RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2792
(173 letters)
>gnl|CDD|206713 cd04146, RERG_RasL11_like, Ras-related and Estrogen-Regulated
Growth inhibitor (RERG) and Ras-like 11 (RasL11)-like
families. RERG (Ras-related and Estrogen- Regulated
Growth inhibitor) and Ras-like 11 are members of a novel
subfamily of Ras that were identified based on their
behavior in breast and prostate tumors, respectively.
RERG expression was decreased or lost in a significant
fraction of primary human breast tumors that lack
estrogen receptor and are correlated with poor clinical
prognosis. Elevated RERG expression correlated with
favorable patient outcome in a breast tumor subtype that
is positive for estrogen receptor expression. In
contrast to most Ras proteins, RERG overexpression
inhibited the growth of breast tumor cells in vitro and
in vivo. RasL11 was found to be ubiquitously expressed
in human tissue, but down-regulated in prostate tumors.
Both RERG and RasL11 lack the C-terminal CaaX
prenylation motif, where a = an aliphatic amino acid and
X = any amino acid, and are localized primarily in the
cytoplasm. Both are believed to have tumor suppressor
activity.
Length = 166
Score = 97.0 bits (242), Expect = 5e-26
Identities = 37/94 (39%), Positives = 52/94 (55%), Gaps = 1/94 (1%)
Query: 16 WADGCIIVYSLIDKESFDYAVSTLQNLQR-HRAVNNVPVMLLANKLDLEHLRQVDESLGR 74
WADG ++VYS+ D+ SFD LQ ++ + +PV+L+ NK DL H RQV G+
Sbjct: 72 WADGFVLVYSITDRSSFDVVSQLLQLIREIKKRDGEIPVILVGNKADLLHSRQVSTEEGQ 131
Query: 75 STAVKYNCTFHEVSVADNSPAIYQAFDHLLTESR 108
A++ C F EVS A+N + F L E R
Sbjct: 132 KLALELGCLFFEVSAAENYLEVQNVFHELCREVR 165
>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 = 78.7 bits (195), Expect = 5e-19
Identities = 29/87 (33%), Positives = 45/87 (51%), Gaps = 2/87 (2%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRST 76
A G I+VY + ++ESF+ L L+ + A N+P++L+ NK DLE RQV +
Sbjct: 73 AHGAILVYDVTNRESFENLDKWLNELKEY-APPNIPIILVGNKSDLEDERQVSTEEAQQF 131
Query: 77 AVKYNCTFHEVSVADNSPAIYQAFDHL 103
A + F E S + +AF+ L
Sbjct: 132 AKENGLLFFETSAKTGE-NVDEAFESL 157
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 78.3 bits (194), Expect = 6e-19
Identities = 31/90 (34%), Positives = 50/90 (55%), Gaps = 2/90 (2%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRST 76
A G ++VY + ++ESF+ + L+ L+ + A NV +ML+ NK DLE RQV +
Sbjct: 73 AVGALLVYDITNRESFENLENWLKELREY-ASPNVVIMLVGNKSDLEEQRQVSREEAEAF 131
Query: 77 AVKYNCTFHEVSVADNSPAIYQAFDHLLTE 106
A ++ F E S N+ + +AF+ L E
Sbjct: 132 AEEHGLPFFETSAKTNT-NVEEAFEELARE 160
>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 = 77.9 bits (193), Expect = 1e-18
Identities = 31/90 (34%), Positives = 48/90 (53%), Gaps = 2/90 (2%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRST 76
A G ++VY + ++SF+ L+ + RH A NVP++L+ NK DLE R V G +
Sbjct: 72 AQGFLLVYDITSRDSFENVKKWLEEILRH-ADENVPIVLVGNKCDLEDQRVVSTEEGEAL 130
Query: 77 AVKYNCTFHEVSVADNSPAIYQAFDHLLTE 106
A + F E S A + + +AF+ L E
Sbjct: 131 AKELGLPFMETS-AKTNENVEEAFEELARE 159
>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 = 74.9 bits (185), Expect = 1e-17
Identities = 33/93 (35%), Positives = 52/93 (55%), Gaps = 1/93 (1%)
Query: 14 ICWADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLG 73
I DG I+VYS+ +ESF+ + + + R + +VP++L+ NK DLE+ RQV G
Sbjct: 68 IRNGDGFILVYSITSRESFEEIKNIREQILRVKDKEDVPIVLVGNKCDLENERQVSTEEG 127
Query: 74 RSTAVKYNCTFHEVSVADNSPAIYQAFDHLLTE 106
+ A ++ C F E S N I + F+ L+ E
Sbjct: 128 EALAEEWGCPFLETSAKTNIN-IDELFNTLVRE 159
>gnl|CDD|197466 smart00010, small_GTPase, Small GTPase of the Ras superfamily;
ill-defined subfamily. SMART predicts Ras-like small
GTPases of the ARF, RAB, RAN, RAS, and SAR subfamilies.
Others that could not be classified in this way are
predicted to be members of the small GTPase superfamily
without predictions of the subfamily.
Length = 166
Score = 75.3 bits (186), Expect = 1e-17
Identities = 30/92 (32%), Positives = 54/92 (58%), Gaps = 3/92 (3%)
Query: 18 DGCIIVYSLIDKESFDYAVSTLQN-LQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRST 76
+G ++VYS+ D++SF+ ++ + + R + ++VP++L+ NK DLE+ R V G+
Sbjct: 75 EGFLLVYSITDRQSFE-EIAKFREQILRVKDRDDVPIVLVGNKCDLENERVVSTEEGKEL 133
Query: 77 AVKYNCTFHEVSVADNSPAIYQAFDHLLTESR 108
A ++ C F E S A + +AF L+ E R
Sbjct: 134 ARQWGCPFLETS-AKERINVDEAFYDLVREIR 164
>gnl|CDD|214541 smart00173, RAS, Ras subfamily of RAS small GTPases. Similar in
fold and function to the bacterial EF-Tu GTPase. p21Ras
couples receptor Tyr kinases and G protein receptors to
protein kinase cascades.
Length = 164
Score = 72.2 bits (178), Expect = 2e-16
Identities = 30/92 (32%), Positives = 52/92 (56%), Gaps = 3/92 (3%)
Query: 18 DGCIIVYSLIDKESFDYAVSTLQN-LQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRST 76
+G ++VYS+ D++SF+ + + + R + ++VP++L+ NK DLE R V G+
Sbjct: 73 EGFLLVYSITDRQSFE-EIKKFREQILRVKDRDDVPIVLVGNKCDLESERVVSTEEGKEL 131
Query: 77 AVKYNCTFHEVSVADNSPAIYQAFDHLLTESR 108
A ++ C F E S A + +AF L+ E R
Sbjct: 132 ARQWGCPFLETS-AKERVNVDEAFYDLVREIR 162
>gnl|CDD|206715 cd04148, RGK, Rem, Rem2, Rad, Gem/Kir (RGK) subfamily of Ras
GTPases. RGK subfamily. The RGK (Rem, Rem2, Rad,
Gem/Kir) subfamily of Ras GTPases are expressed in a
tissue-specific manner and are dynamically regulated by
transcriptional and posttranscriptional mechanisms in
response to environmental cues. RGK proteins bind to the
beta subunit of L-type calcium channels, causing
functional down-regulation of these voltage-dependent
calcium channels, and either termination of
calcium-dependent secretion or modulation of electrical
conduction and contractile function. Inhibition of
L-type calcium channels by Rem2 may provide a mechanism
for modulating calcium-triggered exocytosis in
hormone-secreting cells, and has been proposed to
influence the secretion of insulin in pancreatic beta
cells. RGK proteins also interact with and inhibit the
Rho/Rho kinase pathway to modulate remodeling of the
cytoskeleton. Two characteristics of RGK proteins cited
in the literature are N-terminal and C-terminal
extensions beyond the GTPase domain typical of Ras
superfamily members. The N-terminal extension is not
conserved among family members; the C-terminal extension
is reported to be conserved among the family and lack
the CaaX prenylation motif typical of
membrane-associated Ras proteins. However, a putative
CaaX motif has been identified in the alignment of the
C-terminal residues of this CD.
Length = 219
Score = 68.2 bits (167), Expect = 2e-14
Identities = 29/74 (39%), Positives = 43/74 (58%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRST 76
D +IVYS+ D+ SF+ A L+R R ++P++L+ NK DL R+V GR+
Sbjct: 73 GDAYVIVYSVTDRSSFEKASELRIQLRRARQAEDIPIILVGNKSDLVRSREVSVQEGRAC 132
Query: 77 AVKYNCTFHEVSVA 90
AV ++C F E S A
Sbjct: 133 AVVFDCKFIETSAA 146
Score = 27.0 bits (60), Expect = 4.3
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 139 PTHQGGTVVVCNKSDLCRSRV 159
++V NKSDL RSR
Sbjct: 103 QAEDIPIILVGNKSDLVRSRE 123
>gnl|CDD|206712 cd04141, Rit_Rin_Ric, Ras-like protein in all tissues (Rit),
Ras-like protein in neurons (Rin) and Ras-related
protein which interacts with calmodulin (Ric). Rit
(Ras-like protein in all tissues), Rin (Ras-like protein
in neurons) and Ric (Ras-related protein which interacts
with calmodulin) form a subfamily with several unique
structural and functional characteristics. These
proteins all lack a the C-terminal CaaX lipid-binding
motif typical of Ras family proteins, and Rin and Ric
contain calmodulin-binding domains. Rin, which is
expressed only in neurons, induces neurite outgrowth in
rat pheochromocytoma cells through its association with
calmodulin and its activation of endogenous Rac/cdc42.
Rit, which is ubiquitously expressed in mammals,
inhibits growth-factor withdrawl-mediated apoptosis and
induces neurite extension in pheochromocytoma cells. Rit
and Rin are both able to form a ternary complex with
PAR6, a cell polarity-regulating protein, and Rac/cdc42.
