RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1416
(177 letters)
>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 = 100 bits (250), Expect = 6e-27
Identities = 52/87 (59%), Positives = 62/87 (71%), Gaps = 3/87 (3%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAITNLVLRSKKEQK 151
LVGNKNDDP++KVV TEDA +FA QMGI LFETSAK+NINVEEMF IT LVLR+KK+
Sbjct: 115 LVGNKNDDPERKVVETEDAYKFAGQMGISLFETSAKENINVEEMFNCITELVLRAKKDNL 174
Query: 152 ER-QVLNSDTVNIRKHTTKPGGKKKCC 177
+ Q + V +K KK+CC
Sbjct: 175 AKQQQQQQNDVVKLPKNSK--RKKRCC 199
Score = 56.4 bits (136), Expect = 3e-10
Identities = 29/60 (48%), Positives = 36/60 (60%), Gaps = 1/60 (1%)
Query: 1 MGIQLFETSAKDNINVEEMFMAITNLVLRSKKEQKER-QVLNSDTVNIRKHTTKPGGKKK 59
MGI LFETSAK+NINVEEMF IT LVLR+KK+ + Q + V +K +
Sbjct: 140 MGISLFETSAKENINVEEMFNCITELVLRAKKDNLAKQQQQQQNDVVKLPKNSKRKKRCC 199
>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 = 72.5 bits (179), Expect = 1e-16
Identities = 24/49 (48%), Positives = 34/49 (69%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAIT 140
LVGNK+D ++ V TE+AQ+FA + G+ FETSAK NV+E F ++
Sbjct: 110 LVGNKSDLEDERQVSTEEAQQFAKENGLLFFETSAKTGENVDEAFESLA 158
Score = 39.4 bits (93), Expect = 2e-04
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 2 GIQLFETSAKDNINVEEMFMAIT 24
G+ FETSAK NV+E F ++
Sbjct: 136 GLLFFETSAKTGENVDEAFESLA 158
>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 = 69.8 bits (172), Expect = 1e-15
Identities = 24/54 (44%), Positives = 34/54 (62%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAITNLVLR 145
LVGNK D ++VV TE+ + A ++G+ ETSAK N NVEE F + +L+
Sbjct: 109 LVGNKCDLEDQRVVSTEEGEALAKELGLPFMETSAKTNENVEEAFEELAREILK 162
Score = 41.3 bits (98), Expect = 4e-05
Identities = 13/29 (44%), Positives = 18/29 (62%)
Query: 1 MGIQLFETSAKDNINVEEMFMAITNLVLR 29
+G+ ETSAK N NVEE F + +L+
Sbjct: 134 LGLPFMETSAKTNENVEEAFEELAREILK 162
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 68.7 bits (169), Expect = 4e-15
Identities = 25/54 (46%), Positives = 36/54 (66%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAITNLVLR 145
LVGNK+D +++ V E+A+ FA + G+ FETSAK N NVEE F + +L+
Sbjct: 110 LVGNKSDLEEQRQVSREEAEAFAEEHGLPFFETSAKTNTNVEEAFEELAREILK 163
Score = 40.6 bits (96), Expect = 1e-04
Identities = 14/28 (50%), Positives = 18/28 (64%)
Query: 2 GIQLFETSAKDNINVEEMFMAITNLVLR 29
G+ FETSAK N NVEE F + +L+
Sbjct: 136 GLPFFETSAKTNTNVEEAFEELAREILK 163
>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 = 68.1 bits (167), Expect = 7e-15
Identities = 26/54 (48%), Positives = 36/54 (66%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAITNLVLR 145
LVGNK D +K+VV E+ + A + GI+ ETSAK NINVEE F+ + +L+
Sbjct: 113 LVGNKCDMEEKRVVSKEEGEALAREYGIKFLETSAKANINVEEAFLTLAKDILK 166
Score = 43.8 bits (104), Expect = 6e-06
Identities = 15/28 (53%), Positives = 20/28 (71%)
Query: 2 GIQLFETSAKDNINVEEMFMAITNLVLR 29
GI+ ETSAK NINVEE F+ + +L+
Sbjct: 139 GIKFLETSAKANINVEEAFLTLAKDILK 166
>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 = 65.3 bits (160), Expect = 6e-14
Identities = 19/53 (35%), Positives = 35/53 (66%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAITNLVL 144
+VGNK D +++VV +A+ +A +G + FETSAK +EE+F+++ ++
Sbjct: 110 IVGNKIDLERQRVVSKSEAEEYAKSVGAKHFETSAKTGKGIEELFLSLAKRMI 162
Score = 38.4 bits (90), Expect = 6e-04
Identities = 10/27 (37%), Positives = 18/27 (66%)
Query: 2 GIQLFETSAKDNINVEEMFMAITNLVL 28
G + FETSAK +EE+F+++ ++
Sbjct: 136 GAKHFETSAKTGKGIEELFLSLAKRMI 162
>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 = 65.4 bits (160), Expect = 7e-14
Identities = 26/49 (53%), Positives = 33/49 (67%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAIT 140
LVGNK D KKVV +A+ FA+++GI ETSAK+ NVEE FM +
Sbjct: 112 LVGNKCDLTDKKVVDYTEAKEFADELGIPFLETSAKNATNVEEAFMTMA 160
Score = 35.0 bits (81), Expect = 0.007
Identities = 13/24 (54%), Positives = 16/24 (66%)
Query: 1 MGIQLFETSAKDNINVEEMFMAIT 24
+GI ETSAK+ NVEE FM +
Sbjct: 137 LGIPFLETSAKNATNVEEAFMTMA 160
>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 = 62.6 bits (153), Expect = 7e-13
Identities = 23/48 (47%), Positives = 30/48 (62%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAI 139
L GNK D K+ V TE+AQ +A++ G+ ETSAK NV E+F I
Sbjct: 111 LAGNKADLESKRQVSTEEAQEYADENGLLFMETSAKTGENVNELFTEI 158
Score = 35.2 bits (82), Expect = 0.007
Identities = 10/18 (55%), Positives = 11/18 (61%)
Query: 6 FETSAKDNINVEEMFMAI 23
ETSAK NV E+F I
Sbjct: 141 METSAKTGENVNELFTEI 158
>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 = 61.8 bits (151), Expect = 1e-12
Identities = 23/48 (47%), Positives = 30/48 (62%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAI 139
LVGNK+D + V TE+A+ FA + G+ ETSA D NVEE F +
Sbjct: 113 LVGNKSDLRHLRAVPTEEAKAFAEKNGLSFIETSALDGTNVEEAFKQL 160
Score = 32.1 bits (74), Expect = 0.079
Identities = 11/22 (50%), Positives = 13/22 (59%)
Query: 2 GIQLFETSAKDNINVEEMFMAI 23
G+ ETSA D NVEE F +
Sbjct: 139 GLSFIETSALDGTNVEEAFKQL 160
>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 = 60.6 bits (148), Expect = 4e-12
Identities = 22/45 (48%), Positives = 29/45 (64%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMF 136
LVGNK D ++VV TE+ + A Q G ETSAK+ +NV+E F
Sbjct: 110 LVGNKCDLESERVVSTEEGKELARQWGCPFLETSAKERVNVDEAF 154
Score = 34.1 bits (79), Expect = 0.017
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 1 MGIQLFETSAKDNINVEEMF 20
G ETSAK+ +NV+E F
Sbjct: 135 WGCPFLETSAKERVNVDEAF 154
>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 = 60.3 bits (147), Expect = 6e-12
Identities = 23/45 (51%), Positives = 29/45 (64%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMF 136
LVGNK D ++VV TE+ + A Q G ETSAK+ INV+E F
Sbjct: 112 LVGNKCDLENERVVSTEEGKELARQWGCPFLETSAKERINVDEAF 156
Score = 33.7 bits (78), Expect = 0.023
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 2 GIQLFETSAKDNINVEEMF 20
G ETSAK+ INV+E F
Sbjct: 138 GCPFLETSAKERINVDEAF 156
>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 = 59.8 bits (146), Expect = 7e-12
Identities = 21/52 (40%), Positives = 31/52 (59%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAITNLV 143
LVGNK D ++ V TE+ + A + G ETSAK NIN++E+F + +
Sbjct: 109 LVGNKCDLENERQVSTEEGEALAEEWGCPFLETSAKTNINIDELFNTLVREI 160
Score = 36.7 bits (86), Expect = 0.002
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 2 GIQLFETSAKDNINVEEMFMAITNLV 27
G ETSAK NIN++E+F + +
Sbjct: 135 GCPFLETSAKTNINIDELFNTLVREI 160
>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 = 58.8 bits (143), Expect = 3e-11
Identities = 26/59 (44%), Positives = 37/59 (62%), Gaps = 1/59 (1%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMG-IQLFETSAKDNINVEEMFMAITNLVLRSKKE 149
++GNK D +K+ V T+ AQ++ G I FETSAK+ INV++ F I L L +KE
Sbjct: 114 VLGNKIDLEEKRQVSTKKAQQWCKSKGNIPYFETSAKEAINVDQAFETIARLALEQEKE 172
Score = 43.8 bits (104), Expect = 8e-06
Identities = 16/31 (51%), Positives = 20/31 (64%)
Query: 3 IQLFETSAKDNINVEEMFMAITNLVLRSKKE 33
I FETSAK+ INV++ F I L L +KE
Sbjct: 142 IPYFETSAKEAINVDQAFETIARLALEQEKE 172
>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 = 57.6 bits (139), Expect = 6e-11
Identities = 22/52 (42%), Positives = 37/52 (71%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAITNLV 143
LVGNK D ++VV E ++ A+Q+G + FE SAK+NINV+++F + +++
Sbjct: 111 LVGNKCDMEDERVVSAERGRQLADQLGFEFFEASAKENINVKQVFERLVDII 162
Score = 34.5 bits (79), Expect = 0.013
Identities = 11/27 (40%), Positives = 21/27 (77%)
Query: 1 MGIQLFETSAKDNINVEEMFMAITNLV 27
+G + FE SAK+NINV+++F + +++
Sbjct: 136 LGFEFFEASAKENINVKQVFERLVDII 162
>gnl|CDD|133345 cd04145, M_R_Ras_like, R-Ras2/TC21, M-Ras/R-Ras3. The
M-Ras/R-Ras-like subfamily contains R-Ras2/TC21,
M-Ras/R-Ras3, and related members of the Ras family.
