RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5810
(250 letters)
>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 = 122 bits (308), Expect = 3e-34
Identities = 53/160 (33%), Positives = 76/160 (47%), Gaps = 24/160 (15%)
Query: 107 FCSQVENFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLE 166
C QV D +VIVYSV +R +F+KA ++ L ++ + +ILV NK+DL
Sbjct: 68 SCMQV--------GDAYVIVYSVTDRSSFEKASELRIQLRRARQAEDIPIILVGNKSDLV 119
Query: 167 RRRQVTHSDGKKLAYAWGVKFVETSVGLVYKTDELLVGIARQAGLNKKRNKL-------- 218
R R+V+ +G+ A + KF+ETS L + DEL GI RQ L + +
Sbjct: 120 RSREVSVQEGRACAVVFDCKFIETSAALQHNVDELFEGIVRQVRLRRDSKEKNTRRMASR 179
Query: 219 -----LAKKQKKMASYI---NNIKQFKWFSKVSCENLLVL 250
+ KK K+ S I NN SC +L VL
Sbjct: 180 KRRESITKKAKRFLSKIVAKNNKGMAFKQKSKSCHDLSVL 219
>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 = 73.7 bits (182), Expect = 2e-16
Identities = 31/92 (33%), Positives = 52/92 (56%), Gaps = 6/92 (6%)
Query: 121 DVFVIVYSVIERKTFKKAE---DMLKTLWDSKYIGEKAVILVANKADLERRRQVTHSDGK 177
D F++VYS+ R++F++ + + + + D + + ++LV NK DLE RQV+ +G+
Sbjct: 72 DGFILVYSITSRESFEEIKNIREQILRVKDKEDV---PIVLVGNKCDLENERQVSTEEGE 128
Query: 178 KLAYAWGVKFVETSVGLVYKTDELLVGIARQA 209
LA WG F+ETS DEL + R+
Sbjct: 129 ALAEEWGCPFLETSAKTNINIDELFNTLVREI 160
>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 = 71.0 bits (175), Expect = 2e-15
Identities = 28/90 (31%), Positives = 47/90 (52%), Gaps = 3/90 (3%)
Query: 121 DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVTHSDGKKL 179
F++VY + R +F+ + L+ + ++ E I LV NK DLE +R V+ +G+ L
Sbjct: 73 QGFLLVYDITSRDSFENVKKWLEEI--LRHADENVPIVLVGNKCDLEDQRVVSTEEGEAL 130
Query: 180 AYAWGVKFVETSVGLVYKTDELLVGIARQA 209
A G+ F+ETS +E +AR+
Sbjct: 131 AKELGLPFMETSAKTNENVEEAFEELAREI 160
>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 = 70.3 bits (173), Expect = 4e-15
Identities = 29/89 (32%), Positives = 49/89 (55%)
Query: 121 DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHSDGKKLA 180
+ F++VYS+ +R++F++ + + K + ++LV NK DLE R V+ +GK+LA
Sbjct: 75 EGFLLVYSITDRQSFEEIAKFREQILRVKDRDDVPIVLVGNKCDLENERVVSTEEGKELA 134
Query: 181 YAWGVKFVETSVGLVYKTDELLVGIARQA 209
WG F+ETS DE + R+
Sbjct: 135 RQWGCPFLETSAKERINVDEAFYDLVREI 163
>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 = 70.3 bits (173), Expect = 5e-15
Identities = 29/89 (32%), Positives = 50/89 (56%)
Query: 121 DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHSDGKKLA 180
+ F++VYS+ +R++F++ + + + K + ++LV NK DLE R V+ +GK+LA
Sbjct: 73 EGFLLVYSITDRQSFEEIKKFREQILRVKDRDDVPIVLVGNKCDLESERVVSTEEGKELA 132
Query: 181 YAWGVKFVETSVGLVYKTDELLVGIARQA 209
WG F+ETS DE + R+
Sbjct: 133 RQWGCPFLETSAKERVNVDEAFYDLVREI 161
>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 = 69.9 bits (171), Expect = 7e-15
Identities = 30/86 (34%), Positives = 51/86 (59%)
Query: 123 FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHSDGKKLAYA 182
F+I YSV +R +F++A + + + + + ++LV NK DLE++RQVT +G+ LA
Sbjct: 77 FIICYSVTDRHSFQEASEFKELITRVRLTEDIPLVLVGNKVDLEQQRQVTTEEGRNLARE 136
Query: 183 WGVKFVETSVGLVYKTDELLVGIARQ 208
+ F ETS L + D+ G+ R+
Sbjct: 137 FNCPFFETSAALRFYIDDAFHGLVRE 162
>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 = 68.4 bits (168), Expect = 3e-14
Identities = 30/74 (40%), Positives = 50/74 (67%), Gaps = 8/74 (10%)
Query: 123 FVIVYSVIERKTFKKAEDMLKTLWDS--KYIGEKAV--ILVANKADLERRRQVTHSDGKK 178
+++VYSV RK+F +++K ++D +G+++V +LV NK+DL RQV+ +GKK
Sbjct: 76 YILVYSVTSRKSF----EVVKVIYDKILDMLGKESVPIVLVGNKSDLHMERQVSAEEGKK 131
Query: 179 LAYAWGVKFVETSV 192
LA +WG F+E+S
Sbjct: 132 LAESWGAAFLESSA 145
>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 = 64.5 bits (157), Expect = 5e-13
Identities = 30/87 (34%), Positives = 47/87 (54%), Gaps = 1/87 (1%)
Query: 123 FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHSDGKKLAYA 182
F +VYS+ +++F +D+ + + K + +ILV NK DLE R V+ +G+ LA
Sbjct: 76 FALVYSITAQQSFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVSKEEGQNLARQ 135
Query: 183 WG-VKFVETSVGLVYKTDELLVGIARQ 208
WG F+ETS DE+ + RQ
Sbjct: 136 WGNCPFLETSAKSKINVDEIFYDLVRQ 162
>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 = 62.9 bits (153), Expect = 3e-12
Identities = 32/86 (37%), Positives = 50/86 (58%)
Query: 123 FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHSDGKKLAYA 182
F++VYS++ ++TF+ + M + K + +ILV NK DLE R+V+ ++G+ LA
Sbjct: 76 FIVVYSLVNQQTFQDIKPMRDQIVRVKGYEKVPIILVGNKVDLESEREVSSAEGRALAEE 135
Query: 183 WGVKFVETSVGLVYKTDELLVGIARQ 208
WG F+ETS +EL I RQ
Sbjct: 136 WGCPFMETSAKSKTMVNELFAEIVRQ 161
>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 = 61.5 bits (150), Expect = 8e-12
Identities = 33/77 (42%), Positives = 44/77 (57%), Gaps = 1/77 (1%)
Query: 121 DVFVIVYSVIERKTFKKAEDMLKTLWDSK-YIGEKAVILVANKADLERRRQVTHSDGKKL 179
D FV+VYS+ +R +F +L+ + + K GE VILV NKADL RQV+ +G+KL
Sbjct: 74 DGFVLVYSITDRSSFDVVSQLLQLIREIKKRDGEIPVILVGNKADLLHSRQVSTEEGQKL 133
Query: 180 AYAWGVKFVETSVGLVY 196
A G F E S Y
Sbjct: 134 ALELGCLFFEVSAAENY 150
>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 = 60.2 bits (147), Expect = 2e-11
Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 3/72 (4%)
Query: 121 DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVTHSDGKKL 179
++VY V R++F+ + L L +Y I LV NK+DLE RQV+ + ++
Sbjct: 74 HGAILVYDVTNRESFENLDKWLNEL--KEYAPPNIPIILVGNKSDLEDERQVSTEEAQQF 131
Query: 180 AYAWGVKFVETS 191
A G+ F ETS
Sbjct: 132 AKENGLLFFETS 143
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 59.5 bits (144), Expect = 5e-11
Identities = 32/103 (31%), Positives = 54/103 (52%)
Query: 123 FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHSDGKKLAYA 182
F+ VYS+ R +F++ + + K +ILV NK DL+ RQV+ +G++LA +
Sbjct: 80 FLCVYSITSRSSFEEIASFREQILRVKDKDRVPMILVGNKCDLDSERQVSTGEGQELAKS 139
Query: 183 WGVKFVETSVGLVYKTDELLVGIARQAGLNKKRNKLLAKKQKK 225
+G+ F+ETS DE + R+ K + K++KK