This ternary complex is proposed to have physiological
function in processes such as tumorigenesis. Activated
Ric is likely to signal in parallel with the Ras pathway
or stimulate the Ras pathway at some upstream point, and
binding of calmodulin to Ric may negatively regulate Ric
activity.
Length = 172
Score = 65.6 bits (160), Expect = 7e-14
Identities = 30/73 (41%), Positives = 44/73 (60%)
Query: 18 DGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRSTA 77
+G II YS+ D+ SF A + + R R ++P++L+ NK+DLE RQV GR+ A
Sbjct: 75 EGFIICYSVTDRHSFQEASEFKELITRVRLTEDIPLVLVGNKVDLEQQRQVTTEEGRNLA 134
Query: 78 VKYNCTFHEVSVA 90
++NC F E S A
Sbjct: 135 REFNCPFFETSAA 147
>gnl|CDD|206709 cd04137, RheB, Ras Homolog Enriched in Brain (RheB) is a small
GTPase. Rheb (Ras Homolog Enriched in Brain) subfamily.
Rheb was initially identified in rat brain, where its
expression is elevated by seizures or by long-term
potentiation. It is expressed ubiquitously, with
elevated levels in muscle and brain. Rheb functions as
an important mediator between the tuberous sclerosis
complex proteins, TSC1 and TSC2, and the mammalian
target of rapamycin (TOR) kinase to stimulate cell
growth. TOR kinase regulates cell growth by controlling
nutrient availability, growth factors, and the energy
status of the cell. TSC1 and TSC2 form a dimeric complex
that has tumor suppressor activity, and TSC2 is a GTPase
activating protein (GAP) for Rheb. The TSC1/TSC2 complex
inhibits the activation of TOR kinase through Rheb. Rheb
has also been shown to induce the formation of large
cytoplasmic vacuoles in a process that is dependent on
the GTPase cycle of Rheb, but independent of the TOR
kinase, suggesting Rheb plays a role in endocytic
trafficking that leads to cell growth and cell-cycle
progression. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras proteins.
Length = 180
Score = 64.2 bits (157), Expect = 3e-13
Identities = 29/99 (29%), Positives = 46/99 (46%), Gaps = 4/99 (4%)
Query: 19 GCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRSTAV 78
G I+VYS+ ++SF+ + +VP++L+ NK DL RQV G+ A
Sbjct: 75 GYILVYSVTSRKSFEVVKVIYDKILDMLGKESVPIVLVGNKSDLHMERQVSAEEGKKLAE 134
Query: 79 KYNCTFHEVSVADNSPAIYQAFDHLLTE---SRGGPPSG 114
+ F E S +N + +AF+ L+ E P G
Sbjct: 135 SWGAAFLESSAKENE-NVEEAFELLIEEIEKVENPLPPG 172
>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 = 62.3 bits (152), Expect = 9e-13
Identities = 30/87 (34%), Positives = 48/87 (55%), Gaps = 2/87 (2%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRST 76
A G I+VY + D++SF+ + ++N+ H A +V ML+ NK D+E R V + G +
Sbjct: 76 AMGIILVYDITDEKSFENIKNWMRNIDEH-ASEDVERMLVGNKCDMEEKRVVSKEEGEAL 134
Query: 77 AVKYNCTFHEVSVADNSPAIYQAFDHL 103
A +Y F E S A + + +AF L
Sbjct: 135 AREYGIKFLETS-AKANINVEEAFLTL 160
>gnl|CDD|206660 cd01868, Rab11_like, Rab GTPase family 11 (Rab11)-like includes
Rab11a, Rab11b, and Rab25. Rab11a, Rab11b, and Rab25
are closely related, evolutionary conserved Rab proteins
that are differentially expressed. Rab11a is
ubiquitously synthesized, Rab11b is enriched in brain
and heart and Rab25 is only found in epithelia. Rab11/25
proteins seem to regulate recycling pathways from
endosomes to the plasma membrane and to the trans-Golgi
network. Furthermore, Rab11a is thought to function in
the histamine-induced fusion of tubulovesicles
containing H+, K+ ATPase with the plasma membrane in
gastric parietal cells and in insulin-stimulated
insertion of GLUT4 in the plasma membrane of
cardiomyocytes. Overexpression of Rab25 has recently
been observed in ovarian cancer and breast cancer, and
has been correlated with worsened outcomes in both
diseases. In addition, Rab25 overexpression has also
been observed in prostate cancer, transitional cell
carcinoma of the bladder, and invasive breast tumor
cells. GTPase activating proteins (GAPs) interact with
GTP-bound Rab and accelerate the hydrolysis of GTP to
GDP. Guanine nucleotide exchange factors (GEFs) interact
with GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 165
Score = 61.4 bits (150), Expect = 2e-12
Identities = 33/90 (36%), Positives = 50/90 (55%), Gaps = 2/90 (2%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRST 76
A G ++VY + K +F+ L+ L+ H A +N+ +ML+ NK DL HLR V ++
Sbjct: 76 AVGALLVYDITKKSTFENVERWLKELRDH-ADSNIVIMLVGNKSDLRHLRAVPTEEAKAF 134
Query: 77 AVKYNCTFHEVSVADNSPAIYQAFDHLLTE 106
A K +F E S A + + +AF LLTE
Sbjct: 135 AEKNGLSFIETS-ALDGTNVEEAFKQLLTE 163
>gnl|CDD|206653 cd01860, Rab5_related, Rab-related GTPase family includes Rab5 and
Rab22; regulates early endosome fusion. The
Rab5-related subfamily includes Rab5 and Rab22 of
mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of plants.
The members of this subfamily are involved in
endocytosis and endocytic-sorting pathways. In mammals,
Rab5 GTPases localize to early endosomes and regulate
fusion of clathrin-coated vesicles to early endosomes
and fusion between early endosomes. In yeast, Ypt51p
family members similarly regulate membrane trafficking
through prevacuolar compartments. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 163
Score = 61.4 bits (150), Expect = 2e-12
Identities = 25/68 (36%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 21 IIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRSTAVKY 80
I+VY + +ESF+ A S ++ LQ H N+ + L NK DLE RQV + A +
Sbjct: 78 IVVYDITSEESFEKAKSWVKELQEH-GPPNIVIALAGNKADLESKRQVSTEEAQEYADEN 136
Query: 81 NCTFHEVS 88
F E S
Sbjct: 137 GLLFMETS 144
>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 = 61.0 bits (148), Expect = 3e-12
Identities = 25/74 (33%), Positives = 42/74 (56%)
Query: 19 GCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRSTAV 78
G I+VYSL+++++F + R + VP++L+ NK+DLE R+V + GR+ A
Sbjct: 75 GFIVVYSLVNQQTFQDIKPMRDQIVRVKGYEKVPIILVGNKVDLESEREVSSAEGRALAE 134
Query: 79 KYNCTFHEVSVADN 92
++ C F E S
Sbjct: 135 EWGCPFMETSAKSK 148
>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 = 56.8 bits (138), Expect = 9e-11
Identities = 27/87 (31%), Positives = 42/87 (48%), Gaps = 2/87 (2%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRST 76
ADG I+VY + D +SF ++ L++ R NN+ ++++ NK+DLE R V +S
Sbjct: 73 ADGAILVYDITDADSFQKVKKWIKELKQMRG-NNISLVIVGNKIDLERQRVVSKSEAEEY 131
Query: 77 AVKYNCTFHEVSVADNSPAIYQAFDHL 103
A E S I + F L
Sbjct: 132 AKSVGAKHFETSAKTGK-GIEELFLSL 157
>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 = 57.0 bits (138), Expect = 9e-11
Identities = 31/84 (36%), Positives = 45/84 (53%), Gaps = 2/84 (2%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRST 76
A G IIVY + D+ESF+ LQ + R+ A NV +L+ NK DL + VD + +
Sbjct: 75 AHGIIIVYDVTDQESFNNVKQWLQEIDRY-ASENVNKLLVGNKCDLTDKKVVDYTEAKEF 133
Query: 77 AVKYNCTFHEVSVADNSPAIYQAF 100
A + F E S A N+ + +AF
Sbjct: 134 ADELGIPFLETS-AKNATNVEEAF 156
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 56.8 bits (137), Expect = 2e-10
Identities = 29/90 (32%), Positives = 46/90 (51%), Gaps = 1/90 (1%)
Query: 19 GCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRSTAV 78
G + VYS+ + SF+ S + + R + + VP++L+ NK DL+ RQV G+ A
Sbjct: 79 GFLCVYSITSRSSFEEIASFREQILRVKDKDRVPMILVGNKCDLDSERQVSTGEGQELAK 138
Query: 79 KYNCTFHEVSVADNSPAIYQAFDHLLTESR 108
+ F E S A + +AF L+ E R
Sbjct: 139 SFGIPFLETS-AKQRVNVDEAFYELVREIR 167
>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 = 55.9 bits (135), Expect = 2e-10
Identities = 26/86 (30%), Positives = 45/86 (52%), Gaps = 1/86 (1%)
Query: 18 DGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRSTA 77
+G ++V+S+ D+ SF+ + R + + P++L+ NK DLEH RQV G+ A
Sbjct: 75 EGFLLVFSVTDRGSFEEVDKFHTQILRVKDRDEFPMILVGNKADLEHQRQVSREEGQELA 134
Query: 78 VKYNCTFHEVSVADNSPAIYQAFDHL 103
+ + E S A + + +AF L
Sbjct: 135 RQLKIPYIETS-AKDRVNVDKAFHDL 159
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 56.5 bits (136), Expect = 3e-10
Identities = 43/136 (31%), Positives = 66/136 (48%), Gaps = 14/136 (10%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRST 76
A G ++VY + +++FD L+ L+ H A +N+ +M+ NK DL HLR V E G++
Sbjct: 85 AVGALLVYDITKRQTFDNVQRWLRELRDH-ADSNIVIMMAGNKSDLNHLRSVAEEDGQAL 143
Query: 77 AVKYNCTFHEVSVADNSPAIYQAFDHLLTESRGGPPSGIHKIRKFSVTKMLGTLIGGSNK 136
A K +F E S A + + +AF +L E I+ I K L +N
Sbjct: 144 AEKEGLSFLETS-ALEATNVEKAFQTILLE--------IYHIIS---KKALAAQEAAANS 191
