RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9378
(522 letters)
>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 = 399 bits (1028), Expect = e-136
Identities = 153/301 (50%), Positives = 184/301 (61%), Gaps = 32/301 (10%)
Query: 210 EDAFYVLDVGEIVRKHEDWKLKLPRVDPYYAVKCNDSQMVLEVLAALGTGFDCAS----- 264
E F V+D+G++VRK+ WK LPRV P+YAVKCN VL LAALG GFDCAS
Sbjct: 1 ETPFLVVDLGDVVRKYRRWKKALPRVRPFYAVKCNPDPAVLRTLAALGAGFDCASKGEIE 60
Query: 265 ------------------KPISHIRYAAEYGIDTMTFDNEIELQKVKQFHPTAQLVIRIR 306
K IS IRYAAE G+ TFD+E EL+K+ + P A+L++RI
Sbjct: 61 LVLGLGVSPERIIFANPCKSISDIRYAAELGVRLFTFDSEDELEKIAKHAPGAKLLLRIA 120
Query: 307 CDAEVAQCQLGMKFGCDPISEAPRLLRLAKSLDLDVVGVSFHVGSGCGDPPVFGRAIYSA 366
D A C L KFG DP EA LLR AK L L+VVGVSFHVGS C DP + AI A
Sbjct: 121 TDDSGALCPLSRKFGADP-EEARELLRRAKELGLNVVGVSFHVGSQCTDPSAYVDAIADA 179
Query: 367 RQIFDLGNSLGFSMRVLDLGGGYPG-YTG--YSMNRIAEIINVALDEYFPVEEGVSIIAE 423
R++FD LGF +++LD+GGG+PG Y G S IA +IN ALDEYFP +EGV IIAE
Sbjct: 180 REVFDEAAELGFKLKLLDIGGGFPGSYDGVVPSFEEIAAVINRALDEYFP-DEGVRIIAE 238
Query: 424 PGRYYVASAFTLATLIHSKRDILGANSSVPTHTMYYINDGVYGSFNCIIYDHAVCTPIPF 483
PGRY VASAFTLA + +KR + YY+NDGVYGSFN I++DH P
Sbjct: 239 PGRYLVASAFTLAVNVIAKRKRGDDD----RERWYYLNDGVYGSFNEILFDHIRYPPRVL 294
Query: 484 N 484
Sbjct: 295 K 295
Score = 99.5 bits (249), Expect = 8e-23
Identities = 37/63 (58%), Positives = 46/63 (73%), Gaps = 1/63 (1%)
Query: 4 RETLVPSSVWGPTCDGLDKVNDDILLPE-MPVGSWLIYRDMGAYTLPVASTFNGFPIPKV 62
L PSS+WGPTCD LD + +D+LLPE + VG WL++ +MGAYT ASTFNGFP PK+
Sbjct: 300 DGELYPSSLWGPTCDSLDVIYEDVLLPEDLAVGDWLLFENMGAYTTAYASTFNGFPPPKI 359
Query: 63 HAV 65
V
Sbjct: 360 VYV 362
>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 = 248 bits (636), Expect = 1e-77
Identities = 118/304 (38%), Positives = 173/304 (56%), Gaps = 33/304 (10%)
Query: 208 MKEDAFYVLDVGEIVRKHEDWKLKLPRVDPYYAVKCNDSQMVLEVLAALGTGFDCAS--- 264
++AF+V D+G+IV+KH W+ + ++ P+Y V+CN + VLE+LAALGTGF C+S
Sbjct: 10 TGKNAFFVGDLGKIVKKHSQWQTVMAQIKPFYTVRCNSTPAVLEILAALGTGFACSSKNE 69
Query: 265 --------------------KPISHIRYAAEYGIDTMTFDNEIELQKVKQFHPTAQLVIR 304
K S I+YAA+ G++ MT DNEIEL+K+ + HP A+L++
Sbjct: 70 MALVQELGVSPENIIYTNPCKQASQIKYAAKVGVNIMTCDNEIELKKIARNHPNAKLLLH 129
Query: 305 IRCDAEVAQCQLGMKFGCDPISEAPRLLRLAKSLDLDVVGVSFHVGSGCGDPPVFGRAIY 364
I + + ++ MKFG + LL AK LD+ +VGV FHV S C + + A+
Sbjct: 130 IATEDNIGGEEMNMKFGTT-LKNCRHLLECAKELDVQIVGVKFHVSSSCKEYQTYVHALS 188
Query: 365 SARQIFDLGNSLGFSMRVLDLGGGYPGYTGYSMNRIAEIINVALDEYFPVEEGVSIIAEP 424
AR +FD+ GF M +LD+GGG+ G + + + +I LD YFP G+ IIAEP
Sbjct: 189 DARCVFDMAEEFGFKMNMLDIGGGFTG-SEIQLEEVNHVIRPLLDVYFPEGSGIQIIAEP 247
Query: 425 GRYYVASAFTLATLIHSKRDI--------LGANSSVPTHTMYYINDGVYGSFNCIIYDHA 476
G YYV+SAFTLA + +K+ + + N S +YY+NDGVYGSF + +
Sbjct: 248 GSYYVSSAFTLAVNVIAKKAVENDKHLSSVEKNGSDEPAFVYYMNDGVYGSFASKLSEKL 307
Query: 477 VCTP 480
TP
Sbjct: 308 NTTP 311
Score = 71.4 bits (175), Expect = 2e-13
Identities = 32/72 (44%), Positives = 47/72 (65%)
Query: 5 ETLVPSSVWGPTCDGLDKVNDDILLPEMPVGSWLIYRDMGAYTLPVASTFNGFPIPKVHA 64
E L SS+WGP+CD LD++ + LLPE+ VG WLI+ +MGA +L STFN F P ++
Sbjct: 321 EPLFTSSLWGPSCDELDQIVESCLLPELNVGDWLIFDNMGAGSLHEPSTFNDFQRPAIYY 380
Query: 65 VIEEHIWLMLKD 76
++ W ++D
Sbjct: 381 MMSFSDWYEMQD 392
>gnl|CDD|217230 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 = 235 bits (602), Expect = 2e-74
Identities = 110/246 (44%), Positives = 141/246 (57%), Gaps = 32/246 (13%)
Query: 217 DVGEIV-RKHEDWKLKLPRVDPYYAVKCNDSQMVLEVLAALGTGFDCAS----------- 264
D+G I+ R H W+ LPR+ P+YAVK N VL +LA LG GFDCAS
Sbjct: 1 DLGRIIERAHALWQAFLPRIQPFYAVKANSDPAVLRLLAELGLGFDCASKGELERVLAAG 60
Query: 265 ------------KPISHIRYAAEYGIDTMTFDNEIELQKVKQFHPTAQLVIRIRCDAEV- 311
K S +RYA E+G+ +T DN EL+K+ + P A+L++R++ D +
Sbjct: 61 VPPERIIFANPCKSRSELRYALEHGVVCVTVDNVEELEKLARLAPEARLLLRVKPDVDAH 120
Query: 312 AQCQLGM----KFGCDPISEAPRLLRLAKSLDLDVVGVSFHVGSGCGDPPVFGRAIYSAR 367
A C L KFG D EA LL+ AK L L+VVGV FHVGSGC D F +A AR
