RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy689
(162 letters)
>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 = 249 bits (638), Expect = 3e-86
Identities = 110/134 (82%), Positives = 124/134 (92%)
Query: 24 LLAILKKLRSSPEKELRILLLGLDNAGKTTILKTLASEDISHITPTQGFNIKSVQSEGFK 83
LL+IL+KL+ S +E+RILLLGLDNAGKTTILK LASEDISHITPTQGFNIK+VQ++GFK
Sbjct: 1 LLSILRKLKPSSRQEVRILLLGLDNAGKTTILKQLASEDISHITPTQGFNIKNVQADGFK 60
Query: 84 LNVWDIGGQRKIRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLL 143
LNVWDIGGQRKIRPYWRNYF+NTD+LIYVIDSAD KRFEE+G EL ELL +EKL GVP+L
Sbjct: 61 LNVWDIGGQRKIRPYWRNYFENTDVLIYVIDSADRKRFEEAGQELVELLEEEKLAGVPVL 120
Query: 144 VYANKQDLLGAAPA 157
V+ANKQDLL AAPA
Sbjct: 121 VFANKQDLLTAAPA 134
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 207 bits (530), Expect = 1e-69
Identities = 74/134 (55%), Positives = 92/134 (68%), Gaps = 1/134 (0%)
Query: 24 LLAILKKLRSSPEKELRILLLGLDNAGKTTILKTLASEDISHITPTQGFNIKSVQSEGFK 83
L+IL KL KE+RIL+LGLDNAGKTTIL L +I PT GFN+++V + K
Sbjct: 1 FLSILAKLFGW-NKEMRILILGLDNAGKTTILYKLKLGEIVTTIPTIGFNVETVTYKNVK 59
Query: 84 LNVWDIGGQRKIRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLL 143
VWD+GGQ +RP WRNYF NTD +I+V+DSAD R EE+ ELH LL++E+L PLL
Sbjct: 60 FTVWDVGGQESLRPLWRNYFPNTDAVIFVVDSADRDRIEEAKEELHALLNEEELADAPLL 119
Query: 144 VYANKQDLLGAAPA 157
+ ANKQDL GA
Sbjct: 120 ILANKQDLPGAMSE 133
>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 = 198 bits (505), Expect = 6e-66
Identities = 78/131 (59%), Positives = 103/131 (78%), Gaps = 1/131 (0%)
Query: 24 LLAILKKLRSSPEKELRILLLGLDNAGKTTILKTLASEDISHITPTQGFNIKSVQSEGFK 83
LL IL+K + E+E+RIL+LGLDNAGKTTILK EDIS I+PT GFNIK+++ G+K
Sbjct: 1 LLTILRKTKQK-EREMRILMLGLDNAGKTTILKKFNGEDISTISPTLGFNIKTLEYNGYK 59
Query: 84 LNVWDIGGQRKIRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLL 143
LN+WD+GGQ+ +R YWRNYF++TD LI+V+DS+D R E+ EL +LL +E+L G LL
Sbjct: 60 LNIWDVGGQKSLRSYWRNYFESTDALIWVVDSSDRARLEDCKRELQKLLVEERLAGATLL 119
Query: 144 VYANKQDLLGA 154
++ANKQDL GA
Sbjct: 120 IFANKQDLPGA 130
>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 = 185 bits (473), Expect = 3e-61
Identities = 65/115 (56%), Positives = 88/115 (76%)
Query: 40 RILLLGLDNAGKTTILKTLASEDISHITPTQGFNIKSVQSEGFKLNVWDIGGQRKIRPYW 99
RIL+LGLD AGKTTIL L ++ PT GFN+++V+ + K VWD+GGQ KIRP W
Sbjct: 1 RILMLGLDGAGKTTILYKLKLGEVVTTIPTIGFNVETVEYKNVKFTVWDVGGQDKIRPLW 60
Query: 100 RNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVYANKQDLLGA 154
++Y++NTD LI+V+DS+D +R EE+ ELH+LL++E+L G PLL+ ANKQDL GA
Sbjct: 61 KHYYENTDGLIFVVDSSDRERIEEAKNELHKLLNEEELKGAPLLILANKQDLPGA 115
>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 = 151 bits (383), Expect = 1e-47
Identities = 62/118 (52%), Positives = 81/118 (68%)
Query: 37 KELRILLLGLDNAGKTTILKTLASEDISHITPTQGFNIKSVQSEGFKLNVWDIGGQRKIR 96
KE+RIL+LGLD AGKTTIL L PT GFN+++V + K NVWD+GGQ KIR
Sbjct: 8 KEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGQDKIR 67
Query: 97 PYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVYANKQDLLGA 154
P WR+Y+ T LI+V+DSAD R +E+ ELH +++D ++ LLV+ANKQDL A
Sbjct: 68 PLWRHYYTGTQGLIFVVDSADRDRIDEARQELHRIINDREMRDALLLVFANKQDLPDA 125
>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 = 150 bits (381), Expect = 2e-47
Identities = 62/119 (52%), Positives = 78/119 (65%)
Query: 40 RILLLGLDNAGKTTILKTLASEDISHITPTQGFNIKSVQSEGFKLNVWDIGGQRKIRPYW 99
RIL+LGLD AGKTTIL L ++ PT GFN+++V + K VWD+GGQ IRPYW
Sbjct: 1 RILILGLDGAGKTTILYRLQVGEVVTTIPTIGFNVETVTYKNLKFQVWDLGGQTSIRPYW 60
Query: 100 RNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVYANKQDLLGAAPAG 158
R Y+ NTD +IYV+DS D R S ELH +L +E+L LLV+ANKQD+ GA
Sbjct: 61 RCYYSNTDAIIYVVDSTDRDRLGISKSELHAMLEEEELKDAVLLVFANKQDMPGALSEA 119
>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 = 139 bits (351), Expect = 8e-43
Identities = 58/119 (48%), Positives = 82/119 (68%), Gaps = 1/119 (0%)
Query: 40 RILLLGLDNAGKTTILKTLASEDISHITPTQGFNIKSVQSEG-FKLNVWDIGGQRKIRPY 98
++LLLGLD+AGK+T+L L ++ PT GFN++ +Q E L VWD+GGQ K+R
Sbjct: 1 QVLLLGLDSAGKSTLLYKLKHAELVTTIPTVGFNVEMLQLEKHLSLTVWDVGGQEKMRTV 60
Query: 99 WRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVYANKQDLLGAAPA 157
W+ Y +NTD L+YV+DS+D R +ES EL +L +E + GVP+++ ANKQDL GA A
Sbjct: 61 WKCYLENTDGLVYVVDSSDEARLDESQKELKHILKNEHIKGVPVVLLANKQDLPGALTA 119
>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 = 138 bits (350), Expect = 1e-42
Identities = 59/116 (50%), Positives = 80/116 (68%)
Query: 39 LRILLLGLDNAGKTTILKTLASEDISHITPTQGFNIKSVQSEGFKLNVWDIGGQRKIRPY 98
+RIL++GLD AGKTTIL L +I PT GFN+++V+ + VWD+GGQ KIRP
Sbjct: 1 MRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPL 60
Query: 99 WRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVYANKQDLLGA 154
WR+YF NT LI+V+DS D +R E+ EL +L++++L LLV+ANKQDL A
Sbjct: 61 WRHYFQNTQGLIFVVDSNDRERIGEAREELQRMLNEDELRDAVLLVFANKQDLPNA 116
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 134 bits (338), Expect = 1e-40
Identities = 58/119 (48%), Positives = 85/119 (71%)
Query: 36 EKELRILLLGLDNAGKTTILKTLASEDISHITPTQGFNIKSVQSEGFKLNVWDIGGQRKI 95
+KE+RIL++GLD AGKTTIL L ++ PT GFN+++V+ + K +WD+GGQ K+
Sbjct: 15 KKEVRILMVGLDAAGKTTILYKLKLGEVVTTIPTIGFNVETVEYKNLKFTMWDVGGQDKL 74
Query: 96 RPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVYANKQDLLGA 154
RP WR+Y+ NT+ LI+V+DS D +R ++ EL +LS+++L LLV+ANKQDL A
Sbjct: 75 RPLWRHYYQNTNGLIFVVDSNDRERIGDAREELERMLSEDELRDAVLLVFANKQDLPNA 133
>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 = 132 bits (335), Expect = 4e-40
Identities = 54/120 (45%), Positives = 77/120 (64%)
Query: 35 PEKELRILLLGLDNAGKTTILKTLASEDISHITPTQGFNIKSVQSEGFKLNVWDIGGQRK 94
P KE +++++GLDNAGKTTIL ++ H +PT G N++ + + + +WDIGGQ
Sbjct: 12 PRKEYKVIIVGLDNAGKTTILYQFLLGEVVHTSPTIGSNVEEIVYKNIRFLMWDIGGQES 71
Query: 95 IRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVYANKQDLLGA 154
+R W Y+ NTD +I VIDS D +R + EL+++L+ E L LLV ANKQDL GA
Sbjct: 72 LRSSWNTYYTNTDAVILVIDSTDRERLPLTKEELYKMLAHEDLRKAVLLVLANKQDLKGA 131
>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 = 133 bits (335), Expect = 4e-40
Identities = 60/121 (49%), Positives = 82/121 (67%)
Query: 37 KELRILLLGLDNAGKTTILKTLASEDISHITPTQGFNIKSVQSEGFKLNVWDIGGQRKIR 96
KE+RIL++GLD AGKTTIL L + PT GFN+++V + VWD+GGQ KIR
Sbjct: 12 KEMRILMVGLDAAGKTTILYKLKLGESVTTIPTIGFNVETVTYKNISFTVWDVGGQDKIR 71
Query: 97 PYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVYANKQDLLGAAP 156
P WR+Y+ NT LI+V+DS D R +E+ ELH +L++++L +LV+ANKQDL A
Sbjct: 72 PLWRHYYTNTQGLIFVVDSNDRDRIDEAREELHRMLNEDELRDAVILVFANKQDLPDAMK 131
Query: 157 A 157
A
Sbjct: 132 A 132
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 132 bits (334), Expect = 7e-40
Identities = 63/122 (51%), Positives = 84/122 (68%)
Query: 36 EKELRILLLGLDNAGKTTILKTLASEDISHITPTQGFNIKSVQSEGFKLNVWDIGGQRKI 95
+KE+RIL++GLD AGKTTIL L +I PT GFN+++V+ + VWD+GGQ KI
Sbjct: 15 KKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKI 74
Query: 96 RPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVYANKQDLLGAA 155
RP WR+YF NT LI+V+DS D R E+ ELH +L++++L LLV+ANKQDL A
Sbjct: 75 RPLWRHYFQNTQGLIFVVDSNDRDRVVEARDELHRMLNEDELRDAVLLVFANKQDLPNAM 134
Query: 156 PA 157
A
Sbjct: 135 NA 136
>gnl|CDD|206645 cd00879, Sar1, Sar1 is an essential component of COPII vesicle
coats. Sar1 is an essential component of COPII vesicle
coats involved in export of cargo from the ER. The
GTPase activity of Sar1 functions as a molecular switch
to control protein-protein and protein-lipid
interactions that direct vesicle budding from the ER.
Activation of the GDP to the GTP-bound form of Sar1
involves the membrane-associated guanine nucleotide
exchange factor (GEF) Sec12. Sar1 is unlike all Ras
superfamily GTPases that use either myristoyl or prenyl
groups to direct membrane association and function, in
that Sar1 lacks such modification. Instead, Sar1
contains a unique nine-amino-acid N-terminal extension.
This extension contains an evolutionarily conserved
cluster of bulky hydrophobic amino acids, referred to as
the Sar1-N-terminal activation recruitment (STAR) motif.
The STAR motif mediates the recruitment of Sar1 to ER
membranes and facilitates its interaction with mammalian
Sec12 GEF leading to activation.
Length = 191
Score = 130 bits (329), Expect = 5e-39
Identities = 48/120 (40%), Positives = 73/120 (60%)
Query: 37 KELRILLLGLDNAGKTTILKTLASEDISHITPTQGFNIKSVQSEGFKLNVWDIGGQRKIR 96
KE +I+ LGLDNAGKTT+L L + ++ PT + + K +D+GG + R
Sbjct: 18 KEAKIVFLGLDNAGKTTLLHMLKDDRLAQHVPTLHPTSEELTIGNVKFTTFDLGGHEQAR 77
Query: 97 PYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVYANKQDLLGAAP 156
W++YF D +++++D+AD +RF+ES EL LL+DE+L VP+L+ NK D GA
Sbjct: 78 RVWKDYFPEVDGIVFLVDAADPERFQESKEELDSLLNDEELANVPILILGNKIDKPGAVS 137
>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 = 127 bits (321), Expect = 4e-38
Identities = 58/127 (45%), Positives = 78/127 (61%), Gaps = 8/127 (6%)
Query: 41 ILLLGLDNAGKTTIL---KTLASEDI-----SHITPTQGFNIKSVQSEGFKLNVWDIGGQ 92
+L+LGLDNAGKTT L KT S++ S ITPT G NI +++ +L WD+GGQ
Sbjct: 2 VLILGLDNAGKTTFLEQTKTKFSKNYKGLNPSKITPTVGLNIGTIEVGKARLMFWDLGGQ 61
Query: 93 RKIRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVYANKQDLL 152
++R W Y+ + +IYVIDS D +RF ES +++++E L GVPLLV ANKQDL
Sbjct: 62 EELRSLWDKYYAESHGVIYVIDSTDRERFNESKSAFEKVINNEALEGVPLLVLANKQDLP 121
Query: 153 GAAPAGY 159
A
Sbjct: 122 DALSVAE 128
>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 = 126 bits (318), Expect = 9e-38
Identities = 51/119 (42%), Positives = 71/119 (59%), Gaps = 1/119 (0%)
Query: 41 ILLLGLDNAGKTTILKTLASEDISHIT-PTQGFNIKSVQSEGFKLNVWDIGGQRKIRPYW 99
I L+GL N+GKTT++ +AS S T PT GFN++ V + VWD+GGQ + R W
Sbjct: 2 ITLVGLQNSGKTTLVNVIASGQFSEDTIPTVGFNMRKVTKGNVTIKVWDLGGQPRFRSMW 61
Query: 100 RNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVYANKQDLLGAAPAG 158
Y + ++YV+D+AD ++ E + ELH+LL L G+PLLV NK DL GA
Sbjct: 62 ERYCRGVNAIVYVVDAADREKLEVAKNELHDLLEKPSLEGIPLLVLGNKNDLPGALSVD 120
>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 = 121 bits (304), Expect = 3e-35
Identities = 55/125 (44%), Positives = 82/125 (65%), Gaps = 5/125 (4%)
Query: 39 LRILLLGLDNAGKTTILKTLASEDISHITPTQGFNIKSVQ-----SEGFKLNVWDIGGQR 93
L I++LGLD+AGKTT+L L + + PT+GFN + ++ ++G + WD+GGQ
Sbjct: 4 LHIVMLGLDSAGKTTVLYRLKFNEFVNTVPTKGFNTEKIKVSLGNAKGVTFHFWDVGGQE 63
Query: 94 KIRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVYANKQDLLG 153
K+RP W++Y TD +++V+DS DV+R EE+ ELH++ + GVP+LV ANKQDL
Sbjct: 64 KLRPLWKSYTRCTDGIVFVVDSVDVERMEEAKTELHKITKFSENQGVPVLVLANKQDLPN 123
Query: 154 AAPAG 158
A P
Sbjct: 124 ALPVS 128
>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 = 116 bits (292), Expect = 8e-34
Identities = 50/121 (41%), Positives = 74/121 (61%), Gaps = 7/121 (5%)
Query: 41 ILLLGLDNAGKTTILKTLASEDISH-ITPTQGFNIKSVQSEGFKLNVWDIGGQRKIRPYW 99
IL+LGLD AGKT++L +L+SE + PT GFN ++ ++ + + +IGG + +R YW
Sbjct: 2 ILVLGLDGAGKTSLLHSLSSERSLESVVPTTGFNSVAIPTQDAIMELLEIGGSQNLRKYW 61
Query: 100 RNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVYANKQDLLGAAPAGY 159
+ Y + LI+V+DSAD +R + ELH+LL +PL+V ANKQDL PA
Sbjct: 62 KRYLSGSQGLIFVVDSADSERLPLARQELHQLLQHP--PDLPLVVLANKQDL----PAAR 115
Query: 160 H 160
Sbjct: 116 S 116
>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 = 115 bits (289), Expect = 2e-33
Identities = 51/117 (43%), Positives = 80/117 (68%)
Query: 40 RILLLGLDNAGKTTILKTLASEDISHITPTQGFNIKSVQSEGFKLNVWDIGGQRKIRPYW 99
R++ LGLD AGKTTIL L ++ PT GFN+++V+ + K +WD+GG+ K+RP W
Sbjct: 1 RVVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLW 60
Query: 100 RNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVYANKQDLLGAAP 156
++Y+ NT +++VIDS+ R E+ EL +LL++++L LL++ANKQD+ GA
Sbjct: 61 KHYYLNTQAVVFVIDSSHRDRVSEAHSELAKLLTEKELRDALLLIFANKQDVAGALS 117
>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 = 111 bits (280), Expect = 6e-32
Identities = 44/114 (38%), Positives = 68/114 (59%)
Query: 41 ILLLGLDNAGKTTILKTLASEDISHITPTQGFNIKSVQSEGFKLNVWDIGGQRKIRPYWR 100
+L +GLDNAGKTT++ L E + PT GF ++ + +++ ++D+GG R W
Sbjct: 2 LLTVGLDNAGKTTLVSALQGEIPKKVAPTVGFTPTKLRLDKYEVCIFDLGGGANFRGIWV 61
Query: 101 NYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVYANKQDLLGA 154
NY+ L++V+DS+D R +E L ELL +++G P+LV ANKQD A
Sbjct: 62 NYYAEAHGLVFVVDSSDDDRVQEVKEILRELLQHPRVSGKPILVLANKQDKKNA 115
>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 = 104 bits (261), Expect = 4e-29
Identities = 50/118 (42%), Positives = 70/118 (59%), Gaps = 4/118 (3%)
Query: 41 ILLLGLDNAGKTTILKTL--ASEDISHITPTQGFNIKSVQSEGFKLNVWDIGGQRKIRPY 98
IL+LGLDN+GKTTI+ L ++ +I PT GFN++S + +D+ GQ K R
Sbjct: 2 ILVLGLDNSGKTTIINQLKPSNAQSQNIVPTVGFNVESFKKGNLSFTAFDMSGQGKYRGL 61
Query: 99 WRNYFDNTDILIYVIDSADVKRFEESGFELHELLS--DEKLTGVPLLVYANKQDLLGA 154
W +Y+ N +I+VIDS+D R + EL LL+ D K +P+L YANK DL A
Sbjct: 62 WEHYYKNIQGIIFVIDSSDRLRMVVAKDELELLLNHPDIKHRRIPILFYANKMDLPDA 119
>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 = 98.5 bits (245), Expect = 1e-26
Identities = 49/120 (40%), Positives = 72/120 (60%)
Query: 36 EKELRILLLGLDNAGKTTILKTLASEDISHITPTQGFNIKSVQSEGFKLNVWDIGGQRKI 95
K +IL LGLDNAGKTT+L L ++ ++ PTQ + + K +D+GG ++
Sbjct: 15 NKHAKILFLGLDNAGKTTLLHMLKNDRLAQHQPTQHPTSEELAIGNIKFTTFDLGGHQQA 74
Query: 96 RPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVYANKQDLLGAA 155
