RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3887
(250 letters)
>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 = 41.3 bits (97), Expect = 2e-04
Identities = 25/72 (34%), Positives = 35/72 (48%), Gaps = 2/72 (2%)
Query: 154 IALKVG-LSLYESSLLLSRPLSGIALSQIAEQLLELHRGQGMEIYWRDNYTCPSEEEYRT 212
A+ G L L ++ L+R S AL +AE LL+L GQ +++ WR Y P+ EEY
Sbjct: 56 EAILAGDLLLADAFEELAREGSPEALEILAEALLDLLEGQLLDLKWRREY-VPTLEEYLE 114
Query: 213 MTIRTVGRSVGY 224
VG
Sbjct: 115 YCRYKTAGLVGA 126
>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 = 40.8 bits (96), Expect = 2e-04
Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 1/57 (1%)
Query: 168 LLSRPLSGIALSQIAEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRTVGRSVGY 224
LL+R AL AE L EL GQ +++ + + T + +EY VG
Sbjct: 77 LLARLGYPRALELFAEALRELLEGQALDLEFERD-TYETLDEYLEYCRYKTAGLVGL 132
>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 = 39.1 bits (92), Expect = 0.001
Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 1/48 (2%)
Query: 169 LSRPLSGIALSQIAEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIR 216
L P AL +E +LEL GQ +++ + T +EEEY +
Sbjct: 101 LGNPYYPRALELFSEAILELVEGQLLDLLSEYD-TDVTEEEYLRIIRL 147
>gnl|CDD|177516 PHA03070, PHA03070, DNA-binding virion core protein; Provisional.
Length = 249
Score = 30.8 bits (70), Expect = 0.56
Identities = 18/43 (41%), Positives = 23/43 (53%), Gaps = 9/43 (20%)
Query: 16 VHSPHRVDAVNRRGFVEAVYGFSHRLCLRVDTALQSDKTFEKY 58
VHSP +N AVYGF+++ LR L SDK E+Y
Sbjct: 184 VHSPSASLTLN------AVYGFTNKNELRK---LSSDKELEEY 217
>gnl|CDD|184408 PRK13937, PRK13937, phosphoheptose isomerase; Provisional.
Length = 188
Score = 30.2 bits (69), Expect = 0.65
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 136 INRFKKYRRPLSGIALS 152
+ RFKK R L IAL+
Sbjct: 61 VGRFKKERPALPAIALT 77
>gnl|CDD|146906 pfam04498, Pox_VP8_L4R, Poxvirus nucleic acid binding protein
VP8/L4R. The 25 kDa product of Vaccinia virus gene L4R
is also known as VP8. VP8 is found in the cores of
Vaccinia virions and is essential for the formation of
transcriptionally competent viral particles. It binds
both single stranded and double stranded DNA and RNA
with similar affinities. Binding is thought to involve
cooperative interactions between protein subunits. The
protein is proteolytically cleaved during viral assembly
at an Ala-Gly-Ala site. Possible roles for VP8 include
packaging and maintaining the DNA genome in a
transcribable configuration; binding ssDNA during
transcription initiation; and cooperation with I8R
protein to unwind early promoter regions. VP8 may also
function in either transcription elongation or release
of mRNA molecules from viral particles.
