RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10504
(286 letters)
>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 = 309 bits (793), Expect = e-108
Identities = 127/164 (77%), Positives = 145/164 (88%), Gaps = 1/164 (0%)
Query: 104 EFKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTE 163
E+KVVVLGSGGVGKSALTVQFVSG F+EKYDPTIEDFYRKEIEVD +P VLEILDTAGTE
Sbjct: 1 EYKVVVLGSGGVGKSALTVQFVSGTFIEKYDPTIEDFYRKEIEVDSSPSVLEILDTAGTE 60
Query: 164 QFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLAS 223
QFASMRDLYIKNGQGF+VVYSL N TFQDIK M++ I RVKG E+VPI+LV NK+DL
Sbjct: 61 QFASMRDLYIKNGQGFIVVYSLVNQQTFQDIKPMRDQIVRVKGYEKVPIILVGNKVDLE- 119
Query: 224 HQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREMN 267
+REV + +G+ALA+ WGCPF+E SAK+KT VNE+FAEIVR+MN
Sbjct: 120 SEREVSSAEGRALAEEWGCPFMETSAKSKTMVNELFAEIVRQMN 163
>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 = 277 bits (710), Expect = 4e-95
Identities = 93/165 (56%), Positives = 131/165 (79%), Gaps = 1/165 (0%)
Query: 103 REFKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGT 162
RE+K+VVLG GGVGKSALT+QFV G F+++YDPTIED YRK+IE+D C+L+ILDTAG
Sbjct: 1 REYKLVVLGGGGVGKSALTIQFVQGHFVDEYDPTIEDSYRKQIEIDGEVCLLDILDTAGQ 60
Query: 163 EQFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLA 222
E+F++MRD Y++ G+GF++VYS+T+ +F++I + +E I RVK + VPI+LV NK DL
Sbjct: 61 EEFSAMRDQYMRTGEGFLLVYSITDRQSFEEIAKFREQILRVKDRDDVPIVLVGNKCDL- 119
Query: 223 SHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREMN 267
++R V T +G+ LA+ WGCPF+E SAK + NV+E F ++VRE+
Sbjct: 120 ENERVVSTEEGKELARQWGCPFLETSAKERINVDEAFYDLVREIR 164
>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 = 270 bits (692), Expect = 2e-92
Identities = 92/163 (56%), Positives = 129/163 (79%), Gaps = 1/163 (0%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTEQ 164
+K+VVLGSGGVGKSALT+QF+ G F++ YDPTIED YRK+IE+D C+L+ILDTAG E+
Sbjct: 1 YKLVVLGSGGVGKSALTIQFIQGHFVDDYDPTIEDSYRKQIEIDGEVCLLDILDTAGQEE 60
Query: 165 FASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLASH 224
F++MRD Y++ G+GF++VYS+T+ +F++IK+ +E I RVK + VPI+LV NK DL
Sbjct: 61 FSAMRDQYMRTGEGFLLVYSITDRQSFEEIKKFREQILRVKDRDDVPIVLVGNKCDL-ES 119
Query: 225 QREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREMN 267
+R V T +G+ LA+ WGCPF+E SAK + NV+E F ++VRE+
Sbjct: 120 ERVVSTEEGKELARQWGCPFLETSAKERVNVDEAFYDLVREIR 162
>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 = 259 bits (663), Expect = 4e-88
Identities = 105/165 (63%), Positives = 133/165 (80%), Gaps = 2/165 (1%)
Query: 104 EFKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTE 163
E+K+VVLGSGGVGKSALTVQFV G F++KYDPTIED YRK+IEVD C+LEILDTAGTE
Sbjct: 1 EYKLVVLGSGGVGKSALTVQFVQGIFVDKYDPTIEDSYRKQIEVDCQQCMLEILDTAGTE 60
Query: 164 QFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLAS 223
QF +MRDLYIKNGQGF +VYS+T +F D++ ++E I RVK +E VP++LV NK DL
Sbjct: 61 QFTAMRDLYIKNGQGFALVYSITAQQSFNDLQDLREQILRVKDTEDVPMILVGNKCDLED 120
Query: 224 HQREVPTLDGQALAQSWG-CPFIEASAKNKTNVNEMFAEIVREMN 267
+R V +GQ LA+ WG CPF+E SAK+K NV+E+F ++VR++N
Sbjct: 121 -ERVVSKEEGQNLARQWGNCPFLETSAKSKINVDEIFYDLVRQIN 164
>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 = 257 bits (660), Expect = 1e-87
Identities = 95/161 (59%), Positives = 129/161 (80%), Gaps = 1/161 (0%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTEQF 165
K+VVLG+GGVGKSALT++FVSG F+E+YDPTIED YRK+I VD L+ILDTAG E+F
Sbjct: 1 KLVVLGAGGVGKSALTIRFVSGEFVEEYDPTIEDSYRKQIVVDGETYTLDILDTAGQEEF 60
Query: 166 ASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLASHQ 225
++MRD YI+NG GF++VYS+T+ +F++IK ++E I RVK E VPI+LV NK DL ++
Sbjct: 61 SAMRDQYIRNGDGFILVYSITSRESFEEIKNIREQILRVKDKEDVPIVLVGNKCDL-ENE 119
Query: 226 REVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREM 266
R+V T +G+ALA+ WGCPF+E SAK N++E+F +VRE+
Sbjct: 120 RQVSTEEGEALAEEWGCPFLETSAKTNINIDELFNTLVREI 160
>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 = 240 bits (615), Expect = 9e-81
Identities = 106/164 (64%), Positives = 131/164 (79%), Gaps = 1/164 (0%)
Query: 104 EFKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTE 163
E+K+VVLGSGGVGKSALTVQFV G F+EKYDPTIED YRK++EVD C+LEILDTAGTE
Sbjct: 1 EYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDGQQCMLEILDTAGTE 60
Query: 164 QFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLAS 223
QF +MRDLY+KNGQGFV+VYS+T TF D++ ++E I RVK +E VP++LV NK DL
Sbjct: 61 QFTAMRDLYMKNGQGFVLVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLED 120
Query: 224 HQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREMN 267
+R V GQ LA+ WGC F+E SAK K NVNE+F ++VR++N
Sbjct: 121 -ERVVGKEQGQNLARQWGCAFLETSAKAKINVNEIFYDLVRQIN 163
>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 = 220 bits (561), Expect = 1e-72
Identities = 91/164 (55%), Positives = 128/164 (78%), Gaps = 2/164 (1%)
Query: 104 EFKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTE 163
++K+VVLG+GGVGKSALTVQFV F+E YDPTIED YRK++E+D C LEILDTAGTE
Sbjct: 1 DYKIVVLGAGGVGKSALTVQFVQNVFIESYDPTIEDSYRKQVEIDGRQCDLEILDTAGTE 60
Query: 164 QFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLAS 223
QF +MR+LYIK+GQGF++VYS+T+ + ++ +++E + R+K S+ VP++LV NK DL
Sbjct: 61 QFTAMRELYIKSGQGFLLVYSVTSEASLNELGELREQVLRIKDSDNVPMVLVGNKADLED 120
Query: 224 HQREVPTLDGQALAQSWG-CPFIEASAKNKTNVNEMFAEIVREM 266
R+V DG +L+Q WG PF E SA+ +TNV+E+F ++VR++
Sbjct: 121 -DRQVSREDGVSLSQQWGNVPFYETSARKRTNVDEVFIDLVRQI 163
>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 = 213 bits (546), Expect = 3e-70
Identities = 79/162 (48%), Positives = 107/162 (66%), Gaps = 3/162 (1%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTI-EDFYRKEIEVDKAPCVLEILDTAGTEQ 164
K+V++G GGVGKS+L ++F F E+Y PTI DFY K IEVD L+I DTAG E+
Sbjct: 1 KLVLVGDGGVGKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAGQER 60
Query: 165 FASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLASH 224
F ++R LY + QGF++VY +T+ +F+++K+ E I R E VPI+LV NK DL
Sbjct: 61 FRALRPLYYRGAQGFLLVYDITSRDSFENVKKWLEEILRHAD-ENVPIVLVGNKCDLE-D 118
Query: 225 QREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREM 266
QR V T +G+ALA+ G PF+E SAK NV E F E+ RE+
Sbjct: 119 QRVVSTEEGEALAKELGLPFMETSAKTNENVEEAFEELAREI 160
>gnl|CDD|133338 cd04138, H_N_K_Ras_like, Ras GTPase family containing H-Ras,N-Ras
and K-Ras4A/4B. H-Ras/N-Ras/K-Ras subfamily. H-Ras,
N-Ras, and K-Ras4A/4B are the prototypical members of
the Ras family. These isoforms generate distinct signal
outputs despite interacting with a common set of
activators and effectors, and are strongly associated
with oncogenic progression in tumor initiation. Mutated
versions of Ras that are insensitive to GAP stimulation
(and are therefore constitutively active) are found in a
significant fraction of human cancers. Many Ras guanine
nucleotide exchange factors (GEFs) have been identified.
They are sequestered in the cytosol until activation by
growth factors triggers recruitment to the plasma
membrane or Golgi, where the GEF colocalizes with Ras.
Active (GTP-bound) Ras interacts with several effector
proteins that stimulate a variety of diverse cytoplasmic
signaling activities. Some are known to positively
mediate the oncogenic properties of Ras, including Raf,
phosphatidylinositol 3-kinase (PI3K), RalGEFs, and
Tiam1. Others are proposed to play negative regulatory
roles in oncogenesis, including RASSF and NORE/MST1.
Most Ras proteins contain a lipid modification site at
the C-terminus, with a typical sequence motif CaaX,
where a = an aliphatic amino acid and X = any amino
acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 162
Score = 210 bits (537), Expect = 5e-69
Identities = 83/163 (50%), Positives = 122/163 (74%), Gaps = 2/163 (1%)
Query: 104 EFKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTE 163
E+K+VV+G+GGVGKSALT+Q + F+++YDPTIED YRK++ +D C+L+ILDTAG E
Sbjct: 1 EYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQE 60
Query: 164 QFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLAS 223
++++MRD Y++ G+GF+ V+++ + +F+DI +E I RVK S+ VP++LV NK DLA+
Sbjct: 61 EYSAMRDQYMRTGEGFLCVFAINSRKSFEDIHTYREQIKRVKDSDDVPMVLVGNKCDLAA 120
Query: 224 HQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREM 266
R V T GQ LA+S+G P+IE SAK + V E F +VRE+
Sbjct: 121 --RTVSTRQGQDLAKSYGIPYIETSAKTRQGVEEAFYTLVREI 161
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 204 bits (521), Expect = 4e-66
Identities = 88/165 (53%), Positives = 127/165 (76%), Gaps = 1/165 (0%)
Query: 102 MREFKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAG 161
E+K+VV+G GGVGKSALT+QF+ F+++YDPTIED YRK+ +D+ C+L+ILDTAG
Sbjct: 3 STEYKLVVVGGGGVGKSALTIQFIQNHFIDEYDPTIEDSYRKQCVIDEETCLLDILDTAG 62
Query: 162 TEQFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDL 221
E++++MRD Y++ GQGF+ VYS+T+ +F++I +E I RVK +RVP++LV NK DL
Sbjct: 63 QEEYSAMRDQYMRTGQGFLCVYSITSRSSFEEIASFREQILRVKDKDRVPMILVGNKCDL 122
Query: 222 ASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREM 266
+R+V T +GQ LA+S+G PF+E SAK + NV+E F E+VRE+
Sbjct: 123 -DSERQVSTGEGQELAKSFGIPFLETSAKQRVNVDEAFYELVREI 166
>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 = 201 bits (512), Expect = 4e-65
Identities = 76/160 (47%), Positives = 115/160 (71%), Gaps = 1/160 (0%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTEQ 164
+K+VV+G GGVGKSALT+QF+ F+ YDPTIED Y K+ E+D L+ILDTAG E+
Sbjct: 3 YKLVVVGGGGVGKSALTIQFIQSYFVTDYDPTIEDSYTKQCEIDGQWARLDILDTAGQEE 62
Query: 165 FASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLASH 224
F++MR+ Y++ G+GF++V+S+T+ +F+++ + I RVK + P++LV NK DL H
Sbjct: 63 FSAMREQYMRTGEGFLLVFSVTDRGSFEEVDKFHTQILRVKDRDEFPMILVGNKADL-EH 121
Query: 225 QREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVR 264
QR+V +GQ LA+ P+IE SAK++ NV++ F ++VR
Sbjct: 122 QRQVSREEGQELARQLKIPYIETSAKDRVNVDKAFHDLVR 161
>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 = 197 bits (503), Expect = 2e-63
Identities = 84/163 (51%), Positives = 117/163 (71%), Gaps = 3/163 (1%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTEQF 165
K+VVLG GGVGK+ALT+Q F+E YDPTIED YRK++ VD PC+LE+LDTAG E++
Sbjct: 1 KLVVLGDGGVGKTALTIQLCLNHFVETYDPTIEDSYRKQVVVDGQPCMLEVLDTAGQEEY 60
Query: 166 ASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVK--GSERVPILLVANKLDLAS 223
++RD +I+ G+GF++VYS+T+ TF+ +++ +E I RVK + VPI++V NK D
Sbjct: 61 TALRDQWIREGEGFILVYSITSRSTFERVERFREQIQRVKDESAADVPIMIVGNKCDK-V 119
Query: 224 HQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREM 266
++REV T +G ALA+ GC FIEASAK NV F +VR +
Sbjct: 120 YEREVSTEEGAALARRLGCEFIEASAKTNVNVERAFYTLVRAL 162
>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 = 194 bits (495), Expect = 1e-62
Identities = 80/164 (48%), Positives = 123/164 (75%), Gaps = 1/164 (0%)
Query: 103 REFKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGT 162
RE+K+V+LG+GGVGKSA+T+QF+S F + +DPTIED Y+ + +D P +L+ILDTAG
Sbjct: 1 REYKIVMLGAGGVGKSAVTMQFISHSFPDYHDPTIEDAYKTQARIDNEPALLDILDTAGQ 60
Query: 163 EQFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLA 222
+F +MRD Y++ G+GF++ YS+T+ H+FQ+ + KELITRV+ +E +P++LV NK+DL
Sbjct: 61 AEFTAMRDQYMRCGEGFIICYSVTDRHSFQEASEFKELITRVRLTEDIPLVLVGNKVDLE 120
Query: 223 SHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREM 266
QR+V T +G+ LA+ + CPF E SA + +++ F +VRE+
Sbjct: 121 Q-QRQVTTEEGRNLAREFNCPFFETSAALRFYIDDAFHGLVREI 163
>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 = 189 bits (481), Expect = 2e-60
Identities = 74/162 (45%), Positives = 114/162 (70%), Gaps = 1/162 (0%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTEQ 164
KV+++GSGGVGKSALT+QF+ F+E Y+PT D YRK++ +D L ILDTAG E
Sbjct: 1 HKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEVQLNILDTAGQED 60
Query: 165 FASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLASH 224
+A++RD Y ++G+GF++V+S+T+ +F + + +E I RVK + VP+LLV NK DL
Sbjct: 61 YAAIRDNYFRSGEGFLLVFSITDMESFTALAEFREQILRVKEDDNVPLLLVGNKCDL-ED 119
Query: 225 QREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREM 266
+R+V + LA+ WG ++E SAK + NV+++F ++VRE+
Sbjct: 120 KRQVSVEEAANLAEQWGVNYVETSAKTRANVDKVFFDLVREI 161
>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 = 168 bits (429), Expect = 1e-52
Identities = 65/162 (40%), Positives = 94/162 (58%), Gaps = 5/162 (3%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTI-EDFYRKEIEVDKAPCVLEILDTAGTE 163
FK+V++G GVGK++L ++FV F E Y TI DF K IEVD L+I DTAG E
Sbjct: 1 FKIVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGVDFKSKTIEVDGKKVKLQIWDTAGQE 60
Query: 164 QFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQ-MKELITRVKGSERVPILLVANKLDLA 222
+F S+ Y + G ++VY +TN +F+++ + + EL + +PI+LV NK DL
Sbjct: 61 RFRSITSSYYRGAHGAILVYDVTNRESFENLDKWLNEL--KEYAPPNIPIILVGNKSDLE 118
Query: 223 SHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVR 264
+R+V T + Q A+ G F E SAK NV+E F + R
Sbjct: 119 D-ERQVSTEEAQQFAKENGLLFFETSAKTGENVDEAFESLAR 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 = 165 bits (420), Expect = 4e-51
Identities = 72/177 (40%), Positives = 105/177 (59%), Gaps = 4/177 (2%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTEQF 165
K+ VLGS VGKS+LTVQFV G F+E Y PTIE+ + K I LEI+DTAG +++
Sbjct: 3 KIAVLGSRSVGKSSLTVQFVEGHFVESYYPTIENTFSKIITYKGQEYHLEIVDTAGQDEY 62
Query: 166 ASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLASHQ 225
+ + Y G+++VYS+T+ +F+ +K + + I + G E VPI+LV NK DL +
Sbjct: 63 SILPQKYSIGIHGYILVYSVTSRKSFEVVKVIYDKILDMLGKESVPIVLVGNKSDL-HME 121
Query: 226 REVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREM---NFNPEKDNASFCW 279
R+V +G+ LA+SWG F+E+SAK NV E F ++ E+ S C
Sbjct: 122 RQVSAEEGKKLAESWGAAFLESSAKENENVEEAFELLIEEIEKVENPLPPGQKSKCS 178
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 164 bits (419), Expect = 4e-51
Identities = 72/164 (43%), Positives = 99/164 (60%), Gaps = 5/164 (3%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIE-DFYRKEIEVDKAPCVLEILDTAGTE 163
FK++++G GVGKS+L +F G F E+Y TI DF K IEVD L+I DTAG E
Sbjct: 1 FKIILIGDSGVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIEVDGKRVKLQIWDTAGQE 60
Query: 164 QFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQ-MKELITRVKGSERVPILLVANKLDLA 222
+F S+ Y + G ++VY +TN +F++++ +KEL R S V I+LV NK DL
Sbjct: 61 RFRSITSSYYRGAVGALLVYDITNRESFENLENWLKEL--REYASPNVVIMLVGNKSDLE 118
Query: 223 SHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREM 266
QR+V + +A A+ G PF E SAK TNV E F E+ RE+
Sbjct: 119 -EQRQVSREEAEAFAEEHGLPFFETSAKTNTNVEEAFEELAREI 161
>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 = 165 bits (418), Expect = 5e-51
Identities = 77/162 (47%), Positives = 112/162 (69%), Gaps = 3/162 (1%)
Query: 104 EFKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTE 163
+++VVV G+GGVGKS+L ++FV G F E Y PTIED YR+ I K+ C L+I DT G+
Sbjct: 1 DYRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCSKSICTLQITDTTGSH 60
Query: 164 QFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGS--ERVPILLVANKLDL 221
QF +M+ L I G F++VYS+T+ + +++K + ELI +KG+ E++PI+LV NK D
Sbjct: 61 QFPAMQRLSISKGHAFILVYSITSKQSLEELKPIYELICEIKGNNLEKIPIMLVGNKCD- 119
Query: 222 ASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIV 263
S REV + +G ALA++W C F+E SAK NV E+F E++
Sbjct: 120 ESPSREVSSSEGAALARTWNCAFMETSAKTNHNVQELFQELL 161
>gnl|CDD|206713 cd04146, RERG_RasL11_like, Ras-related and Estrogen-Regulated
Growth inhibitor (RERG) and Ras-like 11 (RasL11)-like
families. RERG (Ras-related and Estrogen- Regulated
Growth inhibitor) and Ras-like 11 are members of a novel
subfamily of Ras that were identified based on their
behavior in breast and prostate tumors, respectively.
RERG expression was decreased or lost in a significant
fraction of primary human breast tumors that lack
estrogen receptor and are correlated with poor clinical
prognosis. Elevated RERG expression correlated with
favorable patient outcome in a breast tumor subtype that
is positive for estrogen receptor expression. In
contrast to most Ras proteins, RERG overexpression
inhibited the growth of breast tumor cells in vitro and
in vivo. RasL11 was found to be ubiquitously expressed
in human tissue, but down-regulated in prostate tumors.
Both RERG and RasL11 lack the C-terminal CaaX
prenylation motif, where a = an aliphatic amino acid and
X = any amino acid, and are localized primarily in the
cytoplasm. Both are believed to have tumor suppressor
activity.
