RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5805
(75 letters)
>gnl|CDD|206715 cd04148, RGK, Rem, Rem2, Rad, Gem/Kir (RGK) subfamily of Ras
GTPases. RGK subfamily. The RGK (Rem, Rem2, Rad,
Gem/Kir) subfamily of Ras GTPases are expressed in a
tissue-specific manner and are dynamically regulated by
transcriptional and posttranscriptional mechanisms in
response to environmental cues. RGK proteins bind to the
beta subunit of L-type calcium channels, causing
functional down-regulation of these voltage-dependent
calcium channels, and either termination of
calcium-dependent secretion or modulation of electrical
conduction and contractile function. Inhibition of
L-type calcium channels by Rem2 may provide a mechanism
for modulating calcium-triggered exocytosis in
hormone-secreting cells, and has been proposed to
influence the secretion of insulin in pancreatic beta
cells. RGK proteins also interact with and inhibit the
Rho/Rho kinase pathway to modulate remodeling of the
cytoskeleton. Two characteristics of RGK proteins cited
in the literature are N-terminal and C-terminal
extensions beyond the GTPase domain typical of Ras
superfamily members. The N-terminal extension is not
conserved among family members; the C-terminal extension
is reported to be conserved among the family and lack
the CaaX prenylation motif typical of
membrane-associated Ras proteins. However, a putative
CaaX motif has been identified in the alignment of the
C-terminal residues of this CD.
Length = 219
Score = 65.5 bits (160), Expect = 7e-15
Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 10/73 (13%)
Query: 1 MASRTSCFTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILV 60
M SC D +VIVYSV +R +F+KA ++ L ++ + +ILV
Sbjct: 63 MWLEDSCMQV----------GDAYVIVYSVTDRSSFEKASELRIQLRRARQAEDIPIILV 112
Query: 61 ANKADLERRRQVT 73
NK+DL R R+V+
Sbjct: 113 GNKSDLVRSREVS 125
>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 = 50.2 bits (121), Expect = 2e-09
Identities = 18/55 (32%), Positives = 34/55 (61%), Gaps = 6/55 (10%)
Query: 22 DVFVIVYSVIERKTFKKAE---DMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
D F++VYS+ R++F++ + + + + D + + ++LV NK DLE RQV+
Sbjct: 72 DGFILVYSITSRESFEEIKNIREQILRVKDKEDV---PIVLVGNKCDLENERQVS 123
>gnl|CDD|206713 cd04146, RERG_RasL11_like, Ras-related and Estrogen-Regulated
Growth inhibitor (RERG) and Ras-like 11 (RasL11)-like
families. RERG (Ras-related and Estrogen- Regulated
Growth inhibitor) and Ras-like 11 are members of a novel
subfamily of Ras that were identified based on their
behavior in breast and prostate tumors, respectively.
RERG expression was decreased or lost in a significant
fraction of primary human breast tumors that lack
estrogen receptor and are correlated with poor clinical
prognosis. Elevated RERG expression correlated with
favorable patient outcome in a breast tumor subtype that
is positive for estrogen receptor expression. In
contrast to most Ras proteins, RERG overexpression
inhibited the growth of breast tumor cells in vitro and
in vivo. RasL11 was found to be ubiquitously expressed
in human tissue, but down-regulated in prostate tumors.
Both RERG and RasL11 lack the C-terminal CaaX
prenylation motif, where a = an aliphatic amino acid and
X = any amino acid, and are localized primarily in the
cytoplasm. Both are believed to have tumor suppressor
activity.
Length = 166
Score = 49.2 bits (118), Expect = 5e-09
Identities = 24/53 (45%), Positives = 33/53 (62%), Gaps = 1/53 (1%)
Query: 22 DVFVIVYSVIERKTFKKAEDMLKTLWDSK-YIGEKAVILVANKADLERRRQVT 73
D FV+VYS+ +R +F +L+ + + K GE VILV NKADL RQV+
Sbjct: 74 DGFVLVYSITDRSSFDVVSQLLQLIREIKKRDGEIPVILVGNKADLLHSRQVS 126
>gnl|CDD|206712 cd04141, Rit_Rin_Ric, Ras-like protein in all tissues (Rit),
Ras-like protein in neurons (Rin) and Ras-related
protein which interacts with calmodulin (Ric). Rit
(Ras-like protein in all tissues), Rin (Ras-like protein
in neurons) and Ric (Ras-related protein which interacts
with calmodulin) form a subfamily with several unique
structural and functional characteristics. These
proteins all lack a the C-terminal CaaX lipid-binding
motif typical of Ras family proteins, and Rin and Ric
contain calmodulin-binding domains. Rin, which is
expressed only in neurons, induces neurite outgrowth in
rat pheochromocytoma cells through its association with
calmodulin and its activation of endogenous Rac/cdc42.
Rit, which is ubiquitously expressed in mammals,
inhibits growth-factor withdrawl-mediated apoptosis and
induces neurite extension in pheochromocytoma cells. Rit
and Rin are both able to form a ternary complex with
PAR6, a cell polarity-regulating protein, and Rac/cdc42.
This ternary complex is proposed to have physiological
function in processes such as tumorigenesis. Activated
Ric is likely to signal in parallel with the Ras pathway
or stimulate the Ras pathway at some upstream point, and
binding of calmodulin to Ric may negatively regulate Ric
activity.
Length = 172
Score = 47.2 bits (112), Expect = 3e-08
Identities = 19/50 (38%), Positives = 33/50 (66%)
Query: 24 FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
F+I YSV +R +F++A + + + + + ++LV NK DLE++RQVT
Sbjct: 77 FIICYSVTDRHSFQEASEFKELITRVRLTEDIPLVLVGNKVDLEQQRQVT 126
>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 = 46.0 bits (110), Expect = 6e-08
Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 3/53 (5%)
Query: 22 DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVT 73
F++VY + R +F+ + L+ + ++ E I LV NK DLE +R V+
Sbjct: 73 QGFLLVYDITSRDSFENVKKWLEEI--LRHADENVPIVLVGNKCDLEDQRVVS 123
>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 = 43.7 bits (104), Expect = 5e-07
Identities = 16/52 (30%), Positives = 31/52 (59%)
Query: 22 DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
+ F++VYS+ +R++F++ + + K + ++LV NK DLE R V+
Sbjct: 75 EGFLLVYSITDRQSFEEIAKFREQILRVKDRDDVPIVLVGNKCDLENERVVS 126
>gnl|CDD|206709 cd04137, RheB, Ras Homolog Enriched in Brain (RheB) is a small
GTPase. Rheb (Ras Homolog Enriched in Brain) subfamily.
Rheb was initially identified in rat brain, where its
expression is elevated by seizures or by long-term
potentiation. It is expressed ubiquitously, with
elevated levels in muscle and brain. Rheb functions as
an important mediator between the tuberous sclerosis
complex proteins, TSC1 and TSC2, and the mammalian
target of rapamycin (TOR) kinase to stimulate cell
growth. TOR kinase regulates cell growth by controlling
nutrient availability, growth factors, and the energy
status of the cell. TSC1 and TSC2 form a dimeric complex
that has tumor suppressor activity, and TSC2 is a GTPase
activating protein (GAP) for Rheb. The TSC1/TSC2 complex
inhibits the activation of TOR kinase through Rheb. Rheb
has also been shown to induce the formation of large
cytoplasmic vacuoles in a process that is dependent on
the GTPase cycle of Rheb, but independent of the TOR
kinase, suggesting Rheb plays a role in endocytic
trafficking that leads to cell growth and cell-cycle
progression. 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 = 180
Score = 43.8 bits (104), Expect = 5e-07
Identities = 20/54 (37%), Positives = 36/54 (66%), Gaps = 8/54 (14%)
Query: 24 FVIVYSVIERKTFKKAEDMLKTLWDS--KYIGEKAV--ILVANKADLERRRQVT 73
+++VYSV RK+F +++K ++D +G+++V +LV NK+DL RQV+
Sbjct: 76 YILVYSVTSRKSF----EVVKVIYDKILDMLGKESVPIVLVGNKSDLHMERQVS 125
>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 = 43.3 bits (103), Expect = 7e-07
Identities = 16/52 (30%), Positives = 32/52 (61%)
Query: 22 DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
+ F++VYS+ +R++F++ + + + K + ++LV NK DLE R V+
Sbjct: 73 EGFLLVYSITDRQSFEEIKKFREQILRVKDRDDVPIVLVGNKCDLESERVVS 124
>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 = 42.8 bits (102), Expect = 1e-06
Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 3/53 (5%)
Query: 22 DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVT 73
++VY V R++F+ + L L +Y I LV NK+DLE RQV+
Sbjct: 74 HGAILVYDVTNRESFENLDKWLNEL--KEYAPPNIPIILVGNKSDLEDERQVS 124
>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 = 42.8 bits (101), Expect = 1e-06
Identities = 20/50 (40%), Positives = 32/50 (64%)
Query: 24 FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
F++V+SV +R +F++ + + K E +ILV NKADLE +RQV+
Sbjct: 77 FLLVFSVTDRGSFEEVDKFHTQILRVKDRDEFPMILVGNKADLEHQRQVS 126
>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 = 39.8 bits (94), Expect = 1e-05
Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 25 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
++VY + ++F+KA+ +K L + L NKADLE +RQV+
Sbjct: 78 IVVYDITSEESFEKAKSWVKEL-QEHGPPNIVIALAGNKADLESKRQVS 125
>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 = 39.9 bits (94), Expect = 1e-05
Identities = 17/52 (32%), Positives = 31/52 (59%), Gaps = 3/52 (5%)
Query: 25 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEK-AVILVANKADLERRRQVTHS 75
++VY + + +F+K + +K L G ++++V NK DLER+R V+ S
Sbjct: 77 ILVYDITDADSFQKVKKWIKELKQM--RGNNISLVIVGNKIDLERQRVVSKS 126
>gnl|CDD|133376 cd04176, Rap2, Rap2 family GTPase consists of Rap2a, Rap2b, and
Rap2c. The Rap2 subgroup is part of the Rap subfamily
of the Ras family. It consists of Rap2a, Rap2b, and
Rap2c. Both isoform 3 of the human mitogen-activated
protein kinase kinase kinase kinase 4 (MAP4K4) and
Traf2- and Nck-interacting kinase (TNIK) are putative
effectors of Rap2 in mediating the activation of c-Jun
N-terminal kinase (JNK) to regulate the actin
cytoskeleton. In human platelets, Rap2 was shown to
interact with the cytoskeleton by binding the actin
filaments. In embryonic Xenopus development, Rap2 is
necessary for the Wnt/beta-catenin signaling pathway.
