RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15036
(179 letters)
>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 = 59.1 bits (143), Expect = 2e-11
Identities = 34/79 (43%), Positives = 43/79 (54%), Gaps = 13/79 (16%)
Query: 70 TVGIVFPAISVTY-SIGP-----RYFRFPLV-------SRFLSLTTGLYRGTMGFLLIFD 116
TVGI F V Y S GP + FR L RF SLTT +R MGFLL+FD
Sbjct: 36 TVGIDFREKRVVYNSQGPDGTSGKAFRVHLQLWDTAGQERFRSLTTAFFRDAMGFLLMFD 95
Query: 117 VTNENSFKDVEKWLLQIKV 135
+T+E SF +V W+ Q++
Sbjct: 96 LTSEQSFLNVRNWMSQLQA 114
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 56.7 bits (138), Expect = 1e-10
Identities = 18/39 (46%), Positives = 30/39 (76%)
Query: 96 RFLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKWLLQIK 134
RF S+T+ YRG +G LL++D+TN SF+++E WL +++
Sbjct: 61 RFRSITSSYYRGAVGALLVYDITNRESFENLENWLKELR 99
>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 = 56.5 bits (136), Expect = 2e-10
Identities = 21/39 (53%), Positives = 29/39 (74%)
Query: 96 RFLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKWLLQIK 134
R+ ++TT YRG MGF+L++D+TNE SF V+ W QIK
Sbjct: 62 RYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIK 100
>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 = 56.0 bits (136), Expect = 2e-10
Identities = 19/39 (48%), Positives = 29/39 (74%)
Query: 96 RFLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKWLLQIK 134
RF +L YRG GFLL++D+T+ +SF++V+KWL +I
Sbjct: 60 RFRALRPLYYRGAQGFLLVYDITSRDSFENVKKWLEEIL 98
>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 = 55.2 bits (134), Expect = 4e-10
Identities = 19/39 (48%), Positives = 30/39 (76%)
Query: 96 RFLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKWLLQIK 134
RF S+T+ YRG G +L++DVTN SF++++KWL ++K
Sbjct: 61 RFRSITSSYYRGAHGAILVYDVTNRESFENLDKWLNELK 99
>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 = 54.6 bits (132), Expect = 7e-10
Identities = 17/39 (43%), Positives = 29/39 (74%)
Query: 96 RFLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKWLLQIK 134
RF ++TT YRG MG +L++D+T+E SF++++ W+ I
Sbjct: 64 RFRTITTSYYRGAMGIILVYDITDEKSFENIKNWMRNID 102
>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 = 51.4 bits (124), Expect = 1e-08
Identities = 15/39 (38%), Positives = 32/39 (82%)
Query: 96 RFLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKWLLQIK 134
R+ ++T+ YRG +G LL++D+T +++F++VE+WL +++
Sbjct: 64 RYRAITSAYYRGAVGALLVYDITKKSTFENVERWLKELR 102
>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 = 48.3 bits (115), Expect = 2e-07
Identities = 18/39 (46%), Positives = 30/39 (76%)
Query: 96 RFLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKWLLQIK 134
RF ++T+ YRGT G ++++DVTN SF +V++WL +I+
Sbjct: 67 RFRTITSTYYRGTHGVIVVYDVTNGESFVNVKRWLQEIE 105
>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 = 46.3 bits (110), Expect = 1e-06
Identities = 18/40 (45%), Positives = 26/40 (65%)
Query: 96 RFLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKWLLQIKV 135
RF S+T YR ++G LL+FD+TN SF+ V WL + +
Sbjct: 64 RFRSITRSYYRNSVGVLLVFDITNRESFEHVHDWLEEARS 103
>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 = 45.0 bits (107), Expect = 3e-06
Identities = 16/38 (42%), Positives = 29/38 (76%)
Query: 96 RFLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKWLLQI 133
RF ++T+ YRG G ++++DVT++ SF +V++WL +I
Sbjct: 63 RFRTITSSYYRGAHGIIIVYDVTDQESFNNVKQWLQEI 100
>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 = 44.3 bits (105), Expect = 3e-06
Identities = 16/35 (45%), Positives = 22/35 (62%)
Query: 96 RFLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKWL 130
RF S+T YRG G LL++D+T+ SF + WL
Sbjct: 61 RFRSVTRSYYRGAAGALLVYDITSRESFNALTNWL 95
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 44.9 bits (106), Expect = 4e-06
Identities = 18/56 (32%), Positives = 34/56 (60%), Gaps = 7/56 (12%)
Query: 96 RFLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKWLLQIKVMDGALFTHFELQIVFM 151
R+ ++T+ YRG +G LL++D+T +F +V++WL +++ H + IV M
Sbjct: 73 RYRAITSAYYRGAVGALLVYDITKRQTFDNVQRWLRELR-------DHADSNIVIM 121
