RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8222
(198 letters)
>gnl|CDD|216454 pfam01363, FYVE, FYVE zinc finger. The FYVE zinc finger is named
after four proteins that it has been found in: Fab1,
YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been
shown to bind two Zn++ ions. The FYVE finger has eight
potential zinc coordinating cysteine positions. Many
members of this family also include two histidines in a
motif R+HHC+XCG, where + represents a charged residue
and X any residue. We have included members which do not
conserve these histidine residues but are clearly
related.
Length = 68
Score = 85.1 bits (211), Expect = 3e-22
Identities = 30/69 (43%), Positives = 40/69 (57%), Gaps = 3/69 (4%)
Query: 54 AVWIPDNEAAVCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKRFLLP--SQSAKPLRVC 111
W+PD++ CM C + F+ RRHHCR CG V C+ CS+K+ L KP+RVC
Sbjct: 1 PRWVPDSDVTNCMGCGKP-FSFFRRRHHCRNCGKVFCSSCSSKKIALLPKLGINKPVRVC 59
Query: 112 LTCYDVLSR 120
CYD L +
Sbjct: 60 DDCYDKLQK 68
>gnl|CDD|214499 smart00064, FYVE, Protein present in Fab1, YOTB, Vac1, and EEA1.
The FYVE zinc finger is named after four proteins where
it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1.
The FYVE finger has been shown to bind two Zn2+ ions.
The FYVE finger has eight potential zinc coordinating
cysteine positions. The FYVE finger is structurally
related to the PHD finger and the RING finger. Many
members of this family also include two histidines in a
motif R+HHC+XCG, where + represents a charged residue
and X any residue. The FYVE finger functions in the
membrane recruitment of cytosolic proteins by binding to
phosphatidylinositol 3-phosphate (PI3P), which is
prominent on endosomes. The R+HHC+XCG motif is critical
for PI3P binding.
Length = 68
Score = 83.3 bits (206), Expect = 2e-21
Identities = 30/69 (43%), Positives = 41/69 (59%), Gaps = 2/69 (2%)
Query: 53 AAVWIPDNEAAVCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKRFLLPSQS-AKPLRVC 111
WIPD E + CM C +F + RRHHCR CG + C+ CS+K+ LP +P+RVC
Sbjct: 1 RPHWIPDEEVSNCMGC-GKEFNLTKRRHHCRNCGRIFCSKCSSKKAPLPKLGIERPVRVC 59
Query: 112 LTCYDVLSR 120
CY+ L+
Sbjct: 60 DDCYENLNG 68
>gnl|CDD|241253 cd01218, PH_Phafin2-like, Phafin2 (also called EAPF, FLJ13187,
ZFYVE18 or PLEKHF2) Pleckstrin Homology (PH) domain.
Phafin2 is differentially expressed in the liver cancer
cell and regulates the structure and function of the
endosomes through Rab5-dependent processes. Phafin2
modulates the cell's response to extracellular
stimulation by modulating the receptor density on the
cell surface. Phafin2 contains a PH domain and a FYVE
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 = 123
Score = 75.0 bits (185), Expect = 9e-18
Identities = 24/36 (66%), Positives = 28/36 (77%)
Query: 1 MELRNGWLIQTSSKSFAVHAATSTEKQEWMAHINKC 36
EL+NGW I + KSF V+AAT+TEK EWM HINKC
Sbjct: 88 GELKNGWQIISPKKSFVVYAATATEKSEWMDHINKC 123
>gnl|CDD|238022 cd00065, FYVE, FYVE domain; Zinc-binding domain; targets proteins
to membrane lipids via interaction with
phosphatidylinositol-3-phosphate, PI3P; present in Fab1,
YOTB, Vac1, and EEA1;.
Length = 57
Score = 69.4 bits (170), Expect = 2e-16
Identities = 28/57 (49%), Positives = 37/57 (64%), Gaps = 2/57 (3%)
Query: 61 EAAVCMHCKRTQFTVLSRRHHCRKCGSVVCAPCSNKRFLLPS-QSAKPLRVCLTCYD 116
+A+ CM C FT+ RRHHCR CG + C+ CS+ R LPS KP+RVC +CY+
Sbjct: 1 DASSCMGC-GKPFTLTRRRHHCRNCGRIFCSKCSSNRIPLPSMGGGKPVRVCDSCYE 56
>gnl|CDD|140324 PTZ00303, PTZ00303, phosphatidylinositol kinase; Provisional.
