RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10443
(195 letters)
>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 = 346 bits (891), Expect = e-124
Identities = 123/174 (70%), Positives = 143/174 (82%)
Query: 9 CVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQEDYD 68
VVVGDG VGKTC+LI YTT++FP +YVPTVF+NYSA VDG PV LGLWDTAGQEDYD
Sbjct: 1 LVVVGDGAVGKTCLLIVYTTNAFPEDYVPTVFENYSADVEVDGKPVELGLWDTAGQEDYD 60
Query: 69 RLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPIILVGTKIDLREDRET 128
RLRPLSYP TDVFLIC+SV SP+SF+NV KWYPE+KH CP+ PIILVGTK+DLR D+ T
Sbjct: 61 RLRPLSYPDTDVFLICFSVDSPASFENVKEKWYPEVKHFCPNVPIILVGTKLDLRNDKST 120
Query: 129 LNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAVLRP 182
L LS++ PV EQGQ LA +I AVKY+ECSALTQ G+R+VF+EA+RA L
Sbjct: 121 LEELSKKKQEPVTYEQGQALAKRIGAVKYLECSALTQEGVREVFEEAIRAALNK 174
>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 = 339 bits (871), Expect = e-121
Identities = 128/172 (74%), Positives = 148/172 (86%), Gaps = 1/172 (0%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQED 66
IK VVVGDG VGKTC+LISYTT+ FP EYVPTVFDNYSA TVDG V+LGLWDTAGQE+
Sbjct: 1 IKIVVVGDGAVGKTCLLISYTTNKFPTEYVPTVFDNYSANVTVDGKQVNLGLWDTAGQEE 60
Query: 67 YDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPIILVGTKIDLREDR 126
YDRLRPLSYPQTDVFL+C+SV SPSSF+NV +KWYPE+KH+CP+ PIILVGTKIDLR+D
Sbjct: 61 YDRLRPLSYPQTDVFLLCFSVDSPSSFENVKTKWYPEIKHYCPNVPIILVGTKIDLRDDG 120
Query: 127 ETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRA 178
TL L E+ P+ E+G+KLA +I AVKYMECSALTQ GL++VFDEA+RA
Sbjct: 121 NTLKKL-EKKQKPITPEEGEKLAKEIGAVKYMECSALTQEGLKEVFDEAIRA 171
>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 = 324 bits (833), Expect = e-115
Identities = 128/173 (73%), Positives = 154/173 (89%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQED 66
IKCVVVGDG VGKTC+LISYTT++FPGEY+PTVFDNYSA VDG PV+LGLWDTAGQED
Sbjct: 2 IKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQED 61
Query: 67 YDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPIILVGTKIDLREDR 126
YDRLRPLSYPQTDVFLIC+S+VSP+SF+NV +KWYPE++HHCP+ PIILVGTK+DLR+D+
Sbjct: 62 YDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDK 121
Query: 127 ETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAV 179
+T+ L E+ L+P+ QG +A +I AVKY+ECSALTQRGL+ VFDEA+RAV
Sbjct: 122 DTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAV 174
>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 = 293 bits (752), Expect = e-103
Identities = 123/189 (65%), Positives = 151/189 (79%), Gaps = 1/189 (0%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQED 66
IKCVVVGDG VGKTC+LI YTT++FP EY+PTVFDNYSA VDG VSL LWDTAGQE+
Sbjct: 4 IKCVVVGDGAVGKTCLLICYTTNAFPKEYIPTVFDNYSAQTAVDGRTVSLNLWDTAGQEE 63
Query: 67 YDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPIILVGTKIDLREDR 126
YDRLR LSYPQT+VF+IC+S+ SPSS++NV KW+PE+ HHCP+ PI+LVGTK DLR D
Sbjct: 64 YDRLRTLSYPQTNVFIICFSIASPSSYENVRHKWHPEVCHHCPNVPILLVGTKKDLRNDA 123
Query: 127 ETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAVLRPEPVK 186
+TL L EQ +P+ +QG LA +I AVKY+ECSAL Q G+++VF EAVRAVL P P+K
Sbjct: 124 DTLKKLKEQGQAPITPQQGGALAKQIHAVKYLECSALNQDGVKEVFAEAVRAVLNPTPIK 183
Query: 187 RRQRKCVII 195
+ CV++
Sbjct: 184 DT-KSCVLL 191
>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 = 279 bits (715), Expect = 2e-97
Identities = 117/174 (67%), Positives = 141/174 (81%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQED 66
IKCVVVGDG VGKTC+LISYTT+ FP EYVPTVFDNY+ + G P +LGL+DTAGQED
Sbjct: 2 IKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTLGLFDTAGQED 61
Query: 67 YDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPIILVGTKIDLREDR 126
YDRLRPLSYPQTDVFL+C+SVVSPSSF+NV KW PE+ HHCP P +LVGT+IDLR+D
Sbjct: 62 YDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQIDLRDDP 121
Query: 127 ETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAVL 180
T+ L++ P+ E G+KLA ++AVKY+ECSALTQ+GL+ VFDEA+ A L
Sbjct: 122 STIEKLAKNKQKPITPETGEKLARDLKAVKYVECSALTQKGLKNVFDEAILAAL 175
>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 = 275 bits (706), Expect = 1e-95
Identities = 105/196 (53%), Positives = 131/196 (66%), Gaps = 5/196 (2%)
Query: 5 RPIKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTV-DGIPVSLGLWDTAG 63
+K VVVGDG GKTC+L+ Y SFP EYVPTVF+NY V +G + L LWDTAG
Sbjct: 2 LKVKIVVVGDGGCGKTCLLMVYAQGSFPEEYVPTVFENYVTTLQVPNGKIIELALWDTAG 61
Query: 64 QEDYDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPIILVGTKIDLR 123
QEDYDRLRPLSYP DV LICYSV +P+S DNV KWYPE+ H CP PI+LVG K DLR
Sbjct: 62 QEDYDRLRPLSYPDVDVILICYSVDNPTSLDNVEDKWYPEVNHFCPGTPIVLVGLKTDLR 121
Query: 124 EDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAVLRPE 183
+D+ +++ L Q L PV EQG+ +A I AV Y+ECSA + +VFD A+ L
Sbjct: 122 KDKNSVSKLRAQGLEPVTPEQGESVAKSIGAVAYIECSAKLMENVDEVFDAAINVALSKS 181
Query: 184 PV----KRRQRKCVII 195
K++++KCVI+
Sbjct: 182 GRAARKKKKKKKCVIL 197
>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 = 255 bits (653), Expect = 8e-88
Identities = 99/172 (57%), Positives = 129/172 (75%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQED 66
+KCV+VGDG VGKT +++SYTT+ +P EYVPT FDN+S VDG PV L L DTAGQ++
Sbjct: 1 LKCVLVGDGAVGKTSLIVSYTTNGYPTEYVPTAFDNFSVVVLVDGKPVRLQLCDTAGQDE 60
Query: 67 YDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPIILVGTKIDLREDR 126
+D+LRPL YP TDVFL+C+SVV+PSSF N++ KW PE++ H P APIILVGT+ DLR D
Sbjct: 61 FDKLRPLCYPDTDVFLLCFSVVNPSSFQNISEKWIPEIRKHNPKAPIILVGTQADLRTDV 120
Query: 127 ETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRA 178
L L+ PV + + + LA KI A +Y+ECSALTQ+ L++VFD A+ A
Sbjct: 121 NVLIQLARYGEKPVSQSRAKALAEKIGACEYIECSALTQKNLKEVFDTAILA 172
>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 = 245 bits (628), Expect = 4e-84
Identities = 102/173 (58%), Positives = 125/173 (72%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQEDY 67
K V+VGDG GKTC+LI ++ D FP YVPTVF+NY A VDG V L LWDTAGQEDY
Sbjct: 3 KLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDY 62
Query: 68 DRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPIILVGTKIDLREDRE 127
DRLRPLSYP TDV L+C+S+ SP S +N+ KW PE+KH CP+ PIILVG K DLR D
Sbjct: 63 DRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEH 122
Query: 128 TLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAVL 180
T+ L++ PVK E+G+ +A KI A Y+ECSA T+ G+R+VF+ A RA L
Sbjct: 123 TIRELAKMKQEPVKPEEGRAMAEKIGAFGYLECSAKTKEGVREVFEMATRAAL 175
>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 = 237 bits (605), Expect = 1e-80
Identities = 111/174 (63%), Positives = 138/174 (79%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQED 66
+KCVVVGDG VGKTC+L+SY D+FP EYVPTVFD+Y+ TV G LGL+DTAGQED
Sbjct: 1 LKCVVVGDGAVGKTCLLMSYANDAFPEEYVPTVFDHYAVSVTVGGKQYLLGLYDTAGQED 60
Query: 67 YDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPIILVGTKIDLREDR 126
YDRLRPLSYP TDVFLIC+SVV+P+SF NV +W PELK + P+ P +L+GT+IDLR+D
Sbjct: 61 YDRLRPLSYPMTDVFLICFSVVNPASFQNVKEEWVPELKEYAPNVPYLLIGTQIDLRDDP 120
Query: 127 ETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAVL 180
+TL L++ P+ EQGQKLA +I A Y+ECSALTQ+GL+ VFDEA+ A+L
Sbjct: 121 KTLARLNDMKEKPITVEQGQKLAKEIGACCYVECSALTQKGLKTVFDEAIIAIL 174
>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 = 228 bits (582), Expect = 4e-77
Identities = 99/174 (56%), Positives = 131/174 (75%), Gaps = 2/174 (1%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQED 66
IKCV VGDG VGKTCMLISYT+++FP +YVPTVFDN+SA VDG V+LGLWDTAGQED
Sbjct: 2 IKCVTVGDGAVGKTCMLISYTSNTFPTDYVPTVFDNFSANVVVDGNTVNLGLWDTAGQED 61
Query: 67 YDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPIILVGTKIDLREDR 126
Y+RLRPLSY DVFL+ +S++S +S++NV KW PEL+H+ P PI+LVGTK+DLR+D+
Sbjct: 62 YNRLRPLSYRGADVFLLAFSLISKASYENVLKKWIPELRHYAPGVPIVLVGTKLDLRDDK 121
Query: 127 ETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAVL 180
+ P+ QG++L +I A Y+ECS+ TQ+ ++ VFD A++ VL
Sbjct: 122 QF--FADHPGAVPITTAQGEELRKQIGAAAYIECSSKTQQNVKAVFDAAIKVVL 173
>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 = 221 bits (566), Expect = 1e-74
Identities = 72/176 (40%), Positives = 100/176 (56%), Gaps = 16/176 (9%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTV-FDNYSAPFTVDGIPVSLGLWDTAGQED 66
K V+VGDG VGK+ +LI +T + FP EY+PT+ D Y+ VDG V L +WDTAGQE
Sbjct: 1 KLVLVGDGGVGKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAGQER 60
Query: 67 YDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPD-APIILVGTKIDLRED 125
+ LRPL Y FL+ Y + S SF+NV KW E+ H + PI+LVG K DL +
Sbjct: 61 FRALRPLYYRGAQGFLLVYDITSRDSFENVK-KWLEEILRHADENVPIVLVGNKCDLEDQ 119
Query: 126 RETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAVLR 181
R V E+G+ LA ++ + +ME SA T + + F+E R +L+
Sbjct: 120 R------------VVSTEEGEALAKEL-GLPFMETSAKTNENVEEAFEELAREILK 162
>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 = 204 bits (521), Expect = 1e-67
Identities = 89/190 (46%), Positives = 116/190 (61%), Gaps = 4/190 (2%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQEDY 67
K V+VGDG GKT +L +T FP EY PTVF+NY VDG PV L LWDTAGQE+Y
Sbjct: 3 KLVIVGDGACGKTSLLYVFTLGEFPEEYHPTVFENYVTDCRVDGKPVQLALWDTAGQEEY 62
Query: 68 DRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPIILVGTKIDLREDRE 127
+RLRPLSY + V LI +++ +P S +NV +KW E++ +CP+ P+ILVG K DLR++
Sbjct: 63 ERLRPLSYSKAHVILIGFAIDTPDSLENVRTKWIEEVRRYCPNVPVILVGLKKDLRQEAV 122
Query: 128 TLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAVL--RPEPV 185
+ V +Q + +A I A KYMECSALT G+ VF+ A RA L R
Sbjct: 123 AKGNYATDEF--VPIQQAKLVARAIGAKKYMECSALTGEGVDDVFEAATRAALLVRKSGK 180
Query: 186 KRRQRKCVII 195
+ C II
Sbjct: 181 EEPGANCCII 190
>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 = 198 bits (506), Expect = 2e-65
Identities = 85/175 (48%), Positives = 110/175 (62%), Gaps = 1/175 (0%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQED 66
K V+VGD GKT +L + DSFP YVPTVF+NY+A F VD + L LWDT+G
Sbjct: 2 CKIVLVGDSQCGKTALLQVFAKDSFPENYVPTVFENYTASFEVDKQRIELSLWDTSGSPY 61
Query: 67 YDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPIILVGTKIDLREDR 126
YD +RPLSYP +D LIC+ + P + D+V KW E++ CP+ P++LVG K DLR D
Sbjct: 62 YDNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEVREFCPNTPVLLVGCKSDLRTDL 121
Query: 127 ETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALT-QRGLRQVFDEAVRAVL 180
TL LS + PV EQG+ LA +I A Y+ECSA T + +R VF+ A A L
Sbjct: 122 STLTELSNKRQIPVSHEQGRNLAKQIGAAAYVECSAKTSENSVRDVFEMATLACL 176
>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 = 188 bits (479), Expect = 3e-61
Identities = 86/187 (45%), Positives = 112/187 (59%), Gaps = 4/187 (2%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQEDY 67
K VV+GDG GKT +L +T FP Y PTVF+NY VDG+ V L LWDTAGQE++
Sbjct: 2 KVVVLGDGACGKTSLLNVFTRGYFPQVYEPTVFENYIHDIFVDGLAVELSLWDTAGQEEF 61
Query: 68 DRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPIILVGTKIDLREDRE 127
DRLR LSY T V ++C+SV +P S +NV SKW E++HHCP ++LV K DLRE R
Sbjct: 62 DRLRSLSYADTHVIMLCFSVDNPDSLENVESKWLAEIRHHCPGVKLVLVALKCDLREPRN 121
Query: 128 TLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAVLRPEPVKR 187
+ + + E+G +A +I A +Y+ECSA RG+ + F EA R L P
Sbjct: 122 ERDRGTHT----ISYEEGLAVAKRINACRYLECSAKLNRGVNEAFTEAARVALNARPPHP 177
Query: 188 RQRKCVI 194
R C I
Sbjct: 178 HSRACTI 184
>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 = 175 bits (445), Expect = 9e-56
Identities = 80/178 (44%), Positives = 113/178 (63%), Gaps = 1/178 (0%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQEDY 67
K VVVGD GKT +L + D++P YVPTVF+NY+A F +D + L +WDT+G Y
Sbjct: 3 KIVVVGDTQCGKTALLHVFAKDNYPESYVPTVFENYTASFEIDKHRIELNMWDTSGSSYY 62
Query: 68 DRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPIILVGTKIDLREDRE 127
D +RPL+YP +D LIC+ + P + D+V KW E + CP+A ++LVG K+D+R D
Sbjct: 63 DNVRPLAYPDSDAVLICFDISRPETLDSVLKKWQGETQEFCPNAKLVLVGCKLDMRTDLS 122
Query: 128 TLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSA-LTQRGLRQVFDEAVRAVLRPEP 184
TL LS+Q L PV EQG LA ++ AV Y+ECS+ +++ +R VF A +R E
Sbjct: 123 TLRELSKQRLIPVTHEQGSLLARQLGAVAYVECSSRMSENSVRDVFHVTTLASVRREH 180
>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 = 165 bits (420), Expect = 2e-52
Identities = 79/172 (45%), Positives = 106/172 (61%), Gaps = 1/172 (0%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQEDY 67
K VVVGD GKT +L + D FP YVPTVF+NY+A F +D + L LWDT+G Y
Sbjct: 7 KIVVVGDSQCGKTALLHVFAKDCFPENYVPTVFENYTASFEIDTQRIELSLWDTSGSPYY 66
Query: 68 DRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPIILVGTKIDLREDRE 127
D +RPLSYP +D LIC+ + P + D+V KW E++ CP+ ++LVG K DLR D
Sbjct: 67 DNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEIQEFCPNTKMLLVGCKSDLRTDVS 126
Query: 128 TLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSAL-TQRGLRQVFDEAVRA 178
TL LS +PV +QG +A +I A Y+ECSAL ++ +R +F A A
Sbjct: 127 TLVELSNHRQTPVSYDQGANMAKQIGAATYIECSALQSENSVRDIFHVATLA 178
>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 = 157 bits (399), Expect = 2e-49
Identities = 57/175 (32%), Positives = 87/175 (49%), Gaps = 20/175 (11%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTV---FDNYSAPFTVDGIPVSLGLWDTAG 63
K V++GD VGKT +L+ + + F Y T+ F + + VDG V L +WDTAG
