RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2967
(101 letters)
>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 = 121 bits (305), Expect = 8e-37
Identities = 51/76 (67%), Positives = 60/76 (78%), Gaps = 12/76 (15%)
Query: 37 SGQFSQDMIPTVGFNMRKITKGNVTIKVWDIGGQPRFRS------------IYMVDAADT 84
SGQFS+D IPTVGFNMRK+TKGNVTIKVWD+GGQPRFRS +Y+VDAAD
Sbjct: 21 SGQFSEDTIPTVGFNMRKVTKGNVTIKVWDLGGQPRFRSMWERYCRGVNAIVYVVDAADR 80
Query: 85 DKLEASRNELHALIEK 100
+KLE ++NELH L+EK
Sbjct: 81 EKLEVAKNELHDLLEK 96
>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 = 81.1 bits (201), Expect = 6e-21
Identities = 26/76 (34%), Positives = 41/76 (53%), Gaps = 12/76 (15%)
Query: 36 LSGQFSQDMIPTVGFNMRKITKGNVTIKVWDIGGQPRFRS------------IYMVDAAD 83
L IPT+GFN+ + NV VWD+GGQ + R I++VD++D
Sbjct: 19 LKLGEVVTTIPTIGFNVETVEYKNVKFTVWDVGGQDKIRPLWKHYYENTDGLIFVVDSSD 78
Query: 84 TDKLEASRNELHALIE 99
+++E ++NELH L+
Sbjct: 79 RERIEEAKNELHKLLN 94
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 70.7 bits (174), Expect = 9e-17
Identities = 28/68 (41%), Positives = 40/68 (58%), Gaps = 12/68 (17%)
Query: 44 MIPTVGFNMRKITKGNVTIKVWDIGGQPRFRS------------IYMVDAADTDKLEASR 91
IPT+GFN+ +T NV VWD+GGQ R I++VD+AD D++E ++
Sbjct: 42 TIPTIGFNVETVTYKNVKFTVWDVGGQESLRPLWRNYFPNTDAVIFVVDSADRDRIEEAK 101
Query: 92 NELHALIE 99
ELHAL+
Sbjct: 102 EELHALLN 109
>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 = 64.0 bits (156), Expect = 2e-14
Identities = 29/67 (43%), Positives = 43/67 (64%), Gaps = 12/67 (17%)
Query: 45 IPTVGFNMRKITKGNVTIKVWDIGGQ----PRFRS--------IYMVDAADTDKLEASRN 92
IPT+GFN+ +T N+ +VWD+GGQ P +R IY+VD+ D D+L S++
Sbjct: 28 IPTIGFNVETVTYKNLKFQVWDLGGQTSIRPYWRCYYSNTDAIIYVVDSTDRDRLGISKS 87
Query: 93 ELHALIE 99
ELHA++E
Sbjct: 88 ELHAMLE 94
>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 = 63.6 bits (155), Expect = 4e-14
Identities = 28/66 (42%), Positives = 40/66 (60%), Gaps = 12/66 (18%)
Query: 45 IPTVGFNMRKITKGNVTIKVWDIGGQPRFRS------------IYMVDAADTDKLEASRN 92
IPTVGFN+ +T NV VWD+GGQ + R I++VD+AD D+++ +R
Sbjct: 38 IPTVGFNVETVTYKNVKFNVWDVGGQDKIRPLWRHYYTGTQGLIFVVDSADRDRIDEARQ 97
Query: 93 ELHALI 98
ELH +I
Sbjct: 98 ELHRII 103
>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 = 56.9 bits (137), Expect = 2e-11
Identities = 24/66 (36%), Positives = 40/66 (60%), Gaps = 12/66 (18%)
Query: 45 IPTVGFNMRKITKGNVTIKVWDIGGQPRFRS------------IYMVDAADTDKLEASRN 92
IPT+GFN+ +T N++ VWD+GGQ + R I++VD+ D D+++ +R
Sbjct: 42 IPTIGFNVETVTYKNISFTVWDVGGQDKIRPLWRHYYTNTQGLIFVVDSNDRDRIDEARE 101
Query: 93 ELHALI 98
ELH ++
Sbjct: 102 ELHRML 107
>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 = 56.6 bits (137), Expect = 2e-11
Identities = 24/76 (31%), Positives = 38/76 (50%), Gaps = 12/76 (15%)
Query: 36 LSGQFSQDMIPTVGFNMRKITKGNVTIKVWDIGGQPRFRS------------IYMVDAAD 83
L+ + + PT GFN++ + + VWDIGGQ + R IY++D+AD
Sbjct: 35 LASEDISHITPTQGFNIKNVQADGFKLNVWDIGGQRKIRPYWRNYFENTDVLIYVIDSAD 94
Query: 84 TDKLEASRNELHALIE 99
+ E + EL L+E
Sbjct: 95 RKRFEEAGQELVELLE 110
>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 = 56.3 bits (136), Expect = 2e-11
Identities = 21/66 (31%), Positives = 37/66 (56%), Gaps = 12/66 (18%)
Query: 45 IPTVGFNMRKITKGNVTIKVWDIGGQPRFRS------------IYMVDAADTDKLEASRN 92
IPT+GFN+ + N++ VWD+GGQ + R I++VD+ D +++ +R
Sbjct: 29 IPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERIGEARE 88
Query: 93 ELHALI 98
EL ++
Sbjct: 89 ELQRML 94
>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 = 55.4 bits (134), Expect = 8e-11
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 14/72 (19%)
Query: 44 MIPTVGFNMRKITKGNVTIKVWDIGGQPRFRS------------IYMVDAADTDKLEASR 91
+PT+ ++T GNV +D+GG + R +++VDAAD ++ + S+
Sbjct: 47 HVPTLHPTSEELTIGNVKFTTFDLGGHEQARRVWKDYFPEVDGIVFLVDAADPERFQESK 106
Query: 92 NELHAL--IEKL 101
EL +L E+L
Sbjct: 107 EELDSLLNDEEL 118
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 54.6 bits (131), Expect = 1e-10
Identities = 23/68 (33%), Positives = 40/68 (58%), Gaps = 12/68 (17%)
Query: 45 IPTVGFNMRKITKGNVTIKVWDIGGQPRFRS------------IYMVDAADTDKLEASRN 92
IPT+GFN+ + N++ VWD+GGQ + R I++VD+ D D++ +R+
