RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1524
(592 letters)
>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 = 176 bits (448), Expect = 6e-52
Identities = 75/159 (47%), Positives = 89/159 (55%), Gaps = 32/159 (20%)
Query: 172 TCSTNEFPAMRALSISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNK 231
T + FPAMR LSI + DAF LVY++DDP SFEE++ +R+ I E K VPIVVVGNK
Sbjct: 54 TSGSYSFPAMRKLSIQNGDAFALVYSVDDPESFEEVKRLREEILEVKEDKFVPIVVVGNK 113
Query: 232 SDLADENRQVDLTGGPFQTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENGFVEA 291
D E QV S V++DW NGFVEA
Sbjct: 114 IDSLAER-------------------------------QVEAADALSTVELDWNNGFVEA 142
Query: 292 SAKDNTNITQVFKELLVQAKVKYNLSPALRRRRRQSLPP 330
SAKDN N+T+VFKELL QA + LSPAL RRRR+S P
Sbjct: 143 SAKDNENVTEVFKELLQQANLPSWLSPAL-RRRRESAPS 180
Score = 95.7 bits (238), Expect = 9e-23
Identities = 38/69 (55%), Positives = 46/69 (66%), Gaps = 2/69 (2%)
Query: 338 VPYDTTESVVQVDWENGFVEASAKDNTNITQVFKELLVQAKVKYNLSPALRRRRRQSLPP 397
V S V++DW NGFVEASAKDN N+T+VFKELL QA + LSPAL RRRR+S P
Sbjct: 122 VEAADALSTVELDWNNGFVEASAKDNENVTEVFKELLQQANLPSWLSPAL-RRRRESAPS 180
Query: 398 VQHSPNPSL 406
+ P +
Sbjct: 181 -EIQRRPPM 188
Score = 87.6 bits (217), Expect = 8e-20
Identities = 30/59 (50%), Positives = 46/59 (77%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHLKLDILDTSGEQS 122
++V MG VGK+++I RFLY+TF PK++RT+EE+H +++ + GV + +DILDTSG S
Sbjct: 1 RLVFMGAAGVGKTALIQRFLYDTFEPKHRRTVEELHSKEYEVAGVKVTIDILDTSGSYS 59
>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 = 150 bits (381), Expect = 9e-43
Identities = 71/247 (28%), Positives = 95/247 (38%), Gaps = 87/247 (35%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHLKLDILDTSGEQSG 123
K+VV+G VGKS++ RF+ F +Y TIE+ + + ++G LDI
Sbjct: 1 KLVVLGAGGVGKSALTIRFVSGEFVEEYDPTIEDSYRKQIVVDGETYTLDI--------- 51
Query: 124 KGLKCGAVLWGPKKWGLDKVCLRRALNQRPMAYKTDVQLPSKLTSLAMTCSTNEFPAMRA 183
LD T EF AMR
Sbjct: 52 ----------------LD------------------------------TAGQEEFSAMRD 65
Query: 184 LSISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADENRQVDL 243
I + D FILVY+I SFEEI+ IR+ I K VPIV+VGNK DL +E RQV
Sbjct: 66 QYIRNGDGFILVYSITSRESFEEIKNIREQILRVKDKEDVPIVLVGNKCDLENE-RQV-- 122
Query: 244 TGGPFQTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENGFVEASAKDNTNITQVF 303
+ G A + W F+E SAK N NI ++F
Sbjct: 123 ------STEEGE---ALAEE--------------------WGCPFLETSAKTNINIDELF 153
Query: 304 KELLVQA 310
L+ +
Sbjct: 154 NTLVREI 160
Score = 37.5 bits (88), Expect = 0.006
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 351 WENGFVEASAKDNTNITQVFKELLVQA 377
W F+E SAK N NI ++F L+ +
Sbjct: 134 WGCPFLETSAKTNINIDELFNTLVREI 160
>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 = 126 bits (320), Expect = 4e-34
Identities = 64/251 (25%), Positives = 96/251 (38%), Gaps = 87/251 (34%)
Query: 63 HKVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHLKLDILDTSGEQS 122
+K+VV+GG VGKS++ +F+ F +Y TIE+ + + ++G LDI
Sbjct: 3 YKLVVLGGGGVGKSALTIQFVQGHFVDEYDPTIEDSYRKQIEIDGEVCLLDI-------- 54
Query: 123 GKGLKCGAVLWGPKKWGLDKVCLRRALNQRPMAYKTDVQLPSKLTSLAMTCSTNEFPAMR 182
LD T EF AMR
Sbjct: 55 -----------------LD------------------------------TAGQEEFSAMR 67
Query: 183 ALSISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADENRQVD 242
+ + + F+LVY+I D SFEEI R+ I K VPIV+VGNK DL +E R V
Sbjct: 68 DQYMRTGEGFLLVYSITDRQSFEEIAKFREQILRVKDRDDVPIVLVGNKCDLENE-RVVS 126
Query: 243 LTGGPFQTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENGFVEASAKDNTNITQV 302
G +++ W F+E SAK+ N+ +
Sbjct: 127 TEEG---------------KELAR----------------QWGCPFLETSAKERINVDEA 155
Query: 303 FKELLVQAKVK 313
F +L+ + +
Sbjct: 156 FYDLVREIRKS 166
Score = 37.2 bits (87), Expect = 0.009
Identities = 9/31 (29%), Positives = 17/31 (54%)
Query: 350 DWENGFVEASAKDNTNITQVFKELLVQAKVK 380
W F+E SAK+ N+ + F +L+ + +
Sbjct: 136 QWGCPFLETSAKERINVDEAFYDLVREIRKS 166
>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 = 125 bits (316), Expect = 1e-33
Identities = 63/249 (25%), Positives = 94/249 (37%), Gaps = 87/249 (34%)
Query: 63 HKVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHLKLDILDTSGEQS 122
+K+VV+G VGKS++ +F+ F Y TIE+ + + ++G LDI
Sbjct: 1 YKLVVLGSGGVGKSALTIQFIQGHFVDDYDPTIEDSYRKQIEIDGEVCLLDI-------- 52
Query: 123 GKGLKCGAVLWGPKKWGLDKVCLRRALNQRPMAYKTDVQLPSKLTSLAMTCSTNEFPAMR 182
LD T EF AMR
Sbjct: 53 -----------------LD------------------------------TAGQEEFSAMR 65
Query: 183 ALSISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADENRQVD 242
+ + + F+LVY+I D SFEEI+ R+ I K VPIV+VGNK DL E R V
Sbjct: 66 DQYMRTGEGFLLVYSITDRQSFEEIKKFREQILRVKDRDDVPIVLVGNKCDLESE-RVVS 124
Query: 243 LTGGPFQTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENGFVEASAKDNTNITQV 302
G + + + W F+E SAK+ N+ +
Sbjct: 125 TEEG------------------------------KELAR-QWGCPFLETSAKERVNVDEA 153
Query: 303 FKELLVQAK 311
F +L+ + +
Sbjct: 154 FYDLVREIR 162
Score = 35.6 bits (83), Expect = 0.029
Identities = 9/29 (31%), Positives = 17/29 (58%)
Query: 350 DWENGFVEASAKDNTNITQVFKELLVQAK 378
W F+E SAK+ N+ + F +L+ + +
Sbjct: 134 QWGCPFLETSAKERVNVDEAFYDLVREIR 162
>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 = 117 bits (296), Expect = 6e-30
Identities = 72/269 (26%), Positives = 112/269 (41%), Gaps = 94/269 (34%)
Query: 63 HKVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHLKLDILDTSGEQS 122
+++VV+G KVGK++I+ RFL F +Y TIE+ H
Sbjct: 1 YRMVVLGASKVGKTAIVSRFLGGRFEEQYTPTIEDFH----------------------- 37
Query: 123 GKGLKCGAVLWGPKKWGLDKVCLRRALNQRPMAYKTDVQLPSKLTSLAMTCSTNEFPAMR 182
R+ + R Y+ D+ S + FPAMR
Sbjct: 38 -----------------------RKLYSIRGEVYQLDILDTSG---------NHPFPAMR 65
Query: 183 ALSISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTA--------VPIVVVGNKSDL 234
LSI + D FILV+++D+ SFEE+ +R+ I ETK+ +P+V+ GNK+D
Sbjct: 66 RLSILTGDVFILVFSLDNRESFEEVCRLREQILETKSCLKNKTKENVKIPMVICGNKADR 125
Query: 235 ADENRQVDLTGGPFQTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENGFVEASAK 294
D R+V + + G D CA + E SAK
Sbjct: 126 -DFPREVQRD--EVEQLVGG--DENCA--------------------------YFEVSAK 154
Query: 295 DNTNITQVFKELLVQAKVKYNLSPALRRR 323
N+N+ ++F+ L AK+ +SP+L R+
Sbjct: 155 KNSNLDEMFRALFSLAKLPNEMSPSLHRK 183
Score = 42.8 bits (101), Expect = 2e-04
Identities = 20/57 (35%), Positives = 31/57 (54%)
Query: 334 SPNPVPYDTTESVVQVDWENGFVEASAKDNTNITQVFKELLVQAKVKYNLSPALRRR 390
P V D E +V D + E SAK N+N+ ++F+ L AK+ +SP+L R+
Sbjct: 127 FPREVQRDEVEQLVGGDENCAYFEVSAKKNSNLDEMFRALFSLAKLPNEMSPSLHRK 183
>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 = 114 bits (289), Expect = 6e-30
Identities = 64/247 (25%), Positives = 95/247 (38%), Gaps = 93/247 (37%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTI-EEMHHEDFSMNGVHLKLDILDTSGEQS 122
K+V++G VGKSS++ RF N F +Y TI + + + ++G +KL I DT+G++
Sbjct: 1 KLVLVGDGGVGKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAGQER 60
Query: 123 GKGLKCGAVLWGPKKWGLDKVCLRRALNQRPMAYKTDVQLPSKLTSLAMTCSTNEFPAMR 182
+ L RP+ Y+
Sbjct: 61 FRAL-------------------------RPLYYRG------------------------ 71
Query: 183 ALSISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADENRQVD 242
A F+LVY I +SFE ++ + I A VPIV+VGNK DL D+ R V
Sbjct: 72 ------AQGFLLVYDITSRDSFENVKKWLEEILRH-ADENVPIVLVGNKCDLEDQ-RVV- 122
Query: 243 LTGGPFQTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENG--FVEASAKDNTNIT 300
+TE + E G F+E SAK N N+
Sbjct: 123 --------------------------------STEEGEALAKELGLPFMETSAKTNENVE 150
Query: 301 QVFKELL 307
+ F+EL
Sbjct: 151 EAFEELA 157
Score = 34.4 bits (80), Expect = 0.064
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 355 FVEASAKDNTNITQVFKELL 374
F+E SAK N N+ + F+EL
Sbjct: 138 FMETSAKTNENVEEAFEELA 157
>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 = 105 bits (263), Expect = 4e-26
Identities = 64/256 (25%), Positives = 97/256 (37%), Gaps = 87/256 (33%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHLKLDILDTSGEQSG 123
K+ V+G VGKSS+ +F+ F Y TIE + + G L+I+DT+
Sbjct: 3 KIAVLGSRSVGKSSLTVQFVEGHFVESYYPTIENTFSKIITYKGQEYHLEIVDTA----- 57
Query: 124 KGLKCGAVLWGPKKWGLDKVCLRRALNQRPMAYKTDVQLPSKLTSLAMTCSTNEFPAMRA 183
G D+ + L Q+ Y +
Sbjct: 58 ---------------GQDEYSI---LPQK---YSIGIH---------------------- 74
Query: 184 LSISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADENRQVDL 243
+ILVY++ SFE +++I D I + +VPIV+VGNKSDL E RQV
Sbjct: 75 -------GYILVYSVTSRKSFEVVKVIYDKILDMLGKESVPIVLVGNKSDLHME-RQVSA 126
Query: 244 TGGPFQTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENGFVEASAKDNTNITQVF 303
G L +S W F+E+SAK+N N+ + F
Sbjct: 127 EEG------KKLAES-------------------------WGAAFLESSAKENENVEEAF 155
Query: 304 KELLVQAKVKYNLSPA 319
+ L+ + + N P
Sbjct: 156 ELLIEEIEKVENPLPP 171
Score = 37.6 bits (88), Expect = 0.007
Identities = 12/36 (33%), Positives = 21/36 (58%)
Query: 351 WENGFVEASAKDNTNITQVFKELLVQAKVKYNLSPA 386
W F+E+SAK+N N+ + F+ L+ + + N P
Sbjct: 136 WGAAFLESSAKENENVEEAFELLIEEIEKVENPLPP 171
>gnl|CDD|190664 pfam03501, S10_plectin, Plectin/S10 domain. This presumed domain
is found at the N-terminus of some isoforms of the
cytoskeletal muscle protein plectin as well as the
ribosomal S10 protein. This domain may be involved in
RNA binding.
Length = 96
Score = 100 bits (251), Expect = 2e-25
Identities = 34/51 (66%), Positives = 43/51 (84%)
Query: 405 SLKSKGWVNEQFAWRHYYWYITNDGIEKLRGVLNIPDEIVPSTLKRQARTT 455
SLKS+G+V EQFAWRHYYWY+TN+GIE LR L++P E+VP+TLK+ AR
Sbjct: 46 SLKSRGYVKEQFAWRHYYWYLTNEGIEYLREYLHLPAEVVPATLKKPARPF 96
>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 = 93.0 bits (231), Expect = 1e-21
Identities = 71/274 (25%), Positives = 105/274 (38%), Gaps = 87/274 (31%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTI-EEMHHEDFSMNGVHLKLDILDTSGEQS 122
+V V+G P VGK++I+ +FL F +Y T ++ ++G L ILD Q
Sbjct: 2 RVAVLGAPGVGKTAIVRQFLAQEFPEEYIPTEHRRLYRPAVVLSGRVYDLHILDVPNMQR 61
Query: 123 GKGLKCGAVLWGPKKWGLDKVCLRRALNQRPMAYKTDVQLPSKLTSLAMTCSTNEFPAMR 182
G ++W R
Sbjct: 62 YPGT-------AGQEW----------------------------------------MDPR 74
Query: 183 ALSISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTA--VPIVVVGNKSDLADENRQ 240
+ ++ AFILVY I P+SF ++L+R I ET+ + PIVVVGNK D
Sbjct: 75 FRGLRNSRAFILVYDICSPDSFHYVKLLRQQILETRPAGNKEPPIVVVGNKRD------- 127
Query: 241 VDLTGGPFQTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENGFVEASAKDNTNIT 300
Q P V + +V+ W+ G++E SAK N +I
Sbjct: 128 --------QQRHRFAPRHVLSV----------------LVRKSWKCGYLECSAKYNWHIL 163
Query: 301 QVFKELLVQAKVK-YNLSPALR-----RRRRQSL 328
+FKELL+ A + + PALR R R S+
Sbjct: 164 LLFKELLISATTRGRSTHPALRLQGALHRERCSI 197
Score = 37.5 bits (87), Expect = 0.009
Identities = 22/56 (39%), Positives = 33/56 (58%), Gaps = 6/56 (10%)
Query: 346 VVQVDWENGFVEASAKDNTNITQVFKELLVQAKVK-YNLSPALR-----RRRRQSL 395
+V+ W+ G++E SAK N +I +FKELL+ A + + PALR R R S+
Sbjct: 142 LVRKSWKCGYLECSAKYNWHILLLFKELLISATTRGRSTHPALRLQGALHRERCSI 197
>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 = 83.7 bits (207), Expect = 8e-19
Identities = 62/250 (24%), Positives = 100/250 (40%), Gaps = 91/250 (36%)
Query: 62 RHKVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHLKLDILDTSGEQ 121
+KVVV+G VGKS++ +F+ TF KY TI EDF
Sbjct: 1 EYKVVVLGSGGVGKSALTVQFVSGTFIEKYDPTI-----EDF------------------ 37
Query: 122 SGKGLKCGAVLWGPKKWGLDKVCLRRALNQRPMAYKTDVQLPSKLTSLAM--TCSTNEFP 179
Y+ ++++ S + L + T T +F
Sbjct: 38 ----------------------------------YRKEIEVDSSPSVLEILDTAGTEQFA 63
Query: 180 AMRALSISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADENR 239
+MR L I + FI+VY++ + +F++I+ +RD I K VPI++VGNK DL E R
Sbjct: 64 SMRDLYIKNGQGFIVVYSLVNQQTFQDIKPMRDQIVRVKGYEKVPIILVGNKVDLESE-R 122
Query: 240 QVDLTGGPFQTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENGFVEASAKDNTNI 299
+V G ++ + +W F+E SAK T +
Sbjct: 123 EVSSAEG------------------------------RALAE-EWGCPFMETSAKSKTMV 151
Query: 300 TQVFKELLVQ 309
++F E++ Q
Sbjct: 152 NELFAEIVRQ 161
Score = 29.4 bits (66), Expect = 3.6
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 351 WENGFVEASAKDNTNITQVFKELLVQ 376
W F+E SAK T + ++F E++ Q
Sbjct: 136 WGCPFMETSAKSKTMVNELFAEIVRQ 161
>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 = 82.1 bits (203), Expect = 3e-18
Identities = 48/157 (30%), Positives = 72/157 (45%), Gaps = 33/157 (21%)
Query: 155 AYKTDVQLPSKLTSLAM--TCSTNEFPAMRALSISSADAFILVYAIDDPNSFEEIRLIRD 212
+Y+ V++ + L + T T +F AMR L I S F+LVY++ S E+ +R+
Sbjct: 37 SYRKQVEIDGRQCDLEILDTAGTEQFTAMRELYIKSGQGFLLVYSVTSEASLNELGELRE 96
Query: 213 HIFETKASTAVPIVVVGNKSDLADENRQVDLTGGPFQTYLSGLPDSVCAHQISGTPDQVP 272
+ K S VP+V+VGNK+DL D+ RQV G +S VP
Sbjct: 97 QVLRIKDSDNVPMVLVGNKADLEDD-RQVSREDG---------------VSLSQQWGNVP 140
Query: 273 YDTTESVVQVDWENGFVEASAKDNTNITQVFKELLVQ 309
F E SA+ TN+ +VF +L+ Q
Sbjct: 141 ---------------FYETSARKRTNVDEVFIDLVRQ 162
Score = 28.2 bits (63), Expect = 7.9
Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 350 DWENG-FVEASAKDNTNITQVFKELLVQ 376
W N F E SA+ TN+ +VF +L+ Q
Sbjct: 135 QWGNVPFYETSARKRTNVDEVFIDLVRQ 162
>gnl|CDD|173331 PTZ00034, PTZ00034, 40S ribosomal protein S10; Provisional.
