RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10117
(135 letters)
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 63.8 bits (155), Expect = 2e-13
Identities = 29/99 (29%), Positives = 47/99 (47%), Gaps = 2/99 (2%)
Query: 2 KIKILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALDTSKTEIELWDTS 61
+ KI++LG GKT L N L E Y PT G + +++LWDT+
Sbjct: 5 EFKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDP--AKTIEPYRRNIKLQLWDTA 62
Query: 62 GDHKFESVWPAFQRDVHGIIFVFNSGVPGHISELLLFYD 100
G ++ S+ P + R +GI+ V++S + EL +
Sbjct: 63 GQEEYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWL 101
>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 = 55.2 bits (134), Expect = 1e-10
Identities = 27/86 (31%), Positives = 44/86 (51%), Gaps = 10/86 (11%)
Query: 3 IKILILGPIMAGKTVLANALCDLTTAEEYHPTQGV----RIVECEHSYALDTSKTEIELW 58
KI+++G GKT L D +E Y T GV + +E +D K ++++W
Sbjct: 1 FKIVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGVDFKSKTIE------VDGKKVKLQIW 54
Query: 59 DTSGDHKFESVWPAFQRDVHGIIFVF 84
DT+G +F S+ ++ R HG I V+
Sbjct: 55 DTAGQERFRSITSSYYRGAHGAILVY 80
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 51.7 bits (125), Expect = 3e-09
Identities = 23/86 (26%), Positives = 45/86 (52%), Gaps = 10/86 (11%)
Query: 3 IKILILGPIMAGKTVLANALCDLTTAEEYHPTQGV----RIVECEHSYALDTSKTEIELW 58
KI+++G GK+ L + D +E+Y T GV + +E +D + ++++W
Sbjct: 1 FKIILIGDSGVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIE------VDGKRVKLQIW 54
Query: 59 DTSGDHKFESVWPAFQRDVHGIIFVF 84
DT+G +F S+ ++ R G + V+
Sbjct: 55 DTAGQERFRSITSSYYRGAVGALLVY 80
>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 = 1e-08
Identities = 29/97 (29%), Positives = 47/97 (48%), Gaps = 5/97 (5%)
Query: 1 MKIKILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVE-CEHSYALDTSKTEIELWD 59
+K KI+++G GKT L + E Y PT + E S+ +DT + E+ LWD
Sbjct: 4 VKCKIVVVGDSQCGKTALLHVFAKDCFPENYVPT----VFENYTASFEIDTQRIELSLWD 59
Query: 60 TSGDHKFESVWPAFQRDVHGIIFVFNSGVPGHISELL 96
TSG +++V P D ++ F+ P + +L
Sbjct: 60 TSGSPYYDNVRPLSYPDSDAVLICFDISRPETLDSVL 96
>gnl|CDD|206699 cd04120, Rab12, Rab GTPase family 12 (Rab12). Rab12 was first
identified in canine cells, where it was localized to
the Golgi complex. The specific function of Rab12
remains unknown, and inconsistent results about its
cellular localization have been reported. More recent
studies have identified Rab12 associated with
post-Golgi vesicles, or with other small vesicle-like
structures but not with the Golgi complex. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins.
Length = 202
Score = 49.6 bits (118), Expect = 3e-08
Identities = 28/85 (32%), Positives = 43/85 (50%), Gaps = 6/85 (7%)
Query: 3 IKILILGPIMAGKTVLANALCDLTTAEEYHPTQGV--RIVECEHSYALDTSKTEIELWDT 60
++++I+G GKT L D T E T GV +I E L K +++WDT
Sbjct: 1 LQVIIIGSRGVGKTSLMERFTDDTFCEACKSTVGVDFKIKTVE----LRGKKIRLQIWDT 56
Query: 61 SGDHKFESVWPAFQRDVHGIIFVFN 85
+G +F S+ A+ R GII V++
Sbjct: 57 AGQERFNSITSAYYRSAKGIILVYD 81
>gnl|CDD|133362 cd04162, Arl9_Arfrp2_like, Arf-like 9 (Arl9)/Arfrp2-like GTPase.
Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first
identified as part of the Human Cancer Genome Project.
It maps to chromosome 4q12 and is sometimes referred to
as Arfrp2 (Arf-related protein 2). This is a novel
subfamily identified in human cancers that is
uncharacterized to date.
Length = 164
Score = 49.0 bits (117), Expect = 3e-08
Identities = 26/82 (31%), Positives = 37/82 (45%), Gaps = 6/82 (7%)
Query: 5 ILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALDTSKTEIELWDTSGDH 64
IL+LG AGKT L ++L + E PT G +S A+ T +EL + G
Sbjct: 2 ILVLGLDGAGKTSLLHSLSSERSLESVVPTTGF------NSVAIPTQDAIMELLEIGGSQ 55
Query: 65 KFESVWPAFQRDVHGIIFVFNS 86
W + G+IFV +S
Sbjct: 56 NLRKYWKRYLSGSQGLIFVVDS 77
>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 = 48.2 bits (115), Expect = 7e-08
Identities = 26/83 (31%), Positives = 45/83 (54%), Gaps = 3/83 (3%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALDTSKTEIELWDTSGD 63
KI+++G GKT L C E T GV E + +D + +++LWDT+G
Sbjct: 4 KIIVIGDSNVGKTCLTYRFCAGRFPERTEATIGVDFRE--RTVEIDGERIKVQLWDTAGQ 61
Query: 64 HKF-ESVWPAFQRDVHGIIFVFN 85
+F +S+ + R+VH ++FV++
Sbjct: 62 ERFRKSMVQHYYRNVHAVVFVYD 84
>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 = 47.9 bits (115), Expect = 9e-08
Identities = 23/85 (27%), Positives = 42/85 (49%), Gaps = 10/85 (11%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQGV----RIVECEHSYALDTSKTEIELWD 59
K++++G GK+ L EEY PT GV + +E +D ++++WD
Sbjct: 1 KLVLVGDGGVGKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIE------VDGKTVKLQIWD 54
Query: 60 TSGDHKFESVWPAFQRDVHGIIFVF 84
T+G +F ++ P + R G + V+
Sbjct: 55 TAGQERFRALRPLYYRGAQGFLLVY 79
>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 = 47.4 bits (113), Expect = 1e-07
Identities = 26/89 (29%), Positives = 42/89 (47%), Gaps = 5/89 (5%)
Query: 2 KIKILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVE-CEHSYALDTSKTEIELWDT 60
+ KI+++G GKT L + E Y PT + E S+ +D + E+ LWDT
Sbjct: 1 RCKIVLVGDSQCGKTALLQVFAKDSFPENYVPT----VFENYTASFEVDKQRIELSLWDT 56
Query: 61 SGDHKFESVWPAFQRDVHGIIFVFNSGVP 89
SG +++V P D ++ F+ P
Sbjct: 57 SGSPYYDNVRPLSYPDSDAVLICFDISRP 85
>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 = 46.7 bits (111), Expect = 3e-07
Identities = 22/103 (21%), Positives = 37/103 (35%), Gaps = 12/103 (11%)
Query: 6 LILGPIMAGKTVLANALCD---LTTAEEYHPTQGVRIVECEHSYALDTSKTEIELWDTSG 62
+++G GK+ L NAL ++ T+ + E LD K ++ L DT G
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKE----LDKGKVKLVLVDTPG 56
Query: 63 DHKFESVWPAFQ-----RDVHGIIFVFNSGVPGHISELLLFYD 100
+F + R I+ V +S + L
Sbjct: 57 LDEFGGLGREELARLLLRGADLILLVVDSTDRESEEDAKLLIL 99
>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 = 46.7 bits (111), Expect = 3e-07
Identities = 23/86 (26%), Positives = 43/86 (50%), Gaps = 4/86 (4%)
Query: 3 IKILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALDTSKTEIE--LWDT 60
IK++++G GK+ + ++Y T GV +E + L S ++ LWDT
Sbjct: 1 IKVIVVGNGNVGKSSMIQRFVKGIFTKDYKKTIGVDFLEKQIF--LRQSDEDVRLMLWDT 58
Query: 61 SGDHKFESVWPAFQRDVHGIIFVFNS 86
+G +F+++ A+ R I VF++
Sbjct: 59 AGQEEFDAITKAYYRGAQACILVFST 84
>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 = 46.6 bits (111), Expect = 3e-07
Identities = 23/84 (27%), Positives = 36/84 (42%), Gaps = 3/84 (3%)
Query: 3 IKILILGPIMAGKTVLANALCDLTTAE-EYHPTQGVRIVECEHSYALDTSKTEIELWDTS 61
IKI+I+G GK+ L N L + EY P V D + L DT+
Sbjct: 2 IKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEE--DGKTYKFNLLDTA 59
Query: 62 GDHKFESVWPAFQRDVHGIIFVFN 85
G ++++ + R V + VF+
Sbjct: 60 GQEDYDAIRRLYYRAVESSLRVFD 83
>gnl|CDD|133361 cd04161, Arl2l1_Arl13_like, Arl2-like protein 1 (Arl2l1) and
Arl13. Arl2l1 (Arl2-like protein 1) and Arl13 form a
subfamily of the Arf family of small GTPases. Arl2l1
was identified in human cells during a search for the
gene(s) responsible for Bardet-Biedl syndrome (BBS).
Like Arl6, the identified BBS gene, Arl2l1 is proposed
to have cilia-specific functions. Arl13 is found on the
X chromosome, but its expression has not been
confirmed; it may be a pseudogene.
Length = 167
Score = 46.2 bits (110), Expect = 4e-07
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 7/82 (8%)
Query: 5 ILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALDTSKTEIELWDTSGDH 64
+L +G AGKT L +AL ++ PT G + L K E+ ++D G
Sbjct: 2 LLTVGLDNAGKTTLVSALQGEIP-KKVAPTVGFTPTK------LRLDKYEVCIFDLGGGA 54
Query: 65 KFESVWPAFQRDVHGIIFVFNS 86
F +W + + HG++FV +S
Sbjct: 55 NFRGIWVNYYAEAHGLVFVVDS 76
>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 = 44.6 bits (106), Expect = 1e-06
Identities = 24/85 (28%), Positives = 44/85 (51%), Gaps = 6/85 (7%)
Query: 3 IKILILGPIMAGKTVLANALCDLTTAEEYHPTQGV--RIVECEHSYALDTSKTEIELWDT 60
+KIL++G GK+ L D T E+ T GV ++ +D K ++ +WDT
Sbjct: 1 LKILLIGDSGVGKSSLLLRFTDDTFDEDLSSTIGVDFKVKTVT----VDGKKVKLAIWDT 56
Query: 61 SGDHKFESVWPAFQRDVHGIIFVFN 85
+G +F ++ ++ R G+I V++
Sbjct: 57 AGQERFRTLTSSYYRGAQGVILVYD 81
>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 = 44.8 bits (106), Expect = 2e-06
Identities = 26/86 (30%), Positives = 45/86 (52%), Gaps = 10/86 (11%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQGV----RIVECEHSYALDTSKTEIELWD 59
K+LI+G GK+ L D T + Y T GV R VE ++ + ++++WD
Sbjct: 8 KLLIIGDSGVGKSSLLLRFADNTFSGSYITTIGVDFKIRTVE------INGERVKLQIWD 61
Query: 60 TSGDHKFESVWPAFQRDVHGIIFVFN 85
T+G +F ++ + R HG+I V++
Sbjct: 62 TAGQERFRTITSTYYRGTHGVIVVYD 87
>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 = 44.2 bits (105), Expect = 2e-06
Identities = 28/86 (32%), Positives = 45/86 (52%), Gaps = 10/86 (11%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQGV----RIVECEHSYALDTSKTEIELWD 59
K+L++G GK+ L D T E Y T GV R +E LD ++++WD
Sbjct: 4 KLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIE------LDGKTVKLQIWD 57
Query: 60 TSGDHKFESVWPAFQRDVHGIIFVFN 85
T+G +F ++ ++ R HGII V++
Sbjct: 58 TAGQERFRTITSSYYRGAHGIIIVYD 83
>gnl|CDD|206693 cd04108, Rab36_Rab34, Rab GTPase families 34 (Rab34) and 36
(Rab36). Rab34/Rab36 subfamily. Rab34, found primarily
in the Golgi, interacts with its effector,
Rab-interacting lysosomal protein (RILP). This enables
its participation in microtubular
dynenin-dynactin-mediated repositioning of lysosomes
from the cell periphery to the Golgi. A Rab34 (Rah)
isoform that lacks the consensus GTP-binding region has
been identified in mice. This isoform is associated
with membrane ruffles and promotes macropinosome
formation. Rab36 has been mapped to human chromosome
22q11.2, a region that is homozygously deleted in
malignant rhabdoid tumors (MRTs). However, experimental
assessments do not implicate Rab36 as a tumor
suppressor that would enable tumor formation through a
loss-of-function mechanism. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab
proteins.
