RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12865
(227 letters)
>gnl|CDD|241394 cd13240, PH1_Kalirin_Trio_like, Triple functional domain pleckstrin
homology pleckstrin homology (PH) domain, repeat 1.
RhoGEFs, Kalirin and Trio, the mammalian homologs of
Drosophila Trio and Caenorhabditis elegans UNC-73
regulate a novel step in secretory granule maturation.
Their signaling modulates the extent to which regulated
cargo enter and remain in the regulated secretory
pathway. This allows for fine tuning of peptides
released by a single secretory cell type with impaired
signaling leading to pathological states. Trio plays an
essential role in regulating the actin cytoskeleton
during axonal guidance and branching. Kalirin and Trio
are encoded by separate genes in mammals and by a single
one in invertebrates. Kalirin and Trio share the same
complex multidomain structure and display several splice
variants. The longest Kalirin and Trio proteins have a
Sec14 domain, a stretch of spectrin repeats, a
RhoGEF(DH)/PH cassette (also called GEF1), an SH3
domain, a second RhoGEF(DH)/PH cassette (also called
GEF2), a second SH3 domain, Ig/FNIII domains, and a
kinase domain. The first RhoGEF(DH)/PH cassette
catalyzes exchange on Rac1 and RhoG while the second
RhoGEF(DH)/PH cassette is specific for RhoA. Kalirin and
Trio are closely related to p63RhoGEF and have PH
domains of similar function. PH domains have diverse
functions, but in general are involved in targeting
proteins to the appropriate cellular location or in the
interaction with a binding partner. They share little
sequence conservation, but all have a common fold, which
is electrostatically polarized. Less than 10% of PH
domains bind phosphoinositide phosphates (PIPs) with
high affinity and specificity. PH domains are
distinguished from other PIP-binding domains by their
specific high-affinity binding to PIPs with two vicinal
phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or
PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved across
all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.not conserved
across all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinases,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, cytoskeletal associated molecules,
and in lipid associated enzymes.
Length = 123
Score = 121 bits (305), Expect = 3e-35
Identities = 47/61 (77%), Positives = 52/61 (85%)
Query: 2 KGRLMTSELGVTEHIEGDECKFAVWTGRAPISDCRILLKASSLEAKQLWVKRLREVIQET 61
K +LMTSELGVTEHIEGD CKFA+WTGR P SD +I+LKASSLE KQ WVK+LREVIQE
Sbjct: 63 KSKLMTSELGVTEHIEGDPCKFALWTGRVPTSDNKIVLKASSLEVKQEWVKKLREVIQER 122
Query: 62 Y 62
Sbjct: 123 I 123
Score = 47.3 bits (113), Expect = 3e-07
Identities = 21/36 (58%), Positives = 23/36 (63%), Gaps = 5/36 (13%)
Query: 104 SGNTTDSD-----KASSLEAKQLWVKRLREVIQETY 134
+G SD KASSLE KQ WVK+LREVIQE
Sbjct: 88 TGRVPTSDNKIVLKASSLEVKQEWVKKLREVIQERI 123
Score = 44.2 bits (105), Expect = 5e-06
Identities = 17/22 (77%), Positives = 18/22 (81%)
Query: 151 ASSLEAKQLWVKRLREVIQETY 172
ASSLE KQ WVK+LREVIQE
Sbjct: 102 ASSLEVKQEWVKKLREVIQERI 123
>gnl|CDD|241261 cd01227, PH_Dbs, DBL's big sister protein pleckstrin homology (PH)
domain. Dbs (also called MCF2-transforming
sequence-like protein 2) is a guanine nucleotide
exchange factor (GEF), which contains spectrin repeats,
a rhoGEF (DH) domain and a PH domain. The Dbs PH domain
participates in binding to both the Cdc42 and RhoA
GTPases. PH domains have diverse functions, but in
general are involved in targeting proteins to the
appropriate cellular location or in the interaction with
a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH domains
bind phosphoinositide phosphates (PIPs) with high
affinity and specificity. PH domains are distinguished
from other PIP-binding domains by their specific
high-affinity binding to PIPs with two vicinal phosphate
groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3
which results in targeting some PH domain proteins to
the plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 132
Score = 48.4 bits (115), Expect = 2e-07
Identities = 20/58 (34%), Positives = 34/58 (58%), Gaps = 5/58 (8%)
Query: 2 KGRLMTSELGVTEHIEGDECKFAVW-TGRAPISDCRILLKASSLEAKQLWVKRLREVI 58
K L S +G+TE+++GD KF +W GR + +++A + E K WV +R+V+
Sbjct: 76 KNSLKMSAVGITENVKGDNKKFEIWYNGREEV----YIIQAPTPEIKAAWVNEIRKVL 129
>gnl|CDD|241393 cd13239, PH_Obscurin, Obscurin pleckstrin homology (PH) domain.
