RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 029266
(196 letters)
>gnl|CDD|178478 PLN02890, PLN02890, geranyl diphosphate synthase.
Length = 422
Score = 291 bits (746), Expect = 1e-98
Identities = 142/223 (63%), Positives = 171/223 (76%), Gaps = 27/223 (12%)
Query: 1 MGNKLAILAGDLLISRALVALASLKHTEVI---------------------------MEC 33
MGNKL++LAGD L+SRA VALA+LK+TEV+ M+
Sbjct: 200 MGNKLSVLAGDFLLSRACVALAALKNTEVVSLLATAVEHLVTGETMQITSSREQRRSMDY 259
Query: 34 YMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSAS 93
YMQKTY KTA+L+SNSCKAVA L+GQ EVA LAFEYG+NLGLA+QLIDD+LDFTGTSAS
Sbjct: 260 YMQKTYYKTASLISNSCKAVAILAGQTAEVAVLAFEYGRNLGLAFQLIDDVLDFTGTSAS 319
Query: 94 LGKASLTDLRNGIITAPILFAMEEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTE 153
LGK SL+D+R+G+ITAPILFAMEEFPQLR ++ DNPANVD+ LEYLGKS GIQRT E
Sbjct: 320 LGKGSLSDIRHGVITAPILFAMEEFPQLREVVDRGFDNPANVDIALEYLGKSRGIQRTRE 379
Query: 154 LALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITRNK 196
LA +HA+LAAAAI+SLPET D D +R AL+ +T+++ITRNK
Sbjct: 380 LAREHANLAAAAIESLPETDDEDVLTSRRALIDLTERVITRNK 422
>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 = 159 bits (403), Expect = 5e-48
Identities = 80/220 (36%), Positives = 124/220 (56%), Gaps = 33/220 (15%)
Query: 2 GNKLAILAGDLLISRALVALASLKHTEVI---------------------------MECY 34
G ++A+LAGD L ++A LA+L++ EV+ +E Y
Sbjct: 107 GTRVAVLAGDFLFAQASWYLANLENLEVVKLISKVITDFAEGEIKQGLNQFDSDLSLEDY 166
Query: 35 MQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASL 94
++K++ KTA+LV+ S KA A LS +VA +EYGK+LGLA+Q++DDILDFTG++ L
Sbjct: 167 LEKSFYKTASLVAASSKAAAVLSDVPSQVANDLYEYGKHLGLAFQVVDDILDFTGSTEQL 226
Query: 95 GKASLTDLRNGIITAPILFAMEEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTEL 154
GK + +DL G +TAP+LFA+EE P+L I +++ L + KS GI++ EL
Sbjct: 227 GKPAGSDLMKGNLTAPVLFALEEEPKLSELIEREFSQKGDLEQALSLVRKSGGIKKAREL 286
Query: 155 ALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITR 194
A + A LA ++ LP + R AL + +++R
Sbjct: 287 AKEQAQLALQSLSFLPP------SPPREALKELVHFVLSR 320
>gnl|CDD|215462 PLN02857, PLN02857, octaprenyl-diphosphate synthase.
Length = 416
Score = 147 bits (372), Expect = 1e-42
Identities = 74/220 (33%), Positives = 119/220 (54%), Gaps = 33/220 (15%)
Query: 2 GNKLAILAGDLLISRALVALASLKHTEVI---------------------------MECY 34
G ++A+LAGD + +++ LA+L + EVI ++ Y
Sbjct: 201 GTRVAVLAGDFMFAQSSWYLANLDNLEVIKLISQVIKDFASGEIKQASSLFDCDVTLDEY 260
Query: 35 MQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASL 94
+ K+Y KTA+L++ S K+ A SG V +EYGKNLGLA+Q++DDILDFT ++ L
Sbjct: 261 LLKSYYKTASLIAASTKSAAIFSGVDSSVKEQMYEYGKNLGLAFQVVDDILDFTQSTEQL 320
Query: 95 GKASLTDLRNGIITAPILFAMEEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTEL 154
GK + +DL G +TAP++FA+E+ P+LR I S +++ +E + + GI+R EL
Sbjct: 321 GKPAGSDLAKGNLTAPVIFALEKEPELREIIESEFCEEGSLEEAIELVNEGGGIERAQEL 380
Query: 155 ALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITR 194
A + A LA ++ LP R++L + + R
Sbjct: 381 AKEKADLAIQNLECLPR------GAFRSSLEDMVDYNLER 414
>gnl|CDD|223220 COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme
metabolism].
