRALAAPVPAERIVFSGVGKTIDEIDLALQ 116 YA+KANS+ +++ LA G ++ S GE+ AA VP ++F G GKT E+ AL Sbjct: 31 YAIKANSDPPILRALAPHVDGFEVASGGEIAHVRAA-VPDAPLIFGGPGKTDSELAQALA 89 Query: 117 SGIYCFNVESESELKTLNQRAVSLGKKAPIAFRVNPDINANTHKKISTGKKEDKFGIPIH 176 G+ +VESE EL+ LN A G+ AP+ RVN + ++ G + FGI Sbjct: 90 QGVERIHVESELELRRLNAVARRAGRTAPVLLRVNLALPDLPSSTLTMGGQPTPFGIDEA 149 Query: 177 QIHSLYAYASTLPGVKISGVDMHIGS-QIDQIESFHKAFKLLRDLTQQLRSNGHNIQHID 235 + LP +++ G H+ S +D L Q +G ++ ++ Sbjct: 150 DLPDALELLRDLPNIRLRGFHFHLMSHNLDAAAHLALVKAYLETARQWAAEHGLDLDVVN 209 Query: 236 VGGGLGIAYHSDHRPPSSSDYA-------SLIHQYFGNLQCKIILEPGRFLVADVGILVT 288 VGGG+G+ Y P D+A L+ +Y + E GR++ A G VT Sbjct: 210 VGGGIGVNY---ADPEEQFDWAGFCEGLDQLLAEY--EPGLTLRFECGRYISAYCGYYVT 264 Query: 289 KVISIKKSADKTFVILDVAMNDFMRPTLYDAYHEINYIVNPAGDRLHIHAD--------- 339 +V+ +K+S + F +L + F P + H + V P + + Sbjct: 265 EVLDLKRSHGEWFAVLRGGTHHFRLPAAWG--HNHPFSVLPVEEWPYPWPRPSVRDTPVT 322 Query: 340 IVGPICETGDFIALNRKIALPRPGDLLYIEKTGAYG 375 +VG +C D +A + + R GDL+ GAYG Sbjct: 323 LVGQLCTPKDVLARDVPVDRLRAGDLVVFPLAGAYG 358 >gnl|CDD|143508 cd06841, PLPDE_III_MccE_like, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme MccE. This subfamily is composed of uncharacterized proteins with similarity to Escherichia coli MccE, a hypothetical protein that is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. ODC participates in the formation of putrescine by catalyzing the decarboxylation of ornithine, the first step in polyamine biosynthesis. DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine. Most members of this subfamily share the same domain architecture as ODC and DapDC. A few members, including Escherichia coli MccE, contain an additional acetyltransferase domain at the C-terminus. Length = 379 Score = 171 bits (436), Expect = 3e-43 Identities = 106/372 (28%), Positives = 173/372 (46%), Gaps = 35/372 (9%) Query: 27 TPFYCYSTTAIEKNYLTFSNAFDGM--DTMVCYALKANSNQAVIKTLAHLGSGLDIVSEG 84 +PF+ + A+ +NY AF + ++ Y+ K N A+ K L G ++VS Sbjct: 7 SPFFVFDEDALRENYRELLGAFKKRYPNVVIAYSYKTNYLPAICKILHEEGGYAEVVSAM 66 Query: 85 ELRRALAAPVPAERIVFSGVGKTIDEIDLALQSGIYCFNVESESELKTLNQRAVSLGKKA 144 E AL VP +RI+F+G K+ +E++ AL+ G N++S EL+ + + A LG+ A Sbjct: 67 EYELALKLGVPGKRIIFNGPYKSKEELEKALEEGAL-INIDSFDELERILEIAKELGRVA 125 Query: 145 PIAFRVNPDINANTHKKISTGKKEDKFGIPIHQIHSLYAYAST---LPGVKISGVDMHIG 201 + R+N + +FG I + A + + G+ H+G Sbjct: 126 KVGIRLNMNY---------GNNVWSRFGFDIEENGEALAALKKIQESKNLSLVGLHCHVG 176 Query: 202 SQIDQIESFHKAFKLLRDLTQQLRSNGHNIQHIDVGGGLG------IAYHSDHRPPSSSD 255 S I E++ A K L +L +L G ++++D+GGG +AY + P D Sbjct: 177 SNILNPEAYSAAAKKLIELLDRLF--GLELEYLDLGGGFPAKTPLSLAYPQEDTVPDPED 234 Query: 256 YASLIHQ----YFGNL--QCKIILEPGRFLVADVGILVTKVISIKKSADKTFVILDVAMN 309 YA I Y+ N + K+ILEPGR LV D G L+ +V+++K + + D +N Sbjct: 235 YAEAIASTLKEYYANKENKPKLILEPGRALVDDAGYLLGRVVAVKNRYGRNIAVTDAGIN 294 Query: 310 DFMRPTLYDAYHEINYIVNPAGDRLHIHADIVGPICETGDFIALNRKIALP--RPGDLLY 367 + PT++ +H I + D + D+ G C D + N + LP GD+L Sbjct: 295 NI--PTIFWYHHPILVLRPGKEDPTSKNYDVYGFNCMESDVLFPN--VPLPPLNVGDILA 350 Query: 368 IEKTGAYGAVQS 379 I GAY QS Sbjct: 351 IRNVGAYNMTQS 362 >gnl|CDD|143505 cd06836, PLPDE_III_ODC_DapDC_like_1, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Uncharacterized Proteins with similarity to Ornithine and Diaminopimelate Decarboxylases. This subfamily contains uncharacterized proteins with similarity to ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. ODC participates in the formation of putrescine by catalyzing the decarboxylation of ornithine, the first step in polyamine biosynthesis. DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine. Proteins in this subfamily may function as PLP-dependent decarboxylases. Homodimer formation and the