RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2300
(221 letters)
>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 = 336 bits (864), Expect = e-119
Identities = 146/165 (88%), Positives = 157/165 (95%)
Query: 21 MFKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQ 80
MFKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTV+R+DKR+KLQIWDTAGQ
Sbjct: 1 MFKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVYRNDKRIKLQIWDTAGQ 60
Query: 81 ERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNKCDMED 140
ERYRTITTAYYRGAMGFILMYD+TNEESF ++QDW TQIKTYSWDNAQVILVGNKCDMED
Sbjct: 61 ERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSWDNAQVILVGNKCDMED 120
Query: 141 ERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDIICDK 185
ERV+S ERG+ LA+ LG EFFE SAK+N+NVK VFERLVDIICDK
Sbjct: 121 ERVVSAERGRQLADQLGFEFFEASAKENINVKQVFERLVDIICDK 165
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 258 bits (663), Expect = 5e-89
Identities = 83/161 (51%), Positives = 120/161 (74%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
FK+++IG+S VGK+S L R+ D F+ + ST+G+DFK KT+ KRVKLQIWDTAGQE
Sbjct: 1 FKIILIGDSGVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIEVDGKRVKLQIWDTAGQE 60
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNKCDMEDE 141
R+R+IT++YYRGA+G +L+YD+TN ESF ++++W+ +++ Y+ N ++LVGNK D+E++
Sbjct: 61 RFRSITSSYYRGAVGALLVYDITNRESFENLENWLKELREYASPNVVIMLVGNKSDLEEQ 120
Query: 142 RVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDII 182
R +S E + AE G+ FFETSAK N NV+ FE L I
Sbjct: 121 RQVSREEAEAFAEEHGLPFFETSAKTNTNVEEAFEELAREI 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 = 257 bits (659), Expect = 2e-88
Identities = 92/167 (55%), Positives = 131/167 (78%)
Query: 19 DYMFKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTA 78
DY+FKLL+IG+S VGK+ L R+++DSF +F+ST+GIDFK++T+ K++KLQIWDTA
Sbjct: 1 DYLFKLLLIGDSGVGKSCLLLRFSEDSFNPSFISTIGIDFKIRTIELDGKKIKLQIWDTA 60
Query: 79 GQERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNKCDM 138
GQER+RTITT+YYRGAMG IL+YD+T+E+SF +I++W+ I ++ ++ + +LVGNKCDM
Sbjct: 61 GQERFRTITTSYYRGAMGIILVYDITDEKSFENIKNWMRNIDEHASEDVERMLVGNKCDM 120
Query: 139 EDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDIICDK 185
E++RV+S E G+ LA G++F ETSAK N+NV+ F L I K
Sbjct: 121 EEKRVVSKEEGEALAREYGIKFLETSAKANINVEEAFLTLAKDILKK 167
>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 = 250 bits (641), Expect = 9e-86
Identities = 78/162 (48%), Positives = 114/162 (70%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQER 82
KL+++G+ VGK+S L R+ + F ++ T+G+DF KT+ K VKLQIWDTAGQER
Sbjct: 1 KLVLVGDGGVGKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAGQER 60
Query: 83 YRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNKCDMEDER 142
+R + YYRGA GF+L+YD+T+ +SF +++ W+ +I ++ +N ++LVGNKCD+ED+R
Sbjct: 61 FRALRPLYYRGAQGFLLVYDITSRDSFENVKKWLEEILRHADENVPIVLVGNKCDLEDQR 120
Query: 143 VISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDIICD 184
V+S E G+ LA+ LG+ F ETSAK N NV+ FE L I
Sbjct: 121 VVSTEEGEALAKELGLPFMETSAKTNENVEEAFEELAREILK 162
>gnl|CDD|206640 cd00154, Rab, Ras-related in brain (Rab) family of small guanosine
triphosphatases (GTPases). Rab GTPases form the largest
family within the Ras superfamily. There are at least 60
Rab genes in the human genome, and a number of Rab
GTPases are conserved from yeast to humans. Rab GTPases
are small, monomeric proteins that function as molecular
switches to regulate vesicle trafficking pathways. The
different Rab GTPases are localized to the cytosolic
face of specific intracellular membranes, where they
regulate distinct steps in membrane traffic pathways. In
the GTP-bound form, Rab GTPases recruit specific sets of
effector proteins onto membranes. Through their
effectors, Rab GTPases regulate vesicle formation,
actin- and tubulin-dependent vesicle movement, and
membrane fusion. GTPase activating proteins (GAPs)
interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which mask C-terminal lipid binding and promote
cytosolic localization. While most unicellular organisms
possess 5-20 Rab members, several have been found to
possess 60 or more Rabs; for many of these Rab isoforms,
homologous proteins are not found in other organisms.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Since crystal
structures often lack C-terminal residues, the lipid
modification site is not available for annotation in
many of the CDs in the hierarchy, but is included where
possible.
Length = 159
Score = 243 bits (623), Expect = 5e-83
Identities = 86/159 (54%), Positives = 115/159 (72%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
FK+++IG+S VGKTS L R+ D+ F+ + ST+G+DFK KT+ K+VKLQIWDTAGQE
Sbjct: 1 FKIVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGVDFKSKTIEVDGKKVKLQIWDTAGQE 60
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNKCDMEDE 141
R+R+IT++YYRGA G IL+YDVTN ESF ++ W+ ++K Y+ N +ILVGNK D+EDE
Sbjct: 61 RFRSITSSYYRGAHGAILVYDVTNRESFENLDKWLNELKEYAPPNIPIILVGNKSDLEDE 120
Query: 142 RVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVD 180
R +S E + A+ G+ FFETSAK NV FE L
Sbjct: 121 RQVSTEEAQQFAKENGLLFFETSAKTGENVDEAFESLAR 159
>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 = 221 bits (564), Expect = 6e-74
Identities = 82/159 (51%), Positives = 122/159 (76%)
Query: 20 YMFKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAG 79
Y+FKLL+IG+S VGK+ L R+ADD++T +++ST+G+DFK++T+ K VKLQIWDTAG
Sbjct: 1 YLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTVKLQIWDTAG 60
Query: 80 QERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNKCDME 139
QER+RTIT++YYRGA G I++YDVT++ESF +++ W+ +I Y+ +N +LVGNKCD+
Sbjct: 61 QERFRTITSSYYRGAHGIIIVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLT 120
Query: 140 DERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERL 178
D++V+ + K A+ LG+ F ETSAK+ NV+ F +
Sbjct: 121 DKKVVDYTEAKEFADELGIPFLETSAKNATNVEEAFMTM 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 = 208 bits (530), Expect = 1e-68
Identities = 80/180 (44%), Positives = 130/180 (72%), Gaps = 11/180 (6%)
Query: 18 FDYMFKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDK--------- 68
+DY+ KLL +G+S VGKT+FL+RY D+ F F++TVGIDF+ K V + +
Sbjct: 1 YDYLIKLLALGDSGVGKTTFLYRYTDNKFNPKFITTVGIDFREKRVVYNSQGPDGTSGKA 60
Query: 69 -RVKLQIWDTAGQERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSW-DN 126
RV LQ+WDTAGQER+R++TTA++R AMGF+LM+D+T+E+SF ++++W++Q++ +++ +N
Sbjct: 61 FRVHLQLWDTAGQERFRSLTTAFFRDAMGFLLMFDLTSEQSFLNVRNWMSQLQAHAYCEN 120
Query: 127 AQVILVGNKCDMEDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDIICDKM 186
++L+GNK D+ D+R +S + + LA+ G+ +FETSA NV+ E L+D+I +M
Sbjct: 121 PDIVLIGNKADLPDQREVSERQARELADKYGIPYFETSAATGQNVEKAVETLLDLIMKRM 180
>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 = 196 bits (501), Expect = 2e-64
Identities = 71/165 (43%), Positives = 111/165 (67%)
Query: 19 DYMFKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTA 78
DY+FK+++IG+S VGK++ L R+ + F ST+G++F +T+ K +K QIWDTA
Sbjct: 1 DYLFKIVLIGDSGVGKSNLLSRFTRNEFNLDSKSTIGVEFATRTIQIDGKTIKAQIWDTA 60
Query: 79 GQERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNKCDM 138
GQERYR IT+AYYRGA+G +L+YD+T + +F +++ W+ +++ ++ N ++LVGNK D+
Sbjct: 61 GQERYRAITSAYYRGAVGALLVYDITKKSTFENVERWLKELRDHADSNIVIMLVGNKSDL 120
Query: 139 EDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDIIC 183
R + E K AE G+ F ETSA D NV+ F++L+ I
Sbjct: 121 RHLRAVPTEEAKAFAEKNGLSFIETSALDGTNVEEAFKQLLTEIY 165
>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 = 195 bits (498), Expect = 2e-63
Identities = 83/194 (42%), Positives = 135/194 (69%), Gaps = 6/194 (3%)
Query: 16 QNFDYMFKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIW 75
+++D++FKLLIIG+S VGK+S L R+AD++F+ ++++T+G+DFK++TV + +RVKLQIW
Sbjct: 1 RDYDHLFKLLIIGDSGVGKSSLLLRFADNTFSGSYITTIGVDFKIRTVEINGERVKLQIW 60
Query: 76 DTAGQERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNK 135
DTAGQER+RTIT+ YYRG G I++YDVTN ESF +++ W+ +I+ + D+ +LVGNK
Sbjct: 61 DTAGQERFRTITSTYYRGTHGVIVVYDVTNGESFVNVKRWLQEIEQ-NCDDVCKVLVGNK 119
Query: 136 CDMEDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDIICDKM-----SESL 190
D + +V+ E A +G+ FETSAK+N+NV+ +F + +++ +
Sbjct: 120 NDDPERKVVETEDAYKFAGQMGISLFETSAKENINVEEMFNCITELVLRAKKDNLAKQQQ 179
Query: 191 DSDPNLVAGPKGTR 204
++V PK ++
Sbjct: 180 QQQNDVVKLPKNSK 193
>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 = 189 bits (483), Expect = 1e-61
Identities = 81/162 (50%), Positives = 111/162 (68%), Gaps = 2/162 (1%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
K+L+IG+S VGK+S L R+ DD+F ST+G+DFKVKTV K+VKL IWDTAGQE
Sbjct: 1 LKILLIGDSGVGKSSLLLRFTDDTFDEDLSSTIGVDFKVKTVTVDGKKVKLAIWDTAGQE 60
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSW-DNAQVILVGNKCDMED 140
R+RT+T++YYRGA G IL+YDVT ++F ++ W+ ++ TYS +A +LVGNK D E
Sbjct: 61 RFRTLTSSYYRGAQGVILVYDVTRRDTFDNLDTWLNELDTYSTNPDAVKMLVGNKIDKE- 119
Query: 141 ERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDII 182
R ++ E G+ A + F ETSAK + V+ FE LV+ I
Sbjct: 120 NREVTREEGQKFARKHNMLFIETSAKTRIGVQQAFEELVEKI 161
>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 = 184 bits (470), Expect = 1e-59
Identities = 67/155 (43%), Positives = 99/155 (63%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
FKL+++G+SSVGK+S + R+ + F+ ST+G F +TV D VK +IWDTAGQE
Sbjct: 2 FKLVLLGDSSVGKSSIVLRFVKNEFSENQESTIGAAFLTQTVNLDDTTVKFEIWDTAGQE 61
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNKCDMEDE 141
RYR++ YYRGA I++YD+T+EESF + W+ +++ + N + L GNK D+E +
Sbjct: 62 RYRSLAPMYYRGAAAAIVVYDITSEESFEKAKSWVKELQEHGPPNIVIALAGNKADLESK 121
Query: 142 RVISFERGKHLAESLGVEFFETSAKDNVNVKGVFE 176
R +S E + A+ G+ F ETSAK NV +F
Sbjct: 122 RQVSTEEAQEYADENGLLFMETSAKTGENVNELFT 156
>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 = 180 bits (459), Expect = 4e-58
Identities = 75/161 (46%), Positives = 111/161 (68%), Gaps = 1/161 (0%)
Query: 19 DYMFKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTA 78
D++FK+++IG+S+VGKT + R+ +F+ +T+G+DF +KT+ KRVKLQIWDTA
Sbjct: 1 DFLFKIILIGDSNVGKTCVVQRFKSGTFSERQGNTIGVDFTMKTLEIQGKRVKLQIWDTA 60
Query: 79 GQERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNKCDM 138
GQER+RTIT +YYR A G I+ YD+T SF S+ WI +++ Y N ++L+GNKCD+
Sbjct: 61 GQERFRTITQSYYRSANGAIIAYDITRRSSFESVPHWIEEVEKYGASNVVLLLIGNKCDL 120
Query: 139 EDERVISFERGKHLAESLGVEF-FETSAKDNVNVKGVFERL 178
E++R + FE LAE G+ ETSAK++ NV+ F +
Sbjct: 121 EEQREVLFEEACTLAEHYGILAVLETSAKESSNVEEAFLLM 161
>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 = 176 bits (449), Expect = 1e-56
Identities = 65/161 (40%), Positives = 106/161 (65%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
KL+ +G+ SVGKTS + R+ D+F + + +T+GIDF KT++ DK V+LQ+WDTAGQE
Sbjct: 1 HKLVFLGDQSVGKTSIITRFMYDTFDNQYQATIGIDFLSKTMYVDDKTVRLQLWDTAGQE 60
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNKCDMEDE 141
R+R++ +Y R + +++YD+TN +SF + WI ++ ++ ++LVGNK D+ D+
Sbjct: 61 RFRSLIPSYIRDSSVAVVVYDITNRQSFDNTDKWIDDVRDERGNDVIIVLVGNKTDLSDK 120
Query: 142 RVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDII 182
R +S E G+ A+ F ETSAK NVK +F+++ +
Sbjct: 121 RQVSTEEGEKKAKENNAMFIETSAKAGHNVKQLFKKIAQAL 161
>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 = 173 bits (441), Expect = 2e-55
Identities = 66/161 (40%), Positives = 98/161 (60%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
FK++++G VGKTS + RY ++ F ST F KTV KR+ L IWDTAGQE
Sbjct: 1 FKVVLLGEGRVGKTSLVLRYVENKFNEKHESTTQASFFQKTVNIGGKRIDLAIWDTAGQE 60
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNKCDMEDE 141
RY + YYR A G IL+YD+T+ +SF ++ WI ++K +N +++VGNK D+E +
Sbjct: 61 RYHALGPIYYRDADGAILVYDITDADSFQKVKKWIKELKQMRGNNISLVIVGNKIDLERQ 120
Query: 142 RVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDII 182
RV+S + A+S+G + FETSAK ++ +F L +
Sbjct: 121 RVVSKSEAEEYAKSVGAKHFETSAKTGKGIEELFLSLAKRM 161
>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 = 172 bits (437), Expect = 2e-54
Identities = 82/165 (49%), Positives = 119/165 (72%), Gaps = 1/165 (0%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQER 82
+++IIG+ VGKTS + R+ DD+F A STVG+DFK+KTV K+++LQIWDTAGQER
Sbjct: 2 QVIIIGSRGVGKTSLMERFTDDTFCEACKSTVGVDFKIKTVELRGKKIRLQIWDTAGQER 61
Query: 83 YRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNKCDMEDER 142
+ +IT+AYYR A G IL+YD+T +E+F + W+ I Y+ ++A+++LVGNK D E +R
Sbjct: 62 FNSITSAYYRSAKGIILVYDITKKETFDDLPKWMKMIDKYASEDAELLLVGNKLDCETDR 121
Query: 143 VISFERGKHLAESL-GVEFFETSAKDNVNVKGVFERLVDIICDKM 186
I+ ++G+ A+ + G+ F E SAKDN NV +F +LVD I KM
Sbjct: 122 EITRQQGEKFAQQITGMRFCEASAKDNFNVDEIFLKLVDDILKKM 166
>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 = 168 bits (428), Expect = 4e-53
Identities = 77/155 (49%), Positives = 108/155 (69%), Gaps = 1/155 (0%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSF-TSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQ 80
FK++++G+S VGKT L R+ D +F +F++TVGI F K V +VKLQIWDTAGQ
Sbjct: 1 FKVMLVGDSGVGKTCLLVRFKDGAFLAGSFIATVGIQFTNKVVTVDGVKVKLQIWDTAGQ 60
Query: 81 ERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNKCDMED 140
ER+R++T AYYR A +L+YDVTN+ SF +I+ W+T+I Y+ + ++L+GNK DM
Sbjct: 61 ERFRSVTHAYYRDAHALLLLYDVTNKSSFDNIRAWLTEILEYAQSDVVIMLLGNKADMSG 120
Query: 141 ERVISFERGKHLAESLGVEFFETSAKDNVNVKGVF 175
ERV+ E G+ LA+ GV F ETSAK +NV+ F
Sbjct: 121 ERVVKREDGERLAKEYGVPFMETSAKTGLNVELAF 155
>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 = 166 bits (423), Expect = 1e-52
Identities = 70/168 (41%), Positives = 105/168 (62%)
Query: 18 FDYMFKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDT 77
+ Y+FK +IIG++ VGK+ L ++ D F T+G++F + + K++KLQIWDT
Sbjct: 1 YAYLFKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDT 60
Query: 78 AGQERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNKCD 137
AGQE +R+IT +YYRGA G +L+YD+T E+F + W+ + +S N ++L+GNKCD
Sbjct: 61 AGQESFRSITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQHSNSNMTIMLIGNKCD 120
Query: 138 MEDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDIICDK 185
+E R +S+E G+ A G+ F ETSAK NV+ F I DK
Sbjct: 121 LESRREVSYEEGEAFAREHGLIFMETSAKTASNVEEAFINTAKEIYDK 168
>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 = 164 bits (416), Expect = 1e-51
Identities = 77/161 (47%), Positives = 113/161 (70%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
F+LL+IG+S VGKT L R+ D+ F S+ +ST+G+DFK+KT+ +V++QIWDTAGQE
Sbjct: 1 FRLLLIGDSGVGKTCLLCRFTDNEFHSSHISTIGVDFKMKTIEVDGIKVRIQIWDTAGQE 60
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNKCDMEDE 141
RY+TIT YYR A G L+YD+++E S+ I W++ + Y+ + Q IL+GNK D E +
Sbjct: 61 RYQTITKQYYRRAQGIFLVYDISSERSYQHIMKWVSDVDEYAPEGVQKILIGNKADEEQK 120
Query: 142 RVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDII 182
R + E+G LA+ G++FFETSA N N+K F RL +++
Sbjct: 121 RQVGDEQGNKLAKEYGMDFFETSACTNKNIKESFTRLTELV 161
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 163 bits (414), Expect = 1e-50
Identities = 72/168 (42%), Positives = 115/168 (68%), Gaps = 1/168 (0%)
Query: 15 DQNFDYMFKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQI 74
D +DY+FK+++IG+S VGK++ L R+ + F ST+G++F +T+ K VK QI
Sbjct: 6 DHEYDYLFKIVLIGDSGVGKSNILSRFTRNEFCLESKSTIGVEFATRTLQVEGKTVKAQI 65
Query: 75 WDTAGQERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGN 134
WDTAGQERYR IT+AYYRGA+G +L+YD+T ++F ++Q W+ +++ ++ N +++ GN
Sbjct: 66 WDTAGQERYRAITSAYYRGAVGALLVYDITKRQTFDNVQRWLRELRDHADSNIVIMMAGN 125
Query: 135 KCDMEDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFER-LVDI 181
K D+ R ++ E G+ LAE G+ F ETSA + NV+ F+ L++I
Sbjct: 126 KSDLNHLRSVAEEDGQALAEKEGLSFLETSALEATNVEKAFQTILLEI 173
>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 = 161 bits (409), Expect = 2e-50
Identities = 69/163 (42%), Positives = 112/163 (68%)
Query: 16 QNFDYMFKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIW 75
+++D++FK+++IGN+ VGKT + R+ F +T+G+DF +KTV +++KLQIW
Sbjct: 2 EDYDFLFKIVLIGNAGVGKTCLVRRFTQGLFPPGQGATIGVDFMIKTVEIKGEKIKLQIW 61
Query: 76 DTAGQERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNK 135
DTAGQER+R+IT +YYR A IL YD+T EESF + +W+ +I+ Y+ + ILVGNK
Sbjct: 62 DTAGQERFRSITQSYYRSANALILTYDITCEESFRCLPEWLREIEQYANNKVITILVGNK 121
Query: 136 CDMEDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERL 178
D+ + R +S +R + +++ + + ETSAK++ NV+ +F L
Sbjct: 122 IDLAERREVSQQRAEEFSDAQDMYYLETSAKESDNVEKLFLDL 164
>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 = 161 bits (410), Expect = 4e-50
Identities = 70/161 (43%), Positives = 111/161 (68%), Gaps = 2/161 (1%)
Query: 20 YMFKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTV-FRHDKRVKLQIWDTA 78
Y F+L++IG+S+VGK+S L R+ + F TVG+DF + + R+KLQ+WDTA
Sbjct: 1 YQFRLIVIGDSTVGKSSLLKRFTEGRFAEVSDPTVGVDFFSRLIEIEPGVRIKLQLWDTA 60
Query: 79 GQERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQV-ILVGNKCD 137
GQER+R+IT +YYR ++G +L++D+TN ESF + DW+ + +++ + V ILVG+KCD
Sbjct: 61 GQERFRSITRSYYRNSVGVLLVFDITNRESFEHVHDWLEEARSHIQPHRPVFILVGHKCD 120
Query: 138 MEDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERL 178
+E +R ++ E + LA+ LG+++ ETSA+ NV+ FE L
Sbjct: 121 LESQRQVTREEAEKLAKDLGMKYIETSARTGDNVEEAFELL 161
>gnl|CDD|206655 cd01862, Rab7, Rab GTPase family 7 (Rab7). Rab7 subfamily. Rab7 is
a small Rab GTPase that regulates vesicular traffic from
early to late endosomal stages of the endocytic pathway.
