RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1169
(218 letters)
>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 = 347 bits (893), Expect = e-124
Identities = 147/166 (88%), Positives = 156/166 (93%)
Query: 14 YIFKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAG 73
YIFKYIIIGDMGVGKSCLLHQFTE+KFM DCPHTIGVEFGTRIIEV+G+KIKLQIWDTAG
Sbjct: 1 YIFKYIIIGDMGVGKSCLLHQFTEKKFMADCPHTIGVEFGTRIIEVNGQKIKLQIWDTAG 60
Query: 74 QERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMDLE 133
QERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTD +NLTNPNTVIFLIGNK DLE
Sbjct: 61 QERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTVIFLIGNKADLE 120
Query: 134 GSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKIYQN 179
RDV Y+EAK+FA+EN L+F+E SA TGENVE AFLETAKKIYQN
Sbjct: 121 AQRDVTYEEAKQFADENGLLFLECSAKTGENVEDAFLETAKKIYQN 166
>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 = 276 bits (709), Expect = 4e-96
Identities = 109/168 (64%), Positives = 133/168 (79%)
Query: 12 YSYIFKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDT 71
Y+Y+FKYIIIGD GVGKSCLL QFT+++F P TIGVEFG R+I + G++IKLQIWDT
Sbjct: 1 YAYLFKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDT 60
Query: 72 AGQERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMD 131
AGQE FR++TRSYYRGAAGAL+VYDITRR T+NHL+SWL D + +N N I LIGNK D
Sbjct: 61 AGQESFRSITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQHSNSNMTIMLIGNKCD 120
Query: 132 LEGSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKIYQN 179
LE R+V Y+E + FA E+ LIF+E SA T NVE+AF+ TAK+IY
Sbjct: 121 LESRREVSYEEGEAFAREHGLIFMETSAKTASNVEEAFINTAKEIYDK 168
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 274 bits (704), Expect = 3e-95
Identities = 93/164 (56%), Positives = 119/164 (72%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQE 75
FK I+IGD GVGKS LL +FT+ KF TIGV+F T+ IEV G+++KLQIWDTAGQE
Sbjct: 1 FKIILIGDSGVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIEVDGKRVKLQIWDTAGQE 60
Query: 76 RFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMDLEGS 135
RFR++T SYYRGA GAL+VYDIT R ++ +L +WL + + +PN VI L+GNK DLE
Sbjct: 61 RFRSITSSYYRGAVGALLVYDITNRESFENLENWLKELREYASPNVVIMLVGNKSDLEEQ 120
Query: 136 RDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKIYQN 179
R V +EA+ FAEE+ L F E SA T NVE+AF E A++I +
Sbjct: 121 RQVSREEAEAFAEEHGLPFFETSAKTNTNVEEAFEELAREILKR 164
>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 = 263 bits (675), Expect = 4e-91
Identities = 104/161 (64%), Positives = 131/161 (81%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQE 75
FK++IIG G GKSCLLHQF E KF D HTIGVEFG+R++ V G+ +KLQIWDTAGQE
Sbjct: 1 FKFLIIGSAGTGKSCLLHQFIENKFKQDSNHTIGVEFGSRVVNVGGKSVKLQIWDTAGQE 60
Query: 76 RFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMDLEGS 135
RFR+VTRSYYRGAAGAL+VYDIT R ++N L++WLTD + L +P+ VI L+GNK DLE
Sbjct: 61 RFRSVTRSYYRGAAGALLVYDITSRESFNALTNWLTDARTLASPDIVIILVGNKKDLEDD 120
Query: 136 RDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKI 176
R+V + EA +FA+EN L+F+E SA+TGENVE+AFL+ A+ I
Sbjct: 121 REVTFLEASRFAQENGLLFLETSALTGENVEEAFLKCARSI 161
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 265 bits (679), Expect = 5e-91
Identities = 117/208 (56%), Positives = 150/208 (72%), Gaps = 2/208 (0%)
Query: 11 SYSYIFKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWD 70
SY+Y+FKYIIIGD GVGKSCLL QFT+++F P TIGVEFG R+I + + IKLQIWD
Sbjct: 2 SYAYLFKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDNKPIKLQIWD 61
Query: 71 TAGQERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKM 130
TAGQE FR++TRSYYRGAAGAL+VYDITRR T+NHL+SWL D + N N I LIGNK
Sbjct: 62 TAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLASWLEDARQHANANMTIMLIGNKC 121
Query: 131 DLEGSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKIYQNIKDGKLNANMT 190
DL R V +E ++FA+E+ LIF+EASA T +NVE+AF++TA KIY+ I+DG + +
Sbjct: 122 DLAHRRAVSTEEGEQFAKEHGLIFMEASAKTAQNVEEAFIKTAAKIYKKIQDGVFDVSNE 181
Query: 191 ESGVQ--HKERGGPASLGDSSSSDKPNC 216
G++ + G + D +SS C
Sbjct: 182 SYGIKVGYGAIPGASGGRDGTSSQGGGC 209
>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 = 253 bits (648), Expect = 7e-87
Identities = 87/159 (54%), Positives = 116/159 (72%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQE 75
FK ++IGD GVGK+ LL +F + KF + TIGV+F ++ IEV G+K+KLQIWDTAGQE
Sbjct: 1 FKIVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGVDFKSKTIEVDGKKVKLQIWDTAGQE 60
Query: 76 RFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMDLEGS 135
RFR++T SYYRGA GA++VYD+T R ++ +L WL + K PN I L+GNK DLE
Sbjct: 61 RFRSITSSYYRGAHGAILVYDVTNRESFENLDKWLNELKEYAPPNIPIILVGNKSDLEDE 120
Query: 136 RDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAK 174
R V +EA++FA+EN L+F E SA TGENV++AF A+
Sbjct: 121 RQVSTEEAQQFAKENGLLFFETSAKTGENVDEAFESLAR 159
>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 = 245 bits (627), Expect = 1e-83
Identities = 83/162 (51%), Positives = 110/162 (67%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQER 76
K +++GD GVGKS LL +FT+ KF + TIGV+F T+ IEV G+ +KLQIWDTAGQER
Sbjct: 1 KLVLVGDGGVGKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAGQER 60
Query: 77 FRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMDLEGSR 136
FRA+ YYRGA G L+VYDIT R ++ ++ WL + + N I L+GNK DLE R
Sbjct: 61 FRALRPLYYRGAQGFLLVYDITSRDSFENVKKWLEEILRHADENVPIVLVGNKCDLEDQR 120
Query: 137 DVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKIYQ 178
V +E + A+E L F+E SA T ENVE+AF E A++I +
Sbjct: 121 VVSTEEGEALAKELGLPFMETSAKTNENVEEAFEELAREILK 162
>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 = 242 bits (621), Expect = 9e-83
Identities = 90/164 (54%), Positives = 119/164 (72%)
Query: 14 YIFKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAG 73
Y+FK ++IGD GVGKS LL +FT +F D TIGVEF TR I++ G+ IK QIWDTAG
Sbjct: 2 YLFKIVLIGDSGVGKSNLLSRFTRNEFNLDSKSTIGVEFATRTIQIDGKTIKAQIWDTAG 61
Query: 74 QERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMDLE 133
QER+RA+T +YYRGA GAL+VYDIT++ST+ ++ WL + ++ + N VI L+GNK DL
Sbjct: 62 QERYRAITSAYYRGAVGALLVYDITKKSTFENVERWLKELRDHADSNIVIMLVGNKSDLR 121
Query: 134 GSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKIY 177
R V +EAK FAE+N L F+E SA+ G NVE+AF + +IY
Sbjct: 122 HLRAVPTEEAKAFAEKNGLSFIETSALDGTNVEEAFKQLLTEIY 165
>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 = 205 bits (524), Expect = 6e-68
Identities = 72/162 (44%), Positives = 106/162 (65%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQE 75
FK +++GD VGKS ++ +F + +F + TIG F T+ + + +K +IWDTAGQE
Sbjct: 2 FKLVLLGDSSVGKSSIVLRFVKNEFSENQESTIGAAFLTQTVNLDDTTVKFEIWDTAGQE 61
Query: 76 RFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMDLEGS 135
R+R++ YYRGAA A++VYDIT ++ SW+ + + PN VI L GNK DLE
Sbjct: 62 RYRSLAPMYYRGAAAAIVVYDITSEESFEKAKSWVKELQEHGPPNIVIALAGNKADLESK 121
Query: 136 RDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKIY 177
R V +EA+++A+EN L+F+E SA TGENV + F E A+K+
Sbjct: 122 RQVSTEEAQEYADENGLLFMETSAKTGENVNELFTEIARKLP 163
>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 = 203 bits (518), Expect = 5e-67
Identities = 79/163 (48%), Positives = 110/163 (67%)
Query: 14 YIFKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAG 73
Y+FK ++IGD GVGKSCLL +F + + TIGV+F R IE+ G+ +KLQIWDTAG
Sbjct: 1 YLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTVKLQIWDTAG 60
Query: 74 QERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMDLE 133
QERFR +T SYYRGA G ++VYD+T + ++N++ WL + + N L+GNK DL
Sbjct: 61 QERFRTITSSYYRGAHGIIIVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLT 120
Query: 134 GSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKI 176
+ V Y EAK+FA+E + F+E SA NVE+AF+ A++I
Sbjct: 121 DKKVVDYTEAKEFADELGIPFLETSAKNATNVEEAFMTMAREI 163
>gnl|CDD|206659 cd01867, Rab8_Rab10_Rab13_like, Rab GTPase families 8, 10, 13
(Rab8, Rab10, Rab13). Rab8/Sec4/Ypt2 are known or
suspected to be involved in post-Golgi transport to the
plasma membrane. It is likely that these Rabs have
functions that are specific to the mammalian lineage and
have no orthologs in plants. Rab8 modulates polarized
membrane transport through reorganization of actin and
microtubules, induces the formation of new surface
extensions, and has an important role in directed
membrane transport to cell surfaces. The Ypt2 gene of
the fission yeast Schizosaccharomyces pombe encodes a
member of the Ypt/Rab family of small GTP-binding
proteins, related in sequence to Sec4p of Saccharomyces
cerevisiae but closer to mammalian Rab8. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 167
Score = 200 bits (511), Expect = 5e-66
Identities = 80/163 (49%), Positives = 108/163 (66%)
Query: 14 YIFKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAG 73
Y+FK ++IGD GVGKSCLL +F+E F P TIG++F R IE+ G+KIKLQIWDTAG
Sbjct: 2 YLFKLLLIGDSGVGKSCLLLRFSEDSFNPSFISTIGIDFKIRTIELDGKKIKLQIWDTAG 61
Query: 74 QERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMDLE 133
QERFR +T SYYRGA G ++VYDIT ++ ++ +W+ + + + L+GNK D+E
Sbjct: 62 QERFRTITTSYYRGAMGIILVYDITDEKSFENIKNWMRNIDEHASEDVERMLVGNKCDME 121
Query: 134 GSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKI 176
R V +E + A E + F+E SA NVE+AFL AK I
Sbjct: 122 EKRVVSKEEGEALAREYGIKFLETSAKANINVEEAFLTLAKDI 164
>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 = 196 bits (501), Expect = 2e-64
Identities = 82/162 (50%), Positives = 115/162 (70%), Gaps = 2/162 (1%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQE 75
K ++IGD GVGKS LL +FT+ F D TIGV+F + + V G+K+KL IWDTAGQE
Sbjct: 1 LKILLIGDSGVGKSSLLLRFTDDTFDEDLSSTIGVDFKVKTVTVDGKKVKLAIWDTAGQE 60
Query: 76 RFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNL-TNPNTVIFLIGNKMDLEG 134
RFR +T SYYRGA G ++VYD+TRR T+++L +WL + TNP+ V L+GNK+D E
Sbjct: 61 RFRTLTSSYYRGAQGVILVYDVTRRDTFDNLDTWLNELDTYSTNPDAVKMLVGNKIDKE- 119
Query: 135 SRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKI 176
+R+V +E +KFA +++++F+E SA T V+QAF E +KI
Sbjct: 120 NREVTREEGQKFARKHNMLFIETSAKTRIGVQQAFEELVEKI 161
>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 = 196 bits (501), Expect = 6e-64
Identities = 93/211 (44%), Positives = 135/211 (63%), Gaps = 6/211 (2%)
Query: 14 YIFKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVH-GEKIKLQIWDTA 72
Y F+ I+IGD VGKS LL +FTE +F T+GV+F +R+IE+ G +IKLQ+WDTA
Sbjct: 1 YQFRLIVIGDSTVGKSSLLKRFTEGRFAEVSDPTVGVDFFSRLIEIEPGVRIKLQLWDTA 60
Query: 73 GQERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIF-LIGNKMD 131
GQERFR++TRSYYR + G L+V+DIT R ++ H+ WL + ++ P+ +F L+G+K D
Sbjct: 61 GQERFRSITRSYYRNSVGVLLVFDITNRESFEHVHDWLEEARSHIQPHRPVFILVGHKCD 120
Query: 132 LEGSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKIYQNIKDGKLNANMTE 191
LE R V +EA+K A++ + ++E SA TG+NVE+AF ++IY+ IK G+L A
Sbjct: 121 LESQRQVTREEAEKLAKDLGMKYIETSARTGDNVEEAFELLTQEIYERIKRGELCALDGW 180
Query: 192 SGV-QHKERGGPASLGDSSSSDKP---NCSC 218
GV G SL + S + +C C
Sbjct: 181 DGVKSGFPAGRAFSLEERSPTFASPEKSCCC 211
>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 = 191 bits (488), Expect = 1e-62
Identities = 76/164 (46%), Positives = 110/164 (67%), Gaps = 1/164 (0%)
Query: 14 YIFKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAG 73
++FK I+IGD VGK+C++ +F F +TIGV+F + +E+ G+++KLQIWDTAG
Sbjct: 2 FLFKIILIGDSNVGKTCVVQRFKSGTFSERQGNTIGVDFTMKTLEIQGKRVKLQIWDTAG 61
Query: 74 QERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMDLE 133
QERFR +T+SYYR A GA++ YDITRRS++ + W+ + + N V+ LIGNK DLE
Sbjct: 62 QERFRTITQSYYRSANGAIIAYDITRRSSFESVPHWIEEVEKYGASNVVLLLIGNKCDLE 121
Query: 134 GSRDVRYDEAKKFAEENDLIFV-EASAMTGENVEQAFLETAKKI 176
R+V ++EA AE ++ V E SA NVE+AFL A ++
Sbjct: 122 EQREVLFEEACTLAEHYGILAVLETSAKESSNVEEAFLLMATEL 165
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 193 bits (492), Expect = 2e-62
Identities = 90/213 (42%), Positives = 132/213 (61%)
Query: 4 MSSSGQYSYSYIFKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEK 63
M+ + Y Y+FK ++IGD GVGKS +L +FT +F + TIGVEF TR ++V G+
Sbjct: 1 MAHRVDHEYDYLFKIVLIGDSGVGKSNILSRFTRNEFCLESKSTIGVEFATRTLQVEGKT 60
Query: 64 IKLQIWDTAGQERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVI 123
+K QIWDTAGQER+RA+T +YYRGA GAL+VYDIT+R T++++ WL + ++ + N VI
Sbjct: 61 VKAQIWDTAGQERYRAITSAYYRGAVGALLVYDITKRQTFDNVQRWLRELRDHADSNIVI 120
Query: 124 FLIGNKMDLEGSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKIYQNIKDG 183
+ GNK DL R V ++ + AE+ L F+E SA+ NVE+AF +IY I
Sbjct: 121 MMAGNKSDLNHLRSVAEEDGQALAEKEGLSFLETSALEATNVEKAFQTILLEIYHIISKK 180
Query: 184 KLNANMTESGVQHKERGGPASLGDSSSSDKPNC 216
L A + +G ++ D+S ++K C
Sbjct: 181 ALAAQEAAANSGLPGQGTTINVADTSGNNKRGC 213
>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 = 174 bits (442), Expect = 1e-55
Identities = 73/165 (44%), Positives = 111/165 (67%)
Query: 12 YSYIFKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDT 71
Y ++FK ++IG+ GVGK+CL+ +FT+ F P TIGV+F + +E+ GEKIKLQIWDT
Sbjct: 4 YDFLFKIVLIGNAGVGKTCLVRRFTQGLFPPGQGATIGVDFMIKTVEIKGEKIKLQIWDT 63
Query: 72 AGQERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMD 131
AGQERFR++T+SYYR A ++ YDIT ++ L WL + + N + L+GNK+D
Sbjct: 64 AGQERFRSITQSYYRSANALILTYDITCEESFRCLPEWLREIEQYANNKVITILVGNKID 123
Query: 132 LEGSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKI 176
L R+V A++F++ D+ ++E SA +NVE+ FL+ A ++
Sbjct: 124 LAERREVSQQRAEEFSDAQDMYYLETSAKESDNVEKLFLDLACRL 168
>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 = 165 bits (419), Expect = 5e-52
Identities = 61/161 (37%), Positives = 102/161 (63%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQE 75
K + +GD VGK+ ++ +F F TIG++F ++ + V + ++LQ+WDTAGQE
Sbjct: 1 HKLVFLGDQSVGKTSIITRFMYDTFDNQYQATIGIDFLSKTMYVDDKTVRLQLWDTAGQE 60
Query: 76 RFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMDLEGS 135
RFR++ SY R ++ A++VYDIT R ++++ W+ D ++ + +I L+GNK DL
Sbjct: 61 RFRSLIPSYIRDSSVAVVVYDITNRQSFDNTDKWIDDVRDERGNDVIIVLVGNKTDLSDK 120
Query: 136 RDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKI 176
R V +E +K A+EN+ +F+E SA G NV+Q F + A+ +
Sbjct: 121 RQVSTEEGEKKAKENNAMFIETSAKAGHNVKQLFKKIAQAL 161
>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 = 163 bits (416), Expect = 2e-51
Identities = 63/171 (36%), Positives = 100/171 (58%), Gaps = 5/171 (2%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQE 75
K II+GD GVGK+ L++Q+ +KF TIG +F T+ + V + LQIWDTAGQE
Sbjct: 1 LKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVTVDDRLVTLQIWDTAGQE 60
Query: 76 RFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTD---TKNLTNPNTVIF-LIGNKMD 131
RF+++ ++YRGA ++VYD+T ++ L SW + + +P F ++GNK+D
Sbjct: 61 RFQSLGVAFYRGADCCVLVYDVTNPKSFESLDSWRDEFLIQASPRDPENFPFVVLGNKID 120
Query: 132 LEGSRDVRYDEAKKFAEEN-DLIFVEASAMTGENVEQAFLETAKKIYQNIK 181
LE R V +A+++ + ++ + E SA NV+QAF A+ + K
Sbjct: 121 LEEKRQVSTKKAQQWCKSKGNIPYFETSAKEAINVDQAFETIARLALEQEK 171
>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 = 163 bits (415), Expect = 4e-51
Identities = 72/170 (42%), Positives = 117/170 (68%), Gaps = 2/170 (1%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMP-DCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQ 74
FK +++GD GVGK+CLL +F + F+ T+G++F +++ V G K+KLQIWDTAGQ
Sbjct: 1 FKVMLVGDSGVGKTCLLVRFKDGAFLAGSFIATVGIQFTNKVVTVDGVKVKLQIWDTAGQ 60
Query: 75 ERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMDLEG 134
ERFR+VT +YYR A L++YD+T +S+++++ +WLT+ + VI L+GNK D+ G
Sbjct: 61 ERFRSVTHAYYRDAHALLLLYDVTNKSSFDNIRAWLTEILEYAQSDVVIMLLGNKADMSG 120
Query: 135 SRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKI-YQNIKDG 183
R V+ ++ ++ A+E + F+E SA TG NVE AF AK++ +++++
Sbjct: 121 ERVVKREDGERLAKEYGVPFMETSAKTGLNVELAFTAVAKELKHRSVEQP 170
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 160 bits (406), Expect = 1e-49
Identities = 88/177 (49%), Positives = 112/177 (63%), Gaps = 4/177 (2%)
Query: 5 SSSGQYS-YSYIFKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEK 63
SSSGQ S Y FK ++IGD GVGKS LL F + D TIGV+F + + V G++
Sbjct: 3 SSSGQSSGYDLSFKILLIGDSGVGKSSLLVSFISSS-VEDLAPTIGVDFKIKQLTVGGKR 61
Query: 64 IKLQIWDTAGQERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNL--TNPNT 121
+KL IWDTAGQERFR +T SYYR A G ++VYD+TRR T+ +LS L TN +
Sbjct: 62 LKLTIWDTAGQERFRTLTSSYYRNAQGIILVYDVTRRETFTNLSDVWGKEVELYSTNQDC 121
Query: 122 VIFLIGNKMDLEGSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKIYQ 178
V L+GNK+D E RDV +E A+E+ +F+E SA T ENVEQ F E A KI +
Sbjct: 122 VKMLVGNKVDRESERDVSREEGMALAKEHGCLFLECSAKTRENVEQCFEELALKIME 178
>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 = 149 bits (379), Expect = 5e-46
Identities = 68/167 (40%), Positives = 102/167 (61%), Gaps = 5/167 (2%)
Query: 15 IFKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQ 74
IFK I+IGD VGK+CL ++F +F TIGV+F R +E+ GE+IK+Q+WDTAGQ
Sbjct: 2 IFKIIVIGDSNVGKTCLTYRFCAGRFPERTEATIGVDFRERTVEIDGERIKVQLWDTAGQ 61
Query: 75 ERFR-AVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVI-FLIGNKMDL 132
ERFR ++ + YYR + VYD+T ++++ L SW+ + + + PN V L+GNK DL
Sbjct: 62 ERFRKSMVQHYYRNVHAVVFVYDVTNMASFHSLPSWIEECEQHSLPNEVPRILVGNKCDL 121
Query: 133 EGSRDVRYDEAKKFAEENDLIFVEASA---MTGENVEQAFLETAKKI 176
V D A++FA+ + + E SA ++VE F+ A K+
Sbjct: 122 REQIQVPTDLAQRFADAHSMPLFETSAKDPSENDHVEAIFMTLAHKL 168
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 150 bits (379), Expect = 2e-45
Identities = 68/226 (30%), Positives = 105/226 (46%), Gaps = 25/226 (11%)
Query: 11 SYSYIFKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWD 70
+ FK +++GD GVGK+ LL++ +F P TIG + IE + IKLQ+WD
Sbjct: 1 LFMKEFKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWD 60
Query: 71 TAGQERFRAVTRSYYRGAAGALMVYDIT-RRSTYNHLSSWLTDTKNLTNPNTVIFLIGNK 129
TAGQE +R++ YYRGA G L+VYD T R S+ WL + + L + I L+GNK
Sbjct: 61 TAGQEEYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVGNK 120
Query: 130 MDLEGSRDVRYDEAKKFAEENDLI---------------FVEASAM--TGENVEQAFLET 172
+DL + + + E L+ +E SA TG NV + F E
Sbjct: 121 IDLFDEQSSSEEILNQLNREVVLLVLAPKAVLPEVANPALLETSAKSLTGPNVNELFKEL 180
Query: 173 AKKIYQNIKDGKLNANMTESGVQHKERGGPASLGDSSSSDKPNCSC 218
+K+ + I+ L + + + + ++ NC
