RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8700
(200 letters)
>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 = 306 bits (785), Expect = e-108
Identities = 140/167 (83%), Positives = 152/167 (91%), Gaps = 2/167 (1%)
Query: 7 DYRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSH 66
DYRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISC+K+ICTLQITDTTGSH
Sbjct: 1 DYRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCSKSICTLQITDTTGSH 60
Query: 67 QFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKC 126
QFPAMQRLSISKGHAFILVYS TS+QSLEEL+PI+E+I E KG N L IPIMLVGNKC
Sbjct: 61 QFPAMQRLSISKGHAFILVYSITSKQSLEELKPIYELICEIKG--NNLEKIPIMLVGNKC 118
Query: 127 DETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLNLEK 173
DE+ +REVS++EG A A+ W C FMETSAKTNHNV+ELF ELLNLEK
Sbjct: 119 DESPSREVSSSEGAALARTWNCAFMETSAKTNHNVQELFQELLNLEK 165
>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 = 230 bits (590), Expect = 3e-78
Identities = 77/170 (45%), Positives = 102/170 (60%), Gaps = 4/170 (2%)
Query: 6 NDYRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGS 65
+Y++VV G GGVGKS+L ++FV+G F + Y PTIED+YR+ I + +C L I DT G
Sbjct: 1 REYKLVVLGGGGVGKSALTIQFVQGHFVDEYDPTIEDSYRKQIEIDGEVCLLDILDTAGQ 60
Query: 66 HQFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNK 125
+F AM+ + G F+LVYS T RQS EE+ E I K +PI+LVGNK
Sbjct: 61 EEFSAMRDQYMRTGEGFLLVYSITDRQSFEEIAKFREQILRVKD----RDDVPIVLVGNK 116
Query: 126 CDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLNLEKNR 175
CD R VS EG+ A+ WGC F+ETSAK NV E F +L+ +
Sbjct: 117 CDLENERVVSTEEGKELARQWGCPFLETSAKERINVDEAFYDLVREIRKS 166
>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 = 228 bits (584), Expect = 2e-77
Identities = 86/161 (53%), Positives = 106/161 (65%), Gaps = 4/161 (2%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSHQF 68
++VV GAGGVGKS+L +RFV G F E Y PTIED+YR+ I + TL I DT G +F
Sbjct: 1 KLVVLGAGGVGKSALTIRFVSGEFVEEYDPTIEDSYRKQIVVDGETYTLDILDTAGQEEF 60
Query: 69 PAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKCDE 128
AM+ I G FILVYS TSR+S EE++ I E I K + +PI+LVGNKCD
Sbjct: 61 SAMRDQYIRNGDGFILVYSITSRESFEEIKNIREQILRVKDKED----VPIVLVGNKCDL 116
Query: 129 TENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELL 169
R+VS EGEA A+ WGC F+ETSAKTN N+ ELF L+
Sbjct: 117 ENERQVSTEEGEALAEEWGCPFLETSAKTNINIDELFNTLV 157
>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 = 225 bits (576), Expect = 3e-76
Identities = 76/166 (45%), Positives = 103/166 (62%), Gaps = 4/166 (2%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSHQ 67
Y++VV G+GGVGKS+L ++F++G F + Y PTIED+YR+ I + +C L I DT G +
Sbjct: 1 YKLVVLGSGGVGKSALTIQFIQGHFVDDYDPTIEDSYRKQIEIDGEVCLLDILDTAGQEE 60
Query: 68 FPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKCD 127
F AM+ + G F+LVYS T RQS EE++ E I K +PI+LVGNKCD
Sbjct: 61 FSAMRDQYMRTGEGFLLVYSITDRQSFEEIKKFREQILRVKD----RDDVPIVLVGNKCD 116
Query: 128 ETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLNLEK 173
R VS EG+ A+ WGC F+ETSAK NV E F +L+ +
Sbjct: 117 LESERVVSTEEGKELARQWGCPFLETSAKERVNVDEAFYDLVREIR 162
>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 = 186 bits (476), Expect = 6e-61
Identities = 76/162 (46%), Positives = 95/162 (58%), Gaps = 6/162 (3%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTI-EDTYRQVISCNKNICTLQITDTTGSHQ 67
++V+ G GGVGKSSL++RF + F E YIPTI D Y + I + LQI DT G +
Sbjct: 1 KLVLVGDGGVGKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAGQER 60
Query: 68 FPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKCD 127
F A++ L F+LVY TSR S E ++ E I ++PI+LVGNKCD
Sbjct: 61 FRALRPLYYRGAQGFLLVYDITSRDSFENVKKWLEEILRHADE-----NVPIVLVGNKCD 115
Query: 128 ETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELL 169
+ R VS EGEA AK G FMETSAKTN NV+E F EL
Sbjct: 116 LEDQRVVSTEEGEALAKELGLPFMETSAKTNENVEEAFEELA 157
>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 = 183 bits (465), Expect = 2e-59
Identities = 81/162 (50%), Positives = 110/162 (67%), Gaps = 4/162 (2%)
Query: 7 DYRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSH 66
+Y+VVV G+GGVGKS+L ++FV GTF E Y PTIED YR+ I + + L+I DT G+
Sbjct: 1 EYKVVVLGSGGVGKSALTVQFVSGTFIEKYDPTIEDFYRKEIEVDSSPSVLEILDTAGTE 60
Query: 67 QFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKC 126
QF +M+ L I G FI+VYS ++Q+ ++++P+ + I KG +PI+LVGNK
Sbjct: 61 QFASMRDLYIKNGQGFIVVYSLVNQQTFQDIKPMRDQIVRVKG----YEKVPIILVGNKV 116
Query: 127 DETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAEL 168
D REVS+AEG A A+ WGC FMETSAK+ V ELFAE+
Sbjct: 117 DLESEREVSSAEGRALAEEWGCPFMETSAKSKTMVNELFAEI 158
>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 = 172 bits (438), Expect = 3e-55
Identities = 77/164 (46%), Positives = 109/164 (66%), Gaps = 5/164 (3%)
Query: 7 DYRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSH 66
+Y++VV G+GGVGKS+L ++FV+G F + Y PTIED+YR+ I + C L+I DT G+
Sbjct: 1 EYKLVVLGSGGVGKSALTVQFVQGIFVDKYDPTIEDSYRKQIEVDCQQCMLEILDTAGTE 60
Query: 67 QFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKC 126
QF AM+ L I G F LVYS T++QS +L+ + E I K + +P++LVGNKC
Sbjct: 61 QFTAMRDLYIKNGQGFALVYSITAQQSFNDLQDLREQILRVK----DTEDVPMILVGNKC 116
Query: 127 DETENREVSAAEGEAEAKMWG-CHFMETSAKTNHNVKELFAELL 169
D + R VS EG+ A+ WG C F+ETSAK+ NV E+F +L+
Sbjct: 117 DLEDERVVSKEEGQNLARQWGNCPFLETSAKSKINVDEIFYDLV 160
>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 = 171 bits (434), Expect = 1e-54
Identities = 76/164 (46%), Positives = 106/164 (64%), Gaps = 5/164 (3%)
Query: 7 DYRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSH 66
DY++VV GAGGVGKS+L ++FV+ F ESY PTIED+YR+ + + C L+I DT G+
Sbjct: 1 DYKIVVLGAGGVGKSALTVQFVQNVFIESYDPTIEDSYRKQVEIDGRQCDLEILDTAGTE 60
Query: 67 QFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKC 126
QF AM+ L I G F+LVYS TS SL EL + E + K N +P++LVGNK
Sbjct: 61 QFTAMRELYIKSGQGFLLVYSVTSEASLNELGELREQVLRIKDSDN----VPMVLVGNKA 116
Query: 127 DETENREVSAAEGEAEAKMWG-CHFMETSAKTNHNVKELFAELL 169
D ++R+VS +G + ++ WG F ETSA+ NV E+F +L+
Sbjct: 117 DLEDDRQVSREDGVSLSQQWGNVPFYETSARKRTNVDEVFIDLV 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 = 168 bits (427), Expect = 1e-53
Identities = 72/163 (44%), Positives = 107/163 (65%), Gaps = 4/163 (2%)
Query: 7 DYRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSH 66
+Y++VV G+GGVGKS+L ++FV+G F E Y PTIED+YR+ + + C L+I DT G+
Sbjct: 1 EYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDGQQCMLEILDTAGTE 60
Query: 67 QFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKC 126
QF AM+ L + G F+LVYS T++ + +L+ + E I K + +P++LVGNKC
Sbjct: 61 QFTAMRDLYMKNGQGFVLVYSITAQSTFNDLQDLREQILRVK----DTEDVPMILVGNKC 116
Query: 127 DETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELL 169
D + R V +G+ A+ WGC F+ETSAK NV E+F +L+
Sbjct: 117 DLEDERVVGKEQGQNLARQWGCAFLETSAKAKINVNEIFYDLV 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 = 164 bits (417), Expect = 7e-52
Identities = 78/193 (40%), Positives = 112/193 (58%), Gaps = 16/193 (8%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSHQF 68
++ V G+ VGKSSL ++FV+G F ESY PTIE+T+ ++I+ L+I DT G ++
Sbjct: 3 KIAVLGSRSVGKSSLTVQFVEGHFVESYYPTIENTFSKIITYKGQEYHLEIVDTAGQDEY 62
Query: 69 PAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKCDE 128
+ + H +ILVYS TSR+S E ++ I++ I + G S+PI+LVGNK D
Sbjct: 63 SILPQKYSIGIHGYILVYSVTSRKSFEVVKVIYDKILDMLG----KESVPIVLVGNKSDL 118
Query: 129 TENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLN-LEKNRNISLQLEKKGQL 187
R+VSA EG+ A+ WG F+E+SAK N NV+E F L+ +EK N +K
Sbjct: 119 HMERQVSAEEGKKLAESWGAAFLESSAKENENVEEAFELLIEEIEKVENPLPPGQKS--- 175
Query: 188 KGTRKLKEKCSVM 200
KCSVM
Sbjct: 176 --------KCSVM 180
>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 = 159 bits (403), Expect = 1e-49
Identities = 82/193 (42%), Positives = 112/193 (58%), Gaps = 4/193 (2%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSHQF 68
++VV G GGVGK++L ++ F E+Y PTIED+YR+ + + C L++ DT G ++
Sbjct: 1 KLVVLGDGGVGKTALTIQLCLNHFVETYDPTIEDSYRKQVVVDGQPCMLEVLDTAGQEEY 60
Query: 69 PAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKCDE 128
A++ I +G FILVYS TSR + E + E I+ K A +PIM+VGNKCD+
Sbjct: 61 TALRDQWIREGEGFILVYSITSRSTFERVERFREQIQRVK--DESAADVPIMIVGNKCDK 118
Query: 129 TENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLN-LEKNRNISLQLEKKGQL 187
REVS EG A A+ GC F+E SAKTN NV+ F L+ L + R Q K G
Sbjct: 119 VYEREVSTEEGAALARRLGCEFIEASAKTNVNVERAFYTLVRALRQQRQGG-QGPKGGPT 177
Query: 188 KGTRKLKEKCSVM 200
K K K KC +M
Sbjct: 178 KKKEKKKRKCVIM 190
>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 = 157 bits (398), Expect = 4e-48
Identities = 89/210 (42%), Positives = 116/210 (55%), Gaps = 27/210 (12%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSHQ 67
YR+VV GA VGK+++V RF+ G F E Y PTIED +R++ S + L I DT+G+H
Sbjct: 1 YRMVVLGASKVGKTAIVSRFLGGRFEEQYTPTIEDFHRKLYSIRGEVYQLDILDTSGNHP 60
Query: 68 FPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGA----NELASIPIMLVG 123
FPAM+RLSI G FILV+S +R+S EE+ + E I ETK E IP+++ G
Sbjct: 61 FPAMRRLSILTGDVFILVFSLDNRESFEEVCRLREQILETKSCLKNKTKENVKIPMVICG 120
Query: 124 NKCDETENREVSAAE-----GEAEAKMWGCHFMETSAKTNHNVKELFAELLNLEK----- 173
NK D REV E G E C + E SAK N N+ E+F L +L K
Sbjct: 121 NKADRDFPREVQRDEVEQLVGGDEN----CAYFEVSAKKNSNLDEMFRALFSLAKLPNEM 176
Query: 174 ----NRNISLQ----LEKKGQLKGTRKLKE 195
+R IS+Q L KK G+RK KE
Sbjct: 177 SPSLHRKISVQYGDALHKK-SRGGSRKRKE 205
>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 = 151 bits (382), Expect = 2e-46
Identities = 75/200 (37%), Positives = 109/200 (54%), Gaps = 13/200 (6%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSHQF 68
R+V GA GVGK++L+ RF+ TF + T+E+ + + T+ I DT+GS+ F
Sbjct: 1 RLVFMGAAGVGKTALIQRFLYDTFEPKHRRTVEELHSKEYEVAGVKVTIDILDTSGSYSF 60
Query: 69 PAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKCDE 128
PAM++LSI G AF LVYS +S EE++ + E I E K E +PI++VGNK D
Sbjct: 61 PAMRKLSIQNGDAFALVYSVDDPESFEEVKRLREEILEVK----EDKFVPIVVVGNKIDS 116
Query: 129 TENREVSAAEGEAEAKM-WGCHFMETSAKTNHNVKELFAELL---NLEKNRNISLQ---- 180
R+V AA+ + ++ W F+E SAK N NV E+F ELL NL + +L+
Sbjct: 117 LAERQVEAADALSTVELDWNNGFVEASAKDNENVTEVFKELLQQANLPSWLSPALRRRRE 176
Query: 181 -LEKKGQLKGTRKLKEKCSV 199
+ Q + CSV
Sbjct: 177 SAPSEIQRRPPMNKTNSCSV 196
>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 = 148 bits (376), Expect = 6e-46
Identities = 67/159 (42%), Positives = 87/159 (54%), Gaps = 6/159 (3%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTI-EDTYRQVISCNKNICTLQITDTTGSH 66
+++V+ G GVGK+SL+LRFV F E+Y TI D + I + LQI DT G
Sbjct: 1 FKIVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGVDFKSKTIEVDGKKVKLQIWDTAGQE 60
Query: 67 QFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKC 126
+F ++ H ILVY T+R+S E L W + E K A +IPI+LVGNK
Sbjct: 61 RFRSITSSYYRGAHGAILVYDVTNRESFENLD-KW--LNELKEYAPP--NIPIILVGNKS 115
Query: 127 DETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELF 165
D + R+VS E + AK G F ETSAKT NV E F
Sbjct: 116 DLEDERQVSTEEAQQFAKENGLLFFETSAKTGENVDEAF 154
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 148 bits (376), Expect = 1e-45
Identities = 75/185 (40%), Positives = 106/185 (57%), Gaps = 4/185 (2%)
Query: 5 SNDYRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTG 64
S +Y++VV G GGVGKS+L ++F++ F + Y PTIED+YR+ ++ C L I DT G
Sbjct: 3 STEYKLVVVGGGGVGKSALTIQFIQNHFIDEYDPTIEDSYRKQCVIDEETCLLDILDTAG 62
Query: 65 SHQFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGN 124
++ AM+ + G F+ VYS TSR S EE+ E I K + +P++LVGN
Sbjct: 63 QEEYSAMRDQYMRTGQGFLCVYSITSRSSFEEIASFREQILRVK----DKDRVPMILVGN 118
Query: 125 KCDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLNLEKNRNISLQLEKK 184
KCD R+VS EG+ AK +G F+ETSAK NV E F EL+ + +K
Sbjct: 119 KCDLDSERQVSTGEGQELAKSFGIPFLETSAKQRVNVDEAFYELVREIRKYLKEDMPSQK 178
Query: 185 GQLKG 189
+ KG
Sbjct: 179 QKKKG 183
>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 = 147 bits (374), Expect = 1e-45
Identities = 64/162 (39%), Positives = 98/162 (60%), Gaps = 5/162 (3%)
Query: 7 DYRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSH 66
+Y++VV GAGGVGKS+L ++ ++ F + Y PTIED+YR+ + + C L I DT G
Sbjct: 1 EYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQE 60
Query: 67 QFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKC 126
++ AM+ + G F+ V++ SR+S E++ E I+ K + +P++LVGNKC
Sbjct: 61 EYSAMRDQYMRTGEGFLCVFAINSRKSFEDIHTYREQIKRVK----DSDDVPMVLVGNKC 116
Query: 127 DETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAEL 168
D R VS +G+ AK +G ++ETSAKT V+E F L
Sbjct: 117 D-LAARTVSTRQGQDLAKSYGIPYIETSAKTRQGVEEAFYTL 157
>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 = 141 bits (358), Expect = 4e-43
Identities = 62/161 (38%), Positives = 88/161 (54%), Gaps = 4/161 (2%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSHQ 67
Y++VV G GGVGKS+L ++F++ F Y PTIED+Y + + L I DT G +
Sbjct: 3 YKLVVVGGGGVGKSALTIQFIQSYFVTDYDPTIEDSYTKQCEIDGQWARLDILDTAGQEE 62
Query: 68 FPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKCD 127
F AM+ + G F+LV+S T R S EE+ I K + P++LVGNK D
Sbjct: 63 FSAMREQYMRTGEGFLLVFSVTDRGSFEEVDKFHTQILRVK----DRDEFPMILVGNKAD 118
Query: 128 ETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAEL 168
R+VS EG+ A+ ++ETSAK NV + F +L
Sbjct: 119 LEHQRQVSREEGQELARQLKIPYIETSAKDRVNVDKAFHDL 159
>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 = 139 bits (353), Expect = 2e-42
Identities = 62/161 (38%), Positives = 93/161 (57%), Gaps = 4/161 (2%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSHQ 67
++V++ G+GGVGKS+L L+F+ F E Y PT D+YR+ + + L I DT G
Sbjct: 1 HKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEVQLNILDTAGQED 60
Query: 68 FPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKCD 127
+ A++ G F+LV+S T +S L E I K E ++P++LVGNKCD
Sbjct: 61 YAAIRDNYFRSGEGFLLVFSITDMESFTALAEFREQILRVK----EDDNVPLLLVGNKCD 116
Query: 128 ETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAEL 168
+ R+VS E A+ WG +++ETSAKT NV ++F +L
Sbjct: 117 LEDKRQVSVEEAANLAEQWGVNYVETSAKTRANVDKVFFDL 157
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 136 bits (345), Expect = 5e-41
Identities = 67/169 (39%), Positives = 92/169 (54%), Gaps = 6/169 (3%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYR-QVISCNKNICTLQITDTTGSH 66
+++++ G GVGKSSL+ RF G F E Y TI ++ + I + LQI DT G
Sbjct: 1 FKIILIGDSGVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIEVDGKRVKLQIWDTAGQE 60
Query: 67 QFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKC 126
+F ++ +LVY T+R+S E L W ++E + A+ ++ IMLVGNK
Sbjct: 61 RFRSITSSYYRGAVGALLVYDITNRESFENLEN-W--LKELREYASP--NVVIMLVGNKS 115
Query: 127 DETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLNLEKNR 175
D E R+VS E EA A+ G F ETSAKTN NV+E F EL R
Sbjct: 116 DLEEQRQVSREEAEAFAEEHGLPFFETSAKTNTNVEEAFEELAREILKR 164
>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 = 125 bits (316), Expect = 9e-37
Identities = 59/162 (36%), Positives = 86/162 (53%), Gaps = 6/162 (3%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTY-RQVISCNKNICTLQITDTTGSH 66
+++V+ G VGKSS+VLRFVK F E+ TI + Q ++ + +I DT G
Sbjct: 2 FKLVLLGDSSVGKSSIVLRFVKNEFSENQESTIGAAFLTQTVNLDDTTVKFEIWDTAGQE 61
Query: 67 QFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKC 126
++ ++ + A I+VY TS +S E+ + W ++E + +I I L GNK
Sbjct: 62 RYRSLAPMYYRGAAAAIVVYDITSEESFEKAKS-W--VKELQEHGPP--NIVIALAGNKA 116
Query: 127 DETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAEL 168
D R+VS E + A G FMETSAKT NV ELF E+
Sbjct: 117 DLESKRQVSTEEAQEYADENGLLFMETSAKTGENVNELFTEI 158
>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 = 122 bits (308), Expect = 2e-35
Identities = 62/163 (38%), Positives = 88/163 (53%), Gaps = 6/163 (3%)
Query: 10 VVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSHQFP 69
+ V GA GVGKS+L +RF+ F Y P +E Y + ++ + +L+I DT G Q
Sbjct: 2 IAVLGASGVGKSALTVRFLTKRFIGEYEPNLESLYSRQVTIDGEQVSLEIQDTPGQQQNE 61
Query: 70 AMQRL--SISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKCD 127
+ L S+ F+LVYS T R S + + + ++IRE K E IP++LVGNK D
Sbjct: 62 DPESLERSLRWADGFVLVYSITDRSSFDVVSQLLQLIREIKKRDGE---IPVILVGNKAD 118
Query: 128 ETENREVSAAEGEAEAKMWGCHFMETSAKTN-HNVKELFAELL 169
+R+VS EG+ A GC F E SA N V+ +F EL
Sbjct: 119 LLHSRQVSTEEGQKLALELGCLFFEVSAAENYLEVQNVFHELC 161
>gnl|CDD|206712 cd04141, Rit_Rin_Ric, Ras-like protein in all tissues (Rit),
Ras-like protein in neurons (Rin) and Ras-related
protein which interacts with calmodulin (Ric). Rit
(Ras-like protein in all tissues), Rin (Ras-like protein
in neurons) and Ric (Ras-related protein which interacts
with calmodulin) form a subfamily with several unique
structural and functional characteristics. These
proteins all lack a the C-terminal CaaX lipid-binding
motif typical of Ras family proteins, and Rin and Ric
contain calmodulin-binding domains. Rin, which is
expressed only in neurons, induces neurite outgrowth in
rat pheochromocytoma cells through its association with
calmodulin and its activation of endogenous Rac/cdc42.
