RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15257
(65 letters)
>gnl|CDD|133275 cd01873, RhoBTB, RhoBTB protein is an atypical member of the Rho
family of small GTPases. Members of the RhoBTB
subfamily of Rho GTPases are present in vertebrates,
Drosophila, and Dictyostelium. RhoBTB proteins are
characterized by a modular organization, consisting of
a GTPase domain, a proline rich region, a tandem of two
BTB (Broad-Complex, Tramtrack, and Bric a brac)
domains, and a C-terminal region of unknown function.
RhoBTB proteins may act as docking points for multiple
components participating in signal transduction
cascades. RhoBTB genes appeared upregulated in some
cancer cell lines, suggesting a participation of RhoBTB
proteins in the pathogenesis of particular tumors. Note
that the Dictyostelium RacA GTPase domain is more
closely related to Rac proteins than to RhoBTB
proteins, where RacA actually belongs. Thus, the
Dictyostelium RacA is not included here. Most Rho
proteins contain a lipid modification site at the
C-terminus; however, RhoBTB is one of few Rho
subfamilies that lack this feature.
Length = 195
Score = 103 bits (258), Expect = 5e-30
Identities = 41/55 (74%), Positives = 47/55 (85%)
Query: 11 ELVKCVVVGDTAVGKTRLICARACNKQVSLSQLLTTHVPTVWAIDQYRIYKDTLE 65
E +KCVVVGD AVGKTRLICARACNK ++ QLL THVPTVWAIDQYR+ ++ LE
Sbjct: 1 ETIKCVVVGDNAVGKTRLICARACNKTLTQYQLLATHVPTVWAIDQYRVCQEVLE 55
>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 = 48.7 bits (117), Expect = 6e-09
Identities = 21/45 (46%), Positives = 26/45 (57%), Gaps = 8/45 (17%)
Query: 13 VKCVVVGDTAVGKTRLICARACNKQVSLSQLLTTHVPTVWAIDQY 57
+K VVVGD AVGKT L+ + NK T +VPTV+ D Y
Sbjct: 1 IKIVVVGDGAVGKTCLLISYTTNK------FPTEYVPTVF--DNY 37
>gnl|CDD|206664 cd01874, Cdc42, cell division cycle 42 (Cdc42) is a small GTPase
of the Rho family. Cdc42 is an essential GTPase that
belongs to the Rho family of Ras-like GTPases. These
proteins act as molecular switches by responding to
exogenous and/or endogenous signals and relaying those
signals to activate downstream components of a
biological pathway. Cdc42 transduces signals to the
actin cytoskeleton to initiate and maintain polarized
growth and to mitogen-activated protein morphogenesis.
In the budding yeast Saccharomyces cerevisiae, Cdc42
plays an important role in multiple actin-dependent
morphogenetic events such as bud emergence,
mating-projection formation, and pseudohyphal growth.
In mammalian cells, Cdc42 regulates a variety of
actin-dependent events and induces the JNK/SAPK protein
kinase cascade, which leads to the activation of
transcription factors within the nucleus. Cdc42
mediates these processes through interactions with a
myriad of downstream effectors, whose number and
regulation we are just starting to understand. In
addition, Cdc42 has been implicated in a number of
human diseases through interactions with its regulators
and downstream effectors. Most Rho proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of
most Rho proteins. Due to the presence of truncated
sequences in this CD, the lipid modification site is
not available for annotation.
Length = 175
Score = 36.4 bits (84), Expect = 2e-04
Identities = 22/47 (46%), Positives = 28/47 (59%), Gaps = 8/47 (17%)
Query: 13 VKCVVVGDTAVGKTRLICARACNKQVSLSQLLTTHVPTVWAIDQYRI 59
+KCVVVGD AVGKT L+ + NK S +VPTV+ D Y +
Sbjct: 2 IKCVVVGDGAVGKTCLLISYTTNKFPS------EYVPTVF--DNYAV 40
>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 = 35.5 bits (82), Expect = 5e-04
Identities = 20/45 (44%), Positives = 25/45 (55%), Gaps = 8/45 (17%)
Query: 13 VKCVVVGDTAVGKTRLICARACNKQVSLSQLLTTHVPTVWAIDQY 57
+KCV+VGD AVGKT LI + N T +VPT A D +
Sbjct: 1 LKCVLVGDGAVGKTSLIVSYTTNG------YPTEYVPT--AFDNF 37
>gnl|CDD|206705 cd04133, Rop_like, Rho-related protein from plants (Rop)-like.
