RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11289
(159 letters)
>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 = 274 bits (703), Expect = 3e-96
Identities = 114/141 (80%), Positives = 128/141 (90%)
Query: 3 IESYFVTDYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFS 62
I+SYFVTDYDPTIEDSYTKQC ID ARLDILDTAGQEEFSAMREQYMR+GEGFLLVFS
Sbjct: 23 IQSYFVTDYDPTIEDSYTKQCEIDGQWARLDILDTAGQEEFSAMREQYMRTGEGFLLVFS 82
Query: 63 VTDRNSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYI 122
VTDR SFEE+ KFH QILRVKDRDEFPM++VGNKADL+HQRQVS + Q +ARQL+IPYI
Sbjct: 83 VTDRGSFEEVDKFHTQILRVKDRDEFPMILVGNKADLEHQRQVSREEGQELARQLKIPYI 142
Query: 123 ECSAKVRINVDQAFHELVRIV 143
E SAK R+NVD+AFH+LVR++
Sbjct: 143 ETSAKDRVNVDKAFHDLVRVI 163
>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 = 257 bits (659), Expect = 2e-89
Identities = 91/141 (64%), Positives = 114/141 (80%)
Query: 3 IESYFVTDYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFS 62
I+ +FV DYDPTIEDSY KQ ID LDILDTAGQEEFSAMR+QYMR+GEGFLLV+S
Sbjct: 21 IQGHFVDDYDPTIEDSYRKQIEIDGEVCLLDILDTAGQEEFSAMRDQYMRTGEGFLLVYS 80
Query: 63 VTDRNSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYI 122
+TDR SFEEI KF QILRVKDRD+ P+++VGNK DL+ +R VS+ + + +ARQ P++
Sbjct: 81 ITDRQSFEEIKKFREQILRVKDRDDVPIVLVGNKCDLESERVVSTEEGKELARQWGCPFL 140
Query: 123 ECSAKVRINVDQAFHELVRIV 143
E SAK R+NVD+AF++LVR +
Sbjct: 141 ETSAKERVNVDEAFYDLVREI 161
>gnl|CDD|197466 smart00010, small_GTPase, Small GTPase of the Ras superfamily;
ill-defined subfamily. SMART predicts Ras-like small
GTPases of the ARF, RAB, RAN, RAS, and SAR subfamilies.
Others that could not be classified in this way are
predicted to be members of the small GTPase superfamily
without predictions of the subfamily.
Length = 166
Score = 256 bits (656), Expect = 5e-89
Identities = 90/141 (63%), Positives = 115/141 (81%)
Query: 3 IESYFVTDYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFS 62
++ +FV +YDPTIEDSY KQ ID LDILDTAGQEEFSAMR+QYMR+GEGFLLV+S
Sbjct: 23 VQGHFVDEYDPTIEDSYRKQIEIDGEVCLLDILDTAGQEEFSAMRDQYMRTGEGFLLVYS 82
Query: 63 VTDRNSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYI 122
+TDR SFEEI KF QILRVKDRD+ P+++VGNK DL+++R VS+ + + +ARQ P++
Sbjct: 83 ITDRQSFEEIAKFREQILRVKDRDDVPIVLVGNKCDLENERVVSTEEGKELARQWGCPFL 142
Query: 123 ECSAKVRINVDQAFHELVRIV 143
E SAK RINVD+AF++LVR +
Sbjct: 143 ETSAKERINVDEAFYDLVREI 163
>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 = 220 bits (563), Expect = 6e-75
Identities = 78/139 (56%), Positives = 107/139 (76%)
Query: 3 IESYFVTDYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFS 62
+ FV +YDPTIEDSY KQ V+D LDILDTAGQEEFSAMR+QY+R+G+GF+LV+S
Sbjct: 20 VSGEFVEEYDPTIEDSYRKQIVVDGETYTLDILDTAGQEEFSAMRDQYIRNGDGFILVYS 79
Query: 63 VTDRNSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYI 122
+T R SFEEI QILRVKD+++ P+++VGNK DL+++RQVS+ + + +A + P++
Sbjct: 80 ITSRESFEEIKNIREQILRVKDKEDVPIVLVGNKCDLENERQVSTEEGEALAEEWGCPFL 139
Query: 123 ECSAKVRINVDQAFHELVR 141
E SAK IN+D+ F+ LVR
Sbjct: 140 ETSAKTNINIDELFNTLVR 158
>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 = 219 bits (560), Expect = 2e-74
Identities = 83/139 (59%), Positives = 105/139 (75%), Gaps = 1/139 (0%)
Query: 3 IESYFVTDYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFS 62
I+++FV +YDPTIEDSY KQ VID LDILDTAGQEE+SAMR+QYMR+GEGFL VF+
Sbjct: 22 IQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFA 81
Query: 63 VTDRNSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYI 122
+ R SFE+I+ + QI RVKD D+ PM++VGNK DL R VS+ Q++A+ IPYI
Sbjct: 82 INSRKSFEDIHTYREQIKRVKDSDDVPMVLVGNKCDLA-ARTVSTRQGQDLAKSYGIPYI 140
Query: 123 ECSAKVRINVDQAFHELVR 141
E SAK R V++AF+ LVR
Sbjct: 141 ETSAKTRQGVEEAFYTLVR 159
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 215 bits (549), Expect = 2e-72
Identities = 89/141 (63%), Positives = 116/141 (82%)
Query: 3 IESYFVTDYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFS 62
I+++F+ +YDPTIEDSY KQCVID+ LDILDTAGQEE+SAMR+QYMR+G+GFL V+S
Sbjct: 26 IQNHFIDEYDPTIEDSYRKQCVIDEETCLLDILDTAGQEEYSAMRDQYMRTGQGFLCVYS 85
Query: 63 VTDRNSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYI 122
+T R+SFEEI F QILRVKD+D PM++VGNK DLD +RQVS+ + Q +A+ IP++
Sbjct: 86 ITSRSSFEEIASFREQILRVKDKDRVPMILVGNKCDLDSERQVSTGEGQELAKSFGIPFL 145
Query: 123 ECSAKVRINVDQAFHELVRIV 143
E SAK R+NVD+AF+ELVR +
Sbjct: 146 ETSAKQRVNVDEAFYELVREI 166
>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 = 204 bits (521), Expect = 2e-68
Identities = 64/143 (44%), Positives = 94/143 (65%), Gaps = 2/143 (1%)
Query: 3 IESYFVTDYDPTI-EDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVF 61
++ F +Y PTI D YTK +D +L I DTAGQE F A+R Y R +GFLLV+
Sbjct: 20 TQNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAGQERFRALRPLYYRGAQGFLLVY 79
Query: 62 SVTDRNSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPY 121
+T R+SFE + K+ +ILR D + P+++VGNK DL+ QR VS+ + + +A++L +P+
Sbjct: 80 DITSRDSFENVKKWLEEILRHAD-ENVPIVLVGNKCDLEDQRVVSTEEGEALAKELGLPF 138
Query: 122 IECSAKVRINVDQAFHELVRIVL 144
+E SAK NV++AF EL R +L
Sbjct: 139 METSAKTNENVEEAFEELAREIL 161
>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 = 172 bits (439), Expect = 4e-56
Identities = 76/135 (56%), Positives = 100/135 (74%)
Query: 7 FVTDYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDR 66
FV DY+PT DSY K+ V+D +L+ILDTAGQE+++A+R+ Y RSGEGFLLVFS+TD
Sbjct: 25 FVEDYEPTKADSYRKKVVLDGEEVQLNILDTAGQEDYAAIRDNYFRSGEGFLLVFSITDM 84
Query: 67 NSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYIECSA 126
SF + +F QILRVK+ D P+L+VGNK DL+ +RQVS +A N+A Q + Y+E SA
Sbjct: 85 ESFTALAEFREQILRVKEDDNVPLLLVGNKCDLEDKRQVSVEEAANLAEQWGVNYVETSA 144
Query: 127 KVRINVDQAFHELVR 141
K R NVD+ F +LVR
Sbjct: 145 KTRANVDKVFFDLVR 159
>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 = 170 bits (431), Expect = 2e-54
Identities = 73/154 (47%), Positives = 107/154 (69%), Gaps = 3/154 (1%)
Query: 5 SYFVTDYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVT 64
++FV YDPTIEDSY KQ V+D P L++LDTAGQEE++A+R+Q++R GEGF+LV+S+T
Sbjct: 22 NHFVETYDPTIEDSYRKQVVVDGQPCMLEVLDTAGQEEYTALRDQWIREGEGFILVYSIT 81
Query: 65 DRNSFEEIYKFHRQILRVKDRDE--FPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYI 122
R++FE + +F QI RVKD P+++VGNK D ++R+VS+ + +AR+L +I
Sbjct: 82 SRSTFERVERFREQIQRVKDESAADVPIMIVGNKCDKVYEREVSTEEGAALARRLGCEFI 141
Query: 123 ECSAKVRINVDQAFHELVRIVLLHTKQCKNSTVY 156
E SAK +NV++AF+ LVR L +Q
Sbjct: 142 EASAKTNVNVERAFYTLVR-ALRQQRQGGQGPKG 174
>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 = 168 bits (426), Expect = 4e-54
Identities = 73/143 (51%), Positives = 102/143 (71%), Gaps = 1/143 (0%)
Query: 3 IESYFVTDYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFS 62
+++ F+ YDPTIEDSY KQ ID L+ILDTAG E+F+AMRE Y++SG+GFLLV+S
Sbjct: 22 VQNVFIESYDPTIEDSYRKQVEIDGRQCDLEILDTAGTEQFTAMRELYIKSGQGFLLVYS 81
Query: 63 VTDRNSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQL-RIPY 121
VT S E+ + Q+LR+KD D PM++VGNKADL+ RQVS D ++++Q +P+
Sbjct: 82 VTSEASLNELGELREQVLRIKDSDNVPMVLVGNKADLEDDRQVSREDGVSLSQQWGNVPF 141
Query: 122 IECSAKVRINVDQAFHELVRIVL 144
E SA+ R NVD+ F +LVR ++
Sbjct: 142 YETSARKRTNVDEVFIDLVRQII 164
>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 = 164 bits (416), Expect = 1e-52
Identities = 72/140 (51%), Positives = 102/140 (72%), Gaps = 1/140 (0%)
Query: 3 IESYFVTDYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFS 62
++ FV YDPTIEDSY KQ +D L+ILDTAG E+F+AMR+ Y+++G+GF LV+S
Sbjct: 22 VQGIFVDKYDPTIEDSYRKQIEVDCQQCMLEILDTAGTEQFTAMRDLYIKNGQGFALVYS 81
Query: 63 VTDRNSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQL-RIPY 121
+T + SF ++ QILRVKD ++ PM++VGNK DL+ +R VS + QN+ARQ P+
Sbjct: 82 ITAQQSFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVSKEEGQNLARQWGNCPF 141
Query: 122 IECSAKVRINVDQAFHELVR 141
+E SAK +INVD+ F++LVR
Sbjct: 142 LETSAKSKINVDEIFYDLVR 161
>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 = 163 bits (414), Expect = 3e-52
Identities = 74/139 (53%), Positives = 101/139 (72%)
Query: 3 IESYFVTDYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFS 62
I F +DPTIED+Y Q ID+ PA LDILDTAGQ EF+AMR+QYMR GEGF++ +S
Sbjct: 23 ISHSFPDYHDPTIEDAYKTQARIDNEPALLDILDTAGQAEFTAMRDQYMRCGEGFIICYS 82
Query: 63 VTDRNSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYI 122
VTDR+SF+E +F I RV+ ++ P+++VGNK DL+ QRQV++ + +N+AR+ P+
Sbjct: 83 VTDRHSFQEASEFKELITRVRLTEDIPLVLVGNKVDLEQQRQVTTEEGRNLAREFNCPFF 142
Query: 123 ECSAKVRINVDQAFHELVR 141
E SA +R +D AFH LVR
Sbjct: 143 ETSAALRFYIDDAFHGLVR 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 = 158 bits (401), Expect = 2e-50
Identities = 69/139 (49%), Positives = 101/139 (72%)
Query: 3 IESYFVTDYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFS 62
++ FV YDPTIEDSY KQ +D L+ILDTAG E+F+AMR+ YM++G+GF+LV+S
Sbjct: 22 VQGIFVEKYDPTIEDSYRKQVEVDGQQCMLEILDTAGTEQFTAMRDLYMKNGQGFVLVYS 81
Query: 63 VTDRNSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYI 122
+T +++F ++ QILRVKD ++ PM++VGNK DL+ +R V QN+ARQ ++
Sbjct: 82 ITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVGKEQGQNLARQWGCAFL 141
Query: 123 ECSAKVRINVDQAFHELVR 141
E SAK +INV++ F++LVR
Sbjct: 142 ETSAKAKINVNEIFYDLVR 160
>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 = 153 bits (389), Expect = 2e-48
Identities = 58/139 (41%), Positives = 100/139 (71%)
Query: 3 IESYFVTDYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFS 62
+ F+ YDPTIED Y K+ +D P+ L+ILDTAG E+F++MR+ Y+++G+GF++V+S
Sbjct: 22 VSGTFIEKYDPTIEDFYRKEIEVDSSPSVLEILDTAGTEQFASMRDLYIKNGQGFIVVYS 81
Query: 63 VTDRNSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYI 122
+ ++ +F++I QI+RVK ++ P+++VGNK DL+ +R+VSS + + +A + P++
Sbjct: 82 LVNQQTFQDIKPMRDQIVRVKGYEKVPIILVGNKVDLESEREVSSAEGRALAEEWGCPFM 141
Query: 123 ECSAKVRINVDQAFHELVR 141
E SAK + V++ F E+VR
Sbjct: 142 ETSAKSKTMVNELFAEIVR 160
>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 = 136 bits (345), Expect = 9e-42
Identities = 53/136 (38%), Positives = 79/136 (58%), Gaps = 2/136 (1%)
Query: 7 FVTDYDPTI-EDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTD 65
F +Y TI D +K +D +L I DTAGQE F ++ Y R G +LV+ VT+
Sbjct: 25 FSENYKSTIGVDFKSKTIEVDGKKVKLQIWDTAGQERFRSITSSYYRGAHGAILVYDVTN 84
Query: 66 RNSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYIECS 125
R SFE + K+ ++ P+++VGNK+DL+ +RQVS+ +AQ A++ + + E S
Sbjct: 85 RESFENLDKWLNELKEYAP-PNIPIILVGNKSDLEDERQVSTEEAQQFAKENGLLFFETS 143
Query: 126 AKVRINVDQAFHELVR 141
AK NVD+AF L R
Sbjct: 144 AKTGENVDEAFESLAR 159
>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 = 130 bits (329), Expect = 3e-39
Identities = 52/139 (37%), Positives = 88/139 (63%)
Query: 3 IESYFVTDYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFS 62
+E +FV Y PTIE++++K L+I+DTAGQ+E+S + ++Y G++LV+S
Sbjct: 22 VEGHFVESYYPTIENTFSKIITYKGQEYHLEIVDTAGQDEYSILPQKYSIGIHGYILVYS 81
Query: 63 VTDRNSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYI 122
VT R SFE + + +IL + ++ P+++VGNK+DL +RQVS+ + + +A ++
Sbjct: 82 VTSRKSFEVVKVIYDKILDMLGKESVPIVLVGNKSDLHMERQVSAEEGKKLAESWGAAFL 141
Query: 123 ECSAKVRINVDQAFHELVR 141
E SAK NV++AF L+
Sbjct: 142 ESSAKENENVEEAFELLIE 160
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 127 bits (322), Expect = 3e-38
Identities = 54/139 (38%), Positives = 80/139 (57%), Gaps = 2/139 (1%)
Query: 7 FVTDYDPTIE-DSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTD 65
F Y TI D TK +D +L I DTAGQE F ++ Y R G LLV+ +T+
Sbjct: 25 FSEQYKSTIGVDFKTKTIEVDGKRVKLQIWDTAGQERFRSITSSYYRGAVGALLVYDITN 84
Query: 66 RNSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYIECS 125
R SFE + + +++ + +++VGNK+DL+ QRQVS +A+ A + +P+ E S
Sbjct: 85 RESFENLENWLKELREYASPN-VVIMLVGNKSDLEEQRQVSREEAEAFAEEHGLPFFETS 143
Query: 126 AKVRINVDQAFHELVRIVL 144
AK NV++AF EL R +L
Sbjct: 144 AKTNTNVEEAFEELAREIL 162
>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 = 121 bits (306), Expect = 6e-36
Identities = 57/141 (40%), Positives = 86/141 (60%), Gaps = 4/141 (2%)
Query: 7 FVTDYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSA--MREQYMRSGEGFLLVFSVT 64
F+ +Y+P +E Y++Q ID L+I DT GQ++ E+ +R +GF+LV+S+T
Sbjct: 24 FIGEYEPNLESLYSRQVTIDGEQVSLEIQDTPGQQQNEDPESLERSLRWADGFVLVYSIT 83
Query: 65 DRNSFEEIYKFHRQILRVKDRD-EFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYIE 123
DR+SF+ + + + I +K RD E P+++VGNKADL H RQVS+ + Q +A +L + E
Sbjct: 84 DRSSFDVVSQLLQLIREIKKRDGEIPVILVGNKADLLHSRQVSTEEGQKLALELGCLFFE 143
Query: 124 CSAKVRIN-VDQAFHELVRIV 143
SA V FHEL R V
Sbjct: 144 VSAAENYLEVQNVFHELCREV 164
>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 = 107 bits (269), Expect = 3e-30
Identities = 57/143 (39%), Positives = 80/143 (55%), Gaps = 5/143 (3%)
Query: 7 FVTDYDPTI-EDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTD 65
F Y TI D TK+ +DD L I DTAGQE F ++ + R + +LV+ VT+
Sbjct: 25 FSNQYKATIGADFLTKEVTVDDRLVTLQIWDTAGQERFQSLGVAFYRGADCCVLVYDVTN 84
Query: 66 RNSFEEIYKFHRQIL---RVKDRDEFPMLMVGNKADLDHQRQVSSMDAQN-VARQLRIPY 121
SFE + + + L +D + FP +++GNK DL+ +RQVS+ AQ + IPY
Sbjct: 85 PKSFESLDSWRDEFLIQASPRDPENFPFVVLGNKIDLEEKRQVSTKKAQQWCKSKGNIPY 144
Query: 122 IECSAKVRINVDQAFHELVRIVL 144
E SAK INVDQAF + R+ L
Sbjct: 145 FETSAKEAINVDQAFETIARLAL 167
>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 = 106 bits (268), Expect = 5e-30
Identities = 45/150 (30%), Positives = 79/150 (52%), Gaps = 17/150 (11%)
Query: 7 FVTDYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMRE-QYMRSGEGFLLVFSVTD 65
F T+Y PT+ D+Y+ +D L + DTAGQEE+ +R Y ++ + FLL FSV
Sbjct: 25 FPTEYVPTVFDNYSANVTVDGKQVNLGLWDTAGQEEYDRLRPLSYPQT-DVFLLCFSVDS 83
Query: 66 RNSFEEI-YKFHRQILRVKDRDEFPMLMVGNKADL-----------DHQRQVSSMDAQNV 113
+SFE + K++ +I P+++VG K DL Q+ ++ + + +
Sbjct: 84 PSSFENVKTKWYPEIKHYCPN--VPIILVGTKIDLRDDGNTLKKLEKKQKPITPEEGEKL 141
Query: 114 ARQLR-IPYIECSAKVRINVDQAFHELVRI 142
A+++ + Y+ECSA + + + F E +R
Sbjct: 142 AKEIGAVKYMECSALTQEGLKEVFDEAIRA 171
>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 = 108 bits (271), Expect = 8e-30
Identities = 56/142 (39%), Positives = 74/142 (52%), Gaps = 9/142 (6%)
Query: 7 FVTDYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDR 66
F Y PTIED + K I +LDILDT+G F AMR + +G+ F+LVFS+ +R
Sbjct: 25 FEEQYTPTIEDFHRKLYSIRGEVYQLDILDTSGNHPFPAMRRLSILTGDVFILVFSLDNR 84
Query: 67 NSFEEIYKFHRQILRVKDRD--------EFPMLMVGNKADLDHQRQVSSMDA-QNVARQL 117
SFEE+ + QIL K + PM++ GNKAD D R+V + Q V
Sbjct: 85 ESFEEVCRLREQILETKSCLKNKTKENVKIPMVICGNKADRDFPREVQRDEVEQLVGGDE 144
Query: 118 RIPYIECSAKVRINVDQAFHEL 139
Y E SAK N+D+ F L
Sbjct: 145 NCAYFEVSAKKNSNLDEMFRAL 166
>gnl|CDD|206714 cd04147, Ras_dva, Ras - dorsal-ventral anterior localization
(Ras-dva) family. Ras-dva subfamily. Ras-dva (Ras -
dorsal-ventral anterior localization) subfamily consists
of a set of proteins characterized only in Xenopus
leavis, to date. In Xenopus Ras-dva expression is
activated by the transcription factor Otx2 and begins
during gastrulation throughout the anterior ectoderm.
