RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1315
(202 letters)
>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 = 287 bits (735), Expect = e-100
Identities = 113/178 (63%), Positives = 145/178 (81%)
Query: 19 SVHIVMLGLDSAGKTTALYRLKFDQYLNTVPTIGFNCEKVKGQIGKCKGINFLIWDVGGQ 78
S+HIVMLGLDSAGKTT LYRLKF++++NTVPT GFN EK+K +G KG+ F WDVGGQ
Sbjct: 3 SLHIVMLGLDSAGKTTVLYRLKFNEFVNTVPTKGFNTEKIKVSLGNAKGVTFHFWDVGGQ 62
Query: 79 EKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLP 138
EKLRPLWKSYTRCTDGI+FV+DS DVERMEE K EL K K ++N VP+L+LANKQDLP
Sbjct: 63 EKLRPLWKSYTRCTDGIVFVVDSVDVERMEEAKTELHKITKFSENQGVPVLVLANKQDLP 122
Query: 139 NAIQIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEGINELYQLILKKRKLQKTNK 196
NA+ + ++EKLL L+EL++ +++Q CAI G+GL EG+ +LY++ILK+RK+ + K
Sbjct: 123 NALPVSEVEKLLALHELSSSTPWHVQPACAIIGEGLQEGLEKLYEMILKRRKMLRQQK 180
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 205 bits (523), Expect = 6e-68
Identities = 82/167 (49%), Positives = 112/167 (67%), Gaps = 6/167 (3%)
Query: 19 SVHIVMLGLDSAGKTTALYRLKFDQYLNTVPTIGFNCEKVKGQIGKCKGINFLIWDVGGQ 78
+ I++LGLD+AGKTT LY+LK + + T+PTIGFN E V K + F +WDVGGQ
Sbjct: 14 EMRILILGLDNAGKTTILYKLKLGEIVTTIPTIGFNVETVT-----YKNVKFTVWDVGGQ 68
Query: 79 EKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLP 138
E LRPLW++Y TD +IFV+DS D +R+EE K EL + + + P+LILANKQDLP
Sbjct: 69 ESLRPLWRNYFPNTDAVIFVVDSADRDRIEEAKEELHALLNEEELADAPLLILANKQDLP 128
Query: 139 NAIQIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEGINELYQLI 185
A+ +I +LLGL+EL + + IQ A+TG+GL EG++ L I
Sbjct: 129 GAMSEAEIRELLGLHELKDRP-WEIQGCSAVTGEGLDEGLDWLSNYI 174
>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 = 203 bits (518), Expect = 2e-67
Identities = 83/164 (50%), Positives = 111/164 (67%), Gaps = 6/164 (3%)
Query: 21 HIVMLGLDSAGKTTALYRLKFDQYLNTVPTIGFNCEKVKGQIGKCKGINFLIWDVGGQEK 80
I+MLGLD AGKTT LY+LK + + T+PTIGFN E V+ K + F +WDVGGQ+K
Sbjct: 1 RILMLGLDGAGKTTILYKLKLGEVVTTIPTIGFNVETVEY-----KNVKFTVWDVGGQDK 55
Query: 81 LRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLPNA 140
+RPLWK Y TDG+IFV+DS+D ER+EE K EL K + + P+LILANKQDLP A
Sbjct: 56 IRPLWKHYYENTDGLIFVVDSSDRERIEEAKNELHKLLNEEELKGAPLLILANKQDLPGA 115
Query: 141 IQIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEGINELYQL 184
+ ++ +LLGL + ++IQ A+TGDGL EG++ L +
Sbjct: 116 LTESELIELLGLESIKG-RRWHIQPCSAVTGDGLDEGLDWLIEQ 158
>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 = 192 bits (489), Expect = 4e-63
Identities = 80/162 (49%), Positives = 116/162 (71%), Gaps = 6/162 (3%)
Query: 20 VHIVMLGLDSAGKTTALYRLKFDQYLNTVPTIGFNCEKVKGQIGKCKGINFLIWDVGGQE 79
+ I+M+GLD+AGKTT LY+LK + + T+PTIGFN E V+ K I+F +WDVGGQ+
Sbjct: 1 MRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVE-----YKNISFTVWDVGGQD 55
Query: 80 KLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLPN 139
K+RPLW+ Y + T G+IFV+DS D ER+ E + EL + + ++ + +L+ ANKQDLPN
Sbjct: 56 KIRPLWRHYFQNTQGLIFVVDSNDRERIGEAREELQRMLNEDELRDAVLLVFANKQDLPN 115
Query: 140 AIQIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEGINEL 181
A+ ++ LGL+ L N + +YIQATCA +GDGL+EG++ L
Sbjct: 116 AMSAAEVTDKLGLHSLRNRN-WYIQATCATSGDGLYEGLDWL 156
>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 = 183 bits (467), Expect = 1e-59
Identities = 76/168 (45%), Positives = 115/168 (68%), Gaps = 6/168 (3%)
Query: 16 GSSSVHIVMLGLDSAGKTTALYRLKFDQYLNTVPTIGFNCEKVKGQIGKCKGINFLIWDV 75
G+ + I+MLGLD+AGKTT LY+LK Q + T+PT+GFN E V K + F +WDV
Sbjct: 6 GNKEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVT-----YKNVKFNVWDV 60
Query: 76 GGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQ 135
GGQ+K+RPLW+ Y T G+IFV+DS D +R++E + EL + I + + + +L+ ANKQ
Sbjct: 61 GGQDKIRPLWRHYYTGTQGLIFVVDSADRDRIDEARQELHRIINDREMRDALLLVFANKQ 120
Query: 136 DLPNAIQIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEGINELYQ 183
DLP+A++ +I++ LGL + + +Y+Q +CA +GDGL+EG+ L
Sbjct: 121 DLPDAMKPHEIQEKLGLTRIRD-RNWYVQPSCATSGDGLYEGLTWLSS 167
>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 = 180 bits (459), Expect = 2e-58
Identities = 68/164 (41%), Positives = 108/164 (65%), Gaps = 4/164 (2%)
Query: 21 HIVMLGLDSAGKTTALYRLKFDQYLNTVPTIGFNCEKVKGQIGKCKGINFLIWDVGGQEK 80
+++LGLDSAGK+T LY+LK + + T+PT+GFN E ++ + K ++ +WDVGGQEK
Sbjct: 1 QVLLLGLDSAGKSTLLYKLKHAELVTTIPTVGFNVEMLQLE----KHLSLTVWDVGGQEK 56
Query: 81 LRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLPNA 140
+R +WK Y TDG+++V+DS+D R++E + EL +KN VP+++LANKQDLP A
Sbjct: 57 MRTVWKCYLENTDGLVYVVDSSDEARLDESQKELKHILKNEHIKGVPVVLLANKQDLPGA 116
Query: 141 IQIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEGINELYQL 184
+ ++I + L + + +Y+Q A+TG+GL E +L
Sbjct: 117 LTAEEITRRFKLKKYCSDRDWYVQPCSAVTGEGLAEAFRKLASF 160
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 180 bits (459), Expect = 3e-58
Identities = 82/190 (43%), Positives = 124/190 (65%), Gaps = 8/190 (4%)
Query: 1 MGKNSAAFFENLQASGSSSVHIVMLGLDSAGKTTALYRLKFDQYLNTVPTIGFNCEKVKG 60
MG ++ F++L G V I+M+GLD+AGKTT LY+LK + + T+PTIGFN E V+
Sbjct: 1 MGLWLSSAFKSL--FGKKEVRILMVGLDAAGKTTILYKLKLGEVVTTIPTIGFNVETVE- 57
Query: 61 QIGKCKGINFLIWDVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKN 120
K + F +WDVGGQ+KLRPLW+ Y + T+G+IFV+DS D ER+ + + EL + +
Sbjct: 58 ----YKNLKFTMWDVGGQDKLRPLWRHYYQNTNGLIFVVDSNDRERIGDAREELERMLSE 113
Query: 121 NDNFNVPILILANKQDLPNAIQIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEGINE 180
++ + +L+ ANKQDLPNA+ ++ + LGL+ + + +YIQ CA T GL+EG++
Sbjct: 114 DELRDAVLLVFANKQDLPNAMSTTEVTEKLGLHSVRQRN-WYIQGCCATTAQGLYEGLDW 172
Query: 181 LYQLILKKRK 190
L I K +
Sbjct: 173 LSANIKKSMQ 182
>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 = 174 bits (443), Expect = 7e-56
Identities = 78/166 (46%), Positives = 117/166 (70%), Gaps = 6/166 (3%)
Query: 16 GSSSVHIVMLGLDSAGKTTALYRLKFDQYLNTVPTIGFNCEKVKGQIGKCKGINFLIWDV 75
G+ + I+M+GLD+AGKTT LY+LK + + T+PTIGFN E V K I+F +WDV
Sbjct: 10 GNKEMRILMVGLDAAGKTTILYKLKLGESVTTIPTIGFNVETVT-----YKNISFTVWDV 64
Query: 76 GGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQ 135
GGQ+K+RPLW+ Y T G+IFV+DS D +R++E + EL + + ++ + IL+ ANKQ
Sbjct: 65 GGQDKIRPLWRHYYTNTQGLIFVVDSNDRDRIDEAREELHRMLNEDELRDAVILVFANKQ 124
Query: 136 DLPNAIQIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEGINEL 181
DLP+A++ +I + LGL+ + + + +YIQ TCA +GDGL+EG+ L
Sbjct: 125 DLPDAMKAAEITEKLGLHSIRDRN-WYIQPTCATSGDGLYEGLTWL 169
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 174 bits (442), Expect = 1e-55
Identities = 84/188 (44%), Positives = 122/188 (64%), Gaps = 8/188 (4%)
Query: 1 MGKNSAAFFENLQASGSSSVHIVMLGLDSAGKTTALYRLKFDQYLNTVPTIGFNCEKVKG 60
MG + F L + I+M+GLD+AGKTT LY+LK + + T+PTIGFN E V+
Sbjct: 1 MGLSFTKLFSRL--FAKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVE- 57
Query: 61 QIGKCKGINFLIWDVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKN 120
K I+F +WDVGGQ+K+RPLW+ Y + T G+IFV+DS D +R+ E + EL + +
Sbjct: 58 ----YKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRDRVVEARDELHRMLNE 113
Query: 121 NDNFNVPILILANKQDLPNAIQIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEGINE 180
++ + +L+ ANKQDLPNA+ +I LGL+ L H +YIQ+TCA +G+GL+EG++
Sbjct: 114 DELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRQRH-WYIQSTCATSGEGLYEGLDW 172
Query: 181 LYQLILKK 188
L I K
Sbjct: 173 LSNNIANK 180
>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 = 162 bits (412), Expect = 2e-51
Identities = 69/160 (43%), Positives = 100/160 (62%), Gaps = 6/160 (3%)
Query: 22 IVMLGLDSAGKTTALYRLKFDQYLNTVPTIGFNCEKVKGQIGKCKGINFLIWDVGGQEKL 81
I++LGLD AGKTT LYRL+ + + T+PTIGFN E V K + F +WD+GGQ +
Sbjct: 2 ILILGLDGAGKTTILYRLQVGEVVTTIPTIGFNVETVT-----YKNLKFQVWDLGGQTSI 56
Query: 82 RPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLPNAI 141
RP W+ Y TD II+V+DSTD +R+ K EL ++ + + +L+ ANKQD+P A+
Sbjct: 57 RPYWRCYYSNTDAIIYVVDSTDRDRLGISKSELHAMLEEEELKDAVLLVFANKQDMPGAL 116
Query: 142 QIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEGINEL 181
++ + LGL EL + + I T A G+GL EG++ L
Sbjct: 117 SEAEVAEKLGLSELKD-RTWQIFKTSATKGEGLDEGMDWL 155
>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 = 160 bits (408), Expect = 1e-50
Identities = 71/157 (45%), Positives = 101/157 (64%), Gaps = 6/157 (3%)
Query: 22 IVMLGLDSAGKTTALYRLKFDQYLNTVPTIGFNCEKVKGQIGKCKGINFLIWDVGGQEKL 81
++++GLD+AGKTT LY+ + ++T PTIG N E++ K I FL+WD+GGQE L
Sbjct: 18 VIIVGLDNAGKTTILYQFLLGEVVHTSPTIGSNVEEIV-----YKNIRFLMWDIGGQESL 72
Query: 82 RPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLPNAI 141
R W +Y TD +I VIDSTD ER+ K EL K + + D +L+LANKQDL A+
Sbjct: 73 RSSWNTYYTNTDAVILVIDSTDRERLPLTKEELYKMLAHEDLRKAVLLVLANKQDLKGAM 132
Query: 142 QIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEGI 178
+I + LGL + + H ++IQ CA+TG+GL EG+
Sbjct: 133 TPAEISESLGLTSIRD-HTWHIQGCCALTGEGLPEGL 168
>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 = 151 bits (383), Expect = 1e-46
Identities = 68/172 (39%), Positives = 103/172 (59%), Gaps = 6/172 (3%)
Query: 8 FFENLQASGSSSVHIVMLGLDSAGKTTALYRLKFDQYLNTVPTIGFNCEKVKGQIGKCKG 67
L+ S V I++LGLD+AGKTT L +L + + PT GFN + V+ G
Sbjct: 4 ILRKLKPSSRQEVRILLLGLDNAGKTTILKQLASEDISHITPTQGFNIKNVQAD-----G 58
Query: 68 INFLIWDVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVP 127
+WD+GGQ K+RP W++Y TD +I+VIDS D +R EE EL++ ++ VP
Sbjct: 59 FKLNVWDIGGQRKIRPYWRNYFENTDVLIYVIDSADRKRFEEAGQELVELLEEEKLAGVP 118
Query: 128 ILILANKQDLPNAIQIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEGIN 179
+L+ ANKQDL A +++ + L L+++ + ++IQA A TG+GL EG+N
Sbjct: 119 VLVFANKQDLLTAAPAEEVAEALNLHDIRD-RSWHIQACSAKTGEGLQEGMN 169
>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 = 144 bits (364), Expect = 6e-44
Identities = 65/165 (39%), Positives = 100/165 (60%), Gaps = 8/165 (4%)
Query: 20 VHIVMLGLDSAGKTTALYRLKFDQYLNTV-PTIGFNCEKVKGQIGKCKGINFLIWDVGGQ 78
+ I+MLGLD+AGKTT L + + ++T+ PT+GFN + ++ G IWDVGGQ
Sbjct: 15 MRILMLGLDNAGKTTILKKFN-GEDISTISPTLGFNIKTLEYN-----GYKLNIWDVGGQ 68
Query: 79 EKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLP 138
+ LR W++Y TD +I+V+DS+D R+E+ K EL K + +LI ANKQDLP
Sbjct: 69 KSLRSYWRNYFESTDALIWVVDSSDRARLEDCKRELQKLLVEERLAGATLLIFANKQDLP 128
Query: 139 NAIQIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEGINELYQ 183
A+ ++I ++L L + + H + I A+TG+ L +GI+ L
Sbjct: 129 GALSPEEIREVLELDSIKSHH-WRIFGCSAVTGENLLDGIDWLVD 172
>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 = 142 bits (359), Expect = 3e-43
Identities = 71/160 (44%), Positives = 104/160 (65%), Gaps = 5/160 (3%)
Query: 22 IVMLGLDSAGKTTALYRLKFDQYLNTVPTIGFNCEKVKGQIGKCKGINFLIWDVGGQEKL 81
+V LGLD AGKTT L++LK D+++ +PTIGFN E V+ K + F IWDVGG+ KL
Sbjct: 2 VVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVE-----YKNLKFTIWDVGGKHKL 56
Query: 82 RPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLPNAI 141
RPLWK Y T ++FVIDS+ +R+ E EL K + + + +LI ANKQD+ A+
Sbjct: 57 RPLWKHYYLNTQAVVFVIDSSHRDRVSEAHSELAKLLTEKELRDALLLIFANKQDVAGAL 116
Query: 142 QIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEGINEL 181
++++ +LL L++L +YIQ A +G GL+EG++ L
Sbjct: 117 SVEEMTELLSLHKLCCGRSWYIQGCDARSGMGLYEGLDWL 156
>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 = 130 bits (328), Expect = 1e-38
Identities = 67/170 (39%), Positives = 96/170 (56%), Gaps = 14/170 (8%)
Query: 22 IVMLGLDSAGKTTALYRLKFDQYLNT--------VPTIGFNCEKVKGQIGKCKGINFLIW 73
+++LGLD+AGKTT L + K N PT+G N + ++GK + + F W
Sbjct: 2 VLILGLDNAGKTTFLEQTKTKFSKNYKGLNPSKITPTVGLNIGTI--EVGKAR-LMF--W 56
Query: 74 DVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILAN 133
D+GGQE+LR LW Y + G+I+VIDSTD ER E K K I N VP+L+LAN
Sbjct: 57 DLGGQEELRSLWDKYYAESHGVIYVIDSTDRERFNESKSAFEKVINNEALEGVPLLVLAN 116
Query: 134 KQDLPNAIQIKQIEKLLGLY-ELNNMHLYYIQATCAITGDGLHEGINELY 182
KQDLP+A+ + +I+++ L +Q A+ G+G+ EGI L
Sbjct: 117 KQDLPDALSVAEIKEVFDDCIALIGRRDCLVQPVSALEGEGVEEGIEWLV 166
>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 = 129 bits (327), Expect = 2e-38
Identities = 69/165 (41%), Positives = 101/165 (61%), Gaps = 10/165 (6%)
Query: 21 HIVMLGLDSAGKTTALYRLK--FDQYLNTVPTIGFNCEKVKGQIGKCKGINFLIWDVGGQ 78
+I++LGLD++GKTT + +LK Q N VPT+GFN E K ++F +D+ GQ
Sbjct: 1 NILVLGLDNSGKTTIINQLKPSNAQSQNIVPTVGFNVESFKKG-----NLSFTAFDMSGQ 55
Query: 79 EKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNND--NFNVPILILANKQD 136
K R LW+ Y + GIIFVIDS+D RM K EL + + D + +PIL ANK D
Sbjct: 56 GKYRGLWEHYYKNIQGIIFVIDSSDRLRMVVAKDELELLLNHPDIKHRRIPILFYANKMD 115
Query: 137 LPNAIQIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEGINEL 181
LP+A+ +I +LL L + + ++I A+ A+TG+GL EG++ L
Sbjct: 116 LPDALTAVKITQLLCLENIKD-KPWHIFASSALTGEGLDEGVDWL 159
>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 = 130 bits (329), Expect = 2e-38
Identities = 62/152 (40%), Positives = 90/152 (59%), Gaps = 10/152 (6%)
Query: 8 FFENLQAS---GSSSVHIVMLGLDSAGKTTALYRLKFDQYLNTVPTIGFNCEKVKGQIGK 64
+F N+ +S IV LGLD+AGKTT L+ LK D+ VPT+ E++ IG
Sbjct: 5 WFYNVLSSLGLYKKEAKIVFLGLDNAGKTTLLHMLKDDRLAQHVPTLHPTSEEL--TIG- 61
Query: 65 CKGINFLIWDVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNF 124
+ F +D+GG E+ R +WK Y DGI+F++D+ D ER +E K EL ++ N++
Sbjct: 62 --NVKFTTFDLGGHEQARRVWKDYFPEVDGIVFLVDAADPERFQESKEEL-DSLLNDEEL 118
Query: 125 -NVPILILANKQDLPNAIQIKQIEKLLGLYEL 155
NVPILIL NK D P A+ +++ + LGLY
Sbjct: 119 ANVPILILGNKIDKPGAVSEEELREALGLYGT 150
>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 = 105 bits (265), Expect = 4e-29
Identities = 54/150 (36%), Positives = 86/150 (57%), Gaps = 8/150 (5%)
Query: 22 IVMLGLDSAGKTTALYRLKFDQYL-NTVPTIGFNCEKVKGQIGKCKGINFLIWDVGGQEK 80
I++LGLD AGKT+ L+ L ++ L + VPT GFN + Q + L ++GG +
Sbjct: 2 ILVLGLDGAGKTSLLHSLSSERSLESVVPTTGFNSVAIPTQDAI---MELL--EIGGSQN 56
Query: 81 LRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLPNA 140
LR WK Y + G+IFV+DS D ER+ + EL + +++ ++P+++LANKQDLP A
Sbjct: 57 LRKYWKRYLSGSQGLIFVVDSADSERLPLARQELHQLLQHPP--DLPLVVLANKQDLPAA 114
Query: 141 IQIKQIEKLLGLYELNNMHLYYIQATCAIT 170
+++I K L L + + +Q T
Sbjct: 115 RSVQEIHKELELEPIARGRRWILQGTSLDD 144
>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 = 104 bits (262), Expect = 1e-28
Identities = 44/137 (32%), Positives = 80/137 (58%), Gaps = 6/137 (4%)
Query: 22 IVMLGLDSAGKTTALYRLKFDQYL-NTVPTIGFNCEKVKGQIGKCKGINFLIWDVGGQEK 80
I ++GL ++GKTT + + Q+ +T+PT+GFN KV + +WD+GGQ +
Sbjct: 2 ITLVGLQNSGKTTLVNVIASGQFSEDTIPTVGFNMRKVTKG-----NVTIKVWDLGGQPR 56
Query: 81 LRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLPNA 140
R +W+ Y R + I++V+D+ D E++E K EL ++ +P+L+L NK DLP A
Sbjct: 57 FRSMWERYCRGVNAIVYVVDAADREKLEVAKNELHDLLEKPSLEGIPLLVLGNKNDLPGA 116
Query: 141 IQIKQIEKLLGLYELNN 157
+ + ++ + + L + +
Sbjct: 117 LSVDELIEQMNLKSITD 133
>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 = 103 bits (258), Expect = 4e-28
Identities = 57/168 (33%), Positives = 92/168 (54%), Gaps = 13/168 (7%)
Query: 22 IVMLGLDSAGKTTALYRLKFDQYLNTVPTIGFNCEKVKGQIGKCKGINFLIWDVGGQEKL 81
++ +GLD+AGKTT + L+ + PT+GF K ++ K I+D+GG
Sbjct: 2 LLTVGLDNAGKTTLVSALQGEIPKKVAPTVGF--TPTKLRLDKY---EVCIFDLGGGANF 56
Query: 82 RPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLPNAI 141
R +W +Y G++FV+DS+D +R++EVK L + +++ PIL+LANKQD NA+
Sbjct: 57 RGIWVNYYAEAHGLVFVVDSSDDDRVQEVKEILRELLQHPRVSGKPILVLANKQDKKNAL 116
Query: 142 QIKQIEKLLGLYELNNMH--LYYIQATCAITGDG------LHEGINEL 181
+ + L L +L N + L +I+ AI G G + EG+ L
Sbjct: 117 LGADVIEYLSLEKLVNENKSLCHIEPCSAIEGLGKKIDPSIVEGLRWL 164
>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 = 95.8 bits (238), Expect = 5e-25
Identities = 52/133 (39%), Positives = 73/133 (54%), Gaps = 5/133 (3%)
Query: 22 IVMLGLDSAGKTTALYRLKFDQYLNTVPTIGFNCEKVKGQIGKCKGINFLIWDVGGQEKL 81
