RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8722
(223 letters)
>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 = 299 bits (768), Expect = e-105
Identities = 116/162 (71%), Positives = 140/162 (86%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE 75
FKVVLLGEG VGKTS+VLRYVE+KFNEKH +T QASF K +NI GKR++LAIWDTAGQE
Sbjct: 1 FKVVLLGEGRVGKTSLVLRYVENKFNEKHESTTQASFFQKTVNIGGKRIDLAIWDTAGQE 60
Query: 76 RFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLEKQ 135
R+HALGPIYYR ++GA+LVYDITD DSF+KVK W+KELK+M GN+I L I GNKIDLE+Q
Sbjct: 61 RYHALGPIYYRDADGAILVYDITDADSFQKVKKWIKELKQMRGNNISLVIVGNKIDLERQ 120
Query: 136 RTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRML 177
R V + +AE+YA+SVGA HF TSAK +GIEE+FL L++RM+
Sbjct: 121 RVVSKSEAEEYAKSVGAKHFETSAKTGKGIEELFLSLAKRMI 162
>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 = 220 bits (564), Expect = 5e-74
Identities = 70/159 (44%), Positives = 112/159 (70%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE 75
FK+VL+G+ VGKTS++LR+V++KF+E + +T+ F +K + + GK++ L IWDTAGQE
Sbjct: 1 FKIVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGVDFKSKTIEVDGKKVKLQIWDTAGQE 60
Query: 76 RFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLEKQ 135
RF ++ YYR ++GA+LVYD+T+ +SFE + W+ ELK+ +I + + GNK DLE +
Sbjct: 61 RFRSITSSYYRGAHGAILVYDVTNRESFENLDKWLNELKEYAPPNIPIILVGNKSDLEDE 120
Query: 136 RTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQ 174
R V E+A+++A+ G + F TSAK ++E F L++
Sbjct: 121 RQVSTEEAQQFAKENGLLFFETSAKTGENVDEAFESLAR 159
>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 = 212 bits (541), Expect = 2e-70
Identities = 74/163 (45%), Positives = 115/163 (70%)
Query: 15 SFKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQ 74
FK+VLLG+ VGK+S+VLR+V+++F+E +T+ A+FL + +N+ + IWDTAGQ
Sbjct: 1 QFKLVLLGDSSVGKSSIVLRFVKNEFSENQESTIGAAFLTQTVNLDDTTVKFEIWDTAGQ 60
Query: 75 ERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLEK 134
ER+ +L P+YYR + A++VYDIT E+SFEK K+WVKEL++ +I + +AGNK DLE
Sbjct: 61 ERYRSLAPMYYRGAAAAIVVYDITSEESFEKAKSWVKELQEHGPPNIVIALAGNKADLES 120
Query: 135 QRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRML 177
+R V E+A++YA G + TSAK + E+F E+++++
Sbjct: 121 KRQVSTEEAQEYADENGLLFMETSAKTGENVNELFTEIARKLP 163
>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 = 209 bits (535), Expect = 1e-69
Identities = 75/162 (46%), Positives = 110/162 (67%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQER 76
K+VL+G+G VGK+S+++R+ ++KF E++I T+ F K + + GK + L IWDTAGQER
Sbjct: 1 KLVLVGDGGVGKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAGQER 60
Query: 77 FHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLEKQR 136
F AL P+YYR + G +LVYDIT DSFE VK W++E+ + ++ + + GNK DLE QR
Sbjct: 61 FRALRPLYYRGAQGFLLVYDITSRDSFENVKKWLEEILRHADENVPIVLVGNKCDLEDQR 120
Query: 137 TVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRMLE 178
V E+ E A+ +G TSAK N +EE F EL++ +L+
Sbjct: 121 VVSTEEGEALAKELGLPFMETSAKTNENVEEAFEELAREILK 162
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 203 bits (519), Expect = 5e-67
Identities = 74/164 (45%), Positives = 117/164 (71%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE 75
FK++L+G+ VGK+S++ R+ + KF+E++ +T+ F K + + GKR+ L IWDTAGQE
Sbjct: 1 FKIILIGDSGVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIEVDGKRVKLQIWDTAGQE 60
Query: 76 RFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLEKQ 135
RF ++ YYR + GA+LVYDIT+ +SFE ++NW+KEL++ ++ + + GNK DLE+Q
Sbjct: 61 RFRSITSSYYRGAVGALLVYDITNRESFENLENWLKELREYASPNVVIMLVGNKSDLEEQ 120
Query: 136 RTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRMLEK 179
R V +E+AE +A+ G F TSAK N +EE F EL++ +L++
Sbjct: 121 RQVSREEAEAFAEEHGLPFFETSAKTNTNVEEAFEELAREILKR 164
>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 = 178 bits (453), Expect = 4e-57
Identities = 72/166 (43%), Positives = 108/166 (65%)
Query: 14 YSFKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAG 73
Y FK++L+G+ VGK+ ++LR+ ED FN I+T+ F + + + GK++ L IWDTAG
Sbjct: 2 YLFKLLLIGDSGVGKSCLLLRFSEDSFNPSFISTIGIDFKIRTIELDGKKIKLQIWDTAG 61
Query: 74 QERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLE 133
QERF + YYR + G +LVYDITDE SFE +KNW++ + + D+ + GNK D+E
Sbjct: 62 QERFRTITTSYYRGAMGIILVYDITDEKSFENIKNWMRNIDEHASEDVERMLVGNKCDME 121
Query: 134 KQRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRMLEK 179
++R V +E+ E A+ G TSAK N +EE FL L++ +L+K
Sbjct: 122 EKRVVSKEEGEALAREYGIKFLETSAKANINVEEAFLTLAKDILKK 167
>gnl|CDD|206654 cd01861, Rab6, Rab GTPase family 6 (Rab6). Rab6 is involved in
microtubule-dependent transport pathways through the
Golgi and from endosomes to the Golgi. Rab6A of mammals
is implicated in retrograde transport through the Golgi
stack, and is also required for a slow,
COPI-independent, retrograde transport pathway from the
Golgi to the endoplasmic reticulum (ER). This pathway
may allow Golgi residents to be recycled through the ER
for scrutiny by ER quality-control systems. Yeast Ypt6p,
the homolog of the mammalian Rab6 GTPase, is not
essential for cell viability. Ypt6p acts in
endosome-to-Golgi, in intra-Golgi retrograde transport,
and possibly also in Golgi-to-ER trafficking. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 161
Score = 169 bits (431), Expect = 7e-54
Identities = 63/159 (39%), Positives = 101/159 (63%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE 75
K+V LG+ VGKTS++ R++ D F+ ++ T+ FL+K + + K + L +WDTAGQE
Sbjct: 1 HKLVFLGDQSVGKTSIITRFMYDTFDNQYQATIGIDFLSKTMYVDDKTVRLQLWDTAGQE 60
Query: 76 RFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLEKQ 135
RF +L P Y R S+ AV+VYDIT+ SF+ W+ +++ GND+ + + GNK DL +
Sbjct: 61 RFRSLIPSYIRDSSVAVVVYDITNRQSFDNTDKWIDDVRDERGNDVIIVLVGNKTDLSDK 120
Query: 136 RTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQ 174
R V E+ EK A+ A+ TSAK ++++F +++Q
Sbjct: 121 RQVSTEEGEKKAKENNAMFIETSAKAGHNVKQLFKKIAQ 159
>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 = 156 bits (397), Expect = 1e-48
Identities = 64/161 (39%), Positives = 100/161 (62%), Gaps = 2/161 (1%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE 75
K++L+G+ VGK+S++LR+ +D F+E +T+ F K + + GK++ LAIWDTAGQE
Sbjct: 1 LKILLIGDSGVGKSSLLLRFTDDTFDEDLSSTIGVDFKVKTVTVDGKKVKLAIWDTAGQE 60
Query: 76 RFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTI-AGNKIDLEK 134
RF L YYR + G +LVYD+T D+F+ + W+ EL N + + GNKID E
Sbjct: 61 RFRTLTSSYYRGAQGVILVYDVTRRDTFDNLDTWLNELDTYSTNPDAVKMLVGNKIDKE- 119
Query: 135 QRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQR 175
R V +E+ +K+A+ + TSAK G+++ F EL ++
Sbjct: 120 NREVTREEGQKFARKHNMLFIETSAKTRIGVQQAFEELVEK 160
>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 = 155 bits (395), Expect = 2e-48
Identities = 61/161 (37%), Positives = 99/161 (61%), Gaps = 2/161 (1%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQER 76
K+V+LG G VGK+++ +R+V +F E++ T++ S+ K++ + G+ L I DTAGQE
Sbjct: 1 KLVVLGAGGVGKSALTIRFVSGEFVEEYDPTIEDSY-RKQIVVDGETYTLDILDTAGQEE 59
Query: 77 FHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLG-NDICLTIAGNKIDLEKQ 135
F A+ Y R +G +LVY IT +SFE++KN +++ ++ D+ + + GNK DLE +
Sbjct: 60 FSAMRDQYIRNGDGFILVYSITSRESFEEIKNIREQILRVKDKEDVPIVLVGNKCDLENE 119
Query: 136 RTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRM 176
R V E+ E A+ G TSAK N I+E+F L + +
Sbjct: 120 RQVSTEEGEALAEEWGCPFLETSAKTNINIDELFNTLVREI 160
>gnl|CDD|206655 cd01862, Rab7, Rab GTPase family 7 (Rab7). Rab7 subfamily. Rab7 is
a small Rab GTPase that regulates vesicular traffic from
early to late endosomal stages of the endocytic pathway.
The yeast Ypt7 and mammalian Rab7 are both involved in
transport to the vacuole/lysosome, whereas Ypt7 is also
required for homotypic vacuole fusion. Mammalian Rab7 is
an essential participant in the autophagic pathway for
sequestration and targeting of cytoplasmic components to
the lytic compartment. Mammalian Rab7 is also proposed
to function as a tumor suppressor. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 172
Score = 154 bits (392), Expect = 9e-48
Identities = 65/172 (37%), Positives = 106/172 (61%), Gaps = 5/172 (2%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE 75
KV++LG+ VGKTS++ +YV KF+ ++ T+ A FL K++ + + + L IWDTAGQE
Sbjct: 1 LKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVTVDDRLVTLQIWDTAGQE 60
Query: 76 RFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLG----NDICLTIAGNKID 131
RF +LG +YR ++ VLVYD+T+ SFE + +W E + + GNKID
Sbjct: 61 RFQSLGVAFYRGADCCVLVYDVTNPKSFESLDSWRDEFLIQASPRDPENFPFVVLGNKID 120
Query: 132 LEKQRTVMQEDAEKYAQSVG-AVHFHTSAKMNRGIEEMFLELSQRMLEKAQE 182
LE++R V + A+++ +S G +F TSAK +++ F +++ LE+ +E
Sbjct: 121 LEEKRQVSTKKAQQWCKSKGNIPYFETSAKEAINVDQAFETIARLALEQEKE 172
>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 = 152 bits (387), Expect = 4e-47
Identities = 64/159 (40%), Positives = 98/159 (61%)
Query: 14 YSFKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAG 73
Y FK+VL+G+ VGK++++ R+ ++FN +T+ F + + I GK + IWDTAG
Sbjct: 2 YLFKIVLIGDSGVGKSNLLSRFTRNEFNLDSKSTIGVEFATRTIQIDGKTIKAQIWDTAG 61
Query: 74 QERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLE 133
QER+ A+ YYR + GA+LVYDIT + +FE V+ W+KEL+ ++I + + GNK DL
Sbjct: 62 QERYRAITSAYYRGAVGALLVYDITKKSTFENVERWLKELRDHADSNIVIMLVGNKSDLR 121
Query: 134 KQRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLEL 172
R V E+A+ +A+ G TSA +EE F +L
Sbjct: 122 HLRAVPTEEAKAFAEKNGLSFIETSALDGTNVEEAFKQL 160
>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 = 151 bits (384), Expect = 1e-46
Identities = 59/166 (35%), Positives = 106/166 (63%)
Query: 14 YSFKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAG 73
Y FK++L+G+ VGK+ ++LR+ +D + E +I+T+ F + + + GK + L IWDTAG
Sbjct: 1 YLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTVKLQIWDTAG 60
Query: 74 QERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLE 133
QERF + YYR ++G ++VYD+TD++SF VK W++E+ + ++ + GNK DL
Sbjct: 61 QERFRTITSSYYRGAHGIIIVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLT 120
Query: 134 KQRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRMLEK 179
++ V +A+++A +G TSAK +EE F+ +++ + ++
Sbjct: 121 DKKVVDYTEAKEFADELGIPFLETSAKNATNVEEAFMTMAREIKKR 166
>gnl|CDD|133267 cd01864, Rab19, Rab GTPase family 19 (Rab19). Rab19 subfamily.
Rab19 proteins are associated with Golgi stacks.
Similarity analysis indicated that Rab41 is closely
related to Rab19. However, the function of these Rabs is
not yet characterized. GTPase activating proteins (GAPs)
interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 165
Score = 150 bits (380), Expect = 4e-46
Identities = 71/161 (44%), Positives = 103/161 (63%), Gaps = 1/161 (0%)
Query: 14 YSFKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAG 73
+ FK++L+G+ VGKT VV R+ F+E+ T+ F K L I GKR+ L IWDTAG
Sbjct: 2 FLFKIILIGDSNVGKTCVVQRFKSGTFSERQGNTIGVDFTMKTLEIQGKRVKLQIWDTAG 61
Query: 74 QERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLE 133
QERF + YYR +NGA++ YDIT SFE V +W++E++K +++ L + GNK DLE
Sbjct: 62 QERFRTITQSYYRSANGAIIAYDITRRSSFESVPHWIEEVEKYGASNVVLLLIGNKCDLE 121
Query: 134 KQRTVMQEDAEKYAQSVGAVH-FHTSAKMNRGIEEMFLELS 173
+QR V+ E+A A+ G + TSAK + +EE FL ++
Sbjct: 122 EQREVLFEEACTLAEHYGILAVLETSAKESSNVEEAFLLMA 162
>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 = 143 bits (363), Expect = 5e-43
Identities = 75/217 (34%), Positives = 119/217 (54%), Gaps = 16/217 (7%)
Query: 14 YSFKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIA-GKRLNLAIWDTA 72
Y F+++++G+ VGK+S++ R+ E +F E T+ F ++ + I G R+ L +WDTA
Sbjct: 1 YQFRLIVIGDSTVGKSSLLKRFTEGRFAEVSDPTVGVDFFSRLIEIEPGVRIKLQLWDTA 60
Query: 73 GQERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKK-MLGNDICLTIAGNKID 131
GQERF ++ YYR S G +LV+DIT+ +SFE V +W++E + + + + G+K D
Sbjct: 61 GQERFRSITRSYYRNSVGVLLVFDITNRESFEHVHDWLEEARSHIQPHRPVFILVGHKCD 120
Query: 132 LEKQRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRMLEKAQEFDLAKASEL 191
LE QR V +E+AEK A+ +G + TSA+ +EE F L+Q + E K EL
Sbjct: 121 LESQRQVTREEAEKLAKDLGMKYIETSARTGDNVEEAFELLTQEIYE------RIKRGEL 174
Query: 192 S--------RRGSMRRNVVVVEDEDLPTSSSTKSGCC 220
+ G +E+ +S KS CC
Sbjct: 175 CALDGWDGVKSGFPAGRAFSLEERSPTFASPEKSCCC 211
>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 = 139 bits (352), Expect = 2e-41
Identities = 66/162 (40%), Positives = 110/162 (67%), Gaps = 1/162 (0%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE 75
FK++++G+ VGK+S++LR+ ++ F+ +ITT+ F + + I G+R+ L IWDTAGQE
Sbjct: 7 FKLLIIGDSGVGKSSLLLRFADNTFSGSYITTIGVDFKIRTVEINGERVKLQIWDTAGQE 66
Query: 76 RFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLEKQ 135
RF + YYR ++G ++VYD+T+ +SF VK W++E+++ +D+C + GNK D ++
Sbjct: 67 RFRTITSTYYRGTHGVIVVYDVTNGESFVNVKRWLQEIEQNC-DDVCKVLVGNKNDDPER 125
Query: 136 RTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRML 177
+ V EDA K+A +G F TSAK N +EEMF +++ +L
Sbjct: 126 KVVETEDAYKFAGQMGISLFETSAKENINVEEMFNCITELVL 167
>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 = 137 bits (347), Expect = 4e-41
Identities = 58/166 (34%), Positives = 103/166 (62%)
Query: 14 YSFKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAG 73
Y FK +++G+ VGK+ ++L++ + +F H T+ F + + I GK++ L IWDTAG
Sbjct: 3 YLFKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAG 62
Query: 74 QERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLE 133
QE F ++ YYR + GA+LVYDIT ++F + +W+++ ++ +++ + + GNK DLE
Sbjct: 63 QESFRSITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQHSNSNMTIMLIGNKCDLE 122
Query: 134 KQRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRMLEK 179
+R V E+ E +A+ G + TSAK +EE F+ ++ + +K
Sbjct: 123 SRREVSYEEGEAFAREHGLIFMETSAKTASNVEEAFINTAKEIYDK 168
>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 = 136 bits (344), Expect = 9e-41
Identities = 60/156 (38%), Positives = 95/156 (60%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE 75
FK +++G GK+ ++ +++E+KF + T+ F ++ +N+ GK + L IWDTAGQE
Sbjct: 1 FKFLIIGSAGTGKSCLLHQFIENKFKQDSNHTIGVEFGSRVVNVGGKSVKLQIWDTAGQE 60
Query: 76 RFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLEKQ 135
RF ++ YYR + GA+LVYDIT +SF + NW+ + + + DI + + GNK DLE
Sbjct: 61 RFRSVTRSYYRGAAGALLVYDITSRESFNALTNWLTDARTLASPDIVIILVGNKKDLEDD 120
Query: 136 RTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLE 171
R V +A ++AQ G + TSA +EE FL+
Sbjct: 121 REVTFLEASRFAQENGLLFLETSALTGENVEEAFLK 156
>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 = 136 bits (345), Expect = 1e-40
Identities = 66/172 (38%), Positives = 104/172 (60%), Gaps = 6/172 (3%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKF-NEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE 75
KVV+LG+ VGKTS+V RYV +F + T+ A+F+ K++ + + + L IWDTAG E
Sbjct: 2 KVVMLGKESVGKTSLVERYVHHRFLVGPYQNTIGAAFVAKRMVVGERVVTLGIWDTAGSE 61
Query: 76 RFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLEKQ 135
R+ A+ IYYR + A++ YD+TD SFE+ K WVKEL+ L + + G K DL +Q
Sbjct: 62 RYEAMSRIYYRGAKAAIVCYDLTDSSSFERAKFWVKELQN-LEEHCKIYLCGTKSDLIEQ 120
Query: 136 ----RTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRMLEKAQEF 183
R V D + +A + A HF TS+K + ++E+F ++++ + +A
Sbjct: 121 DRSLRQVDFHDVQDFADEIKAQHFETSSKTGQNVDELFQKVAEDFVSRANNQ 172
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 132 bits (334), Expect = 1e-38
Identities = 82/228 (35%), Positives = 127/228 (55%), Gaps = 19/228 (8%)
Query: 2 MANSLDRNSSSTYSFKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAG 61
MA+ +D Y FK+VL+G+ VGK++++ R+ ++F + +T+ F + L + G
Sbjct: 1 MAHRVDHEYD--YLFKIVLIGDSGVGKSNILSRFTRNEFCLESKSTIGVEFATRTLQVEG 58
Query: 62 KRLNLAIWDTAGQERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDI 121
K + IWDTAGQER+ A+ YYR + GA+LVYDIT +F+ V+ W++EL+ ++I
Sbjct: 59 KTVKAQIWDTAGQERYRAITSAYYRGAVGALLVYDITKRQTFDNVQRWLRELRDHADSNI 118
Query: 122 CLTIAGNKIDLEKQRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMF----LELSQRML 177
+ +AGNK DL R+V +ED + A+ G TSA +E+ F LE+ +
Sbjct: 119 VIMMAGNKSDLNHLRSVAEEDGQALAEKEGLSFLETSALEATNVEKAFQTILLEIYHIIS 178
Query: 178 EK---AQEFDLAKASELSRRGSMRRNVVVVEDEDLPTSSSTKSGCCLT 222
+K AQE A S L +G+ + V D TS + K GCC T
Sbjct: 179 KKALAAQE--AAANSGLPGQGT----TINVAD----TSGNNKRGCCST 216
>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 = 131 bits (330), Expect = 1e-38
Identities = 63/164 (38%), Positives = 104/164 (63%)
Query: 14 YSFKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAG 73
+ FK+VL+G VGKT +V R+ + F T+ F+ K + I G+++ L IWDTAG
Sbjct: 6 FLFKIVLIGNAGVGKTCLVRRFTQGLFPPGQGATIGVDFMIKTVEIKGEKIKLQIWDTAG 65
Query: 74 QERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLE 133
QERF ++ YYR +N +L YDIT E+SF + W++E+++ N + + GNKIDL
Sbjct: 66 QERFRSITQSYYRSANALILTYDITCEESFRCLPEWLREIEQYANNKVITILVGNKIDLA 125
Query: 134 KQRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRML 177
++R V Q+ AE+++ + + TSAK + +E++FL+L+ R++
Sbjct: 126 ERREVSQQRAEEFSDAQDMYYLETSAKESDNVEKLFLDLACRLI 169
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 132 bits (333), Expect = 2e-38
Identities = 66/212 (31%), Positives = 118/212 (55%), Gaps = 5/212 (2%)
Query: 11 SSTYSFKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWD 70
S Y FK +++G+ VGK+ ++L++ + +F H T+ F + + I K + L IWD