Rit, which is ubiquitously expressed in mammals,
inhibits growth-factor withdrawl-mediated apoptosis and
induces neurite extension in pheochromocytoma cells. Rit
and Rin are both able to form a ternary complex with
PAR6, a cell polarity-regulating protein, and Rac/cdc42.
This ternary complex is proposed to have physiological
function in processes such as tumorigenesis. Activated
Ric is likely to signal in parallel with the Ras pathway
or stimulate the Ras pathway at some upstream point, and
binding of calmodulin to Ric may negatively regulate Ric
activity.
Length = 172
Score = 121 bits (306), Expect = 3e-35
Identities = 57/158 (36%), Positives = 87/158 (55%), Gaps = 4/158 (2%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSHQ 67
Y++V+ GAGGVGKS++ ++F+ +F + + PTIED Y+ + L I DT G +
Sbjct: 3 YKIVMLGAGGVGKSAVTMQFISHSFPDYHDPTIEDAYKTQARIDNEPALLDILDTAGQAE 62
Query: 68 FPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKCD 127
F AM+ + G FI+ YS T R S +E E+I + + IP++LVGNK D
Sbjct: 63 FTAMRDQYMRCGEGFIICYSVTDRHSFQEASEFKELITRVRLTED----IPLVLVGNKVD 118
Query: 128 ETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELF 165
+ R+V+ EG A+ + C F ETSA + + F
Sbjct: 119 LEQQRQVTTEEGRNLAREFNCPFFETSAALRFYIDDAF 156
>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 = 118 bits (298), Expect = 4e-34
Identities = 56/159 (35%), Positives = 86/159 (54%), Gaps = 6/159 (3%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTI-EDTYRQVISCNKNICTLQITDTTGSH 66
+++V G VGK+S++ RF+ TF Y TI D + + + LQ+ DT G
Sbjct: 1 HKLVFLGDQSVGKTSIITRFMYDTFDNQYQATIGIDFLSKTMYVDDKTVRLQLWDTAGQE 60
Query: 67 QFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKC 126
+F ++ I ++VY T+RQS + + +R+ +G + I+LVGNK
Sbjct: 61 RFRSLIPSYIRDSSVAVVVYDITNRQSFDNTDKWIDDVRDERG-----NDVIIVLVGNKT 115
Query: 127 DETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELF 165
D ++ R+VS EGE +AK F+ETSAK HNVK+LF
Sbjct: 116 DLSDKRQVSTEEGEKKAKENNAMFIETSAKAGHNVKQLF 154
>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 = 115 bits (291), Expect = 4e-33
Identities = 57/164 (34%), Positives = 82/164 (50%), Gaps = 6/164 (3%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYR-QVISCNKNICTLQITDTTGSH 66
++++ G GVGKSSL+LRF TF E TI ++ + ++ + L I DT G
Sbjct: 1 LKILLIGDSGVGKSSLLLRFTDDTFDEDLSSTIGVDFKVKTVTVDGKKVKLAIWDTAGQE 60
Query: 67 QFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKC 126
+F + ILVY T R + + L W + E + MLVGNK
Sbjct: 61 RFRTLTSSYYRGAQGVILVYDVTRRDTFDNL-DTW--LNELDTYSTN-PDAVKMLVGNKI 116
Query: 127 DETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLN 170
D+ ENREV+ EG+ A+ F+ETSAKT V++ F EL+
Sbjct: 117 DK-ENREVTREEGQKFARKHNMLFIETSAKTRIGVQQAFEELVE 159
>gnl|CDD|206659 cd01867, Rab8_Rab10_Rab13_like, Rab GTPase families 8, 10, 13
(Rab8, Rab10, Rab13). Rab8/Sec4/Ypt2 are known or
suspected to be involved in post-Golgi transport to the
plasma membrane. It is likely that these Rabs have
functions that are specific to the mammalian lineage and
have no orthologs in plants. Rab8 modulates polarized
membrane transport through reorganization of actin and
microtubules, induces the formation of new surface
extensions, and has an important role in directed
membrane transport to cell surfaces. The Ypt2 gene of
the fission yeast Schizosaccharomyces pombe encodes a
member of the Ypt/Rab family of small GTP-binding
proteins, related in sequence to Sec4p of Saccharomyces
cerevisiae but closer to mammalian Rab8. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 167
Score = 115 bits (291), Expect = 6e-33
Identities = 66/170 (38%), Positives = 90/170 (52%), Gaps = 8/170 (4%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTY--RQVISCNKNICTLQITDTTGS 65
+++++ G GVGKS L+LRF + +F S+I TI + R + K I LQI DT G
Sbjct: 4 FKLLLIGDSGVGKSCLLLRFSEDSFNPSFISTIGIDFKIRTIELDGKKI-KLQIWDTAGQ 62
Query: 66 HQFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNK 125
+F + ILVY T +S E ++ W +R A+E + MLVGNK
Sbjct: 63 ERFRTITTSYYRGAMGIILVYDITDEKSFENIKN-W--MRNIDEHASE--DVERMLVGNK 117
Query: 126 CDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLNLEKNR 175
CD E R VS EGEA A+ +G F+ETSAK N NV+E F L +
Sbjct: 118 CDMEEKRVVSKEEGEALAREYGIKFLETSAKANINVEEAFLTLAKDILKK 167
>gnl|CDD|206641 cd00157, Rho, Ras homology family (Rho) of small guanosine
triphosphatases (GTPases). Members of the Rho (Ras
homology) family include RhoA, Cdc42, Rac, Rnd, Wrch1,
RhoBTB, and Rop. There are 22 human Rho family members
identified currently. These proteins are all involved in
the reorganization of the actin cytoskeleton in response
to external stimuli. They also have roles in cell
transformation by Ras in cytokinesis, in focal adhesion
formation and in the stimulation of stress-activated
kinase. These various functions are controlled through
distinct effector proteins and mediated through a
GTP-binding/GTPase cycle involving three classes of
regulating proteins: GAPs (GTPase-activating proteins),
GEFs (guanine nucleotide exchange factors), and GDIs
(guanine nucleotide dissociation inhibitors). Most Rho
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. Since crystal structures
often lack C-terminal residues, this feature is not
available for annotation in many of the CDs in the
hierarchy.
Length = 171
Score = 114 bits (289), Expect = 1e-32
Identities = 51/172 (29%), Positives = 82/172 (47%), Gaps = 21/172 (12%)
Query: 10 VVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSHQFP 69
+VV G G VGK+ L++ + F Y+PT+ D Y ++ + L + DT G ++
Sbjct: 3 IVVVGDGAVGKTCLLISYTTNKFPTEYVPTVFDNYSANVTVDGKQVNLGLWDTAGQEEYD 62
Query: 70 AMQRLSISKGHAFILVYSCTSRQSLEELRPIW--EVIRETKGGANELASIPIMLVGNKCD 127
++ LS + F+L +S S S E ++ W E+ ++PI+LVG K D
Sbjct: 63 RLRPLSYPQTDVFLLCFSVDSPSSFENVKTKWYPEIKH-------YCPNVPIILVGTKID 115
Query: 128 -----------ETENREVSAAEGEAEAKMWGCH-FMETSAKTNHNVKELFAE 167
E + + ++ EGE AK G +ME SA T +KE+F E
Sbjct: 116 LRDDGNTLKKLEKKQKPITPEEGEKLAKEIGAVKYMECSALTQEGLKEVFDE 167
>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 = 113 bits (284), Expect = 6e-32
Identities = 59/163 (36%), Positives = 86/163 (52%), Gaps = 8/163 (4%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTY--RQVISCNKNICTLQITDTTGS 65
++VV+ G G VGK+SLVLR+V+ F E + T + ++ + V K I L I DT G
Sbjct: 1 FKVVLLGEGRVGKTSLVLRYVENKFNEKHESTTQASFFQKTVNIGGKRI-DLAIWDTAGQ 59
Query: 66 HQFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNK 125
++ A+ + ILVY T S ++++ W I+E K +I +++VGNK
Sbjct: 60 ERYHALGPIYYRDADGAILVYDITDADSFQKVK-KW--IKELKQMRGN--NISLVIVGNK 114
Query: 126 CDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAEL 168
D R VS +E E AK G ETSAKT ++ELF L
Sbjct: 115 IDLERQRVVSKSEAEEYAKSVGAKHFETSAKTGKGIEELFLSL 157
>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 = 111 bits (279), Expect = 1e-30
Identities = 65/186 (34%), Positives = 95/186 (51%), Gaps = 5/186 (2%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRES-YIPTIEDTYRQVISCNKNICTLQITDTTGSH 66
YRVV+ G GVGKSSL F G + +S Y + +DTY + +S + TL + D
Sbjct: 1 YRVVLLGDSGVGKSSLANIFTAGVYEDSAYEASGDDTYERTVSVDGEEATLVVYDHWEQE 60
Query: 67 QFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKC 126
++ + G A+++VYS T R S E+ + +R + IPI+LVGNK
Sbjct: 61 DGMWLEDSCMQVGDAYVIVYSVTDRSSFEKASELRIQLRRA----RQAEDIPIILVGNKS 116
Query: 127 DETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLNLEKNRNISLQLEKKGQ 186
D +REVS EG A A ++ C F+ETSA HNV ELF ++ + R S + +
Sbjct: 117 DLVRSREVSVQEGRACAVVFDCKFIETSAALQHNVDELFEGIVRQVRLRRDSKEKNTRRM 176
Query: 187 LKGTRK 192
R+
Sbjct: 177 ASRKRR 182
>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 = 109 bits (274), Expect = 2e-30
Identities = 58/161 (36%), Positives = 83/161 (51%), Gaps = 10/161 (6%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYR-QVISCNKNICTLQITDTTGSH 66
+++++ G GVGKS L+LRF T+ ESYI TI ++ + I + LQI DT G
Sbjct: 3 FKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTVKLQIWDTAGQE 62
Query: 67 QFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIW--EVIRETKGGANELASIPIMLVGN 124
+F + H I+VY T ++S ++ W E+ R N+L LVGN
Sbjct: 63 RFRTITSSYYRGAHGIIIVYDVTDQESFNNVKQ-WLQEIDRYASENVNKL------LVGN 115
Query: 125 KCDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELF 165
KCD T+ + V E + A G F+ETSAK NV+E F
Sbjct: 116 KCDLTDKKVVDYTEAKEFADELGIPFLETSAKNATNVEEAF 156
>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 = 107 bits (268), Expect = 1e-29
Identities = 65/161 (40%), Positives = 90/161 (55%), Gaps = 10/161 (6%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTI--EDTYRQVISCNKNICTLQITDTTGS 65
++ ++ G GVGKS L+L+F F+ + TI E R + K I LQI DT G
Sbjct: 5 FKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQI-KLQIWDTAGQ 63
Query: 66 HQFPAMQRLSISKGHA-FILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGN 124
F ++ R S +G A +LVY T R++ L W + + + +N +++ IML+GN
Sbjct: 64 ESFRSITR-SYYRGAAGALLVYDITRRETFNHL-TSW--LEDARQHSN--SNMTIMLIGN 117
Query: 125 KCDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELF 165
KCD REVS EGEA A+ G FMETSAKT NV+E F
Sbjct: 118 KCDLESRREVSYEEGEAFAREHGLIFMETSAKTASNVEEAF 158
>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 = 106 bits (268), Expect = 1e-29
Identities = 60/172 (34%), Positives = 86/172 (50%), Gaps = 22/172 (12%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTI--EDTYRQVISCNKNICTLQITDTTGS 65
+++V+ G GVGKS+L+ RF + F TI E R + K I QI DT G
Sbjct: 4 FKIVLIGDSGVGKSNLLSRFTRNEFNLDSKSTIGVEFATRTIQIDGKTI-KAQIWDTAGQ 62
Query: 66 HQFPAMQRLSISKGH------AFILVYSCTSRQSLEEL-RPIWEVIRETKGGANELASIP 118
++ A I+ + A LVY T + + E + R W ++E + A+ ++I
Sbjct: 63 ERYRA-----ITSAYYRGAVGAL-LVYDITKKSTFENVER--W--LKELRDHAD--SNIV 110
Query: 119 IMLVGNKCDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLN 170
IMLVGNK D R V E +A A+ G F+ETSA NV+E F +LL
Sbjct: 111 IMLVGNKSDLRHLRAVPTEEAKAFAEKNGLSFIETSALDGTNVEEAFKQLLT 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 = 101 bits (253), Expect = 3e-27
Identities = 49/173 (28%), Positives = 79/173 (45%), Gaps = 22/173 (12%)
Query: 10 VVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSHQFP 69
+VV G G VGK+ L++ + F E Y+PT+ + Y + + L + DT G +
Sbjct: 1 LVVVGDGAVGKTCLLIVYTTNAFPEDYVPTVFENYSADVEVDGKPVELGLWDTAGQEDYD 60
Query: 70 AMQRLSISKGHAFILVYSCTSRQSLEELRPIW--EVIRETKGGANELASIPIMLVGNKCD 127
++ LS F++ +S S S E ++ W EV +PI+LVG K D
Sbjct: 61 RLRPLSYPDTDVFLICFSVDSPASFENVKEKWYPEVKHFCPN-------VPIILVGTKLD 113
Query: 128 ------------ETENREVSAAEGEAEAKMWG-CHFMETSAKTNHNVKELFAE 167
+ + V+ +G+A AK G ++E SA T V+E+F E
Sbjct: 114 LRNDKSTLEELSKKKQEPVTYEQGQALAKRIGAVKYLECSALTQEGVREVFEE 166
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 101 bits (252), Expect = 9e-27
Identities = 61/211 (28%), Positives = 92/211 (43%), Gaps = 25/211 (11%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIE-DTYRQVISCNKNICTLQITDTTGSH 66
+++VV G GGVGK++L+ R V F E Y PTI + I + LQ+ DT G
Sbjct: 6 FKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQE 65
Query: 67 QFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIW-EVIRETKGGANELASIPIMLVGNK 125
++ +++ + ++VY T R+S +EL W E +RE +PI+LVGNK
Sbjct: 66 EYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAP-----DDVPILLVGNK 120
Query: 126 CDETENREVSAAEGEAEAKM---------------WGCHFMETSAK--TNHNVKELFAEL 168
D + + S + +ETSAK T NV ELF EL
Sbjct: 121 IDLFDEQSSSEEILNQLNREVVLLVLAPKAVLPEVANPALLETSAKSLTGPNVNELFKEL 180
Query: 169 LN-LEKNRNISLQLEKKGQLKGTRKLKEKCS 198
L L + + + QL E+ +
Sbjct: 181 LRKLLEEIEKLVLKNELRQLDRLNNPIEQAA 211
>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 = 100 bits (251), Expect = 9e-27
Identities = 57/209 (27%), Positives = 94/209 (44%), Gaps = 33/209 (15%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKN-ICTLQITDTTGSHQ 67
++VV G GG GK+ L++ + +G+F E Y+PT+ + Y + I L + DT G
Sbjct: 5 KIVVVGDGGCGKTCLLMVYAQGSFPEEYVPTVFENYVTTLQVPNGKIIELALWDTAGQED 64
Query: 68 FPAMQRLSISKGHAFILVYSCTSRQSLEELRPIW--EVIRETKGGANELASIPIMLVGNK 125
+ ++ LS ++ YS + SL+ + W EV G PI+LVG K
Sbjct: 65 YDRLRPLSYPDVDVILICYSVDNPTSLDNVEDKWYPEVNHFCPG-------TPIVLVGLK 117
Query: 126 CDETENRE------------VSAAEGEAEAKMWGC-HFMETSAKTNHNVKELFAELLNLE 172
D +++ V+ +GE+ AK G ++E SAK NV E+F +N+
Sbjct: 118 TDLRKDKNSVSKLRAQGLEPVTPEQGESVAKSIGAVAYIECSAKLMENVDEVFDAAINV- 176
Query: 173 KNRNISLQLEKKGQLKGTRKLKE-KCSVM 200
K +K K+ KC ++
Sbjct: 177 --------ALSKSGRAARKKKKKKKCVIL 197
>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 = 99 bits (249), Expect = 2e-26
Identities = 68/211 (32%), Positives = 96/211 (45%), Gaps = 31/211 (14%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTI-EDTYRQVISCNKNICTLQITDTTGSH 66
RV V GA GVGK+++V +F+ F E YIPT YR + + + L I D
Sbjct: 1 VRVAVLGAPGVGKTAIVRQFLAQEFPEEYIPTEHRRLYRPAVVLSGRVYDLHILD----- 55
Query: 67 QFPAMQRLSISKG--------------HAFILVYSCTSRQSLEELRPIWEVIRETKGGAN 112
P MQR + G AFILVY S S ++ + + I ET+ N
Sbjct: 56 -VPNMQRYPGTAGQEWMDPRFRGLRNSRAFILVYDICSPDSFHYVKLLRQQILETRPAGN 114
Query: 113 ELASIPIMLVGNKCDETENREVSA-AEGEAEAKMWGCHFMETSAKTNHNVKELFAELLN- 170
PI++VGNK D+ +R K W C ++E SAK N ++ LF ELL
Sbjct: 115 --KEPPIVVVGNKRDQQRHRFAPRHVLSVLVRKSWKCGYLECSAKYNWHILLLFKELLIS 172
Query: 171 -LEKNRNISLQLEKKGQLKGTRKLKEKCSVM 200
+ R+ L +G L +E+CS+M
Sbjct: 173 ATTRGRSTHPALRLQGALH-----RERCSIM 198
>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 = 96.8 bits (241), Expect = 1e-25
Identities = 58/170 (34%), Positives = 75/170 (44%), Gaps = 19/170 (11%)
Query: 11 VVFGAGGVGKSSLVLRFVKGTFRES---YIPTI-EDTYRQVISCNKNICTLQITDTTGSH 66
VV G GGVGKSSL+ + G E T D Y +K L + DT G
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYV--KELDKGKVKLVLVDTPGLD 58
Query: 67 QFPAMQ-----RLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIML 121
+F + RL + +LV T R+S E+ + + +G IPI+L
Sbjct: 59 EFGGLGREELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLRKEG-------IPIIL 111
Query: 122 VGNKCDETENREVSAAE-GEAEAKMWGCHFMETSAKTNHNVKELFAELLN 170
VGNK D E REV E AK+ G E SAKT V ELF +L+
Sbjct: 112 VGNKIDLLEEREVEELLRLEELAKILGVPVFEVSAKTGEGVDELFEKLIE 161
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 95.8 bits (238), Expect = 9e-25
Identities = 67/163 (41%), Positives = 88/163 (53%), Gaps = 10/163 (6%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTI--EDTYRQVISCNKNICTLQITDTTGS 65
++ ++ G GVGKS L+L+F F+ + TI E R + NK I LQI DT G
Sbjct: 7 FKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDNKPI-KLQIWDTAGQ 65
Query: 66 HQFPAMQRLSISKGHA-FILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGN 124
F ++ R S +G A +LVY T R++ L E R+ AN A++ IML+GN
Sbjct: 66 ESFRSITR-SYYRGAAGALLVYDITRRETFNHLASWLEDARQH---AN--ANMTIMLIGN 119
Query: 125 KCDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAE 167
