RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12927
(75 letters)
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 88.7 bits (221), Expect = 2e-24
Identities = 27/54 (50%), Positives = 39/54 (72%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
+KI+++GDS VGK+ ++ RF D + + Y STIG+DFK K I++D KLQIW
Sbjct: 1 FKIILIGDSGVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIEVDGKRVKLQIW 54
>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 = 87.9 bits (219), Expect = 4e-24
Identities = 28/54 (51%), Positives = 39/54 (72%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
+KI+++GDS VGKT ++ RF D + + Y STIG+DFK K I++D KLQIW
Sbjct: 1 FKIVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGVDFKSKTIEVDGKKVKLQIW 54
>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 = 82.4 bits (204), Expect = 9e-22
Identities = 31/54 (57%), Positives = 44/54 (81%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
+K+L++GDS VGK+C++ RF D+TY ++YISTIG+DFK + I+LD KLQIW
Sbjct: 3 FKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTVKLQIW 56
>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 = 79.1 bits (196), Expect = 1e-20
Identities = 23/53 (43%), Positives = 35/53 (66%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
K++++GD VGK+ ++ RF + + YI TIG+DF K I++D KLQIW
Sbjct: 1 KLVLVGDGGVGKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIW 53
>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 = 78.5 bits (194), Expect = 3e-20
Identities = 28/54 (51%), Positives = 43/54 (79%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
+K+L++GDS VGK+C++ RF ++++ ++ISTIGIDFK + I+LD KLQIW
Sbjct: 4 FKLLLIGDSGVGKSCLLLRFSEDSFNPSFISTIGIDFKIRTIELDGKKIKLQIW 57
>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 = 74.8 bits (184), Expect = 8e-19
Identities = 24/56 (42%), Positives = 42/56 (75%)
Query: 6 QTYKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
+ +KI+V+GDSNVGKTC+ +RFC + + +TIG+DF+++ +++D K+Q+W
Sbjct: 1 RIFKIIVIGDSNVGKTCLTYRFCAGRFPERTEATIGVDFRERTVEIDGERIKVQLW 56
>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 = 70.4 bits (172), Expect = 3e-17
Identities = 26/54 (48%), Positives = 43/54 (79%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
+++L++GDS VGKTC++ RF D ++ ++ISTIG+DFK K I++D + ++QIW
Sbjct: 1 FRLLLIGDSGVGKTCLLCRFTDNEFHSSHISTIGVDFKMKTIEVDGIKVRIQIW 54
>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 = 70.3 bits (173), Expect = 4e-17
Identities = 25/54 (46%), Positives = 38/54 (70%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
+K++ LGD +VGKT I+ RF +T+ + Y +TIGIDF K + +DD +LQ+W
Sbjct: 1 HKLVFLGDQSVGKTSIITRFMYDTFDNQYQATIGIDFLSKTMYVDDKTVRLQLW 54
>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 = 69.0 bits (169), Expect = 1e-16
Identities = 26/54 (48%), Positives = 38/54 (70%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
+KI+++GDSNVGKTC+V RF T+ + +TIG+DF K +++ KLQIW
Sbjct: 4 FKIILIGDSNVGKTCVVQRFKSGTFSERQGNTIGVDFTMKTLEIQGKRVKLQIW 57
>gnl|CDD|133310 cd04110, Rab35, Rab GTPase family 35 (Rab35). Rab35 is one of
several Rab proteins to be found to participate in the
regulation of osteoclast cells in rats. In addition,
Rab35 has been identified as a protein that interacts
with nucleophosmin-anaplastic lymphoma kinase (NPM-ALK)
in human cells. Overexpression of NPM-ALK is a key
oncogenic event in some anaplastic large-cell
lymphomas; since Rab35 interacts with N|PM-ALK, it may
provide a target for cancer treatments. 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 = 199
Score = 66.0 bits (161), Expect = 3e-15
Identities = 26/59 (44%), Positives = 43/59 (72%)
Query: 3 DCNQTYKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
D + +K+L++GDS VGK+ ++ RF D T+ +YI+TIG+DFK + ++++ KLQIW
Sbjct: 2 DYDHLFKLLIIGDSGVGKSSLLLRFADNTFSGSYITTIGVDFKIRTVEINGERVKLQIW 60
>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 = 65.0 bits (159), Expect = 4e-15
Identities = 26/54 (48%), Positives = 37/54 (68%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
KIL++GDS VGK+ ++ RF D+T+ + STIG+DFK K + +D KL IW
Sbjct: 1 LKILLIGDSGVGKSSLLLRFTDDTFDEDLSSTIGVDFKVKTVTVDGKKVKLAIW 54
>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 = 64.5 bits (158), Expect = 7e-15
Identities = 23/55 (41%), Positives = 35/55 (63%)
Query: 7 TYKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
+K+++LGDS+VGK+ IV RF + + STIG F + ++LDD K +IW
Sbjct: 1 QFKLVLLGDSSVGKSSIVLRFVKNEFSENQESTIGAAFLTQTVNLDDTTVKFEIW 55
>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 = 64.2 bits (157), Expect = 1e-14
Identities = 22/54 (40%), Positives = 37/54 (68%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
K+++LGDS VGKT +++++ ++ + + Y +TIG DF K + +DD LQIW
Sbjct: 1 LKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVTVDDRLVTLQIW 54
>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 = 63.1 bits (154), Expect = 3e-14
Identities = 23/55 (41%), Positives = 35/55 (63%), Gaps = 1/55 (1%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDD-VPTKLQIW 61
+K+LV+GD VGKT I+ R+ + Y +TIG+DF K+I+ D +LQ+W
Sbjct: 1 FKVLVIGDLGVGKTSIIKRYVHGVFSQHYKATIGVDFALKVIEWDPNTVVRLQLW 55
>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 = 60.9 bits (148), Expect = 1e-13
Identities = 17/54 (31%), Positives = 34/54 (62%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
+K L++G + GK+C++H+F + + TIG++F +++++ KLQIW
Sbjct: 1 FKFLIIGSAGTGKSCLLHQFIENKFKQDSNHTIGVEFGSRVVNVGGKSVKLQIW 54
>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 = 59.9 bits (145), Expect = 3e-13
Identities = 24/54 (44%), Positives = 40/54 (74%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
+K+L++G+S+VGKT + R+ D+++ ++ST+GIDFK K + +D KLQIW
Sbjct: 2 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVYRNDKRIKLQIW 55
>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 = 58.9 bits (143), Expect = 1e-12
Identities = 20/62 (32%), Positives = 38/62 (61%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIWTLNALLT 68
K++ +G+S VGK+CI+ R+C+ + Y+ TIGID+ K + + + ++ + L+
Sbjct: 2 KVISMGNSGVGKSCIIKRYCEGRFVSKYLPTIGIDYGVKKVSVRNKEVRVNFFDLSGHPE 61
Query: 69 YL 70
YL
Sbjct: 62 YL 63
>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 = 57.9 bits (140), Expect = 3e-12
Identities = 19/39 (48%), Positives = 29/39 (74%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQK 47
K+L LGDS VGKT ++R+ D + +I+T+GIDF++K
Sbjct: 6 KLLALGDSGVGKTTFLYRYTDNKFNPKFITTVGIDFREK 44
>gnl|CDD|206695 cd04112, Rab26, Rab GTPase family 26 (Rab26). Rab26 subfamily.
First identified in rat pancreatic acinar cells, Rab26
is believed to play a role in recruiting mature
granules to the plasma membrane upon beta-adrenergic
stimulation. Rab26 belongs to the Rab functional group
III, which are considered key regulators of
intracellular vesicle transport during exocytosis.
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 = 191
Score = 58.0 bits (140), Expect = 3e-12
Identities = 25/55 (45%), Positives = 40/55 (72%), Gaps = 1/55 (1%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYY-DTYISTIGIDFKQKIIDLDDVPTKLQIW 61
+K++++GDS VGKTC++ RF D + ++I+T+GI F K++ +D V KLQIW
Sbjct: 1 FKVMLVGDSGVGKTCLLVRFKDGAFLAGSFIATVGIQFTNKVVTVDGVKVKLQIW 55
>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 = 57.9 bits (140), Expect = 4e-12
Identities = 23/55 (41%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDL-DDVPTKLQIW 61
KI+VLGD GKT ++ RF E + +Y TIG+DF + I L + LQ+W
Sbjct: 1 IKIVVLGDGASGKTSLIRRFAQEGFGKSYKQTIGLDFFSRRITLPGSLNVTLQVW 55
>gnl|CDD|206693 cd04108, Rab36_Rab34, Rab GTPase families 34 (Rab34) and 36
(Rab36). Rab34/Rab36 subfamily. Rab34, found primarily
in the Golgi, interacts with its effector,
Rab-interacting lysosomal protein (RILP). This enables
its participation in microtubular
dynenin-dynactin-mediated repositioning of lysosomes
from the cell periphery to the Golgi. A Rab34 (Rah)
isoform that lacks the consensus GTP-binding region has
been identified in mice. This isoform is associated
with membrane ruffles and promotes macropinosome
formation. Rab36 has been mapped to human chromosome
22q11.2, a region that is homozygously deleted in
malignant rhabdoid tumors (MRTs). However, experimental
assessments do not implicate Rab36 as a tumor
suppressor that would enable tumor formation through a
loss-of-function mechanism. 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 = 170
Score = 57.2 bits (138), Expect = 4e-12
Identities = 23/53 (43%), Positives = 39/53 (73%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
K++V+GD +VGKTC+++RFC + + Y +TIG+DF+ + ++ VP LQ+W
Sbjct: 2 KVIVVGDLSVGKTCLINRFCKDVFDKNYKATIGVDFEMERFEVLGVPFSLQLW 54
>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 = 56.0 bits (135), Expect = 1e-11
Identities = 20/54 (37%), Positives = 37/54 (68%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
+K +++GD VGK+C++H+F ++ + TIG++F +II+++ KLQIW
Sbjct: 3 FKYIIIGDMGVGKSCLLHQFTEKKFMADCPHTIGVEFGTRIIEVNGQKIKLQIW 56
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 56.5 bits (136), Expect = 1e-11
Identities = 21/54 (38%), Positives = 39/54 (72%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
+K +++GD+ VGK+C++ +F D+ + + TIG++F ++I +D+ P KLQIW
Sbjct: 7 FKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDNKPIKLQIW 60
>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 = 56.7 bits (137), Expect = 1e-11
Identities = 19/55 (34%), Positives = 38/55 (69%), Gaps = 1/55 (1%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDD-VPTKLQIW 61
++++V+GDS VGK+ ++ RF + + + T+G+DF ++I+++ V KLQ+W
Sbjct: 3 FRLIVIGDSTVGKSSLLKRFTEGRFAEVSDPTVGVDFFSRLIEIEPGVRIKLQLW 57
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins
[General function prediction only].
