RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15625
(223 letters)
>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 = 338 bits (870), Expect = e-120
Identities = 141/213 (66%), Positives = 151/213 (70%), Gaps = 51/213 (23%)
Query: 9 DYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTA 68
DYLFK+VLIGDSGVGKSNLLSRFTRNEFNL+SKSTIGVEFATR+IQ+D KTIKAQIWDTA
Sbjct: 1 DYLFKIVLIGDSGVGKSNLLSRFTRNEFNLDSKSTIGVEFATRTIQIDGKTIKAQIWDTA 60
Query: 69 GQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLL 128
GQERYRAITSA
Sbjct: 61 GQERYRAITSA------------------------------------------------- 71
Query: 129 RRYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPAD 188
YYRGAVGALLVYDI K T+ENVERWL+ELRDHAD NIVIMLVGNKSDLRHLRAVP +
Sbjct: 72 --YYRGAVGALLVYDITKKSTFENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTE 129
Query: 189 EAKTFAERNNLSFIETSALDSTNVETAFQNILT 221
EAK FAE+N LSFIETSALD TNVE AF+ +LT
Sbjct: 130 EAKAFAEKNGLSFIETSALDGTNVEEAFKQLLT 162
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 276 bits (708), Expect = 3e-95
Identities = 131/222 (59%), Positives = 149/222 (67%), Gaps = 52/222 (23%)
Query: 1 MGTRED-EYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKT 59
M R D EYDYLFK+VLIGDSGVGKSN+LSRFTRNEF LESKSTIGVEFATR++QV+ KT
Sbjct: 1 MAHRVDHEYDYLFKIVLIGDSGVGKSNILSRFTRNEFCLESKSTIGVEFATRTLQVEGKT 60
Query: 60 IKAQIWDTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVI 119
+KAQIWDTAGQERYRAITSAYYRGAVGALLVYDI K T
Sbjct: 61 VKAQIWDTAGQERYRAITSAYYRGAVGALLVYDITKRQT--------------------- 99
Query: 120 MLVGPPSLLRRYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDL 179
++NV+RWLRELRDHAD NIVIM+ GNKSDL
Sbjct: 100 ------------------------------FDNVQRWLRELRDHADSNIVIMMAGNKSDL 129
Query: 180 RHLRAVPADEAKTFAERNNLSFIETSALDSTNVETAFQNILT 221
HLR+V ++ + AE+ LSF+ETSAL++TNVE AFQ IL
Sbjct: 130 NHLRSVAEEDGQALAEKEGLSFLETSALEATNVEKAFQTILL 171
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 268 bits (689), Expect = 6e-93
Identities = 100/210 (47%), Positives = 127/210 (60%), Gaps = 51/210 (24%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQE 71
FK++LIGDSGVGKS+LLSRFT +F+ + KSTIGV+F T++I+VD K +K QIWDTAGQE
Sbjct: 1 FKIILIGDSGVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIEVDGKRVKLQIWDTAGQE 60
Query: 72 RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRY 131
R+R+ITS+YYRGAVGALLVYDI +
Sbjct: 61 RFRSITSSYYRGAVGALLVYDITNRES--------------------------------- 87
Query: 132 YRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAK 191
+EN+E WL+ELR++A N+VIMLVGNKSDL R V +EA+
Sbjct: 88 ------------------FENLENWLKELREYASPNVVIMLVGNKSDLEEQRQVSREEAE 129
Query: 192 TFAERNNLSFIETSALDSTNVETAFQNILT 221
FAE + L F ETSA +TNVE AF+ +
Sbjct: 130 AFAEEHGLPFFETSAKTNTNVEEAFEELAR 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 = 232 bits (595), Expect = 1e-78
Identities = 87/210 (41%), Positives = 114/210 (54%), Gaps = 51/210 (24%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
K+VL+GD GVGKS+LL RFT+N+F E TIGV+F T++I+VD KT+K QIWDTAGQER
Sbjct: 1 KLVLVGDGGVGKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAGQER 60
Query: 73 YRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRYY 132
+RA+ YYRGA G LLVYDI +
Sbjct: 61 FRALRPLYYRGAQGFLLVYDITSRDS---------------------------------- 86
Query: 133 RGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAKT 192
+ENV++WL E+ HAD+N+ I+LVGNK DL R V +E +
Sbjct: 87 -----------------FENVKKWLEEILRHADENVPIVLVGNKCDLEDQRVVSTEEGEA 129
Query: 193 FAERNNLSFIETSALDSTNVETAFQNILTA 222
A+ L F+ETSA + NVE AF+ +
Sbjct: 130 LAKELGLPFMETSAKTNENVEEAFEELARE 159
>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 = 231 bits (593), Expect = 2e-78
Identities = 91/208 (43%), Positives = 123/208 (59%), Gaps = 51/208 (24%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQE 71
FK+VLIGDSGVGK++LL RF N+F+ KSTIGV+F +++I+VD K +K QIWDTAGQE
Sbjct: 1 FKIVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGVDFKSKTIEVDGKKVKLQIWDTAGQE 60
Query: 72 RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRY 131
R+R+ITS+YYRGA GA+LVYD +T
Sbjct: 61 RFRSITSSYYRGAHGAILVYD----VTNRE------------------------------ 86
Query: 132 YRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAK 191
++EN+++WL EL+++A NI I+LVGNKSDL R V +EA+
Sbjct: 87 -----------------SFENLDKWLNELKEYAPPNIPIILVGNKSDLEDERQVSTEEAQ 129
Query: 192 TFAERNNLSFIETSALDSTNVETAFQNI 219
FA+ N L F ETSA NV+ AF+++
Sbjct: 130 QFAKENGLLFFETSAKTGENVDEAFESL 157
>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 = 195 bits (499), Expect = 5e-64
Identities = 79/208 (37%), Positives = 108/208 (51%), Gaps = 51/208 (24%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQE 71
FK+VL+GDS VGKS+++ RF +NEF+ +STIG F T+++ +D T+K +IWDTAGQE
Sbjct: 2 FKLVLLGDSSVGKSSIVLRFVKNEFSENQESTIGAAFLTQTVNLDDTTVKFEIWDTAGQE 61
Query: 72 RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRY 131
RYR++ YYRGA A++VYDI S +
Sbjct: 62 RYRSLAPMYYRGAAAAIVVYDITS----------------------------EESFEK-- 91
Query: 132 YRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAK 191
AK W++EL++H NIVI L GNK+DL R V +EA+
Sbjct: 92 -------------AKS--------WVKELQEHGPPNIVIALAGNKADLESKRQVSTEEAQ 130
Query: 192 TFAERNNLSFIETSALDSTNVETAFQNI 219
+A+ N L F+ETSA NV F I
Sbjct: 131 EYADENGLLFMETSAKTGENVNELFTEI 158
>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 = 191 bits (487), Expect = 3e-62
Identities = 87/212 (41%), Positives = 109/212 (51%), Gaps = 51/212 (24%)
Query: 8 YDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDT 67
Y YLFK ++IGD+GVGKS LL +FT F TIGVEF R I +D K IK QIWDT
Sbjct: 1 YAYLFKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDT 60
Query: 68 AGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSL 127
AGQE +R+IT
Sbjct: 61 AGQESFRSIT-------------------------------------------------- 70
Query: 128 LRRYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPA 187
R YYRGA GALLVYDI + T+ ++ WL + R H++ N+ IML+GNK DL R V
Sbjct: 71 -RSYYRGAAGALLVYDITRRETFNHLTSWLEDARQHSNSNMTIMLIGNKCDLESRREVSY 129
Query: 188 DEAKTFAERNNLSFIETSALDSTNVETAFQNI 219
+E + FA + L F+ETSA ++NVE AF N
Sbjct: 130 EEGEAFAREHGLIFMETSAKTASNVEEAFINT 161
>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 = 190 bits (484), Expect = 8e-62
Identities = 87/208 (41%), Positives = 115/208 (55%), Gaps = 51/208 (24%)
Query: 9 DYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTA 68
DYLFK++LIGDSGVGKS LL RF+ + FN STIG++F R+I++D K IK QIWDTA
Sbjct: 1 DYLFKLLLIGDSGVGKSCLLLRFSEDSFNPSFISTIGIDFKIRTIELDGKKIKLQIWDTA 60
Query: 69 GQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLL 128
GQER+R IT++YYRGA+G +LVYDI ++EN++ W+R + +HA
Sbjct: 61 GQERFRTITTSYYRGAMGIILVYDITDEKSFENIKNWMRNIDEHAS-------------- 106
Query: 129 RRYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPAD 188
E+VER MLVGNK D+ R V +
Sbjct: 107 ----------------------EDVER---------------MLVGNKCDMEEKRVVSKE 129
Query: 189 EAKTFAERNNLSFIETSALDSTNVETAF 216
E + A + F+ETSA + NVE AF
Sbjct: 130 EGEALAREYGIKFLETSAKANINVEEAF 157
>gnl|CDD|206661 cd01869, Rab1_Ypt1, Rab GTPase family 1 includes the yeast homolog
Ypt1. Rab1/Ypt1 subfamily. Rab1 is found in every
eukaryote and is a key regulatory component for the
transport of vesicles from the ER to the Golgi
apparatus. Studies on mutations of Ypt1, the yeast
homolog of Rab1, showed that this protein is necessary
for the budding of vesicles of the ER as well as for
their transport to, and fusion with, the Golgi
apparatus. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation of
the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 166
Score = 188 bits (480), Expect = 3e-61
Identities = 85/210 (40%), Positives = 117/210 (55%), Gaps = 51/210 (24%)
Query: 10 YLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAG 69
YLFK++LIGDSGVGKS LL RF + + STIGV+F R+I++D KT+K QIWDTAG
Sbjct: 1 YLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTVKLQIWDTAG 60
Query: 70 QERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLR 129
QER+R ITS+YYRGA G ++VYD+ ++ NV++WL+E
Sbjct: 61 QERFRTITSSYYRGAHGIIIVYDVTDQESFNNVKQWLQE--------------------- 99
Query: 130 RYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADE 189
++R+ A +N+ +LVGNK DL + V E
Sbjct: 100 -----------------------IDRY-------ASENVNKLLVGNKCDLTDKKVVDYTE 129
Query: 190 AKTFAERNNLSFIETSALDSTNVETAFQNI 219
AK FA+ + F+ETSA ++TNVE AF +
Sbjct: 130 AKEFADELGIPFLETSAKNATNVEEAFMTM 159
>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 = 177 bits (450), Expect = 8e-57
Identities = 86/207 (41%), Positives = 109/207 (52%), Gaps = 51/207 (24%)
Query: 10 YLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAG 69
Y+FK ++IGD GVGKS LL +FT +F + TIGVEF TR I+V+ + IK QIWDTAG
Sbjct: 1 YIFKYIIIGDMGVGKSCLLHQFTEKKFMADCPHTIGVEFGTRIIEVNGQKIKLQIWDTAG 60
Query: 70 QERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLR 129
QER+RA+T R
Sbjct: 61 QERFRAVT---------------------------------------------------R 69
Query: 130 RYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADE 189
YYRGA GAL+VYDI + TY ++ WL + R+ + N VI L+GNK+DL R V +E
Sbjct: 70 SYYRGAAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTVIFLIGNKADLEAQRDVTYEE 129
Query: 190 AKTFAERNNLSFIETSALDSTNVETAF 216
AK FA+ N L F+E SA NVE AF
Sbjct: 130 AKQFADENGLLFLECSAKTGENVEDAF 156
>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 = 174 bits (442), Expect = 2e-55
Identities = 78/210 (37%), Positives = 113/210 (53%), Gaps = 51/210 (24%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQE 71
K++LIGDSGVGKS+LL RFT + F+ + STIGV+F +++ VD K +K IWDTAGQE
Sbjct: 1 LKILLIGDSGVGKSSLLLRFTDDTFDEDLSSTIGVDFKVKTVTVDGKKVKLAIWDTAGQE 60
Query: 72 RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRY 131
R+R +TS+YYRGA G +LVYD+ + T++N++ WL EL ++
Sbjct: 61 RFRTLTSSYYRGAQGVILVYDVTRRDTFDNLDTWLNELDTYST----------------- 103
Query: 132 YRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAK 191
+ + V MLVGNK D + R V +E +
Sbjct: 104 ---------------------------------NPDAVKMLVGNKID-KENREVTREEGQ 129
Query: 192 TFAERNNLSFIETSALDSTNVETAFQNILT 221
FA ++N+ FIETSA V+ AF+ ++
Sbjct: 130 KFARKHNMLFIETSAKTRIGVQQAFEELVE 159
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 173 bits (441), Expect = 9e-55
Identities = 88/211 (41%), Positives = 109/211 (51%), Gaps = 51/211 (24%)
Query: 8 YDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDT 67
Y YLFK ++IGD+GVGKS LL +FT F TIGVEF R I +D K IK QIWDT
Sbjct: 3 YAYLFKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDNKPIKLQIWDT 62
Query: 68 AGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSL 127
AGQE +R+IT
Sbjct: 63 AGQESFRSIT-------------------------------------------------- 72
Query: 128 LRRYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPA 187
R YYRGA GALLVYDI + T+ ++ WL + R HA+ N+ IML+GNK DL H RAV
Sbjct: 73 -RSYYRGAAGALLVYDITRRETFNHLASWLEDARQHANANMTIMLIGNKCDLAHRRAVST 131
Query: 188 DEAKTFAERNNLSFIETSALDSTNVETAFQN 218
+E + FA+ + L F+E SA + NVE AF
Sbjct: 132 EEGEQFAKEHGLIFMEASAKTAQNVEEAFIK 162
>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 = 170 bits (432), Expect = 4e-54
Identities = 83/205 (40%), Positives = 104/205 (50%), Gaps = 51/205 (24%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQE 71
FK ++IG +G GKS LL +F N+F +S TIGVEF +R + V K++K QIWDTAGQE
Sbjct: 1 FKFLIIGSAGTGKSCLLHQFIENKFKQDSNHTIGVEFGSRVVNVGGKSVKLQIWDTAGQE 60
Query: 72 RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRY 131
R+R++T R Y
Sbjct: 61 RFRSVT---------------------------------------------------RSY 69
Query: 132 YRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAK 191
YRGA GALLVYDI ++ + WL + R A +IVI+LVGNK DL R V EA
Sbjct: 70 YRGAAGALLVYDITSRESFNALTNWLTDARTLASPDIVIILVGNKKDLEDDREVTFLEAS 129
Query: 192 TFAERNNLSFIETSALDSTNVETAF 216
FA+ N L F+ETSAL NVE AF
Sbjct: 130 RFAQENGLLFLETSALTGENVEEAF 154
>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 = 166 bits (423), Expect = 1e-52
Identities = 74/209 (35%), Positives = 109/209 (52%), Gaps = 52/209 (24%)
Query: 9 DYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTA 68
D+LFK++LIGDS VGK+ ++ RF F+ +TIGV+F +++++ K +K QIWDTA
Sbjct: 1 DFLFKIILIGDSNVGKTCVVQRFKSGTFSERQGNTIGVDFTMKTLEIQGKRVKLQIWDTA 60
Query: 69 GQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLL 128
GQER+R IT +YYR A GA++ YDI + ++E+V W+ E+ + N
Sbjct: 61 GQERFRTITQSYYRSANGAIIAYDITRRSSFESVPHWIEEVEKYGASN------------ 108
Query: 129 RRYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPAD 188
+V++L+GNK DL R V +
Sbjct: 109 ---------------------------------------VVLLLIGNKCDLEEQREVLFE 129
Query: 189 EAKTFAERNN-LSFIETSALDSTNVETAF 216
EA T AE L+ +ETSA +S+NVE AF
Sbjct: 130 EACTLAEHYGILAVLETSAKESSNVEEAF 158
>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 = 162 bits (411), Expect = 3e-50
Identities = 77/208 (37%), Positives = 104/208 (50%), Gaps = 51/208 (24%)
Query: 10 YLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQV-DQKTIKAQIWDTA 68
Y F++++IGDS VGKS+LL RFT F S T+GV+F +R I++ IK Q+WDTA
Sbjct: 1 YQFRLIVIGDSTVGKSSLLKRFTEGRFAEVSDPTVGVDFFSRLIEIEPGVRIKLQLWDTA 60
Query: 69 GQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLL 128
GQER+R+IT +YYR +VG LLV+DI ++E+V WL E R H + P
Sbjct: 61 GQERFRSITRSYYRNSVGVLLVFDITNRESFEHVHDWLEEARSH---------IQPHR-- 109
Query: 129 RRYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPAD 188
V +LVG+K DL R V +
Sbjct: 110 ---------------------------------------PVFILVGHKCDLESQRQVTRE 130
Query: 189 EAKTFAERNNLSFIETSALDSTNVETAF 216
EA+ A+ + +IETSA NVE AF
Sbjct: 131 EAEKLAKDLGMKYIETSARTGDNVEEAF 158
>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 = 158 bits (403), Expect = 1e-49
Identities = 66/211 (31%), Positives = 110/211 (52%), Gaps = 51/211 (24%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQE 71
K+V +GD VGK+++++RF + F+ + ++TIG++F ++++ VD KT++ Q+WDTAGQE
Sbjct: 1 HKLVFLGDQSVGKTSIITRFMYDTFDNQYQATIGIDFLSKTMYVDDKTVRLQLWDTAGQE 60
Query: 72 RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRY 131
R+R SL+ Y
Sbjct: 61 RFR---------------------------------------------------SLIPSY 69
Query: 132 YRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAK 191
R + A++VYDI +++N ++W+ ++RD +++I+LVGNK+DL R V +E +
Sbjct: 70 IRDSSVAVVVYDITNRQSFDNTDKWIDDVRDERGNDVIIVLVGNKTDLSDKRQVSTEEGE 129
Query: 192 TFAERNNLSFIETSALDSTNVETAFQNILTA 222
A+ NN FIETSA NV+ F+ I A
Sbjct: 130 KKAKENNAMFIETSAKAGHNVKQLFKKIAQA 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 = 153 bits (388), Expect = 2e-47
Identities = 63/211 (29%), Positives = 89/211 (42%), Gaps = 51/211 (24%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNE-FNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQ 70
K+V++GD VGKS LL+R N+ E K + T I+ D KT K + DTAGQ
Sbjct: 2 IKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAGQ 61
Query: 71 ERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRR 130
E Y AI YYR +L V+DI
Sbjct: 62 EDYDAIRRLYYRAVESSLRVFDIV------------------------------------ 85
Query: 131 YYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEA 190
+LV D E +E+ +E+ HA+ + I+LVGNK DLR + + A
Sbjct: 86 --------ILVLD-----VEEILEKQTKEIIHHAESGVPIILVGNKIDLRDAK-LKTHVA 131
Query: 191 KTFAERNNLSFIETSALDSTNVETAFQNILT 221
FA+ N I SA N+++AF+ +
Sbjct: 132 FLFAKLNGEPIIPLSAETGKNIDSAFKIVEA 162
>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 = 147 bits (373), Expect = 4e-45
Identities = 72/216 (33%), Positives = 113/216 (52%), Gaps = 51/216 (23%)
Query: 6 DEYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIW 65
++YD+LFK+VLIG++GVGK+ L+ RFT+ F +TIGV+F +++++ + IK QIW
Sbjct: 2 EDYDFLFKIVLIGNAGVGKTCLVRRFTQGLFPPGQGATIGVDFMIKTVEIKGEKIKLQIW 61
Query: 66 DTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPP 125
DTAGQER+R+IT +YYR A +A
Sbjct: 62 DTAGQERFRSITQSYYRSA---------------------------NA------------ 82
Query: 126 SLLRRYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAV 185
+L YDI ++ + WLRE+ +A+ ++ +LVGNK DL R V
Sbjct: 83 ------------LILTYDITCEESFRCLPEWLREIEQYANNKVITILVGNKIDLAERREV 130
Query: 186 PADEAKTFAERNNLSFIETSALDSTNVETAFQNILT 221
A+ F++ ++ ++ETSA +S NVE F ++
Sbjct: 131 SQQRAEEFSDAQDMYYLETSAKESDNVEKLFLDLAC 166
>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 = 146 bits (369), Expect = 5e-44
Identities = 77/213 (36%), Positives = 112/213 (52%), Gaps = 52/213 (24%)
Query: 7 EYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWD 66
+YD+LFK+++IGDSGVGKS+LL RF N F+ +TIGV+F R+++++ + +K QIWD
Sbjct: 2 DYDHLFKLLIIGDSGVGKSSLLLRFADNTFSGSYITTIGVDFKIRTVEINGERVKLQIWD 61
Query: 67 TAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPS 126
TAGQER+R ITS YYRG G ++VYD+ ++ NV+RWL+E+ + D
Sbjct: 62 TAGQERFRTITSTYYRGTHGVIVVYDVTNGESFVNVKRWLQEIEQNCD------------ 109
Query: 127 LLRRYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVP 186
V +LV GNK+D + V
Sbjct: 110 --------DVCKVLV--------------------------------GNKNDDPERKVVE 129
Query: 187 ADEAKTFAERNNLSFIETSALDSTNVETAFQNI 219
++A FA + +S ETSA ++ NVE F I
Sbjct: 130 TEDAYKFAGQMGISLFETSAKENINVEEMFNCI 162
>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 = 144 bits (365), Expect = 8e-44
Identities = 65/208 (31%), Positives = 98/208 (47%), Gaps = 51/208 (24%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQE 71
FKVVL+G+ VGK++L+ R+ N+FN + +ST F +++ + K I IWDTAGQE
Sbjct: 1 FKVVLLGEGRVGKTSLVLRYVENKFNEKHESTTQASFFQKTVNIGGKRIDLAIWDTAGQE 60
Query: 72 RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRY 131
RY A+ YYR A GA+LVYDI T +
Sbjct: 61 RYHALGPIYYRDADGAILVYDI----TDAD------------------------------ 86
Query: 132 YRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAK 191
+++ V++W++EL+ NI +++VGNK DL R V EA+
Sbjct: 87 -----------------SFQKVKKWIKELKQMRGNNISLVIVGNKIDLERQRVVSKSEAE 129
Query: 192 TFAERNNLSFIETSALDSTNVETAFQNI 219
+A+ ETSA +E F ++
Sbjct: 130 EYAKSVGAKHFETSAKTGKGIEELFLSL 157
>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 = 136 bits (344), Expect = 1e-40
Identities = 61/216 (28%), Positives = 105/216 (48%), Gaps = 56/216 (25%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQE 71
KV+++GDSGVGK++L++++ +F+ + K+TIG +F T+ + VD + + QIWDTAGQE
Sbjct: 1 LKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVTVDDRLVTLQIWDTAGQE 60
Query: 72 RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRY 131
R++++ A+YR
Sbjct: 61 RFQSLGVAFYR------------------------------------------------- 71
Query: 132 YRGAVGALLVYDIAKHLTYENVERWLRELRDHADQ----NIVIMLVGNKSDLRHLRAVPA 187
GA +LVYD+ ++E+++ W E A N +++GNK DL R V
Sbjct: 72 --GADCCVLVYDVTNPKSFESLDSWRDEFLIQASPRDPENFPFVVLGNKIDLEEKRQVST 129
Query: 188 DEAKTFAE-RNNLSFIETSALDSTNVETAFQNILTA 222
+A+ + + + N+ + ETSA ++ NV+ AF+ I
Sbjct: 130 KKAQQWCKSKGNIPYFETSAKEAINVDQAFETIARL 165
>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 = 130 bits (328), Expect = 3e-38
Identities = 66/209 (31%), Positives = 100/209 (47%), Gaps = 54/209 (25%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQE 71
FK+++IGDS VGK+ L RF F +++TIGV+F R++++D + IK Q+WDTAGQE
Sbjct: 3 FKIIVIGDSNVGKTCLTYRFCAGRFPERTEATIGVDFRERTVEIDGERIKVQLWDTAGQE 62
Query: 72 RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRY 131
R+R S+++ Y
Sbjct: 63 RFRK--------------------------------------------------SMVQHY 72
Query: 132 YRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVI-MLVGNKSDLRHLRAVPADEA 190
YR + VYD+ ++ ++ W+ E H+ N V +LVGNK DLR VP D A
Sbjct: 73 YRNVHAVVFVYDVTNMASFHSLPSWIEECEQHSLPNEVPRILVGNKCDLREQIQVPTDLA 132
Query: 191 KTFAERNNLSFIETSALD---STNVETAF 216
+ FA+ +++ ETSA D + +VE F
Sbjct: 133 QRFADAHSMPLFETSAKDPSENDHVEAIF 161
>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 = 130 bits (329), Expect = 5e-38
Identities = 68/219 (31%), Positives = 108/219 (49%), Gaps = 54/219 (24%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTI-KAQIWDTAGQ 70
FKV++IGD GVGK++++ R+ F+ K+TIGV+FA + I+ D T+ + Q+WD AGQ
Sbjct: 1 FKVLVIGDLGVGKTSIIKRYVHGVFSQHYKATIGVDFALKVIEWDPNTVVRLQLWDIAGQ 60
Query: 71 ERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRR 130
ER+ +T YY+GAVGA++V+D+ + T+E V +W +L + V + G P
Sbjct: 61 ERFGGMTRVYYKGAVGAIIVFDVTRPSTFEAVLKWKADL-----DSKVTLPNGEP----- 110
Query: 131 YYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLR-AVPADE 189
I +L+ NK DL+ R A ++
Sbjct: 111 -------------------------------------IPALLLANKCDLKKERLAKDPEQ 133
Query: 190 AKTFAERNNLS-FIETSALDSTNVETAFQ----NILTAN 223
F + N + ETSA ++ N+E A + NIL +
Sbjct: 134 MDQFCKENGFIGWFETSAKENINIEEAMRFLVKNILKND 172
>gnl|CDD|206695 cd04112, Rab26, Rab GTPase family 26 (Rab26). Rab26 subfamily.