Length = 124
Score = 79.7 bits (197), Expect = 7e-18
Identities = 33/79 (41%), Positives = 51/79 (64%), Gaps = 3/79 (3%)
Query: 405 SLKSKGWVNEQFAWRHYYWYITNDGIEKLRGVLNIPDEIVPSTLKRQARTTDASKVPRQM 464
SLKS+G V EQFAW+HYY+Y+T++GIE LR L++P ++ P+T K+++ K +
Sbjct: 49 SLKSRGLVKEQFAWQHYYYYLTDEGIEYLRTYLHLPPDVFPATHKKKSVNF-ERKTEEEG 107
Query: 465 TQRPDGGRGADDRMSYRKG 483
++ GGRG Y +G
Sbjct: 108 SRGGRGGRGRGR--GYGRG 124
>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 = 79.9 bits (197), Expect = 2e-17
Identities = 60/250 (24%), Positives = 92/250 (36%), Gaps = 92/250 (36%)
Query: 63 HKVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHLKLDILDTSGEQS 122
+K+VV+G VGKS++ +F+ F KY TI ED
Sbjct: 2 YKLVVLGSGGVGKSALTVQFVQGIFVDKYDPTI-----EDS------------------- 37
Query: 123 GKGLKCGAVLWGPKKWGLDKVCLRRALNQRPMAYKTDVQLPSKLTSLAM--TCSTNEFPA 180
Y+ +++ + L + T T +F A
Sbjct: 38 ---------------------------------YRKQIEVDCQQCMLEILDTAGTEQFTA 64
Query: 181 MRALSISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADENRQ 240
MR L I + F LVY+I SF +++ +R+ I K + VP+++VGNK DL DE R
Sbjct: 65 MRDLYIKNGQGFALVYSITAQQSFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDE-RV 123
Query: 241 VDLTGGPFQTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWEN-GFVEASAKDNTNI 299
V G + W N F+E SAK N+
Sbjct: 124 VSKEEG-------------------------------QNLARQWGNCPFLETSAKSKINV 152
Query: 300 TQVFKELLVQ 309
++F +L+ Q
Sbjct: 153 DEIFYDLVRQ 162
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 77.6 bits (191), Expect = 2e-16
Identities = 64/258 (24%), Positives = 97/258 (37%), Gaps = 88/258 (34%)
Query: 61 TRHKVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHLKLDILDTSGE 120
T +K+VV+GG VGKS++ +F+ N F +Y TIE+ + + ++
Sbjct: 4 TEYKLVVVGGGGVGKSALTIQFIQNHFIDEYDPTIEDSYRKQCVID-------------- 49
Query: 121 QSGKGLKCGAVLWGPKKWGLDKVCLRRALNQRPMAYKTDVQLPSKLTSLAMTCSTNEFPA 180
++ CL L+ T E+ A
Sbjct: 50 --------------------EETCLLDILD---------------------TAGQEEYSA 68
Query: 181 MRALSISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADENRQ 240
MR + + F+ VY+I +SFEEI R+ I K VP+++VGNK DL D RQ
Sbjct: 69 MRDQYMRTGQGFLCVYSITSRSSFEEIASFREQILRVKDKDRVPMILVGNKCDL-DSERQ 127
Query: 241 VDLTGGPFQTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENGFVEASAKDNTNIT 300
V + G Q G P F+E SAK N+
Sbjct: 128 V--STGEGQELAKSF----------GIP-------------------FLETSAKQRVNVD 156
Query: 301 QVFKELLVQAKVKYNLSP 318
+ F EL+ + + KY
Sbjct: 157 EAFYELVREIR-KYLKED 173
>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 = 75.0 bits (185), Expect = 9e-16
Identities = 46/185 (24%), Positives = 75/185 (40%), Gaps = 55/185 (29%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHLKLDILDTSGEQSG 123
K+ V+G VGKS++ RFL F +Y+ +E ++ +++G + L+I DT G+Q
Sbjct: 1 KIAVLGASGVGKSALTVRFLTKRFIGEYEPNLESLYSRQVTIDGEQVSLEIQDTPGQQQN 60
Query: 124 KGLKCGAVLWGPKKWGLDKVCLRRALNQRPMAYKTDVQLPSKLTSLAMTCSTNEFPAMRA 183
+ S
Sbjct: 61 ED----------------------------------------------PESLER------ 68
Query: 184 LSISSADAFILVYAIDDPNSFEEIRLIRDHIFETK-ASTAVPIVVVGNKSDLADENRQVD 242
S+ AD F+LVY+I D +SF+ + + I E K +P+++VGNK+DL +RQV
Sbjct: 69 -SLRWADGFVLVYSITDRSSFDVVSQLLQLIREIKKRDGEIPVILVGNKADL-LHSRQVS 126
Query: 243 LTGGP 247
G
Sbjct: 127 TEEGQ 131
>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 = 74.1 bits (182), Expect = 2e-15
Identities = 46/138 (33%), Positives = 67/138 (48%), Gaps = 34/138 (24%)
Query: 172 TCSTNEFPAMRALSISSADAFILVYAIDDPNSFEEIRLIRDHIFETKAST--AVPIVVVG 229
T +++FPAM+ LSIS AFILVY+I S EE++ I + I E K + +PI++VG
Sbjct: 56 TTGSHQFPAMQRLSISKGHAFILVYSITSKQSLEELKPIYELICEIKGNNLEKIPIMLVG 115
Query: 230 NKSDLADENRQVDLTGGPFQTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENGFV 289
NK D +R+V + G + A W F+
Sbjct: 116 NKCD-ESPSREVSSSEG-----------AALA--------------------RTWNCAFM 143
Query: 290 EASAKDNTNITQVFKELL 307
E SAK N N+ ++F+ELL
Sbjct: 144 ETSAKTNHNVQELFQELL 161
Score = 47.5 bits (113), Expect = 3e-06
Identities = 23/65 (35%), Positives = 35/65 (53%)
Query: 63 HKVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHLKLDILDTSGEQS 122
++VVV G VGKSS++ RF+ TF Y TIE+ + + S + L I DT+G
Sbjct: 2 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCSKSICTLQITDTTGSHQ 61
Query: 123 GKGLK 127
++
Sbjct: 62 FPAMQ 66
Score = 32.5 bits (74), Expect = 0.32
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 351 WENGFVEASAKDNTNITQVFKELL 374
W F+E SAK N N+ ++F+ELL
Sbjct: 138 WNCAFMETSAKTNHNVQELFQELL 161
>gnl|CDD|133375 cd04175, Rap1, Rap1 family GTPase consists of Rap1a and Rap1b
isoforms. The Rap1 subgroup is part of the Rap
subfamily of the Ras family. It can be further divided
into the Rap1a and Rap1b isoforms. In humans, Rap1a and
Rap1b share 95% sequence homology, but are products of
two different genes located on chromosomes 1 and 12,
respectively. Rap1a is sometimes called smg p21 or Krev1
in the older literature. Rap1 proteins are believed to
perform different cellular functions, depending on the
isoform, its subcellular localization, and the effector
proteins it binds. For example, in rat salivary gland,
neutrophils, and platelets, Rap1 localizes to secretory
granules and is believed to regulate exocytosis or the
formation of secretory granules. Rap1 has also been
shown to localize in the Golgi of rat fibroblasts,
zymogen granules, plasma membrane, and the microsomal
membrane of pancreatic acini, as well as in the
endocytic compartment of skeletal muscle cells and
fibroblasts. High expression of Rap1 has been observed
in the nucleus of human oropharyngeal squamous cell
carcinomas (SCCs) and cell lines; interestingly, in the
SCCs, the active GTP-bound form localized to the
nucleus, while the inactive GDP-bound form localized to
the cytoplasm. Rap1 plays a role in phagocytosis by
controlling the binding of adhesion receptors (typically
integrins) to their ligands. In yeast, Rap1 has been
implicated in multiple functions, including activation
and silencing of transcription and maintenance of
telomeres. Rap1a, which is stimulated by T-cell receptor
(TCR) activation, is a positive regulator of T cells by
directing integrin activation and augmenting lymphocyte
responses. In murine hippocampal neurons, Rap1b
determines which neurite will become the axon and
directs the recruitment of Cdc42, which is required for
formation of dendrites and axons. In murine platelets,
Rap1b is required for normal homeostasis in vivo and is
involved in integrin activation. Most Ras proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 164
Score = 70.2 bits (172), Expect = 3e-14
Identities = 44/157 (28%), Positives = 72/157 (45%), Gaps = 34/157 (21%)
Query: 155 AYKTDVQLPSKLTSLAM--TCSTNEFPAMRALSISSADAFILVYAIDDPNSFEEIRLIRD 212
+Y+ V++ + L + T T +F AMR L + + F+LVY+I ++F +++ +R+
Sbjct: 37 SYRKQVEVDGQQCMLEILDTAGTEQFTAMRDLYMKNGQGFVLVYSITAQSTFNDLQDLRE 96
Query: 213 HIFETKASTAVPIVVVGNKSDLADENRQVDLTGGPFQTYLSGLPDSVCAHQISGTPDQVP 272
I K + VP+++VGNK DL DE R V G A Q
Sbjct: 97 QILRVKDTEDVPMILVGNKCDLEDE-RVVGKEQG-----------QNLARQ--------- 135
Query: 273 YDTTESVVQVDWENGFVEASAKDNTNITQVFKELLVQ 309
W F+E SAK N+ ++F +L+ Q
Sbjct: 136 -----------WGCAFLETSAKAKINVNEIFYDLVRQ 161
Score = 48.7 bits (116), Expect = 9e-07
Identities = 24/60 (40%), Positives = 38/60 (63%), Gaps = 1/60 (1%)
Query: 63 HKVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHLKLDILDTSG-EQ 121
+K+VV+G VGKS++ +F+ F KY TIE+ + + ++G L+ILDT+G EQ
Sbjct: 2 YKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDGQQCMLEILDTAGTEQ 61
Score = 28.6 bits (64), Expect = 5.6
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 351 WENGFVEASAKDNTNITQVFKELLVQ 376
W F+E SAK N+ ++F +L+ Q
Sbjct: 136 WGCAFLETSAKAKINVNEIFYDLVRQ 161
>gnl|CDD|133345 cd04145, M_R_Ras_like, R-Ras2/TC21, M-Ras/R-Ras3. The
M-Ras/R-Ras-like subfamily contains R-Ras2/TC21,
M-Ras/R-Ras3, and related members of the Ras family.
M-Ras is expressed in lympho-hematopoetic cells. It
interacts with some of the known Ras effectors, but
appears to also have its own effectors. Expression of
mutated M-Ras leads to transformation of several types
of cell lines, including hematopoietic cells, mammary
epithelial cells, and fibroblasts. Overexpression of
M-Ras is observed in carcinomas from breast, uterus,
thyroid, stomach, colon, kidney, lung, and rectum. In
addition, expression of a constitutively active M-Ras
mutant in murine bone marrow induces a malignant mast
cell leukemia that is distinct from the monocytic
leukemia induced by H-Ras. TC21, along with H-Ras, has
been shown to regulate the branching morphogenesis of
ureteric bud cell branching in mice. Most Ras proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 164
Score = 69.4 bits (170), Expect = 6e-14
Identities = 39/135 (28%), Positives = 58/135 (42%), Gaps = 32/135 (23%)
Query: 172 TCSTNEFPAMRALSISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNK 231
T EF AMR + + + F+LV+++ D SFEE+ I K P+++VGNK
Sbjct: 57 TAGQEEFSAMREQYMRTGEGFLLVFSVTDRGSFEEVDKFHTQILRVKDRDEFPMILVGNK 116
Query: 232 SDLADENRQVDLTGGPFQTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENGFVEA 291
+DL + RQV G A Q+ +PY +E
Sbjct: 117 ADL-EHQRQVSREEG-----------QELARQLK-----IPY---------------IET 144
Query: 292 SAKDNTNITQVFKEL 306
SAKD N+ + F +L
Sbjct: 145 SAKDRVNVDKAFHDL 159
Score = 51.6 bits (124), Expect = 9e-08
Identities = 23/60 (38%), Positives = 40/60 (66%)
Query: 62 RHKVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHLKLDILDTSGEQ 121
+K+VV+GG VGKS++ +F+ + F Y TIE+ + + ++G +LDILDT+G++
Sbjct: 2 TYKLVVVGGGGVGKSALTIQFIQSYFVTDYDPTIEDSYTKQCEIDGQWARLDILDTAGQE 61
>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 = 69.4 bits (170), Expect = 7e-14
Identities = 47/244 (19%), Positives = 85/244 (34%), Gaps = 87/244 (35%)
Query: 63 HKVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHLKLDILDTSGEQS 122
HKV+++G VGKS++ +F+Y+ F Y+ T + + + ++G ++L+ILDT+G++
Sbjct: 1 HKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEVQLNILDTAGQED 60
Query: 123 GKGLKCGAVLWGPKKWGLDKVCLRRALNQRPMAYKTDVQLPSKLTSLAMTCSTNEFPAMR 182
++ + L ++
Sbjct: 61 YAAIRDNYF------RSGEGFLLVFSITDM------------------------------ 84
Query: 183 ALSISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADENRQVD 242
SF + R+ I K VP+++VGNK DL ++ RQV
Sbjct: 85 -------------------ESFTALAEFREQILRVKEDDNVPLLLVGNKCDL-EDKRQV- 123
Query: 243 LTGGPFQTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENGFVEASAKDNTNITQV 302
+ + W +VE SAK N+ +V
Sbjct: 124 ------------------------------SVEEAANLAEQWGVNYVETSAKTRANVDKV 153
Query: 303 FKEL 306
F +L
Sbjct: 154 FFDL 157
Score = 28.5 bits (64), Expect = 6.2
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 349 VDWENGFVEASAKDNTNITQVFKEL 373
W +VE SAK N+ +VF +L
Sbjct: 133 EQWGVNYVETSAKTRANVDKVFFDL 157
>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 = 67.8 bits (166), Expect = 2e-13
Identities = 28/71 (39%), Positives = 39/71 (54%), Gaps = 2/71 (2%)
Query: 172 TCSTNEFPAMRALSISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNK 231
T E+ AMR + + + F+ V+AI+ SFE+I R+ I K S VP+V+VGNK
Sbjct: 56 TAGQEEYSAMRDQYMRTGEGFLCVFAINSRKSFEDIHTYREQIKRVKDSDDVPMVLVGNK 115
Query: 232 SDLADENRQVD 242
DL R V
Sbjct: 116 CDL--AARTVS 124
Score = 44.7 bits (106), Expect = 2e-05
Identities = 22/59 (37%), Positives = 38/59 (64%)
Query: 63 HKVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHLKLDILDTSGEQ 121
+K+VV+G VGKS++ + + N F +Y TIE+ + + ++G LDILDT+G++
Sbjct: 2 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQE 60
>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 = 67.1 bits (165), Expect = 4e-13
Identities = 33/122 (27%), Positives = 48/122 (39%), Gaps = 39/122 (31%)
Query: 188 SADAFILVYAIDDPNSFEEIR-LIRDHIFETKASTAVPIVVVGNKSDLADENRQVDLTGG 246
A ILVY + + SFE + + + + A +PI++VGNKSDL DE
Sbjct: 72 GAHGAILVYDVTNRESFENLDKWLNE--LKEYAPPNIPIILVGNKSDLEDE--------- 120
Query: 247 PFQTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENG--FVEASAKDNTNITQVFK 304
QV + + + ENG F E SAK N+ + F+
Sbjct: 121 ----------------------RQVSTEEAQQFAK---ENGLLFFETSAKTGENVDEAFE 155
Query: 305 EL 306
L
Sbjct: 156 SL 157
Score = 59.8 bits (146), Expect = 1e-10
Identities = 23/57 (40%), Positives = 36/57 (63%), Gaps = 1/57 (1%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTI-EEMHHEDFSMNGVHLKLDILDTSG 119
K+V++G VGK+S++ RF+ N FS YK TI + + ++G +KL I DT+G
Sbjct: 2 KIVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGVDFKSKTIEVDGKKVKLQIWDTAG 58
Score = 31.3 bits (72), Expect = 0.70
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 355 FVEASAKDNTNITQVFKEL 373
F E SAK N+ + F+ L
Sbjct: 139 FFETSAKTGENVDEAFESL 157
>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 = 67.1 bits (164), Expect = 4e-13
Identities = 45/246 (18%), Positives = 77/246 (31%), Gaps = 90/246 (36%)
Query: 66 VVMGGPKVGKSSIIHRFLYNTF---SPKYKRTIEE-MHHEDFSMNGVHLKLDILDTSGEQ 121
VV+G VGKSS+++ L S T + ++ ++ V KL ++DT
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKV--KLVLVDTP--- 55
Query: 122 SGKGLKCGAVLWGPKKWGLDKVCLRRALNQRPMAYKTDVQLPSKLTSLAMTCSTNEFPAM 181
GLD+ + +
Sbjct: 56 -----------------GLDEFGGLGREELARLLLRG----------------------- 75
Query: 182 RALSISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADENRQV 241
AD +LV D S E+ +L+ + +PI++VGNK DL +E
Sbjct: 76 -------ADLILLVVDSTDRESEEDAKLLILRRLRKEG---IPIILVGNKIDLLEEREVE 125
Query: 242 DLTGGPFQTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENGFVEASAKDNTNITQ 301
+L + G+P E SAK + +
Sbjct: 126 ELLRLEELAKILGVP-------------------------------VFEVSAKTGEGVDE 154
Query: 302 VFKELL 307
+F++L+
Sbjct: 155 LFEKLI 160
>gnl|CDD|206641 cd00157, Rho, Ras homology family (Rho) of small guanosine
triphosphatases (GTPases). Members of the Rho (Ras
homology) family include RhoA, Cdc42, Rac, Rnd, Wrch1,
RhoBTB, and Rop. There are 22 human Rho family members
identified currently. These proteins are all involved in
the reorganization of the actin cytoskeleton in response
to external stimuli. They also have roles in cell
transformation by Ras in cytokinesis, in focal adhesion
formation and in the stimulation of stress-activated
kinase. These various functions are controlled through
distinct effector proteins and mediated through a
GTP-binding/GTPase cycle involving three classes of
regulating proteins: GAPs (GTPase-activating proteins),
GEFs (guanine nucleotide exchange factors), and GDIs
(guanine nucleotide dissociation inhibitors). Most Rho
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. Since crystal structures
often lack C-terminal residues, this feature is not
available for annotation in many of the CDs in the
hierarchy.
