RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1355
(76 letters)
>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 = 82.2 bits (204), Expect = 8e-22
Identities = 26/35 (74%), Positives = 32/35 (91%)
Query: 29 QYKLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
Q+KLVLLG+S+VGKSS+VLRFV+ +F E QESTIG
Sbjct: 1 QFKLVLLGDSSVGKSSIVLRFVKNEFSENQESTIG 35
>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 = 62.5 bits (153), Expect = 4e-14
Identities = 18/33 (54%), Positives = 24/33 (72%)
Query: 31 KLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
KLVL+G+ VGKSSL++RF + +F E TIG
Sbjct: 1 KLVLVGDGGVGKSSLLIRFTQNKFPEEYIPTIG 33
>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 = 60.2 bits (147), Expect = 3e-13
Identities = 20/34 (58%), Positives = 28/34 (82%)
Query: 30 YKLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
+K+VL+G+S VGK+SL+LRFV +F E +STIG
Sbjct: 1 FKIVLIGDSGVGKTSLLLRFVDNKFSENYKSTIG 34
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 59.1 bits (144), Expect = 9e-13
Identities = 19/34 (55%), Positives = 27/34 (79%)
Query: 30 YKLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
+K++L+G+S VGKSSL+ RF G+F E +STIG
Sbjct: 1 FKIILIGDSGVGKSSLLSRFTDGKFSEQYKSTIG 34
>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 = 55.3 bits (134), Expect = 2e-11
Identities = 20/33 (60%), Positives = 26/33 (78%)
Query: 30 YKLVLLGESAVGKSSLVLRFVRGQFHEYQESTI 62
+K+VLLGE VGK+SLVLR+V +F+E EST
Sbjct: 1 FKVVLLGEGRVGKTSLVLRYVENKFNEKHESTT 33
>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 = 54.9 bits (133), Expect = 3e-11
Identities = 18/34 (52%), Positives = 27/34 (79%)
Query: 30 YKLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
+K+VL+G+S VGKS+L+ RF R +F+ +STIG
Sbjct: 4 FKIVLIGDSGVGKSNLLSRFTRNEFNLDSKSTIG 37
>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 = 53.1 bits (128), Expect = 2e-10
Identities = 19/34 (55%), Positives = 24/34 (70%)
Query: 30 YKLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
K++L+G+S VGKSSL+LRF F E STIG
Sbjct: 1 LKILLIGDSGVGKSSLLLRFTDDTFDEDLSSTIG 34
>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 = 50.2 bits (121), Expect = 2e-09
Identities = 16/33 (48%), Positives = 24/33 (72%)
Query: 30 YKLVLLGESAVGKSSLVLRFVRGQFHEYQESTI 62
YKLV+LG VGKS+L ++F++G F + + TI
Sbjct: 1 YKLVVLGSGGVGKSALTIQFIQGHFVDDYDPTI 33
>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 = 49.9 bits (120), Expect = 3e-09
Identities = 17/33 (51%), Positives = 24/33 (72%)
Query: 30 YKLVLLGESAVGKSSLVLRFVRGQFHEYQESTI 62
YKLV+LG VGKS+L ++FV+G F + + TI
Sbjct: 3 YKLVVLGGGGVGKSALTIQFVQGHFVDEYDPTI 35
>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 = 49.4 bits (119), Expect = 4e-09
Identities = 18/32 (56%), Positives = 23/32 (71%)
Query: 31 KLVLLGESAVGKSSLVLRFVRGQFHEYQESTI 62
KLV+LG VGKS+L +RFV G+F E + TI
Sbjct: 1 KLVVLGAGGVGKSALTIRFVSGEFVEEYDPTI 32
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins
[General function prediction only].
Length = 219
Score = 48.8 bits (116), Expect = 1e-08
Identities = 15/35 (42%), Positives = 24/35 (68%)
Query: 29 QYKLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
++K+V+LG+ VGK++L+ R V +F E TIG
Sbjct: 5 EFKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIG 39
>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 = 45.7 bits (109), Expect = 9e-08
Identities = 15/34 (44%), Positives = 24/34 (70%)
Query: 30 YKLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
+KLV LG+ +VGK+S++ RF+ F ++TIG
Sbjct: 1 HKLVFLGDQSVGKTSIITRFMYDTFDNQYQATIG 34
>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 = 44.6 bits (106), Expect = 2e-07
Identities = 18/34 (52%), Positives = 24/34 (70%)
Query: 30 YKLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
+KL+L+G+S VGKS L+LRF + E STIG
Sbjct: 3 FKLLLIGDSGVGKSCLLLRFADDTYTESYISTIG 36
>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 = 44.8 bits (106), Expect = 3e-07
Identities = 17/35 (48%), Positives = 27/35 (77%)
Query: 29 QYKLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
Q++L+++G+S VGKSSL+ RF G+F E + T+G
Sbjct: 2 QFRLIVIGDSTVGKSSLLKRFTEGRFAEVSDPTVG 36
>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 = 43.8 bits (104), Expect = 6e-07
Identities = 18/34 (52%), Positives = 24/34 (70%)
Query: 30 YKLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
+KL+L+G+S VGKS L+LRF F+ STIG
Sbjct: 4 FKLLLIGDSGVGKSCLLLRFSEDSFNPSFISTIG 37
>gnl|CDD|206709 cd04137, RheB, Ras Homolog Enriched in Brain (RheB) is a small
GTPase. Rheb (Ras Homolog Enriched in Brain)
subfamily. Rheb was initially identified in rat brain,
where its expression is elevated by seizures or by
long-term potentiation. It is expressed ubiquitously,
with elevated levels in muscle and brain. Rheb
functions as an important mediator between the tuberous
sclerosis complex proteins, TSC1 and TSC2, and the
mammalian target of rapamycin (TOR) kinase to stimulate
cell growth. TOR kinase regulates cell growth by
controlling nutrient availability, growth factors, and
the energy status of the cell. TSC1 and TSC2 form a
dimeric complex that has tumor suppressor activity, and
TSC2 is a GTPase activating protein (GAP) for Rheb. The
TSC1/TSC2 complex inhibits the activation of TOR kinase
through Rheb. Rheb has also been shown to induce the
formation of large cytoplasmic vacuoles in a process
that is dependent on the GTPase cycle of Rheb, but
independent of the TOR kinase, suggesting Rheb plays a
role in endocytic trafficking that leads to cell growth
and cell-cycle progression. Most Ras proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of
most Ras proteins.
