RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8274
(228 letters)
>gnl|CDD|206663 cd01871, Rac1_like, Ras-related C3 botulinum toxin substrate 1 (rho
family, small GTP binding protein Rac1)-like consists of
Rac1, Rac2 and Rac3. The Rac1-like subfamily consists
of Rac1, Rac2, and Rac3 proteins, plus the splice
variant Rac1b that contains a 19-residue insertion near
switch II relative to Rac1. While Rac1 is ubiquitously
expressed, Rac2 and Rac3 are largely restricted to
hematopoietic and neural tissues respectively. Rac1
stimulates the formation of actin lamellipodia and
membrane ruffles. It also plays a role in cell-matrix
adhesion and cell anoikis. In intestinal epithelial
cells, Rac1 is an important regulator of migration and
mediates apoptosis. Rac1 is also essential for
RhoA-regulated actin stress fiber and focal adhesion
complex formation. In leukocytes, Rac1 and Rac2 have
distinct roles in regulating cell morphology, migration,
and invasion, but are not essential for macrophage
migration or chemotaxis. Rac3 has biochemical properties
that are closely related to Rac1, such as effector
interaction, nucleotide binding, and hydrolysis; Rac2
has a slower nucleotide association and is more
efficiently activated by the RacGEF Tiam1. Both Rac1 and
Rac3 have been implicated in the regulation of cell
migration and invasion in human metastatic breast
cancer. Most Rho proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Rho proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 174
Score = 342 bits (880), Expect = e-122
Identities = 156/212 (73%), Positives = 162/212 (76%), Gaps = 48/212 (22%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKP+NLGLWDTAGQEDYDRLRPLSY
Sbjct: 11 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSY 70
Query: 61 PQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSL 120
PQT DVF ICFSL
Sbjct: 71 PQT------------------------------------------------DVFLICFSL 82
Query: 121 VNPASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLS 180
V+PASFENVRAKWYPEVRHHCP+TPIILVGTKLDLRDDK+TIEKLKEKKL PITYPQGL+
Sbjct: 83 VSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLA 142
Query: 181 MAKEIGAVKYLECSALTQKGLKTVFDEAIRAV 212
MAKEIGAVKYLECSALTQ+GLKTVFDEAIRAV
Sbjct: 143 MAKEIGAVKYLECSALTQRGLKTVFDEAIRAV 174
>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 = 321 bits (825), Expect = e-113
Identities = 125/215 (58%), Positives = 146/215 (67%), Gaps = 48/215 (22%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
AVGKTCLLI YTTNAFP +Y+PTVF+NYSA+V VDGKP+ LGLWDTAGQEDYDRLRPLSY
Sbjct: 8 AVGKTCLLIVYTTNAFPEDYVPTVFENYSADVEVDGKPVELGLWDTAGQEDYDRLRPLSY 67
Query: 61 PQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSL 120
P T DVF ICFS+
Sbjct: 68 PDT------------------------------------------------DVFLICFSV 79
Query: 121 VNPASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLS 180
+PASFENV+ KWYPEV+H CP+ PIILVGTKLDLR+DK T+E+L +KK P+TY QG +
Sbjct: 80 DSPASFENVKEKWYPEVKHFCPNVPIILVGTKLDLRNDKSTLEELSKKKQEPVTYEQGQA 139
Query: 181 MAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCP 215
+AK IGAVKYLECSALTQ+G++ VF+EAIRA L
Sbjct: 140 LAKRIGAVKYLECSALTQEGVREVFEEAIRAALNK 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 = 298 bits (766), Expect = e-104
Identities = 126/211 (59%), Positives = 145/211 (68%), Gaps = 49/211 (23%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
AVGKTCLLISYTTN FP EY+PTVFDNYSANV VDGK +NLGLWDTAGQE+YDRLRPLSY
Sbjct: 10 AVGKTCLLISYTTNKFPTEYVPTVFDNYSANVTVDGKQVNLGLWDTAGQEEYDRLRPLSY 69
Query: 61 PQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSL 120
PQT DVF +CFS+
Sbjct: 70 PQT------------------------------------------------DVFLLCFSV 81
Query: 121 VNPASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLS 180
+P+SFENV+ KWYPE++H+CP+ PIILVGTK+DLRDD T++KL EKK PIT +G
Sbjct: 82 DSPSSFENVKTKWYPEIKHYCPNVPIILVGTKIDLRDDGNTLKKL-EKKQKPITPEEGEK 140
Query: 181 MAKEIGAVKYLECSALTQKGLKTVFDEAIRA 211
+AKEIGAVKY+ECSALTQ+GLK VFDEAIRA
Sbjct: 141 LAKEIGAVKYMECSALTQEGLKEVFDEAIRA 171
>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 = 262 bits (670), Expect = 1e-89
Identities = 125/228 (54%), Positives = 148/228 (64%), Gaps = 49/228 (21%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
AVGKTCLLI YTTNAFP EYIPTVFDNYSA VDG+ ++L LWDTAGQE+YDRLR LSY
Sbjct: 13 AVGKTCLLICYTTNAFPKEYIPTVFDNYSAQTAVDGRTVSLNLWDTAGQEEYDRLRTLSY 72
Query: 61 PQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSL 120
PQT +VF ICFS+
Sbjct: 73 PQT------------------------------------------------NVFIICFSI 84
Query: 121 VNPASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLS 180
+P+S+ENVR KW+PEV HHCP+ PI+LVGTK DLR+D +T++KLKE+ APIT QG +
Sbjct: 85 ASPSSYENVRHKWHPEVCHHCPNVPILLVGTKKDLRNDADTLKKLKEQGQAPITPQQGGA 144
Query: 181 MAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCVLL 228
+AK+I AVKYLECSAL Q G+K VF EA+RAVL P P + K CVLL
Sbjct: 145 LAKQIHAVKYLECSALNQDGVKEVFAEAVRAVLNPTP-IKDTKSCVLL 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 = 256 bits (655), Expect = 1e-87
Identities = 117/213 (54%), Positives = 137/213 (64%), Gaps = 48/213 (22%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
AVGKTCLLISYTTN FP EY+PTVFDNY+ VM+ G+P LGL+DTAGQEDYDRLRPLSY
Sbjct: 11 AVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTLGLFDTAGQEDYDRLRPLSY 70
Query: 61 PQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSL 120
PQT DVF +CFS+
Sbjct: 71 PQT------------------------------------------------DVFLVCFSV 82
Query: 121 VNPASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLS 180
V+P+SFENV+ KW PE+ HHCP TP +LVGT++DLRDD TIEKL + K PIT G
Sbjct: 83 VSPSSFENVKEKWVPEITHHCPKTPFLLVGTQIDLRDDPSTIEKLAKNKQKPITPETGEK 142
Query: 181 MAKEIGAVKYLECSALTQKGLKTVFDEAIRAVL 213
+A+++ AVKY+ECSALTQKGLK VFDEAI A L
Sbjct: 143 LARDLKAVKYVECSALTQKGLKNVFDEAILAAL 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 = 232 bits (594), Expect = 5e-78
Identities = 101/233 (43%), Positives = 121/233 (51%), Gaps = 54/233 (23%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMV-DGKPINLGLWDTAGQEDYDRLRPLS 59
GKTCLL+ Y +FP EY+PTVF+NY + V +GK I L LWDTAGQEDYDRLRPLS
Sbjct: 13 GCGKTCLLMVYAQGSFPEEYVPTVFENYVTTLQVPNGKIIELALWDTAGQEDYDRLRPLS 72
Query: 60 YPQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFS 119
YP DV IC+S
Sbjct: 73 YPDV------------------------------------------------DVILICYS 84
Query: 120 LVNPASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGL 179
+ NP S +NV KWYPEV H CP TPI+LVG K DLR DK ++ KL+ + L P+T QG
Sbjct: 85 VDNPTSLDNVEDKWYPEVNHFCPGTPIVLVGLKTDLRKDKNSVSKLRAQGLEPVTPEQGE 144
Query: 180 SMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVL-----CPVPTVPKKKRCVL 227
S+AK IGAV Y+ECSA + + VFD AI L KKK +L
Sbjct: 145 SVAKSIGAVAYIECSAKLMENVDEVFDAAINVALSKSGRAARKKKKKKKCVIL 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 = 223 bits (570), Expect = 9e-75
Identities = 94/211 (44%), Positives = 123/211 (58%), Gaps = 48/211 (22%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
AVGKT L++SYTTN +P EY+PT FDN+S V+VDGKP+ L L DTAGQ+++D+LRPL Y
Sbjct: 10 AVGKTSLIVSYTTNGYPTEYVPTAFDNFSVVVLVDGKPVRLQLCDTAGQDEFDKLRPLCY 69
Query: 61 PQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSL 120
P T DVF +CFS+
Sbjct: 70 PDT------------------------------------------------DVFLLCFSV 81
Query: 121 VNPASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLS 180
VNP+SF+N+ KW PE+R H P PIILVGT+ DLR D + +L P++ + +
Sbjct: 82 VNPSSFQNISEKWIPEIRKHNPKAPIILVGTQADLRTDVNVLIQLARYGEKPVSQSRAKA 141
Query: 181 MAKEIGAVKYLECSALTQKGLKTVFDEAIRA 211
+A++IGA +Y+ECSALTQK LK VFD AI A
Sbjct: 142 LAEKIGACEYIECSALTQKNLKEVFDTAILA 172
>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 = 212 bits (540), Expect = 3e-70
Identities = 105/213 (49%), Positives = 128/213 (60%), Gaps = 50/213 (23%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
AVGKTC+LISYT+N FP +Y+PTVFDN+SANV+VDG +NLGLWDTAGQEDY+RLRPLSY
Sbjct: 11 AVGKTCMLISYTSNTFPTDYVPTVFDNFSANVVVDGNTVNLGLWDTAGQEDYNRLRPLSY 70
Query: 61 PQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSL 120
GA DVF + FSL
Sbjct: 71 R----------GA--------------------------------------DVFLLAFSL 82
Query: 121 VNPASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLS 180
++ AS+ENV KW PE+RH+ P PI+LVGTKLDLRDDK+ PIT QG
Sbjct: 83 ISKASYENVLKKWIPELRHYAPGVPIVLVGTKLDLRDDKQFF--ADHPGAVPITTAQGEE 140
Query: 181 MAKEIGAVKYLECSALTQKGLKTVFDEAIRAVL 213
+ K+IGA Y+ECS+ TQ+ +K VFD AI+ VL
Sbjct: 141 LRKQIGAAAYIECSSKTQQNVKAVFDAAIKVVL 173
>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 = 211 bits (538), Expect = 7e-70
Identities = 96/213 (45%), Positives = 124/213 (58%), Gaps = 48/213 (22%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
A GKTCLLI ++ + FP Y+PTVF+NY A++ VDGK + L LWDTAGQEDYDRLRPLSY
Sbjct: 11 ACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLRPLSY 70
Query: 61 PQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSL 120
P T DV +CFS+
Sbjct: 71 PDT------------------------------------------------DVILMCFSI 82
Query: 121 VNPASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLS 180
+P S EN+ KW PEV+H CP+ PIILVG K DLR+D+ TI +L + K P+ +G +
Sbjct: 83 DSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTIRELAKMKQEPVKPEEGRA 142
Query: 181 MAKEIGAVKYLECSALTQKGLKTVFDEAIRAVL 213
MA++IGA YLECSA T++G++ VF+ A RA L
Sbjct: 143 MAEKIGAFGYLECSAKTKEGVREVFEMATRAAL 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 = 209 bits (534), Expect = 2e-69
Identities = 109/213 (51%), Positives = 135/213 (63%), Gaps = 48/213 (22%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
AVGKTCLL+SY +AFP EY+PTVFD+Y+ +V V GK LGL+DTAGQEDYDRLRPLSY
Sbjct: 10 AVGKTCLLMSYANDAFPEEYVPTVFDHYAVSVTVGGKQYLLGLYDTAGQEDYDRLRPLSY 69
Query: 61 PQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSL 120
P T DVF ICFS+
Sbjct: 70 PMT------------------------------------------------DVFLICFSV 81
Query: 121 VNPASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLS 180
VNPASF+NV+ +W PE++ + P+ P +L+GT++DLRDD +T+ +L + K PIT QG
Sbjct: 82 VNPASFQNVKEEWVPELKEYAPNVPYLLIGTQIDLRDDPKTLARLNDMKEKPITVEQGQK 141
Query: 181 MAKEIGAVKYLECSALTQKGLKTVFDEAIRAVL 213
+AKEIGA Y+ECSALTQKGLKTVFDEAI A+L
Sbjct: 142 LAKEIGACCYVECSALTQKGLKTVFDEAIIAIL 174
>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 = 184 bits (470), Expect = 1e-59
Identities = 66/215 (30%), Positives = 97/215 (45%), Gaps = 64/215 (29%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLS 59
VGK+ LLI +T N FP EYIPT+ D Y+ + VDGK + L +WDTAGQE + LRPL
Sbjct: 9 GVGKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAGQERFRALRPLY 68
Query: 60 YPQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFS 119
Y F + +
Sbjct: 69 YRGA------------------------------------------------QGFLLVYD 80
Query: 120 LVNPASFENVRAKWYPEVRHHCP-STPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQG 178
+ + SFENV+ KW E+ H + PI+LVG K DL D + ++ +G
Sbjct: 81 ITSRDSFENVK-KWLEEILRHADENVPIVLVGNKCDLEDQR------------VVSTEEG 127
Query: 179 LSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVL 213
++AKE+G + ++E SA T + ++ F+E R +L
Sbjct: 128 EALAKELG-LPFMETSAKTNENVEEAFEELAREIL 161
>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 = 168 bits (428), Expect = 4e-53
Identities = 77/212 (36%), Positives = 109/212 (51%), Gaps = 49/212 (23%)
Query: 3 GKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSYPQ 62
GKT LL + ++FP Y+PTVF+NY+A+ VD + I L LWDT+G YD +RPLSYP
Sbjct: 13 GKTALLQVFAKDSFPENYVPTVFENYTASFEVDKQRIELSLWDTSGSPYYDNVRPLSYPD 72
Query: 63 TGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSLVN 122
+ D ICF +
Sbjct: 73 S------------------------------------------------DAVLICFDISR 84
Query: 123 PASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLSMA 182
P + ++V KW EVR CP+TP++LVG K DLR D T+ +L K+ P+++ QG ++A
Sbjct: 85 PETLDSVLKKWKGEVREFCPNTPVLLVGCKSDLRTDLSTLTELSNKRQIPVSHEQGRNLA 144
Query: 183 KEIGAVKYLECSALT-QKGLKTVFDEAIRAVL 213
K+IGA Y+ECSA T + ++ VF+ A A L
Sbjct: 145 KQIGAAAYVECSAKTSENSVRDVFEMATLACL 176
>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 = 168 bits (427), Expect = 8e-53
Identities = 86/213 (40%), Positives = 106/213 (49%), Gaps = 50/213 (23%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
A GKT LL +T FP EY PTVF+NY + VDGKP+ L LWDTAGQE+Y+RLRPLSY
Sbjct: 11 ACGKTSLLYVFTLGEFPEEYHPTVFENYVTDCRVDGKPVQLALWDTAGQEEYERLRPLSY 70
Query: 61 PQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSL 120
+ V I F++
Sbjct: 71 SKA------------------------------------------------HVILIGFAI 82
Query: 121 VNPASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLS 180
P S ENVR KW EVR +CP+ P+ILVG K DLR + + PI Q
Sbjct: 83 DTPDSLENVRTKWIEEVRRYCPNVPVILVGLKKDLRQEAVAKGNYATDEFVPIQ--QAKL 140
Query: 181 MAKEIGAVKYLECSALTQKGLKTVFDEAIRAVL 213
