RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2599
(78 letters)
>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 = 56.3 bits (137), Expect = 8e-12
Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 2/66 (3%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGGKANESSAGLVKTY 71
G + R+ ++F+ Y T G DF K + + + VKL +WD G+ E + +Y
Sbjct: 12 GKTSLLLRFVDNKFSENYKSTIGVDFKSKTIEVDGKKVKLQIWDTAGQ--ERFRSITSSY 69
Query: 72 LSSANI 77
A+
Sbjct: 70 YRGAHG 75
>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 = 55.7 bits (135), Expect = 2e-11
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGGKANESSAGLVKTY 71
G + TR+ D F QY T G DF K + + ++ V+L LWD G+ S L+ +Y
Sbjct: 12 GKTSIITRFMYDTFDNQYQATIGIDFLSKTMYVDDKTVRLQLWDTAGQERFRS--LIPSY 69
Query: 72 LSSANI 77
+ +++
Sbjct: 70 IRDSSV 75
>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 = 52.1 bits (126), Expect = 4e-10
Identities = 19/47 (40%), Positives = 28/47 (59%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGG 58
G S R+TQ++F +Y PT G DF+ K + + + VKL +WD G
Sbjct: 11 GKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAG 57
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 48.7 bits (117), Expect = 7e-09
Identities = 18/47 (38%), Positives = 26/47 (55%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGG 58
G S +R+T +F+ QY T G DF K + + + VKL +WD G
Sbjct: 12 GKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIEVDGKRVKLQIWDTAG 58
>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 = 45.9 bits (109), Expect = 1e-07
Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 4/58 (6%)
Query: 6 IKVLTEGTS---CFSTRYTQDEFTRQYYPTSGPDFHLKLLTI-QNRGVKLILWDIGGK 59
I VL +G S R+ Q+ F + Y T G DF + +T+ + V L +WDIGG+
Sbjct: 3 IVVLGDGASGKTSLIRRFAQEGFGKSYKQTIGLDFFSRRITLPGSLNVTLQVWDIGGQ 60
>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 = 44.6 bits (106), Expect = 3e-07
Identities = 15/48 (31%), Positives = 27/48 (56%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGGK 59
G SC R+++D F + T G DF ++ + + + +KL +WD G+
Sbjct: 15 GKSCLLLRFSEDSFNPSFISTIGIDFKIRTIELDGKKIKLQIWDTAGQ 62
>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 = 44.2 bits (105), Expect = 5e-07
Identities = 19/48 (39%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTI-QNRGVKLILWDIGG 58
G + RY F++ Y T G DF LK++ N V+L LWDI G
Sbjct: 12 GKTSIIKRYVHGVFSQHYKATIGVDFALKVIEWDPNTVVRLQLWDIAG 59
>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 = 43.5 bits (103), Expect = 7e-07
Identities = 18/47 (38%), Positives = 24/47 (51%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGG 58
G S R+T D F T G DF +K +T+ + VKL +WD G
Sbjct: 12 GKSSLLLRFTDDTFDEDLSSTIGVDFKVKTVTVDGKKVKLAIWDTAG 58
>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 = 42.7 bits (101), Expect = 2e-06
Identities = 17/48 (35%), Positives = 26/48 (54%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGGK 59
G SC R+ D +T Y T G DF ++ + + + VKL +WD G+
Sbjct: 14 GKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTVKLQIWDTAGQ 61
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins
[General function prediction only].
Length = 219
Score = 43.0 bits (101), Expect = 2e-06
Identities = 17/47 (36%), Positives = 20/47 (42%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGG 58
G + R DEF Y PT G K + R +KL LWD G
Sbjct: 17 GKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAG 63
>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 = 41.7 bits (98), Expect = 3e-06
Identities = 21/66 (31%), Positives = 31/66 (46%), Gaps = 4/66 (6%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRG--VKLILWDIGGKANESSAGLVK 69
G S R+ + FT+ Y T G DF K + ++ V+L+LWD G+ E + K
Sbjct: 12 GKSSMIQRFVKGIFTKDYKKTIGVDFLEKQIFLRQSDEDVRLMLWDTAGQ--EEFDAITK 69
Query: 70 TYLSSA 75
Y A
Sbjct: 70 AYYRGA 75
>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 = 41.0 bits (96), Expect = 7e-06
Identities = 22/65 (33%), Positives = 33/65 (50%), Gaps = 2/65 (3%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGGKANESSAGLVKTY 71
G +C R+TQ F T G DF +K + I+ +KL +WD G+ E + ++Y
Sbjct: 19 GKTCLVRRFTQGLFPPGQGATIGVDFMIKTVEIKGEKIKLQIWDTAGQ--ERFRSITQSY 76
Query: 72 LSSAN 76
SAN
Sbjct: 77 YRSAN 81
>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 = 40.7 bits (96), Expect = 8e-06
Identities = 17/47 (36%), Positives = 25/47 (53%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGG 58
G + +Y +F+ QY T G DF K +T+ +R V L +WD G
Sbjct: 12 GKTSLMNQYVNKKFSNQYKATIGADFLTKEVTVDDRLVTLQIWDTAG 58
>gnl|CDD|133319 cd04119, RJL, Rab GTPase family J-like (RabJ-like). RJLs are
found in many protists and as chimeras with C-terminal
DNAJ domains in deuterostome metazoa. They are not
found in plants, fungi, and protostome metazoa,
suggesting a horizontal gene transfer between protists
and deuterostome metazoa. RJLs lack any known membrane
targeting signal and contain a degenerate
phosphate/magnesium-binding 3 (PM3) motif, suggesting
an impaired ability to hydrolyze GTP. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization.
