RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy871
(249 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 = 267 bits (685), Expect = 1e-91
Identities = 121/245 (49%), Positives = 140/245 (57%), Gaps = 55/245 (22%)
Query: 4 IWDWFTGVLGYLGLWTKSGKLLFLGLDNAGKTTLLHMLKDDRLAQPVPTLHPILGYLGLW 63
I+DWF VL LGL+ K K++FLGLDNAGKTTLLHMLKDDRLAQ VPTLHP L +
Sbjct: 2 IFDWFYNVLSSLGLYKKEAKIVFLGLDNAGKTTLLHMLKDDRLAQHVPTLHPTSEELTI- 60
Query: 64 TKSGKLLFLGLDNAGKTTLLHMLKDDRLAQPVPTLHPTRRVWKDYFPAVDAIVFLVDTSD 123
G + F D G RRVWKDYFP VD
Sbjct: 61 ---GNVKFTTFDLGGHEQA-------------------RRVWKDYFPEVDG--------- 89
Query: 124 RERFEESKSELQCLLTDESLASSIVFLVDTSDRERFEESKSELQCLLTDESLASCPVLIL 183
IVFLVD +D ERF+ESK EL LL DE LA+ P+LIL
Sbjct: 90 -----------------------IVFLVDAADPERFQESKEELDSLLNDEELANVPILIL 126
Query: 184 GNKIDKHGAASEEEIRQYFGLYGLTTGKVATPRSEMSGRPIELFMCSVLMRQGYGDGFRW 243
GNKIDK GA SEEE+R+ GLYG TTGK + RP+E+FMCSV+ RQGYG+GFRW
Sbjct: 127 GNKIDKPGAVSEEELREALGLYGTTTGKGGVSLKVSNIRPVEVFMCSVVKRQGYGEGFRW 186
Query: 244 LANYI 248
L+ Y+
Sbjct: 187 LSQYL 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 = 212 bits (540), Expect = 1e-69
Identities = 110/243 (45%), Positives = 131/243 (53%), Gaps = 60/243 (24%)
Query: 6 DWFTGVLGYLGLWTKSGKLLFLGLDNAGKTTLLHMLKDDRLAQPVPTLHPILGYLGLWTK 65
DWF +L LGLW K K+LFLGLDNAGKTTLLHMLK+DRLAQ PT HP L +
Sbjct: 2 DWFYDILASLGLWNKHAKILFLGLDNAGKTTLLHMLKNDRLAQHQPTQHPTSEELAI--- 58
Query: 66 SGKLLFLGLDNAGKTTLLHMLKDDRLAQPVPTLHPTRRVWKDYFPAVDAIVFLVDTSDRE 125
G + F D G RR+WKDYFP V+
Sbjct: 59 -GNIKFTTFDLGGHQQ-------------------ARRLWKDYFPEVNG----------- 87
Query: 126 RFEESKSELQCLLTDESLASSIVFLVDTSDRERFEESKSELQCLLTDESLASCPVLILGN 185
IV+LVD D+ERF ESK EL LL+DE LA+ P LILGN
Sbjct: 88 ---------------------IVYLVDAYDKERFAESKRELDALLSDEELATVPFLILGN 126
Query: 186 KIDKHGAASEEEIRQYFGLYGLTTGKVATPRSEMSGRPIELFMCSVLMRQGYGDGFRWLA 245
KID AASE+E+R GL TTGK ++ RP+E+FMCSV+ R GYG+GF+WL+
Sbjct: 127 KIDAPYAASEDELRYALGLTNTTTGK-----GKVGVRPVEVFMCSVVRRMGYGEGFKWLS 181
Query: 246 NYI 248
YI
Sbjct: 182 QYI 184
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 186 bits (475), Expect = 6e-60
Identities = 73/215 (33%), Positives = 99/215 (46%), Gaps = 66/215 (30%)
Query: 56 ILGYLGLWTKSGKLLFLGLDNAGKTTLLHMLKDDRLAQPVPTLHPT-------------- 101
IL L W K ++L LGLDNAGKTT+L+ LK + +PT+
Sbjct: 4 ILAKLFGWNKEMRILILGLDNAGKTTILYKLKLGEIVTTIPTIGFNVETVTYKNVKFTVW 63
Query: 102 --------RRVWKDYFPAVDAIVFLVDTSDRERFEESKSELQCLLTDESLASSIVFLVDT 153
R +W++YFP DA++F+VD++DR+R EE+K EL LL +E
Sbjct: 64 DVGGQESLRPLWRNYFPNTDAVIFVVDSADRDRIEEAKEELHALLNEE------------ 111
Query: 154 SDRERFEESKSELQCLLTDESLASCPVLILGNKIDKHGAASEEEIRQYFGLYGLTTGKVA 213
EL P+LIL NK D GA SE EIR+ GL+ L
Sbjct: 112 -----------ELAD---------APLLILANKQDLPGAMSEAEIRELLGLHELKD---- 147
Query: 214 TPRSEMSGRPIELFMCSVLMRQGYGDGFRWLANYI 248
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 = 126 bits (318), Expect = 2e-36
Identities = 59/201 (29%), Positives = 84/201 (41%), Gaps = 66/201 (32%)
Query: 68 KLLFLGLDNAGKTTLLHMLKDDRLAQPVPTLH----------------------PTRRVW 105
++L LGLD AGKTT+L+ LK + +PT+ R +W
Sbjct: 1 RILMLGLDGAGKTTILYKLKLGEVVTTIPTIGFNVETVEYKNVKFTVWDVGGQDKIRPLW 60
Query: 106 KDYFPAVDAIVFLVDTSDRERFEESKSELQCLLTDESLASSIVFLVDTSDRERFEESKSE 165
K Y+ D ++F+VD+SDRER EE+K+EL LL +E E
Sbjct: 61 KHYYENTDGLIFVVDSSDRERIEEAKNELHKLLNEE-----------------------E 97
Query: 166 LQCLLTDESLASCPVLILGNKIDKHGAASEEEIRQYFGLYGLTTGKVATPRSEMSGRPIE 225
L+ P+LIL NK D GA +E E+ + GL + GR
Sbjct: 98 LKG---------APLLILANKQDLPGALTESELIELLGLESIK------------GRRWH 136
Query: 226 LFMCSVLMRQGYGDGFRWLAN 246
+ CS + G +G WL
Sbjct: 137 IQPCSAVTGDGLDEGLDWLIE 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 = 86.2 bits (214), Expect = 5e-21
Identities = 63/235 (26%), Positives = 92/235 (39%), Gaps = 89/235 (37%)
Query: 23 KLLFLGLDNAGKTTLLHMLKDDRLAQPVPTLHPILGY-----------LGLWTKSGKLLF 71
++L LGLDNAGKTT+L + + T+ P LG+ L +W
Sbjct: 16 RILMLGLDNAGKTTILKKFNG----EDISTISPTLGFNIKTLEYNGYKLNIW-------- 63
Query: 72 LGLDNAGKTTLLHMLKDDRLAQPVPTLHPTRRVWKDYFPAVDAIVFLVDTSDRERFEESK 131
D G+ +L R W++YF + DA++++VD+SDR R E+ K
Sbjct: 64 ---DVGGQKSL-------------------RSYWRNYFESTDALIWVVDSSDRARLEDCK 101
Query: 132 SELQCLLTDESLASSIVFLVDTSDRERFEESKSELQCLLTDESLASCPVLILGNKIDKHG 191
ELQ LL +E LA + +LI NK D G
Sbjct: 102 RELQKLLVEERLAGA--------------------------------TLLIFANKQDLPG 129
Query: 192 AASEEEIRQYFGLYGLTTGKVATPRSEMSGRPIELFMCSVLMRQGYGDGFRWLAN 246
A S EEIR+ L + + +F CS + + DG WL +
Sbjct: 130 ALSPEEIREVLELDSIKS------------HHWRIFGCSAVTGENLLDGIDWLVD 172
>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 = 85.9 bits (213), Expect = 6e-21
Identities = 56/201 (27%), Positives = 81/201 (40%), Gaps = 66/201 (32%)
Query: 68 KLLFLGLDNAGKTTLLHMLKDDRLAQPVPTL-----------------------HPTRRV 104
++L LGLD+AGK+TLL+ LK L +PT+ R V
Sbjct: 1 QVLLLGLDSAGKSTLLYKLKHAELVTTIPTVGFNVEMLQLEKHLSLTVWDVGGQEKMRTV 60
Query: 105 WKDYFPAVDAIVFLVDTSDRERFEESKSELQCLLTDESLASSIVFLVDTSDRERFEESKS 164
WK Y D +V++VD+SD R +ES+ EL+ +L +E +
Sbjct: 61 WKCYLENTDGLVYVVDSSDEARLDESQKELKHILKNEHIKGV------------------ 102
Query: 165 ELQCLLTDESLASCPVLILGNKIDKHGAASEEEIRQYFGLYGLTTGKVATPRSEMSGRPI 224
PV++L NK D GA + EEI + F L S R
Sbjct: 103 --------------PVVLLANKQDLPGALTAEEITRRFKLKKYC-----------SDRDW 137
Query: 225 ELFMCSVLMRQGYGDGFRWLA 245
+ CS + +G + FR LA
Sbjct: 138 YVQPCSAVTGEGLAEAFRKLA 158
>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 = 84.0 bits (208), Expect = 3e-20
Identities = 54/201 (26%), Positives = 82/201 (40%), Gaps = 66/201 (32%)
Query: 68 KLLFLGLDNAGKTTLLHMLKDDRLAQPVPTL----------------------HPTRRVW 105
++L LGLD AGKTT+L+ L+ + +PT+ R W
Sbjct: 1 RILILGLDGAGKTTILYRLQVGEVVTTIPTIGFNVETVTYKNLKFQVWDLGGQTSIRPYW 60
Query: 106 KDYFPAVDAIVFLVDTSDRERFEESKSELQCLLTDESLASSIVFLVDTSDRERFEESKSE 165
+ Y+ DAI+++VD++DR+R SKSEL +L +E L +
Sbjct: 61 RCYYSNTDAIIYVVDSTDRDRLGISKSELHAMLEEEELKDA------------------- 101
Query: 166 LQCLLTDESLASCPVLILGNKIDKHGAASEEEIRQYFGLYGLTTGKVATPRSEMSGRPIE 225
+L+ NK D GA SE E+ + GL SE+ R +
Sbjct: 102 -------------VLLVFANKQDMPGALSEAEVAEKLGL------------SELKDRTWQ 136
Query: 226 LFMCSVLMRQGYGDGFRWLAN 246
+F S +G +G WL N
Sbjct: 137 IFKTSATKGEGLDEGMDWLVN 157
>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 = 80.9 bits (200), Expect = 5e-19
Identities = 52/200 (26%), Positives = 79/200 (39%), Gaps = 66/200 (33%)
Query: 68 KLLFLGLDNAGKTTLLHMLKDDRLAQPVPT----------------------LHPTRRVW 105
++L LGLDNAGKTT+L L + ++ PT R W
Sbjct: 17 RILLLGLDNAGKTTILKQLASEDISHITPTQGFNIKNVQADGFKLNVWDIGGQRKIRPYW 76
Query: 106 KDYFPAVDAIVFLVDTSDRERFEESKSELQCLLTDESLASSIVFLVDTSDRERFEESKSE 165
++YF D +++++D++DR+RFEE+ EL E
Sbjct: 77 RNYFENTDVLIYVIDSADRKRFEEAGQEL------------------------VE----- 107
Query: 166 LQCLLTDESLASCPVLILGNKIDKHGAASEEEIRQYFGLYGLTTGKVATPRSEMSGRPIE 225
LL +E LA PVL+ NK D AA EE+ + L ++ R
Sbjct: 108 ---LLEEEKLAGVPVLVFANKQDLLTAAPAEEVAEALNL------------HDIRDRSWH 152
Query: 226 LFMCSVLMRQGYGDGFRWLA 245
+ CS +G +G W+
Sbjct: 153 IQACSAKTGEGLQEGMNWVC 172
>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 = 80.1 bits (198), Expect = 1e-18
Identities = 50/144 (34%), Positives = 80/144 (55%), Gaps = 13/144 (9%)
Query: 72 LGLDNAGKTTLLHMLKDDRLAQP-VPTL-HPTRRVWKDYFPAVDAIVFLVDTSDRERFEE 129
+GL N+GKTTL++++ + ++ +PT+ R+V K V V+ D + RF