+A+ IGA KY+ECSALT +G+ VF+ A RA L
Sbjct: 141 VARAIGAKKYMECSALTGEGVDDVFEAATRAAL 173
>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 = 168 bits (426), Expect = 8e-53
Identities = 84/227 (37%), Positives = 110/227 (48%), Gaps = 52/227 (22%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
A GKT LL +T FP Y PTVF+NY ++ VDG + L LWDTAGQE++DRLR LSY
Sbjct: 10 ACGKTSLLNVFTRGYFPQVYEPTVFENYIHDIFVDGLAVELSLWDTAGQEEFDRLRSLSY 69
Query: 61 PQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSL 120
T V +CFS+
Sbjct: 70 ADT------------------------------------------------HVIMLCFSV 81
Query: 121 VNPASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLS 180
NP S ENV +KW E+RHHCP ++LV K DLR+ + E+ + I+Y +GL+
Sbjct: 82 DNPDSLENVESKWLAEIRHHCPGVKLVLVALKCDLREPRN--ERDRGTHT--ISYEEGLA 137
Query: 181 MAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCVL 227
+AK I A +YLECSA +G+ F EA R L P P + C +
Sbjct: 138 VAKRINACRYLECSAKLNRGVNEAFTEAARVALNARPPHPHSRACTI 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 = 135 bits (342), Expect = 1e-39
Identities = 64/204 (31%), Positives = 103/204 (50%), Gaps = 49/204 (24%)
Query: 3 GKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSYPQ 62
GKT LL + + +P Y+PTVF+NY+A+ +D I L +WDT+G YD +RPL+YP
Sbjct: 13 GKTALLHVFAKDNYPESYVPTVFENYTASFEIDKHRIELNMWDTSGSSYYDNVRPLAYPD 72
Query: 63 TGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSLVN 122
D ICF +
Sbjct: 73 ------------------------------------------------SDAVLICFDISR 84
Query: 123 PASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLSMA 182
P + ++V KW E + CP+ ++LVG KLD+R D T+ +L +++L P+T+ QG +A
Sbjct: 85 PETLDSVLKKWQGETQEFCPNAKLVLVGCKLDMRTDLSTLRELSKQRLIPVTHEQGSLLA 144
Query: 183 KEIGAVKYLECSA-LTQKGLKTVF 205
+++GAV Y+ECS+ +++ ++ VF
Sbjct: 145 RQLGAVAYVECSSRMSENSVRDVF 168
>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 = 132 bits (332), Expect = 1e-38
Identities = 72/210 (34%), Positives = 105/210 (50%), Gaps = 49/210 (23%)
Query: 3 GKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSYPQ 62
GKT LL + + FP Y+PTVF+NY+A+ +D + I L LWDT+G YD +RPLSYP
Sbjct: 17 GKTALLHVFAKDCFPENYVPTVFENYTASFEIDTQRIELSLWDTSGSPYYDNVRPLSYPD 76
Query: 63 TGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSLVN 122
+ D ICF +
Sbjct: 77 S------------------------------------------------DAVLICFDISR 88
Query: 123 PASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLSMA 182
P + ++V KW E++ CP+T ++LVG K DLR D T+ +L + P++Y QG +MA
Sbjct: 89 PETLDSVLKKWKGEIQEFCPNTKMLLVGCKSDLRTDVSTLVELSNHRQTPVSYDQGANMA 148
Query: 183 KEIGAVKYLECSAL-TQKGLKTVFDEAIRA 211
K+IGA Y+ECSAL ++ ++ +F A A
Sbjct: 149 KQIGAATYIECSALQSENSVRDIFHVATLA 178
>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 = 124 bits (312), Expect = 3e-35
Identities = 71/221 (32%), Positives = 106/221 (47%), Gaps = 49/221 (22%)
Query: 3 GKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSYPQ 62
GKT +L + +P Y+PTVF+NY+A + + + + L LWDT+G YD +RPL Y
Sbjct: 25 GKTAMLQVLAKDCYPETYVPTVFENYTACLETEEQRVELSLWDTSGSPYYDNVRPLCYSD 84
Query: 63 TGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSLVN 122
+ D +CF +
Sbjct: 85 S------------------------------------------------DAVLLCFDISR 96
Query: 123 PASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLSMA 182
P F++ KW E+ +CPST I+L+G K DLR D T+ +L +K API+Y QG +MA
Sbjct: 97 PEIFDSALKKWRAEILDYCPSTRILLIGCKTDLRTDLSTLMELSNQKQAPISYEQGCAMA 156
Query: 183 KEIGAVKYLECSALT-QKGLKTVFDEAIRAVLCPVPTVPKK 222
K++GA YLECSA T +K + ++F A + + + KK
Sbjct: 157 KQLGAEAYLECSAFTSEKSIHSIFRTASLLCINKLSPLAKK 197
Score = 38.5 bits (89), Expect = 0.001
Identities = 30/87 (34%), Positives = 48/87 (55%), Gaps = 5/87 (5%)
Query: 57 PLSYPQTGLSMAKEIGAVKYLECSALT-QKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQ 115
P+SY Q G +MAK++GA YLECSA T +K + ++F A ++LC P K+ V
Sbjct: 146 PISYEQ-GCAMAKQLGAEAYLECSAFTSEKSIHSIFRTA--SLLCINKLSPLAKKSPVRS 202
Query: 116 ICFSLVN-PASFENVRAKWYPEVRHHC 141
+ L++ P+ E + + + E C
Sbjct: 203 LSKRLLHLPSRSELISSTFKKEKAKSC 229
>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 = 120 bits (304), Expect = 1e-34
Identities = 54/212 (25%), Positives = 80/212 (37%), Gaps = 64/212 (30%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVF-DNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLS 59
VGKT LL+ + N F Y T+ D S + VDGK + L +WDTAGQE + +
Sbjct: 10 GVGKTSLLLRFVDNKFSENYKSTIGVDFKSKTIEVDGKKVKLQIWDTAGQERFRSITSSY 69
Query: 60 YPQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFS 119
Y + + +
Sbjct: 70 Y------------------------------------------------RGAHGAILVYD 81
Query: 120 LVNPASFENVRAKWYPEVRHHCPS-TPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQG 178
+ N SFEN+ KW E++ + P PIILVG K DL D+++ ++ +
Sbjct: 82 VTNRESFENLD-KWLNELKEYAPPNIPIILVGNKSDLEDERQ------------VSTEEA 128
Query: 179 LSMAKEIGAVKYLECSALTQKGLKTVFDEAIR 210
AKE G + E SA T + + F+ R
Sbjct: 129 QQFAKENGL-LFFETSAKTGENVDEAFESLAR 159
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 103 bits (257), Expect = 4e-27
Identities = 54/219 (24%), Positives = 82/219 (37%), Gaps = 54/219 (24%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSA-NVMVDGKPINLGLWDTAGQEDYDRLRPLS 59
VGKT LL + FP Y PT+ + A + + I L LWDTAGQE+Y LRP
Sbjct: 15 GVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQEEYRSLRPEY 74
Query: 60 YPQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFS 119
Y + I +
Sbjct: 75 YRG------------------------------------------------ANGILIVYD 86
Query: 120 LVNPASFENVRAKWYPEVRHHCP-STPIILVGTKLDLRDDKETIEKLKEKKLAPITYP-- 176
S + + +W E+R P PI+LVG K+DL D++ + E++ + +
Sbjct: 87 STLRESSDELTEEWLEELRELAPDDVPILLVGNKIDLFDEQSSSEEILNQLNREVVLLVL 146
Query: 177 QGLSMAKEIGAVKYLECSA--LTQKGLKTVFDEAIRAVL 213
++ E+ LE SA LT + +F E +R +L
Sbjct: 147 APKAVLPEVANPALLETSAKSLTGPNVNELFKELLRKLL 185
>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 = 100 bits (250), Expect = 1e-26
Identities = 51/200 (25%), Positives = 63/200 (31%), Gaps = 55/200 (27%)
Query: 1 AVGKTCLLISYTTN-AFPGEYIPTVFDNY-SANVMVDGKPINLGLWDTAGQEDYDRLRPL 58
VGK+ LL N EY P NY + + DGK L DTAGQEDYD +R L
Sbjct: 11 NVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAGQEDYDAIRRL 70
Query: 59 SYPQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICF 118
Y + F
Sbjct: 71 YYRAV------------------------------------------------ESSLRVF 82
Query: 119 SLVNPA-SFENVRAKWYPEVRHHCPS-TPIILVGTKLDLRD---DKETIEKLKEKKLAPI 173
+V E + K E+ HH S PIILVG K+DLRD + PI
Sbjct: 83 DIVILVLDVEEILEKQTKEIIHHAESGVPIILVGNKIDLRDAKLKTHVAFLFAKLNGEPI 142
Query: 174 TYPQGLSMAKEIGAVKYLEC 193
+ A K +E
Sbjct: 143 IPLSAETGKNIDSAFKIVEA 162
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 98.3 bits (246), Expect = 6e-26
Identities = 54/217 (24%), Positives = 86/217 (39%), Gaps = 68/217 (31%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPL- 58
VGK+ LL +T F +Y T+ D + + VDGK + L +WDTAGQE R R +
Sbjct: 10 GVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIEVDGKRVKLQIWDTAGQE---RFRSIT 66
Query: 59 -SYPQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQIC 117
SY Y R + + +
Sbjct: 67 SSY---------------Y-------------------RGAVGAL-------------LV 79
Query: 118 FSLVNPASFENVRAKWYPEVRHHCPST-PIILVGTKLDLRDDKETIEKLKEKKLAPITYP 176
+ + N SFEN+ W E+R + I+LVG K DL + ++ ++
Sbjct: 80 YDITNRESFENLE-NWLKELREYASPNVVIMLVGNKSDLEEQRQ------------VSRE 126
Query: 177 QGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVL 213
+ + A+E G + + E SA T ++ F+E R +L
Sbjct: 127 EAEAFAEEHG-LPFFETSAKTNTNVEEAFEELAREIL 162
>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 = 98.0 bits (245), Expect = 7e-26
Identities = 50/213 (23%), Positives = 86/213 (40%), Gaps = 66/213 (30%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
VGK+ L I + + F EY PT+ D+Y ++VDG+ L + DTAGQE++ +R
Sbjct: 9 GVGKSALTIRFVSGEFVEEYDPTIEDSYRKQIVVDGETYTLDILDTAGQEEFSAMRDQYI 68
Query: 61 PQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSL 120
+ D F + +S+
Sbjct: 69 ------------------------------------------------RNGDGFILVYSI 80
Query: 121 VNPASFENV---RAKWYPEVRHHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQ 177
+ SFE + R + V+ PI+LVG K DL ++++ ++ +
Sbjct: 81 TSRESFEEIKNIREQIL-RVK-DKEDVPIVLVGNKCDLENERQ------------VSTEE 126
Query: 178 GLSMAKEIGAVKYLECSALTQKGLKTVFDEAIR 210
G ++A+E G +LE SA T + +F+ +R
Sbjct: 127 GEALAEEWG-CPFLETSAKTNINIDELFNTLVR 158
>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 = 96.6 bits (240), Expect = 7e-25
Identities = 76/234 (32%), Positives = 103/234 (44%), Gaps = 74/234 (31%)
Query: 1 AVGKTCLLISYTTNAFPGEYI------PTVF--DNY--------SANVMVDGKPINLGLW 44
AVGKT L+ + N +Y PTV+ D Y + +VDG ++L LW
Sbjct: 12 AVGKTRLICARACNKTLTQYQLLATHVPTVWAIDQYRVCQEVLERSRDVVDGVSVSLRLW 71
Query: 45 DTAGQEDYDRLRPLSYPQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPT 104
DT G D+D+ R +Y
Sbjct: 72 DTFG--DHDKDRRFAY-------------------------------------------- 85
Query: 105 VPKKKRCDVFQICFSLVNPASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRD-DKETIE 163
R DV +CFS+ +P S NV+ WYPE+RH CP P+ILVG KLDLR D + +
Sbjct: 86 ----GRSDVVLLCFSIASPNSLRNVKTMWYPEIRHFCPRVPVILVGCKLDLRYADLDEVN 141
Query: 164 KLKEKKLAPITY------PQGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRA 211
+ + PI G ++AKE+G + Y E S +TQ G+K VFD AIRA
Sbjct: 142 RARRPLARPIKNADILPPETGRAVAKELG-IPYYETSVVTQFGVKDVFDNAIRA 194
>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 = 87.7 bits (218), Expect = 8e-22
Identities = 55/208 (26%), Positives = 80/208 (38%), Gaps = 64/208 (30%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLS 59
+VGKT ++ + + F +Y T+ D S + VD K + L LWDTAGQE + L P S
Sbjct: 10 SVGKTSIITRFMYDTFDNQYQATIGIDFLSKTMYVDDKTVRLQLWDTAGQERFRSLIP-S 68
Query: 60 YPQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFS 119
Y IR V + +
Sbjct: 69 Y----------------------------------IRDSSVAV-------------VVYD 81
Query: 120 LVNPASFENVRAKWYPEVRHHCPSTPII-LVGTKLDLRDDKETIEKLKEKKLAPITYPQG 178
+ N SF+N KW +VR + II LVG K DL D ++ ++ +G
Sbjct: 82 ITNRQSFDNTD-KWIDDVRDERGNDVIIVLVGNKTDLSDKRQ------------VSTEEG 128
Query: 179 LSMAKEIGAVKYLECSALTQKGLKTVFD 206
AKE A ++E SA +K +F
Sbjct: 129 EKKAKENNA-MFIETSAKAGHNVKQLFK 155
>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 = 80.7 bits (200), Expect = 4e-19
Identities = 47/218 (21%), Positives = 83/218 (38%), Gaps = 72/218 (33%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
VGK+ L I + F +Y PT+ D+Y + +DG+ L + DTAGQE++ +R Y
Sbjct: 10 GVGKSALTIQFIQGHFVDDYDPTIEDSYRKQIEIDGEVCLLDILDTAGQEEFSAMRDQ-Y 68
Query: 61 PQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSL 120
+TG + F + +S+
Sbjct: 69 MRTG-----------------------------------------------EGFLLVYSI 81
Query: 121 VNPASFENVRAKWYPEVRHH------CPSTPIILVGTKLDLRDDKETIEKLKEKKLAPIT 174
+ SFE ++ + R PI+LVG K DL ++ ++
Sbjct: 82 TDRQSFEEIK-----KFREQILRVKDRDDVPIVLVGNKCDLESERV------------VS 124
Query: 175 YPQGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAV 212
+G +A++ G +LE SA + + F + +R +
Sbjct: 125 TEEGKELARQWG-CPFLETSAKERVNVDEAFYDLVREI 161
>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 = 79.1 bits (196), Expect = 1e-18
Identities = 48/213 (22%), Positives = 85/213 (39%), Gaps = 64/213 (30%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSYP 61
VGK+ L I + F EY PT+ D+Y + +DG+ L + DTAGQE++ +R Y
Sbjct: 13 VGKSALTIQFVQGHFVDEYDPTIEDSYRKQIEIDGEVCLLDILDTAGQEEFSAMRDQ-YM 71
Query: 62 QTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSLV 121
+TG + F + +S+
Sbjct: 72 RTG-----------------------------------------------EGFLLVYSIT 84
Query: 122 NPASFENVRAKWYPEVRH--HCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGL 179
+ SFE + K+ ++ PI+LVG K DL +++ ++ +G
Sbjct: 85 DRQSFEEIA-KFREQILRVKDRDDVPIVLVGNKCDLENERV------------VSTEEGK 131
Query: 180 SMAKEIGAVKYLECSALTQKGLKTVFDEAIRAV 212
+A++ G +LE SA + + F + +R +
Sbjct: 132 ELARQWG-CPFLETSAKERINVDEAFYDLVREI 163
>gnl|CDD|206659 cd01867, Rab8_Rab10_Rab13_like, Rab GTPase families 8, 10, 13
(Rab8, Rab10, Rab13). Rab8/Sec4/Ypt2 are known or
suspected to be involved in post-Golgi transport to the
plasma membrane. It is likely that these Rabs have
functions that are specific to the mammalian lineage and
have no orthologs in plants. Rab8 modulates polarized
membrane transport through reorganization of actin and
microtubules, induces the formation of new surface
extensions, and has an important role in directed
membrane transport to cell surfaces. The Ypt2 gene of
the fission yeast Schizosaccharomyces pombe encodes a
member of the Ypt/Rab family of small GTP-binding
proteins, related in sequence to Sec4p of Saccharomyces
cerevisiae but closer to mammalian Rab8. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 167
Score = 75.8 bits (187), Expect = 2e-17
Identities = 53/217 (24%), Positives = 90/217 (41%), Gaps = 68/217 (31%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPL- 58