KCD R VS EGE AK G FME SAKT NV+E F +
Sbjct: 120 KCDLAHRRAVSTEEGEQFAKEHGLIFMEASAKTAQNVEEAFIK 162
>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 = 93.4 bits (232), Expect = 5e-24
Identities = 61/200 (30%), Positives = 92/200 (46%), Gaps = 17/200 (8%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYR-QVISCNKNICTLQITDTTGSH 66
+++++ G GVGKSSL+LRF TF SYI TI ++ + + N LQI DT G
Sbjct: 7 FKLLIIGDSGVGKSSLLLRFADNTFSGSYITTIGVDFKIRTVEINGERVKLQIWDTAGQE 66
Query: 67 QFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKC 126
+F + H I+VY T+ +S ++ + I + +LVGNK
Sbjct: 67 RFRTITSTYYRGTHGVIVVYDVTNGESFVNVKRWLQEIE------QNCDDVCKVLVGNKN 120
Query: 127 DETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELF---------AELLNLEKNRNI 177
D+ E + V + A G ETSAK N NV+E+F A+ NL K +
Sbjct: 121 DDPERKVVETEDAYKFAGQMGISLFETSAKENINVEEMFNCITELVLRAKKDNLAKQQ-Q 179
Query: 178 SLQLEKKGQLKGTRKLKEKC 197
Q + K +++ K C
Sbjct: 180 QQQNDVVKLPKNSKRKKRCC 199
>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 = 92.2 bits (229), Expect = 1e-23
Identities = 55/171 (32%), Positives = 78/171 (45%), Gaps = 18/171 (10%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSHQF 68
+VVV G G GK+SL+ F +G F + Y PT+ + Y I + L + DT G +F
Sbjct: 2 KVVVLGDGACGKTSLLNVFTRGYFPQVYEPTVFENYIHDIFVDGLAVELSLWDTAGQEEF 61
Query: 69 PAMQRLSISKGHAFILVYSCTSRQSLEELRPIW--EVIRETKGGANELASIPIMLVGNKC 126
++ LS + H +L +S + SLE + W E+ G + ++LV KC
Sbjct: 62 DRLRSLSYADTHVIMLCFSVDNPDSLENVESKWLAEIRHHCPG-------VKLVLVALKC 114
Query: 127 DETENREVSAA--------EGEAEAKMWG-CHFMETSAKTNHNVKELFAEL 168
D E R EG A AK C ++E SAK N V E F E
Sbjct: 115 DLREPRNERDRGTHTISYEEGLAVAKRINACRYLECSAKLNRGVNEAFTEA 165
>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 = 90.6 bits (225), Expect = 3e-23
Identities = 56/160 (35%), Positives = 80/160 (50%), Gaps = 9/160 (5%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTY--RQV-ISCNKNICTLQITDTTGS 65
+V+V G G VGKSS++ RFVKG F + Y TI + +Q+ + + L + DT G
Sbjct: 2 KVIVVGNGNVGKSSMIQRFVKGIFTKDYKKTIGVDFLEKQIFLRQSDEDVRLMLWDTAGQ 61
Query: 66 HQFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNK 125
+F A+ + A ILV+S T R+S E + W+ E E IP++LV K
Sbjct: 62 EEFDAITKAYYRGAQACILVFSTTDRESFEAI-ESWKEKVE-----AECGDIPMVLVQTK 115
Query: 126 CDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELF 165
D + ++ E EA AK TS K + NV ELF
Sbjct: 116 IDLLDQAVITNEEAEALAKRLQLPLFRTSVKDDFNVTELF 155
>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 = 90.6 bits (225), Expect = 3e-23
Identities = 56/168 (33%), Positives = 85/168 (50%), Gaps = 13/168 (7%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTI--EDTYRQVISCNKNICTLQITDTTGS 65
+++++ G VGK+ +V RF GTF E TI + T + + K + LQI DT G
Sbjct: 4 FKIILIGDSNVGKTCVVQRFKSGTFSERQGNTIGVDFTMKTLEIQGKRV-KLQIWDTAGQ 62
Query: 66 HQFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETK--GGANELASIPIMLVG 123
+F + + + I+ Y T R S E + P W I E + G +N + ++L+G
Sbjct: 63 ERFRTITQSYYRSANGAIIAYDITRRSSFESV-PHW--IEEVEKYGASN----VVLLLIG 115
Query: 124 NKCDETENREVSAAEGEAEAKMWGCHF-METSAKTNHNVKELFAELLN 170
NKCD E REV E A+ +G +ETSAK + NV+E F +
Sbjct: 116 NKCDLEEQREVLFEEACTLAEHYGILAVLETSAKESSNVEEAFLLMAT 163
>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 = 90.7 bits (225), Expect = 6e-23
Identities = 62/194 (31%), Positives = 100/194 (51%), Gaps = 8/194 (4%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRE-SYIPTIEDTYR-QVISCNKNICTLQITDTTGS 65
++V++ G GVGK+ L++RF G F S+I T+ + +V++ + LQI DT G
Sbjct: 1 FKVMLVGDSGVGKTCLLVRFKDGAFLAGSFIATVGIQFTNKVVTVDGVKVKLQIWDTAGQ 60
Query: 66 HQFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNK 125
+F ++ HA +L+Y T++ S + +R I E + + IML+GNK
Sbjct: 61 ERFRSVTHAYYRDAHALLLLYDVTNKSSFDNIRAWLTEILEYAQ-----SDVVIMLLGNK 115
Query: 126 CDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLNLEKNRNISLQLEKKG 185
D + R V +GE AK +G FMETSAKT NV+ F + K+R++ E K
Sbjct: 116 ADMSGERVVKREDGERLAKEYGVPFMETSAKTGLNVELAFTAVAKELKHRSVEQPDEPKF 175
Query: 186 QLKG-TRKLKEKCS 198
+++ K K+
Sbjct: 176 KIQDYVEKQKKSSG 189
>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 = 89.4 bits (222), Expect = 7e-23
Identities = 62/165 (37%), Positives = 89/165 (53%), Gaps = 14/165 (8%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTI--EDTYRQVISCNKNICTLQITDTTGS 65
++ ++ G+ G GKS L+ +F++ F++ TI E R V K++ LQI DT G
Sbjct: 1 FKFLIIGSAGTGKSCLLHQFIENKFKQDSNHTIGVEFGSRVVNVGGKSV-KLQIWDTAGQ 59
Query: 66 HQFPAMQRLSISKGHA-FILVYSCTSRQSLEELRPIWEVIRETKGGANELAS--IPIMLV 122
+F ++ R S +G A +LVY TSR+S L W A LAS I I+LV
Sbjct: 60 ERFRSVTR-SYYRGAAGALLVYDITSRESFNALTN-W------LTDARTLASPDIVIILV 111
Query: 123 GNKCDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAE 167
GNK D ++REV+ E A+ G F+ETSA T NV+E F +
Sbjct: 112 GNKKDLEDDREVTFLEASRFAQENGLLFLETSALTGENVEEAFLK 156
>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 = 89.2 bits (221), Expect = 1e-22
Identities = 57/162 (35%), Positives = 83/162 (51%), Gaps = 6/162 (3%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIE-DTYRQVISCNKNICTLQITDTTGSH 66
+++V+ G GVGK+ LV RF +G F TI D + + LQI DT G
Sbjct: 8 FKIVLIGNAGVGKTCLVRRFTQGLFPPGQGATIGVDFMIKTVEIKGEKIKLQIWDTAGQE 67
Query: 67 QFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKC 126
+F ++ + +A IL Y T +S L P W +RE + AN + +LVGNK
Sbjct: 68 RFRSITQSYYRSANALILTYDITCEESFRCL-PEW--LREIEQYANN--KVITILVGNKI 122
Query: 127 DETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAEL 168
D E REVS E + +++ETSAK + NV++LF +L
Sbjct: 123 DLAERREVSQQRAEEFSDAQDMYYLETSAKESDNVEKLFLDL 164
>gnl|CDD|206655 cd01862, Rab7, Rab GTPase family 7 (Rab7). Rab7 subfamily. Rab7 is
a small Rab GTPase that regulates vesicular traffic from
early to late endosomal stages of the endocytic pathway.
The yeast Ypt7 and mammalian Rab7 are both involved in
transport to the vacuole/lysosome, whereas Ypt7 is also
required for homotypic vacuole fusion. Mammalian Rab7 is
an essential participant in the autophagic pathway for
sequestration and targeting of cytoplasmic components to
the lytic compartment. Mammalian Rab7 is also proposed
to function as a tumor suppressor. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 172
Score = 86.6 bits (215), Expect = 1e-21
Identities = 54/174 (31%), Positives = 84/174 (48%), Gaps = 25/174 (14%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTI-EDTYRQVISCNKNICTLQITDTTGSH 66
+V++ G GVGK+SL+ ++V F Y TI D + ++ + + TLQI DT G
Sbjct: 1 LKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVTVDDRLVTLQIWDTAGQE 60
Query: 67 QFPAMQRLSISKGHAF-------ILVYSCTSRQSLEELRPIWEVIRE---TKGGANELAS 116
+F S G AF +LVY T+ +S E L + R+ + + +
Sbjct: 61 RF-------QSLGVAFYRGADCCVLVYDVTNPKSFESL----DSWRDEFLIQASPRDPEN 109
Query: 117 IPIMLVGNKCDETENREVSAAEGEAEAKMWGC--HFMETSAKTNHNVKELFAEL 168
P +++GNK D E R+VS + + K G +F ETSAK NV + F +
Sbjct: 110 FPFVVLGNKIDLEEKRQVSTKKAQQWCKSKGNIPYF-ETSAKEAINVDQAFETI 162
>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 = 86.3 bits (214), Expect = 2e-21
Identities = 47/168 (27%), Positives = 78/168 (46%), Gaps = 18/168 (10%)
Query: 11 VVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSHQFPA 70
V+ G G VGK+SL++ + + Y+PT D + V+ + LQ+ DT G +F
Sbjct: 4 VLVGDGAVGKTSLIVSYTTNGYPTEYVPTAFDNFSVVVLVDGKPVRLQLCDTAGQDEFDK 63
Query: 71 MQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKCDETE 130
++ L F+L +S + S + + W I E + PI+LVG + D
Sbjct: 64 LRPLCYPDTDVFLLCFSVVNPSSFQNISEKW--IPEIRKH---NPKAPIILVGTQADLRT 118
Query: 131 N------------REVSAAEGEAEAKMWG-CHFMETSAKTNHNVKELF 165
+ + VS + +A A+ G C ++E SA T N+KE+F
Sbjct: 119 DVNVLIQLARYGEKPVSQSRAKALAEKIGACEYIECSALTQKNLKEVF 166
>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 = 85.9 bits (213), Expect = 2e-21
Identities = 50/166 (30%), Positives = 70/166 (42%), Gaps = 14/166 (8%)
Query: 6 NDYRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGS 65
D R+V+ G GVGKSSL++ V F E+ + + I DT+
Sbjct: 1 KDVRIVLIGDEGVGKSSLIMSLVSEEFPENVPRVLPE-ITIPADVTPERVPTTIVDTSSR 59
Query: 66 HQFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNK 125
Q A I K + LVYS +LE +R W + + + +PI+LVGNK
Sbjct: 60 PQDRANLAAEIRKANVICLVYSVDRPSTLERIRTKW--LPLIRRLGVK---VPIILVGNK 114
Query: 126 CDETENREVSAAEGEAEAKMWGCHF------METSAKTNHNVKELF 165
D + + E E M F +E SAKT NV E+F
Sbjct: 115 SDLRDGSSQAGLEEEMLPIM--NEFREIETCVECSAKTLINVSEVF 158
>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 = 86.0 bits (213), Expect = 4e-21
Identities = 56/163 (34%), Positives = 83/163 (50%), Gaps = 6/163 (3%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIE-DTYRQVISCNKNI-CTLQITDTTGS 65
+R++V G VGKSSL+ RF +G F E PT+ D + ++I + LQ+ DT G
Sbjct: 3 FRLIVIGDSTVGKSSLLKRFTEGRFAEVSDPTVGVDFFSRLIEIEPGVRIKLQLWDTAGQ 62
Query: 66 HQFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNK 125
+F ++ R +LV+ T+R+S E + E R +LVG+K
Sbjct: 63 ERFRSITRSYYRNSVGVLLVFDITNRESFEHVHDWLEEARSHIQPH----RPVFILVGHK 118
Query: 126 CDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAEL 168
CD R+V+ E E AK G ++ETSA+T NV+E F L
Sbjct: 119 CDLESQRQVTREEAEKLAKDLGMKYIETSARTGDNVEEAFELL 161
>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 = 82.5 bits (204), Expect = 1e-20
Identities = 35/119 (29%), Positives = 54/119 (45%), Gaps = 4/119 (3%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTY-RQVISCNKNICTLQITDTTGSHQ 67
+VVV G G GKSSL+ + V G F + DT + + + L I D G +
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREE 60
Query: 68 FPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKC 126
+ + A +LVY T R+SL E+ + + + + IP++LVGNK
Sbjct: 61 LKFEHIIFMKWADAILLVYDLTDRESLNEVSRLIAWLPNLRKLGGK---IPVILVGNKL 116
>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 = 84.0 bits (208), Expect = 2e-20
Identities = 54/170 (31%), Positives = 81/170 (47%), Gaps = 18/170 (10%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSHQF 68
++V+ G G GK+ L++ F K F E Y+PT+ + Y I + L + DT G +
Sbjct: 3 KLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDY 62
Query: 69 PAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNK--- 125
++ LS ++ +S S SLE + W E K + ++PI+LVGNK
Sbjct: 63 DRLRPLSYPDTDVILMCFSIDSPDSLENIPEKW--TPEVK---HFCPNVPIILVGNKKDL 117
Query: 126 -CDETENRE--------VSAAEGEAEAKMWGCH-FMETSAKTNHNVKELF 165
DE RE V EG A A+ G ++E SAKT V+E+F
Sbjct: 118 RNDEHTIRELAKMKQEPVKPEEGRAMAEKIGAFGYLECSAKTKEGVREVF 167
>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 = 84.3 bits (209), Expect = 2e-20
Identities = 57/202 (28%), Positives = 86/202 (42%), Gaps = 14/202 (6%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIE-DTYRQVISCNKN-ICTLQITDTTGS 65
++V+V G GVGK+S++ R+V G F + Y TI D +VI + N + LQ+ D G
Sbjct: 1 FKVLVIGDLGVGKTSIIKRYVHGVFSQHYKATIGVDFALKVIEWDPNTVVRLQLWDIAGQ 60
Query: 66 HQFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNK 125
+F M R+ I+V+ T + E + W+ ++K IP +L+ NK
Sbjct: 61 ERFGGMTRVYYKGAVGAIIVFDVTRPSTFEAVL-KWKADLDSKVTLPNGEPIPALLLANK 119
Query: 126 CDETENREVSAAEG----EAEAKMWGCHFMETSAKTNHNVKELFAELLNL----EKNRNI 177
CD + R E E G ETSAK N N++E L+ +K
Sbjct: 120 CDLKKERLAKDPEQMDQFCKENGFIGW--FETSAKENINIEEAMRFLVKNILKNDKGLQS 177
Query: 178 SLQLEKKG-QLKGTRKLKEKCS 198
E LK + S
Sbjct: 178 PEPDEDNVIDLKQETTTSKSKS 199
>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 = 83.1 bits (205), Expect = 2e-20
Identities = 54/165 (32%), Positives = 81/165 (49%), Gaps = 6/165 (3%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIE-DTYRQVISCNKNICTLQITDTTGSH 66
+R+++ G GVGK+ L+ RF F S+I TI D + I + +QI DT G
Sbjct: 1 FRLLLIGDSGVGKTCLLCRFTDNEFHSSHISTIGVDFKMKTIEVDGIKVRIQIWDTAGQE 60
Query: 67 QFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKC 126
++ + + + LVY +S +S + I + + + A E L+GNK
Sbjct: 61 RYQTITKQYYRRAQGIFLVYDISSERSYQH---IMKWVSDVDEYAPEGVQKI--LIGNKA 115
Query: 127 DETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLNL 171
DE + R+V +G AK +G F ETSA TN N+KE F L L
Sbjct: 116 DEEQKRQVGDEQGNKLAKEYGMDFFETSACTNKNIKESFTRLTEL 160
>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 = 83.2 bits (206), Expect = 2e-20
Identities = 51/164 (31%), Positives = 83/164 (50%), Gaps = 3/164 (1%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTY--RQVISCNKNICTLQITDTTGSH 66
+V+ G GVGKS ++ R+ +G F Y+PTI Y ++V NK + + D +G
Sbjct: 2 KVISMGNSGVGKSCIIKRYCEGRFVSKYLPTIGIDYGVKKVSVRNKEV-RVNFFDLSGHP 60
Query: 67 QFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKC 126
++ ++ +LVY T RQS E L + +++ G + +I +++ NK
Sbjct: 61 EYLEVRNEFYKDTQGVLLVYDVTDRQSFEALDSWLKEMKQEGGPHGNMENIVVVVCANKI 120
Query: 127 DETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLN 170
D T++R VS EG A+ G + ETSA T V E+F L +
Sbjct: 121 DLTKHRAVSEDEGRLWAESKGFKYFETSACTGEGVNEMFQTLFS 164
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 84.3 bits (208), Expect = 2e-20
Identities = 56/162 (34%), Positives = 80/162 (49%), Gaps = 5/162 (3%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYR-QVISCNKNICTLQITDTTGSH 66
+++++ G GVGKSSL++ F+ + E PTI ++ + ++ L I DT G
Sbjct: 15 FKILLIGDSGVGKSSLLVSFISSSV-EDLAPTIGVDFKIKQLTVGGKRLKLTIWDTAGQE 73
Query: 67 QFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKC 126
+F + ILVY T R++ L +W E + MLVGNK
Sbjct: 74 RFRTLTSSYYRNAQGIILVYDVTRRETFTNLSDVWGKEVELYSTNQDCVK---MLVGNKV 130
Query: 127 DETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAEL 168
D R+VS EG A AK GC F+E SAKT NV++ F EL
Sbjct: 131 DRESERDVSREEGMALAKEHGCLFLECSAKTRENVEQCFEEL 172
>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 = 82.6 bits (204), Expect = 4e-20
Identities = 49/166 (29%), Positives = 81/166 (48%), Gaps = 16/166 (9%)
Query: 11 VVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSHQFPA 70
V G G VGK+ +++ + TF Y+PT+ D + + + N L + DT G +
Sbjct: 5 VTVGDGAVGKTCMLISYTSNTFPTDYVPTVFDNFSANVVVDGNTVNLGLWDTAGQEDYNR 64
Query: 71 MQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKCDETE 130
++ LS F+L +S S+ S E + W I E + A +PI+LVG K D +
Sbjct: 65 LRPLSYRGADVFLLAFSLISKASYENVLKKW--IPELRHYA---PGVPIVLVGTKLDLRD 119
Query: 131 NRE----------VSAAEGEAEAKMWG-CHFMETSAKTNHNVKELF 165
+++ ++ A+GE K G ++E S+KT NVK +F
Sbjct: 120 DKQFFADHPGAVPITTAQGEELRKQIGAAAYIECSSKTQQNVKAVF 165
>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 = 81.9 bits (202), Expect = 6e-20
Identities = 52/166 (31%), Positives = 84/166 (50%), Gaps = 8/166 (4%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPT--IEDTYRQVISCNKNICTLQITDTTGS 65
+++++ G VGK+S + R+ +F +++ T I+ + V +K I LQI DT G
Sbjct: 2 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVYRNDKRI-KLQIWDTAGQ 60
Query: 66 HQFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNK 125
++ + FIL+Y T+ +S ++ W +T N ++LVGNK
Sbjct: 61 ERYRTITTAYYRGAMGFILMYDITNEESFNAVQD-WSTQIKTYSWDNA----QVILVGNK 115
Query: 126 CDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLNL 171
