RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16649
(83 letters)
>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 = 132 bits (333), Expect = 3e-41
Identities = 48/59 (81%), Positives = 58/59 (98%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENASANVEKMLLGN 83
DTAGQERFRTITT+YYRGAMGI+LVYDIT+EKSF+NIKNW+RNI+E+AS +VE+ML+GN
Sbjct: 58 DTAGQERFRTITTSYYRGAMGIILVYDITDEKSFENIKNWMRNIDEHASEDVERMLVGN 116
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 116 bits (294), Expect = 3e-35
Identities = 38/59 (64%), Positives = 51/59 (86%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENASANVEKMLLGN 83
DTAGQERFR+IT++YYRGA+G +LVYDITN +SF+N++NW++ + E AS NV ML+GN
Sbjct: 55 DTAGQERFRSITSSYYRGAVGALLVYDITNRESFENLENWLKELREYASPNVVIMLVGN 113
>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 = 107 bits (269), Expect = 1e-31
Identities = 33/59 (55%), Positives = 42/59 (71%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENASANVEKMLLGN 83
DTAGQERFR + YYRGA G +LVYDIT+ SF+N+K W+ I +A NV +L+GN
Sbjct: 54 DTAGQERFRALRPLYYRGAQGFLLVYDITSRDSFENVKKWLEEILRHADENVPIVLVGN 112
>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 = 106 bits (268), Expect = 2e-31
Identities = 33/59 (55%), Positives = 47/59 (79%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENASANVEKMLLGN 83
DTAGQERFR+IT++YYRGA G +LVYD+TN +SF+N+ W+ ++E A N+ +L+GN
Sbjct: 55 DTAGQERFRSITSSYYRGAHGAILVYDVTNRESFENLDKWLNELKEYAPPNIPIILVGN 113
>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 = 100 bits (252), Expect = 6e-29
Identities = 37/59 (62%), Positives = 52/59 (88%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENASANVEKMLLGN 83
DTAGQERFRTIT++YYRGA GI++VYD+T+++SF+N+K W++ I+ AS NV K+L+GN
Sbjct: 57 DTAGQERFRTITSSYYRGAHGIIIVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGN 115
>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 = 96.5 bits (241), Expect = 3e-27
Identities = 32/59 (54%), Positives = 49/59 (83%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENASANVEKMLLGN 83
DTAGQER+R IT+AYYRGA+G +LVYDIT + +F+N++ W++ + ++A +N+ ML+GN
Sbjct: 58 DTAGQERYRAITSAYYRGAVGALLVYDITKKSTFENVERWLKELRDHADSNIVIMLVGN 116
>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 = 88.6 bits (220), Expect = 4e-24
Identities = 31/59 (52%), Positives = 44/59 (74%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENASANVEKMLLGN 83
DTAGQERFRTIT +YYR A G ++ YDIT SF+++ +WI +E+ ++NV +L+GN
Sbjct: 58 DTAGQERFRTITQSYYRSANGAIIAYDITRRSSFESVPHWIEEVEKYGASNVVLLLIGN 116
>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 = 87.8 bits (218), Expect = 8e-24
Identities = 31/60 (51%), Positives = 46/60 (76%), Gaps = 1/60 (1%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENA-SANVEKMLLGN 83
DTAGQERFRT+T++YYRGA G++LVYD+T +FDN+ W+ ++ + + + KML+GN
Sbjct: 55 DTAGQERFRTLTSSYYRGAQGVILVYDVTRRDTFDNLDTWLNELDTYSTNPDAVKMLVGN 114
>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 = 84.2 bits (208), Expect = 2e-22
Identities = 35/59 (59%), Positives = 48/59 (81%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENASANVEKMLLGN 83
DTAGQER+RTITTAYYRGAMG +L+YDITNE+SF+ +++W I+ + N + +L+GN
Sbjct: 56 DTAGQERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSWDNAQVILVGN 114
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 85.4 bits (211), Expect = 2e-22
Identities = 33/59 (55%), Positives = 48/59 (81%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENASANVEKMLLGN 83
DTAGQER+R IT+AYYRGA+G +LVYDIT ++FDN++ W+R + ++A +N+ M+ GN
Sbjct: 67 DTAGQERYRAITSAYYRGAVGALLVYDITKRQTFDNVQRWLRELRDHADSNIVIMMAGN 125
>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 = 84.3 bits (208), Expect = 4e-22
Identities = 33/59 (55%), Positives = 48/59 (81%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENASANVEKMLLGN 83
DTAGQERF +IT+AYYR A GI+LVYDIT +++FD++ W++ I++ AS + E +L+GN
Sbjct: 55 DTAGQERFNSITSAYYRSAKGIILVYDITKKETFDDLPKWMKMIDKYASEDAELLLVGN 113
>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 = 83.0 bits (205), Expect = 1e-21
Identities = 35/59 (59%), Positives = 46/59 (77%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENASANVEKMLLGN 83
DTAGQERFR++T AYYR A ++L+YD+TN+ SFDNI+ W+ I E A ++V MLLGN
Sbjct: 56 DTAGQERFRSVTHAYYRDAHALLLLYDVTNKSSFDNIRAWLTEILEYAQSDVVIMLLGN 114
>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 = 81.8 bits (202), Expect = 4e-21
Identities = 35/59 (59%), Positives = 47/59 (79%), Gaps = 1/59 (1%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENASANVEKMLLGN 83
DTAGQERFRTIT+ YYRG G+++VYD+TN +SF N+K W++ IE+N V K+L+GN
Sbjct: 61 DTAGQERFRTITSTYYRGTHGVIVVYDVTNGESFVNVKRWLQEIEQNCDD-VCKVLVGN 118
>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 = 81.4 bits (201), Expect = 4e-21
Identities = 31/68 (45%), Positives = 51/68 (75%), Gaps = 1/68 (1%)
Query: 17 HNFHINYRDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENA-SAN 75
H+ DTAGQERFR++TTA++R AMG +L++D+T+E+SF N++NW+ ++ +A N
Sbjct: 61 FRVHLQLWDTAGQERFRSLTTAFFRDAMGFLLMFDLTSEQSFLNVRNWMSQLQAHAYCEN 120
Query: 76 VEKMLLGN 83
+ +L+GN
Sbjct: 121 PDIVLIGN 128
>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 = 80.7 bits (200), Expect = 4e-21
Identities = 28/59 (47%), Positives = 43/59 (72%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENASANVEKMLLGN 83
DTAGQER+R++ YYRGA ++VYDIT+E+SF+ K+W++ ++E+ N+ L GN
Sbjct: 56 DTAGQERYRSLAPMYYRGAAAAIVVYDITSEESFEKAKSWVKELQEHGPPNIVIALAGN 114
>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 = 79.9 bits (197), Expect = 9e-21
Identities = 32/59 (54%), Positives = 43/59 (72%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENASANVEKMLLGN 83
DTAGQERFR+IT +YYR A ++L YDIT E+SF + W+R IE+ A+ V +L+GN
Sbjct: 62 DTAGQERFRSITQSYYRSANALILTYDITCEESFRCLPEWLREIEQYANNKVITILVGN 120
>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 = 79.8 bits (197), Expect = 3e-20
Identities = 24/47 (51%), Positives = 38/47 (80%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEEN 71
DTAGQERFR+IT +YYR ++G++LV+DITN +SF+++ +W+ +
Sbjct: 58 DTAGQERFRSITRSYYRNSVGVLLVFDITNRESFEHVHDWLEEARSH 104
>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 = 78.2 bits (193), Expect = 4e-20
Identities = 31/59 (52%), Positives = 45/59 (76%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENASANVEKMLLGN 83
DTAGQERFR++T +YYRGA G +LVYDIT+ +SF+ + NW+ + AS ++ +L+GN
Sbjct: 55 DTAGQERFRSVTRSYYRGAAGALLVYDITSRESFNALTNWLTDARTLASPDIVIILVGN 113
>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 = 77.5 bits (191), Expect = 9e-20
Identities = 29/59 (49%), Positives = 47/59 (79%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENASANVEKMLLGN 83
DTAGQE FR+IT +YYRGA G +LVYDIT ++F+++ +W+ + +++++N+ ML+GN
Sbjct: 59 DTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQHSNSNMTIMLIGN 117
>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 = 77.3 bits (190), Expect = 1e-19
Identities = 33/63 (52%), Positives = 47/63 (74%)
Query: 21 INYRDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENASANVEKML 80
I DTAGQER++TIT YYR A GI LVYDI++E+S+ +I W+ +++E A V+K+L
Sbjct: 51 IQIWDTAGQERYQTITKQYYRRAQGIFLVYDISSERSYQHIMKWVSDVDEYAPEGVQKIL 110
Query: 81 LGN 83
+GN
Sbjct: 111 IGN 113
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 75.7 bits (186), Expect = 9e-19
Identities = 31/59 (52%), Positives = 47/59 (79%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENASANVEKMLLGN 83
DTAGQE FR+IT +YYRGA G +LVYDIT ++F+++ +W+ + ++A+AN+ ML+GN
Sbjct: 61 DTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLASWLEDARQHANANMTIMLIGN 119
>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 = 73.0 bits (180), Expect = 4e-18
Identities = 27/59 (45%), Positives = 40/59 (67%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENASANVEKMLLGN 83
DTAGQERFR++ +Y R + ++VYDITN +SFDN WI ++ + +V +L+GN
Sbjct: 55 DTAGQERFRSLIPSYIRDSSVAVVVYDITNRQSFDNTDKWIDDVRDERGNDVIIVLVGN 113
>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 = 73.4 bits (180), Expect = 4e-18
Identities = 35/59 (59%), Positives = 43/59 (72%), Gaps = 1/59 (1%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENASANVEKMLLGN 83
DT+GQ RF TI +Y RGA GI+LVYDITN SFD I WI+ I+E+A V K+L+GN
Sbjct: 61 DTSGQGRFCTIFRSYSRGAQGIILVYDITNRWSFDGIDRWIKEIDEHAPG-VPKILVGN 118
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 72.4 bits (177), Expect = 2e-17
Identities = 31/61 (50%), Positives = 46/61 (75%), Gaps = 2/61 (3%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKN-WIRNIE-ENASANVEKMLLG 82
DTAGQERFRT+T++YYR A GI+LVYD+T ++F N+ + W + +E + + + KML+G
Sbjct: 68 DTAGQERFRTLTSSYYRNAQGIILVYDVTRRETFTNLSDVWGKEVELYSTNQDCVKMLVG 127
Query: 83 N 83
N
Sbjct: 128 N 128
>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 = 70.7 bits (174), Expect = 4e-17
Identities = 26/59 (44%), Positives = 39/59 (66%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENASANVEKMLLGN 83
DTAGQER+ + YYR A G +LVYDIT+ SF +K WI+ +++ N+ +++GN
Sbjct: 55 DTAGQERYHALGPIYYRDADGAILVYDITDADSFQKVKKWIKELKQMRGNNISLVIVGN 113
>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 = 70.3 bits (172), Expect = 5e-17
Identities = 26/59 (44%), Positives = 40/59 (67%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENASANVEKMLLGN 83
DTAGQERFR +T +YYRGA G ++VYDIT +++++ +W+ + + N L+GN
Sbjct: 57 DTAGQERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTVIFLIGN 115
>gnl|CDD|206655 cd01862, Rab7, Rab GTPase family 7 (Rab7). Rab7 subfamily. Rab7
is a small Rab GTPase that regulates vesicular traffic
from early to late endosomal stages of the endocytic
pathway. The yeast Ypt7 and mammalian Rab7 are both
involved in transport to the vacuole/lysosome, whereas
Ypt7 is also required for homotypic vacuole fusion.