presence of the PLP cofactor may be required for catalytic activity. Length = 379 Score = 161 bits (408), Expect = 5e-40 Identities = 108/377 (28%), Positives = 171/377 (45%), Gaps = 40/377 (10%) Query: 37 IEKNYLTFSNAFDGMDTMVCYALKANSNQAVIKTLAHLGSGLDIVSEGELRRALAAPVPA 96 + AF + +A+KAN V++ LA G+G ++ S GEL ALAA P Sbjct: 13 FRALVARLTAAFPA-PVLHTFAVKANPLVPVLRLLAEAGAGAEVASPGELELALAAGFPP 71 Query: 97 ERIVFSGVGKTIDEIDLALQSGIYCFNVESESELKTLNQRAVSLGK-KAPIAFRVNPDIN 155 ERIVF KT E+ AL+ G+ N+++ EL+ ++ + + I RVNP + Sbjct: 72 ERIVFDSPAKTRAELREALELGVA-INIDNFQELERIDALVAEFKEASSRIGLRVNPQVG 130 Query: 156 ANTHKKISTGKKEDKFGIPIHQIHS---LYAYASTLPGVKISGVDMHIGSQ---IDQI-E 208 A +ST KFG+ + + A+A P + G+ +H+GSQ + + E Sbjct: 131 AGKIGALSTATATSKFGVALEDGARDEIIDAFARR-PWLN--GLHVHVGSQGCELSLLAE 187 Query: 209 SFHKAFKLLRDLTQQLRSNGHNIQHIDVGGGLGIAYHSDHRPPSSSDYASLIHQYFGNL- 267 + L ++ +++ I ID+GGGL + + S+ P+ +DYA+ + L Sbjct: 188 GIRRVVDLAEEINRRVGRR--QITRIDIGGGLPVNFESEDITPTFADYAAALKAAVPELF 245 Query: 268 --QCKIILEPGRFLVADVGILVTKVISIKKSADKTFVIL----DVAMNDFMRP------- 314 + +++ E GR L+A G +V++V K S + I VA P Sbjct: 246 DGRYQLVTEFGRSLLAKCGTIVSRVEYTKSSGGRRIAITHAGAQVATRTAYAPDDWPLRV 305 Query: 315 TLYDAYHEINYIVNPAGDRLHIHADIVGPICETGDFIALNRKIALPR--PGDLLYIEKTG 372 T++DA E P + D+ GP C GD +A R ALP PGD + + TG Sbjct: 306 TVFDANGE------PKTGPEVVT-DVAGPCCFAGDVLAKER--ALPPLEPGDYVAVHDTG 356 Query: 373 AYGAVQSGTYNSRLLIP 389 AY +YNS Sbjct: 357 AYYFSSHSSYNSLPRPA 373 >gnl|CDD|143484 cd06808, PLPDE_III, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes. The fold type III PLP-dependent enzyme family is predominantly composed of two-domain proteins with similarity to bacterial alanine racemases (AR) including eukaryotic ornithine decarboxylases (ODC), prokaryotic diaminopimelate decarboxylases (DapDC), biosynthetic arginine decarboxylases (ADC), carboxynorspermidine decarboxylases (CANSDC), and similar proteins. AR-like proteins contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. These proteins play important roles in the biosynthesis of amino acids and polyamine. The family also includes the single-domain YBL036c-like proteins, which contain a single PLP-binding TIM-barrel domain without any N- or C-terminal extensions. Due to the lack of a second domain, these proteins may possess only limited D- to L-alanine racemase activity or non-specific racemase activity. Length = 211 Score = 155 bits (395), Expect = 2e-38 Identities = 68/241 (28%), Positives = 105/241 (43%), Gaps = 30/241 (12%) Query: 37 IEKNYLTFSNAFDGMDTMVCYALKANSNQAVIKTLAHLGSGLDIVSEGELRRALAAPVPA 96 I NY A + +KAN+N V +TLA LG+G D+ S GE AA +P Sbjct: 1 IRHNYRRLREAA-PAGITLFAVVKANANPEVARTLAALGTGFDVASLGEALLLRAAGIPP 59 Query: 97 ERIVFSGVGKTIDEIDLALQSGIYCFNVESESELKTLNQRAVSLGKKAPIAFRVNPDINA 156 E I+F G K + E++ A + G+ V+S EL+ L + A+ G A + R++ Sbjct: 60 EPILFLGPCKQVSELEDAAEQGVIVVTVDSLEELEKLEEAALKAGPPARVLLRID----- 114 Query: 157 NTHKKISTGKKEDKFGIPIHQIHSLYAYASTLPGVKISGVDMHIGSQIDQIESFHKAFKL 216 TG + KFG+ ++ +L A LP +++ G+ H GS + F +A Sbjct: 115 -------TGDENGKFGVRPEELKALLERAKELPHLRLVGLHTHFGSADEDYSPFVEALSR 167 Query: 217 LRDLTQQLRSNGHNIQHIDVGGGLGIAYHSDHRPPSSSDYASLIHQYFGNLQCKIILEPG 276 QL G +++ + +GG I Y P II+EPG Sbjct: 168 FVAALDQLGELGIDLEQLSIGGSFAILYLQ-ELPL----------------GTFIIVEPG 210 Query: 277 R 277 R Sbjct: 211 R 211 >gnl|CDD|143509 cd06842, PLPDE_III_Y4yA_like, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Y4yA. This subfamily is composed of the hypothetical Rhizobium sp. protein Y4yA and similar uncharacterized bacterial proteins. These proteins are homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. ODC participates in the formation of putrescine by catalyzing the decarboxylation of ornithine, the first step in polyamine