The Rop (Rho-related protein from plants) subfamily
plays a role in diverse cellular processes, including
cytoskeletal organization, pollen and vegetative cell
growth, hormone responses, stress responses, and
pathogen resistance. Rops are able to regulate several
downstream pathways to amplify a specific signal by
acting as master switches early in the signaling
cascade. They transmit a variety of extracellular and
intracellular signals. Rops are involved in
establishing cell polarity in root-hair development,
root-hair elongation, pollen-tube growth, cell-shape
formation, responses to hormones such as abscisic acid
(ABA) and auxin, responses to abiotic stresses such as
oxygen deprivation, and disease resistance and disease
susceptibility. An individual Rop can have a unique
function or an overlapping function shared with other
Rop proteins; in addition, a given Rop-regulated
function can be controlled by one or multiple Rop
proteins. For example, Rop1, Rop3, and Rop5 are all
involved in pollen-tube growth; Rop2 plays a role in
response to low-oxygen environments, cell-morphology,
and root-hair development; root-hair development is
also regulated by Rop4 and Rop6; Rop6 is also
responsible for ABA response, and ABA response is also
regulated by Rop10. Plants retain some of the
regulatory mechanisms that are shared by other members
of the Rho family, but have also developed a number of
unique modes for regulating Rops. Unique RhoGEFs have
been identified that are exclusively active toward Rop
proteins, such as those containing the domain PRONE
(plant-specific Rop nucleotide exchanger). Most Rho
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 173
Score = 34.1 bits (78), Expect = 0.001
Identities = 17/40 (42%), Positives = 21/40 (52%), Gaps = 6/40 (15%)
Query: 13 VKCVVVGDTAVGKTRLICARACNKQVSLSQLLTTHVPTVW 52
+KCV VGD AVGKT C + T +VPTV+
Sbjct: 2 IKCVTVGDGAVGKT---CMLISYTSNTFP---TDYVPTVF 35
>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 = 33.2 bits (77), Expect = 0.003
Identities = 13/36 (36%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 13 VKCVVVGDTAVGKTRLICARACNKQVSLSQLLTTHV 48
K V++GD+ VGKT L+ R + + S + T V
Sbjct: 1 FKIVLIGDSGVGKTSLLL-RFVDNKFSENYKSTIGV 35
>gnl|CDD|206663 cd01871, Rac1_like, Ras-related C3 botulinum toxin substrate 1
(rho family, small GTP binding protein Rac1)-like
consists of Rac1, Rac2 and Rac3. The Rac1-like
subfamily consists of Rac1, Rac2, and Rac3 proteins,
plus the splice variant Rac1b that contains a
19-residue insertion near switch II relative to Rac1.
While Rac1 is ubiquitously expressed, Rac2 and Rac3 are
largely restricted to hematopoietic and neural tissues
respectively. Rac1 stimulates the formation of actin
lamellipodia and membrane ruffles. It also plays a role
in cell-matrix adhesion and cell anoikis. In intestinal
epithelial cells, Rac1 is an important regulator of
migration and mediates apoptosis. Rac1 is also
essential for RhoA-regulated actin stress fiber and
focal adhesion complex formation. In leukocytes, Rac1
and Rac2 have distinct roles in regulating cell
morphology, migration, and invasion, but are not
essential for macrophage migration or chemotaxis. Rac3
has biochemical properties that are closely related to
Rac1, such as effector interaction, nucleotide binding,
and hydrolysis; Rac2 has a slower nucleotide
association and is more efficiently activated by the
RacGEF Tiam1. Both Rac1 and Rac3 have been implicated
in the regulation of cell migration and invasion in
human metastatic breast cancer. Most Rho proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 174
Score = 33.2 bits (76), Expect = 0.003
Identities = 14/23 (60%), Positives = 17/23 (73%)
Query: 13 VKCVVVGDTAVGKTRLICARACN 35
+KCVVVGD AVGKT L+ + N
Sbjct: 2 IKCVVVGDGAVGKTCLLISYTTN 24
>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 = 31.3 bits (72), Expect = 0.013
Identities = 13/45 (28%), Positives = 24/45 (53%), Gaps = 7/45 (15%)
Query: 14 KCVVVGDTAVGKTRLICARACNKQVSLSQLLTTHVPTVWAIDQYR 58
K V+VGD VGK+ L+ + + ++ ++PT+ +D Y
Sbjct: 1 KLVLVGDGGVGKSSLLI------RFTQNKFPEEYIPTI-GVDFYT 38
>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 = 31.4 bits (72), Expect = 0.013
Identities = 16/37 (43%), Positives = 18/37 (48%), Gaps = 6/37 (16%)
Query: 15 CVVVGDTAVGKTRLICARACNKQVSLSQLLTTHVPTV 51
VVVGD AVGKT L+ N +VPTV
Sbjct: 1 LVVVGDGAVGKTCLLIVYTTNA------FPEDYVPTV 31
>gnl|CDD|133277 cd01875, RhoG, Ras homolog family, member G (RhoG) of small
guanosine triphosphatases (GTPases). RhoG is a GTPase
with high sequence similarity to members of the Rac
subfamily, including the regions involved in effector
recognition and binding. However, RhoG does not bind to
known Rac1 and Cdc42 effectors, including proteins
containing a Cdc42/Rac interacting binding (CRIB)
motif. Instead, RhoG interacts directly with Elmo, an
upstream regulator of Rac1, in a GTP-dependent manner
and forms a ternary complex with Dock180 to induce
activation of Rac1. The RhoG-Elmo-Dock180 pathway is
required for activation of Rac1 and cell spreading
mediated by integrin, as well as for neurite outgrowth
induced by nerve growth factor. Thus RhoG activates
Rac1 through Elmo and Dock180 to control cell
morphology. RhoG has also been shown to play a role in
caveolar trafficking and has a novel role in signaling
the neutrophil respiratory burst stimulated by G
protein-coupled receptor (GPCR) agonists. Most Rho
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins.