Ras-dva expression is inhibited in the anterior neural
plate by factor Xanf1. Downregulation of Ras-dva results
in head development abnormalities through the inhibition
of several regulators of the anterior neural plate and
folds patterning, including Otx2, BF-1, Xag2, Pax6,
Slug, and Sox9. Downregulation of Ras-dva also
interferes with the FGF-8a signaling within the anterior
ectoderm. Most Ras proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins.
Length = 197
Score = 104 bits (262), Expect = 5e-29
Identities = 49/136 (36%), Positives = 80/136 (58%), Gaps = 1/136 (0%)
Query: 7 FVTDYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDR 66
F + T+E+ ++K+ + + +DILDT+G F AMR+ +++G+ F LV+SV D
Sbjct: 24 FEPKHRRTVEELHSKEYEVAGVKVTIDILDTSGSYSFPAMRKLSIQNGDAFALVYSVDDP 83
Query: 67 NSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVAR-QLRIPYIECS 125
SFEE+ + +IL VK+ P+++VGNK D +RQV + DA + ++E S
Sbjct: 84 ESFEEVKRLREEILEVKEDKFVPIVVVGNKIDSLAERQVEAADALSTVELDWNNGFVEAS 143
Query: 126 AKVRINVDQAFHELVR 141
AK NV + F EL++
Sbjct: 144 AKDNENVTEVFKELLQ 159
>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 = 103 bits (260), Expect = 7e-29
Identities = 53/142 (37%), Positives = 75/142 (52%), Gaps = 2/142 (1%)
Query: 4 ESYFVTDYDPTIE-DSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFS 62
E F + TI D + +D +L I DTAGQE F + Y R G +LV+
Sbjct: 25 EDSFNPSFISTIGIDFKIRTIELDGKKIKLQIWDTAGQERFRTITTSYYRGAMGIILVYD 84
Query: 63 VTDRNSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYI 122
+TD SFE I + R I D ML VGNK D++ +R VS + + +AR+ I ++
Sbjct: 85 ITDEKSFENIKNWMRNIDEHASEDVERML-VGNKCDMEEKRVVSKEEGEALAREYGIKFL 143
Query: 123 ECSAKVRINVDQAFHELVRIVL 144
E SAK INV++AF L + +L
Sbjct: 144 ETSAKANINVEEAFLTLAKDIL 165
>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 = 103 bits (258), Expect = 9e-29
Identities = 48/136 (35%), Positives = 73/136 (53%), Gaps = 2/136 (1%)
Query: 7 FVTDYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDR 66
F Y PTIED+Y + L I DT G +F AM+ + G F+LV+S+T +
Sbjct: 26 FRESYIPTIEDTYRQVISCSKSICTLQITDTTGSHQFPAMQRLSISKGHAFILVYSITSK 85
Query: 67 NSFEEIYKFHRQILRVK--DRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYIEC 124
S EE+ + I +K + ++ P+++VGNK D R+VSS + +AR ++E
Sbjct: 86 QSLEELKPIYELICEIKGNNLEKIPIMLVGNKCDESPSREVSSSEGAALARTWNCAFMET 145
Query: 125 SAKVRINVDQAFHELV 140
SAK NV + F EL+
Sbjct: 146 SAKTNHNVQELFQELL 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 = 99.7 bits (249), Expect = 2e-27
Identities = 49/140 (35%), Positives = 73/140 (52%), Gaps = 2/140 (1%)
Query: 3 IESYFVTDYDPTIE-DSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVF 61
+ F D TI D K +D +L I DTAGQE F + Y R +G +LV+
Sbjct: 21 TDDTFDEDLSSTIGVDFKVKTVTVDGKKVKLAIWDTAGQERFRTLTSSYYRGAQGVILVY 80
Query: 62 SVTDRNSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPY 121
VT R++F+ + + ++ + ++VGNK D + R+V+ + Q AR+ + +
Sbjct: 81 DVTRRDTFDNLDTWLNELDTYSTNPDAVKMLVGNKIDKE-NREVTREEGQKFARKHNMLF 139
Query: 122 IECSAKVRINVDQAFHELVR 141
IE SAK RI V QAF ELV
Sbjct: 140 IETSAKTRIGVQQAFEELVE 159
>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 = 99.6 bits (249), Expect = 3e-27
Identities = 42/121 (34%), Positives = 70/121 (57%), Gaps = 1/121 (0%)
Query: 20 TKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQI 79
T+ ID + I DTAGQE + A+ Y R G LLV+ +T +++FE + ++ ++
Sbjct: 42 TRTIQIDGKTIKAQIWDTAGQERYRAITSAYYRGAVGALLVYDITKKSTFENVERWLKE- 100
Query: 80 LRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYIECSAKVRINVDQAFHEL 139
LR +++VGNK+DL H R V + +A+ A + + +IE SA NV++AF +L
Sbjct: 101 LRDHADSNIVIMLVGNKSDLRHLRAVPTEEAKAFAEKNGLSFIETSALDGTNVEEAFKQL 160
Query: 140 V 140
+
Sbjct: 161 L 161
>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 = 98.6 bits (246), Expect = 7e-27
Identities = 43/117 (36%), Positives = 67/117 (57%), Gaps = 1/117 (0%)
Query: 25 IDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQILRVKD 84
+D +L I DTAGQE F + Y R G ++V+ VTD+ SF + ++ ++I R
Sbjct: 46 LDGKTVKLQIWDTAGQERFRTITSSYYRGAHGIIIVYDVTDQESFNNVKQWLQEIDRYAS 105
Query: 85 RDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYIECSAKVRINVDQAFHELVR 141
+ L+VGNK DL ++ V +A+ A +L IP++E SAK NV++AF + R
Sbjct: 106 EN-VNKLLVGNKCDLTDKKVVDYTEAKEFADELGIPFLETSAKNATNVEEAFMTMAR 161
>gnl|CDD|133323 cd04123, Rab21, Rab GTPase family 21 (Rab21). The localization and
function of Rab21 are not clearly defined, with
conflicting data reported. Rab21 has been reported to
localize in the ER in human intestinal epithelial cells,
with partial colocalization with alpha-glucosidase, a
late endosomal/lysosomal marker. More recently, Rab21
was shown to colocalize with and affect the morphology
of early endosomes. In Dictyostelium, GTP-bound Rab21,
together with two novel LIM domain proteins, LimF and
ChLim, has been shown to regulate phagocytosis. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 162
Score = 97.7 bits (244), Expect = 1e-26
Identities = 41/132 (31%), Positives = 76/132 (57%), Gaps = 2/132 (1%)
Query: 14 TIEDS-YTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEI 72
T + S + K I L I DTAGQE + A+ Y R +G +LV+ +TD +SF+++
Sbjct: 32 TTQASFFQKTVNIGGKRIDLAIWDTAGQERYHALGPIYYRDADGAILVYDITDADSFQKV 91
Query: 73 YKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYIECSAKVRINV 132
K+ +++ +++ + +++VGNK DL+ QR VS +A+ A+ + + E SAK +
Sbjct: 92 KKWIKELKQMRG-NNISLVIVGNKIDLERQRVVSKSEAEEYAKSVGAKHFETSAKTGKGI 150
Query: 133 DQAFHELVRIVL 144
++ F L + ++
Sbjct: 151 EELFLSLAKRMI 162
>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 = 97.3 bits (243), Expect = 2e-26
Identities = 46/157 (29%), Positives = 77/157 (49%), Gaps = 24/157 (15%)
Query: 6 YFVTDYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTD 65
F DY PT+ ++Y+ +D P L + DTAGQE++ +R + FL+ FSV
Sbjct: 22 AFPEDYVPTVFENYSADVEVDGKPVELGLWDTAGQEDYDRLRPLSYPDTDVFLICFSVDS 81
Query: 66 RNSFEEI-YKFHRQILRVKDRDEF----PMLMVGNKADL----------DHQRQ--VSSM 108
SFE + K++ ++ F P+++VG K DL ++Q V+
Sbjct: 82 PASFENVKEKWYPEVK------HFCPNVPIILVGTKLDLRNDKSTLEELSKKKQEPVTYE 135
Query: 109 DAQNVARQLR-IPYIECSAKVRINVDQAFHELVRIVL 144
Q +A+++ + Y+ECSA + V + F E +R L
Sbjct: 136 QGQALAKRIGAVKYLECSALTQEGVREVFEEAIRAAL 172
>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 = 93.8 bits (234), Expect = 5e-25
Identities = 43/139 (30%), Positives = 77/139 (55%), Gaps = 2/139 (1%)
Query: 7 FVTDYDPTIEDSY-TKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTD 65
F + + TI ++ T+ +DD + +I DTAGQE + ++ Y R ++V+ +T
Sbjct: 26 FSENQESTIGAAFLTQTVNLDDTTVKFEIWDTAGQERYRSLAPMYYRGAAAAIVVYDITS 85
Query: 66 RNSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYIECS 125
SFE+ + ++ L+ + + GNKADL+ +RQVS+ +AQ A + + ++E S
Sbjct: 86 EESFEKAKSWVKE-LQEHGPPNIVIALAGNKADLESKRQVSTEEAQEYADENGLLFMETS 144
Query: 126 AKVRINVDQAFHELVRIVL 144
AK NV++ F E+ R +
Sbjct: 145 AKTGENVNELFTEIARKLP 163
>gnl|CDD|206715 cd04148, RGK, Rem, Rem2, Rad, Gem/Kir (RGK) subfamily of Ras
GTPases. RGK subfamily. The RGK (Rem, Rem2, Rad,
Gem/Kir) subfamily of Ras GTPases are expressed in a
tissue-specific manner and are dynamically regulated by
transcriptional and posttranscriptional mechanisms in
response to environmental cues. RGK proteins bind to the
beta subunit of L-type calcium channels, causing
functional down-regulation of these voltage-dependent
calcium channels, and either termination of
calcium-dependent secretion or modulation of electrical
conduction and contractile function. Inhibition of
L-type calcium channels by Rem2 may provide a mechanism
for modulating calcium-triggered exocytosis in
hormone-secreting cells, and has been proposed to
influence the secretion of insulin in pancreatic beta
cells. RGK proteins also interact with and inhibit the
Rho/Rho kinase pathway to modulate remodeling of the
cytoskeleton. Two characteristics of RGK proteins cited
in the literature are N-terminal and C-terminal
extensions beyond the GTPase domain typical of Ras
superfamily members. The N-terminal extension is not
conserved among family members; the C-terminal extension
is reported to be conserved among the family and lack
the CaaX prenylation motif typical of
membrane-associated Ras proteins. However, a putative
CaaX motif has been identified in the alignment of the
C-terminal residues of this CD.
