RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12173
(224 letters)
>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 = 159 bits (404), Expect = 9e-50
Identities = 55/140 (39%), Positives = 87/140 (62%), Gaps = 3/140 (2%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKGEYTLNIFELGGQENVR 113
+IL+LGLD +GK+T++ ++ G PT GFN+ ++ ++++GGQ+ +R
Sbjct: 1 RILMLGLDGAGKTTILYKLKLGEVV---TTIPTIGFNVETVEYKNVKFTVWDVGGQDKIR 57
Query: 114 RFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQDVPGALS 173
W Y+E+TD L+FVVDS+D ++ A EL LL ++ L P+L++ANKQD+PGAL+
Sbjct: 58 PLWKHYYENTDGLIFVVDSSDRERIEEAKNELHKLLNEEELKGAPLLILANKQDLPGALT 117
Query: 174 AEEVGVALDLSSISSRQHRI 193
E+ L L SI R+ I
Sbjct: 118 ESELIELLGLESIKGRRWHI 137
>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 = 158 bits (401), Expect = 3e-49
Identities = 65/144 (45%), Positives = 100/144 (69%), Gaps = 3/144 (2%)
Query: 52 QRKILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKGEYTLNIFELGGQEN 111
+ +IL+LGLDN+GK+T++KQ++S + S ++ PT+GFNI +Q + LN++++GGQ
Sbjct: 15 EVRILLLGLDNAGKTTILKQLASEDIS---HITPTQGFNIKNVQADGFKLNVWDIGGQRK 71
Query: 112 VRRFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQDVPGA 171
+R +W YFE+TD+L++V+DSAD + A EL LL +++L+ VP+LV ANKQD+ A
Sbjct: 72 IRPYWRNYFENTDVLIYVIDSADRKRFEEAGQELVELLEEEKLAGVPVLVFANKQDLLTA 131
Query: 172 LSAEEVGVALDLSSISSRQHRIKL 195
AEEV AL+L I R I+
Sbjct: 132 APAEEVAEALNLHDIRDRSWHIQA 155
>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 = 157 bits (398), Expect = 1e-48
Identities = 66/140 (47%), Positives = 98/140 (70%), Gaps = 3/140 (2%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKGEYTLNIFELGGQENVR 113
+IL+LGLDN+GK+T++K+ + + S + PT GFNI L+ Y LNI+++GGQ+++R
Sbjct: 16 RILMLGLDNAGKTTILKKFNGEDIS---TISPTLGFNIKTLEYNGYKLNIWDVGGQKSLR 72
Query: 114 RFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQDVPGALS 173
+W YFE TD L++VVDS+D ++L EL+ LL ++RL+ +L+ ANKQD+PGALS
Sbjct: 73 SYWRNYFESTDALIWVVDSSDRARLEDCKRELQKLLVEERLAGATLLIFANKQDLPGALS 132
Query: 174 AEEVGVALDLSSISSRQHRI 193
EE+ L+L SI S RI
Sbjct: 133 PEEIREVLELDSIKSHHWRI 152
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 155 bits (394), Expect = 4e-48
Identities = 55/136 (40%), Positives = 85/136 (62%), Gaps = 3/136 (2%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKGEYTLNIFELGGQENVR 113
+ILILGLDN+GK+T++ ++ G PT GFN+ + ++++GGQE++R
Sbjct: 16 RILILGLDNAGKTTILYKLKLGEIV---TTIPTIGFNVETVTYKNVKFTVWDVGGQESLR 72
Query: 114 RFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQDVPGALS 173
W YF +TD ++FVVDSAD ++ A EL LL ++ L+ P+L++ANKQD+PGA+S
Sbjct: 73 PLWRNYFPNTDAVIFVVDSADRDRIEEAKEELHALLNEEELADAPLLILANKQDLPGAMS 132
Query: 174 AEEVGVALDLSSISSR 189
E+ L L + R
Sbjct: 133 EAEIRELLGLHELKDR 148
>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 = 130 bits (329), Expect = 2e-38
Identities = 57/139 (41%), Positives = 93/139 (66%), Gaps = 5/139 (3%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQ-KGEYTLNIFELGGQENV 112
++L+LGLD++GKSTL+ ++ + PT GFN+ +LQ + +L ++++GGQE +
Sbjct: 1 QVLLLGLDSAGKSTLLYKLKHAELVTT---IPTVGFNVEMLQLEKHLSLTVWDVGGQEKM 57
Query: 113 RRFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQDVPGAL 172
R W Y E+TD LV+VVDS+D ++L + ELK++L ++ + VP++++ANKQD+PGAL
Sbjct: 58 RTVWKCYLENTDGLVYVVDSSDEARLDESQKELKHILKNEHIKGVPVVLLANKQDLPGAL 117
Query: 173 SAEEVGVALDLSSI-SSRQ 190
+AEE+ L S R
Sbjct: 118 TAEEITRRFKLKKYCSDRD 136
>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 = 129 bits (325), Expect = 9e-38
Identities = 51/140 (36%), Positives = 84/140 (60%), Gaps = 3/140 (2%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKGEYTLNIFELGGQENVR 113
K++I+GLDN+GK+T++ Q G + PT G N+ + ++++GGQE++R
Sbjct: 17 KVIIVGLDNAGKTTILYQFLLGEVVHTS---PTIGSNVEEIVYKNIRFLMWDIGGQESLR 73
Query: 114 RFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQDVPGALS 173
WNTY+ +TD ++ V+DS D +LP+ EL +L + L +LV+ANKQD+ GA++
Sbjct: 74 SSWNTYYTNTDAVILVIDSTDRERLPLTKEELYKMLAHEDLRKAVLLVLANKQDLKGAMT 133
Query: 174 AEEVGVALDLSSISSRQHRI 193
E+ +L L+SI I
Sbjct: 134 PAEISESLGLTSIRDHTWHI 153
>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 = 127 bits (321), Expect = 3e-37
Identities = 59/135 (43%), Positives = 85/135 (62%), Gaps = 2/135 (1%)
Query: 55 ILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKGEYTLNIFELGGQENVRR 114
I ++GL NSGK+TL+ I+SG S + PT GFN+ + KG T+ +++LGGQ R
Sbjct: 2 ITLVGLQNSGKTTLVNVIASGQFS--EDTIPTVGFNMRKVTKGNVTIKVWDLGGQPRFRS 59
Query: 115 FWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQDVPGALSA 174
W Y + +V+VVD+AD KL VA EL +LL L +P+LV+ NK D+PGALS
Sbjct: 60 MWERYCRGVNAIVYVVDAADREKLEVAKNELHDLLEKPSLEGIPLLVLGNKNDLPGALSV 119
Query: 175 EEVGVALDLSSISSR 189
+E+ ++L SI+ R
Sbjct: 120 DELIEQMNLKSITDR 134
>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 = 124 bits (313), Expect = 4e-36
Identities = 54/140 (38%), Positives = 85/140 (60%), Gaps = 3/140 (2%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKGEYTLNIFELGGQENVR 113
+ILILGLD +GK+T++ ++ G + PT GFN+ + +++LGGQ ++R
Sbjct: 1 RILILGLDGAGKTTILYRLQVGEVVTT---IPTIGFNVETVTYKNLKFQVWDLGGQTSIR 57
Query: 114 RFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQDVPGALS 173
+W Y+ +TD +++VVDS D +L ++ EL +L ++ L +LV ANKQD+PGALS
Sbjct: 58 PYWRCYYSNTDAIIYVVDSTDRDRLGISKSELHAMLEEEELKDAVLLVFANKQDMPGALS 117
Query: 174 AEEVGVALDLSSISSRQHRI 193
EV L LS + R +I
Sbjct: 118 EAEVAEKLGLSELKDRTWQI 137
>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 = 123 bits (311), Expect = 1e-35
Identities = 58/149 (38%), Positives = 89/149 (59%), Gaps = 5/149 (3%)
Query: 55 ILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKGEYTLNIFELGGQENVRR 114
IL+LGLD +GK++L+ +S SL ++ PT GFN + + + + E+GG +N+R+
Sbjct: 2 ILVLGLDGAGKTSLLHSLS-SERSL-ESVVPTTGFNSVAIPTQDAIMELLEIGGSQNLRK 59
Query: 115 FWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQDVPGALSA 174
+W Y + L+FVVDSAD +LP+A EL LL Q +P++V+ANKQD+P A S
Sbjct: 60 YWKRYLSGSQGLIFVVDSADSERLPLARQELHQLL--QHPPDLPLVVLANKQDLPAARSV 117
Query: 175 EEVGVALDLSSISSRQHRIKLIATQAPSN 203
+E+ L+L I +R R L T +
Sbjct: 118 QEIHKELELEPI-ARGRRWILQGTSLDDD 145
>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 = 123 bits (310), Expect = 3e-35
Identities = 55/131 (41%), Positives = 74/131 (56%), Gaps = 3/131 (2%)
Query: 53 RKILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKGEYTLNIFELGGQENV 112
KI+ LGLDN+GK+TL+ + PT L G F+LGG E
Sbjct: 20 AKIVFLGLDNAGKTTLLHMLKDDRL---AQHVPTLHPTSEELTIGNVKFTTFDLGGHEQA 76
Query: 113 RRFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQDVPGAL 172
RR W YF + D +VF+VD+ADP + + EL +LL D+ L+ VPIL++ NK D PGA+
Sbjct: 77 RRVWKDYFPEVDGIVFLVDAADPERFQESKEELDSLLNDEELANVPILILGNKIDKPGAV 136
Query: 173 SAEEVGVALDL 183
S EE+ AL L
Sbjct: 137 SEEELREALGL 147
>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 = 118 bits (299), Expect = 8e-34
Identities = 46/135 (34%), Positives = 79/135 (58%), Gaps = 5/135 (3%)
Query: 55 ILILGLDNSGKSTLIKQISSGNTSLS-----HNLKPTEGFNITILQKGEYTLNIFELGGQ 109
+LILGLDN+GK+T ++Q + + + PT G NI ++ G+ L ++LGGQ
Sbjct: 2 VLILGLDNAGKTTFLEQTKTKFSKNYKGLNPSKITPTVGLNIGTIEVGKARLMFWDLGGQ 61
Query: 110 ENVRRFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQDVP 169
E +R W+ Y+ ++ +++V+DS D + + + ++ ++ L VP+LV+ANKQD+P
Sbjct: 62 EELRSLWDKYYAESHGVIYVIDSTDRERFNESKSAFEKVINNEALEGVPLLVLANKQDLP 121
Query: 170 GALSAEEVGVALDLS 184
ALS E+ D
Sbjct: 122 DALSVAEIKEVFDDC 136
>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 = 117 bits (295), Expect = 2e-33
Identities = 55/137 (40%), Positives = 83/137 (60%), Gaps = 3/137 (2%)
Query: 55 ILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKGEYTLNIFELGGQENVRR 114
IL+LGLDNSGK+T+I Q+ N S N+ PT GFN+ +KG + F++ GQ R
Sbjct: 2 ILVLGLDNSGKTTIINQLKPSNAQ-SQNIVPTVGFNVESFKKGNLSFTAFDMSGQGKYRG 60
Query: 115 FWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLG--DQRLSTVPILVIANKQDVPGAL 172
W Y+++ ++FV+DS+D ++ VA EL+ LL D + +PIL ANK D+P AL
Sbjct: 61 LWEHYYKNIQGIIFVIDSSDRLRMVVAKDELELLLNHPDIKHRRIPILFYANKMDLPDAL 120
Query: 173 SAEEVGVALDLSSISSR 189
+A ++ L L +I +
Sbjct: 121 TAVKITQLLCLENIKDK 137
>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 = 112 bits (282), Expect = 2e-31
Identities = 49/136 (36%), Positives = 80/136 (58%), Gaps = 3/136 (2%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKGEYTLNIFELGGQENVR 113
+IL+LGLD +GK+T++ ++ G + + PT GFN+ + N++++GGQ+ +R
Sbjct: 11 RILMLGLDAAGKTTILYKLKLGQSVTT---IPTVGFNVETVTYKNVKFNVWDVGGQDKIR 67
Query: 114 RFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQDVPGALS 173
W Y+ T L+FVVDSAD ++ A EL ++ D+ + +LV ANKQD+P A+
Sbjct: 68 PLWRHYYTGTQGLIFVVDSADRDRIDEARQELHRIINDREMRDALLLVFANKQDLPDAMK 127
Query: 174 AEEVGVALDLSSISSR 189
E+ L L+ I R
Sbjct: 128 PHEIQEKLGLTRIRDR 143
>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 = 107 bits (270), Expect = 1e-29
Identities = 53/143 (37%), Positives = 88/143 (61%), Gaps = 7/143 (4%)
Query: 54 KILILGLDNSGKSTLIKQISSGN--TSLSHNLKPTEGFNITILQKGEYTLNIFELGGQEN 111
+IL++GLD +GK+T++ ++ G T++ PT GFN+ ++ + ++++GGQ+
Sbjct: 2 RILMVGLDAAGKTTILYKLKLGEIVTTI-----PTIGFNVETVEYKNISFTVWDVGGQDK 56
Query: 112 VRRFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQDVPGA 171
+R W YF++T L+FVVDS D ++ A EL+ +L + L +LV ANKQD+P A
Sbjct: 57 IRPLWRHYFQNTQGLIFVVDSNDRERIGEAREELQRMLNEDELRDAVLLVFANKQDLPNA 116
Query: 172 LSAEEVGVALDLSSISSRQHRIK 194
+SA EV L L S+ +R I+
Sbjct: 117 MSAAEVTDKLGLHSLRNRNWYIQ 139
>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 = 105 bits (265), Expect = 8e-29
Identities = 50/123 (40%), Positives = 70/123 (56%), Gaps = 3/123 (2%)
Query: 55 ILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKGEYTLNIFELGGQENVRR 114
+L +GLDN+GK+TL+ + + PT GF T L+ +Y + IF+LGG N R
Sbjct: 2 LLTVGLDNAGKTTLVSALQGEIPK---KVAPTVGFTPTKLRLDKYEVCIFDLGGGANFRG 58
Query: 115 FWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQDVPGALSA 174
W Y+ + LVFVVDS+D ++ L+ LL R+S PILV+ANKQD AL
Sbjct: 59 IWVNYYAEAHGLVFVVDSSDDDRVQEVKEILRELLQHPRVSGKPILVLANKQDKKNALLG 118
Query: 175 EEV 177
+V
Sbjct: 119 ADV 121
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 105 bits (263), Expect = 2e-28
Identities = 50/141 (35%), Positives = 84/141 (59%), Gaps = 3/141 (2%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKGEYTLNIFELGGQENVR 113
+IL++GLD +GK+T++ ++ G + PT GFN+ ++ ++++GGQ+ +R
Sbjct: 19 RILMVGLDAAGKTTILYKLKLGEVVTT---IPTIGFNVETVEYKNLKFTMWDVGGQDKLR 75
Query: 114 RFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQDVPGALS 173
W Y+++T+ L+FVVDS D ++ A EL+ +L + L +LV ANKQD+P A+S
Sbjct: 76 PLWRHYYQNTNGLIFVVDSNDRERIGDAREELERMLSEDELRDAVLLVFANKQDLPNAMS 135
Query: 174 AEEVGVALDLSSISSRQHRIK 194
EV L L S+ R I+
Sbjct: 136 TTEVTEKLGLHSVRQRNWYIQ 156
>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 = 105 bits (262), Expect = 2e-28
Identities = 50/136 (36%), Positives = 80/136 (58%), Gaps = 3/136 (2%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKGEYTLNIFELGGQENVR 113
+IL++GLD +GK+T++ ++ G + + PT GFN+ + + ++++GGQ+ +R
Sbjct: 15 RILMVGLDAAGKTTILYKLKLGESVTT---IPTIGFNVETVTYKNISFTVWDVGGQDKIR 71
Query: 114 RFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQDVPGALS 173
W Y+ +T L+FVVDS D ++ A EL +L + L ILV ANKQD+P A+
Sbjct: 72 PLWRHYYTNTQGLIFVVDSNDRDRIDEAREELHRMLNEDELRDAVILVFANKQDLPDAMK 131
Query: 174 AEEVGVALDLSSISSR 189
A E+ L L SI R
Sbjct: 132 AAEITEKLGLHSIRDR 147
>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 = 101 bits (254), Expect = 5e-27
Identities = 51/137 (37%), Positives = 79/137 (57%), Gaps = 3/137 (2%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKGEYTLNIFELGGQENVR 113
KIL LGLDN+GK+TL+ + N L+ +PT+ L G F+LGG + R
Sbjct: 19 KILFLGLDNAGKTTLLHMLK--NDRLA-QHQPTQHPTSEELAIGNIKFTTFDLGGHQQAR 75
Query: 114 RFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQDVPGALS 173
R W YF + + +V++VD+ D + + EL LL D+ L+TVP L++ NK D P A S
Sbjct: 76 RLWKDYFPEVNGIVYLVDAYDKERFAESKRELDALLSDEELATVPFLILGNKIDAPYAAS 135
Query: 174 AEEVGVALDLSSISSRQ 190
+E+ AL L++ ++ +
Sbjct: 136 EDELRYALGLTNTTTGK 152