Length = 180
Score = 43.4 bits (103), Expect = 1e-06
Identities = 17/34 (50%), Positives = 22/34 (64%)
Query: 29 QYKLVLLGESAVGKSSLVLRFVRGQFHEYQESTI 62
Q K+ +LG +VGKSSL ++FV G F E TI
Sbjct: 1 QRKIAVLGSRSVGKSSLTVQFVEGHFVESYYPTI 34
>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 = 42.5 bits (100), Expect = 1e-06
Identities = 14/34 (41%), Positives = 24/34 (70%)
Query: 29 QYKLVLLGESAVGKSSLVLRFVRGQFHEYQESTI 62
+YK+V+LG VGKS++ ++F+ F +Y + TI
Sbjct: 2 EYKIVMLGAGGVGKSAVTMQFISHSFPDYHDPTI 35
>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 = 42.5 bits (100), Expect = 2e-06
Identities = 17/31 (54%), Positives = 22/31 (70%)
Query: 31 KLVLLGESAVGKSSLVLRFVRGQFHEYQEST 61
K++LLG+SAVGKS LV RF+ + Q ST
Sbjct: 2 KIILLGDSAVGKSKLVERFLMDGYEPQQLST 32
>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 = 42.0 bits (99), Expect = 2e-06
Identities = 17/34 (50%), Positives = 25/34 (73%)
Query: 30 YKLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
+K++L+G+S VGK+ +V RF G F E Q +TIG
Sbjct: 4 FKIILIGDSNVGKTCVVQRFKSGTFSERQGNTIG 37
>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 = 42.1 bits (99), Expect = 3e-06
Identities = 19/33 (57%), Positives = 23/33 (69%)
Query: 30 YKLVLLGESAVGKSSLVLRFVRGQFHEYQESTI 62
Y++V+ G VGKSSLVLRFV+G F E TI
Sbjct: 2 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTI 34
>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 = 41.7 bits (98), Expect = 3e-06
Identities = 18/34 (52%), Positives = 25/34 (73%)
Query: 29 QYKLVLLGESAVGKSSLVLRFVRGQFHEYQESTI 62
+YKLV+LG VGKS+L ++FV+G F E + TI
Sbjct: 1 EYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTI 34
>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 = 42.4 bits (100), Expect = 3e-06
Identities = 16/33 (48%), Positives = 24/33 (72%)
Query: 30 YKLVLLGESAVGKSSLVLRFVRGQFHEYQESTI 62
Y++V+LG S VGK+++V RF+ G+F E TI
Sbjct: 1 YRMVVLGASKVGKTAIVSRFLGGRFEEQYTPTI 33
>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 = 41.9 bits (99), Expect = 3e-06
Identities = 14/34 (41%), Positives = 25/34 (73%)
Query: 30 YKLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
K+++LG+S VGK+SL+ ++V +F ++TIG
Sbjct: 1 LKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIG 34
>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 = 41.5 bits (98), Expect = 5e-06
Identities = 13/34 (38%), Positives = 27/34 (79%)
Query: 30 YKLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
+K++++G+ VGK+S++ R+V G F ++ ++TIG
Sbjct: 1 FKVLVIGDLGVGKTSIIKRYVHGVFSQHYKATIG 34
>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 = 40.5 bits (95), Expect = 9e-06
Identities = 15/33 (45%), Positives = 24/33 (72%)
Query: 31 KLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
K++++G VGKSS++ RFV+G F + + TIG
Sbjct: 2 KVIVVGNGNVGKSSMIQRFVKGIFTKDYKKTIG 34
>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 = 40.5 bits (95), Expect = 1e-05
Identities = 16/34 (47%), Positives = 25/34 (73%)
Query: 30 YKLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
+K++++G+S VGK+ L RF G+F E E+TIG
Sbjct: 3 FKIIVIGDSNVGKTCLTYRFCAGRFPERTEATIG 36
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 40.3 bits (94), Expect = 2e-05
Identities = 17/34 (50%), Positives = 26/34 (76%)
Query: 30 YKLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
+K+VL+G+S VGKS+++ RF R +F +STIG
Sbjct: 13 FKIVLIGDSGVGKSNILSRFTRNEFCLESKSTIG 46
>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 = 39.9 bits (93), Expect = 2e-05
Identities = 17/34 (50%), Positives = 25/34 (73%)
Query: 29 QYKLVLLGESAVGKSSLVLRFVRGQFHEYQESTI 62
+YKLV+LG VGKS+L ++FV+G F + + TI
Sbjct: 1 EYKLVVLGSGGVGKSALTVQFVQGIFVDKYDPTI 34
>gnl|CDD|133376 cd04176, Rap2, Rap2 family GTPase consists of Rap2a, Rap2b, and
Rap2c. The Rap2 subgroup is part of the Rap subfamily
of the Ras family. It consists of Rap2a, Rap2b, and
Rap2c. Both isoform 3 of the human mitogen-activated
protein kinase kinase kinase kinase 4 (MAP4K4) and
Traf2- and Nck-interacting kinase (TNIK) are putative
effectors of Rap2 in mediating the activation of c-Jun
N-terminal kinase (JNK) to regulate the actin
cytoskeleton. In human platelets, Rap2 was shown to
interact with the cytoskeleton by binding the actin
filaments. In embryonic Xenopus development, Rap2 is
necessary for the Wnt/beta-catenin signaling pathway.
The Rap2 interacting protein 9 (RPIP9) is highly
expressed in human breast carcinomas and correlates
with a poor prognosis, suggesting a role for Rap2 in
breast cancer oncogenesis. Rap2b, but not Rap2a, Rap2c,
Rap1a, or Rap1b, is expressed in human red blood cells,
where it is believed to be involved in vesiculation. A
number of additional effector proteins for Rap2 have
been identified, including the RalGEFs RalGDS, RGL, and
Rlf, which also interact with Rap1 and Ras. Most Ras
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 163
Score = 39.8 bits (93), Expect = 2e-05
Identities = 17/34 (50%), Positives = 24/34 (70%)
Query: 29 QYKLVLLGESAVGKSSLVLRFVRGQFHEYQESTI 62
+YK+V+LG VGKS+L ++FV G F E + TI
Sbjct: 1 EYKVVVLGSGGVGKSALTVQFVSGTFIEKYDPTI 34
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 39.7 bits (93), Expect = 3e-05
Identities = 14/42 (33%), Positives = 27/42 (64%)
Query: 22 QTQAKICQYKLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
Q ++ ++KL+L+G+ VGK++ V R + G+F + T+G
Sbjct: 2 QQMDEVPEFKLILVGDGGVGKTTFVKRHLTGEFEKKYIPTLG 43
>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 = 39.2 bits (91), Expect = 3e-05
Identities = 16/34 (47%), Positives = 24/34 (70%)
Query: 30 YKLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
++L+L+G+S VGK+ L+ RF +FH STIG
Sbjct: 1 FRLLLIGDSGVGKTCLLCRFTDNEFHSSHISTIG 34
>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 = 39.1 bits (91), Expect = 3e-05
Identities = 16/35 (45%), Positives = 25/35 (71%), Gaps = 1/35 (2%)
Query: 31 KLVLLGESAVGKSSLVLRFVRGQF-HEYQESTIGG 64
K+V+LG+ +VGK+SLV R+V +F ++TIG
Sbjct: 2 KVVMLGKESVGKTSLVERYVHHRFLVGPYQNTIGA 36
>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 = 38.7 bits (90), Expect = 4e-05
Identities = 17/34 (50%), Positives = 24/34 (70%)
Query: 30 YKLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
+K+VL+G + VGK+ LV RF +G F Q +TIG
Sbjct: 8 FKIVLIGNAGVGKTCLVRRFTQGLFPPGQGATIG 41
>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 = 38.5 bits (90), Expect = 6e-05
Identities = 14/34 (41%), Positives = 22/34 (64%)
Query: 29 QYKLVLLGESAVGKSSLVLRFVRGQFHEYQESTI 62
YKLV++G VGKS+L ++F++ F + TI
Sbjct: 2 TYKLVVVGGGGVGKSALTIQFIQSYFVTDYDPTI 35
>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 = 38.2 bits (89), Expect = 7e-05
Identities = 16/34 (47%), Positives = 23/34 (67%)
