RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13093
(111 letters)
>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 = 161 bits (410), Expect = 2e-52
Identities = 62/63 (98%), Positives = 63/63 (100%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKP+NLGLWDTAGQEDYDRLRPLSY
Sbjct: 11 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSY 70
Query: 61 PQT 63
PQT
Sbjct: 71 PQT 73
>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 = 157 bits (399), Expect = 1e-50
Identities = 53/63 (84%), Positives = 58/63 (92%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
AVGKTCLLI YTTNAFP +Y+PTVF+NYSA+V VDGKP+ LGLWDTAGQEDYDRLRPLSY
Sbjct: 8 AVGKTCLLIVYTTNAFPEDYVPTVFENYSADVEVDGKPVELGLWDTAGQEDYDRLRPLSY 67
Query: 61 PQT 63
P T
Sbjct: 68 PDT 70
>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 = 152 bits (387), Expect = 7e-49
Identities = 56/63 (88%), Positives = 59/63 (93%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
AVGKTCLLISYTTN FP EY+PTVFDNYSANV VDGK +NLGLWDTAGQE+YDRLRPLSY
Sbjct: 10 AVGKTCLLISYTTNKFPTEYVPTVFDNYSANVTVDGKQVNLGLWDTAGQEEYDRLRPLSY 69
Query: 61 PQT 63
PQT
Sbjct: 70 PQT 72
>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 = 131 bits (330), Expect = 3e-40
Identities = 51/63 (80%), Positives = 56/63 (88%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
AVGKTCLLISYTTN FP EY+PTVFDNY+ VM+ G+P LGL+DTAGQEDYDRLRPLSY
Sbjct: 11 AVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTLGLFDTAGQEDYDRLRPLSY 70
Query: 61 PQT 63
PQT
Sbjct: 71 PQT 73
>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 = 128 bits (322), Expect = 8e-39
Identities = 51/63 (80%), Positives = 55/63 (87%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
AVGKTCLLI YTTNAFP EYIPTVFDNYSA VDG+ ++L LWDTAGQE+YDRLR LSY
Sbjct: 13 AVGKTCLLICYTTNAFPKEYIPTVFDNYSAQTAVDGRTVSLNLWDTAGQEEYDRLRTLSY 72
Query: 61 PQT 63
PQT
Sbjct: 73 PQT 75
>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 = 124 bits (313), Expect = 1e-37
Identities = 48/60 (80%), Positives = 56/60 (93%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
AVGKTC+LISYT+N FP +Y+PTVFDN+SANV+VDG +NLGLWDTAGQEDY+RLRPLSY
Sbjct: 11 AVGKTCMLISYTSNTFPTDYVPTVFDNFSANVVVDGNTVNLGLWDTAGQEDYNRLRPLSY 70
>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 = 118 bits (298), Expect = 4e-35
Identities = 41/64 (64%), Positives = 47/64 (73%), Gaps = 1/64 (1%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMV-DGKPINLGLWDTAGQEDYDRLRPLS 59
GKTCLL+ Y +FP EY+PTVF+NY + V +GK I L LWDTAGQEDYDRLRPLS
Sbjct: 13 GCGKTCLLMVYAQGSFPEEYVPTVFENYVTTLQVPNGKIIELALWDTAGQEDYDRLRPLS 72
Query: 60 YPQT 63
YP
Sbjct: 73 YPDV 76
>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 = 114 bits (287), Expect = 1e-33
Identities = 41/63 (65%), Positives = 52/63 (82%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
AVGKT L++SYTTN +P EY+PT FDN+S V+VDGKP+ L L DTAGQ+++D+LRPL Y
Sbjct: 10 AVGKTSLIVSYTTNGYPTEYVPTAFDNFSVVVLVDGKPVRLQLCDTAGQDEFDKLRPLCY 69
Query: 61 PQT 63
P T
Sbjct: 70 PDT 72
>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 = 114 bits (286), Expect = 1e-33
Identities = 43/63 (68%), Positives = 51/63 (80%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
A GKTCLLI ++ + FP Y+PTVF+NY A++ VDGK + L LWDTAGQEDYDRLRPLSY
Sbjct: 11 ACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLRPLSY 70
Query: 61 PQT 63
P T
Sbjct: 71 PDT 73
>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 = 109 bits (274), Expect = 8e-32
Identities = 34/64 (53%), Positives = 42/64 (65%), Gaps = 1/64 (1%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLS 59
VGK+ LLI +T N FP EYIPT+ D Y+ + VDGK + L +WDTAGQE + LRPL
Sbjct: 9 GVGKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAGQERFRALRPLY 68
Query: 60 YPQT 63
Y
Sbjct: 69 YRGA 72
>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 = 107 bits (268), Expect = 6e-31
Identities = 46/63 (73%), Positives = 53/63 (84%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
AVGKTCLL+SY +AFP EY+PTVFD+Y+ +V V GK LGL+DTAGQEDYDRLRPLSY
Sbjct: 10 AVGKTCLLMSYANDAFPEEYVPTVFDHYAVSVTVGGKQYLLGLYDTAGQEDYDRLRPLSY 69
Query: 61 PQT 63
P T
Sbjct: 70 PMT 72
>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 = 99 bits (249), Expect = 9e-28
Identities = 39/62 (62%), Positives = 46/62 (74%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
A GKT LL +T FP EY PTVF+NY + VDGKP+ L LWDTAGQE+Y+RLRPLSY
Sbjct: 11 ACGKTSLLYVFTLGEFPEEYHPTVFENYVTDCRVDGKPVQLALWDTAGQEEYERLRPLSY 70
Query: 61 PQ 62
+
Sbjct: 71 SK 72
>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 = 92.5 bits (230), Expect = 4e-25
Identities = 32/61 (52%), Positives = 43/61 (70%)
Query: 3 GKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSYPQ 62
GKT LL + ++FP Y+PTVF+NY+A+ VD + I L LWDT+G YD +RPLSYP
Sbjct: 13 GKTALLQVFAKDSFPENYVPTVFENYTASFEVDKQRIELSLWDTSGSPYYDNVRPLSYPD 72
Query: 63 T 63
+
Sbjct: 73 S 73
>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 = 86.5 bits (214), Expect = 1e-22
Identities = 36/63 (57%), Positives = 43/63 (68%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
A GKT LL +T FP Y PTVF+NY ++ VDG + L LWDTAGQE++DRLR LSY
Sbjct: 10 ACGKTSLLNVFTRGYFPQVYEPTVFENYIHDIFVDGLAVELSLWDTAGQEEFDRLRSLSY 69
Query: 61 PQT 63
T
Sbjct: 70 ADT 72
>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 = 81.3 bits (201), Expect = 8e-21
Identities = 35/110 (31%), Positives = 48/110 (43%), Gaps = 8/110 (7%)
Query: 1 AVGKTCLLISYTTN-AFPGEYIPTVFDNY-SANVMVDGKPINLGLWDTAGQEDYDRLRPL 58
VGK+ LL N EY P NY + + DGK L DTAGQEDYD +R L
Sbjct: 11 NVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAGQEDYDAIRRL 70
Query: 59 SYPQTW-SLRSFALHAGHPVRFPRGRKIRIMQMIGFRD----RLLWGSKQ 103
Y SLR F + + + + ++I + +L G+K
Sbjct: 71 YYRAVESSLRVFDI-VILVLDVEEILEKQTKEIIHHAESGVPIILVGNKI 119
>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 = 76.6 bits (188), Expect = 6e-19
Identities = 31/61 (50%), Positives = 42/61 (68%)
Query: 3 GKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSYPQ 62
GKT LL + + FP Y+PTVF+NY+A+ +D + I L LWDT+G YD +RPLSYP
Sbjct: 17 GKTALLHVFAKDCFPENYVPTVFENYTASFEIDTQRIELSLWDTSGSPYYDNVRPLSYPD 76
Query: 63 T 63
+
Sbjct: 77 S 77
>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 = 75.1 bits (184), Expect = 5e-18
Identities = 28/59 (47%), Positives = 40/59 (67%)
Query: 3 GKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSYP 61
GKT LL + + +P Y+PTVF+NY+A+ +D I L +WDT+G YD +RPL+YP
Sbjct: 13 GKTALLHVFAKDNYPESYVPTVFENYTASFEIDKHRIELNMWDTSGSSYYDNVRPLAYP 71
>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 = 71.7 bits (177), Expect = 3e-17
Identities = 25/61 (40%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVF-DNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLS 59
VGKT LL+ + N F Y T+ D S + VDGK + L +WDTAGQE + +
Sbjct: 10 GVGKTSLLLRFVDNKFSENYKSTIGVDFKSKTIEVDGKKVKLQIWDTAGQERFRSITSSY 69
Query: 60 Y 60
Y
Sbjct: 70 Y 70
>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 = 70.2 bits (173), Expect = 1e-16
Identities = 23/60 (38%), Positives = 35/60 (58%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
VGK+ L I + + F EY PT+ D+Y ++VDG+ L + DTAGQE++ +R
Sbjct: 9 GVGKSALTIRFVSGEFVEEYDPTIEDSYRKQIVVDGETYTLDILDTAGQEEFSAMRDQYI 68
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins
[General function prediction only].