R W++YF + ++Y++D+ D +RF ES EL LLSDE+L VP L+ NK D AA
Sbjct: 75 RRLWKDYFPEVNGIVYLVDAYDKERFAESKRELDALLSDEELATVPFLILGNKIDAPYAA 134
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 91.9 bits (228), Expect = 1e-23
Identities = 35/130 (26%), Positives = 53/130 (40%), Gaps = 5/130 (3%)
Query: 36 EKELRILLLGLDNAGKTTILKTLASEDISHITPTQGFN-----IKSVQSEGFKLNVWDIG 90
KE +I++LG GKTT+L L ++ P N KL +WD
Sbjct: 3 MKEFKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTA 62
Query: 91 GQRKIRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVYANKQD 150
GQ + R Y+ + ++ V DS + +E E E L + VP+L+ NK D
Sbjct: 63 GQEEYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVGNKID 122
Query: 151 LLGAAPAGYH 160
L +
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 = 62.9 bits (153), Expect = 4e-13
Identities = 26/126 (20%), Positives = 54/126 (42%), Gaps = 14/126 (11%)
Query: 42 LLLGLDNAGKTTILKTLASEDISHIT----PTQGFNIKSVQ--SEGFKLNVWDIGGQRKI 95
+++G GK+++L L ++ ++ T+ ++ + KL + D G +
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPGLDEF 60
Query: 96 RPYW-----RNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVYANKQD 150
R D+++ V+DS D + E++ + L E G+P+++ NK D
Sbjct: 61 GGLGREELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLRKE---GIPIILVGNKID 117
Query: 151 LLGAAP 156
LL
Sbjct: 118 LLEERE 123
>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 = 62.4 bits (152), Expect = 7e-13
Identities = 32/124 (25%), Positives = 56/124 (45%), Gaps = 7/124 (5%)
Query: 38 ELRILLLGLDNAGKTTILKTLA----SEDISHITPTQGFNIKSVQSEG--FKLNVWDIGG 91
E++I+++G N GK+T+L L S T+ + ++ +G +K N+ D G
Sbjct: 1 EIKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAG 60
Query: 92 QRKIRPYWRNYFDNTDILIYVIDSAD-VKRFEESGFELHELLSDEKLTGVPLLVYANKQD 150
Q R Y+ + + V D V EE + + + +GVP+++ NK D
Sbjct: 61 QEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAESGVPIILVGNKID 120
Query: 151 LLGA 154
L A
Sbjct: 121 LRDA 124
>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 = 59.3 bits (144), Expect = 2e-11
Identities = 37/126 (29%), Positives = 62/126 (49%), Gaps = 9/126 (7%)
Query: 41 ILLLGLDNAGKTTILKTLAS----EDISHITPTQGFNIKSVQSEGFKLNVWDIGGQRKIR 96
+LLLG ++GKT + L + ++ I P S S+G KL + D+ G K+R
Sbjct: 3 VLLLGPSDSGKTALFTKLTTGKVRSTVTSIEPNVAS-FYSNSSKGKKLTLVDVPGHEKLR 61
Query: 97 P-YWRNYFDNTDILIYVIDSADV-KRFEESGFELHELLSDEKL--TGVPLLVYANKQDLL 152
+ +++V+DSA K + L+++L+D + +P+L+ NKQDL
Sbjct: 62 DKLLEYLKASLKAIVFVVDSATFQKNIRDVAEFLYDILTDLEKIKNKIPILIACNKQDLF 121
Query: 153 GAAPAG 158
A PA
Sbjct: 122 TAKPAK 127
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 52.5 bits (126), Expect = 5e-09
Identities = 30/135 (22%), Positives = 55/135 (40%), Gaps = 18/135 (13%)
Query: 37 KELRILLLGLDNAGKTTILKTLASE-------DISHITPTQGFNIKSVQS-------EGF 82
E +I+++G AGKTT ++ L+ + D S ++ E
Sbjct: 9 IETKIVVIGPVGAGKTTFVRALSDKPLVITEADASSVSGKGKRPTTVAMDFGSIELDEDT 68
Query: 83 KLNVWDIGGQRKIRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVPL 142
++++ GQ + + W I ++DS+ F E+ + L+ +P+
Sbjct: 69 GVHLFGTPGQERFKFMWEILSRGAVGAIVLVDSSRPITFHA--EEIIDFLTSRN--PIPV 124
Query: 143 LVYANKQDLLGAAPA 157
+V NKQDL A P
Sbjct: 125 VVAINKQDLFDALPP 139
>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 = 50.7 bits (122), Expect = 3e-08
Identities = 25/86 (29%), Positives = 38/86 (44%), Gaps = 10/86 (11%)
Query: 40 RILLLGLDNAGKTTILKTLASE----DISHITPTQGFNIKSVQSEGF-KLNVWDIGGQRK 94
++LL+GL +GK+++ + S D + T V+ G LN+WD GQ
Sbjct: 1 KVLLMGLRGSGKSSMRSIIFSNYSPRDTLRLGATIDVEQSHVRFLGNLTLNLWDCPGQDD 60
Query: 95 I-RPYWR----NYFDNTDILIYVIDS 115
Y + F N +LIYV D
Sbjct: 61 FMENYLTRQKEHIFSNVGVLIYVFDV 86
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 49.3 bits (117), Expect = 8e-08
Identities = 28/86 (32%), Positives = 43/86 (50%), Gaps = 4/86 (4%)
Query: 33 SSPEKELRILLLGLDNAGKTTILKTLASEDISHITPTQG--FNIKSVQSEG--FKLNVWD 88
S + +ILL+G GK+++L + S + + PT G F IK + G KL +WD
Sbjct: 9 SGYDLSFKILLIGDSGVGKSSLLVSFISSSVEDLAPTIGVDFKIKQLTVGGKRLKLTIWD 68
Query: 89 IGGQRKIRPYWRNYFDNTDILIYVID 114
GQ + R +Y+ N +I V D
Sbjct: 69 TAGQERFRTLTSSYYRNAQGIILVYD 94
>gnl|CDD|215955 pfam00503, G-alpha, G-protein alpha subunit. G proteins couple
receptors of extracellular signals to intracellular
signaling pathways. The G protein alpha subunit binds
guanyl nucleotide and is a weak GTPase. A set of
residues that are unique to G-alpha as compared to its
ancestor the Arf-like family form a ring of residues
centered on the nucleotide binding site. A Ggamma is
found fused to an inactive Galpha in the Dictyostelium
protein gbqA.
Length = 329
Score = 49.2 bits (118), Expect = 1e-07
Identities = 28/105 (26%), Positives = 48/105 (45%), Gaps = 15/105 (14%)
Query: 61 EDISHI-TPTQGFNIKSVQSEGFKLNVWDIGGQRKIRPYWRNYFDNTDILIYVIDSAD-- 117
+DI T G +G K ++D+GGQR R W + F++ +I+V+ ++
Sbjct: 146 QDILRARVKTTGIIETKFDFKGLKFRLFDVGGQRSERKKWIHCFEDVTAIIFVVSLSEYD 205
Query: 118 --------VKRFEES--GFELHELLSDEKLTGVPLLVYANKQDLL 152
R EES FE E+ + P++++ NK+DL
Sbjct: 206 QVLYEDDSTNRLEESLNLFE--EICNSPWFKNTPIILFLNKKDLF 248
Score = 31.1 bits (71), Expect = 0.23
Identities = 11/20 (55%), Positives = 17/20 (85%)
Query: 37 KELRILLLGLDNAGKTTILK 56
+E+++LLLG +GK+TILK
Sbjct: 1 REIKLLLLGAGESGKSTILK 20
>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 = 45.7 bits (109), Expect = 4e-07
Identities = 27/122 (22%), Positives = 52/122 (42%), Gaps = 18/122 (14%)
Query: 40 RILLLGLDNAGKTTILKTLASEDISHITPTQG---FNIKSVQSEGFKLNVWDIGGQRK-- 94
R+ L+G N GK+T++ L ++ ++ G I V G ++ + D G +
Sbjct: 1 RVALVGRPNVGKSTLINALTGAKVAIVSDYPGTTRDPILGVLGLGRQIILVDTPGLIEGA 60
Query: 95 --------IRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVYA 146
+ D+++ V+D+++ E E+ E L EKL P+++
Sbjct: 61 SEGKGVEGFNRFLEAI-READLILLVVDASEG--LTEDDEEILEEL--EKLPKKPIILVL 115
Query: 147 NK 148
NK
Sbjct: 116 NK 117
>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 = 46.6 bits (111), Expect = 6e-07
Identities = 31/129 (24%), Positives = 58/129 (44%), Gaps = 14/129 (10%)
Query: 40 RILLLGLDNAGKTTILKTLASEDISHITPTQ-----GFNIKSVQSEGFKLNVWDIGGQRK 94
+++ GL ++GKT++ L + + T K + +GF + D G K
Sbjct: 5 AVIIAGLCDSGKTSLFTLLTTGT---VKKTVTSQEPSAAYKYMLHKGFSFTLIDFPGHVK 61
Query: 95 IRPYWRNYF---DNTDILIYVIDS-ADVKRFEESGFELHELLSDEKLT--GVPLLVYANK 148
+R + +++V+DS A K ++ L+E+LS +L G+ +L+ NK
Sbjct: 62 LRQKLLETIKDSSSLRGIVFVVDSTAFPKEVTDTAEFLYEILSITELLKNGIDILIACNK 121
Query: 149 QDLLGAAPA 157
Q+ A P
Sbjct: 122 QESFTARPP 130
>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 = 43.1 bits (102), Expect = 9e-06
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 6/61 (9%)
Query: 38 ELRILLLGLDNAGKTTILKTL------ASEDISHITPTQGFNIKSVQSEGFKLNVWDIGG 91
E +++L+G GKT++ K L E +H Q + I + + + +LNVWD GG
Sbjct: 1 EAKLMLVGQGGVGKTSLCKQLIGEKFDGDESSTHGINVQDWKIPAPERKKIRLNVWDFGG 60
Query: 92 Q 92
Q
Sbjct: 61 Q 61
>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 = 42.6 bits (101), Expect = 1e-05
Identities = 30/127 (23%), Positives = 56/127 (44%), Gaps = 20/127 (15%)
Query: 43 LLGLDNAGKTTILKTLASEDISHITPTQGFNIKSVQSEGFKLN------------VWDIG 90
+ G N GK+++L L +++ ++P G + + ++L + + G
Sbjct: 2 IFGRPNVGKSSLLNALLGQNVGIVSPIPGTT-RDPVRKEWELLPLGPVVLIDTPGLDEEG 60
Query: 91 GQRKIRPY-WRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVYANKQ 149
G + R R D D+++ V+DS D+ EE LL + G P+L+ NK
Sbjct: 61 GLGRERVEEARQVADRADLVLLVVDS-DLTPVEE--EAKLGLL---RERGKPVLLVLNKI 114
Query: 150 DLLGAAP 156
DL+ +
Sbjct: 115 DLVPESE 121
>gnl|CDD|206640 cd00154, Rab, Ras-related in brain (Rab) family of small guanosine
triphosphatases (GTPases). Rab GTPases form the largest
family within the Ras superfamily. There are at least 60
Rab genes in the human genome, and a number of Rab
GTPases are conserved from yeast to humans. Rab GTPases
are small, monomeric proteins that function as molecular
switches to regulate vesicle trafficking pathways. The
different Rab GTPases are localized to the cytosolic
face of specific intracellular membranes, where they
regulate distinct steps in membrane traffic pathways. In
the GTP-bound form, Rab GTPases recruit specific sets of
effector proteins onto membranes. Through their
effectors, Rab GTPases regulate vesicle formation,
actin- and tubulin-dependent vesicle movement, and
membrane fusion. GTPase activating proteins (GAPs)
interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which mask C-terminal lipid binding and promote
cytosolic localization. While most unicellular organisms
possess 5-20 Rab members, several have been found to
possess 60 or more Rabs; for many of these Rab isoforms,
homologous proteins are not found in other organisms.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Since crystal
structures often lack C-terminal residues, the lipid
modification site is not available for annotation in
many of the CDs in the hierarchy, but is included where
possible.
Length = 159
Score = 42.1 bits (100), Expect = 2e-05
Identities = 34/122 (27%), Positives = 54/122 (44%), Gaps = 14/122 (11%)
Query: 39 LRILLLGLDNAGKTTILKTLASEDIS-HITPTQG--FNIKSVQSEG--FKLNVWDIGGQR 93
+I+L+G GKT++L S + T G F K+++ +G KL +WD GQ
Sbjct: 1 FKIVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGVDFKSKTIEVDGKKVKLQIWDTAGQE 60
Query: 94 KIRPYWRNYFDNTDILIYVIDSADVKRFEESGFE----LHELLSDEKLTGVPLLVYANKQ 149
+ R +Y+ I V D + ES FE L + +P+++ NK
Sbjct: 61 RFRSITSSYYRGAHGAILVYDVTN----RES-FENLDKWLNELKEYAPPNIPIILVGNKS 115
Query: 150 DL 151
DL
Sbjct: 116 DL 117
>gnl|CDD|206661 cd01869, Rab1_Ypt1, Rab GTPase family 1 includes the yeast homolog
Ypt1. Rab1/Ypt1 subfamily. Rab1 is found in every
eukaryote and is a key regulatory component for the
transport of vesicles from the ER to the Golgi
apparatus. Studies on mutations of Ypt1, the yeast
homolog of Rab1, showed that this protein is necessary
for the budding of vesicles of the ER as well as for
their transport to, and fusion with, the Golgi
apparatus. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation of
the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 166
Score = 41.2 bits (97), Expect = 4e-05
Identities = 35/121 (28%), Positives = 58/121 (47%), Gaps = 12/121 (9%)
Query: 39 LRILLLGLDNAGKTTILKTLASEDI--SHITPTQG--FNIKSVQSEG--FKLNVWDIGGQ 92
++LL+G GK+ +L A + S+I+ T G F I++++ +G KL +WD GQ
Sbjct: 3 FKLLLIGDSGVGKSCLLLRFADDTYTESYIS-TIGVDFKIRTIELDGKTVKLQIWDTAGQ 61
Query: 93 RKIRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLT--GVPLLVYANKQD 150
+ R +Y+ +I V D D + F L E+ ++ V L+ NK D
Sbjct: 62 ERFRTITSSYYRGAHGIIIVYDVTDQESFNNVKQWLQEI---DRYASENVNKLLVGNKCD 118
Query: 151 L 151
L
Sbjct: 119 L 119
>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 = 41.3 bits (97), Expect = 5e-05
Identities = 31/121 (25%), Positives = 54/121 (44%), Gaps = 8/121 (6%)
Query: 39 LRILLLGLDNAGKTTILKTLASEDIS---HITPTQGFNIKSVQ---SEGFKLNVWDIGGQ 92
++I++LG +GKT++++ A E T F + + S L VWDIGGQ
Sbjct: 1 IKIVVLGDGASGKTSLIRRFAQEGFGKSYKQTIGLDFFSRRITLPGSLNVTLQVWDIGGQ 60
Query: 93 RKIRPYWRNYFDNTDILIYVIDSADVKRFE--ESGFELHELLSDEKLTGVPLLVYANKQD 150
+ Y + V D + + FE E + + +++E T +++ NK D
Sbjct: 61 QIGGKMLDKYIYGAQAVCLVYDITNSQSFENLEDWLSVVKKVNEESETKPKMVLVGNKTD 120
Query: 151 L 151
L
Sbjct: 121 L 121
>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 = 40.8 bits (96), Expect = 6e-05
Identities = 25/81 (30%), Positives = 41/81 (50%), Gaps = 5/81 (6%)
Query: 39 LRILLLGLDNAGKTTILKTLASEDI-SHITPTQG--FNIKSVQSEG--FKLNVWDIGGQR 93
L+ILL+G GK+++L + ++ T G F +K+V +G KL +WD GQ
Sbjct: 1 LKILLIGDSGVGKSSLLLRFTDDTFDEDLSSTIGVDFKVKTVTVDGKKVKLAIWDTAGQE 60
Query: 94 KIRPYWRNYFDNTDILIYVID 114
+ R +Y+ +I V D
Sbjct: 61 RFRTLTSSYYRGAQGVILVYD 81
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 40.6 bits (96), Expect = 6e-05
Identities = 31/120 (25%), Positives = 53/120 (44%), Gaps = 10/120 (8%)
Query: 39 LRILLLGLDNAGKTTILKTLAS-EDISHITPTQG--FNIKSVQSEG--FKLNVWDIGGQR 93
+I+L+G GK+++L + T G F K+++ +G KL +WD GQ
Sbjct: 1 FKIILIGDSGVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIEVDGKRVKLQIWDTAGQE 60
Query: 94 KIRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELL--SDEKLTGVPLLVYANKQDL 151
+ R +Y+ + V D + + FE L EL + V +++ NK DL
Sbjct: 61 RFRSITSSYYRGAVGALLVYDITNRESFENLENWLKELREYASP---NVVIMLVGNKSDL 117
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 41.0 bits (97), Expect = 1e-04
Identities = 34/156 (21%), Positives = 68/156 (43%), Gaps = 36/156 (23%)
Query: 23 GLLAILKKLRSSPEK------ELRILLLGLDNAGKTTILKTLASEDISHITPTQG----- 71
L+A L +L ++ ++ L+++++G N GK+++L L D + +T G
Sbjct: 196 ELIAELDELLATAKQGKILREGLKVVIIGRPNVGKSSLLNALLGRDRAIVTDIAGTTRDV 255
Query: 72 ----FNIKSVQSEGFKLNVWDIGGQRK---------IRPYWRNYFDNTDILIYVIDSADV 118
N+ G + + D G R+ I + D++++V+D++
Sbjct: 256 IEEDINLN-----GIPVRLVDTAGIRETDDVVERIGIERAK-KAIEEADLVLFVLDASQP 309
Query: 119 KRFEESGFELHELLSDEKLTGVPLLVYANKQDLLGA 154
++ L ELL +K P++V NK DL+
Sbjct: 310 --LDKEDLALIELLPKKK----PIIVVLNKADLVSK 339
>gnl|CDD|219856 pfam08477, Miro, Miro-like protein. Mitochondrial Rho proteins
(Miro-1, and Miro-2), are atypical Rho GTPases. They
have a unique domain organisation, with tandem
GTP-binding domains and two EF hand domains (pfam00036),
that may bind calcium. They are also larger than
classical small GTPases. It has been proposed that they
are involved in mitochondrial homeostasis and apoptosis.
