RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9521
(125 letters)
>gnl|CDD|206725 cd04160, Arfrp1, Arf-related protein 1 (Arfrp1). Arfrp1
(Arf-related protein 1), formerly known as ARP, is a
membrane-associated Arf family member that lacks the
N-terminal myristoylation motif. Arfrp1 is mainly
associated with the trans-Golgi compartment and the
trans-Golgi network, where it regulates the targeting of
Arl1 and the GRIP domain-containing proteins, golgin-97
and golgin-245, onto Golgi membranes. It is also
involved in the anterograde transport of the vesicular
stomatitis virus G protein from the Golgi to the plasma
membrane, and in the retrograde transport of TGN38 and
Shiga toxin from endosomes to the trans-Golgi network.
Arfrp1 also inhibits Arf/Sec7-dependent activation of
phospholipase D. Deletion of Arfrp1 in mice causes
embryonic lethality at the gastrulation stage and
apoptosis of mesodermal cells, indicating its importance
in development.
Length = 168
Score = 165 bits (419), Expect = 2e-53
Identities = 74/155 (47%), Positives = 86/155 (55%), Gaps = 49/155 (31%)
Query: 19 CVLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITTTVGLNIGQIDINTVRLNFWDLGG 78
CVLILGLDNAGKTT+LE KTKF+KNYKG+NPSKIT TVGLNIG I++ RL FWDLGG
Sbjct: 1 CVLILGLDNAGKTTFLEQTKTKFSKNYKGLNPSKITPTVGLNIGTIEVGKARLMFWDLGG 60
Query: 79 QLELQSLWDK------------------------------------------------DI 90
Q EL+SLWDK D+
Sbjct: 61 QEELRSLWDKYYAESHGVIYVIDSTDRERFNESKSAFEKVINNEALEGVPLLVLANKQDL 120
Query: 91 RDCMGVREVKPIFNKNSAHLIGRRDCMVMPVSALT 125
D + V E+K +F+ LIGRRDC+V PVSAL
Sbjct: 121 PDALSVAEIKEVFDD-CIALIGRRDCLVQPVSALE 154
>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 = 74.5 bits (184), Expect = 5e-18
Identities = 24/78 (30%), Positives = 37/78 (47%), Gaps = 8/78 (10%)
Query: 19 CVLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITTTVGLNIGQIDINTVRLNFWDLGG 78
+L+LGLD AGKTT L K T+G N+ ++ V+ WD+GG
Sbjct: 1 RILMLGLDGAGKTTILYKLKLGE--------VVTTIPTIGFNVETVEYKNVKFTVWDVGG 52
Query: 79 QLELQSLWDKDIRDCMGV 96
Q +++ LW + G+
Sbjct: 53 QDKIRPLWKHYYENTDGL 70
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 68.0 bits (167), Expect = 2e-15
Identities = 28/80 (35%), Positives = 35/80 (43%), Gaps = 8/80 (10%)
Query: 8 FYKYMLRKDEFCVLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITTTVGLNIGQIDIN 67
K E +LILGLDNAGKTT L K T+G N+ +
Sbjct: 5 LAKLFGWNKEMRILILGLDNAGKTTIL--------YKLKLGEIVTTIPTIGFNVETVTYK 56
Query: 68 TVRLNFWDLGGQLELQSLWD 87
V+ WD+GGQ L+ LW
Sbjct: 57 NVKFTVWDVGGQESLRPLWR 76
>gnl|CDD|206720 cd04154, Arl2, Arf-like 2 (Arl2) GTPase. Arl2 (Arf-like 2)
GTPases are members of the Arf family that bind GDP and
GTP with very low affinity. Unlike most Arf family
proteins, Arl2 is not myristoylated at its N-terminal
helix. The protein PDE-delta, first identified in
photoreceptor rod cells, binds specifically to Arl2 and
is structurally very similar to RhoGDI. Despite the
high structural similarity between Arl2 and Rho
proteins and between PDE-delta and RhoGDI, the
interactions between the GTPases and their effectors
are very different. In its GTP bound form, Arl2
interacts with the protein Binder of Arl2 (BART), and
the complex is believed to play a role in mitochondrial
adenine nucleotide transport. In its GDP bound form,
Arl2 interacts with tubulin- folding Cofactor D; this
interaction is believed to play a role in regulation of
microtubule dynamics that impact the cytoskeleton, cell
division, and cytokinesis.
Length = 173
Score = 68.1 bits (167), Expect = 2e-15
Identities = 33/77 (42%), Positives = 46/77 (59%), Gaps = 8/77 (10%)
Query: 10 KYMLRKDEFCVLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITTTVGLNIGQIDINTV 69
K ++ E +L+LGLDNAGKTT L K + G + S I+ T+G NI ++ N
Sbjct: 7 KTKQKEREMRILMLGLDNAGKTTIL--------KKFNGEDISTISPTLGFNIKTLEYNGY 58
Query: 70 RLNFWDLGGQLELQSLW 86
+LN WD+GGQ L+S W
Sbjct: 59 KLNIWDVGGQKSLRSYW 75
>gnl|CDD|133353 cd04153, Arl5_Arl8, Arf-like 5 (Arl5) and 8 (Arl8) GTPases.
Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like
Arl4 and Arl7, are localized to the nucleus and
nucleolus. Arl5 is developmentally regulated during
embryogenesis in mice. Human Arl5 interacts with the
heterochromatin protein 1-alpha (HP1alpha), a
nonhistone chromosomal protein that is associated with
heterochromatin and telomeres, and prevents telomere
fusion. Arl5 may also play a role in embryonic nuclear
dynamics and/or signaling cascades. Arl8 was identified
from a fetal cartilage cDNA library. It is found in
brain, heart, lung, cartilage, and kidney. No function
has been assigned for Arl8 to date.
Length = 174
Score = 62.4 bits (152), Expect = 3e-13
Identities = 30/86 (34%), Positives = 44/86 (51%), Gaps = 12/86 (13%)
Query: 3 TLVSGFYKYMLRKDEFCVLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITT--TVGLN 60
L S + + E+ V+I+GLDNAGKTT L Y+ + + T T+G N
Sbjct: 1 LLFSSLWSLFFPRKEYKVIIVGLDNAGKTTIL----------YQFLLGEVVHTSPTIGSN 50
Query: 61 IGQIDINTVRLNFWDLGGQLELQSLW 86
+ +I +R WD+GGQ L+S W
Sbjct: 51 VEEIVYKNIRFLMWDIGGQESLRSSW 76
>gnl|CDD|206721 cd04155, Arl3, Arf-like 3 (Arl3) GTPase. Arl3 (Arf-like 3) is an
Arf family protein that differs from most Arf family
members in the N-terminal extension. In is inactive,
GDP-bound form, the N-terminal extension forms an
elongated loop that is hydrophobically anchored into
the membrane surface; however, it has been proposed
that this region might form a helix in the GTP-bound
form. The delta subunit of the rod-specific cyclic GMP
phosphodiesterase type 6 (PDEdelta) is an Arl3
effector. Arl3 binds microtubules in a regulated manner
to alter specific aspects of cytokinesis via
interactions with retinitis pigmentosa 2 (RP2). It has
been proposed that RP2 functions in concert with Arl3
to link the cell membrane and the cytoskeleton in
photoreceptors as part of the cell signaling or
vesicular transport machinery. In mice, the absence of
Arl3 is associated with abnormal epithelial cell
proliferation and cyst formation.
Length = 174
Score = 59.3 bits (144), Expect = 5e-12
Identities = 32/84 (38%), Positives = 44/84 (52%), Gaps = 9/84 (10%)
Query: 4 LVSGFYKYMLR-KDEFCVLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITTTVGLNIG 62
L+S K + E +L+LGLDNAGKTT L K + S IT T G NI
Sbjct: 1 LLSILRKLKPSSRQEVRILLLGLDNAGKTTIL--------KQLASEDISHITPTQGFNIK 52
Query: 63 QIDINTVRLNFWDLGGQLELQSLW 86
+ + +LN WD+GGQ +++ W
Sbjct: 53 NVQADGFKLNVWDIGGQRKIRPYW 76
>gnl|CDD|206716 cd04149, Arf6, ADP ribosylation factor 6 (Arf6). Arf6 subfamily.
Arf6 (ADP ribosylation factor 6) proteins localize to
the plasma membrane, where they perform a wide variety
of functions. In its active, GTP-bound form, Arf6 is
involved in cell spreading, Rac-induced formation of
plasma membrane ruffles, cell migration, wound healing,
and Fc-mediated phagocytosis. Arf6 appears to change
the actin structure at the plasma membrane by
activating Rac, a Rho family protein involved in
membrane ruffling. Arf6 is required for and enhances
Rac formation of ruffles. Arf6 can regulate dendritic
branching in hippocampal neurons, and in yeast it
localizes to the growing bud, where it plays a role in
polarized growth and bud site selection. In leukocytes,
Arf6 is required for chemokine-stimulated migration
across endothelial cells. Arf6 also plays a role in
down-regulation of beta2-adrenergic receptors and
luteinizing hormone receptors by facilitating the
release of sequestered arrestin to allow endocytosis.
