RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17477
(108 letters)
>gnl|CDD|241271 cd01238, PH_Btk, Bruton's tyrosine kinase pleckstrin homology
(PH) domain. Btk is a member of the Tec family of
cytoplasmic protein tyrosine kinases that includes BMX,
IL2-inducible T-cell kinase (Itk) and Tec. Btk plays a
role in the maturation of B cells. Tec proteins general
have an N-terminal PH domain, followed by a Tek
homology (TH) domain, a SH3 domain, a SH2 domain and a
kinase domain. The Btk PH domain binds
phosphatidylinositol 3,4,5-trisphosphate and responds
to signalling via phosphatidylinositol 3-kinase. The PH
domain is also involved in membrane anchoring which is
confirmed by the discovery of a mutation of a critical
arginine residue in the BTK PH domain. This results in
severe human immunodeficiency known as X-linked
agammaglobulinemia (XLA) in humans and a related
disorder is mice.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 = 71.5 bits (176), Expect = 3e-17
Identities = 27/57 (47%), Positives = 33/57 (57%), Gaps = 10/57 (17%)
Query: 44 RQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYYDTDSE--------IFLSGIR 92
++G L+KRSQ KKRF N YK+RWFVLT L YY+ D I LS I+
Sbjct: 1 KEGLLVKRSQGKKRFGPVN--YKERWFVLTKSSLSYYEGDGGKRGKEKGSIDLSKIK 55
>gnl|CDD|241409 cd13255, PH_TAAP2-like, Tandem PH-domain-containing protein 2
Pleckstrin homology (PH) domain. The binding of TAPP2
(also called PLEKHA2) adaptors to PtdIns(3,4)P(2), but
not PI(3,4, 5)P3, function as negative regulators of
insulin and PI3K signalling pathways (i.e.
TAPP/utrophin/syntrophin complex). TAPP2 contains two
sequential PH domains in which the C-terminal PH domain
specifically binds PtdIns(3,4)P2 with high affinity.
The N-terminal PH domain does not interact with any
phosphoinositide tested. They also contain a C-terminal
PDZ-binding motif that interacts with several
PDZ-binding proteins, including PTPN13 (known
previously as PTPL1 or FAP-1) as well as the
scaffolding proteins MUPP1 (multiple
PDZ-domain-containing protein 1), syntrophin and
utrophin. The members here are most sequence similar to
TAPP2 proteins, but may not be actual TAPP2 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 = 110
Score = 48.2 bits (115), Expect = 1e-08
Identities = 24/62 (38%), Positives = 35/62 (56%), Gaps = 9/62 (14%)
Query: 37 LISDDILRQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYYDTDSEIFLSGIRLSDL 96
+IS+ +L+ G+L K+ + +K +K+RWFVL L YY D E L +RL DL
Sbjct: 1 MISEAVLKAGYLEKKGERRKT-------WKKRWFVLRPTKLAYYKNDKEYRL--LRLIDL 51
Query: 97 PD 98
D
Sbjct: 52 TD 53
>gnl|CDD|241522 cd13371, PH_GAP1_mammal-like, GAP1(IP4BP) pleckstrin homology
(PH) domain. GAP1 (also called IP4BP, RASA3/Ras
GTPase-activating protein 3, and RAS p21 protein
activator (GTPase activating protein)
3/GAPIII/MGC46517/MGC47588)) is a member of the GAP1
family of GTPase-activating proteins, along with
RASAL1, GAP1(m), and CAPRI. With the notable exception
of GAP1(m), they all possess an arginine
finger-dependent GAP activity on the Ras-related
protein Rap1. GAP1(IP4BP) contains two C2 domains, a PH
domain, a RasGAP domain, and a BTK domain. Its C2
domains, like those of GAP1M, do not contain the C2
motif that is known to be required for
calcium-dependent phospholipid binding. GAP1(IP4BP) is
regulated by the binding of its PH domains to
phophoinositides, PIP3 (phosphatidylinositol
3,4,5-trisphosphate) and PIP2 (phosphatidylinositol
4,5-bisphosphate). It suppresses RAS, enhancing the
weak intrinsic GTPase activity of RAS proteins
resulting in the inactive GDP-bound form of RAS,
allowing control of cellular proliferation and
differentiation. GAP1(IP4BP) binds tyrosine-protein
kinase, HCK. Members here include humans, chickens,
frogs, and fish. 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 = 46.6 bits (110), Expect = 7e-08
Identities = 20/55 (36%), Positives = 34/55 (61%), Gaps = 2/55 (3%)
Query: 42 ILRQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYYDTDSEIFLSGIRLSDL 96
+L++GF+IKR+Q +KRF N+K+RWF LT Y+ + + L I + ++
Sbjct: 16 LLKEGFMIKRAQGRKRFGM--KNFKKRWFRLTNHEFTYHKSKGDHPLCSIPIENI 68
>gnl|CDD|241277 cd01244, PH_GAP1-like, RAS p21 protein activator (GTPase
activating protein) family pleckstrin homology (PH)
domain. RASAL1, GAP1(m), GAP1(IP4BP), and CAPRI are
all members of the GAP1 family of GTPase-activating
proteins. They contain N-terminal SH2-SH3-SH2 domains,
followed by two C2 domains, a PH domain, a RasGAP
domain, and a BTK domain. With the notable exception of
GAP1(m), they all possess an arginine finger-dependent
GAP activity on the Ras-related protein Rap1. They act
as a suppressor of RAS enhancing the weak intrinsic
GTPase activity of RAS proteins resulting in the
inactive GDP-bound form of RAS, allowing control of
cellular proliferation and differentiation. PH domains
share little sequence conservation, but all have a
common fold, which is electrostatically polarized. 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 = 45.7 bits (109), Expect = 1e-07
Identities = 19/53 (35%), Positives = 29/53 (54%), Gaps = 3/53 (5%)
Query: 44 RQGFLIKRSQN-KKRFSTSNNNYKQRWFVLTTKHLIYYDTDSEIFLSGIRLSD 95
++G+LIKR+Q K + N +K+R+F LT + L Y + L I L D
Sbjct: 1 KEGYLIKRAQGRKGKLGRKN--FKKRYFRLTNEALSYSKSKGSQPLCSIPLQD 51
>gnl|CDD|215766 pfam00169, PH, PH domain. PH stands for pleckstrin homology.
Length = 101
Score = 45.2 bits (107), Expect = 2e-07
Identities = 17/66 (25%), Positives = 36/66 (54%), Gaps = 14/66 (21%)
Query: 42 ILRQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYYDTDSE--------IFLSGIRL 93
++++G+L+K+ ++ ++K+R+FVL L+YY + I LSG ++
Sbjct: 1 VIKEGWLLKKGSGGRK------SWKKRYFVLFDGVLLYYKDSKKSSSRPKGSIPLSGCQV 54
Query: 94 SDLPDQ 99
+ +PD
Sbjct: 55 TKVPDS 60
>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 = 44.5 bits (105), Expect = 4e-07
Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 15/71 (21%)
Query: 42 ILRQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYYDTDSE---------IFLSGIR 92
++++G+L K+S K+ ++K+R+FVL L+YY + + I LSG
Sbjct: 1 VIKEGWLYKKSGGGKK------SWKKRYFVLFNSTLLYYKSKKDKKSYKPKGSIDLSGCT 54
Query: 93 LSDLPDQIFHD 103
+ + PD
Sbjct: 55 VREAPDPDSSK 65
>gnl|CDD|241431 cd13277, PH_Bem3, Bud emergence protein 3 (Bem3) Pleckstrin
homology (PH) domain. Bud emergence in Saccharomyces
cerevisiae involves cell cycle-regulated reorganizations
of cortical cytoskeletal elements and requires the
action of the Rho-type GTPase Cdc42. Bem3 contains a
RhoGAP domain and a PH domain. Though Bem3 and Bem2 both
contain a RhoGAP, but only Bem3 is able to stimulate the
hydrolysis of GTP on Cdc42. Bem3 is thought to be the
GAP for Cdc42. 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 = 111
Score = 42.7 bits (101), Expect = 2e-06
Identities = 19/71 (26%), Positives = 33/71 (46%), Gaps = 11/71 (15%)
Query: 40 DDILRQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYYDTDSEIFLSGIRL------ 93
D +++G+L+KR +K+ S +K R+ VL L Y++ L I+L
Sbjct: 1 GDSVKEGYLLKR---RKKTLGSTGGWKLRYGVLDGNILELYESRGGQLLESIKLRNAQIE 57
Query: 94 --SDLPDQIFH 102
+LPD +
Sbjct: 58 RQPNLPDDKYG 68
>gnl|CDD|241450 cd13296, PH2_MyoX, Myosin X Pleckstrin homology (PH) domain,
repeat 2. MyoX, a MyTH-FERM myosin, is a molecular
motor that has crucial functions in the transport
and/or tethering of integrins in the actin-based
extensions known as filopodia, microtubule binding, and
in netrin-mediated axon guidance. It functions as a
dimer. MyoX walks on bundles of actin, rather than
single filaments, unlike the other unconventional
myosins. MyoX is present in organisms ranging from
humans to choanoflagellates, but not in Drosophila and
Caenorhabditis elegans.MyoX consists of a N-terminal
motor/head region, a neck made of 3 IQ motifs, and a
tail consisting of a coiled-coil domain, a PEST region,
3 PH domains, a myosin tail homology 4 (MyTH4), and a
FERM domain at its very C-terminus. The first PH domain
in the MyoX tail is a split-PH domain, interupted by
the second PH domain such that PH 1a and PH 1b flanks
PH 2. The third PH domain (PH 3) follows the PH 1b
domain. This cd contains the second PH repeat. 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 = 111
Score = 42.4 bits (100), Expect = 3e-06
Identities = 17/45 (37%), Positives = 23/45 (51%), Gaps = 2/45 (4%)
Query: 41 DILRQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYYDTDSE 85
+ L+ G+L K+ S N+K RWFVL L YY+ D E
Sbjct: 6 EALKSGWLYKKGGGSSTLS--RKNWKSRWFVLRDTVLKYYENDQE 48
>gnl|CDD|241427 cd13273, PH_SWAP-70, Switch-associated protein-70 Pleckstrin
homology (PH) domain. SWAP-70 (also called
Differentially expressed in FDCP 6/DEF-6 or
IRF4-binding protein) functions in cellular signal
transduction pathways (in conjunction with Rac),
regulates cell motility through actin rearrangement,
and contributes to the transformation and invasion
activity of mouse embryo fibroblasts. Metazoan SWAP-70
is found in B lymphocytes, mast cells, and in a variety
of organs. Metazoan SWAP-70 contains an N-terminal
EF-hand motif, a centrally located PH domain, and a
C-terminal coiled-coil domain. The PH domain of
Metazoan SWAP-70 contains a phosphoinositide-binding
site and a nuclear localization signal (NLS), which
localize SWAP-70 to the plasma membrane and nucleus,
respectively. The NLS is a sequence of four Lys
residues located at the N-terminus of the C-terminal
a-helix; this is a unique characteristic of the
Metazoan SWAP-70 PH domain. The SWAP-70 PH domain binds
PtdIns(3,4,5)P3 and PtdIns(4,5)P2 embedded in lipid
bilayer vesicles. There are additional plant SWAP70
proteins, but these are not included in this hierarchy.
