RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17773
(165 letters)
>gnl|CDD|216485 pfam01412, ArfGap, Putative GTPase activating protein for Arf.
Putative zinc fingers with GTPase activating proteins
(GAPs) towards the small GTPase, Arf. The GAP of ARD1
stimulates GTPase hydrolysis for ARD1 but not ARFs.
Length = 117
Score = 100 bits (252), Expect = 3e-28
Identities = 36/62 (58%), Positives = 46/62 (74%), Gaps = 1/62 (1%)
Query: 65 LQSIRSRVPGNLTCADCAEAGPTWASLNLGLLLCIQCCGVHRCLGAHVSRVRSLELDEWP 124
L+ +R ++PGN CADC PTWASLNLG+ +CI+C GVHR LG H+S+VRSL LD+W
Sbjct: 4 LRELR-KLPGNKVCADCGAPNPTWASLNLGIFICIRCSGVHRSLGVHISKVRSLTLDKWT 62
Query: 125 ES 126
Sbjct: 63 PE 64
>gnl|CDD|214518 smart00105, ArfGap, Putative GTP-ase activating proteins for the
small GTPase, ARF. Putative zinc fingers with GTPase
activating proteins (GAPs) towards the small GTPase,
Arf. The GAP of ARD1 stimulates GTPase hydrolysis for
ARD1 but not ARFs.
Length = 119
Score = 91.2 bits (227), Expect = 2e-24
Identities = 36/61 (59%), Positives = 45/61 (73%), Gaps = 1/61 (1%)
Query: 65 LQSIRSRVPGNLTCADCAEAGPTWASLNLGLLLCIQCCGVHRCLGAHVSRVRSLELDEWP 124
L+ +RS +PGN C DC PTWAS+NLG+ LCI+C G+HR LG H+S+VRSL LD W
Sbjct: 1 LKLLRS-IPGNKKCFDCGAPNPTWASVNLGVFLCIECSGIHRSLGVHISKVRSLTLDTWT 59
Query: 125 E 125
E
Sbjct: 60 E 60
>gnl|CDD|133303 cd04103, Centaurin_gamma, Centaurin gamma (CENTG) GTPase. The
centaurins (alpha, beta, gamma, and delta) are large,
multi-domain proteins that all contain an ArfGAP domain
and ankyrin repeats, and in some cases, numerous
additional domains. Centaurin gamma contains an
additional GTPase domain near its N-terminus. The
specific function of this GTPase domain has not been
well characterized, but centaurin gamma 2 (CENTG2) may
play a role in the development of autism. Centaurin
gamma 1 is also called PIKE (phosphatidyl inositol (PI)
3-kinase enhancer) and centaurin gamma 2 is also known
as AGAP (ArfGAP protein with a GTPase-like domain,
ankyrin repeats and a Pleckstrin homology domain) or
GGAP. Three isoforms of PIKE have been identified.
PIKE-S (short) and PIKE-L (long) are brain-specific
isoforms, with PIKE-S restricted to the nucleus and
PIKE-L found in multiple cellular compartments. A third
isoform, PIKE-A was identified in human glioblastoma
brain cancers and has been found in various tissues.
GGAP has been shown to have high GTPase activity due to
a direct intramolecular interaction between the
N-terminal GTPase domain and the C-terminal ArfGAP
domain. In human tissue, AGAP mRNA was detected in
skeletal muscle, kidney, placenta, brain, heart, colon,
and lung. Reduced expression levels were also observed
in the spleen, liver, and small intestine.
Length = 158
Score = 89.9 bits (223), Expect = 2e-23
Identities = 33/45 (73%), Positives = 40/45 (88%)
Query: 121 DEWPESNPRIIDEARARRLASDLKRCSYYETCATYGLNVDRVFQD 165
D SNPR+ID+ARAR+L +D+KRCSYYETCATYGLNV+RVFQ+
Sbjct: 109 DAISASNPRVIDDARARQLCADMKRCSYYETCATYGLNVERVFQE 153
Score = 39.4 bits (92), Expect = 2e-04
Identities = 15/22 (68%), Positives = 19/22 (86%)
Query: 1 MSHYRNAAEIPIILVGTQDSDS 22
+S YRN +EIP+ILVGTQD+ S
Sbjct: 91 LSSYRNISEIPLILVGTQDAIS 112
>gnl|CDD|227651 COG5347, COG5347, GTPase-activating protein that regulates ARFs
(ADP-ribosylation factors), involved in ARF-mediated
vesicular transport [Intracellular trafficking and
secretion].
Length = 319
Score = 86.8 bits (215), Expect = 6e-21
Identities = 33/63 (52%), Positives = 41/63 (65%), Gaps = 1/63 (1%)
Query: 65 LQSIRSRVPGNLTCADCAEAGPTWASLNLGLLLCIQCCGVHRCLGAHVSRVRSLELDEWP 124
L+ ++ N CADC PTWAS+NLG+ LCI C GVHR LG H+S+V+SL LD W
Sbjct: 11 LKLLK-SDSSNKKCADCGAPNPTWASVNLGVFLCIDCAGVHRSLGVHISKVKSLTLDNWT 69
Query: 125 ESN 127
E
Sbjct: 70 EEE 72
>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 = 75.0 bits (185), Expect = 3e-18
Identities = 29/40 (72%), Positives = 36/40 (90%)
Query: 22 SFELLIVSLDNKQWQFEAANSEERDDWIAAIQQQILSSLQ 61
+FE +IVSLD KQW FEAA+SEERD+W+ AI+QQIL+SLQ
Sbjct: 75 AFEFIIVSLDGKQWHFEAASSEERDEWVQAIEQQILASLQ 114
>gnl|CDD|178661 PLN03114, PLN03114, ADP-ribosylation factor GTPase-activating
protein AGD10; Provisional.
Length = 395
Score = 66.4 bits (161), Expect = 2e-13
Identities = 27/49 (55%), Positives = 30/49 (61%)
Query: 75 NLTCADCAEAGPTWASLNLGLLLCIQCCGVHRCLGAHVSRVRSLELDEW 123
N C DC PTWAS+ G+ LCI C VHR LG H+S VRS LD W
Sbjct: 22 NKICFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSW 70
>gnl|CDD|215766 pfam00169, PH, PH domain. PH stands for pleckstrin homology.
Length = 101
Score = 37.4 bits (87), Expect = 5e-04
Identities = 10/36 (27%), Positives = 18/36 (50%)
Query: 21 DSFELLIVSLDNKQWQFEAANSEERDDWIAAIQQQI 56
I + D + + +A + EER +W+ AI+ I
Sbjct: 65 RKNCFEIRTGDRETFLLQAESEEERKEWVKAIRSAI 100
>gnl|CDD|133377 cd04177, RSR1, RSR1/Bud1p family GTPase. RSR1/Bud1p is a member of
the Rap subfamily of the Ras family that is found in
fungi. In budding yeasts, RSR1 is involved in selecting
a site for bud growth on the cell cortex, which directs
the establishment of cell polarization. The Rho family
GTPase cdc42 and its GEF, cdc24, then establish an axis
of polarized growth by organizing the actin cytoskeleton
and secretory apparatus at the bud site. It is believed
that cdc42 interacts directly with RSR1 in vivo. In
filamentous fungi, polar growth occurs at the tips of
hypha and at novel growth sites along the extending
hypha. In Ashbya gossypii, RSR1 is a key regulator of
hyphal growth, localizing at the tip region and
regulating in apical polarization of the actin
cytoskeleton. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras proteins.
Length = 168
Score = 37.1 bits (86), Expect = 0.001
Identities = 12/39 (30%), Positives = 16/39 (41%)
Query: 127 NPRIIDEARARRLASDLKRCSYYETCATYGLNVDRVFQD 165
+ R + L+ +YET A NVD VF D
Sbjct: 120 DDRQVSREDGVSLSQQWGNVPFYETSARKRTNVDEVFID 158
>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 = 35.6 bits (82), Expect = 0.002
Identities = 10/30 (33%), Positives = 18/30 (60%)
Query: 27 IVSLDNKQWQFEAANSEERDDWIAAIQQQI 56
I + D K +A + EER+ W+ A+++ I
Sbjct: 72 IKTSDRKTLLLQAESEEEREKWVEALRKAI 101
>gnl|CDD|178677 PLN03131, PLN03131, hypothetical protein; Provisional.