Length = 170
Score = 44.5 bits (105), Expect = 2e-06
Identities = 26/82 (31%), Positives = 41/82 (50%), Gaps = 2/82 (2%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALDTSKTEIELWDTSGD 63
K++++G + GKT L N C + Y T GV E E L + ++LWDT+G
Sbjct: 2 KVIVVGDLSVGKTCLINRFCKDVFDKNYKATIGVDF-EMERFEVLGVPFS-LQLWDTAGQ 59
Query: 64 HKFESVWPAFQRDVHGIIFVFN 85
+F+ + + R II VF+
Sbjct: 60 ERFKCIASTYYRGAQAIIIVFD 81
>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 = 43.8 bits (104), Expect = 3e-06
Identities = 22/90 (24%), Positives = 42/90 (46%), Gaps = 6/90 (6%)
Query: 5 ILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALDTSKTEIELWDTSGDH 64
I ++G +GKT L N + +E+ PT G + + + I++WD G
Sbjct: 2 ITLVGLQNSGKTTLVNVIASGQFSEDTIPTVGFNMRK------VTKGNVTIKVWDLGGQP 55
Query: 65 KFESVWPAFQRDVHGIIFVFNSGVPGHISE 94
+F S+W + R V+ I++V ++ +
Sbjct: 56 RFRSMWERYCRGVNAIVYVVDAADREKLEV 85
>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 = 43.6 bits (103), Expect = 5e-06
Identities = 24/86 (27%), Positives = 46/86 (53%), Gaps = 9/86 (10%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQGV----RIVECEHSYALDTSKTEIELWD 59
+++++G GK+ L + AE PT GV R++E E + +++LWD
Sbjct: 4 RLIVIGDSTVGKSSLLKRFTEGRFAEVSDPTVGVDFFSRLIEIEPGV-----RIKLQLWD 58
Query: 60 TSGDHKFESVWPAFQRDVHGIIFVFN 85
T+G +F S+ ++ R+ G++ VF+
Sbjct: 59 TAGQERFRSITRSYYRNSVGVLLVFD 84
>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 = 43.3 bits (102), Expect = 6e-06
Identities = 27/87 (31%), Positives = 39/87 (44%), Gaps = 5/87 (5%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIV-ECEHSYALDTSKTEIELWDTSG 62
K++I+G GKT L EEYHPT V +C +D ++ LWDT+G
Sbjct: 3 KLVIVGDGACGKTSLLYVFTLGEFPEEYHPTVFENYVTDCR----VDGKPVQLALWDTAG 58
Query: 63 DHKFESVWPAFQRDVHGIIFVFNSGVP 89
++E + P H I+ F P
Sbjct: 59 QEEYERLRPLSYSKAHVILIGFAIDTP 85
>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 = 42.2 bits (100), Expect = 1e-05
Identities = 25/91 (27%), Positives = 39/91 (42%), Gaps = 7/91 (7%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALDTSKTEIELWDTSGD 63
+IL+LG AGKT + L L PT G + + ++ + +WD G
Sbjct: 1 RILMLGLDGAGKTTILYKLK-LGEVVTTIPTIGFNV----ET--VEYKNVKFTVWDVGGQ 53
Query: 64 HKFESVWPAFQRDVHGIIFVFNSGVPGHISE 94
K +W + + G+IFV +S I E
Sbjct: 54 DKIRPLWKHYYENTDGLIFVVDSSDRERIEE 84
>gnl|CDD|206736 cd04173, Rnd2_Rho7, Rnd2/Rho7 GTPases. Rnd2/Rho7 is a member of
the novel Rho subfamily Rnd, together with Rnd1/Rho6
and Rnd3/RhoE/Rho8. Rnd2/Rho7 is transiently expressed
in radially migrating cells in the brain while they are
within the subventricular zone of the hippocampus and
cerebral cortex. These migrating cells typically
develop into pyramidal neurons. Cells that exogenously
expressed Rnd2/Rho7 failed to migrate to upper layers
of the brain, suggesting that Rnd2/Rho7 plays a role in
the radial migration and morphological changes of
developing pyramidal neurons, and that Rnd2/Rho7
degradation is necessary for proper cellular migration.
The Rnd2/Rho7 GEF Rapostlin is found primarily in the
brain and together with Rnd2/Rho7 induces dendrite
branching. Unlike Rnd1/Rho6 and Rnd3/RhoE/Rho8, which
are RhoA antagonists, Rnd2/Rho7 binds the GEF Pragmin
and significantly stimulates RhoA activity and Rho-A
mediated cell contraction. Rnd2/Rho7 is also found to
be expressed in spermatocytes and early spermatids,
with male-germ-cell Rac GTPase-activating protein
(MgcRacGAP), where it localizes to the Golgi-derived
pro-acrosomal vesicle. Most Rho proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of
most Rho proteins.
Length = 221
Score = 42.7 bits (100), Expect = 1e-05
Identities = 26/96 (27%), Positives = 45/96 (46%), Gaps = 5/96 (5%)
Query: 2 KIKILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVE-CEHSYALDTSKTEIELWDT 60
+ KI+++G GKT L + E Y PT + E S+ +D + E+ +WDT
Sbjct: 1 RCKIVVVGDTQCGKTALLHVFAKDNYPESYVPT----VFENYTASFEIDKHRIELNMWDT 56
Query: 61 SGDHKFESVWPAFQRDVHGIIFVFNSGVPGHISELL 96
SG +++V P D ++ F+ P + +L
Sbjct: 57 SGSSYYDNVRPLAYPDSDAVLICFDISRPETLDSVL 92
>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 = 42.7 bits (100), Expect = 1e-05
Identities = 23/89 (25%), Positives = 40/89 (44%), Gaps = 3/89 (3%)
Query: 1 MKIKILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALDTSKTEIELWDT 60
++ K++++G + GKT + L E Y PT C + + E+ LWDT
Sbjct: 12 VRCKLVLVGDVQCGKTAMLQVLAKDCYPETYVPTVFENYTAC---LETEEQRVELSLWDT 68
Query: 61 SGDHKFESVWPAFQRDVHGIIFVFNSGVP 89
SG +++V P D ++ F+ P
Sbjct: 69 SGSPYYDNVRPLCYSDSDAVLLCFDISRP 97
>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 = 42.1 bits (99), Expect = 1e-05
Identities = 26/91 (28%), Positives = 42/91 (46%), Gaps = 8/91 (8%)
Query: 3 IKILILGPIMAGKTVLANALCDLTTAEEYHPTQGV-----RIV---ECEHSYALDTSKTE 54
IK+L LG GKT D ++ T G+ R+V + + +
Sbjct: 5 IKLLALGDSGVGKTTFLYRYTDNKFNPKFITTVGIDFREKRVVYNSQGPDGTSGKAFRVH 64
Query: 55 IELWDTSGDHKFESVWPAFQRDVHGIIFVFN 85
++LWDT+G +F S+ AF RD G + +F+
Sbjct: 65 LQLWDTAGQERFRSLTTAFFRDAMGFLLMFD 95
>gnl|CDD|133321 cd04121, Rab40, Rab GTPase family 40 (Rab40) contains Rab40a,
Rab40b and Rab40c. The Rab40 subfamily contains
Rab40a, Rab40b, and Rab40c, which are all highly
homologous. In rat, Rab40c is localized to the
perinuclear recycling compartment (PRC), and is
distributed in a tissue-specific manor, with high
expression in brain, heart, kidney, and testis, low
expression in lung and liver, and no expression in
spleen and skeletal muscle. Rab40c is highly expressed
in differentiated oligodendrocytes but minimally
expressed in oligodendrocyte progenitors, suggesting a
role in the vesicular transport of myelin components.
Unlike most other Ras-superfamily proteins, Rab40c was
shown to have a much lower affinity for GTP, and an
affinity for GDP that is lower than for GTP. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins.
Length = 189
Score = 42.2 bits (99), Expect = 2e-05
Identities = 24/83 (28%), Positives = 44/83 (53%), Gaps = 2/83 (2%)
Query: 3 IKILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALDTSKTEIELWDTSG 62
+K L++G GK + +L D +T Y G+ + LD + +++LWDTSG
Sbjct: 7 LKFLLVGDSDVGKGEILASLQDGSTESPYGYNMGIDYKTT--TILLDGRRVKLQLWDTSG 64
Query: 63 DHKFESVWPAFQRDVHGIIFVFN 85
+F +++ ++ R GII V++
Sbjct: 65 QGRFCTIFRSYSRGAQGIILVYD 87
>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 = 40.5 bits (95), Expect = 3e-05
Identities = 17/83 (20%), Positives = 33/83 (39%), Gaps = 2/83 (2%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALDTSKTEIELWDTSGD 63
K++++G +GK+ L + L E QG + DT + +WD G
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGL--LNIWDFGGR 58
Query: 64 HKFESVWPAFQRDVHGIIFVFNS 86
+ + F + I+ V++
Sbjct: 59 EELKFEHIIFMKWADAILLVYDL 81
>gnl|CDD|206721 cd04155, Arl3, Arf-like 3 (Arl3) GTPase. Arl3 (Arf-like 3) is an
Arf family protein that differs from most Arf family
members in the N-terminal extension. In is inactive,
GDP-bound form, the N-terminal extension forms an
elongated loop that is hydrophobically anchored into the
membrane surface; however, it has been proposed that
this region might form a helix in the GTP-bound form.
The delta subunit of the rod-specific cyclic GMP
phosphodiesterase type 6 (PDEdelta) is an Arl3 effector.
Arl3 binds microtubules in a regulated manner to alter
specific aspects of cytokinesis via interactions with
retinitis pigmentosa 2 (RP2). It has been proposed that
RP2 functions in concert with Arl3 to link the cell
membrane and the cytoskeleton in photoreceptors as part
of the cell signaling or vesicular transport machinery.
In mice, the absence of Arl3 is associated with abnormal
epithelial cell proliferation and cyst formation.
Length = 174
Score = 41.2 bits (97), Expect = 3e-05
Identities = 26/94 (27%), Positives = 39/94 (41%), Gaps = 11/94 (11%)
Query: 3 IKILILGPIMAGKTVLANALCDLTTAEEYH--PTQGVRIVECEHSYALDTSKTEIELWDT 60
++IL+LG AGKT + L + H PTQG I + D K + +WD
Sbjct: 16 VRILLLGLDNAGKTTILKQLAS---EDISHITPTQGFNIKNVQA----DGFK--LNVWDI 66
Query: 61 SGDHKFESVWPAFQRDVHGIIFVFNSGVPGHISE 94
G K W + + +I+V +S E
Sbjct: 67 GGQRKIRPYWRNYFENTDVLIYVIDSADRKRFEE 100
>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 = 41.1 bits (96), Expect = 3e-05
Identities = 24/84 (28%), Positives = 45/84 (53%), Gaps = 6/84 (7%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRI-VECE-HSYALDTSKTEIELWDTS 61
++L++G GKT L LC T E+H + I V+ + + +D K I++WDT+
Sbjct: 2 RLLLIGDSGVGKTCL---LCRFTD-NEFHSSHISTIGVDFKMKTIEVDGIKVRIQIWDTA 57
Query: 62 GDHKFESVWPAFQRDVHGIIFVFN 85
G +++++ + R GI V++
Sbjct: 58 GQERYQTITKQYYRRAQGIFLVYD 81
>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 = 40.7 bits (96), Expect = 4e-05
Identities = 32/118 (27%), Positives = 54/118 (45%), Gaps = 5/118 (4%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALDTSKTEIELWDTSGD 63
K++ILG GKT L N + + +Y T G + E +D +++WDT+G
Sbjct: 2 KVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKE--VTVDDRLVTLQIWDTAGQ 59
Query: 64 HKFESVWPAFQRDVHGIIFVFNSGVPGHISELLLFYDYFVTQ---SDLNNHKCLLIDN 118
+F+S+ AF R + V++ P L + D F+ Q D N +++ N
Sbjct: 60 ERFQSLGVAFYRGADCCVLVYDVTNPKSFESLDSWRDEFLIQASPRDPENFPFVVLGN 117
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 40.8 bits (95), Expect = 6e-05
Identities = 23/87 (26%), Positives = 47/87 (54%), Gaps = 7/87 (8%)
Query: 1 MKIKILILGPIMAGKTVLANALCDLTTAEEYHPTQGV--RIVECEHSYALDTSKTEIELW 58
+ KIL++G GK+ L + ++ E+ PT GV +I + + + ++ +W
Sbjct: 13 LSFKILLIGDSGVGKSSLLVSFIS-SSVEDLAPTIGVDFKIKQ----LTVGGKRLKLTIW 67
Query: 59 DTSGDHKFESVWPAFQRDVHGIIFVFN 85
DT+G +F ++ ++ R+ GII V++
Sbjct: 68 DTAGQERFRTLTSSYYRNAQGIILVYD 94
>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 = 39.9 bits (94), Expect = 8e-05
Identities = 23/87 (26%), Positives = 44/87 (50%), Gaps = 10/87 (11%)
Query: 3 IKILILGPIMAGKTVLANALCDLTTAEEYHPTQGV----RIVECEHSYALDTSKTEIELW 58
K+L++G GK+ L + + + T G+ R +E LD K ++++W
Sbjct: 4 FKLLLIGDSGVGKSCLLLRFSEDSFNPSFISTIGIDFKIRTIE------LDGKKIKLQIW 57
Query: 59 DTSGDHKFESVWPAFQRDVHGIIFVFN 85
DT+G +F ++ ++ R GII V++
Sbjct: 58 DTAGQERFRTITTSYYRGAMGIILVYD 84
>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 = 39.5 bits (93), Expect = 1e-04
Identities = 22/85 (25%), Positives = 39/85 (45%), Gaps = 10/85 (11%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQGV----RIVECEHSYALDTSKTEIELWD 59
K++ LG GKT + T +Y T G+ + + +D ++LWD
Sbjct: 2 KLVFLGDQSVGKTSIITRFMYDTFDNQYQATIGIDFLSKTMY------VDDKTVRLQLWD 55
Query: 60 TSGDHKFESVWPAFQRDVHGIIFVF 84
T+G +F S+ P++ RD + V+
Sbjct: 56 TAGQERFRSLIPSYIRDSSVAVVVY 80
>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 = 39.1 bits (91), Expect = 1e-04
Identities = 20/85 (23%), Positives = 39/85 (45%), Gaps = 6/85 (7%)
Query: 3 IKILILGPIMAGKTVLANALCDLTTAEEYHPTQ--GVRIVECEHSYALDTSKTEIELWDT 60
+KI++LG GK+ L + Y P Q + +H+ + ++ WDT
Sbjct: 1 VKIILLGDSAVGKSKLVERF----LMDGYEPQQLSTYALTLYKHNAKFEGKTILVDFWDT 56
Query: 61 SGDHKFESVWPAFQRDVHGIIFVFN 85
+G +F+++ ++ H I VF+
Sbjct: 57 AGQERFQTMHASYYHKAHACILVFD 81
>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 = 39.1 bits (91), Expect = 2e-04
Identities = 24/81 (29%), Positives = 36/81 (44%), Gaps = 3/81 (3%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALDTSKTEIELWDTSGD 63
K+++LG GKT L N + Y PT + H +D E+ LWDT+G
Sbjct: 2 KVVVLGDGACGKTSLLNVFTRGYFPQVYEPTVFENYI---HDIFVDGLAVELSLWDTAGQ 58
Query: 64 HKFESVWPAFQRDVHGIIFVF 84
+F+ + D H I+ F
Sbjct: 59 EEFDRLRSLSYADTHVIMLCF 79
>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 = 38.7 bits (90), Expect = 2e-04
Identities = 23/90 (25%), Positives = 41/90 (45%), Gaps = 18/90 (20%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRI--------VECEHSYALDTSKTEI 55
KI+++G GKT L T + P QG I VE + K ++
Sbjct: 9 KIVLIGNAGVGKTCLVRRF----TQGLFPPGQGATIGVDFMIKTVEIKGE------KIKL 58
Query: 56 ELWDTSGDHKFESVWPAFQRDVHGIIFVFN 85
++WDT+G +F S+ ++ R + +I ++
Sbjct: 59 QIWDTAGQERFRSITQSYYRSANALILTYD 88
>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 = 37.9 bits (88), Expect = 4e-04
Identities = 13/38 (34%), Positives = 26/38 (68%)
Query: 48 LDTSKTEIELWDTSGDHKFESVWPAFQRDVHGIIFVFN 85
+D K ++++WDT+G +F SV A+ RD H ++ +++
Sbjct: 45 VDGVKVKLQIWDTAGQERFRSVTHAYYRDAHALLLLYD 82
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 37.8 bits (87), Expect = 5e-04
Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 26 TTAEEYHPTQGVRIVECEHSYALDTSKTEIELWDTSGDHKFESVWPAFQRDVHGIIFVFN 85
T Y T G+ + + LD ++LWDT+G +F S+ P++ RD I V++
Sbjct: 4 TFDNNYQSTIGIDFLS--KTLYLDEGPVRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYD 61
>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 = 37.8 bits (88), Expect = 5e-04
Identities = 23/84 (27%), Positives = 38/84 (45%), Gaps = 7/84 (8%)
Query: 5 ILILGPIMAGKTVLANAL-CDLTTAEEYHPTQGVRIVECEHSYALDTSKTEIELWDTSGD 63
IL+LG +GKT + N L ++ PT G + + +D SG
Sbjct: 2 ILVLGLDNSGKTTIINQLKPSNAQSQNIVPTVGFNVESFK------KGNLSFTAFDMSGQ 55
Query: 64 HKFESVWPAFQRDVHGIIFVFNSG 87
K+ +W + +++ GIIFV +S
Sbjct: 56 GKYRGLWEHYYKNIQGIIFVIDSS 79
>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 = 37.1 bits (87), Expect = 7e-04
Identities = 22/84 (26%), Positives = 35/84 (41%), Gaps = 9/84 (10%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVEC-EHSYALDTSKTEIELWDTSG 62
K+++LG GK+ L EEY PT I + +D +++ DT+G
Sbjct: 1 KLVVLGAGGVGKSALTIRFVSGEFVEEYDPT----IEDSYRKQIVVDGETYTLDILDTAG 56
Query: 63 DHKFESVWPAFQ--RDVHGIIFVF 84
+F Q R+ G I V+
Sbjct: 57 QEEFS--AMRDQYIRNGDGFILVY 78
>gnl|CDD|223562 COG0488, Uup, ATPase components of ABC transporters with duplicated
ATPase domains [General function prediction only].