>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 = 44.2 bits (105), Expect = 4e-06
Identities = 15/34 (44%), Positives = 21/34 (61%)
Query: 96 RFLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKW 129
RF SL YRG +L++DVTN SF+ ++ W
Sbjct: 61 RFQSLGVAFYRGADCCVLVYDVTNPKSFESLDSW 94
>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 = 43.8 bits (104), Expect = 7e-06
Identities = 16/43 (37%), Positives = 29/43 (67%)
Query: 96 RFLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKWLLQIKVMDG 138
R+ +L YR G +L++D+T+ +SF+ V+KW+ ++K M G
Sbjct: 61 RYHALGPIYYRDADGAILVYDITDADSFQKVKKWIKELKQMRG 103
>gnl|CDD|206699 cd04120, Rab12, Rab GTPase family 12 (Rab12). Rab12 was first
identified in canine cells, where it was localized to
the Golgi complex. The specific function of Rab12
remains unknown, and inconsistent results about its
cellular localization have been reported. More recent
studies have identified Rab12 associated with post-Golgi
vesicles, or with other small vesicle-like structures
but not with the Golgi complex. Most Rab GTPases contain
a lipid modification site at the C-terminus, with
sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation of
the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins.
Length = 202
Score = 43.8 bits (103), Expect = 8e-06
Identities = 15/38 (39%), Positives = 25/38 (65%)
Query: 96 RFLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKWLLQI 133
RF S+T+ YR G +L++D+T + +F D+ KW+ I
Sbjct: 61 RFNSITSAYYRSAKGIILVYDITKKETFDDLPKWMKMI 98
>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 = 42.3 bits (100), Expect = 2e-05
Identities = 15/40 (37%), Positives = 27/40 (67%)
Query: 96 RFLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKWLLQIKV 135
RF +LT+ YRG G +L++DVT ++F +++ WL ++
Sbjct: 61 RFRTLTSSYYRGAQGVILVYDVTRRDTFDNLDTWLNELDT 100
>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 = 41.4 bits (97), Expect = 6e-05
Identities = 17/38 (44%), Positives = 25/38 (65%)
Query: 96 RFLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKWLLQI 133
RF S+T YR LL++DVTN++SF ++ WL +I
Sbjct: 62 RFRSVTHAYYRDAHALLLLYDVTNKSSFDNIRAWLTEI 99
>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 = 40.0 bits (94), Expect = 1e-04
Identities = 13/31 (41%), Positives = 22/31 (70%)
Query: 105 YRGTMGFLLIFDVTNENSFKDVEKWLLQIKV 135
Y+ T G LL++DVT+ SF+ ++ WL ++K
Sbjct: 70 YKDTQGVLLVYDVTDRQSFEALDSWLKEMKQ 100
>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 = 38.6 bits (90), Expect = 7e-04
Identities = 11/28 (39%), Positives = 18/28 (64%)
Query: 107 GTMGFLLIFDVTNENSFKDVEKWLLQIK 134
G L++D+TN SF+++E WL +K
Sbjct: 73 GAQAVCLVYDITNSQSFENLEDWLSVVK 100
>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 = 38.2 bits (89), Expect = 7e-04
Identities = 14/34 (41%), Positives = 20/34 (58%)
Query: 97 FLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKWL 130
F S+T YRG G LL++D+T +F + WL
Sbjct: 66 FRSITRSYYRGAAGALLVYDITRRETFNHLTSWL 99
>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 = 37.9 bits (88), Expect = 8e-04
Identities = 12/35 (34%), Positives = 22/35 (62%)
Query: 96 RFLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKWL 130
RF ++T YRG G L+++D+T +++ + WL
Sbjct: 63 RFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWL 97
>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 = 37.7 bits (88), Expect = 0.001
Identities = 14/34 (41%), Positives = 23/34 (67%)
Query: 96 RFLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKW 129
RF +T Y+G +G +++FDVT ++F+ V KW
Sbjct: 62 RFGGMTRVYYKGAVGAIIVFDVTRPSTFEAVLKW 95
>gnl|CDD|133321 cd04121, Rab40, Rab GTPase family 40 (Rab40) contains Rab40a,
Rab40b and Rab40c. The Rab40 subfamily contains Rab40a,
Rab40b, and Rab40c, which are all highly homologous. In
rat, Rab40c is localized to the perinuclear recycling
compartment (PRC), and is distributed in a
tissue-specific manor, with high expression in brain,
heart, kidney, and testis, low expression in lung and
liver, and no expression in spleen and skeletal muscle.
