RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 015304
(409 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 = 452 bits (1165), Expect = e-159
Identities = 181/377 (48%), Positives = 232/377 (61%), Gaps = 20/377 (5%)
Query: 31 EVPFYILDLGVVVTLYNQMISKLPMIHPHYAVKCNPEPALLEALAALGSNFDCASRSEIE 90
E PF ++DLG VV Y + LP + P YAVKCNP+PA+L LAALG+ FDCAS+ EIE
Sbjct: 1 ETPFLVVDLGDVVRKYRRWKKALPRVRPFYAVKCNPDPAVLRTLAALGAGFDCASKGEIE 60
Query: 91 AVLALGVSPDRIIYANPCKPVSHIKYAANVGVNLTTFDSVEELHKIRKWHPKCDLLIRIK 150
VL LGVSP+RII+ANPCK +S I+YAA +GV L TFDS +EL KI K P LL+RI
Sbjct: 61 LVLGLGVSPERIIFANPCKSISDIRYAAELGVRLFTFDSEDELEKIAKHAPGAKLLLRIA 120
Query: 151 PPDDSGAKHPLDSKYGVDHHPQEIVPLLEAAEASGLSVVGVAFHIGSAATKFAAYRGAIA 210
DDSGA PL K+G P+E LL A+ GL+VVGV+FH+GS T +AY AIA
Sbjct: 121 -TDDSGALCPLSRKFGA--DPEEARELLRRAKELGLNVVGVSFHVGSQCTDPSAYVDAIA 177
Query: 211 AAKAVFETAARLGNNKMRVLDIGGGFSFTNSNTK-SFQEAASIIKEALHAYFPNELLPGS 269
A+ VF+ AA LG K+++LDIGGGF + SF+E A++I AL YFP+E
Sbjct: 178 DAREVFDEAAELG-FKLKLLDIGGGFPGSYDGVVPSFEEIAAVINRALDEYFPDE----- 231
Query: 270 SLRVISEPGRFFTYSAFTLYTQIIGKRVHGE---MRNYWINDGKYGSFDWVNYDEAIAKC 326
+R+I+EPGR+ SAFTL +I KR G+ R Y++NDG YGSF+ + +D
Sbjct: 232 GVRIIAEPGRYLVASAFTLAVNVIAKRKRGDDDRERWYYLNDGVYGSFNEILFDHIRYPP 291
Query: 327 TPLTLASSLTTSKGLSRTYNSKVFGPTCDAADEVFSGHKLPE-LEVTDWLVFSEMGAYTR 385
L Y S ++GPTCD+ D ++ LPE L V DWL+F MGAYT
Sbjct: 292 RV------LKDGGRDGELYPSSLWGPTCDSLDVIYEDVLLPEDLAVGDWLLFENMGAYTT 345
Query: 386 ARGTNFNGYNTAAIPTY 402
A + FNG+ I
Sbjct: 346 AYASTFNGFPPPKIVYV 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 = 259 bits (662), Expect = 6e-83
Identities = 141/385 (36%), Positives = 206/385 (53%), Gaps = 40/385 (10%)
Query: 34 FYILDLGVVVTLYNQMISKLPMIHPHYAVKCNPEPALLEALAALGSNFDCASRSEIEAVL 93
F++ DLG +V ++Q + + I P Y V+CN PA+LE LAALG+ F C+S++E+ V
Sbjct: 15 FFVGDLGKIVKKHSQWQTVMAQIKPFYTVRCNSTPAVLEILAALGTGFACSSKNEMALVQ 74
Query: 94 ALGVSPDRIIYANPCKPVSHIKYAANVGVNLTTFDSVEELHKIRKWHPKCDLLIRIKPPD 153
LGVSP+ IIY NPCK S IKYAA VGVN+ T D+ EL KI + HP LL+ I D
Sbjct: 75 ELGVSPENIIYTNPCKQASQIKYAAKVGVNIMTCDNEIELKKIARNHPNAKLLLHIATED 134
Query: 154 DSGAKHPLDSKYGVD----HHPQEIVPLLEAAEASGLSVVGVAFHIGSAATKFAAYRGAI 209
+ G + ++ K+G H LLE A+ + +VGV FH+ S+ ++ Y A+
Sbjct: 135 NIGGEE-MNMKFGTTLKNCRH------LLECAKELDVQIVGVKFHVSSSCKEYQTYVHAL 187
Query: 210 AAAKAVFETAARLGNNKMRVLDIGGGFSFTNSNTKSFQEAASIIKEALHAYFPNELLPGS 269
+ A+ VF+ A G KM +LDIGGGF+ + + E +I+ L YFP GS
Sbjct: 188 SDARCVFDMAEEFG-FKMNMLDIGGGFTGSEIQLE---EVNHVIRPLLDVYFPE----GS 239
Query: 270 SLRVISEPGRFFTYSAFTLYTQIIGKRV---------HGEMRN------YWINDGKYGSF 314
+++I+EPG ++ SAFTL +I K+ + + Y++NDG YGSF
Sbjct: 240 GIQIIAEPGSYYVSSAFTLAVNVIAKKAVENDKHLSSVEKNGSDEPAFVYYMNDGVYGSF 299
Query: 315 DWVNYDEAIAKCTPLTLASSLTTSKGLSRTYNSKVFGPTCDAADEVFSGHKLPELEVTDW 374
++ T K + S ++GP+CD D++ LPEL V DW
Sbjct: 300 ASKLSEKLN------TTPEVHKKYKEDEPLFTSSLWGPSCDELDQIVESCLLPELNVGDW 353
Query: 375 LVFSEMGAYTRARGTNFNGYNTAAI 399
L+F MGA + + FN + AI
Sbjct: 354 LIFDNMGAGSLHEPSTFNDFQRPAI 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 = 246 bits (631), Expect = 1e-78
Identities = 125/378 (33%), Positives = 184/378 (48%), Gaps = 25/378 (6%)
Query: 33 PFYILDLGVVVTLYNQMISKLPMIH-PHYAVKCNPEPALLEALAALGSNFDCASRSEIEA 91
PFY+ DL ++ Y + LP YAVK NP P +L LA G+ FD AS+ E+
Sbjct: 2 PFYVYDLDIIRAHYAALKEALPSGVKLFYAVKANPNPHVLRTLAEAGTGFDVASKGELAL 61
Query: 92 VLALGVSPDRIIYANPCKPVSHIKYAANVGVNLTTFDSVEELHKI----RKWHPKCDLLI 147
LA GV P+RII+ P K VS I+ A GV+ DS++EL ++ +K PK +L+
Sbjct: 62 ALAAGVPPERIIFTGPAKSVSEIEAALASGVDHIVVDSLDELERLNELAKKLGPKARILL 121
Query: 148 RIKPPDDSGAKHP----LDSKYGVDHHPQEIVPLLEAAEASGLSVVGVAFHIGSAATKFA 203
R+ P +G L SK+G+ E LE A+ L +VG+ FH+GS
Sbjct: 122 RVNPDVSAGTHKISTGGLKSKFGLS--LSEARAALERAKELDLRLVGLHFHVGSQILDLE 179
Query: 204 AYRGAIAAAKAVFETAARLGNNKMRVLDIGGGFSFT-NSNTKSFQEAASIIKEALHAYFP 262
A++ A+ + E +G + +LD+GGG + F+E A++I L YFP
Sbjct: 180 TIVQALSDARELIEELVEMG-FPLEMLDLGGGLGIPYDEQPLDFEEYAALINPLLKKYFP 238
Query: 263 NELLPGSSLRVISEPGRFFTYSAFTLYTQIIGKRVHGEMRNYWINDGKYGSF-DWVNYDE 321
N + +I EPGR+ A L T+++ +V+G ++ G SF + YD
Sbjct: 239 N----DPGVTLILEPGRYIVAQAGVLVTRVVAVKVNGGRFFAVVDGGMNHSFRPALAYDA 294
Query: 322 AIAKCTPLTLASSLTTSKGLSRTYNSKVFGPTCDAADEVFSGHKLPELEVTDWLVFSEMG 381
P+T L + + GP CD+ D + LPELEV D LVF +MG
Sbjct: 295 Y----HPITP---LKAPGPDEPLVPATLAGPLCDSGDVIGRDRLLPELEVGDLLVFEDMG 347
Query: 382 AYTRARGTNFNGYNTAAI 399
AY + +NFN + A
Sbjct: 348 AYGFSESSNFNSHPRPAE 365
>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 = 238 bits (610), Expect = 4e-77
Identities = 106/234 (45%), Positives = 142/234 (60%), Gaps = 11/234 (4%)
Query: 53 LPMIHPHYAVKCNPEPALLEALAALGSNFDCASRSEIEAVLALGVSPDRIIYANPCKPVS 112
LP I P YAVK N +PA+L LA LG FDCAS+ E+E VLA GV P+RII+ANPCK S
Sbjct: 17 LPRIQPFYAVKANSDPAVLRLLAELGLGFDCASKGELERVLAAGVPPERIIFANPCKSRS 76
Query: 113 HIKYAANVGVNLTTFDSVEELHKIRKWHPKCDLLIRIKPPDDSGAKHPL----DSKYGVD 168
++YA GV T D+VEEL K+ + P+ LL+R+KP D+ A L DSK+G D
Sbjct: 77 ELRYALEHGVVCVTVDNVEELEKLARLAPEARLLLRVKPDVDAHAHCYLSTGQDSKFGAD 136
Query: 169 HHPQEIVPLLEAAEASGLSVVGVAFHIGSAATKFAAYRGAIAAAKAVFETAARLGNNKMR 228
+E LL+AA+ GL+VVGV FH+GS T A+ A A+ VF+ A LG ++
Sbjct: 137 --LEEAEALLKAAKELGLNVVGVHFHVGSGCTDAEAFVKAARDARNVFDQGAELGFE-LK 193
Query: 229 VLDIGGGFSFTNSNTKSFQEAASIIKEALHAYFPNELLPGSSLRVISEPGRFFT 282
+LD+GGGF + + F+E A +I AL FP+ +I+EPGR+
Sbjct: 194 ILDLGGGFGVDYTGAEDFEEYAEVINAALEEVFPH----DPHPTIIAEPGRYIV 243
>gnl|CDD|223098 COG0019, LysA, Diaminopimelate decarboxylase [Amino acid transport
and metabolism].
