RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 014581
(422 letters)
>gnl|CDD|215273 PLN02495, PLN02495, oxidoreductase, acting on the CH-CH group of
donors.
Length = 385
Score = 790 bits (2041), Expect = 0.0
Identities = 330/383 (86%), Positives = 359/383 (93%), Gaps = 1/383 (0%)
Query: 40 SASAEPDLSITVNGLQMPNPFVIGSGPPGTNYTVMKRAFDEGWGAVVAKTVSLDAAKVIN 99
A++EPDLS+TVNGL+MPNPFVIGSGPPGTNYTVMKRAFDEGWG V+AKTVSLDA+KVIN
Sbjct: 4 LAASEPDLSVTVNGLKMPNPFVIGSGPPGTNYTVMKRAFDEGWGGVIAKTVSLDASKVIN 63
Query: 100 VTPRYARLRAGANGSAKGQIIGWENIELISDRPLETMLKEFKQLKALYPDKILIASIMEE 159
VTPRYARLRAGANGSAKG++IGW+NIELISDRP ETML EFKQLK YPD+ILIASIMEE
Sbjct: 64 VTPRYARLRAGANGSAKGRVIGWQNIELISDRPFETMLAEFKQLKEEYPDRILIASIMEE 123
Query: 160 YNKAAWEELIDRVEETGIDAIEVNFSCPHGMPERKMGAAVGQDCRLLEEVCGWINAKATV 219
YNK AWEE+I+RVEETG+DA+E+NFSCPHGMPERKMGAAVGQDC LLEEVCGWINAKATV
Sbjct: 124 YNKDAWEEIIERVEETGVDALEINFSCPHGMPERKMGAAVGQDCDLLEEVCGWINAKATV 183
Query: 220 PVWAKMTPNITDITEPARVALRSGSEGVSAINTIMSVMGIDLKTLRPEPCVEGYSTPGGY 279
PVWAKMTPNITDIT+PARVAL+SG EGV+AINTIMSVMGI+L TLRPEPCVEGYSTPGGY
Sbjct: 184 PVWAKMTPNITDITQPARVALKSGCEGVAAINTIMSVMGINLDTLRPEPCVEGYSTPGGY 243
Query: 280 SCKAVHPIALGKVMSIAKMMKSEFNDKDYSLSGIGGVETGGDAAEFILLGANTVQVCTGV 339
S KAV PIAL KVM+IAKMMKSEF + D SLSGIGGVETGGDAAEFILLGA+TVQVCTGV
Sbjct: 244 SSKAVRPIALAKVMAIAKMMKSEFPE-DRSLSGIGGVETGGDAAEFILLGADTVQVCTGV 302
Query: 340 MMHGYGLVKRLCEELKDFMKMHNFSSIEDFRGASIEYFTTHTELVRMQQEAIQQRKAVRK 399
MMHGY LVK LC EL+DFMK HNFSSIEDFRGAS+ YFTTHT+LV+ Q+EAI+QRKA+RK
Sbjct: 303 MMHGYPLVKNLCAELQDFMKKHNFSSIEDFRGASLPYFTTHTDLVQRQKEAIRQRKAIRK 362
Query: 400 GLQSDKDWTGDGFVKETLSMVSN 422
GL SDKDWTGDGFVKET SMVSN
Sbjct: 363 GLASDKDWTGDGFVKETESMVSN 385
>gnl|CDD|239244 cd02940, DHPD_FMN, Dihydropyrimidine dehydrogenase (DHPD)
FMN-binding domain. DHPD catalyzes the first step in
pyrimidine degradation: the NADPH-dependent reduction of
uracil and thymine to the corresponding
5,6-dihydropyrimidines. DHPD contains two FAD, two FMN,
and eight [4Fe-4S] clusters, arranged in two electron
transfer chains that pass the dimer interface twice. Two
of the Fe-S clusters show a hitherto unobserved
coordination involving a glutamine residue.
Length = 299
Score = 484 bits (1248), Expect = e-172
Identities = 171/309 (55%), Positives = 211/309 (68%), Gaps = 10/309 (3%)
Query: 46 DLSITVNGLQMPNPFVIGSGPPGTNYTVMKRAFDEGWGAVVAKTVSLDAAKVINVTPRYA 105
DLS+T G++ PNPF + S PP T+Y +++RAF+ GWG V KT+ LD V NV+PR A
Sbjct: 1 DLSVTFCGIKFPNPFGLASAPPTTSYPMIRRAFEAGWGGAVTKTLGLDKDIVTNVSPRIA 60
Query: 106 RLRAGANGSAKGQIIGWENIELISDRPLETMLKEFKQLKALYPDKILIASIMEEYNKAAW 165
RLR IG+ NIELIS++PLE LKE ++LK +PDKILIASIM EYNK W
Sbjct: 61 RLRTSGR-----GQIGFNNIELISEKPLEYWLKEIRELKKDFPDKILIASIMCEYNKEDW 115
Query: 166 EELIDRVEETGIDAIEVNFSCPHGMPERKMGAAVGQDCRLLEEVCGWINAKATVPVWAKM 225
EL VEE G DA+E+NFSCPHGMPER MGAAVGQD L+EE+C W+ +PV AK+
Sbjct: 116 TELAKLVEEAGADALELNFSCPHGMPERGMGAAVGQDPELVEEICRWVREAVKIPVIAKL 175
Query: 226 TPNITDITEPARVALRSGSEGVSAINTIMSVMGIDLKTLRPEPCVEGYSTPGGYSCKAVH 285
TPNITDI E AR A G++GVSAINT+ S+MG+DL P P VEG +T GGYS AV
Sbjct: 176 TPNITDIREIARAAKEGGADGVSAINTVNSLMGVDLDGTPPAPGVEGKTTYGGYSGPAVK 235
Query: 286 PIALGKVMSIAKMMKSEFNDKDYSLSGIGGVETGGDAAEFILLGANTVQVCTGVMMHGYG 345
PIAL V IA+ + +SGIGG+E+ DAAEF+LLGA+ VQVCT VM G+
Sbjct: 236 PIALRAVSQIARAPE-----PGLPISGIGGIESWEDAAEFLLLGASVVQVCTAVMNQGFT 290
Query: 346 LVKRLCEEL 354
+V +C L
Sbjct: 291 IVDDMCTGL 299
>gnl|CDD|236237 PRK08318, PRK08318, dihydropyrimidine dehydrogenase subunit B;
Validated.
Length = 420
Score = 395 bits (1018), Expect = e-136
Identities = 163/339 (48%), Positives = 214/339 (63%), Gaps = 13/339 (3%)
Query: 46 DLSITVNGLQMPNPFVIGSGPPGTNYTVMKRAFDEGWGAVVAKTVSLDAAKVINVT-PRY 104
DLSIT G++ PNPF + S PP Y + RAF+ GWG VV KT+ ++NV+ PR+
Sbjct: 3 DLSITFCGIKSPNPFWLASAPPTNKYYNVARAFEAGWGGVVWKTLG---PPIVNVSSPRF 59
Query: 105 ARLRAGANGSAKGQIIGWENIELISDRPLETMLKEFKQLKALYPDKILIASIMEEYNKAA 164
GA + IG+ NIELI+DRPLE L+E +++K YPD+ LIASIM E N+
Sbjct: 60 -----GALVKEDRRFIGFNNIELITDRPLEVNLREIRRVKRDYPDRALIASIMVECNEEE 114
Query: 165 WEELIDRVEETGIDAIEVNFSCPHGMPERKMGAAVGQDCRLLEEVCGWINAKATVPVWAK 224
W+E+ VEETG D IE+NF CPHGM ER MG+AVGQ L+E W+ + +PV K
Sbjct: 115 WKEIAPLVEETGADGIELNFGCPHGMSERGMGSAVGQVPELVEMYTRWVKRGSRLPVIVK 174
Query: 225 MTPNITDITEPARVALRSGSEGVSAINTIMSVMGIDLKTLRPEPCVEGYSTPGGYSCKAV 284
+TPNITDI EPAR A R G++ VS INTI S+ G+DL + P P V G S+ GGY AV
Sbjct: 175 LTPNITDIREPARAAKRGGADAVSLINTINSITGVDLDRMIPMPIVNGKSSHGGYCGPAV 234
Query: 285 HPIALGKVMSIAKMMKSEFNDKDYSLSGIGGVETGGDAAEFILLGANTVQVCTGVMMHGY 344
PIAL V IA+ ++ + +SGIGG+ET DAAEFILLGA TVQVCT M +G+
Sbjct: 235 KPIALNMVAEIARDPET----RGLPISGIGGIETWRDAAEFILLGAGTVQVCTAAMQYGF 290
Query: 345 GLVKRLCEELKDFMKMHNFSSIEDFRGASIEYFTTHTEL 383
+V+ + L +M F+S+ED G ++ T +L
Sbjct: 291 RIVEDMISGLSHYMDEKGFASLEDMVGLAVPNVTDWEDL 329
>gnl|CDD|223245 COG0167, PyrD, Dihydroorotate dehydrogenase [Nucleotide transport
and metabolism].