Sbjct: 46 IPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRDRVVEARD 105
Query: 93 ELHALIEK 100
ELH ++ +
Sbjct: 106 ELHRMLNE 113
>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 = 54.0 bits (130), Expect = 2e-10
Identities = 24/78 (30%), Positives = 42/78 (53%), Gaps = 13/78 (16%)
Query: 36 LSGQFSQD-MIPTVGFNMRKITKGNVTIKVWDIGGQPRFRS------------IYMVDAA 82
LS + S + ++PT GFN I + +++ +IGG R I++VD+A
Sbjct: 19 LSSERSLESVVPTTGFNSVAIPTQDAIMELLEIGGSQNLRKYWKRYLSGSQGLIFVVDSA 78
Query: 83 DTDKLEASRNELHALIEK 100
D+++L +R ELH L++
Sbjct: 79 DSERLPLARQELHQLLQH 96
>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 = 53.9 bits (130), Expect = 2e-10
Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 12/65 (18%)
Query: 46 PTVGFNMRKITKGNVTIKVWDIGGQPRFRS------------IYMVDAADTDKLEASRNE 93
PTVG N+ I G + WD+GGQ RS IY++D+ D ++ S++
Sbjct: 37 PTVGLNIGTIEVGKARLMFWDLGGQEELRSLWDKYYAESHGVIYVIDSTDRERFNESKSA 96
Query: 94 LHALI 98
+I
Sbjct: 97 FEKVI 101
>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 = 53.7 bits (129), Expect = 3e-10
Identities = 24/68 (35%), Positives = 37/68 (54%), Gaps = 17/68 (25%)
Query: 45 IPTVGFNMRKI--TKGN---VTIKVWDIGGQPRFRS------------IYMVDAADTDKL 87
+PT GFN KI + GN VT WD+GGQ + R +++VD+ D +++
Sbjct: 32 VPTKGFNTEKIKVSLGNAKGVTFHFWDVGGQEKLRPLWKSYTRCTDGIVFVVDSVDVERM 91
Query: 88 EASRNELH 95
E ++ ELH
Sbjct: 92 EEAKTELH 99
>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 = 52.0 bits (125), Expect = 1e-09
Identities = 22/63 (34%), Positives = 39/63 (61%), Gaps = 13/63 (20%)
Query: 45 IPTVGFNMRKI-TKGNVTIKVWDIGGQPRFRS------------IYMVDAADTDKLEASR 91
IPTVGFN+ + + ++++ VWD+GGQ + R+ +Y+VD++D +L+ S+
Sbjct: 28 IPTVGFNVEMLQLEKHLSLTVWDVGGQEKMRTVWKCYLENTDGLVYVVDSSDEARLDESQ 87
Query: 92 NEL 94
EL
Sbjct: 88 KEL 90
>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 = 51.3 bits (123), Expect = 2e-09
Identities = 21/71 (29%), Positives = 42/71 (59%), Gaps = 12/71 (16%)
Query: 41 SQDMIPTVGFNMRKITKGNVTIKVWDIGGQPRFRS------------IYMVDAADTDKLE 88
SQ+++PTVGFN+ KGN++ +D+ GQ ++R I+++D++D ++
Sbjct: 26 SQNIVPTVGFNVESFKKGNLSFTAFDMSGQGKYRGLWEHYYKNIQGIIFVIDSSDRLRMV 85
Query: 89 ASRNELHALIE 99
+++EL L+
Sbjct: 86 VAKDELELLLN 96
>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 = 51.6 bits (124), Expect = 2e-09
Identities = 23/70 (32%), Positives = 38/70 (54%), Gaps = 14/70 (20%)
Query: 46 PTVGFNMRKITKGNVTIKVWDIGGQPRFRS------------IYMVDAADTDKLEASRNE 93
PT+GFN++ + + +WD+GGQ RS I++VD++D +LE + E
Sbjct: 44 PTLGFNIKTLEYNGYKLNIWDVGGQKSLRSYWRNYFESTDALIWVVDSSDRARLEDCKRE 103
Query: 94 LHALI--EKL 101
L L+ E+L
Sbjct: 104 LQKLLVEERL 113
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 51.8 bits (124), Expect = 2e-09
Identities = 20/66 (30%), Positives = 36/66 (54%), Gaps = 12/66 (18%)
Query: 45 IPTVGFNMRKITKGNVTIKVWDIGGQPRFRS------------IYMVDAADTDKLEASRN 92
IPT+GFN+ + N+ +WD+GGQ + R I++VD+ D +++ +R
Sbjct: 46 IPTIGFNVETVEYKNLKFTMWDVGGQDKLRPLWRHYYQNTNGLIFVVDSNDRERIGDARE 105
Query: 93 ELHALI 98
EL ++
Sbjct: 106 ELERML 111
>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 = 48.5 bits (116), Expect = 3e-08
Identities = 20/65 (30%), Positives = 35/65 (53%), Gaps = 12/65 (18%)
Query: 46 PTVGFNMRKITKGNVTIKVWDIGGQPRFRS------------IYMVDAADTDKLEASRNE 93
PT+G N+ +I N+ +WDIGGQ RS I ++D+ D ++L ++ E
Sbjct: 45 PTIGSNVEEIVYKNIRFLMWDIGGQESLRSSWNTYYTNTDAVILVIDSTDRERLPLTKEE 104
Query: 94 LHALI 98
L+ ++
Sbjct: 105 LYKML 109
>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 = 46.3 bits (111), Expect = 1e-07
Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 4/43 (9%)
Query: 38 GQFSQDMIPTVG--FNMRKITKGNVTIK--VWDIGGQPRFRSI 76
+FS++ T+G F + I +K +WD GQ RFRSI
Sbjct: 23 NKFSENYKSTIGVDFKSKTIEVDGKKVKLQIWDTAGQERFRSI 65
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 45.2 bits (108), Expect = 3e-07
Identities = 17/44 (38%), Positives = 23/44 (52%), Gaps = 4/44 (9%)
Query: 37 SGQFSQDMIPTVG--FNMRKITKGNVTIK--VWDIGGQPRFRSI 76
G+FS+ T+G F + I +K +WD GQ RFRSI
Sbjct: 22 DGKFSEQYKSTIGVDFKTKTIEVDGKRVKLQIWDTAGQERFRSI 65
>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 = 43.5 bits (102), Expect = 2e-06
