RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5772
(654 letters)
>gnl|CDD|216028 pfam00621, RhoGEF, RhoGEF domain. Guanine nucleotide exchange
factor for Rho/Rac/Cdc42-like GTPases Also called
Dbl-homologous (DH) domain. It appears that pfam00169
domains invariably occur C-terminal to RhoGEF/DH
domains.
Length = 179
Score = 154 bits (391), Expect = 1e-43
Identities = 58/181 (32%), Positives = 96/181 (53%), Gaps = 4/181 (2%)
Query: 394 FELITSEASYFKSLTVLEKHFIASPLLDDVNILSKNDRKHLFGNVTAVRKCSERLLAALE 453
EL+ +E SY + L +L + F+ L + ILS+ + K +F N+ + + + L LE
Sbjct: 3 QELLQTERSYVRDLKILVEVFLKP--LRESPILSEEEIKTIFSNIEEILELHQEFLEELE 60
Query: 454 QCWQDSILLTNICEIVYQHVTNKSFNIYIKYCSNQFHIDRTLKSLRETNPKFIEALTELE 513
+ ++ + I +I + F +Y YCSN LK LR+ NP+F + L E E
Sbjct: 61 ERLEEWPDIQRIGDIFLKFAPF--FKVYSTYCSNYPRALELLKKLRKKNPRFAKFLKECE 118
Query: 514 SDPVCQSLSLHSFLMLPMQRVTRLPLLFDAILTRLRPNHSEYETCHTTLATLNKIVHECN 573
+ P+C+ L L+SFL+ P+QR+ R PLL +L P+H +YE L + ++ + N
Sbjct: 119 ASPLCRGLDLNSFLIKPVQRIPRYPLLLKELLKHTPPDHPDYEDLKKALEAIKEVASQIN 178
Query: 574 E 574
E
Sbjct: 179 E 179
Score = 68.8 bits (169), Expect = 1e-13
Identities = 23/63 (36%), Positives = 37/63 (58%)
Query: 10 LESDPVCQSLSLHSFLMLPMQRVTRLPLLFDAILTRLRPNHSEYETCHTTLATLNKIVHE 69
E+ P+C+ L L+SFL+ P+QR+ R PLL +L P+H +YE L + ++ +
Sbjct: 117 CEASPLCRGLDLNSFLIKPVQRIPRYPLLLKELLKHTPPDHPDYEDLKKALEAIKEVASQ 176
Query: 70 CNE 72
NE
Sbjct: 177 INE 179
>gnl|CDD|241256 cd01221, PH_ephexin, Ephexin Pleckstrin homology (PH) domain.
Ephexin-1 (also called NGEF/ neuronal guanine nucleotide
exchange factor) plays a role in the homeostatic
modulation of presynaptic neurotransmitter release.