Arf6 is believed to function at multiple sites on the
plasma membrane through interaction with a specific set
of GEFs, GAPs, and effectors. Arf6 has been implicated
in breast cancer and melanoma cell invasion, and in
actin remodelling at the invasion site of Chlamydia
infection.
Length = 168
Score = 55.2 bits (133), Expect = 2e-10
Identities = 28/71 (39%), Positives = 38/71 (53%), Gaps = 10/71 (14%)
Query: 17 EFCVLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITT-TVGLNIGQIDINTVRLNFWD 75
E +L+LGLD AGKTT L K + S T TVG N+ + V+ N WD
Sbjct: 9 EMRILMLGLDAAGKTTILYKLK---------LGQSVTTIPTVGFNVETVTYKNVKFNVWD 59
Query: 76 LGGQLELQSLW 86
+GGQ +++ LW
Sbjct: 60 VGGQDKIRPLW 70
>gnl|CDD|206718 cd04151, Arl1, ADP ribosylation factor 1 (Arf1). Arl1 subfamily.
Arl1 (Arf-like 1) localizes to the Golgi complex, where
it is believed to recruit effector proteins to the
trans-Golgi network. Like most members of the Arf
family, Arl1 is myristoylated at its N-terminal helix
and mutation of the myristoylation site disrupts Golgi
targeting. In humans, the Golgi-localized proteins
golgin-97 and golgin-245 have been identified as Arl1
effectors. Golgins are large coiled-coil proteins found
in the Golgi, and these golgins contain a C-terminal
GRIP domain, which is the site of Arl1 binding.
Additional Arl1 effectors include the GARP
(Golgi-associated retrograde protein)/VFT (Vps53)
vesicle-tethering complex and Arfaptin 2. Arl1 is not
required for exocytosis, but appears necessary for
trafficking from the endosomes to the Golgi. In
Drosophila zygotes, mutation of Arl1 is lethal, and in
the host-bloodstream form of Trypanosoma brucei, Arl1
is essential for viability.
Length = 158
Score = 53.6 bits (129), Expect = 5e-10
Identities = 25/69 (36%), Positives = 35/69 (50%), Gaps = 12/69 (17%)
Query: 20 VLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITT--TVGLNIGQIDINTVRLNFWDLG 77
+LILGLD AGKTT L Y+ +TT T+G N+ + ++ WDLG
Sbjct: 2 ILILGLDGAGKTTIL----------YRLQVGEVVTTIPTIGFNVETVTYKNLKFQVWDLG 51
Query: 78 GQLELQSLW 86
GQ ++ W
Sbjct: 52 GQTSIRPYW 60
>gnl|CDD|133356 cd04156, ARLTS1, Arf-like tumor suppressor gene 1 (ARLTS1 or
Arl11). ARLTS1 (Arf-like tumor suppressor gene 1),
also known as Arl11, is a member of the Arf family of
small GTPases that is believed to play a major role in
apoptotic signaling. ARLTS1 is widely expressed and
functions as a tumor suppressor gene in several human
cancers. ARLTS1 is a low-penetrance suppressor that
accounts for a small percentage of familial melanoma or
familial chronic lymphocytic leukemia (CLL). ARLTS1
inactivation seems to occur most frequently through
biallelic down-regulation by hypermethylation of the
promoter. In breast cancer, ARLTS1 alterations were
typically a combination of a hypomorphic polymorphism
plus loss of heterozygosity. In a case of thyroid
adenoma, ARLTS1 alterations were polymorphism plus
promoter hypermethylation. The nonsense polymorphism
Trp149Stop occurs with significantly greater frequency
in familial cancer cases than in sporadic cancer cases,
and the Cys148Arg polymorphism is associated with an
increase in high-risk familial breast cancer.
Length = 160
Score = 52.8 bits (127), Expect = 1e-09
Identities = 27/80 (33%), Positives = 45/80 (56%), Gaps = 13/80 (16%)
Query: 20 VLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITT--TVGLNIGQIDINT-VRLNFWDL 76
VL+LGLD+AGK+T L YK + +TT TVG N+ + + + L WD+
Sbjct: 2 VLLLGLDSAGKSTLL----------YKLKHAELVTTIPTVGFNVEMLQLEKHLSLTVWDV 51
Query: 77 GGQLELQSLWDKDIRDCMGV 96
GGQ +++++W + + G+
Sbjct: 52 GGQEKMRTVWKCYLENTDGL 71
>gnl|CDD|206722 cd04157, Arl6, Arf-like 6 (Arl6) GTPase. Arl6 (Arf-like 6) forms
a subfamily of the Arf family of small GTPases. Arl6
expression is limited to the brain and kidney in adult
mice, but it is expressed in the neural plate and
somites during embryogenesis, suggesting a possible
role for Arl6 in early development. Arl6 is also
believed to have a role in cilia or flagella function.
Several proteins have been identified that bind Arl6,
including Arl6 interacting protein (Arl6ip), and
SEC61beta, a subunit of the heterotrimeric conducting
channel SEC61p. Based on Arl6 binding to these
effectors, Arl6 is also proposed to play a role in
protein transport, membrane trafficking, or cell
signaling during hematopoietic maturation. At least
three specific homozygous Arl6 mutations in humans have
been found to cause Bardet-Biedl syndrome, a disorder
characterized by obesity, retinopathy, polydactyly,
renal and cardiac malformations, learning disabilities,
and hypogenitalism. Older literature suggests that Arl6
is a part of the Arl4/Arl7 subfamily, but analyses
based on more recent sequence data place Arl6 in its
own subfamily.
Length = 162
Score = 51.7 bits (124), Expect = 3e-09
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 6/77 (7%)
Query: 20 VLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITTTVGLNIGQIDINTVRLNFWDLGGQ 79
+L+LGLDN+GKTT + K ++ I TVG N+ + +D+ GQ
Sbjct: 2 ILVLGLDNSGKTTIINQLKPSNAQS------QNIVPTVGFNVESFKKGNLSFTAFDMSGQ 55
Query: 80 LELQSLWDKDIRDCMGV 96
+ + LW+ ++ G+
Sbjct: 56 GKYRGLWEHYYKNIQGI 72
>gnl|CDD|128474 smart00177, ARF, ARF-like small GTPases; ARF, ADP-ribosylation
factor. Ras homologues involved in vesicular
transport. Activator of phospholipase D isoforms.
Unlike Ras proteins they lack cysteine residues at
their C-termini and therefore are unlikely to be
prenylated. ARFs are N-terminally myristoylated.
Contains ATP/GTP-binding motif (P-loop).
Length = 175
Score = 51.1 bits (122), Expect = 6e-09
Identities = 26/93 (27%), Positives = 42/93 (45%), Gaps = 12/93 (12%)
Query: 6 SGFYKYMLRKDEFCVLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITT--TVGLNIGQ 63
+ + E +L++GLD AGKTT L YK +TT T+G N+
Sbjct: 2 GKLFSKLFGNKEMRILMVGLDAAGKTTIL----------YKLKLGESVTTIPTIGFNVET 51
Query: 64 IDINTVRLNFWDLGGQLELQSLWDKDIRDCMGV 96
+ + WD+GGQ +++ LW + G+
Sbjct: 52 VTYKNISFTVWDVGGQDKIRPLWRHYYTNTQGL 84
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins
[General function prediction only].
Length = 219
Score = 50.0 bits (119), Expect = 2e-08
Identities = 25/85 (29%), Positives = 36/85 (42%), Gaps = 5/85 (5%)
Query: 13 LRKDEFCVLILGLDNAGKTTYLESAKT-KFTKNYKGMNPSKITTTVGLNIGQIDINTVRL 71
L EF +++LG GKTT L +F + Y P+ I N ++L
Sbjct: 1 LFMKEFKIVVLGDGGVGKTTLLNRLVGDEFPEGYP---PTIGNLDPAKTIEPYRRN-IKL 56
Query: 72 NFWDLGGQLELQSLWDKDIRDCMGV 96
WD GQ E +SL + R G+
Sbjct: 57 QLWDTAGQEEYRSLRPEYYRGANGI 81
>gnl|CDD|206719 cd04152, Arl4_Arl7, Arf-like 4 (Arl4) and 7 (Arl7) GTPases. Arl4
(Arf-like 4) is highly expressed in testicular germ
cells, and is found in the nucleus and nucleolus. In
mice, Arl4 is developmentally expressed during
embryogenesis, and a role in somite formation and
central nervous system differentiation has been
proposed. Arl7 has been identified as the only Arf/Arl
protein to be induced by agonists of liver X-receptor
and retinoid X-receptor and by cholesterol loading in
human macrophages. Arl7 is proposed to play a role in
transport between a perinuclear compartment and the
plasma membrane, apparently linked to the
ABCA1-mediated cholesterol secretion pathway. Older
literature suggests that Arl6 is a part of the
Arl4/Arl7 subfamily, but analyses based on more recent
sequence data place Arl6 in its own subfamily.