M-Ras is expressed in lympho-hematopoetic cells. It
interacts with some of the known Ras effectors, but
appears to also have its own effectors. Expression of
mutated M-Ras leads to transformation of several types
of cell lines, including hematopoietic cells, mammary
epithelial cells, and fibroblasts. Overexpression of
M-Ras is observed in carcinomas from breast, uterus,
thyroid, stomach, colon, kidney, lung, and rectum. In
addition, expression of a constitutively active M-Ras
mutant in murine bone marrow induces a malignant mast
cell leukemia that is distinct from the monocytic
leukemia induced by H-Ras. TC21, along with H-Ras, has
been shown to regulate the branching morphogenesis of
ureteric bud cell branching in mice. Most Ras proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 164
Score = 54.7 bits (132), Expect = 6e-10
Identities = 23/58 (39%), Positives = 34/58 (58%), Gaps = 2/58 (3%)
Query: 86 FPSGLRLVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAITNLV 143
FP + LVGNK D ++ V E+ Q A Q+ I ETSAKD +NV++ F + ++
Sbjct: 108 FP--MILVGNKADLEHQRQVSREEGQELARQLKIPYIETSAKDRVNVDKAFHDLVRVI 163
Score = 30.8 bits (70), Expect = 0.22
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 3 IQLFETSAKDNINVEEMFMAITNLV 27
I ETSAKD +NV++ F + ++
Sbjct: 139 IPYIETSAKDRVNVDKAFHDLVRVI 163
>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 = 54.2 bits (131), Expect = 9e-10
Identities = 19/45 (42%), Positives = 27/45 (60%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMF 136
LVGNK D K+ V TE+ ++ A + ETSAK NV+++F
Sbjct: 110 LVGNKTDLSDKRQVSTEEGEKKAKENNAMFIETSAKAGHNVKQLF 154
>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 = 53.1 bits (128), Expect = 4e-09
Identities = 28/89 (31%), Positives = 41/89 (46%), Gaps = 5/89 (5%)
Query: 92 LVGNKND-DPQKKVVLTEDAQRFANQMG-IQLFETSAKDNINVEEMFMAITNLVLRSKKE 149
L+ NK D ++ E +F + G I FETSAK+NIN+EE + +L++ K
Sbjct: 115 LLANKCDLKKERLAKDPEQMDQFCKENGFIGWFETSAKENINIEEAMRFLVKNILKNDKG 174
Query: 150 -QKERQVLNSDTVNIRKHTTKPGGKKKCC 177
Q ++ V K T K CC
Sbjct: 175 LQSPEPDEDN--VIDLKQETTTSKSKSCC 201
Score = 40.0 bits (94), Expect = 2e-04
Identities = 20/60 (33%), Positives = 28/60 (46%), Gaps = 3/60 (5%)
Query: 3 IQLFETSAKDNINVEEMFMAITNLVLRSKKE-QKERQVLNSDTVNIRKHTTKPGGKKKVC 61
I FETSAK+NIN+EE + +L++ K Q ++ V K T K C
Sbjct: 144 IGWFETSAKENINIEEAMRFLVKNILKNDKGLQSPEPDEDN--VIDLKQETTTSKSKSCC 201
>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 = 52.6 bits (127), Expect = 4e-09
Identities = 21/63 (33%), Positives = 33/63 (52%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAITNLVLRSKKEQK 151
LVGNK+D ++ V E+ ++ A G E+SAK+N NVEE F + + + +
Sbjct: 111 LVGNKSDLHMERQVSAEEGKKLAESWGAAFLESSAKENENVEEAFELLIEEIEKVENPLP 170
Query: 152 ERQ 154
Q
Sbjct: 171 PGQ 173
Score = 29.1 bits (66), Expect = 0.77
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 7 ETSAKDNINVEEMFMAITNLVLRSKKEQKERQ 38
E+SAK+N NVEE F + + + + Q
Sbjct: 142 ESSAKENENVEEAFELLIEEIEKVENPLPPGQ 173
>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 = 52.9 bits (127), Expect = 5e-09
Identities = 32/90 (35%), Positives = 43/90 (47%), Gaps = 9/90 (10%)
Query: 90 LRLVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAITNLVLRSKKE 149
+ L+GNK D ++VV ED +R A + G+ ETSAK +NVE F A+ KE
Sbjct: 109 IMLLGNKADMSGERVVKREDGERLAKEYGVPFMETSAKTGLNVELAFTAVA-------KE 161
Query: 150 QKERQVLNSD--TVNIRKHTTKPGGKKKCC 177
K R V D I+ + K CC
Sbjct: 162 LKHRSVEQPDEPKFKIQDYVEKQKKSSGCC 191
Score = 28.3 bits (63), Expect = 1.5
Identities = 20/62 (32%), Positives = 25/62 (40%), Gaps = 9/62 (14%)
Query: 2 GIQLFETSAKDNINVEEMFMAITNLVLRSKKEQKERQVLNSD--TVNIRKHTTKPGGKKK 59
G+ ETSAK +NVE F A+ KE K R V D I+ + K
Sbjct: 137 GVPFMETSAKTGLNVELAFTAVA-------KELKHRSVEQPDEPKFKIQDYVEKQKKSSG 189
Query: 60 VC 61
C
Sbjct: 190 CC 191
>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 = 51.3 bits (123), Expect = 1e-08
Identities = 20/54 (37%), Positives = 29/54 (53%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAITNLVLR 145
L+GNK D ++ V E+ + FA + G+ ETSAK NVEE F+ +
Sbjct: 114 LIGNKCDLESRREVSYEEGEAFAREHGLIFMETSAKTASNVEEAFINTAKEIYD 167
Score = 28.9 bits (65), Expect = 1.0
Identities = 11/28 (39%), Positives = 14/28 (50%)
Query: 2 GIQLFETSAKDNINVEEMFMAITNLVLR 29
G+ ETSAK NVEE F+ +
Sbjct: 140 GLIFMETSAKTASNVEEAFINTAKEIYD 167
>gnl|CDD|133344 cd04144, Ras2, Rat sarcoma (Ras) family 2 of small guanosine
triphosphatases (GTPases). The Ras2 subfamily, found
exclusively in fungi, was first identified in Ustilago
maydis. In U. maydis, Ras2 is regulated by Sql2, a
protein that is homologous to GEFs (guanine nucleotide
exchange factors) of the CDC25 family. Ras2 has been
shown to induce filamentous growth, but the signaling
cascade through which Ras2 and Sql2 regulate cell
morphology is not known. Most Ras proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Ras proteins.
Length = 190
Score = 51.4 bits (123), Expect = 2e-08
Identities = 26/85 (30%), Positives = 43/85 (50%), Gaps = 8/85 (9%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAITNLVLRSKKEQK 151
+VGNK D ++ V TE+ A ++G + E SAK N+NVE F ++R+ ++Q+
Sbjct: 111 IVGNKCDKVYEREVSTEEGAALARRLGCEFIEASAKTNVNVERAFYT----LVRALRQQR 166
Query: 152 ERQVLNSDTVNIRKHTTKPGGKKKC 176
+ +K K K+KC
Sbjct: 167 QGGQGPKGGPTKKKE--KK--KRKC 187
Score = 32.5 bits (74), Expect = 0.069
Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 9/64 (14%)
Query: 1 MGIQLFETSAKDNINVEEMFMAITNLVLRSKKEQKERQVLNSDTVNIRKHTTKPGGKKKV 60
+G + E SAK N+NVE F ++R+ ++Q++ T K KK+
Sbjct: 136 LGCEFIEASAKTNVNVERAFYT----LVRALRQQRQGGQGPKGGP-----TKKKEKKKRK 186
Query: 61 CTVL 64
C ++
Sbjct: 187 CVIM 190
>gnl|CDD|133338 cd04138, H_N_K_Ras_like, Ras GTPase family containing H-Ras,N-Ras
and K-Ras4A/4B. H-Ras/N-Ras/K-Ras subfamily. H-Ras,
N-Ras, and K-Ras4A/4B are the prototypical members of
the Ras family. These isoforms generate distinct signal
outputs despite interacting with a common set of
activators and effectors, and are strongly associated
with oncogenic progression in tumor initiation. Mutated
versions of Ras that are insensitive to GAP stimulation
(and are therefore constitutively active) are found in a
significant fraction of human cancers. Many Ras guanine
nucleotide exchange factors (GEFs) have been identified.