First identified in rat pancreatic acinar cells, Rab26
is believed to play a role in recruiting mature granules
to the plasma membrane upon beta-adrenergic stimulation.
Rab26 belongs to the Rab functional group III, which are
considered key regulators of intracellular vesicle
transport during exocytosis. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 191
Score = 129 bits (326), Expect = 1e-37
Identities = 72/209 (34%), Positives = 105/209 (50%), Gaps = 52/209 (24%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKS-TIGVEFATRSIQVDQKTIKAQIWDTAGQ 70
FKV+L+GDSGVGK+ LL RF F S T+G++F + + VD +K QIWDTAGQ
Sbjct: 1 FKVMLVGDSGVGKTCLLVRFKDGAFLAGSFIATVGIQFTNKVVTVDGVKVKLQIWDTAGQ 60
Query: 71 ERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRR 130
ER+R++T AYYR A HA
Sbjct: 61 ERFRSVTHAYYRDA---------------------------HA----------------- 76
Query: 131 YYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEA 190
LL+YD+ +++N+ WL E+ ++A ++VIML+GNK+D+ R V ++
Sbjct: 77 -------LLLLYDVTNKSSFDNIRAWLTEILEYAQSDVVIMLLGNKADMSGERVVKREDG 129
Query: 191 KTFAERNNLSFIETSALDSTNVETAFQNI 219
+ A+ + F+ETSA NVE AF +
Sbjct: 130 ERLAKEYGVPFMETSAKTGLNVELAFTAV 158
>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 = 127 bits (319), Expect = 4e-37
Identities = 68/208 (32%), Positives = 107/208 (51%), Gaps = 51/208 (24%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQE 71
F+++LIGDSGVGK+ LL RFT NEF+ STIGV+F ++I+VD ++ QIWDTAGQE
Sbjct: 1 FRLLLIGDSGVGKTCLLCRFTDNEFHSSHISTIGVDFKMKTIEVDGIKVRIQIWDTAGQE 60
Query: 72 RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRY 131
RY+ IT ++Y
Sbjct: 61 RYQTIT---------------------------------------------------KQY 69
Query: 132 YRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAK 191
YR A G LVYDI+ +Y+++ +W+ ++ ++A + + +L+GNK+D R V ++
Sbjct: 70 YRRAQGIFLVYDISSERSYQHIMKWVSDVDEYAPEGVQKILIGNKADEEQKRQVGDEQGN 129
Query: 192 TFAERNNLSFIETSALDSTNVETAFQNI 219
A+ + F ETSA + N++ +F +
Sbjct: 130 KLAKEYGMDFFETSACTNKNIKESFTRL 157
>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 = 126 bits (318), Expect = 8e-37
Identities = 66/210 (31%), Positives = 105/210 (50%), Gaps = 51/210 (24%)
Query: 11 LFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQ 70
+FK+++IG+S VGK++ L R+ + F ST+G++F +++ + K IK QIWDTAGQ
Sbjct: 1 MFKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVYRNDKRIKLQIWDTAGQ 60
Query: 71 ERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRR 130
ERYR IT+AYYRGA+G +L+YDI ++ V+ W +++
Sbjct: 61 ERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIK-------------------- 100
Query: 131 YYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEA 190
TY W N ++LVGNK D+ R V A+
Sbjct: 101 ------------------TYS----W---------DNAQVILVGNKCDMEDERVVSAERG 129
Query: 191 KTFAERNNLSFIETSALDSTNVETAFQNIL 220
+ A++ F E SA ++ NV+ F+ ++
Sbjct: 130 RQLADQLGFEFFEASAKENINVKQVFERLV 159
>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 = 123 bits (311), Expect = 1e-35
Identities = 69/224 (30%), Positives = 112/224 (50%), Gaps = 62/224 (27%)
Query: 8 YDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKT-------- 59
YDYL K++ +GDSGVGK+ L R+T N+FN + +T+G++F + + + +
Sbjct: 1 YDYLIKLLALGDSGVGKTTFLYRYTDNKFNPKFITTVGIDFREKRVVYNSQGPDGTSGKA 60
Query: 60 --IKAQIWDTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNI 117
+ Q+WDTAGQER+R++T+A++R A+G LL++D LT E
Sbjct: 61 FRVHLQLWDTAGQERFRSLTTAFFRDAMGFLLMFD----LTSEQ---------------- 100
Query: 118 VIMLVGPPSLLRRYYRGAVGALLVYDIAKHLTYENVERWLRELRDHA-DQNIVIMLVGNK 176
++ NV W+ +L+ HA +N I+L+GNK
Sbjct: 101 -------------------------------SFLNVRNWMSQLQAHAYCENPDIVLIGNK 129
Query: 177 SDLRHLRAVPADEAKTFAERNNLSFIETSALDSTNVETAFQNIL 220
+DL R V +A+ A++ + + ETSA NVE A + +L
Sbjct: 130 ADLPDQREVSERQARELADKYGIPYFETSAATGQNVEKAVETLL 173
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 124 bits (312), Expect = 2e-35
Identities = 71/213 (33%), Positives = 101/213 (47%), Gaps = 52/213 (24%)
Query: 8 YDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDT 67
YD FK++LIGDSGVGKS+LL F + + TIGV+F + + V K +K IWDT
Sbjct: 11 YDLSFKILLIGDSGVGKSSLLVSFISSSVE-DLAPTIGVDFKIKQLTVGGKRLKLTIWDT 69
Query: 68 AGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSL 127
AGQER+R +TS+YYR A G +LVYD+ + T+ N+
Sbjct: 70 AGQERFRTLTSSYYRNAQGIILVYDVTRRETFTNL------------------------- 104
Query: 128 LRRYYRGAVGALLVYDIAKHLTYENVERWLRELRDHA-DQNIVIMLVGNKSDLRHLRAVP 186
+ W +E+ ++ +Q+ V MLVGNK D R V
Sbjct: 105 -------------------------SDVWGKEVELYSTNQDCVKMLVGNKVDRESERDVS 139
Query: 187 ADEAKTFAERNNLSFIETSALDSTNVETAFQNI 219
+E A+ + F+E SA NVE F+ +
Sbjct: 140 REEGMALAKEHGCLFLECSAKTRENVEQCFEEL 172
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 123 bits (309), Expect = 6e-35
Identities = 52/117 (44%), Positives = 73/117 (62%), Gaps = 1/117 (0%)
Query: 8 YDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDT 67
+ FK+V++GD GVGK+ LL+R +EF TIG ++I+ ++ IK Q+WDT
Sbjct: 2 FMKEFKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDT 61
Query: 68 AGQERYRAITSAYYRGAVGALLVYDIAKHL-TYENVERWLRELRDHADQNIVIMLVG 123
AGQE YR++ YYRGA G L+VYD + E E WL ELR+ A ++ I+LVG
Sbjct: 62 AGQEEYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVG 118
>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 = 118 bits (297), Expect = 1e-33
Identities = 64/208 (30%), Positives = 104/208 (50%), Gaps = 49/208 (23%)
Query: 11 LFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQ 70
L KV+L+GD GVGKS+L++R+ N+F+ + TIGVEF + ++VD + QIWDTAGQ
Sbjct: 5 LLKVILLGDGGVGKSSLMNRYVTNKFDTQLFHTIGVEFLNKDLEVDGHFVTLQIWDTAGQ 64
Query: 71 ERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRR 130
ER+R++ + +YRG+ LL + + +++N+ W +E +AD
Sbjct: 65 ERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYAD---------------- 108
Query: 131 YYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEA 190
+ E + +++GNK D+ R V +EA
Sbjct: 109 -------------------VKEPESF------------PFVILGNKIDIPE-RQVSTEEA 136
Query: 191 KTFAERN-NLSFIETSALDSTNVETAFQ 217
+ + N + + ETSA D+TNV AF+
Sbjct: 137 QAWCRDNGDYPYFETSAKDATNVAAAFE 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 = 117 bits (295), Expect = 5e-33
Identities = 67/205 (32%), Positives = 105/205 (51%), Gaps = 52/205 (25%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
+V++IG GVGK++L+ RFT + F KST+GV+F +++++ K I+ QIWDTAGQER
Sbjct: 2 QVIIIGSRGVGKTSLMERFTDDTFCEACKSTVGVDFKIKTVELRGKKIRLQIWDTAGQER 61
Query: 73 YRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRYY 132
+ +ITSAYYR A G +LVYDI K T++++ +W++ + +A
Sbjct: 62 FNSITSAYYRSAKGIILVYDITKKETFDDLPKWMKMIDKYAS------------------ 103
Query: 133 RGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAKT 192
E+ E ++LVGNK D R + + +
Sbjct: 104 ------------------EDAE---------------LLLVGNKLDCETDREITRQQGEK 130
Query: 193 FAER-NNLSFIETSALDSTNVETAF 216
FA++ + F E SA D+ NV+ F
Sbjct: 131 FAQQITGMRFCEASAKDNFNVDEIF 155
>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 = 61/209 (29%), Positives = 98/209 (46%), Gaps = 52/209 (24%)
Query: 8 YDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDT 67
YDYL K +L+GDS VGK +L+ +G+++ T +I +D + +K Q+WDT
Sbjct: 3 YDYLLKFLLVGDSDVGKGEILASLQDGSTESPYGYNMGIDYKTTTILLDGRRVKLQLWDT 62
Query: 68 AGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSL 127
+GQ R+ I +Y RGA G +LVYDI +++ ++RW++E+ +HA G P +
Sbjct: 63 SGQGRFCTIFRSYSRGAQGIILVYDITNRWSFDGIDRWIKEIDEHAP--------GVPKI 114
Query: 128 LRRYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPA 187
LVGN+ L R V
Sbjct: 115 --------------------------------------------LVGNRLHLAFKRQVAT 130
Query: 188 DEAKTFAERNNLSFIETSALDSTNVETAF 216
++A+ +AERN ++F E S L + N+ +F
Sbjct: 131 EQAQAYAERNGMTFFEVSPLCNFNITESF 159
>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 = 114 bits (286), Expect = 5e-32
Identities = 58/207 (28%), Positives = 88/207 (42%), Gaps = 54/207 (26%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQK--TIKAQIWDTAGQ 70
KV+++G+ VGKS+++ RF + F + K TIGV+F + I + Q ++ +WDTAGQ
Sbjct: 2 KVIVVGNGNVGKSSMIQRFVKGIFTKDYKKTIGVDFLEKQIFLRQSDEDVRLMLWDTAGQ 61
Query: 71 ERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRR 130
E + AIT AYYRGA +LV+ ++E +E W + V G
Sbjct: 62 EEFDAITKAYYRGAQACILVFSTTDRESFEAIESWKEK---------VEAECG------- 105
Query: 131 YYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEA 190
+I ++LV K DL + +EA
Sbjct: 106 ------------------------------------DIPMVLVQTKIDLLDQAVITNEEA 129
Query: 191 KTFAERNNLSFIETSALDSTNVETAFQ 217
+ A+R L TS D NV F+
Sbjct: 130 EALAKRLQLPLFRTSVKDDFNVTELFE 156
>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 = 113 bits (286), Expect = 5e-32
Identities = 58/209 (27%), Positives = 89/209 (42%), Gaps = 51/209 (24%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
K+V++G GVGKS L RF EF E TI + + I VD +T I DTAGQE
Sbjct: 1 KLVVLGAGGVGKSALTIRFVSGEFVEEYDPTIE-DSYRKQIVVDGETYTLDILDTAGQEE 59
Query: 73 YRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRYY 132
+ A+ Y R G +LVY I ++E ++ +R+
Sbjct: 60 FSAMRDQYIRNGDGFILVYSITSRESFEEIKN----IREQ-------------------- 95
Query: 133 RGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAKT 192
+ ++D +++ I+LVGNK DL + R V +E +
Sbjct: 96 ------------------------ILRVKD--KEDVPIVLVGNKCDLENERQVSTEEGEA 129
Query: 193 FAERNNLSFIETSALDSTNVETAFQNILT 221
AE F+ETSA + N++ F ++
Sbjct: 130 LAEEWGCPFLETSAKTNINIDELFNTLVR 158
>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 = 110 bits (276), Expect = 2e-30
Identities = 53/208 (25%), Positives = 89/208 (42%), Gaps = 46/208 (22%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
KV+ +G+SGVGKS ++ R+ F + TIG+++ + + V K ++ +D +G
Sbjct: 2 KVISMGNSGVGKSCIIKRYCEGRFVSKYLPTIGIDYGVKKVSVRNKEVRVNFFDLSGHPE 61
Query: 73 YRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRYY 132
Y + + +Y+ G LLVYD+ ++E ++ WL+E++ GP +
Sbjct: 62 YLEVRNEFYKDTQGVLLVYDVTDRQSFEALDSWLKEMKQE---------GGPHGNME--- 109
Query: 133 RGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAKT 192
NIV+++ NK DL RAV DE +
Sbjct: 110 ----------------------------------NIVVVVCANKIDLTKHRAVSEDEGRL 135
Query: 193 FAERNNLSFIETSALDSTNVETAFQNIL 220
+AE + ETSA V FQ +
Sbjct: 136 WAESKGFKYFETSACTGEGVNEMFQTLF 163
>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 = 103 bits (259), Expect = 4e-28
Identities = 59/210 (28%), Positives = 90/210 (42%), Gaps = 55/210 (26%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
K++L+GDS VGKS L+ RF + + + ST + + + + KTI WDTAGQER
Sbjct: 2 KIILLGDSAVGKSKLVERFLMDGYEPQQLSTYALTLYKHNAKFEGKTILVDFWDTAGQER 61
Query: 73 YRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRYY 132
++ + ++YY A +LV+D+ + +TY+N+ +W E
Sbjct: 62 FQTMHASYYHKAHACILVFDVTRKITYKNLSKWYEE------------------------ 97
Query: 133 RGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAKT 192
LRE R I ++V NK DL +
Sbjct: 98 ------------------------LREYRPE----IPCIVVANKIDL-DPSVT--QKKFN 126
Query: 193 FAERNNLSFIETSALDSTNVETAFQNILTA 222
FAE++NL SA D TNV FQ+ +
Sbjct: 127 FAEKHNLPLYYVSAADGTNVVKLFQDAIKL 156
>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 = 102 bits (257), Expect = 1e-27
Identities = 60/209 (28%), Positives = 91/209 (43%), Gaps = 51/209 (24%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQE 71
+K+V++G GVGKS L +F + F + TI + + I++D + I DTAGQE
Sbjct: 1 YKLVVLGSGGVGKSALTIQFIQGHFVDDYDPTIE-DSYRKQIEIDGEVCLLDILDTAGQE 59
Query: 72 RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRY 131
+ A+ Y R G LLVY I ++E +++ RE +LR
Sbjct: 60 EFSAMRDQYMRTGEGFLLVYSITDRQSFEEIKK-FREQ-----------------ILR-- 99
Query: 132 YRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAK 191
V D ++ I+LVGNK DL R V +E K
Sbjct: 100 ---------VKD---------------------RDDVPIVLVGNKCDLESERVVSTEEGK 129
Query: 192 TFAERNNLSFIETSALDSTNVETAFQNIL 220
A + F+ETSA + NV+ AF +++
Sbjct: 130 ELARQWGCPFLETSAKERVNVDEAFYDLV 158
>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 = 102 bits (256), Expect = 2e-27
Identities = 61/209 (29%), Positives = 91/209 (43%), Gaps = 51/209 (24%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQE 71
+K+V++G GVGKS L +F + F E TI + + I++D + I DTAGQE
Sbjct: 3 YKLVVLGGGGVGKSALTIQFVQGHFVDEYDPTIE-DSYRKQIEIDGEVCLLDILDTAGQE 61
Query: 72 RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRY 131
+ A+ Y R G LLVY I ++E + + RE +LR
Sbjct: 62 EFSAMRDQYMRTGEGFLLVYSITDRQSFEEIAK-FREQ-----------------ILR-- 101
Query: 132 YRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAK 191
V D ++ I+LVGNK DL + R V +E K
Sbjct: 102 ---------VKD---------------------RDDVPIVLVGNKCDLENERVVSTEEGK 131
Query: 192 TFAERNNLSFIETSALDSTNVETAFQNIL 220
A + F+ETSA + NV+ AF +++
Sbjct: 132 ELARQWGCPFLETSAKERINVDEAFYDLV 160
>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 = 100 bits (251), Expect = 2e-26
Identities = 59/212 (27%), Positives = 93/212 (43%), Gaps = 57/212 (26%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEF-NLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQE 71
KVV++G VGK++L+ R+ + F ++TIG F + + V ++ + IWDTAG E
Sbjct: 2 KVVMLGKESVGKTSLVERYVHHRFLVGPYQNTIGAAFVAKRMVVGERVVTLGIWDTAGSE 61
Query: 72 RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRY 131
RY A++ YYRGA A++ YD+ ++E + W++EL+
Sbjct: 62 RYEAMSRIYYRGAKAAIVCYDLTDSSSFERAKFWVKELQ--------------------- 100
Query: 132 YRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDL----RHLRAVPA 187
N+E ++ I L G KSDL R LR V
Sbjct: 101 --------------------NLE-----------EHCKIYLCGTKSDLIEQDRSLRQVDF 129
Query: 188 DEAKTFAERNNLSFIETSALDSTNVETAFQNI 219
+ + FA+ ETS+ NV+ FQ +
Sbjct: 130 HDVQDFADEIKAQHFETSSKTGQNVDELFQKV 161
>gnl|CDD|206693 cd04108, Rab36_Rab34, Rab GTPase families 34 (Rab34) and 36
(Rab36). Rab34/Rab36 subfamily. Rab34, found primarily
in the Golgi, interacts with its effector,
Rab-interacting lysosomal protein (RILP). This enables
its participation in microtubular
dynenin-dynactin-mediated repositioning of lysosomes
from the cell periphery to the Golgi. A Rab34 (Rah)
isoform that lacks the consensus GTP-binding region has
been identified in mice. This isoform is associated with
membrane ruffles and promotes macropinosome formation.
