RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy549
(253 letters)
>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 = 237 bits (606), Expect = 2e-79
Identities = 105/205 (51%), Positives = 136/205 (66%), Gaps = 10/205 (4%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
R+V MG A VGK+++I +FLYD F +++ TVEELH EYE G ++T+DILDTSG+Y
Sbjct: 1 RLVFMGAAGVGKTALIQRFLYDTFEPKHRRTVEELHSKEYE-VAGVKVTIDILDTSGSYS 59
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVN-KRGLMVPIVVVGNKCE-LEF 168
FPAMR+LSI DAF LVY+VDD +++ VK LRE+I+ K VPIVVVGNK + L
Sbjct: 60 FPAMRKLSIQNGDAFALVYSVDDPESFEEVKRLREEILEVKEDKFVPIVVVGNKIDSLAE 119
Query: 169 KDVRREIAETIALYDWQCGFVECSAKENYNIVQVFKELLAQAKVQYNLSPAVRRRRQSLP 228
+ V A + DW GFVE SAK+N N+ +VFKELL QA + LSPA+RRRR+S P
Sbjct: 120 RQVEAADALSTVELDWNNGFVEASAKDNENVTEVFKELLQQANLPSWLSPALRRRRESAP 179
Query: 229 NYIGTTGSASSKGRYMLKRNSCTVA 253
S + M K NSC+V+
Sbjct: 180 -------SEIQRRPPMNKTNSCSVS 197
>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 = 176 bits (448), Expect = 6e-56
Identities = 64/166 (38%), Positives = 99/166 (59%), Gaps = 12/166 (7%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
++VV+G VGKS++ +F+ F+ Y T+E+ +R + + DG TLDILDT+G +
Sbjct: 1 KLVVLGAGGVGKSALTIRFVSGEFVEEYDPTIEDSYRKQIVV-DGETYTLDILDTAGQEE 59
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVN-KRGLMVPIVVVGNKCELE-- 167
F AMR+ I D F+LVY++ +++ +K++REQI+ K VPIV+VGNKC+LE
Sbjct: 60 FSAMRDQYIRNGDGFILVYSITSRESFEEIKNIREQILRVKDKEDVPIVLVGNKCDLENE 119
Query: 168 ---FKDVRREIAETIALYDWQCGFVECSAKENYNIVQVFKELLAQA 210
+ +AE W C F+E SAK N NI ++F L+ +
Sbjct: 120 RQVSTEEGEALAEE-----WGCPFLETSAKTNINIDELFNTLVREI 160
>gnl|CDD|197466 smart00010, small_GTPase, Small GTPase of the Ras superfamily;
ill-defined subfamily. SMART predicts Ras-like small
GTPases of the ARF, RAB, RAN, RAS, and SAR subfamilies.
Others that could not be classified in this way are
predicted to be members of the small GTPase superfamily
without predictions of the subfamily.
Length = 166
Score = 163 bits (415), Expect = 7e-51
Identities = 64/164 (39%), Positives = 102/164 (62%), Gaps = 4/164 (2%)
Query: 50 RRVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAY 109
++VV+GG VGKS++ QF+ F+ Y T+E+ +R + E+ DG LDILDT+G
Sbjct: 3 YKLVVLGGGGVGKSALTIQFVQGHFVDEYDPTIEDSYRKQIEI-DGEVCLLDILDTAGQE 61
Query: 110 QFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLM-VPIVVVGNKCELEF 168
+F AMR+ + T + F+LVY++ D +++ + REQI+ + VPIV+VGNKC+LE
Sbjct: 62 EFSAMRDQYMRTGEGFLLVYSITDRQSFEEIAKFREQILRVKDRDDVPIVLVGNKCDLEN 121
Query: 169 K-DVRREIAETIALYDWQCGFVECSAKENYNIVQVFKELLAQAK 211
+ V E + +A W C F+E SAKE N+ + F +L+ + +
Sbjct: 122 ERVVSTEEGKELA-RQWGCPFLETSAKERINVDEAFYDLVREIR 164
>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 = 161 bits (410), Expect = 4e-50
Identities = 64/164 (39%), Positives = 102/164 (62%), Gaps = 4/164 (2%)
Query: 50 RRVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAY 109
++VV+G VGKS++ QF+ F+ Y T+E+ +R + E+ DG LDILDT+G
Sbjct: 1 YKLVVLGSGGVGKSALTIQFIQGHFVDDYDPTIEDSYRKQIEI-DGEVCLLDILDTAGQE 59
Query: 110 QFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLM-VPIVVVGNKCELEF 168
+F AMR+ + T + F+LVY++ D +++ +K REQI+ + VPIV+VGNKC+LE
Sbjct: 60 EFSAMRDQYMRTGEGFLLVYSITDRQSFEEIKKFREQILRVKDRDDVPIVLVGNKCDLES 119
Query: 169 K-DVRREIAETIALYDWQCGFVECSAKENYNIVQVFKELLAQAK 211
+ V E + +A W C F+E SAKE N+ + F +L+ + +
Sbjct: 120 ERVVSTEEGKELA-RQWGCPFLETSAKERVNVDEAFYDLVREIR 162
>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 = 159 bits (405), Expect = 2e-48
Identities = 73/184 (39%), Positives = 118/184 (64%), Gaps = 11/184 (5%)
Query: 50 RRVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAY 109
R+VV+G ++VGK++I+S+FL RF +Y T+E+ HR Y + G LDILDTSG +
Sbjct: 1 YRMVVLGASKVGKTAIVSRFLGGRFEEQYTPTIEDFHRKLYSI-RGEVYQLDILDTSGNH 59
Query: 110 QFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVN---------KRGLMVPIVVV 160
FPAMR LSI T D F+LV+++D+ +++ V LREQI+ K + +P+V+
Sbjct: 60 PFPAMRRLSILTGDVFILVFSLDNRESFEEVCRLREQILETKSCLKNKTKENVKIPMVIC 119
Query: 161 GNKCELEF-KDVRREIAETIALYDWQCGFVECSAKENYNIVQVFKELLAQAKVQYNLSPA 219
GNK + +F ++V+R+ E + D C + E SAK+N N+ ++F+ L + AK+ +SP+
Sbjct: 120 GNKADRDFPREVQRDEVEQLVGGDENCAYFEVSAKKNSNLDEMFRALFSLAKLPNEMSPS 179
Query: 220 VRRR 223
+ R+
Sbjct: 180 LHRK 183
>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 = 134 bits (341), Expect = 9e-40
Identities = 57/163 (34%), Positives = 91/163 (55%), Gaps = 4/163 (2%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETV-EELHRGEYELPDGAQLTLDILDTSGAY 109
++V++G VGKSS++ +F ++F Y T+ + + E+ DG + L I DT+G
Sbjct: 1 KLVLVGDGGVGKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIEV-DGKTVKLQIWDTAGQE 59
Query: 110 QFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCELEFK 169
+F A+R L A F+LVY + +++ VK E+I+ VPIV+VGNKC+LE +
Sbjct: 60 RFRALRPLYYRGAQGFLLVYDITSRDSFENVKKWLEEILRHADENVPIVLVGNKCDLEDQ 119
Query: 170 D-VRREIAETIALYDWQCGFVECSAKENYNIVQVFKELLAQAK 211
V E E +A + F+E SAK N N+ + F+EL +
Sbjct: 120 RVVSTEEGEALA-KELGLPFMETSAKTNENVEEAFEELAREIL 161
>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 = 127 bits (320), Expect = 1e-36
Identities = 66/161 (40%), Positives = 105/161 (65%), Gaps = 4/161 (2%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
++VV+G VGKS++ QF+ F+ +Y T+E+ +R + E+ DG Q L+ILDT+G Q
Sbjct: 3 KLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEV-DGQQCMLEILDTAGTEQ 61
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLM-VPIVVVGNKCELEFK 169
F AMR+L + FVLVY++ ST++ ++DLREQI+ + VP+++VGNKC+LE +
Sbjct: 62 FTAMRDLYMKNGQGFVLVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDE 121
Query: 170 D-VRREIAETIALYDWQCGFVECSAKENYNIVQVFKELLAQ 209
V +E + +A W C F+E SAK N+ ++F +L+ Q
Sbjct: 122 RVVGKEQGQNLA-RQWGCAFLETSAKAKINVNEIFYDLVRQ 161
>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 = 126 bits (317), Expect = 2e-36
Identities = 62/163 (38%), Positives = 101/163 (61%), Gaps = 4/163 (2%)
Query: 49 KRRVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGA 108
+ +VVV+G VGKS++ QF+ FI +Y T+E+ +R E E+ D + L+ILDT+G
Sbjct: 1 EYKVVVLGSGGVGKSALTVQFVSGTFIEKYDPTIEDFYRKEIEV-DSSPSVLEILDTAGT 59
Query: 109 YQFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLM-VPIVVVGNKCELE 167
QF +MR+L I F++VY++ + T+ +K +R+QIV +G VPI++VGNK +LE
Sbjct: 60 EQFASMRDLYIKNGQGFIVVYSLVNQQTFQDIKPMRDQIVRVKGYEKVPIILVGNKVDLE 119
Query: 168 F-KDVRREIAETIALYDWQCGFVECSAKENYNIVQVFKELLAQ 209
++V +A +W C F+E SAK + ++F E++ Q
Sbjct: 120 SEREVSSAEGRALA-EEWGCPFMETSAKSKTMVNELFAEIVRQ 161
>gnl|CDD|133377 cd04177, RSR1, RSR1/Bud1p family GTPase. RSR1/Bud1p is a member of
the Rap subfamily of the Ras family that is found in
fungi. In budding yeasts, RSR1 is involved in selecting
a site for bud growth on the cell cortex, which directs
the establishment of cell polarization. The Rho family
GTPase cdc42 and its GEF, cdc24, then establish an axis
of polarized growth by organizing the actin cytoskeleton
and secretory apparatus at the bud site. It is believed
that cdc42 interacts directly with RSR1 in vivo. In
filamentous fungi, polar growth occurs at the tips of
hypha and at novel growth sites along the extending
hypha. In Ashbya gossypii, RSR1 is a key regulator of
hyphal growth, localizing at the tip region and
regulating in apical polarization of the actin
cytoskeleton. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras proteins.
Length = 168
Score = 125 bits (316), Expect = 4e-36
Identities = 65/162 (40%), Positives = 102/162 (62%), Gaps = 5/162 (3%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
++VV+G VGKS++ QF+ + FI Y T+E+ +R + E+ DG Q L+ILDT+G Q
Sbjct: 3 KIVVLGAGGVGKSALTVQFVQNVFIESYDPTIEDSYRKQVEI-DGRQCDLEILDTAGTEQ 61
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVN-KRGLMVPIVVVGNKCELEF- 168
F AMREL I + F+LVY+V ++ + + +LREQ++ K VP+V+VGNK +LE
Sbjct: 62 FTAMRELYIKSGQGFLLVYSVTSEASLNELGELREQVLRIKDSDNVPMVLVGNKADLEDD 121
Query: 169 KDVRREIAETIALYDW-QCGFVECSAKENYNIVQVFKELLAQ 209
+ V RE +++ W F E SA++ N+ +VF +L+ Q
Sbjct: 122 RQVSREDGVSLS-QQWGNVPFYETSARKRTNVDEVFIDLVRQ 162
>gnl|CDD|206709 cd04137, RheB, Ras Homolog Enriched in Brain (RheB) is a small
GTPase. Rheb (Ras Homolog Enriched in Brain) subfamily.
Rheb was initially identified in rat brain, where its
expression is elevated by seizures or by long-term
potentiation. It is expressed ubiquitously, with
elevated levels in muscle and brain. Rheb functions as
an important mediator between the tuberous sclerosis
complex proteins, TSC1 and TSC2, and the mammalian
target of rapamycin (TOR) kinase to stimulate cell
growth. TOR kinase regulates cell growth by controlling
nutrient availability, growth factors, and the energy
status of the cell. TSC1 and TSC2 form a dimeric complex
that has tumor suppressor activity, and TSC2 is a GTPase
activating protein (GAP) for Rheb. The TSC1/TSC2 complex
inhibits the activation of TOR kinase through Rheb. Rheb
has also been shown to induce the formation of large
cytoplasmic vacuoles in a process that is dependent on
the GTPase cycle of Rheb, but independent of the TOR
kinase, suggesting Rheb plays a role in endocytic
trafficking that leads to cell growth and cell-cycle
progression. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras proteins.
Length = 180
Score = 120 bits (304), Expect = 4e-34
Identities = 54/175 (30%), Positives = 94/175 (53%), Gaps = 8/175 (4%)
Query: 49 KRRVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGA 108
+R++ V+G VGKSS+ QF+ F+ Y T+E G + L+I+DT+G
Sbjct: 1 QRKIAVLGSRSVGKSSLTVQFVEGHFVESYYPTIENTFSKIITY-KGQEYHLEIVDTAGQ 59
Query: 109 YQFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLM-VPIVVVGNKCELE 167
++ + + ++LVY+V +++VVK + ++I++ G VPIV+VGNK +L
Sbjct: 60 DEYSILPQKYSIGIHGYILVYSVTSRKSFEVVKVIYDKILDMLGKESVPIVLVGNKSDL- 118
Query: 168 FKDVRREI--AETIALYD-WQCGFVECSAKENYNIVQVFKELLAQAKVQYNLSPA 219
+ R++ E L + W F+E SAKEN N+ + F+ L+ + + N P
Sbjct: 119 --HMERQVSAEEGKKLAESWGAAFLESSAKENENVEEAFELLIEEIEKVENPLPP 171
>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 = 118 bits (297), Expect = 3e-33
Identities = 63/161 (39%), Positives = 101/161 (62%), Gaps = 3/161 (1%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
++VV+G VGKS++ QF+ F+ +Y T+E+ +R + E+ D Q L+ILDT+G Q
Sbjct: 3 KLVVLGSGGVGKSALTVQFVQGIFVDKYDPTIEDSYRKQIEV-DCQQCMLEILDTAGTEQ 61
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVN-KRGLMVPIVVVGNKCELEF- 168
F AMR+L I F LVY++ +++ ++DLREQI+ K VP+++VGNKC+LE
Sbjct: 62 FTAMRDLYIKNGQGFALVYSITAQQSFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDE 121
Query: 169 KDVRREIAETIALYDWQCGFVECSAKENYNIVQVFKELLAQ 209
+ V +E + +A C F+E SAK N+ ++F +L+ Q
Sbjct: 122 RVVSKEEGQNLARQWGNCPFLETSAKSKINVDEIFYDLVRQ 162
>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 = 115 bits (290), Expect = 3e-32
Identities = 63/161 (39%), Positives = 94/161 (58%), Gaps = 6/161 (3%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
RVVV G VGKSS++ +F+ F Y T+E+ +R TL I DT+G++Q
Sbjct: 3 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCSKSI-CTLQITDTTGSHQ 61
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLM---VPIVVVGNKC-EL 166
FPAM+ LSIS AF+LVY++ + + +K + E I +G +PI++VGNKC E
Sbjct: 62 FPAMQRLSISKGHAFILVYSITSKQSLEELKPIYELICEIKGNNLEKIPIMLVGNKCDES 121
Query: 167 EFKDVRREIAETIALYDWQCGFVECSAKENYNIVQVFKELL 207
++V +A W C F+E SAK N+N+ ++F+ELL
Sbjct: 122 PSREVSSSEGAALAR-TWNCAFMETSAKTNHNVQELFQELL 161
>gnl|CDD|206713 cd04146, RERG_RasL11_like, Ras-related and Estrogen-Regulated
Growth inhibitor (RERG) and Ras-like 11 (RasL11)-like
families. RERG (Ras-related and Estrogen- Regulated
Growth inhibitor) and Ras-like 11 are members of a novel
subfamily of Ras that were identified based on their
behavior in breast and prostate tumors, respectively.
RERG expression was decreased or lost in a significant
fraction of primary human breast tumors that lack
estrogen receptor and are correlated with poor clinical
prognosis. Elevated RERG expression correlated with
favorable patient outcome in a breast tumor subtype that
is positive for estrogen receptor expression. In
contrast to most Ras proteins, RERG overexpression
inhibited the growth of breast tumor cells in vitro and
in vivo. RasL11 was found to be ubiquitously expressed
in human tissue, but down-regulated in prostate tumors.
Both RERG and RasL11 lack the C-terminal CaaX
prenylation motif, where a = an aliphatic amino acid and
X = any amino acid, and are localized primarily in the
cytoplasm. Both are believed to have tumor suppressor
activity.