Sbjct: 2 SYAYLFKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDNKPIKLQIWD 61
Query: 71 TAGQERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKI 130
TAGQE F ++ YYR + GA+LVYDIT ++F + +W+++ ++ ++ + + GNK
Sbjct: 62 TAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLASWLEDARQHANANMTIMLIGNKC 121
Query: 131 DLEKQRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRMLEKAQE--FDLAKA 188
DL +R V E+ E++A+ G + SAK + +EE F++ + ++ +K Q+ FD++
Sbjct: 122 DLAHRRAVSTEEGEQFAKEHGLIFMEASAKTAQNVEEAFIKTAAKIYKKIQDGVFDVSNE 181
Query: 189 SELSRRGSMRRNVVVVEDEDLPTSSSTKSGCC 220
S + G + +SS GCC
Sbjct: 182 SYGIKVGYGAIPGASGGRD---GTSSQGGGCC 210
>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 = 130 bits (327), Expect = 1e-37
Identities = 64/164 (39%), Positives = 104/164 (63%), Gaps = 1/164 (0%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQER 76
+V+++G VGKTS++ R+ +D F E +T+ F K + + GK++ L IWDTAGQER
Sbjct: 2 QVIIIGSRGVGKTSLMERFTDDTFCEACKSTVGVDFKIKTVELRGKKIRLQIWDTAGQER 61
Query: 77 FHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLEKQR 136
F+++ YYR + G +LVYDIT +++F+ + W+K + K D L + GNK+D E R
Sbjct: 62 FNSITSAYYRSAKGIILVYDITKKETFDDLPKWMKMIDKYASEDAELLLVGNKLDCETDR 121
Query: 137 TVMQEDAEKYAQSVGAVHF-HTSAKMNRGIEEMFLELSQRMLEK 179
+ ++ EK+AQ + + F SAK N ++E+FL+L +L+K
Sbjct: 122 EITRQQGEKFAQQITGMRFCEASAKDNFNVDEIFLKLVDDILKK 165
>gnl|CDD|206657 cd01865, Rab3, Rab GTPase family 3 contains Rab3A, Rab3B, Rab3C and
Rab3D. The Rab3 subfamily contains Rab3A, Rab3B, Rab3C,
and Rab3D. All four isoforms were found in mouse brain
and endocrine tissues, with varying levels of
expression. Rab3A, Rab3B, and Rab3C localized to
synaptic and secretory vesicles; Rab3D was expressed at
high levels only in adipose tissue, exocrine glands, and
the endocrine pituitary, where it is localized to
cytoplasmic secretory granules. Rab3 appears to control
Ca2+-regulated exocytosis. The appropriate GDP/GTP
exchange cycle of Rab3A is required for Ca2+-regulated
exocytosis to occur, and interaction of the GTP-bound
form of Rab3A with effector molecule(s) is widely
believed to be essential for this process. Functionally,
most studies point toward a role for Rab3 in the
secretion of hormones and neurotransmitters. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 165
Score = 128 bits (322), Expect = 2e-37
Identities = 60/164 (36%), Positives = 96/164 (58%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE 75
FK++++G VGKTS + RY +D F ++T+ F K + KR+ L IWDTAGQE
Sbjct: 2 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVYRNDKRIKLQIWDTAGQE 61
Query: 76 RFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLEKQ 135
R+ + YYR + G +L+YDIT+E+SF V++W ++K ++ + + GNK D+E +
Sbjct: 62 RYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSWDNAQVILVGNKCDMEDE 121
Query: 136 RTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRMLEK 179
R V E + A +G F SAK N ++++F L + +K
Sbjct: 122 RVVSAERGRQLADQLGFEFFEASAKENINVKQVFERLVDIICDK 165
>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 = 124 bits (313), Expect = 6e-36
Identities = 56/158 (35%), Positives = 96/158 (60%), Gaps = 2/158 (1%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE 75
+K+V+LG G VGK+++ +++++ F + + T++ S+ K++ I G+ L I DTAGQE
Sbjct: 1 YKLVVLGSGGVGKSALTIQFIQGHFVDDYDPTIEDSYR-KQIEIDGEVCLLDILDTAGQE 59
Query: 76 RFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGND-ICLTIAGNKIDLEK 134
F A+ Y R G +LVY ITD SFE++K + +++ ++ D + + + GNK DLE
Sbjct: 60 EFSAMRDQYMRTGEGFLLVYSITDRQSFEEIKKFREQILRVKDRDDVPIVLVGNKCDLES 119
Query: 135 QRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLEL 172
+R V E+ ++ A+ G TSAK ++E F +L
Sbjct: 120 ERVVSTEEGKELARQWGCPFLETSAKERVNVDEAFYDL 157
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 125 bits (314), Expect = 1e-35
Identities = 76/223 (34%), Positives = 121/223 (54%), Gaps = 17/223 (7%)
Query: 2 MANSLDRNSSSTYSFKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAG 61
M +S ++S SFK++L+G+ VGK+S+++ ++ E T+ F K+L + G
Sbjct: 1 MGSSSGQSSGYDLSFKILLIGDSGVGKSSLLVSFISSSV-EDLAPTIGVDFKIKQLTVGG 59
Query: 62 KRLNLAIWDTAGQERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKN-WVKELKKMLGND 120
KRL L IWDTAGQERF L YYR + G +LVYD+T ++F + + W KE++ N
Sbjct: 60 KRLKLTIWDTAGQERFRTLTSSYYRNAQGIILVYDVTRRETFTNLSDVWGKEVELYSTNQ 119
Query: 121 ICL-TIAGNKIDLEKQRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRMLEK 179
C+ + GNK+D E +R V +E+ A+ G + SAK +E+ F EL+ +++E
Sbjct: 120 DCVKMLVGNKVDRESERDVSREEGMALAKEHGCLFLECSAKTRENVEQCFEELALKIME- 178
Query: 180 AQEFDLAKASELSRRGS--MRRNVVVVEDEDLPTSSSTKSGCC 220
L GS ++RN++ + E P + GCC
Sbjct: 179 --------VPSLLEEGSTAVKRNILKQKPEHQPPPN---GGCC 210
>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 = 122 bits (308), Expect = 2e-35
Identities = 56/166 (33%), Positives = 99/166 (59%)
Query: 14 YSFKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAG 73
Y FK +++G+ VGK+ ++ ++ E KF T+ F + + + G+++ L IWDTAG
Sbjct: 1 YIFKYIIIGDMGVGKSCLLHQFTEKKFMADCPHTIGVEFGTRIIEVNGQKIKLQIWDTAG 60
Query: 74 QERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLE 133
QERF A+ YYR + GA++VYDIT ++ + +W+ + + + + + + GNK DLE
Sbjct: 61 QERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTVIFLIGNKADLE 120
Query: 134 KQRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRMLEK 179
QR V E+A+++A G + SAK +E+ FLE ++++ +
Sbjct: 121 AQRDVTYEEAKQFADENGLLFLECSAKTGENVEDAFLETAKKIYQN 166
>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 = 121 bits (307), Expect = 4e-35
Identities = 56/158 (35%), Positives = 96/158 (60%), Gaps = 2/158 (1%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE 75
+K+V+LG G VGK+++ +++V+ F +++ T++ S+ K++ I G+ L I DTAGQE
Sbjct: 3 YKLVVLGGGGVGKSALTIQFVQGHFVDEYDPTIEDSYR-KQIEIDGEVCLLDILDTAGQE 61
Query: 76 RFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGND-ICLTIAGNKIDLEK 134
F A+ Y R G +LVY ITD SFE++ + +++ ++ D + + + GNK DLE
Sbjct: 62 EFSAMRDQYMRTGEGFLLVYSITDRQSFEEIAKFREQILRVKDRDDVPIVLVGNKCDLEN 121
Query: 135 QRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLEL 172
+R V E+ ++ A+ G TSAK ++E F +L
Sbjct: 122 ERVVSTEEGKELARQWGCPFLETSAKERINVDEAFYDL 159
>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 = 122 bits (307), Expect = 6e-35
Identities = 67/206 (32%), Positives = 109/206 (52%), Gaps = 16/206 (7%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKF-NEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQ 74
FKV+L+G+ VGKT +++R+ + F I T+ F NK + + G ++ L IWDTAGQ
Sbjct: 1 FKVMLVGDSGVGKTCLLVRFKDGAFLAGSFIATVGIQFTNKVVTVDGVKVKLQIWDTAGQ 60
Query: 75 ERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLEK 134
ERF ++ YYR ++ +L+YD+T++ SF+ ++ W+ E+ + +D+ + + GNK D+
Sbjct: 61 ERFRSVTHAYYRDAHALLLLYDVTNKSSFDNIRAWLTEILEYAQSDVVIMLLGNKADMSG 120
Query: 135 QRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRMLEKAQEFDLAKASELSRR 194
+R V +ED E+ A+ G TSAK +E F A A EL R
Sbjct: 121 ERVVKREDGERLAKEYGVPFMETSAKTGLNVELAF---------------TAVAKELKHR 165
Query: 195 GSMRRNVVVVEDEDLPTSSSTKSGCC 220
+ + + +D SGCC
Sbjct: 166 SVEQPDEPKFKIQDYVEKQKKSSGCC 191
>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 = 121 bits (305), Expect = 9e-35
Identities = 65/167 (38%), Positives = 95/167 (56%), Gaps = 10/167 (5%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE 75
KV+LLG+G VGK+S++ RYV +KF+ + T+ FLNK L + G + L IWDTAGQE
Sbjct: 6 LKVILLGDGGVGKSSLMNRYVTNKFDTQLFHTIGVEFLNKDLEVDGHFVTLQIWDTAGQE 65
Query: 76 RFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDI------CLTIAGNK 129
RF +L +YR S+ +L + + D SF+ + NW KE + D+ I GNK
Sbjct: 66 RFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEF--IYYADVKEPESFPFVILGNK 123
Query: 130 IDLEKQRTVMQEDAEKYAQSVG-AVHFHTSAKMNRGIEEMFLELSQR 175
ID+ +R V E+A+ + + G +F TSAK + F E +R
Sbjct: 124 IDIP-ERQVSTEEAQAWCRDNGDYPYFETSAKDATNVAAAFEEAVRR 169
>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 = 121 bits (305), Expect = 2e-34
Identities = 66/213 (30%), Positives = 107/213 (50%), Gaps = 20/213 (9%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRL-NLAIWDTAGQ 74
FKV+++G+ VGKTS++ RYV F++ + T+ F K + + L +WD AGQ
Sbjct: 1 FKVLVIGDLGVGKTSIIKRYVHGVFSQHYKATIGVDFALKVIEWDPNTVVRLQLWDIAGQ 60
Query: 75 ERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKEL-KKMLGND----ICLTIAGNK 129
ERF + +YY+ + GA++V+D+T +FE V W +L K+ + L +A NK
Sbjct: 61 ERFGGMTRVYYKGAVGAIIVFDVTRPSTFEAVLKWKADLDSKVTLPNGEPIPALLLA-NK 119
Query: 130 IDLEKQRT-VMQEDAEKYAQSVGAV-HFHTSAKMNRGIEEMFLELSQRMLEKAQEFDLAK 187
DL+K+R E +++ + G + F TSAK N IEE L + +L+ + +
Sbjct: 120 CDLKKERLAKDPEQMDQFCKENGFIGWFETSAKENINIEEAMRFLVKNILKNDKGLQSPE 179
Query: 188 ASELSRRGSMRRNVVVVEDEDLPTSSSTKSGCC 220
E + V D T++S CC
Sbjct: 180 PDEDN-----------VIDLKQETTTSKSKSCC 201
>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 = 120 bits (301), Expect = 2e-34
Identities = 58/163 (35%), Positives = 98/163 (60%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE 75
F+++L+G+ VGKT ++ R+ +++F+ HI+T+ F K + + G ++ + IWDTAGQE
Sbjct: 1 FRLLLIGDSGVGKTCLLCRFTDNEFHSSHISTIGVDFKMKTIEVDGIKVRIQIWDTAGQE 60
Query: 76 RFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLEKQ 135
R+ + YYR + G LVYDI+ E S++ + WV ++ + + + GNK D E++
Sbjct: 61 RYQTITKQYYRRAQGIFLVYDISSERSYQHIMKWVSDVDEYAPEGVQKILIGNKADEEQK 120
Query: 136 RTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRMLE 178
R V E K A+ G F TSA N+ I+E F L++ +L+
Sbjct: 121 RQVGDEQGNKLAKEYGMDFFETSACTNKNIKESFTRLTELVLQ 163
>gnl|CDD|133315 cd04115, Rab33B_Rab33A, Rab GTPase family 33 includes Rab33A and
Rab33B. Rab33B/Rab33A subfamily. Rab33B is ubiquitously
expressed in mouse tissues and cells, where it is
localized to the medial Golgi cisternae. It colocalizes
with alpha-mannose II. Together with the other cisternal
Rabs, Rab6A and Rab6A', it is believed to regulate the
Golgi response to stress and is likely a molecular
target in stress-activated signaling pathways. Rab33A
(previously known as S10) is expressed primarily in the
brain and immune system cells. In humans, it is located
on the X chromosome at Xq26 and its expression is
down-regulated in tuberculosis patients. Experimental
evidence suggests that Rab33A is a novel CD8+ T cell
factor that likely plays a role in tuberculosis disease
processes. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation of
the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 170
Score = 118 bits (298), Expect = 1e-33
Identities = 56/166 (33%), Positives = 98/166 (59%), Gaps = 5/166 (3%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE 75
FK++++G+ VGKT + R+ +F E+ T+ F + + I G+R+ + +WDTAGQE
Sbjct: 3 FKIIVIGDSNVGKTCLTYRFCAGRFPERTEATIGVDFRERTVEIDGERIKVQLWDTAGQE 62
Query: 76 RF-HALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKK-MLGNDICLTIAGNKIDLE 133
RF ++ YYR + V VYD+T+ SF + +W++E ++ L N++ + GNK DL
Sbjct: 63 RFRKSMVQHYYRNVHAVVFVYDVTNMASFHSLPSWIEECEQHSLPNEVPRILVGNKCDLR 122
Query: 134 KQRTVMQEDAEKYAQSVGAVHFHTSAKM---NRGIEEMFLELSQRM 176
+Q V + A+++A + F TSAK N +E +F+ L+ ++
Sbjct: 123 EQIQVPTDLAQRFADAHSMPLFETSAKDPSENDHVEAIFMTLAHKL 168
>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 = 118 bits (297), Expect = 2e-33
Identities = 62/168 (36%), Positives = 97/168 (57%), Gaps = 17/168 (10%)
Query: 14 YSFKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKL--------NIAGK--R 63
Y K++ LG+ VGKT+ + RY ++KFN K ITT+ F K++ +GK R
Sbjct: 3 YLIKLLALGDSGVGKTTFLYRYTDNKFNPKFITTVGIDFREKRVVYNSQGPDGTSGKAFR 62
Query: 64 LNLAIWDTAGQERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDIC- 122
++L +WDTAGQERF +L ++R + G +L++D+T E SF V+NW+ +L+ + C
Sbjct: 63 VHLQLWDTAGQERFRSLTTAFFRDAMGFLLMFDLTSEQSFLNVRNWMSQLQA---HAYCE 119
Query: 123 ---LTIAGNKIDLEKQRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEE 167
+ + GNK DL QR V + A + A G +F TSA + +E+
Sbjct: 120 NPDIVLIGNKADLPDQREVSERQARELADKYGIPYFETSAATGQNVEK 167
>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 = 115 bits (290), Expect = 1e-32
Identities = 57/161 (35%), Positives = 94/161 (58%), Gaps = 3/161 (1%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKK--LNIAGKRLNLAIWDTAGQ 74
KV+++G G VGK+S++ R+V+ F + + T+ FL K+ L + + + L +WDTAGQ
Sbjct: 2 KVIVVGNGNVGKSSMIQRFVKGIFTKDYKKTIGVDFLEKQIFLRQSDEDVRLMLWDTAGQ 61
Query: 75 ERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLEK 134
E F A+ YYR + +LV+ TD +SFE +++W KE + DI + + KIDL
Sbjct: 62 EEFDAITKAYYRGAQACILVFSTTDRESFEAIESW-KEKVEAECGDIPMVLVQTKIDLLD 120
Query: 135 QRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQR 175
Q + E+AE A+ + F TS K + + E+F L+++
Sbjct: 121 QAVITNEEAEALAKRLQLPLFRTSVKDDFNVTELFEYLAEK 161
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 111 bits (279), Expect = 2e-30
Identities = 57/174 (32%), Positives = 95/174 (54%), Gaps = 1/174 (0%)
Query: 13 TYSFKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTA 72
FK+V+LG+G VGKT+++ R V D+F E + T+ K + + + L +WDTA
Sbjct: 3 MKEFKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTA 62
Query: 73 GQERFHALGPIYYRMSNGAVLVYDITD-EDSFEKVKNWVKELKKMLGNDICLTIAGNKID 131
GQE + +L P YYR +NG ++VYD T E S E + W++EL+++ +D+ + + GNKID
Sbjct: 63 GQEEYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVGNKID 122
Query: 132 LEKQRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRMLEKAQEFDL 185
L +++ +E + + V + A + LE S + L +L
Sbjct: 123 LFDEQSSSEEILNQLNREVVLLVLAPKAVLPEVANPALLETSAKSLTGPNVNEL 176
>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 = 109 bits (274), Expect = 4e-30
Identities = 53/158 (33%), Positives = 92/158 (58%), Gaps = 5/158 (3%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQER 76
KV+ +G VGK+ ++ RY E +F K++ T+ + KK+++ K + + +D +G
Sbjct: 2 KVISMGNSGVGKSCIIKRYCEGRFVSKYLPTIGIDYGVKKVSVRNKEVRVNFFDLSGHPE 61
Query: 77 FHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLG-----NDICLTIAGNKID 131
+ + +Y+ + G +LVYD+TD SFE + +W+KE+K+ G +I + + NKID
Sbjct: 62 YLEVRNEFYKDTQGVLLVYDVTDRQSFEALDSWLKEMKQEGGPHGNMENIVVVVCANKID 121
Query: 132 LEKQRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMF 169
L K R V +++ +A+S G +F TSA G+ EMF
Sbjct: 122 LTKHRAVSEDEGRLWAESKGFKYFETSACTGEGVNEMF 159
>gnl|CDD|206694 cd04109, Rab28, Rab GTPase family 28 (Rab28). Rab28 subfamily.
First identified in maize, Rab28 has been shown to be a
late embryogenesis-abundant (Lea) protein that is
regulated by the plant hormone abcisic acid (ABA). In
Arabidopsis, Rab28 is expressed during embryo
development and is generally restricted to provascular
tissues in mature embryos. Unlike maize Rab28, it is not
ABA-inducible. Characterization of the human Rab28
homolog revealed two isoforms, which differ by a 95-base
pair insertion, producing an alternative sequence for
the 30 amino acids at the C-terminus. The two human
isoforms are presumably the result of alternative
splicing. Since they differ at the C-terminus but not in
the GTP-binding region, they are predicted to be
targeted to different cellular locations. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins.
Length = 213
Score = 107 bits (268), Expect = 9e-29
Identities = 57/192 (29%), Positives = 94/192 (48%), Gaps = 13/192 (6%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGK-RLNLAIWDTAGQ 74
K+V+LG+G GKTS++ R+ ++ F + + T+ F ++++ + G + L +WD GQ
Sbjct: 1 IKIVVLGDGASGKTSLIRRFAQEGFGKSYKQTIGLDFFSRRITLPGSLNVTLQVWDIGGQ 60
Query: 75 ERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGN---DICLTIAGNKID 131
+ + Y + LVYDIT+ SFE +++W+ +KK+ + + GNK D
Sbjct: 61 QIGGKMLDKYIYGAQAVCLVYDITNSQSFENLEDWLSVVKKVNEESETKPKMVLVGNKTD 120
Query: 132 LEKQRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMF---------LELSQRMLEKAQE 182
LE R V E ++AQ SAK + F ++LSQ LE++Q
Sbjct: 121 LEHNRQVTAEKHARFAQENDMESIFVSAKTGDRVFLCFQRIAAELLGVKLSQAELEQSQR 180
Query: 183 FDLAKASELSRR 194
A S S R
Sbjct: 181 VVKADVSRYSER 192
>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 = 104 bits (261), Expect = 3e-28
Identities = 55/158 (34%), Positives = 96/158 (60%), Gaps = 2/158 (1%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE 75
KV+++G G VGK+++ L+++ D+F E + T S+ KK+ + G+ + L I DTAGQE
Sbjct: 1 HKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSY-RKKVVLDGEEVQLNILDTAGQE 59
Query: 76 RFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGND-ICLTIAGNKIDLEK 134
+ A+ Y+R G +LV+ ITD +SF + + +++ ++ +D + L + GNK DLE
Sbjct: 60 DYAAIRDNYFRSGEGFLLVFSITDMESFTALAEFREQILRVKEDDNVPLLLVGNKCDLED 119
Query: 135 QRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLEL 172
+R V E+A A+ G + TSAK ++++F +L
Sbjct: 120 KRQVSVEEAANLAEQWGVNYVETSAKTRANVDKVFFDL 157
>gnl|CDD|133376 cd04176, Rap2, Rap2 family GTPase consists of Rap2a, Rap2b, and
Rap2c. The Rap2 subgroup is part of the Rap subfamily
of the Ras family. It consists of Rap2a, Rap2b, and
Rap2c. Both isoform 3 of the human mitogen-activated
protein kinase kinase kinase kinase 4 (MAP4K4) and
Traf2- and Nck-interacting kinase (TNIK) are putative
effectors of Rap2 in mediating the activation of c-Jun
N-terminal kinase (JNK) to regulate the actin
cytoskeleton. In human platelets, Rap2 was shown to
interact with the cytoskeleton by binding the actin
filaments. In embryonic Xenopus development, Rap2 is
necessary for the Wnt/beta-catenin signaling pathway.