The Rap2 interacting protein 9 (RPIP9) is highly
expressed in human breast carcinomas and correlates with
a poor prognosis, suggesting a role for Rap2 in breast
cancer oncogenesis. Rap2b, but not Rap2a, Rap2c, Rap1a,
or Rap1b, is expressed in human red blood cells, where
it is believed to be involved in vesiculation. A number
of additional effector proteins for Rap2 have been
identified, including the RalGEFs RalGDS, RGL, and Rlf,
which also interact with Rap1 and Ras. 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 = 163
Score = 39.4 bits (92), Expect = 2e-05
Identities = 18/49 (36%), Positives = 30/49 (61%)
Query: 24 FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV 72
F++VYS++ ++TF+ + M + K + +ILV NK DLE R+V
Sbjct: 76 FIVVYSLVNQQTFQDIKPMRDQIVRVKGYEKVPIILVGNKVDLESEREV 124
>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 = 38.7 bits (90), Expect = 4e-05
Identities = 17/52 (32%), Positives = 29/52 (55%)
Query: 24 FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHS 75
F +VYS+ +++F +D+ + + K + +ILV NK DLE R V+
Sbjct: 76 FALVYSITAQQSFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVSKE 127
>gnl|CDD|133375 cd04175, Rap1, Rap1 family GTPase consists of Rap1a and Rap1b
isoforms. The Rap1 subgroup is part of the Rap
subfamily of the Ras family. It can be further divided
into the Rap1a and Rap1b isoforms. In humans, Rap1a and
Rap1b share 95% sequence homology, but are products of
two different genes located on chromosomes 1 and 12,
respectively. Rap1a is sometimes called smg p21 or Krev1
in the older literature. Rap1 proteins are believed to
perform different cellular functions, depending on the
isoform, its subcellular localization, and the effector
proteins it binds. 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 the microsomal
membrane of pancreatic acini, as well as in the
endocytic compartment of skeletal muscle cells and
fibroblasts. High expression of Rap1 has been observed
in the nucleus of human oropharyngeal squamous cell
carcinomas (SCCs) and cell lines; interestingly, in the
SCCs, the active GTP-bound form localized to the
nucleus, while the inactive GDP-bound form localized to
the cytoplasm. 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. Rap1a, which is stimulated by T-cell receptor
(TCR) activation, is a positive regulator of T cells by
directing integrin activation and augmenting lymphocyte
responses. In murine hippocampal neurons, Rap1b
determines which neurite will become the axon and
directs the recruitment of Cdc42, which is required for
formation of dendrites and axons. In murine platelets,
Rap1b is required for normal homeostasis in vivo and is
involved in integrin activation. 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 = 37.9 bits (88), Expect = 8e-05
Identities = 19/50 (38%), Positives = 28/50 (56%)
Query: 24 FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
FV+VYS+ + TF +D+ + + K + +ILV NK DLE R V
Sbjct: 76 FVLVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVG 125
>gnl|CDD|206641 cd00157, Rho, Ras homology family (Rho) of small guanosine
triphosphatases (GTPases). Members of the Rho (Ras
homology) family include RhoA, Cdc42, Rac, Rnd, Wrch1,
RhoBTB, and Rop. There are 22 human Rho family members
identified currently. These proteins are all involved in
the reorganization of the actin cytoskeleton in response
to external stimuli. They also have roles in cell
transformation by Ras in cytokinesis, in focal adhesion
formation and in the stimulation of stress-activated
kinase. These various functions are controlled through
distinct effector proteins and mediated through a
GTP-binding/GTPase cycle involving three classes of
regulating proteins: GAPs (GTPase-activating proteins),
GEFs (guanine nucleotide exchange factors), and GDIs
(guanine nucleotide dissociation inhibitors). 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. Since crystal structures
often lack C-terminal residues, this feature is not
available for annotation in many of the CDs in the
hierarchy.
Length = 171
Score = 37.9 bits (89), Expect = 8e-05
Identities = 14/50 (28%), Positives = 21/50 (42%), Gaps = 7/50 (14%)
Query: 20 HPDVFVIVYSVIERKTFKKAEDMLKTLWD---SKYIGEKAVILVANKADL 66
DVF++ +SV +F+ + W Y +ILV K DL
Sbjct: 71 QTDVFLLCFSVDSPSSFENVKTK----WYPEIKHYCPNVPIILVGTKIDL 116
>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 = 37.4 bits (87), Expect = 1e-04
Identities = 13/51 (25%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 22 DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV 72
D+ ++V +R++ + A+ ++ +ILV NK DL R+V
Sbjct: 77 DLILLVVDSTDRESEEDAKLLIL---RRLRKEGIPIILVGNKIDLLEEREV 124
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 37.5 bits (88), Expect = 1e-04
Identities = 21/51 (41%), Positives = 32/51 (62%), Gaps = 3/51 (5%)
Query: 24 FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVT 73
++VY + R++F+ E+ LK L +Y VI LV NK+DLE +RQV+
Sbjct: 76 ALLVYDITNRESFENLENWLKEL--REYASPNVVIMLVGNKSDLEEQRQVS 124
>gnl|CDD|206654 cd01861, Rab6, Rab GTPase family 6 (Rab6). Rab6 is involved in
microtubule-dependent transport pathways through the
Golgi and from endosomes to the Golgi. Rab6A of mammals
is implicated in retrograde transport through the Golgi
stack, and is also required for a slow,
COPI-independent, retrograde transport pathway from the
Golgi to the endoplasmic reticulum (ER). This pathway
may allow Golgi residents to be recycled through the ER
for scrutiny by ER quality-control systems. Yeast Ypt6p,
the homolog of the mammalian Rab6 GTPase, is not
essential for cell viability. Ypt6p acts in
endosome-to-Golgi, in intra-Golgi retrograde transport,
and possibly also in Golgi-to-ER trafficking. 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 = 161
Score = 36.8 bits (86), Expect = 2e-04
Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 3/52 (5%)
Query: 23 VFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVT 73
V V+VY + R++F + + + D + G +I LV NK DL +RQV+
Sbjct: 75 VAVVVYDITNRQSFDNTDKWIDDVRDER--GNDVIIVLVGNKTDLSDKRQVS 124
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 36.8 bits (85), Expect = 2e-04
Identities = 17/50 (34%), Positives = 27/50 (54%)
Query: 24 FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 73
F+ VYS+ R +F++ + + K +ILV NK DL+ RQV+
Sbjct: 80 FLCVYSITSRSSFEEIASFREQILRVKDKDRVPMILVGNKCDLDSERQVS 129
>gnl|CDD|206694 cd04109, Rab28, Rab GTPase family 28 (Rab28). Rab28 subfamily.
First identified in maize, Rab28 has been shown to be a
late embryogenesis-abundant (Lea) protein that is
regulated by the plant hormone abcisic acid (ABA). In
Arabidopsis, Rab28 is expressed during embryo
development and is generally restricted to provascular
tissues in mature embryos. Unlike maize Rab28, it is not
ABA-inducible. Characterization of the human Rab28
homolog revealed two isoforms, which differ by a 95-base
pair insertion, producing an alternative sequence for
the 30 amino acids at the C-terminus. The two human
isoforms are presumably the result of alternative
splicing. Since they differ at the C-terminus but not in
the GTP-binding region, they are predicted to be
targeted to different cellular locations. 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.
Length = 213
Score = 36.7 bits (85), Expect = 3e-04
Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 2/57 (3%)
Query: 19 YHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEK--AVILVANKADLERRRQVT 73
Y +VY + ++F+ ED L + E ++LV NK DLE RQVT
Sbjct: 72 YGAQAVCLVYDITNSQSFENLEDWLSVVKKVNEESETKPKMVLVGNKTDLEHNRQVT 128
>gnl|CDD|206688 cd04101, RabL4, Rab GTPase-like family 4 (Rab-like4). RabL4
(Rab-like4) subfamily. RabL4s are novel proteins that
have high sequence similarity with Rab family members,
but display features that are distinct from Rabs, and
have been termed Rab-like. As in other Rab-like
proteins, RabL4 lacks a prenylation site at the
C-terminus. The specific function of RabL4 remains
unknown.