Specific functions are still unknown for Ephexin-2 (also
called RhoGEF19) and Ephexin-3 (also called Rho guanine
nucleotide exchange factor 5/RhoGEF5, Transforming
immortalized mammary oncogene/p60 TIM, and
NGEF/neuronalGEF). Ephexin-4 (also called RhoGEF16) acts
downstream of EphA2 to promote ligand-independent breast
cancer cell migration and invasion toward epidermal
growth factor through activation of RhoG. This in turn
results in the activation of RhoG which recruits ELMO2
and Dock4 to form a complex with EphA2 at the tips of
cortactin-rich protrusions in migrating breast cancer
cells. Ephexin-5 is the specific GEF for RhoA activation
and the regulation of vascular smooth muscle
contractility. It interacts with EPHA4 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. The
members of the Ephexin family contains a RhoGEF (DH)
followed by a PH domain and an SH3 domain. The ephexin
PH domain is believed to act with the DH domain in
mediating protein-protein interactions. 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 = 130
Score = 134 bits (340), Expect = 3e-37
Identities = 57/119 (47%), Positives = 80/119 (67%), Gaps = 7/119 (5%)
Query: 96 EVKCLPVISSSRWLVRSGSMNFVNVD-SKMTFARKLNKTHFYAKLNLFLFTDLLVITKKK 154
++K P+IS SRWLV+ G + + D +TF +K KT Y LFLF DLL+ITKKK
Sbjct: 1 KIKPFPLISQSRWLVKRGELTELVEDGGSLTFKKKKKKTPVY----LFLFNDLLLITKKK 56
Query: 155 SNGSYSVIDYCTRAMMQMAAIEDSVPPTN--KYLILLTILENHEQKTVEIVLSCDTESE 211
S Y+V+DY R+++Q+ +ED +P K L LLT+LENHE KTVE++LS ++ES+
Sbjct: 57 SEERYTVLDYAPRSLLQVEEVEDPLPLQGSGKNLFLLTLLENHEGKTVELLLSAESESD 115
Score = 50.7 bits (122), Expect = 1e-07
Identities = 23/53 (43%), Positives = 31/53 (58%), Gaps = 5/53 (9%)
Query: 598 EVKCLPVISSSRWLVRSGSMNFVNVD-SKMTFARKLNKTHFYAKLNLFLFTDL 649
++K P+IS SRWLV+ G + + D +TF +K KT Y LFLF DL
Sbjct: 1 KIKPFPLISQSRWLVKRGELTELVEDGGSLTFKKKKKKTPVY----LFLFNDL 49
>gnl|CDD|214619 smart00325, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases. Guanine nucleotide exchange
factor for Rho/Rac/Cdc42-like GTPases Also called
Dbl-homologous (DH) domain. It appears that PH domains
invariably occur C-terminal to RhoGEF/DH domains.
Improved coverage.
Length = 180
Score = 134 bits (339), Expect = 2e-36
Identities = 56/183 (30%), Positives = 96/183 (52%), Gaps = 7/183 (3%)
Query: 394 FELITSEASYFKSLTVLEKHFIASPLLDDVNILSKNDRKHLFGNVTAVRKCSERLLAALE 453
EL+ +E +Y + L +L + F+ PL ++ +LS N+ + LFGN+ + + L LE
Sbjct: 3 KELLQTERNYVRDLKLLVEVFLK-PLKKELKLLSPNELETLFGNIEEIYEFHRDFLDELE 61
Query: 454 QCWQDSILLTNICEIVYQHVTNKS--FNIYIKYCSNQFHIDRTLKSLRETNPKFIEALTE 511
+ ++ + E + F IY +YCSN LK L++ NP+F + L E
Sbjct: 62 ERIEEW---DDSVERIGDVFLKLEEFFKIYSEYCSNHPDALELLKKLKK-NPRFQKFLKE 117
Query: 512 LESDPVCQSLSLHSFLMLPMQRVTRLPLLFDAILTRLRPNHSEYETCHTTLATLNKIVHE 571
+ES P C+ L+L S L+ P+QR+T+ PLL +L +H + E L + ++ ++
Sbjct: 118 IESSPQCRRLTLESLLLKPVQRLTKYPLLLKELLKHTPEDHEDREDLKKALKAIKELANQ 177
Query: 572 CNE 574
NE
Sbjct: 178 VNE 180
Score = 59.2 bits (144), Expect = 4e-10
Identities = 21/63 (33%), Positives = 36/63 (57%)
Query: 10 LESDPVCQSLSLHSFLMLPMQRVTRLPLLFDAILTRLRPNHSEYETCHTTLATLNKIVHE 69
+ES P C+ L+L S L+ P+QR+T+ PLL +L +H + E L + ++ ++
Sbjct: 118 IESSPQCRRLTLESLLLKPVQRLTKYPLLLKELLKHTPEDHEDREDLKKALKAIKELANQ 177
Query: 70 CNE 72
NE
Sbjct: 178 VNE 180
>gnl|CDD|238091 cd00160, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous
(DH) domain. It appears that PH domains invariably occur
C-terminal to RhoGEF/DH domains.