Length = 530
Score = 37.6 bits (88), Expect = 0.001
Identities = 19/71 (26%), Positives = 29/71 (40%), Gaps = 6/71 (8%)
Query: 4 KILILGPIMAGKTVLANALCDLT--TAEEYHPTQGVRI--VECEHSYALDTSKTEIE-LW 58
+I I+GP AGK+ L L + + V+I + LD KT +E L
Sbjct: 350 RIAIVGPNGAGKSTLLKLLAGELGPLSGTVKVGETVKIGYFDQHRD-ELDPDKTVLEELS 408
Query: 59 DTSGDHKFESV 69
+ D + V
Sbjct: 409 EGFPDGDEQEV 419
>gnl|CDD|206725 cd04160, Arfrp1, Arf-related protein 1 (Arfrp1). Arfrp1
(Arf-related protein 1), formerly known as ARP, is a
membrane-associated Arf family member that lacks the
N-terminal myristoylation motif. Arfrp1 is mainly
associated with the trans-Golgi compartment and the
trans-Golgi network, where it regulates the targeting of
Arl1 and the GRIP domain-containing proteins, golgin-97
and golgin-245, onto Golgi membranes. It is also
involved in the anterograde transport of the vesicular
stomatitis virus G protein from the Golgi to the plasma
membrane, and in the retrograde transport of TGN38 and
Shiga toxin from endosomes to the trans-Golgi network.
Arfrp1 also inhibits Arf/Sec7-dependent activation of
phospholipase D. Deletion of Arfrp1 in mice causes
embryonic lethality at the gastrulation stage and
apoptosis of mesodermal cells, indicating its importance
in development.
Length = 168
Score = 36.9 bits (86), Expect = 0.001
Identities = 27/121 (22%), Positives = 47/121 (38%), Gaps = 13/121 (10%)
Query: 5 ILILGPIMAGKTVLANALCDLTTA-------EEYHPTQGVRIVECEHSYALDTSKTEIEL 57
+LILG AGKT + + PT G+ I ++ K +
Sbjct: 2 VLILGLDNAGKTTFLEQTKTKFSKNYKGLNPSKITPTVGLNIGT------IEVGKARLMF 55
Query: 58 WDTSGDHKFESVWPAFQRDVHGIIFVFNSGVPGHISELLLFYDYFVTQSDLNNHKCLLID 117
WD G + S+W + + HG+I+V +S +E ++ + L L++
Sbjct: 56 WDLGGQEELRSLWDKYYAESHGVIYVIDSTDRERFNESKSAFEKVINNEALEGVPLLVLA 115
Query: 118 N 118
N
Sbjct: 116 N 116
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 36.8 bits (86), Expect = 0.001
Identities = 23/88 (26%), Positives = 36/88 (40%), Gaps = 11/88 (12%)
Query: 1 MKIKILILGPIMAGKTVLANALCDLTTAEEYH--PTQGVRIVECEHSYALDTSKTEIELW 58
+++ILILG AGKT + L L E PT G + + + +W
Sbjct: 13 KEMRILILGLDNAGKTTI---LYKLKLGEIVTTIPTIGFNVETVTYK------NVKFTVW 63
Query: 59 DTSGDHKFESVWPAFQRDVHGIIFVFNS 86
D G +W + + +IFV +S
Sbjct: 64 DVGGQESLRPLWRNYFPNTDAVIFVVDS 91
>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 = 36.7 bits (85), Expect = 0.001
Identities = 24/90 (26%), Positives = 45/90 (50%), Gaps = 18/90 (20%)
Query: 4 KILILGPIMAGKTVLAN--------ALCDLTTAEEYHPTQGVRIVECEHSYALDTSKTEI 55
K +I+G + GK+ L + A C T E+ G RI+E ++ K ++
Sbjct: 4 KYIIIGDMGVGKSCLLHQFTEKKFMADCPHTIGVEF----GTRIIE------VNGQKIKL 53
Query: 56 ELWDTSGDHKFESVWPAFQRDVHGIIFVFN 85
++WDT+G +F +V ++ R G + V++
Sbjct: 54 QIWDTAGQERFRAVTRSYYRGAAGALMVYD 83
>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 = 36.6 bits (85), Expect = 0.001
Identities = 25/87 (28%), Positives = 40/87 (45%), Gaps = 10/87 (11%)
Query: 2 KIKILILGPIMAGKTVLANALCDLTTAEEYHPT---QGVRIVECEHSYALDTSKT-EIEL 57
K+KI+++G GKT L + EEY PT V ++ + K E+ L
Sbjct: 3 KVKIVVVGDGGCGKTCLLMVYAQGSFPEEYVPTVFENYVTTLQ------VPNGKIIELAL 56
Query: 58 WDTSGDHKFESVWPAFQRDVHGIIFVF 84
WDT+G ++ + P DV I+ +
Sbjct: 57 WDTAGQEDYDRLRPLSYPDVDVILICY 83
>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 = 36.3 bits (84), Expect = 0.001
Identities = 19/82 (23%), Positives = 40/82 (48%), Gaps = 2/82 (2%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALDTSKTEIELWDTSGD 63
KI+++G GKT + T +E T GV + + + ++++WDT+G
Sbjct: 5 KIILIGDSNVGKTCVVQRFKSGTFSERQGNTIGVDFTM--KTLEIQGKRVKLQIWDTAGQ 62
Query: 64 HKFESVWPAFQRDVHGIIFVFN 85
+F ++ ++ R +G I ++
Sbjct: 63 ERFRTITQSYYRSANGAIIAYD 84
>gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol
utilisation. Members of this family function in
ethanolamine and propanediol degradation pathways,
however the exact roles of these proteins is poorly
understood.
Length = 143
Score = 35.7 bits (83), Expect = 0.002
Identities = 16/50 (32%), Positives = 22/50 (44%), Gaps = 7/50 (14%)
Query: 1 MKIKILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALDT 50
MK KI+++G GKT L AL +Y TQ + +DT
Sbjct: 1 MK-KIMLIGRSGCGKTTLTQALNGEEL--KYKKTQAIEF----SDNMIDT 43
>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 = 35.9 bits (83), Expect = 0.002
Identities = 26/96 (27%), Positives = 44/96 (45%), Gaps = 16/96 (16%)
Query: 4 KILILGPIMAGKTVLANAL---CDLTTAEEYHPTQG--VRIVECEHSYALDTSKTEIELW 58
++L+LG AGK+ L L +TT PT G V +++ E +L +W
Sbjct: 1 QVLLLGLDSAGKSTLLYKLKHAELVTTI----PTVGFNVEMLQLEKHLSL-------TVW 49
Query: 59 DTSGDHKFESVWPAFQRDVHGIIFVFNSGVPGHISE 94
D G K +VW + + G+++V +S + E
Sbjct: 50 DVGGQEKMRTVWKCYLENTDGLVYVVDSSDEARLDE 85
>gnl|CDD|128474 smart00177, ARF, ARF-like small GTPases; ARF, ADP-ribosylation
factor. Ras homologues involved in vesicular
transport. Activator 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.
Contains ATP/GTP-binding motif (P-loop).
Length = 175
Score = 35.7 bits (82), Expect = 0.003
Identities = 24/93 (25%), Positives = 39/93 (41%), Gaps = 7/93 (7%)
Query: 2 KIKILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALDTSKTEIELWDTS 61
+++IL++G AGKT + L L + PT G + + +WD
Sbjct: 13 EMRILMVGLDAAGKTTILYKL-KLGESVTTIPTIGFNVETVTYK------NISFTVWDVG 65
Query: 62 GDHKFESVWPAFQRDVHGIIFVFNSGVPGHISE 94
G K +W + + G+IFV +S I E
Sbjct: 66 GQDKIRPLWRHYYTNTQGLIFVVDSNDRDRIDE 98
>gnl|CDD|206691 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta), together with SR-alpha, forms the
heterodimeric signal recognition particle (SRP). Signal
recognition particle receptor, beta subunit (SR-beta).
SR-beta and SR-alpha form the heterodimeric signal
recognition particle (SRP or SR) receptor that binds SRP
to regulate protein translocation across the ER
membrane. Nascent polypeptide chains are synthesized
with an N-terminal hydrophobic signal sequence that
binds SRP54, a component of the SRP. SRP directs
targeting of the ribosome-nascent chain complex (RNC) to
the ER membrane via interaction with the SR, which is
localized to the ER membrane. The RNC is then
transferred to the protein-conducting channel, or
translocon, which facilitates polypeptide translation
across the ER membrane or integration into the ER
membrane. SR-beta is found only in eukaryotes; it is
believed to control the release of the signal sequence
from SRP54 upon binding of the ribosome to the
translocon. High expression of SR-beta has been observed
in human colon cancer, suggesting it may play a role in
the development of this type of cancer.
Length = 202
Score = 35.8 bits (83), Expect = 0.003
Identities = 29/116 (25%), Positives = 49/116 (42%), Gaps = 9/116 (7%)
Query: 5 ILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALDTSK-TEIELWDTSGD 63
+L+LGP +GKT L L T + T I S+ ++SK ++ L D G
Sbjct: 3 VLLLGPSDSGKTALFTKL----TTGKVRSTV-TSIEPNVASFYSNSSKGKKLTLVDVPGH 57
Query: 64 HKF-ESVWPAFQRDVHGIIFVFNS-GVPGHISEL-LLFYDYFVTQSDLNNHKCLLI 116
K + + + + I+FV +S +I ++ YD + N +LI
Sbjct: 58 EKLRDKLLEYLKASLKAIVFVVDSATFQKNIRDVAEFLYDILTDLEKIKNKIPILI 113
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 35.7 bits (82), Expect = 0.003
Identities = 24/93 (25%), Positives = 40/93 (43%), Gaps = 7/93 (7%)
Query: 2 KIKILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALDTSKTEIELWDTS 61
+++IL++G AGKT + L L PT G + E+ +WD
Sbjct: 17 EMRILMVGLDAAGKTTILYKL-KLGEIVTTIPTIGFNVETVEYK------NISFTVWDVG 69
Query: 62 GDHKFESVWPAFQRDVHGIIFVFNSGVPGHISE 94
G K +W + ++ G+IFV +S + E
Sbjct: 70 GQDKIRPLWRHYFQNTQGLIFVVDSNDRDRVVE 102
>gnl|CDD|133353 cd04153, Arl5_Arl8, Arf-like 5 (Arl5) and 8 (Arl8) GTPases.
Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like
Arl4 and Arl7, are localized to the nucleus and
nucleolus. Arl5 is developmentally regulated during
embryogenesis in mice. Human Arl5 interacts with the
heterochromatin protein 1-alpha (HP1alpha), a
nonhistone chromosomal protein that is associated with
heterochromatin and telomeres, and prevents telomere
fusion. Arl5 may also play a role in embryonic nuclear
dynamics and/or signaling cascades. Arl8 was identified
from a fetal cartilage cDNA library. It is found in
brain, heart, lung, cartilage, and kidney. No function
has been assigned for Arl8 to date.