Length = 167
Score = 35.2 bits (81), Expect = 8e-04
Identities = 18/66 (27%), Positives = 29/66 (43%), Gaps = 2/66 (3%)
Query: 8 FTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE 67
F+++V N + P V +VY V +F + + + +LV NK DL
Sbjct: 66 FSDMVENVWE--QPAVVCVVYDVTNEVSFNNCSRWINRVRTHSHGLHTPGVLVGNKCDLT 123
Query: 68 RRRQVT 73
RR+V
Sbjct: 124 DRREVD 129
>gnl|CDD|206659 cd01867, Rab8_Rab10_Rab13_like, Rab GTPase families 8, 10, 13
(Rab8, Rab10, Rab13). Rab8/Sec4/Ypt2 are known or
suspected to be involved in post-Golgi transport to the
plasma membrane. It is likely that these Rabs have
functions that are specific to the mammalian lineage and
have no orthologs in plants. Rab8 modulates polarized
membrane transport through reorganization of actin and
microtubules, induces the formation of new surface
extensions, and has an important role in directed
membrane transport to cell surfaces. The Ypt2 gene of
the fission yeast Schizosaccharomyces pombe encodes a
member of the Ypt/Rab family of small GTP-binding
proteins, related in sequence to Sec4p of Saccharomyces
cerevisiae but closer to mammalian Rab8. 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 = 167
Score = 34.6 bits (80), Expect = 0.001
Identities = 13/50 (26%), Positives = 30/50 (60%), Gaps = 3/50 (6%)
Query: 25 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV-ILVANKADLERRRQVT 73
++VY + + K+F+ ++ ++ + ++ E +LV NK D+E +R V+
Sbjct: 80 ILVYDITDEKSFENIKNWMRNI--DEHASEDVERMLVGNKCDMEEKRVVS 127
>gnl|CDD|206700 cd04127, Rab27A, Rab GTPase family 27a (Rab27a). The Rab27a
subfamily consists of Rab27a and its highly homologous
isoform, Rab27b. Unlike most Rab proteins whose
functions remain poorly defined, Rab27a has many known
functions. Rab27a has multiple effector proteins, and
depending on which effector it binds, Rab27a has
different functions as well as tissue distribution
and/or cellular localization. Putative functions have
been assigned to Rab27a when associated with the
effector proteins Slp1, Slp2, Slp3, Slp4, Slp5, DmSlp,
rabphilin, Dm/Ce-rabphilin, Slac2-a, Slac2-b, Slac2-c,
Noc2, JFC1, and Munc13-4. Rab27a has been associated
with several human diseases, including hemophagocytic
syndrome (Griscelli syndrome or GS), Hermansky-Pudlak
syndrome, and choroidermia. In the case of GS, a rare,
autosomal recessive disease, a Rab27a mutation is
directly responsible for the disorder. When Rab27a is
localized to the secretory granules of pancreatic beta
cells, it is believed to mediate glucose-stimulated
insulin secretion, making it a potential target for
diabetes therapy. When bound to JFC1 in prostate cells,
Rab27a is believed to regulate the exocytosis of
prostate- specific markers. 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 = 180
Score = 34.4 bits (79), Expect = 0.002
Identities = 12/52 (23%), Positives = 27/52 (51%)
Query: 24 FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHS 75
F++++ + ++F + + L Y ++L+ NKADL +R+V+
Sbjct: 90 FLLMFDLTSEQSFLNVRNWMSQLQAHAYCENPDIVLIGNKADLPDQREVSER 141
>gnl|CDD|206696 cd04113, Rab4, Rab GTPase family 4 (Rab4). Rab4 subfamily. Rab4
has been implicated in numerous functions within the
cell. It helps regulate endocytosis through the sorting,
recycling, and degradation of early endosomes. Mammalian
Rab4 is involved in the regulation of many surface
proteins including G-protein-coupled receptors,
transferrin receptor, integrins, and surfactant protein
A. Experimental data implicate Rab4 in regulation of the
recycling of internalized receptors back to the plasma
membrane. It is also believed to influence
receptor-mediated antigen processing in B-lymphocytes,
in calcium-dependent exocytosis in platelets, in
alpha-amylase secretion in pancreatic cells, and in
insulin-induced translocation of Glut4 from internal
vesicles to the cell surface. Rab4 is known to share
effector proteins with Rab5 and Rab11. 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 = 161
Score = 34.3 bits (79), Expect = 0.002
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 5/52 (9%)
Query: 25 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEK--AVILVANKADLERRRQVTH 74
++VY + R++F + L D++ + +ILV NK DLE R+VT
Sbjct: 77 LLVYDITSRESF---NALTNWLTDARTLASPDIVIILVGNKKDLEDDREVTF 125
>gnl|CDD|133311 cd04111, Rab39, Rab GTPase family 39 (Rab39). Found in eukaryotes,
Rab39 is mainly found in epithelial cell lines, but is
distributed widely in various human tissues and cell
lines. It is believed to be a novel Rab protein involved
in regulating Golgi-associated vesicular transport
during cellular endocytosis. 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.
Length = 211
Score = 33.2 bits (76), Expect = 0.005
Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 4/51 (7%)
Query: 25 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV--ILVANKADLERRRQVT 73
++V+ + R++F+ D L+ +I ILV +K DLE +RQVT
Sbjct: 80 LLVFDITNRESFEHVHDWLEEA--RSHIQPHRPVFILVGHKCDLESQRQVT 128
>gnl|CDD|206660 cd01868, Rab11_like, Rab GTPase family 11 (Rab11)-like includes
Rab11a, Rab11b, and Rab25. Rab11a, Rab11b, and Rab25
are closely related, evolutionary conserved Rab proteins
that are differentially expressed. Rab11a is
ubiquitously synthesized, Rab11b is enriched in brain
and heart and Rab25 is only found in epithelia. Rab11/25
proteins seem to regulate recycling pathways from
endosomes to the plasma membrane and to the trans-Golgi
network. Furthermore, Rab11a is thought to function in
the histamine-induced fusion of tubulovesicles
containing H+, K+ ATPase with the plasma membrane in
gastric parietal cells and in insulin-stimulated
insertion of GLUT4 in the plasma membrane of
cardiomyocytes. Overexpression of Rab25 has recently
been observed in ovarian cancer and breast cancer, and
has been correlated with worsened outcomes in both
diseases. In addition, Rab25 overexpression has also
been observed in prostate cancer, transitional cell
carcinoma of the bladder, and invasive breast tumor
cells. 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 = 165
Score = 32.5 bits (75), Expect = 0.007
Identities = 19/49 (38%), Positives = 26/49 (53%), Gaps = 3/49 (6%)
Query: 26 IVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVT 73
+VY + ++ TF+ E LK L D + VI LV NK+DL R V
Sbjct: 81 LVYDITKKSTFENVERWLKELRD--HADSNIVIMLVGNKSDLRHLRAVP 127
>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 = 32.0 bits (73), Expect = 0.013
Identities = 14/59 (23%), Positives = 33/59 (55%), Gaps = 8/59 (13%)
Query: 22 DVFVIVYSVIERKTFKKAEDMLKTLWD--------SKYIGEKAVILVANKADLERRRQV 72
DVF++V+S+ R++F++ + + + + +K + +++ NKAD + R+V
Sbjct: 73 DVFILVFSLDNRESFEEVCRLREQILETKSCLKNKTKENVKIPMVICGNKADRDFPREV 131
>gnl|CDD|206658 cd01866, Rab2, Rab GTPase family 2 (Rab2). Rab2 is localized on
cis-Golgi membranes and interacts with Golgi matrix
proteins. Rab2 is also implicated in the maturation of
vesicular tubular clusters (VTCs), which are
microtubule-associated intermediates in transport
between the ER and Golgi apparatus. In plants, Rab2
regulates vesicle trafficking between the ER and the
Golgi bodies and is important to pollen tube growth.
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 = 168
Score = 31.6 bits (72), Expect = 0.014
Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 3/50 (6%)
Query: 25 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVT 73
++VY + R+TF L+ ++ I L+ NK DLE RR+V+
Sbjct: 81 LLVYDITRRETFNHLTSWLEDA--RQHSNSNMTIMLIGNKCDLESRREVS 128
>gnl|CDD|206699 cd04120, Rab12, Rab GTPase family 12 (Rab12). Rab12 was first
identified in canine cells, where it was localized to
the Golgi complex. The specific function of Rab12
remains unknown, and inconsistent results about its
cellular localization have been reported. More recent
studies have identified Rab12 associated with post-Golgi
vesicles, or with other small vesicle-like structures
but not with the Golgi complex. 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. 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.
Length = 202
Score = 31.5 bits (71), Expect = 0.017
Identities = 17/50 (34%), Positives = 29/50 (58%), Gaps = 3/50 (6%)
Query: 25 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKA-VILVANKADLERRRQVT 73
++VY + +++TF +K + KY E A ++LV NK D E R++T
Sbjct: 77 ILVYDITKKETFDDLPKWMKMI--DKYASEDAELLLVGNKLDCETDREIT 124
>gnl|CDD|206714 cd04147, Ras_dva, Ras - dorsal-ventral anterior localization
(Ras-dva) family. Ras-dva subfamily. Ras-dva (Ras -
dorsal-ventral anterior localization) subfamily consists
of a set of proteins characterized only in Xenopus
leavis, to date. In Xenopus Ras-dva expression is
activated by the transcription factor Otx2 and begins
during gastrulation throughout the anterior ectoderm.
Ras-dva expression is inhibited in the anterior neural
plate by factor Xanf1. Downregulation of Ras-dva results
in head development abnormalities through the inhibition
of several regulators of the anterior neural plate and
folds patterning, including Otx2, BF-1, Xag2, Pax6,
Slug, and Sox9. Downregulation of Ras-dva also
interferes with the FGF-8a signaling within the anterior
ectoderm. 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 = 197
Score = 31.7 bits (72), Expect = 0.017
Identities = 15/51 (29%), Positives = 29/51 (56%)
Query: 22 DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV 72
D F +VYSV + ++F++ + + + + + K +++V NK D RQV
Sbjct: 72 DAFALVYSVDDPESFEEVKRLREEILEVKEDKFVPIVVVGNKIDSLAERQV 122
>gnl|CDD|133338 cd04138, H_N_K_Ras_like, Ras GTPase family containing H-Ras,N-Ras
and K-Ras4A/4B. H-Ras/N-Ras/K-Ras subfamily. H-Ras,
N-Ras, and K-Ras4A/4B are the prototypical members of
the Ras family. These isoforms generate distinct signal
outputs despite interacting with a common set of
activators and effectors, and are strongly associated
with oncogenic progression in tumor initiation. Mutated
versions of Ras that are insensitive to GAP stimulation
(and are therefore constitutively active) are found in a
significant fraction of human cancers. Many Ras guanine
nucleotide exchange factors (GEFs) have been identified.