Length = 183
Score = 49.4 bits (118), Expect = 2e-08
Identities = 29/70 (41%), Positives = 41/70 (58%), Gaps = 9/70 (12%)
Query: 20 VLILGLDNAGKTTYLESAK-TKF--TKNYKGMNPSKITTTVGLNIGQIDINTVRLNFWDL 76
+++LGLD+AGKTT L K +F T KG N KI ++G + V +FWD+
Sbjct: 6 IVMLGLDSAGKTTVLYRLKFNEFVNTVPTKGFNTEKIKVSLG------NAKGVTFHFWDV 59
Query: 77 GGQLELQSLW 86
GGQ +L+ LW
Sbjct: 60 GGQEKLRPLW 69
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 49.2 bits (117), Expect = 3e-08
Identities = 27/88 (30%), Positives = 43/88 (48%), Gaps = 12/88 (13%)
Query: 1 MYTLVSGFYKYMLRKDEFCVLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITT--TVG 58
M + + + K E +L++GLD AGKTT L YK +TT T+G
Sbjct: 1 MGLSFTKLFSRLFAKKEMRILMVGLDAAGKTTIL----------YKLKLGEIVTTIPTIG 50
Query: 59 LNIGQIDINTVRLNFWDLGGQLELQSLW 86
N+ ++ + WD+GGQ +++ LW
Sbjct: 51 FNVETVEYKNISFTVWDVGGQDKIRPLW 78
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 48.7 bits (116), Expect = 4e-08
Identities = 30/88 (34%), Positives = 46/88 (52%), Gaps = 12/88 (13%)
Query: 1 MYTLVSGFYKYMLRKDEFCVLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITT--TVG 58
M +S +K + K E +L++GLD AGKTT L YK +TT T+G
Sbjct: 1 MGLWLSSAFKSLFGKKEVRILMVGLDAAGKTTIL----------YKLKLGEVVTTIPTIG 50
Query: 59 LNIGQIDINTVRLNFWDLGGQLELQSLW 86
N+ ++ ++ WD+GGQ +L+ LW
Sbjct: 51 FNVETVEYKNLKFTMWDVGGQDKLRPLW 78
>gnl|CDD|206724 cd04159, Arl10_like, Arf-like 9 (Arl9) and 10 (Arl10) GTPases.
Arl10-like subfamily. Arl9/Arl10 was identified from a
human cancer-derived EST dataset. No functional
information about the subfamily is available at the
current time, but crystal structures of human Arl10b
and Arl10c have been solved.
Length = 159
Score = 46.5 bits (111), Expect = 2e-07
Identities = 27/76 (35%), Positives = 41/76 (53%), Gaps = 12/76 (15%)
Query: 22 ILGLDNAGKTTYLES-AKTKFTKNYKGMNPSKITTTVGLNIGQIDINTVRLNFWDLGGQL 80
++GL N+GKTT + A +F++ P TVG N+ ++ V + WDLGGQ
Sbjct: 4 LVGLQNSGKTTLVNVIASGQFSE---DTIP-----TVGFNMRKVTKGNVTIKVWDLGGQP 55
Query: 81 ELQSLWDKDIRDCMGV 96
+S+W+ R C GV
Sbjct: 56 RFRSMWE---RYCRGV 68
>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 = 46.9 bits (112), Expect = 2e-07
Identities = 24/91 (26%), Positives = 38/91 (41%), Gaps = 8/91 (8%)
Query: 6 SGFYKYMLRKDEFCVLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITTTVGLNIGQID 65
+ L K E ++ LGLDNAGKTT L K + T+ ++
Sbjct: 8 NVLSSLGLYKKEAKIVFLGLDNAGKTTLLHMLKDDRLAQH--------VPTLHPTSEELT 59
Query: 66 INTVRLNFWDLGGQLELQSLWDKDIRDCMGV 96
I V+ +DLGG + + +W + G+
Sbjct: 60 IGNVKFTTFDLGGHEQARRVWKDYFPEVDGI 90
>gnl|CDD|206717 cd04150, Arf1_5_like, ADP-ribosylation factor-1 (Arf1) and
ADP-ribosylation factor-5 (Arf5). The Arf1-Arf5-like
subfamily contains Arf1, Arf2, Arf3, Arf4, Arf5, and
related proteins. Arfs1-5 are soluble proteins that are
crucial for assembling coat proteins during vesicle
formation. Each contains an N-terminal myristoylated
amphipathic helix that is folded into the protein in
the GDP-bound state. GDP/GTP exchange exposes the
helix, which anchors to the membrane. Following GTP
hydrolysis, the helix dissociates from the membrane and
folds back into the protein. A general feature of
Arf1-5 signaling may be the cooperation of two Arfs at
the same site. Arfs1-5 are generally considered to be
interchangeable in function and location, but some
specific functions have been assigned. Arf1 localizes
to the early/cis-Golgi, where it is activated by GBF1
and recruits the coat protein COPI. It also localizes
to the trans-Golgi network (TGN), where it is activated
by BIG1/BIG2 and recruits the AP1, AP3, AP4, and GGA
proteins. Humans, but not rodents and other lower
eukaryotes, lack Arf2. Human Arf3 shares 96% sequence
identity with Arf1 and is believed to generally
function interchangeably with Arf1. Human Arf4 in the
activated (GTP-bound) state has been shown to interact
with the cytoplasmic domain of epidermal growth factor
receptor (EGFR) and mediate the EGF-dependent
activation of phospholipase D2 (PLD2), leading to
activation of the activator protein 1 (AP-1)
transcription factor. Arf4 has also been shown to
recognize the C-terminal sorting signal of rhodopsin
and regulate its incorporation into specialized
post-Golgi rhodopsin transport carriers (RTCs). There
is some evidence that Arf5 functions at the early-Golgi
and the trans-Golgi to affect Golgi-associated
alpha-adaptin homology Arf-binding proteins (GGAs).
Length = 159
Score = 45.1 bits (107), Expect = 7e-07
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 12/69 (17%)
Query: 20 VLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITT--TVGLNIGQIDINTVRLNFWDLG 77
+L++GLD AGKTT L YK +TT T+G N+ ++ + WD+G
Sbjct: 3 ILMVGLDAAGKTTIL----------YKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVG 52
Query: 78 GQLELQSLW 86
GQ +++ LW
Sbjct: 53 GQDKIRPLW 61
>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 = 44.7 bits (106), Expect = 1e-06
Identities = 19/82 (23%), Positives = 31/82 (37%), Gaps = 6/82 (7%)
Query: 20 VLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITTTVGLNIGQIDIN--TVRLNFWDLG 77
++I+G N GK+T L + N + K TT I+ + T + N D
Sbjct: 4 IVIVGDPNVGKSTLLN----RLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTA 59
Query: 78 GQLELQSLWDKDIRDCMGVREV 99
GQ + ++ R V
Sbjct: 60 GQEDYDAIRRLYYRAVESSLRV 81
>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 = 45.0 bits (106), Expect = 1e-06
Identities = 24/67 (35%), Positives = 36/67 (53%), Gaps = 8/67 (11%)
Query: 20 VLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITTTVGLNIGQIDINTVRLNFWDLGGQ 79
V+ LGLD AGKTT L K + M P T+G N+ ++ ++ WD+GG+
Sbjct: 2 VVTLGLDGAGKTTILFKLKQD-----EFMQP---IPTIGFNVETVEYKNLKFTIWDVGGK 53
Query: 80 LELQSLW 86
+L+ LW
Sbjct: 54 HKLRPLW 60
>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 = 43.6 bits (103), Expect = 3e-06
Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 7/67 (10%)
Query: 20 VLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITTTVGLNIGQIDINTVRLNFWDLGGQ 79
+L+LGLD AGKT+ L S ++ + + T G N I + ++GG
Sbjct: 2 ILVLGLDGAGKTSLLHSLSSERS-------LESVVPTTGFNSVAIPTQDAIMELLEIGGS 54
Query: 80 LELQSLW 86
L+ W
Sbjct: 55 QNLRKYW 61
>gnl|CDD|197556 smart00178, SAR, Sar1p-like members of the Ras-family of small
GTPases. Yeast SAR1 is an essential gene required for
transport of secretory proteins from the endoplasmic
reticulum to the Golgi apparatus.
Length = 184
Score = 41.8 bits (98), Expect = 1e-05
Identities = 26/67 (38%), Positives = 33/67 (49%), Gaps = 8/67 (11%)
Query: 20 VLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITTTVGLNIGQIDINTVRLNFWDLGGQ 79
+L LGLDNAGKTT L K P++ T+ L IG I T +DLGG
Sbjct: 20 ILFLGLDNAGKTTLLHMLK---NDRLAQHQPTQHPTSEELAIGNIKFTT-----FDLGGH 71
Query: 80 LELQSLW 86
+ + LW
Sbjct: 72 QQARRLW 78
>gnl|CDD|133361 cd04161, Arl2l1_Arl13_like, Arl2-like protein 1 (Arl2l1) and
Arl13. Arl2l1 (Arl2-like protein 1) and Arl13 form a
subfamily of the Arf family of small GTPases. Arl2l1
was identified in human cells during a search for the
gene(s) responsible for Bardet-Biedl syndrome (BBS).
Like Arl6, the identified BBS gene, Arl2l1 is proposed
to have cilia-specific functions. Arl13 is found on the
X chromosome, but its expression has not been
confirmed; it may be a pseudogene.