They are sequestered in the cytosol until activation by
growth factors triggers recruitment to the plasma
membrane or Golgi, where the GEF colocalizes with Ras.
Active (GTP-bound) Ras interacts with several effector
proteins that stimulate a variety of diverse cytoplasmic
signaling activities. Some are known to positively
mediate the oncogenic properties of Ras, including Raf,
phosphatidylinositol 3-kinase (PI3K), RalGEFs, and
Tiam1. Others are proposed to play negative regulatory
roles in oncogenesis, including RASSF and NORE/MST1.
Most Ras proteins contain a lipid modification site at
the C-terminus, with a typical sequence motif CaaX,
where a = an aliphatic amino acid and X = any amino
acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 162
Score = 48.6 bits (116), Expect = 1e-07
Identities = 21/45 (46%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMF 136
LVGNK D + V T Q A GI ETSAK VEE F
Sbjct: 111 LVGNKCDLA-ARTVSTRQGQDLAKSYGIPYIETSAKTRQGVEEAF 154
Score = 30.1 bits (68), Expect = 0.44
Identities = 11/20 (55%), Positives = 11/20 (55%)
Query: 1 MGIQLFETSAKDNINVEEMF 20
GI ETSAK VEE F
Sbjct: 135 YGIPYIETSAKTRQGVEEAF 154
>gnl|CDD|133375 cd04175, Rap1, Rap1 family GTPase consists of Rap1a and Rap1b
isoforms. The Rap1 subgroup is part of the Rap
subfamily of the Ras family. It can be further divided
into the Rap1a and Rap1b isoforms. In humans, Rap1a and
Rap1b share 95% sequence homology, but are products of
two different genes located on chromosomes 1 and 12,
respectively. Rap1a is sometimes called smg p21 or Krev1
in the older literature. Rap1 proteins are believed to
perform different cellular functions, depending on the
isoform, its subcellular localization, and the effector
proteins it binds. For example, in rat salivary gland,
neutrophils, and platelets, Rap1 localizes to secretory
granules and is believed to regulate exocytosis or the
formation of secretory granules. Rap1 has also been
shown to localize in the Golgi of rat fibroblasts,
zymogen granules, plasma membrane, and the microsomal
membrane of pancreatic acini, as well as in the
endocytic compartment of skeletal muscle cells and
fibroblasts. High expression of Rap1 has been observed
in the nucleus of human oropharyngeal squamous cell
carcinomas (SCCs) and cell lines; interestingly, in the
SCCs, the active GTP-bound form localized to the
nucleus, while the inactive GDP-bound form localized to
the cytoplasm. Rap1 plays a role in phagocytosis by
controlling the binding of adhesion receptors (typically
integrins) to their ligands. In yeast, Rap1 has been
implicated in multiple functions, including activation
and silencing of transcription and maintenance of
telomeres. Rap1a, which is stimulated by T-cell receptor
(TCR) activation, is a positive regulator of T cells by
directing integrin activation and augmenting lymphocyte
responses. In murine hippocampal neurons, Rap1b
determines which neurite will become the axon and
directs the recruitment of Cdc42, which is required for
formation of dendrites and axons. In murine platelets,
Rap1b is required for normal homeostasis in vivo and is
involved in integrin activation. Most Ras proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 164
Score = 48.3 bits (115), Expect = 2e-07
Identities = 23/45 (51%), Positives = 26/45 (57%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMF 136
LVGNK D ++VV E Q A Q G ETSAK INV E+F
Sbjct: 111 LVGNKCDLEDERVVGKEQGQNLARQWGCAFLETSAKAKINVNEIF 155
Score = 26.7 bits (59), Expect = 5.8
Identities = 11/19 (57%), Positives = 12/19 (63%)
Query: 2 GIQLFETSAKDNINVEEMF 20
G ETSAK INV E+F
Sbjct: 137 GCAFLETSAKAKINVNEIF 155
>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 = 47.0 bits (112), Expect = 4e-07
Identities = 22/51 (43%), Positives = 32/51 (62%), Gaps = 1/51 (1%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGI-QLFETSAKDNINVEEMFMAITN 141
L+GNK D +++ VL E+A A GI + ETSAK++ NVEE F+ +
Sbjct: 113 LIGNKCDLEEQREVLFEEACTLAEHYGILAVLETSAKESSNVEEAFLLMAT 163
Score = 30.1 bits (68), Expect = 0.38
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 7 ETSAKDNINVEEMFMAITN 25
ETSAK++ NVEE F+ +
Sbjct: 145 ETSAKESSNVEEAFLLMAT 163
>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 = 46.9 bits (111), Expect = 5e-07
Identities = 24/55 (43%), Positives = 35/55 (63%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAITNLVLRS 146
L+GNK D+ QK+ V E + A + G+ FETSA N N++E F +T LVL++
Sbjct: 110 LIGNKADEEQKRQVGDEQGNKLAKEYGMDFFETSACTNKNIKESFTRLTELVLQA 164
Score = 28.8 bits (64), Expect = 1.0
Identities = 14/29 (48%), Positives = 20/29 (68%)
Query: 2 GIQLFETSAKDNINVEEMFMAITNLVLRS 30
G+ FETSA N N++E F +T LVL++
Sbjct: 136 GMDFFETSACTNKNIKESFTRLTELVLQA 164
>gnl|CDD|206711 cd04140, ARHI_like, A Ras homolog member I (ARHI). ARHI (A Ras
homolog member I) is a member of the Ras family with
several unique structural and functional properties.
ARHI is expressed in normal human ovarian and breast
tissue, but its expression is decreased or eliminated in
breast and ovarian cancer. ARHI contains an N-terminal
extension of 34 residues (human) that is required to
retain its tumor suppressive activity. Unlike most other
Ras family members, ARHI is maintained in the
constitutively active (GTP-bound) state in resting cells
and has modest GTPase activity. ARHI inhibits STAT3
(signal transducers and activators of transcription 3),
a latent transcription factor whose abnormal activation
plays a critical role in oncogenesis. Most Ras proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 165
Score = 46.7 bits (111), Expect = 6e-07
Identities = 20/51 (39%), Positives = 27/51 (52%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAITNL 142
LVGNK D+ + V + + A ETSAK N NV+E+F + NL
Sbjct: 113 LVGNKCDESPSREVSSSEGAALARTWNCAFMETSAKTNHNVQELFQELLNL 163
Score = 29.4 bits (66), Expect = 0.63
Identities = 12/20 (60%), Positives = 15/20 (75%)
Query: 7 ETSAKDNINVEEMFMAITNL 26
ETSAK N NV+E+F + NL
Sbjct: 144 ETSAKTNHNVQELFQELLNL 163
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 46.9 bits (111), Expect = 9e-07
Identities = 20/46 (43%), Positives = 29/46 (63%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFM 137
L+GNK D ++ V TE+ ++FA + G+ E SAK NVEE F+
Sbjct: 116 LIGNKCDLAHRRAVSTEEGEQFAKEHGLIFMEASAKTAQNVEEAFI 161
>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 = 45.4 bits (108), Expect = 2e-06
Identities = 19/45 (42%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMF 136
LVGNK D + V E+ Q+FA + + ETSAK I V++ F
Sbjct: 111 LVGNKIDKENR-EVTREEGQKFARKHNMLFIETSAKTRIGVQQAF 154
>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 = 45.1 bits (107), Expect = 2e-06
Identities = 22/47 (46%), Positives = 28/47 (59%)
Query: 90 LRLVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMF 136
L LVGNK D K+ V E+A A Q G+ ETSAK NV+++F
Sbjct: 108 LLLVGNKCDLEDKRQVSVEEAANLAEQWGVNYVETSAKTRANVDKVF 154
Score = 29.3 bits (66), Expect = 0.72
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 2 GIQLFETSAKDNINVEEMF 20
G+ ETSAK NV+++F
Sbjct: 136 GVNYVETSAKTRANVDKVF 154
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 45.6 bits (108), Expect = 2e-06
Identities = 24/63 (38%), Positives = 32/63 (50%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAITNLVLRSKKEQK 151
LVGNK D ++ V T + Q A GI ETSAK +NV+E F + + + KE
Sbjct: 115 LVGNKCDLDSERQVSTGEGQELAKSFGIPFLETSAKQRVNVDEAFYELVREIRKYLKEDM 174
Query: 152 ERQ 154
Q
Sbjct: 175 PSQ 177
Score = 30.2 bits (68), Expect = 0.41
Identities = 18/64 (28%), Positives = 25/64 (39%), Gaps = 14/64 (21%)
Query: 1 MGIQLFETSAKDNINVEEMFMAITNLVLRSKKEQKERQVLNSDTVNIRKHTTKPGGKKKV 60
GI ETSAK +NV+E F + + + KE Q K K +
Sbjct: 140 FGIPFLETSAKQRVNVDEAFYELVREIRKYLKEDMPSQ--------------KQKKKGGL 185
Query: 61 CTVL 64
C +L
Sbjct: 186 CLIL 189
>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 = 45.5 bits (108), Expect = 2e-06
