RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3877
(145 letters)
>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 = 64.1 bits (157), Expect = 4e-13
Identities = 21/104 (20%), Positives = 41/104 (39%), Gaps = 14/104 (13%)
Query: 1 MMAIRLMQLFSDTKSDFTTLAGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFP 60
+ A+ L + LGL FQ++DD +L + K DL EGK + P
Sbjct: 159 LGAL-LAGADEEEAEALKRFGRNLGLAFQIQDDILDLFGDPETLGKPVGSDLREGKCTLP 217
Query: 61 IIHAIQSRPDDRQVIQILRQRTR-------DVEVKKYCISLLDR 97
++ A+ R++ + ++ + ++ +L D
Sbjct: 218 VLLAL------RELAREYEEKALEALKALPESPAREALRALADF 255
>gnl|CDD|215873 pfam00348, polyprenyl_synt, Polyprenyl synthetase.
Length = 260
Score = 60.8 bits (148), Expect = 5e-12
Identities = 20/87 (22%), Positives = 39/87 (44%), Gaps = 3/87 (3%)
Query: 23 ILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPDDRQVIQILRQRT 82
LGL FQ++DD +L K DL EGK + P++ A++ R+ + L +
Sbjct: 177 DLGLAFQIQDDILDLTGDTEELGKPVGTDLQEGKSTLPVLLALEG---AREEQRKLLREA 233
Query: 83 RDVEVKKYCISLLDRFGSFEHTREVLK 109
+ ++ + + + E E ++
Sbjct: 234 YEQKLSEAAAQGVALTKALEALAEYIE 260
>gnl|CDD|223220 COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme
metabolism].
Length = 322
Score = 61.2 bits (149), Expect = 6e-12
Identities = 30/116 (25%), Positives = 60/116 (51%), Gaps = 6/116 (5%)
Query: 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPDDRQVIQILRQRTR 83
LGL FQ++DD ++ E K DL EGK + P++ A++ +D+++++IL +
Sbjct: 206 LGLAFQIQDDILDITGDEEELGKPVGSDLKEGKPTLPVLLALEKANEDQKLLRILLEGGG 265
Query: 84 DVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNP---LLEAILDELL 136
+VE + LL + G+ E+ + + K A+ + +L + L + D ++
Sbjct: 266 EVEE---ALELLRKSGAIEYAKNLAKTYVEKAKEALEKLPDSEAKEALLELADFII 318
>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 = 47.1 bits (112), Expect = 6e-07
Identities = 30/110 (27%), Positives = 52/110 (47%), Gaps = 3/110 (2%)
Query: 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPDDRQVIQILRQRTR 83
LGL FQV DD + K DL +G + P++ A++ P ++I+ +
Sbjct: 206 LGLAFQVVDDILDFTGSTEQLGKPAGSDLMKGNLTAPVLFALEEEPKLSELIEREFSQKG 265
Query: 84 DVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAILD 133
D+E +SL+ + G + RE+ KE A ++ L +P EA+ +
Sbjct: 266 DLE---QALSLVRKSGGIKKARELAKEQAQLALQSLSFLPPSPPREALKE 312
>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 = 45.0 bits (107), Expect = 2e-06
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQ 66
LGL FQ+ DD ++ K DL EG+ + P+I A +
Sbjct: 158 LGLAFQLTDDLLDVFGDAEELGK-VGSDLREGRITLPVILARE 199
>gnl|CDD|164542 CHL00151, preA, prenyl transferase; Reviewed.
Length = 323
Score = 42.1 bits (99), Expect = 3e-05
Identities = 26/111 (23%), Positives = 46/111 (41%), Gaps = 7/111 (6%)
Query: 9 LFSDTK----SDFTTLAGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHA 64
L SD +DF LGL FQ+ DD ++ S S K DL G + P++ A
Sbjct: 188 LLSDADEKDHNDFYLYGKHLGLAFQIIDDVLDITSSTESLGKPIGSDLKNGNLTAPVLFA 247
Query: 65 IQSRPDDRQVIQILRQRTRDVEVKKYCISLLDRFGSFEHTREVLKELDVSA 115
+ ++I+ T+D+ + ++ E +++ E +A
Sbjct: 248 LTQNSKLAKLIEREFCETKDIS---QALQIIKETNGIEKAKDLALEHMQAA 295
>gnl|CDD|215462 PLN02857, PLN02857, octaprenyl-diphosphate synthase.