Length = 167
Score = 41.2 bits (97), Expect = 2e-05
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 8/77 (10%)
Query: 20 VLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITTTVGLNIGQIDINTVRLNFWDLGGQ 79
+L +GLDNAGKTT + + +G P K+ TVG ++ ++ + +DLGG
Sbjct: 2 LLTVGLDNAGKTTLVSA--------LQGEIPKKVAPTVGFTPTKLRLDKYEVCIFDLGGG 53
Query: 80 LELQSLWDKDIRDCMGV 96
+ +W + G+
Sbjct: 54 ANFRGIWVNYYAEAHGL 70
>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 = 38.2 bits (89), Expect = 1e-04
Identities = 17/77 (22%), Positives = 33/77 (42%), Gaps = 9/77 (11%)
Query: 20 VLILGLDNAGKTTYLES-AKTKFTKNYKGMNPSKITTTVGLNIGQIDINTVRLNFWDLGG 78
V+++G +GK++ L +F + T+ ++ ++D +T LN WD GG
Sbjct: 2 VVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQG----DTLAVDTLEVDGDTGLLNIWDFGG 57
Query: 79 QLELQSLWDKDIRDCMG 95
+ E + M
Sbjct: 58 REE----LKFEHIIFMK 70
>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 = 37.4 bits (87), Expect = 5e-04
Identities = 14/69 (20%), Positives = 25/69 (36%), Gaps = 6/69 (8%)
Query: 21 LILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITTTVGLNIG--QIDINTVRLNFWDLGG 78
+++G GK++ L + G TT ++ ++D V+L D G
Sbjct: 1 VVVGRGGVGKSSLLNA----LLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPG 56
Query: 79 QLELQSLWD 87
E L
Sbjct: 57 LDEFGGLGR 65
>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 = 35.4 bits (82), Expect = 0.002
Identities = 20/66 (30%), Positives = 29/66 (43%), Gaps = 14/66 (21%)
Query: 20 VLILGLDNAGKTTYLES-AKTKFTKNYKGMNPSKITTTVGLNIGQIDI-----NTVRLNF 73
++++G GKT+ + KF G S T G+N+ I +RLN
Sbjct: 4 LMLVGQGGVGKTSLCKQLIGEKF----DGDESS----THGINVQDWKIPAPERKKIRLNV 55
Query: 74 WDLGGQ 79
WD GGQ
Sbjct: 56 WDFGGQ 61
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 35.5 bits (82), Expect = 0.003
Identities = 22/75 (29%), Positives = 36/75 (48%), Gaps = 13/75 (17%)
Query: 18 FCVLILGLDNAGKTTYLESAKT-KFTKNYKGMNPSKITTTVGLNIGQIDINT----VRLN 72
F ++I+G GKTT+++ T +F K Y+ T+G+ + +D T +R
Sbjct: 14 FKLVIVGDGGTGKTTFVKRHLTGEFEKKYE--------PTIGVEVHPLDFFTNCGKIRFY 65
Query: 73 FWDLGGQLELQSLWD 87
WD GQ + L D
Sbjct: 66 CWDTAGQEKFGGLRD 80
>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 = 34.6 bits (80), Expect = 0.004
Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 13/67 (19%)
Query: 18 FCVLILGLDNAGKTTYLESAKTK-FTKNYKGMNPSKITTTVGLNIGQIDINT----VRLN 72
F ++++G GKTT+++ T F K Y T+G+ + +D +T +R N
Sbjct: 1 FKLVLVGDGGTGKTTFVKRHLTGEFEKKYV--------ATLGVEVHPLDFHTNRGKIRFN 52
Query: 73 FWDLGGQ 79
WD GQ
Sbjct: 53 VWDTAGQ 59
>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 = 34.8 bits (80), Expect = 0.004
Identities = 31/101 (30%), Positives = 43/101 (42%), Gaps = 26/101 (25%)
Query: 9 YKYMLRKDEFCVLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITTTVGLNIGQIDI-- 66
Y Y+++ +L LG GKTT+L ++T N NP K TTVG++ + +
Sbjct: 1 YDYLIK-----LLALGDSGVGKTTFLY----RYTDNK--FNP-KFITTVGIDFREKRVVY 48
Query: 67 ------------NTVRLNFWDLGGQLELQSLWDKDIRDCMG 95
V L WD GQ +SL RD MG
Sbjct: 49 NSQGPDGTSGKAFRVHLQLWDTAGQERFRSLTTAFFRDAMG 89
>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 = 34.0 bits (78), Expect = 0.009
Identities = 23/80 (28%), Positives = 37/80 (46%), Gaps = 15/80 (18%)
Query: 20 VLILGLDNAGKTTYLES-AKTKFTKNYKGMNPSKITTTVGLNIGQIDI------NTVRLN 72
V+++G N GK++ ++ K FTK+YK T+G++ + I VRL
Sbjct: 3 VIVVGNGNVGKSSMIQRFVKGIFTKDYK--------KTIGVDFLEKQIFLRQSDEDVRLM 54
Query: 73 FWDLGGQLELQSLWDKDIRD 92
WD GQ E ++ R
Sbjct: 55 LWDTAGQEEFDAITKAYYRG 74
>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 = 33.0 bits (75), Expect = 0.020
Identities = 27/93 (29%), Positives = 44/93 (47%), Gaps = 9/93 (9%)
Query: 18 FCVLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITTT-VGLNIGQIDIN--TVRLNFW 74
F +L++G GKT L +FT N + S I+T V + I+++ VR+ W
Sbjct: 1 FRLLLIGDSGVGKTCLL----CRFTDNE--FHSSHISTIGVDFKMKTIEVDGIKVRIQIW 54
Query: 75 DLGGQLELQSLWDKDIRDCMGVREVKPIFNKNS 107
D GQ Q++ + R G+ V I ++ S
Sbjct: 55 DTAGQERYQTITKQYYRRAQGIFLVYDISSERS 87
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 32.8 bits (75), Expect = 0.022
Identities = 18/82 (21%), Positives = 38/82 (46%), Gaps = 6/82 (7%)
Query: 12 MLRKDEFCVLILGLDNAGKTTYLESAKTKFTKNYKGMNPS-----KITTTVGLNIGQIDI 66
+ E ++++G AGKTT++ + K + S K TTV ++ G I++
Sbjct: 5 ANKMIETKIVVIGPVGAGKTTFVRALSDKPLVITEADASSVSGKGKRPTTVAMDFGSIEL 64
Query: 67 N-TVRLNFWDLGGQLELQSLWD 87
+ ++ + GQ + +W+
Sbjct: 65 DEDTGVHLFGTPGQERFKFMWE 86
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 32.4 bits (74), Expect = 0.033
Identities = 21/76 (27%), Positives = 35/76 (46%), Gaps = 13/76 (17%)
Query: 17 EFCVLILGLDNAGKTTYLESAKT-KFTKNYKGMNPSKITTTVGLNIGQIDINT----VRL 71
EF ++++G GKTT+++ T +F K Y T+G+ + + T +
Sbjct: 9 EFKLILVGDGGVGKTTFVKRHLTGEFEKKY--------IPTLGVEVHPLKFYTNCGPICF 60
Query: 72 NFWDLGGQLELQSLWD 87
N WD GQ + L D
Sbjct: 61 NVWDTAGQEKFGGLRD 76
>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 = 31.4 bits (71), Expect = 0.077
Identities = 29/94 (30%), Positives = 42/94 (44%), Gaps = 11/94 (11%)
Query: 18 FCVLILGLDNAGKTTYL-ESAKTKFTKNYKGMNPSKITTT-VGLNIGQIDIN--TVRLNF 73
F +LI+G GK++ L A F+ +Y ITT V I ++IN V+L
Sbjct: 7 FKLLIIGDSGVGKSSLLLRFADNTFSGSY-------ITTIGVDFKIRTVEINGERVKLQI 59
Query: 74 WDLGGQLELQSLWDKDIRDCMGVREVKPIFNKNS 107
WD GQ +++ R GV V + N S
Sbjct: 60 WDTAGQERFRTITSTYYRGTHGVIVVYDVTNGES 93
>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 = 30.9 bits (71), Expect = 0.11
Identities = 20/71 (28%), Positives = 34/71 (47%), Gaps = 13/71 (18%)
Query: 20 VLILGLDNAGKTTYLES-AKTKFTKNYKGMNPSKITTTVGLNIGQIDIN----TVRLNFW 74
++++G GKT+ L KF++NYK +T+G++ I V+L W
Sbjct: 3 IVLIGDSGVGKTSLLLRFVDNKFSENYK--------STIGVDFKSKTIEVDGKKVKLQIW 54
Query: 75 DLGGQLELQSL 85
D GQ +S+
Sbjct: 55 DTAGQERFRSI 65
>gnl|CDD|213207 cd03240, ABC_Rad50, ATP-binding cassette domain of Rad50. The
catalytic domains of Rad50 are similar to the
ATP-binding cassette of ABC transporters, but are not
associated with membrane-spanning domains. The
conserved ATP-binding motifs common to Rad50 and the
ABC transporter family include the Walker A and Walker
B motifs, the Q loop, a histidine residue in the switch
region, a D-loop, and a conserved LSGG sequence. This
conserved sequence, LSGG, is the most specific and
characteristic motif of this family and is thus known
as the ABC signature sequence.