biosynthesis. DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine. Proteins in this subfamily may function as PLP-dependent decarboxylases. Length = 423 Score = 139 bits (353), Expect = 1e-33 Identities = 104/423 (24%), Positives = 165/423 (39%), Gaps = 89/423 (21%) Query: 21 LAHVVQ---TPFYCYSTTAIEKNYLTFSNAFD--GMDTMVCYALKANSNQAVIKTLAHLG 75 L +V+ +P +N D G+D V +A KAN + A+++ A G Sbjct: 1 LVALVEAYGSPLNVLFPQTFRENIAALRAVLDRHGVDGRVYFARKANKSLALVRAAAAAG 60 Query: 76 SGLDIVSEGELRRALAAPVPAERIVFSGVGKTIDEIDLALQSGIYCFNVESESELKTLNQ 135 G+D+ S ELR+ALAA V +RIV +G KT + + LA++ G V+S EL L Sbjct: 61 IGVDVASLAELRQALAAGVRGDRIVATGPAKTDEFLWLAVRHGA-TIAVDSLDELDRLLA 119 Query: 136 RA-VSLGKKAPIAFRVNPDINANTHKKISTGKKEDKFGIPIHQI-HSLYAYASTLPGVKI 193 A A + R++P S +FG+P ++ +L A V++ Sbjct: 120 LARGYTTGPARVLLRLSPF----PASLPS------RFGMPAAEVRTALERLAQLRERVRL 169 Query: 194 SGVDMHIG--SQIDQIESFHKAFKLLRDLTQQLRSNGHNIQHIDVGGGLGIAYHSD---- 247 G H+ S ++ + + L+ + R+ G + ID+GGG ++Y +D Sbjct: 170 VGFHFHLDGYSAAQRVAALQECLPLID----RARALGLAPRFIDIGGGFPVSYLADAAEW 225 Query: 248 ------------------------------------HRPPSSSDY--ASLIHQYFGN--- 266 +P ++D+ A L Sbjct: 226 EAFLAALTEALYGYGRPLTWRNEGGTLRGPDDFYPYGQPLVAADWLRAILSAPLPQGRTI 285 Query: 267 ----LQCKIIL--EPGRFLVADVGILVTKVISIKKSADKTFVILDVAMNDFMRPTLYDAY 320 I L EPGR L+ G+ V +V +K+ D +I + N F + + Sbjct: 286 AERLRDNGITLALEPGRALLDQCGLTVARVAFVKQLGDGNHLIG-LEGNSF---SACEFS 341 Query: 321 HE--INYIVNPAGDRLHIHADI----VGPICETGDFIALNRKIALPR---PGDLLYIEKT 371 E ++ ++ PA + A I G C D I RKI PR PGDLL T Sbjct: 342 SEFLVDPLLIPAPEPTTDGAPIEAYLAGASCLESDLI-TRRKIPFPRLPKPGDLLVFPNT 400 Query: 372 GAY 374 Y Sbjct: 401 AGY 403 >gnl|CDD|144023 pfam00278, Orn_DAP_Arg_deC, Pyridoxal-dependent decarboxylase, C-terminal sheet domain. These pyridoxal-dependent decarboxylases act on ornithine, lysine, arginine and related substrates. Length = 110 Score = 95.8 bits (239), Expect = 2e-20 Identities = 39/113 (34%), Positives = 54/113 (47%), Gaps = 7/113 (6%) Query: 285 ILVTKVISIKK-SADKTFVILDVAMNDFMRPTLYDAYHEINYIVNPAGDRLHIHADIVGP 343 LVT+VI +K+ D+ FV LD + P LYDA H I V+ D + GP Sbjct: 1 TLVTEVIDVKERGDDRKFVYLDDGVYGSPDPALYDALHPI-LPVSRLDDEPLRPYTLAGP 59 Query: 344 ICETGDFIALNRKIALP---RPGDLLYIEKTGAYGAVQSGTYNSRLLIPEIMV 393 C++GD +A R ++LP GD L GAY S +N E++V Sbjct: 60 TCDSGDVLA--RDVSLPLELEVGDWLVFFDAGAYTISLSSNFNGFPRPAEVLV 110 >gnl|CDD|143503 cd06830, PLPDE_III_ADC, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase. This subfamily includes plants and biosynthetic prokaryotic arginine decarboxylases (ADC, EC 4.1.1.19). ADC is involved in the biosynthesis of putrescine, which is the precursor of aliphatic polyamines in many organisms. It catalyzes the decarboxylation of L-arginine to agmatine, which is then hydrolyzed to putrescine by agmatinase. ADC is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC), which are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. Homodimer formation and the presence of both PLP and Mg2+ cofactors may be required for catalytic activity. Prokaryotic ADCs (biodegradative), which are fold type I PLP-dependent enzymes, are not included in this family. Length = 409 Score = 95.3 bits (238), Expect = 3e-20 Identities = 81/278 (29%), Positives = 129/278 (46%), Gaps = 41/278 (14%) Query: 56 CYALKANSNQAVIKTLAHLGS----GLDIVSEGELRRALAAPVPAER-IVFSGVGKTIDE 110 Y +K N + V++ + G GL+ S+ EL ALA + I+ +G K + Sbjct: 42 VYPIKVNQQREVVEEIVKAGKRYNIGLEAGSKPELLAALALLKTPDALIICNGY-KDDEY 100 Query: 111 IDLALQSGIYCFNV----ESESELKTLNQRAVSLGKKAPIAFRVNPDINANTHKKISTGK 166 I+LAL + NV E SEL + + A LG K + R+ + + S G Sbjct: 101 IELALLARKLGHNVIIVIEKLSELDLILELAKKLGVKPLLGVRIKLASKGSGKWQESGGD 160 Query: 167 KEDKFGIPIHQIHSLY---AYASTLPGVKISGVDMHIGSQIDQIESFHKAFKLLRDLTQ- 222 + KFG+ +I + A L +K+ + HIGSQI