Query: 29 QYKLVLLGESAVGKSSLVLRFVRGQFHEYQESTI 62
YK+V+LG VGKS+L ++FV+ F E + TI
Sbjct: 1 DYKIVVLGAGGVGKSALTVQFVQNVFIESYDPTI 34
>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 = 38.3 bits (89), Expect = 8e-05
Identities = 17/34 (50%), Positives = 24/34 (70%)
Query: 30 YKLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
+KL+++G+S VGKSSL+LRF F +TIG
Sbjct: 7 FKLLIIGDSGVGKSSLLLRFADNTFSGSYITTIG 40
>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 = 36.8 bits (86), Expect = 2e-04
Identities = 11/29 (37%), Positives = 20/29 (68%), Gaps = 1/29 (3%)
Query: 31 KLVLLGESAVGKSSLVLRFVRGQF-HEYQ 58
K+V++G+ AVGK+ L++ + +F EY
Sbjct: 2 KIVVVGDGAVGKTCLLISYTTNKFPTEYV 30
>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 = 36.4 bits (84), Expect = 3e-04
Identities = 16/33 (48%), Positives = 22/33 (66%)
Query: 31 KLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
K++LLG+ VGKSSL+ R+V +F TIG
Sbjct: 7 KVILLGDGGVGKSSLMNRYVTNKFDTQLFHTIG 39
>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 = 36.4 bits (84), Expect = 4e-04
Identities = 16/34 (47%), Positives = 25/34 (73%), Gaps = 1/34 (2%)
Query: 31 KLVLLGESAVGKSSLVLRFVRGQFHEYQESTIGG 64
K+VLLG+ VGK+SL+ R++ +F + ST+GG
Sbjct: 2 KVVLLGDMNVGKTSLLHRYMERRFKDT-VSTVGG 34
>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 = 36.4 bits (84), Expect = 4e-04
Identities = 15/32 (46%), Positives = 22/32 (68%)
Query: 31 KLVLLGESAVGKSSLVLRFVRGQFHEYQESTI 62
K+V+LG+ A GK+SL+ F RG F + E T+
Sbjct: 2 KVVVLGDGACGKTSLLNVFTRGYFPQVYEPTV 33
>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 = 36.2 bits (84), Expect = 4e-04
Identities = 13/34 (38%), Positives = 23/34 (67%)
Query: 30 YKLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
+K +++G++ VGKS L+L+F +F + TIG
Sbjct: 5 FKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIG 38
>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 = 35.1 bits (81), Expect = 5e-04
Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 4/48 (8%)
Query: 31 KLVLLGESAVGKSSLVLRFVRGQF----HEYQESTIGGCGNVPGRDRQ 74
K+V++G+ GKSSL+ + V G+F E Q T+ D
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTG 48
>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 = 35.4 bits (82), Expect = 7e-04
Identities = 14/33 (42%), Positives = 25/33 (75%)
Query: 31 KLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
K+ LLG++ +GK+SL++++V G+F E T+G
Sbjct: 2 KIGLLGDAQIGKTSLMVKYVEGEFDEEYIQTLG 34
>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 = 35.5 bits (82), Expect = 8e-04
Identities = 15/34 (44%), Positives = 23/34 (67%)
Query: 30 YKLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
K+V+LG+ A GK+SL+ RF + F + + TIG
Sbjct: 1 IKIVVLGDGASGKTSLIRRFAQEGFGKSYKQTIG 34
>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 = 35.1 bits (81), Expect = 9e-04
Identities = 13/33 (39%), Positives = 22/33 (66%)
Query: 30 YKLVLLGESAVGKSSLVLRFVRGQFHEYQESTI 62
+K++++G VGKS+L L+F+ +F E E T
Sbjct: 1 HKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTK 33
>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 = 35.1 bits (81), Expect = 0.001
Identities = 13/34 (38%), Positives = 23/34 (67%)
Query: 29 QYKLVLLGESAVGKSSLVLRFVRGQFHEYQESTI 62
+YKLV++G VGKS+L ++ ++ F + + TI
Sbjct: 1 EYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTI 34
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 35.1 bits (81), Expect = 0.001
Identities = 18/45 (40%), Positives = 27/45 (60%), Gaps = 1/45 (2%)
Query: 19 PNDQTQAKICQYKLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
PN QT +KLV++G+ GK++ V R + G+F + E TIG
Sbjct: 4 PNQQTVDYP-SFKLVIVGDGGTGKTTFVKRHLTGEFEKKYEPTIG 47
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 34.5 bits (79), Expect = 0.002
Identities = 14/34 (41%), Positives = 24/34 (70%)
Query: 29 QYKLVLLGESAVGKSSLVLRFVRGQFHEYQESTI 62
+YKLV++G VGKS+L ++F++ F + + TI
Sbjct: 5 EYKLVVVGGGGVGKSALTIQFIQNHFIDEYDPTI 38
>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 = 34.1 bits (78), Expect = 0.002
Identities = 12/25 (48%), Positives = 20/25 (80%)
Query: 30 YKLVLLGESAVGKSSLVLRFVRGQF 54
+K++L+G+S VGK+ L++RF G F
Sbjct: 1 FKVMLVGDSGVGKTCLLVRFKDGAF 25
>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 = 33.5 bits (77), Expect = 0.004
Identities = 14/23 (60%), Positives = 17/23 (73%)
Query: 30 YKLVLLGESAVGKSSLVLRFVRG 52
Y++VLLG+S VGKSSL F G
Sbjct: 1 YRVVLLGDSGVGKSSLANIFTAG 23
>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 = 33.2 bits (76), Expect = 0.005
Identities = 12/26 (46%), Positives = 19/26 (73%)
Query: 31 KLVLLGESAVGKSSLVLRFVRGQFHE 56
KLV++G+ A GK+ L++ F + QF E
Sbjct: 3 KLVIVGDGACGKTCLLIVFSKDQFPE 28
>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 = 33.2 bits (76), Expect = 0.005
Identities = 11/34 (32%), Positives = 21/34 (61%)
Query: 30 YKLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
+K +++G + GKS L+ +F+ +F + TIG
Sbjct: 1 FKFLIIGSAGTGKSCLLHQFIENKFKQDSNHTIG 34
>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 = 33.1 bits (76), Expect = 0.005
Identities = 12/26 (46%), Positives = 19/26 (73%)
Query: 31 KLVLLGESAVGKSSLVLRFVRGQFHE 56
++VL+G+ VGKSSL++ V +F E
Sbjct: 4 RIVLIGDEGVGKSSLIMSLVSEEFPE 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 = 32.9 bits (75), Expect = 0.006
Identities = 14/32 (43%), Positives = 21/32 (65%)
Query: 31 KLVLLGESAVGKSSLVLRFVRGQFHEYQESTI 62
KLV++G+ A GK+SL+ F G+F E T+
Sbjct: 3 KLVIVGDGACGKTSLLYVFTLGEFPEEYHPTV 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 = 32.7 bits (75), Expect = 0.007
Identities = 13/34 (38%), Positives = 23/34 (67%)
Query: 30 YKLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
+KLVL+G+ GK++ V R + G+F + +T+G
Sbjct: 1 FKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLG 34
>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 = 0.007
Identities = 12/32 (37%), Positives = 20/32 (62%)
Query: 31 KLVLLGESAVGKSSLVLRFVRGQFHEYQESTI 62
K+VL+G+S GK++L+ F + F E T+
Sbjct: 3 KIVLVGDSQCGKTALLQVFAKDSFPENYVPTV 34
>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 = 32.5 bits (74), Expect = 0.008
Identities = 12/33 (36%), Positives = 22/33 (66%)
Query: 31 KLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
KL+ LG+S VGK++ + R+ +F+ +T+G
Sbjct: 6 KLLALGDSGVGKTTFLYRYTDNKFNPKFITTVG 38
>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 = 32.3 bits (74), Expect = 0.009
Identities = 10/34 (29%), Positives = 21/34 (61%)
Query: 29 QYKLVLLGESAVGKSSLVLRFVRGQFHEYQESTI 62
+ K+V++G+ GK+ L++ + +G F E T+
Sbjct: 3 KVKIVVVGDGGCGKTCLLMVYAQGSFPEEYVPTV 36
>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 = 31.8 bits (72), Expect = 0.012
Identities = 13/34 (38%), Positives = 22/34 (64%)