They 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 that stimulate a variety of diverse cytoplasmic
signaling activities. Some are known to positively
mediate the oncogenic properties of Ras, including Raf,
phosphatidylinositol 3-kinase (PI3K), RalGEFs, and
Tiam1. Others are proposed to play negative regulatory
roles in oncogenesis, including RASSF 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 = 162
Score = 31.2 bits (71), Expect = 0.023
Identities = 13/46 (28%), Positives = 24/46 (52%)
Query: 24 FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR 69
F+ V+++ RK+F+ + + K + ++LV NK DL R
Sbjct: 76 FLCVFAINSRKSFEDIHTYREQIKRVKDSDDVPMVLVGNKCDLAAR 121
>gnl|CDD|206710 cd04139, RalA_RalB, Ral (Ras-like) family containing highly
homologous RalA and RalB. The Ral (Ras-like) subfamily
consists of the highly homologous RalA and RalB. Ral
proteins are believed to play a crucial role in
tumorigenesis, metastasis, endocytosis, and actin
cytoskeleton dynamics. Despite their high sequence
similarity (>80% sequence identity), nonoverlapping and
opposing functions have been assigned to RalA and RalBs
in tumor migration. In human bladder and prostate cancer
cells, RalB promotes migration while RalA inhibits it. A
Ral-specific set of GEFs has been identified that are
activated by Ras binding. This RalGEF activity is
enhanced by Ras binding to another of its target
proteins, phosphatidylinositol 3-kinase (PI3K). Ral
effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and
the exocyst (Sec6/8) complex, a heterooctomeric protein
complex that is involved in tethering vesicles to
specific sites on the plasma membrane prior to
exocytosis. In rat kidney cells, RalB is required for
functional assembly of the exocyst and for localizing
the exocyst to the leading edge of migrating cells. In
human cancer cells, RalA is required to support
anchorage-independent proliferation and RalB is required
to suppress apoptosis. RalA has been shown to localize
to the plasma membrane while RalB is localized to the
intracellular vesicles. 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 = 163
Score = 30.9 bits (70), Expect = 0.029
Identities = 15/54 (27%), Positives = 30/54 (55%)
Query: 22 DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHS 75
+ F++V+S+ + ++F + + + K ++LV NK DLE +RQV+
Sbjct: 73 EGFLLVFSITDMESFTALAEFREQILRVKEDDNVPLLLVGNKCDLEDKRQVSVE 126
>gnl|CDD|133267 cd01864, Rab19, Rab GTPase family 19 (Rab19). Rab19 subfamily.
Rab19 proteins are associated with Golgi stacks.
Similarity analysis indicated that Rab41 is closely
related to Rab19. However, the function of these Rabs is
not yet characterized. 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 = 165
Score = 30.5 bits (69), Expect = 0.037
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 3/50 (6%)
Query: 25 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV-ILVANKADLERRRQVT 73
+I Y + R +F+ ++ + KY V +L+ NK DLE +R+V
Sbjct: 80 IIAYDITRRSSFESVPHWIEEV--EKYGASNVVLLLIGNKCDLEEQREVL 127
>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 = 30.5 bits (69), Expect = 0.040
Identities = 17/49 (34%), Positives = 27/49 (55%)
Query: 24 FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV 72
F++VYSV + + ++ + + K ++LV NKADLE RQV
Sbjct: 76 FLLVYSVTSEASLNELGELREQVLRIKDSDNVPMVLVGNKADLEDDRQV 124
>gnl|CDD|133342 cd04142, RRP22, Ras-related protein on chromosome 22 (RRP22)
family. RRP22 (Ras-related protein on chromosome 22)
subfamily consists of proteins that inhibit cell growth
and promote caspase-independent cell death. Unlike most
Ras proteins, RRP22 is down-regulated in many human
tumor cells due to promoter methylation. RRP22 localizes
to the nucleolus in a GTP-dependent manner, suggesting a
novel function in modulating transport of nucleolar
components. 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.
Like most Ras family proteins, RRP22 is farnesylated.
Length = 198
Score = 30.6 bits (69), Expect = 0.044
Identities = 12/51 (23%), Positives = 27/51 (52%), Gaps = 2/51 (3%)
Query: 22 DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIG--EKAVILVANKADLERRR 70
F++VY + +F + + + + +++ G E +++V NK D +R R
Sbjct: 82 RAFILVYDICSPDSFHYVKLLRQQILETRPAGNKEPPIVVVGNKRDQQRHR 132
>gnl|CDD|206656 cd01863, Rab18, Rab GTPase family 18 (Rab18). Rab18 subfamily.
Mammalian Rab18 is implicated in endocytic transport and
is expressed most highly in polarized epithelial cells.
However, trypanosomal Rab, TbRAB18, is upregulated in
the BSF (Blood Stream Form) stage and localized
predominantly to elements of the Golgi complex. In human
and mouse cells, Rab18 has been identified in lipid
droplets, organelles that store neutral lipids. 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 = 161
Score = 30.4 bits (69), Expect = 0.047
Identities = 16/47 (34%), Positives = 20/47 (42%), Gaps = 4/47 (8%)
Query: 25 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI--LVANKADLERR 69
++VY V R TF + L L Y + LV NK D E R
Sbjct: 77 ILVYDVTRRDTFDNLDTWLNEL--DTYSTNPDAVKMLVGNKIDKENR 121
>gnl|CDD|206680 cd01893, Miro1, Mitochondrial Rho family 1 (Miro1), N-terminal.
Miro1 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the N-terminal
GTPase domain of Miro proteins. These atypical Rho
GTPases have roles in mitochondrial homeostasis and
apoptosis. Most Rho proteins contain a lipid
modification site at the C-terminus; however, Miro is
one of few Rho subfamilies that lack this feature.
Length = 168
Score = 30.0 bits (68), Expect = 0.063
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 7/48 (14%)
Query: 22 DVFVIVYSVIERKTFKKAEDMLKTLW--DSKYIGEKA-VILVANKADL 66
+V +VYSV T ++ ++T W + +G K +ILV NK+DL
Sbjct: 74 NVICLVYSVDRPSTLER----IRTKWLPLIRRLGVKVPIILVGNKSDL 117
>gnl|CDD|197554 smart00174, RHO, Rho (Ras homology) subfamily of Ras-like small
GTPases. Members of this subfamily of Ras-like small
GTPases include Cdc42 and Rac, as well as Rho isoforms.
Length = 174
Score = 29.1 bits (66), Expect = 0.11
Identities = 17/60 (28%), Positives = 25/60 (41%), Gaps = 16/60 (26%)
Query: 22 DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGE-------KAVILVANKADLERRRQVTH 74
DVF+I +SV +F+ + K+ E +ILV K DL R + T
Sbjct: 71 DVFLICFSVDSPASFENVK--------EKWYPEVKHFCPNVPIILVGTKLDL-RNDKSTL 121
>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 = 29.4 bits (66), Expect = 0.11
Identities = 14/58 (24%), Positives = 31/58 (53%), Gaps = 10/58 (17%)
Query: 24 FVIVYSVIERKTFKKAEDMLKTLWD------SKYIGEKAVILVANKADLERRRQVTHS 75
F++VYS+ +++ ++ LK +++ + + ++LV NK D R+V+ S
Sbjct: 76 FILVYSITSKQSLEE----LKPIYELICEIKGNNLEKIPIMLVGNKCDESPSREVSSS 129
>gnl|CDD|133353 cd04153, Arl5_Arl8, Arf-like 5 (Arl5) and 8 (Arl8) GTPases.
Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like
Arl4 and Arl7, are localized to the nucleus and
nucleolus. Arl5 is developmentally regulated during
embryogenesis in mice. Human Arl5 interacts with the
heterochromatin protein 1-alpha (HP1alpha), a
nonhistone chromosomal protein that is associated with
heterochromatin and telomeres, and prevents telomere
fusion. Arl5 may also play a role in embryonic nuclear
dynamics and/or signaling cascades. Arl8 was identified
from a fetal cartilage cDNA library. It is found in
brain, heart, lung, cartilage, and kidney. No function
has been assigned for Arl8 to date.
Length = 174
Score = 29.2 bits (66), Expect = 0.12
Identities = 11/29 (37%), Positives = 18/29 (62%)
Query: 40 EDMLKTLWDSKYIGEKAVILVANKADLER 68
++ L++ W++ Y AVILV + D ER
Sbjct: 69 QESLRSSWNTYYTNTDAVILVIDSTDRER 97
>gnl|CDD|133322 cd04122, Rab14, Rab GTPase family 14 (Rab14). Rab14 GTPases are
localized to biosynthetic compartments, including the
rough ER, the Golgi complex, and the trans-Golgi
network, and to endosomal compartments, including early
endosomal vacuoles and associated vesicles. Rab14 is
believed to function in both the biosynthetic and
recycling pathways between the Golgi and endosomal
compartments. Rab14 has also been identified on GLUT4
vesicles, and has been suggested to help regulate GLUT4
translocation. In addition, Rab14 is believed to play a
role in the regulation of 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 = 166
Score = 29.4 bits (66), Expect = 0.12
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 5/52 (9%)
Query: 25 VIVYSVIERKTFKKAEDMLKTLWDSKYIG--EKAVILVANKADLERRRQVTH 74
++VY + R T+ L D++ + + L+ NKADLE +R VT+
Sbjct: 79 LMVYDITRRSTYNHLSSWLT---DARNLTNPNTVIFLIGNKADLEAQRDVTY 127
>gnl|CDD|133361 cd04161, Arl2l1_Arl13_like, Arl2-like protein 1 (Arl2l1) and Arl13.
Arl2l1 (Arl2-like protein 1) and Arl13 form a subfamily
of the Arf family of small GTPases. Arl2l1 was
identified in human cells during a search for the
gene(s) responsible for Bardet-Biedl syndrome (BBS).
Like Arl6, the identified BBS gene, Arl2l1 is proposed
to have cilia-specific functions. Arl13 is found on the
X chromosome, but its expression has not been confirmed;
it may be a pseudogene.
Length = 167
Score = 28.9 bits (65), Expect = 0.13
Identities = 15/61 (24%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 13 VNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV 72
VN+ H VFV+ S +R ++ +++L+ L + K ++++ANK D +
Sbjct: 61 VNYYAEAHGLVFVVDSSDDDR--VQEVKEILRELLQHPRVSGKPILVLANKQDKKNALLG 118
Query: 73 T 73
Sbjct: 119 A 119
>gnl|CDD|133344 cd04144, Ras2, Rat sarcoma (Ras) family 2 of small guanosine
triphosphatases (GTPases). The Ras2 subfamily, found
exclusively in fungi, was first identified in Ustilago
maydis. In U. maydis, Ras2 is regulated by Sql2, a
protein that is homologous to GEFs (guanine nucleotide
exchange factors) of the CDC25 family. Ras2 has been
shown to induce filamentous growth, but the signaling
cascade through which Ras2 and Sql2 regulate cell
morphology is not known. 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 = 190
Score = 29.0 bits (65), Expect = 0.14
Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 24 FVIVYSVIERKTFKKAEDMLKTLWDSK--YIGEKAVILVANKADLERRRQVT 73
F++VYS+ R TF++ E + + K + +++V NK D R+V+
Sbjct: 74 FILVYSITSRSTFERVERFREQIQRVKDESAADVPIMIVGNKCDKVYEREVS 125
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 28.9 bits (65), Expect = 0.17
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 49 SKYIGEKAVILVANKADL 66
+ + EK +LV NKADL
Sbjct: 56 ERIVKEKPKLLVLNKADL 73
>gnl|CDD|221709 pfam12684, DUF3799, PDDEXK-like domain of unknown function
(DUF3799). This family of proteins is functionally
uncharacterized. This family of proteins is found in
bacteria and viruses. Proteins in this family are
typically between 265 and 420 amino acids in length. It
appears that these proteins are distantly related to the
PDDEXK superfamily and so these domains are likely to be
nucleases. This family has a C-terminal cysteine cluster
similar to that found in pfam01930.