Sbjct: 181 LRKLLEEIEKLVLKNELRQLDRLNNP-------IEQAALASFNCVL 219
>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 = 148 bits (376), Expect = 3e-45
Identities = 74/199 (37%), Positives = 110/199 (55%), Gaps = 8/199 (4%)
Query: 12 YSYIFKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDT 71
Y ++FK +IIGD GVGKS LL +F + F TIGV+F R +E++GE++KLQIWDT
Sbjct: 3 YDHLFKLLIIGDSGVGKSSLLLRFADNTFSGSYITTIGVDFKIRTVEINGERVKLQIWDT 62
Query: 72 AGQERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVI-FLIGNKM 130
AGQERFR +T +YYRG G ++VYD+T ++ ++ WL + + N + V L+GNK
Sbjct: 63 AGQERFRTITSTYYRGTHGVIVVYDVTNGESFVNVKRWLQEIEQ--NCDDVCKVLVGNKN 120
Query: 131 DLEGSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKIYQNIKDGKLNANMT 190
D + V ++A KFA + + E SA NVE+ F + + + KD N+
Sbjct: 121 DDPERKVVETEDAYKFAGQMGISLFETSAKENINVEEMFNCITELVLRAKKD-----NLA 175
Query: 191 ESGVQHKERGGPASLGDSS 209
+ Q +
Sbjct: 176 KQQQQQQNDVVKLPKNSKR 194
>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 = 146 bits (370), Expect = 9e-45
Identities = 68/164 (41%), Positives = 101/164 (61%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQE 75
F+ ++IGD GVGK+CLL +FT+ +F TIGV+F + IEV G K+++QIWDTAGQE
Sbjct: 1 FRLLLIGDSGVGKTCLLCRFTDNEFHSSHISTIGVDFKMKTIEVDGIKVRIQIWDTAGQE 60
Query: 76 RFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMDLEGS 135
R++ +T+ YYR A G +VYDI+ +Y H+ W++D LIGNK D E
Sbjct: 61 RYQTITKQYYRRAQGIFLVYDISSERSYQHIMKWVSDVDEYAPEGVQKILIGNKADEEQK 120
Query: 136 RDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKIYQN 179
R V ++ K A+E + F E SA T +N++++F + + Q
Sbjct: 121 RQVGDEQGNKLAKEYGMDFFETSACTNKNIKESFTRLTELVLQA 164
>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 = 147 bits (373), Expect = 9e-45
Identities = 67/163 (41%), Positives = 105/163 (64%), Gaps = 1/163 (0%)
Query: 19 IIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQERFR 78
IIIG GVGK+ L+ +FT+ F C T+GV+F + +E+ G+KI+LQIWDTAGQERF
Sbjct: 4 IIIGSRGVGKTSLMERFTDDTFCEACKSTVGVDFKIKTVELRGKKIRLQIWDTAGQERFN 63
Query: 79 AVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMDLEGSRDV 138
++T +YYR A G ++VYDIT++ T++ L W+ + + + L+GNK+D E R++
Sbjct: 64 SITSAYYRSAKGIILVYDITKKETFDDLPKWMKMIDKYASEDAELLLVGNKLDCETDREI 123
Query: 139 RYDEAKKFAEE-NDLIFVEASAMTGENVEQAFLETAKKIYQNI 180
+ +KFA++ + F EASA NV++ FL+ I + +
Sbjct: 124 TRQQGEKFAQQITGMRFCEASAKDNFNVDEIFLKLVDDILKKM 166
>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 = 146 bits (370), Expect = 3e-44
Identities = 65/175 (37%), Positives = 98/175 (56%), Gaps = 7/175 (4%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEV-HGEKIKLQIWDTAGQ 74
FK ++IGD+GVGK+ ++ ++ F TIGV+F ++IE ++LQ+WD AGQ
Sbjct: 1 FKVLVIGDLGVGKTSIIKRYVHGVFSQHYKATIGVDFALKVIEWDPNTVVRLQLWDIAGQ 60
Query: 75 ERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTD--TKNLTNPNTVI--FLIGNKM 130
ERF +TR YY+GA GA++V+D+TR ST+ + W D +K I L+ NK
Sbjct: 61 ERFGGMTRVYYKGAVGAIIVFDVTRPSTFEAVLKWKADLDSKVTLPNGEPIPALLLANKC 120
Query: 131 DLEGSRD-VRYDEAKKFAEENDLI-FVEASAMTGENVEQAFLETAKKIYQNIKDG 183
DL+ R ++ +F +EN I + E SA N+E+A K I +N K
Sbjct: 121 DLKKERLAKDPEQMDQFCKENGFIGWFETSAKENINIEEAMRFLVKNILKNDKGL 175
>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 = 143 bits (364), Expect = 8e-44
Identities = 60/161 (37%), Positives = 96/161 (59%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQE 75
FK +++G+ VGK+ L+ ++ E KF T F + + + G++I L IWDTAGQE
Sbjct: 1 FKVVLLGEGRVGKTSLVLRYVENKFNEKHESTTQASFFQKTVNIGGKRIDLAIWDTAGQE 60
Query: 76 RFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMDLEGS 135
R+ A+ YYR A GA++VYDIT ++ + W+ + K + N + ++GNK+DLE
Sbjct: 61 RYHALGPIYYRDADGAILVYDITDADSFQKVKKWIKELKQMRGNNISLVIVGNKIDLERQ 120
Query: 136 RDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKI 176
R V EA+++A+ E SA TG+ +E+ FL AK++
Sbjct: 121 RVVSKSEAEEYAKSVGAKHFETSAKTGKGIEELFLSLAKRM 161
>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 = 140 bits (354), Expect = 2e-42
Identities = 61/155 (39%), Positives = 95/155 (61%)
Query: 15 IFKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQ 74
+FK +IIG+ VGK+ L ++ + F T+G++F + + + ++IKLQIWDTAGQ
Sbjct: 1 MFKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVYRNDKRIKLQIWDTAGQ 60
Query: 75 ERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMDLEG 134
ER+R +T +YYRGA G +++YDIT ++N + W T K + N + L+GNK D+E
Sbjct: 61 ERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSWDNAQVILVGNKCDMED 120
Query: 135 SRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAF 169
R V + ++ A++ F EASA NV+Q F
Sbjct: 121 ERVVSAERGRQLADQLGFEFFEASAKENINVKQVF 155
>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 = 140 bits (354), Expect = 4e-42
Identities = 61/170 (35%), Positives = 103/170 (60%), Gaps = 15/170 (8%)
Query: 12 YSYIFKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEF----------GTRIIEVHG 61
Y Y+ K + +GD GVGK+ L+++T+ KF P T+G++F G
Sbjct: 1 YDYLIKLLALGDSGVGKTTFLYRYTDNKFNPKFITTVGIDFREKRVVYNSQGPDGTSGKA 60
Query: 62 EKIKLQIWDTAGQERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKN---LTN 118
++ LQ+WDTAGQERFR++T +++R A G L+++D+T ++ ++ +W++ + N
Sbjct: 61 FRVHLQLWDTAGQERFRSLTTAFFRDAMGFLLMFDLTSEQSFLNVRNWMSQLQAHAYCEN 120
Query: 119 PNTVIFLIGNKMDLEGSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQA 168
P+ V LIGNK DL R+V +A++ A++ + + E SA TG+NVE+A
Sbjct: 121 PDIV--LIGNKADLPDQREVSERQARELADKYGIPYFETSAATGQNVEKA 168
>gnl|CDD|133319 cd04119, RJL, Rab GTPase family J-like (RabJ-like). RJLs are found
in many protists and as chimeras with C-terminal DNAJ
domains in deuterostome metazoa. They are not found in
plants, fungi, and protostome metazoa, suggesting a
horizontal gene transfer between protists and
deuterostome metazoa. RJLs lack any known membrane
targeting signal and contain a degenerate
phosphate/magnesium-binding 3 (PM3) motif, suggesting an
impaired ability to hydrolyze GTP. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization.
Length = 168
Score = 132 bits (335), Expect = 3e-39
Identities = 53/158 (33%), Positives = 88/158 (55%), Gaps = 5/158 (3%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQER 76
K I +G+ GVGKSC++ ++ E +F+ TIG+++G + + V +++++ +D +G
Sbjct: 2 KVISMGNSGVGKSCIIKRYCEGRFVSKYLPTIGIDYGVKKVSVRNKEVRVNFFDLSGHPE 61
Query: 77 FRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNP-----NTVIFLIGNKMD 131
+ V +Y+ G L+VYD+T R ++ L SWL + K P N V+ + NK+D
Sbjct: 62 YLEVRNEFYKDTQGVLLVYDVTDRQSFEALDSWLKEMKQEGGPHGNMENIVVVVCANKID 121
Query: 132 LEGSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAF 169
L R V DE + +AE + E SA TGE V + F
Sbjct: 122 LTKHRAVSEDEGRLWAESKGFKYFETSACTGEGVNEMF 159
>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 = 128 bits (323), Expect = 1e-37
Identities = 64/169 (37%), Positives = 99/169 (58%), Gaps = 6/169 (3%)
Query: 13 SYIFKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTA 72
S + K I++GD GVGKS L++++ KF HTIGVEF + +EV G + LQIWDTA
Sbjct: 3 SSLLKVILLGDGGVGKSSLMNRYVTNKFDTQLFHTIGVEFLNKDLEVDGHFVTLQIWDTA 62
Query: 73 GQERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKN---LTNPNTVIFLI-GN 128
GQERFR++ +YRG+ L+ + + ++ +LS+W + + P + F+I GN
Sbjct: 63 GQERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVILGN 122
Query: 129 KMDLEGSRDVRYDEAKKFAEEN-DLIFVEASAMTGENVEQAFLETAKKI 176
K+D+ R V +EA+ + +N D + E SA NV AF E +++
Sbjct: 123 KIDIP-ERQVSTEEAQAWCRDNGDYPYFETSAKDATNVAAAFEEAVRRV 170
>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 = 126 bits (319), Expect = 4e-37
Identities = 57/161 (35%), Positives = 84/161 (52%), Gaps = 2/161 (1%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQER 76
K +++G GVGKS L +F +F+ + TI + + I V GE L I DTAGQE
Sbjct: 1 KLVVLGAGGVGKSALTIRFVSGEFVEEYDPTIE-DSYRKQIVVDGETYTLDILDTAGQEE 59
Query: 77 FRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTV-IFLIGNKMDLEGS 135
F A+ Y R G ++VY IT R ++ + + + + V I L+GNK DLE
Sbjct: 60 FSAMRDQYIRNGDGFILVYSITSRESFEEIKNIREQILRVKDKEDVPIVLVGNKCDLENE 119
Query: 136 RDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKI 176
R V +E + AEE F+E SA T N+++ F ++I
Sbjct: 120 RQVSTEEGEALAEEWGCPFLETSAKTNINIDELFNTLVREI 160
>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 = 124 bits (312), Expect = 5e-36
Identities = 50/158 (31%), Positives = 73/158 (46%), Gaps = 4/158 (2%)
Query: 15 IFKYIIIGDMGVGKSCLLHQFTEQKFMPDCPH-TIGVEFGTRIIEVHGEKIKLQIWDTAG 73
K +I+GD VGKS LL++ K + T +IE G+ K + DTAG
Sbjct: 1 EIKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAG 60
Query: 74 QERFRAVTRSYYRGAAGALMVYDITRR--STYNHLSSWLTDTKNLTNPNTVIFLIGNKMD 131
QE + A+ R YYR +L V+DI L + + I L+GNK+D
Sbjct: 61 QEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAESGVPIILVGNKID 120
Query: 132 LEGSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAF 169
L ++ A FA+ N + SA TG+N++ AF
Sbjct: 121 LRD-AKLKTHVAFLFAKLNGEPIIPLSAETGKNIDSAF 157
>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 = 119 bits (301), Expect = 3e-34
Identities = 65/162 (40%), Positives = 94/162 (58%), Gaps = 7/162 (4%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQER 76
K I++GD+ VGK+CL+++F + F + TIGV+F EV G LQ+WDTAGQER
Sbjct: 2 KVIVVGDLSVGKTCLINRFCKDVFDKNYKATIGVDFEMERFEVLGVPFSLQLWDTAGQER 61
Query: 77 FRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTV-IFLIGNKMDLEGS 135
F+ + +YYRGA ++V+D+T ++ H WL D +P++V +FL+G K DL S
Sbjct: 62 FKCIASTYYRGAQAIIIVFDLTDVASLEHTRQWLEDALKENDPSSVLLFLVGTKKDL--S 119
Query: 136 RDVRYD----EAKKFAEENDLIFVEASAMTGENVEQAFLETA 173
+Y +A K A E + SA+TGENV F A
Sbjct: 120 SPAQYALMEQDAIKLAREMKAEYWAVSALTGENVRDFFFRVA 161
>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 = 117 bits (296), Expect = 2e-33
Identities = 59/157 (37%), Positives = 84/157 (53%), Gaps = 6/157 (3%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQE 75
+K +++G GVGKS L QF + F+ D TI + + IE+ GE L I DTAGQE
Sbjct: 1 YKLVVLGSGGVGKSALTIQFIQGHFVDDYDPTIE-DSYRKQIEIDGEVCLLDILDTAGQE 59
Query: 76 RFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSW---LTDTKNLTNPNTVIFLIGNKMDL 132
F A+ Y R G L+VY IT R ++ + + + K+ + I L+GNK DL
Sbjct: 60 EFSAMRDQYMRTGEGFLLVYSITDRQSFEEIKKFREQILRVKDRDD--VPIVLVGNKCDL 117
Query: 133 EGSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAF 169
E R V +E K+ A + F+E SA NV++AF
Sbjct: 118 ESERVVSTEEGKELARQWGCPFLETSAKERVNVDEAF 154
>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 = 116 bits (294), Expect = 3e-33
Identities = 58/157 (36%), Positives = 85/157 (54%), Gaps = 6/157 (3%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQE 75
+K +++G GVGKS L QF + F+ + TI + + IE+ GE L I DTAGQE
Sbjct: 3 YKLVVLGGGGVGKSALTIQFVQGHFVDEYDPTIE-DSYRKQIEIDGEVCLLDILDTAGQE 61
Query: 76 RFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSW---LTDTKNLTNPNTVIFLIGNKMDL 132
F A+ Y R G L+VY IT R ++ ++ + + K+ + I L+GNK DL
Sbjct: 62 EFSAMRDQYMRTGEGFLLVYSITDRQSFEEIAKFREQILRVKDRDD--VPIVLVGNKCDL 119
Query: 133 EGSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAF 169
E R V +E K+ A + F+E SA NV++AF
Sbjct: 120 ENERVVSTEEGKELARQWGCPFLETSAKERINVDEAF 156
>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 = 116 bits (293), Expect = 3e-33
Identities = 52/161 (32%), Positives = 85/161 (52%), Gaps = 3/161 (1%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVH--GEKIKLQIWDTAGQ 74
K I++G+ VGKS ++ +F + F D TIGV+F + I + E ++L +WDTAGQ
Sbjct: 2 KVIVVGNGNVGKSSMIQRFVKGIFTKDYKKTIGVDFLEKQIFLRQSDEDVRLMLWDTAGQ 61
Query: 75 ERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMDLEG 134
E F A+T++YYRGA ++V+ T R ++ + SW + + + L+ K+DL
Sbjct: 62 EEFDAITKAYYRGAQACILVFSTTDRESFEAIESWKEKVEAECG-DIPMVLVQTKIDLLD 120
Query: 135 SRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKK 175
+ +EA+ A+ L S NV + F A+K
Sbjct: 121 QAVITNEEAEALAKRLQLPLFRTSVKDDFNVTELFEYLAEK 161
>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 = 117 bits (295), Expect = 3e-33
Identities = 60/183 (32%), Positives = 98/183 (53%), Gaps = 10/183 (5%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFM-PDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQE 75
K +++G VGK+ L+ ++ +F+ +TIG F + + V + L IWDTAG E
Sbjct: 2 KVVMLGKESVGKTSLVERYVHHRFLVGPYQNTIGAAFVAKRMVVGERVVTLGIWDTAGSE 61
Query: 76 RFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMDL--- 132
R+ A++R YYRGA A++ YD+T S++ W+ + +NL + I+L G K DL
Sbjct: 62 RYEAMSRIYYRGAKAAIVCYDLTDSSSFERAKFWVKELQNL-EEHCKIYLCGTKSDLIEQ 120
Query: 133 -EGSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKIYQNIKDGKLNANMTE 191
R V + + + FA+E E S+ TG+NV++ F +K+ ++ N TE
Sbjct: 121 DRSLRQVDFHDVQDFADEIKAQHFETSSKTGQNVDELF----QKVAEDFVSRANNQMNTE 176
Query: 192 SGV 194
GV
Sbjct: 177 KGV 179
>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 = 116 bits (293), Expect = 7e-33
Identities = 55/164 (33%), Positives = 95/164 (57%), Gaps = 1/164 (0%)
Query: 11 SYSYIFKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWD 70
+Y Y+ K++++GD VGK +L + + +G+++ T I + G ++KLQ+WD
Sbjct: 2 AYDYLLKFLLVGDSDVGKGEILASLQDGSTESPYGYNMGIDYKTTTILLDGRRVKLQLWD 61
Query: 71 TAGQERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKM 130
T+GQ RF + RSY RGA G ++VYDIT R +++ + W+ + P L+GN++
Sbjct: 62 TSGQGRFCTIFRSYSRGAQGIILVYDITNRWSFDGIDRWIKEIDEHA-PGVPKILVGNRL 120
Query: 131 DLEGSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAK 174
L R V ++A+ +AE N + F E S + N+ ++F E A+
Sbjct: 121 HLAFKRQVATEQAQAYAERNGMTFFEVSPLCNFNITESFTELAR 164
>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 = 113 bits (284), Expect = 9e-32
Identities = 57/164 (34%), Positives = 91/164 (55%), Gaps = 2/164 (1%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQE 75
K I++G GVGKS L QF +F+ D T + +++ + GE+++L I DTAGQE
Sbjct: 1 HKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVV-LDGEEVQLNILDTAGQE 59
Query: 76 RFRAVTRSYYRGAAGALMVYDITRRSTYNHLSS-WLTDTKNLTNPNTVIFLIGNKMDLEG 134
+ A+ +Y+R G L+V+ IT ++ L+ + + N + L+GNK DLE
Sbjct: 60 DYAAIRDNYFRSGEGFLLVFSITDMESFTALAEFREQILRVKEDDNVPLLLVGNKCDLED 119
Query: 135 SRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKIYQ 178
R V +EA AE+ + +VE SA T NV++ F + ++I Q
Sbjct: 120 KRQVSVEEAANLAEQWGVNYVETSAKTRANVDKVFFDLVREIRQ 163
>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 = 110 bits (276), Expect = 1e-30
Identities = 54/162 (33%), Positives = 89/162 (54%), Gaps = 2/162 (1%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQE 75
+K +++G GVGKS L QF + F+ D TI + T+ E+ G+ +L I DTAGQE
Sbjct: 3 YKLVVVGGGGVGKSALTIQFIQSYFVTDYDPTIEDSY-TKQCEIDGQWARLDILDTAGQE 61
Query: 76 RFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTV-IFLIGNKMDLEG 134
F A+ Y R G L+V+ +T R ++ + + T + + + + L+GNK DLE
Sbjct: 62 EFSAMREQYMRTGEGFLLVFSVTDRGSFEEVDKFHTQILRVKDRDEFPMILVGNKADLEH 121
Query: 135 SRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKI 176
R V +E ++ A + + ++E SA NV++AF + + I
Sbjct: 122 QRQVSREEGQELARQLKIPYIETSAKDRVNVDKAFHDLVRVI 163
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 108 bits (270), Expect = 1e-29
Identities = 52/130 (40%), Positives = 83/130 (63%)
Query: 47 TIGVEFGTRIIEVHGEKIKLQIWDTAGQERFRAVTRSYYRGAAGALMVYDITRRSTYNHL 106
TIG++F ++ + + ++LQ+WDTAGQERFR++ SY R +A A++VYDIT R ++ +
Sbjct: 12 TIGIDFLSKTLYLDEGPVRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDITNRQSFENT 71
Query: 107 SSWLTDTKNLTNPNTVIFLIGNKMDLEGSRDVRYDEAKKFAEENDLIFVEASAMTGENVE 166
+ W+ D N + +I L+GNK DL R V Y+E + A+E + +F E SA G N++
Sbjct: 72 TKWIQDILNERGKDVIIALVGNKTDLGDLRKVTYEEGMQKAQEYNTMFHETSAKAGHNIK 131
Query: 167 QAFLETAKKI 176
F + A K+
Sbjct: 132 VLFKKIAAKL 141
>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 = 106 bits (267), Expect = 3e-29
Identities = 54/159 (33%), Positives = 82/159 (51%), Gaps = 6/159 (3%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQER 76
K I++GD VGKS L+ +F + P T + + G+ I + WDTAGQER
Sbjct: 2 KIILLGDSAVGKSKLVERFLMDGYEPQQLSTYALTLYKHNAKFEGKTILVDFWDTAGQER 61
Query: 77 FRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMDLEGSR 136
F+ + SYY A ++V+D+TR+ TY +LS W + + P ++ NK+DL
Sbjct: 62 FQTMHASYYHKAHACILVFDVTRKITYKNLSKWYEELREY-RPEIPCIVVANKIDL---- 116
Query: 137 DVRYDEAK-KFAEENDLIFVEASAMTGENVEQAFLETAK 174
D + K FAE+++L SA G NV + F + K
Sbjct: 117 DPSVTQKKFNFAEKHNLPLYYVSAADGTNVVKLFQDAIK 155
>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 = 106 bits (267), Expect = 9e-29
Identities = 54/165 (32%), Positives = 89/165 (53%), Gaps = 4/165 (2%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGE-KIKLQIWDTAGQ 74
K +++GD GK+ L+ +F ++ F TIG++F +R I + G + LQ+WD GQ
Sbjct: 1 IKIVVLGDGASGKTSLIRRFAQEGFGKSYKQTIGLDFFSRRITLPGSLNVTLQVWDIGGQ 60
Query: 75 ERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTV---IFLIGNKMD 131
+ + Y GA +VYDIT ++ +L WL+ K + + + L+GNK D
Sbjct: 61 QIGGKMLDKYIYGAQAVCLVYDITNSQSFENLEDWLSVVKKVNEESETKPKMVLVGNKTD 120
Query: 132 LEGSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKI 176
LE +R V ++ +FA+END+ + SA TG+ V F A ++
Sbjct: 121 LEHNRQVTAEKHARFAQENDMESIFVSAKTGDRVFLCFQRIAAEL 165
>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 = 101 bits (254), Expect = 3e-27
Identities = 51/165 (30%), Positives = 83/165 (50%), Gaps = 3/165 (1%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQE 75
FK +++GD G GK+ + + +F T+GVE + KI+ +WDTAGQE
Sbjct: 1 FKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLDFHTNRGKIRFNVWDTAGQE 60
Query: 76 RFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMDLEGS 135
+F + YY A++++D+T R TY ++ +W D + N I L GNK+D+
Sbjct: 61 KFGGLRDGYYIQGQCAIIMFDVTSRVTYKNVPNWHRDLVRVCE-NIPIVLCGNKVDI--K 117
Query: 136 RDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKIYQNI 180
+ F + +L + E SA + N E+ FL A+K+ N
Sbjct: 118 DRKVKPKQITFHRKKNLQYYEISAKSNYNFEKPFLWLARKLLGNP 162
>gnl|CDD|206648 cd00882, Ras_like_GTPase, Rat sarcoma (Ras)-like superfamily of
small guanosine triphosphatases (GTPases). Ras-like
GTPase superfamily. The Ras-like superfamily of small
GTPases consists of several families with an extremely
high degree of structural and functional similarity. The
Ras superfamily is divided into at least four families
in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families.