Length = 168
Score = 40.4 bits (95), Expect = 1e-05
Identities = 19/58 (32%), Positives = 34/58 (58%), Gaps = 5/58 (8%)
Query: 6 IKVLTEGT-----SCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGG 58
IKV++ G SC RY + F +Y PT G D+ +K ++++N+ V++ +D+ G
Sbjct: 1 IKVISMGNSGVGKSCIIKRYCEGRFVSKYLPTIGIDYGVKKVSVRNKEVRVNFFDLSG 58
>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 = 40.3 bits (94), Expect = 1e-05
Identities = 17/48 (35%), Positives = 26/48 (54%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGGK 59
G + F RY D FT + T G DF +K + ++ +KL +WD G+
Sbjct: 13 GKTSFLFRYADDSFTSAFVSTVGIDFKVKTVYRNDKRIKLQIWDTAGQ 60
>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 = 39.7 bits (93), Expect = 2e-05
Identities = 13/48 (27%), Positives = 27/48 (56%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGGK 59
G SC ++ +++F + T G +F +++ + + VKL +WD G+
Sbjct: 12 GKSCLLHQFIENKFKQDSNHTIGVEFGSRVVNVGGKSVKLQIWDTAGQ 59
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 38.4 bits (89), Expect = 7e-05
Identities = 20/64 (31%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGGKANESSAGLVKTY 71
G SC ++T F + T G +F +++TI N+ +KL +WD G+ ES + ++Y
Sbjct: 18 GKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDNKPIKLQIWDTAGQ--ESFRSITRSY 75
Query: 72 LSSA 75
A
Sbjct: 76 YRGA 79
>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 = 37.6 bits (87), Expect = 1e-04
Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 2/64 (3%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGGKANESSAGLVKTY 71
G +C R+T +EF + T G DF +K + + V++ +WD G+ E + K Y
Sbjct: 12 GKTCLLCRFTDNEFHSSHISTIGVDFKMKTIEVDGIKVRIQIWDTAGQ--ERYQTITKQY 69
Query: 72 LSSA 75
A
Sbjct: 70 YRRA 73
>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 = 37.4 bits (87), Expect = 1e-04
Identities = 23/65 (35%), Positives = 34/65 (52%), Gaps = 2/65 (3%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGGKANESSAGLVKTY 71
G +C R+ F+ + T G DF +K L IQ + VKL +WD G+ E + ++Y
Sbjct: 15 GKTCVVQRFKSGTFSERQGNTIGVDFTMKTLEIQGKRVKLQIWDTAGQ--ERFRTITQSY 72
Query: 72 LSSAN 76
SAN
Sbjct: 73 YRSAN 77
>gnl|CDD|206653 cd01860, Rab5_related, Rab-related GTPase family includes Rab5
and Rab22; regulates early endosome fusion. The
Rab5-related subfamily includes Rab5 and Rab22 of
mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of
plants. The members of this subfamily are involved in
endocytosis and endocytic-sorting pathways. In mammals,
Rab5 GTPases localize to early endosomes and regulate
fusion of clathrin-coated vesicles to early endosomes
and fusion between early endosomes. In yeast, Ypt51p
family members similarly regulate membrane trafficking
through prevacuolar compartments. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 163
Score = 36.8 bits (86), Expect = 2e-04
Identities = 13/47 (27%), Positives = 22/47 (46%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGG 58
G S R+ ++EF+ T G F + + + + VK +WD G
Sbjct: 13 GKSSIVLRFVKNEFSENQESTIGAAFLTQTVNLDDTTVKFEIWDTAG 59
>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 = 37.0 bits (86), Expect = 2e-04
Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 10 TEGTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQ-NRGVKLILWDIGGK 59
T G S R+T+ F PT G DF +L+ I+ +KL LWD G+
Sbjct: 12 TVGKSSLLKRFTEGRFAEVSDPTVGVDFFSRLIEIEPGVRIKLQLWDTAGQ 62
>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 = 36.6 bits (85), Expect = 3e-04
Identities = 14/48 (29%), Positives = 23/48 (47%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGGK 59
G +C + R+ F + T G DF + + I +K+ LWD G+
Sbjct: 14 GKTCLTYRFCAGRFPERTEATIGVDFRERTVEIDGERIKVQLWDTAGQ 61
>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 = 36.8 bits (85), Expect = 3e-04
Identities = 16/48 (33%), Positives = 24/48 (50%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGGK 59
G S R+ + F+ Y T G DF ++ + I VKL +WD G+
Sbjct: 18 GKSSLLLRFADNTFSGSYITTIGVDFKIRTVEINGERVKLQIWDTAGQ 65
>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 = 34.7 bits (80), Expect = 0.001
Identities = 14/47 (29%), Positives = 25/47 (53%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGG 58
G + +Y + EF +Y T G +F K ++I+ + +WD+GG
Sbjct: 12 GKTSLMVKYVEGEFDEEYIQTLGVNFMEKTISIRGTEITFSIWDLGG 58
>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 = 34.5 bits (79), Expect = 0.002
Identities = 16/51 (31%), Positives = 25/51 (49%)
Query: 9 LTEGTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGGK 59
L+ G +C R+ +D F + Y T G DF ++ + L LWD G+
Sbjct: 9 LSVGKTCLINRFCKDVFDKNYKATIGVDFEMERFEVLGVPFSLQLWDTAGQ 59