Length = 237
Score = 28.8 bits (65), Expect = 0.18
Identities = 20/71 (28%), Positives = 29/71 (40%), Gaps = 20/71 (28%)
Query: 11 LVVNFVQTY-------------HPDVFVIVYS--VIERKTFKKAEDMLKTLWDSK----- 50
LV N+V +Y HP++F + FK AE M++ L +
Sbjct: 36 LVGNYVHSYFESPEAHDEFKKEHPEMFTTRGDNKGELKAEFKIAEQMIEALKADELFNRL 95
Query: 51 YIGEKAVILVA 61
Y GEK VI+
Sbjct: 96 YQGEKEVIVTG 106
>gnl|CDD|206661 cd01869, Rab1_Ypt1, Rab GTPase family 1 includes the yeast homolog
Ypt1. Rab1/Ypt1 subfamily. Rab1 is found in every
eukaryote and is a key regulatory component for the
transport of vesicles from the ER to the Golgi
apparatus. Studies on mutations of Ypt1, the yeast
homolog of Rab1, showed that this protein is necessary
for the budding of vesicles of the ER as well as for
their transport to, and fusion with, the Golgi
apparatus. 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 = 166
Score = 28.4 bits (64), Expect = 0.19
Identities = 15/52 (28%), Positives = 29/52 (55%), Gaps = 3/52 (5%)
Query: 25 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV-ILVANKADLERRRQVTHS 75
+IVY V ++++F + L+ + +Y E +LV NK DL ++ V ++
Sbjct: 79 IIVYDVTDQESFNNVKQWLQEI--DRYASENVNKLLVGNKCDLTDKKVVDYT 128
>gnl|CDD|206748 cd01855, YqeH, Circularly permuted YqeH GTPase. YqeH is an
essential GTP-binding protein. Depletion of YqeH
induces an excess initiation of DNA replication,
suggesting that it negatively controls initiation of
chromosome replication. The YqeH subfamily is common in
eukaryotes and sporadically present in bacteria with
probable acquisition by plants from chloroplasts.
Proteins of the YqeH family contain all sequence motifs
typical of the vast class of P-loop-containing GTPases,
but show a circular permutation, with a G4-G1-G3
pattern of motifs as opposed to the regular G1-G3-G4
pattern seen in most GTPases.
Length = 191
Score = 28.4 bits (64), Expect = 0.23
Identities = 11/17 (64%), Positives = 12/17 (70%)
Query: 50 KYIGEKAVILVANKADL 66
+ IG K VILV NK DL
Sbjct: 56 ELIGAKPVILVGNKIDL 72
>gnl|CDD|206657 cd01865, Rab3, Rab GTPase family 3 contains Rab3A, Rab3B, Rab3C and
Rab3D. The Rab3 subfamily contains Rab3A, Rab3B, Rab3C,
and Rab3D. All four isoforms were found in mouse brain
and endocrine tissues, with varying levels of
expression. Rab3A, Rab3B, and Rab3C localized to
synaptic and secretory vesicles; Rab3D was expressed at
high levels only in adipose tissue, exocrine glands, and
the endocrine pituitary, where it is localized to
cytoplasmic secretory granules. Rab3 appears to control
Ca2+-regulated exocytosis. The appropriate GDP/GTP
exchange cycle of Rab3A is required for Ca2+-regulated
exocytosis to occur, and interaction of the GTP-bound
form of Rab3A with effector molecule(s) is widely
believed to be essential for this process. Functionally,
most studies point toward a role for Rab3 in the
secretion of hormones and neurotransmitters. 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 = 165
Score = 28.3 bits (63), Expect = 0.23
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 3/51 (5%)
Query: 24 FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKA-VILVANKADLERRRQVT 73
F+++Y + ++F +D + Y + A VILV NK D+E R V+
Sbjct: 77 FILMYDITNEESFNAVQDWSTQI--KTYSWDNAQVILVGNKCDMEDERVVS 125
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 28.6 bits (65), Expect = 0.23
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 50 KYIGEKAVILVANKADL 66
K IG K +L+ NK+DL
Sbjct: 47 KIIGNKPRLLILNKSDL 63
>gnl|CDD|237511 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 28.3 bits (64), Expect = 0.27
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 49 SKYIGEKAVILVANKADL 66
+++G V+LV NKADL
Sbjct: 91 HRFVGNNPVLLVGNKADL 108
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 28.2 bits (62), Expect = 0.28
Identities = 15/51 (29%), Positives = 30/51 (58%), Gaps = 3/51 (5%)
Query: 25 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVTH 74
++VY + R++F+ ++ + + + G+ +I LV NK DL R+VT+
Sbjct: 57 IVVYDITNRQSFENTTKWIQDILNER--GKDVIIALVGNKTDLGDLRKVTY 105
>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 = 27.8 bits (62), Expect = 0.36
Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 7/50 (14%)
Query: 20 HPDVFVIVYSVIERKTFKKAEDMLKTLWDS---KYIGEKAVILVANKADL 66
DVF++ +SV+ +F+ + W K+ + +ILV +ADL
Sbjct: 71 DTDVFLLCFSVVNPSSFQN----ISEKWIPEIRKHNPKAPIILVGTQADL 116
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 27.7 bits (61), Expect = 0.45
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 25 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV-ILVANKADLERRRQVT 73
++VY V R+TF D+ + + V +LV NK D E R V+
Sbjct: 90 ILVYDVTRRETFTNLSDVWGKEVELYSTNQDCVKMLVGNKVDRESERDVS 139
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 27.6 bits (61), Expect = 0.50
Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 3/49 (6%)
Query: 25 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVA-NKADLERRRQV 72
++VY + +R+TF + L+ L D + VI++A NK+DL R V
Sbjct: 89 LLVYDITKRQTFDNVQRWLRELRD--HADSNIVIMMAGNKSDLNHLRSV 135
>gnl|CDD|236539 PRK09490, metH, B12-dependent methionine synthase; Provisional.
Length = 1229
Score = 27.4 bits (62), Expect = 0.57
Identities = 9/26 (34%), Positives = 14/26 (53%)
Query: 33 RKTFKKAEDMLKTLWDSKYIGEKAVI 58
RK F A+ ML + K++ + VI
Sbjct: 980 RKLFADAQAMLDKIIAEKWLTARGVI 1005
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 27.2 bits (60), Expect = 0.71
Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 25 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEK--AVILVANKADLERRRQVT 73
++VY + R+TF L+ D++ ++L+ NK DL RR V+
Sbjct: 83 LLVYDITRRETFNHLASWLE---DARQHANANMTIMLIGNKCDLAHRRAVS 130
>gnl|CDD|206692 cd04107, Rab32_Rab38, Rab GTPase families 18 (Rab18) and 32
(Rab32). Rab38/Rab32 subfamily. Rab32 and Rab38 are
members of the Rab family of small GTPases. Human Rab32
was first identified in platelets but it is expressed in
a variety of cell types, where it functions as an
A-kinase anchoring protein (AKAP). Rab38 has been shown
to be melanocyte-specific. 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.
Length = 201
Score = 26.9 bits (60), Expect = 0.73
Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 5/50 (10%)
Query: 25 VIVYSVIERKTFKKAEDMLKTLWDSK--YIGEKAV--ILVANKADLERRR 70
+IV+ V TF+ A K DSK + + +L+ANK DL++ R
Sbjct: 78 IIVFDVTRPSTFE-AVLKWKADLDSKVTLPNGEPIPALLLANKCDLKKER 126
>gnl|CDD|213833 TIGR03596, GTPase_YlqF, ribosome biogenesis GTP-binding protein
YlqF. Members of this protein family are GTP-binding
proteins involved in ribosome biogenesis, including the
essential YlqF protein of Bacillus subtilis, which is
an essential protein. They are related to Era, EngA,
and other GTPases of ribosome biogenesis, but are
circularly permuted. This family is not universal, and
is not present in Escherichia coli, and so is not as
well studied as some other GTPases. This model is built
for bacterial members [Protein synthesis, Other].
Length = 276
Score = 26.7 bits (60), Expect = 0.91
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 50 KYIGEKAVILVANKADL 66
+ G K ++V NKADL
Sbjct: 44 EIRGNKPRLIVLNKADL 60
>gnl|CDD|206681 cd01894, EngA1, EngA1 GTPase contains the first domain of EngA.
This EngA1 subfamily CD represents the first GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. Since the sequences of the
two domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family. Although the exact function of
these proteins has not been elucidated, studies have
revealed that the E. coli EngA homolog, Der, and
Neisseria gonorrhoeae EngA are essential for cell
viability. A recent report suggests that E. coli Der
functions in ribosome assembly and stability.
Length = 157
Score = 26.6 bits (60), Expect = 0.97
Identities = 8/20 (40%), Positives = 10/20 (50%)
Query: 55 KAVILVANKADLERRRQVTH 74
K VILV NK D + +
Sbjct: 106 KPVILVVNKIDNIKEEEEAA 125
>gnl|CDD|213834 TIGR03597, GTPase_YqeH, ribosome biogenesis GTPase YqeH. This
family describes YqeH, a member of a larger family of
GTPases involved in ribosome biogenesis. Like YqlF, it
shows a cyclical permutation relative to GTPases EngA
(in which the GTPase domain is duplicated), Era, and
others. Members of this protein family are found in a
relatively small number of bacterial species, including
Bacillus subtilis but not Escherichia coli [Protein
synthesis, Other].