Length = 394
Score = 221 bits (566), Expect = 1e-68
Identities = 119/412 (28%), Positives = 174/412 (42%), Gaps = 42/412 (10%)
Query: 7 TTVVTKEELTEFVRSTILKRQEFDEVPFYILDLGVVVTLYNQMISKLPMIH--PHYAVKC 64
ELT +EF P Y+ D + ++ S P YAVK
Sbjct: 3 FFRNKDGELTIEGVDLPALAEEF-GTPVYVYDEATLRRNARELKSAFPGSGAKVFYAVKA 61
Query: 65 NPEPALLEALAALGSNFDCASRSEIEAVLALGVSPDRIIYANPCKPVSHIKYAANVGVNL 124
N PA+L LA GS FD AS E+E LA G P+RI+++ P K I +A +G+ L
Sbjct: 62 NSNPAILRLLAEEGSGFDVASLGELELALAAGFPPERIVFSGPAKSEEEIAFALELGIKL 121
Query: 125 TTFDSVEELHKIRKWHPKC--DLLIRIKPPDDSGAKH-------PLDSKYGVDHHPQEIV 175
DS EEL ++ P + +RI P A SK+G+ P+E +
Sbjct: 122 INVDSEEELERLSAIAPGLVARVSLRINP--GVSAGTHEYIATGGKSSKFGIS--PEEAL 177
Query: 176 PLLE-AAEASGLSVVGVAFHIGSAATKFAAYRGAIAAAKAVFETAARLGNNKMRVLDIGG 234
+LE AA+ GL +VG+ FHIGS T + A+A + +F A ++ L++GG
Sbjct: 178 DVLERAAKLLGLELVGLHFHIGSQITDLDPFEEALAKVEELFGRLAEELGIQLEWLNLGG 237
Query: 235 GFSFT---NSNTKSFQEAASIIKEALHAYFPNELLPGSSLRVISEPGRFFTYSAFTLYTQ 291
G T + A +KEA Y + + +I EPGR +A L T+
Sbjct: 238 GLGITYEDEYDPPDLAAYAKALKEAFGEYAED-------VELILEPGRAIVANAGVLVTE 290
Query: 292 IIG-KRVHGEMRNYWINDGKYGSF--DWVNYDEAIAKCTPLTLASSLTTSKGLSRTYNSK 348
++ K RN+ I DG + L + +
Sbjct: 291 VLDVKENGE--RNFVIVDGGMNDLMRPALYGAY---------HHIRLNRTDEDAEREEYD 339
Query: 349 VFGPTCDAADEVFSGHKLPE-LEVTDWLVFSEMGAYTRARGTNFNGYNTAAI 399
V GPTC++ D + LPE L+V D LV + GAY + +N+NG A
Sbjct: 340 VVGPTCESGDVLARDRALPEPLKVGDLLVILDAGAYGASMSSNYNGRPRPAE 391
>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 = 152 bits (387), Expect = 2e-42
Identities = 96/395 (24%), Positives = 153/395 (38%), Gaps = 58/395 (14%)
Query: 33 PFYILDLGVVVTLYNQMISKLPMI--HPHYAVKCNPEPALLEALAALGSNFDCASRSEIE 90
P Y+ D + Y ++ YAVK N A+L+ LA G D S E+
Sbjct: 4 PLYVYDEATIRENYRRLKEAFSGPGFKICYAVKANSNLAILKLLAEEGLGADVVSGGELY 63
Query: 91 AVLALGVSPDRIIYANPCKPVSHIKYAANVGVNLTTFDSVEELHKI----RKWHPKCDLL 146
L G P+RI++ K ++ A +G+ DS+ EL ++ + +
Sbjct: 64 RALKAGFPPERIVFTGNGKSDEELELALELGILRINVDSLSELERLGEIAPELGKGAPVA 123
Query: 147 IRIKPPDDSGAKH-------PLDSKYGVDHHPQEIVPLLE-AAEASGLSVVGVAFHIGSA 198
+R+ P A DSK+G+ ++ + A E GL +VG+ HIGS
Sbjct: 124 LRVNP--GVDAGTHPYISTGGKDSKFGIPL--EQALEAYRRAKELPGLKLVGLHCHIGSQ 179
Query: 199 ATKFAAYRGAIAAAKAVFETAARLGNN--KMRVLDIGGGFSFT---NSNTKSFQEAASII 253
+ AA+ + + AA L + LD+GGG +E A I
Sbjct: 180 ILDLEPFV---EAAEKLLDLAAELRELGIDLEFLDLGGGLGIPYRDEDEPLDIEEYAEAI 236
Query: 254 KEALHAYFPNELLPGSSLRVISEPGRFFTYSAFTLYTQIIG-KRVHGEMRNYWINDGK-- 310
EAL G L++I EPGR+ +A L T++ K G + + D
Sbjct: 237 AEALKELCEG----GPDLKLIIEPGRYIVANAGVLLTRVGYVKETGG--KTFVGVDAGMN 290
Query: 311 -------YGSFDWVNYDEAIAKCTPLTLASSLTTSKGLSRTYNSKVFGPTCDAADEVFSG 363
YG++ ++ P+ T + V GP C++ D
Sbjct: 291 DLIRPALYGAY----HE-----IVPVNKPGEGET-----EKVD--VVGPICESGDVFAKD 334
Query: 364 HKLPELEVTDWLVFSEMGAYTRARGTNFNGYNTAA 398
+LPE+E D L + GAY + +N+N A
Sbjct: 335 RELPEVEEGDLLAIHDAGAYGYSMSSNYNSRPRPA 369
>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 = 137 bits (347), Expect = 2e-38
Identities = 76/240 (31%), Positives = 109/240 (45%), Gaps = 39/240 (16%)
Query: 46 YNQMISKLPM-IHPHYAVKCNPEPALLEALAALGSNFDCASRSEIEAVLALGVSPDRIIY 104
Y ++ P I VK N P + LAALG+ FD AS E + A G+ P+ I++
Sbjct: 5 YRRLREAAPAGITLFAVVKANANPEVARTLAALGTGFDVASLGEALLLRAAGIPPEPILF 64
Query: 105 ANPCKPVSHIKYAANVGVNLTTFDSVEELHKIR----KWHPKCDLLIRIKPPDDSGAKHP 160
PCK VS ++ AA GV + T DS+EEL K+ K P +L+RI D+G +
Sbjct: 65 LGPCKQVSELEDAAEQGVIVVTVDSLEELEKLEEAALKAGPPARVLLRI----DTGDE-- 118
Query: 161 LDSKYGVDHHPQEIVPLLEAA-EASGLSVVGVAFHIGSAATKFAAYRGAIAAAKAVFETA 219
+ K+GV P+E+ LLE A E L +VG+ H GSA ++ + A++ A +
Sbjct: 119 -NGKFGVR--PEELKALLERAKELPHLRLVGLHTHFGSADEDYSPFVEALSRFVAALDQL 175
Query: 220 ARLGNNKMRVLDIGGGFSFTNSNTKSFQEAASIIKEALHAYFPNELLPGSSLRVISEPGR 279
LG + L IGG F+ Y +I EPGR
Sbjct: 176 GELG-IDLEQLSIGGSFAIL--------------------YLQ---ELPLGTFIIVEPGR 211
>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 = 139 bits (353), Expect = 3e-37
Identities = 102/368 (27%), Positives = 152/368 (41%), Gaps = 58/368 (15%)
Query: 58 PHYAVKCNPEPALLEALAALGSNFDCASRSEIEAVLALGVSPDRIIYANPCKPVSHIKYA 117
YAVK N A+L LA LGS FD S E+ LA G P++I+++ K + ++ A
