RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9717
(127 letters)
>gnl|CDD|238036 cd00083, HLH, Helix-loop-helix domain, found in specific DNA-
binding proteins that act as transcription factors;
60-100 amino acids long. A DNA-binding basic region is
followed by two alpha-helices separated by a variable
loop region; HLH forms homo- and heterodimers,
dimerization creates a parallel, left-handed, four
helix bundle; the basic region N-terminal to the first
amphipathic helix mediates high-affinity DNA-binding;
there are several groups of HLH proteins: those
(E12/E47) which bind specific hexanucleotide sequences
such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3),
those lacking the basic domain (Emc, Id) function as
negative regulators since they fail to bind DNA, those
(hairy, E(spl), deadpan) which repress transcription
although they can bind specific hexanucleotide
sequences such as N-box (5-CACGc/aG-3), those which
have a COE domain (Collier/Olf-1/EBF) which is involved
in both in dimerization and in DNA binding, and those
which bind pentanucleotides ACGTG or GCGTG and have a
PAS domain which allows the dimerization between PAS
proteins, the binding of small molecules (e.g.,
dioxin), and interactions with non-PAS proteins.
Length = 60
Score = 37.6 bits (88), Expect = 1e-04
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 53 LLLQPARHSKLEKADILEMTVKHLENMQRQQ 83
LL KL KA+IL V +++++Q
Sbjct: 29 LLPTLPPSKKLSKAEILRKAVDYIKSLQELL 59
>gnl|CDD|215654 pfam00010, HLH, Helix-loop-helix DNA-binding domain.
Length = 52
Score = 35.5 bits (83), Expect = 4e-04
Identities = 9/27 (33%), Positives = 19/27 (70%)
Query: 54 LLQPARHSKLEKADILEMTVKHLENMQ 80
LL + KL KA+IL + +++++++Q
Sbjct: 26 LLPTPPNKKLSKAEILRLAIEYIKHLQ 52
>gnl|CDD|197674 smart00353, HLH, helix loop helix domain.
Length = 53
Score = 33.7 bits (78), Expect = 0.003
Identities = 10/34 (29%), Positives = 22/34 (64%)
Query: 50 LLFLLLQPARHSKLEKADILEMTVKHLENMQRQQ 83
L LL ++ KL KA+IL + +++++++Q +
Sbjct: 18 LRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEEL 51
>gnl|CDD|219453 pfam07527, Hairy_orange, Hairy Orange. The Orange domain is found
in the Drosophila proteins Hesr-1, Hairy, and Enhancer
of Split. The Orange domain is proposed to mediate
specific protein-protein interaction between Hairy and
Scute.
Length = 42
Score = 31.8 bits (73), Expect = 0.010
Identities = 12/16 (75%), Positives = 12/16 (75%)
Query: 97 KFRAGFSECAGEVGRF 112
KFRAGF EC EV RF
Sbjct: 1 KFRAGFRECLNEVARF 16
>gnl|CDD|128787 smart00511, ORANGE, Orange domain. This domain confers specificity
among members of the Hairy/E(SPL) family.
Length = 45
Score = 29.4 bits (67), Expect = 0.073
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 97 KFRAGFSECAGEVGRF 112
FR+G+ ECA EV RF
Sbjct: 2 SFRSGYRECANEVSRF 17
>gnl|CDD|217662 pfam03657, UPF0113, Uncharacterized protein family (UPF0113).
Length = 161
Score = 29.8 bits (67), Expect = 0.25
Identities = 14/35 (40%), Positives = 16/35 (45%), Gaps = 2/35 (5%)
Query: 95 LNKFRAGFS--ECAGEVGRFPGLHFFFFFWLNCGS 127
LN + AG + GE GR L FF L C S
Sbjct: 57 LNPYSAGLNVGSIIGERGRRFRLSLEGFFALLCNS 91
>gnl|CDD|225459 COG2907, COG2907, Predicted NAD/FAD-binding protein [General
function prediction only].