Mammalian Rab7 is an essential participant in the
autophagic pathway for sequestration and targeting of
cytoplasmic components to the lytic compartment.
Mammalian Rab7 is also proposed to function as a tumor
suppressor. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation
of the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs),
which facilitate Rab recycling by masking C-terminal
lipid binding and promoting cytosolic localization.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Due to the presence
of truncated sequences in this CD, the lipid
modification site is not available for annotation.
Length = 172
Score = 67.7 bits (166), Expect = 5e-16
Identities = 27/58 (46%), Positives = 38/58 (65%), Gaps = 13/58 (22%)
Query: 7 TLQIFRGCFQHNFHINYRDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNW 64
TLQI+ DTAGQERF+++ A+YRGA +LVYD+TN KSF+++ +W
Sbjct: 50 TLQIW-------------DTAGQERFQSLGVAFYRGADCCVLVYDVTNPKSFESLDSW 94
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 65.0 bits (158), Expect = 2e-14
Identities = 27/60 (45%), Positives = 39/60 (65%), Gaps = 1/60 (1%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITN-EKSFDNIKNWIRNIEENASANVEKMLLGN 83
DTAGQE +R++ YYRGA GI++VYD T E S + + W+ + E A +V +L+GN
Sbjct: 60 DTAGQEEYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVGN 119
>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 = 62.5 bits (152), Expect = 7e-14
Identities = 27/61 (44%), Positives = 41/61 (67%), Gaps = 2/61 (3%)
Query: 25 DTAGQERFR-TITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENASAN-VEKMLLG 82
DTAGQERFR ++ YYR ++ VYD+TN SF ++ +WI E+++ N V ++L+G
Sbjct: 57 DTAGQERFRKSMVQHYYRNVHAVVFVYDVTNMASFHSLPSWIEECEQHSLPNEVPRILVG 116
Query: 83 N 83
N
Sbjct: 117 N 117
>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 = 61.9 bits (151), Expect = 2e-13
Identities = 21/63 (33%), Positives = 36/63 (57%), Gaps = 4/63 (6%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEE----NASANVEKML 80
D AGQERF +T YY+GA+G ++V+D+T +F+ + W +++ + +L
Sbjct: 56 DIAGQERFGGMTRVYYKGAVGAIIVFDVTRPSTFEAVLKWKADLDSKVTLPNGEPIPALL 115
Query: 81 LGN 83
L N
Sbjct: 116 LAN 118
>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 = 60.1 bits (146), Expect = 4e-13
Identities = 23/46 (50%), Positives = 31/46 (67%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEE 70
DTAGQE F IT AYYRGA +LV+ T+ +SF+ I++W +E
Sbjct: 57 DTAGQEEFDAITKAYYRGAQACILVFSTTDRESFEAIESWKEKVEA 102
>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 = 59.9 bits (145), Expect = 6e-13
Identities = 26/65 (40%), Positives = 44/65 (67%), Gaps = 1/65 (1%)
Query: 19 FHINYRDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRN-IEENASANVE 77
F + DTAGQERF+ I + YYRGA I++V+D+T+ S ++ + W+ + ++EN ++V
Sbjct: 49 FSLQLWDTAGQERFKCIASTYYRGAQAIIIVFDLTDVASLEHTRQWLEDALKENDPSSVL 108
Query: 78 KMLLG 82
L+G
Sbjct: 109 LFLVG 113
>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 = 56.8 bits (138), Expect = 7e-12
Identities = 25/60 (41%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEE-NASANVEKMLLGN 83
DTAGQE F + Y R G +LVY IT+ +SF+ IKN I +V +L+GN
Sbjct: 53 DTAGQEEFSAMRDQYIRNGDGFILVYSITSRESFEEIKNIREQILRVKDKEDVPIVLVGN 112
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 56.7 bits (136), Expect = 1e-11
Identities = 27/59 (45%), Positives = 39/59 (66%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENASANVEKMLLGN 83
DTAGQERFR++ +Y R + ++VYDITN +SF+N WI++I +V L+GN
Sbjct: 35 DTAGQERFRSLIPSYIRDSAAAIVVYDITNRQSFENTTKWIQDILNERGKDVIIALVGN 93
>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 = 52.9 bits (127), Expect = 2e-10
Identities = 19/51 (37%), Positives = 33/51 (64%)
Query: 21 INYRDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEEN 71
+++ DTAGQERF+T+ +YY A +LV+D+T + ++ N+ W + E
Sbjct: 51 VDFWDTAGQERFQTMHASYYHKAHACILVFDVTRKITYKNLSKWYEELREY 101
>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 = 49.9 bits (119), Expect = 4e-09
Identities = 19/40 (47%), Positives = 29/40 (72%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNW 64
DTAGQERFR++ T +YRG+ +L + + + +SF N+ NW
Sbjct: 60 DTAGQERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNW 99
>gnl|CDD|133318 cd04118, Rab24, Rab GTPase family 24 (Rab24). Rab24 is distinct
from other Rabs in several ways. It exists primarily in
the GTP-bound state, having a low intrinsic GTPase
activity; it is not efficiently geranyl-geranylated at
the C-terminus; it does not form a detectable complex
with Rab GDP-dissociation inhibitors (GDIs); and it has
recently been shown to undergo tyrosine phosphorylation
when overexpressed in vitro. The specific function of
Rab24 still remains unknown. It is found in a transport
route between ER-cis-Golgi and late endocytic
compartments. It is putatively involved in an autophagic
pathway, possibly directing misfolded proteins in the ER
to degradative pathways. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 193
Score = 49.9 bits (119), Expect = 4e-09
Identities = 18/47 (38%), Positives = 30/47 (63%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEEN 71
DTAG ER+ ++ YYRGA ++ YD+T+ SF+ K W++ ++
Sbjct: 56 DTAGSERYEAMSRIYYRGAKAAIVCYDLTDSSSFERAKFWVKELQNL 102
>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 = 47.9 bits (114), Expect = 3e-08
Identities = 21/62 (33%), Positives = 36/62 (58%), Gaps = 3/62 (4%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNW---IRNIEENASANVEKMLL 81
D GQ+ + Y GA + LVYDITN +SF+N+++W ++ + E + + +L+
Sbjct: 56 DIGGQQIGGKMLDKYIYGAQAVCLVYDITNSQSFENLEDWLSVVKKVNEESETKPKMVLV 115
Query: 82 GN 83
GN
Sbjct: 116 GN 117
>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 = 47.5 bits (113), Expect = 4e-08
Identities = 20/62 (32%), Positives = 39/62 (62%), Gaps = 3/62 (4%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNW---IRNIEENASANVEKMLL 81
DTAGQE + + + R G +LVY IT+ +F+ ++ + I+ +++ ++A+V M++
Sbjct: 53 DTAGQEEYTALRDQWIREGEGFILVYSITSRSTFERVERFREQIQRVKDESAADVPIMIV 112
Query: 82 GN 83
GN
Sbjct: 113 GN 114
>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 = 45.6 bits (109), Expect = 1e-07
Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 2/66 (3%)
Query: 19 FHINYRDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKN-WIRNIEENASANVE 77
++ DTAGQE + + Y +L + + + SF+N+K W I+ NV
Sbjct: 48 VNLGLWDTAGQEEYDRLRPLSYPQTDVFLLCFSVDSPSSFENVKTKWYPEIKHYCP-NVP 106
Query: 78 KMLLGN 83
+L+G
Sbjct: 107 IILVGT 112
>gnl|CDD|206709 cd04137, RheB, Ras Homolog Enriched in Brain (RheB) is a small
GTPase. Rheb (Ras Homolog Enriched in Brain) subfamily.
