RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17510
(113 letters)
>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 = 230 bits (589), Expect = 1e-79
Identities = 103/110 (93%), Positives = 108/110 (98%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
DVGGQDKIRPLWRHYYTGTQGLIFVVD ADRDRIDEARQELHRIINDREMRDA++L+FAN
Sbjct: 59 DVGGQDKIRPLWRHYYTGTQGLIFVVDSADRDRIDEARQELHRIINDREMRDALLLVFAN 118
Query: 61 KQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATTADGLYEGLTWLTSN 110
KQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCAT+ DGLYEGLTWL+SN
Sbjct: 119 KQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATSGDGLYEGLTWLSSN 168
>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 = 227 bits (580), Expect = 3e-78
Identities = 89/112 (79%), Positives = 101/112 (90%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
DVGGQDKIRPLWRHYYT TQGLIFVVD DRDRIDEAR+ELHR++N+ E+RDA+IL+FAN
Sbjct: 63 DVGGQDKIRPLWRHYYTNTQGLIFVVDSNDRDRIDEAREELHRMLNEDELRDAVILVFAN 122
Query: 61 KQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATTADGLYEGLTWLTSNHK 112
KQDLPDAMK EI EKLGL IRDRNWY+QP+CAT+ DGLYEGLTWL++N K
Sbjct: 123 KQDLPDAMKAAEITEKLGLHSIRDRNWYIQPTCATSGDGLYEGLTWLSNNLK 174
>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 = 199 bits (507), Expect = 3e-67
Identities = 74/110 (67%), Positives = 94/110 (85%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
DVGGQDKIRPLWRHY+ TQGLIFVVD DR+RI EAR+EL R++N+ E+RDA++L+FAN
Sbjct: 50 DVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERIGEAREELQRMLNEDELRDAVLLVFAN 109
Query: 61 KQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATTADGLYEGLTWLTSN 110
KQDLP+AM E+ +KLGL +R+RNWY+Q +CAT+ DGLYEGL WL++N
Sbjct: 110 KQDLPNAMSAAEVTDKLGLHSLRNRNWYIQATCATSGDGLYEGLDWLSNN 159
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 195 bits (497), Expect = 2e-65
Identities = 62/111 (55%), Positives = 82/111 (73%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
DVGGQ+ +RPLWR+Y+ T +IFVVD ADRDRI+EA++ELH ++N+ E+ DA +LI AN
Sbjct: 64 DVGGQESLRPLWRNYFPNTDAVIFVVDSADRDRIEEAKEELHALLNEEELADAPLLILAN 123
Query: 61 KQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATTADGLYEGLTWLTSNH 111
KQDLP AM EI+E LGL ++DR W +Q A T +GL EGL WL++
Sbjct: 124 KQDLPGAMSEAEIRELLGLHELKDRPWEIQGCSAVTGEGLDEGLDWLSNYI 174
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 191 bits (487), Expect = 7e-64
Identities = 73/110 (66%), Positives = 91/110 (82%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
DVGGQDK+RPLWRHYY T GLIFVVD DR+RI +AR+EL R++++ E+RDA++L+FAN
Sbjct: 67 DVGGQDKLRPLWRHYYQNTNGLIFVVDSNDRERIGDAREELERMLSEDELRDAVLLVFAN 126
Query: 61 KQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATTADGLYEGLTWLTSN 110
KQDLP+AM E+ EKLGL +R RNWY+Q CATTA GLYEGL WL++N
Sbjct: 127 KQDLPNAMSTTEVTEKLGLHSVRQRNWYIQGCCATTAQGLYEGLDWLSAN 176
>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 = 188 bits (479), Expect = 5e-63
Identities = 65/110 (59%), Positives = 82/110 (74%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
DVGGQDKIRPLW+HYY T GLIFVVD +DR+RI+EA+ ELH+++N+ E++ A +LI AN
Sbjct: 49 DVGGQDKIRPLWKHYYENTDGLIFVVDSSDRERIEEAKNELHKLLNEEELKGAPLLILAN 108
Query: 61 KQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATTADGLYEGLTWLTSN 110
KQDLP A+ E+ E LGL I+ R W++QP A T DGL EGL WL
Sbjct: 109 KQDLPGALTESELIELLGLESIKGRRWHIQPCSAVTGDGLDEGLDWLIEQ 158
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 182 bits (464), Expect = 2e-60
Identities = 74/110 (67%), Positives = 93/110 (84%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
DVGGQDKIRPLWRHY+ TQGLIFVVD DRDR+ EAR ELHR++N+ E+RDA++L+FAN
Sbjct: 67 DVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRDRVVEARDELHRMLNEDELRDAVLLVFAN 126
Query: 61 KQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATTADGLYEGLTWLTSN 110
KQDLP+AM EI +KLGL +R R+WY+Q +CAT+ +GLYEGL WL++N
Sbjct: 127 KQDLPNAMNAAEITDKLGLHSLRQRHWYIQSTCATSGEGLYEGLDWLSNN 176
>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 = 157 bits (398), Expect = 2e-50
Identities = 52/110 (47%), Positives = 74/110 (67%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
D+GGQ+ +R W YYT T +I V+D DR+R+ ++EL++++ ++R A++L+ AN
Sbjct: 65 DIGGQESLRSSWNTYYTNTDAVILVIDSTDRERLPLTKEELYKMLAHEDLRKAVLLVLAN 124
Query: 61 KQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATTADGLYEGLTWLTSN 110
KQDL AM P EI E LGLT IRD W++Q CA T +GL EGL W+ S
Sbjct: 125 KQDLKGAMTPAEISESLGLTSIRDHTWHIQGCCALTGEGLPEGLDWIASR 174
>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 = 144 bits (365), Expect = 9e-46
Identities = 52/107 (48%), Positives = 77/107 (71%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
D+GGQ IRP WR YY+ T +I+VVD DRDR+ ++ ELH ++ + E++DA++L+FAN
Sbjct: 49 DLGGQTSIRPYWRCYYSNTDAIIYVVDSTDRDRLGISKSELHAMLEEEELKDAVLLVFAN 108
Query: 61 KQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATTADGLYEGLTWL 107
KQD+P A+ E+ EKLGL+ ++DR W + + AT +GL EG+ WL
Sbjct: 109 KQDMPGALSEAEVAEKLGLSELKDRTWQIFKTSATKGEGLDEGMDWL 155
>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 = 142 bits (359), Expect = 2e-44
Identities = 52/110 (47%), Positives = 72/110 (65%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
D+GGQ KIRP WR+Y+ T LI+V+D ADR R +EA QEL ++ + ++ +L+FAN
Sbjct: 65 DIGGQRKIRPYWRNYFENTDVLIYVIDSADRKRFEEAGQELVELLEEEKLAGVPVLVFAN 124
Query: 61 KQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATTADGLYEGLTWLTSN 110
KQDL A E+ E L L IRDR+W++Q A T +GL EG+ W+ N
Sbjct: 125 KQDLLTAAPAEEVAEALNLHDIRDRSWHIQACSAKTGEGLQEGMNWVCKN 174
>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 = 134 bits (339), Expect = 1e-41
Identities = 46/110 (41%), Positives = 69/110 (62%), Gaps = 1/110 (0%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
DVGGQ+K+R +W+ Y T GL++VVD +D R+DE+++EL I+ + ++ +++ AN
Sbjct: 50 DVGGQEKMRTVWKCYLENTDGLVYVVDSSDEARLDESQKELKHILKNEHIKGVPVVLLAN 109
Query: 61 KQDLPDAMKPHEIQEKLGLTRIRD-RNWYVQPSCATTADGLYEGLTWLTS 109
KQDLP A+ EI + L + R+WYVQP A T +GL E L S
Sbjct: 110 KQDLPGALTAEEITRRFKLKKYCSDRDWYVQPCSAVTGEGLAEAFRKLAS 159
>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 = 127 bits (321), Expect = 9e-39
Identities = 46/107 (42%), Positives = 70/107 (65%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
DVGGQ +R WR+Y+ T LI+VVD +DR R+++ ++EL +++ + + A +LIFAN
Sbjct: 64 DVGGQKSLRSYWRNYFESTDALIWVVDSSDRARLEDCKRELQKLLVEERLAGATLLIFAN 123
Query: 61 KQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATTADGLYEGLTWL 107
KQDLP A+ P EI+E L L I+ +W + A T + L +G+ WL
Sbjct: 124 KQDLPGALSPEEIREVLELDSIKSHHWRIFGCSAVTGENLLDGIDWL 170
>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 = 122 bits (306), Expect = 1e-36
Identities = 54/109 (49%), Positives = 79/109 (72%), Gaps = 1/109 (0%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