Length = 191
Score = 31.1 bits (70), Expect = 0.021
Identities = 14/23 (60%), Positives = 16/23 (69%)
Query: 13 VKCVVVGDTAVGKTRLICARACN 35
+KCVVVGD AVGKT L+ N
Sbjct: 4 IKCVVVGDGAVGKTCLLICYTTN 26
>gnl|CDD|206707 cd04135, Tc10, Rho GTPase TC10 (Tc10). TC10 is a Rho family
protein that has been shown to induce microspike
formation and neurite outgrowth in vitro. Its
expression changes dramatically after peripheral nerve
injury, suggesting an important role in promoting
axonal outgrowth and regeneration. TC10 regulates
translocation of insulin-stimulated GLUT4 in adipocytes
and has also been shown to bind directly to Golgi COPI
coat proteins. GTP-bound TC10 in vitro can bind
numerous potential effectors. Depending on its
subcellular localization and distinct functional
domains, TC10 can differentially regulate two types of
filamentous actin in adipocytes. TC10 mRNAs are highly
expressed in three types of mouse muscle tissues: leg
skeletal muscle, cardiac muscle, and uterus; they were
also present in brain, with higher levels in adults
than in newborns. TC10 has also been shown to play a
role in regulating the expression of cystic fibrosis
transmembrane conductance regulator (CFTR) through
interactions with CFTR-associated ligand (CAL). The
GTP-bound form of TC10 directs the trafficking of CFTR
from the juxtanuclear region to the secretory pathway
toward the plasma membrane, away from CAL-mediated DFTR
degradation in the lysosome. Most Rho proteins contain
a lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of
most Rho proteins. Due to the presence of truncated
sequences in this CD, the lipid modification site is
not available for annotation.
Length = 174
Score = 30.4 bits (68), Expect = 0.036
Identities = 20/47 (42%), Positives = 27/47 (57%), Gaps = 8/47 (17%)
Query: 13 VKCVVVGDTAVGKTRLICARACNKQVSLSQLLTTHVPTVWAIDQYRI 59
+KCVVVGD AVGKT L+ + A + +VPTV+ D Y +
Sbjct: 1 LKCVVVGDGAVGKTCLLMSYANDA------FPEEYVPTVF--DHYAV 39
>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 = 29.3 bits (66), Expect = 0.062
Identities = 17/53 (32%), Positives = 22/53 (41%), Gaps = 12/53 (22%)
Query: 14 KCVVVGDTAVGKTRLICARACNKQVSLSQLLT-THVPTVWAIDQYRIYKDTLE 65
K VV+GD GK+ L+ SQL+ P I + DTLE
Sbjct: 1 KVVVIGDKGSGKSSLL-----------SQLVGGEFPPEPLEIQGDTLAVDTLE 42
>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 = 29.4 bits (66), Expect = 0.074
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 6/39 (15%)
Query: 14 KCVVVGDTAVGKTRLICARACNKQVSLSQLLTTHVPTVW 52
K V+VGD A GKT L+ L + + PTV+
Sbjct: 3 KLVIVGDGACGKTSLLYVFT------LGEFPEEYHPTVF 35
>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 = 29.1 bits (66), Expect = 0.087
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 12 LVKCVVVGDTAVGKTRL 28
L K V++GD+ VGK+ L
Sbjct: 3 LFKIVLIGDSGVGKSNL 19
>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 = 29.2 bits (66), Expect = 0.092
Identities = 11/17 (64%), Positives = 12/17 (70%)
Query: 13 VKCVVVGDTAVGKTRLI 29
VK VVVGD GKT L+
Sbjct: 4 VKIVVVGDGGCGKTCLL 20
>gnl|CDD|206688 cd04101, RabL4, Rab GTPase-like family 4 (Rab-like4). RabL4
(Rab-like4) subfamily. RabL4s are novel proteins that
have high sequence similarity with Rab family members,
but display features that are distinct from Rabs, and
have been termed Rab-like. As in other Rab-like
proteins, RabL4 lacks a prenylation site at the
C-terminus. The specific function of RabL4 remains
unknown.