Obscurin (also called Obscurin-RhoGEF; Obscurin-myosin
light chain kinase/Obscurin-MLCK) is a giant muscle
protein that is concentrated at the peripheries of
Z-disks and M-lines. It binds small ankyrin I, a
component of the sarcoplasmic reticulum (SR) membrane.
It is associated with the contractile apparatus through
binding with titin and sarcomeric myosin. It plays
important roles in the organization and assembly of the
myofibril and the SR. Obscurin has been observed as
alternatively-spliced isoforms. The major isoform in
sleletal muscle, approximately 800 kDa in size, is
composed of many adhesion modules and signaling domains.
It harbors 49 Ig and 2 FNIII repeats at the N-terminues,
a complex middle region with additional Ig domains, an
IQ motif, and a conserved SH3 domain near RhoGEF and PH
domains, and a non-modular C-terminus with
phosphorylation motifs. The obscurin gene also encodes
two kinase domains, which are not part of the 800 kDa
form of the protein, but is part of smaller spliced
products that present in heart muscle. PH domains have
diverse functions, but in general are involved in
targeting proteins to the appropriate cellular location
or in the interaction with a binding partner. They share
little sequence conservation, but all have a common
fold, which is electrostatically polarized. Less than
10% of PH domains bind phosphoinositide phosphates
(PIPs) with high affinity and specificity. PH domains
are distinguished from other PIP-binding domains by
their specific high-affinity binding to PIPs with two
vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2
or PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved across
all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 125
Score = 48.2 bits (115), Expect = 2e-07
Identities = 18/60 (30%), Positives = 34/60 (56%), Gaps = 1/60 (1%)
Query: 2 KGRLMTSELGVTEHIEGDECKFAVWTGRAPISDCRILLKASSLEAKQLWVKRLREVIQET 61
K ++ +++ V + +EGD+ F +W R S + L+A ++ K WVK +R++ Q T
Sbjct: 67 KNKMKLNDIDVNDTVEGDDRAFELWHER-EDSVRKYTLQARTIIVKNSWVKEIRDIQQRT 125
>gnl|CDD|241396 cd13242, PH_puratrophin-1, Puratrophin-1 pleckstrin homology (PH)
domain. Puratrophin-1 (also called Purkinje cell
atrophy-associated protein 1 or PLEKHG4/Pleckstrin
homology domain-containing family G member 4) contains a
spectrin repeat, a RhoGEF (DH) domain, and a PH domain.
It is thought to function in intracellular signaling and
cytoskeleton dynamics at the Golgi. Puratrophin-1 is
expressed in kidney, Leydig cells in the testis,
epithelial cells in the prostate gland and Langerhans
islet in the pancreas. A single nucleotide substitution
in the puratrophin-1 gene were once thought to result in
autosomal dominant cerebellar ataxia (ADCA), but now it
has been demonstrated that this ataxia is a result of
defects in the BEAN gene. Puratrophin contains a domain
architecture similar to that of Dbl family members Dbs
and Trio. Dbs is a guanine nucleotide exchange factor
(GEF), which contains spectrin repeats, a RhoGEF (DH)
domain and a PH domain. The Dbs PH domain participates
in binding to both the Cdc42 and RhoA GTPases. Trio
plays an essential role in regulating the actin
cytoskeleton during axonal guidance and branching. Trio
is a multidomain signaling protein that contains two
RhoGEF(DH)-PH domains in tandem. PH domains have diverse
functions, but in general are involved in targeting
proteins to the appropriate cellular location or in the
interaction with a binding partner. They share little
sequence conservation, but all have a common fold, which
is electrostatically polarized. Less than 10% of PH
domains bind phosphoinositide phosphates (PIPs) with
high affinity and specificity. PH domains are
distinguished from other PIP-binding domains by their
specific high-affinity binding to PIPs with two vicinal
phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or
PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved across
all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 136
Score = 40.7 bits (96), Expect = 1e-04
Identities = 18/51 (35%), Positives = 30/51 (58%), Gaps = 3/51 (5%)
Query: 2 KGRLMTSELGVTEHIEGDE-CKFAVWTGRAPISDCRILLKASSLEAKQLWV 51
K + T+++G+TE++ GD KF +W R D +L+A+S E K+ W
Sbjct: 73 KHSIKTADIGLTENV-GDSGLKFEIWFRRRKSRDT-YILQATSPEIKEAWT 121
>gnl|CDD|241395 cd13241, PH2_Kalirin_Trio_p63RhoGEF, p63RhoGEF pleckstrin homology
(PH) domain, repeat 2. The guanine nucleotide exchange
factor p63RhoGEF is an effector of the heterotrimeric G
protein, Galphaq and linking Galphaq-coupled receptors
(GPCRs) to the activation of RhoA. The Dbl(DH) and PH
domains of p63RhoGEF interact with the effector-binding
site and the C-terminal region of Galphaq and appear to
relieve autoinhibition of the catalytic DH domain by the
PH domain. Trio, Duet, and p63RhoGEF are shown to
constitute a family of Galphaq effectors that appear to
activate RhoA both in vitro and in intact cells. Dbs is
a guanine nucleotide exchange factor (GEF), which
contains spectrin repeats, a rhoGEF (DH) domain and a PH
domain. The Dbs PH domain participates in binding to
both the Cdc42 and RhoA GTPases. Trio plays an essential
role in regulating the actin cytoskeleton during axonal
guidance and branching. Trio is a multidomain signaling
protein that contains two RhoGEF(DH)-PH domains in
tandem. PH domains have diverse functions, but in
general are involved in targeting proteins to the
appropriate cellular location or in the interaction with
a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH domains
bind phosphoinositide phosphates (PIPs) with high
affinity and specificity. PH domains are distinguished
from other PIP-binding domains by their specific
high-affinity binding to PIPs with two vicinal phosphate
groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3
which results in targeting some PH domain proteins to
the plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 140
Score = 40.3 bits (95), Expect = 1e-04
Identities = 14/58 (24%), Positives = 32/58 (55%)
Query: 2 KGRLMTSELGVTEHIEGDECKFAVWTGRAPISDCRILLKASSLEAKQLWVKRLREVIQ 59
K + +++ + E+++GD C+FA+ + +L+A S E +Q WV + +++
Sbjct: 68 KNSIKVNKMSLEENVDGDPCRFALRSRDPNKPGESFVLQAPSPEIRQEWVDTINQILD 125
>gnl|CDD|241397 cd13243, PH_PLEKHG1_G2_G3, Pleckstrin homology domain-containing
family G members 1, 2, and 3 pleckstrin homology (PH)
domain. PLEKHG1 (also called ARHGEF41), PLEKHG2 (also
called ARHGEF42 or CLG/common-site lymphoma/leukemia
guanine nucleotide exchange factor2), and PLEKHG3 (also
called ARHGEF43) have RhoGEF DH/double-homology domains
in tandem with a PH domain which is involved in
phospholipid binding. They function as a guanine
nucleotide exchange factor (GEF) and are involved in the
regulation of Rho protein signal transduction. Mutations
in PLEKHG1 have been associated panic disorder (PD), an
anxiety disorder characterized by panic attacks and
anticipatory anxiety. PH domains have diverse functions,
but in general are involved in targeting proteins to the
appropriate cellular location or in the interaction with
a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH domains
bind phosphoinositide phosphates (PIPs) with high
affinity and specificity. PH domains are distinguished
from other PIP-binding domains by their specific
high-affinity binding to PIPs with two vicinal phosphate
groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3
which results in targeting some PH domain proteins to
the plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 147
Score = 34.6 bits (80), Expect = 0.015