Query: 137 SPPTHQGGTVVVCNKS 152
P QG T+ V + S
Sbjct: 192 GLPG-QGTTINVADTS 206
>gnl|CDD|133375 cd04175, Rap1, Rap1 family GTPase consists of Rap1a and Rap1b
isoforms. The Rap1 subgroup is part of the Rap
subfamily of the Ras family. It can be further divided
into the Rap1a and Rap1b isoforms. In humans, Rap1a and
Rap1b share 95% sequence homology, but are products of
two different genes located on chromosomes 1 and 12,
respectively. Rap1a is sometimes called smg p21 or Krev1
in the older literature. Rap1 proteins are believed to
perform different cellular functions, depending on the
isoform, its subcellular localization, and the effector
proteins it binds. For example, in rat salivary gland,
neutrophils, and platelets, Rap1 localizes to secretory
granules and is believed to regulate exocytosis or the
formation of secretory granules. Rap1 has also been
shown to localize in the Golgi of rat fibroblasts,
zymogen granules, plasma membrane, and the microsomal
membrane of pancreatic acini, as well as in the
endocytic compartment of skeletal muscle cells and
fibroblasts. High expression of Rap1 has been observed
in the nucleus of human oropharyngeal squamous cell
carcinomas (SCCs) and cell lines; interestingly, in the
SCCs, the active GTP-bound form localized to the
nucleus, while the inactive GDP-bound form localized to
the cytoplasm. Rap1 plays a role in phagocytosis by
controlling the binding of adhesion receptors (typically
integrins) to their ligands. In yeast, Rap1 has been
implicated in multiple functions, including activation
and silencing of transcription and maintenance of
telomeres. Rap1a, which is stimulated by T-cell receptor
(TCR) activation, is a positive regulator of T cells by
directing integrin activation and augmenting lymphocyte
responses. In murine hippocampal neurons, Rap1b
determines which neurite will become the axon and
directs the recruitment of Cdc42, which is required for
formation of dendrites and axons. In murine platelets,
Rap1b is required for normal homeostasis in vivo and is
involved in integrin activation. Most Ras proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 164
Score = 53.7 bits (129), Expect = 2e-09
Identities = 22/70 (31%), Positives = 40/70 (57%)
Query: 19 GCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRSTAV 78
G ++VYS+ + +F+ + + R + +VP++L+ NK DLE R V + G++ A
Sbjct: 75 GFVLVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVGKEQGQNLAR 134
Query: 79 KYNCTFHEVS 88
++ C F E S
Sbjct: 135 QWGCAFLETS 144
>gnl|CDD|206710 cd04139, RalA_RalB, Ral (Ras-like) family containing highly
homologous RalA and RalB. The Ral (Ras-like) subfamily
consists of the highly homologous RalA and RalB. Ral
proteins are believed to play a crucial role in
tumorigenesis, metastasis, endocytosis, and actin
cytoskeleton dynamics. Despite their high sequence
similarity (>80% sequence identity), nonoverlapping and
opposing functions have been assigned to RalA and RalBs
in tumor migration. In human bladder and prostate cancer
cells, RalB promotes migration while RalA inhibits it. A
Ral-specific set of GEFs has been identified that are
activated by Ras binding. This RalGEF activity is
enhanced by Ras binding to another of its target
proteins, phosphatidylinositol 3-kinase (PI3K). Ral
effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and
the exocyst (Sec6/8) complex, a heterooctomeric protein
complex that is involved in tethering vesicles to
specific sites on the plasma membrane prior to
exocytosis. In rat kidney cells, RalB is required for
functional assembly of the exocyst and for localizing
the exocyst to the leading edge of migrating cells. In
human cancer cells, RalA is required to support
anchorage-independent proliferation and RalB is required
to suppress apoptosis. RalA has been shown to localize
to the plasma membrane while RalB is localized to the
intracellular vesicles. Most Ras proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Ras proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 163
Score = 53.6 bits (129), Expect = 2e-09
Identities = 23/71 (32%), Positives = 39/71 (54%)
Query: 18 DGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRSTA 77
+G ++V+S+ D ESF + + R + +NVP++L+ NK DLE RQV + A
Sbjct: 73 EGFLLVFSITDMESFTALAEFREQILRVKEDDNVPLLLVGNKCDLEDKRQVSVEEAANLA 132
Query: 78 VKYNCTFHEVS 88
++ + E S
Sbjct: 133 EQWGVNYVETS 143
>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 = 51.9 bits (125), Expect = 7e-09
Identities = 29/89 (32%), Positives = 46/89 (51%), Gaps = 2/89 (2%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRST 76
A G I+VY + +++FD + L L + + ML+ NK+D E+ R+V G+
Sbjct: 73 AQGVILVYDVTRRDTFDNLDTWLNELDTYSTNPDAVKMLVGNKIDKEN-REVTREEGQKF 131
Query: 77 AVKYNCTFHEVSVADNSPAIYQAFDHLLT 105
A K+N F E S A + QAF+ L+
Sbjct: 132 ARKHNMLFIETS-AKTRIGVQQAFEELVE 159
>gnl|CDD|133338 cd04138, H_N_K_Ras_like, Ras GTPase family containing H-Ras,N-Ras
and K-Ras4A/4B. H-Ras/N-Ras/K-Ras subfamily. H-Ras,
N-Ras, and K-Ras4A/4B are the prototypical members of
the Ras family. These isoforms generate distinct signal
outputs despite interacting with a common set of
activators and effectors, and are strongly associated
with oncogenic progression in tumor initiation. Mutated
versions of Ras that are insensitive to GAP stimulation
(and are therefore constitutively active) are found in a
significant fraction of human cancers. Many Ras guanine
nucleotide exchange factors (GEFs) have been identified.
They are sequestered in the cytosol until activation by
growth factors triggers recruitment to the plasma
membrane or Golgi, where the GEF colocalizes with Ras.
Active (GTP-bound) Ras interacts with several effector
proteins that stimulate a variety of diverse cytoplasmic
signaling activities. Some are known to positively
mediate the oncogenic properties of Ras, including Raf,
phosphatidylinositol 3-kinase (PI3K), RalGEFs, and
Tiam1. Others are proposed to play negative regulatory
roles in oncogenesis, including RASSF and NORE/MST1.
Most Ras proteins contain a lipid modification site at
the C-terminus, with a typical sequence motif CaaX,
where a = an aliphatic amino acid and X = any amino
acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 162
Score = 51.7 bits (124), Expect = 8e-09
Identities = 25/91 (27%), Positives = 48/91 (52%), Gaps = 2/91 (2%)
Query: 18 DGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRSTA 77
+G + V+++ ++SF+ + + ++R + ++VP++L+ NK DL R V G+ A
Sbjct: 74 EGFLCVFAINSRKSFEDIHTYREQIKRVKDSDDVPMVLVGNKCDLAA-RTVSTRQGQDLA 132
Query: 78 VKYNCTFHEVSVADNSPAIYQAFDHLLTESR 108
Y + E S A + +AF L+ E R
Sbjct: 133 KSYGIPYIETS-AKTRQGVEEAFYTLVREIR 162
>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 = 51.1 bits (123), Expect = 1e-08
Identities = 25/82 (30%), Positives = 40/82 (48%), Gaps = 2/82 (2%)
Query: 20 CIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRSTAVK 79
++VY + +++SFD + ++ R N+V ++L+ NK DL RQV G A +
Sbjct: 76 AVVVYDITNRQSFDNTDKWIDDV-RDERGNDVIIVLVGNKTDLSDKRQVSTEEGEKKAKE 134
Query: 80 YNCTFHEVSVADNSPAIYQAFD 101
N F E S A + Q F
Sbjct: 135 NNAMFIETS-AKAGHNVKQLFK 155
>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 = 51.0 bits (122), Expect = 1e-08
Identities = 24/71 (33%), Positives = 41/71 (57%), Gaps = 1/71 (1%)
Query: 19 GCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRSTAV 78
G +VYS+ ++SF+ + + R + +VP++L+ NK DLE R V + G++ A
Sbjct: 75 GFALVYSITAQQSFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVSKEEGQNLAR 134
Query: 79 KY-NCTFHEVS 88
++ NC F E S
Sbjct: 135 QWGNCPFLETS 145
>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 = 50.8 bits (122), Expect = 2e-08
Identities = 25/76 (32%), Positives = 37/76 (48%), Gaps = 4/76 (5%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTL----QNLQRHRAVNNVPVMLLANKLDLEHLRQVDESL 72
G ++VY + D++SF+ S L Q H + N+ V++ ANK+DL R V E
Sbjct: 73 TQGVLLVYDVTDRQSFEALDSWLKEMKQEGGPHGNMENIVVVVCANKIDLTKHRAVSEDE 132
Query: 73 GRSTAVKYNCTFHEVS 88
GR A + E S
Sbjct: 133 GRLWAESKGFKYFETS 148
>gnl|CDD|206711 cd04140, ARHI_like, A Ras homolog member I (ARHI). ARHI (A Ras
homolog member I) is a member of the Ras family with
several unique structural and functional properties.
