RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 014706
(420 letters)
>gnl|CDD|215462 PLN02857, PLN02857, octaprenyl-diphosphate synthase.
Length = 416
Score = 712 bits (1840), Expect = 0.0
Identities = 317/418 (75%), Positives = 354/418 (84%), Gaps = 5/418 (1%)
Query: 2 MSMTSHNLDFGRSVLDLVACGCSSSASIHRSSVRKIAMTGSRKSNRDCGARRLVCCRQNL 61
MSM+ N+D G S LVACGCSS+AS R VR A + +R + V R+++
Sbjct: 1 MSMSCRNIDLGTS---LVACGCSSNASSRRRVVRNGATPVCKSCSRSYASSL-VTSRRDI 56
Query: 62 ARCRVYSTKTPETLLN-VGQIPPAVLNLKEKSRSPISLANIFEVVAEDLQTLNQNLKSIV 120
RCRV S +L+N +GQ P L+LK +S+ PISL+ +FE VA+DLQ LN NL+SIV
Sbjct: 57 GRCRVVSPSPETSLVNGIGQGPTVALDLKAESKEPISLSELFEPVADDLQQLNDNLQSIV 116
Query: 121 GAENPVLMSAAEQIFGAGGKRLRPALVFLVSRATAELVGLKELTTKHRRLAEIIEMIHTA 180
GAENPVLMSAAEQIFGAGGKR+RPALVFLVSRATAEL GLKELTT+HRRLAEI EMIHTA
Sbjct: 117 GAENPVLMSAAEQIFGAGGKRMRPALVFLVSRATAELAGLKELTTEHRRLAEITEMIHTA 176
Query: 181 SLIHDDVLDESDMRRGQETVHQLYGTRVAVLAGDFMFAQSSWYLANLENLEVIKLISQVI 240
SLIHDDVLDESDMRRG+ETVHQLYGTRVAVLAGDFMFAQSSWYLANL+NLEVIKLISQVI
Sbjct: 177 SLIHDDVLDESDMRRGKETVHQLYGTRVAVLAGDFMFAQSSWYLANLDNLEVIKLISQVI 236
Query: 241 KDFASGEIKQASSLFDCDLELEEYLIKSYYKTASLIAASTKGAAIFSGVDGSLSKQMYEY 300
KDFASGEIKQASSLFDCD+ L+EYL+KSYYKTASLIAASTK AAIFSGVD S+ +QMYEY
Sbjct: 237 KDFASGEIKQASSLFDCDVTLDEYLLKSYYKTASLIAASTKSAAIFSGVDSSVKEQMYEY 296
Query: 301 GRNLGLSFQIVDDILDFTQSAEQLGKPAASDLAKGNLTAPVIFALEKEPKLREIIESEFC 360
G+NLGL+FQ+VDDILDFTQS EQLGKPA SDLAKGNLTAPVIFALEKEP+LREIIESEFC
Sbjct: 297 GKNLGLAFQVVDDILDFTQSTEQLGKPAGSDLAKGNLTAPVIFALEKEPELREIIESEFC 356
Query: 361 ETGSLDEAIKLVKTSGGIEEAQELAKEKANLAIHNLHCLPRSPFRVALEDMVMFNLER 418
E GSL+EAI+LV GGIE AQELAKEKA+LAI NL CLPR FR +LEDMV +NLER
Sbjct: 357 EEGSLEEAIELVNEGGGIERAQELAKEKADLAIQNLECLPRGAFRSSLEDMVDYNLER 414
>gnl|CDD|131796 TIGR02749, prenyl_cyano, solanesyl diphosphate synthase. Members
of this family all are from cyanobacteria or
plastid-containing eukaryotes. A member from Arabidopsis
(where both plastoquinone and ubiquinone contain the
C(45) prenyl moiety) was characterized by heterologous
expression as a solanesyl diphosphate synthase
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Menaquinone and ubiquinone].
Length = 322
Score = 522 bits (1347), Expect = 0.0
Identities = 214/323 (66%), Positives = 262/323 (81%), Gaps = 3/323 (0%)
Query: 96 ISLANIFEVVAEDLQTLNQNLKSIVGAENPVLMSAAEQIFGAGGKRLRPALVFLVSRATA 155
S ++F V +DL L NLKS+VGA +P+L +AAE +F AGGKRLRPA+V LVSRATA
Sbjct: 1 ASATSLFAPVEDDLYLLTDNLKSLVGARHPILYAAAEHLFSAGGKRLRPAIVLLVSRATA 60
Query: 156 ELVGLKELTTKHRRLAEIIEMIHTASLIHDDVLDESDMRRGQETVHQLYGTRVAVLAGDF 215
E +ELT +HRRLAEI EMIHTASL+HDDV+DESD RRG ETVH L+GTRVAVLAGDF
Sbjct: 61 EQ---QELTPRHRRLAEITEMIHTASLVHDDVIDESDTRRGIETVHSLFGTRVAVLAGDF 117
Query: 216 MFAQSSWYLANLENLEVIKLISQVIKDFASGEIKQASSLFDCDLELEEYLIKSYYKTASL 275
+FAQ+SWYLANLENLEV+KLIS+VI DFA GEIKQ + FD DL LE+YL KS+YKTASL
Sbjct: 118 LFAQASWYLANLENLEVVKLISKVITDFAEGEIKQGLNQFDSDLSLEDYLEKSFYKTASL 177
Query: 276 IAASTKGAAIFSGVDGSLSKQMYEYGRNLGLSFQIVDDILDFTQSAEQLGKPAASDLAKG 335
+AAS+K AA+ S V ++ +YEYG++LGL+FQ+VDDILDFT S EQLGKPA SDL KG
Sbjct: 178 VAASSKAAAVLSDVPSQVANDLYEYGKHLGLAFQVVDDILDFTGSTEQLGKPAGSDLMKG 237
Query: 336 NLTAPVIFALEKEPKLREIIESEFCETGSLDEAIKLVKTSGGIEEAQELAKEKANLAIHN 395
NLTAPV+FALE+EPKL E+IE EF + G L++A+ LV+ SGGI++A+ELAKE+A LA+ +
Sbjct: 238 NLTAPVLFALEEEPKLSELIEREFSQKGDLEQALSLVRKSGGIKKARELAKEQAQLALQS 297
Query: 396 LHCLPRSPFRVALEDMVMFNLER 418
L LP SP R AL+++V F L R
Sbjct: 298 LSFLPPSPPREALKELVHFVLSR 320
>gnl|CDD|164542 CHL00151, preA, prenyl transferase; Reviewed.