Rab40c is highly expressed in differentiated
oligodendrocytes but minimally expressed in
oligodendrocyte progenitors, suggesting a role in the
vesicular transport of myelin components. Unlike most
other Ras-superfamily proteins, Rab40c was shown to have
a much lower affinity for GTP, and an affinity for GDP
that is lower than for GTP. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 189
Score = 37.2 bits (86), Expect = 0.002
Identities = 13/38 (34%), Positives = 24/38 (63%)
Query: 96 RFLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKWLLQI 133
RF ++ RG G +L++D+TN SF +++W+ +I
Sbjct: 67 RFCTIFRSYSRGAQGIILVYDITNRWSFDGIDRWIKEI 104
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 37.2 bits (86), Expect = 0.002
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 3/67 (4%)
Query: 67 HGKTVGIVFPAISVTYSIGPRYFRFPLVS---RFLSLTTGLYRGTMGFLLIFDVTNENSF 123
H T+G+ F A +T P + + F S+T YRG G LL++D+T +F
Sbjct: 35 HDLTIGVEFGARMITIDNKPIKLQIWDTAGQESFRSITRSYYRGAAGALLVYDITRRETF 94
Query: 124 KDVEKWL 130
+ WL
Sbjct: 95 NHLASWL 101
>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 = 36.8 bits (86), Expect = 0.002
Identities = 12/39 (30%), Positives = 25/39 (64%)
Query: 96 RFLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKWLLQIK 134
R+ SL YRG ++++D+T+E SF+ + W+ +++
Sbjct: 62 RYRSLAPMYYRGAAAAIVVYDITSEESFEKAKSWVKELQ 100
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 36.6 bits (84), Expect = 0.003
Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 7/69 (10%)
Query: 70 TVGIVFPAISVTYSIGPRYFRFPL-----VSRFLSLTTGLYRGTMGFLLIFDVTNENSFK 124
T+GI F + ++ GP R L RF SL R + ++++D+TN SF+
Sbjct: 12 TIGIDFLSKTLYLDEGP--VRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDITNRQSFE 69
Query: 125 DVEKWLLQI 133
+ KW+ I
Sbjct: 70 NTTKWIQDI 78
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 36.9 bits (85), Expect = 0.003
Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 8/71 (11%)
Query: 70 TVGIVFPAISVTYSIGPRYFRFPLV-----SRFLSLTTGLYRGTMGFLLIFDVTNENSFK 124
T+G + PA T R + L + SL YRG G L+++D T S
Sbjct: 37 TIGNLDPA--KTIEPYRRNIKLQLWDTAGQEEYRSLRPEYYRGANGILIVYDSTLRESSD 94
Query: 125 DV-EKWLLQIK 134
++ E+WL +++
Sbjct: 95 ELTEEWLEELR 105
>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 = 36.0 bits (83), Expect = 0.004
Identities = 15/39 (38%), Positives = 24/39 (61%)
Query: 96 RFLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKWLLQIK 134
RF S+T YR +L +D+T E SF+ + +WL +I+
Sbjct: 68 RFRSITQSYYRSANALILTYDITCEESFRCLPEWLREIE 106
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 35.4 bits (81), Expect = 0.008
Identities = 12/31 (38%), Positives = 20/31 (64%)
Query: 96 RFLSLTTGLYRGTMGFLLIFDVTNENSFKDV 126
RF +LT+ YR G +L++DVT +F ++
Sbjct: 74 RFRTLTSSYYRNAQGIILVYDVTRRETFTNL 104
>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 = 35.0 bits (80), Expect = 0.008
Identities = 11/34 (32%), Positives = 22/34 (64%)
Query: 96 RFLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKW 129
R+ ++T YR G L++D+++E S++ + KW