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 99.3 bits (247), Expect = 4e-26
Identities = 50/143 (34%), Positives = 85/143 (59%), Gaps = 3/143 (2%)
Query: 52 QRKILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKGEYTLNIFELGGQEN 111
+ +IL++GLD +GK+T++ ++ G + PT GFN+ ++ + ++++GGQ+
Sbjct: 17 EMRILMVGLDAAGKTTILYKLKLGEIVTT---IPTIGFNVETVEYKNISFTVWDVGGQDK 73
Query: 112 VRRFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQDVPGA 171
+R W YF++T L+FVVDS D ++ A EL +L + L +LV ANKQD+P A
Sbjct: 74 IRPLWRHYFQNTQGLIFVVDSNDRDRVVEARDELHRMLNEDELRDAVLLVFANKQDLPNA 133
Query: 172 LSAEEVGVALDLSSISSRQHRIK 194
++A E+ L L S+ R I+
Sbjct: 134 MNAAEITDKLGLHSLRQRHWYIQ 156
>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 = 91.4 bits (227), Expect = 4e-23
Identities = 52/139 (37%), Positives = 79/139 (56%), Gaps = 8/139 (5%)
Query: 55 ILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFN-----ITILQKGEYTLNIFELGGQ 109
I++LGLD++GK+T++ ++ N PT+GFN +++ T + +++GGQ
Sbjct: 6 IVMLGLDSAGKTTVLYRLKFNEFV---NTVPTKGFNTEKIKVSLGNAKGVTFHFWDVGGQ 62
Query: 110 ENVRRFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQDVP 169
E +R W +Y TD +VFVVDS D ++ A EL + VP+LV+ANKQD+P
Sbjct: 63 EKLRPLWKSYTRCTDGIVFVVDSVDVERMEEAKTELHKITKFSENQGVPVLVLANKQDLP 122
Query: 170 GALSAEEVGVALDLSSISS 188
AL EV L L +SS
Sbjct: 123 NALPVSEVEKLLALHELSS 141
>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 = 83.5 bits (206), Expect = 4e-20
Identities = 45/133 (33%), Positives = 75/133 (56%), Gaps = 3/133 (2%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKGEYTLNIFELGGQENVR 113
+++ LGLD +GK+T++ ++ PT GFN+ ++ I+++GG+ +R
Sbjct: 1 RVVTLGLDGAGKTTILFKLKQDEFM---QPIPTIGFNVETVEYKNLKFTIWDVGGKHKLR 57
Query: 114 RFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQDVPGALS 173
W Y+ +T +VFV+DS+ ++ A EL LL ++ L +L+ ANKQDV GALS
Sbjct: 58 PLWKHYYLNTQAVVFVIDSSHRDRVSEAHSELAKLLTEKELRDALLLIFANKQDVAGALS 117
Query: 174 AEEVGVALDLSSI 186
EE+ L L +
Sbjct: 118 VEEMTELLSLHKL 130
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 74.4 bits (183), Expect = 1e-16
Identities = 34/145 (23%), Positives = 63/145 (43%), Gaps = 15/145 (10%)
Query: 54 KILILGLDNSGKSTLIKQIS---SGNTSLSHN-LKPTEGFNITILQ-------KGEYTLN 102
KI+++G +GK+T ++ +S T + + T+ + ++
Sbjct: 12 KIVVIGPVGAGKTTFVRALSDKPLVITEADASSVSGKGKRPTTVAMDFGSIELDEDTGVH 71
Query: 103 IFELGGQENVRRFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVI 162
+F GQE + W + +VDS+ P A E+ + L + +P++V
Sbjct: 72 LFGTPGQERFKFMWEILSRGAVGAIVLVDSSRPITF--HAEEIIDFL--TSRNPIPVVVA 127
Query: 163 ANKQDVPGALSAEEVGVALDLSSIS 187
NKQD+ AL E++ AL L +S
Sbjct: 128 INKQDLFDALPPEKIREALKLELLS 152
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 72.3 bits (177), Expect = 1e-15
Identities = 31/130 (23%), Positives = 51/130 (39%), Gaps = 6/130 (4%)
Query: 52 QRKILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNI----TILQKGEYTLNIFELG 107
+ KI++LG GK+TL+ ++ PT G + L +++
Sbjct: 5 EFKIVVLGDGGVGKTTLLNRLVGD--EFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTA 62
Query: 108 GQENVRRFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQD 167
GQE R Y+ + ++ V DS E L + VPIL++ NK D
Sbjct: 63 GQEEYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVGNKID 122
Query: 168 VPGALSAEEV 177
+ S+ E
Sbjct: 123 LFDEQSSSEE 132
>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 = 70.2 bits (172), Expect = 3e-15
Identities = 31/156 (19%), Positives = 55/156 (35%), Gaps = 15/156 (9%)
Query: 56 LILGLDNSGKSTLIKQISSGNTSL-SHNLKPTEGFNIT--ILQKGEYTLNIFELGGQENV 112
+++G GKS+L+ + G S T ++ L KG+ L + + G +
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPGLDEF 60
Query: 113 RRFWNT-----YFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQD 167
DL++ VVDS D +L R +PI+++ NK D
Sbjct: 61 GGLGREELARLLLRGADLILLVVDSTDR---ESEEDAKLLILRRLRKEGIPIILVGNKID 117
Query: 168 VPGALSAEEVGVALDLSSISSRQHRIKLIATQAPSN 203
L E L ++ + + A +
Sbjct: 118 ----LLEEREVEELLRLEELAKILGVPVFEVSAKTG 149
>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 = 64.7 bits (158), Expect = 3e-13
Identities = 37/143 (25%), Positives = 59/143 (41%), Gaps = 16/143 (11%)
Query: 53 RKILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNI---TILQKGE-YTLNIFELGG 108
KI+I+G N GKSTL+ ++ GN KP N I + G+ Y N+ + G
Sbjct: 2 IKIVIVGDPNVGKSTLLNRLL-GNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAG 60
Query: 109 QENVRRFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRL------STVPILVI 162
QE+ Y+ + + V D + V +E + L + S VPI+++
Sbjct: 61 QEDYDAIRRLYYRAVESSLRVFDIV----ILVLDVE-EILEKQTKEIIHHAESGVPIILV 115
Query: 163 ANKQDVPGALSAEEVGVALDLSS 185
NK D+ A V +
Sbjct: 116 GNKIDLRDAKLKTHVAFLFAKLN 138
>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 = 52.2 bits (126), Expect = 1e-08
Identities = 38/154 (24%), Positives = 55/154 (35%), Gaps = 21/154 (13%)
Query: 57 ILGLDNSGKSTLIKQISSGNTSLSHNLKPT----EGFNITILQKGEYTL----NIFELG- 107
I G N GKS+L+ + N + + T +L G L + E G
Sbjct: 2 IFGRPNVGKSSLLNALLGQNVGIVSPIPGTTRDPVRKEWELLPLGPVVLIDTPGLDEEGG 61
Query: 108 -GQENVRRFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQ 166
G+E V + DL++ VVDS PV LL R P+L++ NK
Sbjct: 62 LGRERVEEARQV-ADRADLVLLVVDS---DLTPVEEEAKLGLL---RERGKPVLLVLNKI 114
Query: 167 DVPGALSAEEVGVALDLSSISSRQHRIKLIATQA 200
D+ E L + +IA A
Sbjct: 115 DLVP----ESEEEELLRERKLELLPDLPVIAVSA 144
>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 = 47.8 bits (114), Expect = 2e-07
Identities = 26/118 (22%), Positives = 53/118 (44%), Gaps = 7/118 (5%)
Query: 54 KILILGLDNSGKSTLIKQISSG----NTSLSHNLKPTEGFNITILQKGEYTLNIFELGGQ 109
K++++G SGKS+L+ Q+ G T + + LNI++ GG+
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQ--GDTLAVDTLEVDGDTGLLNIWDFGGR 58
Query: 110 ENVRRFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLST-VPILVIANKQ 166
E ++ + + D ++ V D D L + + L ++L +P++++ NK
Sbjct: 59 EELKFEHIIFMKWADAILLVYDLTDRESLNEVSRLIAWLPNLRKLGGKIPVILVGNKL 116
>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 = 48.9 bits (117), Expect = 3e-07
Identities = 36/132 (27%), Positives = 64/132 (48%), Gaps = 6/132 (4%)
Query: 55 ILILGLDNSGKSTLIKQISSGNTSLSH-NLKPTEGFNITILQKGEYTLNIFELGGQENVR 113
+L+LG +SGK+ L ++++G + +++P + KG L + ++ G E +R
Sbjct: 3 VLLLGPSDSGKTALFTKLTTGKVRSTVTSIEPNVASFYSNSSKG-KKLTLVDVPGHEKLR 61
Query: 114 -RFWNTYFEDTDLLVFVVDSAD-PSKLPVAAMELKNLLGDQRLST--VPILVIANKQDVP 169
+ +VFVVDSA + A L ++L D +PIL+ NKQD+
Sbjct: 62 DKLLEYLKASLKAIVFVVDSATFQKNIRDVAEFLYDILTDLEKIKNKIPILIACNKQDLF 121
Query: 170 GALSAEEVGVAL 181
A A+++ L
Sbjct: 122 TAKPAKKIKELL 133
>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 = 43.6 bits (103), Expect = 2e-05
Identities = 35/138 (25%), Positives = 67/138 (48%), Gaps = 9/138 (6%)
Query: 52 QRKILILGLDNSGKSTLIKQISSGNTSLSH-NLKPTEGFNITILQKGEYTLNIFELGGQE 110
Q ++I GL +SGK++L +++G + + +P+ + + + +TL + G
Sbjct: 3 QPAVIIAGLCDSGKTSLFTLLTTGTVKKTVTSQEPSAAYKYMLHKGFSFTL--IDFPGHV 60
Query: 111 NVRRFWNTYFEDTDL---LVFVVDS-ADPSKLPVAAMELKNLLGDQRLS--TVPILVIAN 164
+R+ +D+ +VFVVDS A P ++ A L +L L + IL+ N
Sbjct: 61 KLRQKLLETIKDSSSLRGIVFVVDSTAFPKEVTDTAEFLYEILSITELLKNGIDILIACN 120
Query: 165 KQDVPGALSAEEVGVALD 182
KQ+ A +++ AL+
Sbjct: 121 KQESFTARPPKKIKQALE 138
>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 = 42.2 bits (99), Expect = 5e-05
Identities = 36/131 (27%), Positives = 60/131 (45%), Gaps = 8/131 (6%)
Query: 54 KILILGLDNSGKSTLIKQISSG--NTSLSHNLKPTEGFNITILQKGE-YTLNIFELGGQE 110
K+++LG GKS+L+ + + +T L H + E N + G TL I++ GQE
Sbjct: 7 KVILLGDGGVGKSSLMNRYVTNKFDTQLFHTIG-VEFLNKDLEVDGHFVTLQIWDTAGQE 65
Query: 111 NVRRFWNTYFEDTD--LLVFVVDSADPSK-LPVAAMELKNLLGDQRLSTVPILVIANKQD 167
R ++ +D LL F VD + + L E + + P +++ NK D
Sbjct: 66 RFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVILGNKID 125
Query: 168 VPG-ALSAEEV 177
+P +S EE
Sbjct: 126 IPERQVSTEEA 136
>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 = 41.6 bits (99), Expect = 6e-05
Identities = 38/144 (26%), Positives = 59/144 (40%), Gaps = 48/144 (33%)
Query: 57 ILGLDNSGKSTLIKQISSGN--------TSLSHNL---KPTEGFNITI-----------L 94
++GL N+GKSTL+ IS+ T+L NL + +G + I
Sbjct: 5 LVGLPNAGKSTLLSAISNAKPKIADYPFTTLVPNLGVVRVDDGRSFVIADIPGLIEGASE 64
Query: 95 QKGEYTLNIFELGGQENVRRFWNTYF----EDTDLLVFVVDSADPSKLPVAAME-LKNLL 149
KG LG + F E T +L+ V+D + PV E ++N L
Sbjct: 65 GKG--------LGHR----------FLRHIERTRVLLHVIDLSGEDD-PVEDYETIRNEL 105
Query: 150 G--DQRLSTVPILVIANKQDVPGA 171
+ L+ P +V+ NK D+ A
Sbjct: 106 EAYNPGLAEKPRIVVLNKIDLLDA 129
>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 = 41.2 bits (97), Expect = 9e-05
Identities = 33/131 (25%), Positives = 56/131 (42%), Gaps = 10/131 (7%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITI----LQKGEYTLNIFELGGQ 109
K++ +G GKS +IK+ G + PT G + + ++ E +N F+L G
Sbjct: 2 KVISMGNSGVGKSCIIKRYCEGRFVSKYL--PTIGIDYGVKKVSVRNKEVRVNFFDLSGH 59
Query: 110 ENVRRFWNTYFEDTD--LLVFVVDSADP-SKLPVAAMELKNLLGDQR-LSTVPILVIANK 165
N +++DT LLV+ V L E+K G + + ++V ANK
Sbjct: 60 PEYLEVRNEFYKDTQGVLLVYDVTDRQSFEALDSWLKEMKQEGGPHGNMENIVVVVCANK 119
Query: 166 QDVPGALSAEE 176
D+ + E
Sbjct: 120 IDLTKHRAVSE 130
>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 = 40.4 bits (95), Expect = 9e-05
Identities = 26/127 (20%), Positives = 49/127 (38%), Gaps = 25/127 (19%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHN-----LKPTEGFNITILQKGEYTLNIFELGG 108
++ ++G N GKSTLI ++ ++ + P G + + + G
Sbjct: 1 RVALVGRPNVGKSTLINALTGAKVAIVSDYPGTTRDPILGVLG-----LGRQIILVDTPG 55
Query: 109 ----------QENVRRFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVP 158
E RF + DL++ VVD+++ E+ L +L P
Sbjct: 56 LIEGASEGKGVEGFNRFLEAI-READLILLVVDASEGLTE--DDEEILEELE--KLPKKP 110
Query: 159 ILVIANK 165
I+++ NK
Sbjct: 111 IILVLNK 117
>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 = 41.5 bits (98), Expect = 1e-04
Identities = 21/95 (22%), Positives = 40/95 (42%), Gaps = 10/95 (10%)
Query: 84 KPTEGFNITILQKGEYTLNIFELGGQENVRRFWNTYFEDTDLLVFVVDSADPSKLPV--- 140
T G T +F++GGQ + R+ W FED ++FVV ++ ++
Sbjct: 153 VKTTGIIETKFDFKGLKFRLFDVGGQRSERKKWIHCFEDVTAIIFVVSLSEYDQVLYEDD 212
Query: 141 ------AAMEL-KNLLGDQRLSTVPILVIANKQDV 168
++ L + + PI++ NK+D+
Sbjct: 213 STNRLEESLNLFEEICNSPWFKNTPIILFLNKKDL 247
Score = 36.1 bits (84), Expect = 0.009
Identities = 11/19 (57%), Positives = 16/19 (84%)
Query: 54 KILILGLDNSGKSTLIKQI 72
K+L+LG SGKST++KQ+
Sbjct: 4 KLLLLGAGESGKSTILKQM 22
>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 = 38.4 bits (90), Expect = 7e-04
Identities = 34/158 (21%), Positives = 59/158 (37%), Gaps = 18/158 (11%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEG--FNITILQKGE--YTLNIFELGGQ 109
KIL++G GKS+L+ + + + +L T G F + + L I++ GQ
Sbjct: 2 KILLIGDSGVGKSSLLLRFTDD--TFDEDLSSTIGVDFKVKTVTVDGKKVKLAIWDTAGQ 59
Query: 110 ENVRRFWNTYFEDTDLLVFVVDSADPS---KLPVAAMELKNLLGDQRLSTVPILVIANKQ 166
E R ++Y+ ++ V D L EL +++ NK
Sbjct: 60 ERFRTLTSSYYRGAQGVILVYDVTRRDTFDNLDTWLNELDTY---STNPDAVKMLVGNKI 116
Query: 167 DVPGALSAEEVGVALDLSSISSRQHRIKLIATQAPSNL 204
D E G +R+H + I T A + +
Sbjct: 117 DKENREVTREEGQKF------ARKHNMLFIETSAKTRI 148
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 39.3 bits (93), Expect = 9e-04
Identities = 40/154 (25%), Positives = 60/154 (38%), Gaps = 56/154 (36%)
Query: 54 KIL----ILGLDNSGKSTLIKQISSGN--------TSLSHNL---KPTEGFNITI----- 93
K+L ++G N GKSTL+ +S+ T+L NL + +G + +
Sbjct: 156 KLLADVGLVGFPNVGKSTLLSVVSNAKPKIANYHFTTLVPNLGVVETDDGRSFVMADIPG 215
Query: 94 ------LQKGEYTLNIFELGGQENVRRFWNTYF----EDTDLLVFVVD-SADPSKLPVAA 142
G LG Q F E T ++V V+D S + P+
Sbjct: 216 LIEGASEGVG--------LGHQ----------FLRHIERTRVIVHVIDMSGSEGRDPIED 257
Query: 143 M-----ELKNLLGDQRLSTVPILVIANKQDVPGA 171
ELK + RL P +V+ANK D+P A
Sbjct: 258 YEKINKELKLY--NPRLLERPQIVVANKMDLPEA 289
>gnl|CDD|215692 pfam00071, Ras, Ras family. Includes sub-families Ras, Rab, Rac,
Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with
GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025,
pfam00063. As regards Rab GTPases, these are important
regulators of vesicle formation, motility and fusion.
