RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9154
(115 letters)
>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 = 201 bits (512), Expect = 6e-68
Identities = 76/104 (73%), Positives = 87/104 (83%)
Query: 12 TYKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQE 71
TYKLVVVG GGVGKSA+TIQF Q FVTDYDPTIEDSY + E+D LD+LDTAGQE
Sbjct: 2 TYKLVVVGGGGVGKSALTIQFIQSYFVTDYDPTIEDSYTKQCEIDGQWARLDILDTAGQE 61
Query: 72 EFSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILRVKDK 115
EFSAMREQYMR G+GFLLV+SVTD+ S+E + F+TQILRVKD+
Sbjct: 62 EFSAMREQYMRTGEGFLLVFSVTDRGSFEEVDKFHTQILRVKDR 105
>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 = 196 bits (501), Expect = 3e-66
Identities = 73/105 (69%), Positives = 87/105 (82%)
Query: 11 TTYKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQ 70
YKLVV+G GGVGKSA+TIQF Q FV +YDPTIEDSY + E+D +C+LD+LDTAGQ
Sbjct: 1 REYKLVVLGGGGVGKSALTIQFVQGHFVDEYDPTIEDSYRKQIEIDGEVCLLDILDTAGQ 60
Query: 71 EEFSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILRVKDK 115
EEFSAMR+QYMR G+GFLLVYS+TD+QS+E I F QILRVKD+
Sbjct: 61 EEFSAMRDQYMRTGEGFLLVYSITDRQSFEEIAKFREQILRVKDR 105
>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 = 194 bits (495), Expect = 3e-65
Identities = 75/103 (72%), Positives = 88/103 (85%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQEE 72
YKLVV+G GGVGKSA+TIQF Q FV DYDPTIEDSY + E+D +C+LD+LDTAGQEE
Sbjct: 1 YKLVVLGSGGVGKSALTIQFIQGHFVDDYDPTIEDSYRKQIEIDGEVCLLDILDTAGQEE 60
Query: 73 FSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILRVKDK 115
FSAMR+QYMR G+GFLLVYS+TD+QS+E IK F QILRVKD+
Sbjct: 61 FSAMRDQYMRTGEGFLLVYSITDRQSFEEIKKFREQILRVKDR 103
>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 = 175 bits (446), Expect = 6e-58
Identities = 67/102 (65%), Positives = 81/102 (79%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQEEF 73
KLVV+G GGVGKSA+TI+F FV +YDPTIEDSY + VD LD+LDTAGQEEF
Sbjct: 1 KLVVLGAGGVGKSALTIRFVSGEFVEEYDPTIEDSYRKQIVVDGETYTLDILDTAGQEEF 60
Query: 74 SAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILRVKDK 115
SAMR+QY+R GDGF+LVYS+T ++S+E IK+ QILRVKDK
Sbjct: 61 SAMRDQYIRNGDGFILVYSITSRESFEEIKNIREQILRVKDK 102
>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 = 171 bits (435), Expect = 3e-56
Identities = 63/103 (61%), Positives = 80/103 (77%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQEE 72
YKLVVVG GGVGKSA+TIQ Q FV +YDPTIEDSY + +D C+LD+LDTAGQEE
Sbjct: 2 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEE 61
Query: 73 FSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILRVKDK 115
+SAMR+QYMR G+GFL V+++ ++S+E+I + QI RVKD
Sbjct: 62 YSAMRDQYMRTGEGFLCVFAINSRKSFEDIHTYREQIKRVKDS 104
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 161 bits (410), Expect = 4e-52
Identities = 70/105 (66%), Positives = 83/105 (79%)
Query: 11 TTYKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQ 70
T YKLVVVG GGVGKSA+TIQF Q F+ +YDPTIEDSY + +D+ C+LD+LDTAGQ
Sbjct: 4 TEYKLVVVGGGGVGKSALTIQFIQNHFIDEYDPTIEDSYRKQCVIDEETCLLDILDTAGQ 63
Query: 71 EEFSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILRVKDK 115
EE+SAMR+QYMR G GFL VYS+T + S+E I F QILRVKDK
Sbjct: 64 EEYSAMRDQYMRTGQGFLCVYSITSRSSFEEIASFREQILRVKDK 108
>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 = 152 bits (386), Expect = 1e-48
Identities = 52/103 (50%), Positives = 67/103 (65%), Gaps = 1/103 (0%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTI-EDSYLQHTEVDDVMCILDVLDTAGQEE 72
KLV+VGDGGVGKS++ I+F Q F +Y PTI D Y + EVD L + DTAGQE
Sbjct: 1 KLVLVGDGGVGKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAGQER 60
Query: 73 FSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILRVKDK 115
F A+R Y R GFLLVY +T + S+EN+K + +ILR D+
Sbjct: 61 FRALRPLYYRGAQGFLLVYDITSRDSFENVKKWLEEILRHADE 103
>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 = 147 bits (372), Expect = 3e-46
Identities = 59/101 (58%), Positives = 80/101 (79%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQEEF 73
KLVV+GDGGVGK+A+TIQ FV YDPTIEDSY + VD C+L+VLDTAGQEE+
Sbjct: 1 KLVVLGDGGVGKTALTIQLCLNHFVETYDPTIEDSYRKQVVVDGQPCMLEVLDTAGQEEY 60
Query: 74 SAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILRVKD 114
+A+R+Q++R+G+GF+LVYS+T + ++E ++ F QI RVKD
Sbjct: 61 TALRDQWIREGEGFILVYSITSRSTFERVERFREQIQRVKD 101
>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 = 140 bits (355), Expect = 4e-44
Identities = 62/102 (60%), Positives = 80/102 (78%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQEE 72
YKLVV+G GGVGKSA+T+QF Q +FV YDPTIEDSY + EVD C+L++LDTAG E+
Sbjct: 2 YKLVVLGSGGVGKSALTVQFVQGIFVDKYDPTIEDSYRKQIEVDCQQCMLEILDTAGTEQ 61
Query: 73 FSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILRVKD 114
F+AMR+ Y++ G GF LVYS+T QQS+ +++ QILRVKD
Sbjct: 62 FTAMRDLYIKNGQGFALVYSITAQQSFNDLQDLREQILRVKD 103
>gnl|CDD|133375 cd04175, Rap1, Rap1 family GTPase consists of Rap1a and Rap1b
isoforms. The Rap1 subgroup is part of the Rap
subfamily of the Ras family. It can be further divided
into the Rap1a and Rap1b isoforms. In humans, Rap1a and
Rap1b share 95% sequence homology, but are products of
two different genes located on chromosomes 1 and 12,
respectively. Rap1a is sometimes called smg p21 or Krev1
in the older literature. Rap1 proteins are believed to
perform different cellular functions, depending on the
isoform, its subcellular localization, and the effector
proteins it binds. For example, in rat salivary gland,
neutrophils, and platelets, Rap1 localizes to secretory
granules and is believed to regulate exocytosis or the
formation of secretory granules. Rap1 has also been
shown to localize in the Golgi of rat fibroblasts,
zymogen granules, plasma membrane, and the microsomal
membrane of pancreatic acini, as well as in the
endocytic compartment of skeletal muscle cells and
fibroblasts. High expression of Rap1 has been observed
in the nucleus of human oropharyngeal squamous cell
carcinomas (SCCs) and cell lines; interestingly, in the
SCCs, the active GTP-bound form localized to the
nucleus, while the inactive GDP-bound form localized to
the cytoplasm. Rap1 plays a role in phagocytosis by
controlling the binding of adhesion receptors (typically
integrins) to their ligands. In yeast, Rap1 has been
implicated in multiple functions, including activation
and silencing of transcription and maintenance of
telomeres. Rap1a, which is stimulated by T-cell receptor
(TCR) activation, is a positive regulator of T cells by
directing integrin activation and augmenting lymphocyte
responses. In murine hippocampal neurons, Rap1b
determines which neurite will become the axon and
directs the recruitment of Cdc42, which is required for
formation of dendrites and axons. In murine platelets,
Rap1b is required for normal homeostasis in vivo and is
involved in integrin activation. Most Ras proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 164
Score = 140 bits (355), Expect = 5e-44
Identities = 61/102 (59%), Positives = 80/102 (78%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQEE 72
YKLVV+G GGVGKSA+T+QF Q +FV YDPTIEDSY + EVD C+L++LDTAG E+
Sbjct: 2 YKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDGQQCMLEILDTAGTEQ 61
Query: 73 FSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILRVKD 114
F+AMR+ YM+ G GF+LVYS+T Q ++ +++ QILRVKD
Sbjct: 62 FTAMRDLYMKNGQGFVLVYSITAQSTFNDLQDLREQILRVKD 103
>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 = 137 bits (347), Expect = 9e-43
Identities = 58/102 (56%), Positives = 76/102 (74%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQEE 72
YK+VV+G GGVGKSA+T+QF Q +F+ YDPTIEDSY + E+D C L++LDTAG E+
Sbjct: 2 YKIVVLGAGGVGKSALTVQFVQNVFIESYDPTIEDSYRKQVEIDGRQCDLEILDTAGTEQ 61
Query: 73 FSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILRVKD 114
F+AMRE Y++ G GFLLVYSVT + S + Q+LR+KD
Sbjct: 62 FTAMRELYIKSGQGFLLVYSVTSEASLNELGELREQVLRIKD 103
>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 = 135 bits (342), Expect = 4e-42
Identities = 52/103 (50%), Positives = 75/103 (72%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQEE 72
+K+++VG GGVGKSA+T+QF FV DY+PT DSY + +D L++LDTAGQE+
Sbjct: 1 HKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEVQLNILDTAGQED 60
Query: 73 FSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILRVKDK 115
++A+R+ Y R G+GFLLV+S+TD +S+ + F QILRVK+
Sbjct: 61 YAAIRDNYFRSGEGFLLVFSITDMESFTALAEFREQILRVKED 103
>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 = 133 bits (337), Expect = 3e-41
Identities = 53/101 (52%), Positives = 73/101 (72%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQEE 72
YK+V++G GGVGKSA+T+QF F +DPTIED+Y +D+ +LD+LDTAGQ E
Sbjct: 3 YKIVMLGAGGVGKSAVTMQFISHSFPDYHDPTIEDAYKTQARIDNEPALLDILDTAGQAE 62
Query: 73 FSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILRVK 113
F+AMR+QYMR G+GF++ YSVTD+ S++ F I RV+
Sbjct: 63 FTAMRDQYMRCGEGFIICYSVTDRHSFQEASEFKELITRVR 103
>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 = 132 bits (333), Expect = 1e-40
Identities = 53/101 (52%), Positives = 77/101 (76%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQEE 72
YK+VV+G GGVGKSA+T+QF F+ YDPTIED Y + EVD +L++LDTAG E+
Sbjct: 2 YKVVVLGSGGVGKSALTVQFVSGTFIEKYDPTIEDFYRKEIEVDSSPSVLEILDTAGTEQ 61
Query: 73 FSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILRVK 113
F++MR+ Y++ G GF++VYS+ +QQ++++IK QI+RVK
Sbjct: 62 FASMRDLYIKNGQGFIVVYSLVNQQTFQDIKPMRDQIVRVK 102
>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 = 100 bits (253), Expect = 1e-28
Identities = 36/104 (34%), Positives = 59/104 (56%), Gaps = 1/104 (0%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHT-EVDDVMCILDVLDTAGQE 71
+K+V++GD GVGK+++ ++F F +Y TI + T EVD L + DTAGQE
Sbjct: 1 FKIVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGVDFKSKTIEVDGKKVKLQIWDTAGQE 60
Query: 72 EFSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILRVKDK 115
F ++ Y R G +LVY VT+++S+EN+ + ++
Sbjct: 61 RFRSITSSYYRGAHGAILVYDVTNRESFENLDKWLNELKEYAPP 104
>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 = 99.6 bits (249), Expect = 9e-28
Identities = 39/98 (39%), Positives = 64/98 (65%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQEEF 73
K+ V+G VGKS++T+QF + FV Y PTIE+++ + L+++DTAGQ+E+
Sbjct: 3 KIAVLGSRSVGKSSLTVQFVEGHFVESYYPTIENTFSKIITYKGQEYHLEIVDTAGQDEY 62
Query: 74 SAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILR 111
S + ++Y G++LVYSVT ++S+E +K Y +IL
Sbjct: 63 SILPQKYSIGIHGYILVYSVTSRKSFEVVKVIYDKILD 100
>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 = 97.7 bits (244), Expect = 4e-27
Identities = 37/102 (36%), Positives = 61/102 (59%), Gaps = 2/102 (1%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQEEF 73
K+ V+G GVGKSA+T++F K F+ +Y+P +E Y + +D L++ DT GQ++
Sbjct: 1 KIAVLGASGVGKSALTVRFLTKRFIGEYEPNLESLYSRQVTIDGEQVSLEIQDTPGQQQN 60
Query: 74 SA--MREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILRVK 113
E+ +R DGF+LVYS+TD+ S++ + I +K
Sbjct: 61 EDPESLERSLRWADGFVLVYSITDRSSFDVVSQLLQLIREIK 102
>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 = 94.5 bits (235), Expect = 7e-26
Identities = 43/101 (42%), Positives = 61/101 (60%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQEE 72
Y++VV G GGVGKS++ ++F + F Y PTIED+Y Q +C L + DT G +
Sbjct: 2 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCSKSICTLQITDTTGSHQ 61
Query: 73 FSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILRVK 113
F AM+ + KG F+LVYS+T +QS E +K Y I +K
Sbjct: 62 FPAMQRLSISKGHAFILVYSITSKQSLEELKPIYELICEIK 102
>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 = 90.7 bits (225), Expect = 4e-24
Identities = 40/100 (40%), Positives = 60/100 (60%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQEEF 73
+LV +G GVGK+A+ +F F + T+E+ + + EV V +D+LDT+G F
Sbjct: 1 RLVFMGAAGVGKTALIQRFLYDTFEPKHRRTVEELHSKEYEVAGVKVTIDILDTSGSYSF 60
Query: 74 SAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILRVK 113
AMR+ ++ GD F LVYSV D +S+E +K +IL VK
Sbjct: 61 PAMRKLSIQNGDAFALVYSVDDPESFEEVKRLREEILEVK 100
>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 = 87.6 bits (218), Expect = 3e-23
Identities = 40/92 (43%), Positives = 55/92 (59%), Gaps = 2/92 (2%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQEEF 73
K+VVVGDG VGK+ + I + F T+Y PT+ D+Y + VD L + DTAGQEE+
Sbjct: 2 KIVVVGDGAVGKTCLLISYTTNKFPTEYVPTVFDNYSANVTVDGKQVNLGLWDTAGQEEY 61
Query: 74 SAMRE-QYMRKGDGFLLVYSVTDQQSYENIKH 104
+R Y + D FLL +SV S+EN+K
Sbjct: 62 DRLRPLSYPQT-DVFLLCFSVDSPSSFENVKT 92
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 87.2 bits (217), Expect = 5e-23
Identities = 36/100 (36%), Positives = 59/100 (59%), Gaps = 1/100 (1%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHT-EVDDVMCILDVLDTAGQE 71
+K++++GD GVGKS++ +F F Y TI + T EVD L + DTAGQE
Sbjct: 1 FKIILIGDSGVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIEVDGKRVKLQIWDTAGQE 60
Query: 72 EFSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILR 111
F ++ Y R G LLVY +T+++S+EN++++ ++
Sbjct: 61 RFRSITSSYYRGAVGALLVYDITNRESFENLENWLKELRE 100
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 86.9 bits (215), Expect = 2e-22
Identities = 36/101 (35%), Positives = 56/101 (55%), Gaps = 1/101 (0%)
Query: 12 TYKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCI-LDVLDTAGQ 70
+K+VV+GDGGVGK+ + + F Y PTI + T I L + DTAGQ
Sbjct: 5 EFKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQ 64
Query: 71 EEFSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILR 111
EE+ ++R +Y R +G L+VY T ++S + + + + LR
Sbjct: 65 EEYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELR 105
>gnl|CDD|232886 TIGR00231, small_GTP, small GTP-binding protein domain. Proteins
with a small GTP-binding domain recognized by this model
include Ras, RhoA, Rab11, translation elongation factor
G, translation initiation factor IF-2, tetratcycline
resistance protein TetM, CDC42, Era, ADP-ribosylation
factors, tdhF, and many others. In some proteins the
domain occurs more than once.This model recognizes a
large number of small GTP-binding proteins and related
domains in larger proteins. Note that the alpha chains
of heterotrimeric G proteins are larger proteins in
which the NKXD motif is separated from the GxxxxGK[ST]
motif (P-loop) by a long insert and are not easily
detected by this model [Unknown function, General].