DVGG+ K+RPLW+HYY TQ ++FV+D + RDR+ EA EL +++ ++E+RDA++LIFAN
Sbjct: 49 DVGGKHKLRPLWKHYYLNTQAVVFVIDSSHRDRVSEAHSELAKLLTEKELRDALLLIFAN 108
Query: 61 KQDLPDAMKPHEIQEKLGLTRI-RDRNWYVQPSCATTADGLYEGLTWLT 108
KQD+ A+ E+ E L L ++ R+WY+Q A + GLYEGL WL+
Sbjct: 109 KQDVAGALSVEEMTELLSLHKLCCGRSWYIQGCDARSGMGLYEGLDWLS 157
>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 = 116 bits (293), Expect = 2e-34
Identities = 49/105 (46%), Positives = 71/105 (67%), Gaps = 1/105 (0%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
DVGGQ+K+RPLW+ Y T G++FVVD D +R++EA+ ELH+I E + +L+ AN
Sbjct: 58 DVGGQEKLRPLWKSYTRCTDGIVFVVDSVDVERMEEAKTELHKITKFSENQGVPVLVLAN 117
Query: 61 KQDLPDAMKPHEIQEKLGLTRIRD-RNWYVQPSCATTADGLYEGL 104
KQDLP+A+ E+++ L L + W+VQP+CA +GL EGL
Sbjct: 118 KQDLPNALPVSEVEKLLALHELSSSTPWHVQPACAIIGEGLQEGL 162
>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 = 113 bits (284), Expect = 3e-33
Identities = 50/111 (45%), Positives = 70/111 (63%), Gaps = 2/111 (1%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIIN--DREMRDAIILIF 58
D+ GQ K R LW HYY QG+IFV+D +DR R+ A+ EL ++N D + R IL +
Sbjct: 51 DMSGQGKYRGLWEHYYKNIQGIIFVIDSSDRLRMVVAKDELELLLNHPDIKHRRIPILFY 110
Query: 59 ANKQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATTADGLYEGLTWLTS 109
ANK DLPDA+ +I + L L I+D+ W++ S A T +GL EG+ WL +
Sbjct: 111 ANKMDLPDALTAVKITQLLCLENIKDKPWHIFASSALTGEGLDEGVDWLQA 161
>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 = 98.6 bits (246), Expect = 2e-27
Identities = 43/109 (39%), Positives = 68/109 (62%), Gaps = 2/109 (1%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
D+GGQ+++R LW YY + G+I+V+D DR+R +E++ ++IN+ + +L+ AN
Sbjct: 57 DLGGQEELRSLWDKYYAESHGVIYVIDSTDRERFNESKSAFEKVINNEALEGVPLLVLAN 116
Query: 61 KQDLPDAMKPHEIQE--KLGLTRIRDRNWYVQPSCATTADGLYEGLTWL 107
KQDLPDA+ EI+E + I R+ VQP A +G+ EG+ WL
Sbjct: 117 KQDLPDALSVAEIKEVFDDCIALIGRRDCLVQPVSALEGEGVEEGIEWL 165
>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 = 96.7 bits (241), Expect = 7e-27
Identities = 41/98 (41%), Positives = 59/98 (60%), Gaps = 3/98 (3%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
++GG +R W+ Y +G+QGLIFVVD AD +R+ ARQELH+++ D +++ AN
Sbjct: 50 EIGGSQNLRKYWKRYLSGSQGLIFVVDSADSERLPLARQELHQLLQ--HPPDLPLVVLAN 107
Query: 61 KQDLPDAMKPHEIQEKLGLTRI-RDRNWYVQPSCATTA 97
KQDLP A EI ++L L I R R W +Q +
Sbjct: 108 KQDLPAARSVQEIHKELELEPIARGRRWILQGTSLDDD 145
>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 = 92.8 bits (231), Expect = 2e-25
Identities = 35/110 (31%), Positives = 57/110 (51%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
D+GGQ + R +W Y G +++VVD ADR++++ A+ ELH ++ + +L+ N
Sbjct: 50 DLGGQPRFRSMWERYCRGVNAIVYVVDAADREKLEVAKNELHDLLEKPSLEGIPLLVLGN 109
Query: 61 KQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATTADGLYEGLTWLTSN 110
K DLP A+ E+ E++ L I DR A + L WL +
Sbjct: 110 KNDLPGALSVDELIEQMNLKSITDREVSCYSISAKEKTNIDIVLDWLIKH 159
>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 = 88.6 bits (220), Expect = 1e-23
Identities = 38/119 (31%), Positives = 62/119 (52%), Gaps = 9/119 (7%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
D+GG R +W +YY GL+FVVD +D DR+ E ++ L ++ + IL+ AN
Sbjct: 49 DLGGGANFRGIWVNYYAEAHGLVFVVDSSDDDRVQEVKEILRELLQHPRVSGKPILVLAN 108
Query: 61 KQDLPDAMKPHEIQEKLGLTRIRDRN---WYVQPSCATTADG------LYEGLTWLTSN 110
KQD +A+ ++ E L L ++ + N +++P A G + EGL WL +
Sbjct: 109 KQDKKNALLGADVIEYLSLEKLVNENKSLCHIEPCSAIEGLGKKIDPSIVEGLRWLLAA 167
>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 = 83.9 bits (208), Expect = 2e-21
Identities = 32/81 (39%), Positives = 52/81 (64%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
D+GG ++ R +W+ Y+ G++F+VD AD +R E+++EL ++ND E+ + ILI N
Sbjct: 69 DLGGHEQARRVWKDYFPEVDGIVFLVDAADPERFQESKEELDSLLNDEELANVPILILGN 128
Query: 61 KQDLPDAMKPHEIQEKLGLTR 81
K D P A+ E++E LGL
Sbjct: 129 KIDKPGAVSEEELREALGLYG 149
>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 = 76.9 bits (189), Expect = 6e-19
Identities = 37/115 (32%), Positives = 59/115 (51%), Gaps = 7/115 (6%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
D+GG + R LW+ Y+ G++++VD D++R E+++EL +++D E+ LI N
Sbjct: 67 DLGGHQQARRLWKDYFPEVNGIVYLVDAYDKERFAESKRELDALLSDEELATVPFLILGN 126
Query: 61 KQDLPDAMKPHEIQEKLGLTRI--RDRNWYVQP----SCATT-ADGLYEGLTWLT 108
K D P A E++ LGLT V+P C+ G EG WL+
Sbjct: 127 KIDAPYAASEDELRYALGLTNTTTGKGKVGVRPVEVFMCSVVRRMGYGEGFKWLS 181
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 73.8 bits (181), Expect = 2e-17
Identities = 25/85 (29%), Positives = 37/85 (43%), Gaps = 3/85 (3%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
D GQ++ R L YY G G++ V D R+ DE +E + + D IL+ N
Sbjct: 60 DTAGQEEYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVGN 119
Query: 61 KQDLPDAMKPHEIQEKLGLTRIRDR 85
K DL D E++ R+
Sbjct: 120 KIDLFDE---QSSSEEILNQLNREV 141
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 60.6 bits (147), Expect = 1e-12
Identities = 31/105 (29%), Positives = 49/105 (46%), Gaps = 9/105 (8%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAI-ILIFA 59
GQ++ + +W G G I +VD + R A II+ R+ I +++
Sbjct: 74 GTPGQERFKFMWEILSRGAVGAIVLVDSS-RPITFHAE----EIIDFLTSRNPIPVVVAI 128
Query: 60 NKQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATTADGLYEGL 104
NKQDL DA+ P +I+E L L + + V AT +G + L
Sbjct: 129 NKQDLFDALPPEKIREALKLELL---SVPVIEIDATEGEGARDQL 170
>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 = 53.6 bits (129), Expect = 3e-10
Identities = 24/114 (21%), Positives = 41/114 (35%), Gaps = 10/114 (8%)
Query: 1 DVGGQDKIRPLW-----RHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAII 55
D G D+ L R G ++ VVD DR+ ++A+ + R + + I
Sbjct: 53 DTPGLDEFGGLGREELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLRKEGIP---I 109
Query: 56 LIFANKQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATTADGLYEGLTWLTS 109
++ NK DL + + + V A T +G+ E L
Sbjct: 110 ILVGNKIDLLEE--REVEELLRLEELAKILGVPVFEVSAKTGEGVDELFEKLIE 161
>gnl|CDD|232886 TIGR00231, small_GTP, small GTP-binding protein domain. Proteins
with a small GTP-binding domain recognized by this model
include Ras, RhoA, Rab11, translation elongation factor
G, translation initiation factor IF-2, tetratcycline
resistance protein TetM, CDC42, Era, ADP-ribosylation
factors, tdhF, and many others. In some proteins the
domain occurs more than once.This model recognizes a
large number of small GTP-binding proteins and related
domains in larger proteins. Note that the alpha chains
of heterotrimeric G proteins are larger proteins in
which the NKXD motif is separated from the GxxxxGK[ST]
motif (P-loop) by a long insert and are not easily
detected by this model [Unknown function, General].