The Rap2 interacting protein 9 (RPIP9) is highly
expressed in human breast carcinomas and correlates with
a poor prognosis, suggesting a role for Rap2 in breast
cancer oncogenesis. Rap2b, but not Rap2a, Rap2c, Rap1a,
or Rap1b, is expressed in human red blood cells, where
it is believed to be involved in vesiculation. A number
of additional effector proteins for Rap2 have been
identified, including the RalGEFs RalGDS, RGL, and Rlf,
which also interact with Rap1 and Ras. Most Ras proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 163
Score = 104 bits (260), Expect = 3e-28
Identities = 49/163 (30%), Positives = 93/163 (57%), Gaps = 2/163 (1%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE 75
+KVV+LG G VGK+++ +++V F EK+ T++ F K++ + L I DTAG E
Sbjct: 2 YKVVVLGSGGVGKSALTVQFVSGTFIEKYDPTIE-DFYRKEIEVDSSPSVLEILDTAGTE 60
Query: 76 RFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGND-ICLTIAGNKIDLEK 134
+F ++ +Y + G ++VY + ++ +F+ +K ++ ++ G + + + + GNK+DLE
Sbjct: 61 QFASMRDLYIKNGQGFIVVYSLVNQQTFQDIKPMRDQIVRVKGYEKVPIILVGNKVDLES 120
Query: 135 QRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRML 177
+R V + A+ G TSAK + E+F E+ ++M
Sbjct: 121 EREVSSAEGRALAEEWGCPFMETSAKSKTMVNELFAEIVRQMN 163
>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 = 104 bits (261), Expect = 4e-28
Identities = 58/170 (34%), Positives = 95/170 (55%), Gaps = 19/170 (11%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLN--KKLNIAGKRLNLAIWDTAGQ 74
K+V++G+G VGKT +++ Y +KF +++ T F N + + GK++NL +WDTAGQ
Sbjct: 2 KIVVVGDGAVGKTCLLISYTTNKFPTEYVPT---VFDNYSANVTVDGKQVNLGLWDTAGQ 58
Query: 75 ERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKN-WVKELKKMLGNDICLTIAGNKIDL- 132
E + L P+ Y ++ +L + + SFE VK W E+K N + + + G KIDL
Sbjct: 59 EEYDRLRPLSYPQTDVFLLCFSVDSPSSFENVKTKWYPEIKHYCPN-VPIILVGTKIDLR 117
Query: 133 ----------EKQRTVMQEDAEKYAQSVGAV-HFHTSAKMNRGIEEMFLE 171
+KQ+ + E+ EK A+ +GAV + SA G++E+F E
Sbjct: 118 DDGNTLKKLEKKQKPITPEEGEKLAKEIGAVKYMECSALTQEGLKEVFDE 167
>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 = 102 bits (257), Expect = 1e-27
Identities = 54/164 (32%), Positives = 104/164 (63%), Gaps = 3/164 (1%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE 75
+K+V+LG G VGK+++ +++V++ F E + T++ S+ K++ I G++ +L I DTAG E
Sbjct: 2 YKIVVLGAGGVGKSALTVQFVQNVFIESYDPTIEDSY-RKQVEIDGRQCDLEILDTAGTE 60
Query: 76 RFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGND-ICLTIAGNKIDLEK 134
+F A+ +Y + G +LVY +T E S ++ +++ ++ +D + + + GNK DLE
Sbjct: 61 QFTAMRELYIKSGQGFLLVYSVTSEASLNELGELREQVLRIKDSDNVPMVLVGNKADLED 120
Query: 135 QRTVMQEDAEKYAQSVGAVHFH-TSAKMNRGIEEMFLELSQRML 177
R V +ED +Q G V F+ TSA+ ++E+F++L ++++
Sbjct: 121 DRQVSREDGVSLSQQWGNVPFYETSARKRTNVDEVFIDLVRQII 164
>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 = 102 bits (257), Expect = 2e-27
Identities = 59/167 (35%), Positives = 97/167 (58%), Gaps = 8/167 (4%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQER 76
K+ +LG VGK+S+ +++VE F E + T++ +F +K + G+ +L I DTAGQ+
Sbjct: 3 KIAVLGSRSVGKSSLTVQFVEGHFVESYYPTIENTF-SKIITYKGQEYHLEIVDTAGQDE 61
Query: 77 FHALGPIYYRMS-NGAVLVYDITDEDSFEKVKNWVKELKKMLGND-ICLTIAGNKIDLEK 134
+ L P Y + +G +LVY +T SFE VK ++ MLG + + + + GNK DL
Sbjct: 62 YSIL-PQKYSIGIHGYILVYSVTSRKSFEVVKVIYDKILDMLGKESVPIVLVGNKSDLHM 120
Query: 135 QRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRMLEKAQ 181
+R V E+ +K A+S GA +SAK N +EE F + ++E+ +
Sbjct: 121 ERQVSAEEGKKLAESWGAAFLESSAKENENVEEAF----ELLIEEIE 163
>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 = 102 bits (256), Expect = 2e-27
Identities = 53/170 (31%), Positives = 86/170 (50%), Gaps = 20/170 (11%)
Query: 18 VVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIA--GKRLNLAIWDTAGQE 75
+V++G+G VGKT +++ Y + F E ++ T F N ++ GK + L +WDTAGQE
Sbjct: 1 LVVVGDGAVGKTCLLIVYTTNAFPEDYVPT---VFENYSADVEVDGKPVELGLWDTAGQE 57
Query: 76 RFHALGPIYYRMSNGAVLVYDITDEDSFEKVKN-WVKELKKMLGNDICLTIAGNKIDL-- 132
+ L P+ Y ++ ++ + + SFE VK W E+K N + + G K+DL
Sbjct: 58 DYDRLRPLSYPDTDVFLICFSVDSPASFENVKEKWYPEVKHFCPNVPIILV-GTKLDLRN 116
Query: 133 ----------EKQRTVMQEDAEKYAQSVGAV-HFHTSAKMNRGIEEMFLE 171
+KQ V E + A+ +GAV + SA G+ E+F E
Sbjct: 117 DKSTLEELSKKKQEPVTYEQGQALAKRIGAVKYLECSALTQEGVREVFEE 166
>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 = 101 bits (254), Expect = 2e-27
Identities = 53/162 (32%), Positives = 99/162 (61%), Gaps = 2/162 (1%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE 75
+K+V+LG G VGK+++ +++V+ F EK+ T++ S+ K++ + G++ L I DTAG E
Sbjct: 2 YKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSY-RKQVEVDGQQCMLEILDTAGTE 60
Query: 76 RFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLG-NDICLTIAGNKIDLEK 134
+F A+ +Y + G VLVY IT + +F +++ +++ ++ D+ + + GNK DLE
Sbjct: 61 QFTAMRDLYMKNGQGFVLVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLED 120
Query: 135 QRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRM 176
+R V +E + A+ G TSAK + E+F +L +++
Sbjct: 121 ERVVGKEQGQNLARQWGCAFLETSAKAKINVNEIFYDLVRQI 162
>gnl|CDD|133326 cd04126, Rab20, Rab GTPase family 20 (Rab20). Rab20 is one of
several Rab proteins that appear to be restricted in
expression to the apical domain of murine polarized
epithelial cells. It is expressed on the apical side of
polarized kidney tubule and intestinal epithelial cells,
and in non-polarized cells. It also localizes to
vesico-tubular structures below the apical brush border
of renal proximal tubule cells and in the apical region
of duodenal epithelial cells. Rab20 has also been shown
to colocalize with vacuolar H+-ATPases (V-ATPases) in
mouse kidney cells, suggesting a role in the regulation
of V-ATPase traffic in specific portions of the nephron.
It was also shown to be one of several proteins whose
expression is upregulated in human myelodysplastic
syndrome (MDS) patients. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 220
Score = 101 bits (254), Expect = 1e-26
Identities = 71/237 (29%), Positives = 111/237 (46%), Gaps = 51/237 (21%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQER 76
KVVLLG+ VGKTS++ RY+E +F + ++T+ +F K+ N++IWDTAG+E+
Sbjct: 2 KVVLLGDMNVGKTSLLHRYMERRFKD-TVSTVGGAFYLKQW----GPYNISIWDTAGREQ 56
Query: 77 FHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDL---- 132
FH LG +Y R + +L YD+++ S E++++ L D + GNK+DL
Sbjct: 57 FHGLGSMYCRGAAAVILTYDVSNVQSLEELEDRFLGLTDTANEDCLFAVVGNKLDLTEEG 116
Query: 133 ---------------EKQRTVMQEDAEKYAQSV--------------GAVHFHTSAKMNR 163
E QR V EDA+ + + + + F TSAK
Sbjct: 117 ALAGQEKDAGDRVSPEDQRQVTLEDAKAFYKRINKYKMLDEDLSPAAEKMCFETSAKTGY 176
Query: 164 GIEEMFLELSQRMLEKAQEFDLAKASELSRRGSMRRNVVVVEDEDLPTSSSTKSGCC 220
++E+F L F+L L++R R V +LP +KS CC
Sbjct: 177 NVDELFEYL----------FNLVLPLILAQRAEANRTQGTV---NLPNPKRSKSKCC 220
>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 = 99 bits (249), Expect = 2e-26
Identities = 53/168 (31%), Positives = 90/168 (53%), Gaps = 2/168 (1%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE 75
+K+V+LG G VGK++V ++++ F + H T++ ++ + I + L I DTAGQ
Sbjct: 3 YKIVMLGAGGVGKSAVTMQFISHSFPDYHDPTIEDAY-KTQARIDNEPALLDILDTAGQA 61
Query: 76 RFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKM-LGNDICLTIAGNKIDLEK 134
F A+ Y R G ++ Y +TD SF++ + + + ++ L DI L + GNK+DLE+
Sbjct: 62 EFTAMRDQYMRCGEGFIICYSVTDRHSFQEASEFKELITRVRLTEDIPLVLVGNKVDLEQ 121
Query: 135 QRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRMLEKAQE 182
QR V E+ A+ F TSA + I++ F L + + K
Sbjct: 122 QRQVTTEEGRNLAREFNCPFFETSAALRFYIDDAFHGLVREIRRKESM 169
>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 = 99.0 bits (247), Expect = 3e-26
Identities = 51/158 (32%), Positives = 94/158 (59%), Gaps = 2/158 (1%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE 75
+K+V++G G VGK+++ +++++ F + T++ S+ K+ I G+ L I DTAGQE
Sbjct: 3 YKLVVVGGGGVGKSALTIQFIQSYFVTDYDPTIEDSYT-KQCEIDGQWARLDILDTAGQE 61
Query: 76 RFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLG-NDICLTIAGNKIDLEK 134
F A+ Y R G +LV+ +TD SFE+V + ++ ++ ++ + + GNK DLE
Sbjct: 62 EFSAMREQYMRTGEGFLLVFSVTDRGSFEEVDKFHTQILRVKDRDEFPMILVGNKADLEH 121
Query: 135 QRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLEL 172
QR V +E+ ++ A+ + + TSAK +++ F +L
Sbjct: 122 QRQVSREEGQELARQLKIPYIETSAKDRVNVDKAFHDL 159
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 97.9 bits (243), Expect = 1e-25
Identities = 50/139 (35%), Positives = 79/139 (56%)
Query: 38 DKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQERFHALGPIYYRMSNGAVLVYDI 97
D F+ + +T+ FL+K L + + L +WDTAGQERF +L P Y R S A++VYDI
Sbjct: 3 DTFDNNYQSTIGIDFLSKTLYLDEGPVRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDI 62
Query: 98 TDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLEKQRTVMQEDAEKYAQSVGAVHFHT 157
T+ SFE W++++ G D+ + + GNK DL R V E+ + AQ + T
Sbjct: 63 TNRQSFENTTKWIQDILNERGKDVIIALVGNKTDLGDLRKVTYEEGMQKAQEYNTMFHET 122
Query: 158 SAKMNRGIEEMFLELSQRM 176
SAK I+ +F +++ ++
Sbjct: 123 SAKAGHNIKVLFKKIAAKL 141
>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 = 96.6 bits (241), Expect = 2e-25
Identities = 51/162 (31%), Positives = 92/162 (56%), Gaps = 3/162 (1%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE 75
FK+VL+G+G GKT+ V R++ +F +K++ TL + ++ +WDTAGQE
Sbjct: 1 FKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLDFHTNRGKIRFNVWDTAGQE 60
Query: 76 RFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLEKQ 135
+F L YY A++++D+T +++ V NW ++L ++ N I + + GNK+D+ K
Sbjct: 61 KFGGLRDGYYIQGQCAIIMFDVTSRVTYKNVPNWHRDLVRVCEN-IPIVLCGNKVDI-KD 118
Query: 136 RTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRML 177
R V + + + ++ SAK N E+ FL L++++L
Sbjct: 119 RKVKPKQIT-FHRKKNLQYYEISAKSNYNFEKPFLWLARKLL 159
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 97.8 bits (244), Expect = 3e-25
Identities = 57/208 (27%), Positives = 102/208 (49%), Gaps = 17/208 (8%)
Query: 15 SFKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQ 74
FK++L+G+G VGKT+ V R++ +F +K+I TL K + +WDTAGQ
Sbjct: 9 EFKLILVGDGGVGKTTFVKRHLTGEFEKKYIPTLGVEVHPLKFYTNCGPICFNVWDTAGQ 68
Query: 75 ERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLEK 134
E+F L YY A++++D+T +++ V NW +++ ++ N I + + GNK+D+ K
Sbjct: 69 EKFGGLRDGYYIKGQCAIIMFDVTSRITYKNVPNWHRDIVRVCEN-IPIVLVGNKVDV-K 126
Query: 135 QRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRMLEKAQ------------- 181
R V + + ++ SAK N E+ FL L++R+
Sbjct: 127 DRQVKARQI-TFHRKKNLQYYDISAKSNYNFEKPFLWLARRLTNDPNLVFVGAPALAPEE 185
Query: 182 -EFDLAKASELSRRGSMRRNVVVVEDED 208
+ D ++ + NV + +D+D
Sbjct: 186 IQIDPELVAQAEKELQAAANVPLPDDDD 213
>gnl|CDD|206704 cd04132, Rho4_like, Ras homology family 4 (Rho4) of small guanosine
triphosphatases (GTPases)-like. Rho4 is a GTPase that
controls septum degradation by regulating secretion of
Eng1 or Agn1 during cytokinesis. Rho4 also plays a role
in cell morphogenesis. Rho4 regulates septation and cell
morphology by controlling the actin cytoskeleton and
cytoplasmic microtubules. The localization of Rho4 is
modulated by Rdi1, which may function as a GDI, and by
Rga9, which is believed to function as a GAP. In S.
pombe, both Rho4 deletion and Rho4 overexpression result
in a defective cell wall, suggesting a role for Rho4 in
maintaining cell wall integrity. Most Rho proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins.
Length = 197
Score = 96.6 bits (241), Expect = 6e-25
Identities = 55/203 (27%), Positives = 92/203 (45%), Gaps = 42/203 (20%)
Query: 14 YSFKVVLLGEGCVGKTSVVLRYVEDKFN--------EKHITTLQASFLNKKLNIAGKRLN 65
K+V++G+G GKT +++ Y + F E ++TTLQ GK +
Sbjct: 2 LKVKIVVVGDGGCGKTCLLMVYAQGSFPEEYVPTVFENYVTTLQVP--------NGKIIE 53
Query: 66 LAIWDTAGQERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKN-WVKELKKMLGNDIC-- 122
LA+WDTAGQE + L P+ Y + ++ Y + + S + V++ W E+ N C
Sbjct: 54 LALWDTAGQEDYDRLRPLSYPDVDVILICYSVDNPTSLDNVEDKWYPEV-----NHFCPG 108
Query: 123 --LTIAGNKIDLEKQRT------------VMQEDAEKYAQSVGAVHF-HTSAKMNRGIEE 167
+ + G K DL K + V E E A+S+GAV + SAK+ ++E
Sbjct: 109 TPIVLVGLKTDLRKDKNSVSKLRAQGLEPVTPEQGESVAKSIGAVAYIECSAKLMENVDE 168
Query: 168 MF---LELSQRMLEKAQEFDLAK 187
+F + ++ +A K
Sbjct: 169 VFDAAINVALSKSGRAARKKKKK 191
>gnl|CDD|206693 cd04108, Rab36_Rab34, Rab GTPase families 34 (Rab34) and 36
(Rab36). Rab34/Rab36 subfamily. Rab34, found primarily
in the Golgi, interacts with its effector,
Rab-interacting lysosomal protein (RILP). This enables
its participation in microtubular
dynenin-dynactin-mediated repositioning of lysosomes
from the cell periphery to the Golgi. A Rab34 (Rah)
isoform that lacks the consensus GTP-binding region has
been identified in mice. This isoform is associated with
membrane ruffles and promotes macropinosome formation.
Rab36 has been mapped to human chromosome 22q11.2, a
region that is homozygously deleted in malignant
rhabdoid tumors (MRTs). However, experimental
assessments do not implicate Rab36 as a tumor suppressor
that would enable tumor formation through a
loss-of-function mechanism. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 170
Score = 95.7 bits (238), Expect = 8e-25
Identities = 51/165 (30%), Positives = 93/165 (56%), Gaps = 3/165 (1%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQER 76
KV+++G+ VGKT ++ R+ +D F++ + T+ F ++ + G +L +WDTAGQER
Sbjct: 2 KVIVVGDLSVGKTCLINRFCKDVFDKNYKATIGVDFEMERFEVLGVPFSLQLWDTAGQER 61
Query: 77 FHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKE-LKKMLGNDICLTIAGNKIDLEK- 134
F + YYR + ++V+D+TD S E + W+++ LK+ + + L + G K DL
Sbjct: 62 FKCIASTYYRGAQAIIIVFDLTDVASLEHTRQWLEDALKENDPSSVLLFLVGTKKDLSSP 121
Query: 135 -QRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRMLE 178
Q +M++DA K A+ + A ++ SA + + F ++ E
Sbjct: 122 AQYALMEQDAIKLAREMKAEYWAVSALTGENVRDFFFRVASLTFE 166
>gnl|CDD|206701 cd04128, Spg1, Septum-promoting GTPase (Spg1). Spg1p. Spg1p
(septum-promoting GTPase) was first identified in the
fission yeast S. pombe, where it regulates septum
formation in the septation initiation network (SIN)
through the cdc7 protein kinase. Spg1p is an essential
gene that localizes to the spindle pole bodies. When
GTP-bound, it binds cdc7 and causes it to translocate to
spindle poles. Sid4p (septation initiation defective) is
required for localization of Spg1p to the spindle pole
body, and the ability of Spg1p to promote septum
formation from any point in the cell cycle depends on
Sid4p. Spg1p is negatively regulated by Byr4 and cdc16,
which form a two-component GTPase activating protein
(GAP) for Spg1p. The existence of a SIN-related pathway
in plants has been proposed. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization.