They share a fold in common with all Ras GTPases: this
is a six-stranded beta-sheet surrounded by five
alpha-helices.
Length = 162
Score = 37.5 bits (88), Expect = 0.002
Identities = 31/125 (24%), Positives = 53/125 (42%), Gaps = 19/125 (15%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGF-----NITILQKGEYTLNIFELGG 108
K++++G GKS+L+ + + + PT G I + K L I++ G
Sbjct: 1 KLVLVGDGGVGKSSLLIRFTQNKFPEEY--IPTIGVDFYTKTIEVDGK-TVKLQIWDTAG 57
Query: 109 QENVRRFWNTYFEDTD--LLVFVVDSADPSKLPVAAMELKNLLGD---QRLSTVPILVIA 163
QE R Y+ LLV+ + S D + +K L + VPI+++
Sbjct: 58 QERFRALRPLYYRGAQGFLLVYDITSRDSFE------NVKKWLEEILRHADENVPIVLVG 111
Query: 164 NKQDV 168
NK D+
Sbjct: 112 NKCDL 116
>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 = 37.3 bits (87), Expect = 0.002
Identities = 17/61 (27%), Positives = 34/61 (55%), Gaps = 5/61 (8%)
Query: 54 KILILGLDNSGKSTLIKQ----ISSGNTSLSHNLKPTEGFNITILQKGEYTLNIFELGGQ 109
K++++G GK++L KQ G+ S +H + + + I ++ + LN+++ GGQ
Sbjct: 3 KLMLVGQGGVGKTSLCKQLIGEKFDGDESSTHGIN-VQDWKIPAPERKKIRLNVWDFGGQ 61
Query: 110 E 110
E
Sbjct: 62 E 62
>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 = 36.7 bits (86), Expect = 0.003
Identities = 30/121 (24%), Positives = 56/121 (46%), Gaps = 13/121 (10%)
Query: 54 KILILGLDNS-GKSTLIKQISSGNTSLSHNLKPTEG--FNITILQKGE--YTLNIFELGG 108
KI+++G D+ GK++L+ + S N K T G F ++ L I++ G
Sbjct: 2 KIVLIG-DSGVGKTSLLLRFVDN--KFSENYKSTIGVDFKSKTIEVDGKKVKLQIWDTAG 58
Query: 109 QENVRRFWNTYFEDTD--LLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQ 166
QE R ++Y+ +LV+ V + + + + N L + +PI+++ NK
Sbjct: 59 QERFRSITSSYYRGAHGAILVYDVTNRESFE---NLDKWLNELKEYAPPNIPIILVGNKS 115
Query: 167 D 167
D
Sbjct: 116 D 116
>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 = 37.4 bits (88), Expect = 0.003
Identities = 43/181 (23%), Positives = 68/181 (37%), Gaps = 60/181 (33%)
Query: 32 RQSTPEDEGFEEVSKVDDIFQRKIL----ILGLDNSGKSTLIKQISSGN--------TSL 79
R +TP + G E + + K+L ++GL N+GKSTLI +S+ T+L
Sbjct: 137 RFATPGEPG--EERWL--RLELKLLADVGLVGLPNAGKSTLISAVSAAKPKIADYPFTTL 192
Query: 80 SHNL---KPTEGFNITI-----------LQKGEYTLNIFELGGQENVRRFWNTYF----E 121
NL + +G + I G LG + F E
Sbjct: 193 VPNLGVVRVDDGRSFVIADIPGLIEGASEGAG--------LGHR----------FLKHIE 234
Query: 122 DTDLLVFVVDSADPSKL-PVAAM-----ELKNLLGDQRLSTVPILVIANKQDVPGALSAE 175
T +L+ ++D + P+ ELK L+ P +V+ NK D+ E
Sbjct: 235 RTRVLLHLIDISPEDGSDPIEDYEIIRNELK--KYSPELAEKPRIVVLNKIDLLDEEELE 292
Query: 176 E 176
E
Sbjct: 293 E 293
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 37.2 bits (87), Expect = 0.004
Identities = 35/125 (28%), Positives = 54/125 (43%), Gaps = 20/125 (16%)
Query: 55 ILILGLDNSGKSTLIKQISSGNTSL-SHNLKP-TEGFNIT-ILQKGEY------TLNIFE 105
+ I+G N GKSTL+ + S+ S KP T I I+ T I +
Sbjct: 9 VAIIGRPNVGKSTLLNALVGQKISIVSP--KPQTTRNRIRGIVTTDNAQIIFVDTPGIHK 66
Query: 106 ---LGGQENVRRFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVI 162
G+ + + +D DL++FVVD+ + P L+ L ++ T ILV+
Sbjct: 67 PKHALGELMNKAARSAL-KDVDLILFVVDADEGWG-PGDEFILEQL---KKTKTPVILVV 121
Query: 163 ANKQD 167
NK D
Sbjct: 122 -NKID 125
>gnl|CDD|206679 cd01892, Miro2, Mitochondrial Rho family 2 (Miro2), C-terminal.
Miro2 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the putative
GTPase domain in the C terminus of Miro proteins. These
atypical Rho GTPases have roles in mitochondrial
homeostasis and apoptosis. Most Rho proteins contain a
lipid modification site at the C-terminus; however, Miro
is one of few Rho subfamilies that lack this feature.
Length = 180
Score = 36.5 bits (85), Expect = 0.004
Identities = 39/183 (21%), Positives = 66/183 (36%), Gaps = 31/183 (16%)
Query: 52 QRKIL---ILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNI---TILQKG-EYTLNIF 104
QR + +LG SGKS L++ G + + PT T+ G E L +
Sbjct: 1 QRNVFLCFVLGAKGSGKSALLQAFL-GRSFSQNAYSPTIKPRYAVNTVEVPGQEKYLILR 59
Query: 105 ELGGQENVRRFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIAN 164
E+G E + D+ V DS+DP+ A E+ L +P L +A
Sbjct: 60 EVGEDEEAILLNDAELAACDVACLVYDSSDPNSFSYCA-EVYKKYFM--LGEIPCLFVAA 116
Query: 165 KQDVPGA-----LSAEEVGVALDLSSISSRQHRIK---LIATQAPSNLHHLHVSVVEAEQ 216
K D+ + +E R+ + +++ + + L + A
Sbjct: 117 KADLDEQQQRAEVQPDEF----------CRKLGLPPPLHFSSRLGDSSNELFTKLATA-- 164
Query: 217 AMY 219
A Y
Sbjct: 165 AQY 167
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 36.4 bits (85), Expect = 0.009
Identities = 32/149 (21%), Positives = 63/149 (42%), Gaps = 27/149 (18%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPT------EGFNITILQKGEYTLNIFELG 107
K++I+G N GKS+L+ + + ++ ++ T E N+ + + +
Sbjct: 219 KVVIIGRPNVGKSSLLNALLGRDRAIVTDIAGTTRDVIEEDINL-----NGIPVRLVDTA 273
Query: 108 G---------QENVRRFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVP 158
G + + R E+ DL++FV+D++ P L + L + P
Sbjct: 274 GIRETDDVVERIGIERAKKA-IEEADLVLFVLDASQP--LDKEDLALI----ELLPKKKP 326
Query: 159 ILVIANKQDVPGALSAEEVGVALDLSSIS 187
I+V+ NK D+ + E +A + IS
Sbjct: 327 IIVVLNKADLVSKIELESEKLANGDAIIS 355
>gnl|CDD|206743 cd11383, YfjP, YfjP GTPase. The Era (E. coli Ras-like
protein)-like YfjP subfamily includes several
uncharacterized bacterial GTPases that are similar to
Era. They 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. Era is
characterized by a distinct derivative of the KH domain
(the pseudo-KH domain) which is located C-terminal to
the GTPase domain.
Length = 140
Score = 35.0 bits (81), Expect = 0.010
Identities = 27/127 (21%), Positives = 50/127 (39%), Gaps = 12/127 (9%)
Query: 56 LILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITI-LQKGEYTLNIFELGGQENVRR 114
++G +GKS+L + + + +PT Q G L + +L G R
Sbjct: 1 GLMGKTGAGKSSLCNALFGTEVAAVGDRRPTTRAAQAYVWQTGGDGLVLLDLPGVGERGR 60
Query: 115 F-------WNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQD 167
+ + DL+++++D+ D + L L G P+L + N+ D
Sbjct: 61 RDREYEELYRRLLPEADLVLWLLDADDRALAADHDFYLLPLAGHDA----PLLFVLNQVD 116
Query: 168 VPGALSA 174
A+SA
Sbjct: 117 PVLAVSA 123
>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 = 35.1 bits (81), Expect = 0.012
Identities = 23/77 (29%), Positives = 35/77 (45%), Gaps = 4/77 (5%)
Query: 93 ILQKGEYTLNIFELGGQENVRRFWNTYFEDTD--LLVFVVDSADPSKLPVAAMELKNLLG 150
+L E LNI + GQE+ + YF + LLVF + D A + +L
Sbjct: 42 VLDGEEVQLNILDTAGQEDYAAIRDNYFRSGEGFLLVFSIT--DMESFTALAEFREQILR 99
Query: 151 DQRLSTVPILVIANKQD 167
+ VP+L++ NK D
Sbjct: 100 VKEDDNVPLLLVGNKCD 116
>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 = 35.2 bits (81), Expect = 0.013
Identities = 28/86 (32%), Positives = 43/86 (50%), Gaps = 4/86 (4%)
Query: 48 DDIFQRKILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNI-TILQKGEYT-LNIFE 105
D +F K+LI+G GKS+L+ + + S S+ F I T+ GE L I++
Sbjct: 4 DHLF--KLLIIGDSGVGKSSLLLRFADNTFSGSYITTIGVDFKIRTVEINGERVKLQIWD 61
Query: 106 LGGQENVRRFWNTYFEDTDLLVFVVD 131
GQE R +TY+ T ++ V D
Sbjct: 62 TAGQERFRTITSTYYRGTHGVIVVYD 87
>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 = 34.5 bits (80), Expect = 0.019
Identities = 43/137 (31%), Positives = 63/137 (45%), Gaps = 21/137 (15%)
Query: 52 QRKILILGLDNSGKSTLIKQISSGNTSLSHNLKPT--EGFNITILQKG-EYTLNIFELGG 108
QRKI +LG + GKS+L Q G+ S+ PT F+ I KG EY L I + G
Sbjct: 1 QRKIAVLGSRSVGKSSLTVQFVEGHFVESYY--PTIENTFSKIITYKGQEYHLEIVDTAG 58
Query: 109 QENVRRFWNTYFEDTD--LLVFVVDSADPSKLPVAAMELKNLLGDQRLST-----VPILV 161
Q+ Y +LV+ V S + E+ ++ D+ L VPI++
Sbjct: 59 QDEYSILPQKYSIGIHGYILVYSVTS-------RKSFEVVKVIYDKILDMLGKESVPIVL 111
Query: 162 IANKQDVPG--ALSAEE 176
+ NK D+ +SAEE
Sbjct: 112 VGNKSDLHMERQVSAEE 128
>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 = 34.3 bits (79), Expect = 0.020
Identities = 30/127 (23%), Positives = 55/127 (43%), Gaps = 16/127 (12%)
Query: 57 ILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKGEY-TLNIFELGG------- 108
++GL N GKSTL+ ++S ++ T N+ + + G+ + I +L G
Sbjct: 2 LVGLPNVGKSTLLSALTSAKVEIASYPFTTLEPNVGVFEFGDGVDIQIIDLPGLLDGASE 61
Query: 109 QENVRRFWNTYFEDTDLLVFVVD-SADPSKLPVAAMELKNL-----LGDQRLSTVPILVI 162
+ + +DL++ V+D S D P+ + K L L P +++
Sbjct: 62 GRGLGEQILAHLYRSDLILHVIDASEDCVGDPLE--DQKTLNEEVSGSFLFLKNKPEMIV 119
Query: 163 ANKQDVP 169
ANK D+
Sbjct: 120 ANKIDMA 126
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 34.8 bits (81), Expect = 0.025
Identities = 46/179 (25%), Positives = 73/179 (40%), Gaps = 58/179 (32%)
Query: 32 RQSTPEDEGFEEVSKVDDIFQRKIL----ILGLDNSGKSTLIKQISSGN--------TSL 79
R +TP + G EE D + K+L ++GL N+GKSTL+ +S+ T+L
Sbjct: 139 RFATPGEPG-EER---DLRLELKLLADVGLVGLPNAGKSTLLSAVSAAKPKIADYPFTTL 194
Query: 80 SHNL---KPTEGFNITI-----------LQKGEYTLNIFELGGQENVRRFWNTYF----E 121
NL + G + + G LG F E
Sbjct: 195 VPNLGVVRVDGGESFVVADIPGLIEGASEGVG--------LG----------LRFLRHIE 236
Query: 122 DTDLLVFVVD-SADPSKLPVAAME-LKNLLG--DQRLSTVPILVIANKQDVPGALSAEE 176
T +L+ V+D S + P+ + ++N L +L+ P +V+ NK D+P L EE
Sbjct: 237 RTRVLLHVIDLSPIDGRDPIEDYQTIRNELEKYSPKLAEKPRIVVLNKIDLP--LDEEE 293
>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 = 33.7 bits (77), Expect = 0.034
Identities = 22/87 (25%), Positives = 39/87 (44%), Gaps = 7/87 (8%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNIT---ILQKGEYTLNIFELGGQE 110
K+L+ G SGKS++ K + N S L+ ++ + G TLN+++ GQ+
Sbjct: 1 KLLLXGRRRSGKSSIRKVVFH-NYSPFDTLRLESTIDVEHSHLSFLGNXTLNLWDCPGQD 59
Query: 111 NVRRFWNTY---FEDTDLLVFVVDSAD 134
F+ L++V+D D
Sbjct: 60 VFFEPTKDKEHIFQXVGALIYVIDVQD 86
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 33.9 bits (77), Expect = 0.034
Identities = 25/82 (30%), Positives = 39/82 (47%), Gaps = 7/82 (8%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQ----KGEYTLNIFELGGQ 109
KIL++G GKS+L+ S S +L PT G + I Q L I++ GQ
Sbjct: 16 KILLIGDSGVGKSSLLVSFIS---SSVEDLAPTIGVDFKIKQLTVGGKRLKLTIWDTAGQ 72
Query: 110 ENVRRFWNTYFEDTDLLVFVVD 131
E R ++Y+ + ++ V D
Sbjct: 73 ERFRTLTSSYYRNAQGIILVYD 94
>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 = 33.4 bits (77), Expect = 0.045
Identities = 26/121 (21%), Positives = 53/121 (43%), Gaps = 9/121 (7%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSH--NLKPTEGFNITILQKGEYTLNIFELGGQEN 111
K+++LG GK++L+ + + H + + + L I++ GQE
Sbjct: 2 KVVLLGEGRVGKTSLVLRYVENKFNEKHESTTQASFFQKTVNIGGKRIDLAIWDTAGQER 61
Query: 112 VRRFWNTYFEDTD--LLVF-VVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQDV 168
Y+ D D +LV+ + D+ K+ ELK + G+ + ++++ NK D+
Sbjct: 62 YHALGPIYYRDADGAILVYDITDADSFQKVKKWIKELKQMRGNN----ISLVIVGNKIDL 117
Query: 169 P 169
Sbjct: 118 E 118
>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 = 33.7 bits (78), Expect = 0.050
Identities = 22/93 (23%), Positives = 39/93 (41%), Gaps = 21/93 (22%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKGEY---------TLNIF 104
K+L++GL SGKS++ I N P + + E TLN++
Sbjct: 1 KVLLMGLRGSGKSSMRSII-------FSNYSPRDTLRLGATIDVEQSHVRFLGNLTLNLW 53
Query: 105 ELGGQEN-----VRRFWNTYFEDTDLLVFVVDS 132
+ GQ++ + R F + +L++V D
Sbjct: 54 DCPGQDDFMENYLTRQKEHIFSNVGVLIYVFDV 86
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 33.3 bits (77), Expect = 0.052
Identities = 30/118 (25%), Positives = 51/118 (43%), Gaps = 7/118 (5%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEG--FNITILQKGEYT--LNIFELGGQ 109
KI+++G GKS+L+ + + G S + K T G F ++ L I++ GQ
Sbjct: 2 KIILIGDSGVGKSSLLSRFTDGKFSEQY--KSTIGVDFKTKTIEVDGKRVKLQIWDTAGQ 59
Query: 110 ENVRRFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQD 167
E R ++Y+ + V D + LK L + V I+++ NK D
Sbjct: 60 ERFRSITSSYYRGAVGALLVYDITNRESFENLENWLKELR-EYASPNVVIMLVGNKSD 116
>gnl|CDD|214595 smart00275, G_alpha, G protein alpha subunit. Subunit of G
proteins that contains the guanine nucleotide binding
site.