Rice SWAP70 (OsSWAP70) exhibits GEF activity toward the
its Rho GTPase, OsRac1, and regulates chitin-induced
production of reactive oxygen species and defense gene
expression in rice. Arabidopsis SWAP70 (AtSWAP70) plays
a role in both PAMP- and effector-triggered immunity.
Plant SWAP70 contains both DH and PH domains, but their
arrangement is the reverse of that in typical
DH-PH-type Rho GEFs, wherein the DH domain is flanked
by a C-terminal PH 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 = 110
Score = 40.3 bits (95), Expect = 1e-05
Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 7/45 (15%)
Query: 36 DLISDDILRQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYY 80
D + D++++G+L K+ +++RWFVL L YY
Sbjct: 2 DELILDVIKKGYLWKKGHLLP-------TWRERWFVLKPNSLSYY 39
>gnl|CDD|241268 cd01235, PH_Sbf1_hMTMR5, Set binding factor 1 (also called Human
MTMR5) Pleckstrin Homology (PH) domain. Sbf1 is a
myotubularin-related pseudo-phosphatase. Both Sbf1 and
myotubularin interact with the SET domains of Hrx and
other epigenetic regulatory proteins, but Sbf1 lacks
phosphatase activity due to several amino acid changes
in its structurally preserved catalytic pocket. It
contains pleckstrin (PH), GEF, and myotubularin
homology domains that are thought to be responsible for
signaling and growth control. Sbf1 functions as an
inhibitor of cellular growth. The N-terminal GEF
homology domain serves to inhibit the transforming
effects of Sbf1. 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 = 106
Score = 38.8 bits (91), Expect = 4e-05
Identities = 18/43 (41%), Positives = 24/43 (55%), Gaps = 9/43 (20%)
Query: 45 QGFLIKRSQNKKRFSTSNNNYKQRWFVL-TTKH-LIYYDTDSE 85
+G+L KR K +KQRWFVL TKH L YY++ +
Sbjct: 6 EGYLYKRGALLK-------GWKQRWFVLDLTKHQLRYYESKED 41
>gnl|CDD|241442 cd13288, PH_Ses, Sesquipedalian family Pleckstrin homology (PH)
domain. The sesquipedalian family has 2 mammalian
members: Ses1 and Ses2, which are also callled 7 kDa
inositol polyphosphate phosphatase-interacting protein
1 and 2. They play a role in endocytic trafficking and
are required for receptor recycling from endosomes,
both to the trans-Golgi network and the plasma
membrane. Members of this family form homodimers and
heterodimers. Sesquipedalian interacts with inositol
polyphosphate 5-phosphatase OCRL-1 (INPP5F) also known
as Lowe oculocerebrorenal syndrome protein, a
phosphatase enzyme that is involved in actin
polymerization and is found in the trans-Golgi network
and INPP5B. Sesquipedalian contains a single PH 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 = 120
Score = 38.7 bits (91), Expect = 7e-05
Identities = 18/64 (28%), Positives = 31/64 (48%), Gaps = 15/64 (23%)
Query: 44 RQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYYD--TDSE----IFLSG--IRLSD 95
++G+L K+ + +Y++RWFVL L Y++ D E I L G + LS+
Sbjct: 10 KEGYLWKKGERNT-------SYQKRWFVLKGNLLFYFEKKGDREPLGVIVLEGCTVELSE 62
Query: 96 LPDQ 99
+
Sbjct: 63 DEEP 66
>gnl|CDD|241521 cd13370, PH_GAP1m_mammal-like, GTPase activating protein 1 m
pleckstrin homology (PH) domain. GAP1(m) (also called
RASA2/RAS p21 protein activator (GTPase activating
protein) 2) is a member of the GAP1 family of
GTPase-activating proteins, along with RASAL1,
GAP1(IP4BP), and CAPRI. With the notable exception of
GAP1(m), they all possess an arginine finger-dependent
GAP activity on the Ras-related protein Rap1. GAP1(m)
contains two C2 domains, a PH domain, a RasGAP domain,
and a BTK domain. Its C2 domains, like those of
GAP1IP4BP, do not contain the C2 motif that is known to
be required for calcium-dependent phospholipid binding.
GAP1(m) is regulated by the binding of its PH domains
to phophoinositides, PIP3 (phosphatidylinositol
3,4,5-trisphosphate). It suppresses RAS, enhancing the
weak intrinsic GTPase activity of RAS proteins
resulting in the inactive GDP-bound form of RAS,
allowing control of cellular proliferation and
differentiation. GAP1(m) binds inositol
tetrakisphosphate (IP4). 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 = 133
Score = 38.4 bits (89), Expect = 1e-04
Identities = 15/39 (38%), Positives = 25/39 (64%), Gaps = 2/39 (5%)
Query: 42 ILRQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYY 80
L++G + KR+Q + R N+K+RWF LT++ L Y+
Sbjct: 16 HLKEGEMHKRAQGRTRIG--KKNFKKRWFCLTSRELTYH 52
>gnl|CDD|241452 cd13298, PH1_PH_fungal, Fungal proteins Pleckstrin homology (PH)
domain, repeat 1. The functions of these fungal
proteins are unknown, but they all contain 2 PH
domains. This cd represents the first PH repeat. 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 = 106
Score = 37.6 bits (88), Expect = 1e-04
Identities = 18/46 (39%), Positives = 26/46 (56%), Gaps = 7/46 (15%)
Query: 40 DDILRQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYYDTDSE 85
D +L+ G+L+KRS+ K +K+RWFVL L YY + E
Sbjct: 4 DRVLKSGWLLKRSRKTK-------TWKKRWFVLRPCQLSYYKDEKE 42
>gnl|CDD|241455 cd13301, PH1_Pleckstrin_2, Pleckstrin 2 Pleckstrin homology (PH)
domain, repeat 1. Pleckstrin is a protein found in
platelets. This name is derived from platelet and
leukocyte C kinase substrate and the KSTR string of
amino acids. Pleckstrin 2 contains two PH domains and a
DEP (dishvelled, egl-10, and pleckstrin) domain. Unlike
pleckstrin 1, pleckstrin 2 does not contain obvious
sites of PKC phosphorylation. Pleckstrin 2 plays a role
in actin rearrangement, large lamellipodia and
peripheral ruffle formation, and may help orchestrate
cytoskeletal arrangement. The PH domains of pleckstrin
2 are thought to contribute to lamellipodia formation.
This cd contains the first PH domain repeat. 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 = 37.3 bits (87), Expect = 2e-04
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 7/39 (17%)
Query: 42 ILRQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYY 80
+L++GFL+K+ NN+K RWFVL L YY
Sbjct: 3 VLKEGFLVKKG-------HVVNNWKARWFVLLEDKLEYY 34
>gnl|CDD|241231 cd00821, PH, Pleckstrin homology (PH) 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 = 92
Score = 36.9 bits (85), Expect = 2e-04
Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 6/57 (10%)
Query: 44 RQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYYDTDSEIFLSGIRLSDLPDQI 100
++G+L KR + ++K+RWFVL L+YY + + L L D +
Sbjct: 1 KEGWLKKRGGKGLK------SWKKRWFVLFDDVLLYYKSKKDSSKKPKGLIPLSDGL 51
>gnl|CDD|241309 cd10573, PH_DAPP1, Dual Adaptor for Phosphotyrosine and
3-Phosphoinositides Pleckstrin homology (PH) domain.
DAPP1 (also known as PHISH/3'
phosphoinositide-interacting SH2 domain-containing
protein or Bam32) plays a role in B-cell activation and
has potential roles in T-cell and mast cell function.
DAPP1 promotes B cell receptor (BCR) induced activation
of Rho GTPases Rac1 and Cdc42, which feed into
mitogen-activated protein kinases (MAPK) activation
pathways and affect cytoskeletal rearrangement.