Identities = 19/59 (32%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 2 KGRLMTSELGVTEHIEGDECKFAVWTGRAPISDCRILLKASSLEAKQLWVKRLREVIQE 60
K +M S L + E I D F V + L+A +LE K+LW + L+ +I E
Sbjct: 90 KTHIMCSNLMLVESIPKDPLSFQVL--PFDNPKAQYTLQAKNLEQKRLWTQHLKRLILE 146
>gnl|CDD|241437 cd13283, PH_GPBP, Goodpasture antigen binding protein Pleckstrin
homology (PH) domain. The GPBP (also called Collagen
type IV alpha-3-binding protein/hCERT; START
domain-containing protein 11/StARD11; StAR-related
lipid transfer protein 11) is a kinase that
phosphorylates an N-terminal region of the alpha 3
chain of type IV collagen, which is commonly known as
the goodpasture antigen. Its splice variant the
ceramide transporter (CERT) mediates the cytosolic
transport of ceramide. There have been additional
splice variants identified, but all of them function as
ceramide transport proteins. GPBP and CERT both contain
an N-terminal PH domain, followed by a serine rich
domain, and a C-terminal START domain. However, GPBP
has an additional serine rich domain just upstream of
its START domain. They are members of the oxysterol
binding protein (OSBP) family which includes OSBP,
OSBP-related proteins (ORP), Goodpasture antigen
binding protein (GPBP), and Four phosphate adaptor
protein 1 (FAPP1). They have a wide range of purported
functions including sterol transport, cell cycle
control, pollen development and vessicle transport from
Golgi recognize both PI lipids and ARF proteins. PH
domains have diverse functions, but in general are
involved in targeting proteins to the appropriate
cellular location or in the interaction with a binding
partner. They share little sequence conservation, but
all have a common fold, which is electrostatically
polarized. Less than 10% of PH domains bind
phosphoinositide phosphates (PIPs) with high affinity
and specificity. PH domains are distinguished from
other PIP-binding domains by their specific
high-affinity binding to PIPs with two vicinal
phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or
PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved
across all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 100
Score = 31.8 bits (73), Expect = 0.067
Identities = 16/44 (36%), Positives = 20/44 (45%), Gaps = 6/44 (13%)
Query: 12 VTEHIEGDECKFAVWTGRAPISDCRILLKASSLEAKQLWVKRLR 55
+ H E DEC+F V D L+A S E +Q WV L
Sbjct: 51 IKPH-EFDECRFDVSVN-----DSVWYLRAESPEERQRWVDALE 88
>gnl|CDD|214574 smart00233, PH, Pleckstrin homology domain. Domain commonly found
in eukaryotic signalling proteins. The domain family
possesses multiple functions including the abilities to
bind inositol phosphates, and various proteins. PH
domains have been found to possess inserted domains
(such as in PLC gamma, syntrophins) and to be inserted
within other domains. Mutations in Brutons tyrosine
kinase (Btk) within its PH domain cause X-linked
agammaglobulinaemia (XLA) in patients. Point mutations
cluster into the positively charged end of the molecule
around the predicted binding site for
phosphatidylinositol lipids.
Length = 102
Score = 30.2 bits (68), Expect = 0.29
Identities = 19/62 (30%), Positives = 28/62 (45%), Gaps = 8/62 (12%)
Query: 2 KGRLMTSELGVTEHIEGDECK----FAVWTGRAPISDCRILLKASSLEAKQLWVKRLREV 57
KG + S V E + D K F + T +LL+A S E ++ WV+ LR+
Sbjct: 45 KGSIDLSGCTVREAPDPDSSKKPHCFEIKTS----DRKTLLLQAESEEEREKWVEALRKA 100
Query: 58 IQ 59
I
Sbjct: 101 IA 102
>gnl|CDD|241447 cd13293, PH_CpORP2-like, Cryptosporidium-like Oxysterol binding
protein related protein 2 Pleckstrin homology (PH)
domain. There are 2 types of ORPs found in
Cryptosporidium: CpORP1 and CpORP2. Cryptosporium
differs from other apicomplexans like Plasmodium,
Toxoplasma, and Eimeria which possess only a single
long-type ORP consisting of an N-terminal PH domain
followed by a C-terminal ligand binding (LB) domain.