Query: 30 YKLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
+KL+++G S+VGK+S + R+ F ST+G
Sbjct: 2 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVG 35
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 31.8 bits (72), Expect = 0.014
Identities = 13/34 (38%), Positives = 23/34 (67%)
Query: 30 YKLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
+K +++G++ VGKS L+L+F +F + TIG
Sbjct: 7 FKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIG 40
>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 = 31.5 bits (72), Expect = 0.015
Identities = 12/24 (50%), Positives = 18/24 (75%)
Query: 31 KLVLLGESAVGKSSLVLRFVRGQF 54
K+ +LG S VGKS+L +RF+ +F
Sbjct: 1 KIAVLGASGVGKSALTVRFLTKRF 24
>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 = 31.3 bits (71), Expect = 0.021
Identities = 11/32 (34%), Positives = 19/32 (59%)
Query: 31 KLVLLGESAVGKSSLVLRFVRGQFHEYQESTI 62
+LV +G + VGK++L+ RF+ F T+
Sbjct: 1 RLVFMGAAGVGKTALIQRFLYDTFEPKHRRTV 32
>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 = 31.0 bits (71), Expect = 0.022
Identities = 10/27 (37%), Positives = 18/27 (66%), Gaps = 1/27 (3%)
Query: 32 LVLLGESAVGKSSLVLRFVRGQF-HEY 57
LV++G+ AVGK+ L++ + F +Y
Sbjct: 1 LVVVGDGAVGKTCLLIVYTTNAFPEDY 27
>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 = 31.2 bits (71), Expect = 0.024
Identities = 13/33 (39%), Positives = 21/33 (63%)
Query: 31 KLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
KL+L+G+ VGK+SL + + +F + ST G
Sbjct: 3 KLMLVGQGGVGKTSLCKQLIGEKFDGDESSTHG 35
>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 = 30.6 bits (69), Expect = 0.033
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 32 LVLLGESAVGKSSLVLRFVRG 52
++L G S GK+SL+ + G
Sbjct: 27 VLLTGPSGTGKTSLLRELLEG 47
>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 = 30.5 bits (69), Expect = 0.039
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 33 VLLGESAVGKSSLVLRFVRGQF 54
V++G VGKSSL+ + G+
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEV 22
>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 = 30.4 bits (69), Expect = 0.045
Identities = 12/29 (41%), Positives = 19/29 (65%), Gaps = 1/29 (3%)
Query: 31 KLVLLGESAVGKSSLVLRFVRGQF-HEYQ 58
K VL+G+ AVGK+SL++ + + EY
Sbjct: 2 KCVLVGDGAVGKTSLIVSYTTNGYPTEYV 30
>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 = 30.2 bits (68), Expect = 0.052
Identities = 12/33 (36%), Positives = 24/33 (72%)
Query: 31 KLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
K++++G+ +VGK+ L+ RF + F + ++TIG
Sbjct: 2 KVIVVGDLSVGKTCLINRFCKDVFDKNYKATIG 34
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 30.4 bits (68), Expect = 0.053
Identities = 11/21 (52%), Positives = 19/21 (90%)
Query: 30 YKLVLLGESAVGKSSLVLRFV 50
+K++L+G+S VGKSSL++ F+
Sbjct: 15 FKILLIGDSGVGKSSLLVSFI 35
>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 = 30.0 bits (68), Expect = 0.055
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 31 KLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
K++ +G S VGKS ++ R+ G+F TIG
Sbjct: 2 KVISMGNSGVGKSCIIKRYCEGRFVSKYLPTIG 34
>gnl|CDD|206747 cd01854, YjeQ_EngC, Ribosomal interacting GTPase YjeQ/EngC, a
circularly permuted subfamily of the Ras GTPases. YjeQ
(YloQ in Bacillus subtilis) is a ribosomal small
subunit-dependent GTPase; hence also known as RsgA. YjeQ
is a late-stage ribosomal biogenesis factor involved in
the 30S subunit maturation, and it represents a protein
family whose members are broadly conserved in bacteria
and have been shown to be essential to the growth of E.
coli and B. subtilis. Proteins of the YjeQ family
contain all sequence motifs typical of the vast class of
P-loop-containing GTPases, but show a circular
permutation, with a G4-G1-G3 pattern of motifs as
opposed to the regular G1-G3-G4 pattern seen in most
GTPases. All YjeQ family proteins display a unique
domain architecture, which includes an N-terminal
OB-fold RNA-binding domain, the central permuted GTPase
domain, and a zinc knuckle-like C-terminal cysteine
domain.
Length = 211
Score = 30.1 bits (69), Expect = 0.066
Identities = 9/14 (64%), Positives = 13/14 (92%)
Query: 33 VLLGESAVGKSSLV 46
VL+G+S VGKS+L+
Sbjct: 89 VLVGQSGVGKSTLL 102
>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 = 29.8 bits (67), Expect = 0.077
Identities = 9/27 (33%), Positives = 18/27 (66%)
Query: 30 YKLVLLGESAVGKSSLVLRFVRGQFHE 56
++ +LG VGK+++V +F+ +F E
Sbjct: 1 VRVAVLGAPGVGKTAIVRQFLAQEFPE 27
>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 = 29.3 bits (66), Expect = 0.10
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 2/34 (5%)
Query: 30 YKLVLLGESAVGKSSL--VLRFVRGQFHEYQEST 61
K+V++G+ VGKS+L L + EY+ T
Sbjct: 2 IKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGT 35
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 28.8 bits (65), Expect = 0.17
Identities = 10/14 (71%), Positives = 13/14 (92%)
Query: 33 VLLGESAVGKSSLV 46
VLLG+S VGKS+L+
Sbjct: 168 VLLGQSGVGKSTLI 181
>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 = 28.7 bits (64), Expect = 0.22
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 31 KLVLLGESAVGKSSLVLRFVRGQFHEYQESTIGGC 65
KLV+LG+ VGK++L ++ F E + TI
Sbjct: 1 KLVVLGDGGVGKTALTIQLCLNHFVETYDPTIEDS 35
>gnl|CDD|226415 COG3899, COG3899, Predicted ATPase [General function prediction
only].
Length = 849
Score = 28.1 bits (63), Expect = 0.31
Identities = 11/37 (29%), Positives = 20/37 (54%), Gaps = 4/37 (10%)
Query: 24 QAKICQYKLVLL-GESAVGKSSL---VLRFVRGQFHE 56
+ + ++VL+ GES +GKS+L V + + Q
Sbjct: 18 RVSKGRGEVVLVAGESGIGKSALVNEVHKPITQQRGY 54
>gnl|CDD|217416 pfam03193, DUF258, Protein of unknown function, DUF258.
Length = 161
Score = 27.9 bits (63), Expect = 0.31
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 33 VLLGESAVGKSSLV 46
VL G+S VGKS+L+
Sbjct: 39 VLAGQSGVGKSTLL 52
>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 = 27.9 bits (62), Expect = 0.39
Identities = 14/33 (42%), Positives = 20/33 (60%)
Query: 31 KLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
K+++LG+S VGKSSLV + Q T+G
Sbjct: 2 KVLVLGDSGVGKSSLVHLLCKNQVLGNPSWTVG 34
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 27.9 bits (63), Expect = 0.40
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 31 KLVLLGESAVGKSSL 45
K+V++G VGKSSL
Sbjct: 219 KVVIIGRPNVGKSSL 233
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 27.5 bits (62), Expect = 0.49
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 33 VLLGESAVGKSSLV 46
VL G+S VGKS+L+
Sbjct: 168 VLAGQSGVGKSTLL 181
>gnl|CDD|222290 pfam13654, AAA_32, AAA domain. This family includes a wide
variety of AAA domains including some that have lost
essential nucleotide binding residues in the P-loop.