This superfamily also includes proteins like the GTP
translation factors, Era-like GTPases, and G-alpha chain
of the heterotrimeric G proteins. Members of the Ras
superfamily regulate a wide variety of cellular
functions: the Ras family regulates gene expression, the
Rho family regulates cytoskeletal reorganization and
gene expression, the Rab and Sar1/Arf families regulate
vesicle trafficking, and the Ran family regulates
nucleocytoplasmic transport and microtubule
organization. The GTP translation factor family
regulates initiation, elongation, termination, and
release in translation, and the Era-like GTPase family
regulates cell division, sporulation, and DNA
replication. Members of the Ras superfamily are
identified by the GTP binding site, which is made up of
five characteristic sequence motifs, and the switch I
and switch II regions.
Length = 161
Score = 100 bits (250), Expect = 8e-27
Identities = 47/160 (29%), Positives = 69/160 (43%), Gaps = 15/160 (9%)
Query: 20 IIGDMGVGKSCLLHQFTEQKFM---PDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQER 76
++G GVGKS LL+ + T + E+ K+KL + DT G +
Sbjct: 2 VVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYV--KELDKGKVKLVLVDTPGLDE 59
Query: 77 F-----RAVTRSYYRGAAGALMVYDIT-RRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKM 130
F + R RGA L+V D T R S + L + L I L+GNK+
Sbjct: 60 FGGLGREELARLLLRGADLILLVVDSTDRESEEDAKLLIL---RRLRKEGIPIILVGNKI 116
Query: 131 DLEGSRDVRYDE-AKKFAEENDLIFVEASAMTGENVEQAF 169
DL R+V ++ A+ + E SA TGE V++ F
Sbjct: 117 DLLEEREVEELLRLEELAKILGVPVFEVSAKTGEGVDELF 156
>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 = 99.8 bits (249), Expect = 2e-26
Identities = 50/162 (30%), Positives = 86/162 (53%), Gaps = 3/162 (1%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQE 75
+K +++G GVGKS L Q + F+ + TI + +++ + GE L I DTAGQE
Sbjct: 2 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVV-IDGETCLLDILDTAGQE 60
Query: 76 RFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTV-IFLIGNKMDLEG 134
+ A+ Y R G L V+ I R ++ + ++ K + + + V + L+GNK DL
Sbjct: 61 EYSAMRDQYMRTGEGFLCVFAINSRKSFEDIHTYREQIKRVKDSDDVPMVLVGNKCDLA- 119
Query: 135 SRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKI 176
+R V + + A+ + ++E SA T + VE+AF ++I
Sbjct: 120 ARTVSTRQGQDLAKSYGIPYIETSAKTRQGVEEAFYTLVREI 161
>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 = 99.5 bits (249), Expect = 2e-26
Identities = 47/171 (27%), Positives = 89/171 (52%), Gaps = 15/171 (8%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQER 76
K +++GD VGK+CLL +T KF + T+ + + + V G+++ L +WDTAGQE
Sbjct: 2 KIVVVGDGAVGKTCLLISYTTNKFPTEYVPTV-FDNYSANVTVDGKQVNLGLWDTAGQEE 60
Query: 77 FRAVTRSYYRGAAGALMVYDITRRSTYNHLSS-WLTDTKNLTNPNTVIFLIGNKMDL--- 132
+ + Y L+ + + S++ ++ + W + K+ PN I L+G K+DL
Sbjct: 61 YDRLRPLSYPQTDVFLLCFSVDSPSSFENVKTKWYPEIKHY-CPNVPIILVGTKIDLRDD 119
Query: 133 --------EGSRDVRYDEAKKFAEENDLI-FVEASAMTGENVEQAFLETAK 174
+ + + +E +K A+E + ++E SA+T E +++ F E +
Sbjct: 120 GNTLKKLEKKQKPITPEEGEKLAKEIGAVKYMECSALTQEGLKEVFDEAIR 170
>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 = 96.9 bits (242), Expect = 2e-25
Identities = 57/157 (36%), Positives = 82/157 (52%), Gaps = 8/157 (5%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQER 76
K ++G VGKS L QF E F+ TI F ++II G++ L+I DTAGQ+
Sbjct: 3 KIAVLGSRSVGKSSLTVQFVEGHFVESYYPTIENTF-SKIITYKGQEYHLEIVDTAGQDE 61
Query: 77 FRAVTRSYYRGAAGALMVYDITRRSTYNHLSSW---LTDTKNLTN-PNTVIFLIGNKMDL 132
+ + + Y G G ++VY +T R ++ + + D + P I L+GNK DL
Sbjct: 62 YSILPQKYSIGIHGYILVYSVTSRKSFEVVKVIYDKILDMLGKESVP---IVLVGNKSDL 118
Query: 133 EGSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAF 169
R V +E KK AE F+E+SA ENVE+AF
Sbjct: 119 HMERQVSAEEGKKLAESWGAAFLESSAKENENVEEAF 155
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 95.7 bits (238), Expect = 1e-24
Identities = 56/168 (33%), Positives = 91/168 (54%), Gaps = 2/168 (1%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQE 75
+K +++G GVGKS L QF + F+ + TI + + + E L I DTAGQE
Sbjct: 6 YKLVVVGGGGVGKSALTIQFIQNHFIDEYDPTIEDSY-RKQCVIDEETCLLDILDTAGQE 64
Query: 76 RFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTV-IFLIGNKMDLEG 134
+ A+ Y R G L VY IT RS++ ++S+ + + + V + L+GNK DL+
Sbjct: 65 EYSAMRDQYMRTGQGFLCVYSITSRSSFEEIASFREQILRVKDKDRVPMILVGNKCDLDS 124
Query: 135 SRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKIYQNIKD 182
R V E ++ A+ + F+E SA NV++AF E ++I + +K+
Sbjct: 125 ERQVSTGEGQELAKSFGIPFLETSAKQRVNVDEAFYELVREIRKYLKE 172
>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 = 93.7 bits (233), Expect = 3e-24
Identities = 52/164 (31%), Positives = 81/164 (49%), Gaps = 6/164 (3%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQE 75
+K +++G GVGKS L QF F+ TI +F + IEV L+I DTAG E
Sbjct: 2 YKVVVLGSGGVGKSALTVQFVSGTFIEKYDPTIE-DFYRKEIEVDSSPSVLEILDTAGTE 60
Query: 76 RFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSW---LTDTKNLTNPNTVIFLIGNKMDL 132
+F ++ Y + G ++VY + + T+ + + K I L+GNK+DL
Sbjct: 61 QFASMRDLYIKNGQGFIVVYSLVNQQTFQDIKPMRDQIVRVKGYEK--VPIILVGNKVDL 118
Query: 133 EGSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKI 176
E R+V E + AEE F+E SA + V + F E +++
Sbjct: 119 ESEREVSSAEGRALAEEWGCPFMETSAKSKTMVNELFAEIVRQM 162
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 92.8 bits (231), Expect = 2e-23
Identities = 56/168 (33%), Positives = 93/168 (55%), Gaps = 17/168 (10%)
Query: 16 FKYIIIGDMGVGKSCLL--H---QFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWD 70
FK I++GD GVGK+ + H +F E+K++P T+GVE + I +WD
Sbjct: 10 FKLILVGDGGVGKTTFVKRHLTGEF-EKKYIP----TLGVEVHPLKFYTNCGPICFNVWD 64
Query: 71 TAGQERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKM 130
TAGQE+F + YY A++++D+T R TY ++ +W D + N I L+GNK+
Sbjct: 65 TAGQEKFGGLRDGYYIKGQCAIIMFDVTSRITYKNVPNWHRDIVRVCE-NIPIVLVGNKV 123
Query: 131 DLEGSRDVRYDEAK--KFAEENDLIFVEASAMTGENVEQAFLETAKKI 176
D++ R V+ A+ F + +L + + SA + N E+ FL A+++
Sbjct: 124 DVK-DRQVK---ARQITFHRKKNLQYYDISAKSNYNFEKPFLWLARRL 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 = 91.0 bits (226), Expect = 4e-23
Identities = 50/163 (30%), Positives = 87/163 (53%), Gaps = 3/163 (1%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQE 75
+K +++G GVGKS L QF + F+ TI + ++ E+ G + L+I DTAG E
Sbjct: 2 YKIVVLGAGGVGKSALTVQFVQNVFIESYDPTIEDSYRKQV-EIDGRQCDLEILDTAGTE 60
Query: 76 RFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTV-IFLIGNKMDLEG 134
+F A+ Y + G L+VY +T ++ N L + + + V + L+GNK DLE
Sbjct: 61 QFTAMRELYIKSGQGFLLVYSVTSEASLNELGELREQVLRIKDSDNVPMVLVGNKADLED 120
Query: 135 SRDVRYDEAKKFAEE-NDLIFVEASAMTGENVEQAFLETAKKI 176
R V ++ +++ ++ F E SA NV++ F++ ++I
Sbjct: 121 DRQVSREDGVSLSQQWGNVPFYETSARKRTNVDEVFIDLVRQI 163
>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 = 90.7 bits (225), Expect = 5e-23
Identities = 54/162 (33%), Positives = 86/162 (53%), Gaps = 2/162 (1%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQE 75
+K +++G GVGKS L QF + F+ TI + + +EV G++ L+I DTAG E
Sbjct: 2 YKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSY-RKQVEVDGQQCMLEILDTAGTE 60
Query: 76 RFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTV-IFLIGNKMDLEG 134
+F A+ Y + G ++VY IT +ST+N L + + V + L+GNK DLE
Sbjct: 61 QFTAMRDLYMKNGQGFVLVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLED 120
Query: 135 SRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKI 176
R V ++ + A + F+E SA NV + F + ++I
Sbjct: 121 ERVVGKEQGQNLARQWGCAFLETSAKAKINVNEIFYDLVRQI 162
>gnl|CDD|133344 cd04144, Ras2, Rat sarcoma (Ras) family 2 of small guanosine
triphosphatases (GTPases). The Ras2 subfamily, found
exclusively in fungi, was first identified in Ustilago
maydis. In U. maydis, Ras2 is regulated by Sql2, a
protein that is homologous to GEFs (guanine nucleotide
exchange factors) of the CDC25 family. Ras2 has been
shown to induce filamentous growth, but the signaling
cascade through which Ras2 and Sql2 regulate cell
morphology is not known. Most Ras proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Ras proteins.
Length = 190
Score = 91.4 bits (227), Expect = 5e-23
Identities = 53/165 (32%), Positives = 85/165 (51%), Gaps = 4/165 (2%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQER 76
K +++GD GVGK+ L Q F+ TI + +++ V G+ L++ DTAGQE
Sbjct: 1 KLVVLGDGGVGKTALTIQLCLNHFVETYDPTIEDSYRKQVV-VDGQPCMLEVLDTAGQEE 59
Query: 77 FRAVTRSYYRGAAGALMVYDITRRSTYNHLSSW---LTDTKNLTNPNTVIFLIGNKMDLE 133
+ A+ + R G ++VY IT RST+ + + + K+ + + I ++GNK D
Sbjct: 60 YTALRDQWIREGEGFILVYSITSRSTFERVERFREQIQRVKDESAADVPIMIVGNKCDKV 119
Query: 134 GSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKIYQ 178
R+V +E A F+EASA T NVE+AF + + Q
Sbjct: 120 YEREVSTEEGAALARRLGCEFIEASAKTNVNVERAFYTLVRALRQ 164
>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 = 89.5 bits (222), Expect = 1e-22
Identities = 50/163 (30%), Positives = 81/163 (49%), Gaps = 5/163 (3%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQ--KFMPDCPHTIGVEFGTRIIEV--HGEKIKLQIWDTA 72
+ ++GD VGKS L+ F F + T G + + + V + ++L I+D+A
Sbjct: 2 QCAVVGDPAVGKSALVQMFHSDGATFQKNYTMTTGCDLVVKTVPVPDTSDSVELFIFDSA 61
Query: 73 GQERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTK-NLTNPNTVIFLIGNKMD 131
GQE F + + + A +VYD+T ++N+ S W+ + + +T L+GNK D
Sbjct: 62 GQELFSDMVENVWEQPAVVCVVYDVTNEVSFNNCSRWINRVRTHSHGLHTPGVLVGNKCD 121
Query: 132 LEGSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAK 174
L R+V +A+ A+ N L F E SA G E FL A+
Sbjct: 122 LTDRREVDAAQAQALAQANTLKFYETSAKEGVGYEAPFLSLAR 164
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 90.6 bits (225), Expect = 2e-22
Identities = 60/180 (33%), Positives = 94/180 (52%), Gaps = 16/180 (8%)
Query: 4 MSSSGQYSYSY-IFKYIIIGDMGVGKSCLLHQFT----EQKFMPDCPHTIGVEFGTRIIE 58
M+ Q + Y FK +I+GD G GK+ + + E+K+ P TIGVE
Sbjct: 1 MALPNQQTVDYPSFKLVIVGDGGTGKTTFVKRHLTGEFEKKYEP----TIGVEVHPLDFF 56
Query: 59 VHGEKIKLQIWDTAGQERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTN 118
+ KI+ WDTAGQE+F + YY A++++D+T R TY ++ +W D +
Sbjct: 57 TNCGKIRFYCWDTAGQEKFGGLRDGYYIHGQCAIIMFDVTARLTYKNVPTWHRDLCRVCE 116
Query: 119 PNTVIFLIGNKMDLEGSRDVRYDEAKK--FAEENDLIFVEASAMTGENVEQAFLETAKKI 176
N I L GNK+D++ R +AK+ F + +L + E SA + N E+ FL A+K+
Sbjct: 117 -NIPIVLCGNKVDVKN----RQVKAKQVTFHRKKNLQYYEISAKSNYNFEKPFLYLARKL 171
>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 = 88.9 bits (221), Expect = 2e-22
Identities = 50/160 (31%), Positives = 80/160 (50%), Gaps = 6/160 (3%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQER 76
K ++G GVGKS L +F ++F+ + + + +R + + GE++ L+I DT GQ++
Sbjct: 1 KIAVLGASGVGKSALTVRFLTKRFIGEYEPNLESLY-SRQVTIDGEQVSLEIQDTPGQQQ 59
Query: 77 FRAV--TRSYYRGAAGALMVYDITRRSTYNHLSSW--LTDTKNLTNPNTVIFLIGNKMDL 132
R A G ++VY IT RS+++ +S L + + L+GNK DL
Sbjct: 60 NEDPESLERSLRWADGFVLVYSITDRSSFDVVSQLLQLIREIKKRDGEIPVILVGNKADL 119
Query: 133 EGSRDVRYDEAKKFAEENDLIFVEASAMTGEN-VEQAFLE 171
SR V +E +K A E +F E SA V+ F E
Sbjct: 120 LHSRQVSTEEGQKLALELGCLFFEVSAAENYLEVQNVFHE 159
>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 = 88.4 bits (219), Expect = 4e-22
Identities = 53/163 (32%), Positives = 86/163 (52%), Gaps = 3/163 (1%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQE 75
+K +++G GVGKS L QF + F+ TI + + IEV ++ L+I DTAG E
Sbjct: 2 YKLVVLGSGGVGKSALTVQFVQGIFVDKYDPTIE-DSYRKQIEVDCQQCMLEILDTAGTE 60
Query: 76 RFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTV-IFLIGNKMDLEG 134
+F A+ Y + G +VY IT + ++N L + + V + L+GNK DLE
Sbjct: 61 QFTAMRDLYIKNGQGFALVYSITAQQSFNDLQDLREQILRVKDTEDVPMILVGNKCDLED 120
Query: 135 SRDVRYDEAKKFAEE-NDLIFVEASAMTGENVEQAFLETAKKI 176
R V +E + A + + F+E SA + NV++ F + ++I
Sbjct: 121 ERVVSKEEGQNLARQWGNCPFLETSAKSKINVDEIFYDLVRQI 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 = 86.9 bits (216), Expect = 2e-21
Identities = 46/170 (27%), Positives = 83/170 (48%), Gaps = 16/170 (9%)
Query: 19 IIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQERFR 78
+++GD VGK+CLL +T F D T+ + +EV G+ ++L +WDTAGQE +
Sbjct: 2 VVVGDGAVGKTCLLIVYTTNAFPEDYVPTVFENYSA-DVEVDGKPVELGLWDTAGQEDYD 60
Query: 79 AVTRSYYRGAAGALMVYDITRRSTYNHLSS-WLTDTKNLTNPNTVIFLIGNKMDL----- 132
+ Y L+ + + +++ ++ W + K+ PN I L+G K+DL
Sbjct: 61 RLRPLSYPDTDVFLICFSVDSPASFENVKEKWYPEVKH-FCPNVPIILVGTKLDLRNDKS 119
Query: 133 -------EGSRDVRYDEAKKFAEE-NDLIFVEASAMTGENVEQAFLETAK 174
+ V Y++ + A+ + ++E SA+T E V + F E +
Sbjct: 120 TLEELSKKKQEPVTYEQGQALAKRIGAVKYLECSALTQEGVREVFEEAIR 169
>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 = 85.3 bits (211), Expect = 2e-20
Identities = 56/190 (29%), Positives = 86/190 (45%), Gaps = 46/190 (24%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQER 76
K +++GDM VGK+ LLH++ E++F D T+G F + + IWDTAG+E+
Sbjct: 2 KVVLLGDMNVGKTSLLHRYMERRF-KDTVSTVGGAFYLK----QWGPYNISIWDTAGREQ 56
Query: 77 FRAVTRSYYRGAAGALMVYDITRRSTYNHLSSW---LTDTKNLTNPNTVIFLIGNKMDLE 133
F + Y RGAA ++ YD++ + L LTDT N + + ++GNK+DL
Sbjct: 57 FHGLGSMYCRGAAAVILTYDVSNVQSLEELEDRFLGLTDT---ANEDCLFAVVGNKLDLT 113
Query: 134 GS-------------------RDVRYDEAKKFAEE---------------NDLIFVEASA 159
R V ++AK F + + F E SA
Sbjct: 114 EEGALAGQEKDAGDRVSPEDQRQVTLEDAKAFYKRINKYKMLDEDLSPAAEKMCF-ETSA 172
Query: 160 MTGENVEQAF 169
TG NV++ F
Sbjct: 173 KTGYNVDELF 182
>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 = 84.7 bits (209), Expect = 2e-20
Identities = 50/158 (31%), Positives = 83/158 (52%), Gaps = 7/158 (4%)
Query: 21 IGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQERFRAV 80
+GD G GK+ + + +F T+GVE + + I+ +WDTAGQE+F +
Sbjct: 1 VGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIRFNVWDTAGQEKFGGL 60
Query: 81 TRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMDLEGSRDVRY 140
YY A++++D+T R TY ++ +W D + N I L GNK+D++ R V+
Sbjct: 61 RDGYYIQGQCAIIMFDVTARVTYKNVPNWHRDLVRVCE-NIPIVLCGNKVDVK-DRKVK- 117
Query: 141 DEAKK--FAEENDLIFVEASAMTGENVEQAFLETAKKI 176
AK F + +L + + SA + N E+ FL A+K+
Sbjct: 118 --AKSITFHRKKNLQYYDISAKSNYNFEKPFLWLARKL 153
>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 = 81.8 bits (202), Expect = 2e-19
Identities = 52/164 (31%), Positives = 78/164 (47%), Gaps = 4/164 (2%)
Query: 15 IFKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQ 74
+K +++G GVGKS + QF F TI + T+ + E L I DTAGQ
Sbjct: 2 EYKIVMLGAGGVGKSAVTMQFISHSFPDYHDPTIEDAYKTQAR-IDNEPALLDILDTAGQ 60
Query: 75 ERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSW--LTDTKNLTNPNTVIFLIGNKMDL 132
F A+ Y R G ++ Y +T R ++ S + L LT + + L+GNK+DL
Sbjct: 61 AEFTAMRDQYMRCGEGFIICYSVTDRHSFQEASEFKELITRVRLTE-DIPLVLVGNKVDL 119
Query: 133 EGSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKI 176
E R V +E + A E + F E SA ++ AF ++I
Sbjct: 120 EQQRQVTTEEGRNLAREFNCPFFETSAALRFYIDDAFHGLVREI 163
>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 = 81.3 bits (201), Expect = 5e-19
Identities = 49/185 (26%), Positives = 82/185 (44%), Gaps = 4/185 (2%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPDCPH-TIGVEFGTRIIEVHGEKIKLQIWDTAGQ 74
++ +++GD GVGKS L + FT + D + G + R + V GE+ L ++D Q
Sbjct: 1 YRVVLLGDSGVGKSSLANIFTAGVYE-DSAYEASGDDTYERTVSVDGEEATLVVYDHWEQ 59
Query: 75 ERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTK-NLTNPNTVIFLIGNKMDLE 133
E + S + ++VY +T RS++ S + + I L+GNK DL
Sbjct: 60 EDGMWLEDSCMQVGDAYVIVYSVTDRSSFEKASELRIQLRRARQAEDIPIILVGNKSDLV 119
Query: 134 GSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKIYQNIKDGKLN-ANMTES 192
SR+V E + A D F+E SA NV++ F +++ + N M
Sbjct: 120 RSREVSVQEGRACAVVFDCKFIETSAALQHNVDELFEGIVRQVRLRRDSKEKNTRRMASR 179
Query: 193 GVQHK 197
+
Sbjct: 180 KRRES 184
>gnl|CDD|206704 cd04132, Rho4_like, Ras homology family 4 (Rho4) of small guanosine
triphosphatases (GTPases)-like. Rho4 is a GTPase that
controls septum degradation by regulating secretion of
Eng1 or Agn1 during cytokinesis. Rho4 also plays a role
in cell morphogenesis. Rho4 regulates septation and cell
morphology by controlling the actin cytoskeleton and
cytoplasmic microtubules. The localization of Rho4 is
modulated by Rdi1, which may function as a GDI, and by
Rga9, which is believed to function as a GAP. In S.