Identities = 20/49 (40%), Positives = 31/49 (63%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAIT 140
LVG+K D ++ V E+A++ A +G++ ETSA+ NVEE F +T
Sbjct: 114 LVGHKCDLESQRQVTREEAEKLAKDLGMKYIETSARTGDNVEEAFELLT 162
Score = 27.4 bits (61), Expect = 3.2
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 2 GIQLFETSAKDNINVEEMFMAIT 24
G++ ETSA+ NVEE F +T
Sbjct: 140 GMKYIETSARTGDNVEEAFELLT 162
>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 = 45.4 bits (107), Expect = 3e-06
Identities = 25/82 (30%), Positives = 46/82 (56%), Gaps = 1/82 (1%)
Query: 90 LRLVGNKNDDPQKKVVLTEDAQRFANQM-GIQLFETSAKDNINVEEMFMAITNLVLRSKK 148
L LVGNK D + + + ++FA Q+ G++ E SAKDN NV+E+F+ + + +L+
Sbjct: 108 LLLVGNKLDCETDREITRQQGEKFAQQITGMRFCEASAKDNFNVDEIFLKLVDDILKKMP 167
Query: 149 EQKERQVLNSDTVNIRKHTTKP 170
R L++ ++++ P
Sbjct: 168 LDILRNELSNSILSLQPEPEIP 189
Score = 31.1 bits (70), Expect = 0.23
Identities = 15/53 (28%), Positives = 30/53 (56%)
Query: 2 GIQLFETSAKDNINVEEMFMAITNLVLRSKKEQKERQVLNSDTVNIRKHTTKP 54
G++ E SAKDN NV+E+F+ + + +L+ R L++ ++++ P
Sbjct: 137 GMRFCEASAKDNFNVDEIFLKLVDDILKKMPLDILRNELSNSILSLQPEPEIP 189
>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 = 43.9 bits (104), Expect = 6e-06
Identities = 15/54 (27%), Positives = 27/54 (50%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAITNLVLR 145
+ NK D + + V ++ + +A G + FETSA V EMF + + ++
Sbjct: 115 VCANKIDLTKHRAVSEDEGRLWAESKGFKYFETSACTGEGVNEMFQTLFSSIVD 168
>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 = 43.6 bits (103), Expect = 7e-06
Identities = 22/47 (46%), Positives = 28/47 (59%), Gaps = 2/47 (4%)
Query: 92 LVGNKND-DPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFM 137
LVGNK D + ++V E A RFA + G+ ETSA NVEE F+
Sbjct: 110 LVGNKKDLEDDREVTFLE-ASRFAQENGLLFLETSALTGENVEEAFL 155
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 44.1 bits (104), Expect = 7e-06
Identities = 27/93 (29%), Positives = 40/93 (43%), Gaps = 7/93 (7%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAITNLVLR--SKKE 149
+ GNK+D + V ED Q A + G+ ETSA + NVE+ F I + SKK
Sbjct: 122 MAGNKSDLNHLRSVAEEDGQALAEKEGLSFLETSALEATNVEKAFQTILLEIYHIISKKA 181
Query: 150 QKERQVLNSDTV-----NIRKHTTKPGGKKKCC 177
++ + + I T K+ CC
Sbjct: 182 LAAQEAAANSGLPGQGTTINVADTSGNNKRGCC 214
>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 = 43.3 bits (102), Expect = 1e-05
Identities = 18/48 (37%), Positives = 32/48 (66%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAI 139
LVGNK D +++ V + A+ F++ + ETSAK++ NVE++F+ +
Sbjct: 117 LVGNKIDLAERREVSQQRAEEFSDAQDMYYLETSAKESDNVEKLFLDL 164
>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 = 43.3 bits (102), Expect = 1e-05
Identities = 26/83 (31%), Positives = 44/83 (53%), Gaps = 4/83 (4%)
Query: 65 NECAWLGC-GWMT-ICPIIYCWLFPSGLRLVGNKNDDPQKKVVLTEDAQRFANQMGIQLF 122
+E ++L WM+ + YC + L+GNK D P ++ V A+ A++ GI F
Sbjct: 98 SEQSFLNVRNWMSQLQAHAYCE--NPDIVLIGNKADLPDQREVSERQARELADKYGIPYF 155
Query: 123 ETSAKDNINVEEMFMAITNLVLR 145
ETSA NVE+ + +L+++
Sbjct: 156 ETSAATGQNVEKAVETLLDLIMK 178
>gnl|CDD|133326 cd04126, Rab20, Rab GTPase family 20 (Rab20). Rab20 is one of
several Rab proteins that appear to be restricted in
expression to the apical domain of murine polarized
epithelial cells. It is expressed on the apical side of
polarized kidney tubule and intestinal epithelial cells,
and in non-polarized cells. It also localizes to
vesico-tubular structures below the apical brush border
of renal proximal tubule cells and in the apical region
of duodenal epithelial cells. Rab20 has also been shown
to colocalize with vacuolar H+-ATPases (V-ATPases) in
mouse kidney cells, suggesting a role in the regulation
of V-ATPase traffic in specific portions of the nephron.
It was also shown to be one of several proteins whose
expression is upregulated in human myelodysplastic
syndrome (MDS) patients. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 220
Score = 43.0 bits (101), Expect = 2e-05
Identities = 27/76 (35%), Positives = 34/76 (44%), Gaps = 6/76 (7%)
Query: 102 KKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAITNLVLRSKKEQKERQVLNSDTV 161
K +L ED A +M FETSAK NV+E+F + NLVL +R N
Sbjct: 151 KYKMLDEDLSPAAEKM---CFETSAKTGYNVDELFEYLFNLVL--PLILAQRAEANRTQG 205
Query: 162 NIRKHTTKPGGKKKCC 177
+ K K KCC
Sbjct: 206 TVNLPNPKR-SKSKCC 220
Score = 34.9 bits (80), Expect = 0.013
Identities = 20/56 (35%), Positives = 25/56 (44%), Gaps = 3/56 (5%)
Query: 6 FETSAKDNINVEEMFMAITNLVLRSKKEQKERQVLNSDTVNIRKHTTKPGGKKKVC 61
FETSAK NV+E+F + NLVL +R N + K K K C
Sbjct: 168 FETSAKTGYNVDELFEYLFNLVL--PLILAQRAEANRTQGTVNLPNPKR-SKSKCC 220
>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 = 42.5 bits (100), Expect = 2e-05
Identities = 19/55 (34%), Positives = 33/55 (60%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAITNLVLRS 146
L+GNK D ++ V E+A++FA++ G+ E SAK NVE+ F+ + ++
Sbjct: 112 LIGNKADLEAQRDVTYEEAKQFADENGLLFLECSAKTGENVEDAFLETAKKIYQN 166
>gnl|CDD|133376 cd04176, Rap2, Rap2 family GTPase consists of Rap2a, Rap2b, and
Rap2c. The Rap2 subgroup is part of the Rap subfamily
of the Ras family. It consists of Rap2a, Rap2b, and
Rap2c. Both isoform 3 of the human mitogen-activated
protein kinase kinase kinase kinase 4 (MAP4K4) and
Traf2- and Nck-interacting kinase (TNIK) are putative
effectors of Rap2 in mediating the activation of c-Jun
N-terminal kinase (JNK) to regulate the actin
cytoskeleton. In human platelets, Rap2 was shown to
interact with the cytoskeleton by binding the actin
filaments. In embryonic Xenopus development, Rap2 is
necessary for the Wnt/beta-catenin signaling pathway.
The Rap2 interacting protein 9 (RPIP9) is highly
expressed in human breast carcinomas and correlates with
a poor prognosis, suggesting a role for Rap2 in breast
cancer oncogenesis. Rap2b, but not Rap2a, Rap2c, Rap1a,
or Rap1b, is expressed in human red blood cells, where
it is believed to be involved in vesiculation. A number
of additional effector proteins for Rap2 have been
identified, including the RalGEFs RalGDS, RGL, and Rlf,
which also interact with Rap1 and Ras. Most Ras proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 163
Score = 41.7 bits (98), Expect = 3e-05
Identities = 18/48 (37%), Positives = 25/48 (52%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAI 139
LVGNK D ++ V + + + A + G ETSAK V E+F I
Sbjct: 111 LVGNKVDLESEREVSSAEGRALAEEWGCPFMETSAKSKTMVNELFAEI 158
Score = 27.5 bits (61), Expect = 2.9
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 7 ETSAKDNINVEEMFMAI 23
ETSAK V E+F I
Sbjct: 142 ETSAKSKTMVNELFAEI 158
>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 = 41.3 bits (97), Expect = 5e-05
Identities = 26/49 (53%), Positives = 33/49 (67%), Gaps = 3/49 (6%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKD---NINVEEMFM 137
LVGNK D ++ V T+ AQRFA+ + LFETSAKD N +VE +FM
Sbjct: 114 LVGNKCDLREQIQVPTDLAQRFADAHSMPLFETSAKDPSENDHVEAIFM 162
>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 = 41.7 bits (98), Expect = 5e-05
Identities = 22/65 (33%), Positives = 30/65 (46%), Gaps = 11/65 (16%)
Query: 79 PIIYCWLFPSGLRLVGNKND-DPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFM 137
P++ C GNK D D ++V E Q FE SAK N N++EMF
Sbjct: 115 PMVIC----------GNKADRDFPREVQRDEVEQLVGGDENCAYFEVSAKKNSNLDEMFR 164
Query: 138 AITNL 142
A+ +L
Sbjct: 165 ALFSL 169
Score = 32.4 bits (74), Expect = 0.090
Identities = 12/22 (54%), Positives = 16/22 (72%)
Query: 5 LFETSAKDNINVEEMFMAITNL 26
FE SAK N N++EMF A+ +L
Sbjct: 148 YFEVSAKKNSNLDEMFRALFSL 169
>gnl|CDD|206713 cd04146, RERG_RasL11_like, Ras-related and Estrogen-Regulated
Growth inhibitor (RERG) and Ras-like 11 (RasL11)-like
families. RERG (Ras-related and Estrogen- Regulated
Growth inhibitor) and Ras-like 11 are members of a novel
subfamily of Ras that were identified based on their
behavior in breast and prostate tumors, respectively.