Sbjct: 140 FGIPFLETSAKQRVNVDEAFYELVREIRKYLKEDMPSQKQKKK 182
>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 = 57.9 bits (140), Expect = 2e-10
Identities = 31/86 (36%), Positives = 45/86 (52%)
Query: 123 FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHSDGKKLAYA 182
FV+VYS+ + TF +D+ + + K + +ILV NK DLE R V G+ LA
Sbjct: 76 FVLVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVGKEQGQNLARQ 135
Query: 183 WGVKFVETSVGLVYKTDELLVGIARQ 208
WG F+ETS +E+ + RQ
Sbjct: 136 WGCAFLETSAKAKINVNEIFYDLVRQ 161
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 56.4 bits (137), Expect = 4e-10
Identities = 27/70 (38%), Positives = 41/70 (58%), Gaps = 3/70 (4%)
Query: 123 FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVTHSDGKKLAY 181
++VY + R++F+ E+ LK L +Y VI LV NK+DLE +RQV+ + + A
Sbjct: 76 ALLVYDITNRESFENLENWLKEL--REYASPNVVIMLVGNKSDLEEQRQVSREEAEAFAE 133
Query: 182 AWGVKFVETS 191
G+ F ETS
Sbjct: 134 EHGLPFFETS 143
>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 = 55.7 bits (135), Expect = 9e-10
Identities = 22/69 (31%), Positives = 44/69 (63%), Gaps = 3/69 (4%)
Query: 124 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV-ILVANKADLERRRQVTHSDGKKLAYA 182
++VY + + K+F+ ++ ++ + ++ E +LV NK D+E +R V+ +G+ LA
Sbjct: 80 ILVYDITDEKSFENIKNWMRNI--DEHASEDVERMLVGNKCDMEEKRVVSKEEGEALARE 137
Query: 183 WGVKFVETS 191
+G+KF+ETS
Sbjct: 138 YGIKFLETS 146
>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 = 55.3 bits (134), Expect = 1e-09
Identities = 30/89 (33%), Positives = 48/89 (53%), Gaps = 9/89 (10%)
Query: 124 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHSDGKKLAYAW 183
++VY + ++F+KA+ +K L + L NKADLE +RQV+ + ++ A
Sbjct: 78 IVVYDITSEESFEKAKSWVKEL-QEHGPPNIVIALAGNKADLESKRQVSTEEAQEYADEN 136
Query: 184 GVKFVETSVGLVYKT----DELLVGIARQ 208
G+ F+ETS KT +EL IAR+
Sbjct: 137 GLLFMETSA----KTGENVNELFTEIARK 161
>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 = 2e-09
Identities = 28/85 (32%), Positives = 48/85 (56%)
Query: 123 FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHSDGKKLAYA 182
F++V+SV +R +F++ + + K E +ILV NKADLE +RQV+ +G++LA
Sbjct: 77 FLLVFSVTDRGSFEEVDKFHTQILRVKDRDEFPMILVGNKADLEHQRQVSREEGQELARQ 136
Query: 183 WGVKFVETSVGLVYKTDELLVGIAR 207
+ ++ETS D+ + R
Sbjct: 137 LKIPYIETSAKDRVNVDKAFHDLVR 161
>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 = 53.3 bits (128), Expect = 7e-09
Identities = 31/87 (35%), Positives = 46/87 (52%), Gaps = 1/87 (1%)
Query: 123 FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHSDGKKLAYA 182
F++VYSV + + ++ + + K ++LV NKADLE RQV+ DG L+
Sbjct: 76 FLLVYSVTSEASLNELGELREQVLRIKDSDNVPMVLVGNKADLEDDRQVSREDGVSLSQQ 135
Query: 183 WG-VKFVETSVGLVYKTDELLVGIARQ 208
WG V F ETS DE+ + + RQ
Sbjct: 136 WGNVPFYETSARKRTNVDEVFIDLVRQ 162
>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 = 52.5 bits (126), Expect = 1e-08
Identities = 39/156 (25%), Positives = 58/156 (37%), Gaps = 11/156 (7%)
Query: 55 IVHSDTNHTQRCLTSMPFCSQVENFVQTYHPD--VFFIVYSDTNHTQRCLTPMPFCSQVE 112
+ HSD Q+ T C V V V ++ Q + M VE
Sbjct: 19 MFHSDGATFQKNYTMTTGCDLVVKTVPVPDTSDSVELFIFDSAG--QELFSDM-----VE 71
Query: 113 NFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 172
N + P V +VY V +F + + + +LV NK DL RR+V
Sbjct: 72 NVWE--QPAVVCVVYDVTNEVSFNNCSRWINRVRTHSHGLHTPGVLVGNKCDLTDRREVD 129
Query: 173 HSDGKKLAYAWGVKFVETSVGLVYKTDELLVGIARQ 208
+ + LA A +KF ETS + + +AR
Sbjct: 130 AAQAQALAQANTLKFYETSAKEGVGYEAPFLSLARA 165
>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 = 52.2 bits (126), Expect = 1e-08
Identities = 25/71 (35%), Positives = 39/71 (54%), Gaps = 3/71 (4%)
Query: 122 VFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVTHSDGKKLA 180
V V+VY + R++F + + + D + G +I LV NK DL +RQV+ +G+K A
Sbjct: 75 VAVVVYDITNRQSFDNTDKWIDDVRDER--GNDVIIVLVGNKTDLSDKRQVSTEEGEKKA 132
Query: 181 YAWGVKFVETS 191
F+ETS
Sbjct: 133 KENNAMFIETS 143
>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 = 52.2 bits (126), Expect = 1e-08
Identities = 26/86 (30%), Positives = 49/86 (56%), Gaps = 3/86 (3%)
Query: 124 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEK-AVILVANKADLERRRQVTHSDGKKLAYA 182
++VY + + +F+K + +K L G ++++V NK DLER+R V+ S+ ++ A +
Sbjct: 77 ILVYDITDADSFQKVKKWIKELKQM--RGNNISLVIVGNKIDLERQRVVSKSEAEEYAKS 134
Query: 183 WGVKFVETSVGLVYKTDELLVGIARQ 208
G K ETS +EL + +A++
Sbjct: 135 VGAKHFETSAKTGKGIEELFLSLAKR 160
>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 = 50.9 bits (122), Expect = 4e-08
Identities = 26/88 (29%), Positives = 47/88 (53%)
Query: 121 DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHSDGKKLA 180
+ F++V+S+ + ++F + + + K ++LV NK DLE +RQV+ + LA
Sbjct: 73 EGFLLVFSITDMESFTALAEFREQILRVKEDDNVPLLLVGNKCDLEDKRQVSVEEAANLA 132
Query: 181 YAWGVKFVETSVGLVYKTDELLVGIARQ 208
WGV +VETS D++ + R+
Sbjct: 133 EQWGVNYVETSAKTRANVDKVFFDLVRE 160
>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 = 50.4 bits (121), Expect = 7e-08
Identities = 25/86 (29%), Positives = 47/86 (54%), Gaps = 3/86 (3%)
Query: 124 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV-ILVANKADLERRRQVTHSDGKKLAYA 182
+IVY V ++++F + L+ + +Y E +LV NK DL ++ V +++ K+ A
Sbjct: 79 IIVYDVTDQESFNNVKQWLQEI--DRYASENVNKLLVGNKCDLTDKKVVDYTEAKEFADE 136
Query: 183 WGVKFVETSVGLVYKTDELLVGIARQ 208
G+ F+ETS +E + +AR+
Sbjct: 137 LGIPFLETSAKNATNVEEAFMTMARE 162
>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 = 50.9 bits (122), Expect = 8e-08
Identities = 29/97 (29%), Positives = 50/97 (51%), Gaps = 4/97 (4%)
Query: 124 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV--ILVANKADLERRRQVTHSDGKKLAY 181
++V+ + R++F+ D L+ +I ILV +K DLE +RQVT + +KLA
Sbjct: 80 LLVFDITNRESFEHVHDWLEEA--RSHIQPHRPVFILVGHKCDLESQRQVTREEAEKLAK 137
Query: 182 AWGVKFVETSVGLVYKTDELLVGIARQAGLNKKRNKL 218
G+K++ETS +E + ++ KR +L
Sbjct: 138 DLGMKYIETSARTGDNVEEAFELLTQEIYERIKRGEL 174