Identities = 17/66 (25%), Positives = 36/66 (54%), Gaps = 12/66 (18%)
Query: 45 IPTVGFNMRKITKGNVTIKVWDIGGQPRFRS------------IYMVDAADTDKLEASRN 92
IPT+GFN+ + N+ +WD+GG+ + R ++++D++ D++ + +
Sbjct: 28 IPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVIDSSHRDRVSEAHS 87
Query: 93 ELHALI 98
EL L+
Sbjct: 88 ELAKLL 93
>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 = 42.8 bits (101), Expect = 3e-06
Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 12/74 (16%)
Query: 36 LSGQFSQDMIPTVGFNMRKITKGNVTIKVWDIGGQPRFRSI------------YMVDAAD 83
L G+ + + PTVGF K+ + ++D+GG FR I ++VD++D
Sbjct: 19 LQGEIPKKVAPTVGFTPTKLRLDKYEVCIFDLGGGANFRGIWVNYYAEAHGLVFVVDSSD 78
Query: 84 TDKLEASRNELHAL 97
D+++ + L L
Sbjct: 79 DDRVQEVKEILREL 92
>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 = 41.0 bits (97), Expect = 1e-05
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 7/51 (13%)
Query: 38 GQFSQDMIPTVG--FNMRKITKGNVTIK--VWDIGGQPRFRSI---YMVDA 81
+F ++ IPT+G F + I T+K +WD GQ RFR++ Y A
Sbjct: 22 NKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAGQERFRALRPLYYRGA 72
>gnl|CDD|206656 cd01863, Rab18, Rab GTPase family 18 (Rab18). Rab18 subfamily.
Mammalian Rab18 is implicated in endocytic transport
and is expressed most highly in polarized epithelial
cells. However, trypanosomal Rab, TbRAB18, is
upregulated in the BSF (Blood Stream Form) stage and
localized predominantly to elements of the Golgi
complex. In human and mouse cells, Rab18 has been
identified in lipid droplets, organelles that store
neutral lipids. GTPase activating proteins (GAPs)
interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab
proteins. Due to the presence of truncated sequences in
this CD, the lipid modification site is not available
for annotation.
Length = 161
Score = 39.2 bits (92), Expect = 6e-05
Identities = 23/77 (29%), Positives = 34/77 (44%), Gaps = 19/77 (24%)
Query: 37 SGQFSQDMIPTVG--FNMRKITKGNVTIKV--WDIGGQPRFRS--------------IYM 78
F +D+ T+G F ++ +T +K+ WD GQ RFR+ +Y
Sbjct: 22 DDTFDEDLSSTIGVDFKVKTVTVDGKKVKLAIWDTAGQERFRTLTSSYYRGAQGVILVYD 81
Query: 79 VDAADT-DKLEASRNEL 94
V DT D L+ NEL
Sbjct: 82 VTRRDTFDNLDTWLNEL 98
>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 = 38.8 bits (91), Expect = 8e-05
Identities = 17/43 (39%), Positives = 22/43 (51%), Gaps = 4/43 (9%)
Query: 38 GQFSQDMIPTVG--FNMRKITKGNVTIK--VWDIGGQPRFRSI 76
F+ I T+G F +R I IK +WD GQ RFR+I
Sbjct: 26 DSFNPSFISTIGIDFKIRTIELDGKKIKLQIWDTAGQERFRTI 68
>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 = 38.6 bits (90), Expect = 1e-04
Identities = 20/54 (37%), Positives = 28/54 (51%), Gaps = 7/54 (12%)
Query: 36 LSGQFSQDMIPTVG--FNMRKITKGNVTIK--VWDIGGQPRFRSI---YMVDAA 82
+ +F QD T+G F R + G ++K +WD GQ RFRS+ Y AA
Sbjct: 21 IENKFKQDSNHTIGVEFGSRVVNVGGKSVKLQIWDTAGQERFRSVTRSYYRGAA 74
>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 = 37.5 bits (88), Expect = 2e-04
Identities = 17/43 (39%), Positives = 23/43 (53%), Gaps = 4/43 (9%)
Query: 38 GQFSQDMIPTVG--FNMRKITKGNVTIK--VWDIGGQPRFRSI 76
+F+ D T+G F R I TIK +WD GQ R+R+I
Sbjct: 26 NEFNLDSKSTIGVEFATRTIQIDGKTIKAQIWDTAGQERYRAI 68
>gnl|CDD|206653 cd01860, Rab5_related, Rab-related GTPase family includes Rab5
and Rab22; regulates early endosome fusion. The
Rab5-related subfamily includes Rab5 and Rab22 of
mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of
plants. The members of this subfamily are involved in
endocytosis and endocytic-sorting pathways. In mammals,
Rab5 GTPases localize to early endosomes and regulate
fusion of clathrin-coated vesicles to early endosomes
and fusion between early endosomes. In yeast, Ypt51p
family members similarly regulate membrane trafficking
through prevacuolar compartments. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 163
Score = 37.5 bits (88), Expect = 2e-04
Identities = 14/43 (32%), Positives = 25/43 (58%), Gaps = 4/43 (9%)
Query: 38 GQFSQDMIPTVG--FNMRKITKGNVTIK--VWDIGGQPRFRSI 76
+FS++ T+G F + + + T+K +WD GQ R+RS+
Sbjct: 24 NEFSENQESTIGAAFLTQTVNLDDTTVKFEIWDTAGQERYRSL 66
>gnl|CDD|133267 cd01864, Rab19, Rab GTPase family 19 (Rab19). Rab19 subfamily.