Length = 181
Score = 119 bits (301), Expect = 4e-31
Identities = 54/186 (29%), Positives = 89/186 (47%), Gaps = 6/186 (3%)
Query: 389 LQEAKFELITSEASYFKSLTVLEKHFIASPLLDDVNILSKNDRKHLFGNVTAVRKCSERL 448
QE EL+ +E +Y + L +L + F+ PL ++ LS + + LFGN+ + +
Sbjct: 1 RQEVIKELLQTERNYVRDLKLLVEVFLK-PLDKELLPLSPEEVELLFGNIEEIYEFHRIF 59
Query: 449 LAALEQCWQDSILLT-NICEIVYQHVTNKSFNIYIKYCSNQFHIDRTLKSLRETNPKFIE 507
L +LE+ ++ I ++ + F IY +YCSN LK L++ N F E
Sbjct: 60 LKSLEERVEEWDKSGPRIGDVFLKL--APFFKIYSEYCSNHPDALELLKKLKKFNKFFQE 117
Query: 508 ALTELESDPVCQSLSLHSFLMLPMQRVTRLPLLFDAILTRLRPNHSEYETCHTTLATLNK 567
L + ES C L L S L+ P+QR+T+ PLL +L H + E L + +
Sbjct: 118 FLEKAES--ECGRLKLESLLLKPVQRLTKYPLLLKELLKHTPDGHEDREDLKKALEAIKE 175
Query: 568 IVHECN 573
+ + N
Sbjct: 176 VASQVN 181
Score = 50.8 bits (122), Expect = 3e-07
Identities = 17/57 (29%), Positives = 27/57 (47%)
Query: 15 VCQSLSLHSFLMLPMQRVTRLPLLFDAILTRLRPNHSEYETCHTTLATLNKIVHECN 71
C L L S L+ P+QR+T+ PLL +L H + E L + ++ + N
Sbjct: 125 ECGRLKLESLLLKPVQRLTKYPLLLKELLKHTPDGHEDREDLKKALEAIKEVASQVN 181
>gnl|CDD|227709 COG5422, ROM1, RhoGEF, Guanine nucleotide exchange factor for
Rho/Rac/Cdc42-like GTPases [Signal transduction
mechanisms].
Length = 1175
Score = 74.5 bits (183), Expect = 1e-13
Identities = 61/227 (26%), Positives = 106/227 (46%), Gaps = 8/227 (3%)
Query: 378 VLDTLDAGERKLQEAKFELITSEASYFKSLTVLEKHFIASPLLDDVNILSKNDR----KH 433
V ++L E K QEA +E+I +E + K L L +I L++ NI+ +N R KH
Sbjct: 474 VWESLPKQEIKRQEAIYEVIYTERDFVKDLEYLRDTWIK--PLEESNIIPENARRNFIKH 531
Query: 434 LFGNVTAVRKCSERLLAALEQCWQDSILLTNICEIVYQHVTNKSFNIYIKYCSNQFHIDR 493
+F N+ + + +LL AL S ++ I +I +V F +IKY ++Q +
Sbjct: 532 VFANINEIYAVNSKLLKALTNRQCLSPIVNGIADIFLDYV--PKFEPFIKYGASQPYAKY 589
Query: 494 TLKSLRETNPKFIEALTELESDPVCQSLSLHSFLMLPMQRVTRLPLLFDAILTRLRPNHS 553
+ + NP F E+E + L L +L P R+ R PLL + +L P++
Sbjct: 590 EFEREKSVNPNFARFDHEVERLDESRKLELDGYLTKPTTRLARYPLLLEEVLKFTDPDNP 649
Query: 554 EYETCHTTLATLNKIVHECNEEARKMERYYEMLLLSRLIKFSLKEVK 600
+ E + L + + N E+ K E ++ L++ + F + V
Sbjct: 650 DTEDIPKVIDMLREFLSRLNFESGKAENRGDLFHLNQQLLFKPEYVN 696
Score = 29.9 bits (67), Expect = 6.4
Identities = 20/82 (24%), Positives = 38/82 (46%)
Query: 17 QSLSLHSFLMLPMQRVTRLPLLFDAILTRLRPNHSEYETCHTTLATLNKIVHECNEEARK 76
+ L L +L P R+ R PLL + +L P++ + E + L + + N E+ K