Length = 182
Score = 94.8 bits (236), Expect = 2e-24
Identities = 47/162 (29%), Positives = 90/162 (55%), Gaps = 14/162 (8%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQER 76
K+ LLG+ +GKTS++++YVE +F+E++I TL +F+ K ++I G + +IWD GQ
Sbjct: 2 KIGLLGDAQIGKTSLMVKYVEGEFDEEYIQTLGVNFMEKTISIRGTEITFSIWDLGGQRE 61
Query: 77 FHALGPIYYRMSNGAVLV---YDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDL- 132
F + P+ + AV + +D+T + + +K W ++ + I + + G K DL
Sbjct: 62 FINMLPL---VCKDAVAILFMFDLTRKSTLNSIKEWYRQARGFNKTAIPILV-GTKYDLF 117
Query: 133 -----EKQRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMF 169
E+Q + ++ A KYA+++ A S + ++++F
Sbjct: 118 ADLPPEEQEEITKQ-ARKYAKAMKAPLIFCSTSHSINVQKIF 158
>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 = 93.6 bits (233), Expect = 4e-24
Identities = 52/158 (32%), Positives = 93/158 (58%), Gaps = 3/158 (1%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE 75
+K+V++G G VGK+++ ++ +++ F +++ T++ S+ K++ I G+ L I DTAGQE
Sbjct: 2 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSY-RKQVVIDGETCLLDILDTAGQE 60
Query: 76 RFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGND-ICLTIAGNKIDLEK 134
+ A+ Y R G + V+ I SFE + + +++K++ +D + + + GNK DL
Sbjct: 61 EYSAMRDQYMRTGEGFLCVFAINSRKSFEDIHTYREQIKRVKDSDDVPMVLVGNKCDLAA 120
Query: 135 QRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLEL 172
RTV + A+S G + TSAK +G+EE F L
Sbjct: 121 -RTVSTRQGQDLAKSYGIPYIETSAKTRQGVEEAFYTL 157
>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 = 92.2 bits (229), Expect = 1e-23
Identities = 53/163 (32%), Positives = 99/163 (60%), Gaps = 3/163 (1%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE 75
+K+V+LG G VGK+++ +++V+ F +K+ T++ S+ K++ + ++ L I DTAG E
Sbjct: 2 YKLVVLGSGGVGKSALTVQFVQGIFVDKYDPTIEDSY-RKQIEVDCQQCMLEILDTAGTE 60
Query: 76 RFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKE-LKKMLGNDICLTIAGNKIDLEK 134
+F A+ +Y + G LVY IT + SF +++ ++ L+ D+ + + GNK DLE
Sbjct: 61 QFTAMRDLYIKNGQGFALVYSITAQQSFNDLQDLREQILRVKDTEDVPMILVGNKCDLED 120
Query: 135 QRTVMQEDAEKYAQSVGAVHF-HTSAKMNRGIEEMFLELSQRM 176
+R V +E+ + A+ G F TSAK ++E+F +L +++
Sbjct: 121 ERVVSKEEGQNLARQWGNCPFLETSAKSKINVDEIFYDLVRQI 163
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 91.8 bits (228), Expect = 3e-23
Identities = 50/158 (31%), Positives = 94/158 (59%), Gaps = 2/158 (1%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE 75
+K+V++G G VGK+++ ++++++ F +++ T++ S+ K+ I + L I DTAGQE
Sbjct: 6 YKLVVVGGGGVGKSALTIQFIQNHFIDEYDPTIEDSY-RKQCVIDEETCLLDILDTAGQE 64
Query: 76 RFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGND-ICLTIAGNKIDLEK 134
+ A+ Y R G + VY IT SFE++ ++ +++ ++ D + + + GNK DL+
Sbjct: 65 EYSAMRDQYMRTGQGFLCVYSITSRSSFEEIASFREQILRVKDKDRVPMILVGNKCDLDS 124
Query: 135 QRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLEL 172
+R V + ++ A+S G TSAK ++E F EL
Sbjct: 125 ERQVSTGEGQELAKSFGIPFLETSAKQRVNVDEAFYEL 162
>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 = 89.9 bits (223), Expect = 1e-22
Identities = 42/143 (29%), Positives = 78/143 (54%), Gaps = 4/143 (2%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQER 76
K++LLG+ VGK+ +V R++ D + + ++T + GK + + WDTAGQER
Sbjct: 2 KIILLGDSAVGKSKLVERFLMDGYEPQQLSTYALTLYKHNAKFEGKTILVDFWDTAGQER 61
Query: 77 FHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLEKQR 136
F + YY ++ +LV+D+T + +++ + W +EL++ C+ +A NKIDL+
Sbjct: 62 FQTMHASYYHKAHACILVFDVTRKITYKNLSKWYEELREYRPEIPCIVVA-NKIDLDPSV 120
Query: 137 TVMQEDAEKYAQSVGAVHFHTSA 159
T + +A+ ++ SA
Sbjct: 121 T---QKKFNFAEKHNLPLYYVSA 140
>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 = 89.8 bits (223), Expect = 1e-22
Identities = 46/165 (27%), Positives = 78/165 (47%), Gaps = 13/165 (7%)
Query: 19 VLLGEGCVGKTSVVLRYVEDKFNE---KHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE 75
V++G G VGK+S++ + + E TT K+L+ +L + DT G +
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLV--LVDTPGLD 58
Query: 76 RFHALGP-----IYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKI 130
F LG + R ++ +LV D TD +S E K L+++ I + + GNKI
Sbjct: 59 EFGGLGREELARLLLRGADLILLVVDSTDRESEEDAKL--LILRRLRKEGIPIILVGNKI 116
Query: 131 DLEKQRTVMQEDAEKYAQSVGAVHFH-TSAKMNRGIEEMFLELSQ 174
DL ++R V + + + V SAK G++E+F +L +
Sbjct: 117 DLLEEREVEELLRLEELAKILGVPVFEVSAKTGEGVDELFEKLIE 161
>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 = 88.7 bits (220), Expect = 2e-22
Identities = 50/160 (31%), Positives = 87/160 (54%), Gaps = 4/160 (2%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE 75
++VV+ G G VGK+S+VLR+V+ F E +I T++ ++ + ++ + L I DT G
Sbjct: 2 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTY-RQVISCSKSICTLQITDTTGSH 60
Query: 76 RFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGND---ICLTIAGNKIDL 132
+F A+ + + +LVY IT + S E++K + + ++ GN+ I + + GNK D
Sbjct: 61 QFPAMQRLSISKGHAFILVYSITSKQSLEELKPIYELICEIKGNNLEKIPIMLVGNKCDE 120
Query: 133 EKQRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLEL 172
R V + A++ TSAK N ++E+F EL
Sbjct: 121 SPSREVSSSEGAALARTWNCAFMETSAKTNHNVQELFQEL 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 = 88.7 bits (220), Expect = 5e-22
Identities = 55/169 (32%), Positives = 92/169 (54%), Gaps = 5/169 (2%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQER 76
K+V+LG+G VGKT++ ++ + F E + T++ S+ K++ + G+ L + DTAGQE
Sbjct: 1 KLVVLGDGGVGKTALTIQLCLNHFVETYDPTIEDSY-RKQVVVDGQPCMLEVLDTAGQEE 59
Query: 77 FHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKEL---KKMLGNDICLTIAGNKIDLE 133
+ AL + R G +LVY IT +FE+V+ + +++ K D+ + I GNK D
Sbjct: 60 YTALRDQWIREGEGFILVYSITSRSTFERVERFREQIQRVKDESAADVPIMIVGNKCDKV 119
Query: 134 KQRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRMLEKAQE 182
+R V E+ A+ +G SAK N +E F L R L + ++
Sbjct: 120 YEREVSTEEGAALARRLGCEFIEASAKTNVNVERAFYTLV-RALRQQRQ 167
>gnl|CDD|206707 cd04135, Tc10, Rho GTPase TC10 (Tc10). TC10 is a Rho family
protein that has been shown to induce microspike
formation and neurite outgrowth in vitro. Its expression
changes dramatically after peripheral nerve injury,
suggesting an important role in promoting axonal
outgrowth and regeneration. TC10 regulates translocation
of insulin-stimulated GLUT4 in adipocytes and has also
been shown to bind directly to Golgi COPI coat proteins.
GTP-bound TC10 in vitro can bind numerous potential
effectors. Depending on its subcellular localization and
distinct functional domains, TC10 can differentially
regulate two types of filamentous actin in adipocytes.
TC10 mRNAs are highly expressed in three types of mouse
muscle tissues: leg skeletal muscle, cardiac muscle, and
uterus; they were also present in brain, with higher
levels in adults than in newborns. TC10 has also been
shown to play a role in regulating the expression of
cystic fibrosis transmembrane conductance regulator
(CFTR) through interactions with CFTR-associated ligand
(CAL). The GTP-bound form of TC10 directs the
trafficking of CFTR from the juxtanuclear region to the
secretory pathway toward the plasma membrane, away from
CAL-mediated DFTR degradation in the lysosome. Most Rho
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 174
Score = 86.6 bits (214), Expect = 2e-21
Identities = 51/170 (30%), Positives = 92/170 (54%), Gaps = 16/170 (9%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE 75
K V++G+G VGKT +++ Y D F E+++ T+ + + + GK+ L ++DTAGQE
Sbjct: 1 LKCVVVGDGAVGKTCLLMSYANDAFPEEYVPTVFDHYA-VSVTVGGKQYLLGLYDTAGQE 59
Query: 76 RFHALGPIYYRMSNGAVLVYDITDEDSFEKVK-NWVKELKKMLGNDICLTIAGNKIDLE- 133
+ L P+ Y M++ ++ + + + SF+ VK WV ELK+ N + + G +IDL
Sbjct: 60 DYDRLRPLSYPMTDVFLICFSVVNPASFQNVKEEWVPELKEYAPN-VPYLLIGTQIDLRD 118
Query: 134 -----------KQRTVMQEDAEKYAQSVGA-VHFHTSAKMNRGIEEMFLE 171
K++ + E +K A+ +GA + SA +G++ +F E
Sbjct: 119 DPKTLARLNDMKEKPITVEQGQKLAKEIGACCYVECSALTQKGLKTVFDE 168
>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 = 87.3 bits (216), Expect = 2e-21
Identities = 53/167 (31%), Positives = 88/167 (52%), Gaps = 3/167 (1%)
Query: 14 YSFKVVLLGEGCVGKTSVVLRYVEDKFNEK-HITTLQASFLNKKLNIAGKRLNLAIWDTA 72
Y K +L+G+ VGK + L ++D E + + + + + G+R+ L +WDT+
Sbjct: 5 YLLKFLLVGDSDVGKGEI-LASLQDGSTESPYGYNMGIDYKTTTILLDGRRVKLQLWDTS 63
Query: 73 GQERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDL 132
GQ RF + Y R + G +LVYDIT+ SF+ + W+KE+ + + + GN++ L
Sbjct: 64 GQGRFCTIFRSYSRGAQGIILVYDITNRWSFDGIDRWIKEIDEH-APGVPKILVGNRLHL 122
Query: 133 EKQRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRMLEK 179
+R V E A+ YA+ G F S N I E F EL++ +L +
Sbjct: 123 AFKRQVATEQAQAYAERNGMTFFEVSPLCNFNITESFTELARIVLMR 169
>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 = 88.3 bits (219), Expect = 3e-21
Identities = 61/209 (29%), Positives = 103/209 (49%), Gaps = 24/209 (11%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE 75
+++V+LG VGKT++V R++ +F E++ T++ F K +I G+ L I DT+G
Sbjct: 1 YRMVVLGASKVGKTAIVSRFLGGRFEEQYTPTIE-DFHRKLYSIRGEVYQLDILDTSGNH 59
Query: 76 RFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKEL---KKMLGN------DICLTIA 126
F A+ + + +LV+ + + +SFE+V +++ K L N I + I
Sbjct: 60 PFPAMRRLSILTGDVFILVFSLDNRESFEEVCRLREQILETKSCLKNKTKENVKIPMVIC 119
Query: 127 GNKIDLEKQRTVMQEDAEKY-AQSVGAVHFHTSAKMNRGIEEMFLELSQRMLEKAQEFDL 185
GNK D + R V +++ E+ +F SAK N ++EMF L F L
Sbjct: 120 GNKADRDFPREVQRDEVEQLVGGDENCAYFEVSAKKNSNLDEMFRAL----------FSL 169
Query: 186 AK-ASELSRRGSMRRNVVVVEDEDLPTSS 213
AK +E+S S+ R + V + L S
Sbjct: 170 AKLPNEMSP--SLHRKISVQYGDALHKKS 196
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 86.0 bits (213), Expect = 1e-20
Identities = 51/165 (30%), Positives = 91/165 (55%), Gaps = 7/165 (4%)
Query: 15 SFKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTL--QASFLNKKLNIAGKRLNLAIWDTA 72
SFK+V++G+G GKT+ V R++ +F +K+ T+ + L+ N R WDTA
Sbjct: 13 SFKLVIVGDGGTGKTTFVKRHLTGEFEKKYEPTIGVEVHPLDFFTNCGKIRFY--CWDTA 70
Query: 73 GQERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDL 132
GQE+F L YY A++++D+T +++ V W ++L ++ N I + + GNK+D+
Sbjct: 71 GQEKFGGLRDGYYIHGQCAIIMFDVTARLTYKNVPTWHRDLCRVCEN-IPIVLCGNKVDV 129
Query: 133 EKQRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRML 177
K R V + + + ++ SAK N E+ FL L++++
Sbjct: 130 -KNRQV-KAKQVTFHRKKNLQYYEISAKSNYNFEKPFLYLARKLA 172
>gnl|CDD|206662 cd01870, RhoA_like, Ras homology family A (RhoA)-like includes
RhoA, RhoB and RhoC. The RhoA subfamily consists of
RhoA, RhoB, and RhoC. RhoA promotes the formation of
stress fibers and focal adhesions, regulating cell
shape, attachment, and motility. RhoA can bind to
multiple effector proteins, thereby triggering different
downstream responses. In many cell types, RhoA mediates
local assembly of the contractile ring, which is
necessary for cytokinesis. RhoA is vital for muscle
contraction; in vascular smooth muscle cells, RhoA plays
a key role in cell contraction, differentiation,
migration, and proliferation. RhoA activities appear to
be elaborately regulated in a time- and space-dependent
manner to control cytoskeletal changes. Most Rho
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. RhoA and RhoC are observed
only in geranylgeranylated forms; however, RhoB can be
present in palmitoylated, farnesylated, and
geranylgeranylated forms. RhoA and RhoC are highly
relevant for tumor progression and invasiveness;
however, RhoB has recently been suggested to be a tumor
suppressor. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 175
Score = 84.8 bits (210), Expect = 1e-20
Identities = 51/167 (30%), Positives = 90/167 (53%), Gaps = 16/167 (9%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQER 76
K+V++G+G GKT +++ + +D+F E ++ T+ +++ + + GK++ LA+WDTAGQE
Sbjct: 3 KLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYV-ADIEVDGKQVELALWDTAGQED 61
Query: 77 FHALGPIYYRMSNGAVLVYDITDEDSFEKVKN-WVKELKKMLGNDICLTIAGNKIDLE-- 133
+ L P+ Y ++ ++ + I DS E + W E+K N + + + GNK DL
Sbjct: 62 YDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPN-VPIILVGNKKDLRND 120
Query: 134 ----------KQRTVMQEDAEKYAQSVGAV-HFHTSAKMNRGIEEMF 169
KQ V E+ A+ +GA + SAK G+ E+F
Sbjct: 121 EHTIRELAKMKQEPVKPEEGRAMAEKIGAFGYLECSAKTKEGVREVF 167
>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 = 83.9 bits (208), Expect = 2e-20
Identities = 50/164 (30%), Positives = 91/164 (55%), Gaps = 12/164 (7%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE- 75
K+ +LG VGK+++ +R++ +F ++ L++ + ++++ I G++++L I DT GQ+
Sbjct: 1 KIAVLGASGVGKSALTVRFLTKRFIGEYEPNLESLY-SRQVTIDGEQVSLEIQDTPGQQQ 59
Query: 76 ---RFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNW---VKELKKMLGNDICLTIAGNK 129
+ + ++G VLVY ITD SF+ V ++E+KK +I + + GNK
Sbjct: 60 NEDPESLERSLRW--ADGFVLVYSITDRSSFDVVSQLLQLIREIKK-RDGEIPVILVGNK 116
Query: 130 IDLEKQRTVMQEDAEKYAQSVGAVHFHTSAKMN-RGIEEMFLEL 172
DL R V E+ +K A +G + F SA N ++ +F EL
Sbjct: 117 ADLLHSRQVSTEEGQKLALELGCLFFEVSAAENYLEVQNVFHEL 160
>gnl|CDD|133330 cd04130, Wrch_1, Wnt-1 responsive Cdc42 homolog (Wrch-1) is a Rho
family GTPase similar to Cdc42. Wrch-1 (Wnt-1
responsive Cdc42 homolog) is a Rho family GTPase that
shares significant sequence and functional similarity
with Cdc42. Wrch-1 was first identified in mouse mammary
epithelial cells, where its transcription is upregulated
in Wnt-1 transformation. Wrch-1 contains N- and
C-terminal extensions relative to cdc42, suggesting
potential differences in cellular localization and
function. The Wrch-1 N-terminal extension contains
putative SH3 domain-binding motifs and has been shown to
bind the SH3 domain-containing protein Grb2, which
increases the level of active Wrch-1 in cells. Unlike
Cdc42, which localizes to the cytosol and perinuclear
membranes, Wrch-1 localizes extensively with the plasma
membrane and endosomes. The membrane association,
localization, and biological activity of Wrch-1 indicate
an atypical model of regulation distinct from other Rho
family GTPases. Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 173
Score = 83.2 bits (206), Expect = 5e-20
Identities = 43/166 (25%), Positives = 88/166 (53%), Gaps = 14/166 (8%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQER 76
K VL+G+G VGKTS+++ Y + + +++ T +F + + + GK + L + DTAGQ+
Sbjct: 2 KCVLVGDGAVGKTSLIVSYTTNGYPTEYVPTAFDNF-SVVVLVDGKPVRLQLCDTAGQDE 60
Query: 77 FHALGPIYYRMSNGAVLVYDITDEDSFEKVKN-WVKELKK--------MLGN--DICLTI 125
F L P+ Y ++ +L + + + SF+ + W+ E++K ++G D+ +
Sbjct: 61 FDKLRPLCYPDTDVFLLCFSVVNPSSFQNISEKWIPEIRKHNPKAPIILVGTQADLRTDV 120
Query: 126 -AGNKIDLEKQRTVMQEDAEKYAQSVGAV-HFHTSAKMNRGIEEMF 169
++ ++ V Q A+ A+ +GA + SA + ++E+F
Sbjct: 121 NVLIQLARYGEKPVSQSRAKALAEKIGACEYIECSALTQKNLKEVF 166
>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 = 82.2 bits (203), Expect = 2e-19
Identities = 58/191 (30%), Positives = 97/191 (50%), Gaps = 9/191 (4%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQER 76
++V +G VGKT+++ R++ D F KH T++ +K+ +AG ++ + I DT+G
Sbjct: 1 RLVFMGAAGVGKTALIQRFLYDTFEPKHRRTVE-ELHSKEYEVAGVKVTIDILDTSGSYS 59
Query: 77 FHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGND-ICLTIAGNKIDLEKQ 135
F A+ + + + LVY + D +SFE+VK +E+ ++ + + + + GNKID +
Sbjct: 60 FPAMRKLSIQNGDAFALVYSVDDPESFEEVKRLREEILEVKEDKFVPIVVVGNKIDSLAE 119
Query: 136 RTVMQEDAEKYAQSVGAVHF-HTSAKMNRGIEEMFLELSQRM-----LEKAQEFDLAKA- 188
R V DA + F SAK N + E+F EL Q+ L A A
Sbjct: 120 RQVEAADALSTVELDWNNGFVEASAKDNENVTEVFKELLQQANLPSWLSPALRRRRESAP 179
Query: 189 SELSRRGSMRR 199
SE+ RR M +
Sbjct: 180 SEIQRRPPMNK 190
>gnl|CDD|206664 cd01874, Cdc42, cell division cycle 42 (Cdc42) is a small GTPase of
the Rho family. Cdc42 is an essential GTPase that
belongs to the Rho family of Ras-like GTPases. These
proteins act as molecular switches by responding to
exogenous and/or endogenous signals and relaying those
signals to activate downstream components of a
biological pathway. Cdc42 transduces signals to the
actin cytoskeleton to initiate and maintain polarized
growth and to mitogen-activated protein morphogenesis.
In the budding yeast Saccharomyces cerevisiae, Cdc42
plays an important role in multiple actin-dependent
morphogenetic events such as bud emergence,
mating-projection formation, and pseudohyphal growth. In
mammalian cells, Cdc42 regulates a variety of
actin-dependent events and induces the JNK/SAPK protein
kinase cascade, which leads to the activation of
transcription factors within the nucleus. Cdc42 mediates
these processes through interactions with a myriad of
downstream effectors, whose number and regulation we are
just starting to understand. In addition, Cdc42 has been
implicated in a number of human diseases through
interactions with its regulators and downstream
effectors. Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 175
Score = 80.7 bits (199), Expect = 4e-19
Identities = 52/173 (30%), Positives = 88/173 (50%), Gaps = 20/173 (11%)
Query: 15 SFKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLN--IAGKRLNLAIWDTA 72
+ K V++G+G VGKT +++ Y +KF +++ T+ F N + I G+ L ++DTA
Sbjct: 1 TIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTV---FDNYAVTVMIGGEPYTLGLFDTA 57
Query: 73 GQERFHALGPIYYRMSNGAVLVYDITDEDSFEKVK-NWVKELKKMLGNDICLTIAGNKID 131
GQE + L P+ Y ++ ++ + + SFE VK WV E+ L + G +ID
Sbjct: 58 GQEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFL-LVGTQID 116
Query: 132 L------------EKQRTVMQEDAEKYAQSVGAVHF-HTSAKMNRGIEEMFLE 171
L KQ+ + E EK A+ + AV + SA +G++ +F E
Sbjct: 117 LRDDPSTIEKLAKNKQKPITPETGEKLARDLKAVKYVECSALTQKGLKNVFDE 169
>gnl|CDD|128473 smart00176, RAN, Ran (Ras-related nuclear proteins) /TC4 subfamily
of small GTPases. Ran is involved in the active
transport of proteins through nuclear pores.