Length = 360
Score = 26.8 bits (60), Expect = 1.1
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 51 YIGEKAVILVANKADL 66
++G V+LV NK DL
Sbjct: 87 FVGGNPVLLVGNKIDL 102
>gnl|CDD|206679 cd01892, Miro2, Mitochondrial Rho family 2 (Miro2), C-terminal.
Miro2 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the putative
GTPase domain in the C terminus of Miro proteins. These
atypical Rho GTPases have roles in mitochondrial
homeostasis and apoptosis. Most Rho proteins contain a
lipid modification site at the C-terminus; however, Miro
is one of few Rho subfamilies that lack this feature.
Length = 180
Score = 26.4 bits (59), Expect = 1.2
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 22 DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV 72
DV +VY + +F ++ K +GE + VA KADL+ ++Q
Sbjct: 79 DVACLVYDSSDPNSFSYCAEVYKK---YFMLGEIPCLFVAAKADLDEQQQR 126
>gnl|CDD|206685 cd01898, Obg, Obg GTPase. The Obg nucleotide binding protein
subfamily has been implicated in stress response,
chromosome partitioning, replication initiation,
mycelium development, and sporulation. Obg proteins are
among a large group of GTP binding proteins conserved
from bacteria to humans. The E. coli homolog, ObgE is
believed to function in ribosomal biogenesis. Members of
the subfamily contain two equally and highly conserved
domains, a C-terminal GTP binding domain and an
N-terminal glycine-rich domain.
Length = 170
Score = 26.2 bits (59), Expect = 1.2
Identities = 8/14 (57%), Positives = 9/14 (64%)
Query: 54 EKAVILVANKADLE 67
EK I+V NK DL
Sbjct: 114 EKPRIVVLNKIDLL 127
>gnl|CDD|133314 cd04114, Rab30, Rab GTPase family 30 (Rab30). Rab30 subfamily.
Rab30 appears to be associated with the Golgi stack. It
is expressed in a wide variety of tissue types and in
humans maps to chromosome 11. 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 = 169
Score = 26.4 bits (58), Expect = 1.2
Identities = 17/59 (28%), Positives = 32/59 (54%), Gaps = 5/59 (8%)
Query: 17 QTYH--PDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV-ILVANKADLERRRQV 72
Q+Y+ + ++ Y + ++F+ + L+ + +Y K + ILV NK DL RR+V
Sbjct: 74 QSYYRSANALILTYDITCEESFRCLPEWLREI--EQYANNKVITILVGNKIDLAERREV 130
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 26.1 bits (58), Expect = 1.6
Identities = 10/15 (66%), Positives = 10/15 (66%)
Query: 54 EKAVILVANKADLER 68
K VIL ANK D ER
Sbjct: 146 GKPVILAANKVDDER 160
>gnl|CDD|217370 pfam03102, NeuB, NeuB family. NeuB is the prokaryotic
N-acetylneuraminic acid (Neu5Ac) synthase. It catalyzes
the direct formation of Neu5Ac (the most common sialic
acid) by condensation of phosphoenolpyruvate (PEP) and
N-acetylmannosamine (ManNAc). This reaction has only
been observed in prokaryotes; eukaryotes synthesise the
9-phosphate form, Neu5Ac-9-P, and utilise ManNAc-6-P
instead of ManNAc. Such eukaryotic enzymes are not
present in this family. This family also contains SpsE
spore coat polysaccharide biosynthesis proteins.
Length = 240
Score = 25.9 bits (58), Expect = 1.8
Identities = 9/38 (23%), Positives = 14/38 (36%), Gaps = 7/38 (18%)
Query: 17 QTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGE 54
QT+ D V + KA+ + LW + E
Sbjct: 15 QTFTADTLVSKNA-------DKADYQIGNLWGGESQYE 45
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 26.1 bits (57), Expect = 1.8
Identities = 11/62 (17%), Positives = 25/62 (40%), Gaps = 10/62 (16%)
Query: 17 QTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKA-----VILVANKADLERRRQ 71
+ +IVY + ++++ + + + E A ++LV NK DL +
Sbjct: 74 YYRGANGILIVYDST---LRESSDELTEEWL--EELRELAPDDVPILLVGNKIDLFDEQS 128
Query: 72 VT 73
+
Sbjct: 129 SS 130
>gnl|CDD|219856 pfam08477, Miro, Miro-like protein. Mitochondrial Rho proteins
(Miro-1, and Miro-2), are atypical Rho GTPases. They
have a unique domain organisation, with tandem
GTP-binding domains and two EF hand domains (pfam00036),
that may bind calcium. They are also larger than
classical small GTPases. It has been proposed that they
are involved in mitochondrial homeostasis and apoptosis.
Length = 116
Score = 25.4 bits (56), Expect = 1.9
Identities = 13/44 (29%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 21 PDVFVIVYSVIERKTFKKAEDMLKTLWD-SKYIGEKAVILVANK 63
D ++VY + +R++ + ++ L + K G+ VILV NK
Sbjct: 72 ADAILLVYDLTDRESLNEVSRLIAWLPNLRKLGGKIPVILVGNK 115
>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 = 25.7 bits (57), Expect = 2.3
Identities = 16/60 (26%), Positives = 30/60 (50%), Gaps = 13/60 (21%)
Query: 22 DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV--------ILVANKADLERRRQVT 73
D V+VY V K+F+ + W +++ + + +++ NK DLE +RQV+
Sbjct: 74 DCCVLVYDVTNPKSFESLDS-----WRDEFLIQASPRDPENFPFVVLGNKIDLEEKRQVS 128
>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 = 25.4 bits (56), Expect = 2.4
Identities = 14/52 (26%), Positives = 26/52 (50%), Gaps = 4/52 (7%)
Query: 25 VIVYSVIERKTF----KKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV 72
++VY V +R++F ++M + + V++ ANK DL + R V
Sbjct: 77 LLVYDVTDRQSFEALDSWLKEMKQEGGPHGNMENIVVVVCANKIDLTKHRAV 128
>gnl|CDD|128474 smart00177, ARF, ARF-like small GTPases; ARF, ADP-ribosylation
factor. Ras homologues involved in vesicular transport.
Activator of phospholipase D isoforms. Unlike Ras
proteins they lack cysteine residues at their C-termini
and therefore are unlikely to be prenylated. ARFs are
N-terminally myristoylated. Contains ATP/GTP-binding
motif (P-loop).
Length = 175
Score = 25.7 bits (56), Expect = 2.5
Identities = 10/38 (26%), Positives = 18/38 (47%), Gaps = 3/38 (7%)
Query: 40 EDMLKTLWDSKYIGEKAVILVANKADLER---RRQVTH 74
+D ++ LW Y + +I V + D +R R+ H
Sbjct: 67 QDKIRPLWRHYYTNTQGLIFVVDSNDRDRIDEAREELH 104
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase. The
Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that generally show sequence
conservation in the region between the Walker A and B
motifs (G1 and G3 box motifs), to the exclusion of other
GTPases. TrmE is ubiquitous in bacteria and is a
widespread mitochondrial protein in eukaryotes, but is
absent from archaea. The yeast member of TrmE family,
MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family.
Length = 161
Score = 25.3 bits (56), Expect = 2.6
Identities = 8/13 (61%), Positives = 9/13 (69%)
Query: 54 EKAVILVANKADL 66
K V+LV NK DL
Sbjct: 104 GKPVLLVLNKIDL 116
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 25.6 bits (57), Expect = 2.8
Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 8/49 (16%)
Query: 23 VFVIVYSVIERKTFKKAEDMLKTLWD-----SKYIGEKAVILVANKADL 66
+ VI S I+ + + +T+ + S + EK I+V NK DL
Sbjct: 242 LHVIDLSPIDGRDPIED---YQTIRNELEKYSPKLAEKPRIVVLNKIDL 287
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 25.4 bits (57), Expect = 3.1
Identities = 8/11 (72%), Positives = 8/11 (72%)
Query: 55 KAVILVANKAD 65
K VILV NK D
Sbjct: 110 KPVILVVNKVD 120
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 25.1 bits (56), Expect = 3.3
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 52 IGEKAVILVANKADLE 67
+ +K VI+V NKADL
Sbjct: 319 LKDKPVIVVLNKADLT 334
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 25.2 bits (56), Expect = 3.5
Identities = 8/15 (53%), Positives = 9/15 (60%)
Query: 51 YIGEKAVILVANKAD 65
+K VILV NK D
Sbjct: 109 RRSKKPVILVVNKID 123
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 25.3 bits (56), Expect = 3.6
Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 1/49 (2%)
Query: 18 TYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADL 66
D+ + V + + +K E + L + E +ILV NK DL
Sbjct: 269 VKEADLLLHVVDASDPEILEKLEAVEDVLAEIG-ADEIPIILVLNKIDL 316
>gnl|CDD|206725 cd04160, Arfrp1, Arf-related protein 1 (Arfrp1). Arfrp1
(Arf-related protein 1), formerly known as ARP, is a
membrane-associated Arf family member that lacks the
N-terminal myristoylation motif. Arfrp1 is mainly
associated with the trans-Golgi compartment and the
trans-Golgi network, where it regulates the targeting
of Arl1 and the GRIP domain-containing proteins,
golgin-97 and golgin-245, onto Golgi membranes. It is
also involved in the anterograde transport of the
vesicular stomatitis virus G protein from the Golgi to
the plasma membrane, and in the retrograde transport of
TGN38 and Shiga toxin from endosomes to the trans-Golgi
network. Arfrp1 also inhibits Arf/Sec7-dependent
activation of phospholipase D. Deletion of Arfrp1 in
mice causes embryonic lethality at the gastrulation
stage and apoptosis of mesodermal cells, indicating its
importance in development.
Length = 168
Score = 24.6 bits (54), Expect = 4.5
Identities = 11/26 (42%), Positives = 14/26 (53%)
Query: 43 LKTLWDSKYIGEKAVILVANKADLER 68
L++LWD Y VI V + D ER
Sbjct: 64 LRSLWDKYYAESHGVIYVIDSTDRER 89
>gnl|CDD|206749 cd01856, YlqF, Circularly permuted YlqF GTPase. Proteins of the
YlqF family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases. The YlqF subfamily is represented in all
eukaryotes as well as a phylogenetically diverse array
of bacteria (including gram-positive bacteria,
proteobacteria, Synechocystis, Borrelia, and
Thermotoga).
