RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5880
(328 letters)
>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 = 291 bits (748), Expect = 6e-98
Identities = 111/190 (58%), Positives = 135/190 (71%), Gaps = 4/190 (2%)
Query: 117 DIADVVLDSVKGILKFGDVAHYFVVNVSSPNTANLRKLQAKDQLKHLLKTVVETRNQLAV 176
+ D V D V G+ K G A Y VVNVSSPNT LR LQ K+ L+ LL V E RN+L
Sbjct: 142 PLEDAVEDYVIGVRKLGPYADYLVVNVSSPNTPGLRDLQGKEALRELLTAVKEERNKLGK 201
Query: 177 KPLPPILVKIAPDLSLDEKKDIADVVLDSKCKVDGLIVSNTTVDRYEYLDARYKEETGGL 236
K P+LVKIAPDLS +E +DIADV L+ VDG+I +NTT+ R L + ETGGL
Sbjct: 202 KV--PLLVKIAPDLSDEELEDIADVALEHG--VDGIIATNTTISRPGLLRSPLANETGGL 257
Query: 237 SGEPLRNKSTELISEMYKLTKGKLPIIGVGGVFSGKDAFEKIKAGASLVQIYTSFVYHGP 296
SG PL+ +STE++ E+YKLT GK+PIIGVGG+ SG+DA+EKI+AGASLVQ+YT VY GP
Sbjct: 258 SGAPLKERSTEVLRELYKLTGGKIPIIGVGGISSGEDAYEKIRAGASLVQLYTGLVYEGP 317
Query: 297 PLVTRIKSEL 306
LV RIK EL
Sbjct: 318 GLVKRIKREL 327
Score = 112 bits (282), Expect = 1e-28
Identities = 48/83 (57%), Positives = 56/83 (67%), Gaps = 3/83 (3%)
Query: 48 GILKFGDVAHYFVVNVSSPNTANLRKLQAKDQLKHLLKTVVETRNQLALKPLPPILVKIA 107
G+ K G A Y VVNVSSPNT LR LQ K+ L+ LL V E RN+L K P+LVKIA
Sbjct: 153 GVRKLGPYADYLVVNVSSPNTPGLRDLQGKEALRELLTAVKEERNKLGKK--VPLLVKIA 210
Query: 108 PDLSLDEKKDIADVVLDS-VKGI 129
PDLS +E +DIADV L+ V GI
Sbjct: 211 PDLSDEELEDIADVALEHGVDGI 233
>gnl|CDD|235388 PRK05286, PRK05286, dihydroorotate dehydrogenase 2; Reviewed.
Length = 344
Score = 279 bits (717), Expect = 7e-93
Identities = 94/198 (47%), Positives = 124/198 (62%), Gaps = 4/198 (2%)
Query: 117 DIADVVLDSVKGILKFGDVAHYFVVNVSSPNTANLRKLQAKDQLKHLLKTVVETRNQLAV 176
+ D V D + + K A YF VN+SSPNT LR LQ + L LL + E + +L
Sbjct: 151 PLEDAVDDYLICLEKLYPYADYFTVNISSPNTPGLRDLQYGEALDELLAALKEAQAELH- 209
Query: 177 KPLPPILVKIAPDLSLDEKKDIADVVLDSKCKVDGLIVSNTTVDRYEYLDARYKEETGGL 236
P+LVKIAPDLS +E DIAD+ L+ +DG+I +NTT+ R +E GGL
Sbjct: 210 -GYVPLLVKIAPDLSDEELDDIADLALEHG--IDGVIATNTTLSRDGLKGLPNADEAGGL 266
Query: 237 SGEPLRNKSTELISEMYKLTKGKLPIIGVGGVFSGKDAFEKIKAGASLVQIYTSFVYHGP 296
SG PL +STE+I +YK G+LPIIGVGG+ S +DA+EKI+AGASLVQIY+ +Y GP
Sbjct: 267 SGRPLFERSTEVIRRLYKELGGRLPIIGVGGIDSAEDAYEKIRAGASLVQIYSGLIYEGP 326
Query: 297 PLVTRIKSELEELLQKEG 314
LV I L LL+++G
Sbjct: 327 GLVKEIVRGLARLLRRDG 344
Score = 108 bits (273), Expect = 3e-27
Identities = 36/74 (48%), Positives = 45/74 (60%), Gaps = 2/74 (2%)
Query: 51 KFGDVAHYFVVNVSSPNTANLRKLQAKDQLKHLLKTVVETRNQLALKPLPPILVKIAPDL 110
K A YF VN+SSPNT LR LQ + L LL + E + +L P+LVKIAPDL
Sbjct: 165 KLYPYADYFTVNISSPNTPGLRDLQYGEALDELLAALKEAQAELHGY--VPLLVKIAPDL 222
Query: 111 SLDEKKDIADVVLD 124
S +E DIAD+ L+
Sbjct: 223 SDEELDDIADLALE 236
>gnl|CDD|178421 PLN02826, PLN02826, dihydroorotate dehydrogenase.
Length = 409
Score = 271 bits (696), Expect = 6e-89
Identities = 111/221 (50%), Positives = 156/221 (70%), Gaps = 5/221 (2%)
Query: 110 LSLDEKKDIADVVLDSVKGILKFGDVAHYFVVNVSSPNTANLRKLQAKDQLKHLLKTVVE 169
++L + K D D V+G+ A Y V+NVSSPNT LRKLQ + QLK LLK V+
Sbjct: 191 VNLGKNKTSEDAAADYVQGVRALSQYADYLVINVSSPNTPGLRKLQGRKQLKDLLKKVLA 250
Query: 170 TRN--QLAVKPLPPILVKIAPDLSLDEKKDIADVVLDSKCKVDGLIVSNTTVDRYEYLDA 227
R+ Q + PP+LVKIAPDLS ++ +DIA V L +DGLI+SNTT+ R + +
Sbjct: 251 ARDEMQWGEEGPPPLLVKIAPDLSKEDLEDIAAVAL--ALGIDGLIISNTTISRPDSVLG 308
Query: 228 -RYKEETGGLSGEPLRNKSTELISEMYKLTKGKLPIIGVGGVFSGKDAFEKIKAGASLVQ 286
+ +E GGLSG+PL + STE++ EMY+LT+GK+P++G GGV SG+DA++KI+AGASLVQ
Sbjct: 309 HPHADEAGGLSGKPLFDLSTEVLREMYRLTRGKIPLVGCGGVSSGEDAYKKIRAGASLVQ 368
Query: 287 IYTSFVYHGPPLVTRIKSELEELLQKEGYNSVSQAVGAAHK 327
+YT+F Y GP L+ RIK+EL L+++G+ S+ +AVGA H+
Sbjct: 369 LYTAFAYEGPALIPRIKAELAACLERDGFKSIQEAVGADHR 409
Score = 94.0 bits (234), Expect = 2e-21
Identities = 40/81 (49%), Positives = 53/81 (65%), Gaps = 2/81 (2%)
Query: 45 WLLGILKFGDVAHYFVVNVSSPNTANLRKLQAKDQLKHLLKTVVETRNQLALK--PLPPI 102
++ G+ A Y V+NVSSPNT LRKLQ + QLK LLK V+ R+++ PP+
Sbjct: 206 YVQGVRALSQYADYLVINVSSPNTPGLRKLQGRKQLKDLLKKVLAARDEMQWGEEGPPPL 265
Query: 103 LVKIAPDLSLDEKKDIADVVL 123
LVKIAPDLS ++ +DIA V L
Sbjct: 266 LVKIAPDLSKEDLEDIAAVAL 286
>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 = 217 bits (554), Expect = 1e-68
Identities = 87/188 (46%), Positives = 114/188 (60%), Gaps = 2/188 (1%)
Query: 119 ADVVLDSVKGILKFGDVAHYFVVNVSSPNTANLRKLQAKDQLKHLLKTVVETRNQLAVKP 178
D + + K A Y VVN+SSPNT LR LQ + L LL + +N L
Sbjct: 150 EQAKDDYLACLRKIYPYAGYIVVNISSPNTPGLRDLQYGEALDDLLTAIKNEQNDLQAHH 209
Query: 179 LPPILVKIAPDLSLDEKKDIADVVLDSKCKVDGLIVSNTTVDRYEYLDARYKEETGGLSG 238
PI VKIAPDLS + IAD ++ + +DG+I +NTTV R + ++TGGLSG
Sbjct: 210 HVPIAVKIAPDLSESDLIQIADSLV--RHGIDGVIATNTTVSRSLVQGPKNCDQTGGLSG 267
Query: 239 EPLRNKSTELISEMYKLTKGKLPIIGVGGVFSGKDAFEKIKAGASLVQIYTSFVYHGPPL 298
+PL+ KSTE+I +Y G+LPIIGVGG+ S +DA EKI AGASL+QIY+ F+Y GPPL
Sbjct: 268 KPLQLKSTEIIRRLYLELNGRLPIIGVGGIDSAQDAREKIAAGASLLQIYSGFIYKGPPL 327
Query: 299 VTRIKSEL 306
V I +
Sbjct: 328 VKEIVKHI 335
Score = 87.9 bits (218), Expect = 9e-20
Identities = 34/78 (43%), Positives = 42/78 (53%)
Query: 45 WLLGILKFGDVAHYFVVNVSSPNTANLRKLQAKDQLKHLLKTVVETRNQLALKPLPPILV 104
+L + K A Y VVN+SSPNT LR LQ + L LL + +N L PI V
Sbjct: 156 YLACLRKIYPYAGYIVVNISSPNTPGLRDLQYGEALDDLLTAIKNEQNDLQAHHHVPIAV 215
Query: 105 KIAPDLSLDEKKDIADVV 122
KIAPDLS + IAD +
Sbjct: 216 KIAPDLSESDLIQIADSL 233
>gnl|CDD|223245 COG0167, PyrD, Dihydroorotate dehydrogenase [Nucleotide transport
and metabolism].