I+ LGLD+AGKTT L+ LK D+ PT E++ IG I F +D+GG ++
Sbjct: 20 ILFLGLDNAGKTTLLHMLKNDRLAQHQPTQHPTSEELA--IGN---IKFTTFDLGGHQQA 74
Query: 82 RPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLPNAI 141
R LWK Y +GI++++D+ D ER E K EL + + + VP LIL NK D P A
Sbjct: 75 RRLWKDYFPEVNGIVYLVDAYDKERFAESKRELDALLSDEELATVPFLILGNKIDAPYAA 134
Query: 142 QIKQIEKLLGLYE 154
++ LGL
Sbjct: 135 SEDELRYALGLTN 147
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 93.5 bits (232), Expect = 9e-24
Identities = 50/194 (25%), Positives = 79/194 (40%), Gaps = 21/194 (10%)
Query: 22 IVMLGLDSAGKTTALYRLKFDQYLNTVPTIGFNCEKVKGQI--GKCKGINFLIWDVGGQE 79
IV+LG GKTT L RL D++ P N + + I +WD GQE
Sbjct: 8 IVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGN--LDPAKTIEPYRRNIKLQLWDTAGQE 65
Query: 80 KLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLPN 139
+ R L Y R +GI+ V DST E +E+ E ++ ++ +VPIL++ NK DL +
Sbjct: 66 EYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVGNKIDLFD 125
Query: 140 A--------------IQIKQIEKLLGLYELNNMHLYYIQATCAIT---GDGLHEGINELY 182
+ + + L E+ N L A + E + +L
Sbjct: 126 EQSSSEEILNQLNREVVLLVLAPKAVLPEVANPALLETSAKSLTGPNVNELFKELLRKLL 185
Query: 183 QLILKKRKLQKTNK 196
+ I K + +
Sbjct: 186 EEIEKLVLKNELRQ 199
>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 = 80.5 bits (199), Expect = 2e-19
Identities = 35/122 (28%), Positives = 56/122 (45%), Gaps = 4/122 (3%)
Query: 22 IVMLGLDSAGKTTALYRLKFDQYLNT--VPTIGFNCEKVKGQIGKCKGINFLIWDVGGQE 79
IV++G + GK+T L RL ++ T P N + K F + D GQE
Sbjct: 4 IVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEE-DGKTYKFNLLDTAGQE 62
Query: 80 KLRPLWKSYTRCTDGIIFVIDSTD-VERMEEVKIELIKTIKNNDNFNVPILILANKQDLP 138
+ + Y R + + V D V +EE+ + K I ++ VPI+++ NK DL
Sbjct: 63 DYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAESGVPIILVGNKIDLR 122
Query: 139 NA 140
+A
Sbjct: 123 DA 124
>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 = 80.2 bits (199), Expect = 3e-19
Identities = 49/168 (29%), Positives = 83/168 (49%), Gaps = 13/168 (7%)
Query: 22 IVMLGLDSA-GKTTALYRLKFDQY-LNTVPTIGFNCEKVKGQIGKCKGINFLIWDVGGQE 79
IV++G DS GKT+ L R +++ N TIG + + ++ K + IWD GQE
Sbjct: 3 IVLIG-DSGVGKTSLLLRFVDNKFSENYKSTIGVDFKSKTIEVDG-KKVKLQIWDTAGQE 60
Query: 80 KLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLPN 139
+ R + SY R G I V D T+ E E + + + +K N+PI+++ NK DL +
Sbjct: 61 RFRSITSSYYRGAHGAILVYDVTNRESFENLD-KWLNELKEYAPPNIPIILVGNKSDLED 119
Query: 140 AIQIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEGINELYQLILK 187
Q+ E+ + N + + T A TG E ++E ++ + +
Sbjct: 120 ERQV-STEEAQQFAKENGLLFF---ETSAKTG----ENVDEAFESLAR 159
>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 = 75.2 bits (185), Expect = 2e-17
Identities = 37/174 (21%), Positives = 82/174 (47%), Gaps = 22/174 (12%)
Query: 23 VMLGLDSAGKTTALYRLKFDQYLNT----VPTIGFNCEKVKGQIGKCKGINFLIWDVGGQ 78
V++G GK++ L L + T + ++ K + ++ D G
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPD--VYVKELDK-GKVKLVLVDTPGL 57
Query: 79 EKLRPLW-----KSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILAN 133
++ L + R D I+ V+DSTD E E+ K+ +++ ++ +PI+++ N
Sbjct: 58 DEFGGLGREELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLRKEG---IPIILVGN 114
Query: 134 KQDLPNAIQIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEGINELYQLILK 187
K DL +++++ +L L ++ + ++ A TG EG++EL++ +++
Sbjct: 115 KIDLLEEREVEELLRLEELAKILGVPVF---EVSAKTG----EGVDELFEKLIE 161
>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 = 72.4 bits (178), Expect = 7e-16
Identities = 43/134 (32%), Positives = 64/134 (47%), Gaps = 6/134 (4%)
Query: 21 HIVMLGLDSAGKTTALYRLKFDQYLNTVPTIGFNCEKVKGQIGKCKGINFLIWDVGGQEK 80
+++LG +GKT +L + +TV +I N K K + + DV G EK
Sbjct: 2 TVLLLGPSDSGKTALFTKLTTGKVRSTVTSIEPNVASFYSNSSKGKKLTLV--DVPGHEK 59
Query: 81 LRP-LWKSYTRCTDGIIFVIDSTDVER-MEEVKIEL--IKTIKNNDNFNVPILILANKQD 136
LR L + I+FV+DS ++ + +V L I T +PILI NKQD
Sbjct: 60 LRDKLLEYLKASLKAIVFVVDSATFQKNIRDVAEFLYDILTDLEKIKNKIPILIACNKQD 119
Query: 137 LPNAIQIKQIEKLL 150
L A K+I++LL
Sbjct: 120 LFTAKPAKKIKELL 133
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 70.2 bits (172), Expect = 3e-15
Identities = 42/180 (23%), Positives = 80/180 (44%), Gaps = 21/180 (11%)
Query: 13 QASGSSSVHIVMLGLDSAGKTTALYRLKFDQYLNTVPTIGFNCEKVKGQIGKCKGINFL- 71
A+ IV++G AGKTT + R D+ L + KG+ ++F
Sbjct: 4 AANKMIETKIVVIGPVGAGKTTFV-RALSDKPLVITEADA-SSVSGKGKRPTTVAMDFGS 61
Query: 72 ----------IWDVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNN 121
++ GQE+ + +W+ +R G I ++DS+ +I T +N
Sbjct: 62 IELDEDTGVHLFGTPGQERFKFMWEILSRGAVGAIVLVDSSRPITFHAEEIIDFLTSRN- 120
Query: 122 DNFNVPILILANKQDLPNAIQIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEGINEL 181
+P+++ NKQDL +A+ ++I + L +L + + I+ A G+G + ++ L
Sbjct: 121 ---PIPVVVAINKQDLFDALPPEKIREAL---KLELLSVPVIE-IDATEGEGARDQLDVL 173
>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 = 66.4 bits (163), Expect = 5e-14
Identities = 52/172 (30%), Positives = 82/172 (47%), Gaps = 17/172 (9%)
Query: 22 IVMLGLDSA-GKTTALYRLKFDQYLNT-VPTIGFNCEKVKGQIGKCKGINFLIWDVGGQE 79
+V++G D GK++ L R +++ +PTIG + K K + IWD GQE
Sbjct: 2 LVLVG-DGGVGKSSLLIRFTQNKFPEEYIPTIGVD-FYTKTIEVDGKTVKLQIWDTAGQE 59
Query: 80 KLRPLWKSYTRCTDGIIFVIDSTDVERMEEVK--IELIKTIKNNDNFNVPILILANKQDL 137
+ R L Y R G + V D T + E VK +E I + NVPI+++ NK DL
Sbjct: 60 RFRALRPLYYRGAQGFLLVYDITSRDSFENVKKWLEEILRHADE---NVPIVLVGNKCDL 116
Query: 138 PN--AIQIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEGINELYQLILK 187
+ + ++ E L + L +++ T A T + + E EL + ILK
Sbjct: 117 EDQRVVSTEEGEAL-----AKELGLPFME-TSAKTNENVEEAFEELAREILK 162
>gnl|CDD|206653 cd01860, Rab5_related, Rab-related GTPase family includes Rab5 and
Rab22; regulates early endosome fusion. The
Rab5-related subfamily includes Rab5 and Rab22 of
mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of plants.
The members of this subfamily are involved in
endocytosis and endocytic-sorting pathways. In mammals,
Rab5 GTPases localize to early endosomes and regulate
fusion of clathrin-coated vesicles to early endosomes
and fusion between early endosomes. In yeast, Ypt51p
family members similarly regulate membrane trafficking
through prevacuolar compartments. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 163
Score = 61.4 bits (150), Expect = 4e-12
Identities = 49/172 (28%), Positives = 81/172 (47%), Gaps = 19/172 (11%)
Query: 22 IVMLGLDSAGKTTALYRLKFDQYL-NTVPTIG--FNCEKVKGQIGKCKGINFLIWDVGGQ 78
+V+LG S GK++ + R +++ N TIG F + V + + F IWD GQ
Sbjct: 4 LVLLGDSSVGKSSIVLRFVKNEFSENQESTIGAAFLTQTVN--LDDT-TVKFEIWDTAGQ 60
Query: 79 EKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLP 138
E+ R L Y R I V D T E E+ K +K ++ + N+ I + NK DL
Sbjct: 61 ERYRSLAPMYYRGAAAAIVVYDITSEESFEKAK-SWVKELQEHGPPNIVIALAGNKADLE 119
Query: 139 N--AIQIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEGINELYQLILKK 188
+ + ++ ++ + L +++ T A TG E +NEL+ I +K
Sbjct: 120 SKRQVSTEEAQEY-----ADENGLLFME-TSAKTG----ENVNELFTEIARK 161
>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 = 61.5 bits (150), Expect = 4e-12
Identities = 50/172 (29%), Positives = 77/172 (44%), Gaps = 19/172 (11%)
Query: 22 IVMLGLDSAGKTTALYRL---KFDQYLNTVPTIGFNCEKVKGQIGKCKGINFLIWDVGGQ 78
+V+LG GKT+ + R KF++ T + + IG + I+ IWD GQ
Sbjct: 3 VVLLGEGRVGKTSLVLRYVENKFNE--KHESTTQASFFQKTVNIGGKR-IDLAIWDTAGQ 59
Query: 79 EKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLP 138
E+ L Y R DG I V D TD + ++VK IK +K N+ ++I+ NK DL
Sbjct: 60 ERYHALGPIYYRDADGAILVYDITDADSFQKVKKW-IKELKQMRGNNISLVIVGNKIDLE 118
Query: 139 N--AIQIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEGINELYQLILKK 188
+ + E+ + T A TG +GI EL+ + K+
Sbjct: 119 RQRVVSKSEAEEYAKSVGAKHFE------TSAKTG----KGIEELFLSLAKR 160
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 61.4 bits (150), Expect = 4e-12
Identities = 39/134 (29%), Positives = 63/134 (47%), Gaps = 23/134 (17%)
Query: 22 IVMLGLDSA-GKTTALYRLKFDQY-LNTVPTIG---------FNCEKVKGQIGKCKGINF 70
I+++G DS GK++ L R ++ TIG + ++VK QI
Sbjct: 3 IILIG-DSGVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIEVDGKRVKLQI-------- 53
Query: 71 LIWDVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILI 130
WD GQE+ R + SY R G + V D T+ E E ++ +K ++ + NV I++
Sbjct: 54 --WDTAGQERFRSITSSYYRGAVGALLVYDITNRESFENLE-NWLKELREYASPNVVIML 110
Query: 131 LANKQDLPNAIQIK 144
+ NK DL Q+
Sbjct: 111 VGNKSDLEEQRQVS 124
>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 = 60.0 bits (146), Expect = 1e-11
Identities = 46/168 (27%), Positives = 78/168 (46%), Gaps = 13/168 (7%)
Query: 22 IVMLGLDSAGKTTALYRL---KFDQYLNTVPTIGFNCEKVKG-QIGKCKGINFLIWDVGG 77
I+++G GK++ L R FD+ + TIG + KVK + K + IWD G
Sbjct: 3 ILLIGDSGVGKSSLLLRFTDDTFDE--DLSSTIGVDF-KVKTVTVDG-KKVKLAIWDTAG 58
Query: 78 QEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDL 137
QE+ R L SY R G+I V D T + + + L + + N + +++ NK D
Sbjct: 59 QERFRTLTSSYYRGAQGVILVYDVTRRDTFDNLDTWLNELDTYSTNPDAVKMLVGNKIDK 118
Query: 138 PNAIQIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEGINELYQLI 185
N +++ + G ++ +I+ T A T G+ + EL + I
Sbjct: 119 EN----REVTREEGQKFARKHNMLFIE-TSAKTRIGVQQAFEELVEKI 161
>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 = 59.9 bits (145), Expect = 2e-11
Identities = 43/135 (31%), Positives = 67/135 (49%), Gaps = 11/135 (8%)
Query: 19 SVHIVMLGLDSAGKTTALYRL---KFDQYLNTVPTIGFNCEKVKGQIGKCKGINF--LIW 73
S IV +G S GKT + R FD+ N TIG + E + ++ G+ F +W
Sbjct: 1 SKVIV-VGDLSVGKTCLINRFCKDVFDK--NYKATIGVDFEMERFEV---LGVPFSLQLW 54
Query: 74 DVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILAN 133
D GQE+ + + +Y R II V D TDV +E + L +K ND +V + ++
Sbjct: 55 DTAGQERFKCIASTYYRGAQAIIIVFDLTDVASLEHTRQWLEDALKENDPSSVLLFLVGT 114
Query: 134 KQDLPNAIQIKQIEK 148
K+DL + Q +E+
Sbjct: 115 KKDLSSPAQYALMEQ 129
>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 = 59.6 bits (145), Expect = 2e-11
Identities = 47/170 (27%), Positives = 78/170 (45%), Gaps = 11/170 (6%)
Query: 22 IVMLGLDSAGKTTALYRLKFDQYLNT-VPTIGFNCEKVKGQIGKCKGINFLIWDVGGQEK 80
++++G GK+ L R D + + + TIG + K++ K I IWD GQE+
Sbjct: 6 LLLIGDSGVGKSCLLLRFSEDSFNPSFISTIGIDF-KIRTIELDGKKIKLQIWDTAGQER 64
Query: 81 LRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLPN- 139
R + SY R GII V D TD + E +K ++ I + + +V +++ NK D+
Sbjct: 65 FRTITTSYYRGAMGIILVYDITDEKSFENIK-NWMRNIDEHASEDVERMLVGNKCDMEEK 123
Query: 140 -AIQIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEGINELYQLILKK 188
+ ++ E L Y + + T A + E L + ILKK
Sbjct: 124 RVVSKEEGEALAREYGIKFLE------TSAKANINVEEAFLTLAKDILKK 167
>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 = 59.2 bits (144), Expect = 2e-11
Identities = 45/172 (26%), Positives = 76/172 (44%), Gaps = 25/172 (14%)
Query: 22 IVMLGLDSAGKTTALYRLKFDQ-YLNTVPTIG--FNCEKVKGQIGKC-----KGINFLIW 73
+V LG S GKT+ + R +D TIG F + K K + +W
Sbjct: 3 LVFLGDQSVGKTSIITRFMYDTFDNQYQATIGIDF--------LSKTMYVDDKTVRLQLW 54
Query: 74 DVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILAN 133
D GQE+ R L SY R + + V D T+ + + + I +++ +V I+++ N
Sbjct: 55 DTAGQERFRSLIPSYIRDSSVAVVVYDITNRQSFDNTD-KWIDDVRDERGNDVIIVLVGN 113
Query: 134 KQDLPNAIQIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEGINELYQLI 185
K DL + Q+ E+ + NN +I+ T A G + +L++ I
Sbjct: 114 KTDLSDKRQVS-TEEGEKKAKENNAM--FIE-TSAKAGH----NVKQLFKKI 157
>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 = 57.7 bits (140), Expect = 8e-11
Identities = 41/124 (33%), Positives = 58/124 (46%), Gaps = 11/124 (8%)
Query: 22 IVMLGLDSAGKTTALYRLKFDQYLNT-VPTIG----FNCEKVKGQIGKCKGINFLIWDVG 76
++++G GK+ L R D Y + + TIG ++ G K + IWD
Sbjct: 5 LLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDG-----KTVKLQIWDTA 59
Query: 77 GQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQD 136
GQE+ R + SY R GII V D TD E VK L + I + NV L++ NK D
Sbjct: 60 GQERFRTITSSYYRGAHGIIIVYDVTDQESFNNVKQWLQE-IDRYASENVNKLLVGNKCD 118
Query: 137 LPNA 140
L +
Sbjct: 119 LTDK 122
>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 = 52.6 bits (126), Expect = 7e-09
Identities = 37/117 (31%), Positives = 59/117 (50%), Gaps = 3/117 (2%)
Query: 22 IVMLGLDSAGKTTALYRLKFDQYLNT-VPTIGFNCEKVKGQIGKCKGINFLIWDVGGQEK 80
++++G S GKT+ L+R D + + V T+G + KVK K I IWD GQE+
Sbjct: 4 LLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDF-KVKTVYRNDKRIKLQIWDTAGQER 62
Query: 81 LRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDL 137
R + +Y R G I + D T+ E V+ + IK N ++++ NK D+
Sbjct: 63 YRTITTAYYRGAMGFILMYDITNEESFNAVQ-DWSTQIKTYSWDNAQVILVGNKCDM 118
>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 = 51.3 bits (123), Expect = 1e-08
Identities = 30/118 (25%), Positives = 56/118 (47%), Gaps = 5/118 (4%)
Query: 21 HIVMLGLDSAGKTTALYRLKFDQYL-NTVPTIGFNCEKVKGQIGKCKGINFLIWDVGGQE 79
+V++G +GK++ L +L ++ + G ++ G+ IWD GG+E
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGL-LNIWDFGGRE 59
Query: 80 KLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKN--NDNFNVPILILANKQ 135
+L+ + + D I+ V D TD E + EV LI + N +P++++ NK
Sbjct: 60 ELKFEHIIFMKWADAILLVYDLTDRESLNEVS-RLIAWLPNLRKLGGKIPVILVGNKL 116
>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 = 52.1 bits (125), Expect = 1e-08
Identities = 50/177 (28%), Positives = 83/177 (46%), Gaps = 20/177 (11%)
Query: 25 LGLDSAGKTTALYRL---KFD-QYLNTVPTIGFNCEKV-------KGQIGKCKGINFLIW 73
LG GKTT LYR KF+ +++ TV I F ++V G GK ++ +W
Sbjct: 10 LGDSGVGKTTFLYRYTDNKFNPKFITTV-GIDFREKRVVYNSQGPDGTSGKAFRVHLQLW 68
Query: 74 DVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILAN 133
D GQE+ R L ++ R G + + D T + V+ + + + N I+++ N
Sbjct: 69 DTAGQERFRSLTTAFFRDAMGFLLMFDLTSEQSFLNVRNWMSQLQAHAYCENPDIVLIGN 128
Query: 134 KQDLPNAIQIK--QIEKLLGLYELNNMHLYYIQATCAITGDGLHEGINELYQLILKK 188
K DLP+ ++ Q +L Y + Y + T A TG + + + L LI+K+
Sbjct: 129 KADLPDQREVSERQARELADKYGIP-----YFE-TSAATGQNVEKAVETLLDLIMKR 179
>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 = 51.7 bits (124), Expect = 2e-08
Identities = 36/126 (28%), Positives = 56/126 (44%), Gaps = 21/126 (16%)
Query: 22 IVMLGLDSAGKTTALYRLKFDQYLN----------TVPTIGFNCEKVKGQIGKCKGINFL 71
I+++G + GKT + R K + T+ T+ ++VK QI
Sbjct: 6 IILIGDSNVGKTCVVQRFKSGTFSERQGNTIGVDFTMKTLEIQGKRVKLQI--------- 56
Query: 72 IWDVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILIL 131
WD GQE+ R + +SY R +G I D T E V I+ ++ NV +L++
Sbjct: 57 -WDTAGQERFRTITQSYYRSANGAIIAYDITRRSSFESVP-HWIEEVEKYGASNVVLLLI 114
Query: 132 ANKQDL 137
NK DL
Sbjct: 115 GNKCDL 120
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 50.7 bits (121), Expect = 5e-08
Identities = 44/169 (26%), Positives = 78/169 (46%), Gaps = 5/169 (2%)
Query: 22 IVMLGLDSAGKTTALYRLKFDQY-LNTVPTIGFNCEKVKGQIGKCKGINFLIWDVGGQEK 80
IV++G GK+ L R +++ L + TIG Q+ + K + IWD GQE+
Sbjct: 15 IVLIGDSGVGKSNILSRFTRNEFCLESKSTIGVEFATRTLQV-EGKTVKAQIWDTAGQER 73
Query: 81 LRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLPNA 140
R + +Y R G + V D T + + V+ ++ ++++ + N+ I++ NK DL N
Sbjct: 74 YRAITSAYYRGAVGALLVYDITKRQTFDNVQ-RWLRELRDHADSNIVIMMAGNKSDL-NH 131
Query: 141 IQIKQIEKLLGLYELNNMHLYYIQATCAITGD-GLHEGINELYQLILKK 188
++ E L E + A A + + E+Y +I KK
Sbjct: 132 LRSVAEEDGQALAEKEGLSFLETSALEATNVEKAFQTILLEIYHIISKK 180
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase. The
Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that generally show sequence
conservation in the region between the Walker A and B
motifs (G1 and G3 box motifs), to the exclusion of other
GTPases. TrmE is ubiquitous in bacteria and is a
widespread mitochondrial protein in eukaryotes, but is
absent from archaea. The yeast member of TrmE family,
MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family.