Length = 219
Score = 70.4 bits (172), Expect = 4e-16
Identities = 27/64 (42%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSA-NVMVDGKPINLGLWDTAGQEDYDRLRPLS 59
VGKT LL + FP Y PT+ + A + + I L LWDTAGQE+Y LRP
Sbjct: 15 GVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQEEYRSLRPEY 74
Query: 60 YPQT 63
Y
Sbjct: 75 YRGA 78
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 64.1 bits (157), Expect = 3e-14
Identities = 22/53 (41%), Positives = 31/53 (58%), Gaps = 1/53 (1%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDY 52
VGK+ LL +T F +Y T+ D + + VDGK + L +WDTAGQE +
Sbjct: 10 GVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIEVDGKRVKLQIWDTAGQERF 62
>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 = 63.9 bits (155), Expect = 1e-13
Identities = 25/58 (43%), Positives = 37/58 (63%)
Query: 3 GKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
GKT +L + +P Y+PTVF+NY+A + + + + L LWDT+G YD +RPL Y
Sbjct: 25 GKTAMLQVLAKDCYPETYVPTVFENYTACLETEEQRVELSLWDTSGSPYYDNVRPLCY 82
>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 = 60.8 bits (148), Expect = 6e-13
Identities = 27/62 (43%), Positives = 35/62 (56%), Gaps = 6/62 (9%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPL-- 58
VGK+ LL+ +T + F + T+ D V VDGK + L +WDTAGQE R R L
Sbjct: 11 VGKSSLLLRFTDDTFDEDLSSTIGVDFKVKTVTVDGKKVKLAIWDTAGQE---RFRTLTS 67
Query: 59 SY 60
SY
Sbjct: 68 SY 69
>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 = 60.7 bits (148), Expect = 6e-13
Identities = 25/60 (41%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDN-YSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
VGKT L++ Y N F ++ T + + V + GK I+L +WDTAGQE Y L P+ Y
Sbjct: 11 VGKTSLVLRYVENKFNEKHESTTQASFFQKTVNIGGKRIDLAIWDTAGQERYHALGPIYY 70
>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 = 60.2 bits (146), Expect = 1e-12
Identities = 28/55 (50%), Positives = 34/55 (61%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLR 56
VGKT L I N F Y PT+ D+Y V+VDG+P L + DTAGQE+Y LR
Sbjct: 10 VGKTALTIQLCLNHFVETYDPTIEDSYRKQVVVDGQPCMLEVLDTAGQEEYTALR 64
>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 = 59.2 bits (144), Expect = 2e-12
Identities = 25/61 (40%), Positives = 35/61 (57%), Gaps = 2/61 (3%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLS 59
+VGKT ++ + + F +Y T+ D S + VD K + L LWDTAGQE + L P S
Sbjct: 10 SVGKTSIITRFMYDTFDNQYQATIGIDFLSKTMYVDDKTVRLQLWDTAGQERFRSLIP-S 68
Query: 60 Y 60
Y
Sbjct: 69 Y 69
>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 = 59.1 bits (144), Expect = 2e-12
Identities = 21/56 (37%), Positives = 33/56 (58%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLR 56
VGK+ L I + F +Y PT+ D+Y + +DG+ L + DTAGQE++ +R
Sbjct: 10 GVGKSALTIQFIQGHFVDDYDPTIEDSYRKQIEIDGEVCLLDILDTAGQEEFSAMR 65
>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 = 58.7 bits (143), Expect = 3e-12
Identities = 22/55 (40%), Positives = 33/55 (60%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLR 56
VGK+ L I + F EY PT+ D+Y + +DG+ L + DTAGQE++ +R
Sbjct: 13 VGKSALTIQFVQGHFVDEYDPTIEDSYRKQIEIDGEVCLLDILDTAGQEEFSAMR 67
>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 = 56.7 bits (137), Expect = 2e-11
Identities = 25/55 (45%), Positives = 34/55 (61%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLR 56
VGK+ L I N F EY PT+ D+Y V++DG+ L + DTAGQE+Y +R
Sbjct: 12 VGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMR 66
>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 = 56.5 bits (137), Expect = 3e-11
Identities = 20/49 (40%), Positives = 30/49 (61%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQE 50
VGK+ L + + T F GEY P + YS V +DG+ ++L + DT GQ+
Sbjct: 10 VGKSALTVRFLTKRFIGEYEPNLESLYSRQVTIDGEQVSLEIQDTPGQQ 58
>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 = 56.1 bits (136), Expect = 4e-11
Identities = 22/51 (43%), Positives = 33/51 (64%), Gaps = 1/51 (1%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQE 50
VGK+CLL+ ++ ++F +I T+ D + +DGK I L +WDTAGQE
Sbjct: 13 GVGKSCLLLRFSEDSFNPSFISTIGIDFKIRTIELDGKKIKLQIWDTAGQE 63
>gnl|CDD|206695 cd04112, Rab26, Rab GTPase family 26 (Rab26). Rab26 subfamily.
First identified in rat pancreatic acinar cells, Rab26
is believed to play a role in recruiting mature
granules to the plasma membrane upon beta-adrenergic
stimulation. Rab26 belongs to the Rab functional group
III, which are considered key regulators of
intracellular vesicle transport during exocytosis.
GTPase activating proteins (GAPs) interact with
GTP-bound Rab and accelerate the hydrolysis of GTP to
GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation
of the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs),
which facilitate Rab recycling by masking C-terminal
lipid binding and promoting cytosolic localization.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins.