Length = 219
Score = 94.8 bits (236), Expect = 9e-25
Identities = 45/136 (33%), Positives = 80/136 (58%)
Query: 10 DYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSF 69
Y+ + +D+Y + +D A L + D QE+ + + M+ G+ +++V+SVTDR+SF
Sbjct: 29 AYEASGDDTYERTVSVDGEEATLVVYDHWEQEDGMWLEDSCMQVGDAYVIVYSVTDRSSF 88
Query: 70 EEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYIECSAKVR 129
E+ + Q+ R + ++ P+++VGNK+DL R+VS + + A +IE SA ++
Sbjct: 89 EKASELRIQLRRARQAEDIPIILVGNKSDLVRSREVSVQEGRACAVVFDCKFIETSAALQ 148
Query: 130 INVDQAFHELVRIVLL 145
NVD+ F +VR V L
Sbjct: 149 HNVDELFEGIVRQVRL 164
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 93.9 bits (233), Expect = 2e-24
Identities = 47/160 (29%), Positives = 76/160 (47%), Gaps = 18/160 (11%)
Query: 3 IESYFVTDYDPTIEDSYTKQCV-IDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVF 61
+ F Y PTI + + + +L + DTAGQEE+ ++R +Y R G L+V+
Sbjct: 26 VGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQEEYRSLRPEYYRGANGILIVY 85
Query: 62 SVTDRNSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQL---- 117
T R S +E+ + + LR D+ P+L+VGNK DL ++ S + R++
Sbjct: 86 DSTLRESSDELTEEWLEELRELAPDDVPILLVGNKIDLFDEQSSSEEILNQLNREVVLLV 145
Query: 118 -----------RIPYIECSAKV--RINVDQAFHELVRIVL 144
+E SAK NV++ F EL+R +L
Sbjct: 146 LAPKAVLPEVANPALLETSAKSLTGPNVNELFKELLRKLL 185
>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 = 89.2 bits (221), Expect = 6e-23
Identities = 43/121 (35%), Positives = 70/121 (57%), Gaps = 1/121 (0%)
Query: 21 KQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQIL 80
K +D + +L I DTAGQE F ++ Y R LL++ VT+++SF+ I + +IL
Sbjct: 41 KVVTVDGVKVKLQIWDTAGQERFRSVTHAYYRDAHALLLLYDVTNKSSFDNIRAWLTEIL 100
Query: 81 RVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYIECSAKVRINVDQAFHELV 140
D ML+ GNKAD+ +R V D + +A++ +P++E SAK +NV+ AF +
Sbjct: 101 EYAQSDVVIMLL-GNKADMSGERVVKREDGERLAKEYGVPFMETSAKTGLNVELAFTAVA 159
Query: 141 R 141
+
Sbjct: 160 K 160
>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 = 88.1 bits (219), Expect = 8e-23
Identities = 48/133 (36%), Positives = 74/133 (55%), Gaps = 6/133 (4%)
Query: 7 FVTDYDPTI-EDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTD 65
F Y TI D +K +DD RL + DTAGQE F ++ Y+R ++V+ +T+
Sbjct: 25 FDNQYQATIGIDFLSKTMYVDDKTVRLQLWDTAGQERFRSLIPSYIRDSSVAVVVYDITN 84
Query: 66 RNSFEEIYKFHRQILRVKDR--DEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYIE 123
R SF+ K+ I V+D ++ +++VGNK DL +RQVS+ + + A++ +IE
Sbjct: 85 RQSFDNTDKW---IDDVRDERGNDVIIVLVGNKTDLSDKRQVSTEEGEKKAKENNAMFIE 141
Query: 124 CSAKVRINVDQAF 136
SAK NV Q F
Sbjct: 142 TSAKAGHNVKQLF 154
>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 = 87.8 bits (218), Expect = 9e-23
Identities = 40/137 (29%), Positives = 65/137 (47%), Gaps = 3/137 (2%)
Query: 7 FVTDYDPTIEDSYTKQCV-IDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTD 65
+T+Y P +Y + D + ++LDTAGQE++ A+R Y R+ E L VF +
Sbjct: 27 SITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAGQEDYDAIRRLYYRAVESSLRVFDIVI 86
Query: 66 R-NSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYIEC 124
EEI + + + P+++VGNK DL ++ + A A+ P I
Sbjct: 87 LVLDVEEILEKQTKEIIHHAESGVPIILVGNKIDLRD-AKLKTHVAFLFAKLNGEPIIPL 145
Query: 125 SAKVRINVDQAFHELVR 141
SA+ N+D AF +
Sbjct: 146 SAETGKNIDSAFKIVEA 162
>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 = 89.0 bits (221), Expect = 1e-22
Identities = 47/132 (35%), Positives = 78/132 (59%), Gaps = 2/132 (1%)
Query: 12 DPTIE-DSYTKQCVIDD-IPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSF 69
DPT+ D +++ I+ + +L + DTAGQE F ++ Y R+ G LLVF +T+R SF
Sbjct: 32 DPTVGVDFFSRLIEIEPGVRIKLQLWDTAGQERFRSITRSYYRNSVGVLLVFDITNRESF 91
Query: 70 EEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYIECSAKVR 129
E ++ + + ++VG+K DL+ QRQV+ +A+ +A+ L + YIE SA+
Sbjct: 92 EHVHDWLEEARSHIQPHRPVFILVGHKCDLESQRQVTREEAEKLAKDLGMKYIETSARTG 151
Query: 130 INVDQAFHELVR 141
NV++AF L +
Sbjct: 152 DNVEEAFELLTQ 163
>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 = 86.8 bits (215), Expect = 4e-22
Identities = 43/114 (37%), Positives = 66/114 (57%), Gaps = 2/114 (1%)
Query: 32 LDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQILRVKDRDEFP-M 90
L + DTAGQE F ++ + R GFLL+F +T SF + + Q L+ E P +
Sbjct: 65 LQLWDTAGQERFRSLTTAFFRDAMGFLLMFDLTSEQSFLNVRNWMSQ-LQAHAYCENPDI 123
Query: 91 LMVGNKADLDHQRQVSSMDAQNVARQLRIPYIECSAKVRINVDQAFHELVRIVL 144
+++GNKADL QR+VS A+ +A + IPY E SA NV++A L+ +++
Sbjct: 124 VLIGNKADLPDQREVSERQARELADKYGIPYFETSAATGQNVEKAVETLLDLIM 177
>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 = 86.5 bits (214), Expect = 4e-22
Identities = 50/127 (39%), Positives = 70/127 (55%), Gaps = 5/127 (3%)
Query: 21 KQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQIL 80
K +D L I DTAGQE F ++R + R + LL FSV D SF+ + + ++ +
Sbjct: 45 KDLEVDGHFVTLQIWDTAGQERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFI 104
Query: 81 R---VKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRI-PYIECSAKVRINVDQAF 136
VK+ + FP +++GNK D+ +RQVS+ +AQ R PY E SAK NV AF
Sbjct: 105 YYADVKEPESFPFVILGNKIDIP-ERQVSTEEAQAWCRDNGDYPYFETSAKDATNVAAAF 163
Query: 137 HELVRIV 143
E VR V
Sbjct: 164 EEAVRRV 170
>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 = 86.0 bits (213), Expect = 5e-22
Identities = 49/133 (36%), Positives = 72/133 (54%), Gaps = 5/133 (3%)
Query: 7 FVTDYDPTI-EDSYTKQCVID--DIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSV 63
F DY TI D KQ + D RL + DTAGQEEF A+ + Y R + +LVFS
Sbjct: 25 FTKDYKKTIGVDFLEKQIFLRQSDEDVRLMLWDTAGQEEFDAITKAYYRGAQACILVFST 84
Query: 64 TDRNSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYIE 123
TDR SFE I + ++ + PM++V K DL Q +++ +A+ +A++L++P
Sbjct: 85 TDRESFEAIESWKEKVEAEC--GDIPMVLVQTKIDLLDQAVITNEEAEALAKRLQLPLFR 142
Query: 124 CSAKVRINVDQAF 136
S K NV + F
Sbjct: 143 TSVKDDFNVTELF 155
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 87.4 bits (216), Expect = 5e-22
Identities = 47/134 (35%), Positives = 72/134 (53%), Gaps = 2/134 (1%)
Query: 8 VTDYDPTIE-DSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDR 66
V D PTI D KQ + +L I DTAGQE F + Y R+ +G +LV+ VT R
Sbjct: 39 VEDLAPTIGVDFKIKQLTVGGKRLKLTIWDTAGQERFRTLTSSYYRNAQGIILVYDVTRR 98
Query: 67 NSFEEIYK-FHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYIECS 125
+F + + +++ + ++VGNK D + +R VS + +A++ ++ECS
Sbjct: 99 ETFTNLSDVWGKEVELYSTNQDCVKMLVGNKVDRESERDVSREEGMALAKEHGCLFLECS 158
Query: 126 AKVRINVDQAFHEL 139
AK R NV+Q F EL
Sbjct: 159 AKTRENVEQCFEEL 172
>gnl|CDD|133330 cd04130, Wrch_1, Wnt-1 responsive Cdc42 homolog (Wrch-1) is a Rho
family GTPase similar to Cdc42. Wrch-1 (Wnt-1
responsive Cdc42 homolog) is a Rho family GTPase that
shares significant sequence and functional similarity
with Cdc42. Wrch-1 was first identified in mouse mammary
epithelial cells, where its transcription is upregulated
in Wnt-1 transformation. Wrch-1 contains N- and
C-terminal extensions relative to cdc42, suggesting
potential differences in cellular localization and
function. The Wrch-1 N-terminal extension contains
putative SH3 domain-binding motifs and has been shown to
bind the SH3 domain-containing protein Grb2, which
increases the level of active Wrch-1 in cells. Unlike
Cdc42, which localizes to the cytosol and perinuclear
membranes, Wrch-1 localizes extensively with the plasma
membrane and endosomes. The membrane association,
localization, and biological activity of Wrch-1 indicate
an atypical model of regulation distinct from other Rho
family GTPases. Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 173
Score = 84.8 bits (210), Expect = 2e-21
Identities = 48/152 (31%), Positives = 80/152 (52%), Gaps = 20/152 (13%)
Query: 3 IESY----FVTDYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFL 58
I SY + T+Y PT D+++ ++D P RL + DTAGQ+EF +R + FL
Sbjct: 17 IVSYTTNGYPTEYVPTAFDNFSVVVLVDGKPVRLQLCDTAGQDEFDKLRPLCYPDTDVFL 76
Query: 59 LVFSVTDRNSFEEIYKFHRQILRVKDRD-EFPMLMVGNKADL------------DHQRQV 105
L FSV + +SF+ I + I ++ + + P+++VG +ADL ++ V
Sbjct: 77 LCFSVVNPSSFQNIS--EKWIPEIRKHNPKAPIILVGTQADLRTDVNVLIQLARYGEKPV 134
Query: 106 SSMDAQNVARQLR-IPYIECSAKVRINVDQAF 136
S A+ +A ++ YIECSA + N+ + F
Sbjct: 135 SQSRAKALAEKIGACEYIECSALTQKNLKEVF 166
>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 = 83.7 bits (207), Expect = 5e-21
Identities = 45/141 (31%), Positives = 75/141 (53%), Gaps = 2/141 (1%)
Query: 4 ESYFVTDYDPTIEDSY-TKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFS 62
E F+ D TI + T+ ++ +L I DTAGQE F A+ Y R G L+V+
Sbjct: 24 EKKFMADCPHTIGVEFGTRIIEVNGQKIKLQIWDTAGQERFRAVTRSYYRGAAGALMVYD 83
Query: 63 VTDRNSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYI 122
+T R+++ + + + + + L +GNKADL+ QR V+ +A+ A + + ++
Sbjct: 84 ITRRSTYNHLSSWLTDARNLTNPNTVIFL-IGNKADLEAQRDVTYEEAKQFADENGLLFL 142
Query: 123 ECSAKVRINVDQAFHELVRIV 143
ECSAK NV+ AF E + +
Sbjct: 143 ECSAKTGENVEDAFLETAKKI 163
>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 = 83.4 bits (206), Expect = 6e-21
Identities = 42/113 (37%), Positives = 64/113 (56%), Gaps = 1/113 (0%)
Query: 31 RLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQILRVKDRDEFPM 90
+L I DTAGQE + + Y R GF+L++ +T+ SF + + QI + D +
Sbjct: 51 KLQIWDTAGQERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQI-KTYSWDNAQV 109
Query: 91 LMVGNKADLDHQRQVSSMDAQNVARQLRIPYIECSAKVRINVDQAFHELVRIV 143
++VGNK D++ +R VS+ + +A QL + E SAK INV Q F LV I+
Sbjct: 110 ILVGNKCDMEDERVVSAERGRQLADQLGFEFFEASAKENINVKQVFERLVDII 162
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 82.3 bits (203), Expect = 5e-20
Identities = 40/121 (33%), Positives = 68/121 (56%), Gaps = 1/121 (0%)
Query: 20 TKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQI 79
T+ ++ + I DTAGQE + A+ Y R G LLV+ +T R +F+ + ++ R+
Sbjct: 51 TRTLQVEGKTVKAQIWDTAGQERYRAITSAYYRGAVGALLVYDITKRQTFDNVQRWLRE- 109
Query: 80 LRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYIECSAKVRINVDQAFHEL 139
LR ++M GNK+DL+H R V+ D Q +A + + ++E SA NV++AF +
Sbjct: 110 LRDHADSNIVIMMAGNKSDLNHLRSVAEEDGQALAEKEGLSFLETSALEATNVEKAFQTI 169
Query: 140 V 140
+
Sbjct: 170 L 170
>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 = 80.6 bits (199), Expect = 6e-20
Identities = 41/128 (32%), Positives = 66/128 (51%), Gaps = 2/128 (1%)
Query: 17 DSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFH 76
D K I +L I DTAGQE F + + Y RS G ++ + +T R+SFE + +
Sbjct: 39 DFTMKTLEIQGKRVKLQIWDTAGQERFRTITQSYYRSANGAIIAYDITRRSSFESVPHWI 98
Query: 77 RQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPY-IECSAKVRINVDQA 135
++ + + +L+ GNK DL+ QR+V +A +A I +E SAK NV++A
Sbjct: 99 EEVEKYGASNVVLLLI-GNKCDLEEQREVLFEEACTLAEHYGILAVLETSAKESSNVEEA 157
Query: 136 FHELVRIV 143
F + +
Sbjct: 158 FLLMATEL 165
>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 = 80.5 bits (199), Expect = 8e-20
Identities = 43/131 (32%), Positives = 69/131 (52%), Gaps = 2/131 (1%)
Query: 7 FVTDYDPTIEDSY-TKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTD 65
F +D TI + + ID +L I DTAGQE F ++ Y R G LLV+ +T
Sbjct: 29 FQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQESFRSITRSYYRGAAGALLVYDITR 88
Query: 66 RNSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYIECS 125
R +F + + R ++++GNK DL+ +R+VS + + AR+ + ++E S
Sbjct: 89 RETFNHLTSWLEDA-RQHSNSNMTIMLIGNKCDLESRREVSYEEGEAFAREHGLIFMETS 147
Query: 126 AKVRINVDQAF 136
AK NV++AF
Sbjct: 148 AKTASNVEEAF 158
>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 = 79.8 bits (197), Expect = 1e-19
Identities = 42/138 (30%), Positives = 64/138 (46%), Gaps = 12/138 (8%)
Query: 11 YDPTI-EDSYTKQCVIDDIPARLDILDTAGQEEFSAMRE-----QYMRSGEGFLLVFSVT 64
T D Y K+ + L ++DT G +EF + +R + LLV T
Sbjct: 29 PGTTRDPDVYVKELDKGKVK--LVLVDTPGLDEFGGLGREELARLLLRGADLILLVVDST 86
Query: 65 DRNSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNV-ARQLRIPYIE 123
DR S E+ ILR ++ P+++VGNK DL +R+V + A+ L +P E
Sbjct: 87 DRESEEDA---KLLILRRLRKEGIPIILVGNKIDLLEEREVEELLRLEELAKILGVPVFE 143
Query: 124 CSAKVRINVDQAFHELVR 141
SAK VD+ F +L+
Sbjct: 144 VSAKTGEGVDELFEKLIE 161
>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 = 79.4 bits (196), Expect = 2e-19
Identities = 45/142 (31%), Positives = 75/142 (52%), Gaps = 2/142 (1%)
Query: 3 IESYFVTDYDPTIEDSYTKQCV-IDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVF 61
IE+ F D + TI + + V + +L I DTAGQE F ++ Y R G LLV+
Sbjct: 21 IENKFKQDSNHTIGVEFGSRVVNVGGKSVKLQIWDTAGQERFRSVTRSYYRGAAGALLVY 80
Query: 62 SVTDRNSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPY 121
+T R SF + + R + +++VGNK DL+ R+V+ ++A A++ + +
Sbjct: 81 DITSRESFNALTNWLTDA-RTLASPDIVIILVGNKKDLEDDREVTFLEASRFAQENGLLF 139
Query: 122 IECSAKVRINVDQAFHELVRIV 143
+E SA NV++AF + R +
Sbjct: 140 LETSALTGENVEEAFLKCARSI 161
>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 = 78.5 bits (194), Expect = 4e-19
Identities = 36/122 (29%), Positives = 62/122 (50%), Gaps = 16/122 (13%)
Query: 29 PARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQILRVKDRDEF 88
R ++ DTAGQE+F +R+ Y G+ +++F VT R +++ + +HR ++RV +
Sbjct: 48 KIRFNVWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRVTYKNVPNWHRDLVRV--CENI 105
Query: 89 PMLMVGNKADLDHQRQVSSMDAQNVARQLRIP------YIECSAKVRINVDQAFHELVRI 142
P+++ GNK D D + +Q+ Y E SAK N ++ F L R
Sbjct: 106 PIVLCGNKVD--------IKDRKVKPKQITFHRKKNLQYYEISAKSNYNFEKPFLWLARK 157
Query: 143 VL 144
+L
Sbjct: 158 LL 159
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 79.6 bits (196), Expect = 4e-19
Identities = 40/112 (35%), Positives = 64/112 (57%), Gaps = 1/112 (0%)
Query: 25 IDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQILRVKD 84
ID+ P +L I DTAGQE F ++ Y R G LLV+ +T R +F + + R
Sbjct: 50 IDNKPIKLQIWDTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLASWLEDA-RQHA 108
Query: 85 RDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYIECSAKVRINVDQAF 136
++++GNK DL H+R VS+ + + A++ + ++E SAK NV++AF
Sbjct: 109 NANMTIMLIGNKCDLAHRRAVSTEEGEQFAKEHGLIFMEASAKTAQNVEEAF 160
>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 = 78.2 bits (193), Expect = 1e-18
Identities = 40/160 (25%), Positives = 70/160 (43%), Gaps = 31/160 (19%)
Query: 7 FVTDYDPTIEDSYTKQCVIDD-IPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTD 65
F +Y PT+ ++Y + + L + DTAGQE++ +R + L+ +SV +
Sbjct: 28 FPEEYVPTVFENYVTTLQVPNGKIIELALWDTAGQEDYDRLRPLSYPDVDVILICYSVDN 87
Query: 66 RNSFE--------EIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQ------------V 105
S + E+ F P+++VG K DL + V
Sbjct: 88 PTSLDNVEDKWYPEVNHFCPGT---------PIVLVGLKTDLRKDKNSVSKLRAQGLEPV 138
Query: 106 SSMDAQNVARQLR-IPYIECSAKVRINVDQAFHELVRIVL 144
+ ++VA+ + + YIECSAK+ NVD+ F + + L
Sbjct: 139 TPEQGESVAKSIGAVAYIECSAKLMENVDEVFDAAINVAL 178
>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 = 77.4 bits (190), Expect = 2e-18
Identities = 41/115 (35%), Positives = 70/115 (60%), Gaps = 2/115 (1%)
Query: 31 RLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQILRVKDRDEFPM 90
RL I DTAGQE F+++ Y RS +G +LV+ +T + +F+++ K+ + I + D +
Sbjct: 50 RLQIWDTAGQERFNSITSAYYRSAKGIILVYDITKKETFDDLPKWMKMIDKYASEDA-EL 108
Query: 91 LMVGNKADLDHQRQVSSMDAQNVARQLR-IPYIECSAKVRINVDQAFHELVRIVL 144
L+VGNK D + R+++ + A+Q+ + + E SAK NVD+ F +LV +L
Sbjct: 109 LLVGNKLDCETDREITRQQGEKFAQQITGMRFCEASAKDNFNVDEIFLKLVDDIL 163
>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 = 76.0 bits (187), Expect = 5e-18
Identities = 51/149 (34%), Positives = 77/149 (51%), Gaps = 12/149 (8%)
Query: 7 FVTDYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDR 66
F TDY PT+ D+++ V+D L + DTAGQE+++ +R R + FLL FS+ +
Sbjct: 26 FPTDYVPTVFDNFSANVVVDGNTVNLGLWDTAGQEDYNRLRPLSYRGADVFLLAFSLISK 85
Query: 67 NSFEEIYKFHRQILRVKDRDEFPMLMVGNKADL--------DHQRQVSSMDAQN--VARQ 116
S+E + K LR P+++VG K DL DH V AQ + +Q
Sbjct: 86 ASYENVLKKWIPELR-HYAPGVPIVLVGTKLDLRDDKQFFADHPGAVPITTAQGEELRKQ 144
Query: 117 LRIP-YIECSAKVRINVDQAFHELVRIVL 144
+ YIECS+K + NV F +++VL
Sbjct: 145 IGAAAYIECSSKTQQNVKAVFDAAIKVVL 173
>gnl|CDD|133321 cd04121, Rab40, Rab GTPase family 40 (Rab40) contains Rab40a,
Rab40b and Rab40c. The Rab40 subfamily contains Rab40a,
Rab40b, and Rab40c, which are all highly homologous. In
rat, Rab40c is localized to the perinuclear recycling
compartment (PRC), and is distributed in a
tissue-specific manor, with high expression in brain,
heart, kidney, and testis, low expression in lung and
liver, and no expression in spleen and skeletal muscle.
