RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 012098
(471 letters)
>gnl|CDD|178152 PLN02537, PLN02537, diaminopimelate decarboxylase.
Length = 410
Score = 834 bits (2157), Expect = 0.0
Identities = 355/385 (92%), Positives = 370/385 (96%)
Query: 75 LYCEDVRVQDVMETVEKRPFYLYSKPQITRNVEAYKQALEGLNSIIGYAIKANNNYKILE 134
LYCE +RVQD+ME+VEKRPFYLYSKPQITRN EAYK+ALEGL SIIGYAIKANNN KILE
Sbjct: 1 LYCEGLRVQDIMESVEKRPFYLYSKPQITRNYEAYKEALEGLRSIIGYAIKANNNLKILE 60
Query: 135 HLRKLGCGAVLVSGNELRLALRAGFDPTKCIFNGNGKLLEDLVLAAQEGVFVNVDSEFDL 194
HLR+LGCGAVLVSGNELRLALRAGFDPT+CIFNGNGKLLEDLVLAAQEGVFVNVDSEFDL
Sbjct: 61 HLRELGCGAVLVSGNELRLALRAGFDPTRCIFNGNGKLLEDLVLAAQEGVFVNVDSEFDL 120
Query: 195 ENIVVASRIAGKKVNVLLRINPDVDPQVHPYVATGNKNSKFGIRNEKLQWFLDAVKAHPN 254
ENIV A+RIAGKKVNVLLRINPDVDPQVHPYVATGNKNSKFGIRNEKLQWFLDAVKAHPN
Sbjct: 121 ENIVEAARIAGKKVNVLLRINPDVDPQVHPYVATGNKNSKFGIRNEKLQWFLDAVKAHPN 180
Query: 255 ELKLVGAHCHLGSTITKVDIFRDAAVLMVNYIDKIRAQGFEVDYLNIGGGLGIDYYHTGA 314
ELKLVGAHCHLGSTITKVDIFRDAAVLMVNY+D+IRAQGFE+ YLNIGGGLGIDYYH GA
Sbjct: 181 ELKLVGAHCHLGSTITKVDIFRDAAVLMVNYVDEIRAQGFELSYLNIGGGLGIDYYHAGA 240
Query: 315 VLPKPRNLIDTVRELVLSRNLNLIIEPGRSLIANTCCLVNHVTGVKTNGTKNFIVIDGSM 374
VLP PR+LIDTVRELVLSR+L LIIEPGRSLIANTCC VN VTGVKTNGTKNFIVIDGSM
Sbjct: 241 VLPTPRDLIDTVRELVLSRDLTLIIEPGRSLIANTCCFVNRVTGVKTNGTKNFIVIDGSM 300
Query: 375 AELIRPSLYDAYQHIELVSPAPQDAEISKFDVVGPVCESADFLGKERELPTPDRGAGLVV 434
AELIRPSLYDAYQHIELVSP P DAE+S FDVVGPVCESADFLGK+RELPTP +GAGLVV
Sbjct: 301 AELIRPSLYDAYQHIELVSPPPPDAEVSTFDVVGPVCESADFLGKDRELPTPPKGAGLVV 360
Query: 435 HDAGAYCMSMASTYNLKMRPPEYWV 459
HDAGAYCMSMASTYNLKMRPPEYWV
Sbjct: 361 HDAGAYCMSMASTYNLKMRPPEYWV 385
>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 = 462 bits (1191), Expect = e-162
Identities = 160/373 (42%), Positives = 217/373 (58%), Gaps = 9/373 (2%)
Query: 93 PFYLYSKPQITRNVEAYKQALEGLNSIIGYAIKANNNYKILEHLRKLGCGAVLVSGNELR 152
P Y+Y + I N K+A G I YA+KAN+N IL+ L + G GA +VSG EL
Sbjct: 4 PLYVYDEATIRENYRRLKEAFSGPGFKICYAVKANSNLAILKLLAEEGLGADVVSGGELY 63
Query: 153 LALRAGFDPTKCIFNGNGKLLEDLVLAAQEGVF-VNVDSEFDLENIVVASRIAGKKVNVL 211
AL+AGF P + +F GNGK E+L LA + G+ +NVDS +LE + + GK V
Sbjct: 64 RALKAGFPPERIVFTGNGKSDEELELALELGILRINVDSLSELERLGEIAPELGKGAPVA 123
Query: 212 LRINPDVDPQVHPYVATGNKNSKFGIRNEKLQWFLDAVKAHPNELKLVGAHCHLGSTITK 271
LR+NP VD HPY++TG K+SKFGI E+ K P LKLVG HCH+GS I
Sbjct: 124 LRVNPGVDAGTHPYISTGGKDSKFGIPLEQALEAYRRAKELPG-LKLVGLHCHIGSQILD 182
Query: 272 VDIFRDAAVLMVNYIDKIRAQGFEVDYLNIGGGLGIDYYHTGAVLPKPRNLIDTVRELV- 330
++ F +AA +++ ++R G ++++L++GGGLGI Y L + + E +
Sbjct: 183 LEPFVEAAEKLLDLAAELRELGIDLEFLDLGGGLGIPYRDEDEPLD-IEEYAEAIAEALK 241
Query: 331 ----LSRNLNLIIEPGRSLIANTCCLVNHVTGVKTNGTKNFIVIDGSMAELIRPSLYDAY 386
+L LIIEPGR ++AN L+ V VK G K F+ +D M +LIRP+LY AY
Sbjct: 242 ELCEGGPDLKLIIEPGRYIVANAGVLLTRVGYVKETGGKTFVGVDAGMNDLIRPALYGAY 301
Query: 387 QHIELVSPAPQDAEISKFDVVGPVCESADFLGKERELPTPDRGAGLVVHDAGAYCMSMAS 446
I V+ P + E K DVVGP+CES D K+RELP + G L +HDAGAY SM+S
Sbjct: 302 HEIVPVNK-PGEGETEKVDVVGPICESGDVFAKDRELPEVEEGDLLAIHDAGAYGYSMSS 360
Query: 447 TYNLKMRPPEYWV 459
YN + RP E V
Sbjct: 361 NYNSRPRPAEVLV 373
>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 = 364 bits (936), Expect = e-123
Identities = 166/395 (42%), Positives = 238/395 (60%), Gaps = 13/395 (3%)
Query: 72 DGFLYCEDVRVQDVMETVEKRPFYLYSKPQITRNVEAYKQALEGLNSIIGYAIKANNNYK 131
DG L+ E V + ++ + P Y+Y + I R AYK+A G S++ YA+KAN+N
Sbjct: 6 DGELFIEGVPLLELAQEF-GTPLYVYDEDTIRRRFRAYKEAFGG-RSLVCYAVKANSNLA 63
Query: 132 ILEHLRKLGCGAVLVSGNELRLALRAGFDPTKCIFNGNGKLLEDLVLAAQEGVFVNVDSE 191
+L L +LG G +VSG EL AL AGF P K +F+GNGK +L A + G+ +NVDS
Sbjct: 64 VLRLLAELGSGFDVVSGGELYRALAAGFPPEKIVFSGNGKSRAELERALELGICINVDSF 123
Query: 192 FDLENIVVASRIAGKKVNVLLRINPDVDPQVHPYVATGNKNSKFGIR-NEKLQWFLDAVK 250
+LE + + GKK + LR+NP VD + HPY++TG K+SKFGI E L+ +L A++
Sbjct: 124 SELERLNEIAPELGKKARISLRVNPGVDAKTHPYISTGLKDSKFGIDVEEALEAYLYALQ 183
Query: 251 AHPNELKLVGAHCHLGSTITKVDIFRDAAVLMVNYIDKIRAQGFEVDYLNIGGGLGIDYY 310
L+LVG HCH+GS IT + F +AA +V + + +G ++++L++GGGLGI Y
Sbjct: 184 LP--HLELVGIHCHIGSQITDLSPFVEAAEKVVKLAESLA-EGIDLEFLDLGGGLGIPYT 240
Query: 311 HTGAVLPKP----RNLIDTV-RELVLSRNLNLIIEPGRSLIANTCCLVNHVTGVKTNGTK 365
P + +++ + L + LI+EPGRS++AN L+ V VK G++
Sbjct: 241 PEEEP-PDLSEYAQAILNALEGYADLGLDPKLILEPGRSIVANAGVLLTRVGFVKETGSR 299
Query: 366 NFIVIDGSMAELIRPSLYDAYQHIELVSPAPQDAEISKFDVVGPVCESADFLGKERELPT 425
NF+++D M +LIRP+LY AY HI +++ DA DVVGPVCES D L K+RELP
Sbjct: 300 NFVIVDAGMNDLIRPALYGAYHHIIVLNR-TNDAPTEVADVVGPVCESGDVLAKDRELPE 358
Query: 426 PDRGAGLVVHDAGAYCMSMASTYNLKMRPPEYWVR 460
+ G L V DAGAY SM+S YN + RP E V
Sbjct: 359 VEPGDLLAVFDAGAYGFSMSSNYNSRPRPAEVLVD 393
>gnl|CDD|223098 COG0019, LysA, Diaminopimelate decarboxylase [Amino acid transport
and metabolism].