Length = 191
Score = 52.9 bits (127), Expect = 9e-10
Identities = 27/62 (43%), Positives = 38/62 (61%), Gaps = 5/62 (8%)
Query: 1 AVGKTCLLISYTTNAF-PGEYIPTVFDNYSANVM-VDGKPINLGLWDTAGQEDYDRLRPL 58
VGKTCLL+ + AF G +I TV ++ V+ VDG + L +WDTAGQE R R +
Sbjct: 10 GVGKTCLLVRFKDGAFLAGSFIATVGIQFTNKVVTVDGVKVKLQIWDTAGQE---RFRSV 66
Query: 59 SY 60
++
Sbjct: 67 TH 68
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 52.6 bits (126), Expect = 1e-09
Identities = 23/55 (41%), Positives = 33/55 (60%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLR 56
VGK+ L I + N F EY PT+ D+Y ++D + L + DTAGQE+Y +R
Sbjct: 16 VGKSALTIQFIQNHFIDEYDPTIEDSYRKQCVIDEETCLLDILDTAGQEEYSAMR 70
>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 = 51.3 bits (123), Expect = 2e-09
Identities = 21/55 (38%), Positives = 34/55 (61%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLR 56
VGK+ L I + + F +Y PT+ D+Y+ +DG+ L + DTAGQE++ +R
Sbjct: 13 VGKSALTIQFIQSYFVTDYDPTIEDSYTKQCEIDGQWARLDILDTAGQEEFSAMR 67
>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 = 51.5 bits (124), Expect = 2e-09
Identities = 21/50 (42%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQE 50
VGKT L+ Y F +Y T+ D + V VD + + L +WDTAGQE
Sbjct: 11 VGKTSLMNQYVNKKFSNQYKATIGADFLTKEVTVDDRLVTLQIWDTAGQE 60
>gnl|CDD|206710 cd04139, RalA_RalB, Ral (Ras-like) family containing highly
homologous RalA and RalB. The Ral (Ras-like) subfamily
consists of the highly homologous RalA and RalB. Ral
proteins are believed to play a crucial role in
tumorigenesis, metastasis, endocytosis, and actin
cytoskeleton dynamics. Despite their high sequence
similarity (>80% sequence identity), nonoverlapping and
opposing functions have been assigned to RalA and RalBs
in tumor migration. In human bladder and prostate
cancer cells, RalB promotes migration while RalA
inhibits it. A Ral-specific set of GEFs has been
identified that are activated by Ras binding. This
RalGEF activity is enhanced by Ras binding to another
of its target proteins, phosphatidylinositol 3-kinase
(PI3K). Ral effectors include RLIP76/RalBP1, a
Rac/cdc42 GAP, and the exocyst (Sec6/8) complex, a
heterooctomeric protein complex that is involved in
tethering vesicles to specific sites on the plasma
membrane prior to exocytosis. In rat kidney cells, RalB
is required for functional assembly of the exocyst and
for localizing the exocyst to the leading edge of
migrating cells. In human cancer cells, RalA is
required to support anchorage-independent proliferation
and RalB is required to suppress apoptosis. RalA has
been shown to localize to the plasma membrane while
RalB is localized to the intracellular vesicles. Most
Ras proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 163
Score = 50.9 bits (122), Expect = 4e-09
Identities = 23/55 (41%), Positives = 35/55 (63%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLR 56
VGK+ L + + + F +Y PT D+Y V++DG+ + L + DTAGQEDY +R
Sbjct: 11 VGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEVQLNILDTAGQEDYAAIR 65
>gnl|CDD|206661 cd01869, Rab1_Ypt1, Rab GTPase family 1 includes the yeast
homolog Ypt1. Rab1/Ypt1 subfamily. Rab1 is found in
every eukaryote and is a key regulatory component for
the transport of vesicles from the ER to the Golgi
apparatus. Studies on mutations of Ypt1, the yeast
homolog of Rab1, showed that this protein is necessary
for the budding of vesicles of the ER as well as for
their transport to, and fusion with, the Golgi
apparatus. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation
of the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs),
which facilitate Rab recycling by masking C-terminal
lipid binding and promoting cytosolic localization.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Due to the presence
of truncated sequences in this CD, the lipid
modification site is not available for annotation.
Length = 166
Score = 50.0 bits (120), Expect = 7e-09
Identities = 23/56 (41%), Positives = 33/56 (58%), Gaps = 4/56 (7%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDYDRLR 56
VGK+CLL+ + + + YI T+ D + +DGK + L +WDTAGQE R R
Sbjct: 13 VGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTVKLQIWDTAGQE---RFR 65
>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 = 50.0 bits (119), Expect = 8e-09
Identities = 24/52 (46%), Positives = 31/52 (59%), Gaps = 1/52 (1%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDY 52
VGKTCLL +T N F +I T+ D + VDG + + +WDTAGQE Y
Sbjct: 11 VGKTCLLCRFTDNEFHSSHISTIGVDFKMKTIEVDGIKVRIQIWDTAGQERY 62
>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 = 49.8 bits (119), Expect = 9e-09
Identities = 22/57 (38%), Positives = 33/57 (57%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPL 58
VGK+ L + + N F Y PT+ D+Y V +DG+ +L + DTAG E + +R L
Sbjct: 12 VGKSALTVQFVQNVFIESYDPTIEDSYRKQVEIDGRQCDLEILDTAGTEQFTAMREL 68
>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 = 49.9 bits (119), Expect = 9e-09
Identities = 20/57 (35%), Positives = 31/57 (54%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPL 58
VGK+ L + + F +Y PT+ D+Y + VD + L + DTAG E + +R L
Sbjct: 12 VGKSALTVQFVQGIFVDKYDPTIEDSYRKQIEVDCQQCMLEILDTAGTEQFTAMRDL 68
>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 = 49.7 bits (119), Expect = 1e-08
Identities = 22/53 (41%), Positives = 33/53 (62%), Gaps = 1/53 (1%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVM-VDGKPINLGLWDTAGQEDY 52
VGK+CLL+ +T F + T+ + A ++ +DGK I L +WDTAGQE +
Sbjct: 14 GVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQESF 66
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 49.9 bits (119), Expect = 2e-08
Identities = 22/52 (42%), Positives = 32/52 (61%), Gaps = 1/52 (1%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSAN-VMVDGKPINLGLWDTAGQEDY 52
VGK+CLL+ +T F + T+ + A + +D KPI L +WDTAGQE +
Sbjct: 17 VGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDNKPIKLQIWDTAGQESF 68
>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 = 48.7 bits (116), Expect = 2e-08
Identities = 21/57 (36%), Positives = 31/57 (54%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPL 58
VGK+ L + + + F +Y PT+ D Y + VD P L + DTAG E + +R L
Sbjct: 12 VGKSALTVQFVSGTFIEKYDPTIEDFYRKEIEVDSSPSVLEILDTAGTEQFASMRDL 68
>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 = 48.3 bits (116), Expect = 3e-08
Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 7/64 (10%)
Query: 1 AVGKTCLLISYTTNAFPGEYI-PTV---FDNYSANVMVDGKPINLGLWDTAGQEDYDRLR 56
+VGK+ +++ + N F E T+ F + V +D + +WDTAGQE Y L
Sbjct: 11 SVGKSSIVLRFVKNEF-SENQESTIGAAFLTQT--VNLDDTTVKFEIWDTAGQERYRSLA 67
Query: 57 PLSY 60
P+ Y
Sbjct: 68 PMYY 71
>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 = 48.6 bits (116), Expect = 4e-08
Identities = 23/51 (45%), Positives = 28/51 (54%), Gaps = 2/51 (3%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTV-FDNYSANV-MVDGKPINLGLWDTAGQE 50
VGK+ LL +T F PTV D +S + + G I L LWDTAGQE
Sbjct: 13 VGKSSLLKRFTEGRFAEVSDPTVGVDFFSRLIEIEPGVRIKLQLWDTAGQE 63
>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 = 48.3 bits (115), Expect = 5e-08
Identities = 22/52 (42%), Positives = 32/52 (61%), Gaps = 1/52 (1%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDY 52
VGK+ LL+ + N F G YI T+ D V ++G+ + L +WDTAGQE +
Sbjct: 17 VGKSSLLLRFADNTFSGSYITTIGVDFKIRTVEINGERVKLQIWDTAGQERF 68
>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 = 47.8 bits (114), Expect = 5e-08
Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVD--GKPINLGLWDTAGQEDYDRLRP 57
VGK+ ++ + F +Y T+ D + + + + L LWDTAGQE++D +
Sbjct: 10 NVGKSSMIQRFVKGIFTKDYKKTIGVDFLEKQIFLRQSDEDVRLMLWDTAGQEEFDAITK 69
Query: 58 LSY 60
Y
Sbjct: 70 AYY 72
>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 = 48.0 bits (115), Expect = 5e-08