Length = 162
Score = 53.1 bits (128), Expect = 5e-10
Identities = 22/97 (22%), Positives = 35/97 (36%), Gaps = 6/97 (6%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADR-DRIDEARQELHRIINDREMRDAIILIFA 59
D GQ+ + R YY + + V D ++E ++ + I I++
Sbjct: 57 DTAGQEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAESGVPIILVG 116
Query: 60 NKQDLPDA-MKPHEIQEKLGLTRIRDRNWYVQPSCAT 95
NK DL DA +K H L + S T
Sbjct: 117 NKIDLRDAKLKTHVAFLFAKLNGEP----IIPLSAET 149
>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 = 53.5 bits (129), Expect = 7e-10
Identities = 30/91 (32%), Positives = 47/91 (51%), Gaps = 6/91 (6%)
Query: 1 DVGGQDKIRP-LWRHYYTGTQGLIFVVDCADRDR-IDEARQELHRIINDREMR-DAI-IL 56
DV G +K+R L + + ++FVVD A + I + + L+ I+ D E + I IL
Sbjct: 53 DVPGHEKLRDKLLEYLKASLKAIVFVVDSATFQKNIRDVAEFLYDILTDLEKIKNKIPIL 112
Query: 57 IFANKQDLPDAMKPHEIQEKL--GLTRIRDR 85
I NKQDL A +I+E L + +R+
Sbjct: 113 IACNKQDLFTAKPAKKIKELLEKEINTLRES 143
>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 = 45.0 bits (107), Expect = 6e-07
Identities = 26/86 (30%), Positives = 36/86 (41%), Gaps = 4/86 (4%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
D GQ++ R L YY G QG+I V D RD D L+ + DA+ ++ N
Sbjct: 55 DTAGQERFRTLTSSYYRGAQGVILVYDVTRRDTFDNLDTWLNELDTYSTNPDAVKMLVGN 114
Query: 61 KQDLPDAMKPHEIQEKLGLTRIRDRN 86
K D E+ + G R N
Sbjct: 115 KIDKE----NREVTREEGQKFARKHN 136
>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 = 44.9 bits (107), Expect = 1e-06
Identities = 24/75 (32%), Positives = 34/75 (45%), Gaps = 12/75 (16%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRD----------RIDEARQELHRIINDREM 50
DVGGQ R W H + +IFVV ++ D R++E+ I N
Sbjct: 174 DVGGQRSERKKWIHCFEDVTAIIFVVSLSEYDQVLYEDDSTNRLEESLNLFEEICNSPWF 233
Query: 51 RDA-IILIFANKQDL 64
++ IIL NK+DL
Sbjct: 234 KNTPIILFL-NKKDL 247
>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 = 43.9 bits (104), Expect = 2e-06
Identities = 25/79 (31%), Positives = 38/79 (48%), Gaps = 5/79 (6%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAII-LIFA 59
D GQ++ R + YY G G+I V D D++ + +Q L I DR + + L+
Sbjct: 57 DTAGQERFRTITSSYYRGAHGIIIVYDVTDQESFNNVKQWLQEI--DRYASENVNKLLVG 114
Query: 60 NKQDLPD--AMKPHEIQEK 76
NK DL D + E +E
Sbjct: 115 NKCDLTDKKVVDYTEAKEF 133
>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 = 42.8 bits (102), Expect = 4e-06
Identities = 21/69 (30%), Positives = 31/69 (44%), Gaps = 7/69 (10%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRD---RIDEARQELHRIINDREMRDAIILI 57
D GQ++ R + YY G G I V D +R+ +D+ EL + I++
Sbjct: 55 DTAGQERFRSITSSYYRGAHGAILVYDVTNRESFENLDKWLNELKEYAPP----NIPIIL 110
Query: 58 FANKQDLPD 66
NK DL D
Sbjct: 111 VGNKSDLED 119
>gnl|CDD|204242 pfam09439, SRPRB, Signal recognition particle receptor beta
subunit. The beta subunit of the signal recognition
particle receptor (SRP) is a transmembrane GTPase which
anchors the alpha subunit to the endoplasmic reticulum
membrane.
Length = 181
Score = 42.4 bits (100), Expect = 7e-06
Identities = 28/93 (30%), Positives = 48/93 (51%), Gaps = 8/93 (8%)
Query: 1 DVGGQDKIRP--LWRHYYT-GTQGLIFVVD-CADRDRIDEARQELHRIINDRE-MRDAI- 54
D G K+R L + +G++FVVD A + + + L+ I++ E +++ I
Sbjct: 55 DFPGHVKLRQKLLETIKDSSSLRGIVFVVDSTAFPKEVTDTAEFLYEILSITELLKNGID 114
Query: 55 ILIFANKQDLPDAMKPHEIQEKL--GLTRIRDR 85
ILI NKQ+ A P +I++ L + IR+R
Sbjct: 115 ILIACNKQESFTARPPKKIKQALEKEINTIRER 147
>gnl|CDD|214595 smart00275, G_alpha, G protein alpha subunit. Subunit of G
proteins that contains the guanine nucleotide binding
site.
Length = 342
Score = 39.9 bits (94), Expect = 7e-05
Identities = 23/74 (31%), Positives = 32/74 (43%), Gaps = 10/74 (13%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRD----------RIDEARQELHRIINDREM 50
DVGGQ R W H + +IF V ++ D R+ E+ I N R
Sbjct: 190 DVGGQRSERKKWIHCFDNVTAIIFCVALSEYDQVLEEDESTNRMQESLNLFESICNSRWF 249
Query: 51 RDAIILIFANKQDL 64
+ I++F NK DL
Sbjct: 250 ANTSIILFLNKIDL 263
>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 = 38.7 bits (90), Expect = 1e-04
Identities = 17/64 (26%), Positives = 31/64 (48%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
D GQ++ + + YY G Q +I V D D ++ RQ L + + + ++ +
Sbjct: 55 DTAGQERFKCIASTYYRGAQAIIIVFDLTDVASLEHTRQWLEDALKENDPSSVLLFLVGT 114
Query: 61 KQDL 64
K+DL
Sbjct: 115 KKDL 118
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 38.6 bits (89), Expect = 2e-04
Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 1/69 (1%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
D GQ++ R L Y + I V D +R + + + I+N+R +D II + N
Sbjct: 35 DTAGQERFRSLIPSYIRDSAAAIVVYDITNRQSFENTTKWIQDILNERG-KDVIIALVGN 93
Query: 61 KQDLPDAMK 69
K DL D K
Sbjct: 94 KTDLGDLRK 102
>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 = 37.5 bits (88), Expect = 4e-04
Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 7/69 (10%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEAR---QELHRIINDREMRDAIILI 57
D GQ++ R L YY G QG + V D RD + + +E+ R ++ + I++
Sbjct: 54 DTAGQERFRALRPLYYRGAQGFLLVYDITSRDSFENVKKWLEEILRHADE----NVPIVL 109
Query: 58 FANKQDLPD 66
NK DL D
Sbjct: 110 VGNKCDLED 118
>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 = 37.2 bits (87), Expect = 4e-04
Identities = 19/71 (26%), Positives = 31/71 (43%), Gaps = 5/71 (7%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMR--DAIILIF 58
D GQ++ L YY G I V D D D + ++ + + ++MR + ++I
Sbjct: 55 DTAGQERYHALGPIYYRDADGAILVYDITDADSFQKVKKWIKEL---KQMRGNNISLVIV 111
Query: 59 ANKQDLPDAMK 69
NK DL
Sbjct: 112 GNKIDLERQRV 122
>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 = 36.9 bits (86), Expect = 7e-04
Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 1/66 (1%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
D GQ++ R + YY G G+I V D D + + + R I++ D ++ N
Sbjct: 58 DTAGQERFRTITTSYYRGAMGIILVYDITDEKSFENIKNWM-RNIDEHASEDVERMLVGN 116
Query: 61 KQDLPD 66
K D+ +
Sbjct: 117 KCDMEE 122
>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 = 36.6 bits (85), Expect = 7e-04
Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 7/69 (10%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREM---RDAIILI 57
D GQ++ R + R YY G G + V D R+ + L + D D +I++
Sbjct: 55 DTAGQERFRSVTRSYYRGAAGALLVYDITSRESFN----ALTNWLTDARTLASPDIVIIL 110
Query: 58 FANKQDLPD 66
NK+DL D
Sbjct: 111 VGNKKDLED 119
>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 = 36.4 bits (85), Expect = 0.001
Identities = 19/69 (27%), Positives = 29/69 (42%), Gaps = 7/69 (10%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEAR---QELHRIINDREMRDAIILI 57
D GQ++ R L YY G I V D + ++A+ +EL + +I +
Sbjct: 56 DTAGQERYRSLAPMYYRGAAAAIVVYDITSEESFEKAKSWVKELQEHGPP----NIVIAL 111
Query: 58 FANKQDLPD 66
NK DL
Sbjct: 112 AGNKADLES 120
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 36.3 bits (85), Expect = 0.001
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 7/69 (10%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADR---DRIDEARQELHRIINDREMRDAIILI 57
D GQ++ R + YY G G + V D +R + ++ +EL + + +I++
Sbjct: 55 DTAGQERFRSITSSYYRGAVGALLVYDITNRESFENLENWLKELREYASP----NVVIML 110
Query: 58 FANKQDLPD 66
NK DL +
Sbjct: 111 VGNKSDLEE 119
>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 = 36.2 bits (84), Expect = 0.001
Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 10/72 (13%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRID-------EARQELHRIINDREMRDA 53
D+ G + + +Y TQG++ V D DR + E +QE N M +
Sbjct: 55 DLSGHPEYLEVRNEFYKDTQGVLLVYDVTDRQSFEALDSWLKEMKQEGGPHGN---MENI 111
Query: 54 IILIFANKQDLP 65
++++ ANK DL
Sbjct: 112 VVVVCANKIDLT 123
>gnl|CDD|206639 cd00066, G-alpha, Alpha subunit of G proteins (guanine nucleotide
binding). The alpha subunit of G proteins contains the
guanine nucleotide binding site. The heterotrimeric
GNP-binding proteins are signal transducers that
communicate signals from many hormones,
neurotransmitters, chemokines, and autocrine and
paracrine factors. Extracellular signals are received by
receptors, which activate the G proteins, which in turn
route the signals to several distinct intracellular
signaling pathways. The alpha subunit of G proteins is a
weak GTPase. In the resting state, heterotrimeric G
proteins are associated at the cytosolic face of the
plasma membrane and the alpha subunit binds to GDP. Upon
activation by a receptor GDP is replaced with GTP, and
the G-alpha/GTP complex dissociates from the beta and
gamma subunits. This results in activation of downstream
signaling pathways, such as cAMP synthesis by adenylyl
cyclase, which is terminated when GTP is hydrolized and
the heterotrimers reconstitute.