Length = 204
Score = 30.7 bits (70), Expect = 0.12
Identities = 17/68 (25%), Positives = 26/68 (38%), Gaps = 11/68 (16%)
Query: 16 DEFCVLILGLDNAGKTTYLESAK-----TKFTKNYKGMNPSKITTTVGLNIGQIDINTVR 70
LI+G + AGKTT +E+ K + G + K+ G Q+
Sbjct: 21 FSPLTLIVGQNGAGKTTIIEALKYALTGELPPNSKGGAHDPKLIRE-GEVRAQVK----- 74
Query: 71 LNFWDLGG 78
L F + G
Sbjct: 75 LAFENANG 82
>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 = 30.1 bits (68), Expect = 0.17
Identities = 24/97 (24%), Positives = 40/97 (41%), Gaps = 5/97 (5%)
Query: 18 FCVLILGLDNAGKTTYLESAKTKFTKN-YKGMNPSKITTTVGLNIGQIDINTVRLNFWDL 76
F LI+G GK+ L +F +N +K + I G + + +V+L WD
Sbjct: 1 FKFLIIGSAGTGKSCLLH----QFIENKFKQDSNHTIGVEFGSRVVNVGGKSVKLQIWDT 56
Query: 77 GGQLELQSLWDKDIRDCMGVREVKPIFNKNSAHLIGR 113
GQ +S+ R G V I ++ S + +
Sbjct: 57 AGQERFRSVTRSYYRGAAGALLVYDITSRESFNALTN 93
>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 = 30.2 bits (68), Expect = 0.23
Identities = 29/94 (30%), Positives = 41/94 (43%), Gaps = 14/94 (14%)
Query: 20 VLILGLDNAGKTTYLES-AKTKFTKNYKGMNPSKITTTVGLNIGQIDIN-----TVRLNF 73
+++LG +GKT+ + A+ F K+YK T+GL+ I V L
Sbjct: 3 IVVLGDGASGKTSLIRRFAQEGFGKSYK--------QTIGLDFFSRRITLPGSLNVTLQV 54
Query: 74 WDLGGQLELQSLWDKDIRDCMGVREVKPIFNKNS 107
WD+GGQ + DK I V V I N S
Sbjct: 55 WDIGGQQIGGKMLDKYIYGAQAVCLVYDITNSQS 88
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 29.7 bits (66), Expect = 0.27
Identities = 17/44 (38%), Positives = 20/44 (45%)
Query: 64 IDINTVRLNFWDLGGQLELQSLWDKDIRDCMGVREVKPIFNKNS 107
+D VRL WD GQ +SL IRD V I N+ S
Sbjct: 24 LDEGPVRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDITNRQS 67
>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 = 29.8 bits (68), Expect = 0.27
Identities = 21/69 (30%), Positives = 29/69 (42%), Gaps = 10/69 (14%)
Query: 20 VLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITTTVGLN---IGQIDINTVRLNFWDL 76
++++G GKT L S +T N P++ TV N +D V L WD
Sbjct: 3 IVVVGDGAVGKTCLLIS----YTTNK---FPTEYVPTVFDNYSANVTVDGKQVNLGLWDT 55
Query: 77 GGQLELQSL 85
GQ E L
Sbjct: 56 AGQEEYDRL 64
>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 = 29.8 bits (68), Expect = 0.27
Identities = 21/79 (26%), Positives = 35/79 (44%), Gaps = 9/79 (11%)
Query: 20 VLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITT-TVGLNIGQIDIN--TVRLNFWDL 76
++++G GK++ L +FT+N I T V I+++ TV+L WD
Sbjct: 2 LVLVGDGGVGKSSLL----IRFTQNK--FPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDT 55
Query: 77 GGQLELQSLWDKDIRDCMG 95
GQ ++L R G
Sbjct: 56 AGQERFRALRPLYYRGAQG 74
>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 = 29.6 bits (67), Expect = 0.28
Identities = 23/68 (33%), Positives = 35/68 (51%), Gaps = 14/68 (20%)
Query: 18 FCVLILGLDNAGKTTYLESAKTK-FTKNYKGMNPSKITTTVG----LNIGQIDINT-VRL 71
F VL++G GKT+ ++ F+++YK T+G L + + D NT VRL
Sbjct: 1 FKVLVIGDLGVGKTSIIKRYVHGVFSQHYK--------ATIGVDFALKVIEWDPNTVVRL 52
Query: 72 NFWDLGGQ 79
WD+ GQ
Sbjct: 53 QLWDIAGQ 60
>gnl|CDD|206706 cd04134, Rho3, Ras homology family 3 (Rho3) of small guanosine
triphosphatases (GTPases). Rho3 is a member of the Rho
family found only in fungi. Rho3 is believed to
regulate cell polarity by interacting with the
diaphanous/formin family protein For3 to control both
the actin cytoskeleton and microtubules. Rho3 is also
believed to have a direct role in exocytosis that is
independent of its role in regulating actin polarity.
The function in exocytosis may be two-pronged: first,
in the transport of post-Golgi vesicles from the mother
cell to the bud, mediated by myosin (Myo2); second, in
the docking and fusion of vesicles to the plasma
membrane, mediated by an exocyst (Exo70) protein. Most
Rho proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins.
Length = 185
Score = 29.4 bits (66), Expect = 0.33
Identities = 23/69 (33%), Positives = 29/69 (42%), Gaps = 10/69 (14%)
Query: 20 VLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITTTVGLN---IGQIDINTVRLNFWDL 76
V++LG GKT+ L FT+ Y P TV N +D V L+ WD
Sbjct: 3 VVVLGDGACGKTSLLNV----FTRGY---FPQVYEPTVFENYIHDIFVDGLAVELSLWDT 55
Query: 77 GGQLELQSL 85
GQ E L
Sbjct: 56 AGQEEFDRL 64
>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 = 29.5 bits (66), Expect = 0.36
Identities = 26/95 (27%), Positives = 42/95 (44%), Gaps = 13/95 (13%)
Query: 18 FCVLILGLDNAGKTTYL-ESAKTKFTKNYKGMNPSKITTTVGLNIGQIDI----NTVRLN 72
F +LI+G + GKT++L A FT S +TVG++ + ++L
Sbjct: 2 FKLLIIGNSSVGKTSFLFRYADDSFT--------SAFVSTVGIDFKVKTVYRNDKRIKLQ 53
Query: 73 FWDLGGQLELQSLWDKDIRDCMGVREVKPIFNKNS 107
WD GQ +++ R MG + I N+ S
Sbjct: 54 IWDTAGQERYRTITTAYYRGAMGFILMYDITNEES 88
>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 = 28.8 bits (65), Expect = 0.55
Identities = 22/71 (30%), Positives = 32/71 (45%), Gaps = 13/71 (18%)
Query: 20 VLILGLDNAGKTTYLESAKTK-FTKNYKGMNPSKITTTVGLNI--GQIDIN--TVRLNFW 74
V+ILG GKT+ + K F+ YK T+G + ++ ++ V L W
Sbjct: 3 VIILGDSGVGKTSLMNQYVNKKFSNQYKA--------TIGADFLTKEVTVDDRLVTLQIW 54
Query: 75 DLGGQLELQSL 85
D GQ QSL
Sbjct: 55 DTAGQERFQSL 65
>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 = 28.7 bits (64), Expect = 0.58
Identities = 29/108 (26%), Positives = 45/108 (41%), Gaps = 14/108 (12%)
Query: 9 YKYMLRKDEFCVLILGLDNAGKTTYLESAKTKFTKN---YKGMNPSKITTTVGLNIGQID 65
Y Y+L+ L++G + GK L S + T++ Y K TT + +D
Sbjct: 3 YDYLLK-----FLLVGDSDVGKGEILASLQDGSTESPYGYNMGIDYKTTTIL------LD 51
Query: 66 INTVRLNFWDLGGQLELQSLWDKDIRDCMGVREVKPIFNKNSAHLIGR 113
V+L WD GQ +++ R G+ V I N+ S I R
Sbjct: 52 GRRVKLQLWDTSGQGRFCTIFRSYSRGAQGIILVYDITNRWSFDGIDR 99
>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 = 28.8 bits (64), Expect = 0.61
Identities = 20/70 (28%), Positives = 32/70 (45%), Gaps = 13/70 (18%)
Query: 23 LGLDNAGKTTYLESAKT-KFTKNYKGMNPSKITTTVGLNIGQIDINT----VRLNFWDLG 77
+G GKTT+++ T +F K Y T+G+ + + +T +R N WD
Sbjct: 1 VGDGGTGKTTFVKRHLTGEFEKKY--------VATLGVEVHPLVFHTNRGPIRFNVWDTA 52
Query: 78 GQLELQSLWD 87
GQ + L D
Sbjct: 53 GQEKFGGLRD 62
>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 = 28.7 bits (64), Expect = 0.69
Identities = 20/81 (24%), Positives = 39/81 (48%), Gaps = 16/81 (19%)
Query: 9 YKYMLRKDEFCVLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITTTVGLN--IGQIDI 66
Y ++ F ++++G GKT + +FT+ G+ P T+G++ I ++I
Sbjct: 4 YDFL-----FKIVLIGNAGVGKTCLVR----RFTQ---GLFPPGQGATIGVDFMIKTVEI 51
Query: 67 N--TVRLNFWDLGGQLELQSL 85
++L WD GQ +S+
Sbjct: 52 KGEKIKLQIWDTAGQERFRSI 72
>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 = 28.1 bits (63), Expect = 0.84
Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 10/63 (15%)
Query: 22 ILGLDNAGKTTYLESAKTKFTK--NYKGMNPSKITTTVGLNIGQID-INTVRLNFWDLGG 78
++GL N GK+T L + + + +Y TT+ N+G + + V + DL G
Sbjct: 2 LVGLPNVGKSTLLSALTSAKVEIASYPF-------TTLEPNVGVFEFGDGVDIQIIDLPG 54
Query: 79 QLE 81
L+
Sbjct: 55 LLD 57
>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 = 28.0 bits (63), Expect = 0.89
Identities = 18/57 (31%), Positives = 24/57 (42%), Gaps = 12/57 (21%)
Query: 40 KFTKNYKGMNPSKITTTVGLN----IGQIDINTVRLNFWDLGGQLELQSLWDKDIRD 92
F Y+ T+G++ +D TVRL WD GQ +SL IRD
Sbjct: 24 TFDNQYQ--------ATIGIDFLSKTMYVDDKTVRLQLWDTAGQERFRSLIPSYIRD 72
>gnl|CDD|218199 pfam04665, Pox_A32, Poxvirus A32 protein. The A32 protein is
thought to be involved in viral DNA packaging.
