RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 037610
(405 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 = 408 bits (1051), Expect = e-142
Identities = 162/371 (43%), Positives = 211/371 (56%), Gaps = 35/371 (9%)
Query: 50 EVPFYLMDLGVVVSLYNHMISNLPMIHPHYAVKCNPEPALLEALAALGSNFDCGSRSEIE 109
E PF ++DLG VV Y LP + P YAVKCNP+PA+L LAALG+ FDC S+ EIE
Sbjct: 1 ETPFLVVDLGDVVRKYRRWKKALPRVRPFYAVKCNPDPAVLRTLAALGAGFDCASKGEIE 60
Query: 110 AVLLLDVSPDRIIYANPCKPVSHIKYAASVGVNLTTVDSVEELDKIRNWHPKSDLLIRIK 169
VL L VSP+RII+ANPCK +S I+YAA +GV L T DS +EL+KI P + LL+RI
Sbjct: 61 LVLGLGVSPERIIFANPCKSISDIRYAAELGVRLFTFDSEDELEKIAKHAPGAKLLLRIA 120
Query: 170 SPDDSGAKYPLDSKYGAGHHPQEIMPLLKAAEASGLSVVGVSFHVGSEATNFAAFRGAIA 229
DDSGA PL K+GA P+E LL+ A+ GL+VVGVSFHVGS+ T+ +A+ AIA
Sbjct: 121 -TDDSGALCPLSRKFGA--DPEEARELLRRAKELGLNVVGVSFHVGSQCTDPSAYVDAIA 177
Query: 230 AAKAVFDTAAR-------------------TSNNKMRKLFKLI---FRELLPGSSLKVIS 267
A+ VFD AA ++ +I E P +++I+
Sbjct: 178 DAREVFDEAAELGFKLKLLDIGGGFPGSYDGVVPSFEEIAAVINRALDEYFPDEGVRIIA 237
Query: 268 EPGRFFAASAFTLYAQIIGKRVRGE---LREYWINDGKFGSLAWVTCDEAIAKCTPLPFA 324
EPGR+ ASAFTL +I KR RG+ R Y++NDG +GS + D L
Sbjct: 238 EPGRYLVASAFTLAVNVIAKRKRGDDDRERWYYLNDGVYGSFNEILFDHIRYPPRVL--- 294
Query: 325 SSFTTSKGLTRTYNSTVFGPTCDAFDEVFTGHKLPE-LEVNDWLVFSEMGAYTTACGTNF 383
Y S+++GPTCD+ D ++ LPE L V DWL+F MGAYTTA + F
Sbjct: 295 ---KDGGRDGELYPSSLWGPTCDSLDVIYEDVLLPEDLAVGDWLLFENMGAYTTAYASTF 351
Query: 384 NGYSTVAIPTY 394
NG+ I
Sbjct: 352 NGFPPPKIVYV 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 = 212 bits (542), Expect = 4e-65
Identities = 126/376 (33%), Positives = 187/376 (49%), Gaps = 49/376 (13%)
Query: 53 FYLMDLGVVVSLYNHMISNLPMIHPHYAVKCNPEPALLEALAALGSNFDCGSRSEIEAVL 112
F++ DLG +V ++ + + I P Y V+CN PA+LE LAALG+ F C S++E+ V
Sbjct: 15 FFVGDLGKIVKKHSQWQTVMAQIKPFYTVRCNSTPAVLEILAALGTGFACSSKNEMALVQ 74
Query: 113 LLDVSPDRIIYANPCKPVSHIKYAASVGVNLTTVDSVEELDKIRNWHPKSDLLIRIKSPD 172
L VSP+ IIY NPCK S IKYAA VGVN+ T D+ EL KI HP + LL+ I + D
Sbjct: 75 ELGVSPENIIYTNPCKQASQIKYAAKVGVNIMTCDNEIELKKIARNHPNAKLLLHIATED 134
Query: 173 DSGAKYPLDSKYGAGHHPQEIMPLLKAAEASGLSVVGVSFHVGSEATNFAAFRGAIAAAK 232
+ G + + G + LL+ A+ + +VGV FHV S + + A++ A+
Sbjct: 135 NIGGE---EMNMKFGTTLKNCRHLLECAKELDVQIVGVKFHVSSSCKEYQTYVHALSDAR 191
Query: 233 AVFDTAA----------------------RTSNNKMRKLFKLIFRELLPGSSLKVISEPG 270
VFD A N+ +R L + F E GS +++I+EPG
Sbjct: 192 CVFDMAEEFGFKMNMLDIGGGFTGSEIQLEEVNHVIRPLLDVYFPE---GSGIQIIAEPG 248
Query: 271 RFFAASAFTLYAQIIGKRV---------RGELRE------YWINDGKFGSLAWVTCDEAI 315
++ +SAFTL +I K+ + Y++NDG +GS A ++
Sbjct: 249 SYYVSSAFTLAVNVIAKKAVENDKHLSSVEKNGSDEPAFVYYMNDGVYGSFASKLSEKLN 308
Query: 316 AKCTPLPFASSFTTSKGLTRTYNSTVFGPTCDAFDEVFTGHKLPELEVNDWLVFSEMGAY 375
TP K + S+++GP+CD D++ LPEL V DWL+F MGA
Sbjct: 309 T--TP----EVHKKYKEDEPLFTSSLWGPSCDELDQIVESCLLPELNVGDWLIFDNMGAG 362
Query: 376 TTACGTNFNGYSTVAI 391
+ + FN + AI
Sbjct: 363 SLHEPSTFNDFQRPAI 378
>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 = 208 bits (531), Expect = 1e-63
Identities = 101/366 (27%), Positives = 159/366 (43%), Gaps = 40/366 (10%)
Query: 52 PFYLMDLGVVVSLYNHMISNLPMIH-PHYAVKCNPEPALLEALAALGSNFDCGSRSEIEA 110
PFY+ DL ++ + Y + LP YAVK NP P +L LA G+ FD S+ E+
Sbjct: 2 PFYVYDLDIIRAHYAALKEALPSGVKLFYAVKANPNPHVLRTLAEAGTGFDVASKGELAL 61
Query: 111 VLLLDVSPDRIIYANPCKPVSHIKYAASVGVNLTTVDSVEELDKIRNWHPKS----DLLI 166
L V P+RII+ P K VS I+ A + GV+ VDS++EL+++ K +L+
Sbjct: 62 ALAAGVPPERIIFTGPAKSVSEIEAALASGVDHIVVDSLDELERLNELAKKLGPKARILL 121
Query: 167 RIKSPDDSGAKYP----LDSKYGAGHHPQEIMPLLKAAEASGLSVVGVSFHVGSEATNFA 222
R+ +G L SK+G E L+ A+ L +VG+ FHVGS+ +
Sbjct: 122 RVNPDVSAGTHKISTGGLKSKFGLS--LSEARAALERAKELDLRLVGLHFHVGSQILDLE 179
Query: 223 AFRGAIAAAKAVFDTAAR----------------TSNNK-------MRKLFKLIFRELLP 259
A++ A+ + + + + + L+ +
Sbjct: 180 TIVQALSDARELIEELVEMGFPLEMLDLGGGLGIPYDEQPLDFEEYAALINPLLKKYFPN 239
Query: 260 GSSLKVISEPGRFFAASAFTLYAQIIGKRVRGELREYWINDGKFGSLAWVTCDEAIAKCT 319
+ +I EPGR+ A A L +++ +V G ++ G S + A
Sbjct: 240 DPGVTLILEPGRYIVAQAGVLVTRVVAVKVNGGRFFAVVDGGMNHSFRPALAYD--AYHP 297
Query: 320 PLPFASSFTTSKGLTRTYNSTVFGPTCDAFDEVFTGHKLPELEVNDWLVFSEMGAYTTAC 379
P + +T+ GP CD+ D + LPELEV D LVF +MGAY +
Sbjct: 298 ITPLKAPGPDEP----LVPATLAGPLCDSGDVIGRDRLLPELEVGDLLVFEDMGAYGFSE 353
Query: 380 GTNFNG 385
+NFN
Sbjct: 354 SSNFNS 359
>gnl|CDD|223098 COG0019, LysA, Diaminopimelate decarboxylase [Amino acid transport
and metabolism].