Length = 219
Score = 55.4 bits (133), Expect = 4e-11
Identities = 21/55 (38%), Positives = 31/55 (56%)
Query: 7 TYKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
+KI+VLGD VGKT +++R + + + Y TIG K I+ KLQ+W
Sbjct: 5 EFKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLW 59
>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 = 54.5 bits (132), Expect = 4e-11
Identities = 23/55 (41%), Positives = 36/55 (65%), Gaps = 2/55 (3%)
Query: 8 YKILVLGDSNVGKTCIVHRFC-DETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
+KI+++GDS VGK+ ++ RF +E D+ STIG++F + I +D K QIW
Sbjct: 4 FKIVLIGDSGVGKSNLLSRFTRNEFNLDSK-STIGVEFATRTIQIDGKTIKAQIW 57
>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 = 54.2 bits (131), Expect = 5e-11
Identities = 17/54 (31%), Positives = 31/54 (57%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
+K+++LG+ VGKT +V R+ + + + + ST F QK +++ L IW
Sbjct: 1 FKVVLLGEGRVGKTSLVLRYVENKFNEKHESTTQASFFQKTVNIGGKRIDLAIW 54
>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 = 54.1 bits (131), Expect = 7e-11
Identities = 18/52 (34%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQI 60
K++VLG VGK+ + RF + + Y TI D +K I +D L I
Sbjct: 1 KLVVLGAGGVGKSALTIRFVSGEFVEEYDPTIE-DSYRKQIVVDGETYTLDI 51
>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 = 53.7 bits (129), Expect = 9e-11
Identities = 24/61 (39%), Positives = 38/61 (62%)
Query: 1 MADCNQTYKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQI 60
M D + +KI+++G++ VGKTC+V RF + +TIG+DF K +++ KLQI
Sbjct: 1 MEDYDFLFKIVLIGNAGVGKTCLVRRFTQGLFPPGQGATIGVDFMIKTVEIKGEKIKLQI 60
Query: 61 W 61
W
Sbjct: 61 W 61
>gnl|CDD|133306 cd04106, Rab23_like, Rab GTPase family 23 (Rab23)-like.
Rab23-like subfamily. Rab23 is a member of the Rab
family of small GTPases. In mouse, Rab23 has been shown
to function as a negative regulator in the sonic
hedgehog (Shh) signaling pathway. Rab23 mediates the
activity of Gli2 and Gli3, transcription factors that
regulate Shh signaling in the spinal cord, primarily by
preventing Gli2 activation in the absence of Shh
ligand. Rab23 also regulates a step in the cytoplasmic
signal transduction pathway that mediates the effect of
Smoothened (one of two integral membrane proteins that
are essential components of the Shh signaling pathway
in vertebrates). In humans, Rab23 is expressed in the
retina. Mice contain an isoform that shares 93%
sequence identity with the human Rab23 and an
alternative splicing isoform that is specific to the
brain. This isoform causes the murine open brain
phenotype, indicating it may have a role in the
development of the central nervous system. 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 = 53.2 bits (128), Expect = 1e-10
Identities = 20/55 (36%), Positives = 32/55 (58%), Gaps = 2/55 (3%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPT--KLQIW 61
K++V+G+ NVGK+ ++ RF + Y TIG+DF +K I L +L +W
Sbjct: 2 KVIVVGNGNVGKSSMIQRFVKGIFTKDYKKTIGVDFLEKQIFLRQSDEDVRLMLW 56
>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 = 52.4 bits (126), Expect = 3e-10
Identities = 20/54 (37%), Positives = 37/54 (68%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
+K +++GD+ VGK+C++ +F D+ + + TIG++F ++I +D KLQIW
Sbjct: 5 FKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIW 58
>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 = 49.5 bits (119), Expect = 3e-09
Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 1/54 (1%)
Query: 7 TYKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQI 60
YK++VLG VGK+ + +F + D Y TI D +K I++D L I
Sbjct: 2 EYKLVVLGGGGVGKSALTIQFVQGHFVDEYDPTIE-DSYRKQIEIDGEVCLLDI 54
>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 = 48.7 bits (117), Expect = 7e-09
Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQI 60
YK++VLG VGK+ + +F + D Y TI D +K I++D L I
Sbjct: 1 YKLVVLGSGGVGKSALTIQFIQGHFVDDYDPTIE-DSYRKQIEIDGEVCLLDI 52
>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 = 47.7 bits (113), Expect = 2e-08
Identities = 21/53 (39%), Positives = 36/53 (67%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
+++++G VGKT ++ RF D+T+ + ST+G+DFK K ++L +LQIW
Sbjct: 2 QVIIIGSRGVGKTSLMERFTDDTFCEACKSTVGVDFKIKTVELRGKKIRLQIW 54
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 46.5 bits (110), Expect = 9e-08
Identities = 20/54 (37%), Positives = 33/54 (61%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
+KI+++GDS VGK+ I+ RF + STIG++F + + ++ K QIW
Sbjct: 13 FKIVLIGDSGVGKSNILSRFTRNEFCLESKSTIGVEFATRTLQVEGKTVKAQIW 66
>gnl|CDD|206697 cd04116, Rab9, Rab GTPase family 9 (Rab9). Rab9 is found in late
endosomes, together with mannose 6-phosphate receptors
(MPRs) and the tail-interacting protein of 47 kD
(TIP47). Rab9 is a key mediator of vesicular transport
from late endosomes to the trans-Golgi network (TGN) by
redirecting the MPRs. Rab9 has been identified as a key
component for the replication of several viruses,
including HIV1, Ebola, Marburg, and measles, making it
a potential target for inhibiting a variety of viruses.
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 = 43.7 bits (103), Expect = 6e-07
Identities = 18/53 (33%), Positives = 32/53 (60%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
K+++LGD VGK+ +++R+ + TIG++F K +++D LQIW
Sbjct: 7 KVILLGDGGVGKSSLMNRYVTNKFDTQLFHTIGVEFLNKDLEVDGHFVTLQIW 59
>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 = 42.9 bits (101), Expect = 1e-06
Identities = 19/53 (35%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQI 60
YK++VLG VGK+ + +F + D Y TI D +K I++D L+I
Sbjct: 2 YKLVVLGSGGVGKSALTVQFVQGIFVDKYDPTIE-DSYRKQIEVDCQQCMLEI 53
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 43.5 bits (102), Expect = 1e-06
Identities = 22/55 (40%), Positives = 33/55 (60%), Gaps = 1/55 (1%)
Query: 7 TYKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
++KIL++GDS VGK+ ++ F + D TIG+DFK K + + KL IW
Sbjct: 14 SFKILLIGDSGVGKSSLLVSFISSSVEDL-APTIGVDFKIKQLTVGGKRLKLTIW 67
>gnl|CDD|206701 cd04128, Spg1, Septum-promoting GTPase (Spg1). Spg1p. Spg1p
(septum-promoting GTPase) was first identified in the
fission yeast S. pombe, where it regulates septum
formation in the septation initiation network (SIN)
through the cdc7 protein kinase. Spg1p is an essential
gene that localizes to the spindle pole bodies. When
GTP-bound, it binds cdc7 and causes it to translocate
to spindle poles. Sid4p (septation initiation
defective) is required for localization of Spg1p to the
spindle pole body, and the ability of Spg1p to promote
septum formation from any point in the cell cycle
depends on Sid4p. Spg1p is negatively regulated by Byr4
and cdc16, which form a two-component GTPase activating
protein (GAP) for Spg1p. The existence of a SIN-related
pathway in plants has been proposed. 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 = 182
Score = 42.8 bits (101), Expect = 2e-06
Identities = 18/55 (32%), Positives = 33/55 (60%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIWTL 63
KI +LGD+ +GKT ++ ++ + + + YI T+G++F +K I + IW L
Sbjct: 2 KIGLLGDAQIGKTSLMVKYVEGEFDEEYIQTLGVNFMEKTISIRGTEITFSIWDL 56
>gnl|CDD|133321 cd04121, Rab40, Rab GTPase family 40 (Rab40) contains Rab40a,
Rab40b and Rab40c. The Rab40 subfamily contains
Rab40a, Rab40b, and Rab40c, which are all highly
homologous. In rat, Rab40c is localized to the
perinuclear recycling compartment (PRC), and is
distributed in a tissue-specific manor, with high
expression in brain, heart, kidney, and testis, low
expression in lung and liver, and no expression in
spleen and skeletal muscle. Rab40c is highly expressed
in differentiated oligodendrocytes but minimally
expressed in oligodendrocyte progenitors, suggesting a
role in the vesicular transport of myelin components.