Length = 342
Score = 33.7 bits (78), Expect = 0.052
Identities = 11/19 (57%), Positives = 16/19 (84%)
Query: 54 KILILGLDNSGKSTLIKQI 72
K+L+LG SGKST++KQ+
Sbjct: 23 KLLLLGAGESGKSTILKQM 41
Score = 28.7 bits (65), Expect = 2.3
Identities = 20/95 (21%), Positives = 39/95 (41%), Gaps = 10/95 (10%)
Query: 84 KPTEGFNITILQKGEYTLNIFELGGQENVRRFWNTYFEDTDLLVFVVDSADPSKLPVAAM 143
PT G T + +F++GGQ + R+ W F++ ++F V ++ ++
Sbjct: 169 VPTTGIQETAFIVKKLFFRMFDVGGQRSERKKWIHCFDNVTAIIFCVALSEYDQVLEEDE 228
Query: 144 ------ELKNLL----GDQRLSTVPILVIANKQDV 168
E NL + + I++ NK D+
Sbjct: 229 STNRMQESLNLFESICNSRWFANTSIILFLNKIDL 263
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 34.1 bits (79), Expect = 0.053
Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 8/47 (17%)
Query: 32 RQSTPEDEGFEEVSKVDDIFQRKIL----ILGLDNSGKSTLIKQISS 74
RQ TP G E ++ + K+L +LGL N+GKST I+ +S+
Sbjct: 139 RQKTPGTPG--EEREL--KLELKLLADVGLLGLPNAGKSTFIRAVSA 181
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 33.5 bits (78), Expect = 0.060
Identities = 12/25 (48%), Positives = 18/25 (72%), Gaps = 4/25 (16%)
Query: 54 KIL----ILGLDNSGKSTLIKQISS 74
K+L ++GL N+GKSTLI +S+
Sbjct: 156 KLLADVGLVGLPNAGKSTLISAVSA 180
>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 = 33.5 bits (77), Expect = 0.060
Identities = 31/123 (25%), Positives = 45/123 (36%), Gaps = 15/123 (12%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNI-TILQKGEYTLNIFELGGQENV 112
+ ILG N GKSTL+ Q+ S++ T I I G + + G
Sbjct: 2 FVAILGRPNVGKSTLLNQLHGQKISITSPKAQTTRNRISGIHTTGASQIIFIDTPGFHEK 61
Query: 113 RRFWNTY--------FEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIAN 164
+ N DL++FVVDS + L Q L P+++ N
Sbjct: 62 KHSLNRLMMKEARSAIGGVDLILFVVDSDQ--WNGDGEF-VLTKL--QNLKR-PVVLTRN 115
Query: 165 KQD 167
K D
Sbjct: 116 KLD 118
>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 = 33.3 bits (77), Expect = 0.070
Identities = 11/19 (57%), Positives = 16/19 (84%)
Query: 54 KILILGLDNSGKSTLIKQI 72
K+L+LG SGKST++KQ+
Sbjct: 2 KLLLLGAGESGKSTILKQM 20
Score = 27.1 bits (61), Expect = 8.7
Identities = 12/31 (38%), Positives = 19/31 (61%)
Query: 100 TLNIFELGGQENVRRFWNTYFEDTDLLVFVV 130
+F++GGQ + R+ W FED ++FVV
Sbjct: 162 KFRMFDVGGQRSERKKWIHCFEDVTAIIFVV 192
>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 = 32.5 bits (74), Expect = 0.077
Identities = 29/130 (22%), Positives = 61/130 (46%), Gaps = 10/130 (7%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKGE-----YTLNIFELGG 108
K++++G + GK+ LI + N K T G + + ++ E ++L +++ G
Sbjct: 2 KVIVVGDLSVGKTCLINRFCKD--VFDKNYKATIGVDFEM-ERFEVLGVPFSLQLWDTAG 58
Query: 109 QENVRRFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQDV 168
QE + +TY+ ++ V D D + L L++ L + S+V + ++ K+D+
Sbjct: 59 QERFKCIASTYYRGAQAIIIVFDLTDVASLEHTRQWLEDALKENDPSSVLLFLVGTKKDL 118
Query: 169 --PGALSAEE 176
P + E
Sbjct: 119 SSPAQYALME 128
>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 = 0.099
Identities = 28/152 (18%), Positives = 66/152 (43%), Gaps = 30/152 (19%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPT-----------EGFNITI-----LQKG 97
K++I G N GKS+L+ ++ + ++ ++ T G + + L++
Sbjct: 5 KVVIAGKPNVGKSSLLNALAGRDRAIVSDIAGTTRDVIEEEIDLGGIPVRLIDTAGLRET 64
Query: 98 EYTLNIFELGGQENVRRFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTV 157
E + E + + R E+ DL++ VVD+++ ++ ++L + +
Sbjct: 65 E---DEIE---KIGIERAREA-IEEADLVLLVVDASEG-------LDEEDLEILELPAKK 110
Query: 158 PILVIANKQDVPGALSAEEVGVALDLSSISSR 189
P++V+ NK D+ + +IS++
Sbjct: 111 PVIVVLNKSDLLSDAEGISELNGKPIIAISAK 142
>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 = 32.7 bits (75), Expect = 0.10
Identities = 35/131 (26%), Positives = 63/131 (48%), Gaps = 20/131 (15%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEG--FNITILQKGEYT---LNIFELGG 108
K+L++G GK+++IK+ G S + K T G F + +++ T L ++++ G
Sbjct: 2 KVLVIGDLGVGKTSIIKRYVHGV--FSQHYKATIGVDFALKVIEWDPNTVVRLQLWDIAG 59
Query: 109 QENVRRFWNT---YFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLST-----VPIL 160
QE RF Y++ + V D PS A ++ K L D +++ +P L
Sbjct: 60 QE---RFGGMTRVYYKGAVGAIIVFDVTRPSTFE-AVLKWKADL-DSKVTLPNGEPIPAL 114
Query: 161 VIANKQDVPGA 171
++ANK D+
Sbjct: 115 LLANKCDLKKE 125
>gnl|CDD|206706 cd04134, Rho3, Ras homology family 3 (Rho3) of small guanosine
triphosphatases (GTPases). Rho3 is a member of the Rho
family found only in fungi. Rho3 is believed to regulate
cell polarity by interacting with the diaphanous/formin
family protein For3 to control both the actin
cytoskeleton and microtubules. Rho3 is also believed to
have a direct role in exocytosis that is independent of
its role in regulating actin polarity. The function in
exocytosis may be two-pronged: first, in the transport
of post-Golgi vesicles from the mother cell to the bud,
mediated by myosin (Myo2); second, in the docking and
fusion of vesicles to the plasma membrane, mediated by
an exocyst (Exo70) protein. Most Rho proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Rho proteins.
Length = 185
Score = 32.5 bits (74), Expect = 0.11
Identities = 25/87 (28%), Positives = 42/87 (48%), Gaps = 7/87 (8%)
Query: 53 RKILILGLDNSGKSTLIKQISSGNTSLSHNLKPT--EGFNITILQKGEY-TLNIFELGGQ 109
RK+++LG GK++L+ + G +PT E + I G L++++ GQ
Sbjct: 1 RKVVVLGDGACGKTSLLNVFTRG--YFPQVYEPTVFENYIHDIFVDGLAVELSLWDTAGQ 58
Query: 110 ENVRRFWNTYFEDTD--LLVFVVDSAD 134
E R + + DT +L F VD+ D
Sbjct: 59 EEFDRLRSLSYADTHVIMLCFSVDNPD 85
>gnl|CDD|213187 cd03220, ABC_KpsT_Wzt, ATP-binding cassette component of
polysaccharide transport system. The KpsT/Wzt ABC
transporter subfamily is involved in extracellular
polysaccharide export. Among the variety of
membrane-linked or extracellular polysaccharides
excreted by bacteria, only capsular polysaccharides,
lipopolysaccharides, and teichoic acids have been shown
to be exported by ABC transporters. A typical system is
made of a conserved integral membrane and an ABC. In
addition to these proteins, capsular polysaccharide
exporter systems require two 'accessory' proteins to
perform their function: a periplasmic (E.coli) or a
lipid-anchored outer membrane protein called OMA
(Neisseria meningitidis and Haemophilus influenza) and a
cytoplasmic membrane protein MPA2.
Length = 224
Score = 31.7 bits (73), Expect = 0.19
Identities = 23/109 (21%), Positives = 42/109 (38%), Gaps = 24/109 (22%)
Query: 18 SVCTYATYQYWKKRRQSTPEDEGFEEVSKVDDI-FQ----RKILILGLDNSGKSTLIKQI 72
S TY K+ E + D+ F+ +I ++G + +GKSTL++ +
Sbjct: 9 SYPTYKGGSSSLKKLGILGRKGEVGEFWALKDVSFEVPRGERIGLIGRNGAGKSTLLRLL 68
Query: 73 SSGNTSLSHNLKPTEGFNITILQKGEYTLNIFELG--------GQENVR 113
+ P G T+ +G + + LG G+EN+
Sbjct: 69 AG-------IYPPDSG---TVTVRGRVSS-LLGLGGGFNPELTGRENIY 106
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 32.2 bits (74), Expect = 0.19
Identities = 17/47 (36%), Positives = 30/47 (63%), Gaps = 3/47 (6%)
Query: 122 DTDLLVFVVDSADPSKLP-VAAMELKNLLGDQRLSTVPILVIANKQD 167
+ DLL+ VVD++DP L + A+E ++L + +PI+++ NK D
Sbjct: 271 EADLLLHVVDASDPEILEKLEAVE--DVLAEIGADEIPIILVLNKID 315
>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 = 31.3 bits (72), Expect = 0.22
Identities = 33/121 (27%), Positives = 58/121 (47%), Gaps = 13/121 (10%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPT--EGFNITILQKGE-YTLNIFELGGQE 110
K+++LG GKS L + SG ++ PT + + I+ GE YTL+I + GQE
Sbjct: 1 KLVVLGAGGVGKSALTIRFVSGEFVEEYD--PTIEDSYRKQIVVDGETYTLDILDTAGQE 58
Query: 111 NVRRFWNTYFEDTD--LLVFVVDSADPSKLPVAAM--ELKNLLGDQRLSTVPILVIANKQ 166
+ Y + D +LV+ + S S + + ++ + + VPI+++ NK
Sbjct: 59 EFSAMRDQYIRNGDGFILVYSITSR-ESFEEIKNIREQILRVKDKE---DVPIVLVGNKC 114
Query: 167 D 167
D
Sbjct: 115 D 115
>gnl|CDD|163431 TIGR03719, ABC_ABC_ChvD, ATP-binding cassette protein, ChvD
family. Members of this protein family have two copies
of the ABC transporter ATP-binding cassette, but are
found outside the common ABC transporter operon
structure that features integral membrane permease
proteins and substrate-binding proteins encoded next to
the ATP-binding cassette (ABC domain) protein. The
member protein ChvD from Agrobacterium tumefaciens was
identified as both a candidate to interact with VirB8,
based on yeast two-hybrid analysis, and as an apparent
regulator of VirG. The general function of this protein
family is unknown.