Length = 200
Score = 79.7 bits (196), Expect = 2e-18
Identities = 46/157 (29%), Positives = 86/157 (54%), Gaps = 3/157 (1%)
Query: 21 LGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQERFHAL 80
+G+G GKT+ V R++ +F +K++ TL + + +WDTAGQE+F L
Sbjct: 1 VGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIRFNVWDTAGQEKFGGL 60
Query: 81 GPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLEKQRTVMQ 140
YY A++++D+T +++ V NW ++L ++ N I + + GNK+D+ K R V
Sbjct: 61 RDGYYIQGQCAIIMFDVTARVTYKNVPNWHRDLVRVCEN-IPIVLCGNKVDV-KDRKVKA 118
Query: 141 EDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRML 177
+ + + ++ SAK N E+ FL L+++++
Sbjct: 119 KSI-TFHRKKNLQYYDISAKSNYNFEKPFLWLARKLI 154
>gnl|CDD|206702 cd04129, Rho2, Ras homology family 2 (Rho2) of small guanosine
triphosphatases (GTPases). Rho2 is a fungal GTPase that
plays a role in cell morphogenesis, control of cell wall
integrity, control of growth polarity, and maintenance
of growth direction. Rho2 activates the protein kinase C
homolog Pck2, and Pck2 controls Mok1, the major (1-3)
alpha-D-glucan synthase. Together with Rho1 (RhoA), Rho2
regulates the construction of the cell wall. Unlike
Rho1, Rho2 is not an essential protein, but its
overexpression is lethal. Most Rho proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for proper intracellular localization via
membrane attachment. As with other Rho family GTPases,
the GDP/GTP cycling is regulated by GEFs (guanine
nucleotide exchange factors), GAPs (GTPase-activating
proteins) and GDIs (guanine nucleotide dissociation
inhibitors).
Length = 190
Score = 79.1 bits (195), Expect = 3e-18
Identities = 50/187 (26%), Positives = 98/187 (52%), Gaps = 17/187 (9%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQER 76
K+V++G+G GKTS++ + +F E++ T+ +++ + GK + LA+WDTAGQE
Sbjct: 3 KLVIVGDGACGKTSLLYVFTLGEFPEEYHPTVFENYVTD-CRVDGKPVQLALWDTAGQEE 61
Query: 77 FHALGPIYYRMSNGAVLVYDITDEDSFEKVK-NWVKELKKMLGNDICLTIAGNKIDLE-- 133
+ L P+ Y ++ ++ + I DS E V+ W++E+++ N + + + G K DL
Sbjct: 62 YERLRPLSYSKAHVILIGFAIDTPDSLENVRTKWIEEVRRYCPN-VPVILVGLKKDLRQE 120
Query: 134 --------KQRTVMQEDAEKYAQSVGAVHFH-TSAKMNRGIEEMFLELSQR--MLEKAQE 182
V + A+ A+++GA + SA G++++F E + R +L +
Sbjct: 121 AVAKGNYATDEFVPIQQAKLVARAIGAKKYMECSALTGEGVDDVF-EAATRAALLVRKSG 179
Query: 183 FDLAKAS 189
+ A+
Sbjct: 180 KEEPGAN 186
>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 = 77.8 bits (192), Expect = 4e-18
Identities = 42/160 (26%), Positives = 77/160 (48%), Gaps = 10/160 (6%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQA----SFLNKKLNIAGKRLNLAIWDT 71
K+V++G+ VGK++++ R N+ IT + +++ + GK + DT
Sbjct: 2 IKIVIVGDPNVGKSTLLNRL---LGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDT 58
Query: 72 AGQERFHALGPIYYRMSNGAVLVYDIT--DEDSFEKVKNWVKELKKMLGNDICLTIAGNK 129
AGQE + A+ +YYR ++ V+DI D E ++ KE+ + + + + GNK
Sbjct: 59 AGQEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAESGVPIILVGNK 118
Query: 130 IDLEKQRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMF 169
IDL + + A +A+ G SA+ + I+ F
Sbjct: 119 IDL-RDAKLKTHVAFLFAKLNGEPIIPLSAETGKNIDSAF 157
>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 = 77.0 bits (190), Expect = 7e-18
Identities = 41/156 (26%), Positives = 83/156 (53%), Gaps = 8/156 (5%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKL-NIAGKRLNLAIWDTAGQE 75
K++L+G+G VGKTS+ + + +KF+ +T + + K+ K++ L +WD GQE
Sbjct: 3 KLMLVGQGGVGKTSLCKQLIGEKFDGDESSTHGINVQDWKIPAPERKKIRLNVWDFGGQE 62
Query: 76 RFHALGPIYYRMSNGAV--LVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLE 133
+HA + +++ ++ LV+D+ D +V W++++K G + + G ID
Sbjct: 63 IYHATHQFF--LTSRSLYLLVFDLRTGDEVSRVPYWLRQIKA-FGGVSPVILVGTHIDES 119
Query: 134 KQRTVMQEDA-EKYAQSVGAVHFHTSAKMNRGIEEM 168
++++ +K+ + +HF S K +GI E+
Sbjct: 120 CDEDILKKALNKKFPAIINDIHF-VSCKNGKGIAEL 154
>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 = 76.0 bits (187), Expect = 2e-17
Identities = 51/172 (29%), Positives = 88/172 (51%), Gaps = 21/172 (12%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIA--GKRLNLAIWDTAGQ 74
K V +G+G VGKT +++ Y + F ++ T+ F N N+ G +NL +WDTAGQ
Sbjct: 3 KCVTVGDGAVGKTCMLISYTSNTFPTDYVPTV---FDNFSANVVVDGNTVNLGLWDTAGQ 59
Query: 75 ERFHALGPIYYRMSNGAVLVYDITDEDSFEKV-KNWVKELKKMLGNDICLTIAGNKIDLE 133
E ++ L P+ YR ++ +L + + + S+E V K W+ EL+ + + + G K+DL
Sbjct: 60 EDYNRLRPLSYRGADVFLLAFSLISKASYENVLKKWIPELRHYAPG-VPIVLVGTKLDL- 117
Query: 134 KQRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRMLE---KAQE 182
++D + +A GAV T+ +G E + +E K Q+
Sbjct: 118 ------RDDKQFFADHPGAVPITTA----QGEELRKQIGAAAYIECSSKTQQ 159
>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 = 75.2 bits (185), Expect = 5e-17
Identities = 51/173 (29%), Positives = 87/173 (50%), Gaps = 20/173 (11%)
Query: 15 SFKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIA--GKRLNLAIWDTA 72
+ K V++G+G VGKT +++ Y + F ++I T+ F N N+ GK +NL +WDTA
Sbjct: 1 AIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTV---FDNYSANVMVDGKPVNLGLWDTA 57
Query: 73 GQERFHALGPIYYRMSNGAVLVYDITDEDSFEKVK-NWVKELKKMLGNDICLTIAGNKID 131
GQE + L P+ Y ++ ++ + + SFE V+ W E++ N + + G K+D
Sbjct: 58 GQEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILV-GTKLD 116
Query: 132 L------------EKQRTVMQEDAEKYAQSVGAV-HFHTSAKMNRGIEEMFLE 171
L +K + A+ +GAV + SA RG++ +F E
Sbjct: 117 LRDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDE 169
>gnl|CDD|133277 cd01875, RhoG, Ras homolog family, member G (RhoG) of small
guanosine triphosphatases (GTPases). RhoG is a GTPase
with high sequence similarity to members of the Rac
subfamily, including the regions involved in effector
recognition and binding. However, RhoG does not bind to
known Rac1 and Cdc42 effectors, including proteins
containing a Cdc42/Rac interacting binding (CRIB) motif.
Instead, RhoG interacts directly with Elmo, an upstream
regulator of Rac1, in a GTP-dependent manner and forms a
ternary complex with Dock180 to induce activation of
Rac1. The RhoG-Elmo-Dock180 pathway is required for
activation of Rac1 and cell spreading mediated by
integrin, as well as for neurite outgrowth induced by
nerve growth factor. Thus RhoG activates Rac1 through
Elmo and Dock180 to control cell morphology. RhoG has
also been shown to play a role in caveolar trafficking
and has a novel role in signaling the neutrophil
respiratory burst stimulated by G protein-coupled
receptor (GPCR) agonists. Most Rho proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Rho proteins.
Length = 191
Score = 74.3 bits (182), Expect = 1e-16
Identities = 47/177 (26%), Positives = 92/177 (51%), Gaps = 16/177 (9%)
Query: 15 SFKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQ 74
S K V++G+G VGKT +++ Y + F +++I T+ ++ + + + G+ ++L +WDTAGQ
Sbjct: 3 SIKCVVVGDGAVGKTCLLICYTTNAFPKEYIPTVFDNY-SAQTAVDGRTVSLNLWDTAGQ 61
Query: 75 ERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKN-WVKELKKMLGNDICLTIAGNKIDLE 133
E + L + Y +N ++ + I S+E V++ W E+ N + + + G K DL
Sbjct: 62 EEYDRLRTLSYPQTNVFIICFSIASPSSYENVRHKWHPEVCHHCPN-VPILLVGTKKDLR 120
Query: 134 KQRTVMQEDAEK------------YAQSVGAVHF-HTSAKMNRGIEEMFLELSQRML 177
+++ E+ A+ + AV + SA G++E+F E + +L
Sbjct: 121 NDADTLKKLKEQGQAPITPQQGGALAKQIHAVKYLECSALNQDGVKEVFAEAVRAVL 177
>gnl|CDD|206706 cd04134, Rho3, Ras homology family 3 (Rho3) of small guanosine
triphosphatases (GTPases). Rho3 is a member of the Rho
family found only in fungi. Rho3 is believed to regulate
cell polarity by interacting with the diaphanous/formin
family protein For3 to control both the actin
cytoskeleton and microtubules. Rho3 is also believed to
have a direct role in exocytosis that is independent of
its role in regulating actin polarity. The function in
exocytosis may be two-pronged: first, in the transport
of post-Golgi vesicles from the mother cell to the bud,
mediated by myosin (Myo2); second, in the docking and
fusion of vesicles to the plasma membrane, mediated by
an exocyst (Exo70) protein. Most Rho proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Rho proteins.
Length = 185
Score = 74.1 bits (182), Expect = 2e-16
Identities = 51/175 (29%), Positives = 91/175 (52%), Gaps = 20/175 (11%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQER 76
KVV+LG+G GKTS++ + F + + T+ ++++ + + G + L++WDTAGQE
Sbjct: 2 KVVVLGDGACGKTSLLNVFTRGYFPQVYEPTVFENYIHD-IFVDGLAVELSLWDTAGQEE 60
Query: 77 FHALGPIYYRMSNGAVLVYDITDEDSFEKVKN-WVKELKKMLGNDIC----LTIAGNKID 131
F L + Y ++ +L + + + DS E V++ W+ E++ C L + K D
Sbjct: 61 FDRLRSLSYADTHVIMLCFSVDNPDSLENVESKWLAEIR-----HHCPGVKLVLVALKCD 115
Query: 132 LEKQR--------TVMQEDAEKYAQSVGAVHF-HTSAKMNRGIEEMFLELSQRML 177
L + R T+ E+ A+ + A + SAK+NRG+ E F E ++ L
Sbjct: 116 LREPRNERDRGTHTISYEEGLAVAKRINACRYLECSAKLNRGVNEAFTEAARVAL 170
>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 = 71.3 bits (175), Expect = 4e-16
Identities = 35/117 (29%), Positives = 61/117 (52%), Gaps = 4/117 (3%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQER 76
KVV++G+ GK+S++ + V +F + + + L + G L IWD G+E
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREE 60
Query: 77 FHALGPIYYRMSNGAVLVYDITDEDSFEKVKN---WVKELKKMLGNDICLTIAGNKI 130
I+ + ++ +LVYD+TD +S +V W+ L+K LG I + + GNK+
Sbjct: 61 LKFEHIIFMKWADAILLVYDLTDRESLNEVSRLIAWLPNLRK-LGGKIPVILVGNKL 116
>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 = 70.7 bits (174), Expect = 2e-15
Identities = 40/167 (23%), Positives = 67/167 (40%), Gaps = 17/167 (10%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQER 76
++++LG GKT+++ + + T F + + + +WD GQ++
Sbjct: 1 RILMLGLDGAGKTTILYKLKLGEVVTTIPTI---GFNVETVEYKNVKFT--VWDVGGQDK 55
Query: 77 FHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGN----DICLTIAGNKIDL 132
L YY ++G + V D +D + E+ KN EL K+L L I NK DL
Sbjct: 56 IRPLWKHYYENTDGLIFVVDSSDRERIEEAKN---ELHKLLNEEELKGAPLLILANKQDL 112
Query: 133 EKQRTVMQEDAEKYAQSVGAVH-FH---TSAKMNRGIEEMFLELSQR 175
T E E +H SA G++E L ++
Sbjct: 113 PGALT-ESELIELLGLESIKGRRWHIQPCSAVTGDGLDEGLDWLIEQ 158
>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 = 69.9 bits (171), Expect = 4e-15
Identities = 45/163 (27%), Positives = 76/163 (46%), Gaps = 5/163 (3%)
Query: 17 KVVLLGEGCVGKTSVVLRYVED--KFNEKHITTLQASFLNKKLNI--AGKRLNLAIWDTA 72
+ ++G+ VGK+++V + D F + + T + K + + + L I+D+A
Sbjct: 2 QCAVVGDPAVGKSALVQMFHSDGATFQKNYTMTTGCDLVVKTVPVPDTSDSVELFIFDSA 61
Query: 73 GQERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELK-KMLGNDICLTIAGNKID 131
GQE F + + +VYD+T+E SF W+ ++ G + GNK D
Sbjct: 62 GQELFSDMVENVWEQPAVVCVVYDVTNEVSFNNCSRWINRVRTHSHGLHTPGVLVGNKCD 121
Query: 132 LEKQRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQ 174
L +R V A+ AQ+ + TSAK G E FL L++
Sbjct: 122 LTDRREVDAAQAQALAQANTLKFYETSAKEGVGYEAPFLSLAR 164
>gnl|CDD|206703 cd04131, Rnd, Rho family GTPase subfamily Rnd includes Rnd1/Rho6,
Rnd2/Rho7, and Rnd3/RhoE/Rho8. The Rnd subfamily
contains Rnd1/Rho6, Rnd2/Rho7, and Rnd3/RhoE/Rho8. These
novel Rho family proteins have substantial structural
differences compared to other Rho members, including N-
and C-terminal extensions relative to other Rhos.
Rnd3/RhoE is farnesylated at the C-terminal prenylation
site, unlike most other Rho proteins that are
geranylgeranylated. In addition, Rnd members are unable
to hydrolyze GTP and are resistant to GAP activity. They
are believed to exist only in the GTP-bound
conformation, and are antagonists of RhoA activity. Most
Rho proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 176
Score = 67.5 bits (165), Expect = 4e-14
Identities = 45/172 (26%), Positives = 84/172 (48%), Gaps = 25/172 (14%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITT----LQASFLNKKLNIAGKRLNLAIWDTA 72
K+VL+G+ GKT+++ + +D F E ++ T ASF + +R+ L++WDT+
Sbjct: 3 KIVLVGDSQCGKTALLQVFAKDSFPENYVPTVFENYTASF-----EVDKQRIELSLWDTS 57
Query: 73 GQERFHALGPIYYRMSNGAVLVYDITDEDSFEKV-KNWVKELKKMLGNDICLTIAGNKID 131
G + + P+ Y S+ ++ +DI+ ++ + V K W E+++ N L + G K D
Sbjct: 58 GSPYYDNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEVREFCPNTPVLLV-GCKSD 116
Query: 132 L------------EKQRTVMQEDAEKYAQSVGAVHF-HTSAK-MNRGIEEMF 169
L ++Q V E A+ +GA + SAK + ++F
Sbjct: 117 LRTDLSTLTELSNKRQIPVSHEQGRNLAKQIGAAAYVECSAKTSENSVRDVF 168
>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 = 58.7 bits (142), Expect = 9e-11
Identities = 44/173 (25%), Positives = 76/173 (43%), Gaps = 11/173 (6%)
Query: 15 SFKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIA---GKRLNLAIWDT 71
S +V+LG GKT+V+ R KFNE T F +K+ ++ K + WD
Sbjct: 3 SLHIVMLGLDSAGKTTVLYRL---KFNEFVNTVPTKGFNTEKIKVSLGNAKGVTFHFWDV 59
Query: 72 AGQERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGND-ICLTIAGNKI 130
GQE+ L Y R ++G V V D D + E+ K + ++ K N + + + NK
Sbjct: 60 GGQEKLRPLWKSYTRCTDGIVFVVDSVDVERMEEAKTELHKITKFSENQGVPVLVLANKQ 119
Query: 131 DLEKQRTVMQEDAEKYAQSVGAVHFH----TSAKMNRGIEEMFLELSQRMLEK 179
DL V + + + + A + G++E +L + +L++
Sbjct: 120 DLPNALPVSEVEKLLALHELSSSTPWHVQPACAIIGEGLQEGLEKLYEMILKR 172
>gnl|CDD|206735 cd04172, Rnd3_RhoE_Rho8, Rnd3/RhoE/Rho8 GTPases. Rnd3/RhoE/Rho8
subfamily. Rnd3/RhoE/Rho8 is a member of the novel Rho
subfamily Rnd, together with Rnd1/Rho6 and Rnd2/Rho7.
Rnd3/RhoE is known to bind the serine-threonine kinase
ROCK I. Unphosphorylated Rnd3/RhoE associates primarily
with membranes, but ROCK I-phosphorylated Rnd3/RhoE
localizes in the cytosol. Phosphorylation of Rnd3/RhoE
correlates with its activity in disrupting RhoA-induced
stress fibers and inhibiting Ras-induced fibroblast
transformation. In cells that lack stress fibers, such
as macrophages and monocytes, Rnd3/RhoE induces a
redistribution of actin, causing morphological changes
in the cell. In addition, Rnd3/RhoE has been shown to
inhibit cell cycle progression in G1 phase at a point
upstream of the pRb family pocket protein checkpoint.
Rnd3/RhoE has also been shown to inhibit Ras- and
Raf-induced fibroblast transformation. In mammary
epithelial tumor cells, Rnd3/RhoE regulates the assembly
of the apical junction complex and tight junction
formation. Rnd3/RhoE is underexpressed in prostate
cancer cells both in vitro and in vivo; re-expression of
Rnd3/RhoE suppresses cell cycle progression and
increases apoptosis, suggesting it may play a role in
tumor suppression. Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 182
Score = 57.8 bits (139), Expect = 1e-10
Identities = 33/126 (26%), Positives = 69/126 (54%), Gaps = 3/126 (2%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQER 76
K+V++G+ GKT+++ + +D F E ++ T+ ++ I +R+ L++WDT+G
Sbjct: 7 KIVVVGDSQCGKTALLHVFAKDCFPENYVPTVFENY-TASFEIDTQRIELSLWDTSGSPY 65
Query: 77 FHALGPIYYRMSNGAVLVYDITDEDSFEKV-KNWVKELKKMLGNDICLTIAGNKIDLEKQ 135
+ + P+ Y S+ ++ +DI+ ++ + V K W E+++ N L + G K DL
Sbjct: 66 YDNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEIQEFCPNTKMLLV-GCKSDLRTD 124
Query: 136 RTVMQE 141
+ + E
Sbjct: 125 VSTLVE 130
>gnl|CDD|206715 cd04148, RGK, Rem, Rem2, Rad, Gem/Kir (RGK) subfamily of Ras
GTPases. RGK subfamily. The RGK (Rem, Rem2, Rad,
Gem/Kir) subfamily of Ras GTPases are expressed in a
tissue-specific manner and are dynamically regulated by
transcriptional and posttranscriptional mechanisms in
response to environmental cues. RGK proteins bind to the
beta subunit of L-type calcium channels, causing
functional down-regulation of these voltage-dependent
calcium channels, and either termination of
calcium-dependent secretion or modulation of electrical
conduction and contractile function. Inhibition of
L-type calcium channels by Rem2 may provide a mechanism
for modulating calcium-triggered exocytosis in
hormone-secreting cells, and has been proposed to
influence the secretion of insulin in pancreatic beta
cells. RGK proteins also interact with and inhibit the
Rho/Rho kinase pathway to modulate remodeling of the
cytoskeleton. Two characteristics of RGK proteins cited
in the literature are N-terminal and C-terminal
extensions beyond the GTPase domain typical of Ras
superfamily members. The N-terminal extension is not
conserved among family members; the C-terminal extension
is reported to be conserved among the family and lack
the CaaX prenylation motif typical of
membrane-associated Ras proteins. However, a putative
CaaX motif has been identified in the alignment of the
C-terminal residues of this CD.