Length = 116
Score = 38.9 bits (91), Expect = 2e-04
Identities = 24/116 (20%), Positives = 51/116 (43%), Gaps = 6/116 (5%)
Query: 40 RILLLGLDNAGKTTILKTLASEDISH-----ITPTQGFNIKSVQSEGFKLNVWDIGGQRK 94
+++++G +GK+++L L + T + V + LN+WD GG+ +
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREE 60
Query: 95 IRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKL-TGVPLLVYANKQ 149
++ + D ++ V D D + E + L + KL +P+++ NK
Sbjct: 61 LKFEHIIFMKWADAILLVYDLTDRESLNEVSRLIAWLPNLRKLGGKIPVILVGNKL 116
>gnl|CDD|133267 cd01864, Rab19, Rab GTPase family 19 (Rab19). Rab19 subfamily.
Rab19 proteins are associated with Golgi stacks.
Similarity analysis indicated that Rab41 is closely
related to Rab19. However, the function of these Rabs is
not yet characterized. GTPase activating proteins (GAPs)
interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 165
Score = 39.0 bits (91), Expect = 2e-04
Identities = 35/122 (28%), Positives = 57/122 (46%), Gaps = 16/122 (13%)
Query: 40 RILLLGLDNAGKTTILKTLASEDISHITPTQG------FNIKSVQSEG--FKLNVWDIGG 91
+I+L+G N GKT +++ S + QG F +K+++ +G KL +WD G
Sbjct: 5 KIILIGDSNVGKTCVVQRFKS---GTFSERQGNTIGVDFTMKTLEIQGKRVKLQIWDTAG 61
Query: 92 QRKIRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTG--VPLLVYANKQ 149
Q + R ++Y+ + + I D FE + E+ EK V LL+ NK
Sbjct: 62 QERFRTITQSYYRSANGAIIAYDITRRSSFESVPHWIEEV---EKYGASNVVLLLIGNKC 118
Query: 150 DL 151
DL
Sbjct: 119 DL 120
>gnl|CDD|206688 cd04101, RabL4, Rab GTPase-like family 4 (Rab-like4). RabL4
(Rab-like4) subfamily. RabL4s are novel proteins that
have high sequence similarity with Rab family members,
but display features that are distinct from Rabs, and
have been termed Rab-like. As in other Rab-like
proteins, RabL4 lacks a prenylation site at the
C-terminus. The specific function of RabL4 remains
unknown.
Length = 167
Score = 39.0 bits (91), Expect = 3e-04
Identities = 23/126 (18%), Positives = 50/126 (39%), Gaps = 9/126 (7%)
Query: 39 LRILLLGLDNAGKTTILKTLASEDIS---HITPTQG--FNIKSVQ----SEGFKLNVWDI 89
+ ++G GK+ +++ S+ + + T T G +K+V S+ +L ++D
Sbjct: 1 AQCAVVGDPAVGKSALVQMFHSDGATFQKNYTMTTGCDLVVKTVPVPDTSDSVELFIFDS 60
Query: 90 GGQRKIRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVYANKQ 149
GQ N ++ ++ V D + F ++ + + P ++ NK
Sbjct: 61 AGQELFSDMVENVWEQPAVVCVVYDVTNEVSFNNCSRWINRVRTHSHGLHTPGVLVGNKC 120
Query: 150 DLLGAA 155
DL
Sbjct: 121 DLTDRR 126
>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 = 38.7 bits (90), Expect = 3e-04
Identities = 25/84 (29%), Positives = 41/84 (48%), Gaps = 11/84 (13%)
Query: 39 LRILLLGLDNAGKTTILKTLASEDISHITPTQG------FNIKSVQSEG--FKLNVWDIG 90
+I+L+G GKT +++ P QG F IK+V+ +G KL +WD
Sbjct: 8 FKIVLIGNAGVGKTCLVRRFTQ---GLFPPGQGATIGVDFMIKTVEIKGEKIKLQIWDTA 64
Query: 91 GQRKIRPYWRNYFDNTDILIYVID 114
GQ + R ++Y+ + + LI D
Sbjct: 65 GQERFRSITQSYYRSANALILTYD 88
>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 = 38.6 bits (91), Expect = 4e-04
Identities = 29/140 (20%), Positives = 55/140 (39%), Gaps = 39/140 (27%)
Query: 39 LRILLLGLDNAGKTTILKTLASEDISHITPTQG---------FNIKSVQSEGFKLNVWD- 88
+++++ G N GK+++L LA D + ++ G ++ G + + D
Sbjct: 4 IKVVIAGKPNVGKSSLLNALAGRDRAIVSDIAGTTRDVIEEEIDL-----GGIPVRLIDT 58
Query: 89 ------------IGGQRKIRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEK 136
IG +R R + D+++ V+D+ G + +L E
Sbjct: 59 AGLRETEDEIEKIGIERA-----REAIEEADLVLLVVDA-------SEGLDEEDLEILEL 106
Query: 137 LTGVPLLVYANKQDLLGAAP 156
P++V NK DLL A
Sbjct: 107 PAKKPVIVVLNKSDLLSDAE 126
>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 = 38.4 bits (90), Expect = 4e-04
Identities = 23/88 (26%), Positives = 39/88 (44%), Gaps = 12/88 (13%)
Query: 40 RILLLGLDNAGKTTILKT----LASEDISHITPTQGFNIKSVQSEGF-KLNVWDIGGQRK 94
RILL+GL +GK++I K ++ + + T + + F +WD GQ
Sbjct: 1 RILLMGLRRSGKSSIQKVVFHKMSPNETLFLESTNKITKDDISNSSFVNFQIWDFPGQ-- 58
Query: 95 IRPYWRNY-----FDNTDILIYVIDSAD 117
+ P+ F L++VID+ D
Sbjct: 59 LDPFDPTLDPEMIFSGCGALVFVIDAQD 86
>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 = 38.6 bits (90), Expect = 4e-04
Identities = 25/91 (27%), Positives = 48/91 (52%), Gaps = 6/91 (6%)
Query: 38 ELRILLLGLDNAGKTTILKTLASEDISHIT-PTQG--FNIKSVQSEG---FKLNVWDIGG 91
+ R++++G GK+++LK + ++ PT G F + ++ E KL +WD G
Sbjct: 2 QFRLIVIGDSTVGKSSLLKRFTEGRFAEVSDPTVGVDFFSRLIEIEPGVRIKLQLWDTAG 61
Query: 92 QRKIRPYWRNYFDNTDILIYVIDSADVKRFE 122
Q + R R+Y+ N+ ++ V D + + FE
Sbjct: 62 QERFRSITRSYYRNSVGVLLVFDITNRESFE 92
>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 = 38.3 bits (89), Expect = 5e-04
Identities = 30/98 (30%), Positives = 48/98 (48%), Gaps = 7/98 (7%)
Query: 40 RILLLGLDNAGKTTILKTLASEDIS--HITPTQG--FNIKSVQSEG--FKLNVWDIGGQR 93
++L++G GK+++L A S +IT T G F I++V+ G KL +WD GQ
Sbjct: 8 KLLIIGDSGVGKSSLLLRFADNTFSGSYIT-TIGVDFKIRTVEINGERVKLQIWDTAGQE 66
Query: 94 KIRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHEL 131
+ R Y+ T +I V D + + F L E+
Sbjct: 67 RFRTITSTYYRGTHGVIVVYDVTNGESFVNVKRWLQEI 104
>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 = 37.5 bits (87), Expect = 8e-04
Identities = 23/78 (29%), Positives = 35/78 (44%), Gaps = 2/78 (2%)
Query: 82 FKLNVWDIGGQRKIRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVP 141
F L +WD GQ + + Y+ +I V D DV E + L + L + + V
Sbjct: 49 FSLQLWDTAGQERFKCIASTYYRGAQAIIIVFDLTDVASLEHTRQWLEDALKENDPSSVL 108
Query: 142 LLVYANKQDLLGAAPAGY 159
L + K+DL +PA Y
Sbjct: 109 LFLVGTKKDLS--SPAQY 124
>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 = 37.9 bits (88), Expect = 8e-04
Identities = 24/86 (27%), Positives = 35/86 (40%), Gaps = 8/86 (9%)
Query: 40 RILLLGLDNAGKTTILKTLASE----DISHITPTQGFNIKSVQSEGF-KLNVWDIGGQRK 94
++LL G +GK++I K + D + T + G LN+WD GQ
Sbjct: 1 KLLLXGRRRSGKSSIRKVVFHNYSPFDTLRLESTIDVEHSHLSFLGNXTLNLWDCPGQDV 60
Query: 95 IRPYWRNY---FDNTDILIYVIDSAD 117
++ F LIYVID D
Sbjct: 61 FFEPTKDKEHIFQXVGALIYVIDVQD 86
>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 = 37.1 bits (87), Expect = 0.001
Identities = 35/130 (26%), Positives = 58/130 (44%), Gaps = 32/130 (24%)
Query: 40 RILLLGLDNAGKTTILKTLASEDISHIT--------PTQG--FNIKSVQSEG--FKLNVW 87
+++L+G GK+++L I PT G F K+++ +G KL +W
Sbjct: 1 KLVLVGDGGVGKSSLL-------IRFTQNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIW 53
Query: 88 DIGGQRKIRPYWRNYFDNTD--ILIYVIDSAD----VKRFEESGFELHELLSDEKLTGVP 141
D GQ + R Y+ +L+Y I S D VK++ E E+ + VP
Sbjct: 54 DTAGQERFRALRPLYYRGAQGFLLVYDITSRDSFENVKKWLE---EILRHADE----NVP 106
Query: 142 LLVYANKQDL 151
+++ NK DL
Sbjct: 107 IVLVGNKCDL 116
>gnl|CDD|133315 cd04115, Rab33B_Rab33A, Rab GTPase family 33 includes Rab33A and
Rab33B. Rab33B/Rab33A subfamily. Rab33B is ubiquitously
expressed in mouse tissues and cells, where it is
localized to the medial Golgi cisternae. It colocalizes
with alpha-mannose II. Together with the other cisternal
Rabs, Rab6A and Rab6A', it is believed to regulate the
Golgi response to stress and is likely a molecular
target in stress-activated signaling pathways. Rab33A
(previously known as S10) is expressed primarily in the
brain and immune system cells. In humans, it is located
on the X chromosome at Xq26 and its expression is
down-regulated in tuberculosis patients. Experimental
evidence suggests that Rab33A is a novel CD8+ T cell
factor that likely plays a role in tuberculosis disease
processes. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation of
the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 170
Score = 36.6 bits (85), Expect = 0.002
Identities = 34/129 (26%), Positives = 59/129 (45%), Gaps = 20/129 (15%)
Query: 40 RILLLGLDNAGKTTI-LKTLASEDISHITPTQG--FNIKSVQSEG--FKLNVWDIGGQRK 94
+I+++G N GKT + + A T G F ++V+ +G K+ +WD GQ +
Sbjct: 4 KIIVIGDSNVGKTCLTYRFCAGRFPERTEATIGVDFRERTVEIDGERIKVQLWDTAGQER 63
Query: 95 IRPYW-RNYFDNTDILIYVIDSADVKRF-------EESGFELHELLSDEKLTGVPLLVYA 146
R ++Y+ N +++V D ++ F EE E H L ++ VP ++
Sbjct: 64 FRKSMVQHYYRNVHAVVFVYDVTNMASFHSLPSWIEEC--EQHSLPNE-----VPRILVG 116
Query: 147 NKQDLLGAA 155
NK DL
Sbjct: 117 NKCDLREQI 125
>gnl|CDD|133318 cd04118, Rab24, Rab GTPase family 24 (Rab24). Rab24 is distinct
from other Rabs in several ways. It exists primarily in
the GTP-bound state, having a low intrinsic GTPase
activity; it is not efficiently geranyl-geranylated at
the C-terminus; it does not form a detectable complex
with Rab GDP-dissociation inhibitors (GDIs); and it has
recently been shown to undergo tyrosine phosphorylation
when overexpressed in vitro. The specific function of
Rab24 still remains unknown. It is found in a transport
route between ER-cis-Golgi and late endocytic
compartments. It is putatively involved in an autophagic
pathway, possibly directing misfolded proteins in the ER
to degradative pathways. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 193
Score = 36.8 bits (85), Expect = 0.002
Identities = 27/121 (22%), Positives = 49/121 (40%), Gaps = 10/121 (8%)
Query: 39 LRILLLGLDNAGKTTILKTLASEDISHITPTQ-----GFNIKSVQSEG--FKLNVWDIGG 91
+++++LG ++ GKT++++ P Q F K + L +WD G
Sbjct: 1 VKVVMLGKESVGKTSLVERYVHHRFLV-GPYQNTIGAAFVAKRMVVGERVVTLGIWDTAG 59
Query: 92 QRKIRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVYANKQDL 151
+ R Y+ I D D FE + F + EL + E+ + + K DL
Sbjct: 60 SERYEAMSRIYYRGAKAAIVCYDLTDSSSFERAKFWVKELQNLEE--HCKIYLCGTKSDL 117
Query: 152 L 152
+
Sbjct: 118 I 118
>gnl|CDD|206696 cd04113, Rab4, Rab GTPase family 4 (Rab4). Rab4 subfamily. Rab4
has been implicated in numerous functions within the
cell. It helps regulate endocytosis through the sorting,
recycling, and degradation of early endosomes. Mammalian
Rab4 is involved in the regulation of many surface
proteins including G-protein-coupled receptors,
transferrin receptor, integrins, and surfactant protein
A. Experimental data implicate Rab4 in regulation of the
recycling of internalized receptors back to the plasma
membrane. It is also believed to influence
receptor-mediated antigen processing in B-lymphocytes,
in calcium-dependent exocytosis in platelets, in
alpha-amylase secretion in pancreatic cells, and in
insulin-induced translocation of Glut4 from internal
vesicles to the cell surface. Rab4 is known to share
effector proteins with Rab5 and Rab11. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 161
Score = 36.6 bits (85), Expect = 0.002
Identities = 34/123 (27%), Positives = 54/123 (43%), Gaps = 16/123 (13%)
Query: 39 LRILLLGLDNAGKTTILKTLAS----EDISH-ITPTQGFNIKSVQSEGFKLNVWDIGGQR 93
+ L++G GK+ +L +D +H I G + +V + KL +WD GQ
Sbjct: 1 FKFLIIGSAGTGKSCLLHQFIENKFKQDSNHTIGVEFGSRVVNVGGKSVKLQIWDTAGQE 60
Query: 94 KIRPYWRNYFDNT--DILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVY---ANK 148
+ R R+Y+ +L+Y I S ES L L+D + P +V NK
Sbjct: 61 RFRSVTRSYYRGAAGALLVYDITS------RESFNALTNWLTDARTLASPDIVIILVGNK 114
Query: 149 QDL 151
+DL
Sbjct: 115 KDL 117
>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 = 37.1 bits (87), Expect = 0.002
Identities = 34/144 (23%), Positives = 56/144 (38%), Gaps = 43/144 (29%)
Query: 39 LRILLLGLDNAGKTTILKTLASEDIS-----------------HITP--------TQGFN 73
L I + G NAGK++++ L +DI+ + P T G +
Sbjct: 7 LHIGIFGRRNAGKSSLINALTGQDIAIVSDVPGTTTDPVYKAMELLPLGPVVLIDTAGLD 66
Query: 74 IKSVQSEGFKLNVWDIGGQRKIRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLS 133
EG ++G R + R D TD+ + V+D+ +EL EL+
Sbjct: 67 -----DEG------ELGELRVEKT--REVLDKTDLALLVVDAG----VGPGEYEL-ELIE 108
Query: 134 DEKLTGVPLLVYANKQDLLGAAPA 157
+ K +P +V NK DL +
Sbjct: 109 ELKERKIPYIVVINKIDLGEESAE 132
>gnl|CDD|133321 cd04121, Rab40, Rab GTPase family 40 (Rab40) contains Rab40a,
Rab40b and Rab40c. The Rab40 subfamily contains Rab40a,
Rab40b, and Rab40c, which are all highly homologous. In
rat, Rab40c is localized to the perinuclear recycling
compartment (PRC), and is distributed in a
tissue-specific manor, with high expression in brain,
heart, kidney, and testis, low expression in lung and
liver, and no expression in spleen and skeletal muscle.
Rab40c is highly expressed in differentiated
oligodendrocytes but minimally expressed in
oligodendrocyte progenitors, suggesting a role in the
vesicular transport of myelin components. Unlike most
other Ras-superfamily proteins, Rab40c was shown to have
a much lower affinity for GTP, and an affinity for GDP
that is lower than for GTP. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 189
Score = 36.5 bits (84), Expect = 0.003
Identities = 34/120 (28%), Positives = 55/120 (45%), Gaps = 11/120 (9%)
Query: 39 LRILLLGLDNAGKTTILKTLASEDISHITP---TQGFNIKS----VQSEGFKLNVWDIGG 91
L+ LL+G + GK IL +L +D S +P G + K+ + KL +WD G
Sbjct: 7 LKFLLVGDSDVGKGEILASL--QDGSTESPYGYNMGIDYKTTTILLDGRRVKLQLWDTSG 64
Query: 92 QRKIRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVYANKQDL 151
Q + +R+Y +I V D + F+ + E+ DE GVP ++ N+ L
Sbjct: 65 QGRFCTIFRSYSRGAQGIILVYDITNRWSFDGIDRWIKEI--DEHAPGVPKILVGNRLHL 122
>gnl|CDD|206698 cd04117, Rab15, Rab GTPase family 15 (Rab15). Rab15 colocalizes
with the transferrin receptor in early endosome
compartments, but not with late endosomal markers. It
codistributes with Rab4 and Rab5 on early/sorting
endosomes, and with Rab11 on pericentriolar recycling
endosomes. It is believed to function as an inhibitory
GTPase that regulates distinct steps in early endocytic
trafficking. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation of
the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 164
Score = 36.1 bits (83), Expect = 0.003
Identities = 26/85 (30%), Positives = 43/85 (50%), Gaps = 9/85 (10%)
Query: 39 LRILLLGLDNAGKTTILKTLASEDI--SHITPTQG--FNIKSVQSEGFK--LNVWDIGGQ 92
R+LL+G GKT +L + SHI+ T G F +K+++ +G K + +WD GQ
Sbjct: 1 FRLLLIGDSGVGKTCLLCRFTDNEFHSSHIS-TIGVDFKMKTIEVDGIKVRIQIWDTAGQ 59
Query: 93 RKIRPYWRNYFDNTD--ILIYVIDS 115
+ + + Y+ L+Y I S
Sbjct: 60 ERYQTITKQYYRRAQGIFLVYDISS 84
>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 = 35.7 bits (83), Expect = 0.003
Identities = 31/90 (34%), Positives = 47/90 (52%), Gaps = 9/90 (10%)
Query: 40 RILLLGLDNAGKTTILKTLASEDI---SHITPTQG--FNIKSVQSEG--FKLNVWDIGGQ 92
++LL+G GK+ +L SED S I+ T G F I++++ +G KL +WD GQ
Sbjct: 5 KLLLIGDSGVGKSCLLLRF-SEDSFNPSFIS-TIGIDFKIRTIELDGKKIKLQIWDTAGQ 62
Query: 93 RKIRPYWRNYFDNTDILIYVIDSADVKRFE 122
+ R +Y+ +I V D D K FE
Sbjct: 63 ERFRTITTSYYRGAMGIILVYDITDEKSFE 92
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 36.2 bits (85), Expect = 0.004
Identities = 35/170 (20%), Positives = 70/170 (41%), Gaps = 41/170 (24%)
Query: 14 ENQVKDLALGLLAILKKLRSSPEKE------LRILLLGLDNAGKTTILKTLASEDISHIT 67
+ ++ + L+A L+ L +S + L++++ G N GK+++L L E+ + +T
Sbjct: 185 DEKILEKLEELIAELEALLASARQGEILREGLKVVIAGRPNVGKSSLLNALLGEERAIVT 244
Query: 68 PTQG---------FNIKSVQSEGFKLNVWDIGGQRK---------IRPYWRNY--FDNTD 107
G N+ +G L + D G R+ I R+ + D
Sbjct: 245 DIAGTTRDVIEEHINL-----DGIPLRLIDTAGIRETDDEVEKIGIE---RSREAIEEAD 296
Query: 108 ILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVYANKQDLLGAAPA 157
+++ V+D+++ + E+L P++V NK DL G
Sbjct: 297 LVLLVLDASE-------PLTEEDDEILEELKDKPVIVVLNKADLTGEIDL 339
>gnl|CDD|232980 TIGR00450, mnmE_trmE_thdF, tRNA modification GTPase TrmE. TrmE,
also called MnmE and previously designated ThdF
(thiophene and furan oxidation protein), is a GTPase
involved in tRNA modification to create
5-methylaminomethyl-2-thiouridine in the wobble position
of some tRNAs. This protein and GidA form an
alpha2/beta2 heterotetramer [Protein synthesis, tRNA and
rRNA base modification].