Length = 1374
Score = 38.1 bits (88), Expect = 0.002
Identities = 29/79 (36%), Positives = 34/79 (43%), Gaps = 16/79 (20%)
Query: 52 HAAVWIPDNEAA-VCMHCKRTQFTVLSR-----RHHCRKCGSVVCAPCSNKR-------F 98
H W D+E++ C C R F LSR HHCR CG +C C KR
Sbjct: 449 HNPSWQKDDESSDSCPSCGRA-FISLSRPLGTRAHHCRSCGIRLCVFCITKRAHYSFAKL 507
Query: 99 LLPSQS--AKPLRVCLTCY 115
P S A+ VC TCY
Sbjct: 508 AKPGSSDEAEERLVCDTCY 526
>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 = 33.7 bits (78), Expect = 0.010
Identities = 9/41 (21%), Positives = 20/41 (48%)
Query: 2 ELRNGWLIQTSSKSFAVHAATSTEKQEWMAHINKCIEDLLR 42
+ R + + + +KS+ + A + ++Q W+ I I L
Sbjct: 58 DRRFCFEVVSPTKSYMLQAESEEDRQAWIQAIQAAIASALN 98
>gnl|CDD|241423 cd13269, PH_alsin, Alsin Pleckstrin homology (PH) domain. The ALS2
gene encodes alsin, a GEF, that has dual specificity for
Rac1 and Rab5 GTPases. Alsin mutations in the form of
truncated proteins are responsible for motor function
disorders including juvenile-onset amyotrophic lateral
sclerosis, familial juvenile primary lateral sclerosis,
and infantile-onset ascending hereditary spastic
paralysis. The alsin protein is widely expressed in the
developing CNS including neurons of the cerebral cortex,
brain stem, spinal cord, and cerebellum. Alsin contains
a regulator of chromosome condensation 1 (RCC1) domain,
a Rho guanine nucleotide exchanging factor (RhoGEF)
domain, a PH domain, a Membrane Occupation and
Recognition Nexus (MORN), a vacuolar protein sorting 9
(Vps9) domain, and a Dbl homology (DH) domain. Alsin
interacts with Rab5 through its Vps9 domain and through
this interaction modulates early endosome fusion and
trafficking. The GEF activity of alsin towards Rab5 is
regulated by Rac1 function. The GEF activity of alsin
for Rac1 occurs via its DH domain and this interaction
plays a role in promoting spinal motor neuron survival
via multiple Rac-dependent signaling pathways. 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 = 32.0 bits (73), Expect = 0.056
Identities = 15/41 (36%), Positives = 22/41 (53%)
Query: 3 LRNGWLIQTSSKSFAVHAATSTEKQEWMAHINKCIEDLLRK 43
+N I T +SF + A+T EK EW+ IN+ I+ L
Sbjct: 66 GQNALKITTPEESFTLVASTPQEKAEWLRAINQAIDQALNG 106
>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 = 31.4 bits (72), Expect = 0.083
Identities = 10/30 (33%), Positives = 18/30 (60%)
Query: 9 IQTSSKSFAVHAATSTEKQEWMAHINKCIE 38
+ T ++F + A T E++EW+ I K +E
Sbjct: 75 LVTPDRTFVLSAETEEERREWITAIQKVLE 104
>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 = 31.5 bits (72), Expect = 0.10
Identities = 11/35 (31%), Positives = 25/35 (71%)
Query: 9 IQTSSKSFAVHAATSTEKQEWMAHINKCIEDLLRK 43
I+++ +SF + A+++ E+ EW+ +++ IED +K
Sbjct: 80 IESTKRSFTLSASSAEERDEWVKALSRAIEDYTKK 114
>gnl|CDD|241255 cd01220, PH1_FARP1-like, FERM, RhoGEF and pleckstrin
domain-containing protein 1 and related proteins
Pleckstrin Homology (PH) domain, repeat 1. Members here
include FARP1 (also called Chondrocyte-derived
ezrin-like protein; PH domain-containing family C member
2), FARP2 (also called FIR/FERM domain including RhoGEF;
FGD1-related Cdc42-GEF/FRG), and FARP6 (also called Zinc
finger FYVE domain-containing protein 24). They are
members of the Dbl family guanine nucleotide exchange
factors (GEFs) which are upstream positive regulators of
Rho GTPases. Little is known about FARP1 and FARP6,