Length = 166
Score = 150 bits (381), Expect = 2e-45
Identities = 67/164 (40%), Positives = 99/164 (60%), Gaps = 5/164 (3%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTEQF 165
K+ VLG+ GVGKSALTV+F++ F+ +Y+P +E Y +++ +D LEI DT G +Q
Sbjct: 1 KIAVLGASGVGKSALTVRFLTKRFIGEYEPNLESLYSRQVTIDGEQVSLEIQDTPGQQQN 60
Query: 166 ASMRDL--YIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVK-GSERVPILLVANKLDLA 222
L ++ GFV+VYS+T+ +F + Q+ +LI +K +P++LV NK DL
Sbjct: 61 EDPESLERSLRWADGFVLVYSITDRSSFDVVSQLLQLIREIKKRDGEIPVILVGNKADLL 120
Query: 223 SHQREVPTLDGQALAQSWGCPFIEASA-KNKTNVNEMFAEIVRE 265
H R+V T +GQ LA GC F E SA +N V +F E+ RE
Sbjct: 121 -HSRQVSTEEGQKLALELGCLFFEVSAAENYLEVQNVFHELCRE 163
>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 = 144 bits (364), Expect = 2e-42
Identities = 62/163 (38%), Positives = 105/163 (64%), Gaps = 2/163 (1%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTEQF 165
++V +G+ GVGK+AL +F+ F K+ T+E+ + KE EV ++ILDT+G+ F
Sbjct: 1 RLVFMGAAGVGKTALIQRFLYDTFEPKHRRTVEELHSKEYEVAGVKVTIDILDTSGSYSF 60
Query: 166 ASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLASHQ 225
+MR L I+NG F +VYS+ + +F+++K+++E I VK + VPI++V NK+D + +
Sbjct: 61 PAMRKLSIQNGDAFALVYSVDDPESFEEVKRLREEILEVKEDKFVPIVVVGNKIDSLA-E 119
Query: 226 REVPTLDGQALAQ-SWGCPFIEASAKNKTNVNEMFAEIVREMN 267
R+V D + + W F+EASAK+ NV E+F E++++ N
Sbjct: 120 RQVEAADALSTVELDWNNGFVEASAKDNENVTEVFKELLQQAN 162
>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 = 141 bits (359), Expect = 4e-42
Identities = 62/165 (37%), Positives = 93/165 (56%), Gaps = 5/165 (3%)
Query: 104 EFKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTI-EDFYRKEIEVDKAPCVLEILDTAGT 162
+FK+V+LG VGKS++ ++FV F E + TI F + + +D EI DTAG
Sbjct: 1 QFKLVLLGDSSVGKSSIVLRFVKNEFSENQESTIGAAFLTQTVNLDDTTVKFEIWDTAGQ 60
Query: 163 EQFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQ-MKELITRVKGSERVPILLVANKLDL 221
E++ S+ +Y + +VVY +T+ +F+ K +KEL + G + I L NK DL
Sbjct: 61 ERYRSLAPMYYRGAAAAIVVYDITSEESFEKAKSWVKEL--QEHGPPNIVIALAGNKADL 118
Query: 222 ASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREM 266
S +R+V T + Q A G F+E SAK NVNE+F EI R++
Sbjct: 119 ES-KRQVSTEEAQEYADENGLLFMETSAKTGENVNELFTEIARKL 162
>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 = 130 bits (328), Expect = 1e-37
Identities = 59/162 (36%), Positives = 86/162 (53%), Gaps = 5/162 (3%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIE-DFYRKEIEVDKAPCVLEILDTAGTE 163
K++++G GVGKS+L ++F F E TI DF K + VD L I DTAG E
Sbjct: 1 LKILLIGDSGVGKSSLLLRFTDDTFDEDLSSTIGVDFKVKTVTVDGKKVKLAIWDTAGQE 60
Query: 164 QFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQ-MKELITRVKGSERVPILLVANKLDLA 222
+F ++ Y + QG ++VY +T TF ++ + EL T + V +LV NK+D
Sbjct: 61 RFRTLTSSYYRGAQGVILVYDVTRRDTFDNLDTWLNELDTYSTNPDAV-KMLVGNKIDKE 119
Query: 223 SHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVR 264
+ REV +GQ A+ FIE SAK + V + F E+V
Sbjct: 120 N--REVTREEGQKFARKHNMLFIETSAKTRIGVQQAFEELVE 159
>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 = 129 bits (327), Expect = 1e-36
Identities = 57/167 (34%), Positives = 95/167 (56%), Gaps = 2/167 (1%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFME-KYDPTIEDFYRKEIEVDKAPCVLEILDTAGTE 163
++VV+LG GVGKS+L F +G + + Y+ + +D Y + + VD L + D E
Sbjct: 1 YRVVLLGDSGVGKSSLANIFTAGVYEDSAYEASGDDTYERTVSVDGEEATLVVYDHWEQE 60
Query: 164 QFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLAS 223
+ D ++ G +V+VYS+T+ +F+ +++ + R + +E +PI+LV NK DL
Sbjct: 61 DGMWLEDSCMQVGDAYVIVYSVTDRSSFEKASELRIQLRRARQAEDIPIILVGNKSDLVR 120
Query: 224 HQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREMNFNP 270
REV +G+A A + C FIE SA + NV+E+F IVR++
Sbjct: 121 S-REVSVQEGRACAVVFDCKFIETSAALQHNVDELFEGIVRQVRLRR 166
>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 = 126 bits (319), Expect = 4e-36
Identities = 59/164 (35%), Positives = 94/164 (57%), Gaps = 5/164 (3%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIE-DFYRKEIEVDKAPCVLEILDTAGTE 163
FK++++G GVGKS L ++F F + TI DF + IE+D L+I DTAG E
Sbjct: 4 FKLLLIGDSGVGKSCLLLRFSEDSFNPSFISTIGIDFKIRTIELDGKKIKLQIWDTAGQE 63
Query: 164 QFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQ-MKELITRVKGSERVPILLVANKLDLA 222
+F ++ Y + G ++VY +T+ +F++IK M+ + SE V +LV NK D+
Sbjct: 64 RFRTITTSYYRGAMGIILVYDITDEKSFENIKNWMRNI--DEHASEDVERMLVGNKCDME 121
Query: 223 SHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREM 266
+R V +G+ALA+ +G F+E SAK NV E F + +++
Sbjct: 122 -EKRVVSKEEGEALAREYGIKFLETSAKANINVEEAFLTLAKDI 164
>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 = 125 bits (317), Expect = 8e-36
Identities = 64/163 (39%), Positives = 93/163 (57%), Gaps = 3/163 (1%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIE-DFYRKEIEVDKAPCVLEILDTAGTE 163
FK++++G GVGKS L ++F + E Y TI DF + IE+D L+I DTAG E
Sbjct: 3 FKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTVKLQIWDTAGQE 62
Query: 164 QFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLAS 223
+F ++ Y + G ++VY +T+ +F ++KQ + I R SE V LLV NK DL
Sbjct: 63 RFRTITSSYYRGAHGIIIVYDVTDQESFNNVKQWLQEIDRY-ASENVNKLLVGNKCDLTD 121
Query: 224 HQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREM 266
++ V + + A G PF+E SAKN TNV E F + RE+
Sbjct: 122 -KKVVDYTEAKEFADELGIPFLETSAKNATNVEEAFMTMAREI 163
>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 = 124 bits (314), Expect = 2e-35
Identities = 58/159 (36%), Positives = 91/159 (57%), Gaps = 3/159 (1%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTI-EDFYRKEIEVDKAPCVLEILDTAGTE 163
K+V LG VGK+++ +F+ F +Y TI DF K + VD L++ DTAG E
Sbjct: 1 HKLVFLGDQSVGKTSIITRFMYDTFDNQYQATIGIDFLSKTMYVDDKTVRLQLWDTAGQE 60
Query: 164 QFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLAS 223
+F S+ YI++ VVVY +TN +F + + + + +G++ V I+LV NK DL+
Sbjct: 61 RFRSLIPSYIRDSSVAVVVYDITNRQSFDNTDKWIDDVRDERGND-VIIVLVGNKTDLSD 119
Query: 224 HQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEI 262
+R+V T +G+ A+ FIE SAK NV ++F +I
Sbjct: 120 -KRQVSTEEGEKKAKENNAMFIETSAKAGHNVKQLFKKI 157
>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 = 122 bits (308), Expect = 1e-34
Identities = 52/163 (31%), Positives = 96/163 (58%), Gaps = 3/163 (1%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIED-FYRKEIEVDKAPCVLEILDTAGTE 163
FKVV+LG G VGK++L +++V F EK++ T + F++K + + L I DTAG E
Sbjct: 1 FKVVLLGEGRVGKTSLVLRYVENKFNEKHESTTQASFFQKTVNIGGKRIDLAIWDTAGQE 60
Query: 164 QFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLAS 223
++ ++ +Y ++ G ++VY +T+ +FQ +K+ + + +++G + +++V NK+DL
Sbjct: 61 RYHALGPIYYRDADGAILVYDITDADSFQKVKKWIKELKQMRG-NNISLVIVGNKIDLER 119
Query: 224 HQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREM 266
QR V + + A+S G E SAK + E+F + + M
Sbjct: 120 -QRVVSKSEAEEYAKSVGAKHFETSAKTGKGIEELFLSLAKRM 161
>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 = 120 bits (303), Expect = 7e-33
Identities = 59/164 (35%), Positives = 96/164 (58%), Gaps = 10/164 (6%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTEQ 164
+++VVLG+ VGK+A+ +F+ G F E+Y PTIEDF+RK + L+ILDT+G
Sbjct: 1 YRMVVLGASKVGKTAIVSRFLGGRFEEQYTPTIEDFHRKLYSIRGEVYQLDILDTSGNHP 60
Query: 165 FASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELI--------TRVKGSERVPILLVA 216
F +MR L I G F++V+SL N +F+++ +++E I + K + ++P+++
Sbjct: 61 FPAMRRLSILTGDVFILVFSLDNRESFEEVCRLREQILETKSCLKNKTKENVKIPMVICG 120
Query: 217 NKLDLASHQREVPTLD-GQALAQSWGCPFIEASAKNKTNVNEMF 259
NK D REV + Q + C + E SAK +N++EMF
Sbjct: 121 NKADRDFP-REVQRDEVEQLVGGDENCAYFEVSAKKNSNLDEMF 163
>gnl|CDD|206660 cd01868, Rab11_like, Rab GTPase family 11 (Rab11)-like includes
Rab11a, Rab11b, and Rab25. Rab11a, Rab11b, and Rab25
are closely related, evolutionary conserved Rab proteins
that are differentially expressed. Rab11a is
ubiquitously synthesized, Rab11b is enriched in brain
and heart and Rab25 is only found in epithelia. Rab11/25
proteins seem to regulate recycling pathways from
endosomes to the plasma membrane and to the trans-Golgi
network. Furthermore, Rab11a is thought to function in
the histamine-induced fusion of tubulovesicles
containing H+, K+ ATPase with the plasma membrane in
gastric parietal cells and in insulin-stimulated
insertion of GLUT4 in the plasma membrane of
cardiomyocytes. Overexpression of Rab25 has recently
been observed in ovarian cancer and breast cancer, and
has been correlated with worsened outcomes in both
diseases. In addition, Rab25 overexpression has also
been observed in prostate cancer, transitional cell
carcinoma of the bladder, and invasive breast tumor
cells. GTPase activating proteins (GAPs) interact with
GTP-bound Rab and accelerate the hydrolysis of GTP to
GDP. Guanine nucleotide exchange factors (GEFs) interact
with GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 165
Score = 115 bits (291), Expect = 6e-32
Identities = 62/167 (37%), Positives = 93/167 (55%), Gaps = 13/167 (7%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIE-DFYRKEIEVD----KAPCVLEILDT 159
FK+V++G GVGKS L +F F TI +F + I++D KA +I DT
Sbjct: 4 FKIVLIGDSGVGKSNLLSRFTRNEFNLDSKSTIGVEFATRTIQIDGKTIKA----QIWDT 59
Query: 160 AGTEQFASMRDLYIKNGQGFVVVYSLTNHHTFQDI-KQMKELITRVKGSERVPILLVANK 218
AG E++ ++ Y + G ++VY +T TF+++ + +KEL R + I+LV NK
Sbjct: 60 AGQERYRAITSAYYRGAVGALLVYDITKKSTFENVERWLKEL--RDHADSNIVIMLVGNK 117
Query: 219 LDLASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVRE 265
DL H R VPT + +A A+ G FIE SA + TNV E F +++ E
Sbjct: 118 SDLR-HLRAVPTEEAKAFAEKNGLSFIETSALDGTNVEEAFKQLLTE 163
>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 = 116 bits (291), Expect = 2e-31
Identities = 57/165 (34%), Positives = 97/165 (58%), Gaps = 5/165 (3%)
Query: 104 EFKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIE-DFYRKEIEVDKAPCV-LEILDTAG 161
+F+++V+G VGKS+L +F G F E DPT+ DF+ + IE++ + L++ DTAG
Sbjct: 2 QFRLIVIGDSTVGKSSLLKRFTEGRFAEVSDPTVGVDFFSRLIEIEPGVRIKLQLWDTAG 61
Query: 162 TEQFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQ-MKELITRVKGSERVPILLVANKLD 220
E+F S+ Y +N G ++V+ +TN +F+ + ++E + ++ V +LV +K D
Sbjct: 62 QERFRSITRSYYRNSVGVLLVFDITNRESFEHVHDWLEEARSHIQPHRPV-FILVGHKCD 120
Query: 221 LASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVRE 265
L S QR+V + + LA+ G +IE SA+ NV E F + +E
Sbjct: 121 LES-QRQVTREEAEKLAKDLGMKYIETSARTGDNVEEAFELLTQE 164
>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 = 113 bits (284), Expect = 7e-31
Identities = 50/172 (29%), Positives = 86/172 (50%), Gaps = 16/172 (9%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTEQF 165
K+VV+G G VGK+ L + + + F +Y PT+ D Y + VD L + DTAG E++
Sbjct: 2 KIVVVGDGAVGKTCLLISYTTNKFPTEYVPTVFDNYSANVTVDGKQVNLGLWDTAGQEEY 61
Query: 166 ASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQM--KELITRVKGSERVPILLVANKLDL-- 221
+R L F++ +S+ + +F+++K E+ VPI+LV K+DL
Sbjct: 62 DRLRPLSYPQTDVFLLCFSVDSPSSFENVKTKWYPEIK---HYCPNVPIILVGTKIDLRD 118
Query: 222 --------ASHQREVPTLDGQALAQSWGC-PFIEASAKNKTNVNEMFAEIVR 264
Q+ + +G+ LA+ G ++E SA + + E+F E +R
Sbjct: 119 DGNTLKKLEKKQKPITPEEGEKLAKEIGAVKYMECSALTQEGLKEVFDEAIR 170
>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 = 109 bits (274), Expect = 1e-29
Identities = 61/166 (36%), Positives = 95/166 (57%), Gaps = 7/166 (4%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIE-DFYRKEIEVDKAPCVLEILDTAGTE 163
KV++LG GGVGKS+L ++V+ F + TI +F K++EVD L+I DTAG E
Sbjct: 6 LKVILLGDGGVGKSSLMNRYVTNKFDTQLFHTIGVEFLNKDLEVDGHFVTLQIWDTAGQE 65
Query: 164 QFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMK-ELI--TRVKGSERVPILLVANKLD 220
+F S+R + + ++ +S+ + +FQ++ K E I VK E P +++ NK+D
Sbjct: 66 RFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVILGNKID 125
Query: 221 LASHQREVPTLDGQALAQSWG-CPFIEASAKNKTNVNEMFAEIVRE 265
+ +R+V T + QA + G P+ E SAK+ TNV F E VR
Sbjct: 126 IP--ERQVSTEEAQAWCRDNGDYPYFETSAKDATNVAAAFEEAVRR 169
>gnl|CDD|206655 cd01862, Rab7, Rab GTPase family 7 (Rab7). Rab7 subfamily. Rab7 is
a small Rab GTPase that regulates vesicular traffic from
early to late endosomal stages of the endocytic pathway.