Rab36 has been mapped to human chromosome 22q11.2, a
region that is homozygously deleted in malignant
rhabdoid tumors (MRTs). However, experimental
assessments do not implicate Rab36 as a tumor suppressor
that would enable tumor formation through a
loss-of-function mechanism. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 170
Score = 95.3 bits (237), Expect = 1e-24
Identities = 43/112 (38%), Positives = 73/112 (65%), Gaps = 1/112 (0%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
KV+++GD VGK+ L++RF ++ F+ K+TIGV+F +V Q+WDTAGQER
Sbjct: 2 KVIVVGDLSVGKTCLINRFCKDVFDKNYKATIGVDFEMERFEVLGVPFSLQLWDTAGQER 61
Query: 73 YRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRE-LRDHADQNIVIMLVG 123
++ I S YYRGA ++V+D+ + E+ +WL + L+++ ++++ LVG
Sbjct: 62 FKCIASTYYRGAQAIIIVFDLTDVASLEHTRQWLEDALKENDPSSVLLFLVG 113
>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 = 95.2 bits (237), Expect = 1e-24
Identities = 59/205 (28%), Positives = 88/205 (42%), Gaps = 51/205 (24%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQE 71
KV+++G GVGKS L +F +EF + + T + + + +D + ++ I DTAGQE
Sbjct: 1 HKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVV-LDGEEVQLNILDTAGQE 59
Query: 72 RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRY 131
Y AI Y+R G LLV+ I ++ L E R
Sbjct: 60 DYAAIRDNYFRSGEGFLLVFSITDMESFTA----LAEFR--------------------- 94
Query: 132 YRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAK 191
E+ LR D N+ ++LVGNK DL R V +EA
Sbjct: 95 ----------------------EQILRVKE---DDNVPLLLVGNKCDLEDKRQVSVEEAA 129
Query: 192 TFAERNNLSFIETSALDSTNVETAF 216
AE+ ++++ETSA NV+ F
Sbjct: 130 NLAEQWGVNYVETSAKTRANVDKVF 154
>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 = 94.1 bits (235), Expect = 3e-24
Identities = 50/217 (23%), Positives = 86/217 (39%), Gaps = 66/217 (30%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
K+V++GD VGK+ LL +T N+F E T+ + + ++ VD K + +WDTAGQE
Sbjct: 2 KIVVVGDGAVGKTCLLISYTTNKFPTEYVPTV-FDNYSANVTVDGKQVNLGLWDTAGQEE 60
Query: 73 YRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRYY 132
Y + L+Y ++
Sbjct: 61 YDRLRP------------------LSYPQT-------------DVF-------------- 75
Query: 133 RGAVGALLVYDIAKHLTYENVER-WLRELRDHADQNIVIMLVGNKSDLR----------- 180
LL + + ++ENV+ W E++ + N+ I+LVG K DLR
Sbjct: 76 ------LLCFSVDSPSSFENVKTKWYPEIKHYC-PNVPIILVGTKIDLRDDGNTLKKLEK 128
Query: 181 HLRAVPADEAKTFAERNNLS-FIETSALDSTNVETAF 216
+ + +E + A+ ++E SAL ++ F
Sbjct: 129 KQKPITPEEGEKLAKEIGAVKYMECSALTQEGLKEVF 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 = 93.5 bits (233), Expect = 4e-24
Identities = 60/209 (28%), Positives = 88/209 (42%), Gaps = 62/209 (29%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKT----IKAQIWDT 67
FK+VL+GD G GK+ + R EF + +T+GVE +D T I+ +WDT
Sbjct: 1 FKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVH----PLDFHTNRGKIRFNVWDT 56
Query: 68 AGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSL 127
AGQE++ LRD
Sbjct: 57 AGQEKFGG---------------------------------LRD---------------- 67
Query: 128 LRRYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPA 187
YY A++++D+ +TY+NV W R+L +NI I+L GNK D++ R V
Sbjct: 68 --GYYIQGQCAIIMFDVTSRVTYKNVPNWHRDLV-RVCENIPIVLCGNKVDIKD-RKVKP 123
Query: 188 DEAKTFAERNNLSFIETSALDSTNVETAF 216
+ TF + NL + E SA + N E F
Sbjct: 124 -KQITFHRKKNLQYYEISAKSNYNFEKPF 151
>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 = 92.6 bits (230), Expect = 2e-23
Identities = 62/211 (29%), Positives = 90/211 (42%), Gaps = 51/211 (24%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATR-SIQVDQKTIKAQIWDTAGQE 71
K+V++GD GVGK+ L + N F TI E + R + VD + ++ DTAGQE
Sbjct: 1 KLVVLGDGGVGKTALTIQLCLNHFVETYDPTI--EDSYRKQVVVDGQPCMLEVLDTAGQE 58
Query: 72 RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRY 131
Y A+ + R G +LVY I T+E VER+
Sbjct: 59 EYTALRDQWIREGEGFILVYSITSRSTFERVERF-------------------------- 92
Query: 132 YRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAK 191
E ++R ++D + ++ IM+VGNK D + R V +E
Sbjct: 93 ------------------REQIQR----VKDESAADVPIMIVGNKCDKVYEREVSTEEGA 130
Query: 192 TFAERNNLSFIETSALDSTNVETAFQNILTA 222
A R FIE SA + NVE AF ++ A
Sbjct: 131 ALARRLGCEFIEASAKTNVNVERAFYTLVRA 161
>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 = 90.2 bits (224), Expect = 8e-23
Identities = 56/211 (26%), Positives = 96/211 (45%), Gaps = 51/211 (24%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQE 71
+K+V++G GVGKS L +F ++ F + TI + T+ ++D + + I DTAGQE
Sbjct: 3 YKLVVVGGGGVGKSALTIQFIQSYFVTDYDPTIEDSY-TKQCEIDGQWARLDILDTAGQE 61
Query: 72 RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRY 131
+ A+ Y R G LLV+ + ++E V+++ + +LR
Sbjct: 62 EFSAMREQYMRTGEGFLLVFSVTDRGSFEEVDKFHTQ------------------ILR-- 101
Query: 132 YRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAK 191
++D + ++ LVGNK+DL H R V +E +
Sbjct: 102 ----------------------------VKDRDEFPMI--LVGNKADLEHQRQVSREEGQ 131
Query: 192 TFAERNNLSFIETSALDSTNVETAFQNILTA 222
A + + +IETSA D NV+ AF +++
Sbjct: 132 ELARQLKIPYIETSAKDRVNVDKAFHDLVRV 162
>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 = 90.6 bits (225), Expect = 1e-22
Identities = 56/209 (26%), Positives = 89/209 (42%), Gaps = 49/209 (23%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQV-DQKTIKAQIWDTAGQ 70
K+V++GD GK++L+ RF + F K TIG++F +R I + + Q+WD GQ
Sbjct: 1 IKIVVLGDGASGKTSLIRRFAQEGFGKSYKQTIGLDFFSRRITLPGSLNVTLQVWDIGGQ 60
Query: 71 ERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRR 130
+ + Y GA LVYDI ++EN+E WL
Sbjct: 61 QIGGKMLDKYIYGAQAVCLVYDITNSQSFENLEDWLSV---------------------- 98
Query: 131 YYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEA 190
++++ + ++ ++LVGNK+DL H R V A++
Sbjct: 99 --------------------------VKKVNEESETKPKMVLVGNKTDLEHNRQVTAEKH 132
Query: 191 KTFAERNNLSFIETSALDSTNVETAFQNI 219
FA+ N++ I SA V FQ I
Sbjct: 133 ARFAQENDMESIFVSAKTGDRVFLCFQRI 161
>gnl|CDD|197554 smart00174, RHO, Rho (Ras homology) subfamily of Ras-like small
GTPases. Members of this subfamily of Ras-like small
GTPases include Cdc42 and Rac, as well as Rho isoforms.
Length = 174
Score = 89.2 bits (222), Expect = 2e-22
Identities = 50/218 (22%), Positives = 85/218 (38%), Gaps = 67/218 (30%)
Query: 14 VVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQERY 73
+V++GD VGK+ LL +T N F + T+ ++ ++VD K ++ +WDTAGQE Y
Sbjct: 1 LVVVGDGAVGKTCLLIVYTTNAFPEDYVPTVFENYSA-DVEVDGKPVELGLWDTAGQEDY 59
Query: 74 RAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRYYR 133
+R LR L + D ++
Sbjct: 60 -----------------------------DR-LRPL-SYPDTDVF--------------- 73
Query: 134 GAVGALLVYDIAKHLTYENV-ERWLRELRDHADQNIVIMLVGNKSDLR---HLRAVPADE 189
L+ + + ++ENV E+W E++ N+ I+LVG K DLR + +
Sbjct: 74 -----LICFSVDSPASFENVKEKWYPEVKHFC-PNVPIILVGTKLDLRNDKSTLEELSKK 127
Query: 190 AKTFAERNN----------LSFIETSALDSTNVETAFQ 217
+ + ++E SAL V F+
Sbjct: 128 KQEPVTYEQGQALAKRIGAVKYLECSALTQEGVREVFE 165
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 89.0 bits (221), Expect = 6e-22
Identities = 40/112 (35%), Positives = 63/112 (56%), Gaps = 1/112 (0%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQE 71
FK++L+GD GVGK+ + R EF + T+GVE + I +WDTAGQE
Sbjct: 10 FKLILVGDGGVGKTTFVKRHLTGEFEKKYIPTLGVEVHPLKFYTNCGPICFNVWDTAGQE 69
Query: 72 RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVG 123
++ + YY A++++D+ +TY+NV W R++ + NI I+LVG
Sbjct: 70 KFGGLRDGYYIKGQCAIIMFDVTSRITYKNVPNWHRDIVRVCE-NIPIVLVG 120
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 89.0 bits (221), Expect = 7e-22
Identities = 41/112 (36%), Positives = 62/112 (55%), Gaps = 1/112 (0%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQE 71
FK+V++GD G GK+ + R EF + + TIGVE + I+ WDTAGQE
Sbjct: 14 FKLVIVGDGGTGKTTFVKRHLTGEFEKKYEPTIGVEVHPLDFFTNCGKIRFYCWDTAGQE 73
Query: 72 RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVG 123
++ + YY A++++D+ LTY+NV W R+L +NI I+L G
Sbjct: 74 KFGGLRDGYYIHGQCAIIMFDVTARLTYKNVPTWHRDLC-RVCENIPIVLCG 124
>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 = 86.9 bits (216), Expect = 2e-21
Identities = 56/208 (26%), Positives = 87/208 (41%), Gaps = 51/208 (24%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
K+ ++G VGKS+L +F F TI F ++ I + +I DTAGQ+
Sbjct: 3 KIAVLGSRSVGKSSLTVQFVEGHFVESYYPTIENTF-SKIITYKGQEYHLEIVDTAGQDE 61
Query: 73 YRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRYY 132
Y + Y G G +LVY + ++E V+
Sbjct: 62 YSILPQKYSIGIHGYILVYSVTSRKSFEVVK----------------------------- 92
Query: 133 RGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAKT 192
++YD L +++ I+LVGNKSDL R V A+E K
Sbjct: 93 -------VIYDKI--------------LDMLGKESVPIVLVGNKSDLHMERQVSAEEGKK 131
Query: 193 FAERNNLSFIETSALDSTNVETAFQNIL 220
AE +F+E+SA ++ NVE AF+ ++
Sbjct: 132 LAESWGAAFLESSAKENENVEEAFELLI 159
>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 = 86.6 bits (215), Expect = 4e-21
Identities = 57/224 (25%), Positives = 93/224 (41%), Gaps = 68/224 (30%)
Query: 9 DYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQV-DQKTIKAQIWDT 67
D K+V++GD G GK+ LL + + F E T+ E ++QV + K I+ +WDT
Sbjct: 1 DLKVKIVVVGDGGCGKTCLLMVYAQGSFPEEYVPTV-FENYVTTLQVPNGKIIELALWDT 59
Query: 68 AGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSL 127
AGQE YD + L+Y +V +++
Sbjct: 60 AGQED------------------YDRLRPLSYPDV-------------DVI--------- 79
Query: 128 LRRYYRGAVGALLVYDIAKHLTYENV-ERWLRELRDHADQNIVIMLVGNKSDLR------ 180
L+ Y + + +NV ++W E+ H I+LVG K+DLR
Sbjct: 80 -----------LICYSVDNPTSLDNVEDKWYPEVN-HFCPGTPIVLVGLKTDLRKDKNSV 127
Query: 181 -HLRA-----VPADEAKTFAER-NNLSFIETSALDSTNVETAFQ 217
LRA V ++ ++ A+ +++IE SA NV+ F
Sbjct: 128 SKLRAQGLEPVTPEQGESVAKSIGAVAYIECSAKLMENVDEVFD 171
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 86.0 bits (212), Expect = 4e-21
Identities = 51/186 (27%), Positives = 88/186 (47%), Gaps = 51/186 (27%)
Query: 34 NEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQERYRAITSAYYRGAVGALLVYDI 93
+ F+ +STIG++F ++++ +D+ ++ Q+WDTAGQER+R
Sbjct: 3 DTFDNNYQSTIGIDFLSKTLYLDEGPVRLQLWDTAGQERFR------------------- 43
Query: 94 AKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRYYRGAVGALLVYDIAKHLTYENV 153
SL+ Y R + A++VYDI ++EN
Sbjct: 44 --------------------------------SLIPSYIRDSAAAIVVYDITNRQSFENT 71
Query: 154 ERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAKTFAERNNLSFIETSALDSTNVE 213
+W++++ + ++++I LVGNK+DL LR V +E A+ N F ETSA N++
Sbjct: 72 TKWIQDILNERGKDVIIALVGNKTDLGDLRKVTYEEGMQKAQEYNTMFHETSAKAGHNIK 131
Query: 214 TAFQNI 219
F+ I
Sbjct: 132 VLFKKI 137
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 83.4 bits (206), Expect = 6e-20
Identities = 57/209 (27%), Positives = 85/209 (40%), Gaps = 51/209 (24%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQE 71
+K+V++G GVGKS L +F +N F E TI + + +D++T I DTAGQE
Sbjct: 6 YKLVVVGGGGVGKSALTIQFIQNHFIDEYDPTIEDSY-RKQCVIDEETCLLDILDTAGQE 64
Query: 72 RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRY 131
Y A+ Y R G L VY I ++E + + ++ D++ V M+
Sbjct: 65 EYSAMRDQYMRTGQGFLCVYSITSRSSFEEIASFREQILRVKDKDRVPMI---------- 114
Query: 132 YRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAK 191
LVGNK DL R V E +
Sbjct: 115 ----------------------------------------LVGNKCDLDSERQVSTGEGQ 134
Query: 192 TFAERNNLSFIETSALDSTNVETAFQNIL 220
A+ + F+ETSA NV+ AF ++
Sbjct: 135 ELAKSFGIPFLETSAKQRVNVDEAFYELV 163
>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 = 81.0 bits (200), Expect = 3e-19
Identities = 48/211 (22%), Positives = 81/211 (38%), Gaps = 54/211 (25%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRN--EFNLESKSTIGVEFATRSIQVDQ--KTIKAQIWDTA 68
+ ++GD VGKS L+ F + F T G + +++ V +++ I+D+A
Sbjct: 2 QCAVVGDPAVGKSALVQMFHSDGATFQKNYTMTTGCDLVVKTVPVPDTSDSVELFIFDSA 61
Query: 69 GQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLL 128
GQE + + + +VYD+ +++ N RW+ +R H+ + G
Sbjct: 62 GQELFSDMVENVWEQPAVVCVVYDVTNEVSFNNCSRWINRVRTHSHG---LHTPG----- 113
Query: 129 RRYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPAD 188
+LVGNK DL R V A
Sbjct: 114 ------------------------------------------VLVGNKCDLTDRREVDAA 131
Query: 189 EAKTFAERNNLSFIETSALDSTNVETAFQNI 219
+A+ A+ N L F ETSA + E F ++
Sbjct: 132 QAQALAQANTLKFYETSAKEGVGYEAPFLSL 162
>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 = 80.7 bits (199), Expect = 3e-19
Identities = 56/208 (26%), Positives = 85/208 (40%), Gaps = 51/208 (24%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQE 71
+KVV++G GVGKS L +F F + TI +F + I+VD +I DTAG E
Sbjct: 2 YKVVVLGSGGVGKSALTVQFVSGTFIEKYDPTIE-DFYRKEIEVDSSPSVLEILDTAGTE 60
Query: 72 RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRY 131
++ ++ Y + G ++VY + T++++ + +RD IV
Sbjct: 61 QFASMRDLYIKNGQGFIVVYSLVNQQTFQDI----KPMRD----QIV------------- 99
Query: 132 YRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAK 191
R + + I+LVGNK DL R V + E +
Sbjct: 100 -----------------------------RVKGYEKVPIILVGNKVDLESEREVSSAEGR 130
Query: 192 TFAERNNLSFIETSALDSTNVETAFQNI 219
AE F+ETSA T V F I
Sbjct: 131 ALAEEWGCPFMETSAKSKTMVNELFAEI 158
>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 = 79.4 bits (196), Expect = 3e-19
Identities = 42/114 (36%), Positives = 56/114 (49%), Gaps = 4/114 (3%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
KVV+IGD G GKS+LLS+ EF E G A +++VD T IWD G+E
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREE 60
Query: 73 YRAITSAYYRGAVGALLVYDIAKHLTYENVER---WLRELRDHADQNIVIMLVG 123
+ + + A LLVYD+ + V R WL LR I ++LVG
Sbjct: 61 LKFEHIIFMKWADAILLVYDLTDRESLNEVSRLIAWLPNLRK-LGGKIPVILVG 113
>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 = 80.4 bits (199), Expect = 4e-19
Identities = 53/211 (25%), Positives = 83/211 (39%), Gaps = 53/211 (25%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
K+ ++G SGVGKS L RF F E + + + +R + +D + + +I DT GQ++
Sbjct: 1 KIAVLGASGVGKSALTVRFLTKRFIGEYEPNLESLY-SRQVTIDGEQVSLEIQDTPGQQQ 59
Query: 73 YRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRYY 132
P L R
Sbjct: 60 NED-------------------------------------------------PESLERSL 70
Query: 133 RGAVGALLVYDIAKHLTYENVERWLRELRDHA--DQNIVIMLVGNKSDLRHLRAVPADEA 190
R A G +LVY I +++ V + L+ +R+ D I ++LVGNK+DL H R V +E
Sbjct: 71 RWADGFVLVYSITDRSSFDVVSQLLQLIREIKKRDGEIPVILVGNKADLLHSRQVSTEEG 130
Query: 191 KTFAERNNLSFIETSA-LDSTNVETAFQNIL 220
+ A F E SA + V+ F +
Sbjct: 131 QKLALELGCLFFEVSAAENYLEVQNVFHELC 161
>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 = 80.1 bits (198), Expect = 7e-19
Identities = 54/206 (26%), Positives = 87/206 (42%), Gaps = 43/206 (20%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
K VL+GD VGK++L+ +T N + E T F+ + VD K ++ Q+ DTAGQ+
Sbjct: 2 KCVLVGDGAVGKTSLIVSYTTNGYPTEYVPTAFDNFSVV-VLVDGKPVRLQLCDTAGQDE 60
Query: 73 YRAITSAYYRGAVGALLVYDIAKHLTYENV-ERWLRELRDHADQNIVIMLVGPPSLLRRY 131
+ + Y LL + + +++N+ E+W+ E+R H + +I LVG + LR
Sbjct: 61 FDKLRPLCYPDTDVFLLCFSVVNPSSFQNISEKWIPEIRKHNPKAPII-LVGTQADLRT- 118
Query: 132 YRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAK 191
D N++I L + V AK
Sbjct: 119 ---------------------------------DVNVLIQLARYGE-----KPVSQSRAK 140
Query: 192 TFAER-NNLSFIETSALDSTNVETAF 216
AE+ +IE SAL N++ F
Sbjct: 141 ALAEKIGACEYIECSALTQKNLKEVF 166
>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 = 79.4 bits (196), Expect = 1e-18
Identities = 56/210 (26%), Positives = 90/210 (42%), Gaps = 52/210 (24%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQE 71
+K+V++G GVGKS L +F +N F TI + + +++D + +I DTAG E
Sbjct: 2 YKIVVLGAGGVGKSALTVQFVQNVFIESYDPTIEDSYRKQ-VEIDGRQCDLEILDTAGTE 60
Query: 72 RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRY 131
++ A+ Y + G LLVY + T E L ELR+
Sbjct: 61 QFTAMRELYIKSGQGFLLVYSV----TSEASLNELGELREQV------------------ 98
Query: 132 YRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAK 191
LR N+ ++LVGNK+DL R V ++
Sbjct: 99 ----------------------------LRIKDSDNVPMVLVGNKADLEDDRQVSREDGV 130
Query: 192 TFAER-NNLSFIETSALDSTNVETAFQNIL 220
+ +++ N+ F ETSA TNV+ F +++
Sbjct: 131 SLSQQWGNVPFYETSARKRTNVDEVFIDLV 160
>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 = 76.3 bits (188), Expect = 2e-17