Length = 509
Score = 27.4 bits (62), Expect = 0.50
Identities = 8/22 (36%), Positives = 15/22 (68%)
Query: 30 YKLVLLGESAVGKSSLVLRFVR 51
Y + +LGE G+++LV R++
Sbjct: 31 YNIFVLGEPGTGRTTLVRRYLE 52
>gnl|CDD|182980 PRK11124, artP, arginine transporter ATP-binding subunit;
Provisional.
Length = 242
Score = 27.7 bits (62), Expect = 0.52
Identities = 11/15 (73%), Positives = 12/15 (80%)
Query: 32 LVLLGESAVGKSSLV 46
LVLLG S GKSSL+
Sbjct: 31 LVLLGPSGAGKSSLL 45
>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 = 27.5 bits (61), Expect = 0.54
Identities = 14/34 (41%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 31 KLVLLGESAVGKSSLVLRFVRGQFHEYQESTIGG 64
KL ++G GKS+LV R++ G + + ES GG
Sbjct: 2 KLGIVGNLRSGKSALVHRYLTGSYVQ-LESPEGG 34
>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 = 27.5 bits (61), Expect = 0.57
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 30 YKLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
+K +++G+ VGKS L+ +F +F TIG
Sbjct: 3 FKYIIIGDMGVGKSCLLHQFTEKKFMADCPHTIG 36
>gnl|CDD|177661 PLN00023, PLN00023, GTP-binding protein; Provisional.
Length = 334
Score = 27.5 bits (61), Expect = 0.59
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 11 GRGGRIQRPNDQTQAKIC-QYKLVLLGESAVGKSSLVLRFVRGQFHEYQESTIG 63
R + +Q C Q +++++G+S VGKSSLV V+G TIG
Sbjct: 7 ERENK-----EQNGGPPCGQVRVLVVGDSGVGKSSLVHLIVKGSSIARPPQTIG 55
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes.
TrmE contains a GTPase domain that forms a canonical
Ras-like fold. It functions a molecular switch GTPase,
and apparently uses a conformational change associated
with GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 27.1 bits (61), Expect = 0.66
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 31 KLVLLGESAVGKSSL 45
K+V+ G+ VGKSSL
Sbjct: 5 KVVIAGKPNVGKSSL 19
>gnl|CDD|221106 pfam11398, DUF2813, Protein of unknown function (DUF2813). This
entry contains YjbD from Escherichia coli, which is
annotated as a nucleotide triphosphate hydrolase.
Length = 373
Score = 26.8 bits (60), Expect = 0.83
Identities = 10/13 (76%), Positives = 12/13 (92%)
Query: 33 VLLGESAVGKSSL 45
VL+GE+A GKSSL
Sbjct: 26 VLIGENAWGKSSL 38
>gnl|CDD|218203 pfam04670, Gtr1_RagA, Gtr1/RagA G protein conserved region. GTR1
was first identified in S. cerevisiae as a suppressor
of a mutation in RCC1. Biochemical analysis revealed
that Gtr1 is in fact a G protein of the Ras family. The
RagA/B proteins are the human homologues of Gtr1.
Included in this family is the human Rag C, a novel
protein that has been shown to interact with RagA/B.
Length = 230
Score = 26.8 bits (60), Expect = 0.83
Identities = 12/39 (30%), Positives = 18/39 (46%), Gaps = 11/39 (28%)
Query: 31 KLVLLGESAVGKSSLVLRFVRGQFHEYQ-------ESTI 62
K++L+G GKSS +R + F Y +TI
Sbjct: 1 KVLLMGLRGSGKSS--MRSI--IFSNYSPRDTLRLGATI 35
>gnl|CDD|235459 PRK05428, PRK05428, HPr kinase/phosphorylase; Provisional.
Length = 308
Score = 27.1 bits (61), Expect = 0.85
Identities = 11/22 (50%), Positives = 14/22 (63%), Gaps = 2/22 (9%)
Query: 33 VLL-GESAVGKSSLVLRFV-RG 52
VL+ GES +GKS L + RG
Sbjct: 149 VLITGESGIGKSETALELIKRG 170
>gnl|CDD|234988 PRK01889, PRK01889, GTPase RsgA; Reviewed.
Length = 356
Score = 26.8 bits (60), Expect = 0.94
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 32 LVLLGESAVGKSSLV 46
+ LLG S VGKS+LV
Sbjct: 198 VALLGSSGVGKSTLV 212
>gnl|CDD|214810 smart00763, AAA_PrkA, PrkA AAA domain. This is a family of PrkA
bacterial and archaeal serine kinases approximately 630
residues long. This is the N-terminal AAA domain.
Length = 361
Score = 26.5 bits (59), Expect = 1.1
Identities = 12/26 (46%), Positives = 14/26 (53%), Gaps = 1/26 (3%)
Query: 32 LVLLGESAVGKSSLVLRFVRGQFHEY 57
L LLG GKSSLV ++ EY
Sbjct: 81 LYLLGPVGGGKSSLV-ECLKRGLEEY 105
>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 = 26.5 bits (58), Expect = 1.1
Identities = 9/29 (31%), Positives = 18/29 (62%)
Query: 35 LGESAVGKSSLVLRFVRGQFHEYQESTIG 63
+G+ GK++ V R + G+F + +T+G
Sbjct: 1 VGDGGTGKTTFVKRHLTGEFEKKYVATLG 29
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 26.4 bits (59), Expect = 1.2
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 31 KLVLLGESAVGKSSLV 46
++V +G S VGKS+LV
Sbjct: 11 EIVFVGRSNVGKSTLV 26
>gnl|CDD|219538 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This
Pfam entry includes some of the AAA proteins not
detected by the pfam00004 model.
Length = 135
Score = 26.1 bits (58), Expect = 1.5
Identities = 7/18 (38%), Positives = 10/18 (55%)
Query: 32 LVLLGESAVGKSSLVLRF 49
++L+G GKS L R
Sbjct: 2 VLLVGPPGTGKSELAERL 19
>gnl|CDD|222036 pfam13304, AAA_21, AAA domain.
Length = 256
Score = 26.3 bits (57), Expect = 1.6
Identities = 7/21 (33%), Positives = 12/21 (57%), Gaps = 2/21 (9%)
Query: 33 VLLGESAVGKSSL--VLRFVR 51
V++G + GKS+L L +
Sbjct: 3 VIIGPNGSGKSNLLKALALLL 23
>gnl|CDD|233088 TIGR00679, hpr-ser, Hpr(Ser) kinase/phosphatase. Members of this
family are the bifunctional enzyme, HPr
kinase/phosphatase. All members of the seed alignment
(n=57) have a gene tightly clustered with a gene for the
phospocarrier protein HPr, its target [Regulatory
functions, Protein interactions, Signal transduction,
PTS].