Length = 315
Score = 36.4 bits (85), Expect = 0.001
Identities = 24/74 (32%), Positives = 35/74 (47%), Gaps = 10/74 (13%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRD----------RIDEARQELHRIINDREM 50
DVGGQ R W H + +IFVV ++ D R+ E+ + I N R
Sbjct: 167 DVGGQRSERKKWIHCFEDVTAIIFVVALSEYDQVLVEDESVNRMQESLKLFDSICNSRWF 226
Query: 51 RDAIILIFANKQDL 64
+ I++F NK+DL
Sbjct: 227 ANTSIILFLNKKDL 240
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 36.4 bits (84), Expect = 0.001
Identities = 22/69 (31%), Positives = 32/69 (46%), Gaps = 11/69 (15%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRD-----AII 55
D GQ++ R + YY G G + V D R D ++ L RE+RD +I
Sbjct: 67 DTAGQERYRAITSAYYRGAVGALLVYDITKRQTFDNVQRWL------RELRDHADSNIVI 120
Query: 56 LIFANKQDL 64
++ NK DL
Sbjct: 121 MMAGNKSDL 129
>gnl|CDD|206685 cd01898, Obg, Obg GTPase. The Obg nucleotide binding protein
subfamily has been implicated in stress response,
chromosome partitioning, replication initiation,
mycelium development, and sporulation. Obg proteins are
among a large group of GTP binding proteins conserved
from bacteria to humans. The E. coli homolog, ObgE is
believed to function in ribosomal biogenesis. Members of
the subfamily contain two equally and highly conserved
domains, a C-terminal GTP binding domain and an
N-terminal glycine-rich domain.
Length = 170
Score = 35.9 bits (84), Expect = 0.001
Identities = 17/63 (26%), Positives = 29/63 (46%), Gaps = 6/63 (9%)
Query: 19 TQGLIFVVDCADRDRIDEA----RQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQ 74
T+ L+ V+D + D E R EL + + + ++ NK DL DA + E
Sbjct: 79 TRVLLHVIDLSGEDDPVEDYETIRNELEAY--NPGLAEKPRIVVLNKIDLLDAEERFEKL 136
Query: 75 EKL 77
++L
Sbjct: 137 KEL 139
>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 = 36.0 bits (83), Expect = 0.002
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 2/66 (3%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
D GQ++ R + YY GT G+I V D + + ++ L I + + +++ N
Sbjct: 61 DTAGQERFRTITSTYYRGTHGVIVVYDVTNGESFVNVKRWLQEIEQNCDDVCKVLV--GN 118
Query: 61 KQDLPD 66
K D P+
Sbjct: 119 KNDDPE 124
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 34.3 bits (78), Expect = 0.006
Identities = 13/32 (40%), Positives = 17/32 (53%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRD 32
D GQ++ R L YY QG+I V D R+
Sbjct: 68 DTAGQERFRTLTSSYYRNAQGIILVYDVTRRE 99
>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 = 34.0 bits (78), Expect = 0.007
Identities = 18/69 (26%), Positives = 29/69 (42%), Gaps = 7/69 (10%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADR---DRIDEARQELHRIINDREMRDAIILI 57
D GQ++ R + R YY G G + V D R + + + + N + +I +
Sbjct: 57 DTAGQERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDARNLTNP----NTVIFL 112
Query: 58 FANKQDLPD 66
NK DL
Sbjct: 113 IGNKADLEA 121
>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 = 33.4 bits (76), Expect = 0.013
Identities = 17/63 (26%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
D GQ++ + YY +G+I V D ++ D+ + + ++I+ DA +L+ N
Sbjct: 55 DTAGQERFNSITSAYYRSAKGIILVYDITKKETFDDLPKWM-KMIDKYASEDAELLLVGN 113
Query: 61 KQD 63
K D
Sbjct: 114 KLD 116
>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 = 0.016
Identities = 22/72 (30%), Positives = 30/72 (41%), Gaps = 15/72 (20%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDR-------IDEARQELHRIINDREMRDA 53
D GQ+ R + R YY G G + V D R+ +++ARQ
Sbjct: 59 DTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQH-------SNSNMT 111
Query: 54 IILIFANKQDLP 65
I+LI NK DL
Sbjct: 112 IMLI-GNKCDLE 122
>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 = 32.6 bits (75), Expect = 0.019
Identities = 19/69 (27%), Positives = 32/69 (46%), Gaps = 1/69 (1%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
D GQ++ R L Y + + V D +R D + + + ++R D II++ N
Sbjct: 55 DTAGQERFRSLIPSYIRDSSVAVVVYDITNRQSFDNTDKWIDDVRDERG-NDVIIVLVGN 113
Query: 61 KQDLPDAMK 69
K DL D +
Sbjct: 114 KTDLSDKRQ 122
>gnl|CDD|206642 cd00876, Ras, Rat sarcoma (Ras) family of small guanosine
triphosphatases (GTPases). The Ras family of the Ras
superfamily includes classical N-Ras, H-Ras, and K-Ras,
as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG,
Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins.