Length = 166
Score = 112 bits (282), Expect = 5e-31
Identities = 66/162 (40%), Positives = 96/162 (59%), Gaps = 8/162 (4%)
Query: 52 VVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQF 111
+ V+G + VGKS++ +FL RFI Y+ +E L+ + + DG Q++L+I DT G Q
Sbjct: 2 IAVLGASGVGKSALTVRFLTKRFIGEYEPNLESLYSRQVTI-DGEQVSLEIQDTPGQQQN 60
Query: 112 --PAMRELSISTADAFVLVYAVDDASTWDVVKDLREQI--VNKRGLMVPIVVVGNKCELE 167
P E S+ AD FVLVY++ D S++DVV L + I + KR +P+++VGNK +L
Sbjct: 61 EDPESLERSLRWADGFVLVYSITDRSSFDVVSQLLQLIREIKKRDGEIPVILVGNKADLL 120
Query: 168 -FKDVRREIAETIALYDWQCGFVECSAKENYNIVQ-VFKELL 207
+ V E + +AL + C F E SA ENY VQ VF EL
Sbjct: 121 HSRQVSTEEGQKLAL-ELGCLFFEVSAAENYLEVQNVFHELC 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 = 106 bits (267), Expect = 6e-29
Identities = 51/157 (32%), Positives = 89/157 (56%), Gaps = 3/157 (1%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
++VV+G VGKS++ Q + + F+ Y T+E+ +R + + DG LDILDT+G +
Sbjct: 3 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVI-DGETCLLDILDTAGQEE 61
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVN-KRGLMVPIVVVGNKCELEFK 169
+ AMR+ + T + F+ V+A++ +++ + REQI K VP+V+VGNKC+L +
Sbjct: 62 YSAMRDQYMRTGEGFLCVFAINSRKSFEDIHTYREQIKRVKDSDDVPMVLVGNKCDLAAR 121
Query: 170 DVRREIAETIALYDWQCGFVECSAKENYNIVQVFKEL 206
V + +A + ++E SAK + + F L
Sbjct: 122 TVSTRQGQDLAK-SYGIPYIETSAKTRQGVEEAFYTL 157
>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 = 106 bits (266), Expect = 1e-28
Identities = 56/158 (35%), Positives = 96/158 (60%), Gaps = 4/158 (2%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
+V+++G VGKS++ QF+YD F+ Y+ T + +R + L DG ++ L+ILDT+G
Sbjct: 2 KVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVL-DGEEVQLNILDTAGQED 60
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVN-KRGLMVPIVVVGNKCELEFK 169
+ A+R+ + + F+LV+++ D ++ + + REQI+ K VP+++VGNKC+LE K
Sbjct: 61 YAAIRDNYFRSGEGFLLVFSITDMESFTALAEFREQILRVKEDDNVPLLLVGNKCDLEDK 120
Query: 170 DVRREIAETIAL-YDWQCGFVECSAKENYNIVQVFKEL 206
+ + E L W +VE SAK N+ +VF +L
Sbjct: 121 -RQVSVEEAANLAEQWGVNYVETSAKTRANVDKVFFDL 157
>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 = 106 bits (267), Expect = 1e-28
Identities = 64/185 (34%), Positives = 94/185 (50%), Gaps = 15/185 (8%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETV-EELHRGEYELPDGAQLTLDILDTSGAY 109
RV V+G VGK++I+ QFL F Y T L+R L G L ILD
Sbjct: 2 RVAVLGAPGVGKTAIVRQFLAQEFPEEYIPTEHRRLYRPAVVL-SGRVYDLHILDVPNMQ 60
Query: 110 QFPA--------MRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLM---VPIV 158
++P R + + AF+LVY + ++ VK LR+QI+ R PIV
Sbjct: 61 RYPGTAGQEWMDPRFRGLRNSRAFILVYDICSPDSFHYVKLLRQQILETRPAGNKEPPIV 120
Query: 159 VVGNKCELE-FKDVRREIAETIALYDWQCGFVECSAKENYNIVQVFKELLAQAKVQ-YNL 216
VVGNK + + + R + + W+CG++ECSAK N++I+ +FKELL A + +
Sbjct: 121 VVGNKRDQQRHRFAPRHVLSVLVRKSWKCGYLECSAKYNWHILLLFKELLISATTRGRST 180
Query: 217 SPAVR 221
PA+R
Sbjct: 181 HPALR 185
>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 = 105 bits (264), Expect = 2e-28
Identities = 57/158 (36%), Positives = 95/158 (60%), Gaps = 4/158 (2%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
++VV+GG VGKS++ QF+ F++ Y T+E+ + + E+ DG LDILDT+G +
Sbjct: 4 KLVVVGGGGVGKSALTIQFIQSYFVTDYDPTIEDSYTKQCEI-DGQWARLDILDTAGQEE 62
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVN-KRGLMVPIVVVGNKCELEF- 168
F AMRE + T + F+LV++V D +++ V QI+ K P+++VGNK +LE
Sbjct: 63 FSAMREQYMRTGEGFLLVFSVTDRGSFEEVDKFHTQILRVKDRDEFPMILVGNKADLEHQ 122
Query: 169 KDVRREIAETIALYDWQCGFVECSAKENYNIVQVFKEL 206
+ V RE + +A + ++E SAK+ N+ + F +L
Sbjct: 123 RQVSREEGQELA-RQLKIPYIETSAKDRVNVDKAFHDL 159
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 103 bits (257), Expect = 4e-27
Identities = 55/165 (33%), Positives = 98/165 (59%), Gaps = 8/165 (4%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
++VV+GG VGKS++ QF+ + FI Y T+E+ +R + + + L LDILDT+G +
Sbjct: 7 KLVVVGGGGVGKSALTIQFIQNHFIDEYDPTIEDSYRKQCVIDEETCL-LDILDTAGQEE 65
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVN-KRGLMVPIVVVGNKCELEFK 169
+ AMR+ + T F+ VY++ S+++ + REQI+ K VP+++VGNKC+L+ +
Sbjct: 66 YSAMRDQYMRTGQGFLCVYSITSRSSFEEIASFREQILRVKDKDRVPMILVGNKCDLDSE 125
Query: 170 DVRREIAETIAL---YDWQCGFVECSAKENYNIVQVFKELLAQAK 211
R+++ + F+E SAK+ N+ + F EL+ + +
Sbjct: 126 ---RQVSTGEGQELAKSFGIPFLETSAKQRVNVDEAFYELVREIR 167
>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 = 97.9 bits (245), Expect = 2e-25
Identities = 45/158 (28%), Positives = 84/158 (53%), Gaps = 4/158 (2%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETV-EELHRGEYELPDGAQLTLDILDTSGAY 109
++V++G + VGK+S++ +F+ ++F YK T+ + E+ DG ++ L I DT+G
Sbjct: 2 KIVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGVDFKSKTIEV-DGKKVKLQIWDTAGQE 60
Query: 110 QFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCELEF- 168
+F ++ A +LVY V + +++ + ++ +PI++VGNK +LE
Sbjct: 61 RFRSITSSYYRGAHGAILVYDVTNRESFENLDKWLNELKEYAPPNIPIILVGNKSDLEDE 120
Query: 169 KDVRREIAETIALYDWQCGFVECSAKENYNIVQVFKEL 206
+ V E A+ A + F E SAK N+ + F+ L
Sbjct: 121 RQVSTEEAQQFAK-ENGLLFFETSAKTGENVDEAFESL 157
>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 = 91.4 bits (227), Expect = 9e-23
Identities = 55/169 (32%), Positives = 96/169 (56%), Gaps = 6/169 (3%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
++VV+G VGK+++ Q + F+ Y T+E+ +R + + DG L++LDT+G +
Sbjct: 1 KLVVLGDGGVGKTALTIQLCLNHFVETYDPTIEDSYRKQVVV-DGQPCMLEVLDTAGQEE 59
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIV---NKRGLMVPIVVVGNKCELE 167
+ A+R+ I + F+LVY++ ST++ V+ REQI ++ VPI++VGNKC+
Sbjct: 60 YTALRDQWIREGEGFILVYSITSRSTFERVERFREQIQRVKDESAADVPIMIVGNKCDKV 119
Query: 168 F-KDVRREIAETIALYDWQCGFVECSAKENYNIVQVFKELLAQAKVQYN 215
+ ++V E +A C F+E SAK N N+ + F L+ + Q
Sbjct: 120 YEREVSTEEGAALA-RRLGCEFIEASAKTNVNVERAFYTLVRALRQQRQ 167
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 89.1 bits (222), Expect = 4e-22
Identities = 48/168 (28%), Positives = 89/168 (52%), Gaps = 14/168 (8%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETV------EELHRGEYELPDGAQLTLDILD 104
+++++G + VGKSS++S+F +F +YK T+ + + DG ++ L I D
Sbjct: 2 KIILIGDSGVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIEV------DGKRVKLQIWD 55
Query: 105 TSGAYQFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKC 164
T+G +F ++ A +LVY + + +++ +++ +++ V I++VGNK
Sbjct: 56 TAGQERFRSITSSYYRGAVGALLVYDITNRESFENLENWLKELREYASPNVVIMLVGNKS 115
Query: 165 ELEFK-DVRREIAETIALYDWQCGFVECSAKENYNIVQVFKELLAQAK 211
+LE + V RE AE A + F E SAK N N+ + F+EL +
Sbjct: 116 DLEEQRQVSREEAEAFAE-EHGLPFFETSAKTNTNVEEAFEELAREIL 162
>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 = 85.2 bits (211), Expect = 1e-20
Identities = 42/164 (25%), Positives = 70/164 (42%), Gaps = 13/164 (7%)
Query: 53 VVMGGARVGKSSIISQFLYDRF---ISRYKETVEELHRGEYELPDGAQLTLDILDTSGAY 109
VV+G VGKSS+++ L T + EL G ++ L ++DT G
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDP-DVYVKELDKG-KVKLVLVDTPGLD 58
Query: 110 QFPAMRE-----LSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKC 164
+F + L + AD +LV D + + K L + R +PI++VGNK
Sbjct: 59 EFGGLGREELARLLLRGADLILLVVDSTDRESEEDAKLLI--LRRLRKEGIPIILVGNKI 116
Query: 165 ELEFKDVRREIAETIALY-DWQCGFVECSAKENYNIVQVFKELL 207
+L + E+ L E SAK + ++F++L+
Sbjct: 117 DLLEEREVEELLRLEELAKILGVPVFEVSAKTGEGVDELFEKLI 160
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 85.0 bits (210), Expect = 5e-20
Identities = 47/215 (21%), Positives = 90/215 (41%), Gaps = 18/215 (8%)
Query: 45 LQKDKRRVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILD 104
L + ++VV+G VGK++++++ + D F Y T+ L + P + L + D
Sbjct: 1 LFMKEFKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWD 60
Query: 105 TSGAYQFPAMRELSISTADAFVLVYAV-DDASTWDVVKDLREQIVNKRGLMVPIVVVGNK 163
T+G ++ ++R A+ ++VY S+ ++ ++ E++ VPI++VGNK
Sbjct: 61 TAGQEEYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVGNK 120
Query: 164 CELEFKDVRREIA------ETIALYDWQC---------GFVECSAK--ENYNIVQVFKEL 206
+L + E E + L +E SAK N+ ++FKEL
Sbjct: 121 IDLFDEQSSSEEILNQLNREVVLLVLAPKAVLPEVANPALLETSAKSLTGPNVNELFKEL 180
Query: 207 LAQAKVQYNLSPAVRRRRQSLPNYIGTTGSASSKG 241
L + + RQ +A +
Sbjct: 181 LRKLLEEIEKLVLKNELRQLDRLNNPIEQAALASF 215
>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 = 83.4 bits (206), Expect = 7e-20
Identities = 48/158 (30%), Positives = 85/158 (53%), Gaps = 4/158 (2%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
++V++G VGKS++ QF+ F + T+E+ ++ + + + L LDILDT+G +
Sbjct: 4 KIVMLGAGGVGKSAVTMQFISHSFPDYHDPTIEDAYKTQARIDNEPAL-LDILDTAGQAE 62
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVN-KRGLMVPIVVVGNKCELE-F 168
F AMR+ + + F++ Y+V D ++ + +E I + +P+V+VGNK +LE
Sbjct: 63 FTAMRDQYMRCGEGFIICYSVTDRHSFQEASEFKELITRVRLTEDIPLVLVGNKVDLEQQ 122
Query: 169 KDVRREIAETIALYDWQCGFVECSAKENYNIVQVFKEL 206
+ V E +A ++ C F E SA + I F L
Sbjct: 123 RQVTTEEGRNLA-REFNCPFFETSAALRFYIDDAFHGL 159
>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 = 82.8 bits (205), Expect = 1e-19
Identities = 51/173 (29%), Positives = 80/173 (46%), Gaps = 18/173 (10%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELP-DG--AQLTLDILDTSG 107
R+V++G VGKSS+I + + F + E +P D ++ I+DTS
Sbjct: 4 RIVLIGDEGVGKSSLIMSLVSEEFPENVPRVLPE-----ITIPADVTPERVPTTIVDTSS 58
Query: 108 AYQFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCELE 167
Q A I A+ LVY+VD ST + ++ ++ + G+ VPI++VGNK +L
Sbjct: 59 RPQDRANLAAEIRKANVICLVYSVDRPSTLERIRTKWLPLIRRLGVKVPIILVGNKSDLR 118
Query: 168 FKDVRREIAETIALYDWQCGF------VECSAKENYNIVQVFKELLAQAKVQY 214
+ + E + F VECSAK N+ +VF AQ V +
Sbjct: 119 DGSSQAGLEEEMLPI--MNEFREIETCVECSAKTLINVSEVF--YYAQKAVLH 167
>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 = 80.3 bits (199), Expect = 7e-19
Identities = 46/157 (29%), Positives = 84/157 (53%), Gaps = 2/157 (1%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
+VV++G RVGK+S++ +++ ++F +++ T + + G ++ L I DT+G +
Sbjct: 2 KVVLLGEGRVGKTSLVLRYVENKFNEKHESTTQASFFQKTVNIGGKRIDLAIWDTAGQER 61
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCELEF-K 169
+ A+ + AD +LVY + DA ++ VK +++ RG + +V+VGNK +LE +
Sbjct: 62 YHALGPIYYRDADGAILVYDITDADSFQKVKKWIKELKQMRGNNISLVIVGNKIDLERQR 121
Query: 170 DVRREIAETIALYDWQCGFVECSAKENYNIVQVFKEL 206
V + AE A E SAK I ++F L
Sbjct: 122 VVSKSEAEEYA-KSVGAKHFETSAKTGKGIEELFLSL 157
>gnl|CDD|219856 pfam08477, Miro, Miro-like protein. Mitochondrial Rho proteins
(Miro-1, and Miro-2), are atypical Rho GTPases. They
have a unique domain organisation, with tandem
GTP-binding domains and two EF hand domains (pfam00036),
that may bind calcium. They are also larger than
classical small GTPases. It has been proposed that they
are involved in mitochondrial homeostasis and apoptosis.
Length = 116
Score = 78.6 bits (194), Expect = 1e-18
Identities = 34/116 (29%), Positives = 55/116 (47%), Gaps = 2/116 (1%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
+VVV+G GKSS++SQ + F E + + DG L+I D G +
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREE 60
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQI--VNKRGLMVPIVVVGNKC 164
+ + ADA +LVY + D + + V L + + K G +P+++VGNK
Sbjct: 61 LKFEHIIFMKWADAILLVYDLTDRESLNEVSRLIAWLPNLRKLGGKIPVILVGNKL 116
>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 = 79.7 bits (197), Expect = 3e-18
Identities = 51/191 (26%), Positives = 87/191 (45%), Gaps = 17/191 (8%)
Query: 49 KRRVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGA 108
K ++VV+G GK+ ++ + F Y TV E + ++P+G + L + DT+G
Sbjct: 3 KVKIVVVGDGGCGKTCLLMVYAQGSFPEEYVPTVFENYVTTLQVPNGKIIELALWDTAGQ 62
Query: 109 YQFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCELEF 168
+ +R LS D ++ Y+VD+ ++ D V+D VN PIV+VG K +L
Sbjct: 63 EDYDRLRPLSYPDVDVILICYSVDNPTSLDNVEDKWYPEVNHFCPGTPIVLVGLKTDLR- 121
Query: 169 KDVRR--------------EIAETIALYDWQCGFVECSAKENYNIVQVFKE--LLAQAKV 212
KD E E++A ++ECSAK N+ +VF +A +K
Sbjct: 122 KDKNSVSKLRAQGLEPVTPEQGESVAKSIGAVAYIECSAKLMENVDEVFDAAINVALSKS 181
Query: 213 QYNLSPAVRRR 223
+++
Sbjct: 182 GRAARKKKKKK 192
>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 = 76.3 bits (188), Expect = 3e-17
Identities = 38/162 (23%), Positives = 77/162 (47%), Gaps = 4/162 (2%)
Query: 50 RRVVVMGGARVGKSSIISQFLY-DRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGA 108
++V++G VGKS+++++ L I+ YK + DG ++LDT+G
Sbjct: 2 IKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAGQ 61
Query: 109 YQFPAMRELSISTADAFVLVYAVDDA--STWDVVKDLREQIVNKRGLMVPIVVVGNKCEL 166
+ A+R L ++ + V+ + ++++ ++I++ VPI++VGNK +L
Sbjct: 62 EDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAESGVPIILVGNKIDL 121
Query: 167 EFKDVRREIAETIALYDWQCGFVECSAKENYNIVQVFKELLA 208
++ +A A + + SA+ NI FK + A
Sbjct: 122 RDAKLKTHVAFLFAKLN-GEPIIPLSAETGKNIDSAFKIVEA 162
>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 = 75.3 bits (186), Expect = 7e-17
Identities = 46/176 (26%), Positives = 80/176 (45%), Gaps = 33/176 (18%)
Query: 52 VVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQF 111
+VV+G VGK+ ++ + ++F + Y TV + + + DG Q+ L + DT+G ++
Sbjct: 3 IVVVGDGAVGKTCLLISYTTNKFPTEYVPTVFDNYSANVTV-DGKQVNLGLWDTAGQEEY 61
Query: 112 PAMRELSISTADAFVLVYAVDDASTWDVVKD-----LREQIVNKRGLMVPIVVVGNKCEL 166
+R LS D F+L ++VD S+++ VK ++ N VPI++VG K
Sbjct: 62 DRLRPLSYPQTDVFLLCFSVDSPSSFENVKTKWYPEIKHYCPN-----VPIILVGTKI-- 114
Query: 167 EFKDVRREIAETIALYDWQ-----------------CGFVECSAKENYNIVQVFKE 205
D+R + L Q ++ECSA + +VF E
Sbjct: 115 ---DLRDDGNTLKKLEKKQKPITPEEGEKLAKEIGAVKYMECSALTQEGLKEVFDE 167
>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 = 73.0 bits (180), Expect = 4e-16
Identities = 49/164 (29%), Positives = 87/164 (53%), Gaps = 9/164 (5%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETV-EELHRGEYELPDGAQLTLDILDTSGAY 109
++V +G VGK+SII++F+YD F ++Y+ T+ + + D + L + DT+G
Sbjct: 2 KLVFLGDQSVGKTSIITRFMYDTFDNQYQATIGIDFLSKTMYV-DDKTVRLQLWDTAGQE 60
Query: 110 QFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCELEFK 169
+F ++ I + V+VY + + ++D + + ++RG V IV+VGNK +L
Sbjct: 61 RFRSLIPSYIRDSSVAVVVYDITNRQSFDNTDKWIDDVRDERGNDVIIVLVGNKTDL--- 117
Query: 170 DVRRE--IAETIALYDWQ-CGFVECSAKENYNIVQVFKELLAQA 210
+R+ E F+E SAK +N+ Q+FK +AQA
Sbjct: 118 SDKRQVSTEEGEKKAKENNAMFIETSAKAGHNVKQLFK-KIAQA 160
>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 = 73.5 bits (181), Expect = 4e-16
Identities = 51/179 (28%), Positives = 91/179 (50%), Gaps = 27/179 (15%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETV------EELHRGEYELPDGAQLTLDILD 104
+V+++G + VGK+S+++Q++ +F ++YK T+ +E+ D +TL I D
Sbjct: 2 KVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEV------TVDDRLVTLQIWD 55
Query: 105 TSGAYQFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLM----VPIVVV 160
T+G +F ++ AD VLVY V + +++ + R++ + + P VV+
Sbjct: 56 TAGQERFQSLGVAFYRGADCCVLVYDVTNPKSFESLDSWRDEFLIQASPRDPENFPFVVL 115
Query: 161 GNKCELEFKDVRREIAETIALYDWQCG------FVECSAKENYNIVQVFKELLAQAKVQ 213
GNK +LE K R+++ A W C + E SAKE N+ Q F+ + A Q
Sbjct: 116 GNKIDLEEK---RQVSTKKAQ-QW-CKSKGNIPYFETSAKEAINVDQAFETIARLALEQ 169
>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 = 72.2 bits (177), Expect = 1e-15
Identities = 44/165 (26%), Positives = 93/165 (56%), Gaps = 8/165 (4%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKET--VEELHRGEYELPDGAQLTLDILDTSGA 108
+V+++G VGKSS++++++ ++F ++ T VE L++ + E+ DG +TL I DT+G
Sbjct: 7 KVILLGDGGVGKSSLMNRYVTNKFDTQLFHTIGVEFLNK-DLEV-DGHFVTLQIWDTAGQ 64
Query: 109 YQFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVN----KRGLMVPIVVVGNKC 164
+F ++R +D +L ++VDD+ ++ + + +++ + K P V++GNK
Sbjct: 65 ERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVILGNKI 124
Query: 165 ELEFKDVRREIAETIALYDWQCGFVECSAKENYNIVQVFKELLAQ 209
++ + V E A+ + + E SAK+ N+ F+E + +
Sbjct: 125 DIPERQVSTEEAQAWCRDNGDYPYFETSAKDATNVAAAFEEAVRR 169
>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 = 71.7 bits (176), Expect = 1e-15
Identities = 44/162 (27%), Positives = 87/162 (53%), Gaps = 5/162 (3%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKET--VEELHRGEYELPDGAQLTLDILDTSGA 108
+V+V+G VGKSS+I +F+ F YK+T V+ L + + + L + DT+G
Sbjct: 2 KVIVVGNGNVGKSSMIQRFVKGIFTKDYKKTIGVDFLEKQIFLRQSDEDVRLMLWDTAGQ 61
Query: 109 YQFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCEL-E 167
+F A+ + A A +LV++ D +++ ++ +E++ + G +P+V+V K +L +
Sbjct: 62 EEFDAITKAYYRGAQACILVFSTTDRESFEAIESWKEKVEAECG-DIPMVLVQTKIDLLD 120
Query: 168 FKDVRREIAETIALYDWQCGFVECSAKENYNIVQVFKELLAQ 209
+ E AE +A Q S K+++N+ ++F+ L +
Sbjct: 121 QAVITNEEAEALAK-RLQLPLFRTSVKDDFNVTELFEYLAEK 161
>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 = 68.8 bits (169), Expect = 2e-14
Identities = 45/167 (26%), Positives = 81/167 (48%), Gaps = 14/167 (8%)
Query: 52 VVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQF 111
+VV+G VGK+ ++ + + F Y TV E + + E+ DG + L + DT+G +
Sbjct: 1 LVVVGDGAVGKTCLLIVYTTNAFPEDYVPTVFENYSADVEV-DGKPVELGLWDTAGQEDY 59
Query: 112 PAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCEL----- 166
+R LS D F++ ++VD ++++ VK+ V VPI++VG K +L
Sbjct: 60 DRLRPLSYPDTDVFLICFSVDSPASFENVKEKWYPEVKHFCPNVPIILVGTKLDLRNDKS 119
Query: 167 --------EFKDVRREIAETIALYDWQCGFVECSAKENYNIVQVFKE 205
+ + V E + +A ++ECSA + +VF+E
Sbjct: 120 TLEELSKKKQEPVTYEQGQALAKRIGAVKYLECSALTQEGVREVFEE 166
>gnl|CDD|206656 cd01863, Rab18, Rab GTPase family 18 (Rab18). Rab18 subfamily.
Mammalian Rab18 is implicated in endocytic transport and
is expressed most highly in polarized epithelial cells.
