RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2161
(155 letters)
>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 = 260 bits (666), Expect = 3e-90
Identities = 102/154 (66%), Positives = 125/154 (81%)
Query: 1 MLKNDRTAQHMPTLHPTSEELSMGDIVFTTHDLGGHVQARRVWRDYFPAVDAIVFIIDAS 60
MLK+DR AQH+PTLHPTSEEL++G++ FTT DLGGH QARRVW+DYFP VD IVF++DA+
Sbjct: 38 MLKDDRLAQHVPTLHPTSEELTIGNVKFTTFDLGGHEQARRVWKDYFPEVDGIVFLVDAA 97
Query: 61 DRSRFPESKYELDSLLADDALTDVPILILGNKIDIFDAASEDEVRHFFGLYGLTTGKEFT 120
D RF ESK ELDSLL D+ L +VPILILGNKID A SE+E+R GLYG TTGK
Sbjct: 98 DPERFQESKEELDSLLNDEELANVPILILGNKIDKPGAVSEEELREALGLYGTTTGKGGV 157
Query: 121 SREILQMRPIELFMCSVLKRQGFGNGFRWLANYI 154
S ++ +RP+E+FMCSV+KRQG+G GFRWL+ Y+
Sbjct: 158 SLKVSNIRPVEVFMCSVVKRQGYGEGFRWLSQYL 191
>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 = 219 bits (560), Expect = 2e-74
Identities = 95/154 (61%), Positives = 119/154 (77%), Gaps = 5/154 (3%)
Query: 1 MLKNDRTAQHMPTLHPTSEELSMGDIVFTTHDLGGHVQARRVWRDYFPAVDAIVFIIDAS 60
MLKNDR AQH PT HPTSEEL++G+I FTT DLGGH QARR+W+DYFP V+ IV+++DA
Sbjct: 36 MLKNDRLAQHQPTQHPTSEELAIGNIKFTTFDLGGHQQARRLWKDYFPEVNGIVYLVDAY 95
Query: 61 DRSRFPESKYELDSLLADDALTDVPILILGNKIDIFDAASEDEVRHFFGLYGLTTGKEFT 120
D+ RF ESK ELD+LL+D+ L VP LILGNKID AASEDE+R+ GL TTGK
Sbjct: 96 DKERFAESKRELDALLSDEELATVPFLILGNKIDAPYAASEDELRYALGLTNTTTGK--- 152
Query: 121 SREILQMRPIELFMCSVLKRQGFGNGFRWLANYI 154
+ +RP+E+FMCSV++R G+G GF+WL+ YI
Sbjct: 153 --GKVGVRPVEVFMCSVVRRMGYGEGFKWLSQYI 184
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 194 bits (495), Expect = 2e-64
Identities = 58/154 (37%), Positives = 85/154 (55%), Gaps = 12/154 (7%)
Query: 1 MLKNDRTAQHMPTLHPTSEELSMGDIVFTTHDLGGHVQARRVWRDYFPAVDAIVFIIDAS 60
LK +PT+ E ++ ++ FT D+GG R +WR+YFP DA++F++D++
Sbjct: 33 KLKLGEIVTTIPTIGFNVETVTYKNVKFTVWDVGGQESLRPLWRNYFPNTDAVIFVVDSA 92
Query: 61 DRSRFPESKYELDSLLADDALTDVPILILGNKIDIFDAASEDEVRHFFGLYGLTTGKEFT 120
DR R E+K EL +LL ++ L D P+LIL NK D+ A SE E+R GL+ L
Sbjct: 93 DRDRIEEAKEELHALLNEEELADAPLLILANKQDLPGAMSEAEIRELLGLHELKD----- 147
Query: 121 SREILQMRPIELFMCSVLKRQGFGNGFRWLANYI 154
RP E+ CS + +G G WL+NYI
Sbjct: 148 -------RPWEIQGCSAVTGEGLDEGLDWLSNYI 174
>gnl|CDD|206644 cd00878, Arf_Arl, ADP-ribosylation factor(Arf)/Arf-like (Arl) small
GTPases. Arf (ADP-ribosylation factor)/Arl (Arf-like)
small GTPases. Arf proteins are activators of
phospholipase D isoforms. Unlike Ras proteins they lack
cysteine residues at their C-termini and therefore are
unlikely to be prenylated. Arfs are N-terminally
myristoylated. Members of the Arf family are regulators
of vesicle formation in intracellular traffic that
interact reversibly with membranes of the secretory and
endocytic compartments in a GTP-dependent manner. They
depart from other small GTP-binding proteins by a unique
structural device, interswitch toggle, that implements
front-back communication from N-terminus to the
nucleotide binding site. Arf-like (Arl) proteins are
close relatives of the Arf, but only Arl1 has been shown
to function in membrane traffic like the Arf proteins.
Arl2 has an unrelated function in the folding of native
tubulin, and Arl4 may function in the nucleus. Most
other Arf family proteins are so far relatively poorly
characterized. Thus, despite their significant sequence
homologies, Arf family proteins may regulate unrelated
functions.
Length = 158
Score = 123 bits (310), Expect = 1e-36
Identities = 46/152 (30%), Positives = 71/152 (46%), Gaps = 12/152 (7%)
Query: 1 MLKNDRTAQHMPTLHPTSEELSMGDIVFTTHDLGGHVQARRVWRDYFPAVDAIVFIIDAS 60
LK +PT+ E + ++ FT D+GG + R +W+ Y+ D ++F++D+S
Sbjct: 18 KLKLGEVVTTIPTIGFNVETVEYKNVKFTVWDVGGQDKIRPLWKHYYENTDGLIFVVDSS 77
Query: 61 DRSRFPESKYELDSLLADDALTDVPILILGNKIDIFDAASEDEVRHFFGLYGLTTGKEFT 120
DR R E+K EL LL ++ L P+LIL NK D+ A +E E+ GL +
Sbjct: 78 DRERIEEAKNELHKLLNEEELKGAPLLILANKQDLPGALTESELIELLGLESIKG----- 132
Query: 121 SREILQMRPIELFMCSVLKRQGFGNGFRWLAN 152
R + CS + G G WL
Sbjct: 133 -------RRWHIQPCSAVTGDGLDEGLDWLIE 157
>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 = 102 bits (256), Expect = 2e-28
Identities = 47/144 (32%), Positives = 70/144 (48%), Gaps = 12/144 (8%)
Query: 9 QHMPTLHPTSEELSMGDIVFTTHDLGGHVQARRVWRDYFPAVDAIVFIIDASDRSRFPES 68
+PT+ E ++ ++ F DLGG R WR Y+ DAI++++D++DR R S
Sbjct: 26 TTIPTIGFNVETVTYKNLKFQVWDLGGQTSIRPYWRCYYSNTDAIIYVVDSTDRDRLGIS 85
Query: 69 KYELDSLLADDALTDVPILILGNKIDIFDAASEDEVRHFFGLYGLTTGKEFTSREILQMR 128
K EL ++L ++ L D +L+ NK D+ A SE EV GL L R
Sbjct: 86 KSELHAMLEEEELKDAVLLVFANKQDMPGALSEAEVAEKLGLSELKD------------R 133
Query: 129 PIELFMCSVLKRQGFGNGFRWLAN 152
++F S K +G G WL N
Sbjct: 134 TWQIFKTSATKGEGLDEGMDWLVN 157
>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 = 93.2 bits (232), Expect = 9e-25
Identities = 41/141 (29%), Positives = 64/141 (45%), Gaps = 12/141 (8%)
Query: 12 PTLHPTSEELSMGDIVFTTHDLGGHVQARRVWRDYFPAVDAIVFIIDASDRSRFPESKYE 71
PT+ EE+ +I F D+GG R W Y+ DA++ +ID++DR R P +K E
Sbjct: 45 PTIGSNVEEIVYKNIRFLMWDIGGQESLRSSWNTYYTNTDAVILVIDSTDRERLPLTKEE 104
Query: 72 LDSLLADDALTDVPILILGNKIDIFDAASEDEVRHFFGLYGLTTGKEFTSREILQMRPIE 131
L +LA + L +L+L NK D+ A + E+ GL +
Sbjct: 105 LYKMLAHEDLRKAVLLVLANKQDLKGAMTPAEISESLGLTSIRD------------HTWH 152
Query: 132 LFMCSVLKRQGFGNGFRWLAN 152
+ C L +G G W+A+
Sbjct: 153 IQGCCALTGEGLPEGLDWIAS 173
>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 = 91.2 bits (227), Expect = 4e-24
Identities = 37/93 (39%), Positives = 53/93 (56%), Gaps = 6/93 (6%)
Query: 32 DLGGHVQARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDSLLADDALTDVPILILGN 91
DLGG + R +W Y V+AIV+++DA+DR + +K EL LL +L +P+L+LGN
Sbjct: 50 DLGGQPRFRSMWERYCRGVNAIVYVVDAADREKLEVAKNELHDLLEKPSLEGIPLLVLGN 109
Query: 92 KIDIFDAASEDEVRHFFGLYGLTTGKEFTSREI 124
K D+ A S DE+ L K T RE+
Sbjct: 110 KNDLPGALSVDELIEQMNL------KSITDREV 136
>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 = 88.2 bits (219), Expect = 9e-23
Identities = 38/120 (31%), Positives = 60/120 (50%), Gaps = 12/120 (10%)
Query: 32 DLGGHVQARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDSLLADDALTDVPILILGN 91
D+GG + R WR+YF D ++++ID++DR RF E+ EL LL ++ L VP+L+ N
Sbjct: 65 DIGGQRKIRPYWRNYFENTDVLIYVIDSADRKRFEEAGQELVELLEEEKLAGVPVLVFAN 124