Length = 447
Score = 29.8 bits (67), Expect = 0.39
Identities = 14/67 (20%), Positives = 23/67 (34%), Gaps = 1/67 (1%)
Query: 61 SKLEKADILEMTVKHLENMQRQQLALSAATDPHVLNKFRAGFSECAGEVGRFPGLHFFFF 120
S L +D L +Q+ A + + A +S + R+P +F F
Sbjct: 138 SDLAPSDNAGQGDTTLAQYLKQRNFGRAFVEDFLQPLVAAIWSTPLADASRYPACNFLVF 197
Query: 121 FWLNCGS 127
N G
Sbjct: 198 T-DNHGL 203
>gnl|CDD|178641 PLN03093, PLN03093, Protein SENSITIVITY TO RED LIGHT REDUCED 1;
Provisional.
Length = 273
Score = 28.3 bits (63), Expect = 1.1
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 2/47 (4%)
Query: 53 LLLQPARHSKLEKADILEMTVKHLENMQRQQLALSAATDPHVLNKFR 99
L P R +KL + +E+ +K +E+ Q Q L P VL+ F
Sbjct: 46 LESDPERQAKLIQK--MEICIKKVESSQFYQAFLEQVKSPEVLDSFH 90
>gnl|CDD|240102 cd04754, Commd6, COMM_Domain containing protein 6. The COMM
Domain is found at the C-terminus of a variety of
proteins; presumably all COMM_Domain containing
proteins are located in the nucleus and the COMM domain
plays a role in protein-protein interactions. Several
family members have been shown to bind and inhibit
NF-kappaB.
Length = 86
Score = 27.2 bits (60), Expect = 1.1
Identities = 19/86 (22%), Positives = 35/86 (40%), Gaps = 12/86 (13%)
Query: 6 CASTAPDDLMFHIGHVIEIQQVFCKMQIICSSKT---LKRHLVQLLCLLFLLLQPARHSK 62
++ D + +IG +++ + K+ + SS T L V + L+ A S
Sbjct: 7 LTASDSVDQVLNIGQLVDFKW---KLGMAVSSDTCRSLNSPYVAVT------LKVADPSG 57
Query: 63 LEKADILEMTVKHLENMQRQQLALSA 88
EMT+ +N RQ ++A
Sbjct: 58 QVVTKSFEMTIPEFQNFSRQFKEMAA 83
>gnl|CDD|182320 PRK10227, PRK10227, DNA-binding transcriptional regulator CueR;
Provisional.
Length = 135
Score = 26.5 bits (58), Expect = 2.8
Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 6/46 (13%)
Query: 50 LLFLLLQPARHS------KLEKADILEMTVKHLENMQRQQLALSAA 89
L+ L P RHS LEK +E ++ L++M+ Q LAL+ A
Sbjct: 66 LVNLFNDPQRHSADVKRRTLEKVAEIERHIEELQSMRDQLLALANA 111
>gnl|CDD|234317 TIGR03703, plsB, glycerol-3-phosphate O-acyltransferase. Members
of this protein family are PlsB, glycerol-3-phosphate
O-acyltransferase, present in E. coli and numerous
related species. In many bacteria, PlsB is not found,
and appears to be replaced by a two enzyme system for
1-acyl-glycerol-3-phosphate biosynthesis, the PlsX/Y
system [Fatty acid and phospholipid metabolism,
Biosynthesis].
Length = 799
Score = 27.2 bits (61), Expect = 2.9
Identities = 14/66 (21%), Positives = 28/66 (42%), Gaps = 1/66 (1%)
Query: 33 IICSSKTLKR-HLVQLLCLLFLLLQPARHSKLEKADILEMTVKHLENMQRQQLALSAATD 91
I+ +K + R L L+ LL+ LL+ + + ++ E+ + L+ + RQ L
Sbjct: 620 IVIHNKKISRAELQALVRLLYPLLKAELFLRWSEEELPEVIDRILDELVRQGLIEQDGDV 679
Query: 92 PHVLNK 97
Sbjct: 680 LTRNAA 685
>gnl|CDD|131099 TIGR02044, CueR, Cu(I)-responsive transcriptional regulator. This
model represents the copper-, silver- and gold- (I)
responsive transcriptional activator of the gamma
proteobacterial copper efflux system. This protein is a
member of the MerR family of transcriptional activators
(pfam00376) and contains a distinctive pattern of
cysteine residues in its metal binding loop, Cys-X7-Cys.
