RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6818
(162 letters)
>gnl|CDD|189650 pfam00645, zf-PARP, Poly(ADP-ribose) polymerase and DNA-Ligase
Zn-finger region. Poly(ADP-ribose) polymerase is an
important regulatory component of the cellular response
to DNA damage. The amino-terminal region of
Poly(ADP-ribose) polymerase consists of two PARP-type
zinc fingers. This region acts as a DNA nick sensor.
Length = 81
Score = 90.4 bits (225), Expect = 1e-24
Identities = 30/84 (35%), Positives = 45/84 (53%), Gaps = 3/84 (3%)
Query: 52 EYAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSCFNAVRLDLEFSA 111
EYAKS R++C+ C+ KIAKGE+R+ K+ G + +WYH CF RL +
Sbjct: 1 EYAKSGRASCKKCKEKIAKGELRIGKVVPSPFFD---GKMKKWYHWGCFTEKRLRNRATE 57
Query: 112 SGKQIPGFGSLEKKDQKIVEATLP 135
+ GF L +DQ+ ++ L
Sbjct: 58 DVDDLDGFEELRPEDQEKIKKALE 81
Score = 48.0 bits (115), Expect = 3e-08
Identities = 22/52 (42%), Positives = 28/52 (53%), Gaps = 6/52 (11%)
Query: 1 SPFFDGKTPKWFHEECFWKKNRPKALL-----DIHNVTSLRHQDQEMIKSKI 47
SPFFDGK KW+H CF +K R + D+ LR +DQE IK +
Sbjct: 30 SPFFDGKMKKWYHWGCFTEK-RLRNRATEDVDDLDGFEELRPEDQEKIKKAL 80
>gnl|CDD|215590 PLN03123, PLN03123, poly [ADP-ribose] polymerase; Provisional.
Length = 981
Score = 88.3 bits (219), Expect = 6e-21
Identities = 49/153 (32%), Positives = 71/153 (46%), Gaps = 32/153 (20%)
Query: 1 SPFFDGKTPKWFHEEC-FWKKNRPKALLDIHNVTSLRHQDQEMIKSKILG---------- 49
S FDG P W H C KKN+ K++ D+ + SLR +DQ+ I+ +
Sbjct: 40 STQFDGFMPMWNHASCILKKKNQIKSIDDVEGIDSLRWEDQQKIRKYVESGGTGTGTASD 99
Query: 50 --------NIEYAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSCFN 101
IE AK++R+TCR C KI KGE+R+S + K W+H CF
Sbjct: 100 AAASSFEYGIEVAKTSRATCRRCSEKILKGEVRISSK-PEGQGYKG----LAWHHAKCF- 153
Query: 102 AVRLDLEFSASG--KQIPGFGSLEKKDQKIVEA 132
LE S S +++ G+ +L DQ+ V
Sbjct: 154 -----LEMSPSTPVEKLSGWDTLSDSDQEAVLP 181
Score = 48.2 bits (115), Expect = 3e-07
Identities = 21/48 (43%), Positives = 31/48 (64%), Gaps = 3/48 (6%)
Query: 52 EYAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQGKMIGGIPEWYHLSC 99
EYAKS+RS+C+ C++ I K E+R+ KM + + G +P W H SC
Sbjct: 11 EYAKSSRSSCKTCKSPIDKDELRLGKMVQST---QFDGFMPMWNHASC 55
>gnl|CDD|221164 pfam11678, DUF3274, Protein of unknown function (DUF3274). This
bacterial family of proteins has no known function.
Length = 280
Score = 28.5 bits (64), Expect = 1.4
Identities = 12/43 (27%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 92 PEWYHLSCFNA-VRLDLEFSASGKQIPGFGSLEKKDQKIVEAT 133
P W L A R D + + ++P FG L + Q++++A+
Sbjct: 225 PVWRQLLIAMADWRTDKKQADKITELPDFGRLSPETQELIDAS 267
>gnl|CDD|212130 cd11665, LamB_like, Aspergillus nidulans lactam utilization protein
LamB and similar proteins. This eukaryotic and
bacterial subfamily of the LamB/YbgL family, includes
Aspergillus nidulans protein LamB. The lamb gene locates
at the lam locus of Aspergillus nidulans, consisting of
two divergently transcribed genes, lamA and lamB, needed
for the utilization of lactams such as 2-pyrrolidinone.