Length = 394
Score = 203 bits (518), Expect = 2e-61
Identities = 108/394 (27%), Positives = 163/394 (41%), Gaps = 45/394 (11%)
Query: 26 TTVVTKDELTEFMQSTILKRQEFDEVPFYLMDLGVVVSLYNHMISNLPMIH--PHYAVKC 83
ELT +EF P Y+ D + + S P YAVK
Sbjct: 3 FFRNKDGELTIEGVDLPALAEEF-GTPVYVYDEATLRRNARELKSAFPGSGAKVFYAVKA 61
Query: 84 NPEPALLEALAALGSNFDCGSRSEIEAVLLLDVSPDRIIYANPCKPVSHIKYAASVGVNL 143
N PA+L LA GS FD S E+E L P+RI+++ P K I +A +G+ L
Sbjct: 62 NSNPAILRLLAEEGSGFDVASLGELELALAAGFPPERIVFSGPAKSEEEIAFALELGIKL 121
Query: 144 TTVDSVEELDKIRNWHP--KSDLLIRIKSPD------DSGAKYPLDSKYGAGHHPQEIMP 195
VDS EEL+++ P + + +RI +P + A SK+G + +
Sbjct: 122 INVDSEEELERLSAIAPGLVARVSLRI-NPGVSAGTHEYIATGGKSSKFGISPE-EALDV 179
Query: 196 LLKAAEASGLSVVGVSFHVGSEATNFAAFRGAIAAAKAVFDTAARTSNNKMRKL------ 249
L +AA+ GL +VG+ FH+GS+ T+ F A+A + +F A ++ L
Sbjct: 180 LERAAKLLGLELVGLHFHIGSQITDLDPFEEALAKVEELFGRLAEELGIQLEWLNLGGGL 239
Query: 250 ------------FKLIFRELLP-----GSSLKVISEPGRFFAASAFTLYAQIIGKRVRGE 292
+ L +++I EPGR A+A L +++ + GE
Sbjct: 240 GITYEDEYDPPDLAAYAKALKEAFGEYAEDVELILEPGRAIVANAGVLVTEVLDVKENGE 299
Query: 293 LREYWINDGKFGSLAWVTCDEAIAKCTPLPFASSFTTSKGLTRTYNSTVFGPTCDAFDEV 352
R + I DG L A + T Y V GPTC++ D +
Sbjct: 300 -RNFVIVDGGMNDLMRPALYGAY-----HHIRLNRTDEDAEREEY--DVVGPTCESGDVL 351
Query: 353 FTGHKLPE-LEVNDWLVFSEMGAYTTACGTNFNG 385
LPE L+V D LV + GAY + +N+NG
Sbjct: 352 ARDRALPEPLKVGDLLVILDAGAYGASMSSNYNG 385
>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 = 192 bits (490), Expect = 3e-59
Identities = 94/234 (40%), Positives = 122/234 (52%), Gaps = 34/234 (14%)
Query: 72 LPMIHPHYAVKCNPEPALLEALAALGSNFDCGSRSEIEAVLLLDVSPDRIIYANPCKPVS 131
LP I P YAVK N +PA+L LA LG FDC S+ E+E VL V P+RII+ANPCK S
Sbjct: 17 LPRIQPFYAVKANSDPAVLRLLAELGLGFDCASKGELERVLAAGVPPERIIFANPCKSRS 76
Query: 132 HIKYAASVGVNLTTVDSVEELDKIRNWHPKSDLLIRIKSPDDSGAKYPL----DSKYGAG 187
++YA GV TVD+VEEL+K+ P++ LL+R+K D+ A L DSK+GA
Sbjct: 77 ELRYALEHGVVCVTVDNVEELEKLARLAPEARLLLRVKPDVDAHAHCYLSTGQDSKFGAD 136
Query: 188 HHPQEIMPLLKAAEASGLSVVGVSFHVGSEATNFAAFRGAIAAAKAVFDTAAR------- 240
+E LLKAA+ GL+VVGV FHVGS T+ AF A A+ VFD A
Sbjct: 137 --LEEAEALLKAAKELGLNVVGVHFHVGSGCTDAEAFVKAARDARNVFDQGAELGFELKI 194
Query: 241 -----------TSNNK-------MRKLFKLIFRELLPGSSLKVISEPGRFFAAS 276
T + + +F +I+EPGR+ A
Sbjct: 195 LDLGGGFGVDYTGAEDFEEYAEVINAALEEVFPHDPH---PTIIAEPGRYIVAP 245
>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 = 117 bits (294), Expect = 7e-31
Identities = 64/212 (30%), Positives = 95/212 (44%), Gaps = 31/212 (14%)
Query: 75 IHPHYAVKCNPEPALLEALAALGSNFDCGSRSEIEAVLLLDVSPDRIIYANPCKPVSHIK 134
I VK N P + LAALG+ FD S E + + P+ I++ PCK VS ++
Sbjct: 16 ITLFAVVKANANPEVARTLAALGTGFDVASLGEALLLRAAGIPPEPILFLGPCKQVSELE 75
Query: 135 YAASVGVNLTTVDSVEELDKIR----NWHPKSDLLIRIKSPDDSGAKYPLDSKYGAGHHP 190
AA GV + TVDS+EEL+K+ P + +L+RI D+G + + K+G P
Sbjct: 76 DAAEQGVIVVTVDSLEELEKLEEAALKAGPPARVLLRI----DTGDE---NGKFGV--RP 126
Query: 191 QEIMPLLKAA-EASGLSVVGVSFHVGSEATNFAAFRGAIAAAKAVFDTAARTSNNKMRKL 249
+E+ LL+ A E L +VG+ H GS +++ F A++ A D
Sbjct: 127 EELKALLERAKELPHLRLVGLHTHFGSADEDYSPFVEALSRFVAALDQLG-------ELG 179
Query: 250 FKL----------IFRELLPGSSLKVISEPGR 271
L I +I EPGR
Sbjct: 180 IDLEQLSIGGSFAILYLQELPLGTFIIVEPGR 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 = 116 bits (294), Expect = 2e-29
Identities = 89/388 (22%), Positives = 143/388 (36%), Gaps = 81/388 (20%)
Query: 52 PFYLMDLGVVVSLYNHMISNLPMI--HPHYAVKCNPEPALLEALAALGSNFDCGSRSEIE 109
P Y+ D + Y + YAVK N A+L+ LA G D S E+
Sbjct: 4 PLYVYDEATIRENYRRLKEAFSGPGFKICYAVKANSNLAILKLLAEEGLGADVVSGGELY 63
Query: 110 AVLLLDVSPDRIIYANPCKPVSHIKYAASVGVNLTTVDSVEELDKI----RNWHPKSDLL 165
L P+RI++ K ++ A +G+ VDS+ EL+++ + +
Sbjct: 64 RALKAGFPPERIVFTGNGKSDEELELALELGILRINVDSLSELERLGEIAPELGKGAPVA 123
Query: 166 IRIKSPD---------DSGAKYPLDSKYGAGHHPQEIMPLLK-AAEASGLSVVGVSFHVG 215
+R+ +P +G K DSK+G ++ + + A E GL +VG+ H+G
Sbjct: 124 LRV-NPGVDAGTHPYISTGGK---DSKFGI--PLEQALEAYRRAKELPGLKLVGLHCHIG 177
Query: 216 SEATNFAAFRGAIAAAKAVFDTAARTSN-------------------------------N 244
S+ + F AA+ + D AA
Sbjct: 178 SQILDLEPFV---EAAEKLLDLAAELRELGIDLEFLDLGGGLGIPYRDEDEPLDIEEYAE 234