Sbjct: 1 FKIVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGVDFKSKT--IEVDGKKVKLQIWDTAG 58
Query: 64 QEDYDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCP-DAPIILVGTKIDL 122
QE + + Y ++ Y V + SF+N+ KW ELK + P + PIILVG K DL
Sbjct: 59 QERFRSITSSYYRGAHGAILVYDVTNRESFENL-DKWLNELKEYAPPNIPIILVGNKSDL 117
Query: 123 REDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVR 177
++R+ V E+ Q+ A + + + E SA T + + F+ R
Sbjct: 118 EDERQ------------VSTEEAQQFAKEN-GLLFFETSAKTGENVDEAFESLAR 159
>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 = 149 bits (377), Expect = 2e-45
Identities = 74/192 (38%), Positives = 105/192 (54%), Gaps = 8/192 (4%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQEDY 67
K V+VGD GKT ML D +P YVPTVF+NY+A + V L LWDT+G Y
Sbjct: 15 KLVLVGDVQCGKTAMLQVLAKDCYPETYVPTVFENYTACLETEEQRVELSLWDTSGSPYY 74
Query: 68 DRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPIILVGTKIDLREDRE 127
D +RPL Y +D L+C+ + P FD+ KW E+ +CP I+L+G K DLR D
Sbjct: 75 DNVRPLCYSDSDAVLLCFDISRPEIFDSALKKWRAEILDYCPSTRILLIGCKTDLRTDLS 134
Query: 128 TLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALT-QRGLRQVFDEAVRAVL------ 180
TL LS Q +P+ EQG +A ++ A Y+ECSA T ++ + +F A +
Sbjct: 135 TLMELSNQKQAPISYEQGCAMAKQLGAEAYLECSAFTSEKSIHSIFRTASLLCINKLSPL 194
Query: 181 -RPEPVKRRQRK 191
+ PV+ ++
Sbjct: 195 AKKSPVRSLSKR 206
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 143 bits (361), Expect = 5e-43
Identities = 62/183 (33%), Positives = 89/183 (48%), Gaps = 6/183 (3%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAP-FTVDGIPVSLGLWDTAGQE 65
K VV+GDG VGKT +L D FP Y PT+ + A + L LWDTAGQE
Sbjct: 6 FKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQE 65
Query: 66 DYDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPD-APIILVGTKIDLRE 124
+Y LRP Y + LI Y S D +T +W EL+ PD PI+LVG KIDL +
Sbjct: 66 EYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVGNKIDLFD 125
Query: 125 DRETLNLLSEQ--NLSPVKREQGQKLANKIRAVKYMECSA--LTQRGLRQVFDEAVRAVL 180
++ + + Q + + + ++ +E SA LT + ++F E +R +L
Sbjct: 126 EQSSSEEILNQLNREVVLLVLAPKAVLPEVANPALLETSAKSLTGPNVNELFKELLRKLL 185
Query: 181 RPE 183
Sbjct: 186 EEI 188
>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 = 139 bits (352), Expect = 3e-42
Identities = 56/172 (32%), Positives = 87/172 (50%), Gaps = 16/172 (9%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQEDY 67
K VV+G G VGK+ + I + + F EY PT+ D+Y VDG +L + DTAGQE++
Sbjct: 1 KLVVLGAGGVGKSALTIRFVSGEFVEEYDPTIEDSYRKQIVVDGETYTLDILDTAGQEEF 60
Query: 68 DRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELK--HHCPDAPIILVGTKIDLRED 125
+R D F++ YS+ S SF+ + ++ D PI+LVG K DL +
Sbjct: 61 SAMRDQYIRNGDGFILVYSITSRESFEEI-KNIREQILRVKDKEDVPIVLVGNKCDLENE 119
Query: 126 RETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVR 177
R+ V E+G+ LA + ++E SA T + ++F+ VR
Sbjct: 120 RQ------------VSTEEGEALAEEWG-CPFLETSAKTNINIDELFNTLVR 158
>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 = 137 bits (346), Expect = 2e-41
Identities = 54/162 (33%), Positives = 70/162 (43%), Gaps = 7/162 (4%)
Query: 6 PIKCVVVGDGTVGKTCMLISYT-TDSFPGEYVPTVFDNY-SAPFTVDGIPVSLGLWDTAG 63
IK V+VGD VGK+ +L EY P NY + DG L DTAG
Sbjct: 1 EIKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAG 60
Query: 64 QEDYDRLRPLSYPQTDVFLICYSVVSP-SSFDNVTSKWYPELKHHCP-DAPIILVGTKID 121
QEDYD +R L Y + L + +V + + K E+ HH PIILVG KID
Sbjct: 61 QEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAESGVPIILVGNKID 120
Query: 122 LR---EDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMEC 160
LR L ++ N P+ + N A K +E
Sbjct: 121 LRDAKLKTHVAFLFAKLNGEPIIPLSAETGKNIDSAFKIVEA 162
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 134 bits (341), Expect = 1e-40
Identities = 55/177 (31%), Positives = 87/177 (49%), Gaps = 16/177 (9%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTV-FDNYSAPFTVDGIPVSLGLWDTAGQE 65
K +++GD VGK+ +L +T F +Y T+ D + VDG V L +WDTAGQE
Sbjct: 1 FKIILIGDSGVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIEVDGKRVKLQIWDTAGQE 60
Query: 66 DYDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHC-PDAPIILVGTKIDLRE 124
+ + Y L+ Y + + SF+N+ W EL+ + P+ I+LVG K DL E
Sbjct: 61 RFRSITSSYYRGAVGALLVYDITNRESFENLE-NWLKELREYASPNVVIMLVGNKSDLEE 119
Query: 125 DRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAVLR 181
R+ V RE+ + A + + + E SA T + + F+E R +L+
Sbjct: 120 QRQ------------VSREEAEAFA-EEHGLPFFETSAKTNTNVEEAFEELAREILK 163
>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 = 130 bits (327), Expect = 3e-38
Identities = 79/195 (40%), Positives = 113/195 (57%), Gaps = 26/195 (13%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSFPGEY------VPTVF--DNY--------SAPFTVD 50
IKCVVVGD VGKT ++ + + +Y VPTV+ D Y + VD
Sbjct: 3 IKCVVVGDNAVGKTRLICARACNKTLTQYQLLATHVPTVWAIDQYRVCQEVLERSRDVVD 62
Query: 51 GIPVSLGLWDTAGQEDYDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPD 110
G+ VSL LWDT G D+D+ R +Y ++DV L+C+S+ SP+S NV + WYPE++H CP
Sbjct: 63 GVSVSLRLWDTFG--DHDKDRRFAYGRSDVVLLCFSIASPNSLRNVKTMWYPEIRHFCPR 120
Query: 111 APIILVGTKIDLRE-DRETLNLLSEQNLSPVKR------EQGQKLANKIRAVKYMECSAL 163
P+ILVG K+DLR D + +N P+K E G+ +A ++ + Y E S +
Sbjct: 121 VPVILVGCKLDLRYADLDEVNRARRPLARPIKNADILPPETGRAVAKEL-GIPYYETSVV 179
Query: 164 TQRGLRQVFDEAVRA 178
TQ G++ VFD A+RA
Sbjct: 180 TQFGVKDVFDNAIRA 194
>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 = 117 bits (296), Expect = 9e-34
Identities = 53/176 (30%), Positives = 87/176 (49%), Gaps = 16/176 (9%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQEDY 67
K VV+G G VGK+ + I + F +Y PT+ D+Y +DG L + DTAGQE++
Sbjct: 2 KLVVLGSGGVGKSALTIQFIQGHFVDDYDPTIEDSYRKQIEIDGEVCLLDILDTAGQEEF 61
Query: 68 DRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKH--HCPDAPIILVGTKIDLRED 125
+R + FL+ YS+ SF+ + K+ ++ D PI+LVG K DL +
Sbjct: 62 SAMRDQYMRTGEGFLLVYSITDRQSFEEI-KKFREQILRVKDRDDVPIVLVGNKCDLESE 120
Query: 126 RETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAVLR 181
R V E+G++LA + ++E SA + + + F + VR + +
Sbjct: 121 RV------------VSTEEGKELARQW-GCPFLETSAKERVNVDEAFYDLVREIRK 163
>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 = 117 bits (295), Expect = 1e-33
Identities = 54/177 (30%), Positives = 88/177 (49%), Gaps = 16/177 (9%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQEDY 67
K VV+G G VGK+ + I + F EY PT+ D+Y +DG L + DTAGQE++
Sbjct: 4 KLVVLGGGGVGKSALTIQFVQGHFVDEYDPTIEDSYRKQIEIDGEVCLLDILDTAGQEEF 63
Query: 68 DRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKH--HCPDAPIILVGTKIDLRED 125
+R + FL+ YS+ SF+ + +K+ ++ D PI+LVG K DL +
Sbjct: 64 SAMRDQYMRTGEGFLLVYSITDRQSFEEI-AKFREQILRVKDRDDVPIVLVGNKCDLENE 122
Query: 126 RETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAVLRP 182
R V E+G++LA + ++E SA + + + F + VR + +
Sbjct: 123 RV------------VSTEEGKELARQW-GCPFLETSAKERINVDEAFYDLVREIRKS 166
>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 = 115 bits (290), Expect = 6e-33
Identities = 64/176 (36%), Positives = 94/176 (53%), Gaps = 18/176 (10%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTV-FDNYSAPFTVDGIPVSLGLWDTAGQE 65
+K +++GD VGK+ +L+ +T D+F + T+ D TVDG V L +WDTAGQE
Sbjct: 1 LKILLIGDSGVGKSSLLLRFTDDTFDEDLSSTIGVDFKVKTVTVDGKKVKLAIWDTAGQE 60
Query: 66 DYDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHC--PDAPIILVGTKIDLR 123
+ L Y ++ Y V +FDN+ W EL + PDA +LVG KID +
Sbjct: 61 RFRTLTSSYYRGAQGVILVYDVTRRDTFDNL-DTWLNELDTYSTNPDAVKMLVGNKID-K 118
Query: 124 EDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAV 179
E+RE V RE+GQK A K + ++E SA T+ G++Q F+E V +
Sbjct: 119 ENRE------------VTREEGQKFARKHNML-FIETSAKTRIGVQQAFEELVEKI 161
>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 = 113 bits (285), Expect = 3e-32
Identities = 57/169 (33%), Positives = 86/169 (50%), Gaps = 18/169 (10%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTV-FDNYSAPFTVDGIPVSLGLWDTAGQED 66
K V +GD +VGKT ++ + D+F +Y T+ D S VD V L LWDTAGQE
Sbjct: 2 KLVFLGDQSVGKTSIITRFMYDTFDNQYQATIGIDFLSKTMYVDDKTVRLQLWDTAGQER 61
Query: 67 YDRLRPLSYPQ-TDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPII-LVGTKIDLRE 124
+ L P SY + + V ++ Y + + SFDN KW +++ + II LVG K DL +
Sbjct: 62 FRSLIP-SYIRDSSVAVVVYDITNRQSFDNTD-KWIDDVRDERGNDVIIVLVGNKTDLSD 119
Query: 125 DRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFD 173
R+ V E+G+K A + ++E SA ++Q+F
Sbjct: 120 KRQ------------VSTEEGEKKAKEN-NAMFIETSAKAGHNVKQLFK 155
>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 = 109 bits (275), Expect = 9e-31
Identities = 57/174 (32%), Positives = 92/174 (52%), Gaps = 16/174 (9%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQEDY 67
K VVVG G VGK+ + I + F +Y PT+ D+Y+ +DG L + DTAGQE++
Sbjct: 4 KLVVVGGGGVGKSALTIQFIQSYFVTDYDPTIEDSYTKQCEIDGQWARLDILDTAGQEEF 63
Query: 68 DRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKH--HCPDAPIILVGTKIDLRED 125
+R + FL+ +SV SF+ V K++ ++ + P+ILVG K DL
Sbjct: 64 SAMREQYMRTGEGFLLVFSVTDRGSFEEV-DKFHTQILRVKDRDEFPMILVGNKADLEHQ 122
Query: 126 RETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAV 179
R+ V RE+GQ+LA +++ + Y+E SA + + + F + VR +
Sbjct: 123 RQ------------VSREEGQELARQLK-IPYIETSAKDRVNVDKAFHDLVRVI 163
>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 = 101 bits (253), Expect = 2e-27
Identities = 51/169 (30%), Positives = 83/169 (49%), Gaps = 16/169 (9%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDN-YSAPFTVDGIPVSLGLWDTAGQE 65
K V++G+G VGKT +++ Y + F ++ T + + + G + L +WDTAGQE
Sbjct: 1 FKVVLLGEGRVGKTSLVLRYVENKFNEKHESTTQASFFQKTVNIGGKRIDLAIWDTAGQE 60
Query: 66 DYDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPD-APIILVGTKIDLRE 124
Y L P+ Y D ++ Y + SF V KW ELK + +++VG KIDL
Sbjct: 61 RYHALGPIYYRDADGAILVYDITDADSFQKVK-KWIKELKQMRGNNISLVIVGNKIDLER 119
Query: 125 DRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFD 173
R V + + ++ A + A K+ E SA T +G+ ++F
Sbjct: 120 QRV------------VSKSEAEEYAKSVGA-KHFETSAKTGKGIEELFL 155
>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 = 100 bits (252), Expect = 3e-27
Identities = 53/179 (29%), Positives = 83/179 (46%), Gaps = 24/179 (13%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPF-----TVDGIPVSLGLWDTA 62
K V++GD +VGK+ +++ + + F T+ A F +D V +WDTA
Sbjct: 3 KLVLLGDSSVGKSSIVLRFVKNEFSENQESTI----GAAFLTQTVNLDDTTVKFEIWDTA 58
Query: 63 GQEDYDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHC-PDAPIILVGTKID 121
GQE Y L P+ Y ++ Y + S SF+ S W EL+ H P+ I L G K D
Sbjct: 59 GQERYRSLAPMYYRGAAAAIVVYDITSEESFEKAKS-WVKELQEHGPPNIVIALAGNKAD 117
Query: 122 LREDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAVL 180
L R+ V E+ Q+ A++ + +ME SA T + ++F E R +
Sbjct: 118 LESKRQ------------VSTEEAQEYADENGLL-FMETSAKTGENVNELFTEIARKLP 163
>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 = 101 bits (252), Expect = 4e-27
Identities = 66/204 (32%), Positives = 103/204 (50%), Gaps = 30/204 (14%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQEDY 67
K VV+GDG VGKT + I + F Y PT+ D+Y VDG P L + DTAGQE+Y
Sbjct: 1 KLVVLGDGGVGKTALTIQLCLNHFVETYDPTIEDSYRKQVVVDGQPCMLEVLDTAGQEEY 60
Query: 68 DRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPEL---KHHCP-DAPIILVGTKIDLR 123
LR + + F++ YS+ S S+F+ V ++ ++ K D PI++VG K D
Sbjct: 61 TALRDQWIREGEGFILVYSITSRSTFERV-ERFREQIQRVKDESAADVPIMIVGNKCDKV 119
Query: 124 EDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAVLRP- 182
+RE V E+G LA ++ +++E SA T + + F VRA+ +
Sbjct: 120 YERE------------VSTEEGAALARRL-GCEFIEASAKTNVNVERAFYTLVRALRQQR 166
Query: 183 -----------EPVKRRQRKCVII 195
+ ++++RKCVI+
Sbjct: 167 QGGQGPKGGPTKKKEKKKRKCVIM 190
>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 = 98.3 bits (245), Expect = 3e-26
Identities = 45/177 (25%), Positives = 67/177 (37%), Gaps = 25/177 (14%)
Query: 10 VVVGDGTVGKTCMLISYTTDSF---PGEYVPTV-FDNYSAPFTVDGIPVSLGLWDTAGQE 65
VVVG G VGK+ +L + T D Y + + L DT G +
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVL--VDTPGLD 58
Query: 66 DYDRLRP-----LSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPIILVGTKI 120
++ L L D+ L+ S ++ K + PIILVG KI
Sbjct: 59 EFGGLGREELARLLLRGADLILLVVDSTDRESEEDA--KLLILRRLRKEGIPIILVGNKI 116
Query: 121 DLREDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVR 177
DL E+RE V+ + KI V E SA T G+ ++F++ +
Sbjct: 117 DLLEERE------------VEELLRLEELAKILGVPVFEVSAKTGEGVDELFEKLIE 161
>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 = 98.1 bits (245), Expect = 4e-26
Identities = 51/180 (28%), Positives = 87/180 (48%), Gaps = 22/180 (12%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTV-FDNYSAPFTVDGIPVSLGLWDTAGQE 65
K +++GD VGK+C+L+ ++ DSF ++ T+ D +DG + L +WDTAGQE
Sbjct: 4 FKLLLIGDSGVGKSCLLLRFSEDSFNPSFISTIGIDFKIRTIELDGKKIKLQIWDTAGQE 63
Query: 66 DYDRLRPLS---YPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHC-PDAPIILVGTKID 121
R R ++ Y ++ Y + SF+N+ W + H D +LVG K D
Sbjct: 64 ---RFRTITTSYYRGAMGIILVYDITDEKSFENI-KNWMRNIDEHASEDVERMLVGNKCD 119
Query: 122 LREDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAVLR 181
+ E R V +E+G+ LA + +K++E SA + + F + +L+
Sbjct: 120 MEEKRV------------VSKEEGEALAREYG-IKFLETSAKANINVEEAFLTLAKDILK 166
>gnl|CDD|206680 cd01893, Miro1, Mitochondrial Rho family 1 (Miro1), N-terminal.
