RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5533
(136 letters)
>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 = 134 bits (338), Expect = 2e-39
Identities = 55/135 (40%), Positives = 88/135 (65%)
Query: 1 MLGGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFA 60
+L +++ +EYG++LG+AFQ+VDD+LDF S++ +GKP +DL G TAPVLFA
Sbjct: 187 VLSDVPSQVANDLYEYGKHLGLAFQVVDDILDFTGSTEQLGKPAGSDLMKGNLTAPVLFA 246
Query: 61 CEKFPELNPMIMRRFQEPGDVEKAFEFVHKSQGLEQTKFLARKHCVEAVRLASGLAESPY 120
E+ P+L+ +I R F + GD+E+A V KS G+++ + LA++ A++ S L SP
Sbjct: 247 LEEEPKLSELIEREFSQKGDLEQALSLVRKSGGIKKARELAKEQAQLALQSLSFLPPSPP 306
Query: 121 QKGLVVLTDLVLNRM 135
++ L L VL+R+
Sbjct: 307 REALKELVHFVLSRL 321
>gnl|CDD|164542 CHL00151, preA, prenyl transferase; Reviewed.
Length = 323
Score = 127 bits (321), Expect = 8e-37
Identities = 50/136 (36%), Positives = 85/136 (62%)
Query: 1 MLGGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFA 60
+L AD+K + YG++LG+AFQ++DD+LD SS++++GKP +DLK G TAPVLFA
Sbjct: 188 LLSDADEKDHNDFYLYGKHLGLAFQIIDDVLDITSSTESLGKPIGSDLKNGNLTAPVLFA 247
Query: 61 CEKFPELNPMIMRRFQEPGDVEKAFEFVHKSQGLEQTKFLARKHCVEAVRLASGLAESPY 120
+ +L +I R F E D+ +A + + ++ G+E+ K LA +H A++ L S
Sbjct: 248 LTQNSKLAKLIEREFCETKDISQALQIIKETNGIEKAKDLALEHMQAAIQCLKFLPPSSA 307
Query: 121 QKGLVVLTDLVLNRMK 136
+ L+ + + ++NR+
Sbjct: 308 KDSLIEIANFIINRLN 323
>gnl|CDD|178478 PLN02890, PLN02890, geranyl diphosphate synthase.
Length = 422
Score = 123 bits (309), Expect = 2e-34
Identities = 58/142 (40%), Positives = 95/142 (66%), Gaps = 6/142 (4%)
Query: 1 MLGGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFA 60
+L G +++ +AFEYGRNLG+AFQL+DD+LDF +S ++GK + +D++ G+ TAP+LFA
Sbjct: 281 ILAGQTAEVAVLAFEYGRNLGLAFQLIDDVLDFTGTSASLGKGSLSDIRHGVITAPILFA 340
Query: 61 CEKFPELNPMIMRRFQEPGDVEKAFEFVHKSQGLEQTKFLARKHCVEAVRLASGLAES-- 118
E+FP+L ++ R F P +V+ A E++ KS+G+++T+ LAR+H A L E+
Sbjct: 341 MEEFPQLREVVDRGFDNPANVDIALEYLGKSRGIQRTRELAREHANLAAAAIESLPETDD 400
Query: 119 ----PYQKGLVVLTDLVLNRMK 136
++ L+ LT+ V+ R K
Sbjct: 401 EDVLTSRRALIDLTERVITRNK 422
>gnl|CDD|215462 PLN02857, PLN02857, octaprenyl-diphosphate synthase.