Length = 394
Score = 345 bits (888), Expect = e-116
Identities = 160/392 (40%), Positives = 221/392 (56%), Gaps = 13/392 (3%)
Query: 72 DGFLYCEDVRVQDVMETVEKRPFYLYSKPQITRNVEAYKQALEGLNSIIGYAIKANNNYK 131
DG L E V + + E P Y+Y + + RN K A G + + YA+KAN+N
Sbjct: 8 DGELTIEGVDLPALAEEFG-TPVYVYDEATLRRNARELKSAFPGSGAKVFYAVKANSNPA 66
Query: 132 ILEHLRKLGCGAVLVSGNELRLALRAGFDPTKCIFNGNGKLLEDLVLAAQEGV-FVNVDS 190
IL L + G G + S EL LAL AGF P + +F+G K E++ A + G+ +NVDS
Sbjct: 67 ILRLLAEEGSGFDVASLGELELALAAGFPPERIVFSGPAKSEEEIAFALELGIKLINVDS 126
Query: 191 EFDLENIVVASRIA-GKKVNVLLRINPDVDPQVHPYVATGNKNSKFGIRNEKLQWFLDAV 249
E +LE + S IA G V LRINP V H Y+ATG K+SKFGI E+ L+
Sbjct: 127 EEELERL---SAIAPGLVARVSLRINPGVSAGTHEYIATGGKSSKFGISPEEALDVLERA 183
Query: 250 KAHPNELKLVGAHCHLGSTITKVDIFRDAAVLMVNYIDKI-RAQGFEVDYLNIGGGLGID 308
L+LVG H H+GS IT +D F +A + ++ G ++++LN+GGGLGI
Sbjct: 184 AKLLG-LELVGLHFHIGSQITDLDPFEEALAKVEELFGRLAEELGIQLEWLNLGGGLGIT 242
Query: 309 YYHTGAVLPKPRNLIDTVRELV--LSRNLNLIIEPGRSLIANTCCLVNHVTGVKTNGTKN 366
Y P ++E + ++ LI+EPGR+++AN LV V VK NG +N
Sbjct: 243 YEDEYDP-PDLAAYAKALKEAFGEYAEDVELILEPGRAIVANAGVLVTEVLDVKENGERN 301
Query: 367 FIVIDGSMAELIRPSLYDAYQHIELVSPAPQDAEISKFDVVGPVCESADFLGKERELPTP 426
F+++DG M +L+RP+LY AY HI L +DAE ++DVVGP CES D L ++R LP P
Sbjct: 302 FVIVDGGMNDLMRPALYGAYHHIRLNRTD-EDAEREEYDVVGPTCESGDVLARDRALPEP 360
Query: 427 -DRGAGLVVHDAGAYCMSMASTYNLKMRPPEY 457
G LV+ DAGAY SM+S YN + RP E
Sbjct: 361 LKVGDLLVILDAGAYGASMSSNYNGRPRPAEV 392
>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 = 274 bits (702), Expect = 2e-88
Identities = 131/372 (35%), Positives = 188/372 (50%), Gaps = 14/372 (3%)
Query: 93 PFYLYSKPQITRNVEAYKQALEGLNSIIGYAIKANNNYKILEHLRKLGCGAVLVSGNELR 152
PFY+Y I + A K+AL + YA+KAN N +L L + G G + S EL
Sbjct: 2 PFYVYDLDIIRAHYAALKEALPS-GVKLFYAVKANPNPHVLRTLAEAGTGFDVASKGELA 60
Query: 153 LALRAGFDPTKCIFNGNGKLLEDLVLAAQEGV-FVNVDSEFDLENIVVASRIAGKKVNVL 211
LAL AG P + IF G K + ++ A GV + VDS +LE + ++ G K +L
Sbjct: 61 LALAAGVPPERIIFTGPAKSVSEIEAALASGVDHIVVDSLDELERLNELAKKLGPKARIL 120
Query: 212 LRINPDVDPQVHPYVATGNKNSKFGIRNEKLQWFLDAVKAHPNELKLVGAHCHLGSTITK 271
LR+NPDV H ++TG SKFG+ + + L+ K +L+LVG H H+GS I
Sbjct: 121 LRVNPDVSAGTH-KISTGGLKSKFGLSLSEARAALERAKEL--DLRLVGLHFHVGSQILD 177
Query: 272 VDIFRDAAVLMVNYIDKIRAQGFEVDYLNIGGGLGIDYYHTGAVLPKPRNLIDTVRELV- 330
++ A I+++ GF ++ L++GGGLGI Y + L+
Sbjct: 178 LETIVQALSDARELIEELVEMGFPLEMLDLGGGLGIPYDEQP---LDFEEYAALINPLLK 234
Query: 331 ----LSRNLNLIIEPGRSLIANTCCLVNHVTGVKTNGTKNFIVIDGSMAELIRPSL-YDA 385
+ LI+EPGR ++A LV V VK NG + F V+DG M RP+L YDA
Sbjct: 235 KYFPNDPGVTLILEPGRYIVAQAGVLVTRVVAVKVNGGRFFAVVDGGMNHSFRPALAYDA 294
Query: 386 YQHIELVSPAPQDAEISKFDVVGPVCESADFLGKERELPTPDRGAGLVVHDAGAYCMSMA 445
Y I + D + + GP+C+S D +G++R LP + G LV D GAY S +
Sbjct: 295 YHPITPLKAPGPDEPLVPATLAGPLCDSGDVIGRDRLLPELEVGDLLVFEDMGAYGFSES 354
Query: 446 STYNLKMRPPEY 457
S +N RP EY
Sbjct: 355 SNFNSHPRPAEY 366
>gnl|CDD|236358 PRK08961, PRK08961, bifunctional aspartate kinase/diaminopimelate
decarboxylase protein; Provisional.
Length = 861
Score = 217 bits (554), Expect = 2e-62
Identities = 124/369 (33%), Positives = 176/369 (47%), Gaps = 25/369 (6%)
Query: 93 PFYLYSKPQITRNVEAYKQALEGLNSIIGYAIKANNNYKILEHLRKLGCGAVLVSGNELR 152
P Y+Y P + A AL ++ YAIKAN + IL L + G G VS ELR
Sbjct: 504 PCYVYHLPTVRARARAL-AALAAVDQRF-YAIKANPHPAILRTLEEEGFGFECVSIGELR 561
Query: 153 LALRA--GFDPTKCIFNGNGKLLEDLVLAAQEGVFVNVDSEFDLENI--VVASRIAGKKV 208
P + +F N + A GV V +D+ L N + R
Sbjct: 562 RVFELFPELSPERVLFTPNFAPRAEYEAAFALGVTVTLDNVEPLRNWPELFRGR------ 615
Query: 209 NVLLRINPDVDPQVHPYVATGNKNSKFGIRNEKLQWFLDAVKAHPNELKLVGAHCHLGST 268
V LRI+P H V TG K SKFG+ ++ F+D K + +VG H HLGS
Sbjct: 616 EVWLRIDPGHGDGHHEKVRTGGKESKFGLSQTRIDEFVDLAKTL--GITVVGLHAHLGSG 673
Query: 269 ITKVDIFRDAAVLMVNYIDKIRAQGFEVDYLNIGGGLGIDYYHTGAVLPKPRNLIDTVRE 328
I + +R A + ++ + +V +++GGGLGI + P + +D
Sbjct: 674 IETGEHWRRMADELASFARRFP----DVRTIDLGGGLGIPE--SAGDEPFDLDALDAGLA 727
Query: 329 LVLSRN--LNLIIEPGRSLIANTCCLVNHVTGVKTNGTKNFIVIDGSMAELIRPSLYDAY 386
V +++ L IEPGR L+A L+ VT VK + ++ M LIRP+LY AY
Sbjct: 728 EVKAQHPGYQLWIEPGRYLVAEAGVLLARVTQVKEKDGVRRVGLETGMNSLIRPALYGAY 787
Query: 387 QHIELVSPAPQDAEISKFDVVGPVCESADFLGKERELPTPDRGAGLVVHDAGAYCMSMAS 446
I +S + A + DVVGP+CES+D LGK R LP G +++ +AGAY SM+S
Sbjct: 788 HEIVNLSRLDEPAAGT-ADVVGPICESSDVLGKRRRLPATAEGDVILIANAGAYGYSMSS 846
Query: 447 TYNLKMRPP 455
TYN +R P
Sbjct: 847 TYN--LREP 853
>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 = 200 bits (511), Expect = 4e-60
Identities = 121/370 (32%), Positives = 176/370 (47%), Gaps = 27/370 (7%)
Query: 93 PFYLYSKPQITRNVEAYKQALEGLNSIIGYAIKANNNYKILEHLRKLGCGAVLVSGNELR 152
P Y+Y + AL+ ++S+ YAIKAN + +L L + G G VS EL
Sbjct: 13 PCYVYDLETVRARARQV-SALKAVDSLF-YAIKANPHPDVLRTLEEAGLGFECVSIGELD 70
Query: 153 LALRA--GFDPTKCIFNGNGKLLEDLVLAAQEGVFVNVDSEFDLENIVVASRIAGKKVNV 210