Length = 162
Score = 82.0 bits (203), Expect = 5e-21
Identities = 32/103 (31%), Positives = 51/103 (49%), Gaps = 3/103 (2%)
Query: 12 TYKLVVVGDGGVGKSAITIQF-FQKLFVTDYDPTIEDSYL-QHTEVDDVMCILDVLDTAG 69
K+V+VGD VGKS + + K+ +T+Y P +Y+ E D ++LDTAG
Sbjct: 1 EIKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAG 60
Query: 70 QEEFSAMREQYMRKGDGFLLVYSVTD-QQSYENIKHFYTQILR 111
QE++ A+R Y R + L V+ + E I T+ +
Sbjct: 61 QEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEII 103
>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 = 82.9 bits (205), Expect = 1e-20
Identities = 39/103 (37%), Positives = 59/103 (57%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQEE 72
Y++VV+G VGK+AI +F F Y PTIED + + + + LD+LDT+G
Sbjct: 1 YRMVVLGASKVGKTAIVSRFLGGRFEEQYTPTIEDFHRKLYSIRGEVYQLDILDTSGNHP 60
Query: 73 FSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILRVKDK 115
F AMR + GD F+LV+S+ +++S+E + QIL K
Sbjct: 61 FPAMRRLSILTGDVFILVFSLDNRESFEEVCRLREQILETKSC 103
>gnl|CDD|197554 smart00174, RHO, Rho (Ras homology) subfamily of Ras-like small
GTPases. Members of this subfamily of Ras-like small
GTPases include Cdc42 and Rac, as well as Rho isoforms.
Length = 174
Score = 81.1 bits (201), Expect = 1e-20
Identities = 37/90 (41%), Positives = 51/90 (56%)
Query: 15 LVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQEEFS 74
LVVVGDG VGK+ + I + F DY PT+ ++Y EVD L + DTAGQE++
Sbjct: 1 LVVVGDGAVGKTCLLIVYTTNAFPEDYVPTVFENYSADVEVDGKPVELGLWDTAGQEDYD 60
Query: 75 AMREQYMRKGDGFLLVYSVTDQQSYENIKH 104
+R D FL+ +SV S+EN+K
Sbjct: 61 RLRPLSYPDTDVFLICFSVDSPASFENVKE 90
>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 = 78.9 bits (195), Expect = 7e-20
Identities = 38/100 (38%), Positives = 58/100 (58%), Gaps = 1/100 (1%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIE-DSYLQHTEVDDVMCILDVLDTAGQE 71
+KL+++GD GVGKS + ++F + Y TI D ++ E+D L + DTAGQE
Sbjct: 3 FKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTVKLQIWDTAGQE 62
Query: 72 EFSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILR 111
F + Y R G ++VY VTDQ+S+ N+K + +I R
Sbjct: 63 RFRTITSSYYRGAHGIIIVYDVTDQESFNNVKQWLQEIDR 102
>gnl|CDD|133277 cd01875, RhoG, Ras homolog family, member G (RhoG) of small
guanosine triphosphatases (GTPases). RhoG is a GTPase
with high sequence similarity to members of the Rac
subfamily, including the regions involved in effector
recognition and binding. However, RhoG does not bind to
known Rac1 and Cdc42 effectors, including proteins
containing a Cdc42/Rac interacting binding (CRIB) motif.
Instead, RhoG interacts directly with Elmo, an upstream
regulator of Rac1, in a GTP-dependent manner and forms a
ternary complex with Dock180 to induce activation of
Rac1. The RhoG-Elmo-Dock180 pathway is required for
activation of Rac1 and cell spreading mediated by
integrin, as well as for neurite outgrowth induced by
nerve growth factor. Thus RhoG activates Rac1 through
Elmo and Dock180 to control cell morphology. RhoG has
also been shown to play a role in caveolar trafficking
and has a novel role in signaling the neutrophil
respiratory burst stimulated by G protein-coupled
receptor (GPCR) agonists. Most Rho proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Rho proteins.
Length = 191
Score = 76.6 bits (188), Expect = 1e-18
Identities = 36/93 (38%), Positives = 55/93 (59%)
Query: 12 TYKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQE 71
+ K VVVGDG VGK+ + I + F +Y PT+ D+Y T VD L++ DTAGQE
Sbjct: 3 SIKCVVVGDGAVGKTCLLICYTTNAFPKEYIPTVFDNYSAQTAVDGRTVSLNLWDTAGQE 62
Query: 72 EFSAMREQYMRKGDGFLLVYSVTDQQSYENIKH 104
E+ +R + + F++ +S+ SYEN++H
Sbjct: 63 EYDRLRTLSYPQTNVFIICFSIASPSSYENVRH 95
>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 = 75.5 bits (186), Expect = 2e-18
Identities = 34/91 (37%), Positives = 51/91 (56%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQEEF 73
K V+VGDG VGK+++ + + + T+Y PT D++ VD L + DTAGQ+EF
Sbjct: 2 KCVLVGDGAVGKTSLIVSYTTNGYPTEYVPTAFDNFSVVVLVDGKPVRLQLCDTAGQDEF 61
Query: 74 SAMREQYMRKGDGFLLVYSVTDQQSYENIKH 104
+R D FLL +SV + S++NI
Sbjct: 62 DKLRPLCYPDTDVFLLCFSVVNPSSFQNISE 92
>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 = 74.6 bits (184), Expect = 3e-18
Identities = 38/98 (38%), Positives = 59/98 (60%), Gaps = 1/98 (1%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIE-DSYLQHTEVDDVMCILDVLDTAGQE 71
+KL+++GD GVGKS + ++F + F + TI D ++ E+D L + DTAGQE
Sbjct: 4 FKLLLIGDSGVGKSCLLLRFSEDSFNPSFISTIGIDFKIRTIELDGKKIKLQIWDTAGQE 63
Query: 72 EFSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQI 109
F + Y R G +LVY +TD++S+ENIK++ I
Sbjct: 64 RFRTITTSYYRGAMGIILVYDITDEKSFENIKNWMRNI 101
>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 = 72.3 bits (178), Expect = 2e-17
Identities = 31/92 (33%), Positives = 56/92 (60%), Gaps = 1/92 (1%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHT-EVDDVMCILDVLDTAGQE 71
+K+V++G+G VGK+++ +++ + F ++ T + S+ Q T + L + DTAGQE
Sbjct: 1 FKVVLLGEGRVGKTSLVLRYVENKFNEKHESTTQASFFQKTVNIGGKRIDLAIWDTAGQE 60
Query: 72 EFSAMREQYMRKGDGFLLVYSVTDQQSYENIK 103
+ A+ Y R DG +LVY +TD S++ +K
Sbjct: 61 RYHALGPIYYRDADGAILVYDITDADSFQKVK 92
>gnl|CDD|206705 cd04133, Rop_like, Rho-related protein from plants (Rop)-like. The
Rop (Rho-related protein from plants) subfamily plays a
role in diverse cellular processes, including
cytoskeletal organization, pollen and vegetative cell
growth, hormone responses, stress responses, and
pathogen resistance. Rops are able to regulate several
downstream pathways to amplify a specific signal by
acting as master switches early in the signaling
cascade. They transmit a variety of extracellular and
intracellular signals. Rops are involved in establishing
cell polarity in root-hair development, root-hair
elongation, pollen-tube growth, cell-shape formation,
responses to hormones such as abscisic acid (ABA) and
auxin, responses to abiotic stresses such as oxygen
deprivation, and disease resistance and disease
susceptibility. An individual Rop can have a unique
function or an overlapping function shared with other
Rop proteins; in addition, a given Rop-regulated
function can be controlled by one or multiple Rop
proteins. For example, Rop1, Rop3, and Rop5 are all
involved in pollen-tube growth; Rop2 plays a role in
response to low-oxygen environments, cell-morphology,
and root-hair development; root-hair development is also
regulated by Rop4 and Rop6; Rop6 is also responsible for
ABA response, and ABA response is also regulated by
Rop10. Plants retain some of the regulatory mechanisms
that are shared by other members of the Rho family, but
have also developed a number of unique modes for
regulating Rops. Unique RhoGEFs have been identified
that are exclusively active toward Rop proteins, such as
those containing the domain PRONE (plant-specific Rop
nucleotide exchanger). Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 173
Score = 72.6 bits (178), Expect = 3e-17
Identities = 37/89 (41%), Positives = 53/89 (59%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQEEF 73
K V VGDG VGK+ + I + F TDY PT+ D++ + VD L + DTAGQE++
Sbjct: 3 KCVTVGDGAVGKTCMLISYTSNTFPTDYVPTVFDNFSANVVVDGNTVNLGLWDTAGQEDY 62
Query: 74 SAMREQYMRKGDGFLLVYSVTDQQSYENI 102
+ +R R D FLL +S+ + SYEN+
Sbjct: 63 NRLRPLSYRGADVFLLAFSLISKASYENV 91
>gnl|CDD|206664 cd01874, Cdc42, cell division cycle 42 (Cdc42) is a small GTPase of
the Rho family. Cdc42 is an essential GTPase that
belongs to the Rho family of Ras-like GTPases. These
proteins act as molecular switches by responding to
exogenous and/or endogenous signals and relaying those
signals to activate downstream components of a
biological pathway. Cdc42 transduces signals to the
actin cytoskeleton to initiate and maintain polarized
growth and to mitogen-activated protein morphogenesis.
In the budding yeast Saccharomyces cerevisiae, Cdc42
plays an important role in multiple actin-dependent
morphogenetic events such as bud emergence,
mating-projection formation, and pseudohyphal growth. In
mammalian cells, Cdc42 regulates a variety of
actin-dependent events and induces the JNK/SAPK protein
kinase cascade, which leads to the activation of
transcription factors within the nucleus. Cdc42 mediates
these processes through interactions with a myriad of
downstream effectors, whose number and regulation we are
just starting to understand. In addition, Cdc42 has been
implicated in a number of human diseases through
interactions with its regulators and downstream
effectors. Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 175
Score = 71.4 bits (175), Expect = 7e-17
Identities = 35/92 (38%), Positives = 52/92 (56%)
Query: 12 TYKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQE 71
T K VVVGDG VGK+ + I + F ++Y PT+ D+Y + L + DTAGQE
Sbjct: 1 TIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTLGLFDTAGQE 60
Query: 72 EFSAMREQYMRKGDGFLLVYSVTDQQSYENIK 103
++ +R + D FL+ +SV S+EN+K
Sbjct: 61 DYDRLRPLSYPQTDVFLVCFSVVSPSSFENVK 92
>gnl|CDD|206643 cd00877, Ran, Ras-related nuclear proteins (Ran)/TC4 family of
small GTPases. Ran GTPase is involved in diverse
biological functions, such as nuclear transport, spindle
formation during mitosis, DNA replication, and cell
division. Among the Ras superfamily, Ran is a unique
small G protein. It does not have a lipid modification
motif at the C-terminus to bind to the membrane, which
is often observed within the Ras superfamily. Ran may
therefore interact with a wide range of proteins in
various intracellular locations. Like other GTPases, Ran
exists in GTP- and GDP-bound conformations that interact
differently with effectors. Conversion between these
forms and the assembly or disassembly of effector
complexes requires the interaction of regulator
proteins. The intrinsic GTPase activity of Ran is very
low, but it is greatly stimulated by a GTPase-activating
protein (RanGAP1) located in the cytoplasm. By contrast,
RCC1, a guanine nucleotide exchange factor that
generates RanGTP, is bound to chromatin and confined to
the nucleus. Ran itself is mobile and is actively
imported into the nucleus by a mechanism involving
NTF-2. Together with the compartmentalization of its
regulators, this is thought to produce a relatively high
concentration of RanGTP in the nucleus.