Identities = 57/205 (27%), Positives = 84/205 (40%), Gaps = 52/205 (25%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQE 71
+K+V++G GVGKS L + +N F E TI + + + +D +T I DTAGQE
Sbjct: 2 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSY-RKQVVIDGETCLLDILDTAGQE 60
Query: 72 RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRY 131
Y A+ Y R G L V+ I ++E++
Sbjct: 61 EYSAMRDQYMRTGEGFLCVFAINSRKSFEDI----------------------------- 91
Query: 132 YRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAK 191
H E ++R ++D D +V LVGNK DL R V + +
Sbjct: 92 ---------------HTYREQIKR----VKDSDDVPMV--LVGNKCDLAA-RTVSTRQGQ 129
Query: 192 TFAERNNLSFIETSALDSTNVETAF 216
A+ + +IETSA VE AF
Sbjct: 130 DLAKSYGIPYIETSAKTRQGVEEAF 154
>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 = 76.4 bits (188), Expect = 2e-17
Identities = 55/209 (26%), Positives = 81/209 (38%), Gaps = 49/209 (23%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQE 71
++VV+ G GVGKS+L+ RF + F TI + + I + QI DT G
Sbjct: 2 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTY-RQVISCSKSICTLQITDTTGSH 60
Query: 72 RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRY 131
++ A+ +LVY I + E EL+
Sbjct: 61 QFPAMQRLSISKGHAFILVYSITSKQSLE-------ELKP-------------------- 93
Query: 132 YRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAK 191
YE + E++ + + I IMLVGNK D R V + E
Sbjct: 94 -----------------IYELI----CEIKGNNLEKIPIMLVGNKCDESPSREVSSSEGA 132
Query: 192 TFAERNNLSFIETSALDSTNVETAFQNIL 220
A N +F+ETSA + NV+ FQ +L
Sbjct: 133 ALARTWNCAFMETSAKTNHNVQELFQELL 161
>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 = 76.6 bits (188), Expect = 2e-17
Identities = 36/107 (33%), Positives = 59/107 (55%), Gaps = 1/107 (0%)
Query: 17 IGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQERYRAI 76
+GD G GK+ + R EF + +T+GVE ++ I+ +WDTAGQE++ +
Sbjct: 1 VGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIRFNVWDTAGQEKFGGL 60
Query: 77 TSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVG 123
YY A++++D+ +TY+NV W R+L +NI I+L G
Sbjct: 61 RDGYYIQGQCAIIMFDVTARVTYKNVPNWHRDLV-RVCENIPIVLCG 106
>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 = 75.9 bits (187), Expect = 3e-17
Identities = 34/111 (30%), Positives = 59/111 (53%), Gaps = 1/111 (0%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
K+ L+GD+ +GK++L+ ++ EF+ E T+GV F ++I + I IWD GQ
Sbjct: 2 KIGLLGDAQIGKTSLMVKYVEGEFDEEYIQTLGVNFMEKTISIRGTEITFSIWDLGGQRE 61
Query: 73 YRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVG 123
+ + + AV L ++D+ + T +++ W R+ R I I LVG
Sbjct: 62 FINMLPLVCKDAVAILFMFDLTRKSTLNSIKEWYRQARGFNKTAIPI-LVG 111
>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 = 74.0 bits (182), Expect = 9e-17
Identities = 47/212 (22%), Positives = 72/212 (33%), Gaps = 56/212 (26%)
Query: 15 VLIGDSGVGKSNLLSRFTRNEFNLESK---STIGVEFATRSIQVDQKTIKAQIWDTAGQE 71
V++G GVGKS+LL+ E S +T + ++D+ +K + DT G +
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDV--YVKELDKGKVKLVLVDTPGLD 58
Query: 72 RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRY 131
+ + G L R
Sbjct: 59 EFGGL----------------------------------------------GREELARLL 72
Query: 132 YRGAVGALLVYDIAKHLTYENVER-WLRELRDHADQNIVIMLVGNKSDLR-HLRAVPADE 189
RGA LLV D + E+ + LR LR I I+LVGNK DL
Sbjct: 73 LRGADLILLVVDSTDRESEEDAKLLILRRLRKE---GIPIILVGNKIDLLEEREVEELLR 129
Query: 190 AKTFAERNNLSFIETSALDSTNVETAFQNILT 221
+ A+ + E SA V+ F+ ++
Sbjct: 130 LEELAKILGVPVFEVSAKTGEGVDELFEKLIE 161
>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 = 71.8 bits (176), Expect = 9e-16
Identities = 45/118 (38%), Positives = 66/118 (55%), Gaps = 3/118 (2%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
K V +GD VGK+ +L +T N F + T+ F+ ++ VD T+ +WDTAGQE
Sbjct: 3 KCVTVGDGAVGKTCMLISYTSNTFPTDYVPTVFDNFSA-NVVVDGNTVNLGLWDTAGQED 61
Query: 73 YRAITSAYYRGAVGALLVYDIAKHLTYENV-ERWLRELRDHADQNIVIMLVGPPSLLR 129
Y + YRGA LL + + +YENV ++W+ ELR +A + I+LVG LR
Sbjct: 62 YNRLRPLSYRGADVFLLAFSLISKASYENVLKKWIPELRHYA-PGVPIVLVGTKLDLR 118
>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 = 70.7 bits (173), Expect = 2e-15
Identities = 54/210 (25%), Positives = 89/210 (42%), Gaps = 52/210 (24%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQE 71
+K+V++G GVGKS L +F + F + TI + + I+VD + +I DTAG E
Sbjct: 2 YKLVVLGSGGVGKSALTVQFVQGIFVDKYDPTIE-DSYRKQIEVDCQQCMLEILDTAGTE 60
Query: 72 RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRY 131
++ A+ Y + G LVY I ++ + L++LR+
Sbjct: 61 QFTAMRDLYIKNGQGFALVYSITAQQSFND----LQDLREQI------------------ 98
Query: 132 YRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAK 191
LR +++ ++LVGNK DL R V +E +
Sbjct: 99 ----------------------------LRVKDTEDVPMILVGNKCDLEDERVVSKEEGQ 130
Query: 192 TFAER-NNLSFIETSALDSTNVETAFQNIL 220
A + N F+ETSA NV+ F +++
Sbjct: 131 NLARQWGNCPFLETSAKSKINVDEIFYDLV 160
>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 = 71.5 bits (175), Expect = 3e-15
Identities = 59/212 (27%), Positives = 95/212 (44%), Gaps = 33/212 (15%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
KVVL+GD VGK++LL R+ F ++ ST+G F + Q I IWDTAG+E+
Sbjct: 2 KVVLLGDMNVGKTSLLHRYMERRFK-DTVSTVGGAFYLK--QWGPYNI--SIWDTAGREQ 56
Query: 73 YRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRYY 132
+ + S Y RGA +L YD++ + E +E L D A+++ + +VG L
Sbjct: 57 FHGLGSMYCRGAAAVILTYDVSNVQSLEELEDRFLGLTDTANEDCLFAVVGNKLDLTEEG 116
Query: 133 RGAV-----GALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPA 187
A G + + + +T E+ + + + + + ML + PA
Sbjct: 117 ALAGQEKDAGDRVSPEDQRQVTLEDAKAFYKRINKY------KMLDED--------LSPA 162
Query: 188 DEAKTFAERNNLSFIETSALDSTNVETAFQNI 219
E F ETSA NV+ F+ +
Sbjct: 163 AEKMCF---------ETSAKTGYNVDELFEYL 185
>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 = 69.9 bits (171), Expect = 4e-15
Identities = 52/209 (24%), Positives = 89/209 (42%), Gaps = 51/209 (24%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQE 71
+K+V++G GVGKS L +F + F + TI + + ++VD + +I DTAG E
Sbjct: 2 YKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSY-RKQVEVDGQQCMLEILDTAGTE 60
Query: 72 RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRY 131
++ A+ Y + G +LVY I T+ + L++LR+
Sbjct: 61 QFTAMRDLYMKNGQGFVLVYSITAQSTFND----LQDLREQI------------------ 98
Query: 132 YRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAK 191
LR +++ ++LVGNK DL R V ++ +
Sbjct: 99 ----------------------------LRVKDTEDVPMILVGNKCDLEDERVVGKEQGQ 130
Query: 192 TFAERNNLSFIETSALDSTNVETAFQNIL 220
A + +F+ETSA NV F +++
Sbjct: 131 NLARQWGCAFLETSAKAKINVNEIFYDLV 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 = 69.4 bits (170), Expect = 8e-15
Identities = 40/118 (33%), Positives = 66/118 (55%), Gaps = 3/118 (2%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
K+VL+GDS GK+ LL F ++ F T+ E T S +VD++ I+ +WDT+G
Sbjct: 3 KIVLVGDSQCGKTALLQVFAKDSFPENYVPTV-FENYTASFEVDKQRIELSLWDTSGSPY 61
Query: 73 YRAITSAYYRGAVGALLVYDIAKHLTYENV-ERWLRELRDHADQNIVIMLVGPPSLLR 129
Y + Y + L+ +DI++ T ++V ++W E+R+ N ++LVG S LR
Sbjct: 62 YDNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEVREFC-PNTPVLLVGCKSDLR 118
>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 = 69.3 bits (169), Expect = 1e-14
Identities = 42/118 (35%), Positives = 64/118 (54%), Gaps = 3/118 (2%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
K V++GD VGK+ LL +T N F E T+ ++ ++ VD +T+ +WDTAGQE
Sbjct: 5 KCVVVGDGAVGKTCLLICYTTNAFPKEYIPTVFDNYSAQTA-VDGRTVSLNLWDTAGQEE 63
Query: 73 YRAITSAYYRGAVGALLVYDIAKHLTYENVE-RWLRELRDHADQNIVIMLVGPPSLLR 129
Y + + Y ++ + IA +YENV +W E+ H N+ I+LVG LR
Sbjct: 64 YDRLRTLSYPQTNVFIICFSIASPSSYENVRHKWHPEVCHHC-PNVPILLVGTKKDLR 120
>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 = 69.1 bits (169), Expect = 1e-14
Identities = 41/118 (34%), Positives = 62/118 (52%), Gaps = 3/118 (2%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
KVV++GD GK++LL+ FTR F + T+ E I VD ++ +WDTAGQE
Sbjct: 2 KVVVLGDGACGKTSLLNVFTRGYFPQVYEPTV-FENYIHDIFVDGLAVELSLWDTAGQEE 60
Query: 73 YRAITSAYYRGAVGALLVYDIAKHLTYENVE-RWLRELRDHADQNIVIMLVGPPSLLR 129
+ + S Y +L + + + ENVE +WL E+R H + ++LV LR
Sbjct: 61 FDRLRSLSYADTHVIMLCFSVDNPDSLENVESKWLAEIRHHC-PGVKLVLVALKCDLR 117
>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 = 69.0 bits (169), Expect = 2e-14
Identities = 53/209 (25%), Positives = 82/209 (39%), Gaps = 50/209 (23%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQE 71
++VVL+GDSGVGKS+L + FT + + G + R++ VD + ++D QE
Sbjct: 1 YRVVLLGDSGVGKSSLANIFTAGVYEDSAYEASGDDTYERTVSVDGEEATLVVYDHWEQE 60
Query: 72 RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRY 131
+ + + ++VY + ++E LR
Sbjct: 61 DGMWLEDSCMQVGDAYVIVYSVTDRSSFEKASE-----------------------LRIQ 97
Query: 132 YRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAK 191
LR R ++I I+LVGNKSDL R V E +
Sbjct: 98 -------------------------LRRARQA--EDIPIILVGNKSDLVRSREVSVQEGR 130
Query: 192 TFAERNNLSFIETSALDSTNVETAFQNIL 220
A + FIETSA NV+ F+ I+
Sbjct: 131 ACAVVFDCKFIETSAALQHNVDELFEGIV 159
>gnl|CDD|206663 cd01871, Rac1_like, Ras-related C3 botulinum toxin substrate 1 (rho
family, small GTP binding protein Rac1)-like consists of
Rac1, Rac2 and Rac3. The Rac1-like subfamily consists
of Rac1, Rac2, and Rac3 proteins, plus the splice
variant Rac1b that contains a 19-residue insertion near
switch II relative to Rac1. While Rac1 is ubiquitously
expressed, Rac2 and Rac3 are largely restricted to
hematopoietic and neural tissues respectively. Rac1
stimulates the formation of actin lamellipodia and
membrane ruffles. It also plays a role in cell-matrix
adhesion and cell anoikis. In intestinal epithelial
cells, Rac1 is an important regulator of migration and
mediates apoptosis. Rac1 is also essential for
RhoA-regulated actin stress fiber and focal adhesion
complex formation. In leukocytes, Rac1 and Rac2 have
distinct roles in regulating cell morphology, migration,
and invasion, but are not essential for macrophage
migration or chemotaxis. Rac3 has biochemical properties
that are closely related to Rac1, such as effector
interaction, nucleotide binding, and hydrolysis; Rac2
has a slower nucleotide association and is more
efficiently activated by the RacGEF Tiam1. Both Rac1 and
Rac3 have been implicated in the regulation of cell
migration and invasion in human metastatic breast
cancer. Most Rho proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Rho proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 174
Score = 67.5 bits (165), Expect = 4e-14
Identities = 59/218 (27%), Positives = 85/218 (38%), Gaps = 67/218 (30%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
K V++GD VGK+ LL +T N F E T+ ++ ++ VD K + +WDTAGQE
Sbjct: 3 KCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSA-NVMVDGKPVNLGLWDTAGQED 61
Query: 73 YRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRYY 132
YD + L+Y + +L I LV P S
Sbjct: 62 ------------------YDRLRPLSYPQTDVFL----------ICFSLVSPAS------ 87
Query: 133 RGAVGALLVYDIAKHLTYENVE-RWLRELRDHADQNIVIMLVGNKSDLRH---------- 181
+ENV +W E+R H N I+LVG K DLR
Sbjct: 88 -----------------FENVRAKWYPEVRHHC-PNTPIILVGTKLDLRDDKDTIEKLKE 129
Query: 182 --LRAVPADEAKTFA-ERNNLSFIETSALDSTNVETAF 216
L + + A E + ++E SAL ++T F
Sbjct: 130 KKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVF 167
>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 = 65.8 bits (161), Expect = 1e-13
Identities = 38/118 (32%), Positives = 59/118 (50%), Gaps = 14/118 (11%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQ-KTIKAQIWDTAGQE 71
K++L+G GVGK++L + +F+ + ST G+ I + K I+ +WD GQE
Sbjct: 3 KLMLVGQGGVGKTSLCKQLIGEKFDGDESSTHGINVQDWKIPAPERKKIRLNVWDFGGQE 62
Query: 72 RYRA-----ITS-AYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVG 123
Y A +TS + Y LLV+D+ V WLR+++ + VI LVG
Sbjct: 63 IYHATHQFFLTSRSLY------LLVFDLRTGDEVSRVPYWLRQIKAFGGVSPVI-LVG 113
Score = 35.0 bits (81), Expect = 0.013
Identities = 15/75 (20%), Positives = 24/75 (32%), Gaps = 1/75 (1%)
Query: 139 LLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAKTFAERNN 198
LLV+D+ V WLR+++ + VI LVG D +
Sbjct: 79 LLVFDLRTGDEVSRVPYWLRQIKAFGGVSPVI-LVGTHIDESCDEDILKKALNKKFPAII 137
Query: 199 LSFIETSALDSTNVE 213
S + +
Sbjct: 138 NDIHFVSCKNGKGIA 152
>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 = 63.1 bits (153), Expect = 2e-12
Identities = 37/118 (31%), Positives = 65/118 (55%), Gaps = 3/118 (2%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
K+V++GDS GK+ LL F ++ F T+ E T S ++D + I+ +WDT+G
Sbjct: 7 KIVVVGDSQCGKTALLHVFAKDCFPENYVPTV-FENYTASFEIDTQRIELSLWDTSGSPY 65
Query: 73 YRAITSAYYRGAVGALLVYDIAKHLTYENV-ERWLRELRDHADQNIVIMLVGPPSLLR 129
Y + Y + L+ +DI++ T ++V ++W E+++ N ++LVG S LR
Sbjct: 66 YDNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEIQEFC-PNTKMLLVGCKSDLR 122
>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 = 62.9 bits (153), Expect = 2e-12
Identities = 42/118 (35%), Positives = 64/118 (54%), Gaps = 3/118 (2%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
K+V++GD GK++LL FT EF E T+ + T +VD K ++ +WDTAGQE
Sbjct: 3 KLVIVGDGACGKTSLLYVFTLGEFPEEYHPTVFENYVT-DCRVDGKPVQLALWDTAGQEE 61
Query: 73 YRAITSAYYRGAVGALLVYDIAKHLTYENVE-RWLRELRDHADQNIVIMLVGPPSLLR 129
Y + Y A L+ + I + ENV +W+ E+R + N+ ++LVG LR
Sbjct: 62 YERLRPLSYSKAHVILIGFAIDTPDSLENVRTKWIEEVRRYCP-NVPVILVGLKKDLR 118
>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 = 62.1 bits (151), Expect = 4e-12
Identities = 56/219 (25%), Positives = 89/219 (40%), Gaps = 67/219 (30%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
K+V++GD GK+ LL F++++F T+ E I+VD K ++ +WDTAGQE
Sbjct: 3 KLVIVGDGACGKTCLLIVFSKDQFPEVYVPTV-FENYVADIEVDGKQVELALWDTAGQED 61
Query: 73 YRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRYY 132
YD + L+Y + + VI
Sbjct: 62 ------------------YDRLRPLSYPDTD--------------VI------------- 76
Query: 133 RGAVGALLVYDIAKHLTYENV-ERWLRELRDHADQNIVIMLVGNKSDLRH---------- 181
L+ + I + EN+ E+W E++ H N+ I+LVGNK DLR+
Sbjct: 77 ------LMCFSIDSPDSLENIPEKWTPEVK-HFCPNVPIILVGNKKDLRNDEHTIRELAK 129
Query: 182 --LRAVPADEAKTFAER-NNLSFIETSALDSTNVETAFQ 217
V +E + AE+ ++E SA V F+
Sbjct: 130 MKQEPVKPEEGRAMAEKIGAFGYLECSAKTKEGVREVFE 168
>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 = 60.6 bits (147), Expect = 1e-11
Identities = 49/205 (23%), Positives = 80/205 (39%), Gaps = 51/205 (24%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQE 71
+K+V++G GVGKS + +F + F TI + T+ ++D + I DTAGQ
Sbjct: 3 YKIVMLGAGGVGKSAVTMQFISHSFPDYHDPTIEDAYKTQ-ARIDNEPALLDILDTAGQA 61
Query: 72 RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRY 131
+ A+ Y R G ++ Y + +++ E ++
Sbjct: 62 EFTAMRDQYMRCGEGFIICYSVTDRHSFQEA----SEFKE-------------------- 97
Query: 132 YRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAK 191
L+ + LT + I ++LVGNK DL R V +E +
Sbjct: 98 --------LITRV--RLTED----------------IPLVLVGNKVDLEQQRQVTTEEGR 131
Query: 192 TFAERNNLSFIETSALDSTNVETAF 216
A N F ETSA ++ AF
Sbjct: 132 NLAREFNCPFFETSAALRFYIDDAF 156
>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 = 55.4 bits (133), Expect = 1e-09
Identities = 37/119 (31%), Positives = 61/119 (51%), Gaps = 3/119 (2%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQE 71
K V++GD VGK+ LL + + F E T+ +A S+ V K ++DTAGQE
Sbjct: 1 LKCVVVGDGAVGKTCLLMSYANDAFPEEYVPTVFDHYAV-SVTVGGKQYLLGLYDTAGQE 59
Query: 72 RYRAITSAYYRGAVGALLVYDIAKHLTYENV-ERWLRELRDHADQNIVIMLVGPPSLLR 129
Y + Y L+ + + +++NV E W+ EL+++A N+ +L+G LR
Sbjct: 60 DYDRLRPLSYPMTDVFLICFSVVNPASFQNVKEEWVPELKEYA-PNVPYLLIGTQIDLR 117
>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 = 55.7 bits (134), Expect = 1e-09
Identities = 29/105 (27%), Positives = 51/105 (48%), Gaps = 9/105 (8%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQV-----DQKTIKAQIWDT 67
KV+++GDSGVGKS+L+ +N+ T+G R ++KT ++WD
Sbjct: 2 KVLVLGDSGVGKSSLVHLLCKNQVLGNPSWTVGCSVDVRHHTYGEGTPEEKTFYVELWDV 61
Query: 68 AGQ----ERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRE 108
G E ++ + +Y G + V+D+ + +N+ RW E
Sbjct: 62 GGSVGSAESVKSTRAVFYNQINGIIFVHDLTNKKSSQNLYRWSLE 106
>gnl|CDD|177661 PLN00023, PLN00023, GTP-binding protein; Provisional.