Length = 310
Score = 257 bits (660), Expect = 1e-83
Identities = 120/331 (36%), Positives = 175/331 (52%), Gaps = 23/331 (6%)
Query: 46 DLSITVNGLQMPNPFVIGSGPPGTNYTVMKRAFDEGWGAVVAKTVSLDAAKVINVTPRYA 105
DLS + GL+ PNP + +G G N + G+GA+V KTV+ + + N PR
Sbjct: 1 DLSTEILGLKFPNPLGLAAGFDGKNGEELDALAALGFGAIVTKTVTPEP-QEGNPKPRLF 59
Query: 106 RLRAGANGSAKGQIIGWENIELISDRPLETMLKEFKQLKALYPDKILIASIMEEYNKAAW 165
RL +G I +D LE + + K P + I ++ AW
Sbjct: 60 RLPE-----DEGLINRMGFNNPGADAFLEELKLAKYEGK---PIGVNIGKNKGGPSEEAW 111
Query: 166 EELIDRVEETG-IDAIEVNFSCPHGMPERKMGAAVGQDCRLLEEVCGWINAKATVPVWAK 224
+ +EE G DAIE+N SCP+ P G A+GQD LLE++ + A VPV+ K
Sbjct: 112 ADYARLLEEAGDADAIELNISCPN-TPG---GRALGQDPELLEKLLEAVKAATKVPVFVK 167
Query: 225 MTPNITDITEPARVALRSGSEGVSAINTIMSVMGIDLKTLRPEPCVEGYSTPGGYSCKAV 284
+ PNITDI E A+ A +G++G+ AINT S M IDL+T +P E GG S +
Sbjct: 168 LAPNITDIDEIAKAAEEAGADGLIAINTTKSGMKIDLETKKPVLANE----TGGLSGPPL 223
Query: 285 HPIALGKVMSIAKMMKSEFNDKDYSLSGIGGVETGGDAAEFILLGANTVQVCTGVMMHGY 344
PIAL +V +A++ K D + G+GG+ETG DA EFIL GA+ VQV T ++ G
Sbjct: 224 KPIAL-RV--VAELYKRLGGDIP--IIGVGGIETGEDALEFILAGASAVQVGTALIYKGP 278
Query: 345 GLVKRLCEELKDFMKMHNFSSIEDFRGASIE 375
G+VK + + L +++ F SI+D G+++
Sbjct: 279 GIVKEIIKGLARWLEEKGFESIQDIIGSALR 309
>gnl|CDD|240091 cd04740, DHOD_1B_like, Dihydroorotate dehydrogenase (DHOD) class 1B
FMN-binding domain. DHOD catalyzes the oxidation of
(S)-dihydroorotate to orotate. This is the fourth step
and the only redox reaction in the de novo biosynthesis
of UMP, the precursor of all pyrimidine nucleotides.
DHOD requires FMN as co-factor. DHOD divides into class
1 and class 2 based on their amino acid sequences and
cellular location. Members of class 1 are cytosolic
enzymes and multimers while class 2 enzymes are membrane
associated and monomeric. The class 1 enzymes can be
further divided into subtypes 1A and 1B which are
homodimers and heterotetrameric proteins, respectively.
Length = 296
Score = 203 bits (518), Expect = 2e-62
Identities = 105/332 (31%), Positives = 166/332 (50%), Gaps = 42/332 (12%)
Query: 48 SITVNGLQMPNPFVIGSGPPGTNYTVMKRAFDEGW-GAVVAKTVSLDAAKVINVTPRYAR 106
S+ + GL++ NP ++ SG G + R D G GA+V K+++L+ + N PR
Sbjct: 1 SVELAGLRLKNPVILASGTFGF-GEELSRVADLGKLGAIVTKSITLEP-REGNPPPRVVE 58
Query: 107 LRAGANGSAKGQIIGWENIELISDRP-LETMLKEFKQLKALYPDKILIASI----MEEYN 161
G + IG +N P +E L+E +IASI +EE+
Sbjct: 59 TPGGMLNA-----IGLQN-------PGVEAFLEELLPWLR-EFGTPVIASIAGSTVEEF- 104
Query: 162 KAAWEELIDRVEETGIDAIEVNFSCPHGMPERKMGAAVGQDCRLLEEVCGWINAKATVPV 221
E+ +++ + G DAIE+N SCP+ + G A G D + E+ + VPV
Sbjct: 105 ----VEVAEKLADAGADAIELNISCPN---VKGGGMAFGTDPEAVAEIVKAVKKATDVPV 157
Query: 222 WAKMTPNITDITEPARVALRSGSEGVSAINTIMSVMGIDLKTLRPEPCVEGYSTPGGYSC 281
K+TPN+TDI E AR A +G++G++ INT+ M ID++T +P + G T GG S
Sbjct: 158 IVKLTPNVTDIVEIARAAEEAGADGLTLINTLK-GMAIDIETRKP---ILGNVT-GGLSG 212
Query: 282 KAVHPIALGKVMSIAKMMKSEFNDKDYSLSGIGGVETGGDAAEFILLGANTVQVCTGVMM 341
A+ PIAL V + K ++ + G+GG+ +G DA EF++ GA+ VQV T +
Sbjct: 213 PAIKPIALRMVYQVYKAVEIP-------IIGVGGIASGEDALEFLMAGASAVQVGTANFV 265
Query: 342 HGYGLVKRLCEELKDFMKMHNFSSIEDFRGAS 373
K + E L+ ++ SIE+ G +
Sbjct: 266 -DPEAFKEIIEGLEAYLDEEGIKSIEELVGLA 296
>gnl|CDD|235982 PRK07259, PRK07259, dihydroorotate dehydrogenase 1B; Reviewed.
Length = 301
Score = 192 bits (491), Expect = 2e-58
Identities = 106/337 (31%), Positives = 161/337 (47%), Gaps = 43/337 (12%)
Query: 46 DLSITVNGLQMPNPFVIGSGPPGTNYTVMKRAFDEGWGAVVAKTVSLDAAKVINVTPRYA 105
LS+ + GL++ NP + SG G + G GA+V K+ +L+ + N TPR A
Sbjct: 1 RLSVELPGLKLKNPVMPASGTFGFGGEYARFYDLNGLGAIVTKSTTLEP-REGNPTPRIA 59
Query: 106 RLRAG---ANGSAKGQIIGWENIELISDRPLETMLKEFKQLKALYPDKILIASI----ME 158
G A G Q G + +E L ++ D +IA++ E
Sbjct: 60 ETPGGMLNAIGL---QNPGVDAF-------IEEELPWLEEF-----DTPIIANVAGSTEE 104
Query: 159 EYNKAAWEELIDRVEETGIDAIEVNFSCPHGMPERKMGAAVGQDCRLLEEVCGWINAKAT 218
EY + A E + + +DAIE+N SCP+ G A G D L EV +
Sbjct: 105 EYAEVA--EKLS--KAPNVDAIELNISCPNVK---HGGMAFGTDPELAYEVVKAVKEVVK 157
Query: 219 VPVWAKMTPNITDITEPARVALRSGSEGVSAINTIMSVMGIDLKTLRPEPCVEGYSTPGG 278
VPV K+TPN+TDI E A+ A +G++G+S INT+ M ID+KT +P + T GG
Sbjct: 158 VPVIVKLTPNVTDIVEIAKAAEEAGADGLSLINTLKG-MAIDIKTRKP---ILANVT-GG 212
Query: 279 YSCKAVHPIALGKVMSIAKMMKSEFNDKDYSLSGIGGVETGGDAAEFILLGANTVQVCTG 338
S A+ PIAL V + + + D + G+GG+ + DA EFI+ GA+ VQV T
Sbjct: 213 LSGPAIKPIALRMVYQVYQAV-------DIPIIGMGGISSAEDAIEFIMAGASAVQVGTA 265
Query: 339 VMMHGYGLVKRLCEELKDFMKMHNFSSIEDFRGASIE 375
++ E L+ ++ + SIE+ G + +
Sbjct: 266 NFY-DPYAFPKIIEGLEAYLDKYGIKSIEEIVGIAHK 301
>gnl|CDD|239204 cd02810, DHOD_DHPD_FMN, Dihydroorotate dehydrogenase (DHOD) and
Dihydropyrimidine dehydrogenase (DHPD) FMN-binding
domain. DHOD catalyzes the oxidation of
(S)-dihydroorotate to orotate. This is the fourth step
and the only redox reaction in the de novo biosynthesis
of UMP, the precursor of all pyrimidine nucleotides.
DHOD requires FMN as co-factor. DHOD divides into class
1 and class 2 based on their amino acid sequences and
cellular location. Members of class 1 are cytosolic
enzymes and multimers while class 2 enzymes are membrane
associated and monomeric. The class 1 enzymes can be
further divided into subtypes 1A and 1B which are
homodimers and heterotetrameric proteins, respectively.
DHPD catalyzes the first step in pyrimidine degradation:
the NADPH-dependent reduction of uracil and thymine to
the corresponding 5,6-dihydropyrimidines. DHPD contains
two FAD, two FMN and eight [4Fe-4S] clusters, arranged
in two electron transfer chains that pass its
homodimeric interface twice. Two of the Fe-S clusters
show a hitherto unobserved coordination involving a
glutamine residue.