Rab19 proteins are associated with Golgi stacks.
Similarity analysis indicated that Rab41 is closely
related to Rab19. However, the function of these Rabs
is not yet characterized. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab
proteins. Due to the presence of truncated sequences in
this CD, the lipid modification site is not available
for annotation.
Length = 165
Score = 35.9 bits (83), Expect = 0.001
Identities = 18/44 (40%), Positives = 26/44 (59%), Gaps = 4/44 (9%)
Query: 37 SGQFSQDMIPTVG--FNMR--KITKGNVTIKVWDIGGQPRFRSI 76
SG FS+ T+G F M+ +I V +++WD GQ RFR+I
Sbjct: 25 SGTFSERQGNTIGVDFTMKTLEIQGKRVKLQIWDTAGQERFRTI 68
>gnl|CDD|206661 cd01869, Rab1_Ypt1, Rab GTPase family 1 includes the yeast
homolog Ypt1. Rab1/Ypt1 subfamily. Rab1 is found in
every eukaryote and is a key regulatory component for
the transport of vesicles from the ER to the Golgi
apparatus. Studies on mutations of Ypt1, the yeast
homolog of Rab1, showed that this protein is necessary
for the budding of vesicles of the ER as well as for
their transport to, and fusion with, the Golgi
apparatus. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation
of the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs),
which facilitate Rab recycling by masking C-terminal
lipid binding and promoting cytosolic localization.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Due to the presence
of truncated sequences in this CD, the lipid
modification site is not available for annotation.
Length = 166
Score = 35.8 bits (83), Expect = 0.001
Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 4/41 (9%)
Query: 40 FSQDMIPTVG--FNMRKITKGNVTIK--VWDIGGQPRFRSI 76
+++ I T+G F +R I T+K +WD GQ RFR+I
Sbjct: 27 YTESYISTIGVDFKIRTIELDGKTVKLQIWDTAGQERFRTI 67
>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 = 35.7 bits (82), Expect = 0.001
Identities = 18/67 (26%), Positives = 30/67 (44%), Gaps = 12/67 (17%)
Query: 44 MIPTVGFNMRKITKGNVTIKVWDIGGQPRFRS------------IYMVDAADTDKLEASR 91
PT ++ GN+ +D+GG + R +Y+VDA D ++ S+
Sbjct: 45 HQPTQHPTSEELAIGNIKFTTFDLGGHQQARRLWKDYFPEVNGIVYLVDAYDKERFAESK 104
Query: 92 NELHALI 98
EL AL+
Sbjct: 105 RELDALL 111
>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 = 35.6 bits (82), Expect = 0.001
Identities = 20/59 (33%), Positives = 29/59 (49%), Gaps = 9/59 (15%)
Query: 27 GNVTIWPVPLSGQFSQDMIP-----TVG--FNMRKITKGNVTIK--VWDIGGQPRFRSI 76
GN + L +F+Q + P T+G F ++ + IK +WD GQ RFRSI
Sbjct: 14 GNAGVGKTCLVRRFTQGLFPPGQGATIGVDFMIKTVEIKGEKIKLQIWDTAGQERFRSI 72
>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 = 35.5 bits (82), Expect = 0.002
Identities = 21/44 (47%), Positives = 26/44 (59%), Gaps = 5/44 (11%)
Query: 38 GQFSQDMIPTVG--FNMRKI-TKGNVTIK--VWDIGGQPRFRSI 76
G+F++ PTVG F R I + V IK +WD GQ RFRSI
Sbjct: 25 GRFAEVSDPTVGVDFFSRLIEIEPGVRIKLQLWDTAGQERFRSI 68
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 35.0 bits (80), Expect = 0.002
Identities = 15/39 (38%), Positives = 26/39 (66%), Gaps = 4/39 (10%)
Query: 42 QDMIPTVG--FNMRKITKGNVTIK--VWDIGGQPRFRSI 76
+D+ PT+G F ++++T G +K +WD GQ RFR++
Sbjct: 40 EDLAPTIGVDFKIKQLTVGGKRLKLTIWDTAGQERFRTL 78
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 35.1 bits (81), Expect = 0.002
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 7/53 (13%)
Query: 36 LSGQFSQDMIPTVGFNMRKI----TKGNVTIKVWDIGGQPRF---RSIYMVDA 81
L+G+F + IPT+G + + G + VWD GQ +F R Y +
Sbjct: 30 LTGEFEKKYIPTLGVEVHPLKFYTNCGPICFNVWDTAGQEKFGGLRDGYYIKG 82
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins
[General function prediction only].
Length = 219
Score = 34.9 bits (80), Expect = 0.003
Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 7/53 (13%)
Query: 36 LSGQFSQDMIPTVGFNMRKIT----KGNVTIKVWDIGGQPRFRSI---YMVDA 81
+ +F + PT+G T + N+ +++WD GQ +RS+ Y A
Sbjct: 26 VGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQEEYRSLRPEYYRGA 78
>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 = 33.7 bits (77), Expect = 0.006
Identities = 17/41 (41%), Positives = 24/41 (58%), Gaps = 4/41 (9%)
Query: 40 FSQDMIPTVG--FNMR--KITKGNVTIKVWDIGGQPRFRSI 76
FS I T+G F +R +I V +++WD GQ RFR+I
Sbjct: 31 FSGSYITTIGVDFKIRTVEINGERVKLQIWDTAGQERFRTI 71
>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 = 33.3 bits (76), Expect = 0.009
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 7/51 (13%)
Query: 36 LSGQFSQDMIPTVGFNMRKITKGNVTIK--VWDIGGQPRFRSI---YMVDA 81
L+G F + + F + +T V +K +WD GQ RFRS+ Y DA
Sbjct: 26 LAGSFIATV--GIQFTNKVVTVDGVKVKLQIWDTAGQERFRSVTHAYYRDA 74
>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 = 33.0 bits (76), Expect = 0.010
Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 7/53 (13%)
Query: 36 LSGQFSQDMIPTVGFNMRKI----TKGNVTIKVWDIGGQPRF---RSIYMVDA 81
L+G+F + + T+G + + +G + VWD GQ +F R Y +
Sbjct: 21 LTGEFEKKYVATLGVEVHPLDFHTNRGKIRFNVWDTAGQEKFGGLRDGYYIQG 73
>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 = 33.1 bits (76), Expect = 0.012
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 5/43 (11%)
Query: 38 GQFSQDMIPTVG--FNMRKIT---KGNVTIKVWDIGGQPRFRS 75
G FSQ T+G F ++ I V +++WDI GQ RF
Sbjct: 23 GVFSQHYKATIGVDFALKVIEWDPNTVVRLQLWDIAGQERFGG 65
>gnl|CDD|206658 cd01866, Rab2, Rab GTPase family 2 (Rab2). Rab2 is localized on
cis-Golgi membranes and interacts with Golgi matrix
proteins. Rab2 is also implicated in the maturation of
vesicular tubular clusters (VTCs), which are
microtubule-associated intermediates in transport
between the ER and Golgi apparatus. In plants, Rab2
regulates vesicle trafficking between the ER and the
Golgi bodies and is important to pollen tube growth.