Query: 92 KIDIFDAASEDEVRHFFGLYGLTTGKEFTSREILQMRPIELFMCSVLKRQGFGNGFRWLA 151
K D+ AA +EV E + ++ R + CS +G G W+
Sbjct: 125 KQDLLTAAPAEEV------------AEALNLHDIRDRSWHIQACSAKTGEGLQEGMNWVC 172
>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 = 86.3 bits (214), Expect = 4e-22
Identities = 44/151 (29%), Positives = 71/151 (47%), Gaps = 14/151 (9%)
Query: 4 NDRTAQHMPTLHPTSEELSMGDIVFTTHDLGGHVQARRVWRDYFPAVDAIVFIIDASDRS 63
N ++ +PT+ E G++ FT D+ G + R +W Y+ + I+F+ID+SDR
Sbjct: 23 NAQSQNIVPTVGFNVESFKKGNLSFTAFDMSGQGKYRGLWEHYYKNIQGIIFVIDSSDRL 82
Query: 64 RFPESKYELDSLL--ADDALTDVPILILGNKIDIFDAASEDEVRHFFGLYGLTTGKEFTS 121
R +K EL+ LL D +PIL NK+D+ DA + ++ L
Sbjct: 83 RMVVAKDELELLLNHPDIKHRRIPILFYANKMDLPDALTAVKITQLLCL----------- 131
Query: 122 REILQMRPIELFMCSVLKRQGFGNGFRWLAN 152
E ++ +P +F S L +G G WL
Sbjct: 132 -ENIKDKPWHIFASSALTGEGLDEGVDWLQA 161
>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 = 86.3 bits (214), Expect = 4e-22
Identities = 45/151 (29%), Positives = 77/151 (50%), Gaps = 12/151 (7%)
Query: 2 LKNDRTAQHMPTLHPTSEELSM-GDIVFTTHDLGGHVQARRVWRDYFPAVDAIVFIIDAS 60
LK+ +PT+ E L + + T D+GG + R VW+ Y D +V+++D+S
Sbjct: 19 LKHAELVTTIPTVGFNVEMLQLEKHLSLTVWDVGGQEKMRTVWKCYLENTDGLVYVVDSS 78
Query: 61 DRSRFPESKYELDSLLADDALTDVPILILGNKIDIFDAASEDEVRHFFGLYGLTTGKEFT 120
D +R ES+ EL +L ++ + VP+++L NK D+ A + +E+ F L K++
Sbjct: 79 DEARLDESQKELKHILKNEHIKGVPVVLLANKQDLPGALTAEEITRRFKL------KKYC 132
Query: 121 SREILQMRPIELFMCSVLKRQGFGNGFRWLA 151
S ++P CS + +G FR LA
Sbjct: 133 SDRDWYVQP-----CSAVTGEGLAEAFRKLA 158
>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 = 84.7 bits (210), Expect = 2e-21
Identities = 37/119 (31%), Positives = 61/119 (51%), Gaps = 10/119 (8%)
Query: 32 DLGGHVQARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDSLLADDALTDVPILILGN 91
DLGG + R +W Y+ ++++ID++DR RF ESK + ++ ++AL VP+L+L N
Sbjct: 57 DLGGQEELRSLWDKYYAESHGVIYVIDSTDRERFNESKSAFEKVINNEALEGVPLLVLAN 116
Query: 92 KIDIFDAASEDEVRHFFGLYGLTTGKEFTSREILQMRPIELFMCSVLKRQGFGNGFRWL 150
K D+ DA S E++ F ++ R + S L+ +G G WL
Sbjct: 117 KQDLPDALSVAEIKEVFDD----------CIALIGRRDCLVQPVSALEGEGVEEGIEWL 165
>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 = 81.0 bits (200), Expect = 5e-20
Identities = 37/151 (24%), Positives = 70/151 (46%), Gaps = 12/151 (7%)
Query: 2 LKNDRTAQHMPTLHPTSEELSMGDIVFTTHDLGGHVQARRVWRDYFPAVDAIVFIIDASD 61
LK ++ +PT+ E ++ ++ F D+GG + R +WR Y+ ++F++D++D
Sbjct: 29 LKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGQDKIRPLWRHYYTGTQGLIFVVDSAD 88
Query: 62 RSRFPESKYELDSLLADDALTDVPILILGNKIDIFDAASEDEVRHFFGLYGLTTGKEFTS 121
R R E++ EL ++ D + D +L+ NK D+ DA E++ GL
Sbjct: 89 RDRIDEARQELHRIINDREMRDALLLVFANKQDLPDAMKPHEIQEKLGL----------- 137
Query: 122 REILQMRPIELFMCSVLKRQGFGNGFRWLAN 152
++ R + G G WL++
Sbjct: 138 -TRIRDRNWYVQPSCATSGDGLYEGLTWLSS 167
>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 = 78.6 bits (194), Expect = 3e-19
Identities = 37/103 (35%), Positives = 59/103 (57%)
Query: 11 MPTLHPTSEELSMGDIVFTTHDLGGHVQARRVWRDYFPAVDAIVFIIDASDRSRFPESKY 70
+PT+ E + +I FT D+GG + R +WR YF ++F++D++DR R E++
Sbjct: 29 IPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERIGEARE 88
Query: 71 ELDSLLADDALTDVPILILGNKIDIFDAASEDEVRHFFGLYGL 113
EL +L +D L D +L+ NK D+ +A S EV GL+ L
Sbjct: 89 ELQRMLNEDELRDAVLLVFANKQDLPNAMSAAEVTDKLGLHSL 131
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 77.6 bits (191), Expect = 1e-18
Identities = 40/144 (27%), Positives = 71/144 (49%), Gaps = 12/144 (8%)
Query: 11 MPTLHPTSEELSMGDIVFTTHDLGGHVQARRVWRDYFPAVDAIVFIIDASDRSRFPESKY 70
+PT+ E + ++ FT D+GG + R +WR Y+ + ++F++D++DR R +++
Sbjct: 46 IPTIGFNVETVEYKNLKFTMWDVGGQDKLRPLWRHYYQNTNGLIFVVDSNDRERIGDARE 105
Query: 71 ELDSLLADDALTDVPILILGNKIDIFDAASEDEVRHFFGLYGLTTGKEFTSREILQMRPI 130
EL+ +L++D L D +L+ NK D+ +A S EV GL+ + +
Sbjct: 106 ELERMLSEDELRDAVLLVFANKQDLPNAMSTTEVTEKLGLHSVRQRNWYIQG-------- 157
Query: 131 ELFMCSVLKRQGFGNGFRWLANYI 154
C QG G WL+ I
Sbjct: 158 ----CCATTAQGLYEGLDWLSANI 177
>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 = 77.3 bits (190), Expect = 1e-18
Identities = 37/112 (33%), Positives = 62/112 (55%)
Query: 2 LKNDRTAQHMPTLHPTSEELSMGDIVFTTHDLGGHVQARRVWRDYFPAVDAIVFIIDASD 61
LK + +PT+ E ++ +I FT D+GG + R +WR Y+ ++F++D++D
Sbjct: 33 LKLGESVTTIPTIGFNVETVTYKNISFTVWDVGGQDKIRPLWRHYYTNTQGLIFVVDSND 92
Query: 62 RSRFPESKYELDSLLADDALTDVPILILGNKIDIFDAASEDEVRHFFGLYGL 113
R R E++ EL +L +D L D IL+ NK D+ DA E+ GL+ +
Sbjct: 93 RDRIDEAREELHRMLNEDELRDAVILVFANKQDLPDAMKAAEITEKLGLHSI 144
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 76.9 bits (189), Expect = 2e-18
Identities = 42/144 (29%), Positives = 70/144 (48%), Gaps = 12/144 (8%)
Query: 11 MPTLHPTSEELSMGDIVFTTHDLGGHVQARRVWRDYFPAVDAIVFIIDASDRSRFPESKY 70
+PT+ E + +I FT D+GG + R +WR YF ++F++D++DR R E++
Sbjct: 46 IPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRDRVVEARD 105
Query: 71 ELDSLLADDALTDVPILILGNKIDIFDAASEDEVRHFFGLYGLTTGKEFTSREILQMRPI 130
EL +L +D L D +L+ NK D+ +A + E+ GL+ L+ R
Sbjct: 106 ELHRMLNEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHS------------LRQRHW 153
Query: 131 ELFMCSVLKRQGFGNGFRWLANYI 154
+ +G G WL+N I
Sbjct: 154 YIQSTCATSGEGLYEGLDWLSNNI 177
>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 = 76.6 bits (188), Expect = 3e-18
Identities = 46/150 (30%), Positives = 70/150 (46%), Gaps = 11/150 (7%)
Query: 2 LKNDRTAQHMPTLHPTSEELSMGDIVFTTHDLGGHVQARRVWRDYFPAVDAIVFIIDASD 61
LK D Q +PT+ E + ++ FT D+GG + R +W+ Y+ A+VF+ID+S
Sbjct: 19 LKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVIDSSH 78
Query: 62 RSRFPESKYELDSLLADDALTDVPILILGNKIDIFDAASEDEVRHFFGLYGLTTGKEFTS 121
R R E+ EL LL + L D +LI NK D+ A S +E+ L+ L G+ +
Sbjct: 79 RDRVSEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEMTELLSLHKLCCGRSWYI 138
Query: 122 REILQMRPIELFMCSVLKRQGFGNGFRWLA 151
+ C G G WL+
Sbjct: 139 QG-----------CDARSGMGLYEGLDWLS 157
>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 = 75.1 bits (185), Expect = 9e-18
Identities = 41/141 (29%), Positives = 67/141 (47%), Gaps = 12/141 (8%)
Query: 12 PTLHPTSEELSMGDIVFTTHDLGGHVQARRVWRDYFPAVDAIVFIIDASDRSRFPESKYE 71
PTL + L D+GG R WR+YF + DA+++++D+SDR+R + K E
Sbjct: 44 PTLGFNIKTLEYNGYKLNIWDVGGQKSLRSYWRNYFESTDALIWVVDSSDRARLEDCKRE 103