>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 = 34.4 bits (79), Expect = 0.002
Identities = 18/58 (31%), Positives = 27/58 (46%), Gaps = 10/58 (17%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRG----------VKLILWDIGGK 59
G + F RYT ++F ++ T G DF K + ++G V L LWD G+
Sbjct: 16 GKTTFLYRYTDNKFNPKFITTVGIDFREKRVVYNSQGPDGTSGKAFRVHLQLWDTAGQ 73
>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 = 34.3 bits (79), Expect = 0.002
Identities = 18/60 (30%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGGKANESSAGLVKTY 71
G SC ++T F + T G +F +++TI + +KL +WD G+ ES + ++Y
Sbjct: 16 GKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQ--ESFRSITRSY 73
>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 = 33.8 bits (77), Expect = 0.003
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 4/61 (6%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRG-VKLILWDIGGKANESSAGLVKT 70
G + F R+ EF ++Y T G + H L+ NRG ++ +WD G+ E GL
Sbjct: 7 GKTTFVKRHLTGEFEKKYVATLGVEVH-PLVFHTNRGPIRFNVWDTAGQ--EKFGGLRDG 63
Query: 71 Y 71
Y
Sbjct: 64 Y 64
>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 = 33.8 bits (77), Expect = 0.003
Identities = 18/64 (28%), Positives = 31/64 (48%), Gaps = 2/64 (3%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGGKANESSAGLVKTY 71
G + R+T D F T G DF +K + ++ + ++L +WD G+ +S + Y
Sbjct: 12 GKTSLMERFTDDTFCEACKSTVGVDFKIKTVELRGKKIRLQIWDTAGQERFNS--ITSAY 69
Query: 72 LSSA 75
SA
Sbjct: 70 YRSA 73
>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 = 33.7 bits (77), Expect = 0.004
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 12 GTSCFSTRYTQDEFTR-QYYPTSGPDFHLKLLTIQNRGVKLILWDIGGK 59
G +C R+ F + T G F K++T+ VKL +WD G+
Sbjct: 12 GKTCLLVRFKDGAFLAGSFIATVGIQFTNKVVTVDGVKVKLQIWDTAGQ 60
>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 = 33.4 bits (77), Expect = 0.004
Identities = 12/47 (25%), Positives = 23/47 (48%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGG 58
G + RY +++F ++ T+ F K + I + + L +WD G
Sbjct: 12 GKTSLVLRYVENKFNEKHESTTQASFFQKTVNIGGKRIDLAIWDTAG 58
>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 = 33.3 bits (76), Expect = 0.005
Identities = 13/48 (27%), Positives = 26/48 (54%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGGK 59
G SC ++T+ +F T G +F +++ + + +KL +WD G+
Sbjct: 14 GKSCLLHQFTEKKFMADCPHTIGVEFGTRIIEVNGQKIKLQIWDTAGQ 61
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 33.1 bits (75), Expect = 0.007
Identities = 17/45 (37%), Positives = 25/45 (55%), Gaps = 2/45 (4%)
Query: 31 PTSGPDFHLKLLTIQNRGVKLILWDIGGKANESSAGLVKTYLSSA 75
PT G DF +K LT+ + +KL +WD G+ E L +Y +A
Sbjct: 44 PTIGVDFKIKQLTVGGKRLKLTIWDTAGQ--ERFRTLTSSYYRNA 86
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 32.7 bits (75), Expect = 0.007
Identities = 22/62 (35%), Positives = 30/62 (48%), Gaps = 6/62 (9%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFH-LKLLTIQNRG-VKLILWDIGGKANESSAGLVK 69
G + F R+ EF ++Y PT G + H LK T N G + +WD G+ E GL
Sbjct: 21 GKTTFVKRHLTGEFEKKYIPTLGVEVHPLKFYT--NCGPICFNVWDTAGQ--EKFGGLRD 76
Query: 70 TY 71
Y
Sbjct: 77 GY 78
>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 = 32.7 bits (74), Expect = 0.008
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGGK 59
G +C YT + F ++Y PT ++ + + R V L LWD G+
Sbjct: 15 GKTCLLICYTTNAFPKEYIPTVFDNYSAQ-TAVDGRTVSLNLWDTAGQ 61
>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 = 32.5 bits (75), Expect = 0.009
Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGG 58
G +C YT ++F +Y PT D + +T+ + V L LWD G
Sbjct: 12 GKTCLLISYTTNKFPTEYVPTVF-DNYSANVTVDGKQVNLGLWDTAG 57
>gnl|CDD|206697 cd04116, Rab9, Rab GTPase family 9 (Rab9). Rab9 is found in late
endosomes, together with mannose 6-phosphate receptors
(MPRs) and the tail-interacting protein of 47 kD
(TIP47). Rab9 is a key mediator of vesicular transport
from late endosomes to the trans-Golgi network (TGN) by
redirecting the MPRs. Rab9 has been identified as a key
component for the replication of several viruses,
including HIV1, Ebola, Marburg, and measles, making it
a potential target for inhibiting a variety of viruses.
GTPase activating proteins (GAPs) interact with
GTP-bound Rab and accelerate the hydrolysis of GTP to
GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation
of the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs),
which facilitate Rab recycling by masking C-terminal
lipid binding and promoting cytosolic localization.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Due to the presence
of truncated sequences in this CD, the lipid
modification site is not available for annotation.