GTPase activating proteins (GAPs) interact with
GTP-bound Rab and accelerate the hydrolysis of GTP to
GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation
of the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs),
which facilitate Rab recycling by masking C-terminal
lipid binding and promoting cytosolic localization.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Due to the presence
of truncated sequences in this CD, the lipid
modification site is not available for annotation.
Length = 168
Score = 32.8 bits (75), Expect = 0.013
Identities = 16/36 (44%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 43 DMIPTVGFNMRKITKGNVTIK--VWDIGGQPRFRSI 76
D+ V F R IT IK +WD GQ FRSI
Sbjct: 34 DLTIGVEFGARMITIDGKQIKLQIWDTAGQESFRSI 69
>gnl|CDD|133323 cd04123, Rab21, Rab GTPase family 21 (Rab21). The localization
and function of Rab21 are not clearly defined, with
conflicting data reported. Rab21 has been reported to
localize in the ER in human intestinal epithelial
cells, with partial colocalization with
alpha-glucosidase, a late endosomal/lysosomal marker.
More recently, Rab21 was shown to colocalize with and
affect the morphology of early endosomes. In
Dictyostelium, GTP-bound Rab21, together with two novel
LIM domain proteins, LimF and ChLim, has been shown to
regulate phagocytosis. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab
proteins. Due to the presence of truncated sequences in
this CD, the lipid modification site is not available
for annotation.
Length = 162
Score = 32.2 bits (74), Expect = 0.020
Identities = 12/52 (23%), Positives = 22/52 (42%), Gaps = 7/52 (13%)
Query: 37 SGQFSQDMIPTV--GFNMRKIT--KGNVTIKVWDIGGQPRFRS---IYMVDA 81
+F++ T F + + + + +WD GQ R+ + IY DA
Sbjct: 22 ENKFNEKHESTTQASFFQKTVNIGGKRIDLAIWDTAGQERYHALGPIYYRDA 73
>gnl|CDD|206701 cd04128, Spg1, Septum-promoting GTPase (Spg1). Spg1p. Spg1p
(septum-promoting GTPase) was first identified in the
fission yeast S. pombe, where it regulates septum
formation in the septation initiation network (SIN)
through the cdc7 protein kinase. Spg1p is an essential
gene that localizes to the spindle pole bodies. When
GTP-bound, it binds cdc7 and causes it to translocate
to spindle poles. Sid4p (septation initiation
defective) is required for localization of Spg1p to the
spindle pole body, and the ability of Spg1p to promote
septum formation from any point in the cell cycle
depends on Sid4p. Spg1p is negatively regulated by Byr4
and cdc16, which form a two-component GTPase activating
protein (GAP) for Spg1p. The existence of a SIN-related
pathway in plants has been proposed. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization.
Length = 182
Score = 32.4 bits (74), Expect = 0.020
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 4/41 (9%)
Query: 38 GQFSQDMIPTVGFNM--RKITKGNVTI--KVWDIGGQPRFR 74
G+F ++ I T+G N + I+ I +WD+GGQ F
Sbjct: 23 GEFDEEYIQTLGVNFMEKTISIRGTEITFSIWDLGGQREFI 63
>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 = 32.1 bits (73), Expect = 0.022
Identities = 17/36 (47%), Positives = 22/36 (61%), Gaps = 5/36 (13%)
Query: 40 FSQDMIPTVG--FNMRKIT---KGNVTIKVWDIGGQ 70
F + T+G F R+IT NVT++VWDIGGQ
Sbjct: 25 FGKSYKQTIGLDFFSRRITLPGSLNVTLQVWDIGGQ 60
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 31.5 bits (71), Expect = 0.038
Identities = 18/40 (45%), Positives = 20/40 (50%), Gaps = 2/40 (5%)
Query: 39 QFSQDMIPTVGFNMRKITKGNVTIK--VWDIGGQPRFRSI 76
Q D+ V F R IT N IK +WD GQ FRSI
Sbjct: 32 QPVHDLTIGVEFGARMITIDNKPIKLQIWDTAGQESFRSI 71
>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 = 31.5 bits (71), Expect = 0.046
Identities = 14/51 (27%), Positives = 24/51 (47%), Gaps = 4/51 (7%)
Query: 27 GNVTIWPVPLSGQFSQDMIPTVGFNMRKI----TKGNVTIKVWDIGGQPRF 73
G T L+G+F + + T+G + + +G + VWD GQ +F
Sbjct: 7 GKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIRFNVWDTAGQEKF 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 = 30.7 bits (70), Expect = 0.064
Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 4/42 (9%)
Query: 39 QFSQDMIPTVG--FNMRKITKGNVTIK--VWDIGGQPRFRSI 76
F T+G F + + + T++ +WD GQ RFRS+
Sbjct: 24 TFDNQYQATIGIDFLSKTMYVDDKTVRLQLWDTAGQERFRSL 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 = 30.4 bits (69), Expect = 0.086
Identities = 14/55 (25%), Positives = 22/55 (40%), Gaps = 15/55 (27%)
Query: 40 FSQDMIPTVGFNMRKITKGN-----VTIKVWDIGGQPRF----------RSIYMV 79
F D T G N++ + + VWD GGQ + RS+Y++
Sbjct: 26 FDGDESSTHGINVQDWKIPAPERKKIRLNVWDFGGQEIYHATHQFFLTSRSLYLL 80
>gnl|CDD|206697 cd04116, Rab9, Rab GTPase family 9 (Rab9). Rab9 is found in late
endosomes, together with mannose 6-phosphate receptors
(MPRs) and the tail-interacting protein of 47 kD
(TIP47). Rab9 is a key mediator of vesicular transport
from late endosomes to the trans-Golgi network (TGN) by
redirecting the MPRs. Rab9 has been identified as a key
component for the replication of several viruses,
including HIV1, Ebola, Marburg, and measles, making it
a potential target for inhibiting a variety of viruses.