Sbjct: 5 VGLQNSGKTTLVNVIASGQFSEDTIPTVGFNMRKVTK---GNVTIKVW--DLGGQPRFR- 58
Query: 130 SKSELQCLLTDESLASSIVFLVDTSDRERFEESKSELQCLLTDESLASCPVLILGNKIDK 189
S E C ++IV++VD +DRE+ E +K+EL LL SL P+L+LGNK D
Sbjct: 59 SMWERYC-----RGVNAIVYVVDAADREKLEVAKNELHDLLEKPSLEGIPLLVLGNKNDL 113
Query: 190 HGAASEEEIRQYFGLYGLTTGKVA 213
GA S +E+ + L +T +V+
Sbjct: 114 PGALSVDELIEQMNLKSITDREVS 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 = 78.9 bits (195), Expect = 2e-18
Identities = 54/180 (30%), Positives = 89/180 (49%), Gaps = 22/180 (12%)
Query: 70 LFLGLDNAGKTTLLHMLKDDRLAQPVPTLHPTRRVWKDYFPAVDAIVFLVDTSD-RERFE 128
L LGLDNAGKTT L K + ++ L+P++ P V + ++ R F
Sbjct: 3 LILGLDNAGKTTFLEQTKT-KFSKNYKGLNPSKIT-----PTVGLNIGTIEVGKARLMFW 56
Query: 129 E--SKSELQCLLTDE--SLASSIVFLVDTSDRERFEESKSELQCLLTDESLASCPVLILG 184
+ + EL+ L D+ + + +++++D++DRERF ESKS + ++ +E+L P+L+L
Sbjct: 57 DLGGQEELRSLW-DKYYAESHGVIYVIDSTDRERFNESKSAFEKVINNEALEGVPLLVLA 115
Query: 185 NKIDKHGAASEEEIRQYFGLYGLTTGKVATPRSEMSGRPIELFMCSVLMRQGYGDGFRWL 244
NK D A S EI++ F G+ R + S L +G +G WL
Sbjct: 116 NKQDLPDALSVAEIKEVFDDCIALIGR----------RDCLVQPVSALEGEGVEEGIEWL 165
>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 = 78.9 bits (195), Expect = 4e-18
Identities = 51/203 (25%), Positives = 79/203 (38%), Gaps = 51/203 (25%)
Query: 61 GLWT-----KSGKLLFLGLDNAGKTTLLHMLKDDRLAQPVPTLHPTRRVWKDYFPAVDAI 115
LW+ K K++ +GLDNAGKTT+L+ + PT+
Sbjct: 5 SLWSLFFPRKEYKVIIVGLDNAGKTTILYQFLLGEVVHTSPTI----------------- 47
Query: 116 VFLVDTSDRERFEESKSELQC--LLTDESLASS----------IVFLVDTSDRERFEESK 163
S+ E + ESL SS ++ ++D++DRER +K
Sbjct: 48 -----GSNVEEIVYKNIRFLMWDIGGQESLRSSWNTYYTNTDAVILVIDSTDRERLPLTK 102
Query: 164 SELQCLLTDESLASCPVLILGNKIDKHGAASEEEIRQYFGLYGLTTGKVATPRSEMSGRP 223
EL +L E L +L+L NK D GA + EI + GL +
Sbjct: 103 EELYKMLAHEDLRKAVLLVLANKQDLKGAMTPAEISESLGLTSIRD------------HT 150
Query: 224 IELFMCSVLMRQGYGDGFRWLAN 246
+ C L +G +G W+A+
Sbjct: 151 WHIQGCCALTGEGLPEGLDWIAS 173
>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 = 72.5 bits (178), Expect = 6e-16
Identities = 54/225 (24%), Positives = 86/225 (38%), Gaps = 67/225 (29%)
Query: 24 LLFLGLDNAGKTTLLHMLK--DDRLAQPVPTLHPILGYLGLWTKSGKLLFLGLDNAGKTT 81
+L LGLDN+GKTT+++ LK + + VPT+ G+ K G L F D +G+
Sbjct: 2 ILVLGLDNSGKTTIINQLKPSNAQSQNIVPTV----GFNVESFKKGNLSFTAFDMSGQGK 57
Query: 82 LLHMLKDDRLAQPVPTLHPTRRVWKDYFPAVDAIVFLVDTSDRERFEESKSELQCLLTDE 141
R +W+ Y+ + I+F++D+SDR R +K EL+ LL
Sbjct: 58 Y-------------------RGLWEHYYKNIQGIIFVIDSSDRLRMVVAKDELELLLNHP 98
Query: 142 SLASSIVFLVDTSDRERFEESKSELQCLLTDESLASCPVLILGNKIDKHGAASEEEIRQY 201
+ + P+L NK+D A + +I Q
Sbjct: 99 DIKHRRI------------------------------PILFYANKMDLPDALTAVKITQL 128
Query: 202 FGLYGLTTGKVATPRSEMSGRPIELFMCSVLMRQGYGDGFRWLAN 246
L + +P +F S L +G +G WL
Sbjct: 129 LCL------------ENIKDKPWHIFASSALTGEGLDEGVDWLQA 161
>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 = 72.8 bits (178), Expect = 7e-16
Identities = 52/151 (34%), Positives = 79/151 (52%), Gaps = 24/151 (15%)
Query: 68 KLLFLGLDNAGKTTLLHMLKDDRLAQPVPTLHPTRRVWKDYFPAVDAIVFLVDTSDRERF 127
+++ LGLD AGKTT+L LK D QP+PT I F V+T + +
Sbjct: 1 RVVTLGLDGAGKTTILFKLKQDEFMQPIPT-----------------IGFNVETVEYKNL 43
Query: 128 EES------KSELQCLLTDESLAS-SIVFLVDTSDRERFEESKSELQCLLTDESLASCPV 180
+ + K +L+ L L + ++VF++D+S R+R E+ SEL LLT++ L +
Sbjct: 44 KFTIWDVGGKHKLRPLWKHYYLNTQAVVFVIDSSHRDRVSEAHSELAKLLTEKELRDALL 103
Query: 181 LILGNKIDKHGAASEEEIRQYFGLYGLTTGK 211
LI NK D GA S EE+ + L+ L G+
Sbjct: 104 LIFANKQDVAGALSVEEMTELLSLHKLCCGR 134
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 73.1 bits (179), Expect = 1e-15
Identities = 39/177 (22%), Positives = 63/177 (35%), Gaps = 17/177 (9%)
Query: 62 LWTKSGKLLFLGLDNAGKTTLLHMLKDDRLAQ------PVPTLHPTRRVWKDYFPAVDAI 115
L+ K K++ LG GKTTLL+ L D + T ++
Sbjct: 1 LFMKEFKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQ--- 57
Query: 116 VFLVDTSDRERFEESKSELQCLLTDESLASSIVFLVDTSDRERFEESKSELQCLLTDESL 175
L DT+ +E + + E A+ I+ + D++ RE +E E L + +
Sbjct: 58 --LWDTAGQEEYRSLRPE------YYRGANGILIVYDSTLRESSDELTEEWLEELRELAP 109
Query: 176 ASCPVLILGNKIDKHGAASEEEIRQYFGLYGLTTGKVATPRSEMSGRPIELFMCSVL 232
P+L++GNKID S E + +A L S
Sbjct: 110 DDVPILLVGNKIDLFDEQSSSEEILNQLNREVVLLVLAPKAVLPEVANPALLETSAK 166
Score = 61.1 bits (148), Expect = 2e-11
Identities = 37/180 (20%), Positives = 63/180 (35%), Gaps = 27/180 (15%)
Query: 17 LWTKSGKLLFLGLDNAGKTTLLHMLKDDRLAQ--PVPTLHPILGYLGLWTKSGKLLFLGL 74
L+ K K++ LG GKTTLL+ L D + P + + +
Sbjct: 1 LFMKEFKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKT-IEPYRRNIKLQLW 59
Query: 75 DNAGKTTLLHMLKDDRLAQPVPTLHPTRRVWKDYFPAVDAIVFLVDTSDRERFEESKSEL 134
D AG + R + +Y+ + I+ + D++ RE +E E
Sbjct: 60 DTAG---------QEEY----------RSLRPEYYRGANGILIVYDSTLRESSDELTEEW 100
Query: 135 QCLLTDESLASSIVFLV-DTSDRERFEESKSELQCLLTDESLASCPVLILGNKIDKHGAA 193
L + + + LV + D + S E+ L E +L+L K A
Sbjct: 101 LEELRELAPDDVPILLVGNKIDLFDEQSSSEEILNQLNREV----VLLVLAPKAVLPEVA 156
>gnl|CDD|206716 cd04149, Arf6, ADP ribosylation factor 6 (Arf6). Arf6 subfamily.
Arf6 (ADP ribosylation factor 6) proteins localize to
the plasma membrane, where they perform a wide variety
of functions. In its active, GTP-bound form, Arf6 is
involved in cell spreading, Rac-induced formation of
plasma membrane ruffles, cell migration, wound healing,
and Fc-mediated phagocytosis. Arf6 appears to change the
actin structure at the plasma membrane by activating
Rac, a Rho family protein involved in membrane ruffling.
Arf6 is required for and enhances Rac formation of
ruffles. Arf6 can regulate dendritic branching in
hippocampal neurons, and in yeast it localizes to the
growing bud, where it plays a role in polarized growth
and bud site selection. In leukocytes, Arf6 is required
for chemokine-stimulated migration across endothelial
cells. Arf6 also plays a role in down-regulation of
beta2-adrenergic receptors and luteinizing hormone
receptors by facilitating the release of sequestered
arrestin to allow endocytosis. Arf6 is believed to
function at multiple sites on the plasma membrane
through interaction with a specific set of GEFs, GAPs,
and effectors. Arf6 has been implicated in breast cancer
and melanoma cell invasion, and in actin remodelling at
the invasion site of Chlamydia infection.
Length = 168
Score = 71.7 bits (176), Expect = 1e-15
Identities = 40/163 (24%), Positives = 67/163 (41%), Gaps = 54/163 (33%)
Query: 64 TKSGKLLFLGLDNAGKTTLLHMLKDDRLAQPVPTL----------------------HPT 101
K ++L LGLD AGKTT+L+ LK + +PT+
Sbjct: 7 NKEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGQDKI 66
Query: 102 RRVWKDYFPAVDAIVFLVDTSDRERFEESKSELQCLLTDESLASSIVFLVDTSDRERFEE 161
R +W+ Y+ ++F+VD++DR+R +E++ EL ++ +DRE
Sbjct: 67 RPLWRHYYTGTQGLIFVVDSADRDRIDEARQELHRII---------------NDRE---- 107
Query: 162 SKSELQCLLTDESLASCPVLILGNKIDKHGAASEEEIRQYFGL 204
+ +L+ NK D A EI++ GL
Sbjct: 108 -------------MRDALLLVFANKQDLPDAMKPHEIQEKLGL 137
>gnl|CDD|133362 cd04162, Arl9_Arfrp2_like, Arf-like 9 (Arl9)/Arfrp2-like GTPase.
Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first
identified as part of the Human Cancer Genome Project.
It maps to chromosome 4q12 and is sometimes referred to
as Arfrp2 (Arf-related protein 2). This is a novel
subfamily identified in human cancers that is
uncharacterized to date.