Rheb was initially identified in rat brain, where its
expression is elevated by seizures or by long-term
potentiation. It is expressed ubiquitously, with
elevated levels in muscle and brain. Rheb functions as
an important mediator between the tuberous sclerosis
complex proteins, TSC1 and TSC2, and the mammalian
target of rapamycin (TOR) kinase to stimulate cell
growth. TOR kinase regulates cell growth by controlling
nutrient availability, growth factors, and the energy
status of the cell. TSC1 and TSC2 form a dimeric complex
that has tumor suppressor activity, and TSC2 is a GTPase
activating protein (GAP) for Rheb. The TSC1/TSC2 complex
inhibits the activation of TOR kinase through Rheb. Rheb
has also been shown to induce the formation of large
cytoplasmic vacuoles in a process that is dependent on
the GTPase cycle of Rheb, but independent of the TOR
kinase, suggesting Rheb plays a role in endocytic
trafficking that leads to cell growth and cell-cycle
progression. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras proteins.
Length = 180
Score = 45.7 bits (109), Expect = 2e-07
Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 3/71 (4%)
Query: 15 FQHNFHINYRDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENA-- 72
+H+ DTAGQ+ + + Y G G +LVY +T+ KSF+ +K I + +
Sbjct: 45 KGQEYHLEIVDTAGQDEYSILPQKYSIGIHGYILVYSVTSRKSFEVVKV-IYDKILDMLG 103
Query: 73 SANVEKMLLGN 83
+V +L+GN
Sbjct: 104 KESVPIVLVGN 114
>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 = 45.4 bits (108), Expect = 2e-07
Identities = 21/65 (32%), Positives = 30/65 (46%), Gaps = 2/65 (3%)
Query: 21 INYRDTAGQERFRTITTAYYRGAMGIMLVYDITN-EKSFDNIKN-WIRNIEENASANVEK 78
N DTAGQE + I YYR + V+DI + I + I +A + V
Sbjct: 53 FNLLDTAGQEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAESGVPI 112
Query: 79 MLLGN 83
+L+GN
Sbjct: 113 ILVGN 117
>gnl|CDD|133376 cd04176, Rap2, Rap2 family GTPase consists of Rap2a, Rap2b, and
Rap2c. The Rap2 subgroup is part of the Rap subfamily
of the Ras family. It consists of Rap2a, Rap2b, and
Rap2c. Both isoform 3 of the human mitogen-activated
protein kinase kinase kinase kinase 4 (MAP4K4) and
Traf2- and Nck-interacting kinase (TNIK) are putative
effectors of Rap2 in mediating the activation of c-Jun
N-terminal kinase (JNK) to regulate the actin
cytoskeleton. In human platelets, Rap2 was shown to
interact with the cytoskeleton by binding the actin
filaments. In embryonic Xenopus development, Rap2 is
necessary for the Wnt/beta-catenin signaling pathway.
The Rap2 interacting protein 9 (RPIP9) is highly
expressed in human breast carcinomas and correlates with
a poor prognosis, suggesting a role for Rap2 in breast
cancer oncogenesis. Rap2b, but not Rap2a, Rap2c, Rap1a,
or Rap1b, is expressed in human red blood cells, where
it is believed to be involved in vesiculation. A number
of additional effector proteins for Rap2 have been
identified, including the RalGEFs RalGDS, RGL, and Rlf,
which also interact with Rap1 and Ras. Most Ras proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 163
Score = 45.2 bits (107), Expect = 2e-07
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEE-NASANVEKMLLGN 83
DTAG E+F ++ Y + G ++VY + N+++F +IK I V +L+GN
Sbjct: 55 DTAGTEQFASMRDLYIKNGQGFIVVYSLVNQQTFQDIKPMRDQIVRVKGYEKVPIILVGN 114
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 45.1 bits (107), Expect = 3e-07
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 3/57 (5%)
Query: 15 FQHNF---HINYRDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNI 68
F N N DTAGQE+F + YY ++++D+T+ ++ N+ NW R+I
Sbjct: 51 FYTNCGPICFNVWDTAGQEKFGGLRDGYYIKGQCAIIMFDVTSRITYKNVPNWHRDI 107
>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 = 44.9 bits (106), Expect = 4e-07
Identities = 19/65 (29%), Positives = 41/65 (63%)
Query: 19 FHINYRDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENASANVEK 78
++I+ DTAG+E+F + + Y RGA ++L YD++N +S + +++ + + A+ +
Sbjct: 44 YNISIWDTAGREQFHGLGSMYCRGAAAVILTYDVSNVQSLEELEDRFLGLTDTANEDCLF 103
Query: 79 MLLGN 83
++GN
Sbjct: 104 AVVGN 108
>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 = 44.3 bits (105), Expect = 4e-07
Identities = 13/55 (23%), Positives = 34/55 (61%)
Query: 21 INYRDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENASAN 75
+N+ D +G + + +Y+ G++LVYD+T+ +SF+ + +W++ +++ +
Sbjct: 51 VNFFDLSGHPEYLEVRNEFYKDTQGVLLVYDVTDRQSFEALDSWLKEMKQEGGPH 105
>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 = 44.3 bits (105), Expect = 5e-07
Identities = 16/44 (36%), Positives = 24/44 (54%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNI 68
DTAGQE F + Y R G +LV+ +T+ SF+ + + I
Sbjct: 56 DTAGQEEFSAMREQYMRTGEGFLLVFSVTDRGSFEEVDKFHTQI 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 = 44.1 bits (104), Expect = 5e-07
Identities = 17/48 (35%), Positives = 27/48 (56%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENA 72
D+AGQE F + + + +VYD+TNE SF+N WI + ++
Sbjct: 59 DSAGQELFSDMVENVWEQPAVVCVVYDVTNEVSFNNCSRWINRVRTHS 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 = 43.9 bits (104), Expect = 6e-07
Identities = 16/44 (36%), Positives = 24/44 (54%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNI 68
DTAGQE + + Y R G + V+ I + KSF++I + I
Sbjct: 55 DTAGQEEYSAMRDQYMRTGEGFLCVFAINSRKSFEDIHTYREQI 98
>gnl|CDD|214541 smart00173, RAS, Ras subfamily of RAS small GTPases. Similar in
fold and function to the bacterial EF-Tu GTPase. p21Ras
couples receptor Tyr kinases and G protein receptors to
protein kinase cascades.
Length = 164
Score = 43.3 bits (103), Expect = 1e-06
Identities = 24/60 (40%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEE-NASANVEKMLLGN 83
DTAGQE F + Y R G +LVY IT+ +SF+ IK + I +V +L+GN
Sbjct: 54 DTAGQEEFSAMRDQYMRTGEGFLLVYSITDRQSFEEIKKFREQILRVKDRDDVPIVLVGN 113
>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 = 42.9 bits (102), Expect = 1e-06
Identities = 18/39 (46%), Positives = 23/39 (58%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKN 63
DTAGQE F + Y R G +LVY IT+ +SF+ I
Sbjct: 56 DTAGQEEFSAMRDQYMRTGEGFLLVYSITDRQSFEEIAK 94
>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 = 42.8 bits (101), Expect = 1e-06
Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 1/64 (1%)
Query: 21 INYRDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKN-WIRNIEENASANVEKM 79
+N DTAGQE + I Y+R G +LV+ IT+ +SF + + + NV +
Sbjct: 50 LNILDTAGQEDYAAIRDNYFRSGEGFLLVFSITDMESFTALAEFREQILRVKEDDNVPLL 109
Query: 80 LLGN 83
L+GN
Sbjct: 110 LVGN 113
>gnl|CDD|128473 smart00176, RAN, Ran (Ras-related nuclear proteins) /TC4 subfamily
of small GTPases. Ran is involved in the active
transport of proteins through nuclear pores.