RERG expression was decreased or lost in a significant
fraction of primary human breast tumors that lack
estrogen receptor and are correlated with poor clinical
prognosis. Elevated RERG expression correlated with
favorable patient outcome in a breast tumor subtype that
is positive for estrogen receptor expression. In
contrast to most Ras proteins, RERG overexpression
inhibited the growth of breast tumor cells in vitro and
in vivo. RasL11 was found to be ubiquitously expressed
in human tissue, but down-regulated in prostate tumors.
Both RERG and RasL11 lack the C-terminal CaaX
prenylation motif, where a = an aliphatic amino acid and
X = any amino acid, and are localized primarily in the
cytoplasm. Both are believed to have tumor suppressor
activity.
Length = 166
Score = 40.3 bits (95), Expect = 1e-04
Identities = 21/55 (38%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNIN-VEEMFMAITNLVLR 145
LVGNK D + V TE+ Q+ A ++G FE SA +N V+ +F + V R
Sbjct: 112 LVGNKADLLHSRQVSTEEGQKLALELGCLFFEVSAAENYLEVQNVFHELCREVRR 166
>gnl|CDD|133318 cd04118, Rab24, Rab GTPase family 24 (Rab24). Rab24 is distinct
from other Rabs in several ways. It exists primarily in
the GTP-bound state, having a low intrinsic GTPase
activity; it is not efficiently geranyl-geranylated at
the C-terminus; it does not form a detectable complex
with Rab GDP-dissociation inhibitors (GDIs); and it has
recently been shown to undergo tyrosine phosphorylation
when overexpressed in vitro. The specific function of
Rab24 still remains unknown. It is found in a transport
route between ER-cis-Golgi and late endocytic
compartments. It is putatively involved in an autophagic
pathway, possibly directing misfolded proteins in the ER
to degradative pathways. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 193
Score = 40.2 bits (94), Expect = 1e-04
Identities = 20/52 (38%), Positives = 29/52 (55%), Gaps = 4/52 (7%)
Query: 92 LVGNKND----DPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAI 139
L G K+D D + V D Q FA+++ Q FETS+K NV+E+F +
Sbjct: 110 LCGTKSDLIEQDRSLRQVDFHDVQDFADEIKAQHFETSSKTGQNVDELFQKV 161
Score = 26.8 bits (59), Expect = 6.6
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 1 MGIQLFETSAKDNINVEEMFMAI 23
+ Q FETS+K NV+E+F +
Sbjct: 139 IKAQHFETSSKTGQNVDELFQKV 161
>gnl|CDD|206688 cd04101, RabL4, Rab GTPase-like family 4 (Rab-like4). RabL4
(Rab-like4) subfamily. RabL4s are novel proteins that
have high sequence similarity with Rab family members,
but display features that are distinct from Rabs, and
have been termed Rab-like. As in other Rab-like
proteins, RabL4 lacks a prenylation site at the
C-terminus. The specific function of RabL4 remains
unknown.
Length = 167
Score = 39.4 bits (92), Expect = 2e-04
Identities = 17/48 (35%), Positives = 27/48 (56%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAI 139
LVGNK D ++ V AQ A ++ +ETSAK+ + E F+++
Sbjct: 115 LVGNKCDLTDRREVDAAQAQALAQANTLKFYETSAKEGVGYEAPFLSL 162
>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 = 39.6 bits (93), Expect = 2e-04
Identities = 24/99 (24%), Positives = 33/99 (33%), Gaps = 29/99 (29%)
Query: 92 LVGNKND------------DPQKKVVLTEDAQRFANQMGIQLF-ETSAKDNINVEEMFMA 138
LVG K D + V E + A +G + E SAK NV+E+F A
Sbjct: 113 LVGLKTDLRKDKNSVSKLRAQGLEPVTPEQGESVAKSIGAVAYIECSAKLMENVDEVFDA 172
Query: 139 ITNLVLRSKKEQKERQVLNSDTVNIRKHTTKPGGKKKCC 177
N+ L ++ KKKC
Sbjct: 173 AINVALSKSGRAARKKK----------------KKKKCV 195
Score = 32.7 bits (75), Expect = 0.064
Identities = 16/58 (27%), Positives = 22/58 (37%), Gaps = 17/58 (29%)
Query: 7 ETSAKDNINVEEMFMAITNLVLRSKKEQKERQVLNSDTVNIRKHTTKPGGKKKVCTVL 64
E SAK NV+E+F A N+ L ++ KKK C +L
Sbjct: 157 ECSAKLMENVDEVFDAAINVALSKSGRAARKKK-----------------KKKKCVIL 197
>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 = 39.5 bits (92), Expect = 3e-04
Identities = 21/53 (39%), Positives = 29/53 (54%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAITNLVL 144
LVGN+ K+ V TE AQ +A + G+ FE S N N+ E F + +VL
Sbjct: 115 LVGNRLHLAFKRQVATEQAQAYAERNGMTFFEVSPLCNFNITESFTELARIVL 167
>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 = 39.0 bits (91), Expect = 3e-04
Identities = 18/45 (40%), Positives = 27/45 (60%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMF 136
LV K D + V+ E+A+ A ++ + LF TS KD+ NV E+F
Sbjct: 111 LVQTKIDLLDQAVITNEEAEALAKRLQLPLFRTSVKDDFNVTELF 155
>gnl|CDD|206648 cd00882, Ras_like_GTPase, Rat sarcoma (Ras)-like superfamily of
small guanosine triphosphatases (GTPases). Ras-like
GTPase superfamily. The Ras-like superfamily of small
GTPases consists of several families with an extremely
high degree of structural and functional similarity. The
Ras superfamily is divided into at least four families
in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families.
This superfamily also includes proteins like the GTP
translation factors, Era-like GTPases, and G-alpha chain
of the heterotrimeric G proteins. Members of the Ras
superfamily regulate a wide variety of cellular
functions: the Ras family regulates gene expression, the
Rho family regulates cytoskeletal reorganization and
gene expression, the Rab and Sar1/Arf families regulate
vesicle trafficking, and the Ran family regulates
nucleocytoplasmic transport and microtubule
organization. The GTP translation factor family
regulates initiation, elongation, termination, and
release in translation, and the Era-like GTPase family
regulates cell division, sporulation, and DNA
replication. Members of the Ras superfamily are
identified by the GTP binding site, which is made up of
five characteristic sequence motifs, and the switch I
and switch II regions.
Length = 161
Score = 38.6 bits (90), Expect = 4e-04
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQM-GIQLFETSAKDNINVEEMFMAITN 141
LVGNK D +++ V ++ G+ +FE SAK V+E+F +
Sbjct: 111 LVGNKIDLLEEREVEELLRLEELAKILGVPVFEVSAKTGEGVDELFEKLIE 161
Score = 28.6 bits (64), Expect = 1.3
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 2 GIQLFETSAKDNINVEEMFMAITN 25
G+ +FE SAK V+E+F +
Sbjct: 138 GVPVFEVSAKTGEGVDELFEKLIE 161
>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 = 38.3 bits (89), Expect = 5e-04
Identities = 23/49 (46%), Positives = 29/49 (59%), Gaps = 1/49 (2%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMG-IQLFETSAKDNINVEEMFMAI 139
LVGNK D ++VV E+ Q A Q G ETSAK INV+E+F +
Sbjct: 111 LVGNKCDLEDERVVSKEEGQNLARQWGNCPFLETSAKSKINVDEIFYDL 159
>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 = 38.1 bits (89), Expect = 8e-04
Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 2/48 (4%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAI 139
L GNK D +KV F + +Q +E SAK N N E+ F+ +
Sbjct: 109 LCGNKVDIKDRKV--KPKQITFHRKKNLQYYEISAKSNYNFEKPFLWL 154
Score = 26.5 bits (59), Expect = 6.1
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 2 GIQLFETSAKDNINVEEMFMAI 23
+Q +E SAK N N E+ F+ +
Sbjct: 133 NLQYYEISAKSNYNFEKPFLWL 154
>gnl|CDD|206712 cd04141, Rit_Rin_Ric, Ras-like protein in all tissues (Rit),
Ras-like protein in neurons (Rin) and Ras-related
protein which interacts with calmodulin (Ric). Rit
(Ras-like protein in all tissues), Rin (Ras-like protein
in neurons) and Ric (Ras-related protein which interacts
with calmodulin) form a subfamily with several unique
structural and functional characteristics. These
proteins all lack a the C-terminal CaaX lipid-binding
motif typical of Ras family proteins, and Rin and Ric
contain calmodulin-binding domains. Rin, which is
expressed only in neurons, induces neurite outgrowth in
rat pheochromocytoma cells through its association with
calmodulin and its activation of endogenous Rac/cdc42.