The yeast Ypt7 and mammalian Rab7 are both involved in
transport to the vacuole/lysosome, whereas Ypt7 is also
required for homotypic vacuole fusion. Mammalian Rab7 is
an essential participant in the autophagic pathway for
sequestration and targeting of cytoplasmic components to
the lytic compartment. Mammalian Rab7 is also proposed
to function as a tumor suppressor. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 172
Score = 160 bits (406), Expect = 5e-50
Identities = 66/160 (41%), Positives = 105/160 (65%), Gaps = 5/160 (3%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
K++I+G+S VGKTS + +Y + F++ + +T+G DF K V D+ V LQIWDTAGQE
Sbjct: 1 LKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVTVDDRLVTLQIWDTAGQE 60
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSIQDW----ITQIKTYSWDNAQVILVGNKCD 137
R++++ A+YRGA +L+YDVTN +SF S+ W + Q +N +++GNK D
Sbjct: 61 RFQSLGVAFYRGADCCVLVYDVTNPKSFESLDSWRDEFLIQASPRDPENFPFVVLGNKID 120
Query: 138 MEDERVISFERGKHLAESLG-VEFFETSAKDNVNVKGVFE 176
+E++R +S ++ + +S G + +FETSAK+ +NV FE
Sbjct: 121 LEEKRQVSTKKAQQWCKSKGNIPYFETSAKEAINVDQAFE 160
>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 = 158 bits (401), Expect = 2e-49
Identities = 68/161 (42%), Positives = 103/161 (63%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
FK LIIG++ GK+ L ++ ++ F T+G++F + V K VKLQIWDTAGQE
Sbjct: 1 FKFLIIGSAGTGKSCLLHQFIENKFKQDSNHTIGVEFGSRVVNVGGKSVKLQIWDTAGQE 60
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNKCDMEDE 141
R+R++T +YYRGA G +L+YD+T+ ESF ++ +W+T +T + + +ILVGNK D+ED+
Sbjct: 61 RFRSVTRSYYRGAAGALLVYDITSRESFNALTNWLTDARTLASPDIVIILVGNKKDLEDD 120
Query: 142 RVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDII 182
R ++F A+ G+ F ETSA NV+ F + I
Sbjct: 121 REVTFLEASRFAQENGLLFLETSALTGENVEEAFLKCARSI 161
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 157 bits (399), Expect = 2e-48
Identities = 79/163 (48%), Positives = 106/163 (65%), Gaps = 3/163 (1%)
Query: 18 FDYMFKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDT 77
+D FK+L+IG+S VGK+S L + S T+G+DFK+K + KR+KL IWDT
Sbjct: 11 YDLSFKILLIGDSGVGKSSLLVSFISSS-VEDLAPTIGVDFKIKQLTVGGKRLKLTIWDT 69
Query: 78 AGQERYRTITTAYYRGAMGFILMYDVTNEESFTSIQD-WITQIKTYSWDNAQV-ILVGNK 135
AGQER+RT+T++YYR A G IL+YDVT E+FT++ D W +++ YS + V +LVGNK
Sbjct: 70 AGQERFRTLTSSYYRNAQGIILVYDVTRRETFTNLSDVWGKEVELYSTNQDCVKMLVGNK 129
Query: 136 CDMEDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERL 178
D E ER +S E G LA+ G F E SAK NV+ FE L
Sbjct: 130 VDRESERDVSREEGMALAKEHGCLFLECSAKTRENVEQCFEEL 172
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 152 bits (386), Expect = 1e-46
Identities = 66/174 (37%), Positives = 107/174 (61%)
Query: 17 NFDYMFKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWD 76
++ Y+FK +IIG++ VGK+ L ++ D F T+G++F + + +K +KLQIWD
Sbjct: 2 SYAYLFKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDNKPIKLQIWD 61
Query: 77 TAGQERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNKC 136
TAGQE +R+IT +YYRGA G +L+YD+T E+F + W+ + ++ N ++L+GNKC
Sbjct: 62 TAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLASWLEDARQHANANMTIMLIGNKC 121
Query: 137 DMEDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDIICDKMSESL 190
D+ R +S E G+ A+ G+ F E SAK NV+ F + I K+ + +
Sbjct: 122 DLAHRRAVSTEEGEQFAKEHGLIFMEASAKTAQNVEEAFIKTAAKIYKKIQDGV 175
>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 = 151 bits (382), Expect = 2e-46
Identities = 59/156 (37%), Positives = 99/156 (63%)
Query: 20 YMFKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAG 79
Y+FK +IIG+ VGK+ L ++ + F + T+G++F + + + +++KLQIWDTAG
Sbjct: 1 YIFKYIIIGDMGVGKSCLLHQFTEKKFMADCPHTIGVEFGTRIIEVNGQKIKLQIWDTAG 60
Query: 80 QERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNKCDME 139
QER+R +T +YYRGA G +++YD+T ++ + W+T + + N + L+GNK D+E
Sbjct: 61 QERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTVIFLIGNKADLE 120
Query: 140 DERVISFERGKHLAESLGVEFFETSAKDNVNVKGVF 175
+R +++E K A+ G+ F E SAK NV+ F
Sbjct: 121 AQRDVTYEEAKQFADENGLLFLECSAKTGENVEDAF 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 = 140 bits (355), Expect = 2e-42
Identities = 61/158 (38%), Positives = 89/158 (56%), Gaps = 2/158 (1%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQER 82
KL+++G VGK++ R+ F + T+ D K + + L I DTAGQE
Sbjct: 1 KLVVLGAGGVGKSALTIRFVSGEFVEEYDPTIE-DSYRKQIVVDGETYTLDILDTAGQEE 59
Query: 83 YRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIK-TYSWDNAQVILVGNKCDMEDE 141
+ + Y R GFIL+Y +T+ ESF I++ QI ++ ++LVGNKCD+E+E
Sbjct: 60 FSAMRDQYIRNGDGFILVYSITSRESFEEIKNIREQILRVKDKEDVPIVLVGNKCDLENE 119
Query: 142 RVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLV 179
R +S E G+ LAE G F ETSAK N+N+ +F LV
Sbjct: 120 RQVSTEEGEALAEEWGCPFLETSAKTNINIDELFNTLV 157
>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 = 140 bits (356), Expect = 5e-42
Identities = 60/180 (33%), Positives = 101/180 (56%), Gaps = 7/180 (3%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTV-FRHDKRVKLQIWDTAGQ 80
FK+L+IG+ VGKTS + RY F+ + +T+G+DF +K + + + V+LQ+WD AGQ
Sbjct: 1 FKVLVIGDLGVGKTSIIKRYVHGVFSQHYKATIGVDFALKVIEWDPNTVVRLQLWDIAGQ 60
Query: 81 ERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQI--KTYSWDNAQV--ILVGNKC 136
ER+ +T YY+GA+G I+++DVT +F ++ W + K + + +L+ NKC
Sbjct: 61 ERFGGMTRVYYKGAVGAIIVFDVTRPSTFEAVLKWKADLDSKVTLPNGEPIPALLLANKC 120
Query: 137 DM--EDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDIICDKMSESLDSDP 194
D+ E + + E+ + +FETSAK+N+N++ LV I +P
Sbjct: 121 DLKKERLAKDPEQMDQFCKENGFIGWFETSAKENINIEEAMRFLVKNILKNDKGLQSPEP 180
>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 = 134 bits (340), Expect = 5e-40
Identities = 56/167 (33%), Positives = 94/167 (56%), Gaps = 5/167 (2%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQER 82
K++ +GNS VGK+ + RY + F S ++ T+GID+ VK V +K V++ +D +G
Sbjct: 2 KVISMGNSGVGKSCIIKRYCEGRFVSKYLPTIGIDYGVKKVSVRNKEVRVNFFDLSGHPE 61
Query: 83 YRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYS-----WDNAQVILVGNKCD 137
Y + +Y+ G +L+YDVT+ +SF ++ W+ ++K +N V++ NK D
Sbjct: 62 YLEVRNEFYKDTQGVLLVYDVTDRQSFEALDSWLKEMKQEGGPHGNMENIVVVVCANKID 121
Query: 138 MEDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDIICD 184
+ R +S + G+ AES G ++FETSA V +F+ L I D
Sbjct: 122 LTKHRAVSEDEGRLWAESKGFKYFETSACTGEGVNEMFQTLFSSIVD 168
>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 = 132 bits (335), Expect = 3e-39
Identities = 62/162 (38%), Positives = 91/162 (56%), Gaps = 2/162 (1%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
+KL+++G+ VGK++ ++ F + T+ D K + + L I DTAGQE
Sbjct: 1 YKLVVLGSGGVGKSALTIQFIQGHFVDDYDPTIE-DSYRKQIEIDGEVCLLDILDTAGQE 59
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQI-KTYSWDNAQVILVGNKCDMED 140
+ + Y R GF+L+Y +T+ +SF I+ + QI + D+ ++LVGNKCD+E
Sbjct: 60 EFSAMRDQYMRTGEGFLLVYSITDRQSFEEIKKFREQILRVKDRDDVPIVLVGNKCDLES 119
Query: 141 ERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDII 182
ERV+S E GK LA G F ETSAK+ VNV F LV I
Sbjct: 120 ERVVSTEEGKELARQWGCPFLETSAKERVNVDEAFYDLVREI 161
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 133 bits (337), Expect = 4e-39
Identities = 63/218 (28%), Positives = 107/218 (49%), Gaps = 22/218 (10%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
FK++++G+ VGKT+ L R D F + T+G KT+ + + +KLQ+WDTAGQE
Sbjct: 6 FKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQE 65
Query: 82 RYRTITTAYYRGAMGFILMYDVTN-EESFTSIQDWITQIKTYSWDNAQVILVGNKCDMED 140
YR++ YYRGA G +++YD T E S ++W+ +++ + D+ ++LVGNK D+ D
Sbjct: 66 EYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVGNKIDLFD 125
Query: 141 ERVISFERGKHLA---------------ESLGVEFFETSAK--DNVNVKGVFERLVDIIC 183
E+ S E L E ETSAK NV +F+ L+ +
Sbjct: 126 EQSSSEEILNQLNREVVLLVLAPKAVLPEVANPALLETSAKSLTGPNVNELFKELLRKLL 185
Query: 184 DKMSESLDSDPNLVAGPKGTRLTEQPQRNNPINPNCNC 221
+++ + + + + ++ + NC
Sbjct: 186 EEIEKLVLKNELRQLDRLNNPI----EQAALASFNCVL 219
>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 = 133 bits (335), Expect = 4e-39
Identities = 67/167 (40%), Positives = 97/167 (58%), Gaps = 1/167 (0%)
Query: 16 QNFDYMFKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIW 75
+ +DY+ K L++G+S VGK L D S S + +GID+K T+ +RVKLQ+W
Sbjct: 1 KAYDYLLKFLLVGDSDVGKGEILASLQDGSTESPYGYNMGIDYKTTTILLDGRRVKLQLW 60
Query: 76 DTAGQERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNK 135
DT+GQ R+ TI +Y RGA G IL+YD+TN SF I WI +I ++ ILVGN+
Sbjct: 61 DTSGQGRFCTIFRSYSRGAQGIILVYDITNRWSFDGIDRWIKEIDEHA-PGVPKILVGNR 119
Query: 136 CDMEDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDII 182
+ +R ++ E+ + AE G+ FFE S N N+ F L I+
Sbjct: 120 LHLAFKRQVATEQAQAYAERNGMTFFEVSPLCNFNITESFTELARIV 166
>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 (329), Expect = 2e-38
Identities = 63/160 (39%), Positives = 101/160 (63%), Gaps = 7/160 (4%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
FK+++IG+S+VGKT +R+ F +T+G+DF+ +TV +R+K+Q+WDTAGQE
Sbjct: 3 FKIIVIGDSNVGKTCLTYRFCAGRFPERTEATIGVDFRERTVEIDGERIKVQLWDTAGQE 62
Query: 82 RYR-TITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQV--ILVGNKCDM 138
R+R ++ YYR + +YDVTN SF S+ WI + + +S +V ILVGNKCD+
Sbjct: 63 RFRKSMVQHYYRNVHAVVFVYDVTNMASFHSLPSWIEECEQHSL-PNEVPRILVGNKCDL 121
Query: 139 EDERVISFERGKHLAESLGVEFFETSAKD---NVNVKGVF 175
++ + + + A++ + FETSAKD N +V+ +F
Sbjct: 122 REQIQVPTDLAQRFADAHSMPLFETSAKDPSENDHVEAIF 161
>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 = 129 bits (327), Expect = 4e-38
Identities = 61/162 (37%), Positives = 90/162 (55%), Gaps = 2/162 (1%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
+KL+++G VGK++ ++ F + T+ D K + + L I DTAGQE
Sbjct: 3 YKLVVLGGGGVGKSALTIQFVQGHFVDEYDPTIE-DSYRKQIEIDGEVCLLDILDTAGQE 61
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQI-KTYSWDNAQVILVGNKCDMED 140
+ + Y R GF+L+Y +T+ +SF I + QI + D+ ++LVGNKCD+E+
Sbjct: 62 EFSAMRDQYMRTGEGFLLVYSITDRQSFEEIAKFREQILRVKDRDDVPIVLVGNKCDLEN 121
Query: 141 ERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDII 182
ERV+S E GK LA G F ETSAK+ +NV F LV I
Sbjct: 122 ERVVSTEEGKELARQWGCPFLETSAKERINVDEAFYDLVREI 163
>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 = 125 bits (316), Expect = 1e-36
Identities = 65/160 (40%), Positives = 99/160 (61%), Gaps = 3/160 (1%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVF--RHDKRVKLQIWDTAGQ 80
K++++GN +VGK+S + R+ FT + T+G+DF K +F + D+ V+L +WDTAGQ
Sbjct: 2 KVIVVGNGNVGKSSMIQRFVKGIFTKDYKKTIGVDFLEKQIFLRQSDEDVRLMLWDTAGQ 61
Query: 81 ERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNKCDMED 140
E + IT AYYRGA IL++ T+ ESF +I+ W +++ D V LV K D+ D
Sbjct: 62 EEFDAITKAYYRGAQACILVFSTTDRESFEAIESWKEKVEAECGDIPMV-LVQTKIDLLD 120
Query: 141 ERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVD 180
+ VI+ E + LA+ L + F TS KD+ NV +FE L +
Sbjct: 121 QAVITNEEAEALAKRLQLPLFRTSVKDDFNVTELFEYLAE 160
>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 = 119 bits (302), Expect = 3e-34
Identities = 56/172 (32%), Positives = 87/172 (50%), Gaps = 15/172 (8%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQER 82
K++++G+ +VGKT L Y + F + +V TV D V K+V L +WDTAGQE
Sbjct: 2 KIVVVGDGAVGKTCLLISYTTNKFPTEYVPTV-FDNYSANVTVDGKQVNLGLWDTAGQEE 60
Query: 83 YRTITTAYYRGAMGFILMYDVTNEESFTSIQD-WITQIKTYSWDNAQVILVGNKCDMEDE 141
Y + Y F+L + V + SF +++ W +IK Y N +ILVG K D+ D+
Sbjct: 61 YDRLRPLSYPQTDVFLLCFSVDSPSSFENVKTKWYPEIKHYC-PNVPIILVGTKIDLRDD 119
Query: 142 R-----------VISFERGKHLAESLG-VEFFETSAKDNVNVKGVFERLVDI 181
I+ E G+ LA+ +G V++ E SA +K VF+ +
Sbjct: 120 GNTLKKLEKKQKPITPEEGEKLAKEIGAVKYMECSALTQEGLKEVFDEAIRA 171
>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 = 117 bits (295), Expect = 4e-33
Identities = 62/176 (35%), Positives = 97/176 (55%), Gaps = 7/176 (3%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQER 82
K+ ++G+ SVGK+S ++ + F ++ T+ F ++ + L+I DTAGQ+
Sbjct: 3 KIAVLGSRSVGKSSLTVQFVEGHFVESYYPTIENTFSKIITYKGQE-YHLEIVDTAGQDE 61
Query: 83 YRTITTAYYRGAMGFILMYDVTNEESF---TSIQDWITQIKTYSWDNAQVILVGNKCDME 139
Y + Y G G+IL+Y VT+ +SF I D I + ++ ++LVGNK D+
Sbjct: 62 YSILPQKYSIGIHGYILVYSVTSRKSFEVVKVIYDKI--LDMLGKESVPIVLVGNKSDLH 119
Query: 140 DERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDIICDKMSESLDSDPN 195
ER +S E GK LAES G F E+SAK+N NV+ FE L++ I +K+ L
Sbjct: 120 MERQVSAEEGKKLAESWGAAFLESSAKENENVEEAFELLIEEI-EKVENPLPPGQK 174
>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 = 116 bits (293), Expect = 6e-33
Identities = 51/167 (30%), Positives = 89/167 (53%), Gaps = 16/167 (9%)
Query: 24 LLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQERY 83
L+++G+ +VGKT L Y ++F +V TV + V K V+L +WDTAGQE Y
Sbjct: 1 LVVVGDGAVGKTCLLIVYTTNAFPEDYVPTV-FENYSADVEVDGKPVELGLWDTAGQEDY 59
Query: 84 RTITTAYYRGAMGFILMYDVTNEESFTSIQD-WITQIKTYSWDNAQVILVGNKCDMEDER 142
+ Y F++ + V + SF ++++ W ++K + N +ILVG K D+ +++
Sbjct: 60 DRLRPLSYPDTDVFLICFSVDSPASFENVKEKWYPEVKHFC-PNVPIILVGTKLDLRNDK 118
Query: 143 V------------ISFERGKHLAESLG-VEFFETSAKDNVNVKGVFE 176
+++E+G+ LA+ +G V++ E SA V+ VFE
Sbjct: 119 STLEELSKKKQEPVTYEQGQALAKRIGAVKYLECSALTQEGVREVFE 165
>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 = 115 bits (290), Expect = 1e-32
Identities = 49/165 (29%), Positives = 77/165 (46%), Gaps = 13/165 (7%)
Query: 25 LIIGNSSVGKTSFLFRYADDSFT---SAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
+++G VGK+S L +T D VK + +VKL + DT G +
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKEL--DKGKVKLVLVDTPGLD 58
Query: 82 RY-----RTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNKC 136
+ + RGA +L+ D T+ ES + I ++ + +ILVGNK
Sbjct: 59 EFGGLGREELARLLLRGADLILLVVDSTDRESEEDAKLLI--LRRLRKEGIPIILVGNKI 116
Query: 137 DMEDERVIS-FERGKHLAESLGVEFFETSAKDNVNVKGVFERLVD 180
D+ +ER + R + LA+ LGV FE SAK V +FE+L++
Sbjct: 117 DLLEEREVEELLRLEELAKILGVPVFEVSAKTGEGVDELFEKLIE 161
>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 = 113 bits (284), Expect = 8e-32
Identities = 58/162 (35%), Positives = 95/162 (58%), Gaps = 2/162 (1%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
+KL+++G+ VGK++ ++ F + T+ ++ K V ++ L+I DTAG E
Sbjct: 2 YKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYR-KQVEVDGQQCMLEILDTAGTE 60
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQI-KTYSWDNAQVILVGNKCDMED 140
++ + Y + GF+L+Y +T + +F +QD QI + ++ +ILVGNKCD+ED
Sbjct: 61 QFTAMRDLYMKNGQGFVLVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLED 120
Query: 141 ERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDII 182
ERV+ E+G++LA G F ETSAK +NV +F LV I
Sbjct: 121 ERVVGKEQGQNLARQWGCAFLETSAKAKINVNEIFYDLVRQI 162
>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 = 113 bits (284), Expect = 9e-32
Identities = 59/162 (36%), Positives = 89/162 (54%), Gaps = 2/162 (1%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
+KL+++G VGK++ ++ F + + T+ D K + +L I DTAGQE
Sbjct: 3 YKLVVVGGGGVGKSALTIQFIQSYFVTDYDPTIE-DSYTKQCEIDGQWARLDILDTAGQE 61
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQI-KTYSWDNAQVILVGNKCDMED 140
+ + Y R GF+L++ VT+ SF + + TQI + D +ILVGNK D+E
Sbjct: 62 EFSAMREQYMRTGEGFLLVFSVTDRGSFEEVDKFHTQILRVKDRDEFPMILVGNKADLEH 121
Query: 141 ERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDII 182
+R +S E G+ LA L + + ETSAKD VNV F LV +I
Sbjct: 122 QRQVSREEGQELARQLKIPYIETSAKDRVNVDKAFHDLVRVI 163
>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 = 112 bits (282), Expect = 2e-31
Identities = 54/163 (33%), Positives = 94/163 (57%), Gaps = 4/163 (2%)
Query: 21 MFKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQ 80
+ K++++G+ VGK+S + RY + F + T+G++F K + V LQIWDTAGQ
Sbjct: 5 LLKVILLGDGGVGKSSLMNRYVTNKFDTQLFHTIGVEFLNKDLEVDGHFVTLQIWDTAGQ 64
Query: 81 ERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYS----WDNAQVILVGNKC 136
ER+R++ T +YRG+ +L + V + +SF ++ +W + Y+ ++ +++GNK
Sbjct: 65 ERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVILGNKI 124
Query: 137 DMEDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLV 179
D+ + +V + E ++ +FETSAKD NV FE V
Sbjct: 125 DIPERQVSTEEAQAWCRDNGDYPYFETSAKDATNVAAAFEEAV 167
>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 = 112 bits (282), Expect = 7e-31
Identities = 51/162 (31%), Positives = 89/162 (54%), Gaps = 4/162 (2%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTV-FRHDKRVKLQIWDTAGQ 80
K++++G+ + GKTS + R+A + F ++ T+G+DF + + V LQ+WD GQ
Sbjct: 1 IKIVVLGDGASGKTSLIRRFAQEGFGKSYKQTIGLDFFSRRITLPGSLNVTLQVWDIGGQ 60
Query: 81 ERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTY---SWDNAQVILVGNKCD 137
+ + Y GA L+YD+TN +SF +++DW++ +K S +++LVGNK D
Sbjct: 61 QIGGKMLDKYIYGAQAVCLVYDITNSQSFENLEDWLSVVKKVNEESETKPKMVLVGNKTD 120
Query: 138 MEDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLV 179
+E R ++ E+ A+ +E SAK V F+R+
Sbjct: 121 LEHNRQVTAEKHARFAQENDMESIFVSAKTGDRVFLCFQRIA 162
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 111 bits (278), Expect = 8e-31
Identities = 58/154 (37%), Positives = 94/154 (61%), Gaps = 1/154 (0%)
Query: 44 DSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQERYRTITTAYYRGAMGFILMYDV 103
D+F + + ST+GIDF KT++ + V+LQ+WDTAGQER+R++ +Y R + I++YD+
Sbjct: 3 DTFDNNYQSTIGIDFLSKTLYLDEGPVRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDI 62
Query: 104 TNEESFTSIQDWITQIKTYSWDNAQVILVGNKCDMEDERVISFERGKHLAESLGVEFFET 163
TN +SF + WI I + + LVGNK D+ D R +++E G A+ F ET
Sbjct: 63 TNRQSFENTTKWIQDILNERGKDVIIALVGNKTDLGDLRKVTYEEGMQKAQEYNTMFHET 122
Query: 164 SAKDNVNVKGVFERLVDIICDKMSESLDSDPNLV 197
SAK N+K +F+++ + + + S +D N+V
Sbjct: 123 SAKAGHNIKVLFKKIAAKLPN-LDNSNSNDANVV 155
>gnl|CDD|206708 cd04136, Rap_like, Rap-like family consists of Rap1, Rap2 and RSR1.