Query: 72 LDSLLADDALTDVPILILGNKIDIFDAASEDEVRHFFGLYGLTTGKEFTSREILQMRPIE 131
L LL ++ L +LI NK D+ A S +E+R L + ++
Sbjct: 104 LQKLLVEERLAGATLLIFANKQDLPGALSPEEIREVLEL------------DSIKSHHWR 151
Query: 132 LFMCSVLKRQGFGNGFRWLAN 152
+F CS + + +G WL +
Sbjct: 152 IFGCSAVTGENLLDGIDWLVD 172
>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 = 68.2 bits (167), Expect = 4e-15
Identities = 29/111 (26%), Positives = 53/111 (47%), Gaps = 2/111 (1%)
Query: 10 HMPTLHPTSEELSMGDIVFTTHDLGGHVQARRVWRDYFPAVDAIVFIIDASDRSRFPESK 69
+PT S + D + ++GG R+ W+ Y ++F++D++D R P ++
Sbjct: 28 VVPTTGFNSVAIPTQDAIMELLEIGGSQNLRKYWKRYLSGSQGLIFVVDSADSERLPLAR 87
Query: 70 YELDSLLADDALTDVPILILGNKIDIFDAASEDEVRHFFGLYGLTTGKEFT 120
EL LL D+P+++L NK D+ A S E+ L + G+ +
Sbjct: 88 QELHQLLQHPP--DLPLVVLANKQDLPAARSVQEIHKELELEPIARGRRWI 136
>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 = 66.3 bits (162), Expect = 2e-14
Identities = 31/94 (32%), Positives = 46/94 (48%)
Query: 11 MPTLHPTSEELSMGDIVFTTHDLGGHVQARRVWRDYFPAVDAIVFIIDASDRSRFPESKY 70
PT+ T +L + DLGG R +W +Y+ +VF++D+SD R E K
Sbjct: 28 APTVGFTPTKLRLDKYEVCIFDLGGGANFRGIWVNYYAEAHGLVFVVDSSDDDRVQEVKE 87
Query: 71 ELDSLLADDALTDVPILILGNKIDIFDAASEDEV 104
L LL ++ PIL+L NK D +A +V
Sbjct: 88 ILRELLQHPRVSGKPILVLANKQDKKNALLGADV 121
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 65.4 bits (159), Expect = 1e-13
Identities = 27/90 (30%), Positives = 42/90 (46%)
Query: 15 HPTSEELSMGDIVFTTHDLGGHVQARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDS 74
+ E +I D G + R + +Y+ + I+ + D++ R E E
Sbjct: 43 PAKTIEPYRRNIKLQLWDTAGQEEYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLE 102
Query: 75 LLADDALTDVPILILGNKIDIFDAASEDEV 104
L + A DVPIL++GNKID+FD S E
Sbjct: 103 ELRELAPDDVPILLVGNKIDLFDEQSSSEE 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 = 56.3 bits (136), Expect = 9e-11
Identities = 27/152 (17%), Positives = 54/152 (35%), Gaps = 28/152 (18%)
Query: 10 HMPTLHPTSEELSM----GDIVFTTHDLGGHVQARRVW-----RDYFPAVDAIVFIIDAS 60
T P + +V D G + + R D I+ ++D++
Sbjct: 29 PGTTRDPDVYVKELDKGKVKLVL--VDTPGLDEFGGLGREELARLLLRGADLILLVVDST 86
Query: 61 DRSRFPESKYELDSLLADDALTDVPILILGNKIDIFDAASEDEVRHFFGLYGLTTGKEFT 120
DR ++K + L + +PI+++GNKID+ + +E+
Sbjct: 87 DRESEEDAKLLILRRLRKE---GIPIILVGNKIDLLEEREVEELL--------------R 129
Query: 121 SREILQMRPIELFMCSVLKRQGFGNGFRWLAN 152
E+ ++ + +F S +G F L
Sbjct: 130 LEELAKILGVPVFEVSAKTGEGVDELFEKLIE 161
>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 = 56.3 bits (136), Expect = 1e-10
Identities = 30/88 (34%), Positives = 45/88 (51%)
Query: 26 IVFTTHDLGGHVQARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDSLLADDALTDVP 85
+ F D+GG + R +W+ Y D IVF++D+ D R E+K EL + VP
Sbjct: 52 VTFHFWDVGGQEKLRPLWKSYTRCTDGIVFVVDSVDVERMEEAKTELHKITKFSENQGVP 111
Query: 86 ILILGNKIDIFDAASEDEVRHFFGLYGL 113
+L+L NK D+ +A EV L+ L
Sbjct: 112 VLVLANKQDLPNALPVSEVEKLLALHEL 139
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 46.7 bits (111), Expect = 6e-07
Identities = 13/74 (17%), Positives = 33/74 (44%), Gaps = 4/74 (5%)
Query: 32 DLGGHVQARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDSLLADDALTDVPILILGN 91
G + + +W + ++D+S P + + + + + +P+++ N
Sbjct: 74 GTPGQERFKFMWEILSRGAVGAIVLVDSSR----PITFHAEEIIDFLTSRNPIPVVVAIN 129
Query: 92 KIDIFDAASEDEVR 105
K D+FDA +++R
Sbjct: 130 KQDLFDALPPEKIR 143
>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 = 44.7 bits (106), Expect = 2e-06
Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 1/78 (1%)
Query: 32 DLGGHVQARRVWRDYFPAVDAIVFIID-ASDRSRFPESKYELDSLLADDALTDVPILILG 90
D G + R Y+ AV++ + + D E + + A + VPI+++G
Sbjct: 57 DTAGQEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAESGVPIILVG 116
Query: 91 NKIDIFDAASEDEVRHFF 108
NKID+ DA + V F
Sbjct: 117 NKIDLRDAKLKTHVAFLF 134
>gnl|CDD|215955 pfam00503, G-alpha, G-protein alpha subunit. G proteins couple
receptors of extracellular signals to intracellular
signaling pathways. The G protein alpha subunit binds
guanyl nucleotide and is a weak GTPase. A set of
residues that are unique to G-alpha as compared to its
ancestor the Arf-like family form a ring of residues
centered on the nucleotide binding site. A Ggamma is
found fused to an inactive Galpha in the Dictyostelium
protein gbqA.
Length = 329
Score = 44.9 bits (107), Expect = 4e-06
Identities = 21/87 (24%), Positives = 36/87 (41%), Gaps = 10/87 (11%)
Query: 20 ELSMGDIVFTTHDLGGHVQARRVWRDYFPAVDAIVFIIDASD----------RSRFPESK 69
+ + F D+GG R+ W F V AI+F++ S+ +R ES
Sbjct: 162 KFDFKGLKFRLFDVGGQRSERKKWIHCFEDVTAIIFVVSLSEYDQVLYEDDSTNRLEESL 221
Query: 70 YELDSLLADDALTDVPILILGNKIDIF 96
+ + + PI++ NK D+F
Sbjct: 222 NLFEEICNSPWFKNTPIILFLNKKDLF 248
>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 = 42.3 bits (100), Expect = 2e-05
Identities = 23/83 (27%), Positives = 41/83 (49%), Gaps = 12/83 (14%)
Query: 32 DLGGHVQAR-RVWRDYFPAVDAIVFIIDASDRSRFPESKYELDSLLADDALTD------- 83
D+ GH + R ++ ++ AIVF++D++ + + + L D LTD
Sbjct: 53 DVPGHEKLRDKLLEYLKASLKAIVFVVDSATFQK--NIRDVAEFLY--DILTDLEKIKNK 108
Query: 84 VPILILGNKIDIFDAASEDEVRH 106
+PILI NK D+F A +++
Sbjct: 109 IPILIACNKQDLFTAKPAKKIKE 131
>gnl|CDD|214595 smart00275, G_alpha, G protein alpha subunit. Subunit of G
proteins that contains the guanine nucleotide binding
site.
Length = 342
Score = 35.6 bits (83), Expect = 0.006
Identities = 26/95 (27%), Positives = 38/95 (40%), Gaps = 10/95 (10%)
Query: 12 PTLHPTSEELSMGDIVFTTHDLGGHVQARRVWRDYFPAVDAIVFIIDAS--------DRS 63
PT + + F D+GG R+ W F V AI+F + S D S
Sbjct: 170 PTTGIQETAFIVKKLFFRMFDVGGQRSERKKWIHCFDNVTAIIFCVALSEYDQVLEEDES 229
Query: 64 --RFPESKYELDSLLADDALTDVPILILGNKIDIF 96
R ES +S+ + I++ NKID+F
Sbjct: 230 TNRMQESLNLFESICNSRWFANTSIILFLNKIDLF 264
>gnl|CDD|206726 cd04163, Era, E. coli Ras-like protein (Era) is a multifunctional
GTPase. Era (E. coli Ras-like protein) is a
multifunctional GTPase found in all bacteria except some
eubacteria. It binds to the 16S ribosomal RNA (rRNA) of
the 30S subunit and appears to play a role in the
assembly of the 30S subunit, possibly by chaperoning the
16S rRNA. It also contacts several assembly elements of
the 30S subunit. Era couples cell growth with
cytokinesis and plays a role in cell division and energy
metabolism. Homologs have also been found in eukaryotes.