Length = 705
Score = 36.3 bits (83), Expect = 0.004
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 3/53 (5%)
Query: 71 RVPGNLTCADCAEAGPTWASLNLGLLLCIQCCGVHRCLGAHVSRVRSLELDEW 123
++P N C +C GP + N +C+ C G+HR RV+S+ + ++
Sbjct: 19 KLPPNRRCINCNSLGPQFVCTNFWTFICMTCSGIHR---EFTHRVKSVSMSKF 68
>gnl|CDD|241426 cd13272, PH_INPP4A_INPP4B, Type I inositol 3,4-bisphosphate
4-phosphatase and Type II inositol 3,4-bisphosphate
4-phosphatase Pleckstrin homology (PH) domain. INPP4A
(also called Inositol polyphosphate 4-phosphatase type
I) and INPP4B (also called Inositol polyphosphate
4-phosphatase type II) both catalyze the hydrolysis of
the 4-position phosphate of phosphatidylinositol
3,4-bisphosphate and inositol 1,3,4-trisphosphate. They
differ in that INPP4A additionally catalyzes the
hydrolysis of the 4-position phosphate of inositol
3,4-bisphosphate, while INPP4B catalyzes the hydrolysis
of the 4-position phosphate of inositol
1,4-bisphosphate. They both have a single PH domain
followed by a C2 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 = 34.5 bits (80), Expect = 0.006
Identities = 17/46 (36%), Positives = 28/46 (60%), Gaps = 8/46 (17%)
Query: 27 IVSLDNKQWQFEAANSEERDDWIAAIQQQILSSLQTASLQSIRSRV 72
+V D K+++F + EERD+WI AI+Q AS + +RS++
Sbjct: 64 LVFKDEKKYRFSCRSEEERDEWIEAIKQ--------ASYEYLRSQL 101
>gnl|CDD|178666 PLN03119, PLN03119, putative ADP-ribosylation factor
GTPase-activating protein AGD14; Provisional.
Length = 648
Score = 35.6 bits (81), Expect = 0.008
Identities = 17/72 (23%), Positives = 32/72 (44%), Gaps = 6/72 (8%)
Query: 71 RVPGNLTCADCAEAGPTWASLNLGLLLCIQCCGVHRCLGAHVSRVRSLELDEWPESNPRI 130
++P N C +C GP + +C+ C G+HR RV+S+ + ++ +
Sbjct: 19 KLPPNRRCINCNSLGPQYVCTTFWTFVCMACSGIHR---EFTHRVKSVSMSKFTSKEVEV 75
Query: 131 IDEA---RARRL 139
+ RAR +
Sbjct: 76 LQNGGNQRAREI 87
>gnl|CDD|206708 cd04136, Rap_like, Rap-like family consists of Rap1, Rap2 and RSR1.
The Rap subfamily consists of the Rap1, Rap2, and RSR1.
Rap subfamily proteins perform different cellular
functions, depending on the isoform and its subcellular
localization. For example, in rat salivary gland,
neutrophils, and platelets, Rap1 localizes to secretory
granules and is believed to regulate exocytosis or the
formation of secretory granules. Rap1 has also been
shown to localize in the Golgi of rat fibroblasts,
zymogen granules, plasma membrane, and microsomal
membrane of the pancreatic acini, as well as in the
endocytic compartment of skeletal muscle cells and
fibroblasts. Rap1 localizes in the nucleus of human
oropharyngeal squamous cell carcinomas (SCCs) and cell
lines. Rap1 plays a role in phagocytosis by controlling
the binding of adhesion receptors (typically integrins)
to their ligands. In yeast, Rap1 has been implicated in
multiple functions, including activation and silencing
of transcription and maintenance of telomeres. Rap2 is
involved in multiple functions, including activation of
c-Jun N-terminal kinase (JNK) to regulate the actin
cytoskeleton and activation of the Wnt/beta-catenin
signaling pathway in embryonic Xenopus. A number of
effector proteins for Rap2 have been identified,
including isoform 3 of the human mitogen-activated
protein kinase kinase kinase kinase 4 (MAP4K4) and
Traf2- and Nck-interacting kinase (TNIK), and the
RalGEFs RalGDS, RGL, and Rlf, which also interact with
Rap1 and Ras. RSR1 is the fungal homolog of Rap1 and
Rap2. In budding yeasts, it is involved in selecting a
site for bud growth, which directs the establishment of
cell polarization. The Rho family GTPase Cdc42 and its
GEF, Cdc24, then establish an axis of polarized growth.
It is believed that Cdc42 interacts directly with RSR1
in vivo. In filamentous fungi such as Ashbya gossypii,
RSR1 is a key regulator of polar growth in the hypha.
Most Ras proteins contain a lipid modification site at
the C-terminus, with a typical sequence motif CaaX,
where a = an aliphatic amino acid and X = any amino
acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 164
Score = 34.5 bits (79), Expect = 0.011
Identities = 12/39 (30%), Positives = 20/39 (51%)
Query: 127 NPRIIDEARARRLASDLKRCSYYETCATYGLNVDRVFQD 165
+ R++ + + LA C + ET A +NVD +F D
Sbjct: 120 DERVVSKEEGQNLARQWGNCPFLETSAKSKINVDEIFYD 158
>gnl|CDD|241444 cd13290, PH_ORP9, Human Oxysterol binding protein related protein
9 Pleckstrin homology (PH) domain. Human ORP9 is
proposed to function in regulation of Akt
phosphorylation. ORP9 has 2 forms, a long (ORP9L) and a
short (ORP9S). ORP9L contains an N-terminal PH domain,
a FFAT motif (two phenylalanines in an acidic tract),
and a C-terminal OSBP-related domain. ORP1S is
truncated and contains a FFAT motif and an OSBP-related
domain. Oxysterol binding proteins are a multigene
family that is conserved in yeast, flies, worms,
mammals and plants. In general OSBPs and ORPs have been
found to be involved in the transport and metabolism of
cholesterol and related lipids in eukaryotes. They all
contain a C-terminal oxysterol binding domain, and most
contain an N-terminal PH domain. OSBP PH domains bind
to membrane phosphoinositides and thus likely play an
important role in intracellular targeting. They are
members of the oxysterol binding protein (OSBP) family
which includes OSBP, OSBP-related proteins (ORP),
Goodpasture antigen binding protein (GPBP), and Four
phosphate adaptor protein 1 (FAPP1). They have a wide
range of purported functions including sterol
transport, cell cycle control, pollen development and
vessicle transport from Golgi recognize both PI lipids
and ARF proteins. PH domains have diverse functions,
but in general are involved in targeting proteins to
the appropriate cellular location or in the interaction
with a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH
domains bind phosphoinositide phosphates (PIPs) with
high affinity and specificity. PH domains are
distinguished from other PIP-binding domains by their
specific high-affinity binding to PIPs with two vicinal
phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or
PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved
across all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 102
Score = 33.2 bits (76), Expect = 0.017
Identities = 16/48 (33%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 14 LVGTQDSDSFELLIVSLDNKQWQFEAANSEERDDWIAAIQQQILSSLQ 61
++G D D +++D K + F+A ++EER+ WI A++ IL Q
Sbjct: 53 VIGIDDEDD-STFTITVDQKTFHFQARDAEERERWIRALEDTILRHSQ 99
>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 = 32.7 bits (75), Expect = 0.031
Identities = 11/35 (31%), Positives = 21/35 (60%), Gaps = 3/35 (8%)
Query: 22 SFELLIVSLDNKQWQFEAANSEERDDWIAAIQQQI 56
+FE VS + + A + +E+++WI+AI + I
Sbjct: 71 AFE---VSTPERTFYLIADSEKEKEEWISAIGRAI 102
>gnl|CDD|133319 cd04119, RJL, Rab GTPase family J-like (RabJ-like). RJLs are found
in many protists and as chimeras with C-terminal DNAJ
domains in deuterostome metazoa. They are not found in
plants, fungi, and protostome metazoa, suggesting a
horizontal gene transfer between protists and
deuterostome metazoa. RJLs lack any known membrane
targeting signal and contain a degenerate
phosphate/magnesium-binding 3 (PM3) motif, suggesting an
impaired ability to hydrolyze GTP. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization.