Length = 166
Score = 70.4 bits (173), Expect = 2e-16
Identities = 34/103 (33%), Positives = 58/103 (56%), Gaps = 5/103 (4%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTI--EDSYLQ-HTEVDDVMCILDVLDTAG 69
+KLV+VGDGG GK+ + F Y T+ E L HT + +V DTAG
Sbjct: 1 FKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLDFHTNRGKI--RFNVWDTAG 58
Query: 70 QEEFSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILRV 112
QE+F +R+ Y +G ++++ VT + +Y+N+ +++ ++RV
Sbjct: 59 QEKFGGLRDGYYIQGQCAIIMFDVTSRVTYKNVPNWHRDLVRV 101
>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 = 69.4 bits (170), Expect = 4e-16
Identities = 37/93 (39%), Positives = 56/93 (60%), Gaps = 3/93 (3%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHT---EVDDVMCILDVLDTAGQ 70
K++VVG+G VGKS++ +F + +F DY TI +L+ D L + DTAGQ
Sbjct: 2 KVIVVGNGNVGKSSMIQRFVKGIFTKDYKKTIGVDFLEKQIFLRQSDEDVRLMLWDTAGQ 61
Query: 71 EEFSAMREQYMRKGDGFLLVYSVTDQQSYENIK 103
EEF A+ + Y R +LV+S TD++S+E I+
Sbjct: 62 EEFDAITKAYYRGAQACILVFSTTDRESFEAIE 94
>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 = 67.8 bits (166), Expect = 5e-16
Identities = 29/97 (29%), Positives = 47/97 (48%), Gaps = 1/97 (1%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSY-LQHTEVDDVMCILDVLDTAGQEE 72
K+VV+GD G GKS++ Q F + D+ + EVD +L++ D G+EE
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREE 60
Query: 73 FSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQI 109
+M+ D LLVY +TD++S + +
Sbjct: 61 LKFEHIIFMKWADAILLVYDLTDRESLNEVSRLIAWL 97
>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 = 69.7 bits (171), Expect = 6e-16
Identities = 31/89 (34%), Positives = 53/89 (59%), Gaps = 1/89 (1%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVT-DYDPTIEDSYLQHTEVDDVMCILDVLDTAGQE 71
Y++V++GD GVGKS++ F ++ Y+ + +D+Y + VD L V D QE
Sbjct: 1 YRVVLLGDSGVGKSSLANIFTAGVYEDSAYEASGDDTYERTVSVDGEEATLVVYDHWEQE 60
Query: 72 EFSAMREQYMRKGDGFLLVYSVTDQQSYE 100
+ + + M+ GD +++VYSVTD+ S+E
Sbjct: 61 DGMWLEDSCMQVGDAYVIVYSVTDRSSFE 89
>gnl|CDD|206697 cd04116, Rab9, Rab GTPase family 9 (Rab9). Rab9 is found in late
endosomes, together with mannose 6-phosphate receptors
(MPRs) and the tail-interacting protein of 47 kD
(TIP47). Rab9 is a key mediator of vesicular transport
from late endosomes to the trans-Golgi network (TGN) by
redirecting the MPRs. Rab9 has been identified as a key
component for the replication of several viruses,
including HIV1, Ebola, Marburg, and measles, making it a
potential target for inhibiting a variety of viruses.
GTPase activating proteins (GAPs) interact with
GTP-bound Rab and accelerate the hydrolysis of GTP to
GDP. Guanine nucleotide exchange factors (GEFs) interact
with GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 170
Score = 68.0 bits (166), Expect = 2e-15
Identities = 37/102 (36%), Positives = 59/102 (57%), Gaps = 1/102 (0%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYL-QHTEVDDVMCILDVLDTAGQEE 72
K++++GDGGVGKS++ ++ F T TI +L + EVD L + DTAGQE
Sbjct: 7 KVILLGDGGVGKSSLMNRYVTNKFDTQLFHTIGVEFLNKDLEVDGHFVTLQIWDTAGQER 66
Query: 73 FSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILRVKD 114
F ++R + R D LL +SV D QS++N+ ++ + + D
Sbjct: 67 FRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYAD 108
>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 = 67.7 bits (166), Expect = 2e-15
Identities = 33/92 (35%), Positives = 51/92 (55%), Gaps = 1/92 (1%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIE-DSYLQHTEVDDVMCILDVLDTAGQE 71
K++++GD GVGKS++ ++F F D TI D ++ VD L + DTAGQE
Sbjct: 1 LKILLIGDSGVGKSSLLLRFTDDTFDEDLSSTIGVDFKVKTVTVDGKKVKLAIWDTAGQE 60
Query: 72 EFSAMREQYMRKGDGFLLVYSVTDQQSYENIK 103
F + Y R G +LVY VT + +++N+
Sbjct: 61 RFRTLTSSYYRGAQGVILVYDVTRRDTFDNLD 92
>gnl|CDD|206655 cd01862, Rab7, Rab GTPase family 7 (Rab7). Rab7 subfamily. Rab7 is
a small Rab GTPase that regulates vesicular traffic from
early to late endosomal stages of the endocytic pathway.
The yeast Ypt7 and mammalian Rab7 are both involved in
transport to the vacuole/lysosome, whereas Ypt7 is also
required for homotypic vacuole fusion. Mammalian Rab7 is
an essential participant in the autophagic pathway for
sequestration and targeting of cytoplasmic components to
the lytic compartment. Mammalian Rab7 is also proposed
to function as a tumor suppressor. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 172
Score = 67.7 bits (166), Expect = 2e-15
Identities = 34/91 (37%), Positives = 55/91 (60%), Gaps = 1/91 (1%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYL-QHTEVDDVMCILDVLDTAGQE 71
K++++GD GVGK+++ Q+ K F Y TI +L + VDD + L + DTAGQE
Sbjct: 1 LKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVTVDDRLVTLQIWDTAGQE 60
Query: 72 EFSAMREQYMRKGDGFLLVYSVTDQQSYENI 102
F ++ + R D +LVY VT+ +S+E++
Sbjct: 61 RFQSLGVAFYRGADCCVLVYDVTNPKSFESL 91
>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 = 67.1 bits (164), Expect = 3e-15
Identities = 34/90 (37%), Positives = 52/90 (57%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQEEF 73
K VVVGDG VGK+ + I + F +Y PT+ D+Y + VD L + DTAGQE++
Sbjct: 3 KCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDY 62
Query: 74 SAMREQYMRKGDGFLLVYSVTDQQSYENIK 103
+R + D FL+ +S+ S+EN++
Sbjct: 63 DRLRPLSYPQTDVFLICFSLVSPASFENVR 92
>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 = 66.6 bits (163), Expect = 8e-15
Identities = 33/91 (36%), Positives = 54/91 (59%), Gaps = 1/91 (1%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCI-LDVLDTAGQEE 72
K+VVVGDGG GK+ + + + Q F +Y PT+ ++Y+ +V + I L + DTAGQE+
Sbjct: 5 KIVVVGDGGCGKTCLLMVYAQGSFPEEYVPTVFENYVTTLQVPNGKIIELALWDTAGQED 64
Query: 73 FSAMREQYMRKGDGFLLVYSVTDQQSYENIK 103
+ +R D L+ YSV + S +N++
Sbjct: 65 YDRLRPLSYPDVDVILICYSVDNPTSLDNVE 95
>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 = 65.6 bits (160), Expect = 1e-14
Identities = 35/96 (36%), Positives = 53/96 (55%), Gaps = 1/96 (1%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHT-EVDDVMCILDVLDTAGQE 71
+K +++GD GVGKS + QF +K F+ D TI + EV+ L + DTAGQE
Sbjct: 3 FKYIIIGDMGVGKSCLLHQFTEKKFMADCPHTIGVEFGTRIIEVNGQKIKLQIWDTAGQE 62
Query: 72 EFSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYT 107
F A+ Y R G L+VY +T + +Y ++ + T
Sbjct: 63 RFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLT 98
>gnl|CDD|206707 cd04135, Tc10, Rho GTPase TC10 (Tc10). TC10 is a Rho family
protein that has been shown to induce microspike
formation and neurite outgrowth in vitro. Its expression
changes dramatically after peripheral nerve injury,
suggesting an important role in promoting axonal
outgrowth and regeneration. TC10 regulates translocation
of insulin-stimulated GLUT4 in adipocytes and has also
been shown to bind directly to Golgi COPI coat proteins.
GTP-bound TC10 in vitro can bind numerous potential
effectors. Depending on its subcellular localization and
distinct functional domains, TC10 can differentially
regulate two types of filamentous actin in adipocytes.
TC10 mRNAs are highly expressed in three types of mouse
muscle tissues: leg skeletal muscle, cardiac muscle, and
uterus; they were also present in brain, with higher
levels in adults than in newborns. TC10 has also been
shown to play a role in regulating the expression of
cystic fibrosis transmembrane conductance regulator
(CFTR) through interactions with CFTR-associated ligand
(CAL). The GTP-bound form of TC10 directs the
trafficking of CFTR from the juxtanuclear region to the
secretory pathway toward the plasma membrane, away from
CAL-mediated DFTR degradation in the lysosome. Most Rho
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 174
Score = 65.4 bits (159), Expect = 2e-14
Identities = 34/98 (34%), Positives = 53/98 (54%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQEEF 73
K VVVGDG VGK+ + + + F +Y PT+ D Y V +L + DTAGQE++
Sbjct: 2 KCVVVGDGAVGKTCLLMSYANDAFPEEYVPTVFDHYAVSVTVGGKQYLLGLYDTAGQEDY 61
Query: 74 SAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILR 111
+R D FL+ +SV + S++N+K + L+
Sbjct: 62 DRLRPLSYPMTDVFLICFSVVNPASFQNVKEEWVPELK 99
>gnl|CDD|206654 cd01861, Rab6, Rab GTPase family 6 (Rab6). Rab6 is involved in
microtubule-dependent transport pathways through the
Golgi and from endosomes to the Golgi. Rab6A of mammals
is implicated in retrograde transport through the Golgi
stack, and is also required for a slow,
COPI-independent, retrograde transport pathway from the
Golgi to the endoplasmic reticulum (ER). This pathway
may allow Golgi residents to be recycled through the ER
for scrutiny by ER quality-control systems. Yeast Ypt6p,
the homolog of the mammalian Rab6 GTPase, is not
essential for cell viability. Ypt6p acts in
endosome-to-Golgi, in intra-Golgi retrograde transport,
and possibly also in Golgi-to-ER trafficking. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 161
Score = 64.6 bits (158), Expect = 2e-14
Identities = 35/95 (36%), Positives = 53/95 (55%), Gaps = 1/95 (1%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHT-EVDDVMCILDVLDTAGQE 71
+KLV +GD VGK++I +F F Y TI +L T VDD L + DTAGQE
Sbjct: 1 HKLVFLGDQSVGKTSIITRFMYDTFDNQYQATIGIDFLSKTMYVDDKTVRLQLWDTAGQE 60
Query: 72 EFSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFY 106
F ++ Y+R ++VY +T++QS++N +
Sbjct: 61 RFRSLIPSYIRDSSVAVVVYDITNRQSFDNTDKWI 95
>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 = 64.6 bits (157), Expect = 2e-14
Identities = 31/91 (34%), Positives = 56/91 (61%), Gaps = 1/91 (1%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIE-DSYLQHTEVDDVMCILDVLDTAGQE 71
++L+++GD GVGK+ + +F F + + TI D ++ EVD + + + DTAGQE
Sbjct: 1 FRLLLIGDSGVGKTCLLCRFTDNEFHSSHISTIGVDFKMKTIEVDGIKVRIQIWDTAGQE 60
Query: 72 EFSAMREQYMRKGDGFLLVYSVTDQQSYENI 102
+ + +QY R+ G LVY ++ ++SY++I
Sbjct: 61 RYQTITKQYYRRAQGIFLVYDISSERSYQHI 91
>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 = 65.3 bits (159), Expect = 2e-14
Identities = 35/98 (35%), Positives = 57/98 (58%), Gaps = 1/98 (1%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIE-DSYLQHTEVDDVMCILDVLDTAGQE 71
+KL+++GD GVGKS++ ++F F Y TI D ++ E++ L + DTAGQE
Sbjct: 7 FKLLIIGDSGVGKSSLLLRFADNTFSGSYITTIGVDFKIRTVEINGERVKLQIWDTAGQE 66
Query: 72 EFSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQI 109
F + Y R G ++VY VT+ +S+ N+K + +I
Sbjct: 67 RFRTITSTYYRGTHGVIVVYDVTNGESFVNVKRWLQEI 104
>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 = 64.5 bits (158), Expect = 3e-14
Identities = 33/92 (35%), Positives = 52/92 (56%), Gaps = 3/92 (3%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTI--EDSYLQHTEVDDVMCILDVLDTAGQ 70
+K+V++GD GVGKS + +F + F D TI E + + ++D + DTAGQ
Sbjct: 4 FKIVLIGDSGVGKSNLLSRFTRNEFNLDSKSTIGVEFAT-RTIQIDGKTIKAQIWDTAGQ 62
Query: 71 EEFSAMREQYMRKGDGFLLVYSVTDQQSYENI 102
E + A+ Y R G LLVY +T + ++EN+
Sbjct: 63 ERYRAITSAYYRGAVGALLVYDITKKSTFENV 94
>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 = 64.8 bits (158), Expect = 3e-14
Identities = 32/91 (35%), Positives = 51/91 (56%), Gaps = 1/91 (1%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHT-EVDDVMCILDVLDTAGQE 71
+K +++GD GVGKS + +QF K F +D TI + +D L + DTAGQE
Sbjct: 5 FKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQE 64
Query: 72 EFSAMREQYMRKGDGFLLVYSVTDQQSYENI 102
F ++ Y R G LLVY +T ++++ ++
Sbjct: 65 SFRSITRSYYRGAAGALLVYDITRRETFNHL 95
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 65.1 bits (158), Expect = 4e-14
Identities = 33/98 (33%), Positives = 54/98 (55%), Gaps = 2/98 (2%)
Query: 12 TYKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIE-DSYLQHTEVDDVMCILDVLDTAGQ 70
++K++++GD GVGKS++ + F V D PTI D ++ V L + DTAGQ
Sbjct: 14 SFKILLIGDSGVGKSSLLVSFISS-SVEDLAPTIGVDFKIKQLTVGGKRLKLTIWDTAGQ 72
Query: 71 EEFSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQ 108
E F + Y R G +LVY VT ++++ N+ + +
Sbjct: 73 ERFRTLTSSYYRNAQGIILVYDVTRRETFTNLSDVWGK 110
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 64.7 bits (158), Expect = 6e-14
Identities = 36/109 (33%), Positives = 63/109 (57%), Gaps = 5/109 (4%)
Query: 7 NNNITTYKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTI--EDSYLQ-HTEVDDVMCILD 63
+ + +KL++VGDGGVGK+ + F Y PT+ E L+ +T + +
Sbjct: 4 MDEVPEFKLILVGDGGVGKTTFVKRHLTGEFEKKYIPTLGVEVHPLKFYTNCGPI--CFN 61
Query: 64 VLDTAGQEEFSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILRV 112
V DTAGQE+F +R+ Y KG ++++ VT + +Y+N+ +++ I+RV
Sbjct: 62 VWDTAGQEKFGGLRDGYYIKGQCAIIMFDVTSRITYKNVPNWHRDIVRV 110
>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 = 64.0 bits (156), Expect = 8e-14
Identities = 31/104 (29%), Positives = 57/104 (54%), Gaps = 2/104 (1%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIE-DSYLQHTEVDDVMCI-LDVLDTAGQ 70
K+VV+GDG GK+++ +F Q+ F Y TI D + + + + + L V D GQ
Sbjct: 1 IKIVVLGDGASGKTSLIRRFAQEGFGKSYKQTIGLDFFSRRITLPGSLNVTLQVWDIGGQ 60
Query: 71 EEFSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILRVKD 114
+ M ++Y+ LVY +T+ QS+EN++ + + + +V +
Sbjct: 61 QIGGKMLDKYIYGAQAVCLVYDITNSQSFENLEDWLSVVKKVNE 104
>gnl|CDD|206662 cd01870, RhoA_like, Ras homology family A (RhoA)-like includes
RhoA, RhoB and RhoC. The RhoA subfamily consists of
RhoA, RhoB, and RhoC. RhoA promotes the formation of
stress fibers and focal adhesions, regulating cell
shape, attachment, and motility. RhoA can bind to
multiple effector proteins, thereby triggering different
downstream responses. In many cell types, RhoA mediates
local assembly of the contractile ring, which is
necessary for cytokinesis. RhoA is vital for muscle
contraction; in vascular smooth muscle cells, RhoA plays
a key role in cell contraction, differentiation,
migration, and proliferation. RhoA activities appear to
be elaborately regulated in a time- and space-dependent
manner to control cytoskeletal changes. Most Rho
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. RhoA and RhoC are observed
only in geranylgeranylated forms; however, RhoB can be
present in palmitoylated, farnesylated, and
geranylgeranylated forms. RhoA and RhoC are highly
relevant for tumor progression and invasiveness;
however, RhoB has recently been suggested to be a tumor
suppressor. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 175
Score = 63.6 bits (155), Expect = 8e-14
Identities = 37/100 (37%), Positives = 52/100 (52%), Gaps = 8/100 (8%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQEEF 73
KLV+VGDG GK+ + I F + F Y PT+ ++Y+ EVD L + DTAGQE++
Sbjct: 3 KLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDY 62
Query: 74 SAMREQYMRKGDGFLLVYSVTDQQSYENI--------KHF 105
+R D L+ +S+ S ENI KHF
Sbjct: 63 DRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHF 102
>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 = 64.0 bits (156), Expect = 9e-14
Identities = 33/96 (34%), Positives = 59/96 (61%), Gaps = 2/96 (2%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIE-DSYLQHTEVDDVMCI-LDVLDTAGQ 70
++L+V+GD VGKS++ +F + F DPT+ D + + E++ + I L + DTAGQ
Sbjct: 3 FRLIVIGDSTVGKSSLLKRFTEGRFAEVSDPTVGVDFFSRLIEIEPGVRIKLQLWDTAGQ 62
Query: 71 EEFSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFY 106
E F ++ Y R G LLV+ +T+++S+E++ +
Sbjct: 63 ERFRSITRSYYRNSVGVLLVFDITNRESFEHVHDWL 98
>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 = 62.8 bits (153), Expect = 1e-13
Identities = 31/96 (32%), Positives = 49/96 (51%), Gaps = 1/96 (1%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHT-EVDDVMCILDVLDTAGQE 71
+K +++G G GKS + QF + F D + TI + V L + DTAGQE
Sbjct: 1 FKFLIIGSAGTGKSCLLHQFIENKFKQDSNHTIGVEFGSRVVNVGGKSVKLQIWDTAGQE 60
Query: 72 EFSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYT 107
F ++ Y R G LLVY +T ++S+ + ++ T
Sbjct: 61 RFRSVTRSYYRGAAGALLVYDITSRESFNALTNWLT 96
>gnl|CDD|206706 cd04134, Rho3, Ras homology family 3 (Rho3) of small guanosine
triphosphatases (GTPases). Rho3 is a member of the Rho
family found only in fungi. Rho3 is believed to regulate
cell polarity by interacting with the diaphanous/formin
family protein For3 to control both the actin
cytoskeleton and microtubules. Rho3 is also believed to
have a direct role in exocytosis that is independent of
its role in regulating actin polarity. The function in
exocytosis may be two-pronged: first, in the transport
of post-Golgi vesicles from the mother cell to the bud,
mediated by myosin (Myo2); second, in the docking and
fusion of vesicles to the plasma membrane, mediated by
an exocyst (Exo70) protein. Most Rho proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Rho proteins.