Query: 245 KMRKLFKLIFRELLPGSSLKVISEPGRFFAASAFTLYAQIIG-KRVRGELREYWINDGKF 303
+ + K G LK+I EPGR+ A+A L ++ K G + + D
Sbjct: 235 AIAEALK---ELCEGGPDLKLIIEPGRYIVANAGVLLTRVGYVKETGG--KTFVGVDAGM 289
Query: 304 GSLAWVTCDEAI------AKCTPLPFASSFTTSKGLTRTYNSTVFGPTCDAFDEVFTGHK 357
L I A +P +G T V GP C++ D +
Sbjct: 290 NDL--------IRPALYGAYHEIVPVNK---PGEGETEKV--DVVGPICESGDVFAKDRE 336
Query: 358 LPELEVNDWLVFSEMGAYTTACGTNFNG 385
LPE+E D L + GAY + +N+N
Sbjct: 337 LPEVEEGDLLAIHDAGAYGYSMSSNYNS 364
>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 = 102 bits (257), Expect = 4e-24
Identities = 83/359 (23%), Positives = 134/359 (37%), Gaps = 79/359 (22%)
Query: 77 PHYAVKCNPEPALLEALAALGSNFDCGSRSEIEAVLLLDVSPDRIIYANPCKPVSHIKYA 136
YAVK N A+L LA LGS FD S E+ L P++I+++ K + ++ A
Sbjct: 52 VCYAVKANSNLAVLRLLAELGSGFDVVSGGELYRALAAGFPPEKIVFSGNGKSRAELERA 111
Query: 137 ASVGVNLTTVDSVEELDKIRNWHP----KSDLLIRIKSPDDSGAKYP------LDSKYGA 186
+G+ VDS EL+++ P K+ + +R+ +P +P DSK+G
Sbjct: 112 LELGI-CINVDSFSELERLNEIAPELGKKARISLRV-NPGVDAKTHPYISTGLKDSKFGI 169
Query: 187 GHHPQEIMPLLKAAEASGLSVVGVSFHVGSEATNFAAFRGAIAAAKAVFDTAAR------ 240
L A + L +VG+ H+GS+ T+ + F + AA+ V A
Sbjct: 170 DVEEALEAYLY-ALQLPHLELVGIHCHIGSQITDLSPF---VEAAEKVVKLAESLAEGID 225
Query: 241 --------------TSNNK-------MRKLFKLIFRELLPGSSLKVISEPGRFFAASAFT 279
T + + + + G K+I EPGR A+A
Sbjct: 226 LEFLDLGGGLGIPYTPEEEPPDLSEYAQAILNALEGYADLGLDPKLILEPGRSIVANAGV 285
Query: 280 LYAQIIGKRVRGELREYWINDGKFG--------------SLAWVTCDEAIAKCTPLPFAS 325
L ++ + G R + I D + T D
Sbjct: 286 LLTRVGFVKETGS-RNFVIVDAGMNDLIRPALYGAYHHIIVLNRTNDAPTEVA------- 337
Query: 326 SFTTSKGLTRTYNSTVFGPTCDAFDEVFTGHKLPELEVNDWLVFSEMGAYTTACGTNFN 384
V GP C++ D + +LPE+E D L + GAY + +N+N
Sbjct: 338 --------------DVVGPVCESGDVLAKDRELPEVEPGDLLAVFDAGAYGFSMSSNYN 382
>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 = 90.8 bits (226), Expect = 4e-20
Identities = 89/395 (22%), Positives = 144/395 (36%), Gaps = 69/395 (17%)
Query: 52 PFYLMDLGVVVSLYNHMISNLPMIHPH----YAVKCNPEPALLEALAALGSNFDCGSRSE 107
PF++ D + Y ++ +P+ Y+ K N PA+ + L G + S E
Sbjct: 8 PFFVFDEDALRENYRELLGAFKKRYPNVVIAYSYKTNYLPAICKILHEEGGYAEVVSAME 67
Query: 108 IEAVLLLDVSPDRIIYANPCKPVSHIKYAASVGVNLTTVDSVEELDKIRNWHPKSDLLIR 167
E L L V RII+ P K ++ A G + +DS +EL++I + + +
Sbjct: 68 YELALKLGVPGKRIIFNGPYKSKEELEKALEEGALI-NIDSFDELERILEIAKELGRVAK 126
Query: 168 --IKSPDDSGAKYPLDSKYG--AGHHPQEIMPLLKAAEASGLSVVGVSFHVGSEATNFAA 223
I+ + G + S++G + + + L K E+ LS+VG+ HVGS N A
Sbjct: 127 VGIRLNMNYG--NNVWSRFGFDIEENGEALAALKKIQESKNLSLVGLHCHVGSNILNPEA 184
Query: 224 FRGAIAAAKAVFDTAART-----------------SNNKMRKLFK--------------L 252
+ AAAK + + R + + +
Sbjct: 185 YS---AAAKKLIELLDRLFGLELEYLDLGGGFPAKTPLSLAYPQEDTVPDPEDYAEAIAS 241
Query: 253 IFRELLP--GSSLKVISEPGRFFAASAFTLYAQIIG-KRVRGELREYWINDGKFGSLAWV 309
+E + K+I EPGR A L +++ K G R + D + +
Sbjct: 242 TLKEYYANKENKPKLILEPGRALVDDAGYLLGRVVAVKNRYG--RNIAVTD---AGINNI 296
Query: 310 TC----DEAIAKCTPLPFASSFTTSKGLTRTYNSTVFGPTCDAFDEVFTGHKLPELEVND 365
I L TSK N V+G C D +F LP L V D
Sbjct: 297 PTIFWYHHPI---LVLRPGKEDPTSK------NYDVYGFNCMESDVLFPNVPLPPLNVGD 347
Query: 366 WLVFSEMGAYTTACGTNFNGYSTVAIPTYVVRSNQ 400
L +GAY T N + Y++ +N
Sbjct: 348 ILAIRNVGAYNM---TQSNQFIRPRPAVYLIDNNG 379
>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 = 78.8 bits (195), Expect = 5e-18
Identities = 39/115 (33%), Positives = 58/115 (50%), Gaps = 10/115 (8%)
Query: 279 TLYAQIIGKRVRGELRE-YWINDGKFGSLAWVTCDEAIAKCTPLPFASSFTTSKGLTRTY 337
TL ++I + RG+ R+ +++DG +GS +A+ P+
Sbjct: 1 TLVTEVIDVKERGDDRKFVYLDDGVYGSPDPAL-YDALHPILPVSRLDD-------EPLR 52
Query: 338 NSTVFGPTCDAFDEVFTGHKLP-ELEVNDWLVFSEMGAYTTACGTNFNGYSTVAI 391
T+ GPTCD+ D + LP ELEV DWLVF + GAYT + +NFNG+ A
Sbjct: 53 PYTLAGPTCDSGDVLARDVSLPLELEVGDWLVFFDAGAYTISLSSNFNGFPRPAE 107
>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 = 84.2 bits (209), Expect = 7e-18
Identities = 92/390 (23%), Positives = 146/390 (37%), Gaps = 84/390 (21%)
Query: 52 PFYLMDLGVVVSLYNHMISNLP-MIHPHYAVKCNPEPALLEALAALGSNFDCGSRSEIEA 110
PFY+ D V Y + + LP I +Y++K NP PAL+ L LG + S E+