Sbjct: 121 AHCYLSTGQDSKFGADLE-EAEALLKAAKELGLNVVGVHFHVGSGCTDAEAFVKAARDAR 179
Query: 368 QIFDLGNSLGFSMRVLDLGGGYPG-YTG-YSMNRIAEIINVALDEYFPVEEGVSIIAEPG 425
+FD G LGF +++LDLGGG+ YTG AE+IN AL+E FP + +IIAEPG
Sbjct: 180 NVFDQGAELGFELKILDLGGGFGVDYTGAEDFEEYAEVINAALEEVFPHDPHPTIIAEPG 239
Query: 426 RYYVAS 431
RY VA
Sbjct: 240 RYIVAP 245
>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 = 210 bits (536), Expect = 4e-63
Identities = 97/309 (31%), Positives = 139/309 (44%), Gaps = 44/309 (14%)
Query: 211 DAFYVLDVGEIVRKHEDWKLKLP-RVDPYYAVKCNDSQMVLEVLAALGTGFDCASKP--- 266
FYV D+ I + K LP V +YAVK N + VL LA GTGFD ASK
Sbjct: 1 TPFYVYDLDIIRAHYAALKEALPSGVKLFYAVKANPNPHVLRTLAEAGTGFDVASKGELA 60
Query: 267 --------------------ISHIRYAAEYGIDTMTFDNEIELQKVKQFH----PTAQLV 302
+S I A G+D + D+ EL+++ + P A+++
Sbjct: 61 LALAAGVPPERIIFTGPAKSVSEIEAALASGVDHIVVDSLDELERLNELAKKLGPKARIL 120
Query: 303 IRIRCDA-----EVAQCQLGMKFGCDPISEAPRLLRLAKSLDLDVVGVSFHVGSGCGDPP 357
+R+ D +++ L KFG SEA L AK LDL +VG+ FHVGS D
Sbjct: 121 LRVNPDVSAGTHKISTGGLKSKFGLSL-SEARAALERAKELDLRLVGLHFHVGSQILDLE 179
Query: 358 VFGRAIYSARQIFDLGNSLGFSMRVLDLGGGYPG-YTG--YSMNRIAEIINVALDEYFPV 414
+A+ AR++ + +GF + +LDLGGG Y A +IN L +YFP
Sbjct: 180 TIVQALSDARELIEELVEMGFPLEMLDLGGGLGIPYDEQPLDFEEYAALINPLLKKYFPN 239
Query: 415 EEGVSIIAEPGRYYVASAFTLATLIHSKRDILGANSSVPTHTMYYINDGVYGSFNCIIYD 474
+ GV++I EPGRY VA A L T + + + G ++ G+ SF +
Sbjct: 240 DPGVTLILEPGRYIVAQAGVLVTRVVAVKVNGGR-------FFAVVDGGMNHSFRPALAY 292
Query: 475 HAVCTPIPF 483
A P
Sbjct: 293 DAYHPITPL 301
Score = 71.6 bits (176), Expect = 2e-13
Identities = 28/62 (45%), Positives = 37/62 (59%)
Query: 4 RETLVPSSVWGPTCDGLDKVNDDILLPEMPVGSWLIYRDMGAYTLPVASTFNGFPIPKVH 63
E LVP+++ GP CD D + D LLPE+ VG L++ DMGAY +S FN P P +
Sbjct: 307 DEPLVPATLAGPLCDSGDVIGRDRLLPELEVGDLLVFEDMGAYGFSESSNFNSHPRPAEY 366
Query: 64 AV 65
V
Sbjct: 367 LV 368
>gnl|CDD|223098 COG0019, LysA, Diaminopimelate decarboxylase [Amino acid transport
and metabolism].
Length = 394
Score = 164 bits (418), Expect = 8e-46
Identities = 85/313 (27%), Positives = 121/313 (38%), Gaps = 45/313 (14%)
Query: 213 FYVLDVGEIVRKHEDWKLKLPRVD--PYYAVKCNDSQMVLEVLAALGTGFDCAS------ 264
YV D + R + K P +YAVK N + +L +LA G+GFD AS
Sbjct: 29 VYVYDEATLRRNARELKSAFPGSGAKVFYAVKANSNPAILRLLAEEGSGFDVASLGELEL 88
Query: 265 -----------------KPISHIRYAAEYGIDTMTFDNEIELQKVKQFHP--TAQLVIRI 305
K I +A E GI + D+E EL+++ P A++ +RI
Sbjct: 89 ALAAGFPPERIVFSGPAKSEEEIAFALELGIKLINVDSEEELERLSAIAPGLVARVSLRI 148
Query: 306 ------RCDAEVAQCQLGMKFGCDPISEAPRLLRLAKSLDLDVVGVSFHVGSGCGDPPVF 359
+A KFG P L R AK L L++VG+ FH+GS D F
Sbjct: 149 NPGVSAGTHEYIATGGKSSKFGISPEEALDVLERAAKLLGLELVGLHFHIGSQITDLDPF 208
Query: 360 GRAIYSARQIFD-LGNSLGFSMRVLDLGGGY--PGYTGYSMNRIAEIINVALDEYFPVEE 416
A+ ++F L LG + L+LGGG Y +A + + E
Sbjct: 209 EEALAKVEELFGRLAEELGIQLEWLNLGGGLGITYEDEYDPPDLAAYAKALKEAFGEYAE 268
Query: 417 GVSIIAEPGRYYVASAFTLATLIHSKRDILGANSSVPTHTMYYINDGVYGSFNCIIYDHA 476
V +I EPGR VA+A L T + ++ N + I DG A
Sbjct: 269 DVELILEPGRAIVANAGVLVTEVLDVKENGERN--------FVIVDGGMNDLMRPALYGA 320
Query: 477 VCTPIPFNVMDDS 489
I N D+
Sbjct: 321 Y-HHIRLNRTDED 332
Score = 56.9 bits (138), Expect = 9e-09
Identities = 22/60 (36%), Positives = 29/60 (48%), Gaps = 1/60 (1%)
Query: 4 RETLVPSSVWGPTCDGLDKVNDDILLPE-MPVGSWLIYRDMGAYTLPVASTFNGFPIPKV 62
V GPTC+ D + D LPE + VG L+ D GAY ++S +NG P P
Sbjct: 332 DAEREEYDVVGPTCESGDVLARDRALPEPLKVGDLLVILDAGAYGASMSSNYNGRPRPAE 391
>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 = 122 bits (309), Expect = 3e-32
Identities = 66/236 (27%), Positives = 90/236 (38%), Gaps = 55/236 (23%)
Query: 221 IVRKHEDWKLKLP-RVDPYYAVKCNDSQMVLEVLAALGTGFDCAS--------------- 264
I + + P + + VK N + V LAALGTGFD AS
Sbjct: 1 IRHNYRRLREAAPAGITLFAVVKANANPEVARTLAALGTGFDVASLGEALLLRAAGIPPE 60
Query: 265 --------KPISHIRYAAEYGIDTMTFDNEIELQKVKQFH----PTAQLVIRIRCDAEVA 312
K +S + AAE G+ +T D+ EL+K+++ P A++++RI E
Sbjct: 61 PILFLGPCKQVSELEDAAEQGVIVVTVDSLEELEKLEEAALKAGPPARVLLRIDTGDEN- 119