However, trypanosomal Rab, TbRAB18, is upregulated in
the BSF (Blood Stream Form) stage and localized
predominantly to elements of the Golgi complex. In human
and mouse cells, Rab18 has been identified in lipid
droplets, organelles that store neutral lipids. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 161
Score = 67.0 bits (164), Expect = 7e-14
Identities = 48/161 (29%), Positives = 78/161 (48%), Gaps = 8/161 (4%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
+++++G + VGKSS++ +F D F T+ + + DG ++ L I DT+G +
Sbjct: 2 KILLIGDSGVGKSSLLLRFTDDTFDEDLSSTIGVDFKVKTVTVDGKKVKLAIWDTAGQER 61
Query: 111 FPAMRELSIS---TADAFVLVYAVDDASTWDVVKD-LREQIVNKRGLMVPIVVVGNKCEL 166
F R L+ S A +LVY V T+D + L E ++VGNK +
Sbjct: 62 F---RTLTSSYYRGAQGVILVYDVTRRDTFDNLDTWLNELDTYSTNPDAVKMLVGNKIDK 118
Query: 167 EFKDVRREIAETIALYDWQCGFVECSAKENYNIVQVFKELL 207
E ++V RE + A F+E SAK + Q F+EL+
Sbjct: 119 ENREVTREEGQKFA-RKHNMLFIETSAKTRIGVQQAFEELV 158
>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 = 67.4 bits (165), Expect = 1e-13
Identities = 53/196 (27%), Positives = 95/196 (48%), Gaps = 29/196 (14%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELP---------DGAQLTLD 101
RVV++G + VGKSS+ + F V E E DG + TL
Sbjct: 2 RVVLLGDSGVGKSSLANIFTAG---------VYEDSAYEASGDDTYERTVSVDGEEATLV 52
Query: 102 ILDTSGAYQFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLM-VPIVVV 160
+ D + + + DA+V+VY+V D S+++ +LR Q+ R +PI++V
Sbjct: 53 VYDHWEQEDGMWLEDSCMQVGDAYVIVYSVTDRSSFEKASELRIQLRRARQAEDIPIILV 112
Query: 161 GNKCEL-EFKDVRREIAETIA-LYDWQCGFVECSAKENYNIVQVFKELLAQAKVQYN--- 215
GNK +L ++V + A ++D C F+E SA +N+ ++F+ ++ Q +++ +
Sbjct: 113 GNKSDLVRSREVSVQEGRACAVVFD--CKFIETSAALQHNVDELFEGIVRQVRLRRDSKE 170
Query: 216 ---LSPAVRRRRQSLP 228
A R+RR+S+
Sbjct: 171 KNTRRMASRKRRESIT 186
>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 = 66.5 bits (162), Expect = 1e-13
Identities = 44/162 (27%), Positives = 85/162 (52%), Gaps = 10/162 (6%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
+++++G + VGK+S + ++ D F S + TV + + + ++ L I DT+G +
Sbjct: 3 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVYRNDKRIKLQIWDTAGQER 62
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCELEFKD 170
+ + A F+L+Y + + +++ V+D QI +++VGNKC++E +
Sbjct: 63 YRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSWDNAQVILVGNKCDMEDER 122
Query: 171 V-----RREIAETIALYDWQCGFVECSAKENYNIVQVFKELL 207
V R++A+ + F E SAKEN N+ QVF+ L+
Sbjct: 123 VVSAERGRQLADQLGFE-----FFEASAKENINVKQVFERLV 159
>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 = 66.7 bits (163), Expect = 1e-13
Identities = 42/169 (24%), Positives = 76/169 (44%), Gaps = 24/169 (14%)
Query: 53 VVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQFP 112
V++G VGK+S+I + + + + Y T + + DG + L + DT+G +F
Sbjct: 4 VLVGDGAVGKTSLIVSYTTNGYPTEYVPTAFDNFSVVVLV-DGKPVRLQLCDTAGQDEFD 62
Query: 113 AMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCELEFKDVR 172
+R L D F+L ++V + S++ + + + K PI++VG + +L DV
Sbjct: 63 KLRPLCYPDTDVFLLCFSVVNPSSFQNISEKWIPEIRKHNPKAPIILVGTQADLR-TDVN 121
Query: 173 ------------------REIAETIALYDWQCGFVECSAKENYNIVQVF 203
+ +AE I C ++ECSA N+ +VF
Sbjct: 122 VLIQLARYGEKPVSQSRAKALAEKIG----ACEYIECSALTQKNLKEVF 166
>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 = 62.6 bits (153), Expect = 3e-12
Identities = 47/183 (25%), Positives = 83/183 (45%), Gaps = 54/183 (29%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGA------------QL 98
++V++G + VGKSSI+ +F+ + F + T+ GA +
Sbjct: 3 KLVLLGDSSVGKSSIVLRFVKNEFSENQESTI------------GAAFLTQTVNLDDTTV 50
Query: 99 TLDILDTSGAYQFPAMRELSISTADAFVLVYAV------DDASTWDVVKDLREQ----IV 148
+I DT+G ++ ++ + A A ++VY + + A +W VK+L+E IV
Sbjct: 51 KFEIWDTAGQERYRSLAPMYYRGAAAAIVVYDITSEESFEKAKSW--VKELQEHGPPNIV 108
Query: 149 NKRGLMVPIVVVGNKCELEFK-----DVRREIAETIALYDWQCGFVECSAKENYNIVQVF 203
I + GNK +LE K + +E A+ L F+E SAK N+ ++F
Sbjct: 109 --------IALAGNKADLESKRQVSTEEAQEYADENGLL-----FMETSAKTGENVNELF 155
Query: 204 KEL 206
E+
Sbjct: 156 TEI 158
>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 = 61.8 bits (150), Expect = 1e-11
Identities = 53/181 (29%), Positives = 86/181 (47%), Gaps = 17/181 (9%)
Query: 50 RRVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAY 109
R+VVV+G GK+S+++ F F Y+ TV E + + + DG + L + DT+G
Sbjct: 1 RKVVVLGDGACGKTSLLNVFTRGYFPQVYEPTVFENYIHDIFV-DGLAVELSLWDTAGQE 59
Query: 110 QFPAMRELSISTADAFVLVYAVDDASTWDVV--KDLREQIVNKRGLMVPIVVVGNKCELE 167
+F +R LS + +L ++VD+ + + V K L E + G V +V+V KC+L
Sbjct: 60 EFDRLRSLSYADTHVIMLCFSVDNPDSLENVESKWLAEIRHHCPG--VKLVLVALKCDLR 117
Query: 168 FKDVRREIAETIALYDW---------QCGFVECSAKENYNIVQVFKELLAQAKVQYNLSP 218
R+ Y+ C ++ECSAK N + + F E A+V N P
Sbjct: 118 EPRNERDRGTHTISYEEGLAVAKRINACRYLECSAKLNRGVNEAFTEA---ARVALNARP 174
Query: 219 A 219
Sbjct: 175 P 175
>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 = 60.5 bits (147), Expect = 2e-11
Identities = 47/177 (26%), Positives = 83/177 (46%), Gaps = 32/177 (18%)
Query: 49 KRRVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGA 108
++++V++G GK+ ++ F D+F Y TV E + + E+ DG Q+ L + DT+G
Sbjct: 1 RKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEV-DGKQVELALWDTAGQ 59
Query: 109 YQFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCELEF 168
+ +R LS D ++ +++D + + + + V VPI++VGNK
Sbjct: 60 EDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNK----- 114
Query: 169 KDVR----------------------REIAETIALYDWQCGFVECSAKENYNIVQVF 203
KD+R R +AE I + G++ECSAK + +VF
Sbjct: 115 KDLRNDEHTIRELAKMKQEPVKPEEGRAMAEKIGAF----GYLECSAKTKEGVREVF 167
>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 = 60.2 bits (146), Expect = 4e-11
Identities = 42/167 (25%), Positives = 80/167 (47%), Gaps = 12/167 (7%)
Query: 49 KRRVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGA 108
+R++V++G GK+S++ F F Y TV E + + + DG + L + DT+G
Sbjct: 1 RRKLVIVGDGACGKTSLLYVFTLGEFPEEYHPTVFENYVTDCRV-DGKPVQLALWDTAGQ 59
Query: 109 YQFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCELEF 168
++ +R LS S A ++ +A+D + + V+ + V + VP+++VG K +L
Sbjct: 60 EEYERLRPLSYSKAHVILIGFAIDTPDSLENVRTKWIEEVRRYCPNVPVILVGLKKDLRQ 119
Query: 169 KD-----------VRREIAETIALYDWQCGFVECSAKENYNIVQVFK 204
+ V + A+ +A ++ECSA + VF+
Sbjct: 120 EAVAKGNYATDEFVPIQQAKLVARAIGAKKYMECSALTGEGVDDVFE 166
>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 = 57.1 bits (138), Expect = 3e-10
Identities = 39/157 (24%), Positives = 81/157 (51%), Gaps = 1/157 (0%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
+++++G + VGK+ ++ +F F R T+ + G ++ L I DT+G +
Sbjct: 5 KIILIGDSNVGKTCVVQRFKSGTFSERQGNTIGVDFTMKTLEIQGKRVKLQIWDTAGQER 64
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCEL-EFK 169
F + + +A+ ++ Y + S+++ V E++ V ++++GNKC+L E +
Sbjct: 65 FRTITQSYYRSANGAIIAYDITRRSSFESVPHWIEEVEKYGASNVVLLLIGNKCDLEEQR 124
Query: 170 DVRREIAETIALYDWQCGFVECSAKENYNIVQVFKEL 206
+V E A T+A + +E SAKE+ N+ + F +
Sbjct: 125 EVLFEEACTLAEHYGILAVLETSAKESSNVEEAFLLM 161
>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 = 56.9 bits (137), Expect = 7e-10
Identities = 44/160 (27%), Positives = 81/160 (50%), Gaps = 3/160 (1%)
Query: 50 RRVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAY 109
+V+++G VGK+S++ +F D F K TV + + G ++ L I DT+G
Sbjct: 1 LQVIIIGSRGVGKTSLMERFTDDTFCEACKSTVGVDFKIKTVELRGKKIRLQIWDTAGQE 60
Query: 110 QFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNK--CELE 167
+F ++ +A +LVY + T+D + + I +++VGNK CE +
Sbjct: 61 RFNSITSAYYRSAKGIILVYDITKKETFDDLPKWMKMIDKYASEDAELLLVGNKLDCETD 120
Query: 168 FKDVRREIAETIALYDWQCGFVECSAKENYNIVQVFKELL 207
+++ R+ E A F E SAK+N+N+ ++F +L+
Sbjct: 121 -REITRQQGEKFAQQITGMRFCEASAKDNFNVDEIFLKLV 159
>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 = 55.0 bits (133), Expect = 2e-09
Identities = 45/173 (26%), Positives = 79/173 (45%), Gaps = 24/173 (13%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
+++++G + VGKS ++ +F D + Y T+ + DG + L I DT+G +
Sbjct: 4 KLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTVKLQIWDTAGQER 63
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQI-------VNKRGLMVPIVVVGNK 163
F + A ++VY V D +++ VK ++I VNK ++VGNK
Sbjct: 64 FRTITSSYYRGAHGIIIVYDVTDQESFNNVKQWLQEIDRYASENVNK-------LLVGNK 116
Query: 164 CELEFK-----DVRREIAETIALYDWQCGFVECSAKENYNIVQVFKELLAQAK 211
C+L K +E A+ + F+E SAK N+ + F + + K
Sbjct: 117 CDLTDKKVVDYTEAKEFADEL-----GIPFLETSAKNATNVEEAFMTMAREIK 164
>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 = 53.3 bits (128), Expect = 6e-09
Identities = 42/169 (24%), Positives = 83/169 (49%), Gaps = 15/169 (8%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVE-ELHRGEYELPDGAQLTLDILDTSGAY 109
+++++G + VGKS ++ +FL D + + T L++ + +G + +D DT+G
Sbjct: 2 KIILLGDSAVGKSKLVERFLMDGYEPQQLSTYALTLYKHNAKF-EGKTILVDFWDTAGQE 60
Query: 110 QFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCELEFK 169
+F M A A +LV+ V T+ + E++ R +P +VV NK +L+
Sbjct: 61 RFQTMHASYYHKAHACILVFDVTRKITYKNLSKWYEELREYRP-EIPCIVVANKIDLDPS 119
Query: 170 DVRREIA----ETIALYDWQCGFVECSAKENYNIVQVFKELLAQAKVQY 214
+++ + LY +V SA + N+V++F++ + A V Y
Sbjct: 120 VTQKKFNFAEKHNLPLY-----YV--SAADGTNVVKLFQDAIKLA-VSY 160
>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 = 53.4 bits (128), Expect = 6e-09
Identities = 43/163 (26%), Positives = 85/163 (52%), Gaps = 8/163 (4%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
++V++G A VGK+ ++ +F F T+ + G ++ L I DT+G +
Sbjct: 9 KIVLIGNAGVGKTCLVRRFTQGLFPPGQGATIGVDFMIKTVEIKGEKIKLQIWDTAGQER 68
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWDVVKD-LRE--QIVNKRGLMVPIVVVGNKCEL- 166
F ++ + +A+A +L Y + ++ + + LRE Q N + V ++VGNK +L
Sbjct: 69 FRSITQSYYRSANALILTYDITCEESFRCLPEWLREIEQYANNK---VITILVGNKIDLA 125
Query: 167 EFKDVRREIAETIALYDWQCGFVECSAKENYNIVQVFKELLAQ 209
E ++V ++ AE + ++E SAKE+ N+ ++F +L +
Sbjct: 126 ERREVSQQRAEEFSDAQ-DMYYLETSAKESDNVEKLFLDLACR 167
>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 = 54.0 bits (130), Expect = 7e-09
Identities = 36/121 (29%), Positives = 62/121 (51%), Gaps = 4/121 (3%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVE-ELHRGEYELPDGAQLTLDILDTSGAY 109
++VV+G GK+S+I +F + F YK+T+ + LP +TL + D G
Sbjct: 2 KIVVLGDGASGKTSLIRRFAQEGFGKSYKQTIGLDFFSRRITLPGSLNVTLQVWDIGGQQ 61
Query: 110 QFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQI--VNKRGLMVP-IVVVGNKCEL 166
M + I A A LVY + ++ +++ ++D + VN+ P +V+VGNK +L
Sbjct: 62 IGGKMLDKYIYGAQAVCLVYDITNSQSFENLEDWLSVVKKVNEESETKPKMVLVGNKTDL 121
Query: 167 E 167
E
Sbjct: 122 E 122
>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 = 52.9 bits (127), Expect = 9e-09
Identities = 48/160 (30%), Positives = 80/160 (50%), Gaps = 10/160 (6%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVE-ELHRGEYELPDGAQLTLDILDTSGAY 109
+ +++G VGKS ++ QF +F++ T+ E E+ +G ++ L I DT+G
Sbjct: 4 KYIIIGDMGVGKSCLLHQFTEKKFMADCPHTIGVEFGTRIIEV-NGQKIKLQIWDTAGQE 62
Query: 110 QFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVP---IVVVGNKCEL 166
+F A+ A ++VY + ST++ L + + R L P I ++GNK +L
Sbjct: 63 RFRAVTRSYYRGAAGALMVYDITRRSTYN---HLSSWLTDARNLTNPNTVIFLIGNKADL 119
Query: 167 E-FKDVRREIAETIALYDWQCGFVECSAKENYNIVQVFKE 205
E +DV E A+ A + F+ECSAK N+ F E
Sbjct: 120 EAQRDVTYEEAKQFADEN-GLLFLECSAKTGENVEDAFLE 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 = 52.7 bits (127), Expect = 1e-08
Identities = 36/169 (21%), Positives = 81/169 (47%), Gaps = 9/169 (5%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVE-ELHRGEYELPDGAQLTLDILDTSGAY 109
++V++G GK++ + + L F +Y T+ E+H ++ + ++ ++ DT+G
Sbjct: 2 KLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLDF-HTNRGKIRFNVWDTAGQE 60
Query: 110 QFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCELEFK 169
+F +R+ ++++ V T+ V + +V +PIV+ GNK +++ +
Sbjct: 61 KFGGLRDGYYIQGQCAIIMFDVTSRVTYKNVPNWHRDLVRVCE-NIPIVLCGNKVDIKDR 119
Query: 170 DVRREIAETIALYDWQCGFVECSAKENYNIVQVF----KELLAQAKVQY 214
V+ + + + E SAK NYN + F ++LL +++
Sbjct: 120 KVKPKQITFHRKKN--LQYYEISAKSNYNFEKPFLWLARKLLGNPNLEF 166
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 53.1 bits (127), Expect = 1e-08
Identities = 56/178 (31%), Positives = 86/178 (48%), Gaps = 16/178 (8%)
Query: 37 SSSGTGVGLQKDKRRVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELP--- 93
SSSG G +++++G + VGKSS++ F IS E + ++++
Sbjct: 3 SSSGQSSGYDL-SFKILLIGDSGVGKSSLLVSF-----ISSSVEDLAPTIGVDFKIKQLT 56
Query: 94 -DGAQLTLDILDTSGAYQFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRG 152
G +L L I DT+G +F + A +LVY V T+ + D+ + V
Sbjct: 57 VGGKRLKLTIWDTAGQERFRTLTSSYYRNAQGIILVYDVTRRETFTNLSDVWGKEVELYS 116
Query: 153 LMVPIV--VVGNKCELEF-KDVRREIAETIALY-DWQCGFVECSAKENYNIVQVFKEL 206
V +VGNK + E +DV RE E +AL + C F+ECSAK N+ Q F+EL
Sbjct: 117 TNQDCVKMLVGNKVDRESERDVSRE--EGMALAKEHGCLFLECSAKTRENVEQCFEEL 172
>gnl|CDD|206695 cd04112, Rab26, Rab GTPase family 26 (Rab26). Rab26 subfamily.
First identified in rat pancreatic acinar cells, Rab26
is believed to play a role in recruiting mature granules
to the plasma membrane upon beta-adrenergic stimulation.