Length = 416
Score = 119 bits (301), Expect = 3e-33
Identities = 54/132 (40%), Positives = 81/132 (61%)
Query: 4 GADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACEK 63
G D + E +EYG+NLG+AFQ+VDD+LDF S++ +GKP +DL G TAPV+FA EK
Sbjct: 284 GVDSSVKEQMYEYGKNLGLAFQVVDDILDFTQSTEQLGKPAGSDLAKGNLTAPVIFALEK 343
Query: 64 FPELNPMIMRRFQEPGDVEKAFEFVHKSQGLEQTKFLARKHCVEAVRLASGLAESPYQKG 123
PEL +I F E G +E+A E V++ G+E+ + LA++ A++ L ++
Sbjct: 344 EPELREIIESEFCEEGSLEEAIELVNEGGGIERAQELAKEKADLAIQNLECLPRGAFRSS 403
Query: 124 LVVLTDLVLNRM 135
L + D L R+
Sbjct: 404 LEDMVDYNLERI 415
>gnl|CDD|223220 COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme
metabolism].
Length = 322
Score = 106 bits (266), Expect = 9e-29
Identities = 52/136 (38%), Positives = 78/136 (57%)
Query: 1 MLGGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFA 60
+L GAD++L E +YGRNLG+AFQ+ DD+LD + +GKP +DLK G T PVL A
Sbjct: 187 ILAGADEELLEALEDYGRNLGLAFQIQDDILDITGDEEELGKPVGSDLKEGKPTLPVLLA 246
Query: 61 CEKFPELNPMIMRRFQEPGDVEKAFEFVHKSQGLEQTKFLARKHCVEAVRLASGLAESPY 120
EK E ++ + G+VE+A E + KS +E K LA+ + +A L +S
Sbjct: 247 LEKANEDQKLLRILLEGGGEVEEALELLRKSGAIEYAKNLAKTYVEKAKEALEKLPDSEA 306
Query: 121 QKGLVVLTDLVLNRMK 136
++ L+ L D ++ R
Sbjct: 307 KEALLELADFIIKRKY 322
>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 = 92.6 bits (231), Expect = 5e-24
Identities = 41/134 (30%), Positives = 61/134 (45%), Gaps = 36/134 (26%)
Query: 1 MLGGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFA 60
+L GAD++ +E +GRNLG+AFQ+ DD+LD + +GKP +DL+ G T PVL A
Sbjct: 162 LLAGADEEEAEALKRFGRNLGLAFQIQDDILDLFGDPETLGKPVGSDLREGKCTLPVLLA 221
Query: 61 CEKFPELNPMIMRRFQEPGDVEKAFEFVHKSQGLEQTKFLARKHCVEAVRLASGLAESPY 120
+ LAR++ +A+ L ESP
Sbjct: 222 LRE------------------------------------LAREYEEKALEALKALPESPA 245
Query: 121 QKGLVVLTDLVLNR 134
++ L L D +L R
Sbjct: 246 REALRALADFILER 259
>gnl|CDD|215873 pfam00348, polyprenyl_synt, Polyprenyl synthetase.
Length = 260
Score = 72.3 bits (178), Expect = 3e-16
Identities = 36/99 (36%), Positives = 56/99 (56%), Gaps = 6/99 (6%)
Query: 2 LGGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFAC 61
+ GAD++ + +++GR+LG+AFQ+ DD+LD ++ +GKP DL+ G +T PVL A
Sbjct: 160 VAGADEEDEKDLYDFGRDLGLAFQIQDDILDLTGDTEELGKPVGTDLQEGKSTLPVLLAL 219
Query: 62 EKFPELNPMIMRRFQEPGDVEKAFEFVHKSQGLEQTKFL 100
E E ++R E E A +QG+ TK L
Sbjct: 220 EGAREEQRKLLREAYEQKLSEAA------AQGVALTKAL 252
>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 = 66.6 bits (163), Expect = 2e-14
Identities = 30/64 (46%), Positives = 41/64 (64%), Gaps = 1/64 (1%)
Query: 1 MLGGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFA 60
L GADD+ +E +YGR LG+AFQL DDLLD ++ +GK +DL+ G T PV+ A
Sbjct: 139 GLSGADDEQAEALKDYGRALGLAFQLTDDLLDVFGDAEELGK-VGSDLREGRITLPVILA 197
Query: 61 CEKF 64
E+
Sbjct: 198 RERA 201
>gnl|CDD|182813 PRK10888, PRK10888, octaprenyl diphosphate synthase; Provisional.