Identities = 17/52 (32%), Positives = 30/52 (57%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDY 52
+VGK+ L + + F Y PT+ + +S + G+ +L + DTAGQ++Y
Sbjct: 11 SVGKSSLTVQFVEGHFVESYYPTIENTFSKIITYKGQEYHLEIVDTAGQDEY 62
>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 = 47.6 bits (113), Expect = 8e-08
Identities = 23/62 (37%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 1 AVGKTCLLISYTTNAF-PGEYIPTVFDNYSANVM-VDGKPINLGLWDTAGQEDYDRLRPL 58
+VGKT L+ Y + F G Y T+ + A M V + + LG+WDTAG E Y+ + +
Sbjct: 10 SVGKTSLVERYVHHRFLVGPYQNTIGAAFVAKRMVVGERVVTLGIWDTAGSERYEAMSRI 69
Query: 59 SY 60
Y
Sbjct: 70 YY 71
>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 = 46.7 bits (111), Expect = 1e-07
Identities = 22/53 (41%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDY 52
VGKTCL + FP T+ D V +DG+ I + LWDTAGQE +
Sbjct: 12 NVGKTCLTYRFCAGRFPERTEATIGVDFRERTVEIDGERIKVQLWDTAGQERF 64
>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 = 46.4 bits (111), Expect = 2e-07
Identities = 22/55 (40%), Positives = 30/55 (54%), Gaps = 5/55 (9%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTV---FDNYSANVMVDGKPINLGLWDTAGQEDY 52
VGK+ LL +T N F + T+ F + + +DGK I +WDTAGQE Y
Sbjct: 13 GVGKSNLLSRFTRNEFNLDSKSTIGVEFATRT--IQIDGKTIKAQIWDTAGQERY 65
>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 = 46.4 bits (110), Expect = 2e-07
Identities = 18/55 (32%), Positives = 33/55 (60%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLR 56
VGK+ + + + +++FP + PT+ D Y +D +P L + DTAGQ ++ +R
Sbjct: 13 VGKSAVTMQFISHSFPDYHDPTIEDAYKTQARIDNEPALLDILDTAGQAEFTAMR 67
>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 = 46.3 bits (110), Expect = 2e-07
Identities = 23/65 (35%), Positives = 31/65 (47%), Gaps = 11/65 (16%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMV-----------DGKPINLGLWDTAGQE 50
VGKT L YT N F ++I TV ++ +V ++L LWDTAGQE
Sbjct: 15 VGKTTFLYRYTDNKFNPKFITTVGIDFREKRVVYNSQGPDGTSGKAFRVHLQLWDTAGQE 74
Query: 51 DYDRL 55
+ L
Sbjct: 75 RFRSL 79
>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 = 45.5 bits (108), Expect = 3e-07
Identities = 24/62 (38%), Positives = 34/62 (54%), Gaps = 6/62 (9%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVM-VDGKPINLGLWDTAGQEDYDRLRPL-- 58
GK+CLL + N F + T+ + + V+ V GK + L +WDTAGQE R R +
Sbjct: 11 TGKSCLLHQFIENKFKQDSNHTIGVEFGSRVVNVGGKSVKLQIWDTAGQE---RFRSVTR 67
Query: 59 SY 60
SY
Sbjct: 68 SY 69
>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 = 44.0 bits (104), Expect = 1e-06
Identities = 22/58 (37%), Positives = 32/58 (55%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPL 58
VGK+ L + + F +Y PT+ D+Y V VDG+ L + DTAG E + +R L
Sbjct: 11 GVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDGQQCMLEILDTAGTEQFTAMRDL 68
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 44.3 bits (105), Expect = 2e-06
Identities = 21/57 (36%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDYDRLR 56
VGKT + + T F +YIPT+ + + + PI +WDTAGQE + LR
Sbjct: 19 GVGKTTFVKRHLTGEFEKKYIPTLGVEVHPLKFYTNCGPICFNVWDTAGQEKFGGLR 75
>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 = 43.3 bits (102), Expect = 3e-06
Identities = 24/58 (41%), Positives = 33/58 (56%), Gaps = 5/58 (8%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTV---FDNYSANVMVDGKPINLGLWDTAGQEDYDRLR 56
VGK+ L+ Y TN F + T+ F N ++ VDG + L +WDTAGQE + LR
Sbjct: 16 VGKSSLMNRYVTNKFDTQLFHTIGVEFLN--KDLEVDGHFVTLQIWDTAGQERFRSLR 71
>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 = 42.9 bits (101), Expect = 4e-06
Identities = 25/62 (40%), Positives = 32/62 (51%), Gaps = 19/62 (30%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFD-NYSANVMVD---------GKPINLGLWDTAGQE 50
+VGKTCL+ + + VFD NY A + VD G P +L LWDTAGQE
Sbjct: 10 SVGKTCLINRFCKD---------VFDKNYKATIGVDFEMERFEVLGVPFSLQLWDTAGQE 60
Query: 51 DY 52
+
Sbjct: 61 RF 62
>gnl|CDD|133314 cd04114, Rab30, Rab GTPase family 30 (Rab30). Rab30 subfamily.
Rab30 appears to be associated with the Golgi stack. It
is expressed in a wide variety of tissue types and in
humans maps to chromosome 11. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 169
Score = 43.0 bits (101), Expect = 4e-06
Identities = 22/52 (42%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 2 VGKTCLLISYTTNAFP-GEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDY 52
VGKTCL+ +T FP G+ D V + G+ I L +WDTAGQE +
Sbjct: 18 VGKTCLVRRFTQGLFPPGQGATIGVDFMIKTVEIKGEKIKLQIWDTAGQERF 69
>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 = 41.8 bits (98), Expect = 8e-06
Identities = 22/53 (41%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDY 52
+VGKT L Y ++F ++ TV D V + K I L +WDTAGQE Y
Sbjct: 11 SVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVYRNDKRIKLQIWDTAGQERY 63
>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 = 41.7 bits (98), Expect = 1e-05
Identities = 20/52 (38%), Positives = 31/52 (59%), Gaps = 1/52 (1%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVM-VDGKPINLGLWDTAGQEDY 52
VGK+CLL +T F + T+ + ++ V+G+ I L +WDTAGQE +
Sbjct: 13 VGKSCLLHQFTEKKFMADCPHTIGVEFGTRIIEVNGQKIKLQIWDTAGQERF 64
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 41.2 bits (96), Expect = 2e-05
Identities = 23/60 (38%), Positives = 35/60 (58%), Gaps = 5/60 (8%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLS 59
VGK+ LL+S+ +++ + PT+ D + V GK + L +WDTAGQE R R L+
Sbjct: 24 GVGKSSLLVSFISSSVE-DLAPTIGVDFKIKQLTVGGKRLKLTIWDTAGQE---RFRTLT 79
>gnl|CDD|206643 cd00877, Ran, Ras-related nuclear proteins (Ran)/TC4 family of
small GTPases. Ran GTPase is involved in diverse
biological functions, such as nuclear transport,
spindle formation during mitosis, DNA replication, and
cell division. Among the Ras superfamily, Ran is a
unique small G protein. It does not have a lipid
modification motif at the C-terminus to bind to the
membrane, which is often observed within the Ras
superfamily. Ran may therefore interact with a wide
range of proteins in various intracellular locations.
Like other GTPases, Ran exists in GTP- and GDP-bound
conformations that interact differently with effectors.
Conversion between these forms and the assembly or
disassembly of effector complexes requires the
interaction of regulator proteins. The intrinsic GTPase
activity of Ran is very low, but it is greatly
stimulated by a GTPase-activating protein (RanGAP1)
located in the cytoplasm. By contrast, RCC1, a guanine
nucleotide exchange factor that generates RanGTP, is
bound to chromatin and confined to the nucleus. Ran
itself is mobile and is actively imported into the
nucleus by a mechanism involving NTF-2. Together with
the compartmentalization of its regulators, this is
thought to produce a relatively high concentration of
RanGTP in the nucleus.
Length = 166
Score = 40.7 bits (96), Expect = 2e-05
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDYDRLR 56
GKT + + T F +Y+ T+ + + + + I +WDTAGQE + LR
Sbjct: 11 TGKTTFVKRHLTGEFEKKYVATLGVEVHPLDFHTNRGKIRFNVWDTAGQEKFGGLR 66
>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 = 40.1 bits (94), Expect = 3e-05
Identities = 13/59 (22%), Positives = 20/59 (33%), Gaps = 6/59 (10%)
Query: 2 VGKTCLLISYTTNAF---PGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDYDRLR 56
VGK+ LL + T D Y + + L DT G +++ L
Sbjct: 8 VGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVL--VDTPGLDEFGGLG 64
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 40.7 bits (95), Expect = 4e-05
Identities = 20/52 (38%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVM-VDGKPINLGLWDTAGQEDY 52
VGK+ +L +T N F E T+ ++ + V+GK + +WDTAGQE Y
Sbjct: 23 VGKSNILSRFTRNEFCLESKSTIGVEFATRTLQVEGKTVKAQIWDTAGQERY 74
>gnl|CDD|133267 cd01864, Rab19, Rab GTPase family 19 (Rab19). Rab19 subfamily.