Rab26 belongs to the Rab functional group III, which are
considered key regulators of intracellular vesicle
transport during exocytosis. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 191
Score = 52.6 bits (126), Expect = 2e-08
Identities = 43/163 (26%), Positives = 85/163 (52%), Gaps = 3/163 (1%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFIS-RYKETVEELHRGEYELPDGAQLTLDILDTSGAY 109
+V+++G + VGK+ ++ +F F++ + TV + DG ++ L I DT+G
Sbjct: 2 KVMLVGDSGVGKTCLLVRFKDGAFLAGSFIATVGIQFTNKVVTVDGVKVKLQIWDTAGQE 61
Query: 110 QFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCELEF- 168
+F ++ A A +L+Y V + S++D ++ +I+ V I+++GNK ++
Sbjct: 62 RFRSVTHAYYRDAHALLLLYDVTNKSSFDNIRAWLTEILEYAQSDVVIMLLGNKADMSGE 121
Query: 169 KDVRREIAETIALYDWQCGFVECSAKENYNIVQVFKELLAQAK 211
+ V+RE E +A ++ F+E SAK N+ F + + K
Sbjct: 122 RVVKREDGERLA-KEYGVPFMETSAKTGLNVELAFTAVAKELK 163
>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 = 52.3 bits (125), Expect = 2e-08
Identities = 43/170 (25%), Positives = 76/170 (44%), Gaps = 18/170 (10%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
+ VV+G VGK+ ++ + D F Y TV + H G Q L + DT+G
Sbjct: 2 KCVVVGDGAVGKTCLLMSYANDAFPEEYVPTVFD-HYAVSVTVGGKQYLLGLYDTAGQED 60
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLM--VPIVVVGNKCEL-- 166
+ +R LS D F++ ++V + +++ VK+ E + + VP +++G + +L
Sbjct: 61 YDRLRPLSYPMTDVFLICFSVVNPASFQNVKE--EWVPELKEYAPNVPYLLIGTQIDLRD 118
Query: 167 -----------EFKDVRREIAETIALYDWQCGFVECSAKENYNIVQVFKE 205
+ K + E + +A C +VECSA + VF E
Sbjct: 119 DPKTLARLNDMKEKPITVEQGQKLAKEIGACCYVECSALTQKGLKTVFDE 168
>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 = 52.5 bits (126), Expect = 3e-08
Identities = 48/164 (29%), Positives = 85/164 (51%), Gaps = 9/164 (5%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVE-ELHRGEYELPDGAQLTLDILDTSGAY 109
R++V+G + VGKSS++ +F RF TV + E+ G ++ L + DT+G
Sbjct: 4 RLIVIGDSTVGKSSLLKRFTEGRFAEVSDPTVGVDFFSRLIEIEPGVRIKLQLWDTAGQE 63
Query: 110 QFPAMRELSISTADAFVLVYAVDDASTWDVVKD-LREQIVNKRGLMVPIVVVGNKCELEF 168
+F ++ + +LV+ + + +++ V D L E + + ++VG+KC+LE
Sbjct: 64 RFRSITRSYYRNSVGVLLVFDITNRESFEHVHDWLEEARSHIQPHRPVFILVGHKCDLES 123
Query: 169 -KDVRREIAETIALYDWQCG--FVECSAKENYNIVQVFKELLAQ 209
+ V RE AE +A G ++E SA+ N+ + F ELL Q
Sbjct: 124 QRQVTREEAEKLAKD---LGMKYIETSARTGDNVEEAF-ELLTQ 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 = 51.5 bits (124), Expect = 3e-08
Identities = 49/170 (28%), Positives = 84/170 (49%), Gaps = 28/170 (16%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVE--------ELHRGEYELPDGAQLTLDI 102
+++++G + VGKS ++ +F D F + T+ EL DG ++ L I
Sbjct: 5 KLLLIGDSGVGKSCLLLRFSEDSFNPSFISTIGIDFKIRTIEL--------DGKKIKLQI 56
Query: 103 LDTSGAYQFPAMRELSIST-----ADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPI 157
DT+G +F +I+T A +LVY + D +++ +K+ I V
Sbjct: 57 WDTAGQERFR-----TITTSYYRGAMGIILVYDITDEKSFENIKNWMRNIDEHASEDVER 111
Query: 158 VVVGNKCELEFK-DVRREIAETIALYDWQCGFVECSAKENYNIVQVFKEL 206
++VGNKC++E K V +E E +A ++ F+E SAK N N+ + F L
Sbjct: 112 MLVGNKCDMEEKRVVSKEEGEALAR-EYGIKFLETSAKANINVEEAFLTL 160
>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 = 51.4 bits (123), Expect = 4e-08
Identities = 46/168 (27%), Positives = 67/168 (39%), Gaps = 13/168 (7%)
Query: 51 RVVVMGGARVGKSSIISQFLYD--RFISRYKETVE-ELHRGEYELPD-GAQLTLDILDTS 106
+ V+G VGKS+++ F D F Y T +L +PD + L I D++
Sbjct: 2 QCAVVGDPAVGKSALVQMFHSDGATFQKNYTMTTGCDLVVKTVPVPDTSDSVELFIFDSA 61
Query: 107 GAYQFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQI-VNKRGLMVPIVVVGNKCE 165
G F M E +VY V + +++ ++ + GL P V+VGNKC+
Sbjct: 62 GQELFSDMVENVWEQPAVVCVVYDVTNEVSFNNCSRWINRVRTHSHGLHTPGVLVGNKCD 121
Query: 166 LEFKDVRREIAETIALYDWQCG----FVECSAKENYNIVQVFKELLAQ 209
L RRE+ A F E SAKE F L
Sbjct: 122 LT---DRREVDAAQA-QALAQANTLKFYETSAKEGVGYEAPFLSLARA 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 = 50.9 bits (122), Expect = 4e-08
Identities = 47/159 (29%), Positives = 75/159 (47%), Gaps = 16/159 (10%)
Query: 53 VVMGGARVGKSSIISQFLYDRFISRYKETVEELHRG-EYELP----DGAQLTLDILDTSG 107
+++G VGKS ++ QF RF + V +L G E+ DG Q+ L I DT+G
Sbjct: 8 IIIGDTGVGKSCLLLQFTDKRF-----QPVHDLTIGVEFGARMITIDGKQIKLQIWDTAG 62
Query: 108 AYQFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCELE 167
F ++ A +LVY + T++ + E + I+++GNKC+LE
Sbjct: 63 QESFRSITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQHSNSNMTIMLIGNKCDLE 122
Query: 168 FK-DVRREIAETIALYDWQCG--FVECSAKENYNIVQVF 203
+ +V E E A + G F+E SAK N+ + F
Sbjct: 123 SRREVSYEEGEAFAR---EHGLIFMETSAKTASNVEEAF 158
>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 = 51.2 bits (122), Expect = 5e-08
Identities = 44/189 (23%), Positives = 88/189 (46%), Gaps = 19/189 (10%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
+ VV+G VGK+ ++ + + F Y TV + + + + DG ++L++ DT+G +
Sbjct: 5 KCVVVGDGAVGKTCLLICYTTNAFPKEYIPTVFDNYSAQTAV-DGRTVSLNLWDTAGQEE 63
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCELEF-K 169
+ +R LS + F++ +++ S+++ V+ V VPI++VG K +L
Sbjct: 64 YDRLRTLSYPQTNVFIICFSIASPSSYENVRHKWHPEVCHHCPNVPILLVGTKKDLRNDA 123
Query: 170 DVRREIAE------------TIALYDWQCGFVECSAKENYNIVQVFKELLAQAKVQYNLS 217
D +++ E +A ++ECSA + +VF E V+ L+
Sbjct: 124 DTLKKLKEQGQAPITPQQGGALAKQIHAVKYLECSALNQDGVKEVFAE-----AVRAVLN 178
Query: 218 PAVRRRRQS 226
P + +S
Sbjct: 179 PTPIKDTKS 187
>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 = 50.8 bits (121), Expect = 6e-08
Identities = 43/174 (24%), Positives = 82/174 (47%), Gaps = 24/174 (13%)
Query: 46 QKDKRRVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDT 105
Q K ++VV+G ++ GK++++ F D F Y TV E + +E+ D ++ L + DT
Sbjct: 2 QNVKCKIVVVGDSQCGKTALLHVFAKDCFPENYVPTVFENYTASFEI-DTQRIELSLWDT 60
Query: 106 SGAYQFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCE 165
SG+ + +R LS +DA ++ + + T D V + + + +++VG K
Sbjct: 61 SGSPYYDNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEIQEFCPNTKMLLVGCK-- 118
Query: 166 LEFKDVRREIAETIAL---------YDWQCG---------FVECSAKENYNIVQ 201
D+R +++ + L YD ++ECSA ++ N V+
Sbjct: 119 ---SDLRTDVSTLVELSNHRQTPVSYDQGANMAKQIGAATYIECSALQSENSVR 169
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 51.5 bits (123), Expect = 6e-08
Identities = 41/160 (25%), Positives = 78/160 (48%), Gaps = 2/160 (1%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
++V++G + VGKS+I+S+F + F K T+ +G + I DT+G +
Sbjct: 14 KIVLIGDSGVGKSNILSRFTRNEFCLESKSTIGVEFATRTLQVEGKTVKAQIWDTAGQER 73
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCEL-EFK 169
+ A+ A +LVY + T+D V+ ++ + + I++ GNK +L +
Sbjct: 74 YRAITSAYYRGAVGALLVYDITKRQTFDNVQRWLRELRDHADSNIVIMMAGNKSDLNHLR 133
Query: 170 DVRREIAETIALYDWQCGFVECSAKENYNIVQVFKELLAQ 209
V E + +A + F+E SA E N+ + F+ +L +
Sbjct: 134 SVAEEDGQALAEKE-GLSFLETSALEATNVEKAFQTILLE 172
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 50.5 bits (120), Expect = 7e-08
Identities = 39/142 (27%), Positives = 72/142 (50%), Gaps = 4/142 (2%)
Query: 70 LYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQFPAMRELSISTADAFVLVY 129
+YD F + Y+ T+ + D + L + DT+G +F ++ I + A ++VY
Sbjct: 1 MYDTFDNNYQSTIGIDFLSKTLYLDEGPVRLQLWDTAGQERFRSLIPSYIRDSAAAIVVY 60
Query: 130 AVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCELEFKDVRREIAE--TIALYDWQCG 187
+ + +++ + I+N+RG V I +VGNK +L D+R+ E ++
Sbjct: 61 DITNRQSFENTTKWIQDILNERGKDVIIALVGNKTDL--GDLRKVTYEEGMQKAQEYNTM 118
Query: 188 FVECSAKENYNIVQVFKELLAQ 209
F E SAK +NI +FK++ A+
Sbjct: 119 FHETSAKAGHNIKVLFKKIAAK 140
>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 = 50.5 bits (121), Expect = 8e-08
Identities = 42/169 (24%), Positives = 80/169 (47%), Gaps = 24/169 (14%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
++V++G ++ GK++++ F D F Y TV E + +E+ D ++ L + DTSG+
Sbjct: 3 KIVLVGDSQCGKTALLQVFAKDSFPENYVPTVFENYTASFEV-DKQRIELSLWDTSGSPY 61
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCELEFKD 170
+ +R LS +DA ++ + + T D V + V + P+++VG K D
Sbjct: 62 YDNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEVREFCPNTPVLLVGCK-----SD 116
Query: 171 VRREIAETIALYDWQC------------------GFVECSAKENYNIVQ 201
+R +++ L + + +VECSAK + N V+
Sbjct: 117 LRTDLSTLTELSNKRQIPVSHEQGRNLAKQIGAAAYVECSAKTSENSVR 165
>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 = 50.4 bits (121), Expect = 1e-07
Identities = 45/162 (27%), Positives = 81/162 (50%), Gaps = 19/162 (11%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRG-EYELP-----DGAQLTLDILD 104
+V+V+G VGK+SII ++++ F YK T+ G ++ L + L + D
Sbjct: 2 KVLVIGDLGVGKTSIIKRYVHGVFSQHYKATI-----GVDFALKVIEWDPNTVVRLQLWD 56
Query: 105 TSGAYQFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNK----RGLMVPIVVV 160
+G +F M + A ++V+ V ST++ V + + +K G +P +++
Sbjct: 57 IAGQERFGGMTRVYYKGAVGAIIVFDVTRPSTFEAVLKWKADLDSKVTLPNGEPIPALLL 116
Query: 161 GNKCELEFKDVRREIAETIALYDWQCGFV---ECSAKENYNI 199
NKC+L+ K+ + E + + + GF+ E SAKEN NI
Sbjct: 117 ANKCDLK-KERLAKDPEQMDQFCKENGFIGWFETSAKENINI 157
>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 = 49.1 bits (117), Expect = 3e-07
Identities = 46/194 (23%), Positives = 85/194 (43%), Gaps = 9/194 (4%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
+++++G + VGKSS++ +F + F Y T+ + +G ++ L I DT+G +
Sbjct: 8 KLLIIGDSGVGKSSLLLRFADNTFSGSYITTIGVDFKIRTVEINGERVKLQIWDTAGQER 67
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCELEFKD 170
F + ++VY V + ++ VK ++I V V+VGNK + D
Sbjct: 68 FRTITSTYYRGTHGVIVVYDVTNGESFVNVKRWLQEIEQNCD-DVCKVLVGNKND----D 122
Query: 171 VRREIAETIALYDW----QCGFVECSAKENYNIVQVFKELLAQAKVQYNLSPAVRRRRQS 226
R++ ET Y + E SAKEN N+ ++F + + A ++++Q
Sbjct: 123 PERKVVETEDAYKFAGQMGISLFETSAKENINVEEMFNCITELVLRAKKDNLAKQQQQQQ 182
Query: 227 LPNYIGTTGSASSK 240
S K
Sbjct: 183 NDVVKLPKNSKRKK 196
>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 = 47.9 bits (114), Expect = 6e-07
Identities = 43/173 (24%), Positives = 77/173 (44%), Gaps = 14/173 (8%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
+ VV+G VGK+ ++ + ++F S Y TV + + + G TL + DT+G
Sbjct: 3 KCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFD-NYAVTVMIGGEPYTLGLFDTAGQED 61
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCEL---- 166
+ +R LS D F++ ++V S+++ VK+ + P ++VG + +L
Sbjct: 62 YDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQIDLRDDP 121
Query: 167 ---------EFKDVRREIAETIALYDWQCGFVECSAKENYNIVQVFKELLAQA 210
+ K + E E +A +VECSA + VF E + A
Sbjct: 122 STIEKLAKNKQKPITPETGEKLARDLKAVKYVECSALTQKGLKNVFDEAILAA 174
>gnl|CDD|133318 cd04118, Rab24, Rab GTPase family 24 (Rab24). Rab24 is distinct
from other Rabs in several ways. It exists primarily in
the GTP-bound state, having a low intrinsic GTPase
activity; it is not efficiently geranyl-geranylated at
the C-terminus; it does not form a detectable complex
with Rab GDP-dissociation inhibitors (GDIs); and it has
recently been shown to undergo tyrosine phosphorylation
when overexpressed in vitro. The specific function of
Rab24 still remains unknown. It is found in a transport
route between ER-cis-Golgi and late endocytic
compartments. It is putatively involved in an autophagic
pathway, possibly directing misfolded proteins in the ER
to degradative pathways. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 193
Score = 47.9 bits (114), Expect = 8e-07
Identities = 37/163 (22%), Positives = 84/163 (51%), Gaps = 10/163 (6%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRF-ISRYKETVEELHRGEYELPDGAQLTLDILDTSGAY 109
+VV++G VGK+S++ ++++ RF + Y+ T+ + + +TL I DT+G+
Sbjct: 2 KVVMLGKESVGKTSLVERYVHHRFLVGPYQNTIGAAFVAKRMVVGERVVTLGIWDTAGSE 61
Query: 110 QFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCEL--E 167
++ AM + A A ++ Y + D+S+++ K +++ N I + G K +L +
Sbjct: 62 RYEAMSRIYYRGAKAAIVCYDLTDSSSFERAKFWVKELQNLEE-HCKIYLCGTKSDLIEQ 120
Query: 168 FKDVRR----EIAETIALYDWQCGFVECSAKENYNIVQVFKEL 206
+ +R+ ++ + Q E S+K N+ ++F+++
Sbjct: 121 DRSLRQVDFHDVQDFADEIKAQ--HFETSSKTGQNVDELFQKV 161
>gnl|CDD|206674 cd01887, IF2_eIF5B, Initiation Factor 2 (IF2)/ eukaryotic
Initiation Factor 5B (eIF5B) family. IF2/eIF5B
contribute to ribosomal subunit joining and function as
GTPases that are maximally activated by the presence of
both ribosomal subunits. As seen in other GTPases,
IF2/IF5B undergoes conformational changes between its
GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess
three characteristic segments, including a divergent
N-terminal region followed by conserved central and
C-terminal segments. This core region is conserved among
all known eukaryotic and archaeal IF2/eIF5Bs and
eubacterial IF2s.
Length = 169
Score = 46.7 bits (112), Expect = 1e-06
Identities = 37/140 (26%), Positives = 57/140 (40%), Gaps = 20/140 (14%)
Query: 86 HRGEYELP-DGAQLTLDILDTSGAYQFPAMRELSISTADAFVLVYAVDD---ASTWDVVK 141
H G Y++P D + +DT G F MR S D +LV A DD T + +
Sbjct: 36 HIGAYQVPIDVKIPGITFIDTPGHEAFTNMRARGASVTDIAILVVAADDGVMPQTIEAIN 95
Query: 142 DLREQIVNKRGLMVPIVVVGNKCELEFKD------VRREIAET-IALYDW--QCGFVECS 192
+ VPI+V NK + + V+ E++E + +W V S
Sbjct: 96 HAK----AAN---VPIIVAINKIDKPYGTEADPERVKNELSELGLVGEEWGGDVSIVPIS 148
Query: 193 AKENYNIVQVFKELLAQAKV 212
AK I + + +L A+V
Sbjct: 149 AKTGEGIDDLLEAILLLAEV 168
>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 = 46.6 bits (111), Expect = 2e-06
Identities = 44/172 (25%), Positives = 75/172 (43%), Gaps = 21/172 (12%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKET------VEELHRGEYELPDGAQLTLDILD 104
+V+ MG + VGKS II ++ RF+S+Y T V+++ ++ ++ D
Sbjct: 2 KVISMGNSGVGKSCIIKRYCEGRFVSKYLPTIGIDYGVKKVSV------RNKEVRVNFFD 55
Query: 105 TSGAYQFPAMRELSISTADAFVLVYAVDDASTWDVV-KDLRE--QIVNKRGLMVPI--VV 159
SG ++ +R +LVY V D +++ + L+E Q G M I VV
Sbjct: 56 LSGHPEYLEVRNEFYKDTQGVLLVYDVTDRQSFEALDSWLKEMKQEGGPHGNMENIVVVV 115
Query: 160 VGNKCELEFKDVRREIAETIALYDWQCGFV--ECSAKENYNIVQVFKELLAQ 209
NK +L E + L+ GF E SA + ++F+ L +
Sbjct: 116 CANKIDLTKHRAVSE--DEGRLWAESKGFKYFETSACTGEGVNEMFQTLFSS 165
>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 = 46.4 bits (110), Expect = 2e-06
Identities = 47/168 (27%), Positives = 76/168 (45%), Gaps = 22/168 (13%)
Query: 53 VVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQFP 112
V +G VGK+ ++ + + F + Y TV + + DG + L + DT+G +
Sbjct: 5 VTVGDGAVGKTCMLISYTSNTFPTDYVPTVFDNFSANVVV-DGNTVNLGLWDTAGQEDYN 63
Query: 113 AMRELSISTADAFVLVYA-VDDASTWDVVK----DLREQIVNKRGLMVPIVVVGNKCELE 167
+R LS AD F+L ++ + AS +V+K +LR VPIV+VG K +L
Sbjct: 64 RLRPLSYRGADVFLLAFSLISKASYENVLKKWIPELRHYAPG-----VPIVLVGTKLDLR 118
Query: 168 -----FKDVRREIAETIALYDWQ------CGFVECSAKENYNIVQVFK 204
F D + T A + ++ECS+K N+ VF
Sbjct: 119 DDKQFFADHPGAVPITTAQGEELRKQIGAAAYIECSSKTQQNVKAVFD 166
>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 = 46.1 bits (109), Expect = 3e-06
Identities = 43/157 (27%), Positives = 75/157 (47%), Gaps = 3/157 (1%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
+ +++G + VGK I++ S Y + ++ L DG ++ L + DTSG +
Sbjct: 8 KFLLVGDSDVGKGEILASLQDGSTESPYGYNMGIDYKTTTILLDGRRVKLQLWDTSGQGR 67
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCELEFK- 169
F + A +LVY + + ++D + ++I ++ VP ++VGN+ L FK
Sbjct: 68 FCTIFRSYSRGAQGIILVYDITNRWSFDGIDRWIKEI-DEHAPGVPKILVGNRLHLAFKR 126
Query: 170 DVRREIAETIALYDWQCGFVECSAKENYNIVQVFKEL 206
V E A+ A + F E S N+NI + F EL
Sbjct: 127 QVATEQAQAYAERN-GMTFFEVSPLCNFNITESFTEL 162
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 46.1 bits (109), Expect = 4e-06
Identities = 50/200 (25%), Positives = 85/200 (42%), Gaps = 10/200 (5%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
+ +++G VGKS ++ QF RF + T+ D + L I DT+G
Sbjct: 8 KYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDNKPIKLQIWDTAGQES 67
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCELEFKD 170
F ++ A +LVY + T++ + E + I+++GNKC+L +
Sbjct: 68 FRSITRSYYRGAAGALLVYDITRRETFNHLASWLEDARQHANANMTIMLIGNKCDLAHRR 127
Query: 171 -VRREIAETIALYDWQCGFVECSAKENYNIVQVFKELLAQ--AKVQ------YNLSPAVR 221
V E E A + F+E SAK N+ + F + A+ K+Q N S ++
Sbjct: 128 AVSTEEGEQFA-KEHGLIFMEASAKTAQNVEEAFIKTAAKIYKKIQDGVFDVSNESYGIK 186
Query: 222 RRRQSLPNYIGTTGSASSKG 241
++P G SS+G
Sbjct: 187 VGYGAIPGASGGRDGTSSQG 206
>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 = 45.5 bits (108), Expect = 5e-06
Identities = 45/185 (24%), Positives = 85/185 (45%), Gaps = 25/185 (13%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKET--VEELHRGEYELPDGAQLTLDILDTSGA 108
++ ++G A++GK+S++ +++ F Y +T V + + G ++T I D G
Sbjct: 2 KIGLLGDAQIGKTSLMVKYVEGEFDEEYIQTLGVNFMEKTIS--IRGTEITFSIWDLGGQ 59
Query: 109 YQFPAMRELSISTADAFVLVYAVD--DASTWDVVKDLREQIVNKRGL---MVPIVVVGNK 163
+F M L + DA +++ D ST + +K+ Q RG +PI+V G K
Sbjct: 60 REFINM--LPLVCKDAVAILFMFDLTRKSTLNSIKEWYRQA---RGFNKTAIPILV-GTK 113
Query: 164 CELEFKDVRREIAETIALYD------WQCGFVECSAKENYNIVQVFKELLAQAKVQYNLS 217
+L F D+ E E I + + CS + N+ ++FK +LA+ ++L
Sbjct: 114 YDL-FADLPPEEQEEITKQARKYAKAMKAPLIFCSTSHSINVQKIFKFVLAKV---FDLP 169
Query: 218 PAVRR 222
+
Sbjct: 170 LTIPE 174
>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 = 44.9 bits (107), Expect = 5e-06
Identities = 33/163 (20%), Positives = 58/163 (35%), Gaps = 21/163 (12%)
Query: 60 VGKSSIISQFLYDRFISRYKETVEELH-------RGEYELPDGAQLTLDILDTSG-AYQF 111
VGKSS+++ L + + V + R E+EL + L +DT G +
Sbjct: 8 VGKSSLLN-ALLGQNVG----IVSPIPGTTRDPVRKEWELLPLGPVVL--IDTPGLDEEG 60
Query: 112 PAMRELSISTADAFV---LVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCEL-E 167
RE LV V D+ V + ++ R P+++V NK +L
Sbjct: 61 GLGRERVEEARQVADRADLVLLVVDSDLTPV--EEEAKLGLLRERGKPVLLVLNKIDLVP 118
Query: 168 FKDVRREIAETIALYDWQCGFVECSAKENYNIVQVFKELLAQA 210
+ + E + SA I ++ K++
Sbjct: 119 ESEEEELLRERKLELLPDLPVIAVSALPGEGIDELRKKIAELL 161
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 45.5 bits (108), Expect = 6e-06
Identities = 42/179 (23%), Positives = 85/179 (47%), Gaps = 19/179 (10%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVE-ELHRGEYELPDGAQLTLDILDTSGAY 109
++V++G GK++ + + L F +Y+ T+ E+H ++ G ++ DT+G
Sbjct: 15 KLVIVGDGGTGKTTFVKRHLTGEFEKKYEPTIGVEVHPLDFFTNCG-KIRFYCWDTAGQE 73
Query: 110 QFPAMRELSISTADAFVLVYAVDDASTWDVV----KDLREQIVNKRGLMVPIVVVGNKCE 165
+F +R+ ++++ V T+ V +DL N +PIV+ GNK +
Sbjct: 74 KFGGLRDGYYIHGQCAIIMFDVTARLTYKNVPTWHRDLCRVCEN-----IPIVLCGNKVD 128
Query: 166 LEFKDVRREIAETIALYDWQC-GFVECSAKENYNIVQVF----KELLAQAKVQYNLSPA 219
++ + V+ A+ + + + + E SAK NYN + F ++L + + SPA
Sbjct: 129 VKNRQVK---AKQVTFHRKKNLQYYEISAKSNYNFEKPFLYLARKLAGDPNLHFVESPA 184
>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 = 44.7 bits (106), Expect = 7e-06
Identities = 48/170 (28%), Positives = 81/170 (47%), Gaps = 13/170 (7%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
+++V+G + VGK+ + +F RF R + T+ R DG ++ + + DT+G +
Sbjct: 4 KIIVIGDSNVGKTCLTYRFCAGRFPERTEATIGVDFRERTVEIDGERIKVQLWDTAGQER 63
Query: 111 F-PAMRELSISTADAFVLVYAVDDASTWDVVKDLREQI--VNKRGL--MVPIVVVGNKCE 165
F +M + A V VY V + +++ L I + L VP ++VGNKC+
Sbjct: 64 FRKSMVQHYYRNVHAVVFVYDVTNMASF---HSLPSWIEECEQHSLPNEVPRILVGNKCD 120
Query: 166 L-EFKDVRREIAETIALYDWQCGFVECSAK---ENYNIVQVFKELLAQAK 211
L E V ++A+ A F E SAK EN ++ +F L + K
Sbjct: 121 LREQIQVPTDLAQRFADAHSMPLF-ETSAKDPSENDHVEAIFMTLAHKLK 169
>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 = 44.5 bits (106), Expect = 8e-06
Identities = 50/166 (30%), Positives = 85/166 (51%), Gaps = 14/166 (8%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKET--VEELHRGEYELPDGAQLTLDILDTSGA 108
++V++G + VGKS+++S+F + F K T VE R DG + I DT+G
Sbjct: 5 KIVLIGDSGVGKSNLLSRFTRNEFNLDSKSTIGVEFATRTIQI--DGKTIKAQIWDTAGQ 62
Query: 109 YQFPAMRELSISTADAFVLVYAVDDASTWDVV----KDLREQIVNKRGLMVPIVVVGNKC 164
++ A+ A +LVY + ST++ V K+LR+ + + I++VGNK
Sbjct: 63 ERYRAITSAYYRGAVGALLVYDITKKSTFENVERWLKELRDHADSN----IVIMLVGNKS 118
Query: 165 ELE-FKDVRREIAETIALYDWQCGFVECSAKENYNIVQVFKELLAQ 209
+L + V E A+ A + F+E SA + N+ + FK+LL +
Sbjct: 119 DLRHLRAVPTEEAKAFAEKN-GLSFIETSALDGTNVEEAFKQLLTE 163
>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 = 44.4 bits (105), Expect = 9e-06
Identities = 40/168 (23%), Positives = 76/168 (45%), Gaps = 14/168 (8%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
+ VV+G VGK+ ++ + + F Y TV + + + DG + L + DT+G
Sbjct: 3 KCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANV-MVDGKPVNLGLWDTAGQED 61
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCEL-EFK 169
+ +R LS D F++ +++ ++++ V+ V PI++VG K +L + K
Sbjct: 62 YDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDK 121
Query: 170 DVRREIAET-IALYDWQCG-----------FVECSAKENYNIVQVFKE 205
D ++ E + + G ++ECSA + VF E
Sbjct: 122 DTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDE 169
>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 = 44.2 bits (104), Expect = 2e-05
Identities = 40/176 (22%), Positives = 83/176 (47%), Gaps = 19/176 (10%)
Query: 55 MGGARVGKSSIISQFLYDRFISRYKETVE-ELHRGEYELPDGAQLTLDILDTSGAYQFPA 113
+G GK++ + + L F +Y T+ E+H + G + ++ DT+G +F
Sbjct: 1 VGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRG-PIRFNVWDTAGQEKFGG 59
Query: 114 MRELSISTADAFVLVYAVDDASTWDVV----KDLREQIVNKRGLMVPIVVVGNKCELEFK 169
+R+ ++++ V T+ V +DL N +PIV+ GNK +++ +
Sbjct: 60 LRDGYYIQGQCAIIMFDVTARVTYKNVPNWHRDLVRVCEN-----IPIVLCGNKVDVKDR 114
Query: 170 DVRREIAETIALYDWQ-CGFVECSAKENYNIVQVF----KELLAQAKVQYNLSPAV 220
V+ A++I + + + + SAK NYN + F ++L+ +++ PA+
Sbjct: 115 KVK---AKSITFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPAL 167
>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 = 43.9 bits (103), Expect = 2e-05
Identities = 25/90 (27%), Positives = 50/90 (55%), Gaps = 1/90 (1%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
++VV+G + GK++++ F D + Y TV E + +E+ D ++ L++ DTSG+
Sbjct: 3 KIVVVGDTQCGKTALLHVFAKDNYPESYVPTVFENYTASFEI-DKHRIELNMWDTSGSSY 61
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWDVV 140
+ +R L+ +DA ++ + + T D V
Sbjct: 62 YDNVRPLAYPDSDAVLICFDISRPETLDSV 91
>gnl|CDD|232995 TIGR00487, IF-2, translation initiation factor IF-2. This model
discriminates eubacterial (and mitochondrial)
translation initiation factor 2 (IF-2), encoded by the
infB gene in bacteria, from similar proteins in the
Archaea and Eukaryotes. In the bacteria and in
organelles, the initiator tRNA is charged with
N-formyl-Met instead of Met. This translation factor
acts in delivering the initator tRNA to the ribosome. It
is one of a number of GTP-binding translation factors
recognized by the pfam model GTP_EFTU [Protein
synthesis, Translation factors].