DAPP1can also regulate BCR-induced activation of
extracellular signal-regulated kinase (ERK), and c-jun
NH2-terminal kinase (JNK). DAPP1 contains an N-terminal
SH2 domain and a C-terminal pleckstrin homology (PH)
domain with a single tyrosine phosphorylation site
located centrally. DAPP1 binds strongly to both
PtdIns(3,4,5)P3 and PtdIns(3,4)P2. The PH domain is
essential for plasma membrane recruitment of PI3K upon
cell activation. 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 = 96
Score = 36.9 bits (86), Expect = 2e-04
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 7/39 (17%)
Query: 44 RQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYYDT 82
++G+L K+ K N+K RWFVL L Y+ T
Sbjct: 5 KEGYLTKQGGIVK-------NWKTRWFVLRKNELKYFKT 36
>gnl|CDD|241283 cd01252, PH_GRP1-like, General Receptor for
Phosphoinositides-1-like Pleckstrin homology (PH)
domain. GRP1/cytohesin3 and the related proteins ARNO
(ARF nucleotide-binding site opener)/cytohesin-2 and
cytohesin-1 are ARF exchange factors that contain a
pleckstrin homology (PH) domain thought to target these
proteins to cell membranes through binding
polyphosphoinositides. The PH domains of all three
proteins exhibit relatively high affinity for
PtdIns(3,4,5)P3. Within the Grp1 family, diglycine (2G)
and triglycine (3G) splice variants, differing only in
the number of glycine residues in the PH domain,
strongly influence the affinity and specificity for
phosphoinositides. The 2G variants selectively bind
PtdIns(3,4,5)P3 with high affinity,the 3G variants bind
PtdIns(3,4,5)P3 with about 30-fold lower affinity and
require the polybasic region for plasma membrane
targeting. These ARF-GEFs share a common, tripartite
structure consisting of an N-terminal coiled-coil
domain, a central domain with homology to the yeast
protein Sec7, a PH domain, and a C-terminal polybasic
region. The Sec7 domain is autoinhibited by conserved
elements proximal to the PH domain. GRP1 binds to the
DNA binding domain of certain nuclear receptors
(TRalpha, TRbeta, AR, ER, but not RXR), and can repress
thyroid hormone receptor (TR)-mediated transactivation
by decreasing TR-complex formation on thyroid hormone
response elements. ARNO promotes sequential activation
of Arf6, Cdc42 and Rac1 and insulin secretion.
Cytohesin acts as a PI 3-kinase effector mediating
biological responses including cell spreading and
adhesion, chemotaxis, protein trafficking, and
cytoskeletal rearrangements, only some of which appear
to depend on their ability to activate ARFs. 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 = 118
Score = 36.9 bits (86), Expect = 3e-04
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 13/61 (21%)
Query: 44 RQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYYD--TDSE----IFLSGIRLSDLP 97
R+G+L+K K ++K+RWF+LT L Y++ TD E I L + + ++
Sbjct: 5 REGWLLKLGGRVK-------SWKRRWFILTDNCLYYFEYTTDKEPRGIIPLENLSVREVE 57
Query: 98 D 98
D
Sbjct: 58 D 58
>gnl|CDD|241404 cd13250, PH_ACAP, ArfGAP with coiled-coil, ankyrin repeat and PH
domains Pleckstrin homology (PH) domain. ACAP (also
called centaurin beta) functions both as a Rab35
effector and as an Arf6-GTPase-activating protein (GAP)
by which it controls actin remodeling and membrane
trafficking. ACAP contain an NH2-terminal
bin/amphiphysin/Rvs (BAR) domain, a phospholipid-binding
domain, a PH domain, a GAP domain, and four ankyrin
repeats. The AZAPs constitute a family of Arf GAPs that
are characterized by an NH2-terminal pleckstrin homology
(PH) domain and a central Arf GAP domain followed by two
or more ankyrin repeats. On the basis of sequence and
domain organization, the AZAP family is further
subdivided into four subfamilies: 1) the ACAPs contain
an NH2-terminal bin/amphiphysin/Rvs (BAR) domain (a
phospholipid-binding domain that is thought to sense
membrane curvature), a single PH domain followed by the
GAP domain, and four ankyrin repeats; 2) the ASAPs also
contain an NH2-terminal BAR domain, the tandem PH
domain/GAP domain, three ankyrin repeats, two
proline-rich regions, and a COOH-terminal Src homology 3
domain; 3) the AGAPs contain an NH2-terminal GTPase-like
domain (GLD), a split PH domain, and the GAP domain
followed by four ankyrin repeats; and 4) the ARAPs
contain both an Arf GAP domain and a Rho GAP domain, as
well as an NH2-terminal sterile-a motif (SAM), a
proline-rich region, a GTPase-binding domain, and five
PH domains. PMID 18003747 and 19055940 Centaurin can
bind to phosphatidlyinositol (3,4,5)P3. 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 = 98
Score = 36.4 bits (85), Expect = 4e-04
Identities = 15/67 (22%), Positives = 29/67 (43%), Gaps = 15/67 (22%)
Query: 44 RQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYYDTDSE---------IFLSGIRLS 94
++G+L KRS S + +K+RWF + L+Y + + L ++
Sbjct: 1 KEGYLFKRS------SNAFKTWKRRWFSIQNGQLVYQKRFKKDTPTVVVEDLRLCTVKPC 54
Query: 95 DLPDQIF 101
+ D+ F
Sbjct: 55 EDIDRRF 61
>gnl|CDD|241529 cd13378, PH_RhoGAP2, Rho GTPase activating protein 2 Pleckstrin
homology (PH) domain. RhoGAP2 (also called RhoGap22 or
ArhGap22) are involved in cell polarity, cell
morphology and cytoskeletal organization. They activate
a GTPase belonging to the RAS superfamily of small
GTP-binding proteins. The encoded protein is
insulin-responsive, is dependent on the kinase Akt, and
requires the Akt-dependent 14-3-3 binding protein which
binds sequentially to two serine residues resulting in
regulation of cell motility. Members here contain an
N-terminal PH domain followed by a RhoGAP domain and
either a BAR or TATA Binding Protein (TBP) Associated
Factor 4 (TAF4) 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 = 116
Score = 36.5 bits (84), Expect = 4e-04
Identities = 21/62 (33%), Positives = 32/62 (51%), Gaps = 13/62 (20%)
Query: 42 ILRQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYYDTDSE------IFLSGIRLSD 95
+L+ G+L K+ K N++QRWFVL L YY + E I L G ++++
Sbjct: 3 VLKAGWLKKQRSIMK-------NWQQRWFVLRGDQLFYYKDEEETKPQGCISLQGSQVNE 55
Query: 96 LP 97
LP
Sbjct: 56 LP 57
>gnl|CDD|241402 cd13248, PH_PEPP1_2_3, Phosphoinositol 3-phosphate binding
proteins 1, 2, and 3 pleckstrin homology (PH) domain.
PEPP1 (also called PLEKHA4/PH domain-containing family
A member 4 and RHOXF1/Rhox homeobox family member 1),
and related homologs PEPP2 (also called PLEKHA5/PH
domain-containing family A member 5) and PEPP3 (also
called PLEKHA6/PH domain-containing family A member 6),
have PH domains that interact specifically with
PtdIns(3,4)P3. Other proteins that bind PtdIns(3,4)P3
specifically are: TAPP1 (tandem PH-domain-containing
protein-1) and TAPP2], PtdIns3P AtPH1, and Ptd-
Ins(3,5)P2 (centaurin-beta2). All of these proteins
contain at least 5 of the 6 conserved amino acids that
make up the putative phosphatidylinositol 3,4,5-
trisphosphate-binding motif (PPBM) located at their
N-terminus. 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 = 104
Score = 35.3 bits (82), Expect = 0.001
Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 6/52 (11%)
Query: 39 SDDILRQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYYDTDSEIFLSG 90
+ ++ G+L K+ + + N+K+RWFVL L YY E G
Sbjct: 4 NAPVVFSGWLHKQGGSGLK------NWKKRWFVLKDNCLYYYKDPEEEKALG 49
>gnl|CDD|241417 cd13263, PH_RhoGap25-like, Rho GTPase activating protein 25 and
related proteins Pleckstrin homology (PH) domain.
RhoGAP25 (also called ArhGap25) like other RhoGaps are
involved in cell polarity, cell morphology and
cytoskeletal organization. They act as GTPase
activators for the Rac-type GTPases by converting them
to an inactive GDP-bound state and control actin
remodeling by inactivating Rac downstream of Rho
leading to suppress leading edge protrusion and
promotes cell retraction to achieve cellular polarity
and are able to suppress RAC1 and CDC42 activity in
vitro. Overexpression of these proteins induces cell
rounding with partial or complete disruption of actin
stress fibers and formation of membrane ruffles,
lamellipodia, and filopodia. This hierarchy contains
RhoGAP22, RhoGAP24, and RhoGAP25. Members here contain
an N-terminal PH domain followed by a RhoGAP domain and
either a BAR or TATA Binding Protein (TBP) Associated
Factor 4 (TAF4) 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 = 114
Score = 35.4 bits (82), Expect = 0.001
Identities = 19/64 (29%), Positives = 30/64 (46%), Gaps = 13/64 (20%)
Query: 41 DILRQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYYDTDSE------IFLSGIRLS 94
+++ G+L K+ K N+++RWFVL L YY + E I L G +
Sbjct: 2 KVIKSGWLKKQGGIVK-------NWQRRWFVLRGDQLYYYKDEDESKPQGCIPLPGNTVK 54
Query: 95 DLPD 98
+LP
Sbjct: 55 ELPF 58
>gnl|CDD|241415 cd13261, PH_RasGRF1_2, Ras-specific guanine nucleotide-releasing
factors 1 and 2 Pleckstrin homology (PH) domain.
RasGRF1 (also called GRF1; CDC25Mm/Ras-specific
nucleotide exchange factor CDC25; GNRP/Guanine
nucleotide-releasing protein) and RasGRF2 (also called
GRF2; Ras guanine nucleotide exchange factor 2) are a
family of guanine nucleotide exchange factors (GEFs).
They both promote the exchange of Ras-bound GDP by GTP,
thereby regulating the RAS signaling pathway. RasGRF1
and RasGRF2 form homooligomers and heterooligomers.