Sbjct: 615 RKLELDGYLTKPTTRLARYPLLLEEVLKFTDPDNPDTEDIPKVIDMLREFLSRLNFESGK 674
Query: 77 MERYYEMLLLSRLIKFSLKEVK 98
E ++ L++ + F + V
Sbjct: 675 AENRGDLFHLNQQLLFKPEYVN 696
>gnl|CDD|241473 cd13319, PH_RARhoGAP, RA and RhoGAP domain-containing protein
Pleckstrin homology PH domain. RARhoGAP (also called
Rho GTPase-activating protein 20 and ARHGAP20 ) is
thought to function in rearrangements of the
cytoskeleton and cell signaling events that occur during
spermatogenesis. RARhoGAP was also shown to be activated
by Rap1 and to induce inactivation of Rho, resulting in
the neurite outgrowth. Recent findings show that
ARHGAP20, even although it is located in the middle of
the MDR on 11q22-23, is expressed at higher levels in
chronic lymphocytic leukemia patients with 11q22-23
and/or 13q14 deletions and its expression pattern
suggests a functional link between cases with 11q22-23
and 13q14 deletions. The mechanism needs to be further
studied. RARhoGAP contains a PH domain, a
Ras-associating domain, a Rho-GAP domain, and ANXL
repeats. 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 = 36.1 bits (84), Expect = 0.008
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 141 LFLFTDLLVITKKKSNGSY 159
LFLF+D+LV+ K KS S+
Sbjct: 31 LFLFSDVLVVAKPKSKNSF 49
>gnl|CDD|241263 cd01229, PH_Ect2, Epithelial cell transforming 2 (Ect2) pleckstrin
homology (PH) domain. Ect2, a mammalian ortholog of
Drosophila pebble, plays a role in neuronal
differentiation and brain development. Pebble and Ect2
have been identified as Rho-family guanine nucleotide
exchange factors (GEF) that mediate activation of Rho
during cytokinesis, but are proposed to play slightly
different roles. 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 = 180
Score = 36.5 bits (85), Expect = 0.020
Identities = 27/94 (28%), Positives = 41/94 (43%), Gaps = 16/94 (17%)
Query: 63 LNKIVHECNEEARKMERYYEMLLLSRLIKFSLKEVKCLP-VISSSRWLVRSGSMNFVNVD 121
L +++ NE+ RK E +M + I+ C P ++SS R V + V +
Sbjct: 1 LKEVMTHINEDKRKTEGQAQMFDIVNEIE------GCPPTLLSSHRSFV--SRLEVVELG 52
Query: 122 SKMTFARKLNKTHFYAKLNLFLFTDLLVITKKKS 155
+ L LFLF+DLL I KK+S
Sbjct: 53 D--SLKSGRGD-----SLALFLFSDLLEICKKRS 79
>gnl|CDD|241398 cd13244, PH_PLEKHG5_G6, Pleckstrin homology domain-containing
family G member 5 and 6 pleckstrin homology (PH) domain.
