RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14768
(452 letters)
>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 = 202 bits (515), Expect = 6e-63
Identities = 75/171 (43%), Positives = 115/171 (67%), Gaps = 4/171 (2%)
Query: 241 YPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIA 300
+ +L+ GD VGKTS ++ +V F +YK T+GVDF+ K++ V+LQ+WDIA
Sbjct: 1 FKVLVIGDLGVGKTSIIKRYVHGVFSQHYKATIGVDFALKVIEWDP--NTVVRLQLWDIA 58
Query: 301 GQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLAS 360
GQ+R+ M+RVYY+ + G II+FD+T +FE+V++WK DLDSK L NG +P LLLA+
Sbjct: 59 GQERFGGMTRVYYKGAVGAIIVFDVTRPSTFEAVLKWKADLDSKVTLPNGEPIPALLLAN 118
Query: 361 KCDLPDRQVEIN--EIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRII 409
KCDL ++ + +++ C + F+ W E S+KE++ IE++M FLV I+
Sbjct: 119 KCDLKKERLAKDPEQMDQFCKENGFIGWFETSAKENINIEEAMRFLVKNIL 169
Score = 70.0 bits (172), Expect = 6e-14
Identities = 24/59 (40%), Positives = 37/59 (62%), Gaps = 2/59 (3%)
Query: 171 YLILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDI 229
+ +L+ GD VGKTS ++ +V F +YK T+GVDF+ K++ V+LQ+WDI
Sbjct: 1 FKVLVIGDLGVGKTSIIKRYVHGVFSQHYKATIGVDFALKVIEWDP--NTVVRLQLWDI 57
Score = 65.4 bits (160), Expect = 2e-12
Identities = 21/44 (47%), Positives = 30/44 (68%)
Query: 109 LKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSH 152
K+LVIGD VGKTS ++ +V F +YK T+GVDF+ K++
Sbjct: 1 FKVLVIGDLGVGKTSIIKRYVHGVFSQHYKATIGVDFALKVIEW 44
>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 = 174 bits (445), Expect = 4e-53
Identities = 62/165 (37%), Positives = 102/165 (61%), Gaps = 9/165 (5%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
I++ GDS VGKTS + FV NKF +NYK+T+GVDF +K + + G+ VKLQIWD AGQ
Sbjct: 3 IVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGVDFKSKTI---EVDGKKVKLQIWDTAGQ 59
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLASKC 362
+R+ ++ YY+ + G I+++D+TNR+SFE++ +W ++L + +P +L+ +K
Sbjct: 60 ERFRSITSSYYRGAHGAILVYDVTNRESFENLDKWLNELKEYAPPN----IPIILVGNKS 115
Query: 363 DLPD-RQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVD 406
DL D RQV E + + + + E S+K ++++ L
Sbjct: 116 DLEDERQVSTEEAQQFAKENG-LLFFETSAKTGENVDEAFESLAR 159
Score = 77.1 bits (191), Expect = 9e-17
Identities = 31/56 (55%), Positives = 41/56 (73%), Gaps = 3/56 (5%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
I++ GDS VGKTS + FV NKF +NYK+T+GVDF +K + + G+ VKLQIWD
Sbjct: 3 IVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGVDFKSKTI---EVDGKKVKLQIWD 55
Score = 65.6 bits (161), Expect = 9e-13
Identities = 25/40 (62%), Positives = 32/40 (80%)
Query: 109 LKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTK 148
KI++IGDS VGKTS + FV NKF +NYK+T+GVDF +K
Sbjct: 1 FKIVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGVDFKSK 40
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 168 bits (428), Expect = 1e-50
Identities = 60/168 (35%), Positives = 100/168 (59%), Gaps = 9/168 (5%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
I++ GDS VGK+S + F KF + YK+T+GVDF TK + G+ VKLQIWD AGQ
Sbjct: 3 IILIGDSGVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIE---VDGKRVKLQIWDTAGQ 59
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLASKC 362
+R+ ++ YY+ + G ++++D+TNR+SFE++ W +L + + +L+ +K
Sbjct: 60 ERFRSITSSYYRGAVGALLVYDITNRESFENLENWLKELREYASPN----VVIMLVGNKS 115
Query: 363 DLPD-RQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRII 409
DL + RQV E EA ++ + + E S+K + +E++ L I+
Sbjct: 116 DLEEQRQVSREEAEAFAEEHG-LPFFETSAKTNTNVEEAFEELAREIL 162
Score = 76.4 bits (189), Expect = 2e-16
Identities = 28/56 (50%), Positives = 37/56 (66%), Gaps = 3/56 (5%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
I++ GDS VGK+S + F KF + YK+T+GVDF TK + G+ VKLQIWD
Sbjct: 3 IILIGDSGVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIE---VDGKRVKLQIWD 55
Score = 65.2 bits (160), Expect = 1e-12
Identities = 22/43 (51%), Positives = 30/43 (69%)
Query: 109 LKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLS 151
KI++IGDS VGK+S + F KF + YK+T+GVDF TK +
Sbjct: 1 FKIILIGDSGVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIE 43
>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 = 138 bits (350), Expect = 4e-39
Identities = 60/168 (35%), Positives = 99/168 (58%), Gaps = 9/168 (5%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
+++ GD VGK+S + F QNKF + Y T+GVDF TK + G+ VKLQIWD AGQ
Sbjct: 2 LVLVGDGGVGKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIE---VDGKTVKLQIWDTAGQ 58
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLASKC 362
+R+ + +YY+ + G ++++D+T+R SFE+V +W ++ +P +L+ +KC
Sbjct: 59 ERFRALRPLYYRGAQGFLLVYDITSRDSFENVKKWLEEILRHA----DENVPIVLVGNKC 114
Query: 363 DLPD-RQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRII 409
DL D R V E EA+ + ++E S+K + +E++ L I+
Sbjct: 115 DLEDQRVVSTEEGEALAKELGLP-FMETSAKTNENVEEAFEELAREIL 161
Score = 67.1 bits (165), Expect = 3e-13
Identities = 29/57 (50%), Positives = 37/57 (64%), Gaps = 4/57 (7%)
Query: 172 LILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
L+L+ GD VGK+S + F QNKF + Y T+GVDF TK + G+ VKLQIWD
Sbjct: 2 LVLV-GDGGVGKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIE---VDGKTVKLQIWD 54
Score = 56.4 bits (137), Expect = 2e-09
Identities = 20/39 (51%), Positives = 28/39 (71%)
Query: 110 KILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTK 148
K++++GD VGK+S + F QNKF + Y T+GVDF TK
Sbjct: 1 KLVLVGDGGVGKSSLLIRFTQNKFPEEYIPTIGVDFYTK 39
>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 = 127 bits (320), Expect = 8e-35
Identities = 56/158 (35%), Positives = 91/158 (57%), Gaps = 4/158 (2%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
++I GDS VGKTS + +V KF + YK T+G DF TK ++ R V LQIWD AGQ
Sbjct: 3 VIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVT---VDDRLVTLQIWDTAGQ 59
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLASKC 362
+R+ + +Y+ +D C++++D+TN KSFES+ W+ + + + P ++L +K
Sbjct: 60 ERFQSLGVAFYRGADCCVLVYDVTNPKSFESLDSWRDEFLIQASPRDPENFPFVVLGNKI 119
Query: 363 DL-PDRQVEINEIEAVCHQYNFMSWIEVSSKEHLMIED 399
DL RQV + + C + + E S+KE + ++
Sbjct: 120 DLEEKRQVSTKKAQQWCKSKGNIPYFETSAKEAINVDQ 157
Score = 65.4 bits (160), Expect = 1e-12
Identities = 27/56 (48%), Positives = 35/56 (62%), Gaps = 3/56 (5%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
++I GDS VGKTS + +V KF + YK T+G DF TK ++ R V LQIWD
Sbjct: 3 VIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVT---VDDRLVTLQIWD 55
Score = 60.0 bits (146), Expect = 1e-10
Identities = 21/40 (52%), Positives = 29/40 (72%)
Query: 109 LKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTK 148
LK++++GDS VGKTS + +V KF + YK T+G DF TK
Sbjct: 1 LKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTK 40
>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 = 126 bits (317), Expect = 2e-34
Identities = 61/160 (38%), Positives = 96/160 (60%), Gaps = 8/160 (5%)
Query: 241 YPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIA 300
+ I++ GDS VGKT VQ F F + NT+GVDF+ K L + G+ VKLQIWD A
Sbjct: 4 FKIILIGDSNVGKTCVVQRFKSGTFSERQGNTIGVDFTMKTLEIQ---GKRVKLQIWDTA 60
Query: 301 GQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLAS 360
GQ+R+ +++ YY++++G II +D+T R SFESV W +++ + + LL+ +
Sbjct: 61 GQERFRTITQSYYRSANGAIIAYDITRRSSFESVPHWIEEVEKY----GASNVVLLLIGN 116
Query: 361 KCDLPD-RQVEINEIEAVCHQYNFMSWIEVSSKEHLMIED 399
KCDL + R+V E + Y ++ +E S+KE +E+
Sbjct: 117 KCDLEEQREVLFEEACTLAEHYGILAVLETSAKESSNVEE 156
Score = 60.1 bits (146), Expect = 9e-11
Identities = 30/57 (52%), Positives = 35/57 (61%), Gaps = 4/57 (7%)
Query: 172 LILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
+ILI GDS VGKT VQ F F + NT+GVDF+ K L G+ VKLQIWD
Sbjct: 6 IILI-GDSNVGKTCVVQRFKSGTFSERQGNTIGVDFTMKTLE---IQGKRVKLQIWD 58
Score = 52.4 bits (126), Expect = 4e-08
Identities = 22/41 (53%), Positives = 27/41 (65%)
Query: 110 KILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLL 150
KI++IGDS VGKT VQ F F + NT+GVDF+ K L
Sbjct: 5 KIILIGDSNVGKTCVVQRFKSGTFSERQGNTIGVDFTMKTL 45
>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 = 119 bits (301), Expect = 1e-31
Identities = 66/216 (30%), Positives = 108/216 (50%), Gaps = 28/216 (12%)
Query: 241 YPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIA 300
+ +++ GDSTVGK+S ++ F + +F + TVGVDF ++L+ + G +KLQ+WD A
Sbjct: 3 FRLIVIGDSTVGKSSLLKRFTEGRFAEVSDPTVGVDFFSRLIEIEP--GVRIKLQLWDTA 60
Query: 301 GQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQW-----KHDLDSKCILDNGAMLPC 355
GQ+R+ ++R YY+NS G +++FD+TNR+SFE V W H + +
Sbjct: 61 GQERFRSITRSYYRNSVGVLLVFDITNRESFEHVHDWLEEARSHIQPHRPVF-------- 112
Query: 356 LLLASKCDLPD-RQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRIICSKRM 414
+L+ KCDL RQV E E + + M +IE S++ +E++ L I +
Sbjct: 113 ILVGHKCDLESQRQVTREEAEKLA-KDLGMKYIETSARTGDNVEEAFELLTQEIYERIKR 171
Query: 415 EEEAVE-----------RKSSIRLSEETLRDDQPKK 439
E + L E + P+K
Sbjct: 172 GELCALDGWDGVKSGFPAGRAFSLEERSPTFASPEK 207
Score = 47.8 bits (114), Expect = 3e-06
Identities = 19/41 (46%), Positives = 31/41 (75%)
Query: 110 KILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLL 150
+++VIGDSTVGK+S ++ F + +F + TVGVDF ++L+
Sbjct: 4 RLIVIGDSTVGKSSLLKRFTEGRFAEVSDPTVGVDFFSRLI 44
>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 = 115 bits (291), Expect = 1e-30
Identities = 52/167 (31%), Positives = 98/167 (58%), Gaps = 9/167 (5%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
+L+ GDS VGK+ + F ++ F ++ +T+G+DF + + + G+ +KLQIWD AGQ
Sbjct: 6 LLLIGDSGVGKSCLLLRFSEDSFNPSFISTIGIDFKIRTI---ELDGKKIKLQIWDTAGQ 62
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLASKC 362
+R+ ++ YY+ + G I+++D+T+ KSFE++ W ++D +L+ +KC
Sbjct: 63 ERFRTITTSYYRGAMGIILVYDITDEKSFENIKNWMRNIDEHA--SEDVER--MLVGNKC 118
Query: 363 DLPD-RQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRI 408
D+ + R V E EA+ +Y ++E S+K ++ +E++ L I
Sbjct: 119 DMEEKRVVSKEEGEALAREYGI-KFLETSAKANINVEEAFLTLAKDI 164
Score = 56.9 bits (138), Expect = 9e-10
Identities = 20/56 (35%), Positives = 36/56 (64%), Gaps = 3/56 (5%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
+L+ GDS VGK+ + F ++ F ++ +T+G+DF + + + G+ +KLQIWD
Sbjct: 6 LLLIGDSGVGKSCLLLRFSEDSFNPSFISTIGIDFKIRTI---ELDGKKIKLQIWD 58
Score = 49.2 bits (118), Expect = 4e-07
Identities = 15/39 (38%), Positives = 27/39 (69%)
Query: 110 KILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTK 148
K+L+IGDS VGK+ + F ++ F ++ +T+G+DF +
Sbjct: 5 KLLLIGDSGVGKSCLLLRFSEDSFNPSFISTIGIDFKIR 43
>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 = 115 bits (290), Expect = 1e-30
Identities = 54/173 (31%), Positives = 102/173 (58%), Gaps = 17/173 (9%)
Query: 241 YPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIA 300
+ I++ GDS VGK++ + F +N+F + K+T+GV+F+T+ + + G+ +K QIWD A
Sbjct: 4 FKIVLIGDSGVGKSNLLSRFTRNEFNLDSKSTIGVEFATRTI---QIDGKTIKAQIWDTA 60
Query: 301 GQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDL----DSKCILDNGAMLPCL 356
GQ+RY ++ YY+ + G ++++D+T + +FE+V +W +L DS ++ +
Sbjct: 61 GQERYRAITSAYYRGAVGALLVYDITKKSTFENVERWLKELRDHADSNIVI--------M 112
Query: 357 LLASKCDLP-DRQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRI 408
L+ +K DL R V E +A + +S+IE S+ + +E++ L+ I
Sbjct: 113 LVGNKSDLRHLRAVPTEEAKAFAEKNG-LSFIETSALDGTNVEEAFKQLLTEI 164
Score = 62.6 bits (153), Expect = 1e-11
Identities = 24/60 (40%), Positives = 41/60 (68%), Gaps = 5/60 (8%)
Query: 171 YL--ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
YL I++ GDS VGK++ + F +N+F + K+T+GV+F+T+ + + G+ +K QIWD
Sbjct: 2 YLFKIVLIGDSGVGKSNLLSRFTRNEFNLDSKSTIGVEFATRTI---QIDGKTIKAQIWD 58
Score = 54.9 bits (133), Expect = 4e-09
Identities = 18/41 (43%), Positives = 32/41 (78%)
Query: 108 VLKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTK 148
+ KI++IGDS VGK++ + F +N+F + K+T+GV+F+T+
Sbjct: 3 LFKIVLIGDSGVGKSNLLSRFTRNEFNLDSKSTIGVEFATR 43
>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 = 115 bits (290), Expect = 2e-30
Identities = 55/170 (32%), Positives = 93/170 (54%), Gaps = 9/170 (5%)
Query: 241 YPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIA 300
+ +++ G+ VGKTS V +V+NKF + +++T F K ++ GG+ + L IWD A
Sbjct: 1 FKVVLLGEGRVGKTSLVLRYVENKFNEKHESTTQASFFQKTVNI---GGKRIDLAIWDTA 57
Query: 301 GQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLAS 360
GQ+RY + +YY+++DG I+++D+T+ SF+ V +W +L K + N L +++ +
Sbjct: 58 GQERYHALGPIYYRDADGAILVYDITDADSFQKVKKWIKEL--KQMRGNNISL--VIVGN 113
Query: 361 KCDLPD-RQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRII 409
K DL R V +E E E S+K IE+ L R+I
Sbjct: 114 KIDLERQRVVSKSEAEEYAKSVG-AKHFETSAKTGKGIEELFLSLAKRMI 162
Score = 50.3 bits (121), Expect = 2e-07
Identities = 24/71 (33%), Positives = 39/71 (54%), Gaps = 8/71 (11%)
Query: 171 YLILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD-- 228
+ +++ G+ VGKTS V +V+NKF + +++T F K ++ GG+ + L IWD
Sbjct: 1 FKVVLLGEGRVGKTSLVLRYVENKFNEKHESTTQASFFQKTVNI---GGKRIDLAIWDTA 57
Query: 229 ---IYCTLSPI 236
Y L PI
Sbjct: 58 GQERYHALGPI 68
Score = 37.6 bits (88), Expect = 0.004
Identities = 15/45 (33%), Positives = 28/45 (62%)
Query: 110 KILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKK 154
K++++G+ VGKTS V +V+NKF + +++T F K ++
Sbjct: 2 KVVLLGEGRVGKTSLVLRYVENKFNEKHESTTQASFFQKTVNIGG 46
>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 = 114 bits (287), Expect = 4e-30
Identities = 54/168 (32%), Positives = 98/168 (58%), Gaps = 7/168 (4%)
Query: 241 YPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIA 300
IL+ GDS VGK+S + F + F ++ +T+GVDF K + G+ VKL IWD A
Sbjct: 1 LKILLIGDSGVGKSSLLLRFTDDTFDEDLSSTIGVDFKVKTV---TVDGKKVKLAIWDTA 57
Query: 301 GQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLAS 360
GQ+R+ ++ YY+ + G I+++D+T R +F+++ W ++LD+ + +L+ +
Sbjct: 58 GQERFRTLTSSYYRGAQGVILVYDVTRRDTFDNLDTWLNELDTYSTNPDAVK---MLVGN 114
Query: 361 KCDLPDRQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRI 408
K D +R+V E + ++N M +IE S+K + ++ + LV++I
Sbjct: 115 KIDKENREVTREEGQKFARKHN-MLFIETSAKTRIGVQQAFEELVEKI 161
Score = 60.0 bits (146), Expect = 8e-11
Identities = 24/56 (42%), Positives = 34/56 (60%), Gaps = 3/56 (5%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
IL+ GDS VGK+S + F + F ++ +T+GVDF K + G+ VKL IWD
Sbjct: 3 ILLIGDSGVGKSSLLLRFTDDTFDEDLSSTIGVDFKVKTV---TVDGKKVKLAIWD 55
Score = 54.2 bits (131), Expect = 9e-09
Identities = 20/43 (46%), Positives = 30/43 (69%)
Query: 109 LKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLS 151
LKIL+IGDS VGK+S + F + F ++ +T+GVDF K ++
Sbjct: 1 LKILLIGDSGVGKSSLLLRFTDDTFDEDLSSTIGVDFKVKTVT 43
>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 = 111 bits (280), Expect = 3e-29
Identities = 51/153 (33%), Positives = 90/153 (58%), Gaps = 9/153 (5%)
Query: 241 YPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIA 300
+ ++ GD +VGKTS + F+ + F + Y+ T+G+DF +K + + V+LQ+WD A
Sbjct: 1 HKLVFLGDQSVGKTSIITRFMYDTFDNQYQATIGIDFLSKTMY---VDDKTVRLQLWDTA 57
Query: 301 GQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLAS 360
GQ+R+ + Y ++S ++++D+TNR+SF++ +W D+ + G + +L+ +
Sbjct: 58 GQERFRSLIPSYIRDSSVAVVVYDITNRQSFDNTDKWIDDV----RDERGNDVIIVLVGN 113
Query: 361 KCDLPD-RQVEINEIEAVCHQYNFMSWIEVSSK 392
K DL D RQV E E + N M +IE S+K
Sbjct: 114 KTDLSDKRQVSTEEGEKKAKENNAM-FIETSAK 145
Score = 62.3 bits (152), Expect = 2e-11
Identities = 20/53 (37%), Positives = 33/53 (62%), Gaps = 3/53 (5%)
Query: 177 GDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDI 229
GD +VGKTS + F+ + F + Y+ T+G+DF +K + + V+LQ+WD
Sbjct: 7 GDQSVGKTSIITRFMYDTFDNQYQATIGIDFLSKTMY---VDDKTVRLQLWDT 56
Score = 51.5 bits (124), Expect = 7e-08
Identities = 16/41 (39%), Positives = 29/41 (70%)
Query: 110 KILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLL 150
K++ +GD +VGKTS + F+ + F + Y+ T+G+DF +K +
Sbjct: 2 KLVFLGDQSVGKTSIITRFMYDTFDNQYQATIGIDFLSKTM 42
>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 = 111 bits (280), Expect = 5e-29
Identities = 56/180 (31%), Positives = 97/180 (53%), Gaps = 14/180 (7%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYG-------GRPVKLQ 295
+L GDS VGKT+++ + NKF + TVG+DF K + + G V LQ
Sbjct: 7 LLALGDSGVGKTTFLYRYTDNKFNPKFITTVGIDFREKRVVYNSQGPDGTSGKAFRVHLQ 66
Query: 296 IWDIAGQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPC 355
+WD AGQ+R+ ++ +++++ G ++MFDLT+ +SF +V W L + +N ++
Sbjct: 67 LWDTAGQERFRSLTTAFFRDAMGFLLMFDLTSEQSFLNVRNWMSQLQAHAYCENPDIVLI 126
Query: 356 LLLASKCDLPD-RQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRIICSKRM 414
+K DLPD R+V + + +Y + + E S+ +E ++ L+D I+ KRM
Sbjct: 127 ---GNKADLPDQREVSERQARELADKYG-IPYFETSAATGQNVEKAVETLLDLIM--KRM 180
Score = 51.3 bits (123), Expect = 1e-07
Identities = 26/67 (38%), Positives = 35/67 (52%), Gaps = 9/67 (13%)
Query: 171 YLI--LITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYG-------GRP 221
YLI L GDS VGKT+++ + NKF + TVG+DF K + + G
Sbjct: 3 YLIKLLALGDSGVGKTTFLYRYTDNKFNPKFITTVGIDFREKRVVYNSQGPDGTSGKAFR 62
Query: 222 VKLQIWD 228
V LQ+WD
Sbjct: 63 VHLQLWD 69
Score = 48.3 bits (115), Expect = 1e-06
Identities = 22/60 (36%), Positives = 34/60 (56%), Gaps = 2/60 (3%)
Query: 108 VLKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPYGTFSPIQ 167
++K+L +GDS VGKT+++ + NKF + TVG+DF K + + G P GT
Sbjct: 4 LIKLLALGDSGVGKTTFLYRYTDNKFNPKFITTVGIDFREKRVVYNSQG--PDGTSGKAF 61
>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 = 110 bits (277), Expect = 1e-28
Identities = 53/164 (32%), Positives = 98/164 (59%), Gaps = 15/164 (9%)
Query: 241 YPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIA 300
+ +L+ GDS VGK+ + F + + ++Y +T+GVDF + + + G+ VKLQIWD A
Sbjct: 3 FKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTI---ELDGKTVKLQIWDTA 59
Query: 301 GQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLD---SKCILDNGAMLPCLL 357
GQ+R+ ++ YY+ + G II++D+T+++SF +V QW ++D S+ + LL
Sbjct: 60 GQERFRTITSSYYRGAHGIIIVYDVTDQESFNNVKQWLQEIDRYASENVNK-------LL 112
Query: 358 LASKCDLPD-RQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDS 400
+ +KCDL D + V+ E + + + ++E S+K +E++
Sbjct: 113 VGNKCDLTDKKVVDYTEAKEFADELG-IPFLETSAKNATNVEEA 155
Score = 54.3 bits (131), Expect = 8e-09
Identities = 24/60 (40%), Positives = 38/60 (63%), Gaps = 5/60 (8%)
Query: 171 YL--ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
YL +L+ GDS VGK+ + F + + ++Y +T+GVDF + + + G+ VKLQIWD