Length = 168
Score = 33.1 bits (76), Expect = 0.034
Identities = 12/41 (29%), Positives = 17/41 (41%), Gaps = 1/41 (2%)
Query: 125 ESNPRIIDEARARRLASDLKRCSYYETCATYGLNVDRVFQD 165
+ R + E R A Y+ET A G V+ +FQ
Sbjct: 122 LTKHRAVSEDEGRLWAESKG-FKYFETSACTGEGVNEMFQT 161
>gnl|CDD|214541 smart00173, RAS, Ras subfamily of RAS small GTPases. Similar in
fold and function to the bacterial EF-Tu GTPase. p21Ras
couples receptor Tyr kinases and G protein receptors to
protein kinase cascades.
Length = 164
Score = 32.9 bits (76), Expect = 0.035
Identities = 12/39 (30%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 127 NPRIIDEARARRLASDLKRCSYYETCATYGLNVDRVFQD 165
+ R++ + LA C + ET A +NVD F D
Sbjct: 119 SERVVSTEEGKELARQWG-CPFLETSAKERVNVDEAFYD 156
>gnl|CDD|241456 cd13302, PH2_Pleckstrin_2, Pleckstrin 2 Pleckstrin homology (PH)
domain, repeat 2. 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 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 = 109
Score = 31.3 bits (71), Expect = 0.068
Identities = 14/38 (36%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 16 GTQDSDSFELLIVSLDNKQWQFEAANSEERDDWIAAIQ 53
G+ + + FE I++ D + +AA ER +WI AIQ
Sbjct: 71 GSVEGNLFE--IITADEVHYYLQAATPAERTEWIKAIQ 106
>gnl|CDD|197466 smart00010, small_GTPase, Small GTPase of the Ras superfamily;
ill-defined subfamily. SMART predicts Ras-like small
GTPases of the ARF, RAB, RAN, RAS, and SAR subfamilies.
Others that could not be classified in this way are
predicted to be members of the small GTPase superfamily
without predictions of the subfamily.
Length = 166
Score = 31.8 bits (73), Expect = 0.081
Identities = 13/39 (33%), Positives = 18/39 (46%), Gaps = 1/39 (2%)
Query: 127 NPRIIDEARARRLASDLKRCSYYETCATYGLNVDRVFQD 165
N R++ + LA C + ET A +NVD F D
Sbjct: 121 NERVVSTEEGKELARQWG-CPFLETSAKERINVDEAFYD 158
>gnl|CDD|206640 cd00154, Rab, Ras-related in brain (Rab) family of small guanosine
triphosphatases (GTPases). Rab GTPases form the largest
family within the Ras superfamily. There are at least 60
Rab genes in the human genome, and a number of Rab
GTPases are conserved from yeast to humans. Rab GTPases
are small, monomeric proteins that function as molecular
switches to regulate vesicle trafficking pathways. The
different Rab GTPases are localized to the cytosolic
face of specific intracellular membranes, where they
regulate distinct steps in membrane traffic pathways. In
the GTP-bound form, Rab GTPases recruit specific sets of
effector proteins onto membranes. Through their
effectors, Rab GTPases regulate vesicle formation,
actin- and tubulin-dependent vesicle movement, and
membrane fusion. GTPase activating proteins (GAPs)
interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which mask C-terminal lipid binding and promote
cytosolic localization. While most unicellular organisms
possess 5-20 Rab members, several have been found to
possess 60 or more Rabs; for many of these Rab isoforms,
homologous proteins are not found in other organisms.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Since crystal
structures often lack C-terminal residues, the lipid
modification site is not available for annotation in
many of the CDs in the hierarchy, but is included where
possible.
Length = 159
Score = 31.3 bits (72), Expect = 0.14
Identities = 11/38 (28%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 127 NPRIIDEARARRLASDLKRCSYYETCATYGLNVDRVFQ 164
+ R + A++ A + ++ET A G NVD F+
Sbjct: 119 DERQVSTEEAQQFAKENG-LLFFETSAKTGENVDEAFE 155
>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 = 30.3 bits (69), Expect = 0.16
Identities = 11/48 (22%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 12 IILVGTQDSDSFELLIVSLDNKQWQFEAANSEERDDWIAAIQQQILSS 59
I V + + FE++ N+ + F A + +ER+ W++ + I
Sbjct: 49 IKTVRSVGDNKFEVVT---GNRTFVFRAESEDERNLWVSTLMAAISEY 93
>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 = 30.0 bits (68), Expect = 0.19
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 12/63 (19%)
Query: 1 MSHYRNAAEI------PIILVG----TQDSDSFELLIVSLDNKQWQFEAANSEERDDWIA 50
+S+YRN AE+ I L G T+DS +F I + + + +A++ ER W+
Sbjct: 27 LSYYRNQAEMAHTCRGTINLAGALIHTEDSCNFV--ISNGGTQTFHLKASSEVERQRWVT 84
Query: 51 AIQ 53
A++
Sbjct: 85 ALE 87
>gnl|CDD|133345 cd04145, M_R_Ras_like, R-Ras2/TC21, M-Ras/R-Ras3. The
M-Ras/R-Ras-like subfamily contains R-Ras2/TC21,
M-Ras/R-Ras3, and related members of the Ras family.
M-Ras is expressed in lympho-hematopoetic cells. It
interacts with some of the known Ras effectors, but
appears to also have its own effectors. Expression of
mutated M-Ras leads to transformation of several types
of cell lines, including hematopoietic cells, mammary
epithelial cells, and fibroblasts. Overexpression of
M-Ras is observed in carcinomas from breast, uterus,
thyroid, stomach, colon, kidney, lung, and rectum. In
addition, expression of a constitutively active M-Ras
mutant in murine bone marrow induces a malignant mast
cell leukemia that is distinct from the monocytic
leukemia induced by H-Ras. TC21, along with H-Ras, has
been shown to regulate the branching morphogenesis of
ureteric bud cell branching in mice. Most Ras proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 164
Score = 30.8 bits (70), Expect = 0.19
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 1/39 (2%)
Query: 127 NPRIIDEARARRLASDLKRCSYYETCATYGLNVDRVFQD 165
+ R + + LA LK Y ET A +NVD+ F D
Sbjct: 121 HQRQVSREEGQELARQLK-IPYIETSAKDRVNVDKAFHD 158
>gnl|CDD|241540 cd13389, PH1_FGD5_FGD6, FYVE, RhoGEF and PH domain
containing/faciogenital dysplasia proteins 5 and 6
Pleckstrin Homology (PH) domain. FGD5 regulates
promotes angiogenesis of vascular endothelial growth
factor (VEGF) in vascular endothelial cells, including
network formation, permeability, directional movement,
and proliferation. The specific function of FGD6 is
unknown. In general, FGDs have a RhoGEF (DH) domain,
followed by a PH domain, a FYVE domain and a C-terminal
PH domain. All FGDs are guanine nucleotide exchange
factors that activate the Rho GTPase Cdc42, an important
regulator of membrane trafficking. The RhoGEF domain is
responsible for GEF catalytic activity, while the PH
domain is involved in intracellular targeting of the DH
domain. PH domains have diverse functions, but in
general are involved in targeting proteins to the
appropriate cellular location or in the interaction with
a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH domains
bind phosphoinositide phosphates (PIPs) with high
affinity and specificity. PH domains are distinguished
from other PIP-binding domains by their specific
high-affinity binding to PIPs with two vicinal phosphate
groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3
which results in targeting some PH domain proteins to
the plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 125
Score = 30.3 bits (69), Expect = 0.22
Identities = 12/40 (30%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 17 TQDSDSFELLIVSLDNKQWQFEAANSEERDDWIAAIQQQI 56
+ S E I S + + A+++EERD+W+ A+ + I
Sbjct: 70 EDEEYSNEFQIES-TKRSFTLSASSAEERDEWVKALSRAI 108
>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 = 30.0 bits (68), Expect = 0.23
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 39 AANSEERDDWIAAIQQQI 56
AA EE D+WI +I+ I
Sbjct: 98 AATEEEMDEWIKSIKASI 115
>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 = 29.9 bits (68), Expect = 0.24