Length = 164
Score = 67.5 bits (165), Expect = 5e-14
Identities = 43/166 (25%), Positives = 61/166 (36%), Gaps = 57/166 (34%)
Query: 69 LLFLGLDNAGKTTLLHMLKDDR-LAQPVPTL----------------------HPTRRVW 105
+L LGLD AGKT+LLH L +R L VPT R+ W
Sbjct: 2 ILVLGLDGAGKTSLLHSLSSERSLESVVPTTGFNSVAIPTQDAIMELLEIGGSQNLRKYW 61
Query: 106 KDYFPAVDAIVFLVDTSDRERFEESKSELQCLLTDESLASSIVFLVDTSDRERFEESKSE 165
K Y ++F+VD++D ER ++ EL LL
Sbjct: 62 KRYLSGSQGLIFVVDSADSERLPLARQELHQLLQHPP----------------------- 98
Query: 166 LQCLLTDESLASCPVLILGNKIDKHGAASEEEIRQYFGLYGLTTGK 211
P+++L NK D A S +EI + L + G+
Sbjct: 99 -----------DLPLVVLANKQDLPAARSVQEIHKELELEPIARGR 133
>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 = 65.9 bits (161), Expect = 2e-13
Identities = 48/204 (23%), Positives = 79/204 (38%), Gaps = 70/204 (34%)
Query: 68 KLLFLGLDNAGKTTLLHMLKDDRLAQPVPTL----------------------HPTRRVW 105
++L +GLD AGKTT+L+ LK + +PT+ R +W
Sbjct: 2 RILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLW 61
Query: 106 KDYFPAVDAIVFLVDTSDRERFEESKSELQCLLTDESLASSIVFLVDTSDRERFEESKSE 165
+ YF ++F+VD++DRER E++ ELQ +L ++ L ++
Sbjct: 62 RHYFQNTQGLIFVVDSNDRERIGEAREELQRMLNEDELRDAV------------------ 103
Query: 166 LQCLLTDESLASCPVLILGNKIDKHGAASEEEIRQYFGLYGLTTGKVATPRSEMSGRPIE 225
+L+ NK D A S E+ GL+ L R
Sbjct: 104 --------------LLVFANKQDLPNAMSAAEVTDKLGLHSL--------------RNRN 135
Query: 226 LFMCSVLMRQGYG--DGFRWLANY 247
++ + G G +G WL+N
Sbjct: 136 WYIQATCATSGDGLYEGLDWLSNN 159
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 63.4 bits (154), Expect = 2e-12
Identities = 49/208 (23%), Positives = 80/208 (38%), Gaps = 70/208 (33%)
Query: 65 KSGKLLFLGLDNAGKTTLLHMLKDDRLAQPVPTL----------------------HPTR 102
K ++L +GLD AGKTT+L+ LK + +PT+ R
Sbjct: 16 KEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIR 75
Query: 103 RVWKDYFPAVDAIVFLVDTSDRERFEESKSELQCLLTDESLASSIVFLVDTSDRERFEES 162
+W+ YF ++F+VD++DR+R E++ EL +L ++ L ++
Sbjct: 76 PLWRHYFQNTQGLIFVVDSNDRDRVVEARDELHRMLNEDELRDAV--------------- 120
Query: 163 KSELQCLLTDESLASCPVLILGNKIDKHGAASEEEIRQYFGLYGLTTGKVATPRSEMSGR 222
+L+ NK D A + EI GL+ L R
Sbjct: 121 -----------------LLVFANKQDLPNAMNAAEITDKLGLHSL--------------R 149
Query: 223 PIELFMCSVLMRQGYG--DGFRWLANYI 248
++ S G G +G WL+N I
Sbjct: 150 QRHWYIQSTCATSGEGLYEGLDWLSNNI 177
>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 = 62.1 bits (151), Expect = 6e-12
Identities = 48/138 (34%), Positives = 65/138 (47%), Gaps = 9/138 (6%)
Query: 72 LGLDNAGKTTLLHMLKDDRLAQPVPTLHPTRRVWKDYFPAVDAIVFLV-DTSDRERFEES 130
LGLD+AGKTT+L+ LK + VPT K + F D +E+
Sbjct: 9 LGLDSAGKTTVLYRLKFNEFVNTVPTKGFNTEKIKVSLGNAKGVTFHFWDVGGQEKLRPL 68
Query: 131 -KSELQCLLTDESLASSIVFLVDTSDRERFEESKSELQCLLTDESLASCPVLILGNKIDK 189
KS +C TD IVF+VD+ D ER EE+K+EL + PVL+L NK D
Sbjct: 69 WKSYTRC--TD-----GIVFVVDSVDVERMEEAKTELHKITKFSENQGVPVLVLANKQDL 121
Query: 190 HGAASEEEIRQYFGLYGL 207
A E+ + L+ L
Sbjct: 122 PNALPVSEVEKLLALHEL 139
>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 = 60.7 bits (147), Expect = 2e-11
Identities = 29/108 (26%), Positives = 55/108 (50%), Gaps = 22/108 (20%)
Query: 65 KSGKLLFLGLDNAGKTTLLHMLKDDRLAQPVPTL----------------------HPTR 102
K ++L +GLD AGKTT+L+ LK +PT+ R
Sbjct: 12 KEMRILMVGLDAAGKTTILYKLKLGESVTTIPTIGFNVETVTYKNISFTVWDVGGQDKIR 71
Query: 103 RVWKDYFPAVDAIVFLVDTSDRERFEESKSELQCLLTDESLASSIVFL 150
+W+ Y+ ++F+VD++DR+R +E++ EL +L ++ L +++ +
Sbjct: 72 PLWRHYYTNTQGLIFVVDSNDRDRIDEAREELHRMLNEDELRDAVILV 119
>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 = 60.2 bits (146), Expect = 2e-11
Identities = 37/133 (27%), Positives = 60/133 (45%), Gaps = 10/133 (7%)
Query: 70 LFLGLDNAGKTTLLHMLKDDRLAQ----PVPTLHPTRRVWKDYFPAVDAIVFLVDTSDRE 125
+ +G GK++LL+ L + + P T P V + V + LVDT +
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVK--LVLVDTPGLD 58
Query: 126 RFEESKSELQCLLTDESLASSIVFLVDTSDRERFEESKSELQCLLTDESLASCPVLILGN 185
F E L A I+ +VD++DRE E++K + L E + P++++GN
Sbjct: 59 EFGGLGREELARLLLRG-ADLILLVVDSTDRESEEDAKLLILRRLRKEGI---PIILVGN 114
Query: 186 KIDKHGAASEEEI 198
KID EE+
Sbjct: 115 KIDLLEEREVEEL 127
>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 = 59.3 bits (144), Expect = 4e-11
Identities = 42/136 (30%), Positives = 63/136 (46%), Gaps = 10/136 (7%)
Query: 69 LLFLGLDNAGKTTLLHMLKDDRLAQPVPTLHPTRRVWKDYFPAVDAIVFLVDTSDRERFE 128
LL +GLDNAGKTTL+ L+ + + PT+ T V + D F
Sbjct: 2 LLTVGLDNAGKTTLVSALQGEIPKKVAPTVGFTP----TKLRLDKYEVCIFDLGGGANFR 57
Query: 129 ESKSELQCLLTDESLASSIVFLVDTSDRERFEESKSELQCLLTDESLASCPVLILGNKID 188
+ A +VF+VD+SD +R +E K L+ LL ++ P+L+L NK D
Sbjct: 58 GIWVNYY------AEAHGLVFVVDSSDDDRVQEVKEILRELLQHPRVSGKPILVLANKQD 111
Query: 189 KHGAASEEEIRQYFGL 204
K A ++ +Y L
Sbjct: 112 KKNALLGADVIEYLSL 127
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 59.5 bits (144), Expect = 6e-11
Identities = 29/108 (26%), Positives = 58/108 (53%), Gaps = 22/108 (20%)
Query: 65 KSGKLLFLGLDNAGKTTLLHMLKDDRLAQPVPTL----------------------HPTR 102
K ++L +GLD AGKTT+L+ LK + +PT+ R
Sbjct: 16 KEVRILMVGLDAAGKTTILYKLKLGEVVTTIPTIGFNVETVEYKNLKFTMWDVGGQDKLR 75
Query: 103 RVWKDYFPAVDAIVFLVDTSDRERFEESKSELQCLLTDESLASSIVFL 150
+W+ Y+ + ++F+VD++DRER +++ EL+ +L+++ L +++ +
Sbjct: 76 PLWRHYYQNTNGLIFVVDSNDRERIGDAREELERMLSEDELRDAVLLV 123
>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 = 55.8 bits (135), Expect = 1e-09
Identities = 33/134 (24%), Positives = 60/134 (44%), Gaps = 9/134 (6%)
Query: 70 LFLGLDNAGKTTLLHMLKDDRLAQPVPTLHPTRRVWKDYFPAVDAIVFLVDTSDRERFEE 129
L LG ++GKT L L ++ V ++ P + + + LVD E+ +
Sbjct: 4 LLLGPSDSGKTALFTKLTTGKVRSTVTSIEPNVASFYSN-SSKGKKLTLVDVPGHEKLRD 62
Query: 130 SKSELQCLLTDESLASSIVFLVDTSDRERFEESKSE-LQCLLTDESLASC--PVLILGNK 186
+ L ++ +IVF+VD++ ++ +E L +LTD P+LI NK
Sbjct: 63 -----KLLEYLKASLKAIVFVVDSATFQKNIRDVAEFLYDILTDLEKIKNKIPILIACNK 117
Query: 187 IDKHGAASEEEIRQ 200
D A ++I++
Sbjct: 118 QDLFTAKPAKKIKE 131
>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 = 47.6 bits (114), Expect = 6e-07
Identities = 47/165 (28%), Positives = 68/165 (41%), Gaps = 32/165 (19%)
Query: 71 FLGLDNAGKTTLLH-MLKDDRLA-QPVP--TLHPTRRVWKDYFPAVDAIVFLVDT----- 121
G N GK++LL+ +L + P+P T P R+ W+ P V L+DT
Sbjct: 2 IFGRPNVGKSSLLNALLGQNVGIVSPIPGTTRDPVRKEWELL-PLGP--VVLIDTPGLDE 58
Query: 122 ---SDRERFEESKSELQCLLTDESLASSIVFLVDTSDRERFEESKSELQCLLTDESLASC 178
RER EE++ A ++ +VD SD EE E + L
Sbjct: 59 EGGLGRERVEEARQVAD-------RADLVLLVVD-SDLTPVEE---EAK--LGLLRERGK 105
Query: 179 PVLILGNKIDKHGAASEEEIRQYFGLYGLTTGKV----ATPRSEM 219
PVL++ NKID + EEE+ + L L V A P +
Sbjct: 106 PVLLVLNKIDLVPESEEEELLRERKLELLPDLPVIAVSALPGEGI 150
>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 = 44.3 bits (105), Expect = 1e-05
Identities = 33/145 (22%), Positives = 61/145 (42%), Gaps = 21/145 (14%)
Query: 67 GKLLFLGLDNAGKTTLLHMLKDDRLA--QPVPTLHPTRRVWKDYFPAVDAIVF---LVDT 121
K++ +G N GK+TLL+ L ++++ + P TR D + L+DT
Sbjct: 2 IKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGT--TRNYVTTVI-EEDGKTYKFNLLDT 58
Query: 122 SDRERFEESKSELQCLLTDESLAS----SIVFLVDTSDRERFEESKSELQCLLTDESLAS 177
+ +E + ++ L +S IV LV EE + + + +
Sbjct: 59 AGQEDY----DAIRRLYYRAVESSLRVFDIVILVL-----DVEEILEKQTKEIIHHAESG 109
Query: 178 CPVLILGNKIDKHGAASEEEIRQYF 202
P++++GNKID A + + F
Sbjct: 110 VPIILVGNKIDLRDAKLKTHVAFLF 134
>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 = 40.5 bits (95), Expect = 1e-04
Identities = 27/123 (21%), Positives = 50/123 (40%), Gaps = 10/123 (8%)
Query: 68 KLLFLGLDNAGKTTLLH-MLKDDRLAQPVPTLHPTRRVWKDYFPAVDAIVFLV-DTSDRE 125
K++ +G +GK++LL ++ + +P+ D + + D RE
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEI-QGDTLAVDTLEVDGDTGLLNIWDFGGRE 59
Query: 126 RFEESKSELQCLLTDESLASSIVFLVDTSDRERFEESKSELQCLLTDESLASC-PVLILG 184
K E + A +I+ + D +DRE E + L L PV+++G
Sbjct: 60 EL---KFEHIIFMKW---ADAILLVYDLTDRESLNEVSRLIAWLPNLRKLGGKIPVILVG 113
Query: 185 NKI 187
NK+
Sbjct: 114 NKL 116
Score = 30.5 bits (69), Expect = 0.28
Identities = 21/108 (19%), Positives = 37/108 (34%), Gaps = 20/108 (18%)
Query: 23 KLLFLGLDNAGKTTLLH-MLKDDRLAQPVPTLHPILGYLGLWTKSGKLLFLGLDNAGKTT 81
K++ +G +GK++LL ++ + +P+ L L L D G+
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREE 60
Query: 82 LLHMLKDDRLAQPVPTLHPTRRVWKDYFPAVDAIVFLVDTSDRERFEE 129
L + DAI+ + D +DRE E
Sbjct: 61 LKFEHII-------------------FMKWADAILLVYDLTDRESLNE 89
>gnl|CDD|216791 pfam01926, MMR_HSR1, 50S ribosome-binding GTPase. The full-length
GTPase protein is required for the complete activity of
the protein of interacting with the 50S ribosome and
binding of both adenine and guanine nucleotides, with a
preference for guanine nucleotide.