CD + R VSA G A G F E SAK N NVK++F L+++
Sbjct: 116 CDMEDERVVSAERGRQLADQLGFEFFEASAKENINVKQVFERLVDI 161
>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 = 81.3 bits (201), Expect = 1e-19
Identities = 41/169 (24%), Positives = 70/169 (41%), Gaps = 12/169 (7%)
Query: 7 DYRVVVFGAGGVGKSSLVLRFVKGT-FRESYIPTIEDTYR-QVISCNKNICTLQITDTTG 64
+ ++V+ G VGKS+L+ R + Y P Y VI + + DT G
Sbjct: 1 EIKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAG 60
Query: 65 SHQFPAMQRLSISKGHAFILVYSCTSRQ-SLEELRPIW--EVIRETKGGANELASIPIML 121
+ A++RL + + V+ +EE+ E+I + G +PI+L
Sbjct: 61 QEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAESG------VPIIL 114
Query: 122 VGNKCDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLN 170
VGNK D + ++ AK+ G + SA+T N+ F +
Sbjct: 115 VGNKID-LRDAKLKTHVAFLFAKLNGEPIIPLSAETGKNIDSAFKIVEA 162
>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 = 79.3 bits (195), Expect = 1e-18
Identities = 51/174 (29%), Positives = 82/174 (47%), Gaps = 22/174 (12%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSHQF 68
+ VV G G VGK+ L++ + F + YIPT+ D Y + + +L + DT G ++
Sbjct: 5 KCVVVGDGAVGKTCLLICYTTNAFPKEYIPTVFDNYSAQTAVDGRTVSLNLWDTAGQEEY 64
Query: 69 PAMQRLSISKGHAFILVYSCTSRQSLEELRPIW--EVIRETKGGANELASIPIMLVGNKC 126
++ LS + + FI+ +S S S E +R W EV + ++PI+LVG K
Sbjct: 65 DRLRTLSYPQTNVFIICFSIASPSSYENVRHKWHPEV-------CHHCPNVPILLVGTKK 117
Query: 127 DETENREV------------SAAEGEAEAKMWGC-HFMETSAKTNHNVKELFAE 167
D + + + +G A AK ++E SA VKE+FAE
Sbjct: 118 DLRNDADTLKKLKEQGQAPITPQQGGALAKQIHAVKYLECSALNQDGVKEVFAE 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 = 77.9 bits (192), Expect = 4e-18
Identities = 52/183 (28%), Positives = 84/183 (45%), Gaps = 19/183 (10%)
Query: 7 DY--RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQ---VISCNKNICT----- 56
DY +++ G GVGK++ + R+ F +I T+ +R+ V + T
Sbjct: 2 DYLIKLLALGDSGVGKTTFLYRYTDNKFNPKFITTVGIDFREKRVVYNSQGPDGTSGKAF 61
Query: 57 ---LQITDTTGSHQFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANE 113
LQ+ DT G +F ++ F+L++ TS QS +R ++ A+
Sbjct: 62 RVHLQLWDTAGQERFRSLTTAFFRDAMGFLLMFDLTSEQSFLNVRNWMSQLQ-----AHA 116
Query: 114 LASIP-IMLVGNKCDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLNLE 172
P I+L+GNK D + REVS + A +G + ETSA T NV++ LL+L
Sbjct: 117 YCENPDIVLIGNKADLPDQREVSERQARELADKYGIPYFETSAATGQNVEKAVETLLDLI 176
Query: 173 KNR 175
R
Sbjct: 177 MKR 179
>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 = 76.5 bits (188), Expect = 9e-18
Identities = 53/166 (31%), Positives = 81/166 (48%), Gaps = 4/166 (2%)
Query: 4 QSNDYRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTY-RQVISCNKNICTLQITDT 62
+S+ +V++ G GGVGKSSL+ R+V F TI + + + + + TLQI DT
Sbjct: 2 KSSLLKVILLGDGGVGKSSLMNRYVTNKFDTQLFHTIGVEFLNKDLEVDGHFVTLQIWDT 61
Query: 63 TGSHQFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLV 122
G +F +++ +L +S QS + L W+ E S P +++
Sbjct: 62 AGQERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLS-NWKKEFIYYADVKEPESFPFVIL 120
Query: 123 GNKCDETENREVSAAEGEAEAKMWGCH-FMETSAKTNHNVKELFAE 167
GNK D E R+VS E +A + G + + ETSAK NV F E
Sbjct: 121 GNKIDIPE-RQVSTEEAQAWCRDNGDYPYFETSAKDATNVAAAFEE 165
>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 = 76.4 bits (188), Expect = 1e-17
Identities = 53/162 (32%), Positives = 80/162 (49%), Gaps = 8/162 (4%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTY-RQVISCNKNICTLQITDTTGSH 66
++ ++ G GVGKS L+ +F + F TI + ++I N LQI DT G
Sbjct: 3 FKYIIIGDMGVGKSCLLHQFTEKKFMADCPHTIGVEFGTRIIEVNGQKIKLQIWDTAGQE 62
Query: 67 QFPAMQRLSISKGHA-FILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNK 125
+F A+ R S +G A ++VY T R + L W + + + N + I L+GNK
Sbjct: 63 RFRAVTR-SYYRGAAGALMVYDITRRSTYNHLSS-W--LTDARNLTN--PNTVIFLIGNK 116
Query: 126 CDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAE 167
D R+V+ E + A G F+E SAKT NV++ F E
Sbjct: 117 ADLEAQRDVTYEEAKQFADENGLLFLECSAKTGENVEDAFLE 158
>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 = 75.2 bits (185), Expect = 5e-17
Identities = 60/215 (27%), Positives = 92/215 (42%), Gaps = 24/215 (11%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIE-DTYRQVISCNKNI-CTLQITDTTGS 65
++VV G G GK+SL+ RF + F +SY TI D + + I+ ++ TLQ+ D G
Sbjct: 1 IKIVVLGDGASGKTSLIRRFAQEGFGKSYKQTIGLDFFSRRITLPGSLNVTLQVWDIGGQ 60
Query: 66 HQFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNK 125
M I A LVY T+ QS E L V++ K ++LVGNK
Sbjct: 61 QIGGKMLDKYIYGAQAVCLVYDITNSQSFENLEDWLSVVK--KVNEESETKPKMVLVGNK 118
Query: 126 CDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELF----AELLNLEKNR------ 175
D NR+V+A + A+ + SAKT V F AELL ++ ++
Sbjct: 119 TDLEHNRQVTAEKHARFAQENDMESIFVSAKTGDRVFLCFQRIAAELLGVKLSQAELEQS 178
Query: 176 -----NISLQLEKKGQLKGTRKLKEK-----CSVM 200
+ ++ + + K C+VM
Sbjct: 179 QRVVKADVSRYSERTLREPVSRSVNKRSNSMCAVM 213
>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 = 75.0 bits (184), Expect = 7e-17
Identities = 55/164 (33%), Positives = 90/164 (54%), Gaps = 7/164 (4%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYR-QVISCNKNICTLQITDTTGSHQ 67
+V++ G+ GVGK+SL+ RF TF E+ T+ ++ + + LQI DT G +
Sbjct: 2 QVIIIGSRGVGKTSLMERFTDDTFCEACKSTVGVDFKIKTVELRGKKIRLQIWDTAGQER 61
Query: 68 FPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKCD 127
F ++ ILVY T +++ ++L P W ++ A+E A ++LVGNK D
Sbjct: 62 FNSITSAYYRSAKGIILVYDITKKETFDDL-PKW--MKMIDKYASEDAE--LLLVGNKLD 116
Query: 128 ETENREVSAAEGEAEA-KMWGCHFMETSAKTNHNVKELFAELLN 170
+RE++ +GE A ++ G F E SAK N NV E+F +L++
Sbjct: 117 CETDREITRQQGEKFAQQITGMRFCEASAKDNFNVDEIFLKLVD 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 = 73.7 bits (181), Expect = 1e-16
Identities = 51/175 (29%), Positives = 82/175 (46%), Gaps = 24/175 (13%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYR-QVISCNKNICTLQITDTTGSHQ 67
+ VV G G VGK+ L++ + F YIPT+ D Y V+ K + L + DT G
Sbjct: 3 KCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPV-NLGLWDTAGQED 61
Query: 68 FPAMQRLSISKGHAFILVYSCTSRQSLEELRPIW--EVIRETKGGANELASIPIMLVGNK 125
+ ++ LS + F++ +S S S E +R W EV + + PI+LVG K
Sbjct: 62 YDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEV-------RHHCPNTPIILVGTK 114
Query: 126 CDETENRE------------VSAAEGEAEAKMWGC-HFMETSAKTNHNVKELFAE 167
D ++++ ++ +G A AK G ++E SA T +K +F E
Sbjct: 115 LDLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDE 169
>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 = 73.7 bits (181), Expect = 2e-16
Identities = 59/200 (29%), Positives = 84/200 (42%), Gaps = 20/200 (10%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRES-YIPTIEDTY-RQVISCNKNICTLQITDTTGSH 66
+VV+ G VGK+SLV R+V F Y TI + + + + + TL I DT GS
Sbjct: 2 KVVMLGKESVGKTSLVERYVHHRFLVGPYQNTIGAAFVAKRMVVGERVVTLGIWDTAGSE 61
Query: 67 QFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELAS----IPIMLV 122
++ AM R+ A I+ Y T S E + W EL + I L
Sbjct: 62 RYEAMSRIYYRGAKAAIVCYDLTDSSSFERAK-FW---------VKELQNLEEHCKIYLC 111
Query: 123 GNKCDETEN----REVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLNLEKNRNIS 178
G K D E R+V + + A ETS+KT NV ELF ++ +R +
Sbjct: 112 GTKSDLIEQDRSLRQVDFHDVQDFADEIKAQHFETSSKTGQNVDELFQKVAEDFVSRANN 171
Query: 179 LQLEKKGQLKGTRKLKEKCS 198
+KG G +K S
Sbjct: 172 QMNTEKGVDLGQKKNSYFYS 191
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 72.7 bits (178), Expect = 6e-16
Identities = 53/164 (32%), Positives = 85/164 (51%), Gaps = 8/164 (4%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTI--EDTYRQVISCNKNICTLQITDTTGS 65
+++V+ G GVGKS+++ RF + F TI E R + K + QI DT G
Sbjct: 13 FKIVLIGDSGVGKSNILSRFTRNEFCLESKSTIGVEFATRTLQVEGKTV-KAQIWDTAGQ 71
Query: 66 HQFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNK 125
++ A+ +LVY T RQ+ + ++ W +RE + A+ ++I IM+ GNK
Sbjct: 72 ERYRAITSAYYRGAVGALLVYDITKRQTFDNVQR-W--LRELRDHAD--SNIVIMMAGNK 126
Query: 126 CDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELL 169
D R V+ +G+A A+ G F+ETSA NV++ F +L
Sbjct: 127 SDLNHLRSVAEEDGQALAEKEGLSFLETSALEATNVEKAFQTIL 170
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 72.4 bits (178), Expect = 6e-16
Identities = 48/172 (27%), Positives = 88/172 (51%), Gaps = 13/172 (7%)
Query: 1 MPEQSNDYRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVI-SCNKNICTLQI 59
++ ++++++ G GGVGK++ V R + G F + YIPT+ + N +
Sbjct: 3 QMDEVPEFKLILVGDGGVGKTTFVKRHLTGEFEKKYIPTLGVEVHPLKFYTNCGPICFNV 62
Query: 60 TDTTGSHQFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIW--EVIRETKGGANELASI 117
DT G +F ++ KG I+++ TSR + + + P W +++R + +I
Sbjct: 63 WDTAGQEKFGGLRDGYYIKGQCAIIMFDVTSRITYKNV-PNWHRDIVRVCE-------NI 114
Query: 118 PIMLVGNKCDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELL 169
PI+LVGNK D ++R+V A + K + + SAK+N+N ++ F L
Sbjct: 115 PIVLVGNKVD-VKDRQVKARQITFHRKK-NLQYYDISAKSNYNFEKPFLWLA 164
>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 = 71.3 bits (175), Expect = 7e-16
Identities = 56/178 (31%), Positives = 83/178 (46%), Gaps = 21/178 (11%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQ--VISCNKNICTLQITDTTGS 65
++++V G VGK+ L RF G F E TI +R+ V + I +Q+ DT G
Sbjct: 3 FKIIVIGDSNVGKTCLTYRFCAGRFPERTEATIGVDFRERTVEIDGERI-KVQLWDTAGQ 61
Query: 66 HQFPAMQRLSISKG-----HAFILVYSCTSRQSLEELRPIWEVIRETKGGANELAS-IPI 119
+F R S+ + HA + VY T+ S L P W I E + + L + +P
Sbjct: 62 ERF----RKSMVQHYYRNVHAVVFVYDVTNMASFHSL-PSW--IEECEQ--HSLPNEVPR 112
Query: 120 MLVGNKCDETENREVSAAEGEAEAKMWGCHFMETSAK---TNHNVKELFAELLNLEKN 174
+LVGNKCD E +V + A ETSAK N +V+ +F L + K+
Sbjct: 113 ILVGNKCDLREQIQVPTDLAQRFADAHSMPLFETSAKDPSENDHVEAIFMTLAHKLKS 170
>gnl|CDD|206702 cd04129, Rho2, Ras homology family 2 (Rho2) of small guanosine
triphosphatases (GTPases). Rho2 is a fungal GTPase that
plays a role in cell morphogenesis, control of cell wall
integrity, control of growth polarity, and maintenance
of growth direction. Rho2 activates the protein kinase C
homolog Pck2, and Pck2 controls Mok1, the major (1-3)
alpha-D-glucan synthase. Together with Rho1 (RhoA), Rho2
regulates the construction of the cell wall. Unlike
Rho1, Rho2 is not an essential protein, but its
overexpression is lethal. Most Rho proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for proper intracellular localization via
membrane attachment. As with other Rho family GTPases,
the GDP/GTP cycling is regulated by GEFs (guanine
nucleotide exchange factors), GAPs (GTPase-activating
proteins) and GDIs (guanine nucleotide dissociation
inhibitors).
Length = 190
Score = 71.8 bits (176), Expect = 9e-16
Identities = 48/169 (28%), Positives = 79/169 (46%), Gaps = 18/169 (10%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSHQF 68
++V+ G G GK+SL+ F G F E Y PT+ + Y + L + DT G ++
Sbjct: 3 KLVIVGDGACGKTSLLYVFTLGEFPEEYHPTVFENYVTDCRVDGKPVQLALWDTAGQEEY 62
Query: 69 PAMQRLSISKGHAFILVYSCTSRQSLEELRPIW-EVIRETKGGANELASIPIMLVGNKCD 127
++ LS SK H ++ ++ + SLE +R W E +R ++P++LVG K D
Sbjct: 63 ERLRPLSYSKAHVILIGFAIDTPDSLENVRTKWIEEVRRYCP------NVPVILVGLKKD 116
Query: 128 ---ETENRE-------VSAAEGEAEAKMWGCH-FMETSAKTNHNVKELF 165
E + V + + A+ G +ME SA T V ++F
Sbjct: 117 LRQEAVAKGNYATDEFVPIQQAKLVARAIGAKKYMECSALTGEGVDDVF 165
>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 = 68.3 bits (167), Expect = 1e-14
Identities = 49/165 (29%), Positives = 70/165 (42%), Gaps = 9/165 (5%)
Query: 9 RVVVFGAGGVGKSSLVLRFVK--GTFRESYIPTI--EDTYRQV-ISCNKNICTLQITDTT 63
+ V G VGKS+LV F TF+++Y T + + V + + L I D+
Sbjct: 2 QCAVVGDPAVGKSALVQMFHSDGATFQKNYTMTTGCDLVVKTVPVPDTSDSVELFIFDSA 61
Query: 64 GSHQFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVG 123
G F M + +VY T+ S +R + P +LVG
Sbjct: 62 GQELFSDMVENVWEQPAVVCVVYDVTNEVSFNNCSRWINRVRT----HSHGLHTPGVLVG 117
Query: 124 NKCDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAEL 168
NKCD T+ REV AA+ +A A+ F ETSAK + F L
Sbjct: 118 NKCDLTDRREVDAAQAQALAQANTLKFYETSAKEGVGYEAPFLSL 162
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 67.5 bits (164), Expect = 3e-14
Identities = 51/151 (33%), Positives = 76/151 (50%), Gaps = 10/151 (6%)
Query: 31 TFRESYIPTIE-DTYRQVISCNKNICTLQITDTTGSHQFPAMQRLSISKGHAFILVYSCT 89
TF +Y TI D + + ++ LQ+ DT G +F ++ I A I+VY T
Sbjct: 4 TFDNNYQSTIGIDFLSKTLYLDEGPVRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDIT 63
Query: 90 SRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKCDETENREVSAAEGEAEAKMWGCH 149
+RQS E + I +G + I LVGNK D + R+V+ EG +A+ +
Sbjct: 64 NRQSFENTTKWIQDILNERG-----KDVIIALVGNKTDLGDLRKVTYEEGMQKAQEYNTM 118
Query: 150 FMETSAKTNHNVKELF----AELLNLEKNRN 176
F ETSAK HN+K LF A+L NL+ + +
Sbjct: 119 FHETSAKAGHNIKVLFKKIAAKLPNLDNSNS 149
>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 = 67.3 bits (164), Expect = 3e-14
Identities = 44/172 (25%), Positives = 81/172 (47%), Gaps = 18/172 (10%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSHQF 68
+ VV G G VGK+ L++ + F E Y+PT+ D Y ++ L + DT G +
Sbjct: 2 KCVVVGDGAVGKTCLLMSYANDAFPEEYVPTVFDHYAVSVTVGGKQYLLGLYDTAGQEDY 61
Query: 69 PAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKCD- 127
++ LS F++ +S + S + ++ W + E K A ++P +L+G + D
Sbjct: 62 DRLRPLSYPMTDVFLICFSVVNPASFQNVKEEW--VPELKEYA---PNVPYLLIGTQIDL 116
Query: 128 -----------ETENREVSAAEGEAEAKMWG-CHFMETSAKTNHNVKELFAE 167
+ + + ++ +G+ AK G C ++E SA T +K +F E
Sbjct: 117 RDDPKTLARLNDMKEKPITVEQGQKLAKEIGACCYVECSALTQKGLKTVFDE 168
>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 = 66.1 bits (161), Expect = 7e-14
Identities = 43/174 (24%), Positives = 74/174 (42%), Gaps = 22/174 (12%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSHQF 68
+ VV G G VGK+ L++ + F Y+PT+ D Y + TL + DT G +
Sbjct: 3 KCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTLGLFDTAGQEDY 62
Query: 69 PAMQRLSISKGHAFILVYSCTSRQSLEELRPIW--EVIRETKGGANELASIPIMLVGNKC 126
++ LS + F++ +S S S E ++ W E+ P +LVG +
Sbjct: 63 DRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCPK-------TPFLLVGTQI 115
Query: 127 D------------ETENREVSAAEGEAEAKMWGC-HFMETSAKTNHNVKELFAE 167
D + + + ++ GE A+ ++E SA T +K +F E
Sbjct: 116 DLRDDPSTIEKLAKNKQKPITPETGEKLARDLKAVKYVECSALTQKGLKNVFDE 169
>gnl|CDD|133326 cd04126, Rab20, Rab GTPase family 20 (Rab20). Rab20 is one of
several Rab proteins that appear to be restricted in
expression to the apical domain of murine polarized
epithelial cells. It is expressed on the apical side of
polarized kidney tubule and intestinal epithelial cells,
and in non-polarized cells. It also localizes to
vesico-tubular structures below the apical brush border
of renal proximal tubule cells and in the apical region
of duodenal epithelial cells. Rab20 has also been shown
to colocalize with vacuolar H+-ATPases (V-ATPases) in
mouse kidney cells, suggesting a role in the regulation
of V-ATPase traffic in specific portions of the nephron.