Length = 167
Score = 27.9 bits (62), Expect = 0.26
Identities = 10/16 (62%), Positives = 13/16 (81%)
Query: 14 KCVVVGDTAVGKTRLI 29
+C VVGD AVGK+ L+
Sbjct: 2 QCAVVGDPAVGKSALV 17
>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 = 27.8 bits (62), Expect = 0.32
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 13/53 (24%)
Query: 14 KCVVVGDTAVGKTRLICARACNKQVSLSQLLTTHVPTVW-------AIDQYRI 59
K V+VGD+ GKT L+ A + +VPTV+ +D+ RI
Sbjct: 3 KIVLVGDSQCGKTALLQVFAKD------SFPENYVPTVFENYTASFEVDKQRI 49
>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 = 27.5 bits (61), Expect = 0.32
Identities = 11/17 (64%), Positives = 13/17 (76%)
Query: 13 VKCVVVGDTAVGKTRLI 29
+K VV+GD A GKT LI
Sbjct: 1 IKIVVLGDGASGKTSLI 17
>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 = 27.3 bits (61), Expect = 0.37
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 14 KCVVVGDTAVGKTRLI 29
K +V+GD VGKT +I
Sbjct: 2 KVLVIGDLGVGKTSII 17
>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 = 27.1 bits (60), Expect = 0.43
Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 8/45 (17%)
Query: 14 KCVVVGDTAVGKTRLICARACNKQVSLSQLLTTHVPTVWAIDQYR 58
K VV+GD VGKT L Q+ L+ + T+ PT+ D YR
Sbjct: 1 KLVVLGDGGVGKTALTI------QLCLNHFVETYDPTIE--DSYR 37
>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 = 27.2 bits (61), Expect = 0.48
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 14 KCVVVGDTAVGKTRLI 29
K V +GD +VGKT +I
Sbjct: 2 KLVFLGDQSVGKTSII 17
>gnl|CDD|236982 PRK11784, PRK11784, tRNA 2-selenouridine synthase; Provisional.
Length = 345
Score = 27.1 bits (61), Expect = 0.56
Identities = 12/37 (32%), Positives = 16/37 (43%), Gaps = 2/37 (5%)
Query: 4 DNEQPHQELVKCVVVGDTAVGKTRLICARACNKQVSL 40
+ LV V+ G+T GKT L+ A A L
Sbjct: 135 EEAPAQFPLV--VLGGNTGSGKTELLQALANAGAQVL 169
>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 = 27.0 bits (60), Expect = 0.57
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 9 HQELVKCVVVGDTAVGKTRLI 29
+ L K +++GDT VGK+ L+
Sbjct: 1 YAYLFKYIIIGDTGVGKSCLL 21
>gnl|CDD|177661 PLN00023, PLN00023, GTP-binding protein; Provisional.
Length = 334
Score = 27.1 bits (60), Expect = 0.57
Identities = 9/17 (52%), Positives = 14/17 (82%)
Query: 13 VKCVVVGDTAVGKTRLI 29
V+ +VVGD+ VGK+ L+
Sbjct: 22 VRVLVVGDSGVGKSSLV 38
>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 = 26.6 bits (59), Expect = 0.61
Identities = 8/17 (47%), Positives = 13/17 (76%)
Query: 13 VKCVVVGDTAVGKTRLI 29
+K +VVG+ VGK+ +I
Sbjct: 1 IKVIVVGNGNVGKSSMI 17
>gnl|CDD|234626 PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate
transferase; Reviewed.
Length = 307
Score = 27.0 bits (61), Expect = 0.61
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 16 VVVGDTAVGKTRL 28
V+VG TA GKT L
Sbjct: 8 VIVGPTASGKTAL 20
>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 = 26.9 bits (60), Expect = 0.64
Identities = 8/17 (47%), Positives = 10/17 (58%)
Query: 13 VKCVVVGDTAVGKTRLI 29
K ++VG VGKT L
Sbjct: 2 AKLMLVGQGGVGKTSLC 18
>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 = 26.8 bits (59), Expect = 0.67
Identities = 9/17 (52%), Positives = 14/17 (82%)
Query: 13 VKCVVVGDTAVGKTRLI 29
VK +V+GD+ VGK+ L+
Sbjct: 1 VKVLVLGDSGVGKSSLV 17
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 26.3 bits (59), Expect = 0.82
Identities = 10/33 (30%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 13 VKCVVVGDTAVGKTRLICARACNKQVSLSQLLT 45
K +++GD+ VGK+ L+ R + + S T
Sbjct: 1 FKIILIGDSGVGKSSLLS-RFTDGKFSEQYKST 32
>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 = 26.1 bits (58), Expect = 1.2
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 13 VKCVVVGDTAVGKTRLICA 31
V+ V++GD VGK+ LI +
Sbjct: 3 VRIVLIGDEGVGKSSLIMS 21
>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 = 25.9 bits (57), Expect = 1.2
Identities = 16/39 (41%), Positives = 20/39 (51%), Gaps = 6/39 (15%)
Query: 14 KCVVVGDTAVGKTRLICARACNKQVSLSQLLTTHVPTVW 52
K V+VGD A GKT L+ S Q +VPTV+
Sbjct: 3 KLVIVGDGACGKTCLLIV------FSKDQFPEVYVPTVF 35
>gnl|CDD|234344 TIGR03754, conj_TOL_TraD, conjugative coupling factor TraD, TOL
family. Members of this protein are assigned by
homology to the TraD family of conjugative coupling
factor. This particular clade serves as a marker for an
extended gene region that occurs occasionally on
plasmids, including the toluene catabolism TOL plasmid.