Length = 241
Score = 27.7 bits (62), Expect = 1.3
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 13 LRKDEFCVLILGLDNAGKTTYLESAKTKFTKNYK 46
L F + I+G +GKTTYL S + +K
Sbjct: 9 LLAAPFRMAIVGGSGSGKTTYLLSLLRTLVRKFK 42
>gnl|CDD|188394 TIGR03864, PQQ_ABC_ATP, ABC transporter, ATP-binding subunit,
PQQ-dependent alcohol dehydrogenase system. Members of
this protein family are the ATP-binding subunit of an
ABC transporter system that is associated with PQQ
biosynthesis and PQQ-dependent alcohol dehydrogenases.
While this family shows homology to several efflux ABC
transporter subunits, the presence of a periplasmic
substrate-binding protein and association with systems
for catabolism of alcohols suggests a role in import
rather than detoxification [Transport and binding
proteins, Carbohydrates, organic alcohols, and acids].
Length = 236
Score = 28.0 bits (63), Expect = 1.3
Identities = 9/20 (45%), Positives = 12/20 (60%), Gaps = 1/20 (5%)
Query: 13 LRKDEFCVLILGLDNAGKTT 32
+R F L LG + AGK+T
Sbjct: 24 VRPGRFVAL-LGPNGAGKST 42
>gnl|CDD|218203 pfam04670, Gtr1_RagA, Gtr1/RagA G protein conserved region. GTR1
was first identified in S. cerevisiae as a suppressor
of a mutation in RCC1. Biochemical analysis revealed
that Gtr1 is in fact a G protein of the Ras family. The
RagA/B proteins are the human homologues of Gtr1.
Included in this family is the human Rag C, a novel
protein that has been shown to interact with RagA/B.
Length = 230
Score = 27.5 bits (62), Expect = 1.6
Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 15/71 (21%)
Query: 20 VLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITTTVGLNIGQIDINTVR------LNF 73
VL++GL +GK++ F+ NY + T +G I ++ + VR LN
Sbjct: 2 VLLMGLRGSGKSSM---RSIIFS-NY----SPRDTLRLGATI-DVEQSHVRFLGNLTLNL 52
Query: 74 WDLGGQLELQS 84
WD GQ +
Sbjct: 53 WDCPGQDDFME 63
>gnl|CDD|161676 TIGR00041, DTMP_kinase, thymidylate kinase. Function:
phosphorylation of DTMP to form DTDP in both de novo
and salvage pathways of DTTP synthesis. Catalytic
activity: ATP + thymidine 5'-phosphate = ADP +
thymidine 5'-diphosphate [Purines, pyrimidines,
nucleosides, and nucleotides, Nucleotide and nucleoside
interconversions].
Length = 195
Score = 27.3 bits (61), Expect = 1.7
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 20 VLILGLDNAGKTTYLESAKTKFTKN 44
++I G+D AGKTT K +N
Sbjct: 6 IVIEGIDGAGKTTQANLLKKLLQEN 30
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 27.6 bits (61), Expect = 1.8
Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 16/75 (21%)
Query: 9 YKYMLRKDEFCVLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITTTVGLNIG----QI 64
Y Y+ F ++++G GK+ L ++FT+N + SK +T+G+ Q+
Sbjct: 9 YDYL-----FKIVLIGDSGVGKSNIL----SRFTRNEFCLE-SK--STIGVEFATRTLQV 56
Query: 65 DINTVRLNFWDLGGQ 79
+ TV+ WD GQ
Sbjct: 57 EGKTVKAQIWDTAGQ 71
>gnl|CDD|238674 cd01378, MYSc_type_I, Myosin motor domain, type I myosins. Myosin I
generates movement at the leading edge in cell motility,
and class I myosins have been implicated in phagocytosis
and vesicle transport. Myosin I, an unconventional
myosin, does not form dimers. This catalytic (head)
domain has ATPase activity and belongs to the larger
group of P-loop NTPases. Myosins are actin-dependent
molecular motors that play important roles in muscle
contraction, cell motility, and organelle transport. The
head domain is a molecular motor, which utilizes ATP
hydrolysis to generate directed movement toward the plus
end along actin filaments. A cyclical interaction
between myosin and actin provides the driving force.
Rates of ATP hydrolysis and consequently the speed of
movement along actin filaments vary widely, from about
0.04 micrometer per second for myosin I to 4.5
micrometer per second for myosin II in skeletal muscle.
Myosin II moves in discrete steps about 5-10 nm long and
generates 1-5 piconewtons of force. Upon ATP binding,
the myosin head dissociates from an actin filament. ATP
hydrolysis causes the head to pivot and associate with a
new actin subunit. The release of Pi causes the head to
pivot and move the filament (power stroke). Release of
ADP completes the cycle.
Length = 674
Score = 27.6 bits (62), Expect = 2.1
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 4/39 (10%)
Query: 1 MYTLVSGFYKYMLRKDE-FCVLILGLDNAGKTTYLESAK 38
+Y L Y+ M ++E CV+I G AGKT E+AK
Sbjct: 69 IYALADNAYRSMKSENENQCVIISGESGAGKT---EAAK 104
>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 = 27.1 bits (60), Expect = 2.1
Identities = 25/95 (26%), Positives = 38/95 (40%), Gaps = 12/95 (12%)
Query: 18 FCVLILGLDNAGKTTYLESAKT-KFTKNYKGMNPSKITTTVGLN----IGQIDINTVRLN 72
F V+++G GKT L K F TVG+ + +D V+L
Sbjct: 1 FKVMLVGDSGVGKTCLLVRFKDGAFL-------AGSFIATVGIQFTNKVVTVDGVKVKLQ 53
Query: 73 FWDLGGQLELQSLWDKDIRDCMGVREVKPIFNKNS 107
WD GQ +S+ RD + + + NK+S
Sbjct: 54 IWDTAGQERFRSVTHAYYRDAHALLLLYDVTNKSS 88
>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 = 26.9 bits (59), Expect = 2.6
Identities = 25/70 (35%), Positives = 28/70 (40%), Gaps = 11/70 (15%)
Query: 19 CVLILGLDNAGKTTYLESAKTK-FTKNYKGMNPSKITTTVGLNIGQ--IDINTVRLNFWD 75
CV++ G GKT L T F K Y I T Q +D TV LN WD
Sbjct: 6 CVVV-GDGAVGKTCLLICYTTNAFPKEY-------IPTVFDNYSAQTAVDGRTVSLNLWD 57
Query: 76 LGGQLELQSL 85
GQ E L
Sbjct: 58 TAGQEEYDRL 67
>gnl|CDD|133315 cd04115, Rab33B_Rab33A, Rab GTPase family 33 includes Rab33A and
Rab33B. Rab33B/Rab33A subfamily. Rab33B is
ubiquitously expressed in mouse tissues and cells,
where it is localized to the medial Golgi cisternae. It
colocalizes with alpha-mannose II. Together with the
other cisternal Rabs, Rab6A and Rab6A', it is believed
to regulate the Golgi response to stress and is likely
a molecular target in stress-activated signaling
pathways. Rab33A (previously known as S10) is expressed
primarily in the brain and immune system cells. In
humans, it is located on the X chromosome at Xq26 and
its expression is down-regulated in tuberculosis
patients. Experimental evidence suggests that Rab33A is
a novel CD8+ T cell factor that likely plays a role in
tuberculosis disease processes. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 170
Score = 26.6 bits (59), Expect = 2.7
Identities = 19/68 (27%), Positives = 32/68 (47%), Gaps = 15/68 (22%)
Query: 18 FCVLILGLDNAGKT--TYLESAKTKFTKNYKGMNPSKITTTVGLNIG----QIDINTVRL 71
F ++++G N GKT TY +F G P + T+G++ +ID +++
Sbjct: 3 FKIIVIGDSNVGKTCLTY------RFCA---GRFPERTEATIGVDFRERTVEIDGERIKV 53
Query: 72 NFWDLGGQ 79
WD GQ
Sbjct: 54 QLWDTAGQ 61
>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 = 26.5 bits (59), Expect = 3.0
Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 4/61 (6%)
Query: 51 SKITTTVGLNIG----QIDINTVRLNFWDLGGQLELQSLWDKDIRDCMGVREVKPIFNKN 106
SK T+G++ G + VR+NF+DL G E + ++ +D GV V + ++
Sbjct: 27 SKYLPTIGIDYGVKKVSVRNKEVRVNFFDLSGHPEYLEVRNEFYKDTQGVLLVYDVTDRQ 86
Query: 107 S 107
S
Sbjct: 87 S 87
>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 = 26.7 bits (59), Expect = 3.1
Identities = 19/64 (29%), Positives = 29/64 (45%), Gaps = 7/64 (10%)
Query: 18 FCVLILGLDNAGKTTYLESAKTKFTKNYKGMN--PSKITTTVGLNIGQIDINTVRLNFWD 75
F +I+G GK+ L +FT+ K M P I G I +++ ++L WD
Sbjct: 3 FKYIIIGDMGVGKSCLLH----QFTEK-KFMADCPHTIGVEFGTRIIEVNGQKIKLQIWD 57
Query: 76 LGGQ 79
GQ
Sbjct: 58 TAGQ 61
>gnl|CDD|206691 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta), together with SR-alpha, forms the
heterodimeric signal recognition particle (SRP).