VGK+CLL+ ++ ++F +I T+ D + +DGK I L +WDTAGQE R R +
Sbjct: 13 GVGKSCLLLRFSEDSFNPSFISTIGIDFKIRTIELDGKKIKLQIWDTAGQE---RFRTIT 69
Query: 59 -SYPQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQIC 117
SY + GA+ G+ V+D
Sbjct: 70 TSYYR---------GAM-----------GIILVYD------------------------- 84
Query: 118 FSLVNPASFENVRAKWYPEV-RHHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYP 176
+ + SFEN++ W + H +LVG K D+ + + ++
Sbjct: 85 --ITDEKSFENIK-NWMRNIDEHASEDVERMLVGNKCDMEEKRV------------VSKE 129
Query: 177 QGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVL 213
+G ++A+E G +K+LE SA ++ F + +L
Sbjct: 130 EGEALAREYG-IKFLETSAKANINVEEAFLTLAKDIL 165
>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 = 72.9 bits (179), Expect = 7e-16
Identities = 59/200 (29%), Positives = 77/200 (38%), Gaps = 66/200 (33%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTV-FDNYSANV-MVDGKPINLGLWDTAGQEDYDRLRPLS 59
VGK+ LL +T F PTV D +S + + G I L LWDTAGQE R R
Sbjct: 13 VGKSSLLKRFTEGRFAEVSDPTVGVDFFSRLIEIEPGVRIKLQLWDTAGQE---RFR--- 66
Query: 60 YPQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFS 119
I Y G+ VFD
Sbjct: 67 ----------SITRSYYRNSV-----GVLLVFD--------------------------- 84
Query: 120 LVNPASFENVRAKWYPEVRHHC-PSTPI-ILVGTKLDLRDDKETIEKLKEKKLAPITYPQ 177
+ N SFE+V W E R H P P+ ILVG K DL ++ +T +
Sbjct: 85 ITNRESFEHVH-DWLEEARSHIQPHRPVFILVGHKCDLESQRQ------------VTREE 131
Query: 178 GLSMAKEIGAVKYLECSALT 197
+AK++G +KY+E SA T
Sbjct: 132 AEKLAKDLG-MKYIETSART 150
>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 = 70.8 bits (174), Expect = 2e-15
Identities = 55/216 (25%), Positives = 88/216 (40%), Gaps = 70/216 (32%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPL-- 58
VGK+ LL+ +T + F + T+ D V VDGK + L +WDTAGQE R R L
Sbjct: 11 VGKSSLLLRFTDDTFDEDLSSTIGVDFKVKTVTVDGKKVKLAIWDTAGQE---RFRTLTS 67
Query: 59 SYPQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICF 118
SY + GA +G+ V+D
Sbjct: 68 SYYR---------GA-----------QGVILVYD-------------------------- 81
Query: 119 SLVNPASFENVRAKWYPEVRHHC--PSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYP 176
+ +F+N+ W E+ + P +LVG K+ DKE E +E
Sbjct: 82 -VTRRDTFDNLD-TWLNELDTYSTNPDAVKMLVGNKI----DKENREVTRE--------- 126
Query: 177 QGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAV 212
+G A++ + ++E SA T+ G++ F+E + +
Sbjct: 127 EGQKFARKHNML-FIETSAKTRIGVQQAFEELVEKI 161
>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 = 70.6 bits (173), Expect = 2e-15
Identities = 42/213 (19%), Positives = 69/213 (32%), Gaps = 63/213 (29%)
Query: 2 VGKTCLLISYTTNAF---PGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDYDRLRP 57
VGK+ LL + T D Y + + L DT G +++ L
Sbjct: 8 VGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVL--VDTPGLDEFGGLG- 64
Query: 58 LSYPQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQIC 117
+ A + + D+ +
Sbjct: 65 --------------------------------REELARLLL----------RGADLILLV 82
Query: 118 FSLVNPASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQ 177
+ S E+ AK R PIILVG K+DL +++E E L+ ++L
Sbjct: 83 VDSTDRESEED--AKLLILRRLRKEGIPIILVGNKIDLLEEREVEELLRLEEL------- 133
Query: 178 GLSMAKEIGAVKYLECSALTQKGLKTVFDEAIR 210
+I V E SA T +G+ +F++ I
Sbjct: 134 -----AKILGVPVFEVSAKTGEGVDELFEKLIE 161
>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 = 70.5 bits (173), Expect = 2e-15
Identities = 53/213 (24%), Positives = 85/213 (39%), Gaps = 65/213 (30%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSYP 61
VGK+ L I N F EY PT+ D+Y V++DG+ L + DTAGQE+Y +R Y
Sbjct: 12 VGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRD-QYM 70
Query: 62 QTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSLV 121
+TG + F F++
Sbjct: 71 RTG-----------------------------------------------EGFLCVFAIN 83
Query: 122 NPASFENVRAKWYPEVRH--HCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGL 179
+ SFE++ + +++ P++LVG K DL ++ QG
Sbjct: 84 SRKSFEDIH-TYREQIKRVKDSDDVPMVLVGNKCDLAART-------------VSTRQGQ 129
Query: 180 SMAKEIGAVKYLECSALTQKGLKTVFDEAIRAV 212
+AK G Y+E SA T++G++ F +R +
Sbjct: 130 DLAKSYGI-PYIETSAKTRQGVEEAFYTLVREI 161
>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 = 70.2 bits (172), Expect = 3e-15
Identities = 56/213 (26%), Positives = 86/213 (40%), Gaps = 64/213 (30%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVM-VDGKPINLGLWDTAGQEDYDRLRPLSY 60
GK+CLL + N F + T+ + + V+ V GK + L +WDTAGQE R R
Sbjct: 11 TGKSCLLHQFIENKFKQDSNHTIGVEFGSRVVNVGGKSVKLQIWDTAGQE---RFR---- 63
Query: 61 PQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSL 120
S+ + Y +A G V+D +
Sbjct: 64 -----SVTRS-----YYRGAA----GALLVYD---------------------------I 82
Query: 121 VNPASFENVRAKWYPEVRH-HCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGL 179
+ SF + W + R P IILVG K DL DD+E +T+ +
Sbjct: 83 TSRESFNAL-TNWLTDARTLASPDIVIILVGNKKDLEDDRE------------VTFLEAS 129
Query: 180 SMAKEIGAVKYLECSALTQKGLKTVFDEAIRAV 212
A+E G + +LE SALT + ++ F + R++
Sbjct: 130 RFAQENG-LLFLETSALTGENVEEAFLKCARSI 161
>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 = 70.1 bits (172), Expect = 3e-15
Identities = 37/107 (34%), Positives = 56/107 (52%), Gaps = 9/107 (8%)
Query: 109 KRCDVFQICFSLVNPASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDKETIEKLKEK 168
++ +V + +S+ P++ E +R KW P +R PIILVG K DLRD E+
Sbjct: 71 RKANVICLVYSVDRPSTLERIRTKWLPLIRRLGVKVPIILVGNKSDLRDGSSQAG--LEE 128
Query: 169 KLAPITYPQGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCP 215
++ PI ++ +EI +ECSA T + VF A +AVL P
Sbjct: 129 EMLPI-----MNEFREIET--CVECSAKTLINVSEVFYYAQKAVLHP 168
Score = 28.8 bits (65), Expect = 1.4
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 76 YLECSALTQKGLKTVFDEAIRAVLCP 101
+ECSA T + VF A +AVL P
Sbjct: 143 CVECSAKTLINVSEVFYYAQKAVLHP 168
>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 = 68.6 bits (168), Expect = 1e-14
Identities = 48/213 (22%), Positives = 87/213 (40%), Gaps = 64/213 (30%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSYP 61
VGK+ L I + + F +Y PT+ D+Y+ +DG+ L + DTAGQE++ +R Y
Sbjct: 13 VGKSALTIQFIQSYFVTDYDPTIEDSYTKQCEIDGQWARLDILDTAGQEEFSAMRE-QYM 71
Query: 62 QTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSLV 121
+TG + F + FS+
Sbjct: 72 RTG-----------------------------------------------EGFLLVFSVT 84
Query: 122 NPASFENVRAKWYPEVRH--HCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGL 179
+ SFE V K++ ++ P+ILVG K DL ++ ++ +G
Sbjct: 85 DRGSFEEVD-KFHTQILRVKDRDEFPMILVGNKADLEHQRQ------------VSREEGQ 131
Query: 180 SMAKEIGAVKYLECSALTQKGLKTVFDEAIRAV 212
+A+++ + Y+E SA + + F + +R +
Sbjct: 132 ELARQL-KIPYIETSAKDRVNVDKAFHDLVRVI 163
>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 = 68.0 bits (167), Expect = 2e-14
Identities = 50/218 (22%), Positives = 83/218 (38%), Gaps = 70/218 (32%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTV---FDNYSANVMVDGKPINLGLWDTAGQEDYDRLRP 57
+VGK+ +++ + N F T+ F + V +D + +WDTAGQE Y L P
Sbjct: 11 SVGKSSIVLRFVKNEFSENQESTIGAAFLTQT--VNLDDTTVKFEIWDTAGQERYRSLAP 68
Query: 58 LSYPQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQIC 117
+ Y GA +A+ V+D
Sbjct: 69 MYYR----------GA-----AAAI------VVYD------------------------- 82
Query: 118 FSLVNPASFENVRAK-WYPEVRHHC-PSTPIILVGTKLDLRDDKETIEKLKEKKLAPITY 175
+ + SFE +AK W E++ H P+ I L G K DL ++ ++
Sbjct: 83 --ITSEESFE--KAKSWVKELQEHGPPNIVIALAGNKADLESKRQ------------VST 126
Query: 176 PQGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVL 213
+ A E G + ++E SA T + + +F E R +
Sbjct: 127 EEAQEYADENGLL-FMETSAKTGENVNELFTEIARKLP 163
>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 = 67.2 bits (164), Expect = 5e-14
Identities = 47/219 (21%), Positives = 83/219 (37%), Gaps = 75/219 (34%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSYP 61
VGK+ L + + F +Y PT+ D+Y + VD + L + DTAG E + +R L Y
Sbjct: 12 VGKSALTVQFVQGIFVDKYDPTIEDSYRKQIEVDCQQCMLEILDTAGTEQFTAMRDL-YI 70
Query: 62 QTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSLV 121
+ G F + +S+
Sbjct: 71 KNGQG-----------------------------------------------FALVYSIT 83
Query: 122 NPASFEN--------VRAKWYPEVRHHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPI 173
SF + +R K +V P+ILVG K DL D++ +
Sbjct: 84 AQQSFNDLQDLREQILRVKDTEDV-------PMILVGNKCDLEDERV------------V 124
Query: 174 TYPQGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAV 212
+ +G ++A++ G +LE SA ++ + +F + +R +
Sbjct: 125 SKEEGQNLARQWGNCPFLETSAKSKINVDEIFYDLVRQI 163
>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 = 65.6 bits (160), Expect = 2e-13
Identities = 54/213 (25%), Positives = 91/213 (42%), Gaps = 59/213 (27%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSYP 61
VGK+ L + + N F Y PT+ D+Y V +DG+ +L + DTAG E + +R L Y
Sbjct: 12 VGKSALTVQFVQNVFIESYDPTIEDSYRKQVEIDGRQCDLEILDTAGTEQFTAMREL-YI 70
Query: 62 QTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSLV 121
++G +G V+ A L + + R V +I S
Sbjct: 71 KSG--------------------QGFLLVYSVTSEASLNELGEL----REQVLRIKDS-- 104
Query: 122 NPASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLSM 181
+NV P++LVG K DL DD++ ++ G+S+
Sbjct: 105 -----DNV---------------PMVLVGNKADLEDDRQ------------VSREDGVSL 132
Query: 182 AKEIGAVKYLECSALTQKGLKTVFDEAIRAVLC 214
+++ G V + E SA + + VF + +R ++C
Sbjct: 133 SQQWGNVPFYETSARKRTNVDEVFIDLVRQIIC 165
>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 = 65.1 bits (159), Expect = 3e-13
Identities = 53/215 (24%), Positives = 86/215 (40%), Gaps = 64/215 (29%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVM-VDGKPINLGLWDTAGQEDYDRLRPLS 59
VGK+CLL+ +T F + T+ + A ++ +DGK I L +WDTAGQE + R S
Sbjct: 14 GVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQESF-RSITRS 72
Query: 60 YPQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFS 119
Y + GA AL V+D R
Sbjct: 73 YYR---------GA-----AGAL------LVYDITRR----------------------- 89
Query: 120 LVNPASFENVRAKWYPEVRHHC-PSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQG 178
+F ++ W + R H + I+L+G K DL +E ++Y +G
Sbjct: 90 ----ETFNHL-TSWLEDARQHSNSNMTIMLIGNKCDLESRRE------------VSYEEG 132
Query: 179 LSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVL 213
+ A+E G + ++E SA T ++ F + +
Sbjct: 133 EAFAREHGLI-FMETSAKTASNVEEAFINTAKEIY 166
>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 = 63.8 bits (156), Expect = 9e-13
Identities = 55/218 (25%), Positives = 81/218 (37%), Gaps = 67/218 (30%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
VGKT L+ Y F +Y T+ D + V VD + + L +WDTAGQE R S
Sbjct: 11 VGKTSLMNQYVNKKFSNQYKATIGADFLTKEVTVDDRLVTLQIWDTAGQE-----RFQS- 64
Query: 61 PQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSL 120
L +A GA +C L V+D +
Sbjct: 65 ----LGVAFYRGA----DCCVL-------VYD---------------------------V 82
Query: 121 VNPASFENVRAKWYPEVRHH-CPST----PIILVGTKLDLRDDKETIEKLKEKKLAPITY 175
NP SFE++ + W E P P +++G K+DL ++K + K ++
Sbjct: 83 TNPKSFESLDS-WRDEFLIQASPRDPENFPFVVLGNKIDL-EEKRQVSTKKAQQW----- 135
Query: 176 PQGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVL 213
K G + Y E SA + F+ R L
Sbjct: 136 ------CKSKGNIPYFETSAKEAINVDQAFETIARLAL 167
>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 = 63.5 bits (155), Expect = 1e-12
Identities = 53/198 (26%), Positives = 80/198 (40%), Gaps = 68/198 (34%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPL-- 58
VGK+CLL+ + + + YI T+ D + +DGK + L +WDTAGQE R R +
Sbjct: 13 VGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTVKLQIWDTAGQE---RFRTITS 69
Query: 59 SYPQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICF 118
SY + GA G+ V+D
Sbjct: 70 SYYR---------GA-----------HGIIIVYD-------------------------- 83
Query: 119 SLVNPASFENVRAKWYPEV-RHHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQ 177
+ + SF NV+ +W E+ R+ + +LVG K DL D K + Y +
Sbjct: 84 -VTDQESFNNVK-QWLQEIDRYASENVNKLLVGNKCDLTDKKV------------VDYTE 129
Query: 178 GLSMAKEIGAVKYLECSA 195
A E+G + +LE SA
Sbjct: 130 AKEFADELG-IPFLETSA 146
>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 = 63.3 bits (154), Expect = 2e-12
Identities = 59/243 (24%), Positives = 100/243 (41%), Gaps = 78/243 (32%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSYP 61
VGKT L I N F Y PT+ D+Y V+VDG+P L + DTAGQE+Y LR
Sbjct: 10 VGKTALTIQLCLNHFVETYDPTIEDSYRKQVVVDGQPCMLEVLDTAGQEEYTALR----- 64
Query: 62 QTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSLV 121
D+ IR + F + +S+
Sbjct: 65 ------------------------------DQWIR-------------EGEGFILVYSIT 81
Query: 122 NPASFENVRAKWYPEVRHHCPST----PIILVGTKLDLRDDKETIEKLKEKKLAPITYPQ 177
+ ++FE V ++ +++ + PI++VG K D ++E ++ +
Sbjct: 82 SRSTFERVE-RFREQIQRVKDESAADVPIMIVGNKCDKVYERE------------VSTEE 128
Query: 178 GLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRA---------VLCPVPTVP---KKKRC 225
G ++A+ +G +++E SA T ++ F +RA PT KK++C