Sbjct: 52 VCYAVKANSNLAVLRLLAELGSGFDVVSGGELYRALAAGFPPEKIVFSGNGKSRAELERA 111
Query: 118 --ANVGVNLTTFDSVEELHKIRKWHP----KCDLLIRIKPPDDSGAK-HP------LDSK 164
+ +N+ DS EL ++ + P K + +R+ P AK HP DSK
Sbjct: 112 LELGICINV---DSFSELERLNEIAPELGKKARISLRVNP--GVDAKTHPYISTGLKDSK 166
Query: 165 YGVDHHPQEIVPLLEAAEASGLSVVGVAFHIGSAATKFAAYRGAIAAAKAVFETAARLGN 224
+G+D L A + L +VG+ HIGS T + + + AA+ V + A L
Sbjct: 167 FGIDVEEALEAYLY-ALQLPHLELVGIHCHIGSQITDLSPF---VEAAEKVVKLAESLAE 222
Query: 225 N-KMRVLDIGGGFS--FTNSN-TKSFQEAASIIKEALHAYFPNELLPGSSLRVISEPGRF 280
+ LD+GGG +T E A I AL G ++I EPGR
Sbjct: 223 GIDLEFLDLGGGLGIPYTPEEEPPDLSEYAQAILNALE----GYADLGLDPKLILEPGRS 278
Query: 281 FTYSAFTLYTQIIG-KRVHGEMRNYWINDGK---------YGSFDWVNYDEAIAKCTPLT 330
+A L T++ K RN+ I D YG+ Y I
Sbjct: 279 IVANAGVLLTRVGFVKETGS--RNFVIVDAGMNDLIRPALYGA-----YHHIIVLNRTND 331
Query: 331 LASSLTTSKGLSRTYNSKVFGPTCDAADEVFSGHKLPELEVTDWLVFSEMGAYTRARGTN 390
+ + V GP C++ D + +LPE+E D L + GAY + +N
Sbjct: 332 APTEVAD-----------VVGPVCESGDVLAKDRELPEVEPGDLLAVFDAGAYGFSMSSN 380
Query: 391 FNGYNTAA 398
+N A
Sbjct: 381 YNSRPRPA 388
>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 = 124 bits (313), Expect = 6e-32
Identities = 101/401 (25%), Positives = 164/401 (40%), Gaps = 54/401 (13%)
Query: 33 PFYILDLGVVVTLYNQMISKLPMIHPH----YAVKCNPEPALLEALAALGSNFDCASRSE 88
PF++ D + Y +++ +P+ Y+ K N PA+ + L G + S E
Sbjct: 8 PFFVFDEDALRENYRELLGAFKKRYPNVVIAYSYKTNYLPAICKILHEEGGYAEVVSAME 67
Query: 89 IEAVLALGVSPDRIIYANPCKPVSHIKYAANVGVNLTTFDSVEELHKIRKWHPKCDLLIR 148
E L LGV RII+ P K ++ A G + DS +EL +I + + + +
Sbjct: 68 YELALKLGVPGKRIIFNGPYKSKEELEKALEEGALINI-DSFDELERILEIAKELGRVAK 126
Query: 149 --IKPPDDSGAKHPLDSKYGVDHHPQEIVPLLEA----AEASGLSVVGVAFHIGSAATKF 202
I+ + G + S++G D +E L A E+ LS+VG+ H+GS
Sbjct: 127 VGIRLNMNYGNN--VWSRFGFD--IEENGEALAALKKIQESKNLSLVGLHCHVGSNILNP 182
Query: 203 AAYRGAIAAAKAVFETAARLGNNKMRVLDIGGGFSFTNS----------NTKSFQEAASI 252
AY AAAK + E RL ++ LD+GGGF + ++ A
Sbjct: 183 EAYS---AAAKKLIELLDRLFGLELEYLDLGGGF-PAKTPLSLAYPQEDTVPDPEDYAEA 238
Query: 253 IKEALHAYFPNEL-LPGSSLRVISEPGRFFTYSAFTLYTQIIG-KRVHGEMRNYWINDGK 310
I L Y+ N+ P ++I EPGR A L +++ K +G RN + D
Sbjct: 239 IASTLKEYYANKENKP----KLILEPGRALVDDAGYLLGRVVAVKNRYG--RNIAVTDAG 292
Query: 311 Y---GSFDWVNYDEAIAKCTPLTLASSLTTSKGLSRTYNSKVFGPTCDAADEVFSGHKLP 367
+ W ++ P+ + S+ Y+ V+G C +D +F LP
Sbjct: 293 INNIPTIFWYHH--------PILVL-RPGKEDPTSKNYD--VYGFNCMESDVLFPNVPLP 341
Query: 368 ELEVTDWLVFSEMGAYTRARGTNFNGYNTAAIPTYVVRSNR 408
L V D L +GAY + F Y++ +N
Sbjct: 342 PLNVGDILAIRNVGAYNMTQSNQFIRPRP---AVYLIDNNG 379
>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 = 114 bits (288), Expect = 2e-28
Identities = 103/377 (27%), Positives = 158/377 (41%), Gaps = 48/377 (12%)
Query: 33 PFYILDLGVVVTLYNQMISKLP-MIHPHYAVKCNPEPALLEALAALGSNFDCASRSEIEA 91
PFY+ D V Y + + LP I +Y++K NP PAL+ L LG + AS E+
Sbjct: 8 PFYVYDRDRVRERYAALRAALPPAIEIYYSLKANPNPALVAHLRQLGDGAEVASAGELAL 67
Query: 92 VLALGVSPDRIIYANPCKPVSHIKYAANVGVNLTTFDSVEELHKIR---KWHPKC-DLLI 147
L GV P++I++A P K + ++ A G+ +S+EEL +I + H + +
Sbjct: 68 ALEAGVPPEKILFAGPGKSDAELRRAIEAGIGTINVESLEELERIDALAEEHGVVARVAL 127
Query: 148 RIKPPDDSGAKHPLD------SKYGVDHHPQEIVPLLEAAEASGLSVVGVAFHI--GSAA 199
RI P D K S++G+D E +P + A A+ ++ V HI G+
Sbjct: 128 RINP--DFELKGSGMKMGGGPSQFGID---VEELPAVLARIAALPNLRFVGLHIYPGTQI 182
Query: 200 TKFAAYRGAIAAAKAVFETAARLGNN---KMRVLDIGGGF--SFTNSNTKSFQEAASIIK 254
A I A + A RL + LD+GGGF + T EA +
Sbjct: 183 LDADA---LIEAFRQTLALALRLAEELGLPLEFLDLGGGFGIPYFPGETPLDLEA---LG 236
Query: 255 EALHAYFPNELLPGSSLRVISEPGRFFTYSAFTLYTQIIG-KRVHGEMRNYWINDGKYG- 312
AL A RV+ E GR+ A T+++ K GE + + DG G
Sbjct: 237 AALAALLAELGDRLPGTRVVLELGRYLVGEAGVYVTRVLDRKVSRGE--TFLVTDG--GM 292
Query: 313 ------SFDWVNYDEAIAKCTPLTLASSLTTSKGLSRTYNSKVFGPTCDAADEVFSGHKL 366
S N+ + + + PL + + + T V GP C D + +L
Sbjct: 293 HHHLAASG---NFGQVLRRNYPLAILNRMGG--EERETVT--VVGPLCTPLDLLGRNVEL 345
Query: 367 PELEVTDWLVFSEMGAY 383
P LE D + + GAY
Sbjct: 346 PPLEPGDLVAVLQSGAY 362
>gnl|CDD|236358 PRK08961, PRK08961, bifunctional aspartate kinase/diaminopimelate
decarboxylase protein; Provisional.