Length = 117
Score = 40.0 bits (94), Expect = 1e-04
Identities = 28/126 (22%), Positives = 52/126 (41%), Gaps = 22/126 (17%)
Query: 71 FLGLDNAGKTTLLHMLKDDRLAQ--PVP--TLHPTRRVWKDYFPAVDAIVFLVDT----S 122
+G N GK+TL++ L ++A P T P V + LVDT
Sbjct: 4 LVGRPNVGKSTLINALTGAKVAIVSDYPGTTRDPILGVLGL-----GRQIILVDTPGLIE 58
Query: 123 DRERFEESKSELQCLLTDESLASS--IVFLVDTSDRERFEESKSELQCLLTDESLASCPV 180
+ + + L E++ + I+ +VD S+ ++ + + L E L P+
Sbjct: 59 GASEGKGVEGFNRFL---EAIREADLILLVVDASE----GLTEDDEEILEELEKLPKKPI 111
Query: 181 LILGNK 186
+++ NK
Sbjct: 112 ILVLNK 117
Score = 30.7 bits (70), Expect = 0.28
Identities = 27/102 (26%), Positives = 46/102 (45%), Gaps = 19/102 (18%)
Query: 26 FLGLDNAGKTTLLHMLKDDRLAQ--PVP--TLHPILGYLGLWTKSGKLLFLGLDNAGKTT 81
+G N GK+TL++ L ++A P T PILG LGL G+ + L +D G
Sbjct: 4 LVGRPNVGKSTLINALTGAKVAIVSDYPGTTRDPILGVLGL----GRQIIL-VDTPG--- 55
Query: 82 LLHMLKDDRLAQPVPTLHPTRRVWKDYFPAVDAIVFLVDTSD 123
+++ + V + ++ D I+ +VD S+
Sbjct: 56 ---LIEGASEGKGVEGFNRFLEAIRE----ADLILLVVDASE 90
>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 = 40.3 bits (94), Expect = 3e-04
Identities = 34/123 (27%), Positives = 56/123 (45%), Gaps = 15/123 (12%)
Query: 68 KLLFLGLDNAGKTTLLHMLKDDRLAQPVPTLHPT--RRVWKDYFPAVDAIVFLVDTSDRE 125
K++ LG N GKT+LLH + R V T+ + W Y ++ DT+ RE
Sbjct: 2 KVVLLGDMNVGKTSLLHRYMERRFKDTVSTVGGAFYLKQWGPYNISI------WDTAGRE 55
Query: 126 RFEESKSELQCLLTDESLASSIVFLVDTSDRERFEESKSELQCLLTDESLASCPVLILGN 185
+F + C A++++ D S+ + EE + LTD + C ++GN
Sbjct: 56 QF-HGLGSMYC-----RGAAAVILTYDVSNVQSLEELEDRF-LGLTDTANEDCLFAVVGN 108
Query: 186 KID 188
K+D
Sbjct: 109 KLD 111
>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 = 39.6 bits (93), Expect = 3e-04
Identities = 33/138 (23%), Positives = 58/138 (42%), Gaps = 12/138 (8%)
Query: 65 KSGKLLFLGLDNAGKTTLLHMLKDDRLAQPVPTLHPTRRVWKDYFPAVDAIVFLVDTSDR 124
K +++ +G + GK++L+ L + + VP + P + D P +VDTS R
Sbjct: 1 KDVRIVLIGDEGVGKSSLIMSLVSEEFPENVPRVLPEITIPADVTPE-RVPTTIVDTSSR 59
Query: 125 ERFEESKSELQCLLTDESLASSIVFLVDTSDRERFEESKSELQCLLTDESLASCPVLILG 184
+ + L E ++++ LV + DR E L P++++G
Sbjct: 60 PQDRAN-------LAAEIRKANVICLVYSVDRPSTLERIRTKWLPLIRRLGVKVPIILVG 112
Query: 185 NKID----KHGAASEEEI 198
NK D A EEE+
Sbjct: 113 NKSDLRDGSSQAGLEEEM 130
>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 = 39.0 bits (92), Expect = 5e-04
Identities = 36/150 (24%), Positives = 61/150 (40%), Gaps = 36/150 (24%)
Query: 68 KLLFLGLDNAGKTTLLHMLKDDRL-AQPVPTLHPTRRVWKDYFPAVDAI------VFLVD 120
K++ +G GKT+LL D++ T+ D+ + + + D
Sbjct: 2 KIVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGV------DFKSKTIEVDGKKVKLQIWD 55
Query: 121 TSDRERFEESKSELQCLLTDESLASS------IVFLV-DTSDRERFEESKSELQCLLTDE 173
T+ +ERF S+ SS LV D ++RE FE L L +
Sbjct: 56 TAGQERFR-------------SITSSYYRGAHGAILVYDVTNRESFENLDKWLN-ELKEY 101
Query: 174 SLASCPVLILGNKIDKHG--AASEEEIRQY 201
+ + P++++GNK D S EE +Q+
Sbjct: 102 APPNIPIILVGNKSDLEDERQVSTEEAQQF 131
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 39.9 bits (94), Expect = 7e-04
Identities = 36/137 (26%), Positives = 61/137 (44%), Gaps = 25/137 (18%)
Query: 64 TKSGKLLFLGLDNAGKTTLLHMLKDDRLA----QPVPTLHPTRRVW--KDYFPAVDAIVF 117
KSG + +G N GK+TLL+ L +++ +P T + R + + I+F
Sbjct: 4 FKSGFVAIIGRPNVGKSTLLNALVGQKISIVSPKPQTTRNRIRGIVTTDNA-----QIIF 58
Query: 118 LVDTSDRERFEESKSELQCLLTDESLASS-----IVFLVDTSDRERFEESKSELQCLLTD 172
VDT + K L L+ + ++ I+F+VD +D + L+ L
Sbjct: 59 -VDTPG---IHKPKHALGELMNKAARSALKDVDLILFVVD-ADEGWGPGDEFILEQL--- 110
Query: 173 ESLASCPVLILGNKIDK 189
PV+++ NKIDK
Sbjct: 111 -KKTKTPVILVVNKIDK 126
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 38.2 bits (89), Expect = 0.002
Identities = 35/152 (23%), Positives = 53/152 (34%), Gaps = 26/152 (17%)
Query: 64 TKSGKLLFLGLDNAGKTTLLHMLKD---DRLAQPVPTLHPTRRVWK----DYFPAV---D 113
K++ +G AGKTT + L D ++ + D+ D
Sbjct: 8 MIETKIVVIGPVGAGKTTFVRALSDKPLVITEADASSVSGKGKRPTTVAMDFGSIELDED 67
Query: 114 AIVFLVDTSDRERFE---ESKSELQCLLTDESLASSIVFLVDTSDRERFEESKSELQCLL 170
V L T +ERF+ E S A + LVD+S F + +
Sbjct: 68 TGVHLFGTPGQERFKFMWEILSRG---------AVGAIVLVDSSRPITFHAEE----IID 114
Query: 171 TDESLASCPVLILGNKIDKHGAASEEEIRQYF 202
S PV++ NK D A E+IR+
Sbjct: 115 FLTSRNPIPVVVAINKQDLFDALPPEKIREAL 146
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 38.0 bits (89), Expect = 0.003
Identities = 40/138 (28%), Positives = 59/138 (42%), Gaps = 23/138 (16%)
Query: 73 GLDNAGKTTLLHMLKDDR--LAQPVP-TLHPTRR--VWKDYFPAV--DAIVFLVDTSDRE 125
G NAGK+TL + L +A + TL PT R D + D + F+ D
Sbjct: 199 GYTNAGKSTLFNALTGADVYVADQLFATLDPTTRRIELGDGRKVLLTDTVGFIRDL-PHP 257
Query: 126 RFEESKSELQCLLTDESL-ASSIVFLVDTSD---RERFEESKSELQCLLTDESLASCPVL 181
E KS L+ E A ++ +VD SD E+ E + L + DE P++
Sbjct: 258 LVEAFKSTLE-----EVKEADLLLHVVDASDPEILEKLEAVEDVLAEIGADEI----PII 308
Query: 182 ILGNKIDKHGAASEEEIR 199
++ NKID EE +
Sbjct: 309 LVLNKIDL--LEDEEILA 324
>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 = 37.1 bits (87), Expect = 0.004
Identities = 39/139 (28%), Positives = 59/139 (42%), Gaps = 26/139 (18%)
Query: 76 NAGKTTLLHML-KDDRLA--QPVPTLHPTRR--VWKDYFPAVDAIVFLVDT----SD--R 124
NAGK+TL + L D LA Q TL PT R + L DT D
Sbjct: 51 NAGKSTLFNALTGADVLAEDQLFATLDPTTRRIKLPGGREVL-----LTDTVGFIRDLPH 105
Query: 125 ERFEESKSELQCLLTDESL-ASSIVFLVDTSDRERFEESKSELQCLLTDESLASCPVLIL 183
+ E +S L+ E A ++ +VD SD EE ++ +L + P++++
Sbjct: 106 QLVEAFRSTLE-----EVAEADLLLHVVDASD-PDREEQIETVEEVLKELGADDIPIILV 159
Query: 184 GNKIDKHGAASEEEIRQYF 202
NKID +EE+ +
Sbjct: 160 LNKIDL---LDDEELEERL 175
>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 = 36.1 bits (84), Expect = 0.011
Identities = 22/87 (25%), Positives = 37/87 (42%), Gaps = 22/87 (25%)
Query: 102 RRVWKDYFPAVDAIVFLVDTSDRERFEESKSELQCLLTDESLASSIVFLVDTSDRERFEE 161
R+ W F V AI+F+V S+ ++ Q L D+S T+ R EE
Sbjct: 182 RKKWIHCFEDVTAIIFVVSLSE---YD------QVLYEDDS----------TN---RLEE 219
Query: 162 SKSELQCLLTDESLASCPVLILGNKID 188
S + + + + P+++ NK D
Sbjct: 220 SLNLFEEICNSPWFKNTPIILFLNKKD 246
Score = 35.3 bits (82), Expect = 0.021
Identities = 23/113 (20%), Positives = 47/113 (41%), Gaps = 5/113 (4%)
Query: 68 KLLFLGLDNAGKTTLLHMLKDDRLAQPVPTLHPTRRVWKD--YFPAVDAIVFLVDTSDRE 125
KLL LG +GK+T+L + ++ R ++ Y + ++ L++ +
Sbjct: 4 KLLLLGAGESGKSTILKQM---KILHGGGFSDEEREQYRAVIYSNIIRSLKTLLEALENL 60
Query: 126 RFEESKSELQCLLTDESLASSIVFLVDTSDRERFEESKSELQCLLTDESLASC 178
E S S+ + + L S + L+D + EE +++ L D +
Sbjct: 61 EIESSNSKPENEEIAKKLKSILDSLLDVDETRFSEELAEDIKELWNDPGIQEV 113
Score = 28.4 bits (64), Expect = 3.5
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 23 KLLFLGLDNAGKTTLLHMLK 42
KLL LG +GK+T+L +K
Sbjct: 4 KLLLLGAGESGKSTILKQMK 23
>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 = 35.6 bits (82), Expect = 0.013
Identities = 38/130 (29%), Positives = 60/130 (46%), Gaps = 16/130 (12%)
Query: 68 KLLFLGLDNAGKTTLL-HMLKD---DRLAQPVPTLHPTRRVWKDYFPA-VDAIVFLVDTS 122
+L+F+G GKT L+ L D + + V LH K+Y A V + ++DTS
Sbjct: 1 RLVFMGAAGVGKTALIQRFLYDTFEPKHRRTVEELHS-----KEYEVAGVKVTIDILDTS 55
Query: 123 DRERFEESKSELQCLLTDESLASSIVFLVDTSDRERFEESKSELQCLLTDESLASCPVLI 182
F ++ L A ++V+ VD D E FEE K + +L + P+++
Sbjct: 56 GSYSF----PAMRKLSIQNGDAFALVYSVD--DPESFEEVKRLREEILEVKEDKFVPIVV 109
Query: 183 LGNKIDKHGA 192
+GNKID
Sbjct: 110 VGNKIDSLAE 119
>gnl|CDD|133319 cd04119, RJL, Rab GTPase family J-like (RabJ-like). RJLs are found
in many protists and as chimeras with C-terminal DNAJ
domains in deuterostome metazoa. They are not found in
plants, fungi, and protostome metazoa, suggesting a
horizontal gene transfer between protists and
deuterostome metazoa. RJLs lack any known membrane
targeting signal and contain a degenerate
phosphate/magnesium-binding 3 (PM3) motif, suggesting an
impaired ability to hydrolyze GTP. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization.
Length = 168
Score = 33.5 bits (77), Expect = 0.052
Identities = 23/61 (37%), Positives = 32/61 (52%), Gaps = 7/61 (11%)
Query: 148 VFLV-DTSDRERFEESKSEL----QCLLTDESLASCPVLILGNKID--KHGAASEEEIRQ 200
V LV D +DR+ FE S L Q ++ + V++ NKID KH A SE+E R
Sbjct: 76 VLLVYDVTDRQSFEALDSWLKEMKQEGGPHGNMENIVVVVCANKIDLTKHRAVSEDEGRL 135
Query: 201 Y 201
+
Sbjct: 136 W 136
>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 = 33.0 bits (76), Expect = 0.058
Identities = 32/131 (24%), Positives = 51/131 (38%), Gaps = 23/131 (17%)
Query: 68 KLLFLGLDNAGKTTLLHMLKDDRLAQPVPTLHPTRRVWKDYFPAVDAIVFLVDTSDRERF 127
K+ LG GK+ L V L T+R +Y P ++++ T D E+
Sbjct: 1 KIAVLGASGVGKSALT-----------VRFL--TKRFIGEYEPNLESLYSRQVTIDGEQV 47
Query: 128 E---ESKSELQCLLTDESLASSI------VFLVDTSDRERFEESKSELQCLLTDESLAS- 177
+ Q ESL S+ V + +DR F+ LQ + +
Sbjct: 48 SLEIQDTPGQQQNEDPESLERSLRWADGFVLVYSITDRSSFDVVSQLLQLIREIKKRDGE 107
Query: 178 CPVLILGNKID 188
PV+++GNK D
Sbjct: 108 IPVILVGNKAD 118
>gnl|CDD|129528 TIGR00436, era, GTP-binding protein Era. Era is an essential
GTPase in Escherichia coli and many other bacteria. It
plays a role in ribosome biogenesis. Few bacteria lack
this protein [Protein synthesis, Other].
Length = 270
Score = 33.5 bits (77), Expect = 0.075
Identities = 42/148 (28%), Positives = 61/148 (41%), Gaps = 21/148 (14%)
Query: 67 GKLLFLGLDNAGKTTLLHMLKDDRLAQPVPTLHPTR-RVWKDYFPAVDAIVFLVDTSDRE 125
G + LG N GK+TLL+ L +++ P TR R+ + I+F +DT
Sbjct: 1 GFVAILGRPNVGKSTLLNQLHGQKISITSPKAQTTRNRISGIHTTGASQIIF-IDTPG-- 57
Query: 126 RFEESKSELQCLLTDESLASS-------IVFLVDTSDRERFEESKSELQCLLTDESLASC 178
F E K L L+ E A S I+F+VD+ E +LT
Sbjct: 58 -FHEKKHSLNRLMMKE--ARSAIGGVDLILFVVDSDQWNGDGEF------VLTKLQNLKR 108
Query: 179 PVLILGNKID-KHGAASEEEIRQYFGLY 205
PV++ NK+D K I +Y L
Sbjct: 109 PVVLTRNKLDNKFKDKLLPLIDKYAILE 136
Score = 27.4 bits (61), Expect = 6.4
Identities = 27/112 (24%), Positives = 45/112 (40%), Gaps = 19/112 (16%)
Query: 22 GKLLFLGLDNAGKTTLLHMLKDDRLA--QPVP--TLHPILGYLGLWTKSGKLLFLGLDNA 77
G + LG N GK+TLL+ L +++ P T + I G T + +++F +D
Sbjct: 1 GFVAILGRPNVGKSTLLNQLHGQKISITSPKAQTTRNRISGIHT--TGASQIIF--IDTP 56
Query: 78 GKTTLLHMLKDDRLAQPVPTLHPTRRVWKDYFPAVDAIVFLVDTSDRERFEE 129
G H L + + + VD I+F+VD+ E
Sbjct: 57 GFHEKKHSLNRLMMKEARSAIG-----------GVDLILFVVDSDQWNGDGE 97
>gnl|CDD|185391 PRK15494, era, GTPase Era; Provisional.