pombe, both Rho4 deletion and Rho4 overexpression result
in a defective cell wall, suggesting a role for Rho4 in
maintaining cell wall integrity. Most Rho proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins.
Length = 197
Score = 79.3 bits (196), Expect = 2e-18
Identities = 46/179 (25%), Positives = 79/179 (44%), Gaps = 17/179 (9%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEV-HGEKIKLQIWDTAGQ 74
K +++GD G GK+CLL + + F + T+ E ++V +G+ I+L +WDTAGQ
Sbjct: 4 VKIVVVGDGGCGKTCLLMVYAQGSFPEEYVPTV-FENYVTTLQVPNGKIIELALWDTAGQ 62
Query: 75 ERFRAVTRSYYRGAAGALMVYDITRRSTY-NHLSSWLTDTKNLTNPNTVIFLIGNKMDL- 132
E + + Y L+ Y + ++ N W + + P T I L+G K DL
Sbjct: 63 EDYDRLRPLSYPDVDVILICYSVDNPTSLDNVEDKWYPEVNHFC-PGTPIVLVGLKTDLR 121
Query: 133 -----------EGSRDVRYDEAKKFAEE-NDLIFVEASAMTGENVEQAFLETAKKIYQN 179
+G V ++ + A+ + ++E SA ENV++ F
Sbjct: 122 KDKNSVSKLRAQGLEPVTPEQGESVAKSIGAVAYIECSAKLMENVDEVFDAAINVALSK 180
>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 = 77.1 bits (190), Expect = 3e-18
Identities = 39/116 (33%), Positives = 57/116 (49%), Gaps = 4/116 (3%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQER 76
K ++IGD G GKS LL Q +F P+ G +EV G+ L IWD G+E
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREE 60
Query: 77 FRAVTRSYYRGAAGALMVYDITRRSTYNHLSS---WLTDTKNLTNPNTVIFLIGNK 129
+ + + A L+VYD+T R + N +S WL + + L + L+GNK
Sbjct: 61 LKFEHIIFMKWADAILLVYDLTDRESLNEVSRLIAWLPNLRKL-GGKIPVILVGNK 115
>gnl|CDD|206741 cd09914, RocCOR, Ras of complex proteins (Roc) C-terminal of Roc
(COR) domain family. RocCOR (or Roco) protein family is
characterized by a superdomain containing a Ras-like
GTPase domain, called Roc (Ras of complex proteins), and
a characteristic second domain called COR (C-terminal of
Roc). A kinase domain and diverse regulatory domains are
also often found in Roco proteins. Their functions are
diverse; in Dictyostelium discoideum, which encodes 11
Roco proteins, they are involved in cell division,
chemotaxis and development, while in human, where 4 Roco
proteins (LRRK1, LRRK2, DAPK1, and MFHAS1) are encoded,
these proteins are involved in epilepsy and cancer.
Mutations in LRRK2 (leucine-rich repeat kinase 2) are
known to cause familial Parkinson's disease.
Length = 161
Score = 77.0 bits (190), Expect = 7e-18
Identities = 44/159 (27%), Positives = 69/159 (43%), Gaps = 18/159 (11%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGT-RIIEVHGEKIKLQIWDTAGQE 75
K +++G GVGK+ L Q +KF D T G+ +I +KI+L +WD GQE
Sbjct: 3 KLMLVGQGGVGKTSLCKQLIGEKFDGDESSTHGINVQDWKIPAPERKKIRLNVWDFGGQE 62
Query: 76 RFRAV------TRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNK 129
+ A +RS Y L+V+D+ + + WL K + + L+G
Sbjct: 63 IYHATHQFFLTSRSLY------LLVFDLRTGDEVSRVPYWLRQIKAF-GGVSPVILVGTH 115
Query: 130 MDLEGSRDVRYDEAKK--FAEENDLIFVEASAMTGENVE 166
+D D+ K A ND+ FV S G+ +
Sbjct: 116 IDESCDEDILKKALNKKFPAIINDIHFV--SCKNGKGIA 152
>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 = 74.5 bits (183), Expect = 8e-17
Identities = 50/174 (28%), Positives = 84/174 (48%), Gaps = 19/174 (10%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQER 76
K + +GD VGK+C+L +T F D T+ F ++ V G + L +WDTAGQE
Sbjct: 3 KCVTVGDGAVGKTCMLISYTSNTFPTDYVPTVFDNFSANVV-VDGNTVNLGLWDTAGQED 61
Query: 77 FRAVTRSYYRGAAGALMVYDITRRSTY-NHLSSWLTDTKNLTNPNTVIFLIGNKMDLEGS 135
+ + YRGA L+ + + +++Y N L W+ + ++ P I L+G K+DL
Sbjct: 62 YNRLRPLSYRGADVFLLAFSLISKASYENVLKKWIPELRHYA-PGVPIVLVGTKLDLRDD 120
Query: 136 RDVRYD-------------EAKKFAEENDLIFVEASAMTGENVEQAFLETAKKI 176
+ D E +K + ++E S+ T +NV+ F + A K+
Sbjct: 121 KQFFADHPGAVPITTAQGEELRK--QIGAAAYIECSSKTQQNVKAVF-DAAIKV 171
>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 = 74.0 bits (182), Expect = 2e-16
Identities = 47/160 (29%), Positives = 76/160 (47%), Gaps = 10/160 (6%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQER 76
K ++GD +GK+ L+ ++ E +F + T+GV F + I + G +I IWD GQ
Sbjct: 2 KIGLLGDAQIGKTSLMVKYVEGEFDEEYIQTLGVNFMEKTISIRGTEITFSIWDLGGQRE 61
Query: 77 FRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMDLEGSR 136
F + + A L ++D+TR+ST N + W + N + L+G K DL
Sbjct: 62 FINMLPLVCKDAVAILFMFDLTRKSTLNSIKEWYRQARGF-NKTAIPILVGTKYDLFADL 120
Query: 137 DVRYDE-----AKKFAE--ENDLIFVEASAMTGENVEQAF 169
E A+K+A+ + LIF S NV++ F
Sbjct: 121 PPEEQEEITKQARKYAKAMKAPLIF--CSTSHSINVQKIF 158
>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 = 73.3 bits (180), Expect = 4e-16
Identities = 56/207 (27%), Positives = 94/207 (45%), Gaps = 18/207 (8%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQER 76
+ + +G GVGK+ L+ +F F P T+ E ++ EV G K+ + I DT+G
Sbjct: 1 RLVFMGAAGVGKTALIQRFLYDTFEPKHRRTVE-ELHSKEYEVAGVKVTIDILDTSGSYS 59
Query: 77 FRAVTR-SYYRGAAGALMVYDITRRSTY---NHLSSWLTDTKNLTNPNTVIFLIGNKMDL 132
F A+ + S G A AL VY + ++ L + + K V+ +GNK+D
Sbjct: 60 FPAMRKLSIQNGDAFAL-VYSVDDPESFEEVKRLREEILEVKEDKFVPIVV--VGNKIDS 116
Query: 133 EGSRDVRYDEAKKFAE-ENDLIFVEASAMTGENVEQAFLETAKKIYQNIKDGKLNANMTE 191
R V +A E + + FVEASA ENV + F E ++ L + ++
Sbjct: 117 LAERQVEAADALSTVELDWNNGFVEASAKDNENVTEVFKEL-------LQQANLPSWLSP 169
Query: 192 SGVQHKERGGPASLGDSSSSDKPNCSC 218
+ ++ + P+ + +K N SC
Sbjct: 170 A-LRRRRESAPSEIQRRPPMNKTN-SC 194
>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 = 72.2 bits (177), Expect = 6e-16
Identities = 50/160 (31%), Positives = 75/160 (46%), Gaps = 6/160 (3%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQE 75
++ ++ G GVGKS L+ +F + F TI + ++I LQI DT G
Sbjct: 2 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTY-RQVISCSKSICTLQITDTTGSH 60
Query: 76 RFRAVTR-SYYRGAAGALMVYDITRRSTYNHLSSW---LTDTKNLTNPNTVIFLIGNKMD 131
+F A+ R S +G A ++VY IT + + L + + K I L+GNK D
Sbjct: 61 QFPAMQRLSISKGHA-FILVYSITSKQSLEELKPIYELICEIKGNNLEKIPIMLVGNKCD 119
Query: 132 LEGSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLE 171
SR+V E A + F+E SA T NV++ F E
Sbjct: 120 ESPSREVSSSEGAALARTWNCAFMETSAKTNHNVQELFQE 159
>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 = 71.7 bits (176), Expect = 1e-15
Identities = 48/171 (28%), Positives = 79/171 (46%), Gaps = 16/171 (9%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQER 76
K +++GD GK+ LL F + F + T+ E T EV ++I+L +WDT+G
Sbjct: 3 KIVLVGDSQCGKTALLQVFAKDSFPENYVPTV-FENYTASFEVDKQRIELSLWDTSGSPY 61
Query: 77 FRAVTRSYYRGAAGALMVYDITRRSTY-NHLSSWLTDTKNLTNPNTVIFLIGNKMDL--- 132
+ V Y + L+ +DI+R T + L W + + PNT + L+G K DL
Sbjct: 62 YDNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEVREFC-PNTPVLLVGCKSDLRTD 120
Query: 133 ---------EGSRDVRYDEAKKFAEE-NDLIFVEASAMTGENVEQAFLETA 173
+ V +++ + A++ +VE SA T EN + E A
Sbjct: 121 LSTLTELSNKRQIPVSHEQGRNLAKQIGAAAYVECSAKTSENSVRDVFEMA 171
>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 = 69.8 bits (171), Expect = 4e-15
Identities = 57/176 (32%), Positives = 84/176 (47%), Gaps = 23/176 (13%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQE- 75
K +I+GD GK+CLL F++ +F P+ E IEV G++++L +WDTAGQE
Sbjct: 3 KLVIVGDGACGKTCLLIVFSKDQF-PEVYVPTVFENYVADIEVDGKQVELALWDTAGQED 61
Query: 76 --RFRAVTRSYYRGAAGALMVYDI-TRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMDL 132
R R ++ Y LM + I + S N W + K+ PN I L+GNK DL
Sbjct: 62 YDRLRPLS---YPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFC-PNVPIILVGNKKDL 117
Query: 133 E------------GSRDVRYDEAKKFAEE-NDLIFVEASAMTGENVEQAFLETAKK 175
V+ +E + AE+ ++E SA T E V + F E A +
Sbjct: 118 RNDEHTIRELAKMKQEPVKPEEGRAMAEKIGAFGYLECSAKTKEGVREVF-EMATR 172
>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 = 68.6 bits (168), Expect = 1e-14
Identities = 44/167 (26%), Positives = 80/167 (47%), Gaps = 16/167 (9%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQER 76
K +++GD VGK+ L+ +T + + T F + V G+ ++LQ+ DTAGQ+
Sbjct: 2 KCVLVGDGAVGKTSLIVSYTTNGYPTEYVPTAFDNFSVVV-LVDGKPVRLQLCDTAGQDE 60
Query: 77 FRAVTRSYYRGAAGALMVYDITRRSTYNHLSS-WLTDTKNLTNPNTVIFLIGNKMDLE-- 133
F + Y L+ + + S++ ++S W+ + + NP I L+G + DL
Sbjct: 61 FDKLRPLCYPDTDVFLLCFSVVNPSSFQNISEKWIPEIRK-HNPKAPIILVGTQADLRTD 119
Query: 134 ----------GSRDVRYDEAKKFAEE-NDLIFVEASAMTGENVEQAF 169
G + V AK AE+ ++E SA+T +N+++ F
Sbjct: 120 VNVLIQLARYGEKPVSQSRAKALAEKIGACEYIECSALTQKNLKEVF 166
>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 = 66.1 bits (162), Expect = 9e-14
Identities = 38/161 (23%), Positives = 67/161 (41%), Gaps = 21/161 (13%)
Query: 19 IIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQERFR 78
+++G G GK+ +L++ + + P TIG + V + +K +WD GQ++ R
Sbjct: 3 LMLGLDGAGKTTILYKLKLGEVVTTIP-TIG----FNVETVEYKNVKFTVWDVGGQDKIR 57
Query: 79 AVTRSYYRGAAGALMVYDITRRS----TYNHLSSWLTDTKNLTNPNTVIFLI-GNKMDLE 133
+ + YY G + V D + R N L L + + P LI NK DL
Sbjct: 58 PLWKHYYENTDGLIFVVDSSDRERIEEAKNELHKLLNEEELKGAP----LLILANKQDLP 113
Query: 134 GSRDVRYDEAKKFAEENDL-----IFVEASAMTGENVEQAF 169
G+ E + + SA+TG+ +++
Sbjct: 114 GALTE--SELIELLGLESIKGRRWHIQPCSAVTGDGLDEGL 152
>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 = 66.0 bits (161), Expect = 1e-13
Identities = 46/172 (26%), Positives = 85/172 (49%), Gaps = 22/172 (12%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQE- 75
K +++GD VGK+CLL +T F + T+ + ++ V G+ + L +WDTAGQE
Sbjct: 3 KCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVM-VDGKPVNLGLWDTAGQED 61
Query: 76 --RFRAVTRSYYRGAAGALMVYDITRRSTYNHLSS-WLTDTKNLTNPNTVIFLIGNKMDL 132
R R ++ Y L+ + + +++ ++ + W + ++ PNT I L+G K+DL
Sbjct: 62 YDRLRPLS---YPQTDVFLICFSLVSPASFENVRAKWYPEVRHHC-PNTPIILVGTKLDL 117
Query: 133 EGSRD------------VRYDEAKKFAEE-NDLIFVEASAMTGENVEQAFLE 171
+D + Y + A+E + ++E SA+T ++ F E
Sbjct: 118 RDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDE 169
>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 = 64.5 bits (157), Expect = 6e-13
Identities = 49/168 (29%), Positives = 75/168 (44%), Gaps = 12/168 (7%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQER 76
K +++GD GK+ LL+ FT F T+ E I V G ++L +WDTAGQE
Sbjct: 2 KVVVLGDGACGKTSLLNVFTRGYFPQVYEPTV-FENYIHDIFVDGLAVELSLWDTAGQEE 60
Query: 77 FRAVTRSYYRGAAGALMVYDI-TRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMDLEGS 135
F + Y ++ + + S N S WL + ++ P + L+ K DL
Sbjct: 61 FDRLRSLSYADTHVIMLCFSVDNPDSLENVESKWLAEIRHHC-PGVKLVLVALKCDLREP 119
Query: 136 RDVR--------YDEAKKFAEE-NDLIFVEASAMTGENVEQAFLETAK 174
R+ R Y+E A+ N ++E SA V +AF E A+
Sbjct: 120 RNERDRGTHTISYEEGLAVAKRINACRYLECSAKLNRGVNEAFTEAAR 167
>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 = 64.3 bits (156), Expect = 6e-13
Identities = 48/162 (29%), Positives = 77/162 (47%), Gaps = 16/162 (9%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQER 76
K +++GD GK+ LLH F + F + T+ E T E+ ++I+L +WDT+G
Sbjct: 7 KIVVVGDSQCGKTALLHVFAKDCFPENYVPTV-FENYTASFEIDTQRIELSLWDTSGSPY 65
Query: 77 FRAVTRSYYRGAAGALMVYDITRRSTY-NHLSSWLTDTKNLTNPNTVIFLIGNKMDL--- 132
+ V Y + L+ +DI+R T + L W + + PNT + L+G K DL
Sbjct: 66 YDNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEIQEFC-PNTKMLLVGCKSDLRTD 124
Query: 133 -----EGSRD----VRYDEAKKFAEE-NDLIFVEASAMTGEN 164
E S V YD+ A++ ++E SA+ EN
Sbjct: 125 VSTLVELSNHRQTPVSYDQGANMAKQIGAATYIECSALQSEN 166
>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 = 62.3 bits (151), Expect = 3e-12
Identities = 53/189 (28%), Positives = 83/189 (43%), Gaps = 28/189 (14%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQER 76
K +++GD VGK+CLL +T F + T+ + + V G + L +WDTAGQE
Sbjct: 5 KCVVVGDGAVGKTCLLICYTTNAFPKEYIPTVFDNYSAQTA-VDGRTVSLNLWDTAGQEE 63
Query: 77 F-RAVTRSYYRGAAGALMVYDITRRSTY-NHLSSWLTDTKNLTNPNTVIFLIGNKMDLEG 134
+ R T SY + ++ + I S+Y N W + + PN I L+G K DL
Sbjct: 64 YDRLRTLSYPQTNV-FIICFSIASPSSYENVRHKWHPEVCHHC-PNVPILLVGTKKDLRN 121
Query: 135 SRDVRYDEAKKFAEEND-----------------LIFVEASAMTGENVEQAFLETAKKI- 176
D KK E+ + ++E SA+ + V++ F E + +
Sbjct: 122 DADT----LKKLKEQGQAPITPQQGGALAKQIHAVKYLECSALNQDGVKEVFAEAVRAVL 177
Query: 177 YQN-IKDGK 184
IKD K
Sbjct: 178 NPTPIKDTK 186
>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 = 62.2 bits (151), Expect = 4e-12
Identities = 50/165 (30%), Positives = 77/165 (46%), Gaps = 14/165 (8%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQER 76
K +I+GD GK+ LL+ FT +F + T+ + T V G+ ++L +WDTAGQE
Sbjct: 3 KLVIVGDGACGKTSLLYVFTLGEFPEEYHPTVFENYVTDC-RVDGKPVQLALWDTAGQEE 61
Query: 77 FRAVTRSYYRGAAGALMVYDI-TRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMDLE-- 133
+ + Y A L+ + I T S N + W+ + + PN + L+G K DL
Sbjct: 62 YERLRPLSYSKAHVILIGFAIDTPDSLENVRTKWIEEVRRYC-PNVPVILVGLKKDLRQE 120
Query: 134 --------GSRDVRYDEAKKFAEE-NDLIFVEASAMTGENVEQAF 169
V +AK A ++E SA+TGE V+ F
Sbjct: 121 AVAKGNYATDEFVPIQQAKLVARAIGAKKYMECSALTGEGVDDVF 165
>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 = 61.7 bits (150), Expect = 4e-12
Identities = 43/163 (26%), Positives = 75/163 (46%), Gaps = 13/163 (7%)
Query: 19 IIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQERFR 78
+++G GKS LL++ + + P T+G F ++++ + L +WD GQE+ R
Sbjct: 3 LLLGLDSAGKSTLLYKLKHAELVTTIP-TVG--FNVEMLQLEK-HLSLTVWDVGGQEKMR 58
Query: 79 AVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNP---NTVIFLIGNKMDLEGS 135
V + Y G + V D + + + L L N + L+ NK DL G+
Sbjct: 59 TVWKCYLENTDGLVYVVDSSDEARLDESQKELKHI--LKNEHIKGVPVVLLANKQDLPGA 116
Query: 136 ---RDV-RYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAK 174
++ R + KK+ + D SA+TGE + +AF + A
Sbjct: 117 LTAEEITRRFKLKKYCSDRDWYVQPCSAVTGEGLAEAFRKLAS 159
>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 = 59.3 bits (144), Expect = 3e-11
Identities = 48/166 (28%), Positives = 70/166 (42%), Gaps = 23/166 (13%)
Query: 19 IIIGDMGVGKSCLLHQFTEQKFMPDCP--------HTIGVEFGTRIIEVHGEKIKLQIWD 70
+I+G GK+ L Q T+ KF + T+G+ GT IEV K +L WD
Sbjct: 3 LILGLDNAGKTTFLEQ-TKTKFSKNYKGLNPSKITPTVGLNIGT--IEV--GKARLMFWD 57
Query: 71 TAGQERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNP---NTVIFLIG 127
GQE R++ YY + G + V D T R +N S K + N + ++
Sbjct: 58 LGGQEELRSLWDKYYAESHGVIYVIDSTDRERFN--ESKSAFEKVINNEALEGVPLLVLA 115
Query: 128 NKMDLEGSRDVRY-----DEAKKFAEENDLIFVEASAMTGENVEQA 168
NK DL + V D+ D + SA+ GE VE+
Sbjct: 116 NKQDLPDALSVAEIKEVFDDCIALIGRRDCLVQPVSALEGEGVEEG 161
>gnl|CDD|206680 cd01893, Miro1, Mitochondrial Rho family 1 (Miro1), N-terminal.