Unlike most other Ras-superfamily proteins, Rab40c was
shown to have a much lower affinity for GTP, and an
affinity for GDP that is lower than for 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. 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 = 189
Score = 41.5 bits (97), Expect = 5e-06
Identities = 22/53 (41%), Positives = 30/53 (56%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
K L++GDS+VGK I+ D + Y +GID+K I LD KLQ+W
Sbjct: 8 KFLLVGDSDVGKGEILASLQDGSTESPYGYNMGIDYKTTTILLDGRRVKLQLW 60
>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 = 41.0 bits (96), Expect = 6e-06
Identities = 21/53 (39%), Positives = 33/53 (62%), Gaps = 1/53 (1%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQI 60
YK++VLG VGK+ + +F T+ + Y TI DF +K I++D P+ L+I
Sbjct: 2 YKVVVLGSGGVGKSALTVQFVSGTFIEKYDPTIE-DFYRKEIEVDSSPSVLEI 53
>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 = 40.6 bits (96), Expect = 8e-06
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
KI+V+GD VGKTC++ + + Y+ T+ D + +D L +W
Sbjct: 2 KIVVVGDGAVGKTCLLISYTTNKFPTEYVPTV-FDNYSANVTVDGKQVNLGLW 53
>gnl|CDD|133326 cd04126, Rab20, Rab GTPase family 20 (Rab20). Rab20 is one of
several Rab proteins that appear to be restricted in
expression to the apical domain of murine polarized
epithelial cells. It is expressed on the apical side of
polarized kidney tubule and intestinal epithelial
cells, and in non-polarized cells. It also localizes to
vesico-tubular structures below the apical brush border
of renal proximal tubule cells and in the apical region
of duodenal epithelial cells. Rab20 has also been shown
to colocalize with vacuolar H+-ATPases (V-ATPases) in
mouse kidney cells, suggesting a role in the regulation
of V-ATPase traffic in specific portions of the
nephron. It was also shown to be one of several
proteins whose expression is upregulated in human
myelodysplastic syndrome (MDS) patients. 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 = 220
Score = 40.7 bits (95), Expect = 1e-05
Identities = 18/39 (46%), Positives = 28/39 (71%), Gaps = 1/39 (2%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQK 47
K+++LGD NVGKT ++HR+ + + DT +ST+G F K
Sbjct: 2 KVVLLGDMNVGKTSLLHRYMERRFKDT-VSTVGGAFYLK 39
>gnl|CDD|206741 cd09914, RocCOR, Ras of complex proteins (Roc) C-terminal of Roc
(COR) domain family. RocCOR (or Roco) protein family
is characterized by a superdomain containing a Ras-like
GTPase domain, called Roc (Ras of complex proteins),
and a characteristic second domain called COR
(C-terminal of Roc). A kinase domain and diverse
regulatory domains are also often found in Roco
proteins. Their functions are diverse; in Dictyostelium
discoideum, which encodes 11 Roco proteins, they are
involved in cell division, chemotaxis and development,
while in human, where 4 Roco proteins (LRRK1, LRRK2,
DAPK1, and MFHAS1) are encoded, these proteins are
involved in epilepsy and cancer. Mutations in LRRK2
(leucine-rich repeat kinase 2) are known to cause
familial Parkinson's disease.
Length = 161
Score = 40.0 bits (94), Expect = 1e-05
Identities = 15/56 (26%), Positives = 27/56 (48%), Gaps = 5/56 (8%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTIGI---DFKQKIIDLDDVPTKLQIW 61
K++++G VGKT + + E + ST GI D+K + + +L +W
Sbjct: 3 KLMLVGQGGVGKTSLCKQLIGEKFDGDESSTHGINVQDWKIPAPERKKI--RLNVW 56
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 39.7 bits (93), Expect = 2e-05
Identities = 16/61 (26%), Positives = 27/61 (44%)
Query: 1 MADCNQTYKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQI 60
D +K++++GD VGKT V R + YI T+G++ + P +
Sbjct: 3 QMDEVPEFKLILVGDGGVGKTTFVKRHLTGEFEKKYIPTLGVEVHPLKFYTNCGPICFNV 62
Query: 61 W 61
W
Sbjct: 63 W 63
>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 = 39.4 bits (92), Expect = 2e-05
Identities = 17/52 (32%), Positives = 32/52 (61%), Gaps = 1/52 (1%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQI 60
K++VLGD VGKT + + C + +TY TI ++++++ +D P L++
Sbjct: 1 KLVVLGDGGVGKTALTIQLCLNHFVETYDPTIEDSYRKQVV-VDGQPCMLEV 51
>gnl|CDD|133318 cd04118, Rab24, Rab GTPase family 24 (Rab24). Rab24 is distinct
from other Rabs in several ways. It exists primarily in
the GTP-bound state, having a low intrinsic GTPase
activity; it is not efficiently geranyl-geranylated at
the C-terminus; it does not form a detectable complex
with Rab GDP-dissociation inhibitors (GDIs); and it has
recently been shown to undergo tyrosine phosphorylation
when overexpressed in vitro. The specific function of
Rab24 still remains unknown. It is found in a transport
route between ER-cis-Golgi and late endocytic
compartments. It is putatively involved in an
autophagic pathway, possibly directing misfolded
proteins in the ER to degradative pathways. 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 = 193
Score = 39.5 bits (92), Expect = 3e-05
Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYD-TYISTIGIDFKQKIIDLDDVPTKLQIW 61
K+++LG +VGKT +V R+ + Y +TIG F K + + + L IW
Sbjct: 2 KVVMLGKESVGKTSLVERYVHHRFLVGPYQNTIGAAFVAKRMVVGERVVTLGIW 55
>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 = 39.0 bits (91), Expect = 4e-05
Identities = 19/41 (46%), Positives = 26/41 (63%), Gaps = 1/41 (2%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKI 48
Y+++VLG S VGKT IV RF + + Y TI DF +K+
Sbjct: 1 YRMVVLGASKVGKTAIVSRFLGGRFEEQYTPTIE-DFHRKL 40
>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 = 38.3 bits (89), Expect = 6e-05
Identities = 16/41 (39%), Positives = 26/41 (63%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKI 48
Y+++V G VGK+ +V RF T+ ++YI TI ++Q I
Sbjct: 2 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVI 42
>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 = 37.2 bits (87), Expect = 1e-04
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 11/53 (20%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTI-----------GIDFKQKIID 50
KI VLG +VGK+ + +F + + ++Y TI G ++ +I+D
Sbjct: 3 KIAVLGSRSVGKSSLTVQFVEGHFVESYYPTIENTFSKIITYKGQEYHLEIVD 55
>gnl|CDD|232886 TIGR00231, small_GTP, small GTP-binding protein domain. Proteins
with a small GTP-binding domain recognized by this
model include Ras, RhoA, Rab11, translation elongation
factor G, translation initiation factor IF-2,
tetratcycline resistance protein TetM, CDC42, Era,
ADP-ribosylation factors, tdhF, and many others. In
some proteins the domain occurs more than once.This
model recognizes a large number of small GTP-binding
proteins and related domains in larger proteins. Note
that the alpha chains of heterotrimeric G proteins are
larger proteins in which the NKXD motif is separated
from the GxxxxGK[ST] motif (P-loop) by a long insert
and are not easily detected by this model [Unknown
function, General].
Length = 162
Score = 37.0 bits (86), Expect = 2e-04
Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 7 TYKILVLGDSNVGKTCIVHRFCDETYYDT-YISTIGIDFKQKIIDLDDVPTKLQIW 61
KI+++GD NVGK+ +++R T Y ++ +I+ D K +
Sbjct: 1 EIKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLL 56
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 37.0 bits (85), Expect = 2e-04
Identities = 16/32 (50%), Positives = 23/32 (71%)
Query: 30 ETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
+T+ + Y STIGIDF K + LD+ P +LQ+W
Sbjct: 3 DTFDNNYQSTIGIDFLSKTLYLDEGPVRLQLW 34
>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 = 37.1 bits (86), Expect = 2e-04
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 2/47 (4%)
Query: 9 KILVLGDSNVGKTCIVHRFCDE--TYYDTYISTIGIDFKQKIIDLDD 53
+ V+GD VGK+ +V F + T+ Y T G D K + + D
Sbjct: 2 QCAVVGDPAVGKSALVQMFHSDGATFQKNYTMTTGCDLVVKTVPVPD 48
>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 = 36.6 bits (85), Expect = 2e-04
Identities = 11/53 (20%), Positives = 23/53 (43%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
K++V+GD GK+ ++ + + + G +++D L IW
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIW 53
>gnl|CDD|206736 cd04173, Rnd2_Rho7, Rnd2/Rho7 GTPases. Rnd2/Rho7 is a member of
the novel Rho subfamily Rnd, together with Rnd1/Rho6
and Rnd3/RhoE/Rho8. Rnd2/Rho7 is transiently expressed
in radially migrating cells in the brain while they are
within the subventricular zone of the hippocampus and
cerebral cortex. These migrating cells typically
develop into pyramidal neurons. Cells that exogenously
expressed Rnd2/Rho7 failed to migrate to upper layers
of the brain, suggesting that Rnd2/Rho7 plays a role in
the radial migration and morphological changes of
developing pyramidal neurons, and that Rnd2/Rho7
degradation is necessary for proper cellular migration.