I A LR+ + Sbjct: 161 R-SKFGLTASEILEVVEKLKEAGMLDRLKL--LHFHIGSQITDIRRIKSA---LREAARI 214 Query: 223 --QLRSNGHNIQHIDVGGGLGIAYH-SDHRPPSSSDYASLIHQYFGN-----LQ--CK-- 270 +LR G N++++D+GGGLG+ Y S SS +Y SL + + N ++ C Sbjct: 215 YAELRKLGANLRYLDIGGGLGVDYDGSRSSSDSSFNY-SL--EEYANDIVKTVKEICDEA 271 Query: 271 ------IILEPGRFLVADVGILVTKVISIKKSADKTFV 302 I+ E GR +VA +L+ +V+ +K+ AD F Sbjct: 272 GVPHPTIVTESGRAIVAHHSVLIFEVLGVKRLADWYFC 309 >gnl|CDD|31360 COG1166, SpeA, Arginine decarboxylase (spermidine biosynthesis) [Amino acid transport and metabolism]. Length = 652 Score = 84.9 bits (210), Expect = 3e-17 Identities = 84/332 (25%), Positives = 139/332 (41%), Gaps = 42/332 (12%) Query: 21 LAHVVQTPFYCYSTTAIEKNYLTFSNAFDGMDTMVCYALKANSNQAVIKTLAHLGS---- 76 L H +++ ++ E Y + + Y +K N ++ V+++L G Sbjct: 90 LQHRLRSLNAAFARAIEEYGY---PGGYFAV-----YPIKVNQHRRVVESLVASGKGYPL 141 Query: 77 GLDIVSEGELRRALA-APVPAERIVFSGVGKTIDEIDLALQSGIYCFNV----ESESELK 131 GL+ S+ EL LA A P IV +G K + I LAL V E SEL Sbjct: 142 GLEAGSKAELMAVLAHAGNPGSLIVCNGY-KDREYIRLALIGEKLGHKVYIVIEKLSELD 200 Query: 132 TLNQRAVSLGKKAPIAFRVNPDINANTHKKISTGKKEDKFGIPIHQIHSLYAY---ASTL 188 + + A LG K + R + + S G+K KFG+ Q+ + A+ L Sbjct: 201 LVLEEAKQLGVKPRLGVRARLASQGSGKWQSSGGEKS-KFGLSATQVLQVVERLREANLL 259 Query: 189 PGVKISGVDMHIGSQIDQIESFHKAFKLLRDLTQQLRSNGHNIQHIDVGGGLGIAYH-SD 247 +++ + H+GSQI I + +LR G NI++ DVGGGLG+ Y + Sbjct: 260 DSLQL--LHFHLGSQISNIRDIKTGVREAARFYVELRKLGANIKYFDVGGGLGVDYDGTR 317 Query: 248 HRPPSSSDYASLIHQYFGNL------QCK--------IILEPGRFLVADVGILVTKVISI 293 + S +Y +++Y ++ C+ II E GR + A +L+ VI + Sbjct: 318 TQSDCSKNYG--LNEYANDVVWALKDACEEKGLPHPTIISESGRAITAHHAVLIANVIGV 375 Query: 294 KKSADKTFVILDVAMNDF-MRPTLYDAYHEIN 324 ++ + D N + TL + Y I Sbjct: 376 ERHEYNDAPLPDAPRNLPPLWRTLQELYESIT 407 >gnl|CDD|143504 cd06831, PLPDE_III_ODC_like_AZI, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase-like Antizyme Inhibitor. Antizyme inhibitor (AZI) is homologous to the fold type III PLP-dependent enzyme ODC but does not retain any decarboxylase activity. Like ODC, AZI is presumed to exist as a homodimer. Antizyme is a regulatory protein that binds directly to the ODC monomer to block its active site, leading to its degradation by the 26S proteasome. AZI binds to Antizyme with a higher affinity than ODC, preventing the formation of the Antizyme-ODC complex. Thus, AZI blocks the ability of Antizyme to promote ODC degradation, which leads to increased ODC enzymatic activity and polyamine levels. AZI also prevents the degradation of other proteins regulated by Antizyme, such as cyclin D1. Length = 394 Score = 63.7 bits (155), Expect = 1e-10 Identities = 65/256 (25%), Positives = 107/256 (41%), Gaps = 41/256 (16%) Query: 57 YALKANSNQAVIKTLAHLGSGLDIVSEGELRRALAAPVPAERIVFSGVGKTIDEIDLALQ 116 Y ++ NS AV++ LA LG+G S+ E+ V E I+++ K +I A + Sbjct: 41 YTVRCNSTPAVLEILAALGTGFACSSKNEMALVQELGVSPENIIYTNPCKQASQIKYAAK 100 Query: 117 SGIYCFNVESESELKTLNQRAVSLGKKAPIAFRVNPD----INANTHKKISTGKKEDKFG 172 G+ ++E ELK IA R +P+ ++ T I + KFG Sbjct: 101 VGVNIMTCDNEIELKK-------------IA-RNHPNAKLLLHIATEDNIGGEEMNMKFG 146 Query: 173 IPIHQIHSLYAYASTLPGVKISGVDMHIGSQIDQIESFHKAFKLLR---DLTQQLRSNGH 229 + L A L V+I GV H+ S + +++ A R D+ ++ G Sbjct: 147 TTLKNCRHLLECAKEL-DVQIVGVKFHVSSSCKEYQTYVHALSDARCVFDMAEEF---GF 202 Query: 230 NIQHIDVGGGLGIA------YHSDHRPPSSSDYASLIHQYFGNLQ-CKIILEPGRFLVAD 282 + +D+GGG + + RP L+ YF +II EPG + V+ Sbjct: 203 KMNMLDIGGGFTGSEIQLEEVNHVIRP--------LLDVYFPEGSGIQIIAEPGSYYVSS 254 Query: 283 VGILVTKVISIKKSAD 298 L VI+ KK+ + Sbjct: 255 AFTLAVNVIA-KKAVE 269 >gnl|CDD|143483 cd00635, PLPDE_III_YBL036c_like, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins. This family contains mostly uncharacterized proteins, widely distributed among eukaryotes, bacteria