Length = 200
Score = 42.3 bits (99), Expect = 3e-06
Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 3/76 (3%)
Query: 8 LQIFRGCFQHNFHINYRDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRN 67
L F N DTAGQE+F + YY ++++D+T ++ N+ NW R+
Sbjct: 35 LVFHTNRGPIRF--NVWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTARVTYKNVPNWHRD 92
Query: 68 IEENASANVEKMLLGN 83
+ N+ +L GN
Sbjct: 93 LVR-VCENIPIVLCGN 107
>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 = 41.7 bits (98), Expect = 4e-06
Identities = 17/76 (22%), Positives = 27/76 (35%), Gaps = 8/76 (10%)
Query: 1 SGENLCTLQIFRGCFQHNFH---INYRDTAGQERF-----RTITTAYYRGAMGIMLVYDI 52
S T + + + DT G + F + RGA I+LV D
Sbjct: 26 SDVPGTTRDPDVYVKELDKGKVKLVLVDTPGLDEFGGLGREELARLLLRGADLILLVVDS 85
Query: 53 TNEKSFDNIKNWIRNI 68
T+ +S ++ K I
Sbjct: 86 TDRESEEDAKLLILRR 101
>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 = 41.4 bits (98), Expect = 5e-06
Identities = 16/60 (26%), Positives = 29/60 (48%), Gaps = 2/60 (3%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKN-WIRNIEENASANVEKMLLGN 83
DTAGQE + + Y ++ + + + SF+N+K W ++ NV +L+G
Sbjct: 52 DTAGQEDYDRLRPLSYPDTDVFLICFSVDSPASFENVKEKWYPEVKHFC-PNVPIILVGT 110
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 41.8 bits (98), Expect = 5e-06
Identities = 16/37 (43%), Positives = 21/37 (56%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNI 61
DTAGQE + + Y R G + VY IT+ SF+ I
Sbjct: 59 DTAGQEEYSAMRDQYMRTGQGFLCVYSITSRSSFEEI 95
>gnl|CDD|206644 cd00878, Arf_Arl, ADP-ribosylation factor(Arf)/Arf-like (Arl)
small GTPases. Arf (ADP-ribosylation factor)/Arl
(Arf-like) small GTPases. Arf proteins are activators
of phospholipase D isoforms. Unlike Ras proteins they
lack cysteine residues at their C-termini and therefore
are unlikely to be prenylated. Arfs are N-terminally
myristoylated. Members of the Arf family are regulators
of vesicle formation in intracellular traffic that
interact reversibly with membranes of the secretory and
endocytic compartments in a GTP-dependent manner. They
depart from other small GTP-binding proteins by a
unique structural device, interswitch toggle, that
implements front-back communication from N-terminus to
the nucleotide binding site. Arf-like (Arl) proteins
are close relatives of the Arf, but only Arl1 has been
shown to function in membrane traffic like the Arf
proteins. Arl2 has an unrelated function in the folding
of native tubulin, and Arl4 may function in the
nucleus. Most other Arf family proteins are so far
relatively poorly characterized. Thus, despite their
significant sequence homologies, Arf family proteins
may regulate unrelated functions.
Length = 158
Score = 41.0 bits (97), Expect = 6e-06
Identities = 12/52 (23%), Positives = 23/52 (44%)
Query: 17 HNFHINYRDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNI 68
N D GQ++ R + YY G++ V D ++ + + KN + +
Sbjct: 41 KNVKFTVWDVGGQDKIRPLWKHYYENTDGLIFVVDSSDRERIEEAKNELHKL 92
>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 = 41.4 bits (97), Expect = 6e-06
Identities = 20/61 (32%), Positives = 36/61 (59%), Gaps = 3/61 (4%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRN--IEENASANVEKMLLG 82
DTAG E+F + Y + G LVY IT ++SF+++++ +R + + +V +L+G
Sbjct: 55 DTAGTEQFTAMRDLYIKNGQGFALVYSITAQQSFNDLQD-LREQILRVKDTEDVPMILVG 113
Query: 83 N 83
N
Sbjct: 114 N 114
>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 = 40.7 bits (96), Expect = 9e-06
Identities = 15/44 (34%), Positives = 28/44 (63%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNI 68
DTAGQE+F + YY ++++D+T+ ++ N+ NW R++
Sbjct: 55 DTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRVTYKNVPNWHRDL 98
>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 = 39.3 bits (92), Expect = 2e-05
Identities = 17/66 (25%), Positives = 32/66 (48%), Gaps = 4/66 (6%)
Query: 21 INYRDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSF---DNIKNWIRNIEENASANVE 77
+N D G+E + + + A I+LVYD+T+ +S + W+ N+ +
Sbjct: 50 LNIWDFGGREELKFEHIIFMKWADAILLVYDLTDRESLNEVSRLIAWLPNL-RKLGGKIP 108
Query: 78 KMLLGN 83
+L+GN
Sbjct: 109 VILVGN 114
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 40.5 bits (95), Expect = 2e-05
Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENASANVEKMLLGN 83
DTAGQE+F + YY ++++D+T ++ N+ W R++ N+ +L GN
Sbjct: 68 DTAGQEKFGGLRDGYYIHGQCAIIMFDVTARLTYKNVPTWHRDLCR-VCENIPIVLCGN 125
>gnl|CDD|206713 cd04146, RERG_RasL11_like, Ras-related and Estrogen-Regulated
Growth inhibitor (RERG) and Ras-like 11 (RasL11)-like
families. RERG (Ras-related and Estrogen- Regulated
Growth inhibitor) and Ras-like 11 are members of a novel
subfamily of Ras that were identified based on their
behavior in breast and prostate tumors, respectively.
RERG expression was decreased or lost in a significant
fraction of primary human breast tumors that lack
estrogen receptor and are correlated with poor clinical
prognosis. Elevated RERG expression correlated with
favorable patient outcome in a breast tumor subtype that
is positive for estrogen receptor expression. In
contrast to most Ras proteins, RERG overexpression
inhibited the growth of breast tumor cells in vitro and
in vivo. RasL11 was found to be ubiquitously expressed
in human tissue, but down-regulated in prostate tumors.
Both RERG and RasL11 lack the C-terminal CaaX
prenylation motif, where a = an aliphatic amino acid and
X = any amino acid, and are localized primarily in the
cytoplasm. Both are believed to have tumor suppressor
activity.
Length = 166
Score = 40.0 bits (94), Expect = 2e-05
Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 4/63 (6%)
Query: 25 DTAGQERFRT--ITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENASA--NVEKML 80
DT GQ++ R A G +LVY IT+ SFD + ++ I E + +L
Sbjct: 53 DTPGQQQNEDPESLERSLRWADGFVLVYSITDRSSFDVVSQLLQLIREIKKRDGEIPVIL 112
Query: 81 LGN 83
+GN
Sbjct: 113 VGN 115
>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 = 38.9 bits (91), Expect = 5e-05
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKN-W 64
DTAGQE + + Y I++ Y + N S DN+++ W
Sbjct: 58 DTAGQEDYDRLRPLSYPDVDVILICYSVDNPTSLDNVEDKW 98
>gnl|CDD|177661 PLN00023, PLN00023, GTP-binding protein; Provisional.
Length = 334
Score = 39.1 bits (91), Expect = 6e-05
Identities = 11/60 (18%), Positives = 31/60 (51%)
Query: 12 RGCFQHNFHINYRDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEEN 71
+G + +F + D +G ER++ + +Y G++ V+D++ ++ +++ W +
Sbjct: 76 KGDSERDFFVELWDVSGHERYKDCRSLFYSQINGVIFVHDLSQRRTKTSLQKWASEVAAT 135
>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 = 37.5 bits (87), Expect = 1e-04
Identities = 20/62 (32%), Positives = 35/62 (56%), Gaps = 5/62 (8%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDN---IKNWIRNIEENASANVEKMLL 81
DTAG E+F + Y + G +LVY +T+E S + ++ + I+++ NV +L+
Sbjct: 55 DTAGTEQFTAMRELYIKSGQGFLLVYSVTSEASLNELGELREQVLRIKDS--DNVPMVLV 112
Query: 82 GN 83
GN
Sbjct: 113 GN 114
>gnl|CDD|206689 cd04102, RabL3, Rab GTPase-like family 3 (Rab-like3). RabL3
(Rab-like3) subfamily. RabL3s are novel proteins that
have high sequence similarity with Rab family members,
but display features that are distinct from Rabs, and
have been termed Rab-like. As in other Rab-like
proteins, RabL3 lacks a prenylation site at the
C-terminus. The specific function of RabL3 remains
unknown.