Era contains two domains: the N-terminal GTPase domain
and a C-terminal domain KH domain that is critical for
RNA binding. Both domains are important for Era
function. Era is functionally able to compensate for
deletion of RbfA, a cold-shock adaptation protein that
is required for efficient processing of the 16S rRNA.
Length = 168
Score = 34.7 bits (81), Expect = 0.008
Identities = 23/106 (21%), Positives = 41/106 (38%), Gaps = 25/106 (23%)
Query: 38 QARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDSLLADDALTDVPILILGNKID-IF 96
A +D VD ++F++DAS+ ++ L+ L + P++++ NKID +
Sbjct: 75 AAWSALKD----VDLVLFVVDASEWIG-EGDEFILELL----KKSKTPVILVLNKIDLVK 125
Query: 97 DAASEDEVRHFFGLYGLTTGKEFTSREILQMRPIELFMCSVLKRQG 142
D + L F E+F S LK +
Sbjct: 126 DKEDLLPLLEK-----LKELHPFA----------EIFPISALKGEN 156
>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 = 33.9 bits (78), Expect = 0.008
Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 9/71 (12%)
Query: 28 FTTHDLGGHVQARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDSLLA-----DDALT 82
D GG + + + DAI+ + D +D ES E+ L+A
Sbjct: 50 LNIWDFGGREELKFEHIIFMKWADAILLVYDLTD----RESLNEVSRLIAWLPNLRKLGG 105
Query: 83 DVPILILGNKI 93
+P++++GNK+
Sbjct: 106 KIPVILVGNKL 116
>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 = 34.5 bits (80), Expect = 0.009
Identities = 16/94 (17%), Positives = 36/94 (38%), Gaps = 20/94 (21%)
Query: 50 VDAIVFIIDASDRSRFPESKYELDSLLADDALTDVPILILGNKIDIFDAASEDEVRHFFG 109
D ++ ++D+ + E ++ L P+L++ NKID+ + E+E
Sbjct: 77 ADLVLLVVDSD------LTPVEEEAKLGLLRERGKPVLLVLNKIDLVPESEEEE------ 124
Query: 110 LYGLTTGKEFTSREILQMRPIELFMCSVLKRQGF 143
R++ + + + S L +G
Sbjct: 125 --------LLRERKLELLPDLPVIAVSALPGEGI 150
>gnl|CDD|182934 PRK11058, PRK11058, GTPase HflX; Provisional.
Length = 426
Score = 34.3 bits (79), Expect = 0.016
Identities = 13/42 (30%), Positives = 27/42 (64%), Gaps = 1/42 (2%)
Query: 56 IIDASDRSRFPESKYELDSLLADDALTDVPILILGNKIDIFD 97
++DA+D R E+ ++++L + ++P L++ NKID+ D
Sbjct: 283 VVDAAD-VRVQENIEAVNTVLEEIDAHEIPTLLVMNKIDMLD 323
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 33.8 bits (78), Expect = 0.024
Identities = 20/79 (25%), Positives = 31/79 (39%), Gaps = 7/79 (8%)
Query: 51 DAIVFIIDASDRSRFP-ESKYELDSLLADDALTDVPILILGNKIDIFDAASEDEVRHFFG 109
I+F+ D S+ + E + L L L PI+++ NKIDI D +E+
Sbjct: 249 GVILFLFDPSETCGYSLEEQISL--LEEIKELFKAPIVVVINKIDIADEEKLEEIEASV- 305
Query: 110 LYGLTTGKEFTSREILQMR 128
L G E +
Sbjct: 306 ---LEEGGEEPLKISATKG 321
>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 = 32.5 bits (75), Expect = 0.038
Identities = 14/56 (25%), Positives = 27/56 (48%), Gaps = 5/56 (8%)
Query: 51 DAIVFIIDASDRSRFP-ESKYEL-DSLLADDALTDVPILILGNKIDIFDAASEDEV 104
A++F ID S+ + E + L + L + P++++ NKID+ E+
Sbjct: 81 AAVLFFIDPSETCGYSIEEQLSLFKEIKP---LFNKPVIVVLNKIDLLTEEDLSEI 133
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 33.0 bits (76), Expect = 0.044
Identities = 18/61 (29%), Positives = 34/61 (55%), Gaps = 8/61 (13%)
Query: 50 VDAIVFIIDASDRSRFPESKYELDS---LLADDALTDVPILILGNKID-IFDAASEDEVR 105
D ++ ++DASD PE +L++ +LA+ ++PI+++ NKID + D E+
Sbjct: 272 ADLLLHVVDASD----PEILEKLEAVEDVLAEIGADEIPIILVLNKIDLLEDEEILAELE 327
Query: 106 H 106
Sbjct: 328 R 328
>gnl|CDD|179843 PRK04390, rnpA, ribonuclease P; Reviewed.
Length = 120
Score = 31.6 bits (72), Expect = 0.057
Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 7/45 (15%)
Query: 40 RRVWRDYF-------PAVDAIVFIIDASDRSRFPESKYELDSLLA 77
+RV R++F P VD +V + DR+ ++ EL L+A
Sbjct: 65 KRVIREWFRLNQHRLPPVDFVVRVQRKFDRATAKQAVAELAQLMA 109
>gnl|CDD|133319 cd04119, RJL, Rab GTPase family J-like (RabJ-like). RJLs are found
in many protists and as chimeras with C-terminal DNAJ
domains in deuterostome metazoa. They are not found in
plants, fungi, and protostome metazoa, suggesting a
horizontal gene transfer between protists and
deuterostome metazoa. RJLs lack any known membrane
targeting signal and contain a degenerate
phosphate/magnesium-binding 3 (PM3) motif, suggesting an
impaired ability to hydrolyze GTP. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization.
Length = 168
Score = 31.9 bits (73), Expect = 0.066
Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 6/80 (7%)
Query: 32 DLGGHVQARRVWRDYFPAVDAIVFIIDASDRSRFPE-SKYEL---DSLLADDALTDVPIL 87
DL GH + V +++ ++ + D +DR F + + ++ ++
Sbjct: 55 DLSGHPEYLEVRNEFYKDTQGVLLVYDVTDRQSFEALDSWLKEMKQEGGPHGNMENIVVV 114
Query: 88 ILGNKIDIFD--AASEDEVR 105
+ NKID+ A SEDE R
Sbjct: 115 VCANKIDLTKHRAVSEDEGR 134
>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 = 32.1 bits (73), Expect = 0.068
Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 8/58 (13%)
Query: 47 FPAV--------DAIVFIIDASDRSRFPESKYELDSLLADDALTDVPILILGNKIDIF 96
FPA+ DA + D F E K + +L VPI+++GNKID
Sbjct: 60 FPAMRKLSIQNGDAFALVYSVDDPESFEEVKRLREEILEVKEDKFVPIVVVGNKIDSL 117
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 31.9 bits (74), Expect = 0.085
Identities = 13/45 (28%), Positives = 26/45 (57%), Gaps = 5/45 (11%)
Query: 50 VDAIVFIIDASDRSRFPESKYELDSLLADDALTDVPILILGNKID 94
VD ++F++DA ++ P ++ L+ L P++++ NKID
Sbjct: 85 VDLVLFVVDADEKIG-PGDEFILEKL----KKVKTPVILVLNKID 124
>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 = 31.2 bits (71), Expect = 0.14
Identities = 21/84 (25%), Positives = 37/84 (44%), Gaps = 6/84 (7%)
Query: 28 FTTHDLGGHVQARRVWRDYFPAVD---AIVFIIDAS-DRSRFPESKYELDSLLADDALTD 83
FT D GHV+ R+ + IVF++D++ ++ L +L+ L
Sbjct: 51 FTLIDFPGHVKLRQKLLETIKDSSSLRGIVFVVDSTAFPKEVTDTAEFLYEILSITELLK 110
Query: 84 --VPILILGNKIDIFDAASEDEVR 105
+ ILI NK + F A +++
Sbjct: 111 NGIDILIACNKQESFTARPPKKIK 134
>gnl|CDD|223597 COG0523, COG0523, Putative GTPases (G3E family) [General function
prediction only].
Length = 323
Score = 31.1 bits (71), Expect = 0.17
Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 6/69 (8%)
Query: 38 QARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDSLLADDALTDVPILILGNKIDIFD 97
D +D +V ++DA+ F E + L A+D L +++L NK D+ D
Sbjct: 106 LTDPELADGV-RLDGVVTVVDAA---HFLEGLDAIAEL-AEDQLAFADVIVL-NKTDLVD 159
Query: 98 AASEDEVRH 106
A + +
Sbjct: 160 AEELEALEA 168
>gnl|CDD|206748 cd01855, YqeH, Circularly permuted YqeH GTPase. YqeH is an
essential GTP-binding protein. Depletion of YqeH induces
an excess initiation of DNA replication, suggesting that
it negatively controls initiation of chromosome
replication. The YqeH subfamily is common in eukaryotes
and sporadically present in bacteria with probable
acquisition by plants from chloroplasts. Proteins of the
YqeH family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases.