Length = 587
Score = 44.4 bits (105), Expect = 3e-05
Identities = 51/174 (29%), Positives = 69/174 (39%), Gaps = 25/174 (14%)
Query: 52 VVVMGGARVGKSSIISQFLYDRFISRYKETVEEL-----HRGEY--ELPDGAQLTLDILD 104
V +MG GK+S++ I + K E H G Y E DG +T LD
Sbjct: 90 VTIMGHVDHGKTSLLD------SIRKTKVAQGEAGGITQHIGAYHVENEDGKMITF--LD 141
Query: 105 TSGAYQFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKC 164
T G F +MR D VLV A DD V+ E I + + VPI+V NK
Sbjct: 142 TPGHEAFTSMRARGAKVTDIVVLVVAADDG----VMPQTIEAISHAKAANVPIIVAINKI 197
Query: 165 ELEFKDVRREIAETIAL----YDW--QCGFVECSAKENYNIVQVFKELLAQAKV 212
+ + R E DW FV SA I ++ +L Q++V
Sbjct: 198 DKPEANPDRVKQELSEYGLVPEDWGGDTIFVPVSALTGDGIDELLDMILLQSEV 251
>gnl|CDD|133303 cd04103, Centaurin_gamma, Centaurin gamma (CENTG) GTPase. The
centaurins (alpha, beta, gamma, and delta) are large,
multi-domain proteins that all contain an ArfGAP domain
and ankyrin repeats, and in some cases, numerous
additional domains. Centaurin gamma contains an
additional GTPase domain near its N-terminus. The
specific function of this GTPase domain has not been
well characterized, but centaurin gamma 2 (CENTG2) may
play a role in the development of autism. Centaurin
gamma 1 is also called PIKE (phosphatidyl inositol (PI)
3-kinase enhancer) and centaurin gamma 2 is also known
as AGAP (ArfGAP protein with a GTPase-like domain,
ankyrin repeats and a Pleckstrin homology domain) or
GGAP. Three isoforms of PIKE have been identified.
PIKE-S (short) and PIKE-L (long) are brain-specific
isoforms, with PIKE-S restricted to the nucleus and
PIKE-L found in multiple cellular compartments. A third
isoform, PIKE-A was identified in human glioblastoma
brain cancers and has been found in various tissues.
GGAP has been shown to have high GTPase activity due to
a direct intramolecular interaction between the
N-terminal GTPase domain and the C-terminal ArfGAP
domain. In human tissue, AGAP mRNA was detected in
skeletal muscle, kidney, placenta, brain, heart, colon,
and lung. Reduced expression levels were also observed
in the spleen, liver, and small intestine.
Length = 158
Score = 42.5 bits (100), Expect = 3e-05
Identities = 39/172 (22%), Positives = 78/172 (45%), Gaps = 37/172 (21%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFIS-------RYKETVEELHRGEYELPDGAQLTLDIL 103
++ ++G R GKS+++ ++L ++ R+K+ V L DG L I
Sbjct: 2 KLGIVGNLRSGKSALVHRYLTGSYVQLESPEGGRFKKEV---------LVDGQSHLLLIR 52
Query: 104 DTSGA--YQFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLM-VPIVVV 160
D GA QF DA + V++++D +++ V L Q+ + R + +P+++V
Sbjct: 53 DEGGAPDAQFA-------GWVDAVIFVFSLEDEASFQTVYRLYHQLSSYRNISEIPLILV 105
Query: 161 GNKCELEFKDVR-------REIAETIALYDWQCGFVECSAKENYNIVQVFKE 205
G + + + R R++ + +C + E A N+ +VF+E
Sbjct: 106 GTQDAISASNPRVIDDARARQLCADMK----RCSYYETCATYGLNVERVFQE 153
>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 = 42.2 bits (99), Expect = 8e-05
Identities = 54/232 (23%), Positives = 93/232 (40%), Gaps = 62/232 (26%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
+VV++G VGK+S++ +++ RF K+TV + G + L + I DT+G Q
Sbjct: 2 KVVLLGDMNVGKTSLLHRYMERRF----KDTVSTVG-GAFYLKQWGPYNISIWDTAGREQ 56
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIV------NKRGLMVPIVVVGNKC 164
F + + A A +L Y D S +++L ++ + N+ L VVGNK
Sbjct: 57 FHGLGSMYCRGAAAVILTY---DVSNVQSLEELEDRFLGLTDTANEDCLF---AVVGNKL 110
Query: 165 EL----------------EFKDVRREIA--ETIALY-----------------DWQCGFV 189
+L + +R++ + A Y + C
Sbjct: 111 DLTEEGALAGQEKDAGDRVSPEDQRQVTLEDAKAFYKRINKYKMLDEDLSPAAEKMC--F 168
Query: 190 ECSAKENYNIVQVFKELLAQAKVQYNLS-PAVRRRRQSLPNYIGTTGSASSK 240
E SAK YN+ ++F+ L +NL P + +R GT + K
Sbjct: 169 ETSAKTGYNVDELFEYL-------FNLVLPLILAQRAEANRTQGTVNLPNPK 213
>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 = 40.9 bits (96), Expect = 1e-04
Identities = 42/158 (26%), Positives = 70/158 (44%), Gaps = 14/158 (8%)
Query: 53 VVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQFP 112
+++G A GKS ++ QF+ ++F T+ G + L I DT+G +F
Sbjct: 4 LIIGSAGTGKSCLLHQFIENKFKQDSNHTIGVEFGSRVVNVGGKSVKLQIWDTAGQERFR 63
Query: 113 AMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVP---IVVVGNKCELEFK 169
++ A +LVY D ++ + L + + R L P I++VGNK +LE
Sbjct: 64 SVTRSYYRGAAGALLVY---DITSRESFNALTNWLTDARTLASPDIVIILVGNKKDLE-- 118
Query: 170 DVRREI----AETIALYDWQCGFVECSAKENYNIVQVF 203
RE+ A A + F+E SA N+ + F
Sbjct: 119 -DDREVTFLEASRFA-QENGLLFLETSALTGENVEEAF 154
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 41.2 bits (97), Expect = 2e-04
Identities = 39/179 (21%), Positives = 84/179 (46%), Gaps = 19/179 (10%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVE-ELHRGEYELPDGAQLTLDILDTSGAY 109
+++++G VGK++ + + L F +Y T+ E+H ++ + + ++ DT+G
Sbjct: 11 KLILVGDGGVGKTTFVKRHLTGEFEKKYIPTLGVEVHPLKFYT-NCGPICFNVWDTAGQE 69
Query: 110 QFPAMRELSISTADAFVLVYAVDDASTWDVV----KDLREQIVNKRGLMVPIVVVGNKCE 165
+F +R+ ++++ V T+ V +D+ N +PIV+VGNK +
Sbjct: 70 KFGGLRDGYYIKGQCAIIMFDVTSRITYKNVPNWHRDIVRVCEN-----IPIVLVGNKVD 124
Query: 166 LEFKDVRREIAETIALY-DWQCGFVECSAKENYN----IVQVFKELLAQAKVQYNLSPA 219
++ + V+ A I + + + SAK NYN + + + L + + +PA
Sbjct: 125 VKDRQVK---ARQITFHRKKNLQYYDISAKSNYNFEKPFLWLARRLTNDPNLVFVGAPA 180
>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 = 40.0 bits (94), Expect = 2e-04
Identities = 35/116 (30%), Positives = 53/116 (45%), Gaps = 8/116 (6%)
Query: 99 TLDILDTSGAYQFPAMRELSISTADAFVLVYAVD--DASTWDVVKDLREQIVNKRGLM-V 155
T+ + D G +F +M E +A +VY VD D +V K+ ++ K L +
Sbjct: 45 TIKVWDLGGQPRFRSMWERYCRGVNA--IVYVVDAADREKLEVAKNELHDLLEKPSLEGI 102
Query: 156 PIVVVGNKCELEFKDVRREIAETIALYDWQCGFVEC---SAKENYNIVQVFKELLA 208
P++V+GNK +L E+ E + L V C SAKE NI V L+
Sbjct: 103 PLLVLGNKNDLPGALSVDELIEQMNLKSITDREVSCYSISAKEKTNIDIVLDWLIK 158
>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 = 38.2 bits (90), Expect = 0.001
Identities = 43/198 (21%), Positives = 68/198 (34%), Gaps = 50/198 (25%)
Query: 47 KDKRRVVVMGGARVGKSSIISQFLYD------------RFISRYKETVEELHRG------ 88
K R + ++G GK+++ LY R + + KE E RG
Sbjct: 1 KRHRNIGIIGHVDHGKTTLTDALLYVTGAISKESAKGARVLDKLKE---ERERGITIKIA 57
Query: 89 --EYELPDGAQLTLDILDTSGAYQFPAMRELSISTADAFVLVYAVDD---AST---WDVV 140
+E ++I+DT G F S AD +LV + T +
Sbjct: 58 AVSFETKKR---LINIIDTPGHVDFTKEMIRGASQADGAILVVDAVEGVMPQTREHLLLA 114
Query: 141 KDLREQIVNKRGLMVPIVVVGNKC----ELEFKDVRREIAET-IALYDWQ---CGFVECS 192
K L VPI+V NK + E ++V EI+ + Y + V S
Sbjct: 115 KTLG----------VPIIVFINKIDRVDDAELEEVVEEISRELLEKYGFGGETVPVVPGS 164
Query: 193 AKENYNIVQVFKELLAQA 210
A I ++ + L
Sbjct: 165 ALTGEGIDELLEALDLYL 182
>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 = 38.3 bits (89), Expect = 0.001
Identities = 26/89 (29%), Positives = 46/89 (51%), Gaps = 6/89 (6%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVE---ELHRGEYELPDGAQLTLDILDTSG 107
+V+V+G VGK+ +I++F D F YK T+ E+ R E G +L + DT+G
Sbjct: 2 KVIVVGDLSVGKTCLINRFCKDVFDKNYKATIGVDFEMERFEVL---GVPFSLQLWDTAG 58
Query: 108 AYQFPAMRELSISTADAFVLVYAVDDAST 136
+F + A A ++V+ + D ++
Sbjct: 59 QERFKCIASTYYRGAQAIIIVFDLTDVAS 87
>gnl|CDD|206647 cd00881, GTP_translation_factor, GTP translation factor family
primarily contains translation initiation, elongation
and release factors. The GTP translation factor family
consists primarily of translation initiation,
elongation, and release factors, which play specific
roles in protein translation. In addition, the family
includes Snu114p, a component of the U5 small nuclear
riboprotein particle which is a component of the
spliceosome and is involved in excision of introns,
TetM, a tetracycline resistance gene that protects the
ribosome from tetracycline binding, and the unusual
subfamily CysN/ATPS, which has an unrelated function
(ATP sulfurylase) acquired through lateral transfer of
the EF1-alpha gene and development of a new function.
Length = 183
Score = 38.4 bits (90), Expect = 0.001
Identities = 43/176 (24%), Positives = 65/176 (36%), Gaps = 34/176 (19%)
Query: 51 RVVVMGGARVGKS----SIISQFLYDRFISRYKETV-----EELHRG--------EYELP 93
V V+G GK+ S++ Q KET EE RG E+E P
Sbjct: 1 NVGVIGHVDHGKTTLTGSLLYQTGAIDRRGTRKETFLDTLKEERERGITIKTGVVEFEWP 60
Query: 94 DGAQLTLDILDTSGAYQFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGL 153
++ +DT G F ++ AD +LV ++ V RE +
Sbjct: 61 K---RRINFIDTPGHEDFSKETVRGLAQADGALLVVDANEG----VEPQTREHLNIALAG 113
Query: 154 MVPIVVVGNKCEL----EFKDVRREIAETIALYDW------QCGFVECSAKENYNI 199
+PI+V NK + +F +V REI E + L + + SA I
Sbjct: 114 GLPIIVAVNKIDRVGEEDFDEVLREIKELLKLIGFTFLKGKDVPIIPISALTGEGI 169
>gnl|CDD|129574 TIGR00483, EF-1_alpha, translation elongation factor EF-1 alpha.
This model represents the counterpart of bacterial EF-Tu
for the Archaea (aEF-1 alpha) and Eukaryotes (eEF-1
alpha). The trusted cutoff is set fairly high so that
incomplete sequences will score between suggested and
trusted cutoff levels [Protein synthesis, Translation
factors].
Length = 426
Score = 39.1 bits (91), Expect = 0.002
Identities = 44/198 (22%), Positives = 78/198 (39%), Gaps = 40/198 (20%)
Query: 43 VGLQKDKRRVVVMGGARVGKSSIISQFLYD------RFISRYKETVEELHRGEYELP--- 93
+ +K+ V +G GKS+ + LY + I ++++ +E + +E
Sbjct: 1 MAKEKEHINVAFIGHVDHGKSTTVGHLLYKCGAIDEQTIEKFEKEAQEKGKASFEFAWVM 60
Query: 94 DGAQ------LTLD--------------ILDTSGAYQFPAMRELSISTADAFVLVYAVDD 133
D + +T+D I+D G F S ADA VLV AV D
Sbjct: 61 DRLKEERERGVTIDVAHWKFETDKYEVTIVDCPGHRDFIKNMITGASQADAAVLVVAVGD 120
Query: 134 ASTWDVVKDLREQIVNKRGLMV-PIVVVGNKCEL------EFKDVRREIAETIALYDW-- 184
+V RE R L + ++V NK + EF+ +++E++ I +
Sbjct: 121 GEF-EVQPQTREHAFLARTLGINQLIVAINKMDSVNYDEEEFEAIKKEVSNLIKKVGYNP 179
Query: 185 -QCGFVECSAKENYNIVQ 201
F+ SA N+++
Sbjct: 180 DTVPFIPISAWNGDNVIK 197
>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 = 37.9 bits (88), Expect = 0.002
Identities = 33/169 (19%), Positives = 75/169 (44%), Gaps = 13/169 (7%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRY----------KETVEELHRGEYELPDGAQLTL 100
+++ +G + VGK++ + ++ ++F ++ K V + ++ L
Sbjct: 6 KLLALGDSGVGKTTFLYRYTDNKFNPKFITTVGIDFREKRVVYNSQGPDGTSGKAFRVHL 65
Query: 101 DILDTSGAYQFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVP-IVV 159
+ DT+G +F ++ A F+L++ + ++ V++ Q+ P IV+
Sbjct: 66 QLWDTAGQERFRSLTTAFFRDAMGFLLMFDLTSEQSFLNVRNWMSQLQAHAYCENPDIVL 125
Query: 160 VGNKCELE-FKDVRREIAETIALYDWQCGFVECSAKENYNIVQVFKELL 207
+GNK +L ++V A +A + + E SA N+ + + LL
Sbjct: 126 IGNKADLPDQREVSERQARELA-DKYGIPYFETSAATGQNVEKAVETLL 173
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 38.3 bits (90), Expect = 0.003
Identities = 51/178 (28%), Positives = 73/178 (41%), Gaps = 29/178 (16%)
Query: 52 VVVMGGARVGKSSIISQFLYDRFISRYKETV---EEL----HRGEY--ELPDGAQLTLDI 102
V +MG GK++++ D+ R K V E H G Y L +
Sbjct: 8 VTIMGHVDHGKTTLL-----DKI--R-KTNVAAGEAGGITQHIGAYQVPLDVIKIPGITF 59
Query: 103 LDTSGAYQFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGN 162
+DT G F AMR S D +LV A DD V+ E I + + VPIVV N
Sbjct: 60 IDTPGHEAFTAMRARGASVTDIAILVVAADDG----VMPQTIEAINHAKAAGVPIVVAIN 115
Query: 163 KCELE----FKDVRREIAE---TIALYDWQCGFVECSAKENYNIVQVFKELLAQAKVQ 213
K + K V++E+ E + FV SAK I ++ + +L A+V
Sbjct: 116 KIDKPEANPDK-VKQELQEYGLVPEEWGGDVIFVPVSAKTGEGIDELLELILLLAEVL 172
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 37.9 bits (88), Expect = 0.004
Identities = 32/112 (28%), Positives = 45/112 (40%), Gaps = 16/112 (14%)
Query: 103 LDTSGAYQFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGN 162
LDT G F +MR + D +L+ A DD V E I + VPI+V N
Sbjct: 300 LDTPGHEAFSSMRSRGANVTDIAILIIAADDG----VKPQTIEAINYIQAANVPIIVAIN 355
Query: 163 KCELEFKDVRREIAETIALY-----DW--QCGFVECSAKENYNIVQVFKELL 207
K + + R I + +A Y W + SA + NI +LL
Sbjct: 356 KIDKANANTER-IKQQLAKYNLIPEKWGGDTPMIPISASQGTNI----DKLL 402
>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 = 36.6 bits (84), Expect = 0.006
Identities = 25/100 (25%), Positives = 52/100 (52%), Gaps = 2/100 (2%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
++V++G + GK++++ D + Y TV E + E + ++ L + DTSG+
Sbjct: 15 KLVLVGDVQCGKTAMLQVLAKDCYPETYVPTVFENYTACLETEE-QRVELSLWDTSGSPY 73
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWD-VVKDLREQIVN 149
+ +R L S +DA +L + + +D +K R +I++
Sbjct: 74 YDNVRPLCYSDSDAVLLCFDISRPEIFDSALKKWRAEILD 113
>gnl|CDD|206644 cd00878, Arf_Arl, ADP-ribosylation factor(Arf)/Arf-like (Arl) small
GTPases. Arf (ADP-ribosylation factor)/Arl (Arf-like)
small GTPases. Arf proteins are activators of
phospholipase D isoforms. Unlike Ras proteins they lack
cysteine residues at their C-termini and therefore are
unlikely to be prenylated. Arfs are N-terminally
myristoylated. Members of the Arf family are regulators
of vesicle formation in intracellular traffic that
interact reversibly with membranes of the secretory and
endocytic compartments in a GTP-dependent manner. They
depart from other small GTP-binding proteins by a unique
structural device, interswitch toggle, that implements
front-back communication from N-terminus to the
nucleotide binding site. Arf-like (Arl) proteins are
close relatives of the Arf, but only Arl1 has been shown
to function in membrane traffic like the Arf proteins.