Length = 171
Score = 67.2 bits (165), Expect = 5e-13
Identities = 49/253 (19%), Positives = 90/253 (35%), Gaps = 98/253 (38%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHLKLDILDTSGEQSG 123
K+VV+G VGK+ ++ + N F +Y T+ + + + +++G + L + DT+G++
Sbjct: 2 KIVVVGDGAVGKTCLLISYTTNKFPTEYVPTVFDNYSANVTVDGKQVNLGLWDTAGQE-- 59
Query: 124 KGLKCGAVLWGPKKWGLDKVCLRRALNQRPMAYKTDVQLPSKLTSLAMTCSTNEFPAMRA 183
D++ RP++Y
Sbjct: 60 ---------------EYDRL--------RPLSY--------------------------- 69
Query: 184 LSISSADAFILVYAIDDPNSFE--------EIRLIRDHIFETKASTAVPIVVVGNKSDLA 235
D F+L +++D P+SFE EI+ H VPI++VG K DL
Sbjct: 70 ---PQTDVFLLCFSVDSPSSFENVKTKWYPEIK----HYCPN-----VPIILVGTKIDLR 117
Query: 236 DENRQVDLTGGPFQTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENG---FVEAS 292
D+ + + + E + + E G ++E S
Sbjct: 118 DDGNTLKKLEKKQ--------------------KPITPEEGEKLAK---EIGAVKYMECS 154
Query: 293 AKDNTNITQVFKE 305
A + +VF E
Sbjct: 155 ALTQEGLKEVFDE 167
>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 = 64.9 bits (159), Expect = 2e-12
Identities = 54/252 (21%), Positives = 90/252 (35%), Gaps = 105/252 (41%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTI------EEMHHEDFSMNGVHLKLDILDT 117
K+V++G VGKSSI+ RF+ N FS + TI + ++ +D + +K +I DT
Sbjct: 3 KLVLLGDSSVGKSSIVLRFVKNEFSENQESTIGAAFLTQTVNLDDTT-----VKFEIWDT 57
Query: 118 SGEQSGKGLKCGAVLWGPKKWGLDKVCLRRALNQRPMAYKTDVQLPSKLTSLAMTCSTNE 177
+G++ + L PM Y+
Sbjct: 58 AGQERYRSLA-------------------------PMYYR-------------------- 72
Query: 178 FPAMRALSISSADAFILVYAIDDPNSFEEIRL-IRDHIFETKASTAVPIVVVGNKSDLAD 236
A A I+VY I SFE+ + +++ + + I + GNK+DL
Sbjct: 73 ----------GAAAAIVVYDITSEESFEKAKSWVKE--LQEHGPPNIVIALAGNKADLES 120
Query: 237 ENRQVDLTGGPFQTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENG--FVEASAK 294
+ QV + + ENG F+E SAK
Sbjct: 121 KR-------------------------------QVSTEEAQEYAD---ENGLLFMETSAK 146
Query: 295 DNTNITQVFKEL 306
N+ ++F E+
Sbjct: 147 TGENVNELFTEI 158
Score = 32.9 bits (76), Expect = 0.23
Identities = 11/24 (45%), Positives = 16/24 (66%), Gaps = 2/24 (8%)
Query: 352 ENG--FVEASAKDNTNITQVFKEL 373
ENG F+E SAK N+ ++F E+
Sbjct: 135 ENGLLFMETSAKTGENVNELFTEI 158
>gnl|CDD|219856 pfam08477, Miro, Miro-like protein. Mitochondrial Rho proteins
(Miro-1, and Miro-2), are atypical Rho GTPases. They
have a unique domain organisation, with tandem
GTP-binding domains and two EF hand domains (pfam00036),
that may bind calcium. They are also larger than
classical small GTPases. It has been proposed that they
are involved in mitochondrial homeostasis and apoptosis.
Length = 116
Score = 62.4 bits (152), Expect = 6e-12
Identities = 32/169 (18%), Positives = 51/169 (30%), Gaps = 55/169 (32%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHLKLDILDTSGEQSG 123
KVVV+G GKSS++ + + F P+ E+ + V DT
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEP----LEIQGDTL---AVDTLEVDGDTGLL--- 50
Query: 124 KGLKCGAVLWGPKKWGLDKVCLRRALNQRPMAYKTDVQLPSKLTSLAMTCSTNEFPAMRA 183
R E
Sbjct: 51 ---------------------NIWDFGGRE-----------------------ELKFEHI 66
Query: 184 LSISSADAFILVYAIDDPNSFEEIRLIRDHIFE-TKASTAVPIVVVGNK 231
+ + ADA +LVY + D S E+ + + K +P+++VGNK
Sbjct: 67 IFMKWADAILLVYDLTDRESLNEVSRLIAWLPNLRKLGGKIPVILVGNK 115
>gnl|CDD|227378 COG5045, COG5045, Ribosomal protein S10E [Translation, ribosomal
structure and biogenesis].
Length = 105
Score = 61.9 bits (150), Expect = 7e-12
Identities = 22/49 (44%), Positives = 28/49 (57%)
Query: 405 SLKSKGWVNEQFAWRHYYWYITNDGIEKLRGVLNIPDEIVPSTLKRQAR 453
SL S G+V WRH Y+ +T +G+E LR L +PDE VPST
Sbjct: 48 SLISYGYVKTIHVWRHSYYTLTPEGVEYLREYLVLPDEGVPSTEAPAVS 96
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 63.3 bits (155), Expect = 9e-12
Identities = 36/122 (29%), Positives = 51/122 (41%), Gaps = 39/122 (31%)
Query: 189 ADAFILVYAIDDPNSFEEI-RLIRDHIFETKASTAVPIVVVGNKSDLADENRQVDLTGGP 247
A +LVY I + SFE + +++ AS V I++VGNKSDL ++ RQV
Sbjct: 73 AVGALLVYDITNRESFENLENWLKE--LREYASPNVVIMLVGNKSDLEEQ-RQV------ 123
Query: 248 FQTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENG--FVEASAKDNTNITQVFKE 305
+ E E+G F E SAK NTN+ + F+E
Sbjct: 124 ---------------------------SREEAEAFAEEHGLPFFETSAKTNTNVEEAFEE 156
Query: 306 LL 307
L
Sbjct: 157 LA 158
Score = 50.6 bits (122), Expect = 2e-07
Identities = 24/61 (39%), Positives = 35/61 (57%), Gaps = 9/61 (14%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDF-----SMNGVHLKLDILDTS 118
K++++G VGKSS++ RF FS +YK TI DF ++G +KL I DT+
Sbjct: 2 KIILIGDSGVGKSSLLSRFTDGKFSEQYKSTIG----VDFKTKTIEVDGKRVKLQIWDTA 57
Query: 119 G 119
G
Sbjct: 58 G 58
Score = 34.0 bits (79), Expect = 0.10
Identities = 11/20 (55%), Positives = 14/20 (70%)
Query: 355 FVEASAKDNTNITQVFKELL 374
F E SAK NTN+ + F+EL
Sbjct: 139 FFETSAKTNTNVEEAFEELA 158
>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 = 62.9 bits (153), Expect = 2e-11
Identities = 63/272 (23%), Positives = 97/272 (35%), Gaps = 101/272 (37%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHLKLDILDTSGEQSG 123
K+VV+G VGK+++ + N F Y TIE+ +
Sbjct: 1 KLVVLGDGGVGKTALTIQLCLNHFVETYDPTIEDSYR----------------------- 37
Query: 124 KGLKCGAVLWGPKKWGLD-KVCLRRALNQRPMAYKTDVQLPSKLTSLAMTCSTNEFPAMR 182
K+ +D + C+ L+ T E+ A+R
Sbjct: 38 ------------KQVVVDGQPCMLEVLD---------------------TAGQEEYTALR 64
Query: 183 ALSISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTA--VPIVVVGNKSDLADENRQ 240
I + FILVY+I ++FE + R+ I K +A VPI++VGNK D E R+
Sbjct: 65 DQWIREGEGFILVYSITSRSTFERVERFREQIQRVKDESAADVPIMIVGNKCDKVYE-RE 123
Query: 241 VDLTGGPFQTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENGFVEASAKDNTNIT 300
V G + A ++ F+EASAK N N+
Sbjct: 124 VSTEEG-----------AALARRLG--------------------CEFIEASAKTNVNVE 152
Query: 301 QVFKELLVQAKVKYNLSPALRRRRRQSLPPVQ 332
+ F Y L ALR++R+ P
Sbjct: 153 RAF----------YTLVRALRQQRQGGQGPKG 174
Score = 31.4 bits (71), Expect = 0.95
Identities = 18/57 (31%), Positives = 24/57 (42%), Gaps = 10/57 (17%)
Query: 354 GFVEASAKDNTNITQVFKELLVQAKVKYNLSPALRRRRRQSLPPVQHSPNPSLKSKG 410
F+EASAK N N+ + F Y L ALR++R+ P K K
Sbjct: 139 EFIEASAKTNVNVERAF----------YTLVRALRQQRQGGQGPKGGPTKKKEKKKR 185
>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 = 62.7 bits (153), Expect = 3e-11
Identities = 42/187 (22%), Positives = 72/187 (38%), Gaps = 43/187 (22%)
Query: 156 YKTDVQLP-SKLTSLAM--TCSTNEFPAMRALSISSADAFILVYAIDDPNSFE------- 205
Y T +Q+P K+ LA+ T ++ +R LS D ++ Y++D+P S +
Sbjct: 40 YVTTLQVPNGKIIELALWDTAGQEDYDRLRPLSYPDVDVILICYSVDNPTSLDNVEDKWY 99
Query: 206 -EIRLIRDHIFETKASTAVPIVVVGNKSDL-ADENRQVDLTGGPFQTYLSGLPDSVCAHQ 263
E+ PIV+VG K+DL D+N S Q
Sbjct: 100 PEVNHFCPG---------TPIVLVGLKTDLRKDKNSV-----------------SKLRAQ 133
Query: 264 ISGTPDQVPYDTTESVVQVDWENGFVEASAKDNTNITQVFKE--LLVQAKVKYNLSPALR 321
+ V + ESV + ++E SAK N+ +VF + +K +
Sbjct: 134 ---GLEPVTPEQGESVAKSIGAVAYIECSAKLMENVDEVFDAAINVALSKSGRAARKKKK 190
Query: 322 RRRRQSL 328
+++ L
Sbjct: 191 KKKCVIL 197
Score = 38.1 bits (89), Expect = 0.006
Identities = 16/78 (20%), Positives = 30/78 (38%), Gaps = 2/78 (2%)
Query: 320 LRRRRRQSLPPVQHSPNPVPYDTTESVVQVDWENGFVEASAKDNTNITQVFKE--LLVQA 377
LR+ + PV + ESV + ++E SAK N+ +VF + +
Sbjct: 120 LRKDKNSVSKLRAQGLEPVTPEQGESVAKSIGAVAYIECSAKLMENVDEVFDAAINVALS 179
Query: 378 KVKYNLSPALRRRRRQSL 395
K ++++ L
Sbjct: 180 KSGRAARKKKKKKKCVIL 197
>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 = 61.1 bits (149), Expect = 7e-11
Identities = 47/248 (18%), Positives = 89/248 (35%), Gaps = 89/248 (35%)
Query: 65 VVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHLKLDILDTSGEQSGK 124
+VV+G VGK+ ++ + N F Y T+ E + D ++G ++L + DT+G++
Sbjct: 1 LVVVGDGAVGKTCLLIVYTTNAFPEDYVPTVFENYSADVEVDGKPVELGLWDTAGQEDYD 60
Query: 125 GLKCGAVLWGPKKWGLDKVCLRRALNQRPMAYKTDVQLPSKLTSLAMTCSTNEFPAMRAL 184
L RP++Y
Sbjct: 61 RL-------------------------RPLSY---------------------------- 67
Query: 185 SISSADAFILVYAIDDPNSFEEIRL-----IRDHIFETKASTAVPIVVVGNKSDLADENR 239
D F++ +++D P SFE ++ ++ VPI++VG K DL +
Sbjct: 68 --PDTDVFLICFSVDSPASFENVKEKWYPEVKHF------CPNVPIILVGTKLDLRN--- 116
Query: 240 QVDLTGGPFQTYLSGLPDSVCAHQISGTPDQVP--YDTTESVVQVDWENGFVEASAKDNT 297
D ++S Q P Y+ +++ + ++E SA
Sbjct: 117 -----------------DKSTLEELSK-KKQEPVTYEQGQALAKRIGAVKYLECSALTQE 158
Query: 298 NITQVFKE 305
+ +VF+E
Sbjct: 159 GVREVFEE 166
Score = 29.9 bits (68), Expect = 2.3
Identities = 9/37 (24%), Positives = 19/37 (51%)
Query: 336 NPVPYDTTESVVQVDWENGFVEASAKDNTNITQVFKE 372
PV Y+ +++ + ++E SA + +VF+E
Sbjct: 130 EPVTYEQGQALAKRIGAVKYLECSALTQEGVREVFEE 166
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 61.5 bits (149), Expect = 1e-10
Identities = 32/138 (23%), Positives = 53/138 (38%), Gaps = 23/138 (16%)
Query: 177 EFPAMRALSISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLAD 236
E+ ++R A+ ++VY S +E+ A VPI++VGNK DL D
Sbjct: 66 EYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVGNKIDLFD 125
Query: 237 ENRQVDLTGGPFQTYLSGLPDSVCAHQISGTPDQVPY--DTTESVVQVDWENGFVEASAK 294
E S ++ +V ++V+ +E SAK
Sbjct: 126 E-------------------QSSSEEILNQLNREVVLLVLAPKAVLPEVANPALLETSAK 166
Query: 295 --DNTNITQVFKELLVQA 310
N+ ++FKELL +
Sbjct: 167 SLTGPNVNELFKELLRKL 184
Score = 52.7 bits (126), Expect = 9e-08
Identities = 18/64 (28%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIE-EMHHEDFSMNGVHLKLDILDTSGEQS 122
K+VV+G VGK+++++R + + F Y TI + ++KL + DT+G++
Sbjct: 7 KIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQEE 66
Query: 123 GKGL 126
+ L
Sbjct: 67 YRSL 70
Score = 29.2 bits (65), Expect = 5.7
Identities = 11/44 (25%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 336 NPVPYDTTESVVQVDWENGFVEASAK--DNTNITQVFKELLVQA 377
+ ++V+ +E SAK N+ ++FKELL +
Sbjct: 141 VVLLVLAPKAVLPEVANPALLETSAKSLTGPNVNELFKELLRKL 184
>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 = 58.7 bits (142), Expect = 3e-10
Identities = 30/89 (33%), Positives = 51/89 (57%), Gaps = 3/89 (3%)
Query: 155 AYKTDVQLPSKLTSLAM--TCSTNEFPAMRALSISSADAFILVYAIDDPNSFEEIRLIRD 212
AYKT ++ ++ L + T EF AMR + + FI+ Y++ D +SF+E ++
Sbjct: 38 AYKTQARIDNEPALLDILDTAGQAEFTAMRDQYMRCGEGFIICYSVTDRHSFQEASEFKE 97
Query: 213 HIFETKASTAVPIVVVGNKSDLADENRQV 241
I + + +P+V+VGNK DL ++ RQV
Sbjct: 98 LITRVRLTEDIPLVLVGNKVDL-EQQRQV 125
Score = 39.8 bits (93), Expect = 0.001
Identities = 19/58 (32%), Positives = 36/58 (62%)
Query: 63 HKVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHLKLDILDTSGE 120
+K+V++G VGKS++ +F+ ++F + TIE+ + ++ LDILDT+G+
Sbjct: 3 YKIVMLGAGGVGKSAVTMQFISHSFPDYHDPTIEDAYKTQARIDNEPALLDILDTAGQ 60
>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 = 58.6 bits (142), Expect = 4e-10
Identities = 60/250 (24%), Positives = 93/250 (37%), Gaps = 94/250 (37%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHLKLDILDTSGEQSG 123
KV+V+G VGKSS+I RF+ F+ YK+TI GV D L+
Sbjct: 2 KVIVVGNGNVGKSSMIQRFVKGIFTKDYKKTI-----------GV----DFLEK------ 40
Query: 124 KGLKCGAVLWGPKKWGLDKVCLRRALNQRPMAYKTDVQLPSKLTSLAMTCSTNEFPAMRA 183
++ LR++ DV+L L T EF A+
Sbjct: 41 ------------------QIFLRQS--------DEDVRL-----MLWDTAGQEEFDAITK 69
Query: 184 LSISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADE----NR 239
A A ILV++ D SFE I ++ + +P+V+V K DL D+ N
Sbjct: 70 AYYRGAQACILVFSTTDRESFEAIESWKEKVEAECGD--IPMVLVQTKIDLLDQAVITNE 127
Query: 240 QVDLTGGPFQTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENGFVEASAKDNTNI 299
+ + L A ++ Q+P S KD+ N+
Sbjct: 128 EAE-----------AL-----AKRL-----QLP---------------LFRTSVKDDFNV 151
Query: 300 TQVFKELLVQ 309
T++F+ L +
Sbjct: 152 TELFEYLAEK 161
>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 = 52.8 bits (127), Expect = 4e-08
Identities = 39/152 (25%), Positives = 65/152 (42%), Gaps = 26/152 (17%)
Query: 156 YKTDVQLPSKLTSLAM--TCSTNEFPAMRALSISSADAFILVYAIDDPNSFEEIRLIRDH 213
Y D+++ K LA+ T ++ +R LS D ++ ++ID P+S E I
Sbjct: 38 YVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIP--EKW 95
Query: 214 IFETKA-STAVPIVVVGNKSDL-ADENRQVDLTGGPFQTYLSGLPDSVCAHQISGTPDQV 271
E K VPI++VGNK DL DE+ +L ++ P V
Sbjct: 96 TPEVKHFCPNVPIILVGNKKDLRNDEHTIREL------------------AKMKQEP--V 135
Query: 272 PYDTTESVVQVDWENGFVEASAKDNTNITQVF 303
+ ++ + G++E SAK + +VF
Sbjct: 136 KPEEGRAMAEKIGAFGYLECSAKTKEGVREVF 167
>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 = 51.2 bits (123), Expect = 1e-07
Identities = 41/177 (23%), Positives = 67/177 (37%), Gaps = 56/177 (31%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSP-KYKRTIEEMHHED-FSMNGVHLKLDILDTSGEQ 121
K+V++G P VGKS++++R L N S +YK + +G K ++LDT+G++
Sbjct: 3 KIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAGQE 62
Query: 122 SGKGLKCGAVLWGPKKWGLDKVCLRRALNQRPMAYKTDVQLPSKLTSLAMTCSTNEFPAM 181
D +RR
Sbjct: 63 -------------------DYDAIRRLYY--RAVES------------------------ 77
Query: 182 RALSISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADEN 238
S+ D ILV +++ ++ + I H A + VPI++VGNK DL D
Sbjct: 78 ---SLRVFDIVILVLDVEEILE-KQTKEIIHH-----AESGVPIILVGNKIDLRDAK 125
>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 = 50.7 bits (122), Expect = 2e-07
Identities = 24/63 (38%), Positives = 39/63 (61%), Gaps = 11/63 (17%)
Query: 63 HKVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTI------EEMHHEDFSMNGVHLKLDILD 116
HK+V +G VGK+SII RF+Y+TF +Y+ TI + M+ +D ++ +L + D
Sbjct: 1 HKLVFLGDQSVGKTSIITRFMYDTFDNQYQATIGIDFLSKTMYVDDKTV-----RLQLWD 55
Query: 117 TSG 119
T+G
Sbjct: 56 TAG 58
Score = 46.5 bits (111), Expect = 6e-06
Identities = 32/127 (25%), Positives = 50/127 (39%), Gaps = 45/127 (35%)
Query: 186 ISSADAFILVYAIDDPNSFEEIR----LIRDHIFETKASTAVPIVVVGNKSDLADENRQV 241
I + ++VY I + SF+ +RD + V IV+VGNK+DL+D+
Sbjct: 70 IRDSSVAVVVYDITNRQSFDNTDKWIDDVRD-----ERGNDVIIVLVGNKTDLSDKR--- 121
Query: 242 DLTGGPFQTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENG--FVEASAKDNTNI 299
QV + E + EN F+E SAK N+
Sbjct: 122 ----------------------------QVSTEEGEKKAK---ENNAMFIETSAKAGHNV 150
Query: 300 TQVFKEL 306
Q+FK++
Sbjct: 151 KQLFKKI 157
>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 = 50.6 bits (121), Expect = 3e-07
Identities = 56/250 (22%), Positives = 96/250 (38%), Gaps = 91/250 (36%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIE-EMHHEDFSMNGVHLKLDILDTSGEQS 122
KV+++G VGKSS+++R++ N F + TI E ++D ++G + L I DT+G++
Sbjct: 7 KVILLGDGGVGKSSLMNRYVTNKFDTQLFHTIGVEFLNKDLEVDGHFVTLQIWDTAGQER 66
Query: 123 GKGLKCGAVLWGPKKWGLDKVCLRRALNQRPMAYKTDVQLPSKLTSLAMTCSTNEFPAMR 182
+ L+ P G D L +++ +++ ++ EF
Sbjct: 67 FRSLRT------PFYRGSDCCLLTFSVDDS-QSFQN------------LSNWKKEF---- 103
Query: 183 ALSISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADENRQVD 242
I AD + +P SF P V++GNK D+ + RQV
Sbjct: 104 ---IYYAD-------VKEPESF-------------------PFVILGNKIDIPE--RQV- 131