Length = 170
Score = 32.5 bits (74), Expect = 0.009
Identities = 16/48 (33%), Positives = 23/48 (47%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGGK 59
G S RY ++F Q + T G +F K L + V L +WD G+
Sbjct: 17 GKSSLMNRYVTNKFDTQLFHTIGVEFLNKDLEVDGHFVTLQIWDTAGQ 64
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 32.6 bits (74), Expect = 0.010
Identities = 15/48 (31%), Positives = 27/48 (56%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGGK 59
G S +R+T++EF + T G +F + L ++ + VK +WD G+
Sbjct: 24 GKSNILSRFTRNEFCLESKSTIGVEFATRTLQVEGKTVKAQIWDTAGQ 71
>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 = 31.8 bits (73), Expect = 0.017
Identities = 12/41 (29%), Positives = 22/41 (53%)
Query: 18 TRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGG 58
+R+T++EF T G +F + + I + +K +WD G
Sbjct: 21 SRFTRNEFNLDSKSTIGVEFATRTIQIDGKTIKAQIWDTAG 61
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 31.3 bits (71), Expect = 0.030
Identities = 21/62 (33%), Positives = 29/62 (46%), Gaps = 6/62 (9%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFH-LKLLTIQNRG-VKLILWDIGGKANESSAGLVK 69
G + F R+ EF ++Y PT G + H L T N G ++ WD G+ E GL
Sbjct: 25 GKTTFVKRHLTGEFEKKYEPTIGVEVHPLDFFT--NCGKIRFYCWDTAGQ--EKFGGLRD 80
Query: 70 TY 71
Y
Sbjct: 81 GY 82
>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 = 30.9 bits (70), Expect = 0.036
Identities = 13/50 (26%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGGKAN 61
G +C +++D+F Y PT ++ + + + + V+L LWD G+ +
Sbjct: 13 GKTCLLIVFSKDQFPEVYVPTVFENY-VADIEVDGKQVELALWDTAGQED 61
>gnl|CDD|133343 cd04143, Rhes_like, Ras homolog enriched in striatum (Rhes) and
activator of G-protein signaling 1 (Dexras1/AGS1).
This subfamily includes Rhes (Ras homolog enriched in
striatum) and Dexras1/AGS1 (activator of G-protein
signaling 1). These proteins are homologous, but
exhibit significant differences in tissue distribution
and subcellular localization. Rhes is found primarily
in the striatum of the brain, but is also expressed in
other areas of the brain, such as the cerebral cortex,
hippocampus, inferior colliculus, and cerebellum. Rhes
expression is controlled by thyroid hormones. In rat
PC12 cells, Rhes is farnesylated and localizes to the
plasma membrane. Rhes binds and activates PI3K, and
plays a role in coupling serpentine membrane receptors
with heterotrimeric G-protein signaling. Rhes has
recently been shown to be reduced under conditions of
dopamine supersensitivity and may play a role in
determining dopamine receptor sensitivity. Dexras1/AGS1
is a dexamethasone-induced Ras protein that is
expressed primarily in the brain, with low expression
levels in other tissues. Dexras1 localizes primarily to
the cytoplasm, and is a critical regulator of the
circadian master clock to photic and nonphotic input.
Most Ras proteins contain a lipid modification site at
the C-terminus, with a typical sequence motif CaaX,
where a = an aliphatic amino acid and X = any amino
acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins.
Length = 247
Score = 30.5 bits (69), Expect = 0.046
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGG 58
G + +R+ F QY PT DFH KL +I+ +L + D G
Sbjct: 12 GKTAIVSRFLGGRFEEQYTPTI-EDFHRKLYSIRGEVYQLDILDTSG 57
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 30.5 bits (68), Expect = 0.047
Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 2/53 (3%)
Query: 23 DEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGGKANESSAGLVKTYLSSA 75
D F Y T G DF K L + V+L LWD G+ E L+ +Y+ +
Sbjct: 3 DTFDNNYQSTIGIDFLSKTLYLDEGPVRLQLWDTAGQ--ERFRSLIPSYIRDS 53
>gnl|CDD|206723 cd04158, ARD1, (ADP-ribosylation factor domain protein 1 (ARD1).
ARD1 (ADP-ribosylation factor domain protein 1) is an
unusual member of the Arf family. In addition to the
C-terminal Arf domain, ARD1 has an additional 46-kDa
N-terminal domain that contains a RING finger domain,
two predicted B-Boxes, and a coiled-coil protein
interaction motif. This domain belongs to the TRIM
(tripartite motif) or RBCC (RING, B-Box, coiled-coil)
family. Like most Arfs, the ARD1 Arf domain lacks
detectable GTPase activity. However, unlike most Arfs,
the full-length ARD1 protein has significant GTPase
activity due to the GAP (GTPase-activating protein)
activity exhibited by the 46-kDa N-terminal domain. The
GAP domain of ARD1 is specific for its own Arf domain
and does not bind other Arfs. The rate of GDP
dissociation from the ARD1 Arf domain is slowed by the
adjacent 15 amino acids, which act as a GDI
(GDP-dissociation inhibitor) domain. ARD1 is
ubiquitously expressed in cells and localizes to the
Golgi and to the lysosomal membrane. Two Tyr-based
motifs in the Arf domain are responsible for Golgi
localization, while the GAP domain controls lysosomal
localization.
Length = 169
Score = 30.4 bits (68), Expect = 0.053
Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 5/48 (10%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGGK 59
G + + QDEF Q PT G F+++ T++ + +K +WD+GGK
Sbjct: 11 GKTTILFKLKQDEFM-QPIPTIG--FNVE--TVEYKNLKFTIWDVGGK 53
>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 = 30.0 bits (68), Expect = 0.061
Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 6/58 (10%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFH-LKLLTIQNRG-VKLILWDIGGKANESSAGL 67
G + F R+ EF ++Y T G + H L T NRG ++ +WD G+ E GL
Sbjct: 12 GKTTFVKRHLTGEFEKKYVATLGVEVHPLDFHT--NRGKIRFNVWDTAGQ--EKFGGL 65
>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 = 29.8 bits (67), Expect = 0.074
Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 1/49 (2%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGGKA 60
G S + ++ Q+ F Y PT D + K + I R L + D G
Sbjct: 13 GKSALTVQFVQNVFIESYDPTI-EDSYRKQVEIDGRQCDLEILDTAGTE 60
>gnl|CDD|206721 cd04155, Arl3, Arf-like 3 (Arl3) GTPase. Arl3 (Arf-like 3) is an
Arf family protein that differs from most Arf family
members in the N-terminal extension. In is inactive,
GDP-bound form, the N-terminal extension forms an
elongated loop that is hydrophobically anchored into
the membrane surface; however, it has been proposed
that this region might form a helix in the GTP-bound
form. The delta subunit of the rod-specific cyclic GMP
phosphodiesterase type 6 (PDEdelta) is an Arl3
effector. Arl3 binds microtubules in a regulated manner
to alter specific aspects of cytokinesis via
interactions with retinitis pigmentosa 2 (RP2). It has
been proposed that RP2 functions in concert with Arl3
to link the cell membrane and the cytoskeleton in
photoreceptors as part of the cell signaling or
vesicular transport machinery. In mice, the absence of
Arl3 is associated with abnormal epithelial cell
proliferation and cyst formation.