Length = 322
Score = 140 bits (356), Expect = 4e-41
Identities = 69/223 (30%), Positives = 104/223 (46%), Gaps = 34/223 (15%)
Query: 2 GNKLAILAGDLLISRALVALASL----------------------------KHTEVIMEC 33
G AILAGD L++ A L+ L ++ V +E
Sbjct: 106 GEATAILAGDALLAAAFELLSKLGSEALEAIKALAEAINGLCGGQALDLAFENKPVTLEE 165
Query: 34 YMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSAS 93
Y++ KTAAL + + A L+G EE+ +YG+NLGLA+Q+ DDILD TG
Sbjct: 166 YLRVIELKTAALFAAAAVLGAILAGADEELLEALEDYGRNLGLAFQIQDDILDITGDEEE 225
Query: 94 LGKASLTDLRNGIITAPILFAMEEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTE 153
LGK +DL+ G T P+L A+E+ + + + + V+ LE L KS I+
Sbjct: 226 LGKPVGSDLKEGKPTLPVLLALEKANEDQKLLRILLEGGGEVEEALELLRKSGAIEYAKN 285
Query: 154 LALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITRNK 196
LA + A A++ LP++ A+ AL+ + II R
Sbjct: 286 LAKTYVEKAKEALEKLPDSE------AKEALLELADFIIKRKY 322
>gnl|CDD|164542 CHL00151, preA, prenyl transferase; Reviewed.
Length = 323
Score = 136 bits (344), Expect = 3e-39
Identities = 73/222 (32%), Positives = 119/222 (53%), Gaps = 33/222 (14%)
Query: 2 GNKLAILAGDLLISRALVALASLKHTEVI---------------------------MECY 34
G K+A+LAGD L +++ LA+L + EV+ + Y
Sbjct: 108 GTKIAVLAGDFLFAQSSWYLANLNNLEVVKLISKVITDFAEGEIRQGLVQFDTTLSILNY 167
Query: 35 MQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASL 94
++K++ KTA+L++ SCKA A LS E+ + YGK+LGLA+Q+IDD+LD T ++ SL
Sbjct: 168 IEKSFYKTASLIAASCKAAALLSDADEKDHNDFYLYGKHLGLAFQIIDDVLDITSSTESL 227
Query: 95 GKASLTDLRNGIITAPILFAMEEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTEL 154
GK +DL+NG +TAP+LFA+ + +L I ++ L+ + +++GI++ +L
Sbjct: 228 GKPIGSDLKNGNLTAPVLFALTQNSKLAKLIEREFCETKDISQALQIIKETNGIEKAKDL 287
Query: 155 ALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITRNK 196
AL+H A + LP + D +L+ I II R
Sbjct: 288 ALEHMQAAIQCLKFLPPSSAKD------SLIEIANFIINRLN 323
>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 = 130 bits (330), Expect = 8e-38
Identities = 67/223 (30%), Positives = 92/223 (41%), Gaps = 72/223 (32%)
Query: 2 GNKLAILAGDLLISRALVALASLKH----------TEVIMEC------------------ 33
GN AILAGD L++RA LA L + +E I+E
Sbjct: 79 GNATAILAGDYLLARAFELLARLGNPYYPRALELFSEAILELVEGQLLDLLSEYDTDVTE 138
Query: 34 --YMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTS 91
Y++ KTAAL + + A L+G EE A +G+NLGLA+Q+ DDILD G
Sbjct: 139 EEYLRIIRLKTAALFAAAPLLGALLAGADEEEAEALKRFGRNLGLAFQIQDDILDLFGDP 198
Query: 92 ASLGKASLTDLRNGIITAPILFAMEEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRT 151
+LGK +DLR G T P+L A+
Sbjct: 199 ETLGKPVGSDLREGKCTLPVLLALR----------------------------------- 223
Query: 152 TELALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITR 194
ELA ++ A A+ +LPE + AR AL + I+ R
Sbjct: 224 -ELAREYEEKALEALKALPE------SPAREALRALADFILER 259
>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 = 103 bits (259), Expect = 2e-27
Identities = 53/144 (36%), Positives = 70/144 (48%), Gaps = 28/144 (19%)
Query: 2 GNKLAILAGDLLISRALVALASLKHTEVI---------------------------MECY 34
GN LAILAGD L++RA LA L + + ++ Y