Length = 289
Score = 179 bits (456), Expect = 2e-53
Identities = 95/303 (31%), Positives = 160/303 (52%), Gaps = 20/303 (6%)
Query: 53 GLQMPNPFVIGSGPPGTNYTVMKRAFDEGWGAVVAKTVSLDAAKVINVTPRYARLRAGAN 112
GL++ NPF + +GP ++ RA G+GAVV KTV+L N PR ARL
Sbjct: 5 GLKLKNPFGVAAGPLLKTGELIARAAAAGFGAVVYKTVTLHPRPG-NPLPRVARLPPEGE 63
Query: 113 GSAKGQIIGWENIELISDRPLETMLKEFKQLKALYPDKILIASIMEEYNKAAWEELIDRV 172
+ +G N + + L+ L++ + K +P + LIAS+ +K + EL ++
Sbjct: 64 SYP--EQLGILNSFGLPNLGLDVWLQDIAKAKKEFPGQPLIASVGGS-SKEDYVELARKI 120
Query: 173 EETGIDAIEVNFSCPHGMPERKMGAAVGQDCRLLEEVCGWINAKATVPVWAKMTPNIT-- 230
E G A+E+N SCP+ R+ +GQD + + + A +P+ K++P
Sbjct: 121 ERAGAKALELNLSCPNVGGGRQ----LGQDPEAVANLLKAVKAAVDIPLLVKLSPYFDLE 176
Query: 231 DITEPARVALRSGSEGVSAINTIMSVMGIDLKTLRPEPCVEGYSTPGGYSCKAVHPIALG 290
DI E A+ A R+G++G++AINTI + +DLKT+ P P GG S + P+AL
Sbjct: 177 DIVELAKAAERAGADGLTAINTISGRV-VDLKTVGPGPK----RGTGGLSGAPIRPLALR 231
Query: 291 KVMSIAKMMKSEFNDKDYSLSGIGGVETGGDAAEFILLGANTVQVCTGVMMHGYGLVKRL 350
+A++ + D + G+GG+++G D E ++ GA+ VQV T +M G +++++
Sbjct: 232 ---WVARL--AARLQLDIPIIGVGGIDSGEDVLEMLMAGASAVQVATALMWDGPDVIRKI 286
Query: 351 CEE 353
+E
Sbjct: 287 KKE 289
>gnl|CDD|130109 TIGR01037, pyrD_sub1_fam, dihydroorotate dehydrogenase (subfamily
1) family protein. This family includes subfamily 1
dihydroorotate dehydrogenases while excluding the
closely related subfamily 2 (TIGR01036). This family
also includes a number of uncharacterized proteins and a
domain of dihydropyrimidine dehydrogenase. The
uncharacterized proteins might all be dihydroorotate
dehydrogenase.
Length = 300
Score = 173 bits (441), Expect = 4e-51
Identities = 108/329 (32%), Positives = 165/329 (50%), Gaps = 36/329 (10%)
Query: 47 LSITVNGLQMPNPFVIGSGPPGTNYTVMKRAFDEGWGAVVAKTVSLDAAKVINVTPRYAR 106
L + + G++ NP ++ SG G+ ++R G GAVV K++ L+ P
Sbjct: 1 LEVELFGIRFKNPLILASGIMGSGVESLRRIDRSGAGAVVTKSIGLEPRPG-YRNPTIVE 59
Query: 107 LRAGANGSAKGQIIGWENIELISDRPLETMLKEFKQLKALYPDKILIASIM----EEYNK 162
G + Q G E LE + ++ LIAS+ EE+ +
Sbjct: 60 TPCGMLNAIGLQNPGVEAF-------LEELKPVREEF-----PTPLIASVYGSSVEEFAE 107
Query: 163 AAWEELIDRVEETGIDAIEVNFSCPHGMPERKMGAAVGQDCRLLEEVCGWINAKATVPVW 222
A E +++ +DA E+N SCPH G A+GQD L +V + K VPV+
Sbjct: 108 VA--EKLEKAPPY-VDAYELNLSCPHVK---GGGIAIGQDPELSADVVKAVKDKTDVPVF 161
Query: 223 AKMTPNITDITEPARVALRSGSEGVSAINTIMSVMGIDLKTLRPEPCVEGYSTPGGYSCK 282
AK++PN+TDITE A+ A +G++G++ INT+ M ID+KT +P + GG S
Sbjct: 162 AKLSPNVTDITEIAKAAEEAGADGLTLINTLRG-MKIDIKTGKPILA----NKTGGLSGP 216
Query: 283 AVHPIALGKVMSIAKMMKSEFNDKDYSLSGIGGVETGGDAAEFILLGANTVQVCTGVMMH 342
A+ PIAL V + KM+ D + G+GG+ + DA EF++ GA+ VQV T V
Sbjct: 217 AIKPIALRMVYDVYKMV-------DIPIIGVGGITSFEDALEFLMAGASAVQVGTAVYYR 269
Query: 343 GYGLVKRLCEELKDFMKMHNFSSIEDFRG 371
G+ K++ E L F+K F+SIE+ G
Sbjct: 270 GF-AFKKIIEGLIAFLKAEGFTSIEELIG 297
>gnl|CDD|216348 pfam01180, DHO_dh, Dihydroorotate dehydrogenase.
Length = 290
Score = 124 bits (313), Expect = 1e-32
Identities = 91/318 (28%), Positives = 149/318 (46%), Gaps = 35/318 (11%)
Query: 47 LSITVNGLQMPNPFVIGSGPPGTNYTVMKRAFDEGWGAVVAKTVSLDAAKVINVTPRYAR 106
L++ + GL+ NP + SG +K +GA+ K+V+ + + N TPR R
Sbjct: 2 LAVKIPGLKFKNPIGLASGFDKFGEEALKWLALGKFGAIEIKSVTPEP-QPGNPTPRVFR 60
Query: 107 LRAGANGSAKGQIIGWENIELISDRPLETMLKEFKQLKALYPDKI-LIASIMEEYNKAAW 165
L G + +G N L D LE +LK K+ YP + +I S +
Sbjct: 61 LPEGVLNA-----MGLNNPGL--DAVLEELLKRRKE----YPRPLGIILSK----AGSTV 105
Query: 166 EELIDRVEETG--IDAIEVNFSCPHGMPERKMGAAVGQDCRLLEEVCGWINAKATVPVWA 223
E+ ++ + G D +E+N SCP+ A+ D L + + + VPV
Sbjct: 106 EDYVEVARKIGPFADYLELNVSCPN----TPGLRALQTDPELAAILLKVVKEVSKVPVLV 161
Query: 224 KMTPNITDITEPARVALRSGSEGVSAI---NTIMSVMGIDLKTLRPEPCVEGYSTPGGYS 280
K+ P++TDI + +G +G++ I NT + M IDLKT P + T GG S
Sbjct: 162 KLAPDLTDIVIIDIADVAAGEDGLTGINATNTTVRGMRIDLKTESP---ILANGT-GGLS 217
Query: 281 CKAVHPIALGKVMSIAKMMKSEFNDKDYSLSGIGGVETGGDAAEFILLGANTVQVCTGVM 340
A+ PIAL + + + + E + G+GG+ TG DA E IL GA+ VQ+ T ++
Sbjct: 218 GPAIKPIALKVIRELYQRVGPEI-----PIIGVGGIFTGEDALEKILAGASAVQIGTALI 272
Query: 341 MHGYGLVKRLCEELKDFM 358
G + ++ +EL + +
Sbjct: 273 FGGPFIFPKIIDELPELL 290
>gnl|CDD|240090 cd04739, DHOD_like, Dihydroorotate dehydrogenase (DHOD) like
proteins. DHOD catalyzes the oxidation of
(S)-dihydroorotate to orotate. This is the fourth step
and the only redox reaction in the de novo biosynthesis
of UMP, the precursor of all pyrimidine nucleotides.
DHOD requires FMN as co-factor. DHOD divides into class
1 and class 2 based on their amino acid sequences and
cellular location. Members of class 1 are cytosolic
enzymes and multimers while class 2 enzymes are membrane
associated and monomeric. The class 1 enzymes can be
further divided into subtypes 1A and 1B which are
homodimers and heterotetrameric proteins, respectively.
This subgroup has the conserved FMN binding site, but
lacks some catalytic residues and may therefore be
inactive.