Sbjct: 129 GAALARRLGC-EFIEASAKTNVNVERAFYTLVRALRQQRQGGQGPKGGPTKKKEKKKRKC 187
Query: 226 VLL 228
V++
Sbjct: 188 VIM 190
>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 = 61.9 bits (151), Expect = 5e-12
Identities = 53/231 (22%), Positives = 92/231 (39%), Gaps = 66/231 (28%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
+VGK+ L + + F Y PT+ + +S + G+ +L + DTAGQ++Y L
Sbjct: 11 SVGKSSLTVQFVEGHFVESYYPTIENTFSKIITYKGQEYHLEIVDTAGQDEYSIL----- 65
Query: 61 PQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSL 120
PQ IG Y+ + +S+
Sbjct: 66 PQKYS-----IGIHGYI--------------------------------------LVYSV 82
Query: 121 VNPASFENVRAKWYPEVRHH-CPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGL 179
+ SFE V+ + + S PI+LVG K DL +++ ++ +G
Sbjct: 83 TSRKSFEVVKVIYDKILDMLGKESVPIVLVGNKSDLHMERQ------------VSAEEGK 130
Query: 180 SMAKEIGAVKYLECSALTQKGLKTVFD---EAIRAVLCPVPTVPKKKRCVL 227
+A+ GA +LE SA + ++ F+ E I V P+P +K +C +
Sbjct: 131 KLAESWGA-AFLESSAKENENVEEAFELLIEEIEKVENPLPP-GQKSKCSV 179
>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 = 61.7 bits (150), Expect = 5e-12
Identities = 56/209 (26%), Positives = 79/209 (37%), Gaps = 75/209 (35%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMV-----------DGKPINLGLWDTAGQE 50
VGKT L YT N F ++I TV ++ +V ++L LWDTAGQE
Sbjct: 15 VGKTTFLYRYTDNKFNPKFITTVGIDFREKRVVYNSQGPDGTSGKAFRVHLQLWDTAGQE 74
Query: 51 DYDRLRPLSYPQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKR 110
R R L +A F +A+
Sbjct: 75 ---RFRSL--------------------TTAF--------FRDAMG-------------- 89
Query: 111 CDVFQICFSLVNPASFENVRAKWYPEVRHH--CPSTPIILVGTKLDLRDDKETIEKLKEK 168
F + F L + SF NVR W +++ H C + I+L+G K DL D +E E+
Sbjct: 90 ---FLLMFDLTSEQSFLNVR-NWMSQLQAHAYCENPDIVLIGNKADLPDQREVSER---- 141
Query: 169 KLAPITYPQGLSMAKEIGAVKYLECSALT 197
Q +A + G + Y E SA T
Sbjct: 142 --------QARELADKYG-IPYFETSAAT 161
>gnl|CDD|206660 cd01868, Rab11_like, Rab GTPase family 11 (Rab11)-like includes
Rab11a, Rab11b, and Rab25. Rab11a, Rab11b, and Rab25
are closely related, evolutionary conserved Rab proteins
that are differentially expressed. Rab11a is
ubiquitously synthesized, Rab11b is enriched in brain
and heart and Rab25 is only found in epithelia. Rab11/25
proteins seem to regulate recycling pathways from
endosomes to the plasma membrane and to the trans-Golgi
network. Furthermore, Rab11a is thought to function in
the histamine-induced fusion of tubulovesicles
containing H+, K+ ATPase with the plasma membrane in
gastric parietal cells and in insulin-stimulated
insertion of GLUT4 in the plasma membrane of
cardiomyocytes. Overexpression of Rab25 has recently
been observed in ovarian cancer and breast cancer, and
has been correlated with worsened outcomes in both
diseases. In addition, Rab25 overexpression has also
been observed in prostate cancer, transitional cell
carcinoma of the bladder, and invasive breast tumor
cells. GTPase activating proteins (GAPs) interact with
GTP-bound Rab and accelerate the hydrolysis of GTP to
GDP. Guanine nucleotide exchange factors (GEFs) interact
with GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 165
Score = 61.0 bits (149), Expect = 9e-12
Identities = 57/212 (26%), Positives = 82/212 (38%), Gaps = 74/212 (34%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTV---FDNYSANVMVDGKPINLGLWDTAGQEDYDRLRP 57
VGK+ LL +T N F + T+ F + + +DGK I +WDTAGQE Y
Sbjct: 13 GVGKSNLLSRFTRNEFNLDSKSTIGVEFATRT--IQIDGKTIKAQIWDTAGQERY----- 65
Query: 58 LSYPQTGLSMAKEIGAVKYLECSALTQ---KGLKTVFDEAIRAVLCPVPTVPKKKRCDVF 114
A+T +G A+ A+L V+
Sbjct: 66 ----------------------RAITSAYYRG-------AVGALL-------------VY 83
Query: 115 QICFSLVNPASFENVRAKWYPEVRHHCPS-TPIILVGTKLDLRDDKETIEKLKEKKLAPI 173
I ++FENV +W E+R H S I+LVG K DLR + + + K A
Sbjct: 84 DIT----KKSTFENV-ERWLKELRDHADSNIVIMLVGNKSDLRHLRA-VPTEEAKAFAE- 136
Query: 174 TYPQGLSMAKEIGAVKYLECSALTQKGLKTVF 205
GLS ++E SAL ++ F
Sbjct: 137 --KNGLS---------FIETSALDGTNVEEAF 157
>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 = 60.6 bits (147), Expect = 1e-11
Identities = 51/210 (24%), Positives = 85/210 (40%), Gaps = 62/210 (29%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSYP 61
VGK+ L + + + F +Y PT+ D Y + VD P L + DTAG E + +R L Y
Sbjct: 12 VGKSALTVQFVSGTFIEKYDPTIEDFYRKEIEVDSSPSVLEILDTAGTEQFASMRDL-YI 70
Query: 62 QTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSLV 121
+ G F + +SLV
Sbjct: 71 KNGQG-----------------------------------------------FIVVYSLV 83
Query: 122 NPASFENVRAKWYPEVR-HHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLS 180
N +F++++ VR PIILVG K+DL ++E ++ +G +
Sbjct: 84 NQQTFQDIKPMRDQIVRVKGYEKVPIILVGNKVDLESERE------------VSSAEGRA 131
Query: 181 MAKEIGAVKYLECSALTQKGLKTVFDEAIR 210
+A+E G ++E SA ++ + +F E +R
Sbjct: 132 LAEEWGC-PFMETSAKSKTMVNELFAEIVR 160
>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 = 60.6 bits (147), Expect = 1e-11
Identities = 45/212 (21%), Positives = 81/212 (38%), Gaps = 68/212 (32%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSYP 61
VGK+ + + + +++FP + PT+ D Y +D +P L + DTAGQ ++ +R
Sbjct: 13 VGKSAVTMQFISHSFPDYHDPTIEDAYKTQARIDNEPALLDILDTAGQAEFTAMRD---- 68
Query: 62 QTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSLV 121
+Y+ C + F IC+S+
Sbjct: 69 -------------QYMRCG-------------------------------EGFIICYSVT 84
Query: 122 NPASFENVRA--KWYPEVRHHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGL 179
+ SF+ + VR P++LVG K+DL ++ +T +G
Sbjct: 85 DRHSFQEASEFKELITRVR-LTEDIPLVLVGNKVDL------------EQQRQVTTEEGR 131
Query: 180 SMAKEIGAVKYLECSALTQKGLKTVFDEAIRA 211
++A+E + E SA L+ D+A
Sbjct: 132 NLAREFNC-PFFETSA----ALRFYIDDAFHG 158
>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 = 60.1 bits (146), Expect = 2e-11
Identities = 52/212 (24%), Positives = 83/212 (39%), Gaps = 62/212 (29%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSYP 61
VGK+ L + + + F +Y PT D+Y V++DG+ + L + DTAGQEDY +R
Sbjct: 11 VGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEVQLNILDTAGQEDYAAIR----- 65
Query: 62 QTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSLV 121
D R+ + F + FS+
Sbjct: 66 ------------------------------DNYFRS-------------GEGFLLVFSIT 82
Query: 122 NPASFENVRAKWYPEVRH-HCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLS 180
+ SF + +R + P++LVG K DL +DK + + LA
Sbjct: 83 DMESFTALAEFREQILRVKEDDNVPLLLVGNKCDL-EDKRQVSVEEAANLA--------- 132
Query: 181 MAKEIGAVKYLECSALTQKGLKTVFDEAIRAV 212
E V Y+E SA T+ + VF + +R +
Sbjct: 133 ---EQWGVNYVETSAKTRANVDKVFFDLVREI 161
>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 = 59.9 bits (146), Expect = 2e-11
Identities = 25/60 (41%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDN-YSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
VGKT L++ Y N F ++ T + + V + GK I+L +WDTAGQE Y L P+ Y
Sbjct: 11 VGKTSLVLRYVENKFNEKHESTTQASFFQKTVNIGGKRIDLAIWDTAGQERYHALGPIYY 70
Score = 43.4 bits (103), Expect = 1e-05
Identities = 23/92 (25%), Positives = 45/92 (48%), Gaps = 15/92 (16%)
Query: 116 ICFSLVNPASFENVRAKWYPEVRHHC-PSTPIILVGTKLDLRDDKETIEKLKEKKLAPIT 174
+ + + + SF+ V+ KW E++ + +++VG K+DL + ++
Sbjct: 78 LVYDITDADSFQKVK-KWIKELKQMRGNNISLVIVGNKIDLERQRV------------VS 124
Query: 175 YPQGLSMAKEIGAVKYLECSALTQKGLKTVFD 206
+ AK +GA K+ E SA T KG++ +F
Sbjct: 125 KSEAEEYAKSVGA-KHFETSAKTGKGIEELFL 155
Score = 30.3 bits (69), Expect = 0.45
Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 61 PQTGLSMAKEIGAVKYLECSALTQKGLKTVFD 92
AK +GA K+ E SA T KG++ +F
Sbjct: 125 KSEAEEYAKSVGA-KHFETSAKTGKGIEELFL 155
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 59.9 bits (145), Expect = 3e-11
Identities = 53/211 (25%), Positives = 86/211 (40%), Gaps = 60/211 (28%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSYP 61
VGK+ L I + N F EY PT+ D+Y ++D + L + DTAGQE+Y +R Y
Sbjct: 16 VGKSALTIQFIQNHFIDEYDPTIEDSYRKQCVIDEETCLLDILDTAGQEEYSAMRD-QYM 74
Query: 62 QTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSLV 121
+TG +L ++T ++ F+E I + + V K R
Sbjct: 75 RTGQG---------FLCVYSITS---RSSFEE-IASFREQILRVKDKDR----------- 110
Query: 122 NPASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLSM 181
P+ILVG K DL +++ ++ +G +
Sbjct: 111 ----------------------VPMILVGNKCDLDSERQ------------VSTGEGQEL 136
Query: 182 AKEIGAVKYLECSALTQKGLKTVFDEAIRAV 212
AK G + +LE SA + + F E +R +
Sbjct: 137 AKSFG-IPFLETSAKQRVNVDEAFYELVREI 166
>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 = 58.7 bits (142), Expect = 1e-10
Identities = 54/200 (27%), Positives = 83/200 (41%), Gaps = 65/200 (32%)
Query: 1 AVGKTCLLISYTTNAF-PGEYIPTVFDNYSANVM-VDGKPINLGLWDTAGQEDYDRLRPL 58
VGKTCLL+ + AF G +I TV ++ V+ VDG + L +WDTAGQE R R +
Sbjct: 10 GVGKTCLLVRFKDGAFLAGSFIATVGIQFTNKVVTVDGVKVKLQIWDTAGQE---RFRSV 66
Query: 59 SYPQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICF 118
++ Y + AL + +
Sbjct: 67 TH-------------AYYRDAHALL--------------------------------LLY 81
Query: 119 SLVNPASFENVRAKWYPEVRHHCPSTPII-LVGTKLDLRDDKETIEKLKEKKLAPITYPQ 177
+ N +SF+N+RA W E+ + S +I L+G K D+ ++ +
Sbjct: 82 DVTNKSSFDNIRA-WLTEILEYAQSDVVIMLLGNKADMSGERV------------VKRED 128
Query: 178 GLSMAKEIGAVKYLECSALT 197
G +AKE G V ++E SA T
Sbjct: 129 GERLAKEYG-VPFMETSAKT 147
>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 = 57.2 bits (138), Expect = 3e-10
Identities = 52/207 (25%), Positives = 83/207 (40%), Gaps = 60/207 (28%)
Query: 1 AVGKTCLLISYTTNAF-PGEYIPTVFDNYSANVM-VDGKPINLGLWDTAGQEDYDRLRPL 58
+VGKT L+ Y + F G Y T+ + A M V + + LG+WDTAG E Y+ + +
Sbjct: 10 SVGKTSLVERYVHHRFLVGPYQNTIGAAFVAKRMVVGERVVTLGIWDTAGSERYEAMSRI 69
Query: 59 SYPQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICF 118
Y +G K AI +C+
Sbjct: 70 YY------------------------RGAKA----AI--------------------VCY 81
Query: 119 SLVNPASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQG 178
L + +SFE + W E+++ I L GTK DL IE +++ L + +
Sbjct: 82 DLTDSSSFERAKF-WVKELQNLEEHCKIYLCGTKSDL------IE--QDRSLRQVDFHDV 132
Query: 179 LSMAKEIGAVKYLECSALTQKGLKTVF 205
A EI A ++ E S+ T + + +F
Sbjct: 133 QDFADEIKA-QHFETSSKTGQNVDELF 158
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 57.3 bits (138), Expect = 3e-10
Identities = 52/206 (25%), Positives = 78/206 (37%), Gaps = 64/206 (31%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSAN-VMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
VGK+CLL+ +T F + T+ + A + +D KPI L +WDTAGQE + R SY
Sbjct: 17 VGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDNKPIKLQIWDTAGQESF-RSITRSY 75
Query: 61 PQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSL 120
+ GA G V+D R
Sbjct: 76 YR---------GAA-----------GALLVYDITRRETF--------------------- 94
Query: 121 VNPASFENVRAKWYPEVRHHC-PSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGL 179
N A W + R H + I+L+G K DL + ++ +G
Sbjct: 95 -------NHLASWLEDARQHANANMTIMLIGNKCDLAHRR------------AVSTEEGE 135
Query: 180 SMAKEIGAVKYLECSALTQKGLKTVF 205
AKE G + ++E SA T + ++ F
Sbjct: 136 QFAKEHGLI-FMEASAKTAQNVEEAF 160
>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 = 56.3 bits (136), Expect = 4e-10
Identities = 40/175 (22%), Positives = 63/175 (36%), Gaps = 56/175 (32%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTV---FDNYSANVMVDGKPINLGLWDTAGQEDYDRLRP 57
VGK+ ++ + F +Y T+ F + + + L LWDTAGQE++D
Sbjct: 10 NVGKSSMIQRFVKGIFTKDYKKTIGVDFLEKQIFLRQSDEDVRLMLWDTAGQEEFD---- 65
Query: 58 LSYPQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQIC 117
A+T+ + A +L
Sbjct: 66 -----------------------AITKA----YYRGAQACIL-----------------V 81
Query: 118 FSLVNPASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDD----KETIEKLKEK 168
FS + SFE + W +V C P++LV TK+DL D E E L ++
Sbjct: 82 FSTTDRESFEAI-ESWKEKVEAECGDIPMVLVQTKIDLLDQAVITNEEAEALAKR 135
>gnl|CDD|206713 cd04146, RERG_RasL11_like, Ras-related and Estrogen-Regulated
Growth inhibitor (RERG) and Ras-like 11 (RasL11)-like
families. RERG (Ras-related and Estrogen- Regulated
Growth inhibitor) and Ras-like 11 are members of a
novel subfamily of Ras that were identified based on
their behavior in breast and prostate tumors,
respectively. RERG expression was decreased or lost in
a significant fraction of primary human breast tumors
that lack estrogen receptor and are correlated with
poor clinical prognosis. Elevated RERG expression
correlated with favorable patient outcome in a breast
tumor subtype that is positive for estrogen receptor
expression. In contrast to most Ras proteins, RERG
overexpression inhibited the growth of breast tumor
cells in vitro and in vivo. RasL11 was found to be
ubiquitously expressed in human tissue, but
down-regulated in prostate tumors. Both RERG and RasL11
lack the C-terminal CaaX prenylation motif, where a =
an aliphatic amino acid and X = any amino acid, and are
localized primarily in the cytoplasm. Both are believed
to have tumor suppressor activity.