Query: 243 LTGGPFQTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENG---FVEASAKDNTNI 299
+TE +NG + E SAKD TN+
Sbjct: 132 --------------------------------STEEAQAWCRDNGDYPYFETSAKDATNV 159
Query: 300 TQVFKELLVQ 309
F+E + +
Sbjct: 160 AAAFEEAVRR 169
>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 = 50.4 bits (121), Expect = 3e-07
Identities = 37/122 (30%), Positives = 50/122 (40%), Gaps = 36/122 (29%)
Query: 189 ADAFILVYAIDDPNSFEEIRLIRDHIFETKAST----AVPIVVVGNKSDLADENRQVDLT 244
AD +LVY + +P SFE + RD F +AS P VV+GNK DL +E RQV
Sbjct: 73 ADCCVLVYDVTNPKSFESLDSWRDE-FLIQASPRDPENFPFVVLGNKIDL-EEKRQVSTK 130
Query: 245 GGPFQTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENGFVEASAKDNTNITQVFK 304
A Q + +PY E SAK+ N+ Q F+
Sbjct: 131 K---------------AQQWCKSKGNIPY---------------FETSAKEAINVDQAFE 160
Query: 305 EL 306
+
Sbjct: 161 TI 162
Score = 28.4 bits (64), Expect = 6.9
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 355 FVEASAKDNTNITQVFKEL 373
+ E SAK+ N+ Q F+ +
Sbjct: 144 YFETSAKEAINVDQAFETI 162
>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 = 50.0 bits (120), Expect = 4e-07
Identities = 36/118 (30%), Positives = 46/118 (38%), Gaps = 33/118 (27%)
Query: 189 ADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADENRQVDLTGGPF 248
A ILVY I D SFE I+ +I E AS V ++VGNK D+ +E R V G
Sbjct: 76 AMGIILVYDITDEKSFENIKNWMRNIDE-HASEDVERMLVGNKCDM-EEKRVVSKEEG-- 131
Query: 249 QTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENGFVEASAKDNTNITQVFKEL 306
L + I F+E SAK N N+ + F L
Sbjct: 132 ----EALARE---YGIK----------------------FLETSAKANINVEEAFLTL 160
Score = 38.4 bits (90), Expect = 0.003
Identities = 21/63 (33%), Positives = 37/63 (58%), Gaps = 9/63 (14%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDF-----SMNGVHLKLDILDTS 118
K++++G VGKS ++ RF ++F+P + TI DF ++G +KL I DT+
Sbjct: 5 KLLLIGDSGVGKSCLLLRFSEDSFNPSFISTI----GIDFKIRTIELDGKKIKLQIWDTA 60
Query: 119 GEQ 121
G++
Sbjct: 61 GQE 63
Score = 30.7 bits (70), Expect = 1.4
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 355 FVEASAKDNTNITQVFKEL 373
F+E SAK N N+ + F L
Sbjct: 142 FLETSAKANINVEEAFLTL 160
>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 = 49.7 bits (119), Expect = 9e-07
Identities = 18/48 (37%), Positives = 32/48 (66%)
Query: 188 SADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLA 235
DA+++VY++ D +SFE+ +R + + + +PI++VGNKSDL
Sbjct: 72 VGDAYVIVYSVTDRSSFEKASELRIQLRRARQAEDIPIILVGNKSDLV 119
>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 = 49.2 bits (118), Expect = 1e-06
Identities = 17/32 (53%), Positives = 23/32 (71%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTI 95
KV+V+G VGK+SII R+++ FS YK TI
Sbjct: 2 KVLVIGDLGVGKTSIIKRYVHGVFSQHYKATI 33
Score = 30.7 bits (70), Expect = 1.6
Identities = 28/125 (22%), Positives = 47/125 (37%), Gaps = 41/125 (32%)
Query: 189 ADAFILVYAIDDPNSFEEIRLIRDHIFETKAST----AVPIVVVGNKSDLADENRQVDLT 244
A I+V+ + P++FE + + + ++K + +P +++ NK DL E D
Sbjct: 74 AVGAIIVFDVTRPSTFEAVLKWKADL-DSKVTLPNGEPIPALLLANKCDLKKERLAKD-- 130
Query: 245 GGPFQTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENGFV---EASAKDNTNITQ 301
D C ENGF+ E SAK+N NI +
Sbjct: 131 --------PEQMDQFCK-----------------------ENGFIGWFETSAKENINIEE 159
Query: 302 VFKEL 306
+ L
Sbjct: 160 AMRFL 164
>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 = 48.7 bits (117), Expect = 1e-06
Identities = 35/123 (28%), Positives = 50/123 (40%), Gaps = 45/123 (36%)
Query: 193 ILVYAIDDPNSFEEIRL----IRDHIFETKASTAVPIVVVGNKSDLADENRQVDLTGGPF 248
+LVY I ++FE + +RDH A + + I++VGNKSDL R V
Sbjct: 80 LLVYDITKKSTFENVERWLKELRDH-----ADSNIVIMLVGNKSDLRHL-RAV------- 126
Query: 249 QTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENG--FVEASAKDNTNITQVFKEL 306
TE +NG F+E SA D TN+ + FK+L
Sbjct: 127 --------------------------PTEEAKAFAEKNGLSFIETSALDGTNVEEAFKQL 160
Query: 307 LVQ 309
L +
Sbjct: 161 LTE 163
Score = 37.9 bits (89), Expect = 0.004
Identities = 21/57 (36%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIE-EMHHEDFSMNGVHLKLDILDTSG 119
K+V++G VGKS+++ RF N F+ K TI E ++G +K I DT+G
Sbjct: 5 KIVLIGDSGVGKSNLLSRFTRNEFNLDSKSTIGVEFATRTIQIDGKTIKAQIWDTAG 61
Score = 31.4 bits (72), Expect = 0.78
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 354 GFVEASAKDNTNITQVFKELLVQ 376
F+E SA D TN+ + FK+LL +
Sbjct: 141 SFIETSALDGTNVEEAFKQLLTE 163
>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 = 48.5 bits (116), Expect = 1e-06
Identities = 24/62 (38%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 183 ALSISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADENRQVD 242
A I A+ LVY++D P++ E IR + VPI++VGNKSDL D + Q
Sbjct: 67 AAEIRKANVICLVYSVDRPSTLERIRTKWLPLIRRLG-VKVPIILVGNKSDLRDGSSQAG 125
Query: 243 LT 244
L
Sbjct: 126 LE 127
Score = 31.2 bits (71), Expect = 0.95
Identities = 11/34 (32%), Positives = 18/34 (52%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEE 97
++V++G VGKSS+I + F R + E
Sbjct: 4 RIVLIGDEGVGKSSLIMSLVSEEFPENVPRVLPE 37
>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 = 48.1 bits (115), Expect = 1e-06
Identities = 31/125 (24%), Positives = 49/125 (39%), Gaps = 33/125 (26%)
Query: 189 ADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADENRQVDLTGGPF 248
A I+VY + D SF ++ I + AS V ++VGNK DL D+ + VD T
Sbjct: 75 AHGIIIVYDVTDQESFNNVKQWLQEI-DRYASENVNKLLVGNKCDLTDK-KVVDYTEA-- 130
Query: 249 QTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENGFVEASAKDNTNITQVFKELLV 308
+ + I F+E SAK+ TN+ + F +
Sbjct: 131 KEFAD-------ELGIP----------------------FLETSAKNATNVEEAFMTMAR 161
Query: 309 QAKVK 313
+ K +
Sbjct: 162 EIKKR 166
Score = 38.1 bits (89), Expect = 0.004
Identities = 21/63 (33%), Positives = 36/63 (57%), Gaps = 9/63 (14%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDF-----SMNGVHLKLDILDTS 118
K++++G VGKS ++ RF +T++ Y TI DF ++G +KL I DT+
Sbjct: 4 KLLLIGDSGVGKSCLLLRFADDTYTESYISTI----GVDFKIRTIELDGKTVKLQIWDTA 59
Query: 119 GEQ 121
G++
Sbjct: 60 GQE 62
Score = 28.4 bits (64), Expect = 7.6
Identities = 9/26 (34%), Positives = 16/26 (61%)
Query: 355 FVEASAKDNTNITQVFKELLVQAKVK 380
F+E SAK+ TN+ + F + + K +
Sbjct: 141 FLETSAKNATNVEEAFMTMAREIKKR 166
>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 = 47.6 bits (114), Expect = 2e-06
Identities = 19/59 (32%), Positives = 38/59 (64%), Gaps = 1/59 (1%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIE-EMHHEDFSMNGVHLKLDILDTSGEQ 121
KVV++G +VGK+S++ R++ N F+ K++ T + + ++ G + L I DT+G++
Sbjct: 2 KVVLLGEGRVGKTSLVLRYVENKFNEKHESTTQASFFQKTVNIGGKRIDLAIWDTAGQE 60
Score = 44.5 bits (106), Expect = 3e-05
Identities = 22/56 (39%), Positives = 31/56 (55%), Gaps = 6/56 (10%)
Query: 189 ADAFILVYAIDDPNSFEEIRLIRDHIFETKAS--TAVPIVVVGNKSDLADENRQVD 242
AD ILVY I D +SF++++ I E K + +V+VGNK DL + R V
Sbjct: 73 ADGAILVYDITDADSFQKVKK---WIKELKQMRGNNISLVIVGNKIDLERQ-RVVS 124
>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 = 47.8 bits (114), Expect = 2e-06
Identities = 37/179 (20%), Positives = 67/179 (37%), Gaps = 66/179 (36%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHLKLDILDTSGEQSG 123
K V++G VGK+S+I + N + +Y T + ++G ++L + DT+G+
Sbjct: 2 KCVLVGDGAVGKTSLIVSYTTNGYPTEYVPTAFDNFSVVVLVDGKPVRLQLCDTAGQDE- 60
Query: 124 KGLKCGAVLWGPKKWGLDKVCLRRALNQRPMAYKTDVQLPSKLTSLAMTCSTNEFPAMRA 183
DK+ RP+ Y
Sbjct: 61 ----------------FDKL--------RPLCY--------------------------- 69
Query: 184 LSISSADAFILVYAIDDPNSFEEIRL-----IRDHIFETKASTAVPIVVVGNKSDLADE 237
D F+L +++ +P+SF+ I IR H + PI++VG ++DL +
Sbjct: 70 ---PDTDVFLLCFSVVNPSSFQNISEKWIPEIRKH------NPKAPIILVGTQADLRTD 119
>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 = 47.2 bits (112), Expect = 3e-06
Identities = 28/71 (39%), Positives = 39/71 (54%), Gaps = 8/71 (11%)
Query: 63 HKVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIE---EMHHEDFSMNGVHLKLDILDTSG 119
KV+V+G VGK+ +I+RF + F YK TI EM E F + GV L + DT+G
Sbjct: 1 SKVIVVGDLSVGKTCLINRFCKDVFDKNYKATIGVDFEM--ERFEVLGVPFSLQLWDTAG 58
Query: 120 EQSGKGLKCGA 130
++ KC A
Sbjct: 59 QER---FKCIA 66
>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 = 46.4 bits (110), Expect = 9e-06
Identities = 30/85 (35%), Positives = 44/85 (51%), Gaps = 5/85 (5%)
Query: 156 YKTDVQLPSKLTSLAM--TCSTNEFPAMRALSISSADAFILVYAIDDPNSFEEIRLIRDH 213
Y TD ++ K LA+ T E+ +R LS S A ++ +AID P+S E +R
Sbjct: 38 YVTDCRVDGKPVQLALWDTAGQEEYERLRPLSYSKAHVILIGFAIDTPDSLENVR--TKW 95
Query: 214 IFE-TKASTAVPIVVVGNKSDLADE 237
I E + VP+++VG K DL E
Sbjct: 96 IEEVRRYCPNVPVILVGLKKDLRQE 120
>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 = 45.2 bits (107), Expect = 2e-05
Identities = 27/69 (39%), Positives = 39/69 (56%), Gaps = 9/69 (13%)
Query: 58 GHDTRHKVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFS-----MNGVHLKL 112
+D K++++G VGKSS++ RF NTFS Y TI DF +NG +KL
Sbjct: 2 DYDHLFKLLIIGDSGVGKSSLLLRFADNTFSGSYITTI----GVDFKIRTVEINGERVKL 57
Query: 113 DILDTSGEQ 121
I DT+G++
Sbjct: 58 QIWDTAGQE 66
>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 = 44.1 bits (104), Expect = 4e-05
Identities = 16/59 (27%), Positives = 33/59 (55%), Gaps = 1/59 (1%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIE-EMHHEDFSMNGVHLKLDILDTSGEQ 121
K++++G VGKS ++ RFL + + P+ T ++ + G + +D DT+G++
Sbjct: 2 KIILLGDSAVGKSKLVERFLMDGYEPQQLSTYALTLYKHNAKFEGKTILVDFWDTAGQE 60
>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 = 44.1 bits (104), Expect = 5e-05
Identities = 41/171 (23%), Positives = 66/171 (38%), Gaps = 39/171 (22%)
Query: 156 YKTDVQLPSKLTSLAM--TCSTNEFPAMRALSISSADAFILVYAIDDPNSFEEIRL---- 209
Y D+ + L++ T EF +R+LS + +L +++D+P+S E +
Sbjct: 37 YIHDIFVDGLAVELSLWDTAGQEEFDRLRSLSYADTHVIMLCFSVDNPDSLENVESKWLA 96
Query: 210 -IRDHIFETKASTAVPIVVVGNKSDLADENRQVDLTGGPFQTYLSGLPDSVCAHQISGTP 268
IR H V +V+V K DL + R G +Y GL A +I+
Sbjct: 97 EIRHH------CPGVKLVLVALKCDLRE-PRNERDRGTHTISYEEGLA---VAKRINACR 146
Query: 269 DQVPYDTTESVVQVDWENGFVEASAKDNTNITQVFKELLVQAKVKYNLSPA 319
++E SAK N + + F E A+V N P
Sbjct: 147 -------------------YLECSAKLNRGVNEAFTEA---ARVALNARPP 175
>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 = 43.3 bits (102), Expect = 9e-05
Identities = 25/94 (26%), Positives = 44/94 (46%), Gaps = 13/94 (13%)
Query: 156 YKTDVQLPSKLTSLAM--TCSTNEFPAMRALSISSADAFILVYAIDDPNSFEEIRL---- 209
Y +V + K +L + T ++ +R LS D F++ +++ P SFE +R
Sbjct: 38 YSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYP 97
Query: 210 -IRDHIFETKASTAVPIVVVGNKSDLADENRQVD 242
+R H PI++VG K DL D+ ++
Sbjct: 98 EVRHH------CPNTPIILVGTKLDLRDDKDTIE 125
>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 = 43.1 bits (101), Expect = 1e-04
Identities = 18/61 (29%), Positives = 35/61 (57%)
Query: 59 HDTRHKVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHLKLDILDTS 118
+ + K+VV+G + GK++++H F + F Y T+ E + F ++ ++L + DTS
Sbjct: 2 QNVKCKIVVVGDSQCGKTALLHVFAKDCFPENYVPTVFENYTASFEIDTQRIELSLWDTS 61
Query: 119 G 119
G
Sbjct: 62 G 62
>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 = 42.7 bits (101), Expect = 1e-04
Identities = 22/67 (32%), Positives = 38/67 (56%), Gaps = 1/67 (1%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIE-EMHHEDFSMNGVHLKLDILDTSGEQS 122
K+V++G GK++ + R L F KY T+ E+H DF N ++ ++ DT+G++
Sbjct: 2 KLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLDFHTNRGKIRFNVWDTAGQEK 61
Query: 123 GKGLKCG 129
GL+ G
Sbjct: 62 FGGLRDG 68
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 44.5 bits (106), Expect = 1e-04
Identities = 41/147 (27%), Positives = 55/147 (37%), Gaps = 46/147 (31%)
Query: 178 FPAMRALSISSADAFILVYAIDD---PNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDL 234
F AMRA S D ILV A DD P + E I + VPIVV NK D
Sbjct: 68 FTAMRARGASVTDIAILVVAADDGVMPQTIEAINHAKA--------AGVPIVVAINKIDK 119
Query: 235 ADENRQVDLTGGPFQTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVD-W--ENGFVEA 291
+ N PD+V + E + + W + FV
Sbjct: 120 PEAN-----------------------------PDKVKQELQEYGLVPEEWGGDVIFVPV 150
Query: 292 SAKDNTNITQVFKELLVQAKV---KYN 315
SAK I ++ + +L+ A+V K N
Sbjct: 151 SAKTGEGIDELLELILLLAEVLELKAN 177
>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 = 42.0 bits (99), Expect = 2e-04
Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 9/63 (14%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSM-----NGVHLKLDILDTS 118
K++++G VGK+ ++ RF TFS + TI DF+M G +KL I DT+
Sbjct: 5 KIILIGDSNVGKTCVVQRFKSGTFSERQGNTI----GVDFTMKTLEIQGKRVKLQIWDTA 60
Query: 119 GEQ 121
G++
Sbjct: 61 GQE 63
Score = 38.2 bits (89), Expect = 0.004
Identities = 24/120 (20%), Positives = 49/120 (40%), Gaps = 34/120 (28%)
Query: 188 SADAFILVYAIDDPNSFEEI-RLIRDHIFETKASTAVPIVVVGNKSDLADENRQVDLTGG 246
SA+ I+ Y I +SFE + I + E ++ V ++++GNK DL ++ R+V
Sbjct: 75 SANGAIIAYDITRRSSFESVPHWIEE--VEKYGASNVVLLLIGNKCDLEEQ-REVLF--- 128
Query: 247 PFQTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENGFVEASAKDNTNITQVFKEL 306
+ ++ + +E SAK+++N+ + F +
Sbjct: 129 ---------------------------EEACTLAEHYGILAVLETSAKESSNVEEAFLLM 161
>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 = 41.5 bits (98), Expect = 2e-04
Identities = 20/59 (33%), Positives = 36/59 (61%), Gaps = 1/59 (1%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIE-EMHHEDFSMNGVHLKLDILDTSGEQ 121
K++++G VGKSS++ RF +TF TI + + +++G +KL I DT+G++
Sbjct: 2 KILLIGDSGVGKSSLLLRFTDDTFDEDLSSTIGVDFKVKTVTVDGKKVKLAIWDTAGQE 60
Score = 38.8 bits (91), Expect = 0.002
Identities = 31/133 (23%), Positives = 48/133 (36%), Gaps = 44/133 (33%)
Query: 182 RALSIS---SADAFILVYAIDDPNSFE--EIRLIRDHIFETKASTAVPIVVVGNKSDLAD 236
R L+ S A ILVY + ++F+ + L + T ++VGNK D
Sbjct: 63 RTLTSSYYRGAQGVILVYDVTRRDTFDNLDTWLNELDTYSTNPDAV--KMLVGNKIDK-- 118
Query: 237 ENRQVDLTGGPFQTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENG--FVEASAK 294
ENR+V T E + ++ F+E SAK
Sbjct: 119 ENREV---------------------------------TREEGQKFARKHNMLFIETSAK 145
Query: 295 DNTNITQVFKELL 307
+ Q F+EL+
Sbjct: 146 TRIGVQQAFEELV 158
Score = 31.1 bits (71), Expect = 0.95
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 355 FVEASAKDNTNITQVFKELL 374
F+E SAK + Q F+EL+
Sbjct: 139 FIETSAKTRIGVQQAFEELV 158
>gnl|CDD|206674 cd01887, IF2_eIF5B, Initiation Factor 2 (IF2)/ eukaryotic
Initiation Factor 5B (eIF5B) family. IF2/eIF5B
contribute to ribosomal subunit joining and function as
GTPases that are maximally activated by the presence of
both ribosomal subunits. As seen in other GTPases,
IF2/IF5B undergoes conformational changes between its
GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess
three characteristic segments, including a divergent
N-terminal region followed by conserved central and
C-terminal segments. This core region is conserved among
all known eukaryotic and archaeal IF2/eIF5Bs and
eubacterial IF2s.