It was also shown to be one of several proteins whose
expression is upregulated in human myelodysplastic
syndrome (MDS) patients. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 220
Score = 64.2 bits (156), Expect = 9e-13
Identities = 64/229 (27%), Positives = 98/229 (42%), Gaps = 51/229 (22%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTY--RQVISCNKNICTLQITDTTGSH 66
+VV+ G VGK+SL+ R+++ F+++ + T+ + +Q N + I DT G
Sbjct: 2 KVVLLGDMNVGKTSLLHRYMERRFKDT-VSTVGGAFYLKQWGPYN-----ISIWDTAGRE 55
Query: 67 QFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKC 126
QF + + A IL Y ++ QSLEEL + + +T ANE +VGNK
Sbjct: 56 QFHGLGSMYCRGAAAVILTYDVSNVQSLEELEDRFLGLTDT---ANE--DCLFAVVGNKL 110
Query: 127 DETEN-------------------REVSAAEGEAEAKMWGCHFM--------------ET 153
D TE R+V+ + +A K + M ET
Sbjct: 111 DLTEEGALAGQEKDAGDRVSPEDQRQVTLEDAKAFYKRINKYKMLDEDLSPAAEKMCFET 170
Query: 154 SAKTNHNVKELFAELLNL-----EKNRNISLQLEKKGQLKGTRKLKEKC 197
SAKT +NV ELF L NL R + + + L ++ K KC
Sbjct: 171 SAKTGYNVDELFEYLFNLVLPLILAQRAEANRTQGTVNLPNPKRSKSKC 219
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 64.0 bits (156), Expect = 1e-12
Identities = 46/168 (27%), Positives = 79/168 (47%), Gaps = 13/168 (7%)
Query: 1 MPEQSNDYRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIE-DTYRQVISCNKNICTLQI 59
+++V+ G GG GK++ V R + G F + Y PTI + + N
Sbjct: 7 QTVDYPSFKLVIVGDGGTGKTTFVKRHLTGEFEKKYEPTIGVEVHPLDFFTNCGKIRFYC 66
Query: 60 TDTTGSHQFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIW--EVIRETKGGANELASI 117
DT G +F ++ G I+++ T+R + + + P W ++ R + +I
Sbjct: 67 WDTAGQEKFGGLRDGYYIHGQCAIIMFDVTARLTYKNV-PTWHRDLCRVCE-------NI 118
Query: 118 PIMLVGNKCDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELF 165
PI+L GNK D +NR+V A + K + E SAK+N+N ++ F
Sbjct: 119 PIVLCGNKVD-VKNRQVKAKQVTFHRKK-NLQYYEISAKSNYNFEKPF 164
>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 = 61.8 bits (150), Expect = 3e-12
Identities = 49/171 (28%), Positives = 80/171 (46%), Gaps = 17/171 (9%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTI----EDTYRQVISCNKNICTLQITDTTG 64
+V+V G VGK+ L+ RF K F ++Y TI E +V+ +LQ+ DT G
Sbjct: 2 KVIVVGDLSVGKTCLINRFCKDVFDKNYKATIGVDFEMERFEVLGVP---FSLQLWDTAG 58
Query: 65 SHQFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIW--EVIRETKGGANELASIPIMLV 122
+F + A I+V+ T SLE R W + ++E N+ +S+ + LV
Sbjct: 59 QERFKCIASTYYRGAQAIIIVFDLTDVASLEHTRQ-WLEDALKE-----NDPSSVLLFLV 112
Query: 123 GNKCDETENREVSAAEGEA--EAKMWGCHFMETSAKTNHNVKELFAELLNL 171
G K D + + + E +A A+ + SA T NV++ F + +L
Sbjct: 113 GTKKDLSSPAQYALMEQDAIKLAREMKAEYWAVSALTGENVRDFFFRVASL 163
>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 = 61.2 bits (149), Expect = 4e-12
Identities = 47/176 (26%), Positives = 86/176 (48%), Gaps = 14/176 (7%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIE-DTYRQVISCNKNICTLQITDTTGSH 66
+++V+ G GG GK++ V R + G F + Y+ T+ + + N+ + DT G
Sbjct: 1 FKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLDFHTNRGKIRFNVWDTAGQE 60
Query: 67 QFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIW--EVIRETKGGANELASIPIMLVGN 124
+F ++ +G I+++ TSR + + + P W +++R + +IPI+L GN
Sbjct: 61 KFGGLRDGYYIQGQCAIIMFDVTSRVTYKNV-PNWHRDLVRVCE-------NIPIVLCGN 112
Query: 125 KCDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLN-LEKNRNISL 179
K D + R+V + K + E SAK+N+N ++ F L L N N+
Sbjct: 113 KVDIKD-RKVKPKQITFHRKK-NLQYYEISAKSNYNFEKPFLWLARKLLGNPNLEF 166
>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 = 61.6 bits (149), Expect = 5e-12
Identities = 41/153 (26%), Positives = 74/153 (48%), Gaps = 9/153 (5%)
Query: 14 GAGGVGKSSLVLRFVKGTFRESYIPTIE-DTYRQVISCNKNICTLQITDTTGSHQFPAMQ 72
G GG GK++ V R + G F + Y+ T+ + + V N+ + DT G +F ++
Sbjct: 2 GDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIRFNVWDTAGQEKFGGLR 61
Query: 73 RLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKCDETENR 132
+G I+++ T+R + + + P W + +IPI+L GNK D ++R
Sbjct: 62 DGYYIQGQCAIIMFDVTARVTYKNV-PNWH-----RDLVRVCENIPIVLCGNKVD-VKDR 114
Query: 133 EVSAAEGEAEAKMWGCHFMETSAKTNHNVKELF 165
+V A K + + SAK+N+N ++ F
Sbjct: 115 KVKAKSITFHRKK-NLQYYDISAKSNYNFEKPF 146
>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 = 57.4 bits (138), Expect = 2e-10
Identities = 47/177 (26%), Positives = 83/177 (46%), Gaps = 21/177 (11%)
Query: 4 QSNDYRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTT 63
Q+ ++VV G GK++L+ F K F E+Y+PT+ + Y + L + DT+
Sbjct: 2 QNVKCKIVVVGDSQCGKTALLHVFAKDCFPENYVPTVFENYTASFEIDTQRIELSLWDTS 61
Query: 64 GSHQFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELA-SIPIMLV 122
GS + ++ LS A ++ + + ++L+ V+++ KG E + ++LV
Sbjct: 62 GSPYYDNVRPLSYPDSDAVLICFDISRPETLD------SVLKKWKGEIQEFCPNTKMLLV 115
Query: 123 GNKCD---------ETENRE---VSAAEGEAEAKMWGCH-FMETSAKTNHN-VKELF 165
G K D E N VS +G AK G ++E SA + N V+++F
Sbjct: 116 GCKSDLRTDVSTLVELSNHRQTPVSYDQGANMAKQIGAATYIECSALQSENSVRDIF 172
>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 = 56.9 bits (137), Expect = 3e-10
Identities = 51/178 (28%), Positives = 82/178 (46%), Gaps = 13/178 (7%)
Query: 4 QSNDY--RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQV-ISCNKNICTLQIT 60
++ DY + ++ G VGK ++ G+ Y + Y+ I + LQ+
Sbjct: 1 KAYDYLLKFLLVGDSDVGKGEILASLQDGSTESPYGYNMGIDYKTTTILLDGRRVKLQLW 60
Query: 61 DTTGSHQFPAMQRLSISKG-HAFILVYSCTSRQSLEEL-RPIWEVIRETKGGANELASIP 118
DT+G +F + R S S+G ILVY T+R S + + R I E+ G +P
Sbjct: 61 DTSGQGRFCTIFR-SYSRGAQGIILVYDITNRWSFDGIDRWIKEIDEHAPG-------VP 112
Query: 119 IMLVGNKCDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLNLEKNRN 176
+LVGN+ R+V+ + +A A+ G F E S N N+ E F EL + R+
Sbjct: 113 KILVGNRLHLAFKRQVATEQAQAYAERNGMTFFEVSPLCNFNITESFTELARIVLMRH 170
>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 = 56.2 bits (136), Expect = 3e-10
Identities = 39/163 (23%), Positives = 67/163 (41%), Gaps = 18/163 (11%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPT----IEDTYRQVISCNKNICTLQITDTTG 64
++++ G GGVGK+SL + + F T ++D K L + D G
Sbjct: 3 KLMLVGQGGVGKTSLCKQLIGEKFDGDESSTHGINVQDWKIPAPERKK--IRLNVWDFGG 60
Query: 65 SHQFPAMQRLSISKGHAFILVYSCTSRQSLEELR-PIWEVIRETKGGANELASIPIMLVG 123
+ A + ++ ++LV+ R E R P W + GG + P++LVG
Sbjct: 61 QEIYHATHQFFLTSRSLYLLVF--DLRTGDEVSRVPYWLRQIKAFGGVS-----PVILVG 113
Query: 124 NKCDETENREVS--AAEGEAEAKMWGCHFMETSAKTNHNVKEL 164
DE+ + ++ A + A + HF S K + EL
Sbjct: 114 THIDESCDEDILKKALNKKFPAIINDIHF--VSCKNGKGIAEL 154
>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 = 54.5 bits (131), Expect = 1e-09
Identities = 42/164 (25%), Positives = 67/164 (40%), Gaps = 10/164 (6%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDT-YRQVISCNKNICTLQITDTTGSHQ 67
++++ G VGKS LV RF+ + + T T Y+ + DT G +
Sbjct: 2 KIILLGDSAVGKSKLVERFLMDGYEPQQLSTYALTLYKHNAKFEGKTILVDFWDTAGQER 61
Query: 68 FPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKCD 127
F M K HA ILV+ T + + + L +E +RE + IP ++V NK D
Sbjct: 62 FQTMHASYYHKAHACILVFDVTRKITYKNLSKWYEELREYR------PEIPCIVVANKID 115
Query: 128 ETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLNL 171
+ + A+ SA NV +LF + + L
Sbjct: 116 LDPS---VTQKKFNFAEKHNLPLYYVSAADGTNVVKLFQDAIKL 156
>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 = 54.4 bits (131), Expect = 2e-09
Identities = 49/172 (28%), Positives = 87/172 (50%), Gaps = 21/172 (12%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSHQF 68
++V+ G GK++L+ F K +F E+Y+PT+ + Y +K L + DT+GS +
Sbjct: 3 KIVLVGDSQCGKTALLQVFAKDSFPENYVPTVFENYTASFEVDKQRIELSLWDTSGSPYY 62
Query: 69 PAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELA-SIPIMLVGNKCD 127
++ LS A ++ + + ++L+ V+++ KG E + P++LVG K D
Sbjct: 63 DNVRPLSYPDSDAVLICFDISRPETLD------SVLKKWKGEVREFCPNTPVLLVGCKSD 116
Query: 128 ---------ETENRE---VSAAEGEAEAKMWGCH-FMETSAKTNHN-VKELF 165
E N+ VS +G AK G ++E SAKT+ N V+++F
Sbjct: 117 LRTDLSTLTELSNKRQIPVSHEQGRNLAKQIGAAAYVECSAKTSENSVRDVF 168
>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 = 49.3 bits (118), Expect = 1e-07
Identities = 48/174 (27%), Positives = 81/174 (46%), Gaps = 18/174 (10%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTY-RQVISCNKNICTLQITDTTGSHQ 67
++ + G +GK+SL++++V+G F E YI T+ + + IS T I D G +
Sbjct: 2 KIGLLGDAQIGKTSLMVKYVEGEFDEEYIQTLGVNFMEKTISIRGTEITFSIWDLGGQRE 61
Query: 68 FPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKCD 127
F M L A + ++ T + +L I E R+ + G N+ A IPI LVG K D
Sbjct: 62 FINMLPLVCKDAVAILFMFDLTRKSTLNS---IKEWYRQAR-GFNKTA-IPI-LVGTKYD 115
Query: 128 E------TENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELF----AELLNL 171
E E++ + AK + S + NV+++F A++ +L
Sbjct: 116 LFADLPPEEQEEIT-KQARKYAKAMKAPLIFCSTSHSINVQKIFKFVLAKVFDL 168
>gnl|CDD|206736 cd04173, Rnd2_Rho7, Rnd2/Rho7 GTPases. Rnd2/Rho7 is a member of
the novel Rho subfamily Rnd, together with Rnd1/Rho6 and
Rnd3/RhoE/Rho8. Rnd2/Rho7 is transiently expressed in
radially migrating cells in the brain while they are
within the subventricular zone of the hippocampus and
cerebral cortex. These migrating cells typically develop
into pyramidal neurons. Cells that exogenously expressed
Rnd2/Rho7 failed to migrate to upper layers of the
brain, suggesting that Rnd2/Rho7 plays a role in the
radial migration and morphological changes of developing
pyramidal neurons, and that Rnd2/Rho7 degradation is
necessary for proper cellular migration. The Rnd2/Rho7
GEF Rapostlin is found primarily in the brain and
together with Rnd2/Rho7 induces dendrite branching.
Unlike Rnd1/Rho6 and Rnd3/RhoE/Rho8, which are RhoA
antagonists, Rnd2/Rho7 binds the GEF Pragmin and
significantly stimulates RhoA activity and Rho-A
mediated cell contraction. Rnd2/Rho7 is also found to be
expressed in spermatocytes and early spermatids, with
male-germ-cell Rac GTPase-activating protein
(MgcRacGAP), where it localizes to the Golgi-derived
pro-acrosomal vesicle. Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Length = 221
Score = 48.5 bits (115), Expect = 4e-07
Identities = 42/172 (24%), Positives = 83/172 (48%), Gaps = 21/172 (12%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSHQF 68
++VV G GK++L+ F K + ESY+PT+ + Y +K+ L + DT+GS +
Sbjct: 3 KIVVVGDTQCGKTALLHVFAKDNYPESYVPTVFENYTASFEIDKHRIELNMWDTSGSSYY 62
Query: 69 PAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELA-SIPIMLVGNKCD 127
++ L+ A ++ + + ++L+ + W+ G E + ++LVG K D
Sbjct: 63 DNVRPLAYPDSDAVLICFDISRPETLDSVLKKWQ------GETQEFCPNAKLVLVGCKLD 116
Query: 128 ETEN----REVSAA--------EGEAEAKMWGC-HFMETSAKTNHN-VKELF 165
+ RE+S +G A+ G ++E S++ + N V+++F
Sbjct: 117 MRTDLSTLRELSKQRLIPVTHEQGSLLARQLGAVAYVECSSRMSENSVRDVF 168
>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 = 2e-06
Identities = 37/171 (21%), Positives = 57/171 (33%), Gaps = 21/171 (12%)
Query: 11 VVFGAGGVGKSSLVLRFVKGTFRE-SYIP-TIEDTYRQVISCNKNICTLQITDTTG---- 64
+FG VGKSSL+ + S IP T D R+ + + DT G
Sbjct: 1 AIFGRPNVGKSSLLNALLGQNVGIVSPIPGTTRDPVRKEWELLPLG-PVVLIDTPGLDEE 59
Query: 65 ---SHQFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIML 121
+ R + +LV EE + +RE P++L
Sbjct: 60 GGLGRERVEEARQVADRADLVLLVVDSDLTPVEEEAKLGL--LRERG--------KPVLL 109
Query: 122 VGNKCDETENREVSAAEGEAEAK-MWGCHFMETSAKTNHNVKELFAELLNL 171
V NK D E E + + + + SA + EL ++ L
Sbjct: 110 VLNKIDLVPESEEEELLRERKLELLPDLPVIAVSALPGEGIDELRKKIAEL 160
>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 = 44.4 bits (105), Expect = 5e-06
Identities = 39/179 (21%), Positives = 63/179 (35%), Gaps = 33/179 (18%)
Query: 10 VVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSHQFP 69
++V G G GK+SL+ ES +PT + + + + L+I GS
Sbjct: 2 ILVLGLDGAGKTSLLHSLSSERSLESVVPTTGFNSVAIPTQDAIMELLEI---GGSQNLR 58
Query: 70 AMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANEL-------ASIPIMLV 122
+ +S I V + L R EL +P++++
Sbjct: 59 KYWKRYLSGSQGLIFVVDSADSERLPLAR-------------QELHQLLQHPPDLPLVVL 105
Query: 123 GNKCDETENREVS------AAEGEAEAKMW---GCH-FMETSAKTNHNVKELFAELLNL 171
NK D R V E A + W G + S VK+L ++L+NL
Sbjct: 106 ANKQDLPAARSVQEIHKELELEPIARGRRWILQGTSLDDDGSPSRMEAVKDLLSQLINL 164
>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 = 43.1 bits (101), Expect = 2e-05
Identities = 56/225 (24%), Positives = 101/225 (44%), Gaps = 40/225 (17%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSHQF 68
++V+ G GK++++ K + E+Y+PT+ + Y + + L + DT+GS +
Sbjct: 15 KLVLVGDVQCGKTAMLQVLAKDCYPETYVPTVFENYTACLETEEQRVELSLWDTSGSPYY 74
Query: 69 PAMQRLSISKGHAFILVYSCTSRQSLEELRPIW--EVIRETKGGANELASIPIMLVGNKC 126
++ L S A +L + + + + W E++ + S I+L+G K
Sbjct: 75 DNVRPLCYSDSDAVLLCFDISRPEIFDSALKKWRAEIL-------DYCPSTRILLIGCKT 127
Query: 127 D---------ETENRE---VSAAEGEAEAKMWGCH-FMETSAKTNH-NVKELF--AELLN 170
D E N++ +S +G A AK G ++E SA T+ ++ +F A LL
Sbjct: 128 DLRTDLSTLMELSNQKQAPISYEQGCAMAKQLGAEAYLECSAFTSEKSIHSIFRTASLLC 187
Query: 171 LEK---------NRNIS---LQLEKKGQLKGTRKLKEK---CSVM 200
+ K R++S L L + +L + KEK CSVM
Sbjct: 188 INKLSPLAKKSPVRSLSKRLLHLPSRSELISSTFKKEKAKSCSVM 232
>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 = 42.3 bits (99), Expect = 4e-05
Identities = 46/194 (23%), Positives = 79/194 (40%), Gaps = 42/194 (21%)
Query: 7 DYRVVVFGAGGVGKSSLVL-RFVKGTFRES-----YIPTIE--DTYR---QVISCNKNIC 55
+ VV G VGK+ L+ R T + ++PT+ D YR +V+ ++++
Sbjct: 2 TIKCVVVGDNAVGKTRLICARACNKTLTQYQLLATHVPTVWAIDQYRVCQEVLERSRDVV 61
Query: 56 -----TLQITDTTGSHQFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGG 110
+L++ DT G H +R + + +L +S S SL ++ +W E +
Sbjct: 62 DGVSVSLRLWDTFGDHD--KDRRFAYGRSDVVLLCFSIASPNSLRNVKTMW--YPEIR-- 115
Query: 111 ANELASIPIMLVGNKCD-------------------ETENREVSAAEGEAEAKMWGCHFM 151
+ +P++LVG K D + G A AK G +
Sbjct: 116 -HFCPRVPVILVGCKLDLRYADLDEVNRARRPLARPIKNADILPPETGRAVAKELGIPYY 174
Query: 152 ETSAKTNHNVKELF 165
ETS T VK++F
Sbjct: 175 ETSVVTQFGVKDVF 188
>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 = 40.6 bits (96), Expect = 1e-04
Identities = 43/186 (23%), Positives = 70/186 (37%), Gaps = 43/186 (23%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKG----------TFRESYIPTIEDTYRQVISCNKNICTL 57
+V+ G VGKSSLV + T + ++ + Y +
Sbjct: 1 RTLVIAGYPNVGKSSLV-NKLTRAKPEVAPYPFTTKSLFVGHFDYKYLRW---------- 49
Query: 58 QITDTTGSHQFPAMQRLSISKGHA------------FILVYSCTSRQSLEELRPIWEVIR 105
Q+ DT G P +R +I A F + S T S+EE +++ I+
Sbjct: 50 QVIDTPGILDRPLEERNTIEM-QAITALAHLRAAVLFFIDPSETCGYSIEEQLSLFKEIK 108
Query: 106 ETKGGANELASIPIMLVGNKCDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELF 165
L + P+++V NK D ++S E E E + G ++ S T V EL
Sbjct: 109 P-------LFNKPVIVVLNKIDLLTEEDLSEIEKELEKE--GEEVIKISTLTEEGVDELK 159
Query: 166 AELLNL 171
+ L
Sbjct: 160 NKACEL 165
>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 = 39.8 bits (94), Expect = 2e-04
Identities = 42/174 (24%), Positives = 68/174 (39%), Gaps = 32/174 (18%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPT-IEDTYRQVISCNKNI--CTLQITDTTGS 65
+VV+ G VGKSSL+ R+ I + I T R VI ++ +++ DT G
Sbjct: 5 KVVIAGKPNVGKSSLLNALAG---RDRAIVSDIAGTTRDVIEEEIDLGGIPVRLIDTAGL 61
Query: 66 HQFP-AMQRLSISKGHAFI-------LVYSCTSRQSLEELRPIWEVIRETKGGANELASI 117
+ ++++ I + I LV + E+L + A
Sbjct: 62 RETEDEIEKIGIERAREAIEEADLVLLVVDASEGLDEEDLEIL-----------ELPAKK 110
Query: 118 PIMLVGNKCDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLNL 171
P+++V NK D + E + G + SAKT + EL LL L
Sbjct: 111 PVIVVLNKSDLLSDAEGISELN-------GKPIIAISAKTGEGIDELKEALLEL 157
>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 = 39.8 bits (93), Expect = 2e-04
Identities = 38/162 (23%), Positives = 69/162 (42%), Gaps = 13/162 (8%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSHQF 68
++ + G GKS+LV R++ G++ + P ++V+ ++ L I D G+
Sbjct: 2 KLGIVGNLRSGKSALVHRYLTGSYVQLESPEGGRFKKEVLVDGQSHLLL-IRDEGGA--- 57
Query: 69 PAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVG--NKC 126
P Q A I V+S S + + ++ + + + IP++LVG +
Sbjct: 58 PDAQFAGWVD--AVIFVFSLEDEASFQTVYRLYHQLSSYRNISE----IPLILVGTQDAI 111
Query: 127 DETENREVSAAEGEA-EAKMWGCHFMETSAKTNHNVKELFAE 167
+ R + A A M C + ET A NV+ +F E
Sbjct: 112 SASNPRVIDDARARQLCADMKRCSYYETCATYGLNVERVFQE 153
>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 = 38.9 bits (92), Expect = 5e-04
Identities = 17/59 (28%), Positives = 24/59 (40%)
Query: 113 ELASIPIMLVGNKCDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLNL 171
LA P ++V NK D + E E ++ G SA T + EL +L L
Sbjct: 111 GLAEKPRIVVLNKIDLLDAEERFEKLKELLKELKGKKVFPISALTGEGLDELLKKLAKL 169
>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 = 38.7 bits (91), Expect = 6e-04
Identities = 35/175 (20%), Positives = 62/175 (35%), Gaps = 29/175 (16%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTI-----EDTYRQVISCNKNICTLQITDTT 63
R+++ G G GK++++ + G + IPTI Y+ V + D
Sbjct: 1 RILMLGLDGAGKTTILYKLKLGEV-VTTIPTIGFNVETVEYKNV--------KFTVWDVG 51
Query: 64 GSHQFPAMQRLSISKGHAFILVYSCTSR----QSLEELRPIWEVIRETKGGANELASIPI 119
G + + + I V + R ++ EL +++ E EL P+
Sbjct: 52 GQDKIRPLWKHYYENTDGLIFVVDSSDRERIEEAKNELH---KLLNE-----EELKGAPL 103
Query: 120 MLVGNKCDETE---NREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLNL 171
+++ NK D E+ G K H SA T + E L+
Sbjct: 104 LILANKQDLPGALTESELIELLGLESIKGRRWHIQPCSAVTGDGLDEGLDWLIEQ 158
>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 = 33.2 bits (77), Expect = 0.047
Identities = 16/58 (27%), Positives = 25/58 (43%), Gaps = 5/58 (8%)
Query: 117 IPIMLVGNKCDETENREVSAAEGEAEAKMWGCHFMET---SAKTNHNVKELFAELLNL 171
P++LV NK D +++E E ++ F E SA NV EL ++
Sbjct: 112 TPVILVLNKIDLVKDKEDLLPLLEKLKELHP--FAEIFPISALKGENVDELLEYIVEY 167
>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 = 33.6 bits (78), Expect = 0.054
Identities = 21/90 (23%), Positives = 32/90 (35%), Gaps = 13/90 (14%)
Query: 82 FILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKCDETENREVSAAEGEA 141
+LV EL + E ++E K IP ++V NK D E +
Sbjct: 89 ALLVVDAGVGPGEYELE-LIEELKERK--------IPYIVVINKIDLGEESAELEKLEKK 139
Query: 142 EAKMWGCHFMETSAKTNHNVKELFAELLNL 171
G + SA T + EL ++ L
Sbjct: 140 F----GLPPIFVSALTGEGIDELKEAIIEL 165
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 33.5 bits (78), Expect = 0.056
Identities = 16/60 (26%), Positives = 24/60 (40%), Gaps = 8/60 (13%)
Query: 112 NELASIPIMLVGNKCDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLNL 171
EL P+++V NK D T ++ G + SAKT + EL + L
Sbjct: 317 EELKDKPVIVVLNKADLTGEIDLEEENG--------KPVIRISAKTGEGIDELREAIKEL 368
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 33.1 bits (77), Expect = 0.066
Identities = 21/65 (32%), Positives = 25/65 (38%), Gaps = 1/65 (1%)
Query: 112 NELASIPIMLVGNKCDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLN- 170
ELA P +LV NK D + E E G SA T + EL L
Sbjct: 267 PELADKPRILVLNKIDLLDEEEEREKRAALELAALGGPVFLISAVTGEGLDELLRALWEL 326
Query: 171 LEKNR 175
LE+ R
Sbjct: 327 LEEAR 331
>gnl|CDD|177661 PLN00023, PLN00023, GTP-binding protein; Provisional.