Length = 166
Score = 56.1 bits (136), Expect = 6e-10
Identities = 20/49 (40%), Positives = 30/49 (61%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQE 50
VGK+ L + + T F GEY P + YS V +DG+ ++L + DT GQ+
Sbjct: 10 VGKSALTVRFLTKRFIGEYEPNLESLYSRQVTIDGEQVSLEIQDTPGQQ 58
Score = 38.8 bits (91), Expect = 7e-04
Identities = 27/105 (25%), Positives = 46/105 (43%), Gaps = 18/105 (17%)
Query: 112 DVFQICFSLVNPASFENVRAKWYPEVRHHCP---STPIILVGTKLDLRDDKETIEKLKEK 168
D F + +S+ + +SF+ V +R P+ILVG K DL ++
Sbjct: 74 DGFVLVYSITDRSSFDVVSQ-LLQLIREIKKRDGEIPVILVGNKADLLHSRQ-------- 124
Query: 169 KLAPITYPQGLSMAKEIGAVKYLECSA-LTQKGLKTVFDEAIRAV 212
++ +G +A E+G + + E SA ++ VF E R V
Sbjct: 125 ----VSTEEGQKLALELGCL-FFEVSAAENYLEVQNVFHELCREV 164
>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 = 54.9 bits (132), Expect = 2e-09
Identities = 45/184 (24%), Positives = 68/184 (36%), Gaps = 50/184 (27%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
VGK+ LL+ + N F G YI T+ D V ++G+ + L +WDTAGQE + + Y
Sbjct: 17 VGKSSLLLRFADNTFSGSYITTIGVDFKIRTVEINGERVKLQIWDTAGQERFRTITSTYY 76
Query: 61 PQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSL 120
T G+ V+D +
Sbjct: 77 RGT---------------------HGVIVVYD---------------------------V 88
Query: 121 VNPASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLS 180
N SF NV+ +W E+ +C +LVG K D + K + K + +
Sbjct: 89 TNGESFVNVK-RWLQEIEQNCDDVCKVLVGNKNDDPERKVVETEDAYKFAGQMGISLFET 147
Query: 181 MAKE 184
AKE
Sbjct: 148 SAKE 151
>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 = 53.3 bits (128), Expect = 5e-09
Identities = 51/213 (23%), Positives = 83/213 (38%), Gaps = 64/213 (30%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVM-VDGKPINLGLWDTAGQEDYDRLRPLSY 60
VGK+CLL +T F + T+ + ++ V+G+ I L +WDTAGQE R R ++
Sbjct: 13 VGKSCLLHQFTEKKFMADCPHTIGVEFGTRIIEVNGQKIKLQIWDTAGQE---RFRAVTR 69
Query: 61 PQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSL 120
Y +A G V+D R+ + +
Sbjct: 70 --------------SYYRGAA----GALMVYDITRRSTYNHLSS---------------- 95
Query: 121 VNPASFENVRAKWYPEVRHHC-PSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGL 179
W + R+ P+T I L+G K DL ++ +TY +
Sbjct: 96 ------------WLTDARNLTNPNTVIFLIGNKADLEAQRD------------VTYEEAK 131
Query: 180 SMAKEIGAVKYLECSALTQKGLKTVFDEAIRAV 212
A E G + +LECSA T + ++ F E + +
Sbjct: 132 QFADENGLL-FLECSAKTGENVEDAFLETAKKI 163
>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 = 53.2 bits (128), Expect = 6e-09
Identities = 46/163 (28%), Positives = 61/163 (37%), Gaps = 51/163 (31%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLS 59
VGKTCL + FP T+ D V +DG+ I + LWDTAGQE R R
Sbjct: 12 NVGKTCLTYRFCAGRFPERTEATIGVDFRERTVEIDGERIKVQLWDTAGQE---RFRK-- 66
Query: 60 YPQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFS 119
SM + + + AV VF +
Sbjct: 67 ------SMVQH--------------------YYRNVHAV--------------VF--VYD 84
Query: 120 LVNPASFENVRAKWYPEVRHHC--PSTPIILVGTKLDLRDDKE 160
+ N ASF ++ + W E H P ILVG K DLR+ +
Sbjct: 85 VTNMASFHSLPS-WIEECEQHSLPNEVPRILVGNKCDLREQIQ 126
>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 = 52.3 bits (125), Expect = 1e-08
Identities = 31/111 (27%), Positives = 52/111 (46%), Gaps = 2/111 (1%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
VGKTCLL +T N F +I T+ D + VDG + + +WDTAGQE Y + Y
Sbjct: 11 VGKTCLLCRFTDNEFHSSHISTIGVDFKMKTIEVDGIKVRIQIWDTAGQERYQTITKQYY 70
Query: 61 PQT-GLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKR 110
+ G+ + +I + + + + E ++ +L ++KR
Sbjct: 71 RRAQGIFLVYDISSERSYQHIMKWVSDVDEYAPEGVQKILIGNKADEEQKR 121
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 53.1 bits (127), Expect = 1e-08
Identities = 52/212 (24%), Positives = 89/212 (41%), Gaps = 69/212 (32%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPL- 58
VGK+ LL+S+ +++ + PT+ D + V GK + L +WDTAGQE R R L
Sbjct: 24 GVGKSSLLVSFISSSVE-DLAPTIGVDFKIKQLTVGGKRLKLTIWDTAGQE---RFRTLT 79
Query: 59 -SYPQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQIC 117
SY + +G+ V+D R
Sbjct: 80 SSYYRNA--------------------QGIILVYDVTRR--------------------- 98
Query: 118 FSLVNPASFENVRAKWYPEVRHHCPSTPII--LVGTKLDLRDDKETIEKLKEKKLAPITY 175
+F N+ W EV + + + LVG K+D +++ ++
Sbjct: 99 ------ETFTNLSDVWGKEVELYSTNQDCVKMLVGNKVDRESERD------------VSR 140
Query: 176 PQGLSMAKEIGAVKYLECSALTQKGLKTVFDE 207
+G+++AKE G + +LECSA T++ ++ F+E
Sbjct: 141 EEGMALAKEHGCL-FLECSAKTRENVEQCFEE 171
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 52.8 bits (127), Expect = 1e-08
Identities = 40/160 (25%), Positives = 64/160 (40%), Gaps = 50/160 (31%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLS 59
VGKT + + T F +YIPT+ + + + PI +WDTAGQE + LR
Sbjct: 19 GVGKTTFVKRHLTGEFEKKYIPTLGVEVHPLKFYTNCGPICFNVWDTAGQEKFGGLRDGY 78
Query: 60 YPQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFS 119
Y I +C AI I F
Sbjct: 79 Y----------IKG----QC--------------AI--------------------IMFD 90
Query: 120 LVNPASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDK 159
+ + +++NV W+ ++ C + PI+LVG K+D++D +
Sbjct: 91 VTSRITYKNV-PNWHRDIVRVCENIPIVLVGNKVDVKDRQ 129
>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 = 52.1 bits (125), Expect = 2e-08
Identities = 44/206 (21%), Positives = 80/206 (38%), Gaps = 63/206 (30%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSA-NVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
VGKTC++ + + F T+ +++ + + GK + L +WDTAGQE R R
Sbjct: 14 VGKTCVVQRFKSGTFSERQGNTIGVDFTMKTLEIQGKRVKLQIWDTAGQE---RFR---- 66
Query: 61 PQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSL 120
+TQ + + A A+ I + +
Sbjct: 67 --------------------TITQ----SYYRSANGAI-----------------IAYDI 85
Query: 121 VNPASFENVRAKWYPEVRHH-CPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGL 179
+SFE+V W EV + + ++L+G K DL + +E + + +
Sbjct: 86 TRRSSFESV-PHWIEEVEKYGASNVVLLLIGNKCDLEEQRE------------VLFEEAC 132
Query: 180 SMAKEIGAVKYLECSALTQKGLKTVF 205
++A+ G + LE SA ++ F
Sbjct: 133 TLAEHYGILAVLETSAKESSNVEEAF 158
>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 = 49.6 bits (119), Expect = 1e-07
Identities = 36/159 (22%), Positives = 61/159 (38%), Gaps = 50/159 (31%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
GKT + + T F +Y+ T+ + + + + I +WDTAGQE + LR Y
Sbjct: 11 TGKTTFVKRHLTGEFEKKYVATLGVEVHPLDFHTNRGKIRFNVWDTAGQEKFGGLRDGYY 70
Query: 61 PQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSL 120
I +C AI I F +
Sbjct: 71 ----------IQG----QC--------------AI--------------------IMFDV 82
Query: 121 VNPASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDK 159
+ +++NV W+ ++ C + PI+L G K+D++D K
Sbjct: 83 TSRVTYKNV-PNWHRDLVRVCENIPIVLCGNKVDIKDRK 120
>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 = 49.4 bits (118), Expect = 1e-07
Identities = 48/213 (22%), Positives = 84/213 (39%), Gaps = 62/213 (29%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
VGK+ L + + F +Y PT+ D+Y V VDG+ L + DTAG E + +R L Y
Sbjct: 11 GVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDGQQCMLEILDTAGTEQFTAMRDL-Y 69
Query: 61 PQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSL 120
+ G +G F + +S+
Sbjct: 70 MKNG--------------------QG---------------------------FVLVYSI 82
Query: 121 VNPASFENVRAKWYPEVR-HHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGL 179
++F +++ +R P+ILVG K DL D++ + QG
Sbjct: 83 TAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDER------------VVGKEQGQ 130
Query: 180 SMAKEIGAVKYLECSALTQKGLKTVFDEAIRAV 212
++A++ G +LE SA + + +F + +R +
Sbjct: 131 NLARQWGC-AFLETSAKAKINVNEIFYDLVRQI 162
>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 = 48.0 bits (114), Expect = 4e-07
Identities = 48/216 (22%), Positives = 83/216 (38%), Gaps = 65/216 (30%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLS 59
+VGKT L Y ++F ++ TV D V + K I L +WDTAGQE Y +
Sbjct: 11 SVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVYRNDKRIKLQIWDTAGQERYRTITTAY 70
Query: 60 YPQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFS 119
Y GA+ ++ + +
Sbjct: 71 YR----------GAMGFI--------------------------------------LMYD 82
Query: 120 LVNPASFENVRAKWYPEVRHHCPSTP-IILVGTKLDLRDDKETIEKLKEKKLAPITYPQG 178
+ N SF V+ W +++ + +ILVG K D+ D++ ++ +G
Sbjct: 83 ITNEESFNAVQ-DWSTQIKTYSWDNAQVILVGNKCDMEDER------------VVSAERG 129
Query: 179 LSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLC 214
+A ++G ++ E SA +K VF E + ++C
Sbjct: 130 RQLADQLG-FEFFEASAKENINVKQVF-ERLVDIIC 163
>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 = 47.5 bits (113), Expect = 5e-07
Identities = 46/196 (23%), Positives = 72/196 (36%), Gaps = 58/196 (29%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPT-VFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLS 59
AVGK+ L+ + + + + + T Y N +GK I + WDTAGQE + + S
Sbjct: 10 AVGKSKLVERFLMDGYEPQQLSTYALTLYKHNAKFEGKTILVDFWDTAGQERFQTMHA-S 68
Query: 60 YPQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFS 119
Y Y + A + F
Sbjct: 69 Y---------------YHKAHACI--------------------------------LVFD 81
Query: 120 LVNPASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDKETIEK---LKEKKLAPITYP 176
+ +++N+ KWY E+R + P P I+V K+DL D +K EK P+ Y
Sbjct: 82 VTRKITYKNLS-KWYEELREYRPEIPCIVVANKIDL--DPSVTQKKFNFAEKHNLPLYY- 137
Query: 177 QGLSMAKEIGAVKYLE 192
+S A VK +
Sbjct: 138 --VSAADGTNVVKLFQ 151
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 47.6 bits (113), Expect = 1e-06
Identities = 53/212 (25%), Positives = 85/212 (40%), Gaps = 68/212 (32%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVM-VDGKPINLGLWDTAGQEDYDRLRPLSY 60
VGK+ +L +T N F E T+ ++ + V+GK + +WDTAGQE Y + Y
Sbjct: 23 VGKSNILSRFTRNEFCLESKSTIGVEFATRTLQVEGKTVKAQIWDTAGQERYRAITSAYY 82
Query: 61 PQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSL 120
GAV G V+D + K++
Sbjct: 83 R----------GAV-----------GALLVYD------------ITKRQ----------- 98
Query: 121 VNPASFENVRAKWYPEVRHHCPSTPII-LVGTKLDLRDDKETIEKLKEKKLAPITYPQGL 179
+F+NV+ +W E+R H S +I + G K DL L + G
Sbjct: 99 ----TFDNVQ-RWLRELRDHADSNIVIMMAGNKSDL------------NHLRSVAEEDGQ 141
Query: 180 SMAKEIGAVKYLECSAL----TQKGLKTVFDE 207
++A++ G + +LE SAL +K +T+ E
Sbjct: 142 ALAEKEG-LSFLETSALEATNVEKAFQTILLE 172
>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 = 46.8 bits (111), Expect = 1e-06
Identities = 50/220 (22%), Positives = 84/220 (38%), Gaps = 74/220 (33%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTV---FDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPL 58
VGK+ L+ Y TN F + T+ F N ++ VDG + L +WDTAGQE + LR
Sbjct: 16 VGKSSLMNRYVTNKFDTQLFHTIGVEFLN--KDLEVDGHFVTLQIWDTAGQERFRSLR-- 71
Query: 59 SYPQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICF 118
P + D + F
Sbjct: 72 ----------------------------------------------TPFYRGSDCCLLTF 85
Query: 119 SLVNPASFENVRAKW------YPEVRHHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAP 172
S+ + SF+N+ + W Y +V+ S P +++G K+D+ + + + E+ +
Sbjct: 86 SVDDSQSFQNL-SNWKKEFIYYADVK-EPESFPFVILGNKIDIPERQVSTEEAQ------ 137
Query: 173 ITYPQGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAV 212
+ ++ G Y E SA + F+EA+R V
Sbjct: 138 -------AWCRDNGDYPYFETSAKDATNVAAAFEEAVRRV 170
>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 = 46.0 bits (109), Expect = 2e-06
Identities = 29/101 (28%), Positives = 43/101 (42%), Gaps = 16/101 (15%)
Query: 113 VFQICFSLVNPASFENVRAKWYPEVRHHCP--STPIILVGTKLDLRDDKETIEKLKEKKL 170
V + + + N SF N ++W VR H TP +LVG K DL D +E
Sbjct: 79 VVCVVYDVTNEVSFNNC-SRWINRVRTHSHGLHTPGVLVGNKCDLTDRRE---------- 127
Query: 171 APITYPQGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRA 211
+ Q ++A+ +K+ E SA G + F RA
Sbjct: 128 --VDAAQAQALAQANT-LKFYETSAKEGVGYEAPFLSLARA 165
>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 = 43.9 bits (104), Expect = 5e-06
Identities = 31/155 (20%), Positives = 45/155 (29%), Gaps = 51/155 (32%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVM-VDGKPINLGLWDTAGQEDYDRLRPLSY 60
GK+ LL FP E + D + + + VDG L +WD G+E+
Sbjct: 10 SGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREE--------- 60
Query: 61 PQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSL 120
+ K D + + L
Sbjct: 61 ------------------------------LKFEHIIFM---------KWADAILLVYDL 81
Query: 121 VNPASFENVRA--KWYPEVRHHCPSTPIILVGTKL 153
+ S V W P +R P+ILVG KL
Sbjct: 82 TDRESLNEVSRLIAWLPNLRKLGGKIPVILVGNKL 116
>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 = 44.7 bits (106), Expect = 6e-06
Identities = 37/169 (21%), Positives = 61/169 (36%), Gaps = 55/169 (32%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNY-SANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
+GKT L++ Y F EYI T+ N+ + + G I +WD GQ ++ + PL
Sbjct: 11 IGKTSLMVKYVEGEFDEEYIQTLGVNFMEKTISIRGTEITFSIWDLGGQREFINMLPL-- 68
Query: 61 PQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSL 120
V +A+ F L
Sbjct: 69 -----------------------------VCKDAV-----------------AILFMFDL 82
Query: 121 VNPASFENVRAKWYPEVRHHCPSTPIILVGTKLDL-----RDDKETIEK 164
++ +++ +WY + R + ILVGTK DL +++E I K
Sbjct: 83 TRKSTLNSIK-EWYRQARGFNKTAIPILVGTKYDLFADLPPEEQEEITK 130