Miro1 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the N-terminal
GTPase domain of Miro proteins. These atypical Rho
GTPases have roles in mitochondrial homeostasis and
apoptosis. Most Rho proteins contain a lipid
modification site at the C-terminus; however, Miro is
one of few Rho subfamilies that lack this feature.
Length = 168
Score = 98.2 bits (245), Expect = 4e-26
Identities = 54/179 (30%), Positives = 90/179 (50%), Gaps = 16/179 (8%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYS--APFTVDGIPVSLGLWDTAGQ 64
++ V++GD VGK+ +++S ++ FP E VP V + A T + +P ++ DT+ +
Sbjct: 3 VRIVLIGDEGVGKSSLIMSLVSEEFP-ENVPRVLPEITIPADVTPERVPTTI--VDTSSR 59
Query: 65 EDYDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPIILVGTKIDLRE 124
+ +V + YSV PS+ + + +KW P ++ PIILVG K DLR+
Sbjct: 60 PQDRANLAAEIRKANVICLVYSVDRPSTLERIRTKWLPLIRRLGVKVPIILVGNKSDLRD 119
Query: 125 DRETLNLLSEQNLSPVKREQGQKLANKIRAVK-YMECSALTQRGLRQVFDEAVRAVLRP 182
L E+ + P+ E R ++ +ECSA T + +VF A +AVL P
Sbjct: 120 GSSQAGL--EEEMLPIMNE--------FREIETCVECSAKTLINVSEVFYYAQKAVLHP 168
>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 = 96.6 bits (241), Expect = 1e-25
Identities = 62/181 (34%), Positives = 88/181 (48%), Gaps = 22/181 (12%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQEDY 67
K V+G VGK+ + + + T F GEY P + YS T+DG VSL + DT GQ+
Sbjct: 1 KIAVLGASGVGKSALTVRFLTKRFIGEYEPNLESLYSRQVTIDGEQVSLEIQDTPGQQQN 60
Query: 68 D----RLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWY--PELKHHCPDAPIILVGTKID 121
+ R L + D F++ YS+ SSFD V+ E+K + P+ILVG K D
Sbjct: 61 EDPESLERSLRW--ADGFVLVYSITDRSSFDVVSQLLQLIREIKKRDGEIPVILVGNKAD 118
Query: 122 LREDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSA-LTQRGLRQVFDEAVRAVL 180
L R+ V E+GQKLA ++ + + E SA ++ VF E R V
Sbjct: 119 LLHSRQ------------VSTEEGQKLALELGCLFF-EVSAAENYLEVQNVFHELCREVR 165
Query: 181 R 181
R
Sbjct: 166 R 166
>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 = 95.6 bits (238), Expect = 3e-25
Identities = 62/176 (35%), Positives = 90/176 (51%), Gaps = 21/176 (11%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQEDY 67
K VVVG G VGK+ + I + F EY PT+ D+Y +DG L + DTAGQE+Y
Sbjct: 3 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEY 62
Query: 68 DRLRPLSYPQT-DVFLICYSVVSPSSFDNVTSKWYPELKHHCPDA---PIILVGTKIDLR 123
+R Y +T + FL +++ S SF+++ + Y E D+ P++LVG K DL
Sbjct: 63 SAMRD-QYMRTGEGFLCVFAINSRKSFEDIHT--YREQIKRVKDSDDVPMVLVGNKCDL- 118
Query: 124 EDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAV 179
R V QGQ LA K + Y+E SA T++G+ + F VR +
Sbjct: 119 AART------------VSTRQGQDLA-KSYGIPYIETSAKTRQGVEEAFYTLVREI 161
>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 = 95.8 bits (239), Expect = 4e-25
Identities = 54/192 (28%), Positives = 90/192 (46%), Gaps = 20/192 (10%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQEDY 67
K V+G +VGK+ + + + F Y PT+ + +S T G L + DTAGQ++Y
Sbjct: 3 KIAVLGSRSVGKSSLTVQFVEGHFVESYYPTIENTFSKIITYKGQEYHLEIVDTAGQDEY 62
Query: 68 DRLRPLSYPQTDV--FLICYSVVSPSSFDNVTSKWYPELKHHCPDA-PIILVGTKIDLRE 124
L P Y + +++ YSV S SF+ V + L ++ PI+LVG K DL
Sbjct: 63 SIL-PQKY-SIGIHGYILVYSVTSRKSFEVVKVIYDKILDMLGKESVPIVLVGNKSDLHM 120
Query: 125 DRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAVLRPE- 183
+R+ V E+G+KLA A ++E SA + + F+ + + + E
Sbjct: 121 ERQ------------VSAEEGKKLAESWGA-AFLESSAKENENVEEAFELLIEEIEKVEN 167
Query: 184 -PVKRRQRKCVI 194
++ KC +
Sbjct: 168 PLPPGQKSKCSV 179
>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 = 95.0 bits (237), Expect = 7e-25
Identities = 56/187 (29%), Positives = 83/187 (44%), Gaps = 27/187 (14%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPF-----TVDGIPVSLGLWDTA 62
K +++GD VGKT ++ Y F +Y T+ A F TVD V+L +WDTA
Sbjct: 2 KVIILGDSGVGKTSLMNQYVNKKFSNQYKATI----GADFLTKEVTVDDRLVTLQIWDTA 57
Query: 63 GQEDYDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHC----PDA-PIILVG 117
GQE + L Y D ++ Y V +P SF+++ S W E P+ P +++G
Sbjct: 58 GQERFQSLGVAFYRGADCCVLVYDVTNPKSFESLDS-WRDEFLIQASPRDPENFPFVVLG 116
Query: 118 TKIDLREDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVR 177
KIDL E R+ V ++ Q+ + Y E SA + Q F+ R
Sbjct: 117 NKIDLEEKRQ------------VSTKKAQQWCKSKGNIPYFETSAKEAINVDQAFETIAR 164
Query: 178 AVLRPEP 184
L E
Sbjct: 165 LALEQEK 171
>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 = 94.0 bits (234), Expect = 1e-24
Identities = 56/175 (32%), Positives = 87/175 (49%), Gaps = 14/175 (8%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQEDY 67
K ++VG G VGK+ + + + D F +Y PT D+Y +DG V L + DTAGQEDY
Sbjct: 2 KVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEVQLNILDTAGQEDY 61
Query: 68 DRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDA-PIILVGTKIDLREDR 126
+R + + FL+ +S+ SF + L+ D P++LVG K DL + R
Sbjct: 62 AAIRDNYFRSGEGFLLVFSITDMESFTALAEFREQILRVKEDDNVPLLLVGNKCDLEDKR 121
Query: 127 ETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAVLR 181
+ V E+ LA + V Y+E SA T+ + +VF + VR + +
Sbjct: 122 Q------------VSVEEAANLAEQ-WGVNYVETSAKTRANVDKVFFDLVREIRQ 163
>gnl|CDD|206660 cd01868, Rab11_like, Rab GTPase family 11 (Rab11)-like includes
Rab11a, Rab11b, and Rab25. Rab11a, Rab11b, and Rab25
are closely related, evolutionary conserved Rab proteins
that are differentially expressed. Rab11a is
ubiquitously synthesized, Rab11b is enriched in brain
and heart and Rab25 is only found in epithelia. Rab11/25
proteins seem to regulate recycling pathways from
endosomes to the plasma membrane and to the trans-Golgi
network. Furthermore, Rab11a is thought to function in
the histamine-induced fusion of tubulovesicles
containing H+, K+ ATPase with the plasma membrane in
gastric parietal cells and in insulin-stimulated
insertion of GLUT4 in the plasma membrane of
cardiomyocytes. Overexpression of Rab25 has recently
been observed in ovarian cancer and breast cancer, and
has been correlated with worsened outcomes in both
diseases. In addition, Rab25 overexpression has also
been observed in prostate cancer, transitional cell
carcinoma of the bladder, and invasive breast tumor
cells. GTPase activating proteins (GAPs) interact with
GTP-bound Rab and accelerate the hydrolysis of GTP to
GDP. Guanine nucleotide exchange factors (GEFs) interact
with GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 165
Score = 93.4 bits (233), Expect = 2e-24
Identities = 53/170 (31%), Positives = 82/170 (48%), Gaps = 22/170 (12%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTV---FDNYSAPFTVDGIPVSLGLWDTAGQ 64
K V++GD VGK+ +L +T + F + T+ F + +DG + +WDTAGQ
Sbjct: 5 KIVLIGDSGVGKSNLLSRFTRNEFNLDSKSTIGVEFATRT--IQIDGKTIKAQIWDTAGQ 62
Query: 65 EDYDRLRPLSYPQTDV-FLICYSVVSPSSFDNVTSKWYPELKHHC-PDAPIILVGTKIDL 122
E Y R +Y + V L+ Y + S+F+NV +W EL+ H + I+LVG K DL
Sbjct: 63 ERY-RAITSAYYRGAVGALLVYDITKKSTFENVE-RWLKELRDHADSNIVIMLVGNKSDL 120
Query: 123 REDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVF 172
R R V E+ + A K + ++E SAL + + F
Sbjct: 121 RHLRA------------VPTEEAKAFAEKNG-LSFIETSALDGTNVEEAF 157
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 93.8 bits (233), Expect = 3e-24
Identities = 63/196 (32%), Positives = 95/196 (48%), Gaps = 21/196 (10%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQEDY 67
K VVVG G VGK+ + I + + F EY PT+ D+Y +D L + DTAGQE+Y
Sbjct: 7 KLVVVGGGGVGKSALTIQFIQNHFIDEYDPTIEDSYRKQCVIDEETCLLDILDTAGQEEY 66
Query: 68 DRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPD-APIILVGTKIDLREDR 126
+R FL YS+ S SSF+ + S L+ D P+ILVG K DL +R
Sbjct: 67 SAMRDQYMRTGQGFLCVYSITSRSSFEEIASFREQILRVKDKDRVPMILVGNKCDLDSER 126
Query: 127 ETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAV------- 179
+ V +GQ+LA K + ++E SA + + + F E VR +
Sbjct: 127 Q------------VSTGEGQELA-KSFGIPFLETSAKQRVNVDEAFYELVREIRKYLKED 173
Query: 180 LRPEPVKRRQRKCVII 195
+ + K++ C+I+
Sbjct: 174 MPSQKQKKKGGLCLIL 189
>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 = 91.9 bits (228), Expect = 9e-24
Identities = 52/173 (30%), Positives = 85/173 (49%), Gaps = 13/173 (7%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQEDY 67
K VV+G G VGK+ + + + F +Y PT+ D+Y VD L + DTAG E +
Sbjct: 3 KLVVLGSGGVGKSALTVQFVQGIFVDKYDPTIEDSYRKQIEVDCQQCMLEILDTAGTEQF 62
Query: 68 DRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELK-HHCPDAPIILVGTKIDLREDR 126
+R L F + YS+ + SF+++ L+ D P+ILVG K DL ++R
Sbjct: 63 TAMRDLYIKNGQGFALVYSITAQQSFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDER 122
Query: 127 ETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAV 179
V +E+GQ LA + ++E SA ++ + ++F + VR +
Sbjct: 123 V------------VSKEEGQNLARQWGNCPFLETSAKSKINVDEIFYDLVRQI 163
>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 = 89.9 bits (223), Expect = 5e-23
Identities = 56/182 (30%), Positives = 86/182 (47%), Gaps = 18/182 (9%)
Query: 5 RPIKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQ 64
R K V++G G VGK+ + + + + SFP + PT+ D Y +D P L + DTAGQ
Sbjct: 1 REYKIVMLGAGGVGKSAVTMQFISHSFPDYHDPTIEDAYKTQARIDNEPALLDILDTAGQ 60
Query: 65 EDYDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPEL---KHHCPDAPIILVGTKID 121
++ +R + F+ICYSV SF + + EL D P++LVG K+D
Sbjct: 61 AEFTAMRDQYMRCGEGFIICYSVTDRHSFQEASE--FKELITRVRLTEDIPLVLVGNKVD 118
Query: 122 LREDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAVLR 181
L + R+ V E+G+ LA + + E SA + + F VR + R
Sbjct: 119 LEQQRQ------------VTTEEGRNLAREF-NCPFFETSAALRFYIDDAFHGLVREIRR 165
Query: 182 PE 183
E
Sbjct: 166 KE 167
>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 = 89.9 bits (223), Expect = 6e-23
Identities = 55/175 (31%), Positives = 88/175 (50%), Gaps = 14/175 (8%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQEDY 67
K VV+G G VGK+ + + + F +Y PT+ D+Y VDG L + DTAG E +
Sbjct: 3 KLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDGQQCMLEILDTAGTEQF 62
Query: 68 DRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELK-HHCPDAPIILVGTKIDLREDR 126
+R L F++ YS+ + S+F+++ L+ D P+ILVG K DL ++R
Sbjct: 63 TAMRDLYMKNGQGFVLVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDER 122
Query: 127 ETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAVLR 181
V +EQGQ LA + ++E SA + + ++F + VR + R
Sbjct: 123 ------------VVGKEQGQNLARQWGC-AFLETSAKAKINVNEIFYDLVRQINR 164
>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 = 89.9 bits (223), Expect = 8e-23
Identities = 58/159 (36%), Positives = 84/159 (52%), Gaps = 15/159 (9%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSF-PGEYVPTV-FDNYSAPFTVDGIPVSLGLWDTAGQE 65
K ++VGD VGKTC+L+ + +F G ++ TV + TVDG+ V L +WDTAGQE
Sbjct: 2 KVMLVGDSGVGKTCLLVRFKDGAFLAGSFIATVGIQFTNKVVTVDGVKVKLQIWDTAGQE 61
Query: 66 DYDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPIILVGTKIDLRED 125
+ + Y L+ Y V + SSFDN+ + L++ D I+L+G K D+ +
Sbjct: 62 RFRSVTHAYYRDAHALLLLYDVTNKSSFDNIRAWLTEILEYAQSDVVIMLLGNKADMSGE 121
Query: 126 RETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALT 164
R VKRE G++LA K V +ME SA T
Sbjct: 122 RV------------VKREDGERLA-KEYGVPFMETSAKT 147
>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 = 89.5 bits (222), Expect = 9e-23
Identities = 55/174 (31%), Positives = 85/174 (48%), Gaps = 13/174 (7%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQEDY 67
K VV+G G VGK+ + + + + F Y PT+ D+Y +DG L + DTAG E +
Sbjct: 3 KIVVLGAGGVGKSALTVQFVQNVFIESYDPTIEDSYRKQVEIDGRQCDLEILDTAGTEQF 62
Query: 68 DRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDA-PIILVGTKIDLREDR 126
+R L FL+ YSV S +S + + L+ D P++LVG K DL +DR
Sbjct: 63 TAMRELYIKSGQGFLLVYSVTSEASLNELGELREQVLRIKDSDNVPMVLVGNKADLEDDR 122
Query: 127 ETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAVL 180
+ V RE G L+ + V + E SA + + +VF + VR ++
Sbjct: 123 Q------------VSREDGVSLSQQWGNVPFYETSARKRTNVDEVFIDLVRQII 164
>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 = 87.1 bits (216), Expect = 6e-22
Identities = 43/150 (28%), Positives = 71/150 (47%), Gaps = 16/150 (10%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTV---FDNYSAPFTVDGIPVSLGLWDTAG 63
IK +VVG+G VGK+ M+ + F +Y T+ F V L LWDTAG
Sbjct: 1 IKVIVVGNGNVGKSSMIQRFVKGIFTKDYKKTIGVDFLEKQIFLRQSDEDVRLMLWDTAG 60
Query: 64 QEDYDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPIILVGTKIDLR 123
QE++D + Y ++ +S SF+ + W +++ C D P++LV TKIDL
Sbjct: 61 QEEFDAITKAYYRGAQACILVFSTTDRESFEAI-ESWKEKVEAECGDIPMVLVQTKIDLL 119
Query: 124 EDRETLNLLSEQNLSPVKREQGQKLANKIR 153
+ + + E+ + LA +++
Sbjct: 120 DQ------------AVITNEEAEALAKRLQ 137
>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 = 87.2 bits (216), Expect = 6e-22