Length = 185
Score = 63.0 bits (153), Expect = 1e-13
Identities = 32/89 (35%), Positives = 50/89 (56%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQEEF 73
K+VV+GDG GK+++ F + F Y+PT+ ++Y+ VD + L + DTAGQEEF
Sbjct: 2 KVVVLGDGACGKTSLLNVFTRGYFPQVYEPTVFENYIHDIFVDGLAVELSLWDTAGQEEF 61
Query: 74 SAMREQYMRKGDGFLLVYSVTDQQSYENI 102
+R +L +SV + S EN+
Sbjct: 62 DRLRSLSYADTHVIMLCFSVDNPDSLENV 90
>gnl|CDD|206702 cd04129, Rho2, Ras homology family 2 (Rho2) of small guanosine
triphosphatases (GTPases). Rho2 is a fungal GTPase that
plays a role in cell morphogenesis, control of cell wall
integrity, control of growth polarity, and maintenance
of growth direction. Rho2 activates the protein kinase C
homolog Pck2, and Pck2 controls Mok1, the major (1-3)
alpha-D-glucan synthase. Together with Rho1 (RhoA), Rho2
regulates the construction of the cell wall. Unlike
Rho1, Rho2 is not an essential protein, but its
overexpression is lethal. Most Rho proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for proper intracellular localization via
membrane attachment. As with other Rho family GTPases,
the GDP/GTP cycling is regulated by GEFs (guanine
nucleotide exchange factors), GAPs (GTPase-activating
proteins) and GDIs (guanine nucleotide dissociation
inhibitors).
Length = 190
Score = 62.9 bits (153), Expect = 2e-13
Identities = 31/90 (34%), Positives = 49/90 (54%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQEEF 73
KLV+VGDG GK+++ F F +Y PT+ ++Y+ VD L + DTAGQEE+
Sbjct: 3 KLVIVGDGACGKTSLLYVFTLGEFPEEYHPTVFENYVTDCRVDGKPVQLALWDTAGQEEY 62
Query: 74 SAMREQYMRKGDGFLLVYSVTDQQSYENIK 103
+R K L+ +++ S EN++
Sbjct: 63 ERLRPLSYSKAHVILIGFAIDTPDSLENVR 92
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 63.4 bits (154), Expect = 2e-13
Identities = 33/92 (35%), Positives = 53/92 (57%), Gaps = 1/92 (1%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHT-EVDDVMCILDVLDTAGQE 71
+K+V++GD GVGKS I +F + F + TI + T +V+ + DTAGQE
Sbjct: 13 FKIVLIGDSGVGKSNILSRFTRNEFCLESKSTIGVEFATRTLQVEGKTVKAQIWDTAGQE 72
Query: 72 EFSAMREQYMRKGDGFLLVYSVTDQQSYENIK 103
+ A+ Y R G LLVY +T +Q+++N++
Sbjct: 73 RYRAITSAYYRGAVGALLVYDITKRQTFDNVQ 104
>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 = 62.1 bits (151), Expect = 2e-13
Identities = 28/94 (29%), Positives = 51/94 (54%), Gaps = 1/94 (1%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIE-DSYLQHTEVDDVMCILDVLDTAGQE 71
+K++++GD VGK+ + +F F TI D ++ E+ L + DTAGQE
Sbjct: 4 FKIILIGDSNVGKTCVVQRFKSGTFSERQGNTIGVDFTMKTLEIQGKRVKLQIWDTAGQE 63
Query: 72 EFSAMREQYMRKGDGFLLVYSVTDQQSYENIKHF 105
F + + Y R +G ++ Y +T + S+E++ H+
Sbjct: 64 RFRTITQSYYRSANGAIIAYDITRRSSFESVPHW 97
>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 = 61.8 bits (151), Expect = 3e-13
Identities = 32/94 (34%), Positives = 55/94 (58%), Gaps = 1/94 (1%)
Query: 12 TYKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHT-EVDDVMCILDVLDTAGQ 70
+KLV++GD VGKS+I ++F + F + + TI ++L T +DD ++ DTAGQ
Sbjct: 1 QFKLVLLGDSSVGKSSIVLRFVKNEFSENQESTIGAAFLTQTVNLDDTTVKFEIWDTAGQ 60
Query: 71 EEFSAMREQYMRKGDGFLLVYSVTDQQSYENIKH 104
E + ++ Y R ++VY +T ++S+E K
Sbjct: 61 ERYRSLAPMYYRGAAAAIVVYDITSEESFEKAKS 94
>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 = 62.2 bits (151), Expect = 3e-13
Identities = 35/105 (33%), Positives = 58/105 (55%), Gaps = 2/105 (1%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVT-DYDPTIEDSYLQHT-EVDDVMCILDVLDTAGQ 70
+K+++VGD GVGK+ + ++F F+ + T+ + VD V L + DTAGQ
Sbjct: 1 FKVMLVGDSGVGKTCLLVRFKDGAFLAGSFIATVGIQFTNKVVTVDGVKVKLQIWDTAGQ 60
Query: 71 EEFSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILRVKDK 115
E F ++ Y R LL+Y VT++ S++NI+ + T+IL
Sbjct: 61 ERFRSVTHAYYRDAHALLLLYDVTNKSSFDNIRAWLTEILEYAQS 105
>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 = 61.3 bits (149), Expect = 5e-13
Identities = 33/109 (30%), Positives = 46/109 (42%), Gaps = 11/109 (10%)
Query: 16 VVVGDGGVGKSAITIQFFQKLFV---TDYDPTI-EDSYLQHTEVDDVMCILDVLDTAGQE 71
VVVG GGVGKS++ T D Y E+D L ++DT G +
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVY--VKELDKGKVKLVLVDTPGLD 58
Query: 72 EFSAMRE-----QYMRKGDGFLLVYSVTDQQSYENIKHFYTQILRVKDK 115
EF + +R D LLV TD++S E+ K + LR +
Sbjct: 59 EFGGLGREELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLRKEGI 107
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 61.9 bits (150), Expect = 5e-13
Identities = 32/91 (35%), Positives = 53/91 (58%), Gaps = 1/91 (1%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSY-LQHTEVDDVMCILDVLDTAGQE 71
+K +++GD GVGKS + +QF K F +D TI + + +D+ L + DTAGQE
Sbjct: 7 FKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDNKPIKLQIWDTAGQE 66
Query: 72 EFSAMREQYMRKGDGFLLVYSVTDQQSYENI 102
F ++ Y R G LLVY +T ++++ ++
Sbjct: 67 SFRSITRSYYRGAAGALLVYDITRRETFNHL 97
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 60.9 bits (148), Expect = 1e-12
Identities = 38/117 (32%), Positives = 60/117 (51%), Gaps = 8/117 (6%)
Query: 1 MAKAPN--NNNITTYKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTI--EDSYLQ-HTEV 55
MA PN + ++KLV+VGDGG GK+ + F Y+PTI E L T
Sbjct: 1 MA-LPNQQTVDYPSFKLVIVGDGGTGKTTFVKRHLTGEFEKKYEPTIGVEVHPLDFFTNC 59
Query: 56 DDVMCILDVLDTAGQEEFSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILRV 112
+ DTAGQE+F +R+ Y G ++++ VT + +Y+N+ ++ + RV
Sbjct: 60 GKI--RFYCWDTAGQEKFGGLRDGYYIHGQCAIIMFDVTARLTYKNVPTWHRDLCRV 114
>gnl|CDD|133314 cd04114, Rab30, Rab GTPase family 30 (Rab30). Rab30 subfamily.
Rab30 appears to be associated with the Golgi stack. It
is expressed in a wide variety of tissue types and in
humans maps to chromosome 11. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 169
Score = 59.5 bits (144), Expect = 2e-12
Identities = 30/98 (30%), Positives = 54/98 (55%), Gaps = 1/98 (1%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIE-DSYLQHTEVDDVMCILDVLDTAGQE 71
+K+V++G+ GVGK+ + +F Q LF TI D ++ E+ L + DTAGQE
Sbjct: 8 FKIVLIGNAGVGKTCLVRRFTQGLFPPGQGATIGVDFMIKTVEIKGEKIKLQIWDTAGQE 67
Query: 72 EFSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQI 109
F ++ + Y R + +L Y +T ++S+ + + +I
Sbjct: 68 RFRSITQSYYRSANALILTYDITCEESFRCLPEWLREI 105
>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 = 58.9 bits (143), Expect = 4e-12
Identities = 31/90 (34%), Positives = 53/90 (58%), Gaps = 1/90 (1%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSY-LQHTEVDDVMCILDVLDTAGQEE 72
K++ +G+ GVGKS I ++ + FV+ Y PTI Y ++ V + ++ D +G E
Sbjct: 2 KVISMGNSGVGKSCIIKRYCEGRFVSKYLPTIGIDYGVKKVSVRNKEVRVNFFDLSGHPE 61
Query: 73 FSAMREQYMRKGDGFLLVYSVTDQQSYENI 102
+ +R ++ + G LLVY VTD+QS+E +
Sbjct: 62 YLEVRNEFYKDTQGVLLVYDVTDRQSFEAL 91
>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 = 57.1 bits (138), Expect = 2e-11
Identities = 30/94 (31%), Positives = 50/94 (53%), Gaps = 2/94 (2%)
Query: 12 TYKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHT-EVDDVMCILDVLDTAGQ 70
+K++V+GD VGK+ +T +F F + TI + + T E+D + + DTAGQ
Sbjct: 2 IFKIIVIGDSNVGKTCLTYRFCAGRFPERTEATIGVDFRERTVEIDGERIKVQLWDTAGQ 61
Query: 71 EEF-SAMREQYMRKGDGFLLVYSVTDQQSYENIK 103
E F +M + Y R + VY VT+ S+ ++
Sbjct: 62 ERFRKSMVQHYYRNVHAVVFVYDVTNMASFHSLP 95
>gnl|CDD|206693 cd04108, Rab36_Rab34, Rab GTPase families 34 (Rab34) and 36
(Rab36). Rab34/Rab36 subfamily. Rab34, found primarily
in the Golgi, interacts with its effector,
Rab-interacting lysosomal protein (RILP). This enables
its participation in microtubular
dynenin-dynactin-mediated repositioning of lysosomes
from the cell periphery to the Golgi. A Rab34 (Rah)
isoform that lacks the consensus GTP-binding region has
been identified in mice. This isoform is associated with
membrane ruffles and promotes macropinosome formation.
Rab36 has been mapped to human chromosome 22q11.2, a
region that is homozygously deleted in malignant
rhabdoid tumors (MRTs). However, experimental
assessments do not implicate Rab36 as a tumor suppressor
that would enable tumor formation through a
loss-of-function mechanism. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 170
Score = 56.4 bits (136), Expect = 3e-11
Identities = 34/102 (33%), Positives = 54/102 (52%), Gaps = 1/102 (0%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIE-DSYLQHTEVDDVMCILDVLDTAGQEE 72
K++VVGD VGK+ + +F + +F +Y TI D ++ EV V L + DTAGQE
Sbjct: 2 KVIVVGDLSVGKTCLINRFCKDVFDKNYKATIGVDFEMERFEVLGVPFSLQLWDTAGQER 61
Query: 73 FSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILRVKD 114
F + Y R ++V+ +TD S E+ + + L+ D
Sbjct: 62 FKCIASTYYRGAQAIIIVFDLTDVASLEHTRQWLEDALKEND 103
>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 = 56.9 bits (138), Expect = 3e-11
Identities = 31/93 (33%), Positives = 50/93 (53%), Gaps = 2/93 (2%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIE-DSYLQHTEVDDVMCI-LDVLDTAGQ 70
+K++V+GD GVGK++I ++ +F Y TI D L+ E D + L + D AGQ
Sbjct: 1 FKVLVIGDLGVGKTSIIKRYVHGVFSQHYKATIGVDFALKVIEWDPNTVVRLQLWDIAGQ 60
Query: 71 EEFSAMREQYMRKGDGFLLVYSVTDQQSYENIK 103
E F M Y + G ++V+ VT ++E +
Sbjct: 61 ERFGGMTRVYYKGAVGAIIVFDVTRPSTFEAVL 93
>gnl|CDD|133324 cd04124, RabL2, Rab GTPase-like family 2 (Rab-like2). RabL2
(Rab-like2) subfamily. RabL2s are novel Rab proteins
identified recently which display features that are
distinct from other Rabs, and have been termed Rab-like.