The Rnd2/Rho7 GEF Rapostlin is found primarily in the
brain and together with Rnd2/Rho7 induces dendrite
branching. Unlike Rnd1/Rho6 and Rnd3/RhoE/Rho8, which
are RhoA antagonists, Rnd2/Rho7 binds the GEF Pragmin
and significantly stimulates RhoA activity and Rho-A
mediated cell contraction. Rnd2/Rho7 is also found to
be expressed in spermatocytes and early spermatids,
with male-germ-cell Rac GTPase-activating protein
(MgcRacGAP), where it localizes to the Golgi-derived
pro-acrosomal vesicle. 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.
Length = 221
Score = 36.5 bits (84), Expect = 3e-04
Identities = 16/53 (30%), Positives = 32/53 (60%), Gaps = 1/53 (1%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
KI+V+GD+ GKT ++H F + Y ++Y+ T+ ++ ++D +L +W
Sbjct: 3 KIVVVGDTQCGKTALLHVFAKDNYPESYVPTVFENYTAS-FEIDKHRIELNMW 54
>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 = 36.4 bits (84), Expect = 3e-04
Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQI 60
YKI++LG VGK+ + +F ++ D + TI +K + +D+ P L I
Sbjct: 3 YKIVMLGAGGVGKSAVTMQFISHSFPDYHDPTIEDAYKTQAR-IDNEPALLDI 54
>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 = 36.3 bits (84), Expect = 3e-04
Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 5/54 (9%)
Query: 11 LVLGDSNVGKTCIVHRFCDETYY---DTYISTIGIDFKQKIIDLDDVPTKLQIW 61
+V+G VGK+ +++ D +T D K +D V KL +
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKV--KLVLV 52
>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 = 36.2 bits (84), Expect = 4e-04
Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 6 QTYKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQI 60
TYK++V+G VGK+ + +F + Y TI D K ++D +L I
Sbjct: 1 PTYKLVVVGGGGVGKSALTIQFIQSYFVTDYDPTIE-DSYTKQCEIDGQWARLDI 54
>gnl|CDD|206689 cd04102, RabL3, Rab GTPase-like family 3 (Rab-like3). RabL3
(Rab-like3) subfamily. RabL3s 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, RabL3 lacks a prenylation site at the
C-terminus. The specific function of RabL3 remains
unknown.
Length = 204
Score = 36.0 bits (83), Expect = 4e-04
Identities = 15/42 (35%), Positives = 20/42 (47%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIID 50
K+LVLGDS VGK+ +VH C T+G +
Sbjct: 2 KVLVLGDSGVGKSSLVHLLCKNQVLGNPSWTVGCSVDVRHHT 43
>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 = 35.5 bits (82), Expect = 6e-04
Identities = 18/53 (33%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQI 60
YKI+VLG VGK+ + +F + ++Y TI D +K +++D L+I
Sbjct: 2 YKIVVLGAGGVGKSALTVQFVQNVFIESYDPTIE-DSYRKQVEIDGRQCDLEI 53
>gnl|CDD|206735 cd04172, Rnd3_RhoE_Rho8, Rnd3/RhoE/Rho8 GTPases. Rnd3/RhoE/Rho8
subfamily. Rnd3/RhoE/Rho8 is a member of the novel Rho
subfamily Rnd, together with Rnd1/Rho6 and Rnd2/Rho7.
Rnd3/RhoE is known to bind the serine-threonine kinase
ROCK I. Unphosphorylated Rnd3/RhoE associates primarily
with membranes, but ROCK I-phosphorylated Rnd3/RhoE
localizes in the cytosol. Phosphorylation of Rnd3/RhoE
correlates with its activity in disrupting RhoA-induced
stress fibers and inhibiting Ras-induced fibroblast
transformation. In cells that lack stress fibers, such
as macrophages and monocytes, Rnd3/RhoE induces a
redistribution of actin, causing morphological changes
in the cell. In addition, Rnd3/RhoE has been shown to
inhibit cell cycle progression in G1 phase at a point
upstream of the pRb family pocket protein checkpoint.
Rnd3/RhoE has also been shown to inhibit Ras- and
Raf-induced fibroblast transformation. In mammary
epithelial tumor cells, Rnd3/RhoE regulates the
assembly of the apical junction complex and tight
junction formation. Rnd3/RhoE is underexpressed in
prostate cancer cells both in vitro and in vivo;
re-expression of Rnd3/RhoE suppresses cell cycle
progression and increases apoptosis, suggesting it may
play a role in tumor suppression. 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 = 182
Score = 35.0 bits (80), Expect = 0.001
Identities = 16/53 (30%), Positives = 31/53 (58%), Gaps = 1/53 (1%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
KI+V+GDS GKT ++H F + + + Y+ T+ ++ ++D +L +W
Sbjct: 7 KIVVVGDSQCGKTALLHVFAKDCFPENYVPTVFENYTAS-FEIDTQRIELSLW 58
>gnl|CDD|133277 cd01875, RhoG, Ras homolog family, member G (RhoG) of small
guanosine triphosphatases (GTPases). RhoG is a GTPase
with high sequence similarity to members of the Rac
subfamily, including the regions involved in effector
recognition and binding. However, RhoG does not bind to
known Rac1 and Cdc42 effectors, including proteins
containing a Cdc42/Rac interacting binding (CRIB)
motif. Instead, RhoG interacts directly with Elmo, an
upstream regulator of Rac1, in a GTP-dependent manner
and forms a ternary complex with Dock180 to induce
activation of Rac1. The RhoG-Elmo-Dock180 pathway is
required for activation of Rac1 and cell spreading
mediated by integrin, as well as for neurite outgrowth
induced by nerve growth factor. Thus RhoG activates
Rac1 through Elmo and Dock180 to control cell
morphology. RhoG has also been shown to play a role in
caveolar trafficking and has a novel role in signaling
the neutrophil respiratory burst stimulated by G
protein-coupled receptor (GPCR) agonists. 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.
Length = 191
Score = 34.6 bits (79), Expect = 0.002
Identities = 13/35 (37%), Positives = 21/35 (60%)
Query: 6 QTYKILVLGDSNVGKTCIVHRFCDETYYDTYISTI 40
Q+ K +V+GD VGKTC++ + + YI T+
Sbjct: 2 QSIKCVVVGDGAVGKTCLLICYTTNAFPKEYIPTV 36
>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 = 33.9 bits (78), Expect = 0.003
Identities = 15/53 (28%), Positives = 28/53 (52%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQI 60
Y++++LGDS VGK+ + + F Y D+ G D ++ + +D L +
Sbjct: 1 YRVVLLGDSGVGKSSLANIFTAGVYEDSAYEASGDDTYERTVSVDGEEATLVV 53
>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 = 33.4 bits (77), Expect = 0.004
Identities = 16/54 (29%), Positives = 30/54 (55%), Gaps = 5/54 (9%)
Query: 10 ILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDL--DDVPTKLQIW 61
++V+GD VGKTC++ + + + Y+ T+ F+ D+ D P +L +W
Sbjct: 1 LVVVGDGAVGKTCLLIVYTTNAFPEDYVPTV---FENYSADVEVDGKPVELGLW 51
>gnl|CDD|206703 cd04131, Rnd, Rho family GTPase subfamily Rnd includes Rnd1/Rho6,
Rnd2/Rho7, and Rnd3/RhoE/Rho8. The Rnd subfamily
contains Rnd1/Rho6, Rnd2/Rho7, and Rnd3/RhoE/Rho8.
These novel Rho family proteins have substantial
structural differences compared to other Rho members,
including N- and C-terminal extensions relative to
other Rhos. Rnd3/RhoE is farnesylated at the C-terminal
prenylation site, unlike most other Rho proteins that
are geranylgeranylated. In addition, Rnd members are
unable to hydrolyze GTP and are resistant to GAP
activity. They are believed to exist only in the
GTP-bound conformation, and are antagonists of RhoA
activity. 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 = 176
Score = 32.8 bits (75), Expect = 0.006
Identities = 11/32 (34%), Positives = 22/32 (68%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTI 40
KI+++GDS GKT ++ F +++ + Y+ T+
Sbjct: 3 KIVLVGDSQCGKTALLQVFAKDSFPENYVPTV 34
>gnl|CDD|177661 PLN00023, PLN00023, GTP-binding protein; Provisional.
Length = 334
Score = 32.9 bits (75), Expect = 0.008
Identities = 12/22 (54%), Positives = 17/22 (77%), Gaps = 1/22 (4%)
Query: 4 CNQTYKILVLGDSNVGKTCIVH 25
C Q ++LV+GDS VGK+ +VH
Sbjct: 19 CGQV-RVLVVGDSGVGKSSLVH 39
>gnl|CDD|133324 cd04124, RabL2, Rab GTPase-like family 2 (Rab-like2). RabL2
(Rab-like2) subfamily. RabL2s are novel Rab proteins
identified recently which display features that are
distinct from other Rabs, and have been termed
Rab-like. RabL2 contains RabL2a and RabL2b, two very
similar Rab proteins that share > 98% sequence identity
in humans. RabL2b maps to the subtelomeric region of
chromosome 22q13.3 and RabL2a maps to 2q13, a region
that suggests it is also a subtelomeric gene. Both
genes are believed to be expressed ubiquitously,
suggesting that RabL2s are the first example of
duplicated genes in human proximal subtelomeric regions
that are both expressed actively. Like other Rab-like
proteins, RabL2s lack a prenylation site at the
C-terminus. The specific functions of RabL2a and RabL2b
remain unknown. 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 = 161
Score = 32.5 bits (74), Expect = 0.008
Identities = 16/53 (30%), Positives = 26/53 (49%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
KI++LGDS VGK+ +V RF + Y +ST + + + + W
Sbjct: 2 KIILLGDSAVGKSKLVERFLMDGYEPQQLSTYALTLYKHNAKFEGKTILVDFW 54
>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 = 32.5 bits (74), Expect = 0.009
Identities = 13/34 (38%), Positives = 19/34 (55%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIG 41
++ VLG VGKT IV +F + + + YI T
Sbjct: 1 VRVAVLGAPGVGKTAIVRQFLAQEFPEEYIPTEH 34
>gnl|CDD|206643 cd00877, Ran, Ras-related nuclear proteins (Ran)/TC4 family of
small GTPases. Ran GTPase is involved in diverse
biological functions, such as nuclear transport,
spindle formation during mitosis, DNA replication, and
cell division. Among the Ras superfamily, Ran is a
unique small G protein. It does not have a lipid
modification motif at the C-terminus to bind to the
membrane, which is often observed within the Ras
superfamily. Ran may therefore interact with a wide
range of proteins in various intracellular locations.