Sbjct: 59 GNALAILAGDYLLARAFQLLARLGYPRALELFAEALRELLEGQALDLEFERDTYETLDEY 118
Query: 35 MQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASL 94
++ KTA LV C A LSG +E A +YG+ LGLA+QL DD+LD G + L
Sbjct: 119 LEYCRYKTAGLVGLLCLLGAGLSGADDEQAEALKDYGRALGLAFQLTDDLLDVFGDAEEL 178
Query: 95 GKASLTDLRNGIITAPILFAMEEF 118
GK +DLR G IT P++ A E
Sbjct: 179 GKV-GSDLREGRITLPVILARERA 201
>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 = 98.6 bits (246), Expect = 6e-25
Identities = 60/222 (27%), Positives = 102/222 (45%), Gaps = 34/222 (15%)
Query: 2 GNKLAILAGDLLISRALVALASLK----HT---EVIMEC--------------------Y 34
GN++A+ GD L +++L + +K H I+E Y
Sbjct: 103 GNRIAMYTGDYLFAKSLETMTEIKDPRAHQILSHTIVEVCRGEIEQIKDKYNFDQNLRTY 162
Query: 35 MQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASL 94
+++ KTA L++ SC+ A SG E + + +G +G++YQ+ DDILDF GT L
Sbjct: 163 LRRIKRKTALLIAASCQLGAIASGANEAIVKKLYWFGYYVGMSYQITDDILDFVGTEEEL 222
Query: 95 GKASLTDLRNGIITAPILFAMEEFPQLRAFINSSSDNPAN-VDVILEYLGKSHGIQRTTE 153
GK + DL G +T P+L+AME+ + + A ++ ++E + KS I+
Sbjct: 223 GKPAGGDLLQGNVTLPVLYAMEDPFLKKRIEQVLEETTAEEMEPLIEEVKKSDAIEYAYA 282
Query: 154 LALKHASLAAAAIDSLPETHDVDATNARTALVHITQKIITRN 195
++ ++ A +D LP A+ L I + I R
Sbjct: 283 VSDRYLKKALELLDGLP------DGRAKKPLQEIAKYIGKRK 318
>gnl|CDD|215873 pfam00348, polyprenyl_synt, Polyprenyl synthetase.
Length = 260
Score = 92.0 bits (229), Expect = 6e-23
Identities = 52/148 (35%), Positives = 70/148 (47%), Gaps = 33/148 (22%)
Query: 2 GNKLAILAGDLLISRALVALASLKH--------------TEVIMEC-------------- 33
G AILAGD L+SRA LA L H V +
Sbjct: 73 GEAGAILAGDALLSRAFQLLALLGHVRPEPKYILISELANAVGAQGEVGQLMDLETEGKD 132
Query: 34 -----YMQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFT 88
Y++ KTAAL S + A ++G EE +++G++LGLA+Q+ DDILD T
Sbjct: 133 ITLEEYLRIVSYKTAALFYASVQLGAIVAGADEEDEKDLYDFGRDLGLAFQIQDDILDLT 192
Query: 89 GTSASLGKASLTDLRNGIITAPILFAME 116
G + LGK TDL+ G T P+L A+E
Sbjct: 193 GDTEELGKPVGTDLQEGKSTLPVLLALE 220
>gnl|CDD|182813 PRK10888, PRK10888, octaprenyl diphosphate synthase; Provisional.
Length = 323
Score = 76.8 bits (189), Expect = 6e-17
Identities = 65/217 (29%), Positives = 99/217 (45%), Gaps = 34/217 (15%)
Query: 2 GNKLAILAGDLLISRA---LVALASLKHTEV---------------IMEC---------Y 34
GN ++L GD + +RA + +L SLK EV +M Y
Sbjct: 104 GNAASVLVGDFIYTRAFQMMTSLGSLKVLEVMSEAVNVIAEGEVLQLMNVNDPDITEENY 163
Query: 35 MQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASL 94
M+ Y+KTA L + + L+G E +YG+ LG A+QLIDD+LD++ +L
Sbjct: 164 MRVIYSKTARLFEAAAQCSGILAGCTPEQEKGLQDYGRYLGTAFQLIDDLLDYSADGETL 223
Query: 95 GKASLTDLRNGIITAPILFAMEE-FPQLRAFINSSSDNPAN---VDVILEYLGKSHGIQR 150
GK DL G T P+L AM P+ A I ++ + ++ +LE + ++
Sbjct: 224 GKNVGDDLNEGKPTLPLLHAMHHGTPEQAAMIRTAIEQGNGRHLLEPVLEAMNACGSLEW 283
Query: 151 TTELALKHASLAAAAIDSLPETHDVDATNARTALVHI 187
T + A + A A AA+ LP+T A L HI
Sbjct: 284 TRQRAEEEADKAIAALQVLPDT---PWREALIGLAHI 317
>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 = 72.5 bits (178), Expect = 9e-16
Identities = 52/218 (23%), Positives = 79/218 (36%), Gaps = 55/218 (25%)