>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 = 50.1 bits (120), Expect = 8e-08
Identities = 21/69 (30%), Positives = 39/69 (56%), Gaps = 1/69 (1%)
Query: 123 FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHSDGKKLAYA 182
F+ V+++ RK+F+ + + K + ++LV NK DL R V+ G+ LA +
Sbjct: 76 FLCVFAINSRKSFEDIHTYREQIKRVKDSDDVPMVLVGNKCDLAAR-TVSTRQGQDLAKS 134
Query: 183 WGVKFVETS 191
+G+ ++ETS
Sbjct: 135 YGIPYIETS 143
>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 = 48.2 bits (115), Expect = 4e-07
Identities = 25/85 (29%), Positives = 43/85 (50%), Gaps = 3/85 (3%)
Query: 124 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVTHSDGKKLAYA 182
++VY + R+TF L+ ++ I L+ NK DLE RR+V++ +G+ A
Sbjct: 81 LLVYDITRRETFNHLTSWLEDA--RQHSNSNMTIMLIGNKCDLESRREVSYEEGEAFARE 138
Query: 183 WGVKFVETSVGLVYKTDELLVGIAR 207
G+ F+ETS +E + A+
Sbjct: 139 HGLIFMETSAKTASNVEEAFINTAK 163
>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 = 48.3 bits (116), Expect = 4e-07
Identities = 26/68 (38%), Positives = 36/68 (52%), Gaps = 3/68 (4%)
Query: 125 IVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVTHSDGKKLAYAW 183
+VY + ++ TF+ E LK L D + VI LV NK+DL R V + K A
Sbjct: 81 LVYDITKKSTFENVERWLKELRD--HADSNIVIMLVGNKSDLRHLRAVPTEEAKAFAEKN 138
Query: 184 GVKFVETS 191
G+ F+ETS
Sbjct: 139 GLSFIETS 146
>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 = 48.3 bits (115), Expect = 5e-07
Identities = 22/86 (25%), Positives = 44/86 (51%), Gaps = 3/86 (3%)
Query: 123 FVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHSDGKKLAYA 182
F++++ + ++F + + L Y ++L+ NKADL +R+V+ ++LA
Sbjct: 90 FLLMFDLTSEQSFLNVRNWMSQLQAHAYCENPDIVLIGNKADLPDQREVSERQARELADK 149
Query: 183 WGVKFVETSVGL---VYKTDELLVGI 205
+G+ + ETS V K E L+ +
Sbjct: 150 YGIPYFETSAATGQNVEKAVETLLDL 175
>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 = 47.9 bits (114), Expect = 6e-07
Identities = 24/85 (28%), Positives = 44/85 (51%), Gaps = 10/85 (11%)
Query: 123 FVIVYSVIERKTFKKAEDMLKTLWD------SKYIGEKAVILVANKADLERRRQVTHSDG 176
F++VYS+ +++ ++ LK +++ + + ++LV NK D R+V+ S+G
Sbjct: 76 FILVYSITSKQSLEE----LKPIYELICEIKGNNLEKIPIMLVGNKCDESPSREVSSSEG 131
Query: 177 KKLAYAWGVKFVETSVGLVYKTDEL 201
LA W F+ETS + EL
Sbjct: 132 AALARTWNCAFMETSAKTNHNVQEL 156
>gnl|CDD|133344 cd04144, Ras2, Rat sarcoma (Ras) family 2 of small guanosine
triphosphatases (GTPases). The Ras2 subfamily, found
exclusively in fungi, was first identified in Ustilago
maydis. In U. maydis, Ras2 is regulated by Sql2, a
protein that is homologous to GEFs (guanine nucleotide
exchange factors) of the CDC25 family. Ras2 has been
shown to induce filamentous growth, but the signaling
cascade through which Ras2 and Sql2 regulate cell
morphology is not known. Most Ras proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Ras proteins.
Length = 190
Score = 47.9 bits (114), Expect = 7e-07
Identities = 31/111 (27%), Positives = 51/111 (45%), Gaps = 8/111 (7%)
Query: 123 FVIVYSVIERKTFKKAEDMLKTLWDSK--YIGEKAVILVANKADLERRRQVTHSDGKKLA 180
F++VYS+ R TF++ E + + K + +++V NK D R+V+ +G LA
Sbjct: 74 FILVYSITSRSTFERVERFREQIQRVKDESAADVPIMIVGNKCDKVYEREVSTEEGAALA 133
Query: 181 YAWGVKFVETS------VGLVYKTDELLVGIARQAGLNKKRNKLLAKKQKK 225
G +F+E S V + T + RQ G K K++KK
Sbjct: 134 RRLGCEFIEASAKTNVNVERAFYTLVRALRQQRQGGQGPKGGPTKKKEKKK 184
>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 = 46.7 bits (111), Expect = 2e-06
Identities = 23/70 (32%), Positives = 38/70 (54%), Gaps = 5/70 (7%)
Query: 124 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEK--AVILVANKADLERRRQVTHSDGKKLAY 181
++VY + R++F + L D++ + +ILV NK DLE R+VT + + A
Sbjct: 77 LLVYDITSRESF---NALTNWLTDARTLASPDIVIILVGNKKDLEDDREVTFLEASRFAQ 133
Query: 182 AWGVKFVETS 191
G+ F+ETS
Sbjct: 134 ENGLLFLETS 143
>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 = 46.1 bits (109), Expect = 3e-06
Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 9/73 (12%)
Query: 123 FVIVYSVIERKTFKKAED---MLKTL-WDSKYIGEKAVILVANKADLERRRQVTHSDGKK 178
F+++Y + ++F +D +KT WD+ VILV NK D+E R V+ G++
Sbjct: 77 FILMYDITNEESFNAVQDWSTQIKTYSWDNA-----QVILVGNKCDMEDERVVSAERGRQ 131
Query: 179 LAYAWGVKFVETS 191
LA G +F E S
Sbjct: 132 LADQLGFEFFEAS 144
>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 = 3e-06
Identities = 29/88 (32%), Positives = 42/88 (47%), Gaps = 9/88 (10%)
Query: 124 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI--LVANKADLERRRQVTHSDGKKLAY 181
++VY V R TF + L L Y + LV NK D E R +VT +G+K A
Sbjct: 77 ILVYDVTRRDTFDNLDTWLNEL--DTYSTNPDAVKMLVGNKIDKENR-EVTREEGQKFAR 133
Query: 182 AWGVKFVETS----VGLVYKTDELLVGI 205
+ F+ETS +G+ +EL+ I
Sbjct: 134 KHNMLFIETSAKTRIGVQQAFEELVEKI 161
>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 = 46.0 bits (109), Expect = 4e-06
Identities = 22/87 (25%), Positives = 44/87 (50%), Gaps = 5/87 (5%)
Query: 124 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILV--ANKADLERRRQVTHSDGKKLAY 181
+++Y V + +F +++ L + + V+++ NKAD+ R V DG++LA
Sbjct: 78 LLLYDVTNKSSF---DNIRAWLTEILEYAQSDVVIMLLGNKADMSGERVVKREDGERLAK 134
Query: 182 AWGVKFVETSVGLVYKTDELLVGIARQ 208
+GV F+ETS + +A++
Sbjct: 135 EYGVPFMETSAKTGLNVELAFTAVAKE 161
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 44.9 bits (106), Expect = 1e-05
Identities = 26/69 (37%), Positives = 40/69 (57%), Gaps = 3/69 (4%)
Query: 124 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVA-NKADLERRRQVTHSDGKKLAYA 182
++VY + +R+TF + L+ L D + VI++A NK+DL R V DG+ LA
Sbjct: 89 LLVYDITKRQTFDNVQRWLRELRD--HADSNIVIMMAGNKSDLNHLRSVAEEDGQALAEK 146
Query: 183 WGVKFVETS 191
G+ F+ETS
Sbjct: 147 EGLSFLETS 155
>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 = 44.2 bits (104), Expect = 1e-05
Identities = 31/101 (30%), Positives = 53/101 (52%), Gaps = 8/101 (7%)
Query: 124 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKA-VILVANKADLERRRQVTHSDGKKLAYA 182