RabL2 contains RabL2a and RabL2b, two very similar Rab
proteins that share > 98% sequence identity in humans.
RabL2b maps to the subtelomeric region of chromosome
22q13.3 and RabL2a maps to 2q13, a region that suggests
it is also a subtelomeric gene. Both genes are believed
to be expressed ubiquitously, suggesting that RabL2s are
the first example of duplicated genes in human proximal
subtelomeric regions that are both expressed actively.
Like other Rab-like proteins, RabL2s lack a prenylation
site at the C-terminus. The specific functions of RabL2a
and RabL2b remain unknown. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization.
Length = 161
Score = 56.0 bits (135), Expect = 4e-11
Identities = 28/97 (28%), Positives = 50/97 (51%), Gaps = 1/97 (1%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHT-EVDDVMCILDVLDTAGQEE 72
K++++GD VGKS + +F + T + +H + + ++D DTAGQE
Sbjct: 2 KIILLGDSAVGKSKLVERFLMDGYEPQQLSTYALTLYKHNAKFEGKTILVDFWDTAGQER 61
Query: 73 FSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQI 109
F M Y K +LV+ VT + +Y+N+ +Y ++
Sbjct: 62 FQTMHASYYHKAHACILVFDVTRKITYKNLSKWYEEL 98
>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 = 52.2 bits (125), Expect = 1e-09
Identities = 28/98 (28%), Positives = 56/98 (57%), Gaps = 1/98 (1%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIE-DSYLQHTEVDDVMCILDVLDTAGQE 71
+KL+++G+ VGK++ ++ F + + T+ D ++ +D L + DTAGQE
Sbjct: 2 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVYRNDKRIKLQIWDTAGQE 61
Query: 72 EFSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQI 109
+ + Y R GF+L+Y +T+++S+ ++ + TQI
Sbjct: 62 RYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQI 99
>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 = 51.7 bits (124), Expect = 2e-09
Identities = 29/107 (27%), Positives = 51/107 (47%), Gaps = 11/107 (10%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTI-----------EDSYLQHTEVDDVMCIL 62
KL+ +GD GVGK+ ++ F + T+ T L
Sbjct: 6 KLLALGDSGVGKTTFLYRYTDNKFNPKFITTVGIDFREKRVVYNSQGPDGTSGKAFRVHL 65
Query: 63 DVLDTAGQEEFSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQI 109
+ DTAGQE F ++ + R GFLL++ +T +QS+ N++++ +Q+
Sbjct: 66 QLWDTAGQERFRSLTTAFFRDAMGFLLMFDLTSEQSFLNVRNWMSQL 112
>gnl|CDD|128473 smart00176, RAN, Ran (Ras-related nuclear proteins) /TC4 subfamily
of small GTPases. Ran is involved in the active
transport of proteins through nuclear pores.
Length = 200
Score = 49.6 bits (118), Expect = 2e-08
Identities = 29/98 (29%), Positives = 52/98 (53%), Gaps = 5/98 (5%)
Query: 18 VGDGGVGKSAITIQFFQKLFVTDYDPTIE---DSYLQHTEVDDVMCILDVLDTAGQEEFS 74
VGDGG GK+ + F Y T+ + HT + +V DTAGQE+F
Sbjct: 1 VGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIR--FNVWDTAGQEKFG 58
Query: 75 AMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILRV 112
+R+ Y +G ++++ VT + +Y+N+ +++ ++RV
Sbjct: 59 GLRDGYYIQGQCAIIMFDVTARVTYKNVPNWHRDLVRV 96
>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 = 48.9 bits (116), Expect = 4e-08
Identities = 26/97 (26%), Positives = 53/97 (54%), Gaps = 1/97 (1%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIE-DSYLQHTEVDDVMCILDVLDTAGQEE 72
+++++G GVGK+++ +F F T+ D ++ E+ L + DTAGQE
Sbjct: 2 QVIIIGSRGVGKTSLMERFTDDTFCEACKSTVGVDFKIKTVELRGKKIRLQIWDTAGQER 61
Query: 73 FSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQI 109
F+++ Y R G +LVY +T +++++++ + I
Sbjct: 62 FNSITSAYYRSAKGIILVYDITKKETFDDLPKWMKMI 98
>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 = 47.5 bits (113), Expect = 8e-08
Identities = 32/99 (32%), Positives = 46/99 (46%), Gaps = 17/99 (17%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDV--------- 64
+ VVGD VGKSA ++F +D T + +Y T D V+ + V
Sbjct: 2 QCAVVGDPAVGKSA-----LVQMFHSD-GATFQKNYTMTTGCDLVVKTVPVPDTSDSVEL 55
Query: 65 --LDTAGQEEFSAMREQYMRKGDGFLLVYSVTDQQSYEN 101
D+AGQE FS M E + +VY VT++ S+ N
Sbjct: 56 FIFDSAGQELFSDMVENVWEQPAVVCVVYDVTNEVSFNN 94
>gnl|CDD|206741 cd09914, RocCOR, Ras of complex proteins (Roc) C-terminal of Roc
(COR) domain family. RocCOR (or Roco) protein family is
characterized by a superdomain containing a Ras-like
GTPase domain, called Roc (Ras of complex proteins), and
a characteristic second domain called COR (C-terminal of
Roc). A kinase domain and diverse regulatory domains are
also often found in Roco proteins. Their functions are
diverse; in Dictyostelium discoideum, which encodes 11
Roco proteins, they are involved in cell division,
chemotaxis and development, while in human, where 4 Roco
proteins (LRRK1, LRRK2, DAPK1, and MFHAS1) are encoded,
these proteins are involved in epilepsy and cancer.
Mutations in LRRK2 (leucine-rich repeat kinase 2) are
known to cause familial Parkinson's disease.
Length = 161
Score = 47.3 bits (113), Expect = 1e-07
Identities = 27/100 (27%), Positives = 47/100 (47%), Gaps = 6/100 (6%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPT----IEDSYLQHTEVDDVMCILDVLDTAG 69
KL++VG GGVGK+++ Q + F D T ++D + E L+V D G
Sbjct: 3 KLMLVGQGGVGKTSLCKQLIGEKFDGDESSTHGINVQDWKIPAPERKK--IRLNVWDFGG 60
Query: 70 QEEFSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQI 109
QE + A + ++ +LLV+ + + ++ QI
Sbjct: 61 QEIYHATHQFFLTSRSLYLLVFDLRTGDEVSRVPYWLRQI 100
>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 = 46.8 bits (111), Expect = 2e-07
Identities = 34/108 (31%), Positives = 49/108 (45%), Gaps = 11/108 (10%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTI-EDSYLQHTEVDDVMCILDVLD----- 66
++ V+G GVGK+AI QF + F +Y PT Y + + L +LD
Sbjct: 1 VRVAVLGAPGVGKTAIVRQFLAQEFPEEYIPTEHRRLYRPAVVLSGRVYDLHILDVPNMQ 60
Query: 67 ----TAGQEEFSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQIL 110
TAGQE R + +R F+LVY + S+ +K QIL
Sbjct: 61 RYPGTAGQEWMDP-RFRGLRNSRAFILVYDICSPDSFHYVKLLRQQIL 107
>gnl|CDD|206703 cd04131, Rnd, Rho family GTPase subfamily Rnd includes Rnd1/Rho6,
Rnd2/Rho7, and Rnd3/RhoE/Rho8. The Rnd subfamily
contains Rnd1/Rho6, Rnd2/Rho7, and Rnd3/RhoE/Rho8. These
novel Rho family proteins have substantial structural
differences compared to other Rho members, including N-
and C-terminal extensions relative to other Rhos.
Rnd3/RhoE is farnesylated at the C-terminal prenylation
site, unlike most other Rho proteins that are
geranylgeranylated. In addition, Rnd members are unable
to hydrolyze GTP and are resistant to GAP activity. They
are believed to exist only in the GTP-bound
conformation, and are antagonists of RhoA activity. Most
Rho proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 176
Score = 46.7 bits (111), Expect = 2e-07
Identities = 25/99 (25%), Positives = 50/99 (50%), Gaps = 1/99 (1%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQEEF 73
K+V+VGD GK+A+ F + F +Y PT+ ++Y EVD L + DT+G +
Sbjct: 3 KIVLVGDSQCGKTALLQVFAKDSFPENYVPTVFENYTASFEVDKQRIELSLWDTSGSPYY 62
Query: 74 SAMREQYMRKGDGFLLVYSVTDQQSYENI-KHFYTQILR 111
+R D L+ + ++ ++ +++ K + ++
Sbjct: 63 DNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEVRE 101
>gnl|CDD|206735 cd04172, Rnd3_RhoE_Rho8, Rnd3/RhoE/Rho8 GTPases. Rnd3/RhoE/Rho8
subfamily. Rnd3/RhoE/Rho8 is a member of the novel Rho
subfamily Rnd, together with Rnd1/Rho6 and Rnd2/Rho7.
Rnd3/RhoE is known to bind the serine-threonine kinase
ROCK I. Unphosphorylated Rnd3/RhoE associates primarily
with membranes, but ROCK I-phosphorylated Rnd3/RhoE
localizes in the cytosol. Phosphorylation of Rnd3/RhoE
correlates with its activity in disrupting RhoA-induced
stress fibers and inhibiting Ras-induced fibroblast
transformation. In cells that lack stress fibers, such
as macrophages and monocytes, Rnd3/RhoE induces a
redistribution of actin, causing morphological changes
in the cell. In addition, Rnd3/RhoE has been shown to
inhibit cell cycle progression in G1 phase at a point
upstream of the pRb family pocket protein checkpoint.
Rnd3/RhoE has also been shown to inhibit Ras- and
Raf-induced fibroblast transformation. In mammary
epithelial tumor cells, Rnd3/RhoE regulates the assembly
of the apical junction complex and tight junction
formation. Rnd3/RhoE is underexpressed in prostate
cancer cells both in vitro and in vivo; re-expression of
Rnd3/RhoE suppresses cell cycle progression and
increases apoptosis, suggesting it may play a role in
tumor suppression. Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 182
Score = 46.6 bits (110), Expect = 2e-07
Identities = 24/89 (26%), Positives = 46/89 (51%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQEEF 73
K+VVVGD GK+A+ F + F +Y PT+ ++Y E+D L + DT+G +
Sbjct: 7 KIVVVGDSQCGKTALLHVFAKDCFPENYVPTVFENYTASFEIDTQRIELSLWDTSGSPYY 66
Query: 74 SAMREQYMRKGDGFLLVYSVTDQQSYENI 102
+R D L+ + ++ ++ +++
Sbjct: 67 DNVRPLSYPDSDAVLICFDISRPETLDSV 95
>gnl|CDD|133318 cd04118, Rab24, Rab GTPase family 24 (Rab24). Rab24 is distinct
from other Rabs in several ways. It exists primarily in
the GTP-bound state, having a low intrinsic GTPase
activity; it is not efficiently geranyl-geranylated at
the C-terminus; it does not form a detectable complex
with Rab GDP-dissociation inhibitors (GDIs); and it has
recently been shown to undergo tyrosine phosphorylation
when overexpressed in vitro. The specific function of
Rab24 still remains unknown. It is found in a transport
route between ER-cis-Golgi and late endocytic
compartments. It is putatively involved in an autophagic
pathway, possibly directing misfolded proteins in the ER
to degradative pathways. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 193
Score = 45.6 bits (108), Expect = 6e-07
Identities = 30/100 (30%), Positives = 52/100 (52%), Gaps = 3/100 (3%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLF-VTDYDPTIEDSYLQHT-EVDDVMCILDVLDTAGQE 71
K+V++G VGK+++ ++ F V Y TI +++ V + + L + DTAG E
Sbjct: 2 KVVMLGKESVGKTSLVERYVHHRFLVGPYQNTIGAAFVAKRMVVGERVVTLGIWDTAGSE 61
Query: 72 EFSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILR 111
+ AM Y R ++ Y +TD S+E K F+ + L+
Sbjct: 62 RYEAMSRIYYRGAKAAIVCYDLTDSSSFERAK-FWVKELQ 100
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 45.1 bits (106), Expect = 7e-07
Identities = 27/80 (33%), Positives = 43/80 (53%), Gaps = 1/80 (1%)
Query: 37 FVTDYDPTIEDSYLQHT-EVDDVMCILDVLDTAGQEEFSAMREQYMRKGDGFLLVYSVTD 95
F +Y TI +L T +D+ L + DTAGQE F ++ Y+R ++VY +T+
Sbjct: 5 FDNNYQSTIGIDFLSKTLYLDEGPVRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDITN 64
Query: 96 QQSYENIKHFYTQILRVKDK 115
+QS+EN + IL + K
Sbjct: 65 RQSFENTTKWIQDILNERGK 84
>gnl|CDD|206737 cd04174, Rnd1_Rho6, Rnd1/Rho6 GTPases. Rnd1/Rho6 is a member of
the novel Rho subfamily Rnd, together with Rnd2/Rho7 and
Rnd3/RhoE/Rho8. Rnd1/Rho6 binds GTP but does not
hydrolyze it to GDP, indicating that it is
constitutively active. In rat, Rnd1/Rho6 is highly
expressed in the cerebral cortex and hippocampus during
synapse formation, and plays a role in spine formation.
Rnd1/Rho6 is also expressed in the liver and in
endothelial cells, and is upregulated in uterine
myometrial cells during pregnancy. Like Rnd3/RhoE/Rho8,
Rnd1/Rho6 is believed to function as an antagonist to
RhoA. Most Rho proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Rho proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 232
Score = 43.1 bits (101), Expect = 5e-06
Identities = 25/98 (25%), Positives = 49/98 (50%), Gaps = 1/98 (1%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQEEF 73
KLV+VGD GK+A+ + + Y PT+ ++Y E ++ L + DT+G +
Sbjct: 15 KLVLVGDVQCGKTAMLQVLAKDCYPETYVPTVFENYTACLETEEQRVELSLWDTSGSPYY 74
Query: 74 SAMREQYMRKGDGFLLVYSVTDQQSYEN-IKHFYTQIL 110
+R D LL + ++ + +++ +K + +IL
Sbjct: 75 DNVRPLCYSDSDAVLLCFDISRPEIFDSALKKWRAEIL 112
>gnl|CDD|206736 cd04173, Rnd2_Rho7, Rnd2/Rho7 GTPases. Rnd2/Rho7 is a member of
the novel Rho subfamily Rnd, together with Rnd1/Rho6 and
Rnd3/RhoE/Rho8. Rnd2/Rho7 is transiently expressed in
radially migrating cells in the brain while they are
within the subventricular zone of the hippocampus and
cerebral cortex. These migrating cells typically develop
into pyramidal neurons. Cells that exogenously expressed
Rnd2/Rho7 failed to migrate to upper layers of the
brain, suggesting that Rnd2/Rho7 plays a role in the
radial migration and morphological changes of developing
pyramidal neurons, and that Rnd2/Rho7 degradation is
necessary for proper cellular migration. The Rnd2/Rho7
GEF Rapostlin is found primarily in the brain and
together with Rnd2/Rho7 induces dendrite branching.