Length = 300
Score = 26.3 bits (59), Expect = 1.6
Identities = 12/22 (54%), Positives = 15/22 (68%), Gaps = 2/22 (9%)
Query: 33 VLL-GESAVGKSSLVLRFV-RG 52
VL+ GES +GKS L L + RG
Sbjct: 146 VLITGESGIGKSELALELIKRG 167
>gnl|CDD|238026 cd00071, GMPK, Guanosine monophosphate kinase (GMPK, EC 2.7.4.8),
also known as guanylate kinase (GKase), catalyzes the
reversible phosphoryl transfer from adenosine
triphosphate (ATP) to guanosine monophosphate (GMP) to
yield adenosine diphosphate (ADP) and guanosine
diphosphate (GDP). It plays an essential role in the
biosynthesis of guanosine triphosphate (GTP). This
enzyme is also important for the activation of some
antiviral and anticancer agents, such as acyclovir,
ganciclovir, carbovir, and thiopurines.
Length = 137
Score = 25.6 bits (57), Expect = 2.2
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 32 LVLLGESAVGKSSLV 46
+VL G S VGKS+L+
Sbjct: 2 IVLSGPSGVGKSTLL 16
>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 = 25.7 bits (56), Expect = 2.2
Identities = 11/32 (34%), Positives = 19/32 (59%)
Query: 31 KLVLLGESAVGKSSLVLRFVRGQFHEYQESTI 62
K V++G+ AVGK+ L++ + F E T+
Sbjct: 2 KCVVVGDGAVGKTCLLMSYANDAFPEEYVPTV 33
>gnl|CDD|226635 COG4161, ArtP, ABC-type arginine transport system, ATPase
component [Amino acid transport and metabolism].
Length = 242
Score = 25.6 bits (56), Expect = 2.3
Identities = 11/15 (73%), Positives = 12/15 (80%)
Query: 32 LVLLGESAVGKSSLV 46
LVLLG S GKSSL+
Sbjct: 31 LVLLGPSGAGKSSLL 45
>gnl|CDD|237039 PRK12288, PRK12288, GTPase RsgA; Reviewed.
Length = 347
Score = 25.6 bits (57), Expect = 2.4
Identities = 8/14 (57%), Positives = 12/14 (85%)
Query: 33 VLLGESAVGKSSLV 46
+ +G+S VGKSSL+
Sbjct: 209 IFVGQSGVGKSSLI 222
>gnl|CDD|238899 cd01918, HprK_C, HprK/P, the bifunctional histidine-containing
protein kinase/phosphatase, controls the
phosphorylation state of the phosphocarrier protein HPr
and regulates the utilization of carbon sources by
gram-positive bacteria. It catalyzes both the
ATP-dependent phosphorylation of Ser-46 of HPr and its
dephosphorylation by phosphorolysis. The latter
reaction uses inorganic phosphate as substrate and
produces pyrophosphate. Phosphoenolpyruvate
carboxykinase (PEPCK) and the C-terminal catalytic
domain of HprK/P are structurally similar with
conserved active site residues suggesting these two
phosphotransferases have related functions. The HprK/P
N-terminal domain is structurally similar to the
N-terminal domains of the MurE and MurF amino acid
ligases.
Length = 149
Score = 25.3 bits (56), Expect = 2.7
Identities = 7/20 (35%), Positives = 13/20 (65%)
Query: 32 LVLLGESAVGKSSLVLRFVR 51
+++ G S +GKS L L ++
Sbjct: 17 VLITGPSGIGKSELALELIK 36
>gnl|CDD|234173 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB. Members
of this protein family are the bacterial ATP-dependent
chaperone ClpB. This protein belongs to the AAA family,
ATPases associated with various cellular activities
(pfam00004). This molecular chaperone does not act as a
protease, but rather serves to disaggregate misfolded
and aggregated proteins [Protein fate, Protein folding
and stabilization].
Length = 852
Score = 25.7 bits (57), Expect = 2.7
Identities = 11/24 (45%), Positives = 15/24 (62%), Gaps = 4/24 (16%)
Query: 33 VLLGESAVGKSSLV----LRFVRG 52
VL+GE VGK+++V R V G
Sbjct: 198 VLIGEPGVGKTAIVEGLAQRIVNG 221
>gnl|CDD|206690 cd04104, p47_IIGP_like, p47 GTPase family includes IGTP,
TGTP/Mg21, IRG-47, GTPI, LRG-47, and IIGP1. The p47
GTPase family consists of several highly homologous
proteins, including IGTP, TGTP/Mg21, IRG-47, GTPI,
LRG-47, and IIGP1. They are found in higher eukaryotes
where they play a role in immune resistance against
intracellular pathogens. p47 proteins exist at low
resting levels in mouse cells, but are strongly induced
by Type II interferon (IFN-gamma). ITGP is critical for
resistance to Toxoplasma gondii infection and in
involved in inhibition of Coxsackievirus-B3-induced
apoptosis. TGTP was shown to limit vesicular stomatitis
virus (VSV) infection of fibroblasts in vitro. IRG-47
is involved in resistance to T. gondii infection.
LRG-47 has been implicated in resistance to T. gondii,
Listeria monocytogenes, Leishmania, and mycobacterial
infections. IIGP1 has been shown to localize to the ER
and to the Golgi membranes in IFN-induced cells and
inflamed tissues. In macrophages, IIGP1 interacts with
hook3, a microtubule binding protein that participates
in the organization of the cis-Golgi compartment.
Length = 197
Score = 25.4 bits (56), Expect = 2.8
Identities = 11/27 (40%), Positives = 15/27 (55%), Gaps = 5/27 (18%)
Query: 36 GESAVGKSSLV--LRFVRGQFHEYQES 60
GES GKSS + LR + HE + +
Sbjct: 8 GESGAGKSSFINALRGIG---HEEEGA 31
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 25.3 bits (56), Expect = 2.9
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 32 LVLLGESAVGKSSLVLRFVR 51
VL GES GK++L+ R R
Sbjct: 7 GVLTGESGSGKTTLLRRLAR 26
>gnl|CDD|234033 TIGR02857, CydD, thiol reductant ABC exporter, CydD subunit. The
gene pair cydCD encodes an ABC-family transporter in
which each gene contains an N-terminal membrane-spanning
domain (pfam00664) and a C-terminal ATP-binding domain
(pfam00005). In E. coli these genes were discovered as
mutants which caused the terminal heme-copper oxidase
complex cytochrome bd to fail to assemble. Recent work
has shown that the transporter is involved in export of
redox-active thiol compounds such as cysteine and
glutathione. The linkage to assembly of the cytochrome
bd complex is further supported by the conserved operon
structure found outside the gammaproteobacteria
(cydABCD) containing both the transporter and oxidase
genes components. The genes used as the seed members for
this model are all either found in the
gammproteobacterial context or the CydABCD context. All
members of this family scoring above trusted at the time
of its creation were from genomes which encode a
cytochrome bd complex. Unfortunately, the gene symbol
nomenclature adopted based on this operon in B. subtilis
assigns cydC to the third gene in the operon where this
gene is actually homologous to the E. coli cydD gene. We
have chosen to name all homologs in this family in
accordance with the precedence of publication of the E.
coli name, CydD.
Length = 529
Score = 25.3 bits (56), Expect = 3.3
Identities = 10/24 (41%), Positives = 15/24 (62%), Gaps = 3/24 (12%)
Query: 31 KLVLLGESAVGKSSL---VLRFVR 51
++ L+G S GKS+L +L FV
Sbjct: 350 RVALVGPSGAGKSTLLNLLLGFVD 373
>gnl|CDD|234172 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
Members of this protein family are homologs of ClpB, an
ATPase associated with chaperone-related functions.
These ClpB homologs, designated ClpV1, are a key
component of the bacterial pathogenicity-associated type
VI secretion system [Protein fate, Protein and peptide
secretion and trafficking, Cellular processes,
Pathogenesis].