Identities = 13/41 (31%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 16 GTQDSDSFELLIVSLDNKQWQFEAANSEERDDWIAAIQQQI 56
G + F +V+ D + + A EER +WI AIQ+ +
Sbjct: 64 GIKGHWGFGFTLVTPD-RTFVLSAETEEERREWITAIQKVL 103
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 30.2 bits (69), Expect = 0.28
Identities = 9/40 (22%), Positives = 15/40 (37%), Gaps = 1/40 (2%)
Query: 125 ESNPRIIDEARARRLASDLKRCSYYETCATYGLNVDRVFQ 164
R + A A + ++ET A NV+ F+
Sbjct: 117 LEEQRQVSREEAEAFAEEHG-LPFFETSAKTNTNVEEAFE 155
>gnl|CDD|241437 cd13283, PH_GPBP, Goodpasture antigen binding protein Pleckstrin
homology (PH) domain. The GPBP (also called Collagen
type IV alpha-3-binding protein/hCERT; START
domain-containing protein 11/StARD11; StAR-related
lipid transfer protein 11) is a kinase that
phosphorylates an N-terminal region of the alpha 3
chain of type IV collagen, which is commonly known as
the goodpasture antigen. Its splice variant the
ceramide transporter (CERT) mediates the cytosolic
transport of ceramide. There have been additional
splice variants identified, but all of them function as
ceramide transport proteins. GPBP and CERT both contain
an N-terminal PH domain, followed by a serine rich
domain, and a C-terminal START domain. However, GPBP
has an additional serine rich domain just upstream of
its START domain. They are members of the oxysterol
binding protein (OSBP) family which includes OSBP,
OSBP-related proteins (ORP), Goodpasture antigen
binding protein (GPBP), and Four phosphate adaptor
protein 1 (FAPP1). They have a wide range of purported
functions including sterol transport, cell cycle
control, pollen development and vessicle transport from
Golgi recognize both PI lipids and ARF proteins. PH
domains have diverse functions, but in general are
involved in targeting proteins to the appropriate
cellular location or in the interaction with a binding
partner. They share little sequence conservation, but
all have a common fold, which is electrostatically
polarized. Less than 10% of PH domains bind
phosphoinositide phosphates (PIPs) with high affinity
and specificity. PH domains are distinguished from
other PIP-binding domains by their specific
high-affinity binding to PIPs with two vicinal
phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or
PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved
across all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 100
Score = 29.5 bits (67), Expect = 0.28
Identities = 9/28 (32%), Positives = 16/28 (57%)
Query: 28 VSLDNKQWQFEAANSEERDDWIAAIQQQ 55
VS+++ W A + EER W+ A++
Sbjct: 63 VSVNDSVWYLRAESPEERQRWVDALEAH 90
>gnl|CDD|241462 cd13308, PH_3BP2, SH3 domain-binding protein 2 Pleckstrin homology
(PH) domain. SH3BP2 (the gene that encodes the adaptor
protein 3BP2), HD, ITU, IT10C3, and ADD1 are located
near the Huntington's Disease Gene on Human Chromosome
4pl6.3. SH3BP2 lies in a region that is often missing in
individuals with Wolf-Hirschhorn syndrome (WHS). Gain of
function mutations in SH3BP2 causes enhanced B-cell
antigen receptor (BCR)-mediated activation of nuclear
factor of activated T cells (NFAT), resulting in a rare,
genetic disorder called cherubism. This results in an
increase in the signaling complex formation with Syk,
phospholipase C-gamma2 (PLC-gamma2), and Vav1. It was
recently discovered that Tankyrase regulates 3BP2
stability through ADP-ribosylation and ubiquitylation by
the E3-ubiquitin ligase. Cherubism mutations uncouple
3BP2 from Tankyrase-mediated protein destruction, which
results in its stabilization and subsequent
hyperactivation of the Src, Syk, and Vav signaling
pathways. SH3BP2 is also a potential negative regulator
of the abl oncogene. 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 = 29.3 bits (66), Expect = 0.41
Identities = 9/35 (25%), Positives = 24/35 (68%)
Query: 22 SFELLIVSLDNKQWQFEAANSEERDDWIAAIQQQI 56
F+++ +S D++ W F A + +E +W+ +++++I
Sbjct: 75 VFKIIHLSKDHRTWYFSAKSEDEMKEWMESLRKEI 109
>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 = 29.3 bits (66), Expect = 0.41
Identities = 8/20 (40%), Positives = 11/20 (55%)
Query: 37 FEAANSEERDDWIAAIQQQI 56
+A + EERD W I + I
Sbjct: 79 LQACSREERDAWAKDITKAI 98
>gnl|CDD|241254 cd01219, PH1_FGD1, FYVE, RhoGEF and PH domain
containing/faciogenital dysplasia protein 1 pleckstrin
homology (PH), N-terminal domain. In general, FGDs have
a RhoGEF (DH) domain, followed by an N-terminal PH
domain, a FYVE domain and a C-terminal PH domain. All
FGDs are guanine nucleotide exchange factors that
activates the Rho GTPase Cdc42, an important regulator
of membrane trafficking. The RhoGEF domain is
responsible for GEF catalytic activity, while the
N-terminal PH domain is involved in intracellular
targeting of the DH domain. Mutations in the FGD1 gene
are responsible for the X-linked disorder known as
faciogenital dysplasia (FGDY). Both FGD1 and FGD3 are
targeted by the ubiquitin ligase SCF(FWD1/beta-TrCP)
upon phosphorylation of two serine residues in its
DSGIDS motif and subsequently degraded by the
proteasome. However, FGD1 and FGD3 induced significantly
different morphological changes in HeLa Tet-Off cells
and while FGD1 induced long finger-like protrusions,
FGD3 induced broad sheet-like protrusions when the level
of GTP-bound Cdc42 was significantly increased by the
inducible expression of FGD3. They also reciprocally
regulated cell motility in inducibly expressed in HeLa
Tet-Off cells, FGD1 stimulated cell migration while FGD3
inhibited it. FGD1 and FGD3 therefore play different
roles to regulate cellular functions, even though their
intracellular levels are tightly controlled by the same
destruction pathway through SCF(FWD1/beta-TrCP). 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 = 29.2 bits (65), Expect = 0.41
Identities = 13/37 (35%), Positives = 19/37 (51%)
Query: 26 LIVSLDNKQWQFEAANSEERDDWIAAIQQQILSSLQT 62
+VS + + +A EE+ DWI AI+ I QT
Sbjct: 67 FLVSGKQRSLELQARTEEEKKDWIQAIEATINRHEQT 103
>gnl|CDD|133323 cd04123, Rab21, Rab GTPase family 21 (Rab21). The localization and
function of Rab21 are not clearly defined, with
conflicting data reported. Rab21 has been reported to
localize in the ER in human intestinal epithelial cells,
with partial colocalization with alpha-glucosidase, a
late endosomal/lysosomal marker. More recently, Rab21
was shown to colocalize with and affect the morphology
of early endosomes. In Dictyostelium, GTP-bound Rab21,
together with two novel LIM domain proteins, LimF and
ChLim, has been shown to regulate phagocytosis. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 162
Score = 29.9 bits (68), Expect = 0.44
Identities = 8/37 (21%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 129 RIIDEARARRLASDLKRCSYYETCATYGLNVDRVFQD 165
R++ ++ A A + ++ET A G ++ +F
Sbjct: 121 RVVSKSEAEEYAKSVG-AKHFETSAKTGKGIEELFLS 156
>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 = 28.9 bits (64), Expect = 0.47
Identities = 9/33 (27%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 19 DSDSFELLIVSLDNKQWQFEAANSEERDDWIAA 51
+ FEL + + + +A + EER++W+ A
Sbjct: 61 KPNCFEL-VTPDRGRTYYLQAESEEEREEWLEA 92
>gnl|CDD|206642 cd00876, Ras, Rat sarcoma (Ras) family of small guanosine
triphosphatases (GTPases). The Ras family of the Ras
superfamily includes classical N-Ras, H-Ras, and K-Ras,
as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG,
Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins.