GTPase activating proteins (GAPs) interact with
GTP-bound Rab and accelerate the hydrolysis of GTP to
GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation
of the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs),
which facilitate Rab recycling by masking C-terminal
lipid binding and promoting cytosolic localization.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Due to the presence
of truncated sequences in this CD, the lipid
modification site is not available for annotation.
Length = 170
Score = 30.2 bits (68), Expect = 0.093
Identities = 10/17 (58%), Positives = 14/17 (82%)
Query: 60 VTIKVWDIGGQPRFRSI 76
VT+++WD GQ RFRS+
Sbjct: 54 VTLQIWDTAGQERFRSL 70
>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 = 30.1 bits (68), Expect = 0.13
Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 4/41 (9%)
Query: 38 GQFSQDMIPTVGFNMRK----ITKGNVTIKVWDIGGQPRFR 74
G+F + T+G + R+ I + +++WD GQ RFR
Sbjct: 25 GRFPERTEATIGVDFRERTVEIDGERIKVQLWDTAGQERFR 65
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 30.1 bits (67), Expect = 0.14
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 7/50 (14%)
Query: 40 FSQDMIPTVGFNMRKIT----KGNVTIKVWDIGGQPRFRSI---YMVDAA 82
F + T+G + T +G V +++WD GQ RFRS+ Y+ D+A
Sbjct: 5 FDNNYQSTIGIDFLSKTLYLDEGPVRLQLWDTAGQERFRSLIPSYIRDSA 54
>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 = 29.8 bits (67), Expect = 0.15
Identities = 16/42 (38%), Positives = 21/42 (50%), Gaps = 4/42 (9%)
Query: 39 QFSQDMIPTVG--FNMRKITKGNVTIK--VWDIGGQPRFRSI 76
+F D T+G F R I IK +WD GQ RFR++
Sbjct: 26 KFMADCPHTIGVEFGTRIIEVNGQKIKLQIWDTAGQERFRAV 67
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 29.7 bits (67), Expect = 0.16
Identities = 12/42 (28%), Positives = 20/42 (47%), Gaps = 4/42 (9%)
Query: 36 LSGQFSQDMIPTVGFNMRKI----TKGNVTIKVWDIGGQPRF 73
L+G+F + PT+G + + G + WD GQ +F
Sbjct: 34 LTGEFEKKYEPTIGVEVHPLDFFTNCGKIRFYCWDTAGQEKF 75
>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 = 0.17
Identities = 12/41 (29%), Positives = 25/41 (60%), Gaps = 4/41 (9%)
Query: 40 FSQDMIPTVG--FNMRKITKGN--VTIKVWDIGGQPRFRSI 76
F+ + TVG F ++ + + + + +++WD GQ R+R+I
Sbjct: 26 FTSAFVSTVGIDFKVKTVYRNDKRIKLQIWDTAGQERYRTI 66
>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 = 29.6 bits (66), Expect = 0.21
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 4/42 (9%)
Query: 39 QFSQDMIPTVG--FNMRKITKG--NVTIKVWDIGGQPRFRSI 76
+F I T+G F M+ I V I++WD GQ R+++I
Sbjct: 24 EFHSSHISTIGVDFKMKTIEVDGIKVRIQIWDTAGQERYQTI 65
>gnl|CDD|218203 pfam04670, Gtr1_RagA, Gtr1/RagA G protein conserved region. GTR1
was first identified in S. cerevisiae as a suppressor
of a mutation in RCC1. Biochemical analysis revealed
that Gtr1 is in fact a G protein of the Ras family. The
RagA/B proteins are the human homologues of Gtr1.
Included in this family is the human Rag C, a novel
protein that has been shown to interact with RagA/B.