Length = 339
Score = 32.8 bits (74), Expect = 0.13
Identities = 31/126 (24%), Positives = 59/126 (46%), Gaps = 7/126 (5%)
Query: 65 KSGKLLFLGLDNAGKTTLLHMLKDDRLAQPVPTLHPTRRVWKDYFPAVDAIVFLVDTSD- 123
K+ + +G N+GK+TLL+ + ++L+ P + TR + D V L DT
Sbjct: 51 KTVSVCIIGRPNSGKSTLLNRIIGEKLSIVTPKVQTTRSIITGIITLKDTQVILYDTPGI 110
Query: 124 -RERFEESKSELQCLLTDESLASSIVFLVDTSDRERFEESKSELQCLLTDESLASCPVLI 182
+ K+ ++C + A ++ ++D+ + F++ + L SL P+ +
Sbjct: 111 FEPKGSLEKAMVRCAWSSLHSADLVLLIIDS--LKSFDDITHNI--LDKLRSLNIVPIFL 166
Query: 183 LGNKID 188
L NKID
Sbjct: 167 L-NKID 171
>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 = 32.0 bits (74), Expect = 0.14
Identities = 37/142 (26%), Positives = 62/142 (43%), Gaps = 35/142 (24%)
Query: 64 TKSGKLLFLGLDNAGKTTLLHMLKDDRLA--QPVPTLHPTR-RVW-----KDYFPAVDAI 115
KSG + +G N GK+TLL+ L +++ P P TR R+ D I
Sbjct: 1 FKSGFVAIIGRPNVGKSTLLNALVGQKISIVSPKP--QTTRNRIRGIYTDDDA-----QI 53
Query: 116 VFLVDT----SDRERFEESKSELQCLLTD--ESLASS--IVFLVDTSDRERFEESKSELQ 167
+F VDT +++ E ++ +L ++F+VD S+ E + L+
Sbjct: 54 IF-VDTPGIHKPKKKLGE------RMVKAAWSALKDVDLVLFVVDASEWIG-EGDEFILE 105
Query: 168 CLLTDESLASCPVLILGNKIDK 189
L + PV+++ NKID
Sbjct: 106 LLKKSK----TPVILVLNKIDL 123
Score = 30.5 bits (70), Expect = 0.48
Identities = 30/115 (26%), Positives = 49/115 (42%), Gaps = 29/115 (25%)
Query: 19 TKSGKLLFLGLDNAGKTTLLHMLKDDRLA--QPVP--TLHPILGYLGLWTKS-GKLLFLG 73
KSG + +G N GK+TLL+ L +++ P P T + I G++T +++F
Sbjct: 1 FKSGFVAIIGRPNVGKSTLLNALVGQKISIVSPKPQTTRNRI---RGIYTDDDAQIIF-- 55
Query: 74 LDNAG----KTTLLHMLKDDRLAQPVPTLHPTRRVWKDYFPAVDAIVFLVDTSDR 124
+D G K L + KD VD ++F+VD S+
Sbjct: 56 VDTPGIHKPKKKLGERMVKA-----------AWSALKD----VDLVLFVVDASEW 95
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 32.1 bits (74), Expect = 0.14
Identities = 30/138 (21%), Positives = 59/138 (42%), Gaps = 40/138 (28%)
Query: 68 KLLFLGLDNAGKTTLLHMLKDDRLAQP-VPTLHP---TRRVWKDYFPAVDAIVFLV---D 120
K++ +G GK++LL D + ++ T+ T+ + VD + D
Sbjct: 2 KIILIGDSGVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTI------EVDGKRVKLQIWD 55
Query: 121 TSDRERFEESKSELQCLLTDESLASS-------IVFLVDTSDRERFEESKS---ELQCLL 170
T+ +ERF S+ SS + + D ++RE FE ++ EL+
Sbjct: 56 TAGQERFR-------------SITSSYYRGAVGALLVYDITNRESFENLENWLKELR--- 99
Query: 171 TDESLASCPVLILGNKID 188
+ + + ++++GNK D
Sbjct: 100 -EYASPNVVIMLVGNKSD 116
>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 = 32.1 bits (74), Expect = 0.14
Identities = 34/131 (25%), Positives = 58/131 (44%), Gaps = 26/131 (19%)
Query: 68 KLLFLGLDNAGKTTLLHMLKDDRLAQPVPTLHPTRRVWKDYFPA---VDAIVF---LVDT 121
KL+ +G GK++LL ++ PT + D++ VD + DT
Sbjct: 1 KLVLVGDGGVGKSSLLIRFTQNKF---PEEYIPT--IGVDFYTKTIEVDGKTVKLQIWDT 55
Query: 122 SDRERFEESKSELQCLLTDESLASSIVFLV--DTSDRERFEESKSELQCLLT--DESLAS 177
+ +ERF L + FL+ D + R+ FE K L+ +L DE++
Sbjct: 56 AGQERFR--------ALRPLYYRGAQGFLLVYDITSRDSFENVKKWLEEILRHADENV-- 105
Query: 178 CPVLILGNKID 188
P++++GNK D
Sbjct: 106 -PIVLVGNKCD 115
>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 = 32.8 bits (76), Expect = 0.16
Identities = 40/137 (29%), Positives = 57/137 (41%), Gaps = 30/137 (21%)
Query: 76 NAGKTTLLHML-KDDRLA--QPVPTLHPT-RRVWKDYFPAVDAIVFLVDT----SDR--- 124
NAGK+TL + L D A Q TL PT RR+ P ++ L DT D
Sbjct: 199 NAGKSTLFNALTGADVYAADQLFATLDPTTRRL---DLPDGGEVL-LTDTVGFIRDLPHE 254
Query: 125 --ERFEESKSELQCLLTDESL-ASSIVFLVDTSDRERFEESKSELQCLLTDESLASCPVL 181
F ++ L+ E A ++ +VD SD EE ++ +L + P L
Sbjct: 255 LVAAF---RATLE-----EVREADLLLHVVDASD-PDREEQIEAVEKVLEELGAEDIPQL 305
Query: 182 ILGNKIDKHGAASEEEI 198
++ NKID E I
Sbjct: 306 LVYNKIDL---LDEPRI 319
>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 = 31.5 bits (72), Expect = 0.19
Identities = 29/126 (23%), Positives = 49/126 (38%), Gaps = 16/126 (12%)
Query: 68 KLLFLGLDNAGKTTLLHMLKDDRLAQPVPTLHPTR-RVWKDYFPAVDAIVFLV-DTSDRE 125
KL+ +G GKT+L L ++ + H + WK P I V D +E
Sbjct: 3 KLMLVGQGGVGKTSLCKQLIGEKFDGDESSTHGINVQDWKIPAPERKKIRLNVWDFGGQE 62
Query: 126 RFEESKSELQCLLTDESLASSIVFLV--DTSDRERFEESKSELQCLLTDESLAS-CPVLI 182
+ + Q LT SL +L+ D + L+ + ++ PV++
Sbjct: 63 IYHATH---QFFLTSRSL-----YLLVFDLRTGDEVSRVPYWLRQI---KAFGGVSPVIL 111
Query: 183 LGNKID 188
+G ID
Sbjct: 112 VGTHID 117
Score = 27.3 bits (61), Expect = 5.6
Identities = 10/34 (29%), Positives = 16/34 (47%)
Query: 23 KLLFLGLDNAGKTTLLHMLKDDRLAQPVPTLHPI 56
KL+ +G GKT+L L ++ + H I
Sbjct: 3 KLMLVGQGGVGKTSLCKQLIGEKFDGDESSTHGI 36
>gnl|CDD|222165 pfam13481, AAA_25, AAA domain. This AAA domain is found in a wide
variety of presumed DNA repair proteins.
Length = 154
Score = 31.5 bits (72), Expect = 0.20
Identities = 17/68 (25%), Positives = 23/68 (33%), Gaps = 9/68 (13%)
Query: 43 DDRLAQPVPTLHPILGYLGLWTKSGKLLFLGLDNAGKTTLL-----HMLKDDRLAQPVPT 97
+ L P P L ++ GL + G L G GK+TL + P P
Sbjct: 12 AEDLDAPPPPLRWLVK--GLLPRGGLTLLAGAPGTGKSTLALDLAAAVATGRPFLGPFPV 69
Query: 98 LHPTRRVW 105
RV
Sbjct: 70 EP--GRVL 75
>gnl|CDD|206642 cd00876, Ras, Rat sarcoma (Ras) family of small guanosine
triphosphatases (GTPases). The Ras family of the Ras
superfamily includes classical N-Ras, H-Ras, and K-Ras,
as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG,
Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins.
Ras proteins regulate cell growth, proliferation and
differentiation. Ras is activated by guanine nucleotide
exchange factors (GEFs) that release GDP and allow GTP
binding. Many RasGEFs have been identified. These are
sequestered in the cytosol until activation by growth
factors triggers recruitment to the plasma membrane or
Golgi, where the GEF colocalizes with Ras. Active
GTP-bound Ras interacts with several effector proteins:
among the best characterized are the Raf kinases,
phosphatidylinositol 3-kinase (PI3K), RalGEFs and
NORE/MST1. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 160
Score = 31.3 bits (72), Expect = 0.24
Identities = 34/144 (23%), Positives = 59/144 (40%), Gaps = 24/144 (16%)
Query: 68 KLLFLGLDNAGKTTLLHMLKDDRLAQP-VPTLHPTRRVWKDYFPAVDAIVF---LVDTSD 123
KL+ LG GK+ L + PT+ + R K VD + ++DT+
Sbjct: 1 KLVVLGAGGVGKSALTIRFVSGEFVEEYDPTIEDSYR--KQI--VVDGETYTLDILDTAG 56
Query: 124 RERFEESKSELQCLLTDESLASS----IVFLVDTSDRERFEESKSELQCLLTDESLASCP 179
+E F + D+ + + +V+ + RE FEE K+ + +L + P
Sbjct: 57 QEEF--------SAMRDQYIRNGDGFILVYSIT--SRESFEEIKNIREQILRVKDKEDVP 106
Query: 180 VLILGNKID--KHGAASEEEIRQY 201
++++GNK D S EE
Sbjct: 107 IVLVGNKCDLENERQVSTEEGEAL 130
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 31.9 bits (73), Expect = 0.25
Identities = 38/144 (26%), Positives = 58/144 (40%), Gaps = 27/144 (18%)
Query: 73 GLDNAGKTTLLHMLKDDRLAQPVPTLHP--TRRVWKDYFPAVDAIVFLVDTS---DRERF 127
G N GK++L+ L A+P +P T+ + +F + ++DT DR
Sbjct: 175 GYPNVGKSSLVRKLTT---AKPEVAPYPFTTKGIHVGHFERGYLRIQVIDTPGLLDRPLE 231
Query: 128 EESKSELQCLLTDESLASSIVFLVDTSD-----RER----FEESKSELQCLLTDESLASC 178
E ++ E Q +L LA I+FL D S+ E EE K
Sbjct: 232 ERNEIERQAILALRHLAGVILFLFDPSETCGYSLEEQISLLEEIKELF----------KA 281
Query: 179 PVLILGNKIDKHGAASEEEIRQYF 202
P++++ NKID EEI
Sbjct: 282 PIVVVINKIDIADEEKLEEIEASV 305
>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 = 30.4 bits (69), Expect = 0.50
Identities = 37/160 (23%), Positives = 65/160 (40%), Gaps = 32/160 (20%)
Query: 68 KLLFLGLDNAGKTTLLHMLKDDRLAQPV-PTLHPTRRVWKDYFPAVDAIVFLVDTSDRER 126
K+L +G GK++LL DD + + T+ +V + + DT+ +ER
Sbjct: 2 KILLIGDSGVGKSSLLLRFTDDTFDEDLSSTIGVDFKVKTVTVDGKKVKLAIWDTAGQER 61
Query: 127 FEESKSELQCLLTDESLASS-------IVFLVDTSDRERFEESK---SELQCLLTDESLA 176
F +L SS ++ + D + R+ F+ +EL T+
Sbjct: 62 FR-------------TLTSSYYRGAQGVILVYDVTRRDTFDNLDTWLNELDTYSTNPDAV 108
Query: 177 SCPVLILGNKIDK--HGAASEEEI---RQYFGLYGLTTGK 211
+++GNKIDK EE R++ L+ T+ K
Sbjct: 109 K---MLVGNKIDKENREVTREEGQKFARKHNMLFIETSAK 145
>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 = 30.5 bits (69), Expect = 0.59
Identities = 41/138 (29%), Positives = 60/138 (43%), Gaps = 38/138 (27%)
Query: 68 KLLFLGLDNAGKTTLLHMLKDDRLAQPVPTLHPTRRVWKDYF-------PAVDAIVFLVD 120
+L+ +G GK++LL + R A PT V D+F P V + L D
Sbjct: 4 RLIVIGDSTVGKSSLLKRFTEGRFA---EVSDPTVGV--DFFSRLIEIEPGVRIKLQLWD 58
Query: 121 TSDRERFEESKSELQCLLTDESLASSI-VFLV-DTSDRERF-------EESKSELQCLLT 171
T+ +ERF +T +S+ V LV D ++RE F EE++S +Q
Sbjct: 59 TAGQERFRS--------ITRSYYRNSVGVLLVFDITNRESFEHVHDWLEEARSHIQP--- 107
Query: 172 DESLASCPVLIL-GNKID 188
PV IL G+K D
Sbjct: 108 -----HRPVFILVGHKCD 120
>gnl|CDD|180712 PRK06820, PRK06820, type III secretion system ATPase; Validated.