CpORP2 is like this, but CpORP1 differs and has a
truncated N-terminus resulting in only having a LB
domain present. The exact functions of these proteins
are largely unknown though CpORP1 is thought to be
involved in lipid transport across the parasitophorous
vacuole membrane. Oxysterol binding proteins are a
multigene family that is conserved in yeast, flies,
worms, mammals and plants. In general OSBPs and ORPs
have been found to be involved in the transport and
metabolism of cholesterol and related lipids in
eukaryotes. They all contain a C-terminal oxysterol
binding domain, and most contain an N-terminal PH
domain. OSBP PH domains bind to membrane
phosphoinositides and thus likely play an important
role in intracellular targeting. They are members of
the oxysterol binding protein (OSBP) family which
includes OSBP, OSBP-related proteins (ORP), Goodpasture
antigen binding protein (GPBP), and Four phosphate
adaptor protein 1 (FAPP1). They have a wide range of
purported functions including sterol transport, cell
cycle control, pollen development and vessicle
transport from Golgi recognize both PI lipids and ARF
proteins. PH domains have diverse functions, but in
general are involved in targeting proteins to the
appropriate cellular location or in the interaction
with a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH
domains bind phosphoinositide phosphates (PIPs) with
high affinity and specificity. PH domains are
distinguished from other PIP-binding domains by their
specific high-affinity binding to PIPs with two vicinal
phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or
PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved
across all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 88
Score = 29.2 bits (66), Expect = 0.46
Identities = 11/38 (28%), Positives = 18/38 (47%), Gaps = 5/38 (13%)
Query: 19 DECKFAVWTGRAPISDCRILLKASSLEAKQLWVKRLRE 56
D + + TG ++ L+ASS+E K W L+
Sbjct: 54 DPLRIIINTG-----TNQLHLRASSVEEKLKWYNALKY 86
>gnl|CDD|215766 pfam00169, PH, PH domain. PH stands for pleckstrin homology.
Length = 101
Score = 29.4 bits (66), Expect = 0.61
Identities = 13/42 (30%), Positives = 19/42 (45%), Gaps = 4/42 (9%)
Query: 17 EGDECKFAVWTGRAPISDCRILLKASSLEAKQLWVKRLREVI 58
+ F + TG LL+A S E ++ WVK +R I
Sbjct: 63 GKRKNCFEIRTGDRE----TFLLQAESEEERKEWVKAIRSAI 100
>gnl|CDD|241540 cd13389, PH1_FGD5_FGD6, FYVE, RhoGEF and PH domain
containing/faciogenital dysplasia proteins 5 and 6
Pleckstrin Homology (PH) domain. FGD5 regulates
promotes angiogenesis of vascular endothelial growth
factor (VEGF) in vascular endothelial cells, including
network formation, permeability, directional movement,
and proliferation. The specific function of FGD6 is
unknown. In general, FGDs have a RhoGEF (DH) domain,
followed by a PH domain, a FYVE domain and a C-terminal
PH domain. All FGDs are guanine nucleotide exchange
factors that activate the Rho GTPase Cdc42, an important
regulator of membrane trafficking. The RhoGEF domain is
responsible for GEF catalytic activity, while the PH
domain is involved in intracellular targeting of the DH
domain. PH domains have diverse functions, but in
general are involved in targeting proteins to the
appropriate cellular location or in the interaction with
a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH domains
bind phosphoinositide phosphates (PIPs) with high
affinity and specificity. PH domains are distinguished
from other PIP-binding domains by their specific
high-affinity binding to PIPs with two vicinal phosphate
groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3
which results in targeting some PH domain proteins to
the plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 125
Score = 28.8 bits (65), Expect = 0.98
Identities = 12/30 (40%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 32 ISDCR-ILLKASSLEAKQLWVKRLREVIQE 60
S R L ASS E + WVK L I++
Sbjct: 81 ESTKRSFTLSASSAEERDEWVKALSRAIED 110
>gnl|CDD|226358 COG3838, VirB2, Type IV secretory pathway, VirB2 components
(pilins) [Intracellular trafficking and secretion].