Length = 416
Score = 38.3 bits (89), Expect = 6e-04
Identities = 26/87 (29%), Positives = 41/87 (47%), Gaps = 3/87 (3%)
Query: 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPDDRQVIQILRQRTR 83
LGL FQV DD + K DL +G + P+I A++ P+ R++I+
Sbjct: 300 LGLAFQVVDDILDFTQSTEQLGKPAGSDLAKGNLTAPVIFALEKEPELREIIESEFCEEG 359
Query: 84 DVEVKKYCISLLDRFGSFEHTREVLKE 110
+E I L++ G E +E+ KE
Sbjct: 360 SLEE---AIELVNEGGGIERAQELAKE 383
>gnl|CDD|182813 PRK10888, PRK10888, octaprenyl diphosphate synthase; Provisional.
Length = 323
Score = 36.0 bits (83), Expect = 0.004
Identities = 28/109 (25%), Positives = 52/109 (47%), Gaps = 1/109 (0%)
Query: 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQ-SRPDDRQVIQILRQRT 82
LG FQ+ DD + + + K+ +DL EGK + P++HA+ P+ +I+ ++
Sbjct: 203 LGTAFQLIDDLLDYSADGETLGKNVGDDLNEGKPTLPLLHAMHHGTPEQAAMIRTAIEQG 262
Query: 83 RDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAI 131
+ + + ++ GS E TR+ +E A + L P EA+
Sbjct: 263 NGRHLLEPVLEAMNACGSLEWTRQRAEEEADKAIAALQVLPDTPWREAL 311
>gnl|CDD|178478 PLN02890, PLN02890, geranyl diphosphate synthase.
Length = 422
Score = 34.5 bits (79), Expect = 0.012
Identities = 23/87 (26%), Positives = 40/87 (45%), Gaps = 3/87 (3%)
Query: 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPDDRQVIQILRQRTR 83
LGL FQ+ DD + S K D+ G + PI+ A++ P R+V+
Sbjct: 300 LGLAFQLIDDVLDFTGTSASLGKGSLSDIRHGVITAPILFAMEEFPQLREVVDRGFDNPA 359
Query: 84 DVEVKKYCISLLDRFGSFEHTREVLKE 110
+V++ + L + + TRE+ +E
Sbjct: 360 NVDI---ALEYLGKSRGIQRTRELARE 383
>gnl|CDD|239332 cd03034, ArsC_ArsC, Arsenate Reductase (ArsC) family, ArsC
subfamily; arsenic reductases similar to that encoded by
arsC on the R733 plasmid of Escherichia coli. E. coli
ArsC catalyzes the reduction of arsenate [As(V)] to
arsenite [As(III)], the first step in the detoxification
of arsenic, using reducing equivalents derived from
glutathione (GSH) via glutaredoxin (GRX). ArsC contains
a single catalytic cysteine, within a thioredoxin fold,
that forms a covalent thiolate-As(V) intermediate, which
is reduced by GRX through a mixed GSH-arsenate
intermediate. This family of predominantly bacterial
enzymes is unrelated to two other families of arsenate
reductases which show similarity to low-molecular-weight
acid phosphatases and phosphotyrosyl phosphatases.
Length = 112
Score = 31.4 bits (72), Expect = 0.061
Identities = 15/63 (23%), Positives = 28/63 (44%), Gaps = 5/63 (7%)
Query: 72 RQVIQILRQRTRDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAI 131
R + +L + + E+ +Y L + RE+L +L +S R ++ R P E
Sbjct: 13 RNALALLEEAGIEPEIVEY----LKTPPTAAELRELLAKLGISPR-DLLRTKEAPYKELG 67
Query: 132 LDE 134
L +
Sbjct: 68 LAD 70
>gnl|CDD|197253 cd09156, PLDc_CLS_unchar1_1, Putative catalytic domain, repeat 1,
of uncharacterized proteins similar to bacterial
cardiolipin synthase. Putative catalytic domain, repeat
1, of uncharacterized proteins similar to bacterial
cardiolipin (CL) synthases, which catalyze the
reversible phosphatidyl group transfer between two
phosphatidylglycerol molecules to form CL and glycerol.