Length = 325
Score = 100 bits (251), Expect = 1e-23
Identities = 87/339 (25%), Positives = 146/339 (43%), Gaps = 49/339 (14%)
Query: 46 DLSITVNGLQMPNPFVIGSGPPGTNYTVMKRAFDEGWGAVVAKTVSLDAAKVINVTPRYA 105
DLS T GL + NP V + P N ++R D G GA+V SL ++
Sbjct: 1 DLSTTYLGLSLKNPLVASASPLSRNLDNIRRLEDAGAGAIVLP--SLFEEQIEREAQELD 58
Query: 106 RLRAGANGSAKGQI----IGWENIELISDRPLETMLKEFKQLKALYPDKILIASIMEEYN 161
R + A+ G N L + LE ++ K+ ++ P +IAS+ N
Sbjct: 59 RFLTYGSSFAEALSYFPEYGRYN--LGPEEYLEL-IRRAKRAVSI-P---VIASL----N 107
Query: 162 KAA---WEELIDRVEETGIDAIEVNFSCPHGMP--ERKMGAAVGQD-CRLLEEVCGWINA 215
+ W + ++EE G DA+E+N + +P GA V Q +L V +
Sbjct: 108 GVSAGGWVDYARQIEEAGADALELNI---YALPTDPDISGAEVEQRYLDILRAVK----S 160
Query: 216 KATVPVWAKMTPNITDITEPARVALRSGSEGVSAINTIMSVMGIDLKTLRPEPCVEGYST 275
T+PV K++P + + A+ +G++G+ N IDL+TL P + S+
Sbjct: 161 AVTIPVAVKLSPFFSALAHMAKQLDAAGADGLVLFNRFYQP-DIDLETLEVVPNLL-LSS 218
Query: 276 PGGYSCKAVHPIAL--GKVMSIAKMMKSEFNDKDYSLSGIGGVETGGDAAEFILLGANTV 333
P + IA+ G+V SL+ GGV D +++L GA+ V
Sbjct: 219 PAEIR-LPLRWIAILSGRV--------------KASLAASGGVHDAEDVVKYLLAGADVV 263
Query: 334 QVCTGVMMHGYGLVKRLCEELKDFMKMHNFSSIEDFRGA 372
+ ++ HG + L L+ +M+ H + S++ RG+
Sbjct: 264 MTTSALLRHGPDYIGTLLAGLEAWMEEHGYESVQQLRGS 302
>gnl|CDD|235045 PRK02506, PRK02506, dihydroorotate dehydrogenase 1A; Reviewed.
Length = 310
Score = 95.8 bits (239), Expect = 3e-22
Identities = 87/346 (25%), Positives = 147/346 (42%), Gaps = 61/346 (17%)
Query: 46 DLSITVNGLQMPNPFVIGSGPPGTNYTVMKRAFDE-------GWGAVVAKTVSLDAAKVI 98
S + G + N + +G V +E GA V K+ +L +
Sbjct: 1 STSTQIAGFKFDNCLMNAAG-------VYCMTKEELEEVEASAAGAFVTKSATL-EPRPG 52
Query: 99 NVTPRYARLRAGANGSAKGQIIGWENIELISDRPLETMLKEFKQLKALYPDKILIASIME 158
N PRYA G+ S +G N+ D L+ + E ++ P + + +
Sbjct: 53 NPEPRYADTPLGSINS-----MGLPNLGF--DYYLD-YVLELQKKGPNKPHFLSVVGLSP 104
Query: 159 EYNKAAWEELIDRVEETG-IDAIEVNFSCPH--GMPERKMGAAVGQDC----RLLEEVCG 211
E ++ +++ + +E+N SCP+ G P+ + D ++LEEV
Sbjct: 105 EET----HTILKKIQASDFNGLVELNLSCPNVPGKPQ------IAYDFETTEQILEEVFT 154
Query: 212 WINAKATVPVWAKMTP--NITDITEPARVALRSGSEGVSAINTIMSVMGIDLKT----LR 265
+ T P+ K+ P +I + A + + V+ IN+I + + ID + ++
Sbjct: 155 YF----TKPLGVKLPPYFDIVHFDQAAAIFNKFPLAFVNCINSIGNGLVIDPEDETVVIK 210
Query: 266 PEPCVEGYSTPGGYSCKAVHPIALGKVMSIAKMMKSEFNDKDYSLSGIGGVETGGDAAEF 325
P+ G+ GG + P AL V + + + + G GGV+TG DA E
Sbjct: 211 PK---NGF---GGIGGDYIKPTALANVRAFYQRLNPSI-----QIIGTGGVKTGRDAFEH 259
Query: 326 ILLGANTVQVCTGVMMHGYGLVKRLCEELKDFMKMHNFSSIEDFRG 371
IL GA+ VQV T + G + +RL +ELK M + S+EDFRG
Sbjct: 260 ILCGASMVQVGTALHKEGPAVFERLTKELKAIMAEKGYQSLEDFRG 305
>gnl|CDD|240092 cd04741, DHOD_1A_like, Dihydroorotate dehydrogenase (DHOD) class 1A
FMN-binding domain. DHOD catalyzes the oxidation of
(S)-dihydroorotate to orotate. This is the fourth step
and the only redox reaction in the de novo biosynthesis
of UMP, the precursor of all pyrimidine nucleotides.
DHOD requires FMN as co-factor. DHOD divides into class
1 and class 2 based on their amino acid sequences and
cellular location. Members of class 1 are cytosolic
enzymes and multimers while class 2 enzymes are membrane
associated and monomeric. The class 1 enzymes can be
further divided into subtypes 1A and 1B which are
homodimers and heterotetrameric proteins, respectively.
Length = 294
Score = 94.3 bits (235), Expect = 9e-22
Identities = 83/316 (26%), Positives = 131/316 (41%), Gaps = 30/316 (9%)
Query: 50 TVNGLQMPNPFVIGSGPPGTNYTVMKRAFDEGWGAVVAKTVSLDAAKVINVTPRYARLRA 109
T GL + P + +GP T + GAV ++ S A + N PRY A
Sbjct: 2 TPPGLTISPPLMNAAGPWCTTLEDLLELAASSTGAVTTRS-STLAGRPGNPEPRY---YA 57
Query: 110 GANGSAKGQIIGWENIELISDRPLETMLKEFKQLKALYPDKILIASIMEEYNKAAWEELI 169
GS +G N+ L D LE + L + + E AA + I
Sbjct: 58 FPLGSINS--LGLPNLGL--DYYLEYIRTISDGLPGSAKPFFISVTGSAEDI-AAMYKKI 112
Query: 170 DRVEETGIDAIEVNFSCPH--GMPERKMGAAVGQDCRLLEEVCGWINAKATVPVWAKMTP 227
++ A+E+N SCP+ G P D E + A ++PV K P
Sbjct: 113 AAHQKQFPLAMELNLSCPNVPGKPPP------AYDFDATLEYLTAVKAAYSIPVGVKTPP 166
Query: 228 NITDITEPARVA--LRSGSEGVS---AINTIMSVMGIDLKTLRPEPCVEGYSTPGGYSCK 282
TD + +A L + + +S A NT+ + + +D R ++ + GG +
Sbjct: 167 -YTDPAQFDTLAEALNAFACPISFITATNTLGNGLVLD--PERETVVLKPKTGFGGLAGA 223
Query: 283 AVHPIALGKVMSIAKMMKSEFNDKDYSLSGIGGVETGGDAAEFILLGANTVQVCTGVMMH 342
+HP+ALG V + +++ SE + G+GGV G A L GA+ VQV T +
Sbjct: 224 YLHPLALGNVRTFRRLLPSEIQ-----IIGVGGVLDGRGAFRMRLAGASAVQVGTALGKE 278
Query: 343 GYGLVKRLCEELKDFM 358
G + R+ +EL+D
Sbjct: 279 GPKVFARIEKELEDIW 294
>gnl|CDD|236051 PRK07565, PRK07565, dihydroorotate dehydrogenase 2; Reviewed.
Length = 334
Score = 89.5 bits (223), Expect = 7e-20
Identities = 87/339 (25%), Positives = 147/339 (43%), Gaps = 48/339 (14%)
Query: 46 DLSITVNGLQMPNPFVIGSGPPGTNYTVMKRAFDEGWGAVVAKT-----VSLDAAKVINV 100
DLS T GL + NP V + P + +KR D G GAVV K+ + +AA++
Sbjct: 2 DLSTTYLGLTLRNPLVASASPLSESVDNVKRLEDAGAGAVVLKSLFEEQIRHEAAELDRH 61
Query: 101 TPRYARLRAGA----NGSAKGQIIGWENIELISDRPLETMLKEFKQLKALYPDKILIASI 156
A A AK + E +ELI ++ K D +IAS+
Sbjct: 62 LTHGTESFAEALDYFPEPAKFYVGPEEYLELI------------RRAKEAV-DIPVIASL 108
Query: 157 MEEYNKAAWEELIDRVEETGIDAIEVNFSCPHGMPERKMGAAVGQD-CRLLEEVCGWINA 215
+ W + ++E+ G DA+E+N P+ GA V Q +L V +
Sbjct: 109 -NGSSAGGWVDYARQIEQAGADALELNIYYLPTDPDIS-GAEVEQRYLDILRAVKSAV-- 164
Query: 216 KATVPVWAKMTPNITDITEPARVALRSGSEGVSAINTIMSVMGIDLKTLRPEPCVEGYST 275
++PV K++P +++ A+ +G++G+ N IDL+TL P + ST
Sbjct: 165 --SIPVAVKLSPYFSNLANMAKRLDAAGADGLVLFNRFYQP-DIDLETLEVVPGLV-LST 220
Query: 276 PGGYSCKAVHPIAL--GKVMSIAKMMKSEFNDKDYSLSGIGGVETGGDAAEFILLGANTV 333
P + IA+ G+V D + + GV D + +L GA+ V
Sbjct: 221 PAELR-LPLRWIAILSGRV------------GADLAATT--GVHDAEDVIKMLLAGADVV 265
Query: 334 QVCTGVMMHGYGLVKRLCEELKDFMKMHNFSSIEDFRGA 372
+ + ++ HG + + L+D+M+ H + S++ FRG+
Sbjct: 266 MIASALLRHGPDYIGTILRGLEDWMERHGYESLQQFRGS 304
>gnl|CDD|240089 cd04738, DHOD_2_like, Dihydroorotate dehydrogenase (DHOD) class 2.