The yeast Ypt7 and mammalian Rab7 are both involved in
transport to the vacuole/lysosome, whereas Ypt7 is also
required for homotypic vacuole fusion. Mammalian Rab7 is
an essential participant in the autophagic pathway for
sequestration and targeting of cytoplasmic components to
the lytic compartment. Mammalian Rab7 is also proposed
to function as a tumor suppressor. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 172
Score = 108 bits (273), Expect = 3e-29
Identities = 62/172 (36%), Positives = 90/172 (52%), Gaps = 20/172 (11%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTI-EDFYRKEIEVDKAPCVLEILDTAGTE 163
KV++LG GVGK++L Q+V+ F +Y TI DF KE+ VD L+I DTAG E
Sbjct: 1 LKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVTVDDRLVTLQIWDTAGQE 60
Query: 164 QFASMRDLYIKNGQGF-------VVVYSLTNHHTFQDIKQMKE--LI-TRVKGSERVPIL 213
+F S+ G F V+VY +TN +F+ + ++ LI + E P +
Sbjct: 61 RFQSL-------GVAFYRGADCCVLVYDVTNPKSFESLDSWRDEFLIQASPRDPENFPFV 113
Query: 214 LVANKLDLASHQREVPTLDGQALAQSWGC-PFIEASAKNKTNVNEMFAEIVR 264
++ NK+DL R+V T Q +S G P+ E SAK NV++ F I R
Sbjct: 114 VLGNKIDLEEK-RQVSTKKAQQWCKSKGNIPYFETSAKEAINVDQAFETIAR 164
>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 = 106 bits (267), Expect = 4e-28
Identities = 56/168 (33%), Positives = 86/168 (51%), Gaps = 6/168 (3%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIE-DFYRKEIEVDKAPCV-LEILDTAGT 162
FKV+V+G GVGK+++ ++V G F + Y TI DF K IE D V L++ D AG
Sbjct: 1 FKVLVIGDLGVGKTSIIKRYVHGVFSQHYKATIGVDFALKVIEWDPNTVVRLQLWDIAGQ 60
Query: 163 EQFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKE-LITRVKGS--ERVPILLVANKL 219
E+F M +Y K G ++V+ +T TF+ + + K L ++V E +P LL+ANK
Sbjct: 61 ERFGGMTRVYYKGAVGAIIVFDVTRPSTFEAVLKWKADLDSKVTLPNGEPIPALLLANKC 120
Query: 220 DLASHQREVPTLDGQALAQSWGCP-FIEASAKNKTNVNEMFAEIVREM 266
DL + + G + E SAK N+ E +V+ +
Sbjct: 121 DLKKERLAKDPEQMDQFCKENGFIGWFETSAKENINIEEAMRFLVKNI 168
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 106 bits (267), Expect = 7e-28
Identities = 68/204 (33%), Positives = 95/204 (46%), Gaps = 17/204 (8%)
Query: 100 FTMREFKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIE-DFYRKEIEVDKAPCVLEILD 158
M+EFK+VVLG GGVGK+ L + V F E Y PTI K IE + L++ D
Sbjct: 1 LFMKEFKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWD 60
Query: 159 TAGTEQFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANK 218
TAG E++ S+R Y + G ++VY T + ++ + R + VPILLV NK
Sbjct: 61 TAGQEEYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVGNK 120
Query: 219 LDLASHQ-----------REVPTLDGQALAQS---WGCPFIEASAKNKT--NVNEMFAEI 262
+DL Q REV L A +E SAK+ T NVNE+F E+
Sbjct: 121 IDLFDEQSSSEEILNQLNREVVLLVLAPKAVLPEVANPALLETSAKSLTGPNVNELFKEL 180
Query: 263 VREMNFNPEKDNASFCWCSSCSIL 286
+R++ EK +
Sbjct: 181 LRKLLEEIEKLVLKNELRQLDRLN 204
>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 = 104 bits (262), Expect = 7e-28
Identities = 53/157 (33%), Positives = 89/157 (56%), Gaps = 6/157 (3%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTI-EDFYRKEIEVDKAPCVLEIL--DTAGT 162
KV+V+G+G VGKS++ +FV G F + Y TI DF K+I + ++ + ++ DTAG
Sbjct: 2 KVIVVGNGNVGKSSMIQRFVKGIFTKDYKKTIGVDFLEKQIFLRQSDEDVRLMLWDTAGQ 61
Query: 163 EQFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLA 222
E+F ++ Y + Q ++V+S T+ +F+ I+ KE + G +P++LV K+DL
Sbjct: 62 EEFDAITKAYYRGAQACILVFSTTDRESFEAIESWKEKVEAECGD--IPMVLVQTKIDLL 119
Query: 223 SHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMF 259
Q + + +ALA+ P S K+ NV E+F
Sbjct: 120 -DQAVITNEEAEALAKRLQLPLFRTSVKDDFNVTELF 155
>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 = 104 bits (261), Expect = 2e-27
Identities = 57/164 (34%), Positives = 90/164 (54%), Gaps = 4/164 (2%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFME-KYDPTIE-DFYRKEIEVDKAPCVLEILDTAGT 162
FKV+++G GVGK+ L V+F G F+ + T+ F K + VD L+I DTAG
Sbjct: 1 FKVMLVGDSGVGKTCLLVRFKDGAFLAGSFIATVGIQFTNKVVTVDGVKVKLQIWDTAGQ 60
Query: 163 EQFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLA 222
E+F S+ Y ++ +++Y +TN +F +I+ I V I+L+ NK D++
Sbjct: 61 ERFRSVTHAYYRDAHALLLLYDVTNKSSFDNIRAWLTEILEY-AQSDVVIMLLGNKADMS 119
Query: 223 SHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREM 266
+R V DG+ LA+ +G PF+E SAK NV F + +E+
Sbjct: 120 G-ERVVKREDGERLAKEYGVPFMETSAKTGLNVELAFTAVAKEL 162
>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 = 103 bits (259), Expect = 2e-27
Identities = 55/164 (33%), Positives = 88/164 (53%), Gaps = 4/164 (2%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIE-DFYRKEIEVDKAPCVLEILDTAGTE 163
FK++++G VGK+ + +F SG F E+ TI DF K +E+ L+I DTAG E
Sbjct: 4 FKIILIGDSNVGKTCVVQRFKSGTFSERQGNTIGVDFTMKTLEIQGKRVKLQIWDTAGQE 63
Query: 164 QFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLAS 223
+F ++ Y ++ G ++ Y +T +F+ + E + + S V +LL+ NK DL
Sbjct: 64 RFRTITQSYYRSANGAIIAYDITRRSSFESVPHWIEEVEKYGASN-VVLLLIGNKCDLEE 122
Query: 224 HQREVPTLDGQALAQSWGCPF-IEASAKNKTNVNEMFAEIVREM 266
QREV + LA+ +G +E SAK +NV E F + E+
Sbjct: 123 -QREVLFEEACTLAEHYGILAVLETSAKESSNVEEAFLLMATEL 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 = 103 bits (259), Expect = 3e-27
Identities = 59/163 (36%), Positives = 86/163 (52%), Gaps = 3/163 (1%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIE-DFYRKEIEVDKAPCVLEILDTAGTE 163
FK +++G GVGKS L +QF F +D TI +F + I +D L+I DTAG E
Sbjct: 5 FKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQE 64
Query: 164 QFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLAS 223
F S+ Y + G ++VY +T TF + E R + + I+L+ NK DL
Sbjct: 65 SFRSITRSYYRGAAGALLVYDITRRETFNHLTSWLE-DARQHSNSNMTIMLIGNKCDL-E 122
Query: 224 HQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREM 266
+REV +G+A A+ G F+E SAK +NV E F +E+
Sbjct: 123 SRREVSYEEGEAFAREHGLIFMETSAKTASNVEEAFINTAKEI 165
>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 = 103 bits (259), Expect = 3e-27
Identities = 46/165 (27%), Positives = 76/165 (46%), Gaps = 7/165 (4%)
Query: 104 EFKVVVLGSGGVGKSALTVQFV-SGCFMEKYDPTIEDFYRKE-IEVDKAPCVLEILDTAG 161
E K+V++G VGKS L + + + + +Y P Y IE D +LDTAG
Sbjct: 1 EIKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAG 60
Query: 162 TEQFASMRDLYIKNGQGFVVVYSLTNHH-TFQDIKQ-MKELITRVKGSERVPILLVANKL 219
E + ++R LY + + + V+ + ++I + + I S VPI+LV NK+
Sbjct: 61 QEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAESG-VPIILVGNKI 119
Query: 220 DLASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVR 264
DL ++ T A+ G P I SA+ N++ F +
Sbjct: 120 DLR--DAKLKTHVAFLFAKLNGEPIIPLSAETGKNIDSAFKIVEA 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 = 103 bits (258), Expect = 4e-27
Identities = 57/171 (33%), Positives = 92/171 (53%), Gaps = 15/171 (8%)
Query: 107 VVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTEQFA 166
+VV+G G VGK+ L + + + F E Y PT+ + Y ++EVD P L + DTAG E +
Sbjct: 1 LVVVGDGAVGKTCLLIVYTTNAFPEDYVPTVFENYSADVEVDGKPVELGLWDTAGQEDYD 60
Query: 167 SMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKG-SERVPILLVANKLDL---- 221
+R L + F++ +S+ + +F+++K ++ VK VPI+LV KLDL
Sbjct: 61 RLRPLSYPDTDVFLICFSVDSPASFENVK--EKWYPEVKHFCPNVPIILVGTKLDLRNDK 118
Query: 222 -----ASHQREVP--TLDGQALAQSWG-CPFIEASAKNKTNVNEMFAEIVR 264
S +++ P GQALA+ G ++E SA + V E+F E +R
Sbjct: 119 STLEELSKKKQEPVTYEQGQALAKRIGAVKYLECSALTQEGVREVFEEAIR 169
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 103 bits (258), Expect = 1e-26
Identities = 61/158 (38%), Positives = 86/158 (54%), Gaps = 3/158 (1%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIE-DFYRKEIEVDKAPCVLEILDTAGTE 163
FK +++G GVGKS L +QF F +D TI +F + I +D P L+I DTAG E
Sbjct: 7 FKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDNKPIKLQIWDTAGQE 66
Query: 164 QFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLAS 223
F S+ Y + G ++VY +T TF + E R + + I+L+ NK DLA
Sbjct: 67 SFRSITRSYYRGAAGALLVYDITRRETFNHLASWLE-DARQHANANMTIMLIGNKCDLA- 124
Query: 224 HQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAE 261
H+R V T +G+ A+ G F+EASAK NV E F +
Sbjct: 125 HRRAVSTEEGEQFAKEHGLIFMEASAKTAQNVEEAFIK 162
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 102 bits (255), Expect = 2e-26
Identities = 63/161 (39%), Positives = 94/161 (58%), Gaps = 6/161 (3%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIE-DFYRKEIEVDKAPCVLEILDTAGTE 163
FK++++G GVGKS+L V F+S +E PTI DF K++ V L I DTAG E
Sbjct: 15 FKILLIGDSGVGKSSLLVSFISSS-VEDLAPTIGVDFKIKQLTVGGKRLKLTIWDTAGQE 73
Query: 164 QFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQM--KELITRVKGSERVPILLVANKLDL 221
+F ++ Y +N QG ++VY +T TF ++ + KE+ + V +LV NK+D
Sbjct: 74 RFRTLTSSYYRNAQGIILVYDVTRRETFTNLSDVWGKEVELYSTNQDCVK-MLVGNKVDR 132
Query: 222 ASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEI 262
S +R+V +G ALA+ GC F+E SAK + NV + F E+
Sbjct: 133 ES-ERDVSREEGMALAKEHGCLFLECSAKTRENVEQCFEEL 172
>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 = 98.3 bits (245), Expect = 2e-25
Identities = 56/161 (34%), Positives = 80/161 (49%), Gaps = 3/161 (1%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTI-EDFYRKEIEVDKAPCVLEILDTAGTE 163
FK +++GS G GKS L QF+ F + + TI +F + + V L+I DTAG E
Sbjct: 1 FKFLIIGSAGTGKSCLLHQFIENKFKQDSNHTIGVEFGSRVVNVGGKSVKLQIWDTAGQE 60
Query: 164 QFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLAS 223
+F S+ Y + G ++VY +T+ +F + R S + I+LV NK DL
Sbjct: 61 RFRSVTRSYYRGAAGALLVYDITSRESFNALTNWLT-DARTLASPDIVIILVGNKKDLED 119
Query: 224 HQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVR 264
REV L+ AQ G F+E SA NV E F + R
Sbjct: 120 -DREVTFLEASRFAQENGLLFLETSALTGENVEEAFLKCAR 159
>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 = 98.3 bits (245), Expect = 3e-25
Identities = 56/151 (37%), Positives = 80/151 (52%), Gaps = 3/151 (1%)
Query: 103 REFKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIE-DFYRKEIEVDKAPCVLEILDTAG 161
R FK++V+G VGK+ LT +F +G F E+ + TI DF + +E+D +++ DTAG
Sbjct: 1 RIFKIIVIGDSNVGKTCLTYRFCAGRFPERTEATIGVDFRERTVEIDGERIKVQLWDTAG 60
Query: 162 TEQF-ASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLD 220
E+F SM Y +N V VY +TN +F + E + VP +LV NK D
Sbjct: 61 QERFRKSMVQHYYRNVHAVVFVYDVTNMASFHSLPSWIEECEQHSLPNEVPRILVGNKCD 120
Query: 221 LASHQREVPTLDGQALAQSWGCPFIEASAKN 251
L Q +VPT Q A + P E SAK+
Sbjct: 121 L-REQIQVPTDLAQRFADAHSMPLFETSAKD 150
>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 = 96.3 bits (240), Expect = 2e-24
Identities = 51/166 (30%), Positives = 87/166 (52%), Gaps = 13/166 (7%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTEQF 165
K V++G G VGK++L V + + + +Y PT D + + VD P L++ DTAG ++F
Sbjct: 2 KCVLVGDGAVGKTSLIVSYTTNGYPTEYVPTAFDNFSVVVLVDGKPVRLQLCDTAGQDEF 61
Query: 166 ASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDL---- 221
+R L + F++ +S+ N +FQ+I + K + K + + PI+LV + DL
Sbjct: 62 DKLRPLCYPDTDVFLLCFSVVNPSSFQNISE-KWIPEIRKHNPKAPIILVGTQADLRTDV 120
Query: 222 -------ASHQREVPTLDGQALAQSWG-CPFIEASAKNKTNVNEMF 259
++ V +ALA+ G C +IE SA + N+ E+F
Sbjct: 121 NVLIQLARYGEKPVSQSRAKALAEKIGACEYIECSALTQKNLKEVF 166
>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 = 96.6 bits (240), Expect = 3e-24
Identities = 60/163 (36%), Positives = 95/163 (58%), Gaps = 4/163 (2%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIE-DFYRKEIEVDKAPCVLEILDTAGTEQ 164
+V+++GS GVGK++L +F F E T+ DF K +E+ L+I DTAG E+
Sbjct: 2 QVIIIGSRGVGKTSLMERFTDDTFCEACKSTVGVDFKIKTVELRGKKIRLQIWDTAGQER 61
Query: 165 FASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLASH 224
F S+ Y ++ +G ++VY +T TF D+ + ++I + SE +LLV NKLD +
Sbjct: 62 FNSITSAYYRSAKGIILVYDITKKETFDDLPKWMKMIDKY-ASEDAELLLVGNKLDCET- 119
Query: 225 QREVPTLDGQALAQS-WGCPFIEASAKNKTNVNEMFAEIVREM 266
RE+ G+ AQ G F EASAK+ NV+E+F ++V ++
Sbjct: 120 DREITRQQGEKFAQQITGMRFCEASAKDNFNVDEIFLKLVDDI 162
>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 = 95.9 bits (239), Expect = 5e-24
Identities = 51/177 (28%), Positives = 83/177 (46%), Gaps = 16/177 (9%)
Query: 103 REFKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKA-PCVLEILDTAG 161
+ K+VV+G GG GK+ L + + G F E+Y PT+ + Y ++V L + DTAG
Sbjct: 2 LKVKIVVVGDGGCGKTCLLMVYAQGSFPEEYVPTVFENYVTTLQVPNGKIIELALWDTAG 61
Query: 162 TEQFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKG-SERVPILLVANKLD 220
E + +R L + ++ YS+ N + +++ V PI+LV K D
Sbjct: 62 QEDYDRLRPLSYPDVDVILICYSVDNPTSLDNVEDK--WYPEVNHFCPGTPIVLVGLKTD 119
Query: 221 LASHQREVPTL-----------DGQALAQSWGC-PFIEASAKNKTNVNEMFAEIVRE 265
L + V L G+++A+S G +IE SAK NV+E+F +
Sbjct: 120 LRKDKNSVSKLRAQGLEPVTPEQGESVAKSIGAVAYIECSAKLMENVDEVFDAAINV 176
>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 = 94.6 bits (235), Expect = 7e-24
Identities = 50/163 (30%), Positives = 86/163 (52%), Gaps = 3/163 (1%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIE-DFYRKEIEVDKAPCVLEILDTAGTE 163
FK+V++G+ GVGK+ L +F G F TI DF K +E+ L+I DTAG E
Sbjct: 8 FKIVLIGNAGVGKTCLVRRFTQGLFPPGQGATIGVDFMIKTVEIKGEKIKLQIWDTAGQE 67
Query: 164 QFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLAS 223
+F S+ Y ++ ++ Y +T +F+ + + I + + +V +LV NK+DLA
Sbjct: 68 RFRSITQSYYRSANALILTYDITCEESFRCLPEWLREIEQY-ANNKVITILVGNKIDLAE 126
Query: 224 HQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREM 266
+REV + + + ++E SAK NV ++F ++ +
Sbjct: 127 -RREVSQQRAEEFSDAQDMYYLETSAKESDNVEKLFLDLACRL 168
>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 = 95.2 bits (237), Expect = 1e-23
Identities = 54/166 (32%), Positives = 80/166 (48%), Gaps = 5/166 (3%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIE-DFYRKEIEVDKAPCV-LEILDTAGT 162
K+VVLG G GK++L +F F + Y TI DF+ + I + + V L++ D G
Sbjct: 1 IKIVVLGDGASGKTSLIRRFAQEGFGKSYKQTIGLDFFSRRITLPGSLNVTLQVWDIGGQ 60
Query: 163 EQFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKG-SERVP-ILLVANKLD 220
+ M D YI Q +VY +TN +F++++ ++ +V SE P ++LV NK D
Sbjct: 61 QIGGKMLDKYIYGAQAVCLVYDITNSQSFENLEDWLSVVKKVNEESETKPKMVLVGNKTD 120
Query: 221 LASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREM 266
L H R+V AQ I SAK V F I E+
Sbjct: 121 L-EHNRQVTAEKHARFAQENDMESIFVSAKTGDRVFLCFQRIAAEL 165
>gnl|CDD|206648 cd00882, Ras_like_GTPase, Rat sarcoma (Ras)-like superfamily of
small guanosine triphosphatases (GTPases). Ras-like
GTPase superfamily. The Ras-like superfamily of small
GTPases consists of several families with an extremely
high degree of structural and functional similarity. The
Ras superfamily is divided into at least four families
in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families.
This superfamily also includes proteins like the GTP
translation factors, Era-like GTPases, and G-alpha chain
of the heterotrimeric G proteins. Members of the Ras
superfamily regulate a wide variety of cellular
functions: the Ras family regulates gene expression, the
Rho family regulates cytoskeletal reorganization and
gene expression, the Rab and Sar1/Arf families regulate
vesicle trafficking, and the Ran family regulates
nucleocytoplasmic transport and microtubule
organization. The GTP translation factor family
regulates initiation, elongation, termination, and
release in translation, and the Era-like GTPase family
regulates cell division, sporulation, and DNA
replication. Members of the Ras superfamily are
identified by the GTP binding site, which is made up of
five characteristic sequence motifs, and the switch I
and switch II regions.