Sbjct: 61 RYQTITKQYYRRAQGIFLVYDISSERSYQHIMKW 94
>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 = 33.9 bits (78), Expect = 0.017
Identities = 12/39 (30%), Positives = 24/39 (61%)
Query: 96 RFLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKWLLQIK 134
RF ++T YR G ++ +D+T +SF+ V W+ +++
Sbjct: 64 RFRTITQSYYRSANGAIIAYDITRRSSFESVPHWIEEVE 102
>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 = 33.3 bits (77), Expect = 0.033
Identities = 10/38 (26%), Positives = 21/38 (55%)
Query: 96 RFLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKWLLQI 133
F ++ R GF+L++ +T+ SF++++ QI
Sbjct: 59 EFSAMRDQYIRNGDGFILVYSITSRESFEEIKNIREQI 96
>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 = 32.4 bits (74), Expect = 0.060
Identities = 14/28 (50%), Positives = 20/28 (71%)
Query: 106 RGTMGFLLIFDVTNENSFKDVEKWLLQI 133
R GFLL+F VT+ SF++V+K+ QI
Sbjct: 72 RTGEGFLLVFSVTDRGSFEEVDKFHTQI 99
>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 = 32.2 bits (74), Expect = 0.063
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 96 RFLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKW 129
RF SL R + ++++D+TN SF + +KW
Sbjct: 61 RFRSLIPSYIRDSSVAVVVYDITNRQSFDNTDKW 94
>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 = 32.4 bits (74), Expect = 0.065
Identities = 16/80 (20%), Positives = 24/80 (30%), Gaps = 8/80 (10%)
Query: 66 THGKTVGIVFPAISVTYSIG-------PRYFRFPLVSRFLSLTTGLYRGTMGFLLIFDVT 118
G T + P F L L RG LL+ D T
Sbjct: 28 VPGTTRDPDVYVKELDKGKVKLVLVDTPGLDEFG-GLGREELARLLLRGADLILLVVDST 86
Query: 119 NENSFKDVEKWLLQIKVMDG 138
+ S +D + +L+ +G
Sbjct: 87 DRESEEDAKLLILRRLRKEG 106
>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 = 32.4 bits (74), Expect = 0.068
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 110 GFLLIFDVTNENSFKDVEKWLLQIK 134
GFL +F + + SF+D+ + QIK
Sbjct: 75 GFLCVFAINSRKSFEDIHTYREQIK 99
>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 = 32.1 bits (74), Expect = 0.074
Identities = 11/33 (33%), Positives = 20/33 (60%)
Query: 106 RGTMGFLLIFDVTNENSFKDVEKWLLQIKVMDG 138
R GFLL++ +T+ SF+++ K+ QI +
Sbjct: 72 RTGEGFLLVYSITDRQSFEEIAKFREQILRVKD 104
>gnl|CDD|133324 cd04124, RabL2, Rab GTPase-like family 2 (Rab-like2). RabL2
(Rab-like2) subfamily. RabL2s are novel Rab proteins
identified recently which display features that are
distinct from other Rabs, and have been termed Rab-like.
RabL2 contains RabL2a and RabL2b, two very similar Rab
proteins that share > 98% sequence identity in humans.
RabL2b maps to the subtelomeric region of chromosome
22q13.3 and RabL2a maps to 2q13, a region that suggests
it is also a subtelomeric gene. Both genes are believed
to be expressed ubiquitously, suggesting that RabL2s are
the first example of duplicated genes in human proximal
subtelomeric regions that are both expressed actively.
Like other Rab-like proteins, RabL2s lack a prenylation
site at the C-terminus. The specific functions of RabL2a
and RabL2b remain unknown. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization.