Rit, which is ubiquitously expressed in mammals,
inhibits growth-factor withdrawl-mediated apoptosis and
induces neurite extension in pheochromocytoma cells. Rit
and Rin are both able to form a ternary complex with
PAR6, a cell polarity-regulating protein, and Rac/cdc42.
This ternary complex is proposed to have physiological
function in processes such as tumorigenesis. Activated
Ric is likely to signal in parallel with the Ras pathway
or stimulate the Ras pathway at some upstream point, and
binding of calmodulin to Ric may negatively regulate Ric
activity.
Length = 172
Score = 37.9 bits (88), Expect = 0.001
Identities = 19/60 (31%), Positives = 30/60 (50%)
Query: 90 LRLVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAITNLVLRSKKE 149
L LVGNK D Q++ V TE+ + A + FETSA +++ F + + R +
Sbjct: 110 LVLVGNKVDLEQQRQVTTEEGRNLAREFNCPFFETSAALRFYIDDAFHGLVREIRRKESM 169
>gnl|CDD|133377 cd04177, RSR1, RSR1/Bud1p family GTPase. RSR1/Bud1p is a member of
the Rap subfamily of the Ras family that is found in
fungi. In budding yeasts, RSR1 is involved in selecting
a site for bud growth on the cell cortex, which directs
the establishment of cell polarization. The Rho family
GTPase cdc42 and its GEF, cdc24, then establish an axis
of polarized growth by organizing the actin cytoskeleton
and secretory apparatus at the bud site. It is believed
that cdc42 interacts directly with RSR1 in vivo. In
filamentous fungi, polar growth occurs at the tips of
hypha and at novel growth sites along the extending
hypha. In Ashbya gossypii, RSR1 is a key regulator of
hyphal growth, localizing at the tip region and
regulating in apical polarization of the actin
cytoskeleton. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras proteins.
Length = 168
Score = 37.8 bits (88), Expect = 0.001
Identities = 19/46 (41%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMG-IQLFETSAKDNINVEEMF 136
LVGNK D + V ED + Q G + +ETSA+ NV+E+F
Sbjct: 111 LVGNKADLEDDRQVSREDGVSLSQQWGNVPFYETSARKRTNVDEVF 156
>gnl|CDD|206697 cd04116, Rab9, Rab GTPase family 9 (Rab9). Rab9 is found in late
endosomes, together with mannose 6-phosphate receptors
(MPRs) and the tail-interacting protein of 47 kD
(TIP47). Rab9 is a key mediator of vesicular transport
from late endosomes to the trans-Golgi network (TGN) by
redirecting the MPRs. Rab9 has been identified as a key
component for the replication of several viruses,
including HIV1, Ebola, Marburg, and measles, making it a
potential target for inhibiting a variety of viruses.
GTPase activating proteins (GAPs) interact with
GTP-bound Rab and accelerate the hydrolysis of GTP to
GDP. Guanine nucleotide exchange factors (GEFs) interact
with GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 170
Score = 36.8 bits (85), Expect = 0.002
Identities = 21/48 (43%), Positives = 28/48 (58%), Gaps = 2/48 (4%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQ-LFETSAKDNINVEEMFMA 138
++GNK D P+++V TE+AQ + G FETSAKD NV F
Sbjct: 119 ILGNKIDIPERQVS-TEEAQAWCRDNGDYPYFETSAKDATNVAAAFEE 165
>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 = 36.6 bits (85), Expect = 0.003
Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 5/57 (8%)
Query: 92 LVGNKND-----DPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAITNLV 143
LVG K D P+++ +T+ A+++A M L S +INV+++F + V
Sbjct: 109 LVGTKYDLFADLPPEEQEEITKQARKYAKAMKAPLIFCSTSHSINVQKIFKFVLAKV 165
>gnl|CDD|206641 cd00157, Rho, Ras homology family (Rho) of small guanosine
triphosphatases (GTPases). Members of the Rho (Ras
homology) family include RhoA, Cdc42, Rac, Rnd, Wrch1,
RhoBTB, and Rop. There are 22 human Rho family members
identified currently. These proteins are all involved in
the reorganization of the actin cytoskeleton in response
to external stimuli. They also have roles in cell
transformation by Ras in cytokinesis, in focal adhesion
formation and in the stimulation of stress-activated
kinase. These various functions are controlled through
distinct effector proteins and mediated through a
GTP-binding/GTPase cycle involving three classes of
regulating proteins: GAPs (GTPase-activating proteins),
GEFs (guanine nucleotide exchange factors), and GDIs
(guanine nucleotide dissociation inhibitors). Most Rho
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. Since crystal structures
often lack C-terminal residues, this feature is not
available for annotation in many of the CDs in the
hierarchy.
Length = 171
Score = 36.0 bits (84), Expect = 0.004
Identities = 14/57 (24%), Positives = 28/57 (49%), Gaps = 12/57 (21%)
Query: 92 LVGNKND-----------DPQKKVVLTEDAQRFANQMG-IQLFETSAKDNINVEEMF 136
LVG K D + ++K + E+ ++ A ++G ++ E SA ++E+F
Sbjct: 109 LVGTKIDLRDDGNTLKKLEKKQKPITPEEGEKLAKEIGAVKYMECSALTQEGLKEVF 165
>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 = 35.3 bits (82), Expect = 0.007
Identities = 20/81 (24%), Positives = 28/81 (34%), Gaps = 23/81 (28%)
Query: 77 ICPIIYCWLFPSGLRLVGNKND------------DPQKKVVLTEDAQRFANQMG-IQLFE 123
PII LVG K D +++ V E Q A ++G ++ E
Sbjct: 102 NVPII----------LVGTKLDLRNDKSTLEELSKKKQEPVTYEQGQALAKRIGAVKYLE 151
Query: 124 TSAKDNINVEEMFMAITNLVL 144
SA V E+F L
Sbjct: 152 CSALTQEGVREVFEEAIRAAL 172
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 35.4 bits (81), Expect = 0.008
Identities = 18/45 (40%), Positives = 23/45 (51%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMF 136
LVGNK D ++ V E+ A + G E SAK NVE+ F
Sbjct: 125 LVGNKVDRESERDVSREEGMALAKEHGCLFLECSAKTRENVEQCF 169
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 34.9 bits (80), Expect = 0.012
Identities = 20/103 (19%), Positives = 31/103 (30%), Gaps = 17/103 (16%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQM---------------GIQLFETSAK--DNINVEE 134
LVGNK D ++ E + ++ L ETSAK NV E
Sbjct: 116 LVGNKIDLFDEQSSSEEILNQLNREVVLLVLAPKAVLPEVANPALLETSAKSLTGPNVNE 175
Query: 135 MFMAITNLVLRSKKEQKERQVLNSDTVNIRKHTTKPGGKKKCC 177
+F + +L ++ + L C
Sbjct: 176 LFKELLRKLLEEIEKLVLKNELRQLDRLNNPIEQAALASFNCV 218
>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 = 34.4 bits (79), Expect = 0.017
Identities = 24/80 (30%), Positives = 34/80 (42%), Gaps = 4/80 (5%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAITNLVLRSKKEQK 151
LVGNK D + V E RFA + ++ SAK V F I +L K Q
Sbjct: 114 LVGNKTDLEHNRQVTAEKHARFAQENDMESIFVSAKTGDRVFLCFQRIAAELLGVKLSQA 173
Query: 152 E----RQVLNSDTVNIRKHT 167
E ++V+ +D + T
Sbjct: 174 ELEQSQRVVKADVSRYSERT 193
>gnl|CDD|232886 TIGR00231, small_GTP, small GTP-binding protein domain. Proteins
with a small GTP-binding domain recognized by this model
include Ras, RhoA, Rab11, translation elongation factor
G, translation initiation factor IF-2, tetratcycline
resistance protein TetM, CDC42, Era, ADP-ribosylation
factors, tdhF, and many others. In some proteins the
domain occurs more than once.This model recognizes a
large number of small GTP-binding proteins and related
domains in larger proteins. Note that the alpha chains
of heterotrimeric G proteins are larger proteins in
which the NKXD motif is separated from the GxxxxGK[ST]
motif (P-loop) by a long insert and are not easily
detected by this model [Unknown function, General].