Identities = 53/171 (30%), Positives = 85/171 (49%), Gaps = 14/171 (8%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQEDY 67
K VV+G G VGK+ + + + + +F +Y PT+ D Y VD P L + DTAG E +
Sbjct: 3 KVVVLGSGGVGKSALTVQFVSGTFIEKYDPTIEDFYRKEIEVDSSPSVLEILDTAGTEQF 62
Query: 68 DRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELK-HHCPDAPIILVGTKIDLREDR 126
+R L F++ YS+V+ +F ++ ++ PIILVG K+DL +R
Sbjct: 63 ASMRDLYIKNGQGFIVVYSLVNQQTFQDIKPMRDQIVRVKGYEKVPIILVGNKVDLESER 122
Query: 127 ETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVR 177
E V +G+ LA + +ME SA ++ + ++F E VR
Sbjct: 123 E------------VSSAEGRALAEEW-GCPFMETSAKSKTMVNELFAEIVR 160
>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 = 87.9 bits (218), Expect = 1e-21
Identities = 60/162 (37%), Positives = 84/162 (51%), Gaps = 24/162 (14%)
Query: 10 VVVGDGTVGKTCMLISYTTDSFPGEYVPTV-FDNYSAPFTV-DGIPVSLGLWDTAGQEDY 67
+V+GD TVGK+ +L +T F PTV D +S + G+ + L LWDTAGQE
Sbjct: 6 IVIGDSTVGKSSLLKRFTEGRFAEVSDPTVGVDFFSRLIEIEPGVRIKLQLWDTAGQE-- 63
Query: 68 DRLRPL--SYPQTDV-FLICYSVVSPSSFDNVTSKWYPELKHHC-PDAPI-ILVGTKIDL 122
R R + SY + V L+ + + + SF++V W E + H P P+ ILVG K DL
Sbjct: 64 -RFRSITRSYYRNSVGVLLVFDITNRESFEHV-HDWLEEARSHIQPHRPVFILVGHKCDL 121
Query: 123 REDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALT 164
R+ V RE+ +KLA K +KY+E SA T
Sbjct: 122 ESQRQ------------VTREEAEKLA-KDLGMKYIETSART 150
>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 = 85.4 bits (211), Expect = 3e-21
Identities = 53/176 (30%), Positives = 86/176 (48%), Gaps = 16/176 (9%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTV-FDNYSAPFTVDGIPVSLGLWDTAGQED 66
+ +++GD VGKTC+L +T + F ++ T+ D VDGI V + +WDTAGQE
Sbjct: 2 RLLLIGDSGVGKTCLLCRFTDNEFHSSHISTIGVDFKMKTIEVDGIKVRIQIWDTAGQER 61
Query: 67 YDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDA-PIILVGTKIDLRED 125
Y + Y + + Y + S S+ ++ KW ++ + P+ IL+G K D +
Sbjct: 62 YQTITKQYYRRAQGIFLVYDISSERSYQHIM-KWVSDVDEYAPEGVQKILIGNKADEEQK 120
Query: 126 RETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAVLR 181
R+ V EQG KLA K + + E SA T + +++ F VL+
Sbjct: 121 RQ------------VGDEQGNKLA-KEYGMDFFETSACTNKNIKESFTRLTELVLQ 163
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 85.1 bits (211), Expect = 9e-21
Identities = 42/122 (34%), Positives = 69/122 (56%), Gaps = 3/122 (2%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTV-FDNYSAPFTVDGIPVSLGLWDTAGQE 65
K ++VGDG VGKT + + T F +Y+PT+ + + F + P+ +WDTAGQE
Sbjct: 10 FKLILVGDGGVGKTTFVKRHLTGEFEKKYIPTLGVEVHPLKFYTNCGPICFNVWDTAGQE 69
Query: 66 DYDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPIILVGTKIDLRED 125
+ LR Y + +I + V S ++ NV W+ ++ C + PI+LVG K+D++ D
Sbjct: 70 KFGGLRDGYYIKGQCAIIMFDVTSRITYKNV-PNWHRDIVRVCENIPIVLVGNKVDVK-D 127
Query: 126 RE 127
R+
Sbjct: 128 RQ 129
>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 = 84.5 bits (209), Expect = 9e-21
Identities = 54/171 (31%), Positives = 78/171 (45%), Gaps = 27/171 (15%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNY-----------SAPFTVDGIPVS 55
IK + +GD VGKT L YT + F +++ TV ++ + V
Sbjct: 5 IKLLALGDSGVGKTTFLYRYTDNKFNPKFITTVGIDFREKRVVYNSQGPDGTSGKAFRVH 64
Query: 56 LGLWDTAGQEDYDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHH--CPDAPI 113
L LWDTAGQE + L + FL+ + + S SF NV W +L+ H C + I
Sbjct: 65 LQLWDTAGQERFRSLTTAFFRDAMGFLLMFDLTSEQSFLNV-RNWMSQLQAHAYCENPDI 123
Query: 114 ILVGTKIDLREDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALT 164
+L+G K DL + RE V Q ++LA+K + Y E SA T
Sbjct: 124 VLIGNKADLPDQRE------------VSERQARELADKYG-IPYFETSAAT 161
>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 = 83.5 bits (207), Expect = 1e-20
Identities = 40/121 (33%), Positives = 64/121 (52%), Gaps = 2/121 (1%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTV-FDNYSAPFTVDGIPVSLGLWDTAGQE 65
K V+VGDG GKT + + T F +YV T+ + + F + + +WDTAGQE
Sbjct: 1 FKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLDFHTNRGKIRFNVWDTAGQE 60
Query: 66 DYDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPIILVGTKIDLRED 125
+ LR Y Q +I + V S ++ NV W+ +L C + PI+L G K+D+++
Sbjct: 61 KFGGLRDGYYIQGQCAIIMFDVTSRVTYKNV-PNWHRDLVRVCENIPIVLCGNKVDIKDR 119
Query: 126 R 126
+
Sbjct: 120 K 120
>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 = 83.1 bits (206), Expect = 2e-20
Identities = 48/179 (26%), Positives = 85/179 (47%), Gaps = 22/179 (12%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTV-FDNYSAPFTVDGIPVSLGLWDTAGQED 66
K +++GD VGK+C+L+ + D++ Y+ T+ D +DG V L +WDTAGQE
Sbjct: 4 KLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTVKLQIWDTAGQE- 62
Query: 67 YDRLRPLS---YPQTDVFLICYSVVSPSSFDNVTSKWYPELKHH-CPDAPIILVGTKIDL 122
R R ++ Y +I Y V SF+NV +W E+ + + +LVG K DL
Sbjct: 63 --RFRTITSSYYRGAHGIIIVYDVTDQESFNNV-KQWLQEIDRYASENVNKLLVGNKCDL 119
Query: 123 REDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAVLR 181
+ + V + ++ A+++ + ++E SA + + F R + +
Sbjct: 120 TDKKV------------VDYTEAKEFADELG-IPFLETSAKNATNVEEAFMTMAREIKK 165
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 83.1 bits (205), Expect = 6e-20
Identities = 50/183 (27%), Positives = 87/183 (47%), Gaps = 16/183 (8%)
Query: 1 MSSGRPIKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPF-TVDGIPVSLGLW 59
MS K +++GD VGK+C+L+ +T F + T+ + A T+D P+ L +W
Sbjct: 1 MSYAYLFKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDNKPIKLQIW 60
Query: 60 DTAGQEDYDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHC-PDAPIILVGT 118
DTAGQE + + Y L+ Y + +F+++ S W + + H + I+L+G
Sbjct: 61 DTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLAS-WLEDARQHANANMTIMLIGN 119
Query: 119 KIDLREDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRA 178
K DL R V E+G++ A K + +ME SA T + + + F +
Sbjct: 120 KCDLAHRR------------AVSTEEGEQFA-KEHGLIFMEASAKTAQNVEEAFIKTAAK 166
Query: 179 VLR 181
+ +
Sbjct: 167 IYK 169
>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 = 81.7 bits (202), Expect = 8e-20
Identities = 49/176 (27%), Positives = 84/176 (47%), Gaps = 16/176 (9%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAP-FTVDGIPVSLGLWDTAGQED 66
K +++GD VGK+C+L+ +T F + T+ + A T+DG + L +WDTAGQE
Sbjct: 6 KYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQES 65
Query: 67 YDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHC-PDAPIILVGTKIDLRED 125
+ + Y L+ Y + +F+++TS W + + H + I+L+G K DL
Sbjct: 66 FRSITRSYYRGAAGALLVYDITRRETFNHLTS-WLEDARQHSNSNMTIMLIGNKCDLESR 124
Query: 126 RETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAVLR 181
RE V E+G+ A + + +ME SA T + + F + +
Sbjct: 125 RE------------VSYEEGEAFARE-HGLIFMETSAKTASNVEEAFINTAKEIYD 167
>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 = 81.4 bits (201), Expect = 1e-19
Identities = 51/178 (28%), Positives = 72/178 (40%), Gaps = 21/178 (11%)
Query: 8 KCVVVGDGTVGKT--CMLISYTTDSFPGEYVPTV---FDNYSAPFTVDGIPVSLGLWDTA 62
+C VVGD VGK+ + +F Y T + P V L ++D+A
Sbjct: 2 QCAVVGDPAVGKSALVQMFHSDGATFQKNYTMTTGCDLVVKTVPVPDTSDSVELFIFDSA 61
Query: 63 GQEDYDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCP--DAPIILVGTKI 120
GQE + + + Q V + Y V + SF+N S+W ++ H P +LVG K
Sbjct: 62 GQELFSDMVENVWEQPAVVCVVYDVTNEVSFNNC-SRWINRVRTHSHGLHTPGVLVGNKC 120
Query: 121 DLREDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRA 178
DL + RE V Q Q LA +K+ E SA G F RA
Sbjct: 121 DLTDRRE------------VDAAQAQALAQA-NTLKFYETSAKEGVGYEAPFLSLARA 165
>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 = 81.1 bits (200), Expect = 1e-19
Identities = 54/175 (30%), Positives = 86/175 (49%), Gaps = 24/175 (13%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGI-----PVSLGLWDTA 62
K +++G+ +VGKT L Y DSF +V TV F V + + L +WDTA
Sbjct: 3 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTV----GIDFKVKTVYRNDKRIKLQIWDTA 58
Query: 63 GQEDYDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPD-APIILVGTKID 121
GQE Y + Y F++ Y + + SF N W ++K + D A +ILVG K D
Sbjct: 59 GQERYRTITTAYYRGAMGFILMYDITNEESF-NAVQDWSTQIKTYSWDNAQVILVGNKCD 117
Query: 122 LREDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAV 176
+ ++R V E+G++LA+++ ++ E SA ++QVF+ V
Sbjct: 118 MEDER------------VVSAERGRQLADQL-GFEFFEASAKENINVKQVFERLV 159
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 81.3 bits (201), Expect = 3e-19
Identities = 38/118 (32%), Positives = 61/118 (51%), Gaps = 2/118 (1%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTV-FDNYSAPFTVDGIPVSLGLWDTAGQE 65
K V+VGDG GKT + + T F +Y PT+ + + F + + WDTAGQE
Sbjct: 14 FKLVIVGDGGTGKTTFVKRHLTGEFEKKYEPTIGVEVHPLDFFTNCGKIRFYCWDTAGQE 73
Query: 66 DYDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPIILVGTKIDLR 123
+ LR Y +I + V + ++ NV + W+ +L C + PI+L G K+D++
Sbjct: 74 KFGGLRDGYYIHGQCAIIMFDVTARLTYKNVPT-WHRDLCRVCENIPIVLCGNKVDVK 130
>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 = 80.7 bits (199), Expect = 3e-19
Identities = 51/168 (30%), Positives = 83/168 (49%), Gaps = 12/168 (7%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSF-PGEYVPTVFDNYSA-PFTVDGIPVSLGLWDTAGQ 64
+K V++G +VGKT ++ Y F G Y T+ + A V V+LG+WDTAG
Sbjct: 1 VKVVMLGKESVGKTSLVERYVHHRFLVGPYQNTIGAAFVAKRMVVGERVVTLGIWDTAGS 60
Query: 65 EDYDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPIILVGTKIDLRE 124
E Y+ + + Y ++CY + SSF+ W EL++ I L GTK DL E
Sbjct: 61 ERYEAMSRIYYRGAKAAIVCYDLTDSSSFERAKF-WVKELQNLEEHCKIYLCGTKSDLIE 119
Query: 125 DRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVF 172
+++L V Q A++I+A ++ E S+ T + + ++F
Sbjct: 120 --------QDRSLRQVDFHDVQDFADEIKA-QHFETSSKTGQNVDELF 158
>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 = 78.6 bits (194), Expect = 3e-19
Identities = 34/116 (29%), Positives = 50/116 (43%), Gaps = 3/116 (2%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAP-FTVDGIPVSLGLWDTAGQED 66
K VV+GD GK+ +L FP E + D + VDG L +WD G+E+
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREE 60
Query: 67 YDRLRPLSYPQTDVFLICYSVVSPSSFDNVTS--KWYPELKHHCPDAPIILVGTKI 120
+ D L+ Y + S + V+ W P L+ P+ILVG K+
Sbjct: 61 LKFEHIIFMKWADAILLVYDLTDRESLNEVSRLIAWLPNLRKLGGKIPVILVGNKL 116
>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 = 79.9 bits (197), Expect = 4e-19
Identities = 58/181 (32%), Positives = 88/181 (48%), Gaps = 24/181 (13%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTV---FDNYSAPFTVDGIPVSLGLWDTAG 63
+K +++GDG VGK+ ++ Y T+ F + T+ F N VDG V+L +WDTAG
Sbjct: 6 LKVILLGDGGVGKSSLMNRYVTNKFDTQLFHTIGVEFLNKD--LEVDGHFVTLQIWDTAG 63
Query: 64 QEDYDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHC----PDA-PIILVGT 118
QE + LR Y +D L+ +SV SF N+ S W E ++ P++ P +++G
Sbjct: 64 QERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNL-SNWKKEFIYYADVKEPESFPFVILGN 122
Query: 119 KIDLREDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRA 178
KID+ +R+ V E+ Q Y E SA + F+EAVR
Sbjct: 123 KIDI-PERQ------------VSTEEAQAWCRDNGDYPYFETSAKDATNVAAAFEEAVRR 169
Query: 179 V 179
V
Sbjct: 170 V 170
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 80.5 bits (198), Expect = 5e-19
Identities = 53/170 (31%), Positives = 84/170 (49%), Gaps = 17/170 (10%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTV-FDNYSAPFTVDGIPVSLGLWDTAGQED 66
K +++GD VGK+ +L+S+ + S + PT+ D TV G + L +WDTAGQE
Sbjct: 16 KILLIGDSGVGKSSLLVSFISSSVE-DLAPTIGVDFKIKQLTVGGKRLKLTIWDTAGQER 74
Query: 67 YDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCP--DAPIILVGTKIDLRE 124
+ L Y ++ Y V +F N++ W E++ + D +LVG K+D
Sbjct: 75 FRTLTSSYYRNAQGIILVYDVTRRETFTNLSDVWGKEVELYSTNQDCVKMLVGNKVDRES 134
Query: 125 DRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDE 174
+R+ V RE+G LA K ++ECSA T+ + Q F+E
Sbjct: 135 ERD------------VSREEGMALA-KEHGCLFLECSAKTRENVEQCFEE 171
>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 = 78.6 bits (194), Expect = 9e-19
Identities = 52/177 (29%), Positives = 84/177 (47%), Gaps = 22/177 (12%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAP-FTVDGIPVSLGLWDTAGQED 66
K +++G GK+C+L + + F + T+ + + V G V L +WDTAGQE
Sbjct: 2 KFLIIGSAGTGKSCLLHQFIENKFKQDSNHTIGVEFGSRVVNVGGKSVKLQIWDTAGQE- 60
Query: 67 YDRLRPL--SYPQTDV-FLICYSVVSPSSFDNVTSKWYPELKH-HCPDAPIILVGTKIDL 122
R R + SY + L+ Y + S SF+ +T W + + PD IILVG K DL
Sbjct: 61 --RFRSVTRSYYRGAAGALLVYDITSRESFNALT-NWLTDARTLASPDIVIILVGNKKDL 117
Query: 123 REDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAV 179
+DRE V + + A + + ++E SALT + + F + R++
Sbjct: 118 EDDRE------------VTFLEASRFAQE-NGLLFLETSALTGENVEEAFLKCARSI 161
>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 = 77.1 bits (190), Expect = 4e-18
Identities = 43/127 (33%), Positives = 62/127 (48%), Gaps = 5/127 (3%)