Length = 334
Score = 56.0 bits (135), Expect = 2e-09
Identities = 30/110 (27%), Positives = 58/110 (52%), Gaps = 13/110 (11%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIG-------VEFAT-----RSIQVD-QKT 59
+V+++GDSGVGKS+L+ + TIG + + + SI+ D ++
Sbjct: 23 RVLVVGDSGVGKSSLVHLIVKGSSIARPPQTIGCTVGVKHITYGSPGSSSNSIKGDSERD 82
Query: 60 IKAQIWDTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLREL 109
++WD +G ERY+ S +Y G + V+D+++ T ++++W E+
Sbjct: 83 FFVELWDVSGHERYKDCRSLFYSQINGVIFVHDLSQRRTKTSLQKWASEV 132
>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 = 54.5 bits (131), Expect = 2e-09
Identities = 43/150 (28%), Positives = 72/150 (48%), Gaps = 5/150 (3%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
K V++GD VGK+ LL +T N+F E T+ +A ++ + + ++DTAGQE
Sbjct: 3 KCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAV-TVMIGGEPYTLGLFDTAGQED 61
Query: 73 YRAITSAYYRGAVGALLVYDIAKHLTYENV-ERWLRELRDHADQNIVIMLVGPPSLLRRY 131
Y + Y L+ + + ++ENV E+W+ E+ H +LVG LR
Sbjct: 62 YDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHC-PKTPFLLVGTQIDLRD- 119
Query: 132 YRGAVGALLVYDIAKHLTYENVERWLRELR 161
+ L + K +T E E+ R+L+
Sbjct: 120 -DPSTIEKLAKNKQKPITPETGEKLARDLK 148
>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 = 53.7 bits (129), Expect = 6e-09
Identities = 49/209 (23%), Positives = 84/209 (40%), Gaps = 52/209 (24%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
++V +G +GVGK+ L+ RF + F + + T+ E ++ +V + I DT+G
Sbjct: 1 RLVFMGAAGVGKTALIQRFLYDTFEPKHRRTVE-ELHSKEYEVAGVKVTIDILDTSGSYS 59
Query: 73 YRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRYY 132
+ A+ + LVY + ++E V+R LR+
Sbjct: 60 FPAMRKLSIQNGDAFALVYSVDDPESFEEVKR----LREE-------------------- 95
Query: 133 RGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAKT 192
+ E+++ IV+ VGNK D R V A +A +
Sbjct: 96 ------------------------ILEVKEDKFVPIVV--VGNKIDSLAERQVEAADALS 129
Query: 193 FAERN-NLSFIETSALDSTNVETAFQNIL 220
E + N F+E SA D+ NV F+ +L
Sbjct: 130 TVELDWNNGFVEASAKDNENVTEVFKELL 158
>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 = 52.4 bits (126), Expect = 2e-08
Identities = 45/212 (21%), Positives = 87/212 (41%), Gaps = 46/212 (21%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQE 71
+++V++G S VGK+ ++SRF F + TI +F + + + + I DT+G
Sbjct: 1 YRMVVLGASKVGKTAIVSRFLGGRFEEQYTPTIE-DFHRKLYSIRGEVYQLDILDTSGNH 59
Query: 72 RYRAITS-AYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRR 130
+ A+ + G V +LV+ + ++E V R ++ +
Sbjct: 60 PFPAMRRLSILTGDV-FILVFSLDNRESFEEVCRLREQILE------------------- 99
Query: 131 YYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEA 190
K+ T ENV+ I +++ GNK+D R V DE
Sbjct: 100 ----------TKSCLKNKTKENVK-------------IPMVICGNKADRDFPREVQRDEV 136
Query: 191 KTF-AERNNLSFIETSALDSTNVETAFQNILT 221
+ N ++ E SA ++N++ F+ + +
Sbjct: 137 EQLVGGDENCAYFEVSAKKNSNLDEMFRALFS 168
>gnl|CDD|206644 cd00878, Arf_Arl, ADP-ribosylation factor(Arf)/Arf-like (Arl) small
GTPases. Arf (ADP-ribosylation factor)/Arl (Arf-like)
small GTPases. Arf proteins are activators of
phospholipase D isoforms. Unlike Ras proteins they lack
cysteine residues at their C-termini and therefore are
unlikely to be prenylated. Arfs are N-terminally
myristoylated. Members of the Arf family are regulators
of vesicle formation in intracellular traffic that
interact reversibly with membranes of the secretory and
endocytic compartments in a GTP-dependent manner. They
depart from other small GTP-binding proteins by a unique
structural device, interswitch toggle, that implements
front-back communication from N-terminus to the
nucleotide binding site. Arf-like (Arl) proteins are
close relatives of the Arf, but only Arl1 has been shown
to function in membrane traffic like the Arf proteins.
Arl2 has an unrelated function in the folding of native
tubulin, and Arl4 may function in the nucleus. Most
other Arf family proteins are so far relatively poorly
characterized. Thus, despite their significant sequence
homologies, Arf family proteins may regulate unrelated
functions.
Length = 158
Score = 50.7 bits (122), Expect = 3e-08
Identities = 26/110 (23%), Positives = 51/110 (46%), Gaps = 5/110 (4%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
+++++G G GK+ +L + E + TIG F +++ K +K +WD GQ++
Sbjct: 1 RILMLGLDGAGKTTILYKLKLGEVV-TTIPTIG--FNVETVEY--KNVKFTVWDVGGQDK 55
Query: 73 YRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLV 122
R + YY G + V D + E + L +L + + +L+
Sbjct: 56 IRPLWKHYYENTDGLIFVVDSSDRERIEEAKNELHKLLNEEELKGAPLLI 105
>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 = 51.6 bits (123), Expect = 4e-08
Identities = 33/112 (29%), Positives = 61/112 (54%), Gaps = 3/112 (2%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
K+V++GD+ GK+ LL F ++ + ES E T S ++D+ I+ +WDT+G
Sbjct: 3 KIVVVGDTQCGKTALLHVFAKDNYP-ESYVPTVFENYTASFEIDKHRIELNMWDTSGSSY 61
Query: 73 YRAITSAYYRGAVGALLVYDIAKHLTYENV-ERWLRELRDHADQNIVIMLVG 123
Y + Y + L+ +DI++ T ++V ++W E ++ N ++LVG
Sbjct: 62 YDNVRPLAYPDSDAVLICFDISRPETLDSVLKKWQGETQEFC-PNAKLVLVG 112
>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 = 51.0 bits (122), Expect = 5e-08
Identities = 27/84 (32%), Positives = 41/84 (48%), Gaps = 6/84 (7%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQV---DQKTIKAQIWDTA 68
+V++G GK+ +L R NEF + + T G F T I+V + K + WD
Sbjct: 4 LHIVMLGLDSAGKTTVLYRLKFNEF-VNTVPTKG--FNTEKIKVSLGNAKGVTFHFWDVG 60
Query: 69 GQERYRAITSAYYRGAVGALLVYD 92
GQE+ R + +Y R G + V D
Sbjct: 61 GQEKLRPLWKSYTRCTDGIVFVVD 84
>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 = 50.4 bits (120), Expect = 1e-07
Identities = 29/118 (24%), Positives = 63/118 (53%), Gaps = 3/118 (2%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
K+VL+GD GK+ +L ++ + T+ E T ++ +++ ++ +WDT+G
Sbjct: 15 KLVLVGDVQCGKTAMLQVLAKDCYPETYVPTV-FENYTACLETEEQRVELSLWDTSGSPY 73
Query: 73 YRAITSAYYRGAVGALLVYDIAKHLTYEN-VERWLRELRDHADQNIVIMLVGPPSLLR 129
Y + Y + LL +DI++ +++ +++W E+ D+ + I+L+G + LR
Sbjct: 74 YDNVRPLCYSDSDAVLLCFDISRPEIFDSALKKWRAEILDYC-PSTRILLIGCKTDLR 130
>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 = 47.3 bits (113), Expect = 7e-07
Identities = 26/83 (31%), Positives = 42/83 (50%), Gaps = 9/83 (10%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIG--VEFATRSIQVDQKTIKAQIWDTAG 69
+KV+++G GK+ +L +F E + + TIG VE ++ K I+ +WD G
Sbjct: 16 YKVIIVGLDNAGKTTILYQFLLGEV-VHTSPTIGSNVE------EIVYKNIRFLMWDIGG 68
Query: 70 QERYRAITSAYYRGAVGALLVYD 92
QE R+ + YY +LV D
Sbjct: 69 QESLRSSWNTYYTNTDAVILVID 91
>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 = 45.4 bits (108), Expect = 3e-06
Identities = 41/147 (27%), Positives = 63/147 (42%), Gaps = 6/147 (4%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
++VLIGD GVGKS+L+ EF + T V + + I DT+ + +
Sbjct: 4 RIVLIGDEGVGKSSLIMSLVSEEFPENVPRV--LPEITIPADVTPERVPTTIVDTSSRPQ 61
Query: 73 YRAITSAYYRGAVGALLVYDIAKHLTYENV-ERWLRELRDHADQNIVIMLVGPPSLLRRY 131
RA +A R A LVY + + T E + +WL +R + I+LVG S LR
Sbjct: 62 DRANLAAEIRKANVICLVYSVDRPSTLERIRTKWLPLIRRLGV-KVPIILVGNKSDLRDG 120
Query: 132 YRGAVGALLVYDIAKHLTYENVERWLR 158
A + I + +E +
Sbjct: 121 SSQAGLEEEMLPIMN--EFREIETCVE 145
Score = 38.1 bits (89), Expect = 0.001
Identities = 28/83 (33%), Positives = 37/83 (44%), Gaps = 6/83 (7%)
Query: 139 LLVYDIAKHLTYENV-ERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAKTFAERN 197
LVY + + T E + +WL +R + I+LVGNKSDLR + E + N
Sbjct: 77 CLVYSVDRPSTLERIRTKWLPLIRRLGV-KVPIILVGNKSDLRDGSSQAGLEEEMLPIMN 135
Query: 198 NLSFIET----SALDSTNVETAF 216
IET SA NV F
Sbjct: 136 EFREIETCVECSAKTLINVSEVF 158
>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 = 45.4 bits (108), Expect = 3e-06
Identities = 28/96 (29%), Positives = 46/96 (47%), Gaps = 4/96 (4%)
Query: 14 VVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQERY 73
+ L+G GK+ L++ +F+ ++ T+G F R + TIK +WD GQ R+
Sbjct: 2 ITLVGLQNSGKTTLVNVIASGQFSEDTIPTVG--FNMRKVTKGNVTIK--VWDLGGQPRF 57
Query: 74 RAITSAYYRGAVGALLVYDIAKHLTYENVERWLREL 109
R++ Y RG + V D A E + L +L
Sbjct: 58 RSMWERYCRGVNAIVYVVDAADREKLEVAKNELHDL 93
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 43.8 bits (104), Expect = 6e-06
Identities = 40/125 (32%), Positives = 59/125 (47%), Gaps = 16/125 (12%)
Query: 14 VVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAG---- 69
VL G+SG GK+ LL R R L ++ + VE + K + +I G
Sbjct: 7 GVLTGESGSGKTTLLRRLARQ---LPNRRVVYVEAPSLG---TPKDLLRKILRALGLPLS 60
Query: 70 ----QERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPP 125
E AI A R LL+ D A+HL+ E +E LR+L D +++ I ++LVG P
Sbjct: 61 GGTTAELLEAILDALKRRGRP-LLIIDEAQHLSLEALE-ELRDLYDLSEKGIQVILVGTP 118
Query: 126 SLLRR 130
L +
Sbjct: 119 ELRKL 123
>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 = 44.2 bits (104), Expect = 1e-05
Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 5/80 (6%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
+VV +G G GK+ +L + ++EF ++ TIG T V+ K +K IWD G+ +
Sbjct: 1 RVVTLGLDGAGKTTILFKLKQDEF-MQPIPTIGFNVET----VEYKNLKFTIWDVGGKHK 55
Query: 73 YRAITSAYYRGAVGALLVYD 92
R + YY + V D
Sbjct: 56 LRPLWKHYYLNTQAVVFVID 75
>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 = 42.6 bits (100), Expect = 4e-05
Identities = 28/110 (25%), Positives = 49/110 (44%), Gaps = 6/110 (5%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
+++++G GK+ +L + E + + TIG T V K I +WD GQ++
Sbjct: 15 RILMVGLDAAGKTTILYKLKLGES-VTTIPTIGFNVET----VTYKNISFTVWDVGGQDK 69
Query: 73 YRAITSAYYRGAVGALLVYDIA-KHLTYENVERWLRELRDHADQNIVIML 121
R + YY G + V D + E E R L + ++ VI++
Sbjct: 70 IRPLWRHYYTNTQGLIFVVDSNDRDRIDEAREELHRMLNEDELRDAVILV 119
>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 = 42.3 bits (99), Expect = 5e-05
Identities = 51/228 (22%), Positives = 81/228 (35%), Gaps = 51/228 (22%)
Query: 11 LFKVVLIGDSGVGKSNLLSRFTRNEFNLESKST--------------IGVEFATRSIQV- 55
K V++GD+ VGK+ L+ N+ + + + E RS V
Sbjct: 2 TIKCVVVGDNAVGKTRLICARACNKTLTQYQLLATHVPTVWAIDQYRVCQEVLERSRDVV 61
Query: 56 DQKTIKAQIWDTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVER-WLRELRDHAD 114
D ++ ++WDT G + + AY R V LL + IA + NV+ W E+R
Sbjct: 62 DGVSVSLRLWDTFG-DHDKDRRFAYGRSDV-VLLCFSIASPNSLRNVKTMWYPEIRHFCP 119
Query: 115 QNIVIMLVGPPSLLRRYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVG 174
+ VI LVG LR + V R R L
Sbjct: 120 RVPVI-LVGCKLDLRYADL-----------------DEVNRARRPLARPIKNA------- 154
Query: 175 NKSDLRHLRAVPADEAKTFAERNNLSFIETSALDSTNVETAFQNILTA 222
+P + + A+ + + ETS + V+ F N + A
Sbjct: 155 --------DILPPETGRAVAKELGIPYYETSVVTQFGVKDVFDNAIRA 194
>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 = 40.9 bits (96), Expect = 1e-04
Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 4/80 (5%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
+V+L+G GKS LL + E + + T+G F +Q+ +K + +WD GQE+
Sbjct: 1 QVLLLGLDSAGKSTLLYKLKHAEL-VTTIPTVG--FNVEMLQL-EKHLSLTVWDVGGQEK 56
Query: 73 YRAITSAYYRGAVGALLVYD 92
R + Y G + V D
Sbjct: 57 MRTVWKCYLENTDGLVYVVD 76
>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 = 40.9 bits (96), Expect = 1e-04
Identities = 27/105 (25%), Positives = 49/105 (46%), Gaps = 11/105 (10%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
+++++G GK+ +L + + ++ + T+G T V K +K +WD GQ++
Sbjct: 11 RILMLGLDAAGKTTILYKLKLGQ-SVTTIPTVGFNVET----VTYKNVKFNVWDVGGQDK 65
Query: 73 YRAITSAYYRGAVGALLVYDIAKHLTYENVERWL------RELRD 111
R + YY G G + V D A + + L RE+RD
Sbjct: 66 IRPLWRHYYTGTQGLIFVVDSADRDRIDEARQELHRIINDREMRD 110
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 40.1 bits (94), Expect = 2e-04
Identities = 29/107 (27%), Positives = 52/107 (48%), Gaps = 23/107 (21%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRN----------------EFNLESKSTIGVEFATRSIQVD 56
K+V+IG G GK+ F R + +T+ ++F SI++D
Sbjct: 12 KIVVIGPVGAGKTT----FVRALSDKPLVITEADASSVSGKGKRPTTVAMDFG--SIELD 65
Query: 57 QKTIKAQIWDTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVE 103
+ T ++ T GQER++ + RGAVGA+++ D ++ +T+ E
Sbjct: 66 EDT-GVHLFGTPGQERFKFMWEILSRGAVGAIVLVDSSRPITFHAEE 111
>gnl|CDD|216791 pfam01926, MMR_HSR1, 50S ribosome-binding GTPase. The full-length
GTPase protein is required for the complete activity of
the protein of interacting with the 50S ribosome and
binding of both adenine and guanine nucleotides, with a
preference for guanine nucleotide.