Miro1 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the N-terminal
GTPase domain of Miro proteins. These atypical Rho
GTPases have roles in mitochondrial homeostasis and
apoptosis. Most Rho proteins contain a lipid
modification site at the C-terminus; however, Miro is
one of few Rho subfamilies that lack this feature.
Length = 168
Score = 57.7 bits (140), Expect = 1e-10
Identities = 48/156 (30%), Positives = 71/156 (45%), Gaps = 8/156 (5%)
Query: 19 IIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQERFR 78
++IGD GVGKS L+ ++F + P + T +V E++ I DT+ + + R
Sbjct: 6 VLIGDEGVGKSSLIMSLVSEEFPENVPRV--LPEITIPADVTPERVPTTIVDTSSRPQDR 63
Query: 79 AVTRSYYRGAAGALMVYDITRRSTYNHLSS-WLTDTKNLTNPNTVIFLIGNKMDL--EGS 135
A + R A +VY + R ST + + WL + L I L+GNK DL S
Sbjct: 64 ANLAAEIRKANVICLVYSVDRPSTLERIRTKWLPLIRRLGV-KVPIILVGNKSDLRDGSS 122
Query: 136 RDVRYDEAKKFAEENDLI--FVEASAMTGENVEQAF 169
+ +E E I VE SA T NV + F
Sbjct: 123 QAGLEEEMLPIMNEFREIETCVECSAKTLINVSEVF 158
>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 = 57.0 bits (137), Expect = 5e-10
Identities = 47/178 (26%), Positives = 78/178 (43%), Gaps = 30/178 (16%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDC-PHT---IGVEFGTRIIEVHGEKIKLQIWDTA 72
K +++GD+ GK+ +L Q DC P T E T +E ++++L +WDT+
Sbjct: 15 KLVLVGDVQCGKTAML-----QVLAKDCYPETYVPTVFENYTACLETEEQRVELSLWDTS 69
Query: 73 GQERFRAVTRSYYRGAAGALMVYDITRRSTYNH-LSSWLTDTKNLTNPNTVIFLIGNKMD 131
G + V Y + L+ +DI+R ++ L W + + P+T I LIG K D
Sbjct: 70 GSPYYDNVRPLCYSDSDAVLLCFDISRPEIFDSALKKWRAEILDYC-PSTRILLIGCKTD 128
Query: 132 L------------EGSRDVRYDE----AKKFAEENDLIFVEASAMTGENVEQAFLETA 173
L + + Y++ AK+ E ++E SA T E + TA
Sbjct: 129 LRTDLSTLMELSNQKQAPISYEQGCAMAKQLGAEA---YLECSAFTSEKSIHSIFRTA 183
>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 = 56.2 bits (135), Expect = 9e-10
Identities = 35/117 (29%), Positives = 59/117 (50%), Gaps = 3/117 (2%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQER 76
K +++GD GK+ LLH F + + T+ E T E+ +I+L +WDT+G
Sbjct: 3 KIVVVGDTQCGKTALLHVFAKDNYPESYVPTV-FENYTASFEIDKHRIELNMWDTSGSSY 61
Query: 77 FRAVTRSYYRGAAGALMVYDITRRSTYNH-LSSWLTDTKNLTNPNTVIFLIGNKMDL 132
+ V Y + L+ +DI+R T + L W +T+ PN + L+G K+D+
Sbjct: 62 YDNVRPLAYPDSDAVLICFDISRPETLDSVLKKWQGETQEFC-PNAKLVLVGCKLDM 117
>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 = 55.3 bits (133), Expect = 1e-09
Identities = 42/169 (24%), Positives = 79/169 (46%), Gaps = 16/169 (9%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQER 76
K +++GD VGK+CLL +T KF + T+ + ++ + GE L ++DTAGQE
Sbjct: 3 KCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVM-IGGEPYTLGLFDTAGQED 61
Query: 77 FRAVTRSYYRGAAGALMVYDITRRSTY-NHLSSWLTDTKNLTNPNTVIFLIGNKMDL--- 132
+ + Y L+ + + S++ N W+ + + P T L+G ++DL
Sbjct: 62 YDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHC-PKTPFLLVGTQIDLRDD 120
Query: 133 ---------EGSRDVRYDEAKKFAEENDLI-FVEASAMTGENVEQAFLE 171
+ + + +K A + + +VE SA+T + ++ F E
Sbjct: 121 PSTIEKLAKNKQKPITPETGEKLARDLKAVKYVECSALTQKGLKNVFDE 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 = 55.5 bits (134), Expect = 2e-09
Identities = 36/164 (21%), Positives = 73/164 (44%), Gaps = 11/164 (6%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQE 75
++ +++G VGK+ ++ +F +F TI +F ++ + GE +L I DT+G
Sbjct: 1 YRMVVLGASKVGKTAIVSRFLGGRFEEQYTPTIE-DFHRKLYSIRGEVYQLDILDTSGNH 59
Query: 76 RFRAVTRSYYRGAAGALMVYDITRRSTYNHLSS---------WLTDTKNLTNPNTVIFLI 126
F A+ R ++V+ + R ++ + K N + +
Sbjct: 60 PFPAMRRLSILTGDVFILVFSLDNRESFEEVCRLREQILETKSCLKNKTKENVKIPMVIC 119
Query: 127 GNKMDLEGSRDVRYDEAKKF-AEENDLIFVEASAMTGENVEQAF 169
GNK D + R+V+ DE ++ + + + E SA N+++ F
Sbjct: 120 GNKADRDFPREVQRDEVEQLVGGDENCAYFEVSAKKNSNLDEMF 163
>gnl|CDD|177661 PLN00023, PLN00023, GTP-binding protein; Provisional.
Length = 334
Score = 55.6 bits (134), Expect = 3e-09
Identities = 46/167 (27%), Positives = 77/167 (46%), Gaps = 33/167 (19%)
Query: 19 IIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHG------EKIK------- 65
+++GD GVGKS L+H + + P TIG G + I +G IK
Sbjct: 25 LVVGDSGVGKSSLVHLIVKGSSIARPPQTIGCTVGVKHIT-YGSPGSSSNSIKGDSERDF 83
Query: 66 -LQIWDTAGQERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSW---LTDTKNLTNPNT 121
+++WD +G ER++ +Y G + V+D+++R T L W + T + P
Sbjct: 84 FVELWDVSGHERYKDCRSLFYSQINGVIFVHDLSQRRTKTSLQKWASEVAATGTFSAPLG 143
Query: 122 --------VIFL-IGNKMDL---EGSRDVR---YDEAKKFAEENDLI 153
V ++ IGNK D+ EG+R D A+++ E+ L+
Sbjct: 144 SGGPGGLPVPYIVIGNKADIAPKEGTRGSSGNLVDAARQWVEKQGLL 190
>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 = 53.5 bits (128), Expect = 5e-09
Identities = 42/176 (23%), Positives = 80/176 (45%), Gaps = 16/176 (9%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQE 75
K +++GD VGK+CLL + F + T+ + + V G++ L ++DTAGQE
Sbjct: 1 LKCVVVGDGAVGKTCLLMSYANDAFPEEYVPTVFDHYAVS-VTVGGKQYLLGLYDTAGQE 59
Query: 76 RFRAVTRSYYRGAAGALMVYDITRRSTYNHL-SSWLTDTKNLTNPNTVIFLIGNKMDLEG 134
+ + Y L+ + + +++ ++ W+ + K PN LIG ++DL
Sbjct: 60 DYDRLRPLSYPMTDVFLICFSVVNPASFQNVKEEWVPELKEYA-PNVPYLLIGTQIDLRD 118
Query: 135 ------------SRDVRYDEAKKFAEE-NDLIFVEASAMTGENVEQAFLETAKKIY 177
+ + ++ +K A+E +VE SA+T + ++ F E I
Sbjct: 119 DPKTLARLNDMKEKPITVEQGQKLAKEIGACCYVECSALTQKGLKTVFDEAIIAIL 174
>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 = 53.0 bits (127), Expect = 9e-09
Identities = 26/103 (25%), Positives = 48/103 (46%), Gaps = 11/103 (10%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGE------KIKLQIWD 70
K +++GD GVGKS L+H + + + + T+G R +GE +++WD
Sbjct: 2 KVLVLGDSGVGKSSLVHLLCKNQVLGNPSWTVGCSVDVRHHT-YGEGTPEEKTFYVELWD 60
Query: 71 TAGQ----ERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSW 109
G E ++ +Y G + V+D+T + + +L W
Sbjct: 61 VGGSVGSAESVKSTRAVFYNQINGIIFVHDLTNKKSSQNLYRW 103
>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 = 51.6 bits (124), Expect = 1e-08
Identities = 35/120 (29%), Positives = 52/120 (43%), Gaps = 5/120 (4%)
Query: 20 IIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQERFRA 79
++G GK+ L++ +F D T+G F R + IK +WD GQ RFR+
Sbjct: 4 LVGLQNSGKTTLVNVIASGQFSEDTIPTVG--FNMRKVTKGNVTIK--VWDLGGQPRFRS 59
Query: 80 VTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLI-GNKMDLEGSRDV 138
+ Y RG + V D R + L D + + L+ GNK DL G+ V
Sbjct: 60 MWERYCRGVNAIVYVVDAADREKLEVAKNELHDLLEKPSLEGIPLLVLGNKNDLPGALSV 119
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 52.1 bits (125), Expect = 2e-08
Identities = 39/166 (23%), Positives = 73/166 (43%), Gaps = 22/166 (13%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFM------------PDCPHTIGVEFGTRIIEVHGEKI 64
K ++IG +G GK+ + +++ + P T+ ++FG+ + E
Sbjct: 12 KIVVIGPVGAGKTTFVRALSDKPLVITEADASSVSGKGKRPTTVAMDFGSIEL---DEDT 68
Query: 65 KLQIWDTAGQERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIF 124
+ ++ T GQERF+ + RGA GA+++ D +R T++ LT+ N +
Sbjct: 69 GVHLFGTPGQERFKFMWEILSRGAVGAIVLVDSSRPITFHAEE----IIDFLTSRNPIPV 124
Query: 125 LIG-NKMDLEGSRDV-RYDEAKKFAEENDLIFVEASAMTGENVEQA 168
++ NK DL + + EA K + + +E A GE
Sbjct: 125 VVAINKQDLFDALPPEKIREALKLELLS-VPVIEIDATEGEGARDQ 169
>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 = 51.6 bits (123), Expect = 2e-08
Identities = 36/126 (28%), Positives = 60/126 (47%), Gaps = 12/126 (9%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQER 76
+ + +G G GK+ +L + + +FM P TIG T V + +K IWD G+ +
Sbjct: 1 RVVTLGLDGAGKTTILFKLKQDEFMQPIP-TIGFNVET----VEYKNLKFTIWDVGGKHK 55
Query: 77 FRAVTRSYYRGAAGALMVYDITRR----STYNHLSSWLTDTKNLTNPNTVIFLIGNKMDL 132
R + + YY + V D + R ++ L+ LT+ K L + +IF NK D+
Sbjct: 56 LRPLWKHYYLNTQAVVFVIDSSHRDRVSEAHSELAKLLTE-KELRDALLLIF--ANKQDV 112
Query: 133 EGSRDV 138
G+ V
Sbjct: 113 AGALSV 118
>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 = 51.4 bits (123), Expect = 4e-08
Identities = 34/129 (26%), Positives = 56/129 (43%), Gaps = 13/129 (10%)
Query: 20 IIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWD--------- 70
++G GVGK+ ++ QF Q+F + T + + G L I D
Sbjct: 5 VLGAPGVGKTAIVRQFLAQEFPEEYIPTEHRRLYRPAVVLSGRVYDLHILDVPNMQRYPG 64
Query: 71 TAGQERFRAVTRSYYRGAAGALMVYDITRRSTYNH---LSSWLTDTKNLTNPNTVIFLIG 127
TAGQE R R + ++VYDI ++++ L + +T+ N I ++G
Sbjct: 65 TAGQEWMDPRFRG-LRNSRAFILVYDICSPDSFHYVKLLRQQILETRPAGNKEPPIVVVG 123
Query: 128 NKMDLEGSR 136
NK D + R
Sbjct: 124 NKRDQQRHR 132
>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 = 50.4 bits (121), Expect = 5e-08
Identities = 38/125 (30%), Positives = 59/125 (47%), Gaps = 14/125 (11%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIG--VEFGTRIIEVHGEKIKLQIWDTAG 73
+K II+G GK+ +L+QF + + P TIG VE E+ + I+ +WD G
Sbjct: 16 YKVIIVGLDNAGKTTILYQFLLGEVVHTSP-TIGSNVE------EIVYKNIRFLMWDIGG 68
Query: 74 QERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNP---NTVIFLIGNKM 130
QE R+ +YY ++V D T R L K L + V+ ++ NK
Sbjct: 69 QESLRSSWNTYYTNTDAVILVIDSTDRERLPLTKEEL--YKMLAHEDLRKAVLLVLANKQ 126
Query: 131 DLEGS 135
DL+G+
Sbjct: 127 DLKGA 131
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 50.3 bits (121), Expect = 6e-08
Identities = 40/166 (24%), Positives = 70/166 (42%), Gaps = 25/166 (15%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIG--VEFGTRIIEVHGEKIKLQIWDTAG 73
+ +I+G GK+ +L++ + + P TIG VE V + +K +WD G
Sbjct: 15 MRILILGLDNAGKTTILYKLKLGEIVTTIP-TIGFNVE------TVTYKNVKFTVWDVGG 67
Query: 74 QERFRAVTRSYYRGAAGALMVYDITRRS----TYNHLSSWLTDTKNLTNPNTVIFLI-GN 128
QE R + R+Y+ + V D R L + L + + LI N
Sbjct: 68 QESLRPLWRNYFPNTDAVIFVVDSADRDRIEEAKEELHALLNEEEL----ADAPLLILAN 123
Query: 129 KMDLEGSRDVRYDEAKKFAEENDL----IFVEA-SAMTGENVEQAF 169
K DL G+ E ++ ++L ++ SA+TGE +++
Sbjct: 124 KQDLPGAMSE--AEIRELLGLHELKDRPWEIQGCSAVTGEGLDEGL 167
>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 = 48.4 bits (115), Expect = 3e-07
Identities = 31/117 (26%), Positives = 50/117 (42%), Gaps = 6/117 (5%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQER 76
+ +++G GK+ +L++ + + P TIG T V + I +WD GQ++
Sbjct: 15 RILMVGLDAAGKTTILYKLKLGESVTTIP-TIGFNVET----VTYKNISFTVWDVGGQDK 69
Query: 77 FRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTN-PNTVIFLIGNKMDL 132
R + R YY G + V D R + L N + VI + NK DL
Sbjct: 70 IRPLWRHYYTNTQGLIFVVDSNDRDRIDEAREELHRMLNEDELRDAVILVFANKQDL 126
>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 = 47.5 bits (113), Expect = 8e-07
Identities = 44/172 (25%), Positives = 75/172 (43%), Gaps = 19/172 (11%)
Query: 19 IIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEV---HGEKIKLQIWDTAGQE 75
+++G GK+ +L++ +F+ P T G F T I+V + + + WD GQE
Sbjct: 7 VMLGLDSAGKTTVLYRLKFNEFVNTVP-TKG--FNTEKIKVSLGNAKGVTFHFWDVGGQE 63
Query: 76 RFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTD-TKNLTNPNTVIFLIGNKMDLEG 134
+ R + +SY R G + V D + L TK N + ++ NK DL
Sbjct: 64 KLRPLWKSYTRCTDGIVFVVDSVDVERMEEAKTELHKITKFSENQGVPVLVLANKQDLPN 123
Query: 135 SRDVRYDEAKKFAEENDLI------FVEASAMTGENVEQAFLETAKKIYQNI 180
+ V E +K ++L A A+ GE ++ E +K+Y+ I
Sbjct: 124 ALPV--SEVEKLLALHELSSSTPWHVQPACAIIGEGLQ----EGLEKLYEMI 169
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 47.2 bits (113), Expect = 2e-06
Identities = 47/185 (25%), Positives = 66/185 (35%), Gaps = 38/185 (20%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQK--FMPDCPHTIGVEFGTR-IIEVH----GEKIKLQI 68
K +IIG VGKS LL+ + + D T TR +IE G I +++
Sbjct: 218 LKVVIIGRPNVGKSSLLNALLGRDRAIVTDIAGT------TRDVIEEDINLNG--IPVRL 269
Query: 69 WDTAGQ-------ERF---RAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTN 118
DTAG ER RA A L V D ++ L L
Sbjct: 270 VDTAGIRETDDVVERIGIERAKKAI--EEADLVLFVLDASQ-----PLDKEDLALIELLP 322
Query: 119 PNTVIFLIGNKMDLEGSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKIYQ 178
I ++ NK DL E + N + SA TGE ++ A E K+++
Sbjct: 323 KKKPIIVVLNKADLVSK-----IELESEKLANGDAIISISAKTGEGLD-ALREAIKQLFG 376
Query: 179 NIKDG 183
Sbjct: 377 KGLGN 381
>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 = 43.9 bits (104), Expect = 8e-06
Identities = 38/156 (24%), Positives = 64/156 (41%), Gaps = 13/156 (8%)
Query: 19 IIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQERFR 78
+I+G G GK+ +L++ + + P TIG T V + +K Q+WD GQ R
Sbjct: 3 LILGLDGAGKTTILYRLQVGEVVTTIP-TIGFNVET----VTYKNLKFQVWDLGGQTSIR 57
Query: 79 AVTRSYYRGAAGALMV---YDITRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMDLEGS 135
R YY + V D R + + + L + ++F NK D+ G+
Sbjct: 58 PYWRCYYSNTDAIIYVVDSTDRDRLGISKSELHAMLEEEELKDAVLLVF--ANKQDMPGA 115
Query: 136 RDV-RYDEAKKFAEENDLIF--VEASAMTGENVEQA 168
E +E D + + SA GE +++
Sbjct: 116 LSEAEVAEKLGLSELKDRTWQIFKTSATKGEGLDEG 151
>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 = 41.7 bits (98), Expect = 6e-05
Identities = 27/113 (23%), Positives = 50/113 (44%), Gaps = 12/113 (10%)
Query: 27 GKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQERFRAVTRSYYR 86
GK+ +L++ + + P T+G T V + +K +WD GQ++ R + R YY
Sbjct: 21 GKTTILYKLKLGQSVTTIP-TVGFNVET----VTYKNVKFNVWDVGGQDKIRPLWRHYYT 75
Query: 87 GAAGALMVYDITRRSTYNHLSSWLTDTKNLTN----PNTVIFLIGNKMDLEGS 135
G G + V D R + + + + N + ++ + NK DL +
Sbjct: 76 GTQGLIFVVDSADR---DRIDEARQELHRIINDREMRDALLLVFANKQDLPDA 125
>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 = 39.6 bits (93), Expect = 3e-04
Identities = 35/132 (26%), Positives = 54/132 (40%), Gaps = 14/132 (10%)
Query: 47 TIGVEFGTRIIEVHGEKIKLQIWDTAGQERFRAVTRSYYRGAAGALMVYDITRRSTYN-- 104
TI G I + KL IWD GQ+ R+ R+Y+ + V D + R+
Sbjct: 41 TISPTLGFNIKTLEYNGYKLNIWDVGGQKSLRSYWRNYFESTDALIWVVDSSDRARLEDC 100
Query: 105 --HLSSWLTDTKNLTNPNTVIFLIGNKMDLEGSRDVRYDEAKKFAEENDL-----IFVEA 157
L L + + L +IF NK DL G+ +E ++ E + +
Sbjct: 101 KRELQKLLVEER-LAGATLLIFA--NKQDLPGALSP--EEIREVLELDSIKSHHWRIFGC 155
Query: 158 SAMTGENVEQAF 169
SA+TGEN+
Sbjct: 156 SAVTGENLLDGI 167
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 39.1 bits (91), Expect = 6e-04
Identities = 30/117 (25%), Positives = 52/117 (44%), Gaps = 10/117 (8%)
Query: 19 IIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQERFR 78
+++G GK+ +L++ + + P TIG T V + +K +WD GQ++ R
Sbjct: 21 LMVGLDAAGKTTILYKLKLGEVVTTIP-TIGFNVET----VEYKNLKFTMWDVGGQDKLR 75
Query: 79 AVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNP---NTVIFLIGNKMDL 132
+ R YY+ G + V D R L + L+ + V+ + NK DL
Sbjct: 76 PLWRHYYQNTNGLIFVVDSNDRERIGDAREEL--ERMLSEDELRDAVLLVFANKQDL 130
>gnl|CDD|215653 pfam00009, GTP_EFTU, Elongation factor Tu GTP binding domain. This
domain contains a P-loop motif, also found in several
other families such as pfam00071, pfam00025 and
pfam00063. Elongation factor Tu consists of three
structural domains, this plus two C-terminal beta barrel
domains.