Query: 313 QCQLGMKFGCDPISEAPRLLRLAKSLD-LDVVGVSFHVGSGCGDPPVFGRAIYSARQIFD 371
KFG P E LL AK L L +VG+ H GS D F A+ D
Sbjct: 120 -----GKFGVRP-EELKALLERAKELPHLRLVGLHTHFGSADEDYSPFVEALSRFVAALD 173
Query: 372 LGNSLGFSMRVLDLGGGYPGYTGYSMNRIAEIINVALDEYFPVE-EGVSIIAEPGR 426
LG + L +GG + Y G II EPGR
Sbjct: 174 QLGELGIDLEQLSIGGSFAIL------------------YLQELPLGTFIIVEPGR 211
>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 = 120 bits (304), Expect = 5e-30
Identities = 77/276 (27%), Positives = 107/276 (38%), Gaps = 49/276 (17%)
Query: 213 FYVLDVGEIVRKHEDWK--LKLPRVDPYYAVKCNDSQMVLEVLAALGTGFDCAS------ 264
YV D I + K P YAVK N + +L++LA G G D S
Sbjct: 5 LYVYDEATIRENYRRLKEAFSGPGFKICYAVKANSNLAILKLLAEEGLGADVVSGGELYR 64
Query: 265 -----------------KPISHIRYAAEYGIDTMTFDNEIELQKVKQFHP----TAQLVI 303
K + A E GI + D+ EL+++ + P A + +
Sbjct: 65 ALKAGFPPERIVFTGNGKSDEELELALELGILRINVDSLSELERLGEIAPELGKGAPVAL 124
Query: 304 RIRCDAEV---AQCQLGM---KFGCDPISEAPRLLRLAKSLD-LDVVGVSFHVGSGCGDP 356
R+ + G KFG P+ +A R AK L L +VG+ H+GS D
Sbjct: 125 RVNPGVDAGTHPYISTGGKDSKFGI-PLEQALEAYRRAKELPGLKLVGLHCHIGSQILDL 183
Query: 357 PVFGRAIYSARQIFDLGNSL---GFSMRVLDLGGGYP-GYTGY----SMNRIAEIINVAL 408
F A A ++ DL L G + LDLGGG Y + AE I AL
Sbjct: 184 EPFVEA---AEKLLDLAAELRELGIDLEFLDLGGGLGIPYRDEDEPLDIEEYAEAIAEAL 240
Query: 409 DEYFPVEEGVSIIAEPGRYYVASA-FTLATLIHSKR 443
E + +I EPGRY VA+A L + + K
Sbjct: 241 KELCEGGPDLKLIIEPGRYIVANAGVLLTRVGYVKE 276
Score = 36.3 bits (85), Expect = 0.037
Identities = 19/56 (33%), Positives = 24/56 (42%)
Query: 5 ETLVPSSVWGPTCDGLDKVNDDILLPEMPVGSWLIYRDMGAYTLPVASTFNGFPIP 60
V GP C+ D D LPE+ G L D GAY ++S +N P P
Sbjct: 313 GETEKVDVVGPICESGDVFAKDRELPEVEEGDLLAIHDAGAYGYSMSSNYNSRPRP 368
>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 = 90.3 bits (225), Expect = 1e-19
Identities = 70/269 (26%), Positives = 113/269 (42%), Gaps = 49/269 (18%)
Query: 213 FYVLDVGEIVRKHEDWKLKLPR-VDPYYAVKCNDSQMVLEVLAALGTGFDCAS------- 264
FYV D + ++ + LP ++ YY++K N + ++ L LG G + AS
Sbjct: 9 FYVYDRDRVRERYAALRAALPPAIEIYYSLKANPNPALVAHLRQLGDGAEVASAGELALA 68
Query: 265 ----------------KPISHIRYAAEYGIDTMTFDNEIELQKV----KQFHPTAQLVIR 304
K + +R A E GI T+ ++ EL+++ ++ A++ +R
Sbjct: 69 LEAGVPPEKILFAGPGKSDAELRRAIEAGIGTINVESLEELERIDALAEEHGVVARVALR 128
Query: 305 IRCDAEVAQCQLGM-----KFGCDPISEAPRLL-RLAKSLDLDVVGVSFHVGSGCGDPPV 358
I D E+ + M +FG D + E P +L R+A +L VG+ + G+ D
Sbjct: 129 INPDFELKGSGMKMGGGPSQFGID-VEELPAVLARIAALPNLRFVGLHIYPGTQILDA-- 185
Query: 359 FGRAIYSA-RQIFDLG----NSLGFSMRVLDLGGG-----YPGYTGYSMNRIAEIINVAL 408
A+ A RQ L LG + LDLGGG +PG T + + + L
Sbjct: 186 --DALIEAFRQTLALALRLAEELGLPLEFLDLGGGFGIPYFPGETPLDLEALGAALAALL 243
Query: 409 DEYFPVEEGVSIIAEPGRYYVASAFTLAT 437
E G ++ E GRY V A T
Sbjct: 244 AELGDRLPGTRVVLELGRYLVGEAGVYVT 272
Score = 31.4 bits (72), Expect = 1.2
Identities = 19/60 (31%), Positives = 26/60 (43%), Gaps = 5/60 (8%)
Query: 4 RETLVPSSVWGPTCDGLDKVNDDILLPEMPVGSWLIYRDMGAYTL---PVASTFNGFPIP 60
E +V GP C LD + ++ LP + G + GAY L P+A F P P
Sbjct: 320 GEERETVTVVGPLCTPLDLLGRNVELPPLEPGDLVAVLQSGAYGLSASPLA--FLSHPAP 377
>gnl|CDD|215835 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 = 75.8 bits (187), Expect = 1e-16
Identities = 29/60 (48%), Positives = 39/60 (65%), Gaps = 1/60 (1%)
Query: 7 LVPSSVWGPTCDGLDKVNDDILLP-EMPVGSWLIYRDMGAYTLPVASTFNGFPIPKVHAV 65
L P ++ GPTCD D + D+ LP E+ VG WL++ D GAYT+ ++S FNGFP P V
Sbjct: 51 LRPYTLAGPTCDSGDVLARDVSLPLELEVGDWLVFFDAGAYTISLSSNFNGFPRPAEVLV 110
Score = 38.8 bits (91), Expect = 7e-04
Identities = 12/45 (26%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 445 ILGANSSVPTHTMYYINDGVYGSFNCIIYDHAVCTPIPFNVMDDS 489
++ Y++DGVYGS + +YD + +P + +DD
Sbjct: 6 VIDVKERGDDRKFVYLDDGVYGSPDPALYDA-LHPILPVSRLDDE 49
>gnl|CDD|233248 TIGR01048, lysA, diaminopimelate decarboxylase. This family
consists of diaminopimelate decarboxylase, an enzyme
which catalyzes the conversion of diaminopimelic acid
into lysine during the last step of lysine biosynthesis
[Amino acid biosynthesis, Aspartate family].