Length = 861
Score = 102 bits (255), Expect = 2e-23
Identities = 97/394 (24%), Positives = 157/394 (39%), Gaps = 76/394 (19%)
Query: 30 DEVPFYILDLGVVVTLYNQMISKLPMIHPHYAVKCNPEPALLEALAALGSNFDCASRSEI 89
P Y+ L V + + + YA+K NP PA+L L G F+C S E+
Sbjct: 501 AGSPCYVYHLPTVRARARALAALAAVDQRFYAIKANPHPAILRTLEEEGFGFECVSIGEL 560
Query: 90 EAVLAL--GVSPDRIIYANPCKPVSHIKYAANVGVNLTTFDSVEELHKIRKWHPKC---- 143
V L +SP+R+++ P + + A +GV + T D+VE L R W P+
Sbjct: 561 RRVFELFPELSPERVLFTPNFAPRAEYEAAFALGVTV-TLDNVEPL---RNW-PELFRGR 615
Query: 144 DLLIRIKPPDDSGAKH-------PLDSKYGVDHHPQEIVPLLEAAEASGLSVVGVAFHIG 196
++ +RI P G H +SK+G+ I ++ A+ G++VVG+ H+G
Sbjct: 616 EVWLRIDP--GHGDGHHEKVRTGGKESKFGL--SQTRIDEFVDLAKTLGITVVGLHAHLG 671
Query: 197 SAATKFAAYRGAIAAAKAVFETAARLGNNKMRVLDIGGGFSFTNS-NTKSFQEAASIIKE 255
S +R A + A R + +R +D+GGG S + F A +
Sbjct: 672 SGIETGEHWRR---MADELASFARRFPD--VRTIDLGGGLGIPESAGDEPFDLDA--LDA 724
Query: 256 ALHAYFPNELLPGSSLRVISEPGRFFTYSAFTLY---TQIIGKRVHGEMRNYWINDGK-- 310
L PG ++ EPGR+ A L TQ+ K +R + G
Sbjct: 725 GLAEV--KAQHPG--YQLWIEPGRYLVAEAGVLLARVTQVKEK---DGVRRVGLETGMNS 777
Query: 311 ------YGSF-DWVNYDEAIAKCTPLTLASSLTTSKGLSRTYNSK-----VFGPTCDAAD 358
YG++ + VN LSR V GP C+++D
Sbjct: 778 LIRPALYGAYHEIVN----------------------LSRLDEPAAGTADVVGPICESSD 815
Query: 359 EVFSGHKLPELEVTDWLVFSEMGAYTRARGTNFN 392
+ +LP D ++ + GAY + + +N
Sbjct: 816 VLGKRRRLPATAEGDVILIANAGAYGYSMSSTYN 849
>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 = 99.8 bits (249), Expect = 3e-23
Identities = 99/396 (25%), Positives = 156/396 (39%), Gaps = 68/396 (17%)
Query: 24 LKRQEFDEVPFYILDLGVVVTLYNQMISKLPMIHPHYAVKCNPEPALLEALAALGSNFDC 83
L R D P Y+ DL V Q+ + + YA+K NP P +L L G F+C
Sbjct: 4 LLRLAPDVGPCYVYDLETVRARARQVSALKAVDSLFYAIKANPHPDVLRTLEEAGLGFEC 63
Query: 84 ASRSEIEAVLAL--GVSPDRIIYANPCKPVSHIKYAANVGVNLTTFDSVEELHKIRKWHP 141
S E++ VL L + P R+++ S + A +GVN+T V+ LH +R+W
Sbjct: 64 VSIGELDLVLKLFPDLDPRRVLFTPNFAARSEYEQALELGVNVT----VDNLHPLREWPE 119
Query: 142 ---KCDLLIRIKPPDDSGAKHPL-------DSKYGVDHHPQEIVPLLEAAEASGLSVVGV 191
++++RI P G H +SK+G+ E+ + A+ +G+ V+G+
Sbjct: 120 LFRGREVILRIDP--GQGEGHHKHVRTGGPESKFGL--DVDELDEARDLAKKAGIIVIGL 175
Query: 192 AFHIGSAATKFAAYRGAIAAAKAVFETAARLGNNKMRVLDIGGGFSFTNSNTKSFQEAAS 251
H GS + + A +R+L++GGG +
Sbjct: 176 HAHSGSGVEDTDHWARHGD---YLASLARHFPA--VRILNVGGGLGIPEAP-----GGRP 225
Query: 252 IIKEALHAYFPN--ELLPGSSLRVISEPGRFFTYSAFTLY---TQIIGKR------VHGE 300
I +AL A P ++ EPGRF + L TQI K +
Sbjct: 226 IDLDALDAALAAAKAAHPQ--YQLWMEPGRFIVAESGVLLARVTQIKHKDGVRFVGLETG 283
Query: 301 MRNYWINDGKYGSF-DWVN---YDEAIAKCTPLTLASSLTTSKGLSRTYNSKVFGPTCDA 356
M N I YG++ + VN DE N+ V GP C++
Sbjct: 284 M-NSLIRPALYGAYHEIVNLSRLDE--------------------PPAGNADVVGPICES 322
Query: 357 ADEVFSGHKLPELEVTDWLVFSEMGAYTRARGTNFN 392
D + LPE E D ++ + GAY + +N
Sbjct: 323 GDVLGRDRLLPETEEGDVILIANAGAYGFCMASTYN 358
>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 = 99.4 bits (248), Expect = 5e-23
Identities = 110/396 (27%), Positives = 155/396 (39%), Gaps = 57/396 (14%)
Query: 33 PFYILDLGVVVTLYNQMISKLP-MIHPHYAVKCNPEPALLEALAALGSNFDCASRSEIEA 91
PFY D G+V + LP + HYAVK NP PALL +A L FD AS E+
Sbjct: 26 PFYAYDRGLVSERVAALRKALPEELAIHYAVKANPMPALLAHMAPLVDGFDVASAGELAV 85
Query: 92 VLALGVSPDRIIYANPCKPVSHIK--YAANVGVNLTTFDSVEEL-HKIRKWHPKCDLLIR 148
L G P I +A P K + ++ AA V +N+ + + L + + +R
Sbjct: 86 ALDTGYDPGCISFAGPGKTDAELRRALAAGVLINVESLRELNRLAALSEALGLRARVAVR 145
Query: 149 IKPP---DDSGAKHPLDSK-YGVDHHPQEIVP-LLEAAEASGLSVVGVAFHIGSAATKFA 203
+ P SG K +K +G+D E VP L +A+ L G FHI + +
Sbjct: 146 VNPDFELKGSGMKMGGGAKQFGID---AEQVPAALAFIKAADLDFQG--FHIFAGSQNLN 200