Sbjct: 8 PFYVYDRDRVRERYAALRAALPPAIEIYYSLKANPNPALVAHLRQLGDGAEVASAGELAL 67
Query: 111 VLLLDVSPDRIIYANPCKPVSHIKYAASVGVNLTTVDSVEELDKI------RNWHPKSDL 164
L V P++I++A P K + ++ A G+ V+S+EEL++I +
Sbjct: 68 ALEAGVPPEKILFAGPGKSDAELRRAIEAGIGTINVESLEELERIDALAEEHGVVA--RV 125
Query: 165 LIRI---KSPDDSGAKY---PLDSKYG--AGHHPQEIMPLLKAAEASGLSVVGVSFHVGS 216
+RI SG K P S++G P ++ + A L VG+ + G+
Sbjct: 126 ALRINPDFELKGSGMKMGGGP--SQFGIDVEELP-AVLARIAALP--NLRFVGLHIYPGT 180
Query: 217 EATNFAAFRGAIAAAKAVFDTAARTSNNKMRKLFKLI----------------------- 253
+ + A I A + A R + L L
Sbjct: 181 QILDADAL---IEAFRQTLALALRLAEELGLPLEFLDLGGGFGIPYFPGETPLDLEALGA 237
Query: 254 --------FRELLPGSSLKVISEPGRFFAASAFTLYAQIIG-KRVRGELREYWIND---- 300
+ LPG+ +V+ E GR+ A +++ K RGE + + D
Sbjct: 238 ALAALLAELGDRLPGT--RVVLELGRYLVGEAGVYVTRVLDRKVSRGET--FLVTDGGMH 293
Query: 301 ------GKFGSLAWVTCDEAIAKCTPLPFASSFTTSKGLTRTYNSTVFGPTCDAFDEVFT 354
G FG + + + PL + T TV GP C D +
Sbjct: 294 HHLAASGNFGQV--------LRRNYPLAILNRMGG--EERETV--TVVGPLCTPLDLLGR 341
Query: 355 GHKLPELEVNDWLVFSEMGAY-TTACGTNF 383
+LP LE D + + GAY +A F
Sbjct: 342 NVELPPLEPGDLVAVLQSGAYGLSASPLAF 371
>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 = 79.4 bits (196), Expect = 3e-16
Identities = 96/391 (24%), Positives = 144/391 (36%), Gaps = 82/391 (20%)
Query: 52 PFYLMDLGVVVSLYNHMISNLP-MIHPHYAVKCNPEPALLEALAALGSNFDCGSRSEIEA 110
PFY D G+V + LP + HYAVK NP PALL +A L FD S E+
Sbjct: 26 PFYAYDRGLVSERVAALRKALPEELAIHYAVKANPMPALLAHMAPLVDGFDVASAGELAV 85
Query: 111 VLLLDVSPDRIIYANPCKPVSHIKYAASVGVNLTTVDSVEELDKIRNWHPKSDL----LI 166
L P I +A P K + ++ A + GV L V+S+ EL+++ L +
Sbjct: 86 ALDTGYDPGCISFAGPGKTDAELRRALAAGV-LINVESLRELNRLAALSEALGLRARVAV 144
Query: 167 RIKSPD----DSGAKYPLDSKYGAGHHP-----QEIMPLLKAAEASGLSVVGVSFHVGSE 217
R+ +PD SG K G G +++ L +A+ L G GS+
Sbjct: 145 RV-NPDFELKGSGM------KMGGGAKQFGIDAEQVPAALAFIKAADLDFQGFHIFAGSQ 197
Query: 218 ATNFAAFRGAIAAAKA-VFDTAARTSN--------------------------------N 244
N AI A+A A R +
Sbjct: 198 NLN----AEAIIEAQAKTLALALRLAESAPAPVRVINIGGGFGIPYFPGNPPLDLAPVGA 253
Query: 245 KMRKLFKLIFRELLPGSSLKVISEPGRFFAASAFTLYAQIIG-KRVRGELREYWINDGKF 303
+ LF R+ LP + + E GR+ A ++I K RGE + + DG
Sbjct: 254 ALAALFAR-LRDALPEVEI--LLELGRYLVGEAGIYVCRVIDRKISRGET--FLVTDGGL 308
Query: 304 -------GSLAWVTCDEAIAKCTPLPFASSFTTSKGLTRTYNSTVFGPTCDAFDEVFTGH 356
G+ V I + P+ + + +++ GP C D +
Sbjct: 309 HHHLSASGNFGQV-----IRRNYPVVIGNRIGGAV----REIASIVGPLCTPLDLLAEKG 359
Query: 357 KLPELEVNDWLVFSEMGAY-TTACGTNFNGY 386
LP E D +V + GAY +A F G+
Sbjct: 360 TLPVAEPGDLVVIFQSGAYGASASPLAFLGH 390
>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 = 77.9 bits (192), Expect = 8e-16
Identities = 93/382 (24%), Positives = 145/382 (37%), Gaps = 67/382 (17%)
Query: 43 LKRQEFDEVPFYLMDLGVVVSLYNHMISNLPMI-HPHYAVKCNPEPALLEALAALGSNFD 101
L R D P Y+ DL V +S L + YA+K NP P +L L G F+
Sbjct: 4 LLRLAPDVGPCYVYDL-ETVRARARQVSALKAVDSLFYAIKANPHPDVLRTLEEAGLGFE 62
Query: 102 CGSRSEIEAVLLL--DVSPDRIIYANPCKPVSHIKYAASVGVNLTTVDSVEELDKIRNWH 159
C S E++ VL L D+ P R+++ S + A +GVN+ TVD++ L R W
Sbjct: 63 CVSIGELDLVLKLFPDLDPRRVLFTPNFAARSEYEQALELGVNV-TVDNLHPL---REWP 118
Query: 160 P---KSDLLIRIKSPDDSGAKYPLDSKYGAGHH---------------PQEIMPLLKAAE 201
++++RI D G GHH E+ A+
Sbjct: 119 ELFRGREVILRI------------DPGQGEGHHKHVRTGGPESKFGLDVDELDEARDLAK 166
Query: 202 ASGLSVVGVSFHVGSEATNFAAFR--GAIAAAKAVFDTAARTSN----------NKMRKL 249
+G+ V+G+ H GS + + G A+ A A R N R +
Sbjct: 167 KAGIIVIGLHAHSGSGVEDTDHWARHGDYLASLARHFPAVRILNVGGGLGIPEAPGGRPI 226
Query: 250 -FKLIFREL------LPGSSLKVISEPGRFFAASAFTLYAQIIGKRVRGELREYWINDGK 302
+ L P ++ EPGRF A + L A++ + + +R + G
Sbjct: 227 DLDALDAALAAAKAAHPQ--YQLWMEPGRFIVAESGVLLARVTQIKHKDGVRFVGLETG- 283
Query: 303 FGSLAWVTCDEAIAKCTPLPFASSFTTSKGLTRTYNSTVFGPTCDAFDEVFTGHKLPELE 362
SL A + L + N+ V GP C++ D + LPE E
Sbjct: 284 MNSLIRPALYGAYHEIVNL-------SRLDEPPAGNADVVGPICESGDVLGRDRLLPETE 336
Query: 363 VNDWLVFSEMGAYTTACGTNFN 384
D ++ + GAY + +N
Sbjct: 337 EGDVILIANAGAYGFCMASTYN 358
>gnl|CDD|236358 PRK08961, PRK08961, bifunctional aspartate kinase/diaminopimelate
decarboxylase protein; Provisional.