Length = 191
Score = 30.3 bits (69), Expect = 0.27
Identities = 13/58 (22%), Positives = 28/58 (48%), Gaps = 12/58 (20%)
Query: 53 IVFIIDASDRSRFPESKYELDSLLAD--DALTDVPILILGNKID-IFDAASEDEVRHF 107
+V ++D D FP SL+ + + P++++GNKID + + ++ +
Sbjct: 37 VVHVVDIFD---FP------GSLIPGLAELIGAKPVILVGNKIDLLPKDVKPNRLKQW 85
>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 = 30.6 bits (70), Expect = 0.28
Identities = 25/86 (29%), Positives = 38/86 (44%), Gaps = 12/86 (13%)
Query: 22 SMGDIVFTTHDLGGHVQARRVWRDYFPAVDAIVFIIDASDR----------SRFPESKYE 71
S+ ++ F D+GG R+ W F V AI+F++ S+ +R ES
Sbjct: 157 SIKNLKFRMFDVGGQRSERKKWIHCFEDVTAIIFVVALSEYDQVLVEDESVNRMQESLKL 216
Query: 72 LDSLLADDALTDVP-ILILGNKIDIF 96
DS+ + IL L NK D+F
Sbjct: 217 FDSICNSRWFANTSIILFL-NKKDLF 241
>gnl|CDD|206668 cd01881, Obg_like, Obg-like family of GTPases consist of five
subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1. The
Obg-like subfamily consists of five well-delimited,
ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210,
and NOG1. Four of these groups (Obg, DRG, YyaF/YchF, and
Ygr210) are characterized by a distinct glycine-rich
motif immediately following the Walker B motif (G3 box).
Obg/CgtA is an essential gene that is involved in the
initiation of sporulation and DNA replication in the
bacteria Caulobacter and Bacillus, but its exact
molecular role is unknown. Furthermore, several OBG
family members possess a C-terminal RNA-binding domain,
the TGS domain, which is also present in threonyl-tRNA
synthetase and in bacterial guanosine polyphosphatase
SpoT. Nog1 is a nucleolar protein that might function in
ribosome assembly. The DRG and Nog1 subfamilies are
ubiquitous in archaea and eukaryotes, the Ygr210
subfamily is present in archaea and fungi, and the Obg
and YyaF/YchF subfamilies are ubiquitous in bacteria and
eukaryotes. The Obg/Nog1 and DRG subfamilies appear to
form one major branch of the Obg family and the Ygr210
and YchF subfamilies form another branch. No GEFs, GAPs,
or GDIs for Obg have been identified.
Length = 167
Score = 30.1 bits (68), Expect = 0.30
Identities = 17/57 (29%), Positives = 27/57 (47%), Gaps = 7/57 (12%)
Query: 51 DAIVFIIDASDRS-RFPESKYEL---DSLLADDALTDVPILILGNKIDIFDAASEDE 103
D I+ +IDAS+ P + + + L + P +I+ NKI D ASE+
Sbjct: 77 DLILHVIDASEDCVGDPLEDQKTLNEEVSGSFLFLKNKPEMIVANKI---DMASENN 130
>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 = 30.1 bits (69), Expect = 0.31
Identities = 17/57 (29%), Positives = 32/57 (56%), Gaps = 2/57 (3%)
Query: 51 DAIVFIIDASDRSRFPESKYELDSLLADDALTDVPILILGNKID-IFDAASEDEVRH 106
D ++ ++DASD E ++ +L + D+PI+++ NKID + D E+ +R
Sbjct: 122 DLLLHVVDASD-PDREEQIETVEEVLKELGADDIPIILVLNKIDLLDDEELEERLRA 177
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 30.2 bits (69), Expect = 0.31
Identities = 16/52 (30%), Positives = 27/52 (51%), Gaps = 5/52 (9%)
Query: 50 VDAIVFIIDASDRSRFPESKYELDSLLADDALTDVPILILGNKIDIFDAASE 101
VD I+F++DA D P ++ L+ L T P++++ NKID +
Sbjct: 86 VDLILFVVDA-DEGWGPGDEFILEQL----KKTKTPVILVVNKIDKVKPKTV 132
>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 = 30.2 bits (69), Expect = 0.32
Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 13/77 (16%)
Query: 35 GHV-QARRVWRDYFPAVDAIVFIIDASDRSRFPESKY--ELDSLLADDALTDVPILILGN 91
GH+ +ARR ++ VD ++ ++DA R P S +D + + P LI+ N
Sbjct: 6 GHMAKARREIKEKLKLVDVVIEVLDA----RIPLSSRNPMIDEIRGNK-----PRLIVLN 56
Query: 92 KIDIFD-AASEDEVRHF 107
K D+ D A ++ +++F
Sbjct: 57 KADLADPAVTKQWLKYF 73
>gnl|CDD|206689 cd04102, RabL3, Rab GTPase-like family 3 (Rab-like3). RabL3
(Rab-like3) subfamily. RabL3s 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, RabL3 lacks a prenylation site at the
C-terminus. The specific function of RabL3 remains
unknown.
Length = 204
Score = 29.9 bits (67), Expect = 0.40
Identities = 19/95 (20%), Positives = 40/95 (42%), Gaps = 22/95 (23%)
Query: 32 DLGGHVQARRVWRD----YFPAVDAIVFIIDASDR-SRFPESKYELDSLLADDALT---- 82
D+GG V + + ++ ++ I+F+ D +++ S ++ L++L D
Sbjct: 60 DVGGSVGSAESVKSTRAVFYNQINGIIFVHDLTNKKSSQNLYRWSLEALNRDTFPAGLLV 119
Query: 83 -------------DVPILILGNKIDIFDAASEDEV 104
VP+L++G K+D A + V
Sbjct: 120 TNGDYDSEQFAGNPVPLLVIGTKLDQIPEAKRNWV 154
>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 = 29.7 bits (68), Expect = 0.43
Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 9/65 (13%)
Query: 46 YFPAVDAIVFIIDASDRSRFPESKYELDSLLAD---DALTDVPILILGNKIDIFD--AAS 100
Y+ + + D ++R ES LD L + A ++PI+++GNK D+ D S
Sbjct: 69 YYRGAHGAILVYDVTNR----ESFENLDKWLNELKEYAPPNIPIILVGNKSDLEDERQVS 124
Query: 101 EDEVR 105
+E +
Sbjct: 125 TEEAQ 129
>gnl|CDD|153105 cd01046, Rubrerythrin_like, rubrerythrin-like, diiron-binding
domain. Rubrerythrin-like domain, similar to
rubrerythrin, a nonheme iron binding domain found in
many air-sensitive bacteria and archaea, and member of a
broad superfamily of ferritin-like diiron-carboxylate
proteins. Rubrerythrin is thought to reduce hydrogen
peroxide as part of an oxidative stress protection
system. The rubrerythrin protein has two domains, a
binuclear metal center located within a four-helix
bundle of the rubrerythrin domain, and a rubredoxin
domain. The Rubrerythrin-like domains in this CD are
singular domains (no C-terminus rubredoxin domain) and
are phylogenetically distinct from rubrerythrin domains
of rubrerythrin-rubredoxin proteins.
Length = 123
Score = 28.8 bits (65), Expect = 0.64
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 93 IDIFDAASEDEVRHFFGLYGL 113
D F A++DE RH L GL
Sbjct: 98 HDFFHEAAKDEARHGKMLKGL 118
>gnl|CDD|206739 cd09912, DLP_2, Dynamin-like protein including dynamins,
mitofusins, and guanylate-binding proteins. The dynamin
family of large mechanochemical GTPases includes the
classical dynamins and dynamin-like proteins (DLPs) that
are found throughout the Eukarya. This family also
includes bacterial DLPs. These proteins catalyze
membrane fission during clathrin-mediated endocytosis.
Dynamin consists of five domains; an N-terminal G domain
that binds and hydrolyzes GTP, a middle domain (MD)
involved in self-assembly and oligomerization, a
pleckstrin homology (PH) domain responsible for
interactions with the plasma membrane, GED, which is
also involved in self-assembly, and a proline arginine
rich domain (PRD) that interacts with SH3 domains on
accessory proteins. To date, three vertebrate dynamin
genes have been identified; dynamin 1, which is brain
specific, mediates uptake of synaptic vesicles in
presynaptic terminals; dynamin-2 is expressed
ubiquitously and similarly participates in membrane
fission; mutations in the MD, PH and GED domains of
dynamin 2 have been linked to human diseases such as
Charcot-Marie-Tooth peripheral neuropathy and rare forms
of centronuclear myopathy. Dynamin 3 participates in
megakaryocyte progenitor amplification, and is also
involved in cytoplasmic enlargement and the formation of
the demarcation membrane system. This family also
includes mitofusins (MFN1 and MFN2 in mammals) that are
involved in mitochondrial fusion. Dynamin oligomerizes
into helical structures around the neck of budding
vesicles in a GTP hydrolysis-dependent manner.
Length = 180
Score = 29.1 bits (66), Expect = 0.69
Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 8/67 (11%)
Query: 44 RDYFPAVDAIVFIIDASDRSRFPESKYELDSLLADDALTDV--PILILGNKIDIFDAASE 101
+ P DA++F++ A D+ P ++ E + L + L I + NKID+
Sbjct: 68 ESFLPRADAVIFVLSA-DQ---PLTESEREFL--KEILKWSGKKIFFVLNKIDLLSEEEL 121
Query: 102 DEVRHFF 108
+EV +
Sbjct: 122 EEVLEYS 128
>gnl|CDD|206642 cd00876, Ras, Rat sarcoma (Ras) family of small guanosine
triphosphatases (GTPases). The Ras family of the Ras
superfamily includes classical N-Ras, H-Ras, and K-Ras,
as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG,
Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins.