Length = 184
Score = 39.0 bits (92), Expect = 7e-04
Identities = 34/134 (25%), Positives = 55/134 (41%), Gaps = 33/134 (24%)
Query: 57 IEVHGEKIKLQIWDTAGQERFRAVTRSYYRGAA---GALMVYDI-------TRRSTYNHL 106
+ +K + I DT G F T+ RGA+ GA++V D TR HL
Sbjct: 59 VSFETKKRLINIIDTPGHVDF---TKEMIRGASQADGAILVVDAVEGVMPQTRE----HL 111
Query: 107 SSWLTDTKNLTNPNTVIFLIGNKMDL-------EGSRDVRYDEAKKFAEENDLI-FVEAS 158
L T + ++F+ NK+D E ++ + +K+ + + V S
Sbjct: 112 --LLAKTLGV---PIIVFI--NKIDRVDDAELEEVVEEISRELLEKYGFGGETVPVVPGS 164
Query: 159 AMTGENVEQAFLET 172
A+TGE + LE
Sbjct: 165 ALTGEGI-DELLEA 177
>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 = 38.0 bits (88), Expect = 0.001
Identities = 37/190 (19%), Positives = 73/190 (38%), Gaps = 40/190 (21%)
Query: 16 FKYIIIGDMGVGKS-------CLLHQFTEQKFMPDCP-------HTIGVEFGTRIIEV-H 60
K +++GD VGK+ C Q P + + E R +V
Sbjct: 3 IKCVVVGDNAVGKTRLICARACNKTLTQYQLLATHVPTVWAIDQYRVCQEVLERSRDVVD 62
Query: 61 GEKIKLQIWDTAG-QERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSS-WLTDTKNLTN 118
G + L++WDT G ++ R R Y + L+ + I ++ ++ + W + ++
Sbjct: 63 GVSVSLRLWDTFGDHDKDR---RFAYGRSDVVLLCFSIASPNSLRNVKTMWYPEIRHFC- 118
Query: 119 PNTVIFLIGNKMDL-------------------EGSRDVRYDEAKKFAEENDLIFVEASA 159
P + L+G K+DL + + + + + A+E + + E S
Sbjct: 119 PRVPVILVGCKLDLRYADLDEVNRARRPLARPIKNADILPPETGRAVAKELGIPYYETSV 178
Query: 160 MTGENVEQAF 169
+T V+ F
Sbjct: 179 VTQFGVKDVF 188
>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 = 37.4 bits (87), Expect = 0.002
Identities = 29/117 (24%), Positives = 50/117 (42%), Gaps = 10/117 (8%)
Query: 19 IIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQERFR 78
+++G GK+ +L++ + + P TIG T V + I +WD GQ++ R
Sbjct: 4 LMVGLDAAGKTTILYKLKLGEIVTTIP-TIGFNVET----VEYKNISFTVWDVGGQDKIR 58
Query: 79 AVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNP---NTVIFLIGNKMDL 132
+ R Y++ G + V D R L + L + V+ + NK DL
Sbjct: 59 PLWRHYFQNTQGLIFVVDSNDRERIGEAREEL--QRMLNEDELRDAVLLVFANKQDL 113
>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 = 37.1 bits (87), Expect = 0.002
Identities = 30/132 (22%), Positives = 50/132 (37%), Gaps = 38/132 (28%)
Query: 54 TR-IIEVH----GEKIKLQIWDTAG---------QERFRAVTRSYYRGAAGA---LMVYD 96
TR +IE G I +++ DTAG + + R+ A L+V D
Sbjct: 38 TRDVIEEEIDLGG--IPVRLIDTAGLRETEDEIEKI---GIERAREA-IEEADLVLLVVD 91
Query: 97 ITRRSTYNHLSSWLTDTKNLTNPNTV-IFLIGNKMDLEGSRDVRYDEAKKFAEENDLIFV 155
+ D + L P + ++ NK DL +A+ +E N +
Sbjct: 92 ASEGLD-------EEDLEILELPAKKPVIVVLNKSDLLS-------DAEGISELNGKPII 137
Query: 156 EASAMTGENVEQ 167
SA TGE +++
Sbjct: 138 AISAKTGEGIDE 149
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 37.3 bits (86), Expect = 0.002
Identities = 22/84 (26%), Positives = 40/84 (47%), Gaps = 5/84 (5%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQER 76
+ +++G GK+ +L++ + + P TIG T V + I +WD GQ++
Sbjct: 19 RILMVGLDAAGKTTILYKLKLGEIVTTIP-TIGFNVET----VEYKNISFTVWDVGGQDK 73
Query: 77 FRAVTRSYYRGAAGALMVYDITRR 100
R + R Y++ G + V D R
Sbjct: 74 IRPLWRHYFQNTQGLIFVVDSNDR 97
>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 = 36.9 bits (86), Expect = 0.003
Identities = 30/126 (23%), Positives = 49/126 (38%), Gaps = 20/126 (15%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQK---FMPDC-PHTIGVEFGTRIIEVHGEKIKLQIWDTA 72
K + +G GK+ LLH + + +P P + + G +K +D
Sbjct: 21 KIVFLGLDNAGKTTLLHMLKDDRLAQHVPTLHPTSEELTIG---------NVKFTTFDLG 71
Query: 73 GQERFRAVTRSYYRGAAGALMVYDITRRSTY----NHLSSWLTDTKNLTNPNTVIFLIGN 128
G E+ R V + Y+ G + + D + L S L D N I ++GN
Sbjct: 72 GHEQARRVWKDYFPEVDGIVFLVDAADPERFQESKEELDSLLND---EELANVPILILGN 128
Query: 129 KMDLEG 134
K+D G
Sbjct: 129 KIDKPG 134
>gnl|CDD|206684 cd01897, NOG, Nucleolar GTP-binding protein (NOG). NOG1 is a
nucleolar GTP-binding protein present in eukaryotes
ranging from trypanosomes to humans. NOG1 is
functionally linked to ribosome biogenesis and found in
association with the nuclear pore complexes and
identified in many preribosomal complexes. Thus, defects
in NOG1 can lead to defects in 60S biogenesis. The S.
cerevisiae NOG1 gene is essential for cell viability,
and mutations in the predicted G motifs abrogate
function. It is a member of the ODN family of
GTP-binding proteins that also includes the bacterial
Obg and DRG proteins.
Length = 167
Score = 35.6 bits (83), Expect = 0.008
Identities = 16/64 (25%), Positives = 29/64 (45%), Gaps = 5/64 (7%)
Query: 114 KNLTNPNTVIFLIGNKMDLEGSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETA 173
K L N ++ L NK+DL + E +K E+ ++ S +T E V++ A
Sbjct: 108 KPLFNKPVIVVL--NKIDL--LTEEDLSEIEKELEKEGEEVIKISTLTEEGVDEL-KNKA 162
Query: 174 KKIY 177
++
Sbjct: 163 CELL 166
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 36.2 bits (85), Expect = 0.010
Identities = 37/148 (25%), Positives = 54/148 (36%), Gaps = 43/148 (29%)
Query: 54 TR-IIEVH----GEKIKLQIWDTAG---------QERFRAVTRSYYRGAAGA---LMVYD 96
TR +IE H G I L++ DTAG + + RS A L+V D
Sbjct: 250 TRDVIEEHINLDG--IPLRLIDTAGIRETDDEVEKI---GIERSREA-IEEADLVLLVLD 303
Query: 97 ITRRSTYNHLSSWLTDTKNLTNPNTV-IFLIGNKMDLEGSRDVRYDEAKKFAEENDLIFV 155
+ T D + L + ++ NK DL G EEN +
Sbjct: 304 ASEPLTEE-------DDEILEELKDKPVIVVLNKADLTG--------EIDLEEENGKPVI 348
Query: 156 EASAMTGENVEQAFLETAKKIYQNIKDG 183
SA TGE +++ L + I + G
Sbjct: 349 RISAKTGEGIDE--LR--EAIKELAFGG 372
>gnl|CDD|235349 PRK05124, cysN, sulfate adenylyltransferase subunit 1; Provisional.
Length = 474
Score = 36.0 bits (84), Expect = 0.010
Identities = 36/122 (29%), Positives = 57/122 (46%), Gaps = 31/122 (25%)
Query: 62 EKIKLQIWDTAGQERFRAVTRSYYRGAAGA-----LM-----VYDITRRSTYNHLSSWLT 111
EK K I DT G E++ TR+ GA+ L+ V D TRR ++ +++ L
Sbjct: 105 EKRKFIIADTPGHEQY---TRNMATGASTCDLAILLIDARKGVLDQTRRHSF--IAT-LL 158
Query: 112 DTKNLTNPNTVIFLIGNKMDLEGSRDVRYDE--------AKKFAEENDLIFVEASAMTGE 163
K+L V+ + NKMDL + ++ A++ D+ FV SA+ G+
Sbjct: 159 GIKHL-----VVAV--NKMDLVDYSEEVFERIREDYLTFAEQLPGNLDIRFVPLSALEGD 211
Query: 164 NV 165
NV
Sbjct: 212 NV 213
>gnl|CDD|206721 cd04155, Arl3, Arf-like 3 (Arl3) GTPase. Arl3 (Arf-like 3) is an
Arf family protein that differs from most Arf family
members in the N-terminal extension. In is inactive,
GDP-bound form, the N-terminal extension forms an
elongated loop that is hydrophobically anchored into the
membrane surface; however, it has been proposed that
this region might form a helix in the GTP-bound form.
The delta subunit of the rod-specific cyclic GMP
phosphodiesterase type 6 (PDEdelta) is an Arl3 effector.
Arl3 binds microtubules in a regulated manner to alter
specific aspects of cytokinesis via interactions with
retinitis pigmentosa 2 (RP2). It has been proposed that
RP2 functions in concert with Arl3 to link the cell
membrane and the cytoskeleton in photoreceptors as part
of the cell signaling or vesicular transport machinery.
In mice, the absence of Arl3 is associated with abnormal
epithelial cell proliferation and cyst formation.
Length = 174
Score = 35.1 bits (81), Expect = 0.011
Identities = 35/149 (23%), Positives = 59/149 (39%), Gaps = 17/149 (11%)
Query: 27 GKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQERFRAVTRSYYR 86
GK+ +L Q + P G I V + KL +WD GQ + R R+Y+
Sbjct: 27 GKTTILKQLASEDISHITPTQ-----GFNIKNVQADGFKLNVWDIGGQRKIRPYWRNYFE 81
Query: 87 GAAGALMVYDITRRSTYNHLSSWLTDT---KNLTNPNTVIFLIGNKMDLEGSRDVRYDEA 143
+ V D R + L + + L ++F NK DL + +E
Sbjct: 82 NTDVLIYVIDSADRKRFEEAGQELVELLEEEKLAGVPVLVF--ANKQDLLTAAPA--EEV 137
Query: 144 KKFAEENDLI----FVEA-SAMTGENVEQ 167
+ +D+ ++A SA TGE +++
Sbjct: 138 AEALNLHDIRDRSWHIQACSAKTGEGLQE 166
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 35.5 bits (83), Expect = 0.017
Identities = 16/72 (22%), Positives = 32/72 (44%), Gaps = 5/72 (6%)
Query: 128 NKMDLEGSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKIYQNIKDGKLNA 187
NKMDL + + + +K + +F SA+TG+ +++ L ++ + + L
Sbjct: 282 NKMDLPEAEENLEEFKEKLGPK---VF-PISALTGQGLDE-LLYAVAELLEETPEFPLEE 336
Query: 188 NMTESGVQHKER 199
E V +K
Sbjct: 337 EEVEEEVYYKFE 348
>gnl|CDD|218203 pfam04670, Gtr1_RagA, Gtr1/RagA G protein conserved region. GTR1
was first identified in S. cerevisiae as a suppressor of
a mutation in RCC1. Biochemical analysis revealed that
Gtr1 is in fact a G protein of the Ras family. The
RagA/B proteins are the human homologues of Gtr1.
Included in this family is the human Rag C, a novel
protein that has been shown to interact with RagA/B.
Length = 230
Score = 34.9 bits (81), Expect = 0.017
Identities = 37/148 (25%), Positives = 63/148 (42%), Gaps = 19/148 (12%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMP-DCPH---TIGVEFGTRIIEVHGE-KIKLQIWDT 71
K +++G G GKS + + P D TI VE V + L +WD
Sbjct: 1 KVLLMGLRGSGKSSM-RSIIFSNYSPRDTLRLGATIDVE----QSHVRFLGNLTLNLWDC 55
Query: 72 AGQERFRAVTRSYYRGA----AGALM-VYDITRRSTYNHLSSWLTDTKNLT--NPNTVIF 124
GQ+ F + + G L+ V+D+ R L++ + + L +PN +F
Sbjct: 56 PGQDDFMENYLTRQKEHIFSNVGVLIYVFDVESREYEEDLATLVKIIEALYQYSPNAKVF 115
Query: 125 LIGNKMDL--EGSRDVRYDEAKKFAEEN 150
++ +KMDL E R +++ K+ E
Sbjct: 116 VLIHKMDLLSEDERKEIFEDRKEEIIEE 143
>gnl|CDD|180120 PRK05506, PRK05506, bifunctional sulfate adenylyltransferase
subunit 1/adenylylsulfate kinase protein; Provisional.
Length = 632
Score = 35.3 bits (82), Expect = 0.020
Identities = 34/121 (28%), Positives = 55/121 (45%), Gaps = 30/121 (24%)
Query: 62 EKIKLQIWDTAGQERFRAVTRSYYRGAAGA-LMVYDI---------TRRSTYNHLSSWLT 111
K K + DT G E++ TR+ GA+ A L + + TRR ++ ++S L
Sbjct: 102 PKRKFIVADTPGHEQY---TRNMVTGASTADLAIILVDARKGVLTQTRRHSF--IAS-LL 155
Query: 112 DTKNLTNPNTVIFLIGNKMDLEGSRDVRYDEAK----KFAEE---NDLIFVEASAMTGEN 164
++ + L NKMDL +DE FA + +D+ F+ SA+ G+N
Sbjct: 156 GIRH-------VVLAVNKMDLVDYDQEVFDEIVADYRAFAAKLGLHDVTFIPISALKGDN 208
Query: 165 V 165
V
Sbjct: 209 V 209
>gnl|CDD|213679 TIGR02034, CysN, sulfate adenylyltransferase, large subunit.
Metabolic assimilation of sulfur from inorganic sulfate,
requires sulfate activation by coupling to a nucleoside,
for the production of high-energy nucleoside
phosphosulfates. This pathway appears to be similar in
all prokaryotic organisms. Activation is first achieved
through sulfation of sulfate with ATP by sulfate
adenylyltransferase (ATP sulfurylase) to produce
5'-phosphosulfate (APS), coupled by GTP hydrolysis.
Subsequently, APS is phosphorylated by an APS kinase to
produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS). In
Escherichia coli, ATP sulfurylase is a heterodimer
composed of two subunits encoded by cysD and cysN, with
APS kinase encoded by cysC. These genes are located in a
unidirectionally transcribed gene cluster, and have been
shown to be required for the synthesis of
sulfur-containing amino acids. Homologous to this E.coli
activation pathway are nodPQH gene products found among
members of the Rhizobiaceae family. These gene products
have been shown to exhibit ATP sulfurase and APS kinase
activity, yet are involved in Nod factor sulfation, and
sulfation of other macromolecules. With members of the
Rhizobiaceae family, nodQ often appears as a fusion of
cysN (large subunit of ATP sulfurase) and cysC (APS
kinase) [Central intermediary metabolism, Sulfur
metabolism].
Length = 406
Score = 34.7 bits (80), Expect = 0.026
Identities = 38/126 (30%), Positives = 56/126 (44%), Gaps = 40/126 (31%)
Query: 62 EKIKLQIWDTAGQERFRAVTRSYYRGAAGALM----------VYDITRRSTYNHLSSWLT 111
+K K + DT G E++ TR+ GA+ A + V + TRR +Y ++S
Sbjct: 78 DKRKFIVADTPGHEQY---TRNMATGASTADLAVLLVDARKGVLEQTRRHSY--IAS--- 129
Query: 112 DTKNLTNPNTVIFLIGNKMDLEGSRDVRYDEA---------KKFAEE---NDLIFVEASA 159
L V+ + NKMDL V YDE FAE+ D+ F+ SA
Sbjct: 130 ----LLGIRHVVLAV-NKMDL-----VDYDEEVFENIKKDYLAFAEQLGFRDVTFIPLSA 179
Query: 160 MTGENV 165
+ G+NV
Sbjct: 180 LKGDNV 185
>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 = 34.0 bits (78), Expect = 0.026
Identities = 34/161 (21%), Positives = 67/161 (41%), Gaps = 11/161 (6%)
Query: 20 IIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQERFRA 79
I+G++ GKS L+H++ ++ G F ++ V G+ L I D G +
Sbjct: 5 IVGNLRSGKSALVHRYLTGSYVQL-ESPEGGRFKKEVL-VDGQSHLLLIRDEGGAPDAQ- 61
Query: 80 VTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTV-IFLIGNKMDLEGSRDV 138
+ + V+ + +++ + + N + + + L+G + + S
Sbjct: 62 ----FAGWVDAVIFVFSLEDEASFQTVYRLYHQLSSYRNISEIPLILVGTQDAISASNPR 117
Query: 139 RYDEAKKFAEENDL---IFVEASAMTGENVEQAFLETAKKI 176
D+A+ D+ + E A G NVE+ F E A+KI
Sbjct: 118 VIDDARARQLCADMKRCSYYETCATYGLNVERVFQEAAQKI 158
>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 = 33.2 bits (76), Expect = 0.043
Identities = 28/121 (23%), Positives = 48/121 (39%), Gaps = 24/121 (19%)
Query: 64 IKLQIWDTAGQERFRAVTRSYYRGAAGALMVYDITRR-----------STYNHLSSWLTD 112
+ +D +GQ ++R + YY+ G + V D + R NH D
Sbjct: 45 LSFTAFDMSGQGKYRGLWEHYYKNIQGIIFVIDSSDRLRMVVAKDELELLLNH-----PD 99
Query: 113 TKNLTNPNTVIFLIGNKMDLEGSRD----VRYDEAKKFAEENDLIFVEASAMTGENVEQA 168
K+ P I NKMDL + + + ++ IF +SA+TGE +++
Sbjct: 100 IKHRRIP---ILFYANKMDLPDALTAVKITQLLCLENIKDKPWHIFA-SSALTGEGLDEG 155
Query: 169 F 169
Sbjct: 156 V 156
>gnl|CDD|206685 cd01898, Obg, Obg GTPase. The Obg nucleotide binding protein
subfamily has been implicated in stress response,
chromosome partitioning, replication initiation,
mycelium development, and sporulation. Obg proteins are
among a large group of GTP binding proteins conserved
from bacteria to humans. The E. coli homolog, ObgE is
believed to function in ribosomal biogenesis. Members of
the subfamily contain two equally and highly conserved
domains, a C-terminal GTP binding domain and an
N-terminal glycine-rich domain.