Length = 161
Score = 49.2 bits (118), Expect = 1e-07
Identities = 35/172 (20%), Positives = 66/172 (38%), Gaps = 24/172 (13%)
Query: 25 LGLDSAGKTTALYRLKFDQYLNTVPTIGFNCEKVKGQIGKCKGINFLIWDVGG------- 77
G + GK++ L L P G + V+ + ++ D G
Sbjct: 3 FGRPNVGKSSLLNALLGQNVGIVSPIPGTTRDPVRKEWELLPLGPVVLIDTPGLDEEGGL 62
Query: 78 -QEKLRPLWKSYTRCTDGIIFVIDST-DVERMEEVKIELIKTIKNNDNFNVPILILANKQ 135
+E++ + R D ++ V+DS E L + P+L++ NK
Sbjct: 63 GRERVEEARQVADR-ADLVLLVVDSDLTPVEEEAKLGLLRER-------GKPVLLVLNKI 114
Query: 136 DLPNAIQIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEGINELYQLILK 187
DL + +++ + L L ++ + A A+ G EGI+EL + I +
Sbjct: 115 DLVPESEEEELLRERKLELLPDLP---VIAVSALPG----EGIDELRKKIAE 159
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 49.7 bits (118), Expect = 1e-07
Identities = 31/87 (35%), Positives = 41/87 (47%), Gaps = 1/87 (1%)
Query: 19 SVHIVMLGLDSAGKTTALYRLKFDQYLNTVPTIGFNCEKVKGQIGKCKGINFLIWDVGGQ 78
S I+++G GK++ L + PTIG + K+K K + IWD GQ
Sbjct: 14 SFKILLIGDSGVGKSSLLVSFISSSVEDLAPTIGVDF-KIKQLTVGGKRLKLTIWDTAGQ 72
Query: 79 EKLRPLWKSYTRCTDGIIFVIDSTDVE 105
E+ R L SY R GII V D T E
Sbjct: 73 ERFRTLTSSYYRNAQGIILVYDVTRRE 99
>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 = 48.3 bits (116), Expect = 2e-07
Identities = 37/127 (29%), Positives = 63/127 (49%), Gaps = 23/127 (18%)
Query: 22 IVMLGLDSA-GKTTALYRLKFDQY-LNTVPTIG---------FNCEKVKGQIGKCKGINF 70
IV++G DS GK+ L R +++ L++ TIG + + +K QI
Sbjct: 6 IVLIG-DSGVGKSNLLSRFTRNEFNLDSKSTIGVEFATRTIQIDGKTIKAQI-------- 56
Query: 71 LIWDVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILI 130
WD GQE+ R + +Y R G + V D T E V+ +K ++++ + N+ I++
Sbjct: 57 --WDTAGQERYRAITSAYYRGAVGALLVYDITKKSTFENVE-RWLKELRDHADSNIVIML 113
Query: 131 LANKQDL 137
+ NK DL
Sbjct: 114 VGNKSDL 120
>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 = 49.2 bits (118), Expect = 3e-07
Identities = 34/101 (33%), Positives = 45/101 (44%), Gaps = 17/101 (16%)
Query: 48 VPTIGFNCEKVKGQIGKCKGINFLIWDVGGQEKLRPLWKSYTRCTDGIIFVI-----DST 102
V T G K KG+ F ++DVGGQ R W IIFV+ D
Sbjct: 153 VKTTGIIETKFD-----FKGLKFRLFDVGGQRSERKKWIHCFEDVTAIIFVVSLSEYDQV 207
Query: 103 DVE-----RMEEVKIELIKTIKNNDNF-NVPILILANKQDL 137
E R+EE + L + I N+ F N PI++ NK+DL
Sbjct: 208 LYEDDSTNRLEE-SLNLFEEICNSPWFKNTPIILFLNKKDL 247
>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 = 47.8 bits (114), Expect = 5e-07
Identities = 38/143 (26%), Positives = 60/143 (41%), Gaps = 15/143 (10%)
Query: 17 SSSVHIVMLGLDSAGKTTALYRLKFDQYLNTVPTIGFNCEKVKGQIGKCKGINFLIWDVG 76
SS +++ GL +GKT+ L TV + + KG +F + D
Sbjct: 1 SSQPAVIIAGLCDSGKTSLFTLLTTGTVKKTVTSQE---PSAAYKYMLHKGFSFTLIDFP 57
Query: 77 GQEKLRPLWKS---YTRCTDGIIFVIDST-DVERMEEV-----KIELIKTIKNNDNFNVP 127
G KLR + GI+FV+DST + + + +I I + N +
Sbjct: 58 GHVKLRQKLLETIKDSSSLRGIVFVVDSTAFPKEVTDTAEFLYEILSITELLKN---GID 114
Query: 128 ILILANKQDLPNAIQIKQIEKLL 150
ILI NKQ+ A K+I++ L
Sbjct: 115 ILIACNKQESFTARPPKKIKQAL 137
>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 = 47.1 bits (112), Expect = 5e-07
Identities = 43/176 (24%), Positives = 74/176 (42%), Gaps = 25/176 (14%)
Query: 23 VMLGLDSAGKTTALYRLKFDQYLNTVP-TIG---------FNCEKVKGQIGKCKGINFLI 72
+++G GK+ L++ +++ P TIG N +K+K QI
Sbjct: 6 IIIGDMGVGKSCLLHQFTEKKFMADCPHTIGVEFGTRIIEVNGQKIKLQI---------- 55
Query: 73 WDVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILA 132
WD GQE+ R + +SY R G + V D T + L +N N N I ++
Sbjct: 56 WDTAGQERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDA-RNLTNPNTVIFLIG 114
Query: 133 NKQDLPNAIQIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEGINELYQLILKK 188
NK DL + E+ + N L +++ + A TG+ + + E + I +
Sbjct: 115 NKADLEAQRDVT-YEEAKQFADENG--LLFLECS-AKTGENVEDAFLETAKKIYQN 166
>gnl|CDD|133318 cd04118, Rab24, Rab GTPase family 24 (Rab24). Rab24 is distinct
from other Rabs in several ways. It exists primarily in
the GTP-bound state, having a low intrinsic GTPase
activity; it is not efficiently geranyl-geranylated at
the C-terminus; it does not form a detectable complex
with Rab GDP-dissociation inhibitors (GDIs); and it has
recently been shown to undergo tyrosine phosphorylation
when overexpressed in vitro. The specific function of
Rab24 still remains unknown. It is found in a transport
route between ER-cis-Golgi and late endocytic
compartments. It is putatively involved in an autophagic
pathway, possibly directing misfolded proteins in the ER
to degradative pathways. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 193
Score = 47.6 bits (113), Expect = 7e-07
Identities = 35/122 (28%), Positives = 57/122 (46%), Gaps = 9/122 (7%)
Query: 20 VHIVMLGLDSAGKTTALYRLKFDQYLN--TVPTIG--FNCEKVKGQIGKCKGINFLIWDV 75
V +VMLG +S GKT+ + R ++L TIG F +++ +G+ + + IWD
Sbjct: 1 VKVVMLGKESVGKTSLVERYVHHRFLVGPYQNTIGAAFVAKRM--VVGE-RVVTLGIWDT 57
Query: 76 GGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQ 135
G E+ + + Y R I D TD E K +K ++N + + I + K
Sbjct: 58 AGSERYEAMSRIYYRGAKAAIVCYDLTDSSSFERAKF-WVKELQNLEE-HCKIYLCGTKS 115
Query: 136 DL 137
DL
Sbjct: 116 DL 117
>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 = 46.8 bits (111), Expect = 1e-06
Identities = 38/127 (29%), Positives = 62/127 (48%), Gaps = 22/127 (17%)
Query: 22 IVMLGLDSAGKTTALYRLKFD----QYLNTV------PTIGFNCEKVKGQIGKCKGINFL 71
++++G GK++ L R + Y+ T+ T+ N E+VK QI
Sbjct: 9 LLIIGDSGVGKSSLLLRFADNTFSGSYITTIGVDFKIRTVEINGERVKLQI--------- 59
Query: 72 IWDVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILIL 131
WD GQE+ R + +Y R T G+I V D T+ E VK ++ I+ N + +V +++
Sbjct: 60 -WDTAGQERFRTITSTYYRGTHGVIVVYDVTNGESFVNVK-RWLQEIEQNCD-DVCKVLV 116
Query: 132 ANKQDLP 138
NK D P
Sbjct: 117 GNKNDDP 123
>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 = 46.3 bits (110), Expect = 1e-06
Identities = 45/161 (27%), Positives = 76/161 (47%), Gaps = 19/161 (11%)
Query: 23 VMLGLDSAGKTTALYRL---KFDQYLNTVPTIG--FNCEKVKGQIGKCKGINFLIWDVGG 77
+++G GK+ L++ KF Q ++ TIG F V +G K + IWD G
Sbjct: 4 LIIGSAGTGKSCLLHQFIENKFKQ--DSNHTIGVEFGSRVVN--VGG-KSVKLQIWDTAG 58
Query: 78 QEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIEL--IKTIKNNDNFNVPILILANKQ 135
QE+ R + +SY R G + V D T E + L +T+ + D + I+++ NK+
Sbjct: 59 QERFRSVTRSYYRGAAGALLVYDITSRESFNALTNWLTDARTLASPD---IVIILVGNKK 115
Query: 136 DLPNAIQIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHE 176
DL + ++ +E E N + T A+TG+ + E
Sbjct: 116 DLEDDREVTFLEASRFAQE-NGLLFL---ETSALTGENVEE 152
>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 = 46.3 bits (110), Expect = 1e-06
Identities = 26/82 (31%), Positives = 40/82 (48%), Gaps = 1/82 (1%)
Query: 66 KGINFLIWDVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFN 125
K I IWD GQE R + +SY R G + V D T E + L + + + N N
Sbjct: 51 KQIKLQIWDTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLTSWL-EDARQHSNSN 109
Query: 126 VPILILANKQDLPNAIQIKQIE 147
+ I+++ NK DL + ++ E
Sbjct: 110 MTIMLIGNKCDLESRREVSYEE 131
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 46.7 bits (111), Expect = 1e-06
Identities = 45/160 (28%), Positives = 63/160 (39%), Gaps = 27/160 (16%)
Query: 11 NLQASGSSSVHIVMLGLDSAGKTTALYRLKFDQY-LNTVPTIGFNCEKVKGQIGKCKGIN 69
N Q S +V++G GKTT + R ++ PTIG + K I
Sbjct: 5 NQQTVDYPSFKLVIVGDGGTGKTTFVKRHLTGEFEKKYEPTIGVEVHPLDFFTNCGK-IR 63
Query: 70 FLIWDVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDN------ 123
F WD GQEK L Y I + D T R+ T KN
Sbjct: 64 FYCWDTAGQEKFGGLRDGYYIHGQCAIIMFDVT--ARL---------TYKNVPTWHRDLC 112
Query: 124 ---FNVPILILANKQDLPN-AIQIKQI----EKLLGLYEL 155
N+PI++ NK D+ N ++ KQ+ +K L YE+
Sbjct: 113 RVCENIPIVLCGNKVDVKNRQVKAKQVTFHRKKNLQYYEI 152
>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 = 46.3 bits (110), Expect = 2e-06
Identities = 34/131 (25%), Positives = 65/131 (49%), Gaps = 9/131 (6%)
Query: 22 IVMLGLDSAGKTTALYRL---KFDQYLNTVPTIG--FNCEKVKGQIGKCKGINFLIWDVG 76
++++G + GK++ L R +F + + PT+G F ++ + G I +WD
Sbjct: 5 LIVIGDSTVGKSSLLKRFTEGRFAEVSD--PTVGVDFFSRLIEIEPGV--RIKLQLWDTA 60
Query: 77 GQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQD 136
GQE+ R + +SY R + G++ V D T+ E E V L + + +++ +K D
Sbjct: 61 GQERFRSITRSYYRNSVGVLLVFDITNRESFEHVHDWLEEARSHIQPHRPVFILVGHKCD 120
Query: 137 LPNAIQIKQIE 147
L + Q+ + E
Sbjct: 121 LESQRQVTREE 131
>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 = 45.6 bits (109), Expect = 2e-06
Identities = 38/124 (30%), Positives = 57/124 (45%), Gaps = 13/124 (10%)
Query: 22 IVMLGLDSAGKTTALYRLKFDQYLNT-VPTIG--FNCE-KVKGQIGKCKGINFLIWDVGG 77
+V+LG GK+ R +++ PTI + + V G+ I D G
Sbjct: 2 LVVLGAGGVGKSALTIRFVSGEFVEEYDPTIEDSYRKQIVVDGET-----YTLDILDTAG 56
Query: 78 QEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVK--IELIKTIKNNDNFNVPILILANKQ 135
QE+ + Y R DG I V T E EE+K E I +K+ + +VPI+++ NK
Sbjct: 57 QEEFSAMRDQYIRNGDGFILVYSITSRESFEEIKNIREQILRVKDKE--DVPIVLVGNKC 114
Query: 136 DLPN 139
DL N
Sbjct: 115 DLEN 118
>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 = 45.5 bits (108), Expect = 2e-06
Identities = 37/138 (26%), Positives = 62/138 (44%), Gaps = 31/138 (22%)
Query: 22 IVMLGLDSAGKTTALYRL---KFDQYLNTVPTIG---------FNCEKVKGQIGKCKGIN 69
I+++G + GKT YR +F + T TIG + E++K Q+
Sbjct: 5 IIVIGDSNVGKTCLTYRFCAGRFPE--RTEATIGVDFRERTVEIDGERIKVQL------- 55
Query: 70 FLIWDVGGQEKLRPLWKS----YTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFN 125
WD GQE+ R KS Y R ++FV D T++ + + + +++
Sbjct: 56 ---WDTAGQERFR---KSMVQHYYRNVHAVVFVYDVTNMASFHSLPSWIEECEQHSLPNE 109
Query: 126 VPILILANKQDLPNAIQI 143
VP +++ NK DL IQ+
Sbjct: 110 VPRILVGNKCDLREQIQV 127
>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 = 45.1 bits (107), Expect = 3e-06
Identities = 28/97 (28%), Positives = 46/97 (47%), Gaps = 7/97 (7%)
Query: 72 IWDVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVK--IELIKTIKNNDNFNVPIL 129
I D GQE+ + + Y R +G + V TD EEV I +K+ D F P++
Sbjct: 54 ILDTAGQEEFSAMREQYMRTGEGFLLVFSVTDRGSFEEVDKFHTQILRVKDRDEF--PMI 111
Query: 130 ILANKQDLPNAIQIKQIEKLLGLYELNNMHLYYIQAT 166
++ NK DL + Q+ + E G + + YI+ +
Sbjct: 112 LVGNKADLEHQRQVSREE---GQELARQLKIPYIETS 145
>gnl|CDD|206694 cd04109, Rab28, Rab GTPase family 28 (Rab28). Rab28 subfamily.
First identified in maize, Rab28 has been shown to be a
late embryogenesis-abundant (Lea) protein that is
regulated by the plant hormone abcisic acid (ABA). In
Arabidopsis, Rab28 is expressed during embryo
development and is generally restricted to provascular
tissues in mature embryos. Unlike maize Rab28, it is not
ABA-inducible. Characterization of the human Rab28
homolog revealed two isoforms, which differ by a 95-base
pair insertion, producing an alternative sequence for
the 30 amino acids at the C-terminus. The two human
isoforms are presumably the result of alternative
splicing. Since they differ at the C-terminus but not in
the GTP-binding region, they are predicted to be
targeted to different cellular locations. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins.
Length = 213
Score = 45.6 bits (108), Expect = 4e-06
Identities = 38/156 (24%), Positives = 68/156 (43%), Gaps = 11/156 (7%)
Query: 22 IVMLGLDSAGKTTALYRL---KFDQYLNTVPTIGFNCEKVKGQIGKCKGINFLIWDVGGQ 78
IV+LG ++GKT+ + R F + TIG + + + + +WD+GGQ
Sbjct: 3 IVVLGDGASGKTSLIRRFAQEGFGKSYKQ--TIGLDFFSRRITLPGSLNVTLQVWDIGGQ 60
Query: 79 EKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVP--ILILANKQD 136
+ + Y + V D T+ + E ++ L K N+ ++++ NK D
Sbjct: 61 QIGGKMLDKYIYGAQAVCLVYDITNSQSFENLEDWLSVVKKVNEESETKPKMVLVGNKTD 120
Query: 137 LPNAIQIKQIEKLLGLYELNNMHLYYIQATCAITGD 172
L + Q+ EK + N+M ++ A TGD
Sbjct: 121 LEHNRQVT-AEKHARFAQENDMESIFVSAK---TGD 152
>gnl|CDD|206641 cd00157, Rho, Ras homology family (Rho) of small guanosine
triphosphatases (GTPases). Members of the Rho (Ras
homology) family include RhoA, Cdc42, Rac, Rnd, Wrch1,
RhoBTB, and Rop. There are 22 human Rho family members
identified currently. These proteins are all involved in
the reorganization of the actin cytoskeleton in response
to external stimuli. They also have roles in cell
transformation by Ras in cytokinesis, in focal adhesion
formation and in the stimulation of stress-activated
kinase. These various functions are controlled through
distinct effector proteins and mediated through a
GTP-binding/GTPase cycle involving three classes of
regulating proteins: GAPs (GTPase-activating proteins),
GEFs (guanine nucleotide exchange factors), and GDIs
(guanine nucleotide dissociation inhibitors). Most Rho
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. Since crystal structures
often lack C-terminal residues, this feature is not
available for annotation in many of the CDs in the
hierarchy.
Length = 171
Score = 44.8 bits (107), Expect = 4e-06
Identities = 42/126 (33%), Positives = 62/126 (49%), Gaps = 22/126 (17%)
Query: 22 IVMLGLDSAGKTTALYRLKFDQYLNT-VPTIGFN----CEKVKGQIGKCKGINFLIWDVG 76
IV++G + GKT L +++ VPT+ F+ V G+ +N +WD
Sbjct: 3 IVVVGDGAVGKTCLLISYTTNKFPTEYVPTV-FDNYSANVTVDGKQ-----VNLGLWDTA 56
Query: 77 GQE---KLRPLWKSYTRCTDGII--FVIDSTDVERMEEVKIELIKTIKNNDNFNVPILIL 131
GQE +LRPL SY + TD + F +DS E VK + IK+ NVPI+++
Sbjct: 57 GQEEYDRLRPL--SYPQ-TDVFLLCFSVDSPS--SFENVKTKWYPEIKHY-CPNVPIILV 110
Query: 132 ANKQDL 137
K DL
Sbjct: 111 GTKIDL 116
>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 = 45.0 bits (106), Expect = 5e-06
Identities = 37/131 (28%), Positives = 62/131 (47%), Gaps = 5/131 (3%)
Query: 22 IVMLGLDSAGKTTALYRLKFDQYLNTVP-TIGFNCEKVKGQIGKCKGINFLIWDVGGQEK 80
++++G GKT+ + R D + T+G + K+K + K I IWD GQE+
Sbjct: 3 VIIIGSRGVGKTSLMERFTDDTFCEACKSTVGVDF-KIKTVELRGKKIRLQIWDTAGQER 61
Query: 81 LRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLPN- 139
+ +Y R GII V D T E +++ + +K I + + +L++ NK D
Sbjct: 62 FNSITSAYYRSAKGIILVYDITKKETFDDLP-KWMKMIDKYASEDAELLLVGNKLDCETD 120
Query: 140 -AIQIKQIEKL 149
I +Q EK
Sbjct: 121 REITRQQGEKF 131
>gnl|CDD|206662 cd01870, RhoA_like, Ras homology family A (RhoA)-like includes
RhoA, RhoB and RhoC. The RhoA subfamily consists of
RhoA, RhoB, and RhoC. RhoA promotes the formation of
stress fibers and focal adhesions, regulating cell
shape, attachment, and motility. RhoA can bind to
multiple effector proteins, thereby triggering different
downstream responses. In many cell types, RhoA mediates
local assembly of the contractile ring, which is
necessary for cytokinesis. RhoA is vital for muscle
contraction; in vascular smooth muscle cells, RhoA plays
a key role in cell contraction, differentiation,
migration, and proliferation. RhoA activities appear to
be elaborately regulated in a time- and space-dependent
manner to control cytoskeletal changes. Most Rho
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. RhoA and RhoC are observed
only in geranylgeranylated forms; however, RhoB can be
present in palmitoylated, farnesylated, and
geranylgeranylated forms. RhoA and RhoC are highly
relevant for tumor progression and invasiveness;
however, RhoB has recently been suggested to be a tumor
suppressor. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 175
Score = 44.3 bits (105), Expect = 6e-06
Identities = 45/126 (35%), Positives = 64/126 (50%), Gaps = 18/126 (14%)
Query: 22 IVMLGLDSAGKTTALYRLKFDQYLNT-VPTIGFNCEKVKGQIGKCKGINFLIWDVGGQE- 79
+V++G + GKT L DQ+ VPT+ N V K + +WD GQE
Sbjct: 4 LVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFEN--YVADIEVDGKQVELALWDTAGQED 61
Query: 80 --KLRPLWKSYTRCTDGII--FVIDSTDVERMEEVKIELIKTIKNNDNF--NVPILILAN 133
+LRPL SY TD I+ F IDS D +E + + +K+ F NVPI+++ N
Sbjct: 62 YDRLRPL--SYPD-TDVILMCFSIDSPD--SLENIPEKWTPEVKH---FCPNVPIILVGN 113
Query: 134 KQDLPN 139
K+DL N
Sbjct: 114 KKDLRN 119
>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 = 43.6 bits (104), Expect = 1e-05
Identities = 30/98 (30%), Positives = 49/98 (50%), Gaps = 10/98 (10%)
Query: 92 TDGIIFVIDSTD----VERMEEVKIELIKTIKNNDNFNVPILILANKQDLPNAIQIKQIE 147
T ++ VID + VE E ++ EL N P +++ NK DL +A + +
Sbjct: 79 TRVLLHVIDLSGEDDPVEDYETIRNELEA--YNPGLAEKPRIVVLNKIDLLDAEERFEKL 136
Query: 148 KLLGLYELNNMHLYYIQATCAITGDGLHEGINELYQLI 185
K L L EL ++ I A+TG+GL E + +L +L+
Sbjct: 137 KEL-LKELKGKKVFPI---SALTGEGLDELLKKLAKLL 170
>gnl|CDD|206710 cd04139, RalA_RalB, Ral (Ras-like) family containing highly
homologous RalA and RalB. The Ral (Ras-like) subfamily
consists of the highly homologous RalA and RalB. Ral
proteins are believed to play a crucial role in
tumorigenesis, metastasis, endocytosis, and actin
cytoskeleton dynamics. Despite their high sequence
similarity (>80% sequence identity), nonoverlapping and
opposing functions have been assigned to RalA and RalBs
in tumor migration. In human bladder and prostate cancer
cells, RalB promotes migration while RalA inhibits it. A
Ral-specific set of GEFs has been identified that are
activated by Ras binding. This RalGEF activity is
enhanced by Ras binding to another of its target
proteins, phosphatidylinositol 3-kinase (PI3K). Ral
effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and
the exocyst (Sec6/8) complex, a heterooctomeric protein
complex that is involved in tethering vesicles to
specific sites on the plasma membrane prior to
exocytosis. In rat kidney cells, RalB is required for
functional assembly of the exocyst and for localizing
the exocyst to the leading edge of migrating cells. In
human cancer cells, RalA is required to support
anchorage-independent proliferation and RalB is required
to suppress apoptosis. RalA has been shown to localize
to the plasma membrane while RalB is localized to the
intracellular vesicles. Most Ras proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Ras proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 163
Score = 42.8 bits (101), Expect = 2e-05
Identities = 36/129 (27%), Positives = 61/129 (47%), Gaps = 7/129 (5%)
Query: 22 IVMLGLDSAGKTTALYRLKFDQYLNTV-PTIGFNCEKVKGQIGKCKGINFLIWDVGGQEK 80
++M+G GK+ + +D+++ PT + K G+ +N L D GQE
Sbjct: 3 VIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEVQLNIL--DTAGQED 60
Query: 81 LRPLWKSYTRCTDGIIFVIDSTDVERMEEVK--IELIKTIKNNDNFNVPILILANKQDLP 138
+ +Y R +G + V TD+E + E I +K +D NVP+L++ NK DL
Sbjct: 61 YAAIRDNYFRSGEGFLLVFSITDMESFTALAEFREQILRVKEDD--NVPLLLVGNKCDLE 118
Query: 139 NAIQIKQIE 147
+ Q+ E
Sbjct: 119 DKRQVSVEE 127
>gnl|CDD|206697 cd04116, Rab9, Rab GTPase family 9 (Rab9). Rab9 is found in late
endosomes, together with mannose 6-phosphate receptors
(MPRs) and the tail-interacting protein of 47 kD
(TIP47). Rab9 is a key mediator of vesicular transport
from late endosomes to the trans-Golgi network (TGN) by
redirecting the MPRs. Rab9 has been identified as a key
component for the replication of several viruses,
including HIV1, Ebola, Marburg, and measles, making it a
potential target for inhibiting a variety of viruses.