Length = 310
Score = 206 bits (526), Expect = 1e-64
Identities = 80/244 (32%), Positives = 122/244 (50%), Gaps = 23/244 (9%)
Query: 91 RNQLALKPLPPILVKIAPDLSLDEKKDIADVVLDSVKGILKFGDVAHYFVVNVSSPNTAN 150
+LA PI V I + ++ AD + + GD A +N+S PNT
Sbjct: 84 ELKLAKYEGKPIGVNIGKNKGGPSEEAWADYAR----LLEEAGD-ADAIELNISCPNTPG 138
Query: 151 LRKLQ-AKDQLKHLLKTVVETRNQLAVKPLPPILVKIAPDLSLDEKKDIADVVLDSKCKV 209
R L + L+ LL+ V P+ VK+AP++ + +IA +
Sbjct: 139 GRALGQDPELLEKLLEAVKAATK-------VPVFVKLAPNI--TDIDEIAKAAEE--AGA 187
Query: 210 DGLIVSNTTVDRYEYLD-----ARYKEETGGLSGEPLRNKSTELISEMYKLTKGKLPIIG 264
DGLI NTT +D ETGGLSG PL+ + +++E+YK G +PIIG
Sbjct: 188 DGLIAINTTKSG-MKIDLETKKPVLANETGGLSGPPLKPIALRVVAELYKRLGGDIPIIG 246
Query: 265 VGGVFSGKDAFEKIKAGASLVQIYTSFVYHGPPLVTRIKSELEELLQKEGYNSVSQAVGA 324
VGG+ +G+DA E I AGAS VQ+ T+ +Y GP +V I L L+++G+ S+ +G+
Sbjct: 247 VGGIETGEDALEFILAGASAVQVGTALIYKGPGIVKEIIKGLARWLEEKGFESIQDIIGS 306
Query: 325 AHKS 328
A ++
Sbjct: 307 ALRN 310
Score = 55.7 bits (135), Expect = 7e-09
Identities = 21/80 (26%), Positives = 35/80 (43%), Gaps = 11/80 (13%)
Query: 46 LLGILKFGDVAHYFVVNVSSPNTANLRKLQ-AKDQLKHLLKTVVETRNQLALKPLPPILV 104
+ + GD A +N+S PNT R L + L+ LL+ V P+ V
Sbjct: 115 ARLLEEAGD-ADAIELNISCPNTPGGRALGQDPELLEKLLEAVKAATK-------VPVFV 166
Query: 105 KIAPDLSLDEKKDIADVVLD 124
K+AP+ + + +IA +
Sbjct: 167 KLAPN--ITDIDEIAKAAEE 184
>gnl|CDD|216348 pfam01180, DHO_dh, Dihydroorotate dehydrogenase.
Length = 290
Score = 193 bits (493), Expect = 4e-60
Identities = 78/192 (40%), Positives = 112/192 (58%), Gaps = 13/192 (6%)
Query: 124 DSVKGILKFGDVAHYFVVNVSSPNTANLRKLQAKDQLKHLLKTVVETRNQLAVKPLPPIL 183
D V+ K G A Y +NVS PNT LR LQ +L +L VV+ ++ P+L
Sbjct: 107 DYVEVARKIGPFADYLELNVSCPNTPGLRALQTDPELAAILLKVVKEVSK------VPVL 160
Query: 184 VKIAPDLSLDEKKDIADVVLDSKCKVDGLIVSNTTVDRYEYLDARYKE-----ETGGLSG 238
VK+APDL+ DIADV + + G+ +NTTV +D + + TGGLSG
Sbjct: 161 VKLAPDLTDIVIIDIADVAA-GEDGLTGINATNTTVRG-MRIDLKTESPILANGTGGLSG 218
Query: 239 EPLRNKSTELISEMYKLTKGKLPIIGVGGVFSGKDAFEKIKAGASLVQIYTSFVYHGPPL 298
++ + ++I E+Y+ ++PIIGVGG+F+G+DA EKI AGAS VQI T+ ++ GP +
Sbjct: 219 PAIKPIALKVIRELYQRVGPEIPIIGVGGIFTGEDALEKILAGASAVQIGTALIFGGPFI 278
Query: 299 VTRIKSELEELL 310
+I EL ELL
Sbjct: 279 FPKIIDELPELL 290
Score = 77.8 bits (192), Expect = 2e-16
Identities = 31/73 (42%), Positives = 40/73 (54%), Gaps = 6/73 (8%)
Query: 51 KFGDVAHYFVVNVSSPNTANLRKLQAKDQLKHLLKTVVETRNQLALKPLPPILVKIAPDL 110
K G A Y +NVS PNT LR LQ +L +L VV+ ++ P+LVK+APDL
Sbjct: 114 KIGPFADYLELNVSCPNTPGLRALQTDPELAAILLKVVKEVSK------VPVLVKLAPDL 167
Query: 111 SLDEKKDIADVVL 123
+ DIADV
Sbjct: 168 TDIVIIDIADVAA 180
>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 = 130 bits (330), Expect = 6e-36
Identities = 58/174 (33%), Positives = 90/174 (51%), Gaps = 13/174 (7%)
Query: 136 AHYFVVNVSSPNTANLRKL-QAKDQLKHLLKTVVETRNQLAVKPLPPILVKIAPDLSLDE 194
A +N+S PN R+L Q + + +LLK V + P+LVK++P L++
Sbjct: 125 AKALELNLSCPNVGGGRQLGQDPEAVANLLKAVKAAVD-------IPLLVKLSPYFDLED 177
Query: 195 KKDIADVVLDSKCKVDGLIVSNTTVDRYEYLDARY---KEETGGLSGEPLRNKSTELISE 251
++A + DGL NT R L K TGGLSG P+R + ++
Sbjct: 178 IVELAKAAERAG--ADGLTAINTISGRVVDLKTVGPGPKRGTGGLSGAPIRPLALRWVAR 235
Query: 252 MYKLTKGKLPIIGVGGVFSGKDAFEKIKAGASLVQIYTSFVYHGPPLVTRIKSE 305
+ + +PIIGVGG+ SG+D E + AGAS VQ+ T+ ++ GP ++ +IK E
Sbjct: 236 LAARLQLDIPIIGVGGIDSGEDVLEMLMAGASAVQVATALMWDGPDVIRKIKKE 289
Score = 46.2 bits (110), Expect = 9e-06
Identities = 19/68 (27%), Positives = 33/68 (48%), Gaps = 8/68 (11%)
Query: 56 AHYFVVNVSSPNTANLRKL-QAKDQLKHLLKTVVETRNQLALKPLPPILVKIAPDLSLDE 114
A +N+S PN R+L Q + + +LLK V + P+LVK++P L++
Sbjct: 125 AKALELNLSCPNVGGGRQLGQDPEAVANLLKAVKAAVD-------IPLLVKLSPYFDLED 177
Query: 115 KKDIADVV 122
++A
Sbjct: 178 IVELAKAA 185
>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 = 86.8 bits (216), Expect = 1e-19
Identities = 64/231 (27%), Positives = 112/231 (48%), Gaps = 31/231 (13%)
Query: 101 PILVKIAPDLSLDEKKDIADVVLDSVKGILKFGDVAHYFVVNVSSPNTANLRKLQAKDQL 160
P++ IA +++E ++A+ + D+ A +N+S PN D
Sbjct: 91 PVIASIAGS-TVEEFVEVAEKLADAG---------ADAIELNISCPNVKGGGMAFGTD-- 138
Query: 161 KHLLKTVVET-RNQLAVKPLPPILVKIAPDLSLDEKKDIADVVLDSKCKVDGLIVSNTTV 219
+ +V+ + V P++VK+ P++ + +IA ++ DGL + NT
Sbjct: 139 PEAVAEIVKAVKKATDV----PVIVKLTPNV--TDIVEIARAAEEAG--ADGLTLINTL- 189
Query: 220 DRYEYLDARYKE-----ETGGLSGEPLRNKSTELISEMYKLTKGKLPIIGVGGVFSGKDA 274
+ +D ++ TGGLSG ++ + ++ ++YK + +PIIGVGG+ SG+DA
Sbjct: 190 -KGMAIDIETRKPILGNVTGGLSGPAIKPIALRMVYQVYKAVE--IPIIGVGGIASGEDA 246
Query: 275 FEKIKAGASLVQIYTSFVYHGPPLVTRIKSELEELLQKEGYNSVSQAVGAA 325
E + AGAS VQ+ T+ + P I LE L +EG S+ + VG A
Sbjct: 247 LEFLMAGASAVQVGTA-NFVDPEAFKEIIEGLEAYLDEEGIKSIEELVGLA 296
>gnl|CDD|235982 PRK07259, PRK07259, dihydroorotate dehydrogenase 1B; Reviewed.