Query: 5 RPIKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTV-FDNYSAPFTVDGIPVSLGLWDTAG 63
R K +V+GD VGKTC+ + FP T+ D +DG + + LWDTAG
Sbjct: 1 RIFKIIVIGDSNVGKTCLTYRFCAGRFPERTEATIGVDFRERTVEIDGERIKVQLWDTAG 60
Query: 64 QEDYDR-LRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHC--PDAPIILVGTKI 120
QE + + + Y + Y V + +SF ++ S W E + H + P ILVG K
Sbjct: 61 QERFRKSMVQHYYRNVHAVVFVYDVTNMASFHSLPS-WIEECEQHSLPNEVPRILVGNKC 119
Query: 121 DLREDRE 127
DLRE +
Sbjct: 120 DLREQIQ 126
>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 = 76.7 bits (189), Expect = 7e-18
Identities = 45/167 (26%), Positives = 78/167 (46%), Gaps = 15/167 (8%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSA-PFTVDGIPVSLGLWDTAGQED 66
K +++GD VGKTC++ + + +F T+ +++ + G V L +WDTAGQE
Sbjct: 5 KIILIGDSNVGKTCVVQRFKSGTFSERQGNTIGVDFTMKTLEIQGKRVKLQIWDTAGQER 64
Query: 67 YDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHH-CPDAPIILVGTKIDLRED 125
+ + Y + +I Y + SSF++V W E++ + + ++L+G K DL E
Sbjct: 65 FRTITQSYYRSANGAIIAYDITRRSSFESV-PHWIEEVEKYGASNVVLLLIGNKCDLEEQ 123
Query: 126 RETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVF 172
RE V E+ LA + +E SA + + F
Sbjct: 124 RE------------VLFEEACTLAEHYGILAVLETSAKESSNVEEAF 158
>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 = 76.1 bits (187), Expect = 1e-17
Identities = 57/172 (33%), Positives = 85/172 (49%), Gaps = 23/172 (13%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTV-FDNYSAPFTVDGIPVSLGLWDTAGQED 66
K +VVGD +VGKTC++ + D F Y T+ D F V G+P SL LWDTAGQE
Sbjct: 2 KVIVVGDLSVGKTCLINRFCKDVFDKNYKATIGVDFEMERFEVLGVPFSLQLWDTAGQER 61
Query: 67 YDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPE-LKHHCPDAPII-LVGTKIDLRE 124
+ + Y +I + + +S ++ T +W + LK + P + ++ LVGTK DL
Sbjct: 62 FKCIASTYYRGAQAIIIVFDLTDVASLEH-TRQWLEDALKENDPSSVLLFLVGTKKDL-- 118
Query: 125 DRETLNLLSEQNLSPVKREQGQ----KLANKIRAVKYMECSALTQRGLRQVF 172
SP + + KLA +++A +Y SALT +R F
Sbjct: 119 ------------SSPAQYALMEQDAIKLAREMKA-EYWAVSALTGENVRDFF 157
>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 = 74.1 bits (182), Expect = 4e-17
Identities = 34/117 (29%), Positives = 60/117 (51%), Gaps = 2/117 (1%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSF-PGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQE 65
+K +++GD VGK+ ++ + D + P + Y +G + + WDTAGQE
Sbjct: 1 VKIILLGDSAVGKSKLVERFLMDGYEPQQLSTYALTLYKHNAKFEGKTILVDFWDTAGQE 60
Query: 66 DYDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPIILVGTKIDL 122
+ + Y + ++ + V ++ N+ SKWY EL+ + P+ P I+V KIDL
Sbjct: 61 RFQTMHASYYHKAHACILVFDVTRKITYKNL-SKWYEELREYRPEIPCIVVANKIDL 116
>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 = 74.1 bits (182), Expect = 1e-16
Identities = 39/115 (33%), Positives = 63/115 (54%), Gaps = 2/115 (1%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTV-FDNYSAPFTVDGIPVSLGLWDTAGQED 66
K +++GD VGK+ +L+ + ++F G Y+ T+ D ++G V L +WDTAGQE
Sbjct: 8 KLLIIGDSGVGKSSLLLRFADNTFSGSYITTIGVDFKIRTVEINGERVKLQIWDTAGQER 67
Query: 67 YDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPIILVGTKID 121
+ + Y T ++ Y V + SF NV +W E++ +C D +LVG K D
Sbjct: 68 FRTITSTYYRGTHGVIVVYDVTNGESFVNV-KRWLQEIEQNCDDVCKVLVGNKND 121
>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 = 73.2 bits (180), Expect = 1e-16
Identities = 45/182 (24%), Positives = 79/182 (43%), Gaps = 21/182 (11%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSA-PFTVDGIPVSLGLWDTAGQE 65
IK + +G+ VGK+C++ Y F +Y+PT+ +Y +V V + +D +G
Sbjct: 1 IKVISMGNSGVGKSCIIKRYCEGRFVSKYLPTIGIDYGVKKVSVRNKEVRVNFFDLSGHP 60
Query: 66 DYDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAP------IILVGTK 119
+Y +R Y T L+ Y V SF+ + W E+K +++ K
Sbjct: 61 EYLEVRNEFYKDTQGVLLVYDVTDRQSFEAL-DSWLKEMKQEGGPHGNMENIVVVVCANK 119
Query: 120 IDLREDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAV 179
IDL + R V ++G+ A + KY E SA T G+ ++F ++
Sbjct: 120 IDLTKHRA------------VSEDEGRLWAES-KGFKYFETSACTGEGVNEMFQTLFSSI 166
Query: 180 LR 181
+
Sbjct: 167 VD 168
>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 = 74.0 bits (182), Expect = 2e-16
Identities = 56/191 (29%), Positives = 86/191 (45%), Gaps = 20/191 (10%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPG-EYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQED 66
+ V++GD VGK+ + +T + Y + D Y +VDG +L ++D QED
Sbjct: 2 RVVLLGDSGVGKSSLANIFTAGVYEDSAYEASGDDTYERTVSVDGEEATLVVYDHWEQED 61
Query: 67 YDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELK--HHCPDAPIILVGTKIDLRE 124
L D ++I YSV SSF+ S+ +L+ D PIILVG K DL
Sbjct: 62 GMWLEDSCMQVGDAYVIVYSVTDRSSFE-KASELRIQLRRARQAEDIPIILVGNKSDLVR 120
Query: 125 DRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAV-LRP- 182
RE V ++G+ A + K++E SA Q + ++F+ VR V LR
Sbjct: 121 SRE------------VSVQEGRACA-VVFDCKFIETSAALQHNVDELFEGIVRQVRLRRD 167
Query: 183 -EPVKRRQRKC 192
+ R+
Sbjct: 168 SKEKNTRRMAS 178
>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 = 72.6 bits (178), Expect = 4e-16
Identities = 53/189 (28%), Positives = 90/189 (47%), Gaps = 18/189 (9%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQEDY 67
+ V +G VGKT ++ + D+F ++ TV + +S + V G+ V++ + DT+G +
Sbjct: 1 RLVFMGAAGVGKTALIQRFLYDTFEPKHRRTVEELHSKEYEVAGVKVTIDILDTSGSYSF 60
Query: 68 DRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDA--PIILVGTKIDLRED 125
+R LS D F + YSV P SF+ V E+ D PI++VG KID +
Sbjct: 61 PAMRKLSIQNGDAFALVYSVDDPESFEEVKR-LREEILEVKEDKFVPIVVVGNKIDSLAE 119
Query: 126 RETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAVLRP--- 182
R+ + + LS V+ + ++E SA + +VF E ++ P
Sbjct: 120 RQ---VEAADALSTVELDWNN---------GFVEASAKDNENVTEVFKELLQQANLPSWL 167
Query: 183 EPVKRRQRK 191
P RR+R+
Sbjct: 168 SPALRRRRE 176
>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 = 71.5 bits (175), Expect = 6e-16
Identities = 46/169 (27%), Positives = 81/169 (47%), Gaps = 16/169 (9%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFP-GEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQED 66
K V++G+ VGKTC++ +T FP G+ D + G + L +WDTAGQE
Sbjct: 9 KIVLIGNAGVGKTCLVRRFTQGLFPPGQGATIGVDFMIKTVEIKGEKIKLQIWDTAGQER 68
Query: 67 YDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPI-ILVGTKIDLRED 125
+ + Y + ++ Y + SF + +W E++ + + I ILVG KIDL E
Sbjct: 69 FRSITQSYYRSANALILTYDITCEESFRCL-PEWLREIEQYANNKVITILVGNKIDLAER 127
Query: 126 RETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDE 174
RE V +++ ++ + + + Y+E SA + ++F +
Sbjct: 128 RE------------VSQQRAEEFS-DAQDMYYLETSAKESDNVEKLFLD 163
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 72.3 bits (177), Expect = 8e-16
Identities = 52/167 (31%), Positives = 78/167 (46%), Gaps = 16/167 (9%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSA-PFTVDGIPVSLGLWDTAGQED 66
K V++GD VGK+ +L +T + F E T+ ++ V+G V +WDTAGQE
Sbjct: 14 KIVLIGDSGVGKSNILSRFTRNEFCLESKSTIGVEFATRTLQVEGKTVKAQIWDTAGQER 73
Query: 67 YDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHC-PDAPIILVGTKIDLRED 125
Y + Y L+ Y + +FDNV +W EL+ H + I++ G K DL
Sbjct: 74 YRAITSAYYRGAVGALLVYDITKRQTFDNV-QRWLRELRDHADSNIVIMMAGNKSDL--- 129
Query: 126 RETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVF 172
+L V E GQ LA K + ++E SAL + + F
Sbjct: 130 ---------NHLRSVAEEDGQALAEK-EGLSFLETSALEATNVEKAF 166
>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 = 71.6 bits (175), Expect = 9e-16
Identities = 51/179 (28%), Positives = 91/179 (50%), Gaps = 17/179 (9%)
Query: 10 VVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVD--GIPVSLGLWDTAGQEDY 67
+++G VGKT ++ +T D+F TV ++ TV+ G + L +WDTAGQE +
Sbjct: 4 IIIGSRGVGKTSLMERFTDDTFCEACKSTVGVDFKIK-TVELRGKKIRLQIWDTAGQERF 62
Query: 68 DRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPEL-KHHCPDAPIILVGTKIDLREDR 126
+ + Y ++ Y + +FD++ KW + K+ DA ++LVG K+D DR
Sbjct: 63 NSITSAYYRSAKGIILVYDITKKETFDDL-PKWMKMIDKYASEDAELLLVGNKLDCETDR 121
Query: 127 ETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAVLRPEPV 185
E + R+QG+K A +I +++ E SA + ++F + V +L+ P+
Sbjct: 122 E------------ITRQQGEKFAQQITGMRFCEASAKDNFNVDEIFLKLVDDILKKMPL 168
>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 = 71.6 bits (176), Expect = 1e-15
Identities = 49/181 (27%), Positives = 78/181 (43%), Gaps = 23/181 (12%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTV-FDNYSAPFTVD-GIPVSLGLWDTAGQE 65
K +V+GD VGKT ++ Y F Y T+ D D V L LWD AGQE
Sbjct: 2 KVLVIGDLGVGKTSIIKRYVHGVFSQHYKATIGVDFALKVIEWDPNTVVRLQLWDIAGQE 61
Query: 66 DYDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPEL--KHHCPDA---PIILVGTKI 120
+ + + Y +I + V PS+F+ V KW +L K P+ P +L+ K
Sbjct: 62 RFGGMTRVYYKGAVGAIIVFDVTRPSTFEAV-LKWKADLDSKVTLPNGEPIPALLLANKC 120
Query: 121 DLREDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAVL 180
DL+++R EQ + + + + E SA + +EA+R ++
Sbjct: 121 DLKKERLA-----------KDPEQMDQFCKENGFIGWFETSAKENINI----EEAMRFLV 165
Query: 181 R 181
+
Sbjct: 166 K 166
>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 = 70.3 bits (172), Expect = 2e-15
Identities = 45/174 (25%), Positives = 84/174 (48%), Gaps = 16/174 (9%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFT-VDGIPVSLGLWDTAGQED 66
K +++GD VGK+C+L +T F + T+ + V+G + L +WDTAGQE
Sbjct: 4 KYIIIGDMGVGKSCLLHQFTEKKFMADCPHTIGVEFGTRIIEVNGQKIKLQIWDTAGQER 63
Query: 67 YDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHC-PDAPIILVGTKIDLRED 125
+ + Y L+ Y + S++++++S W + ++ P+ I L+G K DL
Sbjct: 64 FRAVTRSYYRGAAGALMVYDITRRSTYNHLSS-WLTDARNLTNPNTVIFLIGNKADLEAQ 122
Query: 126 RETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAV 179
R+ V E+ ++ A++ + ++ECSA T + F E + +
Sbjct: 123 RD------------VTYEEAKQFADE-NGLLFLECSAKTGENVEDAFLETAKKI 163
>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 = 70.4 bits (172), Expect = 2e-15
Identities = 38/114 (33%), Positives = 62/114 (54%), Gaps = 2/114 (1%)
Query: 12 VGDGTVGKTCMLISYTTDSFPGEYVPTV-FDNYSAPFTVDGIPVSLGLWDTAGQEDYDRL 70
VGDG GKT + + T F +YV T+ + + F + P+ +WDTAGQE + L
Sbjct: 1 VGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIRFNVWDTAGQEKFGGL 60
Query: 71 RPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPIILVGTKIDLRE 124
R Y Q +I + V + ++ NV + W+ +L C + PI+L G K+D+++
Sbjct: 61 RDGYYIQGQCAIIMFDVTARVTYKNVPN-WHRDLVRVCENIPIVLCGNKVDVKD 113
>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 = 67.2 bits (164), Expect = 2e-14
Identities = 46/170 (27%), Positives = 78/170 (45%), Gaps = 16/170 (9%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQEDY 67
+ VV G G VGK+ +++ + +F Y+PT+ D Y + +L + DT G +
Sbjct: 3 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCSKSICTLQITDTTGSHQF 62
Query: 68 DRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKW--YPELK-HHCPDAPIILVGTKIDLRE 124
++ LS + F++ YS+ S S + + + E+K ++ PI+LVG K D
Sbjct: 63 PAMQRLSISKGHAFILVYSITSKQSLEELKPIYELICEIKGNNLEKIPIMLVGNKCDESP 122
Query: 125 DRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDE 174
RE V +G LA +ME SA T ++++F E
Sbjct: 123 SRE------------VSSSEGAALARTWN-CAFMETSAKTNHNVQELFQE 159
>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 = 67.9 bits (166), Expect = 3e-14
Identities = 36/126 (28%), Positives = 61/126 (48%), Gaps = 7/126 (5%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTV-FDNYSAPFTVDG-IPVSLGLWDTAGQ 64
IK VV+GDG GKT ++ + + F Y T+ D +S T+ G + V+L +WD GQ
Sbjct: 1 IKIVVLGDGASGKTSLIRRFAQEGFGKSYKQTIGLDFFSRRITLPGSLNVTLQVWDIGGQ 60
Query: 65 EDYDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAP----IILVGTKI 120
+ ++ + Y + + SF+N+ W +K ++ ++LVG K
Sbjct: 61 QIGGKMLDKYIYGAQAVCLVYDITNSQSFENL-EDWLSVVKKVNEESETKPKMVLVGNKT 119
Query: 121 DLREDR 126
DL +R
Sbjct: 120 DLEHNR 125
>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 = 65.9 bits (161), Expect = 9e-14
Identities = 34/129 (26%), Positives = 63/129 (48%), Gaps = 7/129 (5%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNY-SAPFTVDGIPVSLGLWDTAGQE 65
+K ++GD +GKT +++ Y F EY+ T+ N+ ++ G ++ +WD GQ
Sbjct: 1 LKIGLLGDAQIGKTSLMVKYVEGEFDEEYIQTLGVNFMEKTISIRGTEITFSIWDLGGQR 60
Query: 66 DYDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPIILVGTKIDL--- 122
++ + PL L + + S+ +++ WY + + A ILVGTK DL
Sbjct: 61 EFINMLPLVCKDAVAILFMFDLTRKSTLNSIKE-WYRQARGFNKTAIPILVGTKYDLFAD 119
Query: 123 --REDRETL 129
E++E +
Sbjct: 120 LPPEEQEEI 128
>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 = 63.0 bits (153), Expect = 1e-12
Identities = 53/176 (30%), Positives = 79/176 (44%), Gaps = 17/176 (9%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNY-SAPFTVDGIPVSLGLWDTAGQE 65
+K ++VGD VGK +L S S Y + +Y + +DG V L LWDT+GQ
Sbjct: 7 LKFLLVGDSDVGKGEILASLQDGSTESPYGYNMGIDYKTTTILLDGRRVKLQLWDTSGQG 66