Length = 414
Score = 80.8 bits (200), Expect = 2e-16
Identities = 73/272 (26%), Positives = 111/272 (40%), Gaps = 43/272 (15%)
Query: 213 FYVLDVGEIVRKHEDWKLKLPRVD-PYYAVKCNDSQMVLEVLAALGTGFDCAS------- 264
YV D I R+ +K YAVK N + VL +LA LG+GFD S
Sbjct: 27 LYVYDEDTIRRRFRAYKEAFGGRSLVCYAVKANSNLAVLRLLAELGSGFDVVSGGELYRA 86
Query: 265 ----------------KPISHIRYAAEYGIDTMTFDNEIELQKVKQFHP----TAQLVIR 304
K + + A E GI + D+ EL+++ + P A++ +R
Sbjct: 87 LAAGFPPEKIVFSGNGKSRAELERALELGI-CINVDSFSELERLNEIAPELGKKARISLR 145
Query: 305 IRCDAEVA---QCQLGM---KFGCDPISEAPRLLRLAKSLD-LDVVGVSFHVGSGCGDPP 357
+ + G+ KFG D EA A L L++VG+ H+GS D
Sbjct: 146 VNPGVDAKTHPYISTGLKDSKFGIDV-EEALEAYLYALQLPHLELVGIHCHIGSQITDLS 204
Query: 358 VFGRAIYSARQIFDLGNSLGFSMRVLDLGGG-----YPGYTGYSMNRIAEIINVALDEYF 412
F A ++ + + G + LDLGGG P ++ A+ I AL+ Y
Sbjct: 205 PFVEAAEKVVKLAESL-AEGIDLEFLDLGGGLGIPYTPEEEPPDLSEYAQAILNALEGYA 263
Query: 413 PVEEGVSIIAEPGRYYVASAFTLATLIHSKRD 444
+ +I EPGR VA+A L T + ++
Sbjct: 264 DLGLDPKLILEPGRSIVANAGVLLTRVGFVKE 295
Score = 35.0 bits (81), Expect = 0.11
Identities = 21/70 (30%), Positives = 32/70 (45%), Gaps = 1/70 (1%)
Query: 8 VPSSVWGPTCDGLDKVNDDILLPEMPVGSWLIYRDMGAYTLPVASTFNGFPIPKVHAVIE 67
+ V GP C+ D + D LPE+ G L D GAY ++S +N P P V +
Sbjct: 335 EVADVVGPVCESGDVLAKDRELPEVEPGDLLAVFDAGAYGFSMSSNYNSRPRPAEVLV-D 393
Query: 68 EHIWLMLKDR 77
+++ R
Sbjct: 394 GGQARLIRRR 403
>gnl|CDD|236358 PRK08961, PRK08961, bifunctional aspartate kinase/diaminopimelate
decarboxylase protein; Provisional.
Length = 861
Score = 69.3 bits (170), Expect = 3e-12
Identities = 57/231 (24%), Positives = 88/231 (38%), Gaps = 46/231 (19%)
Query: 238 YYAVKCNDSQMVLEVLAALGTGFDCAS-------------------------KPISHIRY 272
+YA+K N +L L G GF+C S P +
Sbjct: 530 FYAIKANPHPAILRTLEEEGFGFECVSIGELRRVFELFPELSPERVLFTPNFAPRAEYEA 589
Query: 273 AAEYGIDTMTFDNEIELQKVKQFHPTAQLVIRI---RCDAEVAQCQLG---MKFGCDPIS 326
A G+ T+T DN L+ + ++ +RI D + + G KFG +
Sbjct: 590 AFALGV-TVTLDNVEPLRNWPELFRGREVWLRIDPGHGDGHHEKVRTGGKESKFGL-SQT 647
Query: 327 EAPRLLRLAKSLDLDVVGVSFHVGSGCGDPPVFGRAIYSARQIFDLGNSLGFSMRVLDLG 386
+ LAK+L + VVG+ H+GSG + R A ++ +R +DLG
Sbjct: 648 RIDEFVDLAKTLGITVVGLHAHLGSGIETGEHWRR---MADELASFARRFP-DVRTIDLG 703
Query: 387 GGYP-----GYTGYSMNRIAEIINVALDEYFPVEEGVSIIAEPGRYYVASA 432
GG G + + + ++ L E G + EPGRY VA A
Sbjct: 704 GGLGIPESAGDEPFDL----DALDAGLAEVKAQHPGYQLWIEPGRYLVAEA 750
Score = 33.5 bits (77), Expect = 0.30
Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 12 VWGPTCDGLDKVNDDILLPEMPVGSWLIYRDMGAYTLPVASTFNGFPIPKVHAVIE 67
V GP C+ D + LP G ++ + GAY ++ST+N + V++
Sbjct: 806 VVGPICESSDVLGKRRRLPATAEGDVILIANAGAYGYSMSSTYNLREPAR-EVVLD 860
>gnl|CDD|132143 TIGR03099, dCO2ase_PEP1, pyridoxal-dependent decarboxylase,
exosortase A system-associated. The sequences in this
family contain the pyridoxal binding domain (pfam02784)
and C-terminal sheet domain (pfam00278) of a family of
Pyridoxal-dependent decarboxylases. Characterized
enzymes in this family decarboxylate substrates such as
ornithine, diaminopimelate and arginine. The genes of
the family modeled here, with the exception of those
observed in certain Burkholderia species, are all found
in the context of exopolysaccharide biosynthesis loci
containing the exosortase/PEP-CTERM protein sorting
system. More specifically, these are characteristic of
the type 1 exosortase system represented by the Genome
Property GenProp0652. The substrate of these enzymes may
be a precursor of the carrier or linker which is
hypothesized to release the PEP-CTERM protein from the
exosortase enzyme. These enzymes are apparently most
closely related to the diaminopimelate decarboxylase
modeled by TIGR01048 which may suggest a similarity (or
identity) of substrate.