PLEKHG5 has a RhoGEF DH/double-homology domain in
tandem with a PH domain which is involved in
phospholipid binding. PLEKHG5 activates the nuclear
factor kappa B (NFKB1) signaling pathway. Mutations in
PLEKHG5 are associated with autosomal recessive distal
spinal muscular atrophy. PLEKHG6 (also called MyoGEF)
has no known function to date. 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 = 154
Score = 31.5 bits (72), Expect = 0.60
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 142 FLFTDLLVITKKKSNGSYSVI 162
FLFTD+L+I K +
Sbjct: 69 FLFTDMLLICKPVKKKEDRKV 89
>gnl|CDD|233592 TIGR01834, PHA_synth_III_E, poly(R)-hydroxyalkanoic acid synthase,
class III, PhaE subunit. This model represents the PhaE
subunit of the heterodimeric class (class III) of
polymerase for poly(R)-hydroxyalkanoic acids (PHAs),
carbon and energy storage polymers of many bacteria. The
most common PHA is polyhydroxybutyrate but about 150
different constituent hydroxyalkanoic acids (HAs) have
been identified in various species. This model must be
designated subfamily to indicate the heterogeneity of
PHAs [Cellular processes, Adaptations to atypical
conditions, Fatty acid and phospholipid metabolism,
Biosynthesis].
Length = 320
Score = 32.2 bits (73), Expect = 0.75
Identities = 19/117 (16%), Positives = 46/117 (39%), Gaps = 4/117 (3%)
Query: 469 VYQHVTNKSFNIYIKYCSNQFHIDRTLKSLRETNPKFIEALTELESDPVC--QSLSLHS- 525
+ + KSF + + + +K+ + ++ A E ++ ++ +H
Sbjct: 201 LEADIGYKSFAALMSDLLARAKSGKPVKTAKALYDLWVIAAEEAYAEVFASEENAKVHGK 260
Query: 526 FLMLPMQRVTRLPLLFDAILTRLR-PNHSEYETCHTTLATLNKIVHECNEEARKMER 581
F+ M+ + + +A+L L P SE + H + L + V + ++E
Sbjct: 261 FINALMRLRIQQQEIVEALLKMLNLPTRSELDEAHQRIQQLRREVKSLKKRLGELEA 317
>gnl|CDD|241393 cd13239, PH_Obscurin, Obscurin pleckstrin homology (PH) domain.
Obscurin (also called Obscurin-RhoGEF; Obscurin-myosin
light chain kinase/Obscurin-MLCK) is a giant muscle
protein that is concentrated at the peripheries of
Z-disks and M-lines. It binds small ankyrin I, a
component of the sarcoplasmic reticulum (SR) membrane.
It is associated with the contractile apparatus through
binding with titin and sarcomeric myosin. It plays
important roles in the organization and assembly of the
myofibril and the SR. Obscurin has been observed as
alternatively-spliced isoforms. The major isoform in
sleletal muscle, approximately 800 kDa in size, is
composed of many adhesion modules and signaling domains.
It harbors 49 Ig and 2 FNIII repeats at the N-terminues,
a complex middle region with additional Ig domains, an
IQ motif, and a conserved SH3 domain near RhoGEF and PH
domains, and a non-modular C-terminus with
phosphorylation motifs. The obscurin gene also encodes
two kinase domains, which are not part of the 800 kDa
form of the protein, but is part of smaller spliced
products that present in heart muscle. PH domains have
diverse functions, but in general are involved in
targeting proteins to the appropriate cellular location
or in the interaction with a binding partner. They share
little sequence conservation, but all have a common
fold, which is electrostatically polarized. Less than
10% of PH domains bind phosphoinositide phosphates
(PIPs) with high affinity and specificity. PH domains
are distinguished from other PIP-binding domains by
their specific high-affinity binding to PIPs with two
vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2
or PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved across
all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 125
Score = 30.1 bits (68), Expect = 1.3
Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 3/50 (6%)
Query: 127 ARKLNKTHFYAKLNLFLFTDLLVITKKKSNGSYSVIDYCTRAMMQMAAIE 176
R +K H ++FLF + +VI K K + Y + M++ I+
Sbjct: 30 VRTSSKGH---HRHVFLFKNCIVICKPKRDSRTDTPTYIFKNKMKLNDID 76
>gnl|CDD|241308 cd10572, PH_RhoGEF3_XPLN, Rho guanine nucleotide exchange factor 3
Pleckstrin homology (PH) domain. RhoGEF3/XPLN, a Rho
family GEF, preferentially stimulates guanine nucleotide
exchange on RhoA and RhoB, but not RhoC, RhoG, Rac1, or
Cdc42 in vitro. It also possesses transforming activity.