Query: 2 GNKLAILAGDLLISRALVALASLKHTEVI---------------------------MECY 34
G AILAGDLL++ A LA E + +E Y
Sbjct: 53 GLPEAILAGDLLLADAFEELAREGSPEALEILAEALLDLLEGQLLDLKWRREYVPTLEEY 112
Query: 35 MQKTYNKTAALVSNSCKAVAYLSGQREEVATLAFEYGKNLGLAYQLIDDILDFTGTSASL 94
++ KTA LV C A LSG E+ + G+ LGLA+QL +D+LD+ G +
Sbjct: 113 LEYCRYKTAGLVGALCLLGAGLSGGEAELLEALRKLGRALGLAFQLTNDLLDYEGDAERG 172
Query: 95 GKASLTDLRNGIITAPILFAMEEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTEL 154
G T P+L+A+E + + KS ++ E
Sbjct: 173 ---------EGKCTLPVLYALEYGVPAEDLL---------------LVEKSGSLEEALEE 208
Query: 155 ALKHASLAAAAIDSLPETHDVDATNARTALVHITQKII 192
K A A ++ L + AL+ + +
Sbjct: 209 LAKLAEEALKELNELILSLPD----VPRALLALALNLY 242
>gnl|CDD|182567 PRK10581, PRK10581, geranyltranstransferase; Provisional.
Length = 299
Score = 46.7 bits (111), Expect = 2e-06
Identities = 28/78 (35%), Positives = 44/78 (56%), Gaps = 1/78 (1%)
Query: 41 KTAALVSNSCKAVAYLSGQREEVATLAFE-YGKNLGLAYQLIDDILDFTGTSASLGKASL 99
KT AL+ + + A +G + A + Y +++GLA+Q+ DDILD G +A+LGK
Sbjct: 181 KTGALIRAAVRLGALSAGDKGRRALPVLDRYAESIGLAFQVQDDILDVVGDTATLGKRQG 240
Query: 100 TDLRNGIITAPILFAMEE 117
D + G T P L +E+
Sbjct: 241 ADQQLGKSTYPALLGLEQ 258
>gnl|CDD|233139 TIGR00814, stp, serine transporter. The Hydroxy/Aromatic Amino
Acid Permease (HAAAP) Family- serine/threonine subfamily
(TC 2.A.42.2) The HAAAP family includes well
characterized aromatic amino acid:H+ symport permeases
and hydroxy amino acid permeases. This subfamily is
specific for hydroxy amino acid transporters and
includes the serine permease, SdaC, of E. coli, and the
threonine permease, TdcC, of E. coli.//added GO terms,
none avaialbelf or ser/thr specifically [SS 2/6/05]
[Transport and binding proteins, Amino acids, peptides
and amines].
Length = 397
Score = 31.5 bits (72), Expect = 0.22
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 5/47 (10%)
Query: 106 IITAPILFAMEEFPQLRAFIN--SSSDNPAN--VDVILEYLGKSHGI 148
++ A I + + F RA SS NP +V+ E+ GK+ GI
Sbjct: 37 VLMAIIAYPLTYFGH-RALARFLLSSKNPCEDITEVVEEHFGKNWGI 82
>gnl|CDD|176554 cd08613, GDPD_GDE4_like_1, Glycerophosphodiester phosphodiesterase
domain of uncharacterized bacterial homologs of
mammalian glycerophosphodiester phosphodiesterase GDE4.
This subfamily corresponds to the glycerophosphodiester
phosphodiesterase domain (GDPD) present in
uncharacterized bacterial homologs of mammalian GDE4, a
transmembrane protein whose cellular function has not
been elucidated yet.
Length = 309
Score = 28.5 bits (64), Expect = 2.1
Identities = 16/71 (22%), Positives = 30/71 (42%), Gaps = 2/71 (2%)
Query: 116 EEFPQLRAFINSSSDNPANVDVILEYLGKSHGIQRTTELALKHASLAAAAI-DSLPETHD 174
FP R IN SD+ A +++ E L + +R L + AA+ + P+
Sbjct: 150 AAFPDRRFLINFKSDDAAEGELLAEKL-ATLPRKRLQVLTVYGGDKPIAALRELTPDLRT 208
Query: 175 VDATNARTALV 185
+ + + L+
Sbjct: 209 LSKASMKDCLI 219
>gnl|CDD|151200 pfam10707, YrbL-PhoP_reg, PhoP regulatory network protein YrbL.
This is a family of proteins that are activated by PhoP.