Length = 219
Score = 57.8 bits (140), Expect = 2e-10
Identities = 40/155 (25%), Positives = 72/155 (46%), Gaps = 1/155 (0%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE 75
++VVLLG+ VGK+S+ + + + + +++ G+ L ++D QE
Sbjct: 1 YRVVLLGDSGVGKSSLANIFTAGVYEDSAYEASGDDTYERTVSVDGEEATLVVYDHWEQE 60
Query: 76 RFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKM-LGNDICLTIAGNKIDLEK 134
L ++ + V+VY +TD SFEK +L++ DI + + GNK DL +
Sbjct: 61 DGMWLEDSCMQVGDAYVIVYSVTDRSSFEKASELRIQLRRARQAEDIPIILVGNKSDLVR 120
Query: 135 QRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMF 169
R V ++ A TSA + ++E+F
Sbjct: 121 SREVSVQEGRACAVVFDCKFIETSAALQHNVDELF 155
>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 = 56.4 bits (136), Expect = 5e-10
Identities = 42/137 (30%), Positives = 65/137 (47%), Gaps = 21/137 (15%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWD----- 70
+V +LG VGKT++V +++ +F E++I T + ++G+ +L I D
Sbjct: 1 VRVAVLGAPGVGKTAIVRQFLAQEFPEEYIPTEHRRLYRPAVVLSGRVYDLHILDVPNMQ 60
Query: 71 ----TAGQE----RFHALGPIYYRMSNGAVLVYDITDEDSFEKVK---NWVKELKKMLGN 119
TAGQE RF L R S +LVYDI DSF VK + E +
Sbjct: 61 RYPGTAGQEWMDPRFRGL-----RNSRAFILVYDICSPDSFHYVKLLRQQILETRPAGNK 115
Query: 120 DICLTIAGNKIDLEKQR 136
+ + + GNK D ++ R
Sbjct: 116 EPPIVVVGNKRDQQRHR 132
>gnl|CDD|206736 cd04173, Rnd2_Rho7, Rnd2/Rho7 GTPases. Rnd2/Rho7 is a member of
the novel Rho subfamily Rnd, together with Rnd1/Rho6 and
Rnd3/RhoE/Rho8. Rnd2/Rho7 is transiently expressed in
radially migrating cells in the brain while they are
within the subventricular zone of the hippocampus and
cerebral cortex. These migrating cells typically develop
into pyramidal neurons. Cells that exogenously expressed
Rnd2/Rho7 failed to migrate to upper layers of the
brain, suggesting that Rnd2/Rho7 plays a role in the
radial migration and morphological changes of developing
pyramidal neurons, and that Rnd2/Rho7 degradation is
necessary for proper cellular migration. The Rnd2/Rho7
GEF Rapostlin is found primarily in the brain and
together with Rnd2/Rho7 induces dendrite branching.
Unlike Rnd1/Rho6 and Rnd3/RhoE/Rho8, which are RhoA
antagonists, Rnd2/Rho7 binds the GEF Pragmin and
significantly stimulates RhoA activity and Rho-A
mediated cell contraction. Rnd2/Rho7 is also found to be
expressed in spermatocytes and early spermatids, with
male-germ-cell Rac GTPase-activating protein
(MgcRacGAP), where it localizes to the Golgi-derived
pro-acrosomal vesicle. Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Length = 221
Score = 55.8 bits (134), Expect = 1e-09
Identities = 47/197 (23%), Positives = 88/197 (44%), Gaps = 33/197 (16%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQER 76
K+V++G+ GKT+++ + +D + E ++ T+ ++ I R+ L +WDT+G
Sbjct: 3 KIVVVGDTQCGKTALLHVFAKDNYPESYVPTVFENY-TASFEIDKHRIELNMWDTSGSSY 61
Query: 77 FHALGPIYYRMSNGAVLVYDITDEDSFEKV-KNWVKELKKMLGNDICLTIAGNKID---- 131
+ + P+ Y S+ ++ +DI+ ++ + V K W E ++ N L + G K+D
Sbjct: 62 YDNVRPLAYPDSDAVLICFDISRPETLDSVLKKWQGETQEFCPN-AKLVLVGCKLDMRTD 120
Query: 132 ------LEKQR--TVMQEDAEKYAQSVGAV------------------HFHTSAKMNRGI 165
L KQR V E A+ +GAV H T A + R
Sbjct: 121 LSTLRELSKQRLIPVTHEQGSLLARQLGAVAYVECSSRMSENSVRDVFHVTTLASVRREH 180
Query: 166 EEMFLELSQRMLEKAQE 182
+ S+R L++ +
Sbjct: 181 PSLKRSTSRRGLKRISQ 197
>gnl|CDD|206737 cd04174, Rnd1_Rho6, Rnd1/Rho6 GTPases. Rnd1/Rho6 is a member of
the novel Rho subfamily Rnd, together with Rnd2/Rho7 and
Rnd3/RhoE/Rho8. Rnd1/Rho6 binds GTP but does not
hydrolyze it to GDP, indicating that it is
constitutively active. In rat, Rnd1/Rho6 is highly
expressed in the cerebral cortex and hippocampus during
synapse formation, and plays a role in spine formation.
Rnd1/Rho6 is also expressed in the liver and in
endothelial cells, and is upregulated in uterine
myometrial cells during pregnancy. Like Rnd3/RhoE/Rho8,
Rnd1/Rho6 is believed to function as an antagonist to
RhoA. Most Rho proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Rho proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 232
Score = 55.8 bits (134), Expect = 1e-09
Identities = 49/193 (25%), Positives = 90/193 (46%), Gaps = 15/193 (7%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQER 76
K+VL+G+ GKT+++ +D + E ++ T+ ++ L +R+ L++WDT+G
Sbjct: 15 KLVLVGDVQCGKTAMLQVLAKDCYPETYVPTVFENY-TACLETEEQRVELSLWDTSGSPY 73
Query: 77 FHALGPIYYRMSNGAVLVYDITDEDSFEK-VKNWVKELKKMLGNDICLTIAGNKIDLEKQ 135
+ + P+ Y S+ +L +DI+ + F+ +K W E+ + L I G K DL
Sbjct: 74 YDNVRPLCYSDSDAVLLCFDISRPEIFDSALKKWRAEILDYCPSTRILLI-GCKTDL--- 129
Query: 136 RTVMQEDAEKYAQSVGAVHFHTSAKMNRGI-EEMFLELSQRMLEK--------AQEFDLA 186
RT + E Q + + M + + E +LE S EK A +
Sbjct: 130 RTDLSTLMELSNQKQAPISYEQGCAMAKQLGAEAYLECSAFTSEKSIHSIFRTASLLCIN 189
Query: 187 KASELSRRGSMRR 199
K S L+++ +R
Sbjct: 190 KLSPLAKKSPVRS 202
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 52.6 bits (127), Expect = 1e-08
Identities = 30/122 (24%), Positives = 52/122 (42%), Gaps = 12/122 (9%)
Query: 15 SFKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQ 74
++++LG GKT+++ + + I T+ F + + + +WD GQ
Sbjct: 14 EMRILILGLDNAGKTTILYKLKLGEIVT-TIPTI--GFNVETVTYKNVKFT--VWDVGGQ 68
Query: 75 ERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGND----ICLTIAGNKI 130
E L Y+ ++ + V D D D E+ K +EL +L + L I NK
Sbjct: 69 ESLRPLWRNYFPNTDAVIFVVDSADRDRIEEAK---EELHALLNEEELADAPLLILANKQ 125
Query: 131 DL 132
DL
Sbjct: 126 DL 127
>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 = 52.3 bits (126), Expect = 1e-08
Identities = 34/136 (25%), Positives = 64/136 (47%), Gaps = 19/136 (13%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEK-----HITTLQASFLNKKLNIAGKRLNLAIWDT 71
++VL+G+ VGK+S+++ V ++F E T+ A +R+ I DT
Sbjct: 4 RIVLIGDEGVGKSSLIMSLVSEEFPENVPRVLPEITIPADVTP-------ERVPTTIVDT 56
Query: 72 --AGQERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKN-WVKELKKMLGNDICLTIAGN 128
Q+R + I R +N LVY + + E+++ W+ +++ LG + + + GN
Sbjct: 57 SSRPQDRANLAAEI--RKANVICLVYSVDRPSTLERIRTKWLPLIRR-LGVKVPIILVGN 113
Query: 129 KIDL-EKQRTVMQEDA 143
K DL + E+
Sbjct: 114 KSDLRDGSSQAGLEEE 129
>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 = 49.3 bits (118), Expect = 1e-07
Identities = 34/124 (27%), Positives = 50/124 (40%), Gaps = 17/124 (13%)
Query: 57 LNIAGKRLN---LAIWDTAGQERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKEL 113
LNI + L WD GQE +L YY S+G + V D TD + F + K+
Sbjct: 41 LNIGTIEVGKARLMFWDLGGQEELRSLWDKYYAESHGVIYVIDSTDRERFNESKS---AF 97
Query: 114 KKMLGN----DICLTIAGNKIDLEKQ------RTVMQEDAEKYAQSVGAVHFHTSAKMNR 163
+K++ N + L + NK DL + V + + V SA
Sbjct: 98 EKVINNEALEGVPLLVLANKQDLPDALSVAEIKEVFDDCIALIGRRDCLVQ-PVSALEGE 156
Query: 164 GIEE 167
G+EE
Sbjct: 157 GVEE 160
>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 = 48.9 bits (117), Expect = 2e-07
Identities = 34/111 (30%), Positives = 48/111 (43%), Gaps = 11/111 (9%)
Query: 27 GKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQERFHALGPIYYR 86
GKT++V +F+E I T+ + + + +WD GQ RF ++ Y R
Sbjct: 11 GKTTLVNVIASGQFSEDTIPTVGFNMRKVTKG----NVTIKVWDLGGQPRFRSMWERYCR 66
Query: 87 MSNGAVLVYDITDEDSFEKVKNWVKELKKMLG----NDICLTIAGNKIDLE 133
N V V D D + E KN EL +L I L + GNK DL
Sbjct: 67 GVNAIVYVVDAADREKLEVAKN---ELHDLLEKPSLEGIPLLVLGNKNDLP 114
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 46.8 bits (111), Expect = 1e-06
Identities = 33/128 (25%), Positives = 60/128 (46%), Gaps = 12/128 (9%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQER 76
+++++G GKT+++ + K E +TT+ N + + K L +WD GQ++
Sbjct: 19 RILMVGLDAAGKTTILYKL---KLGEV-VTTIPTIGFNVE-TVEYKNLKFTMWDVGGQDK 73
Query: 77 FHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGND----ICLTIAGNKIDL 132
L YY+ +NG + V D D + + +EL++ML D L + NK DL
Sbjct: 74 LRPLWRHYYQNTNGLIFVVDSNDRERIGDAR---EELERMLSEDELRDAVLLVFANKQDL 130
Query: 133 EKQRTVMQ 140
+ +
Sbjct: 131 PNAMSTTE 138
>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 = 46.5 bits (111), Expect = 2e-06
Identities = 43/177 (24%), Positives = 76/177 (42%), Gaps = 27/177 (15%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQER 76
K+V LG GKT+++ +D+ + H+ TL + +++L I + +D G E+
Sbjct: 21 KIVFLGLDNAGKTTLLHMLKDDRLAQ-HVPTLHPT--SEELTIGN--VKFTTFDLGGHEQ 75
Query: 77 FHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGND----ICLTIAGNKIDL 132
+ Y+ +G V + D D + F++ K +EL +L ++ + + I GNKID
Sbjct: 76 ARRVWKDYFPEVDGIVFLVDAADPERFQESK---EELDSLLNDEELANVPILILGNKIDK 132
Query: 133 ------EKQRTVM-----QEDAEKYAQSVGAVH----FHTSAKMNRGIEEMFLELSQ 174
E+ R + + V + F S +G E F LSQ
Sbjct: 133 PGAVSEEELREALGLYGTTTGKGGVSLKVSNIRPVEVFMCSVVKRQGYGEGFRWLSQ 189
>gnl|CDD|206716 cd04149, Arf6, ADP ribosylation factor 6 (Arf6). Arf6 subfamily.
Arf6 (ADP ribosylation factor 6) proteins localize to
the plasma membrane, where they perform a wide variety
of functions. In its active, GTP-bound form, Arf6 is
involved in cell spreading, Rac-induced formation of
plasma membrane ruffles, cell migration, wound healing,
and Fc-mediated phagocytosis. Arf6 appears to change the
actin structure at the plasma membrane by activating
Rac, a Rho family protein involved in membrane ruffling.
Arf6 is required for and enhances Rac formation of
ruffles. Arf6 can regulate dendritic branching in
hippocampal neurons, and in yeast it localizes to the
growing bud, where it plays a role in polarized growth
and bud site selection. In leukocytes, Arf6 is required
for chemokine-stimulated migration across endothelial
cells. Arf6 also plays a role in down-regulation of
beta2-adrenergic receptors and luteinizing hormone
receptors by facilitating the release of sequestered
arrestin to allow endocytosis. Arf6 is believed to
function at multiple sites on the plasma membrane
through interaction with a specific set of GEFs, GAPs,
and effectors. Arf6 has been implicated in breast cancer
and melanoma cell invasion, and in actin remodelling at
the invasion site of Chlamydia infection.
Length = 168
Score = 44.8 bits (106), Expect = 6e-06
Identities = 30/120 (25%), Positives = 58/120 (48%), Gaps = 12/120 (10%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQER 76
++++LG GKT+++ + K + +TT+ N + + K + +WD GQ++
Sbjct: 11 RILMLGLDAAGKTTILYKL---KLG-QSVTTIPTVGFNVE-TVTYKNVKFNVWDVGGQDK 65
Query: 77 FHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGN----DICLTIAGNKIDL 132
L YY + G + V D D D ++ + +EL +++ + D L + NK DL
Sbjct: 66 IRPLWRHYYTGTQGLIFVVDSADRDRIDEAR---QELHRIINDREMRDALLLVFANKQDL 122
>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 = 43.6 bits (103), Expect = 1e-05
Identities = 34/120 (28%), Positives = 60/120 (50%), Gaps = 11/120 (9%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQER 76
+V+LLG GK++++ + + +TT+ N ++ K L+L +WD GQE+
Sbjct: 1 QVLLLGLDSAGKSTLLYKLKHAEL----VTTIPTVGFNVEMLQLEKHLSLTVWDVGGQEK 56
Query: 77 FHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGN----DICLTIAGNKIDL 132
+ Y ++G V V D +DE ++ + KELK +L N + + + NK DL
Sbjct: 57 MRTVWKCYLENTDGLVYVVDSSDEARLDESQ---KELKHILKNEHIKGVPVVLLANKQDL 113
>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 = 43.4 bits (102), Expect = 2e-05
Identities = 31/120 (25%), Positives = 58/120 (48%), Gaps = 12/120 (10%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQER 76
+++++G GKT+++ + K E +TT+ N + + K ++ +WD GQ++
Sbjct: 15 RILMVGLDAAGKTTILYKL---KLGES-VTTIPTIGFNVE-TVTYKNISFTVWDVGGQDK 69
Query: 77 FHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGN----DICLTIAGNKIDL 132
L YY + G + V D D D ++ + +EL +ML D + + NK DL
Sbjct: 70 IRPLWRHYYTNTQGLIFVVDSNDRDRIDEAR---EELHRMLNEDELRDAVILVFANKQDL 126
>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 = 42.4 bits (100), Expect = 4e-05
Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 7/75 (9%)
Query: 62 KRLNLAIWDTAGQERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGND- 120
K ++ +WD GQ++ L Y++ + G + V D D + + + EL++ML D
Sbjct: 42 KNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERIGEARE---ELQRMLNEDE 98
Query: 121 ---ICLTIAGNKIDL 132
L + NK DL
Sbjct: 99 LRDAVLLVFANKQDL 113
>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 = 42.0 bits (99), Expect = 6e-05
Identities = 33/122 (27%), Positives = 55/122 (45%), Gaps = 12/122 (9%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQE 75
+KV+++G GKT+++ Y +F + + + I K + +WD GQE
Sbjct: 16 YKVIIVGLDNAGKTTIL--Y---QFLLGEVVHTSPTIGSNVEEIVYKNIRFLMWDIGGQE 70
Query: 76 RFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGN----DICLTIAGNKID 131
+ YY ++ +LV D TD + K +EL KML + L + NK D
Sbjct: 71 SLRSSWNTYYTNTDAVILVIDSTDRERLPLTK---EELYKMLAHEDLRKAVLLVLANKQD 127
Query: 132 LE 133
L+
Sbjct: 128 LK 129
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 41.1 bits (96), Expect = 1e-04
Identities = 31/120 (25%), Positives = 58/120 (48%), Gaps = 12/120 (10%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQER 76
+++++G GKT+++ + K E +TT+ N + + K ++ +WD GQ++
Sbjct: 19 RILMVGLDAAGKTTILYKL---KLGEI-VTTIPTIGFNVE-TVEYKNISFTVWDVGGQDK 73
Query: 77 FHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGN----DICLTIAGNKIDL 132
L Y++ + G + V D D D + ++ EL +ML D L + NK DL
Sbjct: 74 IRPLWRHYFQNTQGLIFVVDSNDRDRVVEARD---ELHRMLNEDELRDAVLLVFANKQDL 130
>gnl|CDD|206723 cd04158, ARD1, (ADP-ribosylation factor domain protein 1 (ARD1).
ARD1 (ADP-ribosylation factor domain protein 1) is an
unusual member of the Arf family. In addition to the
C-terminal Arf domain, ARD1 has an additional 46-kDa
N-terminal domain that contains a RING finger domain,
two predicted B-Boxes, and a coiled-coil protein
interaction motif. This domain belongs to the TRIM
(tripartite motif) or RBCC (RING, B-Box, coiled-coil)
family. Like most Arfs, the ARD1 Arf domain lacks
detectable GTPase activity. However, unlike most Arfs,
the full-length ARD1 protein has significant GTPase
activity due to the GAP (GTPase-activating protein)
activity exhibited by the 46-kDa N-terminal domain. The
GAP domain of ARD1 is specific for its own Arf domain
and does not bind other Arfs. The rate of GDP
dissociation from the ARD1 Arf domain is slowed by the
adjacent 15 amino acids, which act as a GDI
(GDP-dissociation inhibitor) domain. ARD1 is
ubiquitously expressed in cells and localizes to the
Golgi and to the lysosomal membrane. Two Tyr-based
motifs in the Arf domain are responsible for Golgi
localization, while the GAP domain controls lysosomal
localization.
Length = 169
Score = 40.8 bits (95), Expect = 2e-04
Identities = 34/121 (28%), Positives = 53/121 (43%), Gaps = 12/121 (9%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQER 76
+VV LG GKT+++ + +D+F + I T+ + + K L IWD G+ +
Sbjct: 1 RVVTLGLDGAGKTTILFKLKQDEFMQP-IPTIGFNVET----VEYKNLKFTIWDVGGKHK 55
Query: 77 FHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGN----DICLTIAGNKIDL 132
L YY + V V D + D + + EL K+L D L I NK D+
Sbjct: 56 LRPLWKHYYLNTQAVVFVIDSSHRDRVSEAHS---ELAKLLTEKELRDALLLIFANKQDV 112
Query: 133 E 133
Sbjct: 113 A 113
>gnl|CDD|133275 cd01873, RhoBTB, RhoBTB protein is an atypical member of the Rho
family of small GTPases. Members of the RhoBTB
subfamily of Rho GTPases are present in vertebrates,
Drosophila, and Dictyostelium. RhoBTB proteins are
characterized by a modular organization, consisting of a
GTPase domain, a proline rich region, a tandem of two
BTB (Broad-Complex, Tramtrack, and Bric a brac) domains,
and a C-terminal region of unknown function. RhoBTB
proteins may act as docking points for multiple
components participating in signal transduction
cascades. RhoBTB genes appeared upregulated in some
cancer cell lines, suggesting a participation of RhoBTB
proteins in the pathogenesis of particular tumors. Note
that the Dictyostelium RacA GTPase domain is more
closely related to Rac proteins than to RhoBTB proteins,
where RacA actually belongs. Thus, the Dictyostelium
RacA is not included here. Most Rho proteins contain a
lipid modification site at the C-terminus; however,
RhoBTB is one of few Rho subfamilies that lack this
feature.
Length = 195
Score = 40.0 bits (93), Expect = 3e-04
Identities = 38/192 (19%), Positives = 74/192 (38%), Gaps = 44/192 (22%)
Query: 16 FKVVLLGEGCVGKTSVVL-----RYVEDK-FNEKHITTL---------QASFLNKKLNIA 60
K V++G+ VGKT ++ + + H+ T+ Q + +
Sbjct: 3 IKCVVVGDNAVGKTRLICARACNKTLTQYQLLATHVPTVWAIDQYRVCQEVLERSRDVVD 62
Query: 61 GKRLNLAIWDTAG---QERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKN-WVKELKKM 116
G ++L +WDT G ++R A G S+ +L + I +S VK W E++
Sbjct: 63 GVSVSLRLWDTFGDHDKDRRFAYG-----RSDVVLLCFSIASPNSLRNVKTMWYPEIRHF 117
Query: 117 LGNDICLTIAGNKIDL-------------------EKQRTVMQEDAEKYAQSVGAVHFHT 157
+ + + G K+DL + + E A+ +G ++ T
Sbjct: 118 C-PRVPVILVGCKLDLRYADLDEVNRARRPLARPIKNADILPPETGRAVAKELGIPYYET 176
Query: 158 SAKMNRGIEEMF 169
S G++++F
Sbjct: 177 SVVTQFGVKDVF 188
>gnl|CDD|177661 PLN00023, PLN00023, GTP-binding protein; Provisional.