Length = 552
Score = 32.2 bits (74), Expect = 0.22
Identities = 13/41 (31%), Positives = 24/41 (58%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITIL 94
KI +LGL+ +GKSTL++ ++ + + +P G + L
Sbjct: 33 KIGVLGLNGAGKSTLLRIMAGVDKEFNGEARPAPGIKVGYL 73
>gnl|CDD|133342 cd04142, RRP22, Ras-related protein on chromosome 22 (RRP22)
family. RRP22 (Ras-related protein on chromosome 22)
subfamily consists of proteins that inhibit cell growth
and promote caspase-independent cell death. Unlike most
Ras proteins, RRP22 is down-regulated in many human
tumor cells due to promoter methylation. RRP22 localizes
to the nucleolus in a GTP-dependent manner, suggesting a
novel function in modulating transport of nucleolar
components. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras proteins.
Like most Ras family proteins, RRP22 is farnesylated.
Length = 198
Score = 31.4 bits (71), Expect = 0.27
Identities = 34/171 (19%), Positives = 63/171 (36%), Gaps = 26/171 (15%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNI----TILQKGEYTLNIFEL--- 106
++ +LG GK+ +++Q + + PTE + +L Y L+I ++
Sbjct: 2 RVAVLGAPGVGKTAIVRQFLAQEFPEEY--IPTEHRRLYRPAVVLSGRVYDLHILDVPNM 59
Query: 107 ------GGQENV-RRFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRL---ST 156
GQE + RF ++ + V D P + L+ + + R
Sbjct: 60 QRYPGTAGQEWMDPRFRG--LRNSRAFILVYDICSPDSFHYVKL-LRQQILETRPAGNKE 116
Query: 157 VPILVIANKQDVPGALSAEEVGVALDLSSISSRQHRIKLIATQAPSNLHHL 207
PI+V+ NK+D LS + + + + A N H L
Sbjct: 117 PPIVVVGNKRD----QQRHRFAPRHVLSVLVRKSWKCGYLECSAKYNWHIL 163
>gnl|CDD|206696 cd04113, Rab4, Rab GTPase family 4 (Rab4). Rab4 subfamily. Rab4
has been implicated in numerous functions within the
cell. It helps regulate endocytosis through the sorting,
recycling, and degradation of early endosomes. Mammalian
Rab4 is involved in the regulation of many surface
proteins including G-protein-coupled receptors,
transferrin receptor, integrins, and surfactant protein
A. Experimental data implicate Rab4 in regulation of the
recycling of internalized receptors back to the plasma
membrane. It is also believed to influence
receptor-mediated antigen processing in B-lymphocytes,
in calcium-dependent exocytosis in platelets, in
alpha-amylase secretion in pancreatic cells, and in
insulin-induced translocation of Glut4 from internal
vesicles to the cell surface. Rab4 is known to share
effector proteins with Rab5 and Rab11. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 161
Score = 30.9 bits (70), Expect = 0.29
Identities = 32/121 (26%), Positives = 51/121 (42%), Gaps = 13/121 (10%)
Query: 54 KILILGLDNSGKSTLIKQISSGN--TSLSHNLKPTEGFNITILQKGEYTLNIFELGGQEN 111
K LI+G +GKS L+ Q +H + G + + L I++ GQE
Sbjct: 2 KFLIIGSAGTGKSCLLHQFIENKFKQDSNHTIGVEFGSRVVNVGGKSVKLQIWDTAGQER 61
Query: 112 VRRFWNTYFEDT--DLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVP---ILVIANKQ 166
R +Y+ LLV+ + S + + L N L D R P I+++ NK+
Sbjct: 62 FRSVTRSYYRGAAGALLVYDITSRE------SFNALTNWLTDARTLASPDIVIILVGNKK 115
Query: 167 D 167
D
Sbjct: 116 D 116
>gnl|CDD|206664 cd01874, Cdc42, cell division cycle 42 (Cdc42) is a small GTPase of
the Rho family. Cdc42 is an essential GTPase that
belongs to the Rho family of Ras-like GTPases. These
proteins act as molecular switches by responding to
exogenous and/or endogenous signals and relaying those
signals to activate downstream components of a
biological pathway. Cdc42 transduces signals to the
actin cytoskeleton to initiate and maintain polarized
growth and to mitogen-activated protein morphogenesis.
In the budding yeast Saccharomyces cerevisiae, Cdc42
plays an important role in multiple actin-dependent
morphogenetic events such as bud emergence,
mating-projection formation, and pseudohyphal growth. In
mammalian cells, Cdc42 regulates a variety of
actin-dependent events and induces the JNK/SAPK protein
kinase cascade, which leads to the activation of
transcription factors within the nucleus. Cdc42 mediates
these processes through interactions with a myriad of
downstream effectors, whose number and regulation we are
just starting to understand. In addition, Cdc42 has been
implicated in a number of human diseases through
interactions with its regulators and downstream
effectors. Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 175
Score = 31.0 bits (70), Expect = 0.32
Identities = 25/80 (31%), Positives = 40/80 (50%), Gaps = 7/80 (8%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPT--EGFNITILQKGE-YTLNIFELGGQE 110
K +++G GK+ L+ IS PT + + +T++ GE YTL +F+ GQE
Sbjct: 3 KCVVVGDGAVGKTCLL--ISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTLGLFDTAGQE 60
Query: 111 NVRRFWNTYFEDTDLLVFVV 130
+ R + TD VF+V
Sbjct: 61 DYDRLRPLSYPQTD--VFLV 78
>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 = 31.3 bits (72), Expect = 0.36
Identities = 32/147 (21%), Positives = 54/147 (36%), Gaps = 46/147 (31%)
Query: 55 ILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKG------EYTLNIFELG- 107
I I G N+GKS+LI ++ ++ I G + + LG
Sbjct: 9 IGIFGRRNAGKSSLINALT--GQDIA----------IVSDVPGTTTDPVYKAMELLPLGP 56
Query: 108 ---------------GQENVRRFWNTY--FEDTDLLVFVVDSADPSKLPVAA-MELKNLL 149
G+ V + T + TDL + VVD+ P +EL L
Sbjct: 57 VVLIDTAGLDDEGELGELRVEK---TREVLDKTDLALLVVDAGVG---PGEYELELIEEL 110
Query: 150 GDQRLSTVPILVIANKQDVPGALSAEE 176
+++ +P +V+ NK D+ + E
Sbjct: 111 KERK---IPYIVVINKIDLGEESAELE 134
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 31.4 bits (72), Expect = 0.37
Identities = 13/33 (39%), Positives = 18/33 (54%)
Query: 40 GFEEVSKVDDIFQRKILILGLDNSGKSTLIKQI 72
EE + ++ KI I+G N GKS+LI I
Sbjct: 166 PDEEEEEEEETDPIKIAIIGRPNVGKSSLINAI 198
Score = 30.2 bits (69), Expect = 0.74
Identities = 34/134 (25%), Positives = 56/134 (41%), Gaps = 25/134 (18%)
Query: 53 RKILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNIT---ILQKGEYTLNIFEL--- 106
+ I+G N GKSTL +++ ++ + +T I E+ F L
Sbjct: 4 PVVAIVGRPNVGKSTLFNRLTGRRIAIVSDTP-----GVTRDRIYGDAEWLGREFILIDT 58
Query: 107 GG---------QENVRRFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTV 157
GG QE +R E+ D+++FVVD + A E+ +L R S
Sbjct: 59 GGLDDGDEDELQELIREQALIAIEEADVILFVVDGR--EGITPADEEIAKIL---RRSKK 113
Query: 158 PILVIANKQDVPGA 171
P++++ NK D A
Sbjct: 114 PVILVVNKIDNLKA 127
>gnl|CDD|213188 cd03221, ABCF_EF-3, ATP-binding cassette domain of elongation
factor 3, subfamily F. Elongation factor 3 (EF-3) is a
cytosolic protein required by fungal ribosomes for in
vitro protein synthesis and for in vivo growth. EF-3
stimulates the binding of the EF-1: GTP: aa-tRNA
ternary complex to the ribosomal A site by facilitated
release of the deacylated tRNA from the E site. The
reaction requires ATP hydrolysis. EF-3 contains two ATP
nucleotide binding sequence (NBS) motifs. NBSI is
sufficient for the intrinsic ATPase activity. NBSII is
essential for the ribosome-stimulated functions.
Length = 144
Score = 30.5 bits (70), Expect = 0.38
Identities = 13/37 (35%), Positives = 21/37 (56%), Gaps = 7/37 (18%)
Query: 53 RKILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGF 89
+I ++G + +GKSTL+K I + L+P EG
Sbjct: 27 DRIGLVGRNGAGKSTLLKLI-------AGELEPDEGI 56
>gnl|CDD|236992 PRK11819, PRK11819, putative ABC transporter ATP-binding protein;
Reviewed.
Length = 556
Score = 31.2 bits (72), Expect = 0.39
Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 12/48 (25%)
Query: 54 KILILGLDNSGKSTLIK------QISSGNTSLSHNLKPTEGFNITILQ 95
KI +LGL+ +GKSTL++ + G +P G + L
Sbjct: 35 KIGVLGLNGAGKSTLLRIMAGVDKEFEGEA------RPAPGIKVGYLP 76
>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 = 30.6 bits (70), Expect = 0.41
Identities = 33/124 (26%), Positives = 53/124 (42%), Gaps = 18/124 (14%)
Query: 53 RKILILGLDNSGKSTLIKQISSGNTSLSHNLKPT--EGFNITILQKGE-YTLNIFELGGQ 109
KI+++G GK+ L+ IS PT + ++ + G+ L +++ GQ
Sbjct: 1 IKIVVVGDGAVGKTCLL--ISYTTNKFPTEYVPTVFDNYSANVTVDGKQVNLGLWDTAGQ 58
Query: 110 ENVRRFWNTYFEDTD--LLVFVVDSADPSKLPVAAM----ELKNLLGDQRLSTVPILVIA 163
E R + TD LL F VDS PS E+K+ + VPI+++
Sbjct: 59 EEYDRLRPLSYPQTDVFLLCFSVDS--PSSFENVKTKWYPEIKHYCPN-----VPIILVG 111
Query: 164 NKQD 167
K D
Sbjct: 112 TKID 115
>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 = 30.5 bits (69), Expect = 0.47
Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 17/76 (22%)
Query: 101 LNIFELGGQENVRRFWNTYFEDTD--LLVFVVDSAD-----PSK-LPVAAMELKNLLGDQ 152
L +++ GQE+ R + DTD L+ F +DS D P K P E+K+ +
Sbjct: 51 LALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTP----EVKHFCPN- 105
Query: 153 RLSTVPILVIANKQDV 168
VPI+++ NK+D+
Sbjct: 106 ----VPIILVGNKKDL 117
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 30.3 bits (69), Expect = 0.47
Identities = 11/21 (52%), Positives = 16/21 (76%)
Query: 53 RKILILGLDNSGKSTLIKQIS 73
+ILILG +GKSTL K+++
Sbjct: 1 MRILILGPPGAGKSTLAKKLA 21
>gnl|CDD|224052 COG1127, Ttg2A, ABC-type transport system involved in resistance to
organic solvents, ATPase component [Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 263
Score = 30.6 bits (70), Expect = 0.58
Identities = 29/87 (33%), Positives = 43/87 (49%), Gaps = 20/87 (22%)
Query: 49 DIFQRKIL-ILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKGEYTLNIFELG 107
D+ + +IL ILG SGKSTL++ I L L+P +G IL GE +I +L
Sbjct: 30 DVPRGEILAILGGSGSGKSTLLRLI----LGL---LRPDKG---EILIDGE---DIPQLS 76
Query: 108 GQEN--VRRFWNTYFED----TDLLVF 128
+E +R+ F+ + L VF
Sbjct: 77 EEELYEIRKRMGVLFQQGALFSSLTVF 103
>gnl|CDD|213192 cd03225, ABC_cobalt_CbiO_domain1, First domain of the ATP-binding
cassette component of cobalt transport system. Domain I
of the ABC component of a cobalt transport family found
in bacteria, archaea, and eukaryota. The transition
metal cobalt is an essential component of many enzymes
and must be transported into cells in appropriate
amounts when needed. This ABC transport system of the
CbiMNQO family is involved in cobalt transport in
association with the cobalamin (vitamin B12)
biosynthetic pathways. Most of cobalt (Cbi) transport
systems possess a separate CbiN component, the
cobalt-binding periplasmic protein, and they are encoded
by the conserved gene cluster cbiMNQO. Both the CbiM and
CbiQ proteins are integral cytoplasmic membrane
proteins, and the CbiO protein has the linker peptide
and the Walker A and B motifs commonly found in the
ATPase components of the ABC-type transport systems.
Length = 211
Score = 30.1 bits (69), Expect = 0.59
Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 8/56 (14%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKGEYTLNIFELGGQ 109
+LI+G + SGKSTL++ ++ L PT G + + K L++ EL +
Sbjct: 29 FVLIVGPNGSGKSTLLRLLNGL-------LGPTSG-EVLVDGKDLTKLSLKELRRK 76
>gnl|CDD|213197 cd03230, ABC_DR_subfamily_A, ATP-binding cassette domain of the
drug resistance transporter and related proteins,
subfamily A. This family of ATP-binding proteins
belongs to a multi-subunit transporter involved in drug
resistance (BcrA and DrrA), nodulation, lipid
transport, and lantibiotic immunity. In bacteria and
archaea, these transporters usually include an
ATP-binding protein and one or two integral membrane
proteins. Eukaryotic systems of the ABCA subfamily
display ABC domains that are quite similar to this
family. The ATP-binding domain shows the highest
similarity between all members of the ABC transporter
family. ABC transporters are a subset of nucleotide
hydrolases that contain a signature motif, Q-loop, and
H-loop/switch region, in addition to, the Walker A
motif/P-loop and Walker B motif commonly found in a
number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 173
Score = 30.1 bits (69), Expect = 0.63
Identities = 15/38 (39%), Positives = 20/38 (52%), Gaps = 8/38 (21%)
Query: 57 ILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITIL 94
+LG + +GK+TLIK I LKP G I +L
Sbjct: 31 LLGPNGAGKTTLIKIILG-------LLKPDSG-EIKVL 60
>gnl|CDD|181235 PRK08118, PRK08118, topology modulation protein; Reviewed.
Length = 167
Score = 30.0 bits (68), Expect = 0.66
Identities = 10/21 (47%), Positives = 16/21 (76%)
Query: 53 RKILILGLDNSGKSTLIKQIS 73
+KI+++G SGKSTL +Q+
Sbjct: 2 KKIILIGSGGSGKSTLARQLG 22
>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 = 29.5 bits (67), Expect = 0.81
Identities = 45/159 (28%), Positives = 75/159 (47%), Gaps = 18/159 (11%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEG--FNI-TI-LQKGEYTLNIFELGGQ 109
K+L++G GKS L+ + S S + + T G F I TI L + L I++ GQ
Sbjct: 5 KLLLIGDSGVGKSCLLLRFSED--SFNPSFISTIGIDFKIRTIELDGKKIKLQIWDTAGQ 62
Query: 110 ENVRRFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLST-VPILVIANKQDV 168
E R +Y+ ++ V D D ++N+ D+ S V +++ NK D+
Sbjct: 63 ERFRTITTSYYRGAMGIILVYDITDEKSFENIKNWMRNI--DEHASEDVERMLVGNKCDM 120
Query: 169 PG--ALSAEEVGVALDLSSISSRQHRIKLIATQAPSNLH 205
+S EE G AL +R++ IK + T A +N++
Sbjct: 121 EEKRVVSKEE-GEAL------AREYGIKFLETSAKANIN 152
>gnl|CDD|224054 COG1131, CcmA, ABC-type multidrug transport system, ATPase
component [Defense mechanisms].