PhoP protein controls the expression of a large number
of genes that mediate adaptation to low Mg2+
environments and/or virulence in several bacterial
species. YbrL is proposed to be acting in a loop
activity with PhoP and PrmA analogous to the
multicomponent loop in Salmonella where the
PhoP-dependent PmrD protein activates the regulatory
protein PmrA, and the activated PmrA then represses
transcription from the PmrD promoter which harbours
binding sites for both the PhoP and PmrA proteins.
Expression of YrbL is induced in low Mg2+ in a
PhoP-dependent fashion and repressed by Fe3+ in a
PmrA-dependent manner.
Length = 199
Score = 28.0 bits (63), Expect = 2.3
Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 8/66 (12%)
Query: 73 NLGLAYQLIDDILDFTGTSASLGKASLTDL-RNGIITAPILFAMEEFPQ--LRAFINSSS 129
+LGL + + I D G + +L DL +NG +TA + A+ EF + L I +
Sbjct: 89 DLGLGL-VTERIRDADGNISP----TLEDLLKNGGLTAALREALNEFKRYLLDNHIVARD 143
Query: 130 DNPANV 135
NP N+
Sbjct: 144 LNPHNI 149
>gnl|CDD|143296 cd05888, Ig1_Nectin-4_like, Frst immunoglobulin (Ig) domain of
nectin-4 (also known as poliovirus receptor related
protein 4, or as LNIR receptor) and similar proteins.
Ig1_Nectin-4_like: domain similar to the first
immunoglobulin (Ig) domain of nectin-4 (also known as
poliovirus receptor related protein 4, or as LNIR
receptor). Nectin-4 belongs to the nectin family, which
is comprised of four transmembrane glycoproteins
(nectins-1 through -4). Nectins are synaptic cell
adhesion molecules (CAMs) which participate in adhesion
and signaling at various intracellular junctions.
Nectins form homophilic cis-dimers, followed by
homophilic and heterophilic trans-dimers involved in
cell-cell adhesion. For example nectin-4
trans-interacts with nectin-1. Nectin-4 has also been
shown to interact with the actin filament-binding
protein, afadin. Unlike the other nectins, which are
widely expressed in adult tissues, nectin-4 is mainly
expressed during embryogenesis, and is not detected in
normal adult tissue or in serum. Nectin-4 is
re-expressed in breast carcinoma, and patients having
metastatic breast cancer have a circulating form of
nectin-4 formed from the ectodomain.
Length = 100
Score = 27.2 bits (60), Expect = 2.5
Identities = 13/57 (22%), Positives = 23/57 (40%), Gaps = 11/57 (19%)
Query: 27 TEVIMECYMQKTYNKTAALVSNSCKAVAYL----SGQREEVATLAFEYGKNLGLAYQ 79
+ + C + +T V ++ G EE+A L F+YG+ AY+
Sbjct: 1 GDTRLPCRYNVSDGETVV-------QVLWIRENAGGVEEEIALLHFKYGQTEFHAYE 50
>gnl|CDD|236601 PRK09637, PRK09637, RNA polymerase sigma factor SigZ; Provisional.
Length = 181
Score = 26.9 bits (60), Expect = 5.3
Identities = 14/29 (48%), Positives = 20/29 (68%), Gaps = 1/29 (3%)
Query: 120 QLRAFINSSSDNPANVDVIL-EYLGKSHG 147
QL+AF++S N A+VD +L E L K+H
Sbjct: 13 QLKAFLHSRVSNEADVDDLLQEVLIKTHS 41
>gnl|CDD|225744 COG3203, OmpC, Outer membrane protein (porin) [Cell envelope
biogenesis, outer membrane].
Length = 354
Score = 27.4 bits (61), Expect = 5.7
Identities = 15/61 (24%), Positives = 22/61 (36%), Gaps = 9/61 (14%)
Query: 57 SGQREEVATLAFE------YGKNLGLAYQLID--DILDFTGTSASLGKASLTDLR-NGII 107
R A L YG+N G+ Y + D L G A+L + R + +
Sbjct: 94 LFTRLAFAGLKGADFGSLDYGRNYGVLYDVAGWTDPLPEFGGDATLVDDNFMTGRADNVA 153
Query: 108 T 108
T
Sbjct: 154 T 154
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 0.131 0.354
Gapped
Lambda K H
0.267 0.0756 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,698,152
Number of extensions: 905391
Number of successful extensions: 905
Number of sequences better than 10.0: 1
Number of HSP's gapped: 891
Number of HSP's successfully gapped: 34
Length of query: 196
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 104
Effective length of database: 6,857,034
Effective search space: 713131536
Effective search space used: 713131536
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: 56 (25.3 bits)