GTPase activating proteins (GAPs) interact with
GTP-bound Rab and accelerate the hydrolysis of GTP to
GDP. Guanine nucleotide exchange factors (GEFs) interact
with GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 170
Score = 42.9 bits (101), Expect = 2e-05
Identities = 41/134 (30%), Positives = 62/134 (46%), Gaps = 21/134 (15%)
Query: 17 SSSVHIVMLGLDSAGKTTALYRL---KFDQYLNTVPTIG---FNCE-KVKGQIGKCKGIN 69
SS + +++LG GK++ + R KFD TIG N + +V G +
Sbjct: 3 SSLLKVILLGDGGVGKSSLMNRYVTNKFDT--QLFHTIGVEFLNKDLEVDGHF-----VT 55
Query: 70 FLIWDVGGQEKLRPLWKSYTRCTDGIIF---VIDSTDVERMEEVKIELI--KTIKNNDNF 124
IWD GQE+ R L + R +D + V DS + + K E I +K ++F
Sbjct: 56 LQIWDTAGQERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPESF 115
Query: 125 NVPILILANKQDLP 138
P +IL NK D+P
Sbjct: 116 --PFVILGNKIDIP 127
>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 = 42.7 bits (101), Expect = 2e-05
Identities = 43/157 (27%), Positives = 62/157 (39%), Gaps = 31/157 (19%)
Query: 22 IVMLGLDSAGKTTALYRLKFDQY-LNTVPTIGFNCEKVK--GQIGKCKGINFLIWDVGGQ 78
+V++G GKTT + R ++ V T+G + GK I F +WD GQ
Sbjct: 3 LVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLDFHTNRGK---IRFNVWDTAGQ 59
Query: 79 EKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDN---------FNVPIL 129
EK L Y I + D T T KN N N+PI+
Sbjct: 60 EKFGGLRDGYYIQGQCAIIMFDVTSRV-----------TYKNVPNWHRDLVRVCENIPIV 108
Query: 130 ILANKQDLPNA-IQIKQIE----KLLGLYELNNMHLY 161
+ NK D+ + ++ KQI K L YE++ Y
Sbjct: 109 LCGNKVDIKDRKVKPKQITFHRKKNLQYYEISAKSNY 145
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 43.4 bits (102), Expect = 2e-05
Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 66 KGINFLIWDVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFN 125
K I IWD GQE R + +SY R G + V D T E + ++ + + N N
Sbjct: 53 KPIKLQIWDTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLA-SWLEDARQHANAN 111
Query: 126 VPILILANKQDL 137
+ I+++ NK DL
Sbjct: 112 MTIMLIGNKCDL 123
>gnl|CDD|206741 cd09914, RocCOR, Ras of complex proteins (Roc) C-terminal of Roc
(COR) domain family. RocCOR (or Roco) protein family is
characterized by a superdomain containing a Ras-like
GTPase domain, called Roc (Ras of complex proteins), and
a characteristic second domain called COR (C-terminal of
Roc). A kinase domain and diverse regulatory domains are
also often found in Roco proteins. Their functions are
diverse; in Dictyostelium discoideum, which encodes 11
Roco proteins, they are involved in cell division,
chemotaxis and development, while in human, where 4 Roco
proteins (LRRK1, LRRK2, DAPK1, and MFHAS1) are encoded,
these proteins are involved in epilepsy and cancer.
Mutations in LRRK2 (leucine-rich repeat kinase 2) are
known to cause familial Parkinson's disease.
Length = 161
Score = 42.3 bits (100), Expect = 3e-05
Identities = 31/153 (20%), Positives = 56/153 (36%), Gaps = 7/153 (4%)
Query: 25 LGLDSAGKTTALYRLKFDQYL-NTVPTIGFNCEKVKGQIGKCKGINFLIWDVGGQEKLRP 83
+G GKT+ +L +++ + T G N + K + K I +WD GGQE
Sbjct: 7 VGQGGVGKTSLCKQLIGEKFDGDESSTHGINVQDWKIPAPERKKIRLNVWDFGGQEIYHA 66
Query: 84 LWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLPNAIQI 143
+ + + V D + + V L + IK P++++ D I
Sbjct: 67 THQFFLTSRSLYLLVFDLRTGDEVSRVPYWL-RQIKAFGG-VSPVILVGTHIDESCDEDI 124
Query: 144 KQIEKLLGLYELNNMHLYYIQATCAITGDGLHE 176
+ K L ++ + G G+ E
Sbjct: 125 LK--KALNKKFPAIINDIHF--VSCKNGKGIAE 153
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 42.4 bits (99), Expect = 3e-05
Identities = 28/91 (30%), Positives = 43/91 (47%), Gaps = 1/91 (1%)
Query: 68 INFLIWDVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVP 127
+ +WD GQE+ R L SY R + I V D T+ + E + I+ I N +V
Sbjct: 29 VRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDITNRQSFENTT-KWIQDILNERGKDVI 87
Query: 128 ILILANKQDLPNAIQIKQIEKLLGLYELNNM 158
I ++ NK DL + ++ E + E N M
Sbjct: 88 IALVGNKTDLGDLRKVTYEEGMQKAQEYNTM 118
>gnl|CDD|214541 smart00173, RAS, Ras subfamily of RAS small GTPases. Similar in
fold and function to the bacterial EF-Tu GTPase. p21Ras
couples receptor Tyr kinases and G protein receptors to
protein kinase cascades.
Length = 164
Score = 41.8 bits (99), Expect = 4e-05
Identities = 26/78 (33%), Positives = 40/78 (51%), Gaps = 4/78 (5%)
Query: 72 IWDVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKI--ELIKTIKNNDNFNVPIL 129
I D GQE+ + Y R +G + V TD + EE+K E I +K+ D+ VPI+
Sbjct: 52 ILDTAGQEEFSAMRDQYMRTGEGFLLVYSITDRQSFEEIKKFREQILRVKDRDD--VPIV 109
Query: 130 ILANKQDLPNAIQIKQIE 147
++ NK DL + + E
Sbjct: 110 LVGNKCDLESERVVSTEE 127
>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 = 41.4 bits (97), Expect = 8e-05
Identities = 39/139 (28%), Positives = 59/139 (42%), Gaps = 27/139 (19%)
Query: 21 HIVMLGLDSA-GKTTALYRLKFDQYL--NTVPTIGFNCE---------KVKGQIGKCKGI 68
VML DS GKT L R K +L + + T+G KVK QI
Sbjct: 1 FKVMLVGDSGVGKTCLLVRFKDGAFLAGSFIATVGIQFTNKVVTVDGVKVKLQI------ 54
Query: 69 NFLIWDVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIEL--IKTIKNNDNFNV 126
WD GQE+ R + +Y R ++ + D T+ + ++ L I +D V
Sbjct: 55 ----WDTAGQERFRSVTHAYYRDAHALLLLYDVTNKSSFDNIRAWLTEILEYAQSD---V 107
Query: 127 PILILANKQDLPNAIQIKQ 145
I++L NK D+ +K+
Sbjct: 108 VIMLLGNKADMSGERVVKR 126
>gnl|CDD|197466 smart00010, small_GTPase, Small GTPase of the Ras superfamily;
ill-defined subfamily. SMART predicts Ras-like small
GTPases of the ARF, RAB, RAN, RAS, and SAR subfamilies.
Others that could not be classified in this way are
predicted to be members of the small GTPase superfamily
without predictions of the subfamily.
Length = 166
Score = 41.0 bits (97), Expect = 9e-05
Identities = 25/70 (35%), Positives = 37/70 (52%), Gaps = 4/70 (5%)
Query: 72 IWDVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKI--ELIKTIKNNDNFNVPIL 129
I D GQE+ + Y R +G + V TD + EE+ E I +K+ D+ VPI+
Sbjct: 54 ILDTAGQEEFSAMRDQYMRTGEGFLLVYSITDRQSFEEIAKFREQILRVKDRDD--VPIV 111
Query: 130 ILANKQDLPN 139
++ NK DL N
Sbjct: 112 LVGNKCDLEN 121
>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 = 40.7 bits (96), Expect = 9e-05
Identities = 22/80 (27%), Positives = 40/80 (50%), Gaps = 5/80 (6%)
Query: 68 INFLIWDVGGQE--KLRPLWKSYTRCTDGIIFVIDSTDVERMEEVK--IELIKTIKNNDN 123
++ I D GQ+ + + R DG + V TD + V ++LI+ IK D
Sbjct: 47 VSLEIQDTPGQQQNEDPESLERSLRWADGFVLVYSITDRSSFDVVSQLLQLIREIKKRDG 106
Query: 124 FNVPILILANKQDLPNAIQI 143
+P++++ NK DL ++ Q+
Sbjct: 107 -EIPVILVGNKADLLHSRQV 125
>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 = 41.0 bits (96), Expect = 1e-04
Identities = 40/127 (31%), Positives = 59/127 (46%), Gaps = 7/127 (5%)
Query: 22 IVMLGLDSAGKTTALYRLKFDQYL---NTVPTIGFNCEKVKGQIGKCKGINFLIWDVGGQ 78
IV++G GKT L R +F Q L TIG + +I K I IWD GQ
Sbjct: 10 IVLIGNAGVGKT-CLVR-RFTQGLFPPGQGATIGVDFMIKTVEIKGEK-IKLQIWDTAGQ 66
Query: 79 EKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLP 138
E+ R + +SY R + +I D T E + E ++ I+ N V +++ NK DL
Sbjct: 67 ERFRSITQSYYRSANALILTYDITCEESFRCLP-EWLREIEQYANNKVITILVGNKIDLA 125
Query: 139 NAIQIKQ 145
++ Q
Sbjct: 126 ERREVSQ 132
>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 = 40.6 bits (95), Expect = 1e-04
Identities = 37/136 (27%), Positives = 59/136 (43%), Gaps = 14/136 (10%)
Query: 22 IVMLGLDSAGKTTALYRL---KFDQYLNTVPTIGFNCEKVKGQIGKCKGINFLIWDVGGQ 78
IVMLG GK+ + F Y + PTI + K + +I + I D GQ
Sbjct: 5 IVMLGAGGVGKSAVTMQFISHSFPDYHD--PTIE-DAYKTQARIDN-EPALLDILDTAGQ 60
Query: 79 EKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVK--IELIKTIKNNDNFNVPILILANKQD 136
+ + Y RC +G I TD +E ELI ++ + ++P++++ NK D
Sbjct: 61 AEFTAMRDQYMRCGEGFIICYSVTDRHSFQEASEFKELITRVRLTE--DIPLVLVGNKVD 118
Query: 137 LPNAIQIKQIEKLLGL 152
L Q +Q+ G
Sbjct: 119 LE---QQRQVTTEEGR 131
>gnl|CDD|133338 cd04138, H_N_K_Ras_like, Ras GTPase family containing H-Ras,N-Ras
and K-Ras4A/4B. H-Ras/N-Ras/K-Ras subfamily. H-Ras,
N-Ras, and K-Ras4A/4B are the prototypical members of
the Ras family. These isoforms generate distinct signal
outputs despite interacting with a common set of
activators and effectors, and are strongly associated
with oncogenic progression in tumor initiation. Mutated
versions of Ras that are insensitive to GAP stimulation
(and are therefore constitutively active) are found in a
significant fraction of human cancers. Many Ras guanine
nucleotide exchange factors (GEFs) have been identified.
They are sequestered in the cytosol until activation by
growth factors triggers recruitment to the plasma
membrane or Golgi, where the GEF colocalizes with Ras.
Active (GTP-bound) Ras interacts with several effector
proteins that stimulate a variety of diverse cytoplasmic
signaling activities. Some are known to positively
mediate the oncogenic properties of Ras, including Raf,
phosphatidylinositol 3-kinase (PI3K), RalGEFs, and
Tiam1. Others are proposed to play negative regulatory
roles in oncogenesis, including RASSF and NORE/MST1.
Most Ras proteins contain a lipid modification site at
the C-terminus, with a typical sequence motif CaaX,
where a = an aliphatic amino acid and X = any amino
acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 162
Score = 40.1 bits (94), Expect = 2e-04
Identities = 21/70 (30%), Positives = 36/70 (51%), Gaps = 4/70 (5%)
Query: 72 IWDVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKI--ELIKTIKNNDNFNVPIL 129
I D GQE+ + Y R +G + V + E++ E IK +K++D+ VP++
Sbjct: 53 ILDTAGQEEYSAMRDQYMRTGEGFLCVFAINSRKSFEDIHTYREQIKRVKDSDD--VPMV 110
Query: 130 ILANKQDLPN 139
++ NK DL
Sbjct: 111 LVGNKCDLAA 120
>gnl|CDD|214595 smart00275, G_alpha, G protein alpha subunit. Subunit of G
proteins that contains the guanine nucleotide binding
site.
Length = 342
Score = 41.0 bits (97), Expect = 2e-04
Identities = 29/86 (33%), Positives = 40/86 (46%), Gaps = 18/86 (20%)
Query: 66 KGINFLIWDVGGQEKLRPLWKSYTRCTDG---IIFVI-----DSTDVE-----RMEEVKI 112
K + F ++DVGGQ R W C D IIF + D E RM+E +
Sbjct: 182 KKLFFRMFDVGGQRSERKKW---IHCFDNVTAIIFCVALSEYDQVLEEDESTNRMQE-SL 237
Query: 113 ELIKTIKNNDNF-NVPILILANKQDL 137
L ++I N+ F N I++ NK DL
Sbjct: 238 NLFESICNSRWFANTSIILFLNKIDL 263
>gnl|CDD|206702 cd04129, Rho2, Ras homology family 2 (Rho2) of small guanosine
triphosphatases (GTPases). Rho2 is a fungal GTPase that
plays a role in cell morphogenesis, control of cell wall
integrity, control of growth polarity, and maintenance
of growth direction. Rho2 activates the protein kinase C
homolog Pck2, and Pck2 controls Mok1, the major (1-3)
alpha-D-glucan synthase. Together with Rho1 (RhoA), Rho2
regulates the construction of the cell wall. Unlike
Rho1, Rho2 is not an essential protein, but its
overexpression is lethal. Most Rho proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for proper intracellular localization via
membrane attachment. As with other Rho family GTPases,
the GDP/GTP cycling is regulated by GEFs (guanine
nucleotide exchange factors), GAPs (GTPase-activating
proteins) and GDIs (guanine nucleotide dissociation
inhibitors).
Length = 190
Score = 40.2 bits (94), Expect = 2e-04
Identities = 41/129 (31%), Positives = 66/129 (51%), Gaps = 28/129 (21%)
Query: 22 IVMLGLDSAGKTTALYRL---KF-DQYLNTVPTIGFN----CEKVKGQIGKCKGINFLIW 73
+V++G + GKT+ LY +F ++Y PT+ N C V G K + +W
Sbjct: 4 LVIVGDGACGKTSLLYVFTLGEFPEEY---HPTVFENYVTDCR-VDG-----KPVQLALW 54
Query: 74 DVGGQ---EKLRPLWKSYTRCTDGII-FVIDSTD-VERMEEVKIELIKTIKNNDNFNVPI 128
D GQ E+LRPL SY++ +I F ID+ D +E + IE ++ NVP+
Sbjct: 55 DTAGQEEYERLRPL--SYSKAHVILIGFAIDTPDSLENVRTKWIEEVRRYCP----NVPV 108
Query: 129 LILANKQDL 137
+++ K+DL
Sbjct: 109 ILVGLKKDL 117
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 39.8 bits (93), Expect = 3e-04
Identities = 21/76 (27%), Positives = 34/76 (44%)
Query: 72 IWDVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILIL 131
I D GQE+ + Y R G + V T EE+ + ++ D VP++++
Sbjct: 57 ILDTAGQEEYSAMRDQYMRTGQGFLCVYSITSRSSFEEIASFREQILRVKDKDRVPMILV 116
Query: 132 ANKQDLPNAIQIKQIE 147
NK DL + Q+ E
Sbjct: 117 GNKCDLDSERQVSTGE 132
>gnl|CDD|197554 smart00174, RHO, Rho (Ras homology) subfamily of Ras-like small
GTPases. Members of this subfamily of Ras-like small
GTPases include Cdc42 and Rac, as well as Rho isoforms.
Length = 174
Score = 39.5 bits (93), Expect = 3e-04
Identities = 44/138 (31%), Positives = 66/138 (47%), Gaps = 24/138 (17%)
Query: 22 IVMLGLDSA-GKTTALYRLKFDQY-LNTVPTIGFN---CEKVKGQIGKCKGINFLIWDVG 76
+V++G D A GKT L + + + VPT+ N +V G+ + +WD
Sbjct: 1 LVVVG-DGAVGKTCLLIVYTTNAFPEDYVPTVFENYSADVEVDGKP-----VELGLWDTA 54
Query: 77 GQE---KLRPLWKSYTRCTDGII--FVIDSTDVERMEEVKIELIKTIKNNDNFNVPILIL 131
GQE +LRPL SY TD + F +DS E VK + +K+ NVPI+++
Sbjct: 55 GQEDYDRLRPL--SYPD-TDVFLICFSVDSPA--SFENVKEKWYPEVKHFCP-NVPIILV 108
Query: 132 ANKQDLPNAIQIKQIEKL 149
K DL N +E+L
Sbjct: 109 GTKLDLRN--DKSTLEEL 124
>gnl|CDD|234395 TIGR03918, GTP_HydF, [FeFe] hydrogenase H-cluster maturation GTPase
HydF. This model describes the family of the [Fe]
hydrogenase maturation protein HypF as characterized in
Chlamydomonas reinhardtii and found, in an operon with
radical SAM proteins HydE and HydG, in numerous
bacteria. It has GTPase activity, can bind an 4Fe-4S
cluster, and is essential for hydrogenase activity
[Protein fate, Protein modification and repair].
Length = 391
Score = 39.8 bits (94), Expect = 5e-04
Identities = 23/97 (23%), Positives = 45/97 (46%), Gaps = 17/97 (17%)
Query: 92 TDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLPNAIQIKQIEKLLG 151
TD + V+D+ E ++ELI+ +K +P +++ NK DL + +
Sbjct: 86 TDLALLVVDAGV--GPGEYELELIEELKER---KIPYIVVINKIDLGEESAELEKLE--- 137
Query: 152 LYELNNMHLYYIQATCAITGDGLHEGINELYQLILKK 188
+ + ++ A+TG EGI+EL + I++
Sbjct: 138 --KKFGLPPIFV---SALTG----EGIDELKEAIIEL 165
>gnl|CDD|206674 cd01887, IF2_eIF5B, Initiation Factor 2 (IF2)/ eukaryotic
Initiation Factor 5B (eIF5B) family. IF2/eIF5B
contribute to ribosomal subunit joining and function as
GTPases that are maximally activated by the presence of
both ribosomal subunits. As seen in other GTPases,
IF2/IF5B undergoes conformational changes between its
GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess
three characteristic segments, including a divergent
N-terminal region followed by conserved central and
C-terminal segments. This core region is conserved among
all known eukaryotic and archaeal IF2/eIF5Bs and
eubacterial IF2s.