GRF1 has 3 isoforms and GRF2 has 2 isoforms. The
longest isoforms of RasGRF1 and RasGRF2 contain the
following domains: a Rho-GEF domain sandwiched between
2 PH domains, IQ domains, a REM (Ras exchanger motif)
domain, and a Ras-GEF domainwhich gives them the
capacity to activate both Ras and Rac GTPases in
response to signals from a variety of neurotransmitter
receptors. Their IQ domains allow them to act as
calcium sensors to mediate the actions of NMDA-type and
calcium-permeable AMPA-type glutamate receptors. GRF1
also mediates the action of dopamine receptors that
signal through cAMP. GRF1 and GRF2 play strikingly
different roles in regulating MAP kinase family
members, neuronal synaptic plasticity, specific forms
of learning and memory, and behavioral responses to
psychoactive drugs. 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 = 35.0 bits (81), Expect = 0.002
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 7/50 (14%)
Query: 44 RQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYYDTDSEIFLSGIRL 93
R+G+L K+S + N+ + +WF L L Y++ +S SG+ L
Sbjct: 7 RRGYLSKKS-------SDNSKWHTKWFALYQNLLFYFENESSSRPSGLYL 49
>gnl|CDD|241531 cd13380, PH_Skap1, Src kinase-associated phosphoprotein 1
Pleckstrin homology (PH) domain. Adaptor protein Skap1
(also called Skap55/Src kinase-associated
phosphoprotein of 55 kDa) and its partner, ADAP
(adhesion and degranulation promoting adapter protein)
help reorganize the cytoskeleton and/or promote
integrin-mediated adhesion upon immunoreceptor
activation. Skap1 is also involved in T Cell Receptor
(TCR)-induced RapL-Rap1 complex formation and LFA-1
activation. Skap1 has an N-terminal coiled-coil
conformation which is proposed to be involved in
homodimer formation, a central PH domain and a
C-terminal SH3 domain that associates with ADAP. The
Skap1 PH domain plays a role in controlling integrin
function via recruitment of ADAP-SKAP complexes to
integrins as well as in controlling the ability of ADAP
to interact with the CBM signalosome and regulate
NF-kappaB. SKAP1 is necessary for RapL binding to
membranes in a PH domain-dependent manner and the PI3K
pathway. Skap adaptor proteins couple receptors to
cytoskeletal rearrangements. Skap55/Skap1, Skap2, and
Skap-homology (Skap-hom) have an N-terminal coiled-coil
conformation, a central PH domain and a C-terminal SH3
domain. Their PH domains bind 3'-phosphoinositides as
well as directly affecting targets such as in Skap55
where it directly affecting integrin regulation by ADAP
and NF-kappaB activation or in Skap-hom where the
dimerization and PH domains comprise a
3'-phosphoinositide-gated molecular switch that
controls ruffle formation. 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 = 106
Score = 34.1 bits (78), Expect = 0.002
Identities = 16/39 (41%), Positives = 25/39 (64%), Gaps = 3/39 (7%)
Query: 42 ILRQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYY 80
I +QG+L KRS++ F + +++RW VLTT+ YY
Sbjct: 1 IFKQGYLEKRSKDHGFFGSE---WQKRWCVLTTRAFYYY 36
>gnl|CDD|241430 cd13276, PH_AtPH1, Arabidopsis thaliana Pleckstrin homolog (PH) 1
(AtPH1) PH domain. AtPH1 is expressed in all plant
tissue and is proposed to be the plant homolog of human
pleckstrin. Pleckstrin consists of two PH domains
separated by a linker region, while AtPH has a single
PH domain with a short N-terminal extension. AtPH1
binds PtdIns3P specifically and is thought to be an
adaptor molecule since it has no obvious catalytic
functions. 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 = 117
Score = 34.3 bits (79), Expect = 0.003
Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 14/59 (23%)
Query: 40 DDILRQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYYDTDSE-------IFLSGI 91
D + G+L K+ + K +++RWFVL L Y+ + I LS
Sbjct: 5 SDPEKAGWLTKQGGSIK-------TWRRRWFVLKQGKLFYFKDEDPDSEPRGVIDLSDC 56
>gnl|CDD|241420 cd13266, PH_Skap_family, Src kinase-associated phosphoprotein
family Pleckstrin homology (PH) domain. Skap adaptor
proteins couple receptors to cytoskeletal
rearrangements. Src kinase-associated phosphoprotein of
55 kDa (Skap55)/Src kinase-associated phosphoprotein 1
(Skap1), Skap2, and Skap-homology (Skap-hom) have an
N-terminal coiled-coil conformation, a central PH
domain and a C-terminal SH3 domain. Their PH domains
bind 3'-phosphoinositides as well as directly affecting
targets such as in Skap55 where it directly affecting
integrin regulation by ADAP and NF-kappaB activation or
in Skap-hom where the dimerization and PH domains
comprise a 3'-phosphoinositide-gated molecular switch
that controls ruffle formation. PH domains are only
found in eukaryotes. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. 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 = 106
Score = 34.0 bits (78), Expect = 0.003
Identities = 13/42 (30%), Positives = 25/42 (59%), Gaps = 3/42 (7%)
Query: 42 ILRQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYYDTD 83
+L+QG+L KR ++ F + +++RW VL+ YY ++
Sbjct: 1 VLKQGYLEKRRKDHSFFG---SEWQKRWCVLSNTAFYYYGSE 39
>gnl|CDD|241282 cd01251, PH2_ADAP, ArfGAP with dual PH domains Pleckstrin
homology (PH) domain, repeat 2. ADAP (also called
centaurin alpha) is a phophatidlyinositide binding
protein consisting of an N-terminal ArfGAP domain and
two PH domains. In response to growth factor
activation, PI3K phosphorylates phosphatidylinositol
4,5-bisphosphate to phosphatidylinositol
3,4,5-trisphosphate. Centaurin alpha 1 is recruited to
the plasma membrane following growth factor stimulation
by specific binding of its PH domain to
phosphatidylinositol 3,4,5-trisphosphate. Centaurin
alpha 2 is constitutively bound to the plasma membrane
since it binds phosphatidylinositol 4,5-bisphosphate
and phosphatidylinositol 3,4,5-trisphosphate with equal
affinity. This cd contains the second PH domain repeat.
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 = 105
Score = 32.9 bits (76), Expect = 0.007
Identities = 15/54 (27%), Positives = 28/54 (51%), Gaps = 12/54 (22%)
Query: 41 DILRQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYYD--TDS----EIFL 88
D L++G+L K + + +++RWF L + L+Y+ D+ EIF+
Sbjct: 1 DFLKEGYLEKTGPKQ------TDGFRKRWFTLDDRRLMYFKDPLDAFPKGEIFI 48
>gnl|CDD|241407 cd13253, PH1_ARAP, ArfGAP with RhoGAP domain, ankyrin repeat and
PH domain Pleckstrin homology (PH) domain, repeat 1.
ARAP proteins (also called centaurin delta) are
phosphatidylinositol 3,4,5-trisphosphate-dependent
GTPase-activating proteins that modulate actin
cytoskeleton remodeling by regulating ARF and RHO
family members. They bind phosphatidylinositol
3,4,5-trisphosphate (PtdIns(3,4,5)P3) and
phosphatidylinositol 3,4-bisphosphate (PtdIns(3,4,5)P2)
binding. There are 3 mammalian ARAP proteins: ARAP1,
ARAP2, and ARAP3. All ARAP proteins contain a
N-terminal SAM (sterile alpha motif) domain, 5 PH
domains, an ArfGAP domain, 2 ankyrin domain, A RhoGap
domain, and a Ras-associating domain. This hierarchy
contains the first PH domain in ARAP. 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 = 93
Score = 31.9 bits (73), Expect = 0.015
Identities = 8/27 (29%), Positives = 17/27 (62%)
Query: 65 YKQRWFVLTTKHLIYYDTDSEIFLSGI 91
+++RW V L Y++++ E++ GI
Sbjct: 17 FQKRWVVFDGDSLRYFNSEKEMYSKGI 43
>gnl|CDD|241435 cd13281, PH_PLEKHD1, Pleckstrin homology (PH) domain containing,
family D (with coiled-coil domains) member 1 PH domain.
Human PLEKHD1 (also called UPF0639, pleckstrin
homology domain containing, family D (with M protein
repeats) member 1) is a single transcript and contains
a single PH domain. PLEKHD1 is conserved in human,
chimpanzee, , dog, cow, mouse, chicken, zebrafish, and
Caenorhabditis elegans. 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 = 31.6 bits (72), Expect = 0.035
Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 5/46 (10%)
Query: 35 DDLISDDILRQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYY 80
D S + G L KR F + + +R+FVL L+YY
Sbjct: 5 LDDFSTKVQLSGVLWKRP-----FGRQSAKWSKRFFVLKECFLLYY 45
>gnl|CDD|241530 cd13379, PH_RhoGap24, Rho GTPase activating protein 24 Pleckstrin
homology (PH) domain. RhoGap24 (also called ARHGAP24,
p73RhoGAp, and Filamin-A-associated RhoGAP) like other
RhoGAPs are involved in cell polarity, cell morphology
and cytoskeletal organization. They act as GTPase
activators for the Rac-type GTPases by converting them
to an inactive GDP-bound state and control actin
remodeling by inactivating Rac downstream of Rho
leading to suppress leading edge protrusion and
promotes cell retraction to achieve cellular polarity
and are able to suppress RAC1 and CDC42 activity in
vitro. Overexpression of these proteins induces cell
rounding with partial or complete disruption of actin
stress fibers and formation of membrane ruffles,
lamellipodia, and filopodia. Members here contain an
N-terminal PH domain followed by a RhoGAP domain and
either a BAR or TATA Binding Protein (TBP) Associated
Factor 4 (TAF4) 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 = 114
Score = 29.9 bits (67), Expect = 0.12
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 13/63 (20%)
Query: 41 DILRQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYYDTDSE------IFLSGIRLS 94
++++ G+L K+ K + T RWFVL L Y+ + E IFL G R++
Sbjct: 2 EVIKCGWLRKQGGFVKTWHT-------RWFVLKGDQLYYFKDEDETKPLGTIFLPGNRVT 54
Query: 95 DLP 97
+ P
Sbjct: 55 EHP 57
>gnl|CDD|241369 cd13215, PH-GRAM1_AGT26, Autophagy-related protein 26/Sterol
3-beta-glucosyltransferase Pleckstrin homology (PH)
domain, repeat 1. ATG26 (also called
UGT51/UDP-glycosyltransferase 51), a member of the
glycosyltransferase 28 family, resulting in the
biosynthesis of sterol glucoside. ATG26 in decane
metabolism and autophagy. There are 32 known
autophagy-related (ATG) proteins, 17 are components of
the core autophagic machinery essential for all
autophagy-related pathways and 15 are the additional
components required only for certain pathways or
species. The core autophagic machinery includes 1) the
ATG9 cycling system (ATG1, ATG2, ATG9, ATG13, ATG18,
and ATG27), 2) the phosphatidylinositol 3-kinase
complex (ATG6/VPS30, ATG14, VPS15, and ATG34), and 3)
the ubiquitin-like protein system (ATG3, ATG4, ATG5,
ATG7, ATG8, ATG10, ATG12, and ATG16). Less is known
about how the core machinery is adapted or modulated
with additional components to accommodate the
nonselective sequestration of bulk cytosol
(autophagosome formation) or selective sequestration of
specific cargos (Cvt vesicle, pexophagosome, or
bacteria-containing autophagosome formation). The
pexophagosome-specific additions include the
ATG30-ATG11-ATG17 receptor-adaptors complex, the
coiled-coil protein ATG25, and the sterol
glucosyltransferase ATG26. ATG26 is necessary for the
degradation of medium peroxisomes. It contains 2 GRAM
domains and a single PH domain. PH domains are only
found in eukaryotes. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. PH domains also have
diverse functions. They are often involved in targeting
proteins to the plasma membrane, but 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 = 130
Score = 29.8 bits (68), Expect = 0.14
Identities = 12/49 (24%), Positives = 25/49 (51%), Gaps = 7/49 (14%)
Query: 39 SDDILRQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYYDTDSEIF 87
++++ G+L KR + R Y + WFVL L +Y + ++++
Sbjct: 26 EGEVVKSGYLSKRGKRTPR-------YNRYWFVLKGDVLSWYRSSTDLY 67
>gnl|CDD|241438 cd13284, PH_OSBP_ORP4, Human Oxysterol binding protein and
OSBP-related protein 4 Pleckstrin homology (PH) domain.