Like other GTPases, Ran exists in GTP- and GDP-bound
conformations that interact differently with effectors.
Conversion between these forms and the assembly or
disassembly of effector complexes requires the
interaction of regulator proteins. The intrinsic GTPase
activity of Ran is very low, but it is greatly
stimulated by a GTPase-activating protein (RanGAP1)
located in the cytoplasm. By contrast, RCC1, a guanine
nucleotide exchange factor that generates RanGTP, is
bound to chromatin and confined to the nucleus. Ran
itself is mobile and is actively imported into the
nucleus by a mechanism involving NTF-2. Together with
the compartmentalization of its regulators, this is
thought to produce a relatively high concentration of
RanGTP in the nucleus.
Length = 166
Score = 32.3 bits (74), Expect = 0.010
Identities = 11/36 (30%), Positives = 22/36 (61%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGID 43
+K++++GD GKT V R + Y++T+G++
Sbjct: 1 FKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVE 36
>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 = 31.9 bits (73), Expect = 0.013
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
KI VLG S VGK+ + RF + + Y + + +++ +D L+I
Sbjct: 1 KIAVLGASGVGKSALTVRFLTKRFIGEYEPNLESLYSRQVT-IDGEQVSLEIQ 52
>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 = 31.7 bits (72), Expect = 0.017
Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQI 60
YK++VLG VGK+ + +F + + Y TI D +K +++D L+I
Sbjct: 2 YKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIE-DSYRKQVEVDGQQCMLEI 53
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 31.4 bits (72), Expect = 0.017
Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 1/37 (2%)
Query: 5 NQTYKILVLGDSNVGKTCIVHRFCDETYYDTYISTIG 41
N+ +IL+LG N GKT I+++ T I TIG
Sbjct: 12 NKEMRILILGLDNAGKTTILYKLKLGE-IVTTIPTIG 47
>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 = 0.018
Identities = 9/32 (28%), Positives = 20/32 (62%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTI 40
+++ +G + VGKT ++ RF +T+ + T+
Sbjct: 1 RLVFMGAAGVGKTALIQRFLYDTFEPKHRRTV 32
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 31.6 bits (72), Expect = 0.018
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 7 TYKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGID 43
++K++++GD GKT V R + Y TIG++
Sbjct: 13 SFKLVIVGDGGTGKTTFVKRHLTGEFEKKYEPTIGVE 49
>gnl|CDD|206663 cd01871, Rac1_like, Ras-related C3 botulinum toxin substrate 1
(rho family, small GTP binding protein Rac1)-like
consists of Rac1, Rac2 and Rac3. The Rac1-like
subfamily consists of Rac1, Rac2, and Rac3 proteins,
plus the splice variant Rac1b that contains a
19-residue insertion near switch II relative to Rac1.
While Rac1 is ubiquitously expressed, Rac2 and Rac3 are
largely restricted to hematopoietic and neural tissues
respectively. Rac1 stimulates the formation of actin
lamellipodia and membrane ruffles. It also plays a role
in cell-matrix adhesion and cell anoikis. In intestinal
epithelial cells, Rac1 is an important regulator of
migration and mediates apoptosis. Rac1 is also
essential for RhoA-regulated actin stress fiber and
focal adhesion complex formation. In leukocytes, Rac1
and Rac2 have distinct roles in regulating cell
morphology, migration, and invasion, but are not
essential for macrophage migration or chemotaxis. Rac3
has biochemical properties that are closely related to
Rac1, such as effector interaction, nucleotide binding,
and hydrolysis; Rac2 has a slower nucleotide
association and is more efficiently activated by the
RacGEF Tiam1. Both Rac1 and Rac3 have been implicated
in the regulation of cell migration and invasion in
human metastatic breast cancer. 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 = 174
Score = 31.3 bits (71), Expect = 0.023
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
K +V+GD VGKTC++ + + YI T+ ++ ++ +D P L +W
Sbjct: 3 KCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVM-VDGKPVNLGLW 54
>gnl|CDD|206707 cd04135, Tc10, Rho GTPase TC10 (Tc10). TC10 is a Rho family
protein that has been shown to induce microspike
formation and neurite outgrowth in vitro. Its
expression changes dramatically after peripheral nerve
injury, suggesting an important role in promoting
axonal outgrowth and regeneration. TC10 regulates
translocation of insulin-stimulated GLUT4 in adipocytes
and has also been shown to bind directly to Golgi COPI
coat proteins. GTP-bound TC10 in vitro can bind
numerous potential effectors. Depending on its
subcellular localization and distinct functional
domains, TC10 can differentially regulate two types of
filamentous actin in adipocytes. TC10 mRNAs are highly
expressed in three types of mouse muscle tissues: leg
skeletal muscle, cardiac muscle, and uterus; they were
also present in brain, with higher levels in adults
than in newborns. TC10 has also been shown to play a
role in regulating the expression of cystic fibrosis
transmembrane conductance regulator (CFTR) through
interactions with CFTR-associated ligand (CAL). The
GTP-bound form of TC10 directs the trafficking of CFTR
from the juxtanuclear region to the secretory pathway
toward the plasma membrane, away from CAL-mediated DFTR
degradation in the lysosome. 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 = 174
Score = 30.8 bits (69), Expect = 0.031
Identities = 11/32 (34%), Positives = 22/32 (68%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTI 40
K +V+GD VGKTC++ + ++ + + Y+ T+
Sbjct: 2 KCVVVGDGAVGKTCLLMSYANDAFPEEYVPTV 33
>gnl|CDD|226003 COG3472, COG3472, Uncharacterized conserved protein [Function
unknown].
Length = 342
Score = 30.2 bits (68), Expect = 0.056
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 36 YISTIGIDFKQKIIDLDDVPTKLQIWTLNALLTYL 70
+I G KQ I+ D+ Q+ L A+ TYL
Sbjct: 74 FIEAAGFLRKQHIVKRDEFIYYEQMVPLLAIYTYL 108
>gnl|CDD|234389 TIGR03903, TOMM_kin_cyc, TOMM system kinase/cyclase fusion protein.
This model represents proteins of 1350 in length, in
multiple species of Burkholderia, in Acidovorax avenae
subsp. citrulli AAC00-1 and Delftia acidovorans SPH-1,
and in multiple copies in Sorangium cellulosum, in
genomic neighborhoods that include a
cyclodehydratase/docking scaffold fusion protein
(TIGR03882) and a member of the thiazole/oxazole
modified metabolite (TOMM) precursor family TIGR03795.
It has a kinase domain in the N-terminal 300 amino
acids, followed by a cyclase homology domain, followed
by regions without named domain definitions. It is a
probable bacteriocin-like metabolite biosynthesis
protein [Cellular processes, Toxin production and
resistance].
Length = 1266
Score = 30.2 bits (68), Expect = 0.056
Identities = 8/19 (42%), Positives = 14/19 (73%)
Query: 10 ILVLGDSNVGKTCIVHRFC 28
ILV+G++ +GK+ +VH
Sbjct: 507 ILVVGEAGIGKSRLVHELV 525
>gnl|CDD|206704 cd04132, Rho4_like, Ras homology family 4 (Rho4) of small
guanosine triphosphatases (GTPases)-like. Rho4 is a
GTPase that controls septum degradation by regulating
secretion of Eng1 or Agn1 during cytokinesis. Rho4 also
plays a role in cell morphogenesis. Rho4 regulates
septation and cell morphology by controlling the actin
cytoskeleton and cytoplasmic microtubules. The
localization of Rho4 is modulated by Rdi1, which may
function as a GDI, and by Rga9, which is believed to
function as a GAP. In S. pombe, both Rho4 deletion and
Rho4 overexpression result in a defective cell wall,
suggesting a role for Rho4 in maintaining cell wall
integrity. 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.
Length = 197
Score = 30.0 bits (68), Expect = 0.057
Identities = 11/32 (34%), Positives = 21/32 (65%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTI 40
KI+V+GD GKTC++ + ++ + Y+ T+
Sbjct: 5 KIVVVGDGGCGKTCLLMVYAQGSFPEEYVPTV 36
>gnl|CDD|133275 cd01873, RhoBTB, RhoBTB protein is an atypical member of the Rho
family of small GTPases. Members of the RhoBTB
subfamily of Rho GTPases are present in vertebrates,
Drosophila, and Dictyostelium. RhoBTB proteins are
characterized by a modular organization, consisting of
a GTPase domain, a proline rich region, a tandem of two
BTB (Broad-Complex, Tramtrack, and Bric a brac)
domains, and a C-terminal region of unknown function.