Rab40c is highly expressed in differentiated
oligodendrocytes but minimally expressed in
oligodendrocyte progenitors, suggesting a role in the
vesicular transport of myelin components. Unlike most
other Ras-superfamily proteins, Rab40c was shown to have
a much lower affinity for GTP, and an affinity for GDP
that is lower than for GTP. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 189
Score = 76.1 bits (187), Expect = 5e-18
Identities = 45/147 (30%), Positives = 75/147 (51%), Gaps = 19/147 (12%)
Query: 12 DPTIEDSY---------TKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFS 62
D + E Y T ++D +L + DT+GQ F + Y R +G +LV+
Sbjct: 28 DGSTESPYGYNMGIDYKTTTILLDGRRVKLQLWDTSGQGRFCTIFRSYSRGAQGIILVYD 87
Query: 63 VTDRNSFEEIYKFHRQILRVKDRDE----FPMLMVGNKADLDHQRQVSSMDAQNVARQLR 118
+T+R SF+ I ++ +K+ DE P ++VGN+ L +RQV++ AQ A +
Sbjct: 88 ITNRWSFDGIDRW------IKEIDEHAPGVPKILVGNRLHLAFKRQVATEQAQAYAERNG 141
Query: 119 IPYIECSAKVRINVDQAFHELVRIVLL 145
+ + E S N+ ++F EL RIVL+
Sbjct: 142 MTFFEVSPLCNFNITESFTELARIVLM 168
>gnl|CDD|133277 cd01875, RhoG, Ras homolog family, member G (RhoG) of small
guanosine triphosphatases (GTPases). RhoG is a GTPase
with high sequence similarity to members of the Rac
subfamily, including the regions involved in effector
recognition and binding. However, RhoG does not bind to
known Rac1 and Cdc42 effectors, including proteins
containing a Cdc42/Rac interacting binding (CRIB) motif.
Instead, RhoG interacts directly with Elmo, an upstream
regulator of Rac1, in a GTP-dependent manner and forms a
ternary complex with Dock180 to induce activation of
Rac1. The RhoG-Elmo-Dock180 pathway is required for
activation of Rac1 and cell spreading mediated by
integrin, as well as for neurite outgrowth induced by
nerve growth factor. Thus RhoG activates Rac1 through
Elmo and Dock180 to control cell morphology. RhoG has
also been shown to play a role in caveolar trafficking
and has a novel role in signaling the neutrophil
respiratory burst stimulated by G protein-coupled
receptor (GPCR) agonists. Most Rho proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Rho proteins.
Length = 191
Score = 75.4 bits (185), Expect = 1e-17
Identities = 48/163 (29%), Positives = 78/163 (47%), Gaps = 21/163 (12%)
Query: 7 FVTDYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDR 66
F +Y PT+ D+Y+ Q +D L++ DTAGQEE+ +R F++ FS+
Sbjct: 28 FPKEYIPTVFDNYSAQTAVDGRTVSLNLWDTAGQEEYDRLRTLSYPQTNVFIICFSIASP 87
Query: 67 NSFEEI-YKFHRQILRVKDRDEFPMLMVGNKADLDHQRQV------------SSMDAQNV 113
+S+E + +K+H ++ P+L+VG K DL + + +
Sbjct: 88 SSYENVRHKWHPEV--CHHCPNVPILLVGTKKDLRNDADTLKKLKEQGQAPITPQQGGAL 145
Query: 114 ARQLR-IPYIECSAKVRINVDQAFHELVRIVLL-----HTKQC 150
A+Q+ + Y+ECSA + V + F E VR VL TK C
Sbjct: 146 AKQIHAVKYLECSALNQDGVKEVFAEAVRAVLNPTPIKDTKSC 188
>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 = 73.9 bits (182), Expect = 3e-17
Identities = 40/146 (27%), Positives = 70/146 (47%), Gaps = 5/146 (3%)
Query: 4 ESYFVTDYDPTIEDSY-TKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFS 62
E FV+ Y PTI Y K+ + + R++ D +G E+ +R ++ + +G LLV+
Sbjct: 22 EGRFVSKYLPTIGIDYGVKKVSVRNKEVRVNFFDLSGHPEYLEVRNEFYKDTQGVLLVYD 81
Query: 63 VTDRNSFEEIYKFHRQI----LRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLR 118
VTDR SFE + + +++ + + +++ NK DL R VS + + A
Sbjct: 82 VTDRQSFEALDSWLKEMKQEGGPHGNMENIVVVVCANKIDLTKHRAVSEDEGRLWAESKG 141
Query: 119 IPYIECSAKVRINVDQAFHELVRIVL 144
Y E SA V++ F L ++
Sbjct: 142 FKYFETSACTGEGVNEMFQTLFSSIV 167
>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 = 73.9 bits (181), Expect = 3e-17
Identities = 42/133 (31%), Positives = 69/133 (51%), Gaps = 11/133 (8%)
Query: 17 DSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFH 76
D K +D I R+ I DTAGQE + + +QY R +G LV+ ++ S++ I K+
Sbjct: 36 DFKMKTIEVDGIKVRIQIWDTAGQERYQTITKQYYRRAQGIFLVYDISSERSYQHIMKW- 94
Query: 77 RQILRVKDRDEF-----PMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYIECSAKVRIN 131
V D DE+ +++GNKAD + +RQV +A++ + + E SA N
Sbjct: 95 -----VSDVDEYAPEGVQKILIGNKADEEQKRQVGDEQGNKLAKEYGMDFFETSACTNKN 149
Query: 132 VDQAFHELVRIVL 144
+ ++F L +VL
Sbjct: 150 IKESFTRLTELVL 162
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 72.1 bits (176), Expect = 2e-16
Identities = 44/134 (32%), Positives = 72/134 (53%), Gaps = 2/134 (1%)
Query: 7 FVTDYDPTIE-DSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTD 65
F +Y TI D +K +D+ P RL + DTAGQE F ++ Y+R ++V+ +T+
Sbjct: 5 FDNNYQSTIGIDFLSKTLYLDEGPVRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDITN 64
Query: 66 RNSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYIECS 125
R SFE K+ + IL + +D + +VGNK DL R+V+ + A++ + E S
Sbjct: 65 RQSFENTTKWIQDILNERGKDVI-IALVGNKTDLGDLRKVTYEEGMQKAQEYNTMFHETS 123
Query: 126 AKVRINVDQAFHEL 139
AK N+ F ++
Sbjct: 124 AKAGHNIKVLFKKI 137
>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 = 71.5 bits (175), Expect = 3e-16
Identities = 41/123 (33%), Positives = 64/123 (52%), Gaps = 1/123 (0%)
Query: 17 DSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFH 76
D K I +L I DTAGQE F ++ + Y RS +L + +T SF + ++
Sbjct: 43 DFMIKTVEIKGEKIKLQIWDTAGQERFRSITQSYYRSANALILTYDITCEESFRCLPEWL 102
Query: 77 RQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYIECSAKVRINVDQAF 136
R+I + + +L VGNK DL +R+VS A+ + + Y+E SAK NV++ F
Sbjct: 103 REIEQYANNKVITIL-VGNKIDLAERREVSQQRAEEFSDAQDMYYLETSAKESDNVEKLF 161
Query: 137 HEL 139
+L
Sbjct: 162 LDL 164
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 72.0 bits (177), Expect = 3e-16
Identities = 38/113 (33%), Positives = 64/113 (56%), Gaps = 4/113 (3%)
Query: 29 PARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQILRVKDRDEF 88
P ++ DTAGQE+F +R+ Y G+ +++F VT R +++ + +HR I+RV +
Sbjct: 57 PICFNVWDTAGQEKFGGLRDGYYIKGQCAIIMFDVTSRITYKNVPNWHRDIVRVC--ENI 114
Query: 89 PMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYIECSAKVRINVDQAFHELVR 141
P+++VGNK D+ RQV + R+ + Y + SAK N ++ F L R
Sbjct: 115 PIVLVGNKVDV-KDRQVKARQIT-FHRKKNLQYYDISAKSNYNFEKPFLWLAR 165
>gnl|CDD|133310 cd04110, Rab35, Rab GTPase family 35 (Rab35). Rab35 is one of
several Rab proteins to be found to participate in the
regulation of osteoclast cells in rats. In addition,
Rab35 has been identified as a protein that interacts
with nucleophosmin-anaplastic lymphoma kinase (NPM-ALK)
in human cells. Overexpression of NPM-ALK is a key
oncogenic event in some anaplastic large-cell lymphomas;
since Rab35 interacts with N|PM-ALK, it may provide a
target for cancer treatments. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 199
Score = 71.8 bits (176), Expect = 3e-16
Identities = 47/143 (32%), Positives = 74/143 (51%), Gaps = 3/143 (2%)
Query: 7 FVTDYDPTIE-DSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTD 65
F Y TI D + I+ +L I DTAGQE F + Y R G ++V+ VT+
Sbjct: 31 FSGSYITTIGVDFKIRTVEINGERVKLQIWDTAGQERFRTITSTYYRGTHGVIVVYDVTN 90
Query: 66 RNSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYIECS 125
SF + ++ ++I ++ D+ ++VGNK D ++ V + DA A Q+ I E S
Sbjct: 91 GESFVNVKRWLQEI--EQNCDDVCKVLVGNKNDDPERKVVETEDAYKFAGQMGISLFETS 148
Query: 126 AKVRINVDQAFHELVRIVLLHTK 148
AK INV++ F+ + +VL K
Sbjct: 149 AKENINVEEMFNCITELVLRAKK 171
>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 = 70.6 bits (173), Expect = 4e-16
Identities = 35/116 (30%), Positives = 54/116 (46%)
Query: 26 DDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQILRVKDR 85
L I D+AGQE FS M E +V+ VT+ SF ++ ++
Sbjct: 49 TSDSVELFIFDSAGQELFSDMVENVWEQPAVVCVVYDVTNEVSFNNCSRWINRVRTHSHG 108
Query: 86 DEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYIECSAKVRINVDQAFHELVR 141
P ++VGNK DL +R+V + AQ +A+ + + E SAK + + F L R
Sbjct: 109 LHTPGVLVGNKCDLTDRREVDAAQAQALAQANTLKFYETSAKEGVGYEAPFLSLAR 164
>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 = 70.3 bits (172), Expect = 7e-16
Identities = 43/148 (29%), Positives = 73/148 (49%), Gaps = 16/148 (10%)
Query: 7 FVTDYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDR 66
F ++Y PT+ D+Y +I P L + DTAGQE++ +R + FL+ FSV
Sbjct: 26 FPSEYVPTVFDNYAVTVMIGGEPYTLGLFDTAGQEDYDRLRPLSYPQTDVFLVCFSVVSP 85
Query: 67 NSFEEIY-KFHRQILRVKDRDEFPMLMVGNKADL------------DHQRQVSSMDAQNV 113
+SFE + K+ +I + P L+VG + DL + Q+ ++ + +
Sbjct: 86 SSFENVKEKWVPEITHHCPK--TPFLLVGTQIDLRDDPSTIEKLAKNKQKPITPETGEKL 143
Query: 114 ARQLR-IPYIECSAKVRINVDQAFHELV 140
AR L+ + Y+ECSA + + F E +
Sbjct: 144 ARDLKAVKYVECSALTQKGLKNVFDEAI 171
>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 = 69.9 bits (171), Expect = 1e-15
Identities = 45/152 (29%), Positives = 68/152 (44%), Gaps = 14/152 (9%)
Query: 6 YFVTDYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTD 65
F +Y PT+ ++Y C +D P +L + DTAGQEE+ +R L+ F++
Sbjct: 25 EFPEEYHPTVFENYVTDCRVDGKPVQLALWDTAGQEEYERLRPLSYSKAHVILIGFAIDT 84
Query: 66 RNSFEEI-YKFHRQILRVKDRDEFPMLMVGNKADL----------DHQRQVSSMDAQNVA 114
+S E + K+ ++ R P+++VG K DL V A+ VA
Sbjct: 85 PDSLENVRTKWIEEVRRYC--PNVPVILVGLKKDLRQEAVAKGNYATDEFVPIQQAKLVA 142
Query: 115 RQLRI-PYIECSAKVRINVDQAFHELVRIVLL 145
R + Y+ECSA VD F R LL
Sbjct: 143 RAIGAKKYMECSALTGEGVDDVFEAATRAALL 174
>gnl|CDD|206706 cd04134, Rho3, Ras homology family 3 (Rho3) of small guanosine
triphosphatases (GTPases). Rho3 is a member of the Rho
family found only in fungi. Rho3 is believed to regulate
cell polarity by interacting with the diaphanous/formin
family protein For3 to control both the actin
cytoskeleton and microtubules. Rho3 is also believed to
have a direct role in exocytosis that is independent of
its role in regulating actin polarity. The function in
exocytosis may be two-pronged: first, in the transport
of post-Golgi vesicles from the mother cell to the bud,
mediated by myosin (Myo2); second, in the docking and
fusion of vesicles to the plasma membrane, mediated by
an exocyst (Exo70) protein. Most Rho proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Rho proteins.