Length = 301
Score = 86.0 bits (214), Expect = 3e-19
Identities = 51/154 (33%), Positives = 82/154 (53%), Gaps = 18/154 (11%)
Query: 181 PILVKIAPDLSLDEKKDIADVVLDSKCKVDGLIVSNT----TVDRYEYLDARY---KEET 233
P++VK+ P ++ + +IA ++ DGL + NT +D + R T
Sbjct: 159 PVIVKLTP--NVTDIVEIAKAAEEAG--ADGLSLINTLKGMAID----IKTRKPILANVT 210
Query: 234 GGLSGEPLRNKSTELISEMYKLTKGKLPIIGVGGVFSGKDAFEKIKAGASLVQIYTSFVY 293
GGLSG ++ + ++ ++Y+ +PIIG+GG+ S +DA E I AGAS VQ+ T+ +
Sbjct: 211 GGLSGPAIKPIALRMVYQVYQAVD--IPIIGMGGISSAEDAIEFIMAGASAVQVGTA-NF 267
Query: 294 HGPPLVTRIKSELEELLQKEGYNSVSQAVGAAHK 327
+ P +I LE L K G S+ + VG AHK
Sbjct: 268 YDPYAFPKIIEGLEAYLDKYGIKSIEEIVGIAHK 301
>gnl|CDD|235045 PRK02506, PRK02506, dihydroorotate dehydrogenase 1A; Reviewed.
Length = 310
Score = 84.2 bits (209), Expect = 1e-18
Identities = 34/92 (36%), Positives = 53/92 (57%), Gaps = 4/92 (4%)
Query: 234 GGLSGEPLRNKSTEL--ISEMYKLTKGKLPIIGVGGVFSGKDAFEKIKAGASLVQIYTSF 291
GG+ G+ + K T L + Y+ + IIG GGV +G+DAFE I GAS+VQ+ T+
Sbjct: 216 GGIGGDYI--KPTALANVRAFYQRLNPSIQIIGTGGVKTGRDAFEHILCGASMVQVGTAL 273
Query: 292 VYHGPPLVTRIKSELEELLQKEGYNSVSQAVG 323
GP + R+ EL+ ++ ++GY S+ G
Sbjct: 274 HKEGPAVFERLTKELKAIMAEKGYQSLEDFRG 305
>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 = 79.8 bits (197), Expect = 5e-17
Identities = 55/199 (27%), Positives = 99/199 (49%), Gaps = 23/199 (11%)
Query: 135 VAHYFVVNVSSPN--TANLRKLQAKDQLKHLLKTVVETRNQLAVKPLPPILVKIAPDLSL 192
+ +N+S P+ + Q + ++K V + P+ K++P+++
Sbjct: 118 YVDAYELNLSCPHVKGGGIAIGQDPELSADVVKAVKD-----KTDV--PVFAKLSPNVT- 169
Query: 193 DEKKDIADVVLDSKCKVDGLIVSNTTVDRYEYLDARYKE-----ETGGLSGEPLRNKSTE 247
+ +IA ++ DGL + NT R +D + + +TGGLSG ++ +
Sbjct: 170 -DITEIAKAAEEAG--ADGLTLINTL--RGMKIDIKTGKPILANKTGGLSGPAIKPIALR 224
Query: 248 LISEMYKLTKGKLPIIGVGGVFSGKDAFEKIKAGASLVQIYTSFVYHGPPLVTRIKSELE 307
++ ++YK +PIIGVGG+ S +DA E + AGAS VQ+ T+ VY+ +I L
Sbjct: 225 MVYDVYK--MVDIPIIGVGGITSFEDALEFLMAGASAVQVGTA-VYYRGFAFKKIIEGLI 281
Query: 308 ELLQKEGYNSVSQAVGAAH 326
L+ EG+ S+ + +G AH
Sbjct: 282 AFLKAEGFTSIEELIGIAH 300
>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 = 66.2 bits (162), Expect = 2e-12
Identities = 48/180 (26%), Positives = 75/180 (41%), Gaps = 20/180 (11%)
Query: 141 VNVSSPNTANLRKLQAKDQLKHLLKTVVETRNQLAVKPLPPILVKIAPDLSLDEKKDIAD 200
+N+S PN + K + +E + P+ VK P + +A+
Sbjct: 125 LNLSCPN------VPGKPPPAYDFDATLEYLTAVKAAYSIPVGVKTPPYTDPAQFDTLAE 178
Query: 201 VVLDSKCKVDGLIVSNT-------TVDRYE-YLDARYKEETGGLSGEPLRNKSTEL--IS 250
+ C + + +NT +R L K GGL+G L L +
Sbjct: 179 ALNAFACPISFITATNTLGNGLVLDPERETVVLKP--KTGFGGLAGAYL--HPLALGNVR 234
Query: 251 EMYKLTKGKLPIIGVGGVFSGKDAFEKIKAGASLVQIYTSFVYHGPPLVTRIKSELEELL 310
+L ++ IIGVGGV G+ AF AGAS VQ+ T+ GP + RI+ ELE++
Sbjct: 235 TFRRLLPSEIQIIGVGGVLDGRGAFRMRLAGASAVQVGTALGKEGPKVFARIEKELEDIW 294
>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 = 57.3 bits (139), Expect = 2e-09
Identities = 24/73 (32%), Positives = 43/73 (58%)
Query: 234 GGLSGEPLRNKSTELISEMYKLTKGKLPIIGVGGVFSGKDAFEKIKAGASLVQIYTSFVY 293
GG SG ++ + +S++ + + LPI G+GG+ S +DA E + GAS+VQ+ T+ +
Sbjct: 227 GGYSGPAVKPIALRAVSQIARAPEPGLPISGIGGIESWEDAAEFLLLGASVVQVCTAVMN 286
Query: 294 HGPPLVTRIKSEL 306
G +V + + L
Sbjct: 287 QGFTIVDDMCTGL 299
>gnl|CDD|215273 PLN02495, PLN02495, oxidoreductase, acting on the CH-CH group of
donors.