Length = 398
Score = 64.8 bits (158), Expect = 4e-11
Identities = 64/293 (21%), Positives = 104/293 (35%), Gaps = 55/293 (18%)
Query: 213 FYVLDVGEIVRKHEDWKLKLP-RVDPYYAVKCNDSQMVLEVLAALGTGFDCAS------- 264
FY D G + + + LP + +YAVK N +L +A L GFD AS
Sbjct: 27 FYAYDRGLVSERVAALRKALPEELAIHYAVKANPMPALLAHMAPLVDGFDVASAGELAVA 86
Query: 265 ----------------KPISHIRYAAEYGIDTMTFDNEIELQKV-----KQFHPTAQLVI 303
K + +R A G+ + ++ EL ++ A++ +
Sbjct: 87 LDTGYDPGCISFAGPGKTDAELRRALAAGV-LINVESLRELNRLAALSEALGLR-ARVAV 144
Query: 304 RIRCDAEVAQCQLGM-----KFGCDPISEAPRLLRLAKSLDLDVVGVSFHVGSGCGDPPV 358
R+ D E+ + M +FG D + P L K+ DLD G GS +
Sbjct: 145 RVNPDFELKGSGMKMGGGAKQFGID-AEQVPAALAFIKAADLDFQGFHIFAGSQNLNAEA 203
Query: 359 FGRAIYSARQI-FDLGNSLGFSMRVLDLGGG-----YPGYTGYSMNRIAEIINVALDEYF 412
A + L S +RV+++GGG +PG + + +
Sbjct: 204 IIEAQAKTLALALRLAESAPAPVRVINIGGGFGIPYFPGNPPLDLAPVGAALAALFARLR 263
Query: 413 PVEEGVSIIAEPGRYYVASA-FTLATLIHSKRDILGANSSVPTHTM-YYINDG 463
V I+ E GRY V A + +I K + + + DG
Sbjct: 264 DALPEVEILLELGRYLVGEAGIYVCRVIDRKI----------SRGETFLVTDG 306
>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 = 64.2 bits (157), Expect = 6e-11
Identities = 43/186 (23%), Positives = 65/186 (34%), Gaps = 40/186 (21%)
Query: 236 DPYYAVKCNDSQMVLEVLAALGTGFDCAS-----------------------KPISHIRY 272
Y+A K N S ++ AA G G D AS K +
Sbjct: 39 RVYFARKANKSLALVRAAAAAGIGVDVASLAELRQALAAGVRGDRIVATGPAKTDEFLWL 98
Query: 273 AAEYGIDTMTFDNEIELQKVKQFHPTAQLVIRIR-CDAEVA------QCQLGMKFGCDPI 325
A +G T+ D+ EL ++ L A V L +FG
Sbjct: 99 AVRHGA-TIAVDSLDELDRL------LALARGYTTGPARVLLRLSPFPASLPSRFGMPAA 151
Query: 326 SEAPRLLRLAKSLD-LDVVGVSFHVGSGCGDPPVFGRAIYSARQIFDLGNSLGFSMRVLD 384
L RLA+ + + +VG FH+ A+ + D +LG + R +D
Sbjct: 152 EVRTALERLAQLRERVRLVGFHFHLDGY--SAAQRVAALQECLPLIDRARALGLAPRFID 209
Query: 385 LGGGYP 390
+GGG+P
Sbjct: 210 IGGGFP 215
>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 = 61.1 bits (149), Expect = 4e-10
Identities = 81/337 (24%), Positives = 124/337 (36%), Gaps = 82/337 (24%)
Query: 210 EDAFYVLDVGEIVRK----HEDWKLKLPRVDPYYAVKCNDSQMVLEVLAALGTG------ 259
F+V D + +K + P V Y+ K N + ++L G
Sbjct: 6 GSPFFVFDEDALRENYRELLGAFKKRYPNVVIAYSYKTNYLPAICKILHEEGGYAEVVSA 65
Query: 260 -----------------FDCASKPISHIRYAAEYG----IDTMTFDNEIELQKVKQFHPT 298
F+ K + A E G ID+ FD EL+++ +
Sbjct: 66 MEYELALKLGVPGKRIIFNGPYKSKEELEKALEEGALINIDS--FD---ELERILEIAKE 120
Query: 299 AQLVIR--IRCDAEVAQCQLGMKFGCDP--ISEA-PRLLRLAKSLDLDVVGVSFHVGSGC 353
V + IR + + +FG D EA L ++ +S +L +VG+ HVGS
Sbjct: 121 LGRVAKVGIRLNMNY-GNNVWSRFGFDIEENGEALAALKKIQESKNLSLVGLHCHVGSNI 179
Query: 354 GDPPVFGRAIYSARQIFDLGNSL-GFSMRVLDLGGGYPG-----------YTGYSMNRIA 401
+P + A A+++ +L + L G + LDLGGG+P T A
Sbjct: 180 LNPEAYSAA---AKKLIELLDRLFGLELEYLDLGGGFPAKTPLSLAYPQEDTVPDPEDYA 236
Query: 402 EIINVALDEYFP-VEEGVSIIAEPGRYYVASAFTLATLIHSKRDILGANS--------SV 452
E I L EY+ E +I EPGR V A L + + ++ G N ++
Sbjct: 237 EAIASTLKEYYANKENKPKLILEPGRALVDDAGYLLGRVVAVKNRYGRNIAVTDAGINNI 296
Query: 453 PTHTMY---------YINDG------VYGSFNCIIYD 474
PT Y D VYG FNC+ D
Sbjct: 297 PTIFWYHHPILVLRPGKEDPTSKNYDVYG-FNCMESD 332
Score = 34.5 bits (80), Expect = 0.12
Identities = 15/54 (27%), Positives = 25/54 (46%)
Query: 1 YPYRETLVPSSVWGPTCDGLDKVNDDILLPEMPVGSWLIYRDMGAYTLPVASTF 54
T V+G C D + ++ LP + VG L R++GAY + ++ F
Sbjct: 312 GKEDPTSKNYDVYGFNCMESDVLFPNVPLPPLNVGDILAIRNVGAYNMTQSNQF 365
>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 = 53.8 bits (130), Expect = 1e-07
Identities = 57/269 (21%), Positives = 101/269 (37%), Gaps = 68/269 (25%)
Query: 214 YVLDVGEIVRKHEDW-KLKLP-RVDPYYAVKCNDSQMVLEVLAALGTGFDCAS------- 264
YV D+ + R H + LP + +YA+K N +L LA GF+ AS
Sbjct: 5 YVYDLAAL-RAHARALRASLPPGCELFYAIKANSDPPILRALAPHVDGFEVASGGEIAHV 63
Query: 265 ---------------KPISHIRYAAEYGIDTMTFDNEIELQKV----KQFHPTAQLVIRI 305
K S + A G++ + ++E+EL+++ ++ TA +++R+
Sbjct: 64 RAAVPDAPLIFGGPGKTDSELAQALAQGVERIHVESELELRRLNAVARRAGRTAPVLLRV 123
Query: 306 RCDAE-VAQCQLGM-----KFGCDPISEAPRLLRLAKSLD-LDVVGVSFHVGSGCGDPPV 358
+ L M FG D ++ P L L + L + + G FH+ S D