Length = 174
Score = 35.4 bits (82), Expect = 0.003
Identities = 21/85 (24%), Positives = 32/85 (37%), Gaps = 11/85 (12%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAE--EYHPTQGVRIVECEHSYALDTSKTEIELWDTS 61
K++I+G AGKT + L E PT G + E + +WD
Sbjct: 17 KVIIVGLDNAGKTTI---LYQFLLGEVVHTSPTIGSNVEE------IVYKNIRFLMWDIG 67
Query: 62 GDHKFESVWPAFQRDVHGIIFVFNS 86
G S W + + +I V +S
Sbjct: 68 GQESLRSSWNTYYTNTDAVILVIDS 92
>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 = 35.3 bits (81), Expect = 0.005
Identities = 15/62 (24%), Positives = 27/62 (43%), Gaps = 3/62 (4%)
Query: 55 IELWDTSGDHKFESVWPAFQRDVHGIIFVFNSGVPGHISELLLFYDYFVTQSDLNNHKCL 114
I +WDT+G +F + + R +I ++ ++ L D F+ +D N CL
Sbjct: 46 ISIWDTAGREQFHGLGSMYCRGAAAVILTYDV---SNVQSLEELEDRFLGLTDTANEDCL 102
Query: 115 LI 116
Sbjct: 103 FA 104
>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 = 34.8 bits (80), Expect = 0.005
Identities = 25/85 (29%), Positives = 39/85 (45%), Gaps = 11/85 (12%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSY----ALDTSKTEIELWD 59
K+++LG GKT L LC E Y PT E SY +D +E+ D
Sbjct: 1 KLVVLGDGGVGKTALTIQLCLNHFVETYDPT-------IEDSYRKQVVVDGQPCMLEVLD 53
Query: 60 TSGDHKFESVWPAFQRDVHGIIFVF 84
T+G ++ ++ + R+ G I V+
Sbjct: 54 TAGQEEYTALRDQWIREGEGFILVY 78
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 34.8 bits (80), Expect = 0.006
Identities = 24/92 (26%), Positives = 41/92 (44%), Gaps = 7/92 (7%)
Query: 3 IKILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALDTSKTEIELWDTSG 62
++IL++G AGKT + L L PT G + E+ + +WD G
Sbjct: 18 VRILMVGLDAAGKTTILYKL-KLGEVVTTIPTIGFNVETVEYK------NLKFTMWDVGG 70
Query: 63 DHKFESVWPAFQRDVHGIIFVFNSGVPGHISE 94
K +W + ++ +G+IFV +S I +
Sbjct: 71 QDKLRPLWRHYYQNTNGLIFVVDSNDRERIGD 102
>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 = 34.4 bits (80), Expect = 0.006
Identities = 24/74 (32%), Positives = 36/74 (48%), Gaps = 13/74 (17%)
Query: 3 IKILILGPIMAGKTVLANALCDLTT---AEEYHPTQGVRIVECEHS--YALDTSKTEIEL 57
IKI+++G GKT L L TT EY PT V +S +D + + L
Sbjct: 1 IKIVVVGDGAVGKTCL---LISYTTNKFPTEYVPT-----VFDNYSANVTVDGKQVNLGL 52
Query: 58 WDTSGDHKFESVWP 71
WDT+G +++ + P
Sbjct: 53 WDTAGQEEYDRLRP 66
>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 = 34.5 bits (80), Expect = 0.006
Identities = 10/32 (31%), Positives = 21/32 (65%)
Query: 54 EIELWDTSGDHKFESVWPAFQRDVHGIIFVFN 85
++ +WDT+G ++ ++ P + RD G I V++
Sbjct: 50 DLAIWDTAGQERYHALGPIYYRDADGAILVYD 81
>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 = 34.4 bits (79), Expect = 0.007
Identities = 24/88 (27%), Positives = 43/88 (48%), Gaps = 11/88 (12%)
Query: 2 KIKILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSY----ALDTSKTEIEL 57
+ K+++LG GK+ L T E+Y PT E Y +D+S + +E+
Sbjct: 1 EYKVVVLGSGGVGKSALTVQFVSGTFIEKYDPT-------IEDFYRKEIEVDSSPSVLEI 53
Query: 58 WDTSGDHKFESVWPAFQRDVHGIIFVFN 85
DT+G +F S+ + ++ G I V++
Sbjct: 54 LDTAGTEQFASMRDLYIKNGQGFIVVYS 81
>gnl|CDD|206645 cd00879, Sar1, Sar1 is an essential component of COPII vesicle
coats. Sar1 is an essential component of COPII vesicle
coats involved in export of cargo from the ER. The
GTPase activity of Sar1 functions as a molecular switch
to control protein-protein and protein-lipid
interactions that direct vesicle budding from the ER.
Activation of the GDP to the GTP-bound form of Sar1
involves the membrane-associated guanine nucleotide
exchange factor (GEF) Sec12. Sar1 is unlike all Ras
superfamily GTPases that use either myristoyl or prenyl
groups to direct membrane association and function, in
that Sar1 lacks such modification. Instead, Sar1
contains a unique nine-amino-acid N-terminal extension.
This extension contains an evolutionarily conserved
cluster of bulky hydrophobic amino acids, referred to as
the Sar1-N-terminal activation recruitment (STAR) motif.
The STAR motif mediates the recruitment of Sar1 to ER
membranes and facilitates its interaction with mammalian
Sec12 GEF leading to activation.
Length = 191
Score = 34.6 bits (80), Expect = 0.007
Identities = 26/91 (28%), Positives = 39/91 (42%), Gaps = 7/91 (7%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALDTSKTEIELWDTSGD 63
KI+ LG AGKT L + L D A+ + PT S L + +D G
Sbjct: 21 KIVFLGLDNAGKTTLLHMLKDDRLAQ-HVPTLH------PTSEELTIGNVKFTTFDLGGH 73
Query: 64 HKFESVWPAFQRDVHGIIFVFNSGVPGHISE 94
+ VW + +V GI+F+ ++ P E
Sbjct: 74 EQARRVWKDYFPEVDGIVFLVDAADPERFQE 104
>gnl|CDD|206719 cd04152, Arl4_Arl7, Arf-like 4 (Arl4) and 7 (Arl7) GTPases. Arl4
(Arf-like 4) is highly expressed in testicular germ
cells, and is found in the nucleus and nucleolus. In
mice, Arl4 is developmentally expressed during
embryogenesis, and a role in somite formation and
central nervous system differentiation has been
proposed. Arl7 has been identified as the only Arf/Arl
protein to be induced by agonists of liver X-receptor
and retinoid X-receptor and by cholesterol loading in
human macrophages. Arl7 is proposed to play a role in
transport between a perinuclear compartment and the
plasma membrane, apparently linked to the
ABCA1-mediated cholesterol secretion pathway. Older
literature suggests that Arl6 is a part of the
Arl4/Arl7 subfamily, but analyses based on more recent
sequence data place Arl6 in its own subfamily.
Length = 183
Score = 34.4 bits (79), Expect = 0.009
Identities = 25/84 (29%), Positives = 36/84 (42%), Gaps = 6/84 (7%)
Query: 5 ILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEH-SYALDTSKT-EIELWDTSG 62
I++LG AGKT + L PT+G E +L +K WD G
Sbjct: 6 IVMLGLDSAGKTTVLYRL-KFNEFVNTVPTKGF---NTEKIKVSLGNAKGVTFHFWDVGG 61
Query: 63 DHKFESVWPAFQRDVHGIIFVFNS 86
K +W ++ R GI+FV +S
Sbjct: 62 QEKLRPLWKSYTRCTDGIVFVVDS 85
>gnl|CDD|206723 cd04158, ARD1, (ADP-ribosylation factor domain protein 1 (ARD1).
ARD1 (ADP-ribosylation factor domain protein 1) is an
unusual member of the Arf family. In addition to the
C-terminal Arf domain, ARD1 has an additional 46-kDa
N-terminal domain that contains a RING finger domain,
two predicted B-Boxes, and a coiled-coil protein
interaction motif. This domain belongs to the TRIM
(tripartite motif) or RBCC (RING, B-Box, coiled-coil)
family. Like most Arfs, the ARD1 Arf domain lacks
detectable GTPase activity. However, unlike most Arfs,
the full-length ARD1 protein has significant GTPase
activity due to the GAP (GTPase-activating protein)
activity exhibited by the 46-kDa N-terminal domain. The
GAP domain of ARD1 is specific for its own Arf domain
and does not bind other Arfs. The rate of GDP
dissociation from the ARD1 Arf domain is slowed by the
adjacent 15 amino acids, which act as a GDI
(GDP-dissociation inhibitor) domain. ARD1 is
ubiquitously expressed in cells and localizes to the
Golgi and to the lysosomal membrane. Two Tyr-based
motifs in the Arf domain are responsible for Golgi
localization, while the GAP domain controls lysosomal
localization.
Length = 169
Score = 33.8 bits (77), Expect = 0.011
Identities = 27/118 (22%), Positives = 49/118 (41%), Gaps = 13/118 (11%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYH---PTQGVRIVECEHSYALDTSKTEIELWDT 60
+++ LG AGKT + L +E+ PT G + E+ + +WD
Sbjct: 1 RVVTLGLDGAGKTTILFKL----KQDEFMQPIPTIGFNVETVEYK------NLKFTIWDV 50
Query: 61 SGDHKFESVWPAFQRDVHGIIFVFNSGVPGHISELLLFYDYFVTQSDLNNHKCLLIDN 118
G HK +W + + ++FV +S +SE +T+ +L + L+ N
Sbjct: 51 GGKHKLRPLWKHYYLNTQAVVFVIDSSHRDRVSEAHSELAKLLTEKELRDALLLIFAN 108
>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 = 34.1 bits (79), Expect = 0.011
Identities = 22/112 (19%), Positives = 43/112 (38%), Gaps = 23/112 (20%)
Query: 4 KILILGPIMAGKT-----VLANALCDLTTAEEYHPTQGVRI---VECEHSYALDTSKTEI 55
K+L++G +GK+ + +N Y P +R+ ++ E S+ +
Sbjct: 1 KVLLMGLRGSGKSSMRSIIFSN----------YSPRDTLRLGATIDVEQSHVRFLGNLTL 50
Query: 56 ELWDTSGDHKFESVWPAFQRD-----VHGIIFVFNSGVPGHISELLLFYDYF 102
LWD G F + Q++ V +I+VF+ + +L
Sbjct: 51 NLWDCPGQDDFMENYLTRQKEHIFSNVGVLIYVFDVESREYEEDLATLVKII 102
>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 = 33.9 bits (78), Expect = 0.012
Identities = 22/90 (24%), Positives = 42/90 (46%), Gaps = 18/90 (20%)
Query: 4 KILILGPIMAGKTVLA--------NALCDLTTAEEYHPTQGVRIVECEHSYALDTSKTEI 55
K +I+G GK+ L + DLT E+ G R++ +D + ++
Sbjct: 6 KYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEF----GARMIT------IDGKQIKL 55
Query: 56 ELWDTSGDHKFESVWPAFQRDVHGIIFVFN 85
++WDT+G F S+ ++ R G + V++
Sbjct: 56 QIWDTAGQESFRSITRSYYRGAAGALLVYD 85
>gnl|CDD|206689 cd04102, RabL3, Rab GTPase-like family 3 (Rab-like3). RabL3
(Rab-like3) subfamily. RabL3s are novel proteins that
have high sequence similarity with Rab family members,
but display features that are distinct from Rabs, and
have been termed Rab-like. As in other Rab-like
proteins, RabL3 lacks a prenylation site at the
C-terminus. The specific function of RabL3 remains
unknown.
Length = 204
Score = 34.1 bits (78), Expect = 0.012
Identities = 26/90 (28%), Positives = 40/90 (44%), Gaps = 7/90 (7%)
Query: 3 IKILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALDTSKTE---IELWD 59
+K+L+LG GK+ L + LC T G + H+Y T + + +ELWD
Sbjct: 1 VKVLVLGDSGVGKSSLVHLLCKNQVLGNPSWTVGCSVDVRHHTYGEGTPEEKTFYVELWD 60
Query: 60 TSG----DHKFESVWPAFQRDVHGIIFVFN 85
G +S F ++GIIFV +
Sbjct: 61 VGGSVGSAESVKSTRAVFYNQINGIIFVHD 90
>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 = 33.5 bits (77), Expect = 0.013
Identities = 20/89 (22%), Positives = 39/89 (43%), Gaps = 10/89 (11%)
Query: 3 IKILILGPIMAGKTVLANALCDLTTAEEYHPT----QGVRIVECEHSYALDTSKTEIELW 58
IK++ +G GK+ + C+ +Y PT GV+ V + + + +
Sbjct: 1 IKVISMGNSGVGKSCIIKRYCEGRFVSKYLPTIGIDYGVKKVS------VRNKEVRVNFF 54
Query: 59 DTSGDHKFESVWPAFQRDVHGIIFVFNSG 87
D SG ++ V F +D G++ V++
Sbjct: 55 DLSGHPEYLEVRNEFYKDTQGVLLVYDVT 83
>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 = 33.6 bits (77), Expect = 0.014
Identities = 22/86 (25%), Positives = 42/86 (48%), Gaps = 10/86 (11%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQGV----RIVECEHSYALDTSKTEIELWD 59
K LI+G GK+ L + + ++ + T GV R+V + ++++WD
Sbjct: 2 KFLIIGSAGTGKSCLLHQFIENKFKQDSNHTIGVEFGSRVVN------VGGKSVKLQIWD 55
Query: 60 TSGDHKFESVWPAFQRDVHGIIFVFN 85
T+G +F SV ++ R G + V++
Sbjct: 56 TAGQERFRSVTRSYYRGAAGALLVYD 81
>gnl|CDD|206694 cd04109, Rab28, Rab GTPase family 28 (Rab28). Rab28 subfamily.
First identified in maize, Rab28 has been shown to be a
late embryogenesis-abundant (Lea) protein that is
regulated by the plant hormone abcisic acid (ABA). In
Arabidopsis, Rab28 is expressed during embryo
development and is generally restricted to provascular
tissues in mature embryos. Unlike maize Rab28, it is
not ABA-inducible. Characterization of the human Rab28
homolog revealed two isoforms, which differ by a
95-base pair insertion, producing an alternative
sequence for the 30 amino acids at the C-terminus. The
two human isoforms are presumably the result of
alternative splicing. Since they differ at the
C-terminus but not in the GTP-binding region, they are
predicted to be targeted to different cellular
locations. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation
of the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs),
which facilitate Rab recycling by masking C-terminal
lipid binding and promoting cytosolic localization.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins.