Signal recognition particle receptor, beta subunit
(SR-beta). SR-beta and SR-alpha form the heterodimeric
signal recognition particle (SRP or SR) receptor that
binds SRP to regulate protein translocation across the
ER membrane. Nascent polypeptide chains are synthesized
with an N-terminal hydrophobic signal sequence that
binds SRP54, a component of the SRP. SRP directs
targeting of the ribosome-nascent chain complex (RNC)
to the ER membrane via interaction with the SR, which
is localized to the ER membrane. The RNC is then
transferred to the protein-conducting channel, or
translocon, which facilitates polypeptide translation
across the ER membrane or integration into the ER
membrane. SR-beta is found only in eukaryotes; it is
believed to control the release of the signal sequence
from SRP54 upon binding of the ribosome to the
translocon. High expression of SR-beta has been
observed in human colon cancer, suggesting it may play
a role in the development of this type of cancer.
Length = 202
Score = 26.5 bits (59), Expect = 3.3
Identities = 11/26 (42%), Positives = 16/26 (61%), Gaps = 3/26 (11%)
Query: 20 VLILGLDNAGKT---TYLESAKTKFT 42
VL+LG ++GKT T L + K + T
Sbjct: 3 VLLLGPSDSGKTALFTKLTTGKVRST 28
>gnl|CDD|215687 pfam00063, Myosin_head, Myosin head (motor domain).
Length = 679
Score = 26.9 bits (60), Expect = 3.5
Identities = 14/31 (45%), Positives = 19/31 (61%), Gaps = 4/31 (12%)
Query: 9 YKYMLRKDEF-CVLILGLDNAGKTTYLESAK 38
Y++MLR E C++I G AGKT E+ K
Sbjct: 76 YRHMLRDKENQCIVISGESGAGKT---ENTK 103
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 26.3 bits (59), Expect = 3.6
Identities = 25/95 (26%), Positives = 44/95 (46%), Gaps = 13/95 (13%)
Query: 18 FCVLILGLDNAGKTTYLES-AKTKFTKNYKGMNPSKITTTVGLNIG----QIDINTVRLN 72
F ++++G GK++ L KF++ YK +T+G++ ++D V+L
Sbjct: 1 FKIILIGDSGVGKSSLLSRFTDGKFSEQYK--------STIGVDFKTKTIEVDGKRVKLQ 52
Query: 73 FWDLGGQLELQSLWDKDIRDCMGVREVKPIFNKNS 107
WD GQ +S+ R +G V I N+ S
Sbjct: 53 IWDTAGQERFRSITSSYYRGAVGALLVYDITNRES 87
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 26.4 bits (58), Expect = 3.7
Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 10/78 (12%)
Query: 9 YKYMLRKDEFCVLILGLDNAGKTTYLESAKTKFT-KNYKGMNPSKITTTVGLNIGQIDIN 67
Y Y+ F +I+G GK+ L +FT K ++ ++ I G + ID
Sbjct: 3 YAYL-----FKYIIIGDTGVGKSCLL----LQFTDKRFQPVHDLTIGVEFGARMITIDNK 53
Query: 68 TVRLNFWDLGGQLELQSL 85
++L WD GQ +S+
Sbjct: 54 PIKLQIWDTAGQESFRSI 71
>gnl|CDD|206649 cd01850, CDC_Septin, CDC/Septin GTPase family. Septins are a
conserved family of GTP-binding proteins associated
with diverse processes in dividing and non-dividing
cells. They were first discovered in the budding yeast
S. cerevisiae as a set of genes (CDC3, CDC10, CDC11 and
CDC12) required for normal bud morphology. Septins are
also present in metazoan cells, where they are required
for cytokinesis in some systems, and implicated in a
variety of other processes involving organization of
the cell cortex and exocytosis. In humans, 12 septin
genes generate dozens of polypeptides, many of which
comprise heterooligomeric complexes. Since septin
mutants are commonly defective in cytokinesis and
formation of the neck formation of the neck
filaments/septin rings, septins have been considered to
be the primary constituents of the neck filaments.
Septins belong to the GTPase superfamily for their
conserved GTPase motifs and enzymatic activities.
Length = 275
Score = 26.7 bits (60), Expect = 3.7
Identities = 14/61 (22%), Positives = 29/61 (47%), Gaps = 4/61 (6%)
Query: 17 EFCVLILGLDNAGKTTYLES--AKTKFTKNYKGMNPSKITTTVGLNI--GQIDINTVRLN 72
+F ++++G GK+T++ + + Y IT TV + I +++ N V+L
Sbjct: 4 QFNIMVVGESGLGKSTFINTLFGTKLYPSKYPPAPGEHITKTVEIKISKAELEENGVKLK 63
Query: 73 F 73
Sbjct: 64 L 64
>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 = 26.1 bits (58), Expect = 4.2
Identities = 25/93 (26%), Positives = 46/93 (49%), Gaps = 9/93 (9%)
Query: 18 FCVLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITTT-VGLNIGQIDIN--TVRLNFW 74
F +L++G GK+ L +F+++ NPS I+T + I I+++ ++L W
Sbjct: 4 FKLLLIGDSGVGKSCLL----LRFSED--SFNPSFISTIGIDFKIRTIELDGKKIKLQIW 57
Query: 75 DLGGQLELQSLWDKDIRDCMGVREVKPIFNKNS 107
D GQ +++ R MG+ V I ++ S
Sbjct: 58 DTAGQERFRTITTSYYRGAMGIILVYDITDEKS 90
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 26.2 bits (59), Expect = 5.4
Identities = 12/29 (41%), Positives = 17/29 (58%), Gaps = 8/29 (27%)
Query: 22 ILGLDNAGKTTYLES---AKTK-----FT 42
++GL NAGK+T + + AK K FT
Sbjct: 163 LVGLPNAGKSTLISAVSAAKPKIADYPFT 191
>gnl|CDD|206744 cd11384, RagA_like, Rag GTPase, subfamily of Ras-related GTPases,
includes Ras-related GTP-binding proteins A and B.
RagA and RagB are closely related Rag GTPases
(ras-related GTP-binding protein A and B) that
constitute a unique subgroup of the Ras superfamily,
and are functional homologs of Saccharomyces cerevisiae
Gtr1. These domains function by forming heterodimers
with RagC or RagD, and similarly, Gtr1 dimerizes with
Gtr2, through the carboxy-terminal segments. They play
an essential role in regulating amino acid-induced
target of rapamycin complex 1 (TORC1) kinase signaling,
exocytic cargo sorting at endosomes, and epigenetic
control of gene expression. In response to amino acids,
the Rag GTPases guide the TORC1 complex to activate the
platform containing Rheb proto-oncogene by driving the
relocalization of mTORC1 from discrete locations in the
cytoplasm to a late endosomal and/or lysosomal
compartment that is Rheb-enriched and contains Rab-7.
Length = 286
Score = 26.0 bits (58), Expect = 5.8
Identities = 21/68 (30%), Positives = 30/68 (44%), Gaps = 19/68 (27%)
Query: 20 VLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITTTVGLNIGQIDINT--VR------L 71
VL++G +GKT S ++ NY + ++ T ID+ VR L
Sbjct: 2 VLLMGKSGSGKT----SMRSIIFANYLARDTRRLGAT-------IDVEHSHVRFLGNLVL 50
Query: 72 NFWDLGGQ 79
N WD GGQ
Sbjct: 51 NLWDCGGQ 58
>gnl|CDD|180366 PRK06043, PRK06043, fumarate hydratase; Provisional.