Members of this subfamily contain two HKD motifs
(H-x-K-x(4)-D, where x represents any amino acid
residue) that characterizes the phospholipase D (PLD)
superfamily. The two motifs may be part of the active
site and may be involved in phosphatidyl group transfer.
Length = 154
Score = 31.5 bits (72), Expect = 0.093
Identities = 18/41 (43%), Positives = 25/41 (60%), Gaps = 5/41 (12%)
Query: 72 RQVIQILRQRTRD-VEVKKYCISLLDRFGSFEHTREVLKEL 111
R+VI L ++ R+ VEV+ LLD GSF +R LK+L
Sbjct: 35 RRVIDALARKAREGVEVR----LLLDALGSFFLSRRALKKL 71
>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 = 31.3 bits (71), Expect = 0.13
Identities = 19/95 (20%), Positives = 37/95 (38%), Gaps = 23/95 (24%)
Query: 20 LAGILGLYFQVRDDYCNLCSKEYSENKSFCEDL--TEGKFSFPIIHAIQSRPDDRQVIQI 77
L LGL FQ+ +D + D EGK + P+++A++ ++ +
Sbjct: 148 LGRALGLAFQLTNDL-----------LDYEGDAERGEGKCTLPVLYALEYGVPAEDLLLV 196
Query: 78 LRQRTRDVEVKKYCISLLDRFGSFEHTREVLKELD 112
+ + + + L + E LKEL+
Sbjct: 197 EKSGSLE-----EALEELA-----KLAEEALKELN 221
>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 = 30.5 bits (69), Expect = 0.28
Identities = 14/61 (22%), Positives = 32/61 (52%)
Query: 24 LGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPDDRQVIQILRQRTR 83
+G+ +Q+ DD + E K DL +G + P+++A++ +++ Q+L + T
Sbjct: 202 VGMSYQITDDILDFVGTEEELGKPAGGDLLQGNVTLPVLYAMEDPFLKKRIEQVLEETTA 261
Query: 84 D 84
+
Sbjct: 262 E 262
>gnl|CDD|235166 PRK03837, PRK03837, transcriptional regulator NanR; Provisional.
Length = 241
Score = 30.0 bits (68), Expect = 0.36
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 110 ELDVSARTEVARLGGNPLLEAILDELLTW 138
D+ +A + GNP+ AI + LL W
Sbjct: 153 RSDMEFHRVIAEIPGNPIFMAIHEALLDW 181
>gnl|CDD|218191 pfam04652, DUF605, Vta1 like. Vta1 (VPS20-associated protein 1) is
a positive regulator of Vps4. Vps4 is an ATPase that is
required in the multivesicular body (MVB) sorting
pathway to dissociate the endosomal sorting complex
required for transport (ESCRT). Vta1 promotes correct
assembly of Vps4 and stimulates its ATPase activity
through its conserved Vta1/SBP1/LIP5 region.
Length = 315
Score = 30.0 bits (68), Expect = 0.38
Identities = 18/59 (30%), Positives = 23/59 (38%), Gaps = 20/59 (33%)
Query: 76 QILRQRTRDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAILDE 134
IL+ + +D EV K+ LLD E K LG N +AI DE
Sbjct: 31 LILKIKLKDGEVTKFLTKLLD-------QLEAFK----------KELGDN---DAITDE 69
>gnl|CDD|215525 PLN02972, PLN02972, Histidyl-tRNA synthetase.
Length = 763
Score = 29.1 bits (65), Expect = 1.0
Identities = 20/65 (30%), Positives = 28/65 (43%), Gaps = 2/65 (3%)
Query: 71 DRQVIQILRQRTRDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEA 130
D+Q + +++ VE K D+ G+F R EL R E + GN A
Sbjct: 511 DKQSFEQVKKEM--VEEKGLSNETADKIGNFVKERGPPLELLSKLRQEGSEFLGNASSRA 568
Query: 131 ILDEL 135
LDEL
Sbjct: 569 ALDEL 573
>gnl|CDD|217651 pfam03635, Vps35, Vacuolar protein sorting-associated protein 35.
Vacuolar protein sorting-associated protein (Vps) 35 is
one of around 50 proteins involved in protein
trafficking. In particular, Vps35 assembles into a
retromer complex with at least four other proteins Vps5,
Vps17, Vps26 and Vps29. Vps35 contains a central region
of weaker sequence similarity, thought to indicate the
presence of at least three domains.