Query: 66 DYDRL-RPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPIILVGTKIDLRE 124
+ + R S + L+ Y + + SFD + +W E+ H P P ILVG ++ L
Sbjct: 67 RFCTIFRSYSRGAQGIILV-YDITNRWSFDGI-DRWIKEIDEHAPGVPKILVGNRLHLAF 124
Query: 125 DRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAVL 180
R+ V EQ Q A + + + E S L + + F E R VL
Sbjct: 125 KRQ------------VATEQAQAYAERN-GMTFFEVSPLCNFNITESFTELARIVL 167
>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 = 63.2 bits (154), Expect = 2e-12
Identities = 44/172 (25%), Positives = 76/172 (44%), Gaps = 21/172 (12%)
Query: 10 VVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQEDYDR 69
VV+G VGKT ++ + F +Y PT+ D + +++ G L + DT+G +
Sbjct: 4 VVLGASKVGKTAIVSRFLGGRFEEQYTPTIEDFHRKLYSIRGEVYQLDILDTSGNHPFPA 63
Query: 70 LRPLSYPQTDVFLICYSVVSPSSFDNV--------TSKWYPELK-HHCPDAPIILVGTKI 120
+R LS DVF++ +S+ + SF+ V +K + K P+++ G K
Sbjct: 64 MRRLSILTGDVFILVFSLDNRESFEEVCRLREQILETKSCLKNKTKENVKIPMVICGNKA 123
Query: 121 DLREDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVF 172
D RE V+R++ ++L Y E SA L ++F
Sbjct: 124 DRDFPRE------------VQRDEVEQLVGGDENCAYFEVSAKKNSNLDEMF 163
>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 = 61.2 bits (149), Expect = 3e-12
Identities = 33/141 (23%), Positives = 59/141 (41%), Gaps = 6/141 (4%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTV---FDNYSAPFTVDGIPVSLGLWDTAG 63
K ++VG G VGKT + + F G+ T ++ P + + L +WD G
Sbjct: 2 AKLMLVGQGGVGKTSLCKQLIGEKFDGDESSTHGINVQDWKIP-APERKKIRLNVWDFGG 60
Query: 64 QEDYDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPIILVGTKIDLR 123
QE Y ++L+ + + + V W ++K +P+ILVGT ID
Sbjct: 61 QEIYHATHQFFLTSRSLYLLVFDLRTGDEVSRV-PYWLRQIKAFGGVSPVILVGTHIDES 119
Query: 124 EDRE-TLNLLSEQNLSPVKRE 143
D + L+++ + +
Sbjct: 120 CDEDILKKALNKKFPAIINDI 140
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 58.6 bits (141), Expect = 5e-11
Identities = 45/148 (30%), Positives = 68/148 (45%), Gaps = 16/148 (10%)
Query: 29 DSFPGEYVPTV-FDNYSAPFTVDGIPVSLGLWDTAGQEDYDRLRPLSYPQTDVFLICYSV 87
D+F Y T+ D S +D PV L LWDTAGQE + L P + ++ Y +
Sbjct: 3 DTFDNNYQSTIGIDFLSKTLYLDEGPVRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDI 62
Query: 88 VSPSSFDNVTSKWYPE-LKHHCPDAPIILVGTKIDLREDRETLNLLSEQNLSPVKREQGQ 146
+ SF+N T+KW + L D I LVG K DL + R+ V E+G
Sbjct: 63 TNRQSFEN-TTKWIQDILNERGKDVIIALVGNKTDLGDLRK------------VTYEEGM 109
Query: 147 KLANKIRAVKYMECSALTQRGLRQVFDE 174
+ A + + + E SA ++ +F +
Sbjct: 110 QKAQEYNTM-FHETSAKAGHNIKVLFKK 136
>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 = 52.2 bits (125), Expect = 1e-08
Identities = 46/203 (22%), Positives = 77/203 (37%), Gaps = 25/203 (12%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQED 66
+K V++GD VGKT +L Y F + V TV A + P ++ +WDTAG+E
Sbjct: 1 LKVVLLGDMNVGKTSLLHRYMERRFK-DTVSTV---GGAFYLKQWGPYNISIWDTAGREQ 56
Query: 67 YDRLRPLSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHHCPDAPIILVGTKIDLREDR 126
+ L + ++ Y V + S + + ++ D +VG K+DL E+
Sbjct: 57 FHGLGSMYCRGAAAVILTYDVSNVQSLEELEDRFLGLTDTANEDCLFAVVGNKLDLTEEG 116
Query: 127 -ETLNLLSEQNLSP------VKREQGQKLANKIRAVK-------------YMECSALTQR 166
+ V E + +I K E SA T
Sbjct: 117 ALAGQEKDAGDRVSPEDQRQVTLEDAKAFYKRINKYKMLDEDLSPAAEKMCFETSAKTGY 176
Query: 167 GLRQVFDEAVRAVLRPEPVKRRQ 189
+ ++F+ VL P + +R
Sbjct: 177 NVDELFEYLFNLVL-PLILAQRA 198
>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 = 48.7 bits (116), Expect = 2e-07
Identities = 49/188 (26%), Positives = 73/188 (38%), Gaps = 28/188 (14%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDN-YSAPFTVDGIPVSLGLWD----- 60
++ V+G VGKT ++ + FP EY+PT Y + G L + D
Sbjct: 1 VRVAVLGAPGVGKTAIVRQFLAQEFPEEYIPTEHRRLYRPAVVLSGRVYDLHILDVPNMQ 60
Query: 61 ----TAGQEDYD-RLRPLSYPQTDVFLICYSVVSPSSFDNVTS---KWYPELKHHCPDAP 112
TAGQE D R R L + F++ Y + SP SF V + + P
Sbjct: 61 RYPGTAGQEWMDPRFRGLR--NSRAFILVYDICSPDSFHYVKLLRQQILETRPAGNKEPP 118
Query: 113 IILVGTKIDLREDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVF 172
I++VG K D++ LS L K Y+ECSA + +F
Sbjct: 119 IVVVGNK----RDQQRHRFAPRHVLS--------VLVRKSWKCGYLECSAKYNWHILLLF 166
Query: 173 DEAVRAVL 180
E + +
Sbjct: 167 KELLISAT 174
>gnl|CDD|133303 cd04103, Centaurin_gamma, Centaurin gamma (CENTG) GTPase. The
centaurins (alpha, beta, gamma, and delta) are large,
multi-domain proteins that all contain an ArfGAP domain
and ankyrin repeats, and in some cases, numerous
additional domains. Centaurin gamma contains an
additional GTPase domain near its N-terminus. The
specific function of this GTPase domain has not been
well characterized, but centaurin gamma 2 (CENTG2) may
play a role in the development of autism. Centaurin
gamma 1 is also called PIKE (phosphatidyl inositol (PI)
3-kinase enhancer) and centaurin gamma 2 is also known
as AGAP (ArfGAP protein with a GTPase-like domain,
ankyrin repeats and a Pleckstrin homology domain) or
GGAP. Three isoforms of PIKE have been identified.
PIKE-S (short) and PIKE-L (long) are brain-specific
isoforms, with PIKE-S restricted to the nucleus and
PIKE-L found in multiple cellular compartments. A third
isoform, PIKE-A was identified in human glioblastoma
brain cancers and has been found in various tissues.
GGAP has been shown to have high GTPase activity due to
a direct intramolecular interaction between the
N-terminal GTPase domain and the C-terminal ArfGAP
domain. In human tissue, AGAP mRNA was detected in
skeletal muscle, kidney, placenta, brain, heart, colon,
and lung. Reduced expression levels were also observed
in the spleen, liver, and small intestine.
Length = 158
Score = 42.1 bits (99), Expect = 3e-05
Identities = 40/175 (22%), Positives = 69/175 (39%), Gaps = 27/175 (15%)
Query: 11 VVGDGTVGKTCMLISYTTDSFPGEYVP---TVFDNYSAPFTVDGIPVSLGLWDTAGQEDY 67
+VG+ GK+ ++ Y T G YV + VDG L + D G D
Sbjct: 5 IVGNLRSGKSALVHRYLT----GSYVQLESPEGGRFKKEVLVDGQSHLLLIRDEGGAPD- 59
Query: 68 DRLRPLSYPQ-TDVFLICYSVVSPSSFDNVTSKWYPELKHHCP--DAPIILVGTKIDLRE 124
+ D + +S+ +SF V + Y +L + + P+ILVGT+
Sbjct: 60 -----AQFAGWVDAVIFVFSLEDEASFQTV-YRLYHQLSSYRNISEIPLILVGTQ----- 108
Query: 125 DRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAV 179
D +S N + + ++L ++ Y E A + +VF EA + +
Sbjct: 109 DA-----ISASNPRVIDDARARQLCADMKRCSYYETCATYGLNVERVFQEAAQKI 158
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 41.4 bits (98), Expect = 6e-05
Identities = 43/186 (23%), Positives = 67/186 (36%), Gaps = 41/186 (22%)
Query: 2 SSGRPIKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIP---VSLGL 58
+ ++ +++G GKT +L +PT+ F V+ + V +
Sbjct: 10 GWNKEMRILILGLDNAGKTTILYKLKLGEI-VTTIPTI------GFNVETVTYKNVKFTV 62
Query: 59 WDTAGQEDYDRLRPL---SYPQTDVFLICYSVVSPSSFDNVTSKWY-----PELKHHCPD 110
WD GQE LRPL +P TD + + + + EL D
Sbjct: 63 WDVGGQE---SLRPLWRNYFPNTDAVIFVVDSADRDRIEEAKEELHALLNEEELA----D 115
Query: 111 APIILVGTKIDLRED---RETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRG 167
AP++++ K DL E LL L K R + CSA+T G
Sbjct: 116 APLLILANKQDLPGAMSEAEIRELLGLHEL-------------KDRPWEIQGCSAVTGEG 162
Query: 168 LRQVFD 173
L + D
Sbjct: 163 LDEGLD 168
>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 = 38.5 bits (90), Expect = 7e-04
Identities = 42/174 (24%), Positives = 61/174 (35%), Gaps = 29/174 (16%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYV---PTVFDNYSAPFTVDGIPVSLGLWDTAGQ 64
K ++VG GKT +L + GE V PT+ N I +WD GQ
Sbjct: 17 KVIIVGLDNAGKTTILYQFLL----GEVVHTSPTIGSNVEE-IVYKNI--RFLMWDIGGQ 69
Query: 65 EDYDRLRP---LSYPQTDVFLICYSVVSPSSFDNVTSKWYPELKHH-CPDAPIILVGTKI 120
E LR Y TD ++ + Y L H A ++++ K
Sbjct: 70 E---SLRSSWNTYYTNTDAVILVIDSTDRERLPLTKEELYKMLAHEDLRKAVLLVLANKQ 126
Query: 121 DLREDRETLNLLSEQ-NLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFD 173
DL + T +SE L+ ++ C ALT GL + D
Sbjct: 127 DL-KGAMTPAEISESLGLTSIRDHTWH----------IQGCCALTGEGLPEGLD 169
>gnl|CDD|206645 cd00879, Sar1, Sar1 is an essential component of COPII vesicle
coats. Sar1 is an essential component of COPII vesicle
coats involved in export of cargo from the ER. The
GTPase activity of Sar1 functions as a molecular switch
to control protein-protein and protein-lipid
interactions that direct vesicle budding from the ER.
Activation of the GDP to the GTP-bound form of Sar1
involves the membrane-associated guanine nucleotide
exchange factor (GEF) Sec12. Sar1 is unlike all Ras
superfamily GTPases that use either myristoyl or prenyl
groups to direct membrane association and function, in
that Sar1 lacks such modification. Instead, Sar1
contains a unique nine-amino-acid N-terminal extension.
This extension contains an evolutionarily conserved
cluster of bulky hydrophobic amino acids, referred to as
the Sar1-N-terminal activation recruitment (STAR) motif.
The STAR motif mediates the recruitment of Sar1 to ER
membranes and facilitates its interaction with mammalian
Sec12 GEF leading to activation.
Length = 191
Score = 38.4 bits (90), Expect = 7e-04
Identities = 45/175 (25%), Positives = 69/175 (39%), Gaps = 21/175 (12%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQEDY 67
K V +G GKT +L D ++VPT+ S T+ + +D G E
Sbjct: 21 KIVFLGLDNAGKTTLLHMLKDDRL-AQHVPTLHPT-SEELTIGNV--KFTTFDLGGHEQA 76
Query: 68 DRLRPLSYPQTD--VFLICYSVVSPSSFDNVTSKWYPELK-----HHCPDAPIILVGTKI 120
R+ +P+ D VFL+ P F EL + PI+++G KI
Sbjct: 77 RRVWKDYFPEVDGIVFLV--DAADPERFQESKE----ELDSLLNDEELANVPILILGNKI 130
Query: 121 DLRE--DRETL-NLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVF 172
D E L L + K K++N IR V+ CS + ++G + F
Sbjct: 131 DKPGAVSEEELREALGLYGTTTGKGGVSLKVSN-IRPVEVFMCSVVKRQGYGEGF 184
>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 = 37.9 bits (88), Expect = 0.001
Identities = 53/211 (25%), Positives = 82/211 (38%), Gaps = 57/211 (27%)
Query: 6 PIKCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLG-------- 57
+ V++G + GKT +L + F VPT F + I VSLG
Sbjct: 3 SLHIVMLGLDSAGKTTVLYRLKFNEFV-NTVPTK------GFNTEKIKVSLGNAKGVTFH 55
Query: 58 LWDTAGQEDYDRLRPL--SYPQ-TD--VFLICYSVVSPSSFDNVTSKWYPELK---H--- 106
WD GQE +LRPL SY + TD VF++ D+V + E K H
Sbjct: 56 FWDVGGQE---KLRPLWKSYTRCTDGIVFVV----------DSVDVERMEEAKTELHKIT 102
Query: 107 HCPD---APIILVGTKIDLRED---RETLNLLSEQNLSPVKREQGQKLANKIRAVKYMEC 160
+ P++++ K DL E LL+ LS Q
Sbjct: 103 KFSENQGVPVLVLANKQDLPNALPVSEVEKLLALHELSSSTPWHVQP------------A 150
Query: 161 SALTQRGLRQVFDEAVRAVLRPEPVKRRQRK 191
A+ GL++ ++ +L+ + R+Q+K
Sbjct: 151 CAIIGEGLQEGLEKLYEMILKRRKMLRQQKK 181
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes. TrmE
contains a GTPase domain that forms a canonical Ras-like
fold. It functions a molecular switch GTPase, and
apparently uses a conformational change associated with
GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 35.5 bits (83), Expect = 0.005
Identities = 26/127 (20%), Positives = 47/127 (37%), Gaps = 29/127 (22%)
Query: 45 APFTVDGIPVSLGLWDTAG---QED----------YDRLRPLSYPQTDVFLICYSVVSPS 91
+ GIPV L DTAG ED + + + D+ L+
Sbjct: 44 EEIDLGGIPVRLI--DTAGLRETEDEIEKIGIERAREAIE-----EADLVLLVVDASEGL 96
Query: 92 SFDNVTSKWYPELKHHCPDAPIILVGTKIDLREDRETLNLLSEQNLSPV--KREQG-QKL 148
++ E+ P+I+V K DL D E ++ L+ + + + K +G +L
Sbjct: 97 DEED------LEILELPAKKPVIVVLNKSDLLSDAEGISELNGKPIIAISAKTGEGIDEL 150
Query: 149 ANKIRAV 155
+ +
Sbjct: 151 KEALLEL 157
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 35.0 bits (82), Expect = 0.013
Identities = 25/82 (30%), Positives = 34/82 (41%), Gaps = 20/82 (24%)
Query: 103 ELKHHCP---DAPIILVGTKIDLREDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYME 159
EL+ + P D P ILV KIDL ++ E +RE+ L
Sbjct: 261 ELEKYSPELADKPRILVLNKIDLLDEEE-------------EREKRAALELAALGGPVFL 307
Query: 160 CSALTQRGLRQVFDEAVRAVLR 181
SA+T GL DE +RA+
Sbjct: 308 ISAVTGEGL----DELLRALWE 325
>gnl|CDD|206644 cd00878, Arf_Arl, ADP-ribosylation factor(Arf)/Arf-like (Arl) small
GTPases. Arf (ADP-ribosylation factor)/Arl (Arf-like)
small GTPases. Arf proteins are activators of
phospholipase D isoforms. Unlike Ras proteins they lack
cysteine residues at their C-termini and therefore are
unlikely to be prenylated. Arfs are N-terminally
myristoylated. Members of the Arf family are regulators
of vesicle formation in intracellular traffic that
interact reversibly with membranes of the secretory and
endocytic compartments in a GTP-dependent manner. They
depart from other small GTP-binding proteins by a unique
structural device, interswitch toggle, that implements
front-back communication from N-terminus to the
nucleotide binding site. Arf-like (Arl) proteins are
close relatives of the Arf, but only Arl1 has been shown
to function in membrane traffic like the Arf proteins.