Length = 174
Score = 29.7 bits (67), Expect = 0.084
Identities = 14/29 (48%), Positives = 19/29 (65%), Gaps = 4/29 (13%)
Query: 31 PTSGPDFHLKLLTIQNRGVKLILWDIGGK 59
PT G F++K +Q G KL +WDIGG+
Sbjct: 45 PTQG--FNIK--NVQADGFKLNVWDIGGQ 69
>gnl|CDD|197228 cd09130, PLDc_unchar2_2, Putative catalytic domain, repeat 2, of
uncharacterized phospholipase D-like proteins. Putative
catalytic domain, repeat 2, of uncharacterized
phospholipase D (PLD, EC 3.1.4.4)-like proteins. PLD
enzymes hydrolyze phospholipid phosphodiester bonds to
yield phosphatidic acid and a free polar head group.
They can also catalyze transphosphatidylation of
phospholipids to acceptor alcohols. Members of this
subfamily contain two HKD motifs (H-x-K-x(4)-D, where x
represents any amino acid residue) that characterizes
the PLD superfamily. The two motifs may be part of the
active site and may be involved in phosphatidyl group
transfer.
Length = 157
Score = 28.7 bits (65), Expect = 0.17
Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 3/44 (6%)
Query: 18 TRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGGKAN 61
+ T+ + ++Y T G FH KLL I+ +G +I IGG AN
Sbjct: 77 MKKTKGKIQIRWYNTGGEQFHTKLLLIKKKGQAII---IGGSAN 117
>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 = 28.6 bits (65), Expect = 0.18
Identities = 13/47 (27%), Positives = 20/47 (42%), Gaps = 1/47 (2%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGG 58
G S + R+ EF +Y PT D + K + + L + D G
Sbjct: 11 GKSALTIRFVSGEFVEEYDPTIE-DSYRKQIVVDGETYTLDILDTAG 56
>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 = 28.7 bits (65), Expect = 0.21
Identities = 11/29 (37%), Positives = 19/29 (65%), Gaps = 4/29 (13%)
Query: 31 PTSGPDFHLKLLTIQNRGVKLILWDIGGK 59
PT G F+++ + +N VK +WD+GG+
Sbjct: 29 PTIG--FNVETVEYKN--VKFTVWDVGGQ 53
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 28.3 bits (64), Expect = 0.23
Identities = 10/29 (34%), Positives = 16/29 (55%), Gaps = 4/29 (13%)
Query: 31 PTSGPDFHLKLLTIQNRGVKLILWDIGGK 59
PT G + T+ + VK +WD+GG+
Sbjct: 44 PTIGFNVE----TVTYKNVKFTVWDVGGQ 68
>gnl|CDD|183125 PRK11413, PRK11413, putative hydratase; Provisional.
Length = 751
Score = 28.4 bits (64), Expect = 0.32
Identities = 8/29 (27%), Positives = 14/29 (48%)
Query: 6 IKVLTEGTSCFSTRYTQDEFTRQYYPTSG 34
+ V+T T+C S+ + DE + G
Sbjct: 240 VDVMTTETTCLSSIWQTDEEVHNWLALHG 268
>gnl|CDD|206663 cd01871, Rac1_like, Ras-related C3 botulinum toxin substrate 1
(rho family, small GTP binding protein Rac1)-like
consists of Rac1, Rac2 and Rac3. The Rac1-like
subfamily consists of Rac1, Rac2, and Rac3 proteins,
plus the splice variant Rac1b that contains a
19-residue insertion near switch II relative to Rac1.
While Rac1 is ubiquitously expressed, Rac2 and Rac3 are
largely restricted to hematopoietic and neural tissues
respectively. Rac1 stimulates the formation of actin
lamellipodia and membrane ruffles. It also plays a role
in cell-matrix adhesion and cell anoikis. In intestinal
epithelial cells, Rac1 is an important regulator of
migration and mediates apoptosis. Rac1 is also
essential for RhoA-regulated actin stress fiber and
focal adhesion complex formation. In leukocytes, Rac1
and Rac2 have distinct roles in regulating cell
morphology, migration, and invasion, but are not
essential for macrophage migration or chemotaxis. Rac3
has biochemical properties that are closely related to
Rac1, such as effector interaction, nucleotide binding,
and hydrolysis; Rac2 has a slower nucleotide
association and is more efficiently activated by the
RacGEF Tiam1. Both Rac1 and Rac3 have been implicated
in the regulation of cell migration and invasion in
human metastatic breast cancer. Most Rho proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 174
Score = 27.9 bits (62), Expect = 0.36
Identities = 14/48 (29%), Positives = 24/48 (50%), Gaps = 1/48 (2%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGGK 59
G +C YT + F +Y PT ++ ++ + + V L LWD G+
Sbjct: 13 GKTCLLISYTTNAFPGEYIPTVFDNYSANVM-VDGKPVNLGLWDTAGQ 59
>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 = 28.0 bits (63), Expect = 0.37
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGG 58
G +C YT + F Y PT + + + + + V+L LWD G
Sbjct: 10 GKTCLLIVYTTNAFPEDYVPTVF-ENYSADVEVDGKPVELGLWDTAG 55
>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 = 27.7 bits (62), Expect = 0.40
Identities = 12/36 (33%), Positives = 21/36 (58%), Gaps = 4/36 (11%)
Query: 23 DEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGG 58
+F+ PT G F+++ +T N V + +WD+GG
Sbjct: 22 GQFSEDTIPTVG--FNMRKVTKGN--VTIKVWDLGG 53
>gnl|CDD|216465 pfam01379, Porphobil_deam, Porphobilinogen deaminase,
dipyromethane cofactor binding domain.