Query: 204 AYRGAIAAAKAVFETAARL---GNNKMRVLDIGGGFSFTNSNTKSFQEAASI----IKEA 256
A A AK A RL +RV++IGGGF F + + A
Sbjct: 201 AEAIIEAQAK-TLALALRLAESAPAPVRVINIGGGFGIP-----YFPGNPPLDLAPVGAA 254
Query: 257 LHAYFP--NELLPGSSLRVISEPGRFFTYSAFTLYTQIIG-KRVHGEMRNYWINDG---- 309
L A F + LP ++ E GR+ A ++I K GE + + DG
Sbjct: 255 LAALFARLRDALPEV--EILLELGRYLVGEAGIYVCRVIDRKISRGET--FLVTDGGLHH 310
Query: 310 ---KYGSFDWV---NYDEAIAKCTPLTLASSLTTSKGLSRTYNSKVFGPTCDAADEVFSG 363
G+F V NY I G + + + GP C D +
Sbjct: 311 HLSASGNFGQVIRRNYPVVIG------------NRIGGAVREIASIVGPLCTPLDLLAEK 358
Query: 364 HKLPELEVTDWLVFSEMGAYTR-ARGTNFNGYNTAA 398
LP E D +V + GAY A F G+ A
Sbjct: 359 GTLPVAEPGDLVVIFQSGAYGASASPLAFLGHPEAV 394
>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 = 96.7 bits (241), Expect = 3e-22
Identities = 96/393 (24%), Positives = 160/393 (40%), Gaps = 55/393 (13%)
Query: 36 ILDLGVVVTLYNQMISKLPMIHPH-YAVKCNPEPALLEALAALGSNFDCASRSEIEAVLA 94
+ DL L ++ + P H +AVK NP +L LA G+ + AS E+E LA
Sbjct: 7 LYDLDGFRALVARLTAAFPAPVLHTFAVKANPLVPVLRLLAEAGAGAEVASPGELELALA 66
Query: 95 LGVSPDRIIYANPCKPVSHIKYAANVGVNLTTFDSVEELHKI-----RKWHPKCDLLIRI 149
G P+RI++ +P K + ++ A +GV + D+ +EL +I + +R+
Sbjct: 67 AGFPPERIVFDSPAKTRAELREALELGVAINI-DNFQELERIDALVAEFKEASSRIGLRV 125
Query: 150 KPPDDSGAKHPL-----DSKYGV---DHHPQEIVPLLEAAEASGLSVVGVAFHIGSAATK 201
P +G L SK+GV D EI+ A A + G+ H+GS +
Sbjct: 126 NPQVGAGKIGALSTATATSKFGVALEDGARDEII----DAFARRPWLNGLHVHVGSQGCE 181
Query: 202 FA-AYRGAIAAAKAVFETAARLGNNKMRVLDIGGGFSF---TNSNTKSFQEAASIIKEAL 257
+ G E R+G ++ +DIGGG + T +F + A+ +K A+
Sbjct: 182 LSLLAEGIRRVVDLAEEINRRVGRRQITRIDIGGGLPVNFESEDITPTFADYAAALKAAV 241
Query: 258 HAYFPNELLPGSSLRVISEPGRFFTYSAFTLYTQIIGKRVHGEMRNYWINDGK------- 310
F +++E GR T+ +++ + G R + G
Sbjct: 242 PELFDGRYQ------LVTEFGRSLLAKCGTIVSRVEYTKSSGGRRIAITHAGAQVATRTA 295
Query: 311 YGSFDWVNYDEAIAKCTPLTLASSLTTSKGLSRTYNSK---VFGPTCDAADEVFSGHKLP 367
Y DW PL + ++ + G +T V GP C A D + LP
Sbjct: 296 YAPDDW-----------PLRV--TVFDANGEPKTGPEVVTDVAGPCCFAGDVLAKERALP 342
Query: 368 ELEVTDWLVFSEMGAYTRARGTNFNGYNTAAIP 400
LE D++ + GAY + + + YN+ P
Sbjct: 343 PLEPGDYVAVHDTGAYYFS---SHSSYNSLPRP 372
>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 = 96.6 bits (241), Expect = 6e-22
Identities = 57/188 (30%), Positives = 84/188 (44%), Gaps = 22/188 (11%)
Query: 58 PHYAVKCNPEPALLEALAALGSNFDCASRSEIEAVLALGVSPDRIIYANPCKPVSHIKYA 117
++A K N AL+ A AA G D AS +E+ LA GV DRI+ P K + A
Sbjct: 40 VYFARKANKSLALVRAAAAAGIGVDVASLAELRQALAAGVRGDRIVATGPAKTDEFLWLA 99
Query: 118 ANVGVNLTTFDSVEELHKI-----RKWHPKCDLLIRIKPPDDSGAKHPLDSKYGVDHHPQ 172
G DS++EL ++ +L+R+ S L S++G+
Sbjct: 100 VRHGA-TIAVDSLDELDRLLALARGYTTGPARVLLRL-----SPFPASLPSRFGMP--AA 151
Query: 173 EIVPLLE--AAEASGLSVVGVAFHIG--SAATKFAAYRGAIAAAKAVFETAARLGNNKMR 228
E+ LE A + +VG FH+ SAA + AA + + + + A LG R
Sbjct: 152 EVRTALERLAQLRERVRLVGFHFHLDGYSAAQRVAALQECL----PLIDRARALGLA-PR 206
Query: 229 VLDIGGGF 236
+DIGGGF
Sbjct: 207 FIDIGGGF 214
>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 = 83.1 bits (206), Expect = 1e-19
Identities = 40/115 (34%), Positives = 58/115 (50%), Gaps = 10/115 (8%)
Query: 287 TLYTQIIGKRV-HGEMRNYWINDGKYGSFDWVNYDEAIAKCTPLTLASSLTTSKGLSRTY 345
TL T++I + + + +++DG YGS D YD A+ P++
Sbjct: 1 TLVTEVIDVKERGDDRKFVYLDDGVYGSPDPALYD-ALHPILPVSRLDD-------EPLR 52
Query: 346 NSKVFGPTCDAADEVFSGHKLP-ELEVTDWLVFSEMGAYTRARGTNFNGYNTAAI 399
+ GPTCD+ D + LP ELEV DWLVF + GAYT + +NFNG+ A
Sbjct: 53 PYTLAGPTCDSGDVLARDVSLPLELEVGDWLVFFDAGAYTISLSSNFNGFPRPAE 107
>gnl|CDD|178152 PLN02537, PLN02537, diaminopimelate decarboxylase.