Length = 323
Score = 67.2 bits (164), Expect = 3e-14
Identities = 44/139 (31%), Positives = 70/139 (50%), Gaps = 6/139 (4%)
Query: 1 MLGGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFA 60
+L G + + +YGR LG AFQL+DDLLD+ + + +GK DL G T P+L A
Sbjct: 184 ILAGCTPEQEKGLQDYGRYLGTAFQLIDDLLDYSADGETLGKNVGDDLNEGKPTLPLLHA 243
Query: 61 CEK-FPELNPMIMRRFQEPGD----VEKAFEFVHKSQGLEQTKFLARKHCVEAVRLASGL 115
PE MI R E G+ +E E ++ LE T+ A + +A+ L
Sbjct: 244 MHHGTPEQAAMI-RTAIEQGNGRHLLEPVLEAMNACGSLEWTRQRAEEEADKAIAALQVL 302
Query: 116 AESPYQKGLVVLTDLVLNR 134
++P+++ L+ L + + R
Sbjct: 303 PDTPWREALIGLAHIAVQR 321
>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 = 67.4 bits (165), Expect = 3e-14
Identities = 36/128 (28%), Positives = 69/128 (53%), Gaps = 11/128 (8%)
Query: 3 GGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACE 62
GA++ + + + +G +G+++Q+ DD+LDF+ + + +GKP DL G T PVL+A E
Sbjct: 185 SGANEAIVKKLYWFGYYVGMSYQITDDILDFVGTEEELGKPAGGDLLQGNVTLPVLYAME 244
Query: 63 KFPELNPMIMRRFQEPG------DVEKAFEFVHKSQGLEQTKFLARKHCVEAVRLASGLA 116
+P + +R ++ ++E E V KS +E ++ ++ +A+ L GL
Sbjct: 245 -----DPFLKKRIEQVLEETTAEEMEPLIEEVKKSDAIEYAYAVSDRYLKKALELLDGLP 299
Query: 117 ESPYQKGL 124
+ +K L
Sbjct: 300 DGRAKKPL 307
>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 = 51.7 bits (124), Expect = 8e-09
Identities = 34/119 (28%), Positives = 48/119 (40%), Gaps = 24/119 (20%)
Query: 1 MLGGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFA 60
L G + +L E + GR LG+AFQL +DLLD+ ++ G T PVL+A
Sbjct: 133 GLSGGEAELLEALRKLGRALGLAFQLTNDLLDYEGDAERGE---------GKCTLPVLYA 183
Query: 61 CEKFPELNPMIMRRFQEPGDVEKAFEFVHKSQGLEQTKFLARKHCVEAVRLASGLAESP 119
E G + V KS LE+ K EA++ + L S
Sbjct: 184 LEY---------------GVPAEDLLLVEKSGSLEEALEELAKLAEEALKELNELILSL 227
>gnl|CDD|182567 PRK10581, PRK10581, geranyltranstransferase; Provisional.
Length = 299
Score = 44.4 bits (105), Expect = 3e-06
Identities = 31/122 (25%), Positives = 47/122 (38%), Gaps = 34/122 (27%)
Query: 16 YGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACEKFPELNPMIMRRF 75
Y ++G+AFQ+ DD+LD + + +GK AD +LG +T P L
Sbjct: 211 YAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKSTYPALL---------------- 254
Query: 76 QEPGDVEKAFEFVHKSQGLEQTKFLARKHCVEAVRLASGLAESPYQKG-LVVLTDLVLNR 134
GLEQ + AR +A + LA L L + ++ R
Sbjct: 255 -----------------GLEQARKKARDLIDDARQSLDQLAAQSLDTSALEALANYIIQR 297
Query: 135 MK 136
K
Sbjct: 298 DK 299
>gnl|CDD|214396 CHL00206, ycf2, Ycf2; Provisional.