Length = 161
Score = 92.9 bits (231), Expect = 3e-23
Identities = 52/166 (31%), Positives = 80/166 (48%), Gaps = 14/166 (8%)
Query: 108 VVLGSGGVGKSALTVQFVSGCFME---KYDPTI-EDFYRKEIEVDKAPCVLEILDTAGTE 163
VV+G GGVGKS+L + G E T D Y KE++ K L ++DT G +
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGK--VKLVLVDTPGLD 58
Query: 164 QFASMRD-----LYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANK 218
+F + L ++ ++V T+ + +D K LI R E +PI+LV NK
Sbjct: 59 EFGGLGREELARLLLRGADLILLVVDSTDRESEEDAK---LLILRRLRKEGIPIILVGNK 115
Query: 219 LDLASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVR 264
+DL + L + LA+ G P E SAK V+E+F +++
Sbjct: 116 IDLLEEREVEELLRLEELAKILGVPVFEVSAKTGEGVDELFEKLIE 161
>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 = 93.0 bits (231), Expect = 6e-23
Identities = 56/161 (34%), Positives = 84/161 (52%), Gaps = 4/161 (2%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIE-DFYRKEIEVDKAPCVLEILDTAGTE 163
FK++++G GVGKS+L ++F F Y TI DF + +E++ L+I DTAG E
Sbjct: 7 FKLLIIGDSGVGKSSLLLRFADNTFSGSYITTIGVDFKIRTVEINGERVKLQIWDTAGQE 66
Query: 164 QFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLAS 223
+F ++ Y + G +VVY +TN +F ++K+ + I + + V +LV NK D
Sbjct: 67 RFRTITSTYYRGTHGVIVVYDVTNGESFVNVKRWLQEIE--QNCDDVCKVLVGNKND-DP 123
Query: 224 HQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVR 264
++ V T D A G E SAK NV EMF I
Sbjct: 124 ERKVVETEDAYKFAGQMGISLFETSAKENINVEEMFNCITE 164
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 93.1 bits (231), Expect = 1e-22
Identities = 56/164 (34%), Positives = 91/164 (55%), Gaps = 5/164 (3%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIE-DFYRKEIEVDKAPCVLEILDTAGTE 163
FK+V++G GVGKS + +F F + TI +F + ++V+ +I DTAG E
Sbjct: 13 FKIVLIGDSGVGKSNILSRFTRNEFCLESKSTIGVEFATRTLQVEGKTVKAQIWDTAGQE 72
Query: 164 QFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQ-MKELITRVKGSERVPILLVANKLDLA 222
++ ++ Y + G ++VY +T TF ++++ ++EL R + I++ NK DL
Sbjct: 73 RYRAITSAYYRGAVGALLVYDITKRQTFDNVQRWLREL--RDHADSNIVIMMAGNKSDL- 129
Query: 223 SHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREM 266
+H R V DGQALA+ G F+E SA TNV + F I+ E+
Sbjct: 130 NHLRSVAEEDGQALAEKEGLSFLETSALEATNVEKAFQTILLEI 173
>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 = 91.3 bits (227), Expect = 1e-22
Identities = 52/166 (31%), Positives = 90/166 (54%), Gaps = 6/166 (3%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIE-DFYRKEIEVDKAPCVLEILDTAGTEQ 164
KV+ +G+ GVGKS + ++ G F+ KY PTI D+ K++ V + D +G +
Sbjct: 2 KVISMGNSGVGKSCIIKRYCEGRFVSKYLPTIGIDYGVKKVSVRNKEVRVNFFDLSGHPE 61
Query: 165 FASMRDLYIKNGQGFVVVYSLTNHHTFQDI----KQMKELITRVKGSERVPILLVANKLD 220
+ +R+ + K+ QG ++VY +T+ +F+ + K+MK+ E + +++ ANK+D
Sbjct: 62 YLEVRNEFYKDTQGVLLVYDVTDRQSFEALDSWLKEMKQEGGPHGNMENIVVVVCANKID 121
Query: 221 LASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREM 266
L H R V +G+ A+S G + E SA VNEMF + +
Sbjct: 122 LTKH-RAVSEDEGRLWAESKGFKYFETSACTGEGVNEMFQTLFSSI 166
>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 = 90.0 bits (223), Expect = 3e-22
Identities = 51/163 (31%), Positives = 83/163 (50%), Gaps = 4/163 (2%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIE-DFYRKEIEVDKAPCVLEILDTAGTE 163
F+++++G GVGK+ L +F F + TI DF K IEVD ++I DTAG E
Sbjct: 1 FRLLLIGDSGVGKTCLLCRFTDNEFHSSHISTIGVDFKMKTIEVDGIKVRIQIWDTAGQE 60
Query: 164 QFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLAS 223
++ ++ Y + QG +VY +++ ++Q I + + E V +L+ NK D
Sbjct: 61 RYQTITKQYYRRAQGIFLVYDISSERSYQHIMKWVSDVDEY-APEGVQKILIGNKAD-EE 118
Query: 224 HQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREM 266
+R+V G LA+ +G F E SA N+ E F + E+
Sbjct: 119 QKRQVGDEQGNKLAKEYGMDFFETSACTNKNIKESFTRL-TEL 160
>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 = 90.5 bits (224), Expect = 5e-22
Identities = 60/190 (31%), Positives = 94/190 (49%), Gaps = 18/190 (9%)
Query: 102 MREFKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAG 161
M+ K VV+G G VGK+ L + + + F ++Y PT+ D Y + VD L + DTAG
Sbjct: 1 MQSIKCVVVGDGAVGKTCLLICYTTNAFPKEYIPTVFDNYSAQTAVDGRTVSLNLWDTAG 60
Query: 162 TEQFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQM--KELITRVKGSERVPILLVANKL 219
E++ +R L F++ +S+ + ++++++ E+ VPILLV K
Sbjct: 61 QEEYDRLRTLSYPQTNVFIICFSIASPSSYENVRHKWHPEVCHHCPN---VPILLVGTKK 117
Query: 220 DLAS---------HQREVPTL--DGQALAQSWGC-PFIEASAKNKTNVNEMFAEIVRE-M 266
DL + Q + P G ALA+ ++E SA N+ V E+FAE VR +
Sbjct: 118 DLRNDADTLKKLKEQGQAPITPQQGGALAKQIHAVKYLECSALNQDGVKEVFAEAVRAVL 177
Query: 267 NFNPEKDNAS 276
N P KD S
Sbjct: 178 NPTPIKDTKS 187
>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 = 89.5 bits (222), Expect = 5e-22
Identities = 54/163 (33%), Positives = 81/163 (49%), Gaps = 3/163 (1%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIE-DFYRKEIEVDKAPCVLEILDTAGTE 163
FK +++G GVGKS L QF FM TI +F + IEV+ L+I DTAG E
Sbjct: 3 FKYIIIGDMGVGKSCLLHQFTEKKFMADCPHTIGVEFGTRIIEVNGQKIKLQIWDTAGQE 62
Query: 164 QFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLAS 223
+F ++ Y + G ++VY +T T+ + + V I L+ NK DL +
Sbjct: 63 RFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTV-IFLIGNKADLEA 121
Query: 224 HQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREM 266
QR+V + + A G F+E SAK NV + F E +++
Sbjct: 122 -QRDVTYEEAKQFADENGLLFLECSAKTGENVEDAFLETAKKI 163
>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 = 88.8 bits (220), Expect = 2e-21
Identities = 52/172 (30%), Positives = 88/172 (51%), Gaps = 13/172 (7%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTI-EDFYRKEIEVDKAPCVLEILD----- 158
+V VLG+ GVGK+A+ QF++ F E+Y PT YR + + L ILD
Sbjct: 1 VRVAVLGAPGVGKTAIVRQFLAQEFPEEYIPTEHRRLYRPAVVLSGRVYDLHILDVPNMQ 60
Query: 159 ---TAGTEQFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELI--TRVKGSERVPIL 213
+++ R ++N + F++VY + + +F +K +++ I TR G++ PI+
Sbjct: 61 RYPGTAGQEWMDPRFRGLRNSRAFILVYDICSPDSFHYVKLLRQQILETRPAGNKEPPIV 120
Query: 214 LVANKLDLASHQREVPTLDGQALA-QSWGCPFIEASAKNKTNVNEMFAEIVR 264
+V NK D H R P L +SW C ++E SAK ++ +F E++
Sbjct: 121 VVGNKRDQQRH-RFAPRHVLSVLVRKSWKCGYLECSAKYNWHILLLFKELLI 171
>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 = 87.2 bits (216), Expect = 6e-21
Identities = 46/163 (28%), Positives = 78/163 (47%), Gaps = 12/163 (7%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIE-DFYRKEIEVDKAPCV----------L 154
K++ LG GVGK+ ++ F K+ T+ DF K + + L
Sbjct: 6 KLLALGDSGVGKTTFLYRYTDNKFNPKFITTVGIDFREKRVVYNSQGPDGTSGKAFRVHL 65
Query: 155 EILDTAGTEQFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILL 214
++ DTAG E+F S+ + ++ GF++++ LT+ +F +++ + E I+L
Sbjct: 66 QLWDTAGQERFRSLTTAFFRDAMGFLLMFDLTSEQSFLNVRNWMSQLQAHAYCENPDIVL 125
Query: 215 VANKLDLASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNE 257
+ NK DL QREV + LA +G P+ E SA NV +
Sbjct: 126 IGNKADL-PDQREVSERQARELADKYGIPYFETSAATGQNVEK 167
>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 = 85.3 bits (211), Expect = 2e-20
Identities = 48/162 (29%), Positives = 86/162 (53%), Gaps = 7/162 (4%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIE-DFYRKEIEVDKAPCVLEILDTAGTE 163
FK++++G+ VGK++ ++ F + T+ DF K + + L+I DTAG E
Sbjct: 2 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVYRNDKRIKLQIWDTAGQE 61
Query: 164 QFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVK--GSERVPILLVANKLDL 221
++ ++ Y + GF+++Y +TN +F + ++ T++K + ++LV NK D+
Sbjct: 62 RYRTITTAYYRGAMGFILMYDITNEESFNAV---QDWSTQIKTYSWDNAQVILVGNKCDM 118
Query: 222 ASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIV 263
+R V G+ LA G F EASAK NV ++F +V
Sbjct: 119 ED-ERVVSAERGRQLADQLGFEFFEASAKENINVKQVFERLV 159
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 83.3 bits (206), Expect = 3e-19
Identities = 46/167 (27%), Positives = 87/167 (52%), Gaps = 6/167 (3%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIE-DFYRKEIEVDKAPCVLEILDTAGTE 163
FK+V++G GG GK+ + ++G F +KY+PTI + + + + DTAG E
Sbjct: 14 FKLVIVGDGGTGKTTFVKRHLTGEFEKKYEPTIGVEVHPLDFFTNCGKIRFYCWDTAGQE 73
Query: 164 QFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLAS 223
+F +RD Y +GQ ++++ +T T++++ + RV E +PI+L NK+D+ +
Sbjct: 74 KFGGLRDGYYIHGQCAIIMFDVTARLTYKNVPTWHRDLCRV--CENIPIVLCGNKVDVKN 131
Query: 224 HQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREMNFNP 270
Q + + + + E SAK+ N + F + R++ +P
Sbjct: 132 RQVKAKQV---TFHRKKNLQYYEISAKSNYNFEKPFLYLARKLAGDP 175
>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 = 81.7 bits (202), Expect = 6e-19
Identities = 53/167 (31%), Positives = 84/167 (50%), Gaps = 15/167 (8%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTEQF 165
K+V++G G GK+ L + F F E Y PT+ + Y +IEVD L + DTAG E +
Sbjct: 3 KLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDY 62
Query: 166 ASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKG-SERVPILLVANKLDLAS- 223
+R L + ++ +S+ + + ++I + + VK VPI+LV NK DL +
Sbjct: 63 DRLRPLSYPDTDVILMCFSIDSPDSLENIPE--KWTPEVKHFCPNVPIILVGNKKDLRND 120
Query: 224 ----------HQREVPTLDGQALAQSWGC-PFIEASAKNKTNVNEMF 259
Q V +G+A+A+ G ++E SAK K V E+F
Sbjct: 121 EHTIRELAKMKQEPVKPEEGRAMAEKIGAFGYLECSAKTKEGVREVF 167
>gnl|CDD|206688 cd04101, RabL4, Rab GTPase-like family 4 (Rab-like4). RabL4
(Rab-like4) subfamily. RabL4s are novel proteins that
have high sequence similarity with Rab family members,
but display features that are distinct from Rabs, and
have been termed Rab-like. As in other Rab-like
proteins, RabL4 lacks a prenylation site at the
C-terminus. The specific function of RabL4 remains
unknown.
Length = 167
Score = 81.0 bits (200), Expect = 1e-18
Identities = 54/165 (32%), Positives = 73/165 (44%), Gaps = 8/165 (4%)
Query: 106 KVVVLGSGGVGKSALTVQFVS--GCFMEKYDPTIE-DFYRKEIEVDKAPCVLE--ILDTA 160
+ V+G VGKSAL F S F + Y T D K + V +E I D+A
Sbjct: 2 QCAVVGDPAVGKSALVQMFHSDGATFQKNYTMTTGCDLVVKTVPVPDTSDSVELFIFDSA 61
Query: 161 GTEQFASMRDLYIKNGQGFVVVYSLTNHHTFQDI-KQMKELITRVKGSERVPILLVANKL 219
G E F+ M + + VVY +TN +F + + + + T G P +LV NK
Sbjct: 62 GQELFSDMVENVWEQPAVVCVVYDVTNEVSFNNCSRWINRVRTHSHGLH-TPGVLVGNKC 120
Query: 220 DLASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVR 264
DL +REV QALAQ+ F E SAK F + R
Sbjct: 121 DLTD-RREVDAAQAQALAQANTLKFYETSAKEGVGYEAPFLSLAR 164
>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 = 79.3 bits (196), Expect = 4e-18
Identities = 47/172 (27%), Positives = 86/172 (50%), Gaps = 16/172 (9%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIE------DFYRKEIEVDKAPCVLEILD 158
FK+V++G GG GK+ + ++G F +KY T+ DF+ ++ + D
Sbjct: 1 FKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLDFH-----TNRGKIRFNVWD 55
Query: 159 TAGTEQFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANK 218
TAG E+F +RD Y GQ ++++ +T+ T++++ + RV + +PI+L NK
Sbjct: 56 TAGQEKFGGLRDGYYIQGQCAIIMFDVTSRVTYKNVPNWHRDLVRVCEN--IPIVLCGNK 113
Query: 219 LDLASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREMNFNP 270
+D+ R+V + + E SAK+ N + F + R++ NP
Sbjct: 114 VDIK--DRKVKPKQITFH-RKKNLQYYEISAKSNYNFEKPFLWLARKLLGNP 162
>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 = 79.3 bits (195), Expect = 4e-18
Identities = 52/172 (30%), Positives = 86/172 (50%), Gaps = 15/172 (8%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTEQ 164
K VV+G G VGK+ L + + + F E+Y PT+ D Y + V +L + DTAG E
Sbjct: 1 LKCVVVGDGAVGKTCLLMSYANDAFPEEYVPTVFDHYAVSVTVGGKQYLLGLYDTAGQED 60
Query: 165 FASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKG-SERVPILLVANKLDLAS 223
+ +R L F++ +S+ N +FQ++K+ E + +K + VP LL+ ++DL
Sbjct: 61 YDRLRPLSYPMTDVFLICFSVVNPASFQNVKE--EWVPELKEYAPNVPYLLIGTQIDLRD 118
Query: 224 ---------HQREVPTL--DGQALAQSWG-CPFIEASAKNKTNVNEMFAEIV 263
+E P GQ LA+ G C ++E SA + + +F E +
Sbjct: 119 DPKTLARLNDMKEKPITVEQGQKLAKEIGACCYVECSALTQKGLKTVFDEAI 170
>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 = 78.7 bits (194), Expect = 9e-18
Identities = 60/184 (32%), Positives = 91/184 (49%), Gaps = 14/184 (7%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTEQF 165
KVVVLG G GK++L F G F + Y+PT+ + Y +I VD L + DTAG E+F
Sbjct: 2 KVVVLGDGACGKTSLLNVFTRGYFPQVYEPTVFENYIHDIFVDGLAVELSLWDTAGQEEF 61
Query: 166 ASMRDLYIKNGQGFVVVYSLTNHHTFQDI--KQMKELITRVKGSERVPILLVANKLDL-- 221
+R L + ++ +S+ N + +++ K + E+ G V ++LVA K DL
Sbjct: 62 DRLRSLSYADTHVIMLCFSVDNPDSLENVESKWLAEIRHHCPG---VKLVLVALKCDLRE 118
Query: 222 --ASHQREVPTLD---GQALAQSWG-CPFIEASAKNKTNVNEMFAEIVR-EMNFNPEKDN 274
R T+ G A+A+ C ++E SAK VNE F E R +N P +
Sbjct: 119 PRNERDRGTHTISYEEGLAVAKRINACRYLECSAKLNRGVNEAFTEAARVALNARPPHPH 178
Query: 275 ASFC 278
+ C
Sbjct: 179 SRAC 182
>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 = 76.7 bits (189), Expect = 1e-17
Identities = 34/116 (29%), Positives = 58/116 (50%), Gaps = 2/116 (1%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIED-FYRKEIEVDKAPCVLEILDTAGTEQ 164
KVVV+G G GKS+L Q V G F + D +EVD +L I D G E+
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREE 60
Query: 165 FASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSE-RVPILLVANKL 219
+++K ++VY LT+ + ++ ++ + ++ ++P++LV NKL
Sbjct: 61 LKFEHIIFMKWADAILLVYDLTDRESLNEVSRLIAWLPNLRKLGGKIPVILVGNKL 116
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 79.0 bits (195), Expect = 1e-17
Identities = 49/169 (28%), Positives = 89/169 (52%), Gaps = 6/169 (3%)
Query: 104 EFKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIE-DFYRKEIEVDKAPCVLEILDTAGT 162
EFK++++G GGVGK+ + ++G F +KY PT+ + + + + P + DTAG
Sbjct: 9 EFKLILVGDGGVGKTTFVKRHLTGEFEKKYIPTLGVEVHPLKFYTNCGPICFNVWDTAGQ 68
Query: 163 EQFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLA 222
E+F +RD Y GQ ++++ +T+ T++++ I RV E +PI+LV NK+D+
Sbjct: 69 EKFGGLRDGYYIKGQCAIIMFDVTSRITYKNVPNWHRDIVRV--CENIPIVLVGNKVDVK 126
Query: 223 SHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREMNFNPE 271
R+V + + + SAK+ N + F + R + +P
Sbjct: 127 --DRQVKARQIT-FHRKKNLQYYDISAKSNYNFEKPFLWLARRLTNDPN 172
>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 = 78.4 bits (193), Expect = 2e-17
Identities = 50/167 (29%), Positives = 80/167 (47%), Gaps = 7/167 (4%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFME-KYDPTI-EDFYRKEIEVDKAPCVLEILDTAGTE 163
KVV+LG VGK++L ++V F+ Y TI F K + V + L I DTAG+E
Sbjct: 2 KVVMLGKESVGKTSLVERYVHHRFLVGPYQNTIGAAFVAKRMVVGERVVTLGIWDTAGSE 61
Query: 164 QFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLAS 223
++ +M +Y + + +V Y LT+ +F+ K + + ++ E I L K DL
Sbjct: 62 RYEAMSRIYYRGAKAAIVCYDLTDSSSFERAKFWVKELQNLE--EHCKIYLCGTKSDLIE 119
Query: 224 HQ---REVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREMN 267
R+V D Q A E S+K NV+E+F ++ +
Sbjct: 120 QDRSLRQVDFHDVQDFADEIKAQHFETSSKTGQNVDELFQKVAEDFV 166
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 77.1 bits (189), Expect = 3e-17
Identities = 51/149 (34%), Positives = 79/149 (53%), Gaps = 6/149 (4%)
Query: 129 FMEKYDPTIE-DFYRKEIEVDKAPCVLEILDTAGTEQFASMRDLYIKNGQGFVVVYSLTN 187
F Y TI DF K + +D+ P L++ DTAG E+F S+ YI++ +VVY +TN
Sbjct: 5 FDNNYQSTIGIDFLSKTLYLDEGPVRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDITN 64
Query: 188 HHTFQDIKQMKELITRVKGSERVPILLVANKLDLASHQREVPTLDGQALAQSWGCPFIEA 247
+F++ + + I +G + V I LV NK DL R+V +G AQ + F E
Sbjct: 65 RQSFENTTKWIQDILNERGKD-VIIALVGNKTDLGD-LRKVTYEEGMQKAQEYNTMFHET 122
Query: 248 SAKNKTNVNEMFAEIVREMNFNPEKDNAS 276
SAK N+ +F +I ++ P DN++
Sbjct: 123 SAKAGHNIKVLFKKIAAKL---PNLDNSN 148
>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 = 76.8 bits (189), Expect = 5e-17
Identities = 49/192 (25%), Positives = 88/192 (45%), Gaps = 23/192 (11%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTEQF 165
K+V++G G GK++L F G F E+Y PT+ + Y + VD P L + DTAG E++
Sbjct: 3 KLVIVGDGACGKTSLLYVFTLGEFPEEYHPTVFENYVTDCRVDGKPVQLALWDTAGQEEY 62
Query: 166 ASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQM-KELITRVKGSERVPILLVANKLDL--- 221
+R L ++ +++ + ++++ E + R + VP++LV K DL
Sbjct: 63 ERLRPLSYSKAHVILIGFAIDTPDSLENVRTKWIEEVRRYCPN--VPVILVGLKKDLRQE 120
Query: 222 ------ASHQREVPTLDGQALAQSWGC-PFIEASAKNKTNVNEMF------AEIVREMNF 268
+ VP + +A++ G ++E SA V+++F A +VR
Sbjct: 121 AVAKGNYATDEFVPIQQAKLVARAIGAKKYMECSALTGEGVDDVFEAATRAALLVR---- 176
Query: 269 NPEKDNASFCWC 280
K+ C
Sbjct: 177 KSGKEEPGANCC 188
>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 = 75.3 bits (185), Expect = 1e-16
Identities = 54/166 (32%), Positives = 83/166 (50%), Gaps = 15/166 (9%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTEQF 165
K V +G G VGK+ + + + S F Y PT+ D + + VD L + DTAG E +
Sbjct: 3 KCVTVGDGAVGKTCMLISYTSNTFPTDYVPTVFDNFSANVVVDGNTVNLGLWDTAGQEDY 62
Query: 166 ASMRDLYIKNGQGFVVVYSLTNHHTFQDI--KQMKELITRVKGSERVPILLVANKLDL-- 221
+R L + F++ +SL + +++++ K + EL G VPI+LV KLDL
Sbjct: 63 NRLRPLSYRGADVFLLAFSLISKASYENVLKKWIPELRHYAPG---VPIVLVGTKLDLRD 119
Query: 222 -----ASHQREVP--TLDGQALAQSWGCP-FIEASAKNKTNVNEMF 259
A H VP T G+ L + G +IE S+K + NV +F
Sbjct: 120 DKQFFADHPGAVPITTAQGEELRKQIGAAAYIECSSKTQQNVKAVF 165