Length = 162
Score = 33.9 bits (78), Expect = 0.021
Identities = 16/49 (32%), Positives = 22/49 (44%), Gaps = 1/49 (2%)
Query: 88 SGLRLVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMF 136
+ LVGNK D K+ T A FA G + SA+ N++ F
Sbjct: 110 VPIILVGNKIDLRDAKL-KTHVAFLFAKLNGEPIIPLSAETGKNIDSAF 157
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 32.8 bits (75), Expect = 0.061
Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 2/46 (4%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFM 137
L GNK D ++V F + +Q +E SAK N N E+ F+
Sbjct: 122 LCGNKVDVKNRQV--KAKQVTFHRKKNLQYYEISAKSNYNFEKPFL 165
>gnl|CDD|206715 cd04148, RGK, Rem, Rem2, Rad, Gem/Kir (RGK) subfamily of Ras
GTPases. RGK subfamily. The RGK (Rem, Rem2, Rad,
Gem/Kir) subfamily of Ras GTPases are expressed in a
tissue-specific manner and are dynamically regulated by
transcriptional and posttranscriptional mechanisms in
response to environmental cues. RGK proteins bind to the
beta subunit of L-type calcium channels, causing
functional down-regulation of these voltage-dependent
calcium channels, and either termination of
calcium-dependent secretion or modulation of electrical
conduction and contractile function. Inhibition of
L-type calcium channels by Rem2 may provide a mechanism
for modulating calcium-triggered exocytosis in
hormone-secreting cells, and has been proposed to
influence the secretion of insulin in pancreatic beta
cells. RGK proteins also interact with and inhibit the
Rho/Rho kinase pathway to modulate remodeling of the
cytoskeleton. Two characteristics of RGK proteins cited
in the literature are N-terminal and C-terminal
extensions beyond the GTPase domain typical of Ras
superfamily members. The N-terminal extension is not
conserved among family members; the C-terminal extension
is reported to be conserved among the family and lack
the CaaX prenylation motif typical of
membrane-associated Ras proteins. However, a putative
CaaX motif has been identified in the alignment of the
C-terminal residues of this CD.
Length = 219
Score = 32.0 bits (73), Expect = 0.11
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAITNLV-LRSKKEQ 150
LVGNK+D + + V ++ + A + ETSA NV+E+F I V LR ++
Sbjct: 111 LVGNKSDLVRSREVSVQEGRACAVVFDCKFIETSAALQHNVDELFEGIVRQVRLRRDSKE 170
Query: 151 K 151
K
Sbjct: 171 K 171
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 30.4 bits (69), Expect = 0.33
Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 6/51 (11%)
Query: 92 LVGNKNDDPQKKVVLTEDAQ--RFANQMGIQLFETSAKDNINVEEMFMAIT 140
LVGNK D ++V A+ F + +Q ++ SAK N N E+ F+ +
Sbjct: 118 LVGNKVDVKDRQV----KARQITFHRKKNLQYYDISAKSNYNFEKPFLWLA 164
>gnl|CDD|206693 cd04108, Rab36_Rab34, Rab GTPase families 34 (Rab34) and 36
(Rab36). Rab34/Rab36 subfamily. Rab34, found primarily
in the Golgi, interacts with its effector,
Rab-interacting lysosomal protein (RILP). This enables
its participation in microtubular
dynenin-dynactin-mediated repositioning of lysosomes
from the cell periphery to the Golgi. A Rab34 (Rah)
isoform that lacks the consensus GTP-binding region has
been identified in mice. This isoform is associated with
membrane ruffles and promotes macropinosome formation.
Rab36 has been mapped to human chromosome 22q11.2, a
region that is homozygously deleted in malignant
rhabdoid tumors (MRTs). However, experimental
assessments do not implicate Rab36 as a tumor suppressor
that would enable tumor formation through a
loss-of-function mechanism. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 170
Score = 30.2 bits (68), Expect = 0.35
Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 90 LRLVGNKND--DPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAITNLVLRS 146
L LVG K D P + ++ +DA + A +M + + SA NV + F + +L
Sbjct: 109 LFLVGTKKDLSSPAQYALMEQDAIKLAREMKAEYWAVSALTGENVRDFFFRVASLTFEL 167
>gnl|CDD|206680 cd01893, Miro1, Mitochondrial Rho family 1 (Miro1), N-terminal.
Miro1 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the N-terminal
GTPase domain of Miro proteins. These atypical Rho
GTPases have roles in mitochondrial homeostasis and
apoptosis. Most Rho proteins contain a lipid
modification site at the C-terminus; however, Miro is
one of few Rho subfamilies that lack this feature.
Length = 168
Score = 30.0 bits (68), Expect = 0.46
Identities = 21/58 (36%), Positives = 26/58 (44%), Gaps = 4/58 (6%)
Query: 92 LVGNKND--DPQKKVVLTEDAQRFANQMG--IQLFETSAKDNINVEEMFMAITNLVLR 145
LVGNK+D D + L E+ N+ E SAK INV E+F VL
Sbjct: 110 LVGNKSDLRDGSSQAGLEEEMLPIMNEFREIETCVECSAKTLINVSEVFYYAQKAVLH 167
>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 = 28.9 bits (65), Expect = 0.87
Identities = 19/62 (30%), Positives = 27/62 (43%), Gaps = 13/62 (20%)
Query: 92 LVGNKND---DPQ---------KKVVLTEDAQRFANQMGIQLF-ETSAKDNINVEEMFMA 138
LVGNK D D ++ V E+ + A ++G + E SAK V E+F
Sbjct: 110 LVGNKKDLRNDEHTIRELAKMKQEPVKPEEGRAMAEKIGAFGYLECSAKTKEGVREVFEM 169
Query: 139 IT 140
T
Sbjct: 170 AT 171
>gnl|CDD|206685 cd01898, Obg, Obg GTPase. The Obg nucleotide binding protein
subfamily has been implicated in stress response,
chromosome partitioning, replication initiation,
mycelium development, and sporulation. Obg proteins are
among a large group of GTP binding proteins conserved
from bacteria to humans. The E. coli homolog, ObgE is
believed to function in ribosomal biogenesis. Members of
the subfamily contain two equally and highly conserved
domains, a C-terminal GTP binding domain and an
N-terminal glycine-rich domain.
Length = 170
Score = 28.9 bits (66), Expect = 0.93
Identities = 9/43 (20%), Positives = 17/43 (39%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEE 134
+V NK D + + + G ++F SA ++E
Sbjct: 119 VVLNKIDLLDAEERFEKLKELLKELKGKKVFPISALTGEGLDE 161
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 28.6 bits (63), Expect = 1.5
Identities = 17/50 (34%), Positives = 25/50 (50%)
Query: 90 LRLVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAI 139
+ LVGNK D + V E+ + A + ETSAK N++ +F I
Sbjct: 88 IALVGNKTDLGDLRKVTYEEGMQKAQEYNTMFHETSAKAGHNIKVLFKKI 137
>gnl|CDD|236692 PRK10431, PRK10431, N-acetylmuramoyl-l-alanine amidase II;
Provisional.
Length = 445
Score = 28.3 bits (63), Expect = 2.2
Identities = 12/22 (54%), Positives = 13/22 (59%)
Query: 97 NDDPQKKVVLTEDAQRFANQMG 118
NDDP K VLT D F + MG
Sbjct: 231 NDDPMFKGVLTRDGDYFISVMG 252
>gnl|CDD|133324 cd04124, RabL2, Rab GTPase-like family 2 (Rab-like2). RabL2
(Rab-like2) subfamily. RabL2s are novel Rab proteins
identified recently which display features that are
distinct from other Rabs, and have been termed Rab-like.
RabL2 contains RabL2a and RabL2b, two very similar Rab
proteins that share > 98% sequence identity in humans.
RabL2b maps to the subtelomeric region of chromosome
22q13.3 and RabL2a maps to 2q13, a region that suggests
it is also a subtelomeric gene. Both genes are believed
to be expressed ubiquitously, suggesting that RabL2s are
the first example of duplicated genes in human proximal
subtelomeric regions that are both expressed actively.
Like other Rab-like proteins, RabL2s lack a prenylation
site at the C-terminus. The specific functions of RabL2a
and RabL2b remain unknown. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization.
Length = 161
Score = 27.9 bits (62), Expect = 2.3
Identities = 19/60 (31%), Positives = 27/60 (45%), Gaps = 12/60 (20%)
Query: 78 CPIIYCWLFPSGLRLVGNKND-DPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMF 136
P I C + V NK D DP +T+ FA + + L+ SA D NV ++F
Sbjct: 102 RPEIPCIV-------VANKIDLDPS----VTQKKFNFAEKHNLPLYYVSAADGTNVVKLF 150
>gnl|CDD|206714 cd04147, Ras_dva, Ras - dorsal-ventral anterior localization
(Ras-dva) family. Ras-dva subfamily. Ras-dva (Ras -
dorsal-ventral anterior localization) subfamily consists
of a set of proteins characterized only in Xenopus
leavis, to date. In Xenopus Ras-dva expression is
activated by the transcription factor Otx2 and begins
during gastrulation throughout the anterior ectoderm.
Ras-dva expression is inhibited in the anterior neural
plate by factor Xanf1. Downregulation of Ras-dva results
in head development abnormalities through the inhibition
of several regulators of the anterior neural plate and
folds patterning, including Otx2, BF-1, Xag2, Pax6,
Slug, and Sox9. Downregulation of Ras-dva also
interferes with the FGF-8a signaling within the anterior
ectoderm. Most Ras proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins.