Length = 117
Score = 38.8 bits (91), Expect = 3e-04
Identities = 31/120 (25%), Positives = 50/120 (41%), Gaps = 16/120 (13%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQ--VDQKTIKAQIWDTAG- 69
+V L+G VGKS L++ T + + S TR V + + DT G
Sbjct: 1 RVALVGRPNVGKSTLINALTGAKVAIVSD----YPGTTRDPILGVLGLGRQIILVDTPGL 56
Query: 70 -----QERYRAITSAY---YRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIML 121
+ + + + R A LLV D ++ LT E+ E L EL + I+++L
Sbjct: 57 IEGASEGKGVEGFNRFLEAIREADLILLVVDASEGLT-EDDEEILEELEKLPKKPIILVL 115
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 38.4 bits (90), Expect = 0.001
Identities = 21/83 (25%), Positives = 38/83 (45%), Gaps = 5/83 (6%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQE 71
+++++G GK+ +L + E + + TIG F ++ K +K +WD GQE
Sbjct: 15 MRILILGLDNAGKTTILYKLKLGEI-VTTIPTIG--FNVETVTY--KNVKFTVWDVGGQE 69
Query: 72 RYRAITSAYYRGAVGALLVYDIA 94
R + Y+ + V D A
Sbjct: 70 SLRPLWRNYFPNTDAVIFVVDSA 92
>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 = 37.3 bits (87), Expect = 0.002
Identities = 24/87 (27%), Positives = 41/87 (47%), Gaps = 13/87 (14%)
Query: 14 VVLIGDSGVGKSNLLSRFTRNEFNLESKS--------TIGVEFATRSIQVDQKTIKAQIW 65
V+++G GK+ L + T+ +F+ K T+G+ T I+V + + W
Sbjct: 2 VLILGLDNAGKTTFLEQ-TKTKFSKNYKGLNPSKITPTVGLNIGT--IEVGKARLM--FW 56
Query: 66 DTAGQERYRAITSAYYRGAVGALLVYD 92
D GQE R++ YY + G + V D
Sbjct: 57 DLGGQEELRSLWDKYYAESHGVIYVID 83
>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 = 36.8 bits (86), Expect = 0.003
Identities = 43/211 (20%), Positives = 78/211 (36%), Gaps = 68/211 (32%)
Query: 14 VVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVE-----FATRSIQV---DQKTIKAQIW 65
+V+ G VGKS+L+++ TR + E F T+S+ V D K ++ Q+
Sbjct: 3 LVIAGYPNVGKSSLVNKLTRAK----------PEVAPYPFTTKSLFVGHFDYKYLRWQVI 52
Query: 66 DTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPP 125
DT G +L D R ++N + M
Sbjct: 53 DTPG------------------IL--D-----------------RPLEERNTIEMQ---- 71
Query: 126 SLLR-RYYRGAVGALLVYDIAKH--LTYENVERWLRELRDHADQNIVIMLVGNKSDLRHL 182
++ + R AV L D ++ + E +E++ ++ ++++L NK DL
Sbjct: 72 AITALAHLRAAV--LFFIDPSETCGYSIEEQLSLFKEIKPLFNKPVIVVL--NKIDLLTE 127
Query: 183 RAVPADEAKTFAERNNLSFIETSALDSTNVE 213
+ E E+ I+ S L V+
Sbjct: 128 EDLSEIE--KELEKEGEEVIKISTLTEEGVD 156
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 36.7 bits (85), Expect = 0.004
Identities = 22/80 (27%), Positives = 40/80 (50%), Gaps = 5/80 (6%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
+++++G GK+ +L + E + + TIG T V+ K +K +WD GQ++
Sbjct: 19 RILMVGLDAAGKTTILYKLKLGEV-VTTIPTIGFNVET----VEYKNLKFTMWDVGGQDK 73
Query: 73 YRAITSAYYRGAVGALLVYD 92
R + YY+ G + V D
Sbjct: 74 LRPLWRHYYQNTNGLIFVVD 93
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 36.5 bits (84), Expect = 0.005
Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 5/80 (6%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
+++++G GK+ +L + E + + TIG T V+ K I +WD GQ++
Sbjct: 19 RILMVGLDAAGKTTILYKLKLGEI-VTTIPTIGFNVET----VEYKNISFTVWDVGGQDK 73
Query: 73 YRAITSAYYRGAVGALLVYD 92
R + Y++ G + V D
Sbjct: 74 IRPLWRHYFQNTQGLIFVVD 93
>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 = 35.8 bits (83), Expect = 0.006
Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 5/80 (6%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
+++++G GK+ +L + E + + TIG T V+ K I +WD GQ++
Sbjct: 2 RILMVGLDAAGKTTILYKLKLGEI-VTTIPTIGFNVET----VEYKNISFTVWDVGGQDK 56
Query: 73 YRAITSAYYRGAVGALLVYD 92
R + Y++ G + V D
Sbjct: 57 IRPLWRHYFQNTQGLIFVVD 76
>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 = 35.8 bits (83), Expect = 0.006
Identities = 24/80 (30%), Positives = 36/80 (45%), Gaps = 5/80 (6%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
+++++G G GK+ +L R E + + TIG T V K +K Q+WD GQ
Sbjct: 1 RILILGLDGAGKTTILYRLQVGEV-VTTIPTIGFNVET----VTYKNLKFQVWDLGGQTS 55
Query: 73 YRAITSAYYRGAVGALLVYD 92
R YY + V D
Sbjct: 56 IRPYWRCYYSNTDAIIYVVD 75
>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 = 35.2 bits (81), Expect = 0.012
Identities = 35/178 (19%), Positives = 60/178 (33%), Gaps = 46/178 (25%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQE 71
+V ++G GVGK+ ++ +F EF E T ++ + + I D +
Sbjct: 1 VRVAVLGAPGVGKTAIVRQFLAQEFPEEYIPTEHRRLYRPAVVLSGRVYDLHILDVPNMQ 60
Query: 72 RYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRY 131
RY A + W R
Sbjct: 61 RY----------PGTAG--------------QEW-------------------MDPRFRG 77
Query: 132 YRGAVGALLVYDIAKHLTYENVE---RWLRELRDHADQNIVIMLVGNKSDLRHLRAVP 186
R + +LVYDI ++ V+ + + E R ++ I++VGNK D + R P
Sbjct: 78 LRNSRAFILVYDICSPDSFHYVKLLRQQILETRPAGNKEPPIVVVGNKRDQQRHRFAP 135
>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 = 0.021
Identities = 26/93 (27%), Positives = 44/93 (47%), Gaps = 19/93 (20%)
Query: 13 KVVLIGDSGVGKSNLLSR-FTRNEFNLESKSTIGVEFATRSIQVDQKTIKA------QIW 65
KV+L+G G GKS++ S F+ N + T+ + AT I V+Q ++ +W
Sbjct: 1 KVLLMGLRGSGKSSMRSIIFS----NYSPRDTLRLG-AT--IDVEQSHVRFLGNLTLNLW 53
Query: 66 DTAGQERYRAITSAYYRGA----VGALL-VYDI 93
D GQ+ + + VG L+ V+D+
Sbjct: 54 DCPGQDDFMENYLTRQKEHIFSNVGVLIYVFDV 86
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 34.1 bits (79), Expect = 0.049
Identities = 19/82 (23%), Positives = 33/82 (40%), Gaps = 10/82 (12%)
Query: 139 LLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAKTFAERNN 198
L V D ++ L E+ L + + I++V NK+DL V E ++ N
Sbjct: 301 LFVLDASQPLDKED-----LALIELLPKKKPIIVVLNKADL-----VSKIELESEKLANG 350
Query: 199 LSFIETSALDSTNVETAFQNIL 220
+ I SA ++ + I
Sbjct: 351 DAIISISAKTGEGLDALREAIK 372
>gnl|CDD|133362 cd04162, Arl9_Arfrp2_like, Arf-like 9 (Arl9)/Arfrp2-like GTPase.
Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first
identified as part of the Human Cancer Genome Project.
It maps to chromosome 4q12 and is sometimes referred to
as Arfrp2 (Arf-related protein 2). This is a novel
subfamily identified in human cancers that is
uncharacterized to date.
Length = 164
Score = 33.2 bits (76), Expect = 0.057
Identities = 20/99 (20%), Positives = 38/99 (38%), Gaps = 4/99 (4%)
Query: 14 VVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQERY 73
++++G G GK++LL + T G S+ + + ++ + G +
Sbjct: 2 ILVLGLDGAGKTSLLHSLSSERSLESVVPTTGFN----SVAIPTQDAIMELLEIGGSQNL 57
Query: 74 RAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDH 112
R Y G+ G + V D A + L +L H
Sbjct: 58 RKYWKRYLSGSQGLIFVVDSADSERLPLARQELHQLLQH 96
Score = 28.2 bits (63), Expect = 2.2
Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 129 RRYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVP 186
+RY G+ G + V D A + L +L H ++ ++++ NK DL R+V
Sbjct: 62 KRYLSGSQGLIFVVDSADSERLPLARQELHQLLQH-PPDLPLVVLANKQDLPAARSVQ 118
>gnl|CDD|206722 cd04157, Arl6, Arf-like 6 (Arl6) GTPase. Arl6 (Arf-like 6) forms a
subfamily of the Arf family of small GTPases. Arl6
expression is limited to the brain and kidney in adult
mice, but it is expressed in the neural plate and
somites during embryogenesis, suggesting a possible role
for Arl6 in early development. Arl6 is also believed to
have a role in cilia or flagella function. Several
proteins have been identified that bind Arl6, including
Arl6 interacting protein (Arl6ip), and SEC61beta, a
subunit of the heterotrimeric conducting channel SEC61p.
Based on Arl6 binding to these effectors, Arl6 is also
proposed to play a role in protein transport, membrane
trafficking, or cell signaling during hematopoietic
maturation. At least three specific homozygous Arl6
mutations in humans have been found to cause
Bardet-Biedl syndrome, a disorder characterized by
obesity, retinopathy, polydactyly, renal and cardiac
malformations, learning disabilities, and
hypogenitalism. Older literature suggests that Arl6 is a
part of the Arl4/Arl7 subfamily, but analyses based on
more recent sequence data place Arl6 in its own
subfamily.
Length = 162
Score = 32.4 bits (74), Expect = 0.100
Identities = 23/112 (20%), Positives = 46/112 (41%), Gaps = 25/112 (22%)
Query: 14 VVLIGDSGVGKSNLLSRF----TRNE-------FNLESKSTIGVEFATRSIQVDQKTIKA 62
++++G GK+ ++++ +++ FN+ES + F
Sbjct: 2 ILVLGLDNSGKTTIINQLKPSNAQSQNIVPTVGFNVESFKKGNLSF-------------- 47
Query: 63 QIWDTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHAD 114
+D +GQ +YR + YY+ G + V D + L + L L +H D
Sbjct: 48 TAFDMSGQGKYRGLWEHYYKNIQGIIFVIDSSDRLRMVVAKDELELLLNHPD 99
>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 = 32.1 bits (74), Expect = 0.10
Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 13/75 (17%)
Query: 139 LLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAKTFAERNN 198
LLV D ++ L E++E L A + +++ V NKSDL +A+ +E N
Sbjct: 87 LLVVDASEGLDEEDLEI----LELPAKKPVIV--VLNKSDL-------LSDAEGISELNG 133
Query: 199 LSFIETSALDSTNVE 213
I SA ++
Sbjct: 134 KPIIAISAKTGEGID 148
Score = 26.3 bits (59), Expect = 8.6
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNE 35
KVV+ G VGKS+LL+ +
Sbjct: 4 IKVVIAGKPNVGKSSLLNALAGRD 27
>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 = 32.5 bits (74), Expect = 0.16
Identities = 17/61 (27%), Positives = 31/61 (50%), Gaps = 7/61 (11%)
Query: 12 FKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSI---QVDQKTIKAQIWDTA 68
FK+ ++G VGKS+LL+ + + + S ++ TR + + I ++ DTA
Sbjct: 204 FKLAIVGSPNVGKSSLLNALLKQDRAIVSD----IKGTTRDVVEGDFELNGILIKLLDTA 259
Query: 69 G 69
G
Sbjct: 260 G 260
>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 = 31.4 bits (72), Expect = 0.24
Identities = 19/64 (29%), Positives = 29/64 (45%), Gaps = 13/64 (20%)
Query: 11 LFKVVLIGDSGVGKSNLLSRFTRNEFNLESKS-TIGVEFATRSIQVDQKTIKAQIWDTAG 69
+F ++G G GKS LL F F+ + S TI +A +++V G
Sbjct: 4 VFLCFVLGAKGSGKSALLQAFLGRSFSQNAYSPTIKPRYAVNTVEV------------PG 51
Query: 70 QERY 73
QE+Y
Sbjct: 52 QEKY 55
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 31.5 bits (72), Expect = 0.30
Identities = 40/166 (24%), Positives = 62/166 (37%), Gaps = 33/166 (19%)
Query: 14 VVLIGDSGVGKSNLLSRFTRNEFNLESKSTIG-VEFATRSI---QVDQKTIKAQIWDT-- 67
V L+G VGKS LL++ T +KS + F T ++ K + Q+ D
Sbjct: 66 VALVGFPSVGKSTLLNKLT------NTKSEVADYPFTTLEPVPGMLEYKGAQIQLLDLPG 119
Query: 68 ----AGQERYR-AITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLV 122
A R R + R A ++V D+ + + + REL D I +
Sbjct: 120 IIEGASSGRGRGRQVLSVARNADLIIIVLDVFEDPH--HRDIIERELE---DVGIRLNKR 174
Query: 123 GPPSLLRRYYRGAVGALLVYDIAK-----HLTYENVERWLRELRDH 163
P +++ G + I HL + V LRE R H
Sbjct: 175 PPDVTIKKKESGGI------RINGTGPLTHLDEDTVRAILREYRIH 214
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 31.1 bits (71), Expect = 0.35
Identities = 30/127 (23%), Positives = 58/127 (45%), Gaps = 23/127 (18%)
Query: 11 LFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQV---DQKTIKAQIWDT 67
L +V+ G VGKS+L+ + T + + F T+ I V ++ ++ Q+ DT
Sbjct: 168 LPTIVVAGYPNVGKSSLVRKLTTAKPEVAP-----YPFTTKGIHVGHFERGYLRIQVIDT 222
Query: 68 AG------QER----YRAITS-AYYRGAVGALLVYDIAKHLTY--ENVERWLRELRDHAD 114
G +ER +AI + + G + L ++D ++ Y E L E+++
Sbjct: 223 PGLLDRPLEERNEIERQAILALRHLAGVI--LFLFDPSETCGYSLEEQISLLEEIKELFK 280
Query: 115 QNIVIML 121
IV+++
Sbjct: 281 APIVVVI 287
>gnl|CDD|217416 pfam03193, DUF258, Protein of unknown function, DUF258.
Length = 161
Score = 30.6 bits (70), Expect = 0.36
Identities = 11/17 (64%), Positives = 12/17 (70%)
Query: 14 VVLIGDSGVGKSNLLSR 30
VL G SGVGKS LL+
Sbjct: 38 SVLAGQSGVGKSTLLNA 54
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 30.7 bits (70), Expect = 0.47
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 14 VVLIGDSGVGKSNLLSRF 31
VL+G SGVGKS L++
Sbjct: 167 TVLLGQSGVGKSTLINAL 184
>gnl|CDD|226124 COG3596, COG3596, Predicted GTPase [General function prediction
only].
Length = 296
Score = 30.9 bits (70), Expect = 0.50
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQ-VDQKTIKAQIWDTAGQE 71
V+L+G +G GKS+L++ + E SK +G + TR D + + +WDT G
Sbjct: 41 NVLLMGATGAGKSSLINALFQGEVKEVSKVGVGTDITTRLRLSYDGENLV--LWDTPGLG 98
>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 = 30.1 bits (68), Expect = 0.54
Identities = 26/99 (26%), Positives = 43/99 (43%), Gaps = 5/99 (5%)
Query: 14 VVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQERY 73
++ +G GK+ L+S + K V F +++D+ + I+D G +
Sbjct: 2 LLTVGLDNAGKTTLVSALQGE---IPKKVAPTVGFTPTKLRLDKYEV--CIFDLGGGANF 56
Query: 74 RAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDH 112
R I YY A G + V D + + V+ LREL H
Sbjct: 57 RGIWVNYYAEAHGLVFVVDSSDDDRVQEVKEILRELLQH 95
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 30.3 bits (69), Expect = 0.54
Identities = 11/28 (39%), Positives = 15/28 (53%)
Query: 5 EDEYDYLFKVVLIGDSGVGKSNLLSRFT 32
E D ++V +G S VGKS L+ T
Sbjct: 3 ETRPDRKPEIVFVGRSNVGKSTLVRELT 30
>gnl|CDD|218745 pfam05783, DLIC, Dynein light intermediate chain (DLIC). This
family consists of several eukaryotic dynein light
intermediate chain proteins. The light intermediate
chains (LICs) of cytoplasmic dynein consist of multiple
isoforms, which undergo post-translational modification
to produce a large number of species. DLIC1 is known to
be involved in assembly, organisation, and function of
centrosomes and mitotic spindles when bound to
pericentrin. DLIC2 is a subunit of cytoplasmic dynein 2
that may play a role in maintaining Golgi organisation
by binding cytoplasmic dynein 2 to its Golgi-associated
cargo.
Length = 490
Score = 30.6 bits (69), Expect = 0.71
Identities = 24/111 (21%), Positives = 54/111 (48%), Gaps = 14/111 (12%)
Query: 14 VVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQ---VDQKTIKAQIWDTAGQ 70
V+++G+ G GK+ L+++ E K G+E+ ++ D +T + +W G
Sbjct: 48 VLVLGEDGSGKTTLIAKLQGVE---HPKKGRGLEYLYLNVHDEDRDDQT-RCNVWILDGD 103
Query: 71 ERYR-----AITSAYYRGAVGALLVYDIAKHLTY-ENVERWLRELRDHADQ 115
++ A+ + + + V D+++ T E++++W LR+H D+
Sbjct: 104 LYHKGLLKFALNAESLADTL-VIFVVDMSRPWTIMESLQKWASVLREHIDK 153
>gnl|CDD|220581 pfam10116, Host_attach, Protein required for attachment to host
cells. Members of this family of bacterial proteins are
required for the attachment of the bacterium to host
cells.
Length = 138
Score = 29.1 bits (66), Expect = 0.97
Identities = 17/61 (27%), Positives = 25/61 (40%), Gaps = 9/61 (14%)
Query: 108 ELRDHADQNIV--IMLVGPPS---LLRRYYRGAVGALLVYDIAKHLTYENVERWLRELRD 162
L A ++LV PP LR++ V +V +I K LT V+ E+
Sbjct: 81 YLNKGALAGRFDRLVLVAPPRFLGELRKHLHKEVRKRVVGEIDKDLTNHPVD----EIEK 136
Query: 163 H 163
H
Sbjct: 137 H 137
>gnl|CDD|216386 pfam01244, Peptidase_M19, Membrane dipeptidase (Peptidase family
M19).
Length = 316
Score = 29.9 bits (68), Expect = 1.00
Identities = 16/66 (24%), Positives = 26/66 (39%), Gaps = 12/66 (18%)
Query: 128 LRRYYRGAVGALLV---------YDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSD 178
L R G VGA Y+ A T E ++ + R +R + +Q + LV D
Sbjct: 37 LERLRAGGVGAQFFAIFVPCDAQYEDAVQATLEQIDIFRRLVRKNPEQ---LRLVRTADD 93
Query: 179 LRHLRA 184
+ +
Sbjct: 94 IERAKK 99
>gnl|CDD|213214 cd03247, ABCC_cytochrome_bd, ATP-binding cassette domain of
CydCD, subfamily C. The CYD subfamily implicated in
cytochrome bd biogenesis. The CydC and CydD proteins
are important for the formation of cytochrome bd
terminal oxidase of E. coli and it has been proposed
that they were necessary for biosynthesis of the
cytochrome bd quinol oxidase and for periplasmic c-type
cytochromes. CydCD were proposed to determine a
heterooligomeric complex important for heme export into
the periplasm or to be involved in the maintenance of
the proper redox state of the periplasmic space. In
Bacillus subtilis, the absence of CydCD does not affect
the presence of halo-cytochrome c in the membrane and
this observation suggests that CydCD proteins are not
involved in the export of heme in this organism.
Length = 178
Score = 29.2 bits (66), Expect = 1.1
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRN 34
K+ L+G SG GKS LL T +
Sbjct: 30 KIALLGRSGSGKSTLLQLLTGD 51
>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 = 29.3 bits (66), Expect = 1.1
Identities = 27/110 (24%), Positives = 48/110 (43%), Gaps = 5/110 (4%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQER 72
+++L+G GK+ +L + + + + T G F +++Q D K +WD GQ +
Sbjct: 17 RILLLGLDNAGKTTILKQLASEDISHIT-PTQG--FNIKNVQADG--FKLNVWDIGGQRK 71
Query: 73 YRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLV 122
R Y+ + V D A +E + L EL + V +LV
Sbjct: 72 IRPYWRNYFENTDVLIYVIDSADRKRFEEAGQELVELLEEEKLAGVPVLV 121
>gnl|CDD|226164 COG3638, COG3638, ABC-type phosphate/phosphonate transport
system, ATPase component [Inorganic ion transport and
metabolism].
Length = 258
Score = 29.5 bits (67), Expect = 1.2
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 14 VVLIGDSGVGKSNLL 28
V +IG SG GKS LL
Sbjct: 33 VAIIGPSGAGKSTLL 47
>gnl|CDD|206747 cd01854, YjeQ_EngC, Ribosomal interacting GTPase YjeQ/EngC, a
circularly permuted subfamily of the Ras GTPases. YjeQ
(YloQ in Bacillus subtilis) is a ribosomal small
subunit-dependent GTPase; hence also known as RsgA. YjeQ
is a late-stage ribosomal biogenesis factor involved in
the 30S subunit maturation, and it represents a protein
family whose members are broadly conserved in bacteria
and have been shown to be essential to the growth of E.
coli and B. subtilis. Proteins of the YjeQ family
contain all sequence motifs typical of the vast class of
P-loop-containing GTPases, but show a circular
permutation, with a G4-G1-G3 pattern of motifs as
opposed to the regular G1-G3-G4 pattern seen in most
GTPases. All YjeQ family proteins display a unique
domain architecture, which includes an N-terminal
OB-fold RNA-binding domain, the central permuted GTPase
domain, and a zinc knuckle-like C-terminal cysteine
domain.