++VY + +++TF +K + KY E A ++LV NK D E R++T G+K A
Sbjct: 77 ILVYDITKKETFDDLPKWMKMI--DKYASEDAELLLVGNKLDCETDREITRQQGEKFAQQ 134
Query: 183 -WGVKFVETSVGLVYKTDELLV----GIARQAGLNKKRNKL 218
G++F E S + DE+ + I ++ L+ RN+L
Sbjct: 135 ITGMRFCEASAKDNFNVDEIFLKLVDDILKKMPLDILRNEL 175
>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 = 42.8 bits (101), Expect = 3e-05
Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 4/88 (4%)
Query: 121 DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTH-SDGKKL 179
D+ ++V +R++ + A+ ++ +ILV NK DL R+V ++L
Sbjct: 77 DLILLVVDSTDRESEEDAKLLIL---RRLRKEGIPIILVGNKIDLLEEREVEELLRLEEL 133
Query: 180 AYAWGVKFVETSVGLVYKTDELLVGIAR 207
A GV E S DEL +
Sbjct: 134 AKILGVPVFEVSAKTGEGVDELFEKLIE 161
>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 = 41.8 bits (99), Expect = 8e-05
Identities = 24/88 (27%), Positives = 40/88 (45%), Gaps = 19/88 (21%)
Query: 119 HPDVFVIVYSVIERKTFKKAEDMLKTLWD---SKYIGEKAVILVANKADL---------- 165
DVF++ +SV +F+ + W Y +ILV K DL
Sbjct: 71 QTDVFLLCFSVDSPSSFENVKTK----WYPEIKHYCPNVPIILVGTKIDLRDDGNTLKKL 126
Query: 166 -ERRRQVTHSDGKKLAYAWG-VKFVETS 191
++++ +T +G+KLA G VK++E S
Sbjct: 127 EKKQKPITPEEGEKLAKEIGAVKYMECS 154
>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 = 41.2 bits (97), Expect = 1e-04
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 4/72 (5%)
Query: 124 VIVYSVIERKTF----KKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHSDGKKL 179
++VY V +R++F ++M + + V++ ANK DL + R V+ +G+
Sbjct: 77 LLVYDVTDRQSFEALDSWLKEMKQEGGPHGNMENIVVVVCANKIDLTKHRAVSEDEGRLW 136
Query: 180 AYAWGVKFVETS 191
A + G K+ ETS
Sbjct: 137 AESKGFKYFETS 148
>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 = 41.4 bits (97), Expect = 1e-04
Identities = 25/92 (27%), Positives = 43/92 (46%), Gaps = 1/92 (1%)
Query: 121 DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHSDGKKLA 180
D F +VYSV + ++F++ + + + + + K +++V NK D RQV +D
Sbjct: 72 DAFALVYSVDDPESFEEVKRLREEILEVKEDKFVPIVVVGNKIDSLAERQVEAADALSTV 131
Query: 181 -YAWGVKFVETSVGLVYKTDELLVGIARQAGL 211
W FVE S E+ + +QA L
Sbjct: 132 ELDWNNGFVEASAKDNENVTEVFKELLQQANL 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 = 41.1 bits (96), Expect = 1e-04
Identities = 25/84 (29%), Positives = 41/84 (48%), Gaps = 5/84 (5%)
Query: 125 IVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV--ILVANKADLERRRQVTHSDGKKLAYA 182
+VY + +++ + ++K + D + V IL+ NKAD E++RQV G KLA
Sbjct: 78 LVYDISSERSY---QHIMKWVSDVDEYAPEGVQKILIGNKADEEQKRQVGDEQGNKLAKE 134
Query: 183 WGVKFVETSVGLVYKTDELLVGIA 206
+G+ F ETS E +
Sbjct: 135 YGMDFFETSACTNKNIKESFTRLT 158
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 41.5 bits (97), Expect = 1e-04
Identities = 23/85 (27%), Positives = 41/85 (48%), Gaps = 5/85 (5%)
Query: 124 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEK--AVILVANKADLERRRQVTHSDGKKLAY 181
++VY + R+TF L+ D++ ++L+ NK DL RR V+ +G++ A
Sbjct: 83 LLVYDITRRETFNHLASWLE---DARQHANANMTIMLIGNKCDLAHRRAVSTEEGEQFAK 139
Query: 182 AWGVKFVETSVGLVYKTDELLVGIA 206
G+ F+E S +E + A
Sbjct: 140 EHGLIFMEASAKTAQNVEEAFIKTA 164
>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 = 40.9 bits (96), Expect = 2e-04
Identities = 24/87 (27%), Positives = 42/87 (48%), Gaps = 4/87 (4%)
Query: 124 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV-ILVANKADLERRRQVTHSDGKKLAYA 182
+I Y + R +F+ ++ + KY V +L+ NK DLE +R+V + LA
Sbjct: 80 IIAYDITRRSSFESVPHWIEEV--EKYGASNVVLLLIGNKCDLEEQREVLFEEACTLAEH 137
Query: 183 WGVKFV-ETSVGLVYKTDELLVGIARQ 208
+G+ V ETS +E + +A +
Sbjct: 138 YGILAVLETSAKESSNVEEAFLLMATE 164
>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 = 40.6 bits (95), Expect = 2e-04
Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 5/70 (7%)
Query: 124 VIVYSVIERKTFKKAEDMLKTLWDSKYIG--EKAVILVANKADLERRRQVTHSDGKKLAY 181
++VY + R T+ L D++ + + L+ NKADLE +R VT+ + K+ A
Sbjct: 79 LMVYDITRRSTYNHLSSWLT---DARNLTNPNTVIFLIGNKADLEAQRDVTYEEAKQFAD 135
Query: 182 AWGVKFVETS 191
G+ F+E S
Sbjct: 136 ENGLLFLECS 145
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 38.6 bits (89), Expect = 0.001
Identities = 21/69 (30%), Positives = 39/69 (56%), Gaps = 3/69 (4%)
Query: 124 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVI-LVANKADLERRRQVTHSDGKKLAYA 182
++VY + R++F+ ++ + + + G+ +I LV NK DL R+VT+ +G + A
Sbjct: 57 IVVYDITNRQSFENTTKWIQDILNER--GKDVIIALVGNKTDLGDLRKVTYEEGMQKAQE 114
Query: 183 WGVKFVETS 191
+ F ETS
Sbjct: 115 YNTMFHETS 123
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 38.5 bits (89), Expect = 0.001
Identities = 23/69 (33%), Positives = 33/69 (47%), Gaps = 1/69 (1%)
Query: 124 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV-ILVANKADLERRRQVTHSDGKKLAYA 182
++VY V R+TF D+ + + V +LV NK D E R V+ +G LA
Sbjct: 90 ILVYDVTRRETFTNLSDVWGKEVELYSTNQDCVKMLVGNKVDRESERDVSREEGMALAKE 149
Query: 183 WGVKFVETS 191
G F+E S
Sbjct: 150 HGCLFLECS 158
>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 = 37.5 bits (87), Expect = 0.002
Identities = 26/109 (23%), Positives = 43/109 (39%), Gaps = 2/109 (1%)
Query: 124 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVTHSDGKKLAYAW 183
++VY V ++F + L+ + + K +LV NK D R+ V D K A
Sbjct: 83 IVVYDVTNGESFVNVKRWLQEIEQNCDDVCK--VLVGNKNDDPERKVVETEDAYKFAGQM 140
Query: 184 GVKFVETSVGLVYKTDELLVGIARQAGLNKKRNKLLAKKQKKMASYINN 232
G+ ETS +E+ I KK N ++Q++
Sbjct: 141 GISLFETSAKENINVEEMFNCITELVLRAKKDNLAKQQQQQQNDVVKLP 189
>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 = 37.5 bits (87), Expect = 0.003
Identities = 20/69 (28%), Positives = 29/69 (42%), Gaps = 2/69 (2%)
Query: 118 YHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEK--AVILVANKADLERRRQVTHSD 175
Y +VY + ++F+ ED L + E ++LV NK DLE RQVT
Sbjct: 72 YGAQAVCLVYDITNSQSFENLEDWLSVVKKVNEESETKPKMVLVGNKTDLEHNRQVTAEK 131
Query: 176 GKKLAYAWG 184
+ A
Sbjct: 132 HARFAQEND 140
>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 = 35.6 bits (82), Expect = 0.009