Length = 204
Score = 36.4 bits (84), Expect = 4e-04
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 4/53 (7%)
Query: 16 QHNFHINYRDTAGQ----ERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNW 64
+ F++ D G E ++ +Y GI+ V+D+TN+KS N+ W
Sbjct: 51 EKTFYVELWDVGGSVGSAESVKSTRAVFYNQINGIIFVHDLTNKKSSQNLYRW 103
>gnl|CDD|133375 cd04175, Rap1, Rap1 family GTPase consists of Rap1a and Rap1b
isoforms. The Rap1 subgroup is part of the Rap
subfamily of the Ras family. It can be further divided
into the Rap1a and Rap1b isoforms. In humans, Rap1a and
Rap1b share 95% sequence homology, but are products of
two different genes located on chromosomes 1 and 12,
respectively. Rap1a is sometimes called smg p21 or Krev1
in the older literature. Rap1 proteins are believed to
perform different cellular functions, depending on the
isoform, its subcellular localization, and the effector
proteins it binds. For example, in rat salivary gland,
neutrophils, and platelets, Rap1 localizes to secretory
granules and is believed to regulate exocytosis or the
formation of secretory granules. Rap1 has also been
shown to localize in the Golgi of rat fibroblasts,
zymogen granules, plasma membrane, and the microsomal
membrane of pancreatic acini, as well as in the
endocytic compartment of skeletal muscle cells and
fibroblasts. High expression of Rap1 has been observed
in the nucleus of human oropharyngeal squamous cell
carcinomas (SCCs) and cell lines; interestingly, in the
SCCs, the active GTP-bound form localized to the
nucleus, while the inactive GDP-bound form localized to
the cytoplasm. Rap1 plays a role in phagocytosis by
controlling the binding of adhesion receptors (typically
integrins) to their ligands. In yeast, Rap1 has been
implicated in multiple functions, including activation
and silencing of transcription and maintenance of
telomeres. Rap1a, which is stimulated by T-cell receptor
(TCR) activation, is a positive regulator of T cells by
directing integrin activation and augmenting lymphocyte
responses. In murine hippocampal neurons, Rap1b
determines which neurite will become the axon and
directs the recruitment of Cdc42, which is required for
formation of dendrites and axons. In murine platelets,
Rap1b is required for normal homeostasis in vivo and is
involved in integrin activation. Most Ras proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 164
Score = 36.0 bits (83), Expect = 6e-04
Identities = 19/60 (31%), Positives = 34/60 (56%), Gaps = 1/60 (1%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNI-EENASANVEKMLLGN 83
DTAG E+F + Y + G +LVY IT + +F+++++ I + +V +L+GN
Sbjct: 55 DTAGTEQFTAMRDLYMKNGQGFVLVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGN 114
>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 = 35.6 bits (82), Expect = 7e-04
Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNI-KNWIRNIEENASANVEKMLLG 82
DTAGQE + + YRGA +L + + ++ S++N+ K WI + A V +L+G
Sbjct: 55 DTAGQEDYNRLRPLSYRGADVFLLAFSLISKASYENVLKKWIPELRHYA-PGVPIVLVG 112
>gnl|CDD|206706 cd04134, Rho3, Ras homology family 3 (Rho3) of small guanosine
triphosphatases (GTPases). Rho3 is a member of the Rho
family found only in fungi. Rho3 is believed to regulate
cell polarity by interacting with the diaphanous/formin
family protein For3 to control both the actin
cytoskeleton and microtubules. Rho3 is also believed to
have a direct role in exocytosis that is independent of
its role in regulating actin polarity. The function in
exocytosis may be two-pronged: first, in the transport
of post-Golgi vesicles from the mother cell to the bud,
mediated by myosin (Myo2); second, in the docking and
fusion of vesicles to the plasma membrane, mediated by
an exocyst (Exo70) protein. Most Rho proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Rho proteins.
Length = 185
Score = 35.6 bits (82), Expect = 7e-04
Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 2/58 (3%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKN-WIRNIEENASANVEKMLL 81
DTAGQE F + + Y IML + + N S +N+++ W+ I + V+ +L+
Sbjct: 54 DTAGQEEFDRLRSLSYADTHVIMLCFSVDNPDSLENVESKWLAEIRHHCPG-VKLVLV 110
>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 = 33.9 bits (78), Expect = 0.003
Identities = 16/50 (32%), Positives = 22/50 (44%), Gaps = 1/50 (2%)
Query: 20 HINYRDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKN-WIRNI 68
+ DTAGQ+ F + Y +L + + N SF NI WI I
Sbjct: 49 RLQLCDTAGQDEFDKLRPLCYPDTDVFLLCFSVVNPSSFQNISEKWIPEI 98
>gnl|CDD|206712 cd04141, Rit_Rin_Ric, Ras-like protein in all tissues (Rit),
Ras-like protein in neurons (Rin) and Ras-related
protein which interacts with calmodulin (Ric). Rit
(Ras-like protein in all tissues), Rin (Ras-like
protein in neurons) and Ric (Ras-related protein which
interacts with calmodulin) form a subfamily with
several unique structural and functional
characteristics. These proteins all lack a the
C-terminal CaaX lipid-binding motif typical of Ras
family proteins, and Rin and Ric contain
calmodulin-binding domains. Rin, which is expressed
only in neurons, induces neurite outgrowth in rat
pheochromocytoma cells through its association with
calmodulin and its activation of endogenous Rac/cdc42.
Rit, which is ubiquitously expressed in mammals,
inhibits growth-factor withdrawl-mediated apoptosis and
induces neurite extension in pheochromocytoma cells.
Rit and Rin are both able to form a ternary complex
with PAR6, a cell polarity-regulating protein, and
Rac/cdc42. This ternary complex is proposed to have
physiological function in processes such as
tumorigenesis. Activated Ric is likely to signal in
parallel with the Ras pathway or stimulate the Ras
pathway at some upstream point, and binding of
calmodulin to Ric may negatively regulate Ric activity.
Length = 172
Score = 34.1 bits (78), Expect = 0.003
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSF 58
DTAGQ F + Y R G ++ Y +T+ SF
Sbjct: 56 DTAGQAEFTAMRDQYMRCGEGFIICYSVTDRHSF 89
>gnl|CDD|206701 cd04128, Spg1, Septum-promoting GTPase (Spg1). Spg1p. Spg1p
(septum-promoting GTPase) was first identified in the
fission yeast S. pombe, where it regulates septum
formation in the septation initiation network (SIN)
through the cdc7 protein kinase. Spg1p is an essential
gene that localizes to the spindle pole bodies. When
GTP-bound, it binds cdc7 and causes it to translocate
to spindle poles. Sid4p (septation initiation
defective) is required for localization of Spg1p to the
spindle pole body, and the ability of Spg1p to promote
septum formation from any point in the cell cycle
depends on Sid4p. Spg1p is negatively regulated by Byr4
and cdc16, which form a two-component GTPase activating
protein (GAP) for Spg1p. The existence of a SIN-related
pathway in plants has been proposed. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization.
Length = 182
Score = 33.5 bits (77), Expect = 0.004
Identities = 12/42 (28%), Positives = 23/42 (54%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIR 66
D GQ F + + A+ I+ ++D+T + + ++IK W R
Sbjct: 55 DLGGQREFINMLPLVCKDAVAILFMFDLTRKSTLNSIKEWYR 96
>gnl|CDD|133356 cd04156, ARLTS1, Arf-like tumor suppressor gene 1 (ARLTS1 or
Arl11). ARLTS1 (Arf-like tumor suppressor gene 1), also
known as Arl11, is a member of the Arf family of small
GTPases that is believed to play a major role in
apoptotic signaling. ARLTS1 is widely expressed and
functions as a tumor suppressor gene in several human
cancers. ARLTS1 is a low-penetrance suppressor that
accounts for a small percentage of familial melanoma or
familial chronic lymphocytic leukemia (CLL). ARLTS1
inactivation seems to occur most frequently through
biallelic down-regulation by hypermethylation of the
promoter. In breast cancer, ARLTS1 alterations were
typically a combination of a hypomorphic polymorphism
plus loss of heterozygosity. In a case of thyroid
adenoma, ARLTS1 alterations were polymorphism plus
promoter hypermethylation. The nonsense polymorphism
Trp149Stop occurs with significantly greater frequency
in familial cancer cases than in sporadic cancer cases,
and the Cys148Arg polymorphism is associated with an
increase in high-risk familial breast cancer.
Length = 160
Score = 32.8 bits (75), Expect = 0.007
Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENAS-ANVEKMLLGN 83
D GQE+ RT+ Y G++ V D ++E D + +++I +N V +LL N
Sbjct: 50 DVGGQEKMRTVWKCYLENTDGLVYVVDSSDEARLDESQKELKHILKNEHIKGVPVVLLAN 109
>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 = 32.4 bits (74), Expect = 0.010
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 2/60 (3%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKN-WIRNIEENASANVEKMLLGN 83
DTAGQE + + Y I++ + I + S +NI W ++ NV +L+GN
Sbjct: 55 DTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCP-NVPIILVGN 113
>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 = 32.3 bits (73), Expect = 0.013
Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 2/59 (3%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIK-NWIRNIEENASANVEKMLLG 82
DTAGQE + + Y ++ + + N SF N+K W+ ++E A NV +L+G
Sbjct: 54 DTAGQEDYDRLRPLSYPMTDVFLICFSVVNPASFQNVKEEWVPELKEYAP-NVPYLLIG 111
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 32.0 bits (73), Expect = 0.013
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYD 51
T GQERF+ + RGA+G +++ D
Sbjct: 74 GTPGQERFKFMWEILSRGAVGAIVLVD 100
>gnl|CDD|206725 cd04160, Arfrp1, Arf-related protein 1 (Arfrp1). Arfrp1
(Arf-related protein 1), formerly known as ARP, is a
membrane-associated Arf family member that lacks the
N-terminal myristoylation motif. Arfrp1 is mainly
associated with the trans-Golgi compartment and the
trans-Golgi network, where it regulates the targeting
of Arl1 and the GRIP domain-containing proteins,
golgin-97 and golgin-245, onto Golgi membranes. It is
also involved in the anterograde transport of the
vesicular stomatitis virus G protein from the Golgi to
the plasma membrane, and in the retrograde transport of
TGN38 and Shiga toxin from endosomes to the trans-Golgi
network. Arfrp1 also inhibits Arf/Sec7-dependent
activation of phospholipase D. Deletion of Arfrp1 in
mice causes embryonic lethality at the gastrulation
stage and apoptosis of mesodermal cells, indicating its
importance in development.
Length = 168
Score = 31.9 bits (73), Expect = 0.014
Identities = 13/43 (30%), Positives = 24/43 (55%)
Query: 21 INYRDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKN 63
+ + D GQE R++ YY + G++ V D T+ + F+ K+
Sbjct: 53 LMFWDLGGQEELRSLWDKYYAESHGVIYVIDSTDRERFNESKS 95
>gnl|CDD|206711 cd04140, ARHI_like, A Ras homolog member I (ARHI). ARHI (A Ras
homolog member I) is a member of the Ras family with
several unique structural and functional properties.