DHOD catalyzes the oxidation of (S)-dihydroorotate to
orotate. This is the fourth step and the only redox
reaction in the de novo biosynthesis of UMP, the
precursor of all pyrimidine nucleotides. DHOD requires
FMN as co-factor. DHOD divides into class 1 and class 2
based on their amino acid sequences, their cellular
location and their natural electron acceptor used to
reoxidize the flavin group. Members of class 1 are
cytosolic enzymes and multimers, while class 2 enzymes
are membrane associated, monomeric and use respiratory
quinones as their physiological electron acceptors.
Length = 327
Score = 72.5 bits (179), Expect = 4e-14
Identities = 94/368 (25%), Positives = 141/368 (38%), Gaps = 96/368 (26%)
Query: 24 GLRLPSRIGLRVLASDSASAEPDLSITVNGLQMPNPFVIGSGPPGTNYTVMKRAFDE--- 80
L+L L +L +P L + V GL PNP + +G FD+
Sbjct: 19 ALKLGLGPPLLLLLVY---DDPRLEVEVFGLTFPNPVGLAAG------------FDKNAE 63
Query: 81 --------GWGAVVAKTVSLDAAKVINVTPRYARL--------RAGANGSAKGQIIGWEN 124
G+G V TV+ N PR RL R G N G
Sbjct: 64 AIDALLALGFGFVEVGTVTPRPQPG-NPKPRLFRLPEDEALINRMGFNN--DG------- 113
Query: 125 IELISDRPLETMLKEFKQLKALYPDKILIASIMEEYNKAAWEELIDRVE--ETGI----- 177
+ + K K+ + L +I NK E D VE G+
Sbjct: 114 --------ADAVAKRLKKRR--PRGGPLGVNI--GKNKDTPLE--DAVEDYVIGVRKLGP 159
Query: 178 --DAIEVNFSCP--HGMPERKMGAAVGQDCRLLEEVCGWINA-----KATVPVWAKMTPN 228
D + VN S P G+ R + Q L E+ + VP+ K+ P+
Sbjct: 160 YADYLVVNVSSPNTPGL--RDL-----QGKEALRELLTAVKEERNKLGKKVPLLVKIAPD 212
Query: 229 ITD--ITEPARVALRSGSEGVSAINTIMSVMGIDLKTLRPEPCVEGYSTPGGYSCKAVHP 286
++D + + A VAL G +G+ A NT +S G+ L E GG S +
Sbjct: 213 LSDEELEDIADVALEHGVDGIIATNTTISRPGLLRSPLANET--------GGLSGAPLKE 264
Query: 287 IALGKVMSIAKMMKSEFNDKDYSLSGIGGVETGGDAAEFILLGANTVQVCTGVMMHGYGL 346
+ +V + ++ + + G+GG+ +G DA E I GA+ VQ+ TG++ G GL
Sbjct: 265 RST-EV--LREL--YKLTGGKIPIIGVGGISSGEDAYEKIRAGASLVQLYTGLVYEGPGL 319
Query: 347 VKRLCEEL 354
VKR+ EL
Sbjct: 320 VKRIKREL 327
>gnl|CDD|235388 PRK05286, PRK05286, dihydroorotate dehydrogenase 2; Reviewed.
Length = 344
Score = 63.3 bits (155), Expect = 5e-11
Identities = 49/191 (25%), Positives = 86/191 (45%), Gaps = 29/191 (15%)
Query: 178 DAIEVNFSCP--HGMPERKMGAAVGQDCRLLEEVCGWINAK-----ATVPVWAKMTPNIT 230
D VN S P G+ R + Q L+E+ + VP+ K+ P+++
Sbjct: 171 DYFTVNISSPNTPGL--RDL-----QYGEALDELLAALKEAQAELHGYVPLLVKIAPDLS 223
Query: 231 D--ITEPARVALRSGSEGVSAINTIMSVMGIDLKTLRPEPCVEGYSTPGGYSCKAVHPIA 288
D + + A +AL G +GV A NT + L+ P + GG S + + +
Sbjct: 224 DEELDDIADLALEHGIDGVIATNTT-----LSRDGLKGLPNADE---AGGLSGRPLFERS 275
Query: 289 LGKVMSIAKMMKSEFNDKDYSLSGIGGVETGGDAAEFILLGANTVQVCTGVMMHGYGLVK 348
+V I ++ + + G+GG+++ DA E I GA+ VQ+ +G++ G GLVK
Sbjct: 276 T-EV--IRRL--YKELGGRLPIIGVGGIDSAEDAYEKIRAGASLVQIYSGLIYEGPGLVK 330
Query: 349 RLCEELKDFMK 359
+ L ++
Sbjct: 331 EIVRGLARLLR 341
Score = 28.6 bits (65), Expect = 7.2
Identities = 14/38 (36%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 24 GLRLPSRIGLR-VLASDSASAEPDLSITVNGLQMPNPF 60
L+ SR L +L +P L +TV GL PNP
Sbjct: 25 ALKRASRTPLLSLLRQRLTYTDPRLPVTVMGLTFPNPV 62
>gnl|CDD|233243 TIGR01036, pyrD_sub2, dihydroorotate dehydrogenase, subfamily 2.
This model describes enzyme protein dihydroorotate
dehydrogenase exclusively for subfamily 2. It includes
members from bacteria, yeast, plants etc. The
subfamilies 1 and 2 share extensive homology,
particularly toward the C-terminus. This subfamily has a
longer N-terminal region [Purines, pyrimidines,
nucleosides, and nucleotides, Pyrimidine ribonucleotide
biosynthesis].
Length = 336
Score = 61.7 bits (150), Expect = 2e-10
Identities = 50/182 (27%), Positives = 88/182 (48%), Gaps = 17/182 (9%)
Query: 178 DAIEVNFSCPH--GMPERKMGAAVGQDCRLLEEVCGWINAKATVPVWAKMTPNIT--DIT 233
I VN S P+ G+ + + G A+ ++ + A VP+ K+ P+++ D+
Sbjct: 168 GYIVVNISSPNTPGLRDLQYGEALDDLLTAIKNEQNDLQAHHHVPIAVKIAPDLSESDLI 227
Query: 234 EPARVALRSGSEGVSAINTIMSVMGIDLKTLRPEPCVEGYSTPGGYSCKAVHPIALGKVM 293
+ A +R G +GV A NT +S + P+ C + GG S K P+ L K
Sbjct: 228 QIADSLVRHGIDGVIATNTTVSRSLV----QGPKNCDQ----TGGLSGK---PLQL-KST 275
Query: 294 SIAKMMKSEFNDKDYSLSGIGGVETGGDAAEFILLGANTVQVCTGVMMHGYGLVKRLCEE 353
I + + E N + + G+GG+++ DA E I GA+ +Q+ +G + G LVK + +
Sbjct: 276 EIIRRLYLELNGR-LPIIGVGGIDSAQDAREKIAAGASLLQIYSGFIYKGPPLVKEIVKH 334
Query: 354 LK 355
+
Sbjct: 335 IV 336
>gnl|CDD|178421 PLN02826, PLN02826, dihydroorotate dehydrogenase.
Length = 409
Score = 54.0 bits (130), Expect = 6e-08
Identities = 45/160 (28%), Positives = 76/160 (47%), Gaps = 20/160 (12%)
Query: 219 VPVWAKMTPNIT--DITEPARVALRSGSEGVSAINTIMSVMGIDLKTLRPEPCVEGYSTP 276
P+ K+ P+++ D+ + A VAL G +G+ NT +S RP+ V G+
Sbjct: 263 PPLLVKIAPDLSKEDLEDIAAVALALGIDGLIISNTTIS---------RPDS-VLGHPHA 312
Query: 277 ---GGYSCKAVHPIALGKVMSIAKMMKSEFNDKDYSLSGIGGVETGGDAAEFILLGANTV 333
GG S K + ++ + + ++ + + L G GGV +G DA + I GA+ V
Sbjct: 313 DEAGGLSGKPLFDLSTEVLREMYRLTRGKI-----PLVGCGGVSSGEDAYKKIRAGASLV 367
Query: 334 QVCTGVMMHGYGLVKRLCEELKDFMKMHNFSSIEDFRGAS 373
Q+ T G L+ R+ EL ++ F SI++ GA
Sbjct: 368 QLYTAFAYEGPALIPRIKAELAACLERDGFKSIQEAVGAD 407
>gnl|CDD|240073 cd04722, TIM_phosphate_binding, TIM barrel proteins share a
structurally conserved phosphate binding motif and in
general share an eight beta/alpha closed barrel
structure. Specific for this family is the conserved
phosphate binding site at the edges of strands 7 and 8.