though FARP1 has increased expression in differentiated
chondrocytes. FARP2 is thought to regulate neurite
remodeling by mediating the signaling pathways from
membrane proteins to Rac. It is found in brain, lung,
and testis, as well as embryonic hippocampal and
cortical neurons. FARP1 and FARP2 are composed of a
N-terminal FERM domain, a proline-rich (PR) domain,
Dbl-homology (DH), and two C-terminal PH domains. FARP6
is composed of Dbl-homology (DH), and two C-terminal PH
domains separated by a FYVE domain. This hierarchy
contains 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 = 123
Score = 30.4 bits (69), Expect = 0.24
Identities = 8/39 (20%), Positives = 22/39 (56%)
Query: 1 MELRNGWLIQTSSKSFAVHAATSTEKQEWMAHINKCIED 39
M + + + I +++ V A++ EK+ W+ +++ I+
Sbjct: 81 MGVPHCFTIYGGNRALTVAASSEEEKERWLEDLSRAIDA 119
>gnl|CDD|215766 pfam00169, PH, PH domain. PH stands for pleckstrin homology.
Length = 101
Score = 29.7 bits (67), Expect = 0.31
Identities = 10/35 (28%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 4 RNGWLIQTSSK-SFAVHAATSTEKQEWMAHINKCI 37
+N + I+T + +F + A + E++EW+ I I
Sbjct: 66 KNCFEIRTGDRETFLLQAESEEERKEWVKAIRSAI 100
>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 = 29.4 bits (66), Expect = 0.47
Identities = 9/38 (23%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 1 MELRNGWLIQTSS-KSFAVHAATSTEKQEWMAHINKCI 37
+ + + I+TS K+ + A + E+++W+ + K I
Sbjct: 64 SKKPHCFEIKTSDRKTLLLQAESEEEREKWVEALRKAI 101
>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 = 29.2 bits (66), Expect = 0.73
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 20 AATSTEKQEWMAHINKCIEDL 40
A T E+ EW+ +N+ + DL
Sbjct: 98 ADTKEERIEWLDALNQTLADL 118
>gnl|CDD|241544 cd13393, PH_RhoGEF2, Rho guanine nucleotide exchange factor 2
Pleckstrin homology (PH) domain. RhoGEF2 acts as
guanine nucleotide exchange factor (GEF) for RhoA
GTPases. It is thought to play a role in actin
cytoskeleton reorganization in different tissues since
its activation induces formation of actin stress fibers.
RhoGEF2 contains a C1 domain followed by Dbl-homology
(DH) and pleckstrin-homology (PH) domains which bind and
catalyze the exchange of GDP for GTP on RhoA. PH domains
have diverse functions, but in generally 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 = 29.0 bits (65), Expect = 0.84
Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 3/40 (7%)
Query: 2 ELRNGWLIQTSSKS---FAVHAATSTEKQEWMAHINKCIE 38
E + +LI SS + VH A+ ++ WM HI + +E
Sbjct: 66 EEKGMFLISASSAGPEMYEVHTASKEDRNTWMRHIQQAVE 105
>gnl|CDD|224123 COG1202, COG1202, Superfamily II helicase, archaea-specific
[General function prediction only].
Length = 830
Score = 29.8 bits (67), Expect = 1.1
Identities = 10/33 (30%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 62 AAVCMHC-KRTQFTVLSRRHHCRKCGSVVCAPC 93
A +C HC ++TVL+ + + G +C C
Sbjct: 95 ARLCRHCLLEGRYTVLTEGNRIKYGGEEICERC 127
>gnl|CDD|180627 PRK06569, PRK06569, F0F1 ATP synthase subunit B'; Validated.
Length = 155
Score = 28.7 bits (64), Expect = 1.4
Identities = 14/29 (48%), Positives = 18/29 (62%), Gaps = 2/29 (6%)
Query: 166 DNIMPADQLSFKVDGLNCNGYYCPEIEGT 194
DNI AD L+ +V+ L N YY EI+ T
Sbjct: 48 DNITQADTLTIEVEKL--NKYYNEEIDKT 74
>gnl|CDD|227458 COG5129, MAK16, Nuclear protein with HMG-like acidic region
[General function prediction only].