Length = 293
Score = 30.0 bits (68), Expect = 0.86
Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 8/40 (20%)
Query: 55 ILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITIL 94
+LG + +GK+TL+K L+ LKPT G I +L
Sbjct: 34 FGLLGPNGAGKTTLLK-------ILAGLLKPTSG-EILVL 65
>gnl|CDD|224045 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport
systems, ATPase components [Inorganic ion transport and
metabolism / Coenzyme metabolism].
Length = 258
Score = 29.8 bits (68), Expect = 0.89
Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 13/54 (24%)
Query: 57 ILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKGEYTLNIFELGGQE 110
ILG + SGKSTL+K L+ LKP G +L G+ +I L +E
Sbjct: 33 ILGPNGSGKSTLLK-------CLAGLLKPKSG---EVLLDGK---DIASLSPKE 73
>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 = 29.5 bits (66), Expect = 0.92
Identities = 24/92 (26%), Positives = 42/92 (45%), Gaps = 15/92 (16%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNI-------TILQKGE-YTLNIFE 105
KI+++G GK+ L+++ + G P +G I T+ KGE L I++
Sbjct: 9 KIVLIGNAGVGKTCLVRRFTQGL------FPPGQGATIGVDFMIKTVEIKGEKIKLQIWD 62
Query: 106 LGGQENVRRFWNTYFEDTDLLVFVVD-SADPS 136
GQE R +Y+ + L+ D + + S
Sbjct: 63 TAGQERFRSITQSYYRSANALILTYDITCEES 94
>gnl|CDD|172200 PRK13652, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 277
Score = 29.8 bits (67), Expect = 1.0
Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 18/77 (23%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKGEYTL--NIFELGGQEN 111
+I ++G + +GKSTL + + LKPT G ++L +GE NI E
Sbjct: 32 RIAVIGPNGAGKSTLFRH-------FNGILKPTSG---SVLIRGEPITKENIRE------ 75
Query: 112 VRRFWNTYFEDTDLLVF 128
VR+F F++ D +F
Sbjct: 76 VRKFVGLVFQNPDDQIF 92
>gnl|CDD|130080 TIGR01007, eps_fam, capsular exopolysaccharide family. This model
describes the capsular exopolysaccharide proteins in
bacteria. The exopolysaccharide gene cluster consists of
several genes which encode a number of proteins which
regulate the exoploysaccharide biosynthesis(EPS).
Atleast 13 genes espA to espM in streptococcus species
seem to direct the EPS proteins and all of which share
high homology. Functional roles were characterized by
gene disruption experiments which resulted in
exopolysaccharide-deficient phenotypes [Transport and
binding proteins, Carbohydrates, organic alcohols, and
acids].
Length = 204
Score = 29.7 bits (67), Expect = 1.0
Identities = 27/98 (27%), Positives = 39/98 (39%), Gaps = 17/98 (17%)
Query: 62 NSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKGEYTLNIFELGGQENVRRFWNT--- 118
+G + + SG T LS + T N+ ++ G N EL N + T
Sbjct: 71 ITGLTNFL----SGTTDLSDAICDTNIENLFVITSGPVPPNPTELLQSSNFKTLIETLRK 126
Query: 119 YFE----DTDLLVFVVDSA------DPSKLPVAAMELK 146
YF+ DT + V D+A D S L A E+K
Sbjct: 127 YFDYIIIDTPPIGTVTDAAIIARACDASILVTDAGEIK 164
>gnl|CDD|226592 COG4107, PhnK, ABC-type phosphonate transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 258
Score = 29.7 bits (67), Expect = 1.1
Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 13/77 (16%)
Query: 40 GFEEVSKVDDIFQRKIL-ILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKGE 98
G +VS D++ ++L I+G SGK+TL+K +S L P G +T +
Sbjct: 21 GCRDVSF--DLYPGEVLGIVGESGSGKTTLLK-------CISGRLTPDAG-TVTYRMRDG 70
Query: 99 YTLNIFELGGQENVRRF 115
+++ + E RR
Sbjct: 71 QPRDLYTMS--EAERRR 85
>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 = 29.4 bits (66), Expect = 1.2
Identities = 27/123 (21%), Positives = 52/123 (42%), Gaps = 9/123 (7%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFN-----ITILQKGEYTLNIFELGG 108
KI++LG SGK++LI++ + + K T G + IT+ TL ++++GG
Sbjct: 2 KIVVLGDGASGKTSLIRRFA--QEGFGKSYKQTIGLDFFSRRITLPGSLNVTLQVWDIGG 59
Query: 109 QENVRRFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVP--ILVIANKQ 166
Q+ + + Y + V D + L + S ++++ NK
Sbjct: 60 QQIGGKMLDKYIYGAQAVCLVYDITNSQSFENLEDWLSVVKKVNEESETKPKMVLVGNKT 119
Query: 167 DVP 169
D+
Sbjct: 120 DLE 122
>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 = 29.3 bits (67), Expect = 1.2
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 6/60 (10%)
Query: 124 DLLVFVVDSADP-SKLPVAAMELKNLLGDQRLSTVPILVIANKQDVPGALSAEEVGVALD 182
DLL+ VVD++DP + + +E +L + +PI+++ NK D L EE+ L
Sbjct: 122 DLLLHVVDASDPDREEQIETVE--EVLKELGADDIPIILVLNKID---LLDDEELEERLR 176
>gnl|CDD|206749 cd01856, YlqF, Circularly permuted YlqF GTPase. Proteins of the
YlqF 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. The YlqF subfamily is represented in all
eukaryotes as well as a phylogenetically diverse array
of bacteria (including gram-positive bacteria,
proteobacteria, Synechocystis, Borrelia, and
Thermotoga).
Length = 171
Score = 29.0 bits (66), Expect = 1.2
Identities = 8/16 (50%), Positives = 13/16 (81%)
Query: 54 KILILGLDNSGKSTLI 69
+ +++G+ N GKSTLI
Sbjct: 117 RAMVVGIPNVGKSTLI 132
>gnl|CDD|237045 PRK12296, obgE, GTPase CgtA; Reviewed.
Length = 500
Score = 29.5 bits (67), Expect = 1.4
Identities = 24/65 (36%), Positives = 32/65 (49%), Gaps = 14/65 (21%)
Query: 121 EDTDLLVFVVDSA--DPSKLPVA---AME---------LKNLLGDQRLSTVPILVIANKQ 166
E +LV VVD A +P + P++ A+E L LG L+ P LV+ NK
Sbjct: 235 ERCAVLVHVVDCATLEPGRDPLSDIDALEAELAAYAPALDGDLGLGDLAERPRLVVLNKI 294
Query: 167 DVPGA 171
DVP A
Sbjct: 295 DVPDA 299
>gnl|CDD|213833 TIGR03596, GTPase_YlqF, ribosome biogenesis GTP-binding protein
YlqF. Members of this protein family are GTP-binding
proteins involved in ribosome biogenesis, including the
essential YlqF protein of Bacillus subtilis, which is an
essential protein. They are related to Era, EngA, and
other GTPases of ribosome biogenesis, but are circularly
permuted. This family is not universal, and is not
present in Escherichia coli, and so is not as well
studied as some other GTPases. This model is built for
bacterial members [Protein synthesis, Other].
Length = 276
Score = 29.4 bits (67), Expect = 1.4
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 54 KILILGLDNSGKSTLI 69
+ +I+G+ N GKSTLI
Sbjct: 120 RAMIVGIPNVGKSTLI 135
>gnl|CDD|237453 PRK13633, PRK13633, cobalt transporter ATP-binding subunit;
Provisional.
Length = 280
Score = 29.3 bits (66), Expect = 1.5
Identities = 21/74 (28%), Positives = 38/74 (51%), Gaps = 20/74 (27%)
Query: 20 CTYATYQYWKKRRQSTPEDEGFEEVSKVDDI-FQRK----ILILGLDNSGKSTLIKQISS 74
C +Y+Y +E E+++ +DD+ + K ++ILG + SGKST+ K +++
Sbjct: 7 CKNVSYKYES-------NEESTEKLA-LDDVNLEVKKGEFLVILGRNGSGKSTIAKHMNA 58
Query: 75 GNTSLSHNLKPTEG 88
L P+EG
Sbjct: 59 -------LLIPSEG 65
>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 = 28.6 bits (65), Expect = 1.5
Identities = 33/136 (24%), Positives = 53/136 (38%), Gaps = 40/136 (29%)
Query: 54 KILILGLDNSGKSTLIKQI--------SSGNTSLSHNLKP-TEGFNIT-ILQKGEYTLNI 103
+ I+G N GKSTL+ + S KP T I I + + I
Sbjct: 5 FVAIIGRPNVGKSTLLNALVGQKISIVSP---------KPQTTRNRIRGIYTDDDAQI-I 54
Query: 104 F----------ELGGQENVRRFWNTYFEDTDLLVFVVDSADPSKLPVA--AMELKNLLGD 151
F + G+ V+ W+ +D DL++FVVD+++ LK
Sbjct: 55 FVDTPGIHKPKKKLGERMVKAAWSAL-KDVDLVLFVVDASEWIGEGDEFILELLKK---- 109
Query: 152 QRLSTVPILVIANKQD 167
S P++++ NK D
Sbjct: 110 ---SKTPVILVLNKID 122
>gnl|CDD|184205 PRK13646, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 286
Score = 29.0 bits (65), Expect = 1.6
Identities = 25/79 (31%), Positives = 39/79 (49%), Gaps = 19/79 (24%)
Query: 24 TYQYWKKRRQSTPEDEGFEEVSKVDDIFQ--RKILILGLDNSGKSTLIKQISSGNTSLSH 81
+Y Y ++ TP + + + V+ F+ + I+G SGKSTLI+ I++
Sbjct: 9 SYTY----QKGTPYE--HQAIHDVNTEFEQGKYYAIVGQTGSGKSTLIQNINA------- 55
Query: 82 NLKPTEGF----NITILQK 96
LKPT G +ITI K
Sbjct: 56 LLKPTTGTVTVDDITITHK 74
>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 = 28.9 bits (65), Expect = 1.7
Identities = 29/117 (24%), Positives = 54/117 (46%), Gaps = 4/117 (3%)
Query: 54 KILILGLDNSGKSTLIKQISSG-NTSLSHNLKPTEGFNITILQKGE-YTLNIFELGGQEN 111
++++LG GKS+L ++G ++ + + T+ GE TL +++ QE+
Sbjct: 2 RVVLLGDSGVGKSSLANIFTAGVYEDSAYEASGDDTYERTVSVDGEEATLVVYDHWEQED 61
Query: 112 VRRFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQR-LSTVPILVIANKQD 167
++ + D V V D S A+ EL+ L R +PI+++ NK D
Sbjct: 62 GMWLEDSCMQVGDAYVIVYSVTDRSSFEKAS-ELRIQLRRARQAEDIPIILVGNKSD 117
>gnl|CDD|183280 PRK11701, phnK, phosphonate C-P lyase system protein PhnK;
Provisional.
Length = 258
Score = 29.1 bits (66), Expect = 1.7
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 13/77 (16%)
Query: 40 GFEEVSKVDDIFQRKIL-ILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKGE 98
G +VS D++ ++L I+G SGK+TL+ +LS L P G + +
Sbjct: 21 GCRDVSF--DLYPGEVLGIVGESGSGKTTLLN-------ALSARLAPDAG-EVHYRMRDG 70
Query: 99 YTLNIFELGGQENVRRF 115
+++ L E RR
Sbjct: 71 QLRDLYALSEAE--RRR 85
>gnl|CDD|236583 PRK09601, PRK09601, GTP-binding protein YchF; Reviewed.
Length = 364
Score = 29.3 bits (67), Expect = 1.8
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 54 KILILGLDNSGKSTL 68
K I+GL N GKSTL
Sbjct: 4 KCGIVGLPNVGKSTL 18
>gnl|CDD|232975 TIGR00437, feoB, ferrous iron transporter FeoB. FeoB (773 amino
acids in E. coli), a cytoplasmic membrane protein
required for iron(II) update, is encoded in an operon
with FeoA (75 amino acids), which is also required, and
is regulated by Fur. There appear to be two copies in
Archaeoglobus fulgidus and Clostridium acetobutylicum
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 591
Score = 29.3 bits (66), Expect = 1.8
Identities = 25/83 (30%), Positives = 39/83 (46%), Gaps = 14/83 (16%)
Query: 62 NSGKSTLIKQISSGNTSLSH------NLK----PTEGFNITILQ-KGEYTLNIFELGGQE 110
N GKSTL ++ N ++ + K +G +I I+ G Y+L F L +E
Sbjct: 4 NVGKSTLFNALTGANQTVGNWPGVTVEKKEGKLGFQGEDIEIVDLPGIYSLTTFSL-EEE 62
Query: 111 NVRRFWNTYFEDTDLLVFVVDSA 133
R + E DL+V VVD++
Sbjct: 63 VARDYLLN--EKPDLVVNVVDAS 83
>gnl|CDD|133311 cd04111, Rab39, Rab GTPase family 39 (Rab39). Found in eukaryotes,
Rab39 is mainly found in epithelial cell lines, but is
distributed widely in various human tissues and cell
lines. It is believed to be a novel Rab protein involved
in regulating Golgi-associated vesicular transport
during cellular endocytosis. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 211
Score = 29.0 bits (65), Expect = 1.9
Identities = 24/86 (27%), Positives = 45/86 (52%), Gaps = 11/86 (12%)
Query: 51 FQRKILILGLDNSGKSTLIKQISSGNTS-LSHNLKPTEG---FNITILQKGEY--TLNIF 104
+Q +++++G GKS+L+K+ + G + +S PT G F+ I + L ++
Sbjct: 1 YQFRLIVIGDSTVGKSSLLKRFTEGRFAEVS---DPTVGVDFFSRLIEIEPGVRIKLQLW 57
Query: 105 ELGGQENVRRFWNTYFEDT--DLLVF 128
+ GQE R +Y+ ++ LLVF
Sbjct: 58 DTAGQERFRSITRSYYRNSVGVLLVF 83
>gnl|CDD|180911 PRK07261, PRK07261, topology modulation protein; Provisional.
Length = 171
Score = 28.5 bits (64), Expect = 1.9
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 54 KILILGLDNSGKSTLIKQIS 73
KI I+G SGKSTL +++S
Sbjct: 2 KIAIIGYSGSGKSTLARKLS 21
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 28.5 bits (63), Expect = 1.9
Identities = 21/130 (16%), Positives = 44/130 (33%), Gaps = 10/130 (7%)
Query: 53 RKILILGLDNSGKSTLIKQI-----SSGNTSLSHNLKPTEGFNITILQKGEYTLNIFELG 107
ILI+G SGK+TL + + G + + + + L
Sbjct: 3 EVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGS 62
Query: 108 GQENVRRFWNTYFEDTDLLVFV--VDSADP---SKLPVAAMELKNLLGDQRLSTVPILVI 162
G+ +R + ++ + + S L + EL+ LL + + +++
Sbjct: 63 GELRLRLALALARKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLTVILT 122
Query: 163 ANKQDVPGAL 172
N + G
Sbjct: 123 TNDEKDLGPA 132
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 28.9 bits (66), Expect = 2.0
Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 9/83 (10%)
Query: 109 QENVRRFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQDV 168
+ + R E+ DL++ V+D+++P E +L + L P++V+ NK D+
Sbjct: 282 KIGIERSREA-IEEADLVLLVLDASEPL-----TEEDDEIL--EELKDKPVIVVLNKADL 333
Query: 169 PGALSAEEVGVALDLSSISSRQH 191
G + EE + IS++
Sbjct: 334 TGEIDLEEENGKPVI-RISAKTG 355
>gnl|CDD|206707 cd04135, Tc10, Rho GTPase TC10 (Tc10). TC10 is a Rho family
protein that has been shown to induce microspike
formation and neurite outgrowth in vitro. Its expression
changes dramatically after peripheral nerve injury,
suggesting an important role in promoting axonal
outgrowth and regeneration. TC10 regulates translocation
of insulin-stimulated GLUT4 in adipocytes and has also
been shown to bind directly to Golgi COPI coat proteins.