More commonly, the gene region is chromosomal, flanked
by various markers of conjugative transfer and
insertion.
Length = 643
Score = 26.2 bits (58), Expect = 1.2
Identities = 9/12 (75%), Positives = 10/12 (83%)
Query: 17 VVGDTAVGKTRL 28
V+G T VGKTRL
Sbjct: 185 VLGTTRVGKTRL 196
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins
[General function prediction only].
Length = 219
Score = 26.1 bits (57), Expect = 1.3
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 10 QELVKCVVVGDTAVGKTRLI 29
+ K VV+GD VGKT L+
Sbjct: 3 MKEFKIVVLGDGGVGKTTLL 22
>gnl|CDD|183703 PRK12724, PRK12724, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 432
Score = 26.1 bits (57), Expect = 1.3
Identities = 20/53 (37%), Positives = 24/53 (45%), Gaps = 9/53 (16%)
Query: 18 VGDTAVGKTRLICARACN------KQVSLSQLLTTHVPTVWAIDQYRIYKDTL 64
VG T GKT I A K VSL TT + AI+Q + Y DT+
Sbjct: 229 VGPTGSGKTTSIAKLAAKYFLHMGKSVSL---YTTDNYRIAAIEQLKRYADTM 278
>gnl|CDD|177443 PHA02653, PHA02653, RNA helicase NPH-II; Provisional.
Length = 675
Score = 26.1 bits (58), Expect = 1.4
Identities = 7/12 (58%), Positives = 8/12 (66%)
Query: 15 CVVVGDTAVGKT 26
V+ G T VGKT
Sbjct: 182 VVLTGGTGVGKT 193
>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 = 25.8 bits (57), Expect = 1.5
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 13 VKCVVVGDTAVGKTRLI 29
+K V+VGD VGK+ L+
Sbjct: 2 IKIVIVGDPNVGKSTLL 18
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 26.1 bits (57), Expect = 1.5
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 15 CVVVGDTAVGKTRLI 29
++VGDT VGKT L+
Sbjct: 1853 LILVGDTGVGKTSLL 1867
>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 = 25.6 bits (56), Expect = 1.6
Identities = 9/17 (52%), Positives = 16/17 (94%)
Query: 13 VKCVVVGDTAVGKTRLI 29
VK +++GD+AVGK++L+
Sbjct: 1 VKIILLGDSAVGKSKLV 17
>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 = 25.6 bits (57), Expect = 1.6
Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 13 VKCVVVGDTAVGKTRLICARACNKQVSLSQLLTTH 47
K V++G+ VGKT L+ R + + TT
Sbjct: 1 FKVVLLGEGRVGKTSLV-LRYVENKFNEKHESTTQ 34
>gnl|CDD|236020 PRK07449, PRK07449,
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-
carboxylate synthase; Validated.
Length = 568
Score = 25.5 bits (57), Expect = 1.8
Identities = 11/54 (20%), Positives = 17/54 (31%), Gaps = 16/54 (29%)
Query: 5 NEQPHQELVKC---VVVGDTAVGKTRLICARACNKQVSLSQLLTTHVPTVWAID 55
N + +EL++ + G K L Q L P W +D
Sbjct: 277 NPKAAEELLQPDIVIQFGSPPTSK-------------RLLQWLADCEPEYWVVD 317
>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 = 25.5 bits (56), Expect = 1.9
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 14 KCVVVGDTAVGKTRL 28
K +V+GD+ VGKT L
Sbjct: 4 KIIVIGDSNVGKTCL 18
>gnl|CDD|237802 PRK14723, flhF, flagellar biosynthesis regulator FlhF; Provisional.