Length = 170
Score = 33.2 bits (77), Expect = 0.050
Identities = 10/45 (22%), Positives = 20/45 (44%)
Query: 123 IFLIGNKMDLEGSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQ 167
++ NK+DL + + + E SA+TGE +++
Sbjct: 117 RIVVLNKIDLLDAEERFEKLKELLKELKGKKVFPISALTGEGLDE 161
>gnl|CDD|225448 COG2895, CysN, GTPases - Sulfate adenylate transferase subunit 1
[Inorganic ion transport and metabolism].
Length = 431
Score = 33.8 bits (78), Expect = 0.051
Identities = 33/121 (27%), Positives = 53/121 (43%), Gaps = 30/121 (24%)
Query: 62 EKIKLQIWDTAGQERFRAVTRSYYRGAAGALM----------VYDITRRSTYNHLSSWLT 111
EK K I DT G E++ TR+ GA+ A + V + TRR ++ ++S L
Sbjct: 84 EKRKFIIADTPGHEQY---TRNMATGASTADLAILLVDARKGVLEQTRRHSF--IASLLG 138
Query: 112 DTKNLTNPNTVIFLIGNKMDLEGSRDVRYDEAKK----FAEE---NDLIFVEASAMTGEN 164
+ + NKMDL + ++ FA + D+ F+ SA+ G+N
Sbjct: 139 IRH--------VVVAVNKMDLVDYSEEVFEAIVADYLAFAAQLGLKDVRFIPISALLGDN 190
Query: 165 V 165
V
Sbjct: 191 V 191
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 33.7 bits (78), Expect = 0.067
Identities = 37/144 (25%), Positives = 53/144 (36%), Gaps = 38/144 (26%)
Query: 70 DTAGQERFRAVTRSYYRGAAGALMVYDITR-------------RSTYNHLSSWLTDTKNL 116
DT G E F A R+ RGA+ V DI NH K
Sbjct: 61 DTPGHEAFTA-MRA--RGAS----VTDIAILVVAADDGVMPQTIEAINHA-------KAA 106
Query: 117 TNPNTVIFLIGNKMDLEGSR--DVRYDEAKK--FAEE--NDLIFVEASAMTGENVEQAFL 170
P V+ + NK+D + V+ + + EE D+IFV SA TGE +++ L
Sbjct: 107 GVP-IVVAI--NKIDKPEANPDKVKQELQEYGLVPEEWGGDVIFVPVSAKTGEGIDE--L 161
Query: 171 ETAKKIYQNIKDGKLNANMTESGV 194
+ + + K N G
Sbjct: 162 LELILLLAEVLELKANPEGPARGT 185
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 32.7 bits (76), Expect = 0.092
Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 11/59 (18%)
Query: 114 KNLTNPNTVIFLIGNKMDLEGSRDV------RYDEAKKFAEENDLIFVEASAMTGENVE 166
+ L T + L+ NK+DL ++ E FAE V SA+ G+NV+
Sbjct: 107 EKLKKVKTPVILVLNKIDLVKDKEELLPLLEELSELMDFAE-----IVPISALKGDNVD 160
>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 = 32.4 bits (75), Expect = 0.096
Identities = 42/165 (25%), Positives = 61/165 (36%), Gaps = 32/165 (19%)
Query: 20 IIGDMGVGKSCLLHQFTEQKF--MPDCPHTIGVEFGTR--IIEVHGEKIKLQI--WDTAG 73
IIG VGKS LL+ QK + P T TR I ++ + QI DT G
Sbjct: 8 IIGRPNVGKSTLLNALVGQKISIVSPKPQT------TRNRIRGIYTDD-DAQIIFVDTPG 60
Query: 74 --------QERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFL 125
ER S + L V D + ++ + L T + L
Sbjct: 61 IHKPKKKLGERMVKAAWSALKDVDLVLFVVDASEWIGEGDE--FILE--LLKKSKTPVIL 116
Query: 126 IGNKMDLEGSRDVRYDEAKKFAEENDLIFVEA----SAMTGENVE 166
+ NK+DL ++ D + +L SA+ GENV+
Sbjct: 117 VLNKIDLVKDKE---DLLPLLEKLKELHPFAEIFPISALKGENVD 158
>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 = 32.4 bits (74), Expect = 0.11
Identities = 28/123 (22%), Positives = 49/123 (39%), Gaps = 14/123 (11%)
Query: 19 IIIGDMGVGKSCLLHQFTEQKFMP-DCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQERF 77
+ +G GK+ L+ Q +P T+G ++ +K ++ I+D G F
Sbjct: 3 LTVGLDNAGKTTLVSAL--QGEIPKKVAPTVGFT----PTKLRLDKYEVCIFDLGGGANF 56
Query: 78 RAVTRSYYRGAAGALMVYD---ITR-RSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMDLE 133
R + +YY A G + V D R + L L + P I ++ NK D +
Sbjct: 57 RGIWVNYYAEAHGLVFVVDSSDDDRVQEVKEILRELLQHPRVSGKP---ILVLANKQDKK 113
Query: 134 GSR 136
+
Sbjct: 114 NAL 116
>gnl|CDD|206729 cd04166, CysN_ATPS, CysN, together with protein CysD, forms the ATP
sulfurylase (ATPS) complex. CysN_ATPS subfamily. CysN,
together with protein CysD, form the ATP sulfurylase
(ATPS) complex in some bacteria and lower eukaryotes.
ATPS catalyzes the production of ATP sulfurylase (APS)
and pyrophosphate (PPi) from ATP and sulfate. CysD,
which catalyzes ATP hydrolysis, is a member of the ATP
pyrophosphatase (ATP PPase) family. CysN hydrolysis of
GTP is required for CysD hydrolysis of ATP; however,
CysN hydrolysis of GTP is not dependent on CysD
hydrolysis of ATP. CysN is an example of lateral gene
transfer followed by acquisition of new function. In
many organisms, an ATPS exists which is not
GTP-dependent and shares no sequence or structural
similarity to CysN.
Length = 209
Score = 32.2 bits (74), Expect = 0.13
Identities = 36/121 (29%), Positives = 55/121 (45%), Gaps = 30/121 (24%)
Query: 62 EKIKLQIWDTAGQERFRAVTRSYYRGAAG---ALMVYDI-------TRRSTYNHLSSWLT 111
K K I DT G E++ TR+ GA+ A+++ D TRR +Y ++S
Sbjct: 76 PKRKFIIADTPGHEQY---TRNMVTGASTADLAILLVDARKGVLEQTRRHSY--IAS--- 127
Query: 112 DTKNLTNPNTVIFLIGNKMDLEGSRDVRYDEAKK----FAEE---NDLIFVEASAMTGEN 164
L V+ + NKMDL + ++E K FA D+ F+ SA+ G+N
Sbjct: 128 ----LLGIRHVVVAV-NKMDLVDYDEEVFEEIKADYLAFAASLGIEDITFIPISALEGDN 182
Query: 165 V 165
V
Sbjct: 183 V 183
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 32.0 bits (74), Expect = 0.18
Identities = 12/44 (27%), Positives = 19/44 (43%)
Query: 124 FLIGNKMDLEGSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQ 167
L+ NK+DL + R A SA+TGE +++
Sbjct: 275 ILVLNKIDLLDEEEEREKRAALELAALGGPVFLISAVTGEGLDE 318
>gnl|CDD|233986 TIGR02729, Obg_CgtA, Obg family GTPase CgtA. This model describes
a univeral, mostly one-gene-per-genome GTP-binding
protein that associates with ribosomal subunits and
appears to play a role in ribosomal RNA maturation. This
GTPase, related to the nucleolar protein Obg, is
designated CgtA in bacteria. Mutations in this gene are
pleiotropic, but it appears that effects on cellular
functions such as chromosome partition may be secondary
to the effect on ribosome structure. Recent work done in
Vibrio cholerae shows an essential role in the stringent
response, in which RelA-dependent ability to synthesize
the alarmone ppGpp is required for deletion of this
GTPase to be lethal [Protein synthesis, Other].
Length = 329
Score = 32.0 bits (74), Expect = 0.22
Identities = 11/45 (24%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 123 IFLIGNKMDLEGSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQ 167
++ NK+DL ++ + K+ E SA+TGE +++
Sbjct: 276 RIVVLNKIDLLDEEELE-ELLKELKEALGKPVFPISALTGEGLDE 319
>gnl|CDD|197556 smart00178, SAR, Sar1p-like members of the Ras-family of small
GTPases. Yeast SAR1 is an essential gene required for
transport of secretory proteins from the endoplasmic
reticulum to the Golgi apparatus.
Length = 184
Score = 31.1 bits (70), Expect = 0.27
Identities = 28/122 (22%), Positives = 45/122 (36%), Gaps = 10/122 (8%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKFMPDCP--HTIGVEFGTRIIEVHGEKIKLQIWDTAGQ 74
K + +G GK+ LLH + P H E IK +D G
Sbjct: 19 KILFLGLDNAGKTTLLHMLKNDRLAQHQPTQHPTSEELAI-------GNIKFTTFDLGGH 71
Query: 75 ERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLI-GNKMDLE 133
++ R + + Y+ G + + D + + L + TV FLI GNK+D
Sbjct: 72 QQARRLWKDYFPEVNGIVYLVDAYDKERFAESKRELDALLSDEELATVPFLILGNKIDAP 131
Query: 134 GS 135
+
Sbjct: 132 YA 133
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 31.4 bits (72), Expect = 0.34
Identities = 16/72 (22%), Positives = 28/72 (38%), Gaps = 2/72 (2%)
Query: 125 LIGNKMDLEGSRDVRYDEAKKFAEENDLIFVEA-SAMTGENVEQAFLETAKKIYQNIKDG 183
++ NK+DL + + K AE SA+T E ++ L ++ + K
Sbjct: 280 VVLNKIDLPLDEEELEELKKALAEALGWEVFYLISALTREGLD-ELLRALAELLEETKAE 338
Query: 184 KLNANMTESGVQ 195
A E V+
Sbjct: 339 AEAAEAEELPVE 350
>gnl|CDD|206691 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta), together with SR-alpha, forms the
heterodimeric signal recognition particle (SRP). Signal
recognition particle receptor, beta subunit (SR-beta).
SR-beta and SR-alpha form the heterodimeric signal
recognition particle (SRP or SR) receptor that binds SRP
to regulate protein translocation across the ER
membrane. Nascent polypeptide chains are synthesized
with an N-terminal hydrophobic signal sequence that
binds SRP54, a component of the SRP. SRP directs
targeting of the ribosome-nascent chain complex (RNC) to
the ER membrane via interaction with the SR, which is
localized to the ER membrane. The RNC is then
transferred to the protein-conducting channel, or
translocon, which facilitates polypeptide translation
across the ER membrane or integration into the ER
membrane. SR-beta is found only in eukaryotes; it is
believed to control the release of the signal sequence
from SRP54 upon binding of the ribosome to the
translocon. High expression of SR-beta has been observed
in human colon cancer, suggesting it may play a role in
the development of this type of cancer.
Length = 202
Score = 30.8 bits (70), Expect = 0.39
Identities = 26/121 (21%), Positives = 44/121 (36%), Gaps = 11/121 (9%)
Query: 19 IIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQERFR 78
+++G GK+ L + T K T + KL + D G E+ R
Sbjct: 4 LLLGPSDSGKTALFTKLTTGKVRST--VTSIEPNVASFYSNSSKGKKLTLVDVPGHEKLR 61
Query: 79 AVTRSYYRGAAGALMVY-----DITR--RSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMD 131
Y + + A+ V+ + R L LTD + + N ++ + NK D
Sbjct: 62 DKLLEYLKASLKAI-VFVVDSATFQKNIRDVAEFLYDILTDLEKIKNKIPIL-IACNKQD 119
Query: 132 L 132
L
Sbjct: 120 L 120
>gnl|CDD|232980 TIGR00450, mnmE_trmE_thdF, tRNA modification GTPase TrmE. TrmE,
also called MnmE and previously designated ThdF
(thiophene and furan oxidation protein), is a GTPase
involved in tRNA modification to create
5-methylaminomethyl-2-thiouridine in the wobble position
of some tRNAs. This protein and GidA form an
alpha2/beta2 heterotetramer [Protein synthesis, tRNA and
rRNA base modification].
Length = 442
Score = 30.9 bits (70), Expect = 0.43
Identities = 21/65 (32%), Positives = 31/65 (47%), Gaps = 15/65 (23%)
Query: 16 FKYIIIGDMGVGKSCLLHQF--TEQKFMPDCPHTIGVEFGTR-----IIEVHGEKIKLQI 68
FK I+G VGKS LL+ ++ + D T TR E++G I +++
Sbjct: 204 FKLAIVGSPNVGKSSLLNALLKQDRAIVSDIKGT------TRDVVEGDFELNG--ILIKL 255
Query: 69 WDTAG 73
DTAG
Sbjct: 256 LDTAG 260
>gnl|CDD|206674 cd01887, IF2_eIF5B, Initiation Factor 2 (IF2)/ eukaryotic
Initiation Factor 5B (eIF5B) family. IF2/eIF5B
contribute to ribosomal subunit joining and function as
GTPases that are maximally activated by the presence of
both ribosomal subunits. As seen in other GTPases,
IF2/IF5B undergoes conformational changes between its
GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess
three characteristic segments, including a divergent
N-terminal region followed by conserved central and
C-terminal segments. This core region is conserved among
all known eukaryotic and archaeal IF2/eIF5Bs and
eubacterial IF2s.
Length = 169
Score = 30.1 bits (69), Expect = 0.54
Identities = 28/114 (24%), Positives = 43/114 (37%), Gaps = 31/114 (27%)
Query: 70 DTAGQERFRAVTRSYYRGAAG---ALMVYDITR------RSTYNHLSSWLTDTKNLTNPN 120
DT G E F R+ RGA+ A++V NH K P
Sbjct: 55 DTPGHEAFTN-MRA--RGASVTDIAILVVAADDGVMPQTIEAINHA-------KAANVP- 103
Query: 121 TVIFLIGNKMDLEGSRD-----VRYDEAKK--FAEEN--DLIFVEASAMTGENV 165
++ + NK+D + V+ + ++ EE D+ V SA TGE +
Sbjct: 104 IIVAI--NKIDKPYGTEADPERVKNELSELGLVGEEWGGDVSIVPISAKTGEGI 155
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the
AAA superfamily.
Length = 154
Score = 29.9 bits (67), Expect = 0.65
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 19 IIIGDMGVGKSCLLHQFTEQ 38
++ G G GK+ LL + E
Sbjct: 28 LLTGPSGTGKTSLLRELLEG 47
>gnl|CDD|206670 cd01883, EF1_alpha, Elongation Factor 1-alpha (EF1-alpha) protein
family. EF1 is responsible for the GTP-dependent
binding of aminoacyl-tRNAs to the ribosomes. EF1 is
composed of four subunits: the alpha chain which binds
GTP and aminoacyl-tRNAs, the gamma chain that probably
plays a role in anchoring the complex to other cellular
components and the beta and delta (or beta') chains.
This subfamily is the alpha subunit, and represents the
counterpart of bacterial EF-Tu for the archaea
(aEF1-alpha) and eukaryotes (eEF1-alpha). eEF1-alpha
interacts with the actin of the eukaryotic cytoskeleton
and may thereby play a role in cellular transformation
and apoptosis. EF-Tu can have no such role in bacteria.
In humans, the isoform eEF1A2 is overexpressed in 2/3 of
breast cancers and has been identified as a putative
oncogene. This subfamily also includes Hbs1, a G protein
known to be important for efficient growth and protein
synthesis under conditions of limiting translation
initiation in yeast, and to associate with Dom34. It has
been speculated that yeast Hbs1 and Dom34 proteins may
function as part of a complex with a role in gene
expression.
Length = 219
Score = 30.2 bits (69), Expect = 0.67
Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 13/50 (26%)
Query: 128 NKMDLEG---SRDVRYDEAKK---------FAEENDLIFVEASAMTGENV 165
NKMD S++ RYDE KK D+ F+ S TG+N+
Sbjct: 145 NKMDDVTVNWSQE-RYDEIKKKVSPFLKKVGYNPKDVPFIPISGFTGDNL 193
>gnl|CDD|204242 pfam09439, SRPRB, Signal recognition particle receptor beta
subunit. The beta subunit of the signal recognition
particle receptor (SRP) is a transmembrane GTPase which
anchors the alpha subunit to the endoplasmic reticulum
membrane.
Length = 181
Score = 29.7 bits (67), Expect = 0.77
Identities = 28/127 (22%), Positives = 39/127 (30%), Gaps = 14/127 (11%)
Query: 19 IIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAGQERFR 78
II G GK+ L T + + + G L D G + R
Sbjct: 7 IIAGLCDSGKTSLFTLLTTGTVKKTVT-SQEPSAAYKYMLHKGFSFTLI--DFPGHVKLR 63
Query: 79 A---VTRSYYRGAAGALMVYDITR-----RSTYNHLSSWLTDTKNLTNPNTVIFLIG-NK 129
T G + V D T T L L+ T+ L N + LI NK
Sbjct: 64 QKLLETIKDSSSLRGIVFVVDSTAFPKEVTDTAEFLYEILSITELL--KNGIDILIACNK 121
Query: 130 MDLEGSR 136
+ +R
Sbjct: 122 QESFTAR 128
>gnl|CDD|130460 TIGR01393, lepA, GTP-binding protein LepA. LepA (GUF1 in
Saccaromyces) is a GTP-binding membrane protein related
to EF-G and EF-Tu. Two types of phylogenetic tree,
rooted by other GTP-binding proteins, suggest that
eukaryotic homologs (including GUF1 of yeast) originated
within the bacterial LepA family. The function is
unknown [Unknown function, General].
Length = 595
Score = 30.4 bits (69), Expect = 0.78
Identities = 37/125 (29%), Positives = 55/125 (44%), Gaps = 19/125 (15%)
Query: 60 HGEKIKLQIWDTAGQERFR-AVTRSYYRGAA--GALMVYDITRRSTYNHLSS-WLTDTKN 115
GE L + DT G F V+RS AA GAL++ D + L++ +L +
Sbjct: 66 DGETYVLNLIDTPGHVDFSYEVSRSL---AACEGALLLVDAAQGIEAQTLANVYLALEND 122
Query: 116 LTNPNTVIFLIGNKMDLEGSRDVRYDEAKKFAEE----NDLIFVEASAMTGENVEQAFLE 171
L I + NK+DL S D + KK EE + + ASA TG +E+
Sbjct: 123 LE-----IIPVINKIDLP-SADP--ERVKKEIEEVIGLDASEAILASAKTGIGIEEILEA 174
Query: 172 TAKKI 176
K++
Sbjct: 175 IVKRV 179
>gnl|CDD|234389 TIGR03903, TOMM_kin_cyc, TOMM system kinase/cyclase fusion protein.
This model represents proteins of 1350 in length, in
multiple species of Burkholderia, in Acidovorax avenae
subsp. citrulli AAC00-1 and Delftia acidovorans SPH-1,
and in multiple copies in Sorangium cellulosum, in
genomic neighborhoods that include a
cyclodehydratase/docking scaffold fusion protein
(TIGR03882) and a member of the thiazole/oxazole
modified metabolite (TOMM) precursor family TIGR03795.
It has a kinase domain in the N-terminal 300 amino
acids, followed by a cyclase homology domain, followed
by regions without named domain definitions. It is a
probable bacteriocin-like metabolite biosynthesis
protein [Cellular processes, Toxin production and
resistance].