Length = 440
Score = 30.9 bits (70), Expect = 0.63
Identities = 33/122 (27%), Positives = 50/122 (40%), Gaps = 28/122 (22%)
Query: 78 GKTTLLHMLKDDRLAQPVPTLHPTRRVWKDYFPAVDAIVF-LVDTSDRERFEESKSELQC 136
GK+TLL ML D A D +V L+ ER E + L+
Sbjct: 175 GKSTLLGMLCADSAA--------------------DVMVLALIG----ERGREVREFLEQ 210
Query: 137 LLTDESLASSIVFLVDTSDRERFEESKSELQCLLTDESLASC--PVLILGNKIDKHGAAS 194
+LT E+ A ++V +V TSDR E K E VL++ + + ++ A+
Sbjct: 211 VLTPEARARTVV-VVATSDRPALERLKGLSTATTIAEYFRDRGKKVLLMADSLTRYARAA 269
Query: 195 EE 196
E
Sbjct: 270 RE 271
>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 = 29.7 bits (67), Expect = 0.95
Identities = 31/135 (22%), Positives = 53/135 (39%), Gaps = 12/135 (8%)
Query: 71 FLGLDNAGKTTLLHML-KDDRLAQPVPTLHPTRRVWKDYFPAVDAIVF-LVDTSD-RERF 127
+GL N GK+TLL L P T F D + ++D +
Sbjct: 2 LVGLPNVGKSTLLSALTSAKVEIASYP--FTTLEPNVGVFEFGDGVDIQIIDLPGLLDGA 59
Query: 128 EESKSELQCLLTDESLASSIVFLVDTSDRER---FEESKS-ELQCLLTDESLASCPVLIL 183
E + + +L + I+ ++D S+ E+ K+ + + L + P +I+
Sbjct: 60 SEGRGLGEQILAHLYRSDLILHVIDASEDCVGDPLEDQKTLNEEVSGSFLFLKNKPEMIV 119
Query: 184 GNKIDKHGAASEEEI 198
NKID ASE +
Sbjct: 120 ANKIDM---ASENNL 131
>gnl|CDD|234814 PRK00698, tmk, thymidylate kinase; Validated.
Length = 205
Score = 29.8 bits (68), Expect = 1.1
Identities = 13/39 (33%), Positives = 21/39 (53%), Gaps = 2/39 (5%)
Query: 65 KSGKLLFL-GLDNAGKTTLLHMLKDDRLAQPVPTLHPTR 102
G + + G+D AGK+T + +LK + L Q + TR
Sbjct: 1 MRGMFITIEGIDGAGKSTQIELLK-ELLEQQGRDVVFTR 38
Score = 28.6 bits (65), Expect = 2.5
Identities = 9/25 (36%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 20 KSGKLLFL-GLDNAGKTTLLHMLKD 43
G + + G+D AGK+T + +LK+
Sbjct: 1 MRGMFITIEGIDGAGKSTQIELLKE 25
>gnl|CDD|151555 pfam11111, CENP-M, Centromere protein M (CENP-M). The prime
candidate for specifying centromere identity is the
array of nucleosomes assembles with CENP-A. CENP-A
recruits a nucleosome associated complex (NAC) comprised
of CENP-M along with two other proteins. Assembly of the
CENP-A NAC at centromeres is partly dependant on CENP-M.
The CENP-A NAC is essential, as disruption of the
complex causes errors of chromosome alignment and
segregation that preclude cell survival.
Length = 176
Score = 29.3 bits (66), Expect = 1.2
Identities = 26/102 (25%), Positives = 46/102 (45%), Gaps = 17/102 (16%)
Query: 66 SGKLLFLGLDNAGKTTLLH-MLKDD-------RLAQ--PVPTLHPTRRVWKDYFPAVDAI 115
+ +L +G + A + L MLK+D LA P+P+ R P +D I
Sbjct: 15 TATVLLVGTEGALQQQLAEAMLKEDKDFELNIHLATSLPLPSERNHLR------PRIDLI 68
Query: 116 VFLVDTSDRERFEESKSELQCLLTDESLASSIVFLVDTSDRE 157
VF+++ + + ++ L+ L D L + FLV + +E
Sbjct: 69 VFVINLHSKLSLQSVEASLKHLDVDFFLG-KVCFLVTGAGQE 109
>gnl|CDD|206711 cd04140, ARHI_like, A Ras homolog member I (ARHI). ARHI (A Ras
homolog member I) is a member of the Ras family with
several unique structural and functional properties.
ARHI is expressed in normal human ovarian and breast
tissue, but its expression is decreased or eliminated in
breast and ovarian cancer. ARHI contains an N-terminal
extension of 34 residues (human) that is required to
retain its tumor suppressive activity. Unlike most other
Ras family members, ARHI is maintained in the
constitutively active (GTP-bound) state in resting cells
and has modest GTPase activity. ARHI inhibits STAT3
(signal transducers and activators of transcription 3),
a latent transcription factor whose abnormal activation
plays a critical role in oncogenesis. Most Ras proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 165
Score = 29.4 bits (66), Expect = 1.3
Identities = 12/35 (34%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 156 RERFEESKS--ELQCLLTDESLASCPVLILGNKID 188
++ EE K EL C + +L P++++GNK D
Sbjct: 85 KQSLEELKPIYELICEIKGNNLEKIPIMLVGNKCD 119
>gnl|CDD|166155 PLN02514, PLN02514, cinnamyl-alcohol dehydrogenase.
Length = 357
Score = 29.8 bits (67), Expect = 1.4
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 44 DRLAQPVPTLHPILGYLGLWTKSGKLLFLGLDNA 77
D + VP HP+ YL L GKL+ +G+ N
Sbjct: 246 DYIIDTVPVFHPLEPYLSLLKLDGKLILMGVINT 279
>gnl|CDD|226952 COG4586, COG4586, ABC-type uncharacterized transport system,
ATPase component [General function prediction only].
Length = 325
Score = 29.7 bits (67), Expect = 1.4
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 24 LLFLGLDNAGKTTLLHML 41
+ FLG + AGK+T L ML
Sbjct: 53 VGFLGANGAGKSTTLKML 70
Score = 29.7 bits (67), Expect = 1.4
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 69 LLFLGLDNAGKTTLLHML 86
+ FLG + AGK+T L ML
Sbjct: 53 VGFLGANGAGKSTTLKML 70
>gnl|CDD|206700 cd04127, Rab27A, Rab GTPase family 27a (Rab27a). The Rab27a
subfamily consists of Rab27a and its highly homologous
isoform, Rab27b. Unlike most Rab proteins whose
functions remain poorly defined, Rab27a has many known
functions. Rab27a has multiple effector proteins, and
depending on which effector it binds, Rab27a has
different functions as well as tissue distribution
and/or cellular localization. Putative functions have
been assigned to Rab27a when associated with the
effector proteins Slp1, Slp2, Slp3, Slp4, Slp5, DmSlp,
rabphilin, Dm/Ce-rabphilin, Slac2-a, Slac2-b, Slac2-c,
Noc2, JFC1, and Munc13-4. Rab27a has been associated
with several human diseases, including hemophagocytic
syndrome (Griscelli syndrome or GS), Hermansky-Pudlak
syndrome, and choroidermia. In the case of GS, a rare,
autosomal recessive disease, a Rab27a mutation is
directly responsible for the disorder. When Rab27a is
localized to the secretory granules of pancreatic beta
cells, it is believed to mediate glucose-stimulated
insulin secretion, making it a potential target for
diabetes therapy. When bound to JFC1 in prostate cells,
Rab27a is believed to regulate the exocytosis of
prostate- specific markers. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 180
Score = 29.0 bits (65), Expect = 1.5
Identities = 36/153 (23%), Positives = 60/153 (39%), Gaps = 19/153 (12%)
Query: 68 KLLFLGLDNAGKTTLLHMLKDDRLAQPVPT-----LHPTRRVWKDYFPAVDA------IV 116
KLL LG GKTT L+ D++ T R V+ P + +
Sbjct: 6 KLLALGDSGVGKTTFLYRYTDNKFNPKFITTVGIDFREKRVVYNSQGPDGTSGKAFRVHL 65
Query: 117 FLVDTSDRERFEESKSELQCLLTDESLASSIVFLVDTSDRERFEESKSELQCLLTDESLA 176
L DT+ +ERF +S D A + + D + + F ++ + L
Sbjct: 66 QLWDTAGQERF---RSLTTAFFRD---AMGFLLMFDLTSEQSFLNVRNWMSQLQAHAYCE 119
Query: 177 SCPVLILGNKID--KHGAASEEEIRQYFGLYGL 207
+ ++++GNK D SE + R+ YG+
Sbjct: 120 NPDIVLIGNKADLPDQREVSERQARELADKYGI 152
Score = 26.7 bits (59), Expect = 8.8
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 23 KLLFLGLDNAGKTTLLHMLKDDR 45
KLL LG GKTT L+ D++
Sbjct: 6 KLLALGDSGVGKTTFLYRYTDNK 28
>gnl|CDD|236167 PRK08154, PRK08154, anaerobic benzoate catabolism transcriptional
regulator; Reviewed.
Length = 309
Score = 29.5 bits (67), Expect = 1.5
Identities = 16/54 (29%), Positives = 24/54 (44%)
Query: 37 LLHMLKDDRLAQPVPTLHPILGYLGLWTKSGKLLFLGLDNAGKTTLLHMLKDDR 90
LL +LA+ L +LG + ++ +GL AGK+TL ML
Sbjct: 104 LLEQASPAQLARVRDALSGMLGAGRRAARRRRIALIGLRGAGKSTLGRMLAARL 157
>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 = 29.4 bits (67), Expect = 1.5
Identities = 10/16 (62%), Positives = 11/16 (68%)
Query: 26 FLGLDNAGKTTLLHML 41
LG + AGKTT L ML
Sbjct: 33 LLGHNGAGKTTTLKML 48
Score = 29.4 bits (67), Expect = 1.5
Identities = 10/16 (62%), Positives = 11/16 (68%)
Query: 71 FLGLDNAGKTTLLHML 86
LG + AGKTT L ML
Sbjct: 33 LLGHNGAGKTTTLKML 48
>gnl|CDD|206748 cd01855, YqeH, Circularly permuted YqeH GTPase. YqeH is an
essential GTP-binding protein. Depletion of YqeH induces
an excess initiation of DNA replication, suggesting that
it negatively controls initiation of chromosome
replication. The YqeH subfamily is common in eukaryotes
and sporadically present in bacteria with probable
acquisition by plants from chloroplasts. Proteins of the
YqeH family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases.
Length = 191
Score = 29.2 bits (66), Expect = 1.6
Identities = 12/54 (22%), Positives = 22/54 (40%), Gaps = 2/54 (3%)
Query: 7 WFTGVLGYL-GLWTKSGKLLFLGLDNAGKTTLLH-MLKDDRLAQPVPTLHPILG 58
++ + L G + +G N GK+TL++ +LK + L L
Sbjct: 110 GVEELIEEIKKLAKYRGDVYVVGATNVGKSTLINALLKSNGGKVQAQALVQRLT 163
>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 = 29.8 bits (67), Expect = 1.6
Identities = 34/140 (24%), Positives = 67/140 (47%), Gaps = 20/140 (14%)
Query: 68 KLLFLGLDNAGKTTLLH-MLKDDR-LAQPVPTLHPTRRVWKDYFPAVDAIVF-LVDTSDR 124
KL +G N GK++LL+ +LK DR + + TR V + F ++ I+ L+DT+
Sbjct: 205 KLAIVGSPNVGKSSLLNALLKQDRAIVSDIKG--TTRDVVEGDF-ELNGILIKLLDTAG- 260
Query: 125 ERFEESKSELQCLLTDESL-----ASSIVFLVDTSDRERFEESKSELQCLLTDESLASCP 179
E ++ L ++S A +++++D S + ++ L+ D + + P
Sbjct: 261 --IREHADFVERLGIEKSFKAIKQADLVIYVLDAS------QPLTKDDFLIIDLNKSKKP 312
Query: 180 VLILGNKIDKHGAASEEEIR 199
+++ NKID + E +
Sbjct: 313 FILVLNKIDLKINSLEFFVS 332
>gnl|CDD|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein D-like (hnRNP DL) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP DL (or hnRNP D-like), also termed AU-rich element
RNA-binding factor, or JKT41-binding protein (protein
laAUF1 or JKTBP), is a dual functional protein that
possesses DNA- and RNA-binding properties. It has been
implicated in mRNA biogenesis at the transcriptional and
post-transcriptional levels. hnRNP DL binds
single-stranded DNA (ssDNA) or double-stranded DNA
(dsDNA) in a non-sequencespecific manner, and interacts
with poly(G) and poly(A) tenaciously. It contains two
putative two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glycine- and tyrosine-rich C-terminus. .
Length = 75
Score = 27.3 bits (60), Expect = 2.3
Identities = 7/13 (53%), Positives = 12/13 (92%)
Query: 194 SEEEIRQYFGLYG 206
+EE+I++YFG +G
Sbjct: 12 TEEQIKEYFGAFG 24
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 28.9 bits (66), Expect = 2.5
Identities = 20/46 (43%), Positives = 25/46 (54%), Gaps = 13/46 (28%)
Query: 23 KLL----FLGLDNAGKTTLLHMLKDDRLAQP----VP--TLHPILG 58
KLL +GL NAGK+TL+ + A+P P TLHP LG
Sbjct: 156 KLLADVGLVGLPNAGKSTLISAVSA---AKPKIADYPFTTLHPNLG 198
>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 = 28.5 bits (64), Expect = 2.6
Identities = 26/135 (19%), Positives = 48/135 (35%), Gaps = 20/135 (14%)
Query: 19 TKSGKLLFLGLDNAGKTTLLHMLKDDRLAQPVPTLHPILGYLGLWTKSGKLLFLGLDNAG 78
+ ++ GL ++GKT+L +L + + V + P Y L
Sbjct: 1 SSQPAVIIAGLCDSGKTSLFTLLTTGTVKKTVTSQEPSAAYK-----------YMLHKGF 49
Query: 79 KTTLLHMLKDDRLAQPVPTLHPTRRVWKDYFPAVDAIVFLVDTSDRERFEESKSEL--QC 136
TL+ +L Q + + IVF+VD++ + +E +
Sbjct: 50 SFTLIDFPGHVKLRQKLLETIKDSSSLR-------GIVFVVDSTAFPKEVTDTAEFLYEI 102
Query: 137 LLTDESLASSIVFLV 151
L E L + I L+
Sbjct: 103 LSITELLKNGIDILI 117
>gnl|CDD|220627 pfam10193, Telomere_reg-2, Telomere length regulation protein.