Rab19 proteins are associated with Golgi stacks.
Similarity analysis indicated that Rab41 is closely
related to Rab19. However, the function of these Rabs
is not yet characterized. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab
proteins. Due to the presence of truncated sequences in
this CD, the lipid modification site is not available
for annotation.
Length = 165
Score = 40.1 bits (94), Expect = 4e-05
Identities = 21/62 (33%), Positives = 34/62 (54%), Gaps = 6/62 (9%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSA-NVMVDGKPINLGLWDTAGQEDYDRLRPL-- 58
VGKTC++ + + F T+ +++ + + GK + L +WDTAGQE R R +
Sbjct: 14 VGKTCVVQRFKSGTFSERQGNTIGVDFTMKTLEIQGKRVKLQIWDTAGQE---RFRTITQ 70
Query: 59 SY 60
SY
Sbjct: 71 SY 72
>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 = 39.7 bits (93), Expect = 6e-05
Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNY-SANVMVDGKPINLGLWDTAGQEDYDRLRPL 58
+GKT L++ Y F EYI T+ N+ + + G I +WD GQ ++ + PL
Sbjct: 11 IGKTSLMVKYVEGEFDEEYIQTLGVNFMEKTISIRGTEITFSIWDLGGQREFINMLPL 68
>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 = 39.2 bits (92), Expect = 1e-04
Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 2/55 (3%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMV--DGKPINLGLWDTAGQEDYD 53
VGKT ++ Y F Y T+ +++ V+ + L LWD AGQE +
Sbjct: 10 GVGKTSIIKRYVHGVFSQHYKATIGVDFALKVIEWDPNTVVRLQLWDIAGQERFG 64
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 38.6 bits (90), Expect = 2e-04
Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 1/56 (1%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDYDRLR 56
GKT + + T F +Y PT+ + + + + I WDTAGQE + LR
Sbjct: 24 TGKTTFVKRHLTGEFEKKYEPTIGVEVHPLDFFTNCGKIRFYCWDTAGQEKFGGLR 79
>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 = 38.1 bits (89), Expect = 2e-04
Identities = 17/56 (30%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSAN-VMVDGKPINLGLWDTAGQEDYDRLR 56
VGK+C++ Y F +Y+PT+ +Y V V K + + +D +G +Y +R
Sbjct: 11 VGKSCIIKRYCEGRFVSKYLPTIGIDYGVKKVSVRNKEVRVNFFDLSGHPEYLEVR 66
>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 = 37.9 bits (88), Expect = 2e-04
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPT-VFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLS 59
AVGK+ L+ + + + + + T Y N +GK I + WDTAGQE + +
Sbjct: 10 AVGKSKLVERFLMDGYEPQQLSTYALTLYKHNAKFEGKTILVDFWDTAGQERFQTMHASY 69
Query: 60 Y 60
Y
Sbjct: 70 Y 70
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 35.9 bits (82), Expect = 0.002
Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 14 NAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDYDRLRP 57
+ F Y T+ D S + +D P+ L LWDTAGQE + L P
Sbjct: 3 DTFDNNYQSTIGIDFLSKTLYLDEGPVRLQLWDTAGQERFRSLIP 47
>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 = 35.6 bits (82), Expect = 0.002
Identities = 17/58 (29%), Positives = 27/58 (46%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLS 59
VGK+ L++ + F YIPT+ D Y + L + DT G + ++ LS
Sbjct: 12 VGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCSKSICTLQITDTTGSHQFPAMQRLS 69
>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 = 35.8 bits (82), Expect = 0.002
Identities = 23/60 (38%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
VGKT L+ +T + F TV D V + GK I L +WDTAGQE ++ + Y
Sbjct: 11 VGKTSLMERFTDDTFCEACKSTVGVDFKIKTVELRGKKIRLQIWDTAGQERFNSITSAYY 70
>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 = 35.8 bits (82), Expect = 0.002
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 3 GKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSYP 61
GKT + + T F +Y+ T+ + + + PI +WDTAGQE + LR Y
Sbjct: 7 GKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIRFNVWDTAGQEKFGGLRDGYYI 66
Query: 62 Q 62
Q
Sbjct: 67 Q 67
>gnl|CDD|206694 cd04109, Rab28, Rab GTPase family 28 (Rab28). Rab28 subfamily.
First identified in maize, Rab28 has been shown to be a
late embryogenesis-abundant (Lea) protein that is
regulated by the plant hormone abcisic acid (ABA). In
Arabidopsis, Rab28 is expressed during embryo
development and is generally restricted to provascular
tissues in mature embryos. Unlike maize Rab28, it is
not ABA-inducible. Characterization of the human Rab28
homolog revealed two isoforms, which differ by a
95-base pair insertion, producing an alternative
sequence for the 30 amino acids at the C-terminus. The
two human isoforms are presumably the result of
alternative splicing. Since they differ at the
C-terminus but not in the GTP-binding region, they are
predicted to be targeted to different cellular
locations. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation
of the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs),
which facilitate Rab recycling by masking C-terminal
lipid binding and promoting cytosolic localization.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins.
Length = 213
Score = 34.0 bits (78), Expect = 0.008
Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGK-PINLGLWDTAGQ 49
A GKT L+ + F Y T+ D +S + + G + L +WD GQ
Sbjct: 10 ASGKTSLIRRFAQEGFGKSYKQTIGLDFFSRRITLPGSLNVTLQVWDIGGQ 60
>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 = 33.2 bits (76), Expect = 0.008
Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 1/51 (1%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVM-VDGKPINLGLWDTAGQED 51
GK+ LL FP E + D + + + VDG L +WD G+E+
Sbjct: 10 SGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREE 60
>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 = 33.3 bits (76), Expect = 0.011
Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 3/70 (4%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSYP 61
VGKT L+ + + F ++ TV + +S V G + + + DT+G + +R LS
Sbjct: 10 VGKTALIQRFLYDTFEPKHRRTVEELHSKEYEVAGVKVTIDILDTSGSYSFPAMRKLSIQ 69
Query: 62 QTWSLRSFAL 71
+FAL
Sbjct: 70 NG---DAFAL 76
>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 = 33.3 bits (76), Expect = 0.012
Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 4/54 (7%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRL 55
VGKT LL Y F + + TV A + P N+ +WDTAG+E + L
Sbjct: 11 VGKTSLLHRYMERRFK-DTVSTV---GGAFYLKQWGPYNISIWDTAGREQFHGL 60
>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 = 32.7 bits (75), Expect = 0.018
Identities = 17/55 (30%), Positives = 22/55 (40%), Gaps = 4/55 (7%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTV---FDNYSANVMVDGKPINLGLWDTAGQEDY 52
VGKT L F G+ T ++ + K I L +WD GQE Y
Sbjct: 11 GVGKTSLCKQLIGEKFDGDESSTHGINVQDWKIPA-PERKKIRLNVWDFGGQEIY 64
>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 = 31.9 bits (72), Expect = 0.040
Identities = 25/70 (35%), Positives = 33/70 (47%), Gaps = 16/70 (22%)
Query: 1 AVGKTCLLISYTTNAFPGEYI------PTVF--DNY--------SANVMVDGKPINLGLW 44
AVGKT L+ + N +Y PTV+ D Y + +VDG ++L LW
Sbjct: 12 AVGKTRLICARACNKTLTQYQLLATHVPTVWAIDQYRVCQEVLERSRDVVDGVSVSLRLW 71
Query: 45 DTAGQEDYDR 54
DT G D DR
Sbjct: 72 DTFGDHDKDR 81
>gnl|CDD|133342 cd04142, RRP22, Ras-related protein on chromosome 22 (RRP22)
family. RRP22 (Ras-related protein on chromosome 22)
subfamily consists of proteins that inhibit cell growth
and promote caspase-independent cell death. Unlike most
Ras proteins, RRP22 is down-regulated in many human
tumor cells due to promoter methylation. RRP22
localizes to the nucleolus in a GTP-dependent manner,
suggesting a novel function in modulating transport of
nucleolar components. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras
proteins. Like most Ras family proteins, RRP22 is
farnesylated.