Length = 169
Score = 38.6 bits (91), Expect = 5e-04
Identities = 29/101 (28%), Positives = 42/101 (41%), Gaps = 14/101 (13%)
Query: 91 CTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLPNAIQ-----IKQ 145
TD I V+ + + V + I+ I + NVPI++ NK D P + +K
Sbjct: 72 VTDIAILVVAA-----DDGVMPQTIEAINHAKAANVPIIVAINKIDKPYGTEADPERVKN 126
Query: 146 IEKLLGLYELNNMHLYYIQATCAITGDGLHEGINELYQLIL 186
LGL I A TG EGI++L + IL
Sbjct: 127 ELSELGLVGEEWGGDVSIVPISAKTG----EGIDDLLEAIL 163
>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 = 39.4 bits (93), Expect = 5e-04
Identities = 35/105 (33%), Positives = 46/105 (43%), Gaps = 25/105 (23%)
Query: 48 VPTIGFNCEKVKGQIGKCKGINFLIWDVGGQEKLRPLWKSYTRCTDG---IIFVI----- 99
V T G K + F ++DVGGQ R W C + IIFV+
Sbjct: 146 VKTTGIIETDFS-----IKNLKFRMFDVGGQRSERKKW---IHCFEDVTAIIFVVALSEY 197
Query: 100 DSTDVE-----RMEEVKIELIKTIKNNDNF-NVP-ILILANKQDL 137
D VE RM+E ++L +I N+ F N IL L NK+DL
Sbjct: 198 DQVLVEDESVNRMQE-SLKLFDSICNSRWFANTSIILFL-NKKDL 240
>gnl|CDD|206701 cd04128, Spg1, Septum-promoting GTPase (Spg1). Spg1p. Spg1p
(septum-promoting GTPase) was first identified in the
fission yeast S. pombe, where it regulates septum
formation in the septation initiation network (SIN)
through the cdc7 protein kinase. Spg1p is an essential
gene that localizes to the spindle pole bodies. When
GTP-bound, it binds cdc7 and causes it to translocate to
spindle poles. Sid4p (septation initiation defective) is
required for localization of Spg1p to the spindle pole
body, and the ability of Spg1p to promote septum
formation from any point in the cell cycle depends on
Sid4p. Spg1p is negatively regulated by Byr4 and cdc16,
which form a two-component GTPase activating protein
(GAP) for Spg1p. The existence of a SIN-related pathway
in plants has been proposed. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization.
Length = 182
Score = 38.9 bits (91), Expect = 5e-04
Identities = 29/114 (25%), Positives = 52/114 (45%), Gaps = 7/114 (6%)
Query: 20 VHIVMLGLDSAGKTTALYRL---KFDQYLNTVPTIGFNCEKVKGQIGKCKGINFLIWDVG 76
+ I +LG GKT+ + + +FD+ + T+G N + I I F IWD+G
Sbjct: 1 LKIGLLGDAQIGKTSLMVKYVEGEFDE--EYIQTLGVNFMEKTISIRG-TEITFSIWDLG 57
Query: 77 GQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILI 130
GQ + + + I+F+ D T + +K E + + + +PIL+
Sbjct: 58 GQREFINMLPLVCKDAVAILFMFDLTRKSTLNSIK-EWYRQARGFNKTAIPILV 110
>gnl|CDD|133377 cd04177, RSR1, RSR1/Bud1p family GTPase. RSR1/Bud1p is a member of
the Rap subfamily of the Ras family that is found in
fungi. In budding yeasts, RSR1 is involved in selecting
a site for bud growth on the cell cortex, which directs
the establishment of cell polarization. The Rho family
GTPase cdc42 and its GEF, cdc24, then establish an axis
of polarized growth by organizing the actin cytoskeleton
and secretory apparatus at the bud site. It is believed
that cdc42 interacts directly with RSR1 in vivo. In
filamentous fungi, polar growth occurs at the tips of
hypha and at novel growth sites along the extending
hypha. In Ashbya gossypii, RSR1 is a key regulator of
hyphal growth, localizing at the tip region and
regulating in apical polarization of the actin
cytoskeleton. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras proteins.
Length = 168
Score = 38.6 bits (90), Expect = 6e-04
Identities = 32/129 (24%), Positives = 59/129 (45%), Gaps = 13/129 (10%)
Query: 21 HIVMLGLDSAGKTTALYRLKFDQYLNTV-PTIGFNCEK---VKGQIGKCKGINFLIWDVG 76
IV+LG GK+ + + ++ + PTI + K + G+ + I D
Sbjct: 3 KIVVLGAGGVGKSALTVQFVQNVFIESYDPTIEDSYRKQVEIDGRQ-----CDLEILDTA 57
Query: 77 GQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKI--ELIKTIKNNDNFNVPILILANK 134
G E+ + + Y + G + V T + E+ E + IK++DN VP++++ NK
Sbjct: 58 GTEQFTAMRELYIKSGQGFLLVYSVTSEASLNELGELREQVLRIKDSDN--VPMVLVGNK 115
Query: 135 QDLPNAIQI 143
DL + Q+
Sbjct: 116 ADLEDDRQV 124
>gnl|CDD|133326 cd04126, Rab20, Rab GTPase family 20 (Rab20). Rab20 is one of
several Rab proteins that appear to be restricted in
expression to the apical domain of murine polarized
epithelial cells. It is expressed on the apical side of
polarized kidney tubule and intestinal epithelial cells,
and in non-polarized cells. It also localizes to
vesico-tubular structures below the apical brush border
of renal proximal tubule cells and in the apical region
of duodenal epithelial cells. Rab20 has also been shown
to colocalize with vacuolar H+-ATPases (V-ATPases) in
mouse kidney cells, suggesting a role in the regulation
of V-ATPase traffic in specific portions of the nephron.
It was also shown to be one of several proteins whose
expression is upregulated in human myelodysplastic
syndrome (MDS) patients. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 220
Score = 38.7 bits (90), Expect = 8e-04
Identities = 34/120 (28%), Positives = 60/120 (50%), Gaps = 10/120 (8%)
Query: 20 VHIVMLGLDSAGKTTALYRLKFDQYLNTVPTIG--FNCEKVKGQIGKCKGINFLIWDVGG 77
+ +V+LG + GKT+ L+R ++ +TV T+G F + Q G N IWD G
Sbjct: 1 LKVVLLGDMNVGKTSLLHRYMERRFKDTVSTVGGAFYLK----QWGP---YNISIWDTAG 53
Query: 78 QEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDL 137
+E+ L Y R +I D ++V+ +EE++ + + + N + ++ NK DL
Sbjct: 54 REQFHGLGSMYCRGAAAVILTYDVSNVQSLEELEDRFL-GLTDTANEDCLFAVVGNKLDL 112
>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 = 38.1 bits (89), Expect = 0.001
Identities = 22/100 (22%), Positives = 46/100 (46%), Gaps = 10/100 (10%)
Query: 90 RCTDGIIFVIDSTDVERMEEVK--IELIKTIKNNDNF--NVPILILANKQDLPNAIQIKQ 145
+D I+ VID+++ + ++ L + + + F N P +I+ANK D+ + +K+
Sbjct: 74 YRSDLILHVIDASEDCVGDPLEDQKTLNEEVSGSFLFLKNKPEMIVANKIDMASENNLKR 133
Query: 146 IEKLLGLYELNNMHLYYIQATCAITGDGLHEGINELYQLI 185
++ + T A+T GL I + +L+
Sbjct: 134 LKL------DKLKRGIPVVPTSALTRLGLDRVIRTIRKLL 167
>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 = 37.8 bits (88), Expect = 0.001
Identities = 31/134 (23%), Positives = 63/134 (47%), Gaps = 6/134 (4%)
Query: 20 VHIVMLGLDSAGKTTALYRLKFDQYLNTV-PTIGFNCEKVKGQIGKCK-GINFLIWDVGG 77
+ ++++G + GK++ + R + TIG + + + + + + ++WD G
Sbjct: 1 IKVIVVGNGNVGKSSMIQRFVKGIFTKDYKKTIGVDFLEKQIFLRQSDEDVRLMLWDTAG 60
Query: 78 QEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDL 137
QE+ + K+Y R I V +TD E E IE K + ++P++++ K DL
Sbjct: 61 QEEFDAITKAYYRGAQACILVFSTTDRESFE--AIESWKEKVEAECGDIPMVLVQTKIDL 118
Query: 138 PN--AIQIKQIEKL 149
+ I ++ E L
Sbjct: 119 LDQAVITNEEAEAL 132
>gnl|CDD|133324 cd04124, RabL2, Rab GTPase-like family 2 (Rab-like2). RabL2
(Rab-like2) subfamily. RabL2s are novel Rab proteins
identified recently which display features that are
distinct from other Rabs, and have been termed Rab-like.
RabL2 contains RabL2a and RabL2b, two very similar Rab
proteins that share > 98% sequence identity in humans.
RabL2b maps to the subtelomeric region of chromosome
22q13.3 and RabL2a maps to 2q13, a region that suggests
it is also a subtelomeric gene. Both genes are believed
to be expressed ubiquitously, suggesting that RabL2s are
the first example of duplicated genes in human proximal
subtelomeric regions that are both expressed actively.
Like other Rab-like proteins, RabL2s lack a prenylation
site at the C-terminus. The specific functions of RabL2a
and RabL2b remain unknown. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization.
Length = 161
Score = 37.5 bits (87), Expect = 0.001
Identities = 44/153 (28%), Positives = 66/153 (43%), Gaps = 20/153 (13%)
Query: 20 VHIVMLGLDSAGKTTALYRLKFDQY----LNTVP-TIGFNCEKVKGQIGKCKGINFLIWD 74
V I++LG + GK+ + R D Y L+T T+ + K +G K I WD
Sbjct: 1 VKIILLGDSAVGKSKLVERFLMDGYEPQQLSTYALTLYKHNAKFEG-----KTILVDFWD 55
Query: 75 VGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNF--NVPILILA 132
GQE+ + + SY I V DV R K L K + + +P +++A
Sbjct: 56 TAGQERFQTMHASYYHKAHACILVF---DVTRKITYK-NLSKWYEELREYRPEIPCIVVA 111
Query: 133 NKQDLPNAIQIKQIEKLLGLYELNNMHLYYIQA 165
NK DL +K E +N+ LYY+ A
Sbjct: 112 NKIDL----DPSVTQKKFNFAEKHNLPLYYVSA 140
>gnl|CDD|206711 cd04140, ARHI_like, A Ras homolog member I (ARHI). ARHI (A Ras
homolog member I) is a member of the Ras family with
several unique structural and functional properties.
ARHI is expressed in normal human ovarian and breast
tissue, but its expression is decreased or eliminated in
breast and ovarian cancer. ARHI contains an N-terminal
extension of 34 residues (human) that is required to
retain its tumor suppressive activity. Unlike most other
Ras family members, ARHI is maintained in the
constitutively active (GTP-bound) state in resting cells
and has modest GTPase activity. ARHI inhibits STAT3
(signal transducers and activators of transcription 3),
a latent transcription factor whose abnormal activation
plays a critical role in oncogenesis. Most Ras proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 165
Score = 37.5 bits (87), Expect = 0.001
Identities = 34/120 (28%), Positives = 54/120 (45%), Gaps = 9/120 (7%)
Query: 22 IVMLGLDSAGKTTALYRLKFDQYLNT-VPTIGFNCEKVKGQIGKC-KGINFL-IWDVGGQ 78
+V+ G GK++ + R + + +PTI E Q+ C K I L I D G
Sbjct: 4 VVVFGAGGVGKSSLVLRFVKGTFRESYIPTI----EDTYRQVISCSKSICTLQITDTTGS 59
Query: 79 EKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVK--IELIKTIKNNDNFNVPILILANKQD 136
+ + + I V T + +EE+K ELI IK N+ +PI+++ NK D
Sbjct: 60 HQFPAMQRLSISKGHAFILVYSITSKQSLEELKPIYELICEIKGNNLEKIPIMLVGNKCD 119
>gnl|CDD|217025 pfam02421, FeoB_N, Ferrous iron transport protein B. Escherichia
coli has an iron(II) transport system (feo) which may
make an important contribution to the iron supply of the
cell under anaerobic conditions. FeoB has been
identified as part of this transport system. FeoB is a
large 700-800 amino acid integral membrane protein. The
N terminus contains a P-loop motif suggesting that iron
transport may be ATP dependent.
Length = 190
Score = 37.5 bits (88), Expect = 0.002
Identities = 24/105 (22%), Positives = 48/105 (45%), Gaps = 20/105 (19%)
Query: 93 DGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLPNA----IQIKQIEK 148
D II V+D+T++ER + ++L++ +P+++ N D I IK++ +
Sbjct: 80 DVIINVVDATNLERNLYLTLQLLE-------LGIPVVVALNMMDEAEKKGIKIDIKKLSE 132
Query: 149 LLGLYELNNMHLYYIQATCAITGDGLHEGINELYQLILKKRKLQK 193
LLG+ + T A G+G+ E + + ++ K
Sbjct: 133 LLGV---------PVVPTSARKGEGIDELKDAIIEVAEGKVPPAP 168
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 38.2 bits (90), Expect = 0.002
Identities = 22/97 (22%), Positives = 43/97 (44%), Gaps = 25/97 (25%)
Query: 93 DGIIFVIDSTDVERMEEVKI-ELIKTIKNNDNFNVPILILANKQDLPNAIQIKQIEKLLG 151
D ++ V+D+++ E+ +I E +K + P++++ NK DL I +++
Sbjct: 296 DLVLLVLDASEPLTEEDDEILEELK--------DKPVIVVLNKADLTGEIDLEEENGKPV 347
Query: 152 LYELNNMHLYYIQATCAITGDGLHEGINELYQLILKK 188
+ A TG EGI+EL + I +
Sbjct: 348 I------------RISAKTG----EGIDELREAIKEL 368
>gnl|CDD|206698 cd04117, Rab15, Rab GTPase family 15 (Rab15). Rab15 colocalizes
with the transferrin receptor in early endosome
compartments, but not with late endosomal markers. It
codistributes with Rab4 and Rab5 on early/sorting
endosomes, and with Rab11 on pericentriolar recycling
endosomes. It is believed to function as an inhibitory
GTPase that regulates distinct steps in early endocytic
trafficking. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation of
the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 164
Score = 37.3 bits (86), Expect = 0.002
Identities = 40/167 (23%), Positives = 75/167 (44%), Gaps = 7/167 (4%)
Query: 22 IVMLGLDSAGKTTALYRLKFDQYLNT-VPTIGFNCEKVKGQIGKCKGINFLIWDVGGQEK 80
++++G GKT L R +++ ++ + TIG + + ++ K + IWD GQE+
Sbjct: 3 LLLIGDSGVGKTCLLCRFTDNEFHSSHISTIGVDFKMKTIEVDGIK-VRIQIWDTAGQER 61
Query: 81 LRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLPNA 140
+ + K Y R GI V D + ER + ++ + + V +++ NK D
Sbjct: 62 YQTITKQYYRRAQGIFLVYDISS-ERSYQHIMKWVSDVDEYAPEGVQKILIGNKADEEQK 120
Query: 141 IQIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEGINELYQLILK 187
Q+ E+ L + M + T A T + E L +L+L+
Sbjct: 121 RQVGD-EQGNKLAKEYGMDFF---ETSACTNKNIKESFTRLTELVLQ 163
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 37.9 bits (89), Expect = 0.002
Identities = 22/95 (23%), Positives = 45/95 (47%), Gaps = 19/95 (20%)
Query: 93 DGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLPNAIQIKQIEKLLGL 152
D ++FV+D++ ++ + LI+ + PI+++ NK DL + I+++ + G
Sbjct: 298 DLVLFVLDASQPL--DKEDLALIELLPKK----KPIIVVLNKADLVSKIELESEKLANG- 350
Query: 153 YELNNMHLYYIQATCAITGDGLHEGINELYQLILK 187
I + A TG EG++ L + I +
Sbjct: 351 --------DAIISISAKTG----EGLDALREAIKQ 373
>gnl|CDD|206692 cd04107, Rab32_Rab38, Rab GTPase families 18 (Rab18) and 32
(Rab32). Rab38/Rab32 subfamily. Rab32 and Rab38 are
members of the Rab family of small GTPases. Human Rab32
was first identified in platelets but it is expressed in
a variety of cell types, where it functions as an
A-kinase anchoring protein (AKAP). Rab38 has been shown
to be melanocyte-specific. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 201
Score = 36.9 bits (86), Expect = 0.003
Identities = 32/122 (26%), Positives = 54/122 (44%), Gaps = 5/122 (4%)
Query: 72 IWDVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEV---KIELIKTIKNNDNFNVPI 128
+WD+ GQE+ + + Y + G I V D T E V K +L + + +P
Sbjct: 54 LWDIAGQERFGGMTRVYYKGAVGAIIVFDVTRPSTFEAVLKWKADLDSKVTLPNGEPIPA 113
Query: 129 LILANKQDLPNAIQIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEGINELYQLILKK 188
L+LANK DL ++ + + + + N + + T A + E + L + ILK
Sbjct: 114 LLLANKCDLKKE-RLAKDPEQMDQFCKENGFIGWF-ETSAKENINIEEAMRFLVKNILKN 171
Query: 189 RK 190
K
Sbjct: 172 DK 173
>gnl|CDD|206655 cd01862, Rab7, Rab GTPase family 7 (Rab7). Rab7 subfamily. Rab7 is
a small Rab GTPase that regulates vesicular traffic from
early to late endosomal stages of the endocytic pathway.
The yeast Ypt7 and mammalian Rab7 are both involved in
transport to the vacuole/lysosome, whereas Ypt7 is also
required for homotypic vacuole fusion. Mammalian Rab7 is
an essential participant in the autophagic pathway for
sequestration and targeting of cytoplasmic components to
the lytic compartment. Mammalian Rab7 is also proposed
to function as a tumor suppressor. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 172
Score = 35.7 bits (83), Expect = 0.005
Identities = 22/69 (31%), Positives = 34/69 (49%), Gaps = 3/69 (4%)
Query: 72 IWDVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEV---KIELIKTIKNNDNFNVPI 128
IWD GQE+ + L ++ R D + V D T+ + E + + E + D N P
Sbjct: 53 IWDTAGQERFQSLGVAFYRGADCCVLVYDVTNPKSFESLDSWRDEFLIQASPRDPENFPF 112
Query: 129 LILANKQDL 137
++L NK DL
Sbjct: 113 VVLGNKIDL 121
>gnl|CDD|206667 cd01879, FeoB, Ferrous iron transport protein B (FeoB) family.
Ferrous iron transport protein B (FeoB) subfamily. E.
coli has an iron(II) transport system, known as feo,
which may make an important contribution to the iron
supply of the cell under anaerobic conditions. FeoB has
been identified as part of this transport system. FeoB
is a large 700-800 amino acid integral membrane protein.
The N terminus contains a P-loop motif suggesting that
iron transport may be ATP dependent.
Length = 159
Score = 35.5 bits (83), Expect = 0.007
Identities = 25/99 (25%), Positives = 46/99 (46%), Gaps = 24/99 (24%)
Query: 93 DGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLPNA----IQIKQIEK 148
D I+ V+D+T++ER + ++L++ +P+++ N D I + ++ +
Sbjct: 77 DLIVNVVDATNLERNLYLTLQLLE-------LGLPVVVALNMIDEAEKRGIKIDLDKLSE 129
Query: 149 LLGLYELNNMHLYYIQATCAITGDGLHEGINELYQLILK 187
LLG+ + T A G EGI+EL I K
Sbjct: 130 LLGV---------PVVPTSARKG----EGIDELLDAIAK 155
>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 = 35.4 bits (82), Expect = 0.007
Identities = 35/148 (23%), Positives = 66/148 (44%), Gaps = 17/148 (11%)
Query: 48 VPTIGFNCEKVKGQIGKCK-GINFLIWDVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVER 106
+PTIG + K + + +NF +D+ G + + + + T G++ V D TD +
Sbjct: 30 LPTIGIDYGVKKVSVRNKEVRVNF--FDLSGHPEYLEVRNEFYKDTQGVLLVYDVTDRQS 87
Query: 107 -------MEEVKIELIKTIKNNDNFNVPILILANKQDLPNAIQIKQIEKLLGLYELNNMH 159
++E+K E + + N+ +++ ANK DL + + E L
Sbjct: 88 FEALDSWLKEMKQEG---GPHGNMENIVVVVCANKIDLTKHRAVSEDEGRLWAESKG--F 142
Query: 160 LYYIQATCAITGDGLHEGINELYQLILK 187
Y+ T A TG+G++E L+ I+
Sbjct: 143 KYF--ETSACTGEGVNEMFQTLFSSIVD 168
>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 = 35.7 bits (82), Expect = 0.008
Identities = 30/125 (24%), Positives = 55/125 (44%), Gaps = 10/125 (8%)
Query: 66 KGINFLIWDVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNF- 124
+ + +WD GQ + +++SY+R GII V D T+ + + + IK D
Sbjct: 53 RRVKLQLWDTSGQGRFCTIFRSYSRGAQGIILVYDITNRWSFDGID----RWIKEIDEHA 108
Query: 125 -NVPILILANKQDLPNAIQIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEGINELYQ 183
VP +++ N+ L Q+ E+ E N M + + C + E EL +
Sbjct: 109 PGVPKILVGNRLHLAFKRQVAT-EQAQAYAERNGMTFFEVSPLCNFN---ITESFTELAR 164
Query: 184 LILKK 188
++L +
Sbjct: 165 IVLMR 169
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 35.8 bits (83), Expect = 0.008
Identities = 37/137 (27%), Positives = 55/137 (40%), Gaps = 28/137 (20%)
Query: 13 QASGSSSVHIVMLGLDSAGKTTALYRL---KFD-QYLNTVPTIGFNCEKVKGQIGKCKGI 68
Q ++++G GKTT + R +F+ +Y +PT+G +K C I
Sbjct: 3 QMDEVPEFKLILVGDGGVGKTTFVKRHLTGEFEKKY---IPTLGVEVHPLKFYT-NCGPI 58
Query: 69 NFLIWDVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNF---- 124
F +WD GQEK L Y I + D T T KN N+
Sbjct: 59 CFNVWDTAGQEKFGGLRDGYYIKGQCAIIMFDVTSRI-----------TYKNVPNWHRDI 107
Query: 125 -----NVPILILANKQD 136
N+PI+++ NK D
Sbjct: 108 VRVCENIPIVLVGNKVD 124
>gnl|CDD|133343 cd04143, Rhes_like, Ras homolog enriched in striatum (Rhes) and
activator of G-protein signaling 1 (Dexras1/AGS1). This
subfamily includes Rhes (Ras homolog enriched in
striatum) and Dexras1/AGS1 (activator of G-protein
signaling 1). These proteins are homologous, but exhibit
significant differences in tissue distribution and
subcellular localization. Rhes is found primarily in the
striatum of the brain, but is also expressed in other
areas of the brain, such as the cerebral cortex,
hippocampus, inferior colliculus, and cerebellum. Rhes
expression is controlled by thyroid hormones. In rat
PC12 cells, Rhes is farnesylated and localizes to the
plasma membrane. Rhes binds and activates PI3K, and
plays a role in coupling serpentine membrane receptors
with heterotrimeric G-protein signaling. Rhes has
recently been shown to be reduced under conditions of
dopamine supersensitivity and may play a role in
determining dopamine receptor sensitivity. Dexras1/AGS1
is a dexamethasone-induced Ras protein that is expressed
primarily in the brain, with low expression levels in
other tissues. Dexras1 localizes primarily to the
cytoplasm, and is a critical regulator of the circadian
master clock to photic and nonphotic input. Most Ras
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins.