Sbjct: 124 NLALPDLPSSTLTMGGQPTPFGIDE-ADLPDALELLRDLPNIRLRGFHFHLMSHNLDAA- 181
Query: 359 FGRAIYSARQIFDLGNSL----GFSMRVLDLGGG-------------YPGYTGYSMNRIA 401
+ + + G + V+++GGG + G+ +A
Sbjct: 182 --AHLALVKAYLETARQWAAEHGLDLDVVNVGGGIGVNYADPEEQFDWAGFCEGLDQLLA 239
Query: 402 EIINVALDEYFPVEEGVSIIAEPGRYYVA 430
E E G+++ E GRY A
Sbjct: 240 E-----------YEPGLTLRFECGRYISA 257
>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 = 53.6 bits (129), Expect = 1e-07
Identities = 64/255 (25%), Positives = 100/255 (39%), Gaps = 46/255 (18%)
Query: 214 YVLDVGEIVRKHEDWKLKLPRVDP-YYAVKCNDSQMVLEVLAALGTGFDCASK------- 265
YV D+ E VR L VD +YA+K N VL L G GF+C S
Sbjct: 15 YVYDL-ETVRARARQVSALKAVDSLFYAIKANPHPDVLRTLEEAGLGFECVSIGELDLVL 73
Query: 266 ------PISHIRYA------AEY------GIDTMTFDNEIELQKVKQFHPTAQLVIRI-- 305
+ + +EY G++ +T DN L++ + ++++RI
Sbjct: 74 KLFPDLDPRRVLFTPNFAARSEYEQALELGVN-VTVDNLHPLREWPELFRGREVILRIDP 132
Query: 306 -RCDAEVAQCQLG---MKFGCDPISEAPRLLRLAKSLDLDVVGVSFHVGSGCGDPPVFGR 361
+ + + G KFG D E LAK + V+G+ H GSG D +
Sbjct: 133 GQGEGHHKHVRTGGPESKFGLDV-DELDEARDLAKKAGIIVIGLHAHSGSGVEDTDHW-- 189
Query: 362 AIYSARQIFDLGNSL--GF-SMRVLDLGGGYPGYTGYSMNRI-AEIINVALDEYFPVEEG 417
+ D SL F ++R+L++GGG I + ++ AL
Sbjct: 190 -----ARHGDYLASLARHFPAVRILNVGGGLGIPEAPGGRPIDLDALDAALAAAKAAHPQ 244
Query: 418 VSIIAEPGRYYVASA 432
+ EPGR+ VA +
Sbjct: 245 YQLWMEPGRFIVAES 259
Score = 32.8 bits (75), Expect = 0.45
Identities = 18/50 (36%), Positives = 25/50 (50%)
Query: 11 SVWGPTCDGLDKVNDDILLPEMPVGSWLIYRDMGAYTLPVASTFNGFPIP 60
V GP C+ D + D LLPE G ++ + GAY +AST+N
Sbjct: 314 DVVGPICESGDVLGRDRLLPETEEGDVILIANAGAYGFCMASTYNLREPA 363
>gnl|CDD|178152 PLN02537, PLN02537, diaminopimelate decarboxylase.
Length = 410
Score = 53.3 bits (128), Expect = 2e-07
Identities = 61/267 (22%), Positives = 104/267 (38%), Gaps = 58/267 (21%)
Query: 213 FYVLDVGEIVRKHEDWKLKLPRVD--PYYAVKCNDSQMVLEVLAALG------------- 257
FY+ +I R +E +K L + YA+K N++ +LE L LG
Sbjct: 20 FYLYSKPQITRNYEAYKEALEGLRSIIGYAIKANNNLKILEHLRELGCGAVLVSGNELRL 79
Query: 258 ---TGFDCA-------SKPISHIRYAAEYGIDTMTFDNEIELQKVKQFHPTA----QLVI 303
GFD K + + AA+ G+ + D+E +L+ + + A +++
Sbjct: 80 ALRAGFDPTRCIFNGNGKLLEDLVLAAQEGV-FVNVDSEFDLENIVEAARIAGKKVNVLL 138
Query: 304 RIRCDAE------VAQCQLGMKFGC---------DPISEAPRLLRLAKSLDLDVVGVSFH 348
RI D + VA KFG D + P L+L VG H
Sbjct: 139 RINPDVDPQVHPYVATGNKNSKFGIRNEKLQWFLDAVKAHPNELKL--------VGAHCH 190
Query: 349 VGSGCGDPPVFGRAIYSARQIFDLGNSLGFSMRVLDLGGGYP---GYTGYSMNRIAEIIN 405
+GS +F A D + GF + L++GGG + G + ++I+
Sbjct: 191 LGSTITKVDIFRDAAVLMVNYVDEIRAQGFELSYLNIGGGLGIDYYHAGAVLPTPRDLID 250
Query: 406 VALDEYFPVEEGVSIIAEPGRYYVASA 432
+ + +++I EPGR +A+
Sbjct: 251 TVRE--LVLSRDLTLIIEPGRSLIANT 275
Score = 37.1 bits (86), Expect = 0.018
Identities = 19/44 (43%), Positives = 26/44 (59%)
Query: 12 VWGPTCDGLDKVNDDILLPEMPVGSWLIYRDMGAYTLPVASTFN 55
V GP C+ D + D LP P G+ L+ D GAY + +AST+N
Sbjct: 332 VVGPVCESADFLGKDRELPTPPKGAGLVVHDAGAYCMSMASTYN 375
>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 = 41.2 bits (97), Expect = 9e-04
Identities = 62/276 (22%), Positives = 100/276 (36%), Gaps = 69/276 (25%)
Query: 240 AVKCNDSQMVLEVLAALGTGFDCAS-----------------------KPISHIRYAAEY 276
AVK N VL +LA G G + AS K + +R A E
Sbjct: 33 AVKANPLVPVLRLLAEAGAGAEVASPGELELALAAGFPPERIVFDSPAKTRAELREALEL 92
Query: 277 GIDTMTFDNEIELQK----VKQFHPTAQLVIRIRCDAEVAQCQLGM--------KFGCDP 324
G+ + DN EL++ V +F + I +R + +V ++G KFG
Sbjct: 93 GV-AINIDNFQELERIDALVAEFKEAS-SRIGLRVNPQVGAGKIGALSTATATSKFGVAL 150
Query: 325 ISEAPRLLRLAKSLDLDVVGVSFHVGS-GCGDPPVFGRAIYSARQIFDLGNSLGFSMR-- 381
A + A + + G+ HVGS GC R++ DL + +
Sbjct: 151 EDGARDEIIDAFARRPWLNGLHVHVGSQGCELS----LLAEGIRRVVDLAEEINRRVGRR 206
Query: 382 ---VLDLGGGYPGYTGYSMNRIAEIINVALDEYFPV---------EEGVSIIAEPGRYYV 429
+D+GGG P +N +E I +Y + ++ E GR +
Sbjct: 207 QITRIDIGGGLP------VNFESEDITPTFADYAAALKAAVPELFDGRYQLVTEFGRSLL 260
Query: 430 ASA-FTLATLIHSKRD------ILGANSSVPTHTMY 458
A ++ + ++K I A + V T T Y
Sbjct: 261 AKCGTIVSRVEYTKSSGGRRIAITHAGAQVATRTAY 296