>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 = 72.6 bits (178), Expect = 1e-15
Identities = 48/159 (30%), Positives = 74/159 (46%), Gaps = 2/159 (1%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIE-DFYRKEIEVDKAPCVLEILDTAGTEQ 164
KV+V+G VGK+ L +F F + Y TI DF + EV P L++ DTAG E+
Sbjct: 2 KVIVVGDLSVGKTCLINRFCKDVFDKNYKATIGVDFEMERFEVLGVPFSLQLWDTAGQER 61
Query: 165 FASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLAS- 223
F + Y + Q ++V+ LT+ + + +Q E + V + LV K DL+S
Sbjct: 62 FKCIASTYYRGAQAIIIVFDLTDVASLEHTRQWLEDALKENDPSSVLLFLVGTKKDLSSP 121
Query: 224 HQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEI 262
Q + D LA+ + SA NV + F +
Sbjct: 122 AQYALMEQDAIKLAREMKAEYWAVSALTGENVRDFFFRV 160
>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 = 72.5 bits (178), Expect = 2e-15
Identities = 50/171 (29%), Positives = 81/171 (47%), Gaps = 13/171 (7%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTEQF 165
K VV+G G VGK+ L + + + F +Y PT+ D Y + VD P L + DTAG E +
Sbjct: 3 KCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDY 62
Query: 166 ASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLASHQ 225
+R L F++ +SL + +F++++ K PI+LV KLDL +
Sbjct: 63 DRLRPLSYPQTDVFLICFSLVSPASFENVRA-KWYPEVRHHCPNTPIILVGTKLDLRDDK 121
Query: 226 REVPTL-----------DGQALAQSWGC-PFIEASAKNKTNVNEMFAEIVR 264
+ L G A+A+ G ++E SA + + +F E +R
Sbjct: 122 DTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIR 172
>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 = 72.2 bits (177), Expect = 2e-15
Identities = 45/170 (26%), Positives = 81/170 (47%), Gaps = 13/170 (7%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTEQF 165
K VV+G G VGK+ L + + + F +Y PT+ D Y + + P L + DTAG E +
Sbjct: 3 KCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTLGLFDTAGQEDY 62
Query: 166 ASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDL---- 221
+R L F+V +S+ + +F+++K+ K + + P LLV ++DL
Sbjct: 63 DRLRPLSYPQTDVFLVCFSVVSPSSFENVKE-KWVPEITHHCPKTPFLLVGTQIDLRDDP 121
Query: 222 -------ASHQREVPTLDGQALAQSWGC-PFIEASAKNKTNVNEMFAEIV 263
+ Q+ + G+ LA+ ++E SA + + +F E +
Sbjct: 122 STIEKLAKNKQKPITPETGEKLARDLKAVKYVECSALTQKGLKNVFDEAI 171
>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 = 70.7 bits (173), Expect = 9e-15
Identities = 55/186 (29%), Positives = 87/186 (46%), Gaps = 9/186 (4%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTI-EDFYRKEIEVDKAPCVLEILDTAGTE 163
K +++G VGK + G Y + D+ I +D L++ DT+G
Sbjct: 7 LKFLLVGDSDVGKGEILASLQDGSTESPYGYNMGIDYKTTTILLDGRRVKLQLWDTSGQG 66
Query: 164 QFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQ-MKELITRVKGSERVPILLVANKLDLA 222
+F ++ Y + QG ++VY +TN +F I + +KE+ G VP +LV N+L LA
Sbjct: 67 RFCTIFRSYSRGAQGIILVYDITNRWSFDGIDRWIKEIDEHAPG---VPKILVGNRLHLA 123
Query: 223 SHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREM---NFNPEKDNASFCW 279
+R+V T QA A+ G F E S N+ E F E+ R + + P + C
Sbjct: 124 -FKRQVATEQAQAYAERNGMTFFEVSPLCNFNITESFTELARIVLMRHGRPPQSPPQNCS 182
Query: 280 CSSCSI 285
+SC I
Sbjct: 183 RNSCKI 188
>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 = 70.0 bits (171), Expect = 2e-14
Identities = 40/162 (24%), Positives = 81/162 (50%), Gaps = 6/162 (3%)
Query: 110 LGSGGVGKSALTVQFVSGCFMEKYDPTIE-DFYRKEIEVDKAPCVLEILDTAGTEQFASM 168
+G GG GK+ + ++G F +KY T+ + + ++ P + DTAG E+F +
Sbjct: 1 VGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIRFNVWDTAGQEKFGGL 60
Query: 169 RDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLASHQREV 228
RD Y GQ ++++ +T T++++ + RV E +PI+L NK+D+ + +
Sbjct: 61 RDGYYIQGQCAIIMFDVTARVTYKNVPNWHRDLVRV--CENIPIVLCGNKVDVKDRKVKA 118
Query: 229 PTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREMNFNP 270
++ + + + SAK+ N + F + R++ +P
Sbjct: 119 KSI---TFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDP 157
>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 = 67.1 bits (164), Expect = 1e-13
Identities = 48/168 (28%), Positives = 81/168 (48%), Gaps = 16/168 (9%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTEQF 165
K+V++G GK+AL F F E Y PT+ + Y EVDK L + DT+G+ +
Sbjct: 3 KIVLVGDSQCGKTALLQVFAKDSFPENYVPTVFENYTASFEVDKQRIELSLWDTSGSPYY 62
Query: 166 ASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKG-SERVPILLVANKLDLA-- 222
++R L + ++ + ++ T + +K+ V+ P+LLV K DL
Sbjct: 63 DNVRPLSYPDSDAVLICFDISRPETLDSV--LKKWKGEVREFCPNTPVLLVGCKSDLRTD 120
Query: 223 -------SHQREVPT--LDGQALAQSWGC-PFIEASAKNKTN-VNEMF 259
S++R++P G+ LA+ G ++E SAK N V ++F
Sbjct: 121 LSTLTELSNKRQIPVSHEQGRNLAKQIGAAAYVECSAKTSENSVRDVF 168
>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 = 65.1 bits (159), Expect = 6e-13
Identities = 43/167 (25%), Positives = 70/167 (41%), Gaps = 19/167 (11%)
Query: 103 REFKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGT 162
++ ++V++G GVGKS+L + VS F E + + +V I+DT+
Sbjct: 1 KDVRIVLIGDEGVGKSSLIMSLVSEEFPENVPRVLPE-ITIPADVTPERVPTTIVDTSSR 59
Query: 163 EQFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLA 222
Q + I+ +VYS+ T + I + K L + +VPI+LV NK DL
Sbjct: 60 PQDRANLAAEIRKANVICLVYSVDRPSTLERI-RTKWLPLIRRLGVKVPIILVGNKSDLR 118
Query: 223 SHQREVPTLDGQALAQSWGCPF----------IEASAKNKTNVNEMF 259
+ + P +E SAK NV+E+F
Sbjct: 119 DGSSQAGLEEEML-------PIMNEFREIETCVECSAKTLINVSEVF 158
>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 = 63.7 bits (155), Expect = 2e-12
Identities = 41/165 (24%), Positives = 78/165 (47%), Gaps = 15/165 (9%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIED-----FYRKEIEVDKAPCVLEILDTA 160
K+++LG VGKS L +F+ M+ Y+P Y+ + + +++ DTA
Sbjct: 2 KIILLGDSAVGKSKLVERFL----MDGYEPQQLSTYALTLYKHNAKFEGKTILVDFWDTA 57
Query: 161 GTEQFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLD 220
G E+F +M Y ++V+ +T T++++ + E + + +P ++VANK+D
Sbjct: 58 GQERFQTMHASYYHKAHACILVFDVTRKITYKNLSKWYEELREYR--PEIPCIVVANKID 115
Query: 221 LASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVRE 265
L T A+ P SA + TNV ++F + ++
Sbjct: 116 LDPSV----TQKKFNFAEKHNLPLYYVSAADGTNVVKLFQDAIKL 156
>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 = 58.5 bits (141), Expect = 2e-10
Identities = 47/168 (27%), Positives = 77/168 (45%), Gaps = 16/168 (9%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTEQF 165
K+VV+G GK+AL F CF E Y PT+ + Y E+D L + DT+G+ +
Sbjct: 7 KIVVVGDSQCGKTALLHVFAKDCFPENYVPTVFENYTASFEIDTQRIELSLWDTSGSPYY 66
Query: 166 ASMRDLYIKNGQGFVVVYSLTNHHTFQDI-KQMKELITRVKGSERVPILLVANKLDLA-- 222
++R L + ++ + ++ T + K+ K I + + +LLV K DL
Sbjct: 67 DNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEIQEFCPNTK--MLLVGCKSDLRTD 124
Query: 223 -------SHQREVPTL--DGQALAQSWG-CPFIEASAKNKTN-VNEMF 259
S+ R+ P G +A+ G +IE SA N V ++F
Sbjct: 125 VSTLVELSNHRQTPVSYDQGANMAKQIGAATYIECSALQSENSVRDIF 172
>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 = 56.6 bits (137), Expect = 7e-10
Identities = 46/161 (28%), Positives = 74/161 (45%), Gaps = 11/161 (6%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIE-DFYRKEIEVDKAPCVLEILDTAGTEQ 164
K+ +LG +GK++L V++V G F E+Y T+ +F K I + I D G +
Sbjct: 2 KIGLLGDAQIGKTSLMVKYVEGEFDEEYIQTLGVNFMEKTISIRGTEITFSIWDLGGQRE 61
Query: 165 FASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPI-LLVANKLDL-- 221
F +M L K+ + ++ LT T I KE + +G + I +LV K DL
Sbjct: 62 FINMLPLVCKDAVAILFMFDLTRKSTLNSI---KEWYRQARGFNKTAIPILVGTKYDLFA 118
Query: 222 ---ASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMF 259
Q E+ T + A++ P I S + NV ++F
Sbjct: 119 DLPPEEQEEI-TKQARKYAKAMKAPLIFCSTSHSINVQKIF 158
>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 = 56.2 bits (135), Expect = 2e-09
Identities = 44/170 (25%), Positives = 78/170 (45%), Gaps = 20/170 (11%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTEQF 165
K+VV+G GK+AL F + E Y PT+ + Y E+DK L + DT+G+ +
Sbjct: 3 KIVVVGDTQCGKTALLHVFAKDNYPESYVPTVFENYTASFEIDKHRIELNMWDTSGSSYY 62
Query: 166 ASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVP---ILLVANKLDLA 222
++R L + ++ + ++ T + + + + E P ++LV KLD+
Sbjct: 63 DNVRPLAYPDSDAVLICFDISRPETLDSVLKKWQ----GETQEFCPNAKLVLVGCKLDMR 118
Query: 223 ---------SHQREVPTL--DGQALAQSWGC-PFIEASAKNKTN-VNEMF 259
S QR +P G LA+ G ++E S++ N V ++F
Sbjct: 119 TDLSTLRELSKQRLIPVTHEQGSLLARQLGAVAYVECSSRMSENSVRDVF 168
>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 = 54.4 bits (131), Expect = 3e-09
Identities = 41/161 (25%), Positives = 76/161 (47%), Gaps = 12/161 (7%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTE-- 163
K+ ++G+ GKSAL ++++G +++ P ++KE+ VD +L I D G
Sbjct: 2 KLGIVGNLRSGKSALVHRYLTGSYVQLESPEGGR-FKKEVLVDGQSHLLLIRDEGGAPDA 60
Query: 164 QFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDL-A 222
QFA D + V+SL + +FQ + ++ ++ + +P++LV + + A
Sbjct: 61 QFAGWVD-------AVIFVFSLEDEASFQTVYRLYHQLSSYRNISEIPLILVGTQDAISA 113
Query: 223 SHQREVPTLDGQAL-AQSWGCPFIEASAKNKTNVNEMFAEI 262
S+ R + + L A C + E A NV +F E
Sbjct: 114 SNPRVIDDARARQLCADMKRCSYYETCATYGLNVERVFQEA 154
>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 = 54.9 bits (132), Expect = 5e-09
Identities = 46/191 (24%), Positives = 77/191 (40%), Gaps = 37/191 (19%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTEQF 165
KVV+LG VGK++L +++ F + FY K+ P + I DTAG EQF
Sbjct: 2 KVVLLGDMNVGKTSLLHRYMERRFKDTVSTVGGAFYLKQW----GPYNISIWDTAGREQF 57
Query: 166 ASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLASH- 224
+ +Y + ++ Y ++N + ++++ +T +E +V NKLDL
Sbjct: 58 HGLGSMYCRGAAAVILTYDVSNVQSLEELEDRFLGLTDT-ANEDCLFAVVGNKLDLTEEG 116
Query: 225 -----------------QREVPTLDGQALAQ--------------SWGCPFIEASAKNKT 253
QR+V D +A + + E SAK
Sbjct: 117 ALAGQEKDAGDRVSPEDQRQVTLEDAKAFYKRINKYKMLDEDLSPAAEKMCFETSAKTGY 176
Query: 254 NVNEMFAEIVR 264
NV+E+F +
Sbjct: 177 NVDELFEYLFN 187
>gnl|CDD|206737 cd04174, Rnd1_Rho6, Rnd1/Rho6 GTPases. Rnd1/Rho6 is a member of
the novel Rho subfamily Rnd, together with Rnd2/Rho7 and
Rnd3/RhoE/Rho8. Rnd1/Rho6 binds GTP but does not
hydrolyze it to GDP, indicating that it is
constitutively active. In rat, Rnd1/Rho6 is highly
expressed in the cerebral cortex and hippocampus during
synapse formation, and plays a role in spine formation.
Rnd1/Rho6 is also expressed in the liver and in
endothelial cells, and is upregulated in uterine
myometrial cells during pregnancy. Like Rnd3/RhoE/Rho8,
Rnd1/Rho6 is believed to function as an antagonist to
RhoA. Most Rho proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Rho proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 232
Score = 50.4 bits (120), Expect = 2e-07
Identities = 40/157 (25%), Positives = 74/157 (47%), Gaps = 15/157 (9%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTEQF 165
K+V++G GK+A+ C+ E Y PT+ + Y +E ++ L + DT+G+ +
Sbjct: 15 KLVLVGDVQCGKTAMLQVLAKDCYPETYVPTVFENYTACLETEEQRVELSLWDTSGSPYY 74
Query: 166 ASMRDLYIKNGQGFVVVYSLTNHHTFQD-IKQMKELITRVKGSERVPILLVANKLDLA-- 222
++R L + ++ + ++ F +K+ + I S R ILL+ K DL
Sbjct: 75 DNVRPLCYSDSDAVLLCFDISRPEIFDSALKKWRAEILDYCPSTR--ILLIGCKTDLRTD 132
Query: 223 -------SHQREVPTL--DGQALAQSWGCP-FIEASA 249
S+Q++ P G A+A+ G ++E SA
Sbjct: 133 LSTLMELSNQKQAPISYEQGCAMAKQLGAEAYLECSA 169
>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 = 47.3 bits (113), Expect = 1e-06
Identities = 35/168 (20%), Positives = 72/168 (42%), Gaps = 13/168 (7%)
Query: 104 EFKVVVLGSGGVGKSALTVQFVSGCFMEKYDPT----IEDFYRKEIEVDKAPCVLEILDT 159
E K++++G GGVGK++L Q + F T ++D+ E K L + D
Sbjct: 1 EAKLMLVGQGGVGKTSLCKQLIGEKFDGDESSTHGINVQDWKIPAPERKK--IRLNVWDF 58
Query: 160 AGTEQFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKG-SERVPILLVANK 218
G E + + ++ + +++V+ L T ++ ++ + ++K P++LV
Sbjct: 59 GGQEIYHATHQFFLTSRSLYLLVFDLR---TGDEVSRVPYWLRQIKAFGGVSPVILVGTH 115
Query: 219 LDLASHQR-EVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVRE 265
+D + + L+ + A S KN + E+ I +E
Sbjct: 116 IDESCDEDILKKALNKKFPAIIND--IHFVSCKNGKGIAELKKAIAKE 161
>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 = 46.9 bits (112), Expect = 1e-06
Identities = 39/163 (23%), Positives = 73/163 (44%), Gaps = 11/163 (6%)
Query: 107 VVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTEQFA 166
+ ++G GK+ L SG F E PT+ RK V K +++ D G +F
Sbjct: 2 ITLVGLQNSGKTTLVNVIASGQFSEDTIPTVGFNMRK---VTKGNVTIKVWDLGGQPRFR 58
Query: 167 SMRDLYIKNGQGFVVVYSLTNHHTFQDIKQ-MKELITRVKGSERVPILLVANKLDLASHQ 225
SM + Y + V V + + K + +L+ + E +P+L++ NK DL
Sbjct: 59 SMWERYCRGVNAIVYVVDAADREKLEVAKNELHDLLEK-PSLEGIPLLVLGNKNDLPGAL 117
Query: 226 RE---VPTLDGQALA-QSWGCPFIEASAKNKTNVNEMFAEIVR 264
+ ++ +++ + C I SAK KTN++ + +++
Sbjct: 118 SVDELIEQMNLKSITDREVSCYSI--SAKEKTNIDIVLDWLIK 158
>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 = 45.3 bits (108), Expect = 6e-06
Identities = 44/179 (24%), Positives = 61/179 (34%), Gaps = 42/179 (23%)
Query: 108 VVLGSGGVGKSAL-------TVQFVSGCFMEKYDPTIEDFYRKEIEVDKA-PCVLEILDT 159
+ G VGKS+L V VS T D RKE E+ P + ++DT
Sbjct: 1 AIFGRPNVGKSSLLNALLGQNVGIVS-----PIPGTTRDPVRKEWELLPLGP--VVLIDT 53
Query: 160 AG---TEQFASMR-----------DLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVK 205
G R DL + VV LT + ++E
Sbjct: 54 PGLDEEGGLGRERVEEARQVADRADLVL-----LVVDSDLTPVEEEAKLGLLRER----- 103
Query: 206 GSERVPILLVANKLDLASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVR 264
P+LLV NK+DL E L + L P I SA ++E+ +I
Sbjct: 104 ---GKPVLLVLNKIDLVPESEEEELLRERKLELLPDLPVIAVSALPGEGIDELRKKIAE 159
>gnl|CDD|217025 pfam02421, FeoB_N, Ferrous iron transport protein B. Escherichia
coli has an iron(II) transport system (feo) which may
make an important contribution to the iron supply of the
cell under anaerobic conditions. FeoB has been
identified as part of this transport system. FeoB is a
large 700-800 amino acid integral membrane protein. The
N terminus contains a P-loop motif suggesting that iron
transport may be ATP dependent.
Length = 190
Score = 44.0 bits (105), Expect = 2e-05
Identities = 12/69 (17%), Positives = 28/69 (40%), Gaps = 2/69 (2%)
Query: 209 RVPILLVANKLDLASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREMNF 268
+P+++ N +D A + +D + L++ G P + SA+ ++E+ I+
Sbjct: 105 GIPVVVALNMMDEAEKKGI--KIDIKKLSELLGVPVVPTSARKGEGIDELKDAIIEVAEG 162
Query: 269 NPEKDNASF 277
Sbjct: 163 KVPPAPLRI 171
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 41.3 bits (97), Expect = 2e-04
Identities = 35/170 (20%), Positives = 65/170 (38%), Gaps = 17/170 (10%)
Query: 99 SFTMREFKVVVLGSGGVGKS----ALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPC-- 152
+ M E K+VV+G G GK+ AL+ + + + + + + +D
Sbjct: 5 ANKMIETKIVVIGPVGAGKTTFVRALSDKPLVITEADASSVSGKGKRPTTVAMDFGSIEL 64
Query: 153 ----VLEILDTAGTEQFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSE 208
+ + T G E+F M ++ + G +V+ + TF +E+I +
Sbjct: 65 DEDTGVHLFGTPGQERFKFMWEILSRGAVGAIVLVDSSRPITFHA----EEIIDFLTSRN 120
Query: 209 RVPILLVANKLDLASHQREVPTLDGQALAQSW-GCPFIEASAKNKTNVNE 257
+P+++ NK DL P +AL P IE A +
Sbjct: 121 PIPVVVAINKQDLFDALP--PEKIREALKLELLSVPVIEIDATEGEGARD 168
>gnl|CDD|206667 cd01879, FeoB, Ferrous iron transport protein B (FeoB) family.
Ferrous iron transport protein B (FeoB) subfamily. E.
coli has an iron(II) transport system, known as feo,
which may make an important contribution to the iron
supply of the cell under anaerobic conditions. FeoB has
been identified as part of this transport system. FeoB
is a large 700-800 amino acid integral membrane protein.
The N terminus contains a P-loop motif suggesting that
iron transport may be ATP dependent.
Length = 159
Score = 39.7 bits (94), Expect = 3e-04
Identities = 15/69 (21%), Positives = 31/69 (44%), Gaps = 10/69 (14%)
Query: 196 QMKELITRVKGSERVPILLVANKLDLASHQREVPTLDGQALAQSWGCPFIEASAKNKTNV 255
Q+ EL +P+++ N +D A + +D L++ G P + SA+ +
Sbjct: 97 QLLEL--------GLPVVVALNMIDEAEKRGI--KIDLDKLSELLGVPVVPTSARKGEGI 146
Query: 256 NEMFAEIVR 264
+E+ I +
Sbjct: 147 DELLDAIAK 155
>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 = 38.8 bits (90), Expect = 0.001
Identities = 49/196 (25%), Positives = 78/196 (39%), Gaps = 41/196 (20%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYD------PTIE--DFYRKEIEV--------D 148
K VV+G VGK+ L + +Y PT+ D YR EV D
Sbjct: 3 IKCVVVGDNAVGKTRLICARACNKTLTQYQLLATHVPTVWAIDQYRVCQEVLERSRDVVD 62
Query: 149 KAPCVLEILDTAGTEQFASMRDLYIKNGQGFVVV--YSLTNHHTFQDIKQMKELITRVKG 206
L + DT G +D G+ VV+ +S+ + ++ +++K M R
Sbjct: 63 GVSVSLRLWDTFGDHD----KDRRFAYGRSDVVLLCFSIASPNSLRNVKTMWYPEIR-HF 117
Query: 207 SERVPILLVANKLDLASHQRE------------------VPTLDGQALAQSWGCPFIEAS 248
RVP++LV KLDL + +P G+A+A+ G P+ E S
Sbjct: 118 CPRVPVILVGCKLDLRYADLDEVNRARRPLARPIKNADILPPETGRAVAKELGIPYYETS 177
Query: 249 AKNKTNVNEMFAEIVR 264
+ V ++F +R
Sbjct: 178 VVTQFGVKDVFDNAIR 193
>gnl|CDD|133362 cd04162, Arl9_Arfrp2_like, Arf-like 9 (Arl9)/Arfrp2-like GTPase.
Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first
identified as part of the Human Cancer Genome Project.
It maps to chromosome 4q12 and is sometimes referred to
as Arfrp2 (Arf-related protein 2). This is a novel
subfamily identified in human cancers that is
uncharacterized to date.