Length = 161
Score = 32.1 bits (73), Expect = 0.081
Identities = 11/39 (28%), Positives = 23/39 (58%)
Query: 96 RFLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKWLLQIK 134
RF ++ Y +L+FDVT + ++K++ KW +++
Sbjct: 61 RFQTMHASYYHKAHACILVFDVTRKITYKNLSKWYEELR 99
>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 = 32.2 bits (73), Expect = 0.084
Identities = 15/34 (44%), Positives = 20/34 (58%)
Query: 96 RFLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKW 129
RF SL T YRG+ LL F V + SF+++ W
Sbjct: 66 RFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNW 99
>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 = 31.6 bits (72), Expect = 0.13
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 97 FLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKW 129
F ++T YRG +L+F T+ SF+ +E W
Sbjct: 64 FDAITKAYYRGAQACILVFSTTDRESFEAIESW 96
>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 = 31.4 bits (72), Expect = 0.15
Identities = 11/29 (37%), Positives = 20/29 (68%)
Query: 106 RGTMGFLLIFDVTNENSFKDVEKWLLQIK 134
R GFLL++ +T+ SF++++K+ QI
Sbjct: 70 RTGEGFLLVYSITDRQSFEEIKKFREQIL 98
>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 = 31.0 bits (71), Expect = 0.19
Identities = 15/37 (40%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 99 SLTTGLYRGTMGFLLIFDVTNENSFKDV-EKWLLQIK 134
L Y T FLL F V + +SF++V KW +IK
Sbjct: 63 RLRPLSYPQTDVFLLCFSVDSPSSFENVKTKWYPEIK 99
>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 = 31.0 bits (70), Expect = 0.20
Identities = 8/24 (33%), Positives = 17/24 (70%)
Query: 111 FLLIFDVTNENSFKDVEKWLLQIK 134
+++DVTNE SF + +W+ +++
Sbjct: 80 VCVVYDVTNEVSFNNCSRWINRVR 103
>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 = 0.21
Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 105 YRGTMGFLLIFDVTNENSFKDV-EKWLLQIK 134
Y T FL+ F V + SF++V EKW ++K
Sbjct: 67 YPDTDVFLICFSVDSPASFENVKEKWYPEVK 97
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 31.2 bits (71), Expect = 0.22
Identities = 11/34 (32%), Positives = 19/34 (55%)
Query: 96 RFLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKW 129
+F L G Y +++FDVT+ ++K+V W
Sbjct: 70 KFGGLRDGYYIKGQCAIIMFDVTSRITYKNVPNW 103
>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 = 0.27
Identities = 14/31 (45%), Positives = 21/31 (67%), Gaps = 1/31 (3%)
Query: 105 YRGTMGFLLIFDVTNENSFKDV-EKWLLQIK 134
Y T FLL F V N +SF+++ EKW+ +I+
Sbjct: 69 YPDTDVFLLCFSVVNPSSFQNISEKWIPEIR 99
>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 = 28.6 bits (64), Expect = 1.3
Identities = 9/33 (27%), Positives = 18/33 (54%)
Query: 94 VSRFLSLTTGLYRGTMGFLLIFDVTNENSFKDV 126
+F ++ + GFLL++ VT+E S ++
Sbjct: 59 TEQFTAMRELYIKSGQGFLLVYSVTSEASLNEL 91
>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 = 28.3 bits (63), Expect = 1.5
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 109 MGFLLIFDVTNENSFKDVEKWLLQI 133
GF L++ +T + SF D++ QI
Sbjct: 74 QGFALVYSITAQQSFNDLQDLREQI 98
>gnl|CDD|233264 TIGR01082, murC, UDP-N-acetylmuramate--alanine ligase. This model
describes the MurC protein in bacterial peptidoglycan
(murein) biosynthesis. In a few species (Mycobacterium
leprae, the Chlamydia), the amino acid may be L-serine
or glycine instead of L-alanine. A related protein,
UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-
diaminopimelate ligase (murein tripeptide ligase) is
described by model TIGR01081 [Cell envelope,
Biosynthesis and degradation of murein sacculus and
peptidoglycan].