Length = 767
Score = 25.5 bits (56), Expect = 1.9
Identities = 21/55 (38%), Positives = 27/55 (49%), Gaps = 12/55 (21%)
Query: 18 VGDTAVGKT--------RLICARACNKQVSLSQLLTTHVPTVWAIDQYRIYKDTL 64
VG T VGKT R + AR Q++L LTT + A++Q RIY L
Sbjct: 191 VGPTGVGKTTTTAKLAARCV-AREGADQLAL---LTTDSFRIGALEQLRIYGRIL 241
>gnl|CDD|234339 TIGR03743, SXT_TraD, conjugative coupling factor TraD, SXT/TOL
subfamily. Members of this protein family are the
putative conjugative coupling factor, TraD (or TraG),
rather distantly related to the well-characterized TraD
of the F plasmid. Members are associated with
conjugative-transposon-like mobile genetic elements of
the class that includes SXT, an antibiotic resistance
transfer element in some Vibrio cholerae strains [Mobile
and extrachromosomal element functions, Other].
Length = 634
Score = 25.3 bits (56), Expect = 2.1
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 15 CVVVGDTAVGKTRL 28
+V+G T VGKTRL
Sbjct: 179 TLVLGTTGVGKTRL 192
>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 = 25.2 bits (55), Expect = 2.3
Identities = 7/28 (25%), Positives = 11/28 (39%), Gaps = 2/28 (7%)
Query: 2 LSDNEQPHQELVKCVVVGDTAVGKTRLI 29
L V ++ G + GKT L+
Sbjct: 16 LRRARSGGPPSV--LLTGPSGTGKTSLL 41
>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 = 25.3 bits (55), Expect = 2.6
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 13 VKCVVVGDTAVGKTRLI 29
+K V++GD VGKT L+
Sbjct: 1 LKVVLLGDMNVGKTSLL 17
>gnl|CDD|234401 TIGR03925, T7SS_EccC_b, type VII secretion protein EccCb. This
model represents the C-terminal domain or EccCb subunit
of the type VII secretion protein EccC as found in the
Actinobacteria. Type VII secretion is defined more
broadly as including secretion systems for ESAT-6-like
proteins in the Firmicutes as well as in the
Actinobacteria, but this family does not show close
homologs in the Firmicutes [Protein fate, Protein and
peptide secretion and trafficking].
Length = 566
Score = 25.3 bits (56), Expect = 2.6
Identities = 11/33 (33%), Positives = 13/33 (39%), Gaps = 8/33 (24%)
Query: 6 EQPHQELVKCVVVGDTAVGKT---RLICARACN 35
E PH +V GD+ GKT R I
Sbjct: 362 ESPH-----LLVFGDSESGKTTLLRAIARGITR 389
>gnl|CDD|206737 cd04174, Rnd1_Rho6, Rnd1/Rho6 GTPases. Rnd1/Rho6 is a member of
the novel Rho subfamily Rnd, together with Rnd2/Rho7
and Rnd3/RhoE/Rho8. Rnd1/Rho6 binds GTP but does not
hydrolyze it to GDP, indicating that it is
constitutively active. In rat, Rnd1/Rho6 is highly
expressed in the cerebral cortex and hippocampus during
synapse formation, and plays a role in spine formation.
Rnd1/Rho6 is also expressed in the liver and in
endothelial cells, and is upregulated in uterine
myometrial cells during pregnancy. Like Rnd3/RhoE/Rho8,
Rnd1/Rho6 is believed to function as an antagonist to
RhoA. Most Rho proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Rho proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for
annotation.
Length = 232
Score = 25.0 bits (54), Expect = 2.7
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 10/50 (20%)
Query: 5 NEQPHQELVKCVVVGDTAVGKTRL--ICARACNKQVSLSQLLTTHVPTVW 52
N QP K V+VGD GKT + + A+ C + T+VPTV+
Sbjct: 6 NPQPLVVRCKLVLVGDVQCGKTAMLQVLAKDCYPE--------TYVPTVF 47
>gnl|CDD|206736 cd04173, Rnd2_Rho7, Rnd2/Rho7 GTPases. Rnd2/Rho7 is a member of
the novel Rho subfamily Rnd, together with Rnd1/Rho6
and Rnd3/RhoE/Rho8. Rnd2/Rho7 is transiently expressed
in radially migrating cells in the brain while they are
within the subventricular zone of the hippocampus and
cerebral cortex. These migrating cells typically
develop into pyramidal neurons. Cells that exogenously
expressed Rnd2/Rho7 failed to migrate to upper layers
of the brain, suggesting that Rnd2/Rho7 plays a role in
the radial migration and morphological changes of
developing pyramidal neurons, and that Rnd2/Rho7
degradation is necessary for proper cellular migration.
The Rnd2/Rho7 GEF Rapostlin is found primarily in the
brain and together with Rnd2/Rho7 induces dendrite
branching. Unlike Rnd1/Rho6 and Rnd3/RhoE/Rho8, which
are RhoA antagonists, Rnd2/Rho7 binds the GEF Pragmin
and significantly stimulates RhoA activity and Rho-A
mediated cell contraction. Rnd2/Rho7 is also found to
be expressed in spermatocytes and early spermatids,
with male-germ-cell Rac GTPase-activating protein
(MgcRacGAP), where it localizes to the Golgi-derived
pro-acrosomal vesicle. Most Rho proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of
most Rho proteins.