Length = 861
Score = 75.1 bits (185), Expect = 2e-14
Identities = 88/387 (22%), Positives = 147/387 (37%), Gaps = 89/387 (22%)
Query: 49 DEVPFYLMDLGVVVSLYNHMISNLPMIHP----HYAVKCNPEPALLEALAALGSNFDCGS 104
P Y+ L V + L + YA+K NP PA+L L G F+C S
Sbjct: 501 AGSPCYVYHLPTVRA----RARALAALAAVDQRFYAIKANPHPAILRTLEEEGFGFECVS 556
Query: 105 RSEIEAV--LLLDVSPDRIIYANPCKPVSHIKYAASVGVNLTTVDSVEELDKIRNWHPK- 161
E+ V L ++SP+R+++ P + + A ++GV + T+D+VE L RNW P+
Sbjct: 557 IGELRRVFELFPELSPERVLFTPNFAPRAEYEAAFALGVTV-TLDNVEPL---RNW-PEL 611
Query: 162 ---SDLLIRIKSPDDSGAKYPLDSKYGAGHH---------------PQEIMPLLKAAEAS 203
++ +RI D +G GHH I + A+
Sbjct: 612 FRGREVWLRI------------DPGHGDGHHEKVRTGGKESKFGLSQTRIDEFVDLAKTL 659
Query: 204 GLSVVGVSFHVGS----------EATNFAAFRGAIAAAKAV-------FDTAARTSNNKM 246
G++VVG+ H+GS A A+F + + +A +
Sbjct: 660 GITVVGLHAHLGSGIETGEHWRRMADELASFARRFPDVRTIDLGGGLGIPESAGDEPFDL 719
Query: 247 RKLFKLI--FRELLPGSSLKVISEPGRFFAASAFTLYAQIIGKRVRGELREYWINDGKFG 304
L + + PG L + EPGR+ A A L A++ + + +R + G
Sbjct: 720 DALDAGLAEVKAQHPGYQLWI--EPGRYLVAEAGVLLARVTQVKEKDGVRRVGLETG-MN 776
Query: 305 SL-------AWVTCDEAIAKCTPLPFASSFTTSKGLTRTYNSTVFGPTCDAFDEVFTGHK 357
SL A+ I + L + V GP C++ D + +
Sbjct: 777 SLIRPALYGAY----HEIVNLSRL----------DEPAAGTADVVGPICESSDVLGKRRR 822
Query: 358 LPELEVNDWLVFSEMGAYTTACGTNFN 384
LP D ++ + GAY + + +N
Sbjct: 823 LPATAEGDVILIANAGAYGYSMSSTYN 849
>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 = 71.7 bits (176), Expect = 1e-13
Identities = 84/400 (21%), Positives = 142/400 (35%), Gaps = 89/400 (22%)
Query: 55 LMDLGVVVSLYNHMISNLPMIHPH-YAVKCNPEPALLEALAALGSNFDCGSRSEIEAVLL 113
L DL +L + + P H +AVK NP +L LA G+ + S E+E L
Sbjct: 7 LYDLDGFRALVARLTAAFPAPVLHTFAVKANPLVPVLRLLAEAGAGAEVASPGELELALA 66
Query: 114 LDVSPDRIIYANPCKPVSHIKYAASVGVNLTTVDSVEELDKI-----RNWHPKSDLLIRI 168
P+RI++ +P K + ++ A +GV + +D+ +EL++I S + +R+
Sbjct: 67 AGFPPERIVFDSPAKTRAELREALELGVAI-NIDNFQELERIDALVAEFKEASSRIGLRV 125
Query: 169 KSPDDSGAKYPL-----DSKYGAG---HHPQEIMPLLKAAEASGLSVVGVSFHVGSEATN 220
+G L SK+G EI+ A A + G+ HVGS+
Sbjct: 126 NPQVGAGKIGALSTATATSKFGVALEDGARDEII----DAFARRPWLNGLHVHVGSQG-- 179
Query: 221 FAAFRGAIAAAKAVFDTAARTSNNKMRKL--------------------------FKLIF 254
+ V D A N ++ + +
Sbjct: 180 -CELSLLAEGIRRVVDLAEEI-NRRVGRRQITRIDIGGGLPVNFESEDITPTFADYAAAL 237
Query: 255 RELLPG---SSLKVISEPGRFFAASAFTLYAQIIGKRVRGELREYWINDGKFGSLAWVTC 311
+ +P ++++E GR A T+ + RV EY + G
Sbjct: 238 KAAVPELFDGRYQLVTEFGRSLLAKCGTIVS-----RV-----EYTKSSG---------- 277
Query: 312 DEAIAKC------------TPLPFASSFT--TSKGLTRTYN---STVFGPTCDAFDEVFT 354
IA P + T + G +T + V GP C A D +
Sbjct: 278 GRRIAITHAGAQVATRTAYAPDDWPLRVTVFDANGEPKTGPEVVTDVAGPCCFAGDVLAK 337
Query: 355 GHKLPELEVNDWLVFSEMGAYTTACGTNFNGYSTVAIPTY 394
LP LE D++ + GAY + +++N A+
Sbjct: 338 ERALPPLEPGDYVAVHDTGAYYFSSHSSYNSLPRPAVYGV 377
>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 = 71.1 bits (175), Expect = 2e-13
Identities = 44/161 (27%), Positives = 68/161 (42%), Gaps = 17/161 (10%)
Query: 77 PHYAVKCNPEPALLEALAALGSNFDCGSRSEIEAVLLLDVSPDRIIYANPCKPVSHIKYA 136
++A K N AL+ A AA G D S +E+ L V DRI+ P K + A
Sbjct: 40 VYFARKANKSLALVRAAAAAGIGVDVASLAELRQALAAGVRGDRIVATGPAKTDEFLWLA 99
Query: 137 ASVGVNLTTVDSVEELDKI-----RNWHPKSDLLIRIKSPDDSGAKYPLDSKYGAGHHPQ 191
G VDS++ELD++ + +L+R+ S L S++G
Sbjct: 100 VRHGA-TIAVDSLDELDRLLALARGYTTGPARVLLRL-----SPFPASLPSRFGMP--AA 151
Query: 192 EIMPLLK--AAEASGLSVVGVSFHVG--SEATNFAAFRGAI 228
E+ L+ A + +VG FH+ S A AA + +
Sbjct: 152 EVRTALERLAQLRERVRLVGFHFHLDGYSAAQRVAALQECL 192
>gnl|CDD|178152 PLN02537, PLN02537, diaminopimelate decarboxylase.