L L+ DP + +F N + A + GV V VD+ L G++V
Sbjct: 71 LVLKLFPDLDPRRVLFTPNFAARSEYEQALELGVNVTVDNLHPLREW--PELFRGREV-- 126
Query: 211 LLRINPDVDPQVHPYVATGNKNSKFGIRNEKLQWFLDAVKAHPNELKLVGAHCHLGSTIT 270
+LRI+P H +V TG SKFG+ ++L D K + ++G H H GS +
Sbjct: 127 ILRIDPGQGEGHHKHVRTGGPESKFGLDVDELDEARDLAKKA--GIIVIGLHAHSGSGVE 184
Query: 271 KVDIFRDAAVLMVNYIDKIRAQGF-EVDYLNIGGGLGIDYYHTGAVLPKPRNLIDTVREL 329
D + + + A+ F V LN+GGGLGI G P + +D
Sbjct: 185 DTDHWARHGDYLASL-----ARHFPAVRILNVGGGLGIPEAPGGR--PIDLDALDAALAA 237
Query: 330 VLSR--NLNLIIEPGRSLIANTCCLVNHVTGVKTNGTKNFIVIDGSMAELIRPSLYDAYQ 387
+ L +EPGR ++A + L+ VT +K F+ ++ M LIRP+LY AY
Sbjct: 238 AKAAHPQYQLWMEPGRFIVAESGVLLARVTQIKHKDGVRFVGLETGMNSLIRPALYGAYH 297
Query: 388 HIELVSPAPQDAEISKF--DVVGPVCESADFLGKERELPTPDRGAGLVVHDAGAYCMSMA 445
I +S + E DVVGP+CES D LG++R LP + G +++ +AGAY MA
Sbjct: 298 EIVNLS---RLDEPPAGNADVVGPICESGDVLGRDRLLPETEEGDVILIANAGAYGFCMA 354
Query: 446 STYNLKMRPP 455
STYNL R P
Sbjct: 355 STYNL--REP 362
>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 = 197 bits (502), Expect = 1e-58
Identities = 112/359 (31%), Positives = 170/359 (47%), Gaps = 15/359 (4%)
Query: 93 PFYLYSKPQITRNVEAYKQALEGLNSIIGYAIKANNNYKILEHLRKLGCGAVLVSGNELR 152
PFY+Y + ++ A + AL I Y++KAN N ++ HLR+LG GA + S EL
Sbjct: 8 PFYVYDRDRVRERYAALRAALPPAIEIY-YSLKANPNPALVAHLRQLGDGAEVASAGELA 66
Query: 153 LALRAGFDPTKCIFNGNGKLLEDLVLAAQEGVF-VNVDSEFDLENIVVASRIAGKKVNVL 211
LAL AG P K +F G GK +L A + G+ +NV+S +LE I + G V
Sbjct: 67 LALEAGVPPEKILFAGPGKSDAELRRAIEAGIGTINVESLEELERIDALAEEHGVVARVA 126
Query: 212 LRINPDVDPQVHPYVATGNKNSKFGIRNEKLQWFLDAVKAHPNELKLVGAHCHLGSTITK 271
LRINPD + + + G S+FGI E+L L + A PN L+ VG H + G+ I
Sbjct: 127 LRINPDFELK-GSGMKMGGGPSQFGIDVEELPAVLARIAALPN-LRFVGLHIYPGTQILD 184
Query: 272 VDIFRDAAVLMVNYIDKIRAQ-GFEVDYLNIGGGLGIDYY--HTGAVLPKPRNLIDTVRE 328
D +A + ++ + G +++L++GGG GI Y+ T L + +
Sbjct: 185 ADALIEAFRQTLALALRLAEELGLPLEFLDLGGGFGIPYFPGETPLDLEALGAALAALLA 244
Query: 329 LVLSR--NLNLIIEPGRSLIANTCCLVNHVTGVKTNGTKNFIVIDGSMAELIRPSLYDAY 386
+ R +++E GR L+ V V K + + F+V DG M + S +
Sbjct: 245 ELGDRLPGTRVVLELGRYLVGEAGVYVTRVLDRKVSRGETFLVTDGGMHHHLAAS-GNFG 303
Query: 387 QHIE-----LVSPAPQDAEISKFDVVGPVCESADFLGKERELPTPDRGAGLVVHDAGAY 440
Q + + E VVGP+C D LG+ ELP + G + V +GAY
Sbjct: 304 QVLRRNYPLAILNRMGGEERETVTVVGPLCTPLDLLGRNVELPPLEPGDLVAVLQSGAY 362
>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 = 188 bits (480), Expect = 3e-55
Identities = 109/383 (28%), Positives = 169/383 (44%), Gaps = 35/383 (9%)
Query: 93 PFYLYSKPQITRNVEAYKQALEGL--NSIIGYAIKANNNYKILEHLRKLGCGAVLVSGNE 150
PF+++ + + N A + N +I Y+ K N I + L + G A +VS E
Sbjct: 8 PFFVFDEDALRENYRELLGAFKKRYPNVVIAYSYKTNYLPAICKILHEEGGYAEVVSAME 67
Query: 151 LRLALRAGFDPTKCIFNGNGKLLEDLVLAAQEGVFVNVDSEFDLENIVVASRIA---GKK 207
LAL+ G + IFNG K E+L A +EG +N+DS + + IA G+
Sbjct: 68 YELALKLGVPGKRIIFNGPYKSKEELEKALEEGALINIDS---FDELERILEIAKELGRV 124
Query: 208 VNVLLRINPDVDPQVHPYVATGNKNSKFGIRNEKLQWFLDAVKAHP--NELKLVGAHCHL 265
V +R+N Y N S+FG E+ L A+K L LVG HCH+
Sbjct: 125 AKVGIRLN-------MNY--GNNVWSRFGFDIEENGEALAALKKIQESKNLSLVGLHCHV 175
Query: 266 GSTITKVDIFRDAAVLMVNYIDKIRAQGFEVDYLNIGGGLGID-----YYHTGAVLPKP- 319
GS I + + AA ++ +D R G E++YL++GGG Y +P P
Sbjct: 176 GSNILNPEAYSAAAKKLIELLD--RLFGLELEYLDLGGGFPAKTPLSLAYPQEDTVPDPE 233
Query: 320 ---RNLIDTVREL--VLSRNLNLIIEPGRSLIANTCCLVNHVTGVKTNGTKNFIVIDGSM 374
+ T++E LI+EPGR+L+ + L+ V VK +N V D +
Sbjct: 234 DYAEAIASTLKEYYANKENKPKLILEPGRALVDDAGYLLGRVVAVKNRYGRNIAVTDAGI 293
Query: 375 AELIRPSLYDAYQHIELVSPAPQDAEISKFDVVGPVCESADFLGKERELPTPDRGAGLVV 434
+ Y + I ++ P +D +DV G C +D L LP + G L +
Sbjct: 294 NNIPTIFWY--HHPILVLRPGKEDPTSKNYDVYGFNCMESDVLFPNVPLPPLNVGDILAI 351
Query: 435 HDAGAYCMSMASTYNLKMRPPEY 457
+ GAY M+ ++ + RP Y
Sbjct: 352 RNVGAYNMTQSNQFIRP-RPAVY 373
>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 = 169 bits (430), Expect = 1e-49
Identities = 85/231 (36%), Positives = 122/231 (52%), Gaps = 13/231 (5%)
Query: 122 YAIKANNNYKILEHLRKLGCGAVLVSGNELRLALRAGFDPTKCIFNGNGKLLEDLVLAAQ 181
YA+KAN++ +L L +LG G S EL L AG P + IF K +L A +
Sbjct: 24 YAVKANSDPAVLRLLAELGLGFDCASKGELERVLAAGVPPERIIFANPCKSRSELRYALE 83
Query: 182 EGV-FVNVDSEFDLENIVVASRIAGKKVNVLLRINPDVDPQVHPYVATGNKNSKFGIRNE 240
GV V VD+ +LE + +R+A + +LLR+ PDVD H Y++TG ++SKFG E
Sbjct: 84 HGVVCVTVDNVEELEKL---ARLA-PEARLLLRVKPDVDAHAHCYLSTG-QDSKFGADLE 138
Query: 241 KLQWFLDAVKAHPNELKLVGAHCHLGSTITKVDIFRDAAVLMVNYIDKIRAQGFEVDYLN 300
+ + L A K L +VG H H+GS T + F AA N D+ GFE+ L+
Sbjct: 139 EAEALLKAAKEL--GLNVVGVHFHVGSGCTDAEAFVKAARDARNVFDQGAELGFELKILD 196
Query: 301 IGGGLGIDYYHTGAV-LPKPRNLIDTVRELVLSR--NLNLIIEPGRSLIAN 348
+GGG G+DY TGA + +I+ E V + +I EPGR ++A
Sbjct: 197 LGGGFGVDY--TGAEDFEEYAEVINAALEEVFPHDPHPTIIAEPGRYIVAP 245
>gnl|CDD|236867 PRK11165, PRK11165, diaminopimelate decarboxylase; Provisional.