Human OSBP is proposed to function is sterol-dependent
regulation of ERK dephosphorylation and sphingomyelin
synthesis as well as modulation of insulin signaling
and hepatic lipogenesis. It contains a N-terminal PH
domain, a FFAT motif (two phenylalanines in an acidic
tract), and a C-terminal OSBP-related domain. OSBPs and
Osh1p PH domains specifically localize to the Golgi
apparatus in a PtdIns4P-dependent manner. ORP4 is
proposed to function in Vimentin-dependent sterol
transport and/or signaling. Human ORP4 has 2 forms, a
long (ORP4L) and a short (ORP4S). ORP4L contains a
N-terminal PH domain, a FFAT motif (two phenylalanines
in an acidic tract), and a C-terminal OSBP-related
domain. ORP4S is truncated and contains only an
OSBP-related domain. Oxysterol binding proteins are a
multigene family that is conserved in yeast, flies,
worms, mammals and plants. 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 = 99
Score = 29.6 bits (67), Expect = 0.14
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 65 YKQRWFVLTTKHLIYYDTDSEI 86
Y++RWFVL+ L YY +E+
Sbjct: 15 YQRRWFVLSNGLLSYYRNQAEM 36
>gnl|CDD|241436 cd13282, PH1_PLEKHH1_PLEKHH2, Pleckstrin homology (PH) domain
containing, family H (with MyTH4 domain) members 1 and
2 (PLEKHH1) PH domain, repeat 1. PLEKHH1 and PLEKHH2
(also called PLEKHH1L) are thought to function in
phospholipid binding and signal transduction. There are
3 Human PLEKHH genes: PLEKHH1, PLEKHH2, and PLEKHH3.
There are many isoforms, the longest of which contain a
FERM domain, a MyTH4 domain, two PH domains, a
peroximal domain, a vacuolar domain, and a coiled coil
stretch. The FERM domain has a cloverleaf tripart
structure (FERM_N, FERM_M, FERM_C/N, alpha-, and
C-lobe/A-lobe, B-lobe, C-lobe/F1, F2, F3). The
C-lobe/F3 within the FERM domain is part of the PH
domain family. 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 = 96
Score = 29.2 bits (66), Expect = 0.16
Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 7/43 (16%)
Query: 44 RQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYYDTDSEI 86
+ G+L K K +K+RWFVL L YY + +++
Sbjct: 1 KAGYLTKLGGKVK-------TWKRRWFVLKNGELFYYKSPNDV 36
>gnl|CDD|241451 cd13297, PH3_MyoX-like, Myosin X-like Pleckstrin homology (PH)
domain, repeat 3. MyoX, a MyTH-FERM myosin, is a
molecular motor that has crucial functions in the
transport and/or tethering of integrins in the
actin-based extensions known as filopodia, microtubule
binding, and in netrin-mediated axon guidance. It
functions as a dimer. MyoX walks on bundles of actin,
rather than single filaments, unlike the other
unconventional myosins. MyoX is present in organisms
ranging from humans to choanoflagellates, but not in
Drosophila and Caenorhabditis elegans.MyoX consists of
a N-terminal motor/head region, a neck made of 3 IQ
motifs, and a tail consisting of a coiled-coil domain,
a PEST region, 3 PH domains, a myosin tail homology 4
(MyTH4), and a FERM domain at its very C-terminus. The
first PH domain in the MyoX tail is a split-PH domain,
interupted by the second PH domain such that PH 1a and
PH 1b flanks PH 2. The third PH domain (PH 3) follows
the PH 1b domain. This cd contains the third MyoX PH
repeat. PLEKHH3/Pleckstrin homology (PH) domain
containing, family H (with MyTH4 domain) member 3 is
also part of this CD and like MyoX contains a FERM
domain, a MyTH4 domain, and a single PH domain. Not
much is known about the function of PLEKHH3. 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 = 123
Score = 29.2 bits (66), Expect = 0.21
Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 6/49 (12%)
Query: 33 NKDDLISD-DILRQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYY 80
D +++ +G+L+K + K+RWFVLT L YY
Sbjct: 3 KGQTDEGDQEVIEKGWLLKEGGKGGNLTK-----KKRWFVLTPNSLDYY 46
>gnl|CDD|241406 cd13252, PH1_ADAP, ArfGAP with dual PH domains Pleckstrin homology
(PH) domain, repeat 1. ADAP (also called centaurin
alpha) is a phophatidlyinositide binding protein
consisting of an N-terminal ArfGAP domain and two PH
domains. In response to growth factor activation, PI3K
phosphorylates phosphatidylinositol 4,5-bisphosphate to
phosphatidylinositol 3,4,5-trisphosphate. Centaurin
alpha 1 is recruited to the plasma membrane following
growth factor stimulation by specific binding of its PH
domain to phosphatidylinositol 3,4,5-trisphosphate.
Centaurin alpha 2 is constitutively bound to the plasma
membrane since it binds phosphatidylinositol
4,5-bisphosphate and phosphatidylinositol
3,4,5-trisphosphate with equal affinity. This cd
contains the first PH domain repeat. 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 = 29.1 bits (66), Expect = 0.27
Identities = 19/68 (27%), Positives = 33/68 (48%), Gaps = 15/68 (22%)
Query: 43 LRQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKH--LIYYDTDSEIF-LSGIRLSDL--- 96
++GFL KR ++ +F KQR FVL+ + L Y+ + + I + +L
Sbjct: 12 SKEGFLWKRGKDNNQF-------KQRKFVLSEREGTLKYFVKEDAKEPKAVISIKELNAV 64
Query: 97 --PDQIFH 102
P++I H
Sbjct: 65 FQPEKIGH 72
>gnl|CDD|241293 cd01262, PH_PDK1, 3-Phosphoinositide dependent protein kinase 1
(PDK1) pleckstrin homology (PH) domain. PDK1 plays an
important role in insulin and growth factor signalling
cascades. It phosphorylates and activates many AGC
(cAMP-dependent, cGMP-dependent, protein kinase C
(PKC)) family of protein kinases members, including
protein kinase B (PKB, also known as Akt), p70
ribosomal S6-kinase (S6K), serum and glucocorticoid
responsive kinase (SGK), p90 ribosomal S6 kinase (RSK),
and PKC. PDK1 contains an N-terminal serine/threonine
kinase domain followed by a PH domain. Following
binding of the PH domain to PtdIns(3,4,5)P3 and
PtdIns(3,4)P2, PDK1 activates these enzymes by
phosphorylating a Ser/Thr residue in their activation
loop. 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 = 28.7 bits (65), Expect = 0.27
Identities = 17/55 (30%), Positives = 22/55 (40%), Gaps = 15/55 (27%)
Query: 42 ILRQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTK-HLIYYDTDS-----EIFLSG 90
IL+ G + KR K F+ K+R +LT L Y D EI S
Sbjct: 17 ILKMGLVDKR---KGLFA------KKRQLILTDGPRLYYVDPVKMVLKGEIPWSP 62
>gnl|CDD|241287 cd01256, PH_dynamin, Dynamin pleckstrin homology (PH) domain.
Dynamin is a GTPase that regulates endocytic vesicle
formation. It has an N-terminal GTPase domain, followed
by a PH domain, a GTPase effector domain and a
C-terminal proline arginine rich domain. Dynamin-like
proteins, which are found in metazoa, plants and yeast
have the same domain architecture as dynamin, but lack
the PH 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 = 112
Score = 28.8 bits (65), Expect = 0.31
Identities = 12/37 (32%), Positives = 20/37 (54%), Gaps = 6/37 (16%)
Query: 66 KQRWFVLTTKHLIYYDTDSE------IFLSGIRLSDL 96
K+ WFVLT + L +Y + E + L ++L D+
Sbjct: 22 KEYWFVLTAESLSWYKDEEEKEKKYMLPLDNLKLRDV 58
>gnl|CDD|241532 cd13381, PH_Skap-hom_Skap2, Src kinase-associated phosphoprotein
homolog and Skap 2 Pleckstrin homology (PH) domain.