Length = 334
Score = 33.3 bits (76), Expect = 0.072
Identities = 38/141 (26%), Positives = 62/141 (43%), Gaps = 23/141 (16%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTI-------EDTYRQVISCNKNICT----- 56
RV+V G GVGKSSLV VKG+ TI TY S + +I
Sbjct: 23 RVLVVGDSGVGKSSLVHLIVKGSSIARPPQTIGCTVGVKHITYGSPGSSSNSIKGDSERD 82
Query: 57 --LQITDTTGSHQFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEV-IRETKGGANE 113
+++ D +G ++ + L S+ + I V+ + R++ L+ W + T +
Sbjct: 83 FFVELWDVSGHERYKDCRSLFYSQINGVIFVHDLSQRRTKTSLQK-WASEVAATGTFSAP 141
Query: 114 LAS-------IPIMLVGNKCD 127
L S +P +++GNK D
Sbjct: 142 LGSGGPGGLPVPYIVIGNKAD 162
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 32.7 bits (76), Expect = 0.087
Identities = 16/58 (27%), Positives = 25/58 (43%), Gaps = 5/58 (8%)
Query: 117 IPIMLVGNKCDETENREVSAAEGEAEAKMWGCHFMET---SAKTNHNVKELFAELLNL 171
P++LV NK D +++E E +++ F E SA NV EL +
Sbjct: 114 TPVILVLNKIDLVKDKEELLPLLEELSELMD--FAEIVPISALKGDNVDELLDVIAKY 169
>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 = 31.7 bits (73), Expect = 0.14
Identities = 13/58 (22%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 117 IPIMLVGNKCDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLNLEKN 174
+P+++ N DE E R + + +++ G + TSA+ + EL + L ++
Sbjct: 103 LPVVVALNMIDEAEKRGIKIDL-DKLSELLGVPVVPTSARKGEGIDELLDAIAKLAES 159
>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 = 32.0 bits (74), Expect = 0.14
Identities = 25/82 (30%), Positives = 36/82 (43%), Gaps = 4/82 (4%)
Query: 93 SLEELRPI--WEVIR-ETKGGANELASIPIMLVGNKCDETENREVSAAEGEAEAKMWGCH 149
+ PI +E+IR E K + ELA P ++V NK D + E+ E + + G
Sbjct: 247 PEDGSDPIEDYEIIRNELKKYSPELAEKPRIVVLNKIDLLDEEELEELLKELKEAL-GKP 305
Query: 150 FMETSAKTNHNVKELFAELLNL 171
SA T + EL L L
Sbjct: 306 VFPISALTGEGLDELLYALAEL 327
>gnl|CDD|206724 cd04159, Arl10_like, Arf-like 9 (Arl9) and 10 (Arl10) GTPases.
Arl10-like subfamily. Arl9/Arl10 was identified from a
human cancer-derived EST dataset. No functional
information about the subfamily is available at the
current time, but crystal structures of human Arl10b and
Arl10c have been solved.
Length = 159
Score = 31.1 bits (71), Expect = 0.20
Identities = 31/119 (26%), Positives = 55/119 (46%), Gaps = 9/119 (7%)
Query: 10 VVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSHQFP 69
+ + G GK++LV G F E IPT+ R+V N T+++ D G +F
Sbjct: 2 ITLVGLQNSGKTTLVNVIASGQFSEDTIPTVGFNMRKVTKGN---VTIKVWDLGGQPRFR 58
Query: 70 AMQRLSISKGHAFILVYSCTSRQSLEELR-PIWEVIRETKGGANELASIPIMLVGNKCD 127
+M +A + V R+ LE + + +++ + L IP++++GNK D
Sbjct: 59 SMWERYCRGVNAIVYVVDAADREKLEVAKNELHDLLEKP-----SLEGIPLLVLGNKND 112
>gnl|CDD|234770 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 31.2 bits (72), Expect = 0.22
Identities = 11/57 (19%), Positives = 21/57 (36%), Gaps = 2/57 (3%)
Query: 117 IPIMLVGNKCDETENREVSAAEGE--AEAKMWGCHFMETSAKTNHNVKELFAELLNL 171
IP+++V K D+ + E + K + S+ + EL A +
Sbjct: 136 IPVLIVLTKADKLKKGERKKQLKKVRKALKFGDDEVILFSSLKKQGIDELRAAIAKW 192
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 31.8 bits (73), Expect = 0.22
Identities = 21/76 (27%), Positives = 31/76 (40%), Gaps = 2/76 (2%)
Query: 113 ELASIPIMLVGNKCDETENREVSAAEGE-AEAKMWGCHFMETSAKTNHNVKELFAELLN- 170
+LA P LV NK D + E EA W SA + VKEL +L+
Sbjct: 272 KLAEKPRWLVFNKIDLLDEEEAEERAKAIVEALGWEGPVYLISAASGLGVKELCWDLMTF 331
Query: 171 LEKNRNISLQLEKKGQ 186
+E+N + + +
Sbjct: 332 IEENPREEAEEAEAPE 347
>gnl|CDD|129833 TIGR00750, lao, LAO/AO transport system ATPase. In E. coli,
mutation of this kinase blocks phosphorylation of two
transporter system periplasmic binding proteins and
consequently inhibits those transporters. This kinase
is also found in Gram-positive bacteria, archaea, and
the roundworm C. elegans. It may have a more general,
but still unknown function. Mutations have also been
found that do not phosphorylate the periplasmic binding
proteins, yet still allow transport. The ATPase
activity of this protein seems to be necessary, however
[Transport and binding proteins, Amino acids, peptides
and amines, Regulatory functions, Protein
interactions].
Length = 300
Score = 31.7 bits (72), Expect = 0.24
Identities = 12/37 (32%), Positives = 16/37 (43%)
Query: 1 MPEQSNDYRVVVFGAGGVGKSSLVLRFVKGTFRESYI 37
MP N +RV + G G GKS+L+ R
Sbjct: 28 MPYTGNAHRVGITGTPGAGKSTLLEALGMELRRRGLR 64
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 31.4 bits (72), Expect = 0.27
Identities = 44/179 (24%), Positives = 73/179 (40%), Gaps = 33/179 (18%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPT-IEDTYRQVISCNKNI--CTLQITDTTGS 65
+VV+ G VGKSSL+ + R+ I T I T R VI + N+ +++ DT G
Sbjct: 219 KVVIIGRPNVGKSSLLNALLG---RDRAIVTDIAGTTRDVIEEDINLNGIPVRLVDTAGI 275
Query: 66 HQFP-AMQRLSISKGHA------FILVYSCTSRQSLEELRPIWEVIRETKGGANELASIP 118
+ ++R+ I + +L S+ +E + E++ + K P
Sbjct: 276 RETDDVVERIGIERAKKAIEEADLVLFVLDASQPLDKEDLALIELLPKKK---------P 326
Query: 119 IMLVGNKCD---ETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLNLEKN 174
I++V NK D + E A G+A + SAKT + L + L
Sbjct: 327 IIVVLNKADLVSKIELESEKLANGDA--------IISISAKTGEGLDALREAIKQLFGK 377
>gnl|CDD|217025 pfam02421, FeoB_N, Ferrous iron transport protein B. Escherichia
coli has an iron(II) transport system (feo) which may
make an important contribution to the iron supply of the
cell under anaerobic conditions. FeoB has been
identified as part of this transport system. FeoB is a
large 700-800 amino acid integral membrane protein. The
N terminus contains a P-loop motif suggesting that iron
transport may be ATP dependent.
Length = 190
Score = 30.5 bits (70), Expect = 0.32
Identities = 12/62 (19%), Positives = 27/62 (43%), Gaps = 1/62 (1%)
Query: 117 IPIMLVGNKCDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLNLEKNRN 176
IP+++ N DE E + + + + G + TSA+ + EL ++ + + +
Sbjct: 106 IPVVVALNMMDEAEKKGIKIDIKKLSELL-GVPVVPTSARKGEGIDELKDAIIEVAEGKV 164
Query: 177 IS 178
Sbjct: 165 PP 166
>gnl|CDD|221955 pfam13173, AAA_14, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily.
Length = 127
Score = 30.2 bits (69), Expect = 0.33
Identities = 10/28 (35%), Positives = 19/28 (67%)
Query: 10 VVVFGAGGVGKSSLVLRFVKGTFRESYI 37
+V+ G VGK++L+L+F+K E+ +
Sbjct: 5 IVITGPRQVGKTTLLLQFLKELLSENIL 32
>gnl|CDD|206734 cd04171, SelB, SelB, the dedicated elongation factor for delivery
of selenocysteinyl-tRNA to the ribosome. SelB is an
elongation factor needed for the co-translational
incorporation of selenocysteine. Selenocysteine is coded
by a UGA stop codon in combination with a specific
downstream mRNA hairpin. In bacteria, the C-terminal
part of SelB recognizes this hairpin, while the
N-terminal part binds GTP and tRNA in analogy with
elongation factor Tu (EF-Tu). It specifically recognizes
the selenocysteine charged tRNAsec, which has a UCA
anticodon, in an EF-Tu like manner. This allows
insertion of selenocysteine at in-frame UGA stop codons.
In E. coli SelB binds GTP, selenocysteyl-tRNAsec, and a
stem-loop structure immediately downstream of the UGA
codon (the SECIS sequence). The absence of active SelB
prevents the participation of selenocysteyl-tRNAsec in
translation. Archaeal and animal mechanisms of
selenocysteine incorporation are more complex. Although
the SECIS elements have different secondary structures
and conserved elements between archaea and eukaryotes,
they do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains bacterial SelBs, as well as, one from archaea.
Length = 170
Score = 30.7 bits (70), Expect = 0.34
Identities = 12/60 (20%), Positives = 21/60 (35%), Gaps = 5/60 (8%)
Query: 119 IMLVGNKCDETENREVSAAEGEAEAKMWGCHFM-----ETSAKTNHNVKELFAELLNLEK 173
++V K D + + E E + G S+ T ++EL L L +
Sbjct: 106 GLVVLTKADLVDEDRLELVEEEILELLAGTFLADAPIFPVSSVTGEGIEELKNYLDELAE 165
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 31.2 bits (72), Expect = 0.36
Identities = 13/65 (20%), Positives = 27/65 (41%), Gaps = 9/65 (13%)
Query: 118 PIMLVGNKCDETENREVSAAEGEAEAKMWGCHFME------TSAKTNHNVKELFAELLNL 171
+++V NK D + + + + E ++ F++ SA T V +L +
Sbjct: 286 ALVIVVNKWDLVDEKTMEEFKKELRRRL---PFLDYAPIVFISALTGQGVDKLLEAIDEA 342
Query: 172 EKNRN 176
+N N
Sbjct: 343 YENAN 347
>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 = 30.3 bits (69), Expect = 0.40
Identities = 16/38 (42%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 4 QSNDYRVVVFGAGGVGKSSLVLRFVKGTF-RESYIPTI 40
Q N + V GA G GKS+L+ F+ +F + +Y PTI
Sbjct: 1 QRNVFLCFVLGAKGSGKSALLQAFLGRSFSQNAYSPTI 38
>gnl|CDD|112137 pfam03308, ArgK, ArgK protein. The ArgK protein acts as an
ATPase enzyme and as a kinase, and phosphorylates
periplasmic binding proteins involved in the LAO
(lysine, arginine, ornithine)/AO transport systems.
Length = 267
Score = 30.4 bits (69), Expect = 0.45
Identities = 11/37 (29%), Positives = 16/37 (43%)
Query: 1 MPEQSNDYRVVVFGAGGVGKSSLVLRFVKGTFRESYI 37
MP +RV + G G GKS+L+ R +
Sbjct: 23 MPLTGRAHRVGITGVPGAGKSTLIEALGMELRRRGHR 59
>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 = 30.1 bits (68), Expect = 0.56
Identities = 35/181 (19%), Positives = 54/181 (29%), Gaps = 35/181 (19%)
Query: 11 VVFGAGGVGKSSL--VLRFVK-------GTFRESYIPTIEDTYRQVISCNKNICTLQITD 61
+ G VGKS+L L K T E + E + +QI D
Sbjct: 1 GLVGLPNVGKSTLLSALTSAKVEIASYPFTTLEPNVGVFEF---------GDGVDIQIID 51
Query: 62 TTG-----------SHQFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGG 110
G Q A S + V + + L + E G
Sbjct: 52 LPGLLDGASEGRGLGEQILAHLYRS----DLILHVIDASEDCVGDPLEDQKTLNEEVSGS 107
Query: 111 ANELASIPIMLVGNKCDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLN 170
L + P M+V NK D + + + + G + TSA T + + +
Sbjct: 108 FLFLKNKPEMIVANKIDMASENNLKRLKLDKLKR--GIPVVPTSALTRLGLDRVIRTIRK 165
Query: 171 L 171
L
Sbjct: 166 L 166
>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 = 29.7 bits (68), Expect = 0.56
Identities = 18/68 (26%), Positives = 28/68 (41%), Gaps = 13/68 (19%)
Query: 115 ASIPIMLVGNKCDETENR---------EVSAAEGEAEAKMWG--CHFMETSAKTNHNVKE 163
A++PI++ NK D+ E+S E WG + SAKT + +
Sbjct: 100 ANVPIIVAINKIDKPYGTEADPERVKNELSELGLVGEE--WGGDVSIVPISAKTGEGIDD 157
Query: 164 LFAELLNL 171
L +L L
Sbjct: 158 LLEAILLL 165
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 30.3 bits (69), Expect = 0.64
Identities = 39/156 (25%), Positives = 58/156 (37%), Gaps = 39/156 (25%)
Query: 10 VVVFGAGGVGKSSLVLRFVKG----------TFRESYIPTIEDTYRQVISCNKNICTLQI 59
+VV G VGKSSLV R + T + ++ E Y ++ Q+
Sbjct: 171 IVVAGYPNVGKSSLV-RKLTTAKPEVAPYPFTTKGIHVGHFERGYLRI----------QV 219
Query: 60 TDTTGSHQFPAMQRLSISKGHA-----------FILVYSCTSRQSLEELRPIWEVIRETK 108
DT G P +R I + F+ S T SLEE + E I+
Sbjct: 220 IDTPGLLDRPLEERNEIERQAILALRHLAGVILFLFDPSETCGYSLEEQISLLEEIK--- 276
Query: 109 GGANELASIPIMLVGNKCDETENREVSAAEGEAEAK 144
EL PI++V NK D + ++ E +
Sbjct: 277 ----ELFKAPIVVVINKIDIADEEKLEEIEASVLEE 308
>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 = 29.7 bits (68), Expect = 0.67
Identities = 16/56 (28%), Positives = 24/56 (42%), Gaps = 2/56 (3%)
Query: 113 ELASIPIMLVGNKCDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAEL 168
E + I ++V NK D ++ E+ E G + SAKT + EL L
Sbjct: 30 EASGIEPVIVLNKADLVDDEELEELLEIYEK--LGYPVLAVSAKTGEGLDELRELL 83
Score = 27.0 bits (61), Expect = 5.4
Identities = 8/17 (47%), Positives = 11/17 (64%), Gaps = 1/17 (5%)
Query: 9 RVVVF-GAGGVGKSSLV 24
+ V G GVGKS+L+
Sbjct: 86 KTSVLVGQSGVGKSTLL 102
>gnl|CDD|237511 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 30.2 bits (69), Expect = 0.68
Identities = 17/66 (25%), Positives = 30/66 (45%), Gaps = 6/66 (9%)
Query: 118 PIMLVGNKCD---ETENREVSAAEGEAEAKMWGCHFME---TSAKTNHNVKELFAELLNL 171
P++LVGNK D ++ + EAK G ++ SA+ H + EL +
Sbjct: 98 PVLLVGNKADLLPKSVKKNKVKNWLRQEAKELGLRPVDVVLISAQKGHGIDELLEAIEKY 157
Query: 172 EKNRNI 177
+ R++
Sbjct: 158 REGRDV 163
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 29.8 bits (68), Expect = 0.77
Identities = 20/63 (31%), Positives = 27/63 (42%), Gaps = 4/63 (6%)
Query: 112 NELASIPIMLVGNKCDETENREVSAAEGEAEAKMWGCHFMET-SAKTNHNVKEL---FAE 167
+LA P ++V NK D + E +A A+ G SA T + EL AE
Sbjct: 271 PKLAEKPRIVVLNKIDLPLDEEELEELKKALAEALGWEVFYLISALTREGLDELLRALAE 330
Query: 168 LLN 170
LL
Sbjct: 331 LLE 333
>gnl|CDD|115510 pfam06858, NOG1, Nucleolar GTP-binding protein 1 (NOG1). This
family represents a conserved region of approximately 60
residues in length within nucleolar GTP-binding protein
1 (NOG1). In S. cerevisiae, the NOG1 gene has been shown
to be essential for cell viability, suggesting that NOG1
may play an important role in nucleolar functions.