Length = 211
Score = 28.9 bits (66), Expect = 1.4
Identities = 11/17 (64%), Positives = 13/17 (76%)
Query: 14 VVLIGDSGVGKSNLLSR 30
VL+G SGVGKS LL+
Sbjct: 88 SVLVGQSGVGKSTLLNA 104
>gnl|CDD|213195 cd03228, ABCC_MRP_Like, ATP-binding cassette domain of multidrug
resistance protein-like transporters. The MRP
(Multidrug Resistance Protein)-like transporters are
involved in drug, peptide, and lipid export. They
belong to the subfamily C of the ATP-binding cassette
(ABC) superfamily of transport proteins. The ABCC
subfamily contains transporters with a diverse
functional spectrum that includes ion transport, cell
surface receptor, and toxin secretion activities. The
MRP-like family, similar to all ABC proteins, have a
common four-domain core structure constituted by two
membrane-spanning domains, each composed of six
transmembrane (TM) helices, and two nucleotide-binding
domains (NBD). ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 171
Score = 28.5 bits (65), Expect = 1.7
Identities = 11/22 (50%), Positives = 13/22 (59%), Gaps = 3/22 (13%)
Query: 13 KVVLIGDSGVGKS---NLLSRF 31
KV ++G SG GKS LL R
Sbjct: 30 KVAIVGPSGSGKSTLLKLLLRL 51
>gnl|CDD|237451 PRK13631, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 320
Score = 29.0 bits (65), Expect = 1.8
Identities = 18/69 (26%), Positives = 24/69 (34%), Gaps = 15/69 (21%)
Query: 6 DEYDYLFK----VVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVE---------FATRS 52
+ Y F+ +IG+SG GKS L++ F N TI V
Sbjct: 43 NNISYTFEKNKIYFIIGNSGSGKSTLVTHF--NGLIKSKYGTIQVGDIYIGDKKNNHELI 100
Query: 53 IQVDQKTIK 61
K IK
Sbjct: 101 TNPYSKKIK 109
>gnl|CDD|234988 PRK01889, PRK01889, GTPase RsgA; Reviewed.
Length = 356
Score = 29.1 bits (66), Expect = 1.9
Identities = 10/14 (71%), Positives = 11/14 (78%)
Query: 14 VVLIGDSGVGKSNL 27
V L+G SGVGKS L
Sbjct: 198 VALLGSSGVGKSTL 211
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase. The
Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that generally show sequence
conservation in the region between the Walker A and B
motifs (G1 and G3 box motifs), to the exclusion of other
GTPases. TrmE is ubiquitous in bacteria and is a
widespread mitochondrial protein in eukaryotes, but is
absent from archaea. The yeast member of TrmE family,
MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family.
Length = 161
Score = 28.4 bits (64), Expect = 2.0
Identities = 43/212 (20%), Positives = 62/212 (29%), Gaps = 60/212 (28%)
Query: 15 VLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQ----VDQKTIKAQIWDTAGQ 70
+ G VGKS+LL+ + S + TR + DT G
Sbjct: 1 AIFGRPNVGKSSLLNALLGQNVGIVSP----IPGTTRDPVRKEWELLPLGPVVLIDTPG- 55
Query: 71 ERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRR 130
D L E VE R++ D AD +++LV L
Sbjct: 56 --------------------LDEEGGLGRERVEE-ARQVADRAD---LVLLVVDSDLTP- 90
Query: 131 YYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLR--HLRAVPAD 188
+ E LRE + ++LV NK DL
Sbjct: 91 -----------------VEEEAKLGLLRE------RGKPVLLVLNKIDLVPESEEEELLR 127
Query: 189 EAKTFAERNNLSFIETSALDSTNVETAFQNIL 220
E K +L I SAL ++ + I
Sbjct: 128 ERK-LELLPDLPVIAVSALPGEGIDELRKKIA 158
>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 = 28.3 bits (63), Expect = 2.0
Identities = 27/159 (16%), Positives = 45/159 (28%), Gaps = 32/159 (20%)
Query: 14 VVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQERY 73
V+L G SG GK++LL G+ A ++ +
Sbjct: 27 VLLTGPSGTGKTSLLRELLE-----------GLLVAAGKCDQAERNPPYAFSQALRE--- 72
Query: 74 RAITSAYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGPPSLLRRYYR 133
L+ + + L E + L ++ L LL R
Sbjct: 73 ---------------LLRQLLRELAAE-LLLLREALLAALGAELIEGLQDLVELLERLLA 116
Query: 134 GAVGALLVYDIAKHLTYENVERWLREL-RDHADQNIVIM 171
A +LV D E L L R ++++
Sbjct: 117 RARPLVLVLDDL-QWADEESLDLLAALLRRLERLPLLVV 154
>gnl|CDD|213179 cd00267, ABC_ATPase, ATP-binding cassette transporter
nucleotide-binding domain. ABC transporters are a
large family of proteins involved in the transport of a
wide variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide-binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and
GTP-binding and hydrolyzing proteins.
Length = 157
Score = 28.0 bits (63), Expect = 2.7
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 14 VVLIGDSGVGKSNLL 28
V L+G +G GKS LL
Sbjct: 28 VALVGPNGSGKSTLL 42
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 28.2 bits (64), Expect = 2.8
Identities = 11/14 (78%), Positives = 11/14 (78%)
Query: 15 VLIGDSGVGKSNLL 28
VL G SGVGKS LL
Sbjct: 168 VLAGQSGVGKSTLL 181
>gnl|CDD|238395 cd00772, ProRS_core, Prolyl-tRNA synthetase (ProRS) class II core
catalytic domain. ProRS is a homodimer. It is
responsible for the attachment of proline to the 3' OH
group of ribose of the appropriate tRNA. This domain is
primarily responsible for ATP-dependent formation of the
enzyme bound aminoacyl-adenylate. Class II assignment is
based upon its structure and the presence of three
characteristic sequence motifs in the core domain.
Length = 264
Score = 28.5 bits (63), Expect = 2.9
Identities = 16/78 (20%), Positives = 27/78 (34%), Gaps = 5/78 (6%)
Query: 79 AYYRGAVGALLVYDIAKHLTYENVERWL-RELRDHADQNIVIMLVGPPSLLR---RYYRG 134
A G + +AK + + +E L + ++H QN + S L + G
Sbjct: 16 ADQGPGRGIINFLPLAKAI-LDKIENVLDKMFKEHGAQNALFPFFILASFLEKEAEHDEG 74
Query: 135 AVGALLVYDIAKHLTYEN 152
L V+ A E
Sbjct: 75 FSKELAVFKDAGDEELEE 92
>gnl|CDD|213223 cd03256, ABC_PhnC_transporter, ATP-binding cassette domain of the
binding protein-dependent phosphonate transport system.
Phosphonates are a class of organophosphorus compounds
characterized by a chemically stable
carbon-to-phosphorus (C-P) bond. Phosphonates are
widespread among naturally occurring compounds in all
kingdoms of wildlife, but only prokaryotic
microorganisms are able to cleave this bond. Certain
bacteria such as E. coli can use alkylphosphonates as a
phosphorus source. ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 241
Score = 28.3 bits (64), Expect = 3.0
Identities = 11/15 (73%), Positives = 11/15 (73%)
Query: 14 VVLIGDSGVGKSNLL 28
V LIG SG GKS LL
Sbjct: 30 VALIGPSGAGKSTLL 44
>gnl|CDD|213229 cd03262, ABC_HisP_GlnQ, ATP-binding cassette domain of the
histidine and glutamine transporters. HisP and GlnQ
are the ATP-binding components of the bacterial
periplasmic histidine and glutamine permeases,
respectively. Histidine permease is a multi-subunit
complex containing the HisQ and HisM integral membrane
subunits and two copies of HisP. HisP has properties
intermediate between those of integral and peripheral
membrane proteins and is accessible from both sides of
the membrane, presumably by its interaction with HisQ
and HisM. The two HisP subunits form a homodimer within
the complex. The domain structure of the amino acid
uptake systems is typical for prokaryotic extracellular
solute binding protein-dependent uptake systems. All of
the amino acid uptake systems also have at least one,
and in a few cases, two extracellular solute binding
proteins located in the periplasm of Gram-negative
bacteria, or attached to the cell membrane of
Gram-positive bacteria. The best-studied member of the
PAAT (polar amino acid transport) family is the HisJQMP
system of S. typhimurium, where HisJ is the
extracellular solute binding proteins and HisP is the
ABC protein.
Length = 213
Score = 28.3 bits (64), Expect = 3.0
Identities = 11/16 (68%), Positives = 12/16 (75%)
Query: 13 KVVLIGDSGVGKSNLL 28
VV+IG SG GKS LL
Sbjct: 28 VVVIIGPSGSGKSTLL 43
>gnl|CDD|239114 cd02648, nuc_hydro_1, NH_1: A subgroup of nucleoside hydrolases.
This group contains fungal proteins similar to
nucleoside hydrolases. Nucleoside hydrolases cleave the
N-glycosidic bond in nucleosides generating ribose and
the respective base. These enzymes vary in their
substrate specificity. .
Length = 367
Score = 28.3 bits (63), Expect = 3.1
Identities = 30/120 (25%), Positives = 44/120 (36%), Gaps = 26/120 (21%)
Query: 25 SNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTA-GQERYRAITSAYYRG 83
N+L F E ++T GV + S +K I A D ER +T++Y+ G
Sbjct: 47 RNVLRLFHVLERERAWRATPGVRYRAFS-ADAEKPIVASGSDQPLEGER---LTASYFHG 102
Query: 84 AVGALLVYDIAKHLTYENVERW-------------------LRELRDHADQNIVIMLVGP 124
G V+ + T VE W L LR+ D + I +GP
Sbjct: 103 RDGLSGVHWLHPDFT--PVETWIPEIVAPLTPSDKPAYDVILDILREEPDHTVTIAALGP 160
>gnl|CDD|181906 PRK09493, glnQ, glutamine ABC transporter ATP-binding protein;
Reviewed.
Length = 240
Score = 28.1 bits (63), Expect = 3.2
Identities = 11/15 (73%), Positives = 12/15 (80%)
Query: 14 VVLIGDSGVGKSNLL 28
VV+IG SG GKS LL
Sbjct: 30 VVIIGPSGSGKSTLL 44
>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 = 27.5 bits (61), Expect = 3.7
Identities = 20/85 (23%), Positives = 38/85 (44%), Gaps = 4/85 (4%)
Query: 139 LLVYDIAKHLTYENVERWLRELRDHAD-QNIVIMLVGNKSDL--RHLRAVPADEAKTF-A 194
+ V+ + +++ V R +L + + I ++LVG + + + R + A+ A
Sbjct: 70 IFVFSLEDEASFQTVYRLYHQLSSYRNISEIPLILVGTQDAISASNPRVIDDARARQLCA 129
Query: 195 ERNNLSFIETSALDSTNVETAFQNI 219
+ S+ ET A NVE FQ
Sbjct: 130 DMKRCSYYETCATYGLNVERVFQEA 154
>gnl|CDD|238863 cd01825, SGNH_hydrolase_peri1, SGNH_peri1; putative periplasmic
member of the SGNH-family of hydrolases, a diverse
family of lipases and esterases. The tertiary fold of
the enzyme is substantially different from that of the
alpha/beta hydrolase family and unique among all known
hydrolases; its active site closely resembles the
Ser-His-Asp(Glu) triad found in other serine hydrolases.
Length = 189
Score = 27.6 bits (62), Expect = 3.8
Identities = 10/33 (30%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 99 YENVERWLRELRDHADQNIVIMLVGPPSLLRRY 131
+ + +++ LR N I+LVGPP L++
Sbjct: 80 RQQLREFIKRLRQIL-PNASILLVGPPDSLQKT 111
>gnl|CDD|183016 PRK11176, PRK11176, lipid transporter ATP-binding/permease protein;
Provisional.
Length = 582
Score = 28.1 bits (63), Expect = 3.8
Identities = 13/21 (61%), Positives = 15/21 (71%), Gaps = 3/21 (14%)
Query: 14 VVLIGDSGVGKS---NLLSRF 31
V L+G SG GKS NLL+RF
Sbjct: 372 VALVGRSGSGKSTIANLLTRF 392
>gnl|CDD|236865 PRK11160, PRK11160, cysteine/glutathione ABC transporter
membrane/ATP-binding component; Reviewed.
Length = 574
Score = 28.3 bits (64), Expect = 3.8
Identities = 12/22 (54%), Positives = 14/22 (63%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRN 34
KV L+G +G GKS LL TR
Sbjct: 368 KVALLGRTGCGKSTLLQLLTRA 389
>gnl|CDD|163293 TIGR03498, FliI_clade3, flagellar protein export ATPase FliI.
Members of this protein family are the FliI protein of
bacterial flagellum systems. This protein acts to drive
protein export for flagellar biosynthesis. The most
closely related family is the YscN family of bacterial
type III secretion systems. This model represents one
(of three) segment of the FliI family tree. These have
been modeled separately in order to exclude the type III
secretion ATPases more effectively.
Length = 418
Score = 28.0 bits (63), Expect = 4.0
Identities = 11/16 (68%), Positives = 11/16 (68%)
Query: 20 SGVGKSNLLSRFTRNE 35
SGVGKS LLS RN
Sbjct: 149 SGVGKSTLLSMLARNT 164
>gnl|CDD|238899 cd01918, HprK_C, HprK/P, the bifunctional histidine-containing
protein kinase/phosphatase, controls the
phosphorylation state of the phosphocarrier protein HPr
and regulates the utilization of carbon sources by
gram-positive bacteria. It catalyzes both the
ATP-dependent phosphorylation of Ser-46 of HPr and its
dephosphorylation by phosphorolysis. The latter
reaction uses inorganic phosphate as substrate and
produces pyrophosphate. Phosphoenolpyruvate
carboxykinase (PEPCK) and the C-terminal catalytic
domain of HprK/P are structurally similar with
conserved active site residues suggesting these two
phosphotransferases have related functions. The HprK/P
N-terminal domain is structurally similar to the
N-terminal domains of the MurE and MurF amino acid
ligases.
Length = 149
Score = 27.2 bits (61), Expect = 4.1
Identities = 8/14 (57%), Positives = 11/14 (78%)
Query: 14 VVLIGDSGVGKSNL 27
V++ G SG+GKS L
Sbjct: 17 VLITGPSGIGKSEL 30
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 28.2 bits (64), Expect = 4.1
Identities = 20/75 (26%), Positives = 31/75 (41%), Gaps = 14/75 (18%)
Query: 139 LLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGNKSDLRHLRAVPADEAKTFAERNN 198
LLV D ++ LT E+ E L + D+ +++ V NK+DL E N
Sbjct: 299 LLVLDASEPLTEEDDE----ILEELKDKPVIV--VLNKADL--------TGEIDLEEENG 344
Query: 199 LSFIETSALDSTNVE 213
I SA ++
Sbjct: 345 KPVIRISAKTGEGID 359
>gnl|CDD|224044 COG1119, ModF, ABC-type molybdenum transport system, ATPase
component/photorepair protein PhrA [Inorganic ion
transport and metabolism].
Length = 257
Score = 27.7 bits (62), Expect = 4.2
Identities = 13/50 (26%), Positives = 20/50 (40%), Gaps = 2/50 (4%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTI-GVEFATRSIQVD-QKTI 60
++G +G GK+ LLS T T+ G F + +K I
Sbjct: 59 HWAIVGPNGAGKTTLLSLLTGEHPPSSGDVTLLGRRFGKGETIFELRKRI 108
>gnl|CDD|236994 PRK11823, PRK11823, DNA repair protein RadA; Provisional.
Length = 446
Score = 28.1 bits (64), Expect = 4.4
Identities = 12/16 (75%), Positives = 13/16 (81%), Gaps = 1/16 (6%)
Query: 14 VVLI-GDSGVGKSNLL 28
VVLI GD G+GKS LL
Sbjct: 82 VVLIGGDPGIGKSTLL 97
>gnl|CDD|215651 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family,
nucleotide-binding domain. This family includes the
ATP synthase alpha and beta subunits, the ATP synthase
associated with flagella and the termination factor
Rho.
Length = 213
Score = 27.4 bits (62), Expect = 4.5
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRN 34
++ + G SG GK+ LL RN
Sbjct: 17 RIGIFGGSGTGKTVLLGMIARN 38
>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 = 27.0 bits (61), Expect = 4.6
Identities = 8/16 (50%), Positives = 12/16 (75%)
Query: 13 KVVLIGDSGVGKSNLL 28
++ L+G +G GKS LL
Sbjct: 28 RIGLVGRNGAGKSTLL 43
>gnl|CDD|226622 COG4138, BtuD, ABC-type cobalamin transport system, ATPase
component [Coenzyme metabolism].
Length = 248
Score = 27.5 bits (61), Expect = 4.7
Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 14/60 (23%)
Query: 16 LIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQERYRA 75
L+G +G GKS LL+R G+ + SIQ + ++A W R+RA
Sbjct: 30 LVGPNGAGKSTLLARMA------------GMTSGSGSIQFAGQPLEA--WSATELARHRA 75
>gnl|CDD|236351 PRK08927, fliI, flagellum-specific ATP synthase; Validated.
Length = 442
Score = 28.0 bits (63), Expect = 4.7
Identities = 11/15 (73%), Positives = 11/15 (73%)
Query: 20 SGVGKSNLLSRFTRN 34
SGVGKS LLS RN
Sbjct: 167 SGVGKSVLLSMLARN 181
>gnl|CDD|222036 pfam13304, AAA_21, AAA domain.
Length = 256
Score = 27.8 bits (61), Expect = 4.8
Identities = 13/56 (23%), Positives = 23/56 (41%), Gaps = 6/56 (10%)
Query: 15 VLIGDSGVGKSNLL------SRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQI 64
V+IG +G GKSNLL L+ +G++ + ++ I +
Sbjct: 3 VIIGPNGSGKSNLLKALALLLLLLSLGLTLDRGLNVGIKLLPFLLDENEIEIPLEF 58
>gnl|CDD|224051 COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase
component [Amino acid transport and metabolism].
Length = 240
Score = 27.5 bits (62), Expect = 5.0
Identities = 11/16 (68%), Positives = 12/16 (75%)
Query: 13 KVVLIGDSGVGKSNLL 28
VV+IG SG GKS LL
Sbjct: 30 VVVIIGPSGSGKSTLL 45
>gnl|CDD|218719 pfam05729, NACHT, NACHT domain. This NTPase domain is found in
apoptosis proteins as well as those involved in MHC
transcription activation. This family is closely
related to pfam00931.
Length = 165
Score = 27.3 bits (61), Expect = 5.0
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 14 VVLIGDSGVGKSNLLSRF 31
V+L G++G GK+ LL +
Sbjct: 3 VILQGEAGSGKTTLLQKI 20
>gnl|CDD|235150 PRK03695, PRK03695, vitamin B12-transporter ATPase; Provisional.
Length = 248
Score = 27.6 bits (62), Expect = 5.2
Identities = 19/60 (31%), Positives = 28/60 (46%), Gaps = 14/60 (23%)
Query: 16 LIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIWDTAGQERYRA 75
L+G +G GKS LL+R G+ + SIQ + ++A W A R+RA
Sbjct: 27 LVGPNGAGKSTLLARMA------------GLLPGSGSIQFAGQPLEA--WSAAELARHRA 72
>gnl|CDD|206750 cd01857, HSR1_MMR1, A circularly permuted subfamily of the Ras
GTPases. Human HSR1 is localized to the human MHC class
I region and is highly homologous to a putative
GTP-binding protein, MMR1 from mouse. These proteins
represent a new subfamily of GTP-binding proteins that
has only eukaryote members. This subfamily shows a
circular permutation of the GTPase signature motifs so
that the C-terminal strands 5, 6, and 7 (strand 6
contains the G4 box with sequence NKXD) are relocated to
the N-terminus.