Ras proteins regulate cell growth, proliferation and
differentiation. Ras is activated by guanine nucleotide
exchange factors (GEFs) that release GDP and allow GTP
binding. Many RasGEFs have been identified. These are
sequestered in the cytosol until activation by growth
factors triggers recruitment to the plasma membrane or
Golgi, where the GEF colocalizes with Ras. Active
GTP-bound Ras interacts with several effector proteins:
among the best characterized are the Raf kinases,
phosphatidylinositol 3-kinase (PI3K), RalGEFs and
NORE/MST1. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 160
Score = 29.0 bits (66), Expect = 0.74
Identities = 14/44 (31%), Positives = 22/44 (50%)
Query: 51 DAIVFIIDASDRSRFPESKYELDSLLADDALTDVPILILGNKID 94
D + + + R F E K + +L DVPI+++GNK D
Sbjct: 72 DGFILVYSITSRESFEEIKNIREQILRVKDKEDVPIVLVGNKCD 115
>gnl|CDD|206749 cd01856, YlqF, Circularly permuted YlqF GTPase. Proteins of the
YlqF family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases. The YlqF subfamily is represented in all
eukaryotes as well as a phylogenetically diverse array
of bacteria (including gram-positive bacteria,
proteobacteria, Synechocystis, Borrelia, and
Thermotoga).
Length = 171
Score = 29.0 bits (66), Expect = 0.74
Identities = 23/77 (29%), Positives = 36/77 (46%), Gaps = 12/77 (15%)
Query: 35 GHVQ-ARRVWRDYFPAVDAIVFIIDASDRSRFPES--KYELDSLLADDALTDVPILILGN 91
GH+ A R ++ VD ++ + DA R P S +LD +L + P LI+ N
Sbjct: 4 GHMAKALRQIKEKLKLVDVVIEVRDA----RIPLSSRNPDLDKILGN-----KPRLIVLN 54
Query: 92 KIDIFDAASEDEVRHFF 108
K D+ D A + +F
Sbjct: 55 KADLADPAKTKKWLKYF 71
>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 = 28.8 bits (65), Expect = 0.78
Identities = 12/46 (26%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 51 DAIVFIIDASDRSRFPESK--YELDSLLADDALTDVPILILGNKID 94
D V + +DRS F +L + ++P++++GNK D
Sbjct: 74 DGFVLVYSITDRSSFDVVSQLLQLIREIKKRDG-EIPVILVGNKAD 118
>gnl|CDD|206743 cd11383, YfjP, YfjP GTPase. The Era (E. coli Ras-like
protein)-like YfjP subfamily includes several
uncharacterized bacterial GTPases that are similar to
Era. They generally show sequence conservation in the
region between the Walker A and B motifs (G1 and G3 box
motifs), to the exclusion of other GTPases. Era is
characterized by a distinct derivative of the KH domain
(the pseudo-KH domain) which is located C-terminal to
the GTPase domain.
Length = 140
Score = 28.5 bits (64), Expect = 0.81
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 11/70 (15%)
Query: 32 DLGGHVQARR-------VWRDYFPAVDAIVFIIDASDRSRFPESKYELDSLLADDALTDV 84
DL G + R ++R P D +++++DA DR+ + + L L DA
Sbjct: 51 DLPGVGERGRRDREYEELYRRLLPEADLVLWLLDADDRALAADHDFYLLPLAGHDA---- 106
Query: 85 PILILGNKID 94
P+L + N++D
Sbjct: 107 PLLFVLNQVD 116
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 28.9 bits (66), Expect = 0.90
Identities = 14/54 (25%), Positives = 24/54 (44%), Gaps = 5/54 (9%)
Query: 53 IVFIIDASDRSRFPESKYE--LDSLLA-DDALTDVPILILGNKIDIFDAASEDE 103
++ ++D P Y+ + L L D P +++ NKID+ D E E
Sbjct: 240 LLHLVDIEAVD--PVEDYKTIRNELEKYSPELADKPRILVLNKIDLLDEEEERE 291
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 28.7 bits (65), Expect = 1.2
Identities = 15/55 (27%), Positives = 24/55 (43%), Gaps = 8/55 (14%)
Query: 53 IVFIIDAS-DRSRFPESKY-----ELDSLLADDALTDVPILILGNKIDIFDAASE 101
++ +ID S R P Y EL+ L + P +++ NKID+ E
Sbjct: 241 LLHVIDLSPIDGRDPIEDYQTIRNELEKY--SPKLAEKPRIVVLNKIDLPLDEEE 293
>gnl|CDD|133090 cd06232, M14-like_5, Peptidase M14-like domain; uncharacterized
subfamily. Peptidase M14-like domain of a functionally
uncharacterized subgroup of the M14 family of
metallocarboxypeptidases (MCPs). The M14 family are
zinc-binding carboxypeptidases (CPs) which hydrolyze
single, C-terminal amino acids from polypeptide chains,
and have a recognition site for the free C-terminal
carboxyl group, which is a key determinant of
specificity. Two major subfamilies of the M14 family,
defined based on sequence and structural homology, are
the A/B and N/E subfamilies. Enzymes belonging to the
A/B subfamily are normally synthesized as inactive
precursors containing preceding signal peptide,
followed by an N-terminal pro-region linked to the
enzyme; these proenzymes are called
procarboxypeptidases. The A/B enzymes can be further
divided based on their substrate specificity;
Carboxypeptidase A-like (CPA-like) enzymes favor
hydrophobic residues while carboxypeptidase B-like
(CPB-like) enzymes only cleave the basic residues
lysine or arginine. The A forms have slightly different
specificities, with Carboxypeptidase A1 (CPA1)
preferring aliphatic and small aromatic residues, and
CPA2 preferring the bulky aromatic side chains. Enzymes
belonging to the N/E subfamily enzymes are not produced
as inactive precursors and instead rely on their
substrate specificity and subcellular
compartmentalization to prevent inappropriate
cleavages. They contain an extra C-terminal
transthyretin-like domain, thought to be involved in
folding or formation of oligomers. MCPs can also be
classified based on their involvement in specific
physiological processes; the pancreatic MCPs
participate only in alimentary digestion and include
carboxypeptidase A and B (A/B subfamily), while others,
namely regulatory MCPs or the N/E subfamily, are
involved in more selective reactions, mainly in
non-digestive tissues and fluids, acting on blood
coagulation/fibrinolysis, inflammation and local
anaphylaxis, pro-hormone and neuropeptide processing,
cellular response and others. Another MCP subfamily,
is that of succinylglutamate desuccinylase
/aspartoacylase, which hydrolyzes N-acetyl-L-aspartate
(NAA), and deficiency in which is the established cause
of Canavan disease. Another subfamily (referred to as
subfamily C) includes an exceptional type of activity
in the MCP family, that of dipeptidyl-peptidase
activity of gamma-glutamyl-(L)-meso-diaminopimelate
peptidase I which is involved in bacterial cell wall
metabolism.
Length = 240
Score = 28.1 bits (63), Expect = 1.5
Identities = 13/42 (30%), Positives = 15/42 (35%), Gaps = 6/42 (14%)
Query: 21 LSMGDIVFTTHDLGG------HVQARRVWRDYFPAVDAIVFI 56
LS G I + L G Q R V Y +D V I
Sbjct: 2 LSAGQIAYELAVLPGIEFAARSRQGRPVTGRYVAGLDHPVVI 43
>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 = 27.5 bits (62), Expect = 2.3
Identities = 9/45 (20%), Positives = 22/45 (48%), Gaps = 7/45 (15%)
Query: 51 DAIVFIIDASDRSRFPESKYELDSLLADDALTDVPILILGNKIDI 95
D ++ ++DAS+ + + L + P++++ NK D+
Sbjct: 84 DLVLLVVDASE-------GLDEEDLEILELPAKKPVIVVLNKSDL 121
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 27.8 bits (63), Expect = 2.7
Identities = 11/54 (20%), Positives = 24/54 (44%), Gaps = 7/54 (12%)
Query: 51 DAIVFIIDASDRSRFPESKYELDSLLADDALTDVPILILGNKIDIFDAASEDEV 104
D ++ ++DAS+ + + L D P++++ NK D+ +E
Sbjct: 296 DLVLLVLDASE-------PLTEEDDEILEELKDKPVIVVLNKADLTGEIDLEEE 342
>gnl|CDD|225176 COG2267, PldB, Lysophospholipase [Lipid metabolism].
Length = 298
Score = 27.7 bits (62), Expect = 2.9
Identities = 14/62 (22%), Positives = 22/62 (35%), Gaps = 7/62 (11%)
Query: 10 HMPTLHPTSEELSMGDIVFTTHDLGGHVQARR-------VWRDYFPAVDAIVFIIDASDR 62
H +++L+ DL GH ++ R + DY +DA V I D
Sbjct: 46 HSGRYEELADDLAARGFDVYALDLRGHGRSPRGQRGHVDSFADYVDDLDAFVETIAEPDP 105
Query: 63 SR 64
Sbjct: 106 GL 107
>gnl|CDD|206667 cd01879, FeoB, Ferrous iron transport protein B (FeoB) family.
Ferrous iron transport protein B (FeoB) subfamily. E.
coli has an iron(II) transport system, known as feo,
which may make an important contribution to the iron
supply of the cell under anaerobic conditions. FeoB has
been identified as part of this transport system. FeoB
is a large 700-800 amino acid integral membrane protein.
The N terminus contains a P-loop motif suggesting that
iron transport may be ATP dependent.