Length = 323
Score = 398 bits (1023), Expect = e-138
Identities = 171/319 (53%), Positives = 229/319 (71%), Gaps = 3/319 (0%)
Query: 100 NIFEVVAEDLQTLNQNLKSIVGAENPVLMSAAEQIFGAGGKRLRPALVFLVSRATAELVG 159
N+ + E+L L NLK ++G+ +P+L +AA+ +F AGGKR+RPA+V LV++AT G
Sbjct: 6 NLLTPIEEELLILEDNLKKLIGSGHPILYAAAKHLFSAGGKRIRPAIVLLVAKATG---G 62
Query: 160 LKELTTKHRRLAEIIEMIHTASLIHDDVLDESDMRRGQETVHQLYGTRVAVLAGDFMFAQ 219
E+ T +RLAEI E+IHTASL+HDDV+DE +RRG TVH+++GT++AVLAGDF+FAQ
Sbjct: 63 NMEIKTSQQRLAEITEIIHTASLVHDDVIDECSIRRGIPTVHKIFGTKIAVLAGDFLFAQ 122
Query: 220 SSWYLANLENLEVIKLISQVIKDFASGEIKQASSLFDCDLELEEYLIKSYYKTASLIAAS 279
SSWYLANL NLEV+KLIS+VI DFA GEI+Q FD L + Y+ KS+YKTASLIAAS
Sbjct: 123 SSWYLANLNNLEVVKLISKVITDFAEGEIRQGLVQFDTTLSILNYIEKSFYKTASLIAAS 182
Query: 280 TKGAAIFSGVDGSLSKQMYEYGRNLGLSFQIVDDILDFTQSAEQLGKPAASDLAKGNLTA 339
K AA+ S D Y YG++LGL+FQI+DD+LD T S E LGKP SDL GNLTA
Sbjct: 183 CKAAALLSDADEKDHNDFYLYGKHLGLAFQIIDDVLDITSSTESLGKPIGSDLKNGNLTA 242
Query: 340 PVIFALEKEPKLREIIESEFCETGSLDEAIKLVKTSGGIEEAQELAKEKANLAIHNLHCL 399
PV+FAL + KL ++IE EFCET + +A++++K + GIE+A++LA E AI L L
Sbjct: 243 PVLFALTQNSKLAKLIEREFCETKDISQALQIIKETNGIEKAKDLALEHMQAAIQCLKFL 302
Query: 400 PRSPFRVALEDMVMFNLER 418
P S + +L ++ F + R
Sbjct: 303 PPSSAKDSLIEIANFIINR 321
>gnl|CDD|223220 COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme
metabolism].
Length = 322
Score = 284 bits (729), Expect = 1e-93
Identities = 124/323 (38%), Positives = 187/323 (57%), Gaps = 6/323 (1%)
Query: 99 ANIFEVVAEDLQTLNQNLKSIV-GAENPVLMSAAEQIFGAGGKRLRPALVFLVSRATAEL 157
+++ ++ + L + + L ++ G++ +L+ A + AGGKRLRP LV L + A
Sbjct: 1 SDLLALLLKRLARIEELLSELLSGSDPELLLEAMRYLLLAGGKRLRPLLVLLAAEALG-- 58
Query: 158 VGLKELTTKHRRLAEIIEMIHTASLIHDDVLDESDMRRGQETVHQLYGTRVAVLAGDFMF 217
+ L+ LA IE+IHTASLIHDD++D+ D+RRG+ TVH +G A+LAGD +
Sbjct: 59 IDLETGGNDALDLAAAIELIHTASLIHDDLMDDDDLRRGKPTVHAKFGEATAILAGDALL 118
Query: 218 AQSSWYLANLEN--LEVIKLISQVIKDFASGEIKQASSLFDCDLELEEYLIKSYYKTASL 275
A + L+ L + LE IK +++ I G+ + + LEEYL KTA+L
Sbjct: 119 AAAFELLSKLGSEALEAIKALAEAINGLCGGQALDLAFENK-PVTLEEYLRVIELKTAAL 177
Query: 276 IAASTKGAAIFSGVDGSLSKQMYEYGRNLGLSFQIVDDILDFTQSAEQLGKPAASDLAKG 335
AA+ AI +G D L + + +YGRNLGL+FQI DDILD T E+LGKP SDL +G
Sbjct: 178 FAAAAVLGAILAGADEELLEALEDYGRNLGLAFQIQDDILDITGDEEELGKPVGSDLKEG 237
Query: 336 NLTAPVIFALEKEPKLREIIESEFCETGSLDEAIKLVKTSGGIEEAQELAKEKANLAIHN 395
T PV+ ALEK + ++++ G ++EA++L++ SG IE A+ LAK A
Sbjct: 238 KPTLPVLLALEKANEDQKLLRILLEGGGEVEEALELLRKSGAIEYAKNLAKTYVEKAKEA 297
Query: 396 LHCLPRSPFRVALEDMVMFNLER 418
L LP S + AL ++ F ++R
Sbjct: 298 LEKLPDSEAKEALLELADFIIKR 320
>gnl|CDD|173833 cd00685, Trans_IPPS_HT, Trans-Isoprenyl Diphosphate Synthases,
head-to-tail. These trans-Isoprenyl Diphosphate
Synthases (Trans_IPPS) catalyze head-to-tail (HT) (1'-4)
condensation reactions. This CD includes all-trans
(E)-isoprenyl diphosphate synthases which synthesize
various chain length (C10, C15, C20, C25, C30, C35, C40,
C45, and C50) linear isoprenyl diphosphates from
precursors, isopentenyl diphosphate (IPP) and
dimethylallyl diphosphate (DMAPP). They catalyze the
successive 1'-4 condensation of the 5-carbon IPP to
allylic substrates geranyl-, farnesyl-, or
geranylgeranyl-diphosphate. Isoprenoid chain elongation
reactions proceed via electrophilic alkylations in which
a new carbon-carbon single bond is generated through
interaction between a highly reactive electron-deficient
allylic carbocation and an electron-rich carbon-carbon
double bond. The catalytic site consists of a large
central cavity formed by mostly antiparallel alpha
helices with two aspartate-rich regions (DDXX(XX)D)
located on opposite walls. These residues mediate
binding of prenyl phosphates via bridging Mg2+ ions,
inducing proposed conformational changes that close the
active site to solvent, protecting and stabilizing
reactive carbocation intermediates. Farnesyl diphosphate
synthases produce the precursors of steroids,
cholesterol, sesquiterpenes, farnsylated proteins, heme,
and vitamin K12; and geranylgeranyl diphosphate and
longer chain synthases produce the precursors of
carotenoids, retinoids, diterpenes, geranylgeranylated
chlorophylls, ubiquinone, and archaeal ether linked
lipids. Isoprenyl diphosphate synthases are widely
distributed among archaea, bacteria, and eukareya.