Length = 852
Score = 25.3 bits (56), Expect = 3.3
Identities = 10/25 (40%), Positives = 15/25 (60%), Gaps = 4/25 (16%)
Query: 33 VLLGESAVGKSSLV----LRFVRGQ 53
+L GE+ VGK+++V LR G
Sbjct: 212 ILTGEAGVGKTAVVEGLALRIAAGD 236
>gnl|CDD|236947 PRK11650, ugpC, glycerol-3-phosphate transporter ATP-binding
subunit; Provisional.
Length = 356
Score = 25.2 bits (56), Expect = 3.4
Identities = 12/21 (57%), Positives = 15/21 (71%), Gaps = 1/21 (4%)
Query: 32 LVLLGESAVGKSSLVLRFVRG 52
+VL+G S GKS+L LR V G
Sbjct: 33 IVLVGPSGCGKSTL-LRMVAG 52
>gnl|CDD|188317 TIGR03415, ABC_choXWV_ATP, choline ABC transporter, ATP-binding
protein. Members of this protein family are the
ATP-binding subunit of a three-protein transporter.
This family belongs, more broadly, to the family of
proline and glycine-betaine transporters, but members
have been identified by direct characterization and by
bioinformatic means as choline transporters. Many
species have several closely-related members of this
family, probably with variable abilities to act
additionally on related quaternary amines [Transport
and binding proteins, Amino acids, peptides and
amines].
Length = 382
Score = 25.1 bits (55), Expect = 3.6
Identities = 12/21 (57%), Positives = 14/21 (66%), Gaps = 1/21 (4%)
Query: 32 LVLLGESAVGKSSLVLRFVRG 52
VL+G S GKS+L LR V G
Sbjct: 53 CVLMGLSGSGKSTL-LRAVNG 72
>gnl|CDD|236828 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit;
Provisional.
Length = 758
Score = 25.2 bits (55), Expect = 3.8
Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 5/35 (14%)
Query: 33 VLLGESAVGKSS----LVLRFVRGQFHE-YQESTI 62
+L+GES VGK++ L R V+G E + TI
Sbjct: 211 LLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTI 245
>gnl|CDD|224041 COG1116, TauB, ABC-type nitrate/sulfonate/bicarbonate transport
system, ATPase component [Inorganic ion transport and
metabolism].
Length = 248
Score = 25.2 bits (56), Expect = 3.9
Identities = 14/43 (32%), Positives = 19/43 (44%), Gaps = 5/43 (11%)
Query: 34 LLGESAVGKSSLVLRFVRGQFHEYQESTI---GGCGNVPGRDR 73
+LG S GKS+L LR + G + + G PG D
Sbjct: 34 ILGPSGCGKSTL-LRLIAG-LEKPTSGEVLLDGRPVTGPGPDI 74
>gnl|CDD|148849 pfam07475, Hpr_kinase_C, HPr Serine kinase C-terminal domain.
This family represents the C terminal kinase domain of
Hpr Serine/threonine kinase PtsK. This kinase is the
sensor in a multicomponent phosphorelay system in
control of carbon catabolic repression in bacteria.
This kinase in unusual in that it recognises the
tertiary structure of its target and is a member of a
novel family unrelated to any previously described
protein phosphorylating enzymes. X-ray analysis of the
full-length crystalline enzyme from Staphylococcus
xylosus at a resolution of 1.95 A shows the enzyme to
consist of two clearly separated domains that are
assembled in a hexameric structure resembling a
three-bladed propeller.
Length = 171
Score = 25.1 bits (56), Expect = 3.9
Identities = 11/22 (50%), Positives = 14/22 (63%), Gaps = 2/22 (9%)
Query: 33 VLL-GESAVGKSSLVLRFV-RG 52
VL+ GES +GKS L + RG
Sbjct: 21 VLITGESGIGKSETALELIKRG 42
>gnl|CDD|224410 COG1493, HprK, Serine kinase of the HPr protein, regulates
carbohydrate metabolism [Signal transduction
mechanisms].
Length = 308
Score = 24.9 bits (55), Expect = 4.0
Identities = 9/20 (45%), Positives = 12/20 (60%), Gaps = 1/20 (5%)
Query: 33 VLL-GESAVGKSSLVLRFVR 51
VL+ G S GKS L L ++
Sbjct: 148 VLITGPSGAGKSELALELIK 167
>gnl|CDD|237040 PRK12289, PRK12289, GTPase RsgA; Reviewed.
Length = 352
Score = 25.0 bits (55), Expect = 4.0
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 33 VLLGESAVGKSSLVLRFV 50
V+ G S VGKSSL+ R +
Sbjct: 176 VVAGPSGVGKSSLINRLI 193
>gnl|CDD|232980 TIGR00450, mnmE_trmE_thdF, tRNA modification GTPase TrmE. TrmE,
also called MnmE and previously designated ThdF
(thiophene and furan oxidation protein), is a GTPase
involved in tRNA modification to create
5-methylaminomethyl-2-thiouridine in the wobble position
of some tRNAs. This protein and GidA form an
alpha2/beta2 heterotetramer [Protein synthesis, tRNA and
rRNA base modification].
Length = 442
Score = 25.1 bits (55), Expect = 4.1
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 30 YKLVLLGESAVGKSSL 45
+KL ++G VGKSSL
Sbjct: 204 FKLAIVGSPNVGKSSL 219
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 24.9 bits (55), Expect = 4.6
Identities = 8/14 (57%), Positives = 9/14 (64%)
Query: 33 VLLGESAVGKSSLV 46
G S VGKSSL+
Sbjct: 28 AFAGRSNVGKSSLI 41
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 25.1 bits (56), Expect = 4.6
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 31 KLVLLGESAVGKSSL 45
K+V+ G VGKSSL
Sbjct: 217 KVVIAGRPNVGKSSL 231
>gnl|CDD|234719 PRK00300, gmk, guanylate kinase; Provisional.
Length = 205
Score = 24.7 bits (55), Expect = 4.7
Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 32 LVLLGESAVGKSSLVLRFVRGQFHEYQES 60
+VL G S GKS+LV + + + Q S
Sbjct: 8 IVLSGPSGAGKSTLV-KALLERDPNLQLS 35
>gnl|CDD|232848 TIGR00157, TIGR00157, ribosome small subunit-dependent GTPase A.
Members of this protein were designated YjeQ and are now
designated RsgA (ribosome small subunit-dependent GTPase
A). The strongest motif in the alignment of these
proteins is GXSGVGKS[ST], a classic P-loop for
nucleotide binding. This protein has been shown to
cleave GTP and remain bound to GDP. A role as a
regulator of translation has been suggested. The Aquifex
aeolicus ortholog is split into consecutive open reading
frames. Consequently, this model was build in fragment
mode (-f option) [Protein synthesis, Translation
factors].
Length = 245
Score = 24.7 bits (54), Expect = 4.9
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 33 VLLGESAVGKSSLVLRFVRGQ 53
V G+S VGKSSL+
Sbjct: 124 VFAGQSGVGKSSLINALDPSV 144
>gnl|CDD|206649 cd01850, CDC_Septin, CDC/Septin GTPase family. Septins are a
conserved family of GTP-binding proteins associated
with diverse processes in dividing and non-dividing
cells. They were first discovered in the budding yeast
S. cerevisiae as a set of genes (CDC3, CDC10, CDC11 and
CDC12) required for normal bud morphology. Septins are
also present in metazoan cells, where they are required
for cytokinesis in some systems, and implicated in a
variety of other processes involving organization of
the cell cortex and exocytosis. In humans, 12 septin
genes generate dozens of polypeptides, many of which
comprise heterooligomeric complexes. Since septin
mutants are commonly defective in cytokinesis and
formation of the neck formation of the neck
filaments/septin rings, septins have been considered to
be the primary constituents of the neck filaments.