Length = 410
Score = 64.4 bits (157), Expect = 3e-11
Identities = 94/379 (24%), Positives = 145/379 (38%), Gaps = 54/379 (14%)
Query: 45 RQEFDEVPFYLMDLGVV---VSLYNHMISNLPMIHPHYAVKCNPEPALLEALAALGSNFD 101
+ ++ PFYL + Y + L I YA+K N +LE L LG
Sbjct: 12 MESVEKRPFYLYSKPQITRNYEAYKEALEGLRSI-IGYAIKANNNLKILEHLRELGCGAV 70
Query: 102 CGSRSEIEAVLLLDVSPDRIIYANPCKPVSHIKYAASVGVNLTTVDSVEELDKI----RN 157
S +E+ L P R I+ K + + AA GV VDS +L+ I R
Sbjct: 71 LVSGNELRLALRAGFDPTRCIFNGNGKLLEDLVLAAQEGV-FVNVDSEFDLENIVEAARI 129
Query: 158 WHPKSDLLIRIKSPDDSGAKYPL------DSKYGA-GHHPQEIMPLLKAAEASGLSVVGV 210
K ++L+RI +PD +P +SK+G Q + +K A + L +VG
Sbjct: 130 AGKKVNVLLRI-NPDVDPQVHPYVATGNKNSKFGIRNEKLQWFLDAVK-AHPNELKLVGA 187
Query: 211 SFHVGSEATNFAAFRGAIAAAKAVFDTAARTSNNKMRKL--------------------F 250
H+GS T FR A A + R ++ L
Sbjct: 188 HCHLGSTITKVDIFRDA-AVLMVNYVDEIRAQGFELSYLNIGGGLGIDYYHAGAVLPTPR 246
Query: 251 KLI--FRELLPGSSLKVISEPGRFFAASAFTLYAQIIGKRVRGELREYWINDGKFGSLAW 308
LI REL+ L +I EPGR A+ ++ G + G + + + DG L
Sbjct: 247 DLIDTVRELVLSRDLTLIIEPGRSLIANTCCFVNRVTGVKTNGT-KNFIVIDGSMAELIR 305
Query: 309 VTCDEA---IAKCTPLPFASSFTTSKGLTRTYNSTVFGPTCDAFDEVFTGHKLPELEVND 365
+ +A I +P P T++ V GP C++ D + +LP
Sbjct: 306 PSLYDAYQHIELVSPPP-------PDAEVSTFD--VVGPVCESADFLGKDRELPTPPKGA 356
Query: 366 WLVFSEMGAYTTACGTNFN 384
LV + GAY + + +N
Sbjct: 357 GLVVHDAGAYCMSMASTYN 375
>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 = 56.5 bits (137), Expect = 8e-09
Identities = 50/221 (22%), Positives = 86/221 (38%), Gaps = 26/221 (11%)
Query: 50 EVPFYLMDLGVVVSLYNHMISNLP-MIHPHYAVKCNPEPALLEALAALGSNFDCGSRSEI 108
+ Y+ DL + + + ++LP YA+K N +P +L ALA F+ S EI
Sbjct: 1 PLCAYVYDLAALRAHARALRASLPPGCELFYAIKANSDPPILRALAPHVDGFEVASGGEI 60
Query: 109 EAVLLLDVSPD-RIIYANPCKPVSHIKYAASVGVNLTTVDSVEELDKI----RNWHPKSD 163
V PD +I+ P K S + A + GV V+S EL ++ R +
Sbjct: 61 AHV--RAAVPDAPLIFGGPGKTDSELAQALAQGVERIHVESELELRRLNAVARRAGRTAP 118
Query: 164 LLIR--IKSPDDSGAKYPLDSKYGA-GHHPQEIMPLLKAA-EASGLSVVGVSFHVGS--- 216
+L+R + PD + + + G ++ L+ + + + G FH+ S
Sbjct: 119 VLLRVNLALPDLPSSTLTMGGQPTPFGIDEADLPDALELLRDLPNIRLRGFHFHLMSHNL 178
Query: 217 EATNFAAFRGAIAAAKAVFDTAARTSNNKMRKLFKLIFREL 257
+A A KA +TA + L +
Sbjct: 179 DAAAHLAL------VKAYLETARQ-----WAAEHGLDLDVV 208
>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 = 54.5 bits (132), Expect = 4e-08
Identities = 43/171 (25%), Positives = 79/171 (46%), Gaps = 20/171 (11%)
Query: 79 YAVKCNPEPALLEALAALGSNFD----CGSRSEIEAVLLLDVSPDRIIYANPCKPVSHIK 134
Y +K N + ++E + G ++ GS+ E+ A L L +PD +I N K +I+
Sbjct: 43 YPIKVNQQREVVEEIVKAGKRYNIGLEAGSKPELLAALALLKTPDALIICNGYKDDEYIE 102
Query: 135 ---YAASVGVNLT-TVDSVEELDKI----RNWHPKSDLLIRIKSPDDSGAKY----PLDS 182
A +G N+ ++ + ELD I + K L +RIK K+ S
Sbjct: 103 LALLARKLGHNVIIVIEKLSELDLILELAKKLGVKPLLGVRIKLASKGSGKWQESGGDRS 162
Query: 183 KYGAGHHPQEIMPLLKAAEASGL--SVVGVSFHVGSEATNFAAFRGAIAAA 231
K+G EI+ +++ + +G+ + + FH+GS+ T+ + A+ A
Sbjct: 163 KFGLT--ASEILEVVEKLKEAGMLDRLKLLHFHIGSQITDIRRIKSALREA 211
>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 = 45.4 bits (108), Expect = 4e-05
Identities = 40/174 (22%), Positives = 73/174 (41%), Gaps = 26/174 (14%)
Query: 79 YAVKCNPEPALLEALAALGSNF----DCGSRSEIEAVLLLDVSPDRIIYANPCKPVSHIK 134
Y +K N ++E + A G + GS+ E+ A + P I N K +I+
Sbjct: 95 YPIKVNQHRRVVEDIVASGKGEPYGLEAGSKPELMAAMAYATKPGAPIVCNGYKDREYIE 154
Query: 135 ---YAASVGVNLT-TVDSVEELDKI------RNWHPKSDLLIRIKSP-----DDSGAKYP 179
+G N+ ++ + ELD + PK L R+ S SG +
Sbjct: 155 LALIGRKLGHNVFIVIEKLSELDLVIDEAKKLGVKPKLGLRARLASKGSGKWASSGGE-- 212
Query: 180 LDSKYGAGHHPQEIMPLLKAAEASGL--SVVGVSFHVGSEATNFAAFRGAIAAA 231
SK+G +++ +++ E +GL S+ + FH+GS+ +N + + A
Sbjct: 213 -KSKFGLS--ATQVLEVVRLLEQNGLLDSLQLLHFHIGSQISNIDDIKKGVREA 263
>gnl|CDD|224088 COG1166, SpeA, Arginine decarboxylase (spermidine biosynthesis)
[Amino acid transport and metabolism].
Length = 652
Score = 40.8 bits (96), Expect = 0.001
Identities = 40/175 (22%), Positives = 75/175 (42%), Gaps = 28/175 (16%)
Query: 79 YAVKCNPEPALLEALAALGSNFDC----GSRSEIEAVLLLDVSPDRIIYANPCKPVSHIK 134
Y +K N ++E+L A G + GS++E+ AVL +P +I N K +I+
Sbjct: 118 YPIKVNQHRRVVESLVASGKGYPLGLEAGSKAELMAVLAHAGNPGSLIVCNGYKDREYIR 177
Query: 135 YA---ASVGVNLT-TVDSVEELDKI----RNWHPKSDLLIRI--------KSPDDSGAKY 178
A +G + ++ + ELD + + K L +R K G K
Sbjct: 178 LALIGEKLGHKVYIVIEKLSELDLVLEEAKQLGVKPRLGVRARLASQGSGKWQSSGGEK- 236
Query: 179 PLDSKYGAGHHPQEIMPLLKAAEASGL--SVVGVSFHVGSEATNFAAFRGAIAAA 231
SK+G +++ +++ + L S+ + FH+GS+ +N + + A
Sbjct: 237 ---SKFGLS--ATQVLQVVERLREANLLDSLQLLHFHLGSQISNIRDIKTGVREA 286
>gnl|CDD|236867 PRK11165, PRK11165, diaminopimelate decarboxylase; Provisional.
Length = 420
Score = 38.0 bits (89), Expect = 0.007
Identities = 20/52 (38%), Positives = 30/52 (57%), Gaps = 9/52 (17%)
Query: 341 VFGPTCDAFDEVFTGH--------KLPELEVNDWLVFSEMGAYTTACGTNFN 384
V GP C++ D VFT LP+++V D+LVF + GAY + +N+N
Sbjct: 337 VAGPLCESGD-VFTQQEGGVVETRALPQVQVGDYLVFHDTGAYGASMSSNYN 387
>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 = 36.0 bits (84), Expect = 0.029
Identities = 21/56 (37%), Positives = 28/56 (50%), Gaps = 5/56 (8%)
Query: 343 GPTCDAFDEVFTGHKLPE-LEVNDWLVFSEMGAYTTACGTNFNGYSTVAIPTYVVR 397
G +C A D V + E L+V D LVF +M YT FNG V +P+ +R
Sbjct: 294 GNSCLAGD-VIGDYSFDEPLQVGDRLVFEDMAHYTMVKTNTFNG---VRLPSIAIR 345
>gnl|CDD|215240 PLN02439, PLN02439, arginine decarboxylase.