Length = 164
Score = 37.8 bits (88), Expect = 0.002
Identities = 30/116 (25%), Positives = 52/116 (44%), Gaps = 5/116 (4%)
Query: 107 VVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTEQFA 166
++VLG G GK++L S +E PT F I A ++E+L+ G++
Sbjct: 2 ILVLGLDGAGKTSLLHSLSSERSLESVVPT-TGFNSVAIPTQDA--IMELLEIGGSQNLR 58
Query: 167 SMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLA 222
Y+ QG + V + +Q EL ++ +P++++ANK DL
Sbjct: 59 KYWKRYLSGSQGLIFVVDSADSERLPLARQ--ELHQLLQHPPDLPLVVLANKQDLP 112
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 39.2 bits (92), Expect = 0.002
Identities = 44/183 (24%), Positives = 79/183 (43%), Gaps = 42/183 (22%)
Query: 102 MREFKVVVLGSGGVGKSALTVQFVSGCFME--KYDP--TIEDFYRKEIEVDKAPCVLEIL 157
M++ V ++G+ VGK+ L ++G + + P T+E +KE ++ +EI+
Sbjct: 1 MKKLTVALVGNPNVGKTTLFNA-LTGANQKVGNW-PGVTVE---KKEGKLKYKGHEIEIV 55
Query: 158 DTAGT---------EQFASMRDLYIKNGQ--GFVVVYSLTN-----HHTFQDIKQMKELI 201
D GT E+ A RD ++ G+ V V TN + T Q + EL
Sbjct: 56 DLPGTYSLTAYSEDEKVA--RD-FLLEGKPDLIVNVVDATNLERNLYLTLQ----LLEL- 107
Query: 202 TRVKGSERVPILLVANKLDLASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAE 261
+P++L N +D A + +D + L++ G P + AK + E+
Sbjct: 108 -------GIPMILALNMIDEAKKRGI--RIDIEKLSKLLGVPVVPTVAKRGEGLEELKRA 158
Query: 262 IVR 264
I+
Sbjct: 159 IIE 161
>gnl|CDD|206689 cd04102, RabL3, Rab GTPase-like family 3 (Rab-like3). RabL3
(Rab-like3) subfamily. RabL3s are novel proteins that
have high sequence similarity with Rab family members,
but display features that are distinct from Rabs, and
have been termed Rab-like. As in other Rab-like
proteins, RabL3 lacks a prenylation site at the
C-terminus. The specific function of RabL3 remains
unknown.
Length = 204
Score = 38.0 bits (88), Expect = 0.002
Identities = 43/203 (21%), Positives = 71/203 (34%), Gaps = 41/203 (20%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTI-------EDFYRKEIEVDKAPCVLEILD 158
KV+VLG GVGKS+L + T+ Y + +K V E+ D
Sbjct: 2 KVLVLGDSGVGKSSLVHLLCKNQVLGNPSWTVGCSVDVRHHTYGEGTPEEKTFYV-ELWD 60
Query: 159 TAGT----EQFASMRDLYIKNGQGFVVVYSLTNHHTFQ------------DIKQMKELIT 202
G+ E S R ++ G + V+ LTN + Q D L+T
Sbjct: 61 VGGSVGSAESVKSTRAVFYNQINGIIFVHDLTNKKSSQNLYRWSLEALNRDTFPAGLLVT 120
Query: 203 RVK------GSERVPILLVANKLDLASH--------QREVPTLDGQALAQSWGCP---FI 245
VP+L++ KLD + + D A + C +
Sbjct: 121 NGDYDSEQFAGNPVPLLVIGTKLDQIPEAKRNWVLTRTAFLSEDFNAEEINLDCTNGRLL 180
Query: 246 EASAKNKTNVNEMFAEIVREMNF 268
A + N ++ F +++ + F
Sbjct: 181 AAGSSNAVKLSRFFDKVIEKRYF 203
>gnl|CDD|234395 TIGR03918, GTP_HydF, [FeFe] hydrogenase H-cluster maturation GTPase
HydF. This model describes the family of the [Fe]
hydrogenase maturation protein HypF as characterized in
Chlamydomonas reinhardtii and found, in an operon with
radical SAM proteins HydE and HydG, in numerous
bacteria. It has GTPase activity, can bind an 4Fe-4S
cluster, and is essential for hydrogenase activity
[Protein fate, Protein modification and repair].
Length = 391
Score = 38.3 bits (90), Expect = 0.003
Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 6/67 (8%)
Query: 198 KELITRVKGSERVPILLVANKLDLASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNE 257
ELI +K ++P ++V NK+DL E+ + L + +G P I SA ++E
Sbjct: 104 LELIEELK-ERKIPYIVVINKIDLGEESAEL-----EKLEKKFGLPPIFVSALTGEGIDE 157
Query: 258 MFAEIVR 264
+ I+
Sbjct: 158 LKEAIIE 164
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 38.3 bits (90), Expect = 0.003
Identities = 44/204 (21%), Positives = 78/204 (38%), Gaps = 59/204 (28%)
Query: 102 MRE-FKVVVLGSGGVGKS----ALT------VQFVSGCFMEKYDPTIEDFYRKEIEVDKA 150
+RE KVV++G VGKS AL V ++G T D ++I ++
Sbjct: 214 LREGLKVVIIGRPNVGKSSLLNALLGRDRAIVTDIAG--------TTRDVIEEDINLNGI 265
Query: 151 PCVLEILDTAG---TEQ----------FASMRD----LYIKNGQGFVVVYSLTNHHTFQD 193
P + ++DTAG T+ ++ + L++ + + ++
Sbjct: 266 P--VRLVDTAGIRETDDVVERIGIERAKKAIEEADLVLFVLDA----------SQPLDKE 313
Query: 194 IKQMKELITRVKGSERVPILLVANKLDLASHQREVPTLDGQALAQSWGCPFIEASAKNKT 253
+ EL+ ++ PI++V NK DL S L+ + LA G I SAK
Sbjct: 314 DLALIELL-----PKKKPIIVVLNKADLVSK----IELESEKLAN--GDAIISISAKTGE 362
Query: 254 NVNEMFAEIVREMNFNPEKDNASF 277
++ + I + F
Sbjct: 363 GLDALREAIKQLFGKGLGNQEGLF 386
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 38.3 bits (90), Expect = 0.004
Identities = 42/156 (26%), Positives = 59/156 (37%), Gaps = 46/156 (29%)
Query: 141 YRKEIEVDKAPCVLEILDTAGTEQFASMRDLYIKNGQGFVVVYSLTNHHTFQDI------ 194
Y+ ++V K P + +DT G E F +MR G S+T DI
Sbjct: 45 YQVPLDVIKIP-GITFIDTPGHEAFTAMR----ARG------ASVT------DIAILVVA 87
Query: 195 ------KQMKELITRVKGSERVPILLVANKLDLASHQREVPTLDGQALAQ------SWG- 241
Q E I K + VPI++ NK+D P Q L + WG
Sbjct: 88 ADDGVMPQTIEAINHAKAA-GVPIVVAINKIDKPEAN---PDKVKQELQEYGLVPEEWGG 143
Query: 242 -CPFIEASAKNKTNVNEMFAEI-----VREMNFNPE 271
F+ SAK ++E+ I V E+ NPE
Sbjct: 144 DVIFVPVSAKTGEGIDELLELILLLAEVLELKANPE 179
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 36.9 bits (87), Expect = 0.006
Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 7/76 (9%)
Query: 198 KELITRVKGSERVPILLVANKLDLASHQREVPTLDGQALAQSWGCPFIEA---SAKNKTN 254
+ ++ ++K + P++LV NK+DL + E+ L + L++ F E SA N
Sbjct: 103 EFILEKLK-KVKTPVILVLNKIDLVKDKEELLPLL-EELSELM--DFAEIVPISALKGDN 158
Query: 255 VNEMFAEIVREMNFNP 270
V+E+ I + + P
Sbjct: 159 VDELLDVIAKYLPEGP 174
>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 = 35.9 bits (84), Expect = 0.008
Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 1/66 (1%)
Query: 198 KELITRVKGSERVPILLVANKLDLASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNE 257
+ ++ +K S+ P++LV NK+DL + ++ L + SA NV+E
Sbjct: 101 EFILELLKKSK-TPVILVLNKIDLVKDKEDLLPLLEKLKELHPFAEIFPISALKGENVDE 159
Query: 258 MFAEIV 263
+ IV
Sbjct: 160 LLEYIV 165
>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 = 35.1 bits (81), Expect = 0.014
Identities = 20/67 (29%), Positives = 31/67 (46%), Gaps = 2/67 (2%)
Query: 158 DTAGTEQFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKG--SERVPILLV 215
D +G ++ + + Y KN QG + V ++ K EL+ R+PIL
Sbjct: 51 DMSGQGKYRGLWEHYYKNIQGIIFVIDSSDRLRMVVAKDELELLLNHPDIKHRRIPILFY 110
Query: 216 ANKLDLA 222
ANK+DL
Sbjct: 111 ANKMDLP 117
>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 = 35.6 bits (83), Expect = 0.014
Identities = 11/67 (16%), Positives = 22/67 (32%), Gaps = 7/67 (10%)
Query: 207 SERVPILLVANKLDLASHQR-------EVPTLDGQALAQSWGCPFIEASAKNKTNVNEMF 259
+ VPI++ NK+D L + P + SA ++E+
Sbjct: 116 TLGVPIIVFINKIDRVDDAELEEVVEEISRELLEKYGFGGETVPVVPGSALTGEGIDELL 175
Query: 260 AEIVREM 266
+ +
Sbjct: 176 EALDLYL 182
>gnl|CDD|133361 cd04161, Arl2l1_Arl13_like, Arl2-like protein 1 (Arl2l1) and Arl13.
Arl2l1 (Arl2-like protein 1) and Arl13 form a subfamily
of the Arf family of small GTPases. Arl2l1 was
identified in human cells during a search for the
gene(s) responsible for Bardet-Biedl syndrome (BBS).
Like Arl6, the identified BBS gene, Arl2l1 is proposed
to have cilia-specific functions. Arl13 is found on the
X chromosome, but its expression has not been confirmed;
it may be a pseudogene.
Length = 167
Score = 35.1 bits (81), Expect = 0.016
Identities = 31/118 (26%), Positives = 53/118 (44%), Gaps = 10/118 (8%)
Query: 107 VVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTEQFA 166
++ +G GK+ L V + G +K PT+ F ++ +DK + I D G F
Sbjct: 2 LLTVGLDNAGKTTL-VSALQGEIPKKVAPTVG-FTPTKLRLDK--YEVCIFDLGGGANFR 57
Query: 167 SMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERV---PILLVANKLDL 221
+ Y G V V + ++++KE++ + RV PIL++ANK D
Sbjct: 58 GIWVNYYAEAHGLVFV---VDSSDDDRVQEVKEILRELLQHPRVSGKPILVLANKQDK 112
>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 = 35.1 bits (82), Expect = 0.018
Identities = 29/128 (22%), Positives = 45/128 (35%), Gaps = 37/128 (28%)
Query: 156 ILDTAGTEQFASMR-------DLYIKNGQGFVVVYSLTNHHTFQDI-----KQMKELITR 203
+DT G E F +MR D+ I +VV Q E I
Sbjct: 53 FIDTPGHEAFTNMRARGASVTDIAI------LVV----------AADDGVMPQTIEAINH 96
Query: 204 VKGSERVPILLVANKLDLASHQREVPTLDGQALAQ------SWG--CPFIEASAKNKTNV 255
K + VPI++ NK+D P L++ WG + SAK +
Sbjct: 97 AK-AANVPIIVAINKIDKPYGTEADPERVKNELSELGLVGEEWGGDVSIVPISAKTGEGI 155
Query: 256 NEMFAEIV 263
+++ I+
Sbjct: 156 DDLLEAIL 163
>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 = 34.9 bits (81), Expect = 0.020
Identities = 36/120 (30%), Positives = 53/120 (44%), Gaps = 7/120 (5%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEK-YDPTIEDFYR-KEIEVDKAPCVLEILDTAGT 162
F VLG+ G GKSAL F+ F + Y PTI+ Y +EV L IL G
Sbjct: 5 FLCFVLGAKGSGKSALLQAFLGRSFSQNAYSPTIKPRYAVNTVEVPGQEKYL-ILREVGE 63
Query: 163 EQFASM-RDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDL 221
++ A + D + +VY ++ ++F E+ + +P L VA K DL
Sbjct: 64 DEEAILLNDAELAACDVACLVYDSSDPNSFSYC---AEVYKKYFMLGEIPCLFVAAKADL 120
>gnl|CDD|232980 TIGR00450, mnmE_trmE_thdF, tRNA modification GTPase TrmE. TrmE,
also called MnmE and previously designated ThdF
(thiophene and furan oxidation protein), is a GTPase
involved in tRNA modification to create
5-methylaminomethyl-2-thiouridine in the wobble position
of some tRNAs. This protein and GidA form an
alpha2/beta2 heterotetramer [Protein synthesis, tRNA and
rRNA base modification].
Length = 442
Score = 35.5 bits (82), Expect = 0.026
Identities = 36/131 (27%), Positives = 61/131 (46%), Gaps = 14/131 (10%)
Query: 105 FKVVVLGSGGVGKSALTVQFV--SGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGT 162
FK+ ++GS VGKS+L + + T D + E++ +++LDTAG
Sbjct: 204 FKLAIVGSPNVGKSSLLNALLKQDRAIVSDIKGTTRDVVEGDFELNGIL--IKLLDTAGI 261
Query: 163 EQFAS-MRDLYIKNG-----QGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVA 216
+ A + L I+ Q +V+Y L Q + + LI + S++ P +LV
Sbjct: 262 REHADFVERLGIEKSFKAIKQADLVIYVLDAS---QPLTKDDFLIIDLNKSKK-PFILVL 317
Query: 217 NKLDLASHQRE 227
NK+DL + E
Sbjct: 318 NKIDLKINSLE 328
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 34.5 bits (80), Expect = 0.029
Identities = 25/120 (20%), Positives = 49/120 (40%), Gaps = 6/120 (5%)
Query: 103 REFKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGT 162
+E ++++LG GK+ + + G + PTI F + + + D G
Sbjct: 13 KEMRILILGLDNAGKTTILYKLKLGEIVT-TIPTI-GFNVETVTYKNVK--FTVWDVGGQ 68
Query: 163 EQFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQ-MKELITRVKGSERVPILLVANKLDL 221
E + Y N + V + ++ K+ + L+ + P+L++ANK DL
Sbjct: 69 ESLRPLWRNYFPNTDAVIFVVDSADRDRIEEAKEELHALLNE-EELADAPLLILANKQDL 127
>gnl|CDD|232995 TIGR00487, IF-2, translation initiation factor IF-2. This model
discriminates eubacterial (and mitochondrial)
translation initiation factor 2 (IF-2), encoded by the
infB gene in bacteria, from similar proteins in the
Archaea and Eukaryotes. In the bacteria and in
organelles, the initiator tRNA is charged with
N-formyl-Met instead of Met. This translation factor
acts in delivering the initator tRNA to the ribosome. It
is one of a number of GTP-binding translation factors
recognized by the pfam model GTP_EFTU [Protein
synthesis, Translation factors].
Length = 587
Score = 35.5 bits (82), Expect = 0.032
Identities = 36/129 (27%), Positives = 52/129 (40%), Gaps = 21/129 (16%)
Query: 157 LDTAGTEQFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVA 216
LDT G E F SMR K V+V + + + Q E I+ K + VPI++
Sbjct: 140 LDTPGHEAFTSMRARGAKVTDIVVLVVAADD----GVMPQTIEAISHAKAAN-VPIIVAI 194
Query: 217 NKLDLASHQREVPTLDGQALAQ------SWG--CPFIEASAKNKTNVNEMFAEI-----V 263
NK+D P Q L++ WG F+ SA ++E+ I V
Sbjct: 195 NKIDKPEAN---PDRVKQELSEYGLVPEDWGGDTIFVPVSALTGDGIDELLDMILLQSEV 251
Query: 264 REMNFNPEK 272
E+ NP
Sbjct: 252 EELKANPNG 260
>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 = 34.2 bits (79), Expect = 0.036
Identities = 37/117 (31%), Positives = 49/117 (41%), Gaps = 6/117 (5%)
Query: 145 IEVDKAPCVLEILDTAGTEQFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRV 204
IEV KA L D G E+ S+ D Y G + V T+ F + K E +
Sbjct: 46 IEVGKA--RLMFWDLGGQEELRSLWDKYYAESHGVIYVIDSTDRERFNESKSAFEKVINN 103
Query: 205 KGSERVPILLVANKLDL--ASHQREVPTL--DGQALAQSWGCPFIEASAKNKTNVNE 257
+ E VP+L++ANK DL A E+ + D AL C SA V E
Sbjct: 104 EALEGVPLLVLANKQDLPDALSVAEIKEVFDDCIALIGRRDCLVQPVSALEGEGVEE 160
>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 = 33.6 bits (78), Expect = 0.053
Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 1/47 (2%)
Query: 211 PILLVANKLDLASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNE 257
P ++V NK+DL E + L + G SA ++E
Sbjct: 116 PRIVVLNKIDLL-DAEERFEKLKELLKELKGKKVFPISALTGEGLDE 161
>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 = 33.5 bits (77), Expect = 0.059
Identities = 29/116 (25%), Positives = 58/116 (50%), Gaps = 3/116 (2%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTEQF 165
+V++LG GKS L + + PT+ F + ++++K L + D G E+
Sbjct: 1 QVLLLGLDSAGKSTLLYKLKHAELVTTI-PTV-GFNVEMLQLEKH-LSLTVWDVGGQEKM 57
Query: 166 ASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDL 221
++ Y++N G V V ++ + ++ + I + + + VP++L+ANK DL
Sbjct: 58 RTVWKCYLENTDGLVYVVDSSDEARLDESQKELKHILKNEHIKGVPVVLLANKQDL 113
>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 = 32.9 bits (76), Expect = 0.078
Identities = 34/155 (21%), Positives = 66/155 (42%), Gaps = 8/155 (5%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTEQF 165
++++LG G GK+ + + G + PTI F + +E K + D G ++
Sbjct: 1 RILMLGLDGAGKTTILYKLKLGEVVTTI-PTI-GFNVETVEY-KNVKFT-VWDVGGQDKI 56
Query: 166 ASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQ-MKELITRVKGSERVPILLVANKLDL--A 222
+ Y +N G + V ++ ++ K + +L+ + P+L++ANK DL A
Sbjct: 57 RPLWKHYYENTDGLIFVVDSSDRERIEEAKNELHKLLNEEELKG-APLLILANKQDLPGA 115
Query: 223 SHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNE 257
+ E+ L G + SA ++E
Sbjct: 116 LTESELIELLGLESIKGRRWHIQPCSAVTGDGLDE 150
>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 = 32.7 bits (75), Expect = 0.10
Identities = 33/129 (25%), Positives = 57/129 (44%), Gaps = 18/129 (13%)
Query: 100 FTMREFKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTI----EDFYRKEIEVDKAPCVLE 155
F +E+KV+++G GK+ + QF+ G + PTI E+ K I
Sbjct: 11 FPRKEYKVIIVGLDNAGKTTILYQFLLGEVVHT-SPTIGSNVEEIVYKNIR-------FL 62
Query: 156 ILDTAGTEQFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSE---RVPI 212
+ D G E S + Y N ++V T+ + + KE + ++ E + +
Sbjct: 63 MWDIGGQESLRSSWNTYYTNTDAVILVIDSTDR---ERLPLTKEELYKMLAHEDLRKAVL 119
Query: 213 LLVANKLDL 221
L++ANK DL
Sbjct: 120 LVLANKQDL 128
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 33.5 bits (78), Expect = 0.11
Identities = 17/70 (24%), Positives = 27/70 (38%), Gaps = 12/70 (17%)
Query: 198 KELITRVKGSERVPILLVANKLDLASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNE 257
E++ +K P+++V NK DL L + G P I SAK ++E
Sbjct: 313 DEILEELKD---KPVIVVLNKADLTGE---------IDLEEENGKPVIRISAKTGEGIDE 360
Query: 258 MFAEIVREMN 267
+ I
Sbjct: 361 LREAIKELAF 370
>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 = 32.9 bits (75), Expect = 0.12
Identities = 29/122 (23%), Positives = 51/122 (41%), Gaps = 5/122 (4%)
Query: 105 FKVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAP---CVLEILDTAG 161
+V+LG GK+ + + F+ PT F ++I+V D G
Sbjct: 4 LHIVMLGLDSAGKTTVLYRLKFNEFVNTV-PTK-GFNTEKIKVSLGNAKGVTFHFWDVGG 61
Query: 162 TEQFASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDL 221
E+ + Y + G V V + ++ K IT+ ++ VP+L++ANK DL
Sbjct: 62 QEKLRPLWKSYTRCTDGIVFVVDSVDVERMEEAKTELHKITKFSENQGVPVLVLANKQDL 121
Query: 222 AS 223
+
Sbjct: 122 PN 123
>gnl|CDD|177089 CHL00189, infB, translation initiation factor 2; Provisional.