ARHI is expressed in normal human ovarian and breast
tissue, but its expression is decreased or eliminated in
breast and ovarian cancer. ARHI contains an N-terminal
extension of 34 residues (human) that is required to
retain its tumor suppressive activity. Unlike most other
Ras family members, ARHI is maintained in the
constitutively active (GTP-bound) state in resting cells
and has modest GTPase activity. ARHI inhibits STAT3
(signal transducers and activators of transcription 3),
a latent transcription factor whose abnormal activation
plays a critical role in oncogenesis. Most Ras proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 165
Score = 31.7 bits (72), Expect = 0.017
Identities = 23/83 (27%), Positives = 36/83 (43%), Gaps = 16/83 (19%)
Query: 4 NLCTLQIFRGCFQHNFHINYRDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIK- 62
++CTLQI DT G +F + +LVY IT+++S + +K
Sbjct: 47 SICTLQI-------------TDTTGSHQFPAMQRLSISKGHAFILVYSITSKQSLEELKP 93
Query: 63 --NWIRNIEENASANVEKMLLGN 83
I I+ N + ML+GN
Sbjct: 94 IYELICEIKGNNLEKIPIMLVGN 116
>gnl|CDD|206724 cd04159, Arl10_like, Arf-like 9 (Arl9) and 10 (Arl10) GTPases.
Arl10-like subfamily. Arl9/Arl10 was identified from a
human cancer-derived EST dataset. No functional
information about the subfamily is available at the
current time, but crystal structures of human Arl10b and
Arl10c have been solved.
Length = 159
Score = 30.0 bits (68), Expect = 0.065
Identities = 18/60 (30%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRN-IEENASANVEKMLLGN 83
D GQ RFR++ Y RG I+ V D + + + KN + + +E+ + + ++LGN
Sbjct: 50 DLGGQPRFRSMWERYCRGVNAIVYVVDAADREKLEVAKNELHDLLEKPSLEGIPLLVLGN 109
>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 = 30.0 bits (68), Expect = 0.076
Identities = 11/55 (20%), Positives = 20/55 (36%)
Query: 19 FHINYRDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENAS 73
+N D GQE + + +LV+D+ + W+R I+
Sbjct: 51 IRLNVWDFGGQEIYHATHQFFLTSRSLYLLVFDLRTGDEVSRVPYWLRQIKAFGG 105
>gnl|CDD|128474 smart00177, ARF, ARF-like small GTPases; ARF, ADP-ribosylation
factor. Ras homologues involved in vesicular
transport. Activator of phospholipase D isoforms.
Unlike Ras proteins they lack cysteine residues at
their C-termini and therefore are unlikely to be
prenylated. ARFs are N-terminally myristoylated.
Contains ATP/GTP-binding motif (P-loop).
Length = 175
Score = 29.1 bits (65), Expect = 0.19
Identities = 10/34 (29%), Positives = 15/34 (44%)
Query: 18 NFHINYRDTAGQERFRTITTAYYRGAMGIMLVYD 51
N D GQ++ R + YY G++ V D
Sbjct: 56 NISFTVWDVGGQDKIRPLWRHYYTNTQGLIFVVD 89
>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 = 28.9 bits (65), Expect = 0.19
Identities = 10/47 (21%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNI-KNWIRNIEE 70
DT+G + + Y + +++ +DI+ ++ D++ K W + E
Sbjct: 55 DTSGSPYYDNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEVRE 101
>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 = 28.6 bits (64), Expect = 0.26
Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIK-NWIRNI 68
DTAGQE + + Y A I++ + I S +N++ WI +
Sbjct: 55 DTAGQEEYERLRPLSYSKAHVILIGFAIDTPDSLENVRTKWIEEV 99
>gnl|CDD|205305 pfam13124, DUF3963, Protein of unknown function (DUF3963). This
family of proteins is functionally uncharacterized.
This family of proteins is found in bacteria. Proteins
in this family are typically between 42 and 85 amino
acids in length. There is a conserved DIQKW sequence
motif.
Length = 40
Score = 26.7 bits (59), Expect = 0.35
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 49 VYDITNEKSFDNIKNWIRNI 68
+ E+ FD+I+ WIRNI
Sbjct: 4 INAAFIERYFDDIQKWIRNI 23
>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 = 28.1 bits (62), Expect = 0.36
Identities = 14/59 (23%), Positives = 31/59 (52%), Gaps = 2/59 (3%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNI-KNWIRNIEENASANVEKMLLG 82
DT+G + + Y + +++ +DI+ ++ D++ K W I+E N + +L+G
Sbjct: 59 DTSGSPYYDNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEIQE-FCPNTKMLLVG 116
>gnl|CDD|206664 cd01874, Cdc42, cell division cycle 42 (Cdc42) is a small GTPase
of the Rho family. Cdc42 is an essential GTPase that
belongs to the Rho family of Ras-like GTPases. These
proteins act as molecular switches by responding to
exogenous and/or endogenous signals and relaying those
signals to activate downstream components of a
biological pathway. Cdc42 transduces signals to the
actin cytoskeleton to initiate and maintain polarized
growth and to mitogen-activated protein morphogenesis.
In the budding yeast Saccharomyces cerevisiae, Cdc42
plays an important role in multiple actin-dependent
morphogenetic events such as bud emergence,
mating-projection formation, and pseudohyphal growth.
In mammalian cells, Cdc42 regulates a variety of
actin-dependent events and induces the JNK/SAPK protein
kinase cascade, which leads to the activation of
transcription factors within the nucleus. Cdc42
mediates these processes through interactions with a
myriad of downstream effectors, whose number and
regulation we are just starting to understand. In
addition, Cdc42 has been implicated in a number of
human diseases through interactions with its regulators
and downstream effectors. Most Rho proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of
most Rho proteins. Due to the presence of truncated
sequences in this CD, the lipid modification site is
not available for annotation.
Length = 175
Score = 28.3 bits (63), Expect = 0.37
Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIK-NWIRNI 68
DTAGQE + + Y ++ + + + SF+N+K W+ I
Sbjct: 55 DTAGQEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEI 99
>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 = 28.1 bits (62), Expect = 0.38
Identities = 12/43 (27%), Positives = 24/43 (55%)
Query: 21 INYRDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKN 63
+N DTAGQE + + T Y ++ + I + S++N+++
Sbjct: 53 LNLWDTAGQEEYDRLRTLSYPQTNVFIICFSIASPSSYENVRH 95
>gnl|CDD|206716 cd04149, Arf6, ADP ribosylation factor 6 (Arf6). Arf6 subfamily.
Arf6 (ADP ribosylation factor 6) proteins localize to
the plasma membrane, where they perform a wide variety
of functions. In its active, GTP-bound form, Arf6 is
involved in cell spreading, Rac-induced formation of
plasma membrane ruffles, cell migration, wound healing,
and Fc-mediated phagocytosis. Arf6 appears to change
the actin structure at the plasma membrane by
activating Rac, a Rho family protein involved in
membrane ruffling. Arf6 is required for and enhances
Rac formation of ruffles. Arf6 can regulate dendritic
branching in hippocampal neurons, and in yeast it
localizes to the growing bud, where it plays a role in
polarized growth and bud site selection. In leukocytes,
Arf6 is required for chemokine-stimulated migration
across endothelial cells. Arf6 also plays a role in
down-regulation of beta2-adrenergic receptors and
luteinizing hormone receptors by facilitating the
release of sequestered arrestin to allow endocytosis.
Arf6 is believed to function at multiple sites on the
plasma membrane through interaction with a specific set
of GEFs, GAPs, and effectors. Arf6 has been implicated
in breast cancer and melanoma cell invasion, and in
actin remodelling at the invasion site of Chlamydia
infection.
Length = 168
Score = 27.8 bits (62), Expect = 0.46
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 18 NFHINYRDTAGQERFRTITTAYYRGAMGIMLVYD 51
N N D GQ++ R + YY G G++ V D
Sbjct: 52 NVKFNVWDVGGQDKIRPLWRHYYTGTQGLIFVVD 85
>gnl|CDD|133361 cd04161, Arl2l1_Arl13_like, Arl2-like protein 1 (Arl2l1) and
Arl13. Arl2l1 (Arl2-like protein 1) and Arl13 form a
subfamily of the Arf family of small GTPases. Arl2l1
was identified in human cells during a search for the
gene(s) responsible for Bardet-Biedl syndrome (BBS).
Like Arl6, the identified BBS gene, Arl2l1 is proposed
to have cilia-specific functions. Arl13 is found on the
X chromosome, but its expression has not been
confirmed; it may be a pseudogene.
Length = 167
Score = 27.7 bits (62), Expect = 0.55
Identities = 11/36 (30%), Positives = 15/36 (41%)
Query: 16 QHNFHINYRDTAGQERFRTITTAYYRGAMGIMLVYD 51
+ + D G FR I YY A G++ V D
Sbjct: 40 LDKYEVCIFDLGGGANFRGIWVNYYAEAHGLVFVVD 75
>gnl|CDD|224535 COG1620, LldP, L-lactate permease [Energy production and
conversion].