Ras proteins regulate cell growth, proliferation and
differentiation. Ras is activated by guanine nucleotide
exchange factors (GEFs) that release GDP and allow GTP
binding. Many RasGEFs have been identified. These are
sequestered in the cytosol until activation by growth
factors triggers recruitment to the plasma membrane or
Golgi, where the GEF colocalizes with Ras. Active
GTP-bound Ras interacts with several effector proteins:
among the best characterized are the Raf kinases,
phosphatidylinositol 3-kinase (PI3K), RalGEFs and
NORE/MST1. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 160
Score = 29.4 bits (67), Expect = 0.52
Identities = 11/41 (26%), Positives = 17/41 (41%), Gaps = 1/41 (2%)
Query: 125 ESNPRIIDEARARRLASDLKRCSYYETCATYGLNVDRVFQD 165
N R + LA + C + ET A +N+D +F
Sbjct: 116 LENERQVSTEEGEALAEEWG-CPFLETSAKTNINIDELFNT 155
>gnl|CDD|133343 cd04143, Rhes_like, Ras homolog enriched in striatum (Rhes) and
activator of G-protein signaling 1 (Dexras1/AGS1). This
subfamily includes Rhes (Ras homolog enriched in
striatum) and Dexras1/AGS1 (activator of G-protein
signaling 1). These proteins are homologous, but exhibit
significant differences in tissue distribution and
subcellular localization. Rhes is found primarily in the
striatum of the brain, but is also expressed in other
areas of the brain, such as the cerebral cortex,
hippocampus, inferior colliculus, and cerebellum. Rhes
expression is controlled by thyroid hormones. In rat
PC12 cells, Rhes is farnesylated and localizes to the
plasma membrane. Rhes binds and activates PI3K, and
plays a role in coupling serpentine membrane receptors
with heterotrimeric G-protein signaling. Rhes has
recently been shown to be reduced under conditions of
dopamine supersensitivity and may play a role in
determining dopamine receptor sensitivity. Dexras1/AGS1
is a dexamethasone-induced Ras protein that is expressed
primarily in the brain, with low expression levels in
other tissues. Dexras1 localizes primarily to the
cytoplasm, and is a critical regulator of the circadian
master clock to photic and nonphotic input. Most Ras
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins.
Length = 247
Score = 29.3 bits (66), Expect = 0.74
Identities = 10/37 (27%), Positives = 18/37 (48%)
Query: 128 PRIIDEARARRLASDLKRCSYYETCATYGLNVDRVFQ 164
PR + +L + C+Y+E A N+D +F+
Sbjct: 128 PREVQRDEVEQLVGGDENCAYFEVSAKKNSNLDEMFR 164
>gnl|CDD|241259 cd01225, PH_Cool_Pix, Cloned out of library/PAK-interactive
exchange factor pleckstrin homology (PH) domain. There
are two forms of Pix proteins: alpha Pix (also called
Rho guanine nucleotide exchange factor (GEF) 6/90Cool-2)
and beta Pix (GEF7/p85Cool-1). betaPix contains an
N-terminal SH3 domain, a RhoGEF/DH domain, a PH domain,
a GIT1 binding domain (GBD), and a C-terminal
coiled-coil (CC) domain. alphaPix differs in that it
contains a calponin homology (CH) domain, which
interacts with beta-parvin, N-terminal to the SH3
domain. alphaPix is an exchange factor for Rac1 and
Cdc42 and mediates Pak activation on cell adhesion to
fibronectin. Mutations in alphaPix can cause X-linked
mental retardation. alphaPix also interacts with
Huntington's disease protein (htt), and enhances the
aggregation of mutant htt (muthtt) by facilitating
SDS-soluble muthtt-muthtt interactions. The DH-PH domain
of a Pix was required for its binding to htt. In the
majority of Rho GEF proteins, the DH-PH domain is
responsible for the exchange activity. 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 = 28.4 bits (64), Expect = 0.82
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 40 ANSEERDDWIAAIQQQILS 58
+S ++ +WI +QQQI
Sbjct: 82 NSSNDQQEWIEHLQQQIKG 100
>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 = 28.0 bits (63), Expect = 1.2
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 3/39 (7%)
Query: 23 FELLIVSLDNKQWQFEAANSEERDDWIAAIQQQILSSLQ 61
FE +VS K + +A + E+R WI AIQ I S+L
Sbjct: 63 FE--VVS-PTKSYMLQAESEEDRQAWIQAIQAAIASALN 98
>gnl|CDD|215692 pfam00071, Ras, Ras family. Includes sub-families Ras, Rab, Rac,
Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with
GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025,
pfam00063. As regards Rab GTPases, these are important
regulators of vesicle formation, motility and fusion.
They share a fold in common with all Ras GTPases: this
is a six-stranded beta-sheet surrounded by five
alpha-helices.
Length = 162
Score = 28.2 bits (64), Expect = 1.2
Identities = 10/37 (27%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 129 RIIDEARARRLASDLKRCSYYETCATYGLNVDRVFQD 165
R++ LA +L + ET A NV+ F++
Sbjct: 120 RVVSTEEGEALAKELG-LPFMETSAKTNENVEEAFEE 155
>gnl|CDD|206702 cd04129, Rho2, Ras homology family 2 (Rho2) of small guanosine
triphosphatases (GTPases). Rho2 is a fungal GTPase that
plays a role in cell morphogenesis, control of cell wall
integrity, control of growth polarity, and maintenance
of growth direction. Rho2 activates the protein kinase C
homolog Pck2, and Pck2 controls Mok1, the major (1-3)
alpha-D-glucan synthase. Together with Rho1 (RhoA), Rho2
regulates the construction of the cell wall. Unlike
Rho1, Rho2 is not an essential protein, but its
overexpression is lethal. Most Rho proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for proper intracellular localization via
membrane attachment. As with other Rho family GTPases,
the GDP/GTP cycling is regulated by GEFs (guanine
nucleotide exchange factors), GAPs (GTPase-activating
proteins) and GDIs (guanine nucleotide dissociation
inhibitors).
Length = 190
Score = 28.6 bits (64), Expect = 1.3
Identities = 10/39 (25%), Positives = 17/39 (43%)
Query: 126 SNPRIIDEARARRLASDLKRCSYYETCATYGLNVDRVFQ 164
+ + +A+ +A + Y E A G VD VF+
Sbjct: 128 ATDEFVPIQQAKLVARAIGAKKYMECSALTGEGVDDVFE 166
>gnl|CDD|99993 cd03823, GT1_ExpE7_like, This family is most closely related to the
GT1 family of glycosyltransferases. ExpE7 in
Sinorhizobium meliloti has been shown to be involved in
the biosynthesis of galactoglucans (exopolysaccharide
II).
Length = 359
Score = 28.8 bits (65), Expect = 1.4
Identities = 11/24 (45%), Positives = 15/24 (62%), Gaps = 3/24 (12%)
Query: 123 WPESNPRIIDEARARR---LASDL 143
WPE+ P +I EA A +ASD+
Sbjct: 272 WPENFPLVIREALAAGVPVIASDI 295
>gnl|CDD|223043 PHA03323, PHA03323, nuclear egress membrane protein UL34;
Provisional.
Length = 272
Score = 28.5 bits (64), Expect = 1.5
Identities = 11/26 (42%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 65 LQSIRSRVPGNLTCADCAEAGPTWAS 90
+Q IR VPGNL C + +AG
Sbjct: 15 IQRIRLVVPGNLRCGEG-DAGLYEPK 39
>gnl|CDD|177868 PLN02222, PLN02222, phosphoinositide phospholipase C 2.