Septins belong to the GTPase superfamily for their
conserved GTPase motifs and enzymatic activities.
Length = 275
Score = 24.8 bits (55), Expect = 5.2
Identities = 7/19 (36%), Positives = 15/19 (78%)
Query: 28 CQYKLVLLGESAVGKSSLV 46
Q+ ++++GES +GKS+ +
Sbjct: 3 FQFNIMVVGESGLGKSTFI 21
>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 = 24.8 bits (54), Expect = 5.2
Identities = 11/26 (42%), Positives = 18/26 (69%), Gaps = 3/26 (11%)
Query: 33 VLLGESAVGKSSLV---LRFVRGQFH 55
+++GE+ +GKS LV + VRG+ H
Sbjct: 508 LVVGEAGIGKSRLVHELVEKVRGRPH 533
>gnl|CDD|224043 COG1118, CysA, ABC-type sulfate/molybdate transport systems,
ATPase component [Inorganic ion transport and
metabolism].
Length = 345
Score = 24.6 bits (54), Expect = 5.8
Identities = 11/21 (52%), Positives = 14/21 (66%), Gaps = 1/21 (4%)
Query: 32 LVLLGESAVGKSSLVLRFVRG 52
+ LLG S GKS+L LR + G
Sbjct: 31 VALLGPSGAGKSTL-LRIIAG 50
>gnl|CDD|206748 cd01855, YqeH, Circularly permuted YqeH GTPase. YqeH is an
essential GTP-binding protein. Depletion of YqeH induces
an excess initiation of DNA replication, suggesting that
it negatively controls initiation of chromosome
replication. The YqeH subfamily is common in eukaryotes
and sporadically present in bacteria with probable
acquisition by plants from chloroplasts. Proteins of the
YqeH family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases.
Length = 191
Score = 24.5 bits (54), Expect = 6.0
Identities = 10/40 (25%), Positives = 18/40 (45%), Gaps = 3/40 (7%)
Query: 34 LLGESAVGKSSLV---LRFVRGQFHEYQESTIGGCGNVPG 70
++G + VGKS+L+ L+ G+ +PG
Sbjct: 130 VVGATNVGKSTLINALLKSNGGKVQAQALVQRLTVSPIPG 169
>gnl|CDD|226646 COG4178, COG4178, ABC-type uncharacterized transport system,
permease and ATPase components [General function
prediction only].
Length = 604
Score = 24.6 bits (54), Expect = 6.0
Identities = 8/15 (53%), Positives = 12/15 (80%)
Query: 32 LVLLGESAVGKSSLV 46
L++ GES GK+SL+
Sbjct: 422 LLITGESGAGKTSLL 436
>gnl|CDD|213268 cd03301, ABC_MalK_N, The N-terminal ATPase domain of the maltose
transporter, MalK. ATP binding cassette (ABC) proteins
function from bacteria to human, mediating the
translocation of substances into and out of cells or
organelles. ABC transporters contain two
transmembrane-spanning domains (TMDs) or subunits and
two nucleotide binding domains (NBDs) or subunits that
couple transport to the hydrolysis of ATP. In the
maltose transport system, the periplasmic maltose
binding protein (MBP) stimulates the ATPase activity of
the membrane-associated transporter, which consists of
two transmembrane subunits, MalF and MalG, and two
copies of the ATP binding subunit, MalK, and becomes
tightly bound to the transporter in the catalytic
transition state, ensuring that maltose is passed to
the transporter as ATP is hydrolyzed.
Length = 213
Score = 24.5 bits (54), Expect = 6.3
Identities = 10/21 (47%), Positives = 14/21 (66%), Gaps = 1/21 (4%)
Query: 32 LVLLGESAVGKSSLVLRFVRG 52
+VLLG S GK++ LR + G
Sbjct: 29 VVLLGPSGCGKTTT-LRMIAG 48
>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 = 24.2 bits (53), Expect = 6.4
Identities = 12/40 (30%), Positives = 24/40 (60%), Gaps = 3/40 (7%)
Query: 29 QYKLVLLGESAVGKSSLVLRFVRGQFHEYQESTIGGCGNV 68
+YK++++G GK++++ +F+ G+ TIG NV
Sbjct: 15 EYKVIIVGLDNAGKTTILYQFLLGEVVHTS-PTIG--SNV 51
>gnl|CDD|223256 COG0178, UvrA, Excinuclease ATPase subunit [DNA replication,
recombination, and repair].
Length = 935
Score = 24.5 bits (54), Expect = 7.1
Identities = 11/22 (50%), Positives = 15/22 (68%), Gaps = 1/22 (4%)
Query: 26 KICQYKLVLL-GESAVGKSSLV 46
+I + KLV++ G S GKSSL
Sbjct: 22 EIPRNKLVVITGLSGSGKSSLA 43
>gnl|CDD|206665 cd01876, YihA_EngB, YihA (EngB) GTPase family. The YihA (EngB)
subfamily of GTPases is typified by the E. coli YihA,
an essential protein involved in cell division control.
YihA and its orthologs are small proteins that
typically contain less than 200 amino acid residues and
consists of the GTPase domain only (some of the
eukaryotic homologs contain an N-terminal extension of
about 120 residues that might be involved in organellar
targeting). Homologs of yihA are found in most
Gram-positive and Gram-negative pathogenic bacteria,
with the exception of Mycobacterium tuberculosis. The
broad-spectrum nature of YihA and its essentiality for
cell viability in bacteria make it an attractive
antibacterial target.
Length = 170
Score = 24.0 bits (53), Expect = 7.4
Identities = 8/14 (57%), Positives = 9/14 (64%)
Query: 33 VLLGESAVGKSSLV 46
G S VGKSSL+
Sbjct: 3 AFAGRSNVGKSSLI 16
>gnl|CDD|213214 cd03247, ABCC_cytochrome_bd, ATP-binding cassette domain of
CydCD, subfamily C. The CYD subfamily implicated in
cytochrome bd biogenesis. The CydC and CydD proteins
are important for the formation of cytochrome bd
terminal oxidase of E. coli and it has been proposed
that they were necessary for biosynthesis of the
cytochrome bd quinol oxidase and for periplasmic c-type
cytochromes. CydCD were proposed to determine a
heterooligomeric complex important for heme export into
the periplasm or to be involved in the maintenance of
the proper redox state of the periplasmic space. In
Bacillus subtilis, the absence of CydCD does not affect
the presence of halo-cytochrome c in the membrane and
this observation suggests that CydCD proteins are not
involved in the export of heme in this organism.
Length = 178
Score = 23.8 bits (52), Expect = 9.3
Identities = 11/22 (50%), Positives = 15/22 (68%), Gaps = 1/22 (4%)
Query: 31 KLVLLGESAVGKSSLVLRFVRG 52
K+ LLG S GKS+L L+ + G
Sbjct: 30 KIALLGRSGSGKSTL-LQLLTG 50
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
0.315 0.134 0.403
Gapped
Lambda K H
0.267 0.0740 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,468,388
Number of extensions: 239488
Number of successful extensions: 455
Number of sequences better than 10.0: 1
Number of HSP's gapped: 455
Number of HSP's successfully gapped: 131
Length of query: 76
Length of database: 10,937,602
Length adjustment: 46
Effective length of query: 30
Effective length of database: 8,897,318
Effective search space: 266919540
Effective search space used: 266919540
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.2 bits)