Length = 522
Score = 27.2 bits (61), Expect = 0.89
Identities = 9/39 (23%), Positives = 16/39 (41%), Gaps = 2/39 (5%)
Query: 44 MGIMLVYDITNEKSFDNIKNWIRNIEENASANVEKMLLG 82
I L +FD I+ + NI + + +L+G
Sbjct: 73 GAIFLYKMSVKSGAFDIIRKSLANITPDRRIQL--LLIG 109
>gnl|CDD|133353 cd04153, Arl5_Arl8, Arf-like 5 (Arl5) and 8 (Arl8) GTPases.
Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like
Arl4 and Arl7, are localized to the nucleus and
nucleolus. Arl5 is developmentally regulated during
embryogenesis in mice. Human Arl5 interacts with the
heterochromatin protein 1-alpha (HP1alpha), a
nonhistone chromosomal protein that is associated with
heterochromatin and telomeres, and prevents telomere
fusion. Arl5 may also play a role in embryonic nuclear
dynamics and/or signaling cascades. Arl8 was identified
from a fetal cartilage cDNA library. It is found in
brain, heart, lung, cartilage, and kidney. No function
has been assigned for Arl8 to date.
Length = 174
Score = 26.9 bits (60), Expect = 1.0
Identities = 12/37 (32%), Positives = 16/37 (43%)
Query: 18 NFHINYRDTAGQERFRTITTAYYRGAMGIMLVYDITN 54
N D GQE R+ YY ++LV D T+
Sbjct: 58 NIRFLMWDIGGQESLRSSWNTYYTNTDAVILVIDSTD 94
>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 = 26.9 bits (59), Expect = 1.1
Identities = 11/41 (26%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDN-IKNW 64
DT+G + + Y + ++L +DI+ + FD+ +K W
Sbjct: 67 DTSGSPYYDNVRPLCYSDSDAVLLCFDISRPEIFDSALKKW 107
>gnl|CDD|182040 PRK09707, PRK09707, putative lipoprotein; Provisional.
Length = 1343
Score = 27.0 bits (59), Expect = 1.3
Identities = 12/43 (27%), Positives = 22/43 (51%)
Query: 6 CTLQIFRGCFQHNFHINYRDTAGQERFRTITTAYYRGAMGIML 48
CTLQ+F+ C + + T + +TT + R +G++L
Sbjct: 11 CTLQVFQACSELTRRVGKTSTVNLRKSSGLTTKFSRLTLGVLL 53
>gnl|CDD|206722 cd04157, Arl6, Arf-like 6 (Arl6) GTPase. Arl6 (Arf-like 6) forms
a subfamily of the Arf family of small GTPases. Arl6
expression is limited to the brain and kidney in adult
mice, but it is expressed in the neural plate and
somites during embryogenesis, suggesting a possible
role for Arl6 in early development. Arl6 is also
believed to have a role in cilia or flagella function.
Several proteins have been identified that bind Arl6,
including Arl6 interacting protein (Arl6ip), and
SEC61beta, a subunit of the heterotrimeric conducting
channel SEC61p. Based on Arl6 binding to these
effectors, Arl6 is also proposed to play a role in
protein transport, membrane trafficking, or cell
signaling during hematopoietic maturation. At least
three specific homozygous Arl6 mutations in humans have
been found to cause Bardet-Biedl syndrome, a disorder
characterized by obesity, retinopathy, polydactyly,
renal and cardiac malformations, learning disabilities,
and hypogenitalism. Older literature suggests that Arl6
is a part of the Arl4/Arl7 subfamily, but analyses
based on more recent sequence data place Arl6 in its
own subfamily.
Length = 162
Score = 26.6 bits (59), Expect = 1.4
Identities = 11/34 (32%), Positives = 17/34 (50%)
Query: 18 NFHINYRDTAGQERFRTITTAYYRGAMGIMLVYD 51
N D +GQ ++R + YY+ GI+ V D
Sbjct: 44 NLSFTAFDMSGQGKYRGLWEHYYKNIQGIIFVID 77
>gnl|CDD|184851 PRK14849, PRK14849, putative lipoprotein/autotransporter
domain-containing protein; Provisional.
Length = 1806
Score = 26.6 bits (58), Expect = 1.5
Identities = 12/43 (27%), Positives = 22/43 (51%)
Query: 6 CTLQIFRGCFQHNFHINYRDTAGQERFRTITTAYYRGAMGIML 48
CTLQ+F+ C + + T + +TT + R +G++L
Sbjct: 11 CTLQVFQACSELTRRVGKTSTVNLRKSSGLTTKFSRLTLGVLL 53
>gnl|CDD|206719 cd04152, Arl4_Arl7, Arf-like 4 (Arl4) and 7 (Arl7) GTPases. Arl4
(Arf-like 4) is highly expressed in testicular germ
cells, and is found in the nucleus and nucleolus. In
mice, Arl4 is developmentally expressed during
embryogenesis, and a role in somite formation and
central nervous system differentiation has been
proposed. Arl7 has been identified as the only Arf/Arl
protein to be induced by agonists of liver X-receptor
and retinoid X-receptor and by cholesterol loading in
human macrophages. Arl7 is proposed to play a role in
transport between a perinuclear compartment and the
plasma membrane, apparently linked to the
ABCA1-mediated cholesterol secretion pathway. Older
literature suggests that Arl6 is a part of the
Arl4/Arl7 subfamily, but analyses based on more recent
sequence data place Arl6 in its own subfamily.
Length = 183
Score = 26.3 bits (58), Expect = 1.5
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 20 HINYRDTAGQERFRTITTAYYRGAMGIMLVYD 51
++ D GQE+ R + +Y R GI+ V D
Sbjct: 53 TFHFWDVGGQEKLRPLWKSYTRCTDGIVFVVD 84
>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 = 26.5 bits (58), Expect = 1.6
Identities = 11/50 (22%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 16 QHNFHINYRDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNI-KNW 64
+H +N DT+G + + Y + +++ +DI+ ++ D++ K W
Sbjct: 46 KHRIELNMWDTSGSSYYDNVRPLAYPDSDAVLICFDISRPETLDSVLKKW 95
>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 = 1.9
Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 2/60 (3%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKN-WIRNIEENASANVEKMLLGN 83
DT+ + + R A R A I LVY + + + I+ W+ I V +L+GN
Sbjct: 55 DTSSRPQDRANLAAEIRKANVICLVYSVDRPSTLERIRTKWLPLIRRLG-VKVPIILVGN 113
>gnl|CDD|133342 cd04142, RRP22, Ras-related protein on chromosome 22 (RRP22)
family. RRP22 (Ras-related protein on chromosome 22)
subfamily consists of proteins that inhibit cell growth
and promote caspase-independent cell death. Unlike most
Ras proteins, RRP22 is down-regulated in many human
tumor cells due to promoter methylation. RRP22 localizes
to the nucleolus in a GTP-dependent manner, suggesting a
novel function in modulating transport of nucleolar
components. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras proteins.
Like most Ras family proteins, RRP22 is farnesylated.
Length = 198
Score = 26.0 bits (57), Expect = 2.1
Identities = 18/44 (40%), Positives = 23/44 (52%), Gaps = 9/44 (20%)
Query: 23 YRDTAGQE----RFRTITTAYYRGAMGIMLVYDITNEKSFDNIK 62
Y TAGQE RFR + R + +LVYDI + SF +K
Sbjct: 62 YPGTAGQEWMDPRFRGL-----RNSRAFILVYDICSPDSFHYVK 100
>gnl|CDD|218734 pfam05758, Ycf1, Ycf1. The chloroplast genomes of most higher
plants contain two giant open reading frames designated
ycf1 and ycf2. Although the function of Ycf1 is unknown,
it is known to be an essential gene.
Length = 832
Score = 25.7 bits (57), Expect = 3.4
Identities = 12/33 (36%), Positives = 15/33 (45%)
Query: 39 YYRGAMGIMLVYDITNEKSFDNIKNWIRNIEEN 71
YRG + +L I N+ S IKN I N
Sbjct: 442 PYRGRIKKLLSPSILNDDSLTLIKNLIDTFWIN 474
>gnl|CDD|206714 cd04147, Ras_dva, Ras - dorsal-ventral anterior localization
(Ras-dva) family. Ras-dva subfamily. Ras-dva (Ras -
dorsal-ventral anterior localization) subfamily consists
of a set of proteins characterized only in Xenopus
leavis, to date. In Xenopus Ras-dva expression is
activated by the transcription factor Otx2 and begins
during gastrulation throughout the anterior ectoderm.
Ras-dva expression is inhibited in the anterior neural
plate by factor Xanf1. Downregulation of Ras-dva results
in head development abnormalities through the inhibition
of several regulators of the anterior neural plate and
folds patterning, including Otx2, BF-1, Xag2, Pax6,
Slug, and Sox9. Downregulation of Ras-dva also
interferes with the FGF-8a signaling within the anterior
ectoderm. Most Ras proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins.
Length = 197
Score = 25.6 bits (56), Expect = 3.4
Identities = 16/65 (24%), Positives = 30/65 (46%), Gaps = 3/65 (4%)
Query: 21 INYRDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRN--IEENASANVEK 78
I+ DT+G F + + LVY + + +SF+ +K +R +E V
Sbjct: 49 IDILDTSGSYSFPAMRKLSIQNGDAFALVYSVDDPESFEEVKR-LREEILEVKEDKFVPI 107
Query: 79 MLLGN 83
+++GN
Sbjct: 108 VVVGN 112
>gnl|CDD|237654 PRK14278, PRK14278, chaperone protein DnaJ; Provisional.