Both genes are under the control of the positive
regulatory gene amdR and are subject to carbon and
nitrogen metabolite repression. Although the exact
molecular function of lamb encoding protein LamB is
unknown, it might be required for conversion of
exogenous 2-pyrrolidinone to endogenous GABA.
Length = 238
Score = 26.9 bits (60), Expect = 4.3
Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 9/54 (16%)
Query: 91 IPEWYHLSCFNAVRLDLEFSASGKQIPGFGSLEKKDQKIVEATLPSLSDGVSKT 144
IPE+Y DL++ GK + ++I E +L+DG +
Sbjct: 157 IPEFY---------ADLDYDPDGKLVITREHKAIDPEEIAERVRRALTDGSVTS 201
>gnl|CDD|143537 cd07163, NR_DBD_TLX, DNA-binding domain of Tailless (TLX) is
composed of two C4-type zinc fingers. DNA-binding
domain of Tailless (TLX) is composed of two C4-type
zinc fingers. Each zinc finger contains a group of four
Cys residues which co-ordinates a single zinc atom. TLX
interacts with specific DNA sites upstream of the
target gene and modulates the rate of transcriptional
initiation. TLX is an orphan receptor that is
expressed by neural stem/progenitor cells in the adult
brain of the subventricular zone (SVZ) and the dentate
gyrus (DG). It plays a key role in neural development
by promoting cell cycle progression and preventing
apoptosis in the developing brain. Like other members
of the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, TLX has a
central well conserved DNA-binding domain (DBD), a
variable N-terminal domain, a flexible hinge and a
C-terminal ligand binding domain (LBD).
Length = 92
Score = 25.9 bits (57), Expect = 5.0
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 4/51 (7%)
Query: 34 SLRHQDQEMIKSKILGNIEYAKSNRSTCRGCEAKIAKGEIRVSKMNYDSDQ 84
S+R Q + KSK G K++R+ CR C K + MN D+ Q
Sbjct: 36 SIRRNRQYVCKSKGQGGCPVDKTHRNQCRACRLK----KCFEVGMNKDAVQ 82
>gnl|CDD|132736 cd06938, NR_LBD_EcR, The ligand binding domain (LBD) of the
Ecdysone receptor, a member of the nuclear receptors
super family. The ligand binding domain (LBD) of the
ecdysone receptor: The ecdysone receptor (EcR) belongs
to the superfamily of nuclear receptors (NRs) of
ligand-dependent transcription factors. Ecdysone
receptor is present only in invertebrates and regulates
the expression of a large number of genes during
development and reproduction. ECR functions as a
heterodimer by partnering with ultraspiracle protein
(USP), the ortholog of the vertebrate retinoid X
receptor (RXR). The natural ligands of ecdysone receptor
are ecdysteroids#the endogenous steroidal hormones found
in invertebrates. In addition, insecticide
bisacylhydrazine used against pests has shown to act on
EcR. EcR must be dimerised with a USP for high-affinity
ligand binding to occur. The ligand binding triggers a
conformational change in the C-terminal part of the EcR
ligand-binding domain that leads to transcriptional
activation of genes controlled by EcR. Like other
members of the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, ec dysone
receptors have a central well conserved DNA binding
domain (DBD), a variable N-terminal domain, a
non-conserved hinge and a C-terminal ligand binding
domain (LBD).
Length = 231
Score = 26.6 bits (59), Expect = 6.5
Identities = 11/25 (44%), Positives = 18/25 (72%), Gaps = 3/25 (12%)
Query: 103 VRLDLEFSASGKQIPGFGSLEKKDQ 127
V+L +EF+ K++PGF L ++DQ
Sbjct: 52 VQLIVEFA---KRLPGFDKLSREDQ 73
>gnl|CDD|132752 cd06954, NR_LBD_LXR, The ligand binding domain of Liver X
receptors, a family of nuclear receptors of
ligand-activated transcription factors. The ligand
binding domain of Liver X receptors: Liver X receptors
(LXRs) belong to a family of nuclear receptors of
ligand-activated transcription factors. LXRs operate as
cholesterol sensors which protect from cholesterol
overload by stimulating reverse cholesterol transport
from peripheral tissues to the liver and its excretion
in the bile. Oxidized cholesterol derivatives or
oxysterols were identified as specific ligands for LXRs.