Length = 218
Score = 28.9 bits (65), Expect = 1.7
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 9/43 (20%)
Query: 16 VHSPHRVDAVNRRGFVEAVYGFSHRLCLRVDTALQSDKTFEKY 58
VHSP V ++ AVYGF+ + L+ L ++K E Y
Sbjct: 153 VHSPSAVLTLS------AVYGFTSKNELK---KLSTNKELENY 186
>gnl|CDD|133228 cd05097, PTKc_DDR_like, Catalytic domain of Discoidin Domain
Receptor-like Protein Tyrosine Kinases. Protein
Tyrosine Kinase (PTK) family; Discoidin Domain Receptor
(DDR)-like proteins; catalytic (c) domain. The PTKc
family is part of a larger superfamily that includes the
catalytic domains of other kinases such as protein
serine/threonine kinases, RIO kinases, and
phosphoinositide 3-kinase (PI3K). PTKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
tyrosine (tyr) residues in protein substrates. DDR-like
proteins are members of the DDR subfamily, which are
receptor tyr kinases (RTKs) containing an extracellular
discoidin homology domain, a transmembrane segment, an
extended juxtamembrane region, and an intracellular
catalytic domain. The binding of the ligand, collagen,
to DDRs results in a slow but sustained receptor
activation. DDRs regulate cell adhesion, proliferation,
and extracellular matrix remodeling. They have been
linked to a variety of human cancers including breast,
colon, ovarian, brain, and lung. There is no evidence
showing that DDRs act as transforming oncogenes. They
are more likely to play a role in the regulation of
tumor growth and metastasis.
Length = 295
Score = 29.2 bits (65), Expect = 2.0
Identities = 17/49 (34%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 159 GLSLYES-SLLLSRPLSGIALSQIAEQLLELHRGQGMEIYWRDNYTCPS 206
G++L+E +L +P S ++ Q+ E E R QG +IY CPS
Sbjct: 218 GVTLWEMFTLCKEQPYSLLSDEQVIENTGEFFRNQGRQIYLSQTPLCPS 266
>gnl|CDD|163431 TIGR03719, ABC_ABC_ChvD, ATP-binding cassette protein, ChvD family.
Members of this protein family have two copies of the
ABC transporter ATP-binding cassette, but are found
outside the common ABC transporter operon structure that
features integral membrane permease proteins and
substrate-binding proteins encoded next to the
ATP-binding cassette (ABC domain) protein. The member
protein ChvD from Agrobacterium tumefaciens was
identified as both a candidate to interact with VirB8,
based on yeast two-hybrid analysis, and as an apparent
regulator of VirG. The general function of this protein
family is unknown.
Length = 552
Score = 28.4 bits (64), Expect = 4.0
Identities = 12/26 (46%), Positives = 16/26 (61%), Gaps = 2/26 (7%)
Query: 178 LSQIAEQLLELHRGQGMEIYWRDNYT 203
L +A +LEL RG+G I W NY+
Sbjct: 221 LDNVAGWILELDRGRG--IPWEGNYS 244
>gnl|CDD|237791 PRK14701, PRK14701, reverse gyrase; Provisional.
Length = 1638
Score = 28.3 bits (63), Expect = 4.5
Identities = 21/71 (29%), Positives = 31/71 (43%), Gaps = 3/71 (4%)
Query: 29 GFVEAVY-GFS--HRLCLRVDTALQSDKTFEKYRERILEPNASLLRSGDLAKVHISIVIN 85
G+VE G+S + L LRV L+ K + P L GD+ + I
Sbjct: 1494 GYVEIEGDGWSRLYSLPLRVLPKLEKGKLKVLEAKIRKAPKVPLYTQGDIVALMKERGIG 1553
Query: 86 RPTTIMRLVRT 96
RP+T ++V T
Sbjct: 1554 RPSTYAKIVDT 1564
>gnl|CDD|236247 PRK08345, PRK08345, cytochrome-c3 hydrogenase subunit gamma;
Provisional.
Length = 289
Score = 27.8 bits (62), Expect = 5.8
Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 4/37 (10%)
Query: 111 FQSHRAGKMR----TDGIFLFLLRLLDPEINRFKKYR 143
+ H A + T+ LFLLR DPE+ ++
Sbjct: 3 YALHDAKILEVYDLTEREKLFLLRFEDPELAESFTFK 39
>gnl|CDD|182754 PRK10815, PRK10815, sensor protein PhoQ; Provisional.