>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 = 45.1 bits (107), Expect = 6e-06
Identities = 28/108 (25%), Positives = 45/108 (41%), Gaps = 24/108 (22%)
Query: 111 CDVFQICFSLVNPASFENVRAKWYPEVR------HHCPSTPIILVGTKLDLRDDKETIEK 164
D + I +S+ + +SFE E+R PIILVG K DL +E
Sbjct: 73 GDAYVIVYSVTDRSSFEKA-----SELRIQLRRARQAEDIPIILVGNKSDLVRSRE---- 123
Query: 165 LKEKKLAPITYPQGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAV 212
++ +G + A K++E SA Q + +F+ +R V
Sbjct: 124 --------VSVQEGRACAVVF-DCKFIETSAALQHNVDELFEGIVRQV 162
>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 = 44.5 bits (105), Expect = 7e-06
Identities = 56/220 (25%), Positives = 84/220 (38%), Gaps = 87/220 (39%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFD-NYSANVMVD---------GKPINLGLWDTAGQE 50
+VGKTCL+ + + VFD NY A + VD G P +L LWDTAGQE
Sbjct: 10 SVGKTCLINRFCKD---------VFDKNYKATIGVDFEMERFEVLGVPFSLQLWDTAGQE 60
Query: 51 DYDRLRPLSYPQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKR 110
+ K I + Y +G + +
Sbjct: 61 RF----------------KCIASTYY--------RGAQAII------------------- 77
Query: 111 CDVFQICFSLVNPASFENVRAKWYPEVRHHCPSTPII-LVGTKLDLRDDKETIEKLKEKK 169
I F L + AS E+ R ++ + PS+ ++ LVGTK DL
Sbjct: 78 -----IVFDLTDVASLEHTRQWLEDALKENDPSSVLLFLVGTKKDL-------------- 118
Query: 170 LAPITYPQ----GLSMAKEIGAVKYLECSALTQKGLKTVF 205
+P Y + +A+E+ A +Y SALT + ++ F
Sbjct: 119 SSPAQYALMEQDAIKLAREMKA-EYWAVSALTGENVRDFF 157
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 44.7 bits (106), Expect = 1e-05
Identities = 34/159 (21%), Positives = 57/159 (35%), Gaps = 50/159 (31%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
GKT + + T F +Y PT+ + + + + I WDTAGQE + LR Y
Sbjct: 24 TGKTTFVKRHLTGEFEKKYEPTIGVEVHPLDFFTNCGKIRFYCWDTAGQEKFGGLRDGYY 83
Query: 61 PQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSL 120
+C+ + +FD R VPT
Sbjct: 84 IHG--------------QCAII-------MFDVTARLTYKNVPT---------------- 106
Query: 121 VNPASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDK 159
W+ ++ C + PI+L G K+D+++ +
Sbjct: 107 ------------WHRDLCRVCENIPIVLCGNKVDVKNRQ 133
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 43.6 bits (102), Expect = 2e-05
Identities = 50/196 (25%), Positives = 72/196 (36%), Gaps = 64/196 (32%)
Query: 14 NAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSYPQTGLSMAKEIG 72
+ F Y T+ D S + +D P+ L LWDTAGQE + L P
Sbjct: 3 DTFDNNYQSTIGIDFLSKTLYLDEGPVRLQLWDTAGQERFRSLIP--------------- 47
Query: 73 AVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSLVNPASFENVRAK 132
Y+ SA AI + + + N SFEN K
Sbjct: 48 --SYIRDSA-----------AAI--------------------VVYDITNRQSFENT-TK 73
Query: 133 WYPEVRHHCPSTPII-LVGTKLDLRDDKETIEKLKEKKLAPITYPQGLSMAKEIGAVKYL 191
W ++ + II LVG K DL D L +TY +G+ A+E + +
Sbjct: 74 WIQDILNERGKDVIIALVGNKTDLGD------------LRKVTYEEGMQKAQEYNTM-FH 120
Query: 192 ECSALTQKGLKTVFDE 207
E SA +K +F +
Sbjct: 121 ETSAKAGHNIKVLFKK 136
>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 = 42.6 bits (100), Expect = 3e-05
Identities = 22/52 (42%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 2 VGKTCLLISYTTNAFP-GEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDY 52
VGKTCL+ +T FP G+ D V + G+ I L +WDTAGQE +
Sbjct: 18 VGKTCLVRRFTQGLFPPGQGATIGVDFMIKTVEIKGEKIKLQIWDTAGQERF 69
>gnl|CDD|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 = 40.8 bits (96), Expect = 1e-04
Identities = 42/219 (19%), Positives = 77/219 (35%), Gaps = 69/219 (31%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSAN-VMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
VGK+C++ Y F +Y+PT+ +Y V V K + + +D +G +Y +R Y
Sbjct: 11 VGKSCIIKRYCEGRFVSKYLPTIGIDYGVKKVSVRNKEVRVNFFDLSGHPEYLEVRNEFY 70
Query: 61 PQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSL 120
T +G+ V+D +
Sbjct: 71 KDT---------------------QGVLLVYD---------------------------V 82
Query: 121 VNPASFENVRAKWYPEVRHHC------PSTPIILVGTKLDLRDDKETIEKLKEKKLAPIT 174
+ SFE + W E++ + +++ K+DL + E
Sbjct: 83 TDRQSFEALD-SWLKEMKQEGGPHGNMENIVVVVCANKIDLTKHRAVSED---------- 131
Query: 175 YPQGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVL 213
+G A+ G KY E SA T +G+ +F +++
Sbjct: 132 --EGRLWAESKGF-KYFETSACTGEGVNEMFQTLFSSIV 167
>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 = 40.8 bits (95), Expect = 2e-04
Identities = 52/218 (23%), Positives = 86/218 (39%), Gaps = 63/218 (28%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
VGKT L+ +T + F TV D V + GK I L +WDTAGQE ++ + Y
Sbjct: 11 VGKTSLMERFTDDTFCEACKSTVGVDFKIKTVELRGKKIRLQIWDTAGQERFNSITSAYY 70
Query: 61 PQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSL 120
+ KG+ V+D + KK+
Sbjct: 71 R---------------------SAKGIILVYD------------ITKKE----------- 86
Query: 121 VNPASFENVRAKWYPEV-RHHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGL 179
+F+++ KW + ++ ++LVG KLD D+E IT QG
Sbjct: 87 ----TFDDL-PKWMKMIDKYASEDAELLLVGNKLDCETDRE------------ITRQQGE 129
Query: 180 SMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVP 217
A++I +++ E SA + +F + + +L +P
Sbjct: 130 KFAQQITGMRFCEASAKDNFNVDEIFLKLVDDILKKMP 167
>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 = 40.4 bits (94), Expect = 3e-04
Identities = 36/158 (22%), Positives = 58/158 (36%), Gaps = 50/158 (31%)
Query: 3 GKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSYP 61
GKT + + T F +Y+ T+ + + + PI +WDTAGQE + LR Y
Sbjct: 7 GKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIRFNVWDTAGQEKFGGLRDGYYI 66
Query: 62 QTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSLV 121
Q +C+ + +FD R VP
Sbjct: 67 QG--------------QCAII-------MFDVTARVTYKNVPN----------------- 88
Query: 122 NPASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDK 159
W+ ++ C + PI+L G K+D++D K
Sbjct: 89 -----------WHRDLVRVCENIPIVLCGNKVDVKDRK 115
>gnl|CDD|206692 cd04107, Rab32_Rab38, Rab GTPase families 18 (Rab18) and 32
(Rab32). Rab38/Rab32 subfamily. Rab32 and Rab38 are
members of the Rab family of small GTPases. Human Rab32
was first identified in platelets but it is expressed in
a variety of cell types, where it functions as an
A-kinase anchoring protein (AKAP). Rab38 has been shown
to be melanocyte-specific. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 201
Score = 39.2 bits (92), Expect = 6e-04
Identities = 44/220 (20%), Positives = 74/220 (33%), Gaps = 75/220 (34%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMV--DGKPINLGLWDTAGQEDYDRLRPL 58
VGKT ++ Y F Y T+ +++ V+ + L LWD AGQE + + +
Sbjct: 10 GVGKTSIIKRYVHGVFSQHYKATIGVDFALKVIEWDPNTVVRLQLWDIAGQERFGGMTRV 69
Query: 59 SYPQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICF 118
Y A+ A+ I F
Sbjct: 70 YYK-------------------------------GAVGAI-----------------IVF 81
Query: 119 SLVNPASFENVRAKWYPEV--RHHCP---STPIILVGTKLDL--RDDKETIEKLKEKKLA 171
+ P++FE V KW ++ + P P +L+ K DL + E++ +
Sbjct: 82 DVTRPSTFEAV-LKWKADLDSKVTLPNGEPIPALLLANKCDLKKERLAKDPEQMDQF--- 137
Query: 172 PITYPQGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRA 211
KE G + + E SA + +EA+R
Sbjct: 138 ----------CKENGFIGWFETSAKENINI----EEAMRF 163
>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 = 37.4 bits (88), Expect = 0.004
Identities = 16/70 (22%), Positives = 30/70 (42%), Gaps = 15/70 (21%)
Query: 145 PIILVGTKLDLRDDKETIEKLKEK---KLAPITYPQGLSMAKEIGAVKYLECSALTQKGL 201
+++V K DL D++T E+ K++ KL + + + SALT +G+
Sbjct: 285 ALVIVVNKWDLVKDEKTREEFKKELRRKLPFLDF------------APIVFISALTGQGV 332
Query: 202 KTVFDEAIRA 211
+ D
Sbjct: 333 DKLLDAIDEV 342
>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 = 36.8 bits (85), Expect = 0.004
Identities = 47/218 (21%), Positives = 76/218 (34%), Gaps = 58/218 (26%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDN-YSANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
VGKT ++ + FP EYIPT Y V++ G+ +L + D ++ Y
Sbjct: 11 VGKTAIVRQFLAQEFPEEYIPTEHRRLYRPAVVLSGRVYDLHI------LDVPNMQR--Y 62
Query: 61 PQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSL 120
P T E +GL+ F + + +
Sbjct: 63 PGTAGQ-----------EWMDPRFRGLRNS---------------------RAFILVYDI 90
Query: 121 VNPASFENVRA--KWYPEVR-HHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQ 177
+P SF V+ + E R PI++VG K D + + AP
Sbjct: 91 CSPDSFHYVKLLRQQILETRPAGNKEPPIVVVGNKRDQ----------QRHRFAP---RH 137
Query: 178 GLS-MAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLC 214
LS + ++ YLECSA + +F E + +
Sbjct: 138 VLSVLVRKSWKCGYLECSAKYNWHILLLFKELLISATT 175
>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 = 36.7 bits (85), Expect = 0.004
Identities = 44/225 (19%), Positives = 79/225 (35%), Gaps = 63/225 (28%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLSYP 61
VGKT L+ + + F ++ TV + +S V G + + + DT+G + +R LS
Sbjct: 10 VGKTALIQRFLYDTFEPKHRRTVEELHSKEYEVAGVKVTIDILDTSGSYSFPAMRKLSIQ 69
Query: 62 QTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSLV 121
D F + +S+
Sbjct: 70 NG------------------------------------------------DAFALVYSVD 81
Query: 122 NPASFENVRA--KWYPEVRHHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGL 179
+P SFE V+ + EV+ PI++VG K+D +++ + L
Sbjct: 82 DPESFEEVKRLREEILEVKED-KFVPIVVVGNKIDSLAERQ------------VEAADAL 128
Query: 180 SMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKR 224
S + ++E SA + + VF E ++ P P +R
Sbjct: 129 STVELDWNNGFVEASAKDNENVTEVFKELLQQANLPSWLSPALRR 173
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 36.2 bits (85), Expect = 0.008
Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 12/64 (18%)
Query: 144 TPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLSMAKEIGAVKYLECSALTQKGLKT 203
TP+ILV K+DL DKE + L E+ +++ + + + SAL +
Sbjct: 114 TPVILVLNKIDLVKDKEELLPLLEE------------LSELMDFAEIVPISALKGDNVDE 161
Query: 204 VFDE 207
+ D
Sbjct: 162 LLDV 165
>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 = 35.5 bits (83), Expect = 0.008
Identities = 17/64 (26%), Positives = 27/64 (42%), Gaps = 12/64 (18%)
Query: 144 TPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLSMAKEIGAVKYLECSALTQKGLKT 203
TP+ILV K+DL DKE + L EK + + + SAL + +
Sbjct: 112 TPVILVLNKIDLVKDKEDLLPLLEK------------LKELHPFAEIFPISALKGENVDE 159
Query: 204 VFDE 207
+ +
Sbjct: 160 LLEY 163
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 36.2 bits (85), Expect = 0.008
Identities = 22/69 (31%), Positives = 30/69 (43%), Gaps = 17/69 (24%)
Query: 145 PIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLSMAKEIGAVKYLECSALTQKGLKTV 204
P ILV K+DL D++E EK +LA SA+T +GL
Sbjct: 273 PRILVLNKIDLLDEEEEREKRAALELA-------------ALGGPVFLISAVTGEGL--- 316
Query: 205 FDEAIRAVL 213
DE +RA+
Sbjct: 317 -DELLRALW 324
>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 = 35.3 bits (82), Expect = 0.010
Identities = 16/66 (24%), Positives = 30/66 (45%), Gaps = 12/66 (18%)
Query: 145 PIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLSMAKEIGAVKYLECSALTQKGLKTV 204
P++LV K+DL + E E L+E+KL + + + + SAL +G+ +
Sbjct: 106 PVLLVLNKIDLVPESEEEELLRERKL------------ELLPDLPVIAVSALPGEGIDEL 153
Query: 205 FDEAIR 210
+
Sbjct: 154 RKKIAE 159
>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 = 34.8 bits (80), Expect = 0.013
Identities = 17/58 (29%), Positives = 27/58 (46%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLS 59
VGK+ L++ + F YIPT+ D Y + L + DT G + ++ LS
Sbjct: 12 VGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCSKSICTLQITDTTGSHQFPAMQRLS 69
>gnl|CDD|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 = 35.3 bits (81), Expect = 0.014
Identities = 47/213 (22%), Positives = 77/213 (36%), Gaps = 63/213 (29%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNY-SANVMVDGKPINLGLWDTAGQEDYDRLRPLSY 60
VGK +L S + Y + +Y + +++DG+ + L LWDT+GQ + + SY
Sbjct: 17 VGKGEILASLQDGSTESPYGYNMGIDYKTTTILLDGRRVKLQLWDTSGQGRFCTIFR-SY 75
Query: 61 PQTGLSMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPKKKRCDVFQICFSL 120
+ GA +G+ V+D +
Sbjct: 76 SR---------GA-----------QGIILVYD---------------------------I 88
Query: 121 VNPASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLS 180
N SF+ + +W E+ H P P ILVG +L L ++ + + Y +
Sbjct: 89 TNRWSFDGID-RWIKEIDEHAPGVPKILVGNRLHLAFKRQVATEQAQ------AYAERNG 141
Query: 181 MAKEIGAVKYLECSALTQKGLKTVFDEAIRAVL 213
M + E S L + F E R VL
Sbjct: 142 MT-------FFEVSPLCNFNITESFTELARIVL 167
>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 = 34.7 bits (81), Expect = 0.016
Identities = 22/58 (37%), Positives = 27/58 (46%), Gaps = 13/58 (22%)
Query: 145 PIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLSMAKEIGAVKYLECSALTQKGLK 202
P I+V K+DL D +E EKLKE KE+ K SALT +GL
Sbjct: 116 PRIVVLNKIDLLDAEERFEKLKELL-------------KELKGKKVFPISALTGEGLD 160
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 35.4 bits (83), Expect = 0.019
Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 16/70 (22%)
Query: 145 PIILVGTKLDLRDDKETIEKLKEK---KLAPITYPQGLSMAKEIGAVKYLECSALTQKGL 201
+++V K DL D+K T+E+ K++ +L + Y + SALT +G+
Sbjct: 286 ALVIVVNKWDLVDEK-TMEEFKKELRRRLPFLDY------------APIVFISALTGQGV 332
Query: 202 KTVFDEAIRA 211
+ + A
Sbjct: 333 DKLLEAIDEA 342
>gnl|CDD|236584 PRK09602, PRK09602, translation-associated GTPase; Reviewed.