and archaea, that bear similarity to the yeast hypothetical protein YBL036c, which is homologous to a Pseudomonas aeruginosa gene that is co-transcribed with a known proline biosynthetic gene. YBL036c is a single domain monomeric protein with a typical TIM barrel fold. It binds the PLP cofactor and has been shown to exhibit amino acid racemase activity. The YBL036c structure is similar to the N-terminal domain of the fold type III PLP-dependent enzymes, bacterial alanine racemase and eukaryotic ornithine decarboxylase, which are two-domain dimeric proteins. The lack of a second domain in YBL036c may explain limited D- to L-alanine racemase or non-specific racemase activity. Length = 222 Score = 48.6 bits (117), Expect = 3e-06 Identities = 27/105 (25%), Positives = 46/105 (43%), Gaps = 13/105 (12%) Query: 124 VESESELKTLNQRAVSLGKKAPIAFRVNPDINANTHKKISTGKKEDKFGIPIHQIHSLYA 183 V+S + LN+RA G+ + +VN G +E K G+ ++ L Sbjct: 97 VDSLKLAEELNKRAEKEGRVLDVLVQVN------------IGGEESKSGVAPEELEELLE 144 Query: 184 YASTLPGVKISGVDMHIGSQIDQIESFHKAFKLLRDLTQQLRSNG 228 + LP ++I G+ M I + E F+ LR+L +L + G Sbjct: 145 EIAALPNLRIRGL-MTIAPLTEDPEEVRPYFRELRELRDELGAKG 188 >gnl|CDD|143502 cd06829, PLPDE_III_CANSDC, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase. Carboxynorspermidine decarboxylase (CANSDC) catalyzes the decarboxylation of carboxynorspermidine, the last step in the biosynthesis of norspermidine. It is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC), which are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. Based on this similarity, CANSDC may require homodimer formation and the presence of the PLP cofactor for its catalytic activity. Length = 346 Score = 44.1 bits (105), Expect = 8e-05 Identities = 84/396 (21%), Positives = 136/396 (34%), Gaps = 100/396 (25%) Query: 27 TPFYCYSTTAIEKNYLTFSNAFDGMDTMVCYALKANSNQAVIKTLAHLGSGLDIVSEGEL 86 TP Y + +N + + ALKA S +V + G S E Sbjct: 1 TPCYVLDEAKLRRNLEILKRVQERSGAKILLALKAFSMWSVFPLIREYLDGTTASSLFEA 60 Query: 87 RRALAAP-VPAERIVFSGVGKTIDEIDLALQSGIYC----FNVESESELKTLNQRAVSLG 141 R L E +S DEID L+ FN S S+L+ RA Sbjct: 61 R--LGREEFGGEVHTYS-PAYRDDEIDEILR---LADHIIFN--SLSQLERFKDRA--KA 110 Query: 142 KKAPIAFRVNPDINANTHKKISTGKKE--------DKFGIPIHQIHSLYAYASTLPGVKI 193 + R+NP + S + + + G+ + ++ L G I Sbjct: 111 AGISVGLRINP--------EYSEVETDLYDPCAPGSRLGVTLDELE-----EEDLDG--I 155 Query: 194 SGVDMHI------GSQIDQIESFHKAF-KLLRDLTQQLRSNGHNIQHIDVGGGLGIAYHS 246 G+ H + +E+ + F + L ++ +++GGG +H Sbjct: 156 EGLHFHTLCEQDFDALERTLEAVEERFGEYL-----------PQLKWLNLGGG----HHI 200 Query: 247 DHRPPSSSDY-----ASLIHQYFG---NLQCKIILEPGRFLVADVGILVTKVISIKKSAD 298 DY +LI + F ++ + LEPG + + G LV V+ I ++ Sbjct: 201 TR-----PDYDVDRLIALI-KRFKEKYGVE--VYLEPGEAVALNTGYLVATVLDIVEN-G 251 Query: 299 KTFVILDVA----MNDFM----RPTLYDAYHEINYIVNPAGDRLHIHADIVGPICETGDF 350 ILD + M D + RP + A G+ H + + G C GD Sbjct: 252 MPIAILDASATAHMPDVLEMPYRPPIRGA--------GEPGEGAHTYR-LGGNSCLAGDV 302 Query: 351 IALNRKIALPRP---GDLLYIEKTGAYGAVQSGTYN 383 I + P GD L E Y V++ T+N Sbjct: 303 IGD---YSFDEPLQVGDRLVFEDMAHYTMVKTNTFN 335 >gnl|CDD|30673 COG0325, COG0325, Predicted enzyme with a TIM-barrel fold [General function prediction only]. Length = 228 Score = 41.4 bits (97), Expect = 4e-04 Identities = 28/118 (23%), Positives = 50/118 (42%), Gaps = 13/118 (11%) Query: 120 YCFNVESESELKTLNQRAVSLGKKAPIAFRVNPDINANTHKKISTGKKEDKFGIPIHQIH 179 + +++ K LN+RA+ L K + +VN +E K G+P ++ Sbjct: 96 WIHSLDRLKLAKELNKRALELPKPLNVLIQVN------------ISGEESKSGVPPEELD 143 Query: 180 SLYAYASTLPGVKISGVDMHIGSQIDQIESFHKAFKLLRDLTQQLRSNGHNIQHIDVG 237 L LP +++ G+ M I D E F+ LR L +L++ I + +G Sbjct: 144 ELAQEVQELPNLELRGL-MTIPPLTDDPEEIFAVFRKLRKLFDELKAKYPPIDELSMG 200 >gnl|CDD|143481 cd00430, PLPDE_III_AR, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase. This