Length = 741
Score = 28.7 bits (65), Expect = 1.3
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 84 DVEVKKYCISLLDRFGSFEHTREVLKELDVSARTE 118
V+VKK I+L+DR ++ R +V + E
Sbjct: 278 GVDVKKILITLMDRLAAY-AERSNEGVAEVESTKE 311
>gnl|CDD|180326 PRK05954, PRK05954, precorrin-8X methylmutase; Provisional.
Length = 203
Score = 28.1 bits (63), Expect = 1.6
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 4/47 (8%)
Query: 98 FGSFEHTREVLKELDV-SARTEVARLGGNPLLEAILDELLT--WDTP 141
F S ++ L +LDV R E R GG+P+ AI++ LL W
Sbjct: 158 FVSVVEAKQALAQLDVPQIRVE-GRKGGSPVAAAIVNALLILAWRDE 203
>gnl|CDD|224993 COG2082, CobH, Precorrin isomerase [Coenzyme metabolism].
Length = 210
Score = 27.3 bits (61), Expect = 2.4
Identities = 12/39 (30%), Positives = 20/39 (51%)
Query: 98 FGSFEHTREVLKELDVSARTEVARLGGNPLLEAILDELL 136
F ++E L+E + T R GG+P+ AI++ L
Sbjct: 165 FVGAAESKEALRESPIPYITVRGRRGGSPVAAAIVNALA 203
>gnl|CDD|234459 TIGR04082, rSAM_for_selen, selenobiotic family peptide radical SAM
maturase. Members of this protein family are radical
SAM (rSAM) enzymes similar in sequence to others with
known or postulated roles in peptide modification, and
regularly found adjacent to members of the GSU_1558
peptide family described by model TIGR04081. GSU_1558
and several other members of that family appear to be
selenoproteins, hence the term selenobiotic.
Length = 516
Score = 27.3 bits (61), Expect = 2.9
Identities = 17/44 (38%), Positives = 22/44 (50%), Gaps = 8/44 (18%)
Query: 92 ISLLDRFGSFEHTREVLKELDVSARTEVARLGGNPLLEAILDEL 135
+++LD F SF R V R +V+ GGNPLL EL
Sbjct: 231 LAVLDDFASFCRERNV--------RGQVSFSGGNPLLYPHFLEL 266
>gnl|CDD|224717 COG1804, CaiB, Predicted acyl-CoA transferases/carnitine
dehydratase [Energy production and conversion].
Length = 396
Score = 27.3 bits (61), Expect = 3.1
Identities = 11/21 (52%), Positives = 13/21 (61%), Gaps = 1/21 (4%)
Query: 102 EHTREVLKELDVSARTEVARL 122
EHT +L EL S R E+A L
Sbjct: 371 EHTEAILAELGYSER-EIAAL 390
>gnl|CDD|236212 PRK08270, PRK08270, anaerobic ribonucleoside triphosphate
reductase; Provisional.
Length = 656
Score = 27.1 bits (61), Expect = 3.4
Identities = 9/22 (40%), Positives = 13/22 (59%), Gaps = 5/22 (22%)
Query: 45 NKSFCEDLTEGK-----FSFPI 61
N++F E + EG F+FPI
Sbjct: 308 NRAFIEVMLEGDANGRVFTFPI 329
>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 = 26.8 bits (60), Expect = 4.4
Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 8/50 (16%)
Query: 61 IIHAIQSRPDDRQVIQILRQRTRDVEVKKYCISLLDRFGSFEHTREVLKE 110
IIHA R + V+ ILR+ V +C + G E +++L
Sbjct: 125 IIHA---RDAEEDVLDILREEKPKVGGVLHCFT-----GDAELAKKLLDL 166
>gnl|CDD|218187 pfam04637, Herpes_pp85, Herpesvirus phosphoprotein 85 (HHV6-7
U14/HCMV UL25). This family includes UL25 proteins from
HCMV, as well as U14 proteins from HHV 6 and HHV7. These
85 kD phosphoproteins appear to act as structural
antigens, but their precise function is otherwise
unknown.