Length = 108
Score = 28.5 bits (64), Expect = 1.2
Identities = 11/47 (23%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 123 VKRLREVIQETYFSSALPLAAPPKSPASASSLEAKQLWVKRLREVIQ 169
R+R I + AL L A +PA+A S + ++++ + +
Sbjct: 5 SSRIRPAIAALIVAVALLLLAAFVAPAAAQSAPWET-PLQQILQSLT 50
>gnl|CDD|241445 cd13291, PH_ORP10_ORP11, Human Oxysterol binding protein (OSBP)
related proteins 10 and 11 (ORP10 and ORP11) Pleckstrin
homology (PH) domain. Human ORP10 is involvedt in
intracellular transport or organelle positioning and is
proposed to function as a regulator of cellular lipid
metabolism. Human ORP11 localizes at the Golgi-late
endosome interface and is thought to form a dimer with
ORP9 functioning as an intracellular lipid sensor or
transporter. Both ORP10 and ORP11 contain a N-terminal
PH domain, a FFAT motif (two phenylalanines in an acidic
tract), and a C-terminal OSBP-related domain. Oxysterol
binding proteins are a multigene family that is
conserved in yeast, flies, worms, mammals and plants. In
general OSBPs and ORPs have been found to be involved in
the transport and metabolism of cholesterol and related
lipids in eukaryotes. They all contain a C-terminal
oxysterol binding domain, and most contain an N-terminal
PH domain. OSBP PH domains bind to membrane
phosphoinositides and thus likely play an important role
in intracellular targeting. They are members of the
oxysterol binding protein (OSBP) family which includes
OSBP, OSBP-related proteins (ORP), Goodpasture antigen
binding protein (GPBP), and Four phosphate adaptor
protein 1 (FAPP1). They have a wide range of purported
functions including sterol transport, cell cycle
control, pollen development and vessicle transport from
Golgi recognize both PI lipids and ARF proteins. PH
domains have diverse functions, but in general are
involved in targeting proteins to the appropriate
cellular location or in the interaction with a binding
partner. They share little sequence conservation, but
all have a common fold, which is electrostatically
polarized. Less than 10% of PH domains bind
phosphoinositide phosphates (PIPs) with high affinity
and specificity. PH domains are distinguished from other
PIP-binding domains by their specific high-affinity
binding to PIPs with two vicinal phosphate groups:
PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which
results in targeting some PH domain proteins to the
plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 107
Score = 27.2 bits (61), Expect = 2.9
Identities = 11/35 (31%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 39 LKASSLEAKQLWVKRLREVIQETYFSSALPLAAPP 73
L+A+ + +Q WV RLR V + + + A+ + P
Sbjct: 75 LRAADAKERQEWVNRLRAVAE--HHTEAIAKSNPS 107
>gnl|CDD|241279 cd01248, PH_PLC_ELMO1, Phospholipase C and Engulfment and cell
motility protein 1 pleckstrin homology domain. The
C-terminal region of ELMO1, the PH domain and Pro-rich
sequences, binds the SH3-containing region of DOCK2
forming a intermolecular five-helix bundle allowing for
DOCK mediated Rac1 activation. ELMO1, a mammalian
homolog of C. elegans CED-12, contains an N-terminal
RhoG-binding region, a ELMO domain, a PH domain, and a
C-terminal sequence with three PxxP motifs. Specificaly,
PLCs catalyze the cleavage of
phosphatidylinositol-4,5-bisphosphate (PIP2) and result
in the release of 1,2-diacylglycerol (DAG) and inositol
1,4,5-triphosphate (IP3). These products trigger the
activation of protein kinase C (PKC) and the release of
Ca2+ from intracellular stores. There are fourteen kinds
of mammalian phospholipase C which are are classified
into six isotypes (beta, gamma, delta, epsilon, zeta,
eta). All PLCs, except for PLCzeta, have a PH domain
which is for most part N-terminally located, though
lipid binding specificity is not conserved between them.
In addition PLC gamma contains a split PH domain within
its catalytic domain that is separated by 2 SH2 domains
and a single SH3 domain. PH domains have diverse
functions, but in general are involved in targeting
proteins to the appropriate cellular location or in the
interaction with a binding partner. They share little
sequence conservation, but all have a common fold, which
is electrostatically polarized. Less than 10% of PH
domains bind phosphoinositide phosphates (PIPs) with
high affinity and specificity. PH domains are
distinguished from other PIP-binding domains by their
specific high-affinity binding to PIPs with two vicinal
phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or
PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved across
all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 108
Score = 26.9 bits (60), Expect = 4.0
Identities = 20/81 (24%), Positives = 32/81 (39%), Gaps = 3/81 (3%)
Query: 47 KQLWVKRLREVIQETYFSSALPLAAPPKSPAKLKSRSNQPNMEDEDNCDRGSLASYGSGN 106