Length = 334
Score = 40.6 bits (95), Expect = 4e-04
Identities = 26/111 (23%), Positives = 54/111 (48%), Gaps = 15/111 (13%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDK------------FNEKHIT--TLQASFLNKKLNIAGK 62
+V+++G+ VGK+S+V V+ KHIT + +S + K + + +
Sbjct: 23 RVLVVGDSGVGKSSLVHLIVKGSSIARPPQTIGCTVGVKHITYGSPGSSSNSIKGD-SER 81
Query: 63 RLNLAIWDTAGQERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKEL 113
+ +WD +G ER+ ++Y NG + V+D++ + ++ W E+
Sbjct: 82 DFFVELWDVSGHERYKDCRSLFYSQINGVIFVHDLSQRRTKTSLQKWASEV 132
>gnl|CDD|206720 cd04154, Arl2, Arf-like 2 (Arl2) GTPase. Arl2 (Arf-like 2) GTPases
are members of the Arf family that bind GDP and GTP with
very low affinity. Unlike most Arf family proteins, Arl2
is not myristoylated at its N-terminal helix. The
protein PDE-delta, first identified in photoreceptor rod
cells, binds specifically to Arl2 and is structurally
very similar to RhoGDI. Despite the high structural
similarity between Arl2 and Rho proteins and between
PDE-delta and RhoGDI, the interactions between the
GTPases and their effectors are very different. In its
GTP bound form, Arl2 interacts with the protein Binder
of Arl2 (BART), and the complex is believed to play a
role in mitochondrial adenine nucleotide transport. In
its GDP bound form, Arl2 interacts with tubulin- folding
Cofactor D; this interaction is believed to play a role
in regulation of microtubule dynamics that impact the
cytoskeleton, cell division, and cytokinesis.
Length = 173
Score = 39.2 bits (92), Expect = 5e-04
Identities = 37/123 (30%), Positives = 59/123 (47%), Gaps = 16/123 (13%)
Query: 16 FKVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQAS--FLNKKLNIAGKRLNLAIWDTAG 73
++++LG GKT+++ KFN + I+T+ + F K L G +LN IWD G
Sbjct: 15 MRILMLGLDNAGKTTILK-----KFNGEDISTISPTLGFNIKTLEYNGYKLN--IWDVGG 67
Query: 74 QERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGND----ICLTIAGNK 129
Q+ + Y+ ++ + V D +D E K EL+K+L + L I NK
Sbjct: 68 QKSLRSYWRNYFESTDALIWVVDSSDRARLEDCKR---ELQKLLVEERLAGATLLIFANK 124
Query: 130 IDL 132
DL
Sbjct: 125 QDL 127
>gnl|CDD|206722 cd04157, Arl6, Arf-like 6 (Arl6) GTPase. Arl6 (Arf-like 6) forms a
subfamily of the Arf family of small GTPases. Arl6
expression is limited to the brain and kidney in adult
mice, but it is expressed in the neural plate and
somites during embryogenesis, suggesting a possible role
for Arl6 in early development. Arl6 is also believed to
have a role in cilia or flagella function. Several
proteins have been identified that bind Arl6, including
Arl6 interacting protein (Arl6ip), and SEC61beta, a
subunit of the heterotrimeric conducting channel SEC61p.
Based on Arl6 binding to these effectors, Arl6 is also
proposed to play a role in protein transport, membrane
trafficking, or cell signaling during hematopoietic
maturation. At least three specific homozygous Arl6
mutations in humans have been found to cause
Bardet-Biedl syndrome, a disorder characterized by
obesity, retinopathy, polydactyly, renal and cardiac
malformations, learning disabilities, and
hypogenitalism. Older literature suggests that Arl6 is a
part of the Arl4/Arl7 subfamily, but analyses based on
more recent sequence data place Arl6 in its own
subfamily.
Length = 162
Score = 38.6 bits (90), Expect = 6e-04
Identities = 21/82 (25%), Positives = 35/82 (42%), Gaps = 9/82 (10%)
Query: 64 LNLAIWDTAGQERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKML------ 117
L+ +D +GQ ++ L YY+ G + V D +D K+ EL+ +L
Sbjct: 45 LSFTAFDMSGQGKYRGLWEHYYKNIQGIIFVIDSSDRLRMVVAKD---ELELLLNHPDIK 101
Query: 118 GNDICLTIAGNKIDLEKQRTVM 139
I + NK+DL T +
Sbjct: 102 HRRIPILFYANKMDLPDALTAV 123
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 39.0 bits (91), Expect = 7e-04
Identities = 29/136 (21%), Positives = 52/136 (38%), Gaps = 22/136 (16%)
Query: 17 KVVLLGEGCVGKTSVV------------LRYVEDKFNEKHITTLQASFLNKKLNIAGKRL 64
K+V++G GKT+ V K TT+ F + +
Sbjct: 12 KIVVIGPVGAGKTTFVRALSDKPLVITEADASSVSGKGKRPTTVAMDFGS---IELDEDT 68
Query: 65 NLAIWDTAGQERFHALGPIYYRMSNGAVLVYDITDEDSFEKVK--NWVKELKKMLGNDIC 122
+ ++ T GQERF + I R + GA+++ D + +F + +++ I
Sbjct: 69 GVHLFGTPGQERFKFMWEILSRGAVGAIVLVDSSRPITFHAEEIIDFLTSRNP-----IP 123
Query: 123 LTIAGNKIDLEKQRTV 138
+ +A NK DL
Sbjct: 124 VVVAINKQDLFDALPP 139
>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 = 36.5 bits (85), Expect = 0.004
Identities = 22/54 (40%), Positives = 29/54 (53%), Gaps = 4/54 (7%)
Query: 91 AVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLEK--QRTVMQED 142
A LVYD +D +SF V + MLG CL +A K DL++ QR +Q D
Sbjct: 81 ACLVYDSSDPNSFSYCAE-VYKKYFMLGEIPCLFVAA-KADLDEQQQRAEVQPD 132
>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 = 33.9 bits (78), Expect = 0.030
Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 5/77 (6%)
Query: 63 RLNLAIWDTAGQERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKEL---KKMLGN 119
+ + I+D G F + YY ++G V V D +D+D ++VK ++EL ++ G
Sbjct: 42 KYEVCIFDLGGGANFRGIWVNYYAEAHGLVFVVDSSDDDRVQEVKEILRELLQHPRVSGK 101
Query: 120 DICLTIAGNKIDLEKQR 136
I L +A NK D +
Sbjct: 102 PI-LVLA-NKQDKKNAL 116
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 33.9 bits (79), Expect = 0.050
Identities = 21/100 (21%), Positives = 36/100 (36%), Gaps = 18/100 (18%)
Query: 92 VLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLEKQRTVMQEDAEKYAQSVG 151
+LV D ++ + E + + K I + NK DL + + +E+ G
Sbjct: 299 LLVLDASEPLTEEDDEILEELKDK---PVIVV---LNKADLTGEIDLEEEN--------G 344
Query: 152 AVHFHTSAKMNRGIEEMFLELSQRMLEKAQEFDLAKASEL 191
SAK GI+ EL + + E A +
Sbjct: 345 KPVIRISAKTGEGID----ELREAIKELAFGGFGGNQEGV 380
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 33.5 bits (78), Expect = 0.074
Identities = 26/96 (27%), Positives = 44/96 (45%), Gaps = 7/96 (7%)
Query: 92 VLVY--DITDEDSFEKVKNWVKELKKM---LGNDICLTIAGNKIDLEKQRTVMQEDAEKY 146
+L++ DI D E K EL+K L + + + NKIDL + ++ A
Sbjct: 239 LLLHLVDIEAVDPVEDYKTIRNELEKYSPELADKPRI-LVLNKIDLLDEEEEREKRAALE 297
Query: 147 AQSVGAVHFHTSAKMNRGIEEMFLELSQRMLEKAQE 182
++G F SA G++E+ L +LE+A+
Sbjct: 298 LAALGGPVFLISAVTGEGLDEL-LRALWELLEEARR 332
>gnl|CDD|206689 cd04102, RabL3, Rab GTPase-like family 3 (Rab-like3). RabL3
(Rab-like3) subfamily. RabL3s are novel proteins that
have high sequence similarity with Rab family members,
but display features that are distinct from Rabs, and
have been termed Rab-like. As in other Rab-like
proteins, RabL3 lacks a prenylation site at the
C-terminus. The specific function of RabL3 remains
unknown.
Length = 204
Score = 32.6 bits (74), Expect = 0.093
Identities = 25/116 (21%), Positives = 44/116 (37%), Gaps = 31/116 (26%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNI----------------A 60
KV++LG+ VGK+S+V H+ N +
Sbjct: 2 KVLVLGDSGVGKSSLV-----------HLLCKNQVLGNPSWTVGCSVDVRHHTYGEGTPE 50
Query: 61 GKRLNLAIWDTAGQ----ERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKE 112
K + +WD G E + ++Y NG + V+D+T++ S + + W E
Sbjct: 51 EKTFYVELWDVGGSVGSAESVKSTRAVFYNQINGIIFVHDLTNKKSSQNLYRWSLE 106
>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 = 32.5 bits (74), Expect = 0.094
Identities = 32/164 (19%), Positives = 67/164 (40%), Gaps = 11/164 (6%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQER 76
K+ ++G GK+++V RY+ + + + K++ + G+ L I D G
Sbjct: 2 KLGIVGNLRSGKSALVHRYLTGSYVQLESP--EGGRFKKEVLVDGQSHLLLIRDEGGA-- 57
Query: 77 FHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLG-NDICLTIAG--NKIDLE 133
+ + + V+ + DE SF+ V +L ++I L + G + I
Sbjct: 58 ---PDAQFAGWVDAVIFVFSLEDEASFQTVYRLYHQLSSYRNISEIPLILVGTQDAISAS 114
Query: 134 KQRTVMQEDAEKYAQSVG-AVHFHTSAKMNRGIEEMFLELSQRM 176
R + A + + ++ T A +E +F E +Q++
Sbjct: 115 NPRVIDDARARQLCADMKRCSYYETCATYGLNVERVFQEAAQKI 158
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 33.2 bits (77), Expect = 0.11
Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 125 IAGNKIDLEKQRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRMLEKAQEFD 184
+ NK+DL + ++E EK V F SA +G++E+ ++ +LE+ EF
Sbjct: 279 VVANKMDLPEAEENLEEFKEKLGPKV----FPISALTGQGLDELLYAVA-ELLEETPEFP 333
Query: 185 L 185
L
Sbjct: 334 L 334
>gnl|CDD|206718 cd04151, Arl1, ADP ribosylation factor 1 (Arf1). Arl1 subfamily.
Arl1 (Arf-like 1) localizes to the Golgi complex, where
it is believed to recruit effector proteins to the
trans-Golgi network. Like most members of the Arf
family, Arl1 is myristoylated at its N-terminal helix
and mutation of the myristoylation site disrupts Golgi
targeting. In humans, the Golgi-localized proteins
golgin-97 and golgin-245 have been identified as Arl1
effectors. Golgins are large coiled-coil proteins found
in the Golgi, and these golgins contain a C-terminal
GRIP domain, which is the site of Arl1 binding.
Additional Arl1 effectors include the GARP
(Golgi-associated retrograde protein)/VFT (Vps53)
vesicle-tethering complex and Arfaptin 2. Arl1 is not
required for exocytosis, but appears necessary for
trafficking from the endosomes to the Golgi. In
Drosophila zygotes, mutation of Arl1 is lethal, and in
the host-bloodstream form of Trypanosoma brucei, Arl1 is
essential for viability.
Length = 158
Score = 32.0 bits (73), Expect = 0.12
Identities = 32/121 (26%), Positives = 51/121 (42%), Gaps = 12/121 (9%)
Query: 17 KVVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQER 76
++++LG GKT+++ R + E +TT+ N + + K L +WD GQ
Sbjct: 1 RILILGLDGAGKTTILYRL---QVGEV-VTTIPTIGFNVE-TVTYKNLKFQVWDLGGQTS 55
Query: 77 FHALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGND----ICLTIAGNKIDL 132
YY ++ + V D TD D K EL ML + L + NK D+
Sbjct: 56 IRPYWRCYYSNTDAIIYVVDSTDRDRLGISK---SELHAMLEEEELKDAVLLVFANKQDM 112
Query: 133 E 133
Sbjct: 113 P 113
>gnl|CDD|238282 cd00508, MopB_CT_Fdh-Nap-like, This CD includes formate
dehydrogenases (Fdh) H and N; nitrate reductases, Nap
and Nas; and other related proteins. Formate
dehydrogenase H is a component of the anaerobic formate
hydrogen lyase complex and catalyzes the reversible
oxidation of formate to CO2 with the release of a proton
and two electrons. Formate dehydrogenase N (alpha
subunit) is the major electron donor to the bacterial
nitrate respiratory chain and nitrate reductases, Nap
and Nas, catalyze the reduction of nitrate to nitrite.
This CD (MopB_CT_Fdh-Nap-like) is of the conserved
molybdopterin_binding C-terminal (MopB_CT) region
present in many, but not all, MopB homologs.
Length = 120
Score = 30.9 bits (71), Expect = 0.16
Identities = 18/64 (28%), Positives = 26/64 (40%), Gaps = 16/64 (25%)
Query: 154 HFHT------SAKMNRGIEEMFLELSQRMLEKAQEF-----DLAKASELSRRGSMRRNVV 202
H+HT S ++ E F+E+ E A DL + S SRRGS+
Sbjct: 15 HWHTGTMTRRSPRLAALAPEPFVEIHP---EDAARLGIKDGDLVRVS--SRRGSVVVRAR 69
Query: 203 VVED 206
V +
Sbjct: 70 VTDR 73
>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 = 31.3 bits (71), Expect = 0.19
Identities = 28/123 (22%), Positives = 50/123 (40%), Gaps = 9/123 (7%)
Query: 18 VVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQERF 77
+++LG GKTS++ ++ E + T F + + + L + G +
Sbjct: 2 ILVLGLDGAGKTSLLHSLSSERSLESVVPT--TGFNSVAIPTQDAIMELL--EIGGSQNL 57
Query: 78 HALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGN--DICLTIAGNKIDLEKQ 135
Y S G + V D D + + EL ++L + D+ L + NK DL
Sbjct: 58 RKYWKRYLSGSQGLIFVVDSADSERLPLARQ---ELHQLLQHPPDLPLVVLANKQDLPAA 114
Query: 136 RTV 138
R+V
Sbjct: 115 RSV 117
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes. TrmE
contains a GTPase domain that forms a canonical Ras-like
fold. It functions a molecular switch GTPase, and
apparently uses a conformational change associated with
GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 31.3 bits (72), Expect = 0.20
Identities = 22/89 (24%), Positives = 33/89 (37%), Gaps = 17/89 (19%)
Query: 92 VLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLEKQRTVMQEDAEKYAQSVG 151
+LV D ++ E ++ KK + + NK DL + E K
Sbjct: 87 LLVVDASEGLDEEDLEILELPAKK------PVIVVLNKSDLLSDAEGISELNGKP----- 135
Query: 152 AVHFHTSAKMNRGIEEMFLELSQRMLEKA 180
SAK GI+ EL + +LE A
Sbjct: 136 --IIAISAKTGEGID----ELKEALLELA 158
>gnl|CDD|206685 cd01898, Obg, Obg GTPase. The Obg nucleotide binding protein
subfamily has been implicated in stress response,
chromosome partitioning, replication initiation,
mycelium development, and sporulation. Obg proteins are
among a large group of GTP binding proteins conserved
from bacteria to humans. The E. coli homolog, ObgE is
believed to function in ribosomal biogenesis. Members of
the subfamily contain two equally and highly conserved
domains, a C-terminal GTP binding domain and an
N-terminal glycine-rich domain.
Length = 170
Score = 31.2 bits (72), Expect = 0.23
Identities = 20/83 (24%), Positives = 33/83 (39%), Gaps = 9/83 (10%)
Query: 92 VLVY--DITDEDS-FEKVKNWVKELKK----MLGNDICLTIAGNKIDLEKQRTVMQEDAE 144
VL++ D++ ED E + EL+ + + NKIDL ++ E
Sbjct: 81 VLLHVIDLSGEDDPVEDYETIRNELEAYNPGLAEKPR--IVVLNKIDLLDAEERFEKLKE 138
Query: 145 KYAQSVGAVHFHTSAKMNRGIEE 167
+ G F SA G++E
Sbjct: 139 LLKELKGKKVFPISALTGEGLDE 161
>gnl|CDD|233163 TIGR00872, gnd_rel, 6-phosphogluconate dehydrogenase
(decarboxylating). This family resembles a larger
family (gnd) of bacterial and eukaryotic
6-phosphogluconate dehydrogenases but differs from it by
a deep split in a UPGMA similarity clustering tree and
the lack of a central region of about 140 residues.
Among complete genomes, it is found is found in Bacillus
subtilis and Mycobacterium tuberculosis, both of which
also contain gnd, and in Aquifex aeolicus. The protein
from Methylobacillus flagellatus KT has been
characterized as a decarboxylating 6-phosphogluconate
dehydrogenase as part of an unusual formaldehyde
oxidation cycle. In some sequenced organisms members of
this family are the sole 6-phosphogluconate
dehydrogenase present and are probably active in the
pentose phosphate cycle [Energy metabolism, Pentose
phosphate pathway].
Length = 298
Score = 31.7 bits (72), Expect = 0.27
Identities = 24/97 (24%), Positives = 45/97 (46%), Gaps = 15/97 (15%)
Query: 116 MLGND--ICLTIAGNKIDLEKQRTVMQEDAEK-----YAQSVGAVHFHTSAKM-NRGIEE 167
+ G + C I G+ + + + A + Y G+ HF KM + GIE
Sbjct: 123 VWGRERGYCFMIGGDGEAFARAEPLFADVAPEEQGYLYCGPCGSGHF---VKMVHNGIEY 179
Query: 168 -MFLELSQ--RMLEKAQ-EFDLAKASELSRRGSMRRN 200
M +++ +L +Q +FD+ + + + RRGS+ R+
Sbjct: 180 GMMAAIAEGFEILRNSQFDFDIPEVARVWRRGSVIRS 216
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 31.9 bits (73), Expect = 0.28
Identities = 26/121 (21%), Positives = 54/121 (44%), Gaps = 12/121 (9%)
Query: 92 VLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLEKQRTVMQEDAEKYAQSVG 151
+ V D +D + EK++ L ++ ++I + + NKIDL + + + E+ + +
Sbjct: 276 LHVVDASDPEILEKLEAVEDVLAEIGADEIPIILVLNKIDL-LEDEEILAELERGSPNPV 334
Query: 152 AVHFHTSAKMNRGIEEMFLELSQRMLEKAQEFDL----AKASELSRRGSMRRNVVVVEDE 207
+ SAK G++ + + + + E L A LS + N +V+E+E
Sbjct: 335 FI----SAKTGEGLDLLRERIIELLSGLRTEVTLELPYTDAGRLSW---LHDNGIVLEEE 387
Query: 208 D 208
Sbjct: 388 Y 388
>gnl|CDD|236582 PRK09599, PRK09599, 6-phosphogluconate dehydrogenase-like protein;
Reviewed.
Length = 301
Score = 30.1 bits (69), Expect = 0.79
Identities = 26/62 (41%), Positives = 32/62 (51%), Gaps = 20/62 (32%)
Query: 146 YAQSVGAVHFHTSAKM--NRGIE--------EMFLELSQRMLEKAQ-EFDLAKASELSRR 194
+A VGA HF KM N GIE E F EL LE ++ + DLA +E+ RR
Sbjct: 162 HAGPVGAGHF---VKMVHN-GIEYGMMQAYAEGF-EL----LEASRFDLDLAAVAEVWRR 212
Query: 195 GS 196
GS
Sbjct: 213 GS 214
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 30.0 bits (68), Expect = 1.2
Identities = 16/46 (34%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 123 LTIAGNKIDLEKQRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEM 168
+ +A N ID K+R + + D EK ++ +G T AK G+EE+
Sbjct: 111 MILALNMIDEAKKRGI-RIDIEKLSKLLGVPVVPTVAKRGEGLEEL 155
>gnl|CDD|237515 PRK13805, PRK13805, bifunctional acetaldehyde-CoA/alcohol
dehydrogenase; Provisional.
Length = 862
Score = 29.8 bits (68), Expect = 1.3
Identities = 11/34 (32%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 98 TDEDSFEKVKNWVKELKKMLGNDICLTIAGNKID 131
T E+ E + ++ELK LG I ++I +D
Sbjct: 790 TTEEKVESLIKAIEELKAELG--IPMSIKEAGVD 821
>gnl|CDD|219538 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This Pfam
entry includes some of the AAA proteins not detected by
the pfam00004 model.