Family members include eukaryotic, bacterial and
archaeal proteins.
Length = 58
Score = 27.6 bits (62), Expect = 0.99
Identities = 12/46 (26%), Positives = 21/46 (45%), Gaps = 6/46 (13%)
Query: 82 FILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKCD 127
F+ S SLEE +++ I+ + P+++V NK D
Sbjct: 19 FVFDPSEQCGYSLEEQLHLFKEIKP------LFKNKPVIVVLNKID 58
>gnl|CDD|206645 cd00879, Sar1, Sar1 is an essential component of COPII vesicle
coats. Sar1 is an essential component of COPII vesicle
coats involved in export of cargo from the ER. The
GTPase activity of Sar1 functions as a molecular switch
to control protein-protein and protein-lipid
interactions that direct vesicle budding from the ER.
Activation of the GDP to the GTP-bound form of Sar1
involves the membrane-associated guanine nucleotide
exchange factor (GEF) Sec12. Sar1 is unlike all Ras
superfamily GTPases that use either myristoyl or prenyl
groups to direct membrane association and function, in
that Sar1 lacks such modification. Instead, Sar1
contains a unique nine-amino-acid N-terminal extension.
This extension contains an evolutionarily conserved
cluster of bulky hydrophobic amino acids, referred to as
the Sar1-N-terminal activation recruitment (STAR) motif.
The STAR motif mediates the recruitment of Sar1 to ER
membranes and facilitates its interaction with mammalian
Sec12 GEF leading to activation.
Length = 191
Score = 29.2 bits (66), Expect = 1.0
Identities = 23/122 (18%), Positives = 52/122 (42%), Gaps = 14/122 (11%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSHQF 68
++V G GK++L+ ++PT+ T ++ N T + G H+
Sbjct: 21 KIVFLGLDNAGKTTLLHMLKDDRL-AQHVPTLHPTSEELTIGNVKFTTFDL----GGHE- 74
Query: 69 PAMQ--RLSISKGHAFILVYSCTSRQSLEELR-PIWEVIRETKGGANELASIPIMLVGNK 125
A + + + + + + +E + + ++ + ELA++PI+++GNK
Sbjct: 75 QARRVWKDYFPEVDGIVFLVDAADPERFQESKEELDSLLND-----EELANVPILILGNK 129
Query: 126 CD 127
D
Sbjct: 130 ID 131
>gnl|CDD|206682 cd01895, EngA2, EngA2 GTPase contains the second domain of EngA.
This EngA2 subfamily CD represents the second GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. 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. Although the exact function of
these proteins has not been elucidated, studies have
revealed that the E. coli EngA homolog, Der, and
Neisseria gonorrhoeae EngA are essential for cell
viability. A recent report suggests that E. coli Der
functions in ribosome assembly and stability.
Length = 174
Score = 28.9 bits (66), Expect = 1.0
Identities = 39/189 (20%), Positives = 65/189 (34%), Gaps = 53/189 (28%)
Query: 9 RVVVFGAGGVGKSSLVLRFVK----------GTFRES-YIP-TIEDTYRQVISCNKNICT 56
++ + G VGKSSL+ + GT R+S +P +
Sbjct: 4 KIAIIGRPNVGKSSLLNALLGEERVIVSDIAGTTRDSIDVPFEYDGQ------------K 51
Query: 57 LQITDTTG----SHQFPAMQRLS-------ISKGHAFILVYSCTSRQSLEE--LRPIWEV 103
+ DT G +++ S I + +LV + + + E LR +
Sbjct: 52 YTLIDTAGIRKKGKVTEGIEKYSVLRTLKAIERADVVLLVLDAS--EGITEQDLRIAGLI 109
Query: 104 IRETKGGANELASIPIMLVGNKCDETENREVSAAEGEAE-----AKMWGCHFMETSAKTN 158
+ E K +++V NK D E E + E E E + + SA T
Sbjct: 110 LEEGKA---------LIIVVNKWDLVEKDEKTMKEFEKELRRKLPFLDYAPIVFISALTG 160
Query: 159 HNVKELFAE 167
V +LF
Sbjct: 161 QGVDKLFDA 169
>gnl|CDD|220660 pfam10261, Scs3p, Inositol phospholipid synthesis and
fat-storage-inducing TM. This is a family of
transmembrane proteins which are variously annotated as
possibly being inositol phospholipid synthesis protein
and fat-storage-inducing. The members are conserved from
yeasts to humans and are localised to the endoplasmic
reticulum where they are involved in triglyceride lipid
droplet formation.
Length = 223
Score = 29.3 bits (66), Expect = 1.1
Identities = 13/32 (40%), Positives = 15/32 (46%), Gaps = 7/32 (21%)
Query: 76 ISKGHAFILVYSCTSRQSL--EELRPIWEVIR 105
IS GH F+LV S L EEL + V
Sbjct: 121 IS-GHVFLLVLSS----LLLWEELGQVARVFD 147
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the
AAA superfamily.
Length = 154
Score = 28.7 bits (64), Expect = 1.2
Identities = 8/21 (38%), Positives = 14/21 (66%)
Query: 10 VVVFGAGGVGKSSLVLRFVKG 30
V++ G G GK+SL+ ++G
Sbjct: 27 VLLTGPSGTGKTSLLRELLEG 47
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 28.7 bits (65), Expect = 1.2
Identities = 9/40 (22%), Positives = 17/40 (42%), Gaps = 5/40 (12%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVI 48
R+V+ G GK++L+ P + + R+ I
Sbjct: 1 RIVITGGPSTGKTTLLEA-----LAARGYPVVPEYGREYI 35
>gnl|CDD|235401 PRK05306, infB, translation initiation factor IF-2; Validated.
Length = 746
Score = 29.4 bits (67), Expect = 1.2
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 6/33 (18%)
Query: 150 FMETSAKTNHNVKELF------AELLNLEKNRN 176
F+ SAKT + EL AE+L L+ N +
Sbjct: 388 FVPVSAKTGEGIDELLEAILLQAEVLELKANPD 420
>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 = 29.2 bits (66), Expect = 1.3
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 2 PEQSNDYRVVVFGAGGVGKSSLV 24
E ++V G GVGKSS +
Sbjct: 26 KELDFSLTILVLGKTGVGKSSTI 48
>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 = 28.6 bits (65), Expect = 1.3
Identities = 11/59 (18%), Positives = 25/59 (42%), Gaps = 4/59 (6%)
Query: 117 IPIMLVGNKCDETENREVSAAEGEAEAKM----WGCHFMETSAKTNHNVKELFAELLNL 171
IP ++V K D+ + E++ + + ++ + S+K + EL A +
Sbjct: 111 IPFLIVLTKADKLKKSELAKVLKKIKEELNLFNILPPVILFSSKKGTGIDELRALIAEW 169
>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 = 29.0 bits (66), Expect = 1.3
Identities = 13/63 (20%), Positives = 23/63 (36%), Gaps = 8/63 (12%)
Query: 117 IPIMLVGNKCDETENREVSAAEGEAEAKMW--------GCHFMETSAKTNHNVKELFAEL 168
+PI++ NK D ++ E+ E ++ + SA T + EL L
Sbjct: 119 VPIIVFINKIDRVDDAELEEVVEEISRELLEKYGFGGETVPVVPGSALTGEGIDELLEAL 178
Query: 169 LNL 171
Sbjct: 179 DLY 181
>gnl|CDD|224617 COG1703, ArgK, Putative periplasmic protein kinase ArgK and
related GTPases of G3E family [Amino acid transport and
metabolism].
Length = 323
Score = 29.2 bits (66), Expect = 1.4
Identities = 8/34 (23%), Positives = 14/34 (41%)
Query: 1 MPEQSNDYRVVVFGAGGVGKSSLVLRFVKGTFRE 34
P N + + + G G GKS+L+ +
Sbjct: 45 YPRTGNAHVIGITGVPGAGKSTLIEALGRELRER 78
>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 = 29.1 bits (65), Expect = 1.4
Identities = 31/156 (19%), Positives = 56/156 (35%), Gaps = 33/156 (21%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTI-------EDTYRQVISCNKNICTLQITD 61
+V+V G GVGKSSLV K + T+ TY + K ++ D
Sbjct: 2 KVLVLGDSGVGKSSLVHLLCKNQVLGNPSWTVGCSVDVRHHTYGEGTPEEKTFYV-ELWD 60
Query: 62 TTGS----HQFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEV-------------- 103
GS + + + ++ + I V+ T+++S + L W +
Sbjct: 61 VGGSVGSAESVKSTRAVFYNQINGIIFVHDLTNKKSSQNLYR-WSLEALNRDTFPAGLLV 119
Query: 104 --IRETKGGANELASIPIMLVGNKCD---ETENREV 134
+P++++G K D E + V
Sbjct: 120 TNGDYDSEQFAGNP-VPLLVIGTKLDQIPEAKRNWV 154
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 28.7 bits (65), Expect = 1.4
Identities = 28/121 (23%), Positives = 47/121 (38%), Gaps = 10/121 (8%)
Query: 8 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSHQ 67
R+++ G GK++++ + G + IPTI V N + D G
Sbjct: 15 MRILILGLDNAGKTTILYKLKLGEIVTT-IPTIGFNVETVTYKN---VKFTVWDVGGQES 70
Query: 68 FPAMQRLSISKGHAFILVYSCTSRQSLEE-LRPIWEVIRETKGGANELASIPIMLVGNKC 126
+ R A I V R +EE + ++ E ELA P++++ NK
Sbjct: 71 LRPLWRNYFPNTDAVIFVVDSADRDRIEEAKEELHALLNE-----EELADAPLLILANKQ 125
Query: 127 D 127
D
Sbjct: 126 D 126
>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 = 29.0 bits (66), Expect = 1.4
Identities = 13/56 (23%), Positives = 20/56 (35%), Gaps = 6/56 (10%)
Query: 113 ELASIPIMLVGNKCDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAEL 168
IP +LV NK D + + E ++ SAKT + L +
Sbjct: 298 GAEDIPQLLVYNKIDLLDEPRIERLEEGYPEAVF------VSAKTGEGLDLLLEAI 347
>gnl|CDD|216506 pfam01443, Viral_helicase1, Viral (Superfamily 1) RNA helicase.
Helicase activity for this family has been demonstrated
and NTPase activity. This helicase has multiple roles
at different stages of viral RNA replication, as
dissected by mutational analysis.
Length = 226
Score = 28.9 bits (65), Expect = 1.5
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 10 VVVFGAGGVGKSSLVLRFVKGTFRESYIPTIED-TYRQVISCNKNICTLQ 58
+VV G G GKS+L+ + ++ T PT E T + N N+ T+
Sbjct: 1 IVVHGVPGCGKSTLIRKLLR-TDLTVIRPTAELRTEGKPDLPNLNVRTVD 49
>gnl|CDD|216619 pfam01637, Arch_ATPase, Archaeal ATPase. This family contain a
conserved P-loop motif that is involved in binding ATP.
This family is almost exclusively found in
archaebacteria and particularly in Methanococcus
jannaschii that encodes sixteen members of this family.
Length = 223
Score = 28.8 bits (65), Expect = 1.6
Identities = 10/31 (32%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 10 VVVFGAGGVGKSSLVLRFVKGTFRESYIPTI 40
+VV+G GK++L+ F++ RE I
Sbjct: 23 IVVYGPRRCGKTALLREFLEE-LRELGYRVI 52
>gnl|CDD|234274 TIGR03594, GTPase_EngA, ribosome-associated GTPase EngA. EngA
(YfgK, Der) is a ribosome-associated essential GTPase
with a duplication of its GTP-binding domain. It is
broadly to universally distributed among bacteria. It
appears to function in ribosome biogenesis or stability
[Protein synthesis, Other].
Length = 429
Score = 28.9 bits (66), Expect = 1.7
Identities = 39/195 (20%), Positives = 65/195 (33%), Gaps = 60/195 (30%)
Query: 18 VGKSSLVLRFVK----------GTFRES-YIP-TIEDTYRQVISCNKNICTLQITDTTG- 64
VGKS+LV + GT R+S IP + DT G
Sbjct: 183 VGKSTLVNALLGEERVIVSDIAGTTRDSIDIPFERNGK------------KYTLIDTAGI 230
Query: 65 ---SHQFPAMQRLS-------ISKGHAFILVYSCTSRQSLEE--LRPIWEVIRETKGGAN 112
+++ S I + +LV + + + E LR + K
Sbjct: 231 RRKGKVTEGVEKYSVLRTLKAIERADVVLLV--LDATEGITEQDLRIAGLALEAGK---- 284
Query: 113 ELASIPIMLVGNKCDETENREVSAA-EGEAEAKMWGCHFME------TSAKTNHNVKELF 165
+++V NK D ++ + + E K+ F++ SA T V +L
Sbjct: 285 -----ALVIVVNKWDLVKDEKTREEFKKELRRKL---PFLDFAPIVFISALTGQGVDKLL 336
Query: 166 --AELLNLEKNRNIS 178
+ + NR IS
Sbjct: 337 DAIDEVYENANRRIS 351
>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 = 28.5 bits (63), Expect = 1.7
Identities = 23/88 (26%), Positives = 37/88 (42%), Gaps = 4/88 (4%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSHQF 68
RVV G G GK++++ + + F + IPTI V KN+ I D G H+
Sbjct: 1 RVVTLGLDGAGKTTILFKLKQDEFMQP-IPTIGFNVETVEY--KNL-KFTIWDVGGKHKL 56
Query: 69 PAMQRLSISKGHAFILVYSCTSRQSLEE 96
+ + A + V + R + E
Sbjct: 57 RPLWKHYYLNTQAVVFVIDSSHRDRVSE 84
>gnl|CDD|222165 pfam13481, AAA_25, AAA domain. This AAA domain is found in a
wide variety of presumed DNA repair proteins.
Length = 154
Score = 28.4 bits (64), Expect = 1.7
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 10 VVVFGAGGVGKSSLVL 25
++ GA G GKS+L L
Sbjct: 36 TLLAGAPGTGKSTLAL 51
>gnl|CDD|169656 PRK09099, PRK09099, type III secretion system ATPase; Provisional.
Length = 441
Score = 29.0 bits (65), Expect = 1.9
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGT 31
R+ +F GVGKS+L+ F +GT
Sbjct: 165 RMGIFAPAGVGKSTLMGMFARGT 187
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 29.0 bits (65), Expect = 2.0
Identities = 25/118 (21%), Positives = 43/118 (36%), Gaps = 10/118 (8%)
Query: 88 CTSRQSLEELRPIW-------EVIRETKGGANELASI--PIMLVGNKCDETENREVSAA- 137
+ LEEL + + ELA + G + E +E+
Sbjct: 420 EELERELEELEEEIKKLEEQINQLESKELMIAELAGAGEKCPVCGQELPEEHEKELLELY 479
Query: 138 EGEAEAKMWGCHFMETSAKTNHNVKELFAELLNLEKNRNISLQLEKKGQLKGTRKLKE 195
E E E + A+ ++EL EL LE+ L+LE+ + + KL++
Sbjct: 480 ELELEELEEELSREKEEAELREEIEELEKELRELEEELIELLELEEALKEELEEKLEK 537
>gnl|CDD|233918 TIGR02546, III_secr_ATP, type III secretion apparatus
H+-transporting two-sector ATPase. [Protein fate,
Protein and peptide secretion and trafficking, Cellular
processes, Pathogenesis].
Length = 422
Score = 28.8 bits (65), Expect = 2.2
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGT 31
R+ +F GVGKS+L+ +G
Sbjct: 147 RIGIFAGAGVGKSTLLGMIARGA 169
>gnl|CDD|176178 cd05188, MDR, Medium chain reductase/dehydrogenase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
The medium chain reductase/dehydrogenases
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH) , quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. ADH-like proteins
typically form dimers (typically higher plants, mammals)
or tetramers (yeast, bacteria), and generally have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. The active site zinc is
coordinated by a histidine, two cysteines, and a water
molecule. The second zinc seems to play a structural
role, affects subunit interactions, and is typically
coordinated by 4 cysteines. Other MDR members have only
a catalytic zinc, and some contain no coordinated zinc.
Length = 271
Score = 28.4 bits (64), Expect = 2.4
Identities = 8/11 (72%), Positives = 9/11 (81%)
Query: 9 RVVVFGAGGVG 19
V+V GAGGVG
Sbjct: 137 TVLVLGAGGVG 147
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 28.3 bits (64), Expect = 2.6
Identities = 41/174 (23%), Positives = 62/174 (35%), Gaps = 28/174 (16%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQI--TDTTGSH 66
V + G VGKS+L+ V G + S + T R I QI DT G H
Sbjct: 8 FVAIIGRPNVGKSTLLNALV-GQ-KISIVSPKPQTTRNRIRGIVTTDNAQIIFVDTPGIH 65
Query: 67 QFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVI---RETKGGANEL------ASI 117
HA + + +R +L+++ I V+ G +
Sbjct: 66 ----------KPKHALGELMNKAARSALKDVDLILFVVDADEGWGPGDEFILEQLKKTKT 115
Query: 118 PIMLVGNKCDETENREVSAAEGEAEAKMWGCHFMET---SAKTNHNVKELFAEL 168
P++LV NK D+ + + V K+ F E SA NV L +
Sbjct: 116 PVILVVNKIDKVKPKTVLLKLIAFLKKLL--PFKEIVPISALKGDNVDTLLEII 167
>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 = 27.0 bits (60), Expect = 2.8
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 10 VVVFGAGGVGKSSLV 24
+VV G GGVGK++L
Sbjct: 2 IVVTGKGGVGKTTLA 16
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a
wide variety of presumed phage proteins.
Length = 201
Score = 28.0 bits (63), Expect = 2.8
Identities = 7/23 (30%), Positives = 15/23 (65%)
Query: 5 SNDYRVVVFGAGGVGKSSLVLRF 27
+ + +V+++G G+GK+SL
Sbjct: 1 TKNIKVLIYGPPGIGKTSLAKTL 23
>gnl|CDD|224911 COG2000, COG2000, Predicted Fe-S protein [General function
prediction only].
Length = 226
Score = 27.9 bits (62), Expect = 3.2
Identities = 15/68 (22%), Positives = 26/68 (38%), Gaps = 14/68 (20%)
Query: 126 CDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLNLEKNRNISLQLEKKG 185
C + E + A + K+ C F+E E FAE + K L++ G
Sbjct: 23 CGYSRCDEFAEALLKKLVKIDDCPFLEL---------ERFAENYDRLKAI-----LKELG 68
Query: 186 QLKGTRKL 193
+ + K+
Sbjct: 69 KAEKEMKI 76
>gnl|CDD|226984 COG4637, COG4637, Predicted ATPase [General function prediction
only].
Length = 373
Score = 28.2 bits (63), Expect = 3.3
Identities = 10/32 (31%), Positives = 15/32 (46%), Gaps = 2/32 (6%)
Query: 11 VVFGAGGVGKSSL--VLRFVKGTFRESYIPTI 40
V+ GA G GKS+ LR + R + +
Sbjct: 26 VIIGANGAGKSNFYDALRLLADAVRGNLQQAL 57
>gnl|CDD|130679 TIGR01618, phage_P_loop, phage nucleotide-binding protein. This
model represents an uncharacterized family of proteins
from a number of phage of Gram-positive bacteria. This
protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near
its amino end. The function of this protein is unknown
[Mobile and extrachromosomal element functions, Prophage
functions].