Length = 247
Score = 35.1 bits (81), Expect = 0.014
Identities = 38/146 (26%), Positives = 62/146 (42%), Gaps = 23/146 (15%)
Query: 22 IVMLGLDSAGKTTALYRL---KF-DQYLNTVPTIGFNCEKVKGQIGKCKGINFLIWDVGG 77
+V+LG GKT + R +F +QY T+ ++G++ + I D G
Sbjct: 3 MVVLGASKVGKTAIVSRFLGGRFEEQYTPTIEDFHRKLYSIRGEVYQLD-----ILDTSG 57
Query: 78 QEKLRPLWKSYTRCT-DGIIFVIDSTDVERMEEVKIELIKTI---------KNNDNFNVP 127
P + + T D I V + E EEV L + I K +N +P
Sbjct: 58 NHPF-PAMRRLSILTGDVFILVFSLDNRESFEEVC-RLREQILETKSCLKNKTKENVKIP 115
Query: 128 ILILANKQDL--PNAIQIKQIEKLLG 151
++I NK D P +Q ++E+L+G
Sbjct: 116 MVICGNKADRDFPREVQRDEVEQLVG 141
>gnl|CDD|206684 cd01897, NOG, Nucleolar GTP-binding protein (NOG). NOG1 is a
nucleolar GTP-binding protein present in eukaryotes
ranging from trypanosomes to humans. NOG1 is
functionally linked to ribosome biogenesis and found in
association with the nuclear pore complexes and
identified in many preribosomal complexes. Thus, defects
in NOG1 can lead to defects in 60S biogenesis. The S.
cerevisiae NOG1 gene is essential for cell viability,
and mutations in the predicted G motifs abrogate
function. It is a member of the ODN family of
GTP-binding proteins that also includes the bacterial
Obg and DRG proteins.
Length = 167
Score = 34.5 bits (80), Expect = 0.017
Identities = 26/94 (27%), Positives = 46/94 (48%), Gaps = 11/94 (11%)
Query: 95 IIFVIDSTD--VERMEEVKIELIKTIKNNDNFNVPILILANKQDLPNAIQIKQIEKLLGL 152
++F ID ++ +EE ++ L K IK FN P++++ NK DL + +IEK L
Sbjct: 83 VLFFIDPSETCGYSIEE-QLSLFKEIKPL--FNKPVIVVLNKIDLLTEEDLSEIEKELEK 139
Query: 153 YELNNMHLYYIQATCAITGDGLHEGINELYQLIL 186
+ +T +G+ E N+ +L+L
Sbjct: 140 EGEEVIK------ISTLTEEGVDELKNKACELLL 167
>gnl|CDD|128473 smart00176, RAN, Ran (Ras-related nuclear proteins) /TC4 subfamily
of small GTPases. Ran is involved in the active
transport of proteins through nuclear pores.
Length = 200
Score = 34.2 bits (78), Expect = 0.026
Identities = 40/151 (26%), Positives = 59/151 (39%), Gaps = 25/151 (16%)
Query: 25 LGLDSAGKTTALYR-LKFDQYLNTVPTIGFNCEKVKGQIGKCKGINFLIWDVGGQEKLRP 83
+G GKTT + R L + V T+G + I F +WD GQEK
Sbjct: 1 VGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHT-NRGPIRFNVWDTAGQEKFGG 59
Query: 84 LWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNF---------NVPILILANK 134
L Y I + D T R+ T KN N+ N+PI++ NK
Sbjct: 60 LRDGYYIQGQCAIIMFDVT--ARV---------TYKNVPNWHRDLVRVCENIPIVLCGNK 108
Query: 135 QDLPNAIQIKQIEKLLGLYELNNMHLYYIQA 165
D+ + ++K K + + N+ Y I A
Sbjct: 109 VDVKDR-KVKA--KSITFHRKKNLQYYDISA 136
>gnl|CDD|206665 cd01876, YihA_EngB, YihA (EngB) GTPase family. The YihA (EngB)
subfamily of GTPases is typified by the E. coli YihA, an
essential protein involved in cell division control.
YihA and its orthologs are small proteins that typically
contain less than 200 amino acid residues and consists
of the GTPase domain only (some of the eukaryotic
homologs contain an N-terminal extension of about 120
residues that might be involved in organellar
targeting). Homologs of yihA are found in most
Gram-positive and Gram-negative pathogenic bacteria,
with the exception of Mycobacterium tuberculosis. The
broad-spectrum nature of YihA and its essentiality for
cell viability in bacteria make it an attractive
antibacterial target.
Length = 170
Score = 33.3 bits (77), Expect = 0.038
Identities = 17/93 (18%), Positives = 41/93 (44%), Gaps = 7/93 (7%)
Query: 94 GIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQD-LPNAIQIKQIEKLLGL 152
G++ +ID+ + +E+++ ++ +P LI+ K D L + K ++K+
Sbjct: 84 GVVLLIDAR--HGPTPIDLEMLEFLEEL---GIPFLIVLTKADKLKKSELAKVLKKIKEE 138
Query: 153 YELNNMHLYYIQATCAITGDGLHEGINELYQLI 185
L N+ + + G G+ E + + +
Sbjct: 139 LNLFNIL-PPVILFSSKKGTGIDELRALIAEWL 170
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 33.8 bits (78), Expect = 0.041
Identities = 16/60 (26%), Positives = 34/60 (56%), Gaps = 3/60 (5%)
Query: 92 TDGIIFVIDSTDVERME-EVKIELIKTIKNNDNFNVPILILANKQDLPNAIQIKQIEKLL 150
I+F+ D ++ E +I L++ IK + F PI+++ NK D+ + ++++IE +
Sbjct: 248 AGVILFLFDPSETCGYSLEEQISLLEEIK--ELFKAPIVVVINKIDIADEEKLEEIEASV 305
>gnl|CDD|206726 cd04163, Era, E. coli Ras-like protein (Era) is a multifunctional
GTPase. Era (E. coli Ras-like protein) is a
multifunctional GTPase found in all bacteria except some
eubacteria. It binds to the 16S ribosomal RNA (rRNA) of
the 30S subunit and appears to play a role in the
assembly of the 30S subunit, possibly by chaperoning the
16S rRNA. It also contacts several assembly elements of
the 30S subunit. Era couples cell growth with
cytokinesis and plays a role in cell division and energy
metabolism. Homologs have also been found in eukaryotes.
Era contains two domains: the N-terminal GTPase domain
and a C-terminal domain KH domain that is critical for
RNA binding. Both domains are important for Era
function. Era is functionally able to compensate for
deletion of RbfA, a cold-shock adaptation protein that
is required for efficient processing of the 16S rRNA.
Length = 168
Score = 33.2 bits (77), Expect = 0.043
Identities = 20/102 (19%), Positives = 46/102 (45%), Gaps = 13/102 (12%)
Query: 85 WKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDL--PNAIQ 142
W + D ++FV+D+++ E + +++ +K + P++++ NK DL
Sbjct: 77 WSALKDV-DLVLFVVDASE-WIGEGDE-FILELLKKS---KTPVILVLNKIDLVKDKEDL 130
Query: 143 IKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEGINELYQL 184
+ +EKL L+ I A+ G+ + E + + +
Sbjct: 131 LPLLEKLKELHPFAE-----IFPISALKGENVDELLEYIVEY 167
>gnl|CDD|206704 cd04132, Rho4_like, Ras homology family 4 (Rho4) of small guanosine
triphosphatases (GTPases)-like. Rho4 is a GTPase that
controls septum degradation by regulating secretion of
Eng1 or Agn1 during cytokinesis. Rho4 also plays a role
in cell morphogenesis. Rho4 regulates septation and cell
morphology by controlling the actin cytoskeleton and
cytoplasmic microtubules. The localization of Rho4 is
modulated by Rdi1, which may function as a GDI, and by
Rga9, which is believed to function as a GAP. In S.
pombe, both Rho4 deletion and Rho4 overexpression result
in a defective cell wall, suggesting a role for Rho4 in
maintaining cell wall integrity. Most Rho proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins.
Length = 197
Score = 33.5 bits (77), Expect = 0.044
Identities = 49/202 (24%), Positives = 77/202 (38%), Gaps = 30/202 (14%)
Query: 19 SVHIVMLGLDSAGKTTAL--Y-RLKF-DQYLNTVPTIGFNCEKVKGQIGKCKGINFLIWD 74
V IV++G GKT L Y + F ++Y VPT+ F Q+ K I +WD
Sbjct: 3 KVKIVVVGDGGCGKTCLLMVYAQGSFPEEY---VPTV-FENYVTTLQVPNGKIIELALWD 58
Query: 75 VGGQE---KLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNF--NVPIL 129
GQE +LRPL SY D I+ + ++ V+ + + +F PI+
Sbjct: 59 TAGQEDYDRLRPL--SYPD-VDVILICYSVDNPTSLDNVEDKWYPEVN---HFCPGTPIV 112
Query: 130 ILANKQDLPNAIQIKQIEKLLGLYELNNMH----------LYYIQATCAITGDGLHEGIN 179
++ K DL + GL + + YI+ A + + E +
Sbjct: 113 LVGLKTDLRKDKNSVSKLRAQGLEPVTPEQGESVAKSIGAVAYIE-CSAKLMENVDEVFD 171
Query: 180 ELYQLILKKRKLQKTNKMNKVK 201
+ L K K K K
Sbjct: 172 AAINVALSKSGRAARKKKKKKK 193
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 33.8 bits (78), Expect = 0.055
Identities = 26/106 (24%), Positives = 51/106 (48%), Gaps = 24/106 (22%)
Query: 93 DGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLPNA----IQIKQIEK 148
D I+ V+D+T++ER + ++L++ +P+++ N D I I+++ K
Sbjct: 83 DLIVNVVDATNLERNLYLTLQLLE-------LGIPMILALNMIDEAKKRGIRIDIEKLSK 135
Query: 149 LLGLYELNNMHLYYIQATCAITGDGLHEGINELYQLILKKRKLQKT 194
LLG+ + T A G EG+ EL + I++ + + T
Sbjct: 136 LLGV---------PVVPTVAKRG----EGLEELKRAIIELAESKTT 168
>gnl|CDD|206709 cd04137, RheB, Ras Homolog Enriched in Brain (RheB) is a small
GTPase. Rheb (Ras Homolog Enriched in Brain) subfamily.
Rheb was initially identified in rat brain, where its
expression is elevated by seizures or by long-term
potentiation. It is expressed ubiquitously, with
elevated levels in muscle and brain. Rheb functions as
an important mediator between the tuberous sclerosis
complex proteins, TSC1 and TSC2, and the mammalian
target of rapamycin (TOR) kinase to stimulate cell
growth. TOR kinase regulates cell growth by controlling
nutrient availability, growth factors, and the energy
status of the cell. TSC1 and TSC2 form a dimeric complex
that has tumor suppressor activity, and TSC2 is a GTPase
activating protein (GAP) for Rheb. The TSC1/TSC2 complex
inhibits the activation of TOR kinase through Rheb. Rheb
has also been shown to induce the formation of large
cytoplasmic vacuoles in a process that is dependent on
the GTPase cycle of Rheb, but independent of the TOR
kinase, suggesting Rheb plays a role in endocytic
trafficking that leads to cell growth and cell-cycle
progression. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras proteins.
Length = 180
Score = 33.0 bits (76), Expect = 0.056
Identities = 36/130 (27%), Positives = 57/130 (43%), Gaps = 7/130 (5%)
Query: 21 HIVMLGLDSAGKTTALYRLKFDQYLNTV-PTIGFNCEKVKGQIGKCKGINFL--IWDVGG 77
I +LG S GK++ + ++ + PTI E +I KG + I D G
Sbjct: 3 KIAVLGSRSVGKSSLTVQFVEGHFVESYYPTI----ENTFSKIITYKGQEYHLEIVDTAG 58
Query: 78 QEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDL 137
Q++ L + Y+ G I V T + E VK+ K + +VPI+++ NK DL
Sbjct: 59 QDEYSILPQKYSIGIHGYILVYSVTSRKSFEVVKVIYDKILDMLGKESVPIVLVGNKSDL 118
Query: 138 PNAIQIKQIE 147
Q+ E
Sbjct: 119 HMERQVSAEE 128
>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 = 33.2 bits (77), Expect = 0.071
Identities = 24/100 (24%), Positives = 49/100 (49%), Gaps = 13/100 (13%)
Query: 92 TDGIIFVIDSTDVER---MEEVKI---ELIKTIKNNDNFNVPILILANKQDLPNAIQIKQ 145
T ++ +ID + + +E+ +I EL K + + P +++ NK DL + ++++
Sbjct: 236 TRVLLHLIDISPEDGSDPIEDYEIIRNELKKY--SPELAEKPRIVVLNKIDLLDEEELEE 293
Query: 146 IEKLLGLYELNNMHLYYIQATCAITGDGLHEGINELYQLI 185
+ K EL + A+TG+GL E + L +L+
Sbjct: 294 LLK-----ELKEALGKPVFPISALTGEGLDELLYALAELL 328
>gnl|CDD|237039 PRK12288, PRK12288, GTPase RsgA; Reviewed.
Length = 347
Score = 32.9 bits (76), Expect = 0.078
Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 5/53 (9%)
Query: 125 NVPILILANKQDLPNAIQIKQIEKLLGLYELNNMHL-YYIQATCAITGDGLHE 176
+ LI+ NK DL + + + L +Y ++ Y + + TG+GL E
Sbjct: 150 GIEPLIVLNKIDLLDDEGRAFVNEQLDIYR----NIGYRVLMVSSHTGEGLEE 198
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes. TrmE
contains a GTPase domain that forms a canonical Ras-like
fold. It functions a molecular switch GTPase, and
apparently uses a conformational change associated with
GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 32.1 bits (74), Expect = 0.11
Identities = 23/94 (24%), Positives = 44/94 (46%), Gaps = 22/94 (23%)
Query: 95 IIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLPNAIQIKQIEKLLGLYE 154
++ V+D+++ E+++I + P++++ NK DL + G+ E
Sbjct: 86 VLLVVDASEGLDEEDLEILELPA-------KKPVIVVLNKSDL--------LSDAEGISE 130
Query: 155 LNNMHLYYIQATCAITGDGLHEGINELYQLILKK 188
LN + I A TG EGI+EL + +L+
Sbjct: 131 LNGKPIIAIS---AKTG----EGIDELKEALLEL 157
>gnl|CDD|206688 cd04101, RabL4, Rab GTPase-like family 4 (Rab-like4). RabL4
(Rab-like4) subfamily. RabL4s are novel proteins that
have high sequence similarity with Rab family members,
but display features that are distinct from Rabs, and
have been termed Rab-like. As in other Rab-like
proteins, RabL4 lacks a prenylation site at the
C-terminus. The specific function of RabL4 remains
unknown.
Length = 167
Score = 31.7 bits (72), Expect = 0.12
Identities = 13/70 (18%), Positives = 28/70 (40%)
Query: 68 INFLIWDVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVP 127
+ I+D GQE + ++ + V D T+ + + ++ + P
Sbjct: 53 VELFIFDSAGQELFSDMVENVWEQPAVVCVVYDVTNEVSFNNCSRWINRVRTHSHGLHTP 112
Query: 128 ILILANKQDL 137
+++ NK DL
Sbjct: 113 GVLVGNKCDL 122
>gnl|CDD|215653 pfam00009, GTP_EFTU, Elongation factor Tu GTP binding domain. This
domain contains a P-loop motif, also found in several
other families such as pfam00071, pfam00025 and
pfam00063. Elongation factor Tu consists of three
structural domains, this plus two C-terminal beta barrel
domains.
Length = 184
Score = 32.1 bits (74), Expect = 0.12
Identities = 24/100 (24%), Positives = 41/100 (41%), Gaps = 13/100 (13%)
Query: 92 TDGIIFVIDSTD-VERM-EEVKIELIKTIKNNDNFNVPILILANKQDLPNAI----QIKQ 145
DG I V+D+ + V E + L KT VPI++ NK D + +++
Sbjct: 90 ADGAILVVDAVEGVMPQTREH-LLLAKT------LGVPIIVFINKIDRVDDAELEEVVEE 142
Query: 146 IEKLLGLYELNNMHLYYIQATCAITGDGLHEGINELYQLI 185
I + L + A+TG+G+ E + L +
Sbjct: 143 ISRELLEKYGFGGETVPVVPGSALTGEGIDELLEALDLYL 182
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 32.1 bits (74), Expect = 0.14
Identities = 24/111 (21%), Positives = 51/111 (45%), Gaps = 13/111 (11%)
Query: 92 TDGIIFVIDSTDVERMEEVKIELIKTIKN-----NDNF-NVPILILANKQDLPNAIQ-IK 144
T ++ VID + ++ + IE +TI+N + P +++ NK DLP + ++
Sbjct: 238 TRVLLHVIDLSPIDGRD--PIEDYQTIRNELEKYSPKLAEKPRIVVLNKIDLPLDEEELE 295
Query: 145 QIEKLLGLYELNNMHLYYIQATCAITGDGLHEGINELYQLILKKRKLQKTN 195
+++K L + A+T +GL E + L +L+ + + +
Sbjct: 296 ELKKALA----EALGWEVFYLISALTREGLDELLRALAELLEETKAEAEAA 342
>gnl|CDD|133344 cd04144, Ras2, Rat sarcoma (Ras) family 2 of small guanosine
triphosphatases (GTPases). The Ras2 subfamily, found
exclusively in fungi, was first identified in Ustilago
maydis. In U. maydis, Ras2 is regulated by Sql2, a
protein that is homologous to GEFs (guanine nucleotide
exchange factors) of the CDC25 family. Ras2 has been
shown to induce filamentous growth, but the signaling
cascade through which Ras2 and Sql2 regulate cell
morphology is not known. Most Ras proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Ras proteins.
Length = 190
Score = 31.7 bits (72), Expect = 0.17
Identities = 39/122 (31%), Positives = 57/122 (46%), Gaps = 13/122 (10%)
Query: 22 IVMLGLDSAGKTTALYRLKFDQYLNTV-PTIGFNCEK---VKGQIGKCKGINFL-IWDVG 76
+V+LG GKT +L + ++ T PTI + K V GQ C L + D
Sbjct: 2 LVVLGDGGVGKTALTIQLCLNHFVETYDPTIEDSYRKQVVVDGQP--C----MLEVLDTA 55
Query: 77 GQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKI--ELIKTIKNNDNFNVPILILANK 134
GQE+ L + R +G I V T E V+ E I+ +K+ +VPI+I+ NK
Sbjct: 56 GQEEYTALRDQWIREGEGFILVYSITSRSTFERVERFREQIQRVKDESAADVPIMIVGNK 115
Query: 135 QD 136
D
Sbjct: 116 CD 117
>gnl|CDD|206663 cd01871, Rac1_like, Ras-related C3 botulinum toxin substrate 1 (rho
family, small GTP binding protein Rac1)-like consists of
Rac1, Rac2 and Rac3. The Rac1-like subfamily consists
of Rac1, Rac2, and Rac3 proteins, plus the splice
variant Rac1b that contains a 19-residue insertion near
switch II relative to Rac1. While Rac1 is ubiquitously
expressed, Rac2 and Rac3 are largely restricted to
hematopoietic and neural tissues respectively. Rac1
stimulates the formation of actin lamellipodia and
membrane ruffles. It also plays a role in cell-matrix
adhesion and cell anoikis. In intestinal epithelial
cells, Rac1 is an important regulator of migration and
mediates apoptosis. Rac1 is also essential for
RhoA-regulated actin stress fiber and focal adhesion
complex formation. In leukocytes, Rac1 and Rac2 have
distinct roles in regulating cell morphology, migration,
and invasion, but are not essential for macrophage
migration or chemotaxis. Rac3 has biochemical properties
that are closely related to Rac1, such as effector
interaction, nucleotide binding, and hydrolysis; Rac2
has a slower nucleotide association and is more
efficiently activated by the RacGEF Tiam1. Both Rac1 and
Rac3 have been implicated in the regulation of cell
migration and invasion in human metastatic breast
cancer. Most Rho proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Rho proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 174
Score = 31.3 bits (71), Expect = 0.17
Identities = 27/87 (31%), Positives = 42/87 (48%), Gaps = 9/87 (10%)
Query: 66 KGINFLIWDVGGQE---KLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNND 122
K +N +WD GQE +LRPL SY + TD + E V+ + ++++
Sbjct: 47 KPVNLGLWDTAGQEDYDRLRPL--SYPQ-TDVFLICFSLVSPASFENVRAKWYPEVRHHC 103
Query: 123 NFNVPILILANKQDLPNAIQIKQIEKL 149
N PI+++ K DL + IEKL
Sbjct: 104 P-NTPIILVGTKLDLRD--DKDTIEKL 127
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 32.0 bits (74), Expect = 0.17
Identities = 21/103 (20%), Positives = 51/103 (49%), Gaps = 11/103 (10%)
Query: 95 IIFVIDSTDVERMEEVKIELIKTIK--NNDNFNVPILILANKQDL--PNAIQIKQIEKLL 150
++ ++D V+ +E+ K + ++ + + + P +++ NK DL + K+ L
Sbjct: 240 LLHLVDIEAVDPVEDYKT-IRNELEKYSPELADKPRILVLNKIDLLDEEEEREKRAALEL 298
Query: 151 GLYELNNMHLYYIQATCAITGDGLHEGINELYQLILKKRKLQK 193
++ I A+TG+GL E + L++L+ + R+ ++
Sbjct: 299 AALGGP---VFLI---SAVTGEGLDELLRALWELLEEARREEE 335
>gnl|CDD|223597 COG0523, COG0523, Putative GTPases (G3E family) [General function
prediction only].