Length = 396
Score = 35.2 bits (82), Expect = 0.021
Identities = 27/87 (31%), Positives = 37/87 (42%), Gaps = 22/87 (25%)
Query: 143 STPIILVGTKLDLRDDKETIEKLKEKKLAPITYP------QGLSMAKEIGAVKYL----- 191
S P+++ K DL +E IE+LKE+K I P L A + G + Y+
Sbjct: 217 SKPMVIAANKADLPPAEENIERLKEEKY-YIVVPTSAEAELALRRAAKAGLIDYIPGDSD 275
Query: 192 -----ECSALTQKGLKTVFDEAIRAVL 213
E S +K L E IR VL
Sbjct: 276 FEILGELSEKQKKAL-----EYIREVL 297
>gnl|CDD|206682 cd01895, EngA2, EngA2 GTPase contains the second domain of EngA.
This EngA2 subfamily CD represents the second GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. Since the sequences of the
two domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family. Although the exact function of
these proteins has not been elucidated, studies have
revealed that the E. coli EngA homolog, Der, and
Neisseria gonorrhoeae EngA are essential for cell
viability. A recent report suggests that E. coli Der
functions in ribosome assembly and stability.
Length = 174
Score = 33.6 bits (78), Expect = 0.039
Identities = 16/71 (22%), Positives = 31/71 (43%), Gaps = 16/71 (22%)
Query: 145 PIILVGTKLDLRDDK-ETIEKLKEK---KLAPITYPQGLSMAKEIGAVKYLECSALTQKG 200
+I+V K DL + +T+++ +++ KL + Y + SALT +G
Sbjct: 115 ALIIVVNKWDLVEKDEKTMKEFEKELRRKLPFLDY------------APIVFISALTGQG 162
Query: 201 LKTVFDEAIRA 211
+ +FD
Sbjct: 163 VDKLFDAIKEV 173
>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 = 33.6 bits (77), Expect = 0.052
Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGK-PINLGLWDTAGQ 49
A GKT L+ + F Y T+ D +S + + G + L +WD GQ
Sbjct: 10 ASGKTSLIRRFAQEGFGKSYKQTIGLDFFSRRITLPGSLNVTLQVWDIGGQ 60
>gnl|CDD|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 = 33.1 bits (76), Expect = 0.059
Identities = 17/55 (30%), Positives = 22/55 (40%), Gaps = 4/55 (7%)
Query: 1 AVGKTCLLISYTTNAFPGEYIPTV---FDNYSANVMVDGKPINLGLWDTAGQEDY 52
VGKT L F G+ T ++ + K I L +WD GQE Y
Sbjct: 11 GVGKTSLCKQLIGEKFDGDESSTHGINVQDWKIPA-PERKKIRLNVWDFGGQEIY 64
Score = 29.6 bits (67), Expect = 0.84
Identities = 12/33 (36%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 142 PSTPIILVGTKLD-LRDDKETIEKLKEKKLAPI 173
+P+ILVGT +D D+ + L +K A I
Sbjct: 105 GVSPVILVGTHIDESCDEDILKKALNKKFPAII 137
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 33.5 bits (78), Expect = 0.077
Identities = 18/66 (27%), Positives = 26/66 (39%), Gaps = 17/66 (25%)
Query: 145 PIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLSMAKEIGAVKYLECSALTQKGLKTV 204
P I+V K+DL + +E +E+ KEK K SALT +GL +
Sbjct: 276 PQIVVANKMDLPEAEENLEEFKEKL-----------------GPKVFPISALTGQGLDEL 318
Query: 205 FDEAIR 210
Sbjct: 319 LYAVAE 324
>gnl|CDD|133326 cd04126, Rab20, Rab GTPase family 20 (Rab20). Rab20 is one of
several Rab proteins that appear to be restricted in
expression to the apical domain of murine polarized
epithelial cells. It is expressed on the apical side of
polarized kidney tubule and intestinal epithelial
cells, and in non-polarized cells. It also localizes to
vesico-tubular structures below the apical brush border
of renal proximal tubule cells and in the apical region
of duodenal epithelial cells. Rab20 has also been shown
to colocalize with vacuolar H+-ATPases (V-ATPases) in
mouse kidney cells, suggesting a role in the regulation
of V-ATPase traffic in specific portions of the
nephron. It was also shown to be one of several
proteins whose expression is upregulated in human
myelodysplastic syndrome (MDS) patients. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins.
Length = 220
Score = 33.0 bits (75), Expect = 0.078
Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 4/54 (7%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRL 55
VGKT LL Y F + + TV A + P N+ +WDTAG+E + L
Sbjct: 11 VGKTSLLHRYMERRFK-DTVSTV---GGAFYLKQWGPYNISIWDTAGREQFHGL 60
>gnl|CDD|206686 cd01899, Ygr210, Ygr210 GTPase. Ygr210 is a member of Obg-like
family and present in archaea and fungi. They are
characterized by a distinct glycine-rich motif
immediately following the Walker B motif. The Ygr210 and
YyaF/YchF subfamilies appear to form one major branch of
the Obg-like family. Among eukaryotes, the Ygr210
subfamily is represented only in fungi. These fungal
proteins form a tight cluster with their archaeal
orthologs, which suggests the possibility of horizontal
transfer from archaea to fungi.
Length = 318
Score = 33.4 bits (77), Expect = 0.086
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 6/53 (11%)
Query: 145 PIILVGTKLDLRDDKETIEKLKEKKLAPITYP------QGLSMAKEIGAVKYL 191
P+++ K D+ D +E I KL+ K I P L A + G +KY+
Sbjct: 216 PMVIAANKADIPDAEENISKLRLKYPDEIVVPTSAEAELALRRAAKQGLIKYV 268
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 32.9 bits (76), Expect = 0.10
Identities = 15/61 (24%), Positives = 25/61 (40%), Gaps = 14/61 (22%)
Query: 145 PIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLSMAKEIG-AVKYLECSALTQKGLKT 203
P LV K+DL D++E E+ K + + +G SA + G+K
Sbjct: 277 PRWLVFNKIDLLDEEEAEERAKA-------------IVEALGWEGPVYLISAASGLGVKE 323
Query: 204 V 204
+
Sbjct: 324 L 324
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 32.5 bits (75), Expect = 0.13
Identities = 23/68 (33%), Positives = 37/68 (54%), Gaps = 16/68 (23%)
Query: 145 PIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLSMAKEIGAVKYLECSALTQKGLKTV 204
P I+V K+DL D+E +E+LK+ +A+ +G + SALT++GL
Sbjct: 277 PRIVVLNKIDLPLDEEELEELKKA------------LAEALGWEVFYLISALTREGL--- 321
Query: 205 FDEAIRAV 212
DE +RA+
Sbjct: 322 -DELLRAL 328
>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 = 31.4 bits (72), Expect = 0.24
Identities = 16/69 (23%), Positives = 32/69 (46%), Gaps = 15/69 (21%)
Query: 145 PIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLSMAKEIGAVKYLECSALTQKGLKTV 204
P+I+V K+DL +++ E KE E + ++ S LT++G+ +
Sbjct: 114 PVIVVLNKIDLLTEEDLSEIEKE---------------LEKEGEEVIKISTLTEEGVDEL 158
Query: 205 FDEAIRAVL 213
++A +L
Sbjct: 159 KNKACELLL 167
>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 = 31.6 bits (73), Expect = 0.26
Identities = 19/58 (32%), Positives = 27/58 (46%), Gaps = 14/58 (24%)
Query: 145 PIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLSMAKEIGAVKYLECSALTQKGLK 202
P I+V K+DL D++E E LKE + + +G SALT +GL
Sbjct: 275 PRIVVLNKIDLLDEEELEELLKE-------------LKEALG-KPVFPISALTGEGLD 318
>gnl|CDD|213833 TIGR03596, GTPase_YlqF, ribosome biogenesis GTP-binding protein
YlqF. Members of this protein family are GTP-binding
proteins involved in ribosome biogenesis, including the
essential YlqF protein of Bacillus subtilis, which is an
essential protein. They are related to Era, EngA, and
other GTPases of ribosome biogenesis, but are circularly
permuted. This family is not universal, and is not
present in Escherichia coli, and so is not as well
studied as some other GTPases. This model is built for
bacterial members [Protein synthesis, Other].
Length = 276
Score = 31.3 bits (72), Expect = 0.28
Identities = 24/98 (24%), Positives = 40/98 (40%), Gaps = 17/98 (17%)
Query: 135 PEVRHHCPSTPIILVGTKLDLRDDKET---IEKLKEKKLAPIT----YPQGLSM----AK 183
P + + P ++V K DL D T ++ +EK + + +G+ AK
Sbjct: 40 PMIDEIRGNKPRLIVLNKADLADPAVTKQWLKYFEEKGIKALAINAKKGKGVKKIIKAAK 99
Query: 184 EIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPK 221
++ K L KGL IRA++ +P V K
Sbjct: 100 KLLKEKN---EKLKAKGLLN---RPIRAMIVGIPNVGK 131
>gnl|CDD|198249 cd10386, SH2_SOCS5, Src homology 2 (SH2) domain found in
suppressor of cytokine signaling (SOCS) family. SH2
domain found in SOCS proteins. SOCS was first
recognized as a group of cytokine-inducible SH2 (CIS)
domain proteins comprising eight family members in
human (CIS and SOCS1-SOCS7). In addition to the SH2
domain, SOCS proteins have a variable N-terminal domain
and a conserved SOCS box in the C-terminal domain. SOCS
proteins bind to a substrate via their SH2 domain. The
prototypical members, CIS and SOCS1-SOCS3, have been
shown to regulate growth hormone signaling in vitro and
in a classic negative feedback response compete for
binding at phosphotyrosine sites in JAK kinase and
receptor pathways to displace effector proteins and
target bound receptors for proteasomal degradation.
Loss of SOCS activity results in excessive cytokine
signaling associated with a variety of hematopoietic,
autoimmune, and inflammatory diseases and certain
cancers. Members (SOCS4-SOCS7) were identified by their
conserved SOCS box, an adapter motif of 3 helices that
associates substrate binding domains, such as the SOCS
SH2 domain, ankryin, and WD40 with ubiquitin ligase
components. These show limited cytokine induction. In
general SH2 domains are involved in signal
transduction. They typically bind pTyr-containing
ligands via two surface pockets, a pTyr and hydrophobic
binding pocket, allowing proteins with SH2 domains to
localize to tyrosine phosphorylated sites.
Length = 81
Score = 29.7 bits (66), Expect = 0.33
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 24 VFDNYSANVMVDGKPINLGLWDTAGQEDY 52
V D Y A +++GKP L + QEDY
Sbjct: 6 VMDRYEAEALLEGKPEGTFLLRDSAQEDY 34
>gnl|CDD|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 = 30.4 bits (70), Expect = 0.48
Identities = 23/85 (27%), Positives = 36/85 (42%), Gaps = 28/85 (32%)
Query: 144 TPIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLSMAKEIGAVKYLECSALTQKGLKT 203
P+I++ K DL DD+E E L+ +++G L SA T +GL
Sbjct: 35 EPVIVL-NKADLVDDEELEELLEI--------------YEKLG-YPVLAVSAKTGEGL-- 76
Query: 204 VFDEAIRAVLCPVPTVPKKKRCVLL 228
+ +R +L K K VL+
Sbjct: 77 ---DELRELL-------KGKTSVLV 91
>gnl|CDD|133343 cd04143, Rhes_like, Ras homolog enriched in striatum (Rhes) and
activator of G-protein signaling 1 (Dexras1/AGS1).
This subfamily includes Rhes (Ras homolog enriched in
striatum) and Dexras1/AGS1 (activator of G-protein
signaling 1). These proteins are homologous, but
exhibit significant differences in tissue distribution
and subcellular localization. Rhes is found primarily
in the striatum of the brain, but is also expressed in
other areas of the brain, such as the cerebral cortex,
hippocampus, inferior colliculus, and cerebellum. Rhes
expression is controlled by thyroid hormones. In rat
PC12 cells, Rhes is farnesylated and localizes to the
plasma membrane. Rhes binds and activates PI3K, and
plays a role in coupling serpentine membrane receptors
with heterotrimeric G-protein signaling. Rhes has
recently been shown to be reduced under conditions of
dopamine supersensitivity and may play a role in
determining dopamine receptor sensitivity. Dexras1/AGS1
is a dexamethasone-induced Ras protein that is
expressed primarily in the brain, with low expression
levels in other tissues. Dexras1 localizes primarily to
the cytoplasm, and is a critical regulator of the
circadian master clock to photic and nonphotic input.
Most Ras proteins contain a lipid modification site at
the C-terminus, with a typical sequence motif CaaX,
where a = an aliphatic amino acid and X = any amino
acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins.
Length = 247
Score = 30.5 bits (69), Expect = 0.65
Identities = 17/58 (29%), Positives = 29/58 (50%)
Query: 2 VGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPLS 59
VGKT ++ + F +Y PT+ D + + G+ L + DT+G + +R LS
Sbjct: 11 VGKTAIVSRFLGGRFEEQYTPTIEDFHRKLYSIRGEVYQLDILDTSGNHPFPAMRRLS 68
>gnl|CDD|218279 pfam04818, CTD_bind, RNA polymerase II-binding domain. This domain
binds to the phosphorylated C-terminal domain (CTD) of
RNA polymerase II.