Length = 213
Score = 27.6 bits (62), Expect = 0.44
Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 21 TQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLI---LWDIGGKA 60
Q E+ ++ PD +++TI+ G K++ L IGGK
Sbjct: 14 IQAEYVKEKLKKLYPDIEFEIVTIKTTGDKILDKPLAKIGGKG 56
>gnl|CDD|129331 TIGR00228, ruvC, crossover junction endodeoxyribonuclease RuvC.
Endonuclease that resolves Holliday junction
intermediates in genetic recombination. The active form
of the protein is a dimer. Structure studies reveals
that the catalytic center, comprised of four acidic
residues, lies at the bottom of a cleft that fits a DNA
duplex. The model hits a single Synechocystis PCC6803
protein at a score of 30, below the trusted cutoff,
that appears orthologous and may act as authentic RuvC
[DNA metabolism, DNA replication, recombination, and
repair].
Length = 156
Score = 27.6 bits (61), Expect = 0.45
Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 3/52 (5%)
Query: 3 PLYIKVLTEGTSCFSTRYTQDEFT-RQYYPTSGPDFHLKLLTIQNRGVKLIL 53
P +K++ G + T++ + F Q + D LKL Q RGV ++
Sbjct: 39 PSRLKLIYAGVTEIITQFQPNYFAIEQVFMAKNADSALKL--GQARGVAIVA 88
>gnl|CDD|206720 cd04154, Arl2, Arf-like 2 (Arl2) GTPase. Arl2 (Arf-like 2)
GTPases are members of the Arf family that bind GDP and
GTP with very low affinity. Unlike most Arf family
proteins, Arl2 is not myristoylated at its N-terminal
helix. The protein PDE-delta, first identified in
photoreceptor rod cells, binds specifically to Arl2 and
is structurally very similar to RhoGDI. Despite the
high structural similarity between Arl2 and Rho
proteins and between PDE-delta and RhoGDI, the
interactions between the GTPases and their effectors
are very different. In its GTP bound form, Arl2
interacts with the protein Binder of Arl2 (BART), and
the complex is believed to play a role in mitochondrial
adenine nucleotide transport. In its GDP bound form,
Arl2 interacts with tubulin- folding Cofactor D; this
interaction is believed to play a role in regulation of
microtubule dynamics that impact the cytoskeleton, cell
division, and cytokinesis.
Length = 173
Score = 27.3 bits (61), Expect = 0.67
Identities = 13/29 (44%), Positives = 20/29 (68%), Gaps = 4/29 (13%)
Query: 31 PTSGPDFHLKLLTIQNRGVKLILWDIGGK 59
PT G F++K T++ G KL +WD+GG+
Sbjct: 44 PTLG--FNIK--TLEYNGYKLNIWDVGGQ 68
>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 = 26.6 bits (59), Expect = 0.93
Identities = 11/47 (23%), Positives = 17/47 (36%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGG 58
G S ++ EF + G + L + L +WD GG
Sbjct: 11 GKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGG 57
>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 = 26.8 bits (60), Expect = 0.94
Identities = 10/42 (23%), Positives = 19/42 (45%), Gaps = 11/42 (26%)
Query: 12 GTSCFSTRYTQDEFTRQYYPT-----------SGPDFHLKLL 42
G S + ++ + F YYPT G ++HL+++
Sbjct: 13 GKSSLTVQFVEGHFVESYYPTIENTFSKIITYKGQEYHLEIV 54
>gnl|CDD|206707 cd04135, Tc10, Rho GTPase TC10 (Tc10). TC10 is a Rho family
protein that has been shown to induce microspike
formation and neurite outgrowth in vitro. Its
expression changes dramatically after peripheral nerve
injury, suggesting an important role in promoting
axonal outgrowth and regeneration. TC10 regulates
translocation of insulin-stimulated GLUT4 in adipocytes
and has also been shown to bind directly to Golgi COPI
coat proteins. GTP-bound TC10 in vitro can bind
numerous potential effectors. Depending on its
subcellular localization and distinct functional
domains, TC10 can differentially regulate two types of
filamentous actin in adipocytes. TC10 mRNAs are highly
expressed in three types of mouse muscle tissues: leg
skeletal muscle, cardiac muscle, and uterus; they were
also present in brain, with higher levels in adults
than in newborns. TC10 has also been shown to play a
role in regulating the expression of cystic fibrosis
transmembrane conductance regulator (CFTR) through
interactions with CFTR-associated ligand (CAL). The
GTP-bound form of TC10 directs the trafficking of CFTR
from the juxtanuclear region to the secretory pathway
toward the plasma membrane, away from CAL-mediated DFTR
degradation in the lysosome. Most Rho proteins contain
a lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of
most Rho proteins. Due to the presence of truncated
sequences in this CD, the lipid modification site is
not available for annotation.
Length = 174
Score = 26.1 bits (57), Expect = 1.7
Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 1/50 (2%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGGKAN 61
G +C Y D F +Y PT D + +T+ + L L+D G+ +
Sbjct: 12 GKTCLLMSYANDAFPEEYVPTVF-DHYAVSVTVGGKQYLLGLYDTAGQED 60
>gnl|CDD|173686 cd05595, STKc_PKB_beta, Catalytic domain of the Protein
Serine/Threonine Kinase, Protein Kinase B beta.