Ras proteins regulate cell growth, proliferation and
differentiation. Ras is activated by guanine nucleotide
exchange factors (GEFs) that release GDP and allow GTP
binding. Many RasGEFs have been identified. These are
sequestered in the cytosol until activation by growth
factors triggers recruitment to the plasma membrane or
Golgi, where the GEF colocalizes with Ras. Active
GTP-bound Ras interacts with several effector proteins:
among the best characterized are the Raf kinases,
phosphatidylinositol 3-kinase (PI3K), RalGEFs and
NORE/MST1. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 160
Score = 32.5 bits (75), Expect = 0.020
Identities = 17/69 (24%), Positives = 29/69 (42%), Gaps = 6/69 (8%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADR---DRIDEARQELHRIINDREMRDAIILI 57
D GQ++ + Y G I V R + I R+++ R+ + D I++
Sbjct: 53 DTAGQEEFSAMRDQYIRNGDGFILVYSITSRESFEEIKNIREQILRVKDKE---DVPIVL 109
Query: 58 FANKQDLPD 66
NK DL +
Sbjct: 110 VGNKCDLEN 118
>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 = 32.5 bits (74), Expect = 0.021
Identities = 20/79 (25%), Positives = 36/79 (45%), Gaps = 2/79 (2%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
D GQ++ R + YY L+ + D ++ D R L I+ + D +I++ N
Sbjct: 56 DTAGQERFRSVTHAYYRDAHALLLLYDVTNKSSFDNIRAWLTEIL-EYAQSDVVIMLLGN 114
Query: 61 KQDLP-DAMKPHEIQEKLG 78
K D+ + + E E+L
Sbjct: 115 KADMSGERVVKREDGERLA 133
>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 = 32.2 bits (73), Expect = 0.025
Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 1/66 (1%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
D GQ++ R + YY G G I + D + + + A Q+ I +A +++ N
Sbjct: 56 DTAGQERYRTITTAYYRGAMGFILMYDITNEESFN-AVQDWSTQIKTYSWDNAQVILVGN 114
Query: 61 KQDLPD 66
K D+ D
Sbjct: 115 KCDMED 120
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 32.2 bits (73), Expect = 0.032
Identities = 20/71 (28%), Positives = 31/71 (43%), Gaps = 15/71 (21%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDR-------IDEARQELHRIINDREMRDA 53
D GQ+ R + R YY G G + V D R+ +++ARQ + +
Sbjct: 61 DTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLASWLEDARQHAN--------ANM 112
Query: 54 IILIFANKQDL 64
I++ NK DL
Sbjct: 113 TIMLIGNKCDL 123
>gnl|CDD|206713 cd04146, RERG_RasL11_like, Ras-related and Estrogen-Regulated
Growth inhibitor (RERG) and Ras-like 11 (RasL11)-like
families. RERG (Ras-related and Estrogen- Regulated
Growth inhibitor) and Ras-like 11 are members of a novel
subfamily of Ras that were identified based on their
behavior in breast and prostate tumors, respectively.
RERG expression was decreased or lost in a significant
fraction of primary human breast tumors that lack
estrogen receptor and are correlated with poor clinical
prognosis. Elevated RERG expression correlated with
favorable patient outcome in a breast tumor subtype that
is positive for estrogen receptor expression. In
contrast to most Ras proteins, RERG overexpression
inhibited the growth of breast tumor cells in vitro and
in vivo. RasL11 was found to be ubiquitously expressed
in human tissue, but down-regulated in prostate tumors.
Both RERG and RasL11 lack the C-terminal CaaX
prenylation motif, where a = an aliphatic amino acid and
X = any amino acid, and are localized primarily in the
cytoplasm. Both are believed to have tumor suppressor
activity.
Length = 166
Score = 31.9 bits (73), Expect = 0.041
Identities = 14/49 (28%), Positives = 20/49 (40%), Gaps = 7/49 (14%)
Query: 21 GLIFVVDCADRDRIDEARQELHRIINDREM----RDAIILIFANKQDLP 65
G + V DR D Q L I RE+ + +++ NK DL
Sbjct: 75 GFVLVYSITDRSSFDVVSQLLQLI---REIKKRDGEIPVILVGNKADLL 120
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 31.0 bits (71), Expect = 0.080
Identities = 16/64 (25%), Positives = 29/64 (45%), Gaps = 10/64 (15%)
Query: 19 TQGLIFVVDCADRDRIDEA------RQELHRIINDREMRDAIILIFANKQDLPDAMKPHE 72
T+ L+ V+D + D D R EL + ++ + ++ NK DLP + E
Sbjct: 238 TRVLLHVIDLSPIDGRDPIEDYQTIRNELEKY--SPKLAEKPRIVVLNKIDLPLDEE--E 293
Query: 73 IQEK 76
++E
Sbjct: 294 LEEL 297
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 30.7 bits (70), Expect = 0.11
Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 11/80 (13%)
Query: 22 LIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQD-LPDAMKPHEIQEKLGLT 80
L+ VVD +D + +++ + ++ + + I++ NK D L D E++
Sbjct: 275 LLHVVDASDPEILEKLEA-VEDVLAEIGADEIPIILVLNKIDLLEDEEILAELE------ 327
Query: 81 RIRDRNWYVQPSCATTADGL 100
R V S A T +GL
Sbjct: 328 --RGSPNPVFIS-AKTGEGL 344
>gnl|CDD|206668 cd01881, Obg_like, Obg-like family of GTPases consist of five
subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1. The
Obg-like subfamily consists of five well-delimited,
ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210,
and NOG1. Four of these groups (Obg, DRG, YyaF/YchF, and
Ygr210) are characterized by a distinct glycine-rich
motif immediately following the Walker B motif (G3 box).
Obg/CgtA is an essential gene that is involved in the
initiation of sporulation and DNA replication in the
bacteria Caulobacter and Bacillus, but its exact
molecular role is unknown. Furthermore, several OBG
family members possess a C-terminal RNA-binding domain,
the TGS domain, which is also present in threonyl-tRNA
synthetase and in bacterial guanosine polyphosphatase
SpoT. Nog1 is a nucleolar protein that might function in
ribosome assembly. The DRG and Nog1 subfamilies are
ubiquitous in archaea and eukaryotes, the Ygr210
subfamily is present in archaea and fungi, and the Obg
and YyaF/YchF subfamilies are ubiquitous in bacteria and
eukaryotes. The Obg/Nog1 and DRG subfamilies appear to
form one major branch of the Obg family and the Ygr210
and YchF subfamilies form another branch. No GEFs, GAPs,
or GDIs for Obg have been identified.
Length = 167
Score = 30.4 bits (69), Expect = 0.13
Identities = 21/104 (20%), Positives = 37/104 (35%), Gaps = 16/104 (15%)
Query: 4 GQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEA------RQELHRIINDREMRDAIILI 57
G+ + H Y + ++ V+D ++ D +E+ + + +I
Sbjct: 62 GRGLGEQILAHLYR-SDLILHVIDASEDCVGDPLEDQKTLNEEVSGSFLFLKNK--PEMI 118
Query: 58 FANKQDLPDAMKPHE-IQEKLGLTRIRDRNWYVQPSCATTADGL 100
ANK D+ +KL R V P+ A T GL
Sbjct: 119 VANKIDMASENNLKRLKLDKL------KRGIPVVPTSALTRLGL 156
>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 = 29.7 bits (67), Expect = 0.22
Identities = 22/81 (27%), Positives = 36/81 (44%), Gaps = 9/81 (11%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRD---RIDEARQELHRIINDREMRDAIILI 57
D GQ++ + + YY G Q I V DR+ I+ ++++ D M ++
Sbjct: 57 DTAGQEEFDAITKAYYRGAQACILVFSTTDRESFEAIESWKEKVEAECGDIPM-----VL 111
Query: 58 FANKQDLPD-AMKPHEIQEKL 77
K DL D A+ +E E L
Sbjct: 112 VQTKIDLLDQAVITNEEAEAL 132
>gnl|CDD|233986 TIGR02729, Obg_CgtA, Obg family GTPase CgtA. This model describes
a univeral, mostly one-gene-per-genome GTP-binding
protein that associates with ribosomal subunits and
appears to play a role in ribosomal RNA maturation. This
GTPase, related to the nucleolar protein Obg, is
designated CgtA in bacteria. Mutations in this gene are
pleiotropic, but it appears that effects on cellular
functions such as chromosome partition may be secondary
to the effect on ribosome structure. Recent work done in
Vibrio cholerae shows an essential role in the stringent
response, in which RelA-dependent ability to synthesize
the alarmone ppGpp is required for deletion of this
GTPase to be lethal [Protein synthesis, Other].
Length = 329
Score = 29.7 bits (68), Expect = 0.27
Identities = 16/64 (25%), Positives = 29/64 (45%), Gaps = 9/64 (14%)
Query: 19 TQGLIFVVDCADRDRIDEARQELHRIIN-----DREMRDAIILIFANKQDLPDAMKPHEI 73
T+ L+ ++D + D D ++ I N E+ + ++ NK DL D E+
Sbjct: 236 TRVLLHLIDISPEDGSD-PIEDYEIIRNELKKYSPELAEKPRIVVLNKIDLLD---EEEL 291
Query: 74 QEKL 77
+E L
Sbjct: 292 EELL 295
>gnl|CDD|237045 PRK12296, obgE, GTPase CgtA; Reviewed.