Length = 448
Score = 28.8 bits (65), Expect = 1.5
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 11/32 (34%)
Query: 50 RRGIPLLKHLKYLG-----------TGTHGKT 70
RGIP+++ + L GTHGKT
Sbjct: 80 ERGIPVIRRAEMLAELMRFRHSIAVAGTHGKT 111
>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 = 28.3 bits (63), Expect = 1.6
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 96 RFLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKWL 130
RF + + YRG +++FD+T+ S + +WL
Sbjct: 61 RFKCIASTYYRGAQAIIIVFDLTDVASLEHTRQWL 95
>gnl|CDD|218779 pfam05853, DUF849, Prokaryotic protein of unknown function
(DUF849). This family consists of several hypothetical
prokaryotic proteins with no known function.
Length = 273
Score = 28.6 bits (65), Expect = 1.7
Identities = 15/72 (20%), Positives = 23/72 (31%), Gaps = 10/72 (13%)
Query: 107 GTMGFLLIFDVTNENSFKDVEKWLLQIKVMDGALFTHFELQIVFMRGCLELLQRCRE--V 164
G+M F D+ N+ DVE M E + F G L + +
Sbjct: 110 GSMNFGAYRDMVFRNTPADVE-EFA--ARM-QEAGVKPEFEC-FDVGHLRNAAALLKRGL 164
Query: 165 VTPD---QIMFG 173
+ Q + G
Sbjct: 165 LKGPLFVQFVLG 176
>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 = 28.6 bits (64), Expect = 1.8
Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 6/43 (13%)
Query: 91 FPLVSRFLSLTTGLYRGTMGFLLIFDVTNENSFKDVEKWLLQI 133
FP + R LS+ TG F+L+F + N SF++V + QI
Sbjct: 61 FPAMRR-LSILTGDV-----FILVFSLDNRESFEEVCRLREQI 97
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 27.9 bits (62), Expect = 2.4
Identities = 11/33 (33%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 106 RGTMGFLLIFDVTNENSFKDVEKWLLQI-KVMD 137
R GFL ++ +T+ +SF+++ + QI +V D
Sbjct: 75 RTGQGFLCVYSITSRSSFEEIASFREQILRVKD 107
>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 = 27.7 bits (62), Expect = 2.5
Identities = 7/19 (36%), Positives = 11/19 (57%), Gaps = 1/19 (5%)
Query: 112 LLIFDVTNENSFKDV-EKW 129
L+ + V N S +V +KW
Sbjct: 80 LICYSVDNPTSLDNVEDKW 98
>gnl|CDD|240626 cd05301, GDH, D-glycerate dehydrogenase/hydroxypyruvate reductase
(GDH). D-glycerate dehydrogenase (GDH, also known as
hydroxypyruvate reductase, HPR) catalyzes the reversible
reaction of (R)-glycerate + NAD+ to hydroxypyruvate +
NADH + H+. In humans, HPR deficiency causes primary
hyperoxaluria type 2, characterized by over-excretion of
L-glycerate and oxalate in the urine, possibly due to an
imbalance in competition with L-lactate dehydrogenase,
another formate dehydrogenase (FDH)-like enzyme. GDH,
like FDH and other members of the D-specific hydroxyacid
dehydrogenase family that also includes L-alanine
dehydrogenase and S-adenosylhomocysteine hydrolase,
typically have a characteristic arrangement of 2 similar
subdomains of the alpha/beta Rossmann-fold NAD+ binding
form, despite often low sequence identity. The NAD+
binding domain is inserted within the linear sequence of
the mostly N-terminal catalytic domain, which has a
similar domain structure to the internal NAD binding
domain. Structurally, these domains are connected by
extended alpha helices and create a cleft in which NAD
is bound, primarily to the C-terminal portion of the 2nd
(internal) domain. Some related proteins have similar
structural subdomain but with a tandem arrangement of
the catalytic and NAD-binding subdomains in the linear
sequence. While many members of this family are dimeric,
alanine DH is hexameric and phosphoglycerate DH is
tetrameric.
Length = 309
Score = 27.7 bits (63), Expect = 2.9
Identities = 10/14 (71%), Positives = 11/14 (78%)
Query: 61 YLGTGTHGKTVGIV 74
LGT HGKT+GIV
Sbjct: 137 LLGTDLHGKTLGIV 150
>gnl|CDD|223844 COG0773, MurC, UDP-N-acetylmuramate-alanine ligase [Cell envelope
biogenesis, outer membrane].