Sbjct: 1 YLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTI---ELDGKTVKLQIWD 57
Score = 45.4 bits (108), Expect = 9e-06
Identities = 16/37 (43%), Positives = 26/37 (70%)
Query: 109 LKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDF 145
K+L+IGDS VGK+ + F + + ++Y +T+GVDF
Sbjct: 3 FKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDF 39
>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 = 110 bits (277), Expect = 3e-28
Identities = 60/199 (30%), Positives = 108/199 (54%), Gaps = 9/199 (4%)
Query: 241 YPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIA 300
+ +LI GDS VGK+S + F N F +Y T+GVDF + + G VKLQIWD A
Sbjct: 7 FKLLIIGDSGVGKSSLLLRFADNTFSGSYITTIGVDFKIRTVE---INGERVKLQIWDTA 63
Query: 301 GQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLAS 360
GQ+R+ ++ YY+ + G I+++D+TN +SF +V +W +++ C +L+ +
Sbjct: 64 GQERFRTITSTYYRGTHGVIVVYDVTNGESFVNVKRWLQEIEQNCDDVCK-----VLVGN 118
Query: 361 KCDLPDRQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRIICSKRMEEEAVE 420
K D P+R+V E +S E S+KE++ +E+ N + + ++ +K + A +
Sbjct: 119 KNDDPERKVVETEDAYKFAGQMGISLFETSAKENINVEEMFNCITELVLRAK-KDNLAKQ 177
Query: 421 RKSSIRLSEETLRDDQPKK 439
++ + ++ + KK
Sbjct: 178 QQQQQNDVVKLPKNSKRKK 196
Score = 52.9 bits (127), Expect = 4e-08
Identities = 26/56 (46%), Positives = 33/56 (58%), Gaps = 3/56 (5%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
+LI GDS VGK+S + F N F +Y T+GVDF + + G VKLQIWD
Sbjct: 9 LLIIGDSGVGKSSLLLRFADNTFSGSYITTIGVDFKIRTVE---INGERVKLQIWD 61
Score = 45.6 bits (108), Expect = 1e-05
Identities = 20/42 (47%), Positives = 28/42 (66%)
Query: 104 DAETVLKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDF 145
D + + K+L+IGDS VGK+S + F N F +Y T+GVDF
Sbjct: 2 DYDHLFKLLIIGDSGVGKSSLLLRFADNTFSGSYITTIGVDF 43
>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 = 108 bits (272), Expect = 5e-28
Identities = 62/174 (35%), Positives = 100/174 (57%), Gaps = 12/174 (6%)
Query: 241 YPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTK-LLSHKKYGGRPVKLQIWDI 299
+ +LI G+S+VGKTS++ + + F + +TVG+DF K + + K +KLQIWD
Sbjct: 2 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVYRNDKR----IKLQIWDT 57
Query: 300 AGQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLA 359
AGQ+RY ++ YY+ + G I+M+D+TN +SF +V W + + DN + +L+
Sbjct: 58 AGQERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYS-WDNAQV---ILVG 113
Query: 360 SKCDLPD-RQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRIICSK 412
+KCD+ D R V + Q F + E S+KE++ ++ LVD IIC K
Sbjct: 114 NKCDMEDERVVSAERGRQLADQLGF-EFFEASAKENINVKQVFERLVD-IICDK 165
Score = 48.8 bits (116), Expect = 7e-07
Identities = 23/57 (40%), Positives = 36/57 (63%), Gaps = 5/57 (8%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTK-LLSHKKYGGRPVKLQIWD 228
+LI G+S+VGKTS++ + + F + +TVG+DF K + + K +KLQIWD
Sbjct: 4 LLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVYRNDKR----IKLQIWD 56
Score = 43.0 bits (101), Expect = 7e-05
Identities = 17/41 (41%), Positives = 29/41 (70%)
Query: 108 VLKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTK 148
+ K+L+IG+S+VGKTS++ + + F + +TVG+DF K
Sbjct: 1 MFKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVK 41
>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 = 106 bits (267), Expect = 2e-27
Identities = 51/166 (30%), Positives = 96/166 (57%), Gaps = 8/166 (4%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
+++ G+ VGK+S +Q FV+ F +YK T+GVDF K + ++ V+L +WD AGQ
Sbjct: 3 VIVVGNGNVGKSSMIQRFVKGIFTKDYKKTIGVDFLEKQIFLRQ-SDEDVRLMLWDTAGQ 61
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLASKC 362
+ + +++ YY+ + CI++F T+R+SFE++ WK ++++C +P +L+ +K
Sbjct: 62 EEFDAITKAYYRGAQACILVFSTTDRESFEAIESWKEKVEAEC-----GDIPMVLVQTKI 116
Query: 363 DLPDRQVEIN-EIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDR 407
DL D+ V N E EA+ + + S K+ + + +L ++
Sbjct: 117 DLLDQAVITNEEAEALAKRLQ-LPLFRTSVKDDFNVTELFEYLAEK 161
Score = 52.4 bits (126), Expect = 4e-08
Identities = 19/40 (47%), Positives = 29/40 (72%)
Query: 109 LKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTK 148
+K++V+G+ VGK+S +Q FV+ F +YK T+GVDF K
Sbjct: 1 IKVIVVGNGNVGKSSMIQRFVKGIFTKDYKKTIGVDFLEK 40
Score = 51.7 bits (124), Expect = 6e-08
Identities = 21/56 (37%), Positives = 35/56 (62%), Gaps = 1/56 (1%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
+++ G+ VGK+S +Q FV+ F +YK T+GVDF K + ++ V+L +WD
Sbjct: 3 VIVVGNGNVGKSSMIQRFVKGIFTKDYKKTIGVDFLEKQIFLRQ-SDEDVRLMLWD 57
>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 = 106 bits (266), Expect = 4e-27
Identities = 52/153 (33%), Positives = 90/153 (58%), Gaps = 15/153 (9%)
Query: 244 LITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQD 303
LI G + GK+ + F++NKF + +T+GV+F ++++ GG+ VKLQIWD AGQ+
Sbjct: 4 LIIGSAGTGKSCLLHQFIENKFKQDSNHTIGVEFGSRVV---NVGGKSVKLQIWDTAGQE 60
Query: 304 RYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHD---LDSKCILDNGAMLPCLLLAS 360
R+ ++R YY+ + G ++++D+T+R+SF ++ W D L S I+ +L+ +
Sbjct: 61 RFRSVTRSYYRGAAGALLVYDITSRESFNALTNWLTDARTLASPDIV-------IILVGN 113
Query: 361 KCDL-PDRQVEINEIEAVCHQYNFMSWIEVSSK 392
K DL DR+V E Q N + ++E S+
Sbjct: 114 KKDLEDDREVTFLEASRFA-QENGLLFLETSAL 145
Score = 57.8 bits (140), Expect = 4e-10
Identities = 22/55 (40%), Positives = 36/55 (65%), Gaps = 3/55 (5%)
Query: 174 LITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
LI G + GK+ + F++NKF + +T+GV+F ++++ GG+ VKLQIWD
Sbjct: 4 LIIGSAGTGKSCLLHQFIENKFKQDSNHTIGVEFGSRVV---NVGGKSVKLQIWD 55
Score = 45.9 bits (109), Expect = 6e-06
Identities = 14/43 (32%), Positives = 29/43 (67%)
Query: 109 LKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLS 151
K L+IG + GK+ + F++NKF + +T+GV+F +++++
Sbjct: 1 FKFLIIGSAGTGKSCLLHQFIENKFKQDSNHTIGVEFGSRVVN 43
>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 = 104 bits (262), Expect = 1e-26
Identities = 52/166 (31%), Positives = 89/166 (53%), Gaps = 3/166 (1%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
+++ GD VGK+S + +V NKF +T+GV+F K L + G V LQIWD AGQ
Sbjct: 8 VILLGDGGVGKSSLMNRYVTNKFDTQLFHTIGVEFLNKDL---EVDGHFVTLQIWDTAGQ 64
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLASKC 362
+R+ + +Y+ SD C++ F + + +SF+++ WK + + P ++L +K
Sbjct: 65 ERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVILGNKI 124
Query: 363 DLPDRQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRI 408
D+P+RQV E +A C + E S+K+ + + V R+
Sbjct: 125 DIPERQVSTEEAQAWCRDNGDYPYFETSAKDATNVAAAFEEAVRRV 170
Score = 46.0 bits (109), Expect = 6e-06
Identities = 23/56 (41%), Positives = 33/56 (58%), Gaps = 3/56 (5%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
+++ GD VGK+S + +V NKF +T+GV+F K L + G V LQIWD
Sbjct: 8 VILLGDGGVGKSSLMNRYVTNKFDTQLFHTIGVEFLNKDL---EVDGHFVTLQIWD 60
Score = 40.6 bits (95), Expect = 4e-04
Identities = 17/41 (41%), Positives = 28/41 (68%)
Query: 108 VLKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTK 148
+LK++++GD VGK+S + +V NKF +T+GV+F K
Sbjct: 5 LLKVILLGDGGVGKSSLMNRYVTNKFDTQLFHTIGVEFLNK 45
>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 = 103 bits (259), Expect = 4e-26
Identities = 49/158 (31%), Positives = 85/158 (53%), Gaps = 17/158 (10%)
Query: 240 TYPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDI 299
+ +++ GDS+VGK+S V FV+N+F +N ++T+G F T+ + VK +IWD
Sbjct: 1 QFKLVLLGDSSVGKSSIVLRFVKNEFSENQESTIGAAFLTQTV---NLDDTTVKFEIWDT 57
Query: 300 AGQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDL----DSKCILDNGAMLPC 355
AGQ+RY ++ +YY+ + I+++D+T+ +SFE W +L ++
Sbjct: 58 AGQERYRSLAPMYYRGAAAAIVVYDITSEESFEKAKSWVKELQEHGPPNIVI-------- 109
Query: 356 LLLASKCDLPD-RQVEINEIEAVCHQYNFMSWIEVSSK 392
L +K DL RQV E + N + ++E S+K
Sbjct: 110 ALAGNKADLESKRQVSTEEAQEYA-DENGLLFMETSAK 146
Score = 55.6 bits (135), Expect = 3e-09
Identities = 25/72 (34%), Positives = 43/72 (59%), Gaps = 8/72 (11%)
Query: 170 SYLILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDI 229
+ +++ GDS+VGK+S V FV+N+F +N ++T+G F T+ + VK +IWD
Sbjct: 1 QFKLVLLGDSSVGKSSIVLRFVKNEFSENQESTIGAAFLTQTV---NLDDTTVKFEIWDT 57
Query: 230 -----YCTLSPI 236
Y +L+P+
Sbjct: 58 AGQERYRSLAPM 69
Score = 46.8 bits (112), Expect = 3e-06
Identities = 18/39 (46%), Positives = 31/39 (79%)
Query: 110 KILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTK 148
K++++GDS+VGK+S V FV+N+F +N ++T+G F T+
Sbjct: 3 KLVLLGDSSVGKSSIVLRFVKNEFSENQESTIGAAFLTQ 41
>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 = 101 bits (253), Expect = 2e-25
Identities = 50/167 (29%), Positives = 89/167 (53%), Gaps = 9/167 (5%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
+++ G VGK++ FV +F++ Y T+ D K + G L I D AGQ
Sbjct: 2 LVVLGAGGVGKSALTIRFVSGEFVEEYDPTIE-DSYRKQIVV---DGETYTLDILDTAGQ 57
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLASKC 362
+ + M Y +N DG I+++ +T+R+SFE + K+ + + + +P +L+ +KC
Sbjct: 58 EEFSAMRDQYIRNGDGFILVYSITSRESFEEI---KNIREQILRVKDKEDVPIVLVGNKC 114
Query: 363 DLPD-RQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRI 408
DL + RQV E EA+ ++ ++E S+K ++ I++ N LV I
Sbjct: 115 DLENERQVSTEEGEALAEEWG-CPFLETSAKTNINIDELFNTLVREI 160
Score = 36.3 bits (85), Expect = 0.009
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 4/56 (7%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
+++ G VGK++ FV +F++ Y T+ D K + G L I D
Sbjct: 2 LVVLGAGGVGKSALTIRFVSGEFVEEYDPTIE-DSYRKQIVV---DGETYTLDILD 53
Score = 36.3 bits (85), Expect = 0.010
Identities = 11/32 (34%), Positives = 20/32 (62%)
Query: 110 KILVIGDSTVGKTSYVQGFVQNKFLDNYKNTV 141
K++V+G VGK++ FV +F++ Y T+
Sbjct: 1 KLVVLGAGGVGKSALTIRFVSGEFVEEYDPTI 32
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 101 bits (253), Expect = 8e-25
Identities = 44/133 (33%), Positives = 71/133 (53%), Gaps = 8/133 (6%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
I++ GD VGKT+ + V ++F + Y T+G K + R +KLQ+WD AGQ
Sbjct: 8 IVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKT---IEPYRRNIKLQLWDTAGQ 64
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQ-WKHDLDSKCILDNGAMLPCLLLASK 361
+ Y + YY+ ++G +I++D T R+S + + + W +L D +P LL+ +K
Sbjct: 65 EEYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDD----VPILLVGNK 120
Query: 362 CDLPDRQVEINEI 374
DL D Q EI
Sbjct: 121 IDLFDEQSSSEEI 133
Score = 52.3 bits (125), Expect = 8e-08
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 3/57 (5%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDI 229
I++ GD VGKT+ + V ++F + Y T+G K + R +KLQ+WD
Sbjct: 8 IVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKT---IEPYRRNIKLQLWDT 61
Score = 47.6 bits (113), Expect = 3e-06
Identities = 15/44 (34%), Positives = 23/44 (52%)
Query: 105 AETVLKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTK 148
KI+V+GD VGKT+ + V ++F + Y T+G K
Sbjct: 2 FMKEFKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAK 45
>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 = 98.3 bits (245), Expect = 4e-24
Identities = 46/158 (29%), Positives = 90/158 (56%), Gaps = 9/158 (5%)
Query: 244 LITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQD 303
+I GD+ VGK+ + F +F + T+GV+F ++++ G+ +KLQIWD AGQ+
Sbjct: 8 IIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMIT---IDGKQIKLQIWDTAGQE 64
Query: 304 RYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLASKCD 363
+ ++R YY+ + G ++++D+T R++F + W D + + + +L+ +KCD
Sbjct: 65 SFRSITRSYYRGAAGALLVYDITRRETFNHLTSWLED----ARQHSNSNMTIMLIGNKCD 120
Query: 364 LP-DRQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDS 400
L R+V E EA ++ + ++E S+K +E++
Sbjct: 121 LESRREVSYEEGEAFAREHGLI-FMETSAKTASNVEEA 157
Score = 45.9 bits (109), Expect = 7e-06
Identities = 21/61 (34%), Positives = 36/61 (59%), Gaps = 5/61 (8%)
Query: 170 SYLI--LITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIW 227
+YL +I GD+ VGK+ + F +F + T+GV+F ++++ G+ +KLQIW
Sbjct: 2 AYLFKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMIT---IDGKQIKLQIW 58
Query: 228 D 228
D
Sbjct: 59 D 59
Score = 33.6 bits (77), Expect = 0.089
Identities = 13/43 (30%), Positives = 26/43 (60%)
Query: 108 VLKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLL 150
+ K ++IGD+ VGK+ + F +F + T+GV+F +++
Sbjct: 4 LFKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMI 46
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 96.9 bits (241), Expect = 3e-23
Identities = 56/180 (31%), Positives = 105/180 (58%), Gaps = 19/180 (10%)
Query: 241 YPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIA 300
+ I++ GDS VGK++ + F +N+F K+T+GV+F+T+ L + G+ VK QIWD A
Sbjct: 13 FKIVLIGDSGVGKSNILSRFTRNEFCLESKSTIGVEFATRTL---QVEGKTVKAQIWDTA 69
Query: 301 GQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDL----DSKCILDNGAMLPCL 356
GQ+RY ++ YY+ + G ++++D+T R++F++V +W +L DS ++ +
Sbjct: 70 GQERYRAITSAYYRGAVGALLVYDITKRQTFDNVQRWLRELRDHADSNIVI--------M 121
Query: 357 LLASKCDLPD-RQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRI--ICSKR 413
+ +K DL R V + +A+ + +S++E S+ E +E + ++ I I SK+
Sbjct: 122 MAGNKSDLNHLRSVAEEDGQALAEKEG-LSFLETSALEATNVEKAFQTILLEIYHIISKK 180
Score = 51.9 bits (124), Expect = 1e-07
Identities = 24/56 (42%), Positives = 38/56 (67%), Gaps = 3/56 (5%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
I++ GDS VGK++ + F +N+F K+T+GV+F+T+ L + G+ VK QIWD
Sbjct: 15 IVLIGDSGVGKSNILSRFTRNEFCLESKSTIGVEFATRTL---QVEGKTVKAQIWD 67
Score = 45.7 bits (108), Expect = 1e-05
Identities = 19/43 (44%), Positives = 32/43 (74%)
Query: 108 VLKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLL 150
+ KI++IGDS VGK++ + F +N+F K+T+GV+F+T+ L
Sbjct: 12 LFKIVLIGDSGVGKSNILSRFTRNEFCLESKSTIGVEFATRTL 54
>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 = 96.0 bits (239), Expect = 6e-23
Identities = 60/204 (29%), Positives = 95/204 (46%), Gaps = 20/204 (9%)
Query: 241 YPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIA 300
I++ GD GKTS ++ F Q F +YK T+G+DF ++ ++ G V LQ+WDI
Sbjct: 1 IKIVVLGDGASGKTSLIRRFAQEGFGKSYKQTIGLDFFSRRITLP--GSLNVTLQVWDIG 58
Query: 301 GQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLL-A 359
GQ M Y + +++D+TN +SFE++ W + + + P ++L
Sbjct: 59 GQQIGGKMLDKYIYGAQAVCLVYDITNSQSFENLEDWLSVVKK--VNEESETKPKMVLVG 116
Query: 360 SKCDLPD-RQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRIICS------K 412
+K DL RQV + + + S I VS+K D + RI
Sbjct: 117 NKTDLEHNRQVTAEKHARFAQENDMES-IFVSAKTG----DRVFLCFQRIAAELLGVKLS 171
Query: 413 RMEEEAVER--KSSI-RLSEETLR 433
+ E E +R K+ + R SE TLR
Sbjct: 172 QAELEQSQRVVKADVSRYSERTLR 195
Score = 50.2 bits (120), Expect = 4e-07
Identities = 18/40 (45%), Positives = 28/40 (70%)
Query: 109 LKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTK 148
+KI+V+GD GKTS ++ F Q F +YK T+G+DF ++
Sbjct: 1 IKIVVLGDGASGKTSLIRRFAQEGFGKSYKQTIGLDFFSR 40
>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 = 94.7 bits (236), Expect = 6e-23
Identities = 46/152 (30%), Positives = 83/152 (54%), Gaps = 10/152 (6%)
Query: 241 YPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIA 300
+ +++ GD GKT++V+ + +F Y T+GV+ L H G ++ +WD A
Sbjct: 1 FKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVH-PLDFHTNRG--KIRFNVWDTA 57
Query: 301 GQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLAS 360
GQ+++ + YY IIMFD+T+R ++++V W DL C +N +P +L +
Sbjct: 58 GQEKFGGLRDGYYIQGQCAIIMFDVTSRVTYKNVPNWHRDLVRVC--EN---IPIVLCGN 112
Query: 361 KCDLPDRQVEINEIEAVCHQYNFMSWIEVSSK 392
K D+ DR+V+ +I H+ + + E+S+K
Sbjct: 113 KVDIKDRKVKPKQITF--HRKKNLQYYEISAK 142
Score = 39.6 bits (93), Expect = 0.001
Identities = 18/57 (31%), Positives = 30/57 (52%), Gaps = 4/57 (7%)
Query: 172 LILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
L+L+ GD GKT++V+ + +F Y T+GV+ L H G ++ +WD
Sbjct: 3 LVLV-GDGGTGKTTFVKRHLTGEFEKKYVATLGVEVH-PLDFHTNRG--KIRFNVWD 55
Score = 36.9 bits (86), Expect = 0.008
Identities = 12/35 (34%), Positives = 23/35 (65%)
Query: 110 KILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVD 144
K++++GD GKT++V+ + +F Y T+GV+
Sbjct: 2 KLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVE 36
>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 = 93.4 bits (233), Expect = 1e-22
Identities = 47/175 (26%), Positives = 87/175 (49%), Gaps = 21/175 (12%)
Query: 241 YPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIA 300
Y +++ G VGK++ F+Q F+D+Y T+ D K + G L I D A
Sbjct: 1 YKLVVLGSGGVGKSALTIQFIQGHFVDDYDPTIE-DSYRKQIE---IDGEVCLLDILDTA 56
Query: 301 GQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKH------DLDSKCILDNGAMLP 354
GQ+ + M Y + +G ++++ +T+R+SFE + +++ D D +P
Sbjct: 57 GQEEFSAMRDQYMRTGEGFLLVYSITDRQSFEEIKKFREQILRVKDRDD---------VP 107
Query: 355 CLLLASKCDLPD-RQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRI 408
+L+ +KCDL R V E + + Q+ ++E S+KE + ++++ LV I
Sbjct: 108 IVLVGNKCDLESERVVSTEEGKELARQWG-CPFLETSAKERVNVDEAFYDLVREI 161
Score = 38.3 bits (90), Expect = 0.002
Identities = 12/32 (37%), Positives = 21/32 (65%)
Query: 110 KILVIGDSTVGKTSYVQGFVQNKFLDNYKNTV 141
K++V+G VGK++ F+Q F+D+Y T+
Sbjct: 2 KLVVLGSGGVGKSALTIQFIQGHFVDDYDPTI 33
Score = 37.9 bits (89), Expect = 0.003
Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 4/58 (6%)
Query: 171 YLILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
Y +++ G VGK++ F+Q F+D+Y T+ D K + G L I D
Sbjct: 1 YKLVVLGSGGVGKSALTIQFIQGHFVDDYDPTIE-DSYRKQIE---IDGEVCLLDILD 54
>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 = 93.4 bits (233), Expect = 1e-22
Identities = 48/177 (27%), Positives = 87/177 (49%), Gaps = 21/177 (11%)
Query: 239 PTYPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 298
Y +++ G VGK++ FVQ F+D Y T+ D K + G L I D
Sbjct: 1 REYKLVVLGGGGVGKSALTIQFVQGHFVDEYDPTIE-DSYRKQIE---IDGEVCLLDILD 56
Query: 299 IAGQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKH------DLDSKCILDNGAM 352
AGQ+ + M Y + +G ++++ +T+R+SFE + +++ D D
Sbjct: 57 TAGQEEFSAMRDQYMRTGEGFLLVYSITDRQSFEEIAKFREQILRVKDRDD--------- 107
Query: 353 LPCLLLASKCDLPD-RQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRI 408
+P +L+ +KCDL + R V E + + Q+ ++E S+KE + ++++ LV I
Sbjct: 108 VPIVLVGNKCDLENERVVSTEEGKELARQWG-CPFLETSAKERINVDEAFYDLVREI 163
Score = 37.9 bits (89), Expect = 0.003
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 110 KILVIGDSTVGKTSYVQGFVQNKFLDNYKNTV 141
K++V+G VGK++ FVQ F+D Y T+
Sbjct: 4 KLVVLGGGGVGKSALTIQFVQGHFVDEYDPTI 35
Score = 37.5 bits (88), Expect = 0.005
Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 4/60 (6%)