Length = 198
Score = 30.6 bits (69), Expect = 0.11
Identities = 25/77 (32%), Positives = 35/77 (45%), Gaps = 17/77 (22%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDN-YSANVMVDGKPINLGLWD---------TAGQED 51
VGKT ++ + FP EYIPT Y V++ G+ +L + D TAGQE
Sbjct: 11 VGKTAIVRQFLAQEFPEEYIPTEHRRLYRPAVVLSGRVYDLHILDVPNMQRYPGTAGQEW 70
Query: 52 YDRLRPLSYPQTWSLRS 68
D P+ LR+
Sbjct: 71 MD-------PRFRGLRN 80
>gnl|CDD|133343 cd04143, Rhes_like, Ras homolog enriched in striatum (Rhes) and
activator of G-protein signaling 1 (Dexras1/AGS1).
This subfamily includes Rhes (Ras homolog enriched in
striatum) and Dexras1/AGS1 (activator of G-protein
signaling 1). These proteins are homologous, but
exhibit significant differences in tissue distribution
and subcellular localization. Rhes is found primarily
in the striatum of the brain, but is also expressed in
other areas of the brain, such as the cerebral cortex,
hippocampus, inferior colliculus, and cerebellum. Rhes
expression is controlled by thyroid hormones. In rat
PC12 cells, Rhes is farnesylated and localizes to the
plasma membrane. Rhes binds and activates PI3K, and
plays a role in coupling serpentine membrane receptors
with heterotrimeric G-protein signaling. Rhes has
recently been shown to be reduced under conditions of
dopamine supersensitivity and may play a role in
determining dopamine receptor sensitivity. Dexras1/AGS1
is a dexamethasone-induced Ras protein that is
expressed primarily in the brain, with low expression
levels in other tissues. Dexras1 localizes primarily to
the cytoplasm, and is a critical regulator of the
circadian master clock to photic and nonphotic input.
Most Ras proteins contain a lipid modification site at
the C-terminus, with a typical sequence motif CaaX,
where a = an aliphatic amino acid and X = any amino
acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins.
Length = 247
Score = 30.5 bits (69), Expect = 0.14
Identities = 17/58 (29%), Positives = 29/58 (50%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLS 59
VGKT ++ + F +Y PT+ D + + G+ L + DT+G + +R LS
Sbjct: 11 VGKTAIVSRFLGGRFEEQYTPTIEDFHRKLYSIRGEVYQLDILDTSGNHPFPAMRRLS 68
>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 = 29.9 bits (67), Expect = 0.18
Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNY-SANVMVDGKPINLGLWDTAGQ 49
VGK +L S + Y + +Y + +++DG+ + L LWDT+GQ
Sbjct: 17 VGKGEILASLQDGSTESPYGYNMGIDYKTTTILLDGRRVKLQLWDTSGQ 65
>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 = 29.8 bits (67), Expect = 0.18
Identities = 22/62 (35%), Positives = 29/62 (46%), Gaps = 8/62 (12%)
Query: 3 GKTCLLISYTTNAFPGEYIPTV-FDNYSANVMV-DGKPINLGLWDTAGQEDYDRLRPL-- 58
GKT +L N F +PT F+ V + + K + WD GQE +LRPL
Sbjct: 15 GKTTVLYRLKFNEFV-NTVPTKGFNTEKIKVSLGNAKGVTFHFWDVGGQE---KLRPLWK 70
Query: 59 SY 60
SY
Sbjct: 71 SY 72
>gnl|CDD|215392 PLN02737, PLN02737, inositol monophosphatase family protein.
Length = 363
Score = 29.8 bits (67), Expect = 0.26
Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 61 PQTWSLRSFALHAGHPVRFPRGRKIRIMQMIGFRDRLL 98
P W+ R+F+ AG F G+KI + Q LL
Sbjct: 196 PMCWNTRTFSASAGGGA-FCNGQKIHVSQTDKVERSLL 232
>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 = 29.2 bits (66), Expect = 0.28
Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 6/56 (10%)
Query: 3 GKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPL 58
GKT L+ + F + IPTV N V + + +WD GQ R R +
Sbjct: 11 GKTTLVNVIASGQFSEDTIPTVGFNMR---KVTKGNVTIKVWDLGGQP---RFRSM 60
>gnl|CDD|198249 cd10386, SH2_SOCS5, Src homology 2 (SH2) domain found in
suppressor of cytokine signaling (SOCS) family. SH2
domain found in SOCS proteins. SOCS was first
recognized as a group of cytokine-inducible SH2 (CIS)
domain proteins comprising eight family members in
human (CIS and SOCS1-SOCS7). In addition to the SH2
domain, SOCS proteins have a variable N-terminal domain
and a conserved SOCS box in the C-terminal domain. SOCS
proteins bind to a substrate via their SH2 domain. The
prototypical members, CIS and SOCS1-SOCS3, have been
shown to regulate growth hormone signaling in vitro and
in a classic negative feedback response compete for
binding at phosphotyrosine sites in JAK kinase and
receptor pathways to displace effector proteins and
target bound receptors for proteasomal degradation.
Loss of SOCS activity results in excessive cytokine
signaling associated with a variety of hematopoietic,
autoimmune, and inflammatory diseases and certain
cancers. Members (SOCS4-SOCS7) were identified by their
conserved SOCS box, an adapter motif of 3 helices that
associates substrate binding domains, such as the SOCS
SH2 domain, ankryin, and WD40 with ubiquitin ligase
components. These show limited cytokine induction. In
general SH2 domains are involved in signal
transduction. They typically bind pTyr-containing
ligands via two surface pockets, a pTyr and hydrophobic
binding pocket, allowing proteins with SH2 domains to
localize to tyrosine phosphorylated sites.
Length = 81
Score = 27.7 bits (61), Expect = 0.54
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 24 VFDNYSANVMVDGKPINLGLWDTAGQEDY 52
V D Y A +++GKP L + QEDY
Sbjct: 6 VMDRYEAEALLEGKPEGTFLLRDSAQEDY 34
>gnl|CDD|206717 cd04150, Arf1_5_like, ADP-ribosylation factor-1 (Arf1) and
ADP-ribosylation factor-5 (Arf5). The Arf1-Arf5-like
subfamily contains Arf1, Arf2, Arf3, Arf4, Arf5, and
related proteins. Arfs1-5 are soluble proteins that are
crucial for assembling coat proteins during vesicle
formation. Each contains an N-terminal myristoylated
amphipathic helix that is folded into the protein in
the GDP-bound state. GDP/GTP exchange exposes the
helix, which anchors to the membrane. Following GTP
hydrolysis, the helix dissociates from the membrane and
folds back into the protein. A general feature of
Arf1-5 signaling may be the cooperation of two Arfs at
the same site. Arfs1-5 are generally considered to be
interchangeable in function and location, but some
specific functions have been assigned. Arf1 localizes
to the early/cis-Golgi, where it is activated by GBF1
and recruits the coat protein COPI. It also localizes
to the trans-Golgi network (TGN), where it is activated
by BIG1/BIG2 and recruits the AP1, AP3, AP4, and GGA
proteins. Humans, but not rodents and other lower
eukaryotes, lack Arf2. Human Arf3 shares 96% sequence
identity with Arf1 and is believed to generally
function interchangeably with Arf1. Human Arf4 in the
activated (GTP-bound) state has been shown to interact
with the cytoplasmic domain of epidermal growth factor
receptor (EGFR) and mediate the EGF-dependent
activation of phospholipase D2 (PLD2), leading to
activation of the activator protein 1 (AP-1)
transcription factor. Arf4 has also been shown to
recognize the C-terminal sorting signal of rhodopsin
and regulate its incorporation into specialized
post-Golgi rhodopsin transport carriers (RTCs). There
is some evidence that Arf5 functions at the early-Golgi
and the trans-Golgi to affect Golgi-associated
alpha-adaptin homology Arf-binding proteins (GGAs).