Length = 259
Score = 271 bits (696), Expect = 1e-89
Identities = 115/300 (38%), Positives = 155/300 (51%), Gaps = 44/300 (14%)
Query: 122 AENPVLMSAAEQIFGAGGKRLRPALVFLVSRATAELVGLKELTTKHRRLAEIIEMIHTAS 181
+E +L A + AGGKRLRP LV L +RA RLA IE++HTAS
Sbjct: 1 SEVELLREALRYLLLAGGKRLRPLLVLLAARALGG-----PELEAALRLAAAIELLHTAS 55
Query: 182 LIHDDVLDESDMRRGQETVHQLYGTRVAVLAGDFMFAQSSWYLANLEN---LEVIKLISQ 238
L+HDDV+D SD+RRG+ TVH+++G A+LAGD++ A++ LA L N ++L S+
Sbjct: 56 LVHDDVMDNSDLRRGKPTVHKVFGNATAILAGDYLLARAFELLARLGNPYYPRALELFSE 115
Query: 239 VIKDFASGEIKQASSLFDCDLELEEYLIKSYYKTASLIAASTKGAAIFSGVDGSLSKQMY 298
I + G++ S +D D+ EEYL KTA+L AA+ A+ +G D ++ +
Sbjct: 116 AILELVEGQLLDLLSEYDTDVTEEEYLRIIRLKTAALFAAAPLLGALLAGADEEEAEALK 175
Query: 299 EYGRNLGLSFQIVDDILDFTQSAEQLGKPAASDLAKGNLTAPVIFALEKEPKLREIIESE 358
+GRNLGL+FQI DDILD E LGKP SDL +G T PV+ AL
Sbjct: 176 RFGRNLGLAFQIQDDILDLFGDPETLGKPVGSDLREGKCTLPVLLALR------------ 223
Query: 359 FCETGSLDEAIKLVKTSGGIEEAQELAKEKANLAIHNLHCLPRSPFRVALEDMVMFNLER 418
ELA+E A+ L LP SP R AL + F LER
Sbjct: 224 ------------------------ELAREYEEKALEALKALPESPAREALRALADFILER 259
>gnl|CDD|178478 PLN02890, PLN02890, geranyl diphosphate synthase.
Length = 422
Score = 257 bits (659), Expect = 4e-82
Identities = 131/314 (41%), Positives = 200/314 (63%), Gaps = 13/314 (4%)
Query: 102 FEVVAEDLQTLNQNLKSIVGAENPVLMSAAEQIF--GAGGKRLRP--------ALVFLVS 151
F +VA++L L L+S+V AE P L SAAE F G GKR RP AL +
Sbjct: 85 FSLVADELSLLANKLRSMVVAEVPKLASAAEYFFKVGVEGKRFRPTVLLLMATALNVPLP 144
Query: 152 RATAELVG---LKELTTKHRRLAEIIEMIHTASLIHDDVLDESDMRRGQETVHQLYGTRV 208
+T V EL T+ + +AEI EMIH ASL+HDDVLD++D RRG +++ + G ++
Sbjct: 145 ESTEGGVLDIVASELRTRQQNIAEITEMIHVASLLHDDVLDDADTRRGVGSLNVVMGNKL 204
Query: 209 AVLAGDFMFAQSSWYLANLENLEVIKLISQVIKDFASGEIKQASSLFDCDLELEEYLIKS 268
+VLAGDF+ +++ LA L+N EV+ L++ ++ +GE Q +S + ++ Y+ K+
Sbjct: 205 SVLAGDFLLSRACVALAALKNTEVVSLLATAVEHLVTGETMQITSSREQRRSMDYYMQKT 264
Query: 269 YYKTASLIAASTKGAAIFSGVDGSLSKQMYEYGRNLGLSFQIVDDILDFTQSAEQLGKPA 328
YYKTASLI+ S K AI +G ++ +EYGRNLGL+FQ++DD+LDFT ++ LGK +
Sbjct: 265 YYKTASLISNSCKAVAILAGQTAEVAVLAFEYGRNLGLAFQLIDDVLDFTGTSASLGKGS 324
Query: 329 ASDLAKGNLTAPVIFALEKEPKLREIIESEFCETGSLDEAIKLVKTSGGIEEAQELAKEK 388
SD+ G +TAP++FA+E+ P+LRE+++ F ++D A++ + S GI+ +ELA+E
Sbjct: 325 LSDIRHGVITAPILFAMEEFPQLREVVDRGFDNPANVDIALEYLGKSRGIQRTRELAREH 384
Query: 389 ANLAIHNLHCLPRS 402
ANLA + LP +
Sbjct: 385 ANLAAAAIESLPET 398
>gnl|CDD|131795 TIGR02748, GerC3_HepT, heptaprenyl diphosphate synthase component
II. Members of this family are component II of the
heterodimeric heptaprenyl diphosphate synthase. The
trusted cutoff was set such that all members identified
are encoded near to a recognizable gene for component I
(in Pfam family pfam07307). This enzyme acts in
menaquinone-7 isoprenoid side chain biosynthesis
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Menaquinone and ubiquinone].
Length = 319
Score = 244 bits (624), Expect = 5e-78
Identities = 116/320 (36%), Positives = 192/320 (60%), Gaps = 11/320 (3%)
Query: 98 LANIFEVVAEDLQTLNQNLKSIVGAENPVLMSAAEQIFGAGGKRLRPALVFLVSR-ATAE 156
LA+I+ + +D+ ++ + L+ V AE+PVL A+ + AGGKR+RP V L + +
Sbjct: 2 LADIYSFLQKDIDSIEKELEKAVQAEHPVLSEASLHLLEAGGKRIRPVFVLLAGKFGDYD 61
Query: 157 LVGLKELTTKHRRLAEIIEMIHTASLIHDDVLDESDMRRGQETVHQLYGTRVAVLAGDFM 216
L +K +A +E+IH ASL+HDDV+D++D+RRG+ T+ +G R+A+ GD++
Sbjct: 62 LDAIK-------HVAVALELIHMASLVHDDVIDDADLRRGRPTIKSKWGNRIAMYTGDYL 114
Query: 217 FAQSSWYLANLENLEVIKLISQVIKDFASGEIKQASSLFDCDLELEEYLIKSYYKTASLI 276
FA+S + +++ +++S I + GEI+Q ++ D L YL + KTA LI
Sbjct: 115 FAKSLETMTEIKDPRAHQILSHTIVEVCRGEIEQIKDKYNFDQNLRTYLRRIKRKTALLI 174
Query: 277 AASTKGAAIFSGVDGSLSKQMYEYGRNLGLSFQIVDDILDFTQSAEQLGKPAASDLAKGN 336
AAS + AI SG + ++ K++Y +G +G+S+QI DDILDF + E+LGKPA DL +GN
Sbjct: 175 AASCQLGAIASGANEAIVKKLYWFGYYVGMSYQITDDILDFVGTEEELGKPAGGDLLQGN 234
Query: 337 LTAPVIFALEKEPKLREIIESEFCETGS--LDEAIKLVKTSGGIEEAQELAKEKANLAIH 394
+T PV++A+E +P L++ IE ET + ++ I+ VK S IE A ++ A+
Sbjct: 235 VTLPVLYAME-DPFLKKRIEQVLEETTAEEMEPLIEEVKKSDAIEYAYAVSDRYLKKALE 293
Query: 395 NLHCLPRSPFRVALEDMVMF 414
L LP + L+++ +
Sbjct: 294 LLDGLPDGRAKKPLQEIAKY 313
>gnl|CDD|215873 pfam00348, polyprenyl_synt, Polyprenyl synthetase.