Query: 169 PSYLILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
Y +++ G VGK++ FVQ F+D Y T+ D K + G L I D
Sbjct: 1 REYKLVVLGGGGVGKSALTIQFVQGHFVDEYDPTIE-DSYRKQIE---IDGEVCLLDILD 56
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 94.4 bits (235), Expect = 2e-22
Identities = 47/156 (30%), Positives = 88/156 (56%), Gaps = 10/156 (6%)
Query: 237 QIPTYPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQI 296
++P + +++ GD VGKT++V+ + +F Y T+GV+ L + G P+ +
Sbjct: 6 EVPEFKLILVGDGGVGKTTFVKRHLTGEFEKKYIPTLGVEVH-PLKFYTNCG--PICFNV 62
Query: 297 WDIAGQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCL 356
WD AGQ+++ + YY IIMFD+T+R ++++V W D+ C +N +P +
Sbjct: 63 WDTAGQEKFGGLRDGYYIKGQCAIIMFDVTSRITYKNVPNWHRDIVRVC--EN---IPIV 117
Query: 357 LLASKCDLPDRQVEINEIEAVCHQYNFMSWIEVSSK 392
L+ +K D+ DRQV+ +I H+ + + ++S+K
Sbjct: 118 LVGNKVDVKDRQVKARQI--TFHRKKNLQYYDISAK 151
Score = 37.4 bits (87), Expect = 0.007
Identities = 18/62 (29%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 167 QTPSYLILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQI 226
+ P + +++ GD VGKT++V+ + +F Y T+GV+ L + G P+ +
Sbjct: 6 EVPEFKLILVGDGGVGKTTFVKRHLTGEFEKKYIPTLGVEVH-PLKFYTNCG--PICFNV 62
Query: 227 WD 228
WD
Sbjct: 63 WD 64
Score = 33.5 bits (77), Expect = 0.15
Identities = 13/35 (37%), Positives = 24/35 (68%)
Query: 110 KILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVD 144
K++++GD VGKT++V+ + +F Y T+GV+
Sbjct: 11 KLILVGDGGVGKTTFVKRHLTGEFEKKYIPTLGVE 45
>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 = 92.0 bits (228), Expect = 5e-22
Identities = 49/162 (30%), Positives = 91/162 (56%), Gaps = 9/162 (5%)
Query: 241 YPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIA 300
+ +L+ GDS VGKT + F N+F ++ +T+GVDF K + + G V++QIWD A
Sbjct: 1 FRLLLIGDSGVGKTCLLCRFTDNEFHSSHISTIGVDFKMKTI---EVDGIKVRIQIWDTA 57
Query: 301 GQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLAS 360
GQ+RY +++ YY+ + G +++D+++ +S++ +++W D+D G L+ +
Sbjct: 58 GQERYQTITKQYYRRAQGIFLVYDISSERSYQHIMKWVSDVDE--YAPEGVQKI--LIGN 113
Query: 361 KCDLPD-RQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSM 401
K D RQV + + +Y M + E S+ + I++S
Sbjct: 114 KADEEQKRQVGDEQGNKLAKEYG-MDFFETSACTNKNIKESF 154
Score = 47.3 bits (112), Expect = 2e-06
Identities = 23/58 (39%), Positives = 36/58 (62%), Gaps = 3/58 (5%)
Query: 171 YLILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
+ +L+ GDS VGKT + F N+F ++ +T+GVDF K + + G V++QIWD
Sbjct: 1 FRLLLIGDSGVGKTCLLCRFTDNEFHSSHISTIGVDFKMKTI---EVDGIKVRIQIWD 55
Score = 41.1 bits (96), Expect = 3e-04
Identities = 18/42 (42%), Positives = 28/42 (66%)
Query: 109 LKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLL 150
++L+IGDS VGKT + F N+F ++ +T+GVDF K +
Sbjct: 1 FRLLLIGDSGVGKTCLLCRFTDNEFHSSHISTIGVDFKMKTI 42
>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 = 91.4 bits (227), Expect = 9e-22
Identities = 48/158 (30%), Positives = 89/158 (56%), Gaps = 9/158 (5%)
Query: 244 LITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQD 303
+I GD VGK+ + F + KF+ + +T+GV+F T+++ + G+ +KLQIWD AGQ+
Sbjct: 6 IIIGDMGVGKSCLLHQFTEKKFMADCPHTIGVEFGTRII---EVNGQKIKLQIWDTAGQE 62
Query: 304 RYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLASKCD 363
R+ ++R YY+ + G ++++D+T R ++ + W D + L N + L+ +K D
Sbjct: 63 RFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDARN---LTNPNTV-IFLIGNKAD 118
Query: 364 LPD-RQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDS 400
L R V E + + + ++E S+K +ED+
Sbjct: 119 LEAQRDVTYEEAKQFADENGLL-FLECSAKTGENVEDA 155
Score = 51.8 bits (124), Expect = 6e-08
Identities = 21/55 (38%), Positives = 36/55 (65%), Gaps = 3/55 (5%)
Query: 174 LITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
+I GD VGK+ + F + KF+ + +T+GV+F T+++ + G+ +KLQIWD
Sbjct: 6 IIIGDMGVGKSCLLHQFTEKKFMADCPHTIGVEFGTRII---EVNGQKIKLQIWD 57
Score = 42.9 bits (101), Expect = 7e-05
Identities = 15/43 (34%), Positives = 29/43 (67%)
Query: 108 VLKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLL 150
+ K ++IGD VGK+ + F + KF+ + +T+GV+F T+++
Sbjct: 2 IFKYIIIGDMGVGKSCLLHQFTEKKFMADCPHTIGVEFGTRII 44
>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 = 91.3 bits (227), Expect = 1e-21
Identities = 49/160 (30%), Positives = 82/160 (51%), Gaps = 19/160 (11%)
Query: 240 TYPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDI 299
+ I++ GDS VGKT F +F + + T+GVDF + + + G +K+Q+WD
Sbjct: 2 IFKIIVIGDSNVGKTCLTYRFCAGRFPERTEATIGVDFRERTV---EIDGERIKVQLWDT 58
Query: 300 AGQDRY-ICMSRVYYQNSDGCIIMFDLTNRKSFESVVQW-----KHDLDSKCILDNGAML 353
AGQ+R+ M + YY+N + ++D+TN SF S+ W +H L +
Sbjct: 59 AGQERFRKSMVQHYYRNVHAVVFVYDVTNMASFHSLPSWIEECEQHSL--------PNEV 110
Query: 354 PCLLLASKCDLPD-RQVEINEIEAVCHQYNFMSWIEVSSK 392
P +L+ +KCDL + QV + + ++ M E S+K
Sbjct: 111 PRILVGNKCDLREQIQVPTDLAQRFADAHS-MPLFETSAK 149
Score = 47.4 bits (113), Expect = 2e-06
Identities = 18/43 (41%), Positives = 26/43 (60%)
Query: 108 VLKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLL 150
+ KI+VIGDS VGKT F +F + + T+GVDF + +
Sbjct: 2 IFKIIVIGDSNVGKTCLTYRFCAGRFPERTEATIGVDFRERTV 44
>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 = 90.3 bits (224), Expect = 2e-21
Identities = 49/141 (34%), Positives = 75/141 (53%), Gaps = 17/141 (12%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
+++ GD +VGKT + F ++ F NYK T+GVDF + + G P LQ+WD AGQ
Sbjct: 3 VIVVGDLSVGKTCLINRFCKDVFDKNYKATIGVDFE---MERFEVLGVPFSLQLWDTAGQ 59
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQW-----KHDLDSKCILDNGAMLPCLL 357
+R+ C++ YY+ + II+FDLT+ S E QW K + S +L L
Sbjct: 60 ERFKCIASTYYRGAQAIIIVFDLTDVASLEHTRQWLEDALKENDPSSVLL--------FL 111
Query: 358 LASKCDL-PDRQVEINEIEAV 377
+ +K DL Q + E +A+
Sbjct: 112 VGTKKDLSSPAQYALMEQDAI 132
Score = 49.1 bits (117), Expect = 6e-07
Identities = 22/56 (39%), Positives = 33/56 (58%), Gaps = 3/56 (5%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
+++ GD +VGKT + F ++ F NYK T+GVDF + + G P LQ+WD
Sbjct: 3 VIVVGDLSVGKTCLINRFCKDVFDKNYKATIGVDFE---MERFEVLGVPFSLQLWD 55
Score = 45.3 bits (107), Expect = 1e-05
Identities = 18/36 (50%), Positives = 26/36 (72%)
Query: 110 KILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDF 145
K++V+GD +VGKT + F ++ F NYK T+GVDF
Sbjct: 2 KVIVVGDLSVGKTCLINRFCKDVFDKNYKATIGVDF 37
>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 = 90.3 bits (224), Expect = 4e-21
Identities = 41/102 (40%), Positives = 61/102 (59%), Gaps = 4/102 (3%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDN-YKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAG 301
+++ G +VGKTS V+ +V ++FL Y+NT+G F K + G R V L IWD AG
Sbjct: 3 VVMLGKESVGKTSLVERYVHHRFLVGPYQNTIGAAFVAKRMV---VGERVVTLGIWDTAG 59
Query: 302 QDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDS 343
+RY MSR+YY+ + I+ +DLT+ SFE W +L +
Sbjct: 60 SERYEAMSRIYYRGAKAAIVCYDLTDSSSFERAKFWVKELQN 101
Score = 46.4 bits (110), Expect = 6e-06
Identities = 23/57 (40%), Positives = 34/57 (59%), Gaps = 4/57 (7%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDN-YKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
+++ G +VGKTS V+ +V ++FL Y+NT+G F K + G R V L IWD
Sbjct: 3 VVMLGKESVGKTSLVERYVHHRFLVGPYQNTIGAAFVAKRMV---VGERVVTLGIWD 56
Score = 41.4 bits (97), Expect = 3e-04
Identities = 17/44 (38%), Positives = 30/44 (68%), Gaps = 1/44 (2%)
Query: 109 LKILVIGDSTVGKTSYVQGFVQNKFLDN-YKNTVGVDFSTKLLS 151
+K++++G +VGKTS V+ +V ++FL Y+NT+G F K +
Sbjct: 1 VKVVMLGKESVGKTSLVERYVHHRFLVGPYQNTIGAAFVAKRMV 44
>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 = 90.1 bits (223), Expect = 6e-21
Identities = 58/184 (31%), Positives = 104/184 (56%), Gaps = 8/184 (4%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
++I G VGKTS ++ F + F + K+TVGVDF K + + G+ ++LQIWD AGQ
Sbjct: 3 VIIIGSRGVGKTSLMERFTDDTFCEACKSTVGVDFKIKTVELR---GKKIRLQIWDTAGQ 59
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLASKC 362
+R+ ++ YY+++ G I+++D+T +++F+ + +W +D D A L LL+ +K
Sbjct: 60 ERFNSITSAYYRSAKGIILVYDITKKETFDDLPKWMKMIDKYASED--AEL--LLVGNKL 115
Query: 363 DL-PDRQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRIICSKRMEEEAVER 421
D DR++ + E Q M + E S+K++ +++ LVD I+ ++ E
Sbjct: 116 DCETDREITRQQGEKFAQQITGMRFCEASAKDNFNVDEIFLKLVDDILKKMPLDILRNEL 175
Query: 422 KSSI 425
+SI
Sbjct: 176 SNSI 179
Score = 41.2 bits (96), Expect = 4e-04
Identities = 23/56 (41%), Positives = 35/56 (62%), Gaps = 3/56 (5%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
++I G VGKTS ++ F + F + K+TVGVDF K + + G+ ++LQIWD
Sbjct: 3 VIIIGSRGVGKTSLMERFTDDTFCEACKSTVGVDFKIKTVELR---GKKIRLQIWD 55
Score = 32.3 bits (73), Expect = 0.30
Identities = 18/40 (45%), Positives = 27/40 (67%)
Query: 109 LKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTK 148
L++++IG VGKTS ++ F + F + K+TVGVDF K
Sbjct: 1 LQVIIIGSRGVGKTSLMERFTDDTFCEACKSTVGVDFKIK 40
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 88.3 bits (219), Expect = 4e-20
Identities = 48/174 (27%), Positives = 91/174 (52%), Gaps = 10/174 (5%)
Query: 235 PIQIPTYPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKL 294
+ P++ ++I GD GKT++V+ + +F Y+ T+GV+ L G ++
Sbjct: 8 TVDYPSFKLVIVGDGGTGKTTFVKRHLTGEFEKKYEPTIGVEVHP-LDFFTNCG--KIRF 64
Query: 295 QIWDIAGQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLP 354
WD AGQ+++ + YY + IIMFD+T R ++++V W DL C +N +P
Sbjct: 65 YCWDTAGQEKFGGLRDGYYIHGQCAIIMFDVTARLTYKNVPTWHRDLCRVC--EN---IP 119
Query: 355 CLLLASKCDLPDRQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRI 408
+L +K D+ +RQV+ ++ H+ + + E+S+K + E +L ++
Sbjct: 120 IVLCGNKVDVKNRQVKAKQVTF--HRKKNLQYYEISAKSNYNFEKPFLYLARKL 171
Score = 38.2 bits (89), Expect = 0.005
Identities = 18/64 (28%), Positives = 32/64 (50%), Gaps = 3/64 (4%)
Query: 165 PIQTPSYLILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKL 224
+ PS+ ++I GD GKT++V+ + +F Y+ T+GV+ L G ++
Sbjct: 8 TVDYPSFKLVIVGDGGTGKTTFVKRHLTGEFEKKYEPTIGVEVHP-LDFFTNCG--KIRF 64
Query: 225 QIWD 228
WD
Sbjct: 65 YCWD 68
Score = 35.5 bits (82), Expect = 0.037
Identities = 15/44 (34%), Positives = 26/44 (59%), Gaps = 5/44 (11%)
Query: 109 LKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGV-----DFST 147
K++++GD GKT++V+ + +F Y+ T+GV DF T
Sbjct: 14 FKLVIVGDGGTGKTTFVKRHLTGEFEKKYEPTIGVEVHPLDFFT 57
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 88.1 bits (218), Expect = 4e-20
Identities = 46/158 (29%), Positives = 88/158 (55%), Gaps = 9/158 (5%)
Query: 244 LITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQD 303
+I GD+ VGK+ + F +F + T+GV+F ++++ +P+KLQIWD AGQ+
Sbjct: 10 IIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMIT---IDNKPIKLQIWDTAGQE 66
Query: 304 RYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLASKCD 363
+ ++R YY+ + G ++++D+T R++F + W D A + +L+ +KCD
Sbjct: 67 SFRSITRSYYRGAAGALLVYDITRRETFNHLASWLEDARQHA----NANMTIMLIGNKCD 122
Query: 364 LPDRQ-VEINEIEAVCHQYNFMSWIEVSSKEHLMIEDS 400
L R+ V E E ++ + ++E S+K +E++
Sbjct: 123 LAHRRAVSTEEGEQFAKEHGLI-FMEASAKTAQNVEEA 159
Score = 45.7 bits (108), Expect = 1e-05
Identities = 19/55 (34%), Positives = 33/55 (60%), Gaps = 3/55 (5%)
Query: 174 LITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
+I GD+ VGK+ + F +F + T+GV+F ++++ +P+KLQIWD
Sbjct: 10 IIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMIT---IDNKPIKLQIWD 61
Score = 32.6 bits (74), Expect = 0.30
Identities = 13/44 (29%), Positives = 27/44 (61%)
Query: 108 VLKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLS 151
+ K ++IGD+ VGK+ + F +F + T+GV+F ++++
Sbjct: 6 LFKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMIT 49
>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 = 84.2 bits (208), Expect = 4e-19
Identities = 47/158 (29%), Positives = 87/158 (55%), Gaps = 7/158 (4%)
Query: 241 YPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIA 300
+ I++ G++ VGKT V+ F Q F T+GVDF K + + G +KLQIWD A
Sbjct: 8 FKIVLIGNAGVGKTCLVRRFTQGLFPPGQGATIGVDFMIKTV---EIKGEKIKLQIWDTA 64
Query: 301 GQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLAS 360
GQ+R+ +++ YY++++ I+ +D+T +SF + +W +++ N ++ +L+ +
Sbjct: 65 GQERFRSITQSYYRSANALILTYDITCEESFRCLPEWLREIEQYA---NNKVIT-ILVGN 120
Query: 361 KCDLPDRQVEINEIEAVCHQYNFMSWIEVSSKEHLMIE 398
K DL +R+ + M ++E S+KE +E
Sbjct: 121 KIDLAERREVSQQRAEEFSDAQDMYYLETSAKESDNVE 158
Score = 47.2 bits (112), Expect = 2e-06
Identities = 23/56 (41%), Positives = 32/56 (57%), Gaps = 3/56 (5%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
I++ G++ VGKT V+ F Q F T+GVDF K + + G +KLQIWD
Sbjct: 10 IVLIGNAGVGKTCLVRRFTQGLFPPGQGATIGVDFMIKTV---EIKGEKIKLQIWD 62
Score = 38.3 bits (89), Expect = 0.002
Identities = 19/45 (42%), Positives = 27/45 (60%)
Query: 104 DAETVLKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTK 148
D + + KI++IG++ VGKT V+ F Q F T+GVDF K
Sbjct: 3 DYDFLFKIVLIGNAGVGKTCLVRRFTQGLFPPGQGATIGVDFMIK 47
>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 = 83.6 bits (207), Expect = 5e-19
Identities = 47/174 (27%), Positives = 82/174 (47%), Gaps = 20/174 (11%)
Query: 241 YPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIA 300
Y +++ G VGK++ +QN F+D Y T+ + +++ G L I D A
Sbjct: 2 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVV----IDGETCLLDILDTA 57
Query: 301 GQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKH------DLDSKCILDNGAMLP 354
GQ+ Y M Y + +G + +F + +RKSFE + ++ D D +P
Sbjct: 58 GQEEYSAMRDQYMRTGEGFLCVFAINSRKSFEDIHTYREQIKRVKDSDD---------VP 108
Query: 355 CLLLASKCDLPDRQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRI 408
+L+ +KCDL R V + + + Y + +IE S+K +E++ LV I
Sbjct: 109 MVLVGNKCDLAARTVSTRQGQDLAKSYG-IPYIETSAKTRQGVEEAFYTLVREI 161
Score = 32.0 bits (73), Expect = 0.33
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 109 LKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTV 141
K++V+G VGK++ +QN F+D Y T+
Sbjct: 2 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTI 34
Score = 28.9 bits (65), Expect = 3.6
Identities = 11/33 (33%), Positives = 19/33 (57%)
Query: 171 YLILITGDSTVGKTSYVQGFVQNKFLDNYKNTV 203
Y +++ G VGK++ +QN F+D Y T+
Sbjct: 2 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTI 34
>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 = 83.8 bits (207), Expect = 8e-19
Identities = 50/160 (31%), Positives = 92/160 (57%), Gaps = 10/160 (6%)
Query: 241 YPILITGDSTVGKTSYVQGFVQNKFL-DNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDI 299
+ +++ GDS VGKT + F FL ++ TVG+ F+ K+++ G VKLQIWD
Sbjct: 1 FKVMLVGDSGVGKTCLLVRFKDGAFLAGSFIATVGIQFTNKVVT---VDGVKVKLQIWDT 57
Query: 300 AGQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLA 359
AGQ+R+ ++ YY+++ ++++D+TN+ SF+++ W ++ D M LL
Sbjct: 58 AGQERFRSVTHAYYRDAHALLLLYDVTNKSSFDNIRAWLTEILEYAQSDVVIM----LLG 113
Query: 360 SKCDLP-DRQVEINEIEAVCHQYNFMSWIEVSSKEHLMIE 398
+K D+ +R V+ + E + +Y + ++E S+K L +E
Sbjct: 114 NKADMSGERVVKREDGERLAKEYG-VPFMETSAKTGLNVE 152
Score = 47.2 bits (112), Expect = 3e-06
Identities = 23/57 (40%), Positives = 34/57 (59%), Gaps = 4/57 (7%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFL-DNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
+++ GDS VGKT + F FL ++ TVG+ F+ K+++ G VKLQIWD
Sbjct: 3 VMLVGDSGVGKTCLLVRFKDGAFLAGSFIATVGIQFTNKVVT---VDGVKVKLQIWD 56
Score = 38.3 bits (89), Expect = 0.003
Identities = 16/43 (37%), Positives = 28/43 (65%), Gaps = 1/43 (2%)
Query: 110 KILVIGDSTVGKTSYVQGFVQNKFL-DNYKNTVGVDFSTKLLS 151
K++++GDS VGKT + F FL ++ TVG+ F+ K+++
Sbjct: 2 KVMLVGDSGVGKTCLLVRFKDGAFLAGSFIATVGIQFTNKVVT 44
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 83.6 bits (206), Expect = 2e-18
Identities = 56/188 (29%), Positives = 104/188 (55%), Gaps = 13/188 (6%)
Query: 240 TYPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDI 299
++ IL+ GDS VGK+S + F+ + +++ T+GVDF K L+ GG+ +KL IWD
Sbjct: 14 SFKILLIGDSGVGKSSLLVSFISSS-VEDLAPTIGVDFKIKQLT---VGGKRLKLTIWDT 69
Query: 300 AGQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQ-WKHDLDSKCILDNGAMLPCLLL 358
AGQ+R+ ++ YY+N+ G I+++D+T R++F ++ W +++ + +L+
Sbjct: 70 AGQERFRTLTSSYYRNAQGIILVYDVTRRETFTNLSDVWGKEVELYSTNQDCVK---MLV 126
Query: 359 ASKCDL-PDRQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRIICSKRMEEE 417
+K D +R V E A+ ++ + ++E S+K +E L +I+ + EE
Sbjct: 127 GNKVDRESERDVSREEGMALAKEHGCL-FLECSAKTRENVEQCFEELALKIMEVPSLLEE 185
Query: 418 ---AVERK 422
AV+R
Sbjct: 186 GSTAVKRN 193
Score = 47.0 bits (111), Expect = 6e-06
Identities = 25/59 (42%), Positives = 38/59 (64%), Gaps = 4/59 (6%)
Query: 170 SYLILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
S+ IL+ GDS VGK+S + F+ + +++ T+GVDF K L+ GG+ +KL IWD
Sbjct: 14 SFKILLIGDSGVGKSSLLVSFISSS-VEDLAPTIGVDFKIKQLT---VGGKRLKLTIWD 68
Score = 38.5 bits (89), Expect = 0.004
Identities = 19/43 (44%), Positives = 29/43 (67%), Gaps = 1/43 (2%)
Query: 109 LKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLS 151
KIL+IGDS VGK+S + F+ + +++ T+GVDF K L+
Sbjct: 15 FKILLIGDSGVGKSSLLVSFISSS-VEDLAPTIGVDFKIKQLT 56
>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 = 82.4 bits (203), Expect = 3e-18
Identities = 50/169 (29%), Positives = 88/169 (52%), Gaps = 10/169 (5%)
Query: 247 GDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQDRYI 306
GD GKT++V+ + +F Y T+GV+ L+ H G P++ +WD AGQ+++
Sbjct: 2 GDGGTGKTTFVKRHLTGEFEKKYVATLGVEVH-PLVFHTNRG--PIRFNVWDTAGQEKFG 58
Query: 307 CMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLASKCDLPD 366
+ YY IIMFD+T R ++++V W DL C +N +P +L +K D+ D
Sbjct: 59 GLRDGYYIQGQCAIIMFDVTARVTYKNVPNWHRDLVRVC--EN---IPIVLCGNKVDVKD 113
Query: 367 RQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRIICSKRME 415
R+V+ I H+ + + ++S+K + E +L ++I +E
Sbjct: 114 RKVKAKSI--TFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLE 160
Score = 31.5 bits (71), Expect = 0.58
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 3/52 (5%)
Query: 177 GDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
GD GKT++V+ + +F Y T+GV+ L+ H G P++ +WD
Sbjct: 2 GDGGTGKTTFVKRHLTGEFEKKYVATLGVEVH-PLVFHTNRG--PIRFNVWD 50
>gnl|CDD|206688 cd04101, RabL4, Rab GTPase-like family 4 (Rab-like4). RabL4
(Rab-like4) subfamily. RabL4s are novel proteins that
have high sequence similarity with Rab family members,
but display features that are distinct from Rabs, and
have been termed Rab-like. As in other Rab-like
proteins, RabL4 lacks a prenylation site at the
C-terminus. The specific function of RabL4 remains
unknown.