Length = 221
Score = 25.0 bits (54), Expect = 3.3
Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 17/55 (30%)
Query: 14 KCVVVGDTAVGKTRL--ICARACNKQVSLSQLLTTHVPTV-------WAIDQYRI 59
K VVVGDT GKT L + A+ + ++VPTV + ID++RI
Sbjct: 3 KIVVVGDTQCGKTALLHVFAKDNYPE--------SYVPTVFENYTASFEIDKHRI 49
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 24.7 bits (54), Expect = 3.3
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 14 KCVVVGDTAVGKTRLI 29
K ++VGD VGKT +
Sbjct: 11 KLILVGDGGVGKTTFV 26
>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 = 24.6 bits (54), Expect = 3.6
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 14 KCVVVGDTAVGKTRLI 29
K V+VGD GKT +
Sbjct: 2 KLVLVGDGGTGKTTFV 17
>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 = 24.7 bits (54), Expect = 4.0
Identities = 14/51 (27%), Positives = 18/51 (35%), Gaps = 6/51 (11%)
Query: 16 VVVGDTAVGKTRLICARA-CNKQVSLSQLLTTHVPTVWAIDQYRIYKDTLE 65
VVVG VGK+ L+ A +V T D Y D +
Sbjct: 1 VVVGRGGVGKSSLL--NALLGGEVGEV--SDVPGTTRD-PDVYVKELDKGK 46
>gnl|CDD|223401 COG0324, MiaA, tRNA delta(2)-isopentenylpyrophosphate transferase
[Translation, ribosomal structure and biogenesis].
Length = 308
Score = 24.5 bits (54), Expect = 4.3
Identities = 8/14 (57%), Positives = 9/14 (64%)
Query: 15 CVVVGDTAVGKTRL 28
V+ G TA GKT L
Sbjct: 6 IVIAGPTASGKTAL 19
>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 = 24.3 bits (53), Expect = 4.6
Identities = 16/45 (35%), Positives = 20/45 (44%), Gaps = 8/45 (17%)
Query: 14 KCVVVGDTAVGKTRLICARACNKQVSLSQLLTTHVPTVWAIDQYR 58
K VVVG VGK+ L Q S +T + PT+ D Y
Sbjct: 4 KLVVVGGGGVGKSALTI------QFIQSYFVTDYDPTIE--DSYT 40
>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 = 24.5 bits (54), Expect = 4.6
Identities = 8/18 (44%), Positives = 14/18 (77%)
Query: 12 LVKCVVVGDTAVGKTRLI 29
L K +++GD+ VGK+ L+
Sbjct: 3 LFKLLLIGDSGVGKSCLL 20
>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 = 24.4 bits (54), Expect = 4.6
Identities = 7/18 (38%), Positives = 14/18 (77%)
Query: 13 VKCVVVGDTAVGKTRLIC 30
K V++GD++VGK+ ++
Sbjct: 2 FKLVLLGDSSVGKSSIVL 19
>gnl|CDD|176247 cd08287, FDH_like_ADH3, formaldehyde dehydrogenase (FDH)-like.
This group contains proteins identified as alcohol
dehydrogenases and glutathione-dependant formaldehyde
dehydrogenases (FDH) of the zinc-dependent/medium chain
alcohol dehydrogenase family. The MDR family uses
NAD(H) as a cofactor in the interconversion of alcohols
and aldehydes, or ketones. FDH converts formaldehyde
and NAD to formate and NADH. The initial step in this
process the spontaneous formation of a
S-(hydroxymethyl)glutathione adduct from formaldehyde
and glutathione, followed by FDH-mediated oxidation (and
detoxification) of the adduct to S-formylglutathione.
The medium chain alcohol dehydrogenase family (MDR) has
a NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The N-terminal region typically has an
all-beta catalytic domain. These proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and have 2 tightly bound zinc atoms
per subunit.
Length = 345
Score = 24.6 bits (54), Expect = 4.8
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 15 CVVVGDTAVGKTRLICAR 32
VVVGD AVG ++ A+
Sbjct: 172 VVVVGDGAVGLCAVLAAK 189
>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 = 24.2 bits (53), Expect = 4.9
Identities = 7/18 (38%), Positives = 14/18 (77%)
Query: 13 VKCVVVGDTAVGKTRLIC 30
+K +++GD+ VGK+ L+
Sbjct: 1 LKILLIGDSGVGKSSLLL 18
>gnl|CDD|110677 pfam01695, IstB_IS21, IstB-like ATP binding protein. This
protein contains an ATP/GTP binding P-loop motif. It is
found associated with IS21 family insertion sequences.
The function of this protein is unknown, but it may
perform a transposase function.