Length = 260
Score = 230 bits (588), Expect = 2e-73
Identities = 97/230 (42%), Positives = 133/230 (57%), Gaps = 13/230 (5%)
Query: 136 GAGGKRLRPALVFLVSRATAELVGLKELTTKHRRLAEIIEMIHTASLIHDDVLDESDMRR 195
AGGKR+RP LV L +RA L LA IEMIHTASL+HDD++D SD+RR
Sbjct: 10 LAGGKRIRPLLVVLAARA------LGVEPETLLYLACAIEMIHTASLVHDDLMDNSDLRR 63
Query: 196 GQETVHQLYGTRVAVLAGDFMFAQSSWYLANLENL----EVIKLISQVIKDFASGEIKQA 251
G+ T H+ +G A+LAGD + +++ LA L ++ + I + A GE+ Q
Sbjct: 64 GKPTCHKKFGEAGAILAGDALLSRAFQLLALLGHVRPEPKYILISELANAVGAQGEVGQL 123
Query: 252 SSLFDCDLE--LEEYLIKSYYKTASLIAASTKGAAIFSGVDGSLSKQMYEYGRNLGLSFQ 309
L + LEEYL YKTA+L AS + AI +G D K +Y++GR+LGL+FQ
Sbjct: 124 MDLETEGKDITLEEYLRIVSYKTAALFYASVQLGAIVAGADEEDEKDLYDFGRDLGLAFQ 183
Query: 310 IVDDILDFTQSAEQLGKPAASDLAKGNLTAPVIFALE-KEPKLREIIESE 358
I DDILD T E+LGKP +DL +G T PV+ ALE + R+++
Sbjct: 184 IQDDILDLTGDTEELGKPVGTDLQEGKSTLPVLLALEGAREEQRKLLREA 233
>gnl|CDD|182813 PRK10888, PRK10888, octaprenyl diphosphate synthase; Provisional.
Length = 323
Score = 205 bits (524), Expect = 3e-63
Identities = 106/328 (32%), Positives = 185/328 (56%), Gaps = 12/328 (3%)
Query: 96 ISLANIFEVVAEDLQTLNQNLKSIVGAENPVLMSAAEQIFGAGGKRLRPALVFLVSRATA 155
++L I E+ A+D+ +N + + ++ ++ I GGKR+RP + L +RA
Sbjct: 1 MNLEKINELTAQDMAGVNAAILEQLNSDVQLINQLGYYIISGGGKRIRPMIAVLAARA-- 58
Query: 156 ELVGLKELTTKHRRLAEIIEMIHTASLIHDDVLDESDMRRGQETVHQLYGTRVAVLAGDF 215
+ H +A +IE IHTA+L+HDDV+DESDMRRG+ T + +G +VL GDF
Sbjct: 59 ----VGYQGNAHVTIAALIEFIHTATLLHDDVVDESDMRRGKATANAAFGNAASVLVGDF 114
Query: 216 MFAQSSWYLANLENLEVIKLISQVIKDFASGEIKQASSLFDCDLELEEYLIKSYYKTASL 275
++ ++ + +L +L+V++++S+ + A GE+ Q ++ D D+ E Y+ Y KTA L
Sbjct: 115 IYTRAFQMMTSLGSLKVLEVMSEAVNVIAEGEVLQLMNVNDPDITEENYMRVIYSKTARL 174
Query: 276 IAASTKGAAIFSGVDGSLSKQMYEYGRNLGLSFQIVDDILDFTQSAEQLGKPAASDLAKG 335
A+ + + I +G K + +YGR LG +FQ++DD+LD++ E LGK DL +G
Sbjct: 175 FEAAAQCSGILAGCTPEQEKGLQDYGRYLGTAFQLIDDLLDYSADGETLGKNVGDDLNEG 234
Query: 336 NLTAPVIFALEK-EPKLREIIESEFCETGS----LDEAIKLVKTSGGIEEAQELAKEKAN 390
T P++ A+ P+ +I + E G+ L+ ++ + G +E ++ A+E+A+
Sbjct: 235 KPTLPLLHAMHHGTPEQAAMIRTAI-EQGNGRHLLEPVLEAMNACGSLEWTRQRAEEEAD 293
Query: 391 LAIHNLHCLPRSPFRVALEDMVMFNLER 418
AI L LP +P+R AL + ++R
Sbjct: 294 KAIAALQVLPDTPWREALIGLAHIAVQR 321
>gnl|CDD|173836 cd00867, Trans_IPPS, Trans-Isoprenyl Diphosphate Synthases.
Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of
class 1 isoprenoid biosynthesis enzymes which either
synthesis geranyl/farnesyl diphosphates (GPP/FPP) or
longer chained products from isoprene precursors,
isopentenyl diphosphate (IPP) and dimethylallyl
diphosphate (DMAPP), or use geranyl (C10)-, farnesyl
(C15)-, or geranylgeranyl (C20)-diphosphate as
substrate. These enzymes produce a myriad of precursors
for such end products as steroids, cholesterol,
sesquiterpenes, heme, carotenoids, retinoids,
diterpenes, ubiquinone, and archaeal ether linked
lipids; and are widely distributed among archaea,
bacteria, and eukareya. The enzymes in this family share
the same 'isoprenoid synthase fold' and include the
head-to-tail (HT) IPPS which catalyze the successive
1'-4 condensation of the 5-carbon IPP to the growing
isoprene chain to form linear, all-trans, C10-, C15-,
C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid
diphosphates. The head-to-head (HH) IPPS catalyze the
successive 1'-1 condensation of 2 farnesyl or 2
geranylgeranyl isoprenoid diphosphates. Isoprenoid chain
elongation reactions proceed via electrophilic
alkylations in which a new carbon-carbon single bond is
generated through interaction between a highly reactive
electron-deficient allylic carbocation and an
electron-rich carbon-carbon double bond. The catalytic
site consists of a large central cavity formed by mostly
antiparallel alpha helices with two aspartate-rich
regions located on opposite walls. These residues
mediate binding of prenyl phosphates via bridging Mg2+
ions, inducing proposed conformational changes that
close the active site to solvent, stabilizing reactive
carbocation intermediates. Mechanistically and
structurally distinct, cis-IPPS are not included in this
CD.