Unlike Rnd1/Rho6 and Rnd3/RhoE/Rho8, which are RhoA
antagonists, Rnd2/Rho7 binds the GEF Pragmin and
significantly stimulates RhoA activity and Rho-A
mediated cell contraction. Rnd2/Rho7 is also found to be
expressed in spermatocytes and early spermatids, with
male-germ-cell Rac GTPase-activating protein
(MgcRacGAP), where it localizes to the Golgi-derived
pro-acrosomal vesicle. Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Length = 221
Score = 42.7 bits (100), Expect = 8e-06
Identities = 23/89 (25%), Positives = 46/89 (51%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQEEF 73
K+VVVGD GK+A+ F + + Y PT+ ++Y E+D L++ DT+G +
Sbjct: 3 KIVVVGDTQCGKTALLHVFAKDNYPESYVPTVFENYTASFEIDKHRIELNMWDTSGSSYY 62
Query: 74 SAMREQYMRKGDGFLLVYSVTDQQSYENI 102
+R D L+ + ++ ++ +++
Sbjct: 63 DNVRPLAYPDSDAVLICFDISRPETLDSV 91
>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 = 42.2 bits (99), Expect = 9e-06
Identities = 29/105 (27%), Positives = 46/105 (43%), Gaps = 17/105 (16%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVD--DVMCILD-------V 64
K ++VGD VGK I D + E Y + +D +LD +
Sbjct: 8 KFLLVGDSDVGKGEILASL--------QDGSTESPYGYNMGIDYKTTTILLDGRRVKLQL 59
Query: 65 LDTAGQEEFSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQI 109
DT+GQ F + Y R G +LVY +T++ S++ I + +I
Sbjct: 60 WDTSGQGRFCTIFRSYSRGAQGIILVYDITNRWSFDGIDRWIKEI 104
>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 = 38.5 bits (90), Expect = 2e-04
Identities = 23/99 (23%), Positives = 48/99 (48%), Gaps = 1/99 (1%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQEEF 73
++V++GD GVGKS++ + + F + + + + +V ++DT+ + +
Sbjct: 4 RIVLIGDEGVGKSSLIMSLVSEEFPENVPRVLPEITIP-ADVTPERVPTTIVDTSSRPQD 62
Query: 74 SAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILRV 112
A +RK + LVYSV + E I+ + ++R
Sbjct: 63 RANLAAEIRKANVICLVYSVDRPSTLERIRTKWLPLIRR 101
>gnl|CDD|206701 cd04128, Spg1, Septum-promoting GTPase (Spg1). Spg1p. Spg1p
(septum-promoting GTPase) was first identified in the
fission yeast S. pombe, where it regulates septum
formation in the septation initiation network (SIN)
through the cdc7 protein kinase. Spg1p is an essential
gene that localizes to the spindle pole bodies. When
GTP-bound, it binds cdc7 and causes it to translocate to
spindle poles. Sid4p (septation initiation defective) is
required for localization of Spg1p to the spindle pole
body, and the ability of Spg1p to promote septum
formation from any point in the cell cycle depends on
Sid4p. Spg1p is negatively regulated by Byr4 and cdc16,
which form a two-component GTPase activating protein
(GAP) for Spg1p. The existence of a SIN-related pathway
in plants has been proposed. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization.
Length = 182
Score = 38.5 bits (90), Expect = 2e-04
Identities = 21/96 (21%), Positives = 48/96 (50%), Gaps = 1/96 (1%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHT-EVDDVMCILDVLDTAGQEE 72
K+ ++GD +GK+++ +++ + F +Y T+ ++++ T + + D GQ E
Sbjct: 2 KIGLLGDAQIGKTSLMVKYVEGEFDEEYIQTLGVNFMEKTISIRGTEITFSIWDLGGQRE 61
Query: 73 FSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQ 108
F M + L ++ +T + + +IK +Y Q
Sbjct: 62 FINMLPLVCKDAVAILFMFDLTRKSTLNSIKEWYRQ 97
>gnl|CDD|133326 cd04126, Rab20, Rab GTPase family 20 (Rab20). Rab20 is one of
several Rab proteins that appear to be restricted in
expression to the apical domain of murine polarized
epithelial cells. It is expressed on the apical side of
polarized kidney tubule and intestinal epithelial cells,
and in non-polarized cells. It also localizes to
vesico-tubular structures below the apical brush border
of renal proximal tubule cells and in the apical region
of duodenal epithelial cells. Rab20 has also been shown
to colocalize with vacuolar H+-ATPases (V-ATPases) in
mouse kidney cells, suggesting a role in the regulation
of V-ATPase traffic in specific portions of the nephron.
It was also shown to be one of several proteins whose
expression is upregulated in human myelodysplastic
syndrome (MDS) patients. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 220
Score = 38.7 bits (90), Expect = 2e-04
Identities = 26/90 (28%), Positives = 49/90 (54%), Gaps = 6/90 (6%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDS-YLQHTEVDDVMCILDVLDTAGQEE 72
K+V++GD VGK+++ ++ ++ F D T+ + YL+ ++ + DTAG+E+
Sbjct: 2 KVVLLGDMNVGKTSLLHRYMERRF-KDTVSTVGGAFYLKQWGPYNI----SIWDTAGREQ 56
Query: 73 FSAMREQYMRKGDGFLLVYSVTDQQSYENI 102
F + Y R +L Y V++ QS E +
Sbjct: 57 FHGLGSMYCRGAAAVILTYDVSNVQSLEEL 86
>gnl|CDD|133275 cd01873, RhoBTB, RhoBTB protein is an atypical member of the Rho
family of small GTPases. Members of the RhoBTB
subfamily of Rho GTPases are present in vertebrates,
Drosophila, and Dictyostelium. RhoBTB proteins are
characterized by a modular organization, consisting of a
GTPase domain, a proline rich region, a tandem of two
BTB (Broad-Complex, Tramtrack, and Bric a brac) domains,
and a C-terminal region of unknown function. RhoBTB
proteins may act as docking points for multiple
components participating in signal transduction
cascades. RhoBTB genes appeared upregulated in some
cancer cell lines, suggesting a participation of RhoBTB
proteins in the pathogenesis of particular tumors. Note
that the Dictyostelium RacA GTPase domain is more
closely related to Rac proteins than to RhoBTB proteins,
where RacA actually belongs. Thus, the Dictyostelium
RacA is not included here. Most Rho proteins contain a
lipid modification site at the C-terminus; however,
RhoBTB is one of few Rho subfamilies that lack this
feature.
Length = 195
Score = 34.9 bits (80), Expect = 0.004
Identities = 35/116 (30%), Positives = 46/116 (39%), Gaps = 18/116 (15%)
Query: 12 TYKLVVVGDGGVGKS------AITIQFFQKLFVTDYDPTIE--DSYLQHTE--------V 55
T K VVVGD VGK+ A Q + + PT+ D Y E V
Sbjct: 2 TIKCVVVGDNAVGKTRLICARACNKTLTQYQLLATHVPTVWAIDQYRVCQEVLERSRDVV 61
Query: 56 DDVMCILDVLDTAGQEEFSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILR 111
D V L + DT G + R Y R D LL +S+ S N+K + +R
Sbjct: 62 DGVSVSLRLWDTFGDHD-KDRRFAYGR-SDVVLLCFSIASPNSLRNVKTMWYPEIR 115
>gnl|CDD|133303 cd04103, Centaurin_gamma, Centaurin gamma (CENTG) GTPase. The
centaurins (alpha, beta, gamma, and delta) are large,
multi-domain proteins that all contain an ArfGAP domain
and ankyrin repeats, and in some cases, numerous
additional domains. Centaurin gamma contains an
additional GTPase domain near its N-terminus. The
specific function of this GTPase domain has not been
well characterized, but centaurin gamma 2 (CENTG2) may
play a role in the development of autism. Centaurin
gamma 1 is also called PIKE (phosphatidyl inositol (PI)
3-kinase enhancer) and centaurin gamma 2 is also known
as AGAP (ArfGAP protein with a GTPase-like domain,
ankyrin repeats and a Pleckstrin homology domain) or
GGAP. Three isoforms of PIKE have been identified.
PIKE-S (short) and PIKE-L (long) are brain-specific
isoforms, with PIKE-S restricted to the nucleus and
PIKE-L found in multiple cellular compartments. A third
isoform, PIKE-A was identified in human glioblastoma
brain cancers and has been found in various tissues.
GGAP has been shown to have high GTPase activity due to
a direct intramolecular interaction between the
N-terminal GTPase domain and the C-terminal ArfGAP
domain. In human tissue, AGAP mRNA was detected in
skeletal muscle, kidney, placenta, brain, heart, colon,
and lung. Reduced expression levels were also observed
in the spleen, liver, and small intestine.
Length = 158
Score = 33.2 bits (76), Expect = 0.013
Identities = 23/96 (23%), Positives = 43/96 (44%), Gaps = 6/96 (6%)
Query: 14 KLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTAGQEEF 73
KL +VG+ GKSA+ ++ +V P + + VD +L + D G +
Sbjct: 2 KLGIVGNLRSGKSALVHRYLTGSYVQLESPEGG-RFKKEVLVDGQSHLLLIRDEGGAPDA 60
Query: 74 SAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQI 109
Q+ D + V+S+ D+ S++ + Y Q+
Sbjct: 61 -----QFAGWVDAVIFVFSLEDEASFQTVYRLYHQL 91
>gnl|CDD|238991 cd02034, CooC, The accessory protein CooC, which contains a
nucleotide-binding domain (P-loop) near the N-terminus,
participates in the maturation of the nickel center of
carbon monoxide dehydrogenase (CODH). CODH from
Rhodospirillum rubrum catalyzes the reversible
oxidation of CO to CO2. CODH contains a
nickel-iron-sulfur cluster (C-center) and an
iron-sulfur cluster (B-center). CO oxidation occurs at
the C-center. Three accessory proteins encoded by
cooCTJ genes are involved in nickel incorporation into
a nickel site. CooC functions as a nickel insertase
that mobilizes nickel to apoCODH using energy released
from ATP hydrolysis. CooC is a homodimer and has NTPase
activities. Mutation at the P-loop abolishs its
function.
Length = 116
Score = 30.7 bits (70), Expect = 0.068
Identities = 11/37 (29%), Positives = 18/37 (48%), Gaps = 7/37 (18%)
Query: 14 KLVVVGDGGVGKSAIT---IQFF----QKLFVTDYDP 43
K+ + G GGVGK+ I ++ + + D DP
Sbjct: 1 KIAITGKGGVGKTTIAALLARYLAEKGKPVLAIDADP 37
>gnl|CDD|226166 COG3640, CooC, CO dehydrogenase maturation factor [Cell division
and chromosome partitioning].
Length = 255
Score = 30.7 bits (70), Expect = 0.11
Identities = 13/39 (33%), Positives = 18/39 (46%), Gaps = 8/39 (20%)
Query: 13 YKLVVVGDGGVGKSAIT----IQFFQK----LFVTDYDP 43
K+ + G GGVGK+ I + K + V D DP
Sbjct: 1 MKIAITGKGGVGKTTIAALLLKRLLSKGGYNVLVVDADP 39
>gnl|CDD|206674 cd01887, IF2_eIF5B, Initiation Factor 2 (IF2)/ eukaryotic
Initiation Factor 5B (eIF5B) family. IF2/eIF5B
contribute to ribosomal subunit joining and function as
GTPases that are maximally activated by the presence of
both ribosomal subunits. As seen in other GTPases,
IF2/IF5B undergoes conformational changes between its
GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess
three characteristic segments, including a divergent
N-terminal region followed by conserved central and
C-terminal segments. This core region is conserved among
all known eukaryotic and archaeal IF2/eIF5Bs and
eubacterial IF2s.
Length = 169
Score = 30.1 bits (69), Expect = 0.16
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 62 LDVLDTAGQEEFSAMREQYMRKGDGFLLVYSVTD---QQSYENIKH 104
+ +DT G E F+ MR + D +LV + D Q+ E I H
Sbjct: 51 ITFIDTPGHEAFTNMRARGASVTDIAILVVAADDGVMPQTIEAINH 96
>gnl|CDD|232995 TIGR00487, IF-2, translation initiation factor IF-2. This model
discriminates eubacterial (and mitochondrial)
translation initiation factor 2 (IF-2), encoded by the
infB gene in bacteria, from similar proteins in the
Archaea and Eukaryotes. In the bacteria and in
organelles, the initiator tRNA is charged with
N-formyl-Met instead of Met. This translation factor
acts in delivering the initator tRNA to the ribosome. It
is one of a number of GTP-binding translation factors
recognized by the pfam model GTP_EFTU [Protein
synthesis, Translation factors].
Length = 587
Score = 29.7 bits (67), Expect = 0.31
Identities = 20/56 (35%), Positives = 28/56 (50%), Gaps = 4/56 (7%)
Query: 52 HTEVDDVMCILDVLDTAGQEEFSAMREQYMRKGDGFLLVYSVTD---QQSYENIKH 104
H E +D I LDT G E F++MR + + D +LV + D Q+ E I H
Sbjct: 128 HVENEDGKMIT-FLDTPGHEAFTSMRARGAKVTDIVVLVVAADDGVMPQTIEAISH 182
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the
AAA superfamily.
Length = 154
Score = 29.1 bits (65), Expect = 0.38
Identities = 6/24 (25%), Positives = 14/24 (58%)
Query: 15 LVVVGDGGVGKSAITIQFFQKLFV 38
+++ G G GK+++ + + L V
Sbjct: 27 VLLTGPSGTGKTSLLRELLEGLLV 50
>gnl|CDD|227352 COG5019, CDC3, Septin family protein [Cell division and
chromosome partitioning / Cytoskeleton].