Length = 230
Score = 29.1 bits (66), Expect = 0.30
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 58 GNVTIKVWDIGGQPRFRSIYMVDAADT 84
GN+T+ +WD GQ F Y+ +
Sbjct: 46 GNLTLNLWDCPGQDDFMENYLTRQKEH 72
>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 = 28.6 bits (64), Expect = 0.39
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 14/53 (26%)
Query: 38 GQFSQDMIPTVGFNMRK-----------ITKG---NVTIKVWDIGGQPRFRSI 76
+F+ I TVG + R+ T G V +++WD GQ RFRS+
Sbjct: 27 NKFNPKFITTVGIDFREKRVVYNSQGPDGTSGKAFRVHLQLWDTAGQERFRSL 79
>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 = 28.3 bits (63), Expect = 0.47
Identities = 19/62 (30%), Positives = 25/62 (40%), Gaps = 3/62 (4%)
Query: 27 GNVTIWPVPLSGQFSQDMIPTVGFNMRKI--TKGN-VTIKVWDIGGQPRFRSIYMVDAAD 83
G ++ V G F Q PTV N G V + +WD GQ F + + AD
Sbjct: 12 GKTSLLNVFTRGYFPQVYEPTVFENYIHDIFVDGLAVELSLWDTAGQEEFDRLRSLSYAD 71
Query: 84 TD 85
T
Sbjct: 72 TH 73
>gnl|CDD|206742 cd09915, Rag, Rag GTPase subfamily of Ras-related GTPases. Rag
GTPases (ras-related GTP-binding proteins) constitute a
unique subgroup of the Ras superfamily, playing 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. This subfamily consists of
RagA and RagB as well as RagC and RagD that are closely
related. Saccharomyces cerevisiae encodes single
orthologs of metazoan RagA/B and RagC/D, Gtr1 and Gtr2,
respectively. Dimer formation is important for their
cellular function; these domains form heterodimers, as
RagA or RagB dimerizes with RagC or RagD, and similarly,
Gtr1 dimerizes with Gtr2. 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 = 175
Score = 28.3 bits (63), Expect = 0.57
Identities = 15/61 (24%), Positives = 24/61 (39%), Gaps = 17/61 (27%)
Query: 56 TKGNVTIKVWDIGGQ-----PRFRS----------IYMVDAADTDKLEASRNELHALIEK 100
GN T+ +WD GQ P IY++D D + L+A L +++
Sbjct: 44 FLGNXTLNLWDCPGQDVFFEPTKDKEHIFQXVGALIYVIDVQD-EYLKAITI-LAKALKQ 101
Query: 101 L 101
Sbjct: 102 A 102
>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 = 28.0 bits (63), Expect = 0.61
Identities = 15/41 (36%), Positives = 25/41 (60%), Gaps = 4/41 (9%)
Query: 39 QFSQDMIPTVG--FNMRKITKGN--VTIKVWDIGGQPRFRS 75
+FS T+G F +++T + VT+++WD GQ RF+S
Sbjct: 24 KFSNQYKATIGADFLTKEVTVDDRLVTLQIWDTAGQERFQS 64
>gnl|CDD|235623 PRK05849, PRK05849, hypothetical protein; Provisional.
Length = 783
Score = 28.0 bits (63), Expect = 0.72
Identities = 15/62 (24%), Positives = 26/62 (41%), Gaps = 10/62 (16%)
Query: 35 PLSGQFSQDMIPTVGFNMRKITKGNVTIKVWDIGGQPRFRSIYMVDAADTDKLEASRNEL 94
L G FS++ I + F++ K+T ++ K ++ D +KLE EL
Sbjct: 377 LLPGGFSENEIKRIEFSLLKLTNRIISPK----------SGLFRKDLEKIEKLEERYKEL 426
Query: 95 HA 96
Sbjct: 427 LN 428
>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 = 27.0 bits (60), Expect = 1.4
Identities = 9/35 (25%), Positives = 12/35 (34%), Gaps = 4/35 (11%)
Query: 46 PTVGFN--MRKITKGNVTIKV--WDIGGQPRFRSI 76
P N I + T K D GQ + +I
Sbjct: 33 PGTTRNYVTTVIEEDGKTYKFNLLDTAGQEDYDAI 67
>gnl|CDD|206735 cd04172, Rnd3_RhoE_Rho8, Rnd3/RhoE/Rho8 GTPases. Rnd3/RhoE/Rho8
subfamily. Rnd3/RhoE/Rho8 is a member of the novel Rho
subfamily Rnd, together with Rnd1/Rho6 and Rnd2/Rho7.
Rnd3/RhoE is known to bind the serine-threonine kinase
ROCK I. Unphosphorylated Rnd3/RhoE associates primarily
with membranes, but ROCK I-phosphorylated Rnd3/RhoE
localizes in the cytosol. Phosphorylation of Rnd3/RhoE
correlates with its activity in disrupting RhoA-induced
stress fibers and inhibiting Ras-induced fibroblast
transformation. In cells that lack stress fibers, such
as macrophages and monocytes, Rnd3/RhoE induces a
redistribution of actin, causing morphological changes
in the cell. In addition, Rnd3/RhoE has been shown to
inhibit cell cycle progression in G1 phase at a point
upstream of the pRb family pocket protein checkpoint.
Rnd3/RhoE has also been shown to inhibit Ras- and
Raf-induced fibroblast transformation. In mammary
epithelial tumor cells, Rnd3/RhoE regulates the
assembly of the apical junction complex and tight
junction formation. Rnd3/RhoE is underexpressed in
prostate cancer cells both in vitro and in vivo;
re-expression of Rnd3/RhoE suppresses cell cycle
progression and increases apoptosis, suggesting it may
play a role in tumor suppression. Most Rho proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 182
Score = 26.9 bits (59), Expect = 1.9
Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 3/49 (6%)
Query: 40 FSQDMIPTVGFNMR---KITKGNVTIKVWDIGGQPRFRSIYMVDAADTD 85
F ++ +PTV N +I + + +WD G P + ++ + D+D
Sbjct: 30 FPENYVPTVFENYTASFEIDTQRIELSLWDTSGSPYYDNVRPLSYPDSD 78
>gnl|CDD|234421 TIGR03970, Rv0697, dehydrogenase, Rv0697 family. This model
describes a set of dehydrogenases belonging to the
glucose-methanol-choline oxidoreductase (GMC
oxidoreductase) family. Members of the present family
are restricted to Actinobacterial genome contexts
containing also members of families TIGR03962 and
TIGR03969 (the mycofactocin system), and are proposed to
be uniform in function.