Length = 236
Score = 196 bits (501), Expect = 8e-61
Identities = 80/206 (38%), Positives = 119/206 (57%), Gaps = 8/206 (3%)
Query: 142 LRPALVFLVSRATAELVGLKELTTKHRRLAEIIEMIHTASLIHDDVLDESDMRRGQETVH 201
RP LV L++RA L RLA +E++H ASL+HDD++D+SD+RRG+ T H
Sbjct: 1 SRPLLVLLLARA------LGGDLEAALRLAAAVELLHAASLVHDDIVDDSDLRRGKPTAH 54
Query: 202 -QLYGTRVAVLAGDFMFAQSSWYLANLENLEVIKLISQVIKDFASGEIKQASSLFDCDLE 260
+ +G +A+LAGD++ A++ LA L ++L ++ +++ G+ D
Sbjct: 55 LRRFGNALAILAGDYLLARAFQLLARLGYPRALELFAEALRELLEGQALDLEFERDTYET 114
Query: 261 LEEYLIKSYYKTASLIAASTKGAAIFSGVDGSLSKQMYEYGRNLGLSFQIVDDILDFTQS 320
L+EYL YKTA L+ A SG D ++ + +YGR LGL+FQ+ DD+LD
Sbjct: 115 LDEYLEYCRYKTAGLVGLLCLLGAGLSGADDEQAEALKDYGRALGLAFQLTDDLLDVFGD 174
Query: 321 AEQLGKPAASDLAKGNLTAPVIFALE 346
AE+LGK SDL +G +T PVI A E
Sbjct: 175 AEELGK-VGSDLREGRITLPVILARE 199
>gnl|CDD|173830 cd00385, Isoprenoid_Biosyn_C1, Isoprenoid Biosynthesis enzymes,
Class 1. Superfamily of trans-isoprenyl diphosphate
synthases (IPPS) and class I terpene cyclases which
either synthesis geranyl/farnesyl diphosphates (GPP/FPP)
or longer chained products from isoprene precursors,
isopentenyl diphosphate (IPP) and dimethylallyl
diphosphate (DMAPP), or use geranyl (C10)-, farnesyl
(C15)-, or geranylgeranyl (C20)-diphosphate as
substrate. These enzymes produce a myriad of precursors
for such end products as steroids, cholesterol,
sesquiterpenes, heme, carotenoids, retinoids, and
diterpenes; and are widely distributed among archaea,
bacteria, and eukaryota.The enzymes in this superfamily
share the same 'isoprenoid synthase fold' and include
several subgroups. The head-to-tail (HT) IPPS catalyze
the successive 1'-4 condensation of the 5-carbon IPP to
the growing isoprene chain to form linear, all-trans,
C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or
C50-isoprenoid diphosphates. Cyclic monoterpenes,
diterpenes, and sesquiterpenes, are formed from their
respective linear isoprenoid diphosphates by class I
terpene cyclases. The head-to-head (HH) IPPS catalyze
the successive 1'-1 condensation of 2 farnesyl or 2
geranylgeranyl isoprenoid diphosphates. Cyclization of
these 30- and 40-carbon linear forms are catalyzed by
class II cyclases. Both the isoprenoid chain elongation
reactions and the class I terpene cyclization reactions
proceed via electrophilic alkylations in which a new
carbon-carbon single bond is generated through
interaction between a highly reactive electron-deficient
allylic carbocation and an electron-rich carbon-carbon
double bond. The catalytic site consists of a large
central cavity formed by mostly antiparallel alpha
helices with two aspartate-rich regions located on
opposite walls. These residues mediate binding of prenyl
phosphates via bridging Mg2+ ions, inducing proposed
conformational changes that close the active site to
solvent, stabilizing reactive carbocation intermediates.
Generally, the enzymes in this family exhibit an
all-trans reaction pathway, an exception, is the
cis-trans terpene cyclase, trichodiene synthase.
Mechanistically and structurally distinct, class II
terpene cyclases and cis-IPPS are not included in this
CD.
Length = 243
Score = 163 bits (415), Expect = 6e-48
Identities = 82/268 (30%), Positives = 123/268 (45%), Gaps = 41/268 (15%)
Query: 142 LRPALVFLVSRATAELVGLKELTTKHRRLAEIIEMIHTASLIHDDVLDESDMRRGQETVH 201
RP V L A RL +E +H ASL+HDD++D+S RRG T H
Sbjct: 1 FRPLAVLLEPEA--------------SRLRAAVEKLHAASLVHDDIVDDSGTRRGLPTAH 46
Query: 202 QL---YGTRVAVLAGDFMFAQSSWYLANLENLEVIKLISQVIKDFASGEIKQASSLFDCD 258
G A+LAGD + A + LA + E ++++++ + D G++ +
Sbjct: 47 LAVAIDGLPEAILAGDLLLADAFEELAREGSPEALEILAEALLDLLEGQLLDLKWRREYV 106
Query: 259 LELEEYLIKSYYKTASLIAASTKGAAIFSGVDGSLSKQMYEYGRNLGLSFQIVDDILDFT 318
LEEYL YKTA L+ A A SG + L + + + GR LGL+FQ+ +D+LD+
Sbjct: 107 PTLEEYLEYCRYKTAGLVGALCLLGAGLSGGEAELLEALRKLGRALGLAFQLTNDLLDYE 166
Query: 319 QSAEQLGKPAASDLAKGNLTAPVIFALEKEPKLREIIESEFCETGSLDEAIKLVKTSGGI 378
AE+ G T PV++ALE +++ LV+ SG +
Sbjct: 167 GDAERGE---------GKCTLPVLYALEYGVPAEDLL---------------LVEKSGSL 202
Query: 379 EEAQELAKEKANLAIHNLHCLPRSPFRV 406
EEA E + A A+ L+ L S V
Sbjct: 203 EEALEELAKLAEEALKELNELILSLPDV 230
>gnl|CDD|182567 PRK10581, PRK10581, geranyltranstransferase; Provisional.