The Rap subfamily consists of the Rap1, Rap2, and RSR1.
Rap subfamily proteins perform different cellular
functions, depending on the isoform and its subcellular
localization. For example, in rat salivary gland,
neutrophils, and platelets, Rap1 localizes to secretory
granules and is believed to regulate exocytosis or the
formation of secretory granules. Rap1 has also been
shown to localize in the Golgi of rat fibroblasts,
zymogen granules, plasma membrane, and microsomal
membrane of the pancreatic acini, as well as in the
endocytic compartment of skeletal muscle cells and
fibroblasts. Rap1 localizes in the nucleus of human
oropharyngeal squamous cell carcinomas (SCCs) and cell
lines. Rap1 plays a role in phagocytosis by controlling
the binding of adhesion receptors (typically integrins)
to their ligands. In yeast, Rap1 has been implicated in
multiple functions, including activation and silencing
of transcription and maintenance of telomeres. Rap2 is
involved in multiple functions, including activation of
c-Jun N-terminal kinase (JNK) to regulate the actin
cytoskeleton and activation of the Wnt/beta-catenin
signaling pathway in embryonic Xenopus. A number of
effector proteins for Rap2 have been identified,
including isoform 3 of the human mitogen-activated
protein kinase kinase kinase kinase 4 (MAP4K4) and
Traf2- and Nck-interacting kinase (TNIK), and the
RalGEFs RalGDS, RGL, and Rlf, which also interact with
Rap1 and Ras. RSR1 is the fungal homolog of Rap1 and
Rap2. In budding yeasts, it is involved in selecting a
site for bud growth, which directs the establishment of
cell polarization. The Rho family GTPase Cdc42 and its
GEF, Cdc24, then establish an axis of polarized growth.
It is believed that Cdc42 interacts directly with RSR1
in vivo. In filamentous fungi such as Ashbya gossypii,
RSR1 is a key regulator of polar growth in the hypha.
Most Ras proteins contain a lipid modification site at
the C-terminus, with a typical sequence motif CaaX,
where a = an aliphatic amino acid and X = any amino
acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 164
Score = 111 bits (278), Expect = 8e-31
Identities = 59/160 (36%), Positives = 93/160 (58%), Gaps = 3/160 (1%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
+KL+++G+ VGK++ ++ F + T+ D K + ++ L+I DTAG E
Sbjct: 2 YKLVVLGSGGVGKSALTVQFVQGIFVDKYDPTIE-DSYRKQIEVDCQQCMLEILDTAGTE 60
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQI-KTYSWDNAQVILVGNKCDMED 140
++ + Y + GF L+Y +T ++SF +QD QI + ++ +ILVGNKCD+ED
Sbjct: 61 QFTAMRDLYIKNGQGFALVYSITAQQSFNDLQDLREQILRVKDTEDVPMILVGNKCDLED 120
Query: 141 ERVISFERGKHLAESLG-VEFFETSAKDNVNVKGVFERLV 179
ERV+S E G++LA G F ETSAK +NV +F LV
Sbjct: 121 ERVVSKEEGQNLARQWGNCPFLETSAKSKINVDEIFYDLV 160
>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 = 110 bits (277), Expect = 9e-31
Identities = 53/161 (32%), Positives = 88/161 (54%), Gaps = 5/161 (3%)
Query: 23 KLLIIGNSSVGKTSF--LFRYADDSFTSAFVSTVGIDFKVKTVF--RHDKRVKLQIWDTA 78
+ ++G+ +VGK++ +F +F + T G D VKTV V+L I+D+A
Sbjct: 2 QCAVVGDPAVGKSALVQMFHSDGATFQKNYTMTTGCDLVVKTVPVPDTSDSVELFIFDSA 61
Query: 79 GQERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQV-ILVGNKCD 137
GQE + + + ++YDVTNE SF + WI +++T+S +LVGNKCD
Sbjct: 62 GQELFSDMVENVWEQPAVVCVVYDVTNEVSFNNCSRWINRVRTHSHGLHTPGVLVGNKCD 121
Query: 138 MEDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERL 178
+ D R + + + LA++ ++F+ETSAK+ V + F L
Sbjct: 122 LTDRREVDAAQAQALAQANTLKFYETSAKEGVGYEAPFLSL 162
>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 = 109 bits (274), Expect = 3e-30
Identities = 64/159 (40%), Positives = 94/159 (59%), Gaps = 2/159 (1%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
K++++G+ VGK++ ++ D F + T D K V + V+L I DTAGQE
Sbjct: 1 HKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKA-DSYRKKVVLDGEEVQLNILDTAGQE 59
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQI-KTYSWDNAQVILVGNKCDMED 140
Y I Y+R GF+L++ +T+ ESFT++ ++ QI + DN ++LVGNKCD+ED
Sbjct: 60 DYAAIRDNYFRSGEGFLLVFSITDMESFTALAEFREQILRVKEDDNVPLLLVGNKCDLED 119
Query: 141 ERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLV 179
+R +S E +LAE GV + ETSAK NV VF LV
Sbjct: 120 KRQVSVEEAANLAEQWGVNYVETSAKTRANVDKVFFDLV 158
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 109 bits (274), Expect = 5e-30
Identities = 59/162 (36%), Positives = 88/162 (54%), Gaps = 2/162 (1%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
+KL+++G VGK++ ++ + F + T+ ++ K ++ L I DTAGQE
Sbjct: 6 YKLVVVGGGGVGKSALTIQFIQNHFIDEYDPTIEDSYR-KQCVIDEETCLLDILDTAGQE 64
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQI-KTYSWDNAQVILVGNKCDMED 140
Y + Y R GF+ +Y +T+ SF I + QI + D +ILVGNKCD++
Sbjct: 65 EYSAMRDQYMRTGQGFLCVYSITSRSSFEEIASFREQILRVKDKDRVPMILVGNKCDLDS 124
Query: 141 ERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDII 182
ER +S G+ LA+S G+ F ETSAK VNV F LV I
Sbjct: 125 ERQVSTGEGQELAKSFGIPFLETSAKQRVNVDEAFYELVREI 166
>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 = 108 bits (272), Expect = 6e-30
Identities = 54/162 (33%), Positives = 90/162 (55%), Gaps = 6/162 (3%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
+K++++G+ VGK++ ++ +F + T+ DF K + L+I DTAG E
Sbjct: 2 YKVVVLGSGGVGKSALTVQFVSGTFIEKYDPTIE-DFYRKEIEVDSSPSVLEILDTAGTE 60
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSI---QDWITQIKTYSWDNAQVILVGNKCDM 138
++ ++ Y + GFI++Y + N+++F I +D I ++K Y + +ILVGNK D+
Sbjct: 61 QFASMRDLYIKNGQGFIVVYSLVNQQTFQDIKPMRDQIVRVKGY--EKVPIILVGNKVDL 118
Query: 139 EDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVD 180
E ER +S G+ LAE G F ETSAK V +F +V
Sbjct: 119 ESEREVSSAEGRALAEEWGCPFMETSAKSKTMVNELFAEIVR 160
>gnl|CDD|133344 cd04144, Ras2, Rat sarcoma (Ras) family 2 of small guanosine
triphosphatases (GTPases). The Ras2 subfamily, found
exclusively in fungi, was first identified in Ustilago
maydis. In U. maydis, Ras2 is regulated by Sql2, a
protein that is homologous to GEFs (guanine nucleotide
exchange factors) of the CDC25 family. Ras2 has been
shown to induce filamentous growth, but the signaling
cascade through which Ras2 and Sql2 regulate cell
morphology is not known. Most Ras proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Ras proteins.
Length = 190
Score = 108 bits (272), Expect = 1e-29
Identities = 58/160 (36%), Positives = 88/160 (55%), Gaps = 4/160 (2%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQER 82
KL+++G+ VGKT+ + + F + T+ ++ + V + L++ DTAGQE
Sbjct: 1 KLVVLGDGGVGKTALTIQLCLNHFVETYDPTIEDSYRKQVVV-DGQPCMLEVLDTAGQEE 59
Query: 83 YRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQI---KTYSWDNAQVILVGNKCDME 139
Y + + R GFIL+Y +T+ +F ++ + QI K S + +++VGNKCD
Sbjct: 60 YTALRDQWIREGEGFILVYSITSRSTFERVERFREQIQRVKDESAADVPIMIVGNKCDKV 119
Query: 140 DERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLV 179
ER +S E G LA LG EF E SAK NVNV+ F LV
Sbjct: 120 YEREVSTEEGAALARRLGCEFIEASAKTNVNVERAFYTLV 159
>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 = 108 bits (270), Expect = 2e-29
Identities = 53/166 (31%), Positives = 90/166 (54%), Gaps = 6/166 (3%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSF-TSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
K++++G SVGKTS + RY F + +T+G F K + ++ V L IWDTAG E
Sbjct: 2 KVVMLGKESVGKTSLVERYVHHRFLVGPYQNTIGAAFVAKRMVVGERVVTLGIWDTAGSE 61
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNKCDM--- 138
RY ++ YYRGA I+ YD+T+ SF + W+ +++ ++ ++ L G K D+
Sbjct: 62 RYEAMSRIYYRGAKAAIVCYDLTDSSSFERAKFWVKELQNLE-EHCKIYLCGTKSDLIEQ 120
Query: 139 -EDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDIIC 183
R + F + A+ + + FETS+K NV +F+++ +
Sbjct: 121 DRSLRQVDFHDVQDFADEIKAQHFETSSKTGQNVDELFQKVAEDFV 166
>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 = 102 bits (256), Expect = 2e-27
Identities = 54/163 (33%), Positives = 80/163 (49%), Gaps = 8/163 (4%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQER 82
K+ ++G S VGK++ R+ F + + + + V ++V L+I DT GQ++
Sbjct: 1 KIAVLGASGVGKSALTVRFLTKRFIGEYEPNLESLYS-RQVTIDGEQVSLEIQDTPGQQQ 59
Query: 83 YRT--ITTAYYRGAMGFILMYDVTNEESFTSIQDW---ITQIKTYSWDNAQVILVGNKCD 137
R A GF+L+Y +T+ SF + I +IK VILVGNK D
Sbjct: 60 NEDPESLERSLRWADGFVLVYSITDRSSFDVVSQLLQLIREIKKRD-GEIPVILVGNKAD 118
Query: 138 MEDERVISFERGKHLAESLGVEFFETSAKDNVN-VKGVFERLV 179
+ R +S E G+ LA LG FFE SA +N V+ VF L
Sbjct: 119 LLHSRQVSTEEGQKLALELGCLFFEVSAAENYLEVQNVFHELC 161
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 103 bits (258), Expect = 2e-27
Identities = 56/180 (31%), Positives = 99/180 (55%), Gaps = 19/180 (10%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
FKL+++G+ VGKT+F+ R+ F ++ T+G++ + + + +WDTAGQE
Sbjct: 10 FKLILVGDGGVGKTTFVKRHLTGEFEKKYIPTLGVEVHPLKFYTNCGPICFNVWDTAGQE 69
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNKCDMEDE 141
++ + YY I+M+DVT+ ++ ++ +W I +N ++LVGNK D++D
Sbjct: 70 KFGGLRDGYYIKGQCAIIMFDVTSRITYKNVPNWHRDI-VRVCENIPIVLVGNKVDVKDR 128
Query: 142 RV----ISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDIICDKMSESLDSDPNLV 197
+V I+F R K+L ++++ SAK N N FE+ + + L +DPNLV
Sbjct: 129 QVKARQITFHRKKNL------QYYDISAKSNYN----FEKPFLWLARR----LTNDPNLV 174
>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 = 100 bits (252), Expect = 5e-27
Identities = 55/162 (33%), Positives = 85/162 (52%), Gaps = 3/162 (1%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
+KL+++G VGK++ + + F + T+ D K V + L I DTAGQE
Sbjct: 2 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIE-DSYRKQVVIDGETCLLDILDTAGQE 60
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIK-TYSWDNAQVILVGNKCDMED 140
Y + Y R GF+ ++ + + +SF I + QIK D+ ++LVGNKCD+
Sbjct: 61 EYSAMRDQYMRTGEGFLCVFAINSRKSFEDIHTYREQIKRVKDSDDVPMVLVGNKCDLAA 120
Query: 141 ERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDII 182
R +S +G+ LA+S G+ + ETSAK V+ F LV I
Sbjct: 121 -RTVSTRQGQDLAKSYGIPYIETSAKTRQGVEEAFYTLVREI 161
>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 = 101 bits (254), Expect = 6e-27
Identities = 51/182 (28%), Positives = 88/182 (48%), Gaps = 15/182 (8%)
Query: 19 DYMFKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTA 78
D K++++G+ GKT L YA SF +V TV ++ + K ++L +WDTA
Sbjct: 1 DLKVKIVVVGDGGCGKTCLLMVYAQGSFPEEYVPTVFENYVTTLQVPNGKIIELALWDTA 60
Query: 79 GQERYRTITTAYYRGAMGFILMYDVTNEESFTSIQD-WITQIKTYSWDNAQVILVGNKCD 137
GQE Y + Y ++ Y V N S +++D W ++ + ++LVG K D
Sbjct: 61 GQEDYDRLRPLSYPDVDVILICYSVDNPTSLDNVEDKWYPEVNHFC-PGTPIVLVGLKTD 119
Query: 138 M------------EDERVISFERGKHLAESLG-VEFFETSAKDNVNVKGVFERLVDIICD 184
+ + ++ E+G+ +A+S+G V + E SAK NV VF+ +++
Sbjct: 120 LRKDKNSVSKLRAQGLEPVTPEQGESVAKSIGAVAYIECSAKLMENVDEVFDAAINVALS 179
Query: 185 KM 186
K
Sbjct: 180 KS 181
>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 = 100 bits (251), Expect = 7e-27
Identities = 58/168 (34%), Positives = 96/168 (57%), Gaps = 4/168 (2%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
+K++++G VGK++ ++ + F ++ T+ ++ K V ++ L+I DTAG E
Sbjct: 2 YKIVVLGAGGVGKSALTVQFVQNVFIESYDPTIEDSYR-KQVEIDGRQCDLEILDTAGTE 60
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQI-KTYSWDNAQVILVGNKCDMED 140
++ + Y + GF+L+Y VT+E S + + Q+ + DN ++LVGNK D+ED
Sbjct: 61 QFTAMRELYIKSGQGFLLVYSVTSEASLNELGELREQVLRIKDSDNVPMVLVGNKADLED 120
Query: 141 ERVISFERGKHLAESLG-VEFFETSAKDNVNVKGVFERLV-DIICDKM 186
+R +S E G L++ G V F+ETSA+ NV VF LV IIC M
Sbjct: 121 DRQVSREDGVSLSQQWGNVPFYETSARKRTNVDEVFIDLVRQIICVIM 168
>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 = 98.5 bits (246), Expect = 5e-26
Identities = 49/156 (31%), Positives = 88/156 (56%), Gaps = 15/156 (9%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKR--VKLQIWDTAG 79
FKL+++G+ GKT+F+ R+ F +V+T+G++ V + H R ++ +WDTAG
Sbjct: 1 FKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVE--VHPLDFHTNRGKIRFNVWDTAG 58
Query: 80 QERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNKCDME 139
QE++ + YY I+M+DVT+ ++ ++ +W + +N ++L GNK D++
Sbjct: 59 QEKFGGLRDGYYIQGQCAIIMFDVTSRVTYKNVPNWHRDL-VRVCENIPIVLCGNKVDIK 117
Query: 140 DERV----ISFERGKHLAESLGVEFFETSAKDNVNV 171
D +V I+F R K ++++E SAK N N
Sbjct: 118 DRKVKPKQITFHRKK------NLQYYEISAKSNYNF 147
>gnl|CDD|232886 TIGR00231, small_GTP, small GTP-binding protein domain. Proteins
with a small GTP-binding domain recognized by this model
include Ras, RhoA, Rab11, translation elongation factor
G, translation initiation factor IF-2, tetratcycline
resistance protein TetM, CDC42, Era, ADP-ribosylation
factors, tdhF, and many others. In some proteins the
domain occurs more than once.This model recognizes a
large number of small GTP-binding proteins and related
domains in larger proteins. Note that the alpha chains
of heterotrimeric G proteins are larger proteins in
which the NKXD motif is separated from the GxxxxGK[ST]
motif (P-loop) by a long insert and are not easily
detected by this model [Unknown function, General].