Length = 213
Score = 33.6 bits (77), Expect = 0.014
Identities = 17/64 (26%), Positives = 27/64 (42%), Gaps = 9/64 (14%)
Query: 3 IKILILGPIMAGKTVLANALCDLTTAEEYHPTQGV----RIVECEHSYALDTSKTEIELW 58
IKI++LG +GKT L + Y T G+ R + S + +++W
Sbjct: 1 IKIVVLGDGASGKTSLIRRFAQEGFGKSYKQTIGLDFFSRRITLPGSLNV-----TLQVW 55
Query: 59 DTSG 62
D G
Sbjct: 56 DIGG 59
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 33.6 bits (77), Expect = 0.016
Identities = 29/125 (23%), Positives = 50/125 (40%), Gaps = 19/125 (15%)
Query: 2 KIKILILGPIMAGKTVLANALCD--------LTTAEEYHPTQGVRIVECEHSYALDTSKT 53
+ KI+++GP+ AGKT AL D ++ + + S LD T
Sbjct: 10 ETKIVVIGPVGAGKTTFVRALSDKPLVITEADASSVSGKGKRPTTVAMDFGSIELD-EDT 68
Query: 54 EIELWDTSGDHKFESVWPAFQRDVHGIIFVFNS--GVPGHISELLLFYDY--------FV 103
+ L+ T G +F+ +W R G I + +S + H E++ F +
Sbjct: 69 GVHLFGTPGQERFKFMWEILSRGAVGAIVLVDSSRPITFHAEEIIDFLTSRNPIPVVVAI 128
Query: 104 TQSDL 108
+ DL
Sbjct: 129 NKQDL 133
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 33.4 bits (76), Expect = 0.022
Identities = 22/90 (24%), Positives = 41/90 (45%), Gaps = 18/90 (20%)
Query: 4 KILILGPIMAGKTVLA--------NALCDLTTAEEYHPTQGVRIVECEHSYALDTSKTEI 55
K +I+G GK+ L + DLT E+ G R++ +D ++
Sbjct: 8 KYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEF----GARMI------TIDNKPIKL 57
Query: 56 ELWDTSGDHKFESVWPAFQRDVHGIIFVFN 85
++WDT+G F S+ ++ R G + V++
Sbjct: 58 QIWDTAGQESFRSITRSYYRGAAGALLVYD 87
>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 = 33.0 bits (75), Expect = 0.024
Identities = 20/82 (24%), Positives = 41/82 (50%), Gaps = 2/82 (2%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALDTSKTEIELWDTSGD 63
K+LI+G GKT D + + T G+ + + Y D + ++++WDT+G
Sbjct: 3 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDF-KVKTVYRND-KRIKLQIWDTAGQ 60
Query: 64 HKFESVWPAFQRDVHGIIFVFN 85
++ ++ A+ R G I +++
Sbjct: 61 ERYRTITTAYYRGAMGFILMYD 82
>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 = 32.3 bits (74), Expect = 0.044
Identities = 20/85 (23%), Positives = 40/85 (47%), Gaps = 9/85 (10%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQGV----RIVECEHSYALDTSKTEIELWD 59
K+L++G + GKT + ++ Y T GV +++E + + + ++LWD
Sbjct: 2 KVLVIGDLGVGKTSIIKRYVHGVFSQHYKATIGVDFALKVIEWDPN-----TVVRLQLWD 56
Query: 60 TSGDHKFESVWPAFQRDVHGIIFVF 84
+G +F + + + G I VF
Sbjct: 57 IAGQERFGGMTRVYYKGAVGAIIVF 81
>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 = 32.1 bits (73), Expect = 0.047
Identities = 20/86 (23%), Positives = 39/86 (45%), Gaps = 11/86 (12%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSY----ALDTSKTEIELWD 59
K+++LG GK+ L ++Y PT E SY +D + +E+ D
Sbjct: 3 KLVVLGSGGVGKSALTVQFVQGIFVDKYDPT-------IEDSYRKQIEVDCQQCMLEILD 55
Query: 60 TSGDHKFESVWPAFQRDVHGIIFVFN 85
T+G +F ++ + ++ G V++
Sbjct: 56 TAGTEQFTAMRDLYIKNGQGFALVYS 81
>gnl|CDD|234189 TIGR03375, type_I_sec_LssB, type I secretion system ATPase, LssB
family. Type I protein secretion is a system in some
Gram-negative bacteria to export proteins (often
proteases) across both inner and outer membranes to the
extracellular medium. This is one of three proteins of
the type I secretion apparatus. Targeted proteins are
not cleaved at the N-terminus, but rather carry signals
located toward the extreme C-terminus to direct type I
secretion. This model is related to models TIGR01842 and
TIGR01846, and to bacteriocin ABC transporters that
cleave their substrates during export [Protein fate,
Protein and peptide secretion and trafficking, Cellular
processes, Pathogenesis].
Length = 694
Score = 32.1 bits (74), Expect = 0.069
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 5/33 (15%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQG 36
K+ I+G I +GK+ L L L Y PT+G
Sbjct: 493 KVAIIGRIGSGKSTLLKLLLGL-----YQPTEG 520
>gnl|CDD|177661 PLN00023, PLN00023, GTP-binding protein; Provisional.
Length = 334
Score = 31.8 bits (72), Expect = 0.073
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 55 IELWDTSGDHKFESVWPAFQRDVHGIIFVFN 85
+ELWD SG +++ F ++G+IFV +
Sbjct: 85 VELWDVSGHERYKDCRSLFYSQINGVIFVHD 115
>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 = 31.5 bits (72), Expect = 0.080
Identities = 18/90 (20%), Positives = 37/90 (41%), Gaps = 5/90 (5%)
Query: 2 KIKILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALDTSKTEIELWDTS 61
+ K++++G GKT L L + T G+ + + + A + K + +WD
Sbjct: 1 EAKLMLVGQGGVGKTSLCKQLIGEKFDGDESSTHGINVQDWKIP-APERKKIRLNVWDFG 59
Query: 62 GDHKFESVWPAF--QRDVHGIIFVFNSGVP 89
G + + F R ++ + VF+
Sbjct: 60 GQEIYHATHQFFLTSRSLY--LLVFDLRTG 87
>gnl|CDD|197556 smart00178, SAR, Sar1p-like members of the Ras-family of small
GTPases. Yeast SAR1 is an essential gene required for
transport of secretory proteins from the endoplasmic
reticulum to the Golgi apparatus.
Length = 184
Score = 31.4 bits (71), Expect = 0.088
Identities = 23/94 (24%), Positives = 38/94 (40%), Gaps = 13/94 (13%)
Query: 4 KILILGPIMAGKTVLANALCD---LTTAEEYHPTQGVRIVECEHSYALDTSKTEIELWDT 60
KIL LG AGKT L + L + HPT S L + +D
Sbjct: 19 KILFLGLDNAGKTTLLHMLKNDRLAQHQPTQHPT----------SEELAIGNIKFTTFDL 68
Query: 61 SGDHKFESVWPAFQRDVHGIIFVFNSGVPGHISE 94
G + +W + +V+GI+++ ++ +E
Sbjct: 69 GGHQQARRLWKDYFPEVNGIVYLVDAYDKERFAE 102
>gnl|CDD|172418 PRK13898, PRK13898, type IV secretion system ATPase VirB4;
Provisional.
Length = 800
Score = 31.7 bits (72), Expect = 0.092
Identities = 13/18 (72%), Positives = 14/18 (77%)
Query: 6 LILGPIMAGKTVLANALC 23
LI+GP AGKTVL N LC
Sbjct: 450 LIIGPTGAGKTVLMNFLC 467
>gnl|CDD|206720 cd04154, Arl2, Arf-like 2 (Arl2) GTPase. Arl2 (Arf-like 2)
GTPases are members of the Arf family that bind GDP and
GTP with very low affinity. Unlike most Arf family
proteins, Arl2 is not myristoylated at its N-terminal
helix. The protein PDE-delta, first identified in
photoreceptor rod cells, binds specifically to Arl2 and
is structurally very similar to RhoGDI. Despite the
high structural similarity between Arl2 and Rho
proteins and between PDE-delta and RhoGDI, the
interactions between the GTPases and their effectors
are very different. In its GTP bound form, Arl2
interacts with the protein Binder of Arl2 (BART), and
the complex is believed to play a role in mitochondrial
adenine nucleotide transport. In its GDP bound form,
Arl2 interacts with tubulin- folding Cofactor D; this
interaction is believed to play a role in regulation of
microtubule dynamics that impact the cytoskeleton, cell
division, and cytokinesis.
Length = 173
Score = 31.1 bits (71), Expect = 0.098
Identities = 25/87 (28%), Positives = 39/87 (44%), Gaps = 13/87 (14%)
Query: 3 IKILILGPIMAGKTVLANALC--DLTTAEEYHPTQGVRIVECEHS-YALDTSKTEIELWD 59
++IL+LG AGKT + D++T PT G I E++ Y L+ +WD
Sbjct: 15 MRILMLGLDNAGKTTILKKFNGEDISTIS---PTLGFNIKTLEYNGYKLN-------IWD 64
Query: 60 TSGDHKFESVWPAFQRDVHGIIFVFNS 86
G S W + +I+V +S
Sbjct: 65 VGGQKSLRSYWRNYFESTDALIWVVDS 91
>gnl|CDD|206716 cd04149, Arf6, ADP ribosylation factor 6 (Arf6). Arf6 subfamily.
Arf6 (ADP ribosylation factor 6) proteins localize to
the plasma membrane, where they perform a wide variety
of functions. In its active, GTP-bound form, Arf6 is
involved in cell spreading, Rac-induced formation of
plasma membrane ruffles, cell migration, wound healing,
and Fc-mediated phagocytosis. Arf6 appears to change
the actin structure at the plasma membrane by
activating Rac, a Rho family protein involved in
membrane ruffling. Arf6 is required for and enhances
Rac formation of ruffles. Arf6 can regulate dendritic
branching in hippocampal neurons, and in yeast it
localizes to the growing bud, where it plays a role in
polarized growth and bud site selection. In leukocytes,
Arf6 is required for chemokine-stimulated migration
across endothelial cells. Arf6 also plays a role in
down-regulation of beta2-adrenergic receptors and
luteinizing hormone receptors by facilitating the
release of sequestered arrestin to allow endocytosis.
Arf6 is believed to function at multiple sites on the
plasma membrane through interaction with a specific set
of GEFs, GAPs, and effectors. Arf6 has been implicated
in breast cancer and melanoma cell invasion, and in
actin remodelling at the invasion site of Chlamydia
infection.
Length = 168
Score = 30.9 bits (70), Expect = 0.13
Identities = 25/93 (26%), Positives = 39/93 (41%), Gaps = 7/93 (7%)
Query: 2 KIKILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALDTSKTEIELWDTS 61
+++IL+LG AGKT + L L + PT G + + + +WD
Sbjct: 9 EMRILMLGLDAAGKTTILYKL-KLGQSVTTIPTVGFNVETVTYK------NVKFNVWDVG 61
Query: 62 GDHKFESVWPAFQRDVHGIIFVFNSGVPGHISE 94
G K +W + G+IFV +S I E
Sbjct: 62 GQDKIRPLWRHYYTGTQGLIFVVDSADRDRIDE 94
>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 = 30.9 bits (70), Expect = 0.13
Identities = 25/89 (28%), Positives = 38/89 (42%), Gaps = 9/89 (10%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPT---QGVRIVECEHSYALDTSKTEIELWDT 60
K++I+G GKT L E Y PT V +E +D + E+ LWDT
Sbjct: 3 KLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIE------VDGKQVELALWDT 56
Query: 61 SGDHKFESVWPAFQRDVHGIIFVFNSGVP 89
+G ++ + P D I+ F+ P
Sbjct: 57 AGQEDYDRLRPLSYPDTDVILMCFSIDSP 85
>gnl|CDD|206739 cd09912, DLP_2, Dynamin-like protein including dynamins,
mitofusins, and guanylate-binding proteins. The dynamin
family of large mechanochemical GTPases includes the
classical dynamins and dynamin-like proteins (DLPs) that
are found throughout the Eukarya. This family also
includes bacterial DLPs. These proteins catalyze
membrane fission during clathrin-mediated endocytosis.
Dynamin consists of five domains; an N-terminal G domain
that binds and hydrolyzes GTP, a middle domain (MD)
involved in self-assembly and oligomerization, a
pleckstrin homology (PH) domain responsible for
interactions with the plasma membrane, GED, which is
also involved in self-assembly, and a proline arginine
rich domain (PRD) that interacts with SH3 domains on
accessory proteins. To date, three vertebrate dynamin
genes have been identified; dynamin 1, which is brain
specific, mediates uptake of synaptic vesicles in
presynaptic terminals; dynamin-2 is expressed
ubiquitously and similarly participates in membrane
fission; mutations in the MD, PH and GED domains of
dynamin 2 have been linked to human diseases such as
Charcot-Marie-Tooth peripheral neuropathy and rare forms
of centronuclear myopathy. Dynamin 3 participates in
megakaryocyte progenitor amplification, and is also
involved in cytoplasmic enlargement and the formation of
the demarcation membrane system. This family also
includes mitofusins (MFN1 and MFN2 in mammals) that are
involved in mitochondrial fusion. Dynamin oligomerizes
into helical structures around the neck of budding
vesicles in a GTP hydrolysis-dependent manner.
Length = 180
Score = 30.6 bits (70), Expect = 0.16
Identities = 30/108 (27%), Positives = 41/108 (37%), Gaps = 21/108 (19%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQGV-----RIVECEHSYALDTSKTEIELW 58
+ ++G AGK+ L NAL EE PT GV I Y L + L
Sbjct: 2 LLAVVGEFSAGKSTLLNALL----GEEVLPT-GVTPTTAVITVL--RYGL---LKGVVLV 51
Query: 59 DTSG-----DHKFESVWPAFQRDVHGIIFVFNSGVPGHISELLLFYDY 101
DT G +H E +F +IFV ++ P SE +
Sbjct: 52 DTPGLNSTIEHHTEITE-SFLPRADAVIFVLSADQPLTESEREFLKEI 98
>gnl|CDD|204242 pfam09439, SRPRB, Signal recognition particle receptor beta
subunit. The beta subunit of the signal recognition
particle receptor (SRP) is a transmembrane GTPase which
anchors the alpha subunit to the endoplasmic reticulum
membrane.
Length = 181
Score = 30.5 bits (69), Expect = 0.17
Identities = 21/90 (23%), Positives = 27/90 (30%), Gaps = 14/90 (15%)
Query: 5 ILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALD---TSKTEIELWDTS 61
++I G +GKT L L T T E S A L D
Sbjct: 6 VIIAGLCDSGKTSLFTLL----TTGTVKKTV----TSQEPSAAYKYMLHKGFSFTLIDFP 57
Query: 62 GDHKFESVW---PAFQRDVHGIIFVFNSGV 88
G K + GI+FV +S
Sbjct: 58 GHVKLRQKLLETIKDSSSLRGIVFVVDSTA 87
>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 = 30.6 bits (69), Expect = 0.17
Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 2/73 (2%)
Query: 3 IKILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALDTSKTEIELWDTSG 62
+K+++LG GK+ L N + T GV + + +D +++WDT+G
Sbjct: 6 LKVILLGDGGVGKSSLMNRYVTNKFDTQLFHTIGVEFLNKD--LEVDGHFVTLQIWDTAG 63
Query: 63 DHKFESVWPAFQR 75
+F S+ F R
Sbjct: 64 QERFRSLRTPFYR 76
>gnl|CDD|206717 cd04150, Arf1_5_like, ADP-ribosylation factor-1 (Arf1) and
ADP-ribosylation factor-5 (Arf5). The Arf1-Arf5-like
subfamily contains Arf1, Arf2, Arf3, Arf4, Arf5, and
related proteins. Arfs1-5 are soluble proteins that are
crucial for assembling coat proteins during vesicle
formation. Each contains an N-terminal myristoylated
amphipathic helix that is folded into the protein in
the GDP-bound state. GDP/GTP exchange exposes the
helix, which anchors to the membrane. Following GTP
hydrolysis, the helix dissociates from the membrane and
folds back into the protein. A general feature of
Arf1-5 signaling may be the cooperation of two Arfs at
the same site. Arfs1-5 are generally considered to be
interchangeable in function and location, but some
specific functions have been assigned. Arf1 localizes
to the early/cis-Golgi, where it is activated by GBF1
and recruits the coat protein COPI. It also localizes
to the trans-Golgi network (TGN), where it is activated
by BIG1/BIG2 and recruits the AP1, AP3, AP4, and GGA
proteins. Humans, but not rodents and other lower
eukaryotes, lack Arf2. Human Arf3 shares 96% sequence
identity with Arf1 and is believed to generally
function interchangeably with Arf1. Human Arf4 in the
activated (GTP-bound) state has been shown to interact
with the cytoplasmic domain of epidermal growth factor
receptor (EGFR) and mediate the EGF-dependent
activation of phospholipase D2 (PLD2), leading to
activation of the activator protein 1 (AP-1)
transcription factor. Arf4 has also been shown to
recognize the C-terminal sorting signal of rhodopsin
and regulate its incorporation into specialized
post-Golgi rhodopsin transport carriers (RTCs). There
is some evidence that Arf5 functions at the early-Golgi
and the trans-Golgi to affect Golgi-associated
alpha-adaptin homology Arf-binding proteins (GGAs).