Length = 299
Score = 100 bits (250), Expect = 9e-24
Identities = 96/301 (31%), Positives = 141/301 (46%), Gaps = 46/301 (15%)
Query: 110 QTLNQNLKSIVGA---ENPVLMSAAEQIFGA--GGKRLRPALVFLVSRATAELVGLKELT 164
Q NQ L + +N ++ A + +GA GGKRLRP LV+ AT ++ G+ T
Sbjct: 12 QQANQALSRFIAPLPFQNTPVVEAMQ--YGALLGGKRLRPFLVY----ATGQMFGVS--T 63
Query: 165 TKHRRLAEIIEMIHTASLIHDDV--LDESDMRRGQETVHQLYGTRVAVLAGDFMFAQSSW 222
A +E IH SLIHDD+ +D+ D+RRG T H +G A+LAGD + +
Sbjct: 64 NTLDAPAAAVECIHAYSLIHDDLPAMDDDDLRRGLPTCHVKFGEANAILAGDALQTLAFS 123
Query: 223 YLANLENLEV-----IKLISQVIKDFASGEIK----QASSLFDCDLELEEYLIK------ 267
L++ EV I +IS++ ASG QA DLE E +
Sbjct: 124 ILSDAPMPEVSDRDRISMISELAS--ASGIAGMCGGQA-----LDLEAEGKQVPLDALER 176
Query: 268 -SYYKTASLIAASTKGAAIFSGVDGSLS-KQMYEYGRNLGLSFQIVDDILDFTQSAEQLG 325
+KT +LI A+ + A+ +G G + + Y ++GL+FQ+ DDILD LG
Sbjct: 177 IHRHKTGALIRAAVRLGALSAGDKGRRALPVLDRYAESIGLAFQVQDDILDVVGDTATLG 236
Query: 326 KPAASDLAKGNLTAPVIFALEK-EPKLREIIESEFCETGSLDEAIKLVKTSGGIEEAQEL 384
K +D G T P + LE+ K R++I+ SLD+ L S + L
Sbjct: 237 KRQGADQQLGKSTYPALLGLEQARKKARDLIDDAR---QSLDQ---LAAQSLDTSALEAL 290
Query: 385 A 385
A
Sbjct: 291 A 291
>gnl|CDD|223009 PHA03211, PHA03211, serine/threonine kinase US3; Provisional.
Length = 461
Score = 32.2 bits (73), Expect = 0.57
Identities = 26/87 (29%), Positives = 37/87 (42%), Gaps = 26/87 (29%)
Query: 139 GKRLRPALVFLVSRATAELVGLKELTTKHRRLAEIIEMIHTASLIHDDVLDESDMRRGQE 198
G RLRP +GL ++T R+L I+ IH +IH D+ E+ + G E
Sbjct: 251 GARLRP-------------LGLAQVTAVARQLLSAIDYIHGEGIIHRDIKTENVLVNGPE 297
Query: 199 TVHQLYGTRVAVLAGDF---MFAQSSW 222
+ GDF FA+ SW
Sbjct: 298 D----------ICLGDFGAACFARGSW 314
>gnl|CDD|234650 PRK00122, rimM, 16S rRNA-processing protein RimM; Provisional.
Length = 172
Score = 29.3 bits (67), Expect = 2.1
Identities = 8/34 (23%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 155 AELVGLKELTTKHRRLAEIIEMIHTASLIHDDVL 188
+L+GL+ + L ++ +++ T + +DVL
Sbjct: 103 HDLIGLEVVDEDGEELGKVTDILETGA---NDVL 133
>gnl|CDD|234022 TIGR02813, omega_3_PfaA, polyketide-type polyunsaturated fatty acid
synthase PfaA. Members of the seed for this alignment
are involved in omega-3 polyunsaturated fatty acid
biosynthesis, such as the protein PfaA from the
eicosapentaenoic acid biosynthesis operon in
Photobacterium profundum strain SS9. PfaA is encoded
together with PfaB, PfaC, and PfaD, and the functions of
the individual polypeptides have not yet been described.
More distant homologs of PfaA, also included with the
reach of this model, appear to be involved in
polyketide-like biosynthetic mechanisms of
polyunsaturated fatty acid biosynthesis, an alternative
to the more familiar iterated mechanism of chain
extension and desaturation, and in most cases are
encoded near genes for homologs of PfaB, PfaC, and/or
PfaD.
Length = 2582
Score = 30.4 bits (68), Expect = 2.5
Identities = 30/103 (29%), Positives = 45/103 (43%), Gaps = 20/103 (19%)
Query: 231 EVIKLISQVIKDFASGEIKQASSLFDCDLELEEYLIKS--YYKTASLIAASTKGAAIFSG 288
E+I ++ Q I +A S EE+ + S Y+ ++L+ S K AA+F+G
Sbjct: 541 ELITMLEQAITQL------EAKSC-------EEWQLPSGISYRKSALVVESGKVAALFAG 587
Query: 289 VDGSLSKQMYEYGRNLGLSF-QIVDDILDFTQSAEQLGKPAAS 330
GS Q GR L +F ++ D Q GK A S
Sbjct: 588 -QGS---QYLNMGRELACNFPEVRQAAADMDSVFTQAGKGALS 626
>gnl|CDD|235945 PRK07139, PRK07139, amidase; Provisional.
Length = 439
Score = 30.0 bits (68), Expect = 2.8
Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 21/77 (27%)
Query: 213 GDFMFAQS----SWYLANLENLEVIKLISQVI-----KDFASGEIKQAS---------SL 254
G F +A S +++ N+ + ++S+V+ D S ++K + +
Sbjct: 167 GLFAYASSLDTVAYFTHNVND---AIILSKVLFGKDENDLTSVDVKINNVKKTKPKKVAY 223
Query: 255 FDCDLELEEYLIKSYYK 271
DC ELEEY+ K Y K
Sbjct: 224 LDCFKELEEYVAKKYKK 240
>gnl|CDD|129953 TIGR00875, fsa_talC_mipB, fructose-6-phosphate aldolase, TalC/MipB
family. This model represents a family that includes
the E. coli transaldolase homologs TalC and MipB, both
shown to be fructose-6-phosphate aldolases rather than
transaldolases as previously thought. It is related to
but distinct from the transaldolase family of E. coli
TalA and TalB. The member from Bacillus subtilis becomes
phosphorylated during early stationary phase but not
during exponential growth [Energy metabolism, Pentose
phosphate pathway].
Length = 213
Score = 29.1 bits (65), Expect = 3.3
Identities = 27/83 (32%), Positives = 37/83 (44%), Gaps = 14/83 (16%)
Query: 318 TQSAEQLGKPAASDLAKGNLTAPVIFALEKEP---KLREIIE----SEFCETGSLDEAIK 370
T + E++ K A + G T P + A E L+EI E ET SLD
Sbjct: 7 TANVEEIKKAAELGILAGVTTNPSLIAKEGRSFWEVLKEIQEAVEGPVSAETISLD---- 62
Query: 371 LVKTSGGIEEAQELAKEKANLAI 393
G +EEA+ELAK N+ +
Sbjct: 63 ---AEGMVEEAKELAKLAPNIVV 82
>gnl|CDD|235369 PRK05231, PRK05231, homoserine kinase; Provisional.
Length = 319
Score = 29.4 bits (67), Expect = 3.5
Identities = 15/44 (34%), Positives = 18/44 (40%), Gaps = 9/44 (20%)
Query: 381 AQELAKEKANLAIHNLHCLPRSP-----FRVALEDMVMFNLERF 419
ELA + A LA LPR FR D V+F +R
Sbjct: 167 EAELAAQLAFLASAAWPALPRGVIHADLFR----DNVLFEGDRL 206
>gnl|CDD|225883 COG3346, COG3346, Uncharacterized conserved protein [Function
unknown].