Length = 2281
Score = 30.3 bits (68), Expect = 0.37
Identities = 15/44 (34%), Positives = 20/44 (45%), Gaps = 1/44 (2%)
Query: 62 EKFPELNPMIMRRFQEPGDV-EKAFEFVHKSQGLEQTKFLARKH 104
E+F E+ + EP V K F F S GL+Q +FL
Sbjct: 612 ERFQEMADLFTLSITEPDLVYHKGFAFSIDSYGLDQKQFLNEVF 655
>gnl|CDD|222241 pfam13583, Reprolysin_4, Metallo-peptidase family M12B
Reprolysin-like. This zinc-binding metallo-peptidase
has the characteristic binding motif HExxGHxxGxxH of
Reprolysin-like peptidases of family M12B.
Length = 195
Score = 28.5 bits (64), Expect = 1.0
Identities = 11/22 (50%), Positives = 16/22 (72%), Gaps = 3/22 (13%)
Query: 8 KLSEVAFEYGRNLGIAFQLVDD 29
+L+EV YGRN+GI+ L+ D
Sbjct: 36 RLNEV---YGRNVGISLTLIGD 54
>gnl|CDD|227544 COG5219, COG5219, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 1525
Score = 28.1 bits (62), Expect = 1.6
Identities = 27/126 (21%), Positives = 39/126 (30%), Gaps = 17/126 (13%)
Query: 11 EVAFEYGRNLGI-AFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACEKFPELNP 69
E F +LG+ +F+ D L+ S P A L P +F
Sbjct: 1044 EKVFSLSGDLGLPSFRCSDRKLE-QSVLLERIGPRAILYVLRKHNVP-----PQFVASVS 1097
Query: 70 MIMRRFQEPGDVEK----AFEFVHKSQGLEQTKFLARKHCVEAVRLASGL----AESPYQ 121
I E D F F H S + + L+R ++ G ES Y
Sbjct: 1098 DIKDCIVESNDSMNYLLLKFLFTHFSY--LRNEALSRAVSQLLLKCRKGFPIKFVESQYF 1155
Query: 122 KGLVVL 127
+G
Sbjct: 1156 EGFPEF 1161
>gnl|CDD|201944 pfam01735, PLA2_B, Lysophospholipase catalytic domain. This family
consists of Lysophospholipase / phospholipase B
EC:3.1.1.5 and cytosolic phospholipase A2 EC:3.1.4 which
also has a C2 domain pfam00168. Phospholipase B enzymes
catalyze the release of fatty acids from
lysophsopholipids and are capable in vitro of
hydrolysing all phospholipids extractable form yeast
cells. Cytosolic phospholipase A2 associates with
natural membranes in response to physiological increases
in Ca2+ and selectively hydrolyses arachidonyl
phospholipids, the aligned region corresponds the the
carboxy-terminal Ca2+-independent catalytic domain of
the protein as discussed in.
Length = 490
Score = 26.9 bits (60), Expect = 3.4
Identities = 17/60 (28%), Positives = 22/60 (36%), Gaps = 14/60 (23%)
Query: 3 GGADDKLSEVAFEYGRNLGIAFQLVDDLLDFISSSDAMGKPTAADLKLGLATAPVLFACE 62
G + E FE + G AF V D F++ LGL T P F C+
Sbjct: 341 GSSLVDTYERQFEPLQVKGKAFPYVPDQNTFVN--------------LGLNTRPTFFGCD 386
>gnl|CDD|132263 TIGR03219, salicylate_mono, salicylate 1-monooxygenase. Members of
this protein family are salicylate 1-monooxygenase, also
called salicylate hydroxylase. This enzyme converts
salicylate to catechol, which is a common intermediate
in the degradation of a number of aromatic compounds
(phenol, toluene, benzoate, etc.). The gene for this
protein may occur in catechol degradation genes, such as
those of the meta-cleavage pathway.