Length = 581
Score = 28.8 bits (64), Expect = 1.5
Identities = 22/79 (27%), Positives = 30/79 (37%), Gaps = 23/79 (29%)
Query: 70 SRVPGNLTCADCAEAGPTWASLNLGLLLCIQCCGVHRCLGAHVSRVRSLELDEWPESNPR 129
S + GN +DC+E P +L G VR +ELD WP S+
Sbjct: 120 SYLTGNQLSSDCSEV-PIIDALKKG--------------------VRVIELDIWPNSDKD 158
Query: 130 IIDEARARRLAS--DLKRC 146
ID L + L +C
Sbjct: 159 DIDVLHGMTLTTPVGLIKC 177
>gnl|CDD|206648 cd00882, Ras_like_GTPase, Rat sarcoma (Ras)-like superfamily of
small guanosine triphosphatases (GTPases). Ras-like
GTPase superfamily. The Ras-like superfamily of small
GTPases consists of several families with an extremely
high degree of structural and functional similarity. The
Ras superfamily is divided into at least four families
in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families.
This superfamily also includes proteins like the GTP
translation factors, Era-like GTPases, and G-alpha chain
of the heterotrimeric G proteins. Members of the Ras
superfamily regulate a wide variety of cellular
functions: the Ras family regulates gene expression, the
Rho family regulates cytoskeletal reorganization and
gene expression, the Rab and Sar1/Arf families regulate
vesicle trafficking, and the Ran family regulates
nucleocytoplasmic transport and microtubule
organization. The GTP translation factor family
regulates initiation, elongation, termination, and
release in translation, and the Era-like GTPase family
regulates cell division, sporulation, and DNA
replication. Members of the Ras superfamily are
identified by the GTP binding site, which is made up of
five characteristic sequence motifs, and the switch I
and switch II regions.
Length = 161
Score = 28.2 bits (63), Expect = 1.5
Identities = 8/39 (20%), Positives = 15/39 (38%)
Query: 127 NPRIIDEARARRLASDLKRCSYYETCATYGLNVDRVFQD 165
R ++E + + +E A G VD +F+
Sbjct: 120 EEREVEELLRLEELAKILGVPVFEVSAKTGEGVDELFEK 158
>gnl|CDD|236548 PRK09525, lacZ, beta-D-galactosidase; Reviewed.
Length = 1027
Score = 28.7 bits (65), Expect = 1.7
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 7/56 (12%)
Query: 6 NAAEIPIILVGTQDSDSFELLIVSLDNKQWQFEAANSEERDDWIAAIQQQILSSLQ 61
+ P + TQD F + L N++WQF S W ++Q+L+ L+
Sbjct: 737 ASHAAPQL---TQDEQDFC---IELGNQRWQF-NRQSGLLSQWWVGGKEQLLTPLR 785
>gnl|CDD|152648 pfam12213, Dpoe2NT, DNA polymerases epsilon N terminal. This
domain is found in eukaryotes, and is approximately 70
amino acids in length. The family is found in
association with pfam04042. There is a single
completely conserved residue F that may be functionally
important. This domain is the N terminal domain of DNA
polymerase epsilon subunit B. It forms a primarily
alpha helical structure in which four helices are
arranged in two hairpins with connecting loops
containing beta strands which form a short parallel
sheet. DNA polymerase epsilon is required in DNA
replication for synthesis of the leading strand. This
domain has close structural relation to AAA+ protein C
terminal domains.
Length = 72
Score = 26.9 bits (60), Expect = 1.8
Identities = 10/28 (35%), Positives = 15/28 (53%), Gaps = 4/28 (14%)
Query: 36 QFEAANSEERDDW----IAAIQQQILSS 59
+ ER+DW I A+++Q LSS
Sbjct: 31 VLLSLGEPEREDWLEKIIEAVEKQPLSS 58
>gnl|CDD|241408 cd13254, PH2_ARAP, ArfGAP with RhoGAP domain, ankyrin repeat and
PH domain Pleckstrin homology (PH) domain, repeat 2.
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 second 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 = 90
Score = 27.3 bits (61), Expect = 1.8
Identities = 10/35 (28%), Positives = 18/35 (51%), Gaps = 3/35 (8%)
Query: 19 DSDSFELLIVSLDNKQWQFEAANSEERDDWIAAIQ 53
D SF+L + + F A + E+ +W+ A+Q
Sbjct: 59 DKRSFDLTTPY---RIFSFTAESEREKQEWVEALQ 90
>gnl|CDD|206655 cd01862, Rab7, Rab GTPase family 7 (Rab7). Rab7 subfamily. Rab7 is
a small Rab GTPase that regulates vesicular traffic from
early to late endosomal stages of the endocytic pathway.
The yeast Ypt7 and mammalian Rab7 are both involved in
transport to the vacuole/lysosome, whereas Ypt7 is also
required for homotypic vacuole fusion. Mammalian Rab7 is
an essential participant in the autophagic pathway for
sequestration and targeting of cytoplasmic components to
the lytic compartment. Mammalian Rab7 is also proposed
to function as a tumor suppressor. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 172
Score = 27.6 bits (62), Expect = 2.0
Identities = 10/37 (27%), Positives = 18/37 (48%)
Query: 129 RIIDEARARRLASDLKRCSYYETCATYGLNVDRVFQD 165
R + +A++ Y+ET A +NVD+ F+
Sbjct: 125 RQVSTKKAQQWCKSKGNIPYFETSAKEAINVDQAFET 161
>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 = 27.4 bits (61), Expect = 2.1
Identities = 9/41 (21%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 27 IVSLDNKQWQFEAANSEERDDWIAAIQQQILSSLQTASLQS 67
IV+ + + +A + E + WI+AI + T + +
Sbjct: 71 IVT-PARTFYVQADSKAEMESWISAINLARQALRATITPNT 110
>gnl|CDD|184651 PRK14370, PRK14370, hypothetical protein; Provisional.
Length = 120
Score = 27.5 bits (61), Expect = 2.1
Identities = 8/12 (66%), Positives = 9/12 (75%)
Query: 145 RCSYYETCATYG 156
RC YY TC+ YG
Sbjct: 31 RCRYYPTCSNYG 42
>gnl|CDD|181668 PRK09135, PRK09135, pteridine reductase; Provisional.
Length = 249
Score = 27.6 bits (62), Expect = 2.7
Identities = 16/53 (30%), Positives = 18/53 (33%), Gaps = 16/53 (30%)
Query: 109 GAHVSRVRSLELD---------------EWPESNPRIIDEARARRLASD-LKR 145
A RSL L+ WPE +EAR LA LKR
Sbjct: 161 AALEMLTRSLALELAPEVRVNAVAPGAILWPEDGNSFDEEARQAILARTPLKR 213
>gnl|CDD|241292 cd01261, PH_SOS, Son of Sevenless (SOS) Pleckstrin homology (PH)
domain. SOS is a Ras guanine nucleotide exchange
factor. SOS is thought to transmit signals from
activated receptor tyrosine kinases to the Ras signaling
pathway. SOS contains a histone domain, Dbl-homology
(DH), a PH domain, Rem domain, Cdc25 domain, and a Grb2
binding domain. The SOS PH domain binds to
phosphatidylinositol-4,5-bisphosphate (PIP2) and
phosphatidic acid (PA). SOS is dependent on Ras binding
to the allosteric site via its histone domain for both a
lower level of activity (Ras GDP) and maximal activity
(Ras GTP). The DH domain blocks the allosteric Ras
binding site in SOS. The PH domain is closely associated
with the DH domain and the action of the DH-PH unit
gates a reciprocal interaction between Ras and SOS. The
C-terminal proline-rich domain of SOS binds to the
adapter protein Grb2 which localizes the Sos protein to
the plasma membrane and diminishes the negative effect
of the C-terminal domain on the guanine nucleotide
exchange activity of the CDC25-homology domain of SOS.