Arl2 has an unrelated function in the folding of native
tubulin, and Arl4 may function in the nucleus. Most
other Arf family proteins are so far relatively poorly
characterized. Thus, despite their significant sequence
homologies, Arf family proteins may regulate unrelated
functions.
Length = 158
Score = 33.7 bits (78), Expect = 0.029
Identities = 46/183 (25%), Positives = 73/183 (39%), Gaps = 47/183 (25%)
Query: 8 KCVVVG-DGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQED 66
+ +++G DG GKT +L +PT+ N TV+ V +WD GQ
Sbjct: 1 RILMLGLDG-AGKTTILYKLKLGEVV-TTIPTIGFNVE---TVEYKNVKFTVWDVGGQ-- 53
Query: 67 YDRLRPL---SYPQTD--VFLICYS-----VVSPSSFDNVTSKWYPELKHHCPDAPIILV 116
D++RPL Y TD +F++ S + + + ++ ELK AP++++
Sbjct: 54 -DKIRPLWKHYYENTDGLIFVVDSSDRERIEEAKNELHKLLNE--EELK----GAPLLIL 106
Query: 117 GTKIDL------REDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQ 170
K DL E E L L S + + CSA+T GL +
Sbjct: 107 ANKQDLPGALTESELIELLGLESIKG-------------RRWHIQP---CSAVTGDGLDE 150
Query: 171 VFD 173
D
Sbjct: 151 GLD 153
>gnl|CDD|206685 cd01898, Obg, Obg GTPase. The Obg nucleotide binding protein
subfamily has been implicated in stress response,
chromosome partitioning, replication initiation,
mycelium development, and sporulation. Obg proteins are
among a large group of GTP binding proteins conserved
from bacteria to humans. The E. coli homolog, ObgE is
believed to function in ribosomal biogenesis. Members of
the subfamily contain two equally and highly conserved
domains, a C-terminal GTP binding domain and an
N-terminal glycine-rich domain.
Length = 170
Score = 33.2 bits (77), Expect = 0.039
Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 16/72 (22%)
Query: 103 ELKHHCP---DAPIILVGTKIDLREDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYME 159
EL+ + P + P I+V KIDL + E L ++L +++ K
Sbjct: 104 ELEAYNPGLAEKPRIVVLNKIDLLDAEERFEKL-------------KELLKELKGKKVFP 150
Query: 160 CSALTQRGLRQV 171
SALT GL ++
Sbjct: 151 ISALTGEGLDEL 162
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 33.7 bits (78), Expect = 0.040
Identities = 26/82 (31%), Positives = 36/82 (43%), Gaps = 19/82 (23%)
Query: 103 ELKHHCP---DAPIILVGTKIDLREDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYME 159
EL+ + P + P I+V KIDL D E L L + LA + +
Sbjct: 265 ELEKYSPKLAEKPRIVVLNKIDLPLDEEELEELKK------------ALAEALGWEVFYL 312
Query: 160 CSALTQRGLRQVFDEAVRAVLR 181
SALT+ GL DE +RA+
Sbjct: 313 ISALTREGL----DELLRALAE 330
>gnl|CDD|206679 cd01892, Miro2, Mitochondrial Rho family 2 (Miro2), C-terminal.
Miro2 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the putative
GTPase domain in the C terminus of Miro proteins. These
atypical Rho GTPases have roles in mitochondrial
homeostasis and apoptosis. Most Rho proteins contain a
lipid modification site at the C-terminus; however, Miro
is one of few Rho subfamilies that lack this feature.
Length = 180
Score = 33.0 bits (76), Expect = 0.052
Identities = 34/123 (27%), Positives = 48/123 (39%), Gaps = 10/123 (8%)
Query: 7 IKCVVVGDGTVGKTCMLISYTTDSF-PGEYVPTVFDNYSAPFTVD--GIPVSLGLWDTAG 63
C V+G GK+ +L ++ SF Y PT+ Y+ TV+ G L L +
Sbjct: 5 FLCFVLGAKGSGKSALLQAFLGRSFSQNAYSPTIKPRYAVN-TVEVPGQEKYLILREVGE 63
Query: 64 QEDYDRLRPLSYPQTDVFLICYSVVSPSSFDNVTS--KWYPELKHHCPDAPIILVGTKID 121
E+ L DV + Y P+SF K Y L + P + V K D
Sbjct: 64 DEEAILLNDAELAACDVACLVYDSSDPNSFSYCAEVYKKYFMLG----EIPCLFVAAKAD 119
Query: 122 LRE 124
L E
Sbjct: 120 LDE 122
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase. The
Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that generally show sequence
conservation in the region between the Walker A and B
motifs (G1 and G3 box motifs), to the exclusion of other
GTPases. TrmE is ubiquitous in bacteria and is a
widespread mitochondrial protein in eukaryotes, but is
absent from archaea. The yeast member of TrmE family,
MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family.
Length = 161
Score = 32.2 bits (74), Expect = 0.079
Identities = 18/66 (27%), Positives = 27/66 (40%), Gaps = 12/66 (18%)
Query: 112 PIILVGTKIDLREDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQV 171
P++LV KIDL + E LL E R+ + AV SAL G+ ++
Sbjct: 106 PVLLVLNKIDLVPESEEEELLRE-------RKLELLPDLPVIAV-----SALPGEGIDEL 153
Query: 172 FDEAVR 177
+
Sbjct: 154 RKKIAE 159
>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 = 31.9 bits (73), Expect = 0.10
Identities = 35/141 (24%), Positives = 58/141 (41%), Gaps = 26/141 (18%)
Query: 11 VVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAGQEDYDRL 70
+VG GKT ++ + F + +PTV N V V++ +WD GQ R
Sbjct: 4 LVGLQNSGKTTLVNVIASGQFSEDTIPTVGFNMR---KVTKGNVTIKVWDLGGQP---RF 57
Query: 71 RPL--SYPQTDVFLICYSVVS--PSSFDNVTSKWY-----PELKHHCPDAPIILVGTKID 121
R + Y + V I Y V + + ++ + P L+ P++++G K D
Sbjct: 58 RSMWERYCRG-VNAIVYVVDAADREKLEVAKNELHDLLEKPSLEG----IPLLVLGNKND 112
Query: 122 L----REDR--ETLNLLSEQN 136
L D E +NL S +
Sbjct: 113 LPGALSVDELIEQMNLKSITD 133
>gnl|CDD|234274 TIGR03594, GTPase_EngA, ribosome-associated GTPase EngA. EngA
(YfgK, Der) is a ribosome-associated essential GTPase
with a duplication of its GTP-binding domain. It is
broadly to universally distributed among bacteria. It
appears to function in ribosome biogenesis or stability
[Protein synthesis, Other].
Length = 429
Score = 32.0 bits (74), Expect = 0.16
Identities = 16/67 (23%), Positives = 29/67 (43%), Gaps = 9/67 (13%)
Query: 112 PIILVGTKIDLREDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQV 171
+++V K DL +D +T K+E +KL + + SALT +G+ ++
Sbjct: 285 ALVIVVNKWDLVKDEKTREE--------FKKELRRKLP-FLDFAPIVFISALTGQGVDKL 335
Query: 172 FDEAVRA 178
D
Sbjct: 336 LDAIDEV 342
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 31.2 bits (72), Expect = 0.31
Identities = 23/76 (30%), Positives = 32/76 (42%), Gaps = 20/76 (26%)
Query: 103 ELKHHCP---DAPIILVGTKIDLREDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYME 159
ELK + P + P I+V K+DL E E L E KL K+ +
Sbjct: 264 ELKLYNPRLLERPQIVVANKMDLPEAEENLEEFKE------------KLGPKVFPI---- 307
Query: 160 CSALTQRGLRQVFDEA 175
SALT +GL ++
Sbjct: 308 -SALTGQGLDELLYAV 322
>gnl|CDD|232980 TIGR00450, mnmE_trmE_thdF, tRNA modification GTPase TrmE. TrmE,
also called MnmE and previously designated ThdF
(thiophene and furan oxidation protein), is a GTPase
involved in tRNA modification to create
5-methylaminomethyl-2-thiouridine in the wobble position
of some tRNAs. This protein and GidA form an
alpha2/beta2 heterotetramer [Protein synthesis, tRNA and
rRNA base modification].
Length = 442
Score = 30.5 bits (69), Expect = 0.47
Identities = 32/131 (24%), Positives = 50/131 (38%), Gaps = 25/131 (19%)
Query: 6 PIKCVVVGDGTVGKTCML--ISYTTDSFPGEYVPTVFDNYSAPFTVDGIPVSLGLWDTAG 63
K +VG VGK+ +L + + + T D F ++GI + L DTAG
Sbjct: 203 GFKLAIVGSPNVGKSSLLNALLKQDRAIVSDIKGTTRDVVEGDFELNGILIKL--LDTAG 260
Query: 64 -QEDYDRLRPL-------SYPQTDVFLICYSVVSPSSFDNVTSKWYPELK----HHCPDA 111
+E D + L + Q D L+ Y + + + + +
Sbjct: 261 IREHADFVERLGIEKSFKAIKQAD--LVIYVL-------DASQPLTKDDFLIIDLNKSKK 311
Query: 112 PIILVGTKIDL 122
P ILV KIDL
Sbjct: 312 PFILVLNKIDL 322
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 29.9 bits (67), Expect = 0.56
Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 13/76 (17%)
Query: 1 MSSGRPIKCVVVGDGTVGKTCMLISYTTDSFPGEYV---PTVFDNYSAPFTVDGIPVSLG 57
+ + + ++ ++VG GKT +L GE V PT+ N TV+ +S
Sbjct: 12 LFAKKEMRILMVGLDAAGKTTILYKLKL----GEIVTTIPTIGFNVE---TVEYKNISFT 64
Query: 58 LWDTAGQEDYDRLRPL 73
+WD GQ D++RPL
Sbjct: 65 VWDVGGQ---DKIRPL 77
>gnl|CDD|206726 cd04163, Era, E. coli Ras-like protein (Era) is a multifunctional
GTPase. Era (E. coli Ras-like protein) is a
multifunctional GTPase found in all bacteria except some
eubacteria. It binds to the 16S ribosomal RNA (rRNA) of
the 30S subunit and appears to play a role in the
assembly of the 30S subunit, possibly by chaperoning the
16S rRNA. It also contacts several assembly elements of
the 30S subunit. Era couples cell growth with
cytokinesis and plays a role in cell division and energy
metabolism. Homologs have also been found in eukaryotes.
Era contains two domains: the N-terminal GTPase domain
and a C-terminal domain KH domain that is critical for
RNA binding. Both domains are important for Era
function. Era is functionally able to compensate for
deletion of RbfA, a cold-shock adaptation protein that
is required for efficient processing of the 16S rRNA.
Length = 168
Score = 29.7 bits (68), Expect = 0.62
Identities = 18/63 (28%), Positives = 26/63 (41%), Gaps = 12/63 (19%)
Query: 112 PIILVGTKIDLREDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQV 171
P+ILV KIDL +D+E L L E KL + SAL + ++
Sbjct: 113 PVILVLNKIDLVKDKEDLLPLLE------------KLKELHPFAEIFPISALKGENVDEL 160
Query: 172 FDE 174
+
Sbjct: 161 LEY 163
>gnl|CDD|206684 cd01897, NOG, Nucleolar GTP-binding protein (NOG). NOG1 is a
nucleolar GTP-binding protein present in eukaryotes
ranging from trypanosomes to humans. NOG1 is
functionally linked to ribosome biogenesis and found in
association with the nuclear pore complexes and
identified in many preribosomal complexes. Thus, defects
in NOG1 can lead to defects in 60S biogenesis. The S.
cerevisiae NOG1 gene is essential for cell viability,
and mutations in the predicted G motifs abrogate
function. It is a member of the ODN family of
GTP-binding proteins that also includes the bacterial
Obg and DRG proteins.
Length = 167
Score = 29.8 bits (68), Expect = 0.62
Identities = 15/66 (22%), Positives = 33/66 (50%), Gaps = 15/66 (22%)
Query: 110 DAPIILVGTKIDLREDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLR 169
+ P+I+V KIDL + + LS +++E + + ++ S LT+ G+
Sbjct: 112 NKPVIVVLNKIDLLTEED---------LSEIEKE------LEKEGEEVIKISTLTEEGVD 156
Query: 170 QVFDEA 175
++ ++A
Sbjct: 157 ELKNKA 162
>gnl|CDD|233986 TIGR02729, Obg_CgtA, Obg family GTPase CgtA. This model describes
a univeral, mostly one-gene-per-genome GTP-binding
protein that associates with ribosomal subunits and
appears to play a role in ribosomal RNA maturation. This
GTPase, related to the nucleolar protein Obg, is
designated CgtA in bacteria. Mutations in this gene are
pleiotropic, but it appears that effects on cellular
functions such as chromosome partition may be secondary
to the effect on ribosome structure. Recent work done in
Vibrio cholerae shows an essential role in the stringent
response, in which RelA-dependent ability to synthesize
the alarmone ppGpp is required for deletion of this
GTPase to be lethal [Protein synthesis, Other].
Length = 329
Score = 30.1 bits (69), Expect = 0.70
Identities = 22/85 (25%), Positives = 34/85 (40%), Gaps = 27/85 (31%)
Query: 103 ELKHHCP---DAPIILVGTKIDLREDRETLNLLSEQNLSPVKREQGQKLANKIRA---VK 156
ELK + P + P I+V KIDL ++ E ++L +++
Sbjct: 263 ELKKYSPELAEKPRIVVLNKIDLLDEEEL-----------------EELLKELKEALGKP 305
Query: 157 YMECSALTQRGLRQVFDEAVRAVLR 181
SALT GL DE + A+
Sbjct: 306 VFPISALTGEGL----DELLYALAE 326
>gnl|CDD|220849 pfam10691, DUF2497, Protein of unknown function (DUF2497). Members
of this family belong to the Alphaproteobacteria. The
function of the family is not known.