Length = 159
Score = 30.5 bits (69), Expect = 0.18
Identities = 25/87 (28%), Positives = 40/87 (45%), Gaps = 13/87 (14%)
Query: 3 IKILILGPIMAGKTVLANALC---DLTTAEEYHPTQGVRIVECEHSYALDTSKTEIELWD 59
++IL++G AGKT + L +TT PT G + E+ T +WD
Sbjct: 1 MRILMVGLDAAGKTTILYKLKLGEIVTTI----PTIGFNVETVEYKNISFT------VWD 50
Query: 60 TSGDHKFESVWPAFQRDVHGIIFVFNS 86
G K +W + ++ G+IFV +S
Sbjct: 51 VGGQDKIRPLWRHYFQNTQGLIFVVDS 77
>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 = 30.3 bits (69), Expect = 0.19
Identities = 21/102 (20%), Positives = 30/102 (29%), Gaps = 17/102 (16%)
Query: 7 ILGPIMAGKTVLANALCD---LTTAEEYHPTQGVRIVECEHSYALDTSKTEIELWDT--- 60
I G GK+ L NAL + T+ E E + L DT
Sbjct: 2 IFGRPNVGKSSLLNALLGQNVGIVSPIPGTTRDPVRKEWELL-----PLGPVVLIDTPGL 56
Query: 61 -----SGDHKFESVWPAFQRDVHGIIFVFNSGVPGHISELLL 97
G + E R ++ V +S + E L
Sbjct: 57 DEEGGLGRERVEEARQVADR-ADLVLLVVDSDLTPVEEEAKL 97
>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 = 30.5 bits (69), Expect = 0.19
Identities = 28/119 (23%), Positives = 52/119 (43%), Gaps = 11/119 (9%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSY----ALDTSKTEIELWD 59
KI++LG GK+ L E Y PT E SY +D + ++E+ D
Sbjct: 3 KIVVLGAGGVGKSALTVQFVQNVFIESYDPT-------IEDSYRKQVEIDGRQCDLEILD 55
Query: 60 TSGDHKFESVWPAFQRDVHGIIFVFNSGVPGHISELLLFYDYFVTQSDLNNHKCLLIDN 118
T+G +F ++ + + G + V++ ++EL + + D +N +L+ N
Sbjct: 56 TAGTEQFTAMRELYIKSGQGFLLVYSVTSEASLNELGELREQVLRIKDSDNVPMVLVGN 114
>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 = 30.1 bits (68), Expect = 0.23
Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 2/83 (2%)
Query: 3 IKILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALDTSKTEIELWDTSG 62
+KI +LG GKT L + EEY T GV +E + ++ ++ +WD G
Sbjct: 1 LKIGLLGDAQIGKTSLMVKYVEGEFDEEYIQTLGVNFME--KTISIRGTEITFSIWDLGG 58
Query: 63 DHKFESVWPAFQRDVHGIIFVFN 85
+F ++ P +D I+F+F+
Sbjct: 59 QREFINMLPLVCKDAVAILFMFD 81
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 29.7 bits (67), Expect = 0.37
Identities = 22/68 (32%), Positives = 30/68 (44%), Gaps = 10/68 (14%)
Query: 3 IKILILGPIMAGKTVLANALCDLTTAEE--YHPTQGVRIVECEHSYALDTSKTEI--ELW 58
K++++G GKT LT E Y PT GV + H T+ I +W
Sbjct: 10 FKLILVGDGGVGKTTFVKR--HLTGEFEKKYIPTLGVEV----HPLKFYTNCGPICFNVW 63
Query: 59 DTSGDHKF 66
DT+G KF
Sbjct: 64 DTAGQEKF 71
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 29.5 bits (66), Expect = 0.38
Identities = 21/85 (24%), Positives = 40/85 (47%), Gaps = 8/85 (9%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAE---EYHPTQGVRIVECEHSYALDTSKTEIELWDT 60
KI+++G GK+ N L T E E T GV + ++ + ++WDT
Sbjct: 14 KIVLIGDSGVGKS---NILSRFTRNEFCLESKSTIGVEFAT--RTLQVEGKTVKAQIWDT 68
Query: 61 SGDHKFESVWPAFQRDVHGIIFVFN 85
+G ++ ++ A+ R G + V++
Sbjct: 69 AGQERYRAITSAYYRGAVGALLVYD 93
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 29.7 bits (67), Expect = 0.41
Identities = 21/68 (30%), Positives = 31/68 (45%), Gaps = 10/68 (14%)
Query: 3 IKILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALD--TSKTEI--ELW 58
K++I+G GKT ++Y PT GV + + LD T+ +I W
Sbjct: 14 FKLVIVGDGGTGKTTFVKRHLTGEFEKKYEPTIGVEV------HPLDFFTNCGKIRFYCW 67
Query: 59 DTSGDHKF 66
DT+G KF
Sbjct: 68 DTAGQEKF 75
>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 = 29.2 bits (65), Expect = 0.58
Identities = 26/91 (28%), Positives = 41/91 (45%), Gaps = 11/91 (12%)
Query: 3 IKILILGPIMAGKTVLANALCDLTTA--EEYHPTQGVRIVECEHS--YALDTSKTEIELW 58
IK +++G GKT L +C T A +EY PT V +S A+D + LW
Sbjct: 4 IKCVVVGDGAVGKTCLL--ICYTTNAFPKEYIPT-----VFDNYSAQTAVDGRTVSLNLW 56
Query: 59 DTSGDHKFESVWPAFQRDVHGIIFVFNSGVP 89
DT+G +++ + + I F+ P
Sbjct: 57 DTAGQEEYDRLRTLSYPQTNVFIICFSIASP 87
>gnl|CDD|238550 cd01130, VirB11-like_ATPase, Type IV secretory pathway component
VirB11, and related ATPases. The homohexamer, VirB11 is
one of eleven Vir proteins, which are required for
T-pilus biogenesis and virulence in the transfer of
T-DNA from the Ti (tumor-inducing) plasmid of bacterial
to plant cells. The pilus is a fibrous cell surface
organelle, which mediates adhesion between bacteria
during conjugative transfer or between bacteria and
host eukaryotic cells during infection. VirB11- related
ATPases include the archaeal flagella biosynthesis
protein and the pilus assembly proteins CpaF/TadA and
TrbB. This alignment contains the C-terminal domain,
which is the ATPase.
Length = 186
Score = 28.8 bits (65), Expect = 0.68
Identities = 15/39 (38%), Positives = 18/39 (46%), Gaps = 7/39 (17%)
Query: 5 ILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECE 43
ILI G +GKT L NAL +E RI+ E
Sbjct: 28 ILISGGTGSGKTTLLNALLAFIPPDE-------RIITIE 59
>gnl|CDD|129208 TIGR00101, ureG, urease accessory protein UreG. This model
represents UreG, a GTP hydrolase that acts in the
assembly of the nickel metallocenter of urease. It is
found only in urease-positive species, although some
urease-positive species (e.g. Bacillus subtilis) lack
this protein. A similar protein, hypB, is an accessory
protein for expression of hydrogenase, which also uses
nickel [Central intermediary metabolism, Nitrogen
metabolism].
Length = 199
Score = 28.7 bits (64), Expect = 0.90
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 3 IKILILGPIMAGKTVLANALC 23
+KI + GP+ +GKT L AL
Sbjct: 2 LKIGVAGPVGSGKTALIEALT 22
>gnl|CDD|172997 PRK14531, PRK14531, adenylate kinase; Provisional.
Length = 183
Score = 28.2 bits (63), Expect = 1.2
Identities = 12/24 (50%), Positives = 14/24 (58%)
Query: 1 MKIKILILGPIMAGKTVLANALCD 24
MK ++L LGP AGK A LC
Sbjct: 1 MKQRLLFLGPPGAGKGTQAARLCA 24
>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 = 27.9 bits (63), Expect = 1.2
Identities = 19/85 (22%), Positives = 37/85 (43%), Gaps = 6/85 (7%)
Query: 2 KIKILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALDTSKTEI--ELWD 59
+ K+++LG GK+ + E+ Q I + ++ T + E+WD
Sbjct: 1 QFKLVLLGDSSVGKSSIVLRFVK----NEFSENQESTIGAAFLTQTVNLDDTTVKFEIWD 56
Query: 60 TSGDHKFESVWPAFQRDVHGIIFVF 84
T+G ++ S+ P + R I V+
Sbjct: 57 TAGQERYRSLAPMYYRGAAAAIVVY 81
>gnl|CDD|238836 cd01673, dNK, Deoxyribonucleoside kinase (dNK) catalyzes the
phosphorylation of deoxyribonucleosides to yield
corresponding monophosphates (dNMPs). This family
consists of various deoxynucleoside kinases including
deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC
2.7.1.113), adenosine (EC 2.7.1.76), and thymidine (EC
2.7.1.21) kinases. They are key enzymes in the salvage
of deoxyribonucleosides originating from extra- or
intracellular breakdown of DNA.
Length = 193
Score = 28.0 bits (63), Expect = 1.3
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 4 KILILGPIMAGKTVLANAL 22
I++ G I AGK+ LA L
Sbjct: 1 VIVVEGNIGAGKSTLAKEL 19
>gnl|CDD|234141 TIGR03185, DNA_S_dndD, DNA sulfur modification protein DndD.
This model describes the DndB protein encoded by an
operon associated with a sulfur-containing modification
to DNA. The operon is sporadically distributed in
bacteria, much like some restriction enzyme operons.
DndD is described as a putative ATPase. The small
number of examples known so far include species from
among the Firmicutes, Actinomycetes, Proteobacteria,
and Cyanobacteria [DNA metabolism,
Restriction/modification].
Length = 650
Score = 28.1 bits (63), Expect = 1.4
Identities = 16/63 (25%), Positives = 22/63 (34%), Gaps = 14/63 (22%)
Query: 5 ILILGPIMAGKTVLANAL----------CDLTTAEEYHPTQGVRIVECEHSYALDTSKTE 54
ILI G AGKT L +A+ C + Y + + A T+
Sbjct: 31 ILIGGLNGAGKTTLLDAIQLALYGKRALCSGRGNKSYEQ----YLRGLINRQAGKTNPAS 86
Query: 55 IEL 57
I L
Sbjct: 87 ITL 89
>gnl|CDD|223401 COG0324, MiaA, tRNA delta(2)-isopentenylpyrophosphate transferase
[Translation, ribosomal structure and biogenesis].
Length = 308
Score = 28.0 bits (63), Expect = 1.4
Identities = 13/29 (44%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 1 MKIKILILGPIMAGKTVLANALCDLTTAE 29
K+ I+I GP +GKT LA AL E
Sbjct: 3 PKL-IVIAGPTASGKTALAIALAKRLGGE 30
>gnl|CDD|222912 PHA02624, PHA02624, large T antigen; Provisional.
Length = 647
Score = 28.0 bits (63), Expect = 1.5
Identities = 12/23 (52%), Positives = 14/23 (60%)
Query: 5 ILILGPIMAGKTVLANALCDLTT 27
L GP+ +GKT LA AL DL
Sbjct: 434 WLFKGPVNSGKTTLAAALLDLCG 456
>gnl|CDD|213179 cd00267, ABC_ATPase, ATP-binding cassette transporter
nucleotide-binding domain. ABC transporters are a
large family of proteins involved in the transport of a
wide variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide-binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and
GTP-binding and hydrolyzing proteins.
Length = 157
Score = 27.6 bits (62), Expect = 1.5
Identities = 10/32 (31%), Positives = 16/32 (50%), Gaps = 5/32 (15%)
Query: 5 ILILGPIMAGKTVLANALCDLTTAEEYHPTQG 36
+ ++GP +GK+ L A+ L PT G
Sbjct: 28 VALVGPNGSGKSTLLRAIAGLLK-----PTSG 54
>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 = 27.7 bits (62), Expect = 1.6
Identities = 18/66 (27%), Positives = 30/66 (45%), Gaps = 6/66 (9%)
Query: 3 IKILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALDTSKTEI--ELWDT 60
K++++G GKT ++Y T GV + H T++ +I +WDT
Sbjct: 1 FKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEV----HPLDFHTNRGKIRFNVWDT 56
Query: 61 SGDHKF 66
+G KF
Sbjct: 57 AGQEKF 62
>gnl|CDD|239198 cd02799, tRNA_bind_EMAP-II_like, tRNA-binding-domain-containing
EMAP2-like proteins. This family contains a diverse
fraction of tRNA binding proteins, including
Caenorhabditis elegans methionyl-tRNA synthetase
(CeMetRS), human tyrosyl- tRNA synthetase (hTyrRS),
Saccharomyces cerevisiae Arc1p, human p43 and EMAP2.
CeMetRS and hTyrRS aminoacylate their cognate tRNAs.
Arc1p is a transactivator of yeast methionyl-tRNA and
glutamyl-tRNA synthetases. This domain has general tRNA
binding properties. In a subset of this family this
domain has the added capability of a cytokine. For
example the p43 component of the Human aminoacyl-tRNA
synthetase complex is cleaved to release EMAP-II
cytokine. EMAP-II has multiple activities during
apoptosis, angiogenesis and inflammation and
participates in malignant transformation. A EMAP-II-like
cytokine also is released from hTyrRS upon cleavage. The
active cytokine heptapeptide locates to this domain.