Length = 442
Score = 36.3 bits (84), Expect = 0.004
Identities = 32/150 (21%), Positives = 64/150 (42%), Gaps = 23/150 (15%)
Query: 19 DLALGLLAILKKLRSSPEKELR-----ILLLGLDNAGKTTILKTLASEDISHITPTQGFN 73
L L ++A LK + +S + E + ++G N GK+++L L +D + ++ +G
Sbjct: 179 QLLLSIIAELKDILNSYKLEKLDDGFKLAIVGSPNVGKSSLLNALLKQDRAIVSDIKGTT 238
Query: 74 IKSVQS----EGFKLNVWDIGGQRKIRPYW--------RNYFDNTDILIYVIDSADVKRF 121
V+ G + + D G R+ + D++IYV+D++
Sbjct: 239 RDVVEGDFELNGILIKLLDTAGIREHADFVERLGIEKSFKAIKQADLVIYVLDASQPLTK 298
Query: 122 EESGFELHELLSDEKLTGVPLLVYANKQDL 151
++ L+ D + P ++ NK DL
Sbjct: 299 DD------FLIIDLNKSKKPFILVLNKIDL 322
>gnl|CDD|206744 cd11384, RagA_like, Rag GTPase, subfamily of Ras-related GTPases,
includes Ras-related GTP-binding proteins A and B. RagA
and RagB are closely related Rag GTPases (ras-related
GTP-binding protein A and B) that constitute a unique
subgroup of the Ras superfamily, and are functional
homologs of Saccharomyces cerevisiae Gtr1. These domains
function by forming heterodimers with RagC or RagD, and
similarly, Gtr1 dimerizes with Gtr2, through the
carboxy-terminal segments. They play an essential role
in regulating amino acid-induced target of rapamycin
complex 1 (TORC1) kinase signaling, exocytic cargo
sorting at endosomes, and epigenetic control of gene
expression. In response to amino acids, the Rag GTPases
guide the TORC1 complex to activate the platform
containing Rheb proto-oncogene by driving the
relocalization of mTORC1 from discrete locations in the
cytoplasm to a late endosomal and/or lysosomal
compartment that is Rheb-enriched and contains Rab-7.
Length = 286
Score = 35.7 bits (83), Expect = 0.006
Identities = 27/87 (31%), Positives = 38/87 (43%), Gaps = 16/87 (18%)
Query: 41 ILLLGLDNAGKTT----ILKTLASEDISHITPTQGFNIKSVQSEG-FKLNVWDIGGQRKI 95
+LL+G +GKT+ I + D + T V+ G LN+WD GGQ
Sbjct: 2 VLLMGKSGSGKTSMRSIIFANYLARDTRRLGATIDVEHSHVRFLGNLVLNLWDCGGQDA- 60
Query: 96 RPYWRNYFD--------NTDILIYVID 114
+ NYF N ++LIYV D
Sbjct: 61 --FMENYFTSQRDHIFRNVEVLIYVFD 85
>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 = 34.5 bits (80), Expect = 0.009
Identities = 32/120 (26%), Positives = 52/120 (43%), Gaps = 12/120 (10%)
Query: 40 RILLLGLDNAGKTTILKTLASE--DISHITPTQ-GFNIKSVQSEG--FKLNVWDIGGQRK 94
+++LLG GKT+++ + H + TQ F K+V G L +WD GQ +
Sbjct: 2 KVVLLGEGRVGKTSLVLRYVENKFNEKHESTTQASFFQKTVNIGGKRIDLAIWDTAGQER 61
Query: 95 IRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHEL---LSDEKLTGVPLLVYANKQDL 151
Y+ + D I V D D F++ + EL + + L++ NK DL
Sbjct: 62 YHALGPIYYRDADGAILVYDITDADSFQKVKKWIKELKQMRGNN----ISLVIVGNKIDL 117
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 34.9 bits (80), Expect = 0.011
Identities = 31/118 (26%), Positives = 50/118 (42%), Gaps = 6/118 (5%)
Query: 39 LRILLLGLDNAGKTTILKTLASEDI---SHITPTQGFNIKSVQSEG--FKLNVWDIGGQR 93
+I+L+G GK+ IL + S T F +++Q EG K +WD GQ
Sbjct: 13 FKIVLIGDSGVGKSNILSRFTRNEFCLESKSTIGVEFATRTLQVEGKTVKAQIWDTAGQE 72
Query: 94 KIRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVYANKQDL 151
+ R Y+ + V D + F+ L E L D + + +++ NK DL
Sbjct: 73 RYRAITSAYYRGAVGALLVYDITKRQTFDNVQRWLRE-LRDHADSNIVIMMAGNKSDL 129
>gnl|CDD|214595 smart00275, G_alpha, G protein alpha subunit. Subunit of G
proteins that contains the guanine nucleotide binding
site.
Length = 342
Score = 34.5 bits (80), Expect = 0.015
Identities = 13/29 (44%), Positives = 22/29 (75%)
Query: 28 LKKLRSSPEKELRILLLGLDNAGKTTILK 56
L++ R ++E+++LLLG +GK+TILK
Sbjct: 11 LEEERKKKKREVKLLLLGAGESGKSTILK 39
Score = 33.7 bits (78), Expect = 0.028
Identities = 24/81 (29%), Positives = 35/81 (43%), Gaps = 14/81 (17%)
Query: 61 EDISHI-TPTQG-----FNIKSVQSEGFKLNVWDIGGQRKIRPYWRNYFDNTDILIYVID 114
+DI PT G F +K ++D+GGQR R W + FDN +I+ +
Sbjct: 162 QDILRSRVPTTGIQETAFIVK-----KLFFRMFDVGGQRSERKKWIHCFDNVTAIIFCVA 216
Query: 115 SA--DVKRFE-ESGFELHELL 132
+ D E ES + E L
Sbjct: 217 LSEYDQVLEEDESTNRMQESL 237
>gnl|CDD|133343 cd04143, Rhes_like, Ras homolog enriched in striatum (Rhes) and
activator of G-protein signaling 1 (Dexras1/AGS1). This
subfamily includes Rhes (Ras homolog enriched in
striatum) and Dexras1/AGS1 (activator of G-protein
signaling 1). These proteins are homologous, but exhibit
significant differences in tissue distribution and
subcellular localization. Rhes is found primarily in the
striatum of the brain, but is also expressed in other
areas of the brain, such as the cerebral cortex,
hippocampus, inferior colliculus, and cerebellum. Rhes
expression is controlled by thyroid hormones. In rat
PC12 cells, Rhes is farnesylated and localizes to the
plasma membrane. Rhes binds and activates PI3K, and
plays a role in coupling serpentine membrane receptors
with heterotrimeric G-protein signaling. Rhes has
recently been shown to be reduced under conditions of
dopamine supersensitivity and may play a role in
determining dopamine receptor sensitivity. Dexras1/AGS1
is a dexamethasone-induced Ras protein that is expressed
primarily in the brain, with low expression levels in
other tissues. Dexras1 localizes primarily to the
cytoplasm, and is a critical regulator of the circadian
master clock to photic and nonphotic input. Most Ras
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins.
Length = 247
Score = 34.3 bits (79), Expect = 0.017
Identities = 32/124 (25%), Positives = 55/124 (44%), Gaps = 12/124 (9%)
Query: 40 RILLLGLDNAGKTTIL-KTLASEDISHITPT-QGFNIK--SVQSEGFKLNVWDIGGQRKI 95
R+++LG GKT I+ + L TPT + F+ K S++ E ++L++ D G
Sbjct: 2 RMVVLGASKVGKTAIVSRFLGGRFEEQYTPTIEDFHRKLYSIRGEVYQLDILDTSGNHPF 61
Query: 96 RPYWRNYFDNTDILIYV--IDSAD----VKRFEESGFELHELLSDEK--LTGVPLLVYAN 147
R D+ I V +D+ + V R E E L ++ +P+++ N
Sbjct: 62 PAMRRLSILTGDVFILVFSLDNRESFEEVCRLREQILETKSCLKNKTKENVKIPMVICGN 121
Query: 148 KQDL 151
K D
Sbjct: 122 KADR 125
>gnl|CDD|206713 cd04146, RERG_RasL11_like, Ras-related and Estrogen-Regulated
Growth inhibitor (RERG) and Ras-like 11 (RasL11)-like
families. RERG (Ras-related and Estrogen- Regulated
Growth inhibitor) and Ras-like 11 are members of a novel
subfamily of Ras that were identified based on their
behavior in breast and prostate tumors, respectively.
RERG expression was decreased or lost in a significant
fraction of primary human breast tumors that lack
estrogen receptor and are correlated with poor clinical
prognosis. Elevated RERG expression correlated with
favorable patient outcome in a breast tumor subtype that
is positive for estrogen receptor expression. In
contrast to most Ras proteins, RERG overexpression
inhibited the growth of breast tumor cells in vitro and
in vivo. RasL11 was found to be ubiquitously expressed
in human tissue, but down-regulated in prostate tumors.
Both RERG and RasL11 lack the C-terminal CaaX
prenylation motif, where a = an aliphatic amino acid and
X = any amino acid, and are localized primarily in the
cytoplasm. Both are believed to have tumor suppressor
activity.
Length = 166
Score = 33.8 bits (78), Expect = 0.019
Identities = 31/131 (23%), Positives = 54/131 (41%), Gaps = 27/131 (20%)
Query: 41 ILLLGLDNAGKTT-ILKTLASEDISHITPTQGFNI----KSVQSEGFKLNVWDIGGQ--- 92
I +LG GK+ ++ L I P ++ ++ E L + D GQ
Sbjct: 2 IAVLGASGVGKSALTVRFLTKRFIGEYEPNLE-SLYSRQVTIDGEQVSLEIQDTPGQQQN 60
Query: 93 -------RKIRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLT--GVPLL 143
R +R W + F +L+Y I D F+ +L +L+ + K +P++
Sbjct: 61 EDPESLERSLR--WADGF----VLVYSIT--DRSSFDVVS-QLLQLIREIKKRDGEIPVI 111
Query: 144 VYANKQDLLGA 154
+ NK DLL +
Sbjct: 112 LVGNKADLLHS 122
>gnl|CDD|130064 TIGR00991, 3a0901s02IAP34, GTP-binding protein (Chloroplast
Envelope Protein Translocase). [Transport and binding
proteins, Nucleosides, purines and pyrimidines].
Length = 313
Score = 34.1 bits (78), Expect = 0.024
Identities = 30/112 (26%), Positives = 50/112 (44%), Gaps = 14/112 (12%)
Query: 24 LLAILKKLRSSPEKELRILLLGLDNAGKTTILKTLASEDISHITPTQGFNIK----SVQS 79
LL +L KL+ L IL++G GK++ + ++ E I+ ++ Q ++ S
Sbjct: 24 LLELLGKLKEEDVSSLTILVMGKGGVGKSSTVNSIIGERIATVSAFQSEGLRPMMVSRTR 83
Query: 80 EGFKLNVWDIGG--------QRKIRPYWRNYFDNT-DILIYVIDSADVKRFE 122
GF LN+ D G + + R T D+L+YV D D R +
Sbjct: 84 AGFTLNIIDTPGLIEGGYINDQAVNIIKRFLLGKTIDVLLYV-DRLDAYRVD 134
>gnl|CDD|206652 cd01853, Toc34_like, Translocon at the Outer-envelope membrane of
Chloroplasts 34-like (Toc34-like). The Toc34-like
(Translocon at the Outer-envelope membrane of
Chloroplasts) family contains several Toc proteins,
including Toc34, Toc33, Toc120, Toc159, Toc86, Toc125,
and Toc90. The Toc complex at the outer envelope
membrane of chloroplasts is a molecular machine of ~500
kDa that contains a single Toc159 protein, four Toc75
molecules, and four or five copies of Toc34. Toc64 and
Toc12 are associated with the translocon, but do not
appear to be part of the core complex. The Toc
translocon initiates the import of nuclear-encoded
preproteins from the cytosol into the organelle. Toc34
and Toc159 are both GTPases, while Toc75 is a
beta-barrel integral membrane protein. Toc159 is equally
distributed between a soluble cytoplasmic form and a
membrane-inserted form, suggesting that assembly of the
Toc complex is dynamic. Toc34 and Toc75 act sequentially
to mediate docking and insertion of Toc159 resulting in
assembly of the functional translocon.
Length = 248
Score = 33.8 bits (78), Expect = 0.025
Identities = 27/129 (20%), Positives = 51/129 (39%), Gaps = 22/129 (17%)
Query: 24 LLAILKKLRSSPEKELRILLLGLDNAGKTTILKTLASEDISHITPTQGFNIKSVQSE--- 80
L + KL+ + L IL+LG GK++ + ++ E ++ Q ++ +
Sbjct: 17 LHELEAKLKKELDFSLTILVLGKTGVGKSSTINSIFGERKVSVSAFQSETLRPREVSRTV 76
Query: 81 -GFKLNVWDIGGQRKIRPYWRNYFDNT--------------DILIYVIDSADVKRFEESG 125
GFKLN+ D G + + D+++YV D D+ R +
Sbjct: 77 DGFKLNIIDTPG---LLESQDQRVNRKILSIIKRFLKKKTIDVVLYV-DRLDMYRVDNLD 132
Query: 126 FELHELLSD 134
L ++D
Sbjct: 133 VPLLRAITD 141
>gnl|CDD|225976 COG3444, COG3444, Phosphotransferase system,
mannose/fructose/N-acetylgalactosamine-specific
component IIB [Carbohydrate transport and metabolism].
Length = 159
Score = 33.0 bits (76), Expect = 0.031
Identities = 11/58 (18%), Positives = 23/58 (39%), Gaps = 2/58 (3%)
Query: 74 IKSVQSEGFKLNVWDIGGQRKIRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHEL 131
+K G KL + + ++ I + +D + + + DV R E G + +
Sbjct: 47 LKQAAPPGVKLRFFSV--EKAIDVINKPKYDGQKVFLLFENPQDVLRLVEGGVPIKTI 102
>gnl|CDD|206657 cd01865, Rab3, Rab GTPase family 3 contains Rab3A, Rab3B, Rab3C and
Rab3D. The Rab3 subfamily contains Rab3A, Rab3B, Rab3C,
and Rab3D. All four isoforms were found in mouse brain
and endocrine tissues, with varying levels of
expression. Rab3A, Rab3B, and Rab3C localized to
synaptic and secretory vesicles; Rab3D was expressed at
high levels only in adipose tissue, exocrine glands, and
the endocrine pituitary, where it is localized to
cytoplasmic secretory granules. Rab3 appears to control
Ca2+-regulated exocytosis. The appropriate GDP/GTP
exchange cycle of Rab3A is required for Ca2+-regulated
exocytosis to occur, and interaction of the GTP-bound
form of Rab3A with effector molecule(s) is widely
believed to be essential for this process. Functionally,
most studies point toward a role for Rab3 in the
secretion of hormones and neurotransmitters. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 165
Score = 32.6 bits (74), Expect = 0.044
Identities = 24/88 (27%), Positives = 40/88 (45%), Gaps = 5/88 (5%)
Query: 39 LRILLLGLDNAGKTTILKTLASEDI-SHITPTQG--FNIKSV--QSEGFKLNVWDIGGQR 93
++L++G + GKT+ L A + S T G F +K+V + KL +WD GQ
Sbjct: 2 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVYRNDKRIKLQIWDTAGQE 61
Query: 94 KIRPYWRNYFDNTDILIYVIDSADVKRF 121
+ R Y+ I + D + + F
Sbjct: 62 RYRTITTAYYRGAMGFILMYDITNEESF 89
>gnl|CDD|182934 PRK11058, PRK11058, GTPase HflX; Provisional.
Length = 426
Score = 33.2 bits (76), Expect = 0.050
Identities = 15/46 (32%), Positives = 29/46 (63%), Gaps = 1/46 (2%)
Query: 107 DILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVYANKQDLL 152
+L++V+D+ADV R +E+ ++ +L + +P L+ NK D+L
Sbjct: 278 TLLLHVVDAADV-RVQENIEAVNTVLEEIDAHEIPTLLVMNKIDML 322
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 32.4 bits (73), Expect = 0.052
Identities = 19/69 (27%), Positives = 35/69 (50%), Gaps = 1/69 (1%)
Query: 83 KLNVWDIGGQRKIRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVPL 142
+L +WD GQ + R +Y ++ I V D + + FE + + ++L +E+ V +
Sbjct: 30 RLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDITNRQSFENTTKWIQDIL-NERGKDVII 88
Query: 143 LVYANKQDL 151
+ NK DL
Sbjct: 89 ALVGNKTDL 97
>gnl|CDD|206654 cd01861, Rab6, Rab GTPase family 6 (Rab6). Rab6 is involved in
microtubule-dependent transport pathways through the
Golgi and from endosomes to the Golgi. Rab6A of mammals
is implicated in retrograde transport through the Golgi
stack, and is also required for a slow,
COPI-independent, retrograde transport pathway from the
Golgi to the endoplasmic reticulum (ER). This pathway
may allow Golgi residents to be recycled through the ER
for scrutiny by ER quality-control systems. Yeast Ypt6p,
the homolog of the mammalian Rab6 GTPase, is not
essential for cell viability. Ypt6p acts in
endosome-to-Golgi, in intra-Golgi retrograde transport,
and possibly also in Golgi-to-ER trafficking. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 161
Score = 32.2 bits (74), Expect = 0.055
Identities = 27/117 (23%), Positives = 56/117 (47%), Gaps = 6/117 (5%)
Query: 40 RILLLGLDNAGKTTILKTLASEDIS-HITPTQG--FNIKSVQSEG--FKLNVWDIGGQRK 94
+++ LG + GKT+I+ + T G F K++ + +L +WD GQ +
Sbjct: 2 KLVFLGDQSVGKTSIITRFMYDTFDNQYQATIGIDFLSKTMYVDDKTVRLQLWDTAGQER 61
Query: 95 IRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVYANKQDL 151
R +Y ++ + + V D + + F ++ + + + DE+ V +++ NK DL
Sbjct: 62 FRSLIPSYIRDSSVAVVVYDITNRQSF-DNTDKWIDDVRDERGNDVIIVLVGNKTDL 117
>gnl|CDD|206680 cd01893, Miro1, Mitochondrial Rho family 1 (Miro1), N-terminal.