Score = 39.7 bits (93), Expect = 0.003
Identities = 19/59 (32%), Positives = 28/59 (47%)
Query: 7 LVPSSVWGPTCDGLDKVNDDILLPEMPVGSWLIYRDMGAYTLPVASTFNGFPIPKVHAV 65
V + V GP C D + + LP + G ++ D GAY S++N P P V+ V
Sbjct: 319 EVVTDVAGPCCFAGDVLAKERALPPLEPGDYVAVHDTGAYYFSSHSSYNSLPRPAVYGV 377
>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 = 40.2 bits (95), Expect = 0.002
Identities = 36/124 (29%), Positives = 53/124 (42%), Gaps = 20/124 (16%)
Query: 347 FHVGSGCGDPPVFGRAIYSARQIF-DLGNSLGFSMRVLDLGGGYP-GYTG---------- 394
FH+GS D A+ A +I+ +L LG ++R LD+GGG Y G
Sbjct: 192 FHIGSQITDIRRIKSALREAARIYAEL-RKLGANLRYLDIGGGLGVDYDGSRSSSDSSFN 250
Query: 395 YSMNRIAEIINVALDEYFPVEEGV---SIIAEPGRYYVA-SAFTLATLI--HSKRDILGA 448
YS+ A I + E E GV +I+ E GR VA + + ++ D
Sbjct: 251 YSLEEYANDIVKTVKEIC-DEAGVPHPTIVTESGRAIVAHHSVLIFEVLGVKRLADWYFC 309
Query: 449 NSSV 452
N S+
Sbjct: 310 NFSL 313
>gnl|CDD|215240 PLN02439, PLN02439, arginine decarboxylase.
Length = 559
Score = 38.5 bits (90), Expect = 0.008
Identities = 36/128 (28%), Positives = 54/128 (42%), Gaps = 25/128 (19%)
Query: 319 KFGCDPISEAPRLLRLAKSLD----LDVVG-VSFHVGSGCGDPPVFGRAIYSARQIFDLG 373
KFG A ++R+ + L LD + + FH+GS + + A QI+
Sbjct: 159 KFGLT----ATEIVRVVRKLRKEGMLDCLQLLHFHIGSQIPSTSLLKDGVSEAAQIYCEL 214
Query: 374 NSLGFSMRVLDLGGG----YPGY--------TGYSMNRIAEIINVALDEYFPVEEGVS-- 419
LG MRV+D+GGG Y G YS+ A + A+ + +GV
Sbjct: 215 VRLGAPMRVIDIGGGLGIDYDGSKSGSSDMSVAYSLEEYANAVVAAVRDVC-DRKGVKHP 273
Query: 420 -IIAEPGR 426
I +E GR
Sbjct: 274 VICSESGR 281
>gnl|CDD|224088 COG1166, SpeA, Arginine decarboxylase (spermidine biosynthesis)
[Amino acid transport and metabolism].
Length = 652
Score = 36.5 bits (85), Expect = 0.036
Identities = 31/131 (23%), Positives = 53/131 (40%), Gaps = 24/131 (18%)
Query: 319 KFGCDP--ISEAPRLLRLAKSLDLDVVGVSFHVGSGCGDPPVFGRAIYSARQIFDLGNSL 376
KFG + + LR A LD + + FH+GS + + A + + L
Sbjct: 238 KFGLSATQVLQVVERLREANLLD-SLQLLHFHLGSQISNIRDIKTGVREAARFYVELRKL 296
Query: 377 GFSMRVLDLGGG----YPGYTGYSMNRIAEIINVALDEY-----FPVEEGV--------S 419
G +++ D+GGG Y G + + N L+EY + +++ +
Sbjct: 297 GANIKYFDVGGGLGVDYDG----TRTQSDCSKNYGLNEYANDVVWALKDACEEKGLPHPT 352
Query: 420 IIAEPGRYYVA 430
II+E GR A
Sbjct: 353 IISESGRAITA 363
>gnl|CDD|233337 TIGR01273, speA, arginine decarboxylase, biosynthetic. Two
alternative pathways can convert arginine to putrescine.
One is decarboxylation by this enzyme followed by
removal of the urea moeity by agmatinase. In the other,
the ureohydrolase (arginase) acts first, followed by
ornithine decarboxylase. This pathway leads to
spermidine biosynthesis, hence the gene symbol speA. A
distinct biodegradative form is also pyridoxal
phosphate-dependent but is not similar in sequence
[Central intermediary metabolism, Polyamine
biosynthesis].
Length = 624
Score = 36.2 bits (84), Expect = 0.049
Identities = 59/254 (23%), Positives = 92/254 (36%), Gaps = 70/254 (27%)
Query: 239 YAVKCNDSQMVLEVLAALGTGF----DCASKP-----ISH------------------IR 271
Y +K N + V+E + A G G + SKP +++ I
Sbjct: 95 YPIKVNQHRRVVEDIVASGKGEPYGLEAGSKPELMAAMAYATKPGAPIVCNGYKDREYIE 154
Query: 272 ---YAAEYGID-TMTFDNEIELQKV----KQFHPTAQLVIRIRCDAEVA---QCQLGM-- 318
+ G + + + EL V K+ +L +R R ++ + G
Sbjct: 155 LALIGRKLGHNVFIVIEKLSELDLVIDEAKKLGVKPKLGLRARLASKGSGKWASSGGEKS 214
Query: 319 KFGCDP--ISEAPRLLR---LAKSLDLDVVGVSFHVGSGCGDPPVFGRAIYSARQIFDLG 373
KFG + E RLL L SL L + FH+GS + + + A + +
Sbjct: 215 KFGLSATQVLEVVRLLEQNGLLDSLQL----LHFHIGSQISNIDDIKKGVREAARFYCEL 270
Query: 374 NSLGFSMRVLDLGGG----YPGYTGYSMNRIAEIINVALDEY-----FPVEE-----GV- 418
LG + +D+GGG Y G + S +N L+EY + E GV
Sbjct: 271 RKLGVKITYVDVGGGLGVDYDGTSSSSDCS----VNYGLEEYANDIVQALREICEEKGVP 326
Query: 419 --SIIAEPGRYYVA 430
II E GR A
Sbjct: 327 HPVIITESGRAITA 340
>gnl|CDD|233247 TIGR01047, nspC, carboxynorspermidine decarboxylase. This protein
is related to diaminopimelate decarboxylase. It is the
last enzyme in norspermidine biosynthesis by an unusual
pathway shown in Vibrio alginolyticus [Central
intermediary metabolism, Polyamine biosynthesis].