Length = 385
Score = 54.8 bits (132), Expect = 2e-08
Identities = 60/204 (29%), Positives = 94/204 (46%), Gaps = 28/204 (13%)
Query: 139 FVVNVSSPNTANLRKL-QAKDQLKHLLKTVVETRNQLAVKPLPPILVKIAPDLSLDEKKD 197
+N S P+ RK+ A Q LL+ V N A P + K+ P+++ D
Sbjct: 144 LEINFSCPHGMPERKMGAAVGQDCDLLEEVCGWINAKATVP---VWAKMTPNIT-----D 195
Query: 198 I---ADVVLDSKCKVDGLIVSNTTVD---------RYEYLDARYKEETGGLSGEPLRNKS 245
I A V L S C +G+ NT + R E Y GG S + +R +
Sbjct: 196 ITQPARVALKSGC--EGVAAINTIMSVMGINLDTLRPEPCVEGY-STPGGYSSKAVRPIA 252
Query: 246 TELISEMYKLTKGKLP----IIGVGGVFSGKDAFEKIKAGASLVQIYTSFVYHGPPLVTR 301
+ + K+ K + P + G+GGV +G DA E I GA VQ+ T + HG PLV
Sbjct: 253 LAKVMAIAKMMKSEFPEDRSLSGIGGVETGGDAAEFILLGADTVQVCTGVMMHGYPLVKN 312
Query: 302 IKSELEELLQKEGYNSVSQAVGAA 325
+ +EL++ ++K ++S+ GA+
Sbjct: 313 LCAELQDFMKKHNFSSIEDFRGAS 336
>gnl|CDD|236237 PRK08318, PRK08318, dihydropyrimidine dehydrogenase subunit B;
Validated.
Length = 420
Score = 55.0 bits (133), Expect = 2e-08
Identities = 28/93 (30%), Positives = 53/93 (56%), Gaps = 1/93 (1%)
Query: 234 GGLSGEPLRNKSTELISEMYKLTKGK-LPIIGVGGVFSGKDAFEKIKAGASLVQIYTSFV 292
GG G ++ + +++E+ + + + LPI G+GG+ + +DA E I GA VQ+ T+ +
Sbjct: 227 GGYCGPAVKPIALNMVAEIARDPETRGLPISGIGGIETWRDAAEFILLGAGTVQVCTAAM 286
Query: 293 YHGPPLVTRIKSELEELLQKEGYNSVSQAVGAA 325
+G +V + S L + ++G+ S+ VG A
Sbjct: 287 QYGFRIVEDMISGLSHYMDEKGFASLEDMVGLA 319
>gnl|CDD|240086 cd04735, OYE_like_4_FMN, Old yellow enzyme (OYE)-related FMN
binding domain, group 4. Each monomer of OYE contains
FMN as a non-covalently bound cofactor, uses NADPH as a
reducing agent with oxygens, quinones, and
alpha,beta-unsaturated aldehydes and ketones, and can
act as electron acceptors in the catalytic reaction.
Other members of OYE family include trimethylamine
dehydrogenase, 2,4-dienoyl-CoA reductase, enoate
reductase, pentaerythriol tetranitrate reductase,
xenobiotic reductase, and morphinone reductase.
Length = 353
Score = 48.4 bits (116), Expect = 2e-06
Identities = 30/126 (23%), Positives = 50/126 (39%), Gaps = 18/126 (14%)
Query: 188 PDLSLDEKKDIADVVLDSKCKVDGLIVSNTTVDRYEYLDARYKEETGGLSGEPLRNKSTE 247
P + +++ + D + D +D L +S DR +
Sbjct: 230 PGIRMEDTLALVDKLAD--KGLDYLHISLWDFDRKSRRGR---------DDNQTIME--- 275
Query: 248 LISEMYKLTKGKLPIIGVGGVFSGKDAFEKIKAGASLVQIYTSFVYHGPPLVTRIKSELE 307
L+ E G+LP+I VG + + DA E ++ GA LV I + P V +IK E
Sbjct: 276 LVKERIA---GRLPLIAVGSINTPDDALEALETGADLVAIGRGLLVD-PDWVEKIKEGRE 331
Query: 308 ELLQKE 313
+ + E
Sbjct: 332 DEINLE 337
>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 = 44.1 bits (105), Expect = 5e-05
Identities = 19/62 (30%), Positives = 33/62 (53%)
Query: 259 KLPIIGVGGVFSGKDAFEKIKAGASLVQIYTSFVYHGPPLVTRIKSELEELLQKEGYNSV 318
K + GGV +D + + AGA +V ++ + HGP + + + LE +++ GY SV
Sbjct: 237 KASLAASGGVHDAEDVVKYLLAGADVVMTTSALLRHGPDYIGTLLAGLEAWMEEHGYESV 296
Query: 319 SQ 320
Q
Sbjct: 297 QQ 298
>gnl|CDD|236051 PRK07565, PRK07565, dihydroorotate dehydrogenase 2; Reviewed.
Length = 334
Score = 43.7 bits (104), Expect = 7e-05
Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 266 GGVFSGKDAFEKIKAGASLVQIYTSFVY-HGPPLVTRIKSELEELLQKEGYNSVSQ 320
GV +D + + AGA +V I S + HGP + I LE+ +++ GY S+ Q
Sbjct: 246 TGVHDAEDVIKMLLAGADVVMI-ASALLRHGPDYIGTILRGLEDWMERHGYESLQQ 300
>gnl|CDD|224981 COG2070, COG2070, Dioxygenases related to 2-nitropropane
dioxygenase [General function prediction only].
Length = 336
Score = 36.2 bits (84), Expect = 0.016
Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 2/63 (3%)
Query: 232 ETGGLSGEPLRNKSTE-LISEMYKLTKGKLPIIGVGGVFSGKDAFEKIKAGASLVQIYTS 290
E GG G ST L+ E+ G +P+I GG+ G+ + GA VQ+ T
Sbjct: 157 EAGGHRGGVDLEVSTFALVPEVVDAVDG-IPVIAAGGIADGRGIAAALALGADGVQMGTR 215
Query: 291 FVY 293
F+
Sbjct: 216 FLA 218
>gnl|CDD|166620 PLN02979, PLN02979, glycolate oxidase.
Length = 366
Score = 36.2 bits (83), Expect = 0.021
Identities = 28/102 (27%), Positives = 47/102 (46%), Gaps = 24/102 (23%)
Query: 211 GLIVSNTTVDRYEYLDARYKEETGGLSGEPLRNKSTELISEMYKLTKGKLPIIGVGGVFS 270
G+IVSN + +Y+ A + + E+ K T+G++P+ GGV
Sbjct: 247 GIIVSNHGARQLDYVPA-----------------TISALEEVVKATQGRIPVFLDGGVRR 289
Query: 271 GKDAFEKIKAGASLVQIYTSFVYHGPPLVTRIKSELEELLQK 312
G D F+ + GAS + I G P+V + +E E ++K
Sbjct: 290 GTDVFKALALGASGIFI-------GRPVVFSLAAEGEAGVRK 324
>gnl|CDD|166134 PLN02493, PLN02493, probable peroxisomal (S)-2-hydroxy-acid
oxidase.
Length = 367
Score = 35.5 bits (81), Expect = 0.036
Identities = 28/102 (27%), Positives = 47/102 (46%), Gaps = 24/102 (23%)
Query: 211 GLIVSNTTVDRYEYLDARYKEETGGLSGEPLRNKSTELISEMYKLTKGKLPIIGVGGVFS 270
G+IVSN + +Y+ A + + E+ K T+G++P+ GGV
Sbjct: 248 GIIVSNHGARQLDYVPA-----------------TISALEEVVKATQGRIPVFLDGGVRR 290
Query: 271 GKDAFEKIKAGASLVQIYTSFVYHGPPLVTRIKSELEELLQK 312
G D F+ + GAS + I G P+V + +E E ++K
Sbjct: 291 GTDVFKALALGASGIFI-------GRPVVFSLAAEGEAGVRK 325
>gnl|CDD|240081 cd04730, NPD_like, 2-Nitropropane dioxygenase (NPD), one of the
nitroalkane oxidizing enzyme families, catalyzes
oxidative denitrification of nitroalkanes to their
corresponding carbonyl compounds and nitrites. NDP is a
member of the NAD(P)H-dependent flavin oxidoreductase
family that reduce a range of alternative electron
acceptors. Most use FAD/FMN as a cofactor and NAD(P)H as
electron donor. Some contain 4Fe-4S cluster to transfer
electron from FAD to FMN.