Miro1 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 N-terminal
GTPase domain 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 = 168
Score = 32.3 bits (74), Expect = 0.059
Identities = 11/32 (34%), Positives = 22/32 (68%)
Query: 37 KELRILLLGLDNAGKTTILKTLASEDISHITP 68
K++RI+L+G + GK++++ +L SE+ P
Sbjct: 1 KDVRIVLIGDEGVGKSSLIMSLVSEEFPENVP 32
>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 = 32.4 bits (75), Expect = 0.061
Identities = 15/46 (32%), Positives = 28/46 (60%), Gaps = 1/46 (2%)
Query: 107 DILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVYANKQDLL 152
D+L++V+D++D EE + E+L + +P+++ NK DLL
Sbjct: 122 DLLLHVVDASD-PDREEQIETVEEVLKELGADDIPIILVLNKIDLL 166
Score = 25.9 bits (58), Expect = 9.3
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 43 LLGLDNAGKTTILKTLASEDI 63
L+G NAGK+T+ L D+
Sbjct: 46 LVGYTNAGKSTLFNALTGADV 66
>gnl|CDD|206695 cd04112, Rab26, Rab GTPase family 26 (Rab26). Rab26 subfamily.
First identified in rat pancreatic acinar cells, Rab26
is believed to play a role in recruiting mature granules
to the plasma membrane upon beta-adrenergic stimulation.
Rab26 belongs to the Rab functional group III, which are
considered key regulators of intracellular vesicle
transport during exocytosis. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 191
Score = 32.1 bits (73), Expect = 0.068
Identities = 32/123 (26%), Positives = 52/123 (42%), Gaps = 13/123 (10%)
Query: 40 RILLLGLDNAGKTTIL---KTLASEDISHITPTQ-GFNIKSVQSEG--FKLNVWDIGGQR 93
+++L+G GKT +L K A S I F K V +G KL +WD GQ
Sbjct: 2 KVMLVGDSGVGKTCLLVRFKDGAFLAGSFIATVGIQFTNKVVTVDGVKVKLQIWDTAGQE 61
Query: 94 KIRPYWRNYFDNTDILIYVIDSADVKRFEESG---FELHELLSDEKLTGVPLLVYANKQD 150
+ R Y+ + L+ + D + F+ E+ E + V +++ NK D
Sbjct: 62 RFRSVTHAYYRDAHALLLLYDVTNKSSFDNIRAWLTEILEYAQSD----VVIMLLGNKAD 117
Query: 151 LLG 153
+ G
Sbjct: 118 MSG 120
>gnl|CDD|223562 COG0488, Uup, ATPase components of ABC transporters with duplicated
ATPase domains [General function prediction only].
Length = 530
Score = 32.2 bits (74), Expect = 0.10
Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 7/59 (11%)
Query: 16 QVKDLALGL---LAILKKLRSSPEKELRILLLGLDNAGKTTILKTLASEDISHITPTQG 71
+ ++++ G +LK L ++ RI ++G + AGK+T+LK LA E + P G
Sbjct: 323 EFENVSKGYDGGRLLLKDLSFRIDRGDRIAIVGPNGAGKSTLLKLLAGE----LGPLSG 377
>gnl|CDD|206653 cd01860, Rab5_related, Rab-related GTPase family includes Rab5 and
Rab22; regulates early endosome fusion. The
Rab5-related subfamily includes Rab5 and Rab22 of
mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of plants.
The members of this subfamily are involved in
endocytosis and endocytic-sorting pathways. In mammals,
Rab5 GTPases localize to early endosomes and regulate
fusion of clathrin-coated vesicles to early endosomes
and fusion between early endosomes. In yeast, Ypt51p
family members similarly regulate membrane trafficking
through prevacuolar compartments. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 163
Score = 31.4 bits (72), Expect = 0.13
Identities = 33/128 (25%), Positives = 53/128 (41%), Gaps = 20/128 (15%)
Query: 38 ELRILLLGLDNAGKTTILKTLASEDISHIT-PTQG--FNIKSV--QSEGFKLNVWDIGGQ 92
+ +++LLG + GK++I+ + S T G F ++V K +WD GQ
Sbjct: 1 QFKLVLLGDSSVGKSSIVLRFVKNEFSENQESTIGAAFLTQTVNLDDTTVKFEIWDTAGQ 60
Query: 93 RKIRP----YWRNYFDNTDILIYVIDSADVKRFEESGF---ELHELLSDEKLTGVPLLVY 145
+ R Y+R I++Y I S + FE++ EL E + L
Sbjct: 61 ERYRSLAPMYYRG--AAAAIVVYDITSEE--SFEKAKSWVKELQEHGPPNIVIA---LA- 112
Query: 146 ANKQDLLG 153
NK DL
Sbjct: 113 GNKADLES 120
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 31.8 bits (73), Expect = 0.13
Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 9/53 (16%)
Query: 106 TDILIYVIDSADVKRFEESGFELHELLSDE--KLTGVPLLVYANKQDLLGAAP 156
TDI I V+ + D G + + K GVP++V NK D A P
Sbjct: 79 TDIAILVVAADD-------GVMPQTIEAINHAKAAGVPIVVAINKIDKPEANP 124
>gnl|CDD|217751 pfam03830, PTSIIB_sorb, PTS system sorbose subfamily IIB component.
Length = 151
Score = 30.9 bits (71), Expect = 0.14
Identities = 12/58 (20%), Positives = 26/58 (44%), Gaps = 2/58 (3%)
Query: 74 IKSVQSEGFKLNVWDIGGQRKIRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHEL 131
+K G K++++ + ++ I + +D + + V + D R E G + EL
Sbjct: 46 LKMAAPAGVKVSIFSV--EKAIEVIKKGKYDKQKVFLLVKNPQDALRLVEGGVPIKEL 101
>gnl|CDD|234321 TIGR03708, poly_P_AMP_trns, polyphosphate:AMP phosphotransferase.
Members of this protein family contain a domain
duplication. The characterized member from
Acinetobacter johnsonii is polyphosphate:AMP
phosphotransferase (PAP), which can transfer the
terminal phosphate from poly(P) to AMP, yielding ADP.
In the opposite direction, this enzyme can synthesize
poly(P). Each domain of this protein family is
homologous to polyphosphate kinase, an enzyme that can
run in the forward direction to extend a polyphosphate
chain with a new terminal phosphate from ATP, or in
reverse to make ATP (or GTP) from ADP (or GDP) [Central
intermediary metabolism, Phosphorus compounds].
Length = 493
Score = 31.5 bits (72), Expect = 0.14
Identities = 16/43 (37%), Positives = 21/43 (48%)
Query: 16 QVKDLALGLLAILKKLRSSPEKELRILLLGLDNAGKTTILKTL 58
QV DL LL + +L S + IL+ G D AGK + L
Sbjct: 18 QVPDLREALLDLQYELLESAGFPVIILIEGWDGAGKGETINLL 60
>gnl|CDD|237975 cd00001, PTS_IIB_man, PTS_IIB, PTS system, Mannose/sorbose specific
IIB subunit. The bacterial phosphoenolpyruvate: sugar
phosphotransferase system (PTS) is a multi-protein
system involved in the regulation of a variety of
metabolic and transcriptional processes. This family is
one of four structurally and functionally distinct group
IIB PTS system cytoplasmic enzymes, necessary for the
uptake of carbohydrates across the cytoplasmic membrane
and their phosphorylation. The active site histidine
receives a phosphate group from the IIA subunit and
transfers it to the substrate.
Length = 151
Score = 31.0 bits (71), Expect = 0.16
Identities = 11/58 (18%), Positives = 23/58 (39%), Gaps = 2/58 (3%)
Query: 74 IKSVQSEGFKLNVWDIGGQRKIRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHEL 131
+K G KL ++ + ++ I +D + + + DV R E G + +
Sbjct: 45 LKLAAPPGVKLRIFTV--EKAIEAINSPKYDKQRVFLLFKNPQDVLRLVEGGVPIKTI 100
>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 = 31.3 bits (72), Expect = 0.17
Identities = 27/110 (24%), Positives = 51/110 (46%), Gaps = 25/110 (22%)
Query: 61 EDISHI-TPTQG-----FNIKSVQSEGFKLNVWDIGGQRKIRPYWRNYFDNTDILIYVID 114
+DI T G F+IK++ K ++D+GGQR R W + F++ +I+V+
Sbjct: 139 QDILRSRVKTTGIIETDFSIKNL-----KFRMFDVGGQRSERKKWIHCFEDVTAIIFVVA 193
Query: 115 SAD----------VKRFEES--GFELHELLSDEKLTGVPLLVYANKQDLL 152
++ V R +ES F+ + + ++++ NK+DL
Sbjct: 194 LSEYDQVLVEDESVNRMQESLKLFD--SICNSRWFANTSIILFLNKKDLF 241
Score = 27.9 bits (63), Expect = 2.3
Identities = 10/20 (50%), Positives = 16/20 (80%)
Query: 39 LRILLLGLDNAGKTTILKTL 58
+++LLLG +GK+TILK +
Sbjct: 1 VKLLLLGAGESGKSTILKQM 20
>gnl|CDD|184132 PRK13547, hmuV, hemin importer ATP-binding subunit; Provisional.
Length = 272
Score = 31.3 bits (71), Expect = 0.17
Identities = 16/36 (44%), Positives = 21/36 (58%)
Query: 26 AILKKLRSSPEKELRILLLGLDNAGKTTILKTLASE 61
AIL+ L E LLG + AGK+T+LK LA +
Sbjct: 15 AILRDLSLRIEPGRVTALLGRNGAGKSTLLKALAGD 50
>gnl|CDD|206699 cd04120, Rab12, Rab GTPase family 12 (Rab12). Rab12 was first
identified in canine cells, where it was localized to
the Golgi complex. The specific function of Rab12
remains unknown, and inconsistent results about its
cellular localization have been reported. More recent
studies have identified Rab12 associated with post-Golgi
vesicles, or with other small vesicle-like structures
but not with the Golgi complex. Most Rab GTPases contain
a lipid modification site at the C-terminus, with
sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation of
the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins.
Length = 202
Score = 31.1 bits (70), Expect = 0.18
Identities = 21/90 (23%), Positives = 42/90 (46%), Gaps = 5/90 (5%)
Query: 39 LRILLLGLDNAGKTTILKTLASEDISHITPTQ---GFNIKSVQSEGFK--LNVWDIGGQR 93
L+++++G GKT++++ + + F IK+V+ G K L +WD GQ
Sbjct: 1 LQVIIIGSRGVGKTSLMERFTDDTFCEACKSTVGVDFKIKTVELRGKKIRLQIWDTAGQE 60
Query: 94 KIRPYWRNYFDNTDILIYVIDSADVKRFEE 123
+ Y+ + +I V D + F++
Sbjct: 61 RFNSITSAYYRSAKGIILVYDITKKETFDD 90
>gnl|CDD|237894 PRK15064, PRK15064, ABC transporter ATP-binding protein;
Provisional.
Length = 530
Score = 31.4 bits (72), Expect = 0.19
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 13/77 (16%)
Query: 4 KQNSYERMEKENQVKDLAL---------GLLAILKKLRSSPEKELRILLLGLDNAGKTTI 54
+QN + R E++ ++ AL + K L E R+ ++G + GKTT+
Sbjct: 302 RQNPFIRFEQDKKLHRNALEVENLTKGFDNGPLFKNLNLLLEAGERLAIIGENGVGKTTL 361
Query: 55 LKTLASEDISHITPTQG 71
L+TL E + P G
Sbjct: 362 LRTLVGE----LEPDSG 374
>gnl|CDD|213230 cd03263, ABC_subfamily_A, ATP-binding cassette domain of the
lipid transporters, subfamily A. The ABCA subfamily
mediates the transport of a variety of lipid compounds.
Mutations of members of ABCA subfamily are associated
with human genetic diseases, such as, familial
high-density lipoprotein (HDL) deficiency, neonatal
surfactant deficiency, degenerative retinopathies, and
congenital keratinization disorders. The ABCA1 protein
is involved in disorders of cholesterol transport and
high-density lipoprotein (HDL) biosynthesis. The ABCA4
(ABCR) protein transports vitamin A derivatives in the
outer segments of photoreceptor cells, and therefore,
performs a crucial step in the visual cycle. The ABCA
genes are not present in yeast. However, evolutionary
studies of ABCA genes indicate that they arose as
transporters that subsequently duplicated and that
certain sets of ABCA genes were lost in different
eukaryotic lineages.
Length = 220
Score = 30.9 bits (71), Expect = 0.20
Identities = 15/29 (51%), Positives = 17/29 (58%), Gaps = 4/29 (13%)
Query: 43 LLGLDNAGKTTILKTLASEDISHITPTQG 71
LLG + AGKTT LK L E + PT G
Sbjct: 33 LLGHNGAGKTTTLKMLTGE----LRPTSG 57
>gnl|CDD|226927 COG4555, NatA, ABC-type Na+ transport system, ATPase component
[Energy production and conversion / Inorganic ion
transport and metabolism].
Length = 245
Score = 30.8 bits (70), Expect = 0.26
Identities = 12/29 (41%), Positives = 18/29 (62%), Gaps = 4/29 (13%)
Query: 43 LLGLDNAGKTTILKTLASEDISHITPTQG 71
LLG + AGKTT+L+ +A + + P G
Sbjct: 33 LLGENGAGKTTLLRMIA----TLLIPDSG 57
>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 = 30.0 bits (68), Expect = 0.28
Identities = 16/62 (25%), Positives = 28/62 (45%), Gaps = 6/62 (9%)
Query: 15 NQVKDLALGLLAILKKLRSSPEKELRILLLGLDNAGKTTILKTLASE------DISHITP 68
N L L +KL+ +K +R+ ++GL N GK++ + L ++ I T
Sbjct: 68 NGQGILKLKAEITKQKLKLKYKKGIRVGVVGLPNVGKSSFINALLNKFKLKVGSIPGTTK 127
Query: 69 TQ 70
Q
Sbjct: 128 LQ 129
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 30.7 bits (70), Expect = 0.31
Identities = 13/46 (28%), Positives = 28/46 (60%), Gaps = 1/46 (2%)
Query: 107 DILIYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVYANKQDLL 152
D+L++V+D++D E + ++L++ +P+++ NK DLL
Sbjct: 273 DLLLHVVDASD-PEILEKLEAVEDVLAEIGADEIPIILVLNKIDLL 317
>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 = 29.8 bits (67), Expect = 0.37
Identities = 26/122 (21%), Positives = 52/122 (42%), Gaps = 10/122 (8%)
Query: 39 LRILLLGLDNAGKTTILKTLAS----EDISHITPTQGFNIKSVQSEG--FKLNVWDIGGQ 92
L+++LLG GK++++ + + H + N K ++ +G L +WD GQ
Sbjct: 6 LKVILLGDGGVGKSSLMNRYVTNKFDTQLFHTIGVEFLN-KDLEVDGHFVTLQIWDTAGQ 64
Query: 93 RKIRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELL--SDEK-LTGVPLLVYANKQ 149
+ R ++ +D + D + F+ E + +D K P ++ NK
Sbjct: 65 ERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVILGNKI 124
Query: 150 DL 151
D+
Sbjct: 125 DI 126
>gnl|CDD|237182 PRK12727, PRK12727, flagellar biosynthesis regulator FlhF;
Provisional.
Length = 559
Score = 30.3 bits (68), Expect = 0.41
Identities = 37/122 (30%), Positives = 55/122 (45%), Gaps = 24/122 (19%)
Query: 20 LALGLLAILKKLRSSPEKELR----ILLLGLDNAGKTTILKTLASEDISHITPTQGFNIK 75
L LGLL+ K+L +P L I L+G AGKTT + LA + P ++
Sbjct: 330 LMLGLLS--KRLPVAPVDPLERGGVIALVGPTGAGKTTTIAKLAQRFAAQHAPR---DVA 384
Query: 76 SVQSEGFKLNVWDIGGQRKIRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDE 135
V ++ + +GG+ ++ Y R I ++ DSA ES +L E L D
Sbjct: 385 LVTTDTQR-----VGGREQLHSYGRQL----GIAVHEADSA------ESLLDLLERLRDY 429
Query: 136 KL 137
KL
Sbjct: 430 KL 431
>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 = 29.7 bits (67), Expect = 0.42
Identities = 21/76 (27%), Positives = 34/76 (44%)
Query: 76 SVQSEGFKLNVWDIGGQRKIRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDE 135
+ E +LN+ D GQ NYF + + + V D++ F ++L +
Sbjct: 42 VLDGEEVQLNILDTAGQEDYAAIRDNYFRSGEGFLLVFSITDMESFTALAEFREQILRVK 101
Query: 136 KLTGVPLLVYANKQDL 151
+ VPLL+ NK DL
Sbjct: 102 EDDNVPLLLVGNKCDL 117
>gnl|CDD|237747 PRK14530, PRK14530, adenylate kinase; Provisional.
Length = 215
Score = 29.8 bits (67), Expect = 0.44
Identities = 15/29 (51%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 40 RILLLGLDNAGKTTILKTLASE-DISHIT 67
RILLLG AGK T LA E + H+T
Sbjct: 5 RILLLGAPGAGKGTQSSNLAEEFGVEHVT 33
>gnl|CDD|133322 cd04122, Rab14, Rab GTPase family 14 (Rab14). Rab14 GTPases are
localized to biosynthetic compartments, including the
rough ER, the Golgi complex, and the trans-Golgi
network, and to endosomal compartments, including early
endosomal vacuoles and associated vesicles. Rab14 is
believed to function in both the biosynthetic and
recycling pathways between the Golgi and endosomal
compartments. Rab14 has also been identified on GLUT4
vesicles, and has been suggested to help regulate GLUT4
translocation. In addition, Rab14 is believed to play a
role in the regulation of phagocytosis. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 166
Score = 29.8 bits (67), Expect = 0.47
Identities = 12/33 (36%), Positives = 17/33 (51%)
Query: 71 GFNIKSVQSEGFKLNVWDIGGQRKIRPYWRNYF 103
G I V + KL +WD GQ + R R+Y+
Sbjct: 40 GTRIIEVNGQKIKLQIWDTAGQERFRAVTRSYY 72
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 29.7 bits (67), Expect = 0.58
Identities = 20/69 (28%), Positives = 27/69 (39%), Gaps = 19/69 (27%)
Query: 38 ELRILLLGLDNAGKTTILKTLASEDISHIT--------PTQGFNIKS----VQSEGFKLN 85
E +++L+G GKTT +K H+T PT G + N
Sbjct: 9 EFKLILVGDGGVGKTTFVK-------RHLTGEFEKKYIPTLGVEVHPLKFYTNCGPICFN 61
Query: 86 VWDIGGQRK 94
VWD GQ K
Sbjct: 62 VWDTAGQEK 70
>gnl|CDD|224054 COG1131, CcmA, ABC-type multidrug transport system, ATPase
component [Defense mechanisms].