Length = 380
Score = 35.9 bits (83), Expect = 0.051
Identities = 15/49 (30%), Positives = 25/49 (51%)
Query: 14 GPTCDGLDKVNDDILLPEMPVGSWLIYRDMGAYTLPVASTFNGFPIPKV 62
G TC D + + + VG +++ DM YT+ +TFNG +P +
Sbjct: 308 GNTCLAGDVMGEYAFDKPLKVGDKIVFLDMIHYTMVKNTTFNGVKLPSL 356
>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 = 34.4 bits (80), Expect = 0.11
Identities = 16/47 (34%), Positives = 24/47 (51%)
Query: 14 GPTCDGLDKVNDDILLPEMPVGSWLIYRDMGAYTLPVASTFNGFPIP 60
G +C D + D + VG L++ DM YT+ +TFNG +P
Sbjct: 294 GNSCLAGDVIGDYSFDEPLQVGDRLVFEDMAHYTMVKTNTFNGVRLP 340
>gnl|CDD|236867 PRK11165, PRK11165, diaminopimelate decarboxylase; Provisional.
Length = 420
Score = 31.8 bits (73), Expect = 1.0
Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 4 RETLVPSSVWGPTCDGLD----KVNDDIL---LPEMPVGSWLIYRDMGAYTLPVASTFNG 56
V + V GP C+ D + + LP++ VG +L++ D GAY ++S +N
Sbjct: 329 EAPTVDTVVAGPLCESGDVFTQQEGGVVETRALPQVQVGDYLVFHDTGAYGASMSSNYNS 388
Query: 57 FP-IPKV 62
P +P+V
Sbjct: 389 RPLLPEV 395
>gnl|CDD|191228 pfam05198, IF3_N, Translation initiation factor IF-3, N-terminal
domain.
Length = 76
Score = 29.0 bits (66), Expect = 1.1
Identities = 19/59 (32%), Positives = 28/59 (47%), Gaps = 17/59 (28%)
Query: 315 QLGMKFGCDPISEAPRLLRLAKSLDLDVVGVSFHVGSGCGDPPV-----FGRAIYSARQ 368
QLG+ +EA LRLA+ LD+V + S DPPV +G+ Y ++
Sbjct: 24 QLGVV----SRAEA---LRLAEEKGLDLVEI-----SPNADPPVCKIMDYGKFKYEQQK 70
>gnl|CDD|235427 PRK05354, PRK05354, arginine decarboxylase; Provisional.
Length = 634
Score = 31.6 bits (73), Expect = 1.3
Identities = 30/100 (30%), Positives = 45/100 (45%), Gaps = 19/100 (19%)
Query: 347 FHVGSGCGDPPVFGRAIYSARQIF-DLGNSLGFSMRVLDLGGGYPG--YTGYSMNRIAEI 403
FH+GS + A+ A + + +L LG ++ LD+GGG G Y G +
Sbjct: 251 FHLGSQIANIRDIKTAVREAARFYVEL-RKLGAPIQYLDVGGGL-GVDYDGTRSQSDSS- 307
Query: 404 INVALDEY-----FPV-----EEGVS---IIAEPGRYYVA 430
+N +L EY + + E GV II+E GR A
Sbjct: 308 VNYSLQEYANDVVYTLKEICEEHGVPHPTIISESGRALTA 347
>gnl|CDD|215795 pfam00215, OMPdecase, Orotidine 5'-phosphate decarboxylase / HUMPS
family. This family includes Orotidine 5'-phosphate
decarboxylase enzymes EC:4.1.1.23 that are involved in
the final step of pyrimidine biosynthesis. The family
also includes enzymes such as hexulose-6-phosphate
synthase. This family appears to be distantly related to
pfam00834.
Length = 217
Score = 29.9 bits (68), Expect = 2.4
Identities = 19/112 (16%), Positives = 30/112 (26%), Gaps = 14/112 (12%)
Query: 270 IRYAAEYG-----IDTMTFDNEIELQKVKQFHPTAQLVIRIR-------CDAEVAQCQLG 317
A EYG + ++ ++LQ+ T ++V R D VA
Sbjct: 97 KEAAEEYGKGLLLVAELSSKGSLDLQEEGDLGYTQEIVHRAADLAAFAGVDGVVASATEP 156
Query: 318 MKFGCDPISEAPRLLRLAKSLDLDVVGVSFH--VGSGCGDPPVFGRAIYSAR 367
+ L V+ D + GR I A
Sbjct: 157 EAALGPDFLLLTPGIGLQGGDAGGQQRVTTPAVAKEAGADIIIVGRGITGAG 208
>gnl|CDD|140327 PTZ00306, PTZ00306, NADH-dependent fumarate reductase; Provisional.
Length = 1167
Score = 30.1 bits (68), Expect = 3.8
Identities = 17/42 (40%), Positives = 21/42 (50%), Gaps = 5/42 (11%)
Query: 216 LDVGEIVRKHEDWKLKLPRVDPYYAVKCNDSQMVLEVLAALG 257
L+ G I RKHED L L V+ Y V V++ L A G
Sbjct: 192 LEEGTIARKHEDAMLDLGGVNKGYTVDY-----VVDRLNAAG 228
>gnl|CDD|200373 TIGR04122, Xnuc_lig_assoc, putative exonuclease, DNA
ligase-associated. Members of this protein family
frequently are found annotated as a putative exonuclease
involved in mRNA processing. This protein is found,
exclusively in bacteria, associated with three other
proteins: an ATP-dependent DNA ligase, a helicase, and
putative phosphoesterase.
Length = 326
Score = 29.1 bits (66), Expect = 5.8
Identities = 14/55 (25%), Positives = 23/55 (41%), Gaps = 9/55 (16%)
Query: 264 SKPISHIRYAAEYGIDTMTFDNEIELQKVK-QFHP------TAQLVIRIRCDAEV 311
+ I +R + I T+ + I + VK HP +AQ +R+ EV
Sbjct: 50 TLAILRLRLGEDIAIQTVAYGETIRINGVKVSLHPAGHVLGSAQ--VRLEYGGEV 102
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.323 0.141 0.445
Gapped
Lambda K H
0.267 0.0859 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 27,754,129
Number of extensions: 2782748
Number of successful extensions: 2201
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2147
Number of HSP's successfully gapped: 52
Length of query: 522
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 421
Effective length of database: 6,457,848
Effective search space: 2718754008
Effective search space used: 2718754008
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 61 (27.0 bits)