family includes predominantly bacterial alanine racemases (AR), some serine racemases (SerRac), and putative bifunctional enzymes containing N-terminal UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase (murF) and C-terminal AR domains. These proteins are fold type III PLP-dependent enzymes that play essential roles in peptidoglycan biosynthesis. AR catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. SerRac converts L-serine into its D-enantiomer (D-serine) for peptidoglycan synthesis. murF catalyzes the addition of D-Ala-D-Ala to UDPMurNAc-tripeptide, the final step in the synthesis of the cytoplasmic precursor of bacterial cell wall peptidoglycan. Members of this family contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. AR and other members of this family require dimer formation and the presence of the PLP cofactor for catalytic activity. Fungal ARs and eukaryotic serine racemases, which are fold types I and II PLP-dependent enzymes respectively, are excluded from this family. Length = 367 Score = 39.4 bits (93), Expect = 0.002 Identities = 44/209 (21%), Positives = 73/209 (34%), Gaps = 38/209 (18%) Query: 36 AIEKNYLTFSNAFDGMDTMVCYALKANSNQA-------VIKTLAHLGS---GLDIVSEG- 84 A+ N G T + +KA+ A V K L G+ + + E Sbjct: 10 ALRHNLRVIRRLL-GPGTKIMAVVKAD---AYGHGAVEVAKALEEAGADYFAVATLEEAL 65 Query: 85 ELRRA-LAAPVPAERIVFSGVGKTIDEIDLALQSGIYCFNVESESELKTLNQRAVSLGKK 143 ELR A + AP+ +V G +E + A++ + V S + + L+ A LGK Sbjct: 66 ELREAGITAPI----LVLGGT--PPEEAEEAIEYDLTPT-VSSLEQAEALSAAAARLGKT 118 Query: 144 APIAFRVNPDINANTHKKISTGKKEDKFGIPIHQIHSLYAYASTLPGVKISGVDMHIG-S 202 + H KI TG + G + L LPG+++ GV H + Sbjct: 119 LKV------------HLKIDTGM--GRLGFRPEEAEELLEALKALPGLELEGVFTHFATA 164 Query: 203 QIDQIESFHKAFKLLRDLTQQLRSNGHNI 231 + + + +L G Sbjct: 165 DEPDKAYTRRQLERFLEALAELEEAGIPP 193 >gnl|CDD|143497 cd06824, PLPDE_III_Yggs_like, Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins. This subfamily contains mainly uncharacterized proteobacterial proteins with similarity to the hypothetical Escherichia coli protein YggS, a homolog of yeast YBL036c, which is homologous to a Pseudomonas aeruginosa gene that is co-transcribed with a known proline biosynthetic gene. Like yeast YBL036c, Yggs is a single domain monomeric protein with a typical TIM-barrel fold. Its structure, which shows a covalently-bound PLP cofactor, is similar to the N-terminal domain of the fold type III PLP-dependent enzymes, bacterial alanine racemase and eukaryotic ornithine decarboxylase, which are two-domain dimeric proteins. YggS has not been characterized extensively and its biological function is still unkonwn. Length = 224 Score = 31.0 bits (71), Expect = 0.59 Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 1/62 (1%) Query: 170 KFGIPIHQIHSLYAYASTLPGVKISGVDMHIGSQIDQIESFHKAFKLLRDLTQQLRSNGH 229 K G+ L S LP +++ G+ M I + D + AFK LR L QL+ Sbjct: 133 KSGVAPEDAAELAEAISQLPNLRLRGL-MAIPAPTDDEAAQRAAFKRLRQLFDQLKKQYP 191 Query: 230 NI 231 ++ Sbjct: 192 DL 193 >gnl|CDD|36360 KOG1145, KOG1145, KOG1145, Mitochondrial translation initiation factor 2 (IF-2; GTPase) [Translation, ribosomal structure and biogenesis]. Length = 683 Score = 30.3 bits (68), Expect = 1.0 Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 3/43 (6%) Query: 98 RIVFSGVGK-TIDEIDLALQSG--IYCFNVESESELKTLNQRA 137 +V SGVG T +++LA S IY FNV++ +K L Sbjct: 502 NVVHSGVGPVTESDLELAQASDAIIYGFNVKASPSVKQLAAAK 544 >gnl|CDD|147007 pfam04637, Herpes_pp85, Herpesvirus phosphoprotein 85 (HHV6-7 U14/HCMV UL25). This family includes UL25 proteins from HCMV, as well as U14 proteins from HHV 6 and HHV7. These 85 kD phosphoproteins appear to act as structural antigens, but their precise function