Length = 420
Score = 163 bits (416), Expect = 9e-46
Identities = 125/389 (32%), Positives = 181/389 (46%), Gaps = 46/389 (11%)
Query: 93 PFYLYSKPQITRNVEAYKQALEGLNSIIGYAIKANNNYKILEHLRKLGCGAVLVSGNELR 152
P ++Y I R + +Q +I +A KA +N IL +R+ G VS E+
Sbjct: 27 PLWVYDADIIRRRIAQLRQF-----DVIRFAQKACSNIHILRLMREQGVKVDAVSLGEIE 81
Query: 153 LALRAGFDPTKC----IFNGNGKLLEDLVLA--AQEGVFVNVDSEFDLENIVVASRIAGK 206
AL AG+ P +F + +++ LA + + VN S L+ + S
Sbjct: 82 RALAAGYKPGTEPDEIVFTAD--VIDRATLARVVELKIPVNAGSIDMLDQLGQVS----P 135
Query: 207 KVNVLLRINPDVDPQVHPYVATGNKNSKFGIRNEKLQWFLDAVKAHPNELKLVGAHCHLG 266
V LRINP TG +NSK GI +E L L ++ + LKLVG H H+G
Sbjct: 136 GHRVWLRINPGFGHGHSQKTNTGGENSKHGIWHEDLPAALAVIQRY--GLKLVGIHMHIG 193
Query: 267 STITKVDIFRDAAVL--MVNYIDKIRAQGFEVDYLNIGGGLGIDYYHTGAVLPKPR--NL 322
S VD V MV + G +++ ++ GGGL I Y + L
Sbjct: 194 S---GVDYGHLEQVCGAMVRQV---IELGQDIEAISAGGGLSIPYREGEEPVDTEHYFGL 247
Query: 323 IDTVRELV---LSRNLNLIIEPGRSLIANTCCLVNHVTGVKTNGTKNFIVIDGSMAELIR 379
D R+ + L + L IEPGR L+A + LV V VK G+++F+++D +L+R
Sbjct: 248 WDAARKRIARHLGHPVKLEIEPGRFLVAESGVLVAQVRAVKQMGSRHFVLVDAGFNDLMR 307
Query: 380 PSLYDAYQHIELVSPAPQD-AEISKFDVV--GPVCESAD-FLGKE------RELPTPDRG 429
P++Y +Y HI +++ + E D V GP+CES D F +E R LP G
Sbjct: 308 PAMYGSYHHISVLAADGRSLEEAPTVDTVVAGPLCESGDVFTQQEGGVVETRALPQVQVG 367
Query: 430 AGLVVHDAGAYCMSMASTYNLKMRP--PE 456
LV HD GAY SM+S YN RP PE
Sbjct: 368 DYLVFHDTGAYGASMSSNYN--SRPLLPE 394
>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 = 148 bits (376), Expect = 3e-42
Identities = 75/243 (30%), Positives = 110/243 (45%), Gaps = 33/243 (13%)
Query: 102 ITRNVEAYKQALEGLNSIIGYAIKANNNYKILEHLRKLGCGAVLVSGNELRLALRAGFDP 161
I N ++A + +KAN N ++ L LG G + S E L AG P
Sbjct: 1 IRHNYRRLREAA-PAGITLFAVVKANANPEVARTLAALGTGFDVASLGEALLLRAAGIPP 59
Query: 162 TKCIFNGNGKLLEDLVLAAQEGVF-VNVDSEFDLENIVVASRIAGKKVNVLLRINPDVDP 220
+F G K + +L AA++GV V VDS +LE + A+ AG VLLRI+
Sbjct: 60 EPILFLGPCKQVSELEDAAEQGVIVVTVDSLEELEKLEEAALKAGPPARVLLRID----- 114
Query: 221 QVHPYVATGNKNSKFGIRNEKLQWFLDAVKAHPNELKLVGAHCHLGSTITKVDIFRDAAV 280
TG++N KFG+R E+L+ L+ K P+ L+LVG H H GS F +A
Sbjct: 115 -------TGDENGKFGVRPEELKALLERAKELPH-LRLVGLHTHFGSADEDYSPFVEALS 166
Query: 281 LMVNYIDKIRAQGFEVDYLNIGGGLGIDYYHTGAVLPKPRNLIDTVRELVLSRNLNLIIE 340
V +D++ G +++ L+IGG I Y + +I+E
Sbjct: 167 RFVAALDQLGELGIDLEQLSIGGSFAILYLQELPLGTF------------------IIVE 208
Query: 341 PGR 343
PGR
Sbjct: 209 PGR 211
>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 = 149 bits (380), Expect = 4e-41
Identities = 103/380 (27%), Positives = 161/380 (42%), Gaps = 33/380 (8%)
Query: 93 PFYLYSKPQITRNVEAYKQALEGLNSIIGYAIKANNNYKILEHLRKLGCGAVLVSGNELR 152
PF + + R +K+AL YA+K N + +L L LG G S E+
Sbjct: 3 PFLVVDLGDVVRKYRRWKKALP--RVRPFYAVKCNPDPAVLRTLAALGAGFDCASKGEIE 60
Query: 153 LALRAGFDPTKCIFNGNGKLLEDLVLAAQEGV--FVNVDSEFDLENIVVASRIAGKKVNV 210
L L G P + IF K + D+ AA+ GV F DSE +LE I + A +
Sbjct: 61 LVLGLGVSPERIIFANPCKSISDIRYAAELGVRLFT-FDSEDELEKIA---KHA-PGAKL 115
Query: 211 LLRINPDVDPQVHPYVATGNKNSKFGIRNEKLQWFLDAVKAHPNELKLVGAHCHLGSTIT 270
LLRI D + P + KFG E+ + L K L +VG H+GS T
Sbjct: 116 LLRIATDDSGALCPL------SRKFGADPEEARELLRRAKEL--GLNVVGVSFHVGSQCT 167
Query: 271 KVDIFRDAAVLMVNYI-DKIRAQGFEVDYLNIGGGLGIDYYHTGAVLPK-PRNLIDTVRE 328
+ DA + + D+ GF++ L+IGGG Y + + + E
Sbjct: 168 DPSAYVDA-IADAREVFDEAAELGFKLKLLDIGGGFPGSYDGVVPSFEEIAAVINRALDE 226
Query: 329 LVLSRNLNLIIEPGRSLIANTCCLVNHVTGVKTNG---TKNFIVID----GSMAELIRPS 381
+ +I EPGR L+A+ L +V + G + + ++ GS E+
Sbjct: 227 YFPDEGVRIIAEPGRYLVASAFTLAVNVIAKRKRGDDDRERWYYLNDGVYGSFNEI---- 282
Query: 382 LYDAYQ-HIELVSPAPQDAEISKFDVVGPVCESADFLGKERELP-TPDRGAGLVVHDAGA 439
L+D + ++ +D E+ + GP C+S D + ++ LP G L+ + GA
Sbjct: 283 LFDHIRYPPRVLKDGGRDGELYPSSLWGPTCDSLDVIYEDVLLPEDLAVGDWLLFENMGA 342
Query: 440 YCMSMASTYNLKMRPPEYWV 459
Y + AST+N P +V
Sbjct: 343 YTTAYASTFNGFPPPKIVYV 362
>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 = 149 bits (378), Expect = 2e-40
Identities = 108/401 (26%), Positives = 169/401 (42%), Gaps = 28/401 (6%)
Query: 71 ADGFLYCEDVRVQDVMETVEKRPFYLYSKPQITRNVEAYKQAL-EGLNSIIGYAIKANNN 129
+G L + + ++ PFY Y + ++ V A ++AL E L I YA+KAN
Sbjct: 4 KNGCLCVGGIPLTELAARAGGTPFYAYDRGLVSERVAALRKALPEELA--IHYAVKANPM 61
Query: 130 YKILEHLRKLGCGAVLVSGNELRLALRAGFDPTKCIFNGNGKLLEDLVLAAQEGVFVNVD 189
+L H+ L G + S EL +AL G+DP F G GK +L A GV +NV+
Sbjct: 62 PALLAHMAPLVDGFDVASAGELAVALDTGYDPGCISFAGPGKTDAELRRALAAGVLINVE 121
Query: 190 SEFDLENIVVASRIAGKKVNVLLRINPDVDPQVHPYVATGNKNSKFGIRNEKLQWFLDAV 249
S +L + S G + V +R+NPD + + + G +FGI E++ L +
Sbjct: 122 SLRELNRLAALSEALGLRARVAVRVNPDFELKGSG-MKMGGGAKQFGIDAEQVPAALAFI 180
Query: 250 KAHPNELKLVGAHCHLGSTITKVD-IFRDAAVLMVNYIDKIRAQGFEVDYLNIGGGLGID 308
KA + + G H GS + I A + + + V +NIGGG GI
Sbjct: 181 KAADLDFQ--GFHIFAGSQNLNAEAIIEAQAKTLALALRLAESAPAPVRVINIGGGFGIP 238
Query: 309 YYHTGAVL---PKPRNLIDTVRELV-LSRNLNLIIEPGRSLIANTCCLVNHVTGVKTNGT 364
Y+ L P L L + +++E GR L+ V V K +
Sbjct: 239 YFPGNPPLDLAPVGAALAALFARLRDALPEVEILLELGRYLVGEAGIYVCRVIDRKISRG 298
Query: 365 KNFIVIDGSM----------AELIRPSLYDAYQHIELVSPAPQDAEISKFDVVGPVCESA 414
+ F+V DG + ++IR + Y ++ A +VGP+C
Sbjct: 299 ETFLVTDGGLHHHLSASGNFGQVIRRN-YPV-----VIGNRIGGAVREIASIVGPLCTPL 352
Query: 415 DFLGKERELPTPDRGAGLVVHDAGAYCMSMASTYNLKMRPP 455
D L ++ LP + G +V+ +GAY S AS P
Sbjct: 353 DLLAEKGTLPVAEPGDLVVIFQSGAYGAS-ASPLAFLGHPE 392
>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 = 144 bits (365), Expect = 7e-39
Identities = 103/351 (29%), Positives = 165/351 (47%), Gaps = 18/351 (5%)
Query: 123 AIKANNNYKILEHLRKLGCGAVLVSGNELRLALRAGFDPTKCIFNGNGKLLEDLVLAAQE 182
A+KAN +L L + G GA + S EL LAL AGF P + +F+ K +L A +
Sbjct: 33 AVKANPLVPVLRLLAEAGAGAEVASPGELELALAAGFPPERIVFDSPAKTRAELREALEL 92
Query: 183 GVFVNVDSEFDLENI-VVASRIAGKKVNVLLRINPDVDPQVHPYVATGNKNSKFGI--RN 239
GV +N+D+ +LE I + + + LR+NP V ++T SKFG+ +
Sbjct: 93 GVAINIDNFQELERIDALVAEFKEASSRIGLRVNPQVGAGKIGALSTATATSKFGVALED 152
Query: 240 EKLQWFLDAVKAHPNELKLVGAHCHLGSTITKVDIFRDAAVLMVNYIDKIRAQG--FEVD 297