Length = 742
Score = 33.3 bits (76), Expect = 0.14
Identities = 30/114 (26%), Positives = 50/114 (43%), Gaps = 16/114 (14%)
Query: 157 LDTAGTEQFASMRDLYIKNGQGFVVVYSLTNH---HTFQDIKQMKELITRVKGSERVPIL 213
LDT G E F+SMR +++ + + T + I ++ + VPI+
Sbjct: 300 LDTPGHEAFSSMRSRGANVTDIAILIIAADDGVKPQTIEAINYIQ--------AANVPII 351
Query: 214 LVANKLD--LASHQREVPTLDGQAL-AQSWG--CPFIEASAKNKTNVNEMFAEI 262
+ NK+D A+ +R L L + WG P I SA TN++++ I
Sbjct: 352 VAINKIDKANANTERIKQQLAKYNLIPEKWGGDTPMIPISASQGTNIDKLLETI 405
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes. TrmE
contains a GTPase domain that forms a canonical Ras-like
fold. It functions a molecular switch GTPase, and
apparently uses a conformational change associated with
GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 32.1 bits (74), Expect = 0.18
Identities = 17/78 (21%), Positives = 35/78 (44%), Gaps = 15/78 (19%)
Query: 180 VVVYSLTNHHTFQDIKQMKELITRVKGSERVPILLVANKLDLASHQREVPTLDGQALAQS 239
++V + +D++ ++ + P+++V NK DL S D + +++
Sbjct: 87 LLVVDASEGLDEEDLEILEL-------PAKKPVIVVLNKSDLLS--------DAEGISEL 131
Query: 240 WGCPFIEASAKNKTNVNE 257
G P I SAK ++E
Sbjct: 132 NGKPIIAISAKTGEGIDE 149
>gnl|CDD|234125 TIGR03156, GTP_HflX, GTP-binding protein HflX. This protein family
is one of a number of homologous small, well-conserved
GTP-binding proteins with pleiotropic effects. Bacterial
members are designated HflX, following the naming
convention in Escherichia coli where HflX is encoded
immediately downstream of the RNA chaperone Hfq, and
immediately upstream of HflKC, a membrane-associated
protease pair with an important housekeeping function.
Over large numbers of other bacterial genomes, the
pairing with hfq is more significant than with hflK and
hlfC. The gene from Homo sapiens in this family has been
named PGPL (pseudoautosomal GTP-binding protein-like)
[Unknown function, General].
Length = 351
Score = 32.8 bits (76), Expect = 0.19
Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 7/61 (11%)
Query: 206 GSERVPILLVANKLDLASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVRE 265
G+E +P LLV NK+DL R +G A + SAK ++ + I
Sbjct: 298 GAEDIPQLLVYNKIDLLDEPRIERLEEGYPEA-------VFVSAKTGEGLDLLLEAIAER 350
Query: 266 M 266
+
Sbjct: 351 L 351
>gnl|CDD|232975 TIGR00437, feoB, ferrous iron transporter FeoB. FeoB (773 amino
acids in E. coli), a cytoplasmic membrane protein
required for iron(II) update, is encoded in an operon
with FeoA (75 amino acids), which is also required, and
is regulated by Fur. There appear to be two copies in
Archaeoglobus fulgidus and Clostridium acetobutylicum
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 591
Score = 32.8 bits (75), Expect = 0.20
Identities = 14/66 (21%), Positives = 29/66 (43%), Gaps = 2/66 (3%)
Query: 210 VPILLVANKLDLASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREMNFN 269
+P++L N +D A +++ +D + L + G P + SA + + I + +
Sbjct: 100 IPMILALNLVDEA--EKKGIRIDEEKLEERLGVPVVPTSATEGRGIERLKDAIRKAIGLK 157
Query: 270 PEKDNA 275
K A
Sbjct: 158 ELKKRA 163
>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 = 31.7 bits (73), Expect = 0.26
Identities = 17/70 (24%), Positives = 29/70 (41%), Gaps = 11/70 (15%)
Query: 197 MKELITRVKGSERVPILLVANKLDLASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVN 256
+KEL G++ +PI+LV NK+DL + L + SAK ++
Sbjct: 146 LKEL-----GADDIPIILVLNKIDLLDDEELEERLRAGRP------DAVFISAKTGEGLD 194
Query: 257 EMFAEIVREM 266
+ I +
Sbjct: 195 LLKEAIEELL 204
>gnl|CDD|234770 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 31.2 bits (72), Expect = 0.41
Identities = 16/83 (19%), Positives = 32/83 (38%), Gaps = 16/83 (19%)
Query: 189 HTFQDI-KQMKELITRVKGSERVPILLVANKLD------LASHQREVPTLDGQALAQSWG 241
H +++ QM E + +P+L+V K D ++V + +
Sbjct: 118 HPLKELDLQMIEWLKEYG----IPVLIVLTKADKLKKGERKKQLKKV-----RKALKFGD 168
Query: 242 CPFIEASAKNKTNVNEMFAEIVR 264
I S+ K ++E+ A I +
Sbjct: 169 DEVILFSSLKKQGIDELRAAIAK 191
>gnl|CDD|206684 cd01897, NOG, Nucleolar GTP-binding protein (NOG). NOG1 is a
nucleolar GTP-binding protein present in eukaryotes
ranging from trypanosomes to humans. NOG1 is
functionally linked to ribosome biogenesis and found in
association with the nuclear pore complexes and
identified in many preribosomal complexes. Thus, defects
in NOG1 can lead to defects in 60S biogenesis. The S.
cerevisiae NOG1 gene is essential for cell viability,
and mutations in the predicted G motifs abrogate
function. It is a member of the ODN family of
GTP-binding proteins that also includes the bacterial
Obg and DRG proteins.
Length = 167
Score = 30.6 bits (70), Expect = 0.49
Identities = 15/64 (23%), Positives = 28/64 (43%), Gaps = 3/64 (4%)
Query: 194 IKQMKELITRVKGSERVPILLVANKLDLASHQREVPTLDGQALAQSWGCPFIEASAKNKT 253
I++ L +K P+++V NK+DL E + + + G I+ S +
Sbjct: 97 IEEQLSLFKEIKPLFNKPVIVVLNKIDLL---TEEDLSEIEKELEKEGEEVIKISTLTEE 153
Query: 254 NVNE 257
V+E
Sbjct: 154 GVDE 157
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 31.0 bits (71), Expect = 0.62
Identities = 42/191 (21%), Positives = 70/191 (36%), Gaps = 56/191 (29%)
Query: 105 FKVVVLGSGGVGKSALT----------VQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVL 154
K+ ++G VGKS+L V ++G T D E E D
Sbjct: 179 IKIAIIGRPNVGKSSLINAILGEERVIVSDIAG--------TTRDSIDIEFERDG--RKY 228
Query: 155 EILDTAG----------TEQFASMRDL-YIKNGQGFVVVYSLTNHHTFQDIKQMKELITR 203
++DTAG E+++ R L I+ ++V T + QD +
Sbjct: 229 VLIDTAGIRRKGKITESVEKYSVARTLKAIERADVVLLVIDATEGISEQD----LRIAGL 284
Query: 204 VKGSERVPILLVANKLDLASHQ------------REVPTLDGQALAQSWGCPFIEASAKN 251
++ + R I++V NK DL R++P LD P + SA
Sbjct: 285 IEEAGR-GIVIVVNKWDLVEEDEATMEEFKKKLRRKLPFLDFA--------PIVFISALT 335
Query: 252 KTNVNEMFAEI 262
++++F I
Sbjct: 336 GQGLDKLFEAI 346
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 30.6 bits (70), Expect = 0.86
Identities = 16/71 (22%), Positives = 29/71 (40%), Gaps = 12/71 (16%)
Query: 211 PILLVANKLDLASHQREVPTLDGQALAQ------SWGCPFIEASAKNKTNVNEMFAEIVR 264
P LV NK+DL + + + A+ W P SA + V E+ +++
Sbjct: 277 PRWLVFNKIDL------LDEEEAEERAKAIVEALGWEGPVYLISAASGLGVKELCWDLMT 330
Query: 265 EMNFNPEKDNA 275
+ NP ++
Sbjct: 331 FIEENPREEAE 341
>gnl|CDD|226054 COG3523, IcmF, Type VI protein secretion system component VasK
[Intracellular trafficking, secretion, and vesicular
transport].
Length = 1188
Score = 30.8 bits (70), Expect = 1.0
Identities = 16/63 (25%), Positives = 27/63 (42%), Gaps = 4/63 (6%)
Query: 209 RVPILLVANKLDLASHQREV-PTLDGQALAQSWGCPFIEASAKNKTNV---NEMFAEIVR 264
R+P+ LV K DL E +L+ + Q WG F + +N + F ++
Sbjct: 256 RLPVYLVLTKADLLPGFEEFFGSLNKEEREQVWGVTFPLDARRNANLAAELEQEFRLLLD 315
Query: 265 EMN 267
+N
Sbjct: 316 RLN 318
>gnl|CDD|206747 cd01854, YjeQ_EngC, Ribosomal interacting GTPase YjeQ/EngC, a
circularly permuted subfamily of the Ras GTPases. YjeQ
(YloQ in Bacillus subtilis) is a ribosomal small
subunit-dependent GTPase; hence also known as RsgA. YjeQ
is a late-stage ribosomal biogenesis factor involved in
the 30S subunit maturation, and it represents a protein
family whose members are broadly conserved in bacteria
and have been shown to be essential to the growth of E.
coli and B. subtilis. Proteins of the YjeQ family
contain all sequence motifs typical of the vast class of
P-loop-containing GTPases, but show a circular
permutation, with a G4-G1-G3 pattern of motifs as
opposed to the regular G1-G3-G4 pattern seen in most
GTPases. All YjeQ family proteins display a unique
domain architecture, which includes an N-terminal
OB-fold RNA-binding domain, the central permuted GTPase
domain, and a zinc knuckle-like C-terminal cysteine
domain.
Length = 211
Score = 30.1 bits (69), Expect = 1.1
Identities = 13/56 (23%), Positives = 25/56 (44%), Gaps = 3/56 (5%)
Query: 207 SERVPILLVANKLDLASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEI 262
+ + ++V NK DL E+ L + + G P + SAK ++E+ +
Sbjct: 31 ASGIEPVIVLNKADLVD-DEELEEL--LEIYEKLGYPVLAVSAKTGEGLDELRELL 83
>gnl|CDD|206652 cd01853, Toc34_like, Translocon at the Outer-envelope membrane of
Chloroplasts 34-like (Toc34-like). The Toc34-like
(Translocon at the Outer-envelope membrane of
Chloroplasts) family contains several Toc proteins,
including Toc34, Toc33, Toc120, Toc159, Toc86, Toc125,
and Toc90. The Toc complex at the outer envelope
membrane of chloroplasts is a molecular machine of ~500
kDa that contains a single Toc159 protein, four Toc75
molecules, and four or five copies of Toc34. Toc64 and
Toc12 are associated with the translocon, but do not
appear to be part of the core complex. The Toc
translocon initiates the import of nuclear-encoded
preproteins from the cytosol into the organelle. Toc34
and Toc159 are both GTPases, while Toc75 is a
beta-barrel integral membrane protein. Toc159 is equally
distributed between a soluble cytoplasmic form and a
membrane-inserted form, suggesting that assembly of the
Toc complex is dynamic. Toc34 and Toc75 act sequentially
to mediate docking and insertion of Toc159 resulting in
assembly of the functional translocon.
Length = 248
Score = 30.0 bits (68), Expect = 1.2
Identities = 9/23 (39%), Positives = 15/23 (65%), Gaps = 3/23 (13%)
Query: 97 DNSFTMREFKVVVLGSGGVGKSA 119
+ F++ ++VLG GVGKS+
Sbjct: 27 ELDFSLT---ILVLGKTGVGKSS 46
>gnl|CDD|215028 PLN00012, PLN00012, chlorophyll synthetase; Provisional.
Length = 375
Score = 30.2 bits (68), Expect = 1.2
Identities = 14/37 (37%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 115 VGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAP 151
V KS + +SG F+ Y TI D+Y +EI+ P
Sbjct: 121 VAKS-IVCMLMSGPFLTGYTQTINDWYDREIDAINEP 156
>gnl|CDD|233986 TIGR02729, Obg_CgtA, Obg family GTPase CgtA. This model describes
a univeral, mostly one-gene-per-genome GTP-binding
protein that associates with ribosomal subunits and
appears to play a role in ribosomal RNA maturation. This
GTPase, related to the nucleolar protein Obg, is
designated CgtA in bacteria. Mutations in this gene are
pleiotropic, but it appears that effects on cellular
functions such as chromosome partition may be secondary
to the effect on ribosome structure. Recent work done in
Vibrio cholerae shows an essential role in the stringent
response, in which RelA-dependent ability to synthesize
the alarmone ppGpp is required for deletion of this
GTPase to be lethal [Protein synthesis, Other].
Length = 329
Score = 30.1 bits (69), Expect = 1.2
Identities = 13/59 (22%), Positives = 25/59 (42%), Gaps = 6/59 (10%)
Query: 211 PILLVANKLDL--ASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREMN 267
P ++V NK+DL E+ + L ++ G P SA ++E+ + +
Sbjct: 275 PRIVVLNKIDLLDEEELEELL----KELKEALGKPVFPISALTGEGLDELLYALAELLE 329
>gnl|CDD|206665 cd01876, YihA_EngB, YihA (EngB) GTPase family. The YihA (EngB)
subfamily of GTPases is typified by the E. coli YihA, an
essential protein involved in cell division control.
YihA and its orthologs are small proteins that typically
contain less than 200 amino acid residues and consists
of the GTPase domain only (some of the eukaryotic
homologs contain an N-terminal extension of about 120
residues that might be involved in organellar
targeting). Homologs of yihA are found in most
Gram-positive and Gram-negative pathogenic bacteria,
with the exception of Mycobacterium tuberculosis. The
broad-spectrum nature of YihA and its essentiality for
cell viability in bacteria make it an attractive
antibacterial target.
Length = 170
Score = 29.4 bits (67), Expect = 1.2
Identities = 19/82 (23%), Positives = 32/82 (39%), Gaps = 14/82 (17%)
Query: 188 HHTFQDI-KQMKELITRVKGSERVPILLVANKLD------LASHQREVPTLDGQALAQSW 240
H I +M E + +P L+V K D LA +++ + +
Sbjct: 92 RHGPTPIDLEMLEFL----EELGIPFLIVLTKADKLKKSELAKVLKKIKE---ELNLFNI 144
Query: 241 GCPFIEASAKNKTNVNEMFAEI 262
P I S+K T ++E+ A I
Sbjct: 145 LPPVILFSSKKGTGIDELRALI 166
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 29.9 bits (68), Expect = 1.4
Identities = 16/65 (24%), Positives = 30/65 (46%), Gaps = 12/65 (18%)
Query: 206 GSERVPILLVANKLDLASHQ---REVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEI 262
G++ +PI+LV NK+DL + E+ + FI SAK ++ + I
Sbjct: 301 GADEIPIILVLNKIDLLEDEEILAELERGSPNPV-------FI--SAKTGEGLDLLRERI 351
Query: 263 VREMN 267
+ ++
Sbjct: 352 IELLS 356
>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 = 28.8 bits (64), Expect = 2.4
Identities = 40/147 (27%), Positives = 61/147 (41%), Gaps = 16/147 (10%)
Query: 106 KVVVLGSGGVGKSALTVQFVSGCFMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAGTEQF 165
+VV LG G GK+ + + FM+ PTI F + +E I D G +
Sbjct: 1 RVVTLGLDGAGKTTILFKLKQDEFMQPI-PTI-GFNVETVEYKNLK--FTIWDVGGKHKL 56
Query: 166 ASMRDLYIKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKGSE-RVPILLV-ANKLDLA- 222
+ Y N Q VV+ + + H + + EL + E R +LL+ ANK D+A
Sbjct: 57 RPLWKHYYLNTQA--VVFVIDSSHRDRVSEAHSELAKLLTEKELRDALLLIFANKQDVAG 114
Query: 223 ----SHQREVPTLDGQALAQSW---GC 242
E+ +L +SW GC
Sbjct: 115 ALSVEEMTELLSLHKLCCGRSWYIQGC 141
>gnl|CDD|234988 PRK01889, PRK01889, GTPase RsgA; Reviewed.
Length = 356
Score = 29.1 bits (66), Expect = 2.5
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 107 VVVLGSGGVGKSALT 121
V +LGS GVGKS L
Sbjct: 198 VALLGSSGVGKSTLV 212
>gnl|CDD|223455 COG0378, HypB, Ni2+-binding GTPase involved in regulation of
expression and maturation of urease and hydrogenase
[Posttranslational modification, protein turnover,
chaperones / Transcription].
Length = 202
Score = 28.7 bits (65), Expect = 2.5
Identities = 14/57 (24%), Positives = 23/57 (40%), Gaps = 1/57 (1%)
Query: 213 LLVANKLDLASH-QREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREMNF 268
LLV NK DLA + ++ + A + P I + K ++E I +
Sbjct: 146 LLVINKTDLAPYVGADLEVMARDAKEVNPEAPIIFTNLKTGEGLDEWLRFIEPQALL 202
>gnl|CDD|234175 TIGR03348, VI_IcmF, type VI secretion protein IcmF. Members of
this protein family are IcmF homologs and tend to be
associated with type VI secretion systems [Cellular
processes, Pathogenesis].
Length = 1169
Score = 29.2 bits (66), Expect = 2.8
Identities = 17/60 (28%), Positives = 21/60 (35%), Gaps = 14/60 (23%)
Query: 209 RVPILLVANKLDLASHQREVP-------TLDGQALAQSWGCPFIEASAKNKTNVNEMFAE 261
R P+ LV K DL + LD + Q WG F A + E FA
Sbjct: 243 RFPVYLVLTKADL------LAGFEEFFADLDAEEREQVWGFTFPLDEADDDNAA-EEFAA 295
>gnl|CDD|226458 COG3949, COG3949, Uncharacterized membrane protein [Function
unknown].
Length = 349
Score = 28.8 bits (65), Expect = 3.0
Identities = 12/69 (17%), Positives = 24/69 (34%), Gaps = 15/69 (21%)
Query: 35 SISKFPIPMGREMEIYAYYQGLVTIEV---------CHLLYKISS------HTASWSLFV 79
+ + IP+ + ++ GLV + L+Y ++S W +
Sbjct: 239 KVVNYDIPLLTIAKNFSPLIGLVMSVIIWLEIYTTTVGLIYGLASRLTSFFPRRYWIIAA 298
Query: 80 ILSVFLVPT 88
I+ V P
Sbjct: 299 IILVIAYPL 307
>gnl|CDD|236563 PRK09554, feoB, ferrous iron transport protein B; Reviewed.
Length = 772
Score = 29.3 bits (66), Expect = 3.1
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 210 VPILLVANKLDLASHQREVPTLDGQALAQSWGCPFI 245
+P ++ N LD+A Q +D AL+ GCP I
Sbjct: 113 IPCIVALNMLDIAEKQN--IRIDIDALSARLGCPVI 146
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 28.6 bits (65), Expect = 3.4
Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 2/52 (3%)
Query: 207 SERVPILLVANKLDLASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEM 258
+ + ++V NK+DL E L AL ++ G +E SAK ++E+
Sbjct: 109 ANGIKPIIVLNKIDLLDDLEEAREL--LALYRAIGYDVLELSAKEGEGLDEL 158
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 29.0 bits (66), Expect = 3.6
Identities = 22/85 (25%), Positives = 36/85 (42%), Gaps = 32/85 (37%)
Query: 210 VPILLVA-NKLD------------LASHQREVPTLDGQALAQSWG--CPFIEASAKNKTN 254
VPI+ VA NK+D L+ + + + + WG F+ SAK
Sbjct: 349 VPII-VAINKIDKPGANPDRVKQELSEY--GL-------VPEEWGGDTIFVPVSAKTGEG 398
Query: 255 VNEMF------AEIVREMNFNPEKD 273
++E+ AE V E+ NP++
Sbjct: 399 IDELLEAILLQAE-VLELKANPDRP 422
>gnl|CDD|206749 cd01856, YlqF, Circularly permuted YlqF GTPase. Proteins of the
YlqF family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases. The YlqF subfamily is represented in all
eukaryotes as well as a phylogenetically diverse array
of bacteria (including gram-positive bacteria,
proteobacteria, Synechocystis, Borrelia, and
Thermotoga).
Length = 171
Score = 28.3 bits (64), Expect = 3.7
Identities = 19/72 (26%), Positives = 29/72 (40%), Gaps = 18/72 (25%)
Query: 211 PILLVANKLDLASHQREVPTLDGQALAQSW-------GCPFIEASAKNKTNVNEMFAEIV 263
P L+V NK DLA D + W G P + +AKN V ++ +
Sbjct: 48 PRLIVLNKADLA---------DPAKTKK-WLKYFKSQGEPVLFVNAKNGKGVKKL-LKKA 96
Query: 264 REMNFNPEKDNA 275
+++ EK A
Sbjct: 97 KKLLKENEKLKA 108
>gnl|CDD|206668 cd01881, Obg_like, Obg-like family of GTPases consist of five
subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1. The
Obg-like subfamily consists of five well-delimited,
ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210,
and NOG1. Four of these groups (Obg, DRG, YyaF/YchF, and
Ygr210) are characterized by a distinct glycine-rich
motif immediately following the Walker B motif (G3 box).