RhoBTB proteins may act as docking points for multiple
components participating in signal transduction
cascades. RhoBTB genes appeared upregulated in some
cancer cell lines, suggesting a participation of RhoBTB
proteins in the pathogenesis of particular tumors. Note
that the Dictyostelium RacA GTPase domain is more
closely related to Rac proteins than to RhoBTB
proteins, where RacA actually belongs. Thus, the
Dictyostelium RacA is not included here. Most Rho
proteins contain a lipid modification site at the
C-terminus; however, RhoBTB is one of few Rho
subfamilies that lack this feature.
Length = 195
Score = 29.9 bits (67), Expect = 0.074
Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 15/71 (21%)
Query: 6 QTYKILVLGDSNVGKT-CIVHRFCDETYYD-----TYISTI-GID--------FKQKIID 50
+T K +V+GD+ VGKT I R C++T T++ T+ ID ++
Sbjct: 1 ETIKCVVVGDNAVGKTRLICARACNKTLTQYQLLATHVPTVWAIDQYRVCQEVLERSRDV 60
Query: 51 LDDVPTKLQIW 61
+D V L++W
Sbjct: 61 VDGVSVSLRLW 71
>gnl|CDD|206737 cd04174, Rnd1_Rho6, Rnd1/Rho6 GTPases. Rnd1/Rho6 is a member of
the novel Rho subfamily Rnd, together with Rnd2/Rho7
and Rnd3/RhoE/Rho8. Rnd1/Rho6 binds GTP but does not
hydrolyze it to GDP, indicating that it is
constitutively active. In rat, Rnd1/Rho6 is highly
expressed in the cerebral cortex and hippocampus during
synapse formation, and plays a role in spine formation.
Rnd1/Rho6 is also expressed in the liver and in
endothelial cells, and is upregulated in uterine
myometrial cells during pregnancy. Like Rnd3/RhoE/Rho8,
Rnd1/Rho6 is believed to function as an antagonist to
RhoA. 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 = 232
Score = 30.0 bits (67), Expect = 0.074
Identities = 12/53 (22%), Positives = 30/53 (56%), Gaps = 1/53 (1%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
K++++GD GKT ++ + Y +TY+ T+ ++ ++ ++ +L +W
Sbjct: 15 KLVLVGDVQCGKTAMLQVLAKDCYPETYVPTVFENY-TACLETEEQRVELSLW 66
>gnl|CDD|206721 cd04155, Arl3, Arf-like 3 (Arl3) GTPase. Arl3 (Arf-like 3) is an
Arf family protein that differs from most Arf family
members in the N-terminal extension. In is inactive,
GDP-bound form, the N-terminal extension forms an
elongated loop that is hydrophobically anchored into
the membrane surface; however, it has been proposed
that this region might form a helix in the GTP-bound
form. The delta subunit of the rod-specific cyclic GMP
phosphodiesterase type 6 (PDEdelta) is an Arl3
effector. Arl3 binds microtubules in a regulated manner
to alter specific aspects of cytokinesis via
interactions with retinitis pigmentosa 2 (RP2). It has
been proposed that RP2 functions in concert with Arl3
to link the cell membrane and the cytoskeleton in
photoreceptors as part of the cell signaling or
vesicular transport machinery. In mice, the absence of
Arl3 is associated with abnormal epithelial cell
proliferation and cyst formation.
Length = 174
Score = 29.7 bits (67), Expect = 0.074
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 5 NQTYKILVLGDSNVGKTCIVHRFCDE 30
Q +IL+LG N GKT I+ + E
Sbjct: 13 RQEVRILLLGLDNAGKTTILKQLASE 38
>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 = 29.7 bits (67), Expect = 0.078
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
K +++GD VGKT ++ + Y Y+ T D ++ +D P +LQ+
Sbjct: 2 KCVLVGDGAVGKTSLIVSYTTNGYPTEYVPT-AFDNFSVVVLVDGKPVRLQLC 53
>gnl|CDD|133362 cd04162, Arl9_Arfrp2_like, Arf-like 9 (Arl9)/Arfrp2-like GTPase.
Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first
identified as part of the Human Cancer Genome Project.
It maps to chromosome 4q12 and is sometimes referred to
as Arfrp2 (Arf-related protein 2). This is a novel
subfamily identified in human cancers that is
uncharacterized to date.
Length = 164
Score = 29.7 bits (67), Expect = 0.080
Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 10 ILVLGDSNVGKTCIVHRFCDETYYDTYISTIG-----IDFKQKIIDLDDV 54
ILVLG GKT ++H E ++ + T G I + I++L ++
Sbjct: 2 ILVLGLDGAGKTSLLHSLSSERSLESVVPTTGFNSVAIPTQDAIMELLEI 51
>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 = 29.3 bits (66), Expect = 0.098
Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 8/54 (14%)
Query: 8 YKILVLGDSNVGKTC-----IVHRFCDE---TYYDTYISTIGIDFKQKIIDLDD 53
YK++V+G VGK+ I + F DE T D+Y + ID + ++D+ D
Sbjct: 2 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILD 55
>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 = 29.0 bits (65), Expect = 0.13
Identities = 15/53 (28%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
K + +GD VGKTC++ + T+ Y+ T+ +F ++ +D L +W
Sbjct: 3 KCVTVGDGAVGKTCMLISYTSNTFPTDYVPTVFDNFSANVV-VDGNTVNLGLW 54
>gnl|CDD|206706 cd04134, Rho3, Ras homology family 3 (Rho3) of small guanosine
triphosphatases (GTPases). Rho3 is a member of the Rho
family found only in fungi. Rho3 is believed to
regulate cell polarity by interacting with the
diaphanous/formin family protein For3 to control both
the actin cytoskeleton and microtubules. Rho3 is also
believed to have a direct role in exocytosis that is
independent of its role in regulating actin polarity.
The function in exocytosis may be two-pronged: first,
in the transport of post-Golgi vesicles from the mother
cell to the bud, mediated by myosin (Myo2); second, in
the docking and fusion of vesicles to the plasma
membrane, mediated by an exocyst (Exo70) protein. 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.
Length = 185
Score = 28.7 bits (64), Expect = 0.17
Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 5/55 (9%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDL--DDVPTKLQIW 61
K++VLGD GKT +++ F + Y T+ F+ I D+ D + +L +W
Sbjct: 2 KVVVLGDGACGKTSLLNVFTRGYFPQVYEPTV---FENYIHDIFVDGLAVELSLW 53
>gnl|CDD|206662 cd01870, RhoA_like, Ras homology family A (RhoA)-like includes
RhoA, RhoB and RhoC. The RhoA subfamily consists of
RhoA, RhoB, and RhoC. RhoA promotes the formation of
stress fibers and focal adhesions, regulating cell
shape, attachment, and motility. RhoA can bind to
multiple effector proteins, thereby triggering
different downstream responses. In many cell types,
RhoA mediates local assembly of the contractile ring,
which is necessary for cytokinesis. RhoA is vital for
muscle contraction; in vascular smooth muscle cells,
RhoA plays a key role in cell contraction,
differentiation, migration, and proliferation. RhoA
activities appear to be elaborately regulated in a
time- and space-dependent manner to control
cytoskeletal changes. 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. RhoA and RhoC are observed only in
geranylgeranylated forms; however, RhoB can be present
in palmitoylated, farnesylated, and geranylgeranylated
forms. RhoA and RhoC are highly relevant for tumor
progression and invasiveness; however, RhoB has
recently been suggested to be a tumor suppressor. Due
to the presence of truncated sequences in this CD, the
lipid modification site is not available for
annotation.
Length = 175
Score = 28.9 bits (65), Expect = 0.17
Identities = 14/46 (30%), Positives = 26/46 (56%), Gaps = 8/46 (17%)
Query: 9 KILVLGDSNVGKTCIVHRFCDE--------TYYDTYISTIGIDFKQ 46
K++++GD GKTC++ F + T ++ Y++ I +D KQ
Sbjct: 3 KLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQ 48
>gnl|CDD|206664 cd01874, Cdc42, cell division cycle 42 (Cdc42) is a small GTPase
of the Rho family. Cdc42 is an essential GTPase that
belongs to the Rho family of Ras-like GTPases. These
proteins act as molecular switches by responding to
exogenous and/or endogenous signals and relaying those
signals to activate downstream components of a
biological pathway. Cdc42 transduces signals to the
actin cytoskeleton to initiate and maintain polarized
growth and to mitogen-activated protein morphogenesis.
In the budding yeast Saccharomyces cerevisiae, Cdc42
plays an important role in multiple actin-dependent
morphogenetic events such as bud emergence,
mating-projection formation, and pseudohyphal growth.
In mammalian cells, Cdc42 regulates a variety of
actin-dependent events and induces the JNK/SAPK protein
kinase cascade, which leads to the activation of
transcription factors within the nucleus. Cdc42
mediates these processes through interactions with a
myriad of downstream effectors, whose number and
regulation we are just starting to understand. In
addition, Cdc42 has been implicated in a number of
human diseases through interactions with its regulators
and downstream effectors. 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 = 175
Score = 28.7 bits (64), Expect = 0.21
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 7 TYKILVLGDSNVGKTCIVHRFCDETYYDTYISTI 40
T K +V+GD VGKTC++ + + Y+ T+
Sbjct: 1 TIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTV 34
>gnl|CDD|133303 cd04103, Centaurin_gamma, Centaurin gamma (CENTG) GTPase. The
centaurins (alpha, beta, gamma, and delta) are large,
multi-domain proteins that all contain an ArfGAP domain
and ankyrin repeats, and in some cases, numerous
additional domains. Centaurin gamma contains an
additional GTPase domain near its N-terminus. The
specific function of this GTPase domain has not been
well characterized, but centaurin gamma 2 (CENTG2) may
play a role in the development of autism. Centaurin
gamma 1 is also called PIKE (phosphatidyl inositol (PI)
3-kinase enhancer) and centaurin gamma 2 is also known
as AGAP (ArfGAP protein with a GTPase-like domain,
ankyrin repeats and a Pleckstrin homology domain) or
GGAP. Three isoforms of PIKE have been identified.