Length = 185
Score = 69.1 bits (169), Expect = 2e-15
Identities = 42/151 (27%), Positives = 71/151 (47%), Gaps = 12/151 (7%)
Query: 6 YFVTDYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTD 65
YF Y+PT+ ++Y +D + L + DTAGQEEF +R +L FSV +
Sbjct: 24 YFPQVYEPTVFENYIHDIFVDGLAVELSLWDTAGQEEFDRLRSLSYADTHVIMLCFSVDN 83
Query: 66 RNSFEEIYKFHRQILRVKDRDE-FPMLMVGNKADL--------DHQRQVSSMDAQNVARQ 116
+S E + + + ++ +++V K DL +S + VA++
Sbjct: 84 PDSLENVES--KWLAEIRHHCPGVKLVLVALKCDLREPRNERDRGTHTISYEEGLAVAKR 141
Query: 117 LR-IPYIECSAKVRINVDQAFHELVRIVLLH 146
+ Y+ECSAK+ V++AF E R+ L
Sbjct: 142 INACRYLECSAKLNRGVNEAFTEAARVALNA 172
>gnl|CDD|206663 cd01871, Rac1_like, Ras-related C3 botulinum toxin substrate 1 (rho
family, small GTP binding protein Rac1)-like consists of
Rac1, Rac2 and Rac3. The Rac1-like subfamily consists
of Rac1, Rac2, and Rac3 proteins, plus the splice
variant Rac1b that contains a 19-residue insertion near
switch II relative to Rac1. While Rac1 is ubiquitously
expressed, Rac2 and Rac3 are largely restricted to
hematopoietic and neural tissues respectively. Rac1
stimulates the formation of actin lamellipodia and
membrane ruffles. It also plays a role in cell-matrix
adhesion and cell anoikis. In intestinal epithelial
cells, Rac1 is an important regulator of migration and
mediates apoptosis. Rac1 is also essential for
RhoA-regulated actin stress fiber and focal adhesion
complex formation. In leukocytes, Rac1 and Rac2 have
distinct roles in regulating cell morphology, migration,
and invasion, but are not essential for macrophage
migration or chemotaxis. Rac3 has biochemical properties
that are closely related to Rac1, such as effector
interaction, nucleotide binding, and hydrolysis; Rac2
has a slower nucleotide association and is more
efficiently activated by the RacGEF Tiam1. Both Rac1 and
Rac3 have been implicated in the regulation of cell
migration and invasion in human metastatic breast
cancer. Most Rho proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Rho proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 174
Score = 67.1 bits (164), Expect = 1e-14
Identities = 40/151 (26%), Positives = 73/151 (48%), Gaps = 16/151 (10%)
Query: 7 FVTDYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDR 66
F +Y PT+ D+Y+ ++D P L + DTAGQE++ +R + FL+ FS+
Sbjct: 26 FPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSYPQTDVFLICFSLVSP 85
Query: 67 NSFEEIY-KFHRQILRVKDRDEFPMLMVGNKADLDHQRQ------------VSSMDAQNV 113
SFE + K++ ++ P+++VG K DL + ++ +
Sbjct: 86 ASFENVRAKWYPEVRH--HCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAM 143
Query: 114 ARQLR-IPYIECSAKVRINVDQAFHELVRIV 143
A+++ + Y+ECSA + + F E +R V
Sbjct: 144 AKEIGAVKYLECSALTQRGLKTVFDEAIRAV 174
>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 = 65.5 bits (160), Expect = 4e-14
Identities = 36/108 (33%), Positives = 55/108 (50%), Gaps = 1/108 (0%)
Query: 21 KQCVIDDIPARLDILDTAGQEEF-SAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQI 79
+ ID ++ + DTAGQE F +M + Y R+ + V+ VT+ SF + + +
Sbjct: 42 RTVEIDGERIKVQLWDTAGQERFRKSMVQHYYRNVHAVVFVYDVTNMASFHSLPSWIEEC 101
Query: 80 LRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYIECSAK 127
+ +E P ++VGNK DL Q QV + AQ A +P E SAK
Sbjct: 102 EQHSLPNEVPRILVGNKCDLREQIQVPTDLAQRFADAHSMPLFETSAK 149
>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 = 64.6 bits (158), Expect = 2e-13
Identities = 39/124 (31%), Positives = 62/124 (50%), Gaps = 7/124 (5%)
Query: 31 RLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQI---LRVKDRDE 87
RL + D AGQE F M Y + G ++VF VT ++FE + K+ + + + + +
Sbjct: 51 RLQLWDIAGQERFGGMTRVYYKGAVGAIIVFDVTRPSTFEAVLKWKADLDSKVTLPNGEP 110
Query: 88 FPMLMVGNKADLDHQR---QVSSMDAQNVARQLRIPYIECSAKVRINVDQAFHELVRIVL 144
P L++ NK DL +R MD I + E SAK IN+++A LV+ +L
Sbjct: 111 IPALLLANKCDLKKERLAKDPEQMDQF-CKENGFIGWFETSAKENINIEEAMRFLVKNIL 169
Query: 145 LHTK 148
+ K
Sbjct: 170 KNDK 173
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 64.8 bits (158), Expect = 2e-13
Identities = 39/115 (33%), Positives = 62/115 (53%), Gaps = 8/115 (6%)
Query: 29 PARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQILRVKDRDEF 88
R DTAGQE+F +R+ Y G+ +++F VT R +++ + +HR + RV +
Sbjct: 61 KIRFYCWDTAGQEKFGGLRDGYYIHGQCAIIMFDVTARLTYKNVPTWHRDLCRVC--ENI 118
Query: 89 PMLMVGNKADLDHQRQVSSMDAQNVA--RQLRIPYIECSAKVRINVDQAFHELVR 141
P+++ GNK D+ RQV A+ V R+ + Y E SAK N ++ F L R
Sbjct: 119 PIVLCGNKVDV-KNRQVK---AKQVTFHRKKNLQYYEISAKSNYNFEKPFLYLAR 169
>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 = 63.5 bits (154), Expect = 4e-13
Identities = 37/115 (32%), Positives = 67/115 (58%), Gaps = 8/115 (6%)
Query: 29 PARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQILRVKDRDEF 88
P R ++ DTAGQE+F +R+ Y G+ +++F VT R +++ + +HR ++RV +
Sbjct: 43 PIRFNVWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTARVTYKNVPNWHRDLVRVC--ENI 100
Query: 89 PMLMVGNKADLDHQRQVSSMDAQNVA--RQLRIPYIECSAKVRINVDQAFHELVR 141
P+++ GNK D+ R+V A+++ R+ + Y + SAK N ++ F L R
Sbjct: 101 PIVLCGNKVDVK-DRKVK---AKSITFHRKKNLQYYDISAKSNYNFEKPFLWLAR 151
>gnl|CDD|206693 cd04108, Rab36_Rab34, Rab GTPase families 34 (Rab34) and 36
(Rab36). Rab34/Rab36 subfamily. Rab34, found primarily
in the Golgi, interacts with its effector,
Rab-interacting lysosomal protein (RILP). This enables
its participation in microtubular
dynenin-dynactin-mediated repositioning of lysosomes
from the cell periphery to the Golgi. A Rab34 (Rah)
isoform that lacks the consensus GTP-binding region has
been identified in mice. This isoform is associated with
membrane ruffles and promotes macropinosome formation.
Rab36 has been mapped to human chromosome 22q11.2, a
region that is homozygously deleted in malignant
rhabdoid tumors (MRTs). However, experimental
assessments do not implicate Rab36 as a tumor suppressor
that would enable tumor formation through a
loss-of-function mechanism. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 170
Score = 60.7 bits (147), Expect = 3e-12
Identities = 41/133 (30%), Positives = 62/133 (46%), Gaps = 3/133 (2%)
Query: 7 FVTDYDPTIE-DSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTD 65
F +Y TI D ++ + +P L + DTAGQE F + Y R + ++VF +TD
Sbjct: 25 FDKNYKATIGVDFEMERFEVLGVPFSLQLWDTAGQERFKCIASTYYRGAQAIIIVFDLTD 84
Query: 66 RNSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSM--DAQNVARQLRIPYIE 123
S E ++ L+ D + +VG K DL Q + M DA +AR+++ Y
Sbjct: 85 VASLEHTRQWLEDALKENDPSSVLLFLVGTKKDLSSPAQYALMEQDAIKLAREMKAEYWA 144
Query: 124 CSAKVRINVDQAF 136
SA NV F
Sbjct: 145 VSALTGENVRDFF 157
>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 = 61.0 bits (148), Expect = 5e-12
Identities = 38/145 (26%), Positives = 69/145 (47%), Gaps = 4/145 (2%)
Query: 4 ESYFVTDYDPTIE-DSYTKQCVI-DDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVF 61
+ F Y TI D ++++ + + L + D GQ+ M ++Y+ + LV+
Sbjct: 22 QEGFGKSYKQTIGLDFFSRRITLPGSLNVTLQVWDIGGQQIGGKMLDKYIYGAQAVCLVY 81
Query: 62 SVTDRNSFEEIYKFHRQILRVKDRDEFP--MLMVGNKADLDHQRQVSSMDAQNVARQLRI 119
+T+ SFE + + + +V + E M++VGNK DL+H RQV++ A++ +
Sbjct: 82 DITNSQSFENLEDWLSVVKKVNEESETKPKMVLVGNKTDLEHNRQVTAEKHARFAQENDM 141
Query: 120 PYIECSAKVRINVDQAFHELVRIVL 144
I SAK V F + +L
Sbjct: 142 ESIFVSAKTGDRVFLCFQRIAAELL 166
>gnl|CDD|219856 pfam08477, Miro, Miro-like protein. Mitochondrial Rho proteins
(Miro-1, and Miro-2), are atypical Rho GTPases. They
have a unique domain organisation, with tandem
GTP-binding domains and two EF hand domains (pfam00036),
that may bind calcium. They are also larger than
classical small GTPases. It has been proposed that they
are involved in mitochondrial homeostasis and apoptosis.
Length = 116
Score = 57.0 bits (138), Expect = 3e-11
Identities = 23/92 (25%), Positives = 42/92 (45%), Gaps = 2/92 (2%)
Query: 7 FVTDYDPTIEDSYTKQCVIDDIPAR-LDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTD 65
F + D+ + D L+I D G+EE +M+ + LLV+ +TD
Sbjct: 24 FPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREELKFEHIIFMKWADAILLVYDLTD 83
Query: 66 RNSFEEIYKFHRQILRVKDRD-EFPMLMVGNK 96
R S E+ + + ++ + P+++VGNK
Sbjct: 84 RESLNEVSRLIAWLPNLRKLGGKIPVILVGNK 115
>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 = 58.2 bits (141), Expect = 3e-11
Identities = 41/152 (26%), Positives = 68/152 (44%), Gaps = 24/152 (15%)
Query: 11 YDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFE 70
Y PT+ ++Y +D L + DTAGQE++ +R + L+ FS+ +S E
Sbjct: 30 YVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLE 89
Query: 71 EI-YKFHRQILRVKDRDEF----PMLMVGNKADLDH------------QRQVSSMDAQNV 113
I K+ ++ F P+++VGNK DL + Q V + + +
Sbjct: 90 NIPEKWTPEVK------HFCPNVPIILVGNKKDLRNDEHTIRELAKMKQEPVKPEEGRAM 143
Query: 114 ARQLR-IPYIECSAKVRINVDQAFHELVRIVL 144
A ++ Y+ECSAK + V + F R L
Sbjct: 144 AEKIGAFGYLECSAKTKEGVREVFEMATRAAL 175
>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 = 57.6 bits (139), Expect = 7e-11
Identities = 43/139 (30%), Positives = 71/139 (51%), Gaps = 7/139 (5%)
Query: 6 YFVTDYDPTIEDSY-TKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVT 64
+ V Y TI ++ K+ V+ + L I DTAG E + AM Y R + ++ + +T
Sbjct: 25 FLVGPYQNTIGAAFVAKRMVVGERVVTLGIWDTAGSERYEAMSRIYYRGAKAAIVCYDLT 84
Query: 65 DRNSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQ----RQVSSMDAQNVARQLRIP 120
D +SFE KF + L+ + + + G K+DL Q RQV D Q+ A +++
Sbjct: 85 DSSSFERA-KFWVKELQ-NLEEHCKIYLCGTKSDLIEQDRSLRQVDFHDVQDFADEIKAQ 142
Query: 121 YIECSAKVRINVDQAFHEL 139
+ E S+K NVD+ F ++
Sbjct: 143 HFETSSKTGQNVDELFQKV 161
>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 = 55.6 bits (134), Expect = 2e-10
Identities = 39/149 (26%), Positives = 67/149 (44%), Gaps = 10/149 (6%)
Query: 3 IESYFVTDYDPTIEDSYT-----KQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGF 57
+E + + Y+P +Y + +D DTAGQE F M Y
Sbjct: 17 VERFLMDGYEPQQLSTYALTLYKHNAKFEGKTILVDFWDTAGQERFQTMHASYYHKAHAC 76
Query: 58 LLVFSVTDRNSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQL 117
+LVF VT + +++ + K++ + LR + R E P ++V NK DLD N A +
Sbjct: 77 ILVFDVTRKITYKNLSKWYEE-LR-EYRPEIPCIVVANKIDLDPSVTQKKF---NFAEKH 131
Query: 118 RIPYIECSAKVRINVDQAFHELVRIVLLH 146
+P SA NV + F + +++ + +
Sbjct: 132 NLPLYYVSAADGTNVVKLFQDAIKLAVSY 160
>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 = 54.5 bits (131), Expect = 8e-10
Identities = 30/109 (27%), Positives = 51/109 (46%), Gaps = 3/109 (2%)
Query: 39 GQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQIL--RVKDRDEFPMLMVGNK 96
+E+ R + +R+ F+LV+ + +SF + +QIL R E P+++VGNK
Sbjct: 66 AGQEWMDPRFRGLRNSRAFILVYDICSPDSFHYVKLLRQQILETRPAGNKEPPIVVVGNK 125
Query: 97 ADLDHQRQVSSMD-AQNVARQLRIPYIECSAKVRINVDQAFHELVRIVL 144
D R + V + + Y+ECSAK ++ F EL+
Sbjct: 126 RDQQRHRFAPRHVLSVLVRKSWKCGYLECSAKYNWHILLLFKELLISAT 174
>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 = 53.8 bits (129), Expect = 2e-09
Identities = 42/163 (25%), Positives = 63/163 (38%), Gaps = 37/163 (22%)
Query: 29 PARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQILRVKDRDEF 88
P + I DTAG+E+F + Y R +L + V++ S EE+ + + D
Sbjct: 43 PYNISIWDTAGREQFHGLGSMYCRGAAAVILTYDVSNVQSLEELEDRFLGLTDTANEDCL 102
Query: 89 PMLMVGNKADL-------------------DHQRQVSSMDAQNVARQL------------ 117
+VGNK DL + QRQV+ DA+ +++
Sbjct: 103 -FAVVGNKLDLTEEGALAGQEKDAGDRVSPEDQRQVTLEDAKAFYKRINKYKMLDEDLSP 161
Query: 118 --RIPYIECSAKVRINVDQAFHELVRIVL---LHTKQCKNSTV 155
E SAK NVD+ F L +VL L + N T
Sbjct: 162 AAEKMCFETSAKTGYNVDELFEYLFNLVLPLILAQRAEANRTQ 204
>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 = 51.7 bits (124), Expect = 5e-09
Identities = 33/125 (26%), Positives = 58/125 (46%), Gaps = 12/125 (9%)
Query: 19 YTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQ 78
+ K+ ++D L I D G + Q+ + + VFS+ D SF+ +Y+ + Q
Sbjct: 36 FKKEVLVDGQSHLLLIRDEGGAPDA-----QFAGWVDAVIFVFSLEDEASFQTVYRLYHQ 90
Query: 79 ILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQL-----RIPYIECSAKVRINVD 133
+ ++ E P+++VG + + DA+ ARQL R Y E A +NV+
Sbjct: 91 LSSYRNISEIPLILVGTQDAISASNPRVIDDAR--ARQLCADMKRCSYYETCATYGLNVE 148
Query: 134 QAFHE 138
+ F E
Sbjct: 149 RVFQE 153
>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 = 51.1 bits (123), Expect = 1e-08
Identities = 23/65 (35%), Positives = 32/65 (49%), Gaps = 9/65 (13%)
Query: 59 LVFSVTDRNSFE---EIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVAR 115
LV+ +D NSF E+YK + E P L V KADLD Q+Q + + R
Sbjct: 83 LVYDSSDPNSFSYCAEVYKKY------FMLGEIPCLFVAAKADLDEQQQRAEVQPDEFCR 136
Query: 116 QLRIP 120
+L +P
Sbjct: 137 KLGLP 141
>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 = 49.6 bits (119), Expect = 3e-08
Identities = 32/116 (27%), Positives = 55/116 (47%), Gaps = 7/116 (6%)
Query: 26 DDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQILRVKDR 85
+ +P I+DT+ + + A +R LV+SV ++ E I ++R
Sbjct: 47 ERVPTT--IVDTSSRPQDRANLAAEIRKANVICLVYSVDRPSTLERIRTKWLPLIRRL-G 103
Query: 86 DEFPMLMVGNKADL-DHQRQVSSMDA-QNVARQLR--IPYIECSAKVRINVDQAFH 137
+ P+++VGNK+DL D Q + + + R +ECSAK INV + F+
Sbjct: 104 VKVPIILVGNKSDLRDGSSQAGLEEEMLPIMNEFREIETCVECSAKTLINVSEVFY 159
>gnl|CDD|206703 cd04131, Rnd, Rho family GTPase subfamily Rnd includes Rnd1/Rho6,
Rnd2/Rho7, and Rnd3/RhoE/Rho8. The Rnd subfamily
contains Rnd1/Rho6, Rnd2/Rho7, and Rnd3/RhoE/Rho8. These
novel Rho family proteins have substantial structural
differences compared to other Rho members, including N-
and C-terminal extensions relative to other Rhos.