This family also lacks a conserved cysteine at the
N-terminal end of the dimerization helix which is
required for the binding of divalent metals such as
zinc; here it is replaced by a serine residue
[Regulatory functions, DNA interactions].
Length = 127
Score = 26.3 bits (58), Expect = 3.6
Identities = 16/46 (34%), Positives = 22/46 (47%), Gaps = 6/46 (13%)
Query: 50 LLFLLLQPARHSK------LEKADILEMTVKHLENMQRQQLALSAA 89
LL L P R S LEK +E + L++M+ Q AL+ A
Sbjct: 66 LLNLWNDPNRTSADVKARTLEKVAEIERKISELQSMRDQLEALAQA 111
>gnl|CDD|189000 cd08662, M13, Peptidase family M13 includes neprilysin,
endothelin-converting enzyme I. M13 family of
metallopeptidases includes neprilysin (neutral
endopeptidase, NEP, enkephalinase, CD10, CALLA, EC
3.4.24.11), endothelin-converting enzyme I (ECE-1, EC
3.4.24.71), erythrocyte surface antigen KELL (ECE-3),
phosphate-regulating gene on the X chromosome (PHEX),
soluble secreted endopeptidase (SEP), and damage-induced
neuronal endopeptidase (DINE)/X-converting enzyme (XCE).
These proteins consist of a short N-terminal cytoplasmic
domain, a single transmembrane helix, and a larger
C-terminal extracellular domain containing the active
site. Proteins in this family fulfill a broad range of
physiological roles due to the greater variation in the
S2' subsite allowing substrate specificity. NEP is
expressed in a variety of tissues including kidney and
brain, and is involved in many physiological and
pathological processes, including blood pressure and
inflammatory response. It degrades a wide array of
substrates such as substance P, enkephalins,
cholecystokinin, neurotensin and somatostatin. It is an
important enzyme in the regulation of amyloid-beta
(Abeta) protein that forms amyloid plaques that are
associated with Alzeimers disease (AD). ECE-1 catalyzes
the final rate-limiting step in the biosynthesis of
endothelins via post-translational conversion of the
biologically inactive big endothelins. Like NEP, it also
hydrolyses bradykinin, substance P, neurotensin and
Abeta. Endothelin-1 overproduction has been implicated
in various diseases, including stroke, asthma,
hypertension, and cardiac and renal failure. Kell is a
homolog of NEP and constitutes a major antigen on human
erythrocytes; it preferentially cleaves big endothelin-3
to produce bioactive endothelin-3, but is also known to
cleave substance P and neurokinin A. PHEX forms a
complex interaction with fibroblast growth factor 23
(FGF23) and matrix extracellular phosphoglycoprotein,
causing bone mineralization. A loss-of-function mutation
in PHEX disrupts this interaction leading to
hypophosphatemic rickets; X-linked hypophosphatemic
(XLH) rickets is the most common form of metabolic
rickets. ECEL1 is a brain metalloprotease involved in
the critical role in the nervous regulation of the
respiratory system, while DINE (damage induced neuronal
endopeptidase) is abundantly expressed in the
hypothalamus and its expression responds to nerve injury
as well. Thus, majority of these M13 proteases are prime
therapeutic targets for selective inhibition.
Length = 611
Score = 26.5 bits (59), Expect = 4.4
Identities = 8/24 (33%), Positives = 10/24 (41%)
Query: 77 ENMQRQQLALSAATDPHVLNKFRA 100
+ + L TDPH KFR
Sbjct: 558 SKYRPEALRQLLLTDPHSPGKFRV 581
>gnl|CDD|133383 cd01108, HTH_CueR, Helix-Turn-Helix DNA binding domain of CueR-like
transcription regulators. Helix-turn-helix (HTH)
transcription regulators CueR and ActP, copper efflux
regulators. In Bacillus subtilis, copper induced CueR
regulates the copZA operon, preventing copper toxicity.