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 = 109
Score = 26.9 bits (60), Expect = 3.1
Identities = 13/39 (33%), Positives = 24/39 (61%), Gaps = 6/39 (15%)
Query: 18 QDSD----SFELLIVSLDNKQWQFEAANSEERDDWIAAI 52
+D+D +FE IV D + A ++EE+++W+AA+
Sbjct: 69 EDTDELKNAFE--IVPRDEPSYILFAKSAEEKNNWMAAL 105
>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 = 26.8 bits (60), Expect = 3.5
Identities = 7/18 (38%), Positives = 14/18 (77%)
Query: 39 AANSEERDDWIAAIQQQI 56
A + E+RD+WI A++++
Sbjct: 85 APSEEDRDEWILALRKEC 102
>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 = 26.4 bits (58), Expect = 3.7
Identities = 11/31 (35%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 23 FELLIVSLDNKQWQFEAANSEERDDWIAAIQ 53
FEL + + + ++F AA+ E DW+ IQ
Sbjct: 71 FEL--TTPNQRTYEFTAASPSEARDWVDQIQ 99
>gnl|CDD|173818 cd07493, Peptidases_S8_9, Peptidase S8 family domain,
uncharacterized subfamily 9. This family is a member
of the Peptidases S8 or Subtilases serine endo- and
exo-peptidase clan. They have an Asp/His/Ser catalytic
triad similar to that found in trypsin-like proteases,
but do not share their three-dimensional structure and
are not homologous to trypsin. The stability of
subtilases may be enhanced by calcium, some members
have been shown to bind up to 4 ions via binding sites
with different affinity. Some members of this clan
contain disulfide bonds. These enzymes can be intra-
and extracellular, some function at extreme
temperatures and pH values.
Length = 261
Score = 27.3 bits (61), Expect = 4.0
Identities = 15/50 (30%), Positives = 22/50 (44%), Gaps = 12/50 (24%)
Query: 7 AAEIPIILVGTQDSDSFELLIVSLDNKQWQFEAANSE---ERDDWIAAIQ 53
A P ++VGT + S+ L E SE E D+W+AA +
Sbjct: 58 AGYTPGVMVGTAPNASYYLART---------EDVASETPVEEDNWVAAAE 98
>gnl|CDD|241538 cd13387, PH1_FGD3, FYVE, RhoGEF and PH domain
containing/faciogenital dysplasia protein 3 pleckstrin
homology (PH), N-terminal domain. In general, FGDs
have a RhoGEF (DH) domain, followed by an N-terminal PH
domain, a FYVE domain and a C-terminal PH domain. All
FGDs are guanine nucleotide exchange factors that
activates the Rho GTPase Cdc42, an important regulator
of membrane trafficking. The RhoGEF domain is
responsible for GEF catalytic activity, while the
N-terminal PH domain is involved in intracellular
targeting of the DH domain. Both FGD1 and FGD3 are
targeted by the ubiquitin ligase SCF(FWD1/beta-TrCP)
upon phosphorylation of two serine residues in its
DSGIDS motif and subsequently degraded by the
proteasome. However, FGD1 and FGD3 induced
significantly different morphological changes in HeLa
Tet-Off cells and while FGD1 induced long finger-like
protrusions, FGD3 induced broad sheet-like protrusions
when the level of GTP-bound Cdc42 was significantly
increased by the inducible expression of FGD3. They
also reciprocally regulated cell motility in inducibly
expressed in HeLa Tet-Off cells, FGD1 stimulated cell
migration while FGD3 inhibited it. FGD1 and FGD3
therefore play different roles to regulate cellular
functions, even though their intracellular levels are
tightly controlled by the same destruction pathway
through SCF(FWD1/beta-TrCP). 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 = 26.5 bits (58), Expect = 4.4
Identities = 9/31 (29%), Positives = 16/31 (51%)
Query: 26 LIVSLDNKQWQFEAANSEERDDWIAAIQQQI 56
I++ + + +A EE+ +WI IQ I
Sbjct: 67 FIITGKKRSLELQARTEEEKKEWIQVIQATI 97
>gnl|CDD|206653 cd01860, Rab5_related, Rab-related GTPase family includes Rab5 and
Rab22; regulates early endosome fusion. The
Rab5-related subfamily includes Rab5 and Rab22 of
mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of plants.
The members of this subfamily are involved in
endocytosis and endocytic-sorting pathways. In mammals,
Rab5 GTPases localize to early endosomes and regulate
fusion of clathrin-coated vesicles to early endosomes
and fusion between early endosomes. In yeast, Ypt51p
family members similarly regulate membrane trafficking
through prevacuolar compartments. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 163
Score = 26.7 bits (60), Expect = 4.5
Identities = 10/40 (25%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 126 SNPRIIDEARARRLASDLKRCSYYETCATYGLNVDRVFQD 165
+ R + A+ A + + ET A G NV+ +F +
Sbjct: 119 ESKRQVSTEEAQEYADENG-LLFMETSAKTGENVNELFTE 157
>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 = 26.3 bits (58), Expect = 4.5
Identities = 11/31 (35%), Positives = 19/31 (61%), Gaps = 2/31 (6%)
Query: 23 FELLIVSLDNKQWQFEAANSEERDDWIAAIQ 53
FE I + D + +QF AA+ +E +W+ I+
Sbjct: 71 FE--ISAPDKRVYQFTAASPKEAREWVDQIK 99
>gnl|CDD|241307 cd10571, PH_beta_spectrin, Beta-spectrin pleckstrin homology (PH)
domain. Beta spectrin binds actin and functions as a
major component of the cytoskeleton underlying cellular
membranes. Beta spectrin consists of multiple spectrin
repeats followed by a PH domain, which binds to
inositol-1,4,5-trisphosphate. The PH domain of
beta-spectrin is thought to play a role in the
association of spectrin with the plasma membrane of
cells. 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 = 26.0 bits (58), Expect = 4.8
Identities = 8/25 (32%), Positives = 15/25 (60%)
Query: 31 DNKQWQFEAANSEERDDWIAAIQQQ 55
D ++ F+A + EE +DW+ +Q
Sbjct: 81 DGSEYLFQAKDEEEMNDWVQKLQAA 105
>gnl|CDD|241401 cd13247, BAR-PH_APPL, Adaptor protein containing PH domain, PTB
domain, and Leucine zipper motif Bin1/amphiphysin/Rvs167
(BAR)-Pleckstrin homology (PH) domain. APPL (also
called DCC-interacting protein (DIP)-13alpha) interacts
with oncoprotein serine/threonine kinase AKT2, tumor
suppressor protein DCC (deleted in colorectal cancer),
Rab5, GIPC (GAIP-interacting protein, C terminus), human
follicle-stimulating hormone receptor (FSHR), and the
adiponectin receptors AdipoR1 and AdipoR2. There are two
isoforms of human APPL: APPL1 and APPL2, which share
about 50% sequence identity. APPL has a BAR and a PH
domain near its N terminus, and the two domains are
thought to function as a unit (BAR-PH domain).
C-terminal to this is a PTB domain. Lipid binding assays
show that the BAR, PH, and PTB domains can bind
phospholipids. 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 = 26.5 bits (59), Expect = 4.9
Identities = 7/20 (35%), Positives = 13/20 (65%)
Query: 33 KQWQFEAANSEERDDWIAAI 52
K +A + ++R++WIA I
Sbjct: 100 KAIVLQAESEKDREEWIATI 119
>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 = 26.1 bits (58), Expect = 5.3
Identities = 6/23 (26%), Positives = 18/23 (78%)
Query: 32 NKQWQFEAANSEERDDWIAAIQQ 54
+K + F+A++ ++ ++W+ AI++
Sbjct: 75 SKNYHFQASSEKDANEWVEAIRE 97
>gnl|CDD|133330 cd04130, Wrch_1, Wnt-1 responsive Cdc42 homolog (Wrch-1) is a Rho
family GTPase similar to Cdc42. Wrch-1 (Wnt-1
responsive Cdc42 homolog) is a Rho family GTPase that
shares significant sequence and functional similarity
with Cdc42. Wrch-1 was first identified in mouse mammary
epithelial cells, where its transcription is upregulated
in Wnt-1 transformation. Wrch-1 contains N- and
C-terminal extensions relative to cdc42, suggesting
potential differences in cellular localization and
function. The Wrch-1 N-terminal extension contains
putative SH3 domain-binding motifs and has been shown to
bind the SH3 domain-containing protein Grb2, which
increases the level of active Wrch-1 in cells. Unlike
Cdc42, which localizes to the cytosol and perinuclear
membranes, Wrch-1 localizes extensively with the plasma
membrane and endosomes. The membrane association,
localization, and biological activity of Wrch-1 indicate
an atypical model of regulation distinct from other Rho
family GTPases. Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 173
Score = 26.6 bits (59), Expect = 5.5
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 131 IDEARARRLASDLKRCSYYETCATYGLNVDRVF 163
+ ++RA+ LA + C Y E A N+ VF
Sbjct: 134 VSQSRAKALAEKIGACEYIECSALTQKNLKEVF 166
>gnl|CDD|177873 PLN02228, PLN02228, Phosphoinositide phospholipase C.