Length = 252
Score = 29.3 bits (66), Expect = 3.9
Identities = 18/72 (25%), Positives = 28/72 (38%), Gaps = 6/72 (8%)
Query: 136 GAGGKRLRPA-LVFLVSRATAELVGL-----KELTTKHRRLAEIIEMIHTASLIHDDVLD 189
+ +R A L+ LV A L+GL + L K +A I +H + +LD
Sbjct: 5 ASTRRRRWLALLLLLVLATFAILLGLGTWQLQRLHWKLALIARIEARLHAPPVPLPKLLD 64
Query: 190 ESDMRRGQETVH 201
+D E
Sbjct: 65 WADSGADLEYRR 76
>gnl|CDD|233805 TIGR02273, 16S_RimM, 16S rRNA processing protein RimM. This family
consists of the bacterial protein RimM (YfjA, 21K), a
30S ribosomal subunit-binding protein implicated in 16S
ribsomal RNA processing. It has been partially
characterized in Escherichia coli, is found with other
translation-associated genes such as trmD. It is broadly
distributed among bacteria, including some minimal
genomes such the aphid endosymbiont Buchnera aphidicola.
The protein contains a PRC-barrel domain that it shares
with other protein families (pfam05239) and a unique
domain (pfam01782). This model describes the full-length
protein. A member from Arabidopsis (plant) has
additional N-terminal sequence likely to represent a
chloroplast transit peptide [Transcription, RNA
processing].
Length = 165
Score = 28.7 bits (65), Expect = 4.0
Identities = 10/33 (30%), Positives = 22/33 (66%), Gaps = 3/33 (9%)
Query: 156 ELVGLKELTTKHRRLAEIIEMIHTASLIHDDVL 188
+L+GL+ +T + L +++E++ T + +DVL
Sbjct: 99 DLIGLEVVTEEGEELGKVVEILETGA---NDVL 128
>gnl|CDD|235249 PRK04194, PRK04194, hypothetical protein; Provisional.
Length = 392
Score = 29.0 bits (66), Expect = 4.7
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 158 VGLKELTTKHRRLAEIIEMIHTASL 182
V LKE HR L+EI +I + L
Sbjct: 63 VELKEHHHPHRHLSEIKALIENSDL 87
>gnl|CDD|213993 cd07438, PHP_HisPPase_AMP, Polymerase and Histidinol Phosphatase
domain of Histidinol phosphate phosphatase (HisPPase)
AMP bound. The PHP domain of this HisPPase family has
an unknown function. It has a second domain inserted in
the middle that binds adenosine 5-monophosphate (AMP).
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
give 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 the 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 = 155
Score = 28.1 bits (64), Expect = 5.5
Identities = 8/16 (50%), Positives = 13/16 (81%)
Query: 363 GSLDEAIKLVKTSGGI 378
GS +EAI+L+ +GG+
Sbjct: 75 GSPEEAIELIHAAGGV 90
>gnl|CDD|235554 PRK05673, dnaE, DNA polymerase III subunit alpha; Validated.
Length = 1135
Score = 28.9 bits (66), Expect = 5.6
Identities = 22/79 (27%), Positives = 34/79 (43%), Gaps = 22/79 (27%)
Query: 301 GRNLGLSFQIVDDILDFTQSAEQLGKPAASDLAKGNLTAPVIFALEKEPKLREIIESEFC 360
GR LG+ + VD I + + LAK A E+EP+LRE+ ES+
Sbjct: 443 GRVLGMPYGFVDRI------TKLIPPDPGITLAK---------AYEEEPELRELYESD-- 485
Query: 361 ETGSLDEAIKLVKTSGGIE 379
E +L+ + +E
Sbjct: 486 -----PEVKRLIDMARKLE 499
>gnl|CDD|232780 TIGR00010, TIGR00010, hydrolase, TatD family. PSI-BLAST, starting
with a urease alpha subunit, finds a large superfamily
of proteins, including a number of different enzymes
that act as hydrolases at C-N bonds other than peptide
bonds (EC 3.5.-.-), many uncharacterized proteins, and
the members of this family. Several genomes have
multiple paralogs related to this family. However, a set
of 17 proteins can be found, one each from 17 of the
first 20 genomes, such that each member forms a
bidirectional best hit across genomes with all other
members of the set. This core set (and one other
near-perfect member), but not the other paralogs, form
the seed for this model. Additionally, members of the
seed alignment and all trusted hits, but not all
paralogs, have a conserved motif DxHxH near the amino
end. The member from E. coli was recently shown to have
DNase activity [Unknown function, Enzymes of unknown
specificity].
Length = 252
Score = 28.4 bits (64), Expect = 6.6
Identities = 14/33 (42%), Positives = 17/33 (51%), Gaps = 5/33 (15%)
Query: 139 GKRLRPALVFLVSRATAELVG-----LKELTTK 166
GKR PA V A AE+ G L ++TTK
Sbjct: 212 GKRNEPAFVRYTVEAIAEIKGMDVEELAQITTK 244
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 28.8 bits (65), Expect = 7.5
Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 6/59 (10%)
Query: 140 KRLRPALVFLVSRATAELVGLKELTTKHRRLAEIIEMIHTASLIHDDVLD-ESDMRRGQ 197
K+ R L+F +R+ AE L + ++L I +H SL + L+ E ++ G+
Sbjct: 251 KKHRTTLIFTNTRSGAER-----LAFRLKKLGPDIIEVHHGSLSRELRLEVEERLKEGE 304
>gnl|CDD|238309 cd00553, NAD_synthase, NAD+ synthase is a homodimer, which
catalyzes the final step in de novo nicotinamide adenine
dinucleotide (NAD+) biosynthesis, an amide transfer from
either ammonia or glutamine to nicotinic acid adenine
dinucleotide (NaAD). The conversion of NaAD to NAD+
occurs via an NAD-adenylate intermediate and requires
ATP and Mg2+. The intemediate is subsequently cleaved
into NAD+ and AMP. In many prokaryotes, such as E. coli
, NAD synthetase consists of a single domain and is
strictly ammonia dependent. In contrast, eukaryotes and
other prokaryotes have an additional N-terminal
amidohydrolase domain that prefer glutamine,
Interestingly, NAD+ synthases in these prokaryotes, can
also utilize ammonia as an amide source .
Length = 248
Score = 28.3 bits (64), Expect = 7.5
Identities = 21/102 (20%), Positives = 32/102 (31%), Gaps = 23/102 (22%)
Query: 261 LEEYLIKSYYK-------------TASLIAASTKGAAIFSGV---DGSLSKQMYEYG--- 301
L +YL KS +K + +A G + S++ E
Sbjct: 14 LRDYLRKSGFKGVVLGLSGGIDSALVAALAVRALGRENVLALFMPSRYSSEETREDAKEL 73
Query: 302 -RNLGLSFQIVDDILDFTQSAEQLGK---PAASDLAKGNLTA 339
LG+ +D LG+ DLA GN+ A
Sbjct: 74 AEALGIEHVNIDIDPAVEAFLALLGESGGSELEDLALGNIQA 115
>gnl|CDD|213910 TIGR04297, thauma_sortase, thaumarchaeosortase. This member of the
archaeosortase/exosortase family occurs exclusively in
the Thaumarchaeota, where the corresponding proposed
sorting signal is PEFG-CTERM (see model TIGR04296). This
family is unusual in that the suspected active site
residue, Cys in every other defined subfamily of
archaeosortases and exosortases is replaced by Ser.