Length = 323
Score = 31.9 bits (73), Expect = 0.18
Identities = 14/59 (23%), Positives = 29/59 (49%), Gaps = 7/59 (11%)
Query: 93 DGIIFVIDSTDV-ERMEEVKIELIKTIKNNDNFNVPILILANKQDLPNAIQIKQIEKLL 150
DG++ V+D+ E ++ + + D +I+ NK DL +A +++ +E L
Sbjct: 118 DGVVTVVDAAHFLEGLDAIAELAEDQLAFAD------VIVLNKTDLVDAEELEALEARL 170
>gnl|CDD|213835 TIGR03598, GTPase_YsxC, ribosome biogenesis GTP-binding protein
YsxC/EngB. Members of this protein family are a GTPase
associated with ribosome biogenesis, typified by YsxC
from Bacillus subutilis. The family is widely but not
universally distributed among bacteria. Members commonly
are called EngB based on homology to EngA, one of
several other GTPases of ribosome biogenesis. Cutoffs as
set find essentially all bacterial members, but also
identify large numbers of eukaryotic (probably
organellar) sequences. This protein is found in about 80
percent of bacterial genomes [Protein synthesis, Other].
Length = 178
Score = 31.3 bits (72), Expect = 0.20
Identities = 18/85 (21%), Positives = 39/85 (45%), Gaps = 12/85 (14%)
Query: 94 GIIFVIDSTDVERME--EVKIELIKTIKNNDNFNVPILILANKQD-LPNAIQIKQIEKLL 150
G++ ++D R E+ +E+I+ ++ +P+LI+ K D L + KQ++K+
Sbjct: 103 GVVLLMDI----RHPLKELDLEMIEWLRER---GIPVLIVLTKADKLKKSELNKQLKKIK 155
Query: 151 GLYELNNMHLYYIQATCAITGDGLH 175
L +Q ++ G+
Sbjct: 156 K--ALKKDADDSVQLFSSLKKTGID 178
>gnl|CDD|234770 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 31.2 bits (72), Expect = 0.21
Identities = 16/70 (22%), Positives = 29/70 (41%), Gaps = 14/70 (20%)
Query: 122 DNFNVPILILANKQD-LPN---AIQIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEG 177
+ +P+LI+ K D L Q+K++ K L + + ++ +G
Sbjct: 132 KEYGIPVLIVLTKADKLKKGERKKQLKKVRKALKFGDDE------VILFSSLKK----QG 181
Query: 178 INELYQLILK 187
I+EL I K
Sbjct: 182 IDELRAAIAK 191
>gnl|CDD|206708 cd04136, Rap_like, Rap-like family consists of Rap1, Rap2 and RSR1.
The Rap subfamily consists of the Rap1, Rap2, and RSR1.
Rap subfamily proteins perform different cellular
functions, depending on the isoform and its subcellular
localization. For example, in rat salivary gland,
neutrophils, and platelets, Rap1 localizes to secretory
granules and is believed to regulate exocytosis or the
formation of secretory granules. Rap1 has also been
shown to localize in the Golgi of rat fibroblasts,
zymogen granules, plasma membrane, and microsomal
membrane of the pancreatic acini, as well as in the
endocytic compartment of skeletal muscle cells and
fibroblasts. Rap1 localizes in the nucleus of human
oropharyngeal squamous cell carcinomas (SCCs) and cell
lines. Rap1 plays a role in phagocytosis by controlling
the binding of adhesion receptors (typically integrins)
to their ligands. In yeast, Rap1 has been implicated in
multiple functions, including activation and silencing
of transcription and maintenance of telomeres. Rap2 is
involved in multiple functions, including activation of
c-Jun N-terminal kinase (JNK) to regulate the actin
cytoskeleton and activation of the Wnt/beta-catenin
signaling pathway in embryonic Xenopus. A number of
effector proteins for Rap2 have been identified,
including isoform 3 of the human mitogen-activated
protein kinase kinase kinase kinase 4 (MAP4K4) and
Traf2- and Nck-interacting kinase (TNIK), and the
RalGEFs RalGDS, RGL, and Rlf, which also interact with
Rap1 and Ras. RSR1 is the fungal homolog of Rap1 and
Rap2. In budding yeasts, it is involved in selecting a
site for bud growth, which directs the establishment of
cell polarization. The Rho family GTPase Cdc42 and its
GEF, Cdc24, then establish an axis of polarized growth.
It is believed that Cdc42 interacts directly with RSR1
in vivo. In filamentous fungi such as Ashbya gossypii,
RSR1 is a key regulator of polar growth in the hypha.
Most Ras proteins contain a lipid modification site at
the C-terminus, with a typical sequence motif CaaX,
where a = an aliphatic amino acid and X = any amino
acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 164
Score = 31.0 bits (70), Expect = 0.25
Identities = 26/120 (21%), Positives = 52/120 (43%), Gaps = 5/120 (4%)
Query: 22 IVMLGLDSAGKTTALYRLKFDQYLNTV-PTIGFNCEKVKGQIG-KCKGINFLIWDVGGQE 79
+V+LG GK+ + +++ PTI + + QI C+ I D G E
Sbjct: 4 LVVLGSGGVGKSALTVQFVQGIFVDKYDPTIE---DSYRKQIEVDCQQCMLEILDTAGTE 60
Query: 80 KLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLPN 139
+ + Y + G V T + +++ + ++ D +VP++++ NK DL +
Sbjct: 61 QFTAMRDLYIKNGQGFALVYSITAQQSFNDLQDLREQILRVKDTEDVPMILVGNKCDLED 120
>gnl|CDD|206742 cd09915, Rag, Rag GTPase subfamily of Ras-related GTPases. Rag
GTPases (ras-related GTP-binding proteins) constitute a
unique subgroup of the Ras superfamily, playing an
essential role in regulating amino acid-induced target
of rapamycin complex 1 (TORC1) kinase signaling,
exocytic cargo sorting at endosomes, and epigenetic
control of gene expression. This subfamily consists of
RagA and RagB as well as RagC and RagD that are closely
related. Saccharomyces cerevisiae encodes single
orthologs of metazoan RagA/B and RagC/D, Gtr1 and Gtr2,
respectively. Dimer formation is important for their
cellular function; these domains form heterodimers, as
RagA or RagB dimerizes with RagC or RagD, and similarly,
Gtr1 dimerizes with Gtr2. In response to amino acids,
the Rag GTPases guide the TORC1 complex to activate the
platform containing Rheb proto-oncogene by driving the
relocalization of mTORC1 from discrete locations in the
cytoplasm to a late endosomal and/or lysosomal
compartment that is Rheb-enriched and contains Rab-7.
Length = 175
Score = 31.0 bits (70), Expect = 0.25
Identities = 16/68 (23%), Positives = 29/68 (42%), Gaps = 5/68 (7%)
Query: 68 INFLIWDVGGQEKLRPLWKSYT---RCTDGIIFVIDSTD--VERMEEVKIELIKTIKNND 122
+WD GQ+ K + +I+VID D ++ + + L + K N
Sbjct: 48 XTLNLWDCPGQDVFFEPTKDKEHIFQXVGALIYVIDVQDEYLKAITILAKALKQAYKVNP 107
Query: 123 NFNVPILI 130
+ N+ +LI
Sbjct: 108 DANIEVLI 115
>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 = 30.6 bits (70), Expect = 0.41
Identities = 26/126 (20%), Positives = 53/126 (42%), Gaps = 14/126 (11%)
Query: 22 IVMLGLDSAGKTTALYRLKFDQYL-NTVPTIGFNCEKVKGQIGKCKGINFLIWDVGGQEK 80
++++GL +GK++ + F Y +G + + + + +WD GQ+
Sbjct: 2 VLLMGLRGSGKSSMRSII-FSNYSPRDTLRLGATIDVEQSHVRFLGNLTLNLWDCPGQDD 60
Query: 81 LRPLWKSYTRCT-----DGIIFVIDSTDVERMEEVKIELIKTI----KNNDNFNVPILIL 131
+ + + +I+V D E E++ L+K I + + N V +LI
Sbjct: 61 FMENYLTRQKEHIFSNVGVLIYVFDVESREYEEDLAT-LVKIIEALYQYSPNAKVFVLI- 118
Query: 132 ANKQDL 137
+K DL
Sbjct: 119 -HKMDL 123
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 30.8 bits (71), Expect = 0.42
Identities = 21/95 (22%), Positives = 45/95 (47%), Gaps = 14/95 (14%)
Query: 93 DGIIFVIDSTD-VERMEEVKIELIKTIKNNDNFNVPILILANKQDL--PNAIQIKQIEKL 149
D ++FV+D+ + + +E +E +K +K P++++ NK DL + +E+L
Sbjct: 86 DLVLFVVDADEKIGPGDEFILEKLKKVK------TPVILVLNKIDLVKDKEELLPLLEEL 139
Query: 150 LGLYELNNMHLYYIQATCAITGDGLHEGINELYQL 184
L + I A+ GD + E ++ + +
Sbjct: 140 SELMDFAE-----IVPISALKGDNVDELLDVIAKY 169
>gnl|CDD|129528 TIGR00436, era, GTP-binding protein Era. Era is an essential
GTPase in Escherichia coli and many other bacteria. It
plays a role in ribosome biogenesis. Few bacteria lack
this protein [Protein synthesis, Other].
Length = 270
Score = 30.4 bits (69), Expect = 0.48
Identities = 20/92 (21%), Positives = 36/92 (39%), Gaps = 12/92 (13%)
Query: 93 DGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLPNAIQ-IKQIEKLLG 151
D I+FV+DS E + ++ +K P+++ NK D + + I+K
Sbjct: 81 DLILFVVDSDQWNGDGEFVLTKLQNLK------RPVVLTRNKLDNKFKDKLLPLIDKYAI 134
Query: 152 LYELNNMHLYYIQATCAITGDGLHEGINELYQ 183
L + + I A+TGD +
Sbjct: 135 LEDFKD-----IVPISALTGDNTSFLAAFIEV 161
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 30.6 bits (70), Expect = 0.51
Identities = 33/106 (31%), Positives = 43/106 (40%), Gaps = 29/106 (27%)
Query: 92 TDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLPNAIQIKQIEKLLG 151
TD I V+ + D M + IE I K VPI++ NK D P A +K+
Sbjct: 79 TDIAILVVAADD-GVMPQT-IEAINHAKA---AGVPIVVAINKIDKPEA----NPDKV-- 127
Query: 152 LYELNNMHLYYIQA-----------TCAITGDGLHEGINELYQLIL 186
EL Y + A TG EGI+EL +LIL
Sbjct: 128 KQELQE---YGLVPEEWGGDVIFVPVSAKTG----EGIDELLELIL 166
>gnl|CDD|223296 COG0218, COG0218, Predicted GTPase [General function prediction
only].
Length = 200
Score = 30.3 bits (69), Expect = 0.54
Identities = 17/87 (19%), Positives = 40/87 (45%), Gaps = 8/87 (9%)
Query: 108 EEVKIELIKTIKNNDNFNVPILILANKQD-LPNAIQIKQIEKLLGLYELNNMHLYYIQAT 166
+++ E+I+ + +P++++ K D L + + KQ+ K+ + ++
Sbjct: 121 KDLDREMIEFLLELG---IPVIVVLTKADKLKKSERNKQLNKVAEELKKPPPDDQWVVLF 177
Query: 167 CAITGDGLHEGINELYQLILKKRKLQK 193
++ +GI+EL IL+ K K
Sbjct: 178 SSLKK----KGIDELKAKILEWLKEAK 200
>gnl|CDD|206733 cd04170, EF-G_bact, Elongation factor G (EF-G) family.
Translocation is mediated by EF-G (also called
translocase). The structure of EF-G closely resembles
that of the complex between EF-Tu and tRNA. This is an
example of molecular mimicry; a protein domain evolved
so that it mimics the shape of a tRNA molecule. EF-G in
the GTP form binds to the ribosome, primarily through
the interaction of its EF-Tu-like domain with the 50S
subunit. The binding of EF-G to the ribosome in this
manner stimulates the GTPase activity of EF-G. On GTP
hydrolysis, EF-G undergoes a conformational change that
forces its arm deeper into the A site on the 30S
subunit. To accommodate this domain, the peptidyl-tRNA
in the A site moves to the P site, carrying the mRNA and
the deacylated tRNA with it. The ribosome may be
prepared for these rearrangements by the initial binding
of EF-G as well. The dissociation of EF-G leaves the
ribosome ready to accept the next aminoacyl-tRNA into
the A site. This group contains only bacterial members.
Length = 268
Score = 30.3 bits (69), Expect = 0.56
Identities = 12/51 (23%), Positives = 22/51 (43%), Gaps = 5/51 (9%)
Query: 90 RCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLPNA 140
R D + V+++ V++ K + D+ +P +I NK D A
Sbjct: 86 RAVDAALIVVEAQS-----GVEVGTEKVWEFLDDAKLPRIIFINKMDRARA 131
>gnl|CDD|206748 cd01855, YqeH, Circularly permuted YqeH GTPase. YqeH is an
essential GTP-binding protein. Depletion of YqeH induces
an excess initiation of DNA replication, suggesting that
it negatively controls initiation of chromosome
replication. The YqeH subfamily is common in eukaryotes
and sporadically present in bacteria with probable
acquisition by plants from chloroplasts. Proteins of the
YqeH family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases.
Length = 191
Score = 29.9 bits (68), Expect = 0.61
Identities = 23/101 (22%), Positives = 42/101 (41%), Gaps = 15/101 (14%)
Query: 95 IIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQD-LP---NAIQIKQ-IEKL 149
++ V+D D LI + P++++ NK D LP ++KQ ++K
Sbjct: 37 VVHVVDIFDFP------GSLIPGLAEL-IGAKPVILVGNKIDLLPKDVKPNRLKQWVKKR 89
Query: 150 LGLYELNNMHLYYIQATCAITGDGLHEGINELYQLILKKRK 190
L + L + + A G G+ E I E+ +L +
Sbjct: 90 LKIGGLKIKDVILVSAK---KGWGVEELIEEIKKLAKYRGD 127
>gnl|CDD|206705 cd04133, Rop_like, Rho-related protein from plants (Rop)-like. The
Rop (Rho-related protein from plants) subfamily plays a
role in diverse cellular processes, including
cytoskeletal organization, pollen and vegetative cell
growth, hormone responses, stress responses, and
pathogen resistance. Rops are able to regulate several
downstream pathways to amplify a specific signal by
acting as master switches early in the signaling
cascade. They transmit a variety of extracellular and
intracellular signals. Rops are involved in establishing
cell polarity in root-hair development, root-hair
elongation, pollen-tube growth, cell-shape formation,
responses to hormones such as abscisic acid (ABA) and
auxin, responses to abiotic stresses such as oxygen
deprivation, and disease resistance and disease
susceptibility. An individual Rop can have a unique
function or an overlapping function shared with other
Rop proteins; in addition, a given Rop-regulated
function can be controlled by one or multiple Rop
proteins. For example, Rop1, Rop3, and Rop5 are all
involved in pollen-tube growth; Rop2 plays a role in
response to low-oxygen environments, cell-morphology,
and root-hair development; root-hair development is also
regulated by Rop4 and Rop6; Rop6 is also responsible for
ABA response, and ABA response is also regulated by
Rop10. Plants retain some of the regulatory mechanisms
that are shared by other members of the Rho family, but
have also developed a number of unique modes for
regulating Rops. Unique RhoGEFs have been identified
that are exclusively active toward Rop proteins, such as
those containing the domain PRONE (plant-specific Rop
nucleotide exchanger). Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 173
Score = 29.8 bits (67), Expect = 0.64
Identities = 30/100 (30%), Positives = 47/100 (47%), Gaps = 23/100 (23%)
Query: 68 INFLIWDVGGQE---KLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNF 124
+N +WD GQE +LRPL SY R D +F++ + + + + L K I ++
Sbjct: 49 VNLGLWDTAGQEDYNRLRPL--SY-RGAD--VFLLAFSLISKASYENV-LKKWIPELRHY 102
Query: 125 --NVPILILANKQDL----------PNAIQIK--QIEKLL 150
VPI+++ K DL P A+ I Q E+L
Sbjct: 103 APGVPIVLVGTKLDLRDDKQFFADHPGAVPITTAQGEELR 142
>gnl|CDD|225808 COG3269, COG3269, Predicted RNA-binding protein, contains TRAM
domain [General function prediction only].
Length = 73
Score = 28.1 bits (63), Expect = 0.72
Identities = 13/37 (35%), Positives = 18/37 (48%), Gaps = 5/37 (13%)
Query: 93 DGII----FVIDSTDVERMEEVKIELIKTIKNNDNFN 125
DGI FV+ E +EVK++ I +K N F
Sbjct: 31 DGIARVEGFVVFVPGAEVGDEVKVK-ITKVKPNFAFA 66
>gnl|CDD|133277 cd01875, RhoG, Ras homolog family, member G (RhoG) of small
guanosine triphosphatases (GTPases). RhoG is a GTPase
with high sequence similarity to members of the Rac
subfamily, including the regions involved in effector
recognition and binding. However, RhoG does not bind to
known Rac1 and Cdc42 effectors, including proteins
containing a Cdc42/Rac interacting binding (CRIB) motif.
Instead, RhoG interacts directly with Elmo, an upstream
regulator of Rac1, in a GTP-dependent manner and forms a
ternary complex with Dock180 to induce activation of
Rac1. The RhoG-Elmo-Dock180 pathway is required for
activation of Rac1 and cell spreading mediated by
integrin, as well as for neurite outgrowth induced by
nerve growth factor. Thus RhoG activates Rac1 through
Elmo and Dock180 to control cell morphology. RhoG has
also been shown to play a role in caveolar trafficking
and has a novel role in signaling the neutrophil
respiratory burst stimulated by G protein-coupled
receptor (GPCR) agonists. Most Rho proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Rho proteins.
Length = 191
Score = 29.6 bits (66), Expect = 0.93
Identities = 40/136 (29%), Positives = 63/136 (46%), Gaps = 14/136 (10%)
Query: 19 SVHIVMLGLDSAGKTTALYRLKFDQYLNT-VPTIGFNCEKVKGQIGKCKGINFLIWDVGG 77
S+ V++G + GKT L + + +PT+ N G+ +N +WD G
Sbjct: 3 SIKCVVVGDGAVGKTCLLICYTTNAFPKEYIPTVFDNYSAQTAVDGRTVSLN--LWDTAG 60
Query: 78 QE---KLRPLWKSYTRCTDGII-FVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILAN 133
QE +LR L SY + II F I S E V+ + + ++ NVPIL++
Sbjct: 61 QEEYDRLRTL--SYPQTNVFIICFSIASP--SSYENVRHKWHPEVCHHCP-NVPILLVGT 115
Query: 134 KQDLPNAIQIKQIEKL 149
K+DL N ++KL
Sbjct: 116 KKDLRN--DADTLKKL 129
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 29.6 bits (68), Expect = 1.2
Identities = 18/84 (21%), Positives = 40/84 (47%), Gaps = 21/84 (25%)
Query: 127 PILILANKQDLPNAIQIKQIEKLLGLYELNNMHLYYIQ-----ATCAITGDGLHEGINEL 181
++I+ NK DL + +++ +K L L ++ A+TG +G+++L
Sbjct: 286 ALVIVVNKWDLVDEKTMEEFKKEL------RRRLPFLDYAPIVFISALTG----QGVDKL 335
Query: 182 YQLILK-----KRKLQKTNKMNKV 200
+ I + R++ T+ +N+V
Sbjct: 336 LEAIDEAYENANRRI-STSVLNRV 358
>gnl|CDD|216791 pfam01926, MMR_HSR1, 50S ribosome-binding GTPase. The full-length
GTPase protein is required for the complete activity of
the protein of interacting with the 50S ribosome and
binding of both adenine and guanine nucleotides, with a
preference for guanine nucleotide.
Length = 117
Score = 28.4 bits (64), Expect = 1.3
Identities = 15/78 (19%), Positives = 34/78 (43%), Gaps = 13/78 (16%)
Query: 66 KGINFLIWDVGG------QEKLRPLWKSYT---RCTDGIIFVIDSTDVERMEEVKIELIK 116
G ++ D G + K + + R D I+ V+D+++ + E E+++
Sbjct: 44 LGRQIILVDTPGLIEGASEGKGVEGFNRFLEAIREADLILLVVDASEG--LTEDDEEILE 101
Query: 117 TIKNNDNFNVPILILANK 134
++ PI+++ NK
Sbjct: 102 ELEK--LPKKPIILVLNK 117
>gnl|CDD|206647 cd00881, GTP_translation_factor, GTP translation factor family
primarily contains translation initiation, elongation
and release factors. The GTP translation factor family
consists primarily of translation initiation,
elongation, and release factors, which play specific
roles in protein translation. In addition, the family
includes Snu114p, a component of the U5 small nuclear
riboprotein particle which is a component of the
spliceosome and is involved in excision of introns,
TetM, a tetracycline resistance gene that protects the
ribosome from tetracycline binding, and the unusual
subfamily CysN/ATPS, which has an unrelated function
(ATP sulfurylase) acquired through lateral transfer of
the EF1-alpha gene and development of a new function.
Length = 183
Score = 28.4 bits (64), Expect = 1.7
Identities = 25/101 (24%), Positives = 41/101 (40%), Gaps = 17/101 (16%)
Query: 93 DGIIFVIDSTD-VERMEEVKIELIKTIKNNDNFNVPILILANKQDLPNAIQI----KQIE 147
DG + V+D+ + VE + + +PI++ NK D ++I+
Sbjct: 87 DGALLVVDANEGVEPQTREHLNIALA------GGLPIIVAVNKIDRVGEEDFDEVLREIK 140
Query: 148 KLLGLYELNNM--HLYYIQATCAITGDGLHEGINELYQLIL 186
+LL L + I A+TG EGI EL I+
Sbjct: 141 ELLKLIGFTFLKGKDVPIIPISALTG----EGIEELLDAIV 177
>gnl|CDD|234175 TIGR03348, VI_IcmF, type VI secretion protein IcmF. Members of
this protein family are IcmF homologs and tend to be
associated with type VI secretion systems [Cellular
processes, Pathogenesis].