Obg/CgtA is an essential gene that is involved in the
initiation of sporulation and DNA replication in the
bacteria Caulobacter and Bacillus, but its exact
molecular role is unknown. Furthermore, several OBG
family members possess a C-terminal RNA-binding domain,
the TGS domain, which is also present in threonyl-tRNA
synthetase and in bacterial guanosine polyphosphatase
SpoT. Nog1 is a nucleolar protein that might function in
ribosome assembly. The DRG and Nog1 subfamilies are
ubiquitous in archaea and eukaryotes, the Ygr210
subfamily is present in archaea and fungi, and the Obg
and YyaF/YchF subfamilies are ubiquitous in bacteria and
eukaryotes. The Obg/Nog1 and DRG subfamilies appear to
form one major branch of the Obg family and the Ygr210
and YchF subfamilies form another branch. No GEFs, GAPs,
or GDIs for Obg have been identified.
Length = 167
Score = 27.7 bits (62), Expect = 4.4
Identities = 35/176 (19%), Positives = 63/176 (35%), Gaps = 26/176 (14%)
Query: 108 VVLGSGGVGKSALTVQFVSGCFMEKYDPTIED--FYRKEIEV----DKAPCVLEILDTAG 161
++G VGKS L + ++ I F E V ++I+D G
Sbjct: 1 GLVGLPNVGKSTL-LSALT-----SAKVEIASYPFTTLEPNVGVFEFGDGVDIQIIDLPG 54
Query: 162 TEQFAS---------MRDLYIKNGQGFVVVYS-LTNHHTFQDIKQMKELITRVK-GSERV 210
AS + LY + V+ S +D K + E ++ +
Sbjct: 55 LLDGASEGRGLGEQILAHLYRSDLILHVIDASEDCVGDPLEDQKTLNEEVSGSFLFLKNK 114
Query: 211 PILLVANKLDLASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREM 266
P ++VANK+D+AS + G P + SA + ++ + I + +
Sbjct: 115 PEMIVANKIDMAS--ENNLKRLKLDKLKR-GIPVVPTSALTRLGLDRVIRTIRKLL 167
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 28.5 bits (65), Expect = 4.5
Identities = 13/64 (20%), Positives = 24/64 (37%), Gaps = 1/64 (1%)
Query: 211 PILLVANKLDLASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEMFAEIVREMNFNP 270
P +LV NK+DL + E + G P SA ++E+ + +
Sbjct: 273 PRILVLNKIDLLD-EEEEREKRAALELAALGGPVFLISAVTGEGLDELLRALWELLEEAR 331
Query: 271 EKDN 274
++
Sbjct: 332 REEE 335
>gnl|CDD|219001 pfam06371, Drf_GBD, Diaphanous GTPase-binding Domain. This domain
is bound to by GTP-attached Rho proteins, leading to
activation of the Drf protein.
Length = 187
Score = 27.7 bits (62), Expect = 5.1
Identities = 7/18 (38%), Positives = 12/18 (66%)
Query: 255 VNEMFAEIVREMNFNPEK 272
+ ++F E++ EMN EK
Sbjct: 9 ILKLFEELMEEMNLPEEK 26
>gnl|CDD|216791 pfam01926, MMR_HSR1, 50S ribosome-binding GTPase. The full-length
GTPase protein is required for the complete activity of
the protein of interacting with the 50S ribosome and
binding of both adenine and guanine nucleotides, with a
preference for guanine nucleotide.
Length = 117
Score = 26.9 bits (60), Expect = 5.4
Identities = 31/132 (23%), Positives = 50/132 (37%), Gaps = 34/132 (25%)
Query: 106 KVVVLGSGGVGKS----ALT---VQFVS---GCFMEKYDPTIEDFYRKEIEVDKAPCVLE 155
+V ++G VGKS ALT V VS G T + + V +
Sbjct: 1 RVALVGRPNVGKSTLINALTGAKVAIVSDYPGT-------TRD----PILGVLGLGRQII 49
Query: 156 ILDTAG------TEQFASMRDLY---IKNGQGFVVVYSLTNHHTFQDIKQMKELITRVKG 206
++DT G + + + I+ ++V + T D + ++EL K
Sbjct: 50 LVDTPGLIEGASEGKGVEGFNRFLEAIREADLILLVVDASEGLTEDDEEILEELEKLPK- 108
Query: 207 SERVPILLVANK 218
PI+LV NK
Sbjct: 109 ---KPIILVLNK 117
>gnl|CDD|236185 PRK08205, sdhA, succinate dehydrogenase flavoprotein subunit;
Reviewed.
Length = 583
Score = 28.4 bits (64), Expect = 5.6
Identities = 14/33 (42%), Positives = 22/33 (66%), Gaps = 2/33 (6%)
Query: 129 FMEKYDPTIEDFYRKEIEVDKAPCVLEILDTAG 161
FME+Y PTI+D ++I V ++ VLE+ + G
Sbjct: 272 FMERYAPTIKDLAPRDI-VARS-MVLEVREGRG 302
>gnl|CDD|151981 pfam11545, HemeBinding_Shp, Cell surface heme-binding protein Shp.
Shp is part of a complex which functions in heme uptake
in Streptococcus pyogenes. During which, Shp transfers
its heme to HtsA which is a component of an ABC
transporter. The heme binding region of Shp contains an
immunoglobulin-like beta-sandwich fold and has a unique
heme-iron coordination with the axial ligands being two
methionine residues from the same Shp molecule.
Surrounding the heme pocket, there is a negative surface
which may serve as a docking interface for heme
transfer.
Length = 151
Score = 27.6 bits (61), Expect = 5.8
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 2/46 (4%)
Query: 13 GRGNENNLGT--IAIEVKSMVLIYSISKFPIPMGREMEIYAYYQGL 56
+G + N T IAI + ++ + S + PMGRE+ Y L
Sbjct: 92 QKGTDTNGTTLDIAISLPTVNSVVRGSMYVEPMGREVVFYLSPSEL 137
>gnl|CDD|181235 PRK08118, PRK08118, topology modulation protein; Reviewed.
Length = 167
Score = 27.7 bits (62), Expect = 5.9
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 106 KVVVLGSGGVGKSALTVQ 123
K++++GSGG GKS L Q
Sbjct: 3 KIILIGSGGSGKSTLARQ 20
>gnl|CDD|232787 TIGR00023, TIGR00023, acyl-phosphate glycerol 3-phosphate
acyltransferase. This model represents the full length
of acylphosphate:glycerol 3-phosphate acyltransferase,
and integral membrane protein about 200 amino acids in
length, called PlsY in Streptococcus pneumoniae, YneS
in Bacillus subtilis, and YgiH in E. coli. It is found
in a single copy in a large number of bacteria,
including the Mycoplasmas but not Mycobacteria or
spirochetes, for example. Its partner is PlsX (see
TIGR00182), and the pair can replace PlsB for
synthesizing 1-acylglycerol-3-phosphate [Fatty acid and
phospholipid metabolism, Biosynthesis].
Length = 196
Score = 27.7 bits (62), Expect = 5.9
Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 2/58 (3%)
Query: 7 KEIVSGGRGNENNLGTIAIEVKSMVLIYSISK--FPIPMGREMEIYAYYQGLVTIEVC 62
+E SG G N L T+ ++ +VLI+ I K + + + ++ + GLV I
Sbjct: 34 REHGSGNPGATNVLRTLGVKAALLVLIFDILKGMLAVALSFLLGLFDFLPGLVAIAAV 91
>gnl|CDD|238991 cd02034, CooC, The accessory protein CooC, which contains a
nucleotide-binding domain (P-loop) near the N-terminus,
participates in the maturation of the nickel center of
carbon monoxide dehydrogenase (CODH). CODH from
Rhodospirillum rubrum catalyzes the reversible oxidation
of CO to CO2. CODH contains a nickel-iron-sulfur cluster
(C-center) and an iron-sulfur cluster (B-center). CO
oxidation occurs at the C-center. Three accessory
proteins encoded by cooCTJ genes are involved in nickel
incorporation into a nickel site. CooC functions as a
nickel insertase that mobilizes nickel to apoCODH using
energy released from ATP hydrolysis. CooC is a homodimer
and has NTPase activities. Mutation at the P-loop
abolishs its function.
Length = 116
Score = 26.8 bits (60), Expect = 6.0
Identities = 7/16 (43%), Positives = 11/16 (68%)
Query: 106 KVVVLGSGGVGKSALT 121
K+ + G GGVGK+ +
Sbjct: 1 KIAITGKGGVGKTTIA 16
>gnl|CDD|213833 TIGR03596, GTPase_YlqF, ribosome biogenesis GTP-binding protein
YlqF. Members of this protein family are GTP-binding
proteins involved in ribosome biogenesis, including the
essential YlqF protein of Bacillus subtilis, which is an
essential protein. They are related to Era, EngA, and
other GTPases of ribosome biogenesis, but are circularly
permuted. This family is not universal, and is not
present in Escherichia coli, and so is not as well
studied as some other GTPases. This model is built for
bacterial members [Protein synthesis, Other].
Length = 276
Score = 27.9 bits (63), Expect = 6.5
Identities = 14/59 (23%), Positives = 21/59 (35%), Gaps = 17/59 (28%)
Query: 211 PILLVANKLDLASHQREVPTLDGQALAQSW-------GCPFIEASAKNKTNVNEMFAEI 262
P L+V NK DLA A+ + W G + +AK V ++
Sbjct: 50 PRLIVLNKADLAD----------PAVTKQWLKYFEEKGIKALAINAKKGKGVKKIIKAA 98
>gnl|CDD|206748 cd01855, YqeH, Circularly permuted YqeH GTPase. YqeH is an
essential GTP-binding protein. Depletion of YqeH induces
an excess initiation of DNA replication, suggesting that
it negatively controls initiation of chromosome
replication. The YqeH subfamily is common in eukaryotes
and sporadically present in bacteria with probable
acquisition by plants from chloroplasts. Proteins of the
YqeH family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases.
Length = 191
Score = 27.2 bits (61), Expect = 7.2
Identities = 21/80 (26%), Positives = 29/80 (36%), Gaps = 17/80 (21%)
Query: 191 FQDIKQMKELITRVKGSERVPILLVANKLDL----ASHQREVPTLDGQALAQSWGCPFIE 246
I + ELI P++LV NK+DL R + + G I+
Sbjct: 48 GSLIPGLAELIGAK------PVILVGNKIDLLPKDVKPNRLKQWVKKRLKI---GGLKIK 98
Query: 247 A----SAKNKTNVNEMFAEI 262
SAK V E+ EI
Sbjct: 99 DVILVSAKKGWGVEELIEEI 118
>gnl|CDD|178389 PLN02792, PLN02792, oxidoreductase.
Length = 536
Score = 28.0 bits (62), Expect = 7.6
Identities = 19/52 (36%), Positives = 24/52 (46%), Gaps = 7/52 (13%)
Query: 137 IEDFYRKEIEVDKAPCVLEILDTAGTEQFASMRDLYIKNGQGFVVVYSLTNH 188
I D+YR+ K ILD G + M D + NGQG VYS+T
Sbjct: 154 IGDWYRRNHTTLKK-----ILD--GGRKLPLMPDGVMINGQGVSYVYSITVD 198
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 27.5 bits (62), Expect = 7.7
Identities = 16/64 (25%), Positives = 27/64 (42%), Gaps = 3/64 (4%)
Query: 211 PILLVANKLDLASHQREVPTLDGQALAQSWGCPFIEASAKNKTNVNEM---FAEIVREMN 267
P ++V NK+DL + E+ L F SA + ++E+ AE++ E
Sbjct: 277 PRIVVLNKIDLPLDEEELEELKKALAEALGWEVFYLISALTREGLDELLRALAELLEETK 336
Query: 268 FNPE 271
E
Sbjct: 337 AEAE 340
>gnl|CDD|133443 cd01065, NAD_bind_Shikimate_DH, NAD(P) binding domain of Shikimate
dehydrogenase. Shikimate dehydrogenase (DH) is an amino
acid DH family member. Shikimate pathway links
metabolism of carbohydrates to de novo biosynthesis of
aromatic amino acids, quinones and folate. It is
essential in plants, bacteria, and fungi but absent in
mammals, thus making enzymes involved in this pathway
ideal targets for broad spectrum antibiotics and
herbicides. Shikimate DH catalyzes the reduction of
3-hydroshikimate to shikimate using the cofactor NADH.
Amino acid DH-like NAD(P)-binding domains are members of
the Rossmann fold superfamily and include glutamate,
leucine, and phenylalanine DHs, methylene
tetrahydrofolate DH, methylene-tetrahydromethanopterin
DH, methylene-tetrahydropholate DH/cyclohydrolase,
Shikimate DH-like proteins, malate oxidoreductases, and
glutamyl tRNA reductase. Amino acid DHs catalyze the
deamination of amino acids to keto acids with NAD(P)+ as
a cofactor. The NAD(P)-binding Rossmann fold superfamily
includes a wide variety of protein families including
NAD(P)- binding domains of alcohol DHs,
tyrosine-dependent oxidoreductases,
glyceraldehyde-3-phosphate DH, lactate/malate DHs,
formate/glycerate DHs, siroheme synthases,
6-phosphogluconate DHs, amino acid DHs, repressor rex,
NAD-binding potassium channel domain, CoA-binding, and
ornithine cyclodeaminase-like domains. These domains
have an alpha-beta-alpha configuration. NAD binding
involves numerous hydrogen and van der Waals contacts.
Length = 155
Score = 26.9 bits (60), Expect = 7.9
Identities = 6/15 (40%), Positives = 11/15 (73%)
Query: 106 KVVVLGSGGVGKSAL 120
KV++LG+GG ++
Sbjct: 21 KVLILGAGGAARAVA 35
>gnl|CDD|206691 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta), together with SR-alpha, forms the
heterodimeric signal recognition particle (SRP). Signal
recognition particle receptor, beta subunit (SR-beta).
SR-beta and SR-alpha form the heterodimeric signal
recognition particle (SRP or SR) receptor that binds SRP
to regulate protein translocation across the ER
membrane. Nascent polypeptide chains are synthesized
with an N-terminal hydrophobic signal sequence that
binds SRP54, a component of the SRP. SRP directs
targeting of the ribosome-nascent chain complex (RNC) to
the ER membrane via interaction with the SR, which is
localized to the ER membrane. The RNC is then
transferred to the protein-conducting channel, or
translocon, which facilitates polypeptide translation
across the ER membrane or integration into the ER
membrane. SR-beta is found only in eukaryotes; it is
believed to control the release of the signal sequence
from SRP54 upon binding of the ribosome to the
translocon. High expression of SR-beta has been observed
in human colon cancer, suggesting it may play a role in
the development of this type of cancer.
Length = 202
Score = 27.3 bits (61), Expect = 8.2
Identities = 33/125 (26%), Positives = 52/125 (41%), Gaps = 17/125 (13%)
Query: 107 VVVLGSGGVGKSALTVQFVSGCFMEKYDPT---IEDFYRKEIEVDKAPCVLEILDTAGTE 163
V++LG GK+AL + +G K T IE L ++D G E
Sbjct: 3 VLLLGPSDSGKTALFTKLTTG----KVRSTVTSIEPNVASFYSNSSKGKKLTLVDVPGHE 58
Query: 164 QFASMRDLYIKNG-QGFV-VVYSLTNHHTFQDIKQMKELITRV-----KGSERVPILLVA 216
+ Y+K + V VV S T ++I+ + E + + K ++PIL+
Sbjct: 59 KLRDKLLEYLKASLKAIVFVVDSATFQ---KNIRDVAEFLYDILTDLEKIKNKIPILIAC 115
Query: 217 NKLDL 221
NK DL
Sbjct: 116 NKQDL 120
>gnl|CDD|213835 TIGR03598, GTPase_YsxC, ribosome biogenesis GTP-binding protein
YsxC/EngB. Members of this protein family are a GTPase
associated with ribosome biogenesis, typified by YsxC
from Bacillus subutilis. The family is widely but not
universally distributed among bacteria. Members commonly
are called EngB based on homology to EngA, one of
several other GTPases of ribosome biogenesis. Cutoffs as
set find essentially all bacterial members, but also
identify large numbers of eukaryotic (probably
organellar) sequences. This protein is found in about 80
percent of bacterial genomes [Protein synthesis, Other].
Length = 178
Score = 27.0 bits (61), Expect = 8.3
Identities = 14/74 (18%), Positives = 29/74 (39%), Gaps = 15/74 (20%)
Query: 189 HTFQDI-KQMKELITRVKGSERVPILLVANKLD------LASHQREVPTLDGQALAQSWG 241
H +++ +M E + +P+L+V K D L +++ +AL +
Sbjct: 112 HPLKELDLEMIEWLRERG----IPVLIVLTKADKLKKSELNKQLKKI----KKALKKDAD 163
Query: 242 CPFIEASAKNKTNV 255
S+ KT +
Sbjct: 164 DSVQLFSSLKKTGI 177
>gnl|CDD|221398 pfam12056, DUF3537, Protein of unknown function (DUF3537). This
family of transmembrane proteins are functionally
uncharacterized. This protein is found in eukaryotes.
Proteins in this family are typically between 427 to 453
amino acids in length.
Length = 398
Score = 27.7 bits (62), Expect = 8.6
Identities = 21/65 (32%), Positives = 29/65 (44%), Gaps = 9/65 (13%)
Query: 73 ASWSLFVILSVFLVP--TDLLPRCSIDNSFTMREFKVVVLGSGGVGKSAL-TVQFVS-GC 128
SWS+F +L+V VP + L C + R F V+V S SA V F+
Sbjct: 28 LSWSVFFLLAV-AVPAISHFLLPCRDCDFDHRRPFDVLVQLS----LSAFAAVSFLCLSR 82
Query: 129 FMEKY 133
+ KY
Sbjct: 83 WFRKY 87
>gnl|CDD|237314 PRK13238, tnaA, tryptophanase/L-cysteine desulfhydrase,
PLP-dependent; Provisional.
Length = 460
Score = 27.5 bits (62), Expect = 9.3
Identities = 29/126 (23%), Positives = 47/126 (37%), Gaps = 47/126 (37%)
Query: 169 RDLYIKNGQGFVVVYSLTNHHTFQ---DIKQMKELITRVKGSERVP--ILLVANKLDLAS 223
DL I + H F+ D+++++ LI V G+E VP ++ + N + A
Sbjct: 141 VDLVIDEA------LDTGSRHPFKGNFDLEKLEALIEEV-GAENVPFIVMTITN--NSAG 191
Query: 224 HQ-------REVPTLDGQALAQSWGCPFI----------------EASAKNKTNVNEMFA 260
Q R V +A+ +G P + E K+K+
Sbjct: 192 GQPVSMANLRAV-----YEIAKKYGIPVVIDAARFAENAYFIKQREPGYKDKS-----IK 241
Query: 261 EIVREM 266
EI REM
Sbjct: 242 EIAREM 247
>gnl|CDD|238994 cd02037, MRP-like, MRP (Multiple Resistance and pH adaptation) is a
homologue of the Fer4_NifH superfamily. Like the other
members of the superfamily, MRP contains a ATP-binding
domain at the N-termini. It is found in bacteria as a
membrane-spanning protein and functions as a Na+/H+
antiporter.
Length = 169
Score = 26.7 bits (60), Expect = 9.5
Identities = 9/19 (47%), Positives = 12/19 (63%), Gaps = 1/19 (5%)
Query: 106 KVVVL-GSGGVGKSALTVQ 123
+ V+ G GGVGKS + V
Sbjct: 1 VIAVMSGKGGVGKSTVAVN 19
>gnl|CDD|181594 PRK08958, sdhA, succinate dehydrogenase flavoprotein subunit;
Reviewed.
Length = 588
Score = 27.4 bits (61), Expect = 9.8
Identities = 11/26 (42%), Positives = 17/26 (65%), Gaps = 1/26 (3%)
Query: 98 NSFTMREFKVVVLGSGGVG-KSALTV 122
+REF VV+G+GG G ++AL +
Sbjct: 1 MKLPVREFDAVVIGAGGAGMRAALQI 26
>gnl|CDD|238941 cd01983, Fer4_NifH, The Fer4_NifH superfamily contains a variety of
proteins which share a common ATP-binding domain.
Functionally, proteins in this superfamily use the
energy from hydrolysis of NTP to transfer electron or
ion.
Length = 99
Score = 26.2 bits (58), Expect = 9.9
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 106 KVVVLGSGGVGKSALTV 122
+VV G GGVGK+ L
Sbjct: 1 VIVVTGKGGVGKTTLAA 17
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
0.321 0.135 0.398
Gapped
Lambda K H
0.267 0.0555 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,280,469
Number of extensions: 1364533
Number of successful extensions: 1947
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1745
Number of HSP's successfully gapped: 180
Length of query: 286
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 190
Effective length of database: 6,679,618
Effective search space: 1269127420
Effective search space used: 1269127420
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 58 (26.5 bits)