In Rhizobium leguminosarum, ActP controls copper
homeostasis; it detects cytoplasmic copper stress and
activates transcription in response to increasing copper
concentrations. These proteins are comprised of two
distinct domains that harbor the regulatory
(effector-binding) site and the active (DNA-binding)
site. Their conserved N-terminal domains contain winged
HTH motifs that mediate DNA binding, while the
C-terminal domains have two conserved cysteines that
define a monovalent copper ion binding site. These
proteins share the N-terminal DNA binding domain with
other transcription regulators of the MerR superfamily
that promote transcription by reconfiguring the spacer
between the -35 and -10 promoter elements.
Length = 127
Score = 25.6 bits (57), Expect = 5.5
Identities = 15/52 (28%), Positives = 23/52 (44%), Gaps = 6/52 (11%)
Query: 44 LVQLLCLLFLLLQPARHSK------LEKADILEMTVKHLENMQRQQLALSAA 89
L ++ LL L P+R S LE LE + L+ M+R L+ +
Sbjct: 60 LEEIRELLALWRDPSRASADVKALALEHIAELERKIAELQAMRRTLQQLADS 111
>gnl|CDD|173683 cd05592, STKc_nPKC_theta_delta, Catalytic domain of the Protein
Serine/Threonine Kinases, Novel Protein Kinase C theta
and delta. Serine/Threonine Kinases (STKs), Novel
Protein Kinase C (nPKC), theta and delta-like isoforms,
catalytic (c) domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The nPKC subfamily is
part of a larger superfamily that includes the catalytic
domains of other protein STKs, protein tyrosine kinases,
RIO kinases, aminoglycoside phosphotransferase, choline
kinase, and phosphoinositide 3-kinase. PKCs are
classified into three groups (classical, atypical, and
novel) depending on their mode of activation and the
structural characteristics of their regulatory domain.
nPKCs are calcium-independent, but require DAG
(1,2-diacylglycerol) and phosphatidylserine (PS) for
activity. There are four nPKC isoforms, delta, epsilon,
eta, and theta. PKC-theta is selectively expressed in
T-cells and plays an important and non-redundant role in
several aspects of T-cell biology. PKC-delta plays a
role in cell cycle regulation and programmed cell death
in many cell types.
Length = 316
Score = 25.9 bits (57), Expect = 7.5
Identities = 18/43 (41%), Positives = 21/43 (48%), Gaps = 8/43 (18%)
Query: 1 MEYLNCASTAPDDLMFHI---GHVIEIQQVFCKMQIICSSKTL 40
MEYLN DLMFHI G E + F +IIC + L
Sbjct: 75 MEYLNGG-----DLMFHIQSSGRFDEARARFYAAEIICGLQFL 112
>gnl|CDD|237603 PRK14083, PRK14083, HSP90 family protein; Provisional.
Length = 601
Score = 25.7 bits (57), Expect = 7.8
Identities = 14/45 (31%), Positives = 19/45 (42%), Gaps = 1/45 (2%)
Query: 55 LQP-ARHSKLEKADILEMTVKHLENMQRQQLALSAATDPHVLNKF 98
L+P A L + D L + L R+ L A TDP L +
Sbjct: 299 LRPTASREALYEDDALAAVREELGEAIRKWLIGLATTDPERLRRL 343
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
0.331 0.141 0.445
Gapped
Lambda K H
0.267 0.0803 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,316,974
Number of extensions: 518899
Number of successful extensions: 661
Number of sequences better than 10.0: 1
Number of HSP's gapped: 661
Number of HSP's successfully gapped: 24
Length of query: 127
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 42
Effective length of database: 7,167,512
Effective search space: 301035504
Effective search space used: 301035504
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 53 (24.1 bits)