is otherwise unknown. Length = 502 Score = 29.3 bits (66), Expect = 1.9 Identities = 13/63 (20%), Positives = 24/63 (38%), Gaps = 8/63 (12%) Query: 207 IESFHKAFKLLRDLTQQLRS--NGHNIQHIDVGGGLGIAYHSDHRPPSSSDYASLIHQYF 264 I ++ +LR + L+S N ++ +D G R SD + + Sbjct: 75 INHYYNGKGILRHMRAALKSLMNPPTMRRLDRG------LRRLCRALQDSDNPPDLSESL 128 Query: 265 GNL 267 G+L Sbjct: 129 GDL 131 >gnl|CDD|31227 COG1024, CaiD, Enoyl-CoA hydratase/carnithine racemase [Lipid metabolism]. Length = 257 Score = 29.3 bits (65), Expect = 2.0 Identities = 14/76 (18%), Positives = 25/76 (32%), Gaps = 4/76 (5%) Query: 194 SGVDMHIGSQIDQIESFHKAFKLLRDLTQQLRSNGH----NIQHIDVGGGLGIAYHSDHR 249 +G D+ + + + +DL + L + +GGGL +A D R Sbjct: 64 AGADLKELLSPEDGNAAENLMQPGQDLLRALADLPKPVIAAVNGYALGGGLELALACDIR 123 Query: 250 PPSSSDYASLIHQYFG 265 + L G Sbjct: 124 IAAEDAKFGLPEVNLG 139 >gnl|CDD|39620 KOG4419, KOG4419, KOG4419, 5' nucleotidase [Nucleotide transport and metabolism]. Length = 602 Score = 28.8 bits (64), Expect = 3.0 Identities = 28/148 (18%), Positives = 45/148 (30%), Gaps = 25/148 (16%) Query: 5 KYFEGSLHAENVSLEKLAHVVQTPFYCYSTTAIEKN--------YLTFS---NAFDGMDT 53 ++G A NV + + PF T + + +L S A + Sbjct: 148 PAWKGPYLASNVQI-FDSSNSFVPFGLEYATFLTPHGVVVLAVGFLCASFSGAANRTVVV 206 Query: 54 MVCYALKANSNQAVIKT------LAHLGSGLDIVSEGELRRALAAPV--PAERIVFSGVG 105 V ++ Q ++ T +A S + E + A V V G Sbjct: 207 PVEEITQSEWEQDMVNTTDIDLIIALGHSPVRDDDEWKSLHAEIRKVHPNTPIQVIGGHS 266 Query: 106 KT-----IDEIDLALQSGIYCFNVESES 128 DE + L+SG Y V S Sbjct: 267 HIRDFAVYDEKSVELESGRYPETVGWLS 294 >gnl|CDD|111911 pfam03069, FmdA_AmdA, Acetamidase/Formamidase family. This family includes amidohydrolases of formamide EC:3.5.1.49 and acetamide. Methylophilus methylotrophus formamidase forms a homotrimer suggesting all the members of this family also do. Length = 331 Score = 28.6 bits (64), Expect = 3.1 Identities = 12/38 (31%), Positives = 18/38 (47%), Gaps = 1/38 (2%) Query: 164 TGKKEDKFGIPIHQIHSLYAYASTLPGVKISGVDMHIG 201 K +K I + +YA + +PGV+I G H G Sbjct: 115 LTDKFEKAAKAIWEFEGIYAVSRHVPGVRIPG-IPHPG 151 >gnl|CDD|119339 cd06558, crotonase-like, Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. Many of these play important roles in fatty acid metabolism. In addition to a conserved structural core and the formation of trimers (or dimers of trimers), a common feature in this superfamily is the stabilization of an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two conserved backbone NH groups in active sites that form an oxyanion hole.. Length = 195 Score = 28.7 bits (65), Expect = 3.5 Identities = 16/66 (24%), Positives = 26/66 (39%), Gaps = 15/66 (22%) Query: 194 SGVDMH-IGSQIDQIESFHKAFKLLRDLTQQLRS---------NGHNIQHIDVGGGLGIA 243 +G D+ + + D E + L++L + L NG + GGGL +A Sbjct: 58 AGADLKELAALSDAGEEARAFIRELQELLRALLRLPKPVIAAVNGAAL-----GGGLELA 112 Query: 244 YHSDHR 249 D R Sbjct: 113 LACDIR 118 >gnl|CDD|100003 cd05844, GT1_like_7, Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility.. Length = 367 Score = 28.4 bits (64), Expect = 3.8 Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 5/47 (10%) Query: 69 KTLAHLGSGLDIVSEGELRRALAAPVPAERIVFSGVGKTIDEIDLAL 115 + LA + VS+ R LA P E++ +G +D A Sbjct: 137 RRLARRAALFIAVSQFIRDRLLALGFPPEKVHVHPIG-----VDTAK 178 >gnl|CDD|173847 cd01158, SCAD_SBCAD, Short chain acyl-CoA dehydrogenases and eukaryotic short/branched chain acyl-CoA dehydrogenases. Short chain acyl-CoA dehydrogenase (SCAD). SCAD is a mitochondrial beta-oxidation enzyme. It catalyzes the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of SCAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. This subgroup also contains the eukaryotic short/branched chain acyl-CoA dehydrogenase(SBCAD), the bacterial butyryl-CoA dehydorgenase(BCAD) and 