RhoGEF3/XPLN contains a tandem Dbl homology and PH
domain, but lacks homology with other known functional
domains or motifs. It is expressed in the brain,
skeletal muscle, heart, kidney, platelets, and
macrophage and neuronal cell lines. 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 = 143
Score = 30.4 bits (69), Expect = 1.3
Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 22/74 (29%)
Query: 79 RYYEMLLLSRLIKFSLKEVKCLPVISSSRWLVRSGSMNFVNVDSKMTFARKLNKTHFYAK 138
+YY +SRL L E + P+I SR L+ G + K + K
Sbjct: 6 QYY----ISRL--EYLDEKQKDPLIDESRALLCHGEL-------------KNKRGT---K 43
Query: 139 LNLFLFTDLLVITK 152
L++FLF D+LV+T+
Sbjct: 44 LHVFLFEDVLVLTR 57
>gnl|CDD|241397 cd13243, PH_PLEKHG1_G2_G3, Pleckstrin homology domain-containing
family G members 1, 2, and 3 pleckstrin homology (PH)
domain. PLEKHG1 (also called ARHGEF41), PLEKHG2 (also
called ARHGEF42 or CLG/common-site lymphoma/leukemia
guanine nucleotide exchange factor2), and PLEKHG3 (also
called ARHGEF43) have RhoGEF DH/double-homology domains
in tandem with a PH domain which is involved in
phospholipid binding. They function as a guanine
nucleotide exchange factor (GEF) and are involved in the
regulation of Rho protein signal transduction. Mutations
in PLEKHG1 have been associated panic disorder (PD), an
anxiety disorder characterized by panic attacks and
anticipatory anxiety. PH domains have diverse functions,
but in general are involved in targeting proteins to the
appropriate cellular location or in the interaction with
a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH domains
bind phosphoinositide phosphates (PIPs) with high
affinity and specificity. PH domains are distinguished
from other PIP-binding domains by their specific
high-affinity binding to PIPs with two vicinal phosphate
groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3
which results in targeting some PH domain proteins to
the plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 147
Score = 30.4 bits (69), Expect = 1.4
Identities = 12/40 (30%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 141 LFLFTDLLVITKKKSNGSYSVIDY--CTRAMMQMAAIEDS 178
LFLF +L+ITKK+ + + C+ M+ + +D
Sbjct: 69 LFLFDKMLLITKKREDDHLVYKTHIMCSNLMLVESIPKDP 108
>gnl|CDD|241262 cd01228, PH_BCR-related, Breakpoint Cluster Region-related
pleckstrin homology (PH) domain. The BCR gene is one of
the two genes in the BCR-ABL complex, which is
associated with the Philadelphia chromosome, a product
of a reciprocal translocation between chromosomes 22 and
9. BCR is a GTPase-activating protein (GAP) for RAC1
(primarily) and CDC42. The Dbl region of BCR has the
most RhoGEF activity for Cdc42, and less activity
towards Rac and Rho. Since BCR possesses both GAP and
GEF activities, it may function to temporally regulate
the activity of these GTPases. It also displays
serine/threonine kinase activity. The BCR protein
contains multiple domains including an N-terminal kinase
domain, a RhoGEF domain, a PH domain, a C1 domain, a C2
domain, and a C-terminal RhoGAP domain. ABR, a related
smaller protein, is structurally similar to BCR, but
lacks the N-terminal kinase domain and has GAP activity
for both Rac and 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 = 179
Score = 30.8 bits (70), Expect = 1.5
Identities = 25/111 (22%), Positives = 40/111 (36%), Gaps = 25/111 (22%)
Query: 141 LFLFTDLLVITKKKS-----NGSYSVIDYC--TRAMMQM----AAIEDSVPPTNKYLILL 189
LFLFTD+L+ K KS G Y Y + A D VP +++ L+ +
Sbjct: 35 LFLFTDVLLCAKLKSSGRGFQGQYECKWYIPLRDLSLHPKDESEAAPDVVPKSSEELVQM 94
Query: 190 TILENHEQKTVEIVLSCDTESESSLNVSNKSDK------------ILNSPS 228
+I +++ + S +K +L SPS
Sbjct: 95 KKAI--SALKQKIKRDSAERKKAASSGSRAIEKLRKKLAEQEAALLLASPS 143
>gnl|CDD|234960 PRK01565, PRK01565, thiamine biosynthesis protein ThiI;
Provisional.