Q+ + ++ ++ + P K R + N E+ C S+ YGS N
Sbjct: 28 TQITWESSKKKSEKKSIDISDIKEVRPGKDTKGFKRKKKSNKPKEERC--FSI-IYGSHN 84
Query: 107 TTDSDKASSLEAKQLWVKRLR 127
T A S + LWV+ LR
Sbjct: 85 KTLDLVAPSEDEANLWVEGLR 105
>gnl|CDD|241432 cd13278, PH_Bud4, Bud4 Pleckstrin homology (PH) domain. Bud4 is an
anillin-like yeast protein involved in the formation and
the disassembly of the double ring structure formed by
the septins during cytokinesis. Bud4 acts with Bud3 and
and in parallel with septin phosphorylation by the
p21-activated kinase Cla4 and the septin-dependent
kinase Gin4. Bud4 is regulated by the cyclin-dependent
protein kinase Cdk1, the master regulator of cell cycle
progression. Bud4 contains an anillin-like domain
followed by a PH domain. In addition there are two
consensus Cdk phosphorylation sites: one at the
N-terminus and one right before the C-terminal PH
domain. Anillins also have C-terminal PH domains. PH
domains have diverse functions, but in general are
involved in targeting proteins to the appropriate
cellular location or in the interaction with a binding
partner. They share little sequence conservation, but
all have a common fold, which is electrostatically
polarized. Less than 10% of PH domains bind
phosphoinositide phosphates (PIPs) with high affinity
and specificity. PH domains are distinguished from other
PIP-binding domains by their specific high-affinity
binding to PIPs with two vicinal phosphate groups:
PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which
results in targeting some PH domain proteins to the
plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 139
Score = 26.8 bits (60), Expect = 5.6
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 36 RILLKASSLEAKQLWVKRLREVIQ 59
I A S E K W +L+EV++
Sbjct: 105 VIDFYADSKEEKADWYSKLKEVVE 128
>gnl|CDD|232853 TIGR00169, leuB, 3-isopropylmalate dehydrogenase. Several NAD- or
NADP-dependent dehydrogenases, including
3-isopropylmalate dehydrogenase, tartrate dehydrogenase,
and the dimeric forms of isocitrate dehydrogenase, share
a nucleotide binding domain unrelated to that of lactate
dehydrogenase and its homologs. These enzymes
dehydrogenate their substates at a H-C-OH site adjacent
to a H-C-COOH site; the latter carbon, now adjacent to a
carbonyl group, readily decarboxylates.Among these
decarboxylating dehydrogenases of hydroxyacids, overall
sequence homology indicates evolutionary history rather
than actual substrate or cofactor specifity, which may
be toggled experimentally by replacement of just a few
amino acids. 3-isopropylmalate dehydrogenase is an
NAD-dependent enzyme and should have a sequence
resembling HGSAPDI around residue 340. The subtrate
binding loop should include a sequence resembling
E[KQR]X(0,1)LLXXR around residue 115. Other contacts of
importance are known from crystallography but not
detailed here.This model will not find all
isopropylmalate dehydrogenases; the enzyme from
Sulfolobus sp. strain 7 is more similar to mitochondrial
NAD-dependent isocitrate dehydrogenases than to other
known isopropylmalate dehydrogenases and was omitted to
improve the specificity of the model. It scores below
the cutoff and below some enzymes known not to be
isopropylmalate dehydrogenase [Amino acid biosynthesis,
Pyruvate family].
Length = 346
Score = 27.4 bits (61), Expect = 7.0
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 108 TDSDKASSLEAKQLWVKRLREVIQE 132
T DKA+ LE+ +LW K + E+ +E
Sbjct: 181 TSVDKANVLESSRLWRKTVEEIAKE 205
>gnl|CDD|198413 cd10431, GHITM, Growth-hormone inducible transmembrane protein.
GHITM appears to be ubiquitiously expressed in mammalian
cells and expression has also been observed in various
cancer cell lines. A cytoprotective function has been
suggested. It is closely related to the BAX inhibitor
(BI)-1 like family of small transmembrane proteins,
which have been shown to have an antiapoptotic effect.
Length = 264
Score = 27.0 bits (60), Expect = 7.3
Identities = 14/56 (25%), Positives = 24/56 (42%), Gaps = 3/56 (5%)
Query: 97 GSLASYGSGNTTDSDKASSLEAKQLWVKRLREVIQETYFSSALPLAAPPKSPASAS 152
G+L YG G S + ++E +W + +R+ I TY L + + S
Sbjct: 14 GALCYYGLGL---SSEIGAIEKAVIWPQYVRDRIHSTYMYFGGSLGLTALAAVALS 66
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
0.310 0.125 0.360
Gapped
Lambda K H
0.267 0.0618 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,032,651
Number of extensions: 977643
Number of successful extensions: 631
Number of sequences better than 10.0: 1
Number of HSP's gapped: 625
Number of HSP's successfully gapped: 31
Length of query: 227
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 134
Effective length of database: 6,812,680
Effective search space: 912899120
Effective search space used: 912899120
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 57 (26.0 bits)