Length = 162
Score = 98.2 bits (245), Expect = 6e-26
Identities = 42/159 (26%), Positives = 72/159 (45%), Gaps = 6/159 (3%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDS-FTSAFVSTVGIDFKVKTVFRHD-KRVKLQIWDTAG 79
K++I+G+ +VGK++ L R + + + ++ V TV D K K + DTAG
Sbjct: 2 IKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNY-VTTVIEEDGKTYKFNLLDTAG 60
Query: 80 QERYRTITTAYYRGAMGFILMYDVTN-EESFTSI-QDWITQIKTYSWDNAQVILVGNKCD 137
QE Y I YYR + ++D+ I + +I ++ +ILVGNK D
Sbjct: 61 QEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAESGVPIILVGNKID 120
Query: 138 MEDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFE 176
+ D ++ + A+ G SA+ N+ F+
Sbjct: 121 LRDAKLKTHVAFL-FAKLNGEPIIPLSAETGKNIDSAFK 158
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 97.5 bits (243), Expect = 4e-25
Identities = 51/167 (30%), Positives = 89/167 (53%), Gaps = 16/167 (9%)
Query: 16 QNFDY-MFKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQI 74
Q DY FKL+I+G+ GKT+F+ R+ F + T+G++ F + +++
Sbjct: 7 QTVDYPSFKLVIVGDGGTGKTTFVKRHLTGEFEKKYEPTIGVEVHPLDFFTNCGKIRFYC 66
Query: 75 WDTAGQERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGN 134
WDTAGQE++ + YY I+M+DVT ++ ++ W + +N ++L GN
Sbjct: 67 WDTAGQEKFGGLRDGYYIHGQCAIIMFDVTARLTYKNVPTWHRDL-CRVCENIPIVLCGN 125
Query: 135 KCDMEDERV----ISFERGKHLAESLGVEFFETSAKDNVNVKGVFER 177
K D+++ +V ++F R K+L +++E SAK N N FE+
Sbjct: 126 KVDVKNRQVKAKQVTFHRKKNL------QYYEISAKSNYN----FEK 162
>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 = 96.3 bits (240), Expect = 5e-25
Identities = 40/159 (25%), Positives = 84/159 (52%), Gaps = 8/159 (5%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQER 82
K+ ++G++ +GKTS + +Y + F ++ T+G++F KT+ + IWD GQ
Sbjct: 2 KIGLLGDAQIGKTSLMVKYVEGEFDEEYIQTLGVNFMEKTISIRGTEITFSIWDLGGQRE 61
Query: 83 YRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNKCDM---- 138
+ + + A+ + M+D+T + + SI++W Q + ++ A ILVG K D+
Sbjct: 62 FINMLPLVCKDAVAILFMFDLTRKSTLNSIKEWYRQARGFN-KTAIPILVGTKYDLFADL 120
Query: 139 --EDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVF 175
E++ I+ ++ + A+++ S ++NV+ +F
Sbjct: 121 PPEEQEEIT-KQARKYAKAMKAPLIFCSTSHSINVQKIF 158
>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 = 94.4 bits (235), Expect = 2e-24
Identities = 55/168 (32%), Positives = 88/168 (52%), Gaps = 16/168 (9%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQER 82
K +++G+ +VGKTS + Y + + + +V T +F V V K V+LQ+ DTAGQ+
Sbjct: 2 KCVLVGDGAVGKTSLIVSYTTNGYPTEYVPTAFDNFSVV-VLVDGKPVRLQLCDTAGQDE 60
Query: 83 YRTITTAYYRGAMGFILMYDVTNEESFTSIQD-WITQIKTYSWDNAQVILVGNKCDMED- 140
+ + Y F+L + V N SF +I + WI +I+ ++ A +ILVG + D+
Sbjct: 61 FDKLRPLCYPDTDVFLLCFSVVNPSSFQNISEKWIPEIRKHN-PKAPIILVGTQADLRTD 119
Query: 141 -----------ERVISFERGKHLAESLG-VEFFETSAKDNVNVKGVFE 176
E+ +S R K LAE +G E+ E SA N+K VF+
Sbjct: 120 VNVLIQLARYGEKPVSQSRAKALAEKIGACEYIECSALTQKNLKEVFD 167
>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 = 93.8 bits (233), Expect = 3e-24
Identities = 47/159 (29%), Positives = 88/159 (55%), Gaps = 14/159 (8%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHD-----KRVKLQIWDT 77
K++++G+S+VGK+ + R+ D + +ST + T+++H+ K + + WDT
Sbjct: 2 KIILLGDSAVGKSKLVERFLMDGYEPQQLSTYAL-----TLYKHNAKFEGKTILVDFWDT 56
Query: 78 AGQERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNKCD 137
AGQER++T+ +YY A IL++DVT + ++ ++ W +++ Y I+V NK D
Sbjct: 57 AGQERFQTMHASYYHKAHACILVFDVTRKITYKNLSKWYEELREYR-PEIPCIVVANKID 115
Query: 138 MEDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFE 176
+ D V ++ + AE + + SA D NV +F+
Sbjct: 116 L-DPSVT--QKKFNFAEKHNLPLYYVSAADGTNVVKLFQ 151
>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 = 93.0 bits (231), Expect = 7e-24
Identities = 50/159 (31%), Positives = 87/159 (54%), Gaps = 3/159 (1%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQER 82
K++++G+ SVGKT + R+ D F + +T+G+DF+++ LQ+WDTAGQER
Sbjct: 2 KVIVVGDLSVGKTCLINRFCKDVFDKNYKATIGVDFEMERFEVLGVPFSLQLWDTAGQER 61
Query: 83 YRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQ-IKTYSWDNAQVILVGNKCDME-- 139
++ I + YYRGA I+++D+T+ S + W+ +K + + LVG K D+
Sbjct: 62 FKCIASTYYRGAQAIIIVFDLTDVASLEHTRQWLEDALKENDPSSVLLFLVGTKKDLSSP 121
Query: 140 DERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERL 178
+ + + LA + E++ SA NV+ F R+
Sbjct: 122 AQYALMEQDAIKLAREMKAEYWAVSALTGENVRDFFFRV 160
>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 = 90.3 bits (224), Expect = 8e-23
Identities = 50/164 (30%), Positives = 87/164 (53%), Gaps = 6/164 (3%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRV-KLQIWDTAGQ 80
+++++ G VGK+S + R+ +F +++ T I+ + V K + LQI DT G
Sbjct: 2 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPT--IEDTYRQVISCSKSICTLQITDTTGS 59
Query: 81 ERYRTITTAYYRGAMGFILMYDVTNEESF---TSIQDWITQIKTYSWDNAQVILVGNKCD 137
++ + FIL+Y +T+++S I + I +IK + + ++LVGNKCD
Sbjct: 60 HQFPAMQRLSISKGHAFILVYSITSKQSLEELKPIYELICEIKGNNLEKIPIMLVGNKCD 119
Query: 138 MEDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDI 181
R +S G LA + F ETSAK N NV+ +F+ L+++
Sbjct: 120 ESPSREVSSSEGAALARTWNCAFMETSAKTNHNVQELFQELLNL 163
>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 = 89.0 bits (221), Expect = 2e-22
Identities = 54/168 (32%), Positives = 86/168 (51%), Gaps = 16/168 (9%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQER 82
KL+I+G+ + GKT L ++ D F +V TV ++ V + K+V+L +WDTAGQE
Sbjct: 3 KLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENY-VADIEVDGKQVELALWDTAGQED 61
Query: 83 YRTITTAYYRGAMGFILMYDVTNEESFTSIQD-WITQIKTYSWDNAQVILVGNKCDM-ED 140
Y + Y ++ + + + +S +I + W ++K + N +ILVGNK D+ D
Sbjct: 62 YDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFC-PNVPIILVGNKKDLRND 120
Query: 141 ERVI-----------SFERGKHLAESLGV-EFFETSAKDNVNVKGVFE 176
E I E G+ +AE +G + E SAK V+ VFE
Sbjct: 121 EHTIRELAKMKQEPVKPEEGRAMAEKIGAFGYLECSAKTKEGVREVFE 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 = 89.1 bits (221), Expect = 3e-22
Identities = 52/170 (30%), Positives = 86/170 (50%), Gaps = 6/170 (3%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
+K++++G VGK++ ++ SF T+ +K + ++ L I DTAGQ
Sbjct: 3 YKIVMLGAGGVGKSAVTMQFISHSFPDYHDPTIEDAYKTQARI-DNEPALLDILDTAGQA 61
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSIQDW---ITQIKTYSWDNAQVILVGNKCDM 138
+ + Y R GFI+ Y VT+ SF ++ IT+++ ++ ++LVGNK D+
Sbjct: 62 EFTAMRDQYMRCGEGFIICYSVTDRHSFQEASEFKELITRVRLT--EDIPLVLVGNKVDL 119
Query: 139 EDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDIICDKMSE 188
E +R ++ E G++LA FFETSA + F LV I K S
Sbjct: 120 EQQRQVTTEEGRNLAREFNCPFFETSAALRFYIDDAFHGLVREIRRKESM 169
>gnl|CDD|133326 cd04126, Rab20, Rab GTPase family 20 (Rab20). Rab20 is one of
several Rab proteins that appear to be restricted in
expression to the apical domain of murine polarized
epithelial cells. It is expressed on the apical side of
polarized kidney tubule and intestinal epithelial cells,
and in non-polarized cells. It also localizes to
vesico-tubular structures below the apical brush border
of renal proximal tubule cells and in the apical region
of duodenal epithelial cells. Rab20 has also been shown
to colocalize with vacuolar H+-ATPases (V-ATPases) in
mouse kidney cells, suggesting a role in the regulation
of V-ATPase traffic in specific portions of the nephron.
It was also shown to be one of several proteins whose
expression is upregulated in human myelodysplastic
syndrome (MDS) patients. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 220
Score = 89.6 bits (222), Expect = 5e-22
Identities = 65/219 (29%), Positives = 101/219 (46%), Gaps = 43/219 (19%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQER 82
K++++G+ +VGKTS L RY + F VSTVG F +K ++ + IWDTAG+E+
Sbjct: 2 KVVLLGDMNVGKTSLLHRYMERRFKDT-VSTVGGAFYLKQWGPYN----ISIWDTAGREQ 56
Query: 83 YRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNKCDM---- 138
+ + + Y RGA IL YDV+N +S ++D + + ++ +VGNK D+
Sbjct: 57 FHGLGSMYCRGAAAVILTYDVSNVQSLEELEDRFLGLTDTANEDCLFAVVGNKLDLTEEG 116
Query: 139 ---------------EDERVISFERGKHLAE------------SLGVE--FFETSAKDNV 169
ED+R ++ E K + S E FETSAK
Sbjct: 117 ALAGQEKDAGDRVSPEDQRQVTLEDAKAFYKRINKYKMLDEDLSPAAEKMCFETSAKTGY 176
Query: 170 NVKGVFERLVD----IICDKMSESLDSDPNLVAGPKGTR 204
NV +FE L + +I + +E+ V P R
Sbjct: 177 NVDELFEYLFNLVLPLILAQRAEANR-TQGTVNLPNPKR 214
>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 = 88.5 bits (219), Expect = 8e-22
Identities = 53/180 (29%), Positives = 92/180 (51%), Gaps = 21/180 (11%)
Query: 27 IGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQERYRTI 86
+G+ GKT+F+ R+ F +V+T+G++ + ++ +WDTAGQE++ +
Sbjct: 1 VGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIRFNVWDTAGQEKFGGL 60
Query: 87 TTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNKCDMEDERV--- 143
YY I+M+DVT ++ ++ +W + +N ++L GNK D++D +V
Sbjct: 61 RDGYYIQGQCAIIMFDVTARVTYKNVPNWHRDLVRVC-ENIPIVLCGNKVDVKDRKVKAK 119
Query: 144 -ISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDIICDKMSESLDSDPNL--VAGP 200
I+F R K+L ++++ SAK N N + F L + L DPNL VA P
Sbjct: 120 SITFHRKKNL------QYYDISAKSNYNFEKPFLWL--------ARKLIGDPNLEFVAMP 165
>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 = 83.7 bits (207), Expect = 2e-20
Identities = 52/173 (30%), Positives = 93/173 (53%), Gaps = 14/173 (8%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQER 82
K + +G+ +VGKT L Y ++F + +V TV +F V + V L +WDTAGQE
Sbjct: 3 KCVTVGDGAVGKTCMLISYTSNTFPTDYVPTVFDNFSANVVVDGNT-VNLGLWDTAGQED 61
Query: 83 YRTITTAYYRGAMGFILMYDVTNEESFTSI-QDWITQIKTYSWDNAQVILVGNKCDMEDE 141
Y + YRGA F+L + + ++ S+ ++ + WI +++ Y+ ++LVG K D+ D+
Sbjct: 62 YNRLRPLSYRGADVFLLAFSLISKASYENVLKKWIPELRHYA-PGVPIVLVGTKLDLRDD 120
Query: 142 R----------VISFERGKHLAESLGVE-FFETSAKDNVNVKGVFERLVDIIC 183
+ I+ +G+ L + +G + E S+K NVK VF+ + ++
Sbjct: 121 KQFFADHPGAVPITTAQGEELRKQIGAAAYIECSSKTQQNVKAVFDAAIKVVL 173
>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 = 83.1 bits (205), Expect = 4e-20
Identities = 52/172 (30%), Positives = 90/172 (52%), Gaps = 16/172 (9%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
K +++G+ +VGKT L YA+D+F +V TV D +V K+ L ++DTAGQE
Sbjct: 1 LKCVVVGDGAVGKTCLLMSYANDAFPEEYVPTV-FDHYAVSVTVGGKQYLLGLYDTAGQE 59
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSIQ-DWITQIKTYSWDNAQVILVGNKCDMED 140
Y + Y F++ + V N SF +++ +W+ ++K Y+ N +L+G + D+ D
Sbjct: 60 DYDRLRPLSYPMTDVFLICFSVVNPASFQNVKEEWVPELKEYA-PNVPYLLIGTQIDLRD 118
Query: 141 ------------ERVISFERGKHLAESLGVE-FFETSAKDNVNVKGVFERLV 179
E+ I+ E+G+ LA+ +G + E SA +K VF+ +
Sbjct: 119 DPKTLARLNDMKEKPITVEQGQKLAKEIGACCYVECSALTQKGLKTVFDEAI 170
>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 = 82.6 bits (204), Expect = 1e-19
Identities = 49/166 (29%), Positives = 80/166 (48%), Gaps = 14/166 (8%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQER 82
KL+I+G+ + GKTS L+ + F + TV + V K V+L +WDTAGQE
Sbjct: 3 KLVIVGDGACGKTSLLYVFTLGEFPEEYHPTV-FENYVTDCRVDGKPVQLALWDTAGQEE 61
Query: 83 YRTITTAYYRGAMGFILMYDVTNEESFTSIQ-DWITQIKTYSWDNAQVILVGNKCDMEDE 141
Y + Y A ++ + + +S +++ WI +++ Y N VILVG K D+ E
Sbjct: 62 YERLRPLSYSKAHVILIGFAIDTPDSLENVRTKWIEEVRRYC-PNVPVILVGLKKDLRQE 120
Query: 142 ----------RVISFERGKHLAESLGVE-FFETSAKDNVNVKGVFE 176
+ ++ K +A ++G + + E SA V VFE
Sbjct: 121 AVAKGNYATDEFVPIQQAKLVARAIGAKKYMECSALTGEGVDDVFE 166
>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 = 80.7 bits (199), Expect = 6e-19
Identities = 45/166 (27%), Positives = 82/166 (49%), Gaps = 12/166 (7%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQER 82
K++++G+ + GKTS L + F + TV ++ + +F V+L +WDTAGQE
Sbjct: 2 KVVVLGDGACGKTSLLNVFTRGYFPQVYEPTVFENY-IHDIFVDGLAVELSLWDTAGQEE 60
Query: 83 YRTITTAYYRGAMGFILMYDVTNEESFTSIQD-WITQIKTYSWDNAQVILVGNKCDMEDE 141
+ + + Y +L + V N +S +++ W+ +I+ + +++LV KCD+ +
Sbjct: 61 FDRLRSLSYADTHVIMLCFSVDNPDSLENVESKWLAEIRHHC-PGVKLVLVALKCDLREP 119
Query: 142 R--------VISFERGKHLAESLG-VEFFETSAKDNVNVKGVFERL 178
R IS+E G +A+ + + E SAK N V F
Sbjct: 120 RNERDRGTHTISYEEGLAVAKRINACRYLECSAKLNRGVNEAFTEA 165
>gnl|CDD|206741 cd09914, RocCOR, Ras of complex proteins (Roc) C-terminal of Roc
(COR) domain family. RocCOR (or Roco) protein family is
characterized by a superdomain containing a Ras-like
GTPase domain, called Roc (Ras of complex proteins), and
a characteristic second domain called COR (C-terminal of
Roc). A kinase domain and diverse regulatory domains are
also often found in Roco proteins. Their functions are
diverse; in Dictyostelium discoideum, which encodes 11
Roco proteins, they are involved in cell division,
chemotaxis and development, while in human, where 4 Roco
proteins (LRRK1, LRRK2, DAPK1, and MFHAS1) are encoded,
these proteins are involved in epilepsy and cancer.
Mutations in LRRK2 (leucine-rich repeat kinase 2) are
known to cause familial Parkinson's disease.