The phosphate comes either from the substrate, as in the
case of inosine monophosphate dehydrogenase (IMPDH), or
from ribulose-5-phosphate 3-epimerase (RPE) or from
cofactors, like FMN.
Length = 200
Score = 41.0 bits (96), Expect = 4e-04
Identities = 47/223 (21%), Positives = 68/223 (30%), Gaps = 46/223 (20%)
Query: 115 AKGQIIGWENIELISDRPLETMLKEFKQLKALYPDKILIASIMEEYNKAAWEELIDRVEE 174
A I + ET KE + A D L + AA +
Sbjct: 24 AGADAIIVGTRSSDPEEA-ETDDKEVLKEVAAETDLPLGVQLAINDAAAAVDIAAAAARA 82
Query: 175 TGIDAIEVNFSCPHGMPERKMGAAVGQDCRLLEEVCGWINAKATVPVWAKMTPNITDITE 234
G D +E++ + + E + R L E A V V K++P
Sbjct: 83 AGADGVEIHGAVGYLARE------DLELIRELRE------AVPDVKVVVKLSPTGELAAA 130
Query: 235 PARVALRSGSEGVSAINTIMSVMGIDLKTLRPEPCVEGYSTPGGYSCKAVHPIALGKVMS 294
A A GV + G GG AV PIA ++
Sbjct: 131 AAEEA------GVDEVGL-------------------GNGGGGGGGRDAV-PIADLLLIL 164
Query: 295 IAKMMKSEFNDKDYSLSGIGGVETGGDAAEFILLGANTVQVCT 337
+ K + GG+ DAAE + LGA+ V V +
Sbjct: 165 AKRGSKVP-------VIAGGGINDPEDAAEALALGADGVIVGS 200
>gnl|CDD|233750 TIGR02151, IPP_isom_2, isopentenyl-diphosphate delta-isomerase,
type 2. Isopentenyl-diphosphate delta-isomerase (IPP
isomerase) interconverts isopentenyl diphosphate and
dimethylallyl diphosphate. This model represents the
type 2 enzyme. FMN, NADPH, and Mg2+ are required by this
form, which lacks homology to the type 1 enzyme
(TIGR02150). IPP is precursor to many compounds,
including enzyme cofactors, sterols, and isoprenoids
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Other].
Length = 333
Score = 38.4 bits (90), Expect = 0.005
Identities = 71/348 (20%), Positives = 121/348 (34%), Gaps = 73/348 (20%)
Query: 43 AEPDLSITVNGLQMPNPFVIGSGPPGTNYTVMKRAFDEGWGAVVAKTVSLDAAKVINVTP 102
+ DL+ G ++ PF I + G+ + A IN
Sbjct: 39 DDIDLTTEFLGKRLKAPFYINAMTGGS-----------------------EEAGKIN--- 72
Query: 103 RYARLRAGANGSAKGQIIGWENIELISDRPLETMLKEFKQLKALYPDKILIASI-----M 157
L A +G + L +T F+ ++ P+ LIA+I +
Sbjct: 73 --RNLARAARELGIPMGVGSQRAALKDPETADT----FEVVREEAPNGPLIANIGAPQLV 126
Query: 158 EEYNKAAWEELIDRVEETGIDAIEVNFSCPHG--MPERKMGAAVGQDCR-LLEEVCGWIN 214
E + A +E ID +E DA+ ++ + PE G + + E+C ++
Sbjct: 127 EGGPEEA-QEAIDMIE---ADALAIHLNVLQELVQPE---GDRNFKGWLEKIAEICSQLS 179
Query: 215 AKATVPVWAKMTPNITDITEPARVALRSGSEGVSAINTIMSVMGIDLKTLRPEPCVEGYS 274
VPV K VA GVSAI+ + G VE Y
Sbjct: 180 ----VPVIVKEVGFGIS----KEVAKLLADAGVSAID-VAGAGGTSWAQ------VENYR 224
Query: 275 TPGGYSCKAVHPIALGKVMSIAKMMKSEFNDKDYSLSGIGGVETGGDAAEFILLGANTVQ 334
G + + S+ ++S+ D + GG+ TG D A+ I LGA+ V
Sbjct: 225 AKGSNLASFFNDWGIPTAASLL-EVRSDAPDA--PIIASGGLRTGLDVAKAIALGADAVG 281
Query: 335 VCTGVM--MHGYG------LVKRLCEELKDFMKMHNFSSIEDFRGASI 374
+ + G ++ + EELK M + +I + + +
Sbjct: 282 MARPFLKAALDEGEEAVIEEIELIIEELKVAMFLTGAKTIAELKKVPL 329
>gnl|CDD|153362 cd07678, F-BAR_FCHSD1, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of FCH and double SH3
domains 1 (FCHSD1). F-BAR domains are dimerization
modules that bind and bend membranes and are found in
proteins involved in membrane dynamics and actin
reorganization. FCH and double SH3 domains 1 (FCHSD1)
contains an N-terminal F-BAR domain and two SH3 domains
at the C-terminus. It has been characterized only in
silico, and its biological function is still unknown.
F-BAR domains form banana-shaped dimers with a
positively-charged concave surface that binds to
negatively-charged lipid membranes. They can induce
membrane deformation in the form of long tubules.
Length = 263
Score = 33.1 bits (75), Expect = 0.22
Identities = 25/97 (25%), Positives = 39/97 (40%), Gaps = 5/97 (5%)
Query: 55 QMPNPFVIGSGPPGTNYTVMKRAFDEGWGAVVAKTVSLDAAKVINVTP--RYARLRAGAN 112
++ + F+ G N T M R+ WGA T + +V + R
Sbjct: 44 RLASQFLKRDWHRGGNETEMDRSVRTVWGAWREGTAATGQGRVTRLEAYRRLRDEAGKTG 103
Query: 113 GSAKGQII--GWENIELISDRPLETMLKEFKQLKALY 147
SAK Q++ E ++ LET+ KE + K LY
Sbjct: 104 RSAKEQVLKKSTEQLQKAQAELLETV-KELSKSKKLY 139
>gnl|CDD|213914 TIGR04301, ODC_inducible, ornithine decarboxylase SpeF. Members of
this family are known or trusted examples of ornithine
decarboxylase, all encoded in the immediate vicinity of
an ornithine-putrescine antiporter. Decarboxylation of
ornithine to putrescine, followed by exchange of a
putrescine for a new ornithine, is a proton-motive cycle
that can be induced by low pH and protect a bacterium
against transient exposure to acidic conditions.
Length = 719
Score = 33.5 bits (77), Expect = 0.23
Identities = 17/61 (27%), Positives = 27/61 (44%), Gaps = 15/61 (24%)
Query: 342 HGYGLVKRLCEELKDFMKMHNFSSI--EDFRG------------ASIEYFTTHTELVRMQ 387
GY + ++LC+E+ D N + E FR A+IE+ ELV ++
Sbjct: 588 KGYTI-RQLCQEMHDLYVSRNVKQLQKEMFRKAHFPEVVMNPQEANIEFVRGEAELVPLE 646
Query: 388 Q 388
Q
Sbjct: 647 Q 647
>gnl|CDD|129820 TIGR00737, nifR3_yhdG, putative TIM-barrel protein, nifR3 family.
This model represents one branch of COG0042 (Predicted
TIM-barrel enzymes, possibly dehydrogenases, nifR3
family). This branch includes NifR3 itself, from
Rhodobacter capsulatus. It excludes a broadly
distributed but more sparsely populated subfamily that
contains sll0926 from Synechocystis PCC6803, HI0634 from
Haemophilus influenzae, and BB0225 from Borrelia
burgdorferi. It also excludes a shorter and more distant
archaeal subfamily.The function of nifR3, a member of
this family, is unknown, but it is found in an operon
with nitrogen-sensing two component regulators in
Rhodobacter capsulatus.Members of this family show a
distant relationship to alpha/beta (TIM) barrel enzymes
such as dihydroorotate dehydrogenase and glycolate
oxidase [Unknown function, General].
Length = 319
Score = 32.7 bits (75), Expect = 0.35
Identities = 28/115 (24%), Positives = 48/115 (41%), Gaps = 24/115 (20%)
Query: 172 VEETGIDAIEVNFSCPHGMPE---RKMGAAVGQDCRLLEEVCGWINAKATVPVWAKMTPN 228
EE G D I++N CP +P+ + G+A+ +D L+ ++ + +PV K+
Sbjct: 84 NEELGADIIDINMGCP--VPKITKKGAGSALLRDPDLIGKIVKAVVDAVDIPVTVKIRIG 141
Query: 229 ITD----ITEPARVALRSGSEGVSAINTIMSVMGIDLKTLRPEPCVEGYSTPGGY 279
D E AR+A +G++ V TL +GYS +
Sbjct: 142 WDDAHINAVEAARIAEDAGAQAV---------------TLHGRTRAQGYSGEANW 181
>gnl|CDD|185321 PRK15423, PRK15423, hypoxanthine phosphoribosyltransferase;
Provisional.