+DA P L G H H+GS ++ + + +V+ ++I + ++
Sbjct: 153 GARDEIIDAFARRP---WLNGLHVHVGSQGCELSLLAEGIRRVVDLAEEINRRVGRRQIT 209
Query: 298 YLNIGGGLGIDYYHTGAVLPKPRNLIDTVRELV---LSRNLNLIIEPGRSLIANTCCLVN 354
++IGGGL +++ + P + ++ V L+ E GRSL+A +V+
Sbjct: 210 RIDIGGGLPVNFESE-DITPTFADYAAALKAAVPELFDGRYQLVTEFGRSLLAKCGTIVS 268
Query: 355 HVTGVKTNGTKNFIVIDGSMAELIRPSLY--DAYQH-IELVSPA--PQDAEISKFDVVGP 409
V K++G + I I + A++ + Y D + + + P+ DV GP
Sbjct: 269 RVEYTKSSGGRR-IAITHAGAQVATRTAYAPDDWPLRVTVFDANGEPKTGPEVVTDVAGP 327
Query: 410 VCESADFLGKERELPTPDRGAGLVVHDAGAYCMSMASTYNLKMRPPEYWVR 460
C + D L KER LP + G + VHD GAY S S+YN RP Y VR
Sbjct: 328 CCFAGDVLAKERALPPLEPGDYVAVHDTGAYYFSSHSSYNSLPRPAVYGVR 378
>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 = 131 bits (332), Expect = 6e-34
Identities = 81/338 (23%), Positives = 133/338 (39%), Gaps = 70/338 (20%)
Query: 93 PFYLYSKPQITRNVEAYKQALE--GLNSIIGYAIKANNNYKILEHLRKLGCGAVLVSGNE 150
P + N+ A + L+ G++ + +A KAN + ++ G G + S E
Sbjct: 11 PLNVLFPQTFRENIAALRAVLDRHGVDGRVYFARKANKSLALVRAAAAAGIGVDVASLAE 70
Query: 151 LRLALRAGFDPTKCIFNGNGKLLEDLVLAAQEGVFVNVDSEFDLENIV-VASRIAGKKVN 209
LR AL AG + + G K E L LA + G + VDS +L+ ++ +A
Sbjct: 71 LRQALAAGVRGDRIVATGPAKTDEFLWLAVRHGATIAVDSLDELDRLLALARGYTTGPAR 130
Query: 210 VLLRINPDVDPQVHPYVATGNKNSKFGIRNEKLQWFLDAVKAHPNELKLVGAHCHLG--S 267
VLLR++P P P S+FG+ +++ L+ + ++LVG H HL S
Sbjct: 131 VLLRLSP--FPASLP--------SRFGMPAAEVRTALERLAQLRERVRLVGFHFHLDGYS 180
Query: 268 TITKVDIFRDAAVLMVNYIDKIRAQGFEVDYLNIGGGLGIDY------------------ 309
+V ++ L ID+ RA G +++IGGG + Y
Sbjct: 181 AAQRVAALQECLPL----IDRARALGLAPRFIDIGGGFPVSYLADAAEWEAFLAALTEAL 236
Query: 310 YHTG--------------------------------AVLPKPRNLIDTVRELVLSRNLNL 337
Y G A+L P T+ E + + L
Sbjct: 237 YGYGRPLTWRNEGGTLRGPDDFYPYGQPLVAADWLRAILSAPLPQGRTIAERLRDNGITL 296
Query: 338 IIEPGRSLIANTCCLVNHVTGVKTNGTKNFIV-IDGSM 374
+EPGR+L+ V V VK G N ++ ++G+
Sbjct: 297 ALEPGRALLDQCGLTVARVAFVKQLGDGNHLIGLEGNS 334
>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 = 108 bits (273), Expect = 9e-29
Identities = 38/111 (34%), Positives = 54/111 (48%), Gaps = 3/111 (2%)
Query: 351 CLVNHVTGVKTN-GTKNFIVIDGSMAELIRPSLYDAYQHIELVSPAPQDAEISKFDVVGP 409
LV V VK + F+ +D + P+LYDA I V D + + + GP
Sbjct: 1 TLVTEVIDVKERGDDRKFVYLDDGVYGSPDPALYDALHPILPV-SRLDDEPLRPYTLAGP 59
Query: 410 VCESADFLGKERELPTP-DRGAGLVVHDAGAYCMSMASTYNLKMRPPEYWV 459
C+S D L ++ LP + G LV DAGAY +S++S +N RP E V
Sbjct: 60 TCDSGDVLARDVSLPLELEVGDWLVFFDAGAYTISLSSNFNGFPRPAEVLV 110
>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 = 113 bits (285), Expect = 1e-27
Identities = 102/372 (27%), Positives = 161/372 (43%), Gaps = 45/372 (12%)
Query: 95 YLYSKPQITRNVEAYKQAL-EGLNSIIGYAIKANNNYKILEHLRKLGCGAVLVSGNELRL 153
Y+Y + + A + +L G + YAIKAN++ IL L G + SG E+
Sbjct: 5 YVYDLAALRAHARALRASLPPGCE--LFYAIKANSDPPILRALAPHVDGFEVASGGEI-A 61
Query: 154 ALRAGFDPTKCIFNGNGKLLEDLVLAAQEGV-FVNVDSEFDLENIVVASRIAGKKVNVLL 212
+RA IF G GK +L A +GV ++V+SE +L + +R AG+ VLL
Sbjct: 62 HVRAAVPDAPLIFGGPGKTDSELAQALAQGVERIHVESELELRRLNAVARRAGRTAPVLL 121
Query: 213 RINPDVDPQVHPYVATGNKNSKFGIRNEKLQWFLDAVKAHPNELKLVGAHCHLGSTITKV 272
R+N + + G + + FGI L L+ ++ PN ++L G H HL S +
Sbjct: 122 RVNLALPDLPSSTLTMGGQPTPFGIDEADLPDALELLRDLPN-IRLRGFHFHLMS--HNL 178
Query: 273 DIFRDAAVLMVNYIDKIRAQ----GFEVDYLNIGGGLGIDYYHTGAVLPKPRNLIDTVRE 328
D A L+ Y++ R G ++D +N+GGG+G++Y A + +
Sbjct: 179 DAAAHLA-LVKAYLETARQWAAEHGLDLDVVNVGGGIGVNY----ADPEEQFDWAGFCEG 233
Query: 329 L-VLSR----NLNLIIEPGRSLIANTCCLVNHVTGVKTNGTKNFIVIDGSMAELIRPSLY 383
L L L L E GR + A V V +K + + F V+ G P+
Sbjct: 234 LDQLLAEYEPGLTLRFECGRYISAYCGYYVTEVLDLKRSHGEWFAVLRGGTHHFRLPA-- 291
Query: 384 DAYQH-------------IELVSPAPQDAEISKFDVVGPVCESADFLGKERELPTPDRGA 430
A+ H P+ +D ++ +VG +C D L R++P A
Sbjct: 292 -AWGHNHPFSVLPVEEWPYPWPRPSVRDTPVT---LVGQLCTPKDVLA--RDVPVDRLRA 345
Query: 431 G--LVVHDAGAY 440
G +V AGAY
Sbjct: 346 GDLVVFPLAGAY 357
>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 = 85.3 bits (212), Expect = 6e-18
Identities = 71/273 (26%), Positives = 122/273 (44%), Gaps = 32/273 (11%)
Query: 122 YAIKANNNYKILEHLRKLG--CGAVLVSGN--ELRLALRAGFDPTKCIF-NG--NGKLLE 174
Y IK N +++E + K G L +G+ EL AL P I NG + + +E
Sbjct: 43 YPIKVNQQREVVEEIVKAGKRYNIGLEAGSKPELLAALALLKTPDALIICNGYKDDEYIE 102
Query: 175 DLVLAAQEG--VFVNVDSEFDLENIVVASRIAGKKVNVLLRINPDVDPQVHPYVATGNKN 232
+LA + G V + ++ +L+ I+ ++ G K + +RI + +G
Sbjct: 103 LALLARKLGHNVIIVIEKLSELDLILELAKKLGVKPLLGVRIKLASKGSGK-WQESGGDR 161
Query: 233 SKFGIRNEKLQWFLDAVKAHPNE-----LKLVGAHCHLGSTITKVDIFRDAAVLMVNYID 287
SKFG+ ++ L+ V+ LKL+ H H+GS IT + + A
Sbjct: 162 SKFGLTASEI---LEVVEKLKEAGMLDRLKLL--HFHIGSQITDIRRIKSALREAARIYA 216
Query: 288 KIRAQGFEVDYLNIGGGLGIDYYHTGAVLPKPRN---------LIDTVRELVLSRNL--- 335
++R G + YL+IGGGLG+DY + + N ++ TV+E+ +
Sbjct: 217 ELRKLGANLRYLDIGGGLGVDYDGSRSSSDSSFNYSLEEYANDIVKTVKEICDEAGVPHP 276
Query: 336 NLIIEPGRSLIANTCCLVNHVTGVKTNGTKNFI 368
++ E GR+++A+ L+ V GVK F
Sbjct: 277 TIVTESGRAIVAHHSVLIFEVLGVKRLADWYFC 309
>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 = 71.2 bits (175), Expect = 4e-13
Identities = 45/212 (21%), Positives = 101/212 (47%), Gaps = 36/212 (16%)
Query: 176 LVLAAQE---GVFVNVDSEFDLENIVVASRIAGKKVNVLLRINPDVDPQVHP-----YVA 227
L L ++ VF+ ++ +L+ ++ + KK+ V ++ + ++ + +
Sbjct: 155 LALIGRKLGHNVFIVIEKLSELDLVIDEA----KKLGVKPKLG--LRARLASKGSGKWAS 208
Query: 228 TGNKNSKFGIRNEKLQWFLDAVKAHPNE-----LKLVGAHCHLGSTITKVDIFRDAAVLM 282
+G + SKFG+ ++ L+ V+ L+L+ H H+GS I+ +D +
Sbjct: 209 SGGEKSKFGLSATQV---LEVVRLLEQNGLLDSLQLL--HFHIGSQISNIDDIKKGVREA 263
Query: 283 VNYIDKIRAQGFEVDYLNIGGGLGIDYYHTGAVLPK---------PRNLIDTVRELVLSR 333
+ ++R G ++ Y+++GGGLG+DY T + +++ +RE+ +
Sbjct: 264 ARFYCELRKLGVKITYVDVGGGLGVDYDGTSSSSDCSVNYGLEEYANDIVQALREICEEK 323
Query: 334 NL---NLIIEPGRSLIANTCCLVNHVTGVKTN 362
+ +I E GR++ A+ L+ +V GV+ +
Sbjct: 324 GVPHPVIITESGRAITAHHAVLITNVLGVERH 355
>gnl|CDD|235427 PRK05354, PRK05354, arginine decarboxylase; Provisional.