Length = 167
Score = 81.4 bits (201), Expect = 4e-18
Identities = 46/154 (29%), Positives = 77/154 (50%), Gaps = 8/154 (5%)
Query: 243 ILITGDSTVGKTSYVQGFVQN--KFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIA 300
+ GD VGK++ VQ F + F NY T G D K + V+L I+D A
Sbjct: 3 CAVVGDPAVGKSALVQMFHSDGATFQKNYTMTTGCDLVVKTVPVPD-TSDSVELFIFDSA 61
Query: 301 GQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLAS 360
GQ+ + M ++ +++D+TN SF + +W + + + +G P +L+ +
Sbjct: 62 GQELFSDMVENVWEQPAVVCVVYDVTNEVSFNNCSRWINRVRTH---SHGLHTPGVLVGN 118
Query: 361 KCDLPDRQVEINEIEAVC-HQYNFMSWIEVSSKE 393
KCDL DR+ E++ +A Q N + + E S+KE
Sbjct: 119 KCDLTDRR-EVDAAQAQALAQANTLKFYETSAKE 151
Score = 40.6 bits (95), Expect = 4e-04
Identities = 16/42 (38%), Positives = 21/42 (50%), Gaps = 2/42 (4%)
Query: 109 LKILVIGDSTVGKTSYVQGFVQN--KFLDNYKNTVGVDFSTK 148
+ V+GD VGK++ VQ F + F NY T G D K
Sbjct: 1 AQCAVVGDPAVGKSALVQMFHSDGATFQKNYTMTTGCDLVVK 42
Score = 36.0 bits (83), Expect = 0.014
Identities = 15/40 (37%), Positives = 19/40 (47%), Gaps = 2/40 (5%)
Query: 173 ILITGDSTVGKTSYVQGFVQN--KFLDNYKNTVGVDFSTK 210
+ GD VGK++ VQ F + F NY T G D K
Sbjct: 3 CAVVGDPAVGKSALVQMFHSDGATFQKNYTMTTGCDLVVK 42
>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 = 80.1 bits (198), Expect = 8e-18
Identities = 50/172 (29%), Positives = 91/172 (52%), Gaps = 10/172 (5%)
Query: 239 PTYPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 298
PTY +++ G VGK++ F+Q+ F+ +Y T+ D TK + G+ +L I D
Sbjct: 1 PTYKLVVVGGGGVGKSALTIQFIQSYFVTDYDPTIE-DSYTK---QCEIDGQWARLDILD 56
Query: 299 IAGQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLL 358
AGQ+ + M Y + +G +++F +T+R SFE V ++ + + + P +L+
Sbjct: 57 TAGQEEFSAMREQYMRTGEGFLLVFSVTDRGSFEEVDKFHTQI---LRVKDRDEFPMILV 113
Query: 359 ASKCDLPD-RQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRII 409
+K DL RQV E + + Q +IE S+K+ + ++ + + LV R+I
Sbjct: 114 GNKADLEHQRQVSREEGQELARQLKIP-YIETSAKDRVNVDKAFHDLV-RVI 163
Score = 32.8 bits (75), Expect = 0.16
Identities = 18/60 (30%), Positives = 32/60 (53%), Gaps = 4/60 (6%)
Query: 169 PSYLILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
P+Y +++ G VGK++ F+Q+ F+ +Y T+ D TK + G+ +L I D
Sbjct: 1 PTYKLVVVGGGGVGKSALTIQFIQSYFVTDYDPTIE-DSYTK---QCEIDGQWARLDILD 56
Score = 32.4 bits (74), Expect = 0.24
Identities = 11/34 (32%), Positives = 21/34 (61%)
Query: 108 VLKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTV 141
K++V+G VGK++ F+Q+ F+ +Y T+
Sbjct: 2 TYKLVVVGGGGVGKSALTIQFIQSYFVTDYDPTI 35
>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 = 80.3 bits (199), Expect = 9e-18
Identities = 43/163 (26%), Positives = 73/163 (44%), Gaps = 22/163 (13%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
I++ GD VGKT + + NKF Y TV ++S + G+ V L +WD AGQ
Sbjct: 3 IVVVGDGAVGKTCLLISYTTNKFPTEYVPTVFDNYSANV----TVDGKQVNLGLWDTAGQ 58
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQ-WKHDLDSKCILDNGAMLPCLLLASK 361
+ Y + + Y +D ++ F + + SFE+V W ++ K N P +L+ +K
Sbjct: 59 EEYDRLRPLSYPQTDVFLLCFSVDSPSSFENVKTKWYPEI--KHYCPNV---PIILVGTK 113
Query: 362 CDLPDRQVEI------------NEIEAVCHQYNFMSWIEVSSK 392
DL D + E E + + + ++E S+
Sbjct: 114 IDLRDDGNTLKKLEKKQKPITPEEGEKLAKEIGAVKYMECSAL 156
Score = 44.5 bits (106), Expect = 2e-05
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 4/56 (7%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
I++ GD VGKT + + NKF Y TV ++S + G+ V L +WD
Sbjct: 3 IVVVGDGAVGKTCLLISYTTNKFPTEYVPTVFDNYSANV----TVDGKQVNLGLWD 54
Score = 42.1 bits (100), Expect = 1e-04
Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 4/52 (7%)
Query: 109 LKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPY 160
+KI+V+GD VGKT + + NKF Y TV ++S + G+
Sbjct: 1 IKIVVVGDGAVGKTCLLISYTTNKFPTEYVPTVFDNYSANV----TVDGKQV 48
>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 = 78.8 bits (195), Expect = 3e-17
Identities = 42/169 (24%), Positives = 82/169 (48%), Gaps = 29/169 (17%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
+++ GD VGKT + + N F ++Y TV ++S + + G+PV+L +WD AGQ
Sbjct: 1 LVVVGDGAVGKTCLLIVYTTNAFPEDYVPTVFENYSADV----EVDGKPVELGLWDTAGQ 56
Query: 303 DRYICMSRV---YYQNSDGCIIMFDLTNRKSFESVV-QWKHDLDSKCILDNGAMLPCLLL 358
+ Y R+ Y ++D +I F + + SFE+V +W ++ C +P +L+
Sbjct: 57 EDY---DRLRPLSYPDTDVFLICFSVDSPASFENVKEKWYPEVKHFC-----PNVPIILV 108
Query: 359 ASKCDLPDRQVEINEI-------------EAVCHQYNFMSWIEVSSKEH 394
+K DL + + + E+ +A+ + + ++E S+
Sbjct: 109 GTKLDLRNDKSTLEELSKKKQEPVTYEQGQALAKRIGAVKYLECSALTQ 157
Score = 47.6 bits (114), Expect = 2e-06
Identities = 18/56 (32%), Positives = 32/56 (57%), Gaps = 4/56 (7%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
+++ GD VGKT + + N F ++Y TV ++S + + G+PV+L +WD
Sbjct: 1 LVVVGDGAVGKTCLLIVYTTNAFPEDYVPTVFENYSADV----EVDGKPVELGLWD 52
Score = 38.4 bits (90), Expect = 0.003
Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 4/50 (8%)
Query: 111 ILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPY 160
++V+GD VGKT + + N F ++Y TV ++S + + G+P
Sbjct: 1 LVVVGDGAVGKTCLLIVYTTNAFPEDYVPTVFENYSADV----EVDGKPV 46
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 77.9 bits (191), Expect = 7e-17
Identities = 46/131 (35%), Positives = 78/131 (59%), Gaps = 9/131 (6%)
Query: 263 NKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQDRYICMSRVYYQNSDGCIIM 322
+ F +NY++T+G+DF +K L + PV+LQ+WD AGQ+R+ + Y ++S I++
Sbjct: 3 DTFDNNYQSTIGIDFLSKTLYLDE---GPVRLQLWDTAGQERFRSLIPSYIRDSAAAIVV 59
Query: 323 FDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLASKCDLPD-RQVEINEIEAVCHQY 381
+D+TNR+SFE+ +W D+ + + G + L+ +K DL D R+V E +Y
Sbjct: 60 YDITNRQSFENTTKWIQDI----LNERGKDVIIALVGNKTDLGDLRKVTYEEGMQKAQEY 115
Query: 382 NFMSWIEVSSK 392
N M + E S+K
Sbjct: 116 NTM-FHETSAK 125
Score = 33.9 bits (77), Expect = 0.092
Identities = 15/36 (41%), Positives = 25/36 (69%), Gaps = 3/36 (8%)
Query: 193 NKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
+ F +NY++T+G+DF +K L + PV+LQ+WD
Sbjct: 3 DTFDNNYQSTIGIDFLSKTLYLDE---GPVRLQLWD 35
>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 = 76.9 bits (190), Expect = 2e-16
Identities = 55/169 (32%), Positives = 91/169 (53%), Gaps = 13/169 (7%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
I + G +VGK+S FV+ F+++Y T+ FS Y G+ L+I D AGQ
Sbjct: 4 IAVLGSRSVGKSSLTVQFVEGHFVESYYPTIENTFS----KIITYKGQEYHLEIVDTAGQ 59
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDN-GAM-LPCLLLAS 360
D Y + + Y G I+++ +T+RKSFE VV+ +D ILD G +P +L+ +
Sbjct: 60 DEYSILPQKYSIGIHGYILVYSVTSRKSFE-VVKVIYDK----ILDMLGKESVPIVLVGN 114
Query: 361 KCDLPD-RQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRI 408
K DL RQV E + + + +++E S+KE+ +E++ L++ I
Sbjct: 115 KSDLHMERQVSAEEGKKLAESWG-AAFLESSAKENENVEEAFELLIEEI 162
Score = 36.5 bits (85), Expect = 0.010
Identities = 17/45 (37%), Positives = 29/45 (64%), Gaps = 1/45 (2%)
Query: 110 KILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKK 154
KI V+G +VGK+S FV+ F+++Y T+ FS K++++K
Sbjct: 3 KIAVLGSRSVGKSSLTVQFVEGHFVESYYPTIENTFS-KIITYKG 46
Score = 33.0 bits (76), Expect = 0.17
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 4/56 (7%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
I + G +VGK+S FV+ F+++Y T+ FS Y G+ L+I D
Sbjct: 4 IAVLGSRSVGKSSLTVQFVEGHFVESYYPTIENTFS----KIITYKGQEYHLEIVD 55
>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 = 73.7 bits (181), Expect = 2e-15
Identities = 42/171 (24%), Positives = 90/171 (52%), Gaps = 8/171 (4%)
Query: 241 YPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIA 300
Y I++ G VGK++ FVQN F+++Y T+ + ++ + GR L+I D A
Sbjct: 2 YKIVVLGAGGVGKSALTVQFVQNVFIESYDPTIEDSYRKQV----EIDGRQCDLEILDTA 57
Query: 301 GQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLAS 360
G +++ M +Y ++ G ++++ +T+ S + + + + + + +P +L+ +
Sbjct: 58 GTEQFTAMRELYIKSGQGFLLVYSVTSEASLNELGELREQV---LRIKDSDNVPMVLVGN 114
Query: 361 KCDL-PDRQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRIIC 410
K DL DRQV + ++ Q+ + + E S+++ +++ LV +IIC
Sbjct: 115 KADLEDDRQVSREDGVSLSQQWGNVPFYETSARKRTNVDEVFIDLVRQIIC 165
Score = 32.1 bits (73), Expect = 0.32
Identities = 14/32 (43%), Positives = 22/32 (68%)
Query: 110 KILVIGDSTVGKTSYVQGFVQNKFLDNYKNTV 141
KI+V+G VGK++ FVQN F+++Y T+
Sbjct: 3 KIVVLGAGGVGKSALTVQFVQNVFIESYDPTI 34
Score = 31.7 bits (72), Expect = 0.39
Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 4/58 (6%)
Query: 171 YLILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
Y I++ G VGK++ FVQN F+++Y T+ + ++ + GR L+I D
Sbjct: 2 YKIVVLGAGGVGKSALTVQFVQNVFIESYDPTIEDSYRKQV----EIDGRQCDLEILD 55
>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 = 72.8 bits (179), Expect = 3e-15
Identities = 34/134 (25%), Positives = 79/134 (58%), Gaps = 7/134 (5%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
++ G+S VGK+ ++ + + +F+ Y T+G+D+ K +S + + V++ +D++G
Sbjct: 3 VISMGNSGVGKSCIIKRYCEGRFVSKYLPTIGIDYGVKKVSVR---NKEVRVNFFDLSGH 59
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAM--LPCLLLAS 360
Y+ + +Y+++ G ++++D+T+R+SFE++ W ++ + +G M + ++ A+
Sbjct: 60 PEYLEVRNEFYKDTQGVLLVYDVTDRQSFEALDSWLKEMKQEG-GPHGNMENIVVVVCAN 118
Query: 361 KCDLPD-RQVEINE 373
K DL R V +E
Sbjct: 119 KIDLTKHRAVSEDE 132
Score = 38.1 bits (89), Expect = 0.003
Identities = 13/43 (30%), Positives = 29/43 (67%)
Query: 109 LKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLS 151
+K++ +G+S VGK+ ++ + + +F+ Y T+G+D+ K +S
Sbjct: 1 IKVISMGNSGVGKSCIIKRYCEGRFVSKYLPTIGIDYGVKKVS 43
Score = 36.9 bits (86), Expect = 0.006
Identities = 14/56 (25%), Positives = 33/56 (58%), Gaps = 3/56 (5%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
++ G+S VGK+ ++ + + +F+ Y T+G+D+ K +S + + V++ +D
Sbjct: 3 VISMGNSGVGKSCIIKRYCEGRFVSKYLPTIGIDYGVKKVSVR---NKEVRVNFFD 55
>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 = 71.8 bits (176), Expect = 6e-15
Identities = 36/129 (27%), Positives = 70/129 (54%), Gaps = 10/129 (7%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHK-KYGGRPVKLQIWDIAG 301
I++ GDS VGK+ V+ F+ + + +T ++ L H K+ G+ + + WD AG
Sbjct: 3 IILLGDSAVGKSKLVERFLMDGYEPQQLST----YALTLYKHNAKFEGKTILVDFWDTAG 58
Query: 302 QDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLASK 361
Q+R+ M YY + CI++FD+T + +++++ +W +L +PC+++A+K
Sbjct: 59 QERFQTMHASYYHKAHACILVFDVTRKITYKNLSKWYEELREYR-----PEIPCIVVANK 113
Query: 362 CDLPDRQVE 370
DL +
Sbjct: 114 IDLDPSVTQ 122
Score = 28.7 bits (64), Expect = 4.2
Identities = 10/25 (40%), Positives = 19/25 (76%)
Query: 109 LKILVIGDSTVGKTSYVQGFVQNKF 133
+KI+++GDS VGK+ V+ F+ + +
Sbjct: 1 VKIILLGDSAVGKSKLVERFLMDGY 25
>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 = 72.3 bits (177), Expect = 7e-15
Identities = 48/151 (31%), Positives = 80/151 (52%), Gaps = 14/151 (9%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTK--LLSHKKYGGRPVKLQIWDIA 300
L+ GDS VGK + Y +G+D+ T LL GR VKLQ+WD +
Sbjct: 9 FLLVGDSDVGKGEILASLQDGSTESPYGYNMGIDYKTTTILLD-----GRRVKLQLWDTS 63
Query: 301 GQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLAS 360
GQ R+ + R Y + + G I+++D+TNR SF+ + +W ++D ++ +P +L+ +
Sbjct: 64 GQGRFCTIFRSYSRGAQGIILVYDITNRWSFDGIDRWIKEID-----EHAPGVPKILVGN 118
Query: 361 KCDLP-DRQVEINEIEAVCHQYNFMSWIEVS 390
+ L RQV + +A + N M++ EVS
Sbjct: 119 RLHLAFKRQVATEQAQAYAER-NGMTFFEVS 148
Score = 33.0 bits (75), Expect = 0.17
Identities = 23/68 (33%), Positives = 31/68 (45%), Gaps = 12/68 (17%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTK--LLSHKKYGGRPVKLQIWDI- 229
L+ GDS VGK + Y +G+D+ T LL GR VKLQ+WD
Sbjct: 9 FLLVGDSDVGKGEILASLQDGSTESPYGYNMGIDYKTTTILLD-----GRRVKLQLWDTS 63
Query: 230 ----YCTL 233
+CT+
Sbjct: 64 GQGRFCTI 71
>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 = 71.3 bits (175), Expect = 1e-14
Identities = 38/175 (21%), Positives = 69/175 (39%), Gaps = 24/175 (13%)
Query: 244 LITGDSTVGKTSYVQGFVQNKFL---DNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIA 300
++ G VGK+S + + + D T D K L K KL + D
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKV-----KLVLVDTP 55
Query: 301 GQDRYICMSRV-----YYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPC 355
G D + + R + +D +++ D T+R+S E K +P
Sbjct: 56 GLDEFGGLGREELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLRK------EGIPI 109
Query: 356 LLLASKCDLPD-RQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRII 409
+L+ +K DL + R+VE + + EVS+K +++ L +++I
Sbjct: 110 ILVGNKIDLLEEREVEELLRLEELAKILGVPVFEVSAKTGEGVDE----LFEKLI 160
Score = 28.6 bits (64), Expect = 4.8
Identities = 14/58 (24%), Positives = 21/58 (36%), Gaps = 8/58 (13%)
Query: 174 LITGDSTVGKTSYVQGFVQNKFL---DNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
++ G VGK+S + + + D T D K L K KL + D
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKV-----KLVLVD 53
>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 = 70.9 bits (174), Expect = 2e-14
Identities = 31/95 (32%), Positives = 54/95 (56%), Gaps = 3/95 (3%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
I + GD+ +GKTS + +V+ +F + Y T+GV+F K +S G + IWD+ GQ
Sbjct: 3 IGLLGDAQIGKTSLMVKYVEGEFDEEYIQTLGVNFMEKTIS---IRGTEITFSIWDLGGQ 59
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQW 337
+I M + +++ + MFDLT + + S+ +W
Sbjct: 60 REFINMLPLVCKDAVAILFMFDLTRKSTLNSIKEW 94
Score = 45.5 bits (108), Expect = 1e-05
Identities = 20/57 (35%), Positives = 33/57 (57%), Gaps = 3/57 (5%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDI 229
I + GD+ +GKTS + +V+ +F + Y T+GV+F K +S G + IWD+
Sbjct: 3 IGLLGDAQIGKTSLMVKYVEGEFDEEYIQTLGVNFMEKTIS---IRGTEITFSIWDL 56
Score = 43.5 bits (103), Expect = 4e-05
Identities = 18/43 (41%), Positives = 30/43 (69%)
Query: 109 LKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLS 151
LKI ++GD+ +GKTS + +V+ +F + Y T+GV+F K +S
Sbjct: 1 LKIGLLGDAQIGKTSLMVKYVEGEFDEEYIQTLGVNFMEKTIS 43
>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 = 70.1 bits (172), Expect = 2e-14
Identities = 38/167 (22%), Positives = 74/167 (44%), Gaps = 15/167 (8%)
Query: 240 TYPILITGDSTVGKTSYVQGFVQNK-FLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 298
I+I GD VGK++ + + NK + YK ++ T ++ + G+ K + D
Sbjct: 1 EIKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVI---EEDGKTYKFNLLD 57
Query: 299 IAGQDRYICMSRVYYQNSDGCIIMFDLTNR-KSFESVVQWKHDLDSKCILDNGAMLPCLL 357
AGQ+ Y + R+YY+ + + +FD+ E +++ K + ++G P +L
Sbjct: 58 TAGQEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILE-KQTKEIIHHAESGV--PIIL 114
Query: 358 LASKCDLPDRQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFL 404
+ +K DL D +++ + + N I +S E N
Sbjct: 115 VGNKIDLRDAKLKTHVAFLF-AKLNGEPIIPLS------AETGKNID 154
Score = 36.6 bits (85), Expect = 0.008
Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 4/57 (7%)
Query: 173 ILITGDSTVGKTSYVQGFVQNK-FLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
I+I GD VGK++ + + NK + YK ++ T ++ + G+ K + D
Sbjct: 4 IVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVI---EEDGKTYKFNLLD 57
Score = 31.6 bits (72), Expect = 0.45
Identities = 16/61 (26%), Positives = 32/61 (52%), Gaps = 5/61 (8%)
Query: 110 KILVIGDSTVGKTSYVQGFVQNK-FLDNYKNTVGVDFSTKLLSHKKYGGRPYGTFSPIQT 168
KI+++GD VGK++ + + NK + YK ++ T ++ + G+ Y F+ + T
Sbjct: 3 KIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVI---EEDGKTY-KFNLLDT 58
Query: 169 P 169
Sbjct: 59 A 59
>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 = 68.6 bits (168), Expect = 9e-14
Identities = 45/170 (26%), Positives = 91/170 (53%), Gaps = 11/170 (6%)
Query: 241 YPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIA 300
+ +++ G VGK++ F+ ++F+++Y+ T + K++ G V+L I D A
Sbjct: 1 HKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVV----LDGEEVQLNILDTA 56
Query: 301 GQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQ-WKHDLDSKCILDNGAMLPCLLLA 359
GQ+ Y + Y+++ +G +++F +T+ +SF ++ + + L K +P LL+
Sbjct: 57 GQEDYAAIRDNYFRSGEGFLLVFSITDMESFTALAEFREQILRVK----EDDNVPLLLVG 112
Query: 360 SKCDLPD-RQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRI 408