Length = 293
Score = 29.6 bits (67), Expect = 0.62
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 8/55 (14%)
Query: 41 ILLLGLDNAGKTTILKTLASEDISHITPTQGFNIKSVQSEGFKLNVWDIGGQRKI 95
LLG + AGKTT+LK LA + PT G + G+ + +R+I
Sbjct: 34 FGLLGPNGAGKTTLLKILAGL----LKPTSG----EILVLGYDVVKEPAKVRRRI 80
>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 = 29.7 bits (68), Expect = 0.62
Identities = 18/47 (38%), Positives = 29/47 (61%), Gaps = 3/47 (6%)
Query: 107 DILIYVIDSADVKRFEESGFELHELLSDEKLTGVP-LLVYANKQDLL 152
D+L++V+D++D EE + ++L + +P LLVY NK DLL
Sbjct: 270 DLLLHVVDASD-PDREEQIEAVEKVLEELGAEDIPQLLVY-NKIDLL 314
>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 = 29.0 bits (66), Expect = 0.63
Identities = 14/33 (42%), Positives = 21/33 (63%), Gaps = 4/33 (12%)
Query: 40 RILLLGLDNAGKTTILKTLASEDISHITPTQGF 72
RI L+G + AGK+T+LK +A E + P +G
Sbjct: 28 RIGLVGRNGAGKSTLLKLIAGE----LEPDEGI 56
>gnl|CDD|206701 cd04128, Spg1, Septum-promoting GTPase (Spg1). Spg1p. Spg1p
(septum-promoting GTPase) was first identified in the
fission yeast S. pombe, where it regulates septum
formation in the septation initiation network (SIN)
through the cdc7 protein kinase. Spg1p is an essential
gene that localizes to the spindle pole bodies. When
GTP-bound, it binds cdc7 and causes it to translocate
to spindle poles. Sid4p (septation initiation
defective) is required for localization of Spg1p to the
spindle pole body, and the ability of Spg1p to promote
septum formation from any point in the cell cycle
depends on Sid4p. Spg1p is negatively regulated by Byr4
and cdc16, which form a two-component GTPase activating
protein (GAP) for Spg1p. The existence of a SIN-related
pathway in plants has been proposed. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization.
Length = 182
Score = 28.9 bits (65), Expect = 0.83
Identities = 20/61 (32%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 39 LRILLLGLDNAGKTTIL-KTLASEDISHITPTQGFNIK----SVQSEGFKLNVWDIGGQR 93
L+I LLG GKT+++ K + E T G N S++ ++WD+GGQR
Sbjct: 1 LKIGLLGDAQIGKTSLMVKYVEGEFDEEYIQTLGVNFMEKTISIRGTEITFSIWDLGGQR 60
Query: 94 K 94
+
Sbjct: 61 E 61
>gnl|CDD|179922 PRK05066, PRK05066, arginine repressor; Provisional.
Length = 156
Score = 28.8 bits (65), Expect = 0.88
Identities = 16/31 (51%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 46 LDNAGKTT-ILKTLASEDISHITPTQGFNIK 75
LD+ GK IL T+A +D ITP GF IK
Sbjct: 112 LDSLGKAEGILGTIAGDDTIFITPASGFTIK 142
>gnl|CDD|224047 COG1122, CbiO, ABC-type cobalt transport system, ATPase component
[Inorganic ion transport and metabolism].
Length = 235
Score = 29.1 bits (66), Expect = 0.90
Identities = 15/34 (44%), Positives = 22/34 (64%)
Query: 26 AILKKLRSSPEKELRILLLGLDNAGKTTILKTLA 59
A LK + EK R+LL+G + +GK+T+LK L
Sbjct: 18 AALKDVSLEIEKGERVLLIGPNGSGKSTLLKLLN 51
>gnl|CDD|213231 cd03264, ABC_drug_resistance_like, ABC-type multidrug transport
system, ATPase component. The biological function of
this family is not well characterized, but display ABC
domains similar to members of ABCA subfamily. 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 = 211
Score = 28.7 bits (65), Expect = 1.0
Identities = 12/29 (41%), Positives = 18/29 (62%), Gaps = 4/29 (13%)
Query: 43 LLGLDNAGKTTILKTLASEDISHITPTQG 71
LLG + AGKTT+++ LA+ P+ G
Sbjct: 30 LLGPNGAGKTTLMRILATL----TPPSSG 54
>gnl|CDD|236729 PRK10636, PRK10636, putative ABC transporter ATP-binding protein;
Provisional.
Length = 638
Score = 29.0 bits (65), Expect = 1.1
Identities = 15/32 (46%), Positives = 20/32 (62%), Gaps = 4/32 (12%)
Query: 40 RILLLGLDNAGKTTILKTLASEDISHITPTQG 71
RI LLG + AGK+T++K LA E + P G
Sbjct: 340 RIGLLGRNGAGKSTLIKLLAGE----LAPVSG 367
>gnl|CDD|185391 PRK15494, era, GTPase Era; Provisional.
Length = 339
Score = 28.9 bits (64), Expect = 1.1
Identities = 12/37 (32%), Positives = 24/37 (64%)
Query: 32 RSSPEKELRILLLGLDNAGKTTILKTLASEDISHITP 68
+ S +K + + ++G N+GK+T+L + E +S +TP
Sbjct: 46 KMSNQKTVSVCIIGRPNSGKSTLLNRIIGEKLSIVTP 82
>gnl|CDD|236167 PRK08154, PRK08154, anaerobic benzoate catabolism transcriptional
regulator; Reviewed.
Length = 309
Score = 28.8 bits (65), Expect = 1.1
Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 4/46 (8%)
Query: 16 QVKDLALGLLAILKKLRSSPEKELRILLLGLDNAGKTTILKTLASE 61
+V+D G+L + RI L+GL AGK+T+ + LA+
Sbjct: 115 RVRDALSGMLG----AGRRAARRRRIALIGLRGAGKSTLGRMLAAR 156
>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 = 28.6 bits (65), Expect = 1.2
Identities = 18/46 (39%), Positives = 29/46 (63%), Gaps = 2/46 (4%)
Query: 16 QVKDLALGL--LAILKKLRSSPEKELRILLLGLDNAGKTTILKTLA 59
+V++L++G +L L S E + +LG + AGK+T+LKTLA
Sbjct: 1 EVENLSVGYGGRTVLDDLSLSIEAGEIVGILGPNGAGKSTLLKTLA 46
>gnl|CDD|223487 COG0410, LivF, ABC-type branched-chain amino acid transport
systems, ATPase component [Amino acid transport and
metabolism].
Length = 237
Score = 28.6 bits (65), Expect = 1.4
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 6/58 (10%)
Query: 16 QVKDL--ALGLLAILKKLRSSPEKELRILLLGLDNAGKTTILKTLASEDISHITPTQG 71
+V++L G + L+ + E+ + LLG + AGKTT+LKT+ + P G
Sbjct: 5 EVENLSAGYGKIQALRGVSLEVERGEIVALLGRNGAGKTTLLKTIM----GLVRPRSG 58
>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 = 28.2 bits (64), Expect = 1.5
Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 4/52 (7%)
Query: 106 TDILIYVIDSADVKRFEESGFEL--HELLS-DEKLTGVPLLVYANKQDLLGA 154
T +L++VID + E +E +EL + + L P +V NK DLL A
Sbjct: 79 TRVLLHVIDLSGEDDPVED-YETIRNELEAYNPGLAEKPRIVVLNKIDLLDA 129
>gnl|CDD|206703 cd04131, Rnd, Rho family GTPase subfamily Rnd includes Rnd1/Rho6,
Rnd2/Rho7, and Rnd3/RhoE/Rho8. The Rnd subfamily
contains Rnd1/Rho6, Rnd2/Rho7, and Rnd3/RhoE/Rho8. These
novel Rho family proteins have substantial structural
differences compared to other Rho members, including N-
and C-terminal extensions relative to other Rhos.
Rnd3/RhoE is farnesylated at the C-terminal prenylation
site, unlike most other Rho proteins that are
geranylgeranylated. In addition, Rnd members are unable
to hydrolyze GTP and are resistant to GAP activity. They
are believed to exist only in the GTP-bound
conformation, and are antagonists of RhoA activity. 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 = 176
Score = 28.2 bits (63), Expect = 1.6
Identities = 21/76 (27%), Positives = 33/76 (43%), Gaps = 12/76 (15%)
Query: 40 RILLLGLDNAGKTTILKTLASEDISHI-TPTQGFNIKS---VQSEGFKLNVWDIGGQRKI 95
+I+L+G GKT +L+ A + PT N + V + +L++WD G
Sbjct: 3 KIVLVGDSQCGKTALLQVFAKDSFPENYVPTVFENYTASFEVDKQRIELSLWDTSGS--- 59
Query: 96 RPYWRNYFDNTDILIY 111
Y+DN L Y
Sbjct: 60 -----PYYDNVRPLSY 70
>gnl|CDD|234041 TIGR02868, CydC, thiol reductant ABC exporter, CydC subunit. The
gene pair cydCD encodes an ABC-family transporter in
which each gene contains an N-terminal membrane-spanning
domain (pfam00664) and a C-terminal ATP-binding domain
(pfam00005). In E. coli these genes were discovered as
mutants which caused the terminal heme-copper oxidase
complex cytochrome bd to fail to assemble. Recent work
has shown that the transporter is involved in export of
redox-active thiol compounds such as cysteine and
glutathione. The linkage to assembly of the cytochrome
bd complex is further supported by the conserved operon
structure found outside the gammaproteobacteria
(cydABCD) containing both the transporter and oxidase
genes components. The genes used as the seed members for
this model are all either found in the
gammproteobacterial context or the CydABCD context. All
members of this family scoring above trusted at the time
of its creation were from genomes which encode a
cytochrome bd complex.
Length = 530
Score = 28.5 bits (64), Expect = 1.7
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 40 RILLLGLDNAGKTTILKTLA 59
R+ +LG +GK+T+L TLA
Sbjct: 363 RVAILGPSGSGKSTLLATLA 382
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 28.0 bits (62), Expect = 1.8
Identities = 22/86 (25%), Positives = 38/86 (44%), Gaps = 11/86 (12%)
Query: 71 GFNIKSVQSEGFKLNVWDIGGQRKIRPYWRNYFDNT--DILIYVIDSADVKRFEESGFEL 128
G + ++ ++ KL +WD GQ R R+Y+ +L+Y D+ R E+ L
Sbjct: 44 GARMITIDNKPIKLQIWDTAGQESFRSITRSYYRGAAGALLVY-----DITR-RETFNHL 97
Query: 129 HELLSDEKLTGVP---LLVYANKQDL 151
L D + +++ NK DL
Sbjct: 98 ASWLEDARQHANANMTIMLIGNKCDL 123
>gnl|CDD|213191 cd03224, ABC_TM1139_LivF_branched, ATP-binding cassette domain of
branched-chain amino acid transporter. LivF (TM1139)
is part of the LIV-I bacterial ABC-type two-component
transport system that imports neutral, branched-chain
amino acids. The E. coli branched-chain amino acid
transporter comprises a heterodimer of ABC transporters
(LivF and LivG), a heterodimer of six-helix TM domains
(LivM and LivH), and one of two alternative soluble
periplasmic substrate binding proteins (LivK or LivJ).
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.
Length = 222
Score = 28.2 bits (64), Expect = 1.8
Identities = 13/29 (44%), Positives = 17/29 (58%), Gaps = 4/29 (13%)
Query: 43 LLGLDNAGKTTILKTLASEDISHITPTQG 71
LLG + AGKTT+LKT+ + P G
Sbjct: 31 LLGRNGAGKTTLLKTIM----GLLPPRSG 55
>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 = 28.0 bits (63), Expect = 1.9
Identities = 25/116 (21%), Positives = 47/116 (40%), Gaps = 13/116 (11%)
Query: 44 LGLDNAGKTTILKTLASEDISH--ITPTQG--FNIKSVQSEGFK--LNVWDIGGQRKIRP 97
LG +GK+ +L+ S +PT + + +V+ G + L + ++G +
Sbjct: 10 LGAKGSGKSALLQAFLGRSFSQNAYSPTIKPRYAVNTVEVPGQEKYLILREVGEDEEAIL 69
Query: 98 YWRNYFDNTDILIYVIDSADVKRFE--ESGFELHELLSDEKLTGVPLLVYANKQDL 151
D+ V DS+D F ++ + +L + +P L A K DL
Sbjct: 70 LNDAELAACDVACLVYDSSDPNSFSYCAEVYKKYFMLGE-----IPCLFVAAKADL 120
>gnl|CDD|221921 pfam13098, Thioredoxin_2, Thioredoxin-like domain.
Length = 105
Score = 27.4 bits (61), Expect = 1.9
Identities = 13/53 (24%), Positives = 20/53 (37%)
Query: 110 IYVIDSADVKRFEESGFELHELLSDEKLTGVPLLVYANKQDLLGAAPAGYHSF 162
+ V DS +V F+ EL + G P +V+ + A GY
Sbjct: 46 VNVDDSKEVTDFDGETLSEKELARKYGVRGTPTIVFLDGDGKEVARLPGYLPP 98
>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 = 28.0 bits (63), Expect = 2.0
Identities = 36/128 (28%), Positives = 54/128 (42%), Gaps = 15/128 (11%)
Query: 39 LRILLLGLDNAGKTTILKTLASEDI--SHITPTQG--FNIKSVQSEGFK---LNVWDIGG 91
++L++G GKT+I+K + H T G F +K ++ + L +WDI G
Sbjct: 1 FKVLVIGDLGVGKTSIIKRY-VHGVFSQHYKATIGVDFALKVIEWDPNTVVRLQLWDIAG 59
Query: 92 QRKIRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTG-----VPLLVYA 146
Q + R Y+ I V D FE +L D K+T +P L+ A
Sbjct: 60 QERFGGMTRVYYKGAVGAIIVFDVTRPSTFEAVLKWKADL--DSKVTLPNGEPIPALLLA 117
Query: 147 NKQDLLGA 154
NK DL
Sbjct: 118 NKCDLKKE 125
>gnl|CDD|237422 PRK13548, hmuV, hemin importer ATP-binding subunit; Provisional.
Length = 258
Score = 27.8 bits (63), Expect = 2.1
Identities = 11/29 (37%), Positives = 19/29 (65%), Gaps = 4/29 (13%)
Query: 43 LLGLDNAGKTTILKTLASEDISHITPTQG 71
+LG + AGK+T+L+ L+ E ++P G
Sbjct: 33 ILGPNGAGKSTLLRALSGE----LSPDSG 57
>gnl|CDD|206714 cd04147, Ras_dva, Ras - dorsal-ventral anterior localization
(Ras-dva) family. Ras-dva subfamily. Ras-dva (Ras -
dorsal-ventral anterior localization) subfamily consists
of a set of proteins characterized only in Xenopus
leavis, to date. In Xenopus Ras-dva expression is
activated by the transcription factor Otx2 and begins
during gastrulation throughout the anterior ectoderm.
Ras-dva expression is inhibited in the anterior neural
plate by factor Xanf1. Downregulation of Ras-dva results
in head development abnormalities through the inhibition
of several regulators of the anterior neural plate and
folds patterning, including Otx2, BF-1, Xag2, Pax6,
Slug, and Sox9. Downregulation of Ras-dva also
interferes with the FGF-8a signaling within the anterior
ectoderm. 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 = 197
Score = 27.9 bits (62), Expect = 2.2
Identities = 30/125 (24%), Positives = 51/125 (40%), Gaps = 16/125 (12%)
Query: 40 RILLLGLDNAGKTTILKTLASEDIS--HITPTQGFNIKSVQSEGFKL--NVWDIGGQRKI 95
R++ +G GKT +++ + H + + K + G K+ ++ D G
Sbjct: 1 RLVFMGAAGVGKTALIQRFLYDTFEPKHRRTVEELHSKEYEVAGVKVTIDILDTSGSYSF 60
Query: 96 RPYWRNYFDNTD--ILIYVIDSAD----VKRFEESGFELHELLSDEKLTGVPLLVYANKQ 149
+ N D L+Y +D + VKR E E+ E+ D VP++V NK
Sbjct: 61 PAMRKLSIQNGDAFALVYSVDDPESFEEVKRLRE---EILEVKED---KFVPIVVVGNKI 114
Query: 150 DLLGA 154
D L
Sbjct: 115 DSLAE 119
>gnl|CDD|213233 cd03266, ABC_NatA_sodium_exporter, ATP-binding cassette domain of
the Na+ transporter. NatA is the ATPase component of a
bacterial ABC-type Na+ transport system called NatAB,
which catalyzes ATP-dependent electrogenic Na+
extrusion without mechanically coupled proton or K+
uptake. NatB possess six putative membrane spanning
regions at its C-terminus. In B. subtilis, NatAB is
inducible by agents such as ethanol and protonophores,
which lower the proton-motive force across the
membrane. The closest sequence similarity to NatA is
exhibited by DrrA of the two-component daunorubicin-
and doxorubicin-efflux system. Hence, the functional
NatAB is presumably assembled with two copies of a
single ATP-binding protein and a single integral
membrane protein.
Length = 218
Score = 27.7 bits (62), Expect = 2.2
Identities = 14/30 (46%), Positives = 17/30 (56%), Gaps = 4/30 (13%)
Query: 43 LLGLDNAGKTTILKTLASEDISHITPTQGF 72
LLG + AGKTT L+ LA + P GF
Sbjct: 36 LLGPNGAGKTTTLRMLAGL----LEPDAGF 61
>gnl|CDD|233208 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family
protein. [Transport and binding proteins, Other].
Length = 1394
Score = 28.2 bits (63), Expect = 2.2
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 41 ILLLGLDNAGKTTILKTLASE 61
++LG +G +T+LKT+AS
Sbjct: 90 TVVLGRPGSGCSTLLKTIASN 110
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 27.9 bits (63), Expect = 2.3
Identities = 12/23 (52%), Positives = 17/23 (73%), Gaps = 4/23 (17%)
Query: 38 ELRIL----LLGLDNAGKTTILK 56
EL++L LLGL NAGK+T ++
Sbjct: 155 ELKLLADVGLLGLPNAGKSTFIR 177
>gnl|CDD|213234 cd03267, ABC_NatA_like, ATP-binding cassette domain of an
uncharacterized transporter similar in sequence to
NatA. NatA is the ATPase component of a bacterial
ABC-type Na+ transport system called NatAB, which
catalyzes ATP-dependent electrogenic Na+ extrusion
without mechanically coupled to proton or K+ uptake.