Length = 159
Score = 27.0 bits (61), Expect = 3.0
Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 13/70 (18%)
Query: 30 THDLGGHVQARRVWRDY--FPAVDAIVFIIDAS--DRSRFPESKYELDSLLADDALTDVP 85
T+ L + + +V RD+ D IV ++DA+ +R+ + L L + +P
Sbjct: 54 TYSLTPYSEDEKVARDFLLGEEPDLIVNVVDATNLERNLY------LTLQLLE---LGLP 104
Query: 86 ILILGNKIDI 95
+++ N ID
Sbjct: 105 VVVALNMIDE 114
>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 = 27.2 bits (60), Expect = 3.1
Identities = 16/69 (23%), Positives = 34/69 (49%), Gaps = 7/69 (10%)
Query: 32 DLGGHVQARRVWRDYFPAVDAIVFIIDASDRSRF---PESKYELDSLLADDALTDVPILI 88
D G + R + + Y+ + +A++ D + F PE E++ + +T ++
Sbjct: 62 DTAGQERFRSITQSYYRSANALILTYDITCEESFRCLPEWLREIEQYANNKVIT----IL 117
Query: 89 LGNKIDIFD 97
+GNKID+ +
Sbjct: 118 VGNKIDLAE 126
>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 = 27.2 bits (61), Expect = 3.1
Identities = 18/54 (33%), Positives = 30/54 (55%), Gaps = 5/54 (9%)
Query: 44 RDYFPAVDAIVFIIDASDRSRFPESKYELDSLLADDALTDVPILILGNKIDIFD 97
RD AV +V+ D ++R F + +D + D+ DV I+++GNK D+ D
Sbjct: 71 RDSSVAV--VVY--DITNRQSFDNTDKWIDDVR-DERGNDVIIVLVGNKTDLSD 119
>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 = 27.2 bits (60), Expect = 3.3
Identities = 13/57 (22%), Positives = 23/57 (40%), Gaps = 1/57 (1%)
Query: 46 YFPAVDAIVFIIDASDRSRFPESKYELDSLLADDALTDVPILILGNKIDIFDAASED 102
Y A++ D S+ E + L D A D ++GNK+D+ + +
Sbjct: 64 YCRGAAAVILTYDVSNVQSLEELEDRFLGLT-DTANEDCLFAVVGNKLDLTEEGALA 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 = 27.1 bits (60), Expect = 3.3
Identities = 13/66 (19%), Positives = 30/66 (45%), Gaps = 2/66 (3%)
Query: 32 DLGGHVQARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDSLLA--DDALTDVPILIL 89
D+GG ++ Y A+ + D ++ F + L + +++ T ++++
Sbjct: 56 DIGGQQIGGKMLDKYIYGAQAVCLVYDITNSQSFENLEDWLSVVKKVNEESETKPKMVLV 115
Query: 90 GNKIDI 95
GNK D+
Sbjct: 116 GNKTDL 121
>gnl|CDD|117515 pfam08948, DUF1859, Domain of unknown function (DUF1859). This
domain has no known function. It is predominantly found
in the N-terminus of bacteriophage spike proteins.
Length = 126
Score = 26.6 bits (58), Expect = 3.5
Identities = 7/48 (14%), Positives = 13/48 (27%), Gaps = 4/48 (8%)
Query: 23 MGDIVFTTHDLGGHVQARRVWRDYFP--AVDAIVFIIDAS--DRSRFP 66
G + G ++ + YFP F+ + P
Sbjct: 66 DGAFEIDVEETGQRIKCPAGKQGYFPLLVPGRAKFVARHLGSGKKSVP 113
>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 = 26.7 bits (60), Expect = 3.6
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 5/51 (9%)
Query: 46 YFPAVDAIVFIIDASDRSRFPESKYELDSLL--ADDALTDVPILILGNKID 94
Y+ + + D + R F K L+ +L AD+ +VPI+++GNK D
Sbjct: 68 YYRGAQGFLLVYDITSRDSFENVKKWLEEILRHADE---NVPIVLVGNKCD 115
>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 = 26.7 bits (60), Expect = 4.1
Identities = 15/65 (23%), Positives = 30/65 (46%), Gaps = 13/65 (20%)
Query: 83 DVPILILGNKIDIFDAASEDEVRHFFGLYGLTTGKEFTSRE-ILQM----RPIELFMCSV 137
+VPI+++G KID+ D + L L ++ + E ++ ++ CS
Sbjct: 104 NVPIILVGTKIDLRDDGNT--------LKKLEKKQKPITPEEGEKLAKEIGAVKYMECSA 155
Query: 138 LKRQG 142
L ++G
Sbjct: 156 LTQEG 160
>gnl|CDD|237536 PRK13873, PRK13873, conjugal transfer ATPase TrbE; Provisional.
Length = 811
Score = 27.2 bits (61), Expect = 4.6
Identities = 12/21 (57%), Positives = 14/21 (66%)
Query: 62 RSRFPESKYELDSLLADDALT 82
R R PE+ LD+LLAD LT
Sbjct: 197 RVRVPETPMYLDALLADQPLT 217
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 27.1 bits (61), Expect = 4.7
Identities = 14/55 (25%), Positives = 25/55 (45%), Gaps = 6/55 (10%)
Query: 51 DAIVFIIDASDRSRFPESKYELDSLLADDALTDVPILILGNKIDIFDAASEDEVR 105
D ++F++DAS P K D L + PI+++ NK D+ + +
Sbjct: 298 DLVLFVLDASQ----PLDK--EDLALIELLPKKKPIIVVLNKADLVSKIELESEK 346
>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 = 4.8
Identities = 15/60 (25%), Positives = 26/60 (43%), Gaps = 4/60 (6%)
Query: 53 IVFIIDASD-RSRFPESKYE--LDSLLA-DDALTDVPILILGNKIDIFDAASEDEVRHFF 108
++ +ID S P YE + L L + P +++ NKID+ D +E+
Sbjct: 239 LLHLIDISPEDGSDPIEDYEIIRNELKKYSPELAEKPRIVVLNKIDLLDEEELEELLKEL 298
>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 = 27.0 bits (61), Expect = 4.8
Identities = 15/44 (34%), Positives = 26/44 (59%), Gaps = 1/44 (2%)
Query: 51 DAIVFIIDASDRSRFPESKYELDSLLADDALTDVPILILGNKID 94
D ++ ++DASD R E ++ +L + D+P L++ NKID
Sbjct: 270 DLLLHVVDASDPDRE-EQIEAVEKVLEELGAEDIPQLLVYNKID 312
>gnl|CDD|197466 smart00010, small_GTPase, Small GTPase of the Ras superfamily;
ill-defined subfamily. SMART predicts Ras-like small
GTPases of the ARF, RAB, RAN, RAS, and SAR subfamilies.
Others that could not be classified in this way are
predicted to be members of the small GTPase superfamily
without predictions of the subfamily.
Length = 166
Score = 26.4 bits (59), Expect = 5.0
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 53 IVFIIDASDRSRFPESKYELDSLLADDALTDVPILILGNKID 94
+V+ I DR F E + +L DVPI+++GNK D
Sbjct: 79 LVYSIT--DRQSFEEIAKFREQILRVKDRDDVPIVLVGNKCD 118
>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 = 26.7 bits (60), Expect = 5.5
Identities = 14/59 (23%), Positives = 29/59 (49%), Gaps = 5/59 (8%)
Query: 50 VDAIVFIIDASDRSRFPESKYELDSLLADDALTDVPILILGNKIDIFDAASEDEVRHFF 108
D + ++DA +YEL+ L+ + +P +++ NKID+ + ++E E
Sbjct: 86 TDLALLVVDA----GVGPGEYELE-LIEELKERKIPYIVVINKIDLGEESAELEKLEKK 139
>gnl|CDD|181721 PRK09242, PRK09242, tropinone reductase; Provisional.
Length = 257
Score = 26.6 bits (59), Expect = 5.9
Identities = 25/95 (26%), Positives = 37/95 (38%), Gaps = 9/95 (9%)
Query: 18 SEELSMG-DIVFTTHDLGGHVQARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDSLL 76
E L +G D++ D QAR + FP + D SD E + + +
Sbjct: 27 REFLGLGADVLIVARDADALAQARDELAEEFPEREVHGLAADVSD----DEDRRAILDWV 82
Query: 77 ADDALTDVPILILGNKIDIFDAA---SEDEVRHFF 108
D + IL+ +I AA +EDE R F
Sbjct: 83 EDHW-DGLHILVNNAGGNIRKAAIDYTEDEWRGIF 116
>gnl|CDD|206715 cd04148, RGK, Rem, Rem2, Rad, Gem/Kir (RGK) subfamily of Ras
GTPases. RGK subfamily. The RGK (Rem, Rem2, Rad,
Gem/Kir) subfamily of Ras GTPases are expressed in a
tissue-specific manner and are dynamically regulated by
transcriptional and posttranscriptional mechanisms in
response to environmental cues. RGK proteins bind to the
beta subunit of L-type calcium channels, causing
functional down-regulation of these voltage-dependent
calcium channels, and either termination of
calcium-dependent secretion or modulation of electrical
conduction and contractile function. Inhibition of
L-type calcium channels by Rem2 may provide a mechanism
for modulating calcium-triggered exocytosis in
hormone-secreting cells, and has been proposed to
influence the secretion of insulin in pancreatic beta
cells. RGK proteins also interact with and inhibit the
Rho/Rho kinase pathway to modulate remodeling of the
cytoskeleton. Two characteristics of RGK proteins cited
in the literature are N-terminal and C-terminal
extensions beyond the GTPase domain typical of Ras
superfamily members. The N-terminal extension is not
conserved among family members; the C-terminal extension
is reported to be conserved among the family and lack
the CaaX prenylation motif typical of
membrane-associated Ras proteins. However, a putative
CaaX motif has been identified in the alignment of the
C-terminal residues of this CD.