+KCDL D RQV + E + Q+ ++++E S+K ++ LV I
Sbjct: 113 NKCDLEDKRQVSVEEAANLAEQWG-VNYVETSAKTRANVDKVFFDLVREI 161
>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 = 68.5 bits (168), Expect = 1e-13
Identities = 35/134 (26%), Positives = 60/134 (44%), Gaps = 9/134 (6%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
I + G S VGK++ F+ +F+ Y+ + +S G V L+I D GQ
Sbjct: 2 IAVLGASGVGKSALTVRFLTKRFIGEYEPNLESLYS----RQVTIDGEQVSLEIQDTPGQ 57
Query: 303 DRYICMSRV--YYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLAS 360
+ + + +DG ++++ +T+R SF+ V Q + D P +L+ +
Sbjct: 58 QQNEDPESLERSLRWADGFVLVYSITDRSSFDVVSQLLQLIREIKKRDGEI--PVILVGN 115
Query: 361 KCDLP-DRQVEINE 373
K DL RQV E
Sbjct: 116 KADLLHSRQVSTEE 129
Score = 31.5 bits (72), Expect = 0.46
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 4/56 (7%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
I + G S VGK++ F+ +F+ Y+ + +S G V L+I D
Sbjct: 2 IAVLGASGVGKSALTVRFLTKRFIGEYEPNLESLYS----RQVTIDGEQVSLEIQD 53
>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 = 68.0 bits (166), Expect = 1e-13
Identities = 45/171 (26%), Positives = 87/171 (50%), Gaps = 10/171 (5%)
Query: 241 YPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIA 300
Y +++ G VGK++ FVQ F+D Y T+ D K + + + L+I D A
Sbjct: 2 YKLVVLGSGGVGKSALTVQFVQGIFVDKYDPTIE-DSYRKQI---EVDCQQCMLEILDTA 57
Query: 301 GQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCI-LDNGAMLPCLLLA 359
G +++ M +Y +N G +++ +T ++SF + DL + + + + +P +L+
Sbjct: 58 GTEQFTAMRDLYIKNGQGFALVYSITAQQSFNDL----QDLREQILRVKDTEDVPMILVG 113
Query: 360 SKCDLPD-RQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRII 409
+KCDL D R V E + + Q+ ++E S+K + +++ LV +I
Sbjct: 114 NKCDLEDERVVSKEEGQNLARQWGNCPFLETSAKSKINVDEIFYDLVRQIN 164
Score = 30.2 bits (68), Expect = 1.4
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 110 KILVIGDSTVGKTSYVQGFVQNKFLDNYKNTV 141
K++V+G VGK++ FVQ F+D Y T+
Sbjct: 3 KLVVLGSGGVGKSALTVQFVQGIFVDKYDPTI 34
>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 = 67.2 bits (164), Expect = 2e-13
Identities = 41/169 (24%), Positives = 85/169 (50%), Gaps = 9/169 (5%)
Query: 241 YPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIA 300
Y +++ G VGK++ FV F++ Y T+ DF K + + P L+I D A
Sbjct: 2 YKVVVLGSGGVGKSALTVQFVSGTFIEKYDPTIE-DFYRKEI---EVDSSPSVLEILDTA 57
Query: 301 GQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLAS 360
G +++ M +Y +N G I+++ L N+++F+ + + + + +P +L+ +
Sbjct: 58 GTEQFASMRDLYIKNGQGFIVVYSLVNQQTFQDIKPMRDQIVRVKGYEK---VPIILVGN 114
Query: 361 KCDLP-DRQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRI 408
K DL +R+V E A+ ++ ++E S+K M+ + +V ++
Sbjct: 115 KVDLESEREVSSAEGRALAEEWG-CPFMETSAKSKTMVNELFAEIVRQM 162
Score = 28.6 bits (64), Expect = 4.1
Identities = 14/39 (35%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 110 KILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTK 148
K++V+G VGK++ FV F++ Y T+ DF K
Sbjct: 3 KVVVLGSGGVGKSALTVQFVSGTFIEKYDPTIE-DFYRK 40
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 68.0 bits (166), Expect = 3e-13
Identities = 47/177 (26%), Positives = 85/177 (48%), Gaps = 25/177 (14%)
Query: 241 YPILITGDSTVGKTSYVQGFVQNKFLDNYKNT--------VGVDFSTKLLSHKKYGGRPV 292
Y +++ G VGK++ F+QN F+D Y T +D T LL
Sbjct: 6 YKLVVVGGGGVGKSALTIQFIQNHFIDEYDPTIEDSYRKQCVIDEETCLLD--------- 56
Query: 293 KLQIWDIAGQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAM 352
I D AGQ+ Y M Y + G + ++ +T+R SFE + ++ + + D
Sbjct: 57 ---ILDTAGQEEYSAMRDQYMRTGQGFLCVYSITSRSSFEEIASFREQILR--VKDKDR- 110
Query: 353 LPCLLLASKCDLP-DRQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRI 408
+P +L+ +KCDL +RQV E + + + + ++E S+K+ + ++++ LV I
Sbjct: 111 VPMILVGNKCDLDSERQVSTGEGQELAKSFG-IPFLETSAKQRVNVDEAFYELVREI 166
Score = 32.1 bits (73), Expect = 0.36
Identities = 15/37 (40%), Positives = 23/37 (62%)
Query: 105 AETVLKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTV 141
A T K++V+G VGK++ F+QN F+D Y T+
Sbjct: 2 ASTEYKLVVVGGGGVGKSALTIQFIQNHFIDEYDPTI 38
Score = 29.8 bits (67), Expect = 1.8
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 171 YLILITGDSTVGKTSYVQGFVQNKFLDNYKNTV 203
Y +++ G VGK++ F+QN F+D Y T+
Sbjct: 6 YKLVVVGGGGVGKSALTIQFIQNHFIDEYDPTI 38
>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 = 67.4 bits (165), Expect = 4e-13
Identities = 44/195 (22%), Positives = 87/195 (44%), Gaps = 24/195 (12%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
I++ GD GKT + + Q F + Y TV ++ T L G+ ++L +WD AGQ
Sbjct: 6 IVVVGDGGCGKTCLLMVYAQGSFPEEYVPTVFENYVTTLQVPN---GKIIELALWDTAGQ 62
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESV-VQWKHDLDSKCILDNGAMLPCLLLASK 361
+ Y + + Y + D +I + + N S ++V +W +++ C P +L+ K
Sbjct: 63 EDYDRLRPLSYPDVDVILICYSVDNPTSLDNVEDKWYPEVNHFC-----PGTPIVLVGLK 117
Query: 362 CDL-PDRQ------------VEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRI 408
DL D+ V + E+V +++IE S+K +++ + ++
Sbjct: 118 TDLRKDKNSVSKLRAQGLEPVTPEQGESVAKSIGAVAYIECSAKLMENVDEVFDAAIN-- 175
Query: 409 ICSKRMEEEAVERKS 423
+ + A ++K
Sbjct: 176 VALSKSGRAARKKKK 190
Score = 35.4 bits (82), Expect = 0.033
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 3/56 (5%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
I++ GD GKT + + Q F + Y TV ++ T L G+ ++L +WD
Sbjct: 6 IVVVGDGGCGKTCLLMVYAQGSFPEEYVPTVFENYVTTLQVPN---GKIIELALWD 58
Score = 34.6 bits (80), Expect = 0.055
Identities = 13/33 (39%), Positives = 19/33 (57%)
Query: 109 LKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTV 141
+KI+V+GD GKT + + Q F + Y TV
Sbjct: 4 VKIVVVGDGGCGKTCLLMVYAQGSFPEEYVPTV 36
>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 = 64.9 bits (158), Expect = 2e-12
Identities = 47/180 (26%), Positives = 84/180 (46%), Gaps = 12/180 (6%)
Query: 241 YPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIA 300
Y I++ G VGK++ F+ + F D + T+ + T+ + P L I D A
Sbjct: 3 YKIVMLGAGGVGKSAVTMQFISHSFPDYHDPTIEDAYKTQA----RIDNEPALLDILDTA 58
Query: 301 GQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLAS 360
GQ + M Y + +G II + +T+R SF+ ++K + + ++ +P +L+ +
Sbjct: 59 GQAEFTAMRDQYMRCGEGFIICYSVTDRHSFQEASEFKELITRVRLTED---IPLVLVGN 115
Query: 361 KCDLPD-RQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRIICSKRMEEEAV 419
K DL RQV E + ++N + E S+ I+D+ + LV I +R E
Sbjct: 116 KVDLEQQRQVTTEEGRNLAREFN-CPFFETSAALRFYIDDAFHGLVREI---RRKESMPA 171
Score = 30.2 bits (68), Expect = 1.6
Identities = 10/34 (29%), Positives = 19/34 (55%)
Query: 108 VLKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTV 141
KI+++G VGK++ F+ + F D + T+
Sbjct: 2 EYKIVMLGAGGVGKSAVTMQFISHSFPDYHDPTI 35
Score = 29.1 bits (65), Expect = 3.5
Identities = 10/33 (30%), Positives = 18/33 (54%)
Query: 171 YLILITGDSTVGKTSYVQGFVQNKFLDNYKNTV 203
Y I++ G VGK++ F+ + F D + T+
Sbjct: 3 YKIVMLGAGGVGKSAVTMQFISHSFPDYHDPTI 35
>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 = 63.7 bits (155), Expect = 4e-12
Identities = 41/171 (23%), Positives = 88/171 (51%), Gaps = 11/171 (6%)
Query: 241 YPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIA 300
Y +++ G VGK++ FVQ F++ Y T+ + ++ + G+ L+I D A
Sbjct: 2 YKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQV----EVDGQQCMLEILDTA 57
Query: 301 GQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCI-LDNGAMLPCLLLA 359
G +++ M +Y +N G ++++ +T + +F + DL + + + + +P +L+
Sbjct: 58 GTEQFTAMRDLYMKNGQGFVLVYSITAQSTFNDL----QDLREQILRVKDTEDVPMILVG 113
Query: 360 SKCDLPD-RQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRII 409
+KCDL D R V + + + Q+ +++E S+K + + + LV +I
Sbjct: 114 NKCDLEDERVVGKEQGQNLARQWG-CAFLETSAKAKINVNEIFYDLVRQIN 163
Score = 30.9 bits (70), Expect = 0.77
Identities = 12/32 (37%), Positives = 20/32 (62%)
Query: 110 KILVIGDSTVGKTSYVQGFVQNKFLDNYKNTV 141
K++V+G VGK++ FVQ F++ Y T+
Sbjct: 3 KLVVLGSGGVGKSALTVQFVQGIFVEKYDPTI 34
Score = 27.9 bits (62), Expect = 7.1
Identities = 11/33 (33%), Positives = 19/33 (57%)
Query: 171 YLILITGDSTVGKTSYVQGFVQNKFLDNYKNTV 203
Y +++ G VGK++ FVQ F++ Y T+
Sbjct: 2 YKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTI 34
>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 = 63.0 bits (154), Expect = 6e-12
Identities = 37/124 (29%), Positives = 62/124 (50%), Gaps = 11/124 (8%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
IL+ G GKT+ + + + T+G F+ + + +K VK +WD+ GQ
Sbjct: 2 ILMLGLDGAGKTTILYKL-KLGEVVTTIPTIG--FNVETVEYKN-----VKFTVWDVGGQ 53
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLASKC 362
D+ + + YY+N+DG I + D ++R+ E H L ++ L P L+LA+K
Sbjct: 54 DKIRPLWKHYYENTDGLIFVVDSSDRERIEEAKNELHKLLNEEELKG---APLLILANKQ 110
Query: 363 DLPD 366
DLP
Sbjct: 111 DLPG 114
>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 = 63.7 bits (155), Expect = 6e-12
Identities = 42/142 (29%), Positives = 65/142 (45%), Gaps = 26/142 (18%)
Query: 244 LITGDSTVGKTSYVQGFVQNKF--------LDNYKNTVGVDFSTKLLSHKKYGGRPVKLQ 295
++ GD VGKT + + N F DNY V VD G+PV L
Sbjct: 5 VVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVD------------GKPVNLG 52
Query: 296 IWDIAGQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESV-VQWKHDLDSKCILDNGAMLP 354
+WD AGQ+ Y + + Y +D +I F L + SFE+V +W ++ C P
Sbjct: 53 LWDTAGQEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHC-----PNTP 107
Query: 355 CLLLASKCDLPDRQVEINEIEA 376
+L+ +K DL D + I +++
Sbjct: 108 IILVGTKLDLRDDKDTIEKLKE 129
Score = 37.5 bits (87), Expect = 0.005
Identities = 27/96 (28%), Positives = 37/96 (38%), Gaps = 25/96 (26%)
Query: 174 LITGDSTVGKTSYVQGFVQNKF--------LDNYKNTVGVDFSTKLLSHKKYGGRPVKLQ 225
++ GD VGKT + + N F DNY V VD G+PV L
Sbjct: 5 VVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVD------------GKPVNLG 52
Query: 226 IWDI-----YCTLSPIQIPTYPILITGDSTVGKTSY 256
+WD Y L P+ P + + S V S+
Sbjct: 53 LWDTAGQEDYDRLRPLSYPQTDVFLICFSLVSPASF 88
Score = 30.9 bits (70), Expect = 0.79
Identities = 16/44 (36%), Positives = 21/44 (47%), Gaps = 8/44 (18%)
Query: 109 LKILVIGDSTVGKTSYVQGFVQNKF--------LDNYKNTVGVD 144
+K +V+GD VGKT + + N F DNY V VD
Sbjct: 2 IKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVD 45
>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 = 64.0 bits (156), Expect = 1e-11
Identities = 49/165 (29%), Positives = 86/165 (52%), Gaps = 10/165 (6%)
Query: 241 YPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIA 300
Y +++ G S VGKT+ V F+ +F + Y T+ DF KL S + G +L I D +
Sbjct: 1 YRMVVLGASKVGKTAIVSRFLGGRFEEQYTPTIE-DFHRKLYSIR---GEVYQLDILDTS 56
Query: 301 GQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHD-LDSKCILDN----GAMLPC 355
G + M R+ D I++F L NR+SFE V + + L++K L N +P
Sbjct: 57 GNHPFPAMRRLSILTGDVFILVFSLDNRESFEEVCRLREQILETKSCLKNKTKENVKIPM 116
Query: 356 LLLASKCDLPD-RQVEINEIEAVCHQYNFMSWIEVSSKEHLMIED 399
++ +K D R+V+ +E+E + ++ EVS+K++ +++
Sbjct: 117 VICGNKADRDFPREVQRDEVEQLVGGDENCAYFEVSAKKNSNLDE 161
Score = 33.2 bits (76), Expect = 0.22
Identities = 17/42 (40%), Positives = 26/42 (61%), Gaps = 1/42 (2%)
Query: 110 KILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLS 151
+++V+G S VGKT+ V F+ +F + Y T+ DF KL S
Sbjct: 2 RMVVLGASKVGKTAIVSRFLGGRFEEQYTPTIE-DFHRKLYS 42
Score = 32.8 bits (75), Expect = 0.28
Identities = 17/43 (39%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 171 YLILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLS 213
Y +++ G S VGKT+ V F+ +F + Y T+ DF KL S
Sbjct: 1 YRMVVLGASKVGKTAIVSRFLGGRFEEQYTPTIE-DFHRKLYS 42
>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 = 62.6 bits (152), Expect = 2e-11
Identities = 43/160 (26%), Positives = 75/160 (46%), Gaps = 19/160 (11%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
+++ GD GKTS + F + F Y+ TV ++ + G V+L +WD AGQ
Sbjct: 3 VVVLGDGACGKTSLLNVFTRGYFPQVYEPTVFENYIHDIFVD----GLAVELSLWDTAGQ 58
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVV-QWKHDLDSKCILDNGAMLPCLLLASK 361
+ + + + Y ++ ++ F + N S E+V +W ++ C G L +L+A K
Sbjct: 59 EEFDRLRSLSYADTHVIMLCFSVDNPDSLENVESKWLAEIRHHC---PGVKL--VLVALK 113
Query: 362 CDLPDRQVEI---------NEIEAVCHQYNFMSWIEVSSK 392
CDL + + E E AV + N ++E S+K
Sbjct: 114 CDLREPRNERDRGTHTISYEEGLAVAKRINACRYLECSAK 153
Score = 32.5 bits (74), Expect = 0.25
Identities = 16/56 (28%), Positives = 27/56 (48%), Gaps = 4/56 (7%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
+++ GD GKTS + F + F Y+ TV ++ + G V+L +WD
Sbjct: 3 VVVLGDGACGKTSLLNVFTRGYFPQVYEPTVFENYIHDIFVD----GLAVELSLWD 54
Score = 31.4 bits (71), Expect = 0.71
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 110 KILVIGDSTVGKTSYVQGFVQNKFLDNYKNTV 141
K++V+GD GKTS + F + F Y+ TV
Sbjct: 2 KVVVLGDGACGKTSLLNVFTRGYFPQVYEPTV 33
>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 = 61.3 bits (149), Expect = 3e-11
Identities = 35/123 (28%), Positives = 66/123 (53%), Gaps = 10/123 (8%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
I++ GDS GKT+ +Q F ++ F +NY TV +++ + + ++L +WD +G
Sbjct: 4 IVLVGDSQCGKTALLQVFAKDSFPENYVPTVFENYTASF----EVDKQRIELSLWDTSGS 59
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVV-QWKHDLDSKCILDNGAMLPCLLLASK 361
Y + + Y +SD +I FD++ ++ +SV+ +WK + + + P LL+ K
Sbjct: 60 PYYDNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGE-----VREFCPNTPVLLVGCK 114
Query: 362 CDL 364
DL
Sbjct: 115 SDL 117
Score = 40.1 bits (94), Expect = 6e-04
Identities = 15/32 (46%), Positives = 23/32 (71%)
Query: 110 KILVIGDSTVGKTSYVQGFVQNKFLDNYKNTV 141
KI+++GDS GKT+ +Q F ++ F +NY TV
Sbjct: 3 KIVLVGDSQCGKTALLQVFAKDSFPENYVPTV 34
Score = 38.6 bits (90), Expect = 0.002
Identities = 17/56 (30%), Positives = 32/56 (57%), Gaps = 4/56 (7%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
I++ GDS GKT+ +Q F ++ F +NY TV +++ + + ++L +WD
Sbjct: 4 IVLVGDSQCGKTALLQVFAKDSFPENYVPTVFENYTASF----EVDKQRIELSLWD 55
>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 = 61.0 bits (148), Expect = 7e-11
Identities = 42/161 (26%), Positives = 71/161 (44%), Gaps = 21/161 (13%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
++I GD GKTS + F +F + Y TV ++ T + G+PV+L +WD AGQ
Sbjct: 4 LVIVGDGACGKTSLLYVFTLGEFPEEYHPTVFENYVTDC----RVDGKPVQLALWDTAGQ 59
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESV-VQWKHDLDSKCILDNGAMLPCLLLASK 361
+ Y + + Y + +I F + S E+V +W ++ C +P +L+ K
Sbjct: 60 EEYERLRPLSYSKAHVILIGFAIDTPDSLENVRTKWIEEVRRYC-----PNVPVILVGLK 114
Query: 362 CDL-----------PDRQVEINEIEAVCHQYNFMSWIEVSS 391
DL D V I + + V ++E S+
Sbjct: 115 KDLRQEAVAKGNYATDEFVPIQQAKLVARAIGAKKYMECSA 155
Score = 35.2 bits (81), Expect = 0.034
Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 4/56 (7%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
++I GD GKTS + F +F + Y TV ++ T + G+PV+L +WD
Sbjct: 4 LVIVGDGACGKTSLLYVFTLGEFPEEYHPTVFENYVTDC----RVDGKPVQLALWD 55
Score = 29.8 bits (67), Expect = 2.2
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 110 KILVIGDSTVGKTSYVQGFVQNKFLDNYKNTV 141
K++++GD GKTS + F +F + Y TV
Sbjct: 3 KLVIVGDGACGKTSLLYVFTLGEFPEEYHPTV 34
>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 = 59.0 bits (143), Expect = 2e-10
Identities = 34/119 (28%), Positives = 60/119 (50%), Gaps = 10/119 (8%)
Query: 247 GDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQDRYI 306
GD VGKTS + + N + Y T +FS +L G+PV+LQ+ D AGQD +
Sbjct: 7 GDGAVGKTSLIVSYTTNGYPTEYVPTAFDNFSVVVLVD----GKPVRLQLCDTAGQDEFD 62
Query: 307 CMSRVYYQNSDGCIIMFDLTNRKSFESVV-QWKHDLDSKCILDNGAMLPCLLLASKCDL 364
+ + Y ++D ++ F + N SF+++ +W ++ P +L+ ++ DL
Sbjct: 63 KLRPLCYPDTDVFLLCFSVVNPSSFQNISEKWIPEIRKHN-----PKAPIILVGTQADL 116
Score = 38.9 bits (91), Expect = 0.002
Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 4/52 (7%)
Query: 177 GDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
GD VGKTS + + N + Y T +FS +L G+PV+LQ+ D
Sbjct: 7 GDGAVGKTSLIVSYTTNGYPTEYVPTAFDNFSVVVLVD----GKPVRLQLCD 54
Score = 31.2 bits (71), Expect = 0.59
Identities = 14/38 (36%), Positives = 21/38 (55%)
Query: 109 LKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFS 146
LK +++GD VGKTS + + N + Y T +FS