Length = 559
Score = 35.0 bits (81), Expect = 0.073
Identities = 26/85 (30%), Positives = 40/85 (47%), Gaps = 10/85 (11%)
Query: 79 YAVKCNPEPALLEALAALGSNF----DCGSRSEIEAVL--LLDVSPDRIIYANPCKPVSH 132
+ VKCN + L+E + GS F + GS+ E+ + L SPD + N K +
Sbjct: 37 FPVKCNQDRFLVEDIVKFGSPFRFGLEAGSKPELLLAMSCLCKGSPDAFLICNGYKDAEY 96
Query: 133 IKYA---ASVGVNLTTV-DSVEELD 153
+ A +G+N V + EELD
Sbjct: 97 VSLALLARKLGLNTVIVLEQEEELD 121
>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 = 32.1 bits (73), Expect = 0.53
Identities = 18/44 (40%), Positives = 23/44 (52%), Gaps = 2/44 (4%)
Query: 343 GPTCDAFDEVFTGHKLPE-LEVNDWLVFSEMGAYTTACGTNFNG 385
G TC A D V + + L+V D +VF +M YT T FNG
Sbjct: 308 GNTCLAGD-VMGEYAFDKPLKVGDKIVFLDMIHYTMVKNTTFNG 350
>gnl|CDD|235427 PRK05354, PRK05354, arginine decarboxylase; Provisional.
Length = 634
Score = 32.0 bits (74), Expect = 0.60
Identities = 38/177 (21%), Positives = 72/177 (40%), Gaps = 38/177 (21%)
Query: 79 YAVKCNPEPALLEALAALGSNFD----CGSRSEIEAVLLLDVSPDRIIYANPCKPVSHIK 134
Y +K N + ++E + A G ++ GS+ E+ AVL L P +I N K +I+
Sbjct: 102 YPIKVNQQRRVVEEIVASGKPYNLGLEAGSKPELMAVLALAGDPGALIVCNGYKDREYIR 161
Query: 135 ---YAASVGVNLT-TVDSVEELDKI----RNWHPKSDLLIRIKSPDDSGAKYPLDSKYGA 186
+G + ++ + EL+ I + K L +R + L S+ G+
Sbjct: 162 LALIGRKLGHKVFIVIEKLSELELILEEAKELGVKPRLGVRAR----------LASQ-GS 210
Query: 187 GH-------------HPQEIMPLLKAAEASGL--SVVGVSFHVGSEATNFAAFRGAI 228
G E++ ++ +GL + + FH+GS+ N + A+
Sbjct: 211 GKWQSSGGEKSKFGLSATEVLEAVERLREAGLLDCLQLLHFHLGSQIANIRDIKTAV 267
>gnl|CDD|214707 smart00518, AP2Ec, AP endonuclease family 2. These endonucleases
play a role in DNA repair. Cleave phosphodiester bonds
at apurinic or apyrimidinic sites.
Length = 273
Score = 30.3 bits (69), Expect = 1.5
Identities = 25/115 (21%), Positives = 41/115 (35%), Gaps = 37/115 (32%)
Query: 75 IHPHYAVKCNPE--------------------PALLEALAALGSNFDCGSRSEIEAVLLL 114
HP +K + E LLE A GS + +++ ++ L
Sbjct: 103 FHPGSYLKQSKEEALNRIIESLNEVIDETKGVVILLETTAGKGSQI-GSTFEDLKEIIDL 161
Query: 115 DVSPDRIIYANPCKPVSHIKYAASVGVNLTTVDSVEE----------LDKIRNWH 159
DRI C HI +AA G ++ TV+ E+ L+ ++ H
Sbjct: 162 IKELDRIG---VCIDTCHI-FAA--GYDINTVEGFEKVLEEFENVLGLEYLKAIH 210
>gnl|CDD|197304 cd10311, PLDc_N_DEXD_c, N-terminal putative catalytic domain of
uncharacterized prokaryotic and archeal HKD family
nucleases fused to a DEAD/DEAH box helicase domain.
N-terminal putative catalytic domain of uncharacterized
prokaryotic and archeal HKD family nucleases fused to a
DEAD/DEAH box helicase domain. All members of this
subfamily are uncharacterized. Other characterized
members of the superfamily that have a related domain
architecture ( containing a DEAD/DEAH box helicase
domain), include the DNA/RNA helicase superfamily II
(SF2) and Res-subunit of type III restriction
endonucleases. In addition to the helicase-like region,
members of this subfamily also contain one copy of the
conserved HKD motif (H-x-K-x(4)-D, where x represents
any amino acid residue) in the N-terminal putative
catalytic domain. The HKD motif characterizes the
phospholipase D (PLD, EC 3.1.4.4) superfamily.
Length = 156
Score = 29.5 bits (67), Expect = 1.7
Identities = 12/40 (30%), Positives = 21/40 (52%), Gaps = 8/40 (20%)
Query: 243 NNKMRKLFKLIFRELLPGSSLKVISEPGRFFAASAFTLYA 282
NN ++ + +EL GS L + AA++F++YA
Sbjct: 1 NNGTDRVGDDLKKELKKGSKLSI--------AAASFSIYA 32
>gnl|CDD|176743 cd08330, CARD_ASC_NALP1, Caspase activation and recruitment domain
found in Human ASC, NALP1, and similar proteins.
Caspase activation and recruitment domain (CARD) similar
to those found in human ASC (Apoptosis-associated
speck-like protein containing a CARD) and NALP1 (CARD7,
NLRP1). ASC, an adaptor molecule, and NALP1, a member of
the Nod-like receptor (NLR) family, are involved in the
assembly of the 'inflammasome', a multiprotein platform,
which is responsible for caspase-1 activation and
regulation of IL-1beta maturation. In general, CARDs are
death domains (DDs) associated with caspases. They are
known to be important in the signaling pathways for
apoptosis, inflammation and host-defense mechanisms. DDs
are protein-protein interaction domains found in a
variety of domain architectures. Their common feature is
that they form homodimers by self-association or
heterodimers by associating with other members of the DD
superfamily including PYRIN and DED (Death Effector
Domain). They serve as adaptors in signaling pathways
and can recruit other proteins into signaling complexes.
Length = 82
Score = 28.0 bits (63), Expect = 2.4
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 237 TAARTSNNKMRKLF 250
A +T+ KMRKLF
Sbjct: 39 RAEKTNQEKMRKLF 52
>gnl|CDD|216074 pfam00710, Asparaginase, Asparaginase.
Length = 318
Score = 29.8 bits (68), Expect = 2.6
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 184 YGAGHHPQEIMPLLKAAEASGLSVVGVS 211
+GAG+ P ++ LK A A G+ VV S
Sbjct: 239 FGAGNVPPALLDALKEAVARGIPVVVAS 266
>gnl|CDD|219970 pfam08689, Med5, Mediator complex subunit Med5. The mediator
complex is required for the expression of nearly all RNA
pol II dependent genes in Saccharomyces cerevisiae.
Deletion of the MED5 gene leads to increased
transcription of nuclear genes encoding components of
the oxidative phosphorylation machinery, and decreased
transcription of mitochondrial genes encoding components
of the same machinery. There is no orthologue from
pombe, and this subunit appears to be fungal specific.
Length = 977
Score = 29.8 bits (67), Expect = 2.9
Identities = 15/74 (20%), Positives = 27/74 (36%), Gaps = 4/74 (5%)
Query: 87 PALLEALAALGSNFDCGSRSEIEAVLLLDVSPDRIIYANPCKPVSHIKYAASVGVNLTTV 146
P L++ L L ++ S+ L + + NP K S +N+
Sbjct: 674 PGLIKILTWLENHLIWEKESDPSLPLKVLHE----LVKNPASISGEAKAIHSTVLNINAR 729
Query: 147 DSVEELDKIRNWHP 160
+++L K R P
Sbjct: 730 PLLKQLKKFRRREP 743
>gnl|CDD|107333 cd06338, PBP1_ABC_ligand_binding_like_5, Type I periplasmic
ligand-binding domain of uncharacterized ABC (ATPase
Binding Cassette)-type active transport systems that are
predicted to be involved in transport of amino acids,
peptides, or inorganic ions. This subgroup includes the
type I periplasmic ligand-binding domain of
uncharacterized ABC (ATPase Binding Cassette)-type
active transport systems that are predicted to be
involved in transport of amino acids, peptides, or
inorganic ions. This subgroup has high sequence
similarity to members of the family of hydrophobic amino
acid transporters (HAAT); however their ligand
specificity has not been determined experimentally.