Length = 220
Score = 27.8 bits (62), Expect = 3.4
Identities = 23/115 (20%), Positives = 43/115 (37%), Gaps = 13/115 (11%)
Query: 4 QSNDYRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTT 63
+ +++G G GK+S + T S+ D +V+ ++N+ I D
Sbjct: 9 KRIPNMYLIYGKPGTGKTSTIKYLPGKTLVLSF-----DMSSKVLIGDENV---DIADHD 60
Query: 64 GSHQFPAM-QRLSISKGHAFILVYSCTSRQSLEELRPIW--EVIRETKGGANELA 115
AM + + A + Y ++ L+ +W + R K G EL
Sbjct: 61 DMPPIQAMVEFYVMQNIQA--VKYDNIVIDNISALQNLWLENIGRAAKNGQPELQ 113
>gnl|CDD|206669 cd01882, BMS1, Bms1, an essential GTPase, promotes assembly of
preribosomal RNA processing complexes. Bms1 is an
essential, evolutionarily conserved, nucleolar protein.
Its depletion interferes with processing of the 35S
pre-rRNA at sites A0, A1, and A2, and the formation of
40S subunits. Bms1, the putative endonuclease Rc11, and
the essential U3 small nucleolar RNA form a stable
subcomplex that is believed to control an early step in
the formation of the 40S subumit. The C-terminal domain
of Bms1 contains a GTPase-activating protein (GAP) that
functions intramolecularly. It is believed that Rc11
activates Bms1 by acting as a guanine-nucleotide
exchange factor (GEF) to promote GDP/GTP exchange, and
that activated (GTP-bound) Bms1 delivers Rc11 to the
preribosomes.
Length = 231
Score = 27.7 bits (62), Expect = 3.5
Identities = 15/34 (44%), Positives = 18/34 (52%), Gaps = 4/34 (11%)
Query: 2 PEQSNDYRVVVFGAGGVGKS----SLVLRFVKGT 31
PE+ VVV G GVGKS SL+ R+ K
Sbjct: 34 PEEPPPLVVVVVGPPGVGKSTLIRSLIKRYTKQN 67
>gnl|CDD|177823 PLN02165, PLN02165, adenylate isopentenyltransferase.
Length = 334
Score = 27.9 bits (62), Expect = 3.6
Identities = 11/23 (47%), Positives = 13/23 (56%)
Query: 1 MPEQSNDYRVVVFGAGGVGKSSL 23
M + D VV+ GA G GKS L
Sbjct: 37 MEQNCKDKVVVIMGATGSGKSRL 59
>gnl|CDD|226617 COG4133, CcmA, ABC-type transport system involved in cytochrome c
biogenesis, ATPase component [Posttranslational
modification, protein turnover, chaperones].
Length = 209
Score = 27.6 bits (62), Expect = 3.7
Identities = 11/46 (23%), Positives = 21/46 (45%), Gaps = 10/46 (21%)
Query: 10 VVVFGAGGVGKSSLVLRFVKG---------TFRESYIPTIEDTYRQ 46
+ + G G GK++L LR + G ++ I + ++Y Q
Sbjct: 31 LQITGPNGAGKTTL-LRILAGLLRPDAGEVYWQGEPIQNVRESYHQ 75
>gnl|CDD|206666 cd01878, HflX, HflX GTPase family. HflX subfamily. A distinct
conserved domain with a glycine-rich segment N-terminal
of the GTPase domain characterizes the HflX subfamily.
The E. coli HflX has been implicated in the control of
the lambda cII repressor proteolysis, but the actual
biological functions of these GTPases remain unclear.
HflX is widespread, but not universally represented in
all three superkingdoms.
Length = 204
Score = 27.4 bits (62), Expect = 3.8
Identities = 17/59 (28%), Positives = 23/59 (38%), Gaps = 5/59 (8%)
Query: 113 ELASIPIMLVGNKCDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLNL 171
IPI+LV NK D ++ E A F+ SAKT + L + L
Sbjct: 150 GADDIPIILVLNKIDLLDD---EELEERLRAGRPDAVFI--SAKTGEGLDLLKEAIEEL 203
>gnl|CDD|225815 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 28.1 bits (63), Expect = 3.8
Identities = 15/65 (23%), Positives = 28/65 (43%), Gaps = 2/65 (3%)
Query: 119 IMLVGNKCDETENREVSAAEGE--AEAKMWGCHFMETSAKTNHNVKELFAELLNLEKNRN 176
++V K D + + + A+ + +TSAKT ++EL EL++L +
Sbjct: 106 GIIVLTKADRVDEARIEQKIKQILADLSLANAKIFKTSAKTGRGIEELKNELIDLLEEIE 165
Query: 177 ISLQL 181
Q
Sbjct: 166 RDEQK 170
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 27.8 bits (63), Expect = 4.0
Identities = 15/59 (25%), Positives = 19/59 (32%), Gaps = 4/59 (6%)
Query: 113 ELASIPIMLVGNKCDETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLNL 171
L P ++V NK D E E E SA T + EL + L
Sbjct: 271 RLLERPQIVVANKMDLPEAEENLEEFKEKLGPK----VFPISALTGQGLDELLYAVAEL 325
>gnl|CDD|176221 cd08260, Zn_ADH6, Alcohol dehydrogenases of the MDR family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. This group has the characteristic
catalytic and structural zinc sites of the
zinc-dependent alcohol dehydrogenases. Alcohol
dehydrogenase in the liver converts ethanol and NAD+ to
acetaldehyde and NADH, while in yeast and some other
microorganisms ADH catalyzes the conversion acetaldehyde
to ethanol in alcoholic fermentation. ADH is a member of
the medium chain alcohol dehydrogenase family (MDR),
which has a NAD(P)(H)-binding domain in a Rossmann fold
of a beta-alpha form. The NAD(H)-binding region is
comprised of 2 structurally similar halves, each of
which contacts a mononucleotide. A GxGxxG motif after
the first mononucleotide contact half allows the close
contact of the coenzyme with the ADH backbone. The
N-terminal catalytic domain has a distant homology to
GroES. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit, a
catalytic zinc at the active site and a structural zinc
in a lobe of the catalytic domain. NAD(H)-binding occurs
in the cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 345
Score = 27.6 bits (62), Expect = 4.5
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 9 RVVVFGAGGVGKSSL 23
V V G GGVG S++
Sbjct: 168 WVAVHGCGGVGLSAV 182
>gnl|CDD|238384 cd00755, YgdL_like, Family of activating enzymes (E1) of
ubiquitin-like proteins related to the E.coli
hypothetical protein ygdL. The common reaction
mechanism catalyzed by E1-like enzymes begins with a
nucleophilic attack of the C-terminal carboxylate of
the ubiquitin-like substrate, on the alpha-phosphate of
an ATP molecule bound at the active site of the
activating enzymes, leading to the formation of a
high-energy acyladenylate intermediate and subsequently
to the formation of a thiocarboxylate at the C termini
of the substrate. The exact function of this family is
unknown.
Length = 231
Score = 27.6 bits (62), Expect = 4.5
Identities = 7/11 (63%), Positives = 7/11 (63%)
Query: 9 RVVVFGAGGVG 19
V V G GGVG
Sbjct: 13 HVAVVGLGGVG 23
>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 = 4.9
Identities = 10/24 (41%), Positives = 12/24 (50%)
Query: 153 TSAKTNHNVKELFAELLNLEKNRN 176
SAK V+EL E+ L K R
Sbjct: 103 VSAKKGWGVEELIEEIKKLAKYRG 126
>gnl|CDD|224422 COG1505, COG1505, Serine proteases of the peptidase family S9A
[Amino acid transport and metabolism].
Length = 648
Score = 27.7 bits (62), Expect = 4.9
Identities = 10/49 (20%), Positives = 20/49 (40%), Gaps = 1/49 (2%)
Query: 84 LVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKCDETENR 132
+Y T+ ++ +P WEV+ + + +L + L G R
Sbjct: 76 GLYRRTTLETYRSAKPEWEVLIDVDALSADL-GDKVALGGASVLPDGTR 123
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 27.5 bits (62), Expect = 5.0
Identities = 41/190 (21%), Positives = 69/190 (36%), Gaps = 59/190 (31%)
Query: 9 RVVVFGAGGVGKSSLVLRFVK----------GTFRESYIPTIEDTYRQVISCNKNICTLQ 58
++ + G VGKSSL+ + GT R+S I IE + +
Sbjct: 180 KIAIIGRPNVGKSSLINAILGEERVIVSDIAGTTRDS-I-DIEFERD-----GRKYVLI- 231
Query: 59 ITDTTG----SHQFPAMQRLSISKGHAFILVYSCTSRQSLEELRPIWEVIRETKG----- 109
DT G ++++ S+++ +++E + VI T+G
Sbjct: 232 --DTAGIRRKGKITESVEKYSVARTL-----------KAIERADVVLLVIDATEGISEQD 278
Query: 110 ----GANELASIPIMLVGNKCDETENREVSAAEGEAE----------AKMWGCHFMETSA 155
G E A I++V NK D E E + E + + A + F SA
Sbjct: 279 LRIAGLIEEAGRGIVIVVNKWDLVEEDEATMEEFKKKLRRKLPFLDFAPI---VF--ISA 333
Query: 156 KTNHNVKELF 165
T + +LF
Sbjct: 334 LTGQGLDKLF 343
>gnl|CDD|130064 TIGR00991, 3a0901s02IAP34, GTP-binding protein (Chloroplast
Envelope Protein Translocase). [Transport and binding
proteins, Nucleosides, purines and pyrimidines].
Length = 313
Score = 27.6 bits (61), Expect = 5.2
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 3 EQSNDYRVVVFGAGGVGKSSLV 24
E + ++V G GGVGKSS V
Sbjct: 34 EDVSSLTILVMGKGGVGKSSTV 55
>gnl|CDD|176239 cd08278, benzyl_alcohol_DH, Benzyl alcohol dehydrogenase. Benzyl
alcohol dehydrogenase is similar to liver alcohol
dehydrogenase, but has some amino acid substitutions
near the active site, which may determine the enzyme's
specificity of oxidizing aromatic substrates. Also
known as aryl-alcohol dehydrogenases, they catalyze the
conversion of an aromatic alcohol + NAD+ to an aromatic
aldehyde + NADH + H+. NAD(P)(H)-dependent
oxidoreductases are the major enzymes in the
interconversion of alcohols and aldehydes, or ketones.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. A GxGxxG motif
after the first mononucleotide contact half allows the
close contact of the coenzyme with the ADH backbone.
The N-terminal catalytic domain has a distant homology
to GroES. These proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and have 2 tightly bound zinc atoms per
subunit, a catalytic zinc at the active site and a
structural zinc in a lobe of the catalytic domain.
NAD(H) binding occurs in the cleft between the catalytic
and coenzyme-binding domains at the active site, and
coenzyme binding induces a conformational closing of
this cleft. Coenzyme binding typically precedes and
contributes to substrate binding. In human ADH
catalysis, the zinc ion helps coordinate the alcohol,
followed by deprotonation of a histidine, the ribose of
NAD, a serine, then the alcohol, which allows the
transfer of a hydride to NAD+, creating NADH and a
zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 365
Score = 27.1 bits (61), Expect = 6.3
Identities = 7/11 (63%), Positives = 8/11 (72%)
Query: 9 RVVVFGAGGVG 19
+ VFGAG VG
Sbjct: 189 SIAVFGAGAVG 199
>gnl|CDD|216186 pfam00910, RNA_helicase, RNA helicase. This family includes RNA
helicases thought to be involved in duplex unwinding
during viral RNA replication. Members of this family
are found in a variety of single stranded RNA viruses.
Length = 105
Score = 26.0 bits (58), Expect = 6.6
Identities = 8/35 (22%), Positives = 16/35 (45%)
Query: 10 VVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTY 44
+ ++G G GKS+L + + +P + Y
Sbjct: 1 IWLYGPPGCGKSTLAKYLARALLKHLGLPKKDSVY 35
>gnl|CDD|216180 pfam00899, ThiF, ThiF family. This family contains a repeated
domain in ubiquitin activating enzyme E1 and members of
the bacterial ThiF/MoeB/HesA family.
Length = 134
Score = 26.4 bits (59), Expect = 6.6
Identities = 8/11 (72%), Positives = 10/11 (90%)
Query: 9 RVVVFGAGGVG 19
RV+V GAGG+G
Sbjct: 3 RVLVVGAGGLG 13
>gnl|CDD|222036 pfam13304, AAA_21, AAA domain.
Length = 256
Score = 27.0 bits (59), Expect = 7.3
Identities = 29/178 (16%), Positives = 44/178 (24%), Gaps = 12/178 (6%)
Query: 11 VVFGAGGVGKSSL--VLRFVKGTFRESYIPTIEDTYRQVISCNKNICTLQITDTTGSHQF 68
V+ G G GKS+L L + N I L +
Sbjct: 3 VIIGPNGSGKSNLLKALALLLLLLSLGLTLDRGL--------NVGIKLLPFLLDENEIEI 54
Query: 69 PAMQRLS--ISKGHAFILVYSCTSRQSLEELRPIWEVIRETKGGANELASIPIMLVGNKC 126
P + + G + + LEEL + E K
Sbjct: 55 PLEFEIEEFLIDGIRYRYGFELDKEDILEELLYEYRKGEELLFERERSKESFEKSPEKKR 114
Query: 127 DETENREVSAAEGEAEAKMWGCHFMETSAKTNHNVKELFAELLNLEKNRNISLQLEKK 184
+ REV + + +E + L NL L L K+
Sbjct: 115 ELRGLREVLLLLNLSLSSFLLLASLEILLSILLPFSFILGNLRNLRNIELKLLDLVKR 172
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 26.1 bits (57), Expect = 7.6
Identities = 6/15 (40%), Positives = 10/15 (66%)
Query: 9 RVVVFGAGGVGKSSL 23
+++ G G GKS+L
Sbjct: 1 IILITGPPGSGKSTL 15
>gnl|CDD|237039 PRK12288, PRK12288, GTPase RsgA; Reviewed.
Length = 347
Score = 26.7 bits (60), Expect = 7.8
Identities = 10/17 (58%), Positives = 13/17 (76%), Gaps = 1/17 (5%)
Query: 9 RVVVF-GAGGVGKSSLV 24
R+ +F G GVGKSSL+
Sbjct: 206 RISIFVGQSGVGKSSLI 222
>gnl|CDD|176240 cd08279, Zn_ADH_class_III, Class III alcohol dehydrogenase.
Glutathione-dependent formaldehyde dehydrogenases (FDHs,
Class III ADH) are members of the zinc-dependent/medium
chain alcohol dehydrogenase family. FDH converts
formaldehyde and NAD(P) to formate and NAD(P)H. The
initial step in this process the spontaneous formation
of a S-(hydroxymethyl)glutathione adduct from
formaldehyde and glutathione, followed by FDH-mediated
oxidation (and detoxification) of the adduct to
S-formylglutathione. NAD(P)(H)-dependent oxidoreductases
are the major enzymes in the interconversion of alcohols
and aldehydes or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. Class III ADH are also known as
glutathione-dependent formaldehyde dehydrogenase (FDH),
which convert aldehydes to corresponding carboxylic acid
and alcohol. ADH is a member of the medium chain
alcohol dehydrogenase family (MDR), which has a
NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding
domains at the active site, and coenzyme binding induces
a conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Length = 363
Score = 26.7 bits (60), Expect = 7.8
Identities = 7/10 (70%), Positives = 7/10 (70%)
Query: 10 VVVFGAGGVG 19
V V G GGVG
Sbjct: 186 VAVIGCGGVG 195
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 26.7 bits (60), Expect = 8.2
Identities = 23/84 (27%), Positives = 36/84 (42%), Gaps = 12/84 (14%)
Query: 115 ASIPIMLVGNKCD------ETENREVSAAEGEAEAKMWG--CHFMETSAKTNHNVKELFA 166
A +PI++ NK D + +E+ E WG F+ SAKT + EL
Sbjct: 106 AGVPIVVAINKIDKPEANPDKVKQELQEYGLVPEE--WGGDVIFVPVSAKTGEGIDELLE 163
Query: 167 ELLNLEKNRNISLQLEKKGQLKGT 190
+L L + L+ +G +GT
Sbjct: 164 LILLLAEVLE--LKANPEGPARGT 185
>gnl|CDD|223082 COG0003, ArsA, Predicted ATPase involved in chromosome
partitioning [Cell division and chromosome
partitioning].
Length = 322
Score = 26.9 bits (60), Expect = 8.4
Identities = 9/17 (52%), Positives = 13/17 (76%), Gaps = 1/17 (5%)
Query: 9 RVVVF-GAGGVGKSSLV 24
R+V F G GGVGK+++
Sbjct: 3 RIVFFTGKGGVGKTTIA 19
>gnl|CDD|217416 pfam03193, DUF258, Protein of unknown function, DUF258.
Length = 161
Score = 26.4 bits (59), Expect = 9.2
Identities = 8/17 (47%), Positives = 11/17 (64%), Gaps = 1/17 (5%)
Query: 9 RVVVF-GAGGVGKSSLV 24
+ V G GVGKS+L+
Sbjct: 36 KTSVLAGQSGVGKSTLL 52
>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 = 25.7 bits (57), Expect = 9.3
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 9 RVVVFGAGGVGKSSLV 24
RV + G VGKS+L+
Sbjct: 1 RVALVGRPNVGKSTLI 16
>gnl|CDD|240360 PTZ00325, PTZ00325, malate dehydrogenase; Provisional.
Length = 321
Score = 26.5 bits (59), Expect = 9.6
Identities = 10/20 (50%), Positives = 15/20 (75%), Gaps = 2/20 (10%)
Query: 9 RVVVFGA-GGVGKS-SLVLR 26
+V V GA GG+G+ SL+L+
Sbjct: 10 KVAVLGAAGGIGQPLSLLLK 29
>gnl|CDD|180762 PRK06936, PRK06936, type III secretion system ATPase; Provisional.
Length = 439
Score = 26.6 bits (59), Expect = 9.6
Identities = 8/23 (34%), Positives = 14/23 (60%)
Query: 9 RVVVFGAGGVGKSSLVLRFVKGT 31
R+ +F A G GKS+L+ ++
Sbjct: 164 RMGIFAAAGGGKSTLLASLIRSA 186
>gnl|CDD|221182 pfam11715, Nup160, Nucleoporin Nup120/160. Nup120 is conserved
from fungi to plants to humans, and is homologous with
the Nup160 of vertebrates. The nuclear core complex, or
NPC, mediates macromolecular transport across the
nuclear envelope. Deletion of the NUP120 gene causes
clustering of NPCs at one side of the nuclear envelope,
moderate nucleolar fragmentation and slower cell growth.
The vertebrate NPC is estimated to contain between 30
and 60 different proteins. most of which are not known.
Two important ones in creating the nucleoporin basket
are Nup98 and Nup153, and Nup120, in conjunction with
Nup 133, interacts with these two and itself plays a
role in mRNA export. Nup160, Nup133, Nup96, and Nup107
are all targets of phosphorylation. The phosphorylation
sites are clustered mainly at the N-terminal regions of
these proteins, which are predicted to be natively
disordered. The entire Nup107-160 subcomplex is stable
throughout the cell cycle, thus it seems unlikely that
phosphorylation affects interactions within the
Nup107-160 subcomplex, but rather that it regulates the
association of the subcomplex with the NPC and other
proteins.
Length = 511
Score = 26.7 bits (59), Expect = 9.9
Identities = 6/44 (13%), Positives = 11/44 (25%)
Query: 56 TLQITDTTGSHQFPAMQRLSISKGHAFILVYSCTSRQSLEELRP 99
TL++ + R + YS S +
Sbjct: 243 TLRVWNLDTGQCAFLPSRADSGGSRYLCVTYSPFSSGEFKFFSV 286
>gnl|CDD|238540 cd01120, RecA-like_NTPases, RecA-like NTPases. This family
includes the NTP binding domain of F1 and V1 H+ATPases,
DnaB and related helicases as well as bacterial RecA
and related eukaryotic and archaeal recombinases. This
group also includes bacterial conjugation proteins and
related DNA transfer proteins involved in type II and
type IV secretion.
Length = 165
Score = 26.3 bits (58), Expect = 10.0
Identities = 10/39 (25%), Positives = 16/39 (41%), Gaps = 4/39 (10%)
Query: 9 RVVVFGAGGVGKS----SLVLRFVKGTFRESYIPTIEDT 43
++VFG G GK+ L L + Y+ E+
Sbjct: 1 LILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEI 39
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.316 0.131 0.377
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: 9,591,226
Number of extensions: 844428
Number of successful extensions: 1660
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1488
Number of HSP's successfully gapped: 200
Length of query: 200
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 108
Effective length of database: 6,857,034
Effective search space: 740559672
Effective search space used: 740559672
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (25.7 bits)