Length = 303
Score = 28.5 bits (63), Expect = 2.5
Identities = 8/31 (25%), Positives = 14/31 (45%)
Query: 134 ATADKDVSRTSRSDSSGEDDSDDDTDDANHN 164
+ + S + S E +SD+D D+ N
Sbjct: 236 GSDQSMETSESEEEESSESESDEDEDEDNKG 266
>gnl|CDD|234616 PRK00076, recR, recombination protein RecR; Reviewed.
Length = 196
Score = 28.1 bits (64), Expect = 2.6
Identities = 8/27 (29%), Positives = 12/27 (44%), Gaps = 4/27 (14%)
Query: 75 VLSRRHHCRKCGSV----VCAPCSNKR 97
+ HC CG++ C CS+ R
Sbjct: 49 AKEKIKHCSVCGNLTEQDPCEICSDPR 75
>gnl|CDD|215628 PLN03196, PLN03196, MOC1-like protein; Provisional.
Length = 487
Score = 28.1 bits (63), Expect = 3.2
Identities = 12/39 (30%), Positives = 15/39 (38%)
Query: 123 TVSGKPMAGNTATADKDVSRTSRSDSSGEDDSDDDTDDA 161
+ G+ M + K S S S EDD DDD
Sbjct: 443 FIEGEEMEPLFSMGGKLEMPGSESVSDEEDDDDDDEVLY 481
>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit.
Transcription initiation factor IIA (TFIIA) is a
heterotrimer, the three subunits being known as alpha,
beta, and gamma, in order of molecular weight. The N and
C-terminal domains of the gamma subunit are represented
in pfam02268 and pfam02751, respectively. This family
represents the precursor that yields both the alpha and
beta subunits. The TFIIA heterotrimer is an essential
general transcription initiation factor for the
expression of genes transcribed by RNA polymerase II.
Together with TFIID, TFIIA binds to the promoter region;
this is the first step in the formation of a
pre-initiation complex (PIC). Binding of the rest of the
transcription machinery follows this step. After
initiation, the PIC does not completely dissociate from
the promoter. Some components, including TFIIA, remain
attached and re-initiate a subsequent round of
transcription.
Length = 332
Score = 28.2 bits (63), Expect = 3.3
Identities = 10/35 (28%), Positives = 14/35 (40%), Gaps = 1/35 (2%)
Query: 133 TATADKDVSRTSRSDSSGEDDSDDDTDDANHNPDN 167
T + S + G DD DDD D + D+
Sbjct: 238 RRTIAQIDGIDSDDEGDGSDD-DDDEDAIESDLDD 271
>gnl|CDD|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein.
This family represents Cwf15/Cwc15 (from
Schizosaccharomyces pombe and Saccharomyces cerevisiae
respectively) and their homologues. The function of
these proteins is unknown, but they form part of the
spliceosome and are thus thought to be involved in mRNA
splicing.
Length = 241
Score = 27.8 bits (62), Expect = 4.0
Identities = 8/25 (32%), Positives = 11/25 (44%)
Query: 136 ADKDVSRTSRSDSSGEDDSDDDTDD 160
AD S + S + D DD D+
Sbjct: 119 ADDSDSSSDSDSSDDDSDDDDSEDE 143
Score = 27.0 bits (60), Expect = 6.2
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 137 DKDVSRTSRSDSSGEDDSDDDTDD 160
D D S +S S +DDSDDD +
Sbjct: 118 DADDSDSSSDSDSSDDDSDDDDSE 141
Score = 26.6 bits (59), Expect = 8.4
Identities = 8/26 (30%), Positives = 10/26 (38%)
Query: 135 TADKDVSRTSRSDSSGEDDSDDDTDD 160
+ D + S S D D D DD
Sbjct: 114 ARNSDADDSDSSSDSDSSDDDSDDDD 139
>gnl|CDD|220775 pfam10479, FSA_C, Fragile site-associated protein C-terminus. This
is the conserved C-terminal half of the protein KIAA1109
which is the fragile site-associated protein FSA.