Length = 171
Score = 24.8 bits (55), Expect = 4.5
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 50 KYIGEKAVILVANKADL 66
K +G K ++V NKADL
Sbjct: 42 KILGNKPRLIVLNKADL 58
>gnl|CDD|133356 cd04156, ARLTS1, Arf-like tumor suppressor gene 1 (ARLTS1 or
Arl11). ARLTS1 (Arf-like tumor suppressor gene 1), also
known as Arl11, is a member of the Arf family of small
GTPases that is believed to play a major role in
apoptotic signaling. ARLTS1 is widely expressed and
functions as a tumor suppressor gene in several human
cancers. ARLTS1 is a low-penetrance suppressor that
accounts for a small percentage of familial melanoma or
familial chronic lymphocytic leukemia (CLL). ARLTS1
inactivation seems to occur most frequently through
biallelic down-regulation by hypermethylation of the
promoter. In breast cancer, ARLTS1 alterations were
typically a combination of a hypomorphic polymorphism
plus loss of heterozygosity. In a case of thyroid
adenoma, ARLTS1 alterations were polymorphism plus
promoter hypermethylation. The nonsense polymorphism
Trp149Stop occurs with significantly greater frequency
in familial cancer cases than in sporadic cancer cases,
and the Cys148Arg polymorphism is associated with an
increase in high-risk familial breast cancer.
Length = 160
Score = 24.7 bits (54), Expect = 4.7
Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 2/50 (4%)
Query: 19 YHPDVFVIVYSV--IERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADL 66
Y + +VY V + +++ LK + +++I V+L+ANK DL
Sbjct: 64 YLENTDGLVYVVDSSDEARLDESQKELKHILKNEHIKGVPVVLLANKQDL 113
>gnl|CDD|173867 cd08502, PBP2_NikA_DppA_OppA_like_16, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 472
Score = 24.8 bits (55), Expect = 4.7
Identities = 10/26 (38%), Positives = 15/26 (57%), Gaps = 3/26 (11%)
Query: 36 FKKAEDMLKTLWDSKYIGEKAVILVA 61
+KA+ +LK ++ Y GE VIL
Sbjct: 317 LEKAKKLLK---EAGYDGEPIVILTP 339
>gnl|CDD|133315 cd04115, Rab33B_Rab33A, Rab GTPase family 33 includes Rab33A and
Rab33B. Rab33B/Rab33A subfamily. Rab33B is ubiquitously
expressed in mouse tissues and cells, where it is
localized to the medial Golgi cisternae. It colocalizes
with alpha-mannose II. Together with the other cisternal
Rabs, Rab6A and Rab6A', it is believed to regulate the
Golgi response to stress and is likely a molecular
target in stress-activated signaling pathways. Rab33A
(previously known as S10) is expressed primarily in the
brain and immune system cells. In humans, it is located
on the X chromosome at Xq26 and its expression is
down-regulated in tuberculosis patients. Experimental
evidence suggests that Rab33A is a novel CD8+ T cell
factor that likely plays a role in tuberculosis disease
processes. 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 = 170
Score = 24.7 bits (54), Expect = 4.8
Identities = 19/59 (32%), Positives = 25/59 (42%), Gaps = 2/59 (3%)
Query: 16 VQTYHPDV--FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQV 72
VQ Y+ +V V VY V +F ++ E ILV NK DL + QV
Sbjct: 69 VQHYYRNVHAVVFVYDVTNMASFHSLPSWIEECEQHSLPNEVPRILVGNKCDLREQIQV 127
>gnl|CDD|133644 CHL00202, argB, acetylglutamate kinase; Provisional.
Length = 284
Score = 24.8 bits (54), Expect = 4.9
Identities = 11/47 (23%), Positives = 21/47 (44%)
Query: 13 VNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVIL 59
+ ++Q + + VI Y K D++K + IG K V++
Sbjct: 15 LPYIQKFRGRIMVIKYGGAAMKNLILKADIIKDILFLSCIGLKIVVV 61
>gnl|CDD|206716 cd04149, Arf6, ADP ribosylation factor 6 (Arf6). Arf6 subfamily.
Arf6 (ADP ribosylation factor 6) proteins localize to
the plasma membrane, where they perform a wide variety
of functions. In its active, GTP-bound form, Arf6 is
involved in cell spreading, Rac-induced formation of
plasma membrane ruffles, cell migration, wound healing,
and Fc-mediated phagocytosis. Arf6 appears to change the
actin structure at the plasma membrane by activating
Rac, a Rho family protein involved in membrane ruffling.
Arf6 is required for and enhances Rac formation of
ruffles. Arf6 can regulate dendritic branching in
hippocampal neurons, and in yeast it localizes to the
growing bud, where it plays a role in polarized growth
and bud site selection. In leukocytes, Arf6 is required
for chemokine-stimulated migration across endothelial
cells. Arf6 also plays a role in down-regulation of
beta2-adrenergic receptors and luteinizing hormone
receptors by facilitating the release of sequestered
arrestin to allow endocytosis. Arf6 is believed to
function at multiple sites on the plasma membrane
through interaction with a specific set of GEFs, GAPs,
and effectors. Arf6 has been implicated in breast cancer
and melanoma cell invasion, and in actin remodelling at
the invasion site of Chlamydia infection.
Length = 168
Score = 24.7 bits (54), Expect = 5.0
Identities = 12/39 (30%), Positives = 20/39 (51%), Gaps = 3/39 (7%)
Query: 40 EDMLKTLWDSKYIGEKAVILVANKAD---LERRRQVTHS 75
+D ++ LW Y G + +I V + AD ++ RQ H
Sbjct: 63 QDKIRPLWRHYYTGTQGLIFVVDSADRDRIDEARQELHR 101
>gnl|CDD|234874 PRK00955, PRK00955, hypothetical protein; Provisional.
Length = 620
Score = 24.9 bits (55), Expect = 5.2
Identities = 14/60 (23%), Positives = 21/60 (35%), Gaps = 15/60 (25%)
Query: 19 YHPDVFVIVYSVIERKTFKKA-------EDMLKTL-----WDSKYIGEKAVILVANKADL 66
PD IVY ++ + E L+ W K + IL+ + ADL
Sbjct: 104 LRPDRATIVYCNKIKEAYPDVPIIIGGIEASLRRFAHYDYWSDKV---RRSILIDSGADL 160
>gnl|CDD|235514 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
Length = 679
Score = 24.7 bits (55), Expect = 5.3
Identities = 9/27 (33%), Positives = 14/27 (51%), Gaps = 1/27 (3%)
Query: 15 FVQTYHPDVFVIVYSVIE-RKTFKKAE 40
+QTYHP+ VI + + F + E
Sbjct: 543 LIQTYHPEHPVIQALLAQDYDAFAEQE 569
>gnl|CDD|206705 cd04133, Rop_like, Rho-related protein from plants (Rop)-like. The
Rop (Rho-related protein from plants) subfamily plays a
role in diverse cellular processes, including
cytoskeletal organization, pollen and vegetative cell
growth, hormone responses, stress responses, and
pathogen resistance. Rops are able to regulate several
downstream pathways to amplify a specific signal by
acting as master switches early in the signaling
cascade. They transmit a variety of extracellular and
intracellular signals. Rops are involved in establishing
cell polarity in root-hair development, root-hair
elongation, pollen-tube growth, cell-shape formation,
responses to hormones such as abscisic acid (ABA) and
auxin, responses to abiotic stresses such as oxygen
deprivation, and disease resistance and disease
susceptibility. An individual Rop can have a unique
function or an overlapping function shared with other
Rop proteins; in addition, a given Rop-regulated
function can be controlled by one or multiple Rop
proteins. For example, Rop1, Rop3, and Rop5 are all
involved in pollen-tube growth; Rop2 plays a role in
response to low-oxygen environments, cell-morphology,
and root-hair development; root-hair development is also
regulated by Rop4 and Rop6; Rop6 is also responsible for
ABA response, and ABA response is also regulated by
Rop10. Plants retain some of the regulatory mechanisms
that are shared by other members of the Rho family, but
have also developed a number of unique modes for
regulating Rops. Unique RhoGEFs have been identified
that are exclusively active toward Rop proteins, such as
those containing the domain PRONE (plant-specific Rop
nucleotide exchanger). 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 = 24.4 bits (53), Expect = 5.5
Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 15/57 (26%)
Query: 22 DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGE-------KAVILVANKADLERRRQ 71
DVF++ +S+I + ++ E++LK K+I E ++LV K DL +Q
Sbjct: 74 DVFLLAFSLISKASY---ENVLK-----KWIPELRHYAPGVPIVLVGTKLDLRDDKQ 122
>gnl|CDD|206698 cd04117, Rab15, Rab GTPase family 15 (Rab15). Rab15 colocalizes
with the transferrin receptor in early endosome
compartments, but not with late endosomal markers. It
codistributes with Rab4 and Rab5 on early/sorting
endosomes, and with Rab11 on pericentriolar recycling
endosomes. It is believed to function as an inhibitory
GTPase that regulates distinct steps in early endocytic
trafficking. 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 = 164
Score = 24.6 bits (53), Expect = 5.6
Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 5/49 (10%)
Query: 26 IVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV--ILVANKADLERRRQV 72
+VY + +++ + ++K + D + V IL+ NKAD E++RQV
Sbjct: 78 LVYDISSERSY---QHIMKWVSDVDEYAPEGVQKILIGNKADEEQKRQV 123
>gnl|CDD|217066 pfam02492, cobW, CobW/HypB/UreG, nucleotide-binding domain. This
domain is found in HypB, a hydrogenase expression /
formation protein, and UreG a urease accessory protein.
Both these proteins contain a P-loop nucleotide binding
motif. HypB has GTPase activity and is a guanine
nucleotide binding protein. It is not known whether UreG
binds GTP or some other nucleotide. Both enzymes are
involved in nickel binding. HypB can store nickel and is
required for nickel dependent hydrogenase expression.
UreG is required for functional incorporation of the
urease nickel metallocenter. GTP hydrolysis may required
by these proteins for nickel incorporation into other
nickel proteins. This family of domains also contains
P47K, a Pseudomonas chlororaphis protein needed for
nitrile hydratase expression, and the cobW gene product,
which may be involved in cobalamin biosynthesis in
Pseudomonas denitrificans.