Length = 485
Score = 27.7 bits (62), Expect = 6.5
Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 128 LLRLLDPEINRFKKYRRPLSGIALSQIALKVGLSLYESSLLLSRPLSGIALSQIAEQLLE 187
L RLL E R+ KYR L+ + S LK L++ +S+L R +++ Q +LE
Sbjct: 252 LNRLLKNERERYTKYRTTLTDLTHS---LKTPLAVLQSTLRSLRSGKQMSVEQAEPIMLE 308
>gnl|CDD|223356 COG0279, GmhA, Phosphoheptose isomerase [Carbohydrate transport and
metabolism].
Length = 176
Score = 26.9 bits (60), Expect = 7.4
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 136 INRFKKYRRPLSGIALS 152
RF+K R L IALS
Sbjct: 64 TGRFEKERPSLPAIALS 80
>gnl|CDD|173837 cd00868, Terpene_cyclase_C1, Terpene cyclases, Class 1. Terpene
cyclases, Class 1 (C1) of the class 1 family of
isoprenoid biosynthesis enzymes, which share the
'isoprenoid synthase fold' and convert linear,
all-trans, isoprenoids, geranyl (C10)-, farnesyl (C15)-,
or geranylgeranyl (C20)-diphosphate into numerous cyclic
forms of monoterpenes, diterpenes, and sesquiterpenes.
Also included in this CD are the cis-trans terpene
cyclases such as trichodiene synthase. 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. Mechanistically and
structurally distinct, class II terpene cyclases and
cis-IPPS are not included in this CD. Taxonomic
distribution includes bacteria, fungi and plants.
Length = 284
Score = 27.3 bits (61), Expect = 7.6
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 4/47 (8%)
Query: 181 IAEQLLELHRGQGMEIYWRDNYTCPSEEEYRTMTIRTVGRSVGYPTI 227
+ E +L R +E W + PS EEY + R V S+GYP +
Sbjct: 127 LKEAWKDLLRAYLVEAKWANEGYVPSFEEY--LENRRV--SIGYPPL 169
>gnl|CDD|236992 PRK11819, PRK11819, putative ABC transporter ATP-binding protein;
Reviewed.
Length = 556
Score = 27.4 bits (62), Expect = 8.9
Identities = 12/26 (46%), Positives = 16/26 (61%), Gaps = 2/26 (7%)
Query: 178 LSQIAEQLLELHRGQGMEIYWRDNYT 203
L +A +LEL RG+G I W NY+
Sbjct: 223 LDNVAGWILELDRGRG--IPWEGNYS 246
>gnl|CDD|218467 pfam05147, LANC_like, Lanthionine synthetase C-like protein.
Lanthionines are thioether bridges that are putatively
generated by dehydration of Ser and Thr residues
followed by addition of cysteine residues within the
peptide. This family contains the lanthionine synthetase
C-like proteins 1 and 2 which are related to the
bacterial lanthionine synthetase components C (LanC).
LANCL1 (P40 seven-transmembrane-domain protein) and
LANCL2 (testes-specific adriamycin sensitivity protein)
are thought to be peptide-modifying enzyme components in
eukaryotic cells. Both proteins are produced in large
quantities in the brain and testes and may have role in
the immune surveillance of these organs. Lanthionines
are found in lantibiotics, which are peptide-derived,
post-translationally modified antimicrobials produced by
several bacterial strains. This region contains seven
internal repeats.
Length = 352
Score = 27.0 bits (60), Expect = 9.9
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 123 GIFLFLLRLLDPEINRFKKY 142
GI FLL LL+PE +RF
Sbjct: 331 GILYFLLDLLNPEESRFPSA 350
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 0.137 0.399
Gapped
Lambda K H
0.267 0.0707 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,742,017
Number of extensions: 1208715
Number of successful extensions: 950
Number of sequences better than 10.0: 1
Number of HSP's gapped: 948
Number of HSP's successfully gapped: 20
Length of query: 250
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 155
Effective length of database: 6,723,972
Effective search space: 1042215660
Effective search space used: 1042215660
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: 58 (26.2 bits)