Length = 169
Score = 41.7 bits (99), Expect = 3e-04
Identities = 25/70 (35%), Positives = 28/70 (40%), Gaps = 16/70 (22%)
Query: 178 FPAMRALSISSADAFILVYAIDD---PNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDL 234
F MRA S D ILV A DD P + E I + VPI+V NK D
Sbjct: 62 FTNMRARGASVTDIAILVVAADDGVMPQTIEAINHAKA--------ANVPIIVAINKIDK 113
Query: 235 -----ADENR 239
AD R
Sbjct: 114 PYGTEADPER 123
>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 = 40.7 bits (95), Expect = 6e-04
Identities = 55/254 (21%), Positives = 88/254 (34%), Gaps = 95/254 (37%)
Query: 57 EGHDTRHKVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHLKLDILD 116
E +D K+V++G VGK+ ++ RF F P TI GV + ++
Sbjct: 2 EDYDFLFKIVLIGNAGVGKTCLVRRFTQGLFPPGQGATI-----------GVDFMIKTVE 50
Query: 117 TSGEQSGKGLKCGAVLWGPKKWGLDKVCLRRALNQRPMAYKTDVQLPSKLTSLAMTCSTN 176
GE K +W T
Sbjct: 51 IKGE------KIKLQIWD-------------------------------------TAGQE 67
Query: 177 EFPAMRALSISSADAFILVYAIDDPNSF----EEIRLIRDHIFETKASTAVPIVVVGNKS 232
F ++ SA+A IL Y I SF E +R I E A+ V ++VGNK
Sbjct: 68 RFRSITQSYYRSANALILTYDITCEESFRCLPEWLREI-----EQYANNKVITILVGNKI 122
Query: 233 DLADENRQVDLTGGPFQTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENGFVEAS 292
DLA+ R+V Q + +++ Q + ++E S
Sbjct: 123 DLAER-REV--------------------------SQQRAEEFSDA--QDMY---YLETS 150
Query: 293 AKDNTNITQVFKEL 306
AK++ N+ ++F +L
Sbjct: 151 AKESDNVEKLFLDL 164
>gnl|CDD|232995 TIGR00487, IF-2, translation initiation factor IF-2. This model
discriminates eubacterial (and mitochondrial)
translation initiation factor 2 (IF-2), encoded by the
infB gene in bacteria, from similar proteins in the
Archaea and Eukaryotes. In the bacteria and in
organelles, the initiator tRNA is charged with
N-formyl-Met instead of Met. This translation factor
acts in delivering the initator tRNA to the ribosome. It
is one of a number of GTP-binding translation factors
recognized by the pfam model GTP_EFTU [Protein
synthesis, Translation factors].
Length = 587
Score = 42.4 bits (100), Expect = 6e-04
Identities = 39/141 (27%), Positives = 56/141 (39%), Gaps = 43/141 (30%)
Query: 178 FPAMRALSISSADAFILVYAIDD---PNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDL 234
F +MRA D +LV A DD P + E I H KA+ VPI+V NK D
Sbjct: 148 FTSMRARGAKVTDIVVLVVAADDGVMPQTIEAI----SH---AKAAN-VPIIVAINKIDK 199
Query: 235 ADENRQVDLTGGPFQTYLSGLPDSVCAHQISGTPDQVPYDTTE-SVVQVDW--ENGFVEA 291
+ N PD+V + +E +V DW + FV
Sbjct: 200 PEAN-----------------------------PDRVKQELSEYGLVPEDWGGDTIFVPV 230
Query: 292 SAKDNTNITQVFKELLVQAKV 312
SA I ++ +L+Q++V
Sbjct: 231 SALTGDGIDELLDMILLQSEV 251
>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 = 40.5 bits (95), Expect = 6e-04
Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTI-EEMHHEDFSMNGVHLKLDILDTSGEQ 121
K +++G GKS ++H+F+ N F TI E ++ G +KL I DT+G++
Sbjct: 2 KFLIIGSAGTGKSCLLHQFIENKFKQDSNHTIGVEFGSRVVNVGGKSVKLQIWDTAGQE 60
Score = 32.4 bits (74), Expect = 0.27
Identities = 19/50 (38%), Positives = 29/50 (58%), Gaps = 4/50 (8%)
Query: 193 ILVYAIDDPNSFEEI-RLIRDHIFETKASTAVPIVVVGNKSDLADENRQV 241
+LVY I SF + + D T AS + I++VGNK DL +++R+V
Sbjct: 77 LLVYDITSRESFNALTNWLTDA--RTLASPDIVIILVGNKKDL-EDDREV 123
>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 = 40.9 bits (96), Expect = 6e-04
Identities = 24/64 (37%), Positives = 34/64 (53%), Gaps = 5/64 (7%)
Query: 181 MRALSISSADAFILVYAIDDPNSFEEI---RLIRDHIFETKASTAVPIVVVGNKSDLADE 237
M I A A LVY I + SFE + + + E ++ T +V+VGNK+DL +
Sbjct: 66 MLDKYIYGAQAVCLVYDITNSQSFENLEDWLSVVKKVNE-ESETKPKMVLVGNKTDL-EH 123
Query: 238 NRQV 241
NRQV
Sbjct: 124 NRQV 127
Score = 38.6 bits (90), Expect = 0.004
Identities = 23/66 (34%), Positives = 31/66 (46%), Gaps = 10/66 (15%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHL------KLDILDT 117
K+VV+G GK+S+I RF F YK+TI DF + L L + D
Sbjct: 2 KIVVLGDGASGKTSLIRRFAQEGFGKSYKQTI----GLDFFSRRITLPGSLNVTLQVWDI 57
Query: 118 SGEQSG 123
G+Q G
Sbjct: 58 GGQQIG 63
>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 = 40.0 bits (94), Expect = 8e-04
Identities = 21/65 (32%), Positives = 29/65 (44%), Gaps = 9/65 (13%)
Query: 63 HKVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDF-----SMNGVHLKLDILDT 117
KV+ MG VGKS II R+ F KY TI D+ S+ ++++ D
Sbjct: 1 IKVISMGNSGVGKSCIIKRYCEGRFVSKYLPTI----GIDYGVKKVSVRNKEVRVNFFDL 56
Query: 118 SGEQS 122
SG
Sbjct: 57 SGHPE 61
Score = 31.2 bits (71), Expect = 0.86
Identities = 16/63 (25%), Positives = 24/63 (38%), Gaps = 11/63 (17%)
Query: 176 NEFPAMRALSISSADAFILVYAIDDPNSFEEI----RLIRDHIFETKASTAVPIVVVGNK 231
NEF +LVY + D SFE + + ++ + +VV NK
Sbjct: 67 NEF-------YKDTQGVLLVYDVTDRQSFEALDSWLKEMKQEGGPHGNMENIVVVVCANK 119
Query: 232 SDL 234
DL
Sbjct: 120 IDL 122
>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 = 39.9 bits (94), Expect = 0.001
Identities = 19/65 (29%), Positives = 28/65 (43%), Gaps = 4/65 (6%)
Query: 177 EFPAMRALSISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLAD 236
E + +++ D LVY DPNSF + F +P + V K+DL D
Sbjct: 66 EAILLNDAELAACDVACLVYDSSDPNSFSYCAEVYKKYFMLG---EIPCLFVAAKADL-D 121
Query: 237 ENRQV 241
E +Q
Sbjct: 122 EQQQR 126
Score = 29.5 bits (67), Expect = 3.7
Identities = 11/45 (24%), Positives = 20/45 (44%), Gaps = 3/45 (6%)
Query: 67 VMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHLK 111
V+G GKS+++ FL +FS +++N V +
Sbjct: 9 VLGAKGSGKSALLQAFLGRSFSQN---AYSPTIKPRYAVNTVEVP 50
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 39.9 bits (93), Expect = 0.001
Identities = 23/64 (35%), Positives = 35/64 (54%), Gaps = 1/64 (1%)
Query: 59 HDTRHKVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIE-EMHHEDFSMNGVHLKLDILDT 117
+D K+V++G VGKS+I+ RF N F + K TI E + G +K I DT
Sbjct: 9 YDYLFKIVLIGDSGVGKSNILSRFTRNEFCLESKSTIGVEFATRTLQVEGKTVKAQIWDT 68
Query: 118 SGEQ 121
+G++
Sbjct: 69 AGQE 72
>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 = 38.7 bits (90), Expect = 0.002
Identities = 35/119 (29%), Positives = 54/119 (45%), Gaps = 33/119 (27%)
Query: 189 ADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADENRQVDLTGGPF 248
A FIL+Y I + SF ++ I +T + +++VGNK D+ DE R V G
Sbjct: 74 AMGFILMYDITNEESFNAVQDWSTQI-KTYSWDNAQVILVGNKCDMEDE-RVVSAERG-- 129
Query: 249 QTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENGFVEASAKDNTNITQVFKELL 307
Q++ DQ+ ++ F EASAK+N N+ QVF+ L+
Sbjct: 130 -------------RQLA---DQLGFE-------------FFEASAKENINVKQVFERLV 159
Score = 34.1 bits (78), Expect = 0.094
Identities = 18/63 (28%), Positives = 36/63 (57%), Gaps = 9/63 (14%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVH-----LKLDILDTS 118
K++++G VGK+S + R+ ++F+ + T+ DF + V+ +KL I DT+
Sbjct: 3 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTV----GIDFKVKTVYRNDKRIKLQIWDTA 58
Query: 119 GEQ 121
G++
Sbjct: 59 GQE 61
Score = 31.4 bits (71), Expect = 0.71
Identities = 12/20 (60%), Positives = 16/20 (80%)
Query: 355 FVEASAKDNTNITQVFKELL 374
F EASAK+N N+ QVF+ L+
Sbjct: 140 FFEASAKENINVKQVFERLV 159
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 39.0 bits (91), Expect = 0.003
Identities = 23/67 (34%), Positives = 37/67 (55%), Gaps = 1/67 (1%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIE-EMHHEDFSMNGVHLKLDILDTSGEQS 122
K+V++G GK++ + R L F KY+ TI E+H DF N ++ DT+G++
Sbjct: 15 KLVIVGDGGTGKTTFVKRHLTGEFEKKYEPTIGVEVHPLDFFTNCGKIRFYCWDTAGQEK 74
Query: 123 GKGLKCG 129
GL+ G
Sbjct: 75 FGGLRDG 81
>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 = 38.2 bits (89), Expect = 0.004
Identities = 17/58 (29%), Positives = 34/58 (58%)
Query: 62 RHKVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHLKLDILDTSG 119
R K+V++G + GK++++ F ++F Y T+ E + F ++ ++L + DTSG
Sbjct: 1 RCKIVLVGDSQCGKTALLQVFAKDSFPENYVPTVFENYTASFEVDKQRIELSLWDTSG 58
>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 = 37.9 bits (88), Expect = 0.005
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIE-EMHHEDFSMNGVHLKLDILDTSGEQ 121
K +++G VGKS ++H+F F TI E +NG +KL I DT+G++
Sbjct: 4 KYIIIGDMGVGKSCLLHQFTEKKFMADCPHTIGVEFGTRIIEVNGQKIKLQIWDTAGQE 62
Score = 28.6 bits (64), Expect = 6.3
Identities = 14/33 (42%), Positives = 16/33 (48%), Gaps = 2/33 (6%)
Query: 342 TTESVVQVDWENG--FVEASAKDNTNITQVFKE 372
T E Q ENG F+E SAK N+ F E
Sbjct: 126 TYEEAKQFADENGLLFLECSAKTGENVEDAFLE 158
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 38.1 bits (88), Expect = 0.006
Identities = 22/76 (28%), Positives = 41/76 (53%)
Query: 51 NESGSSEGHDTRHKVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHL 110
+ SG S G+D K++++G VGKSS++ F+ ++ + + ++ G L
Sbjct: 3 SSSGQSSGYDLSFKILLIGDSGVGKSSLLVSFISSSVEDLAPTIGVDFKIKQLTVGGKRL 62
Query: 111 KLDILDTSGEQSGKGL 126
KL I DT+G++ + L
Sbjct: 63 KLTIWDTAGQERFRTL 78
>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 = 38.1 bits (88), Expect = 0.007
Identities = 18/58 (31%), Positives = 35/58 (60%)
Query: 62 RHKVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHLKLDILDTSG 119
R K+VV+G + GK++++H F + + Y T+ E + F ++ ++L++ DTSG
Sbjct: 1 RCKIVVVGDTQCGKTALLHVFAKDNYPESYVPTVFENYTASFEIDKHRIELNMWDTSG 58
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 38.3 bits (89), Expect = 0.012
Identities = 28/94 (29%), Positives = 41/94 (43%), Gaps = 15/94 (15%)
Query: 151 QRPMAYKTDVQLPS---KLTSLAMTCSTNEFPAMRALSISSADAFILVYAIDD---PNSF 204
Q+ AY+ + + K+ L T F +MR+ + D IL+ A DD P +
Sbjct: 279 QKIGAYEVEFEYKDENQKIVFLD-TPGHEAFSSMRSRGANVTDIAILIIAADDGVKPQTI 337
Query: 205 EEIRLIRDHIFETKASTAVPIVVVGNKSDLADEN 238
E I I+ VPI+V NK D A+ N
Sbjct: 338 EAINYIQA--------ANVPIIVAINKIDKANAN 363
>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 = 36.9 bits (85), Expect = 0.014
Identities = 43/168 (25%), Positives = 63/168 (37%), Gaps = 33/168 (19%)
Query: 172 TCSTNEFPAMRALSISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNK 231
T F ++ + SA ILVY I +F+++ I + AS +++VGNK
Sbjct: 56 TAGQERFNSITSAYYRSAKGIILVYDITKKETFDDLPKWMKMI-DKYASEDAELLLVGNK 114
Query: 232 SDLADENRQVDLTGGPFQTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENGFVEA 291
D + G F A QI+G F EA
Sbjct: 115 LDCETDREITRQQGEKF------------AQQITGMR-------------------FCEA 143
Query: 292 SAKDNTNITQVFKELLVQAKVKYNLSPALRRRRRQSLPPVQHSPNPVP 339
SAKDN N+ ++F +L+ K L LR S+ +Q P P
Sbjct: 144 SAKDNFNVDEIFLKLVDDILKKMPLD-ILRNELSNSILSLQPEPEIPP 190
Score = 28.1 bits (62), Expect = 9.9
Identities = 18/48 (37%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 355 FVEASAKDNTNITQVFKELLVQAKVKYNLSPALRRRRRQSLPPVQHSP 402
F EASAKDN N+ ++F +L+ K L LR S+ +Q P
Sbjct: 140 FCEASAKDNFNVDEIFLKLVDDILKKMPLD-ILRNELSNSILSLQPEP 186
>gnl|CDD|206645 cd00879, Sar1, Sar1 is an essential component of COPII vesicle
coats. Sar1 is an essential component of COPII vesicle
coats involved in export of cargo from the ER. The
GTPase activity of Sar1 functions as a molecular switch
to control protein-protein and protein-lipid
interactions that direct vesicle budding from the ER.
Activation of the GDP to the GTP-bound form of Sar1
involves the membrane-associated guanine nucleotide
exchange factor (GEF) Sec12. Sar1 is unlike all Ras
superfamily GTPases that use either myristoyl or prenyl
groups to direct membrane association and function, in
that Sar1 lacks such modification. Instead, Sar1
contains a unique nine-amino-acid N-terminal extension.
This extension contains an evolutionarily conserved
cluster of bulky hydrophobic amino acids, referred to as
the Sar1-N-terminal activation recruitment (STAR) motif.
The STAR motif mediates the recruitment of Sar1 to ER
membranes and facilitates its interaction with mammalian
Sec12 GEF leading to activation.