Length = 500
Score = 29.8 bits (68), Expect = 0.28
Identities = 29/101 (28%), Positives = 40/101 (39%), Gaps = 23/101 (22%)
Query: 22 LIFVVDCA----DRD---RIDEARQELHRIINDREMRDAII-------LIFANKQDLPDA 67
L+ VVDCA RD ID EL + + L+ NK D+PDA
Sbjct: 240 LVHVVDCATLEPGRDPLSDIDALEAELAAYAPALDGDLGLGDLAERPRLVVLNKIDVPDA 299
Query: 68 MKPHEIQEKLGLTR--IRDRNWYVQPSCATTADGLYEGLTW 106
+E R + R W V A + +GL E L++
Sbjct: 300 ------RELAEFVRPELEARGWPVFEVSAASREGLRE-LSF 333
>gnl|CDD|132868 cd07230, Pat_TGL4-5_like, Triacylglycerol lipase 4 and 5. TGL4
and TGL5 are triacylglycerol lipases that are involved
in triacylglycerol mobilization and degradation; they
are found in lipid particles. Tgl4 is a functional
ortholog of mammalian adipose TG lipase (ATGL) and is
phosphorylated and activated by cyclin-dependent kinase
1 (Cdk1/Cdc28). TGL4 is 30% homologus to TGL3, whereas
TGL5 is 26% homologus to TGL3. This family includes
TGL4 (STC1) and TGL5 (STC2) from Saccharomyces
cerevisiae.
Length = 421
Score = 29.5 bits (67), Expect = 0.32
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 8/49 (16%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDRE 49
D+G + L+RH + GT+ LI I EA L +++D E
Sbjct: 12 DLGNMGNVN-LYRHSHVGTKKLI-------ERYITEALLTLEYLVDDDE 52
>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 = 29.1 bits (65), Expect = 0.40
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 3/44 (6%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADR---DRIDEARQEL 41
D GQ + ++R Y G QG+I V D +R D ID +E+
Sbjct: 61 DTSGQGRFCTIFRSYSRGAQGIILVYDITNRWSFDGIDRWIKEI 104
>gnl|CDD|133345 cd04145, M_R_Ras_like, R-Ras2/TC21, M-Ras/R-Ras3. The
M-Ras/R-Ras-like subfamily contains R-Ras2/TC21,
M-Ras/R-Ras3, and related members of the Ras family.
M-Ras is expressed in lympho-hematopoetic cells. It
interacts with some of the known Ras effectors, but
appears to also have its own effectors. Expression of
mutated M-Ras leads to transformation of several types
of cell lines, including hematopoietic cells, mammary
epithelial cells, and fibroblasts. Overexpression of
M-Ras is observed in carcinomas from breast, uterus,
thyroid, stomach, colon, kidney, lung, and rectum. In
addition, expression of a constitutively active M-Ras
mutant in murine bone marrow induces a malignant mast
cell leukemia that is distinct from the monocytic
leukemia induced by H-Ras. TC21, along with H-Ras, has
been shown to regulate the branching morphogenesis of
ureteric bud cell branching in mice. Most Ras proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 164
Score = 28.9 bits (65), Expect = 0.42
Identities = 17/67 (25%), Positives = 29/67 (43%), Gaps = 6/67 (8%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRII---NDREMRDAIILI 57
D GQ++ + Y +G + V DR +E + H I DR+ + +++
Sbjct: 56 DTAGQEEFSAMREQYMRTGEGFLLVFSVTDRGSFEEVDK-FHTQILRVKDRD--EFPMIL 112
Query: 58 FANKQDL 64
NK DL
Sbjct: 113 VGNKADL 119
>gnl|CDD|206712 cd04141, Rit_Rin_Ric, Ras-like protein in all tissues (Rit),
Ras-like protein in neurons (Rin) and Ras-related
protein which interacts with calmodulin (Ric). Rit
(Ras-like protein in all tissues), Rin (Ras-like protein
in neurons) and Ric (Ras-related protein which interacts
with calmodulin) form a subfamily with several unique
structural and functional characteristics. These
proteins all lack a the C-terminal CaaX lipid-binding
motif typical of Ras family proteins, and Rin and Ric
contain calmodulin-binding domains. Rin, which is
expressed only in neurons, induces neurite outgrowth in
rat pheochromocytoma cells through its association with
calmodulin and its activation of endogenous Rac/cdc42.
Rit, which is ubiquitously expressed in mammals,
inhibits growth-factor withdrawl-mediated apoptosis and
induces neurite extension in pheochromocytoma cells. Rit
and Rin are both able to form a ternary complex with
PAR6, a cell polarity-regulating protein, and Rac/cdc42.
This ternary complex is proposed to have physiological
function in processes such as tumorigenesis. Activated
Ric is likely to signal in parallel with the Ras pathway
or stimulate the Ras pathway at some upstream point, and
binding of calmodulin to Ric may negatively regulate Ric
activity.
Length = 172
Score = 28.7 bits (64), Expect = 0.43
Identities = 17/64 (26%), Positives = 24/64 (37%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
D GQ + + Y +G I DR EA + I R D +++ N
Sbjct: 56 DTAGQAEFTAMRDQYMRCGEGFIICYSVTDRHSFQEASEFKELITRVRLTEDIPLVLVGN 115
Query: 61 KQDL 64
K DL
Sbjct: 116 KVDL 119
>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 = 0.46
Identities = 18/78 (23%), Positives = 29/78 (37%), Gaps = 4/78 (5%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
D GQ++ R + + YY LI D + E R I I ++ N
Sbjct: 62 DTAGQERFRSITQSYYRSANALILTYDITCEESFR-CLPEWLREIEQYANNKVITILVGN 120
Query: 61 KQDLPDAMKPHEIQEKLG 78
K DL + E+ ++
Sbjct: 121 KIDLAER---REVSQQRA 135
>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 = 29.0 bits (65), Expect = 0.49
Identities = 17/54 (31%), Positives = 28/54 (51%), Gaps = 9/54 (16%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADR-------DRIDEARQEL--HRII 45
D GQ++ R + R YY + G++ V D +R D ++EAR + HR +
Sbjct: 58 DTAGQERFRSITRSYYRNSVGVLLVFDITNRESFEHVHDWLEEARSHIQPHRPV 111
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 28.9 bits (66), Expect = 0.54
Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 5/62 (8%)
Query: 19 TQGLIFVVDCADRDRIDEA---RQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQE 75
T+ L+ +VD D +++ R EL + E+ D ++ NK DL D + E +
Sbjct: 237 TRLLLHLVDIEAVDPVEDYKTIRNELEKY--SPELADKPRILVLNKIDLLDEEEEREKRA 294
Query: 76 KL 77
L
Sbjct: 295 AL 296
>gnl|CDD|206666 cd01878, HflX, HflX GTPase family. HflX subfamily. A distinct
conserved domain with a glycine-rich segment N-terminal
of the GTPase domain characterizes the HflX subfamily.
The E. coli HflX has been implicated in the control of
the lambda cII repressor proteolysis, but the actual
biological functions of these GTPases remain unclear.
HflX is widespread, but not universally represented in
all three superkingdoms.
Length = 204
Score = 28.6 bits (65), Expect = 0.55
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 22 LIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAMKPHE 72
L+ VVD +D DR +E + + ++ + D I++ NK DL D + E
Sbjct: 124 LLHVVDASDPDR-EEQIETVEEVLKELGADDIPIILVLNKIDLLDDEELEE 173
>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 = 28.1 bits (63), Expect = 0.63
Identities = 13/63 (20%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAI-ILIFA 59
D GG+++++ + ++ V D DR+ ++E + + + N R++ I +++
Sbjct: 54 DFGGREELKFEHIIFMKWADAILLVYDLTDRESLNEVSRLIAWLPNLRKLGGKIPVILVG 113
Query: 60 NKQ 62
NK
Sbjct: 114 NKL 116
>gnl|CDD|184920 PRK14956, PRK14956, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 484
Score = 28.4 bits (63), Expect = 0.73
Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 9/82 (10%)
Query: 4 GQDKIRPLWRHYYTGTQGLIFVVD-CADRDRIDEARQELHRIINDREMRDAIILIFANKQ 62
GQD + LW T L + D ADR+ ++ +++L ++ +D E D+ L F
Sbjct: 278 GQDIYKFLW-DSIEFTHTLNLIRDSLADRESVNFPKEDLQKMKSDFENVDSSKLNFL--- 333
Query: 63 DLPDAMKPHEIQEKLGLTRIRD 84
+ K EI EK+ R+R+
Sbjct: 334 ----SGKLFEIYEKIKTIRLRN 351
>gnl|CDD|219158 pfam06745, KaiC, KaiC. This family represents a conserved region
within bacterial and archaeal proteins, most of which
are hypothetical. More than one copy is sometimes found
in each protein. This family includes KaiC, which is one
of the Kai proteins among which direct protein-protein
association may be a critical process in the generation
of circadian rhythms in cyanobacteria.