Length = 140
Score = 26.8 bits (60), Expect = 5.3
Identities = 12/64 (18%), Positives = 30/64 (46%), Gaps = 10/64 (15%)
Query: 151 ENVERWLRELRDHADQNIVIMLVGNKSDL--RHLRAVPADEAKTFAERNNLSFIETSALD 208
++E++++E+ D + +L+ NK+DL R + ++ + + SAL+
Sbjct: 30 PDLEKYVKEV----DPSKENVLLLNKADLVTEEQR----KAWARYFKKEGIVVLFFSALN 81
Query: 209 STNV 212
+
Sbjct: 82 EATI 85
>gnl|CDD|153313 cd07629, BAR_Atg20p, The Bin/Amphiphysin/Rvs (BAR) domain of yeast
Sorting Nexin Atg20p. BAR domains are dimerization,
lipid binding and curvature sensing modules found in
many different proteins with diverse functions. Sorting
nexins (SNXs) are Phox homology (PX) domain containing
proteins that are involved in regulating membrane
traffic and protein sorting in the endosomal system.
SNXs differ from each other in their lipid-binding
specificity, subcellular localization and specific
function in the endocytic pathway. A subset of SNXs also
contain BAR domains. The PX-BAR structural unit
determines the specific membrane targeting of SNXs. The
function of Atg20p is unknown but it has been shown to
interact with Atg11p, which plays a role in linking
cargo molecules with vesicle-forming components. BAR
domains form dimers that bind to membranes, induce
membrane bending and curvature, and may also be involved
in protein-protein interactions.
Length = 187
Score = 27.4 bits (61), Expect = 5.8
Identities = 26/94 (27%), Positives = 37/94 (39%), Gaps = 11/94 (11%)
Query: 78 SAYYRGAVGALLVYDIAKHLTYENVERWLRELRDH-ADQNIVIMLVGPPSLLRRYYRGAV 136
SA + G V LL Y KH+ YE + L E A ++VI L R+ R
Sbjct: 97 SAQFAGVVRELLKYRKLKHVQYEMTKDSLLESALVAASDDLVISSTIKQKDLPRFQRERE 156
Query: 137 GALLVYDIAKHLTYENVERWLRELRDHADQNIVI 170
L +I K+ + +D A QN+
Sbjct: 157 ADL--REILKNY--------SKYHKDWAKQNLEA 180
>gnl|CDD|205733 pfam13555, AAA_29, P-loop containing region of AAA domain.
Length = 60
Score = 25.6 bits (57), Expect = 6.0
Identities = 8/13 (61%), Positives = 9/13 (69%)
Query: 16 LIGDSGVGKSNLL 28
L G SG GKS L+
Sbjct: 26 LTGPSGSGKSTLI 38
>gnl|CDD|172577 PRK14087, dnaA, chromosomal replication initiation protein;
Provisional.
Length = 450
Score = 27.6 bits (61), Expect = 6.0
Identities = 20/58 (34%), Positives = 34/58 (58%), Gaps = 7/58 (12%)
Query: 8 YDYLFKVVLIGDSGVGKSNLLS---RFTRNEFN-LESKSTIGVEFATRSIQVDQKTIK 61
Y+ LF + G+SG+GK++LL + + F+ L+ G EFA +++ + QKT K
Sbjct: 141 YNPLF---IYGESGMGKTHLLKAAKNYIESNFSDLKVSYMSGDEFARKAVDILQKTHK 195
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 27.2 bits (61), Expect = 6.1
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 11 LFKVVLIGDSGVGKSNLLSRFTRN 34
L ++ G S VGKS+L++ T
Sbjct: 24 LPEIAFAGRSNVGKSSLINALTNQ 47
>gnl|CDD|224550 COG1635, THI4, Ribulose 1,5-bisphosphate synthetase, converts PRPP
to RuBP, flavoprotein [Carbohydrate transport and
metabolism].
Length = 262
Score = 27.3 bits (61), Expect = 6.2
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 102 VERWLRELRDHADQNIVIMLVGPPSLLRRYY 132
ER+ +L D+ + +++I+ GP L YY
Sbjct: 18 TERYFEDLLDYLESDVIIVGAGPSGLTAAYY 48
>gnl|CDD|237457 PRK13647, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 274
Score = 27.4 bits (61), Expect = 6.3
Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 6/49 (12%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIK 61
K L+G +G GKS LL N L + + V +V+ + K
Sbjct: 33 KTALLGPNGAGKSTLLLHL--NGIYLPQRGRVKV----MGREVNAENEK 75
>gnl|CDD|232848 TIGR00157, TIGR00157, ribosome small subunit-dependent GTPase A.
Members of this protein were designated YjeQ and are now
designated RsgA (ribosome small subunit-dependent GTPase
A). The strongest motif in the alignment of these
proteins is GXSGVGKS[ST], a classic P-loop for
nucleotide binding. This protein has been shown to
cleave GTP and remain bound to GDP. A role as a
regulator of translation has been suggested. The Aquifex
aeolicus ortholog is split into consecutive open reading
frames. Consequently, this model was build in fragment
mode (-f option) [Protein synthesis, Translation
factors].
Length = 245
Score = 27.4 bits (61), Expect = 6.4
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 15 VLIGDSGVGKSNLLSR 30
V G SGVGKS+L++
Sbjct: 124 VFAGQSGVGKSSLINA 139
>gnl|CDD|213218 cd03251, ABCC_MsbA, ATP-binding cassette domain of the bacterial
lipid flippase and related proteins, subfamily C. MsbA
is an essential ABC transporter, closely related to
eukaryotic MDR proteins. ABC transporters are a large
family of proteins involved in the transport of a wide
variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and
GTP-binding and hydrolyzing proteins.
Length = 234
Score = 27.2 bits (61), Expect = 6.5
Identities = 12/21 (57%), Positives = 14/21 (66%), Gaps = 3/21 (14%)
Query: 14 VVLIGDSGVGKS---NLLSRF 31
V L+G SG GKS NL+ RF
Sbjct: 31 VALVGPSGSGKSTLVNLIPRF 51
>gnl|CDD|234608 PRK00064, recF, recombination protein F; Reviewed.
Length = 361
Score = 27.4 bits (62), Expect = 6.8
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 13 KVVLIGDSGVGKSNLL 28
VL+G++G GK+NLL
Sbjct: 25 VNVLVGENGQGKTNLL 40
>gnl|CDD|238026 cd00071, GMPK, Guanosine monophosphate kinase (GMPK, EC 2.7.4.8),
also known as guanylate kinase (GKase), catalyzes the
reversible phosphoryl transfer from adenosine
triphosphate (ATP) to guanosine monophosphate (GMP) to
yield adenosine diphosphate (ADP) and guanosine
diphosphate (GDP). It plays an essential role in the
biosynthesis of guanosine triphosphate (GTP). This
enzyme is also important for the activation of some
antiviral and anticancer agents, such as acyclovir,
ganciclovir, carbovir, and thiopurines.
Length = 137
Score = 26.7 bits (60), Expect = 7.1
Identities = 13/27 (48%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 14 VVLIGDSGVGKSNLLSR-FTRNEFNLE 39
+VL G SGVGKS LL R + N
Sbjct: 2 IVLSGPSGVGKSTLLKRLLEEFDPNFG 28
>gnl|CDD|148849 pfam07475, Hpr_kinase_C, HPr Serine kinase C-terminal domain.
This family represents the C terminal kinase domain of
Hpr Serine/threonine kinase PtsK. This kinase is the
sensor in a multicomponent phosphorelay system in
control of carbon catabolic repression in bacteria.
This kinase in unusual in that it recognises the
tertiary structure of its target and is a member of a
novel family unrelated to any previously described
protein phosphorylating enzymes. X-ray analysis of the
full-length crystalline enzyme from Staphylococcus
xylosus at a resolution of 1.95 A shows the enzyme to
consist of two clearly separated domains that are
assembled in a hexameric structure resembling a
three-bladed propeller.
Length = 171
Score = 26.6 bits (60), Expect = 7.2
Identities = 7/12 (58%), Positives = 11/12 (91%)
Query: 14 VVLIGDSGVGKS 25
V++ G+SG+GKS
Sbjct: 21 VLITGESGIGKS 32
>gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol
utilisation. Members of this family function in
ethanolamine and propanediol degradation pathways,
however the exact roles of these proteins is poorly
understood.
Length = 143
Score = 26.4 bits (59), Expect = 7.3
Identities = 16/41 (39%), Positives = 22/41 (53%), Gaps = 2/41 (4%)
Query: 13 KVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSI 53
K++LIG SG GK+ L E L+ K T +EF+ I
Sbjct: 3 KIMLIGRSGCGKTTLTQAL-NGE-ELKYKKTQAIEFSDNMI 41
>gnl|CDD|235316 PRK04863, mukB, cell division protein MukB; Provisional.
Length = 1486
Score = 27.6 bits (62), Expect = 7.5
Identities = 21/76 (27%), Positives = 33/76 (43%), Gaps = 19/76 (25%)
Query: 51 RSIQVDQKTIKAQIWDTAGQERY-----RAITSAYYRGAVGALLVYDIAK------HLTY 99
+ + + +K+Q+ D Q+ RAI Y+ AV AL + AK LT
Sbjct: 386 EAAEEEVDELKSQLADY--QQALDVQQTRAIQ---YQQAVQAL---ERAKQLCGLPDLTA 437
Query: 100 ENVERWLRELRDHADQ 115
+N E WL E + +
Sbjct: 438 DNAEDWLEEFQAKEQE 453
>gnl|CDD|218648 pfam05592, Bac_rhamnosid, Bacterial alpha-L-rhamnosidase. This
family consists of bacterial rhamnosidase A and B
enzymes. L-Rhamnose is abundant in biomass as a common
constituent of glycolipids and glycosides, such as plant
pigments, pectic polysaccharides, gums or
biosurfactants. Some rhamnosides are important bioactive
compounds. For example, terpenyl glycosides, the
glycosidic precursor of aromatic terpenoids, act as
important flavouring substances in grapes. Other
rhamnosides act as cytotoxic rhamnosylated terpenoids,
as signal substances in plants or play a role in the
antigenicity of pathogenic bacteria.
Length = 509
Score = 27.2 bits (61), Expect = 7.5
Identities = 23/103 (22%), Positives = 33/103 (32%), Gaps = 32/103 (31%)
Query: 83 GAVGALLVYDIAKHLTYENVERWLRELRDHADQNIVIMLVGP------------------ 124
A A YD +WLR+L D +N + V P
Sbjct: 157 FAPTASYNYD-----VSAFYAKWLRDLADEQRENGAVPDVVPSVWGPGSPGPEWGDAIVI 211
Query: 125 -PSLLRRYYRGAVGALLVYDIAKHLTYENVERWLRELRDHADQ 166
P +L R Y G L Y +++RWL + +D
Sbjct: 212 VPWVLYRNY-GDERIL-----KDQ--YPSMKRWLDYILQRSDD 246
>gnl|CDD|213260 cd03293, ABC_NrtD_SsuB_transporters, ATP-binding cassette domain
of the nitrate and sulfonate transporters. NrtD and
SsuB are the ATP-binding subunits of the bacterial
ABC-type nitrate and sulfonate transport systems,
respectively. ABC transporters are a large family of
proteins involved in the transport of a wide variety of
different compounds, like sugars, ions, peptides, and
more complex organic molecules. The nucleotide binding
domain shows the highest similarity between all members
of the family. ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 220
Score = 27.1 bits (61), Expect = 7.7
Identities = 10/16 (62%), Positives = 11/16 (68%)
Query: 14 VVLIGDSGVGKSNLLS 29
V L+G SG GKS LL
Sbjct: 33 VALVGPSGCGKSTLLR 48
>gnl|CDD|237456 PRK13641, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 287
Score = 27.1 bits (60), Expect = 7.7
Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 2/49 (4%)
Query: 14 VVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDQKTIKA 62
V L+G +G GKS L+ F N S TI + + + K +K
Sbjct: 36 VALVGHTGSGKSTLMQHF--NALLKPSSGTITIAGYHITPETGNKNLKK 82
>gnl|CDD|184593 PRK14258, PRK14258, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 261
Score = 26.9 bits (59), Expect = 8.2
Identities = 16/39 (41%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 16 LIGDSGVGKSNLLSRFTR-NEFNLESKSTIGVEFATRSI 53
+IG SG GKS L R NE E + VEF ++I
Sbjct: 38 IIGPSGCGKSTFLKCLNRMNELESEVRVEGRVEFFNQNI 76
>gnl|CDD|224079 COG1157, FliI, Flagellar biosynthesis/type III secretory pathway
ATPase [Cell motility and secretion / Intracellular
trafficking and secretion].
Length = 441
Score = 27.2 bits (61), Expect = 8.2
Identities = 10/15 (66%), Positives = 10/15 (66%)
Query: 20 SGVGKSNLLSRFTRN 34
SGVGKS LL RN
Sbjct: 172 SGVGKSTLLGMIARN 186
>gnl|CDD|224973 COG2062, SixA, Phosphohistidine phosphatase SixA [Signal
transduction mechanisms].
Length = 163
Score = 26.5 bits (59), Expect = 8.4
Identities = 15/77 (19%), Positives = 20/77 (25%), Gaps = 13/77 (16%)
Query: 104 RWLRELRDHADQNIVIMLVGPPSLLRRYYRGAVGALLVYDIAK-----HLTYE-NVERWL 157
WL D +V S R + A K L + L
Sbjct: 39 AWLAGQGVEPDLVLV-------SPAVRARQTAEIVAEHLGEKKVEVFEELLPNGDPGTVL 91
Query: 158 RELRDHADQNIVIMLVG 174
L D ++LVG
Sbjct: 92 DYLEALGDGVGSVLLVG 108
Score = 26.5 bits (59), Expect = 8.5
Identities = 7/29 (24%), Positives = 10/29 (34%), Gaps = 1/29 (3%)
Query: 96 HLTYE-NVERWLRELRDHADQNIVIMLVG 123
L + L L D ++LVG
Sbjct: 80 ELLPNGDPGTVLDYLEALGDGVGSVLLVG 108
>gnl|CDD|206665 cd01876, YihA_EngB, YihA (EngB) GTPase family. The YihA (EngB)
subfamily of GTPases is typified by the E. coli YihA,
an essential protein involved in cell division control.
YihA and its orthologs are small proteins that
typically contain less than 200 amino acid residues and
consists of the GTPase domain only (some of the
eukaryotic homologs contain an N-terminal extension of
about 120 residues that might be involved in organellar
targeting). Homologs of yihA are found in most
Gram-positive and Gram-negative pathogenic bacteria,
with the exception of Mycobacterium tuberculosis. The
broad-spectrum nature of YihA and its essentiality for
cell viability in bacteria make it an attractive
antibacterial target.
Length = 170
Score = 26.7 bits (60), Expect = 8.5
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 14 VVLIGDSGVGKSNLLSRFTRN 34
V G S VGKS+L++ T
Sbjct: 2 VAFAGRSNVGKSSLINALTNR 22
>gnl|CDD|236947 PRK11650, ugpC, glycerol-3-phosphate transporter ATP-binding
subunit; Provisional.
Length = 356
Score = 27.1 bits (61), Expect = 8.6
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 14 VVLIGDSGVGKSNLL 28
+VL+G SG GKS LL
Sbjct: 33 IVLVGPSGCGKSTLL 47
>gnl|CDD|224041 COG1116, TauB, ABC-type nitrate/sulfonate/bicarbonate transport
system, ATPase component [Inorganic ion transport and
metabolism].
Length = 248
Score = 26.8 bits (60), Expect = 8.9
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 14 VVLIGDSGVGKSNLL 28
V ++G SG GKS LL
Sbjct: 32 VAILGPSGCGKSTLL 46
>gnl|CDD|182692 PRK10744, pstB, phosphate transporter ATP-binding protein;
Provisional.
Length = 260
Score = 26.9 bits (60), Expect = 9.0
Identities = 11/18 (61%), Positives = 11/18 (61%)
Query: 16 LIGDSGVGKSNLLSRFTR 33
IG SG GKS LL F R
Sbjct: 44 FIGPSGCGKSTLLRTFNR 61
>gnl|CDD|234789 PRK00549, PRK00549, competence damage-inducible protein A;
Provisional.
Length = 414
Score = 27.1 bits (61), Expect = 9.0
Identities = 13/47 (27%), Positives = 16/47 (34%), Gaps = 2/47 (4%)
Query: 112 HADQNIVIMLVGPPSLLRRYYRGAVGALLVYDIAKHLTYENVERWLR 158
D I+L GPPS L+ + V L R LR
Sbjct: 140 EVDGKTYIVLPGPPSELKPMFEEYVVPYLSSAKGTGEVL--YSRVLR 184
>gnl|CDD|182980 PRK11124, artP, arginine transporter ATP-binding subunit;
Provisional.
Length = 242
Score = 26.9 bits (60), Expect = 9.0
Identities = 10/15 (66%), Positives = 13/15 (86%)
Query: 14 VVLIGDSGVGKSNLL 28
+VL+G SG GKS+LL
Sbjct: 31 LVLLGPSGAGKSSLL 45
>gnl|CDD|172749 PRK14261, PRK14261, phosphate ABC transporter ATP-binding
protein; Provisional.
Length = 253
Score = 26.7 bits (59), Expect = 9.1
Identities = 12/18 (66%), Positives = 12/18 (66%)
Query: 16 LIGDSGVGKSNLLSRFTR 33
LIG SG GKS LL F R
Sbjct: 37 LIGPSGCGKSTLLRCFNR 54
>gnl|CDD|233088 TIGR00679, hpr-ser, Hpr(Ser) kinase/phosphatase. Members of this
family are the bifunctional enzyme, HPr
kinase/phosphatase. All members of the seed alignment
(n=57) have a gene tightly clustered with a gene for the
phospocarrier protein HPr, its target [Regulatory
functions, Protein interactions, Signal transduction,
PTS].
Length = 300
Score = 26.7 bits (60), Expect = 9.3
Identities = 7/12 (58%), Positives = 11/12 (91%)
Query: 14 VVLIGDSGVGKS 25
V++ G+SG+GKS
Sbjct: 146 VLITGESGIGKS 157
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 26.9 bits (60), Expect = 9.6
Identities = 17/73 (23%), Positives = 30/73 (41%), Gaps = 17/73 (23%)
Query: 13 KVVLIGDSGVGKSNLLSR--FTRNEFNLESKSTIGVEFATRSIQVDQKTIKAQIW----- 65
+V IG GKS L+ R + E + K T+ ++ + K + + +
Sbjct: 9 NLVFIGHVDAGKSTLVGRLLYDLGEID---KRTM------EKLEKEAKELGKESFKFAWV 59
Query: 66 -DTAGQERYRAIT 77
D +ER R +T
Sbjct: 60 LDKTKEERERGVT 72
>gnl|CDD|234033 TIGR02857, CydD, thiol reductant ABC exporter, CydD subunit. The
gene pair cydCD encodes an ABC-family transporter in
which each gene contains an N-terminal membrane-spanning
domain (pfam00664) and a C-terminal ATP-binding domain
(pfam00005). In E. coli these genes were discovered as
mutants which caused the terminal heme-copper oxidase
complex cytochrome bd to fail to assemble. Recent work
has shown that the transporter is involved in export of
redox-active thiol compounds such as cysteine and
glutathione. The linkage to assembly of the cytochrome
bd complex is further supported by the conserved operon
structure found outside the gammaproteobacteria
(cydABCD) containing both the transporter and oxidase
genes components. The genes used as the seed members for
this model are all either found in the
gammproteobacterial context or the CydABCD context. All
members of this family scoring above trusted at the time
of its creation were from genomes which encode a
cytochrome bd complex. Unfortunately, the gene symbol
nomenclature adopted based on this operon in B. subtilis
assigns cydC to the third gene in the operon where this
gene is actually homologous to the E. coli cydD gene. We
have chosen to name all homologs in this family in
accordance with the precedence of publication of the E.
coli name, CydD.
Length = 529
Score = 26.9 bits (60), Expect = 9.6
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 13 KVVLIGDSGVGKSNLLS 29
+V L+G SG GKS LL+
Sbjct: 350 RVALVGPSGAGKSTLLN 366
>gnl|CDD|235459 PRK05428, PRK05428, HPr kinase/phosphorylase; Provisional.
Length = 308
Score = 26.7 bits (60), Expect = 9.8
Identities = 7/12 (58%), Positives = 11/12 (91%)
Query: 14 VVLIGDSGVGKS 25
V++ G+SG+GKS
Sbjct: 149 VLITGESGIGKS 160
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
0.319 0.135 0.384
Gapped
Lambda K H
0.267 0.0751 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,500,218
Number of extensions: 1104188
Number of successful extensions: 2216
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2079
Number of HSP's successfully gapped: 366
Length of query: 223
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 130
Effective length of database: 6,812,680
Effective search space: 885648400
Effective search space used: 885648400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (25.7 bits)