Length = 191
Score = 36.9 bits (86), Expect = 0.015
Identities = 14/44 (31%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 193 ILVYAID--DPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDL 234
+V+ +D DP F+E + D + + VPI+++GNK D
Sbjct: 89 GIVFLVDAADPERFQESKEELDSLLNDEELANVPILILGNKIDK 132
>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 = 36.9 bits (85), Expect = 0.015
Identities = 24/84 (28%), Positives = 40/84 (47%), Gaps = 9/84 (10%)
Query: 156 YKTDVQLPSKLTSLAM--TCSTNEFPAMRALSISSADAFILVYAIDDPNSFEEIRLIRDH 213
Y + + SL + T E+ +R LS + FI+ ++I P+S+E +R H
Sbjct: 40 YSAQTAVDGRTVSLNLWDTAGQEEYDRLRTLSYPQTNVFIICFSIASPSSYENVR----H 95
Query: 214 IFETKAS---TAVPIVVVGNKSDL 234
+ + VPI++VG K DL
Sbjct: 96 KWHPEVCHHCPNVPILLVGTKKDL 119
Score = 32.3 bits (73), Expect = 0.40
Identities = 16/58 (27%), Positives = 34/58 (58%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHLKLDILDTSGEQ 121
K VV+G VGK+ ++ + N F +Y T+ + + +++G + L++ DT+G++
Sbjct: 5 KCVVVGDGAVGKTCLLICYTTNAFPKEYIPTVFDNYSAQTAVDGRTVSLNLWDTAGQE 62
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 37.0 bits (86), Expect = 0.016
Identities = 21/67 (31%), Positives = 37/67 (55%), Gaps = 1/67 (1%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIE-EMHHEDFSMNGVHLKLDILDTSGEQS 122
K++++G VGK++ + R L F KY T+ E+H F N + ++ DT+G++
Sbjct: 11 KLILVGDGGVGKTTFVKRHLTGEFEKKYIPTLGVEVHPLKFYTNCGPICFNVWDTAGQEK 70
Query: 123 GKGLKCG 129
GL+ G
Sbjct: 71 FGGLRDG 77
Score = 29.3 bits (66), Expect = 4.8
Identities = 12/19 (63%), Positives = 15/19 (78%), Gaps = 2/19 (10%)
Query: 223 VPIVVVGNKSDLADENRQV 241
+PIV+VGNK D+ D RQV
Sbjct: 114 IPIVLVGNKVDVKD--RQV 130
>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 = 36.4 bits (84), Expect = 0.016
Identities = 27/125 (21%), Positives = 50/125 (40%), Gaps = 15/125 (12%)
Query: 172 TCSTNEFPAMRALSISSADAFILVYAIDDPNSFEEIR-----LIRDHIFETKASTAVPIV 226
T ++ +R LS D F++ +++ P+SFE ++ I H P +
Sbjct: 56 TAGQEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHH------CPKTPFL 109
Query: 227 VVGNKSDLADENRQVDLTGGPFQTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWEN 286
+VG + DL D+ ++ Q ++ A + V Y ++ Q +N
Sbjct: 110 LVGTQIDLRDDPSTIEKLAKNKQKPITPETGEKLARDLKA----VKYVECSALTQKGLKN 165
Query: 287 GFVEA 291
F EA
Sbjct: 166 VFDEA 170
>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 = 36.4 bits (84), Expect = 0.021
Identities = 20/53 (37%), Positives = 33/53 (62%), Gaps = 2/53 (3%)
Query: 189 ADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADENRQV 241
A A +L+Y + + +SF+ IR I E A + V I+++GNK+D++ E R V
Sbjct: 74 AHALLLLYDVTNKSSFDNIRAWLTEILEY-AQSDVVIMLLGNKADMSGE-RVV 124
Score = 32.9 bits (75), Expect = 0.26
Identities = 18/61 (29%), Positives = 36/61 (59%), Gaps = 2/61 (3%)
Query: 63 HKVVVMGGPKVGKSSIIHRFLYNTFSP-KYKRTIE-EMHHEDFSMNGVHLKLDILDTSGE 120
KV+++G VGK+ ++ RF F + T+ + ++ +++GV +KL I DT+G+
Sbjct: 1 FKVMLVGDSGVGKTCLLVRFKDGAFLAGSFIATVGIQFTNKVVTVDGVKVKLQIWDTAGQ 60
Query: 121 Q 121
+
Sbjct: 61 E 61
>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 = 36.5 bits (84), Expect = 0.022
Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 68 MGGPKVGKSSIIHRFLYNTFSPKYKRTIE-EMHHEDFSMNGVHLKLDILDTSGEQSGKGL 126
+G GK++ + R L F KY T+ E+H F N ++ ++ DT+G++ GL
Sbjct: 1 VGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIRFNVWDTAGQEKFGGL 60
Query: 127 KCGAVLWG 134
+ G + G
Sbjct: 61 RDGYYIQG 68
>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 = 35.8 bits (82), Expect = 0.024
Identities = 19/73 (26%), Positives = 38/73 (52%), Gaps = 3/73 (4%)
Query: 166 LTSLAMTCSTNEFPAMRALSISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTA-VP 224
L L T ++ +R LS D F++ +++ +P SF+ ++ + + E K VP
Sbjct: 49 LLGLYDTAGQEDYDRLRPLSYPMTDVFLICFSVVNPASFQNVK--EEWVPELKEYAPNVP 106
Query: 225 IVVVGNKSDLADE 237
+++G + DL D+
Sbjct: 107 YLLIGTQIDLRDD 119
>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 = 35.9 bits (83), Expect = 0.024
Identities = 38/182 (20%), Positives = 65/182 (35%), Gaps = 53/182 (29%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHLKLDILDTSGEQSG 123
K++ +G VGK++ ++R+ N F+PK+ T+ DF V SG
Sbjct: 6 KLLALGDSGVGKTTFLYRYTDNKFNPKFITTV----GIDFREKRVVYNSQ---GPDGTSG 58
Query: 124 KGLKCGAVLWGPKKWGLDKVCLRRALNQRPMAYKTDVQLPSKLTSLAMTCSTNEFPAMRA 183
K + LW T F ++
Sbjct: 59 KAFRVHLQLWD-------------------------------------TAGQERFRSLTT 81
Query: 184 LSISSADAFILVYAIDDPNSFEEIR----LIRDHIFETKASTAVPIVVVGNKSDLADENR 239
A F+L++ + SF +R ++ H + IV++GNK+DL D+ R
Sbjct: 82 AFFRDAMGFLLMFDLTSEQSFLNVRNWMSQLQAHAYCENPD----IVLIGNKADLPDQ-R 136
Query: 240 QV 241
+V
Sbjct: 137 EV 138
>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 = 36.3 bits (84), Expect = 0.027
Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 16/67 (23%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPK---------YKRTIEEMHHEDFSMNGVHLKLDI 114
+++V+G VGKSS++ RF F+ + R IE GV +KL +
Sbjct: 4 RLIVIGDSTVGKSSLLKRFTEGRFAEVSDPTVGVDFFSRLIE-------IEPGVRIKLQL 56
Query: 115 LDTSGEQ 121
DT+G++
Sbjct: 57 WDTAGQE 63
Score = 32.0 bits (73), Expect = 0.53
Identities = 30/135 (22%), Positives = 50/135 (37%), Gaps = 44/135 (32%)
Query: 193 ILVYAIDDPNSFEEIRL----IRDHIFETKASTAVPIVVVGNKSDLADENRQVDLTGGPF 248
+LV+ I + SFE + R HI + V ++VG+K DL +
Sbjct: 80 LLVFDITNRESFEHVHDWLEEARSHI---QPHRPV-FILVGHKCDLESQR---------- 125
Query: 249 QTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENGFVEASAKDNTNITQVFKELL- 307
QV + E + + D ++E SA+ N+ + F ELL
Sbjct: 126 ---------------------QVTREEAEKLAK-DLGMKYIETSARTGDNVEEAF-ELLT 162
Query: 308 --VQAKVKYNLSPAL 320
+ ++K AL
Sbjct: 163 QEIYERIKRGELCAL 177
>gnl|CDD|206721 cd04155, Arl3, Arf-like 3 (Arl3) GTPase. Arl3 (Arf-like 3) is an
Arf family protein that differs from most Arf family
members in the N-terminal extension. In is inactive,
GDP-bound form, the N-terminal extension forms an
elongated loop that is hydrophobically anchored into the
membrane surface; however, it has been proposed that
this region might form a helix in the GTP-bound form.
The delta subunit of the rod-specific cyclic GMP
phosphodiesterase type 6 (PDEdelta) is an Arl3 effector.
Arl3 binds microtubules in a regulated manner to alter
specific aspects of cytokinesis via interactions with
retinitis pigmentosa 2 (RP2). It has been proposed that
RP2 functions in concert with Arl3 to link the cell
membrane and the cytoskeleton in photoreceptors as part
of the cell signaling or vesicular transport machinery.
In mice, the absence of Arl3 is associated with abnormal
epithelial cell proliferation and cyst formation.
Length = 174
Score = 35.4 bits (82), Expect = 0.031
Identities = 16/46 (34%), Positives = 22/46 (47%), Gaps = 2/46 (4%)
Query: 193 ILVYAID--DPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLAD 236
+L+Y ID D FEE + E + VP++V NK DL
Sbjct: 85 VLIYVIDSADRKRFEEAGQELVELLEEEKLAGVPVLVFANKQDLLT 130
>gnl|CDD|232980 TIGR00450, mnmE_trmE_thdF, tRNA modification GTPase TrmE. TrmE,
also called MnmE and previously designated ThdF
(thiophene and furan oxidation protein), is a GTPase
involved in tRNA modification to create
5-methylaminomethyl-2-thiouridine in the wobble position
of some tRNAs. This protein and GidA form an
alpha2/beta2 heterotetramer [Protein synthesis, tRNA and
rRNA base modification].
Length = 442
Score = 36.7 bits (85), Expect = 0.031
Identities = 21/62 (33%), Positives = 35/62 (56%), Gaps = 4/62 (6%)
Query: 60 DTRHKVVVMGGPKVGKSSIIHRFLYNTFS--PKYKRTIEEMHHEDFSMNGVHLKLDILDT 117
D K+ ++G P VGKSS+++ L + K T ++ DF +NG+ +K +LDT
Sbjct: 201 DDGFKLAIVGSPNVGKSSLLNALLKQDRAIVSDIKGTTRDVVEGDFELNGILIK--LLDT 258
Query: 118 SG 119
+G
Sbjct: 259 AG 260
>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 = 35.2 bits (81), Expect = 0.035
Identities = 18/66 (27%), Positives = 25/66 (37%), Gaps = 1/66 (1%)
Query: 177 EFPAMRALSISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLAD 236
F M +VY + + SF + + P V+VGNK DL D
Sbjct: 65 LFSDMVENVWEQPAVVCVVYDVTNEVSFNNCSRWINRVRTHSHGLHTPGVLVGNKCDLTD 124
Query: 237 ENRQVD 242
R+VD
Sbjct: 125 R-REVD 129
>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 = 35.2 bits (81), Expect = 0.037
Identities = 22/67 (32%), Positives = 37/67 (55%), Gaps = 3/67 (4%)
Query: 172 TCSTNEFPAMRALSISSADAFILVYAIDDPNSFEEIRLIRDHIFETKA-STAVPIVVVGN 230
T ++ +R LS AD F+L +++ S+E + ++ I E + + VPIV+VG
Sbjct: 56 TAGQEDYNRLRPLSYRGADVFLLAFSLISKASYENV--LKKWIPELRHYAPGVPIVLVGT 113
Query: 231 KSDLADE 237
K DL D+
Sbjct: 114 KLDLRDD 120
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 36.8 bits (86), Expect = 0.039
Identities = 42/142 (29%), Positives = 58/142 (40%), Gaps = 45/142 (31%)
Query: 178 FPAMRALSISSADAFILVYAIDD---PNSFEEIRLIRDHIFETKASTA-VPIVVVGNKSD 233
F AMRA D +LV A DD P + E I +H KA A VPI+V NK D
Sbjct: 309 FTAMRARGAQVTDIVVLVVAADDGVMPQTIEAI----NH---AKA--AGVPIIVAINKID 359
Query: 234 LADENRQVDLTGGPFQTYLSGLPDSVCAHQISGTPDQVPYDTTE-SVVQVDW--ENGFVE 290
N PD+V + +E +V +W + FV
Sbjct: 360 KPGAN-----------------------------PDRVKQELSEYGLVPEEWGGDTIFVP 390
Query: 291 ASAKDNTNITQVFKELLVQAKV 312
SAK I ++ + +L+QA+V
Sbjct: 391 VSAKTGEGIDELLEAILLQAEV 412
>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 = 34.7 bits (80), Expect = 0.062
Identities = 30/128 (23%), Positives = 52/128 (40%), Gaps = 48/128 (37%)
Query: 193 ILVYAIDDPNSFEEIRL----IRDHIFETKASTAVPIVVVGNKSDLADENRQVDLTGGPF 248
+LVY I +F + R H +++ + I+++GNK DL E+R+
Sbjct: 81 LLVYDITRRETFNHLTSWLEDARQH-----SNSNMTIMLIGNKCDL--ESRR-------- 125
Query: 249 QTYLSGLPDSVCAHQISGTPDQVPYDTTESVVQVDWENG--FVEASAKDNTNITQVFKEL 306
+V Y+ E+ + E+G F+E SAK +N+ + F
Sbjct: 126 ---------------------EVSYEEGEAFAR---EHGLIFMETSAKTASNVEEAF--- 158
Query: 307 LVQAKVKY 314
+ AK Y
Sbjct: 159 INTAKEIY 166
Score = 32.8 bits (75), Expect = 0.24
Identities = 20/60 (33%), Positives = 34/60 (56%), Gaps = 1/60 (1%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIE-EMHHEDFSMNGVHLKLDILDTSGEQS 122
K +++G VGKS ++ +F F P + TI E +++G +KL I DT+G++S
Sbjct: 6 KYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQES 65
>gnl|CDD|237040 PRK12289, PRK12289, GTPase RsgA; Reviewed.
Length = 352
Score = 35.4 bits (82), Expect = 0.067
Identities = 20/56 (35%), Positives = 32/56 (57%), Gaps = 5/56 (8%)
Query: 186 ISSADAFILVYAIDDPNSFEEIRLIRDHIFETKA-STAVPIVVVGNKSDLADENRQ 240
+++AD +LV+A+ +P + +L R F KA ST + IV+ NK+DL Q
Sbjct: 87 VANADQILLVFALAEP-PLDPWQLSR---FLVKAESTGLEIVLCLNKADLVSPTEQ 138
>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 = 34.2 bits (78), Expect = 0.092
Identities = 18/63 (28%), Positives = 35/63 (55%), Gaps = 9/63 (14%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSM-----NGVHLKLDILDTS 118
+++++G VGK+ ++ RF N F + TI DF M +G+ +++ I DT+
Sbjct: 2 RLLLIGDSGVGKTCLLCRFTDNEFHSSHISTI----GVDFKMKTIEVDGIKVRIQIWDTA 57
Query: 119 GEQ 121
G++
Sbjct: 58 GQE 60
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 34.5 bits (79), Expect = 0.094
Identities = 19/60 (31%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIE-EMHHEDFSMNGVHLKLDILDTSGEQS 122
K +++G VGKS ++ +F F P + TI E +++ +KL I DT+G++S
Sbjct: 8 KYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDNKPIKLQIWDTAGQES 67
>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 = 33.6 bits (77), Expect = 0.16
Identities = 16/59 (27%), Positives = 33/59 (55%), Gaps = 1/59 (1%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIE-EMHHEDFSMNGVHLKLDILDTSGEQ 121
K++V+G VGK+ + +RF F + + TI + ++G +K+ + DT+G++
Sbjct: 4 KIIVIGDSNVGKTCLTYRFCAGRFPERTEATIGVDFRERTVEIDGERIKVQLWDTAGQE 62
Score = 28.2 bits (63), Expect = 7.6
Identities = 13/49 (26%), Positives = 24/49 (48%)
Query: 191 AFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADENR 239
A + VY + + SF + + + VP ++VGNK DL ++ +
Sbjct: 78 AVVFVYDVTNMASFHSLPSWIEECEQHSLPNEVPRILVGNKCDLREQIQ 126
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 33.6 bits (77), Expect = 0.17
Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 4/59 (6%)
Query: 178 FPAMRALSISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLAD 236
F M + A I++ P +F +I ++ +P+VV NK DL D
Sbjct: 81 FKFMWEILSRGAVGAIVLVDSSRPITFHAEEIID--FLTSRNP--IPVVVAINKQDLFD 135
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 34.3 bits (80), Expect = 0.17
Identities = 18/68 (26%), Positives = 30/68 (44%), Gaps = 8/68 (11%)
Query: 182 RALS-ISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADENRQ 240
R+ I AD +LV +P + E+ ++ + P++VV NK+DL E
Sbjct: 287 RSREAIEEADLVLLVLDASEPLTEEDDEILEELK-------DKPVIVVLNKADLTGEIDL 339
Query: 241 VDLTGGPF 248
+ G P
Sbjct: 340 EEENGKPV 347
>gnl|CDD|133303 cd04103, Centaurin_gamma, Centaurin gamma (CENTG) GTPase. The
centaurins (alpha, beta, gamma, and delta) are large,
multi-domain proteins that all contain an ArfGAP domain
and ankyrin repeats, and in some cases, numerous
additional domains. Centaurin gamma contains an
additional GTPase domain near its N-terminus. The
specific function of this GTPase domain has not been
well characterized, but centaurin gamma 2 (CENTG2) may
play a role in the development of autism. Centaurin
gamma 1 is also called PIKE (phosphatidyl inositol (PI)
3-kinase enhancer) and centaurin gamma 2 is also known
as AGAP (ArfGAP protein with a GTPase-like domain,
ankyrin repeats and a Pleckstrin homology domain) or
GGAP. Three isoforms of PIKE have been identified.
PIKE-S (short) and PIKE-L (long) are brain-specific
isoforms, with PIKE-S restricted to the nucleus and
PIKE-L found in multiple cellular compartments. A third
isoform, PIKE-A was identified in human glioblastoma
brain cancers and has been found in various tissues.
GGAP has been shown to have high GTPase activity due to
a direct intramolecular interaction between the
N-terminal GTPase domain and the C-terminal ArfGAP
domain. In human tissue, AGAP mRNA was detected in
skeletal muscle, kidney, placenta, brain, heart, colon,
and lung. Reduced expression levels were also observed
in the spleen, liver, and small intestine.
Length = 158
Score = 32.5 bits (74), Expect = 0.33
Identities = 12/53 (22%), Positives = 30/53 (56%)
Query: 189 ADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADENRQV 241
DA I V++++D SF+ + + + + + +P+++VG + ++ N +V
Sbjct: 66 VDAVIFVFSLEDEASFQTVYRLYHQLSSYRNISEIPLILVGTQDAISASNPRV 118
Score = 29.4 bits (66), Expect = 3.5
Identities = 8/26 (30%), Positives = 18/26 (69%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSP 89
K+ ++G + GKS+++HR+L ++
Sbjct: 2 KLGIVGNLRSGKSALVHRYLTGSYVQ 27
>gnl|CDD|224776 COG1863, MnhE, Multisubunit Na+/H+ antiporter, MnhE subunit
[Inorganic ion transport and metabolism].