Adaptor protein Skap-hom, a homolog of Skap55, which
interacts with actin and with ADAP (adhesion and
degranulation promoting adapter protein) undergoes
tyrosine phosphorylation in response to plating of bone
marrow-derived macrophages on fibronectin. Skap-hom has
an N-terminal coiled-coil conformation that is involved
in homodimer formation, a central PH domain and a
C-terminal SH3 domain that associates with ADAP. The
Skap-hom PH domain regulates intracellular targeting;
its interaction with the DM domain inhibits Skap-hom
actin-based ruffles in macrophages and its binding to
3'-phosphoinositides reverses this autoinhibition. The
Skap-hom PH domain binds PI[3,4]P2 and PI[3,4,5]P3, but
not to PI[3]P, PI[5]P, or PI[4,5]P2. Skap2 is a
downstream target of Heat shock transcription factor 4
(HSF4) and functions in the regulation of actin
reorganization during lens differentiation. It is
thought that SKAP2 anchors the complex of tyrosine
kinase adaptor protein 2 (NCK20/focal adhesion to
fibroblast growth factor receptors at the lamellipodium
in lens epithelial cells. Skap2 has an N-terminal
coiled-coil conformation which interacts with the SH2
domain of NCK2, a central PH domain and a C-terminal
SH3 domain that associates with ADAP (adhesion and
degranulation promoting adapter protein)/FYB (the Fyn
binding protein). Skap2 PH domain binds to membrane
lipids. Skap adaptor proteins couple receptors to
cytoskeletal rearrangements. Src kinase-associated
phosphoprotein of 55 kDa (Skap55)/Src kinase-associated
phosphoprotein 1 (Skap1), Skap2, and Skap-hom have an
N-terminal coiled-coil conformation, a central PH
domain and a C-terminal SH3 domain. Their PH domains
bind 3'-phosphoinositides as well as directly affecting
targets such as in Skap55 where it directly affecting
integrin regulation by ADAP and NF-kappaB activation or
in Skap-hom where the dimerization and PH domains
comprise a 3'-phosphoinositide-gated molecular switch
that controls ruffle formation. 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 = 106
Score = 28.7 bits (64), Expect = 0.31
Identities = 13/44 (29%), Positives = 23/44 (52%), Gaps = 3/44 (6%)
Query: 42 ILRQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYYDTDSE 85
+L+ G+L KR +K S +++RW L+ YY +D +
Sbjct: 1 VLKAGYLEKR---RKDHSFLGFEWQKRWCALSKTVFYYYGSDKD 41
>gnl|CDD|241453 cd13299, PH2_PH_fungal, Fungal proteins Pleckstrin homology (PH)
domain, repeat 2. The functions of these fungal
proteins are unknown, but they all contain 2 PH
domains. This cd represents the second PH repeat. 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 = 102
Score = 28.4 bits (64), Expect = 0.32
Identities = 14/44 (31%), Positives = 22/44 (50%), Gaps = 6/44 (13%)
Query: 42 ILRQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYYDTDSE 85
++ QG+L KK+ N +K+ W VL + L +Y SE
Sbjct: 6 VIEQGYLQVL---KKK---GVNQWKKYWLVLRNRSLSFYKDQSE 43
>gnl|CDD|241470 cd13316, PH_Boi, Boi family Pleckstrin homology domain. Yeast
Boi proteins Boi1 and Boi2 are functionally redundant
and important for cell growth with Boi mutants
displaying defects in bud formation and in the
maintenance of cell polarity.They appear to be linked
to Rho-type GTPase, Cdc42 and Rho3. Boi1 and Boi2
display two-hybrid interactions with the GTP-bound
("active") form of Cdc42, while Rho3 can suppress of
the lethality caused by deletion of Boi1 and Boi2.
These findings suggest that Boi1 and Boi2 are targets
of Cdc42 that promote cell growth in a manner that is
regulated by Rho3. Boi proteins contain a N-terminal
SH3 domain, followed by a SAM (sterile alpha motif)
domain, a proline-rich region, which mediates binding
to the second SH3 domain of Bem1, and C-terminal PH
domain. The PH domain is essential for its function in
cell growth and is important for localization to the
bud, while the SH3 domain is needed for localization to
the neck. 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 = 95
Score = 27.7 bits (62), Expect = 0.54
Identities = 10/31 (32%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 55 KKRFSTSNNNYKQRWFVLTTKHLIYYDTDSE 85
KKR +K R+FVL L Y ++++
Sbjct: 6 KKR-GERYGTWKTRYFVLKGTRLYYLKSEND 35
>gnl|CDD|128354 smart00039, CRF, corticotropin-releasing factor.
Length = 40
Score = 26.6 bits (59), Expect = 0.70
Identities = 6/28 (21%), Positives = 17/28 (60%)
Query: 41 DILRQGFLIKRSQNKKRFSTSNNNYKQR 68
D+LRQ +++++ ++ + +N N+
Sbjct: 12 DLLRQRLELEKAERRREQAQANRNFLDD 39
>gnl|CDD|241446 cd13292, PH_Osh1p_Osh2p_yeast, Yeast oxysterol binding protein
homologs 1 and 2 Pleckstrin homology (PH) domain.
Yeast Osh1p is proposed to function in postsynthetic
sterol regulation, piecemeal microautophagy of the
nucleus, and cell polarity establishment. Yeast Osh2p
is proposed to function in sterol metabolism and cell
polarity establishment. Both Osh1p and Osh2p contain 3
N-terminal ankyrin repeats, a PH domain, a FFAT motif
(two phenylalanines in an acidic tract), and a
C-terminal OSBP-related domain. OSBP andOsh1p PH
domains specifically localize to the Golgi apparatus in
a PtdIns4P-dependent manner. 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 = 103
Score = 27.7 bits (62), Expect = 0.75
Identities = 12/22 (54%), Positives = 12/22 (54%), Gaps = 1/22 (4%)
Query: 65 YKQRWFVLTTKHLIYY-DTDSE 85
YK RWFVL L YY D E
Sbjct: 18 YKTRWFVLEDGVLSYYRHQDDE 39
>gnl|CDD|239817 cd04322, LysRS_N, LysRS_N: N-terminal, anticodon recognition
domain of lysyl-tRNA synthetases (LysRS). These enzymes
are homodimeric class 2b aminoacyl-tRNA synthetases
(aaRSs). This domain is a beta-barrel domain (OB fold)
involved in binding the tRNA anticodon stem-loop.
aaRSs catalyze the specific attachment of amino acids
(AAs) to their cognate tRNAs during protein
biosynthesis. This 2-step reaction involves i) the
activation of the AA by ATP in the presence of
magnesium ions, followed by ii) the transfer of the
activated AA to the terminal ribose of tRNA. In the
case of the class2b aaRSs, the activated AA is attached
to the 3'OH of the terminal ribose. Included in this
group are E. coli LysS and LysU. These two isoforms of
LysRS are encoded by distinct genes which are
differently regulated. Eukaryotes contain 2 sets of
aaRSs, both of which encoded by the nuclear genome. One
set concerns with cytoplasmic protein synthesis,
whereas the other exclusively with mitochondrial
protein synthesis. Saccharomyces cerevisiae cytoplasmic
and mitochondrial LysRSs have been shown to participate
in the mitochondrial import of the only nuclear-encoded
tRNA of S. cerevisiae (tRNAlysCUU). The gene for human
LysRS encodes both the cytoplasmic and the
mitochondrial isoforms of LysRS. In addition to their
housekeeping role, human lysRS may function as a
signaling molecule that activates immune cells and
tomato LysRS may participate in a root-specific process
possibly connected to conditions of oxidative-stress
conditions or heavy metal uptake. It is known that
human tRNAlys and LysRS are specifically packaged into
HIV-1 suggesting a role for LysRS in tRNA packaging.
Length = 108
Score = 27.4 bits (62), Expect = 0.86
Identities = 13/23 (56%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 16 AATFLDLEDESGKC-GMANKDDL 37
+F DL+DESGK NKDDL
Sbjct: 16 KLSFADLQDESGKIQVYVNKDDL 38
>gnl|CDD|241291 cd01260, PH_CNK_mammalian-like, Connector enhancer of KSR (Kinase
suppressor of ras) (CNK) pleckstrin homology (PH)
domain. CNK family members function as protein
scaffolds, regulating the activity and the subcellular
localization of RAS activated RAF. There is a single
CNK protein present in Drosophila and Caenorhabditis
elegans in contrast to mammals which have 3 CNK
proteins (CNK1, CNK2, and CNK3). All of the CNK members
contain a sterile a motif (SAM), a conserved region in
CNK (CRIC) domain, and a PSD-95/DLG-1/ZO-1 (PDZ)
domain, and, with the exception of CNK3, a PH domain. A
CNK2 splice variant CNK2A also has a PDZ domain-binding
motif at its C terminus and Drosophila CNK (D-CNK) also
has a domain known as the Raf-interacting region (RIR)
that mediates binding of the Drosophila Raf kinase.
This cd contains CNKs from mammals, chickens,
amphibians, fish, and crustacea. 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 = 114
Score = 27.3 bits (61), Expect = 0.95
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 4/52 (7%)
Query: 45 QGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYYDTDSEIFLSG-IRLSD 95
G+L K+ + K F +K+ WFVL L +Y+ + G I L D
Sbjct: 16 DGWLWKKKEAKGFFG---QKWKRYWFVLKGSSLYWYNNPQDEKAEGFINLPD 64
>gnl|CDD|241421 cd13267, PH_DOCK-D, Dedicator of cytokinesis-D subfamily
Pleckstrin homology (PH) domain. DOCK-D subfamily
(also called Zizimin subfamily) consists of
Dock9/Zizimin1, Dock10/Zizimin3, and Dock11/Zizimin2.
DOCK-D has a N-terminal DUF3398 domain, a PH-like
domain, a Dock Homology Region 1, DHR1 (also called
CZH1), a C2 domain, and a C-terminal DHR2 domain (also
called CZH2). Zizimin1 is enriched in the brain, lung,
and kidney; zizimin2 is found in B and T lymphocytes,
and zizimin3 is enriched in brain, lung, spleen and
thymus. Zizimin1 functions in autoinhibition and
membrane targeting. Zizimin2 is an immune-related and
age-regulated guanine nucleotide exchange factor, which
facilitates filopodial formation through activation of
Cdc42, which results in activation of cell migration.
No function has been determined for Zizimin3 to date.