ARHI is expressed in normal human ovarian and breast
tissue, but its expression is decreased or eliminated in
breast and ovarian cancer. ARHI contains an N-terminal
extension of 34 residues (human) that is required to
retain its tumor suppressive activity. Unlike most other
Ras family members, ARHI is maintained in the
constitutively active (GTP-bound) state in resting cells
and has modest GTPase activity. ARHI inhibits STAT3
(signal transducers and activators of transcription 3),
a latent transcription factor whose abnormal activation
plays a critical role in oncogenesis. Most Ras proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 165
Score = 49.1 bits (117), Expect = 7e-08
Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 21 IIVYSLIDKESFDYAVSTLQNLQRHRAVN--NVPVMLLANKLDLEHLRQVDESLGRSTAV 78
I+VYS+ K+S + + + + N +P+ML+ NK D R+V S G + A
Sbjct: 77 ILVYSITSKQSLEELKPIYELICEIKGNNLEKIPIMLVGNKCDESPSREVSSSEGAALAR 136
Query: 79 KYNCTFHEVSVADN 92
+NC F E S N
Sbjct: 137 TWNCAFMETSAKTN 150
>gnl|CDD|206658 cd01866, Rab2, Rab GTPase family 2 (Rab2). Rab2 is localized on
cis-Golgi membranes and interacts with Golgi matrix
proteins. Rab2 is also implicated in the maturation of
vesicular tubular clusters (VTCs), which are
microtubule-associated intermediates in transport
between the ER and Golgi apparatus. In plants, Rab2
regulates vesicle trafficking between the ER and the
Golgi bodies and is important to pollen tube growth.
GTPase activating proteins (GAPs) interact with
GTP-bound Rab and accelerate the hydrolysis of GTP to
GDP. Guanine nucleotide exchange factors (GEFs) interact
with GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 168
Score = 49.0 bits (117), Expect = 8e-08
Identities = 25/77 (32%), Positives = 45/77 (58%), Gaps = 1/77 (1%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRST 76
A G ++VY + +E+F++ S L++ ++H + +N+ +ML+ NK DLE R+V G +
Sbjct: 77 AAGALLVYDITRRETFNHLTSWLEDARQH-SNSNMTIMLIGNKCDLESRREVSYEEGEAF 135
Query: 77 AVKYNCTFHEVSVADNS 93
A ++ F E S S
Sbjct: 136 AREHGLIFMETSAKTAS 152
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 49.2 bits (117), Expect = 1e-07
Identities = 28/84 (33%), Positives = 47/84 (55%), Gaps = 2/84 (2%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRST 76
A G ++VY + +E+F++ S L++ ++H A N+ +ML+ NK DL H R V G
Sbjct: 79 AAGALLVYDITRRETFNHLASWLEDARQH-ANANMTIMLIGNKCDLAHRRAVSTEEGEQF 137
Query: 77 AVKYNCTFHEVSVADNSPAIYQAF 100
A ++ F E S A + + +AF
Sbjct: 138 AKEHGLIFMEAS-AKTAQNVEEAF 160
>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 = 47.1 bits (112), Expect = 4e-07
Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 2/78 (2%)
Query: 18 DGCIIVYSLIDKESFDYAVSTLQNLQR--HRAVNNVPVMLLANKLDLEHLRQVDESLGRS 75
+G I+VYS+ + +F+ + +QR + +VP+M++ NK D + R+V G +
Sbjct: 72 EGFILVYSITSRSTFERVERFREQIQRVKDESAADVPIMIVGNKCDKVYEREVSTEEGAA 131
Query: 76 TAVKYNCTFHEVSVADNS 93
A + C F E S N
Sbjct: 132 LARRLGCEFIEASAKTNV 149
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 47.0 bits (111), Expect = 5e-07
Identities = 24/68 (35%), Positives = 38/68 (55%), Gaps = 1/68 (1%)
Query: 21 IIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRSTAVKY 80
I+VY + +++SF+ +Q++ R +V + L+ NK DL LR+V G A +Y
Sbjct: 57 IVVYDITNRQSFENTTKWIQDILNERG-KDVIIALVGNKTDLGDLRKVTYEEGMQKAQEY 115
Query: 81 NCTFHEVS 88
N FHE S
Sbjct: 116 NTMFHETS 123
>gnl|CDD|206714 cd04147, Ras_dva, Ras - dorsal-ventral anterior localization
(Ras-dva) family. Ras-dva subfamily. Ras-dva (Ras -
dorsal-ventral anterior localization) subfamily consists
of a set of proteins characterized only in Xenopus
leavis, to date. In Xenopus Ras-dva expression is
activated by the transcription factor Otx2 and begins
during gastrulation throughout the anterior ectoderm.
Ras-dva expression is inhibited in the anterior neural
plate by factor Xanf1. Downregulation of Ras-dva results
in head development abnormalities through the inhibition
of several regulators of the anterior neural plate and
folds patterning, including Otx2, BF-1, Xag2, Pax6,
Slug, and Sox9. Downregulation of Ras-dva also
interferes with the FGF-8a signaling within the anterior
ectoderm. Most Ras proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins.
Length = 197
Score = 45.6 bits (108), Expect = 2e-06
Identities = 27/93 (29%), Positives = 46/93 (49%), Gaps = 2/93 (2%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRST 76
D +VYS+ D ESF+ + + + VP++++ NK+D RQV+ + ST
Sbjct: 71 GDAFALVYSVDDPESFEEVKRLREEILEVKEDKFVPIVVVGNKIDSLAERQVEAADALST 130
Query: 77 A-VKYNCTFHEVSVADNSPAIYQAFDHLLTESR 108
+ +N F E S DN + + F LL ++
Sbjct: 131 VELDWNNGFVEASAKDNE-NVTEVFKELLQQAN 162
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 45.7 bits (108), Expect = 2e-06
Identities = 18/58 (31%), Positives = 29/58 (50%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGR 74
A+G +IVY +ES D R A ++VP++L+ NK+DL + E +
Sbjct: 78 ANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVGNKIDLFDEQSSSEEILN 135
>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 = 45.2 bits (107), Expect = 3e-06
Identities = 29/94 (30%), Positives = 45/94 (47%), Gaps = 1/94 (1%)
Query: 11 TAMICWADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDE 70
TA A G ++++ L ++SF + + LQ H N ++L+ NK DL R+V E
Sbjct: 81 TAFFRDAMGFLLMFDLTSEQSFLNVRNWMSQLQAHAYCENPDIVLIGNKADLPDQREVSE 140
Query: 71 SLGRSTAVKYNCTFHEVSVADNSPAIYQAFDHLL 104
R A KY + E S A + +A + LL
Sbjct: 141 RQARELADKYGIPYFETSAA-TGQNVEKAVETLL 173
>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 = 44.0 bits (104), Expect = 5e-06
Identities = 30/90 (33%), Positives = 46/90 (51%), Gaps = 7/90 (7%)
Query: 6 TEGT--LTAM----ICWADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANK 59
T GT TAM I G ++VYS+ + S + + + R + +NVP++L+ NK
Sbjct: 56 TAGTEQFTAMRELYIKSGQGFLLVYSVTSEASLNELGELREQVLRIKDSDNVPMVLVGNK 115
Query: 60 LDLEHLRQVDESLGRSTAVKYNCT-FHEVS 88
DLE RQV G S + ++ F+E S
Sbjct: 116 ADLEDDRQVSREDGVSLSQQWGNVPFYETS 145
>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 = 43.6 bits (103), Expect = 6e-06
Identities = 19/76 (25%), Positives = 36/76 (47%), Gaps = 2/76 (2%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRST 76
A CI+V+S D+ESF+ S + ++ ++P++L+ K+DL + +
Sbjct: 75 AQACILVFSTTDRESFEAIESWKEKVE--AECGDIPMVLVQTKIDLLDQAVITNEEAEAL 132
Query: 77 AVKYNCTFHEVSVADN 92
A + SV D+
Sbjct: 133 AKRLQLPLFRTSVKDD 148
>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 = 43.6 bits (103), Expect = 7e-06
Identities = 24/90 (26%), Positives = 40/90 (44%), Gaps = 5/90 (5%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRST 76
AD ++V D+ES + A + R +P++L+ NK+DL R+V+E L
Sbjct: 76 ADLILLVVDSTDRESEEDAKLLILRRLRKE---GIPIILVGNKIDLLEEREVEELLRLEE 132
Query: 77 AVK-YNCTFHEVSVADNSPAIYQAFDHLLT 105
K EVS + + F+ L+
Sbjct: 133 LAKILGVPVFEVSAKTGE-GVDELFEKLIE 161
>gnl|CDD|206688 cd04101, RabL4, Rab GTPase-like family 4 (Rab-like4). RabL4
(Rab-like4) subfamily. RabL4s are novel proteins that
have high sequence similarity with Rab family members,
but display features that are distinct from Rabs, and
have been termed Rab-like. As in other Rab-like
proteins, RabL4 lacks a prenylation site at the
C-terminus. The specific function of RabL4 remains
unknown.
Length = 167
Score = 43.3 bits (102), Expect = 1e-05
Identities = 18/69 (26%), Positives = 34/69 (49%)
Query: 21 IIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRSTAVKY 80
+VY + ++ SF+ + ++ H + P +L+ NK DL R+VD + ++ A
Sbjct: 81 CVVYDVTNEVSFNNCSRWINRVRTHSHGLHTPGVLVGNKCDLTDRREVDAAQAQALAQAN 140
Query: 81 NCTFHEVSV 89
F+E S
Sbjct: 141 TLKFYETSA 149
>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 = 3e-05
Identities = 24/72 (33%), Positives = 37/72 (51%), Gaps = 2/72 (2%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRST 76
A G I+VY + ++ SFD ++ + H VP +L+ N+L L RQV ++
Sbjct: 79 AQGIILVYDITNRWSFDGIDRWIKEIDEH--APGVPKILVGNRLHLAFKRQVATEQAQAY 136
Query: 77 AVKYNCTFHEVS 88
A + TF EVS
Sbjct: 137 AERNGMTFFEVS 148
>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 = 40.9 bits (96), Expect = 4e-05
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 16 WADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVN-NVPVMLLANKL 60
WAD ++VY L D+ES + + L R + +PV+L+ NKL
Sbjct: 71 WADAILLVYDLTDRESLNEVSRLIAWLPNLRKLGGKIPVILVGNKL 116
>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 = 40.8 bits (96), Expect = 8e-05
Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 5/77 (6%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLE---HLRQVDESLG 73
+ G I V D+E F+ + S + + + A+ VP+++LANK DL + ++ E
Sbjct: 75 SHGVIYVIDSTDRERFNESKSAFEKVINNEALEGVPLLVLANKQDLPDALSVAEIKEVFD 134
Query: 74 RSTAV--KYNCTFHEVS 88
A+ + +C VS
Sbjct: 135 DCIALIGRRDCLVQPVS 151
>gnl|CDD|133267 cd01864, Rab19, Rab GTPase family 19 (Rab19). Rab19 subfamily.