Length = 394
Score = 30.9 bits (71), Expect = 2.0
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 127 ARKLNKTHFYAKLNLFLFTDLLVITKKKSNGSYSVIDYCTRAMMQMA 173
AR L K KL++ FT++ KKK SY + R MM++A
Sbjct: 226 ARILAKYGGRIKLHVVPFTEIQEEIKKKVPESYLMTLM-RRFMMRIA 271
>gnl|CDD|241472 cd13318, PH_IQSEC, IQ motif and SEC7 domain-containing protein
family Pleckstrin homology domain. The IQSEC (also
called BRAG/Brefeldin A-resistant Arf-gunanine
nucleotide exchange factor) family are a subset of Arf
GEFs that have been shown to activate Arf6, which acts
in the endocytic pathway to control the trafficking of a
subset of cargo proteins including integrins and have
key roles in the function and organization of distinct
excitatory and inhibitory synapses in the retina. The
family consists of 3 members: IQSEC1 (also called
BRAG2/GEP100), IQSEC2 (also called BRAG1), and IQSEC3
(also called SynArfGEF, BRAG3, or KIAA1110). IQSEC1
interacts with clathrin and modulates cell adhesion by
regulating integrin surface expression and in addition
to Arf6, it also activates the class II Arfs, Arf4 and
Arf5. Mutations in IQSEC2 cause non-syndromic X-linked
intellectual disability as well as reduced activation of
Arf substrates (Arf1, Arf6). IQSEC3 regulates Arf6 at
inhibitory synapses and associates with the
dystrophin-associated glycoprotein complex and S-SCAM.
These members contains a IQ domain that may bind
calmodulin, a PH domain that is thought to mediate
membrane localization by binding of phosphoinositides,
and a SEC7 domain that can promote GEF activity on ARF.
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 = 128
Score = 28.8 bits (65), Expect = 4.5
Identities = 22/88 (25%), Positives = 36/88 (40%), Gaps = 26/88 (29%)
Query: 141 LFLFTDLLVITK----KKSNGSYSVIDYCTRAM---MQMAAIEDSVPPTNKYLILLTILE 193
+FLF DLLV+TK KKS+ +Y+ + MQ+ E+S
Sbjct: 30 VFLFNDLLVVTKIFSKKKSSVTYT---FRQSFPLLGMQVLLFENS--------------- 71
Query: 194 NHEQKTVEIVLSCDTESESSLNVSNKSD 221
+ + + D + + N N+SD
Sbjct: 72 -YYPHGIRLTSPLDNKVLITFNAPNESD 98
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
0.320 0.134 0.398
Gapped
Lambda K H
0.267 0.0734 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 32,554,317
Number of extensions: 3129901
Number of successful extensions: 2378
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2363
Number of HSP's successfully gapped: 24
Length of query: 654
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 551
Effective length of database: 6,369,140
Effective search space: 3509396140
Effective search space used: 3509396140
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 62 (27.7 bits)