Length = 72
Score = 28.0 bits (63), Expect = 0.83
Identities = 16/54 (29%), Positives = 22/54 (40%), Gaps = 11/54 (20%)
Query: 130 NLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFDEAVRAVLRPE 183
L+SE+ V G KLA IR R + ++ VR +LRP
Sbjct: 3 ALISEETAEAVAAAFG-KLARAIR----------ISRSGGRTLEDLVREMLRPM 45
>gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol
utilisation. Members of this family function in
ethanolamine and propanediol degradation pathways,
however the exact roles of these proteins is poorly
understood.
Length = 143
Score = 29.1 bits (66), Expect = 0.83
Identities = 26/100 (26%), Positives = 39/100 (39%), Gaps = 30/100 (30%)
Query: 79 DVFLICYSVVSPSS-----FDNVTSKWYPELKHHCPDAPIILVGTKIDLREDRETLNLLS 133
DV + P S F ++ +K P+I + TKIDL +D
Sbjct: 65 DVIALVQDATEPWSVFPPGFASMFNK------------PVIGIITKIDLAKD-------- 104
Query: 134 EQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQVFD 173
E N+ V+ A KI E SA+T G+ ++F
Sbjct: 105 EANIEMVEEWLNNAGAEKI-----FEVSAVTNEGIDELFA 139
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 29.6 bits (68), Expect = 0.91
Identities = 16/66 (24%), Positives = 28/66 (42%), Gaps = 12/66 (18%)
Query: 109 PDAPIILVGTKIDLREDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGL 168
P+ILV KIDL +D+E L ++L+ + + + SAL +
Sbjct: 112 VKTPVILVLNKIDLVKDKEELL------------PLLEELSELMDFAEIVPISALKGDNV 159
Query: 169 RQVFDE 174
++ D
Sbjct: 160 DELLDV 165
>gnl|CDD|206747 cd01854, YjeQ_EngC, Ribosomal interacting GTPase YjeQ/EngC, a
circularly permuted subfamily of the Ras GTPases. YjeQ
(YloQ in Bacillus subtilis) is a ribosomal small
subunit-dependent GTPase; hence also known as RsgA. YjeQ
is a late-stage ribosomal biogenesis factor involved in
the 30S subunit maturation, and it represents a protein
family whose members are broadly conserved in bacteria
and have been shown to be essential to the growth of E.
coli and B. subtilis. Proteins of the YjeQ family
contain all sequence motifs typical of the vast class of
P-loop-containing GTPases, but show a circular
permutation, with a G4-G1-G3 pattern of motifs as
opposed to the regular G1-G3-G4 pattern seen in most
GTPases. All YjeQ family proteins display a unique
domain architecture, which includes an N-terminal
OB-fold RNA-binding domain, the central permuted GTPase
domain, and a zinc knuckle-like C-terminal cysteine
domain.
Length = 211
Score = 28.9 bits (66), Expect = 1.4
Identities = 15/75 (20%), Positives = 26/75 (34%), Gaps = 24/75 (32%)
Query: 110 DAPIILVGTKIDLREDRETLNLLSEQNLSPVKREQGQKLANKIRAVKY--MECSALTQRG 167
++V K DL +D E ++L + Y + SA T G
Sbjct: 33 GIEPVIVLNKADLVDDEEL-----------------EELLEIYEKLGYPVLAVSAKTGEG 75
Query: 168 LRQVFDEAVRAVLRP 182
L + +R +L+
Sbjct: 76 L-----DELRELLKG 85
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 28.7 bits (65), Expect = 2.0
Identities = 15/73 (20%), Positives = 29/73 (39%), Gaps = 17/73 (23%)
Query: 103 ELKHHCP---DAPIILVGTKIDLREDRETLNLLSEQNLSPVKREQGQKLANKI-RAVKYM 158
EL+ + P + P LV KIDL ++ E E+ + + +
Sbjct: 265 ELEKYSPKLAEKPRWLVFNKIDLLDEEEA-------------EERAKAIVEALGWEGPVY 311
Query: 159 ECSALTQRGLRQV 171
SA + G++++
Sbjct: 312 LISAASGLGVKEL 324
>gnl|CDD|215653 pfam00009, GTP_EFTU, Elongation factor Tu GTP binding domain. This
domain contains a P-loop motif, also found in several
other families such as pfam00071, pfam00025 and
pfam00063. Elongation factor Tu consists of three
structural domains, this plus two C-terminal beta barrel
domains.
Length = 184
Score = 28.2 bits (64), Expect = 2.0
Identities = 19/66 (28%), Positives = 29/66 (43%), Gaps = 5/66 (7%)
Query: 112 PIILVGTKIDLREDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQV 171
PII+ KID R D L + E+ + RE +K V + SALT G+ ++
Sbjct: 120 PIIVFINKID-RVDDAELEEVVEE----ISRELLEKYGFGGETVPVVPGSALTGEGIDEL 174
Query: 172 FDEAVR 177
+
Sbjct: 175 LEALDL 180
>gnl|CDD|213834 TIGR03597, GTPase_YqeH, ribosome biogenesis GTPase YqeH. This
family describes YqeH, a member of a larger family of
GTPases involved in ribosome biogenesis. Like YqlF, it
shows a cyclical permutation relative to GTPases EngA
(in which the GTPase domain is duplicated), Era, and
others. Members of this protein family are found in a
relatively small number of bacterial species, including
Bacillus subtilis but not Escherichia coli [Protein
synthesis, Other].
Length = 360
Score = 28.0 bits (63), Expect = 3.1
Identities = 14/35 (40%), Positives = 18/35 (51%)
Query: 100 WYPELKHHCPDAPIILVGTKIDLREDRETLNLLSE 134
PELK P++LVG KIDL L+ + E
Sbjct: 80 LIPELKRFVGGNPVLLVGNKIDLLPKSVNLSKIKE 114
>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 = 27.9 bits (63), Expect = 3.4
Identities = 20/75 (26%), Positives = 30/75 (40%), Gaps = 29/75 (38%)
Query: 8 KCVVVGDGTVGKTCMLISYTTDSFPGEYVPTVFDNYSA---PF---TVD---------GI 52
K +++G GK+ M S +F NYS T+D G
Sbjct: 1 KVLLMGLRGSGKSSM-RS------------IIFSNYSPRDTLRLGATIDVEQSHVRFLGN 47
Query: 53 PVSLGLWDTAGQEDY 67
++L LWD GQ+D+
Sbjct: 48 -LTLNLWDCPGQDDF 61
>gnl|CDD|215790 pfam00209, SNF, Sodium:neurotransmitter symporter family.
Length = 506
Score = 28.0 bits (63), Expect = 3.4
Identities = 13/35 (37%), Positives = 17/35 (48%), Gaps = 4/35 (11%)
Query: 17 VGKTCMLIS--YTTDSFPGEYVPTVFDNYSAPFTV 49
V LI T+ G YV T+FD Y+A F +
Sbjct: 375 VCVISFLIGLILVTEG--GIYVFTLFDYYAASFGL 407
>gnl|CDD|206748 cd01855, YqeH, Circularly permuted YqeH GTPase. YqeH is an
essential GTP-binding protein. Depletion of YqeH induces
an excess initiation of DNA replication, suggesting that
it negatively controls initiation of chromosome
replication. The YqeH subfamily is common in eukaryotes
and sporadically present in bacteria with probable
acquisition by plants from chloroplasts. Proteins of the
YqeH family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases.
Length = 191
Score = 27.2 bits (61), Expect = 4.1
Identities = 11/23 (47%), Positives = 12/23 (52%)
Query: 100 WYPELKHHCPDAPIILVGTKIDL 122
P L P+ILVG KIDL
Sbjct: 50 LIPGLAELIGAKPVILVGNKIDL 72
>gnl|CDD|215063 PLN00120, PLN00120, fucoxanthin-chlorophyll a-c binding protein;
Provisional.
Length = 202
Score = 27.4 bits (61), Expect = 4.3
Identities = 10/16 (62%), Positives = 11/16 (68%)
Query: 56 LGLWDTAGQEDYDRLR 71
LGL D QE +DRLR
Sbjct: 50 LGLVDDGDQEKFDRLR 65
>gnl|CDD|225623 COG3081, COG3081, Nucleoid-associated protein [General function
prediction only].
Length = 335
Score = 27.4 bits (61), Expect = 4.6
Identities = 11/41 (26%), Positives = 18/41 (43%)
Query: 116 VGTKIDLREDRETLNLLSEQNLSPVKREQGQKLANKIRAVK 156
G +I+L+E + L L+E E+G L A +
Sbjct: 236 AGEEIELQELSKELPGLNEVAFYDFTAEKGYGLEESFPADR 276
>gnl|CDD|240352 PTZ00302, PTZ00302, N-acetylglucosamine-phosphate mutase;
Provisional.
Length = 585
Score = 27.7 bits (62), Expect = 5.1
Identities = 14/48 (29%), Positives = 18/48 (37%), Gaps = 10/48 (20%)
Query: 150 NKIRAVKYMECSALTQRGLRQVFDEAV-------RAVLRP---EPVKR 187
+ E L +GL+ D V RA +RP EPV R
Sbjct: 509 RTLITNTEDETRLLEPKGLQDKIDAIVSKYDNAARAFIRPSGTEPVVR 556
>gnl|CDD|237535 PRK13868, PRK13868, type IV secretion system single-stranded DNA
binding protein VirE2; Provisional.
Length = 556
Score = 27.6 bits (61), Expect = 5.2
Identities = 22/83 (26%), Positives = 38/83 (45%), Gaps = 9/83 (10%)
Query: 114 ILVGTKIDLREDR----ETLNLLSEQNLSPVKR-EQGQKLANKIRAVKY----MECSALT 164
++V +LR+ R E L LS++++ R E+GQ+ +Y M+
Sbjct: 453 VIVANGPNLRDIRDLSPEKLQQLSQKDVLIADRNEKGQRTGTYTSVAEYERLMMKLPDDA 512
Query: 165 QRGLRQVFDEAVRAVLRPEPVKR 187
+ L + D+ R +RPEP R
Sbjct: 513 AQLLAEPTDKYSRDFVRPEPALR 535
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 27.3 bits (62), Expect = 5.2
Identities = 12/67 (17%), Positives = 30/67 (44%), Gaps = 10/67 (14%)
Query: 112 PIILVGTKIDLREDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGLRQV 171
+++V K DL ++ +T+ ++ ++R + + SALT +G+ ++
Sbjct: 286 ALVIVVNKWDLVDE-KTMEEFKKE----LRRRLPF-----LDYAPIVFISALTGQGVDKL 335
Query: 172 FDEAVRA 178
+ A
Sbjct: 336 LEAIDEA 342
>gnl|CDD|227434 COG5103, CDC39, Cell division control protein, negative regulator of
transcription [Cell division and chromosome partitioning
/ Transcription].
Length = 2005
Score = 27.7 bits (61), Expect = 5.8
Identities = 8/27 (29%), Positives = 10/27 (37%)
Query: 80 VFLICYSVVSPSSFDNVTSKWYPELKH 106
V + + PS F T W L H
Sbjct: 1645 VVYSIFEALQPSRFPGFTFAWLELLSH 1671
>gnl|CDD|171679 PRK12717, flgL, flagellar hook-associated protein FlgL;
Provisional.
Length = 523
Score = 27.0 bits (60), Expect = 6.5
Identities = 10/34 (29%), Positives = 15/34 (44%), Gaps = 6/34 (17%)
Query: 30 SFPGEYV------PTVFDNYSAPFTVDGIPVSLG 57
+FP T ++ Y+ P T D P+S G
Sbjct: 336 TFPSSGAVLKFTSATAYELYAQPVTADSKPISSG 369
>gnl|CDD|129567 TIGR00475, selB, selenocysteine-specific elongation factor SelB.
In prokaryotes, the incorporation of selenocysteine as
the 21st amino acid, encoded by TGA, requires several
elements: SelC is the tRNA itself, SelD acts as a donor
of reduced selenium, SelA modifies a serine residue on
SelC into selenocysteine, and SelB is a
selenocysteine-specific translation elongation factor.
3-prime or 5-prime non-coding elements of mRNA have been
found as probable structures for directing
selenocysteine incorporation. This model describes the
elongation factor SelB, a close homolog rf EF-Tu. It may
function by replacing EF-Tu. A C-terminal domain not
found in EF-Tu is in all SelB sequences in the seed
alignment except that from Methanococcus jannaschii.
This model does not find an equivalent protein for
eukaryotes [Protein synthesis, Translation factors].
Length = 581
Score = 27.1 bits (60), Expect = 6.7
Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 2/60 (3%)
Query: 110 DAPIILV-GTKIDLREDRETLNLLSEQNLSPVKREQGQKLANKIRA-VKYMECSALTQRG 167
DAP+IL G K+ LR+ + PV+ ++ +A I+A L +RG
Sbjct: 309 DAPLILAKGDKLVLRDSSGNFLAGARVLEPPVRVKRKAFIAELIKAGDSCYCIFLLLERG 368
>gnl|CDD|235751 PRK06241, PRK06241, phosphoenolpyruvate synthase; Validated.
Length = 871
Score = 27.2 bits (61), Expect = 7.0
Identities = 15/41 (36%), Positives = 20/41 (48%), Gaps = 7/41 (17%)
Query: 118 TKIDLREDRETL--NLLS-----EQNLSPVKREQGQKLANK 151
TK RED TL +L+ E S K EQG++ A +
Sbjct: 593 TKPRWREDPSTLVPMILNNIKNFEPGASKRKFEQGRQEALE 633
>gnl|CDD|213781 TIGR03170, flgA_cterm, flagella basal body P-ring formation protein
FlgA. This model describes a conserved C-terminal
region of the flagellar basal body P-ring formation
protein FlgA. This sequence region contains a SAF
domain, now described by pfam08666 [Cellular processes,
Chemotaxis and motility].
Length = 122
Score = 26.0 bits (58), Expect = 7.4
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 1 MSSGRPIKCVVVGDGTV 17
+SSG+ I +V GTV
Sbjct: 104 LSSGKIISGIVTAPGTV 120
>gnl|CDD|237045 PRK12296, obgE, GTPase CgtA; Reviewed.
Length = 500
Score = 26.8 bits (60), Expect = 8.4
Identities = 23/93 (24%), Positives = 35/93 (37%), Gaps = 30/93 (32%)
Query: 109 PDAPIILVGTKIDLREDRETLNLLSEQNLSPVKREQGQKLANKIRAVKYMECSALTQRGL 168
+ P ++V KID+ + RE V+ E R E SA ++ GL
Sbjct: 283 AERPRLVVLNKIDVPDARELAEF--------VRPELEA------RGWPVFEVSAASREGL 328
Query: 169 RQ--------VFD--------EAVRAVLRPEPV 185
R+ V + E R V+RP+ V
Sbjct: 329 RELSFALAELVEEARAAEPEAEPTRIVIRPKAV 361
>gnl|CDD|222318 pfam13685, Fe-ADH_2, Iron-containing alcohol dehydrogenase.
Length = 247
Score = 26.4 bits (59), Expect = 8.7
Identities = 16/55 (29%), Positives = 21/55 (38%), Gaps = 10/55 (18%)
Query: 10 VVVGDGTVGKTCMLISYTTDSFPGEY--VPTV-----FDNYSAPFTVDGIPVSLG 57
V VG GT+ ++ Y VPT + + A TVDG SL
Sbjct: 78 VAVGGGTINDIAKYAAFKLGK---PYISVPTAASMDGYASPGASLTVDGKKTSLP 129
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 26.3 bits (59), Expect = 9.8
Identities = 17/93 (18%), Positives = 35/93 (37%), Gaps = 23/93 (24%)
Query: 102 PELKHHCPDAPIILVGTKIDLREDRET---LNLLSEQNLSPVKREQGQKLANKIRAVKYM 158
P + + P +L+ K DL + T + EQ +K +
Sbjct: 43 PMIDKIIGNKPRLLILNKSDLADPEVTKKWIEYFEEQG------------------IKAL 84
Query: 159 ECSALTQRGLRQVFDEAVRAVLRPEPVKRRQRK 191
+A +G++++ A + + E +RR+ K
Sbjct: 85 AINAKKGQGVKKILKAAKKLL--KEKNERRKAK 115
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
0.320 0.137 0.417
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: 10,024,849
Number of extensions: 919584
Number of successful extensions: 1275
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1095
Number of HSP's successfully gapped: 142
Length of query: 195
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 103
Effective length of database: 6,857,034
Effective search space: 706274502
Effective search space used: 706274502
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (25.7 bits)