Length = 373
Score = 28.1 bits (63), Expect = 0.99
Identities = 19/75 (25%), Positives = 29/75 (38%), Gaps = 12/75 (16%)
Query: 6 NNNNITTYKLVVVGDGGVGKSAITIQFFQKLFVTD----------YDPTIE-DSYLQHTE 54
+ I + ++VVG+ G+GK+ F V + PT+E E
Sbjct: 18 SKKGID-FTIMVVGESGLGKTTFINTLFGTSLVDETEIDDIRAEGTSPTLEIKITKAELE 76
Query: 55 VDDVMCILDVLDTAG 69
D L V+DT G
Sbjct: 77 EDGFHLNLTVIDTPG 91
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 27.9 bits (63), Expect = 1.0
Identities = 17/54 (31%), Positives = 21/54 (38%), Gaps = 23/54 (42%)
Query: 64 VLDTAGQEEFSAMREQYMRKGDGFLLVYSVTD-------------QQSYENIKH 104
+DT G E F+AMR +G SVTD Q+ E I H
Sbjct: 59 FIDTPGHEAFTAMR----ARG------ASVTDIAILVVAADDGVMPQTIEAINH 102
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 27.8 bits (62), Expect = 1.1
Identities = 25/93 (26%), Positives = 34/93 (36%), Gaps = 10/93 (10%)
Query: 8 NNITTYKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSY--LQHTEV--DDVMCILD 63
N + K+VV+G G GK+ K V S + T V D LD
Sbjct: 6 NKMIETKIVVIGPVGAGKTTFVRALSDKPLVITEADASSVSGKGKRPTTVAMDFGSIELD 65
Query: 64 ------VLDTAGQEEFSAMREQYMRKGDGFLLV 90
+ T GQE F M E R G +++
Sbjct: 66 EDTGVHLFGTPGQERFKFMWEILSRGAVGAIVL 98
>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 = 27.7 bits (62), Expect = 1.1
Identities = 24/87 (27%), Positives = 33/87 (37%), Gaps = 12/87 (13%)
Query: 13 YKLVVVGDGGVGKSAITIQFFQKLFVTDYDPTIEDSYLQHTEVD----DVMCILDVLDTA 68
YK+++VG GK+ I QF V PTI + E+ + D
Sbjct: 16 YKVIIVGLDNAGKTTILYQFLLGEVVHT-SPTIGSN---VEEIVYKNIRFLMW----DIG 67
Query: 69 GQEEFSAMREQYMRKGDGFLLVYSVTD 95
GQE + Y D +LV TD
Sbjct: 68 GQESLRSSWNTYYTNTDAVILVIDSTD 94
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 27.9 bits (62), Expect = 1.2
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 65 LDTAGQEEFSAMREQYMRKGDGFLLVYSVTD---QQSYENIKH 104
LDT G E FS+MR + D +L+ + D Q+ E I +
Sbjct: 300 LDTPGHEAFSSMRSRGANVTDIAILIIAADDGVKPQTIEAINY 342
>gnl|CDD|206722 cd04157, Arl6, Arf-like 6 (Arl6) GTPase. Arl6 (Arf-like 6) forms a
subfamily of the Arf family of small GTPases. Arl6
expression is limited to the brain and kidney in adult
mice, but it is expressed in the neural plate and
somites during embryogenesis, suggesting a possible role
for Arl6 in early development. Arl6 is also believed to
have a role in cilia or flagella function. Several
proteins have been identified that bind Arl6, including
Arl6 interacting protein (Arl6ip), and SEC61beta, a
subunit of the heterotrimeric conducting channel SEC61p.
Based on Arl6 binding to these effectors, Arl6 is also
proposed to play a role in protein transport, membrane
trafficking, or cell signaling during hematopoietic
maturation. At least three specific homozygous Arl6
mutations in humans have been found to cause
Bardet-Biedl syndrome, a disorder characterized by
obesity, retinopathy, polydactyly, renal and cardiac
malformations, learning disabilities, and
hypogenitalism. Older literature suggests that Arl6 is a
part of the Arl4/Arl7 subfamily, but analyses based on
more recent sequence data place Arl6 in its own
subfamily.
Length = 162
Score = 27.4 bits (61), Expect = 1.3
Identities = 11/51 (21%), Positives = 20/51 (39%)
Query: 64 VLDTAGQEEFSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILRVKD 114
D +GQ ++ + E Y + G + V +D+ K +L D
Sbjct: 49 AFDMSGQGKYRGLWEHYYKNIQGIIFVIDSSDRLRMVVAKDELELLLNHPD 99
>gnl|CDD|176233 cd08272, MDR6, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 326
Score = 27.5 bits (62), Expect = 1.3
Identities = 21/83 (25%), Positives = 29/83 (34%), Gaps = 27/83 (32%)
Query: 15 LVVVGDGGVGKSAITI-----------------QFFQKL---FVTDYDPTIEDSYLQHTE 54
L+ G GGVG A+ + F + L + Y T+ + +HT
Sbjct: 149 LIHGGAGGVGHVAVQLAKAAGARVYATASSEKAAFARSLGADPIIYYRETVVEYVAEHTG 208
Query: 55 VD--DVMCILDVLDTAGQEEFSA 75
DV V DT G E A
Sbjct: 209 GRGFDV-----VFDTVGGETLDA 226
>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ
chaperones [Posttranslational modification, protein
turnover, chaperones].
Length = 786
Score = 27.6 bits (62), Expect = 1.4
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 16 VVVGDGGVGKSAITIQFFQK 35
V+VG+ GVGK+AI Q+
Sbjct: 195 VLVGEPGVGKTAIVEGLAQR 214
>gnl|CDD|215653 pfam00009, GTP_EFTU, Elongation factor Tu GTP binding domain. This
domain contains a P-loop motif, also found in several
other families such as pfam00071, pfam00025 and
pfam00063. Elongation factor Tu consists of three
structural domains, this plus two C-terminal beta barrel
domains.
Length = 184
Score = 27.1 bits (61), Expect = 1.6
Identities = 10/44 (22%), Positives = 21/44 (47%), Gaps = 3/44 (6%)
Query: 64 VLDTAGQEEFSAMREQYMRKGDGFLLVYSVTD---QQSYENIKH 104
++DT G +F+ + + DG +LV + Q+ E++
Sbjct: 70 IIDTPGHVDFTKEMIRGASQADGAILVVDAVEGVMPQTREHLLL 113
>gnl|CDD|223840 COG0769, MurE, UDP-N-acetylmuramyl tripeptide synthase [Cell
envelope biogenesis, outer membrane].
Length = 475
Score = 27.7 bits (62), Expect = 1.7
Identities = 14/46 (30%), Positives = 18/46 (39%), Gaps = 8/46 (17%)
Query: 10 ITTYKLVVV----GDGGVGK----SAITIQFFQKLFVTDYDPTIED 47
+L+VV GD K AI Q + VT +P ED
Sbjct: 356 HAAGRLIVVFGCGGDRDKSKRPDMGAIAEQLADIVIVTSDNPRSED 401
>gnl|CDD|226126 COG3598, RepA, RecA-family ATPase [DNA replication, recombination,
and repair].
Length = 402
Score = 27.2 bits (60), Expect = 1.9
Identities = 7/23 (30%), Positives = 12/23 (52%)
Query: 9 NITTYKLVVVGDGGVGKSAITIQ 31
Y ++ GD GVGK+ + +
Sbjct: 86 FRKGYVSILYGDSGVGKTTLLLY 108
>gnl|CDD|206649 cd01850, CDC_Septin, CDC/Septin GTPase family. Septins are a
conserved family of GTP-binding proteins associated
with diverse processes in dividing and non-dividing
cells. They were first discovered in the budding yeast
S. cerevisiae as a set of genes (CDC3, CDC10, CDC11 and
CDC12) required for normal bud morphology. Septins are
also present in metazoan cells, where they are required
for cytokinesis in some systems, and implicated in a
variety of other processes involving organization of
the cell cortex and exocytosis. In humans, 12 septin
genes generate dozens of polypeptides, many of which
comprise heterooligomeric complexes. Since septin
mutants are commonly defective in cytokinesis and
formation of the neck formation of the neck
filaments/septin rings, septins have been considered to
be the primary constituents of the neck filaments.
Septins belong to the GTPase superfamily for their
conserved GTPase motifs and enzymatic activities.
Length = 275
Score = 27.1 bits (61), Expect = 2.1
Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 10/68 (14%)
Query: 12 TYKLVVVGDGGVGKSA-ITIQFFQKLFVTDYDPTIEDSYLQHTEV---------DDVMCI 61
+ ++VVG+ G+GKS I F KL+ + Y P + + E+ + V
Sbjct: 4 QFNIMVVGESGLGKSTFINTLFGTKLYPSKYPPAPGEHITKTVEIKISKAELEENGVKLK 63
Query: 62 LDVLDTAG 69
L V+DT G
Sbjct: 64 LTVIDTPG 71
>gnl|CDD|238994 cd02037, MRP-like, MRP (Multiple Resistance and pH adaptation) is
a homologue of the Fer4_NifH superfamily. Like the
other members of the superfamily, MRP contains a
ATP-binding domain at the N-termini. It is found in
bacteria as a membrane-spanning protein and functions
as a Na+/H+ antiporter.
Length = 169
Score = 26.7 bits (60), Expect = 2.2
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 15 LVVVGDGGVGKSAITIQ 31
V+ G GGVGKS + +
Sbjct: 3 AVMSGKGGVGKSTVAVN 19
>gnl|CDD|213512 TIGR00174, miaA, tRNA dimethylallyltransferase. Alternate names
include delta(2)-isopentenylpyrophosphate transferase,
IPP transferase, 2-methylthio-N6-isopentyladenosine
tRNA modification enzyme. Catalyzes the first step in
the modification of an adenosine near the anticodon to
2-methylthio-N6-isopentyladenosine. Understanding of
substrate specificity has changed [Protein synthesis,
tRNA and rRNA base modification].
Length = 287
Score = 27.0 bits (60), Expect = 2.3
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 15 LVVVGDGGVGKSAITIQFFQKL 36
+ ++G GKS ++IQ QKL
Sbjct: 2 IFLMGPTASGKSQLSIQLAQKL 23
>gnl|CDD|233672 TIGR01989, COQ6, ubiquinone biosynthesis monooxygenase COQ6. This
model represents the monooxygenase responsible for the
4-hydroxylateion of the phenol ring in the aerobic
biosynthesis of ubiquinone.
Length = 437
Score = 27.0 bits (60), Expect = 2.7
Identities = 8/34 (23%), Positives = 16/34 (47%)
Query: 30 IQFFQKLFVTDYDPTIEDSYLQHTEVDDVMCILD 63
IQ F ++ V D + + +D+ CI++
Sbjct: 82 IQPFGRMQVWDGCSLALIRFDRDNGKEDMACIIE 115
>gnl|CDD|206689 cd04102, RabL3, Rab GTPase-like family 3 (Rab-like3). RabL3
(Rab-like3) subfamily. RabL3s are novel proteins that
have high sequence similarity with Rab family members,
but display features that are distinct from Rabs, and
have been termed Rab-like. As in other Rab-like
proteins, RabL3 lacks a prenylation site at the
C-terminus. The specific function of RabL3 remains
unknown.
Length = 204
Score = 26.4 bits (58), Expect = 3.6
Identities = 9/15 (60%), Positives = 14/15 (93%)
Query: 14 KLVVVGDGGVGKSAI 28
K++V+GD GVGKS++
Sbjct: 2 KVLVLGDSGVGKSSL 16
>gnl|CDD|206724 cd04159, Arl10_like, Arf-like 9 (Arl9) and 10 (Arl10) GTPases.
Arl10-like subfamily. Arl9/Arl10 was identified from a
human cancer-derived EST dataset. No functional
information about the subfamily is available at the
current time, but crystal structures of human Arl10b and
Arl10c have been solved.
Length = 159
Score = 26.1 bits (58), Expect = 3.6
Identities = 12/39 (30%), Positives = 19/39 (48%)
Query: 62 LDVLDTAGQEEFSAMREQYMRKGDGFLLVYSVTDQQSYE 100
+ V D GQ F +M E+Y R + + V D++ E
Sbjct: 46 IKVWDLGGQPRFRSMWERYCRGVNAIVYVVDAADREKLE 84
>gnl|CDD|177661 PLN00023, PLN00023, GTP-binding protein; Provisional.
Length = 334
Score = 26.4 bits (58), Expect = 4.2
Identities = 9/15 (60%), Positives = 14/15 (93%)
Query: 14 KLVVVGDGGVGKSAI 28
+++VVGD GVGKS++
Sbjct: 23 RVLVVGDSGVGKSSL 37
>gnl|CDD|206719 cd04152, Arl4_Arl7, Arf-like 4 (Arl4) and 7 (Arl7) GTPases. Arl4
(Arf-like 4) is highly expressed in testicular germ
cells, and is found in the nucleus and nucleolus. In
mice, Arl4 is developmentally expressed during
embryogenesis, and a role in somite formation and
central nervous system differentiation has been
proposed. Arl7 has been identified as the only Arf/Arl
protein to be induced by agonists of liver X-receptor
and retinoid X-receptor and by cholesterol loading in
human macrophages. Arl7 is proposed to play a role in
transport between a perinuclear compartment and the
plasma membrane, apparently linked to the ABCA1-mediated
cholesterol secretion pathway. Older literature suggests
that Arl6 is a part of the Arl4/Arl7 subfamily, but
analyses based on more recent sequence data place Arl6
in its own subfamily.
Length = 183
Score = 25.9 bits (57), Expect = 4.2
Identities = 13/51 (25%), Positives = 21/51 (41%)
Query: 64 VLDTAGQEEFSAMREQYMRKGDGFLLVYSVTDQQSYENIKHFYTQILRVKD 114
D GQE+ + + Y R DG + V D + E K +I + +
Sbjct: 56 FWDVGGQEKLRPLWKSYTRCTDGIVFVVDSVDVERMEEAKTELHKITKFSE 106
>gnl|CDD|223531 COG0455, flhG, Antiactivator of flagellar biosynthesis FleN, an
ATPase [Cell motility].
Length = 262
Score = 26.1 bits (58), Expect = 4.2
Identities = 11/20 (55%), Positives = 13/20 (65%), Gaps = 1/20 (5%)
Query: 12 TYKLVVV-GDGGVGKSAITI 30
T + VV G GGVGK+ IT
Sbjct: 2 TKVIAVVSGKGGVGKTTITA 21
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 26.4 bits (59), Expect = 4.2
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 65 LDTAGQEEFSAMR 77
LDT G E F+AMR
Sbjct: 301 LDTPGHEAFTAMR 313
>gnl|CDD|221329 pfam11938, DUF3456, TLR4 regulator and MIR-interacting MSAP. This
family of proteins, found from plants to humans, is
PRAT4 (A and B), a Protein Associated with Toll-like
receptor 4. The Toll family of receptors - TLRs - plays
an essential role in innate recognition of microbial
products, the first line of defence against bacterial
infection. PRAT4A influences the subcellular
distribution and the strength of TLR responses and
alters the relative activity of each TLR. PRAT4B
regulates TLR4 trafficking to the cell surface and the
extent of its expression there. TLR4 recognizes
lipopolysaccharide (LPS), one of the most
immuno-stimulatory glycolipids constituting the outer
membrane of the Gram-negative bacteria. This family has
also been described as a SAP-like MIR-interacting
protein family.