Length = 459
Score = 27.5 bits (62), Expect = 3.7
Identities = 11/32 (34%), Positives = 14/32 (43%), Gaps = 11/32 (34%)
Query: 50 RRGIPLLKHLKYLG-----------TGTHGKT 70
RGIP++ + L GTHGKT
Sbjct: 88 ERGIPVISRAEMLAELMRFRTSIAVAGTHGKT 119
>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 = 27.4 bits (61), Expect = 3.9
Identities = 12/56 (21%), Positives = 26/56 (46%), Gaps = 7/56 (12%)
Query: 110 GFLLIFDVTNENSFKDVEKWLLQIKVMDGALFTHFELQI-VFMRGCLELLQRCREV 164
+++++ VT+ +SF+ + +Q++ I + + G L R REV
Sbjct: 75 AYVIVYSVTDRSSFEKASELRIQLRR------ARQAEDIPIILVGNKSDLVRSREV 124
>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 = 27.0 bits (60), Expect = 4.1
Identities = 9/26 (34%), Positives = 14/26 (53%)
Query: 105 YRGTMGFLLIFDVTNENSFKDVEKWL 130
YR + ++DVTN SF + W+
Sbjct: 73 YRNVHAVVFVYDVTNMASFHSLPSWI 98
>gnl|CDD|226837 COG4403, LcnDR2, Lantibiotic modifying enzyme [Defense mechanisms].
Length = 963
Score = 27.4 bits (61), Expect = 4.7
Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 4/37 (10%)
Query: 100 LTTGLYRGTMGFLLIFD----VTNENSFKDVEKWLLQ 132
L LY G+ G L F VT ++ +K++ LQ
Sbjct: 641 LGNDLYDGSAGIALFFAYLALVTGKDYYKEIAIKALQ 677
>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 = 26.6 bits (59), Expect = 5.8
Identities = 11/29 (37%), Positives = 18/29 (62%)
Query: 105 YRGTMGFLLIFDVTNENSFKDVEKWLLQI 133
+R GFLL+F +T+ SF + ++ QI
Sbjct: 69 FRSGEGFLLVFSITDMESFTALAEFREQI 97
>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 = 26.8 bits (59), Expect = 5.9
Identities = 13/31 (41%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 105 YRGTMGFLLIFDVTNENSFKDV-EKWLLQIK 134
Y T FL+ F V + +SF++V EKW+ +I
Sbjct: 70 YPQTDVFLVCFSVVSPSSFENVKEKWVPEIT 100
>gnl|CDD|165398 PHA03126, PHA03126, dUTPase; Provisional.
Length = 326
Score = 26.5 bits (58), Expect = 7.8
Identities = 12/24 (50%), Positives = 15/24 (62%)
Query: 2 FADLAIMFADSRPESTFWIFGKPT 25
F DL I+FA S P T IFG+ +
Sbjct: 197 FVDLPIVFASSNPAVTPCIFGRSS 220
>gnl|CDD|215627 PLN03195, PLN03195, fatty acid omega-hydroxylase; Provisional.
Length = 516
Score = 26.7 bits (59), Expect = 8.2
Identities = 17/57 (29%), Positives = 24/57 (42%), Gaps = 4/57 (7%)
Query: 68 GKTVGIVFPAISVTYSIGPRYFRFPLVSRFLSLTTG-LYRGTMGFLL---IFDVTNE 120
+TV + P + TY P L + F + G +Y M LL IF+V E
Sbjct: 65 DRTVVVKMPFTTYTYIADPVNVEHVLKTNFANYPKGEVYHSYMEVLLGDGIFNVDGE 121
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
0.329 0.142 0.438
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: 9,169,017
Number of extensions: 840112
Number of successful extensions: 997
Number of sequences better than 10.0: 1
Number of HSP's gapped: 996
Number of HSP's successfully gapped: 76
Length of query: 179
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 88
Effective length of database: 6,901,388
Effective search space: 607322144
Effective search space used: 607322144
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 56 (25.2 bits)