Sbjct: 1 LKCVLVGDGAVGKTSLIVSYTTNGYPTEYVPTAFDNFS 38
>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 = 57.0 bits (138), Expect = 3e-10
Identities = 27/120 (22%), Positives = 53/120 (44%), Gaps = 5/120 (4%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
+++ GD GK+S + V +F G + L G L IWD G+
Sbjct: 2 VVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTG---LLNIWDFGGR 58
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLASKC 362
+ ++ + +D ++++DLT+R+S V + L + + G +P +L+ +K
Sbjct: 59 EELKFEHIIFMKWADAILLVYDLTDRESLNEVSRLIAWLPN--LRKLGGKIPVILVGNKL 116
Score = 35.1 bits (81), Expect = 0.017
Identities = 25/82 (30%), Positives = 34/82 (41%), Gaps = 11/82 (13%)
Query: 110 KILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVG---------VDFSTKLLSHKKYGGRPY 160
K++VIGD GK+S + V +F G VD T LL+ +GGR
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREE 60
Query: 161 GTFSPIQTP--SYLILITGDST 180
F I + IL+ D T
Sbjct: 61 LKFEHIIFMKWADAILLVYDLT 82
Score = 28.9 bits (65), Expect = 2.4
Identities = 17/69 (24%), Positives = 26/69 (37%), Gaps = 9/69 (13%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVG---------VDFSTKLLSHKKYGGRPVK 223
+++ GD GK+S + V +F G VD T LL+ +GGR
Sbjct: 2 VVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREEL 61
Query: 224 LQIWDIYCT 232
I+
Sbjct: 62 KFEHIIFMK 70
>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 = 59.1 bits (143), Expect = 4e-10
Identities = 45/195 (23%), Positives = 91/195 (46%), Gaps = 15/195 (7%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKY--GGRPVKLQIWDIA 300
++ G + VGKT+ +Q F+ + F ++ TV + L K+Y G V + I D +
Sbjct: 2 LVFMGAAGVGKTALIQRFLYDTFEPKHRRTV------EELHSKEYEVAGVKVTIDILDTS 55
Query: 301 GQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHD-LDSKCILDNGAMLPCLLLA 359
G + M ++ QN D +++ + + +SFE V + + + L+ K +P +++
Sbjct: 56 GSYSFPAMRKLSIQNGDAFALVYSVDDPESFEEVKRLREEILEVK----EDKFVPIVVVG 111
Query: 360 SKCD-LPDRQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRIICSKRMEEEA 418
+K D L +RQVE + + ++E S+K++ + + L+ + + A
Sbjct: 112 NKIDSLAERQVEAADALSTVELDWNNGFVEASAKDNENVTEVFKELLQQANLPSWL-SPA 170
Query: 419 VERKSSIRLSEETLR 433
+ R+ SE R
Sbjct: 171 LRRRRESAPSEIQRR 185
Score = 33.3 bits (76), Expect = 0.18
Identities = 10/32 (31%), Positives = 21/32 (65%)
Query: 110 KILVIGDSTVGKTSYVQGFVQNKFLDNYKNTV 141
+++ +G + VGKT+ +Q F+ + F ++ TV
Sbjct: 1 RLVFMGAAGVGKTALIQRFLYDTFEPKHRRTV 32
Score = 31.7 bits (72), Expect = 0.58
Identities = 17/58 (29%), Positives = 29/58 (50%), Gaps = 8/58 (13%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKY--GGRPVKLQIWD 228
++ G + VGKT+ +Q F+ + F ++ TV + L K+Y G V + I D
Sbjct: 2 LVFMGAAGVGKTALIQRFLYDTFEPKHRRTV------EELHSKEYEVAGVKVTIDILD 53
>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 = 57.5 bits (139), Expect = 1e-09
Identities = 41/167 (24%), Positives = 90/167 (53%), Gaps = 7/167 (4%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
+++ GD VGKT+ N F++ Y T+ + +++ G+P L++ D AGQ
Sbjct: 2 LVVLGDGGVGKTALTIQLCLNHFVETYDPTIEDSYRKQVV----VDGQPCMLEVLDTAGQ 57
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLASKC 362
+ Y + + + +G I+++ +T+R +FE V +++ + + ++ A +P +++ +KC
Sbjct: 58 EEYTALRDQWIREGEGFILVYSITSRSTFERVERFREQI-QRVKDESAADVPIMIVGNKC 116
Query: 363 D-LPDRQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFLVDRI 408
D + +R+V E A+ + +IE S+K ++ +E + LV +
Sbjct: 117 DKVYEREVSTEEGAALARRLG-CEFIEASAKTNVNVERAFYTLVRAL 162
Score = 29.8 bits (67), Expect = 2.0
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 110 KILVIGDSTVGKTSYVQGFVQNKFLDNYKNTV 141
K++V+GD VGKT+ N F++ Y T+
Sbjct: 1 KLVVLGDGGVGKTALTIQLCLNHFVETYDPTI 32
>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 = 58.0 bits (140), Expect = 1e-09
Identities = 29/101 (28%), Positives = 52/101 (51%), Gaps = 6/101 (5%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGG--RPVKLQIWDIA 300
+L+ GDS VGK+S V +N+ L N TVG + ++ + + +++WD+
Sbjct: 3 VLVLGDSGVGKSSLVHLLCKNQVLGNPSWTVGCSVDVRHHTYGEGTPEEKTFYVELWDVG 62
Query: 301 GQ----DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQW 337
G + V+Y +G I + DLTN+KS +++ +W
Sbjct: 63 GSVGSAESVKSTRAVFYNQINGIIFVHDLTNKKSSQNLYRW 103
Score = 37.2 bits (86), Expect = 0.008
Identities = 17/45 (37%), Positives = 26/45 (57%)
Query: 109 LKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHK 153
+K+LV+GDS VGK+S V +N+ L N TVG + ++
Sbjct: 1 VKVLVLGDSGVGKSSLVHLLCKNQVLGNPSWTVGCSVDVRHHTYG 45
Score = 35.3 bits (81), Expect = 0.037
Identities = 17/59 (28%), Positives = 31/59 (52%), Gaps = 2/59 (3%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGG--RPVKLQIWDI 229
+L+ GDS VGK+S V +N+ L N TVG + ++ + + +++WD+
Sbjct: 3 VLVLGDSGVGKSSLVHLLCKNQVLGNPSWTVGCSVDVRHHTYGEGTPEEKTFYVELWDV 61
>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 = 58.0 bits (140), Expect = 1e-09
Identities = 26/92 (28%), Positives = 50/92 (54%), Gaps = 8/92 (8%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
+++ GD VGKTS + +++ +F D +TVG F K P + IWD AG+
Sbjct: 3 VVLLGDMNVGKTSLLHRYMERRFKDTV-STVGGAFYLKQW-------GPYNISIWDTAGR 54
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESV 334
+++ + +Y + + I+ +D++N +S E +
Sbjct: 55 EQFHGLGSMYCRGAAAVILTYDVSNVQSLEEL 86
Score = 34.9 bits (80), Expect = 0.047
Identities = 16/40 (40%), Positives = 26/40 (65%), Gaps = 1/40 (2%)
Query: 109 LKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTK 148
LK++++GD VGKTS + +++ +F D +TVG F K
Sbjct: 1 LKVVLLGDMNVGKTSLLHRYMERRFKDTV-STVGGAFYLK 39
Score = 33.3 bits (76), Expect = 0.19
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 8/56 (14%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
+++ GD VGKTS + +++ +F D +TVG F K P + IWD
Sbjct: 3 VVLLGDMNVGKTSLLHRYMERRFKDTV-STVGGAFYLKQW-------GPYNISIWD 50
>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 = 56.8 bits (137), Expect = 2e-09
Identities = 37/128 (28%), Positives = 63/128 (49%), Gaps = 10/128 (7%)
Query: 240 TYPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDI 299
T ++ GD VGKT + + NKF Y TV +++ ++ GG P L ++D
Sbjct: 1 TIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVM----IGGEPYTLGLFDT 56
Query: 300 AGQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQ-WKHDLDSKCILDNGAMLPCLLL 358
AGQ+ Y + + Y +D ++ F + + SFE+V + W ++ C P LL+
Sbjct: 57 AGQEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHC-----PKTPFLLV 111
Query: 359 ASKCDLPD 366
++ DL D
Sbjct: 112 GTQIDLRD 119
Score = 33.7 bits (77), Expect = 0.084
Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 4/52 (7%)
Query: 109 LKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPY 160
+K +V+GD VGKT + + NKF Y TV +++ ++ GG PY
Sbjct: 2 IKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVM----IGGEPY 49
Score = 33.7 bits (77), Expect = 0.10
Identities = 24/88 (27%), Positives = 40/88 (45%), Gaps = 9/88 (10%)
Query: 174 LITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDI---- 229
++ GD VGKT + + NKF Y TV +++ ++ GG P L ++D
Sbjct: 5 VVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVM----IGGEPYTLGLFDTAGQE 60
Query: 230 -YCTLSPIQIPTYPILITGDSTVGKTSY 256
Y L P+ P + + S V +S+
Sbjct: 61 DYDRLRPLSYPQTDVFLVCFSVVSPSSF 88
>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 = 56.2 bits (135), Expect = 3e-09
Identities = 36/123 (29%), Positives = 65/123 (52%), Gaps = 10/123 (8%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
I++ GDS GKT+ + F ++ F +NY TV +++ + ++L +WD +G
Sbjct: 8 IVVVGDSQCGKTALLHVFAKDCFPENYVPTVFENYTASFEIDTQR----IELSLWDTSGS 63
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVV-QWKHDLDSKCILDNGAMLPCLLLASK 361
Y + + Y +SD +I FD++ ++ +SV+ +WK ++ C N M LL+ K
Sbjct: 64 PYYDNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEIQEFC--PNTKM---LLVGCK 118
Query: 362 CDL 364
DL
Sbjct: 119 SDL 121
Score = 33.9 bits (77), Expect = 0.093
Identities = 15/32 (46%), Positives = 22/32 (68%)
Query: 110 KILVIGDSTVGKTSYVQGFVQNKFLDNYKNTV 141
KI+V+GDS GKT+ + F ++ F +NY TV
Sbjct: 7 KIVVVGDSQCGKTALLHVFAKDCFPENYVPTV 38
Score = 32.7 bits (74), Expect = 0.23
Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 9/72 (12%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDI--- 229
I++ GDS GKT+ + F ++ F +NY TV +++ + ++L +WD
Sbjct: 8 IVVVGDSQCGKTALLHVFAKDCFPENYVPTVFENYTASFEIDTQR----IELSLWDTSGS 63
Query: 230 --YCTLSPIQIP 239
Y + P+ P
Sbjct: 64 PYYDNVRPLSYP 75
>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 = 56.2 bits (135), Expect = 3e-09
Identities = 37/122 (30%), Positives = 60/122 (49%), Gaps = 10/122 (8%)
Query: 244 LITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQD 303
++ GD VGKT + + N F Y TV ++S + GR V L +WD AGQ+
Sbjct: 7 VVVGDGAVGKTCLLICYTTNAFPKEYIPTVFDNYSAQT----AVDGRTVSLNLWDTAGQE 62
Query: 304 RYICMSRVYYQNSDGCIIMFDLTNRKSFESVV-QWKHDLDSKCILDNGAMLPCLLLASKC 362
Y + + Y ++ II F + + S+E+V +W ++ C +P LL+ +K
Sbjct: 63 EYDRLRTLSYPQTNVFIICFSIASPSSYENVRHKWHPEVCHHC-----PNVPILLVGTKK 117
Query: 363 DL 364
DL
Sbjct: 118 DL 119
Score = 36.1 bits (83), Expect = 0.016
Identities = 25/88 (28%), Positives = 36/88 (40%), Gaps = 9/88 (10%)
Query: 174 LITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDI---- 229
++ GD VGKT + + N F Y TV ++S + GR V L +WD
Sbjct: 7 VVVGDGAVGKTCLLICYTTNAFPKEYIPTVFDNYSAQT----AVDGRTVSLNLWDTAGQE 62
Query: 230 -YCTLSPIQIPTYPILITGDSTVGKTSY 256
Y L + P + I S +SY
Sbjct: 63 EYDRLRTLSYPQTNVFIICFSIASPSSY 90
Score = 31.9 bits (72), Expect = 0.44
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 109 LKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTK 148
+K +V+GD VGKT + + N F Y TV ++S +
Sbjct: 4 IKCVVVGDGAVGKTCLLICYTTNAFPKEYIPTVFDNYSAQ 43
>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 = 53.9 bits (130), Expect = 9e-09
Identities = 33/115 (28%), Positives = 55/115 (47%), Gaps = 10/115 (8%)
Query: 252 GKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQDRYICMSRV 311
GKT+ V +F ++ TVG F+ + + G V +++WD+ GQ R+ M
Sbjct: 11 GKTTLVNVIASGQFSEDTIPTVG--FNMRKV---TKGN--VTIKVWDLGGQPRFRSMWER 63
Query: 312 YYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLASKCDLPD 366
Y + + + + D +R+ E HDL K L+ +P L+L +K DLP
Sbjct: 64 YCRGVNAIVYVVDAADREKLEVAKNELHDLLEKPSLEG---IPLLVLGNKNDLPG 115
>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 = 53.7 bits (129), Expect = 1e-08
Identities = 40/153 (26%), Positives = 77/153 (50%), Gaps = 7/153 (4%)
Query: 241 YPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIA 300
Y +++ G VGK+S V FV+ F ++Y T+ + + K LQI D
Sbjct: 2 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCSKSIC----TLQITDTT 57
Query: 301 GQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLAS 360
G ++ M R+ I+++ +T+++S E + ++L + +N +P +L+ +
Sbjct: 58 GSHQFPAMQRLSISKGHAFILVYSITSKQSLEELKPI-YELICEIKGNNLEKIPIMLVGN 116
Query: 361 KCD-LPDRQVEINEIEAVCHQYNFMSWIEVSSK 392
KCD P R+V +E A+ +N +++E S+K
Sbjct: 117 KCDESPSREVSSSEGAALARTWN-CAFMETSAK 148
Score = 27.9 bits (62), Expect = 8.0
Identities = 12/32 (37%), Positives = 20/32 (62%)
Query: 110 KILVIGDSTVGKTSYVQGFVQNKFLDNYKNTV 141
+++V G VGK+S V FV+ F ++Y T+
Sbjct: 3 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTI 34
>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 = 52.2 bits (125), Expect = 5e-08
Identities = 37/121 (30%), Positives = 62/121 (51%), Gaps = 10/121 (8%)
Query: 247 GDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQDRYI 306
GD VGKT + + N F +Y TV +FS ++ G V L +WD AGQ+ Y
Sbjct: 8 GDGAVGKTCMLISYTSNTFPTDYVPTVFDNFSANVV----VDGNTVNLGLWDTAGQEDYN 63
Query: 307 CMSRVYYQNSDGCIIMFDLTNRKSFESVV-QWKHDLDSKCILDNGAMLPCLLLASKCDLP 365
+ + Y+ +D ++ F L ++ S+E+V+ +W +L +P +L+ +K DL
Sbjct: 64 RLRPLSYRGADVFLLAFSLISKASYENVLKKWIPELRHY-----APGVPIVLVGTKLDLR 118
Query: 366 D 366
D
Sbjct: 119 D 119
Score = 32.9 bits (75), Expect = 0.17
Identities = 25/85 (29%), Positives = 36/85 (42%), Gaps = 9/85 (10%)
Query: 177 GDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDI-----YC 231
GD VGKT + + N F +Y TV +FS ++ G V L +WD Y
Sbjct: 8 GDGAVGKTCMLISYTSNTFPTDYVPTVFDNFSANVV----VDGNTVNLGLWDTAGQEDYN 63
Query: 232 TLSPIQIPTYPILITGDSTVGKTSY 256
L P+ + + S + K SY
Sbjct: 64 RLRPLSYRGADVFLLAFSLISKASY 88
Score = 29.4 bits (66), Expect = 2.8
Identities = 23/87 (26%), Positives = 35/87 (40%), Gaps = 9/87 (10%)
Query: 109 LKILVIGDSTVGKTSYVQGFVQNKF--------LDNYKNTVGVDFSTKLLSHKKYGGRP- 159
+K + +GD VGKT + + N F DN+ V VD +T L G+
Sbjct: 2 IKCVTVGDGAVGKTCMLISYTSNTFPTDYVPTVFDNFSANVVVDGNTVNLGLWDTAGQED 61
Query: 160 YGTFSPIQTPSYLILITGDSTVGKTSY 186
Y P+ + + S + K SY
Sbjct: 62 YNRLRPLSYRGADVFLLAFSLISKASY 88
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 51.5 bits (124), Expect = 1e-07
Identities = 36/124 (29%), Positives = 58/124 (46%), Gaps = 11/124 (8%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
ILI G GKT+ + + T+G F+ + +++K VK +WD+ GQ
Sbjct: 17 ILILGLDNAGKTTILYKLKLGEI-VTTIPTIG--FNVETVTYKN-----VKFTVWDVGGQ 68
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLASKC 362
+ + R Y+ N+D I + D +R E K +L + + A P L+LA+K
Sbjct: 69 ESLRPLWRNYFPNTDAVIFVVDSADRDRIEEA---KEELHALLNEEELADAPLLILANKQ 125
Query: 363 DLPD 366
DLP
Sbjct: 126 DLPG 129
>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 = 51.2 bits (123), Expect = 1e-07
Identities = 45/168 (26%), Positives = 73/168 (43%), Gaps = 16/168 (9%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
IL+ G GKT+ ++ F + + T+G F+ K L + Y KL IWD+ GQ
Sbjct: 17 ILMLGLDNAGKTTILKKF-NGEDISTISPTLG--FNIKTLEYNGY-----KLNIWDVGGQ 68
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLASKC 362
R Y++++D I + D ++R E K +L + + A L+ A+K
Sbjct: 69 KSLRSYWRNYFESTDALIWVVDSSDRARLEDC---KRELQKLLVEERLAGATLLIFANKQ 125
Query: 363 DLPDRQVEINEIEAVCH--QYNFMSW--IEVSSKEHLMIEDSMNFLVD 406
DLP + EI V W S+ + D +++LVD
Sbjct: 126 DLPG-ALSPEEIREVLELDSIKSHHWRIFGCSAVTGENLLDGIDWLVD 172
>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 = 50.4 bits (121), Expect = 2e-07
Identities = 33/167 (19%), Positives = 65/167 (38%), Gaps = 13/167 (7%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
+++ G VGKTS + + KF + +T G++ + ++L +WD GQ
Sbjct: 4 LMLVGQGGVGKTSLCKQLIGEKFDGDESSTHGINVQDW--KIPAPERKKIRLNVWDFGGQ 61
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLASKC 362
+ Y + + + +++FDL V W I G + P +L+ +
Sbjct: 62 EIYHATHQFFLTSRSLYLLVFDLRTGDEVSRVPYWLR-----QIKAFGGVSPVILVGTHI 116
Query: 363 D-LPDRQVEINEIEAVCHQYNFMSW--IEVSSKEHLMIEDSMNFLVD 406
D D I + +A+ ++ + VS K I + +
Sbjct: 117 DESCDED--ILK-KALNKKFPAIINDIHFVSCKNGKGIAELKKAIAK 160
Score = 38.1 bits (89), Expect = 0.003
Identities = 13/56 (23%), Positives = 26/56 (46%), Gaps = 2/56 (3%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWD 228
+++ G VGKTS + + KF + +T G++ + ++L +WD
Sbjct: 4 LMLVGQGGVGKTSLCKQLIGEKFDGDESSTHGINVQDW--KIPAPERKKIRLNVWD 57
Score = 34.6 bits (80), Expect = 0.037
Identities = 11/39 (28%), Positives = 21/39 (53%)
Query: 110 KILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTK 148
K++++G VGKTS + + KF + +T G++
Sbjct: 3 KLMLVGQGGVGKTSLCKQLIGEKFDGDESSTHGINVQDW 41
>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 = 50.4 bits (121), Expect = 2e-07
Identities = 49/185 (26%), Positives = 85/185 (45%), Gaps = 38/185 (20%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKN--------TVGVDFSTKLLSHKKYGGRPVKL 294
+LI G GKT++++ + KF NYK TVG++ T + +L
Sbjct: 2 VLILGLDNAGKTTFLEQ-TKTKFSKNYKGLNPSKITPTVGLNIGTIEVGK-------ARL 53
Query: 295 QIWDIAGQDRYICMSRVYYQNSDGCIIMFDLTNRKSF-ESVVQWKHDLDSKCILDNGAML 353
WD+ GQ+ + YY S G I + D T+R+ F ES ++ ++++ + +
Sbjct: 54 MFWDLGGQEELRSLWDKYYAESHGVIYVIDSTDRERFNESKSAFEKVINNEALEG----V 109
Query: 354 PCLLLASKCDLPDRQVEINEIEAVCHQYNFMSWIEVSSKEHLM-----------IEDSMN 402
P L+LA+K DLPD + + EI+ V F I + + + +E+ +
Sbjct: 110 PLLVLANKQDLPDA-LSVAEIKEV-----FDDCIALIGRRDCLVQPVSALEGEGVEEGIE 163
Query: 403 FLVDR 407
+LVD
Sbjct: 164 WLVDC 168
>gnl|CDD|177661 PLN00023, PLN00023, GTP-binding protein; Provisional.