Length = 236
Score = 33.6 bits (78), Expect = 0.094
Identities = 19/84 (22%), Positives = 30/84 (35%), Gaps = 17/84 (20%)
Query: 209 VDGLIVSNTTVDRYEYLDARYKEETGGLSGEPLRNKSTELISEMYKLTKGKLPIIGVGGV 268
D L+ E GG G + L+ E+ +P+I GG+
Sbjct: 123 ADALVAQGA--------------EAGGHRGTFDIG-TFALVPEVRDAVD--IPVIAAGGI 165
Query: 269 FSGKDAFEKIKAGASLVQIYTSFV 292
G+ + GA VQ+ T F+
Sbjct: 166 ADGRGIAAALALGADGVQMGTRFL 189
>gnl|CDD|233103 TIGR00722, ttdA_fumA_fumB, hydro-lyases, Fe-S type,
tartrate/fumarate subfamily, alpha region. A number of
Fe-S cluster-containing hydro-lyases share a conserved
motif, including argininosuccinate lyase,
adenylosuccinate lyase, aspartase, class I fumarate
hydratase (fumarase), and tartrate dehydratase (see
PROSITE:PDOC00147). This model represents a subset of
closely related proteins or modules, including the E.
coli tartrate dehydratase alpha chain and the N-terminal
region of the class I fumarase (where the C-terminal
region is homologous to the tartrate dehydratase beta
chain). The activity of archaeal proteins in this
subfamily has not been established.
Length = 273
Score = 32.4 bits (74), Expect = 0.22
Identities = 15/42 (35%), Positives = 24/42 (57%)
Query: 145 SPNTANLRKLQAKDQLKHLLKTVVETRNQLAVKPLPPILVKI 186
S N + L+ L+ D ++ + K V+ET KP PPI+V +
Sbjct: 142 SENPSALKMLKPSDGIEGVKKFVLETVKNAGGKPCPPIIVGV 183
Score = 30.9 bits (70), Expect = 0.80
Identities = 15/42 (35%), Positives = 24/42 (57%)
Query: 65 SPNTANLRKLQAKDQLKHLLKTVVETRNQLALKPLPPILVKI 106
S N + L+ L+ D ++ + K V+ET KP PPI+V +
Sbjct: 142 SENPSALKMLKPSDGIEGVKKFVLETVKNAGGKPCPPIIVGV 183
>gnl|CDD|223120 COG0042, COG0042, tRNA-dihydrouridine synthase [Translation,
ribosomal structure and biogenesis].
Length = 323
Score = 32.7 bits (75), Expect = 0.23
Identities = 30/135 (22%), Positives = 52/135 (38%), Gaps = 36/135 (26%)
Query: 154 LQAKDQLKHLLKTVVETRNQLAVKPLPPILVKI-----APDLSLDEKKDIADVVLDSKCK 208
L+ + L ++K +VE AV +P + VKI D+ +IA ++ D+
Sbjct: 117 LKNPELLAEIVKAMVE-----AVGDIP-VTVKIRLGWDDDDI---LALEIARILEDAGA- 166
Query: 209 VDGLIV-SNTTVDRYEYLDARYKEETGGLSGEPLRNKSTELISEMYKLTKGKLPIIGVGG 267
D L V T Y A + + I E+ + +P+I G
Sbjct: 167 -DALTVHGRTRAQGYLG-PADW-----------------DYIKELKEAVP-SIPVIANGD 206
Query: 268 VFSGKDAFEKIKAGA 282
+ S +DA E ++
Sbjct: 207 IKSLEDAKEMLEYTG 221
>gnl|CDD|217344 pfam03060, NMO, Nitronate monooxygenase. Nitronate monooxygenase
(NMO), formerly referred to as 2-nitropropane
dioxygenase (NPD) (EC:1.13.11.32), is an FMN-dependent
enzyme that uses molecular oxygen to oxidize (anionic)
alkyl nitronates and, in the case of the enzyme from
Neurospora crassa, (neutral) nitroalkanes to the
corresponding carbonyl compounds and nitrite. Previously
classified as 2-nitropropane dioxygenase, but it is now
recognized that this was the result of the slow
ionization of nitroalkanes to their nitronate (anionic)
forms. The enzymes from the fungus Neurospora crassa and
the yeast Williopsis saturnus var. mrakii (formerly
classified as Hansenula mrakii) contain non-covalently
bound FMN as the cofactor. Active towards linear alkyl
nitronates of lengths between 2 and 6 carbon atoms and,
with lower activity, towards propyl-2-nitronate. The
enzyme from N. crassa can also utilize neutral
nitroalkanes, but with lower activity. One atom of
oxygen is incorporated into the carbonyl group of the
aldehyde product. The reaction appears to involve the
formation of an enzyme-bound nitronate radical and an
a-peroxynitroethane species, which then decomposes,
either in the active site of the enzyme or after
release, to acetaldehyde and nitrite.
Length = 329
Score = 32.4 bits (74), Expect = 0.26
Identities = 17/61 (27%), Positives = 27/61 (44%), Gaps = 2/61 (3%)
Query: 232 ETGGLSGEPLRNKSTELISEMYKLTKGKLPIIGVGGVFSGKDAFEKIKAGASLVQIYTSF 291
E GG G + + L+ + +P+I GG+ G+ + GA VQI T F
Sbjct: 167 EAGGHIGTFVGVTTFLLVPTVVDAVD--IPVIAAGGIADGRGIAAALALGAEGVQIGTRF 224
Query: 292 V 292
+
Sbjct: 225 L 225
>gnl|CDD|215294 PLN02535, PLN02535, glycolate oxidase.
Length = 364
Score = 32.5 bits (74), Expect = 0.31
Identities = 21/85 (24%), Positives = 37/85 (43%), Gaps = 17/85 (20%)
Query: 209 VDGLIVSNTTVDRYEYLDARYKEETGGLSGEPLRNKSTELISEMYKLTKGKLPIIGVGGV 268
V G+IVSN + +Y A + ++ E+ + G++P++ GGV
Sbjct: 245 VAGIIVSNHGARQLDYSPA-----------------TISVLEEVVQAVGGRVPVLLDGGV 287
Query: 269 FSGKDAFEKIKAGASLVQIYTSFVY 293
G D F+ + GA V + +Y
Sbjct: 288 RRGTDVFKALALGAQAVLVGRPVIY 312
>gnl|CDD|184807 PRK14730, coaE, dephospho-CoA kinase; Provisional.
Length = 195
Score = 31.0 bits (71), Expect = 0.59
Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 8/46 (17%)
Query: 79 QLKHLLKTVVETRNQLALKPLPPILVKIAPDLSLDEKKDIADVVLD 124
QL+ L+K R+ L + +I L+EK +ADVVLD
Sbjct: 139 QLQRLIK-----RDGLTEEE---AEARINAQWPLEEKVKLADVVLD 176
Score = 29.5 bits (67), Expect = 1.8
Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 8/46 (17%)
Query: 159 QLKHLLKTVVETRNQLAVKPLPPILVKIAPDLSLDEKKDIADVVLD 204
QL+ L+K R+ L + +I L+EK +ADVVLD
Sbjct: 139 QLQRLIK-----RDGLTEEE---AEARINAQWPLEEKVKLADVVLD 176
>gnl|CDD|130373 TIGR01306, GMP_reduct_2, guanosine monophosphate reductase,
bacterial. A deep split separates two families of GMP
reductase. The other (TIGR01305) is found in eukaryotic
and some proteobacterial lineages, including E. coli,
while this family is found in a variety of bacterial
lineages [Purines, pyrimidines, nucleosides, and
nucleotides, Nucleotide and nucleoside
interconversions].
Length = 321
Score = 31.1 bits (70), Expect = 0.85
Identities = 22/68 (32%), Positives = 33/68 (48%), Gaps = 2/68 (2%)
Query: 261 PIIGVGGVFSGKDAFEKIKAGASLVQIYTSFVYHGPPLVTRIKSELEELLQKEGYNSVSQ 320
PII GG+ + D + I+ GAS+V I + F H + E + L KE + S S+
Sbjct: 200 PIIADGGIRTHGDIAKSIRFGASMVMIGSLFAGHEESPGETV--EKDGKLYKEYFGSASE 257
Query: 321 AVGAAHKS 328
HK+
Sbjct: 258 FQKGEHKN 265
>gnl|CDD|227559 COG5234, CIN1, Beta-tubulin folding cofactor D [Posttranslational
modification, protein turnover, chaperones /
Cytoskeleton].