The N-terminal half of zizimin1 binds to the GEF domain
through three distinct areas, including CZH1, to
inhibit the interaction with Cdc42. In addition its PH
domain binds phosphoinositides and mediates zizimin1
membrane targeting. DOCK is a family of proteins
involved in intracellular signalling networks. They act
as guanine nucleotide exchange factors for small G
proteins of the Rho family, such as Rac and Cdc42.
There are 4 subfamilies of DOCK family proteins based
on their sequence homology: A-D. 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 = 27.3 bits (61), Expect = 1.0
Identities = 11/33 (33%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 42 ILRQGFLIKRSQNKKRF-STSNNNYKQRWFVLT 73
I ++G+L K +N F S + ++K+R+F L
Sbjct: 6 ITKEGYLYKGPENSSMFISLAMKSFKRRFFHLK 38
>gnl|CDD|241465 cd13311, PH_Slm1, Slm1 Pleckstrin homology (PH) domain. Slm1 is
a component of the target of rapamycin complex 2
(TORC2) signaling pathway. It plays a role in the
regulation of actin organization and is a target of
sphingolipid signaling during the heat shock response.
Slm1 contains a single PH domain that binds
PtdIns(4,5)P2, PtdIns(4)P, and dihydrosphingosine
1-phosphate (DHS-1P). Slm1 possesses two binding sites
for anionic lipids. The non-canonical binding site of
the PH domain of Slm1 is used for ligand binding, and
it is proposed that beta-spectrin, Tiam1 and ArhGAP9
also have this type of phosphoinositide binding site.
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 = 110
Score = 27.0 bits (60), Expect = 1.4
Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 8/36 (22%)
Query: 43 LRQGFLIKRSQNKKRFSTSNNNYKQRWFVLT-TKHL 77
L GFL + K +F +Y + ++VLT +L
Sbjct: 4 LISGFLER----KSKF---LKSYSKGYYVLTPAGYL 32
>gnl|CDD|241429 cd13275, PH_M-RIP, Myosin phosphatase-RhoA Interacting Protein
Pleckstrin homology (PH) domain. M-RIP is proposed to
play a role in myosin phosphatase regulation by RhoA.
M-RIP contains 2 PH domains followed by a Rho binding
domain (Rho-BD), and a C-terminal myosin binding
subunit (MBS) binding domain (MBS-BD). The amino
terminus of M-RIP with its adjacent PH domains and
polyproline motifs mediates binding to both actin and
Galpha. M-RIP brings RhoA and MBS into close proximity
where M-RIP can target RhoA to the myosin phosphatase
complex to regulate the myosin phosphorylation state.
M-RIP does this via its C-terminal coiled-coil domain
which interacts with the MBS leucine zipper domain of
myosin phosphatase, while its Rho-BD, directly binds
RhoA in a nucleotide-independent manner. 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 = 103
Score = 26.9 bits (60), Expect = 1.4
Identities = 15/58 (25%), Positives = 24/58 (41%), Gaps = 17/58 (29%)
Query: 44 RQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYY---------DTDSEIFLSGIR 92
++G+L+K+ + +K+ WFVL L YY + D I LS
Sbjct: 1 KKGWLMKQD--------EDGEWKKHWFVLRDASLRYYRDSVAEEAGELDGVIDLSTCT 50
>gnl|CDD|241278 cd01247, PH_FAPP1_FAPP2, Four phosphate adaptor protein 1 and 2
Pleckstrin homology (PH) domain. Human FAPP1 (also
called PLEKHA3/Pleckstrin homology domain-containing,
family A member 3) regulates secretory transport from
the trans-Golgi network to the plasma membrane. It is
recruited through binding of PH domain to
phosphatidylinositol 4-phosphate (PtdIns(4)P) and a
small GTPase ADP-ribosylation factor 1 (ARF1). These
two binding sites have little overlap the FAPP1 PH
domain to associate with both ligands simultaneously
and independently. FAPP1 has a N-terminal PH domain
followed by a short proline-rich region. FAPP1 is a
member of the oxysterol binding protein (OSBP) family
which includes OSBP, OSBP-related proteins (ORP), and
Goodpasture antigen binding protein (GPBP). 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. FAPP2 (also called PLEKHA8/Pleckstrin
homology domain-containing, family A member 8), a
member of the Glycolipid lipid transfer protein(GLTP)
family has an N-terminal PH domain that targets the TGN
and C-terminal GLTP domain. FAPP2 functions to traffic
glucosylceramide (GlcCer) which is made in the Golgi.
It's interaction with vesicle-associated membrane
protein-associated protein (VAP) could be a means of
regulation. Some FAPP2s share the FFAT-like motifs
found in GLTP. 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 = 26.6 bits (59), Expect = 1.6
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 62 NNNYKQRWFVLTTKHLIYYDTDSEI 86
+ ++ RWFVL L YY + E+
Sbjct: 12 LSGWQPRWFVLDDGVLSYYKSQEEV 36
>gnl|CDD|241284 cd01253, PH_ARHGAP21-like, ARHGAP21 and related proteins
pleckstrin homology (PH) domain. ARHGAP family genes
encode Rho/Rac/Cdc42-like GTPase activating proteins
with a RhoGAP domain. These proteins functions as a
GTPase-activating protein (GAP) for RHOA and CDC42.
ARHGAP21 controls the Arp2/3 complex and F-actin
dynamics at the Golgi complex by regulating the
activity of the small GTPase Cdc42. It is recruited to
the Golgi by to GTPase, ARF1, through its PH domain and
its helical motif. It is also required for CTNNA1
recruitment to adherens junctions. ARHGAP21 and it
related proteins all contains a PH domain and a RhoGAP
domain. Some of the members have additional N-terminal
domains including PDZ, SH3, and SPEC. The ARHGAP21 PH
domain interacts with the GTPbound forms of both ARF1
and ARF6 ARF-binding domain/ArfBD. The members here
include: ARHGAP15, ARHGAP21, and ARHGAP23. 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 = 113
Score = 26.5 bits (59), Expect = 1.8
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 44 RQGFL-IKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYYDTDS 84
R+G+L K+S +K S+ ++KQ W VL H +Y D
Sbjct: 2 REGWLHFKQSVLEKGKRASDRSWKQVWAVL-RGHSLYLYKDK 42
>gnl|CDD|241410 cd13256, PH3_ARAP, ArfGAP with RhoGAP domain, ankyrin repeat and
PH domain Pleckstrin homology (PH) domain, repeat 3.
ARAP proteins (also called centaurin delta) are
phosphatidylinositol 3,4,5-trisphosphate-dependent
GTPase-activating proteins that modulate actin
cytoskeleton remodeling by regulating ARF and RHO
family members. They bind phosphatidylinositol
3,4,5-trisphosphate (PtdIns(3,4,5)P3) and
phosphatidylinositol 3,4-bisphosphate (PtdIns(3,4,5)P2)
binding. There are 3 mammalian ARAP proteins: ARAP1,
ARAP2, and ARAP3. All ARAP proteins contain a
N-terminal SAM (sterile alpha motif) domain, 5 PH
domains, an ArfGAP domain, 2 ankyrin domain, A RhoGap
domain, and a Ras-associating domain. This hierarchy
contains the third PH domain in ARAP. 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 = 110
Score = 26.2 bits (58), Expect = 2.8
Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 3/53 (5%)
Query: 46 GFLIKRSQNKKRFS--TSNNNYKQRWFVLTTKHLIYYDTD-SEIFLSGIRLSD 95
GFL K + K + + +RW VL L YY++D S I +S+
Sbjct: 6 GFLYKTASMAKPTTERKGKEEFSRRWCVLEDGFLSYYESDKSTTPNGEIDISE 58
>gnl|CDD|241419 cd13265, PH_evt, Evectin Pleckstrin homology (PH) domain. There
are 2 members of the evectin family (also called
pleckstrin homology domain containing, family B): evt-1
(also called PLEKHB1) and evt-2 (also called PLEKHB2).
evt-1 is specific to the nervous system, where it is
expressed in photoreceptors and myelinating glia. evt-2
is widely expressed in both neural and nonneural
tissues. Evectins possess a single N-terminal PH domain
and a C-terminal hydrophobic region. evt-1 is thought
to function as a mediator of post-Golgi trafficking in
cells that produce large membrane-rich organelles. It
is a candidate gene for the inherited human retinopathy
autosomal dominant familial exudative vitreoretinopathy
and a susceptibility gene for multiple sclerosis. evt-2
is essential for retrograde endosomal membrane
transport from the plasma membrane (PM) to the Golgi.
Two membrane trafficking pathways pass through
recycling endosomes: a recycling pathway and a
retrograde pathway that links the PM to the Golgi/ER.