Length = 231
Score = 28.0 bits (63), Expect = 0.84
Identities = 12/29 (41%), Positives = 14/29 (48%)
Query: 24 FVVDCADRDRIDEARQELHRIINDREMRD 52
FVVD R + E EL R I +MR
Sbjct: 179 FVVDGVIRLDLKEIEGELVRTIEIVKMRG 207
>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 = 27.8 bits (62), Expect = 1.1
Identities = 18/69 (26%), Positives = 29/69 (42%), Gaps = 7/69 (10%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDA---IILI 57
D GQ++ R + + YY G I D R + + I + E A ++L+
Sbjct: 58 DTAGQERFRTITQSYYRSANGAIIAYDITRRSSFE----SVPHWIEEVEKYGASNVVLLL 113
Query: 58 FANKQDLPD 66
NK DL +
Sbjct: 114 IGNKCDLEE 122
>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 = 27.5 bits (61), Expect = 1.2
Identities = 22/103 (21%), Positives = 40/103 (38%), Gaps = 12/103 (11%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
D GQ++ R L ++ G + + D R + ++ + I++ N
Sbjct: 69 DTAGQERFRSLTTAFFRDAMGFLLMFDLTSEQSFLNVRNWMSQLQAHAYCENPDIVLIGN 128
Query: 61 KQDLPD-----AMKPHEIQEKLGLTRIRDRNWYVQPSCATTAD 98
K DLPD + E+ +K G+ Y + S AT +
Sbjct: 129 KADLPDQREVSERQARELADKYGIP-------YFETSAATGQN 164
>gnl|CDD|182934 PRK11058, PRK11058, GTPase HflX; Provisional.
Length = 426
Score = 27.8 bits (62), Expect = 1.4
Identities = 25/91 (27%), Positives = 42/91 (46%), Gaps = 19/91 (20%)
Query: 22 LIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQEKLGLTR 81
L+ VVD AD R+ E + ++ ++ + + + L+ NK D+ D +P R
Sbjct: 280 LLHVVDAAD-VRVQENIEAVNTVLEEIDAHEIPTLLVMNKIDMLDDFEP----------R 328
Query: 82 IRDRNWYVQPSC----ATTADG---LYEGLT 105
I DR+ +P A T G L++ LT
Sbjct: 329 I-DRDEENKPIRVWLSAQTGAGIPLLFQALT 358
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 27.5 bits (61), Expect = 1.4
Identities = 14/64 (21%), Positives = 26/64 (40%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAIILIFAN 60
D GQ++ + Y QG + V R +E +I+ ++ +++ N
Sbjct: 59 DTAGQEEYSAMRDQYMRTGQGFLCVYSITSRSSFEEIASFREQILRVKDKDRVPMILVGN 118
Query: 61 KQDL 64
K DL
Sbjct: 119 KCDL 122
>gnl|CDD|226834 COG4399, COG4399, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 376
Score = 27.4 bits (61), Expect = 1.9
Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 3/41 (7%)
Query: 14 HYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMRDAI 54
H GT +FVV+ + DR+ +QEL +++N E + +
Sbjct: 197 HGKLGTMVQMFVVNESLADRL---QQELLKLLNREETKKIL 234
>gnl|CDD|212555 cd11656, FBX4_GTPase_like, C-terminal GTPase-like domain of F-Box
Only Protein 4. F-box proteins are involved in
substrate recognition as part of SCF
(Skp1-Cul1-Rbx1-F-box protein) ubiquitin ligase
complexes. Fbx4 (or Fbxo4) binds to the telomere repeat
binding factor 1 (TRF1), whose activity at telomeres is
regulated in part by selective ubiquitination and
degradation. This ubiquitination of TRF1 is mediated by
Fbx4, which binds to the TRFH domain of TRF1, via the
C-terminal domain characterized by this model, a module
resembling a small GTPase domain that lacks the
GTP-binding site. When bound to telomeres, TIN2 acts to
protect TRF1 from SCF-Fbx4 mediated ubiquitination.
Tankyrase-mediated ADP-ribosylation releases TRF1 from
telomeres, rendering them susceptible to ubiquitination
and degradation, which in turn promotes telomere
elongation. Fbx4 has also been reported to target cyclin
D1 for degradation by the proteasome, a mechanism
ensuring the fidelity of DNA replication. More recently,
these findings have been disputed.
Length = 223
Score = 27.1 bits (60), Expect = 2.1
Identities = 12/33 (36%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 75 EKLGLTRIRDRNWYVQPSCATTADGLYEGLTWL 107
+L L + R W VQ + A T GL +G+ W+
Sbjct: 185 HELHLNLL-PRPWLVQDTEAETLAGLLDGIAWI 216
>gnl|CDD|236795 PRK10920, PRK10920, putative uroporphyrinogen III
C-methyltransferase; Provisional.
Length = 390
Score = 27.0 bits (60), Expect = 2.5
Identities = 14/35 (40%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 63 DLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATTA 97
DLP+ ++ I EKL TR+ RN QP+ T
Sbjct: 342 DLPETLQSQPILEKLMQTRV--RNLLAQPAAGATE 374
>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 = 26.4 bits (59), Expect = 3.3
Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 11/69 (15%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADR---DRIDEARQELHRIINDREMRDA--II 55
D GQ++ R + YY G G + V D + + ++ +EL R+ D+ +I
Sbjct: 58 DTAGQERYRAITSAYYRGAVGALLVYDITKKSTFENVERWLKEL------RDHADSNIVI 111
Query: 56 LIFANKQDL 64
++ NK DL
Sbjct: 112 MLVGNKSDL 120
>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 = 26.4 bits (59), Expect = 3.6
Identities = 21/93 (22%), Positives = 33/93 (35%), Gaps = 9/93 (9%)
Query: 1 DVGGQDKIRPLWRHYYTGT-----QGLIFVVDCADRDRIDEARQELHRII-NDREM-RDA 53
D GQD + LI+V D R+ +E L +II + +A
Sbjct: 54 DCPGQDDFMENYLTRQKEHIFSNVGVLIYVFDVESRE-YEEDLATLVKIIEALYQYSPNA 112
Query: 54 IILIFANKQDLPDAMKPHEIQEKLGLTRIRDRN 86
+ + +K DL + EI E I +
Sbjct: 113 KVFVLIHKMDLLSEDERKEIFEDR-KEEIIEEI 144
>gnl|CDD|151400 pfam10953, DUF2754, Protein of unknown function (DUF2754). This
family of proteins with unknown function appear to be
restricted to Enterobacteriaceae.
Length = 70
Score = 25.3 bits (55), Expect = 3.8
Identities = 12/22 (54%), Positives = 15/22 (68%), Gaps = 1/22 (4%)
Query: 6 DKIRPLWRHYYTGTQGLIFVVD 27
DKIR W HYY GLIF+++
Sbjct: 5 DKIRRDW-HYYAVALGLIFILN 25
>gnl|CDD|215096 PLN00192, PLN00192, aldehyde oxidase.
Length = 1344
Score = 26.2 bits (58), Expect = 4.6
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 26 VDCADRDRIDEARQELH 42
V CA R I EAR++L
Sbjct: 1286 VHCATRAAIREARKQLL 1302
>gnl|CDD|212725 cd11791, SH3_UBASH3, Src homology 3 domain of Ubiquitin-associated
and SH3 domain-containing proteins, also called TULA (T
cell Ubiquitin LigAnd) family of proteins. UBASH3 or
TULA proteins are also referred to as Suppressor of T
cell receptor Signaling (STS) proteins. They contain an
N-terminal UBA domain, a central SH3 domain, and a
C-terminal histidine phosphatase domain. They bind c-Cbl
through the SH3 domain and to ubiquitin via UBA. In some
vertebrates, there are two TULA family proteins, called
UBASH3A (also called TULA or STS-2) and UBASH3B (also
called TULA-2 or STS-1), which show partly overlapping
as well as distinct functions. UBASH3B is widely
expressed while UBASH3A is only found in lymphoid cells.
UBASH3A facilitates apoptosis induced in T cells through
its interaction with the apoptosis-inducing factor AIF.
UBASH3B is an active phosphatase while UBASH3A is not.
SH3 domains are protein interaction domains that bind to
proline-rich ligands with moderate affinity and
selectivity, preferentially to PxxP motifs. They play
versatile and diverse roles in the cell including the
regulation of enzymes, changing the subcellular
localization of signaling pathway components, and
mediating the formation of multiprotein complex
assemblies.
Length = 59
Score = 24.6 bits (54), Expect = 4.8
Identities = 14/40 (35%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 70 PHEIQEKLGLTRIRDRNWYVQPS-CATTADGLYEGLTWLT 108
P+ QE+ L + YV P +++DG EG +WLT
Sbjct: 7 PYTPQEEDELELVPGDYIYVSPEELDSSSDGWVEGTSWLT 46
>gnl|CDD|217711 pfam03748, FliL, Flagellar basal body-associated protein FliL.
This FliL protein controls the rotational direction of
the flagella during chemotaxis. FliL is a cytoplasmic
membrane protein associated with the basal body.