Length = 410
Score = 80.6 bits (199), Expect = 1e-16
Identities = 89/356 (25%), Positives = 146/356 (41%), Gaps = 47/356 (13%)
Query: 58 PHYAVKCNPEPALLEALAALGSNFDCASRSEIEAVLALGVSPDRIIYANPCKPVSHIKYA 117
YA+K N +LE L LG S +E+ L G P R I+ K + + A
Sbjct: 46 IGYAIKANNNLKILEHLRELGCGAVLVSGNELRLALRAGFDPTRCIFNGNGKLLEDLVLA 105
Query: 118 ANVGVNLTTFDSVEELHKI----RKWHPKCDLLIRIKPPDDSGAKHPL------DSKYGV 167
A GV DS +L I R K ++L+RI P D HP +SK+G+
Sbjct: 106 AQEGV-FVNVDSEFDLENIVEAARIAGKKVNVLLRINPDVDPQV-HPYVATGNKNSKFGI 163
Query: 168 DHHPQEIVPLLEA--AEASGLSVVGVAFHIGSAATKFAAYRGAIAAAKAVFETAARLGNN 225
+ +++ L+A A + L +VG H+GS TK +R A A + R
Sbjct: 164 RN--EKLQWFLDAVKAHPNELKLVGAHCHLGSTITKVDIFRDA-AVLMVNYVDEIRAQGF 220
Query: 226 KMRVLDIGGGFSFTNSNTKSFQEAASIIKEALHAYFPNELLPGSSLRVISEPGRFFTYSA 285
++ L+IGGG + + + + + EL+ L +I EPGR +
Sbjct: 221 ELSYLNIGGGLGIDYYHAGAVLPTPRDLIDTVR-----ELVLSRDLTLIIEPGRSLIANT 275
Query: 286 FTLYTQIIGKRVHGEMRNYWINDGK---------YGSFDWVNYDEAIAKCTPLTLASSLT 336
++ G + +G +N+ + DG Y ++ + E ++ P S
Sbjct: 276 CCFVNRVTGVKTNGT-KNFIVIDGSMAELIRPSLYDAYQHI---ELVSPPPPDAEVS--- 328
Query: 337 TSKGLSRTYNSKVFGPTCDAADEVFSGHKLPELEVTDWLVFSEMGAYTRARGTNFN 392
T++ V GP C++AD + +LP LV + GAY + + +N
Sbjct: 329 -------TFD--VVGPVCESADFLGKDRELPTPPKGAGLVVHDAGAYCMSMASTYN 375
>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 = 78.0 bits (193), Expect = 9e-16
Identities = 67/276 (24%), Positives = 121/276 (43%), Gaps = 36/276 (13%)
Query: 60 YAVKCNPEPALLEALAALGSNFD----CASRSEIEAVLALGVSPDRIIYANPCKPVSHIK 115
Y +K N + ++E + G ++ S+ E+ A LAL +PD +I N K +I+
Sbjct: 43 YPIKVNQQREVVEEIVKAGKRYNIGLEAGSKPELLAALALLKTPDALIICNGYKDDEYIE 102
Query: 116 ---YAANVGVNLT-TFDSVEELHKI----RKWHPKCDLLIRIKPPDDSGAK----HPLDS 163
A +G N+ + + EL I +K K L +RIK K S
Sbjct: 103 LALLARKLGHNVIIVIEKLSELDLILELAKKLGVKPLLGVRIKLASKGSGKWQESGGDRS 162
Query: 164 KYGVDHHPQEIVPLLEAAEASGL--SVVGVAFHIGSAATKFAAYRGAIAAAKAVFETAAR 221
K+G+ EI+ ++E + +G+ + + FHIGS T + A+ A ++ +
Sbjct: 163 KFGLT--ASEILEVVEKLKEAGMLDRLKLLHFHIGSQITDIRRIKSALREAARIYAELRK 220
Query: 222 LGNNKMRVLDIGGGFSFTNSNTKS---------FQEAASIIKEALHAYFPNELLPGSSLR 272
LG N +R LDIGGG ++S +E A+ I + + +P ++
Sbjct: 221 LGAN-LRYLDIGGGLGVDYDGSRSSSDSSFNYSLEEYANDIVKTVKEICDEAGVPHPTI- 278
Query: 273 VISEPGRFFT-YSAFTLYTQIIGKRVHGEMRNYWIN 307
++E GR + + ++ +++G V Y+ N
Sbjct: 279 -VTESGRAIVAHHSVLIF-EVLG--VKRLADWYFCN 310
>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 = 77.3 bits (191), Expect = 1e-15
Identities = 71/292 (24%), Positives = 117/292 (40%), Gaps = 39/292 (13%)
Query: 31 EVPFYILDLGVVVTLYNQMISKLP-MIHPHYAVKCNPEPALLEALAALGSNFDCASRSEI 89
+ Y+ DL + + + LP YA+K N +P +L ALA F+ AS EI
Sbjct: 1 PLCAYVYDLAALRAHARALRASLPPGCELFYAIKANSDPPILRALAPHVDGFEVASGGEI 60
Query: 90 EAVLALGVSPD-RIIYANPCKPVSHIKYAANVGVNLTTFDSVEELHKI----RKWHPKCD 144
V A PD +I+ P K S + A GV +S EL ++ R+
Sbjct: 61 AHVRAA--VPDAPLIFGGPGKTDSELAQALAQGVERIHVESELELRRLNAVARRAGRTAP 118
Query: 145 LLIRIKP--PDDSGAKHPLDSK---YGVDHHPQEIVPLLEAA-EASGLSVVGVAFHIGSA 198
+L+R+ PD + + + +G+D ++ LE + + + G FH+ S
Sbjct: 119 VLLRVNLALPDLPSSTLTMGGQPTPFGID--EADLPDALELLRDLPNIRLRGFHFHLMSH 176
Query: 199 ---ATKFAAYRGAIAAAKAVFETA---ARLGNNKMRVLDIGGGFSFTNSNTKS---FQEA 249
A A KA ETA A + V+++GGG ++ + +
Sbjct: 177 NLDAAAHLAL------VKAYLETARQWAAEHGLDLDVVNVGGGIGVNYADPEEQFDWAGF 230
Query: 250 ASIIKEALHAYFPNELLPGSSLRVISEPGRFFT-YSAFTLYTQIIGKRVHGE 300
+ + L Y P L + E GR+ + Y + + + KR HGE
Sbjct: 231 CEGLDQLLAEYEP-------GLTLRFECGRYISAYCGYYVTEVLDLKRSHGE 275
>gnl|CDD|224088 COG1166, SpeA, Arginine decarboxylase (spermidine biosynthesis)
[Amino acid transport and metabolism].
Length = 652
Score = 52.7 bits (127), Expect = 2e-07
Identities = 60/270 (22%), Positives = 103/270 (38%), Gaps = 48/270 (17%)
Query: 60 YAVKCNPEPALLEALAALGSNFDCA----SRSEIEAVLALGVSPDRIIYANPCKPVSHIK 115
Y +K N ++E+L A G + S++E+ AVLA +P +I N K +I+
Sbjct: 118 YPIKVNQHRRVVESLVASGKGYPLGLEAGSKAELMAVLAHAGNPGSLIVCNGYKDREYIR 177
Query: 116 YA---ANVGVNLT-TFDSVEELHKI------RKWHPKCDLLIRI------KPPDDSGAKH 159
A +G + + + EL + P+ + R+ K G K
Sbjct: 178 LALIGEKLGHKVYIVIEKLSELDLVLEEAKQLGVKPRLGVRARLASQGSGKWQSSGGEK- 236
Query: 160 PLDSKYGVDHHPQEIVPLLEAAEASGL--SVVGVAFHIGSAATKFAAYRGAIAAAKAVFE 217
SK+G+ +++ ++E + L S+ + FH+GS + + + A +
Sbjct: 237 ---SKFGLS--ATQVLQVVERLREANLLDSLQLLHFHLGSQISNIRDIKTGVREAARFYV 291
Query: 218 TAARLGNNKMRVLDIGGG---------FSFTNSNTKSFQEAA----SIIKEALHAYFPNE 264
+LG N ++ D+GGG S E A +K+A
Sbjct: 292 ELRKLGAN-IKYFDVGGGLGVDYDGTRTQSDCSKNYGLNEYANDVVWALKDACEEK---G 347
Query: 265 LLPGSSLRVISEPGRFFTYSAFTLYTQIIG 294
L +ISE GR T L +IG
Sbjct: 348 LPHP---TIISESGRAITAHHAVLIANVIG 374
>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 = 52.0 bits (125), Expect = 4e-07
Identities = 58/273 (21%), Positives = 104/273 (38%), Gaps = 38/273 (13%)
Query: 60 YAVKCNPEPALLEALAALGSNF----DCASRSEIEAVLALGVSPDRIIYANPCKPVSHIK 115
Y +K N ++E + A G + S+ E+ A +A P I N K +I+
Sbjct: 95 YPIKVNQHRRVVEDIVASGKGEPYGLEAGSKPELMAAMAYATKPGAPIVCNGYKDREYIE 154
Query: 116 ---YAANVGVNLT-TFDSVEELHKI----RKWHPKCDLLIRIKPPD-------DSGAKHP 160
+G N+ + + EL + +K K L +R + SG +
Sbjct: 155 LALIGRKLGHNVFIVIEKLSELDLVIDEAKKLGVKPKLGLRARLASKGSGKWASSGGEK- 213
Query: 161 LDSKYGVDHHPQEIVPLLEAAEASGL--SVVGVAFHIGSAATKFAAYRGAIAAAKAVFET 218
SK+G+ +++ ++ E +GL S+ + FHIGS + + + A +
Sbjct: 214 --SKFGLS--ATQVLEVVRLLEQNGLLDSLQLLHFHIGSQISNIDDIKKGVREAARFYCE 269
Query: 219 AARLGNNKMRVLDIGGGFSFTNSNTKSFQEAASIIKEALHAYFPNELLPGSSL------- 271
+LG K+ +D+GGG T S + + L Y + + +
Sbjct: 270 LRKLG-VKITYVDVGGGLGVDYDGTSS--SSDCSVNYGLEEYANDIVQALREICEEKGVP 326
Query: 272 --RVISEPGRFFTYSAFTLYTQIIGKRVHGEMR 302
+I+E GR T L T ++G H
Sbjct: 327 HPVIITESGRAITAHHAVLITNVLGVERHEYDP 359
>gnl|CDD|236867 PRK11165, PRK11165, diaminopimelate decarboxylase; Provisional.