Length = 307
Score = 28.4 bits (63), Expect = 7.7
Identities = 16/29 (55%), Positives = 20/29 (68%), Gaps = 4/29 (13%)
Query: 145 ALVFLVSRATAELVGLKELTTKHRRLAEI 173
ALVF+V AEL+GLK + +K R LA I
Sbjct: 36 ALVFVV----AELIGLKIIISKKRLLAVI 60
>gnl|CDD|176187 cd05284, arabinose_DH_like, D-arabinose dehydrogenase. This group
contains arabinose dehydrogenase (AraDH) and related
alcohol dehydrogenases. AraDH is a member of the medium
chain dehydrogenase/reductase family and catalyzes the
NAD(P)-dependent oxidation of D-arabinose and other
pentoses, the initial step in the metabolism of
d-arabinose into 2-oxoglutarate. Like the alcohol
dehydrogenases, AraDH binds a zinc in the catalytic
cleft as well as a distal structural zinc. AraDH forms
homotetramers as a dimer of dimers. AraDH replaces a
conserved catalytic His with replace with Arg, compared
to the canonical ADH site. 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. A GxGxxG motif
after the first mononucleotide contact half allows the
close contact of the coenzyme with the ADH backbone.
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. In human ADH
catalysis, the zinc ion helps coordinate the alcohol,
followed by deprotonation of a histidine, the ribose of
NAD, a serine, then the alcohol, which allows the
transfer of a hydride to NAD+, creating NADH and a
zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 340
Score = 28.3 bits (64), Expect = 8.2
Identities = 24/100 (24%), Positives = 37/100 (37%), Gaps = 20/100 (20%)
Query: 311 VDDILDFTQSAEQLGKPAASDLAK----------GNLTAPVIFALEKEPKLREIIESEFC 360
D ++DF S E L A LAK G+ P + E +
Sbjct: 236 ADAVIDFVGSDETLALAAKL-LAKGGRYVIVGYGGHGRLPTSDLVPTEIS----VIGSL- 289
Query: 361 ETGSLDEAIKLVK--TSGGIE-EAQELAKEKANLAIHNLH 397
G+ E +++V SG ++ E + E AN A+ L
Sbjct: 290 -WGTRAELVEVVALAESGKVKVEITKFPLEDANEALDRLR 328
>gnl|CDD|118696 pfam10168, Nup88, Nuclear pore component. Nup88 can be divided
into two structural domains; the N-terminal two-thirds
of the protein has no obvious structural motifs but is
the region for binding to Nup98, one of the components
of the nuclear pore. the C-terminal end is a predicted
coiled-coil domain. Nup88 is overexpressed in tumour
cells.
Length = 717
Score = 28.3 bits (63), Expect = 8.3
Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 1/59 (1%)
Query: 65 RVYSTKTPETLLNVGQIPPAVLNLKEKSRSPISLANIFEV-VAEDLQTLNQNLKSIVGA 122
RVY+ P VG + A ++ + SLA++ E VA D L + K++ G
Sbjct: 174 RVYNLSKPRHPWQVGPLSQADDESVLRNGANSSLASLGETAVAFDFGPLAASPKTLFGQ 232
>gnl|CDD|240327 PTZ00243, PTZ00243, ABC transporter; Provisional.
Length = 1560
Score = 28.6 bits (64), Expect = 9.3
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 391 LAIHNLHCLPRSPFRVALED 410
LA H +H +PR+ + VAL D
Sbjct: 837 LATHQVHVVPRADYVVALGD 856
>gnl|CDD|132952 cd06621, PKc_MAPKK_Pek1_like, Catalytic domain of fungal Pek1-like
dual-specificity MAP kinase kinases. Protein kinases
(PKs), MAP kinase kinase(MAPKK) subfamily, fungal
Pek1-like proteins, catalytic (c) domain. PKs catalyze
the transfer of the gamma-phosphoryl group from ATP to
serine/threonine or tyrosine residues on protein
substrates. The MAPKK subfamily is part of a larger
superfamily that includes the catalytic domains of other
protein serine/threonine kinases, protein tyrosine
kinases, RIO kinases, aminoglycoside phosphotransferase,
choline kinase, and phosphoinositide 3-kinase. The
mitogen-activated protein (MAP) kinase signaling
pathways are important mediators of cellular responses
to extracellular signals. The pathways involve a triple
kinase core cascade comprising of the MAP kinase (MAPK),
which is phosphorylated and activated by a MAPK kinase
(MAPKK or MKK), which itself is phosphorylated and
activated by a MAPK kinase kinase (MAPKKK or MKKK).
Members of this group include the MAPKKs Pek1/Skh1 from
Schizosaccharomyces pombe and MKK2 from Saccharomyces
cerevisiae, and related proteins. Both fission yeast
Pek1 and baker's yeast MKK2 are components of the cell
integrity MAPK pathway. In fission yeast, Pek1
phosphorylates and activates the MAPK Pmk1/Spm1 and is
regulated by the MAPKKK Mkh1. In baker's yeast, the
pathway involves the MAPK Slt2, the MAPKKs MKK1 and
MKK2, and the MAPKKK Bck1. The cell integrity MAPK
cascade is activated by multiple stress conditions, and
is essential in cell wall construction, morphogenesis,
cytokinesis, and ion homeostasis.
Length = 287
Score = 27.8 bits (62), Expect = 9.8
Identities = 13/24 (54%), Positives = 14/24 (58%)
Query: 355 IESEFCETGSLDEAIKLVKTSGGI 378
I E+CE GSLD K VK GG
Sbjct: 78 IAMEYCEGGSLDSIYKKVKKRGGR 101
>gnl|CDD|170568 PRK10610, PRK10610, chemotaxis regulatory protein CheY;
Provisional.
Length = 129
Score = 27.2 bits (60), Expect = 9.8
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 212 AGDFMFAQSSWYLANLENLEVIKLI 236
AG F F S W + N++ LE++K I
Sbjct: 48 AGGFGFVISDWNMPNMDGLELLKTI 72
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.133 0.368
Gapped
Lambda K H
0.267 0.0704 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,983,953
Number of extensions: 2055767
Number of successful extensions: 2069
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2043
Number of HSP's successfully gapped: 50
Length of query: 420
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 321
Effective length of database: 6,546,556
Effective search space: 2101444476
Effective search space used: 2101444476
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 60 (26.9 bits)