Serine/Threonine Kinases (STKs), Protein Kinase B (PKB)
or Akt subfamily, beta (or Akt2) isoform, catalytic (c)
domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The PKB subfamily is
part of a larger superfamily that includes the catalytic
domains of other protein STKs, protein tyrosine kinases,
RIO kinases, aminoglycoside phosphotransferase, choline
kinase, and phosphoinositide 3-kinase. There are three
PKB isoforms from different genes, PKB-alpha (or Akt1),
PKB-beta (or Akt2), and PKB-gamma (or Akt3). PKB
contains an N-terminal pleckstrin homology (PH) domain
and a C-terminal catalytic domain. PKB-beta is the
predominant PKB isoform expressed in insulin-responsive
tissues. It plays a critical role in the regulation of
glucose homeostasis. It is also implicated in muscle
cell differentiation. Mice deficient in PKB-beta display
normal growth weights but exhibit severe insulin
resistance and diabetes, accompanied by lipoatrophy and
B-cell failure.
Length = 323
Score = 26.1 bits (57), Expect = 2.1
Identities = 12/24 (50%), Positives = 13/24 (54%)
Query: 13 TSCFSTRYTQDEFTRQYYPTSGPD 36
TS TRY DEFT Q + PD
Sbjct: 276 TSEVDTRYFDDEFTAQSITITPPD 299
>gnl|CDD|217946 pfam04183, IucA_IucC, IucA / IucC family. IucA and IucC catalyze
discrete steps in biosynthesis of the siderophore
aerobactin from N epsilon-acetyl-N epsilon-hydroxylysine
and citrate. This family represents the N-terminal
region. The C-terminal region appears to be related to
iron transporter proteins.
Length = 241
Score = 26.0 bits (58), Expect = 2.1
Identities = 13/41 (31%), Positives = 18/41 (43%), Gaps = 14/41 (34%)
Query: 24 EFTRQYYPTS---------GPDFHLKL-LTIQN----RGVK 50
E Y PTS P+ HLKL L+++N R +
Sbjct: 121 EGGDAYLPTSSVRTLYNPDAPEPHLKLSLSVRNTNSVRTLS 161
>gnl|CDD|236416 PRK09222, PRK09222, isocitrate dehydrogenase; Validated.
Length = 482
Score = 25.2 bits (56), Expect = 3.4
Identities = 8/31 (25%), Positives = 15/31 (48%), Gaps = 2/31 (6%)
Query: 21 TQDEFTRQYYPTSGPDFHLKLLTIQNRGVKL 51
+E + + + LK+ I NRG+K+
Sbjct: 388 DANELAAKLEKLALGNLKLKM--ISNRGLKV 416
>gnl|CDD|215463 PLN02858, PLN02858, fructose-bisphosphate aldolase.
Length = 1378
Score = 25.6 bits (56), Expect = 3.4
Identities = 12/29 (41%), Positives = 15/29 (51%), Gaps = 5/29 (17%)
Query: 30 YPTSGPDFHLKLL-----TIQNRGVKLIL 53
YP SGP+ L LL +GV L+L
Sbjct: 1278 YPASGPNLRLDLLKELRALSSKKGVLLVL 1306
>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 = 25.2 bits (55), Expect = 3.7
Identities = 15/48 (31%), Positives = 21/48 (43%), Gaps = 1/48 (2%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGGK 59
G +C YT + F Y PT +F + + V L LWD G+
Sbjct: 13 GKTCMLISYTSNTFPTDYVPTVFDNFSAN-VVVDGNTVNLGLWDTAGQ 59
>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 = 24.9 bits (54), Expect = 4.1
Identities = 11/31 (35%), Positives = 15/31 (48%)
Query: 29 YYPTSGPDFHLKLLTIQNRGVKLILWDIGGK 59
Y G D+ + + R VKL LWD G+
Sbjct: 35 YGYNMGIDYKTTTILLDGRRVKLQLWDTSGQ 65
>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 = 24.8 bits (54), Expect = 4.2
Identities = 12/49 (24%), Positives = 21/49 (42%), Gaps = 1/49 (2%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGGKA 60
G S + ++ Q F +Y PT D + K + + + L + D G
Sbjct: 13 GKSALTVQFVQGIFVDKYDPTI-EDSYRKQIEVDCQQCMLEILDTAGTE 60
>gnl|CDD|238915 cd01940, Fructoselysine_kinase_like, Fructoselysine kinase-like.
Fructoselysine is a fructoseamine formed by glycation, a
non-enzymatic reaction of glucose with a primary amine
followed by an Amadori rearrangement, resulting in a
protein that is modified at the amino terminus and at
the lysine side chains. Fructoseamines are typically
metabolized by fructoseamine-3-kinase, especially in
higher eukaryotes. In E. coli, fructoselysine kinase has
been shown in vitro to catalyze the phosphorylation of
fructoselysine. It is proposed that fructoselysine is
released from glycated proteins during human digestion
and is partly metabolized by bacteria in the hind gut
using a protein such as fructoselysine kinase. This
family is found only in bacterial sequences, and its
oligomeric state is currently unknown.