Length = 105
Score = 27.2 bits (61), Expect = 1.7
Identities = 9/28 (32%), Positives = 14/28 (50%), Gaps = 2/28 (7%)
Query: 102 FVTQSDLNNHKCLLIDNVKPG--RGDSS 127
FV + N +++ N+KP RG S
Sbjct: 47 FVPLEQMQNRLVVVLCNLKPRKMRGVKS 74
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a
wide variety of presumed phage proteins.
Length = 201
Score = 27.6 bits (62), Expect = 1.7
Identities = 13/25 (52%), Positives = 14/25 (56%)
Query: 2 KIKILILGPIMAGKTVLANALCDLT 26
IK+LI GP GKT LA L T
Sbjct: 3 NIKVLIYGPPGIGKTSLAKTLPPKT 27
>gnl|CDD|225713 COG3172, NadR, Predicted ATPase/kinase involved in NAD metabolism
[Coenzyme metabolism].
Length = 187
Score = 27.4 bits (61), Expect = 1.8
Identities = 13/34 (38%), Positives = 20/34 (58%), Gaps = 4/34 (11%)
Query: 1 MKIKILILGPIMAGKTVLANALCDL---TTAEEY 31
+K + ILG +GK+ L N L ++ T+A EY
Sbjct: 8 VKT-VAILGGESSGKSTLVNKLANIFNTTSAWEY 40
>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 = 27.8 bits (62), Expect = 1.8
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 11/74 (14%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHS--YALDTSKTEIELWDTS 61
++++LG GKT + + E+Y PT +E H Y++ ++++ DTS
Sbjct: 2 RMVVLGASKVGKTAIVSRFLGGRFEEQYTPT-----IEDFHRKLYSIRGEVYQLDILDTS 56
Query: 62 GDHKFESVWPAFQR 75
G+H F PA +R
Sbjct: 57 GNHPF----PAMRR 66
>gnl|CDD|224345 COG1428, COG1428, Deoxynucleoside kinases [Nucleotide transport
and metabolism].
Length = 216
Score = 27.7 bits (62), Expect = 1.8
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 5 ILILGPIMAGKTVLANAL 22
I+I G I AGK+ LA AL
Sbjct: 7 IVIEGMIGAGKSTLAQAL 24
>gnl|CDD|206718 cd04151, Arl1, ADP ribosylation factor 1 (Arf1). Arl1 subfamily.
Arl1 (Arf-like 1) localizes to the Golgi complex, where
it is believed to recruit effector proteins to the
trans-Golgi network. Like most members of the Arf
family, Arl1 is myristoylated at its N-terminal helix
and mutation of the myristoylation site disrupts Golgi
targeting. In humans, the Golgi-localized proteins
golgin-97 and golgin-245 have been identified as Arl1
effectors. Golgins are large coiled-coil proteins found
in the Golgi, and these golgins contain a C-terminal
GRIP domain, which is the site of Arl1 binding.
Additional Arl1 effectors include the GARP
(Golgi-associated retrograde protein)/VFT (Vps53)
vesicle-tethering complex and Arfaptin 2. Arl1 is not
required for exocytosis, but appears necessary for
trafficking from the endosomes to the Golgi. In
Drosophila zygotes, mutation of Arl1 is lethal, and in
the host-bloodstream form of Trypanosoma brucei, Arl1
is essential for viability.
Length = 158
Score = 27.4 bits (61), Expect = 1.9
Identities = 25/85 (29%), Positives = 35/85 (41%), Gaps = 11/85 (12%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAE--EYHPTQGVRIVECEHSYALDTSKTEIELWDTS 61
+ILILG AGKT + L L E PT G VE + + ++WD
Sbjct: 1 RILILGLDGAGKTTI---LYRLQVGEVVTTIPTIGFN-VE-----TVTYKNLKFQVWDLG 51
Query: 62 GDHKFESVWPAFQRDVHGIIFVFNS 86
G W + + II+V +S
Sbjct: 52 GQTSIRPYWRCYYSNTDAIIYVVDS 76
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 27.5 bits (62), Expect = 2.0
Identities = 11/30 (36%), Positives = 13/30 (43%), Gaps = 2/30 (6%)
Query: 4 KILILGPIMAGKTVLANALCDL--TTAEEY 31
+I+I G GKT L AL EY
Sbjct: 1 RIVITGGPSTGKTTLLEALAARGYPVVPEY 30
>gnl|CDD|131580 TIGR02528, EutP, ethanolamine utilization protein, EutP. This
protein is found within operons which code for
polyhedral organelles containing the enzyme
ethanolamine ammonia lyase. The function of this gene
is unknown, although the presence of an N-terminal
GxxGxGK motif implies a GTP-binding site [Energy
metabolism, Amino acids and amines].
Length = 142
Score = 27.0 bits (60), Expect = 2.0
Identities = 12/34 (35%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQGV 37
+I+ +G + GKT L AL Y TQ V
Sbjct: 2 RIMFIGSVGCGKTTLTQALQGEEI--LYKKTQAV 33
>gnl|CDD|226970 COG4619, COG4619, ABC-type uncharacterized transport system,
ATPase component [General function prediction only].
Length = 223
Score = 27.5 bits (61), Expect = 2.2
Identities = 12/55 (21%), Positives = 16/55 (29%), Gaps = 8/55 (14%)
Query: 5 ILILGPIMAGKTVLANALCDLTTAEEYH--------PTQGVRIVECEHSYALDTS 51
I I GP GK+ L + L + T + SY T
Sbjct: 32 IAITGPSGCGKSTLLKIVASLISPTSGTLLFEGEDVSTLKPEAYRQQVSYCAQTP 86
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only
detects a fraction of this vast family. The poorly
conserved N-terminal helix is missing from the
alignment.
Length = 148
Score = 27.0 bits (59), Expect = 2.5
Identities = 18/45 (40%), Positives = 22/45 (48%), Gaps = 6/45 (13%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQ-GVRIVECEHSYA 47
ILI+GP +GKT LA AL A E P GV ++ E
Sbjct: 4 VILIVGPPGSGKTTLARAL-----ARELGPPGGGVIYIDGEDILE 43
>gnl|CDD|213212 cd03245, ABCC_bacteriocin_exporters, ATP-binding cassette domain
of bacteriocin exporters, subfamily C. Many
non-lantibiotic bacteriocins of lactic acid bacteria
are produced as precursors which have N-terminal leader
peptides that share similarities in amino acid sequence
and contain a conserved processing site of two glycine
residues in positions -1 and -2. A dedicated
ATP-binding cassette (ABC) transporter is responsible
for the proteolytic cleavage of the leader peptides and
subsequent translocation of the bacteriocins across the
cytoplasmic membrane.
Length = 220
Score = 27.2 bits (61), Expect = 2.6
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 6/37 (16%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQG-VRI 39
K+ I+G + +GK+ L L L Y PT G V +
Sbjct: 32 KVAIIGRVGSGKSTLLKLLAGL-----YKPTSGSVLL 63
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 27.3 bits (61), Expect = 2.7
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 1 MKIKILILGPIMAGKTVLANALC 23
K+ + ++G GKT L NAL
Sbjct: 2 KKLTVALVGNPNVGKTTLFNALT 24
>gnl|CDD|233193 TIGR00929, VirB4_CagE, type IV secretion/conjugal transfer ATPase,
VirB4 family. Type IV secretion systems are found in
Gram-negative pathogens. They export proteins, DNA, or
complexes in different systems and are related to
plasmid conjugation systems. This model represents
related ATPases that include VirB4 in Agrobacterium
tumefaciens (DNA export) CagE in Helicobacter pylori
(protein export) and plasmid TraB (conjugation).
Length = 785
Score = 27.3 bits (61), Expect = 2.7
Identities = 10/18 (55%), Positives = 11/18 (61%)
Query: 6 LILGPIMAGKTVLANALC 23
LI GP +GKT L N L
Sbjct: 438 LIFGPTGSGKTTLLNFLL 455
>gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme
subunit McrB; Provisional.
Length = 459
Score = 27.4 bits (60), Expect = 2.9
Identities = 17/49 (34%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 1 MKIKILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALD 49
+K I++ GP GKT +A L L T E+ Q V +V+ SY+ +
Sbjct: 193 IKKNIILQGPPGVGKTFVARRLAYLLTGEK--APQRVNMVQFHQSYSYE 239
>gnl|CDD|115108 pfam06431, Polyoma_lg_T_C, Polyomavirus large T antigen C-terminus.
Length = 417
Score = 27.2 bits (60), Expect = 2.9
Identities = 13/20 (65%), Positives = 14/20 (70%)
Query: 6 LILGPIMAGKTVLANALCDL 25
L GPI +GKT LA AL DL
Sbjct: 159 LFKGPIDSGKTTLAAALLDL 178
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 26.9 bits (60), Expect = 3.0
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 5/32 (15%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQ 35
+ILILGP AGK+ LA L A++
Sbjct: 2 RILILGPPGAGKSTLAKKL-----AKKLGLPH 28
>gnl|CDD|206733 cd04170, EF-G_bact, Elongation factor G (EF-G) family.
Translocation is mediated by EF-G (also called
translocase). The structure of EF-G closely resembles
that of the complex between EF-Tu and tRNA. This is an
example of molecular mimicry; a protein domain evolved
so that it mimics the shape of a tRNA molecule. EF-G in
the GTP form binds to the ribosome, primarily through
the interaction of its EF-Tu-like domain with the 50S
subunit. The binding of EF-G to the ribosome in this
manner stimulates the GTPase activity of EF-G. On GTP
hydrolysis, EF-G undergoes a conformational change that
forces its arm deeper into the A site on the 30S
subunit. To accommodate this domain, the peptidyl-tRNA
in the A site moves to the P site, carrying the mRNA and
the deacylated tRNA with it. The ribosome may be
prepared for these rearrangements by the initial binding
of EF-G as well. The dissociation of EF-G leaves the
ribosome ready to accept the next aminoacyl-tRNA into
the A site. This group contains only bacterial members.
Length = 268
Score = 27.2 bits (61), Expect = 3.1
Identities = 29/107 (27%), Positives = 39/107 (36%), Gaps = 30/107 (28%)
Query: 5 ILILGPIMAGKTVLANALC-------------DLTTAEEYHPTQGVRIVECEHSYALDTS 51
I ++G +GKT LA AL D T +Y P E + +++TS
Sbjct: 2 IALVGHSGSGKTTLAEALLYATGAIDRLGRVEDGNTVSDYDP------EEKKRKMSIETS 55
Query: 52 -------KTEIELWDTSGDHKF-ESVWPAFQRDVHGIIFVFN--SGV 88
+I L DT G F A R V + V SGV
Sbjct: 56 VAPLEWNGHKINLIDTPGYADFVGETLSAL-RAVDAALIVVEAQSGV 101
>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 = 26.6 bits (59), Expect = 3.2
Identities = 26/119 (21%), Positives = 49/119 (41%), Gaps = 11/119 (9%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSY----ALDTSKTEIELWD 59
K++++G GK+ L +Y PT E SY +D +++ D
Sbjct: 4 KLVVVGGGGVGKSALTIQFIQSYFVTDYDPT-------IEDSYTKQCEIDGQWARLDILD 56
Query: 60 TSGDHKFESVWPAFQRDVHGIIFVFNSGVPGHISELLLFYDYFVTQSDLNNHKCLLIDN 118
T+G +F ++ + R G + VF+ G E+ F+ + D + +L+ N
Sbjct: 57 TAGQEEFSAMREQYMRTGEGFLLVFSVTDRGSFEEVDKFHTQILRVKDRDEFPMILVGN 115
>gnl|CDD|213213 cd03246, ABCC_Protease_Secretion, ATP-binding cassette domain of
PrtD, subfamily C. This family represents the ABC
component of the protease secretion system PrtD, a
60-kDa integral membrane protein sharing 37% identity
with HlyB, the ABC component of the alpha-hemolysin
secretion pathway, in the C-terminal domain. They
export degradative enzymes by using a type I protein
secretion system and lack an N-terminal signal peptide,
but contain a C-terminal secretion signal. The Type I
secretion apparatus is made up of three components, an
ABC transporter, a membrane fusion protein (MFP), and
an outer membrane protein (OMP). For the HlyA
transporter complex, HlyB (ABC transporter) and HlyD
(MFP) reside in the inner membrane of E. coli. The OMP
component is TolC, which is thought to interact with
the MFP to form a continuous channel across the
periplasm from the cytoplasm to the exterior. HlyB
belongs to the family of ABC transporters, which are
ubiquitous, ATP-dependent transmembrane pumps or
channels. The spectrum of transport substrates ranges
from inorganic ions, nutrients such as amino acids,
sugars, or peptides, hydrophobic drugs, to large
polypeptides, such as HlyA.
Length = 173
Score = 26.8 bits (60), Expect = 3.2
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 6/34 (17%)
Query: 7 ILGPIMAGKTVLANALCDLTTAEEYHPTQG-VRI 39
I+GP +GK+ LA + L PT G VR+
Sbjct: 33 IIGPSGSGKSTLARLILGLLR-----PTSGRVRL 61
>gnl|CDD|235825 PRK06547, PRK06547, hypothetical protein; Provisional.
Length = 172
Score = 26.6 bits (59), Expect = 3.7
Identities = 13/30 (43%), Positives = 16/30 (53%)
Query: 3 IKILILGPIMAGKTVLANALCDLTTAEEYH 32
I +LI G +GKT LA AL T + H
Sbjct: 16 ITVLIDGRSGSGKTTLAGALAARTGFQLVH 45
>gnl|CDD|226124 COG3596, COG3596, Predicted GTPase [General function prediction
only].
Length = 296
Score = 26.7 bits (59), Expect = 4.0
Identities = 19/62 (30%), Positives = 26/62 (41%), Gaps = 5/62 (8%)
Query: 2 KIKILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIV-ECEHSYALDTSKTEIELWDT 60
+ +L++G AGK+ L NAL E G I SY + + LWDT
Sbjct: 39 PVNVLLMGATGAGKSSLINALFQGEVKEVSKVGVGTDITTRLRLSYDGEN----LVLWDT 94
Query: 61 SG 62
G
Sbjct: 95 PG 96
>gnl|CDD|224145 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
[Transcription].