Length = 487
Score = 27.1 bits (60), Expect = 1.9
Identities = 14/48 (29%), Positives = 19/48 (39%)
Query: 52 MRKITKGNVTIKVWDIGGQPRFRSIYMVDAADTDKLEASRNELHALIE 99
MR ++G + + D PR Y AAD L A H L+
Sbjct: 350 MRPHSRGRIRLASADPADPPRIEHRYDSSAADRAALRAGAALAHELLG 397
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 26.8 bits (59), Expect = 2.1
Identities = 12/31 (38%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 48 VGFNMRKITKGNVTIK--VWDIGGQPRFRSI 76
V F R + T+K +WD GQ R+R+I
Sbjct: 47 VEFATRTLQVEGKTVKAQIWDTAGQERYRAI 77
>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 = 2.4
Identities = 11/43 (25%), Positives = 25/43 (58%), Gaps = 4/43 (9%)
Query: 38 GQFSQDMIPTVG--FNMRKITKGNVTIKV--WDIGGQPRFRSI 76
G+F +PT+G + ++K++ N ++V +D+ G P + +
Sbjct: 23 GRFVSKYLPTIGIDYGVKKVSVRNKEVRVNFFDLSGHPEYLEV 65
>gnl|CDD|206693 cd04108, Rab36_Rab34, Rab GTPase families 34 (Rab34) and 36
(Rab36). Rab34/Rab36 subfamily. Rab34, found primarily
in the Golgi, interacts with its effector,
Rab-interacting lysosomal protein (RILP). This enables
its participation in microtubular
dynenin-dynactin-mediated repositioning of lysosomes
from the cell periphery to the Golgi. A Rab34 (Rah)
isoform that lacks the consensus GTP-binding region has
been identified in mice. This isoform is associated
with membrane ruffles and promotes macropinosome
formation. Rab36 has been mapped to human chromosome
22q11.2, a region that is homozygously deleted in
malignant rhabdoid tumors (MRTs). However, experimental
assessments do not implicate Rab36 as a tumor
suppressor that would enable tumor formation through a
loss-of-function mechanism. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab
proteins.
Length = 170
Score = 26.4 bits (58), Expect = 2.4
Identities = 13/43 (30%), Positives = 22/43 (51%), Gaps = 4/43 (9%)
Query: 38 GQFSQDMIPTVG--FNMRKITKGNV--TIKVWDIGGQPRFRSI 76
F ++ T+G F M + V ++++WD GQ RF+ I
Sbjct: 23 DVFDKNYKATIGVDFEMERFEVLGVPFSLQLWDTAGQERFKCI 65
>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 = 26.1 bits (57), Expect = 3.5
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 5/32 (15%)
Query: 45 IPTVGFNMRKITKGNVTIKVWDIGGQPRFRSI 76
I TV +KI +++WD GQ RF SI
Sbjct: 39 IKTVELRGKKIR-----LQIWDTAGQERFNSI 65
>gnl|CDD|205485 pfam13305, WHG, WHG domain. This presumed domain is around 80
amino acids in length. It is found to the C-terminus of
a DNA-binding helix-turn-helix domain. This domain may
be involved in binding to an as yet unknown ligand that
allows a transcriptional regulation response to that
molecule. The domain is named WHG after three conserved
residues near the C-terminus of the domain.
Length = 80
Score = 24.9 bits (55), Expect = 4.4
Identities = 9/30 (30%), Positives = 16/30 (53%)
Query: 72 RFRSIYMVDAADTDKLEASRNELHALIEKL 101
FR ++ D D +L+ + L L+E+L
Sbjct: 17 LFRLMFGADLEDDPELDEAFELLVELLEEL 46
>gnl|CDD|215955 pfam00503, G-alpha, G-protein alpha subunit. G proteins couple
receptors of extracellular signals to intracellular
signaling pathways. The G protein alpha subunit binds
guanyl nucleotide and is a weak GTPase. A set of
residues that are unique to G-alpha as compared to its
ancestor the Arf-like family form a ring of residues
centered on the nucleotide binding site. A Ggamma is
found fused to an inactive Galpha in the Dictyostelium
protein gbqA.
Length = 329
Score = 25.3 bits (56), Expect = 6.6
Identities = 7/26 (26%), Positives = 13/26 (50%)
Query: 45 IPTVGFNMRKITKGNVTIKVWDIGGQ 70
+ T G K + +++D+GGQ
Sbjct: 153 VKTTGIIETKFDFKGLKFRLFDVGGQ 178
>gnl|CDD|148984 pfam07680, DoxA, TQO small subunit DoxA. Thiosulphate:quinone
oxidoreductase (TQO) is one of the early steps in
elemental sulphur oxidation. A novel TQO enzyme was
purified from the thermo-acidophilic archaeon Acidianus
ambivalens and shown to consist of a large subunit
(DoxD) and a smaller subunit (DoxA). The DoxD- and
DoxA-like two subunits are fused together in a single
polypeptide in BT_0515.
Length = 133
Score = 24.6 bits (54), Expect = 8.3
Identities = 5/18 (27%), Positives = 9/18 (50%)
Query: 55 ITKGNVTIKVWDIGGQPR 72
+ G +K++D GQ
Sbjct: 110 LPPGTYEVKLYDPAGQSA 127
>gnl|CDD|188130 TIGR01323, nitrile_alph, nitrile hydratase, alpha subunit. This
model describes both iron- and cobalt-containing nitrile
hydratase alpha chains. It excludes the thiocyanate
hydrolase gamma subunit of Thiobacillus thioparus, a
sequence that appears to have evolved from within the
family of nitrile hydratase alpha subunits but which
differs by several indels and a more rapid accumulation
of point mutations [Energy metabolism, Amino acids and
amines].
Length = 189
Score = 24.6 bits (54), Expect = 8.9
Identities = 11/42 (26%), Positives = 21/42 (50%), Gaps = 3/42 (7%)
Query: 59 NVTIKVWDIGGQPRFRSIYMVDAADTDKLEASRNELHALIEK 100
+V ++VWD + R+ + M A T+ S +L L+ +
Sbjct: 139 DVEVRVWDSSAETRYLVLPM-RPAGTEGW--SEEQLAELVTR 177
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
0.320 0.136 0.402
Gapped
Lambda K H
0.267 0.0585 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,067,648
Number of extensions: 411873
Number of successful extensions: 448
Number of sequences better than 10.0: 1
Number of HSP's gapped: 424
Number of HSP's successfully gapped: 88
Length of query: 101
Length of database: 10,937,602
Length adjustment: 67
Effective length of query: 34
Effective length of database: 7,965,884
Effective search space: 270840056
Effective search space used: 270840056
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 (21.8 bits)
S2: 53 (24.5 bits)