Rnd3/RhoE is farnesylated at the C-terminal prenylation
site, unlike most other Rho proteins that are
geranylgeranylated. In addition, Rnd members are unable
to hydrolyze GTP and are resistant to GAP activity. They
are believed to exist only in the GTP-bound
conformation, and are antagonists of RhoA activity. Most
Rho proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 176
Score = 48.6 bits (116), Expect = 9e-08
Identities = 37/146 (25%), Positives = 67/146 (45%), Gaps = 17/146 (11%)
Query: 7 FVTDYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDR 66
F +Y PT+ ++YT +D L + DT+G + +R + L+ F ++
Sbjct: 26 FPENYVPTVFENYTASFEVDKQRIELSLWDTSGSPYYDNVRPLSYPDSDAVLICFDISRP 85
Query: 67 NSFEEIY-KFHRQILRVKDRDEFPMLMVGNKAD----------LDHQRQ--VSSMDAQNV 113
+ + + K+ ++ P+L+VG K+D L ++RQ VS +N+
Sbjct: 86 ETLDSVLKKWKGEVREFCPNT--PVLLVGCKSDLRTDLSTLTELSNKRQIPVSHEQGRNL 143
Query: 114 ARQL-RIPYIECSAKV-RINVDQAFH 137
A+Q+ Y+ECSAK +V F
Sbjct: 144 AKQIGAAAYVECSAKTSENSVRDVFE 169
>gnl|CDD|206735 cd04172, Rnd3_RhoE_Rho8, Rnd3/RhoE/Rho8 GTPases. Rnd3/RhoE/Rho8
subfamily. Rnd3/RhoE/Rho8 is a member of the novel Rho
subfamily Rnd, together with Rnd1/Rho6 and Rnd2/Rho7.
Rnd3/RhoE is known to bind the serine-threonine kinase
ROCK I. Unphosphorylated Rnd3/RhoE associates primarily
with membranes, but ROCK I-phosphorylated Rnd3/RhoE
localizes in the cytosol. Phosphorylation of Rnd3/RhoE
correlates with its activity in disrupting RhoA-induced
stress fibers and inhibiting Ras-induced fibroblast
transformation. In cells that lack stress fibers, such
as macrophages and monocytes, Rnd3/RhoE induces a
redistribution of actin, causing morphological changes
in the cell. In addition, Rnd3/RhoE has been shown to
inhibit cell cycle progression in G1 phase at a point
upstream of the pRb family pocket protein checkpoint.
Rnd3/RhoE has also been shown to inhibit Ras- and
Raf-induced fibroblast transformation. In mammary
epithelial tumor cells, Rnd3/RhoE regulates the assembly
of the apical junction complex and tight junction
formation. Rnd3/RhoE is underexpressed in prostate
cancer cells both in vitro and in vivo; re-expression of
Rnd3/RhoE suppresses cell cycle progression and
increases apoptosis, suggesting it may play a role in
tumor suppression. Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 182
Score = 46.6 bits (110), Expect = 6e-07
Identities = 41/149 (27%), Positives = 63/149 (42%), Gaps = 23/149 (15%)
Query: 7 FVTDYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDR 66
F +Y PT+ ++YT ID L + DT+G + +R + L+ F ++
Sbjct: 30 FPENYVPTVFENYTASFEIDTQRIELSLWDTSGSPYYDNVRPLSYPDSDAVLICFDISRP 89
Query: 67 NSFEEIYKFHRQILRVKDRDEF----PMLMVGNKADL------------DHQRQVSSMDA 110
+ + + K + + EF ML+VG K+DL Q VS
Sbjct: 90 ETLDSVLKKWK-----GEIQEFCPNTKMLLVGCKSDLRTDVSTLVELSNHRQTPVSYDQG 144
Query: 111 QNVARQLR-IPYIECSAKVRIN-VDQAFH 137
N+A+Q+ YIECSA N V FH
Sbjct: 145 ANMAKQIGAATYIECSALQSENSVRDIFH 173
>gnl|CDD|206701 cd04128, Spg1, Septum-promoting GTPase (Spg1). Spg1p. Spg1p
(septum-promoting GTPase) was first identified in the
fission yeast S. pombe, where it regulates septum
formation in the septation initiation network (SIN)
through the cdc7 protein kinase. Spg1p is an essential
gene that localizes to the spindle pole bodies. When
GTP-bound, it binds cdc7 and causes it to translocate to
spindle poles. Sid4p (septation initiation defective) is
required for localization of Spg1p to the spindle pole
body, and the ability of Spg1p to promote septum
formation from any point in the cell cycle depends on
Sid4p. Spg1p is negatively regulated by Byr4 and cdc16,
which form a two-component GTPase activating protein
(GAP) for Spg1p. The existence of a SIN-related pathway
in plants has been proposed. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization.
Length = 182
Score = 46.2 bits (110), Expect = 7e-07
Identities = 34/122 (27%), Positives = 55/122 (45%), Gaps = 9/122 (7%)
Query: 21 KQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQIL 80
K I I D GQ EF M + L +F +T +++ I +++RQ
Sbjct: 40 KTISIRGTEITFSIWDLGGQREFINMLPLVCKDAVAILFMFDLTRKSTLNSIKEWYRQA- 98
Query: 81 RVKDRDEFPMLMVGNKADL------DHQRQVSSMDAQNVARQLRIPYIECSAKVRINVDQ 134
R ++ P+L VG K DL + Q +++ A+ A+ ++ P I CS INV +
Sbjct: 99 RGFNKTAIPIL-VGTKYDLFADLPPEEQEEITK-QARKYAKAMKAPLIFCSTSHSINVQK 156
Query: 135 AF 136
F
Sbjct: 157 IF 158
>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 = 45.4 bits (107), Expect = 2e-06
Identities = 37/151 (24%), Positives = 68/151 (45%), Gaps = 14/151 (9%)
Query: 7 FVTDYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDR 66
F +Y PT+ D Y + L + DTAGQE++ +R + FL+ FSV +
Sbjct: 25 FPEEYVPTVFDHYAVSVTVGGKQYLLGLYDTAGQEDYDRLRPLSYPMTDVFLICFSVVNP 84
Query: 67 NSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLD------------HQRQVSSMDAQNVA 114
SF+ + + L+ + P L++G + DL ++ ++ Q +A
Sbjct: 85 ASFQNVKEEWVPELK-EYAPNVPYLLIGTQIDLRDDPKTLARLNDMKEKPITVEQGQKLA 143
Query: 115 RQLRIP-YIECSAKVRINVDQAFHELVRIVL 144
+++ Y+ECSA + + F E + +L
Sbjct: 144 KEIGACCYVECSALTQKGLKTVFDEAIIAIL 174
>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 = 41.5 bits (98), Expect = 3e-05
Identities = 31/137 (22%), Positives = 52/137 (37%), Gaps = 18/137 (13%)
Query: 22 QCVIDDIPA-------------RLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNS 68
Q D IP + + D GQ F +M E+Y R + V DR
Sbjct: 23 QFSEDTIPTVGFNMRKVTKGNVTIKVWDLGGQPRFRSMWERYCRGVNAIVYVVDAADREK 82
Query: 69 FEEIYKFHRQILRVKDRDEFPMLMVGNKADL----DHQRQVSSMDAQNVARQLRIPYIEC 124
E +L + P+L++GNK DL + M+ +++ + +
Sbjct: 83 LEVAKNELHDLLEKPSLEGIPLLVLGNKNDLPGALSVDELIEQMNLKSITDR-EVSCYSI 141
Query: 125 SAKVRINVDQAFHELVR 141
SAK + N+D L++
Sbjct: 142 SAKEKTNIDIVLDWLIK 158
>gnl|CDD|206741 cd09914, RocCOR, Ras of complex proteins (Roc) C-terminal of Roc
(COR) domain family. RocCOR (or Roco) protein family is
characterized by a superdomain containing a Ras-like
GTPase domain, called Roc (Ras of complex proteins), and
a characteristic second domain called COR (C-terminal of
Roc). A kinase domain and diverse regulatory domains are
also often found in Roco proteins. Their functions are
diverse; in Dictyostelium discoideum, which encodes 11
Roco proteins, they are involved in cell division,
chemotaxis and development, while in human, where 4 Roco
proteins (LRRK1, LRRK2, DAPK1, and MFHAS1) are encoded,
these proteins are involved in epilepsy and cancer.
Mutations in LRRK2 (leucine-rich repeat kinase 2) are
known to cause familial Parkinson's disease.
Length = 161
Score = 40.8 bits (96), Expect = 6e-05
Identities = 21/111 (18%), Positives = 38/111 (34%), Gaps = 4/111 (3%)
Query: 24 VIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQILRVK 83
+ RL++ D GQE + A + ++ S +LLVF + + + + RQI K
Sbjct: 45 APERKKIRLNVWDFGGQEIYHATHQFFLTSRSLYLLVFDLRTGDEVSRVPYWLRQI---K 101
Query: 84 DRDEFPMLM-VGNKADLDHQRQVSSMDAQNVARQLRIPYIECSAKVRINVD 133
++ VG D + + S K +
Sbjct: 102 AFGGVSPVILVGTHIDESCDEDILKKALNKKFPAIINDIHFVSCKNGKGIA 152
>gnl|CDD|206644 cd00878, Arf_Arl, ADP-ribosylation factor(Arf)/Arf-like (Arl) small
GTPases. Arf (ADP-ribosylation factor)/Arl (Arf-like)
small GTPases. Arf proteins are activators of
phospholipase D isoforms. Unlike Ras proteins they lack
cysteine residues at their C-termini and therefore are
unlikely to be prenylated. Arfs are N-terminally
myristoylated. Members of the Arf family are regulators
of vesicle formation in intracellular traffic that
interact reversibly with membranes of the secretory and
endocytic compartments in a GTP-dependent manner. They
depart from other small GTP-binding proteins by a unique
structural device, interswitch toggle, that implements
front-back communication from N-terminus to the
nucleotide binding site. Arf-like (Arl) proteins are
close relatives of the Arf, but only Arl1 has been shown
to function in membrane traffic like the Arf proteins.
Arl2 has an unrelated function in the folding of native
tubulin, and Arl4 may function in the nucleus. Most
other Arf family proteins are so far relatively poorly
characterized. Thus, despite their significant sequence
homologies, Arf family proteins may regulate unrelated
functions.
Length = 158
Score = 40.3 bits (95), Expect = 8e-05
Identities = 23/114 (20%), Positives = 46/114 (40%), Gaps = 13/114 (11%)
Query: 31 RLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQILRVKDRDEFPM 90
+ + D GQ++ + + Y + +G + V +DR EE ++L ++ P+
Sbjct: 44 KFTVWDVGGQDKIRPLWKHYYENTDGLIFVVDSSDRERIEEAKNELHKLLNEEELKGAPL 103
Query: 91 LMVGNKADLDHQRQVSSMDAQNVARQLRIPYI--------ECSAKVRINVDQAF 136
L++ NK DL ++ + L + I CSA +D+
Sbjct: 104 LILANKQDLPG-----ALTESELIELLGLESIKGRRWHIQPCSAVTGDGLDEGL 152
>gnl|CDD|206737 cd04174, Rnd1_Rho6, Rnd1/Rho6 GTPases. Rnd1/Rho6 is a member of
the novel Rho subfamily Rnd, together with Rnd2/Rho7 and
Rnd3/RhoE/Rho8. Rnd1/Rho6 binds GTP but does not
hydrolyze it to GDP, indicating that it is
constitutively active. In rat, Rnd1/Rho6 is highly
expressed in the cerebral cortex and hippocampus during
synapse formation, and plays a role in spine formation.
Rnd1/Rho6 is also expressed in the liver and in
endothelial cells, and is upregulated in uterine
myometrial cells during pregnancy. Like Rnd3/RhoE/Rho8,
Rnd1/Rho6 is believed to function as an antagonist to
RhoA. Most Rho proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Rho proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 232
Score = 39.3 bits (91), Expect = 3e-04
Identities = 37/148 (25%), Positives = 66/148 (44%), Gaps = 25/148 (16%)
Query: 11 YDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFE 70
Y PT+ ++YT ++ L + DT+G + +R + LL F ++ F+
Sbjct: 42 YVPTVFENYTACLETEEQRVELSLWDTSGSPYYDNVRPLCYSDSDAVLLCFDISRPEIFD 101
Query: 71 E-IYKFHRQILRVKDRDEFP---MLMVGNKAD----------LDHQRQ--VSSMDAQNVA 114
+ K+ +IL D P +L++G K D L +Q+Q +S +A
Sbjct: 102 SALKKWRAEIL-----DYCPSTRILLIGCKTDLRTDLSTLMELSNQKQAPISYEQGCAMA 156
Query: 115 RQLRIP-YIECSAKVRINVDQAFHELVR 141
+QL Y+ECSA +++ H + R
Sbjct: 157 KQLGAEAYLECSA---FTSEKSIHSIFR 181
>gnl|CDD|206719 cd04152, Arl4_Arl7, Arf-like 4 (Arl4) and 7 (Arl7) GTPases. Arl4
(Arf-like 4) is highly expressed in testicular germ
cells, and is found in the nucleus and nucleolus. In
mice, Arl4 is developmentally expressed during
embryogenesis, and a role in somite formation and
central nervous system differentiation has been
proposed. Arl7 has been identified as the only Arf/Arl
protein to be induced by agonists of liver X-receptor
and retinoid X-receptor and by cholesterol loading in
human macrophages. Arl7 is proposed to play a role in
transport between a perinuclear compartment and the
plasma membrane, apparently linked to the ABCA1-mediated
cholesterol secretion pathway. Older literature suggests
that Arl6 is a part of the Arl4/Arl7 subfamily, but
analyses based on more recent sequence data place Arl6
in its own subfamily.