Identities = 23/94 (24%), Positives = 49/94 (52%), Gaps = 5/94 (5%)
Query: 116 QTYH--PDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV-ILVANKADLERRRQVT 172
Q+Y+ + ++ Y + ++F+ + L+ + +Y K + ILV NK DL RR+V+
Sbjct: 74 QSYYRSANALILTYDITCEESFRCLPEWLREI--EQYANNKVITILVGNKIDLAERREVS 131
Query: 173 HSDGKKLAYAWGVKFVETSVGLVYKTDELLVGIA 206
++ + A + ++ETS ++L + +A
Sbjct: 132 QQRAEEFSDAQDMYYLETSAKESDNVEKLFLDLA 165
>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 = 35.8 bits (83), Expect = 0.011
Identities = 31/121 (25%), Positives = 47/121 (38%), Gaps = 20/121 (16%)
Query: 121 DVFVIVYSVIERKTFKKAEDMLKTLW--DSKYIGEKA-VILVANKADLERRRQ------- 170
DV +I YSV + ED W + + ++LV K DL + +
Sbjct: 77 DVILICYSVDNPTSLDNVEDK----WYPEVNHFCPGTPIVLVGLKTDLRKDKNSVSKLRA 132
Query: 171 -----VTHSDGKKLAYAWG-VKFVETSVGLVYKTDELLVGIARQAGLNKKRNKLLAKKQK 224
VT G+ +A + G V ++E S L+ DE+ A R KK+K
Sbjct: 133 QGLEPVTPEQGESVAKSIGAVAYIECSAKLMENVDEVFDAAINVALSKSGRAARKKKKKK 192
Query: 225 K 225
K
Sbjct: 193 K 193
>gnl|CDD|133330 cd04130, Wrch_1, Wnt-1 responsive Cdc42 homolog (Wrch-1) is a Rho
family GTPase similar to Cdc42. Wrch-1 (Wnt-1
responsive Cdc42 homolog) is a Rho family GTPase that
shares significant sequence and functional similarity
with Cdc42. Wrch-1 was first identified in mouse mammary
epithelial cells, where its transcription is upregulated
in Wnt-1 transformation. Wrch-1 contains N- and
C-terminal extensions relative to cdc42, suggesting
potential differences in cellular localization and
function. The Wrch-1 N-terminal extension contains
putative SH3 domain-binding motifs and has been shown to
bind the SH3 domain-containing protein Grb2, which
increases the level of active Wrch-1 in cells. Unlike
Cdc42, which localizes to the cytosol and perinuclear
membranes, Wrch-1 localizes extensively with the plasma
membrane and endosomes. The membrane association,
localization, and biological activity of Wrch-1 indicate
an atypical model of regulation distinct from other Rho
family GTPases. Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 173
Score = 34.3 bits (79), Expect = 0.023
Identities = 22/89 (24%), Positives = 38/89 (42%), Gaps = 20/89 (22%)
Query: 119 HPDVFVIVYSVIERKTFKKAEDMLKTLWDS---KYIGEKAVILVANKADLE--------- 166
DVF++ +SV+ +F+ + W K+ + +ILV +ADL
Sbjct: 71 DTDVFLLCFSVVNPSSFQN----ISEKWIPEIRKHNPKAPIILVGTQADLRTDVNVLIQL 126
Query: 167 ---RRRQVTHSDGKKLAYAWG-VKFVETS 191
+ V+ S K LA G +++E S
Sbjct: 127 ARYGEKPVSQSRAKALAEKIGACEYIECS 155
>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 = 34.7 bits (80), Expect = 0.025
Identities = 21/100 (21%), Positives = 46/100 (46%), Gaps = 9/100 (9%)
Query: 121 DVFVIVYSVIERKTFKKAEDMLKTLWD--------SKYIGEKAVILVANKADLERRRQVT 172
DVF++V+S+ R++F++ + + + + +K + +++ NKAD + R+V
Sbjct: 73 DVFILVFSLDNRESFEEVCRLREQILETKSCLKNKTKENVKIPMVICGNKADRDFPREVQ 132
Query: 173 HSDGKKL-AYAWGVKFVETSVGLVYKTDELLVGIARQAGL 211
+ ++L + E S DE+ + A L
Sbjct: 133 RDEVEQLVGGDENCAYFEVSAKKNSNLDEMFRALFSLAKL 172
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 33.8 bits (77), Expect = 0.048
Identities = 25/151 (16%), Positives = 53/151 (35%), Gaps = 29/151 (19%)
Query: 116 QTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKA-----VILVANKADLERRRQ 170
+ +IVY + ++++ + + + E A ++LV NK DL +
Sbjct: 74 YYRGANGILIVYDST---LRESSDELTEEWL--EELRELAPDDVPILLVGNKIDLFDEQS 128
Query: 171 VTHSDGKKLAYA---------------WGVKFVETSV--GLVYKTDELLVGIARQAGLNK 213
+ +L +ETS +EL + R+ L +
Sbjct: 129 SSEEILNQLNREVVLLVLAPKAVLPEVANPALLETSAKSLTGPNVNELFKELLRK--LLE 186
Query: 214 KRNKLLAKKQKKMASYINNIKQFKWFSKVSC 244
+ KL+ K + + +NN + + +C
Sbjct: 187 EIEKLVLKNELRQLDRLNNPIEQAALASFNC 217
>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 = 33.4 bits (77), Expect = 0.049
Identities = 26/91 (28%), Positives = 40/91 (43%), Gaps = 28/91 (30%)
Query: 121 DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGE-------KAVILVANKADL-------- 165
DVF+I +SV +F+ + K+ E +ILV K DL
Sbjct: 71 DVFLICFSVDSPASFENVK--------EKWYPEVKHFCPNVPIILVGTKLDLRNDKSTLE 122
Query: 166 --ERRRQ--VTHSDGKKLAYAWG-VKFVETS 191
+++Q VT+ G+ LA G VK++E S
Sbjct: 123 ELSKKKQEPVTYEQGQALAKRIGAVKYLECS 153
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 32.6 bits (75), Expect = 0.19
Identities = 16/57 (28%), Positives = 23/57 (40%), Gaps = 1/57 (1%)
Query: 153 EKAVILVANKADLERRRQVTHSDGKKLAYAWGVKFVETSVGLVYKTDELLVGIARQA 209
+IL N D ++R + D +KL+ GV V T +EL I A
Sbjct: 108 GIPMILALNMIDEAKKRGI-RIDIEKLSKLLGVPVVPTVAKRGEGLEELKRAIIELA 163
>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 = 31.2 bits (71), Expect = 0.30
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 7/48 (14%)
Query: 121 DVFVIVYSVIERKTFKKAEDMLKTLW--DSKYIGEKA-VILVANKADL 165
+V +VYSV T ++ ++T W + +G K +ILV NK+DL
Sbjct: 74 NVICLVYSVDRPSTLER----IRTKWLPLIRRLGVKVPIILVGNKSDL 117
>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 = 30.5 bits (69), Expect = 0.43
Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 8/72 (11%)
Query: 124 VIVYSVIERKTFKKAEDMLKTLWDSKY---IGEKAVILVANKADLERRRQVTHSDGKKLA 180
++V+S +R++F+ E W K G+ ++LV K DL + +T+ + + LA
Sbjct: 79 ILVFSTTDRESFEAIES-----WKEKVEAECGDIPMVLVQTKIDLLDQAVITNEEAEALA 133
Query: 181 YAWGVKFVETSV 192
+ TSV
Sbjct: 134 KRLQLPLFRTSV 145
>gnl|CDD|133342 cd04142, RRP22, Ras-related protein on chromosome 22 (RRP22)
family. RRP22 (Ras-related protein on chromosome 22)
subfamily consists of proteins that inhibit cell growth
and promote caspase-independent cell death. Unlike most
Ras proteins, RRP22 is down-regulated in many human
tumor cells due to promoter methylation. RRP22 localizes
to the nucleolus in a GTP-dependent manner, suggesting a
novel function in modulating transport of nucleolar
components. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras proteins.