Arl2 has an unrelated function in the folding of native
tubulin, and Arl4 may function in the nucleus. Most
other Arf family proteins are so far relatively poorly
characterized. Thus, despite their significant sequence
homologies, Arf family proteins may regulate unrelated
functions.
Length = 158
Score = 34.5 bits (80), Expect = 0.020
Identities = 19/92 (20%), Positives = 36/92 (39%), Gaps = 10/92 (10%)
Query: 126 VLVYAVD--DASTWDVVKD-LREQIVNKRGLMVPIVVVGNKCELEFKDVRREIAETIALY 182
L++ VD D + K+ L + + + P++++ NK +L E+ E + L
Sbjct: 69 GLIFVVDSSDRERIEEAKNELHKLLNEEELKGAPLLILANKQDLPGALTESELIELLGLE 128
Query: 183 -----DWQCGFVECSAKENYNIVQVFKELLAQ 209
W CSA + + L+ Q
Sbjct: 129 SIKGRRWHI--QPCSAVTGDGLDEGLDWLIEQ 158
>gnl|CDD|232980 TIGR00450, mnmE_trmE_thdF, tRNA modification GTPase TrmE. TrmE,
also called MnmE and previously designated ThdF
(thiophene and furan oxidation protein), is a GTPase
involved in tRNA modification to create
5-methylaminomethyl-2-thiouridine in the wobble position
of some tRNAs. This protein and GidA form an
alpha2/beta2 heterotetramer [Protein synthesis, tRNA and
rRNA base modification].
Length = 442
Score = 35.2 bits (81), Expect = 0.029
Identities = 36/141 (25%), Positives = 66/141 (46%), Gaps = 18/141 (12%)
Query: 40 GTGVGLQKDKRRVVVMGGARVGKSSIISQFL-YDRFI-SRYKETVEELHRGEYELPDGAQ 97
+ D ++ ++G VGKSS+++ L DR I S K T ++ G++EL +G
Sbjct: 194 SYKLEKLDDGFKLAIVGSPNVGKSSLLNALLKQDRAIVSDIKGTTRDVVEGDFEL-NG-- 250
Query: 98 LTLDILDTSGAYQFPAMREL--------SISTADAFVLVYAVDDASTWDVVKDLREQIVN 149
+ + +LDT+G + E +I AD +++Y +D + KD I++
Sbjct: 251 ILIKLLDTAGIREHADFVERLGIEKSFKAIKQAD--LVIYVLDASQPLT--KDD-FLIID 305
Query: 150 KRGLMVPIVVVGNKCELEFKD 170
P ++V NK +L+
Sbjct: 306 LNKSKKPFILVLNKIDLKINS 326
>gnl|CDD|206685 cd01898, Obg, Obg GTPase. The Obg nucleotide binding protein
subfamily has been implicated in stress response,
chromosome partitioning, replication initiation,
mycelium development, and sporulation. Obg proteins are
among a large group of GTP binding proteins conserved
from bacteria to humans. The E. coli homolog, ObgE is
believed to function in ribosomal biogenesis. Members of
the subfamily contain two equally and highly conserved
domains, a C-terminal GTP binding domain and an
N-terminal glycine-rich domain.
Length = 170
Score = 33.9 bits (79), Expect = 0.031
Identities = 20/92 (21%), Positives = 32/92 (34%), Gaps = 19/92 (20%)
Query: 126 VLVYAVDDASTWDVVKDLR----------EQIVNKRGLMVPIVVVGNKCELEFKDVRREI 175
VL++ +D + D V+D + K P +VV NK +L + R E
Sbjct: 81 VLLHVIDLSGEDDPVEDYETIRNELEAYNPGLAEK-----PRIVVLNKIDLLDAEERFEK 135
Query: 176 AETIALYDWQCGFVECSAKENYNIVQVFKELL 207
+ + SA + ELL
Sbjct: 136 LKELLKELKGKKVFPISALTGEGL----DELL 163
>gnl|CDD|206698 cd04117, Rab15, Rab GTPase family 15 (Rab15). Rab15 colocalizes
with the transferrin receptor in early endosome
compartments, but not with late endosomal markers. It
codistributes with Rab4 and Rab5 on early/sorting
endosomes, and with Rab11 on pericentriolar recycling
endosomes. It is believed to function as an inhibitory
GTPase that regulates distinct steps in early endocytic
trafficking. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation of
the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 164
Score = 33.8 bits (77), Expect = 0.035
Identities = 40/166 (24%), Positives = 76/166 (45%), Gaps = 9/166 (5%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQ 110
R++++G + VGK+ ++ +F + F S + T+ + + DG ++ + I DT+G +
Sbjct: 2 RLLLIGDSGVGKTCLLCRFTDNEFHSSHISTIGVDFKMKTIEVDGIKVRIQIWDTAGQER 61
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKC-ELEFK 169
+ + + A LVY + ++ + + V +++GNK E + +
Sbjct: 62 YQTITKQYYRRAQGIFLVYDISSERSYQHIMKWVSDVDEYAPEGVQKILIGNKADEEQKR 121
Query: 170 DVRREIAETIALYDWQCG--FVECSAKENYNIVQVF---KELLAQA 210
V E +A + G F E SA N NI + F EL+ QA
Sbjct: 122 QVGDEQGNKLAK---EYGMDFFETSACTNKNIKESFTRLTELVLQA 164
>gnl|CDD|206741 cd09914, RocCOR, Ras of complex proteins (Roc) C-terminal of Roc
(COR) domain family. RocCOR (or Roco) protein family is
characterized by a superdomain containing a Ras-like
GTPase domain, called Roc (Ras of complex proteins), and
a characteristic second domain called COR (C-terminal of
Roc). A kinase domain and diverse regulatory domains are
also often found in Roco proteins. Their functions are
diverse; in Dictyostelium discoideum, which encodes 11
Roco proteins, they are involved in cell division,
chemotaxis and development, while in human, where 4 Roco
proteins (LRRK1, LRRK2, DAPK1, and MFHAS1) are encoded,
these proteins are involved in epilepsy and cancer.
Mutations in LRRK2 (leucine-rich repeat kinase 2) are
known to cause familial Parkinson's disease.
Length = 161
Score = 32.7 bits (75), Expect = 0.078
Identities = 27/154 (17%), Positives = 69/154 (44%), Gaps = 10/154 (6%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELP--DGAQLTLDILDTSGA 108
+++++G VGK+S+ Q + ++F + + ++ ++++P + ++ L++ D G
Sbjct: 3 KLMLVGQGGVGKTSLCKQLIGEKF-DGDESSTHGINVQDWKIPAPERKKIRLNVWDFGGQ 61
Query: 109 YQFPAMRELSISTADAFVLVYAVDDASTWDVVKDLRE--QIVNKRGLMVPIVVVGNKC-E 165
+ A + +++ ++LV+ D T D V + + + G + P+++VG E
Sbjct: 62 EIYHATHQFFLTSRSLYLLVF---DLRTGDEVSRVPYWLRQIKAFGGVSPVILVGTHIDE 118
Query: 166 LEFKDVRREIAETIALYDWQCGFVECSAKENYNI 199
+D+ ++ S K I
Sbjct: 119 SCDEDILKKALNKKFPAIIN-DIHFVSCKNGKGI 151
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 33.0 bits (76), Expect = 0.15
Identities = 44/160 (27%), Positives = 67/160 (41%), Gaps = 46/160 (28%)
Query: 52 VVVMGGARVGKSSIISQFLYDRFISRYKETVEEL-----HRGEYE-LPDGAQLTLDILDT 105
V V+G VGKS+ L +R + R + VE++ R Y+ +G + T+ +DT
Sbjct: 41 VAVVGRPNVGKST-----LVNRILGRREAVVEDVPGVTRDRVSYDAEWNGRRFTV--VDT 93
Query: 106 SG--------AYQFPAMRELSISTADAFVLVY-------AVDDASTWDVVKDLREQIVNK 150
G E+++ TADA + V A D+A V + LR +
Sbjct: 94 GGWEPDAKGLQASVAEQAEVAMRTADAVLFVVDATVGATATDEA----VARVLR-----R 144
Query: 151 RGLMVPIVVVGNKCELEFKDVRREIAETIALYDWQCGFVE 190
G P+++ NK D R E A+ AL W G E
Sbjct: 145 SG--KPVILAANK----VDDERGE-ADAAAL--WSLGLGE 175
>gnl|CDD|206722 cd04157, Arl6, Arf-like 6 (Arl6) GTPase. Arl6 (Arf-like 6) forms a
subfamily of the Arf family of small GTPases. Arl6
expression is limited to the brain and kidney in adult
mice, but it is expressed in the neural plate and
somites during embryogenesis, suggesting a possible role
for Arl6 in early development. Arl6 is also believed to
have a role in cilia or flagella function. Several
proteins have been identified that bind Arl6, including
Arl6 interacting protein (Arl6ip), and SEC61beta, a
subunit of the heterotrimeric conducting channel SEC61p.
Based on Arl6 binding to these effectors, Arl6 is also
proposed to play a role in protein transport, membrane
trafficking, or cell signaling during hematopoietic
maturation. At least three specific homozygous Arl6
mutations in humans have been found to cause
Bardet-Biedl syndrome, a disorder characterized by
obesity, retinopathy, polydactyly, renal and cardiac
malformations, learning disabilities, and
hypogenitalism. Older literature suggests that Arl6 is a
part of the Arl4/Arl7 subfamily, but analyses based on
more recent sequence data place Arl6 in its own
subfamily.
Length = 162
Score = 32.0 bits (73), Expect = 0.15
Identities = 17/73 (23%), Positives = 28/73 (38%), Gaps = 3/73 (4%)
Query: 98 LTLDILDTSGAYQFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLM--- 154
L+ D SG ++ + E + V D V KD E ++N +
Sbjct: 45 LSFTAFDMSGQGKYRGLWEHYYKNIQGIIFVIDSSDRLRMVVAKDELELLLNHPDIKHRR 104
Query: 155 VPIVVVGNKCELE 167
+PI+ NK +L
Sbjct: 105 IPILFYANKMDLP 117
>gnl|CDD|237040 PRK12289, PRK12289, GTPase RsgA; Reviewed.
Length = 352
Score = 32.7 bits (75), Expect = 0.17
Identities = 29/98 (29%), Positives = 43/98 (43%), Gaps = 23/98 (23%)
Query: 41 TGVGLQKDKRRV-----VVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGE------ 89
TG+GL+ ++ VV G + VGKSS+I++ L R + +L RG
Sbjct: 159 TGIGLEALLEQLRNKITVVAGPSGVGKSSLINR-LIPDVELRVGKVSGKLGRGRHTTRHV 217
Query: 90 --YELPDGA---------QLTLDILDTSGAYQFPAMRE 116
+ELP+G Q LD A+ FP R+
Sbjct: 218 ELFELPNGGLLADTPGFNQPDLDCSPRELAHYFPEARQ 255
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 32.9 bits (76), Expect = 0.17
Identities = 39/137 (28%), Positives = 53/137 (38%), Gaps = 50/137 (36%)
Query: 103 LDTSGAYQFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLM-------- 154
LDT G F AMR D VLV A DD G+M
Sbjct: 301 LDTPGHEAFTAMRARGAQVTDIVVLVVAADD------------------GVMPQTIEAIN 342
Query: 155 ------VPIVVVGNKCELEFKD---VRREIAETIALY-----DWQCG----FVECSAKEN 196
VPI+V NK + + V++E++E Y +W G FV SAK
Sbjct: 343 HAKAAGVPIIVAINKIDKPGANPDRVKQELSE----YGLVPEEW--GGDTIFVPVSAKTG 396
Query: 197 YNIVQVFKELLAQAKVQ 213
I ++ + +L QA+V
Sbjct: 397 EGIDELLEAILLQAEVL 413
>gnl|CDD|149409 pfam08337, Plexin_cytopl, Plexin cytoplasmic RasGAP domain. This
family features the C-terminal regions of various
plexins. Plexins are receptors for semaphorins, and
plexin signalling is important in path finding and
patterning of both neurons and developing blood vessels.
The cytoplasmic region, which has been called a SEX
domain in some members of this family, is involved in
downstream signalling pathways, by interaction with
proteins such as Rac1, RhoD, Rnd1 and other plexins.
This domain acts as a RasGAP domain.
Length = 538
Score = 32.4 bits (74), Expect = 0.21
Identities = 13/35 (37%), Positives = 22/35 (62%)
Query: 59 RVGKSSIISQFLYDRFISRYKETVEELHRGEYELP 93
R+GK S ++ LY + I RYK+ VE ++ ++P
Sbjct: 462 RLGKDSPSNKLLYAKDIPRYKKMVERYYKDIRQMP 496
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 32.2 bits (74), Expect = 0.26
Identities = 46/190 (24%), Positives = 83/190 (43%), Gaps = 43/190 (22%)
Query: 52 VVVMGGARVGKSSIISQFLYD------RFISRYKETVEELHRGEYE---LPDGAQ----- 97
+ V+G GKS+++ + LY+ I +E +E + ++ + D +
Sbjct: 9 LAVIGHVDHGKSTLVGRLLYETGAIDEHIIEELREEAKEKGKESFKFAWVMDRLKEERER 68
Query: 98 -LTLDI----LDTSGAYQF-----PAMREL------SISTADAFVLVYAVDDASTWDVVK 141
+T+D+ +T Y F P R+ S ADA VLV A DDA V+
Sbjct: 69 GVTIDLAHKKFET-DKYYFTIVDCPGHRDFVKNMITGASQADAAVLVVAADDAGG--VMP 125
Query: 142 DLREQIVNKRGLMVPIVVVG-NKC------ELEFKDVRREIAETIALYDW---QCGFVEC 191
RE + R L + ++V NK E +++V+ E+++ + + + F+
Sbjct: 126 QTREHVFLARTLGINQLIVAINKMDAVNYDEKRYEEVKEEVSKLLKMVGYKPDDIPFIPV 185
Query: 192 SAKENYNIVQ 201
SA E N+V+
Sbjct: 186 SAFEGDNVVK 195
>gnl|CDD|234395 TIGR03918, GTP_HydF, [FeFe] hydrogenase H-cluster maturation GTPase
HydF. This model describes the family of the [Fe]
hydrogenase maturation protein HypF as characterized in
Chlamydomonas reinhardtii and found, in an operon with
radical SAM proteins HydE and HydG, in numerous
bacteria. It has GTPase activity, can bind an 4Fe-4S
cluster, and is essential for hydrogenase activity
[Protein fate, Protein modification and repair].
Length = 391
Score = 31.7 bits (73), Expect = 0.29
Identities = 18/94 (19%), Positives = 37/94 (39%), Gaps = 13/94 (13%)
Query: 119 ISTADAFVLVYAVDDASTWDVVKDLREQIVNK-RGLMVPIVVVGNKCEL-EFKDVRREIA 176
+ D +LV VD + +++ + + +P +VV NK +L E ++
Sbjct: 83 LDKTDLALLV--VDAGVGP---GEYELELIEELKERKIPYIVVINKIDLGEESAELEKLE 137
Query: 177 ETIALYDWQCGFVECSAKENYNIVQVFKELLAQA 210
+ L + SA I ++ KE + +
Sbjct: 138 KKFGL-----PPIFVSALTGEGIDEL-KEAIIEL 165
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 31.6 bits (72), Expect = 0.34
Identities = 13/23 (56%), Positives = 16/23 (69%)
Query: 44 GLQKDKRRVVVMGGARVGKSSII 66
GL K K RV V+G VGKS++I
Sbjct: 127 GLLKRKIRVGVVGYPNVGKSTLI 149
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 31.2 bits (72), Expect = 0.49
Identities = 24/110 (21%), Positives = 37/110 (33%), Gaps = 17/110 (15%)
Query: 119 ISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCELEFKDVRREIAET 178
I AD LV V DAS +D K P++VV NK +L + E
Sbjct: 292 IEEAD---LVLLVLDASEPLTEEDDEILEELKD---KPVIVVLNKADLTGEIDLEEEN-- 343
Query: 179 IALYDWQCGFVECSAKENYNIVQVFKELLAQAKVQYNLS---PAVRRRRQ 225
+ SAK I ++ + + A + + + R
Sbjct: 344 ------GKPVIRISAKTGEGIDELREAIKELAFGGFGGNQEGVFLTNARH 387
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 31.3 bits (71), Expect = 0.54
Identities = 51/225 (22%), Positives = 83/225 (36%), Gaps = 39/225 (17%)
Query: 9 DKGLQTDYRKMPGACERLRLHSLGTESTSSSGTGVGLQKDKRR----VVVMGGARVGKSS 64
D + +Y + E L + SG G +K + V ++G VGKS+
Sbjct: 231 DAIEEQEYDQYAANLEGYELDEGDEDLLEGSGFVAGDEKAGPKAVGVVAIVGRPNVGKST 290
Query: 65 IISQFLYDRFISRYKETVEEL-----HRGEYELPDGAQLTLDILDTSG--------AYQF 111
++ +R + R + VE+ R Y + A ++DT G
Sbjct: 291 LV-----NRILGRREAVVEDTPGVTRDRVSY-DAEWAGTDFKLVDTGGWEADVEGIDSAI 344
Query: 112 PAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNK-RGLMVPIVVVGNKCELEFKD 170
+ ++++S ADA V V D D E+IV R P+V+ NK +
Sbjct: 345 ASQAQIAVSLADAVVFVV---DGQVGLTSTD--ERIVRMLRRAGKPVVLAVNKID----- 394
Query: 171 VRREIAETIALYDWQCGFVE---CSAKENYNIVQVFKELLAQAKV 212
+ +E A W+ G E SA + + E L KV
Sbjct: 395 --DQASEYDAAEFWKLGLGEPYPISAMHGRGVGDLLDEALDSLKV 437
>gnl|CDD|213347 cd12787, RasGAP_plexin_B, Ras-GTPase Activating Domain of type B
plexins. Plexins form a conserved family of
transmembrane receptors for semaphorins and may be the
ancestors of semaphorins. Plexins are divided into four
types (A-D) according to sequence similarity.There are
three members of the Plexin-B subfamily, namely B1, B2
and B3. Plexins-B1, B2 and B3 are receptors for Sema4D,
Sema4C and Sema4G, and Sema5A, respectively. The
activation of plexin-B1 by Sema4D produces an acute
collapse of axonal growth cones in hippocampal and
retinal neurons over the early stages of neurite
outgrowth and promotes branching and complexity. By
signaling the effect of Sema4C and Sema4G, the plexin-B2
receptor is critically involved in neural tube closure
and cerebellar granule cell development. Plexin-B3, the
receptor of Sema5A, is a highly potent stimulator of
neurite outgrowth of primary murine cerebellar neurons.