Length = 183
Score = 35.9 bits (83), Expect = 0.003
Identities = 20/76 (26%), Positives = 34/76 (44%)
Query: 36 DTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQILRVKDRDEFPMLMVGN 95
D GQE+ + + Y R +G + V D EE +I + + P+L++ N
Sbjct: 58 DVGGQEKLRPLWKSYTRCTDGIVFVVDSVDVERMEEAKTELHKITKFSENQGVPVLVLAN 117
Query: 96 KADLDHQRQVSSMDAQ 111
K DL + VS ++
Sbjct: 118 KQDLPNALPVSEVEKL 133
>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 = 0.005
Identities = 28/105 (26%), Positives = 47/105 (44%), Gaps = 13/105 (12%)
Query: 31 RLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQILRVKDRDEFPM 90
+L++ D GQ + Y + + + V DR FEE + ++L + P+
Sbjct: 60 KLNVWDIGGQRKIRPYWRNYFENTDVLIYVIDSADRKRFEEAGQELVELLEEEKLAGVPV 119
Query: 91 LMVGNKADLDHQRQVSSMDAQNVARQL-------RIPYIE-CSAK 127
L+ NK DL +++ A+ VA L R +I+ CSAK
Sbjct: 120 LVFANKQDL-----LTAAPAEEVAEALNLHDIRDRSWHIQACSAK 159
>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 = 35.0 bits (80), Expect = 0.007
Identities = 36/145 (24%), Positives = 65/145 (44%), Gaps = 21/145 (14%)
Query: 10 DYDPTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSF 69
Y PT+ ++YT ID L++ DT+G + +R + L+ F ++ +
Sbjct: 29 SYVPTVFENYTASFEIDKHRIELNMWDTSGSSYYDNVRPLAYPDSDAVLICFDISRPETL 88
Query: 70 EEIYKFHRQILRVKDRDEFP---MLMVGNKAD----------LDHQRQVSSMDAQN--VA 114
+ + K + + ++ P +++VG K D L QR + Q +A
Sbjct: 89 DSVLK----KWQGETQEFCPNAKLVLVGCKLDMRTDLSTLRELSKQRLIPVTHEQGSLLA 144
Query: 115 RQL-RIPYIECSAKVRIN-VDQAFH 137
RQL + Y+ECS+++ N V FH
Sbjct: 145 RQLGAVAYVECSSRMSENSVRDVFH 169
>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 = 34.9 bits (81), Expect = 0.011
Identities = 14/62 (22%), Positives = 28/62 (45%), Gaps = 17/62 (27%)
Query: 70 EEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRI-----PYIEC 124
E++ + R++ + + PM++ NKAD+ DA+ +LR+ +
Sbjct: 201 EDLLRLARELRKRR----KPMVIAANKADI--------PDAEENISKLRLKYPDEIVVPT 248
Query: 125 SA 126
SA
Sbjct: 249 SA 250
>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 = 33.5 bits (77), Expect = 0.020
Identities = 22/70 (31%), Positives = 35/70 (50%)
Query: 30 ARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQILRVKDRDEFP 89
ARL D GQEE ++ ++Y G + V TDR F E +++ + + P
Sbjct: 51 ARLMFWDLGGQEELRSLWDKYYAESHGVIYVIDSTDRERFNESKSAFEKVINNEALEGVP 110
Query: 90 MLMVGNKADL 99
+L++ NK DL
Sbjct: 111 LLVLANKQDL 120
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 33.2 bits (76), Expect = 0.030
Identities = 20/77 (25%), Positives = 32/77 (41%), Gaps = 8/77 (10%)
Query: 32 LDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSF--EEIYKFHRQILRVKDRDEFP 89
+ + T GQE F M E R G +++ + +F EEI F + R+ P
Sbjct: 70 VHLFGTPGQERFKFMWEILSRGAVGAIVLVDSSRPITFHAEEIIDF------LTSRNPIP 123
Query: 90 MLMVGNKADLDHQRQVS 106
+++ NK DL
Sbjct: 124 VVVAINKQDLFDALPPE 140
>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 = 32.6 bits (75), Expect = 0.042
Identities = 17/66 (25%), Positives = 29/66 (43%), Gaps = 4/66 (6%)
Query: 36 DTAGQEEFSAMR--EQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQILRVKDRDEFPMLMV 93
D G E A R + Y +G + + D F+E + +L ++ P+L++
Sbjct: 69 DLGGHE--QARRVWKDYFPEVDGIVFLVDAADPERFQESKEELDSLLNDEELANVPILIL 126
Query: 94 GNKADL 99
GNK D
Sbjct: 127 GNKIDK 132
>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 = 32.2 bits (74), Expect = 0.051
Identities = 25/121 (20%), Positives = 46/121 (38%), Gaps = 16/121 (13%)
Query: 32 LDILDTAG--------QEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQILRVK 83
+ ++DT G +E R+ R+ + LLV EE L +
Sbjct: 48 VVLIDTPGLDEEGGLGRERVEEARQVADRA-DLVLLVVDSDLTPVEEE------AKLGLL 100
Query: 84 DRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLR-IPYIECSAKVRINVDQAFHELVRI 142
P+L+V NK DL + + + + L +P I SA +D+ ++ +
Sbjct: 101 RERGKPVLLVLNKIDLVPESEEEELLRERKLELLPDLPVIAVSALPGEGIDELRKKIAEL 160
Query: 143 V 143
+
Sbjct: 161 L 161
>gnl|CDD|133353 cd04153, Arl5_Arl8, Arf-like 5 (Arl5) and 8 (Arl8) GTPases.
Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like
Arl4 and Arl7, are localized to the nucleus and
nucleolus. Arl5 is developmentally regulated during
embryogenesis in mice. Human Arl5 interacts with the
heterochromatin protein 1-alpha (HP1alpha), a nonhistone
chromosomal protein that is associated with
heterochromatin and telomeres, and prevents telomere
fusion. Arl5 may also play a role in embryonic nuclear
dynamics and/or signaling cascades. Arl8 was identified
from a fetal cartilage cDNA library. It is found in
brain, heart, lung, cartilage, and kidney. No function
has been assigned for Arl8 to date.
Length = 174
Score = 32.3 bits (74), Expect = 0.063
Identities = 28/91 (30%), Positives = 43/91 (47%), Gaps = 11/91 (12%)
Query: 13 PTIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSF--- 69
PTI S ++ V +I R + D GQE + Y + + +LV TDR
Sbjct: 45 PTI-GSNVEEIVYKNI--RFLMWDIGGQESLRSSWNTYYTNTDAVILVIDSTDRERLPLT 101
Query: 70 -EEIYKFHRQILRVKDRDEFPMLMVGNKADL 99
EE+YK +L +D + +L++ NK DL
Sbjct: 102 KEELYK----MLAHEDLRKAVLLVLANKQDL 128
>gnl|CDD|133356 cd04156, ARLTS1, Arf-like tumor suppressor gene 1 (ARLTS1 or
Arl11). ARLTS1 (Arf-like tumor suppressor gene 1), also
known as Arl11, is a member of the Arf family of small
GTPases that is believed to play a major role in
apoptotic signaling. ARLTS1 is widely expressed and
functions as a tumor suppressor gene in several human
cancers. ARLTS1 is a low-penetrance suppressor that
accounts for a small percentage of familial melanoma or
familial chronic lymphocytic leukemia (CLL). ARLTS1
inactivation seems to occur most frequently through
biallelic down-regulation by hypermethylation of the
promoter. In breast cancer, ARLTS1 alterations were
typically a combination of a hypomorphic polymorphism
plus loss of heterozygosity. In a case of thyroid
adenoma, ARLTS1 alterations were polymorphism plus
promoter hypermethylation. The nonsense polymorphism
Trp149Stop occurs with significantly greater frequency
in familial cancer cases than in sporadic cancer cases,
and the Cys148Arg polymorphism is associated with an
increase in high-risk familial breast cancer.
Length = 160
Score = 32.0 bits (73), Expect = 0.066
Identities = 27/117 (23%), Positives = 56/117 (47%), Gaps = 14/117 (11%)
Query: 32 LDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQILRVKDRDEFPML 91
L + D GQE+ + + Y+ + +G + V +D +E K + IL+ + P++
Sbjct: 46 LTVWDVGGQEKMRTVWKCYLENTDGLVYVVDSSDEARLDESQKELKHILKNEHIKGVPVV 105
Query: 92 MVGNKADLDHQRQVSSMDAQNVARQLRIP--------YIE-CSAKVRINVDQAFHEL 139
++ NK DL ++ A+ + R+ ++ Y++ CSA + +AF +L
Sbjct: 106 LLANKQDLP-----GALTAEEITRRFKLKKYCSDRDWYVQPCSAVTGEGLAEAFRKL 157
>gnl|CDD|206722 cd04157, Arl6, Arf-like 6 (Arl6) GTPase. Arl6 (Arf-like 6) forms a
subfamily of the Arf family of small GTPases. Arl6
expression is limited to the brain and kidney in adult
mice, but it is expressed in the neural plate and
somites during embryogenesis, suggesting a possible role
for Arl6 in early development. Arl6 is also believed to
have a role in cilia or flagella function. Several
proteins have been identified that bind Arl6, including
Arl6 interacting protein (Arl6ip), and SEC61beta, a
subunit of the heterotrimeric conducting channel SEC61p.
Based on Arl6 binding to these effectors, Arl6 is also
proposed to play a role in protein transport, membrane
trafficking, or cell signaling during hematopoietic
maturation. At least three specific homozygous Arl6
mutations in humans have been found to cause
Bardet-Biedl syndrome, a disorder characterized by
obesity, retinopathy, polydactyly, renal and cardiac
malformations, learning disabilities, and
hypogenitalism. Older literature suggests that Arl6 is a
part of the Arl4/Arl7 subfamily, but analyses based on
more recent sequence data place Arl6 in its own
subfamily.
Length = 162
Score = 31.6 bits (72), Expect = 0.093
Identities = 18/67 (26%), Positives = 30/67 (44%), Gaps = 4/67 (5%)
Query: 36 DTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQILR---VKDRDEFPMLM 92
D +GQ ++ + E Y ++ +G + V +DR +L +K R P+L
Sbjct: 51 DMSGQGKYRGLWEHYYKNIQGIIFVIDSSDRLRMVVAKDELELLLNHPDIKHRR-IPILF 109
Query: 93 VGNKADL 99
NK DL
Sbjct: 110 YANKMDL 116
>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 = 31.5 bits (71), Expect = 0.11
Identities = 35/136 (25%), Positives = 52/136 (38%), Gaps = 20/136 (14%)
Query: 24 VIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNS--------FEEIYKF 75
V+D + L + DT G + R Y RS + LL FS+ NS + EI F
Sbjct: 60 VVDGVSVSLRLWDTFGDHD-KDRRFAYGRS-DVVLLCFSIASPNSLRNVKTMWYPEIRHF 117
Query: 76 HRQI----------LRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYIECS 125
++ LR D DE + + + + VA++L IPY E S
Sbjct: 118 CPRVPVILVGCKLDLRYADLDEVNRARRPLARPIKNADILPPETGRAVAKELGIPYYETS 177
Query: 126 AKVRINVDQAFHELVR 141
+ V F +R
Sbjct: 178 VVTQFGVKDVFDNAIR 193
>gnl|CDD|206674 cd01887, IF2_eIF5B, Initiation Factor 2 (IF2)/ eukaryotic
Initiation Factor 5B (eIF5B) family. IF2/eIF5B
contribute to ribosomal subunit joining and function as
GTPases that are maximally activated by the presence of
both ribosomal subunits. As seen in other GTPases,
IF2/IF5B undergoes conformational changes between its
GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess
three characteristic segments, including a divergent
N-terminal region followed by conserved central and
C-terminal segments. This core region is conserved among
all known eukaryotic and archaeal IF2/eIF5Bs and
eubacterial IF2s.
Length = 169
Score = 30.9 bits (71), Expect = 0.19
Identities = 27/133 (20%), Positives = 48/133 (36%), Gaps = 36/133 (27%)
Query: 31 RLDILDTAGQEEFSAMREQYMRSGEG---FLLVFSVTD---RNSFEEIYKFHRQILRVKD 84
+ +DT G E F+ MR R +LV + D + E I + +
Sbjct: 50 GITFIDTPGHEAFTNMRA---RGASVTDIAILVVAADDGVMPQTIEAI-----NHAKAAN 101
Query: 85 RDEFPMLMVGNKADLDHQRQVSSMDAQNVARQL------------RIPYIECSAKVRINV 132
P+++ NK D + + D + V +L + + SAK +
Sbjct: 102 ---VPIIVAINKIDKPYGTEA---DPERVKNELSELGLVGEEWGGDVSIVPISAKTGEGI 155
Query: 133 DQAFHELVRIVLL 145
D +L+ +LL
Sbjct: 156 D----DLLEAILL 164
>gnl|CDD|128474 smart00177, ARF, ARF-like small GTPases; ARF, ADP-ribosylation
factor. Ras homologues involved in vesicular transport.
Activator of phospholipase D isoforms. Unlike Ras
proteins they lack cysteine residues at their C-termini
and therefore are unlikely to be prenylated. ARFs are
N-terminally myristoylated. Contains ATP/GTP-binding
motif (P-loop).
Length = 175
Score = 30.7 bits (69), Expect = 0.20
Identities = 15/69 (21%), Positives = 31/69 (44%)
Query: 31 RLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQILRVKDRDEFPM 90
+ D GQ++ + Y + +G + V DR+ +E + ++L + + +
Sbjct: 58 SFTVWDVGGQDKIRPLWRHYYTNTQGLIFVVDSNDRDRIDEAREELHRMLNEDELRDAVI 117
Query: 91 LMVGNKADL 99
L+ NK DL
Sbjct: 118 LVFANKQDL 126
>gnl|CDD|238931 cd01971, Nitrogenase_VnfN_like, Nitrogenase_vnfN_like: VnfN subunit
of the VnfEN complex-like. This group in addition to
VnfN contains a subset of the beta subunit of the
nitrogenase MoFe protein and NifN-like proteins. The
nitrogenase enzyme system catalyzes the ATP-dependent
reduction of dinitrogen to ammonia. NifEN participates
in the synthesis of the iron-molybdenum cofactor
(FeMoco) of MoFe protein of the
molybdenum(Mo)-nitrogenase. NifB-co (an iron and sulfur
containing precursor of the FeMoco) from NifB is
transferred to NifEN where it is further processed to
FeMoco. VnfEN may similarly be a scaffolding protien
for the iron-vanadium cofactor (FeVco) of the
vanadium-dependent (V)-nitrogenase. NifE and NifN are
essential for the Mo-nitrogenase, VnfE and VnfN are not
essential for the V-nitrogenase. NifE and NifN can
substitute when the vnfEN genes are inactivated.
Length = 427
Score = 31.2 bits (71), Expect = 0.20
Identities = 26/111 (23%), Positives = 49/111 (44%), Gaps = 22/111 (19%)
Query: 28 IPARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQILRVKDRDE 87
+PA+ I D ++ SA+ ++ G +VFS E+ Y Q LR D
Sbjct: 319 VPAKQVITDNPPEKYRSAIENEFEAEGVSAEVVFS-------EDGYAIG-QSLRQSDFKY 370
Query: 88 FPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYIECSAKV--RINVDQAF 136
P ++ G SS + +++A++L +E S V R+ +++ +
Sbjct: 371 KPPIIFG-----------SSWE-RDLAKELGGKILEVSFPVTNRVVLNRGY 409
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 29.9 bits (67), Expect = 0.38
Identities = 18/76 (23%), Positives = 35/76 (46%), Gaps = 2/76 (2%)
Query: 34 ILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIY-KFHRQILRVKDRDEFPMLM 92
+ D GQ++ + Y ++ +G + V DR+ E + HR + + RD +L+
Sbjct: 65 VWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRDRVVEARDELHRMLNEDELRDAV-LLV 123
Query: 93 VGNKADLDHQRQVSSM 108
NK DL + + +
Sbjct: 124 FANKQDLPNAMNAAEI 139
>gnl|CDD|133362 cd04162, Arl9_Arfrp2_like, Arf-like 9 (Arl9)/Arfrp2-like GTPase.
Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first
identified as part of the Human Cancer Genome Project.
It maps to chromosome 4q12 and is sometimes referred to
as Arfrp2 (Arf-related protein 2). This is a novel
subfamily identified in human cancers that is
uncharacterized to date.
Length = 164
Score = 28.6 bits (64), Expect = 0.91
Identities = 21/101 (20%), Positives = 42/101 (41%), Gaps = 6/101 (5%)
Query: 30 ARLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQILRVKDRDEFP 89
A +++L+ G + ++Y+ +G + V D + Q+L+ D P
Sbjct: 44 AIMELLEIGGSQNLRKYWKRYLSGSQGLIFVVDSADSERLPLARQELHQLLQ-HPPD-LP 101
Query: 90 MLMVGNKADLDHQRQV----SSMDAQNVARQLRIPYIECSA 126
++++ NK DL R V ++ + +AR R S
Sbjct: 102 LVVLANKQDLPAARSVQEIHKELELEPIARGRRWILQGTSL 142
>gnl|CDD|237358 PRK13351, PRK13351, elongation factor G; Reviewed.