Length = 993
Score = 31.1 bits (70), Expect = 1.0
Identities = 7/35 (20%), Positives = 12/35 (34%)
Query: 2 VGLDESTCSRILSRVFRSGEWGCTPTHNMLSSFAR 36
+ E C+R + S +GC P +
Sbjct: 853 ILSSEDECARFYFPIMESFAYGCFPDFQVKGMSKA 887
>gnl|CDD|240088 cd04737, LOX_like_FMN, L-Lactate oxidase (LOX) FMN-binding domain.
LOX is a member of the family of FMN-containing
alpha-hydroxyacid oxidases and catalyzes the oxidation
of l-lactate using molecular oxygen to generate pyruvate
and H2O2. This family occurs in both prokaryotes and
eukaryotes. Members of this family include
flavocytochrome b2 (FCB2), glycolate oxidase (GOX),
lactate monooxygenase (LMO), mandelate dehydrogenase
(MDH), and long chain hydroxyacid oxidase (LCHAO).
Length = 351
Score = 30.5 bits (69), Expect = 1.1
Identities = 18/53 (33%), Positives = 24/53 (45%), Gaps = 15/53 (28%)
Query: 249 ISEMYKLTKGK--------------LPIIGVGGVFSGKDAFEKIKAGASLVQI 287
ISE+Y K K LP+I V G+ S +DA I AGA + +
Sbjct: 197 ISEIYAAAKQKLSPADIEFIAKISGLPVI-VKGIQSPEDADVAINAGADGIWV 248
>gnl|CDD|224560 COG1646, COG1646, Predicted phosphate-binding enzymes, TIM-barrel
fold [General function prediction only].
Length = 240
Score = 30.3 bits (69), Expect = 1.2
Identities = 16/51 (31%), Positives = 23/51 (45%), Gaps = 7/51 (13%)
Query: 232 ETGGLSGEPLRNKSTELISEMYKLTKGKLPIIGVGGVFSGKDAFEKIKAGA 282
E G +G+P+ EM P+I GG+ S + A E +AGA
Sbjct: 171 EAGSGAGDPVPV-------EMVSRVLSDTPLIVGGGIRSPEQAREMAEAGA 214
>gnl|CDD|107029 PHA01351, PHA01351, putative minor structural protein.
Length = 1070
Score = 30.7 bits (69), Expect = 1.2
Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 118 IADVVLDSVKGILKFGDVAHYFVVNVSSPNTANLRKLQAKDQLKHLLKTVVE 169
I D++ GIL D+ Y N+ +P TA KL ++Q LL+ VVE
Sbjct: 329 IRDLITGVQYGILNISDLEKYAYNNLITPKTA---KLMYQNQTARLLQRVVE 377
>gnl|CDD|233564 TIGR01768, GGGP-family, geranylgeranylglyceryl phosphate synthase
family protein. This model represents a family of
sequences including geranylgeranylglyceryl phosphate
synthase which catalyzes the first committed step in the
synthesis of ether-linked membrane lipids in archaea.
The clade of bacterial sequences may have the same
function or a closely related function. This model
supercedes TIGR00265, which has been retired.
Length = 223
Score = 30.1 bits (68), Expect = 1.3
Identities = 17/54 (31%), Positives = 28/54 (51%), Gaps = 4/54 (7%)
Query: 232 ETGGLSGEPLRNKSTELISEMYKLTKGKLPIIGVGGVFSGKDAFEKIKAGASLV 285
E G + EP+ EL++E+ K+ +G GG+ S + A E +AGA +
Sbjct: 156 EAGSGAPEPVP---PELVAEVKKVLDKARLFVG-GGIRSVEKAREMAEAGADTI 205
>gnl|CDD|183033 PRK11197, lldD, L-lactate dehydrogenase; Provisional.
Length = 381
Score = 30.4 bits (69), Expect = 1.4
Identities = 13/37 (35%), Positives = 19/37 (51%)
Query: 257 KGKLPIIGVGGVFSGKDAFEKIKAGASLVQIYTSFVY 293
KG + I+ G+ +G D I GA V + +FVY
Sbjct: 298 KGDITILADSGIRNGLDVVRMIALGADTVLLGRAFVY 334
>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 = 29.9 bits (67), Expect = 1.5
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 259 KLPIIGVGGVFSGKDAFEKIKAGASLVQI 287
K+P+I GG+ +DA E + GA V +
Sbjct: 170 KVPVIAGGGINDPEDAAEALALGADGVIV 198
>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 = 1.9
Identities = 19/88 (21%), Positives = 35/88 (39%), Gaps = 7/88 (7%)
Query: 206 KCKVDGLIVSNTTVDRYEYLDARYKEETGGLSGEPLRNKSTELISEMYKLTKGKLPIIGV 265
D T D E + ++ G+S + + + E+ + ++ +I
Sbjct: 227 LAPEDAAGAGGTGADGIEVSNHGGRQLDWGIS-------TADSLPEIVEAVGDRIEVIAD 279
Query: 266 GGVFSGKDAFEKIKAGASLVQIYTSFVY 293
GG+ SG D + + GA V I F+Y
Sbjct: 280 GGIRSGLDVAKALALGADAVGIGRPFLY 307
>gnl|CDD|232984 TIGR00462, genX, EF-P lysine aminoacylase GenX. Many
Gram-negative bacteria have a protein closely
homologous to the C-terminal region of lysyl-tRNA
synthetase (LysS). Multiple sequence alignment of these
proteins with the homologous regions of collected LysS
proteins shows that these proteins form a distinct set
rather than just similar truncations of LysS. The
protein is termed GenX after its designation in E.
coli. Interestingly, genX often is located near a
homolog of lysine-2,3-aminomutase. Its function is
unknown [Unknown function, General].
Length = 290
Score = 29.8 bits (68), Expect = 2.0
Identities = 10/23 (43%), Positives = 13/23 (56%), Gaps = 6/23 (26%)
Query: 13 LSRVFRSGEWGCTPTHN----ML 31
+ +VFR+GE G HN ML
Sbjct: 66 ICKVFRNGERG--RRHNPEFTML 86
>gnl|CDD|188630 cd00408, DHDPS-like, Dihydrodipicolinate synthase family.
Dihydrodipicolinate synthase family. A member of the
class I aldolases, which use an active-site lysine which
stabilizes a reaction intermediate via Schiff base
formation, and have TIM beta/alpha barrel fold. The
dihydrodipicolinate synthase family comprises several
pyruvate-dependent class I aldolases that use the same
catalytic step to catalyze different reactions in
different pathways and includes such proteins as
N-acetylneuraminate lyase, MosA protein,
5-keto-4-deoxy-glucarate dehydratase,
trans-o-hydroxybenzylidenepyruvate hydratase-aldolase,
trans-2'-carboxybenzalpyruvate hydratase-aldolase, and
2-keto-3-deoxy- gluconate aldolase. The family is also
referred to as the N-acetylneuraminate lyase (NAL)
family.
Length = 281
Score = 29.4 bits (67), Expect = 2.1
Identities = 10/51 (19%), Positives = 26/51 (50%), Gaps = 9/51 (17%)
Query: 110 LSLDEKKDIADVVLDSVKGILKFGDVAHYFVVNVSSPNTANLRKL--QAKD 158
L+ +E+K++ + V+++V G + + V + +T +L A++
Sbjct: 47 LTDEERKEVIEAVVEAVAGRVP-------VIAGVGANSTREAIELARHAEE 90
>gnl|CDD|223406 COG0329, DapA, Dihydrodipicolinate synthase/N-acetylneuraminate
lyase [Amino acid transport and metabolism / Cell
envelope biogenesis, outer membrane].
Length = 299
Score = 29.5 bits (67), Expect = 2.1
Identities = 11/41 (26%), Positives = 23/41 (56%), Gaps = 7/41 (17%)
Query: 110 LSLDEKKDIADVVLDSVKGILKFGDVAHYFVVNVSSPNTAN 150
L+L+E+K++ + V+++V G + + V S +TA
Sbjct: 54 LTLEERKEVLEAVVEAVGGRVP-------VIAGVGSNSTAE 87
>gnl|CDD|215600 PLN03141, PLN03141, 3-epi-6-deoxocathasterone 23-monooxygenase;
Provisional.