Length = 64
Score = 28.3 bits (64), Expect = 0.70
Identities = 12/33 (36%), Positives = 16/33 (48%)
Query: 107 KKKRCDVFQICFSLVNPASFENVRAKWYPEVRH 139
K K D F FS V P +F +V + EV+
Sbjct: 16 KHKNKDEFVKAFSPVLPDAFAHVYKEGDEEVKK 48
>gnl|CDD|206717 cd04150, Arf1_5_like, ADP-ribosylation factor-1 (Arf1) and
ADP-ribosylation factor-5 (Arf5). The Arf1-Arf5-like
subfamily contains Arf1, Arf2, Arf3, Arf4, Arf5, and
related proteins. Arfs1-5 are soluble proteins that are
crucial for assembling coat proteins during vesicle
formation. Each contains an N-terminal myristoylated
amphipathic helix that is folded into the protein in
the GDP-bound state. GDP/GTP exchange exposes the
helix, which anchors to the membrane. Following GTP
hydrolysis, the helix dissociates from the membrane and
folds back into the protein. A general feature of
Arf1-5 signaling may be the cooperation of two Arfs at
the same site. Arfs1-5 are generally considered to be
interchangeable in function and location, but some
specific functions have been assigned. Arf1 localizes
to the early/cis-Golgi, where it is activated by GBF1
and recruits the coat protein COPI. It also localizes
to the trans-Golgi network (TGN), where it is activated
by BIG1/BIG2 and recruits the AP1, AP3, AP4, and GGA
proteins. Humans, but not rodents and other lower
eukaryotes, lack Arf2. Human Arf3 shares 96% sequence
identity with Arf1 and is believed to generally
function interchangeably with Arf1. Human Arf4 in the
activated (GTP-bound) state has been shown to interact
with the cytoplasmic domain of epidermal growth factor
receptor (EGFR) and mediate the EGF-dependent
activation of phospholipase D2 (PLD2), leading to
activation of the activator protein 1 (AP-1)
transcription factor. Arf4 has also been shown to
recognize the C-terminal sorting signal of rhodopsin
and regulate its incorporation into specialized
post-Golgi rhodopsin transport carriers (RTCs). There
is some evidence that Arf5 functions at the early-Golgi
and the trans-Golgi to affect Golgi-associated
alpha-adaptin homology Arf-binding proteins (GGAs).
Length = 159
Score = 29.7 bits (67), Expect = 0.74
Identities = 22/61 (36%), Positives = 29/61 (47%), Gaps = 13/61 (21%)
Query: 1 AVGKTCLLISYTTNAFPGEY---IPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRP 57
A GKT +L GE IPT+ N V+ K I+ +WD GQ D++RP
Sbjct: 10 AAGKTTILYKLKL----GEIVTTIPTIGFNVET---VEYKNISFTVWDVGGQ---DKIRP 59
Query: 58 L 58
L
Sbjct: 60 L 60
>gnl|CDD|198248 cd10385, SH2_SOCS4, Src homology 2 (SH2) domain found in
suppressor of cytokine signaling (SOCS) proteins. SH2
domain found in SOCS proteins. SOCS was first
recognized as a group of cytokine-inducible SH2 (CIS)
domain proteins comprising eight family members in
human (CIS and SOCS1-SOCS7). In addition to the SH2
domain, SOCS proteins have a variable N-terminal domain
and a conserved SOCS box in the C-terminal domain. SOCS
proteins bind to a substrate via their SH2 domain. The
prototypical members, CIS and SOCS1-SOCS3, have been
shown to regulate growth hormone signaling in vitro and
in a classic negative feedback response compete for
binding at phosphotyrosine sites in JAK kinase and
receptor pathways to displace effector proteins and
target bound receptors for proteasomal degradation.
Loss of SOCS activity results in excessive cytokine
signaling associated with a variety of hematopoietic,
autoimmune, and inflammatory diseases and certain
cancers. Members (SOCS4-SOCS7) were identified by their
conserved SOCS box, an adapter motif of 3 helices that
associates substrate binding domains, such as the SOCS
SH2 domain, ankryin, and WD40 with ubiquitin ligase
components. These show limited cytokine induction. In
general SH2 domains are involved in signal
transduction. They typically bind pTyr-containing
ligands via two surface pockets, a pTyr and hydrophobic
binding pocket, allowing proteins with SH2 domains to
localize to tyrosine phosphorylated sites.
Length = 101
Score = 28.5 bits (63), Expect = 1.2
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 24 VFDNYSANVMVDGKPINLGLWDTAGQEDY 52
V D Y+A +++GKP L + QEDY
Sbjct: 16 VMDKYAAEALLEGKPEGTFLLRDSAQEDY 44
>gnl|CDD|206719 cd04152, Arl4_Arl7, Arf-like 4 (Arl4) and 7 (Arl7) GTPases. Arl4
(Arf-like 4) is highly expressed in testicular germ
cells, and is found in the nucleus and nucleolus. In
mice, Arl4 is developmentally expressed during
embryogenesis, and a role in somite formation and
central nervous system differentiation has been
proposed. Arl7 has been identified as the only Arf/Arl
protein to be induced by agonists of liver X-receptor
and retinoid X-receptor and by cholesterol loading in
human macrophages. Arl7 is proposed to play a role in
transport between a perinuclear compartment and the
plasma membrane, apparently linked to the
ABCA1-mediated cholesterol secretion pathway. Older
literature suggests that Arl6 is a part of the
Arl4/Arl7 subfamily, but analyses based on more recent
sequence data place Arl6 in its own subfamily.
Length = 183
Score = 29.4 bits (66), Expect = 1.2
Identities = 22/62 (35%), Positives = 29/62 (46%), Gaps = 8/62 (12%)
Query: 3 GKTCLLISYTTNAFPGEYIPTV-FDNYSANVMV-DGKPINLGLWDTAGQEDYDRLRPL-- 58
GKT +L N F +PT F+ V + + K + WD GQE +LRPL
Sbjct: 15 GKTTVLYRLKFNEFV-NTVPTKGFNTEKIKVSLGNAKGVTFHFWDVGGQE---KLRPLWK 70
Query: 59 SY 60
SY
Sbjct: 71 SY 72
>gnl|CDD|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 = 28.8 bits (65), Expect = 1.3
Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 6/56 (10%)
Query: 3 GKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRPL 58
GKT L+ + F + IPTV N V + + +WD GQ R R +
Sbjct: 11 GKTTLVNVIASGQFSEDTIPTVGFNMR---KVTKGNVTIKVWDLGGQP---RFRSM 60
>gnl|CDD|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 = 28.7 bits (65), Expect = 1.3
Identities = 21/62 (33%), Positives = 32/62 (51%), Gaps = 13/62 (20%)
Query: 145 PIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLSMAKEIGAVKYLECSALTQKGLKTV 204
P+I + TK+DL D+ IE ++E L+ A GA K E SA+T +G+ +
Sbjct: 91 PVIGIITKIDLAKDEANIEMVEEW----------LNNA---GAEKIFEVSAVTNEGIDEL 137
Query: 205 FD 206
F
Sbjct: 138 FA 139
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 29.4 bits (67), Expect = 1.3
Identities = 29/110 (26%), Positives = 46/110 (41%), Gaps = 23/110 (20%)
Query: 123 PASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDKET---IEKLKEKKLAPIT----Y 175
P S EN P + + P +L+ K DL D + T IE +E+ + +
Sbjct: 37 PLSSEN------PMIDKIIGNKPRLLILNKSDLADPEVTKKWIEYFEEQGIKALAINAKK 90
Query: 176 PQGL----SMAKEIGAVKYLECSALTQKGLKTVFDEAIRAVLCPVPTVPK 221
QG+ AK++ K KG++ AIRA++ +P V K
Sbjct: 91 GQGVKKILKAAKKLLKEKNER---RKAKGMR---PRAIRAMIIGIPNVGK 134
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 28.8 bits (64), Expect = 1.8
Identities = 22/61 (36%), Positives = 29/61 (47%), Gaps = 13/61 (21%)
Query: 1 AVGKTCLLISYTTNAFPGEY---IPTVFDNYSANVMVDGKPINLGLWDTAGQEDYDRLRP 57
A GKT +L GE IPT+ N V+ K I+ +WD GQ D++RP
Sbjct: 27 AAGKTTILYKLKL----GEIVTTIPTIGFNVET---VEYKNISFTVWDVGGQ---DKIRP 76
Query: 58 L 58
L
Sbjct: 77 L 77
>gnl|CDD|131580 TIGR02528, EutP, ethanolamine utilization protein, EutP. This
protein is found within operons which code for
polyhedral organelles containing the enzyme ethanolamine
ammonia lyase. The function of this gene is unknown,
although the presence of an N-terminal GxxGxGK motif
implies a GTP-binding site [Energy metabolism, Amino
acids and amines].
Length = 142
Score = 27.8 bits (62), Expect = 2.6
Identities = 19/62 (30%), Positives = 30/62 (48%), Gaps = 13/62 (20%)
Query: 145 PIILVGTKLDLRDDKETIEKLKEKKLAPITYPQGLSMAKEIGAVKYLECSALTQKGLKTV 204
P+I + TK+DL + IE+ KE L A GA E S++ ++GL+ +
Sbjct: 90 PVIGLVTKIDLAEADVDIERAKEL----------LETA---GAEPIFEISSVDEQGLEAL 136
Query: 205 FD 206
D
Sbjct: 137 VD 138
>gnl|CDD|218203 pfam04670, Gtr1_RagA, Gtr1/RagA G protein conserved region. GTR1
was first identified in S. cerevisiae as a suppressor
of a mutation in RCC1. Biochemical analysis revealed
that Gtr1 is in fact a G protein of the Ras family. The
RagA/B proteins are the human homologues of Gtr1.
Included in this family is the human Rag C, a novel
protein that has been shown to interact with RagA/B.
Length = 230
Score = 28.3 bits (64), Expect = 3.1
Identities = 13/45 (28%), Positives = 17/45 (37%), Gaps = 16/45 (35%)
Query: 23 TVFDNYSAN---------------VMVDGKPINLGLWDTAGQEDY 52
+F NYS V G + L LWD GQ+D+
Sbjct: 18 IIFSNYSPRDTLRLGATIDVEQSHVRFLGN-LTLNLWDCPGQDDF 61
>gnl|CDD|219841 pfam08438, MMR_HSR1_C, GTPase of unknown function C-terminal. This
domain is found at the C-terminus of pfam01926 in
archaeal and eukaryotic GTP-binding proteins. The
C-terminal domain of the GTP-binding proteins is
necessary for the complete activity of the protein of
interacting with the 50S ribosome and binding of both
adenine and guanine nucleotides, with a preference for
guanine nucleotides.
Length = 109
Score = 26.8 bits (60), Expect = 4.3
Identities = 17/50 (34%), Positives = 19/50 (38%), Gaps = 6/50 (12%)
Query: 149 VGTKLDLRDDKETIEKLKEKKLAPITYP------QGLSMAKEIGAVKYLE 192
K DL E IEKLKEK P L A + G + YL
Sbjct: 1 AANKADLPAADENIEKLKEKYPDEPVVPTSAEAELALRKAAKAGLIDYLP 50
>gnl|CDD|215653 pfam00009, GTP_EFTU, Elongation factor Tu GTP binding domain. This
domain contains a P-loop motif, also found in several
other families such as pfam00071, pfam00025 and
pfam00063. Elongation factor Tu consists of three
structural domains, this plus two C-terminal beta barrel
domains.
Length = 184
Score = 27.5 bits (62), Expect = 4.4
Identities = 16/69 (23%), Positives = 29/69 (42%), Gaps = 11/69 (15%)
Query: 145 PIILVGTKLDLRDD---KETIEKLKEKKLAPITYPQGLSMAKEIGAVKYLECSALTQKGL 201
PII+ K+D DD +E +E++ + L + V + SALT +G+
Sbjct: 120 PIIVFINKIDRVDDAELEEVVEEISRELLEKYGFGGET--------VPVVPGSALTGEGI 171
Query: 202 KTVFDEAIR 210
+ +
Sbjct: 172 DELLEALDL 180
>gnl|CDD|215063 PLN00120, PLN00120, fucoxanthin-chlorophyll a-c binding protein;
Provisional.
Length = 202
Score = 27.4 bits (61), Expect = 5.7
Identities = 10/16 (62%), Positives = 11/16 (68%)
Query: 41 LGLWDTAGQEDYDRLR 56
LGL D QE +DRLR
Sbjct: 50 LGLVDDGDQEKFDRLR 65
>gnl|CDD|185310 PRK15412, PRK15412, thiol:disulfide interchange protein DsbE;
Provisional.
Length = 185
Score = 27.3 bits (60), Expect = 6.3
Identities = 11/30 (36%), Positives = 17/30 (56%), Gaps = 7/30 (23%)
Query: 17 PGEYIPTVFDNYSANVMVDGKPINLGLWDT 46
PG++ Y A+V+ GKP+ L +W T
Sbjct: 56 PGQF-------YQADVLTQGKPVLLNVWAT 78
>gnl|CDD|211373 cd09262, AP_stonin-1_MHD, Mu homology domain (MHD) of adaptor-like
protein (AP-like), stonin-1 (also called Stoned B-like
factor). A small family of proteins named stonins has
been characterized as clathrin-dependent AP-2 mu2 chain
related factors, which may act as cargo-specific sorting
adaptors in endocytosis. Stonins include stonin 1 and
stonin 2, which are the only mammalian homologs of
Drosophila stoned B, a presynaptic protein implicated in
neurotransmission and synaptic vesicle (SV) recycling.
They are conserved from C. elegans to humans, but are
not found in prokaryotes or yeasts. This family
corresponds to the mu homology domain of stonin 1, which
is distantly related to the C-terminal domain of mu
chains among AP complexes. Due to the low degree of
sequence conservation of the corresponding binding site,
the mu homology domain of stonin-1 is unable to
recognize tyrosine-based endocytic sorting signals. To
data, little is known about the localization and
function of stonin-1.
Length = 309
Score = 27.5 bits (61), Expect = 6.9
Identities = 19/103 (18%), Positives = 38/103 (36%), Gaps = 9/103 (8%)
Query: 71 IGAVKYLECSALTQKGLKTV-FDEAIRAVLCPVPTVP-KKKRCDVFQICFSLVNPASFEN 128
+G+ E + Q + T ++ A RAV+ + +P K D + S +
Sbjct: 201 LGSALEAESEPVIQVSVGTAKYENAYRAVVWKIDRLPDKNSAVDHPHSLSCKLELGSDQE 260
Query: 129 VRAKWYPEVRHHC-------PSTPIILVGTKLDLRDDKETIEK 164
+ + WYP T + +G + D++ K +
Sbjct: 261 IPSDWYPFATVEFEVEDTCASGTRVKSLGIESDMQPQKHVTSR 303
>gnl|CDD|223009 PHA03211, PHA03211, serine/threonine kinase US3; Provisional.
Length = 461
Score = 27.5 bits (61), Expect = 7.0
Identities = 10/36 (27%), Positives = 17/36 (47%)
Query: 54 RLRPLSYPQTGLSMAKEIGAVKYLECSALTQKGLKT 89
RLRPL Q + + A+ Y+ + + +KT
Sbjct: 253 RLRPLGLAQVTAVARQLLSAIDYIHGEGIIHRDIKT 288
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 26.9 bits (60), Expect = 8.5
Identities = 12/33 (36%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 144 TPIILVGTKLDLRDDKETIEKLKEKKLAPITYP 176
P+I++ K+DL DD+E K ++ I YP
Sbjct: 112 EPVIVL-NKIDLLDDEEAAVKELLREYEDIGYP 143
>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 = 26.3 bits (59), Expect = 9.3
Identities = 12/33 (36%), Positives = 16/33 (48%)
Query: 141 CPSTPIILVGTKLDLRDDKETIEKLKEKKLAPI 173
P+I+V K DL D E I +L K + I
Sbjct: 107 PAKKPVIVVLNKSDLLSDAEGISELNGKPIIAI 139
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: 11,617,476
Number of extensions: 1073165
Number of successful extensions: 1334
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1246
Number of HSP's successfully gapped: 236
Length of query: 228
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 134
Effective length of database: 6,768,326
Effective search space: 906955684
Effective search space used: 906955684
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: 57 (26.1 bits)