Rab19 proteins are associated with Golgi stacks.
Similarity analysis indicated that Rab41 is closely
related to Rab19. However, the function of these Rabs is
not yet characterized. GTPase activating proteins (GAPs)
interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 165
Score = 40.5 bits (95), Expect = 8e-05
Identities = 26/90 (28%), Positives = 41/90 (45%), Gaps = 1/90 (1%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRST 76
A+G II Y + + SF+ +V +NV ++L+ NK DLE R+V +
Sbjct: 76 ANGAIIAYDITRRSSFE-SVPHWIEEVEKYGASNVVLLLIGNKCDLEEQREVLFEEACTL 134
Query: 77 AVKYNCTFHEVSVADNSPAIYQAFDHLLTE 106
A Y + A S + +AF + TE
Sbjct: 135 AEHYGILAVLETSAKESSNVEEAFLLMATE 164
>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 = 40.9 bits (96), Expect = 1e-04
Identities = 22/94 (23%), Positives = 43/94 (45%), Gaps = 10/94 (10%)
Query: 21 IIVYSLIDKESFDYAVSTLQN--------LQRHRAVNNVPVMLLANKLDLEHLRQVD-ES 71
I+V+SL ++ESF+ + + + +P+++ NK D + R+V +
Sbjct: 76 ILVFSLDNRESFEEVCRLREQILETKSCLKNKTKENVKIPMVICGNKADRDFPREVQRDE 135
Query: 72 LGRSTAVKYNCTFHEVSVADNSPAIYQAFDHLLT 105
+ + NC + EVS NS + + F L +
Sbjct: 136 VEQLVGGDENCAYFEVSAKKNS-NLDEMFRALFS 168
>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 = 39.9 bits (94), Expect = 1e-04
Identities = 22/90 (24%), Positives = 33/90 (36%), Gaps = 4/90 (4%)
Query: 18 DGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDE---SLGR 74
DG I V D+E + A + L L + P+++LANK DL E LG
Sbjct: 68 DGLIFVVDSSDRERIEEAKNELHKLLNEEELKGAPLLILANKQDLPGALTESELIELLGL 127
Query: 75 STAVKYNCTFHEVSVADNSPAIYQAFDHLL 104
+ S + + D L+
Sbjct: 128 ESIKGRRWHIQPCSAVTGD-GLDEGLDWLI 156
>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 = 38.7 bits (90), Expect = 4e-04
Identities = 30/94 (31%), Positives = 47/94 (50%), Gaps = 2/94 (2%)
Query: 11 TAMICWADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDE 70
TA A G I++Y + ++ESF+ AV + + +N V+L+ NK D+E R V
Sbjct: 68 TAYYRGAMGFILMYDITNEESFN-AVQDWSTQIKTYSWDNAQVILVGNKCDMEDERVVSA 126
Query: 71 SLGRSTAVKYNCTFHEVSVADNSPAIYQAFDHLL 104
GR A + F E S +N + Q F+ L+
Sbjct: 127 ERGRQLADQLGFEFFEASAKENI-NVKQVFERLV 159
>gnl|CDD|133303 cd04103, Centaurin_gamma, Centaurin gamma (CENTG) GTPase. The
centaurins (alpha, beta, gamma, and delta) are large,
multi-domain proteins that all contain an ArfGAP domain
and ankyrin repeats, and in some cases, numerous
additional domains. Centaurin gamma contains an
additional GTPase domain near its N-terminus. The
specific function of this GTPase domain has not been
well characterized, but centaurin gamma 2 (CENTG2) may
play a role in the development of autism. Centaurin
gamma 1 is also called PIKE (phosphatidyl inositol (PI)
3-kinase enhancer) and centaurin gamma 2 is also known
as AGAP (ArfGAP protein with a GTPase-like domain,
ankyrin repeats and a Pleckstrin homology domain) or
GGAP. Three isoforms of PIKE have been identified.
PIKE-S (short) and PIKE-L (long) are brain-specific
isoforms, with PIKE-S restricted to the nucleus and
PIKE-L found in multiple cellular compartments. A third
isoform, PIKE-A was identified in human glioblastoma
brain cancers and has been found in various tissues.
GGAP has been shown to have high GTPase activity due to
a direct intramolecular interaction between the
N-terminal GTPase domain and the C-terminal ArfGAP
domain. In human tissue, AGAP mRNA was detected in
skeletal muscle, kidney, placenta, brain, heart, colon,
and lung. Reduced expression levels were also observed
in the spleen, liver, and small intestine.
Length = 158
Score = 38.2 bits (89), Expect = 5e-04
Identities = 21/86 (24%), Positives = 40/86 (46%), Gaps = 6/86 (6%)
Query: 8 GTLTAMIC-WADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLA--NKLDLEH 64
G A W D I V+SL D+ SF L +R ++ +P++L+ + + +
Sbjct: 56 GAPDAQFAGWVDAVIFVFSLEDEASFQTVYRLYHQLSSYRNISEIPLILVGTQDAISASN 115
Query: 65 LRQVDESLGR--STAVKYNCTFHEVS 88
R +D++ R +K C+++E
Sbjct: 116 PRVIDDARARQLCADMK-RCSYYETC 140
>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 = 37.6 bits (88), Expect = 0.001
Identities = 28/97 (28%), Positives = 46/97 (47%), Gaps = 13/97 (13%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRH-------RAVNNVPVMLLANKLDLEHLRQVD 69
AD C++VY + + +SF+ +L + + R N P ++L NK+DLE RQV
Sbjct: 73 ADCCVLVYDVTNPKSFE----SLDSWRDEFLIQASPRDPENFPFVVLGNKIDLEEKRQVS 128
Query: 70 ESLGRSTAV-KYNCTFHEVSVADNSPAIYQAFDHLLT 105
+ K N + E S A + + QAF+ +
Sbjct: 129 TKKAQQWCKSKGNIPYFETS-AKEAINVDQAFETIAR 164
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 38.1 bits (88), Expect = 0.001
Identities = 27/88 (30%), Positives = 39/88 (44%), Gaps = 2/88 (2%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPV-MLLANKLDLEHLRQVDESLGRS 75
A G I+VY + +E+F + N V ML+ NK+D E R V G +
Sbjct: 86 AQGIILVYDVTRRETFTNLSDVWGKEVELYSTNQDCVKMLVGNKVDRESERDVSREEGMA 145
Query: 76 TAVKYNCTFHEVSVADNSPAIYQAFDHL 103
A ++ C F E S A + Q F+ L
Sbjct: 146 LAKEHGCLFLECS-AKTRENVEQCFEEL 172
>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 = 37.0 bits (86), Expect = 0.002
Identities = 25/89 (28%), Positives = 39/89 (43%), Gaps = 5/89 (5%)
Query: 21 IIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRSTAVKY 80
+ VY + + SF S ++ ++H N VP +L+ NK DL QV L + A +
Sbjct: 80 VFVYDVTNMASFHSLPSWIEECEQHSLPNEVPRILVGNKCDLREQIQVPTDLAQRFADAH 139
Query: 81 NCTFHEVSV-----ADNSPAIYQAFDHLL 104
+ E S D+ AI+ H L
Sbjct: 140 SMPLFETSAKDPSENDHVEAIFMTLAHKL 168
>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 = 0.002
Identities = 23/84 (27%), Positives = 38/84 (45%), Gaps = 2/84 (2%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRST 76
A G ++VY + + ++++ S L + + N V + L+ NK DLE R V +
Sbjct: 75 AAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTV-IFLIGNKADLEAQRDVTYEEAKQF 133
Query: 77 AVKYNCTFHEVSVADNSPAIYQAF 100
A + F E S A + AF
Sbjct: 134 ADENGLLFLECS-AKTGENVEDAF 156
>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 = 36.8 bits (85), Expect = 0.002
Identities = 23/90 (25%), Positives = 42/90 (46%), Gaps = 2/90 (2%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRST 76
A+ I+ Y + +ESF L+ ++++ A N V +L+ NK+DL R+V +
Sbjct: 80 ANALILTYDITCEESFRCLPEWLREIEQY-ANNKVITILVGNKIDLAERREVSQQRAEEF 138
Query: 77 AVKYNCTFHEVSVADNSPAIYQAFDHLLTE 106
+ + + E S A S + + F L
Sbjct: 139 SDAQDMYYLETS-AKESDNVEKLFLDLACR 167
>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 = 35.9 bits (83), Expect = 0.004
Identities = 18/52 (34%), Positives = 31/52 (59%), Gaps = 1/52 (1%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQV 68
A G ++VY + +ESF+ A++ R A ++ ++L+ NK DLE R+V
Sbjct: 73 AAGALLVYDITSRESFN-ALTNWLTDARTLASPDIVIILVGNKKDLEDDREV 123
>gnl|CDD|206680 cd01893, Miro1, Mitochondrial Rho family 1 (Miro1), N-terminal.
Miro1 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the N-terminal
GTPase domain of Miro proteins. These atypical Rho
GTPases have roles in mitochondrial homeostasis and
apoptosis. Most Rho proteins contain a lipid
modification site at the C-terminus; however, Miro is
one of few Rho subfamilies that lack this feature.