Length = 334
Score = 51.4 bits (123), Expect = 3e-07
Identities = 28/105 (26%), Positives = 52/105 (49%), Gaps = 10/105 (9%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGG----------RPV 292
+L+ GDS VGK+S V V+ + T+G K +++ G R
Sbjct: 24 VLVVGDSGVGKSSLVHLIVKGSSIARPPQTIGCTVGVKHITYGSPGSSSNSIKGDSERDF 83
Query: 293 KLQIWDIAGQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQW 337
+++WD++G +RY ++Y +G I + DL+ R++ S+ +W
Sbjct: 84 FVELWDVSGHERYKDCRSLFYSQINGVIFVHDLSQRRTKTSLQKW 128
Score = 32.5 bits (74), Expect = 0.45
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 109 LKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPYGTFSPIQT 168
+++LV+GDS VGK+S V V+ + T+G K +++ G P + + I+
Sbjct: 22 VRVLVVGDSGVGKSSLVHLIVKGSSIARPPQTIGCTVGVKHITY----GSPGSSSNSIKG 77
Query: 169 PS 170
S
Sbjct: 78 DS 79
Score = 28.7 bits (64), Expect = 5.9
Identities = 14/47 (29%), Positives = 23/47 (48%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGG 219
+L+ GDS VGK+S V V+ + T+G K +++ G
Sbjct: 24 VLVVGDSGVGKSSLVHLIVKGSSIARPPQTIGCTVGVKHITYGSPGS 70
>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 = 49.6 bits (118), Expect = 4e-07
Identities = 36/124 (29%), Positives = 62/124 (50%), Gaps = 10/124 (8%)
Query: 244 LITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQD 303
++ GD VGKT + + + F + Y TV ++ + GG+ L ++D AGQ+
Sbjct: 4 VVVGDGAVGKTCLLMSYANDAFPEEYVPTVFDHYAVSV----TVGGKQYLLGLYDTAGQE 59
Query: 304 RYICMSRVYYQNSDGCIIMFDLTNRKSFESVV-QWKHDLDSKCILDNGAMLPCLLLASKC 362
Y + + Y +D +I F + N SF++V +W +L K N +P LL+ ++
Sbjct: 60 DYDRLRPLSYPMTDVFLICFSVVNPASFQNVKEEWVPEL--KEYAPN---VPYLLIGTQI 114
Query: 363 DLPD 366
DL D
Sbjct: 115 DLRD 118
Score = 32.7 bits (74), Expect = 0.21
Identities = 23/87 (26%), Positives = 35/87 (40%), Gaps = 9/87 (10%)
Query: 109 LKILVIGDSTVGKTSYVQGFVQNKF--------LDNYKNTVGVDFSTKLLS-HKKYGGRP 159
LK +V+GD VGKT + + + F D+Y +V V LL + G
Sbjct: 1 LKCVVVGDGAVGKTCLLMSYANDAFPEEYVPTVFDHYAVSVTVGGKQYLLGLYDTAGQED 60
Query: 160 YGTFSPIQTPSYLILITGDSTVGKTSY 186
Y P+ P + + S V S+
Sbjct: 61 YDRLRPLSYPMTDVFLICFSVVNPASF 87
Score = 30.4 bits (68), Expect = 1.3
Identities = 21/88 (23%), Positives = 37/88 (42%), Gaps = 9/88 (10%)
Query: 174 LITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDI---- 229
++ GD VGKT + + + F + Y TV ++ + GG+ L ++D
Sbjct: 4 VVVGDGAVGKTCLLMSYANDAFPEEYVPTVFDHYAVSV----TVGGKQYLLGLYDTAGQE 59
Query: 230 -YCTLSPIQIPTYPILITGDSTVGKTSY 256
Y L P+ P + + S V S+
Sbjct: 60 DYDRLRPLSYPMTDVFLICFSVVNPASF 87
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 48.3 bits (115), Expect = 1e-06
Identities = 30/106 (28%), Positives = 49/106 (46%), Gaps = 19/106 (17%)
Query: 290 RPVKLQIWDIAGQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDN 349
+ +K +WD+ GQD+ + R YYQN++G I + D +R+ + + S+ L +
Sbjct: 59 KNLKFTMWDVGGQDKLRPLWRHYYQNTNGLIFVVDSNDRERIGDAREELERMLSEDELRD 118
Query: 350 GAMLPCLLLASKCDLPDRQVEINEIEAVCHQYNFMSWIEVSSKEHL 395
+ L+ A+K DLP N MS EV+ K L
Sbjct: 119 AVL---LVFANKQDLP----------------NAMSTTEVTEKLGL 145
>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 = 48.5 bits (115), Expect = 2e-06
Identities = 26/104 (25%), Positives = 56/104 (53%), Gaps = 5/104 (4%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
I++ GD+ GKT+ + F ++ + ++Y TV +++ K ++L +WD +G
Sbjct: 4 IVVVGDTQCGKTALLHVFAKDNYPESYVPTVFENYTASFEIDK----HRIELNMWDTSGS 59
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVV-QWKHDLDSKC 345
Y + + Y +SD +I FD++ ++ +SV+ +W+ + C
Sbjct: 60 SYYDNVRPLAYPDSDAVLICFDISRPETLDSVLKKWQGETQEFC 103
Score = 31.1 bits (70), Expect = 0.98
Identities = 12/32 (37%), Positives = 22/32 (68%)
Query: 110 KILVIGDSTVGKTSYVQGFVQNKFLDNYKNTV 141
KI+V+GD+ GKT+ + F ++ + ++Y TV
Sbjct: 3 KIVVVGDTQCGKTALLHVFAKDNYPESYVPTV 34
Score = 30.0 bits (67), Expect = 2.2
Identities = 17/72 (23%), Positives = 35/72 (48%), Gaps = 9/72 (12%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDI--- 229
I++ GD+ GKT+ + F ++ + ++Y TV +++ K ++L +WD
Sbjct: 4 IVVVGDTQCGKTALLHVFAKDNYPESYVPTVFENYTASFEIDK----HRIELNMWDTSGS 59
Query: 230 --YCTLSPIQIP 239
Y + P+ P
Sbjct: 60 SYYDNVRPLAYP 71
>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 = 46.6 bits (111), Expect = 3e-06
Identities = 34/125 (27%), Positives = 66/125 (52%), Gaps = 12/125 (9%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
+L+ G + GK++ + + + TVG F+ ++L +K+ + L +WD+ GQ
Sbjct: 2 VLLLGLDSAGKSTLLYKLKHAELVTTIP-TVG--FNVEMLQLEKH----LSLTVWDVGGQ 54
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSF-ESVVQWKHDLDSKCILDNGAMLPCLLLASK 361
++ + + Y +N+DG + + D ++ ES + KH L ++ I +P +LLA+K
Sbjct: 55 EKMRTVWKCYLENTDGLVYVVDSSDEARLDESQKELKHILKNEHIKG----VPVVLLANK 110
Query: 362 CDLPD 366
DLP
Sbjct: 111 QDLPG 115
>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 = 46.5 bits (110), Expect = 5e-06
Identities = 36/141 (25%), Positives = 64/141 (45%), Gaps = 29/141 (20%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVG--------VDFSTKLLSHKKYGGRPVKL 294
IL+ G GKT+ + YK +G + F+ + +++K +
Sbjct: 16 ILMVGLDAAGKTTIL-----------YKLKLGESVTTIPTIGFNVETVTYKN-----ISF 59
Query: 295 QIWDIAGQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLP 354
+WD+ GQD+ + R YY N+ G I + D +R + + H + ++ L + +
Sbjct: 60 TVWDVGGQDKIRPLWRHYYTNTQGLIFVVDSNDRDRIDEAREELHRMLNEDELRDAVI-- 117
Query: 355 CLLLASKCDLPD--RQVEINE 373
L+ A+K DLPD + EI E
Sbjct: 118 -LVFANKQDLPDAMKAAEITE 137
>gnl|CDD|206679 cd01892, Miro2, Mitochondrial Rho family 2 (Miro2), C-terminal.
Miro2 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the putative
GTPase domain in the C terminus of Miro proteins. These
atypical Rho GTPases have roles in mitochondrial
homeostasis and apoptosis. Most Rho proteins contain a
lipid modification site at the C-terminus; however, Miro
is one of few Rho subfamilies that lack this feature.
Length = 180
Score = 46.1 bits (110), Expect = 6e-06
Identities = 30/154 (19%), Positives = 65/154 (42%), Gaps = 23/154 (14%)
Query: 247 GDSTVGKTSYVQGFVQNKF-LDNYKNTVGVDF---STKLLSHKKYGGRPVKLQIWDIAGQ 302
G GK++ +Q F+ F + Y T+ + + ++ +KY L + ++
Sbjct: 11 GAKGSGKSALLQAFLGRSFSQNAYSPTIKPRYAVNTVEVPGQEKY------LILREVGED 64
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQW--KHDLDSKCILDNGAMLPCLLLAS 360
+ I ++ D +++D ++ SF + K+ + + +PCL +A+
Sbjct: 65 EEAILLNDAELAACDVACLVYDSSDPNSFSYCAEVYKKYFMLGE--------IPCLFVAA 116
Query: 361 KCDLPDRQVEINEIE--AVCHQYNFMSWIEVSSK 392
K DL D Q + E++ C + + SS+
Sbjct: 117 KADL-DEQQQRAEVQPDEFCRKLGLPPPLHFSSR 149
Score = 28.0 bits (63), Expect = 6.6
Identities = 12/52 (23%), Positives = 24/52 (46%), Gaps = 4/52 (7%)
Query: 108 VLKILVIGDSTVGKTSYVQGFVQNKF-LDNYKNTVGVDF---STKLLSHKKY 155
V V+G GK++ +Q F+ F + Y T+ + + ++ +KY
Sbjct: 4 VFLCFVLGAKGSGKSALLQAFLGRSFSQNAYSPTIKPRYAVNTVEVPGQEKY 55
>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 = 45.9 bits (109), Expect = 7e-06
Identities = 38/126 (30%), Positives = 60/126 (47%), Gaps = 15/126 (11%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
IL+ G GKT+ + + + TVG F+ + +++K VK +WD+ GQ
Sbjct: 12 ILMLGLDAAGKTTILYKLKLGQSVTTIP-TVG--FNVETVTYKN-----VKFNVWDVGGQ 63
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLL--AS 360
D+ + R YY + G I + D +R + Q H I+++ M LLL A+
Sbjct: 64 DKIRPLWRHYYTGTQGLIFVVDSADRDRIDEARQELHR-----IINDREMRDALLLVFAN 118
Query: 361 KCDLPD 366
K DLPD
Sbjct: 119 KQDLPD 124
>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 = 45.1 bits (107), Expect = 1e-05
Identities = 27/104 (25%), Positives = 46/104 (44%), Gaps = 19/104 (18%)
Query: 292 VKLQIWDIAGQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGA 351
+ +WD+ GQD+ + R Y+QN+ G I + D +R+ + + ++ L +
Sbjct: 44 ISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERIGEAREELQRMLNEDELRDAV 103
Query: 352 MLPCLLLASKCDLPDRQVEINEIEAVCHQYNFMSWIEVSSKEHL 395
+ L+ A+K DLP N MS EV+ K L
Sbjct: 104 L---LVFANKQDLP----------------NAMSAAEVTDKLGL 128
>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 = 45.1 bits (107), Expect = 1e-05
Identities = 34/133 (25%), Positives = 69/133 (51%), Gaps = 10/133 (7%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
++I GD GKT + F +++F + Y TV ++ + + G+ V+L +WD AGQ
Sbjct: 4 LVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADI----EVDGKQVELALWDTAGQ 59
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQ-WKHDLDSKCILDNGAMLPCLLLASK 361
+ Y + + Y ++D ++ F + + S E++ + W ++ C +P +L+ +K
Sbjct: 60 EDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFC-----PNVPIILVGNK 114
Query: 362 CDLPDRQVEINEI 374
DL + + I E+
Sbjct: 115 KDLRNDEHTIREL 127
>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 = 44.7 bits (105), Expect = 3e-05
Identities = 32/123 (26%), Positives = 64/123 (52%), Gaps = 10/123 (8%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
+++ GD GKT+ +Q ++ + + Y TV +++ L + ++ V+L +WD +G
Sbjct: 16 LVLVGDVQCGKTAMLQVLAKDCYPETYVPTVFENYTACLETEEQR----VELSLWDTSGS 71
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVV-QWKHDLDSKCILDNGAMLPCLLLASK 361
Y + + Y +SD ++ FD++ + F+S + +W+ + ILD LL+ K
Sbjct: 72 PYYDNVRPLCYSDSDAVLLCFDISRPEIFDSALKKWRAE-----ILDYCPSTRILLIGCK 126
Query: 362 CDL 364
DL
Sbjct: 127 TDL 129
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 41.9 bits (98), Expect = 2e-04
Identities = 33/124 (26%), Positives = 59/124 (47%), Gaps = 11/124 (8%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
IL+ G GKT+ + + + T+G F+ + + +K + +WD+ GQ
Sbjct: 20 ILMVGLDAAGKTTILYKLKLGEIVTTIP-TIG--FNVETVEYKN-----ISFTVWDVGGQ 71
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLASKC 362
D+ + R Y+QN+ G I + D +R + VV+ + +L D L+ A+K
Sbjct: 72 DKIRPLWRHYFQNTQGLIFVVDSNDR---DRVVEARDELHRMLNEDELRDAVLLVFANKQ 128
Query: 363 DLPD 366
DLP+
Sbjct: 129 DLPN 132
>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 = 41.3 bits (97), Expect = 3e-04
Identities = 35/134 (26%), Positives = 67/134 (50%), Gaps = 9/134 (6%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTV-GVDFSTKLLSHKKYGGRPVKLQIWDIAG 301
I++ G + GKT+ + N+F+ NTV F+T+ + + V WD+ G
Sbjct: 6 IVMLGLDSAGKTTVLYRLKFNEFV----NTVPTKGFNTEKIKVSLGNAKGVTFHFWDVGG 61
Query: 302 QDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLASK 361
Q++ + + Y + +DG + + D + + E H + +K + G +P L+LA+K
Sbjct: 62 QEKLRPLWKSYTRCTDGIVFVVDSVDVERMEEAKTELHKI-TKFSENQG--VPVLVLANK 118
Query: 362 CDLPDRQVEINEIE 375
DLP + ++E+E
Sbjct: 119 QDLP-NALPVSEVE 131
>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 = 41.2 bits (97), Expect = 5e-04
Identities = 33/133 (24%), Positives = 57/133 (42%), Gaps = 24/133 (18%)
Query: 241 YPILITGDSTVGKTSYVQGFVQNKFL---------DNYKNTVGVDFSTKLLSHKKYGGRP 291
Y +++ GDS VGK+S F + D Y+ TV VD G
Sbjct: 1 YRVVLLGDSGVGKSSLANIFTAGVYEDSAYEASGDDTYERTVSVD------------GEE 48
Query: 292 VKLQIWDIAGQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGA 351
L ++D Q+ + + Q D +I++ +T+R SFE + + L ++
Sbjct: 49 ATLVVYDHWEQEDGMWLEDSCMQVGDAYVIVYSVTDRSSFEKASELRIQLRRARQAED-- 106
Query: 352 MLPCLLLASKCDL 364
+P +L+ +K DL
Sbjct: 107 -IPIILVGNKSDL 118
>gnl|CDD|206722 cd04157, Arl6, Arf-like 6 (Arl6) GTPase. Arl6 (Arf-like 6) forms a
subfamily of the Arf family of small GTPases. Arl6
expression is limited to the brain and kidney in adult
mice, but it is expressed in the neural plate and
somites during embryogenesis, suggesting a possible role
for Arl6 in early development. Arl6 is also believed to
have a role in cilia or flagella function. Several
proteins have been identified that bind Arl6, including
Arl6 interacting protein (Arl6ip), and SEC61beta, a
subunit of the heterotrimeric conducting channel SEC61p.
Based on Arl6 binding to these effectors, Arl6 is also
proposed to play a role in protein transport, membrane
trafficking, or cell signaling during hematopoietic
maturation. At least three specific homozygous Arl6
mutations in humans have been found to cause
Bardet-Biedl syndrome, a disorder characterized by
obesity, retinopathy, polydactyly, renal and cardiac
malformations, learning disabilities, and
hypogenitalism. Older literature suggests that Arl6 is a
part of the Arl4/Arl7 subfamily, but analyses based on
more recent sequence data place Arl6 in its own
subfamily.
Length = 162
Score = 40.1 bits (94), Expect = 7e-04
Identities = 23/91 (25%), Positives = 43/91 (47%), Gaps = 9/91 (9%)
Query: 292 VKLQIWDIAGQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDN-- 349
+ +D++GQ +Y + YY+N G I + D ++R K +L+ +L++
Sbjct: 45 LSFTAFDMSGQGKYRGLWEHYYKNIQGIIFVIDSSDRLRMVVA---KDELEL--LLNHPD 99
Query: 350 --GAMLPCLLLASKCDLPDRQVEINEIEAVC 378
+P L A+K DLPD + + +C
Sbjct: 100 IKHRRIPILFYANKMDLPDALTAVKITQLLC 130
>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 = 40.1 bits (94), Expect = 7e-04
Identities = 35/124 (28%), Positives = 55/124 (44%), Gaps = 11/124 (8%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
IL+ G GKT+ + + + + T+ + K KL +WDI GQ
Sbjct: 18 ILLLGLDNAGKTT-----ILKQLASEDISHI---TPTQGFNIKNVQADGFKLNVWDIGGQ 69
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLASKC 362
+ R Y++N+D I + D +RK FE Q +L + L A +P L+ A+K
Sbjct: 70 RKIRPYWRNYFENTDVLIYVIDSADRKRFEEAGQELVELLEEEKL---AGVPVLVFANKQ 126
Query: 363 DLPD 366
DL
Sbjct: 127 DLLT 130
>gnl|CDD|133353 cd04153, Arl5_Arl8, Arf-like 5 (Arl5) and 8 (Arl8) GTPases.
Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like
Arl4 and Arl7, are localized to the nucleus and
nucleolus. Arl5 is developmentally regulated during
embryogenesis in mice. Human Arl5 interacts with the
heterochromatin protein 1-alpha (HP1alpha), a nonhistone
chromosomal protein that is associated with
heterochromatin and telomeres, and prevents telomere
fusion. Arl5 may also play a role in embryonic nuclear
dynamics and/or signaling cascades. Arl8 was identified
from a fetal cartilage cDNA library. It is found in
brain, heart, lung, cartilage, and kidney. No function
has been assigned for Arl8 to date.
Length = 174
Score = 39.3 bits (92), Expect = 0.001
Identities = 32/135 (23%), Positives = 61/135 (45%), Gaps = 13/135 (9%)
Query: 241 YPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIA 300
Y ++I G GKT+ + F+ + + T+G + ++ + ++ +WDI
Sbjct: 16 YKVIIVGLDNAGKTTILYQFLLGEVVHT-SPTIGSN-------VEEIVYKNIRFLMWDIG 67
Query: 301 GQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLAS 360
GQ+ YY N+D I++ D T+R+ + + + + L + L+LA+
Sbjct: 68 GQESLRSSWNTYYTNTDAVILVIDSTDRERLPLTKEELYKMLAHEDLRKAVL---LVLAN 124
Query: 361 KCDLPDRQ--VEINE 373
K DL EI+E
Sbjct: 125 KQDLKGAMTPAEISE 139
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 39.4 bits (92), Expect = 0.002
Identities = 26/138 (18%), Positives = 51/138 (36%), Gaps = 25/138 (18%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFL--------DNYK----NTVGVDFSTKLLSHKKYGGR 290
I++ G GKT++V+ + + K TV +DF S +
Sbjct: 13 IVVIGPVGAGKTTFVRALSDKPLVITEADASSVSGKGKRPTTVAMDF----GSIELDEDT 68
Query: 291 PVKLQIWDIAGQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNG 350
+ ++ GQ+R+ M + + + G I++ D + +F + I
Sbjct: 69 --GVHLFGTPGQERFKFMWEILSRGAVGAIVLVDSSRPITFHAEEIIDFLTSRNPI---- 122
Query: 351 AMLPCLLLASKCDLPDRQ 368
P ++ +K DL D
Sbjct: 123 ---PVVVAINKQDLFDAL 137
>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 = 39.2 bits (92), Expect = 0.002
Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 5/76 (6%)
Query: 292 VKLQIWDIAGQDRYICMSRVYYQNSDGCIIMFDLTNRKSF-ESVVQWKHDLDSKCILDNG 350
VK +D+ G ++ + + Y+ DG + + D + + F ES K +LDS +
Sbjct: 63 VKFTTFDLGGHEQARRVWKDYFPEVDGIVFLVDAADPERFQES----KEELDSLLNDEEL 118
Query: 351 AMLPCLLLASKCDLPD 366
A +P L+L +K D P
Sbjct: 119 ANVPILILGNKIDKPG 134
>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 = 38.2 bits (89), Expect = 0.002
Identities = 34/132 (25%), Positives = 57/132 (43%), Gaps = 27/132 (20%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVG--------VDFSTKLLSHKKYGGRPVKL 294
ILI G GKT+ + Y+ VG + F+ + +++K +K
Sbjct: 2 ILILGLDGAGKTTIL-----------YRLQVGEVVTTIPTIGFNVETVTYKN-----LKF 45
Query: 295 QIWDIAGQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLP 354
Q+WD+ GQ R YY N+D I + D T+R + + K +L + +
Sbjct: 46 QVWDLGGQTSIRPYWRCYYSNTDAIIYVVDSTDR---DRLGISKSELHAMLEEEELKDAV 102
Query: 355 CLLLASKCDLPD 366
L+ A+K D+P
Sbjct: 103 LLVFANKQDMPG 114
>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 = 37.8 bits (88), Expect = 0.003
Identities = 30/125 (24%), Positives = 51/125 (40%), Gaps = 12/125 (9%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
IL+ G GKTS + + L++ T G F++ + + +++ +I G
Sbjct: 2 ILVLGLDGAGKTSLLHSLSSERSLESVVPTTG--FNSVAIPTQDA-----IMELLEIGGS 54
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCLLLASKC 362
+ Y S G I + D + + Q H L L + LP ++LA+K
Sbjct: 55 QNLRKYWKRYLSGSQGLIFVVDSADSERLPLARQELHQL-----LQHPPDLPLVVLANKQ 109
Query: 363 DLPDR 367
DLP
Sbjct: 110 DLPAA 114
>gnl|CDD|133303 cd04103, Centaurin_gamma, Centaurin gamma (CENTG) GTPase. The
centaurins (alpha, beta, gamma, and delta) are large,
multi-domain proteins that all contain an ArfGAP domain
and ankyrin repeats, and in some cases, numerous
additional domains. Centaurin gamma contains an
additional GTPase domain near its N-terminus. The
specific function of this GTPase domain has not been
well characterized, but centaurin gamma 2 (CENTG2) may
play a role in the development of autism. Centaurin
gamma 1 is also called PIKE (phosphatidyl inositol (PI)
3-kinase enhancer) and centaurin gamma 2 is also known
as AGAP (ArfGAP protein with a GTPase-like domain,
ankyrin repeats and a Pleckstrin homology domain) or
GGAP. Three isoforms of PIKE have been identified.