GTP-bound TC10 in vitro can bind numerous potential
effectors. Depending on its subcellular localization and
distinct functional domains, TC10 can differentially
regulate two types of filamentous actin in adipocytes.
TC10 mRNAs are highly expressed in three types of mouse
muscle tissues: leg skeletal muscle, cardiac muscle, and
uterus; they were also present in brain, with higher
levels in adults than in newborns. TC10 has also been
shown to play a role in regulating the expression of
cystic fibrosis transmembrane conductance regulator
(CFTR) through interactions with CFTR-associated ligand
(CAL). The GTP-bound form of TC10 directs the
trafficking of CFTR from the juxtanuclear region to the
secretory pathway toward the plasma membrane, away from
CAL-mediated DFTR degradation in the lysosome. Most Rho
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 174
Score = 28.4 bits (63), Expect = 2.0
Identities = 26/118 (22%), Positives = 52/118 (44%), Gaps = 6/118 (5%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPT--EGFNITILQKG-EYTLNIFELGGQE 110
K +++G GK+ L+ +S N + PT + + +++ G +Y L +++ GQE
Sbjct: 2 KCVVVGDGAVGKTCLL--MSYANDAFPEEYVPTVFDHYAVSVTVGGKQYLLGLYDTAGQE 59
Query: 111 NVRRFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQDV 168
+ R + TD+ + +P+ E L + VP L+I + D+
Sbjct: 60 DYDRLRPLSYPMTDVFLICFSVVNPASFQNVKEEWVPEL-KEYAPNVPYLLIGTQIDL 116
>gnl|CDD|206655 cd01862, Rab7, Rab GTPase family 7 (Rab7). Rab7 subfamily. Rab7 is
a small Rab GTPase that regulates vesicular traffic from
early to late endosomal stages of the endocytic pathway.
The yeast Ypt7 and mammalian Rab7 are both involved in
transport to the vacuole/lysosome, whereas Ypt7 is also
required for homotypic vacuole fusion. Mammalian Rab7 is
an essential participant in the autophagic pathway for
sequestration and targeting of cytoplasmic components to
the lytic compartment. Mammalian Rab7 is also proposed
to function as a tumor suppressor. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 172
Score = 28.4 bits (64), Expect = 2.1
Identities = 33/123 (26%), Positives = 52/123 (42%), Gaps = 11/123 (8%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEG--F---NITILQKGEYTLNIFELGG 108
K++ILG GK++L+ Q N S+ K T G F +T+ + TL I++ G
Sbjct: 2 KVIILGDSGVGKTSLMNQYV--NKKFSNQYKATIGADFLTKEVTVDDR-LVTLQIWDTAG 58
Query: 109 QENVRRFWNTYFEDTDLLVFVVDSADPS---KLPVAAMELKNLLGDQRLSTVPILVIANK 165
QE + ++ D V V D +P L E + P +V+ NK
Sbjct: 59 QERFQSLGVAFYRGADCCVLVYDVTNPKSFESLDSWRDEFLIQASPRDPENFPFVVLGNK 118
Query: 166 QDV 168
D+
Sbjct: 119 IDL 121
>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 = 28.3 bits (64), Expect = 2.2
Identities = 25/96 (26%), Positives = 40/96 (41%), Gaps = 23/96 (23%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKGEY---------TLNIF 104
+IL++GL SGKS+ I+++ + H + P E + K I+
Sbjct: 1 RILLMGLRRSGKSS-IQKV------VFHKMSPNETLFLESTNKITKDDISNSSFVNFQIW 53
Query: 105 ELGGQENVRRFWNTY-----FEDTDLLVFVVDSADP 135
+ GQ + F T F LVFV+D+ D
Sbjct: 54 DFPGQLDP--FDPTLDPEMIFSGCGALVFVIDAQDD 87
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 28.6 bits (65), Expect = 2.3
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 54 KILILGLDNSGKSTLI 69
+ +I+G+ N GKSTLI
Sbjct: 123 RAMIIGIPNVGKSTLI 138
>gnl|CDD|216619 pfam01637, Arch_ATPase, Archaeal ATPase. This family contain a
conserved P-loop motif that is involved in binding ATP.
This family is almost exclusively found in
archaebacteria and particularly in Methanococcus
jannaschii that encodes sixteen members of this family.
Length = 223
Score = 28.4 bits (64), Expect = 2.3
Identities = 5/18 (27%), Positives = 11/18 (61%)
Query: 55 ILILGLDNSGKSTLIKQI 72
I++ G GK+ L+++
Sbjct: 23 IVVYGPRRCGKTALLREF 40
>gnl|CDD|213214 cd03247, ABCC_cytochrome_bd, ATP-binding cassette domain of CydCD,
subfamily C. The CYD subfamily implicated in cytochrome
bd biogenesis. The CydC and CydD proteins are important
for the formation of cytochrome bd terminal oxidase of
E. coli and it has been proposed that they were
necessary for biosynthesis of the cytochrome bd quinol
oxidase and for periplasmic c-type cytochromes. CydCD
were proposed to determine a heterooligomeric complex
important for heme export into the periplasm or to be
involved in the maintenance of the proper redox state of
the periplasmic space. In Bacillus subtilis, the absence
of CydCD does not affect the presence of halo-cytochrome
c in the membrane and this observation suggests that
CydCD proteins are not involved in the export of heme in
this organism.
Length = 178
Score = 28.4 bits (64), Expect = 2.4
Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 16/61 (26%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKGEYTLNIFELGGQENVR 113
KI +LG SGKSTL++ ++ +LKP Q+GE TL+ + E
Sbjct: 30 KIALLGRSGSGKSTLLQLLTG-------DLKP---------QQGEITLDGVPVSDLEKAL 73
Query: 114 R 114
Sbjct: 74 S 74
>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 = 28.4 bits (64), Expect = 2.4
Identities = 13/44 (29%), Positives = 23/44 (52%), Gaps = 7/44 (15%)
Query: 34 STPEDEGFEEVSKVDDIFQ-----RKILILGLDNSGKSTLIKQI 72
S + G EE+ +++I + + ++G N GKSTLI +
Sbjct: 104 SAKKGWGVEEL--IEEIKKLAKYRGDVYVVGATNVGKSTLINAL 145
>gnl|CDD|213181 cd03214, ABC_Iron-Siderophores_B12_Hemin, ATP-binding component
of iron-siderophores, vitamin B12 and hemin
transporters and related proteins. ABC transporters,
involved in the uptake of siderophores, heme, and
vitamin B12, are widely conserved in bacteria and
archaea. Only very few species lack representatives of
the siderophore family transporters. The E. coli BtuCD
protein is an ABC transporter mediating vitamin B12
uptake. The two ATP-binding cassettes (BtuD) are in
close contact with each other, as are the two
membrane-spanning subunits (BtuC); this arrangement is
distinct from that observed for the E. coli lipid
flippase MsbA. The BtuC subunits provide 20
transmembrane helices grouped around a translocation
pathway that is closed to the cytoplasm by a gate
region, whereas the dimer arrangement of the BtuD
subunits resembles the ATP-bound form of the Rad50 DNA
repair enzyme. A prominent cytoplasmic loop of BtuC
forms the contact region with the ATP-binding cassette
and represent a conserved motif among the ABC
transporters.
Length = 180
Score = 28.2 bits (64), Expect = 2.9
Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 8/41 (19%)
Query: 49 DIFQRKIL-ILGLDNSGKSTLIKQISSGNTSLSHNLKPTEG 88
I +I+ ILG + +GKSTL+K +L+ LKP+ G
Sbjct: 21 SIEAGEIVGILGPNGAGKSTLLK-------TLAGLLKPSSG 54
>gnl|CDD|234125 TIGR03156, GTP_HflX, GTP-binding protein HflX. This protein family
is one of a number of homologous small, well-conserved
GTP-binding proteins with pleiotropic effects. Bacterial
members are designated HflX, following the naming
convention in Escherichia coli where HflX is encoded
immediately downstream of the RNA chaperone Hfq, and
immediately upstream of HflKC, a membrane-associated
protease pair with an important housekeeping function.
Over large numbers of other bacterial genomes, the
pairing with hfq is more significant than with hflK and
hlfC. The gene from Homo sapiens in this family has been
named PGPL (pseudoautosomal GTP-binding protein-like)
[Unknown function, General].
Length = 351
Score = 28.6 bits (65), Expect = 3.0
Identities = 14/45 (31%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 124 DLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQDV 168
DLL+ VVD++DP + ++ +L + +P L++ NK D+
Sbjct: 270 DLLLHVVDASDPDREEQIE-AVEKVLEELGAEDIPQLLVYNKIDL 313
>gnl|CDD|225907 COG3372, COG3372, Predicted nuclease of restriction
endonuclease-like fold [General function prediction
only].
Length = 396
Score = 28.5 bits (64), Expect = 3.4
Identities = 11/33 (33%), Positives = 16/33 (48%), Gaps = 4/33 (12%)
Query: 188 SRQHRIKLIATQAPSNLHHLHVSVVEAEQAMYA 220
S + R +++ A H VS E E A+YA
Sbjct: 99 SEEERQRVLQEAA----DHFSVSPEEIEDALYA 127
>gnl|CDD|233394 TIGR01394, TypA_BipA, GTP-binding protein TypA/BipA. This
bacterial (and Arabidopsis) protein, termed TypA or
BipA, a GTP-binding protein, is phosphorylated on a
tyrosine residue under some cellular conditions. Mutants
show altered regulation of some pathways, but the
precise function is unknown [Regulatory functions,
Other, Cellular processes, Adaptations to atypical
conditions, Protein synthesis, Translation factors].
Length = 594
Score = 28.4 bits (64), Expect = 3.6
Identities = 41/153 (26%), Positives = 59/153 (38%), Gaps = 33/153 (21%)
Query: 53 RKILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGF----------NITILQKG----- 97
R I I+ + GK+TL+ + + + N E ITIL K
Sbjct: 2 RNIAIIAHVDHGKTTLVDALLKQSGTFRANEAVAERVMDSNDLERERGITILAKNTAIRY 61
Query: 98 -EYTLNIFE------LGGQENVRRFWNTYFEDTDLLVFVVDSADPSKLPVAAMELKNLLG 150
+NI + GG+ V R D ++ +VD+++ +P LK L
Sbjct: 62 NGTKINIVDTPGHADFGGE--VERVLGM----VDGVLLLVDASE-GPMPQTRFVLKKAL- 113
Query: 151 DQRLSTVPILVIANKQDVPGALSAEEVGVALDL 183
L PI+VI NK D P A E V DL
Sbjct: 114 --ELGLKPIVVI-NKIDRPSARPDEVVDEVFDL 143
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 27.8 bits (62), Expect = 3.6
Identities = 29/128 (22%), Positives = 55/128 (42%), Gaps = 14/128 (10%)
Query: 49 DIFQRKILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQ----KGEYTLNIF 104
D K++I+G +GK+T +K+ +G +PT G + L G+ +
Sbjct: 10 DYPSFKLVIVGDGGTGKTTFVKRHLTG--EFEKKYEPTIGVEVHPLDFFTNCGKIRFYCW 67
Query: 105 ELGGQENVRRFWNTYF--EDTDLLVFVVDSADPSK-LPVAAMELKNLLGDQRLSTVPILV 161
+ GQE + Y+ +++F V + K +P +L + + +PI++
Sbjct: 68 DTAGQEKFGGLRDGYYIHGQCAIIMFDVTARLTYKNVPTWHRDLCRVCEN-----IPIVL 122
Query: 162 IANKQDVP 169
NK DV
Sbjct: 123 CGNKVDVK 130
>gnl|CDD|213179 cd00267, ABC_ATPase, ATP-binding cassette transporter
nucleotide-binding domain. ABC transporters are a
large family of proteins involved in the transport of a
wide variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide-binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and
GTP-binding and hydrolyzing proteins.
Length = 157
Score = 27.6 bits (62), Expect = 3.7
Identities = 8/21 (38%), Positives = 15/21 (71%)
Query: 53 RKILILGLDNSGKSTLIKQIS 73
+ ++G + SGKSTL++ I+
Sbjct: 26 EIVALVGPNGSGKSTLLRAIA 46
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction
only].
Length = 365
Score = 28.0 bits (63), Expect = 3.9
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 4/46 (8%)
Query: 29 KKRRQSTPEDEGFEEVSKVDDIFQRKILILGLDNSGKSTLIKQISS 74
K++ +S GF V K D L+ G + GKSTL+ ++++
Sbjct: 44 KRKSKSGGGGSGFA-VKKSGDA--TVALV-GFPSVGKSTLLNKLTN 85
>gnl|CDD|200516 cd11255, Sema_3G, The Sema domain, a protein interacting module, of
semaphorin 3G (Sema3G). Semaphorin 3G is identified as
a primarily endothelial cell- expressed class 3
semaphorin that controls endothelial and smooth muscle
cell functions in autocrine and paracrine manners,
respectively. It is mainly expressed in the lung and
kidney, and a little in the brain. Semaphorins are
regulatory molecules in the development of the nervous
system and in axonal guidance. They also play important
roles in other biological processes, such as
angiogenesis, immune regulation, respiration systems and
cancer. The Sema domain is located at the N-terminus and
contains four disulfide bonds formed by eight conserved
cysteine residues. It serves as a receptor-recognition
and -binding module.
Length = 474
Score = 28.0 bits (62), Expect = 4.3
Identities = 11/35 (31%), Positives = 14/35 (40%)
Query: 185 SISSRQHRIKLIATQAPSNLHHLHVSVVEAEQAMY 219
+ R L+ T P L + V VEAE Y
Sbjct: 369 PVYPSHRRPVLVKTGLPYRLTQIVVDRVEAEDGYY 403
>gnl|CDD|232931 TIGR00344, alaS, alanine--tRNA ligase. The model describes
alanine--tRNA ligase. This enzyme catalyzes the reaction
(tRNAala + L-alanine + ATP = L-alanyl-tRNAala +
pyrophosphate + AMP) [Protein synthesis, tRNA
aminoacylation].
Length = 851
Score = 28.1 bits (63), Expect = 4.8
Identities = 16/55 (29%), Positives = 22/55 (40%), Gaps = 6/55 (10%)
Query: 120 FEDTDLLVFVVDSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQDVPGALSA 174
+LV VVD+ D L A LK+ LG I V+A+ + L
Sbjct: 764 INGVKVLVEVVDAKDMKSLKTMADRLKSKLGSA------IYVLASFANGKVKLVC 812
>gnl|CDD|223562 COG0488, Uup, ATPase components of ABC transporters with duplicated
ATPase domains [General function prediction only].
Length = 530
Score = 28.0 bits (63), Expect = 4.9
Identities = 13/35 (37%), Positives = 19/35 (54%), Gaps = 7/35 (20%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEG 88
+I I+G + +GKSTL+K L+ L P G
Sbjct: 350 RIAIVGPNGAGKSTLLK-------LLAGELGPLSG 377
>gnl|CDD|226643 COG4175, ProV, ABC-type proline/glycine betaine transport system,
ATPase component [Amino acid transport and metabolism].