Length = 168
Score = 35.8 bits (83), Expect = 0.004
Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 1/57 (1%)
Query: 6 TEGTLTAMICWADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDL 62
L A I A+ +VYS+ + + + T R VP++L+ NK DL
Sbjct: 62 DRANLAAEIRKANVICLVYSVDRPSTLE-RIRTKWLPLIRRLGVKVPIILVGNKSDL 117
>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 = 36.3 bits (84), Expect = 0.004
Identities = 23/88 (26%), Positives = 41/88 (46%), Gaps = 2/88 (2%)
Query: 19 GCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRSTAV 78
G ++V+ + ++ESF++ L+ + H + +L+ +K DLE RQV A
Sbjct: 78 GVLLVFDITNRESFEHVHDWLEEARSHIQPHRPVFILVGHKCDLESQRQVTREEAEKLAK 137
Query: 79 KYNCTFHEVSVADNSPAIYQAFDHLLTE 106
+ E S + +AF LLT+
Sbjct: 138 DLGMKYIETSARTGDN-VEEAF-ELLTQ 163
>gnl|CDD|206699 cd04120, Rab12, Rab GTPase family 12 (Rab12). Rab12 was first
identified in canine cells, where it was localized to
the Golgi complex. The specific function of Rab12
remains unknown, and inconsistent results about its
cellular localization have been reported. More recent
studies have identified Rab12 associated with post-Golgi
vesicles, or with other small vesicle-like structures
but not with the Golgi complex. Most Rab GTPases contain
a lipid modification site at the C-terminus, with
sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation of
the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins.
Length = 202
Score = 35.8 bits (82), Expect = 0.005
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 2/77 (2%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRST 76
A G I+VY + KE+FD ++ + ++ A + ++L+ NKLD E R++ G
Sbjct: 73 AKGIILVYDITKKETFDDLPKWMKMIDKY-ASEDAELLLVGNKLDCETDREITRQQGEKF 131
Query: 77 AVKYN-CTFHEVSVADN 92
A + F E S DN
Sbjct: 132 AQQITGMRFCEASAKDN 148
>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 = 35.9 bits (83), Expect = 0.005
Identities = 16/54 (29%), Positives = 28/54 (51%), Gaps = 2/54 (3%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQR--HRAVNNVPVMLLANKLDLEHLRQV 68
A +VY + + +SF+ L +++ + ++L+ NK DLEH RQV
Sbjct: 74 AQAVCLVYDITNSQSFENLEDWLSVVKKVNEESETKPKMVLVGNKTDLEHNRQV 127
>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 = 35.6 bits (82), Expect = 0.006
Identities = 31/114 (27%), Positives = 48/114 (42%), Gaps = 6/114 (5%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRST 76
A +++Y + +K SFD + L + A ++V +MLL NK D+ R V G
Sbjct: 74 AHALLLLYDVTNKSSFDNIRAWLTEI-LEYAQSDVVIMLLGNKADMSGERVVKREDGERL 132
Query: 77 AVKYNCTFHEVSVADNSPAIYQAFDHLLTE--SRGG--PPSGIHKIRKFSVTKM 126
A +Y F E S A + AF + E R P KI+ + +
Sbjct: 133 AKEYGVPFMETS-AKTGLNVELAFTAVAKELKHRSVEQPDEPKFKIQDYVEKQK 185
>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 = 33.9 bits (78), Expect = 0.017
Identities = 16/46 (34%), Positives = 26/46 (56%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDL 62
DG + V D+ D + L+++ ++ + VPV+LLANK DL
Sbjct: 68 TDGLVYVVDSSDEARLDESQKELKHILKNEHIKGVPVVLLANKQDL 113
>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 = 34.2 bits (79), Expect = 0.019
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 3/49 (6%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNN---VPVMLLANKLDL 62
A G IIV+ + +F+ + +L + N +P +LLANK DL
Sbjct: 74 AVGAIIVFDVTRPSTFEAVLKWKADLDSKVTLPNGEPIPALLLANKCDL 122
>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 = 33.8 bits (78), Expect = 0.020
Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 8/63 (12%)
Query: 8 GTLTAMICW----ADGCIIVYSLID---KESFDYAVSTLQNLQRHRAVNNVPVMLLANKL 60
G A W + IV+ L+D E F + L +L + NVP+++L NK+
Sbjct: 72 GHEQARRVWKDYFPEVDGIVF-LVDAADPERFQESKEELDSLLNDEELANVPILILGNKI 130
Query: 61 DLE 63
D
Sbjct: 131 DKP 133
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 33.7 bits (78), Expect = 0.025
Identities = 14/45 (31%), Positives = 22/45 (48%)
Query: 18 DGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDL 62
D I V D++ + A L L + + P+++LANK DL
Sbjct: 83 DAVIFVVDSADRDRIEEAKEELHALLNEEELADAPLLILANKQDL 127
>gnl|CDD|133318 cd04118, Rab24, Rab GTPase family 24 (Rab24). Rab24 is distinct
from other Rabs in several ways. It exists primarily in
the GTP-bound state, having a low intrinsic GTPase
activity; it is not efficiently geranyl-geranylated at
the C-terminus; it does not form a detectable complex
with Rab GDP-dissociation inhibitors (GDIs); and it has
recently been shown to undergo tyrosine phosphorylation
when overexpressed in vitro. The specific function of
Rab24 still remains unknown. It is found in a transport
route between ER-cis-Golgi and late endocytic
compartments. It is putatively involved in an autophagic
pathway, possibly directing misfolded proteins in the ER
to degradative pathways. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 193
Score = 33.7 bits (77), Expect = 0.027
Identities = 26/79 (32%), Positives = 32/79 (40%), Gaps = 12/79 (15%)
Query: 17 ADGCIIVYSLIDKESFDYA---VSTLQNLQRHRAVNNVPVMLLANKLDL----EHLRQVD 69
A I+ Y L D SF+ A V LQNL+ H + L K DL LRQVD
Sbjct: 74 AKAAIVCYDLTDSSSFERAKFWVKELQNLEEH-----CKIYLCGTKSDLIEQDRSLRQVD 128
Query: 70 ESLGRSTAVKYNCTFHEVS 88
+ A + E S
Sbjct: 129 FHDVQDFADEIKAQHFETS 147
>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 = 32.3 bits (74), Expect = 0.060
Identities = 11/48 (22%), Positives = 20/48 (41%), Gaps = 1/48 (2%)
Query: 44 RHRAVNNVPVMLLANKLDLEHLRQVDESLGRSTAVKYNCTFHEVSVAD 91
H A + VP++L+ NK+DL + + + A +S
Sbjct: 103 IHHAESGVPIILVGNKIDLRDAK-LKTHVAFLFAKLNGEPIIPLSAET 149
>gnl|CDD|133342 cd04142, RRP22, Ras-related protein on chromosome 22 (RRP22)
family. RRP22 (Ras-related protein on chromosome 22)
subfamily consists of proteins that inhibit cell growth
and promote caspase-independent cell death. Unlike most
Ras proteins, RRP22 is down-regulated in many human
tumor cells due to promoter methylation. RRP22 localizes
to the nucleolus in a GTP-dependent manner, suggesting a
novel function in modulating transport of nucleolar
components. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras proteins.
Like most Ras family proteins, RRP22 is farnesylated.
Length = 198
Score = 32.1 bits (73), Expect = 0.096
Identities = 16/63 (25%), Positives = 25/63 (39%), Gaps = 12/63 (19%)
Query: 16 WADGC----------IIVYSLIDKESFDYAVSTLQNLQRHRAVNN--VPVMLLANKLDLE 63
W D I+VY + +SF Y Q + R N P++++ NK D +
Sbjct: 70 WMDPRFRGLRNSRAFILVYDICSPDSFHYVKLLRQQILETRPAGNKEPPIVVVGNKRDQQ 129
Query: 64 HLR 66
R
Sbjct: 130 RHR 132
>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 = 31.2 bits (71), Expect = 0.16
Identities = 16/46 (34%), Positives = 22/46 (47%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDL 62
D I V D++ F+ A L L + VPV++ ANK DL
Sbjct: 83 TDVLIYVIDSADRKRFEEAGQELVELLEEEKLAGVPVLVFANKQDL 128
>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 = 31.0 bits (70), Expect = 0.19
Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 5/77 (6%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRST 76
A CI+V+ + K ++ + L+ +R +P +++ANK+DL+ + +
Sbjct: 73 AHACILVFDVTRKITYKNLSKWYEELREYRP--EIPCIVVANKIDLD-PSVTQKKF--NF 127
Query: 77 AVKYNCTFHEVSVADNS 93
A K+N + VS AD +
Sbjct: 128 AEKHNLPLYYVSAADGT 144
>gnl|CDD|206705 cd04133, Rop_like, Rho-related protein from plants (Rop)-like. The
Rop (Rho-related protein from plants) subfamily plays a
role in diverse cellular processes, including
cytoskeletal organization, pollen and vegetative cell
growth, hormone responses, stress responses, and
pathogen resistance. Rops are able to regulate several
downstream pathways to amplify a specific signal by
acting as master switches early in the signaling
cascade. They transmit a variety of extracellular and
intracellular signals. Rops are involved in establishing
cell polarity in root-hair development, root-hair
elongation, pollen-tube growth, cell-shape formation,
responses to hormones such as abscisic acid (ABA) and
auxin, responses to abiotic stresses such as oxygen
deprivation, and disease resistance and disease
susceptibility. An individual Rop can have a unique
function or an overlapping function shared with other
Rop proteins; in addition, a given Rop-regulated
function can be controlled by one or multiple Rop
proteins. For example, Rop1, Rop3, and Rop5 are all
involved in pollen-tube growth; Rop2 plays a role in
response to low-oxygen environments, cell-morphology,
and root-hair development; root-hair development is also
regulated by Rop4 and Rop6; Rop6 is also responsible for
ABA response, and ABA response is also regulated by
Rop10. Plants retain some of the regulatory mechanisms
that are shared by other members of the Rho family, but
have also developed a number of unique modes for
regulating Rops. Unique RhoGEFs have been identified
that are exclusively active toward Rop proteins, such as
those containing the domain PRONE (plant-specific Rop
nucleotide exchanger). Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 173
Score = 31.0 bits (70), Expect = 0.22
Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQ 67
AD ++ +SLI K S++ + RH A VP++L+ KLDL +Q
Sbjct: 73 ADVFLLAFSLISKASYENVLKKWIPELRHYA-PGVPIVLVGTKLDLRDDKQ 122
>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 = 30.6 bits (70), Expect = 0.23
Identities = 10/43 (23%), Positives = 23/43 (53%), Gaps = 3/43 (6%)
Query: 21 IIVYSLIDKESFDYAVST-LQNLQRHRAVNNVPVMLLANKLDL 62
++ +S+ SF+ + ++ + NVP++L+ K+DL
Sbjct: 76 LLCFSVDSPSSFENVKTKWYPEIKHY--CPNVPIILVGTKIDL 116
>gnl|CDD|237511 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 31.4 bits (72), Expect = 0.23
Identities = 17/42 (40%), Positives = 25/42 (59%), Gaps = 5/42 (11%)
Query: 21 IIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDL 62
++V ++D FD+ S + L HR V N PV+L+ NK DL
Sbjct: 72 LVVN-VVD--IFDFNGSWIPGL--HRFVGNNPVLLVGNKADL 108
>gnl|CDD|206679 cd01892, Miro2, Mitochondrial Rho family 2 (Miro2), C-terminal.