Length = 378
Score = 25.4 bits (56), Expect = 3.9
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 25 DTAGQERFRTITTAY 39
D QE+F+ I+ AY
Sbjct: 38 DEEAQEKFKEISVAY 52
>gnl|CDD|219275 pfam07034, ORC3_N, Origin recognition complex (ORC) subunit 3
N-terminus. This family represents the N-terminus
(approximately 300 residues) of subunit 3 of the
eukaryotic origin recognition complex (ORC). Origin
recognition complex (ORC) is composed of six subunits
that are essential for cell viability. They
collectively bind to the autonomously replicating
sequence (ARS) in a sequence-specific manner and lead
to the chromatin loading of other replication factors
that are essential for initiation of DNA replication.
Length = 313
Score = 25.0 bits (55), Expect = 4.5
Identities = 12/55 (21%), Positives = 21/55 (38%)
Query: 24 RDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEENASANVEK 78
D Q RF + + I + D +N K FD + ++IR + +
Sbjct: 24 EDLTSQLRFEAYQRLWEKIKSHIERLQDESNAKIFDQLLDFIRESHASRQSEARD 78
>gnl|CDD|206717 cd04150, Arf1_5_like, ADP-ribosylation factor-1 (Arf1) and
ADP-ribosylation factor-5 (Arf5). The Arf1-Arf5-like
subfamily contains Arf1, Arf2, Arf3, Arf4, Arf5, and
related proteins. Arfs1-5 are soluble proteins that are
crucial for assembling coat proteins during vesicle
formation. Each contains an N-terminal myristoylated
amphipathic helix that is folded into the protein in
the GDP-bound state. GDP/GTP exchange exposes the
helix, which anchors to the membrane. Following GTP
hydrolysis, the helix dissociates from the membrane and
folds back into the protein. A general feature of
Arf1-5 signaling may be the cooperation of two Arfs at
the same site. Arfs1-5 are generally considered to be
interchangeable in function and location, but some
specific functions have been assigned. Arf1 localizes
to the early/cis-Golgi, where it is activated by GBF1
and recruits the coat protein COPI. It also localizes
to the trans-Golgi network (TGN), where it is activated
by BIG1/BIG2 and recruits the AP1, AP3, AP4, and GGA
proteins. Humans, but not rodents and other lower
eukaryotes, lack Arf2. Human Arf3 shares 96% sequence
identity with Arf1 and is believed to generally
function interchangeably with Arf1. Human Arf4 in the
activated (GTP-bound) state has been shown to interact
with the cytoplasmic domain of epidermal growth factor
receptor (EGFR) and mediate the EGF-dependent
activation of phospholipase D2 (PLD2), leading to
activation of the activator protein 1 (AP-1)
transcription factor. Arf4 has also been shown to
recognize the C-terminal sorting signal of rhodopsin
and regulate its incorporation into specialized
post-Golgi rhodopsin transport carriers (RTCs). There
is some evidence that Arf5 functions at the early-Golgi
and the trans-Golgi to affect Golgi-associated
alpha-adaptin homology Arf-binding proteins (GGAs).
Length = 159
Score = 25.1 bits (55), Expect = 4.6
Identities = 8/27 (29%), Positives = 15/27 (55%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYD 51
D GQ++ R + Y++ G++ V D
Sbjct: 50 DVGGQDKIRPLWRHYFQNTQGLIFVVD 76
>gnl|CDD|219567 pfam07775, PaRep2b, PaRep2b protein. This is a family of proteins,
expressed in the crenarchaeon Pyrobaculum aerophilum,
whose members are variable in length and level of
conservation. The presence of numerous frameshifts and
internal stop codons in multiple alignments are thought
to indicate that most family members are no longer
functional.
Length = 510
Score = 25.2 bits (55), Expect = 5.0
Identities = 8/30 (26%), Positives = 16/30 (53%)
Query: 37 TAYYRGAMGIMLVYDITNEKSFDNIKNWIR 66
+ YY+ + IM+ Y +E S + N ++
Sbjct: 203 SVYYKRSKRIMIKYQPRSEASKNAAVNALK 232
>gnl|CDD|219017 pfam06418, CTP_synth_N, CTP synthase N-terminus. This family
consists of the N-terminal region of the CTP synthase
protein (EC:6.3.4.2). This family is found in
conjunction with pfam00117 located in the C-terminal
region of the protein. CTP synthase catalyzes the
synthesis of CTP from UTP by amination of the pyrimidine
ring at the 4-position.
Length = 276
Score = 24.7 bits (55), Expect = 5.9
Identities = 8/25 (32%), Positives = 11/25 (44%), Gaps = 5/25 (20%)
Query: 52 ITNEKSFDNIKNWIRNIEENASANV 76
IT+E IK IR + +V
Sbjct: 117 ITDE-----IKERIRRVAAKPGPDV 136
>gnl|CDD|215358 PLN02666, PLN02666, 5-oxoprolinase.
Length = 1275
Score = 24.7 bits (54), Expect = 6.8
Identities = 9/36 (25%), Positives = 21/36 (58%)
Query: 45 GIMLVYDITNEKSFDNIKNWIRNIEENASANVEKML 80
GI L+ ++ +E ++ ++ +++ NA V +ML
Sbjct: 944 GISLIKELIDEYGLGTVQAYMGHVQANAELAVREML 979
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 24.4 bits (53), Expect = 7.0
Identities = 9/27 (33%), Positives = 15/27 (55%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYD 51
D GQ++ R + YY+ G++ V D
Sbjct: 67 DVGGQDKLRPLWRHYYQNTNGLIFVVD 93
>gnl|CDD|234293 TIGR03648, Na_symport_lg, probable sodium:solute symporter, VC_2705
subfamily. This family belongs to a larger family of
transporters of the sodium:solute symporter superfamily,
TC 2.A.21. Members of this strictly bacterial protein
subfamily are found almost invariably immediately
downstream from a member of family TIGR03647.
Occasionally, the two genes are fused.
Length = 552
Score = 24.5 bits (54), Expect = 7.3
Identities = 8/34 (23%), Positives = 12/34 (35%)
Query: 36 TTAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIE 69
TTA A + N + + W+ N E
Sbjct: 287 TTAPAVAAFARYNLITTVNGTPYAELPGWVANWE 320
>gnl|CDD|225940 COG3405, CelA, Endoglucanase Y [Carbohydrate transport and
metabolism].
Length = 360
Score = 24.4 bits (53), Expect = 8.4
Identities = 11/43 (25%), Positives = 18/43 (41%), Gaps = 4/43 (9%)
Query: 25 DTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNIKNWIRN 67
D +G + T Y G+ ++ +FD I NW +N
Sbjct: 45 DPSGNRKITTSEGQSY----GMFFAVLADDKDAFDRIWNWTQN 83
>gnl|CDD|206721 cd04155, Arl3, Arf-like 3 (Arl3) GTPase. Arl3 (Arf-like 3) is an
Arf family protein that differs from most Arf family
members in the N-terminal extension. In is inactive,
GDP-bound form, the N-terminal extension forms an
elongated loop that is hydrophobically anchored into the
membrane surface; however, it has been proposed that
this region might form a helix in the GTP-bound form.
The delta subunit of the rod-specific cyclic GMP
phosphodiesterase type 6 (PDEdelta) is an Arl3 effector.
Arl3 binds microtubules in a regulated manner to alter
specific aspects of cytokinesis via interactions with
retinitis pigmentosa 2 (RP2). It has been proposed that
RP2 functions in concert with Arl3 to link the cell
membrane and the cytoskeleton in photoreceptors as part
of the cell signaling or vesicular transport machinery.
In mice, the absence of Arl3 is associated with abnormal
epithelial cell proliferation and cyst formation.
Length = 174
Score = 24.3 bits (53), Expect = 9.1
Identities = 16/66 (24%), Positives = 28/66 (42%), Gaps = 1/66 (1%)
Query: 19 FHINYRDTAGQERFRTITTAYYRGAMGIMLVYDITNEKSFDNI-KNWIRNIEENASANVE 77
F +N D GQ + R Y+ ++ V D + K F+ + + +EE A V
Sbjct: 59 FKLNVWDIGGQRKIRPYWRNYFENTDVLIYVIDSADRKRFEEAGQELVELLEEEKLAGVP 118
Query: 78 KMLLGN 83
++ N
Sbjct: 119 VLVFAN 124
>gnl|CDD|235437 PRK05380, pyrG, CTP synthetase; Validated.
Length = 533
Score = 24.2 bits (54), Expect = 9.8
Identities = 7/21 (33%), Positives = 9/21 (42%), Gaps = 5/21 (23%)
Query: 52 ITNEKSFDNIKNWIRNIEENA 72
IT+E IK I +A
Sbjct: 118 ITDE-----IKERILAAGTDA 133
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
0.322 0.136 0.414
Gapped
Lambda K H
0.267 0.0591 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,100,622
Number of extensions: 314241
Number of successful extensions: 483
Number of sequences better than 10.0: 1
Number of HSP's gapped: 480
Number of HSP's successfully gapped: 121
Length of query: 83
Length of database: 10,937,602
Length adjustment: 52
Effective length of query: 31
Effective length of database: 8,631,194
Effective search space: 267567014
Effective search space used: 267567014
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 (24.5 bits)