Length = 161
Score = 77.4 bits (191), Expect = 5e-18
Identities = 40/165 (24%), Positives = 70/165 (42%), Gaps = 10/165 (6%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGI---DFKVKTVFRHDKRVKLQIWDTAG 79
KL+++G VGKTS + + F ST GI D+K+ K+++L +WD G
Sbjct: 3 KLMLVGQGGVGKTSLCKQLIGEKFDGDESSTHGINVQDWKIPA--PERKKIRLNVWDFGG 60
Query: 80 QERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNKCDME 139
QE Y + ++L++D+ + + + W+ QIK + + VILVG D
Sbjct: 61 QEIYHATHQFFLTSRSLYLLVFDLRTGDEVSRVPYWLRQIKAFGGVSP-VILVGTHIDES 119
Query: 140 DERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDIICD 184
+ I + ++ + S K+ + L I
Sbjct: 120 CDEDILKKALNKKFPAIINDIHFVSCKNGKGIA----ELKKAIAK 160
>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 = 77.9 bits (192), Expect = 5e-18
Identities = 51/170 (30%), Positives = 90/170 (52%), Gaps = 19/170 (11%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDK-RVKLQIWDTAGQE 81
K++++G+S GKT+ L +A DSF +V TV ++ F DK R++L +WDT+G
Sbjct: 3 KIVLVGDSQCGKTALLQVFAKDSFPENYVPTVFENY--TASFEVDKQRIELSLWDTSGSP 60
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSIQD-WITQIKTYSWDNAQVILVGNKCDMED 140
Y + Y + ++ +D++ E+ S+ W +++ + N V+LVG K D+
Sbjct: 61 YYDNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEVREFC-PNTPVLLVGCKSDLRT 119
Query: 141 E------------RVISFERGKHLAESLG-VEFFETSAKDNVN-VKGVFE 176
+ +S E+G++LA+ +G + E SAK + N V+ VFE
Sbjct: 120 DLSTLTELSNKRQIPVSHEQGRNLAKQIGAAAYVECSAKTSENSVRDVFE 169
>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 = 74.4 bits (183), Expect = 2e-17
Identities = 32/117 (27%), Positives = 53/117 (45%), Gaps = 4/117 (3%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQER 82
K+++IG+ GK+S L + F + G V T+ L IWD G+E
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREE 60
Query: 83 YRTITTAYYRGAMGFILMYDVTNEESF---TSIQDWITQIKTYSWDNAQVILVGNKC 136
+ + + A +L+YD+T+ ES + + W+ ++ VILVGNK
Sbjct: 61 LKFEHIIFMKWADAILLVYDLTDRESLNEVSRLIAWLPNLRKLG-GKIPVILVGNKL 116
>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 = 77.1 bits (190), Expect = 2e-17
Identities = 41/159 (25%), Positives = 77/159 (48%), Gaps = 1/159 (0%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
++++++G+S VGK+S + + + G D +TV + L ++D QE
Sbjct: 1 YRVVLLGDSGVGKSSLANIFTAGVYEDSAYEASGDDTYERTVSVDGEEATLVVYDHWEQE 60
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIK-TYSWDNAQVILVGNKCDMED 140
+ + + ++++Y VT+ SF + Q++ ++ +ILVGNK D+
Sbjct: 61 DGMWLEDSCMQVGDAYVIVYSVTDRSSFEKASELRIQLRRARQAEDIPIILVGNKSDLVR 120
Query: 141 ERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLV 179
R +S + G+ A +F ETSA NV +FE +V
Sbjct: 121 SREVSVQEGRACAVVFDCKFIETSAALQHNVDELFEGIV 159
>gnl|CDD|206663 cd01871, Rac1_like, Ras-related C3 botulinum toxin substrate 1 (rho
family, small GTP binding protein Rac1)-like consists of
Rac1, Rac2 and Rac3. The Rac1-like subfamily consists
of Rac1, Rac2, and Rac3 proteins, plus the splice
variant Rac1b that contains a 19-residue insertion near
switch II relative to Rac1. While Rac1 is ubiquitously
expressed, Rac2 and Rac3 are largely restricted to
hematopoietic and neural tissues respectively. Rac1
stimulates the formation of actin lamellipodia and
membrane ruffles. It also plays a role in cell-matrix
adhesion and cell anoikis. In intestinal epithelial
cells, Rac1 is an important regulator of migration and
mediates apoptosis. Rac1 is also essential for
RhoA-regulated actin stress fiber and focal adhesion
complex formation. In leukocytes, Rac1 and Rac2 have
distinct roles in regulating cell morphology, migration,
and invasion, but are not essential for macrophage
migration or chemotaxis. Rac3 has biochemical properties
that are closely related to Rac1, such as effector
interaction, nucleotide binding, and hydrolysis; Rac2
has a slower nucleotide association and is more
efficiently activated by the RacGEF Tiam1. Both Rac1 and
Rac3 have been implicated in the regulation of cell
migration and invasion in human metastatic breast
cancer. Most Rho proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Rho proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 174
Score = 75.6 bits (186), Expect = 4e-17
Identities = 48/168 (28%), Positives = 85/168 (50%), Gaps = 16/168 (9%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQER 82
K +++G+ +VGKT L Y ++F ++ TV D V K V L +WDTAGQE
Sbjct: 3 KCVVVGDGAVGKTCLLISYTTNAFPGEYIPTV-FDNYSANVMVDGKPVNLGLWDTAGQED 61
Query: 83 YRTITTAYYRGAMGFILMYDVTNEESFTSIQ-DWITQIKTYSWDNAQVILVGNKCDMEDE 141
Y + Y F++ + + + SF +++ W +++ + N +ILVG K D+ D+
Sbjct: 62 YDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHC-PNTPIILVGTKLDLRDD 120
Query: 142 RV------------ISFERGKHLAESLG-VEFFETSAKDNVNVKGVFE 176
+ I++ +G +A+ +G V++ E SA +K VF+
Sbjct: 121 KDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVFD 168
>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 = 74.0 bits (182), Expect = 4e-16
Identities = 47/172 (27%), Positives = 78/172 (45%), Gaps = 21/172 (12%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
++++++G S VGKT+ + R+ F + T+ DF K + +L I DT+G
Sbjct: 1 YRMVVLGASKVGKTAIVSRFLGGRFEEQYTPTIE-DFHRKLYSIRGEVYQLDILDTSGNH 59
Query: 82 -----RYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSW-------DNAQV 129
R +I T G + FIL++ + N ESF + QI +N ++
Sbjct: 60 PFPAMRRLSILT----GDV-FILVFSLDNRESFEEVCRLREQILETKSCLKNKTKENVKI 114
Query: 130 --ILVGNKCDMEDER-VISFERGKHLAESLGVEFFETSAKDNVNVKGVFERL 178
++ GNK D + R V E + + +FE SAK N N+ +F L
Sbjct: 115 PMVICGNKADRDFPREVQRDEVEQLVGGDENCAYFEVSAKKNSNLDEMFRAL 166
>gnl|CDD|206714 cd04147, Ras_dva, Ras - dorsal-ventral anterior localization
(Ras-dva) family. Ras-dva subfamily. Ras-dva (Ras -
dorsal-ventral anterior localization) subfamily consists
of a set of proteins characterized only in Xenopus
leavis, to date. In Xenopus Ras-dva expression is
activated by the transcription factor Otx2 and begins
during gastrulation throughout the anterior ectoderm.
Ras-dva expression is inhibited in the anterior neural
plate by factor Xanf1. Downregulation of Ras-dva results
in head development abnormalities through the inhibition
of several regulators of the anterior neural plate and
folds patterning, including Otx2, BF-1, Xag2, Pax6,
Slug, and Sox9. Downregulation of Ras-dva also
interferes with the FGF-8a signaling within the anterior
ectoderm. Most Ras proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins.
Length = 197
Score = 72.6 bits (178), Expect = 6e-16
Identities = 47/163 (28%), Positives = 75/163 (46%), Gaps = 11/163 (6%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTV----GIDFKVKTVFRHDKRVKLQIWDTA 78
+L+ +G + VGKT+ + R+ D+F TV +++V V +V + I DT+
Sbjct: 1 RLVFMGAAGVGKTALIQRFLYDTFEPKHRRTVEELHSKEYEVAGV-----KVTIDILDTS 55
Query: 79 GQERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNA-QVILVGNKCD 137
G + + + F L+Y V + ESF ++ +I D +++VGNK D
Sbjct: 56 GSYSFPAMRKLSIQNGDAFALVYSVDDPESFEEVKRLREEILEVKEDKFVPIVVVGNKID 115
Query: 138 MEDERVISFERGKHLAE-SLGVEFFETSAKDNVNVKGVFERLV 179
ER + E F E SAKDN NV VF+ L+
Sbjct: 116 SLAERQVEAADALSTVELDWNNGFVEASAKDNENVTEVFKELL 158
>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 = 71.1 bits (174), Expect = 2e-15
Identities = 49/168 (29%), Positives = 84/168 (50%), Gaps = 16/168 (9%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQER 82
K +++G+ +VGKT L Y + F S +V TV ++ V TV + L ++DTAGQE
Sbjct: 3 KCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAV-TVMIGGEPYTLGLFDTAGQED 61
Query: 83 YRTITTAYYRGAMGFILMYDVTNEESFTSIQD-WITQIKTYSWDNAQVILVGNKCDMEDE 141
Y + Y F++ + V + SF ++++ W+ +I + +LVG + D+ D+
Sbjct: 62 YDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHC-PKTPFLLVGTQIDLRDD 120
Query: 142 ------------RVISFERGKHLAESLG-VEFFETSAKDNVNVKGVFE 176
+ I+ E G+ LA L V++ E SA +K VF+
Sbjct: 121 PSTIEKLAKNKQKPITPETGEKLARDLKAVKYVECSALTQKGLKNVFD 168
>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 = 70.4 bits (172), Expect = 4e-15
Identities = 49/172 (28%), Positives = 87/172 (50%), Gaps = 18/172 (10%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKR-VKLQIWDTAGQE 81
K +++G+ +VGKT L Y ++F ++ TV ++ +T D R V L +WDTAGQE
Sbjct: 5 KCVVVGDGAVGKTCLLICYTTNAFPKEYIPTVFDNYSAQTAV--DGRTVSLNLWDTAGQE 62
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSIQ-DWITQIKTYSWDNAQVILVGNKCDMED 140
Y + T Y FI+ + + + S+ +++ W ++ + N ++LVG K D+ +
Sbjct: 63 EYDRLRTLSYPQTNVFIICFSIASPSSYENVRHKWHPEV-CHHCPNVPILLVGTKKDLRN 121
Query: 141 ER------------VISFERGKHLAESLG-VEFFETSAKDNVNVKGVFERLV 179
+ I+ ++G LA+ + V++ E SA + VK VF V
Sbjct: 122 DADTLKKLKEQGQAPITPQQGGALAKQIHAVKYLECSALNQDGVKEVFAEAV 173
>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 = 70.8 bits (173), Expect = 5e-15
Identities = 49/169 (28%), Positives = 92/169 (54%), Gaps = 19/169 (11%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDK-RVKLQIWDTAGQE 81
K++++G++ GKT+ L +A D++ ++V TV ++ F DK R++L +WDT+G
Sbjct: 3 KIVVVGDTQCGKTALLHVFAKDNYPESYVPTVFENYTAS--FEIDKHRIELNMWDTSGSS 60
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSI-QDWITQIKTYSWDNAQVILVGNKCDME- 139
Y + Y + ++ +D++ E+ S+ + W + + + NA+++LVG K DM
Sbjct: 61 YYDNVRPLAYPDSDAVLICFDISRPETLDSVLKKWQGETQEFC-PNAKLVLVGCKLDMRT 119
Query: 140 ---------DERVI--SFERGKHLAESLG-VEFFETSAKDNVN-VKGVF 175
+R+I + E+G LA LG V + E S++ + N V+ VF
Sbjct: 120 DLSTLRELSKQRLIPVTHEQGSLLARQLGAVAYVECSSRMSENSVRDVF 168
>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 = 70.5 bits (172), Expect = 7e-15
Identities = 44/157 (28%), Positives = 81/157 (51%), Gaps = 16/157 (10%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQER 82
KL+++G+ GKT+ L A D + +V TV ++ + ++RV+L +WDT+G
Sbjct: 15 KLVLVGDVQCGKTAMLQVLAKDCYPETYVPTVFENY-TACLETEEQRVELSLWDTSGSPY 73
Query: 83 YRTITTAYYRGAMGFILMYDVTNEESFTS-IQDWITQIKTYSWDNAQVILVGNKCDM--- 138
Y + Y + +L +D++ E F S ++ W +I Y + +++L+G K D+
Sbjct: 74 YDNVRPLCYSDSDAVLLCFDISRPEIFDSALKKWRAEILDYC-PSTRILLIGCKTDLRTD 132
Query: 139 ---------EDERVISFERGKHLAESLGVE-FFETSA 165
+ + IS+E+G +A+ LG E + E SA
Sbjct: 133 LSTLMELSNQKQAPISYEQGCAMAKQLGAEAYLECSA 169
>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 = 67.8 bits (165), Expect = 4e-14
Identities = 44/169 (26%), Positives = 88/169 (52%), Gaps = 19/169 (11%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDK-RVKLQIWDTAGQE 81
K++++G+S GKT+ L +A D F +V TV ++ F D R++L +WDT+G
Sbjct: 7 KIVVVGDSQCGKTALLHVFAKDCFPENYVPTVFENYTAS--FEIDTQRIELSLWDTSGSP 64
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSI-QDWITQIKTYSWDNAQVILVGNKCDMED 140
Y + Y + ++ +D++ E+ S+ + W +I+ + N +++LVG K D+
Sbjct: 65 YYDNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEIQEFC-PNTKMLLVGCKSDLRT 123
Query: 141 ERV------------ISFERGKHLAESLGVE-FFETSAKDNVN-VKGVF 175
+ +S+++G ++A+ +G + E SA + N V+ +F
Sbjct: 124 DVSTLVELSNHRQTPVSYDQGANMAKQIGAATYIECSALQSENSVRDIF 172
>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 = 60.7 bits (148), Expect = 9e-12
Identities = 39/167 (23%), Positives = 72/167 (43%), Gaps = 19/167 (11%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQER 82
++L++G GKT+ L++ + + T+G F V+TV K VK +WD GQ++
Sbjct: 1 RILMLGLDGAGKTTILYKLKLGEVVTT-IPTIG--FNVETV--EYKNVKFTVWDVGGQDK 55
Query: 83 YRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQI-KTYSWDNAQVILVGNKCDMEDE 141
R + YY G I + D ++ E ++ + ++ A ++++ NK D+
Sbjct: 56 IRPLWKHYYENTDGLIFVVDSSDRERIEEAKNELHKLLNEEELKGAPLLILANKQDLPGA 115
Query: 142 RVISFERGKHLAESLGVE--------FFETSAKDNVNVKGVFERLVD 180
S L E LG+E SA + + L++
Sbjct: 116 LTES-----ELIELLGLESIKGRRWHIQPCSAVTGDGLDEGLDWLIE 157
>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 = 52.3 bits (126), Expect = 8e-09
Identities = 39/162 (24%), Positives = 75/162 (46%), Gaps = 16/162 (9%)
Query: 26 IIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQERYRT 85
++G + GKT+ + A F+ + TVG F ++ V + V +++WD GQ R+R+
Sbjct: 4 LVGLQNSGKTTLVNVIASGQFSEDTIPTVG--FNMRKVTK--GNVTIKVWDLGGQPRFRS 59
Query: 86 ITTAYYRGAMGFILMYDVTNEESF----TSIQDWITQIKTYSWDNAQVILVGNKCDMED- 140
+ Y RG + + D + E + D + K S + ++++GNK D+
Sbjct: 60 MWERYCRGVNAIVYVVDAADREKLEVAKNELHDLL--EKP-SLEGIPLLVLGNKNDLPGA 116
Query: 141 ---ERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLV 179
+ +I K + + V + SAK+ N+ V + L+
Sbjct: 117 LSVDELIEQMNLKSITDR-EVSCYSISAKEKTNIDIVLDWLI 157
>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 = 50.4 bits (120), Expect = 7e-08
Identities = 46/190 (24%), Positives = 80/190 (42%), Gaps = 38/190 (20%)
Query: 22 FKLLIIGNSSVGKTSFLFRYA------DDSFTSAFVSTV-GID--------FKVKTVFRH 66
K +++G+++VGKT + A + V TV ID +
Sbjct: 3 IKCVVVGDNAVGKTRLICARACNKTLTQYQLLATHVPTVWAIDQYRVCQEVLERSRDVVD 62
Query: 67 DKRVKLQIWDTAGQERYRTITTAYYRGAMGFILMYDVTNEESFTSIQD-WITQIKTYSWD 125
V L++WDT G + + AY R + +L + + + S +++ W +I+ +
Sbjct: 63 GVSVSLRLWDTFG-DHDKDRRFAYGRSDV-VLLCFSIASPNSLRNVKTMWYPEIRHFCPR 120
Query: 126 NAQVILVGNKCDME----DE---------------RVISFERGKHLAESLGVEFFETSAK 166
VILVG K D+ DE ++ E G+ +A+ LG+ ++ETS
Sbjct: 121 -VPVILVGCKLDLRYADLDEVNRARRPLARPIKNADILPPETGRAVAKELGIPYYETSVV 179
Query: 167 DNVNVKGVFE 176
VK VF+
Sbjct: 180 TQFGVKDVFD 189
>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 = 49.8 bits (119), Expect = 1e-07
Identities = 33/120 (27%), Positives = 59/120 (49%), Gaps = 5/120 (4%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDF-KVKTVFRHDKRVKLQIWDTAGQ 80
++++G S GKT+ L+R + F + V T G + K+K + K V WD GQ
Sbjct: 4 LHIVMLGLDSAGKTTVLYRLKFNEFVNT-VPTKGFNTEKIKVSLGNAKGVTFHFWDVGGQ 62
Query: 81 ERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDN--AQVILVGNKCDM 138
E+ R + +Y R G + + D + E + + +I +S +N V+++ NK D+
Sbjct: 63 EKLRPLWKSYTRCTDGIVFVVDSVDVERMEEAKTELHKITKFS-ENQGVPVLVLANKQDL 121
>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 = 49.0 bits (117), Expect = 1e-07
Identities = 29/81 (35%), Positives = 45/81 (55%), Gaps = 7/81 (8%)
Query: 23 KLLIIGNSSVGKTSFLFRYA-DDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
++L++G + GKT+ L++ S T+ + TVG F V+TV K VK +WD GQ+
Sbjct: 11 RILMLGLDAAGKTTILYKLKLGQSVTT--IPTVG--FNVETVTY--KNVKFNVWDVGGQD 64
Query: 82 RYRTITTAYYRGAMGFILMYD 102
+ R + YY G G I + D
Sbjct: 65 KIRPLWRHYYTGTQGLIFVVD 85
>gnl|CDD|177661 PLN00023, PLN00023, GTP-binding protein; Provisional.
Length = 334
Score = 49.9 bits (119), Expect = 3e-07
Identities = 29/112 (25%), Positives = 53/112 (47%), Gaps = 17/112 (15%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTV---------------FRHD 67
++L++G+S VGK+S + S + T+G VK + D
Sbjct: 23 RVLVVGDSGVGKSSLVHLIVKGSSIARPPQTIGCTVGVKHITYGSPGSSSNSIKGDSERD 82
Query: 68 KRVKLQIWDTAGQERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQI 119
V+L WD +G ERY+ + +Y G I ++D++ + TS+Q W +++
Sbjct: 83 FFVEL--WDVSGHERYKDCRSLFYSQINGVIFVHDLSQRRTKTSLQKWASEV 132
>gnl|CDD|128474 smart00177, ARF, ARF-like small GTPases; ARF, ADP-ribosylation
factor. Ras homologues involved in vesicular transport.
Activator of phospholipase D isoforms. Unlike Ras
proteins they lack cysteine residues at their C-termini
and therefore are unlikely to be prenylated. ARFs are
N-terminally myristoylated. Contains ATP/GTP-binding
motif (P-loop).