Length = 567
Score = 26.9 bits (59), Expect = 6.0
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 115 VRSLELDEWPESNPRIIDEARARRLAS--DLKRC 146
V+ +ELD WP + + R L S DL++C
Sbjct: 147 VKVIELDLWPNPSGNAAEVRHGRTLTSHEDLQKC 180
>gnl|CDD|239216 cd02865, Heme_Cu_Oxidase_III_2, Heme-copper oxidase subunit III
subfamily. Heme-copper oxidases are transmembrane
protein complexes in the respiratory chains of
prokaryotes and mitochondria which couple the reduction
of molecular oxygen to water to, proton pumping across
the membrane. The heme-copper oxidase superfamily is
diverse in terms of electron donors, subunit
composition, and heme types. This superfamily includes
cytochrome c and ubiquinol oxidases. Bacterial oxidases
typically contain 3 or 4 subunits in contrast to the 13
subunit bovine cytochrome c oxidase (CcO). Subunits I,
II, and III of mammalian CcO are encoded within the
mitochondrial genome and the remaining 10 subunits are
encoded within the nuclear genome. Subunits I, II and
III of ubiquinol oxidase are homologous to the
corresponding subunits in CcO. Although not required
for catalytic activity, subunit III is believed to play
a role in assembly of the multimer complex. Rhodobacter
CcO subunit III stabilizes the integrity of the
binuclear center in subunit I. It has been proposed
that Archaea acquired heme-copper oxidases through gene
transfer from Gram-positive bacteria.
Length = 184
Score = 26.6 bits (59), Expect = 6.3
Identities = 6/27 (22%), Positives = 8/27 (29%), Gaps = 1/27 (3%)
Query: 84 AGPTWASLNLGLLLCIQCCGVHRCLGA 110
P SLN +L + A
Sbjct: 47 PLPNLLSLNTAVLAAS-SVAMQWARRA 72
>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 = 25.7 bits (57), Expect = 6.8
Identities = 10/34 (29%), Positives = 18/34 (52%)
Query: 23 FELLIVSLDNKQWQFEAANSEERDDWIAAIQQQI 56
FE+ + + +W +A + E WI A+Q+ I
Sbjct: 64 FEVSSKTSGSPKWYLKANHPVEAARWIQALQKAI 97
>gnl|CDD|179118 PRK00771, PRK00771, signal recognition particle protein Srp54;
Provisional.
Length = 437
Score = 26.7 bits (60), Expect = 7.0
Identities = 10/22 (45%), Positives = 14/22 (63%), Gaps = 5/22 (22%)
Query: 119 ELDEWPESNPRIIDEARARRLA 140
EL+ NP II+ +R RR+A
Sbjct: 378 ELE-----NPEIINASRIRRIA 394
>gnl|CDD|241413 cd13259, PH5_ARAP, ArfGAP with RhoGAP domain, ankyrin repeat and PH
domain Pleckstrin homology (PH) domain, repeat 5. 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 five
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 = 121
Score = 25.8 bits (57), Expect = 7.1
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 26 LIVSLDNKQWQFEAANSEERDDWIAAI 52
V L+ +QW EE +W+A+I
Sbjct: 84 FTVILEKQQWYLCCDTQEELWEWMASI 110
>gnl|CDD|206711 cd04140, ARHI_like, A Ras homolog member I (ARHI). ARHI (A Ras
homolog member I) is a member of the Ras family with
several unique structural and functional properties.
ARHI is expressed in normal human ovarian and breast
tissue, but its expression is decreased or eliminated in
breast and ovarian cancer. ARHI contains an N-terminal
extension of 34 residues (human) that is required to
retain its tumor suppressive activity. Unlike most other
Ras family members, ARHI is maintained in the
constitutively active (GTP-bound) state in resting cells
and has modest GTPase activity. ARHI inhibits STAT3
(signal transducers and activators of transcription 3),
a latent transcription factor whose abnormal activation
plays a critical role in oncogenesis. Most Ras proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 165
Score = 26.3 bits (58), Expect = 7.4
Identities = 13/40 (32%), Positives = 18/40 (45%), Gaps = 1/40 (2%)
Query: 125 ESNPRIIDEARARRLASDLKRCSYYETCATYGLNVDRVFQ 164
ES R + + LA C++ ET A NV +FQ
Sbjct: 120 ESPSREVSSSEGAALARTWN-CAFMETSAKTNHNVQELFQ 158
>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 = 25.3 bits (56), Expect = 7.7
Identities = 5/22 (22%), Positives = 12/22 (54%)
Query: 35 WQFEAANSEERDDWIAAIQQQI 56
+ A EE D+W+ ++ ++
Sbjct: 75 FYMYAKTEEEADEWVKLLKWKL 96
>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 = 25.7 bits (57), Expect = 8.0
Identities = 12/39 (30%), Positives = 16/39 (41%), Gaps = 6/39 (15%)
Query: 22 SFELLIVSLDNKQWQFEAANSEERDDWI----AAIQQQI 56
FEL + D K + A + E DDWI +Q
Sbjct: 80 CFELRMQ--DGKSYVLAAESESEMDDWISKLNKILQINK 116
>gnl|CDD|238509 cd01038, Endonuclease_DUF559, Domain of unknown function, appears
to be related to a diverse group of endonucleases.
Length = 108
Score = 25.7 bits (57), Expect = 8.4
Identities = 11/26 (42%), Positives = 14/26 (53%)
Query: 26 LIVSLDNKQWQFEAANSEERDDWIAA 51
L+V LD Q + A ERD W+ A
Sbjct: 54 LVVELDGGQHDEQIAYDAERDAWLEA 79
>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 = 25.7 bits (57), Expect = 8.5
Identities = 7/18 (38%), Positives = 13/18 (72%)
Query: 39 AANSEERDDWIAAIQQQI 56
A +ERD+W++A+ + I
Sbjct: 93 AETDKERDEWVSALSEYI 110
>gnl|CDD|241294 cd01263, PH_anillin, Anillin Pleckstrin homology (PH) domain.
Anillin (Rhotekin/RTKN; also called PLEKHK/Pleckstrin
homology domain-containing family K) is an actin binding
protein involved in cytokinesis. It interacts with
GTP-bound Rho proteins and results in the inhibition of
their GTPase activity. Dysregulation of the Rho signal
transduction pathway has been implicated in many forms
of cancer. Anillin proteins have a N-terminal HRI
domain/ACC (anti-parallel coiled-coil) finger domain or
Rho-binding domain binds small GTPases from the Rho
family. The C-terminal PH domain helps target anillin to
ectopic septin containing foci. 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 = 119
Score = 25.7 bits (57), Expect = 8.7
Identities = 11/41 (26%), Positives = 17/41 (41%), Gaps = 8/41 (19%)
Query: 22 SFELLIVSLDN--------KQWQFEAANSEERDDWIAAIQQ 54
+FEL + K+ A EER +W+ A+ Q
Sbjct: 73 TFELETLRPAEDSDGTNEKKRVLLSADTKEERIEWLDALNQ 113
>gnl|CDD|237860 PRK14939, gyrB, DNA gyrase subunit B; Provisional.
Length = 756
Score = 26.2 bits (59), Expect = 9.6
Identities = 16/37 (43%), Positives = 19/37 (51%), Gaps = 11/37 (29%)
Query: 120 LDEWPESNP--------RIIDEARAR---RLASDLKR 145
L E+ E NP +IID ARAR R A +L R
Sbjct: 358 LSEFLEENPNEAKIIVGKIIDAARAREAARKARELTR 394
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
0.321 0.133 0.411
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: 8,076,194
Number of extensions: 683595
Number of successful extensions: 888
Number of sequences better than 10.0: 1
Number of HSP's gapped: 888
Number of HSP's successfully gapped: 88
Length of query: 165
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 75
Effective length of database: 6,945,742
Effective search space: 520930650
Effective search space used: 520930650
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.2 bits)