Plexin-B3 has been linked to verbal performance and
white matter volume in human brain. Small GTPases play
important roles in plexin-B signaling. Plexin-B1
activates Rho through Rho-specific guanine nucleotide
exchange factors, leading to neurite retraction.
Plexin-B1 possesses an intrinsic GTPase-activating
protein activity for R-Ras and induces growth cone
collapse through R-Ras inactivation. Plexins contain a
C-terminal RasGAP domain, which functions as an enhancer
of the hydrolysis of GTP that is bound to Ras-GTPases.
Plexins display GAP activity towards the Ras homolog
Rap. Although the Rho (Ras homolog) GTPases are most
closely related to members of the Ras family, RhoGAP and
RasGAP show no sequence homology at their amino acid
level. RasGTPases function as molecular switches in a
large number of of signaling pathways. When bound to GTP
they are in the on state and when bound to GDP they are
in the off state. The RasGAP domain speeds up the
hydrolysis of GTP in Ras-like proteins acting as a
negative regulator.
Length = 391
Score = 31.1 bits (70), Expect = 0.61
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 59 RVGKSSIISQFLYDRFISRYKETVEELHRG 88
++G+ S ++ LY R I RYK+ VE +
Sbjct: 287 KLGRDSPSNKLLYAREIPRYKKMVERYYAD 316
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 30.7 bits (70), Expect = 0.64
Identities = 41/204 (20%), Positives = 74/204 (36%), Gaps = 48/204 (23%)
Query: 43 VGLQKDKRRVVVMGGARVGKSSIISQFLYD------RFISRYKE---------------- 80
+ +K +V +G GKS+++ + LYD R + + ++
Sbjct: 1 MASEKPHLNLVFIGHVDAGKSTLVGRLLYDLGEIDKRTMEKLEKEAKELGKESFKFAWVL 60
Query: 81 --TVEELHRGE--------YELPDGAQLTLDILDTSGAYQFPAMRELSISTADAFVLVYA 130
T EE RG +E + I+D G F S AD VLV
Sbjct: 61 DKTKEERERGVTIDVAHSKFETD---KYNFTIIDAPGHRDFVKNMITGASQADVAVLVVD 117
Query: 131 VDDAS---TWDVVKDLREQIVNKRGLMVP-IVVVGNKCEL------EFKDVRREIAETIA 180
D + V RE R L + ++V NK +L F+++ E+++ +
Sbjct: 118 ARDGEFEAGFGVGGQTREHAFLARTLGIKQLIVAVNKMDLVSWDEERFEEIVSEVSKLLK 177
Query: 181 LYDWQCG---FVECSAKENYNIVQ 201
+ + F+ S + N+ +
Sbjct: 178 MVGYNPKDVPFIPISGFKGDNLTK 201
>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 = 30.3 bits (68), Expect = 0.69
Identities = 27/135 (20%), Positives = 60/135 (44%), Gaps = 17/135 (12%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKETV---------------EELHRGEYELPDG 95
+ VV+G VGK+ +I ++ +++Y+ +E+ ++ DG
Sbjct: 4 KCVVVGDNAVGKTRLICARACNKTLTQYQLLATHVPTVWAIDQYRVCQEVLERSRDVVDG 63
Query: 96 AQLTLDILDTSGAYQFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMV 155
++L + DT G + R + +D +L +++ ++ VK + + V
Sbjct: 64 VSVSLRLWDTFGDHD--KDRRFAYGRSDVVLLCFSIASPNSLRNVKTMWYPEIRHFCPRV 121
Query: 156 PIVVVGNKCELEFKD 170
P+++VG K +L + D
Sbjct: 122 PVILVGCKLDLRYAD 136
>gnl|CDD|218790 pfam05876, Terminase_GpA, Phage terminase large subunit (GpA).
This family consists of several phage terminase large
subunit proteins as well as related sequences from
several bacterial species. The DNA packaging enzyme of
bacteriophage lambda, terminase, is a heteromultimer
composed of a small subunit, gpNu1, and a large
subunit, gpA, products of the Nu1 and A genes,
respectively. Terminase is involved in the
site-specific binding and cutting of the DNA in the
initial stages of packaging. It is now known that gpA
is actively involved in late stages of packaging,
including DNA translocation, and that this enzyme
contains separate functional domains for its early and
late packaging activities.
Length = 552
Score = 30.7 bits (70), Expect = 0.86
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 50 RRVVVMGGARVGKSSII 66
RVV M A+VGK+ ++
Sbjct: 34 ERVVFMKSAQVGKTELL 50
>gnl|CDD|213351 cd12791, RasGAP_plexin_B3, Ras-GTPase Activating Domain of
plexin-B3. Plexins form a conserved family of
transmembrane receptors for semaphorins and may be the
ancestors of semaphorins. Plexins are divided into four
types (A-D) according to sequence similarity. Plexin-B3
is the receptor of semaphorin 5A. It is a highly potent
stimulator of neurite outgrowth of primary murine
cerebellar neurons. Plexin-B3 has been linked to verbal
performance and white matter volume in human brain.
Furthermore, Sema5A and plexin-B3 have been implicated
in the progression of various types of cancer. They play
an important role in the invasion and metastasis of
gastric carcinoma. The protein and mRNA expression of
Sema5A and its receptor plexin-B3 increased gradually in
non-neoplastic mucosa, primary gastric carcinoma, and
lymph node metastasis, and their expression is
correlated. The stimulation of plexin-B3 by Sema5A
binding in human glioma cells results in the inhibition
of cell migration and invasion. Plexins contain a
C-terminal RasGAP domain, which functions as an enhancer
of the hydrolysis of GTP that is bound to Ras-GTPases.
Plexins display GAP activity towards the Ras homolog
Rap. Although the Rho (Ras homolog) GTPases are most
closely related to members of the Ras family, RhoGAP and
RasGAP show no sequence homology at their amino acid
level. RasGTPases function as molecular switches in a
large number of of signaling pathways. When bound to GTP
they are in the on state and when bound to GDP they are
in the off state. The RasGAP domain speeds up the
hydrolysis of GTP in Ras-like proteins acting as a
negative regulator.
Length = 397
Score = 30.2 bits (68), Expect = 0.97
Identities = 12/25 (48%), Positives = 18/25 (72%)
Query: 59 RVGKSSIISQFLYDRFISRYKETVE 83
+VG+ S +++ LY R I RYK+ VE
Sbjct: 289 KVGRDSPVNKLLYAREIPRYKQMVE 313
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 30.2 bits (69), Expect = 1.1
Identities = 44/195 (22%), Positives = 77/195 (39%), Gaps = 41/195 (21%)
Query: 51 RVVVMGGARVGKSSIISQFL-YDRFI-SRYKETVEELHRGEYELPDGAQLTLDILDTSGA 108
+VV++G VGKSS+++ L DR I + T ++ + L +G + + ++DT+G
Sbjct: 219 KVVIIGRPNVGKSSLLNALLGRDRAIVTDIAGTTRDVIEEDINL-NG--IPVRLVDTAG- 274
Query: 109 YQFPAMRE--------------LSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLM 154
+RE +I AD LV V DAS +DL ++
Sbjct: 275 -----IRETDDVVERIGIERAKKAIEEAD---LVLFVLDASQPLDKEDLA--LIELLPKK 324
Query: 155 VPIVVVGNKCEL--EFKDVRREIAETIALYDWQCGFVECSAKENYNIVQVFKELLAQAKV 212
PI+VV NK +L + + ++A A + SAK + + + +
Sbjct: 325 KPIIVVLNKADLVSKIELESEKLANGDA-------IISISAKTGEGLDALREAIKQLFGK 377
Query: 213 QYNLS--PAVRRRRQ 225
+ R
Sbjct: 378 GLGNQEGLFLSNLRH 392
>gnl|CDD|206679 cd01892, Miro2, Mitochondrial Rho family 2 (Miro2), C-terminal.
Miro2 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the putative
GTPase domain in the C terminus of Miro proteins. These
atypical Rho GTPases have roles in mitochondrial
homeostasis and apoptosis. Most Rho proteins contain a
lipid modification site at the C-terminus; however, Miro
is one of few Rho subfamilies that lack this feature.
Length = 180
Score = 29.1 bits (66), Expect = 1.5
Identities = 30/132 (22%), Positives = 52/132 (39%), Gaps = 26/132 (19%)
Query: 50 RRVV---VMGGARVGKSSIISQFLYDRF-ISRYKETVEELHRGEY------ELPDGAQLT 99
R V V+G GKS+++ FL F + Y T E+P G +
Sbjct: 2 RNVFLCFVLGAKGSGKSALLQAFLGRSFSQNAYSPT-----IKPRYAVNTVEVP-GQEKY 55
Query: 100 LDILDTSGA-YQFPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLM---V 155
L IL G + + + ++ D LVY D +++ ++ K+ M +
Sbjct: 56 L-ILREVGEDEEAILLNDAELAACDVACLVYDSSDPNSFSYCAEVY-----KKYFMLGEI 109
Query: 156 PIVVVGNKCELE 167
P + V K +L+
Sbjct: 110 PCLFVAAKADLD 121
>gnl|CDD|217416 pfam03193, DUF258, Protein of unknown function, DUF258.
Length = 161
Score = 29.1 bits (66), Expect = 1.5
Identities = 27/104 (25%), Positives = 43/104 (41%), Gaps = 28/104 (26%)
Query: 36 TSSSGTGVGLQK-----DKRRVVVMGGARVGKSSIISQFL--YDRFISRYKETVEELHRG 88
S+ TG G+++ + V+ G + VGKS++++ L D E E+L RG
Sbjct: 17 VVSAKTGEGIEELKPLLKGKTSVLAGQSGVGKSTLLNALLPELDLRTG---EISEKLGRG 73
Query: 89 E--------YELPDGAQLTLDILDTSGAYQFPAMRELSISTADA 124
+ LP G ++DT P REL + D
Sbjct: 74 RHTTTHVELFPLPGGG----LLIDT------PGFRELGLWHLDP 107
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 29.0 bits (65), Expect = 1.9
Identities = 32/175 (18%), Positives = 59/175 (33%), Gaps = 18/175 (10%)
Query: 45 LQKDKRRVVVMGGARVGKSSIISQFLYDRFI-----------SRYKETVEELHRGEYELP 93
+ + ++VV+G GK++ + + + T + G EL
Sbjct: 6 NKMIETKIVVIGPVGAGKTTFVRALSDKPLVITEADASSVSGKGKRPTTVAMDFGSIELD 65
Query: 94 DGAQLTLDILDTSGAYQFPAMRELSISTADAFVLVYAVDDASTWDVVKDLRE-QIVNKRG 152
+ + L T G +F M E+ A +++ T+ + + N
Sbjct: 66 EDTGVHL--FGTPGQERFKFMWEILSRGAVGAIVLVDSSRPITFHAEEIIDFLTSRNP-- 121
Query: 153 LMVPIVVVGNKCELEFKDVRREIAETIALYDWQCGFVECSAKENYNIVQVFKELL 207
+P+VV NK +L +I E + L +E A E LL
Sbjct: 122 --IPVVVAINKQDLFDALPPEKIREALKLELLSVPVIEIDATEGEGARDQLDVLL 174
>gnl|CDD|213344 cd12205, RasGAP_plexin, Ras-GTPase Activating Domain of plexins.
Plexins form a conserved family of transmembrane
receptors for semaphorins and may be the ancestors of
semaphorins. Ligand binding activates signal
transduction pathways controlling axon guidance in the
nervous system and other developmental processes,
including cell migration and morphogenesis, immune
function, and tumor progression. Plexins are divided
into four types (A-D) according to sequence similarity.
In vertebrates, type A Plexins serve as the co-receptors
for neuropilins to mediate the signaling of class 3
semaphorins except Sema3E, which signals through Plexin
D1. Plexins serve as direct receptors for several other
members of the semaphorin family: class 6 semaphorins
signal through type A plexins and class 4 semaphorins
through type B. Plexin C1 serves as the receptor of
Sema7A and plays regulation roles in both immune and
nervous systems. Plexins contain a C-terminal RasGAP
domain, which functions as an enhancer of the hydrolysis
of GTP that is bound to Ras-GTPases. Plexins display GAP
activity towards the Ras homolog Rap. Other proteins
having a RasGAP domain include p120GAP, IQGAP,
Rab5-activating protein 6, and Neurofibromin. Although
the Rho (Ras homolog) GTPases are most closely related
to members of the Ras family, RhoGAP and RasGAP show no
sequence homology at their amino acid level. RasGTPases
function as molecular switches in a large number of of
signaling pathways. When bound to GTP they are in the on
state and when bound to GDP they are in the off state.
The RasGAP domain speeds up the hydrolysis of GTP in
Ras-like proteins acting as a negative regulator.
Length = 382
Score = 29.1 bits (66), Expect = 2.0
Identities = 10/29 (34%), Positives = 18/29 (62%)
Query: 59 RVGKSSIISQFLYDRFISRYKETVEELHR 87
++GK S ++ L+ + I RY+E V +R
Sbjct: 282 KLGKDSPSNKLLFAKDIPRYREMVANFYR 310
>gnl|CDD|219447 pfam07520, SrfB, Virulence factor SrfB. This family includes
homologues of SsrAB is a two-component regulatory system
encoded within the Salmonella pathogenicity island
SPI-2. Among the products of genes activated by SsrAB
within epithelial and macrophage cells is Salmonella
typhimurium srfB. Homologues are found in several other
proteobacteria.
Length = 999
Score = 29.6 bits (67), Expect = 2.0
Identities = 12/20 (60%), Positives = 14/20 (70%), Gaps = 1/20 (5%)
Query: 205 ELLAQAKVQYNLSPAVRRRR 224
E+LAQA +Q N SPA R R
Sbjct: 430 EILAQALMQIN-SPAQRLRM 448
>gnl|CDD|221744 pfam12736, CABIT, Cell-cycle sustaining, positive selection,. The
'CABIT' domain (for 'cysteine-containing, all- in
Themis') is found in a newly identified gene family that
has three mammalian homologues (Themis, Icb1 and
9130404H23Rik) that encode proteins with two CABIT
domains and a highly conserved proline-rich region. In
contrast, Fam59A, Fam59B and related proteins from
mammals to cnidarians, including the insect Serrano
proteins, have a single copy of the CABIT domain, a
proline-rich region and often a C-terminal SAM
(sterile-motif) domain. Multiple-sequence alignment has
predicted that the CABIT domain adopts an all-strand
structure with at least 12 strands, ie a dyad of
six-stranded beta-barrel units. The CABIT domain
contains a nearly absolutely conserved cysteine residue
which is likely to be central to its function. CABIT
domain proteins function downstream of tyrosine kinase
signalling and interact with GRB2.
Length = 251
Score = 28.9 bits (65), Expect = 2.1
Identities = 22/105 (20%), Positives = 38/105 (36%), Gaps = 8/105 (7%)
Query: 111 FPAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRG--LMVPIVVVGNKCEL-E 167
F ++ EL VLV S+ +QI+ G L + V +L
Sbjct: 71 FESVEELLARVFPGRVLVTEDIRTSSDLSSSSDVDQILVPAGDELRLLGVEKRKGTDLGR 130
Query: 168 FKDVRREIAETIAL-YDWQCGFVECSAKENYNIVQVFKELLAQAK 211
+ E + L D + F E + E Y + KE++ + +
Sbjct: 131 CLVCLNQTNEPVTLPLDCKGRFSEVAPDEQYTL----KEIVEKFR 171
>gnl|CDD|206665 cd01876, YihA_EngB, YihA (EngB) GTPase family. The YihA (EngB)
subfamily of GTPases is typified by the E. coli YihA, an
essential protein involved in cell division control.
YihA and its orthologs are small proteins that typically
contain less than 200 amino acid residues and consists
of the GTPase domain only (some of the eukaryotic
homologs contain an N-terminal extension of about 120
residues that might be involved in organellar
targeting). Homologs of yihA are found in most
Gram-positive and Gram-negative pathogenic bacteria,
with the exception of Mycobacterium tuberculosis. The
broad-spectrum nature of YihA and its essentiality for
cell viability in bacteria make it an attractive
antibacterial target.
Length = 170
Score = 28.2 bits (64), Expect = 2.8
Identities = 11/57 (19%), Positives = 26/57 (45%), Gaps = 4/57 (7%)
Query: 155 VPIVVVGNKC----ELEFKDVRREIAETIALYDWQCGFVECSAKENYNIVQVFKELL 207
+P ++V K + E V ++I E + L++ + S+K+ I ++ +
Sbjct: 111 IPFLIVLTKADKLKKSELAKVLKKIKEELNLFNILPPVILFSSKKGTGIDELRALIA 167
>gnl|CDD|130064 TIGR00991, 3a0901s02IAP34, GTP-binding protein (Chloroplast
Envelope Protein Translocase). [Transport and binding
proteins, Nucleosides, purines and pyrimidines].
Length = 313
Score = 28.7 bits (64), Expect = 3.0
Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 1/81 (1%)
Query: 52 VVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQF 111
++VMG VGKSS ++ + +R + E L R A TL+I+DT G +
Sbjct: 41 ILVMGKGGVGKSSTVNSIIGERIATVSAFQSEGL-RPMMVSRTRAGFTLNIIDTPGLIEG 99
Query: 112 PAMRELSISTADAFVLVYAVD 132
+ + +++ F+L +D
Sbjct: 100 GYINDQAVNIIKRFLLGKTID 120
>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 = 28.6 bits (65), Expect = 3.2
Identities = 10/59 (16%), Positives = 25/59 (42%), Gaps = 8/59 (13%)
Query: 156 PIVVVGNKCEL-----EFKDVRREIAETIALYDW-QCGFVECSAKENYNIVQVFKELLA 208
+V+V NK +L ++ ++E+ + D+ F+ SA + ++ +
Sbjct: 285 ALVIVVNKWDLVKDEKTREEFKKELRRKLPFLDFAPIVFI--SALTGQGVDKLLDAIDE 341
>gnl|CDD|213353 cd12793, RasGAP_plexin_B1, Ras-GTPase Activating Domain of
plexin-B1. Plexins form a conserved family of
transmembrane receptors for semaphorins and may be the
ancestors of semaphorins. Plexins are divided into four
types (A-D) according to sequence similarity. Plexin-B1
serves as the Semaphorin 4D receptor and functions as a
regulator of developing neurons and a tumor suppressor
protein for melanoma. The Sema4D and plexin-B1 signaling
complex regulates dendritic and axonal complexity. The
activation of Plexin-B1 by Sema4D produces an acute
collapse of axonal growth cones in hippocampal and
retinal neurons over the early stages of neurite
outgrowth and promotes branching and complexity. As a
tumor suppressor, plexin-B1 abrogates activation of the
oncogenic receptor, c-Met, by its ligand, hepatocyte
growth factor (HGF), in melanoma. Furthermore, plexin-B1
suppresses integrin-dependent migration and activation
of pp125FAK and inhibits Rho activity. Plexin-B1 is
highly expressed in endothelial cells and its activation
by Sema4D elicits a potent proangiogenic response.
Plexins contain a C-terminal RasGAP domain, which
functions as an enhancer of the hydrolysis of GTP that
is bound to Ras-GTPases. Plexins display GAP activity
towards the Ras homolog Rap. Although the Rho (Ras
homolog) GTPases are most closely related to members of
the Ras family, RhoGAP and RasGAP show no sequence
homology at their amino acid level. RasGTPases function
as molecular switches in a large number of of signaling
pathways. When bound to GTP they are in the on state and
when bound to GDP they are in the off state. The RasGAP
domain speeds up the hydrolysis of GTP in Ras-like
proteins acting as a negative regulator.
Length = 394
Score = 28.5 bits (63), Expect = 3.3
Identities = 12/28 (42%), Positives = 19/28 (67%)
Query: 59 RVGKSSIISQFLYDRFISRYKETVEELH 86
++G+ S I++ LY R I RYK+ VE +
Sbjct: 286 KLGRDSPINKLLYARDIPRYKQMVERYY 313
>gnl|CDD|206748 cd01855, YqeH, Circularly permuted YqeH GTPase. YqeH is an
essential GTP-binding protein. Depletion of YqeH induces
an excess initiation of DNA replication, suggesting that
it negatively controls initiation of chromosome
replication. The YqeH subfamily is common in eukaryotes
and sporadically present in bacteria with probable
acquisition by plants from chloroplasts. Proteins of the
YqeH family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases.
Length = 191
Score = 28.0 bits (63), Expect = 3.4
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 47 KDKRRVVVMGGARVGKSSIISQFL 70
K + V V+G VGKS++I+ L
Sbjct: 123 KYRGDVYVVGATNVGKSTLINALL 146
Score = 27.6 bits (62), Expect = 4.8
Identities = 23/102 (22%), Positives = 39/102 (38%), Gaps = 27/102 (26%)
Query: 125 FVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCELEFKD---------VRREI 175
LV V D D L + G P+++VGNK +L KD V++ +
Sbjct: 34 NALVVHVVDIF--DFPGSLIPGLAELIGA-KPVILVGNKIDLLPKDVKPNRLKQWVKKRL 90
Query: 176 AET------IALYDWQCGFVECSAKENYNIVQVFKELLAQAK 211
+ L SAK+ + + ++ +E+ AK
Sbjct: 91 KIGGLKIKDVILV---------SAKKGWGVEELIEEIKKLAK 123
>gnl|CDD|223557 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 28.7 bits (65), Expect = 3.6
Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 5/56 (8%)
Query: 157 IVVVGNKCELEFKD---VRREIAETIALYDWQCGFVECSAKENYNIVQVFKELLAQ 209
I+ V NK +L D V++EI + I + D V SAK I V + ++ +
Sbjct: 131 IIPVLNKIDLPAADPERVKQEIEDIIGI-D-ASDAVLVSAKTGIGIEDVLEAIVEK 184
>gnl|CDD|221955 pfam13173, AAA_14, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily.