Length = 345
Score = 29.5 bits (67), Expect = 3.2
Identities = 14/63 (22%), Positives = 24/63 (38%), Gaps = 4/63 (6%)
Query: 186 AGHHPQEIMPLLKAAEASGLSVVGVSFHVGSEATNFAAFRGAI-AAAKAVFDTAARTSNN 244
H + + L++ + G + + VG F AF A+ A A+ VF T
Sbjct: 202 VAGHFPDAVLLVRQMKELGYNPKALYMTVG---PAFPAFVKALGADAEGVFGPTQWTPAL 258
Query: 245 KMR 247
+
Sbjct: 259 DYK 261
>gnl|CDD|214862 smart00858, SAF, This domain family includes a range of different
proteins. Such as antifreeze proteins and flagellar FlgA
proteins, and CpaB pilus proteins.
Length = 63
Score = 26.8 bits (60), Expect = 4.3
Identities = 9/40 (22%), Positives = 17/40 (42%)
Query: 256 ELLPGSSLKVISEPGRFFAASAFTLYAQIIGKRVRGELRE 295
E++ L++ R T Y Q+IG+ R ++
Sbjct: 14 EVITAEDLRLGHVALRDLPGGGLTPYGQVIGRVARRDIAA 53
>gnl|CDD|223084 COG0005, Pnp, Purine nucleoside phosphorylase [Nucleotide transport
and metabolism].
Length = 262
Score = 28.8 bits (65), Expect = 4.3
Identities = 17/65 (26%), Positives = 26/65 (40%), Gaps = 6/65 (9%)
Query: 193 IMPLLKAAEASGLSVVGVSFHVGSEATNFAAFRGAIAAAKAVFDTAARTSNNKMRKLFKL 252
+P + A GL V +S TN+AA G + V + A + K+ KL
Sbjct: 204 TVPEVILARELGLCVAALSL-----VTNYAAGIGQPLTHEEVLEVAKENA-EKIAKLLAA 257
Query: 253 IFREL 257
+L
Sbjct: 258 AIAKL 262
>gnl|CDD|233528 TIGR01684, viral_ppase, viral phosphatase. This model represents a
family of viral proteins of unknown function. These
proteins are members, however, of the IIIC (TIGR01681)
subfamily of the haloacid dehalogenase (HAD) superfamily
of aspartate nucleophile hydrolases. All characterized
members of the III subfamilies (IIIA, TIGR01662; IIIB,
pfam03767) are phosphatases, including MDP-1, a member
of subfamily IIIC (TIGR01681). No member of this
subfamily is characterized with respect to particular
function. All of the active site residues characteristic
of HAD-superfamily phosphatases are present in subfamily
IIIC. These proteins also include an N-terminal domain
(ca. 125 aas) that is unique to this clade.
Length = 301
Score = 28.6 bits (64), Expect = 5.8
Identities = 12/44 (27%), Positives = 17/44 (38%), Gaps = 7/44 (15%)
Query: 333 LTRTYNSTVFGPTCDAFDEVFTGHKLPELE-VNDWLVFSEMGAY 375
L + ++ FG T F HK +N+W VF Y
Sbjct: 77 LKTAFKTSYFGHTFVLF------HKPAMYACLNEWYVFELEEIY 114
>gnl|CDD|163701 cd08070, MPN_like, Mpr1p, Pad1p N-terminal (MPN) domains with
catalytic isopeptidase activity (metal-binding). This
family contains archaeal and bacterial MPN (also known
as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These
domains contain the signature JAB1/MPN/Mov34
metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is
involved in zinc ion coordination and provides the
active site for isopeptidase activity for the release of
ubiquitin from ubiquitinated proteins (thus having
deubiquitinating (DUB) activity) that are tagged for
degradation. The JAMM proteins likely hydrolyze
ubiquitin conjugates in a manner similar to thermolysin,
in which the zinc-polarized aqua ligand serves as the
nucleophile, compared with the classical DUBs that do so
with a cysteine residue in the active site.
Length = 128
Score = 27.6 bits (62), Expect = 6.0
Identities = 9/24 (37%), Positives = 13/24 (54%), Gaps = 1/24 (4%)
Query: 190 PQEIMPLLKAAEASGLSVVGVSFH 213
P E + + A GL VVG+ +H
Sbjct: 55 PAEQLAAQREARERGLEVVGI-YH 77
>gnl|CDD|214873 smart00870, Asparaginase, Asparaginase, found in various plant,
animal and bacterial cells. Asparaginase catalyses the
deamination of asparagine to yield aspartic acid and an
ammonium ion, resulting in a depletion of free
circulatory asparagine in plasma. The enzyme is
effective in the treatment of human malignant lymphomas,
which have a diminished capacity to produce asparagine
synthetase: in order to survive, such cells absorb
asparagine from blood plasma..- if Asn levels have been
depleted by injection of asparaginase, the lymphoma
cells die.
Length = 323
Score = 28.3 bits (64), Expect = 7.6
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 184 YGAGHHPQEIMPLLKAAEASGLSVVGVS 211
GAG+ P +++ LK A G+ VV S
Sbjct: 244 TGAGNVPPDLLEALKEALERGIPVVRTS 271
>gnl|CDD|216395 pfam01261, AP_endonuc_2, Xylose isomerase-like TIM barrel. This
TIM alpha/beta barrel structure is found in xylose
isomerase and in endonuclease IV (EC:3.1.21.2). This
domain is also found in the N termini of bacterial
myo-inositol catabolism proteins. These are involved in
the myo-inositol catabolism pathway, and is required for
growth on myo-inositol in Rhizobium leguminosarum bv.
viciae.
Length = 202
Score = 27.7 bits (62), Expect = 8.0
Identities = 9/45 (20%), Positives = 17/45 (37%)
Query: 196 LLKAAEASGLSVVGVSFHVGSEATNFAAFRGAIAAAKAVFDTAAR 240
L + GL + ++ +G + A+ A K + AA
Sbjct: 31 LKALLKEYGLEISSLNPSLGLLEPDEHERAAALEALKRAIELAAA 75
>gnl|CDD|202344 pfam02675, AdoMet_dc, S-adenosylmethionine decarboxylase. This
family contains several S-adenosylmethionine
decarboxylase proteins from bacterial and
archaebacterial species. S-adenosylmethionine
decarboxylase (AdoMetDC), a key enzyme in the
biosynthesis of spermidine and spermine, is first
synthesised as a proenzyme, which is cleaved post
translationally to form alpha and beta subunits. The
alpha subunit contains a covalently bound pyruvoyl group
derived from serine that is essential for activity.
Length = 107
Score = 26.7 bits (60), Expect = 8.1
Identities = 8/18 (44%), Positives = 16/18 (88%)
Query: 196 LLKAAEASGLSVVGVSFH 213
L +AA+A+G +++G++FH
Sbjct: 24 LREAAKAAGATLLGIAFH 41
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
0.319 0.134 0.400
Gapped
Lambda K H
0.267 0.0824 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,805,426
Number of extensions: 2032816
Number of successful extensions: 1996
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1955
Number of HSP's successfully gapped: 59
Length of query: 405
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 306
Effective length of database: 6,546,556
Effective search space: 2003246136
Effective search space used: 2003246136
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: 60 (26.7 bits)