Length = 197
Score = 27.9 bits (62), Expect = 2.3
Identities = 18/46 (39%), Positives = 22/46 (47%), Gaps = 1/46 (2%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFAN-QMGIQLFETSAKDNINVEEMF 136
+VGNK D ++ V DA E SAKDN NV E+F
Sbjct: 109 VVGNKIDSLAERQVEAADALSTVELDWNNGFVEASAKDNENVTEVF 154
Score = 26.7 bits (59), Expect = 6.8
Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 9/61 (14%)
Query: 7 ETSAKDNINVEEMF---MAITNLVLR-SKKEQKERQVLNSDTVNIRKHTTKPGGKKKVCT 62
E SAKDN NV E+F + NL S ++ R+ S+ + R P K C+
Sbjct: 141 EASAKDNENVTEVFKELLQQANLPSWLSPALRRRRESAPSE-IQRR----PPMNKTNSCS 195
Query: 63 V 63
V
Sbjct: 196 V 196
>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 = 27.7 bits (61), Expect = 2.6
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 2/46 (4%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFM 137
L GNK D +KV + F + +Q ++ SAK N N E+ F+
Sbjct: 104 LCGNKVDVKDRKV--KAKSITFHRKKNLQYYDISAKSNYNFEKPFL 147
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 28.1 bits (64), Expect = 2.8
Identities = 14/65 (21%), Positives = 30/65 (46%), Gaps = 8/65 (12%)
Query: 93 VGNKNDDP--QKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAITNLVLRSKKEQ 150
V NK D P ++ + + F ++G ++F SA ++E+ A+ L+ + +
Sbjct: 280 VANKMDLPEAEENL------EEFKEKLGPKVFPISALTGQGLDELLYAVAELLEETPEFP 333
Query: 151 KERQV 155
E +
Sbjct: 334 LEEEE 338
>gnl|CDD|220524 pfam10021, DUF2263, Uncharacterized protein conserved in bacteria
(DUF2263). This domain, found in various hypothetical
bacterial and eukaryotic proteins, has no known
function.
Length = 149
Score = 27.3 bits (61), Expect = 3.0
Identities = 11/42 (26%), Positives = 17/42 (40%), Gaps = 1/42 (2%)
Query: 24 TNLVLRSKKEQKERQVLNSDTVNIRKHTTKPGGKKKVCTVLN 65
+L + + +V+N DT+ KVC VLN
Sbjct: 43 ESLPEIASSVRTAVEVVNEDTLEAAIRLANSEDGGKVC-VLN 83
>gnl|CDD|129313 TIGR00209, galT_1, galactose-1-phosphate uridylyltransferase,
family 1. This enzyme is involved in glucose and
galactose interconversion. This model describes one of
two extremely distantly related branches of the model
pfam01087 [Energy metabolism, Sugars].
Length = 347
Score = 27.6 bits (61), Expect = 3.6
Identities = 10/27 (37%), Positives = 13/27 (48%)
Query: 83 CWLFPSGLRLVGNKNDDPQKKVVLTED 109
C+L P R+ G+ N D V T D
Sbjct: 52 CYLCPGNKRVTGDLNPDYTGTYVFTND 78
>gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol
utilisation. Members of this family function in
ethanolamine and propanediol degradation pathways,
however the exact roles of these proteins is poorly
understood.
Length = 143
Score = 26.8 bits (60), Expect = 3.7
Identities = 10/31 (32%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 107 TEDAQRFANQMGI-QLFETSAKDNINVEEMF 136
E + + N G ++FE SA N ++E+F
Sbjct: 108 IEMVEEWLNNAGAEKIFEVSAVTNEGIDELF 138
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes. TrmE
contains a GTPase domain that forms a canonical Ras-like
fold. It functions a molecular switch GTPase, and
apparently uses a conformational change associated with
GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 27.1 bits (61), Expect = 3.9
Identities = 14/52 (26%), Positives = 23/52 (44%), Gaps = 7/52 (13%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAITNLV 143
+V NK+D L DA+ + G + SAK ++E+ A+ L
Sbjct: 114 VVLNKSD-------LLSDAEGISELNGKPIIAISAKTGEGIDELKEALLELA 158
>gnl|CDD|233986 TIGR02729, Obg_CgtA, Obg family GTPase CgtA. This model describes
a univeral, mostly one-gene-per-genome GTP-binding
protein that associates with ribosomal subunits and
appears to play a role in ribosomal RNA maturation. This
GTPase, related to the nucleolar protein Obg, is
designated CgtA in bacteria. Mutations in this gene are
pleiotropic, but it appears that effects on cellular
functions such as chromosome partition may be secondary
to the effect on ribosome structure. Recent work done in
Vibrio cholerae shows an essential role in the stringent
response, in which RelA-dependent ability to synthesize
the alarmone ppGpp is required for deletion of this
GTPase to be lethal [Protein synthesis, Other].
Length = 329
Score = 27.4 bits (62), Expect = 4.3
Identities = 13/52 (25%), Positives = 24/52 (46%), Gaps = 1/52 (1%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAITNLV 143
+V NK D ++ L E + +G +F SA ++E+ A+ L+
Sbjct: 278 VVLNKIDLLDEEE-LEELLKELKEALGKPVFPISALTGEGLDELLYALAELL 328
>gnl|CDD|219964 pfam08670, MEKHLA, MEKHLA domain. The MEKHLA domain shares
similarity with the PAS domain and is found in the 3'
end of plant HD-ZIP III homeobox genes, and bacterial
proteins.
Length = 148
Score = 26.4 bits (59), Expect = 5.3
Identities = 6/13 (46%), Positives = 9/13 (69%)
Query: 113 FANQMGIQLFETS 125
+ANQ + L ET+
Sbjct: 57 YANQAALDLLETT 69
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 27.0 bits (61), Expect = 6.7
Identities = 14/60 (23%), Positives = 29/60 (48%)
Query: 92 LVGNKNDDPQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAITNLVLRSKKEQK 151
LV NK D ++ + A +G +F SA ++E+ A+ L+ +++E++
Sbjct: 276 LVLNKIDLLDEEEEREKRAALELAALGGPVFLISAVTGEGLDELLRALWELLEEARREEE 335
>gnl|CDD|237405 PRK13508, PRK13508, tagatose-6-phosphate kinase; Provisional.
Length = 309
Score = 26.6 bits (59), Expect = 7.2
Identities = 13/29 (44%), Positives = 15/29 (51%), Gaps = 2/29 (6%)
Query: 40 LNSDTVNIRKHTTK-PGGKK-KVCTVLNE 66
L DTVN +K GGK V VL+E
Sbjct: 20 LKLDTVNRVVDVSKTAGGKGLNVTRVLSE 48
>gnl|CDD|206726 cd04163, Era, E. coli Ras-like protein (Era) is a multifunctional
GTPase. Era (E. coli Ras-like protein) is a
multifunctional GTPase found in all bacteria except some
eubacteria. It binds to the 16S ribosomal RNA (rRNA) of
the 30S subunit and appears to play a role in the
assembly of the 30S subunit, possibly by chaperoning the
16S rRNA. It also contacts several assembly elements of
the 30S subunit. Era couples cell growth with
cytokinesis and plays a role in cell division and energy
metabolism. Homologs have also been found in eukaryotes.
Era contains two domains: the N-terminal GTPase domain
and a C-terminal domain KH domain that is critical for
RNA binding. Both domains are important for Era
function. Era is functionally able to compensate for
deletion of RbfA, a cold-shock adaptation protein that
is required for efficient processing of the 16S rRNA.
Length = 168
Score = 26.3 bits (59), Expect = 8.5
Identities = 14/52 (26%), Positives = 21/52 (40%), Gaps = 1/52 (1%)
Query: 92 LVGNKNDD-PQKKVVLTEDAQRFANQMGIQLFETSAKDNINVEEMFMAITNL 142
LV NK D K+ +L + ++F SA NV+E+ I
Sbjct: 116 LVLNKIDLVKDKEDLLPLLEKLKELHPFAEIFPISALKGENVDELLEYIVEY 167
>gnl|CDD|219609 pfam07856, Orai-1, Mediator of CRAC channel activity. ORAI-1 is a
protein homologue of Drosophila Orai and human Orai1,
Orai2 and Orai3. ORAI-1 GFP reporters are co- expressed
with STIM-1 (ER CA(2+) sensors) in the gonad and
intestine. The protein has four predicted transmembrane
domains with a highly conserved region between TM2 ad
TM3. This conserved domain is thought to function in
channel regulation. ORAI1- related proteins are required
for the production of the calcium channel, CRAC, along
with STIM1-related proteins.
Length = 175
Score = 26.1 bits (58), Expect = 8.8
Identities = 15/47 (31%), Positives = 20/47 (42%), Gaps = 4/47 (8%)
Query: 77 ICPIIYCWLFPSGLRLVGNKNDDPQKKV-VLTEDAQRFANQMGIQLF 122
I P I C F L + P ++ E RF+ +MGI LF
Sbjct: 78 ILPNIECVTFVHNYNLT---PESPHRRFERYCELDWRFSTRMGIPLF 121
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.318 0.132 0.396
Gapped
Lambda K H
0.267 0.0723 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,355,975
Number of extensions: 721054
Number of successful extensions: 806
Number of sequences better than 10.0: 1
Number of HSP's gapped: 798
Number of HSP's successfully gapped: 138
Length of query: 177
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 86
Effective length of database: 6,901,388
Effective search space: 593519368
Effective search space used: 593519368
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: 56 (25.4 bits)