Length = 634
Score = 65.9 bits (162), Expect = 2e-11
Identities = 48/185 (25%), Positives = 87/185 (47%), Gaps = 33/185 (17%)
Query: 227 ATGNKNSKFGIRNEKLQWFLDAV---KAHP--NELKLVGAHCHLGSTITKVDIFRDAAVL 281
++G + SKFG+ ++ L+AV + + L+L+ H HLGS I + + A
Sbjct: 215 SSGGEKSKFGLSATEV---LEAVERLREAGLLDCLQLL--HFHLGSQIANIRDIKTAVRE 269
Query: 282 MVNYIDKIRAQGFEVDYLNIGGGLGIDY------------YHTG--AVLPKPRNLIDTVR 327
+ ++R G + YL++GGGLG+DY Y A +++ T++
Sbjct: 270 AARFYVELRKLGAPIQYLDVGGGLGVDYDGTRSQSDSSVNYSLQEYA-----NDVVYTLK 324
Query: 328 ELVLSRNL---NLIIEPGRSLIANTCCLVNHVTGVKTNGTKNFIVIDGSMAELIRPSLYD 384
E+ + +I E GR+L A+ LV +V GV++ + L++ +L++
Sbjct: 325 EICEEHGVPHPTIISESGRALTAHHAVLVFNVLGVESQEYEEPPAPAEDAPPLLQ-NLWE 383
Query: 385 AYQHI 389
YQ I
Sbjct: 384 TYQEI 388
>gnl|CDD|224088 COG1166, SpeA, Arginine decarboxylase (spermidine biosynthesis)
[Amino acid transport and metabolism].
Length = 652
Score = 58.1 bits (141), Expect = 6e-09
Identities = 42/184 (22%), Positives = 78/184 (42%), Gaps = 29/184 (15%)
Query: 228 TGNKNSKFGIRNEKLQWFLDAVKAHPNELK-------LVGAHCHLGSTITKVDIFRDAAV 280
+G + SKFG+ ++ L V L+ L H HLGS I+ + +
Sbjct: 232 SGGEKSKFGLSATQV---LQVV----ERLREANLLDSLQLLHFHLGSQISNIRDIKTGVR 284
Query: 281 LMVNYIDKIRAQGFEVDYLNIGGGLGIDYYHTGAVLPKPRN---------LIDTVRELVL 331
+ ++R G + Y ++GGGLG+DY T +N ++ +++
Sbjct: 285 EAARFYVELRKLGANIKYFDVGGGLGVDYDGTRTQSDCSKNYGLNEYANDVVWALKDACE 344
Query: 332 SRNL---NLIIEPGRSLIANTCCLVNHVTGVKTN--GTKNFIVIDGSMAELIRPSLYDAY 386
+ L +I E GR++ A+ L+ +V GV+ + ++ L R +L + Y
Sbjct: 345 EKGLPHPTIISESGRAITAHHAVLIANVIGVERHEYNDAPLPDAPRNLPPLWR-TLQELY 403
Query: 387 QHIE 390
+ I
Sbjct: 404 ESIT 407
>gnl|CDD|216340 pfam01168, Ala_racemase_N, Alanine racemase, N-terminal domain.
Length = 217
Score = 51.0 bits (123), Expect = 2e-07
Identities = 46/216 (21%), Positives = 74/216 (34%), Gaps = 43/216 (19%)
Query: 101 QITRNVEAYKQALEGLNSIIGYAIKANNNYKILEHLRKLGCGAVLVSGNELR-------- 152
+ N+ A ++ + + +KAN Y G GAV V+
Sbjct: 5 ALRHNIRALRERAGP-VAKLMAVVKANA-Y---------GHGAVRVARALAAGADGFGVA 53
Query: 153 -----LALRAGFDPTKCIFNGNGKLLEDLVLAAQEGVFVNVDSEFDLENIVVASRIAGKK 207
L LR P I E+L A+ + VDS E + A+ AG+
Sbjct: 54 TLQEALELREAGAP---ILVLGFFPPEELAALAEYDLIPTVDSLEQAEALSAAAAKAGRP 110
Query: 208 VNVLLRINPDVDPQVHPYVATGNKNSKFGIRNEKLQWFLDAVKAHPNELKLVGAHCHLGS 267
+ V L+++ TG + G E+L +A+ A P L+L G H
Sbjct: 111 LRVHLKVD------------TG--MGRLGFTPEELPALAEALAALPG-LRLEGLMTHFAC 155
Query: 268 TITKVDIFRDAAVLMVNYIDKIRAQGFEVDYLNIGG 303
+ D D++ A G L++G
Sbjct: 156 A-DEPDYTERQLARFRELADRLEAAGLAPPVLSLGN 190
>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 = 47.9 bits (114), Expect = 7e-06
Identities = 81/357 (22%), Positives = 136/357 (38%), Gaps = 31/357 (8%)
Query: 122 YAIKANNNYKILEHLRKLGCGAVLVSGNELRLALRAGFDPTKCIFNGNGKLLEDLVLAAQ 181
Y ++ N+ +LE L LG G S NE+ L G P I+ K + AA+
Sbjct: 41 YTVRCNSTPAVLEILAALGTGFACSSKNEMALVQELGVSPENIIYTNPCKQASQIKYAAK 100
Query: 182 EGV-FVNVDSEFDLENIVVASRIAGKKVNVLLRINPDVDPQVHPYVATGNKNSKFGIRNE 240
GV + D+E +L+ I A +LL I + + + N KFG +
Sbjct: 101 VGVNIMTCDNEIELKKIARNHPNA----KLLLHIATEDN------IGGEEMNMKFGTTLK 150
Query: 241 KLQWFLDAVKAHPNELKLVGAHCHLGSTITKVDIFRDAAVLMVNYIDKIRAQGFEVDYLN 300
+ L+ K ++++VG H+ S+ + + A D GF+++ L+
Sbjct: 151 NCRHLLECAKEL--DVQIVGVKFHVSSSCKEYQTYVHALSDARCVFDMAEEFGFKMNMLD 208
Query: 301 IGGGLGIDYYHTGAVLPKPRNLIDTVRELVLSRNLNLIIEPGRSLIANTCCLVNHVTGVK 360
IGGG V R L+D + +I EPG +++ L +V K
Sbjct: 209 IGGGFTGSEIQLEEVNHVIRPLLDVY--FPEGSGIQIIAEPGSYYVSSAFTLAVNVIAKK 266
Query: 361 T--------NGTKN--------FIVIDGSMAELIRPSLYDAYQHIELVSPAPQDAEISKF 404
+ KN + + DG E+ +D +
Sbjct: 267 AVENDKHLSSVEKNGSDEPAFVYYMNDGVYGSFASKLSEKLNTTPEVHKKYKEDEPLFTS 326
Query: 405 DVVGPVCESADFLGKERELPTPDRGAGLVVHDAGAYCMSMASTYNLKMRPPEYWVRS 461
+ GP C+ D + + LP + G L+ + GA + ST+N RP Y++ S
Sbjct: 327 SLWGPSCDELDQIVESCLLPELNVGDWLIFDNMGAGSLHEPSTFNDFQRPAIYYMMS 383
>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 = 46.4 bits (111), Expect = 2e-05
Identities = 60/271 (22%), Positives = 98/271 (36%), Gaps = 65/271 (23%)
Query: 202 RIAGKKVNVLLRINPDVDPQVHPYVATGNKNSKFGIRNEKLQWFLDAVKAHPNELKLV-G 260
R ++V LRINP+ S+ G+ + +L + G
Sbjct: 107 RAKAAGISVGLRINPEYSEVETDLYDPCAPGSRLGVT---------LDELEEEDLDGIEG 157
Query: 261 AHCH---------LGSTITKV-DIFRDAAVLMVNYIDKIRAQGFEVDYLNIGGGLGIDYY 310
H H L T+ V + F + Y+ +++ +LN+GGG +
Sbjct: 158 LHFHTLCEQDFDALERTLEAVEERFGE-------YLPQLK-------WLNLGGG-----H 198
Query: 311 H-TGAVLPKPRNLIDTVRELVLSRNLNLIIEPGRSLIANTCCLVNHVTGVKTNGTKNFIV 369
H T R LI ++ + + +EPG ++ NT LV V + NG I+
Sbjct: 199 HITRPDYDVDR-LIALIKRFKEKYGVEVYLEPGEAVALNTGYLVATVLDIVENGMPIAIL 257
Query: 370 IDGSMA-------ELI-RPSLYDAYQHIELVSPAPQDAEISKFDVVGPVCESADFLGK-- 419
D S E+ RP + A P + + + + G C + D +G
Sbjct: 258 -DASATAHMPDVLEMPYRPPIRGA--------GEPGEGAHT-YRLGGNSCLAGDVIGDYS 307
Query: 420 -ERELPTPDRGAGLVVHDAGAYCMSMASTYN 449
+ L DR LV D Y M +T+N
Sbjct: 308 FDEPLQVGDR---LVFEDMAHYTMVKTNTFN 335
>gnl|CDD|215240 PLN02439, PLN02439, arginine decarboxylase.