This family is the central conserved 110 amino acid
region of a group of proteins called telomere-length
regulation or clock abnormal protein-2 which are
conserved from plants to humans. The full-length protein
regulates telomere length and contributes to silencing
of sub-telomeric regions. In vitro the protein binds to
telomeric DNA repeats.
Length = 114
Score = 27.6 bits (62), Expect = 2.7
Identities = 19/65 (29%), Positives = 29/65 (44%), Gaps = 14/65 (21%)
Query: 117 FLVDTSDRERFEES----------KSELQCLLTD--ESLASSIVFLVDTSDRERFEESKS 164
DT + ERFE + K++ + + E LA ++ L + D E FEE +
Sbjct: 12 LRSDTENYERFELALKTAPTLIRQKADFGTEVAEHAEELAKILLGLQNKFDLEDFEELR- 70
Query: 165 ELQCL 169
LQ L
Sbjct: 71 -LQAL 74
>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 = 28.3 bits (63), Expect = 2.7
Identities = 19/130 (14%), Positives = 42/130 (32%), Gaps = 21/130 (16%)
Query: 116 VFLVDTSDRERFEESKSELQCLLTDESLASSIVFLVDTSDRERFEESKSELQCLLTDESL 175
+F+ D++ +E F + + + + + D ++ F + + T
Sbjct: 55 LFIFDSAGQELFSDMVENVW------EQPAVVCVVYDVTNEVSFNNCSRWINRVRTHSHG 108
Query: 176 ASCPVLILGNKIDKHGAASEEEIRQYFGLYGLTTGKVATPRSEMSGRPIELFMCSVLMRQ 235
P +++GNK D + A ++ ++ + S
Sbjct: 109 LHTPGVLVGNKCDLTDRREVDA---------------AQAQALAQANTLKFYETSAKEGV 153
Query: 236 GYGDGFRWLA 245
GY F LA
Sbjct: 154 GYEAPFLSLA 163
>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 = 28.3 bits (64), Expect = 3.5
Identities = 26/128 (20%), Positives = 56/128 (43%), Gaps = 11/128 (8%)
Query: 68 KLLFLGLDNAGKTTLLHMLKDDRLAQPVPTLHPTRRVWKDYFPAVDAIVF-LVDTSDRER 126
K+L +GL +GK+++ ++ + + L T V + + + + L D ++
Sbjct: 1 KVLLMGLRGSGKSSMRSIIFSNYSPRDTLRLGATIDVEQSHVRFLGNLTLNLWDCPGQDD 60
Query: 127 FEESKSELQ--CLLTDESLASSIVFLVDTSDRERFEESKSELQ---CLLTDESLASCPVL 181
F E+ Q + ++ ++++ D RE +EE + L L S + V
Sbjct: 61 FMENYLTRQKEHIFSN---VGVLIYVFDVESRE-YEEDLATLVKIIEALYQYSPNAK-VF 115
Query: 182 ILGNKIDK 189
+L +K+D
Sbjct: 116 VLIHKMDL 123
>gnl|CDD|130256 TIGR01188, drrA, daunorubicin resistance ABC transporter
ATP-binding subunit. This model describes daunorubicin
resistance ABC transporter, ATP binding subunit in
bacteria and archaea. This model is restricted in its
scope to preferentially recognize the ATP binding
subunit associated with effux of the drug,
daunorubicin. 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. In eukaryotes
proteins of similar function include p-gyco proteins,
multidrug resistance protein etc [Transport and binding
proteins, Other].
Length = 302
Score = 28.1 bits (63), Expect = 3.9
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 26 FLGLDNAGKTTLLHML 41
FLG + AGKTT + ML
Sbjct: 24 FLGPNGAGKTTTIRML 39
Score = 28.1 bits (63), Expect = 3.9
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 71 FLGLDNAGKTTLLHML 86
FLG + AGKTT + ML
Sbjct: 24 FLGPNGAGKTTTIRML 39
>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 = 27.9 bits (63), Expect = 4.1
Identities = 36/150 (24%), Positives = 60/150 (40%), Gaps = 45/150 (30%)
Query: 68 KLLFLGLDNAGKTTLL-HMLKDDRLAQPVPTLHPTRRVWKDYFPAVDAIVFL-------- 118
L +G +AGK+TLL +L ++ L PT P I L
Sbjct: 2 LLAVVGEFSAGKSTLLNALLGEEVL--------PTGVT-----PTTAVITVLRYGLLKGV 48
Query: 119 --VDT-----SDRERFEESKSELQCLLTDESLASSIVFLVDTSDRERFEESKSELQCLLT 171
VDT + E ++S L A +++F++ +D+ ++SE + L
Sbjct: 49 VLVDTPGLNSTIEHHTEITESFL-------PRADAVIFVLS-ADQP---LTESERE-FLK 96
Query: 172 DESLASCP-VLILGNKIDKHGAASEEEIRQ 200
+ S + + NKID SEEE+ +
Sbjct: 97 EILKWSGKKIFFVLNKIDLL---SEEELEE 123
>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 = 28.2 bits (64), Expect = 4.3
Identities = 19/46 (41%), Positives = 24/46 (52%), Gaps = 13/46 (28%)
Query: 23 KLL----FLGLDNAGKTTLLHMLKDDRLAQP----VP--TLHPILG 58
KLL +GL NAGK+TL+ + A+P P TL P LG
Sbjct: 155 KLLADVGLVGLPNAGKSTLISAVSA---AKPKIADYPFTTLVPNLG 197
>gnl|CDD|213232 cd03265, ABC_DrrA, Daunorubicin/doxorubicin resistance
ATP-binding protein. DrrA is the ATP-binding protein
component of a bacterial exporter complex that confers
resistance to the antibiotics daunorubicin and
doxorubicin. In addition to DrrA, the complex includes
an integral membrane protein called DrrB. DrrA belongs
to the ABC family of transporters and shares sequence
and functional similarities with a protein found in
cancer cells called P-glycoprotein. 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 = 220
Score = 27.7 bits (62), Expect = 4.3
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 26 FLGLDNAGKTTLLHML 41
LG + AGKTT + ML
Sbjct: 31 LLGPNGAGKTTTIKML 46
Score = 27.7 bits (62), Expect = 4.3
Identities = 9/16 (56%), Positives = 11/16 (68%)
Query: 71 FLGLDNAGKTTLLHML 86
LG + AGKTT + ML
Sbjct: 31 LLGPNGAGKTTTIKML 46
>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 = 28.3 bits (64), Expect = 4.5
Identities = 23/88 (26%), Positives = 34/88 (38%), Gaps = 24/88 (27%)
Query: 102 RRVWKDYFPAVDAIVFLVDTSDRERFEESKSELQCLLTDESLASSIVFLVDTSDRERFEE 161
R+ W F V AI+F+V S+ + Q L+ DES+ R +E
Sbjct: 175 RKKWIHCFEDVTAIIFVVALSEYD---------QVLVEDESVN-------------RMQE 212
Query: 162 SKSELQCLLTDESLASCPV-LILGNKID 188
S + A+ + L L NK D
Sbjct: 213 SLKLFDSICNSRWFANTSIILFL-NKKD 239
>gnl|CDD|226631 COG4152, COG4152, ABC-type uncharacterized transport system,
ATPase component [General function prediction only].
Length = 300
Score = 28.1 bits (63), Expect = 4.5
Identities = 9/23 (39%), Positives = 13/23 (56%), Gaps = 1/23 (4%)
Query: 20 KSGKLL-FLGLDNAGKTTLLHML 41
G++ LG + AGKTT M+
Sbjct: 26 PPGEIFGLLGPNGAGKTTTFRMI 48
Score = 28.1 bits (63), Expect = 4.5
Identities = 9/23 (39%), Positives = 13/23 (56%), Gaps = 1/23 (4%)
Query: 65 KSGKLL-FLGLDNAGKTTLLHML 86
G++ LG + AGKTT M+
Sbjct: 26 PPGEIFGLLGPNGAGKTTTFRMI 48
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 28.3 bits (64), Expect = 4.7
Identities = 34/145 (23%), Positives = 61/145 (42%), Gaps = 30/145 (20%)
Query: 68 KLLFLGLDNAGKTTLLH-MLKDDR-LAQPVP-TLHPTRRVWKDYFPAVDAI-VFLVDT-- 121
K++ +G N GK++LL+ +L DR + + T TR V ++ ++ I V LVDT
Sbjct: 219 KVVIIGRPNVGKSSLLNALLGRDRAIVTDIAGT---TRDVIEEDI-NLNGIPVRLVDTAG 274
Query: 122 ----SD---RERFEESKSELQCLLTDESLASSIVFLVDTSDRERFEESKSELQCLLTDES 174
D R E +K ++ A ++F++D S + L +
Sbjct: 275 IRETDDVVERIGIERAKKAIE-------EADLVLFVLDASQPL------DKEDLALIELL 321
Query: 175 LASCPVLILGNKIDKHGAASEEEIR 199
P++++ NK D E +
Sbjct: 322 PKKKPIIVVLNKADLVSKIELESEK 346
>gnl|CDD|238835 cd01672, TMPK, Thymidine monophosphate kinase (TMPK), also known
as thymidylate kinase, catalyzes the phosphorylation of
thymidine monophosphate (TMP) to thymidine diphosphate
(TDP) utilizing ATP as its preferred phophoryl donor.
TMPK represents the rate-limiting step in either de
novo or salvage biosynthesis of thymidine triphosphate
(TTP).
Length = 200
Score = 27.6 bits (62), Expect = 4.8
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 28 GLDNAGKTTLLHMLKD 43
G+D AGKTTL+ +L +
Sbjct: 7 GIDGAGKTTLIELLAE 22
Score = 27.6 bits (62), Expect = 4.8
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 73 GLDNAGKTTLLHMLKD 88
G+D AGKTTL+ +L +
Sbjct: 7 GIDGAGKTTLIELLAE 22
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 27.9 bits (63), Expect = 4.9
Identities = 18/43 (41%), Positives = 22/43 (51%), Gaps = 7/43 (16%)
Query: 23 KLL----FLGLDNAGKTTLLHMLKDDR---LAQPVPTLHPILG 58
KLL +GL NAGK+TLL + + P TL P LG
Sbjct: 157 KLLADVGLVGLPNAGKSTLLSAVSAAKPKIADYPFTTLVPNLG 199
>gnl|CDD|226121 COG3593, COG3593, Predicted ATP-dependent endonuclease of the OLD
family [DNA replication, recombination, and repair].
Length = 581
Score = 28.1 bits (63), Expect = 4.9
Identities = 28/144 (19%), Positives = 50/144 (34%), Gaps = 25/144 (17%)
Query: 60 LGLWTKSGKLLFLGLDNAGKTTLLHMLKDDRLAQPVPTLHPTRRVWKD-YFPAVDA---- 114
L L + G + +G +N+GK++LL L+ L P L+ D +FP +
Sbjct: 17 LSLEFEEGLNVLIGENNSGKSSLLDALR--LLLDPESDLYSF--TLDDFHFPISEFDEKS 72
Query: 115 --IVFLVDTSDRERFEES------KSELQCLLTDESLASSIVFLVDTSDRERFEESKSEL 166
+ + ++ + E + + + I R R E E
Sbjct: 73 QHLHIELTFAESDPNERAVVRYRLLEPGALWIPNLDGIEKI--------RYRLEGEALED 124
Query: 167 QCLLTDESLASCPVLILGNKIDKH 190
++T S + GN I K
Sbjct: 125 GIVMTLRSFLNLGRNKDGNPIAKE 148
>gnl|CDD|224054 COG1131, CcmA, ABC-type multidrug transport system, ATPase
component [Defense mechanisms].