Length = 159
Score = 28.1 bits (63), Expect = 0.62
Identities = 22/61 (36%), Positives = 29/61 (47%), Gaps = 13/61 (21%)
Query: 1 AVGKTCLLISYTTNAFPGEY---IPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRP 57
A GKT +L GE IPT+ N V+ K I+ +WD GQ D++RP
Sbjct: 10 AAGKTTILYKLKL----GEIVTTIPTIGFNVET---VEYKNISFTVWDVGGQ---DKIRP 59
Query: 58 L 58
L
Sbjct: 60 L 60
>gnl|CDD|198248 cd10385, SH2_SOCS4, Src homology 2 (SH2) domain found in
suppressor of cytokine signaling (SOCS) proteins. SH2
domain found in SOCS proteins. SOCS was first
recognized as a group of cytokine-inducible SH2 (CIS)
domain proteins comprising eight family members in
human (CIS and SOCS1-SOCS7). In addition to the SH2
domain, SOCS proteins have a variable N-terminal domain
and a conserved SOCS box in the C-terminal domain. SOCS
proteins bind to a substrate via their SH2 domain. The
prototypical members, CIS and SOCS1-SOCS3, have been
shown to regulate growth hormone signaling in vitro and
in a classic negative feedback response compete for
binding at phosphotyrosine sites in JAK kinase and
receptor pathways to displace effector proteins and
target bound receptors for proteasomal degradation.
Loss of SOCS activity results in excessive cytokine
signaling associated with a variety of hematopoietic,
autoimmune, and inflammatory diseases and certain
cancers. Members (SOCS4-SOCS7) were identified by their
conserved SOCS box, an adapter motif of 3 helices that
associates substrate binding domains, such as the SOCS
SH2 domain, ankryin, and WD40 with ubiquitin ligase
components. These show limited cytokine induction. In
general SH2 domains are involved in signal
transduction. They typically bind pTyr-containing
ligands via two surface pockets, a pTyr and hydrophobic
binding pocket, allowing proteins with SH2 domains to
localize to tyrosine phosphorylated sites.
Length = 101
Score = 27.7 bits (61), Expect = 0.66
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 24 VFDNYSANVMVDGKPINLGLWDTAGQEDY 52
V D Y+A +++GKP L + QEDY
Sbjct: 16 VMDKYAAEALLEGKPEGTFLLRDSAQEDY 44
>gnl|CDD|218203 pfam04670, Gtr1_RagA, Gtr1/RagA G protein conserved region. GTR1
was first identified in S. cerevisiae as a suppressor
of a mutation in RCC1. Biochemical analysis revealed
that Gtr1 is in fact a G protein of the Ras family. The
RagA/B proteins are the human homologues of Gtr1.
Included in this family is the human Rag C, a novel
protein that has been shown to interact with RagA/B.
Length = 230
Score = 28.3 bits (64), Expect = 0.76
Identities = 13/45 (28%), Positives = 17/45 (37%), Gaps = 16/45 (35%)
Query: 23 TVFDNYSAN---------------VMVDGKPINLGLWDTAGQEDY 52
+F NYS V G + L LWD GQ+D+
Sbjct: 18 IIFSNYSPRDTLRLGATIDVEQSHVRFLGN-LTLNLWDCPGQDDF 61
>gnl|CDD|204089 pfam08900, DUF1845, Domain of unknown function (DUF1845). This
family of proteins are functionally uncharacterized.
Length = 217
Score = 27.6 bits (62), Expect = 1.3
Identities = 15/41 (36%), Positives = 20/41 (48%), Gaps = 8/41 (19%)
Query: 65 SLRS---FALHAGHPVRFPRGR-----KIRIMQMIGFRDRL 97
SLRS LH + +R +GR K I+ + GF RL
Sbjct: 6 SLRSEVTLTLHTHYAIRLWQGRRREENKPAIIGLPGFASRL 46
>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 = 27.1 bits (60), Expect = 1.7
Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 5/58 (8%)
Query: 1 AVGKTCLLISYTTNA--FPGEYIPTV---FDNYSANVMVDGKPINLGLWDTAGQEDYD 53
AVGK+ L+ + ++ F Y T + V + L ++D+AGQE +
Sbjct: 10 AVGKSALVQMFHSDGATFQKNYTMTTGCDLVVKTVPVPDTSDSVELFIFDSAGQELFS 67
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 26.9 bits (59), Expect = 2.3
Identities = 22/61 (36%), Positives = 29/61 (47%), Gaps = 13/61 (21%)
Query: 1 AVGKTCLLISYTTNAFPGEY---IPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRP 57
A GKT +L GE IPT+ N V+ K I+ +WD GQ D++RP
Sbjct: 27 AAGKTTILYKLKL----GEIVTTIPTIGFNVET---VEYKNISFTVWDVGGQ---DKIRP 76
Query: 58 L 58
L
Sbjct: 77 L 77
>gnl|CDD|212040 cd10332, SLC6sbd-B0AT-like, System B(0) neutral amino acid
transporter AT1, 2 and 3, and related proteins;
solute-binding domain. This subgroup includes the
solute-binding domain of transmembrane transporters,
which transport, i) neutral amino acids: NTT4 (also
called XT1), SBAT1 (also called B0AT2, v7-3, NTT7-3),
and B0AT1 (also called HND); the human genes encoding
these are SLC6A17, SLC6A15, and SLC6A19 respectively,
ii) glycine: B0AT3 (also called Xtrp2, XT2), iii) imino
acids, such as proline, pipecolate, MeAIB, and
sarcosine: SIT1 (also called XTRP3, XT3, IMINO). The
human genes encoding B0AT3 and SIT1 are SLC6A18 and
SLC6A20 respectively. Transporters in this subgroup may
play a role in disorders including major depression,
Hartnup disorder, increased susceptibility to myocardial
infarction, and iminoglycinuria. This subgroup belongs
to the solute carrier 6 (SLC6) transporter family.
Length = 565
Score = 26.9 bits (60), Expect = 2.9
Identities = 10/29 (34%), Positives = 15/29 (51%), Gaps = 4/29 (13%)
Query: 6 CLLIS--YTTNAFPGEYIPTVFDNYSANV 32
C LI +T + G Y +FD+YS +
Sbjct: 430 CFLIGLIFTQRS--GNYWVQMFDSYSGTL 456
>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 = 26.6 bits (59), Expect = 3.1
Identities = 19/60 (31%), Positives = 25/60 (41%), Gaps = 9/60 (15%)
Query: 2 VGKTCLLISYTTNAFPGEYI-----PTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLR 56
VGK+ L +T G Y + D Y V VDG+ L ++D QED L
Sbjct: 11 VGKSSLANIFTA----GVYEDSAYEASGDDTYERTVSVDGEEATLVVYDHWEQEDGMWLE 66
>gnl|CDD|215063 PLN00120, PLN00120, fucoxanthin-chlorophyll a-c binding protein;
Provisional.
Length = 202
Score = 26.2 bits (58), Expect = 3.2
Identities = 10/16 (62%), Positives = 11/16 (68%)
Query: 41 LGLWDTAGQEDYDRLR 56
LGL D QE +DRLR
Sbjct: 50 LGLVDDGDQEKFDRLR 65
>gnl|CDD|216033 pfam00630, Filamin, Filamin/ABP280 repeat.
Length = 93
Score = 25.4 bits (56), Expect = 3.7
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 19 EYIPTVFDNYSANVMVDGKPI 39
Y PT +Y+ +V +G+ I
Sbjct: 67 SYTPTEPGDYTVSVKFNGQHI 87
>gnl|CDD|185310 PRK15412, PRK15412, thiol:disulfide interchange protein DsbE;
Provisional.