Like most Ras family proteins, RRP22 is farnesylated.
Length = 198
Score = 30.6 bits (69), Expect = 0.48
Identities = 12/51 (23%), Positives = 27/51 (52%), Gaps = 2/51 (3%)
Query: 121 DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIG--EKAVILVANKADLERRR 169
F++VY + +F + + + + +++ G E +++V NK D +R R
Sbjct: 82 RAFILVYDICSPDSFHYVKLLRQQILETRPAGNKEPPIVVVGNKRDQQRHR 132
>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 = 30.3 bits (69), Expect = 0.56
Identities = 26/103 (25%), Positives = 47/103 (45%), Gaps = 14/103 (13%)
Query: 121 DVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAV--------ILVANKADLERRRQVT 172
D V+VY V K+F+ + W +++ + + +++ NK DLE +RQV+
Sbjct: 74 DCCVLVYDVTNPKSFESLDS-----WRDEFLIQASPRDPENFPFVVLGNKIDLEEKRQVS 128
Query: 173 HSDGKKLAYAWG-VKFVETSVGLVYKTDELLVGIARQAGLNKK 214
++ + G + + ETS D+ IAR A +K
Sbjct: 129 TKKAQQWCKSKGNIPYFETSAKEAINVDQAFETIARLALEQEK 171
>gnl|CDD|221161 pfam11661, DUF2986, Protein of unknown function (DUF2986). This
family of proteins has no known function.
Length = 44
Score = 28.0 bits (63), Expect = 0.57
Identities = 11/29 (37%), Positives = 17/29 (58%)
Query: 213 KKRNKLLAKKQKKMASYINNIKQFKWFSK 241
KK N+ L KK KK + ++ + K+ SK
Sbjct: 5 KKINQKLKKKAKKANAKLHPSNKPKYISK 33
>gnl|CDD|133353 cd04153, Arl5_Arl8, Arf-like 5 (Arl5) and 8 (Arl8) GTPases.
Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like
Arl4 and Arl7, are localized to the nucleus and
nucleolus. Arl5 is developmentally regulated during
embryogenesis in mice. Human Arl5 interacts with the
heterochromatin protein 1-alpha (HP1alpha), a nonhistone
chromosomal protein that is associated with
heterochromatin and telomeres, and prevents telomere
fusion. Arl5 may also play a role in embryonic nuclear
dynamics and/or signaling cascades. Arl8 was identified
from a fetal cartilage cDNA library. It is found in
brain, heart, lung, cartilage, and kidney. No function
has been assigned for Arl8 to date.
Length = 174
Score = 29.6 bits (67), Expect = 0.86
Identities = 11/29 (37%), Positives = 18/29 (62%)
Query: 139 EDMLKTLWDSKYIGEKAVILVANKADLER 167
++ L++ W++ Y AVILV + D ER
Sbjct: 69 QESLRSSWNTYYTNTDAVILVIDSTDRER 97
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 30.0 bits (68), Expect = 1.0
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 148 SKYIGEKAVILVANKADL 165
+ + EK +LV NKADL
Sbjct: 56 ERIVKEKPKLLVLNKADL 73
>gnl|CDD|133361 cd04161, Arl2l1_Arl13_like, Arl2-like protein 1 (Arl2l1) and Arl13.
Arl2l1 (Arl2-like protein 1) and Arl13 form a subfamily
of the Arf family of small GTPases. Arl2l1 was
identified in human cells during a search for the
gene(s) responsible for Bardet-Biedl syndrome (BBS).
Like Arl6, the identified BBS gene, Arl2l1 is proposed
to have cilia-specific functions. Arl13 is found on the
X chromosome, but its expression has not been confirmed;
it may be a pseudogene.
Length = 167
Score = 29.3 bits (66), Expect = 1.3
Identities = 13/54 (24%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 119 HPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERRRQVT 172
H VFV+ S +R ++ +++L+ L + K ++++ANK D +
Sbjct: 68 HGLVFVVDSSDDDR--VQEVKEILRELLQHPRVSGKPILVLANKQDKKNALLGA 119
>gnl|CDD|185309 PRK15411, rcsA, colanic acid capsular biosynthesis activation
protein A; Provisional.
Length = 207
Score = 29.3 bits (66), Expect = 1.4
Identities = 13/62 (20%), Positives = 19/62 (30%), Gaps = 7/62 (11%)
Query: 75 QVENFVQTYHPDVFFIVYSDTNHTQRCLTPMPFCSQVENFVQTYHPDVFVIVYSVIERKT 134
+ + P V FI + C SQ + HP+ IV+ I
Sbjct: 38 DLAIACDSLRPSVVFI-------NEDCFIHDASNSQRIKQIINQHPNTLFIVFMAIANIH 90
Query: 135 FK 136
F
Sbjct: 91 FD 92
>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 = 28.9 bits (65), Expect = 1.6
Identities = 24/83 (28%), Positives = 35/83 (42%), Gaps = 2/83 (2%)
Query: 109 SQVENFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVILVANKADLERR 168
S V+++ + H VFV Y V +F ++ E ILV NK DL +
Sbjct: 67 SMVQHYYRNVHAVVFV--YDVTNMASFHSLPSWIEECEQHSLPNEVPRILVGNKCDLREQ 124
Query: 169 RQVTHSDGKKLAYAWGVKFVETS 191
QV ++ A A + ETS
Sbjct: 125 IQVPTDLAQRFADAHSMPLFETS 147
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 29.4 bits (67), Expect = 1.7
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 149 KYIGEKAVILVANKADL 165
K IG K +L+ NK+DL
Sbjct: 47 KIIGNKPRLLILNKSDL 63
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase. The
Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that generally show sequence
conservation in the region between the Walker A and B
motifs (G1 and G3 box motifs), to the exclusion of other
GTPases. TrmE is ubiquitous in bacteria and is a
widespread mitochondrial protein in eukaryotes, but is
absent from archaea. The yeast member of TrmE family,
MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family.
Length = 161
Score = 28.4 bits (64), Expect = 2.2
Identities = 17/63 (26%), Positives = 23/63 (36%), Gaps = 11/63 (17%)
Query: 153 EKAVILVANKADL--ERRRQVTHSDGKKLAYAWGVKFVETS----VGLVYKTDELLVGIA 206
K V+LV NK DL E + + K + + S G+ DEL IA
Sbjct: 104 GKPVLLVLNKIDLVPESEEEELLRERKLELLP-DLPVIAVSALPGEGI----DELRKKIA 158
Query: 207 RQA 209
Sbjct: 159 ELL 161
>gnl|CDD|206748 cd01855, YqeH, Circularly permuted YqeH GTPase. YqeH is an
essential GTP-binding protein. Depletion of YqeH induces
an excess initiation of DNA replication, suggesting that
it negatively controls initiation of chromosome
replication. The YqeH subfamily is common in eukaryotes
and sporadically present in bacteria with probable
acquisition by plants from chloroplasts. Proteins of the
YqeH family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases.
Length = 191
Score = 28.4 bits (64), Expect = 2.5
Identities = 11/17 (64%), Positives = 12/17 (70%)
Query: 149 KYIGEKAVILVANKADL 165
+ IG K VILV NK DL
Sbjct: 56 ELIGAKPVILVGNKIDL 72
>gnl|CDD|173022 PRK14557, pyrH, uridylate kinase; Provisional.