NatB possess six putative membrane spanning regions at
its C-terminus. In B. subtilis, NatAB is inducible by
agents such as ethanol and protonophores, which lower
the proton-motive force across the membrane. The
closest sequence similarity to NatA is exhibited by
DrrA of the two-component daunorubicin- and
doxorubicin-efflux system. Hence, the functional NatAB
is presumably assembled with two copies of the single
ATP-binding protein and the single integral membrane
protein.
Length = 236
Score = 27.7 bits (62), Expect = 2.3
Identities = 12/29 (41%), Positives = 16/29 (55%), Gaps = 4/29 (13%)
Query: 43 LLGLDNAGKTTILKTLASEDISHITPTQG 71
+G + AGKTT LK L+ + PT G
Sbjct: 52 FIGPNGAGKTTTLKILSGL----LQPTSG 76
>gnl|CDD|133326 cd04126, Rab20, Rab GTPase family 20 (Rab20). Rab20 is one of
several Rab proteins that appear to be restricted in
expression to the apical domain of murine polarized
epithelial cells. It is expressed on the apical side of
polarized kidney tubule and intestinal epithelial cells,
and in non-polarized cells. It also localizes to
vesico-tubular structures below the apical brush border
of renal proximal tubule cells and in the apical region
of duodenal epithelial cells. Rab20 has also been shown
to colocalize with vacuolar H+-ATPases (V-ATPases) in
mouse kidney cells, suggesting a role in the regulation
of V-ATPase traffic in specific portions of the nephron.
It was also shown to be one of several proteins whose
expression is upregulated in human myelodysplastic
syndrome (MDS) patients. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 220
Score = 27.6 bits (61), Expect = 2.5
Identities = 30/120 (25%), Positives = 50/120 (41%), Gaps = 11/120 (9%)
Query: 39 LRILLLGLDNAGKTTILKTLASEDISHITPTQG--FNIKSVQSEGFKLNVWDIGGQRKIR 96
L+++LLG N GKT++L T G F +K Q + +++WD G+ +
Sbjct: 1 LKVVLLGDMNVGKTSLLHRYMERRFKDTVSTVGGAFYLK--QWGPYNISIWDTAGREQFH 58
Query: 97 PYWRNYFDNTDILIYVIDSADVKRFEE---SGFELHELLSDEKLTGVPLLVYANKQDLLG 153
Y +I D ++V+ EE L + +++ L V NK DL
Sbjct: 59 GLGSMYCRGAAAVILTYDVSNVQSLEELEDRFLGLTDTANEDCL----FAVVGNKLDLTE 114
>gnl|CDD|234401 TIGR03925, T7SS_EccC_b, type VII secretion protein EccCb. This
model represents the C-terminal domain or EccCb subunit
of the type VII secretion protein EccC as found in the
Actinobacteria. Type VII secretion is defined more
broadly as including secretion systems for ESAT-6-like
proteins in the Firmicutes as well as in the
Actinobacteria, but this family does not show close
homologs in the Firmicutes [Protein fate, Protein and
peptide secretion and trafficking].
Length = 566
Score = 28.0 bits (63), Expect = 2.5
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 41 ILLLGLDNAGKTTILKTLASEDISHITPTQ 70
+L+ G +GKTT+L+ +A +P Q
Sbjct: 366 LLVFGDSESGKTTLLRAIARGITRRYSPQQ 395
>gnl|CDD|187769 cd09638, Cas2_I_II_III, CRISPR/Cas system-associated protein
Cas2. CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Cas2 is present in majority of CRISPR/Cas systems along
with Cas1; RNAse specific to U-rich regions; Possesses
an RRM/ferredoxin fold.
Length = 90
Score = 26.6 bits (59), Expect = 2.6
Identities = 14/55 (25%), Positives = 21/55 (38%), Gaps = 6/55 (10%)
Query: 2 FQKQNS-YERMEKENQVKDLALGLLAILKKLRSSPEKELRILLLGLDNAGKTTIL 55
F+ Q S +E + + N + L L I+ E +RI L IL
Sbjct: 31 FRVQYSVFEGILEPNLLASLIERLKKIIP-----DEDSIRIYPLTEKQKTAIRIL 80
>gnl|CDD|227910 COG5623, CLP1, Predicted GTPase subunit of the pre-mRNA cleavage
complex [Translation, ribosomal structure and
biogenesis].
Length = 424
Score = 28.0 bits (62), Expect = 2.6
Identities = 14/42 (33%), Positives = 20/42 (47%), Gaps = 1/42 (2%)
Query: 20 LALGLLAILKKLRSSP-EKELRILLLGLDNAGKTTILKTLAS 60
L L L+K R EK ++++G GKT+ TL S
Sbjct: 80 LIFNLHFFLEKRRMFNYEKGPTVMVVGGSQNGKTSFCFTLIS 121
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 27.8 bits (63), Expect = 2.6
Identities = 13/52 (25%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 15 NQVKDLALGLLAILKKLRSSP---EKELRILLLGLDNAGKTTILKTLASEDI 63
++ A LL + R + + +R +++G+ N GK+T++ LA + I
Sbjct: 95 KKILKAAKKLLKEKNERRKAKGMRPRAIRAMIIGIPNVGKSTLINRLAGKKI 146
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 28.0 bits (63), Expect = 2.8
Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 6/54 (11%)
Query: 24 LLAILKKLRSSPEKEL------RILLLGLDNAGKTTILKTLASEDISHITPTQG 71
L A+L L P R+ L+G N GK+++L LA E+ S + G
Sbjct: 191 LDAVLAALPEVPRVGSASGGPRRVALVGKPNVGKSSLLNKLAGEERSVVDDVAG 244
>gnl|CDD|238977 cd02019, NK, Nucleoside/nucleotide kinase (NK) is a protein
superfamily consisting of multiple families of enzymes
that share structural similarity and are functionally
related to the catalysis of the reversible phosphate
group transfer from nucleoside triphosphates to
nucleosides/nucleotides, nucleoside monophosphates, or
sugars. Members of this family play a wide variety of
essential roles in nucleotide metabolism, the
biosynthesis of coenzymes and aromatic compounds, as
well as the metabolism of sugar and sulfate.
Length = 69
Score = 26.1 bits (58), Expect = 3.0
Identities = 8/27 (29%), Positives = 13/27 (48%)
Query: 40 RILLLGLDNAGKTTILKTLASEDISHI 66
I + G +GK+T+ K LA +
Sbjct: 1 IIAITGGSGSGKSTVAKKLAEQLGGRS 27
>gnl|CDD|233458 TIGR01540, portal_PBSX, phage portal protein, PBSX family. This
model represents one of several distantly related
families of phage portal protein. This protein forms a
hole, or portal, that enables DNA passage during
packaging and ejection. It also forms the junction
between the phage head (capsid) and the tail proteins.
It functions as a dodecamer of a single polypeptide of
average mol. wt. of 40-90 KDa. This family shows clear
homology to TIGR01537. The alignment for this group was
trimmed of poorly alignable N-terminal sequence of about
50 residues and of C-terminal regions present in some
but not all members of up 180 residues [Mobile and
extrachromosomal element functions, Prophage functions].
Length = 320
Score = 27.6 bits (61), Expect = 3.0
Identities = 17/49 (34%), Positives = 23/49 (46%)
Query: 91 GQRKIRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLSDEKLTG 139
RK + R YF N + ++I D EES EL E ++D K G
Sbjct: 162 LNRKATEFNRMYFKNGRHVGFIITVTDGMLSEESYRELQEYMNDLKGVG 210
>gnl|CDD|226372 COG3854, SpoIIIAA, ncharacterized protein conserved in bacteria
[Function unknown].
Length = 308
Score = 27.5 bits (61), Expect = 3.0
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 38 ELRILLLGLDNAGKTTILKTLA---SEDISHITP 68
L L++G GKTT+L+ +A S+ I+ P
Sbjct: 137 WLNTLIIGPPQVGKTTLLRDIARLLSDGINQFLP 170
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 27.5 bits (62), Expect = 3.1
Identities = 12/27 (44%), Positives = 20/27 (74%), Gaps = 4/27 (14%)
Query: 38 ELRIL----LLGLDNAGKTTILKTLAS 60
EL++L L+GL NAGK+T+L +++
Sbjct: 155 ELKLLADVGLVGLPNAGKSTLLSAVSA 181
>gnl|CDD|213235 cd03268, ABC_BcrA_bacitracin_resist, ATP-binding cassette domain
of the bacitracin-resistance transporter. The BcrA
subfamily represents ABC transporters involved in
peptide antibiotic resistance. Bacitracin is a
dodecapeptide antibiotic produced by B. licheniformis
and B. subtilis. The synthesis of bacitracin is
non-ribosomally catalyzed by a multi-enzyme complex
BcrABC. Bacitracin has potent antibiotic activity
against gram-positive bacteria. The inhibition of
peptidoglycan biosynthesis is the best characterized
bacterial effect of bacitracin. The bacitracin
resistance of B. licheniformis is mediated by the ABC
transporter Bcr which is composed of two identical BcrA
ATP-binding subunits and one each of the integral
membrane proteins, BcrB and BcrC. B. subtilis cells
carrying bcr genes on high-copy number plasmids develop
collateral detergent sensitivity, a similar phenomenon
in human cells with overexpressed multi-drug resistance
P-glycoprotein.
Length = 208
Score = 27.2 bits (61), Expect = 3.1
Identities = 16/47 (34%), Positives = 20/47 (42%), Gaps = 7/47 (14%)
Query: 43 LLGLDNAGKTTILKTLASEDISHITPTQG---FNIKSVQSEGFKLNV 86
LG + AGKTT +K + I P G F+ KS Q L
Sbjct: 31 FLGPNGAGKTTTMKIIL----GLIKPDSGEITFDGKSYQKNIEALRR 73
>gnl|CDD|213223 cd03256, ABC_PhnC_transporter, ATP-binding cassette domain of the
binding protein-dependent phosphonate transport system.
Phosphonates are a class of organophosphorus compounds
characterized by a chemically stable
carbon-to-phosphorus (C-P) bond. Phosphonates are
widespread among naturally occurring compounds in all
kingdoms of wildlife, but only prokaryotic
microorganisms are able to cleave this bond. Certain
bacteria such as E. coli can use alkylphosphonates as a
phosphorus source. 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 = 241
Score = 27.5 bits (62), Expect = 3.2
Identities = 17/57 (29%), Positives = 27/57 (47%), Gaps = 8/57 (14%)
Query: 40 RILLLGLDNAGKTTILKTLASEDISHITPTQGFNIKSVQSEGFKLNVWDIGGQRKIR 96
+ L+G AGK+T+L+ L + PT G SV +G +N R++R
Sbjct: 29 FVALIGPSGAGKSTLLRCLNGL----VEPTSG----SVLIDGTDINKLKGKALRQLR 77
>gnl|CDD|224044 COG1119, ModF, ABC-type molybdenum transport system, ATPase
component/photorepair protein PhrA [Inorganic ion
transport and metabolism].
Length = 257
Score = 27.3 bits (61), Expect = 3.4
Identities = 12/36 (33%), Positives = 16/36 (44%)
Query: 26 AILKKLRSSPEKELRILLLGLDNAGKTTILKTLASE 61
IL L ++G + AGKTT+L L E
Sbjct: 45 KILGDLSWQVNPGEHWAIVGPNGAGKTTLLSLLTGE 80
>gnl|CDD|226952 COG4586, COG4586, ABC-type uncharacterized transport system,
ATPase component [General function prediction only].
Length = 325
Score = 27.3 bits (61), Expect = 3.5
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 40 RILLLGLDNAGKTTILKTL 58
+ LG + AGK+T LK L
Sbjct: 52 IVGFLGANGAGKSTTLKML 70
>gnl|CDD|206658 cd01866, Rab2, Rab GTPase family 2 (Rab2). Rab2 is localized on
cis-Golgi membranes and interacts with Golgi matrix
proteins. Rab2 is also implicated in the maturation of
vesicular tubular clusters (VTCs), which are
microtubule-associated intermediates in transport
between the ER and Golgi apparatus. In plants, Rab2
regulates vesicle trafficking between the ER and the
Golgi bodies and is important to pollen tube growth.
GTPase activating proteins (GAPs) interact with
GTP-bound Rab and accelerate the hydrolysis of GTP to
GDP. Guanine nucleotide exchange factors (GEFs) interact
with GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 168
Score = 27.0 bits (60), Expect = 3.8
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 77 VQSEGFKLNVWDIGGQRKIRPYWRNYF 103
+ + KL +WD GQ R R+Y+
Sbjct: 48 IDGKQIKLQIWDTAGQESFRSITRSYY 74
>gnl|CDD|224043 COG1118, CysA, ABC-type sulfate/molybdate transport systems,
ATPase component [Inorganic ion transport and
metabolism].
Length = 345
Score = 27.3 bits (61), Expect = 4.1
Identities = 12/29 (41%), Positives = 16/29 (55%), Gaps = 4/29 (13%)
Query: 43 LLGLDNAGKTTILKTLASEDISHITPTQG 71
LLG AGK+T+L+ +A TP G
Sbjct: 33 LLGPSGAGKSTLLRIIA----GLETPDAG 57
>gnl|CDD|240327 PTZ00243, PTZ00243, ABC transporter; Provisional.
Length = 1560
Score = 27.4 bits (61), Expect = 4.1
Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 6/70 (8%)
Query: 1 MFQKQNSYERMEKENQVKDLALGLLAILKKLR----SSPEKELRILLLGLDNAGKTTILK 56
+ + ER K ++K L LR S P +L ++L G +GK+T+L+
Sbjct: 646 GHEATPTSERSAKTPKMKTDDFFELEPKVLLRDVSVSVPRGKLTVVL-GATGSGKSTLLQ 704
Query: 57 TLASE-DISH 65
+L S+ +IS
Sbjct: 705 SLLSQFEISE 714
>gnl|CDD|130492 TIGR01425, SRP54_euk, signal recognition particle protein SRP54.
This model represents examples from the eukaryotic
cytosol of the signal recognition particle protein
component, SRP54. This GTP-binding protein is a
component of the eukaryotic signal recognition particle,
along with several other protein subunits and a 7S RNA.
Some species, including Arabidopsis, have several
closely related forms. The extreme C-terminal region is
glycine-rich and lower in complexity, poorly conserved
between species, and excluded from this model.
Length = 429
Score = 27.1 bits (60), Expect = 4.3
Identities = 23/103 (22%), Positives = 47/103 (45%), Gaps = 11/103 (10%)
Query: 29 KKLRSSPEKELRILLLGLDNAGKTTILKTLASEDISHITPTQGFNIKSVQSEGFKLNVWD 88
+ K+ I+ +GL +GKTT LA + +GF V ++ F+ +D
Sbjct: 91 EAFTPKKGKQNVIMFVGLQGSGKTTTCTKLA-----YYYQRKGFKPCLVCADTFRAGAFD 145
Query: 89 IGGQRKIR---PYWRNYFDNTDILIYVIDSADVKRFEESGFEL 128
Q + P++ +Y ++ + I S V++F++ F++
Sbjct: 146 QLKQNATKARIPFYGSYTESDPV---KIASEGVEKFKKENFDI 185
>gnl|CDD|234814 PRK00698, tmk, thymidylate kinase; Validated.
Length = 205
Score = 27.1 bits (61), Expect = 4.3
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 41 ILLLGLDNAGKTTILKTLAS 60
I + G+D AGK+T ++ L
Sbjct: 6 ITIEGIDGAGKSTQIELLKE 25
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 27.4 bits (62), Expect = 4.4
Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 4/54 (7%)
Query: 106 TDILIYVID-SADVKRFEESGFEL--HEL-LSDEKLTGVPLLVYANKQDLLGAA 155
T ++++VID S R +E EL L + +L P +V ANK DL A
Sbjct: 237 TRVIVHVIDMSGSEGRDPIEDYEKINKELKLYNPRLLERPQIVVANKMDLPEAE 290
>gnl|CDD|226124 COG3596, COG3596, Predicted GTPase [General function prediction
only].
Length = 296
Score = 27.1 bits (60), Expect = 4.5
Identities = 23/109 (21%), Positives = 50/109 (45%), Gaps = 17/109 (15%)
Query: 23 GLLAILKKLRSSPEKELRILLLGLDNAGKTTILKTLASEDISHIT-------PTQGFNIK 75
+L L+ L+ + ++ + +LL+G AGK++++ L ++ ++ T
Sbjct: 24 RILEQLRMLQLTEKEPVNVLLMGATGAGKSSLINALFQGEVKEVSKVGVGTDITTRL-RL 82
Query: 76 SVQSEGFKLNVWDIGG----QRKIRPYWRNYFD---NTDILIYVIDSAD 117
S E L +WD G + K + + Y D D+++++I + D
Sbjct: 83 SYDGEN--LVLWDTPGLGDGKDKDAEHRQLYRDYLPKLDLVLWLIKADD 129
>gnl|CDD|183231 PRK11614, livF, leucine/isoleucine/valine transporter ATP-binding
subunit; Provisional.
Length = 237
Score = 27.2 bits (60), Expect = 4.5
Identities = 10/21 (47%), Positives = 15/21 (71%)
Query: 41 ILLLGLDNAGKTTILKTLASE 61
+ L+G + AGKTT+L TL +
Sbjct: 34 VTLIGANGAGKTTLLGTLCGD 54
>gnl|CDD|234199 TIGR03410, urea_trans_UrtE, urea ABC transporter, ATP-binding
protein UrtE. Members of this protein family are ABC
transporter ATP-binding subunits associated with urea
transport and metabolism. This protein is found in a
conserved five-gene transport operon typically found
adjacent to urease genes. It was shown in Cyanobacteria
that disruption leads to the loss of high-affinity urea
transport activity [Transport and binding proteins,
Amino acids, peptides and amines].