Length = 1266
Score = 30.2 bits (68), Expect = 1.0
Identities = 8/20 (40%), Positives = 16/20 (80%)
Query: 19 IIIGDMGVGKSCLLHQFTEQ 38
+++G+ G+GKS L+H+ E+
Sbjct: 508 LVVGEAGIGKSRLVHELVEK 527
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 29.6 bits (67), Expect = 1.3
Identities = 13/55 (23%), Positives = 22/55 (40%), Gaps = 10/55 (18%)
Query: 120 NTVIFLIGNKMDLEGSRDVRYDEAKKFAE---------ENDLIFVEASAMTGENV 165
+I + NKMDL + R++E D+ F+ S G+N+
Sbjct: 146 KQLIVAV-NKMDLVSWDEERFEEIVSEVSKLLKMVGYNPKDVPFIPISGFKGDNL 199
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 29.5 bits (67), Expect = 1.4
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 9/47 (19%)
Query: 128 NKMDLEGSRDVRYDEAKKFAEE---------NDLIFVEASAMTGENV 165
NKMD + RY+E K+ + +D+ F+ SA G+NV
Sbjct: 147 NKMDAVNYDEKRYEEVKEEVSKLLKMVGYKPDDIPFIPVSAFEGDNV 193
>gnl|CDD|188695 cd08741, RGS_RGS10, Regulator of G protein signaling (RGS) domain
found in the RGS10 protein. RGS (Regulator of G-protein
Signaling) domain is an essential part of the RGS10
protein. RGS10 is a member of the RA/RGS subfamily of
RGS proteins family, a diverse group of multifunctional
proteins that regulate cellular signaling events
downstream of G-protein coupled receptors (GPCRs). As a
major G-protein regulator, RGS domain containing
proteins are involved in many crucial cellular processes
such as regulation of intracellular trafficking, glial
differentiation, embryonic axis formation, skeletal and
muscle development, and cell migration during early
embryogenesis. RGS10 belong to the R12 RGS subfamily,
which includes RGS12 and RGS14, all of which are highly
selective for G-alpha-i1 over G-alpha-q. RGS10 exists in
2 splice isoforms. RGS10A is specifically expressed in
osteoclasts and is a key component in the RANKL
signaling mechanism for osteoclast differentiation,
whereas RGS10B expressed in brain and in immune tissues
and has been implicated in diverse processes including:
promoting of dopaminergic neuron survival via
regulation of the microglial inflammatory response,
modulation of presynaptic and postsynaptic G-protein
signalling, as well as a possible role in regulation of
gene expression.
Length = 113
Score = 28.1 bits (62), Expect = 1.7
Identities = 17/63 (26%), Positives = 27/63 (42%)
Query: 131 DLEGSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKIYQNIKDGKLNANMT 190
D EG + R K+F+EEN L ++ + E AK+IY K ++ +
Sbjct: 7 DPEGVKRFREFLKKEFSEENVLFWLACEDFKKMQDKTQMQEKAKEIYMTFLSSKASSQVN 66
Query: 191 ESG 193
G
Sbjct: 67 VEG 69
>gnl|CDD|237451 PRK13631, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 320
Score = 28.7 bits (64), Expect = 2.1
Identities = 13/28 (46%), Positives = 16/28 (57%), Gaps = 4/28 (14%)
Query: 12 YSYIFK----YIIIGDMGVGKSCLLHQF 35
SY F+ Y IIG+ G GKS L+ F
Sbjct: 45 ISYTFEKNKIYFIIGNSGSGKSTLVTHF 72
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 28.7 bits (65), Expect = 2.3
Identities = 15/56 (26%), Positives = 24/56 (42%), Gaps = 5/56 (8%)
Query: 115 NLTNPNTVIFLIGNKMDLEGSRDVRYDEAKKFAEENDLIF---VEASAMTGENVEQ 167
L T + L+ NK+D + F ++ L F V SA+ G+NV+
Sbjct: 109 QLKKTKTPVILVVNKIDKV-KPKTVLLKLIAFLKK-LLPFKEIVPISALKGDNVDT 162
>gnl|CDD|206677 cd01890, LepA, LepA also known as Elongation Factor 4 (EF4). LepA
(also known as elongation factor 4, EF4) belongs to the
GTPase family and exhibits significant homology to the
translation factors EF-G and EF-Tu, indicating its
possible involvement in translation and association with
the ribosome. LepA is ubiquitous in bacteria and
eukaryota (e.g. yeast GUF1p), but is missing from
archaea. This pattern of phyletic distribution suggests
that LepA evolved through a duplication of the EF-G gene
in bacteria, followed by early transfer into the
eukaryotic lineage, most likely from the
promitochondrial endosymbiont. Yeast GUF1p is not
essential and mutant cells did not reveal any marked
phenotype.
Length = 179
Score = 28.3 bits (64), Expect = 2.4
Identities = 40/120 (33%), Positives = 55/120 (45%), Gaps = 27/120 (22%)
Query: 60 HGEKIKLQIWDTAGQERFR-AVTRSYYRGAA--GALMVYDITR---RSTYNHLSSWLTDT 113
GE+ L + DT G F V+RS AA GAL+V D T+ T + +L
Sbjct: 63 DGEEYLLNLIDTPGHVDFSYEVSRSL---AACEGALLVVDATQGVEAQTLANF--YLALE 117
Query: 114 KNLTNPNTVIFLIGNKMDLEGSRDVRYDEAKKFAEE------NDLIFVEASAMTGENVEQ 167
NL +I +I NK+DL + D D K+ E+ ++ I V SA TG VE
Sbjct: 118 NNLE----IIPVI-NKIDLPAA-DP--DRVKQEIEDVLGLDASEAILV--SAKTGLGVED 167
>gnl|CDD|129794 TIGR00711, efflux_EmrB, drug resistance transporter, EmrB/QacA
subfamily. This subfamily of drug efflux proteins, a
part of the major faciliator family, is predicted to
have 14 potential membrane-spanning regions. Members
with known activities include EmrB (multiple drug
resistance efflux pump) in E. coli, FarB (antibacterial
fatty acid resistance) in Neisseria gonorrhoeae, TcmA
(tetracenomycin C resistance) in Streptomyces
glaucescens, etc. In most cases, the efflux pump is
described as having a second component encoded in the
same operon, such as EmrA of E. coli [Cellular
processes, Toxin production and resistance, Transport
and binding proteins, Other].
Length = 485
Score = 28.5 bits (64), Expect = 2.7
Identities = 15/35 (42%), Positives = 22/35 (62%), Gaps = 3/35 (8%)
Query: 87 GAAG-ALMVYDITRRSTYNHLSSWLTDTKNLTNPN 120
G+ G AL+ +T R+ ++H S LT+T N NPN
Sbjct: 397 GSIGTALITTILTNRTQFHH--SQLTETINPVNPN 429
>gnl|CDD|213188 cd03221, ABCF_EF-3, ATP-binding cassette domain of elongation
factor 3, subfamily F. Elongation factor 3 (EF-3) is a
cytosolic protein required by fungal ribosomes for in
vitro protein synthesis and for in vivo growth. EF-3
stimulates the binding of the EF-1: GTP: aa-tRNA
ternary complex to the ribosomal A site by facilitated
release of the deacylated tRNA from the E site. The
reaction requires ATP hydrolysis. EF-3 contains two ATP
nucleotide binding sequence (NBS) motifs. NBSI is
sufficient for the intrinsic ATPase activity. NBSII is
essential for the ribosome-stimulated functions.
Length = 144
Score = 27.8 bits (63), Expect = 3.1
Identities = 7/17 (41%), Positives = 10/17 (58%)
Query: 17 KYIIIGDMGVGKSCLLH 33
+ ++G G GKS LL
Sbjct: 28 RIGLVGRNGAGKSTLLK 44
>gnl|CDD|129528 TIGR00436, era, GTP-binding protein Era. Era is an essential
GTPase in Escherichia coli and many other bacteria. It
plays a role in ribosome biogenesis. Few bacteria lack
this protein [Protein synthesis, Other].
Length = 270
Score = 28.1 bits (63), Expect = 3.3
Identities = 41/172 (23%), Positives = 64/172 (37%), Gaps = 18/172 (10%)
Query: 20 IIGDMGVGKSCLLHQFTEQK--FMPDCPHTIGVEFGTRIIEVHGEKIKLQIWDTAG-QER 76
I+G VGKS LL+Q QK T + I + DT G E+
Sbjct: 5 ILGRPNVGKSTLLNQLHGQKISITSPKAQTTRNRISGIHTTGASQIIFI---DTPGFHEK 61
Query: 77 FRAVTRSYYRGAAGA-----LMVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMD 131
++ R + A A L+++ + LT +NL P + L NK+D
Sbjct: 62 KHSLNRLMMKEARSAIGGVDLILFVVDSDQWNGDGEFVLTKLQNLKRP---VVLTRNKLD 118
Query: 132 LEGSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKIYQNIKDG 183
+ + K E+ V SA+TG+N A I ++ +G
Sbjct: 119 NKFKDKLLPLIDKYAILEDFKDIVPISALTGDNTS----FLAAFIEVHLPEG 166
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 27.2 bits (61), Expect = 3.3
Identities = 9/33 (27%), Positives = 15/33 (45%), Gaps = 3/33 (9%)
Query: 19 IIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVE 51
++ G+ G GK+ LL + Q + VE
Sbjct: 8 VLTGESGSGKTTLLRRLARQL---PNRRVVYVE 37
>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 = 27.6 bits (62), Expect = 3.9
Identities = 22/85 (25%), Positives = 33/85 (38%), Gaps = 15/85 (17%)
Query: 108 SWLTDTKNLTNPNTVIFLIGNKMDL--EGSRDVRYDE------AKKFAEENDLIFVEASA 159
S + L VI L+GNK+DL + + R + + D+I V SA
Sbjct: 49 SLIPGLAELIGAKPVI-LVGNKIDLLPKDVKPNRLKQWVKKRLKIGGLKIKDVILV--SA 105
Query: 160 MTGENVEQAFLETAKKIYQNIKDGK 184
G VE E ++I + K
Sbjct: 106 KKGWGVE----ELIEEIKKLAKYRG 126
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 28.0 bits (63), Expect = 4.1
Identities = 15/67 (22%), Positives = 25/67 (37%), Gaps = 5/67 (7%)
Query: 128 NKMDLEGSRDVRYDEAKKFAEENDLIFVEASAMTGENVEQAFLETAKKIYQNIKDGKLNA 187
NK+DL + +E E V SA TGE ++ + + + L
Sbjct: 312 NKIDL-----LEDEEILAELERGSPNPVFISAKTGEGLDLLRERIIELLSGLRTEVTLEL 366
Query: 188 NMTESGV 194
T++G
Sbjct: 367 PYTDAGR 373
>gnl|CDD|215243 PLN02444, PLN02444, HMP-P synthase.
Length = 642
Score = 28.0 bits (62), Expect = 4.8
Identities = 20/74 (27%), Positives = 30/74 (40%), Gaps = 16/74 (21%)
Query: 141 DEAKKFAEENDLIFVEASAMTG-ENVEQAFLETAKKIYQNIKDGKLNANMTESGVQHKER 199
++ +K+AEE+ E + G + + FL K I SG QH E
Sbjct: 582 EDVRKYAEEHGYGSAEEAVKQGMDAMSAEFLAAKKTI---------------SGEQHGES 626
Query: 200 GGPASLGDSSSSDK 213
GG L +S + K
Sbjct: 627 GGEIYLPESYVASK 640
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 27.5 bits (62), Expect = 5.7
Identities = 17/47 (36%), Positives = 26/47 (55%), Gaps = 8/47 (17%)
Query: 128 NKMDLEGS---RDVRYDEAKK--FAEE--NDLIFVEASAMTGENVEQ 167
NK+D G+ R V+ + ++ EE D IFV SA TGE +++
Sbjct: 356 NKIDKPGANPDR-VKQELSEYGLVPEEWGGDTIFVPVSAKTGEGIDE 401
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a
wide variety of presumed phage proteins.
Length = 201
Score = 27.3 bits (61), Expect = 6.0
Identities = 13/55 (23%), Positives = 25/55 (45%), Gaps = 6/55 (10%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEVHGEKIKLQIWD 70
K +I G G+GK+ L K +P + ++ GT + G+ + ++ W
Sbjct: 4 IKVLIYGPPGIGKTSLA------KTLPPKTLFLDLDAGTTKVLSRGDNVDIRSWQ 52
>gnl|CDD|224193 COG1274, PckA, Phosphoenolpyruvate carboxykinase (GTP) [Energy
production and conversion].
Length = 608
Score = 27.7 bits (62), Expect = 6.1
Identities = 13/60 (21%), Positives = 20/60 (33%), Gaps = 2/60 (3%)
Query: 93 MVYDITRRSTYNHLSSWLTDTKNLTNPNTVIFLIGNKMDLEGSRD--VRYDEAKKFAEEN 150
D L SW+ + LT P+ V+ G+ + + V E K E
Sbjct: 7 DGLDKLAPINNQGLKSWIEEVAELTEPDDVVVCDGSPEEYDYLCWKMVEAGEEIKLNPEK 66
>gnl|CDD|130679 TIGR01618, phage_P_loop, phage nucleotide-binding protein. This
model represents an uncharacterized family of proteins
from a number of phage of Gram-positive bacteria. This
protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near
its amino end. The function of this protein is unknown
[Mobile and extrachromosomal element functions,
Prophage functions].
Length = 220
Score = 27.1 bits (60), Expect = 6.6
Identities = 8/44 (18%), Positives = 17/44 (38%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPDCPHTIGVEFGTRIIEV 59
Y+I G G GK+ + + + + V G +++
Sbjct: 13 NMYLIYGKPGTGKTSTIKYLPGKTLVLSFDMSSKVLIGDENVDI 56
>gnl|CDD|180061 PRK05412, PRK05412, putative nucleotide-binding protein; Reviewed.
Length = 161
Score = 26.6 bits (60), Expect = 7.3
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 171 ETAKKIYQNIKDGKL 185
E AKKI + IKD KL
Sbjct: 103 ELAKKIVKLIKDSKL 117
>gnl|CDD|223886 COG0816, COG0816, Predicted endonuclease involved in recombination
(possible Holliday junction resolvase in Mycoplasmas and
B. subtilis) [DNA replication, recombination, and
repair].
Length = 141
Score = 26.4 bits (59), Expect = 7.5
Identities = 10/32 (31%), Positives = 20/32 (62%), Gaps = 2/32 (6%)
Query: 118 NPNTVIFLIGNKMDLEGSRDVRYDEAKKFAEE 149
+TV+ +G ++++G+ R + A+KFAE
Sbjct: 53 QVDTVV--VGLPLNMDGTEGPRAELARKFAER 82
>gnl|CDD|201420 pfam00735, Septin, Septin. Members of this family include CDC3,
CDC10, CDC11 and CDC12/Septin. Members of this family
bind GTP. As regards the septins, these are
polypeptides of 30-65kDa with three characteristic
GTPase motifs (G-1, G-3 and G-4) that are similar to
those of the Ras family. The G-4 motif is strictly
conserved with a unique septin consensus of AKAD. Most
septins are thought to have at least one coiled-coil
region, which in some cases is necessary for
intermolecular interactions that allow septins to
polymerise to form rod-shaped complexes. In turn, these
are arranged into tandem arrays to form filaments. They
are multifunctional proteins, with roles in
cytokinesis, sporulation, germ cell development,
exocytosis and apoptosis.
Length = 280
Score = 26.9 bits (60), Expect = 7.8
Identities = 17/67 (25%), Positives = 32/67 (47%), Gaps = 9/67 (13%)
Query: 16 FKYIIIGDMGVGKSCLLHQFTEQKFMPD---------CPHTIGVEFGTRIIEVHGEKIKL 66
F +++G+ G+GK+ L++ +P+ T+ ++ T IE G K+ L
Sbjct: 5 FTLMVVGESGLGKTTLINTLFLTDLIPERGIPGPSEKIKKTVEIKATTVEIEEDGVKLNL 64
Query: 67 QIWDTAG 73
+ DT G
Sbjct: 65 TVIDTPG 71
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 26.8 bits (60), Expect = 7.8
Identities = 11/49 (22%), Positives = 18/49 (36%), Gaps = 10/49 (20%)
Query: 17 KYIIIGDMGVGKSCLLHQFTEQKF--MPDCPHTIGVEFGTRIIEVHGEK 63
+ +I G GK+ LL + + +P E+G IE
Sbjct: 1 RIVITGGPSTGKTTLLEALAARGYPVVP--------EYGREYIEEQLAD 41
>gnl|CDD|215436 PLN02815, PLN02815, L-aspartate oxidase.
Length = 594
Score = 27.4 bits (61), Expect = 8.1
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 155 VEASAMTGENVEQAFLETAK 174
V A+ MTG +E+A LE K
Sbjct: 147 VHAADMTGREIERALLEAVK 166
>gnl|CDD|216197 pfam00926, DHBP_synthase, 3,4-dihydroxy-2-butanone 4-phosphate
synthase. 3,4-Dihydroxy-2-butanone 4-phosphate is
biosynthesised from ribulose 5-phosphate and serves as
the biosynthetic precursor for the xylene ring of
riboflavin. Sometimes found as a bifunctional enzyme
with pfam00925.
Length = 193
Score = 26.7 bits (60), Expect = 8.2
Identities = 5/18 (27%), Positives = 11/18 (61%)
Query: 139 RYDEAKKFAEENDLIFVE 156
R + ++FA+E+ L +
Sbjct: 168 RLPDLEEFAKEHGLPLIT 185
>gnl|CDD|240125 cd04821, PA_M28_1_2, PA_M28_1_2: Protease-associated (PA) domain,
peptidase family M28, subfamily-1, subgroup 2. A
subgroup of PA-domain containing proteins belonging to
the peptidase family M28. Family M28 contains
aminopeptidases and carboxypeptidases, and has
co-catalytic zinc ions. The PA domain is an insert
domain in a diverse fraction of proteases. The
significance of the PA domain to many of the proteins in
which it is inserted is undetermined. It may be a
protein-protein interaction domain. At peptidase active
sites, the PA domain may participate in substrate
binding and/or promoting conformational changes, which
influence the stability and accessibility of the site to
substrate. Proteins into which the PA domain is inserted
include the following members of the peptidase family
M28: i) prostate-specific membrane antigen (PSMA), ii)
yeast aminopeptidase Y, and ii) human TfR (transferrin
receptor)1 and human TfR2. The proteins listed above
belong to other subgroups; relatively little is known
about proteins in this subgroup.
Length = 157
Score = 26.5 bits (59), Expect = 8.2
Identities = 11/40 (27%), Positives = 17/40 (42%), Gaps = 12/40 (30%)
Query: 69 WDTAGQERFRAVTRSYY------------RGAAGALMVYD 96
+ T F +YY +GAAGAL+V++
Sbjct: 62 FATPDSGLFNGKAMTYYGRWTYKYEEAARQGAAGALIVHE 101
>gnl|CDD|206744 cd11384, RagA_like, Rag GTPase, subfamily of Ras-related GTPases,
includes Ras-related GTP-binding proteins A and B. RagA
and RagB are closely related Rag GTPases (ras-related
GTP-binding protein A and B) that constitute a unique
subgroup of the Ras superfamily, and are functional
homologs of Saccharomyces cerevisiae Gtr1. These domains
function by forming heterodimers with RagC or RagD, and
similarly, Gtr1 dimerizes with Gtr2, through the
carboxy-terminal segments. They play an essential role
in regulating amino acid-induced target of rapamycin
complex 1 (TORC1) kinase signaling, exocytic cargo
sorting at endosomes, and epigenetic control of gene
expression. In response to amino acids, the Rag GTPases
guide the TORC1 complex to activate the platform
containing Rheb proto-oncogene by driving the
relocalization of mTORC1 from discrete locations in the
cytoplasm to a late endosomal and/or lysosomal
compartment that is Rheb-enriched and contains Rab-7.
Length = 286
Score = 26.8 bits (60), Expect = 9.1
Identities = 23/106 (21%), Positives = 47/106 (44%), Gaps = 19/106 (17%)
Query: 65 KLQIWDTAGQERFRAVTRSY--------YRGAAGALMVYDITRRSTYNHLSSWLTDTKNL 116
L +WD GQ+ F +Y +R + V+D+ R L+ + + + L
Sbjct: 49 VLNLWDCGGQDAFME---NYFTSQRDHIFRNVEVLIYVFDVESRELEKDLTYFRSCLEAL 105
Query: 117 T--NPNTVIFLIGNKMDL--EGSRD----VRYDEAKKFAEENDLIF 154
+P+ +F++ +KMDL E R+ + E ++ +E ++
Sbjct: 106 RQNSPDAKVFVLIHKMDLVQEDEREAVFERKEKELRRLSEPLEVTC 151
>gnl|CDD|180800 PRK07030, PRK07030, adenosylmethionine--8-amino-7-oxononanoate
transaminase; Provisional.
Length = 466
Score = 27.0 bits (60), Expect = 9.4
Identities = 22/72 (30%), Positives = 32/72 (44%), Gaps = 8/72 (11%)
Query: 53 GTRIIEVHGEKIKLQIWDTAGQE---RFRAVTRSYYRGAAGALMVYDITR-RSTYNHLSS 108
G+ IEV K+ W G+ RF +T SY+ A+ V D+ TY L
Sbjct: 116 GSSAIEV-ALKMSFHYWRNRGKPRKKRFVTLTNSYHGETLAAMSVGDVALFTETYKPL-- 172
Query: 109 WLTDTKNLTNPN 120
L DT + +P+
Sbjct: 173 -LLDTIKVPSPD 183
>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 = 26.4 bits (59), Expect = 9.7
Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 20 IIGDMGVGKSCLLHQFTEQKFMPDC-PHTIGVEFGTRIIEVHGEK 63
++G G GKS LL F + F + TI + +EV G++
Sbjct: 9 VLGAKGSGKSALLQAFLGRSFSQNAYSPTIKPRYAVNTVEVPGQE 53
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 0.132 0.386
Gapped
Lambda K H
0.267 0.0585 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,779,450
Number of extensions: 989806
Number of successful extensions: 1542
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1380
Number of HSP's successfully gapped: 186
Length of query: 218
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 125
Effective length of database: 6,812,680
Effective search space: 851585000
Effective search space used: 851585000
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 (26.1 bits)