Length = 247
Score = 28.7 bits (64), Expect = 2.5
Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 2/34 (5%)
Query: 21 IVYSDTNHTQRCLTSIPFCSTVENFVQ--TYHHV 52
++ S TN R +TSIPF + E +++ HH+
Sbjct: 89 VLTSKTNKEVRVMTSIPFNAVAEPYIRLRAVHHL 122
>gnl|CDD|188086 TIGR00819, ydaH, p-Aminobenzoyl-glutamate transporter family. The
p-Aminobenzoyl-glutamate transporter family includes two
transporters, the AbgT (YdaH) protein of E. coli and
MtrF of Neisseria gonorrhoea. AbgT is apparently cryptic
in wild type cells, but when expressed on a high copy
number plasmid, or when expressed at higher levels due
to mutation, it allows utilization of
p-aminobenzoyl-glutamate as a source of p-aminobenzoate
for p-aminobenzoate auxotrophs. p-Aminobenzoate is a
constituent of and a precursor for the biosynthesis of
folic acid [Hypothetical proteins, Conserved].
Length = 525
Score = 28.8 bits (64), Expect = 3.2
Identities = 8/46 (17%), Positives = 15/46 (32%), Gaps = 1/46 (2%)
Query: 83 YHPDVFFIVYSDTNHTQRCLTPM-PFCSQVENFVQTYHPDVFVIVY 127
+ P + + + + PM PF F+ Y D +
Sbjct: 439 FAPAFAQAAFRIADSSTLIIAPMMPFFGLFLAFLMKYKKDAGLGTL 484
>gnl|CDD|237511 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 28.3 bits (64), Expect = 3.6
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 148 SKYIGEKAVILVANKADL 165
+++G V+LV NKADL
Sbjct: 91 HRFVGNNPVLLVGNKADL 108
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 28.3 bits (64), Expect = 3.7
Identities = 18/73 (24%), Positives = 27/73 (36%), Gaps = 18/73 (24%)
Query: 148 SKYIGEKAVILVANKADLERRRQVTHSDGKKLAYAWGVKFVETSVGLVYKTDELLVGIAR 207
+K +I+V NKADL V+ + + A G + S KT E
Sbjct: 319 ELLPKKKPIIVVLNKADL-----VSKIELESEKLANGDAIISISA----KTGE------- 362
Query: 208 QAGLNKKRNKLLA 220
GL+ R +
Sbjct: 363 --GLDALREAIKQ 373
>gnl|CDD|206681 cd01894, EngA1, EngA1 GTPase contains the first domain of EngA.
This EngA1 subfamily CD represents the first GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. Since the sequences of the
two domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family. Although the exact function of
these proteins has not been elucidated, studies have
revealed that the E. coli EngA homolog, Der, and
Neisseria gonorrhoeae EngA are essential for cell
viability. A recent report suggests that E. coli Der
functions in ribosome assembly and stability.
Length = 157
Score = 27.4 bits (62), Expect = 4.2
Identities = 8/20 (40%), Positives = 10/20 (50%)
Query: 154 KAVILVANKADLERRRQVTH 173
K VILV NK D + +
Sbjct: 106 KPVILVVNKIDNIKEEEEAA 125
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family. Emg1 and Nop14 are novel
proteins whose interaction is required for the
maturation of the 18S rRNA and for 40S ribosome
production.
Length = 809
Score = 28.4 bits (64), Expect = 4.3
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 197 KTDELLVGIARQAGLNKKRNKLLAKKQKK 225
K D G++R K++ LL +K++K
Sbjct: 34 KGDRGRPGVSRSRAEEKRKQTLLKEKKQK 62
>gnl|CDD|206692 cd04107, Rab32_Rab38, Rab GTPase families 18 (Rab18) and 32
(Rab32). Rab38/Rab32 subfamily. Rab32 and Rab38 are
members of the Rab family of small GTPases. Human Rab32
was first identified in platelets but it is expressed in
a variety of cell types, where it functions as an
A-kinase anchoring protein (AKAP). Rab38 has been shown
to be melanocyte-specific. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 201
Score = 27.7 bits (62), Expect = 4.9
Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 5/50 (10%)
Query: 124 VIVYSVIERKTFKKAEDMLKTLWDSK--YIGEKAV--ILVANKADLERRR 169
+IV+ V TF+ A K DSK + + +L+ANK DL++ R
Sbjct: 78 IIVFDVTRPSTFE-AVLKWKADLDSKVTLPNGEPIPALLLANKCDLKKER 126
>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 = 27.6 bits (61), Expect = 5.1
Identities = 25/99 (25%), Positives = 38/99 (38%), Gaps = 10/99 (10%)
Query: 124 VIVYSVIERKTFKKAEDMLKTLWDSKYIGEKA----VILVANKADLERRRQVTHSDGKKL 179
++VY + R +F + +K I E A ILV N+ L +RQV +
Sbjct: 83 ILVYDITNRWSFDGIDRWIKE------IDEHAPGVPKILVGNRLHLAFKRQVATEQAQAY 136
Query: 180 AYAWGVKFVETSVGLVYKTDELLVGIARQAGLNKKRNKL 218
A G+ F E S + E +AR + R
Sbjct: 137 AERNGMTFFEVSPLCNFNITESFTELARIVLMRHGRPPQ 175
>gnl|CDD|221709 pfam12684, DUF3799, PDDEXK-like domain of unknown function
(DUF3799). This family of proteins is functionally
uncharacterized. This family of proteins is found in
bacteria and viruses. Proteins in this family are
typically between 265 and 420 amino acids in length. It
appears that these proteins are distantly related to the
PDDEXK superfamily and so these domains are likely to be
nucleases. This family has a C-terminal cysteine cluster
similar to that found in pfam01930.
Length = 237
Score = 27.7 bits (62), Expect = 5.1
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 5/34 (14%)
Query: 132 RKTFKKAEDMLKTLWDSK-----YIGEKAVILVA 160
+ FK AE M++ L + Y GEK VI+
Sbjct: 73 KAEFKIAEQMIEALKADELFNRLYQGEKEVIVTG 106
>gnl|CDD|236539 PRK09490, metH, B12-dependent methionine synthase; Provisional.
Length = 1229
Score = 28.2 bits (64), Expect = 5.4
Identities = 9/26 (34%), Positives = 14/26 (53%)
Query: 132 RKTFKKAEDMLKTLWDSKYIGEKAVI 157
RK F A+ ML + K++ + VI
Sbjct: 980 RKLFADAQAMLDKIIAEKWLTARGVI 1005
>gnl|CDD|215563 PLN03081, PLN03081, pentatricopeptide (PPR) repeat-containing
protein; Provisional.
Length = 697
Score = 27.9 bits (62), Expect = 5.4
Identities = 21/87 (24%), Positives = 42/87 (48%), Gaps = 3/87 (3%)
Query: 99 QRCLTPMPFCSQVENFVQTYHPDVFVIVYSVIERKTFKKAEDMLKTLWDSKYIGEKAVIL 158
++ L+ P C+ +E Q H R+ ++K ++++K + + Y+ E+ +L
Sbjct: 556 RKGLSMHPACTWIEVKKQD-HSFFSGDRLHPQSREIYQKLDELMKEISEYGYVAEENELL 614
Query: 159 VANKADLERRRQVTHSDGKKLAYAWGV 185
D E+ HS+ KLA A+G+
Sbjct: 615 PDVDEDEEKVSGRYHSE--KLAIAFGL 639
>gnl|CDD|225905 COG3370, COG3370, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 113
Score = 26.6 bits (59), Expect = 5.5
Identities = 25/102 (24%), Positives = 44/102 (43%), Gaps = 10/102 (9%)
Query: 87 VFFIVYSDTNHTQRCLTPMPFCSQVENFVQ-TYHPDVFVIVYSVIERKTFKKAEDMLKTL 145
V I+ S + ++ LT + F N V+ + DV +I + E+ K D LK L
Sbjct: 4 VLVIISSGKENIEKALTALNFAY---NSVKNKWFEDVELIFFGPSEKLLAKNDGDSLKML 60
Query: 146 WDSKYIGEK--AVILVAN----KADLERRRQVTHSDGKKLAY 181
+ + +G K A +VA + +L G+++A
Sbjct: 61 QELRSLGIKPLACKVVAENLGIEDELIFLGVELEMVGERIAA 102
>gnl|CDD|213833 TIGR03596, GTPase_YlqF, ribosome biogenesis GTP-binding protein
YlqF. Members of this protein family are GTP-binding
proteins involved in ribosome biogenesis, including the
essential YlqF protein of Bacillus subtilis, which is an
essential protein. They are related to Era, EngA, and
other GTPases of ribosome biogenesis, but are circularly
permuted. This family is not universal, and is not
present in Escherichia coli, and so is not as well
studied as some other GTPases. This model is built for
bacterial members [Protein synthesis, Other].