Its PH domain that is unique in that it specifically
recognizes phosphatidylserine (PS), but not
polyphosphoinositides. PS is an anionic phospholipid
class in eukaryotic biomembranes, is highly enriched in
the PM, and plays key roles in various physiological
processes such as the coagulation cascade, recruitment
and activation of signaling molecules, and clearance of
apoptotic cells. PH domains are only found in
eukaryotes. They share little sequence conservation,
but all have a common fold, which is electrostatically
polarized. 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 = 25.7 bits (57), Expect = 3.2
Identities = 14/44 (31%), Positives = 26/44 (59%), Gaps = 8/44 (18%)
Query: 42 ILRQGFLIKRSQNKKRFSTSNNNYKQRWFVL-TTKHLIYYDTDS 84
+++ G+L+++S KR +K+ WFVL + L YY+ +S
Sbjct: 3 LVKSGWLLRQSTILKR-------WKKNWFVLYSDGELSYYEDES 39
>gnl|CDD|241425 cd13271, PH2_TAPP1_2, Tandem PH-domain-containing proteins 1 and
2 Pleckstrin homology (PH) domain, C-terminal repeat.
The binding of TAPP1 (also called PLEKHA1/pleckstrin
homology domain containing, family A (phosphoinositide
binding specific) member 1) and TAPP2 (also called
PLEKHA2) adaptors to PtdIns(3,4)P(2), but not PI(3,4,
5)P3, function as negative regulators of insulin and
PI3K signalling pathways (i.e. TAPP/utrophin/syntrophin
complex). TAPP1 and TAPP2 contain two sequential PH
domains in which the C-terminal PH domain specifically
binds PtdIns(3,4)P2 with high affinity. The N-terminal
PH domain does not interact with any phosphoinositide
tested. They also contain a C-terminal PDZ-binding
motif that interacts with several PDZ-binding proteins,
including PTPN13 (known previously as PTPL1 or FAP-1)
as well as the scaffolding proteins MUPP1 (multiple
PDZ-domain-containing protein 1), syntrophin and
utrophin. 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 = 114
Score = 25.8 bits (57), Expect = 3.8
Identities = 10/44 (22%), Positives = 26/44 (59%), Gaps = 7/44 (15%)
Query: 42 ILRQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYYDTDSE 85
+++ G+ +K+ +K N+K+R+F+L + YY ++++
Sbjct: 8 VIKSGYCVKQGAVRK-------NWKRRYFILDDNTISYYKSETD 44
>gnl|CDD|241296 cd01265, PH_TBC1D2A, TBC1 domain family member 2A pleckstrin
homology (PH) domain. TBC1D2A (also called
PARIS-1/Prostate antigen recognized and identified by
SEREX 1 and ARMUS) contains a PH domain and a TBC-type
GTPase catalytic domain. TBC1D2A integrates signaling
between Arf6, Rac1, and Rab7 during junction
disassembly. Activated Rac1 recruits TBC1D2A to locally
inactivate Rab7 via its C-terminal TBC/RabGAP domain
and facilitate E-cadherin degradation in lysosomes. The
TBC1D2A PH domain mediates localization at cell-cell
contacts and coprecipitates with cadherin complexes. 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 = 101
Score = 25.7 bits (57), Expect = 3.8
Identities = 13/34 (38%), Positives = 16/34 (47%), Gaps = 3/34 (8%)
Query: 65 YKQRWFVL--TTKHLIYYDTDSEI-FLSGIRLSD 95
+K RWFV L YY + +I L I LS
Sbjct: 18 WKSRWFVFDERKCQLYYYRSPQDITPLGSIDLSG 51
>gnl|CDD|201220 pfam00427, PBS_linker_poly, Phycobilisome Linker polypeptide.
Length = 131
Score = 25.5 bits (57), Expect = 4.1
Identities = 10/24 (41%), Positives = 14/24 (58%), Gaps = 4/24 (16%)
Query: 55 KKRFSTSNNNYKQRWFV-LTTKHL 77
+KRF N+NY+ + L KHL
Sbjct: 61 RKRFFEPNSNYR---VIELNFKHL 81
>gnl|CDD|241281 cd01250, PH_AGAP, Arf-GAP with GTPase, ANK repeat and PH
domain-containing protein Pleckstrin homology (PH)
domain. AGAP (also called centaurin gamma;
PIKE/Phosphatidylinositol-3-kinase enhancer) reside
mainly in the nucleus and are known to activate
phosphoinositide 3-kinase, a key regulator of cell
proliferation, motility and vesicular trafficking.
There are 3 isoforms of AGAP (PIKE-A, PIKE-L, and
PIKE-S) the longest of which PIKE-L consists of
N-terminal proline rich domains (PRDs), followed by a
GTPase domain, a split PH domain (PHN and PHC), an
ArfGAP domain and two ankyrin repeats. PIKE-S
terminates after the PHN domain and PIKE-A is missing
the PRD region. Centaurin binds phosphatidlyinositol
(3,4,5)P3. 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 = 114
Score = 25.4 bits (56), Expect = 4.7
Identities = 10/39 (25%), Positives = 17/39 (43%), Gaps = 4/39 (10%)
Query: 42 ILRQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYY 80
++QG+L KRS S + K+ + L Y+
Sbjct: 4 PIKQGYLYKRSSK----SLNKEWKKKYVTLCDDGRLTYH 38
>gnl|CDD|241270 cd01237, PH_fermitin, Fermitin family pleckstrin homology (PH)
domain. Fermitin functions as a mediator of integrin
inside-out signalling. The recruitment of Fermitin
proteins and Talin to the membrane mediates the
terminal event of integrin signalling, via interaction
with integrin beta subunits. Fermatin has FERM domain
interrupted with a pleckstrin homology (PH) domain.
Fermitin family homologs (Fermt1, 2, and 3, also known
as Kindlins) are each encoded by a different gene. In
mammalian studies, Fermt1 is generally expressed in
epithelial cells, Fermt2 is expressed inmuscle tissues,
and Fermt3 is expressed in hematopoietic lineages.
Specifically Fermt2 is expressed in smooth and striated
muscle tissues in mice and in the somites (a trunk
muscle precursor) and neural crest in Xenopus embryos.
As such it has been proposed that Fermt2 plays a role
in cardiomyocyte and neural crest differentiation.
Expression of mammalian Fermt3 is associated with
hematopoietic lineages: the anterior ventral blood
islands, vitelline veins, and early myeloid cells. In
Xenopus embryos this expression, also include the
notochord and cement gland. 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 = 110
Score = 25.4 bits (56), Expect = 5.0
Identities = 11/30 (36%), Positives = 16/30 (53%), Gaps = 2/30 (6%)
Query: 56 KRFSTSNNNYKQRWFVLTTKHLIYYDTDSE 85
K+F+ +K+ WFV HL YY + E
Sbjct: 13 KKFTL--KGFKRYWFVFKDTHLSYYKSKEE 40
>gnl|CDD|241443 cd13289, PH_Osh3p_yeast, Yeast oxysterol binding protein homolog 3
Pleckstrin homology (PH) domain. Yeast Osh3p is
proposed to function in sterol transport and regulation
of nuclear fusion during mating and of pseudohyphal
growth as well as sphingolipid metabolism. Osh3 contains
a N-GOLD (Golgi dynamics) domain, a PH domain, a FFAT
motif (two phenylalanines in an acidic tract), and a
C-terminal OSBP-related domain. GOLD domains are thought
to mediate protein-protein interactions, but their role
in ORPs are unknown. 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 = 90
Score = 24.9 bits (55), Expect = 5.2
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 17/59 (28%)
Query: 45 QGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKH--LIYYDTDSEIFLSGIRLSDLPDQIF 101
+G+L+K+ + K + + +R+FVL K+ L YY + S +R QI
Sbjct: 3 EGWLLKKRRKKMQ------GFARRYFVLNFKYGTLSYYFNPN----SPVR-----GQIP 46
>gnl|CDD|235553 PRK05672, dnaE2, error-prone DNA polymerase; Validated.
Length = 1046
Score = 26.0 bits (58), Expect = 5.5
Identities = 10/16 (62%), Positives = 11/16 (68%), Gaps = 3/16 (18%)
Query: 18 TFLDLEDESGKCGMAN 33
TFL LEDE+ GM N
Sbjct: 975 TFLTLEDET---GMVN 987
>gnl|CDD|222879 PHA02563, PHA02563, DNA polymerase; Provisional.
Length = 630
Score = 25.9 bits (57), Expect = 5.8
Identities = 11/28 (39%), Positives = 12/28 (42%), Gaps = 1/28 (3%)
Query: 77 LIYYDTDSEIFLSGIRLSDLPDQIFHDI 104
IY DTDS I L G LP +
Sbjct: 476 FIYCDTDS-IHLEGAETPKLPKDMIDPK 502
>gnl|CDD|237417 PRK13533, PRK13533, 7-cyano-7-deazaguanine tRNA-ribosyltransferase;
Provisional.
Length = 487
Score = 25.6 bits (57), Expect = 6.0
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 9 LWTNPVAAATFLDLEDESGK 28
LW PV T+ DL +ES +
Sbjct: 159 LWVAPVQGGTYPDLREESAR 178
>gnl|CDD|202662 pfam03483, B3_4, B3/4 domain. This domain is found in tRNA
synthetase beta subunits as well as in some non tRNA
synthetase proteins.
Length = 159
Score = 24.8 bits (55), Expect = 8.6
Identities = 15/57 (26%), Positives = 29/57 (50%), Gaps = 9/57 (15%)
Query: 36 DLISDDILRQGFLIKRSQNKKRFSTSNNNYKQRWFVLTTKHLIYYDTDSEIFLSGIR 92
D I+ DI+ ++ ++ ++F+T + K+R L L+ D D + L+GI
Sbjct: 44 DKIAGDIV-----VRLAKGGEKFTTLDG--KER--ELDPGDLVIADDDGPVALAGIM 91
>gnl|CDD|213067 cd11751, GH94N_like_4, Glycoside hydrolase family 94
N-terminal-like domain of uncharacterized function. The
glycoside hydrolase family 94 (previously known as
glycosyltransferase family 36) includes cellobiose
phosphorylase (EC:2.4.1.20), cellodextrin phosphorylase
(EC:2.4.1.49), chitobiose phosphorylase (EC:2.4.1.-),
amongst other members. Their N-terminal domain is
involved in oligomerization and may play a role in
catalysis, but it is separate from the catalytic domain
[an (alpha/alpha)(6) barrel]. The GH64N domain, as
represented by this model, is found near the N-terminus
of GH94 members and related proteins with
uncharacterized specificities.
Length = 223
Score = 25.0 bits (55), Expect = 9.8
Identities = 10/41 (24%), Positives = 19/41 (46%)
Query: 61 SNNNYKQRWFVLTTKHLIYYDTDSEIFLSGIRLSDLPDQIF 101
+N N+ F ++ ++ YD D E F+ + PD +
Sbjct: 139 NNRNWPYVAFHAASEPVVSYDGDKESFIGMYGSEENPDAVA 179
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
0.319 0.136 0.408
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: 5,670,727
Number of extensions: 473471
Number of successful extensions: 427
Number of sequences better than 10.0: 1
Number of HSP's gapped: 411
Number of HSP's successfully gapped: 72
Length of query: 108
Length of database: 10,937,602
Length adjustment: 73
Effective length of query: 35
Effective length of database: 7,699,760
Effective search space: 269491600
Effective search space used: 269491600
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 (21.8 bits)
S2: 53 (24.4 bits)