Length = 185
Score = 26.1 bits (57), Expect = 3.7
Identities = 11/30 (36%), Positives = 17/30 (56%), Gaps = 7/30 (23%)
Query: 17 PGEYIPTVFDNYSANVMVDGKPINLGLWDT 46
PG++ Y A+V+ GKP+ L +W T
Sbjct: 56 PGQF-------YQADVLTQGKPVLLNVWAT 78
>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 = 25.8 bits (57), Expect = 4.6
Identities = 20/68 (29%), Positives = 29/68 (42%), Gaps = 20/68 (29%)
Query: 3 GKTCLLISYTTNAFPGEYI---PTVFDNYSANV-MVDGKPINLGLWDTAGQEDYDRLRPL 58
GKT +L + GE + PT+ +NV + K I +WD GQE LR
Sbjct: 27 GKTTILYQFLL----GEVVHTSPTI----GSNVEEIVYKNIRFLMWDIGGQE---SLR-- 73
Query: 59 SYPQTWSL 66
+W+
Sbjct: 74 ---SSWNT 78
>gnl|CDD|216953 pfam02265, S1-P1_nuclease, S1/P1 Nuclease. This family contains
both S1 and P1 nucleases (EC:3.1.30.1) which cleave RNA
and single stranded DNA with no base specificity.
Length = 251
Score = 26.1 bits (58), Expect = 4.7
Identities = 9/35 (25%), Positives = 12/35 (34%), Gaps = 1/35 (2%)
Query: 31 NVMVDGKPINL-GLWDTAGQEDYDRLRPLSYPQTW 64
V G+ NL +WD+ E S W
Sbjct: 137 KVRWFGRKTNLHSVWDSGIIETALGDYYRSSLSEW 171
>gnl|CDD|212034 cd10324, SLC6sbd, Solute carrier 6 family, neurotransmitter
transporters; solute-binding domain. This family
represents the solute-binding domain of SLC6 proteins
(also called the sodium- and chloride-dependent
neurotransmitter transporter family or Na+/Cl--dependent
transporter family). These use sodium and chloride
electrochemical gradients to catalyze the
thermodynamically uphill movement of a variety of
substrates, and include neurotransmitter transporters
(NTTs). The latter are Na+/Cl--dependent plasma membrane
transporters for the monoamine neurotransmitters
serotonin (5-hydroxytryptamine), dopamine, and
norepinephrine, and the amino acid neurotransmitters
GABA and glycine. NTTs are widely expressed in the
mammalian brain, and are involved in regulating
neurotransmitter signaling and homeostasis, through
facilitating the uptake of released neurotransmitters
from the extracellular space into neurons and glial
cells. NTTs are the target of a range of therapeutic
drugs for the treatment of psychiatric diseases, such as
major depression, anxiety disorders, attention deficit
hyperactivity disorder and epilepsy. In addition, they
are the primary targets of cocaine, amphetamines and
other psychostimulants. This family also includes
Drosophila Blot which is expressed primarily in
epithelial tissues of ectodermal origin and in the
nervous system of the embryo and larvae, but in addition
found in the developing oocyte and the freshly laid egg.
A lack or reduction of Blot function during oogenesis
results in early arrest of embryonic development. 12
transmembrane helices (TMs) appears to be common for
eukaryotic and some prokaryotic and archaeal SLC6s, (a
core inverted topology repeat, TM1-5 and TM6-10, plus
TMs11-12; TMs numbered to conform to the SLC6 Aquifex
aeolicus LeuT), although a majority of bacterial, and
some archaeal SLC6s lack TM12, for example the
functional Fusobacterium nucleatum tyrosine transporter
Tyt1.
Length = 417
Score = 25.5 bits (57), Expect = 6.1
Identities = 9/29 (31%), Positives = 13/29 (44%), Gaps = 2/29 (6%)
Query: 6 CLLISYTTNAFPGEYIPTVFDNYSANVMV 34
L + Y T G YI + D Y+A +
Sbjct: 335 LLGLPYVTQG--GIYILDLLDYYAATFSL 361
>gnl|CDD|180892 PRK07220, PRK07220, DNA topoisomerase I; Validated.
Length = 740
Score = 25.9 bits (57), Expect = 6.2
Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 6/32 (18%)
Query: 76 PVRFPRGRKIRIMQMIGFRDRLLWGSKQAREE 107
P R+ +GR I++M+ +G G+K R E
Sbjct: 466 PGRYGQGRLIKLMEDLGL------GTKATRHE 491
>gnl|CDD|236201 PRK08248, PRK08248, O-acetylhomoserine
aminocarboxypropyltransferase; Validated.
Length = 431
Score = 25.6 bits (56), Expect = 7.8
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 3/41 (7%)
Query: 58 LSYPQTWSLRSFALHAGH---PVRFPRGRKIRIMQMIGFRD 95
+S +T+ L + A+HAG P R I GFRD
Sbjct: 1 MSEERTFRLETLAIHAGQEIDPTTGSRAVPIYQTTSYGFRD 41
>gnl|CDD|177661 PLN00023, PLN00023, GTP-binding protein; Provisional.
Length = 334
Score = 25.2 bits (55), Expect = 9.3
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 43 LWDTAGQEDYDRLRPLSYPQ 62
LWD +G E Y R L Y Q
Sbjct: 87 LWDVSGHERYKDCRSLFYSQ 106
>gnl|CDD|220677 pfam10291, muHD, Muniscin C-terminal mu homology domain. The
muniscins are a family of endocytic adaptors that is
conserved from yeast to humans.This C-terminal domain is
structurally similar to mu homology domains, and is the
region of the muniscin proteins involved in the
interactions with the endocytic adaptor-scaffold
proteins Ede1-eps15. This interaction influences
muniscin localisation. The muniscins provide a combined
adaptor-membrane-tubulation activity that is important
for regulating endocytosis.
Length = 251
Score = 24.9 bits (55), Expect = 9.6
Identities = 10/34 (29%), Positives = 15/34 (44%)
Query: 3 GKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDG 36
+T L++ Y N P V N +V +DG
Sbjct: 118 HQTSLILDYKLNPSPASSSSLVLLNLVVSVNLDG 151
>gnl|CDD|217652 pfam03636, Glyco_hydro_65N, Glycosyl hydrolase family 65,
N-terminal domain. This family of glycosyl hydrolases
contains vacuolar acid trehalase and maltose
phosphorylase.Maltose phosphorylase (MP) is a dimeric
enzyme that catalyzes the conversion of maltose and
inorganic phosphate into beta-D-glucose-1-phosphate and
glucose. This domain is believed to be essential for
catalytic activity although its precise function remains
unknown.
Length = 259
Score = 25.0 bits (55), Expect = 9.7
Identities = 21/92 (22%), Positives = 37/92 (40%), Gaps = 12/92 (13%)
Query: 10 SYTTNAFPGEYIPTVFDNYSANVMVDGKP------INLGLW-----DTAGQE-DYDRLRP 57
Y+ +++PG YI V+ V +G P INL W G+ D +
Sbjct: 35 DYSGDSYPGTYIAGVYFPDKTRVGKNGYPEYFEKVINLPNWIGLKILIDGEVFDLSTVEV 94
Query: 58 LSYPQTWSLRSFALHAGHPVRFPRGRKIRIMQ 89
S+ +T +++ L R G+ +R+
Sbjct: 95 ESFERTLDMKAGVLTRSLRWRSLGGKGVRVTS 126
>gnl|CDD|220767 pfam10459, Peptidase_S46, Peptidase S46. Dipeptidyl-peptidase 7
(DPP-7) is the best characterized member of this family.
It is a serine peptidase that is located on the cell
surface and is predicted to have two N-terminal
transmembrane domains.
Length = 696
Score = 25.3 bits (56), Expect = 9.9
Identities = 10/25 (40%), Positives = 12/25 (48%)
Query: 84 KIRIMQMIGFRDRLLWGSKQAREEK 108
K I + G +D L KQARE
Sbjct: 309 KNSIGMLEGLKDLDLLARKQAREAA 333
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.322 0.139 0.440
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: 5,862,043
Number of extensions: 496943
Number of successful extensions: 513
Number of sequences better than 10.0: 1
Number of HSP's gapped: 473
Number of HSP's successfully gapped: 114
Length of query: 111
Length of database: 10,937,602
Length adjustment: 75
Effective length of query: 36
Effective length of database: 7,611,052
Effective search space: 273997872
Effective search space used: 273997872
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.6 bits)