Length = 1169
Score = 29.2 bits (66), Expect = 1.9
Identities = 9/21 (42%), Positives = 13/21 (61%), Gaps = 2/21 (9%)
Query: 23 VMLGLDSAGKTTALYR--LKF 41
+++G +GKTT L LKF
Sbjct: 115 LVIGPPGSGKTTLLQNSGLKF 135
>gnl|CDD|226833 COG4398, COG4398, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 389
Score = 29.0 bits (65), Expect = 1.9
Identities = 10/31 (32%), Positives = 14/31 (45%), Gaps = 3/31 (9%)
Query: 41 FDQYLNTVPTIGFNCEKVKGQIGKCKGINFL 71
++ L +P GF G+IG G N L
Sbjct: 348 IEELLGGIPLAGFFA---AGEIGPVAGRNAL 375
>gnl|CDD|206747 cd01854, YjeQ_EngC, Ribosomal interacting GTPase YjeQ/EngC, a
circularly permuted subfamily of the Ras GTPases. YjeQ
(YloQ in Bacillus subtilis) is a ribosomal small
subunit-dependent GTPase; hence also known as RsgA. YjeQ
is a late-stage ribosomal biogenesis factor involved in
the 30S subunit maturation, and it represents a protein
family whose members are broadly conserved in bacteria
and have been shown to be essential to the growth of E.
coli and B. subtilis. Proteins of the YjeQ family
contain all sequence motifs typical of the vast class of
P-loop-containing GTPases, but show a circular
permutation, with a G4-G1-G3 pattern of motifs as
opposed to the regular G1-G3-G4 pattern seen in most
GTPases. All YjeQ family proteins display a unique
domain architecture, which includes an N-terminal
OB-fold RNA-binding domain, the central permuted GTPase
domain, and a zinc knuckle-like C-terminal cysteine
domain.
Length = 211
Score = 28.5 bits (65), Expect = 2.1
Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 6/52 (11%)
Query: 125 NVPILILANKQDLPNAIQIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHE 176
+ +I+ NK DL + +++E+LL +YE Y + A A TG+GL E
Sbjct: 33 GIEPVIVLNKADLVDD---EELEELLEIYEKLG---YPVLAVSAKTGEGLDE 78
>gnl|CDD|234353 TIGR03788, marine_srt_targ, marine proteobacterial sortase target
protein. Members of this protein family are restricted
to the Proteobacteria. Each contains a C-terminal
sortase-recognition motif, transmembrane domain, and
basic residues cluster at the the C-terminus, and is
encoded adjacent to a sortase gene. This protein is
frequently the only sortase target in its genome, which
is as unusual its occurrence in Gram-negative rather
than Gram-positive genomes. Many bacteria with this
system are marine. In addition to the LPXTG signal,
members carry a vault protein inter-alpha-trypsin
inhibitor domain (pfam08487) and a von Willebrand factor
type A domain (pfam00092).
Length = 596
Score = 28.9 bits (65), Expect = 2.1
Identities = 12/38 (31%), Positives = 20/38 (52%), Gaps = 6/38 (15%)
Query: 95 IIFVID---STDVERMEEVKIEL---IKTIKNNDNFNV 126
++FVID S E +E+ K L + ++ D FN+
Sbjct: 274 LVFVIDTSGSMAGESIEQAKSALLLALDQLRPGDRFNI 311
>gnl|CDD|206715 cd04148, RGK, Rem, Rem2, Rad, Gem/Kir (RGK) subfamily of Ras
GTPases. RGK subfamily. The RGK (Rem, Rem2, Rad,
Gem/Kir) subfamily of Ras GTPases are expressed in a
tissue-specific manner and are dynamically regulated by
transcriptional and posttranscriptional mechanisms in
response to environmental cues. RGK proteins bind to the
beta subunit of L-type calcium channels, causing
functional down-regulation of these voltage-dependent
calcium channels, and either termination of
calcium-dependent secretion or modulation of electrical
conduction and contractile function. Inhibition of
L-type calcium channels by Rem2 may provide a mechanism
for modulating calcium-triggered exocytosis in
hormone-secreting cells, and has been proposed to
influence the secretion of insulin in pancreatic beta
cells. RGK proteins also interact with and inhibit the
Rho/Rho kinase pathway to modulate remodeling of the
cytoskeleton. Two characteristics of RGK proteins cited
in the literature are N-terminal and C-terminal
extensions beyond the GTPase domain typical of Ras
superfamily members. The N-terminal extension is not
conserved among family members; the C-terminal extension
is reported to be conserved among the family and lack
the CaaX prenylation motif typical of
membrane-associated Ras proteins. However, a putative
CaaX motif has been identified in the alignment of the
C-terminal residues of this CD.
Length = 219
Score = 28.1 bits (63), Expect = 2.3
Identities = 27/122 (22%), Positives = 51/122 (41%), Gaps = 12/122 (9%)
Query: 22 IVMLGLDSAGKTTALYRLKFDQY-LNTVPTIGFN-CEKVKGQIGKCKGINFL-IWDVGGQ 78
+V+LG GK++ Y + G + E+ G+ + W+
Sbjct: 3 VVLLGDSGVGKSSLANIFTAGVYEDSAYEASGDDTYERTVSVDGEEATLVVYDHWEQEDG 62
Query: 79 EKLRPLWKSYTRCTDG--IIF-VIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQ 135
L S + D I++ V D + E+ E++I+L + + D +PI+++ NK
Sbjct: 63 MWLE---DSCMQVGDAYVIVYSVTDRSSFEKASELRIQLRRARQAED---IPIILVGNKS 116
Query: 136 DL 137
DL
Sbjct: 117 DL 118
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 28.5 bits (65), Expect = 2.5
Identities = 28/104 (26%), Positives = 49/104 (47%), Gaps = 21/104 (20%)
Query: 95 IIFVIDSTDVERMEEVKIELIKTIKNND--NFNV-----PILILANKQDLPNAIQ-IKQI 146
I+ VID + E IE + I N + +N P +++ANK DLP A + +++
Sbjct: 240 IVHVIDMSGSE--GRDPIEDYEKI-NKELKLYNPRLLERPQIVVANKMDLPEAEENLEEF 296
Query: 147 EKLLGLYELNNMHLYYIQATCAITGDGLHEGINELYQLILKKRK 190
++ LG + A+TG GL E + + +L L++
Sbjct: 297 KEKLG---------PKVFPISALTGQGLDELLYAVAEL-LEETP 330
>gnl|CDD|240834 cd12388, RRM1_RAVER, RNA recognition motif 1 in ribonucleoprotein
PTB-binding raver-1, raver-2 and similar proteins. This
subfamily corresponds to the RRM1 of raver-1 and
raver-2. Raver-1 is a ubiquitously expressed
heterogeneous nuclear ribonucleoprotein (hnRNP) that
serves as a co-repressor of the nucleoplasmic splicing
repressor polypyrimidine tract-binding protein
(PTB)-directed splicing of select mRNAs. It shuttles
between the cytoplasm and the nucleus and can accumulate
in the perinucleolar compartment, a dynamic nuclear
substructure that harbors PTB. Raver-1 also modulates
focal adhesion assembly by binding to the cytoskeletal
proteins, including alpha-actinin, vinculin, and
metavinculin (an alternatively spliced isoform of
vinculin) at adhesion complexes, particularly in
differentiated muscle tissue. Raver-2 is a novel member
of the heterogeneous nuclear ribonucleoprotein (hnRNP)
family. It shows high sequence homology to raver-1.
Raver-2 exerts a spatio-temporal expression pattern
during embryogenesis and is mainly limited to
differentiated neurons and glia cells. Although it
displays nucleo-cytoplasmic shuttling in heterokaryons,
raver2 localizes to the nucleus in glia cells and
neurons. Raver-2 can interact with PTB and may
participate in PTB-mediated RNA-processing. However,
there is no evidence indicating that raver-2 can bind to
cytoplasmic proteins. Both, raver-1 and raver-2, contain
three N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), two putative nuclear
localization signals (NLS) at the N- and C-termini, a
central leucine-rich region, and a C-terminal region
harboring two [SG][IL]LGxxP motifs. They binds to RNA
through the RRMs. In addition, the two [SG][IL]LGxxP
motifs serve as the PTB-binding motifs in raver1.
However, raver-2 interacts with PTB through the SLLGEPP
motif only. .
Length = 70
Score = 26.7 bits (59), Expect = 2.6
Identities = 15/60 (25%), Positives = 30/60 (50%), Gaps = 3/60 (5%)
Query: 135 QDLPNAIQIKQIEKLLGLYELNNMHLYYIQATCAIT---GDGLHEGINELYQLILKKRKL 191
++LP + +++ LL Y++ + + T +T GD I +L+Q K+RK+
Sbjct: 5 RNLPADVTKQEVHDLLSDYQVKYCDVDKSKRTAQVTLLNGDQASRAIAKLHQSSYKERKI 64
>gnl|CDD|206666 cd01878, HflX, HflX GTPase family. HflX subfamily. A distinct
conserved domain with a glycine-rich segment N-terminal
of the GTPase domain characterizes the HflX subfamily.
The E. coli HflX has been implicated in the control of
the lambda cII repressor proteolysis, but the actual
biological functions of these GTPases remain unclear.
HflX is widespread, but not universally represented in
all three superkingdoms.
Length = 204
Score = 27.8 bits (63), Expect = 2.9
Identities = 24/98 (24%), Positives = 44/98 (44%), Gaps = 18/98 (18%)
Query: 93 DGIIFVIDSTD--VERMEEVKIELIKTIKNNDNFNVPILILANKQDLPNAIQIKQIEKLL 150
D ++ V+D++D E E E++K + +D +PI+++ NK DL + E
Sbjct: 122 DLLLHVVDASDPDREEQIETVEEVLKELGADD---IPIILVLNKIDL-----LDDEELEE 173
Query: 151 GLYELNNMHLYYIQATCAITGDGLHEGINELYQLILKK 188
L ++ A TG EG++ L + I +
Sbjct: 174 RLRAGRPDAVFI----SAKTG----EGLDLLKEAIEEL 203
>gnl|CDD|232995 TIGR00487, IF-2, translation initiation factor IF-2. This model
discriminates eubacterial (and mitochondrial)
translation initiation factor 2 (IF-2), encoded by the
infB gene in bacteria, from similar proteins in the
Archaea and Eukaryotes. In the bacteria and in
organelles, the initiator tRNA is charged with
N-formyl-Met instead of Met. This translation factor
acts in delivering the initator tRNA to the ribosome. It
is one of a number of GTP-binding translation factors
recognized by the pfam model GTP_EFTU [Protein
synthesis, Translation factors].
Length = 587
Score = 28.2 bits (63), Expect = 3.0
Identities = 23/75 (30%), Positives = 34/75 (45%), Gaps = 7/75 (9%)
Query: 66 KGINFLIWDVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFN 125
K I FL D G E + + TD ++ V+ + D V + I+ I + N
Sbjct: 135 KMITFL--DTPGHEAFTSMRARGAKVTDIVVLVVAADD-----GVMPQTIEAISHAKAAN 187
Query: 126 VPILILANKQDLPNA 140
VPI++ NK D P A
Sbjct: 188 VPIIVAINKIDKPEA 202
>gnl|CDD|239467 cd03370, NADH_oxidase, NADPH_oxidase. Nitroreductase family
containing NADH oxidase and other, uncharacterized
proteins that are similar to nitroreductase.
Nitroreductase catalyzes the reduction of nitroaromatic
compounds such as nitrotoluenes, nitrofurans and
nitroimidazoles. This process requires NAD(P)H as
electron donor in an obligatory two-electron transfer
and uses FMN as cofactor. The enzyme is typically a
homodimer. Members of this family are also called NADH
dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or
dihydropteridine reductase.
Length = 156
Score = 27.8 bits (62), Expect = 3.0
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 45 LNTVPTIGFNCEKVKGQIG 63
L T P GF+ EKVK +G
Sbjct: 107 LATSPMTGFDEEKVKEALG 125
>gnl|CDD|236584 PRK09602, PRK09602, translation-associated GTPase; Reviewed.
Length = 396
Score = 28.2 bits (64), Expect = 3.1
Identities = 12/23 (52%), Positives = 16/23 (69%), Gaps = 2/23 (8%)
Query: 127 PILILANKQDLPNAIQIKQIEKL 149
P++I ANK DLP A + IE+L
Sbjct: 219 PMVIAANKADLPPA--EENIERL 239
>gnl|CDD|203185 pfam05161, MOFRL, MOFRL family. MOFRL(multi-organism fragment with
rich Leucine) family exists in bacteria and eukaryotes.
The function of this domain is not clear, although it
exists in some putative enzymes such as reductases and
kinases.
Length = 107
Score = 26.8 bits (60), Expect = 3.3
Identities = 10/41 (24%), Positives = 19/41 (46%), Gaps = 7/41 (17%)
Query: 92 TDGIIFV-------IDSTDVERMEEVKIELIKTIKNNDNFN 125
TDGI +D + R+ ++ +T+ NND++
Sbjct: 47 TDGIDGPTDAAGAIVDPDTLSRLRAAGLDPRETLANNDSYT 87
>gnl|CDD|223556 COG0480, FusA, Translation elongation factors (GTPases)
[Translation, ribosomal structure and biogenesis].
Length = 697
Score = 28.0 bits (63), Expect = 3.9
Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 5/52 (9%)
Query: 89 TRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLPNA 140
R DG + V+D+ VE +E + + D + VP ++ NK D A
Sbjct: 97 LRVLDGAVVVVDA--VEGVEPQTETVWRQA---DKYGVPRILFVNKMDRLGA 143
>gnl|CDD|133376 cd04176, Rap2, Rap2 family GTPase consists of Rap2a, Rap2b, and
Rap2c. The Rap2 subgroup is part of the Rap subfamily
of the Ras family. It consists of Rap2a, Rap2b, and
Rap2c. Both isoform 3 of the human mitogen-activated
protein kinase kinase kinase kinase 4 (MAP4K4) and
Traf2- and Nck-interacting kinase (TNIK) are putative
effectors of Rap2 in mediating the activation of c-Jun
N-terminal kinase (JNK) to regulate the actin
cytoskeleton. In human platelets, Rap2 was shown to
interact with the cytoskeleton by binding the actin
filaments. In embryonic Xenopus development, Rap2 is
necessary for the Wnt/beta-catenin signaling pathway.
The Rap2 interacting protein 9 (RPIP9) is highly
expressed in human breast carcinomas and correlates with
a poor prognosis, suggesting a role for Rap2 in breast
cancer oncogenesis. Rap2b, but not Rap2a, Rap2c, Rap1a,
or Rap1b, is expressed in human red blood cells, where
it is believed to be involved in vesiculation. A number
of additional effector proteins for Rap2 have been
identified, including the RalGEFs RalGDS, RGL, and Rlf,
which also interact with Rap1 and Ras. Most Ras proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 163
Score = 27.5 bits (61), Expect = 4.0
Identities = 17/76 (22%), Positives = 34/76 (44%)
Query: 72 IWDVGGQEKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKNNDNFNVPILIL 131
I D G E+ + Y + G I V + + +++K + ++ VPI+++
Sbjct: 53 ILDTAGTEQFASMRDLYIKNGQGFIVVYSLVNQQTFQDIKPMRDQIVRVKGYEKVPIILV 112
Query: 132 ANKQDLPNAIQIKQIE 147
NK DL + ++ E
Sbjct: 113 GNKVDLESEREVSSAE 128
>gnl|CDD|206686 cd01899, Ygr210, Ygr210 GTPase. Ygr210 is a member of Obg-like
family and present in archaea and fungi. They are
characterized by a distinct glycine-rich motif
immediately following the Walker B motif. The Ygr210 and
YyaF/YchF subfamilies appear to form one major branch of
the Obg-like family. Among eukaryotes, the Ygr210
subfamily is represented only in fungi. These fungal
proteins form a tight cluster with their archaeal
orthologs, which suggests the possibility of horizontal
transfer from archaea to fungi.
Length = 318
Score = 27.6 bits (62), Expect = 4.9
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 127 PILILANKQDLPNAIQIKQIEKLLGLYE 154
P++I ANK D+P+A + +L E
Sbjct: 216 PMVIAANKADIPDAEENISKLRLKYPDE 243
>gnl|CDD|215245 PLN02446, PLN02446,
(5-phosphoribosyl)-5-[(5-
phosphoribosylamino)methylideneamino]
imidazole-4-carboxamide isomerase.
Length = 262
Score = 27.4 bits (61), Expect = 5.7
Identities = 13/34 (38%), Positives = 19/34 (55%)
Query: 3 KNSAAFFENLQASGSSSVHIVMLGLDSAGKTTAL 36
K++A F E + G + H++MLG D A AL
Sbjct: 43 KSAAEFAEMYKRDGLTGGHVIMLGADDASLAAAL 76
>gnl|CDD|206745 cd11385, RagC_like, Rag GTPase, subfamily of Ras-related GTPases,
includes Ras-related GTP-binding proteins C and D. RagC
and RagD are closely related Rag GTPases (ras-related
GTP-binding protein C and D) that constitute a unique
subgroup of the Ras superfamily, and are functional
homologs of Saccharomyces cerevisiae Gtr2. These domains
form heterodimers with RagA or RagB, and similarly, Gtr2
dimerizes with Gtr1 in order to function. They play an
essential role in regulating amino acid-induced target
of rapamycin complex 1 (TORC1) kinase signaling,
exocytic cargo sorting at endosomes, and epigenetic
control of gene expression. In response to amino acids,
the Rag GTPases guide the TORC1 complex to activate the
platform containing Rheb proto-oncogene by driving the
relocalization of mTORC1 from discrete locations in the
cytoplasm to a late endosomal and/or lysosomal
compartment that is Rheb-enriched and contains Rab-7.
Length = 175
Score = 26.8 bits (60), Expect = 6.3
Identities = 32/125 (25%), Positives = 56/125 (44%), Gaps = 27/125 (21%)
Query: 22 IVMLGLDSAGKTTALYRLKFDQ-------YLNTVPTIGFNCEKVKGQIGKCKGINFLIWD 74
I+++GL +GK++ + ++ F + +L + I K I +NF IWD
Sbjct: 2 ILLMGLRRSGKSS-IQKVVFHKMSPNETLFLESTNKI------TKDDISNSSFVNFQIWD 54
Query: 75 VGGQ-----EKLRPLWKSYTRCTDGIIFVIDSTDVERMEEVKIELIKTIKN----NDNFN 125
GQ L P ++ C ++FVID+ D + E + L++T+ N N N
Sbjct: 55 FPGQLDPFDPTLDPE-MIFSGCG-ALVFVIDAQD-DYDEAIA-RLVETVTKAYKVNPNIN 110
Query: 126 VPILI 130
+ I
Sbjct: 111 FEVFI 115
>gnl|CDD|185539 PTZ00286, PTZ00286, 6-phospho-1-fructokinase; Provisional.
Length = 459
Score = 27.3 bits (61), Expect = 7.0
Identities = 10/23 (43%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 169 ITGDGLHEGINELYQLILKKRKL 191
+ GDG H G +Y+ L++RKL
Sbjct: 183 LGGDGTHRGALAIYK-ELRRRKL 204
>gnl|CDD|223091 COG0012, COG0012, Predicted GTPase, probable translation factor
[Translation, ribosomal structure and biogenesis].
Length = 372
Score = 27.1 bits (61), Expect = 7.0
Identities = 13/69 (18%), Positives = 26/69 (37%), Gaps = 7/69 (10%)
Query: 97 FVIDSTDVERMEEVKIELIKTIKNNDNFNVPILILANKQDLPNAIQIKQIEKLLGLYELN 156
+ E +E + + T K P+L +AN + A + +++L L
Sbjct: 185 LDLSKWSEEDLEALASLNLLTAK-------PMLYVANVSEDDLANLNEYVKRLKELAAKE 237
Query: 157 NMHLYYIQA 165
N + + A
Sbjct: 238 NAEVVPVSA 246
>gnl|CDD|236500 PRK09405, aceE, pyruvate dehydrogenase subunit E1; Reviewed.
Length = 891
Score = 26.6 bits (60), Expect = 9.8
Identities = 9/22 (40%), Positives = 12/22 (54%), Gaps = 3/22 (13%)
Query: 160 LYYIQATCAITGDGLHEGINEL 181
+YY ++ G L EGINE
Sbjct: 557 MYYKESK---DGQILQEGINEA 575
>gnl|CDD|206677 cd01890, LepA, LepA also known as Elongation Factor 4 (EF4). LepA
(also known as elongation factor 4, EF4) belongs to the
GTPase family and exhibits significant homology to the
translation factors EF-G and EF-Tu, indicating its
possible involvement in translation and association with
the ribosome. LepA is ubiquitous in bacteria and
eukaryota (e.g. yeast GUF1p), but is missing from
archaea. This pattern of phyletic distribution suggests
that LepA evolved through a duplication of the EF-G gene
in bacteria, followed by early transfer into the
eukaryotic lineage, most likely from the
promitochondrial endosymbiont. Yeast GUF1p is not
essential and mutant cells did not reveal any marked
phenotype.
Length = 179
Score = 26.3 bits (59), Expect = 9.8
Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 13/67 (19%)
Query: 125 NVPILILANKQDLPNA---IQIKQIEKLLGLYELNNMHLYYIQATCAITGDGLHEGINEL 181
N+ I+ + NK DLP A ++IE +LGL A TG G+ +L
Sbjct: 119 NLEIIPVINKIDLPAADPDRVKQEIEDVLGLDASE------AILVSAKTG----LGVEDL 168
Query: 182 YQLILKK 188
+ I+++
Sbjct: 169 LEAIVER 175
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
0.319 0.137 0.398
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: 10,049,475
Number of extensions: 932398
Number of successful extensions: 1215
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1110
Number of HSP's successfully gapped: 190
Length of query: 202
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 110
Effective length of database: 6,857,034
Effective search space: 754273740
Effective search space used: 754273740
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 (21.7 bits)
S2: 56 (25.2 bits)