Length = 230
Score = 26.7 bits (60), Expect = 4.7
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 13/41 (31%)
Query: 43 LLGLDNAGKTTILKTL-------------ASEDISHITPTQ 70
+LG + GKTT+LKTL EDI+ + P +
Sbjct: 31 VLGRNGVGKTTLLKTLMGLLPVKSGSIRLDGEDITKLPPHE 71
>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 = 27.1 bits (61), Expect = 4.8
Identities = 11/48 (22%), Positives = 24/48 (50%), Gaps = 3/48 (6%)
Query: 15 NQVKDLALGLLAILKKLRSSP---EKELRILLLGLDNAGKTTILKTLA 59
++ A LL + + + +R +++G+ N GK+T++ LA
Sbjct: 92 KKIIKAAKKLLKEKNEKLKAKGLLNRPIRAMIVGIPNVGKSTLINRLA 139
>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 = 27.0 bits (61), Expect = 4.9
Identities = 11/27 (40%), Positives = 20/27 (74%), Gaps = 4/27 (14%)
Query: 38 ELRIL----LLGLDNAGKTTILKTLAS 60
EL++L L+GL NAGK+T++ +++
Sbjct: 153 ELKLLADVGLVGLPNAGKSTLISAVSA 179
Score = 27.0 bits (61), Expect = 5.3
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 4/53 (7%)
Query: 106 TDILIYVIDSADVKRFE-ESGFE--LHELLS-DEKLTGVPLLVYANKQDLLGA 154
T +L+++ID + + +E +EL +L P +V NK DLL
Sbjct: 236 TRVLLHLIDISPEDGSDPIEDYEIIRNELKKYSPELAEKPRIVVLNKIDLLDE 288
>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 = 26.6 bits (60), Expect = 5.1
Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 4/29 (13%)
Query: 43 LLGLDNAGKTTILKTLASEDISHITPTQG 71
LLG + AGKTT++K + + P G
Sbjct: 31 LLGPNGAGKTTLIKIILGL----LKPDSG 55
>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 = 26.6 bits (59), Expect = 5.1
Identities = 26/87 (29%), Positives = 38/87 (43%), Gaps = 25/87 (28%)
Query: 77 VQSEGFKLNVWDIGGQR---KIRPYWRNYFDNTDILI-YVIDSADVKRFEESGFELHELL 132
V + +L +WD GQ ++RP +Y D IL+ + IDS D E
Sbjct: 44 VDGKQVELALWDTAGQEDYDRLRPL--SYPDTDVILMCFSIDSPD--SLENI-------- 91
Query: 133 SDEKLT--------GVPLLVYANKQDL 151
EK T VP+++ NK+DL
Sbjct: 92 -PEKWTPEVKHFCPNVPIILVGNKKDL 117
>gnl|CDD|237457 PRK13647, cbiO, cobalt transporter ATP-binding subunit;
Provisional.
Length = 274
Score = 27.0 bits (60), Expect = 5.2
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 28 LKKLRSSPEKELRILLLGLDNAGKTTIL 55
LK L S + + LLG + AGK+T+L
Sbjct: 21 LKGLSLSIPEGSKTALLGPNGAGKSTLL 48
>gnl|CDD|180660 PRK06696, PRK06696, uridine kinase; Validated.
Length = 223
Score = 26.9 bits (60), Expect = 5.2
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 31 LRSSPEKELRILLLGLDNAGKTTILKTLASE 61
L + + LR+ + G+ +GKTT LA E
Sbjct: 15 LTLNLTRPLRVAIDGITASGKTTFADELAEE 45
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 26.8 bits (60), Expect = 5.8
Identities = 19/102 (18%), Positives = 43/102 (42%), Gaps = 29/102 (28%)
Query: 26 AILKKLRSSPEKE-------LRILLLGLDNAGKTTILKTLASEDISHITPTQGFNIKSVQ 78
A+L+ L E+E ++I ++G N GK++++ + E+ ++ G S+
Sbjct: 159 AVLELLPPDEEEEEEEETDPIKIAIIGRPNVGKSSLINAILGEERVIVSDIAGTTRDSID 218
Query: 79 SEGFKLNVWDIGGQRKIRPYWRNYFDNTDILIYVIDSADVKR 120
E ++ G++ +ID+A ++R
Sbjct: 219 IE------FERDGRK----------------YVLIDTAGIRR 238
>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 = 26.4 bits (59), Expect = 5.9
Identities = 13/51 (25%), Positives = 22/51 (43%), Gaps = 9/51 (17%)
Query: 107 DILIYVIDSADVKRFEESGFELHE----LLSDEKLTGVPLLVYANKQDLLG 153
+++ ID + E G+ + E + L P++V NK DLL
Sbjct: 81 AAVLFFIDPS-----ETCGYSIEEQLSLFKEIKPLFNKPVIVVLNKIDLLT 126
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 26.5 bits (59), Expect = 6.0
Identities = 13/29 (44%), Positives = 20/29 (68%), Gaps = 1/29 (3%)
Query: 39 LRILLLGLDNAGKTTILKTLASE-DISHI 66
+RIL+LG AGK+T+ K LA + + H+
Sbjct: 1 MRILILGPPGAGKSTLAKKLAKKLGLPHL 29
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 26.6 bits (60), Expect = 6.0
Identities = 11/27 (40%), Positives = 20/27 (74%), Gaps = 4/27 (14%)
Query: 38 ELRIL----LLGLDNAGKTTILKTLAS 60
EL++L L+GL NAGK+T++ +++
Sbjct: 154 ELKLLADVGLVGLPNAGKSTLISAVSA 180
>gnl|CDD|223615 COG0541, Ffh, Signal recognition particle GTPase [Intracellular
trafficking and secretion].
Length = 451
Score = 26.7 bits (60), Expect = 6.1
Identities = 11/34 (32%), Positives = 19/34 (55%), Gaps = 4/34 (11%)
Query: 24 LLAIL----KKLRSSPEKELRILLLGLDNAGKTT 53
L+ +L +L + + IL++GL +GKTT
Sbjct: 82 LVKLLGGENSELNLAKKPPTVILMVGLQGSGKTT 115
>gnl|CDD|140006 PRK13949, PRK13949, shikimate kinase; Provisional.
Length = 169
Score = 26.2 bits (58), Expect = 6.2
Identities = 13/22 (59%), Positives = 15/22 (68%)
Query: 40 RILLLGLDNAGKTTILKTLASE 61
RI L+G AGKTT+ K LA E
Sbjct: 3 RIFLVGYMGAGKTTLGKALARE 24
>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 = 26.6 bits (59), Expect = 6.4
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 39 LRILLLGLDNAGKTTILKTLASEDISHITP 68
+ +LG N GK+T+L L + IS +P
Sbjct: 1 GFVAILGRPNVGKSTLLNQLHGQKISITSP 30
>gnl|CDD|163483 TIGR03771, anch_rpt_ABC, anchored repeat-type ABC transporter,
ATP-binding subunit. This protein family is the
ATP-binding cassette subunit of binding
protein-dependent ABC transporter complex that strictly
co-occurs with TIGR03769. TIGRFAMs model TIGR03769
describes a protein domain that occurs singly or as one
of up to three repeats in proteins of a number of
Actinobacteria, including Propionibacterium acnes
KPA171202. The TIGR03769 domain occurs both in an
adjacent gene for the substrate-binding protein and in
additional (often nearby) proteins, often with
LPXTG-like sortase recognition signals. Homologous
ATP-binding subunits outside the scope of this family
include manganese transporter MntA in Synechocystis sp.
PCC 6803 and chelated iron transporter subunits. The
function of this transporter complex is unknown
[Transport and binding proteins, Unknown substrate].
Length = 223
Score = 26.4 bits (58), Expect = 6.5
Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 5/33 (15%)
Query: 43 LLGLDNAGKTTILKTLASEDISHITPTQGFNIK 75
LLG + AGKTT+L+ + + I P +G +K
Sbjct: 11 LLGPNGAGKTTLLRAI----LGLIPPAKG-TVK 38
>gnl|CDD|224045 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport
systems, ATPase components [Inorganic ion transport and
metabolism / Coenzyme metabolism].
Length = 258
Score = 26.4 bits (59), Expect = 6.8
Identities = 9/17 (52%), Positives = 14/17 (82%)
Query: 43 LLGLDNAGKTTILKTLA 59
+LG + +GK+T+LK LA
Sbjct: 33 ILGPNGSGKSTLLKCLA 49
>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 = 26.2 bits (58), Expect = 7.1
Identities = 28/128 (21%), Positives = 55/128 (42%), Gaps = 25/128 (19%)
Query: 43 LLGLDNAGKTTILKTLASEDI---SHITPTQGFNIKSVQS-EGFKLNVWDIGG------- 91
L+GL N GK+T+L L S + S+ T N+ + +G + + D+ G
Sbjct: 2 LVGLPNVGKSTLLSALTSAKVEIASYPFTTLEPNVGVFEFGDGVDIQIIDLPGLLDGASE 61
Query: 92 -QRKIRPYWRNYFDNTDILIYVIDSADVKRFEESGFELHELLS--------DEKLTGVPL 142
+ + + +D++++VID+++ + G L + + L P
Sbjct: 62 GRGLGEQILAHLY-RSDLILHVIDASE----DCVGDPLEDQKTLNEEVSGSFLFLKNKPE 116
Query: 143 LVYANKQD 150
++ ANK D
Sbjct: 117 MIVANKID 124
>gnl|CDD|236992 PRK11819, PRK11819, putative ABC transporter ATP-binding protein;
Reviewed.
Length = 556
Score = 26.6 bits (60), Expect = 7.2
Identities = 11/22 (50%), Positives = 17/22 (77%)
Query: 41 ILLLGLDNAGKTTILKTLASED 62
I +LGL+ AGK+T+L+ +A D
Sbjct: 36 IGVLGLNGAGKSTLLRIMAGVD 57
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 26.6 bits (59), Expect = 7.5
Identities = 12/58 (20%), Positives = 29/58 (50%), Gaps = 2/58 (3%)
Query: 6 NSYERMEKENQVKDLALGLLAILKKLRS--SPEKELRILLLGLDNAGKTTILKTLASE 61
++ R + K L +K+L+ ++++R+ ++G N GK+T++ L +
Sbjct: 98 SAKSRQGGKKIRKALEKLSEEKIKRLKKKGLLKRKIRVGVVGYPNVGKSTLINRLLGK 155
>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 = 26.4 bits (59), Expect = 7.6
Identities = 15/44 (34%), Positives = 26/44 (59%), Gaps = 7/44 (15%)
Query: 40 RILLLGLDNAGKTTILKTLASEDISHITPTQGFNIKSVQSEGFK 83
+I +LGL+ AGK+T+L+ +A D + FN ++ + G K
Sbjct: 33 KIGVLGLNGAGKSTLLRIMAGVD-------KEFNGEARPAPGIK 69
>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 = 26.1 bits (58), Expect = 7.7
Identities = 10/32 (31%), Positives = 19/32 (59%), Gaps = 4/32 (12%)
Query: 40 RILLLGLDNAGKTTILKTLASEDISHITPTQG 71
+ L+G + +GK+T+L+ +A + PT G
Sbjct: 27 IVALVGPNGSGKSTLLRAIAGL----LKPTSG 54
>gnl|CDD|181541 PRK08727, PRK08727, hypothetical protein; Validated.
Length = 233
Score = 26.3 bits (58), Expect = 7.8
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 23 GLLAILKKLRSSPEKELRILLLGLDNAGKTTILKTLA 59
GL +L LRS + +RI L LD+ + +L+ A
Sbjct: 139 GLALVLPDLRSRLAQCIRIGLPVLDDVARAAVLRERA 175
>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 = 26.0 bits (58), Expect = 7.8
Identities = 22/91 (24%), Positives = 41/91 (45%), Gaps = 22/91 (24%)
Query: 39 LRILLLGLDNAGKTTILKTLAS-----EDISHITPT----QGFNIKSVQSEGFKLNVWDI 89
++I+++G GKT +L + + E + PT N+ V + L +WD
Sbjct: 1 IKIVVVGDGAVGKTCLLISYTTNKFPTEYV----PTVFDNYSANVT-VDGKQVNLGLWDT 55
Query: 90 GGQ---RKIRPYWRNYFDNTDILI--YVIDS 115
GQ ++RP + TD+ + + +DS
Sbjct: 56 AGQEEYDRLRPL---SYPQTDVFLLCFSVDS 83
>gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol
utilisation. Members of this family function in
ethanolamine and propanediol degradation pathways,
however the exact roles of these proteins is poorly
understood.
Length = 143
Score = 26.1 bits (58), Expect = 7.8
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 40 RILLLGLDNAGKTTILKTLASEDISHITPTQGFNI 74
+I+L+G GKTT+ + L E++ TQ
Sbjct: 3 KIMLIGRSGCGKTTLTQALNGEEL-KYKKTQAIEF 36
>gnl|CDD|206647 cd00881, GTP_translation_factor, GTP translation factor family
primarily contains translation initiation, elongation
and release factors. The GTP translation factor family
consists primarily of translation initiation,
elongation, and release factors, which play specific
roles in protein translation. In addition, the family
includes Snu114p, a component of the U5 small nuclear
riboprotein particle which is a component of the
spliceosome and is involved in excision of introns,
TetM, a tetracycline resistance gene that protects the
ribosome from tetracycline binding, and the unusual
subfamily CysN/ATPS, which has an unrelated function
(ATP sulfurylase) acquired through lateral transfer of
the EF1-alpha gene and development of a new function.
Length = 183
Score = 26.1 bits (58), Expect = 8.1
Identities = 25/136 (18%), Positives = 43/136 (31%), Gaps = 42/136 (30%)
Query: 48 NAGKTTILKTLAS---------------------EDISHITPTQGFNIKSVQSEGFKLNV 86
+ GKTT+ +L E IT G + ++N
Sbjct: 9 DHGKTTLTGSLLYQTGAIDRRGTRKETFLDTLKEERERGITIKTGV--VEFEWPKRRINF 66
Query: 87 WDIGGQRKIRPYWRNYFDNT-------DILIYVIDSADVKRFEESGFELHELLSDEKLTG 139
D G ++ T D + V+D+ + E H ++ G
Sbjct: 67 IDTPGH-------EDFSKETVRGLAQADGALLVVDANE---GVEPQTREHLNIA--LAGG 114
Query: 140 VPLLVYANKQDLLGAA 155
+P++V NK D +G
Sbjct: 115 LPIIVAVNKIDRVGEE 130
>gnl|CDD|234711 PRK00279, adk, adenylate kinase; Reviewed.
Length = 215
Score = 26.3 bits (59), Expect = 8.4
Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 39 LRILLLGLDNAGKTTILKTLASE-DISHI 66
+R++LLG AGK T K +A + I HI
Sbjct: 1 MRLILLGPPGAGKGTQAKFIAEKYGIPHI 29
>gnl|CDD|238985 cd02027, APSK, Adenosine 5'-phosphosulfate kinase (APSK)
catalyzes the phosphorylation of adenosine
5'-phosphosulfate to form 3'-phosphoadenosine
5'-phosphosulfate (PAPS). The end-product PAPS is a
biologically "activated" sulfate form important for the
assimilation of inorganic sulfate.
Length = 149
Score = 25.9 bits (58), Expect = 8.5
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 41 ILLLGLDNAGKTTILKTLA 59
I L GL +GK+TI + L
Sbjct: 2 IWLTGLSGSGKSTIARALE 20
>gnl|CDD|235450 PRK05416, PRK05416, glmZ(sRNA)-inactivating NTPase; Provisional.
Length = 288
Score = 26.2 bits (59), Expect = 8.6
Identities = 10/31 (32%), Positives = 18/31 (58%), Gaps = 3/31 (9%)
Query: 34 SPEKELRILLL-GLDNAGKTTILKTLASEDI 63
+R++++ GL AGK+ L+ L ED+
Sbjct: 1 MTAAPMRLVIVTGLSGAGKSVALRAL--EDL 29
>gnl|CDD|226164 COG3638, COG3638, ABC-type phosphate/phosphonate transport
system, ATPase component [Inorganic ion transport and
metabolism].
Length = 258
Score = 26.1 bits (58), Expect = 8.9
Identities = 11/49 (22%), Positives = 22/49 (44%), Gaps = 6/49 (12%)
Query: 35 PEKELRILLLGLDNAGKTTILKTLAS-EDIS----HITPTQGFNIKSVQ 78
+ E + ++G AGK+T+L++L D + Q +K +
Sbjct: 28 NQGE-MVAIIGPSGAGKSTLLRSLNGLVDPTSGEILFNGVQITKLKGKE 75
>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 = 26.0 bits (58), Expect = 9.0
Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 15 NQVKDLALGLLAILKKLRSSPEK--ELRILLLGLDNAGKTTILKTLA 59
++ A LL +KL++ LR +++G+ N GK+T++ L
Sbjct: 90 KKLLKKAKKLLKENEKLKAKGLLPRPLRAMVVGIPNVGKSTLINRLR 136
>gnl|CDD|162242 TIGR01187, potA, spermidine/putrescine ABC transporter
ATP-binding subunit. This model describes
spermidine/putrescine ABC transporter, 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 transporter is the
obligatory coupling of ATP hydrolysis to substrate
translocation. The minimal configuration of bacterial
ABC transport system: an ATPase or ATP binding subunit;
An integral membrane protein; a hydrophilic
polypetpide, which likely functions as substrate
binding protein. Polyamines like spermidine and
putrescine play vital role in cell proliferation,
differentiation, and ion homeostasis. The concentration
of polyamines within the cell are regulated by
biosynthesis, degradation and transport (uptake and
efflux included) [Transport and binding proteins, Amino
acids, peptides and amines].
Length = 325
Score = 26.3 bits (58), Expect = 9.4
Identities = 13/39 (33%), Positives = 19/39 (48%), Gaps = 13/39 (33%)
Query: 43 LLGLDNAGKTTILKTLA-------------SEDISHITP 68
LLG GKTT+L+ LA ED++++ P
Sbjct: 1 LLGPSGCGKTTLLRLLAGFEQPDSGSIMLDGEDVTNVPP 39
>gnl|CDD|215925 pfam00448, SRP54, SRP54-type protein, GTPase domain. This family
includes relatives of the G-domain of the SRP54 family
of proteins.
Length = 196
Score = 26.0 bits (58), Expect = 9.7
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 41 ILLLGLDNAGKTTILKTLA 59
ILL+GL +GKTT + LA
Sbjct: 4 ILLVGLQGSGKTTTIAKLA 22
>gnl|CDD|215599 PLN03140, PLN03140, ABC transporter G family member; Provisional.
Length = 1470
Score = 26.3 bits (58), Expect = 10.0
Identities = 15/58 (25%), Positives = 29/58 (50%)
Query: 2 FQKQNSYERMEKENQVKDLALGLLAILKKLRSSPEKELRILLLGLDNAGKTTILKTLA 59
F N + M E + + + L +L+++ + + L+G+ AGKTT++ LA
Sbjct: 870 FDDVNYFVDMPAEMKEQGVTEDRLQLLREVTGAFRPGVLTALMGVSGAGKTTLMDVLA 927
>gnl|CDD|232995 TIGR00487, IF-2, translation initiation factor IF-2. This model
discriminates eubacterial (and mitochondrial)
translation initiation factor 2 (IF-2), encoded by the
infB gene in bacteria, from similar proteins in the
Archaea and Eukaryotes. In the bacteria and in
organelles, the initiator tRNA is charged with
N-formyl-Met instead of Met. This translation factor
acts in delivering the initator tRNA to the ribosome. It
is one of a number of GTP-binding translation factors
recognized by the pfam model GTP_EFTU [Protein
synthesis, Translation factors].
Length = 587
Score = 26.3 bits (58), Expect = 10.0
Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 7/52 (13%)
Query: 106 TDILIYVIDSAD-VKRFEESGFELHELLSDEKLTGVPLLVYANKQDLLGAAP 156
TDI++ V+ + D V + E +S K VP++V NK D A P
Sbjct: 159 TDIVVLVVAADDGVMP------QTIEAISHAKAANVPIIVAINKIDKPEANP 204
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
0.317 0.137 0.389
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: 8,307,017
Number of extensions: 759777
Number of successful extensions: 1362
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1312
Number of HSP's successfully gapped: 271
Length of query: 162
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 73
Effective length of database: 6,990,096
Effective search space: 510277008
Effective search space used: 510277008
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: 55 (25.4 bits)