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)