Length = 502
Score = 27.0 bits (60), Expect = 4.7
Identities = 7/28 (25%), Positives = 12/28 (42%), Gaps = 3/28 (10%)
Query: 27 YFQV---RDDYCNLCSKEYSENKSFCED 51
Y QV R+ + +L + + S D
Sbjct: 261 YTQVPETRETFLDLAREVANMISSNSPD 288
>gnl|CDD|215613 PLN03174, PLN03174, Chalcone-flavanone isomerase-related;
Provisional.
Length = 278
Score = 26.4 bits (58), Expect = 6.1
Identities = 9/27 (33%), Positives = 13/27 (48%)
Query: 29 QVRDDYCNLCSKEYSENKSFCEDLTEG 55
+ + Y L + E NK F +DL E
Sbjct: 130 LLGEKYGKLSASELKGNKEFIDDLMEA 156
>gnl|CDD|219942 pfam08626, TRAPPC9-Trs120, Transport protein Trs120 or TRAPPC9,
TRAPP II complex subunit. This region is found at the N
terminal of Saccharomyces cerevisiae Trs120 protein.
Trs120 is a subunit of the multiprotein complex TRAPP
(transport particle protein) which functions in ER to
Golgi traffic. Trs120 is specific to the larger TRAPP
complex, TRAPP II, along with Trs65p and
Trs130p(TRAPPC10). It is suggested that Trs120p is
required for the stability of the Trs130p subunit,
suggesting that these two proteins might interact in
some way. It is likely that there is a complex function
for TRAPP II in multiple pathways.
Length = 1183
Score = 26.6 bits (58), Expect = 6.4
Identities = 13/61 (21%), Positives = 19/61 (31%)
Query: 59 FPIIHAIQSRPDDRQVIQILRQRTRDVEVKKYCISLLDRFGSFEHTREVLKELDVSARTE 118
P+ S D + I + YC+ LLD S++ E E
Sbjct: 925 LPLNSDSVSENSDSVISYITSIKADSKGSWDYCLLLLDFRNSWDEGLECNVSYSTFESNE 984
Query: 119 V 119
V
Sbjct: 985 V 985
>gnl|CDD|182567 PRK10581, PRK10581, geranyltranstransferase; Provisional.
Length = 299
Score = 26.3 bits (58), Expect = 6.5
Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 1/82 (1%)
Query: 21 AGILGLYFQVRDDYCNLCSKEYSENKSFCEDLTEGKFSFPIIHAI-QSRPDDRQVIQILR 79
A +GL FQV+DD ++ + K D GK ++P + + Q+R R +I R
Sbjct: 212 AESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKSTYPALLGLEQARKKARDLIDDAR 271
Query: 80 QRTRDVEVKKYCISLLDRFGSF 101
Q + + S L+ ++
Sbjct: 272 QSLDQLAAQSLDTSALEALANY 293
>gnl|CDD|215174 PLN02305, PLN02305, lipoxygenase.
Length = 918
Score = 26.4 bits (58), Expect = 7.2
Identities = 13/46 (28%), Positives = 19/46 (41%)
Query: 36 NLCSKEYSENKSFCEDLTEGKFSFPIIHAIQSRPDDRQVIQILRQR 81
NL KE+ + +G FP I SR D+ + I R +
Sbjct: 176 NLHGKEFYLMEIVIHGFDDGPIFFPANTWIHSRKDNPESRIIFRNQ 221
>gnl|CDD|236311 PRK08609, PRK08609, hypothetical protein; Provisional.
Length = 570
Score = 26.1 bits (58), Expect = 9.1
Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 4/54 (7%)
Query: 62 IHAIQSRPDDRQVIQILRQRTRDVEVKKYCISLLDRF---GSFEHTREVLKELD 112
+ + RP+ R I + +++E I + RF GS RE +K+LD
Sbjct: 143 VKELGKRPE-RLPIAQVLPIAQEIEEYLATIDEIIRFSRAGSLRRARETVKDLD 195
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
0.322 0.138 0.405
Gapped
Lambda K H
0.267 0.0790 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,486,822
Number of extensions: 670943
Number of successful extensions: 784
Number of sequences better than 10.0: 1
Number of HSP's gapped: 779
Number of HSP's successfully gapped: 49
Length of query: 145
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 57
Effective length of database: 7,034,450
Effective search space: 400963650
Effective search space used: 400963650
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 (24.5 bits)