Length = 178
Score = 30.4 bits (68), Expect = 1.1
Identities = 17/62 (27%), Positives = 28/62 (45%)
Query: 4 LNLNQIISNSNTSFAVNRRPGLRLPSRIGLRVLASDSASAEPDLSITVNGLQMPNPFVIG 63
L + II + NT V LR P + + L + E ++ + G +P+ FV+G
Sbjct: 96 LIVEDIIDSGNTLSKVREILSLREPKSLAICTLLDKPSRREVNVPVEFIGFSIPDEFVVG 155
Query: 64 SG 65
G
Sbjct: 156 YG 157
>gnl|CDD|239200 cd02801, DUS_like_FMN, Dihydrouridine synthase-like (DUS-like)
FMN-binding domain. Members of this family catalyze the
reduction of the 5,6-double bond of a uridine residue on
tRNA. Dihydrouridine modification of tRNA is widely
observed in prokaryotes and eukaryotes, and also in some
archaea. Most dihydrouridines are found in the D loop of
t-RNAs. The role of dihydrouridine in tRNA is currently
unknown, but may increase conformational flexibility of
the tRNA. It is likely that different family members
have different substrate specificities, which may
overlap. 1VHN, a putative flavin oxidoreductase, has
high sequence similarity to DUS. The enzymatic
mechanism of 1VHN is not known at the present.
Length = 231
Score = 30.5 bits (70), Expect = 1.3
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 171 RVEETGIDAIEVNFSCPHGMPERK-MGAAVGQDCRLLEEVCGWINAKATVPVWAKM 225
VEE G D I++N CP + GAA+ +D L+ E+ + +PV K+
Sbjct: 75 IVEELGADGIDLNMGCPSPKVTKGGAGAALLKDPELVAEIVRAVREAVPIPVTVKI 130
>gnl|CDD|217151 pfam02624, YcaO, YcaO-like family.
Length = 332
Score = 30.4 bits (69), Expect = 1.7
Identities = 6/28 (21%), Positives = 14/28 (50%)
Query: 161 NKAAWEELIDRVEETGIDAIEVNFSCPH 188
+ EL+ R++ G++ V+ + P
Sbjct: 290 LEEDLAELVARLKAAGLEVYVVDLTRPD 317
>gnl|CDD|216365 pfam01207, Dus, Dihydrouridine synthase (Dus). Members of this
family catalyze the reduction of the 5,6-double bond of
a uridine residue on tRNA. Dihydrouridine modification
of tRNA is widely observed in prokaryotes and
eukaryotes, and also in some archae. Most
dihydrouridines are found in the D loop of t-RNAs. The
role of dihydrouridine in tRNA is currently unknown, but
may increase conformational flexibility of the tRNA. It
is likely that different family members have different
substrate specificities, which may overlap. Dus 1 from
Saccharomyces cerevisiae acts on pre-tRNA-Phe, while Dus
2 acts on pre-tRNA-Tyr and pre-tRNA-Leu. Dus 1 is active
as a single subunit, requiring NADPH or NADH, and is
stimulated by the presence of FAD. Some family members
may be targeted to the mitochondria and even have a role
in mitochondria.
Length = 309
Score = 30.4 bits (69), Expect = 1.8
Identities = 18/61 (29%), Positives = 29/61 (47%), Gaps = 11/61 (18%)
Query: 171 RVEETGIDAIEVNFSCPHGMPERKM-GAAVGQD----CRLLEEVCGWINAKAT-VPVWAK 224
V + G D I++N CP R GAA+ +D ++++ V KA +PV K
Sbjct: 74 LVADLGADIIDINMGCPAKKVTRGGAGAALLRDPDLVAQIVKAV-----VKAVDIPVTVK 128
Query: 225 M 225
+
Sbjct: 129 I 129
>gnl|CDD|153397 cd08028, LARP_3, La RNA-binding domain of La-related protein 3.
This domain is found at the N-terminus of the La
autoantigen and similar proteins, and co-occurs with an
RNA-recognition motif (RRM). Together these domains
function to bind primary transcripts of RNA polymerase
III at their 3' terminus and protect them from
exonucleolytic degradation. Binding is specific for the
3'-terminal UUU-OH motif. The La autoantigen is also
called Lupus La protein, LARP3, or Sjoegren syndrome
type B antigen (SS-B).
Length = 82
Score = 28.4 bits (64), Expect = 1.8
Identities = 12/28 (42%), Positives = 19/28 (67%), Gaps = 1/28 (3%)
Query: 132 PLETMLKEFKQLKALYPDKILIASIMEE 159
P+E MLK F +LK+L D +IA +++
Sbjct: 39 PMEVMLK-FNRLKSLSSDPEVIAKALKK 65
>gnl|CDD|221887 pfam12998, ING, Inhibitor of growth proteins N-terminal
histone-binding. Histones undergo numerous
post-translational modifications, including acetylation
and methylation, at residues which are then probable
docking sites for various chromatin remodelling
complexes. Inhibitor of growth proteins (INGs)
specifically bind to residues that have been thus
modified. INGs carry a well-characterized C-terminal
PHD-type zinc-finger domain, binding with lysine
4-tri-methylated histone H3 (H3K4me3), as well as this
N-terminal domain that binds unmodified H3 tails.
Although these two regions can bind histones
independently, together they increase the apparent
association of the ING for the H3 tail.
Length = 104
Score = 28.6 bits (65), Expect = 2.1
Identities = 8/42 (19%), Positives = 20/42 (47%), Gaps = 8/42 (19%)
Query: 130 DRPLETMLKEFKQLKALYPDKILIASIMEEYNKAAWEELIDR 171
+ L+ + +E + + L +K+ +A+ EL+D+
Sbjct: 59 EELLKRIQEELIKAQELQDEKVQLANQA--------YELVDK 92
>gnl|CDD|214697 smart00498, FH2, Formin Homology 2 Domain. FH proteins control
rearrangements of the actin cytoskeleton, especially in
the context of cytokinesis and cell polarisation.
Members of this family have been found to interact with
Rho-GTPases, profilin and other actin-assoziated
proteins. These interactions are mediated by the
proline-rich FH1 domain, usually located in front of FH2
(but not listed in SMART). Despite this cytosolic
function, vertebrate formins have been assigned
functions within the nucleus. A set of Formin-Binding
Proteins (FBPs) has been shown to bind FH1 with their WW
domain.
Length = 392
Score = 30.0 bits (68), Expect = 2.5
Identities = 13/57 (22%), Positives = 24/57 (42%), Gaps = 3/57 (5%)
Query: 346 LVKRLCEELKDFMKMHNFSSIEDFRGASIEYFTTHTELVRMQQEAIQQRKAVRKGLQ 402
LV+ E+ KD F +F E+ E ++ ++E ++RK + K
Sbjct: 303 LVEYYGEDPKDTSPEEFFKDFNEFL---KEFSKAAEENIKKEEEEEERRKKLVKETT 356
>gnl|CDD|224223 COG1304, idi, Isopentenyl diphosphate isomerase (BS_ypgA, MTH48 and
related proteins) [Coenzyme transport and metabolism].
Length = 360
Score = 29.9 bits (68), Expect = 2.6
Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 8/69 (11%)
Query: 314 GGVETGGDAAEFILLGANTV----QVCTGVMMHGYGLVKRLCE----ELKDFMKMHNFSS 365
GG+ +G D A+ + LGA+ V G+ G V+R+ E ELK M + +
Sbjct: 280 GGIRSGLDVAKALALGADAVGIGRPFLYGLAAGGEAGVERVLEIIRKELKIAMALTGAKN 339
Query: 366 IEDFRGASI 374
IE+ + +
Sbjct: 340 IEELKRVPL 348
>gnl|CDD|237434 PRK13578, PRK13578, ornithine decarboxylase; Provisional.
Length = 720
Score = 29.9 bits (68), Expect = 2.7
Identities = 19/61 (31%), Positives = 27/61 (44%), Gaps = 15/61 (24%)
Query: 342 HGYGLVKRLCEELKDFMKMHNFSSI--EDFRGAS------------IEYFTTHTELVRMQ 387
GY L ++LC+E+ D H+ + E FR AS I Y ELVR+
Sbjct: 588 RGYTL-RQLCQEMHDLYVSHDVKQLQKEMFRKASFPRVVMNPQDANIAYIRGEVELVRLS 646
Query: 388 Q 388
+
Sbjct: 647 E 647
>gnl|CDD|179400 PRK02261, PRK02261, methylaspartate mutase subunit S; Provisional.