Length = 452
Score = 29.7 bits (67), Expect = 2.3
Identities = 43/157 (27%), Positives = 65/157 (41%), Gaps = 37/157 (23%)
Query: 79 QLKHLLKTVVETRNQLAL---KPLPPILVKIAPDLSLDEKKDIADVVLDSVKGILKF--G 133
LK + +E +L + PP+LV+ DE K IA VL VK ++ G
Sbjct: 117 HLKAQITRDMERYVSESLDSWRDDPPVLVQ-------DETKKIAFEVL--VKALISLEPG 167
Query: 134 DVAHY-------FVVNVSS-----PNTANLRKLQAKDQLKHLLKTVVETRNQLAVKPLPP 181
+ + F+ + S P T R LQAK ++ L+K ++E + + A+K
Sbjct: 168 EEMEFLKKEFQEFIKGLMSLPIKLPGTRLYRSLQAKKRMVKLVKKIIEEK-RRAMKNKEE 226
Query: 182 ILVKIAPDLSLDEKKDIADVVLD--SKCKVDGLIVSN 216
I KD+ DV+L S D LI N
Sbjct: 227 DETGIP--------KDVVDVLLRDGSDELTDDLISDN 255
>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 = 29.2 bits (66), Expect = 3.3
Identities = 16/56 (28%), Positives = 24/56 (42%), Gaps = 5/56 (8%)
Query: 259 KLPIIGVGGVFSGKDAFEKIKAGASLVQIYTSF---VYHGPP--LVTRIKSELEEL 309
PII GG+ +G D + I GA V + F ++ I+ +EEL
Sbjct: 254 DAPIIASGGLRTGLDVAKAIALGADAVGMARPFLKAALDEGEEAVIEEIELIIEEL 309
>gnl|CDD|188634 cd00945, Aldolase_Class_I, Class I aldolases. Class I aldolases.
The class I aldolases use an active-site lysine which
stabilizes a reaction intermediates via Schiff base
formation, and have TIM beta/alpha barrel fold. The
members of this family include
2-keto-3-deoxy-6-phosphogluconate (KDPG) and
2-keto-4-hydroxyglutarate (KHG) aldolases,
transaldolase, dihydrodipicolinate synthase sub-family,
Type I 3-dehydroquinate dehydratase, DeoC and DhnA
proteins, and metal-independent
fructose-1,6-bisphosphate aldolase. Although
structurally similar, the class II aldolases use a
different mechanism and are believed to have an
independent evolutionary origin.
Length = 201
Score = 28.4 bits (64), Expect = 3.7
Identities = 12/48 (25%), Positives = 23/48 (47%)
Query: 238 GEPLRNKSTELISEMYKLTKGKLPIIGVGGVFSGKDAFEKIKAGASLV 285
G + E + M + G++ + GG+ + +DA I+AGA +
Sbjct: 151 GFGGGGATVEDVKLMKEAVGGRVGVKAAGGIKTLEDALAAIEAGADGI 198
>gnl|CDD|215524 PLN02970, PLN02970, serine racemase.
Length = 328
Score = 28.9 bits (65), Expect = 3.9
Identities = 24/82 (29%), Positives = 38/82 (46%), Gaps = 17/82 (20%)
Query: 206 KCKVD------GLIV-SNTTVDRYEYLDARYKEETGGLSGEPLRNK---------STELI 249
CKVD G+I TV+ E + AR ++ETG + P + + E +
Sbjct: 111 ACKVDAVIRYGGIITWCEPTVESREAVAARVQQETGAVLIHPYNDGRVISGQGTIALEFL 170
Query: 250 SEMYKLTKGKLPIIGVGGVFSG 271
++ +L +PI G GG+ SG
Sbjct: 171 EQVPELDVIIVPISG-GGLISG 191
>gnl|CDD|217008 pfam02384, N6_Mtase, N-6 DNA Methylase. Restriction-modification
(R-M) systems protect a bacterial cell against invasion
of foreign DNA by endonucleolytic cleavage of DNA that
lacks a site specific modification. The R-M system is a
complex containing three polypeptides: M (this family),
S (pfam01420), and R. This family consists of N-6
adenine-specific DNA methylase EC:2.1.1.72 from Type I
and Type IC restriction systems. These methylases have
the same sequence specificity as their corresponding
restriction enzymes.
Length = 312
Score = 28.4 bits (64), Expect = 4.6
Identities = 23/74 (31%), Positives = 33/74 (44%), Gaps = 5/74 (6%)
Query: 220 DRYEYLDARYKEETGGLSGEPLRNKS-TELISEMYKLTKGKL---PIIGVGGVFSGKDAF 275
D YEYL ++ E G GE + ++LI E+ + G+ P G GG D F
Sbjct: 8 DAYEYLLGKFAPEEGKSGGEFYTPREVSKLIVELLEPKPGESIYDPACGSGGFLIQADKF 67
Query: 276 EKIKAG-ASLVQIY 288
K G + + IY
Sbjct: 68 VKSHDGDTNDISIY 81
>gnl|CDD|238341 cd00608, GalT, Galactose-1-phosphate uridyl transferase (GalT):
This enzyme plays a key role in galactose metabolism by
catalysing the transfer of a uridine 5'-phosphoryl group
from UDP-galactose 1-phosphate. The structure of E.coli
GalT reveals that the enzyme contains two identical
subunits. It also demonstrates that the active site is
formed by amino acid residues from both subunits of the
dimer.
Length = 329
Score = 28.4 bits (64), Expect = 5.9
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 11/58 (18%)
Query: 167 VVETRNQLAVKPLP---PILVKIAP--------DLSLDEKKDIADVVLDSKCKVDGLI 213
VVE + +AV P P V I P DL+ +E++D+A+++ + D L
Sbjct: 203 VVENEHFVAVVPFWARWPFEVHILPKRHVSRFTDLTDEEREDLAEILKRLLARYDNLF 260
>gnl|CDD|176179 cd05195, enoyl_red, enoyl reductase of polyketide synthase.
Putative enoyl reductase of polyketide synthase.
Polyketide synthases produce polyketides in step by step
mechanism that is similar to fatty acid synthesis. Enoyl
reductase reduces a double to single bond. Erythromycin
is one example of a polyketide generated by 3 complex
enzymes (megasynthases). 2-enoyl thioester reductase
(ETR) catalyzes the NADPH-dependent dependent conversion
of trans-2-enoyl acyl carrier protein/coenzyme A
(ACP/CoA) to acyl-(ACP/CoA) in fatty acid synthesis.
2-enoyl thioester reductase activity has been linked in
Candida tropicalis as essential in maintaining
mitiochondrial respiratory function. This ETR family is
a part of the medium chain dehydrogenase/reductase
family, but lack the zinc coordination sites
characteristic of the alcohol dehydrogenases in this
family. NAD(P)(H)-dependent oxidoreductases are the
major enzymes in the interconversion of alcohols and
aldehydes or ketones. Alcohol dehydrogenase in the liver
converts ethanol and NAD+ to acetaldehyde and NADH,
while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. The N-terminal catalytic domain has a
distant homology to GroES. These proteins typically
form dimers (typically higher plants, mammals) or
tetramers (yeast, bacteria), and have 2 tightly bound
zinc atoms per subunit, a catalytic zinc at the active
site, and a structural zinc in a lobe of the catalytic
domain. NAD(H) binding occurs in the cleft between the
catalytic and coenzyme-binding domains, at the active
site, and coenzyme binding induces a conformational
closing of this cleft. Coenzyme binding typically
precedes and contributes to substrate binding.
Length = 293
Score = 27.9 bits (63), Expect = 6.4
Identities = 25/99 (25%), Positives = 37/99 (37%), Gaps = 16/99 (16%)
Query: 13 LSRVFRSGEWGCTPTHNMLSSFARM----RAWVLQFWLLGILKFGDVAHYFVVNVSSPNT 68
LS W C L+ F R + +L LG+ F + V++
Sbjct: 187 LSGELLRASWRC------LAPFGRFVEIGKRDILSNSKLGMRPFLRNVSFSSVDLDQLAR 240
Query: 69 ANLRKLQAKDQLKHLLKTVVETRNQLALKPLPPILVKIA 107
+ L+ LL+ V+E LKPLPP +V A
Sbjct: 241 ER------PELLRELLREVLELLEAGVLKPLPPTVVPSA 273
>gnl|CDD|221851 pfam12916, DUF3834, Protein of unknown function (DUF3834). This
family is likely to be related to solute-binding
lipo-proteins.