Length = 178
Score = 24.5 bits (54), Expect = 5.6
Identities = 12/45 (26%), Positives = 17/45 (37%), Gaps = 11/45 (24%)
Query: 23 VFVI-VYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADL 66
V V+ V +KA D + A ++V NK DL
Sbjct: 119 VTVVDVAETEGEDIPEKAPDQI----------AFADLIVINKTDL 153
>gnl|CDD|234135 TIGR03172, TIGR03172, probable selenium-dependent hydroxylase
accessory protein YqeC. This uncharacterized protein
family includes YqeC from Escherichia coli. A
phylogenetic profiling analysis shows correlation with
SelD, the selenium donor protein, even in species where
SelD contributes to neither selenocysteine nor
selenouridine biosynthesis. Instead, this family, and
families TIGR03309 and TIGR03310 appear to mark
selenium-dependent molybdenum hydroxylase maturation
systems [Unknown function, General].
Length = 210
Score = 24.5 bits (54), Expect = 6.0
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 53 GEKAVILVANKADLERRRQ 71
E I++ N+AD E R Q
Sbjct: 180 PEARFIILLNQADTEERIQ 198
>gnl|CDD|206752 cd01859, MJ1464, An uncharacterized, circularly permuted
subfamily of the Ras GTPases. This family represents
archaeal GTPase typified by the protein MJ1464 from
Methanococcus jannaschii. The members of this family
show a circular permutation of the GTPase signature
motifs so that C-terminal strands 5, 6, and 7 (strands
6 contain the NKxD motif) are relocated to the N
terminus.
Length = 157
Score = 24.2 bits (53), Expect = 6.6
Identities = 12/30 (40%), Positives = 15/30 (50%), Gaps = 7/30 (23%)
Query: 37 KKAEDMLKTLWDSKYIGEKAVILVANKADL 66
+K E M L K +I+V NKADL
Sbjct: 30 RKLERMALEL-------GKKLIIVLNKADL 52
>gnl|CDD|234274 TIGR03594, GTPase_EngA, ribosome-associated GTPase EngA. EngA
(YfgK, Der) is a ribosome-associated essential GTPase
with a duplication of its GTP-binding domain. It is
broadly to universally distributed among bacteria. It
appears to function in ribosome biogenesis or stability
[Protein synthesis, Other].
Length = 429
Score = 24.3 bits (54), Expect = 6.8
Identities = 9/11 (81%), Positives = 9/11 (81%)
Query: 55 KAVILVANKAD 65
K VILVANK D
Sbjct: 108 KPVILVANKID 118
>gnl|CDD|102471 PRK06628, PRK06628, lipid A biosynthesis lauroyl acyltransferase;
Provisional.
Length = 290
Score = 24.5 bits (53), Expect = 7.2
Identities = 11/35 (31%), Positives = 22/35 (62%), Gaps = 2/35 (5%)
Query: 40 EDMLKTLWDS--KYIGEKAVILVANKADLERRRQV 72
E ++ WD+ ++IGE + ++A+LERR ++
Sbjct: 68 EKIIDQTWDNFGRFIGEFTYVNKMDEAELERRIEI 102
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 24.4 bits (54), Expect = 7.5
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 49 SKYIGEKAVILVANKADLE 67
+K +I+V NKADL
Sbjct: 319 ELLPKKKPIIVVLNKADLV 337
>gnl|CDD|234685 PRK00197, proA, gamma-glutamyl phosphate reductase; Provisional.
Length = 417
Score = 24.3 bits (54), Expect = 8.1
Identities = 8/18 (44%), Positives = 8/18 (44%)
Query: 54 EKAVILVANKADLERRRQ 71
A IL AN DL R
Sbjct: 42 NAAEILAANAKDLAAARA 59
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes. TrmE
contains a GTPase domain that forms a canonical Ras-like
fold. It functions a molecular switch GTPase, and
apparently uses a conformational change associated with
GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 24.0 bits (53), Expect = 8.7
Identities = 8/13 (61%), Positives = 11/13 (84%)
Query: 54 EKAVILVANKADL 66
+K VI+V NK+DL
Sbjct: 109 KKPVIVVLNKSDL 121
>gnl|CDD|206750 cd01857, HSR1_MMR1, A circularly permuted subfamily of the Ras
GTPases. Human HSR1 is localized to the human MHC
class I region and is highly homologous to a putative
GTP-binding protein, MMR1 from mouse. These proteins
represent a new subfamily of GTP-binding proteins that
has only eukaryote members. This subfamily shows a
circular permutation of the GTPase signature motifs so
that the C-terminal strands 5, 6, and 7 (strand 6
contains the G4 box with sequence NKXD) are relocated
to the N-terminus.
Length = 140
Score = 23.7 bits (52), Expect = 9.2
Identities = 11/29 (37%), Positives = 14/29 (48%), Gaps = 4/29 (13%)
Query: 50 KYIGE----KAVILVANKADLERRRQVTH 74
KY+ E K +L+ NKADL Q
Sbjct: 34 KYVKEVDPSKENVLLLNKADLVTEEQRKA 62
>gnl|CDD|200499 cd11238, Sema_2A, The Sema domain, a protein interacting module, of
semaphorin 2A (Sema2A). Sema2A, a secreted semaphorin,
signals through its receptor plexin B (PlexB) to
regulate central and peripheral axon pathfinding. In the
Drosophila embryo, Sema2A secreted by oenocytes
interacts with PlexB to guide sensory axons. Sema2A is a
member of the semaphorin family of proteins. Semaphorins
are regulatory molecules in the development of the
nervous system and in axonal guidance. They also play
important roles in other biological processes, such as
angiogenesis, immune regulation, respiration systems and
cancer. The Sema domain is located at the N-terminus and
contains four disulfide bonds formed by eight conserved
cysteine residues. It serves as a receptor-recognition
and -binding module.
Length = 452
Score = 23.9 bits (52), Expect = 9.2
Identities = 9/50 (18%), Positives = 18/50 (36%)
Query: 8 FTNLVVNFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV 57
FT+LVV+ ++ + V + K +K S + +
Sbjct: 372 FTHLVVDKLRIDDQEYVVFYAGSNDGKVYKIVHWKDAGESKSNLLDVFEL 421
>gnl|CDD|238174 cd00280, TRFH, Telomeric Repeat binding Factor or TTAGGG Repeat
binding Factor, central (dimerization) domain Homology;
TRFH. Telomeres are protein/DNA complexes that make up
the physical ends of eukaryotic linear chromosomes and
are essential for chromosome stability, protecting the
chromosome ends from degradation and end-to-end fusion.
Proteins TRF1, TRF2 and Taz1 bind telomeric DNA and are
also involved in recruiting interacting proteins, TIN2,
and Rap1, to the telomeres. It has also been
demonstrated that PARP1 associates with TRF2 and is
capable of poly(ADP-ribosyl)ation of TRF2, which affects
binding of TRF2 to telomeric DNA. TRF1, TRF2 and Taz1
proteins contain three functional domains: an N-terminal
acidic domain, a central TRF-specific/dimerization
domain, and a C-terminal DNA binding domain with a
single Myb-like repeat. Homodimerization, a prerequisite
to DNA binding, results in the juxtaposition of two Myb
DNA binding domains.
Length = 200
Score = 23.9 bits (52), Expect = 9.4
Identities = 11/25 (44%), Positives = 15/25 (60%), Gaps = 2/25 (8%)
Query: 25 VIVYSVIERKTFKKAEDMLKTLWDS 49
V V +E FKKAE++LK L+
Sbjct: 118 VAVC--MENGEFKKAEEVLKRLFSD 140
>gnl|CDD|220781 pfam10493, Rod_C, Rough deal protein C-terminal region. Rod, the
Rough deal protein, displays a dynamic intracellular
staining pattern, localising first to kinetochores in
pro-metaphase, but moving to kinetochore microtubules at
metaphase. Early in anaphase the protein is once again
restricted to the kinetochores, where it persists until
the end of telophase. This behaviour is in all respects
similar to that described for ZW10, and indeed the two
proteins function together, localisation of each
depending upon the other. These two proteins are found
at the kinetochore in complex with a third, Zwilch, in
both flies and humans. The C-terminus is the most
conserved part of the protein. During pro-metaphase, the
ZW10-Rod complex, dynein/dynactin, and Mad2 all
accumulate on unattached kinetochores; microtubule
capture leads to Mad2 depletion as it is carried off by
dynein/dynactin; ZW10-Rod complex accumulation
continues, replenishing kinetochore dynein. The
continuing recruitment of the ZW10-Rod complex during
metaphase may serve to maintain adequate dynein/dynactin
complex on kinetochores for assisting chromatid movement
during anaphase. The ZW10-Rod complex acts as a bridge
whose association with Zwint-1 links Mad1 and Mad2,
components that are directly responsible for generating
the diffusible 'wait anaphase' signal, to a structural,
inner kinetochore complex containing Mis12 and
KNL-1AF15q14, the last of which has been proved to be
essential for kinetochore assembly in C. elegans.
Removal of ZW10 or Rod inactivates the mitotic
checkpoint.
Length = 555
Score = 24.0 bits (52), Expect = 9.7
Identities = 16/72 (22%), Positives = 28/72 (38%), Gaps = 16/72 (22%)
Query: 7 CFTNL----VVNFVQTYHPDVFVIVYSVIERKTFK------------KAEDMLKTLWDSK 50
CF+ L +F +T+ + ++ + V K E +LK LW +
Sbjct: 321 CFSKLDDDTCNSFTKTFIQEQYIYLKCVHFLKALGFLNITVEKFESTPKEGLLKGLWQNH 380
Query: 51 YIGEKAVILVAN 62
KA+ +VA
Sbjct: 381 AHEPKALEVVAE 392
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
0.323 0.133 0.381
Gapped
Lambda K H
0.267 0.0797 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,670,727
Number of extensions: 275113
Number of successful extensions: 558
Number of sequences better than 10.0: 1
Number of HSP's gapped: 531
Number of HSP's successfully gapped: 110
Length of query: 75
Length of database: 10,937,602
Length adjustment: 45
Effective length of query: 30
Effective length of database: 8,941,672
Effective search space: 268250160
Effective search space used: 268250160
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.1 bits)