Length = 414
Score = 27.1 bits (60), Expect = 3.8
Identities = 22/62 (35%), Positives = 25/62 (40%), Gaps = 5/62 (8%)
Query: 45 AADLKLGLATAPVLFACEKFPELNPMIMRRFQEPGDVEKAFEFVHK----SQGLEQTKFL 100
AA L AP L+A EL + R GD A H+ QGLE FL
Sbjct: 272 AARALLECIPAPTLWALHDLAELPGYVHGRVALIGDAAHAM-LPHQGAGAGQGLEDAYFL 330
Query: 101 AR 102
AR
Sbjct: 331 AR 332
>gnl|CDD|233595 TIGR01845, outer_NodT, efflux transporter, outer membrane factor
(OMF) lipoprotein, NodT family. Members of This model
comprise a subfamily of the Outer Membrane Factor (TCDB
1.B.17) porins. OMF proteins operate in conjunction with
a primary transporter of the RND, MFS, ABC, or PET
systems, and a MFP (membrane fusion protein) to tranport
substrates across membranes. The complex thus formed
allows transport (export) of various solutes (heavy
metal cations; drugs, oligosaccharides, proteins, etc.)
across the two envelopes of the Gram-negative bacterial
cell envelope in a single energy-coupled step. Current
data suggest that the OMF (and not the MFP) is largely
responsible for the formation of both the trans-outer
membrane and trans-periplasmic channels. The roles
played by the MFP have yet to be determined [Cellular
processes, Detoxification, Transport and binding
proteins, Porins].
Length = 454
Score = 26.2 bits (58), Expect = 6.2
Identities = 11/43 (25%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 88 VHKSQGLEQTKFLARKHCVEAVRLASGLAESPYQKGLVVLTDL 130
+ Q L + A++ VE + A LA++ Y+ GL +
Sbjct: 378 LVALQALARR-LDAQRQAVEQAQEALSLAQTRYRAGLDSYLTV 419
>gnl|CDD|215193 PLN02337, PLN02337, lipoxygenase.
Length = 866
Score = 26.2 bits (58), Expect = 6.4
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 59 FACEKFPELNPMIMRRFQE 77
FA E +NP+++RR E
Sbjct: 368 FAREMLAGVNPVVIRRLTE 386
>gnl|CDD|217376 pfam03122, Herpes_MCP, Herpes virus major capsid protein. This
family represents the major capsid protein (MCP) of
herpes viruses. The capsid shell consists of 150 MCP
hexamers and 12 MCP pentamers. One pentamer is found at
each of the 12 apices of the icosahedral shell, and the
hexamers form the edges and 20 faces.
Length = 1352
Score = 26.0 bits (58), Expect = 8.1
Identities = 13/23 (56%), Positives = 15/23 (65%), Gaps = 3/23 (13%)
Query: 48 LKLGLATAPVLFACEKFPELNPM 70
L+ GLA A V C KFP+LN M
Sbjct: 57 LETGLAVACV---CTKFPDLNYM 76
>gnl|CDD|130405 TIGR01338, phycocy_alpha, phycocyanin, alpha subunit. This model
describes the phycocyanin alpha subunit. Other,
homologous phyobiliproteins of the phycobilisome include
phycocyanin alpha chain and the allophycocyanin and
phycoerythrin alpha and beta chains. This model excludes
the closely related phycoerythrocyanin alpha subunit
[Energy metabolism, Photosynthesis].
Length = 161
Score = 25.7 bits (56), Expect = 8.4
Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 5/50 (10%)
Query: 74 RFQEPGDVEKAF-EFVHKSQGLEQTKFLARKHCVEAVRLASGLAESPYQK 122
RF G+++ F F + LE K L A RL SG A++ Y K
Sbjct: 16 RFLSNGELQSIFGRFQRATASLEAAKSLTSN----AQRLISGAAQAVYSK 61
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
0.321 0.138 0.392
Gapped
Lambda K H
0.267 0.0684 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,985,607
Number of extensions: 627011
Number of successful extensions: 573
Number of sequences better than 10.0: 1
Number of HSP's gapped: 571
Number of HSP's successfully gapped: 30
Length of query: 136
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 49
Effective length of database: 7,078,804
Effective search space: 346861396
Effective search space used: 346861396
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 (21.9 bits)
S2: 54 (24.7 bits)