PIKE-S (short) and PIKE-L (long) are brain-specific
isoforms, with PIKE-S restricted to the nucleus and
PIKE-L found in multiple cellular compartments. A third
isoform, PIKE-A was identified in human glioblastoma
brain cancers and has been found in various tissues.
GGAP has been shown to have high GTPase activity due to
a direct intramolecular interaction between the
N-terminal GTPase domain and the C-terminal ArfGAP
domain. In human tissue, AGAP mRNA was detected in
skeletal muscle, kidney, placenta, brain, heart, colon,
and lung. Reduced expression levels were also observed
in the spleen, liver, and small intestine.
Length = 158
Score = 28.2 bits (63), Expect = 0.23
Identities = 8/24 (33%), Positives = 16/24 (66%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETY 32
K+ ++G+ GK+ +VHR+ +Y
Sbjct: 2 KLGIVGNLRSGKSALVHRYLTGSY 25
>gnl|CDD|206720 cd04154, Arl2, Arf-like 2 (Arl2) GTPase. Arl2 (Arf-like 2)
GTPases are members of the Arf family that bind GDP and
GTP with very low affinity. Unlike most Arf family
proteins, Arl2 is not myristoylated at its N-terminal
helix. The protein PDE-delta, first identified in
photoreceptor rod cells, binds specifically to Arl2 and
is structurally very similar to RhoGDI. Despite the
high structural similarity between Arl2 and Rho
proteins and between PDE-delta and RhoGDI, the
interactions between the GTPases and their effectors
are very different. In its GTP bound form, Arl2
interacts with the protein Binder of Arl2 (BART), and
the complex is believed to play a role in mitochondrial
adenine nucleotide transport. In its GDP bound form,
Arl2 interacts with tubulin- folding Cofactor D; this
interaction is believed to play a role in regulation of
microtubule dynamics that impact the cytoskeleton, cell
division, and cytokinesis.
Length = 173
Score = 28.4 bits (64), Expect = 0.24
Identities = 21/53 (39%), Positives = 26/53 (49%), Gaps = 5/53 (9%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
+IL+LG N GKT I+ +F E ISTI I L+ KL IW
Sbjct: 16 RILMLGLDNAGKTTILKKFNGED-----ISTISPTLGFNIKTLEYNGYKLNIW 63
>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 = 28.1 bits (63), Expect = 0.31
Identities = 9/23 (39%), Positives = 17/23 (73%)
Query: 5 NQTYKILVLGDSNVGKTCIVHRF 27
+ YK++++G N GKT I+++F
Sbjct: 13 RKEYKVIIVGLDNAGKTTILYQF 35
>gnl|CDD|128473 smart00176, RAN, Ran (Ras-related nuclear proteins) /TC4
subfamily of small GTPases. Ran is involved in the
active transport of proteins through nuclear pores.
Length = 200
Score = 28.1 bits (62), Expect = 0.31
Identities = 12/49 (24%), Positives = 23/49 (46%)
Query: 13 LGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIW 61
+GD GKT V R + Y++T+G++ + + P + +W
Sbjct: 1 VGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIRFNVW 49
>gnl|CDD|206644 cd00878, Arf_Arl, ADP-ribosylation factor(Arf)/Arf-like (Arl)
small GTPases. Arf (ADP-ribosylation factor)/Arl
(Arf-like) small GTPases. Arf proteins are activators
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. Members of the Arf family are regulators
of vesicle formation in intracellular traffic that
interact reversibly with membranes of the secretory and
endocytic compartments in a GTP-dependent manner. They
depart from other small GTP-binding proteins by a
unique structural device, interswitch toggle, that
implements front-back communication from N-terminus to
the nucleotide binding site. Arf-like (Arl) proteins
are close relatives of the Arf, but only Arl1 has been
shown to function in membrane traffic like the Arf
proteins. Arl2 has an unrelated function in the folding
of native tubulin, and Arl4 may function in the
nucleus. Most other Arf family proteins are so far
relatively poorly characterized. Thus, despite their
significant sequence homologies, Arf family proteins
may regulate unrelated functions.
Length = 158
Score = 27.5 bits (62), Expect = 0.42
Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 5/55 (9%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIWTL 63
+IL+LG GKT I+++ T I TIG F + ++ +V K +W +
Sbjct: 1 RILMLGLDGAGKTTILYKLKLGE-VVTTIPTIG--FNVETVEYKNV--KFTVWDV 50
>gnl|CDD|206718 cd04151, Arl1, ADP ribosylation factor 1 (Arf1). Arl1 subfamily.
Arl1 (Arf-like 1) localizes to the Golgi complex, where
it is believed to recruit effector proteins to the
trans-Golgi network. Like most members of the Arf
family, Arl1 is myristoylated at its N-terminal helix
and mutation of the myristoylation site disrupts Golgi
targeting. In humans, the Golgi-localized proteins
golgin-97 and golgin-245 have been identified as Arl1
effectors. Golgins are large coiled-coil proteins found
in the Golgi, and these golgins contain a C-terminal
GRIP domain, which is the site of Arl1 binding.
Additional Arl1 effectors include the GARP
(Golgi-associated retrograde protein)/VFT (Vps53)
vesicle-tethering complex and Arfaptin 2. Arl1 is not
required for exocytosis, but appears necessary for
trafficking from the endosomes to the Golgi. In
Drosophila zygotes, mutation of Arl1 is lethal, and in
the host-bloodstream form of Trypanosoma brucei, Arl1
is essential for viability.
Length = 158
Score = 27.8 bits (62), Expect = 0.44
Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 7/56 (12%)
Query: 9 KILVLGDSNVGKTCIVHRF-CDETYYDTYISTIGIDFKQKIIDLDDVPTKLQIWTL 63
+IL+LG GKT I++R E T I TIG F + + ++ K Q+W L
Sbjct: 1 RILILGLDGAGKTTILYRLQVGEVV--TTIPTIG--FNVETVTYKNL--KFQVWDL 50
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the
AAA superfamily.
Length = 154
Score = 27.5 bits (61), Expect = 0.53
Identities = 6/23 (26%), Positives = 11/23 (47%)
Query: 10 ILVLGDSNVGKTCIVHRFCDETY 32
+L+ G S GKT ++ +
Sbjct: 27 VLLTGPSGTGKTSLLRELLEGLL 49
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 27.1 bits (60), Expect = 0.73
Identities = 16/46 (34%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDF-KQKIIDLD 52
YK++V+G VGK+ + +F + D Y TI + KQ +ID +
Sbjct: 6 YKLVVVGGGGVGKSALTIQFIQNHFIDEYDPTIEDSYRKQCVIDEE 51
>gnl|CDD|241251 cd01215, PTB_Dab, Disabled (Dab) Phosphotyrosine-binding domain.
Dab is a cystosolic adaptor protein, which binds to the
cytoplasmic tails of lipoprotein receptors, such as
ApoER2 and VLDLR, via its PTB domain. The dab PTB
domain has a preference for unphosphorylated tyrosine
within an NPxY motif. Additionally, the Dab PTB
domain, which is structurally similar to PH domains,
binds to phosphatidlyinositol phosphate 4,5
bisphosphate in a manner characteristic of
phosphoinositide binding PH domains. PTB domains have a
common PH-like fold and are found in various eukaryotic
signaling molecules. This domain was initially shown to
binds peptides with a NPXY motif with differing
requirements for phosphorylation of the tyrosine,
although more recent studies have found that some types
of PTB domains can bind to peptides lack tyrosine
residues altogether. In contrast to SH2 domains, which
recognize phosphotyrosine and adjacent carboxy-terminal
residues, PTB-domain binding specificity is conferred
by residues amino-terminal to the phosphotyrosine. PTB
domains are classified into three groups:
phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains. This
cd is part of the Dab-like subgroup.
Length = 150
Score = 26.1 bits (58), Expect = 1.3
Identities = 8/15 (53%), Positives = 12/15 (80%)
Query: 41 GIDFKQKIIDLDDVP 55
G+ FK K+I +D+VP
Sbjct: 15 GVRFKAKLIGIDEVP 29
>gnl|CDD|206702 cd04129, Rho2, Ras homology family 2 (Rho2) of small guanosine
triphosphatases (GTPases). Rho2 is a fungal GTPase
that plays a role in cell morphogenesis, control of
cell wall integrity, control of growth polarity, and
maintenance of growth direction. Rho2 activates the
protein kinase C homolog Pck2, and Pck2 controls Mok1,
the major (1-3) alpha-D-glucan synthase. Together with
Rho1 (RhoA), Rho2 regulates the construction of the
cell wall. Unlike Rho1, Rho2 is not an essential
protein, but its overexpression is lethal. Most Rho
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for proper intracellular
localization via membrane attachment. As with other Rho
family GTPases, the GDP/GTP cycling is regulated by
GEFs (guanine nucleotide exchange factors), GAPs
(GTPase-activating proteins) and GDIs (guanine
nucleotide dissociation inhibitors).