Length = 137
Score = 28.8 bits (65), Expect = 3.2
Identities = 19/45 (42%), Positives = 20/45 (44%), Gaps = 10/45 (22%)
Query: 166 EELIDRVEETGIDAIEVNFSCPHGMPERKMGAAVGQDCRLLEEVC 210
EE ID ET DAI V S +G E DCR L E C
Sbjct: 44 EEFIDAAIETDADAILV--SSLYGHGE--------IDCRGLREKC 78
>gnl|CDD|220248 pfam09455, Cas_DxTHG, CRISPR-associated (Cas) DxTHG family. CRISPR
is a term for Clustered Regularly Interspaced Short
Palidromic Repeats. A number of protein families appear
only in association with these repeats and are
designated Cas (CRISPR associated) proteins. The family
describes Cas proteins of about 400 residues that
include the motif [VIL]-D-x-[ST]-H-[GS]. The CRISPR and
associated proteins are thought to be involved in the
evolution of host resistance. The exact molecular
function of this family is currently unknown.
Length = 370
Score = 29.7 bits (67), Expect = 3.2
Identities = 15/57 (26%), Positives = 29/57 (50%), Gaps = 8/57 (14%)
Query: 144 KALYPDKILI---ASIMEEYNK--AAWEELIDRVEETGIDAIEVNFSC---PHGMPE 192
+ L PDK+++ S+ E+ N +++EEL ++E + ++ N P G E
Sbjct: 35 ELLNPDKVIVLLTDSLAEKKNDDPSSYEELKKELKEELKNFLKNNIEVVVIPDGKSE 91
>gnl|CDD|176355 cd01611, GABARAP, Ubiquitin domain of GABA-receptor-associated
protein. GABARAP (GABA-receptor-associated protein)
belongs ot a large family of proteins that mediate
intracellular membrane trafficking and/or fusion.
GABARAP binds not only to GABA, type A but also to
tubulin, gephrin, and ULK1. Orthologues of GABARAP
include Gate-16 (golgi-associated ATPase enhancer), LC3
(microtubule-associated protein light chain 3), and ATG8
(autophagy protein 8). ATG8 is a ubiquitin-like protein
that is conjugated to the membrane phospholipid,
phosphatidylethanolamine as part of a ubiquitin-like
conjugation system essential for
autophagosome-formation.
Length = 112
Score = 28.0 bits (63), Expect = 3.5
Identities = 12/35 (34%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 129 SDRPLETMLKEFKQLKALYPDKILIASIMEEYNKA 163
P E E ++++A YPD+I + I+E Y K+
Sbjct: 3 ERHPFEKRKAEVERIRAKYPDRIPV--IVERYPKS 35
>gnl|CDD|216321 pfam01136, Peptidase_U32, Peptidase family U32.
Length = 232
Score = 29.2 bits (66), Expect = 3.8
Identities = 7/20 (35%), Positives = 13/20 (65%)
Query: 164 AWEELIDRVEETGIDAIEVN 183
A E ++++ E G+DA+ V
Sbjct: 3 ALREYLEKLAEIGVDAVIVA 22
>gnl|CDD|173000 PRK14534, cysS, cysteinyl-tRNA synthetase; Provisional.
Length = 481
Score = 29.4 bits (66), Expect = 4.1
Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 4/50 (8%)
Query: 128 ISDRPLETMLKEFKQLKALYPDKILIASIMEEYNKAAWEELIDRVEETGI 177
IS E + K+L +YPDK+L+AS EY E++ +EE G
Sbjct: 97 ISRFFTEAFFDDCKKLNIVYPDKVLVAS---EY-IPIMIEVVKVLEENGF 142
>gnl|CDD|227500 COG5173, SEC6, Exocyst complex subunit SEC6 [Intracellular
trafficking and secretion].
Length = 742
Score = 29.5 bits (66), Expect = 4.1
Identities = 13/36 (36%), Positives = 20/36 (55%), Gaps = 2/36 (5%)
Query: 125 IELISDRPLETMLKEFKQLKALYPD--KILIASIME 158
I L+ R + + E K LK +Y D K LI +I++
Sbjct: 662 IPLMDTRNDDLFIVEVKSLKEIYWDIKKSLIKTILK 697
>gnl|CDD|183708 PRK12735, PRK12735, elongation factor Tu; Reviewed.
Length = 396
Score = 29.4 bits (67), Expect = 4.3
Identities = 14/44 (31%), Positives = 18/44 (40%), Gaps = 9/44 (20%)
Query: 308 YSLSGIGGVETG---------GDAAEFILLGANTVQVCTGVMMH 342
+S+SG G V TG GD E + + TGV M
Sbjct: 221 FSISGRGTVVTGRVERGIVKVGDEVEIVGIKETQKTTVTGVEMF 264
>gnl|CDD|216366 pfam01208, URO-D, Uroporphyrinogen decarboxylase (URO-D).
Length = 338
Score = 28.7 bits (65), Expect = 5.5
Identities = 8/48 (16%), Positives = 22/48 (45%), Gaps = 6/48 (12%)
Query: 140 FKQLKALYPDKILIASIMEEYNKAAWEELIDRVEETGIDAIEVNFSCP 187
++KA P +++ + +++ + ETG D I ++++
Sbjct: 224 VDEVKARGPGPVIL------HICGNGTPILEDMAETGADVISLDWTVD 265
>gnl|CDD|213994 cd12110, PHP_HisPPase_Hisj_like, Polymerase and Histidinol
Phosphatase domain of Histidinol phosphate phosphatase
of Hisj like. Bacillus subtilis YtvP HisJ has strong
histidinol phosphate phosphatase (HisPPase) activity.
The PHP (also called histidinol phosphatase-2/HIS2)
domain is associated with several types of DNA
polymerases, such as PolIIIA and family X DNA
polymerases, stand alone histidinol phosphate
phosphatases (HisPPases), and a number of
uncharacterized protein families. HisPPase catalyzes the
eighth step of histidine biosynthesis, in which
L-histidinol phosphate undergoes dephosphorylation to
produce histidinol. The PHP domain has four conserved
sequence motifs and contains an invariant histidine that
is involved in metal ion coordination. The PHP domain of
HisPPase is structurally homologous to other members of
the PHP family that have a distorted (beta/alpha)7
barrel fold with a trinuclear metal site on the
C-terminal side of the barrel.
Length = 244
Score = 27.9 bits (63), Expect = 8.1
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 133 LETMLKEFKQLKALYPDKILIASIME-EYNKAAWEELIDRVEETGID 178
LE ++E ++LK Y D+I I +E +Y EEL + + +D
Sbjct: 57 LEDYVEEIRRLKEKYADQIEIKLGLEVDYFPGYEEELRELLYGYPLD 103
>gnl|CDD|227345 COG5012, COG5012, Predicted cobalamin binding protein [General
function prediction only].
Length = 227
Score = 28.1 bits (63), Expect = 8.4
Identities = 17/57 (29%), Positives = 35/57 (61%), Gaps = 4/57 (7%)
Query: 121 GWENIELISDRPLETMLKEFKQLKALYPDKILIASIMEEYNKAAWEELIDRVEETGI 177
G+E I+L D P+E +++ K+LK PD + ++++M +++I+ ++E GI
Sbjct: 132 GFEVIDLGRDVPVEEFVEKAKELK---PDLVSMSALMTT-TMIGMKDVIELLKEEGI 184
>gnl|CDD|239434 cd03318, MLE, Muconate Lactonizing Enzyme (MLE), an homooctameric
enzyme, catalyses the conversion of cis,cis-muconate
(CCM) to muconolactone (ML) in the catechol branch of
the beta-ketoadipate pathway. This pathway is used in
soil microbes to breakdown lignin-derived aromatics,
catechol and protocatechuate, to citric acid cycle
intermediates. Some bacterial species are also capable
of dehalogenating chloroaromatic compounds by the action
of chloromuconate lactonizing enzymes (Cl-MLEs). MLEs
are members of the enolase superfamily characterized by
the presence of an enolate anion intermediate which is
generated by abstraction of the alpha-proton of the
carboxylate substrate by an active site residue and that
is stabilized by coordination to the essential Mg2+ ion.
Length = 365
Score = 28.1 bits (63), Expect = 9.4
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 9/56 (16%)
Query: 131 RPLETMLKEFKQLKALYPDKILIASIMEEYNKAAWEEL-----IDRVEETGIDAIE 181
RP L + + D+ AS+ + N AW+E + R+E G++ IE
Sbjct: 169 RPPADDLAHVEAIAKALGDR---ASVRVDVN-QAWDESTAIRALPRLEAAGVELIE 220
>gnl|CDD|223896 COG0826, COG0826, Collagenase and related proteases
[Posttranslational modification, protein turnover,
chaperones].
Length = 347
Score = 28.0 bits (63), Expect = 9.9
Identities = 8/33 (24%), Positives = 17/33 (51%)
Query: 151 ILIASIMEEYNKAAWEELIDRVEETGIDAIEVN 183
+ + +++ E +DR+ E G+DA+ V
Sbjct: 67 VAVNTLLHNDELETLERYLDRLVELGVDAVIVA 99
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
0.317 0.133 0.389
Gapped
Lambda K H
0.267 0.0709 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 21,539,398
Number of extensions: 2122883
Number of successful extensions: 2343
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2291
Number of HSP's successfully gapped: 69
Length of query: 422
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 323
Effective length of database: 6,546,556
Effective search space: 2114537588
Effective search space used: 2114537588
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 60 (26.9 bits)