Length = 264
Score = 25.0 bits (55), Expect = 4.3
Identities = 14/61 (22%), Positives = 20/61 (32%), Gaps = 10/61 (16%)
Query: 16 FSTRYTQDEFTR-----QYYPTSGPDF-----HLKLLTIQNRGVKLILWDIGGKANESSA 65
FS R+ D + S D KL +RG KL++ G +
Sbjct: 145 FSDRWDDDYLQLVCPYVDFAFFSASDLSDEEVKAKLKEAVSRGAKLVIVTRGEDGAIAYD 204
Query: 66 G 66
G
Sbjct: 205 G 205
>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 = 25.1 bits (55), Expect = 4.4
Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 3/63 (4%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGGKANESSAGLVKTY 71
G S + ++ DEF Y PT D + K + + V+L + D G+ E A + Y
Sbjct: 12 GKSALTLQFMYDEFVEDYEPTKA-DSYRKKVVLDGEEVQLNILDTAGQ--EDYAAIRDNY 68
Query: 72 LSS 74
S
Sbjct: 69 FRS 71
>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 = 24.6 bits (54), Expect = 4.7
Identities = 9/48 (18%), Positives = 18/48 (37%), Gaps = 1/48 (2%)
Query: 12 GTSCFSTRYTQDE-FTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGG 58
G S R ++ +Y P + ++ ++ + K L D G
Sbjct: 13 GKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAG 60
>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 = 24.6 bits (54), Expect = 5.8
Identities = 11/29 (37%), Positives = 17/29 (58%), Gaps = 4/29 (13%)
Query: 31 PTSGPDFHLKLLTIQNRGVKLILWDIGGK 59
PT G L + TI+ +L+ WD+GG+
Sbjct: 37 PTVG----LNIGTIEVGKARLMFWDLGGQ 61
>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 = 24.4 bits (54), Expect = 5.8
Identities = 13/47 (27%), Positives = 19/47 (40%), Gaps = 1/47 (2%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGG 58
G S + ++ Q F Y PT D + K + I L + D G
Sbjct: 12 GKSALTIQFIQGHFVDDYDPTI-EDSYRKQIEIDGEVCLLDILDTAG 57
>gnl|CDD|226284 COG3761, COG3761, NADH:ubiquinone oxidoreductase 17.2 kD subunit
[Energy production and conversion].
Length = 118
Score = 24.5 bits (53), Expect = 5.9
Identities = 7/21 (33%), Positives = 9/21 (42%)
Query: 16 FSTRYTQDEFTRQYYPTSGPD 36
F + +DEF YY D
Sbjct: 12 FHKKVGEDEFGNVYYEGRNID 32
>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 = 24.6 bits (54), Expect = 6.3
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 6/50 (12%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQ---NRGVKLILWDIGG 58
G +C Y Q F +Y PT F + T+Q + ++L LWD G
Sbjct: 15 GKTCLLMVYAQGSFPEEYVPTV---FENYVTTLQVPNGKIIELALWDTAG 61
>gnl|CDD|221790 pfam12819, Malectin_like, Carbohydrate-binding protein of the ER.
Malectin is a membrane-anchored protein of the
endoplasmic reticulum that recognises and binds
Glc2-N-glycan. The domain is found on a number of plant
receptor kinases.
Length = 335
Score = 24.6 bits (54), Expect = 6.8
Identities = 8/35 (22%), Positives = 14/35 (40%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQN 46
G S + RY D + R + P ++ T +
Sbjct: 178 GGSEGTIRYPDDVYDRIWEPFFSSPGWSQISTSLS 212
>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 = 24.5 bits (53), Expect = 6.9
Identities = 7/28 (25%), Positives = 15/28 (53%)
Query: 32 TSGPDFHLKLLTIQNRGVKLILWDIGGK 59
T+ P + T+ + + +WD+GG+
Sbjct: 40 TTIPTIGFNVETVTYKNISFTVWDVGGQ 67
>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 = 24.4 bits (54), Expect = 7.3
Identities = 13/47 (27%), Positives = 20/47 (42%), Gaps = 1/47 (2%)
Query: 12 GTSCFSTRYTQDEFTRQYYPTSGPDFHLKLLTIQNRGVKLILWDIGG 58
G S + ++ Q F +Y PT D + K + I L + D G
Sbjct: 14 GKSALTIQFVQGHFVDEYDPTI-EDSYRKQIEIDGEVCLLDILDTAG 59
>gnl|CDD|187598 cd05339, 17beta-HSDXI-like_SDR_c, human 17-beta-hydroxysteroid
dehydrogenase XI-like, classical (c) SDRs.
17-beta-hydroxysteroid dehydrogenases (17betaHSD) are a
group of isozymes that catalyze activation and
inactivation of estrogen and androgens. 17betaHSD type
XI, a classical SDR, preferentially converts
3alpha-adiol to androsterone but not numerous other
tested steroids. This subgroup of classical SDRs also
includes members identified as retinol dehydrogenases,
which convert retinol to retinal, a property that
overlaps with 17betaHSD activity. SDRs are a
functionally diverse family of oxidoreductases that
have a single domain with a structurally conserved
Rossmann fold (alpha/beta folding pattern with a
central beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRS are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes have a
3-glycine N-terminal NAD(P)(H)-binding pattern
(typically, TGxxxGxG in classical SDRs and TGxxGxxG in
extended SDRs), while substrate binding is in the
C-terminal region. A critical catalytic Tyr residue
(Tyr-151, human 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering), is often found in a conserved
YXXXK pattern. In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is
not generally found among SDRs.
Length = 243
Score = 24.1 bits (53), Expect = 8.1
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 47 RGVKLILWDIGGKANESSAGLVK 69
RG K+++ DI K E +A V+
Sbjct: 22 RGAKVVILDINEKGAEETANNVR 44
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
0.317 0.133 0.392
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: 3,596,016
Number of extensions: 255724
Number of successful extensions: 276
Number of sequences better than 10.0: 1
Number of HSP's gapped: 269
Number of HSP's successfully gapped: 80
Length of query: 78
Length of database: 10,937,602
Length adjustment: 47
Effective length of query: 31
Effective length of database: 8,852,964
Effective search space: 274441884
Effective search space used: 274441884
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.5 bits)