Upon ligand binding a conformational change leads to
recruitment of co-factors, which stimulates expression
of target genes. Among the LXR target genes are several
genes involved in cholesterol efflux from peripheral
tissues such as the ATP-binding-cassette transporters
ABCA1, ABCG1 and ApoE. There are two LXR isoforms in
mammals, LXRalpha and LXRbeta. LXRalpha is expressed
mainly in the liver, intestine, kidney, spleen, and
adipose tissue, whereas LXRbeta is ubiquitously
expressed at lower level. Both LXRalpha and LXRbeta
function as heterodimers with the retinoid X receptor
(RX R) which may be activated by either LXR ligands or
9-cis retinoic acid, a specific RXR ligand. The LXR/RXR
complex binds to a liver X receptor response element
(LXRE) in the promoter region of target genes. LXR has
typical NR modular structure with a central well
conserved DNA binding domain (DBD), a variable
N-terminal domain, a flexible hinge and the ligand
binding domain (LBD) at the C-terminal.
Length = 236
Score = 26.3 bits (58), Expect = 6.9
Identities = 10/25 (40%), Positives = 18/25 (72%), Gaps = 3/25 (12%)
Query: 103 VRLDLEFSASGKQIPGFGSLEKKDQ 127
V+ ++F+ KQ+PGF +L ++DQ
Sbjct: 56 VQEIVDFA---KQLPGFLTLTREDQ 77
>gnl|CDD|218888 pfam06087, Tyr-DNA_phospho, Tyrosyl-DNA phosphodiesterase.
Covalent intermediates between topoisomerase I and DNA
can become dead-end complexes that lead to cell death.
Tyrosyl-DNA phosphodiesterase can hydrolyse the bond
between topoisomerase I and DNA.
Length = 433
Score = 26.6 bits (59), Expect = 7.3
Identities = 10/43 (23%), Positives = 18/43 (41%)
Query: 6 GKTPKWFHEECFWKKNRPKALLDIHNVTSLRHQDQEMIKSKIL 48
G TPK + + F P + +S+ Q + K +I+
Sbjct: 243 GVTPKDWLKSNFLGSLYPASFSSEGQESSINQQKERKPKPRII 285
>gnl|CDD|132753 cd07068, NR_LBD_ER_like, The ligand binding domain of estrogen
receptor and estrogen receptor-related receptors. The
ligand binding domain of estrogen receptor (ER) and
estrogen receptor-related receptors (ERRs): Estrogen
receptors are a group of receptors which are activated
by the hormone estrogen. Estrogen regulates many
physiological processes including reproduction, bone
integrity, cardiovascular health, and behavior. The main
mechanism of action of the estrogen receptor is as a
transcription factor by binding to the estrogen response
element of target genes upon activation by estrogen and
then recruiting coactivator proteins which are
responsible for the transcription of target genes.
Additionally some ERs may associate with other membrane
proteins and can be rapidly activated by exposure of
cells to estrogen. ERRs are closely related to the
estrogen receptor (ER) family. But, it lacks the ability
to bind estrogen. ERRs can interfere with the classic
ER-mediated estrogen signaling pathway, positively or
negatively. ERRs share target genes, co-regulators and
promoters with the estrogen receptor (ER) family. Like
other members of the nuclear receptor (NR) superfamily
of ligand-activated transcription factors, ER and ERRs
have a central well conserved DNA binding domain (DBD),
a variable N-terminal domain, a non-conserved hinge and
a C-terminal ligand binding domain (LBD).
Length = 221
Score = 26.0 bits (58), Expect = 9.5
Identities = 8/15 (53%), Positives = 8/15 (53%)
Query: 113 GKQIPGFGSLEKKDQ 127
K IPGF L DQ
Sbjct: 47 AKHIPGFSDLSLNDQ 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
0.318 0.135 0.410
Gapped
Lambda K H
0.267 0.0689 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,937,223
Number of extensions: 674565
Number of successful extensions: 536
Number of sequences better than 10.0: 1
Number of HSP's gapped: 529
Number of HSP's successfully gapped: 19
Length of query: 162
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 73
Effective length of database: 6,990,096
Effective search space: 510277008
Effective search space used: 510277008
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: 55 (25.0 bits)