Length = 199
Score = 27.7 bits (62), Expect = 6.6
Identities = 22/98 (22%), Positives = 36/98 (36%), Gaps = 11/98 (11%)
Query: 101 PILVKIAPDLSLD---EKKDIADVVLDSVKGILKFGDVAHYFVV--------NVSSPNTA 149
P++ +D K+ ADVVLDS ++K G + + S
Sbjct: 11 PLIAATMKYKDIDIIFSKEGNADVVLDSTVSLVKRGLRIDAVTIKKLYSIYPKIGSGKIG 70
Query: 150 NLRKLQAKDQLKHLLKTVVETRNQLAVKPLPPILVKIA 187
RK A D L L + + ++ P +VK+
Sbjct: 71 VWRKGSAADVLARALLDLKGIKAEVVYADDPDEIVKML 108
>gnl|CDD|218676 pfam05649, Peptidase_M13_N, Peptidase family M13. M13 peptidases
are well-studied proteases found in a wide range of
organisms including mammals and bacteria. In mammals
they participate in processes such as cardiovascular
development, blood-pressure regulation, nervous control
of respiration, and regulation of the function of
neuropeptides in the central nervous system. In bacteria
they may be used for digestion of milk.
Length = 380
Score = 28.1 bits (63), Expect = 6.7
Identities = 17/57 (29%), Positives = 26/57 (45%), Gaps = 7/57 (12%)
Query: 88 VETRNQLALKPLPPILVKIAPDLSLDEKKDIADVVLDSVKGILKFGDVAHYFVVNVS 144
+ +L LKPL P+L KI ++ K D+AD + + + G F VS
Sbjct: 69 TDAIEKLGLKPLKPLLKKIG---AIKSKFDLADALAK----LERGGSNGPLFGFGVS 118
>gnl|CDD|220311 pfam09609, Cas_GSU0054, CRISPR-associated protein, GSU0054 family
(Cas_GSU0054). This entry represents a rare
CRISPR-associated protein. So far, members are found in
Geobacter sulfurreducens and in two unpublished genomes:
Gemmata obscuriglobus and Actinomyces naeslundii.
CRISPR-associated proteins typically are found near
CRISPR repeats and other CRISPR-associated proteins,
have low levels of sequence identify, have sequence
relationships that suggest lateral transfer, and show
some sequence similarity to DNA-active proteins such as
helicases and repair proteins.
Length = 519
Score = 28.0 bits (62), Expect = 6.9
Identities = 29/96 (30%), Positives = 38/96 (39%), Gaps = 5/96 (5%)
Query: 60 VVNVSSPNTANLRKLQAKDQLKHLLKTVVETRNQLALKPLPPI--LVKIAPDLSLDEKKD 117
+VNV PN +L +L AK + K L V PP+ LV L E
Sbjct: 185 IVNVRVPNEGSLDELDAKGENKLPLLIVGSILPTQPKNLYPPMSRLVAYERSLDCFEPSK 244
Query: 118 IADVVLDSVKGILKFGDVAHYFVVNVSSPNTANLRK 153
I+ VV G K VN +P T +LR+
Sbjct: 245 ISHVV---DWGERKVNVPRRLLDVNALTPVTDSLRR 277
>gnl|CDD|176513 cd08571, GDPD_SHV3_plant, Glycerophosphodiester phosphodiesterase
domain of glycerophosphodiester phosphodiesterase-like
protein SHV3 and SHV3-like proteins. This subfamily
corresponds to the glycerophosphodiester
phosphodiesterase (GDPD) domain present in
glycerophosphodiester phosphodiesterase (GP-GDE)-like
protein SHV3 and SHV3-like proteins (SVLs), which may
play an important role in cell wall organization. The
prototype of this family is a
glycosylphosphatidylinositol (GPI) anchored protein SHV3
encoded by shaven3 (shv3) gene from Arabidopsis
thaliana. Members in this family show sequence homology
to bacterial GP-GDEs (EC 3.1.4.46) that catalyze the
hydrolysis of various glycerophosphodiesters, and
produce sn-glycerol-3-phosphate (G3P) and the
corresponding alcohols. Both, SHV3 and SVLs, have two
tandemly repeated GDPD domains whose biochemical
functions remain unclear. The residues essential for
interactions with the substrates and calcium ions in
bacterial GP-GDEs are not conserved in SHV3 and SVLs,
which suggests that the function of GDPD domains in
these proteins might be distinct from those in typical
bacterial GP-GDEs. In addition, the two tandem repeats
show low sequence similarity to each other, suggesting
they have different biochemical function. Most members
of this family are Arabidopsis-specific gene products.
To date, SHV3 orthologues are only found in
Physcomitrella patens.
Length = 302
Score = 27.6 bits (62), Expect = 8.8
Identities = 26/144 (18%), Positives = 51/144 (35%), Gaps = 14/144 (9%)
Query: 63 VSSPNTANLRKLQAKDQLKHLLKTVVETRNQLALKPLPPILVKIAPDLSLDEKKDIADVV 122
+S+P + R + + K + T+ + K L + + + L E K + V
Sbjct: 96 ISNPFSVLFRNPRNDNAGK--ILTLEDFLTLAKPKSLSGVWINVENAAFLAEHKGL-LSV 152
Query: 123 LDSVKGILKFGDVAHYFVVNVSSPNTANLRKLQAKDQLKHLLKTVVETRNQLAVKPLPPI 182
+ + K G V +SSP+++ L+ + + K + + +
Sbjct: 153 DAVLTSLSKAGYDQTAKKVYISSPDSSVLKSFKKRVGTKLVFRVLDVDDT---------- 202
Query: 183 LVKIAPDLSLDEKKDIADVVLDSK 206
+L E K A VL K
Sbjct: 203 -EPDTLLSNLTEIKKFASGVLVPK 225
>gnl|CDD|131432 TIGR02379, ECA_wecE, TDP-4-keto-6-deoxy-D-glucose transaminase.
This family consists of TDP-4-keto-6-deoxy-D-glucose
transaminases, the WecE (formerly RffA) protein of
enterobacterial common antigen (ECA) biosynthesis, from
enterobacteria. It also includes closely matching
sequence from species not expected to make ECA, but
which contain other genes for the biosynthesis of
TDP-4-keto-6-deoxy-D-Glc, an intermediate in the
biosynthesis of other compounds as well and the
substrate of WecA. This family belongs to the
DegT/DnrJ/EryC1/StrS aminotransferase family (pfam01041)
[Cell envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 376
Score = 27.9 bits (62), Expect = 9.0
Identities = 20/71 (28%), Positives = 30/71 (42%), Gaps = 6/71 (8%)
Query: 69 ANLRKLQAKDQLKHLLKTVVETRNQLALKPLPPILVKIAPD-LSLDEKKDIADVVLDSVK 127
A L +Q D++ T V T N L+ + V I PD +++DE I + K
Sbjct: 63 ALLLDIQPGDEVIMPSYTFVSTANAFVLRGAKIVFVDIRPDTMNIDETL-IESAITHRTK 121
Query: 128 GILKFGDVAHY 138
I+ HY
Sbjct: 122 AIV----PVHY 128
>gnl|CDD|181670 PRK09140, PRK09140, 2-dehydro-3-deoxy-6-phosphogalactonate
aldolase; Reviewed.
Length = 206
Score = 27.1 bits (61), Expect = 9.6
Identities = 10/40 (25%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 267 GVFSGKDAFEKIKAGASLVQIYTSFVYHGPPLVTRIKSEL 306
GV + +AF ++AGA ++++ + GP + +++ L
Sbjct: 110 GVATPTEAFAALRAGAQALKLFPASQL-GPAGIKALRAVL 148
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 0.135 0.384
Gapped
Lambda K H
0.267 0.0691 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,613,544
Number of extensions: 1622075
Number of successful extensions: 1846
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1820
Number of HSP's successfully gapped: 90
Length of query: 328
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 231
Effective length of database: 6,635,264
Effective search space: 1532745984
Effective search space used: 1532745984
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: 59 (26.6 bits)