Length = 151
Score = 25.8 bits (57), Expect = 4.5
Identities = 12/59 (20%), Positives = 26/59 (44%), Gaps = 1/59 (1%)
Query: 1 MAKAPNNNNITTYKLVVVGDGGVGKSAIT-IQFFQKLFVTDYDPTIEDSYLQHTEVDDV 58
AK + T + LV+ G + + ++F + + +++ IE+ Y DD+
Sbjct: 80 FAKGMSPTFQTLHGLVLKGVKVDPSAEVAELKFQCERLLEEHEDEIEEWYKNEQLEDDL 138
>gnl|CDD|223562 COG0488, Uup, ATPase components of ABC transporters with duplicated
ATPase domains [General function prediction only].
Length = 530
Score = 26.1 bits (58), Expect = 4.6
Identities = 16/85 (18%), Positives = 26/85 (30%), Gaps = 12/85 (14%)
Query: 17 VVGDGGVGKS----AIT--IQFFQKLFVTDYDPTIEDSYL-QHTEVDDVMCILDVLDTAG 69
+VG G GKS + ++ + YL Q +D +LD +
Sbjct: 34 LVGRNGAGKSTLLKILAGELEPDSGEVTRPKGLRVG--YLSQEPPLDPEKTVLDYVIEGF 91
Query: 70 QEEFSAMRE---QYMRKGDGFLLVY 91
E + E Y D +
Sbjct: 92 GELRELLAELEEAYALLADPDDELL 116
>gnl|CDD|223563 COG0489, Mrp, ATPases involved in chromosome partitioning [Cell
division and chromosome partitioning].
Length = 265
Score = 25.8 bits (57), Expect = 5.0
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 15 LVVVGDGGVGKSAITI 30
V G GGVGKS + +
Sbjct: 61 AVTSGKGGVGKSTVAV 76
>gnl|CDD|222165 pfam13481, AAA_25, AAA domain. This AAA domain is found in a
wide variety of presumed DNA repair proteins.
Length = 154
Score = 25.7 bits (57), Expect = 5.2
Identities = 5/16 (31%), Positives = 9/16 (56%)
Query: 16 VVVGDGGVGKSAITIQ 31
++ G G GKS + +
Sbjct: 37 LLAGAPGTGKSTLALD 52
>gnl|CDD|215893 pfam00389, 2-Hacid_dh, D-isomer specific 2-hydroxyacid
dehydrogenase, catalytic domain. This family represents
the largest portion of the catalytic domain of
2-hydroxyacid dehydrogenases as the NAD binding domain
is inserted within the structural domain.
Length = 312
Score = 26.1 bits (58), Expect = 5.3
Identities = 16/68 (23%), Positives = 22/68 (32%), Gaps = 14/68 (20%)
Query: 15 LVVVGDGGVGKSAITIQFFQKLFVTDYDP--------------TIEDSYLQHTEVDDVMC 60
L V+G GG+G I + V YDP + D L + D +
Sbjct: 139 LGVIGGGGIGGIGAAIAKALGMGVVAYDPYPNPERAEEGGVEVLLLDLLLLDLKESDDLI 198
Query: 61 ILDVLDTA 68
L T
Sbjct: 199 NLAPPTTM 206
>gnl|CDD|218141 pfam04548, AIG1, AIG1 family. Arabidopsis protein AIG1 appears
to be involved in plant resistance to bacteria.
Length = 211
Score = 25.6 bits (57), Expect = 5.8
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 15 LVVVGDGGVGKSA 27
+V+VG G GKSA
Sbjct: 3 IVLVGKTGNGKSA 15
>gnl|CDD|176224 cd08263, Zn_ADH10, Alcohol dehydrogenases of the MDR family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. ADH is a member of the medium
chain alcohol dehydrogenase family (MDR), which have a
NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H)-binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 367
Score = 25.8 bits (57), Expect = 6.9
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 15 LVVVGDGGVGKSAITI 30
+ V+G GGVG SAI +
Sbjct: 191 VAVIGVGGVGSSAIQL 206
>gnl|CDD|232980 TIGR00450, mnmE_trmE_thdF, tRNA modification GTPase TrmE. TrmE,
also called MnmE and previously designated ThdF
(thiophene and furan oxidation protein), is a GTPase
involved in tRNA modification to create
5-methylaminomethyl-2-thiouridine in the wobble position
of some tRNAs. This protein and GidA form an
alpha2/beta2 heterotetramer [Protein synthesis, tRNA and
rRNA base modification].
Length = 442
Score = 25.5 bits (56), Expect = 7.1
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 4/61 (6%)
Query: 11 TTYKLVVVGDGGVGKSAITIQFF--QKLFVTDYDPTIEDSYLQHTEVDDVMCILDVLDTA 68
+KL +VG VGKS++ + V+D T D E++ ++ + +LDTA
Sbjct: 202 DGFKLAIVGSPNVGKSSLLNALLKQDRAIVSDIKGTTRDVVEGDFELNGIL--IKLLDTA 259
Query: 69 G 69
G
Sbjct: 260 G 260
>gnl|CDD|176221 cd08260, Zn_ADH6, Alcohol dehydrogenases of the MDR family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. This group has the characteristic
catalytic and structural zinc sites of the
zinc-dependent alcohol dehydrogenases. Alcohol
dehydrogenase in the liver converts ethanol and NAD+ to
acetaldehyde and NADH, while in yeast and some other
microorganisms ADH catalyzes the conversion acetaldehyde
to ethanol in alcoholic fermentation. ADH is a member of
the medium chain alcohol dehydrogenase family (MDR),
which has a NAD(P)(H)-binding domain in a Rossmann fold
of a beta-alpha form. The NAD(H)-binding region is
comprised of 2 structurally similar halves, each of
which contacts a mononucleotide. A GxGxxG motif after
the first mononucleotide contact half allows the close
contact of the coenzyme with the ADH backbone. The
N-terminal catalytic domain has a distant homology to
GroES. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit, a
catalytic zinc at the active site and a structural zinc
in a lobe of the catalytic domain. NAD(H)-binding occurs
in the cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 345
Score = 25.6 bits (57), Expect = 7.2
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 15 LVVVGDGGVGKSAITI 30
+ V G GGVG SA+ I
Sbjct: 169 VAVHGCGGVGLSAVMI 184
>gnl|CDD|241435 cd13281, PH_PLEKHD1, Pleckstrin homology (PH) domain containing,
family D (with coiled-coil domains) member 1 PH domain.
Human PLEKHD1 (also called UPF0639, pleckstrin homology
domain containing, family D (with M protein repeats)
member 1) is a single transcript and contains a single
PH domain. PLEKHD1 is conserved in human, chimpanzee, ,
dog, cow, mouse, chicken, zebrafish, and Caenorhabditis
elegans. PH domains have diverse functions, but in
general are involved in targeting proteins to the
appropriate cellular location or in the interaction with
a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH domains
bind phosphoinositide phosphates (PIPs) with high
affinity and specificity. PH domains are distinguished
from other PIP-binding domains by their specific
high-affinity binding to PIPs with two vicinal phosphate
groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3
which results in targeting some PH domain proteins to
the plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 139
Score = 25.0 bits (55), Expect = 7.8
Identities = 6/21 (28%), Positives = 14/21 (66%)
Query: 85 DGFLLVYSVTDQQSYENIKHF 105
+ FLL Y+ ++++ +E + F
Sbjct: 39 ECFLLYYAESEKKDFEKTRRF 59
>gnl|CDD|129575 TIGR00484, EF-G, translation elongation factor EF-G. After peptide
bond formation, this elongation factor of bacteria and
organelles catalyzes the translocation of the tRNA-mRNA
complex, with its attached nascent polypeptide chain,
from the A-site to the P-site of the ribosome. Every
completed bacterial genome has at least one copy, but
some species have additional EF-G-like proteins. The
closest homolog to canonical (e.g. E. coli) EF-G in the
spirochetes clusters as if it is derived from
mitochondrial forms, while a more distant second copy is
also present. Synechocystis PCC6803 has a few proteins
more closely related to EF-G than to any other
characterized protein. Two of these resemble E. coli
EF-G more closely than does the best match from the
spirochetes; it may be that both function as authentic
EF-G [Protein synthesis, Translation factors].
Length = 689
Score = 25.5 bits (56), Expect = 8.4
Identities = 9/32 (28%), Positives = 18/32 (56%)
Query: 60 CILDVLDTAGQEEFSAMREQYMRKGDGFLLVY 91
++++DT G +F+ E+ +R DG + V
Sbjct: 75 HRINIIDTPGHVDFTVEVERSLRVLDGAVAVL 106
>gnl|CDD|176247 cd08287, FDH_like_ADH3, formaldehyde dehydrogenase (FDH)-like.
This group contains proteins identified as alcohol
dehydrogenases and glutathione-dependant formaldehyde
dehydrogenases (FDH) of the zinc-dependent/medium chain
alcohol dehydrogenase family. The MDR family uses
NAD(H) as a cofactor in the interconversion of alcohols
and aldehydes, or ketones. FDH converts formaldehyde
and NAD to formate and NADH. The initial step in this
process the spontaneous formation of a
S-(hydroxymethyl)glutathione adduct from formaldehyde
and glutathione, followed by FDH-mediated oxidation (and
detoxification) of the adduct to S-formylglutathione.
The medium chain alcohol dehydrogenase family (MDR) has
a NAD(P)(H)-binding domain in a Rossmann fold of a
beta-alpha form. The N-terminal region typically has an
all-beta catalytic domain. These proteins typically form
dimers (typically higher plants, mammals) or tetramers
(yeast, bacteria), and have 2 tightly bound zinc atoms
per subunit.
Length = 345
Score = 25.3 bits (56), Expect = 8.4
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 16 VVVGDGGVGKSAI 28
VVVGDG VG A+
Sbjct: 173 VVVGDGAVGLCAV 185
>gnl|CDD|206652 cd01853, Toc34_like, Translocon at the Outer-envelope membrane of
Chloroplasts 34-like (Toc34-like). The Toc34-like
(Translocon at the Outer-envelope membrane of
Chloroplasts) family contains several Toc proteins,
including Toc34, Toc33, Toc120, Toc159, Toc86, Toc125,
and Toc90. The Toc complex at the outer envelope
membrane of chloroplasts is a molecular machine of ~500
kDa that contains a single Toc159 protein, four Toc75
molecules, and four or five copies of Toc34. Toc64 and
Toc12 are associated with the translocon, but do not
appear to be part of the core complex. The Toc
translocon initiates the import of nuclear-encoded
preproteins from the cytosol into the organelle. Toc34
and Toc159 are both GTPases, while Toc75 is a
beta-barrel integral membrane protein. Toc159 is
equally distributed between a soluble cytoplasmic form
and a membrane-inserted form, suggesting that assembly
of the Toc complex is dynamic. Toc34 and Toc75 act
sequentially to mediate docking and insertion of Toc159
resulting in assembly of the functional translocon.
Length = 248
Score = 25.4 bits (56), Expect = 8.6
Identities = 7/13 (53%), Positives = 10/13 (76%)
Query: 16 VVVGDGGVGKSAI 28
+V+G GVGKS+
Sbjct: 35 LVLGKTGVGKSST 47
>gnl|CDD|234790 PRK00550, rpsE, 30S ribosomal protein S5; Validated.
Length = 168
Score = 25.1 bits (56), Expect = 8.7
Identities = 10/18 (55%), Positives = 11/18 (61%), Gaps = 6/18 (33%)
Query: 15 LVVVGDG------GVGKS 26
LVVVGDG G GK+
Sbjct: 38 LVVVGDGKGRVGFGYGKA 55
>gnl|CDD|129594 TIGR00503, prfC, peptide chain release factor 3. This
translation releasing factor, RF-3 (prfC) was
originally described as stop codon-independent, in
contrast to peptide chain release factor 1 (RF-1, prfA)
and RF-2 (prfB). RF-1 and RF-2 are closely related to
each other, while RF-3 is similar to elongation factors
EF-Tu and EF-G; RF-1 is active at UAA and UAG and RF-2
is active at UAA and UGA. More recently, RF-3 was shown
to be active primarily at UGA stop codons in E. coli.
All bacteria and organelles have RF-1. The Mycoplasmas
and organelles, which translate UGA as Trp rather than
as a stop codon, lack RF-2. RF-3, in contrast, seems to
be rare among bacteria and is found so far only in
Escherichia coli and some other gamma subdivision
Proteobacteria, in Synechocystis PCC6803, and in
Staphylococcus aureus [Protein synthesis, Translation
factors].
Length = 527
Score = 25.3 bits (55), Expect = 8.7
Identities = 8/15 (53%), Positives = 13/15 (86%)
Query: 60 CILDVLDTAGQEEFS 74
C++++LDT G E+FS
Sbjct: 80 CLVNLLDTPGHEDFS 94
>gnl|CDD|206679 cd01892, Miro2, Mitochondrial Rho family 2 (Miro2), C-terminal.
Miro2 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 putative
GTPase domain in the C terminus 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 = 180
Score = 25.3 bits (56), Expect = 8.9
Identities = 30/100 (30%), Positives = 43/100 (43%), Gaps = 9/100 (9%)
Query: 17 VVGDGGVGKSAITIQFFQKLFVTD-YDPTIEDSYLQHT-EVDDVMCILDVLDTAG-QEEF 73
V+G G GKSA+ F + F + Y PTI+ Y +T EV L +L G EE
Sbjct: 9 VLGAKGSGKSALLQAFLGRSFSQNAYSPTIKPRYAVNTVEVPGQEKYL-ILREVGEDEEA 67
Query: 74 SAMREQYMRKGDGFLLVYSVTDQQSYENI-----KHFYTQ 108
+ + + D LVY +D S+ K+F
Sbjct: 68 ILLNDAELAACDVACLVYDSSDPNSFSYCAEVYKKYFMLG 107
>gnl|CDD|234172 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
Members of this protein family are homologs of ClpB, an
ATPase associated with chaperone-related functions.
These ClpB homologs, designated ClpV1, are a key
component of the bacterial pathogenicity-associated type
VI secretion system [Protein fate, Protein and peptide
secretion and trafficking, Cellular processes,
Pathogenesis].
Length = 852
Score = 25.3 bits (56), Expect = 9.4
Identities = 9/22 (40%), Positives = 13/22 (59%), Gaps = 6/22 (27%)
Query: 7 NNNITTYKLVVVGDGGVGKSAI 28
NN I + G+ GVGK+A+
Sbjct: 209 NNPI------LTGEAGVGKTAV 224
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
0.319 0.136 0.386
Gapped
Lambda K H
0.267 0.0555 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,819,114
Number of extensions: 505562
Number of successful extensions: 867
Number of sequences better than 10.0: 1
Number of HSP's gapped: 805
Number of HSP's successfully gapped: 164
Length of query: 115
Length of database: 10,937,602
Length adjustment: 79
Effective length of query: 36
Effective length of database: 7,433,636
Effective search space: 267610896
Effective search space used: 267610896
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.6 bits)