Length = 420
Score = 46.8 bits (112), Expect = 1e-05
Identities = 85/380 (22%), Positives = 143/380 (37%), Gaps = 90/380 (23%)
Query: 60 YAVKCNPEPALLEALAALGSNFDCASRSEIEAVLALGVSPDR----------IIYANPCK 109
+A K +L + G D S EIE LA G P +I
Sbjct: 51 FAQKACSNIHILRLMREQGVKVDAVSLGEIERALAAGYKPGTEPDEIVFTADVIDRATLA 110
Query: 110 PVSHIKYAANVGVNLTTFDSVEELHKIRKWHPKCDLLIRIKP--------PDDSGAKHPL 161
V +K N G S++ L ++ + P + +RI P ++G ++
Sbjct: 111 RVVELKIPVNAG-------SIDMLDQLGQVSPGHRVWLRINPGFGHGHSQKTNTGGEN-- 161
Query: 162 DSKYGVDHHPQEIVPLLEAAEASGLSVVGVAFHIGSAATKFAAYRGAIAAAKAVFETAAR 221
SK+G+ H +++ L + GL +VG+ HIGS Y A+
Sbjct: 162 -SKHGIWH--EDLPAALAVIQRYGLKLVGIHMHIGSGVD----YGHLEQVCGAMVRQVIE 214
Query: 222 LGNNKMRVLDIGGGFSF------TNSNTKSFQEAASIIKEALHAYFPNELLPGSSLRVIS 275
LG + + GGG S +T+ + ++ + + G +++
Sbjct: 215 LG-QDIEAISAGGGLSIPYREGEEPVDTEHYFGLWDAARKRIARHL------GHPVKLEI 267
Query: 276 EPGRFFTYSAFTLYTQIIGKRVHGEM--RNYWI-----ND----GKYGSFDWVNYDEAIA 324
EPGRF + L Q+ R +M R++ + ND YGS+ +
Sbjct: 268 EPGRFLVAESGVLVAQV---RAVKQMGSRHFVLVDAGFNDLMRPAMYGSYHHI------- 317
Query: 325 KCTPLTLASSLTTSKGLSRTYNSK----VFGPTCDAADEVFSGH--------KLPELEVT 372
S+ + G S V GP C++ D VF+ LP+++V
Sbjct: 318 ---------SVLAADGRSLEEAPTVDTVVAGPLCESGD-VFTQQEGGVVETRALPQVQVG 367
Query: 373 DWLVFSEMGAYTRARGTNFN 392
D+LVF + GAY + +N+N
Sbjct: 368 DYLVFHDTGAYGASMSSNYN 387
>gnl|CDD|215240 PLN02439, PLN02439, arginine decarboxylase.
Length = 559
Score = 45.4 bits (108), Expect = 4e-05
Identities = 54/213 (25%), Positives = 87/213 (40%), Gaps = 23/213 (10%)
Query: 60 YAVKCNPEPALLEALAALGS--NFDCASRSEIEAVLALGV----SPDRIIYANPCKPVSH 113
+ VKCN + L+E + GS F + S+ E +LA+ SPD + N K +
Sbjct: 37 FPVKCNQDRFLVEDIVKFGSPFRFGLEAGSKPELLLAMSCLCKGSPDAFLICNGYKDAEY 96
Query: 114 IKYA---ANVGVN-------LTTFDSVEELHKIRKWHPKCDLL--IRIKPPDDSGAKHPL 161
+ A +G+N D V E + P + +R K G+
Sbjct: 97 VSLALLARKLGLNTVIVLEQEEELDLVIEASQRLGVRPVIGVRAKLRTKHSGHFGSTSGE 156
Query: 162 DSKYGVDHHPQEIVPLLEAAEASGLS--VVGVAFHIGSAATKFAAYRGAIAAAKAVFETA 219
K+G+ EIV ++ G+ + + FHIGS + + ++ A ++
Sbjct: 157 KGKFGLT--ATEIVRVVRKLRKEGMLDCLQLLHFHIGSQIPSTSLLKDGVSEAAQIYCEL 214
Query: 220 ARLGNNKMRVLDIGGGFSFTNSNTKSFQEAASI 252
RLG MRV+DIGGG +KS S+
Sbjct: 215 VRLGAP-MRVIDIGGGLGIDYDGSKSGSSDMSV 246
>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 = 38.7 bits (91), Expect = 0.004
Identities = 19/50 (38%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 351 GPTCDAADEVFSGHKLPE-LEVTDWLVFSEMGAYTRARGTNFNGYNTAAI 399
G +C A D V + E L+V D LVF +M YT + FNG +I
Sbjct: 294 GNSCLAGD-VIGDYSFDEPLQVGDRLVFEDMAHYTMVKTNTFNGVRLPSI 342
>gnl|CDD|235427 PRK05354, PRK05354, arginine decarboxylase; Provisional.
Length = 634
Score = 36.6 bits (86), Expect = 0.021
Identities = 65/271 (23%), Positives = 110/271 (40%), Gaps = 50/271 (18%)
Query: 60 YAVKCNPEPALLEALAALGSNFD----CASRSEIEAVLALGVSPDRIIYANPCKPVSHIK 115
Y +K N + ++E + A G ++ S+ E+ AVLAL P +I N K +I+
Sbjct: 102 YPIKVNQQRRVVEEIVASGKPYNLGLEAGSKPELMAVLALAGDPGALIVCNGYKDREYIR 161
Query: 116 ---YAANVGVNLT-TFDSVEELHKI----RKWHPKCDLLIRIKP--------PDDSGAKH 159
+G + + + EL I ++ K L +R + G K
Sbjct: 162 LALIGRKLGHKVFIVIEKLSELELILEEAKELGVKPRLGVRARLASQGSGKWQSSGGEK- 220
Query: 160 PLDSKYGVDHHPQEIVPLLEAAEASGL--SVVGVAFHIGSAATKFAAYRGAIAAAKAVFE 217
SK+G+ E++ +E +GL + + FH+GS + A+ A +
Sbjct: 221 ---SKFGL--SATEVLEAVERLREAGLLDCLQLLHFHLGSQIANIRDIKTAVREAARFYV 275
Query: 218 TAARLGNNKMRVLDIGGG----FSFTNSNTK-----SFQE-AASI---IKEALHAYFPNE 264
+LG ++ LD+GGG + T S + S QE A + +KE +
Sbjct: 276 ELRKLGAP-IQYLDVGGGLGVDYDGTRSQSDSSVNYSLQEYANDVVYTLKEICEEH--GV 332
Query: 265 LLPGSSLRVISEPGRFFT-YSAFTLYTQIIG 294
P +ISE GR T + A L ++G
Sbjct: 333 PHP----TIISESGRALTAHHAV-LVFNVLG 358
>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 = 35.4 bits (82), Expect = 0.025
Identities = 16/81 (19%), Positives = 25/81 (30%), Gaps = 2/81 (2%)
Query: 177 LLEAAEASGLSVVGVAFHIGSAATKFAAYRGAIAAAKAVFETAARLGNNKMRVLDIGGGF 236
L + GL + + +G A+ A K E AA LG + V G
Sbjct: 31 LKALLKEYGLEISSLNPSLGLLEPDEHERAAALEALKRAIELAAALGAKVVVV--HPGSA 88
Query: 237 SFTNSNTKSFQEAASIIKEAL 257
++ A + E
Sbjct: 89 PAGKDREEALDRLAESLNELA 109
>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 = 34.8 bits (80), Expect = 0.073
Identities = 18/44 (40%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 351 GPTCDAADEVFSGHKLPE-LEVTDWLVFSEMGAYTRARGTNFNG 393
G TC A D V + + L+V D +VF +M YT + T FNG
Sbjct: 308 GNTCLAGD-VMGEYAFDKPLKVGDKIVFLDMIHYTMVKNTTFNG 350
>gnl|CDD|143494 cd06820, PLPDE_III_LS_D-TA_like, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzymes, Low Specificity D-Threonine
Aldolase-like. This subfamily is composed of
uncharacterized bacterial proteins with similarity to
low specificity D-threonine aldolase (D-TA), which is a
fold type III PLP-dependent enzyme that catalyzes the
interconversion between D-threonine/D-allo-threonine and
glycine plus acetaldehyde. Both PLP and divalent cations
(eg. Mn2+) are required for catalytic activity. Low
specificity D-TAs show similarity to bacterial alanine
racemase (AR), which contains an N-terminal PLP-binding
TIM-barrel domain and a C-terminal beta-sandwich domain.