Length = 158
Score = 32.3 bits (74), Expect = 0.36
Identities = 18/75 (24%), Positives = 30/75 (40%), Gaps = 4/75 (5%)
Query: 142 KVCLRRALNQRPM--AYKTDVQLPSKLTSLAMTCSTNEFPAMRALSISSADAFILVYAID 199
K+ LR P A T+++ +T LA S P L +S ++ V+AID
Sbjct: 77 KIVLRPKRPINPGIVAVPTELKSDLAITLLAN--SITLTPGTLTLDVSDDRKYLYVHAID 134
Query: 200 DPNSFEEIRLIRDHI 214
+ I++
Sbjct: 135 VEDKEAARESIKNRF 149
>gnl|CDD|206752 cd01859, MJ1464, An uncharacterized, circularly permuted subfamily
of the Ras GTPases. This family represents archaeal
GTPase typified by the protein MJ1464 from Methanococcus
jannaschii. The members of this family show a circular
permutation of the GTPase signature motifs so that
C-terminal strands 5, 6, and 7 (strands 6 contain the
NKxD motif) are relocated to the N terminus.
Length = 157
Score = 31.9 bits (73), Expect = 0.40
Identities = 12/16 (75%), Positives = 13/16 (81%)
Query: 64 KVVVMGGPKVGKSSII 79
V V+G PKVGKSSII
Sbjct: 101 IVGVVGYPKVGKSSII 116
>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 = 31.5 bits (72), Expect = 0.55
Identities = 27/117 (23%), Positives = 42/117 (35%), Gaps = 33/117 (28%)
Query: 194 LVYAID--DPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADENRQVDLTGGPFQTY 251
+VY +D D E + + E + +P++V+GNK+DL +L Q
Sbjct: 71 IVYVVDAADREKLEVAKNELHDLLEKPSLEGIPLLVLGNKNDLPGALSVDELIE---QMN 127
Query: 252 LSGLPD-SVCAHQISGTPDQVPYDTTESVVQVDWENGFVEASAKDNTNITQVFKELL 307
L + D V + I SAK+ TNI V L+
Sbjct: 128 LKSITDREVSCYSI---------------------------SAKEKTNIDIVLDWLI 157
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes. TrmE
contains a GTPase domain that forms a canonical Ras-like
fold. It functions a molecular switch GTPase, and
apparently uses a conformational change associated with
GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 31.7 bits (73), Expect = 0.58
Identities = 19/75 (25%), Positives = 31/75 (41%), Gaps = 8/75 (10%)
Query: 182 RAL-SISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADENRQ 240
RA +I AD +++ +D +E L + K P++VV NKSDL +
Sbjct: 75 RAREAIEEAD--LVLLVVDASEGLDEEDLEILELPAKK-----PVIVVLNKSDLLSDAEG 127
Query: 241 VDLTGGPFQTYLSGL 255
+ G +S
Sbjct: 128 ISELNGKPIIAISAK 142
>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 = 31.8 bits (72), Expect = 0.59
Identities = 21/74 (28%), Positives = 33/74 (44%), Gaps = 5/74 (6%)
Query: 172 TCSTNEFPAMRALSISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNK 231
T + + AM + A A I+ Y + D +SFE + + I + G K
Sbjct: 57 TAGSERYEAMSRIYYRGAKAAIVCYDLTDSSSFERAKFWVKEL--QNLEEHCKIYLCGTK 114
Query: 232 SDLADEN---RQVD 242
SDL +++ RQVD
Sbjct: 115 SDLIEQDRSLRQVD 128
Score = 29.8 bits (67), Expect = 3.2
Identities = 18/60 (30%), Positives = 33/60 (55%), Gaps = 2/60 (3%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTF-SPKYKRTI-EEMHHEDFSMNGVHLKLDILDTSGEQ 121
KVV++G VGK+S++ R++++ F Y+ TI + + + L I DT+G +
Sbjct: 2 KVVMLGKESVGKTSLVERYVHHRFLVGPYQNTIGAAFVAKRMVVGERVVTLGIWDTAGSE 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 = 32.2 bits (73), Expect = 0.59
Identities = 11/24 (45%), Positives = 18/24 (75%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTF 87
KVV++G VGK+S++HR++ F
Sbjct: 2 KVVLLGDMNVGKTSLLHRYMERRF 25
Score = 30.3 bits (68), Expect = 2.4
Identities = 35/161 (21%), Positives = 57/161 (35%), Gaps = 13/161 (8%)
Query: 172 TCSTNEFPAMRALSISSADAFILVYAIDDPNSFEEI--RLIRDHIFETKASTAVPIVVVG 229
T +F + ++ A A IL Y + + S EE+ R + + +T A+ VVG
Sbjct: 51 TAGREQFHGLGSMYCRGAAAVILTYDVSNVQSLEELEDRFL--GLTDT-ANEDCLFAVVG 107
Query: 230 NKSDLADENRQVDLTGGPFQTYLSGLPDSVCAHQISGTPDQV-PYDTTESVVQVDWENGF 288
NK DL +E V ++ Y + + E
Sbjct: 108 NKLDLTEEGALAGQEKDAGDRVSPEDQRQVTLEDAKAFYKRINKYKMLDEDLSPAAEKMC 167
Query: 289 VEASAKDNTNITQVFKELLVQAKVKYNLSPALRRRRRQSLP 329
E SAK N+ ++F+ L +NL L +R
Sbjct: 168 FETSAKTGYNVDELFEYL-------FNLVLPLILAQRAEAN 201
>gnl|CDD|215653 pfam00009, GTP_EFTU, Elongation factor Tu GTP binding domain. This
domain contains a P-loop motif, also found in several
other families such as pfam00071, pfam00025 and
pfam00063. Elongation factor Tu consists of three
structural domains, this plus two C-terminal beta barrel
domains.
Length = 184
Score = 31.7 bits (73), Expect = 0.70
Identities = 18/65 (27%), Positives = 24/65 (36%), Gaps = 11/65 (16%)
Query: 178 FPAMRALSISSADAFILVYAIDD---PNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDL 234
F S AD ILV + P + E + L + VPI+V NK D
Sbjct: 79 FTKEMIRGASQADGAILVVDAVEGVMPQTREHLLLAKTL--------GVPIIVFINKIDR 130
Query: 235 ADENR 239
D+
Sbjct: 131 VDDAE 135
>gnl|CDD|185214 PRK15314, PRK15314, outer membrane protein RatB; Provisional.
Length = 2435
Score = 32.5 bits (73), Expect = 0.88
Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 3/75 (4%)
Query: 197 AIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADENRQVDL---TGGPFQTYLS 253
A + F+ +RL ++ TKA+TA + + + DL+ E D+ G P
Sbjct: 1834 ATHSDSQFQYVRLSDNNTLTTKANTATAQLCLAKRRDLSIELTSSDMDADKGAPVAKKGE 1893
Query: 254 GLPDSVCAHQISGTP 268
LP +V SGTP
Sbjct: 1894 SLPLTVTVRDGSGTP 1908
>gnl|CDD|206739 cd09912, DLP_2, Dynamin-like protein including dynamins,
mitofusins, and guanylate-binding proteins. The dynamin
family of large mechanochemical GTPases includes the
classical dynamins and dynamin-like proteins (DLPs) that
are found throughout the Eukarya. This family also
includes bacterial DLPs. These proteins catalyze
membrane fission during clathrin-mediated endocytosis.
Dynamin consists of five domains; an N-terminal G domain
that binds and hydrolyzes GTP, a middle domain (MD)
involved in self-assembly and oligomerization, a
pleckstrin homology (PH) domain responsible for
interactions with the plasma membrane, GED, which is
also involved in self-assembly, and a proline arginine
rich domain (PRD) that interacts with SH3 domains on
accessory proteins. To date, three vertebrate dynamin
genes have been identified; dynamin 1, which is brain
specific, mediates uptake of synaptic vesicles in
presynaptic terminals; dynamin-2 is expressed
ubiquitously and similarly participates in membrane
fission; mutations in the MD, PH and GED domains of
dynamin 2 have been linked to human diseases such as
Charcot-Marie-Tooth peripheral neuropathy and rare forms
of centronuclear myopathy. Dynamin 3 participates in
megakaryocyte progenitor amplification, and is also
involved in cytoplasmic enlargement and the formation of
the demarcation membrane system. This family also
includes mitofusins (MFN1 and MFN2 in mammals) that are
involved in mitochondrial fusion. Dynamin oligomerizes
into helical structures around the neck of budding
vesicles in a GTP hydrolysis-dependent manner.
Length = 180
Score = 31.0 bits (71), Expect = 0.93
Identities = 15/53 (28%), Positives = 22/53 (41%), Gaps = 4/53 (7%)
Query: 186 ISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADEN 238
+ ADA I V + D P + E +++ + I V NK DL E
Sbjct: 71 LPRADAVIFVLSADQPLTESEREFLKEI----LKWSGKKIFFVLNKIDLLSEE 119
>gnl|CDD|197556 smart00178, SAR, Sar1p-like members of the Ras-family of small
GTPases. Yeast SAR1 is an essential gene required for
transport of secretory proteins from the endoplasmic
reticulum to the Golgi apparatus.
Length = 184
Score = 31.1 bits (70), Expect = 0.94
Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 2/42 (4%)
Query: 194 LVYAID--DPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSD 233
+VY +D D F E + D + + VP +++GNK D
Sbjct: 88 IVYLVDAYDKERFAESKRELDALLSDEELATVPFLILGNKID 129
>gnl|CDD|223091 COG0012, COG0012, Predicted GTPase, probable translation factor
[Translation, ribosomal structure and biogenesis].
Length = 372
Score = 31.4 bits (72), Expect = 1.2
Identities = 8/34 (23%), Positives = 14/34 (41%), Gaps = 4/34 (11%)
Query: 205 EEIRLIRDHIFETKASTAVPIVVVGNKSDLADEN 238
E++ + T A P++ V N S+ N
Sbjct: 193 EDLEALASLNLLT----AKPMLYVANVSEDDLAN 222
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 31.3 bits (72), Expect = 1.3
Identities = 8/18 (44%), Positives = 15/18 (83%)
Query: 64 KVVVMGGPKVGKSSIIHR 81
+ +++G P VGKS++I+R
Sbjct: 123 RAMIIGIPNVGKSTLINR 140
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 31.4 bits (72), Expect = 1.3
Identities = 12/40 (30%), Positives = 20/40 (50%)
Query: 44 LVSASSENESGSSEGHDTRHKVVVMGGPKVGKSSIIHRFL 83
++ +E E K+ ++G P VGKSS+I+ L
Sbjct: 160 VLELLPPDEEEEEEEETDPIKIAIIGRPNVGKSSLINAIL 199
>gnl|CDD|206647 cd00881, GTP_translation_factor, GTP translation factor family
primarily contains translation initiation, elongation
and release factors. The GTP translation factor family
consists primarily of translation initiation,
elongation, and release factors, which play specific
roles in protein translation. In addition, the family
includes Snu114p, a component of the U5 small nuclear
riboprotein particle which is a component of the
spliceosome and is involved in excision of introns,
TetM, a tetracycline resistance gene that protects the
ribosome from tetracycline binding, and the unusual
subfamily CysN/ATPS, which has an unrelated function
(ATP sulfurylase) acquired through lateral transfer of
the EF1-alpha gene and development of a new function.
Length = 183
Score = 30.7 bits (70), Expect = 1.4
Identities = 15/55 (27%), Positives = 25/55 (45%), Gaps = 5/55 (9%)
Query: 185 SISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADENR 239
++ AD +LV ++ E + R+H+ A +PI+V NK D E
Sbjct: 82 GLAQADGALLVVDANE---GVEPQT-REHLNIALA-GGLPIIVAVNKIDRVGEED 131
>gnl|CDD|234125 TIGR03156, GTP_HflX, GTP-binding protein HflX. This protein family
is one of a number of homologous small, well-conserved
GTP-binding proteins with pleiotropic effects. Bacterial
members are designated HflX, following the naming
convention in Escherichia coli where HflX is encoded
immediately downstream of the RNA chaperone Hfq, and
immediately upstream of HflKC, a membrane-associated
protease pair with an important housekeeping function.
Over large numbers of other bacterial genomes, the
pairing with hfq is more significant than with hflK and
hlfC. The gene from Homo sapiens in this family has been
named PGPL (pseudoautosomal GTP-binding protein-like)
[Unknown function, General].
Length = 351
Score = 31.3 bits (72), Expect = 1.4
Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 4/69 (5%)
Query: 188 SADAFILVYAID--DPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADENR-QVDLT 244
+A +L++ +D DP+ E+I + + E A +P ++V NK DL DE R +
Sbjct: 266 VREADLLLHVVDASDPDREEQIEAVEKVLEELGA-EDIPQLLVYNKIDLLDEPRIERLEE 324
Query: 245 GGPFQTYLS 253
G P ++S
Sbjct: 325 GYPEAVFVS 333
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 31.2 bits (71), Expect = 1.7
Identities = 10/18 (55%), Positives = 15/18 (83%)
Query: 64 KVVVMGGPKVGKSSIIHR 81
+V V+G P VGKS++I+R
Sbjct: 134 RVGVVGYPNVGKSTLINR 151
>gnl|CDD|206686 cd01899, Ygr210, Ygr210 GTPase. Ygr210 is a member of Obg-like
family and present in archaea and fungi. They are
characterized by a distinct glycine-rich motif
immediately following the Walker B motif. The Ygr210 and
YyaF/YchF subfamilies appear to form one major branch of
the Obg-like family. Among eukaryotes, the Ygr210
subfamily is represented only in fungi. These fungal
proteins form a tight cluster with their archaeal
orthologs, which suggests the possibility of horizontal
transfer from archaea to fungi.
Length = 318
Score = 31.0 bits (71), Expect = 1.8
Identities = 10/40 (25%), Positives = 16/40 (40%), Gaps = 8/40 (20%)
Query: 199 DDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADEN 238
DD + R +R P+V+ NK+D+ D
Sbjct: 199 DDEDLLRLARELRKRRK--------PMVIAANKADIPDAE 230
>gnl|CDD|227581 COG5256, TEF1, Translation elongation factor EF-1alpha (GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 428
Score = 30.7 bits (70), Expect = 2.0
Identities = 18/60 (30%), Positives = 23/60 (38%), Gaps = 5/60 (8%)
Query: 185 SISSADAFILVYAIDDPN---SFEEIRLIRDHIFETKASTAVPIVVVGNKSDLA--DENR 239
S AD +LV D F R+H F + ++V NK DL DE R
Sbjct: 105 GASQADVAVLVVDARDGEFEAGFGVGGQTREHAFLARTLGIKQLIVAVNKMDLVSWDEER 164
>gnl|CDD|235878 PRK06851, PRK06851, hypothetical protein; Provisional.
Length = 367
Score = 30.7 bits (70), Expect = 2.2
Identities = 11/52 (21%), Positives = 21/52 (40%), Gaps = 12/52 (23%)
Query: 62 RHKVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEEMHHEDFSMNGVHLKLD 113
++ GGP GKS+++ K+ EE + + + +H D
Sbjct: 30 NRIFILKGGPGTGKSTLM------------KKIGEEFLEKGYDVEFLHCSSD 69
>gnl|CDD|213833 TIGR03596, GTPase_YlqF, ribosome biogenesis GTP-binding protein
YlqF. Members of this protein family are GTP-binding
proteins involved in ribosome biogenesis, including the
essential YlqF protein of Bacillus subtilis, which is an
essential protein. They are related to Era, EngA, and
other GTPases of ribosome biogenesis, but are circularly
permuted. This family is not universal, and is not
present in Escherichia coli, and so is not as well
studied as some other GTPases. This model is built for
bacterial members [Protein synthesis, Other].
Length = 276
Score = 30.6 bits (70), Expect = 2.3
Identities = 8/20 (40%), Positives = 15/20 (75%)
Query: 64 KVVVMGGPKVGKSSIIHRFL 83
+ +++G P VGKS++I+R
Sbjct: 120 RAMIVGIPNVGKSTLINRLA 139
>gnl|CDD|206748 cd01855, YqeH, Circularly permuted YqeH GTPase. YqeH is an
essential GTP-binding protein. Depletion of YqeH induces
an excess initiation of DNA replication, suggesting that
it negatively controls initiation of chromosome
replication. The YqeH subfamily is common in eukaryotes
and sporadically present in bacteria with probable
acquisition by plants from chloroplasts. Proteins of the
YqeH family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases.
Length = 191
Score = 29.9 bits (68), Expect = 2.3
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 62 RHKVVVMGGPKVGKSSIIHRFL 83
R V V+G VGKS++I+ L
Sbjct: 125 RGDVYVVGATNVGKSTLINALL 146
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 30.1 bits (67), Expect = 2.4
Identities = 23/66 (34%), Positives = 33/66 (50%), Gaps = 3/66 (4%)
Query: 172 TCSTNEFPAMRALSISSADAFILVYAIDDPNSFEEI-RLIRDHIFETKASTAVPIVVVGN 230
T F ++ I + A I+VY I + SFE + I+D + E V I +VGN
Sbjct: 36 TAGQERFRSLIPSYIRDSAAAIVVYDITNRQSFENTTKWIQDILNERGKD--VIIALVGN 93
Query: 231 KSDLAD 236
K+DL D
Sbjct: 94 KTDLGD 99
>gnl|CDD|227395 COG5063, CTH1, CCCH-type Zn-finger protein [General function
prediction only].
Length = 351
Score = 30.4 bits (68), Expect = 2.4
Identities = 11/50 (22%), Positives = 19/50 (38%), Gaps = 1/50 (2%)
Query: 14 PSLHSQFFVSAENAGSQFLQPSLNFNRILNLVSASSENESGSSEGHDTRH 63
S + + + + +PSLN I +L ++ E SSE
Sbjct: 37 LSRRTSYLRNICECSEYYKKPSLN-ETISHLSASLDNKEQSSSEKRQKAE 85
>gnl|CDD|188527 TIGR04012, poly_gGlu_PgsB, poly-gamma-glutamate synthase PgsB/CapB.
Of four genes commonly found to be involved in
biosynthesis and export of poly-gamma-glutamate,
pgsB(capB) and pgsC(capC) are found to be involved in
the synthesis per se. Members of this family are
designated PgsB, a nomeclature that covers both cases in
which the poly-gamma-glutamate is secreted and those in
which it is retained to form capsular material.PgsB has
been shown to have poly-gamma-glutamate activity by
itself but is bound tightly by PgsC (TIGR04011) [Cell
envelope, Other].