Length = 450
Score = 26.9 bits (60), Expect = 4.1
Identities = 20/52 (38%), Positives = 24/52 (46%), Gaps = 7/52 (13%)
Query: 5 ILILGPIMAGKTVLANALCDLTTAEEYHP-TQGVRIVECEHSYALDTSKTEI 55
ILI+GP GKT LA + A E V I E Y+L+ KTE
Sbjct: 68 ILIVGPPGTGKTALAMGI-----ARELGEDVPFVAISGSE-IYSLEVKKTEA 113
>gnl|CDD|213221 cd03254, ABCC_Glucan_exporter_like, ATP-binding cassette domain
of glucan transporter and related proteins, subfamily
C. Glucan exporter ATP-binding protein. In A.
tumefaciens cyclic beta-1, 2-glucan must be transported
into the periplasmic space to exert its action as a
virulence factor. This subfamily belongs to the
MRP-like family and is involved in drug, peptide, and
lipid export. The MRP-like family, similar to all ABC
proteins, have a common four-domain core structure
constituted by two membrane-spanning domains each
composed of six transmembrane (TM) helices and two
nucleotide-binding domains (NBD). ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and
GTP-binding and hydrolyzing proteins.
Length = 229
Score = 26.4 bits (59), Expect = 4.2
Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 5/33 (15%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQG 36
+ I+GP AGKT L N L Y P +G
Sbjct: 31 TVAIVGPTGAGKTTLINLLMRF-----YDPQKG 58
>gnl|CDD|224847 COG1936, COG1936, Predicted nucleotide kinase (related to CMP and
AMP kinases) [Nucleotide transport and metabolism].
Length = 180
Score = 26.5 bits (59), Expect = 4.3
Identities = 20/101 (19%), Positives = 33/101 (32%), Gaps = 16/101 (15%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECEHSYALDTSKTEIELWDTSGD 63
I I G GKT + L +L + + + Y TE + S
Sbjct: 2 LIAITGTPGVGKTTVCKLLRELGY-KVIE---LNELAKENGLY------TEYDELRKSVI 51
Query: 64 HKFESVWPAFQRD-VHGIIFVFNSGVPGHISELLLFYDYFV 103
+ + R + ++ + V H+S LL D V
Sbjct: 52 VDVDKL-----RKRLEELLREGSGIVDSHLSHLLPDCDLVV 87
>gnl|CDD|182330 PRK10246, PRK10246, exonuclease subunit SbcC; Provisional.
Length = 1047
Score = 26.7 bits (59), Expect = 4.5
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 7 ILGPIMAGKTVLANALC 23
I GP AGKT L +A+C
Sbjct: 35 ITGPTGAGKTTLLDAIC 51
>gnl|CDD|234626 PRK00091, miaA, tRNA delta(2)-isopentenylpyrophosphate
transferase; Reviewed.
Length = 307
Score = 26.2 bits (59), Expect = 5.0
Identities = 13/23 (56%), Positives = 16/23 (69%), Gaps = 1/23 (4%)
Query: 1 MKIK-ILILGPIMAGKTVLANAL 22
MK K I+I+GP +GKT LA L
Sbjct: 2 MKPKVIVIVGPTASGKTALAIEL 24
>gnl|CDD|215920 pfam00437, T2SE, Type II/IV secretion system protein. This family
contains both type II and type IV pathway secretion
proteins from bacteria. VirB11 ATPase is a subunit of
the Agrobacterium tumefaciens transfer DNA (T-DNA)
transfer system, a type IV secretion pathway required
for delivery of T-DNA and effector proteins to plant
cells during infection.
Length = 273
Score = 26.5 bits (59), Expect = 5.5
Identities = 14/39 (35%), Positives = 17/39 (43%), Gaps = 6/39 (15%)
Query: 5 ILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVECE 43
IL+ G +GKT L AL + T RIV E
Sbjct: 132 ILVSGGTGSGKTTLLYALLNEI------NTDDERIVTIE 164
>gnl|CDD|233448 TIGR01526, nadR_NMN_Atrans, nicotinamide-nucleotide
adenylyltransferase, NadR type. The NadR protein of E.
coli and closely related bacteria is both enzyme and
regulatory protein. The first 60 or so amino acids,
N-terminal to the region covered by this model, is a
DNA-binding helix-turn-helix domain (pfam01381)
responsible for repressing the nadAB genes of NAD de
novo biosynthesis. The NadR homologs in Mycobacterium
tuberculosis, Haemophilus influenzae, and others appear
to lack the repressor domain. NadR has recently been
shown to act as an enzyme of the salvage pathway of NAD
biosynthesis, nicotinamide-nucleotide
adenylyltransferase; members of this family are presumed
to share this activity. E. coli NadR has also been found
to regulate the import of its substrate, nicotinamide
ribonucleotide, but it is not known if the other members
of this model share that activity.
Length = 325
Score = 26.3 bits (58), Expect = 5.7
Identities = 12/28 (42%), Positives = 15/28 (53%), Gaps = 3/28 (10%)
Query: 7 ILGPIMAGKTVLANALCDL---TTAEEY 31
ILG GK+ L N L + T+A EY
Sbjct: 167 ILGGESTGKSTLVNKLAAVFNTTSAWEY 194
>gnl|CDD|184377 PRK13894, PRK13894, conjugal transfer ATPase TrbB; Provisional.
Length = 319
Score = 26.2 bits (58), Expect = 5.7
Identities = 14/37 (37%), Positives = 23/37 (62%), Gaps = 2/37 (5%)
Query: 5 ILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVE 41
IL++G +GKT L NA+ + ++ PT+ V I+E
Sbjct: 151 ILVIGGTGSGKTTLVNAIINEMVIQD--PTERVFIIE 185
>gnl|CDD|182993 PRK11144, modC, molybdate transporter ATP-binding protein;
Provisional.
Length = 352
Score = 26.4 bits (59), Expect = 5.8
Identities = 14/28 (50%), Positives = 16/28 (57%), Gaps = 6/28 (21%)
Query: 13 AGKTVLANALCDLTTAEEYHPTQGVRIV 40
AGKT L NA+ LT P +G RIV
Sbjct: 35 AGKTSLINAISGLTR-----PQKG-RIV 56
>gnl|CDD|234011 TIGR02782, TrbB_P, P-type conjugative transfer ATPase TrbB. The
TrbB protein is found in the trb locus of Agrobacterium
Ti plasmids where it is involved in the type IV
secretion system for plasmid conjugative transfer. TrbB
is a homolog of the vir system VirB11 ATPase , and the
Flp pilus sytem ATPase TadA [Cellular processes,
Conjugation].
Length = 299
Score = 26.2 bits (58), Expect = 5.8
Identities = 17/37 (45%), Positives = 22/37 (59%), Gaps = 2/37 (5%)
Query: 5 ILILGPIMAGKTVLANALCDLTTAEEYHPTQGVRIVE 41
IL++G +GKT LANAL L + PT V I+E
Sbjct: 135 ILVVGGTGSGKTTLANAL--LAEIAKNDPTDRVVIIE 169
>gnl|CDD|232949 TIGR00382, clpX, endopeptidase Clp ATP-binding regulatory subunit
(clpX). A member of the ATP-dependent proteases, ClpX
has ATP-dependent chaperone activity and is required for
specific ATP-dependent proteolytic activities expressed
by ClpPX. The gene is also found to be involved in
stress tolerance in Bacillus subtilis and is essential
for the efficient acquisition of genes specifying type
IA and IB restriction [Protein fate, Protein folding and
stabilization, Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 413
Score = 26.3 bits (58), Expect = 5.8
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 2 KIKILILGPIMAGKTVLANAL 22
K IL++GP +GKT+LA L
Sbjct: 116 KSNILLIGPTGSGKTLLAQTL 136
>gnl|CDD|169652 PRK09087, PRK09087, hypothetical protein; Validated.
Length = 226
Score = 26.2 bits (58), Expect = 6.1
Identities = 11/31 (35%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 5 ILIL-GPIMAGKTVLANALCDLTTAEEYHPT 34
+++L GP+ +GKT LA+ + + A HP
Sbjct: 46 VVVLAGPVGSGKTHLASIWREKSDALLIHPN 76
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 26.3 bits (58), Expect = 6.2
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 5 ILILGPIMAGKTVLANALCDLTTA 28
+L+ GP GKT+LA A+ TTA
Sbjct: 182 VLLYGPPGTGKTMLAKAVAHHTTA 205
>gnl|CDD|132060 TIGR03015, pepcterm_ATPase, putative secretion ATPase, PEP-CTERM
locus subfamily. Members of this protein are marked as
probable ATPases by the nucleotide binding P-loop motif
GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of
helicases, and extensive homology to ATPases of
MSHA-type pilus systems and to GspA proteins associated
with type II protein secretion systems [Protein fate,
Protein and peptide secretion and trafficking].
Length = 269
Score = 26.2 bits (58), Expect = 6.5
Identities = 20/71 (28%), Positives = 25/71 (35%), Gaps = 17/71 (23%)
Query: 38 RIVECEHSYALDTSKTE--IELWDTSGDHKFESV-W---PAFQRDVHGIIFVFNSGVPGH 91
RI+ H LD +T IE H+ E P F I F+ G+P
Sbjct: 182 RIIASCHLGPLDREETREYIE-------HRLERAGNRDAPVFSEGAFDAIHRFSRGIPRL 234
Query: 92 I----SELLLF 98
I LLL
Sbjct: 235 INILCDRLLLS 245
>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
cellular Activities) superfamily represents an ancient
group of ATPases belonging to the ASCE (for additional
strand, catalytic E) division of the P-loop NTPase
fold. The ASCE division also includes ABC, RecA-like,
VirD4-like, PilT-like, and SF1/2 helicases. Members of
the AAA+ ATPases function as molecular chaperons,
ATPase subunits of proteases, helicases, or
nucleic-acid stimulated ATPases. The AAA+ proteins
contain several distinct features in addition to the
conserved alpha-beta-alpha core domain structure and
the Walker A and B motifs of the P-loop NTPases.
Length = 151
Score = 26.0 bits (57), Expect = 6.5
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 5 ILILGPIMAGKTVLANALC 23
+L+ GP GKT LA A+
Sbjct: 22 LLLYGPPGTGKTTLARAIA 40
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 26.3 bits (59), Expect = 6.6
Identities = 13/28 (46%), Positives = 14/28 (50%), Gaps = 5/28 (17%)
Query: 5 ILILGPIMAGKTVLANALCDLTTAEEYH 32
ILI G AGK+ A AL AE Y
Sbjct: 260 ILIAGAPGAGKSTFAQAL-----AEFYA 282
>gnl|CDD|234988 PRK01889, PRK01889, GTPase RsgA; Reviewed.
Length = 356
Score = 26.0 bits (58), Expect = 6.6
Identities = 13/34 (38%), Positives = 16/34 (47%), Gaps = 4/34 (11%)
Query: 5 ILILGPIMAGKTVLANALCDLTTAEEYHPTQGVR 38
+ +LG GK+ L NAL EE T VR
Sbjct: 198 VALLGSSGVGKSTLVNALLG----EEVQKTGAVR 227
>gnl|CDD|213180 cd03213, ABCG_EPDR, Eye pigment and drug resistance transporter
subfamily G of the ATP-binding cassette superfamily.
ABCG transporters are involved in eye pigment (EP)
precursor transport, regulation of lipid-trafficking
mechanisms, and pleiotropic drug resistance (DR). DR is
a well-described phenomenon occurring in fungi and
shares several similarities with processes in bacteria
and higher eukaryotes. Compared to other members of the
ABC transporter subfamilies, the ABCG transporter
family is composed of proteins that have an ATP-binding
cassette domain at the N-terminus and a TM
(transmembrane) domain at the C-terminus.
Length = 194
Score = 26.0 bits (58), Expect = 6.6
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 5 ILILGPIMAGKTVLANAL 22
I+GP AGK+ L NAL
Sbjct: 38 TAIMGPSGAGKSTLLNAL 55
>gnl|CDD|223679 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 26.0 bits (58), Expect = 6.8
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 5 ILILGPIMAGKTVLANALCDL 25
+L++GP GKT+LA+ L L
Sbjct: 201 LLLVGPPGTGKTMLASRLPGL 221
>gnl|CDD|213195 cd03228, ABCC_MRP_Like, ATP-binding cassette domain of multidrug
resistance protein-like transporters. The MRP
(Multidrug Resistance Protein)-like transporters are
involved in drug, peptide, and lipid export. They
belong to the subfamily C of the ATP-binding cassette
(ABC) superfamily of transport proteins. The ABCC
subfamily contains transporters with a diverse
functional spectrum that includes ion transport, cell
surface receptor, and toxin secretion activities. The
MRP-like family, similar to all ABC proteins, have a
common four-domain core structure constituted by two
membrane-spanning domains, each composed of six
transmembrane (TM) helices, and two nucleotide-binding
domains (NBD). ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 171
Score = 25.8 bits (58), Expect = 7.0
Identities = 14/37 (37%), Positives = 19/37 (51%), Gaps = 6/37 (16%)
Query: 4 KILILGPIMAGKTVLANALCDLTTAEEYHPTQG-VRI 39
K+ I+GP +GK+ L L L Y PT G + I
Sbjct: 30 KVAIVGPSGSGKSTLLKLLLRL-----YDPTSGEILI 61
>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 = 25.7 bits (56), Expect = 7.7
Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 6/40 (15%)
Query: 29 EEYHPTQGVRIVECEHSYALDTSKTEIEL--WDTSGDHKF 66
++Y T GV + H T++ I WDT+G KF
Sbjct: 22 KKYVATLGVEV----HPLVFHTNRGPIRFNVWDTAGQEKF 57
>gnl|CDD|225982 COG3451, VirB4, Type IV secretory pathway, VirB4 components
[Intracellular trafficking and secretion].
Length = 796
Score = 26.2 bits (58), Expect = 8.2
Identities = 11/18 (61%), Positives = 13/18 (72%)
Query: 6 LILGPIMAGKTVLANALC 23
LI+GP AGKTVL + L
Sbjct: 440 LIIGPTGAGKTVLLSFLL 457
>gnl|CDD|224140 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 408
Score = 25.6 bits (57), Expect = 9.7
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 2 KIKILILGPIMAGKTVLANAL 22
K IL++GP +GKT+LA L
Sbjct: 97 KSNILLIGPTGSGKTLLAQTL 117
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
0.321 0.138 0.428
Gapped
Lambda K H
0.267 0.0740 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,717,983
Number of extensions: 571245
Number of successful extensions: 862
Number of sequences better than 10.0: 1
Number of HSP's gapped: 822
Number of HSP's successfully gapped: 180
Length of query: 135
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 48
Effective length of database: 7,078,804
Effective search space: 339782592
Effective search space used: 339782592
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.2 bits)