Length = 175
Score = 48.4 bits (115), Expect = 3e-07
Identities = 30/120 (25%), Positives = 61/120 (50%), Gaps = 8/120 (6%)
Query: 23 KLLIIGNSSVGKTSFLFRYA-DDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
++L++G + GKT+ L++ +S T+ + T+G F V+TV K + +WD GQ+
Sbjct: 15 RILMVGLDAAGKTTILYKLKLGESVTT--IPTIG--FNVETV--TYKNISFTVWDVGGQD 68
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQ-IKTYSWDNAQVILVGNKCDMED 140
+ R + YY G I + D + + ++ + + + +A +++ NK D+ D
Sbjct: 69 KIRPLWRHYYTNTQGLIFVVDSNDRDRIDEAREELHRMLNEDELRDAVILVFANKQDLPD 128
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 48.0 bits (115), Expect = 4e-07
Identities = 29/122 (23%), Positives = 56/122 (45%), Gaps = 10/122 (8%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
++LI+G + GKT+ L++ + + T+G F V+TV K VK +WD GQE
Sbjct: 15 MRILILGLDNAGKTTILYKLKLGEIVTT-IPTIG--FNVETV--TYKNVKFTVWDVGGQE 69
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSIQ---DWITQIKTYSWDNAQVILVGNKCDM 138
R + Y+ I + D + + + + + + +A ++++ NK D+
Sbjct: 70 SLRPLWRNYFPNTDAVIFVVDSADRDRIEEAKEELHALLNEEELA--DAPLLILANKQDL 127
Query: 139 ED 140
Sbjct: 128 PG 129
>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 = 48.3 bits (115), Expect = 5e-07
Identities = 42/175 (24%), Positives = 75/175 (42%), Gaps = 22/175 (12%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWD----- 76
++ ++G VGKT+ + ++ F ++ T V + L I D
Sbjct: 1 VRVAVLGAPGVGKTAIVRQFLAQEFPEEYIPTEHRRLYRPAVVLSGRVYDLHILDVPNMQ 60
Query: 77 ----TAGQE----RYRTITTAYYRGAMGFILMYDVTNEESF---TSIQDWITQIKTYSWD 125
TAGQE R+R + R + FIL+YD+ + +SF ++ I + +
Sbjct: 61 RYPGTAGQEWMDPRFRGL-----RNSRAFILVYDICSPDSFHYVKLLRQQILETRPAGNK 115
Query: 126 NAQVILVGNKCDMEDERVISFERGKHLA-ESLGVEFFETSAKDNVNVKGVFERLV 179
+++VGNK D + R L +S + E SAK N ++ +F+ L+
Sbjct: 116 EPPIVVVGNKRDQQRHRFAPRHVLSVLVRKSWKCGYLECSAKYNWHILLLFKELL 170
>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 = 47.4 bits (113), Expect = 6e-07
Identities = 32/119 (26%), Positives = 58/119 (48%), Gaps = 5/119 (4%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQER 82
++L++G S GK++ L++ + + TVG F V+ + + +K + L +WD GQE+
Sbjct: 1 QVLLLGLDSAGKSTLLYKLKHAELVTT-IPTVG--FNVEML-QLEKHLSLTVWDVGGQEK 56
Query: 83 YRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQI-KTYSWDNAQVILVGNKCDMED 140
RT+ Y G + + D ++E Q + I K V+L+ NK D+
Sbjct: 57 MRTVWKCYLENTDGLVYVVDSSDEARLDESQKELKHILKNEHIKGVPVVLLANKQDLPG 115
>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 = 47.6 bits (113), Expect = 8e-07
Identities = 37/170 (21%), Positives = 70/170 (41%), Gaps = 30/170 (17%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVG--IDFKVKTVFR---HDKRVKLQIWDT 77
K+L++G+S VGK+S + + TVG +D + T +K +++WD
Sbjct: 2 KVLVLGDSGVGKSSLVHLLCKNQVLGNPSWTVGCSVDVRHHTYGEGTPEEKTFYVELWDV 61
Query: 78 AGQ----ERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQ------------IKT 121
G E ++ +Y G I ++D+TN++S ++ W + +
Sbjct: 62 GGSVGSAESVKSTRAVFYNQINGIIFVHDLTNKKSSQNLYRWSLEALNRDTFPAGLLVTN 121
Query: 122 YSWDNAQ-------VILVGNKCDM--EDERVISFERGKHLAESLGVEFFE 162
+D+ Q ++++G K D E +R R L+E E
Sbjct: 122 GDYDSEQFAGNPVPLLVIGTKLDQIPEAKRNWVLTRTAFLSEDFNAEEIN 171
>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 = 46.9 bits (112), Expect = 8e-07
Identities = 43/160 (26%), Positives = 67/160 (41%), Gaps = 12/160 (7%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQER 82
++++IG+ VGK+S + + F V V + + + RV I DT+ + +
Sbjct: 4 RIVLIGDEGVGKSSLIMSLVSEEF-PENVPRVLPEITIPADVTPE-RVPTTIVDTSSRPQ 61
Query: 83 YRTITTAYYRGAMGFILMYDVTNEESFTSIQD-WITQIKTYSWDNAQVILVGNKCDMEDE 141
R A R A L+Y V + I+ W+ I+ +ILVGNK D+ D
Sbjct: 62 DRANLAAEIRKANVICLVYSVDRPSTLERIRTKWLPLIRR-LGVKVPIILVGNKSDLRDG 120
Query: 142 RVISFERGKHLAESLGVEF------FETSAKDNVNVKGVF 175
S + + EF E SAK +NV VF
Sbjct: 121 S--SQAGLEEEMLPIMNEFREIETCVECSAKTLINVSEVF 158
>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 = 47.0 bits (112), Expect = 9e-07
Identities = 42/154 (27%), Positives = 66/154 (42%), Gaps = 21/154 (13%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTV-GIDFKVKTVFRHDKRVKLQIWDTAGQE 81
++LI+G GKT+ L+R V+T+ I F V+TV K +K Q+WD GQ
Sbjct: 1 RILILGLDGAGKTTILYRLQ----VGEVVTTIPTIGFNVETV--TYKNLKFQVWDLGGQT 54
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESF-TSIQDWITQIKTYSWDNAQVILVGNKCDMED 140
R YY I + D T+ + S + ++ +A +++ NK DM
Sbjct: 55 SIRPYWRCYYSNTDAIIYVVDSTDRDRLGISKSELHAMLEEEELKDAVLLVFANKQDMPG 114
Query: 141 ERVISFERGKHLAESLGVE--------FFETSAK 166
+ +AE LG+ F+TSA
Sbjct: 115 ALSEA-----EVAEKLGLSELKDRTWQIFKTSAT 143
>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 = 46.3 bits (110), Expect = 1e-06
Identities = 43/160 (26%), Positives = 69/160 (43%), Gaps = 15/160 (9%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQER 82
KL I+GN GK++ + RY S+ S G FK K V + L I D G
Sbjct: 2 KLGIVGNLRSGKSALVHRYLTGSYV-QLESPEGGRFK-KEVLVDGQSHLLLIRDEGGAPD 59
Query: 83 YRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQ---VILVG--NKCD 137
+ + I ++ + +E SF ++ Q+ +Y N +ILVG +
Sbjct: 60 AQ-----FAGWVDAVIFVFSLEDEASFQTVYRLYHQLSSYR--NISEIPLILVGTQDAIS 112
Query: 138 MEDERVISFERGKHLAESLG-VEFFETSAKDNVNVKGVFE 176
+ RVI R + L + ++ET A +NV+ VF+
Sbjct: 113 ASNPRVIDDARARQLCADMKRCSYYETCATYGLNVERVFQ 152
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 46.7 bits (111), Expect = 1e-06
Identities = 40/172 (23%), Positives = 71/172 (41%), Gaps = 23/172 (13%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVS------------TVGIDFKVKTVFRHDKRV 70
K+++IG GKT+F+ +D TV +DF + D+
Sbjct: 12 KIVVIGPVGAGKTTFVRALSDKPLVITEADASSVSGKGKRPTTVAMDFGSIEL---DEDT 68
Query: 71 KLQIWDTAGQERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVI 130
+ ++ T GQER++ + RGA+G I++ D + +F + + I + N +
Sbjct: 69 GVHLFGTPGQERFKFMWEILSRGAVGAIVLVDSSRPITFHAEEI----IDFLTSRNPIPV 124
Query: 131 LVG-NKCDMEDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDI 181
+V NK D+ D R E L V E A + +G ++L +
Sbjct: 125 VVAINKQDLFDALPPEKIREALKLELLSVPVIEIDATEG---EGARDQLDVL 173
>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 = 45.8 bits (108), Expect = 2e-06
Identities = 29/118 (24%), Positives = 56/118 (47%), Gaps = 6/118 (5%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQER 82
+++ +G GKT+ LF+ D F + T+G F V+TV K +K IWD G+ +
Sbjct: 1 RVVTLGLDGAGKTTILFKLKQDEFMQP-IPTIG--FNVETV--EYKNLKFTIWDVGGKHK 55
Query: 83 YRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKT-YSWDNAQVILVGNKCDME 139
R + YY + + D ++ + + + ++ T +A +++ NK D+
Sbjct: 56 LRPLWKHYYLNTQAVVFVIDSSHRDRVSEAHSELAKLLTEKELRDALLLIFANKQDVA 113
>gnl|CDD|133353 cd04153, Arl5_Arl8, Arf-like 5 (Arl5) and 8 (Arl8) GTPases.
Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like
Arl4 and Arl7, are localized to the nucleus and
nucleolus. Arl5 is developmentally regulated during
embryogenesis in mice. Human Arl5 interacts with the
heterochromatin protein 1-alpha (HP1alpha), a nonhistone
chromosomal protein that is associated with
heterochromatin and telomeres, and prevents telomere
fusion. Arl5 may also play a role in embryonic nuclear
dynamics and/or signaling cascades. Arl8 was identified
from a fetal cartilage cDNA library. It is found in
brain, heart, lung, cartilage, and kidney. No function
has been assigned for Arl8 to date.
Length = 174
Score = 45.8 bits (109), Expect = 2e-06
Identities = 27/121 (22%), Positives = 60/121 (49%), Gaps = 8/121 (6%)
Query: 22 FKLLIIGNSSVGKTSFLFRYA-DDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQ 80
+K++I+G + GKT+ L+++ + ++ T+G + + K ++ +WD GQ
Sbjct: 16 YKVIIVGLDNAGKTTILYQFLLGEVVHTS--PTIGSNVEEIVY----KNIRFLMWDIGGQ 69
Query: 81 ERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTY-SWDNAQVILVGNKCDME 139
E R+ YY IL+ D T+ E ++ + ++ + A ++++ NK D++
Sbjct: 70 ESLRSSWNTYYTNTDAVILVIDSTDRERLPLTKEELYKMLAHEDLRKAVLLVLANKQDLK 129
Query: 140 D 140
Sbjct: 130 G 130
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 44.2 bits (104), Expect = 9e-06
Identities = 24/93 (25%), Positives = 46/93 (49%), Gaps = 7/93 (7%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTV-GIDFKVKTVFRHDKRVKLQIWDTAGQE 81
++L++G + GKT+ L++ V+T+ I F V+TV K + +WD GQ+
Sbjct: 19 RILMVGLDAAGKTTILYKLK----LGEIVTTIPTIGFNVETV--EYKNISFTVWDVGGQD 72
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSIQD 114
+ R + Y++ G I + D + + +D
Sbjct: 73 KIRPLWRHYFQNTQGLIFVVDSNDRDRVVEARD 105
>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 = 43.9 bits (104), Expect = 1e-05
Identities = 34/125 (27%), Positives = 57/125 (45%), Gaps = 14/125 (11%)
Query: 25 LIIGNSSVGKTSFLFRYADDSFT--------SAFVSTVGIDFKVKTVFRHDKRVKLQIWD 76
LI+G + GKT+FL + F+ S TVG++ V + +L WD
Sbjct: 3 LILGLDNAGKTTFLEQ-TKTKFSKNYKGLNPSKITPTVGLNIGTIEV----GKARLMFWD 57
Query: 77 TAGQERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQ-IKTYSWDNAQVILVGNK 135
GQE R++ YY + G I + D T+ E F + + I + + ++++ NK
Sbjct: 58 LGGQEELRSLWDKYYAESHGVIYVIDSTDRERFNESKSAFEKVINNEALEGVPLLVLANK 117
Query: 136 CDMED 140
D+ D
Sbjct: 118 QDLPD 122
>gnl|CDD|206645 cd00879, Sar1, Sar1 is an essential component of COPII vesicle
coats. Sar1 is an essential component of COPII vesicle
coats involved in export of cargo from the ER. The
GTPase activity of Sar1 functions as a molecular switch
to control protein-protein and protein-lipid
interactions that direct vesicle budding from the ER.
Activation of the GDP to the GTP-bound form of Sar1
involves the membrane-associated guanine nucleotide
exchange factor (GEF) Sec12. Sar1 is unlike all Ras
superfamily GTPases that use either myristoyl or prenyl
groups to direct membrane association and function, in
that Sar1 lacks such modification. Instead, Sar1
contains a unique nine-amino-acid N-terminal extension.
This extension contains an evolutionarily conserved
cluster of bulky hydrophobic amino acids, referred to as
the Sar1-N-terminal activation recruitment (STAR) motif.
The STAR motif mediates the recruitment of Sar1 to ER
membranes and facilitates its interaction with mammalian
Sec12 GEF leading to activation.
Length = 191
Score = 42.7 bits (101), Expect = 3e-05
Identities = 41/175 (23%), Positives = 75/175 (42%), Gaps = 21/175 (12%)
Query: 9 WQKDAADQNFDYMFKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDK 68
++K+A K++ +G + GKT+ L DD + V T+ + T+
Sbjct: 16 YKKEA---------KIVFLGLDNAGKTTLLHMLKDDR-LAQHVPTLHPTSEELTI----G 61
Query: 69 RVKLQIWDTAGQERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQI-KTYSWDNA 127
VK +D G E+ R + Y+ G + + D + E F ++ + + N
Sbjct: 62 NVKFTTFDLGGHEQARRVWKDYFPEVDGIVFLVDAADPERFQESKEELDSLLNDEELANV 121
Query: 128 QVILVGNKCDMEDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDII 182
++++GNK D +S E L E+LG+ T K V++K R V++
Sbjct: 122 PILILGNKIDKPGA--VSEEE---LREALGLYGTTTG-KGGVSLKVSNIRPVEVF 170
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 42.1 bits (99), Expect = 6e-05
Identities = 30/118 (25%), Positives = 60/118 (50%), Gaps = 8/118 (6%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTV-GIDFKVKTVFRHDKRVKLQIWDTAGQE 81
++L++G + GKT+ L++ V+T+ I F V+TV K +K +WD GQ+
Sbjct: 19 RILMVGLDAAGKTTILYKLK----LGEVVTTIPTIGFNVETV--EYKNLKFTMWDVGGQD 72
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTY-SWDNAQVILVGNKCDM 138
+ R + YY+ G I + D + E ++ + ++ + +A +++ NK D+
Sbjct: 73 KLRPLWRHYYQNTNGLIFVVDSNDRERIGDAREELERMLSEDELRDAVLLVFANKQDL 130
>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 = 41.6 bits (98), Expect = 6e-05
Identities = 28/118 (23%), Positives = 58/118 (49%), Gaps = 8/118 (6%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTV-GIDFKVKTVFRHDKRVKLQIWDTAGQE 81
++L++G + GKT+ L++ V+T+ I F V+TV K + +WD GQ+
Sbjct: 2 RILMVGLDAAGKTTILYKLK----LGEIVTTIPTIGFNVETV--EYKNISFTVWDVGGQD 55
Query: 82 RYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQ-IKTYSWDNAQVILVGNKCDM 138
+ R + Y++ G I + D + E ++ + + + +A +++ NK D+
Sbjct: 56 KIRPLWRHYFQNTQGLIFVVDSNDRERIGEAREELQRMLNEDELRDAVLLVFANKQDL 113
>gnl|CDD|233986 TIGR02729, Obg_CgtA, Obg family GTPase CgtA. This model describes
a univeral, mostly one-gene-per-genome GTP-binding
protein that associates with ribosomal subunits and
appears to play a role in ribosomal RNA maturation. This
GTPase, related to the nucleolar protein Obg, is
designated CgtA in bacteria. Mutations in this gene are
pleiotropic, but it appears that effects on cellular
functions such as chromosome partition may be secondary
to the effect on ribosome structure. Recent work done in
Vibrio cholerae shows an essential role in the stringent
response, in which RelA-dependent ability to synthesize
the alarmone ppGpp is required for deletion of this
GTPase to be lethal [Protein synthesis, Other].
Length = 329
Score = 42.4 bits (101), Expect = 8e-05
Identities = 24/87 (27%), Positives = 42/87 (48%), Gaps = 8/87 (9%)
Query: 102 DVTNEESFTSIQDW---ITQIKTYS---WDNAQVILVGNKCDMEDERVISFERGKHLAES 155
D++ E+ I+D+ ++K YS + + I+V NK D+ DE + E K L E+
Sbjct: 244 DISPEDGSDPIEDYEIIRNELKKYSPELAEKPR-IVVLNKIDLLDEEEL-EELLKELKEA 301
Query: 156 LGVEFFETSAKDNVNVKGVFERLVDII 182
LG F SA + + L +++
Sbjct: 302 LGKPVFPISALTGEGLDELLYALAELL 328
>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 = 41.0 bits (97), Expect = 1e-04
Identities = 46/175 (26%), Positives = 76/175 (43%), Gaps = 29/175 (16%)
Query: 24 LLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVF-RH--DKRVKLQIWDTAG- 79
L+I G +VGK+S + + T A F K++F H K ++ Q+ DT G
Sbjct: 3 LVIAGYPNVGKSSLV-----NKLTRAKPEVAPYPFTTKSLFVGHFDYKYLRWQVIDTPGI 57
Query: 80 -----QER----YRTITT-AYYRGAMGFILMYDVTNEESFTSIQDWIT---QIKTYSWDN 126
+ER + IT A+ R A+ F + D + E SI++ ++ +IK N
Sbjct: 58 LDRPLEERNTIEMQAITALAHLRAAVLFFI--DPS-ETCGYSIEEQLSLFKEIKPLF--N 112
Query: 127 AQVILVGNKCDMEDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDI 181
VI+V NK D+ E +S + E G E + S V + + ++
Sbjct: 113 KPVIVVLNKIDLLTEEDLS--EIEKELEKEGEEVIKISTLTEEGVDELKNKACEL 165
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 38.5 bits (91), Expect = 0.002
Identities = 18/87 (20%), Positives = 38/87 (43%), Gaps = 11/87 (12%)
Query: 102 DVTNEESFTSIQDWIT---QIKTYS---WDNAQVILVGNKCDMEDERVISFERGKHLAES 155
D++ E I+D+ ++K Y+ + Q++ V NK D+ + E + E
Sbjct: 245 DMSGSEGRDPIEDYEKINKELKLYNPRLLERPQIV-VANKMDLPEAE----ENLEEFKEK 299
Query: 156 LGVEFFETSAKDNVNVKGVFERLVDII 182
LG + F SA + + + +++
Sbjct: 300 LGPKVFPISALTGQGLDELLYAVAELL 326
>gnl|CDD|206685 cd01898, Obg, Obg GTPase. The Obg nucleotide binding protein
subfamily has been implicated in stress response,
chromosome partitioning, replication initiation,
mycelium development, and sporulation. Obg proteins are
among a large group of GTP binding proteins conserved
from bacteria to humans. The E. coli homolog, ObgE is
believed to function in ribosomal biogenesis. Members of
the subfamily contain two equally and highly conserved
domains, a C-terminal GTP binding domain and an
N-terminal glycine-rich domain.
Length = 170
Score = 37.4 bits (88), Expect = 0.002
Identities = 15/62 (24%), Positives = 25/62 (40%), Gaps = 8/62 (12%)
Query: 129 VILVGNKCDMEDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDIICDKMSE 188
I+V NK D+ D + + L E G + F SA +D + K+++
Sbjct: 117 RIVVLNKIDLLDAEERFEKLKELLKELKGKKVFPISALTGEG--------LDELLKKLAK 168
Query: 189 SL 190
L
Sbjct: 169 LL 170
>gnl|CDD|206691 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta), together with SR-alpha, forms the
heterodimeric signal recognition particle (SRP). Signal
recognition particle receptor, beta subunit (SR-beta).
SR-beta and SR-alpha form the heterodimeric signal
recognition particle (SRP or SR) receptor that binds SRP
to regulate protein translocation across the ER
membrane. Nascent polypeptide chains are synthesized
with an N-terminal hydrophobic signal sequence that
binds SRP54, a component of the SRP. SRP directs
targeting of the ribosome-nascent chain complex (RNC) to
the ER membrane via interaction with the SR, which is
localized to the ER membrane. The RNC is then
transferred to the protein-conducting channel, or
translocon, which facilitates polypeptide translation
across the ER membrane or integration into the ER
membrane. SR-beta is found only in eukaryotes; it is
believed to control the release of the signal sequence
from SRP54 upon binding of the ribosome to the
translocon. High expression of SR-beta has been observed
in human colon cancer, suggesting it may play a role in
the development of this type of cancer.
Length = 202
Score = 37.3 bits (87), Expect = 0.003
Identities = 26/119 (21%), Positives = 47/119 (39%), Gaps = 9/119 (7%)
Query: 25 LIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRH-DKRVKLQIWDTAGQERY 83
L++G S GKT+ + S S I+ V + + + K KL + D G E+
Sbjct: 4 LLLGPSDSGKTALFTKLTTGKVRSTVTS---IEPNVASFYSNSSKGKKLTLVDVPGHEKL 60
Query: 84 RTITTAYYRG-AMGFILMYD-VTNEESFTSIQDWITQIKTYSWDNAQVI---LVGNKCD 137
R Y + + + D T +++ + +++ I T I + NK D
Sbjct: 61 RDKLLEYLKASLKAIVFVVDSATFQKNIRDVAEFLYDILTDLEKIKNKIPILIACNKQD 119
>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 = 37.2 bits (87), Expect = 0.003
Identities = 41/169 (24%), Positives = 69/169 (40%), Gaps = 32/169 (18%)
Query: 23 KLLIIGNSSVGKTS-----FLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDT 77
K+L++G GK+S F D T +T+ ++ ++ R + L +WD
Sbjct: 1 KVLLMGLRGSGKSSMRSIIFSNYSPRD--TLRLGATIDVE---QSHVRFLGNLTLNLWDC 55
Query: 78 AGQERYRTITTAYYR-------GAMGFILMYDVTN---EESFTSIQDWITQIKTYSWDNA 127
GQ+ + + G + ++ DV + EE ++ I + YS NA
Sbjct: 56 PGQDDFMENYLTRQKEHIFSNVGVLIYVF--DVESREYEEDLATLVKIIEALYQYS-PNA 112
Query: 128 QVILVGNKCDM--EDERVISFERGKHLAESL-------GVEFFETSAKD 167
+V ++ +K D+ EDER FE K + FF TS D
Sbjct: 113 KVFVLIHKMDLLSEDERKEIFEDRKEEIIEEIEDFGIEDLTFFLTSIWD 161
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 37.0 bits (87), Expect = 0.004
Identities = 16/59 (27%), Positives = 25/59 (42%), Gaps = 4/59 (6%)
Query: 130 ILVGNKCDMEDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDIICDKMSE 188
ILV NK D+ DE +R +LG F SA + + L+ + + + E
Sbjct: 275 ILVLNKIDLLDEEEEREKRAALELAALGGPVFLISAVTGEGL----DELLRALWELLEE 329
>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 = 36.6 bits (85), Expect = 0.004
Identities = 23/87 (26%), Positives = 39/87 (44%), Gaps = 5/87 (5%)
Query: 23 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQER 82
++L++G + GKT+ L + A + + T G F +K V KL +WD GQ +
Sbjct: 17 RILLLGLDNAGKTTILKQLASEDISHIT-PTQG--FNIKNVQADGF--KLNVWDIGGQRK 71
Query: 83 YRTITTAYYRGAMGFILMYDVTNEESF 109
R Y+ I + D + + F
Sbjct: 72 IRPYWRNYFENTDVLIYVIDSADRKRF 98
>gnl|CDD|206668 cd01881, Obg_like, Obg-like family of GTPases consist of five
subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1. The
Obg-like subfamily consists of five well-delimited,
ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210,
and NOG1. Four of these groups (Obg, DRG, YyaF/YchF, and
Ygr210) are characterized by a distinct glycine-rich
motif immediately following the Walker B motif (G3 box).