Length = 190
Score = 25.9 bits (57), Expect = 1.7
Identities = 15/55 (27%), Positives = 30/55 (54%), Gaps = 5/55 (9%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIID--LDDVPTKLQIW 61
K++++GD GKT +++ F + + Y T+ F+ + D +D P +L +W
Sbjct: 3 KLVIVGDGACGKTSLLYVFTLGEFPEEYHPTV---FENYVTDCRVDGKPVQLALW 54
>gnl|CDD|197556 smart00178, SAR, Sar1p-like members of the Ras-family of small
GTPases. Yeast SAR1 is an essential gene required for
transport of secretory proteins from the endoplasmic
reticulum to the Golgi apparatus.
Length = 184
Score = 26.1 bits (57), Expect = 1.9
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 5 NQTYKILVLGDSNVGKTCIVHRFCDE 30
N+ KIL LG N GKT ++H ++
Sbjct: 15 NKHAKILFLGLDNAGKTTLLHMLKND 40
>gnl|CDD|216241 pfam01010, Oxidored_q1_C, NADH-Ubiquinone oxidoreductase (complex
I) subunit C-terminus. This sub-family represents a
carboxyl terminal extension of pfam00361. It includes
subunit 5 from chloroplasts, and bacterial subunit L.
This sub-family is part of complex I which catalyzes the
transfer of two electrons from NADH to ubiquinone in a
reaction that is associated with proton translocation
across the membrane.
Length = 242
Score = 25.6 bits (57), Expect = 2.3
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 36 YISTIGIDFKQKIIDLD 52
++ IGI F Q+ IDLD
Sbjct: 112 FVGFIGIPFNQEGIDLD 128
>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 = 25.4 bits (56), Expect = 2.8
Identities = 7/26 (26%), Positives = 16/26 (61%)
Query: 9 KILVLGDSNVGKTCIVHRFCDETYYD 34
+I+++GD VGK+ ++ E + +
Sbjct: 4 RIVLIGDEGVGKSSLIMSLVSEEFPE 29
>gnl|CDD|217465 pfam03266, NTPase_1, NTPase. This domain is found across all
species from bacteria to human, and the function was
determined first in a hyperthermophilic bacterium to be
an NTPase. The structure of one member-sequence
represents a variation of the RecA fold, and implies
that the function might be that of a DNA/RNA modifying
enzyme. The sequence carries both a Walker A and Walker
B motif which together are characteristic of ATPases or
GTPases. The protein exhibits an increased expression
profile in human liver cholangiocarcinoma when compared
to normal tissue.
Length = 168
Score = 24.9 bits (55), Expect = 3.6
Identities = 7/22 (31%), Positives = 12/22 (54%)
Query: 9 KILVLGDSNVGKTCIVHRFCDE 30
+I + G VGKT +V + +
Sbjct: 1 RIFITGPPGVGKTTLVKKVIEL 22
>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
replication, recombination, and repair /
Posttranslational modification, protein turnover,
chaperones].
Length = 366
Score = 25.0 bits (55), Expect = 4.8
Identities = 7/21 (33%), Positives = 11/21 (52%)
Query: 10 ILVLGDSNVGKTCIVHRFCDE 30
I++ G + GKT V +E
Sbjct: 45 IIIYGPTGTGKTATVKFVMEE 65
>gnl|CDD|185524 PTZ00242, PTZ00242, protein tyrosine phosphatase; Provisional.
Length = 166
Score = 24.6 bits (54), Expect = 4.9
Identities = 16/55 (29%), Positives = 19/55 (34%), Gaps = 3/55 (5%)
Query: 3 DCNQTYKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIIDLDDVPTK 57
N I L NV T +V R C TY + GI+ D P K
Sbjct: 26 PSNLPLYIKELQRYNV--THLV-RVCGPTYDAELLEKNGIEVHDWPFDDGAPPPK 77
>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 = 24.7 bits (54), Expect = 5.0
Identities = 9/43 (20%), Positives = 25/43 (58%)
Query: 8 YKILVLGDSNVGKTCIVHRFCDETYYDTYISTIGIDFKQKIID 50
+K++++G VGK+ + +F + + + Y T +++K++
Sbjct: 1 HKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVL 43
>gnl|CDD|181459 PRK08533, PRK08533, flagellar accessory protein FlaH; Reviewed.
Length = 230
Score = 24.6 bits (54), Expect = 5.2
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 4/34 (11%)
Query: 10 ILVLGDSNVGKTCIVHR----FCDETYYDTYIST 39
IL+ GD + GK+ + R F Y +Y+ST
Sbjct: 27 ILIEGDESTGKSILSQRLAYGFLQNGYSVSYVST 60
>gnl|CDD|204242 pfam09439, SRPRB, Signal recognition particle receptor beta
subunit. The beta subunit of the signal recognition
particle receptor (SRP) is a transmembrane GTPase which
anchors the alpha subunit to the endoplasmic reticulum
membrane.
Length = 181
Score = 24.7 bits (54), Expect = 5.5
Identities = 7/29 (24%), Positives = 12/29 (41%)
Query: 10 ILVLGDSNVGKTCIVHRFCDETYYDTYIS 38
+++ G + GKT + T T S
Sbjct: 6 VIIAGLCDSGKTSLFTLLTTGTVKKTVTS 34
>gnl|CDD|224260 COG1341, COG1341, Predicted GTPase or GTP-binding protein [General
function prediction only].
Length = 398
Score = 24.7 bits (54), Expect = 5.6
Identities = 11/51 (21%), Positives = 20/51 (39%), Gaps = 12/51 (23%)
Query: 4 CNQTYKILVLGDSNVGKTCIVHRFCDETYYDTYIST--IGIDFKQKIIDLD 52
+ ++V+G + GK + TY++ + K IID D
Sbjct: 70 AGKVGVVMVVGPVDSGK----------STLTTYLANKLLARGRKVAIIDAD 110
>gnl|CDD|234565 PRK00002, aroB, 3-dehydroquinate synthase; Reviewed.
Length = 358
Score = 24.7 bits (55), Expect = 5.9
Identities = 8/20 (40%), Positives = 9/20 (45%)
Query: 55 PTKLQIWTLNALLTYLLLDK 74
PT L ALL + DK
Sbjct: 300 PTSLPDLDAEALLEAMKRDK 319
>gnl|CDD|227352 COG5019, CDC3, Septin family protein [Cell division and
chromosome partitioning / Cytoskeleton].
Length = 373
Score = 24.6 bits (54), Expect = 6.1
Identities = 15/64 (23%), Positives = 27/64 (42%), Gaps = 10/64 (15%)
Query: 7 TYKILVLGDSNVGKTCIVHRFC-----DETYYDTYI-----STIGIDFKQKIIDLDDVPT 56
+ I+V+G+S +GKT ++ DET D T+ I + ++ D
Sbjct: 23 DFTIMVVGESGLGKTTFINTLFGTSLVDETEIDDIRAEGTSPTLEIKITKAELEEDGFHL 82
Query: 57 KLQI 60
L +
Sbjct: 83 NLTV 86
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 24.6 bits (53), Expect = 6.3
Identities = 9/23 (39%), Positives = 17/23 (73%), Gaps = 1/23 (4%)
Query: 5 NQTYKILVLGDSNVGKTCIVHRF 27
N + ++++GD+ VGKT ++ RF
Sbjct: 1848 NMNWPLILVGDTGVGKTSLL-RF 1869
>gnl|CDD|179732 PRK04056, PRK04056, Maf-like protein; Reviewed.
Length = 180
Score = 24.2 bits (53), Expect = 7.9
Identities = 7/12 (58%), Positives = 10/12 (83%)
Query: 41 GIDFKQKIIDLD 52
GI+F+QK +D D
Sbjct: 19 GIEFEQKSLDFD 30
>gnl|CDD|206645 cd00879, Sar1, Sar1 is an essential component of COPII vesicle
coats. Sar1 is an essential component of COPII vesicle
coats involved in export of cargo from the ER. The
GTPase activity of Sar1 functions as a molecular switch
to control protein-protein and protein-lipid
interactions that direct vesicle budding from the ER.
Activation of the GDP to the GTP-bound form of Sar1
involves the membrane-associated guanine nucleotide
exchange factor (GEF) Sec12. Sar1 is unlike all Ras
superfamily GTPases that use either myristoyl or prenyl
groups to direct membrane association and function, in
that Sar1 lacks such modification. Instead, Sar1
contains a unique nine-amino-acid N-terminal extension.
This extension contains an evolutionarily conserved
cluster of bulky hydrophobic amino acids, referred to
as the Sar1-N-terminal activation recruitment (STAR)
motif. The STAR motif mediates the recruitment of Sar1
to ER membranes and facilitates its interaction with
mammalian Sec12 GEF leading to activation.
Length = 191
Score = 24.2 bits (53), Expect = 8.0
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 5 NQTYKILVLGDSNVGKTCIVHRFCDE 30
+ KI+ LG N GKT ++H D+
Sbjct: 17 KKEAKIVFLGLDNAGKTTLLHMLKDD 42
>gnl|CDD|226415 COG3899, COG3899, Predicted ATPase [General function prediction
only].
Length = 849
Score = 23.9 bits (52), Expect = 9.4
Identities = 7/21 (33%), Positives = 14/21 (66%)
Query: 5 NQTYKILVLGDSNVGKTCIVH 25
+ +LV G+S +GK+ +V+
Sbjct: 22 GRGEVVLVAGESGIGKSALVN 42
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
0.325 0.143 0.440
Gapped
Lambda K H
0.267 0.0585 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,736,983
Number of extensions: 282018
Number of successful extensions: 582
Number of sequences better than 10.0: 1
Number of HSP's gapped: 570
Number of HSP's successfully gapped: 126
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: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.5 bits)