PIKE-S (short) and PIKE-L (long) are brain-specific
isoforms, with PIKE-S restricted to the nucleus and
PIKE-L found in multiple cellular compartments. A third
isoform, PIKE-A was identified in human glioblastoma
brain cancers and has been found in various tissues.
GGAP has been shown to have high GTPase activity due to
a direct intramolecular interaction between the
N-terminal GTPase domain and the C-terminal ArfGAP
domain. In human tissue, AGAP mRNA was detected in
skeletal muscle, kidney, placenta, brain, heart, colon,
and lung. Reduced expression levels were also observed
in the spleen, liver, and small intestine.
Length = 158
Score = 32.9 bits (75), Expect = 0.16
Identities = 27/125 (21%), Positives = 49/125 (39%), Gaps = 29/125 (23%)
Query: 245 ITGDSTVGKTSYVQGFVQNKFL-------DNYKNTVGVDFSTKLLSHKKYGGRP-VKLQI 296
I G+ GK++ V ++ ++ +K V VD + LL + GG P +
Sbjct: 5 IVGNLRSGKSALVHRYLTGSYVQLESPEGGRFKKEVLVDGQSHLLLIRDEGGAPDAQFAG 64
Query: 297 WDIAGQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGAMLPCL 356
W D I +F L + SF++V + H L N + +P +
Sbjct: 65 W------------------VDAVIFVFSLEDEASFQTVYRLYHQL---SSYRNISEIPLI 103
Query: 357 LLASK 361
L+ ++
Sbjct: 104 LVGTQ 108
>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 = 32.3 bits (73), Expect = 0.31
Identities = 31/133 (23%), Positives = 65/133 (48%), Gaps = 14/133 (10%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDFSTKLLSHKKYGGRPVKLQIWDIAGQ 302
++ G GKT+ + Q++F+ T+G F+ + + +K +K IWD+ G+
Sbjct: 2 VVTLGLDGAGKTTILFKLKQDEFMQPIP-TIG--FNVETVEYKN-----LKFTIWDVGGK 53
Query: 303 DRYICMSRVYYQNSDGCIIMFDLTNR-KSFESVVQWKHDLDSKCILDNGAMLPCLLLASK 361
+ + + YY N+ + + D ++R + E+ + L K + D A+L L+ A+K
Sbjct: 54 HKLRPLWKHYYLNTQAVVFVIDSSHRDRVSEAHSELAKLLTEKELRD--ALL--LIFANK 109
Query: 362 CDLPDRQVEINEI 374
D+ + + E+
Sbjct: 110 QDV-AGALSVEEM 121
>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 = 31.9 bits (73), Expect = 0.31
Identities = 11/28 (39%), Positives = 19/28 (67%)
Query: 109 LKILVIGDSTVGKTSYVQGFVQNKFLDN 136
++I++IGD VGK+S + V +F +N
Sbjct: 3 VRIVLIGDEGVGKSSLIMSLVSEEFPEN 30
Score = 27.7 bits (62), Expect = 8.1
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 173 ILITGDSTVGKTSYVQGFVQNKFLDN 198
I++ GD VGK+S + V +F +N
Sbjct: 5 IVLIGDEGVGKSSLIMSLVSEEFPEN 30
Score = 27.7 bits (62), Expect = 8.1
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 243 ILITGDSTVGKTSYVQGFVQNKFLDN 268
I++ GD VGK+S + V +F +N
Sbjct: 5 IVLIGDEGVGKSSLIMSLVSEEFPEN 30
>gnl|CDD|241257 cd01223, PH_Vav, Vav pleckstrin homology (PH) domain. Vav acts as
a guanosine nucleotide exchange factor (GEF) for Rho/Rac
proteins. They control processes including T cell
activation, phagocytosis, and migration of cells. The
Vav subgroup of Dbl GEFs consists of three family
members (Vav1, Vav2, and Vav3) in mammals. Vav1 is
preferentially expressed in the hematopoietic system,
while Vav2 and Vav3 are described by broader expression
patterns. Mammalian Vav proteins consist of a calponin
homology (CH) domain, an acidic region, a catalytic Dbl
homology (DH) domain, a PH domain, a zinc finger
cysteine rich domain (C1/CRD), and an SH2 domain,
flanked by two SH3 domains. In invertebrates such as
Drosophila and C. elegans, Vav is missing the N-terminal
SH3 domain. The DH domain is involved in RhoGTPase
recognition and selectivity and stimulates the
reorganization of the switch regions for GDP/GTP
exchange. The PH domain is implicated in directing
membrane localization, allosteric regulation of guanine
nucleotide exchange activity, and as a phospholipid-
dependent regulator of GEF activity. Vavs bind
RhoGTPases including Rac1, RhoA, RhoG, and Cdc42, while
other members of the GEF family are specific for a
single RhoGTPase. This promiscuity is thought to be a
result of its CRD. PH domains have diverse functions,
but in general are involved in targeting proteins to the
appropriate cellular location or in the interaction with
a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH domains
bind phosphoinositide phosphates (PIPs) with high
affinity and specificity. PH domains are distinguished
from other PIP-binding domains by their specific
high-affinity binding to PIPs with two vicinal phosphate
groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3
which results in targeting some PH domain proteins to
the plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.polarized. PH domains also have
diverse functions. They are often involved in targeting
proteins to the plasma membrane, but only a few (less
than 10%) display strong specificity in binding inositol
phosphates. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinases, tyrosine kinases,
regulators of G-proteins, endocytotic GTPases, adaptors,
cytoskeletal associated molecules, and in lipid
associated enzymes.
Length = 127
Score = 31.1 bits (71), Expect = 0.44
Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 3/51 (5%)
Query: 403 FLVDR--IICSKRMEEEAVERKSSIRLSEETLRDDQPKKLVPADKVSTYCW 451
FL D+ ++C KR+ + E K I LSE + DD ++ + DK +Y +
Sbjct: 41 FLFDKVLLVC-KRLRGDQYEYKEIINLSEYKIEDDPSRRTLKRDKRWSYQF 90
>gnl|CDD|220193 pfam09346, SMI1_KNR4, SMI1 / KNR4 family (SUKH-1). Proteins in
this family are involved in the regulation of
1,3-beta-glucan synthase activity and cell-wall
formation. Genome contextual information showed that
SMI1 are primary immunity proteins in bacterial toxin
systems.
Length = 121
Score = 30.1 bits (68), Expect = 0.81
Identities = 8/32 (25%), Positives = 13/32 (40%)
Query: 313 YQNSDGCIIMFDLTNRKSFESVVQWKHDLDSK 344
+ G + DL++ V W H+ D K
Sbjct: 77 ADDGGGNYLCLDLSDGPEGGEVYFWDHEDDEK 108
>gnl|CDD|214361 CHL00095, clpC, Clp protease ATP binding subunit.
Length = 821
Score = 32.0 bits (73), Expect = 0.89
Identities = 25/79 (31%), Positives = 38/79 (48%), Gaps = 21/79 (26%)
Query: 95 VIGFEPRPSDAETVLKIL---------VIGDSTVGKTSYVQGFVQ---NK----FLDNYK 138
VIG R + E V++IL +IG+ VGKT+ +G Q N+ L++ K
Sbjct: 181 VIG---REKEIERVIQILGRRTKNNPILIGEPGVGKTAIAEGLAQRIVNRDVPDILED-K 236
Query: 139 NTVGVDFSTKLLSHKKYGG 157
+ +D LL+ KY G
Sbjct: 237 LVITLDIGL-LLAGTKYRG 254
Score = 30.0 bits (68), Expect = 3.3
Identities = 20/55 (36%), Positives = 29/55 (52%), Gaps = 10/55 (18%)
Query: 242 PILITGDSTVGKTSYVQGFVQ---NK----FLDNYKNTVGVDFSTKLLSHKKYGG 289
PILI G+ VGKT+ +G Q N+ L++ K + +D LL+ KY G
Sbjct: 203 PILI-GEPGVGKTAIAEGLAQRIVNRDVPDILED-KLVITLDIGL-LLAGTKYRG 254
>gnl|CDD|223718 COG0645, COG0645, Predicted kinase [General function prediction
only].
Length = 170
Score = 30.5 bits (69), Expect = 0.96
Identities = 11/51 (21%), Positives = 21/51 (41%), Gaps = 2/51 (3%)
Query: 73 KHINALPARELCKSNSPSPRASVIGFEPRPSDAETVLK--ILVIGDSTVGK 121
K + +P + SP A+ ++ AE +L V+ D+T +
Sbjct: 37 KRLFGVPEETRGPAGLYSPAATAAVYDELLGRAELLLSSGHSVVLDATFDR 87
>gnl|CDD|181459 PRK08533, PRK08533, flagellar accessory protein FlaH; Reviewed.
Length = 230
Score = 30.8 bits (70), Expect = 1.1
Identities = 21/56 (37%), Positives = 29/56 (51%), Gaps = 14/56 (25%)
Query: 152 HKKYGGR-PYGTFSPIQTPSYLILITGDSTVGKTSYVQ----GFVQNKFLDNYKNT 202
HK+ GG P G+ LILI GD + GK+ Q GF+QN + +Y +T
Sbjct: 14 HKRLGGGIPAGS---------LILIEGDESTGKSILSQRLAYGFLQNGYSVSYVST 60
>gnl|CDD|197556 smart00178, SAR, Sar1p-like members of the Ras-family of small
GTPases. Yeast SAR1 is an essential gene required for
transport of secretory proteins from the endoplasmic
reticulum to the Golgi apparatus.
Length = 184
Score = 30.7 bits (69), Expect = 1.2
Identities = 20/92 (21%), Positives = 40/92 (43%), Gaps = 4/92 (4%)
Query: 292 VKLQIWDIAGQDRYICMSRVYYQNSDGCIIMFDLTNRKSFESVVQWKHDLDSKCILDNGA 351
+K +D+ G + + + Y+ +G + + D + E + K +LD+ + A
Sbjct: 61 IKFTTFDLGGHQQARRLWKDYFPEVNGIVYLVDAYD---KERFAESKRELDALLSDEELA 117
Query: 352 MLPCLLLASKCDLPDRQVEINEIEAVCHQYNF 383
+P L+L +K D P E +E+ N
Sbjct: 118 TVPFLILGNKIDAPYAASE-DELRYALGLTNT 148
>gnl|CDD|177060 CHL00138, rps5, ribosomal protein S5; Validated.
Length = 143
Score = 29.2 bits (66), Expect = 2.6
Identities = 15/53 (28%), Positives = 22/53 (41%), Gaps = 7/53 (13%)
Query: 111 ILVIGDST------VGKTSYVQGFVQNKFLDNYKNTVGVD-FSTKLLSHKKYG 156
I+VIG+ VGK VQ V+ D KN + + + + H G
Sbjct: 49 IVVIGNENGWVGVGVGKADDVQNAVKKAVTDAKKNLITIPLTKSNSIPHNITG 101
>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 = 29.6 bits (66), Expect = 3.0
Identities = 35/141 (24%), Positives = 53/141 (37%), Gaps = 26/141 (18%)
Query: 240 TYPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVG------------VDFSTKLLSHKKY 287
T ++ GD+ VGKT + NK L Y+ V S
Sbjct: 2 TIKCVVVGDNAVGKTRLICARACNKTLTQYQLLATHVPTVWAIDQYRVCQEVLERSRDVV 61
Query: 288 GGRPVKLQIWDIAG---QDRYICMSRVYYQNSDGCIIMFDLTNRKSFESV-VQWKHDLDS 343
G V L++WD G +DR R Y SD ++ F + + S +V W ++
Sbjct: 62 DGVSVSLRLWDTFGDHDKDR-----RFAYGRSDVVLLCFSIASPNSLRNVKTMWYPEIRH 116
Query: 344 KCILDNGAMLPCLLLASKCDL 364
C +P +L+ K DL
Sbjct: 117 FC-----PRVPVILVGCKLDL 132
>gnl|CDD|152459 pfam12024, DUF3512, Domain of unknown function (DUF3512). This
presumed domain is functionally uncharacterized. This
domain is found in eukaryotes. This domain is typically
between 231 to 249 amino acids in length. This domain is
found associated with pfam00439.
Length = 245
Score = 29.7 bits (67), Expect = 3.1
Identities = 30/105 (28%), Positives = 44/105 (41%), Gaps = 31/105 (29%)
Query: 93 ASVIGFEPRPSDAETVLKILVIGD--------------STVGK----TSYVQGFVQNKFL 134
S IGF R SD T L +L D S VGK T+ +QGF +++
Sbjct: 52 NSKIGFLRRKSDGTTTLNVLNPVDPEAGEEGTHPVDLGSLVGKLQTGTTTLQGFKEDR-- 109
Query: 135 DNYKNTVGVDFSTKLLSHKKYGGRPYGTFSPIQTPSYLILITGDS 179
+N V +S+ YG PY +F+P ++ L +S
Sbjct: 110 ---RNKV------TPVSYLNYG--PYSSFAPTYDSTFANLSKEES 143
>gnl|CDD|219871 pfam08504, RunxI, Runx inhibition domain. This domain lies to
the C-terminus of Runx-related transcription factors
and homologous proteins (AML, CBF-alpha, PEBP2). Its
function might be to interact with functional
cofactors.
Length = 102
Score = 28.3 bits (63), Expect = 3.1
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 2/44 (4%)
Query: 12 TPPLLLSPAESESTRSKKLLEPLNTQAVDLAEDAGDGSKSNSPS 55
+P +L P + ST S + L Q+ E DGS SNSP+
Sbjct: 45 SPTRMLPPCTNASTGSSLMNPNLPNQSDGGVE--ADGSHSNSPT 86
>gnl|CDD|206683 cd01896, DRG, Developmentally Regulated GTP-binding protein (DRG).
The developmentally regulated GTP-binding protein (DRG)
subfamily is an uncharacterized member of the Obg
family, an evolutionary branch of GTPase superfamily
proteins. GTPases act as molecular switches regulating
diverse cellular processes. DRG2 and DRG1 comprise the
DRG subfamily in eukaryotes. In view of their widespread
expression in various tissues and high conservation
among distantly related species in eukaryotes and
archaea, DRG proteins may regulate fundamental cellular
processes. It is proposed that the DRG subfamily
proteins play their physiological roles through RNA
binding.
Length = 233
Score = 29.4 bits (67), Expect = 3.3
Identities = 16/64 (25%), Positives = 33/64 (51%), Gaps = 11/64 (17%)
Query: 345 CILDNGAMLPCLLLASKCDLPDRQVEINEIEAVCHQYNFMSWIEVSSKEHLMIEDSMNFL 404
I N +PCL + +K DL + I E++ + N + +S+++ L +++ L
Sbjct: 169 VIEGNRVYIPCLYVYNKIDL----ISIEELDRLARIPNS---VVISAEKDLNLDE----L 217
Query: 405 VDRI 408
++RI
Sbjct: 218 LERI 221
>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 = 29.1 bits (65), Expect = 3.4
Identities = 26/107 (24%), Positives = 41/107 (38%), Gaps = 21/107 (19%)
Query: 241 YPILITGDSTVGKTSYVQGFVQNKFLDNYKNTVGVDF--STKLLSHKKYGGRPVKLQIWD 298
+ + G VGKT+ V+ F+ +F + Y T +LS GR L I D
Sbjct: 1 VRVAVLGAPGVGKTAIVRQFLAQEFPEEYIPTEHRRLYRPAVVLS-----GRVYDLHILD 55
Query: 299 IAGQDRY-----------ICMSRVYYQNSDGCIIMFDLTNRKSFESV 334
+ RY +NS I+++D+ + SF V
Sbjct: 56 VPNMQRYPGTAGQEWMDPRFRG---LRNSRAFILVYDICSPDSFHYV 99
>gnl|CDD|225401 COG2845, COG2845, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 354
Score = 29.4 bits (66), Expect = 4.1
Identities = 13/57 (22%), Positives = 23/57 (40%), Gaps = 9/57 (15%)
Query: 88 SPSPRASVIGFEPRPSDAE---TVLKILVIGDSTVGKTSYVQGFVQNKFLDNYKNTV 141
+P P A+ EP + A K+LV+GDS + + + + T+
Sbjct: 96 APRPGATA---EPATTIAAKSRDADKVLVVGDSLMQ---GLAEGLDKALATSPGITI 146
>gnl|CDD|129254 TIGR00150, T6A_YjeE, tRNA threonylcarbamoyl adenosine modification
protein YjeE. This protein family belongs to a
four-gene system responsible for the threonylcarbamoyl
adenosine (t6A) tRNA modification. Members of this
family have a conserved nucleotide-binding motif
GXXGXGKT and a nucleotide-binding fold. Member protein
YjeE of Haemophilus influenzae (HI0065) was shown to
have (weak) ATPase activity [Protein synthesis, tRNA and
rRNA base modification].
Length = 133
Score = 27.8 bits (62), Expect = 5.5
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 172 LILITGDSTVGKTSYVQGFVQN 193
++L+ GD GKT+ VQG +Q
Sbjct: 24 VVLLKGDLGAGKTTLVQGLLQG 45
Score = 27.8 bits (62), Expect = 6.0
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 243 ILITGDSTVGKTSYVQGFVQN 263
+L+ GD GKT+ VQG +Q
Sbjct: 25 VLLKGDLGAGKTTLVQGLLQG 45
>gnl|CDD|216999 pfam02367, UPF0079, Uncharacterized P-loop hydrolase UPF0079. This
uncharacterized family contains a P-loop.
Length = 123
Score = 27.6 bits (62), Expect = 6.1
Identities = 9/26 (34%), Positives = 16/26 (61%)
Query: 168 TPSYLILITGDSTVGKTSYVQGFVQN 193
++L++GD GKT++V+G Q
Sbjct: 13 KAGDVVLLSGDLGAGKTTFVRGLAQG 38
>gnl|CDD|176254 cd08294, leukotriene_B4_DH_like, 13-PGR is a bifunctional enzyme
with delta-13 15-prostaglandin reductase and leukotriene
B4 12 hydroxydehydrogenase activity. Prostaglandins and
related eicosanoids are metabolized by the oxidation of
the 15(S)-hydroxyl group of the NAD+-dependent (type I
15-PGDH) 15-prostaglandin dehydrogenase (15-PGDH)
followed by reduction by NADPH/NADH-dependent (type II
15-PGDH) delta-13 15-prostaglandin reductase (13-PGR) to
15-keto- 13,14,-dihydroprostaglandins. 13-PGR is a
bifunctional enzyme, since it also has leukotriene B(4)
12-hydroxydehydrogenase activity. These 15-PGDH and
related enzymes are members of the medium chain
dehydrogenase/reductase family. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES.
Length = 329
Score = 28.8 bits (65), Expect = 6.2
Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 4/26 (15%)
Query: 133 FLDNYKNTVGVDFSTKLLSHKKYGGR 158
+ DN VG +FS+ +LSH GR
Sbjct: 215 YFDN----VGGEFSSTVLSHMNDFGR 236
Score = 28.8 bits (65), Expect = 6.2
Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 4/26 (15%)
Query: 195 FLDNYKNTVGVDFSTKLLSHKKYGGR 220
+ DN VG +FS+ +LSH GR
Sbjct: 215 YFDN----VGGEFSSTVLSHMNDFGR 236
Score = 28.8 bits (65), Expect = 6.2
Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 4/26 (15%)
Query: 265 FLDNYKNTVGVDFSTKLLSHKKYGGR 290
+ DN VG +FS+ +LSH GR
Sbjct: 215 YFDN----VGGEFSSTVLSHMNDFGR 236
>gnl|CDD|226473 COG3964, COG3964, Predicted amidohydrolase [General function
prediction only].
Length = 386
Score = 28.6 bits (64), Expect = 6.5
Identities = 11/46 (23%), Positives = 15/46 (32%), Gaps = 6/46 (13%)
Query: 1 GREAPGTVTNIT------PPLLLSPAESESTRSKKLLEPLNTQAVD 40
G APG +IT + A +S + LL P
Sbjct: 323 GTLAPGAFADITVFKLKNRHVEFVDAHGDSLTATHLLVPQMAIKAG 368
>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA. [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 730
Score = 28.8 bits (65), Expect = 7.0
Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 8/54 (14%)
Query: 242 PILITGDSTVGKTSYVQGF----VQNKFLDNYKNTV--GVDFSTKLLSHKKYGG 289
P+L+ G+ VGKT+ V+G + K + KN +D T LL+ KY G
Sbjct: 205 PLLV-GEPGVGKTAIVEGLALRIAEGKVPERLKNAKIYSLDMGT-LLAGTKYRG 256
>gnl|CDD|220888 pfam10846, DUF2722, Protein of unknown function (DUF2722). This
eukaryotic family of proteins has no known function.
Length = 373
Score = 28.3 bits (63), Expect = 9.2
Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 4/46 (8%)
Query: 62 SRKNCAETYAHKHINALPARELCK----SNSPSPRASVIGFEPRPS 103
R+ + H+ +LP+ SN P P SV+ F+P P+
Sbjct: 205 LRRKKFGSQLHQRNMSLPSNTPTSGNTNSNIPKPATSVLNFKPSPA 250
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
0.317 0.134 0.399
Gapped
Lambda K H
0.267 0.0585 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,283,235
Number of extensions: 2101997
Number of successful extensions: 2454
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2270
Number of HSP's successfully gapped: 302
Length of query: 452
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 352
Effective length of database: 6,502,202
Effective search space: 2288775104
Effective search space used: 2288775104
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 61 (27.6 bits)