Length = 99
Score = 25.2 bits (56), Expect = 4.9
Identities = 7/36 (19%), Positives = 18/36 (50%), Gaps = 7/36 (19%)
Query: 49 EMRDAIILIFANKQDLPDAMKPHEIQEKLGLTRIRD 84
+RDAI+L+ ++K ++ G ++++
Sbjct: 45 LIRDAILLLLSSK-------TAEDLSTPEGKEKLKE 73
>gnl|CDD|236254 PRK08384, PRK08384, thiamine biosynthesis protein ThiI;
Provisional.
Length = 381
Score = 26.1 bits (57), Expect = 5.2
Identities = 12/41 (29%), Positives = 24/41 (58%), Gaps = 3/41 (7%)
Query: 6 DKIRPLW---RHYYTGTQGLIFVVDCADRDRIDEARQELHR 43
+K+R +W + Y+ G + + VV +R+RI + +EL +
Sbjct: 220 EKVRKIWNQLKKYHYGGKAELIVVKPQERERIIQKLKELKK 260
>gnl|CDD|213182 cd03215, ABC_Carb_Monos_II, Second domain of the ATP-binding
cassette component of monosaccharide transport system.
This family represents domain II of the carbohydrate
uptake proteins that transport only monosaccharides
(Monos). The Carb_Monos family is involved in the uptake
of monosaccharides, such as pentoses (such as xylose,
arabinose, and ribose) and hexoses (such as xylose,
arabinose, and ribose), that cannot be broken down to
simple sugars by hydrolysis. In members of Carb_Monos
family the single hydrophobic gene product forms a
homodimer, while the ABC protein represents a fusion of
two nucleotide-binding domains. However, it is assumed
that two copies of the ABC domains are present in the
assembled transporter.
Length = 182
Score = 25.5 bits (57), Expect = 6.2
Identities = 11/28 (39%), Positives = 19/28 (67%), Gaps = 6/28 (21%)
Query: 34 ID-EARQELHRIINDREMRD---AIILI 57
+D A+ E++R+I RE+ D A++LI
Sbjct: 135 VDVGAKAEIYRLI--RELADAGKAVLLI 160
>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 = 24.6 bits (54), Expect = 6.4
Identities = 8/56 (14%), Positives = 19/56 (33%), Gaps = 13/56 (23%)
Query: 13 RHYYTGTQGLIFVVDCADRDRIDEARQELHRII---------NDREMRDAIILIFA 59
+ L+F D D +DEA + L ++ + + +++
Sbjct: 15 PALFR----LMFGADLEDDPELDEAFELLVELLEELLAAGGLSPEDAERLARALWS 66
>gnl|CDD|176462 cd01357, Aspartase, Aspartase. This subgroup contains Escherichia
coli aspartase (L-aspartate ammonia-lyase), Bacillus
aspartase and related proteins. It is a member of the
Lyase class I family, which includes both aspartase
(L-aspartate ammonia-lyase) and fumarase class II
enzymes. Members of this family for the most part
catalyze similar beta-elimination reactions in which a
C-N or C-O bond is cleaved with the release of fumarate
as one of the products. These proteins are active as
tetramers. The four active sites of the homotetrameric
enzyme are each formed by residues from three different
subunits. Aspartase catalyzes the reversible deamination
of aspartic acid.
Length = 450
Score = 25.6 bits (57), Expect = 6.6
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 30 DRDRIDEARQELHRI 44
DR RI +AR+ L +
Sbjct: 206 DRARIYKARERLREV 220
>gnl|CDD|180707 PRK06811, PRK06811, RNA polymerase factor sigma-70; Validated.
Length = 189
Score = 25.3 bits (56), Expect = 7.6
Identities = 19/48 (39%), Positives = 28/48 (58%), Gaps = 4/48 (8%)
Query: 34 IDEARQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQEKLGLTR 81
+ E ++E+ ++IND E D I I ++ L K EI +KLGLTR
Sbjct: 118 LKENKEEILKLINDLEKLDREIFI---RRYL-LGEKIEEIAKKLGLTR 161
>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 = 25.1 bits (55), Expect = 7.7
Identities = 10/28 (35%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 1 DVGGQDKIR-PLWRHYYTGTQGLIFVVD 27
D GQ++ R + +HYY ++FV D
Sbjct: 57 DTAGQERFRKSMVQHYYRNVHAVVFVYD 84
>gnl|CDD|236117 PRK07857, PRK07857, hypothetical protein; Provisional.
Length = 106
Score = 25.0 bits (55), Expect = 7.7
Identities = 8/21 (38%), Positives = 13/21 (61%), Gaps = 2/21 (9%)
Query: 34 IDEARQELHRIINDREMRDAI 54
IDE R+E+ R+ D E+ +
Sbjct: 30 IDELREEIDRL--DAEILALV 48
>gnl|CDD|219519 pfam07693, KAP_NTPase, KAP family P-loop domain. The KAP (after
Kidins220/ARMS and PifA) family of predicted NTPases are
sporadically distributed across a wide phylogenetic
range in bacteria and in animals. Many of the
prokaryotic KAP NTPases are encoded in plasmids and tend
to undergo disruption to form pseudogenes. A unique
feature of all eukaryotic and certain bacterial KAP
NTPases is the presence of two or four transmembrane
helices inserted into the P-loop NTPase domain. These
transmembrane helices anchor KAP NTPases in the membrane
such that the P-loop domain is located on the
intracellular side.
Length = 301
Score = 25.4 bits (56), Expect = 8.3
Identities = 9/47 (19%), Positives = 14/47 (29%)
Query: 5 QDKIRPLWRHYYTGTQGLIFVVDCADRDRIDEARQELHRIINDREMR 51
+ + L+ GT D E IN RE++
Sbjct: 242 RRFLMTLFDALEKGTPSEDRDRGLRADDLNIILDSEDKSNINPRELK 288
>gnl|CDD|219423 pfam07477, Glyco_hydro_67C, Glycosyl hydrolase family 67
C-terminus. Alpha-glucuronidases, components of an
ensemble of enzymes central to the recycling of
photosynthetic biomass, remove the alpha-1,2 linked
4-O-methyl glucuronic acid from xylans. This family
represents the C terminal region of alpha-glucuronidase
which is mainly alpha-helical. It wraps around the
catalytic domain (pfam07488), making additional
interactions both with the N-terminal domain (pfam03648)
of its parent monomer and also forming the majority of
the dimer-surface with the equivalent C-terminal domain
of the other monomer of the dimer.
Length = 225
Score = 25.3 bits (56), Expect = 8.4
Identities = 13/46 (28%), Positives = 17/46 (36%), Gaps = 6/46 (13%)
Query: 31 RDRIDEAR--QELHR----IINDREMRDAIILIFANKQDLPDAMKP 70
+ID R + L R + RDAI L F +PD
Sbjct: 177 EGKIDPERFEEVLARLKIQAEHAIWWRDAINLYFQRFSGIPDEKGR 222
>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 = 25.0 bits (55), Expect = 8.6
Identities = 11/31 (35%), Positives = 13/31 (41%)
Query: 1 DVGGQDKIRPLWRHYYTGTQGLIFVVDCADR 31
D GQ+K L YY Q I + D R
Sbjct: 55 DTAGQEKFGGLRDGYYIQGQCAIIMFDVTSR 85
>gnl|CDD|180576 PRK06463, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Provisional.
Length = 255
Score = 25.1 bits (55), Expect = 8.6
Identities = 3/26 (11%), Positives = 12/26 (46%)
Query: 21 GLIFVVDCADRDRIDEARQELHRIIN 46
D +RD++ ++++ + +
Sbjct: 53 VFTIKCDVGNRDQVKKSKEVVEKEFG 78
>gnl|CDD|237478 PRK13709, PRK13709, conjugal transfer nickase/helicase TraI;
Provisional.
Length = 1747
Score = 25.5 bits (56), Expect = 9.1
Identities = 10/49 (20%), Positives = 18/49 (36%), Gaps = 5/49 (10%)
Query: 36 EARQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQEKLGLTRIRD 84
A+Q +H + E ++ L F+ L +A E T +
Sbjct: 862 PAQQAIHLALPVLESKN---LAFSMVDLLTEAKSFA--AEGTSFTELGG 905
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
0.323 0.140 0.442
Gapped
Lambda K H
0.267 0.0791 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,019,641
Number of extensions: 528036
Number of successful extensions: 771
Number of sequences better than 10.0: 1
Number of HSP's gapped: 751
Number of HSP's successfully gapped: 128
Length of query: 113
Length of database: 10,937,602
Length adjustment: 77
Effective length of query: 36
Effective length of database: 7,522,344
Effective search space: 270804384
Effective search space used: 270804384
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 (24.1 bits)