AR 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. Based on its similarity to AR, it is possible
that low specificity D-TAs also form dimers in solution.
Experimental data show that the monomeric form of low
specificity D-TAs exhibit full catalytic activity.
Length = 353
Score = 30.7 bits (70), Expect = 1.3
Identities = 20/71 (28%), Positives = 29/71 (40%), Gaps = 2/71 (2%)
Query: 166 GVDHHPQEIVPLLEA-AEASGLSVVGVAFHIGSAATKFAAYRGAIAAAKAVFETAARLGN 224
GV P++ V L A A A GL G+ + G + A A A+A+ A L
Sbjct: 136 GV-QTPEDAVALARAIASAPGLRFRGIFTYPGHSYAPGALEEAAADEAEALLAAAGILEE 194
Query: 225 NKMRVLDIGGG 235
+ + GG
Sbjct: 195 AGLEPPVVSGG 205
>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 = 27.9 bits (63), Expect = 3.3
Identities = 10/18 (55%), Positives = 16/18 (88%)
Query: 177 LLEAAEASGLSVVGVAFH 194
L EAA+A+G +++G+AFH
Sbjct: 24 LREAAKAAGATLLGIAFH 41
>gnl|CDD|219922 pfam08595, RXT2_N, RXT2-like, N-terminal. The family represents
the N-terminal region of RXT2-like proteins. In S.
cerevisiae, RXT2 has been demonstrated to be involved in
conjugation with cellular fusion (mating) and invasive
growth. A high throughput localisation study has
localised RXT2 to the nucleus.
Length = 141
Score = 28.1 bits (63), Expect = 4.3
Identities = 11/24 (45%), Positives = 13/24 (54%)
Query: 327 TPLTLASSLTTSKGLSRTYNSKVF 350
PLT S L T +SRT+ SK
Sbjct: 87 APLTHPSDLPTHPAISRTFKSKTL 110
>gnl|CDD|213852 TIGR03707, PPK2_P_aer, polyphosphate kinase 2, PA0141 family.
Members of this protein family are designated
polyphosphate kinase 2 (PPK2) after the characterized
protein in Pseudomonas aeruginosa. This family comprises
one of three well-separated clades in the larger family
described by pfam03976. PA0141 from this family has been
shown capable of operating in reverse, with GDP
preferred (over ADP) as a substrate, producing GTP (or
ATP) by transfer of a phosphate residue from
polyphosphate. Most species with a member of this family
also encode a polyphosphate kinase 1 (PPK1) [Central
intermediary metabolism, Phosphorus compounds].
Length = 230
Score = 28.4 bits (64), Expect = 5.5
Identities = 11/26 (42%), Positives = 14/26 (53%)
Query: 382 AYTRARGTNFNGYNTAAIPTYVVRSN 407
YTRA+ F +T P VVRS+
Sbjct: 179 DYTRAKDEMFARTDTEEAPWTVVRSD 204
>gnl|CDD|107313 cd06318, PBP1_ABC_sugar_binding_like_9, Periplasmic sugar-binding
domain of uncharacterized ABC-type transport systems.
Periplasmic sugar-binding domain of uncharacterized
ABC-type transport systems that share homology with a
family of pentose/hexose sugar-binding proteins of the
type I periplasmic binding protein superfamily, which
consists of two domains connected by a three-stranded
hinge. The substrate specificity of this group is not
known, but it is predicted to be involved in the
transport of sugar-containing molecules and chemotaxis.
Length = 282
Score = 28.6 bits (64), Expect = 5.6
Identities = 18/67 (26%), Positives = 30/67 (44%), Gaps = 4/67 (5%)
Query: 171 PQEIVPLLEAAEASGLSVVGVAFHIGSAATKFAAYRGA--IAAAKAVFETAA-RLGNNKM 227
P+ +VP + AA+A+G+ VV V I A + V E LG+ M
Sbjct: 66 PEGLVPAVAAAKAAGVPVVVVDSSINLEA-GVVTQVQSSNAKNGNLVGEWVVGELGDKPM 124
Query: 228 RVLDIGG 234
+++ + G
Sbjct: 125 KIILLSG 131
>gnl|CDD|180921 PRK07306, PRK07306, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 720
Score = 28.9 bits (65), Expect = 6.7
Identities = 13/47 (27%), Positives = 18/47 (38%), Gaps = 6/47 (12%)
Query: 345 YNSKVFGPTCDAADEVFSGHKLPELEVTDWLVFSEM----GAYTRAR 387
Y + F P D E+F G +P DW + G Y + R
Sbjct: 531 YVTGDFVPKSDKVKELFKGIFIPTAA--DWAALRDAVMKDGLYHQNR 575
>gnl|CDD|223866 COG0795, COG0795, Predicted permeases [General function prediction
only].
Length = 364
Score = 28.5 bits (64), Expect = 6.8
Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 3/46 (6%)
Query: 58 PHYAVKCNPEPALLEALAALGSNFDCASRSEIEAVLALGVSPDRII 103
P P L+ AL LG + SE+ + A GVS R++
Sbjct: 59 PTLLPLVLPLALLIAALLTLGR---LSRESELVVLRASGVSLKRLL 101
>gnl|CDD|233812 TIGR02290, M3_fam_3, oligoendopeptidase, pepF/M3 family. The M3
family of metallopeptidases contains several distinct
clades. Oligoendopeptidase F as characterized in
Lactococcus, the functionally equivalent
oligoendopeptidase B of group B Streptococcus, and
closely related sequences are described by TIGR00181.
The present family is quite similar but forms a distinct
clade, and a number of species have one member of each.
A greater sequence difference separates members of
TIGR02289, probable oligoendopeptidases of the M3 family
that probably should not be designated PepF.
Length = 587
Score = 28.5 bits (64), Expect = 8.2
Identities = 12/45 (26%), Positives = 21/45 (46%)
Query: 219 AARLGNNKMRVLDIGGGFSFTNSNTKSFQEAASIIKEALHAYFPN 263
A LG K+ D+ +++ T +F EA ++ EA + P
Sbjct: 282 AKLLGKEKLDFYDLYAPLGDSSAKTYTFDEAKELVLEAFGKFSPE 326
>gnl|CDD|218480 pfam05176, ATP-synt_10, ATP10 protein. ATP 10 is essential for the
assembly of a functional mitochondrial ATPase complex.
Length = 255
Score = 28.0 bits (63), Expect = 8.6
Identities = 12/36 (33%), Positives = 15/36 (41%), Gaps = 2/36 (5%)
Query: 237 SFTNSNTKSFQEAASIIKEALHAYFPNELLPGSSLR 272
F +N K F S+ K YFPN G +L
Sbjct: 79 EFRKTNGKLFLAPPSLFKADKALYFPN--FSGRTLA 112
>gnl|CDD|224165 COG1244, COG1244, Predicted Fe-S oxidoreductase [General function
prediction only].
Length = 358
Score = 28.1 bits (63), Expect = 9.4
Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 9/40 (22%)
Query: 217 ETAARLGNNKMRVLDIGGGFSFTNSNTKSFQEAASIIKEA 256
ETA N+K+R I GF+F + F AA II+
Sbjct: 172 ETA----NDKIREDSINKGFTFED-----FVRAAEIIRNY 202
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 0.0690 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,241,650
Number of extensions: 2088310
Number of successful extensions: 2284
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2207
Number of HSP's successfully gapped: 59
Length of query: 409
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 310
Effective length of database: 6,546,556
Effective search space: 2029432360
Effective search space used: 2029432360
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 (27.0 bits)