Length = 386
Score = 27.7 bits (62), Expect = 5.5
Identities = 11/26 (42%), Positives = 19/26 (73%), Gaps = 1/26 (3%)
Query: 49 DIFQRKIL-ILGLDNSGKSTLIKQIS 73
D+ + +I I+GL SGKSTL++ ++
Sbjct: 50 DVEEGEIFVIMGLSGSGKSTLVRLLN 75
>gnl|CDD|221955 pfam13173, AAA_14, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily.
Length = 127
Score = 26.8 bits (60), Expect = 5.8
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 53 RKILILGLDNSGKSTLIKQI 72
+ I+I G GK+TL+ Q
Sbjct: 3 KIIVITGPRQVGKTTLLLQF 22
>gnl|CDD|236151 PRK08099, PRK08099, bifunctional DNA-binding transcriptional
repressor/ NMN adenylyltransferase; Provisional.
Length = 399
Score = 27.7 bits (62), Expect = 5.9
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 51 FQRKILILGLDNSGKSTLI 69
F R + ILG ++SGKSTL+
Sbjct: 218 FVRTVAILGGESSGKSTLV 236
>gnl|CDD|226637 COG4167, SapF, ABC-type antimicrobial peptide transport system,
ATPase component [Defense mechanisms].
Length = 267
Score = 27.5 bits (61), Expect = 6.1
Identities = 19/64 (29%), Positives = 28/64 (43%), Gaps = 12/64 (18%)
Query: 41 FEEVSKVDDIFQRK--ILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEG---FNITILQ 95
E V V + + I+G + SGKSTL K ++ ++PT G N L
Sbjct: 26 VEAVKPVSFTLREGQTLAIIGENGSGKSTLAKMLAG-------MIEPTSGEILINDHPLH 78
Query: 96 KGEY 99
G+Y
Sbjct: 79 FGDY 82
>gnl|CDD|213261 cd03294, ABC_Pro_Gly_Betaine, ATP-binding cassette domain of the
osmoprotectant proline/glycine betaine uptake system.
This family comprises the glycine betaine/L-proline ATP
binding subunit in bacteria and its equivalents in
archaea. This transport system belong to the larger
ATP-Binding Cassette (ABC) transporter superfamily. The
characteristic feature of these transporters is the
obligatory coupling of ATP hydrolysis to substrate
translocation. ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 269
Score = 27.2 bits (61), Expect = 6.3
Identities = 10/17 (58%), Positives = 14/17 (82%)
Query: 57 ILGLDNSGKSTLIKQIS 73
I+GL SGKSTL++ I+
Sbjct: 55 IMGLSGSGKSTLLRCIN 71
>gnl|CDD|184134 PRK13549, PRK13549, xylose transporter ATP-binding subunit;
Provisional.
Length = 506
Score = 27.6 bits (62), Expect = 6.9
Identities = 49/180 (27%), Positives = 73/180 (40%), Gaps = 46/180 (25%)
Query: 41 FEEVSKVDDI-FQ-RKILILGL---DNSGKSTLIKQIS--------------SGNTSLSH 81
F V +D++ + R I+ L + +GKSTL+K +S G +
Sbjct: 15 FGGVKALDNVSLKVRAGEIVSLCGENGAGKSTLMKVLSGVYPHGTYEGEIIFEGEELQAS 74
Query: 82 NLKPTEGFNITILQKGEYTL--------NIFELGGQ--ENVRRFWNT-YFEDTDLLVFVV 130
N++ TE I I+ + E L NIF LG + ++ Y LL +
Sbjct: 75 NIRDTERAGIAIIHQ-ELALVKELSVLENIF-LGNEITPGGIMDYDAMYLRAQKLLAQLK 132
Query: 131 DSADPSKLPVAAMELKNLLGDQRLSTVPILVIANKQ------DVP-GALSAEEVGVALDL 183
+P+ PV L LG Q+L V I NKQ D P +L+ E V LD+
Sbjct: 133 LDINPA-TPV--GNLG--LGQQQL--VEIAKALNKQARLLILDEPTASLTESETAVLLDI 185
>gnl|CDD|184633 PRK14338, PRK14338, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 459
Score = 27.5 bits (61), Expect = 7.0
Identities = 12/41 (29%), Positives = 20/41 (48%)
Query: 19 VCTYATYQYWKKRRQSTPEDEGFEEVSKVDDIFQRKILILG 59
C+Y + R +S P E EEV ++ ++I +LG
Sbjct: 168 SCSYCVIPLRRGRERSRPLAEIVEEVRRIAARGAKEITLLG 208
>gnl|CDD|234274 TIGR03594, GTPase_EngA, ribosome-associated GTPase EngA. EngA
(YfgK, Der) is a ribosome-associated essential GTPase
with a duplication of its GTP-binding domain. It is
broadly to universally distributed among bacteria. It
appears to function in ribosome biogenesis or stability
[Protein synthesis, Other].
Length = 429
Score = 27.4 bits (62), Expect = 7.1
Identities = 16/37 (43%), Positives = 21/37 (56%), Gaps = 4/37 (10%)
Query: 36 PEDEGFEEVSKVDDIFQRKILILGLDNSGKSTLIKQI 72
PE+E EE + D KI I+G N GKSTL+ +
Sbjct: 160 PEEE--EEEEEEDGPI--KIAIIGRPNVGKSTLVNAL 192
>gnl|CDD|237678 PRK14335, PRK14335, (dimethylallyl)adenosine tRNA
methylthiotransferase; Provisional.
Length = 455
Score = 27.6 bits (61), Expect = 7.2
Identities = 11/40 (27%), Positives = 19/40 (47%)
Query: 20 CTYATYQYWKKRRQSTPEDEGFEEVSKVDDIFQRKILILG 59
C+Y Y + R S D +E+ + + R+I +LG
Sbjct: 166 CSYCIVPYVRGREISRDLDAILQEIDVLSEKGVREITLLG 205
>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 = 26.8 bits (60), Expect = 7.2
Identities = 8/24 (33%), Positives = 15/24 (62%)
Query: 53 RKILILGLDNSGKSTLIKQISSGN 76
R ++I G N GKS+L+ +++
Sbjct: 1 RTLVIAGYPNVGKSSLVNKLTRAK 24
>gnl|CDD|224057 COG1134, TagH, ABC-type polysaccharide/polyol phosphate transport
system, ATPase component [Carbohydrate transport and
metabolism / Cell envelope biogenesis, outer membrane].
Length = 249
Score = 27.2 bits (61), Expect = 7.2
Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 19/68 (27%)
Query: 54 KILILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKGEYTLNIFELG------ 107
++ I+G + +GKSTL+K I+ KPT G + G+ + ELG
Sbjct: 55 RVGIIGHNGAGKSTLLKLIAGI-------YKPTSG---KVKVTGKVA-PLIELGAGFDPE 103
Query: 108 --GQENVR 113
G+EN+
Sbjct: 104 LTGRENIY 111
>gnl|CDD|130261 TIGR01193, bacteriocin_ABC, ABC-type bacteriocin transporter. This
model describes ABC-type bacteriocin transporter. The
amino terminal domain (pfam03412) processes the
N-terminal leader peptide from the bacteriocin while
C-terminal domains resemble ABC transporter membrane
protein and ATP-binding cassette domain. In general,
bacteriocins are agents which are responsible for
killing or inhibiting the closely related species or
even different strains of the same species. Bacteriocins
are usually encoded by bacterial plasmids. Bacteriocins
are named after the species and hence in literature one
encounters various names e.g., leucocin from Leuconostic
geldium; pedicocin from Pedicoccus acidilactici; sakacin
from Lactobacillus sake etc [Protein fate, Protein and
peptide secretion and trafficking, Protein fate, Protein
modification and repair, Transport and binding proteins,
Other].
Length = 708
Score = 27.4 bits (61), Expect = 7.3
Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 8/49 (16%)
Query: 54 KILILGLDNSGKSTLIK------QISSGNTSLSHNLKPTEGFNITILQK 96
K I+G+ SGKSTL K Q SG L+ + + L++
Sbjct: 502 KTTIVGMSGSGKSTLAKLLVGFFQARSGEILLNG--FSLKDIDRHTLRQ 548
>gnl|CDD|220063 pfam08895, DUF1840, Domain of unknown function (DUF1840). This
family of proteins are functionally uncharacterized.
Length = 105
Score = 26.0 bits (58), Expect = 7.8
Identities = 11/42 (26%), Positives = 21/42 (50%), Gaps = 2/42 (4%)
Query: 167 DVPGALSAEEVGVALDL--SSISSRQHRIKLIATQAPSNLHH 206
VPGA++AEE+ A+ ++I++ + R A +
Sbjct: 32 TVPGAITAEELPAAIARLEAAIAAEEARRAPPAEDEDDDEDE 73
>gnl|CDD|234814 PRK00698, tmk, thymidylate kinase; Validated.
Length = 205
Score = 26.7 bits (60), Expect = 8.0
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 55 ILILGLDNSGKSTLIKQISS 74
I I G+D +GKST I+ +
Sbjct: 6 ITIEGIDGAGKSTQIELLKE 25
>gnl|CDD|206746 cd01849, YlqF_related_GTPase, Circularly permuted YlqF-related
GTPases. These proteins are found in bacteria,
eukaryotes, and archaea. They all exhibit a circular
permutation of the GTPase signature motifs so that the
order of the conserved G box motifs is G4-G5-G1-G2-G3,
with G4 and G5 being permuted from the C-terminal region
of proteins in the Ras superfamily to the N-terminus of
YlqF-related GTPases.
Length = 146
Score = 26.6 bits (59), Expect = 8.1
Identities = 7/23 (30%), Positives = 14/23 (60%)
Query: 54 KILILGLDNSGKSTLIKQISSGN 76
++ ++GL N GKS+ I + +
Sbjct: 93 RVGVVGLPNVGKSSFINALLNKF 115
>gnl|CDD|237511 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 27.1 bits (61), Expect = 8.2
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 53 RKILILGLDNSGKSTLIKQI 72
R + ++G+ N GKSTLI +I
Sbjct: 161 RDVYVVGVTNVGKSTLINRI 180
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 27.0 bits (60), Expect = 8.9
Identities = 8/21 (38%), Positives = 13/21 (61%)
Query: 49 DIFQRKILILGLDNSGKSTLI 69
+ ++ ++G N GKSTLI
Sbjct: 129 LKRKIRVGVVGYPNVGKSTLI 149
>gnl|CDD|238835 cd01672, TMPK, Thymidine monophosphate kinase (TMPK), also known
as thymidylate kinase, catalyzes the phosphorylation of
thymidine monophosphate (TMP) to thymidine diphosphate
(TDP) utilizing ATP as its preferred phophoryl donor.
TMPK represents the rate-limiting step in either de
novo or salvage biosynthesis of thymidine triphosphate
(TTP).
Length = 200
Score = 26.5 bits (59), Expect = 9.0
Identities = 9/32 (28%), Positives = 19/32 (59%)
Query: 55 ILILGLDNSGKSTLIKQISSGNTSLSHNLKPT 86
I+ G+D +GK+TLI+ ++ + + + T
Sbjct: 3 IVFEGIDGAGKTTLIELLAERLEARGYEVVLT 34
>gnl|CDD|225713 COG3172, NadR, Predicted ATPase/kinase involved in NAD metabolism
[Coenzyme metabolism].
Length = 187
Score = 26.6 bits (59), Expect = 9.2
Identities = 10/22 (45%), Positives = 17/22 (77%)
Query: 51 FQRKILILGLDNSGKSTLIKQI 72
F + + ILG ++SGKSTL+ ++
Sbjct: 7 FVKTVAILGGESSGKSTLVNKL 28
>gnl|CDD|236584 PRK09602, PRK09602, translation-associated GTPase; Reviewed.
Length = 396
Score = 27.1 bits (61), Expect = 9.5
Identities = 10/28 (35%), Positives = 17/28 (60%)
Query: 144 ELKNLLGDQRLSTVPILVIANKQDVPGA 171
+L L + R + P+++ ANK D+P A
Sbjct: 205 DLLELARELRKISKPMVIAANKADLPPA 232
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 26.2 bits (58), Expect = 9.5
Identities = 15/80 (18%), Positives = 28/80 (35%), Gaps = 3/80 (3%)
Query: 55 ILILGLDNSGKSTLIKQISS-GNTSLSHNLKPTEGFNITILQKGEYTLNIFELGGQENVR 113
ILI G SGK+TL K+++ L K G + + ++ + +
Sbjct: 1 ILITGTPGSGKTTLAKELAERLGDVLRDLAK-ENGLVLELDEEITDESKRLDEDKLAKLL 59
Query: 114 RFW-NTYFEDTDLLVFVVDS 132
E + ++D
Sbjct: 60 DKLEKIIEELAEGENVIIDG 79
>gnl|CDD|213251 cd03284, ABC_MutS1, ATP-binding cassette domain of MutS1 homolog.
The MutS protein initiates DNA mismatch repair by
recognizing mispaired and unpaired bases embedded in
duplex DNA and activating endo- and exonucleases to
remove the mismatch. Members of the MutS family possess
C-terminal domain with a conserved ATPase activity that
belongs to the ATP binding cassette (ABC) superfamily.
MutS homologs (MSH) have been identified in most
prokaryotic and all eukaryotic organisms examined.
Prokaryotes have two homologs (MutS1 and MutS2),
whereas seven MSH proteins (MSH1 to MSH7) have been
identified in eukaryotes. The homodimer MutS1 and
heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily
involved in mitotic mismatch repair, whereas MSH4-MSH5
is involved in resolution of Holliday junctions during
meiosis. All members of the MutS family contain the
highly conserved Walker A/B ATPase domain, and many
share a common mechanism of action. MutS1, MSH2-MSH3,
MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding
clamps, and recognition of specific DNA structures or
lesions results in ADP/ATP exchange.
Length = 216
Score = 26.5 bits (59), Expect = 9.7
Identities = 8/21 (38%), Positives = 16/21 (76%)
Query: 52 QRKILILGLDNSGKSTLIKQI 72
++ +LI G + +GKST ++Q+
Sbjct: 30 RQILLITGPNMAGKSTYLRQV 50
>gnl|CDD|213184 cd03217, ABC_FeS_Assembly, ABC-type transport system involved in
Fe-S cluster assembly, ATPase component. Biosynthesis
of iron-sulfur clusters (Fe-S) depends on multi-protein
systems. The SUF system of E. coli and Erwinia
chrysanthemi is important for Fe-S biogenesis under
stressful conditions. The SUF system is made of six
proteins: SufC is an atypical cytoplasmic ABC-ATPase,
which forms a complex with SufB and SufD; SufA plays the
role of a scaffold protein for assembly of iron-sulfur
clusters and delivery to target proteins; SufS is a
cysteine desulfurase which mobilizes the sulfur atom
from cysteine and provides it to the cluster; SufE has
no associated function yet.
Length = 200
Score = 26.3 bits (59), Expect = 9.8
Identities = 22/58 (37%), Positives = 30/58 (51%), Gaps = 11/58 (18%)
Query: 57 ILGLDNSGKSTLIKQISSGNTSLSHNLKPTEGFNITILQKGEYTLNIFELGGQENVRR 114
++G + SGKSTL K I G+ + TEG IL KGE +I +L +E R
Sbjct: 31 LMGPNGSGKSTLAKTI-MGH----PKYEVTEG---EILFKGE---DITDLPPEERARL 77
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.316 0.131 0.361
Gapped
Lambda K H
0.267 0.0534 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,047,593
Number of extensions: 1029042
Number of successful extensions: 1635
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1570
Number of HSP's successfully gapped: 229
Length of query: 224
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 131
Effective length of database: 6,812,680
Effective search space: 892461080
Effective search space used: 892461080
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (26.2 bits)