Length = 559
Score = 38.5 bits (90), Expect = 0.007
Identities = 23/94 (24%), Positives = 40/94 (42%), Gaps = 24/94 (25%)
Query: 228 TGNKNSKFGIRNEKLQWFLDAVKAHP--NELKLVGAHCHLGSTITKVDIFRDAA------ 279
T + KFG+ ++ + ++ + L+L+ H H+GS I + +D
Sbjct: 153 TSGEKGKFGLTATEIVRVVRKLRKEGMLDCLQLL--HFHIGSQIPSTSLLKDGVSEAAQI 210
Query: 280 ----VLMVNYIDKIRAQGFEVDYLNIGGGLGIDY 309
V + G + ++IGGGLGIDY
Sbjct: 211 YCELVRL----------GAPMRVIDIGGGLGIDY 234
>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 = 37.1 bits (86), Expect = 0.018
Identities = 55/260 (21%), Positives = 93/260 (35%), Gaps = 37/260 (14%)
Query: 204 AGKKVNVLLRINPDVDPQVHPYVATGNKNSKFGIR----NEKLQWFLDAVKAHPNELKLV 259
V + LRINP+ + S+ G++ E L ++ + H K
Sbjct: 113 KNSAVKLGLRINPEYSEVPTDLYNPCGRFSRLGVQAKDFEEVLLDGIEGLHFHTLCEKDA 172
Query: 260 GAHCHLGSTITKVDIFRDAAVLMVNYIDKIRAQGFEVDYLNIGGGLGIDYYHTGAVLPKP 319
A I + F + Y+ ++ ++N GGG I G + K
Sbjct: 173 DALERTLEVIEE--KFGE-------YLPQM-------KWVNFGGGHHITK--KGYDVEK- 213
Query: 320 RNLIDTVRELVLSRNLNLIIEPGRSLIANTCCLVNHVTGVKTNGTKNFIVIDGSMAELI- 378
LI ++ + +I+EPG ++ T LV V + N + I+ A +
Sbjct: 214 --LIAVIKAFSERHGVQVILEPGEAIGWQTGFLVASVVDIVENEKQIAILDVSFEAHMPD 271
Query: 379 ------RPSLYDAY--QHIELVSPAPQDAEISKFDVVGPVCESADFLGKERELPTP-DRG 429
RP + A E + ++ E S + G C + D +G E P G
Sbjct: 272 TLEMPYRPEVLGARDPATRENEEISDKEGEFSYL-LGGNTCLAGDVMG-EYAFDKPLKVG 329
Query: 430 AGLVVHDAGAYCMSMASTYN 449
+V D Y M +T+N
Sbjct: 330 DKIVFLDMIHYTMVKNTTFN 349
>gnl|CDD|143481 cd00430, PLPDE_III_AR, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzyme Alanine Racemase. This family
includes predominantly bacterial alanine racemases (AR),
some serine racemases (SerRac), and putative
bifunctional enzymes containing N-terminal
UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine
ligase (murF) and C-terminal AR domains. These proteins
are fold type III PLP-dependent enzymes that play
essential roles in peptidoglycan biosynthesis. AR
catalyzes the interconversion between L- and D-alanine,
which is an essential component of the peptidoglycan
layer of bacterial cell walls. SerRac converts L-serine
into its D-enantiomer (D-serine) for peptidoglycan
synthesis. murF catalyzes the addition of D-Ala-D-Ala to
UDPMurNAc-tripeptide, the final step in the synthesis of
the cytoplasmic precursor of bacterial cell wall
peptidoglycan. Members of this family contain an
N-terminal PLP-binding TIM-barrel domain and a
C-terminal beta-sandwich domain. They exist as
homodimers with active sites that lie at the interface
between the TIM barrel domain of one subunit and the
beta-sandwich domain of the other subunit. AR and other
members of this family require dimer formation and the
presence of the PLP cofactor for catalytic activity.
Fungal ARs and eukaryotic serine racemases, which are
fold types I and II PLP-dependent enzymes respectively,
are excluded from this family.
Length = 367
Score = 35.6 bits (83), Expect = 0.048
Identities = 41/175 (23%), Positives = 69/175 (39%), Gaps = 31/175 (17%)
Query: 102 ITRNVEAYKQALEGLNSIIGYAIKANNNY-----KILEHLRKLGCGAVLVS----GNELR 152
+ N+ ++ L G + I +KA+ Y ++ + L + G V+ ELR
Sbjct: 11 LRHNLRVIRRLL-GPGTKIMAVVKADA-YGHGAVEVAKALEEAGADYFAVATLEEALELR 68
Query: 153 LALRAGFDPTKCIFNGNGKLLEDLVLAAQEGVFVNVDSEFDLENIVVASRIAGKKVNVLL 212
AG + G E+ A + + V S E + A+ GK + V L
Sbjct: 69 ---EAGITAPILVLGGT--PPEEAEEAIEYDLTPTVSSLEQAEALSAAAARLGKTLKVHL 123
Query: 213 RINPDVDPQVHPYVATGNKNSKFGIRNEKLQWFLDAVKAHPNELKLVGAHCHLGS 267
+I+ TG + G R E+ + L+A+KA P L+L G H +
Sbjct: 124 KID------------TG--MGRLGFRPEEAEELLEALKALPG-LELEGVFTHFAT 163
>gnl|CDD|143483 cd00635, PLPDE_III_YBL036c_like, Type III Pyridoxal 5-phosphate
(PLP)-Dependent Enzymes, YBL036c-like proteins. This
family contains mostly uncharacterized proteins, widely
distributed among eukaryotes, bacteria and archaea, that
bear similarity to the yeast hypothetical protein
YBL036c, which is homologous to a Pseudomonas aeruginosa
gene that is co-transcribed with a known proline
biosynthetic gene. YBL036c is a single domain monomeric
protein with a typical TIM barrel fold. It binds the PLP
cofactor and has been shown to exhibit amino acid
racemase activity. The YBL036c structure is similar to
the N-terminal domain of the fold type III PLP-dependent
enzymes, bacterial alanine racemase and eukaryotic
ornithine decarboxylase, which are two-domain dimeric
proteins. The lack of a second domain in YBL036c may
explain limited D- to L-alanine racemase or non-specific
racemase activity.
Length = 222
Score = 34.4 bits (80), Expect = 0.079
Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 13/73 (17%)
Query: 188 VDSEFDLENIVVASRIAGKKVNVLLRINPDVDPQVHPYVATGNKNSKFGIRNEKLQWFLD 247
VDS E + + G+ ++VL+++N G + SK G+ E+L+ L+
Sbjct: 97 VDSLKLAEELNKRAEKEGRVLDVLVQVN------------IGGEESKSGVAPEELEELLE 144
Query: 248 AVKAHPNELKLVG 260
+ A PN L++ G
Sbjct: 145 EIAALPN-LRIRG 156
>gnl|CDD|180579 PRK06467, PRK06467, dihydrolipoamide dehydrogenase; Reviewed.
Length = 471
Score = 31.8 bits (73), Expect = 0.71
Identities = 26/91 (28%), Positives = 32/91 (35%), Gaps = 40/91 (43%)
Query: 169 NGKLLEDLVLAAQEGV------FVNVDSEF-----------DL------------ENIVV 199
NGKLL A + GV F+ VD + D+ E V
Sbjct: 275 NGKLL----DAEKAGVEVDERGFIRVDKQCRTNVPHIFAIGDIVGQPMLAHKGVHEGHVA 330
Query: 200 ASRIAGKKVNVLLRINPDVDPQV---HPYVA 227
A IAGKK +P V P + P VA
Sbjct: 331 AEVIAGKKHYF----DPKVIPSIAYTEPEVA 357
>gnl|CDD|238932 cd01972, Nitrogenase_VnfE_like, Nitrogenase_VnfE_like: VnfE subunit
of the VnfEN complex_like. This group in addition to
VnfE contains a subset of the alpha subunit of the
nitrogenase MoFe protein and NifE-like proteins. The
nitrogenase enzyme system catalyzes the ATP-dependent
reduction of dinitrogen to ammonia. NifEN participates
in the synthesis of the iron-molybdenum cofactor
(FeMoco) of MoFe protein of the
molybdenum(Mo)-nitrogenase. NifB-co (an iron and sulfur
containing precursor of the FeMoco) from NifB is
transferred to NifEN where it is further processed to
FeMoco. VnfEN may similarly be a scaffolding protein
for the iron-vanadium cofactor (FeVco) of the
vanadium-dependent (V)-nitrogenase. NifE and NifN are
essential for the Mo-nitrogenase, VnfE and VnfN are not
essential for the V-nitrogenase. NifE and NifN can
substitute when the vnfEN genes are inactivated.
Length = 426
Score = 32.0 bits (73), Expect = 0.77
Identities = 30/119 (25%), Positives = 46/119 (38%), Gaps = 24/119 (20%)
Query: 99 KPQITRNVEAYKQALEGLNSIIGYAIKANNNYKILEHLRKLGCGAVLVSGNELRLALRAG 158
P+I E ++AL+G +I+ A + ++ LR+LG G V V
Sbjct: 281 APEI----EELRKALKGKKAIV--ETGAAYGHLLIAVLRELGFGEVPVVLVFHHDPTYDR 334
Query: 159 FDPTKCIFNGNGKLLEDLVLAAQEGVFVNVDSEFDLENIVVASRIAGKKVNVLLRINPD 217
D K LLE V D E D+ V++ + N+L R+ PD
Sbjct: 335 GDSEK-------DLLEHGV-----------DPEIDITKYTVSNGQYYQFYNLLKRVKPD 375
>gnl|CDD|225056 COG2145, ThiM, Hydroxyethylthiazole kinase, sugar kinase family
[Coenzyme metabolism].
Length = 265
Score = 31.1 bits (71), Expect = 1.0
Identities = 21/96 (21%), Positives = 38/96 (39%), Gaps = 18/96 (18%)
Query: 174 EDLVLAAQEGVFVNVDSEFDLENIVVASRIAGKKVNVLLRINPDVDPQVHPYVATGNKNS 233
E LA + G VD+ + + A++ A +K ++ + +VD Y++ G +
Sbjct: 123 EIAALAGEAGGGKGVDAGDGAADAIEAAKKAAQKYGTVVVVTGEVD-----YISDGTRV- 176
Query: 234 KFGIRNEKLQWFLDAVKAHPNELKLVGAHCHLGSTI 269
I N P K+ G C LG+ +
Sbjct: 177 -VVIHN-----------GSPLLGKITGTGCLLGAVV 200
>gnl|CDD|163642 cd07399, MPP_YvnB, Bacillus subtilis YvnB and related proteins,
metallophosphatase domain. YvnB (BSU35040) is an
uncharacterized Bacillus subtilis protein with a
metallophosphatase domain. This family includes
bacterial and eukaryotic proteins similar to YvnB. YvnB
belongs to the metallophosphatase (MPP) superfamily.