Miro2 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the putative
GTPase domain in the C terminus of Miro proteins. These
atypical Rho GTPases have roles in mitochondrial
homeostasis and apoptosis. Most Rho proteins contain a
lipid modification site at the C-terminus; however, Miro
is one of few Rho subfamilies that lack this feature.
Length = 180
Score = 30.7 bits (70), Expect = 0.26
Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 3/52 (5%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQV 68
D +VY D SF Y + ++ + +P + +A K DL+ +Q
Sbjct: 78 CDVACLVYDSSDPNSFSYCAEVYK---KYFMLGEIPCLFVAAKADLDEQQQR 126
>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 = 30.4 bits (69), Expect = 0.26
Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 2/51 (3%)
Query: 22 IVY--SLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDE 70
IVY D+E + A + L +L ++ +P+++L NK DL VDE
Sbjct: 71 IVYVVDAADREKLEVAKNELHDLLEKPSLEGIPLLVLGNKNDLPGALSVDE 121
>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 = 30.5 bits (69), Expect = 0.27
Identities = 16/46 (34%), Positives = 24/46 (52%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDL 62
DG + V +D E + A + L + + VPV++LANK DL
Sbjct: 76 TDGIVFVVDSVDVERMEEAKTELHKITKFSENQGVPVLVLANKQDL 121
>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 = 30.6 bits (69), Expect = 0.29
Identities = 19/74 (25%), Positives = 35/74 (47%), Gaps = 2/74 (2%)
Query: 19 GCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRSTAV 78
G I+VY + + ESF LQ ++++ ++V +L+ NK D + V+ A
Sbjct: 81 GVIVVYDVTNGESFVNVKRWLQEIEQN--CDDVCKVLVGNKNDDPERKVVETEDAYKFAG 138
Query: 79 KYNCTFHEVSVADN 92
+ + E S +N
Sbjct: 139 QMGISLFETSAKEN 152
>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 = 29.9 bits (67), Expect = 0.49
Identities = 15/53 (28%), Positives = 24/53 (45%)
Query: 18 DGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDE 70
+G + + DKE F + L L + VP ++L NK+D + DE
Sbjct: 86 NGIVYLVDAYDKERFAESKRELDALLSDEELATVPFLILGNKIDAPYAASEDE 138
>gnl|CDD|182557 PRK10569, PRK10569, NAD(P)H-dependent FMN reductase; Provisional.
Length = 191
Score = 29.6 bits (67), Expect = 0.56
Identities = 24/67 (35%), Positives = 34/67 (50%), Gaps = 7/67 (10%)
Query: 9 TLTAMICWADGCII---VYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHL 65
T T + ADG I+ VY K SF A+ TL +L RA+ + V+ LA + H+
Sbjct: 59 TFTEQLAQADGLIVATPVY----KASFSGALKTLLDLLPERALEHKVVLPLATGGSVAHM 114
Query: 66 RQVDESL 72
VD +L
Sbjct: 115 LAVDYAL 121
>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 = 29.6 bits (67), Expect = 0.62
Identities = 17/76 (22%), Positives = 36/76 (47%), Gaps = 4/76 (5%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRST 76
II++ + + ++ + ++L R N+P++L NK+D++ R+V
Sbjct: 73 GQCAIIMFDVTSRVTYKNVPNWHRDLVR--VCENIPIVLCGNKVDIKD-RKVKPKQITFH 129
Query: 77 AVKYNCTFHEVSVADN 92
K N ++E+S N
Sbjct: 130 R-KKNLQYYEISAKSN 144
>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 = 29.2 bits (65), Expect = 0.72
Identities = 22/76 (28%), Positives = 36/76 (47%), Gaps = 1/76 (1%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRST 76
A G +VY + + S+ + + + ++ + A V +L+ NK D E RQV + G
Sbjct: 73 AQGIFLVYDISSERSYQHIMKWVSDVDEY-APEGVQKILIGNKADEEQKRQVGDEQGNKL 131
Query: 77 AVKYNCTFHEVSVADN 92
A +Y F E S N
Sbjct: 132 AKEYGMDFFETSACTN 147
>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 = 28.9 bits (65), Expect = 0.89
Identities = 10/26 (38%), Positives = 17/26 (65%)
Query: 38 TLQNLQRHRAVNNVPVMLLANKLDLE 63
L+ L +H V+ P+++LANK D +
Sbjct: 88 ILRELLQHPRVSGKPILVLANKQDKK 113
>gnl|CDD|215599 PLN03140, PLN03140, ABC transporter G family member; Provisional.
Length = 1470
Score = 29.4 bits (66), Expect = 1.1
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 5/29 (17%)
Query: 82 CTFHEVSVADNSPAIYQAFDHLLTESRGG 110
CT H+ S+ I++AFD LL RGG
Sbjct: 1074 CTIHQPSID-----IFEAFDELLLMKRGG 1097
>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 = 28.1 bits (63), Expect = 1.6
Identities = 7/42 (16%), Positives = 13/42 (30%)
Query: 52 PVMLLANKLDLEHLRQVDESLGRSTAVKYNCTFHEVSVADNS 93
PV+L+ +D + + H VS +
Sbjct: 108 PVILVGTHIDESCDEDILKKALNKKFPAIINDIHFVSCKNGK 149
>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 = 28.1 bits (63), Expect = 1.7
Identities = 13/46 (28%), Positives = 21/46 (45%)
Query: 18 DGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLE 63
D I+V D+E L + H + +++LANK DL+
Sbjct: 84 DAVILVIDSTDRERLPLTKEELYKMLAHEDLRKAVLLVLANKQDLK 129
>gnl|CDD|197554 smart00174, RHO, Rho (Ras homology) subfamily of Ras-like small
GTPases. Members of this subfamily of Ras-like small
GTPases include Cdc42 and Rac, as well as Rho isoforms.
Length = 174
Score = 28.0 bits (63), Expect = 1.8
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 15/53 (28%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQ-------RHRAVNNVPVMLLANKLDL 62
D +I +S+ SF+ N++ +H NVP++L+ KLDL
Sbjct: 70 TDVFLICFSVDSPASFE-------NVKEKWYPEVKHFC-PNVPIILVGTKLDL 114
>gnl|CDD|133003 cd02509, GDP-M1P_Guanylyltransferase, GDP-M1P_Guanylyltransferase
catalyzes the formation of GDP-Mannose.
GDP-mannose-1-phosphate guanylyltransferase, also called
GDP-mannose pyrophosphorylase (GDP-MP), catalyzes the
formation of GDP-Mannose from mannose-1-phosphate and
GTP. Mannose is a key monosaccharide for glycosylation
of proteins and lipids. GDP-Mannose is the activated
donor for mannosylation of various biomolecules. This
enzyme is known to be bifunctional, as both
mannose-6-phosphate isomerase and mannose-1-phosphate
guanylyltransferase. This CD covers the N-terminal
GDP-mannose-1-phosphate guanylyltransferase domain,
whereas the isomerase function is located at the
C-terminal half. GDP-MP is a member of the
nucleotidyltransferase family of enzymes.
Length = 274
Score = 28.3 bits (64), Expect = 2.2
Identities = 6/14 (42%), Positives = 8/14 (57%)
Query: 23 VYSLIDKESFDYAV 36
++ I S DYAV
Sbjct: 236 AFAKIPSISIDYAV 249
>gnl|CDD|206647 cd00881, GTP_translation_factor, GTP translation factor family
primarily contains translation initiation, elongation
and release factors. The GTP translation factor family
consists primarily of translation initiation,
elongation, and release factors, which play specific
roles in protein translation. In addition, the family
includes Snu114p, a component of the U5 small nuclear
riboprotein particle which is a component of the
spliceosome and is involved in excision of introns,
TetM, a tetracycline resistance gene that protects the
ribosome from tetracycline binding, and the unusual
subfamily CysN/ATPS, which has an unrelated function
(ATP sulfurylase) acquired through lateral transfer of
the EF1-alpha gene and development of a new function.