Length = 192
Score = 25.9 bits (57), Expect = 6.1
Identities = 13/38 (34%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 11 YMLRKDEFCVLILGLDNAGKTTYLESAKTKFTKNYKGM 48
++L +EF LI+G+D G Y E + K KN++ +
Sbjct: 154 WVLEVEEFGPLIVGIDAKGNDLYSE-VREKAEKNFEKI 190
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 26.0 bits (58), Expect = 6.5
Identities = 13/28 (46%), Positives = 17/28 (60%), Gaps = 8/28 (28%)
Query: 23 LGLDNAGKTTYLES---AKTK-----FT 42
LGL NAGK+T++ + AK K FT
Sbjct: 165 LGLPNAGKSTFIRAVSAAKPKVADYPFT 192
>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 = 25.7 bits (56), Expect = 6.6
Identities = 22/89 (24%), Positives = 37/89 (41%), Gaps = 5/89 (5%)
Query: 20 VLILGLDNAGKTTYLESAKTKFTKN-YKGMNPSKITTTVGLNIGQIDINTVRLNFWDLGG 78
V+I+G GKT+ +E +FT + + S + + ++ +RL WD G
Sbjct: 3 VIIIGSRGVGKTSLME----RFTDDTFCEACKSTVGVDFKIKTVELRGKKIRLQIWDTAG 58
Query: 79 QLELQSLWDKDIRDCMGVREVKPIFNKNS 107
Q S+ R G+ V I K +
Sbjct: 59 QERFNSITSAYYRSAKGIILVYDITKKET 87
>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 = 25.6 bits (56), Expect = 6.7
Identities = 7/22 (31%), Positives = 13/22 (59%)
Query: 64 IDINTVRLNFWDLGGQLELQSL 85
+ T+ ++FWD GQ Q++
Sbjct: 44 FEGKTILVDFWDTAGQERFQTM 65
>gnl|CDD|213266 cd03299, ABC_ModC_like, ATP-binding cassette domain similar to
the molybdate transporter. Archaeal protein closely
related to ModC. ModC is an ABC-type transporter and
the ATPase component of a molybdate transport system
that also includes the periplasmic binding protein ModA
and the membrane protein ModB. ABC transporters are a
large family of proteins involved in the transport of a
wide variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and
GTP-binding and hydrolyzing proteins.
Length = 235
Score = 25.8 bits (57), Expect = 7.5
Identities = 8/23 (34%), Positives = 14/23 (60%), Gaps = 1/23 (4%)
Query: 13 LRKDEFCVLILGLDNAGKTTYLE 35
+ + ++ V ILG +GK+ LE
Sbjct: 22 VERGDYFV-ILGPTGSGKSVLLE 43
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 25.8 bits (56), Expect = 7.6
Identities = 21/81 (25%), Positives = 36/81 (44%), Gaps = 8/81 (9%)
Query: 18 FCVLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITTTVGLNIGQIDINTVRLNF--WD 75
F +L++G GK++ L S + + + + P T V I Q+ + RL WD
Sbjct: 15 FKILLIGDSGVGKSSLLVSF---ISSSVEDLAP---TIGVDFKIKQLTVGGKRLKLTIWD 68
Query: 76 LGGQLELQSLWDKDIRDCMGV 96
GQ ++L R+ G+
Sbjct: 69 TAGQERFRTLTSSYYRNAQGI 89
>gnl|CDD|143649 cd07933, RHD-n_c-Rel, N-terminal sub-domain of the Rel homology
domain (RHD) of c-Rel. Proteins containing the Rel
homology domain (RHD) are metazoan transcription
factors. The RHD is composed of two structural
sub-domains; this model characterizes the N-terminal RHD
sub-domain of the c-Rel family of transcription factors,
categorized as a class II member of the NF-kappa B
family. In class II NF-kappa Bs, the RHD domain
co-occurs with a C-terminal transactivation domain
(TAD). NF-kappa B proteins are part of a protein complex
that acts as a transcription factor, which is
responsible for regulating a host of cellular responses
to a variety of stimuli. This complex tightly regulates
the expression of a large number of genes, and is
involved in processes such as adaptive and innate
immunity, stress response, inflammation, cell adhesion,
proliferation and apoptosis. The cytosolic NF-kappa B
complex is activated via phosphorylation of the
ankyrin-repeat containing inhibitory protein I-kappa B,
which dissociates from the complex and exposes the
nuclear localization signal of the heterodimer (NF-kappa
B and Rel). c-Rel plays an important role in B cell
proliferation and survival.
Length = 172
Score = 25.6 bits (56), Expect = 8.0
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 46 KGMNPSKITTTVGLNIGQIDINTVRLNF 73
+G+NP + L I + D+N VRL F
Sbjct: 118 RGINPFNVPEEQLLQIEEYDLNVVRLCF 145
>gnl|CDD|221941 pfam13154, DUF3991, Protein of unknown function (DUF3991). This
family of proteins is often associated with family
Toprim, pfam01751.
Length = 76
Score = 24.5 bits (54), Expect = 8.3
Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 2/50 (4%)
Query: 3 TLVSGFYKY-MLRKDEF-CVLILGLDNAGKTTYLESAKTKFTKNYKGMNP 50
V F + +L +D++ V+ G D GK E T K +KG+
Sbjct: 12 ETVRAFIRQGLLYEDKYGNVVFPGKDEDGKVVGAEKRGTGEGKPFKGIAK 61
>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 = 25.5 bits (56), Expect = 8.5
Identities = 13/39 (33%), Positives = 20/39 (51%)
Query: 69 VRLNFWDLGGQLELQSLWDKDIRDCMGVREVKPIFNKNS 107
++L WD GQ +S+ R+ +GV V I N+ S
Sbjct: 52 IKLQLWDTAGQERFRSITRSYYRNSVGVLLVFDITNRES 90
>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 = 25.2 bits (56), Expect = 8.9
Identities = 20/70 (28%), Positives = 31/70 (44%), Gaps = 19/70 (27%)
Query: 18 FCVLILGLDNAGKTTYLESAKTKFTKNYKGMNPSKITTTVGLNIG--------QIDINTV 69
F ++++G GK+ L ++FT+N N +T IG QID T+
Sbjct: 4 FKIVLIGDSGVGKSNLL----SRFTRNE--FNLDSKST-----IGVEFATRTIQIDGKTI 52
Query: 70 RLNFWDLGGQ 79
+ WD GQ
Sbjct: 53 KAQIWDTAGQ 62
>gnl|CDD|234141 TIGR03185, DNA_S_dndD, DNA sulfur modification protein DndD.
This model describes the DndB protein encoded by an
operon associated with a sulfur-containing modification
to DNA. The operon is sporadically distributed in
bacteria, much like some restriction enzyme operons.
DndD is described as a putative ATPase. The small
number of examples known so far include species from
among the Firmicutes, Actinomycetes, Proteobacteria,
and Cyanobacteria [DNA metabolism,
Restriction/modification].
Length = 650
Score = 25.8 bits (57), Expect = 9.1
Identities = 10/17 (58%), Positives = 14/17 (82%)
Query: 20 VLILGLDNAGKTTYLES 36
+LI GL+ AGKTT L++
Sbjct: 31 ILIGGLNGAGKTTLLDA 47
>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 = 25.3 bits (56), Expect = 9.6
Identities = 10/57 (17%), Positives = 20/57 (35%), Gaps = 13/57 (22%)
Query: 18 FCVLILGLDNAGKTTYLES--AKTKFTKNYKGMNPSKITTTVGLNIGQIDINTVRLN 72
F +LG +GK+ L++ ++ Y + +NTV +
Sbjct: 5 FLCFVLGAKGSGKSALLQAFLGRSFSQNAYSPTIKPRYA-----------VNTVEVP 50
>gnl|CDD|206746 cd01849, YlqF_related_GTPase, Circularly permuted YlqF-related
GTPases. These proteins are found in bacteria,
eukaryotes, and archaea. They all exhibit a circular
permutation of the GTPase signature motifs so that the
order of the conserved G box motifs is G4-G5-G1-G2-G3,
with G4 and G5 being permuted from the C-terminal region
of proteins in the Ras superfamily to the N-terminus of
YlqF-related GTPases.
Length = 146
Score = 25.0 bits (55), Expect = 9.9
Identities = 11/49 (22%), Positives = 21/49 (42%), Gaps = 3/49 (6%)
Query: 20 VLILGLDNAGKTTYLESAKTKF---TKNYKGMNPSKITTTVGLNIGQID 65
V ++GL N GK++++ + KF + G + + I D
Sbjct: 94 VGVVGLPNVGKSSFINALLNKFKLKVGSIPGTTKLQQDVKLDKEIYLYD 142
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
0.322 0.139 0.420
Gapped
Lambda K H
0.267 0.0809 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,087,912
Number of extensions: 501470
Number of successful extensions: 632
Number of sequences better than 10.0: 1
Number of HSP's gapped: 606
Number of HSP's successfully gapped: 107
Length of query: 125
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 40
Effective length of database: 7,167,512
Effective search space: 286700480
Effective search space used: 286700480
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.0 bits)