Genome-wide-association studies showed this protein to
linked to the susceptibility to coeliac disease. The
protein may also be associated with polycystic kidney
disease.
Length = 615
Score = 28.0 bits (62), Expect = 4.4
Identities = 18/57 (31%), Positives = 26/57 (45%), Gaps = 2/57 (3%)
Query: 128 PMAGNTATADKDVSRTSRSDSSGEDDSDDDTDDANHNPDNI--MPADQLSFKVDGLN 182
P++ N A S SR SG + + NHN + I +P+ QL FK + L
Sbjct: 387 PISENENEAKSPTSSISRFRGSGSSSAKEKGQATNHNREVIFALPSLQLHFKSEHLQ 443
>gnl|CDD|223146 COG0068, HypF, Hydrogenase maturation factor [Posttranslational
modification, protein turnover, chaperones].
Length = 750
Score = 27.7 bits (62), Expect = 4.6
Identities = 13/34 (38%), Positives = 14/34 (41%), Gaps = 7/34 (20%)
Query: 58 PDNEAAVCMHCKRTQFTVLSRRHH-----CRKCG 86
PD AA C C F SRR+ C CG
Sbjct: 99 PD--AATCEDCLEEIFDPNSRRYLYPFINCTNCG 130
>gnl|CDD|234777 PRK00481, PRK00481, NAD-dependent deacetylase; Provisional.
Length = 242
Score = 27.5 bits (62), Expect = 4.7
Identities = 8/30 (26%), Positives = 12/30 (40%), Gaps = 3/30 (10%)
Query: 63 AVCMHCKRT---QFTVLSRRHHCRKCGSVV 89
A C C +T + C KCG ++
Sbjct: 123 ARCTKCGQTYDLDEYLKPEPPRCPKCGGIL 152
>gnl|CDD|241266 cd01233, PH_KIFIA_KIFIB, KIFIA and KIFIB protein pleckstrin
homology (PH) domain. The kinesin-3 family motors KIFIA
(Caenorhabditis elegans homolog unc-104) and KIFIB
transport synaptic vesicle precursors that contain
synaptic vesicle proteins, such as synaptophysin,
synaptotagmin and the small GTPase RAB3A, but they do
not transport organelles that contain plasma membrane
proteins. They have a N-terminal motor domain, followed
by a coiled-coil domain, and a C-terminal PH domain.
KIF1A adopts a monomeric form in vitro, but acts as a
processive dimer in vivo. KIF1B has alternatively
spliced isoforms distinguished by the presence or
absence of insertion sequences in the conserved
amino-terminal region of the protein; this results in
their different motor activities. KIF1A and KIF1B bind
to RAB3 proteins through the adaptor protein
mitogen-activated protein kinase (MAPK) -activating
death domain (MADD; also calledDENN), which was first
identified as a RAB3 guanine nucleotide exchange factor
(GEF). 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 = 26.4 bits (59), Expect = 4.7
Identities = 6/24 (25%), Positives = 13/24 (54%)
Query: 11 TSSKSFAVHAATSTEKQEWMAHIN 34
T + S+ + A + E +W+ I+
Sbjct: 84 TPTNSYLLQARSEKEMHDWLYAID 107
>gnl|CDD|221323 pfam11931, DUF3449, Domain of unknown function (DUF3449). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is typically
between 181 to 207 amino acids in length. This domain
has two conserved sequence motifs: PIP and CEICG. The
domain carries a zinc-finger domain of the C2H2-type.
Length = 187
Score = 27.2 bits (61), Expect = 5.2
Identities = 22/66 (33%), Positives = 31/66 (46%), Gaps = 10/66 (15%)
Query: 135 TADKDVSRTSRSDSSGEDDSDDDTDDANHNPDNIMP--ADQLS-----FKVDGLNCNGYY 187
A D S S+ +DDSDDD ++ +NP N +P D +K+ GL +
Sbjct: 37 QASADESSEDASEDGSDDDSDDDEEEPIYNPLN-LPLGWDGKPIPYWLYKLHGLG-KEFK 94
Query: 188 CPEIEG 193
C EI G
Sbjct: 95 C-EICG 99
>gnl|CDD|215643 PLN03241, PLN03241, magnesium chelatase subunit H; Provisional.