Length = 276
Score = 27.5 bits (62), Expect = 5.8
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 149 KYIGEKAVILVANKADL 165
+ G K ++V NKADL
Sbjct: 44 EIRGNKPRLIVLNKADL 60
>gnl|CDD|206663 cd01871, Rac1_like, Ras-related C3 botulinum toxin substrate 1 (rho
family, small GTP binding protein Rac1)-like consists of
Rac1, Rac2 and Rac3. The Rac1-like subfamily consists
of Rac1, Rac2, and Rac3 proteins, plus the splice
variant Rac1b that contains a 19-residue insertion near
switch II relative to Rac1. While Rac1 is ubiquitously
expressed, Rac2 and Rac3 are largely restricted to
hematopoietic and neural tissues respectively. Rac1
stimulates the formation of actin lamellipodia and
membrane ruffles. It also plays a role in cell-matrix
adhesion and cell anoikis. In intestinal epithelial
cells, Rac1 is an important regulator of migration and
mediates apoptosis. Rac1 is also essential for
RhoA-regulated actin stress fiber and focal adhesion
complex formation. In leukocytes, Rac1 and Rac2 have
distinct roles in regulating cell morphology, migration,
and invasion, but are not essential for macrophage
migration or chemotaxis. Rac3 has biochemical properties
that are closely related to Rac1, such as effector
interaction, nucleotide binding, and hydrolysis; Rac2
has a slower nucleotide association and is more
efficiently activated by the RacGEF Tiam1. Both Rac1 and
Rac3 have been implicated in the regulation of cell
migration and invasion in human metastatic breast
cancer. Most Rho proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Rho proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 174
Score = 27.5 bits (61), Expect = 6.0
Identities = 22/87 (25%), Positives = 39/87 (44%), Gaps = 20/87 (22%)
Query: 121 DVFVIVYSVIERKTFKKAEDMLKTLWD---SKYIGEKAVILVANKADL-----------E 166
DVF+I +S++ +F + ++ W + +ILV K DL E
Sbjct: 74 DVFLICFSLVSPASF----ENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKE 129
Query: 167 RRRQ-VTHSDGKKLAYAWG-VKFVETS 191
++ +T+ G +A G VK++E S
Sbjct: 130 KKLTPITYPQGLAMAKEIGAVKYLECS 156
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 27.6 bits (62), Expect = 6.1
Identities = 13/29 (44%), Positives = 15/29 (51%), Gaps = 4/29 (13%)
Query: 139 EDMLKTLWDSKYIGEKAVILVANKADLER 167
E + + L S K VIL ANK D ER
Sbjct: 136 EAVARVLRRSG----KPVILAANKVDDER 160
>gnl|CDD|206750 cd01857, HSR1_MMR1, A circularly permuted subfamily of the Ras
GTPases. Human HSR1 is localized to the human MHC class
I region and is highly homologous to a putative
GTP-binding protein, MMR1 from mouse. These proteins
represent a new subfamily of GTP-binding proteins that
has only eukaryote members. This subfamily shows a
circular permutation of the GTPase signature motifs so
that the C-terminal strands 5, 6, and 7 (strand 6
contains the G4 box with sequence NKXD) are relocated to
the N-terminus.
Length = 140
Score = 26.8 bits (60), Expect = 6.7
Identities = 16/57 (28%), Positives = 24/57 (42%), Gaps = 12/57 (21%)
Query: 149 KYIGE----KAVILVANKADLERRRQVTHSDGKKLAYAWGVKFV------ETSVGLV 195
KY+ E K +L+ NKADL Q + G+ + E ++GLV
Sbjct: 34 KYVKEVDPSKENVLLLNKADLVTEEQRKA--WARYFKKEGIVVLFFSALNEATIGLV 88
>gnl|CDD|217474 pfam03283, PAE, Pectinacetylesterase.
Length = 362
Score = 27.3 bits (61), Expect = 7.3
Identities = 15/94 (15%), Positives = 33/94 (35%), Gaps = 19/94 (20%)
Query: 43 ENFVQTYHHVFFIVHSDTNHTQRCLTSMP-----FCSQVENFVQT--------YHPDVFF 89
++ + Y V + +S+ N + C + F + +++T Y D +
Sbjct: 206 QSLRRFYSGVVGLQNSEKNLPESCTVKLNPTECFFPQYLIEYIKTPIFILNSAY--DSWQ 263
Query: 90 IVYS---DTNHTQRCLTPMPFCSQVE-NFVQTYH 119
I + C + CS + F+Q +
Sbjct: 264 IQNILAPPSGSWISCKLDLQPCSSSQLQFLQGFR 297
>gnl|CDD|219856 pfam08477, Miro, Miro-like protein. Mitochondrial Rho proteins
(Miro-1, and Miro-2), are atypical Rho GTPases. They
have a unique domain organisation, with tandem
GTP-binding domains and two EF hand domains (pfam00036),
that may bind calcium. They are also larger than
classical small GTPases. It has been proposed that they
are involved in mitochondrial homeostasis and apoptosis.
Length = 116
Score = 26.2 bits (58), Expect = 7.8
Identities = 13/44 (29%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 120 PDVFVIVYSVIERKTFKKAEDMLKTLWD-SKYIGEKAVILVANK 162
D ++VY + +R++ + ++ L + K G+ VILV NK
Sbjct: 72 ADAILLVYDLTDRESLNEVSRLIAWLPNLRKLGGKIPVILVGNK 115
>gnl|CDD|206752 cd01859, MJ1464, An uncharacterized, circularly permuted subfamily
of the Ras GTPases. This family represents archaeal
GTPase typified by the protein MJ1464 from Methanococcus
jannaschii. The members of this family show a circular
permutation of the GTPase signature motifs so that
C-terminal strands 5, 6, and 7 (strands 6 contain the
NKxD motif) are relocated to the N terminus.
Length = 157
Score = 26.5 bits (59), Expect = 8.5
Identities = 12/30 (40%), Positives = 15/30 (50%), Gaps = 7/30 (23%)
Query: 136 KKAEDMLKTLWDSKYIGEKAVILVANKADL 165
+K E M L K +I+V NKADL
Sbjct: 30 RKLERMALEL-------GKKLIIVLNKADL 52
>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 = 26.6 bits (60), Expect = 9.3
Identities = 8/14 (57%), Positives = 9/14 (64%)
Query: 153 EKAVILVANKADLE 166
EK I+V NK DL
Sbjct: 114 EKPRIVVLNKIDLL 127
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 27.2 bits (61), Expect = 9.4
Identities = 21/88 (23%), Positives = 34/88 (38%), Gaps = 15/88 (17%)
Query: 85 PDVFFIVYSDTN-------HTQRCLTPMPFCSQVENFVQTYHPDVFVIVYSVIERKTFKK 137
D ++ +DT H L F S +E + D+ + V + + +K
Sbjct: 237 GDGRKVLLTDTVGFIRDLPHP---LVEA-FKSTLE---EVKEADLLLHVVDASDPEILEK 289
Query: 138 AEDMLKTLWDSKYIGEKAVILVANKADL 165
E + L + E +ILV NK DL
Sbjct: 290 LEAVEDVLAEIG-ADEIPIILVLNKIDL 316
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
0.325 0.135 0.418
Gapped
Lambda K H
0.267 0.0830 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,294,542
Number of extensions: 1122144
Number of successful extensions: 1624
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1584
Number of HSP's successfully gapped: 106
Length of query: 250
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 155
Effective length of database: 6,723,972
Effective search space: 1042215660
Effective search space used: 1042215660
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 58 (25.9 bits)