Length = 219
Score = 26.6 bits (59), Expect = 5.9
Identities = 15/45 (33%), Positives = 24/45 (53%)
Query: 51 DAIVFIIDASDRSRFPESKYELDSLLADDALTDVPILILGNKIDI 95
DA V + +DRS F ++ L D+PI+++GNK D+
Sbjct: 74 DAYVIVYSVTDRSSFEKASELRIQLRRARQAEDIPIILVGNKSDL 118
>gnl|CDD|226590 COG4105, ComL, DNA uptake lipoprotein [General function prediction
only].
Length = 254
Score = 26.5 bits (59), Expect = 6.4
Identities = 16/67 (23%), Positives = 22/67 (32%), Gaps = 13/67 (19%)
Query: 14 LHPTSEELSMGDIVFTTHDLGGHVQARRVWRDYFPAVDAIV----FIIDASDRSRFPESK 69
L+PT D + L Q V RD A A + R+P S+
Sbjct: 100 LYPTHPNA---DYAYYLKGLSYFFQIDDVTRDQSAARAAFAAFKELV------QRYPNSR 150
Query: 70 YELDSLL 76
Y D+
Sbjct: 151 YAPDAKA 157
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 26.6 bits (60), Expect = 6.5
Identities = 27/94 (28%), Positives = 40/94 (42%), Gaps = 23/94 (24%)
Query: 53 IVFIIDAS-DRSRFPESKYEL--DSL-LADDALTDVPILILGNKIDIFDAASEDEVRHFF 108
IV +ID S R P YE L L + L + P +++ NK+D+ +A E+ + F
Sbjct: 240 IVHVIDMSGSEGRDPIEDYEKINKELKLYNPRLLERPQIVVANKMDLPEA--EENLEEF- 296
Query: 109 GLYGLTTGKEFTSREILQMRPIELFMCSVLKRQG 142
KE ++ PI S L QG
Sbjct: 297 --------KEKLGPKVF---PI-----SALTGQG 314
>gnl|CDD|153428 cd08001, WGR_PARP1_like, WGR domain of poly(ADP-ribose) polymerase
1 and similar proteins. The WGR domain is found in a
variety of eukaryotic poly(ADP-ribose) polymerases
(PARPs). It has been called WGR after the most conserved
central motif of the domain. The domain typically occurs
together with a catalytic PARP domain, and is between 70
and 80 residues in length. It has been proposed to
function as a nucleic acid binding domain. PARPs
catalyze the NAD(+)-dependent synthesis of ADP-ribose
polymers and their addition to various nuclear proteins.
Higher eukaryotes contain several PARPs and and there
may be up to 17 human PARP-like proteins, with three of
them (PARP-1, PARP-2, and PARP-3) containing a WGR
domain. The synthesis of poly-ADP-ribose requires
multiple enzymatic activities for initiation,
trans-ADP-ribosylation, elongation, branching, and
release of the polymer from the enzyme. This subfamily
is composed of vertebrate PARP-1 and similar proteins,
including Arabidopsis thaliana PARP-1 and PARP-3. PARP-1
is the best-studied among the PARPs. It is a widely
expressed nuclear chromatin-associated enzyme that
possesses auto-mono-ADP-ribosylation (initiation),
elongation, and branching activities. PARP-1 is
implicated in DNA damage and cell death pathways and is
important in maintaining genomic stability and
regulating cell proliferation, differentiation, neuronal
function, inflammation, and aging.
Length = 104
Score = 25.6 bits (57), Expect = 7.4
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 87 LILGNKIDIFDAASEDEVRHFFGLYGLTTGKEFTSREILQMRP 129
I GNK++ F + E+ F LY TG +F +R+ + +P
Sbjct: 53 TIGGNKLEEFSS-LEEAKMAFEELYEEKTGNDFENRKNFKKKP 94
>gnl|CDD|188547 TIGR04032, toxin_SdpC, antimicrobial peptide, SdpC family. This
protein family contains the antimicrobial peptide SdpC,
used in cannibalistic killing by Bacillus subtilis, and
related sequences in species as distant as Myxococcus
xanthus from the Deltaproteobacteria. A conserved gene
neighborhood includes proteins associated with immunity.
Length = 172
Score = 25.8 bits (57), Expect = 8.0
Identities = 13/48 (27%), Positives = 19/48 (39%), Gaps = 7/48 (14%)
Query: 57 IDASDRSRFPESKYELDSLLADDALTDVPILILGNKIDIFDAASEDEV 104
D + R E+ Y D L D+ LT L+ +AA+E
Sbjct: 59 KDPAYFDRLKEAVYSGDPLKVDELLTKGGELLQ-------EAAAESTA 99
>gnl|CDD|133344 cd04144, Ras2, Rat sarcoma (Ras) family 2 of small guanosine
triphosphatases (GTPases). The Ras2 subfamily, found
exclusively in fungi, was first identified in Ustilago
maydis. In U. maydis, Ras2 is regulated by Sql2, a
protein that is homologous to GEFs (guanine nucleotide
exchange factors) of the CDC25 family. Ras2 has been
shown to induce filamentous growth, but the signaling
cascade through which Ras2 and Sql2 regulate cell
morphology is not known. Most Ras proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Ras proteins.
Length = 190
Score = 26.0 bits (57), Expect = 8.3
Identities = 20/54 (37%), Positives = 28/54 (51%), Gaps = 7/54 (12%)
Query: 53 IVFIIDASDRSRFP--ESKYELDSLLADDALTDVPILILGNKIDIFDAASEDEV 104
+V+ I + RS F E E + D++ DVPI+I+GNK D E EV
Sbjct: 76 LVYSI--TSRSTFERVERFREQIQRVKDESAADVPIMIVGNKCDKV---YEREV 124
>gnl|CDD|115510 pfam06858, NOG1, Nucleolar GTP-binding protein 1 (NOG1). This
family represents a conserved region of approximately
60 residues in length within nucleolar GTP-binding
protein 1 (NOG1). In S. cerevisiae, the NOG1 gene has
been shown to be essential for cell viability,
suggesting that NOG1 may play an important role in
nucleolar functions. Family members include eukaryotic,
bacterial and archaeal proteins.
Length = 58
Score = 24.5 bits (54), Expect = 8.3
Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 10/49 (20%)
Query: 51 DAIVFIIDASDRSRFPESK-----YELDSLLADDALTDVPILILGNKID 94
A++F+ D S++ + + E+ L + P++++ NKID
Sbjct: 15 AAVLFVFDPSEQCGYSLEEQLHLFKEIKPLFK-----NKPVIVVLNKID 58
>gnl|CDD|132262 TIGR03218, catechol_dmpH, 4-oxalocrotonate decarboxylase. Members
of this protein family are 4-oxalocrotonate
decarboxylase. Note that this protein, as characterized
(indirectly) in Pseudomonas sp. strain CF600, was
inactive except when coexpressed with DmpE,
2-oxopent-4-enoate hydratase, a homologous protein from
the same operon. Both of these enzymes are active in the
degradation of catechol, a common intermediate in the
degradation of aromatic compounds such as benzoate,
toluene, phenol, dimethylphenol (dmp), salicylate, etc
[Energy metabolism, Other].
Length = 263
Score = 26.3 bits (58), Expect = 8.5
Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 17/72 (23%)
Query: 14 LHPTSEELSMGDIVFTT-HDLGG---HVQARRVWRDY-FPAVDAIVFIIDASDRSRFPES 68
+HP E +I F T L G H+ D+ PAV+ +ID SR+ +
Sbjct: 104 IHPKVE----AEIAFVTKAPLKGPGCHIGDVLAATDFVMPAVE----VID----SRYRDF 151
Query: 69 KYELDSLLADDA 80
K++L S++AD+
Sbjct: 152 KFDLKSVIADNT 163
>gnl|CDD|234593 PRK00046, murB, UDP-N-acetylenolpyruvoylglucosamine reductase;
Provisional.
Length = 334
Score = 25.9 bits (58), Expect = 9.0
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 67 ESKYELDSLLADDALTDVPILILG 90
ES+ +L LAD +P+L+LG
Sbjct: 28 ESEEQLLEALADARAAGLPVLVLG 51
>gnl|CDD|217066 pfam02492, cobW, CobW/HypB/UreG, nucleotide-binding domain. This
domain is found in HypB, a hydrogenase expression /
formation protein, and UreG a urease accessory protein.
Both these proteins contain a P-loop nucleotide binding
motif. HypB has GTPase activity and is a guanine
nucleotide binding protein. It is not known whether UreG
binds GTP or some other nucleotide. Both enzymes are
involved in nickel binding. HypB can store nickel and is
required for nickel dependent hydrogenase expression.
UreG is required for functional incorporation of the
urease nickel metallocenter. GTP hydrolysis may required
by these proteins for nickel incorporation into other
nickel proteins. This family of domains also contains
P47K, a Pseudomonas chlororaphis protein needed for
nitrile hydratase expression, and the cobW gene product,
which may be involved in cobalamin biosynthesis in
Pseudomonas denitrificans.
Length = 178
Score = 25.7 bits (57), Expect = 9.8
Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 11/52 (21%)
Query: 50 VDAIVFIIDASDRSRFPESKYELDSLLADDALT--DVPILILGNKIDIFDAA 99
+D +V ++D + E++ E A D + D LI+ NK D+ A
Sbjct: 115 LDGVVTVVDVA------ETEGEDIPEKAPDQIAFAD---LIVINKTDLAPAV 157
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
0.324 0.141 0.427
Gapped
Lambda K H
0.267 0.0791 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,351,081
Number of extensions: 784584
Number of successful extensions: 1092
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1064
Number of HSP's successfully gapped: 118
Length of query: 155
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 66
Effective length of database: 6,990,096
Effective search space: 461346336
Effective search space used: 461346336
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 55 (24.8 bits)