Length = 127
Score = 27.5 bits (62), Expect = 3.7
Identities = 9/31 (29%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 49 KRRVVVMGGAR-VGKSSIISQFLYDRFISRY 78
+++V+ G R VGK++++ QFL +
Sbjct: 1 NNKIIVITGPRQVGKTTLLLQFLKELLSENI 31
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 28.2 bits (64), Expect = 3.7
Identities = 8/23 (34%), Positives = 15/23 (65%)
Query: 44 GLQKDKRRVVVMGGARVGKSSII 66
G++ R +++G VGKS++I
Sbjct: 116 GMRPRAIRAMIIGIPNVGKSTLI 138
>gnl|CDD|227812 COG5525, COG5525, Phage terminase, large subunit GpA
[Replication, recombination and repair].
Length = 611
Score = 28.6 bits (64), Expect = 4.3
Identities = 7/18 (38%), Positives = 11/18 (61%)
Query: 50 RRVVVMGGARVGKSSIIS 67
R V + ARVGK+ ++
Sbjct: 65 RAVNFVKSARVGKTKMLL 82
>gnl|CDD|239172 cd02771, MopB_NDH-1_NuoG2-N7, MopB_NDH-1_NuoG2-N7: The second
domain of the NuoG subunit (with a [4Fe-4S] cluster, N7)
of the NADH-quinone oxidoreductase/NADH dehydrogenase-1
(NDH-1) found in various bacteria. The NDH-1 is the
first energy-transducting complex in the respiratory
chain and functions as a redox pump that uses the redox
energy to translocate H+ ions across the membrane,
resulting in a significant contribution to energy
production. In Escherichia coli NDH-1, the largest
subunit is encoded by the nuoG gene, and is part of the
14 distinct subunits constituting the functional enzyme.
The NuoG subunit is made of two domains: the first
contains three binding sites for FeS clusters (the fer2
domain), the second domain (this CD), is of unknown
function or, as postulated, has lost an ancestral
formate dehydrogenase activity that became redundant
during the evolution of the complex I enzyme. Unique to
this group, compared to the other prokaryotic and
eukaryotic groups in this domain protein family
(NADH-Q-OR-NuoG2), is an N-terminal [4Fe-4S] cluster
(N7/N1c) present in the second domain. Although only
vestigial sequence evidence remains of a molybdopterin
binding site, this protein domain belongs to the
molybdopterin_binding (MopB) superfamily of proteins.
Length = 472
Score = 28.1 bits (63), Expect = 4.6
Identities = 20/85 (23%), Positives = 35/85 (41%), Gaps = 13/85 (15%)
Query: 44 GLQKDKRRVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDIL 103
L++ K +V +G R S S + + + T HR L +IL
Sbjct: 81 RLKEAKDKVGGIGSPRA---SNESNYALQKLVGAVLGTNNVDHRARR-------LIAEIL 130
Query: 104 DTSGAYQFPAMRELSISTADAFVLV 128
Y P++R+ I +ADA +++
Sbjct: 131 RNGPIYI-PSLRD--IESADAVLVL 152
>gnl|CDD|206681 cd01894, EngA1, EngA1 GTPase contains the first domain of EngA.
This EngA1 subfamily CD represents the first GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. Since the sequences of the
two domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family. Although the exact function of
these proteins has not been elucidated, studies have
revealed that the E. coli EngA homolog, Der, and
Neisseria gonorrhoeae EngA are essential for cell
viability. A recent report suggests that E. coli Der
functions in ribosome assembly and stability.
Length = 157
Score = 27.4 bits (62), Expect = 4.6
Identities = 30/126 (23%), Positives = 48/126 (38%), Gaps = 37/126 (29%)
Query: 60 VGKSSIISQFLYDRFISRYKETVEEL-------HRGEYELPDGAQLTLDILDTSG----- 107
VGKS+ L++R R V + GE E ++DT G
Sbjct: 8 VGKST-----LFNRLTGRRDAIVSDTPGVTRDRKYGEAEWGG---REFILIDTGGIEPDD 59
Query: 108 AYQFPAMRE---LSISTADAFVLVYAVD-----DASTWDVVKDLREQIVNKRGLMVPIVV 159
+RE ++I AD + V VD + ++ K LR+ K P+++
Sbjct: 60 EGISKEIREQAEIAIEEADVILFV--VDGREGLTPADEEIAKYLRKS--KK-----PVIL 110
Query: 160 VGNKCE 165
V NK +
Sbjct: 111 VVNKID 116
>gnl|CDD|234433 TIGR03992, Arch_glmU, UDP-N-acetylglucosamine
diphosphorylase/glucosamine-1-phosphate
N-acetyltransferase. The MJ_1101 protein from
Methanococcus jannaschii has been characterized as the
GlmU enzyme catalyzing the final two steps of UDP-GlcNAc
biosynthesis. Many of the genes identified by this model
are in proximity to the GlmS and GlmM genes and are also
presumed to be GlmU. However, some archaeal genomes
contain multiple closely-related homologs from this
family and it is not clear what the substrate
specificity is for each of them.
Length = 393
Score = 27.9 bits (63), Expect = 4.8
Identities = 20/61 (32%), Positives = 26/61 (42%), Gaps = 11/61 (18%)
Query: 52 VVVMGGARV---------GKSSIISQFLY--DRFISRYKETVEELHRGEYELPDGAQLTL 100
VV G RV S++I+ +Y I E + RGEYEL D QL +
Sbjct: 138 VVETDGGRVTGIVEKPENPPSNLINAGIYLFSPEIFELLEKTKLSPRGEYELTDALQLLI 197
Query: 101 D 101
D
Sbjct: 198 D 198
>gnl|CDD|206670 cd01883, EF1_alpha, Elongation Factor 1-alpha (EF1-alpha) protein
family. EF1 is responsible for the GTP-dependent
binding of aminoacyl-tRNAs to the ribosomes. EF1 is
composed of four subunits: the alpha chain which binds
GTP and aminoacyl-tRNAs, the gamma chain that probably
plays a role in anchoring the complex to other cellular
components and the beta and delta (or beta') chains.
This subfamily is the alpha subunit, and represents the
counterpart of bacterial EF-Tu for the archaea
(aEF1-alpha) and eukaryotes (eEF1-alpha). eEF1-alpha
interacts with the actin of the eukaryotic cytoskeleton
and may thereby play a role in cellular transformation
and apoptosis. EF-Tu can have no such role in bacteria.
In humans, the isoform eEF1A2 is overexpressed in 2/3
of breast cancers and has been identified as a putative
oncogene. This subfamily also includes Hbs1, a G
protein known to be important for efficient growth and
protein synthesis under conditions of limiting
translation initiation in yeast, and to associate with
Dom34. It has been speculated that yeast Hbs1 and Dom34
proteins may function as part of a complex with a role
in gene expression.
Length = 219
Score = 27.8 bits (63), Expect = 4.9
Identities = 12/47 (25%), Positives = 24/47 (51%), Gaps = 6/47 (12%)
Query: 52 VVVMGGARVGKSSIISQFLYD------RFISRYKETVEELHRGEYEL 92
+VV+G GKS++ LY R I +Y++ +E+ + ++
Sbjct: 2 LVVIGHVDAGKSTLTGHLLYKLGGVDKRTIEKYEKEAKEMGKESFKY 48
>gnl|CDD|133356 cd04156, ARLTS1, Arf-like tumor suppressor gene 1 (ARLTS1 or
Arl11). ARLTS1 (Arf-like tumor suppressor gene 1), also
known as Arl11, is a member of the Arf family of small
GTPases that is believed to play a major role in
apoptotic signaling. ARLTS1 is widely expressed and
functions as a tumor suppressor gene in several human
cancers. ARLTS1 is a low-penetrance suppressor that
accounts for a small percentage of familial melanoma or
familial chronic lymphocytic leukemia (CLL). ARLTS1
inactivation seems to occur most frequently through
biallelic down-regulation by hypermethylation of the
promoter. In breast cancer, ARLTS1 alterations were
typically a combination of a hypomorphic polymorphism
plus loss of heterozygosity. In a case of thyroid
adenoma, ARLTS1 alterations were polymorphism plus
promoter hypermethylation. The nonsense polymorphism
Trp149Stop occurs with significantly greater frequency
in familial cancer cases than in sporadic cancer cases,
and the Cys148Arg polymorphism is associated with an
increase in high-risk familial breast cancer.
Length = 160
Score = 27.4 bits (61), Expect = 4.9
Identities = 39/167 (23%), Positives = 73/167 (43%), Gaps = 21/167 (12%)
Query: 51 RVVVMGGARVGKSSIISQFLYDRFISRYKE---TVEELHRGEYELPDGAQLTLDILDTSG 107
+V+++G GKS+++ + + ++ VE L ++ L+L + D G
Sbjct: 1 QVLLLGLDSAGKSTLLYKLKHAELVTTIPTVGFNVEMLQLEKH-------LSLTVWDVGG 53
Query: 108 AYQFPAMRELSIS-TADAFVLVYAVD---DASTWDVVKDLREQIVNKRGLMVPIVVVGNK 163
Q MR + + LVY VD +A + K+L+ + N+ VP+V++ NK
Sbjct: 54 --QEK-MRTVWKCYLENTDGLVYVVDSSDEARLDESQKELKHILKNEHIKGVPVVLLANK 110
Query: 164 CELEFKDVRREIAETIAL---YDWQCGFVE-CSAKENYNIVQVFKEL 206
+L EI L + +V+ CSA + + F++L
Sbjct: 111 QDLPGALTAEEITRRFKLKKYCSDRDWYVQPCSAVTGEGLAEAFRKL 157
>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 = 27.7 bits (63), Expect = 5.0
Identities = 30/102 (29%), Positives = 44/102 (43%), Gaps = 28/102 (27%)
Query: 38 SSGTGVGLQK-----DKRRVVVMG--GARVGKSSIISQFLYDRFISRYKETVEELHRG-- 88
S+ TG GL + + V++G G VGKS++++ L + E E+L RG
Sbjct: 69 SAKTGEGLDELRELLKGKTSVLVGQSG--VGKSTLLNALL-PELVLATGEISEKLGRGRH 125
Query: 89 -----E-YELPDGAQLTLDILDTSGAYQFPAMRELSISTADA 124
E + LP G I+DT P REL + D
Sbjct: 126 TTTHRELFPLPGGG----LIIDT------PGFRELGLLHIDP 157
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 28.0 bits (63), Expect = 5.2
Identities = 25/91 (27%), Positives = 40/91 (43%), Gaps = 19/91 (20%)
Query: 48 DKRRVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGE--------YELPDGAQLT 99
+ V++G + VGKS++I+ L + + E E+L RG + LP G
Sbjct: 163 AGKITVLLGQSGVGKSTLINALLPELNQ-KTGEISEKLGRGRHTTTHVELFPLPGGGW-- 219
Query: 100 LDILDTSGAYQFPAMRELSISTADAFVLVYA 130
I+DT P R L ++ + LV A
Sbjct: 220 --IIDT------PGFRSLGLAHLEPEDLVQA 242
>gnl|CDD|185122 PRK15200, PRK15200, fimbrial protein FimI; Provisional.
Length = 177
Score = 27.5 bits (61), Expect = 5.6
Identities = 12/55 (21%), Positives = 27/55 (49%)
Query: 34 ESTSSSGTGVGLQKDKRRVVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRG 88
E ++G G+ L D++R ++ + + I++ + F +RY+ E + G
Sbjct: 110 EGIGNAGIGLALFDDQQRQIIPNTLPLHYAPILTSEMTLHFTARYRAISENMTPG 164
>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 = 27.1 bits (61), Expect = 5.7
Identities = 20/92 (21%), Positives = 33/92 (35%), Gaps = 14/92 (15%)
Query: 118 SISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMVPIVVVGNKCELEFKDVRREIAE 177
+I AD +++ VD + D ++ K+ P++VV NK +L
Sbjct: 79 AIEEAD--LVLLVVDASEGLDEEDLEILELPAKK----PVIVVLNKSDLLSDAEGISELN 132
Query: 178 TIALYDWQCGFVECSAKENYNIVQVFKELLAQ 209
+ SAK I KE L +
Sbjct: 133 -------GKPIIAISAKTGEGI-DELKEALLE 156
>gnl|CDD|143442 cd07124, ALDH_PutA-P5CDH-RocA, Delta(1)-pyrroline-5-carboxylate
dehydrogenase, RocA. Delta(1)-pyrroline-5-carboxylate
dehydrogenase (EC=1.5.1.12 ), RocA: a proline catabolic
enzyme of the aldehyde dehydrogenase (ALDH) protein
superfamily. The proline catabolic enzymes, proline
dehydrogenase and Delta(1)-pyrroline-5-carboxylate
dehydrogenase (P5CDH), catalyze the two-step oxidation
of proline to glutamate; P5CDH catalyzes the oxidation
of glutamate semialdehyde, utilizing NAD+ as the
electron acceptor. In some bacteria, the two enzymes are
fused into the bifunctional flavoenzyme, proline
utilization A (PutA). In this CD, monofunctional enzyme
sequences such as seen in the Bacillus subtilis RocA
P5CDH are also present. These enzymes play important
roles in cellular redox control, superoxide generation,
and apoptosis.
Length = 512
Score = 28.0 bits (63), Expect = 5.8
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 65 IISQFLYDRFISRYKETVEELHRGEYELPD 94
I+ + +YD F+ R E + L G+ E P+
Sbjct: 322 IVHESVYDEFLERLVERTKALKVGDPEDPE 351
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 28.0 bits (62), Expect = 6.8
Identities = 11/29 (37%), Positives = 20/29 (68%), Gaps = 1/29 (3%)
Query: 75 ISRYKETVEELHRGEYELPDGAQLTLDIL 103
I+++K VE+LH G Y+LP G +++ +
Sbjct: 1047 IAQFKRKVEKLHEG-YDLPQGVSMSVKVF 1074
>gnl|CDD|206677 cd01890, LepA, LepA also known as Elongation Factor 4 (EF4). LepA
(also known as elongation factor 4, EF4) belongs to the
GTPase family and exhibits significant homology to the
translation factors EF-G and EF-Tu, indicating its
possible involvement in translation and association with
the ribosome. LepA is ubiquitous in bacteria and
eukaryota (e.g. yeast GUF1p), but is missing from
archaea. This pattern of phyletic distribution suggests
that LepA evolved through a duplication of the EF-G gene
in bacteria, followed by early transfer into the
eukaryotic lineage, most likely from the
promitochondrial endosymbiont. Yeast GUF1p is not
essential and mutant cells did not reveal any marked
phenotype.
Length = 179
Score = 27.1 bits (61), Expect = 7.0
Identities = 13/53 (24%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 157 IVVVGNKCELEFKD---VRREIAETIALYDWQCGFVECSAKENYNIVQVFKEL 206
I+ V NK +L D V++EI + + L + + SAK + + + +
Sbjct: 122 IIPVINKIDLPAADPDRVKQEIEDVLGLDASEA--ILVSAKTGLGVEDLLEAI 172
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 27.5 bits (62), Expect = 7.0
Identities = 30/138 (21%), Positives = 50/138 (36%), Gaps = 38/138 (27%)
Query: 49 KRRVVVMGGARVGKSSIISQFLYDRFISRYKETVEEL-------HRGEYELPDGAQLTLD 101
V ++G VGKS+ L++R R V + G+ E
Sbjct: 3 TPVVAIVGRPNVGKST-----LFNRLTGRRIAIVSDTPGVTRDRIYGDAEWLG---REFI 54
Query: 102 ILDTSG------AYQFPAMRE---LSISTADAFVLVYAVD-----DASTWDVVKDLREQI 147
++DT G +RE ++I AD + V VD + ++ K LR
Sbjct: 55 LIDTGGLDDGDEDELQELIREQALIAIEEADVILFV--VDGREGITPADEEIAKILRRS- 111
Query: 148 VNKRGLMVPIVVVGNKCE 165
P+++V NK +
Sbjct: 112 ------KKPVILVVNKID 123
>gnl|CDD|218203 pfam04670, Gtr1_RagA, Gtr1/RagA G protein conserved region. GTR1
was first identified in S. cerevisiae as a suppressor
of a mutation in RCC1. Biochemical analysis revealed
that Gtr1 is in fact a G protein of the Ras family. The
RagA/B proteins are the human homologues of Gtr1.
Included in this family is the human Rag C, a novel
protein that has been shown to interact with RagA/B.
Length = 230
Score = 27.2 bits (61), Expect = 7.3
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 51 RVVVMGGARVGKSSIIS 67
+V++MG GKSS+ S
Sbjct: 1 KVLLMGLRGSGKSSMRS 17
>gnl|CDD|213834 TIGR03597, GTPase_YqeH, ribosome biogenesis GTPase YqeH. This
family describes YqeH, a member of a larger family of
GTPases involved in ribosome biogenesis. Like YqlF, it
shows a cyclical permutation relative to GTPases EngA
(in which the GTPase domain is duplicated), Era, and
others. Members of this protein family are found in a
relatively small number of bacterial species, including
Bacillus subtilis but not Escherichia coli [Protein
synthesis, Other].
Length = 360
Score = 27.2 bits (61), Expect = 8.6
Identities = 11/24 (45%), Positives = 18/24 (75%)
Query: 47 KDKRRVVVMGGARVGKSSIISQFL 70
++K+ V V+G VGKSS+I++ L
Sbjct: 152 RNKKDVYVVGVTNVGKSSLINKLL 175
>gnl|CDD|182827 PRK10906, PRK10906, DNA-binding transcriptional repressor GlpR;
Provisional.
Length = 252
Score = 27.1 bits (60), Expect = 8.7
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 56 GGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGA 108
GGA + SS+ + + +DR ++ +E + ++P+GA L +DI T A
Sbjct: 54 GGAALPSSSVNTPW-HDRKATQTEEKERIARKVASQIPNGATLFIDIGTTPEA 105
>gnl|CDD|206752 cd01859, MJ1464, An uncharacterized, circularly permuted subfamily
of the Ras GTPases. This family represents archaeal
GTPase typified by the protein MJ1464 from Methanococcus
jannaschii. The members of this family show a circular
permutation of the GTPase signature motifs so that
C-terminal strands 5, 6, and 7 (strands 6 contain the
NKxD motif) are relocated to the N terminus.
Length = 157
Score = 26.5 bits (59), Expect = 8.9
Identities = 13/67 (19%), Positives = 28/67 (41%), Gaps = 4/67 (5%)
Query: 145 EQIVNKRGLMVPIVVVGNKCELEFKDVRREIAETIALYDWQCGFVECSAKENYNIVQVFK 204
E++ + G +++V NK +L ++V + E +V SA+E + +
Sbjct: 33 ERMALELGK--KLIIVLNKADLVPREVLEKWKEVFESEGLPVVYV--SARERLGTRILRR 88
Query: 205 ELLAQAK 211
+ A
Sbjct: 89 TIKELAI 95
>gnl|CDD|235424 PRK05347, PRK05347, glutaminyl-tRNA synthetase; Provisional.
Length = 554
Score = 27.4 bits (62), Expect = 9.5
Identities = 10/21 (47%), Positives = 11/21 (52%), Gaps = 7/21 (33%)
Query: 164 CELEFKDVRREIAETIALYDW 184
C LEF+D R LYDW
Sbjct: 232 CTLEFEDHRP-------LYDW 245
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the AAA
superfamily.
Length = 154
Score = 26.4 bits (58), Expect = 9.7
Identities = 17/104 (16%), Positives = 36/104 (34%), Gaps = 7/104 (6%)
Query: 52 VVVMGGARVGKSSIISQFLYDRFISRYKETVEELHRGEYELPDGAQLTLDILDTSGAYQF 111
V++ G + GK+S++ + L ++ K E + +L +L A
Sbjct: 27 VLLTGPSGTGKTSLLRELLEGLLVAAGKCDQAERNPPYAFSQALRELLRQLLRELAAELL 86
Query: 112 PAMRELSISTADAFVLVYAVDDASTWDVVKDLREQIVNKRGLMV 155
L + + D+V+ L + R L++
Sbjct: 87 LLREALLAALGAELIE-------GLQDLVELLERLLARARPLVL 123
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
0.318 0.133 0.381
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: 12,827,338
Number of extensions: 1220452
Number of successful extensions: 1593
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1407
Number of HSP's successfully gapped: 170
Length of query: 253
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 158
Effective length of database: 6,723,972
Effective search space: 1062387576
Effective search space used: 1062387576
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.5 bits)