Obg/CgtA is an essential gene that is involved in the
initiation of sporulation and DNA replication in the
bacteria Caulobacter and Bacillus, but its exact
molecular role is unknown. Furthermore, several OBG
family members possess a C-terminal RNA-binding domain,
the TGS domain, which is also present in threonyl-tRNA
synthetase and in bacterial guanosine polyphosphatase
SpoT. Nog1 is a nucleolar protein that might function in
ribosome assembly. The DRG and Nog1 subfamilies are
ubiquitous in archaea and eukaryotes, the Ygr210
subfamily is present in archaea and fungi, and the Obg
and YyaF/YchF subfamilies are ubiquitous in bacteria and
eukaryotes. The Obg/Nog1 and DRG subfamilies appear to
form one major branch of the Obg family and the Ygr210
and YchF subfamilies form another branch. No GEFs, GAPs,
or GDIs for Obg have been identified.
Length = 167
Score = 35.1 bits (81), Expect = 0.012
Identities = 37/173 (21%), Positives = 59/173 (34%), Gaps = 27/173 (15%)
Query: 26 IIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKT----VFRHDKRVKLQIWDTAG-- 79
++G +VGK++ L + TSA V F VF V +QI D G
Sbjct: 2 LVGLPNVGKSTLL-----SALTSAKVEIASYPFTTLEPNVGVFEFGDGVDIQIIDLPGLL 56
Query: 80 ------QERYRTITTAYYR-GAMGFILMYDVTNEESFTSIQDWIT-----QIKTYSWDNA 127
+ I YR + ++ D + + ++D T N
Sbjct: 57 DGASEGRGLGEQILAHLYRSDLILHVI--DASEDCVGDPLEDQKTLNEEVSGSFLFLKNK 114
Query: 128 QVILVGNKCDMEDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVD 180
++V NK DM E + R K G+ TSA + + V +
Sbjct: 115 PEMIVANKIDMASENNLK--RLKLDKLKRGIPVVPTSALTRLGLDRVIRTIRK 165
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 35.2 bits (82), Expect = 0.015
Identities = 17/75 (22%), Positives = 33/75 (44%), Gaps = 13/75 (17%)
Query: 128 QVILVGNKCDMEDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDIICDKMS 187
+ I+V NK D+ D+ L ++G + E SAK+ + + L ++ K++
Sbjct: 113 KPIIVLNKIDLLDDLE-EARELLALYRAIGYDVLELSAKEGEGL----DELKPLLAGKVT 167
Query: 188 ESLDSDPNLVAGPKG 202
++AG G
Sbjct: 168 --------VLAGQSG 174
>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 = 34.7 bits (81), Expect = 0.019
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 2/53 (3%)
Query: 126 NAQVILVGNKCDMEDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERL 178
+ ++V NK D+ D+ + E + E LG SAK + + E L
Sbjct: 33 GIEPVIVLNKADLVDDEEL--EELLEIYEKLGYPVLAVSAKTGEGLDELRELL 83
>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 = 34.3 bits (79), Expect = 0.021
Identities = 25/121 (20%), Positives = 50/121 (41%), Gaps = 8/121 (6%)
Query: 24 LLIIGNSSVGKTSFLFRYADDSFTSAFVS-TVGIDFKVKTVFRHDKRVKLQIWDTAGQER 82
+L++G + GKT+ + + + S + TVG F+ + +D +GQ +
Sbjct: 2 ILVLGLDNSGKTTIINQLKPSNAQSQNIVPTVGF---NVESFK-KGNLSFTAFDMSGQGK 57
Query: 83 YRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQI---KTYSWDNAQVILVGNKCDME 139
YR + YY+ G I + D ++ +D + + ++ NK D+
Sbjct: 58 YRGLWEHYYKNIQGIIFVIDSSDRLRMVVAKDELELLLNHPDIKHRRIPILFYANKMDLP 117
Query: 140 D 140
D
Sbjct: 118 D 118
>gnl|CDD|206720 cd04154, Arl2, Arf-like 2 (Arl2) GTPase. Arl2 (Arf-like 2) GTPases
are members of the Arf family that bind GDP and GTP with
very low affinity. Unlike most Arf family proteins, Arl2
is not myristoylated at its N-terminal helix. The
protein PDE-delta, first identified in photoreceptor rod
cells, binds specifically to Arl2 and is structurally
very similar to RhoGDI. Despite the high structural
similarity between Arl2 and Rho proteins and between
PDE-delta and RhoGDI, the interactions between the
GTPases and their effectors are very different. In its
GTP bound form, Arl2 interacts with the protein Binder
of Arl2 (BART), and the complex is believed to play a
role in mitochondrial adenine nucleotide transport. In
its GDP bound form, Arl2 interacts with tubulin- folding
Cofactor D; this interaction is believed to play a role
in regulation of microtubule dynamics that impact the
cytoskeleton, cell division, and cytokinesis.
Length = 173
Score = 33.8 bits (78), Expect = 0.030
Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 5/81 (6%)
Query: 22 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQE 81
++L++G + GKT+ L ++ + S T+G F +KT+ KL IWD GQ+
Sbjct: 15 MRILMLGLDNAGKTTILKKFNGED-ISTISPTLG--FNIKTL--EYNGYKLNIWDVGGQK 69
Query: 82 RYRTITTAYYRGAMGFILMYD 102
R+ Y+ I + D
Sbjct: 70 SLRSYWRNYFESTDALIWVVD 90
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 34.1 bits (79), Expect = 0.043
Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 7/57 (12%)
Query: 130 ILVGNKCDM--EDERVISFERGKHLAESLG--VEFFETSAKDNVNVKGVFERLVDII 182
LV NK D+ E+E ER K + E+LG + SA + VK + L+ I
Sbjct: 279 WLVFNKIDLLDEEEA---EERAKAIVEALGWEGPVYLISAASGLGVKELCWDLMTFI 332
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 33.9 bits (79), Expect = 0.045
Identities = 18/62 (29%), Positives = 28/62 (45%), Gaps = 5/62 (8%)
Query: 129 VILVGNKCDMEDERVISFERGKHLAESLG-VEFFETSAKDNVNVKGVFERLVDIICDKMS 187
VILV NK D+ ++ + L+E + E SA NV + L+D+I +
Sbjct: 116 VILVLNKIDLVKDKEELLPLLEELSELMDFAEIVPISALKGDNV----DELLDVIAKYLP 171
Query: 188 ES 189
E
Sbjct: 172 EG 173
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 32.0 bits (72), Expect = 0.11
Identities = 21/144 (14%), Positives = 40/144 (27%), Gaps = 9/144 (6%)
Query: 23 KLLIIGNSSVGKTSF---LFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAG 79
+LI+G GKT+ L R + V + +G
Sbjct: 4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSG 63
Query: 80 QERYRTITTAYYRGAMGFIL------MYDVTNEESFTSIQDWITQIKTYSWDNAQVILVG 133
+ R R + ++ + D E +++ + S N VIL
Sbjct: 64 ELRLRLALALARKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLTVILTT 123
Query: 134 NKCDMEDERVISFERGKHLAESLG 157
N ++ + + L
Sbjct: 124 NDEKDLGPALLRRRFDRRIVLLLI 147
>gnl|CDD|206742 cd09915, Rag, Rag GTPase subfamily of Ras-related GTPases. Rag
GTPases (ras-related GTP-binding proteins) constitute a
unique subgroup of the Ras superfamily, playing an
essential role in regulating amino acid-induced target
of rapamycin complex 1 (TORC1) kinase signaling,
exocytic cargo sorting at endosomes, and epigenetic
control of gene expression. This subfamily consists of
RagA and RagB as well as RagC and RagD that are closely
related. Saccharomyces cerevisiae encodes single
orthologs of metazoan RagA/B and RagC/D, Gtr1 and Gtr2,
respectively. Dimer formation is important for their
cellular function; these domains form heterodimers, as
RagA or RagB dimerizes with RagC or RagD, and similarly,
Gtr1 dimerizes with Gtr2. In response to amino acids,
the Rag GTPases guide the TORC1 complex to activate the
platform containing Rheb proto-oncogene by driving the
relocalization of mTORC1 from discrete locations in the
cytoplasm to a late endosomal and/or lysosomal
compartment that is Rheb-enriched and contains Rab-7.
Length = 175
Score = 32.1 bits (73), Expect = 0.13
Identities = 39/181 (21%), Positives = 71/181 (39%), Gaps = 29/181 (16%)
Query: 23 KLLIIGNSSVGKTSF---LFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAG 79
KLL+ G GK+S +F T ST+ ++ + L +WD G
Sbjct: 1 KLLLXGRRRSGKSSIRKVVFHNYSPFDTLRLESTIDVE---HSHLSFLGNXTLNLWDCPG 57
Query: 80 QERYRTITTAY---YRGAMGFILMYDVTNE--ESFTSIQDWITQIKTYSWD-NAQVILVG 133
Q+ + T ++ I + DV +E ++ T + + Q + D N +V++
Sbjct: 58 QDVFFEPTKDKEHIFQXVGALIYVIDVQDEYLKAITILAKALKQAYKVNPDANIEVLI-- 115
Query: 134 NKCD-------MEDERVISFERGKHLAES----LGVEFFETSAKDNVNVKGVFERLVDII 182
+K D E +R I + L+E + F+ TS D+ ++E I+
Sbjct: 116 HKVDGLSLDKKEELQRDIXQRLSETLSEFGLEFPNLSFYLTSIWDH----SIYEAFSQIV 171
Query: 183 C 183
Sbjct: 172 Q 172
>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 = 31.8 bits (73), Expect = 0.15
Identities = 31/168 (18%), Positives = 50/168 (29%), Gaps = 25/168 (14%)
Query: 26 IIGNSSVGKTSFLFRYADDSFTSAFVS-----TVGIDFKVKTVFRHDKRVKLQIWDTAG- 79
I G +VGK+S L VS T V+ + + + DT G
Sbjct: 2 IFGRPNVGKSSLLNALLGQ--NVGIVSPIPGTTRDP---VRKEWELLPLGPVVLIDTPGL 56
Query: 80 -----QERYRTITT-AYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVG 133
R R A +L+ D + ++ V+LV
Sbjct: 57 DEEGGLGRERVEEARQVADRADLVLLVVDSDLTPV-----EEEAKLGLLRERGKPVLLVL 111
Query: 134 NKCDM--EDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLV 179
NK D+ E E K L + SA + + +++
Sbjct: 112 NKIDLVPESEEEELLRERK-LELLPDLPVIAVSALPGEGIDELRKKIA 158
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes. TrmE
contains a GTPase domain that forms a canonical Ras-like
fold. It functions a molecular switch GTPase, and
apparently uses a conformational change associated with
GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 31.3 bits (72), Expect = 0.20
Identities = 15/85 (17%), Positives = 27/85 (31%), Gaps = 13/85 (15%)
Query: 98 ILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNKCDMEDERVISFERGKHLAESLG 157
+L+ D + +D VI+V NK D+ + E
Sbjct: 87 LLVVDASEGLD---EEDLEILELP---AKKPVIVVLNKSDLLSDAEGISELNGK------ 134
Query: 158 VEFFETSAKDNVNVKGVFERLVDII 182
SAK + + E L+++
Sbjct: 135 -PIIAISAKTGEGIDELKEALLELA 158
>gnl|CDD|217025 pfam02421, FeoB_N, Ferrous iron transport protein B. Escherichia
coli has an iron(II) transport system (feo) which may
make an important contribution to the iron supply of the
cell under anaerobic conditions. FeoB has been
identified as part of this transport system. FeoB is a
large 700-800 amino acid integral membrane protein. The
N terminus contains a P-loop motif suggesting that iron
transport may be ATP dependent.
Length = 190
Score = 30.5 bits (70), Expect = 0.45
Identities = 14/57 (24%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 129 VILVGNKCDMEDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDIICDK 185
V++ N D +++ I + K L+E LGV TSA+ + + + ++++ K
Sbjct: 108 VVVALNMMDEAEKKGIKIDIKK-LSELLGVPVVPTSARKGEGIDELKDAIIEVAEGK 163
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 30.8 bits (71), Expect = 0.49
Identities = 20/100 (20%), Positives = 36/100 (36%), Gaps = 18/100 (18%)
Query: 98 ILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILVGNKCDMEDERVISFERGKHLAESLG 157
+L+ D + E + + ++K + VI+V NK D+ E + E GK
Sbjct: 299 LLVLDAS-EPLTEEDDEILEELK-----DKPVIVVLNKADLTGEIDLEEENGKP------ 346
Query: 158 VEFFETSAKDNVNVKGVFERLVDIICDKMSESLDSDPNLV 197
SAK + + L + I + + V
Sbjct: 347 --VIRISAKTGEGI----DELREAIKELAFGGFGGNQEGV 380
>gnl|CDD|235545 PRK05650, PRK05650, short chain dehydrogenase; Provisional.
Length = 270
Score = 30.8 bits (70), Expect = 0.53
Identities = 9/45 (20%), Positives = 18/45 (40%), Gaps = 3/45 (6%)
Query: 74 IWDTAGQERYRTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQ 118
+ + G+E + + A G GF DV + T++ +
Sbjct: 32 VNEEGGEETLKLLREA---GGDGFYQRCDVRDYSQLTALAQACEE 73
>gnl|CDD|131580 TIGR02528, EutP, ethanolamine utilization protein, EutP. This
protein is found within operons which code for
polyhedral organelles containing the enzyme ethanolamine
ammonia lyase. The function of this gene is unknown,
although the presence of an N-terminal GxxGxGK motif
implies a GTP-binding site [Energy metabolism, Amino
acids and amines].
Length = 142
Score = 29.7 bits (67), Expect = 0.58
Identities = 24/89 (26%), Positives = 35/89 (39%), Gaps = 19/89 (21%)
Query: 98 ILMYDVTNEES-----FTSIQDWITQIKTYSWDNAQVILVGNKCDMEDERVISFERGKHL 152
L+ T+ ES F SI VI + K D+ + V ER K L
Sbjct: 67 ALVQSATDPESRFPPGFASIF------------VKPVIGLVTKIDLAEADV-DIERAKEL 113
Query: 153 AESLGVE-FFETSAKDNVNVKGVFERLVD 180
E+ G E FE S+ D ++ + + L
Sbjct: 114 LETAGAEPIFEISSVDEQGLEALVDYLNS 142
>gnl|CDD|225918 COG3383, COG3383, Uncharacterized anaerobic dehydrogenase [General
function prediction only].
Length = 978
Score = 30.9 bits (70), Expect = 0.59
Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 3/38 (7%)
Query: 75 WDTAGQ---ERYRTITTAYYRGAMGFILMYDVTNEESF 109
W+ A R R I Y ++GFI TNEE++
Sbjct: 335 WEEALDLVASRLREIKEKYGGDSIGFIASSKCTNEENY 372
>gnl|CDD|213190 cd03223, ABCD_peroxisomal_ALDP, ATP-binding cassette domain of
peroxisomal transporter, subfamily D. Peroxisomal
ATP-binding cassette transporter (Pat) is involved in
the import of very long-chain fatty acids (VLCFA) into
the peroxisome. The peroxisomal membrane forms a
permeability barrier for a wide variety of metabolites
required for and formed during fatty acid
beta-oxidation. To communicate with the cytoplasm and
mitochondria, peroxisomes need dedicated proteins to
transport such hydrophilic molecules across their
membranes. X-linked adrenoleukodystrophy (X-ALD) is
caused by mutations in the ALD gene, which encodes ALDP
(adrenoleukodystrophy protein ), a peroxisomal integral
membrane protein that is a member of the ATP-binding
cassette (ABC) transporter protein family. The disease
is characterized by a striking and unpredictable
variation in phenotypic expression. Phenotypes include
the rapidly progressive childhood cerebral form
(CCALD), the milder adult form, adrenomyeloneuropathy
(AMN), and variants without neurologic involvement
(i.e. asymptomatic).
Length = 166
Score = 29.8 bits (68), Expect = 0.60
Identities = 11/17 (64%), Positives = 12/17 (70%), Gaps = 1/17 (5%)
Query: 24 LLIIGNSSVGKTSFLFR 40
LLI G S GK+S LFR
Sbjct: 30 LLITGPSGTGKSS-LFR 45
>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 = 30.1 bits (68), Expect = 0.62
Identities = 21/84 (25%), Positives = 35/84 (41%), Gaps = 4/84 (4%)
Query: 24 LLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQERY 83
+L++G GKTS L + + + V T G F + D ++L + G +
Sbjct: 2 ILVLGLDGAGKTSLLHSLSSERSLESVVPTTG--FNSVAIPTQDAIMELL--EIGGSQNL 57
Query: 84 RTITTAYYRGAMGFILMYDVTNEE 107
R Y G+ G I + D + E
Sbjct: 58 RKYWKRYLSGSQGLIFVVDSADSE 81
>gnl|CDD|177659 PLN00021, PLN00021, chlorophyllase.
Length = 313
Score = 30.0 bits (68), Expect = 0.76
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 23 KLLIIGNSSVGKTSF--LFRYADDSFTSAFVSTVGID 57
KL + G+S GKT+F A S F + +G+D
Sbjct: 127 KLALAGHSRGGKTAFALALGKAAVSLPLKFSALIGLD 163
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 30.2 bits (69), Expect = 0.80
Identities = 18/65 (27%), Positives = 27/65 (41%), Gaps = 5/65 (7%)
Query: 126 NAQVILVGNKCDMEDERVISFERGKHLAESLG-VEFFETSAKDNVNVKGVFERLVDIICD 184
VILV NK D + + + L + L E SA NV + L++II +
Sbjct: 114 KTPVILVVNKIDKVKPKTVLLKLIAFLKKLLPFKEIVPISALKGDNV----DTLLEIIKE 169
Query: 185 KMSES 189
+ E
Sbjct: 170 YLPEG 174
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 30.2 bits (69), Expect = 0.82
Identities = 23/92 (25%), Positives = 44/92 (47%), Gaps = 8/92 (8%)
Query: 98 ILMYDVTNEESFTSIQDWIT---QIKTYS---WDNAQVILVGNKCDMEDERVISFERGKH 151
+ + D++ + I+D+ T +++ YS + + I+V NK D+ + E K
Sbjct: 242 LHVIDLSPIDGRDPIEDYQTIRNELEKYSPKLAEKPR-IVVLNKIDLPLDEEELEELKKA 300
Query: 152 LAESLGVEFFET-SAKDNVNVKGVFERLVDII 182
LAE+LG E F SA + + L +++
Sbjct: 301 LAEALGWEVFYLISALTREGLDELLRALAELL 332
>gnl|CDD|206647 cd00881, GTP_translation_factor, GTP translation factor family
primarily contains translation initiation, elongation
and release factors. The GTP translation factor family
consists primarily of translation initiation,
elongation, and release factors, which play specific
roles in protein translation. In addition, the family
includes Snu114p, a component of the U5 small nuclear
riboprotein particle which is a component of the
spliceosome and is involved in excision of introns,
TetM, a tetracycline resistance gene that protects the
ribosome from tetracycline binding, and the unusual
subfamily CysN/ATPS, which has an unrelated function
(ATP sulfurylase) acquired through lateral transfer of
the EF1-alpha gene and development of a new function.
Length = 183
Score = 29.2 bits (66), Expect = 1.1
Identities = 23/117 (19%), Positives = 38/117 (32%), Gaps = 9/117 (7%)
Query: 56 IDFKVKTVFRHDKRVKLQIWDTAGQERYRTITTAYYRGAMGFILMYDVTNEESFTSI-QD 114
I V +R+ DT G E + T A G +L+ D E ++
Sbjct: 50 IKTGVVEFEWPKRRI--NFIDTPGHEDFSKETVRGLAQADGALLVVDA--NEGVEPQTRE 105
Query: 115 WITQIKTYSWDNAQVILVGNKCDMEDERVISFERGKHLAESLGVEFFETSAKDNVNV 171
+ +I+ NK D E E + + E L + F +V +
Sbjct: 106 HLNIALAG---GLPIIVAVNKIDRVGEEDFD-EVLREIKELLKLIGFTFLKGKDVPI 158
>gnl|CDD|133361 cd04161, Arl2l1_Arl13_like, Arl2-like protein 1 (Arl2l1) and Arl13.
Arl2l1 (Arl2-like protein 1) and Arl13 form a subfamily
of the Arf family of small GTPases. Arl2l1 was
identified in human cells during a search for the
gene(s) responsible for Bardet-Biedl syndrome (BBS).
Like Arl6, the identified BBS gene, Arl2l1 is proposed
to have cilia-specific functions. Arl13 is found on the
X chromosome, but its expression has not been confirmed;
it may be a pseudogene.