Length = 687
Score = 28.8 bits (65), Expect = 1.4
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 10/62 (16%)
Query: 8 VTDYDP-------TIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLV 60
VTD+ P TIE + T C D+ R++++DT G +F+ E+ +R +G ++V
Sbjct: 47 VTDWMPQEQERGITIESAATS-CDWDNH--RINLIDTPGHIDFTGEVERSLRVLDGAVVV 103
Query: 61 FS 62
F
Sbjct: 104 FD 105
>gnl|CDD|206716 cd04149, Arf6, ADP ribosylation factor 6 (Arf6). Arf6 subfamily.
Arf6 (ADP ribosylation factor 6) proteins localize to
the plasma membrane, where they perform a wide variety
of functions. In its active, GTP-bound form, Arf6 is
involved in cell spreading, Rac-induced formation of
plasma membrane ruffles, cell migration, wound healing,
and Fc-mediated phagocytosis. Arf6 appears to change the
actin structure at the plasma membrane by activating
Rac, a Rho family protein involved in membrane ruffling.
Arf6 is required for and enhances Rac formation of
ruffles. Arf6 can regulate dendritic branching in
hippocampal neurons, and in yeast it localizes to the
growing bud, where it plays a role in polarized growth
and bud site selection. In leukocytes, Arf6 is required
for chemokine-stimulated migration across endothelial
cells. Arf6 also plays a role in down-regulation of
beta2-adrenergic receptors and luteinizing hormone
receptors by facilitating the release of sequestered
arrestin to allow endocytosis. Arf6 is believed to
function at multiple sites on the plasma membrane
through interaction with a specific set of GEFs, GAPs,
and effectors. Arf6 has been implicated in breast cancer
and melanoma cell invasion, and in actin remodelling at
the invasion site of Chlamydia infection.
Length = 168
Score = 28.2 bits (63), Expect = 1.5
Identities = 17/70 (24%), Positives = 34/70 (48%), Gaps = 2/70 (2%)
Query: 31 RLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEI-YKFHRQILRVKDRDEFP 89
+ ++ D GQ++ + Y +G + V DR+ +E + HR I+ ++ +
Sbjct: 54 KFNVWDVGGQDKIRPLWRHYYTGTQGLIFVVDSADRDRIDEARQELHR-IINDREMRDAL 112
Query: 90 MLMVGNKADL 99
+L+ NK DL
Sbjct: 113 LLVFANKQDL 122
>gnl|CDD|222509 pfam14040, DNase_NucA_NucB, Deoxyribonuclease NucA/NucB. Members
of this family act as deoxyribonucleases.
Length = 103
Score = 27.3 bits (61), Expect = 1.6
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 9/38 (23%)
Query: 83 KDRDEFPMLMV---GNKADL------DHQRQVSSMDAQ 111
DRDE+PM M G A + D++ S + Q
Sbjct: 51 YDRDEWPMAMCKEGGTGASVRYIPPSDNRGAGSWVGNQ 88
>gnl|CDD|236584 PRK09602, PRK09602, translation-associated GTPase; Reviewed.
Length = 396
Score = 28.2 bits (64), Expect = 1.6
Identities = 10/32 (31%), Positives = 19/32 (59%), Gaps = 6/32 (18%)
Query: 70 EEIYKFHRQILRV-KDRDEFPMLMVGNKADLD 100
E++ + R++ ++ K PM++ NKADL
Sbjct: 204 EDLLELARELRKISK-----PMVIAANKADLP 230
>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 = 27.4 bits (62), Expect = 2.5
Identities = 9/46 (19%), Positives = 16/46 (34%)
Query: 89 PMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYIECSAKVRINVDQ 134
P ++V NK DL + + + SA +D+
Sbjct: 116 PRIVVLNKIDLLDAEERFEKLKELLKELKGKKVFPISALTGEGLDE 161
>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 = 27.4 bits (62), Expect = 2.8
Identities = 14/57 (24%), Positives = 26/57 (45%), Gaps = 5/57 (8%)
Query: 77 RQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLRIPYIECSAKVRINVD 133
++L+ D+ P+++V NK DL + + + R R + SAK +D
Sbjct: 143 EEVLKELGADDIPIILVLNKIDL-----LDDEELEERLRAGRPDAVFISAKTGEGLD 194
>gnl|CDD|206720 cd04154, Arl2, Arf-like 2 (Arl2) GTPase. Arl2 (Arf-like 2) GTPases
are members of the Arf family that bind GDP and GTP with
very low affinity. Unlike most Arf family proteins, Arl2
is not myristoylated at its N-terminal helix. The
protein PDE-delta, first identified in photoreceptor rod
cells, binds specifically to Arl2 and is structurally
very similar to RhoGDI. Despite the high structural
similarity between Arl2 and Rho proteins and between
PDE-delta and RhoGDI, the interactions between the
GTPases and their effectors are very different. In its
GTP bound form, Arl2 interacts with the protein Binder
of Arl2 (BART), and the complex is believed to play a
role in mitochondrial adenine nucleotide transport. In
its GDP bound form, Arl2 interacts with tubulin- folding
Cofactor D; this interaction is believed to play a role
in regulation of microtubule dynamics that impact the
cytoskeleton, cell division, and cytokinesis.
Length = 173
Score = 27.3 bits (61), Expect = 3.3
Identities = 29/119 (24%), Positives = 48/119 (40%), Gaps = 15/119 (12%)
Query: 31 RLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQILRVKDRDEFPM 90
+L+I D GQ+ + Y S + + V +DR E+ K Q L V++R
Sbjct: 59 KLNIWDVGGQKSLRSYWRNYFESTDALIWVVDSSDRARLEDC-KRELQKLLVEERLAGAT 117
Query: 91 LMV-GNKADLDHQRQVSSMDAQNVARQLRIPYIE--------CSAKVRINVDQAFHELV 140
L++ NK DL ++ + + L + I+ CSA N+ LV
Sbjct: 118 LLIFANKQDLP-----GALSPEEIREVLELDSIKSHHWRIFGCSAVTGENLLDGIDWLV 171
>gnl|CDD|224679 COG1765, COG1765, Predicted redox protein, regulator of disulfide
bond formation [Posttranslational modification, protein
turnover, chaperones].
Length = 137
Score = 27.0 bits (60), Expect = 3.6
Identities = 5/38 (13%), Positives = 15/38 (39%), Gaps = 1/38 (2%)
Query: 106 SSMDAQNVARQLRIPYIECSAKVRINV-DQAFHELVRI 142
S++ + + ++ RI + +V ++ I
Sbjct: 53 SAITVRLILKKKRIDVEDLEVEVTGERREEEPRGFTEI 90
>gnl|CDD|206723 cd04158, ARD1, (ADP-ribosylation factor domain protein 1 (ARD1).
ARD1 (ADP-ribosylation factor domain protein 1) is an
unusual member of the Arf family. In addition to the
C-terminal Arf domain, ARD1 has an additional 46-kDa
N-terminal domain that contains a RING finger domain,
two predicted B-Boxes, and a coiled-coil protein
interaction motif. This domain belongs to the TRIM
(tripartite motif) or RBCC (RING, B-Box, coiled-coil)
family. Like most Arfs, the ARD1 Arf domain lacks
detectable GTPase activity. However, unlike most Arfs,
the full-length ARD1 protein has significant GTPase
activity due to the GAP (GTPase-activating protein)
activity exhibited by the 46-kDa N-terminal domain. The
GAP domain of ARD1 is specific for its own Arf domain
and does not bind other Arfs. The rate of GDP
dissociation from the ARD1 Arf domain is slowed by the
adjacent 15 amino acids, which act as a GDI
(GDP-dissociation inhibitor) domain. ARD1 is
ubiquitously expressed in cells and localizes to the
Golgi and to the lysosomal membrane. Two Tyr-based
motifs in the Arf domain are responsible for Golgi
localization, while the GAP domain controls lysosomal
localization.
Length = 169
Score = 26.9 bits (59), Expect = 4.1
Identities = 15/78 (19%), Positives = 33/78 (42%)
Query: 31 RLDILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQILRVKDRDEFPM 90
+ I D G+ + + + Y + + + V + R+ E + ++L K+ + +
Sbjct: 44 KFTIWDVGGKHKLRPLWKHYYLNTQAVVFVIDSSHRDRVSEAHSELAKLLTEKELRDALL 103
Query: 91 LMVGNKADLDHQRQVSSM 108
L+ NK D+ V M
Sbjct: 104 LIFANKQDVAGALSVEEM 121
>gnl|CDD|206717 cd04150, Arf1_5_like, ADP-ribosylation factor-1 (Arf1) and
ADP-ribosylation factor-5 (Arf5). The Arf1-Arf5-like
subfamily contains Arf1, Arf2, Arf3, Arf4, Arf5, and
related proteins. Arfs1-5 are soluble proteins that are
crucial for assembling coat proteins during vesicle
formation. Each contains an N-terminal myristoylated
amphipathic helix that is folded into the protein in the
GDP-bound state. GDP/GTP exchange exposes the helix,
which anchors to the membrane. Following GTP hydrolysis,
the helix dissociates from the membrane and folds back
into the protein. A general feature of Arf1-5 signaling
may be the cooperation of two Arfs at the same site.
Arfs1-5 are generally considered to be interchangeable
in function and location, but some specific functions
have been assigned. Arf1 localizes to the
early/cis-Golgi, where it is activated by GBF1 and
recruits the coat protein COPI. It also localizes to the
trans-Golgi network (TGN), where it is activated by
BIG1/BIG2 and recruits the AP1, AP3, AP4, and GGA
proteins. Humans, but not rodents and other lower
eukaryotes, lack Arf2. Human Arf3 shares 96% sequence
identity with Arf1 and is believed to generally function
interchangeably with Arf1. Human Arf4 in the activated
(GTP-bound) state has been shown to interact with the
cytoplasmic domain of epidermal growth factor receptor
(EGFR) and mediate the EGF-dependent activation of
phospholipase D2 (PLD2), leading to activation of the
activator protein 1 (AP-1) transcription factor. Arf4
has also been shown to recognize the C-terminal sorting
signal of rhodopsin and regulate its incorporation into
specialized post-Golgi rhodopsin transport carriers
(RTCs). There is some evidence that Arf5 functions at
the early-Golgi and the trans-Golgi to affect
Golgi-associated alpha-adaptin homology Arf-binding
proteins (GGAs).
Length = 159
Score = 26.6 bits (59), Expect = 5.3
Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 6/67 (8%)
Query: 36 DTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFHRQILRVKDRDEFP---MLM 92
D GQ++ + Y ++ +G L+F V D N E I + ++ R+ + DE +L+
Sbjct: 50 DVGGQDKIRPLWRHYFQNTQG--LIF-VVDSNDRERIGEAREELQRMLNEDELRDAVLLV 106
Query: 93 VGNKADL 99
NK DL
Sbjct: 107 FANKQDL 113
>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 = 26.3 bits (59), Expect = 6.0
Identities = 22/85 (25%), Positives = 37/85 (43%), Gaps = 7/85 (8%)
Query: 59 LVFSVTDRNSFEEIYKFHRQILRVKDRDEFPMLMVGNKADLDHQRQVSSMDAQNVARQLR 118
LV V D + E I + IL + + + P+++V NK DL ++ + +
Sbjct: 85 LVLFVVDAS--EWIGEGDEFILELLKKSKTPVILVLNKIDLVKDKEDLLPLLE--KLKEL 140
Query: 119 IPYIE---CSAKVRINVDQAFHELV 140
P+ E SA NVD+ +V
Sbjct: 141 HPFAEIFPISALKGENVDELLEYIV 165
>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 26.8 bits (60), Expect = 6.3
Identities = 21/98 (21%), Positives = 40/98 (40%), Gaps = 14/98 (14%)
Query: 8 VTDYDP-------TIEDSYTKQCVIDDIPARLDILDTAGQEEFSAMREQYMRSGEGFLLV 60
D+ TI + T D R++++DT G +F+ E+ +R +G ++V
Sbjct: 49 TMDWMEQEQERGITITSAATTLFWKGDY--RINLIDTPGHVDFTIEVERSLRVLDGAVVV 106
Query: 61 FSVTDRNSFEEIYKFHRQILRVKDRDEFPMLMVGNKAD 98
+ E + + R D+ P ++ NK D
Sbjct: 107 VDAVE--GVEPQTE---TVWRQADKYGVPRILFVNKMD 139
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 26.7 bits (60), Expect = 6.8
Identities = 11/27 (40%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 22 QCVIDDIPAR-LDILDTAGQEEFSAMR 47
Q +D I + +DT G E F+AMR
Sbjct: 46 QVPLDVIKIPGITFIDTPGHEAFTAMR 72
>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 = 26.3 bits (59), Expect = 7.3
Identities = 21/122 (17%), Positives = 42/122 (34%), Gaps = 19/122 (15%)
Query: 34 ILDTAGQEEFSAMREQYMRSGEGFLLVFSVTDRNSFEEIYKFH-RQILRVKDRDEFPMLM 92
I+DT G +F+ + +G +LV + + H + P+++
Sbjct: 70 IIDTPGHVDFTKEMIRGASQADGAILVVDAVE--GVMPQTREHLLLAKTLG----VPIIV 123
Query: 93 VGNKADLDHQ-------RQVSSMDAQN-VARQLRIPYIECSAKVRINVDQAFHELVRIVL 144
NK D ++S + +P + SA +D EL+ +
Sbjct: 124 FINKIDRVDDAELEEVVEEISRELLEKYGFGGETVPVVPGSALTGEGID----ELLEALD 179
Query: 145 LH 146
L+
Sbjct: 180 LY 181
>gnl|CDD|239123 cd02658, Peptidase_C19B, A subfamily of Peptidase C19. Peptidase
C19 contains ubiquitinyl hydrolases. They are
intracellular peptidases that remove ubiquitin molecules
from polyubiquinated peptides by cleavage of isopeptide
bonds. They hydrolyze bonds involving the carboxyl group
of the C-terminal Gly residue of ubiquitin. The purpose
of the de-ubiquitination is thought to be editing of the
ubiquitin conjugates, which could rescue them from
degradation, as well as recycling of the ubiquitin. The
ubiquitin/proteasome system is responsible for most
protein turnover in the mammalian cell, and with over 50
members, family C19 is one of the largest families of
peptidases in the human genome.
Length = 311
Score = 26.5 bits (59), Expect = 7.4
Identities = 20/103 (19%), Positives = 34/103 (33%), Gaps = 18/103 (17%)
Query: 38 AGQEEFSAMREQYMRSGEGFLLVFSVTDRNSF-EEIYKFHRQILRVKDRDEFPMLMVGNK 96
G EFS MR+Q + E L + DR SF + + + M+ ++
Sbjct: 90 KGHPEFSTMRQQ--DALEFLLHLIDKLDRESFKNLGLNPND-LFKF---------MIEDR 137
Query: 97 ADLDHQRQVSSMDAQNVARQLRIPY-----IECSAKVRINVDQ 134
+ ++V + L +P E V V
Sbjct: 138 LECLSCKKVKYTSELSEILSLPVPKDEATEKEEGELVYEPVPL 180
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 26.4 bits (59), Expect = 8.3
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 35 LDTAGQEEFSAMR 47
LDT G E F+AMR
Sbjct: 301 LDTPGHEAFTAMR 313
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 26.2 bits (59), Expect = 8.5
Identities = 11/49 (22%), Positives = 18/49 (36%), Gaps = 10/49 (20%)
Query: 89 PMLMVGNKADLDHQRQVSSMDAQNVAR---QLRIPYIECSAKVRINVDQ 134
P ++V NK DL +N+ +L SA +D+
Sbjct: 276 PQIVVANKMDLP-------EAEENLEEFKEKLGPKVFPISALTGQGLDE 317
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
0.324 0.137 0.393
Gapped
Lambda K H
0.267 0.0734 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,088,979
Number of extensions: 732973
Number of successful extensions: 1097
Number of sequences better than 10.0: 1
Number of HSP's gapped: 987
Number of HSP's successfully gapped: 140
Length of query: 159
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 70
Effective length of database: 6,990,096
Effective search space: 489306720
Effective search space used: 489306720
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 55 (25.0 bits)