MPPs are functionally diverse, but all share a conserved
domain with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 214
Score = 30.8 bits (70), Expect = 1.1
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 235 FGIRNEKLQWFLDAVKAHPNELKLVGAH 262
FG R+E LQW + +K HP+ ++ H
Sbjct: 87 FGPRDEVLQWANEVLKKHPDRPAILTTH 114
>gnl|CDD|190271 pfam02296, Alpha_adaptin_C, Alpha adaptin AP2, C-terminal domain.
Alpha adaptin is a hetero tetramer which regulates
clathrin-bud formation. The carboxyl-terminal appendage
of the alpha subunit regulates translocation of
endocytic accessory proteins to the bud site.
Length = 113
Score = 28.8 bits (65), Expect = 2.0
Identities = 21/67 (31%), Positives = 26/67 (38%), Gaps = 12/67 (17%)
Query: 165 IF---NGNGKLLEDLVLAAQEG----VFVNVDSEFDLENIVVASRIAGK---KVNVLLRI 214
IF N + V EG + VD + ENIV A I KV LLR+
Sbjct: 29 IFKLQAANRPIDIAFVRRVLEGFGWAILDGVDP--NPENIVGAGVIHTSVSGKVGCLLRL 86
Query: 215 NPDVDPQ 221
P+ Q
Sbjct: 87 EPNYQAQ 93
>gnl|CDD|223402 COG0325, COG0325, Predicted enzyme with a TIM-barrel fold [General
function prediction only].
Length = 228
Score = 29.5 bits (67), Expect = 2.9
Identities = 24/101 (23%), Positives = 41/101 (40%), Gaps = 20/101 (19%)
Query: 205 GKKVNVLLRINPDVDPQVHPYVATGNKNSKFGIRNEKLQWFLDAVKAHPNELKLVGAHC- 263
K +NVL+++N + SK G+ E+L V+ PN L+L G
Sbjct: 117 PKPLNVLIQVN------------ISGEESKSGVPPEELDELAQEVQELPN-LELRGLMTI 163
Query: 264 --HLGSTITKVDIFRDAAVLMVNYIDKIRAQGFEVDYLNIG 302
+FR L D+++A+ +D L++G
Sbjct: 164 PPLTDDPEEIFAVFRKLRKLF----DELKAKYPPIDELSMG 200
>gnl|CDD|226143 COG3616, COG3616, Predicted amino acid aldolase or racemase [Amino
acid transport and metabolism].
Length = 368
Score = 29.3 bits (66), Expect = 4.7
Identities = 29/120 (24%), Positives = 48/120 (40%), Gaps = 16/120 (13%)
Query: 184 VFVNVDSEFDLENIVVASRIAGKKVNVLLRINPDVDPQVHPYVATGNKNSKFGIRNEKLQ 243
+ V +DS L+ + +R AGK + VL+ ++D +H + G+R ++
Sbjct: 114 ISVLIDSVEQLDALAALARDAGKPLRVLI----EIDSGLH----------RSGVRTPEVA 159
Query: 244 WFLDAVKAHPNELKLVGAHCHLGSTITKVDIFRDAAVLMVNYIDKIRAQGFEVDYLNIGG 303
L A A L+L G + G + AA V+ + A G L GG
Sbjct: 160 EALAAEIAAAPGLRLAGVMTYPGHSYGPGSEV--AAAERVHAAALLGAVGRAAPVLTSGG 217
>gnl|CDD|185673 cd00560, PanC, Pantoate-beta-alanine ligase. PanC
Pantoate-beta-alanine ligase, also known as pantothenate
synthase, catalyzes the formation of pantothenate from
pantoate and alanine. PanC belongs to a large
superfamily of nucleotidyltransferases that includes ,
ATP sulfurylase (ATPS), phosphopantetheine
adenylyltransferase (PPAT), and the amino-acyl tRNA
synthetases. The enzymes of this family are structurally
similar and share a dinucleotide-binding domain.
Length = 277
Score = 28.7 bits (65), Expect = 7.2
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 276 RDAAVLMVNYIDKIRAQGFEVDYLNI 301
RDA ++ D + A GF VDYL I
Sbjct: 219 RDAEDIIAAARDVLEAAGFRVDYLEI 244
>gnl|CDD|223874 COG0803, LraI, ABC-type metal ion transport system, periplasmic
component/surface adhesin [Inorganic ion transport and
metabolism].
Length = 303
Score = 28.5 bits (64), Expect = 7.4
Identities = 13/30 (43%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 199 VASRIAGKKVNVLLRINPDVDPQVHPYVAT 228
V IAG KV+V+ + P DP H Y T
Sbjct: 45 VVKNIAGDKVDVVSLVPPGADP--HSYEPT 72
>gnl|CDD|197200 cd00138, PLDc_SF, Catalytic domain of phospholipase D superfamily
proteins. Catalytic domain of phospholipase D (PLD)
superfamily proteins. The PLD superfamily is composed of
a large and diverse group of proteins including plant,
mammalian and bacterial PLDs, bacterial cardiolipin (CL)
synthases, bacterial phosphatidylserine synthases (PSS),
eukaryotic phosphatidylglycerophosphate (PGP) synthase,
eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and
some bacterial endonucleases (Nuc and BfiI), among
others. PLD enzymes hydrolyze phospholipid
phosphodiester bonds to yield phosphatidic acid and a
free polar head group. They can also catalyze the
transphosphatidylation of phospholipids to acceptor
alcohols. The majority of members in this superfamily
contain a short conserved sequence motif (H-x-K-x(4)-D,
where x represents any amino acid residue), called the
HKD signature motif. There are varying expanded forms of
this motif in different family members. Some members
contain variant HKD motifs. Most PLD enzymes are
monomeric proteins with two HKD motif-containing
domains. Two HKD motifs from two domains form a single
active site. Some PLD enzymes have only one copy of the
HKD motif per subunit but form a functionally active
dimer, which has a single active site at the dimer
interface containing the two HKD motifs from both
subunits. Different PLD enzymes may have evolved through
domain fusion of a common catalytic core with separate
substrate recognition domains. Despite their various
catalytic functions and a very broad range of substrate
specificities, the diverse group of PLD enzymes can bind
to a phosphodiester moiety. Most of them are active as
bi-lobed monomers or dimers, and may possess similar
core structures for catalytic activity. They are
generally thought to utilize a common two-step ping-pong
catalytic mechanism, involving an enzyme-substrate
intermediate, to cleave phosphodiester bonds. The two
histidine residues from the two HKD motifs play key
roles in the catalysis. Upon substrate binding, a
histidine from one HKD motif could function as the
nucleophile, attacking the phosphodiester bond to create
a covalent phosphohistidine intermediate, while the
other histidine residue from the second HKD motif could
serve as a general acid, stabilizing the leaving group.
Length = 119
Score = 27.1 bits (60), Expect = 9.0
Identities = 12/73 (16%), Positives = 31/73 (42%), Gaps = 5/73 (6%)
Query: 171 KLLEDLVLAAQEGVFV-----NVDSEFDLENIVVASRIAGKKVNVLLRINPDVDPQVHPY 225
+ L +L+ A+E +F+ + +S L ++A+ G V +++ P+ +
Sbjct: 1 EALLELLKNAKESIFIATPNFSFNSADRLLKALLAAAERGVDVRLIIDKPPNAAGSLSAA 60
Query: 226 VATGNKNSKFGIR 238
+ + +R
Sbjct: 61 LLEALLRAGVNVR 73
>gnl|CDD|226480 COG3971, COG3971, 2-keto-4-pentenoate hydratase [Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 264
Score = 28.1 bits (63), Expect = 9.2
Identities = 13/68 (19%), Positives = 24/68 (35%), Gaps = 14/68 (20%)
Query: 381 SLYDAYQHIELVSPA--------PQDAEISKFDVVGPVCESADF-LGKERELPTPDRGAG 431
++ D + V PA QD ++ D + +A F +G +
Sbjct: 123 TVADVLNATDYVLPALELIDSRIKQDWQVKFPDTIADNAANAGFVIG-----GRAVKPDD 177
Query: 432 LVVHDAGA 439
L + + GA
Sbjct: 178 LDLRNVGA 185
>gnl|CDD|237088 PRK12393, PRK12393, amidohydrolase; Provisional.
Length = 457
Score = 28.5 bits (64), Expect = 9.2
Identities = 15/48 (31%), Positives = 17/48 (35%), Gaps = 11/48 (22%)
Query: 244 WFLDAVKAHPNELKLVG------AHC-----HLGSTITKVDIFRDAAV 280
WF VK E+ L+ AHC LGS I A V
Sbjct: 271 WFAHLVKLDAEEIALLAQTGTGIAHCPQSNGRLGSGIAPALAMEAAGV 318
>gnl|CDD|180458 PRK06194, PRK06194, hypothetical protein; Provisional.
Length = 287
Score = 28.1 bits (63), Expect = 9.7
Identities = 17/69 (24%), Positives = 29/69 (42%), Gaps = 5/69 (7%)
Query: 51 QNPAKSQTHTAP--VEHCFSKKA--DGFLYCEDVRVQDVMETVEKRPFYLYSKPQITRNV 106
+ A + T + S+KA G + E+V Q V + + FY+YS PQ +V
Sbjct: 209 ADLANTAPPTRSQLIAQAMSQKAVGSGKVTAEEV-AQLVFDAIRAGRFYIYSHPQALASV 267
Query: 107 EAYKQALEG 115
+ +
Sbjct: 268 RTRMEDIVQ 276
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
0.320 0.137 0.405
Gapped
Lambda K H
0.267 0.0751 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 24,182,677
Number of extensions: 2419072
Number of successful extensions: 2067
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1977
Number of HSP's successfully gapped: 57
Length of query: 471
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 371
Effective length of database: 6,502,202
Effective search space: 2412316942
Effective search space used: 2412316942
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: 61 (27.2 bits)