Length = 366
Score = 30.4 bits (69), Expect = 2.6
Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 3/49 (6%)
Query: 192 FILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADENRQ 240
F+ +A +DP S E I D + T P++++ ++D D +Q
Sbjct: 242 FVNAFAANDPVSTE---RIWDRVCAKGYPTDKPVLIMNCRADRVDRTKQ 287
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 30.4 bits (70), Expect = 2.7
Identities = 12/58 (20%), Positives = 23/58 (39%), Gaps = 5/58 (8%)
Query: 185 SISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADENRQVD 242
S+ D + V D+ + + I E P+++V NK DL + ++
Sbjct: 81 SLKDVDLVLFVVDADEKIGPGD-----EFILEKLKKVKTPVILVLNKIDLVKDKEELL 133
>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 = 29.9 bits (67), Expect = 2.9
Identities = 15/54 (27%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 182 RALSISSADAFILVYAIDDPNSFEEIRLIRDHIFETKA-STAVPIVVVGNKSDL 234
R + +D +L ++I PNS ++ + E + VP+++VG K DL
Sbjct: 81 RRFAYGRSDVVLLCFSIASPNSLRNVKTMWYP--EIRHFCPRVPVILVGCKLDL 132
>gnl|CDD|234274 TIGR03594, GTPase_EngA, ribosome-associated GTPase EngA. EngA
(YfgK, Der) is a ribosome-associated essential GTPase
with a duplication of its GTP-binding domain. It is
broadly to universally distributed among bacteria. It
appears to function in ribosome biogenesis or stability
[Protein synthesis, Other].
Length = 429
Score = 30.5 bits (70), Expect = 3.0
Identities = 15/64 (23%), Positives = 27/64 (42%), Gaps = 8/64 (12%)
Query: 20 FFVSAENAGSQFLQPSLNFNRILNLVSASSENESGSSEGHDTRHKVVVMGGPKVGKSSII 79
+SAE+ +L+ + E E D K+ ++G P VGKS+++
Sbjct: 138 IPISAEH--------GRGIGDLLDAILELLPEEEEEEEEEDGPIKIAIIGRPNVGKSTLV 189
Query: 80 HRFL 83
+ L
Sbjct: 190 NALL 193
>gnl|CDD|206669 cd01882, BMS1, Bms1, an essential GTPase, promotes assembly of
preribosomal RNA processing complexes. Bms1 is an
essential, evolutionarily conserved, nucleolar protein.
Its depletion interferes with processing of the 35S
pre-rRNA at sites A0, A1, and A2, and the formation of
40S subunits. Bms1, the putative endonuclease Rc11, and
the essential U3 small nucleolar RNA form a stable
subcomplex that is believed to control an early step in
the formation of the 40S subumit. The C-terminal domain
of Bms1 contains a GTPase-activating protein (GAP) that
functions intramolecularly. It is believed that Rc11
activates Bms1 by acting as a guanine-nucleotide
exchange factor (GEF) to promote GDP/GTP exchange, and
that activated (GTP-bound) Bms1 delivers Rc11 to the
preribosomes.
Length = 231
Score = 30.0 bits (68), Expect = 3.1
Identities = 13/33 (39%), Positives = 21/33 (63%), Gaps = 4/33 (12%)
Query: 65 VVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIEE 97
VVV+G P VGKS++I R L ++ K+ + +
Sbjct: 42 VVVVGPPGVGKSTLI-RSLIKRYT---KQNLSD 70
>gnl|CDD|206753 cd04178, Nucleostemin_like, A circularly permuted subfamily of the
Ras GTPases. Nucleostemin (NS) is a nucleolar protein
that functions as a regulator of cell growth and
proliferation in stem cells and in several types of
cancer cells, but is not expressed in the differentiated
cells of most mammalian adult tissues. NS shuttles
between the nucleolus and nucleoplasm bidirectionally at
a rate that is fast and independent of cell type.
Lowering GTP levels decreases the nucleolar retention of
NS, and expression of NS is abruptly down-regulated
during differentiation prior to terminal cell division.
Found only in eukaryotes, NS consists of an N-terminal
basic domain, a coiled-coil domain, a GTP-binding
domain, an intermediate domain, and a C-terminal acidic
domain. Experimental evidence indicates that NS uses its
GTP-binding property as a molecular switch to control
the transition between the nucleolus and nucleoplasm,
and this process involves interaction between the basic,
GTP-binding, and intermediate domains of the protein.
Length = 171
Score = 29.1 bits (66), Expect = 4.0
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 56 SEGHDTRHKVVVMGGPKVGKSSII 79
++G T V V+G P VGKSS+I
Sbjct: 110 NKGIKTSITVGVVGYPNVGKSSVI 133
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 29.1 bits (66), Expect = 4.0
Identities = 11/41 (26%), Positives = 19/41 (46%), Gaps = 2/41 (4%)
Query: 64 KVVVMGGPKVGKSSIIHRF--LYNTFSPKYKRTIEEMHHED 102
++V+ GGP GK++++ P+Y R E D
Sbjct: 1 RIVITGGPSTGKTTLLEALAARGYPVVPEYGREYIEEQLAD 41
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 29.1 bits (66), Expect = 4.2
Identities = 9/45 (20%), Positives = 21/45 (46%), Gaps = 2/45 (4%)
Query: 194 LVYAID--DPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLAD 236
+++ +D D + EE + + + P++++ NK DL
Sbjct: 85 VIFVVDSADRDRIEEAKEELHALLNEEELADAPLLILANKQDLPG 129
>gnl|CDD|183452 PRK12337, PRK12337, 2-phosphoglycerate kinase; Provisional.
Length = 475
Score = 29.7 bits (67), Expect = 4.5
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 203 SFEEIRLIRDHIFETKASTAVPIVVVGNKSDLAD 236
FEEIRLI+DH+ VP++ + + D
Sbjct: 420 HFEEIRLIQDHLLRLARQEGVPVLPGEDLDESID 453
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 29.9 bits (68), Expect = 4.6
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 2/50 (4%)
Query: 187 SSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLAD 236
S ADA +LV A DD R+H+F + ++V NK D +
Sbjct: 106 SQADAAVLVVAADDAGGVMP--QTREHVFLARTLGINQLIVAINKMDAVN 153
>gnl|CDD|234395 TIGR03918, GTP_HydF, [FeFe] hydrogenase H-cluster maturation GTPase
HydF. This model describes the family of the [Fe]
hydrogenase maturation protein HypF as characterized in
Chlamydomonas reinhardtii and found, in an operon with
radical SAM proteins HydE and HydG, in numerous
bacteria. It has GTPase activity, can bind an 4Fe-4S
cluster, and is essential for hydrogenase activity
[Protein fate, Protein modification and repair].
Length = 391
Score = 29.8 bits (68), Expect = 4.6
Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 5/58 (8%)
Query: 186 ISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADENRQVDL 243
+ D +LV E+ LI + + E K +P +VV NK DL +E+ +++
Sbjct: 83 LDKTDLALLVVDAGVGPGEYELELI-EELKERK----IPYIVVINKIDLGEESAELEK 135
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 29.8 bits (68), Expect = 4.9
Identities = 21/78 (26%), Positives = 31/78 (39%), Gaps = 9/78 (11%)
Query: 181 MRAL-SISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDL--ADE 237
RA +I AD + V P +E + + + + K PI+VV NK+DL E
Sbjct: 288 ERAKKAIEEADLVLFVLDASQPLD-KEDLALIELLPKKK-----PIIVVLNKADLVSKIE 341
Query: 238 NRQVDLTGGPFQTYLSGL 255
L G +S
Sbjct: 342 LESEKLANGDAIISISAK 359
Score = 29.1 bits (66), Expect = 7.4
Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 24/69 (34%)
Query: 63 HKVVVMGGPKVGKSSIIHRFLYNTFSPKYKR------------TIEEMHHEDFSMNGVHL 110
KVV++G P VGKSS+++ L R IE ED ++NG+ +
Sbjct: 218 LKVVIIGRPNVGKSSLLNALL------GRDRAIVTDIAGTTRDVIE----EDINLNGIPV 267
Query: 111 KLDILDTSG 119
+ ++DT+G
Sbjct: 268 R--LVDTAG 274
>gnl|CDD|206666 cd01878, HflX, HflX GTPase family. HflX subfamily. A distinct
conserved domain with a glycine-rich segment N-terminal
of the GTPase domain characterizes the HflX subfamily.
The E. coli HflX has been implicated in the control of
the lambda cII repressor proteolysis, but the actual
biological functions of these GTPases remain unclear.
HflX is widespread, but not universally represented in
all three superkingdoms.
Length = 204
Score = 29.0 bits (66), Expect = 5.1
Identities = 17/49 (34%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 189 ADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADE 237
AD + V DP+ E+I + + + E A +PI++V NK DL D+
Sbjct: 121 ADLLLHVVDASDPDREEQIETVEEVLKELGAD-DIPIILVLNKIDLLDD 168
>gnl|CDD|218203 pfam04670, Gtr1_RagA, Gtr1/RagA G protein conserved region. GTR1
was first identified in S. cerevisiae as a suppressor of
a mutation in RCC1. Biochemical analysis revealed that
Gtr1 is in fact a G protein of the Ras family. The
RagA/B proteins are the human homologues of Gtr1.
Included in this family is the human Rag C, a novel
protein that has been shown to interact with RagA/B.
Length = 230
Score = 29.1 bits (66), Expect = 5.2
Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 5/59 (8%)
Query: 64 KVVVMGGPKVGKSSIIHRFLYNTFSPKYKRTIE---EMHHEDFSMNGVHLKLDILDTSG 119
KV++MG GKSS+ N +SP+ + ++ G +L L++ D G
Sbjct: 1 KVLLMGLRGSGKSSMRSIIFSN-YSPRDTLRLGATIDVEQSHVRFLG-NLTLNLWDCPG 57
>gnl|CDD|206749 cd01856, YlqF, Circularly permuted YlqF GTPase. Proteins of the
YlqF family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases. The YlqF subfamily is represented in all
eukaryotes as well as a phylogenetically diverse array
of bacteria (including gram-positive bacteria,
proteobacteria, Synechocystis, Borrelia, and
Thermotoga).
Length = 171
Score = 28.6 bits (65), Expect = 5.5
Identities = 9/20 (45%), Positives = 15/20 (75%)
Query: 64 KVVVMGGPKVGKSSIIHRFL 83
+ +V+G P VGKS++I+R
Sbjct: 117 RAMVVGIPNVGKSTLINRLR 136
>gnl|CDD|235281 PRK04328, PRK04328, hypothetical protein; Provisional.
Length = 249
Score = 29.3 bits (66), Expect = 5.7
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 62 RHKVVVMGGPKVGKSSIIHRFLYN 85
R+ V++ GGP GKS +FL+N
Sbjct: 23 RNVVLLSGGPGTGKSIFSQQFLWN 46
>gnl|CDD|234031 TIGR02840, spore_YtaF, putative sporulation protein YtaF. This
protein family was identified, at the time of the
publication of the Carboxydothermus hydrogenoformans
genome, as having a phylogenetic profile that exactly
matches the subset of the Firmicutes capable of forming
endospores. The species include Bacillus anthracis,
Clostridium tetani, Thermoanaerobacter tengcongensis,
Geobacillus kaustophilus, etc. This protein, previously
named YtaF, is therefore a putative sporulation protein
[Cellular processes, Sporulation and germination].
Length = 206
Score = 28.8 bits (65), Expect = 6.3
Identities = 13/53 (24%), Positives = 18/53 (33%), Gaps = 9/53 (16%)
Query: 81 RFLYNTFSPKYKRTIEEMHHE-DFSMNGVHLKLDIL--------DTSGEQSGK 124
+YN F PK + + + + IL D SG SGK
Sbjct: 77 WIIYNAFRPKKEVKDRSSEPDSTKELKSFGFVIQILRNPEVADLDKSGNISGK 129
>gnl|CDD|218485 pfam05187, ETF_QO, Electron transfer flavoprotein-ubiquinone
oxidoreductase. Electron-transfer
flavoprotein-ubiquinone oxidoreductase (ETF-QO) in the
inner mitochondrial membrane accepts electrons from
electron-transfer flavoprotein which is located in the
mitochondrial matrix and reduces ubiquinone in the
mitochondrial membrane. The two redox centres in the
protein, FAD and a [4Fe4S] cluster, are present in a
64-kDa monomer.
Length = 110
Score = 27.9 bits (63), Expect = 6.3
Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 3/50 (6%)
Query: 129 GAVLWGPKKWGLDKVCLRRALNQRPMAY-KTDVQLP-SKLTSLAMTCSTN 176
G W K D L+ A +P+ Y K D +L +L+S+ ++ +TN
Sbjct: 18 GKSPWTLKHHKPDHAALKPASECKPIDYPKPDGKLTFDRLSSVFLS-NTN 66
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 29.4 bits (66), Expect = 6.6
Identities = 12/40 (30%), Positives = 19/40 (47%)
Query: 44 LVSASSENESGSSEGHDTRHKVVVMGGPKVGKSSIIHRFL 83
L+ S G V ++G P VGKS++++R L
Sbjct: 257 LLEGSGFVAGDEKAGPKAVGVVAIVGRPNVGKSTLVNRIL 296
>gnl|CDD|206726 cd04163, Era, E. coli Ras-like protein (Era) is a multifunctional
GTPase. Era (E. coli Ras-like protein) is a
multifunctional GTPase found in all bacteria except some
eubacteria. It binds to the 16S ribosomal RNA (rRNA) of
the 30S subunit and appears to play a role in the
assembly of the 30S subunit, possibly by chaperoning the
16S rRNA. It also contacts several assembly elements of
the 30S subunit. Era couples cell growth with
cytokinesis and plays a role in cell division and energy
metabolism. Homologs have also been found in eukaryotes.
Era contains two domains: the N-terminal GTPase domain
and a C-terminal domain KH domain that is critical for
RNA binding. Both domains are important for Era
function. Era is functionally able to compensate for
deletion of RbfA, a cold-shock adaptation protein that
is required for efficient processing of the 16S rRNA.
Length = 168
Score = 28.6 bits (65), Expect = 6.9
Identities = 14/73 (19%), Positives = 27/73 (36%), Gaps = 9/73 (12%)
Query: 185 SISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADENRQVDLT 244
++ D + V + E I + + ++K P+++V NK DL + +
Sbjct: 79 ALKDVDLVLFVVDASEWIG-EGDEFILELLKKSK----TPVILVLNKIDLVKDKEDLL-- 131
Query: 245 GGPFQTYLSGLPD 257
P L L
Sbjct: 132 --PLLEKLKELHP 142
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 29.2 bits (66), Expect = 7.0
Identities = 16/35 (45%), Positives = 20/35 (57%), Gaps = 4/35 (11%)
Query: 205 EEIRLIRDHIFETKASTAVPIVVVGNKSDLADENR 239
E+I L+ E K PIVVV NK D+ADE +
Sbjct: 267 EQISLLE----EIKELFKAPIVVVINKIDIADEEK 297
>gnl|CDD|223492 COG0415, PhrB, Deoxyribodipyrimidine photolyase [DNA replication,
recombination, and repair].
Length = 461
Score = 29.2 bits (66), Expect = 7.1
Identities = 11/50 (22%), Positives = 18/50 (36%), Gaps = 9/50 (18%)
Query: 382 NLSPALR------RRRRQSLPPVQHSPNPSLKSKGWVNEQFAWRHYYWYI 425
LSP L R +L + + +NE WR +Y ++
Sbjct: 232 RLSPYLAFGVISPREVYAALL--AAESDAREGTAALINE-LIWREFYQHL 278
>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 = 28.5 bits (64), Expect = 7.3
Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 2/50 (4%)
Query: 189 ADAFILVYAID--DPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLAD 236
A++ ++Y ID D F E + + + +A VP++V+ NK DL D
Sbjct: 73 AESHGVIYVIDSTDRERFNESKSAFEKVINNEALEGVPLLVLANKQDLPD 122
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 29.2 bits (66), Expect = 7.3
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 189 ADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADE 237
AD + V DP E++ + D + E A PI++V NK DL ++
Sbjct: 272 ADLLLHVVDASDPEILEKLEAVEDVLAEIGADEI-PIILVLNKIDLLED 319
>gnl|CDD|163589 TIGR03877, thermo_KaiC_1, KaiC domain protein, Ph0284 family.
Members of this family contain a single copy of the
KaiC domain (pfam06745) that occurs in two copies of
the circadian clock protein kinase KaiC itself. Members
occur primarily in thermophilic archaea and in
Thermotoga.
Length = 237
Score = 28.6 bits (64), Expect = 8.7
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 62 RHKVVVMGGPKVGKSSIIHRFLYN 85
R+ V++ GGP GKS +FL+N
Sbjct: 21 RNVVLLSGGPGTGKSIFSQQFLWN 44
>gnl|CDD|206685 cd01898, Obg, Obg GTPase. The Obg nucleotide binding protein
subfamily has been implicated in stress response,
chromosome partitioning, replication initiation,
mycelium development, and sporulation. Obg proteins are
among a large group of GTP binding proteins conserved
from bacteria to humans. The E. coli homolog, ObgE is
believed to function in ribosomal biogenesis. Members of
the subfamily contain two equally and highly conserved
domains, a C-terminal GTP binding domain and an
N-terminal glycine-rich domain.
Length = 170
Score = 28.2 bits (64), Expect = 8.8
Identities = 17/56 (30%), Positives = 23/56 (41%), Gaps = 18/56 (32%)
Query: 193 ILVYAID-----DPNSFEEIRLIR------DHIFETKASTAVPIVVVGNKSDLADE 237
+L++ ID DP E+ IR + K P +VV NK DL D
Sbjct: 81 VLLHVIDLSGEDDP--VEDYETIRNELEAYNPGLAEK-----PRIVVLNKIDLLDA 129
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase. The
Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that generally show sequence
conservation in the region between the Walker A and B
motifs (G1 and G3 box motifs), to the exclusion of other
GTPases. TrmE is ubiquitous in bacteria and is a
widespread mitochondrial protein in eukaryotes, but is
absent from archaea. The yeast member of TrmE family,
MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family.
Length = 161
Score = 28.0 bits (63), Expect = 9.0
Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 6/58 (10%)
Query: 186 ISSADAFILVYAIDDPNSFEEIRLIRDHIFETKASTAVPIVVVGNKSDLADENRQVDL 243
AD +LV D EE +L + E P+++V NK DL E+ + +L
Sbjct: 74 ADRADLVLLVVDSDLTPVEEEAKLGL--LRERG----KPVLLVLNKIDLVPESEEEEL 125
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.316 0.133 0.397
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: 30,051,577
Number of extensions: 2887580
Number of successful extensions: 2874
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2799
Number of HSP's successfully gapped: 278
Length of query: 592
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 490
Effective length of database: 6,413,494
Effective search space: 3142612060
Effective search space used: 3142612060
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: 62 (28.0 bits)