Length = 293
Score = 28.0 bits (63), Expect = 5.0
Identities = 11/23 (47%), Positives = 16/23 (69%), Gaps = 1/23 (4%)
Query: 20 KSGKLL-FLGLDNAGKTTLLHML 41
+ G++ LG + AGKTTLL +L
Sbjct: 29 EPGEIFGLLGPNGAGKTTLLKIL 51
Score = 28.0 bits (63), Expect = 5.0
Identities = 11/23 (47%), Positives = 16/23 (69%), Gaps = 1/23 (4%)
Query: 65 KSGKLL-FLGLDNAGKTTLLHML 86
+ G++ LG + AGKTTLL +L
Sbjct: 29 EPGEIFGLLGPNGAGKTTLLKIL 51
>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 = 27.1 bits (61), Expect = 5.6
Identities = 34/136 (25%), Positives = 57/136 (41%), Gaps = 37/136 (27%)
Query: 68 KLLFLGLDNAGKTTLLHMLKDDR-LAQPVPTLHPTRRVWKDYF--PAVDAIVF---LVDT 121
K++ +G GKT LL ++ + VPT V+ +Y VD L DT
Sbjct: 2 KIVVVGDGAVGKTCLLISYTTNKFPTEYVPT------VFDNYSANVTVDGKQVNLGLWDT 55
Query: 122 SDRERFEESKSELQCLL---TDESLASSIVFLV--DTSDRERFE--ESK--SELQCLLTD 172
+ +E ++ L+ L TD VFL+ FE ++K E++ +
Sbjct: 56 AGQEEYD----RLRPLSYPQTD-------VFLLCFSVDSPSSFENVKTKWYPEIKHYCPN 104
Query: 173 ESLASCPVLILGNKID 188
P++++G KID
Sbjct: 105 -----VPIILVGTKID 115
>gnl|CDD|213199 cd03232, ABCG_PDR_domain2, Second domain of the pleiotropic drug
resistance-like (PDR) subfamily G of ATP-binding
cassette transporters. The pleiotropic drug resistance
(PDR) is a well-described phenomenon occurring in fungi
and shares several similarities with processes in
bacteria and higher eukaryotes. This PDR subfamily
represents domain I of its (ABC-IM)2 organization. ABC
transporters are a large family of proteins involved in
the transport of a wide variety of different compounds
including 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 = 192
Score = 27.6 bits (62), Expect = 5.8
Identities = 17/35 (48%), Positives = 20/35 (57%), Gaps = 5/35 (14%)
Query: 53 LHPILGYLGLWTKSGKLLFL-GLDNAGKTTLLHML 86
L+ I GY+ K G L L G AGKTTLL +L
Sbjct: 23 LNNISGYV----KPGTLTALMGESGAGKTTLLDVL 53
>gnl|CDD|129668 TIGR00578, ku70, ATP-dependent DNA helicase II, 70 kDa subunit
(ku70). Proteins in this family are involved in
non-homologous end joining, a process used for the
repair of double stranded DNA breaks. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University). Cutoff does not
detect the putative ku70 homologs in yeast [DNA
metabolism, DNA replication, recombination, and repair].
Length = 584
Score = 27.9 bits (62), Expect = 5.9
Identities = 13/28 (46%), Positives = 19/28 (67%), Gaps = 2/28 (7%)
Query: 107 DY-FPAVDAIVFLVDTSDRERFEESKSE 133
DY + D+++FLVD S + FEES+ E
Sbjct: 4 DYKYSGRDSLIFLVDAS-KAMFEESQGE 30
>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 = 27.2 bits (61), Expect = 6.4
Identities = 12/26 (46%), Positives = 17/26 (65%), Gaps = 4/26 (15%)
Query: 26 FLGLDNAGKTTLL-HMLKDDRLAQPV 50
FLG +GKTTLL H+L+ +R +
Sbjct: 8 FLG---SGKTTLLEHLLEKNREGLKI 30
Score = 27.2 bits (61), Expect = 6.4
Identities = 12/26 (46%), Positives = 17/26 (65%), Gaps = 4/26 (15%)
Query: 71 FLGLDNAGKTTLL-HMLKDDRLAQPV 95
FLG +GKTTLL H+L+ +R +
Sbjct: 8 FLG---SGKTTLLEHLLEKNREGLKI 30
>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 = 27.1 bits (61), Expect = 6.9
Identities = 17/73 (23%), Positives = 32/73 (43%), Gaps = 9/73 (12%)
Query: 133 ELQCLLTDESLASSIVFLVDTSDRERFEES----KSELQCLLTDESLASCPVLILGNKID 188
E+Q + L ++++F +D S E + +L + L + PV+++ NKID
Sbjct: 69 EMQAITALAHLRAAVLFFIDPS-----ETCGYSIEEQLSLFKEIKPLFNKPVIVVLNKID 123
Query: 189 KHGAASEEEIRQY 201
EI +
Sbjct: 124 LLTEEDLSEIEKE 136
>gnl|CDD|133345 cd04145, M_R_Ras_like, R-Ras2/TC21, M-Ras/R-Ras3. The
M-Ras/R-Ras-like subfamily contains R-Ras2/TC21,
M-Ras/R-Ras3, and related members of the Ras family.
M-Ras is expressed in lympho-hematopoetic cells. It
interacts with some of the known Ras effectors, but
appears to also have its own effectors. Expression of
mutated M-Ras leads to transformation of several types
of cell lines, including hematopoietic cells, mammary
epithelial cells, and fibroblasts. Overexpression of
M-Ras is observed in carcinomas from breast, uterus,
thyroid, stomach, colon, kidney, lung, and rectum. In
addition, expression of a constitutively active M-Ras
mutant in murine bone marrow induces a malignant mast
cell leukemia that is distinct from the monocytic
leukemia induced by H-Ras. TC21, along with H-Ras, has
been shown to regulate the branching morphogenesis of
ureteric bud cell branching in mice. Most Ras proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 164
Score = 27.0 bits (60), Expect = 7.1
Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 6/75 (8%)
Query: 114 AIVFLVDTSDRERFEESKSELQCLLTDESLASSIVFLVDTSDRERFEESKSELQCLLTDE 173
A + ++DT+ +E F S Q + T E +VF V +DR FEE +L +
Sbjct: 50 ARLDILDTAGQEEF--SAMREQYMRTGEGFL--LVFSV--TDRGSFEEVDKFHTQILRVK 103
Query: 174 SLASCPVLILGNKID 188
P++++GNK D
Sbjct: 104 DRDEFPMILVGNKAD 118
>gnl|CDD|131721 TIGR02673, FtsE, cell division ATP-binding protein FtsE. This
model describes FtsE, a member of the ABC transporter
ATP-binding protein family. This protein, and its
permease partner FtsX, localize to the division site.
In a number of species, the ftsEX gene pair is located
next to FtsY, the signal recognition particle-docking
protein [Cellular processes, Cell division].
Length = 214
Score = 27.2 bits (61), Expect = 7.5
Identities = 16/37 (43%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 51 PTLHPILGYLGLWTKSGKLLFL-GLDNAGKTTLLHML 86
P L + L + G+ LFL G AGKTTLL +L
Sbjct: 12 PGGVAALHDVSLHIRKGEFLFLTGPSGAGKTTLLKLL 48
>gnl|CDD|232967 TIGR00418, thrS, threonyl-tRNA synthetase. This model represents
the threonyl-tRNA synthetase found in most organisms.
This protein is a class II tRNA synthetase, and is
recognized by the pfam model tRNA-synt_2b. Note that B.
subtilis has closely related isozymes thrS and thrZ. The
N-terminal regions are quite dissimilar between archaeal
and eubacterial forms, while some eukaryotic forms are
missing sequence there altogether. [Protein synthesis,
tRNA aminoacylation].
Length = 563
Score = 27.7 bits (62), Expect = 7.6
Identities = 12/51 (23%), Positives = 18/51 (35%), Gaps = 7/51 (13%)
Query: 17 LWTKSGKLLFLGLDNAGKTTLLHMLKDDRLAQPVPTLHPILGYLGLWTKSG 67
W G + L++ + + V T PI+ L LW SG
Sbjct: 194 FWLPKGATIRNLLED-----FVRQKQIKYGYMEVET--PIMYDLELWEISG 237
>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 = 27.0 bits (61), Expect = 7.7
Identities = 8/16 (50%), Positives = 12/16 (75%)
Query: 26 FLGLDNAGKTTLLHML 41
LG + AGKTTL+ ++
Sbjct: 31 LLGPNGAGKTTLIKII 46
Score = 27.0 bits (61), Expect = 7.7
Identities = 8/16 (50%), Positives = 12/16 (75%)
Query: 71 FLGLDNAGKTTLLHML 86
LG + AGKTTL+ ++
Sbjct: 31 LLGPNGAGKTTLIKII 46
>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 = 26.8 bits (60), Expect = 7.8
Identities = 12/42 (28%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 147 IVFLVDTSDRERFEESKSELQCLLTDESLASCPVLILGNKID 188
+V+ + DR+ FEE + +L + P++++GNK D
Sbjct: 79 LVYSIT--DRQSFEEIAKFREQILRVKDRDDVPIVLVGNKCD 118
>gnl|CDD|189055 cd09885, PIN_Smg6, PIN domain of human telomerase-binding protein
EST1, Smg6, and other similar eukaryotic homologs.
Nonsense-mediated decay (NMD) factors, Smg5 and Smg6 are
essential to the post-transcriptional regulatory
pathway, NMD, which recognizes and rapidly degrades
mRNAs containing premature translation termination
codons. In vivo, the Smg6 PIN (PilT N terminus) domain
elicits degradation of bound mRNAs, as well as, metal
ion dependent, degradation of single-stranded RNA, in
vitro. These PIN domains are structural homologs of flap
endonuclease-1 (FEN1)-like PIN domains, but lack the
extensive arch/clamp region and the H3TH
(helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region, seen in FEN1-like PIN
domains. PIN domains within this subgroup contain four
highly conserved acidic residues (putative
metal-binding, active site residues) which cluster at
the C-terminal end of the beta-sheet and form a
negatively charged pocket near the center of the
molecule. Point mutation studies of the conserved
aspartate residues in the catalytic center of the Smg6
PIN domain revealed that Smg6 is the endonuclease
involved in human NMD. However, Smg5 lacks several of
these key catalytic residues and does not degrade
single-stranded RNA, in vivo. Eukaryotic Smg6 PIN
domains are present at the C-terminal end of the
telomerase activating proteins, Est1.
Length = 182
Score = 27.0 bits (60), Expect = 8.3
Identities = 25/96 (26%), Positives = 38/96 (39%), Gaps = 19/96 (19%)
Query: 89 DRLAQPVPTLHPTRRVWKD-YFPAV-----DAIVFLVDTSDRERFEESKSELQCLLTDES 142
D L++ P P+ + V +A+ FL +ERFE+ S L+ L + S
Sbjct: 44 DGLSKGSPLDSPSNGTLSPAHDREVQERAKEAVAFL-----KERFEKRDSCLRALTSRGS 98
Query: 143 LASSIVFLVDTSDRERFEESKSELQCLLTDESLASC 178
+I F R E+ + E D LA C
Sbjct: 99 FLETIAF--------RSEDLEGEEGGTNDDVILACC 126
>gnl|CDD|223597 COG0523, COG0523, Putative GTPases (G3E family) [General function
prediction only].
Length = 323
Score = 27.3 bits (61), Expect = 8.8
Identities = 11/19 (57%), Positives = 14/19 (73%), Gaps = 4/19 (21%)
Query: 26 FLGLDNAGKTTLL-HMLKD 43
FLG +GKTTLL H+L +
Sbjct: 9 FLG---SGKTTLLNHLLAN 24
Score = 27.3 bits (61), Expect = 8.8
Identities = 11/19 (57%), Positives = 14/19 (73%), Gaps = 4/19 (21%)
Query: 71 FLGLDNAGKTTLL-HMLKD 88
FLG +GKTTLL H+L +
Sbjct: 9 FLG---SGKTTLLNHLLAN 24
>gnl|CDD|226927 COG4555, NatA, ABC-type Na+ transport system, ATPase component
[Energy production and conversion / Inorganic ion
transport and metabolism].
Length = 245
Score = 27.0 bits (60), Expect = 9.1
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 27 LGLDNAGKTTLLHML 41
LG + AGKTTLL M+
Sbjct: 34 LGENGAGKTTLLRMI 48
Score = 27.0 bits (60), Expect = 9.1
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 72 LGLDNAGKTTLLHML 86
LG + AGKTTLL M+
Sbjct: 34 LGENGAGKTTLLRMI 48
>gnl|CDD|206734 cd04171, SelB, SelB, the dedicated elongation factor for delivery
of selenocysteinyl-tRNA to the ribosome. SelB is an
elongation factor needed for the co-translational
incorporation of selenocysteine. Selenocysteine is coded
by a UGA stop codon in combination with a specific
downstream mRNA hairpin. In bacteria, the C-terminal
part of SelB recognizes this hairpin, while the
N-terminal part binds GTP and tRNA in analogy with
elongation factor Tu (EF-Tu). It specifically recognizes
the selenocysteine charged tRNAsec, which has a UCA
anticodon, in an EF-Tu like manner. This allows
insertion of selenocysteine at in-frame UGA stop codons.
In E. coli SelB binds GTP, selenocysteyl-tRNAsec, and a
stem-loop structure immediately downstream of the UGA
codon (the SECIS sequence). The absence of active SelB
prevents the participation of selenocysteyl-tRNAsec in
translation. Archaeal and animal mechanisms of
selenocysteine incorporation are more complex. Although
the SECIS elements have different secondary structures
and conserved elements between archaea and eukaryotes,
they do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains bacterial SelBs, as well as, one from archaea.
Length = 170
Score = 26.8 bits (60), Expect = 9.5
Identities = 18/55 (32%), Positives = 26/55 (47%)
Query: 120 DTSDRERFEESKSELQCLLTDESLASSIVFLVDTSDRERFEESKSELQCLLTDES 174
D D +R E + E+ LL LA + +F V + E EE K+ L L +S
Sbjct: 114 DLVDEDRLELVEEEILELLAGTFLADAPIFPVSSVTGEGIEELKNYLDELAEPQS 168
>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 = 26.6 bits (60), Expect = 9.6
Identities = 13/34 (38%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 54 HPILGYLGLWTKSGKLL-FLGLDNAGKTTLLHML 86
+L L L ++G+++ LG + AGK+TLL L
Sbjct: 12 RTVLDDLSLSIEAGEIVGILGPNGAGKSTLLKTL 45
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
0.322 0.139 0.429
Gapped
Lambda K H
0.267 0.0694 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,946,666
Number of extensions: 1218960
Number of successful extensions: 2089
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2024
Number of HSP's successfully gapped: 206
Length of query: 249
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 155
Effective length of database: 6,768,326
Effective search space: 1049090530
Effective search space used: 1049090530
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 58 (26.2 bits)