Length = 183
Score = 28.0 bits (63), Expect = 2.2
Identities = 13/64 (20%), Positives = 26/64 (40%), Gaps = 6/64 (9%)
Query: 9 TLTAMICWADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQV 68
T+ + ADG ++V +D + + + +P+++ NK+D
Sbjct: 79 TVRGL-AQADGALLV---VD--ANEGVEPQTREHLNIALAGGLPIIVAVNKIDRVGEEDF 132
Query: 69 DESL 72
DE L
Sbjct: 133 DEVL 136
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 27.8 bits (62), Expect = 2.8
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 8/50 (16%)
Query: 46 RAVNNVPVMLLANKLDLEHLRQVDE---SLGRSTAVKYNCTFHEVSVADN 92
R N+P++L NK+D+++ RQV + R K N ++E+S N
Sbjct: 113 RVCENIPIVLCGNKVDVKN-RQVKAKQVTFHR----KKNLQYYEISAKSN 157
>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 = 27.6 bits (61), Expect = 3.1
Identities = 18/89 (20%), Positives = 37/89 (41%), Gaps = 4/89 (4%)
Query: 18 DGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHL---RQVDESLGR 74
G I V D++ D A L + + + +++ ANK DL ++ E LG
Sbjct: 82 QGLIFVVDSNDRDRIDEAREELHRMLNEDELRDAVILVFANKQDLPDAMKAAEITEKLGL 141
Query: 75 STAVKYNCTFHEVSVADNSPAIYQAFDHL 103
+++ + + + A + +Y+ L
Sbjct: 142 -HSIRDRNWYIQPTCATSGDGLYEGLTWL 169
>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 = 27.4 bits (61), Expect = 3.3
Identities = 20/92 (21%), Positives = 39/92 (42%), Gaps = 4/92 (4%)
Query: 18 DGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEH---LRQVDESLGR 74
G I V D+E A LQ + + + +++ ANK DL + +V + LG
Sbjct: 69 QGLIFVVDSNDRERIGEAREELQRMLNEDELRDAVLLVFANKQDLPNAMSAAEVTDKLGL 128
Query: 75 STAVKYNCTFHEVSVADNSPAIYQAFDHLLTE 106
+ ++ + + + A + +Y+ D L
Sbjct: 129 HS-LRNRNWYIQATCATSGDGLYEGLDWLSNN 159
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 27.1 bits (60), Expect = 3.6
Identities = 21/89 (23%), Positives = 39/89 (43%), Gaps = 4/89 (4%)
Query: 18 DGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEH---LRQVDESLGR 74
+G I V D+E A L+ + + + +++ ANK DL + +V E LG
Sbjct: 86 NGLIFVVDSNDRERIGDAREELERMLSEDELRDAVLLVFANKQDLPNAMSTTEVTEKLGL 145
Query: 75 STAVKYNCTFHEVSVADNSPAIYQAFDHL 103
+ V+ + + A + +Y+ D L
Sbjct: 146 HS-VRQRNWYIQGCCATTAQGLYEGLDWL 173
>gnl|CDD|213834 TIGR03597, GTPase_YqeH, ribosome biogenesis GTPase YqeH. This
family describes YqeH, a member of a larger family of
GTPases involved in ribosome biogenesis. Like YqlF, it
shows a cyclical permutation relative to GTPases EngA
(in which the GTPase domain is duplicated), Era, and
others. Members of this protein family are found in a
relatively small number of bacterial species, including
Bacillus subtilis but not Escherichia coli [Protein
synthesis, Other].
Length = 360
Score = 27.2 bits (61), Expect = 4.7
Identities = 17/42 (40%), Positives = 25/42 (59%), Gaps = 5/42 (11%)
Query: 21 IIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDL 62
+IVY ++D FD+ S + L R V PV+L+ NK+DL
Sbjct: 66 LIVY-VVD--IFDFEGSLIPEL--KRFVGGNPVLLVGNKIDL 102
>gnl|CDD|206730 cd04167, Snu114p, Snu114p, a spliceosome protein, is a GTPase.
Snu114p subfamily. Snu114p is one of several proteins
that make up the U5 small nuclear ribonucleoprotein
(snRNP) particle. U5 is a component of the spliceosome,
which catalyzes the splicing of pre-mRNA to remove
introns. Snu114p is homologous to EF-2, but typically
contains an additional N-terminal domain not found in
Ef-2. This protein is part of the GTP translation factor
family and the Ras superfamily, characterized by five
G-box motifs.
Length = 213
Score = 26.8 bits (60), Expect = 4.8
Identities = 12/45 (26%), Positives = 24/45 (53%), Gaps = 5/45 (11%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLD 61
DG ++V +++ + S + L RH +P++L+ NK+D
Sbjct: 95 CDGVVLVVDVVEGLT-----SVTERLIRHAIQEGLPMVLVINKID 134
>gnl|CDD|206663 cd01871, Rac1_like, Ras-related C3 botulinum toxin substrate 1 (rho
family, small GTP binding protein Rac1)-like consists of
Rac1, Rac2 and Rac3. The Rac1-like subfamily consists
of Rac1, Rac2, and Rac3 proteins, plus the splice
variant Rac1b that contains a 19-residue insertion near
switch II relative to Rac1. While Rac1 is ubiquitously
expressed, Rac2 and Rac3 are largely restricted to
hematopoietic and neural tissues respectively. Rac1
stimulates the formation of actin lamellipodia and
membrane ruffles. It also plays a role in cell-matrix
adhesion and cell anoikis. In intestinal epithelial
cells, Rac1 is an important regulator of migration and
mediates apoptosis. Rac1 is also essential for
RhoA-regulated actin stress fiber and focal adhesion
complex formation. In leukocytes, Rac1 and Rac2 have
distinct roles in regulating cell morphology, migration,
and invasion, but are not essential for macrophage
migration or chemotaxis. Rac3 has biochemical properties
that are closely related to Rac1, such as effector
interaction, nucleotide binding, and hydrolysis; Rac2
has a slower nucleotide association and is more
efficiently activated by the RacGEF Tiam1. Both Rac1 and
Rac3 have been implicated in the regulation of cell
migration and invasion in human metastatic breast
cancer. Most Rho proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Rho proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 174
Score = 26.7 bits (59), Expect = 4.9
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 21 IIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESL 72
+I +SL+ SF+ + RH N P++L+ KLDL + E L
Sbjct: 77 LICFSLVSPASFENVRAKWYPEVRHHC-PNTPIILVGTKLDLRDDKDTIEKL 127
>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 = 26.8 bits (59), Expect = 5.2
Identities = 20/88 (22%), Positives = 37/88 (42%), Gaps = 19/88 (21%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRA----------VNNVPVMLLANKLDLEHLR 66
+D C++ +S+ D +SF QNL + + P ++L NK+D+ R
Sbjct: 78 SDCCLLTFSVDDSQSF-------QNLSNWKKEFIYYADVKEPESFPFVILGNKIDIPE-R 129
Query: 67 QVDESLGRS-TAVKYNCTFHEVSVADNS 93
QV ++ + + E S D +
Sbjct: 130 QVSTEEAQAWCRDNGDYPYFETSAKDAT 157
>gnl|CDD|216035 pfam00632, HECT, HECT-domain (ubiquitin-transferase). The name
HECT comes from Homologous to the E6-AP Carboxyl
Terminus.
Length = 298
Score = 26.9 bits (60), Expect = 6.4
Identities = 10/22 (45%), Positives = 12/22 (54%)
Query: 54 MLLANKLDLEHLRQVDESLGRS 75
LL + LE L +VD L RS
Sbjct: 69 KLLGKPITLEDLEEVDPELYRS 90
>gnl|CDD|206748 cd01855, YqeH, Circularly permuted YqeH GTPase. YqeH is an
essential GTP-binding protein. Depletion of YqeH
induces an excess initiation of DNA replication,
suggesting that it negatively controls initiation of
chromosome replication. The YqeH subfamily is common in
eukaryotes and sporadically present in bacteria with
probable acquisition by plants from chloroplasts.
Proteins of the YqeH family contain all sequence motifs
typical of the vast class of P-loop-containing GTPases,
but show a circular permutation, with a G4-G1-G3
pattern of motifs as opposed to the regular G1-G3-G4
pattern seen in most GTPases.
Length = 191
Score = 26.5 bits (59), Expect = 6.9
Identities = 14/45 (31%), Positives = 25/45 (55%), Gaps = 5/45 (11%)
Query: 18 DGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDL 62
D ++V+ ++D FD+ S + L + PV+L+ NK+DL
Sbjct: 33 DNALVVH-VVD--IFDFPGSLIPGLAEL--IGAKPVILVGNKIDL 72
>gnl|CDD|221178 pfam11709, Mit_ribos_Mrp51, Mitochondrial ribosomal protein
subunit. This family is the mitochondrial ribosomal
small-subunit protein Mrp51. Its function is not
entirely clear, but deletion of the MRP51 gene
completely blocked mitochondrial gene expression.
Length = 302
Score = 26.6 bits (59), Expect = 7.1
Identities = 14/39 (35%), Positives = 16/39 (41%), Gaps = 3/39 (7%)
Query: 119 RKFSVTKMLGTLIGGSNKSPPTHQGGTVVVCNKSDLCRS 157
R V L L G+ S PTHQ V+ S L R
Sbjct: 14 RLAQVATPLSPLPRGNPSSHPTHQ---VITTPPSSLKRG 49
>gnl|CDD|180750 PRK06921, PRK06921, hypothetical protein; Provisional.
Length = 266
Score = 26.3 bits (58), Expect = 8.0
Identities = 12/61 (19%), Positives = 36/61 (59%), Gaps = 3/61 (4%)
Query: 33 DYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDESLGRSTAVKYNCTFHEVSVADN 92
++ + + ++ +R +N+ P+++ +++L ++ L +DE+LG + + C + V + +
Sbjct: 198 EWQIEQMYSVLNYRYLNHKPILI-SSELTIDELLDIDEALG--SRIVEMCKDYLVIIKGD 254
Query: 93 S 93
S
Sbjct: 255 S 255
>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 = 25.9 bits (57), Expect = 9.4
Identities = 19/54 (35%), Positives = 25/54 (46%), Gaps = 2/54 (3%)
Query: 17 ADGCIIVYSLIDKESFDYAVSTLQNLQRHRAVNNVPVMLLANKLDLEHLRQVDE 70
+ G I V D E A L L +H +P+++LANK DL R V E
Sbjct: 68 SQGLIFVVDSADSERLPLARQELHQLLQHPPD--LPLVVLANKQDLPAARSVQE 119
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.134 0.396
Gapped
Lambda K H
0.267 0.0585 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,476,338
Number of extensions: 743647
Number of successful extensions: 782
Number of sequences better than 10.0: 1
Number of HSP's gapped: 744
Number of HSP's successfully gapped: 110
Length of query: 173
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 83
Effective length of database: 6,945,742
Effective search space: 576496586
Effective search space used: 576496586
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.3 bits)