Length = 135
Score = 28.4 bits (64), Expect = 1.6
Identities = 17/122 (13%), Positives = 36/122 (29%), Gaps = 11/122 (9%)
Query: 18 VVLLGEGCVGKTSVVLRYVEDKFNEKHITTLQASFLNKKLNIAGKRLNLAIWDTAGQERF 77
V+L+G GK+ + R + + + +Q L + L +
Sbjct: 2 VLLVGPPGTGKSELAERLAA-ALSNRPVFYVQ---LTRDTTEE--DL-KGRRNIDPGGAS 54
Query: 78 HALGPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLEKQRT 137
GP+ G + V ++ + + L +L L G ++
Sbjct: 55 WVDGPLVRAAREGEIAV----LDEINRANPDVLNSLLSLLDERRLLLPEGGELVKAAPDG 110
Query: 138 VM 139
Sbjct: 111 FR 112
>gnl|CDD|232975 TIGR00437, feoB, ferrous iron transporter FeoB. FeoB (773 amino
acids in E. coli), a cytoplasmic membrane protein
required for iron(II) update, is encoded in an operon
with FeoA (75 amino acids), which is also required, and
is regulated by Fur. There appear to be two copies in
Archaeoglobus fulgidus and Clostridium acetobutylicum
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 591
Score = 29.3 bits (66), Expect = 2.0
Identities = 20/89 (22%), Positives = 38/89 (42%), Gaps = 4/89 (4%)
Query: 125 IAGNKIDLEKQRTVMQEDAEKYAQSVGAVHFHTSAKMNRGIEEMFLELSQRMLEKAQEFD 184
+A N +D +++ + + D EK + +G TSA RGIE + + + + +
Sbjct: 104 LALNLVDEAEKKGI-RIDEEKLEERLGVPVVPTSATEGRGIERLKDAIRKAI---GLKEL 159
Query: 185 LAKASELSRRGSMRRNVVVVEDEDLPTSS 213
+A E+ VV E + + S
Sbjct: 160 KKRAIEIVPEAYQVVEVVEGLIEIIYSIS 188
>gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol
utilisation. Members of this family function in
ethanolamine and propanediol degradation pathways,
however the exact roles of these proteins is poorly
understood.
Length = 143
Score = 28.0 bits (63), Expect = 2.1
Identities = 18/48 (37%), Positives = 23/48 (47%), Gaps = 6/48 (12%)
Query: 129 KIDLEK--QRTVMQEDAEKYAQSVGAVH-FHTSAKMNRGIEEMFLELS 173
KIDL K M E++ + GA F SA N GI+E+F L
Sbjct: 98 KIDLAKDEANIEM---VEEWLNNAGAEKIFEVSAVTNEGIDELFAYLE 142
>gnl|CDD|206726 cd04163, Era, E. coli Ras-like protein (Era) is a multifunctional
GTPase. Era (E. coli Ras-like protein) is a
multifunctional GTPase found in all bacteria except some
eubacteria. It binds to the 16S ribosomal RNA (rRNA) of
the 30S subunit and appears to play a role in the
assembly of the 30S subunit, possibly by chaperoning the
16S rRNA. It also contacts several assembly elements of
the 30S subunit. Era couples cell growth with
cytokinesis and plays a role in cell division and energy
metabolism. Homologs have also been found in eukaryotes.
Era contains two domains: the N-terminal GTPase domain
and a C-terminal domain KH domain that is critical for
RNA binding. Both domains are important for Era
function. Era is functionally able to compensate for
deletion of RbfA, a cold-shock adaptation protein that
is required for efficient processing of the 16S rRNA.
Length = 168
Score = 28.2 bits (64), Expect = 2.6
Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 1/50 (2%)
Query: 128 NKIDLEKQRTVMQEDAEKYAQSVGAVH-FHTSAKMNRGIEEMFLELSQRM 176
NKIDL K + + EK + F SA ++E+ + + +
Sbjct: 119 NKIDLVKDKEDLLPLLEKLKELHPFAEIFPISALKGENVDELLEYIVEYL 168
>gnl|CDD|234173 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB. Members
of this protein family are the bacterial ATP-dependent
chaperone ClpB. This protein belongs to the AAA family,
ATPases associated with various cellular activities
(pfam00004). This molecular chaperone does not act as a
protease, but rather serves to disaggregate misfolded
and aggregated proteins [Protein fate, Protein folding
and stabilization].
Length = 852
Score = 28.4 bits (64), Expect = 3.3
Identities = 28/97 (28%), Positives = 47/97 (48%), Gaps = 31/97 (31%)
Query: 98 TDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLEKQRTVMQE--DAEKYAQSVGAVHF 155
DE S E++++ KEL +LE++ ++E AEK ++ +
Sbjct: 428 KDEASKERLEDLEKELA----------------ELEEEYADLEEQWKAEK--AAIQGI-- 467
Query: 156 HTSAKMNRGIEEMFLELSQRMLEKAQ-EFDLAKASEL 191
++ IE++ LEL E+A+ E DLAKA+EL
Sbjct: 468 ---QQIKEEIEQVRLEL-----EQAEREGDLAKAAEL 496
>gnl|CDD|213834 TIGR03597, GTPase_YqeH, ribosome biogenesis GTPase YqeH. This
family describes YqeH, a member of a larger family of
GTPases involved in ribosome biogenesis. Like YqlF, it
shows a cyclical permutation relative to GTPases EngA
(in which the GTPase domain is duplicated), Era, and
others. Members of this protein family are found in a
relatively small number of bacterial species, including
Bacillus subtilis but not Escherichia coli [Protein
synthesis, Other].
Length = 360
Score = 28.4 bits (64), Expect = 3.6
Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 3/34 (8%)
Query: 104 EKVKNWVKELKKMLG---NDICLTIAGNKIDLEK 134
K+K W+K+ K LG DI L A +++
Sbjct: 110 SKIKEWMKKRAKELGLKPVDIILVSAKKGNGIDE 143
>gnl|CDD|173937 cd08178, AAD_C, C-terminal alcohol dehydrogenase domain of the
acetaldehyde dehydrogenase-alcohol dehydrogenase
bifunctional two-domain protein (AAD). Alcohol
dehydrogenase domain located on the C-terminal of a
bifunctional two-domain protein. The N-terminal of the
protein contains an acetaldehyde-CoA dehydrogenase
domain. This protein is involved in pyruvate metabolism.
Pyruvate is converted to acetyl-CoA and formate by
pyruvate formate-lysase (PFL). Under anaerobic
condition, acetyl-CoA is reduced to acetaldehyde and
ethanol by this two-domain protein. Acetyl-CoA is first
converted into an enzyme-bound thiohemiacetal by the
N-terminal acetaldehyde dehydrogenase domain. The
enzyme-bound thiohemiacetal is subsequently reduced by
the C-terminal NAD+-dependent alcohol dehydrogenase
domain. In E. coli, this protein is called AdhE and was
shown pyruvate formate-lysase (PFL) deactivase activity,
which is involved in the inactivation of PFL, a key
enzyme in anaerobic metabolism. In Escherichia coli and
Entamoeba histolytica, this enzyme forms homopolymeric
peptides composed of more than 20 protomers associated
in a helical rod-like structure.
Length = 398
Score = 28.3 bits (64), Expect = 3.6
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 2/34 (5%)
Query: 98 TDEDSFEKVKNWVKELKKMLGNDICLTIAGNKID 131
TDE+ E + ++ELKK LG I +I +D
Sbjct: 329 TDEEKVESLIKAIEELKKKLG--IPKSIKDAGVD 360
>gnl|CDD|233953 TIGR02621, cas3_GSU0051, CRISPR-associated helicase Cas3, subtype
Dpsyc. This model describes a CRISPR-associated
putative DEAH-box helicase, or Cas3, of a subtype found
in Actinomyces naeslundii MG1, Geobacter sulfurreducens
PCA, Gemmata obscuriglobus UQM 2246, and Desulfotalea
psychrophila. This protein includes both DEAH and HD
motifs [Mobile and extrachromosomal element functions,
Other].
Length = 862
Score = 28.0 bits (62), Expect = 5.1
Identities = 12/55 (21%), Positives = 17/55 (30%), Gaps = 1/55 (1%)
Query: 86 RMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLEKQRTVMQ 140
+ V + D E+ K WV+ L + A DL K Q
Sbjct: 682 KDDADEVTLCGHLD-RVGERAKQWVRALGLGELLVEAVVTAARHHDLGKDDPRFQ 735
>gnl|CDD|187585 cd05324, carb_red_PTCR-like_SDR_c, Porcine testicular carbonyl
reductase (PTCR)-like, classical (c) SDRs. PTCR is a
classical SDR which catalyzes the NADPH-dependent
reduction of ketones on steroids and prostaglandins.
Unlike most SDRs, PTCR functions as a monomer. This
subgroup also includes human carbonyl reductase 1 (CBR1)
and CBR3. CBR1 is an NADPH-dependent SDR with broad
substrate specificity and may be responsible for the in
vivo reduction of quinones, prostaglandins, and other
carbonyl-containing compounds. In addition it includes
poppy NADPH-dependent salutaridine reductase which
catalyzes the stereospecific reduction of salutaridine
to 7(S)-salutaridinol in the biosynthesis of morphine,
and Arabidopsis SDR1,a menthone reductase, which
catalyzes the reduction of menthone to neomenthol, a
compound with antimicrobial activity; SDR1 can also
carry out neomenthol oxidation. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, 15-hydroxyprostaglandin dehydrogenase
(15-PGDH) numbering). In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-PGDH numbering)
contributing to the active site; while substrate binding
is in the C-terminal region, which determines
specificity. The standard reaction mechanism is a
4-pro-S hydride transfer and proton relay involving the
conserved Tyr and Lys, a water molecule stabilized by
Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 225
Score = 27.2 bits (61), Expect = 5.7
Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 2/51 (3%)
Query: 96 DITDEDSFEKVKNWVKELKKMLGNDICLTIAGNKIDLEKQRTVMQEDAEKY 146
D+TD+ S E ++V+E L DI + AG T +E A +
Sbjct: 58 DVTDDASIEAAADFVEEKYGGL--DILVNNAGIAFKGFDDSTPTREQARET 106
>gnl|CDD|206748 cd01855, YqeH, Circularly permuted YqeH GTPase. YqeH is an
essential GTP-binding protein. Depletion of YqeH induces
an excess initiation of DNA replication, suggesting that
it negatively controls initiation of chromosome
replication. The YqeH subfamily is common in eukaryotes
and sporadically present in bacteria with probable
acquisition by plants from chloroplasts. Proteins of the
YqeH family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases.
Length = 191
Score = 27.2 bits (61), Expect = 6.1
Identities = 20/88 (22%), Positives = 30/88 (34%), Gaps = 20/88 (22%)
Query: 92 VLVYDITD-EDSF-EKVKNWVKELKKMLGNDICLTIAGNKIDL--------EKQRTVMQE 141
V V DI D S + + + + GNKIDL ++ V +
Sbjct: 38 VHVVDIFDFPGSLIPGLAELIGAKP--------VILVGNKIDLLPKDVKPNRLKQWVKKR 89
Query: 142 DAEKYAQSVGAVHFHTSAKMNRGIEEMF 169
+ V SAK G+EE+
Sbjct: 90 LKIGGLKIKD-VIL-VSAKKGWGVEELI 115
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 27.2 bits (61), Expect = 7.1
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 99 DEDSFEKVKNWVKELKKMLG 118
DE +E+VK V +L KM+G
Sbjct: 155 DEKRYEEVKEEVSKLLKMVG 174
>gnl|CDD|206734 cd04171, SelB, SelB, the dedicated elongation factor for delivery
of selenocysteinyl-tRNA to the ribosome. SelB is an
elongation factor needed for the co-translational
incorporation of selenocysteine. Selenocysteine is coded
by a UGA stop codon in combination with a specific
downstream mRNA hairpin. In bacteria, the C-terminal
part of SelB recognizes this hairpin, while the
N-terminal part binds GTP and tRNA in analogy with
elongation factor Tu (EF-Tu). It specifically recognizes
the selenocysteine charged tRNAsec, which has a UCA
anticodon, in an EF-Tu like manner. This allows
insertion of selenocysteine at in-frame UGA stop codons.
In E. coli SelB binds GTP, selenocysteyl-tRNAsec, and a
stem-loop structure immediately downstream of the UGA
codon (the SECIS sequence). The absence of active SelB
prevents the participation of selenocysteyl-tRNAsec in
translation. Archaeal and animal mechanisms of
selenocysteine incorporation are more complex. Although
the SECIS elements have different secondary structures
and conserved elements between archaea and eukaryotes,
they do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains bacterial SelBs, as well as, one from archaea.
Length = 170
Score = 26.8 bits (60), Expect = 8.2
Identities = 33/133 (24%), Positives = 51/133 (38%), Gaps = 26/133 (19%)
Query: 65 NLAIWDTAGQERFHA-----LGPIYYRMSNGAVLVYDITD---EDSFEKVKNWVKELKKM 116
L D G E+F G I + +LV + + E + E+ ++
Sbjct: 51 RLGFIDVPGHEKFVKNMLAGAGGI-----DAVLLVVAADEGIMPQTREHL-----EILEL 100
Query: 117 LGNDICLTIAGNKIDL-EKQRT--VMQEDAEKYAQSVGAVH--FHTSAKMNRGIEEMFLE 171
LG L + K DL ++ R V +E E A + A F S+ GIEE+
Sbjct: 101 LGIKKGL-VVLTKADLVDEDRLELVEEEILELLAGTFLADAPIFPVSSVTGEGIEELKNY 159
Query: 172 LSQRMLEKAQEFD 184
L + L + Q D
Sbjct: 160 LDE--LAEPQSKD 170
>gnl|CDD|218203 pfam04670, Gtr1_RagA, Gtr1/RagA G protein conserved region. GTR1
was first identified in S. cerevisiae as a suppressor of
a mutation in RCC1. Biochemical analysis revealed that
Gtr1 is in fact a G protein of the Ras family. The
RagA/B proteins are the human homologues of Gtr1.
Included in this family is the human Rag C, a novel
protein that has been shown to interact with RagA/B.
Length = 230
Score = 26.8 bits (60), Expect = 8.3
Identities = 37/171 (21%), Positives = 67/171 (39%), Gaps = 40/171 (23%)
Query: 17 KVVLLGEGCVGKTS---VVLRYVEDKFNEKHITTLQAS---------FLNKKLNIAGKRL 64
KV+L+G GK+S ++ ++ + L A+ FL L
Sbjct: 1 KVLLMGLRGSGKSSMRSIIF----SNYSPRDTLRLGATIDVEQSHVRFLGN--------L 48
Query: 65 NLAIWDTAGQERFHALGPIYYR---MSNGAVLVY--DITDEDSFEKVKNWVKELKKMLGN 119
L +WD GQ+ F + SN VL+Y D+ + E + VK ++ +
Sbjct: 49 TLNLWDCPGQDDFMENYLTRQKEHIFSNVGVLIYVFDVESREYEEDLATLVKIIEALYQY 108
Query: 120 --DICLTIAGNKIDL--EKQRTVMQEDAEKYAQS------VGAVHFH-TSA 159
+ + + +K+DL E +R + ED ++ + + F TS
Sbjct: 109 SPNAKVFVLIHKMDLLSEDERKEIFEDRKEEIIEEIEDFGIEDLTFFLTSI 159
>gnl|CDD|206114 pfam13943, WPP, WPP domain.
Length = 100
Score = 25.7 bits (57), Expect = 8.4
Identities = 16/74 (21%), Positives = 34/74 (45%), Gaps = 9/74 (12%)
Query: 114 KKMLGNDICLTIAGNKIDLEKQRTVMQEDAEKYAQSVGAVHF------HTSAKMNRGIEE 167
+ + + T++ I ++ + +E+AE+ A+++ F + GI
Sbjct: 12 RDAVVERLTETLSTPSILSKRYGLLSKEEAEEAAKAIEEEAFAAANAHASKEPDGDGISA 71
Query: 168 MFL---ELSQRMLE 178
+ L E+S+RMLE
Sbjct: 72 LQLYSKEISKRMLE 85
>gnl|CDD|235190 PRK03991, PRK03991, threonyl-tRNA synthetase; Validated.
Length = 613
Score = 27.1 bits (61), Expect = 8.4
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 92 VLVYDITDEDSFEKVKNWVKELKKMLGNDICLTI 125
+ T ED +E+ K+W+ EL K G + L I
Sbjct: 374 EVAIRFT-EDFYEENKDWIVELVKREGKPVLLEI 406
>gnl|CDD|238542 cd01122, GP4d_helicase, GP4d_helicase is a homohexameric 5'-3'
helicases. Helicases couple NTP hydrolysis to the
unwinding of nucleic acid duplexes into their component
strands.
Length = 271
Score = 26.6 bits (59), Expect = 9.4
Identities = 25/112 (22%), Positives = 38/112 (33%), Gaps = 13/112 (11%)
Query: 26 VGKTSVVLRYVEDKFNEKHITTLQASF--LNKKL------NIAGKRLNLAIWDTAGQERF 77
VGKT+ + Y D + + S + AGKRL+L DT
Sbjct: 41 VGKTTFLREYALDLITQHGVRVGTISLEEPVVRTARRLLGQYAGKRLHLP--DTVFIYTL 98
Query: 78 HALGPIYYRM-SNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDICLTIAGN 128
+ G + +YD E S + V V+ + + I I N
Sbjct: 99 EEFDAAFDEFEGTGRLFMYDSFGEYSMDSVLEKVRYMAVS--HGIQHIIIDN 148
>gnl|CDD|232926 TIGR00337, PyrG, CTP synthase. CTP synthase is involved in
pyrimidine ribonucleotide/ribonucleoside metabolism. The
enzyme catalyzes the reaction L-glutamine + H2O + UTP +
ATP = CTP + phosphate + ADP + L-glutamate. The enzyme
exists as a dimer of identical chains that aggregates as
a tetramer. This gene has been found circa 500 bp 5'
upstream of enolase in both beta (Nitrosomonas europaea)
and gamma (E.coli) subdivisions of proteobacterium (FEMS
Microbiol Lett 1998 Aug 1;165(1):153-7) [Purines,
pyrimidines, nucleosides, and nucleotides, Pyrimidine
ribonucleotide biosynthesis].
Length = 525
Score = 26.9 bits (60), Expect = 9.5
Identities = 12/38 (31%), Positives = 21/38 (55%), Gaps = 6/38 (15%)
Query: 97 ITDEDSFEKVKNWVKELKKMLGNDICLT-IAGNKIDLE 133
IT+E +K+ +K + K+ G D+ + I G D+E
Sbjct: 117 ITNE-----IKDRIKRVAKISGPDVVIVEIGGTVGDIE 149
>gnl|CDD|234274 TIGR03594, GTPase_EngA, ribosome-associated GTPase EngA. EngA
(YfgK, Der) is a ribosome-associated essential GTPase
with a duplication of its GTP-binding domain. It is
broadly to universally distributed among bacteria. It
appears to function in ribosome biogenesis or stability
[Protein synthesis, Other].
Length = 429
Score = 27.0 bits (61), Expect = 9.5
Identities = 11/49 (22%), Positives = 21/49 (42%), Gaps = 4/49 (8%)
Query: 125 IAGNKIDL---EKQRTVMQEDAEKYAQSVGAVHFH-TSAKMNRGIEEMF 169
I NK DL EK R +++ + + SA +G++++
Sbjct: 288 IVVNKWDLVKDEKTREEFKKELRRKLPFLDFAPIVFISALTGQGVDKLL 336
>gnl|CDD|221746 pfam12739, TRAPPC-Trs85, ER-Golgi trafficking TRAPP I complex 85
kDa subunit. This family is one of the subunits of the
TRAPP Golgi trafficking complex. TRAPP subunits are
found in two different sized complexes, TRAPP I and
TRAPP II, and this Trs85 is in the smaller complex.
TRAPP I, but Not TRAPP II, functions in ER-Golgi
transport. Trs85p was reported to function in the
cytosol-to-vacuole targeting pathway, suggesting a role
for this subunit in autophagy as well as in secretion.
The overall architecture of TRAPP I shows the other
components to be Bet3p (TRAPPC3), Bet5p (TRAPPC1),
Trs20p (TRAPPC2), Trs23p (TRAPPC4), Trs31p (TRAPPC5),
Trs33p (TRAPPC6a and b) and Trs85p.
Length = 390
Score = 26.9 bits (60), Expect = 9.6
Identities = 12/42 (28%), Positives = 21/42 (50%), Gaps = 6/42 (14%)
Query: 81 GPIYYRMSNGAVLVYDITDEDSFEKVKNWVKELKKMLGNDIC 122
+Y VLV+D +D D E+ + +++LK+ G C
Sbjct: 31 ILRHY------VLVHDESDGDDEERSQALLEQLKRTFGLCNC 66
>gnl|CDD|176232 cd08271, MDR5, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 325
Score = 26.9 bits (60), Expect = 9.8
Identities = 16/48 (33%), Positives = 20/48 (41%), Gaps = 6/48 (12%)
Query: 62 KRLNLAIWDTAGQERFHALGPIYYRMSNGAVLVYDITDEDSFEKVKNW 109
KR L + T + F Y S GA V D DED E++K
Sbjct: 163 KRAGLRVITTCSKRNFE------YVKSLGADHVIDYNDEDVCERIKEI 204
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
0.316 0.131 0.366
Gapped
Lambda K H
0.267 0.0591 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,939,627
Number of extensions: 1026855
Number of successful extensions: 1506
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1368
Number of HSP's successfully gapped: 168
Length of query: 223
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 130
Effective length of database: 6,812,680
Effective search space: 885648400
Effective search space used: 885648400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (26.0 bits)