Length = 167
Score = 28.9 bits (65), Expect = 1.2
Identities = 30/120 (25%), Positives = 54/120 (45%), Gaps = 6/120 (5%)
Query: 24 LLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQERY 83
LL +G + GKT+ L TVG T R DK ++ I+D G +
Sbjct: 2 LLTVGLDNAGKTT-LVSALQGEIPKKVAPTVGF---TPTKLRLDK-YEVCIFDLGGGANF 56
Query: 84 RTITTAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYSWDNAQVILV-GNKCDMEDER 142
R I YY A G + + D ++++ +++ + ++ + + + ILV NK D ++
Sbjct: 57 RGIWVNYYAEAHGLVFVVDSSDDDRVQEVKEILRELLQHPRVSGKPILVLANKQDKKNAL 116
>gnl|CDD|213672 TIGR01990, bPGM, beta-phosphoglucomutase. This model represents
the beta-phosphoglucomutase enzyme which catalyzes the
interconverison of beta-D-glucose-1-phosphate and
beta-D-glucose-6-phosphate. The 6-phosphate is capable
of non-enzymatic anomerization (alpha <-> beta) while
the 1-phosphate is not. A separate enzyme is responsible
for the isomerization of the alpha anomers.
Beta-D-glucose-1-phosphate results from the
phosphorylysis of maltose (2.4.1.8), trehalose
(2.4.1.64) or trehalose-6-phosphate (2.4.1.216).
Alternatively, these reactions can be run in the
synthetic direction to create the disaccharides. All
sequenced genomes which contain a member of this family
also appear to contain at least one putative maltose or
trehalose phosphorylase. Three species, Lactococcus,
Enterococcus and Neisseria appear to contain a pair of
paralogous beta-PGM's. Beta-phosphoglucomutase is a
member of the haloacid dehalogenase superfamily of
hydrolase enzymes. These enzymes are characterized by a
series of three catalytic motifs positioned within an
alpha-beta (Rossman) fold. beta-PGM contains an inserted
alpha helical domain in between the first and second
conserved motifs and thus is a member of subfamily IA of
the superfamily. The third catalytic motif comes in
three variants, the third of which, containing a
conserved DD or ED, is the only one found here as well
as in several other related enzymes (TIGR01509). The
enzyme from L. lactis has been extensively characterized
including a remarkable crystal structure which traps the
pentacoordinate transition state [Energy metabolism,
Biosynthesis and degradation of polysaccharides].
Length = 185
Score = 28.8 bits (65), Expect = 1.6
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 4/41 (9%)
Query: 146 FERGKHLAESLGVEFFETSAKDNVNVKGVF-ERLVDIICDK 185
+ KHLA+ LG+ F + N ++KGV E ++ I D
Sbjct: 18 YLAWKHLADELGIPF---DEEFNESLKGVSREESLERILDL 55
>gnl|CDD|224770 COG1857, COG1857, CRISPR system related protein [Defense
mechanisms].
Length = 334
Score = 29.4 bits (66), Expect = 1.7
Identities = 13/50 (26%), Positives = 19/50 (38%)
Query: 124 WDNAQVILVGNKCDMEDERVISFERGKHLAESLGVEFFETSAKDNVNVKG 173
+V+L K + + IS E KH + VE F+ VN
Sbjct: 29 HRRVRVVLKDRKLKVYEVPAISGESLKHWHQEYLVELFQKEGGLPVNELC 78
>gnl|CDD|204242 pfam09439, SRPRB, Signal recognition particle receptor beta
subunit. The beta subunit of the signal recognition
particle receptor (SRP) is a transmembrane GTPase which
anchors the alpha subunit to the endoplasmic reticulum
membrane.
Length = 181
Score = 28.5 bits (64), Expect = 1.7
Identities = 15/83 (18%), Positives = 23/83 (27%), Gaps = 6/83 (7%)
Query: 25 LIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFRHDKRVKLQIWDTAGQERYR 84
+I G GKTS + S + + K + D G + R
Sbjct: 7 IIAGLCDSGKTSLFTLLTTGTVKKTVTS---QEPSAAYKYMLHKGFSFTLIDFPGHVKLR 63
Query: 85 T---ITTAYYRGAMGFILMYDVT 104
T G + + D T
Sbjct: 64 QKLLETIKDSSSLRGIVFVVDST 86
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 29.3 bits (66), Expect = 1.8
Identities = 12/46 (26%), Positives = 21/46 (45%), Gaps = 1/46 (2%)
Query: 129 VILVGNKCDMEDERVISFERGKHLAESLGVEFFETSAKDNVNVKGV 174
+LV NK D+ + V + K+ + G++ SAK K +
Sbjct: 64 KLLVLNKADLAPKEVTK-KWKKYFKKEEGIKPIFVSAKSRQGGKKI 108
>gnl|CDD|222578 pfam14175, YaaC, YaaC-like Protein. The YaaC-like protein family
includes the B. subtilis YaaC protein, which is
functionally uncharacterized. This family of proteins is
found in bacteria. Proteins in this family are typically
between 320 and 333 amino acids in length.
Length = 326
Score = 28.9 bits (65), Expect = 2.1
Identities = 15/62 (24%), Positives = 25/62 (40%), Gaps = 3/62 (4%)
Query: 115 WITQIKTYSWDNAQVILVGNKCDMEDERVISFERGKHLAESL--GVEFFETSAKDNVNVK 172
W + S + AQ L + + ED SFE + L F+E + K + +K
Sbjct: 1 WKRLLTFSSAEYAQKYLK-KRYEKEDAEEKSFENCEGFIYYLEQAESFYEAAEKAPLEIK 59
Query: 173 GV 174
+
Sbjct: 60 PL 61
>gnl|CDD|233980 TIGR02712, urea_carbox, urea carboxylase. Members of this family
are ATP-dependent urea carboxylase, including
characterized members from Oleomonas sagaranensis (alpha
class Proteobacterium) and yeasts such as Saccharomyces
cerevisiae. The allophanate hydrolase domain of the
yeast enzyme is not included in this model and is
represented by an adjacent gene in Oleomonas
sagaranensis. The fusion of urea carboxylase and
allophanate hydrolase is designated urea amidolyase. The
enzyme from Oleomonas sagaranensis was shown to be
highly active on acetamide and formamide as well as urea
[Central intermediary metabolism, Nitrogen metabolism].
Length = 1201
Score = 29.2 bits (66), Expect = 2.2
Identities = 18/47 (38%), Positives = 21/47 (44%), Gaps = 13/47 (27%)
Query: 135 KCDMEDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVF-ERLVD 180
KCD E +FE K L ES FF + GVF ER V+
Sbjct: 168 KCDSAAELAEAFETVKRLGES----FFGDA--------GVFLERFVE 202
>gnl|CDD|206649 cd01850, CDC_Septin, CDC/Septin GTPase family. Septins are a
conserved family of GTP-binding proteins associated
with diverse processes in dividing and non-dividing
cells. They were first discovered in the budding yeast
S. cerevisiae as a set of genes (CDC3, CDC10, CDC11 and
CDC12) required for normal bud morphology. Septins are
also present in metazoan cells, where they are required
for cytokinesis in some systems, and implicated in a
variety of other processes involving organization of
the cell cortex and exocytosis. In humans, 12 septin
genes generate dozens of polypeptides, many of which
comprise heterooligomeric complexes. Since septin
mutants are commonly defective in cytokinesis and
formation of the neck formation of the neck
filaments/septin rings, septins have been considered to
be the primary constituents of the neck filaments.
Septins belong to the GTPase superfamily for their
conserved GTPase motifs and enzymatic activities.
Length = 275
Score = 28.7 bits (65), Expect = 2.3
Identities = 16/69 (23%), Positives = 29/69 (42%), Gaps = 13/69 (18%)
Query: 22 FKLLIIGNSSVGKTSF---LFRYADDSFTSAFVSTVGIDFKVKTVFRHDK--------RV 70
F ++++G S +GK++F LF + S + G + K ++
Sbjct: 5 FNIMVVGESGLGKSTFINTLF--GTKLYPSKYPPAPGEHITKTVEIKISKAELEENGVKL 62
Query: 71 KLQIWDTAG 79
KL + DT G
Sbjct: 63 KLTVIDTPG 71
>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 = 29.0 bits (65), Expect = 2.3
Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 13/64 (20%)
Query: 22 FKLLIIGNSSVGKTSFL--FRYADDSFTSAFVST----VGIDFKVKTVFRHDKRVKLQIW 75
FKL I+G+ +VGK+S L D + S T V DF++ + +++
Sbjct: 204 FKLAIVGSPNVGKSSLLNALLKQDRAIVSDIKGTTRDVVEGDFELNGIL-------IKLL 256
Query: 76 DTAG 79
DTAG
Sbjct: 257 DTAG 260
>gnl|CDD|178268 PLN02662, PLN02662, cinnamyl-alcohol dehydrogenase family protein.
Length = 322
Score = 28.5 bits (64), Expect = 2.7
Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 135 KCDMEDERVISFERGKHLAESLGVEF--FETSAKDNVN 170
KC + V +++ K A+SLG+EF E S KD V
Sbjct: 276 KCADDKPYVPTYQVSKEKAKSLGIEFIPLEVSLKDTVE 313
>gnl|CDD|227922 COG5635, COG5635, Predicted NTPase (NACHT family) [Signal
transduction mechanisms].
Length = 824
Score = 28.2 bits (63), Expect = 3.7
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 23 KLLIIGNSSVGKTSFLFRYA 42
KLLI+G GKT+FL R A
Sbjct: 224 KLLILGAPGSGKTTFLQRLA 243
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 28.0 bits (63), Expect = 4.0
Identities = 12/53 (22%), Positives = 24/53 (45%)
Query: 126 NAQVILVGNKCDMEDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERL 178
+ ++V NK D+ D+ + + E +G SAK+ ++ + E L
Sbjct: 110 GIEPVIVLNKIDLLDDEEAAVKELLREYEDIGYPVLFVSAKNGDGLEELAELL 162
>gnl|CDD|206726 cd04163, Era, E. coli Ras-like protein (Era) is a multifunctional
GTPase. Era (E. coli Ras-like protein) is a
multifunctional GTPase found in all bacteria except some
eubacteria. It binds to the 16S ribosomal RNA (rRNA) of
the 30S subunit and appears to play a role in the
assembly of the 30S subunit, possibly by chaperoning the
16S rRNA. It also contacts several assembly elements of
the 30S subunit. Era couples cell growth with
cytokinesis and plays a role in cell division and energy
metabolism. Homologs have also been found in eukaryotes.
Era contains two domains: the N-terminal GTPase domain
and a C-terminal domain KH domain that is critical for
RNA binding. Both domains are important for Era
function. Era is functionally able to compensate for
deletion of RbfA, a cold-shock adaptation protein that
is required for efficient processing of the 16S rRNA.
Length = 168
Score = 27.4 bits (62), Expect = 4.1
Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 5/59 (8%)
Query: 129 VILVGNKCDMEDERVISFERGKHLAESLG-VEFFETSAKDNVNVKGVFERLVDIICDKM 186
VILV NK D+ ++ + L E E F SA NV + L++ I + +
Sbjct: 114 VILVLNKIDLVKDKEDLLPLLEKLKELHPFAEIFPISALKGENV----DELLEYIVEYL 168
>gnl|CDD|206667 cd01879, FeoB, Ferrous iron transport protein B (FeoB) family.
Ferrous iron transport protein B (FeoB) subfamily. E.
coli has an iron(II) transport system, known as feo,
which may make an important contribution to the iron
supply of the cell under anaerobic conditions. FeoB has
been identified as part of this transport system. FeoB
is a large 700-800 amino acid integral membrane protein.
The N terminus contains a P-loop motif suggesting that
iron transport may be ATP dependent.
Length = 159
Score = 27.4 bits (62), Expect = 4.2
Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 126 NAQVILVGNKCDMEDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDI 181
V++ N D ++R I + K L+E LGV TSA+ + + + + +
Sbjct: 102 GLPVVVALNMIDEAEKRGIKIDLDK-LSELLGVPVVPTSARKGEGIDELLDAIAKL 156
>gnl|CDD|215653 pfam00009, GTP_EFTU, Elongation factor Tu GTP binding domain. This
domain contains a P-loop motif, also found in several
other families such as pfam00071, pfam00025 and
pfam00063. Elongation factor Tu consists of three
structural domains, this plus two C-terminal beta barrel
domains.
Length = 184
Score = 27.5 bits (62), Expect = 4.4
Identities = 13/62 (20%), Positives = 20/62 (32%), Gaps = 8/62 (12%)
Query: 129 VILVGNKCDMED----ERVISFERG----KHLAESLGVEFFETSAKDNVNVKGVFERLVD 180
+I+ NK D D E V+ K+ V SA + + E L
Sbjct: 121 IIVFINKIDRVDDAELEEVVEEISRELLEKYGFGGETVPVVPGSALTGEGIDELLEALDL 180
Query: 181 II 182
+
Sbjct: 181 YL 182
>gnl|CDD|181300 PRK08221, PRK08221, anaerobic sulfite reductase subunit B;
Provisional.
Length = 263
Score = 27.6 bits (62), Expect = 5.2
Identities = 19/75 (25%), Positives = 33/75 (44%), Gaps = 18/75 (24%)
Query: 91 YRGAMGFILMYDVTNEESFTS----IQDWITQIKTYSWDNAQVILVGN------------ 134
+R + IL D EE + + +I ++ DN QVI+VG
Sbjct: 154 WREKINLILTLD-EGEEGYRGNVGLVTKYIPELTLKDIDNMQVIVVGPPIMMKFTVLEFL 212
Query: 135 KCDMEDERV-ISFER 148
K +++E + +S+ER
Sbjct: 213 KRGIKEENIWVSYER 227
>gnl|CDD|216362 pfam01204, Trehalase, Trehalase. Trehalase (EC:3.2.1.28) is known
to recycle trehalose to glucose. Trehalose is a
physiological hallmark of heat-shock response in yeast
and protects of proteins and membranes against a variety
of stresses. This family is found in conjunction with
pfam07492 in fungi.
Length = 509
Score = 27.6 bits (62), Expect = 6.0
Identities = 18/90 (20%), Positives = 29/90 (32%), Gaps = 12/90 (13%)
Query: 73 QIWDTAGQERYRTITTAYYRGAMGFILMYDV-----TNEESFTSIQDWITQIKTYSWDNA 127
IW+ + R I + G YD+ N S ++ S D A
Sbjct: 332 AIWEERAEARRDAIDKYLWNEEDGIWYDYDLKKQKHRNYFSASNF--VPLWAGLASPDQA 389
Query: 128 Q-VILVGNKCDMEDERVISFERGKHLAESL 156
V V +E ++ + G + SL
Sbjct: 390 AKVAKVLPY--LERSGLLVYPGG--IPTSL 415
>gnl|CDD|178049 PLN02430, PLN02430, long-chain-fatty-acid-CoA ligase.
Length = 660
Score = 27.5 bits (61), Expect = 6.8
Identities = 23/72 (31%), Positives = 31/72 (43%), Gaps = 19/72 (26%)
Query: 56 IDFKVKTVFRHDKRVK-LQIWDTAGQERYRTITTAYYRGAMGFILMYDVTNEESFTSIQD 114
IDF VF DK++K L D +R + I + VT EES + Q
Sbjct: 149 IDF----VFVQDKKIKELLEPDCKSAKRLKAI-----------VSFTSVTEEESDKASQ- 192
Query: 115 WITQIKTYSWDN 126
+KTYSW +
Sbjct: 193 --IGVKTYSWID 202
>gnl|CDD|218528 pfam05272, VirE, Virulence-associated protein E. This family
contains several bacterial virulence-associated protein
E like proteins. These proteins contain a P-loop motif.
Length = 198
Score = 27.0 bits (60), Expect = 7.2
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 18 FDYMFKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVK 61
FD++ L G GK++FL + + FT + S G D K
Sbjct: 51 FDHVLIL--QGAQGSGKSTFLKKLGGEWFTDSIRSFEGKDAYEK 92
>gnl|CDD|235175 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 27.3 bits (61), Expect = 7.3
Identities = 43/210 (20%), Positives = 81/210 (38%), Gaps = 37/210 (17%)
Query: 25 LIIGNSSVGKTSFL------FRYADDSFTSA-----FVSTVGIDFKVKTVFRHDKRVKLQ 73
LIIG + GK+S L + S F G +++ F + R K +
Sbjct: 27 LIIGQNGSGKSSILEAILVGLYWGHGSKPKGLKKDDFTRIGGSGTEIELKFEKNGR-KYR 85
Query: 74 IWDTAGQERYRTIT--TAYYRGAMGFILMYDVTNEESFTSIQDWITQIKTYS-WDNAQVI 130
I R+ +Y + G EE +S+++W+ ++ Y + NA I
Sbjct: 86 I--------VRSFNRGESYLKYLDGS-----EVLEEGDSSVREWVERLIPYHVFLNAIYI 132
Query: 131 LVG--NKCDMEDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFERLVDIICDKMSE 188
G + DE R K + + LG++ +E + K+ V +R ++ + +
Sbjct: 133 RQGEIDAILESDES-----REKVVRQILGLDDYENAYKNLGEVIKEIKRRIERLEKFIKR 187
Query: 189 SLDSDPNLVAGPKGTRLTEQPQRNNPINPN 218
+ + + L+ K L E + N I+
Sbjct: 188 TENIE-ELI-KEKEKELEEVLREINEISSE 215
>gnl|CDD|70841 pfam07390, P30, Mycoplasma P30 protein. This family consists of
several P30 proteins which seem to be specific to
Mycoplasma agalactiae. P30 is a 30-kDa immunodominant
antigen and is known to be a transmembrane protein.
Length = 266
Score = 27.1 bits (59), Expect = 8.1
Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 6/58 (10%)
Query: 120 KTYSWDNAQVILVGNKCDMEDERVISFERGKHLAESLGVEFFETSAKDNVNVKGVFER 177
K +D ++V + +K D++DE +IS ++G H + F + KD V G E+
Sbjct: 133 KDIDFDISKVKITIDKKDLKDEDLISPKKGSH------KQLFFNTYKDKTKVSGKLEK 184
>gnl|CDD|227910 COG5623, CLP1, Predicted GTPase subunit of the pre-mRNA cleavage
complex [Translation, ribosomal structure and
biogenesis].
Length = 424
Score = 27.2 bits (60), Expect = 8.3
Identities = 9/23 (39%), Positives = 15/23 (65%)
Query: 17 NFDYMFKLLIIGNSSVGKTSFLF 39
N++ ++++G S GKTSF F
Sbjct: 95 NYEKGPTVMVVGGSQNGKTSFCF 117
>gnl|CDD|234274 TIGR03594, GTPase_EngA, ribosome-associated GTPase EngA. EngA
(YfgK, Der) is a ribosome-associated essential GTPase
with a duplication of its GTP-binding domain. It is
broadly to universally distributed among bacteria. It
appears to function in ribosome biogenesis or stability
[Protein synthesis, Other].
Length = 429
Score = 27.0 bits (61), Expect = 8.7
Identities = 20/74 (27%), Positives = 30/74 (40%), Gaps = 10/74 (13%)
Query: 129 VILVGNKCDMEDERVISFERGKHLAESLGV-EFFETSAKDNVNVKGVFERLVDIICDKMS 187
VILV NK D + E ++ E SLG E SA+ + L+D I + +
Sbjct: 110 VILVANKIDGKKEDAVAAE-----FYSLGFGEPIPISAEHGRGIGD----LLDAILELLP 160
Query: 188 ESLDSDPNLVAGPK 201
E + + K
Sbjct: 161 EEEEEEEEEDGPIK 174
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 26.8 bits (60), Expect = 9.4
Identities = 15/68 (22%), Positives = 28/68 (41%), Gaps = 6/68 (8%)
Query: 129 VILVGNKCDMEDERVISFERGKHLAESLGV-EFFETSAKDNVNVKGVFERLVDIICDKMS 187
VILV NK D E + SLG E SA+ + + + +++++
Sbjct: 115 VILVVNKIDNLKA-----EELAYEFYSLGFGEPVPISAEHGRGIGDLLDAVLELLPPDEE 169
Query: 188 ESLDSDPN 195
E + + +
Sbjct: 170 EEEEEETD 177
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 0.403
Gapped
Lambda K H
0.267 0.0534 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,933,851
Number of extensions: 990484
Number of successful extensions: 1364
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1199
Number of HSP's successfully gapped: 178
Length of query: 221
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 128
Effective length of database: 6,812,680
Effective search space: 872023040
Effective search space used: 872023040
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 (26.2 bits)