Length = 178
Score = 24.1 bits (53), Expect = 5.1
Identities = 10/23 (43%), Positives = 14/23 (60%), Gaps = 3/23 (13%)
Query: 15 CVVVGDTAVGKTRLICA---RAC 34
+++G VGKT L CA +AC
Sbjct: 50 LLLLGPPGVGKTHLACALGHQAC 72
>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 = 24.4 bits (53), Expect = 5.2
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 12 LVKCVVVGDTAVGKTRLI 29
L+K + +GD+ VGKT +
Sbjct: 4 LIKLLALGDSGVGKTTFL 21
>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 = 24.2 bits (53), Expect = 5.3
Identities = 8/16 (50%), Positives = 13/16 (81%)
Query: 14 KCVVVGDTAVGKTRLI 29
K +++GD+ VGKT L+
Sbjct: 2 KVIILGDSGVGKTSLM 17
>gnl|CDD|237951 PRK15347, PRK15347, two component system sensor kinase SsrA;
Provisional.
Length = 921
Score = 24.2 bits (53), Expect = 6.4
Identities = 9/31 (29%), Positives = 15/31 (48%)
Query: 29 ICARACNKQVSLSQLLTTHVPTVWAIDQYRI 59
I A +K ++L + HVP +D R+
Sbjct: 484 IQGPAQSKSLTLRTFVGAHVPLYLHLDSLRL 514
>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 = 23.9 bits (52), Expect = 6.7
Identities = 8/15 (53%), Positives = 12/15 (80%)
Query: 12 LVKCVVVGDTAVGKT 26
L K +++GD+ VGKT
Sbjct: 3 LFKIILIGDSNVGKT 17
>gnl|CDD|206735 cd04172, Rnd3_RhoE_Rho8, Rnd3/RhoE/Rho8 GTPases. Rnd3/RhoE/Rho8
subfamily. Rnd3/RhoE/Rho8 is a member of the novel Rho
subfamily Rnd, together with Rnd1/Rho6 and Rnd2/Rho7.
Rnd3/RhoE is known to bind the serine-threonine kinase
ROCK I. Unphosphorylated Rnd3/RhoE associates primarily
with membranes, but ROCK I-phosphorylated Rnd3/RhoE
localizes in the cytosol. Phosphorylation of Rnd3/RhoE
correlates with its activity in disrupting RhoA-induced
stress fibers and inhibiting Ras-induced fibroblast
transformation. In cells that lack stress fibers, such
as macrophages and monocytes, Rnd3/RhoE induces a
redistribution of actin, causing morphological changes
in the cell. In addition, Rnd3/RhoE has been shown to
inhibit cell cycle progression in G1 phase at a point
upstream of the pRb family pocket protein checkpoint.
Rnd3/RhoE has also been shown to inhibit Ras- and
Raf-induced fibroblast transformation. In mammary
epithelial tumor cells, Rnd3/RhoE regulates the
assembly of the apical junction complex and tight
junction formation. Rnd3/RhoE is underexpressed in
prostate cancer cells both in vitro and in vivo;
re-expression of Rnd3/RhoE suppresses cell cycle
progression and increases apoptosis, suggesting it may
play a role in tumor suppression. Most Rho proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 182
Score = 23.9 bits (51), Expect = 7.6
Identities = 11/22 (50%), Positives = 15/22 (68%), Gaps = 1/22 (4%)
Query: 9 HQEL-VKCVVVGDTAVGKTRLI 29
+Q + K VVVGD+ GKT L+
Sbjct: 1 NQNVKCKIVVVGDSQCGKTALL 22
>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 = 23.7 bits (52), Expect = 9.1
Identities = 14/45 (31%), Positives = 19/45 (42%), Gaps = 8/45 (17%)
Query: 14 KCVVVGDTAVGKTRLICARACNKQVSLSQLLTTHVPTVWAIDQYR 58
K VV+G VGK+ L Q + + PT+ D YR
Sbjct: 2 KLVVLGSGGVGKSALTI------QFIQGHFVDDYDPTIE--DSYR 38
>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 = 23.3 bits (51), Expect = 9.6
Identities = 14/45 (31%), Positives = 19/45 (42%), Gaps = 8/45 (17%)
Query: 14 KCVVVGDTAVGKTRLICARACNKQVSLSQLLTTHVPTVWAIDQYR 58
K VV+G VGK+ L Q + + PT+ D YR
Sbjct: 4 KLVVLGGGGVGKSALTI------QFVQGHFVDEYDPTIE--DSYR 40
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.132 0.398
Gapped
Lambda K H
0.267 0.0830 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,022,633
Number of extensions: 193622
Number of successful extensions: 292
Number of sequences better than 10.0: 1
Number of HSP's gapped: 292
Number of HSP's successfully gapped: 65
Length of query: 65
Length of database: 10,937,602
Length adjustment: 36
Effective length of query: 29
Effective length of database: 9,340,858
Effective search space: 270884882
Effective search space used: 270884882
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.0 bits)