Length = 1315
Score = 27.5 bits (61), Expect = 5.2
Identities = 3/53 (5%), Positives = 14/53 (26%), Gaps = 2/53 (3%)
Query: 117 VLSRDKTVSGKPMA-GNTATADKDVSRTSRSDSSGEDDSDDDTDDANHNPDNI 168
L + + +P A + + +++ + ++
Sbjct: 18 TLLGSRRSARRPAGSRPCHAAPTFAALAAVAEADEDSAG-SPQPKKHNTARTR 69
>gnl|CDD|216353 pfam01190, Pollen_Ole_e_I, Pollen proteins Ole e I like.
Length = 95
Score = 25.9 bits (57), Expect = 6.9
Identities = 18/57 (31%), Positives = 22/57 (38%), Gaps = 13/57 (22%)
Query: 86 GSVVCAPCSNKRFLLPSQSAKPL---RVCLTCYDVLSRDKTVSGKPMAGNTATADKD 139
GSV C C F L SA PL +V + C D R T + A D+
Sbjct: 3 GSVYCDTCRASGFEL---SAYPLPGAKVKIECKDGDGRVVTSA-------EAVTDEK 49
>gnl|CDD|215239 PLN02436, PLN02436, cellulose synthase A.
Length = 1094
Score = 27.1 bits (60), Expect = 7.1
Identities = 21/85 (24%), Positives = 35/85 (41%), Gaps = 9/85 (10%)
Query: 82 CRKCGSVVCAPCSNKRFLLPSQSAKPLRVCLTCYDVLSRDKTVSGKPMAGNTATADKDVS 141
C+ CG + + F+ ++ A P VC CY+ R+ G T K +
Sbjct: 39 CQICGDEIELTVDGEPFVACNECAFP--VCRPCYEYERRE----GNQACPQCKTRYKRIK 92
Query: 142 RTSRSDSSGEDDSDDDTDDANHNPD 166
+ R + D+ +DD DD + D
Sbjct: 93 GSPRVEG---DEEEDDIDDLENEFD 114
>gnl|CDD|221398 pfam12056, DUF3537, Protein of unknown function (DUF3537). This
family of transmembrane proteins are functionally
uncharacterized. This protein is found in eukaryotes.
Proteins in this family are typically between 427 to 453
amino acids in length.
Length = 398
Score = 27.0 bits (60), Expect = 7.4
Identities = 22/61 (36%), Positives = 27/61 (44%), Gaps = 5/61 (8%)
Query: 110 VCLTCYDVLSRDKTVSGKPMAGNTATADKDVSRTSRSDSSGEDDSDDDTDDANHNPDNIM 169
C TC S D TV P + A V R S SS D+S D+ DD ++ IM
Sbjct: 300 ACATCS---SFDTTVDETPTSVLLPAASNLVLRPVSSSSSSSDESGDEEDDLDNT--KIM 354
Query: 170 P 170
P
Sbjct: 355 P 355
>gnl|CDD|241258 cd01224, PH_Collybistin_ASEF, Collybistin/APC-stimulated guanine
nucleotide exchange factor pleckstrin homology (PH)
domain. Collybistin (also called PEM2) is homologous to
the Dbl proteins ASEF (also called ARHGEF4/RhoGEF4) and
SPATA13 (Spermatogenesis-associated protein 13; also
called ASEF2). It activates CDC42 specifically and not
any other Rho-family GTPases. Collybistin consists of an
SH3 domain, followed by a RhoGEF/DH and PH domain. In
Dbl proteins, the DH and PH domains catalyze the
exchange of GDP for GTP in Rho GTPases, allowing them to
signal to downstream effectors. It induces submembrane
clustering of the receptor-associated peripheral
membrane protein gephyrin, which is thought to form a
scaffold underneath the postsynaptic membrane linking
receptors to the cytoskeleton. It also acts as a tumor
suppressor that links adenomatous polyposis coli (APC)
protein, a negative regulator of the Wnt signaling
pathway and promotes the phosphorylation and degradation
of beta-catenin, to Cdc42. Autoinhibition of collybistin
is accomplished by the binding of its SH3 domain with
both the RhoGEF and PH domains to block access of Cdc42
to the GTPase-binding site. Inactivation promotes cancer
progression. PH domains have diverse functions, but in
general are involved in targeting proteins to the
appropriate cellular location or in the interaction with
a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH domains
bind phosphoinositide phosphates (PIPs) with high
affinity and specificity. PH domains are distinguished
from other PIP-binding domains by their specific
high-affinity binding to PIPs with two vicinal phosphate
groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3
which results in targeting some PH domain proteins to
the plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 139
Score = 26.4 bits (59), Expect = 7.7
Identities = 10/33 (30%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 3 LRNGWLIQTSS--KSFAVHAATSTEKQEWMAHI 33
++N W I +S K + + A ++ EKQ W+
Sbjct: 97 VKNAWKIYNTSKNKWYLLCAKSAEEKQRWLEAF 129
>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 = 26.1 bits (58), Expect = 7.7
Identities = 8/19 (42%), Positives = 9/19 (47%)
Query: 19 HAATSTEKQEWMAHINKCI 37
AAT E EW+ I I
Sbjct: 97 SAATEEEMDEWIKSIKASI 115
>gnl|CDD|241425 cd13271, PH2_TAPP1_2, Tandem PH-domain-containing proteins 1 and 2
Pleckstrin homology (PH) domain, C-terminal repeat. The
binding of TAPP1 (also called PLEKHA1/pleckstrin
homology domain containing, family A (phosphoinositide
binding specific) member 1) and TAPP2 (also called
PLEKHA2) adaptors to PtdIns(3,4)P(2), but not PI(3,4,
5)P3, function as negative regulators of insulin and
PI3K signalling pathways (i.e. TAPP/utrophin/syntrophin
complex). TAPP1 and TAPP2 contain two sequential PH
domains in which the C-terminal PH domain specifically
binds PtdIns(3,4)P2 with high affinity. The N-terminal
PH domain does not interact with any phosphoinositide
tested. They also contain a C-terminal PDZ-binding motif
that interacts with several PDZ-binding proteins,
including PTPN13 (known previously as PTPL1 or FAP-1) as
well as the scaffolding proteins MUPP1 (multiple
PDZ-domain-containing protein 1), syntrophin and
utrophin. PH domains have diverse functions, but in
general are involved in targeting proteins to the
appropriate cellular location or in the interaction with
a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH domains
bind phosphoinositide phosphates (PIPs) with high
affinity and specificity. PH domains are distinguished
from other PIP-binding domains by their specific
high-affinity binding to PIPs with two vicinal phosphate
groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3
which results in targeting some PH domain proteins to
the plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 114
Score = 26.1 bits (58), Expect = 7.8
Identities = 8/37 (21%), Positives = 16/37 (43%)
Query: 9 IQTSSKSFAVHAATSTEKQEWMAHINKCIEDLLRKSG 45
I T+S++F + A + + W+ I+ I
Sbjct: 76 IITTSRTFYIQADSPEDMHSWIKAISGAIVARRGPYR 112
>gnl|CDD|234949 PRK01388, PRK01388, arginine deiminase; Provisional.
Length = 406
Score = 26.7 bits (60), Expect = 8.3
Identities = 17/45 (37%), Positives = 19/45 (42%), Gaps = 6/45 (13%)
Query: 37 IEDLLRKSGKKPAATHA-AVWIPDNEAA-----VCMHCKRTQFTV 75
IE L R KK AA AV IP + A V +FTV
Sbjct: 240 IEQLARSLFKKGAAKRVLAVEIPKSRAFMHLDTVFTMVDYDKFTV 284
>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 = 25.8 bits (57), Expect = 8.7
Identities = 9/34 (26%), Positives = 19/34 (55%)
Query: 4 RNGWLIQTSSKSFAVHAATSTEKQEWMAHINKCI 37
+ + T ++F + A + EK+EW++ I + I
Sbjct: 69 EFAFEVSTPERTFYLIADSEKEKEEWISAIGRAI 102
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
0.316 0.129 0.403
Gapped
Lambda K H
0.267 0.0672 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,275,978
Number of extensions: 775134
Number of successful extensions: 1163
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1132
Number of HSP's successfully gapped: 63
Length of query: 198
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 106
Effective length of database: 6,857,034
Effective search space: 726845604
Effective search space used: 726845604
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (25.5 bits)