2-methylbutyryl-CoA dehydrogenase, which is involved in isoleucine catabolism. These enzymes are homotetramers. Length = 373 Score = 28.0 bits (63), Expect = 5.4 Identities = 15/35 (42%), Positives = 17/35 (48%), Gaps = 5/35 (14%) Query: 139 SLGKKAPIAFRVNPDINANTHKKISTGKKEDKFGI 173 S G + AF V D +S GKKEDK GI Sbjct: 169 SKGYRGITAFIVERD-----TPGLSVGKKEDKLGI 198 >gnl|CDD|58581 cd04281, ZnMc_BMP1_TLD, Zinc-dependent metalloprotease; BMP1/TLD-like subfamily. BMP1 (Bone morphogenetic protein 1) and TLD (tolloid)-like metalloproteases play vital roles in extracellular matrix formation, by cleaving precursor proteins such as enzymes, structural proteins, and proteins involved in the mineralization of the extracellular matrix. The drosophila protein tolloid and its Xenopus homologue xolloid cleave and inactivate Sog and chordin, respectively, which are inhibitors of Dpp (the Drosophila decapentaplegic gene product) and its homologue BMP4, involved in dorso-ventral patterning.. Length = 200 Score = 28.0 bits (62), Expect = 5.5 Identities = 11/24 (45%), Positives = 15/24 (62%) Query: 155 NANTHKKISTGKKEDKFGIPIHQI 178 N + IS GK DKFGI +H++ Sbjct: 72 RGNGPQAISIGKNCDKFGIVVHEL 95 >gnl|CDD|48147 cd03312, CIMS_N_terminal_like, CIMS - Cobalamine-independent methonine synthase, or MetE, N-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme catalyses the last step in the production of methionine by transferring a methyl group from 5-methyltetrahydrofolate to L-homocysteine without using an intermediate methyl carrier. The active enzyme has a dual (beta-alpha)8-barrel structure, and this model covers the N-terminal barrel, and a few single-barrel sequences most similar to the N-terminal barrel. It is assumed that the homologous N-terminal barrel has evolved from the C-terminus via gene duplication and has subsequently lost binding sites, and it seems as if the two barrels forming the active enzyme may sometimes reside on different polypeptides. The C-terminal domain incorporates the Zinc ion, which binds and activates homocysteine. Side chains from both barrels contribute to the binding of the folate substrate.. Length = 360 Score = 27.4 bits (61), Expect = 7.7 Identities = 21/82 (25%), Positives = 38/82 (46%), Gaps = 3/82 (3%) Query: 36 AIEKNYLTFSNAFDGMDTMV-CYALKANSNQAVIKTLAHLGSGLDIVSEGELRRALAAPV 94 A ++ Y + A G+ ++ Y N ++ +L G LD+V E A+ Sbjct: 217 AFKRAYEELAKAAPGLKLLLATYFGSLGENLDLLASLPVDGLHLDLVRGPENLEAVLKAG 276 Query: 95 PAERIVFSGV--GKTIDEIDLA 114 A++++ +GV G+ I DLA Sbjct: 277 FADKVLSAGVVDGRNIWRADLA 298 >gnl|CDD|145563 pfam02489, Herpes_glycop_H, Herpesvirus glycoprotein H. Herpesvirus glycoprotein H (gH) is a virion associated envelope glycoprotein. Complex formation between gH and gL has been demonstrated in both virions and infected cells. Length = 655 Score = 27.3 bits (61), Expect = 9.5 Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 1/58 (1%) Query: 309 NDFMRPTLYDAYHEINYIVNPAGDRLHIHADIVGPICETGDFIALNRKIALPRPGDLL 366 + R TL+ AY +N + + I I +C + + +A P LL Sbjct: 369 SGSDRKTLFLAYEVLNNETLNSSNLRLILLLITS-MCSAVEISSWIELLAKKDPLSLL 425 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 0.137 0.397 Gapped Lambda K H 0.267 0.0685 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 5,129,764 Number of extensions: 274148 Number of successful extensions: 660 Number of sequences better than 10.0: 1 Number of HSP's gapped: 597 Number of HSP's successfully gapped: 38 Length of query: 431 Length of database: 6,263,737 Length adjustment: 97 Effective length of query: 334 Effective length of database: 4,167,664 Effective search space: 1391999776 Effective search space used: 1391999776 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: 59 (26.6 bits)