RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2159
(194 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 = 308 bits (792), Expect = e-109
Identities = 122/190 (64%), Positives = 150/190 (78%)
Query: 4 IWTKFREVLLRLGLWKKSGKLLFLGLDNAGKTFLLQMLKNDRTAQHMPTLHPTSEELSMG 63
I+ F VL LGL+KK K++FLGLDNAGKT LL MLK+DR AQH+PTLHPTSEEL++G
Sbjct: 2 IFDWFYNVLSSLGLYKKEAKIVFLGLDNAGKTTLLHMLKDDRLAQHVPTLHPTSEELTIG 61
Query: 64 DIVFTTHDLGGHVQARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDV 123
++ FTT DLGGH QARRVW+DYFP VD IVF++DA+D RF ESK ELD+LL D+ L +V
Sbjct: 62 NVKFTTFDLGGHEQARRVWKDYFPEVDGIVFLVDAADPERFQESKEELDSLLNDEELANV 121
Query: 124 PILILGNKIDIFDAASEDEVRHFFGLYGLTTGKEFTPREILQMRPMELFMCSVLKRQGFG 183
PILILGNKID A SE+E+R GLYG TTGK ++ +RP+E+FMCSV+KRQG+G
Sbjct: 122 PILILGNKIDKPGAVSEEELREALGLYGTTTGKGGVSLKVSNIRPVEVFMCSVVKRQGYG 181
Query: 184 NGFRWLANYI 193
GFRWL+ Y+
Sbjct: 182 EGFRWLSQYL 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 = 262 bits (670), Expect = 2e-90
Identities = 116/186 (62%), Positives = 142/186 (76%), Gaps = 5/186 (2%)
Query: 8 FREVLLRLGLWKKSGKLLFLGLDNAGKTFLLQMLKNDRTAQHMPTLHPTSEELSMGDIVF 67
F ++L LGLW K K+LFLGLDNAGKT LL MLKNDR AQH PT HPTSEEL++G+I F
Sbjct: 4 FYDILASLGLWNKHAKILFLGLDNAGKTTLLHMLKNDRLAQHQPTQHPTSEELAIGNIKF 63
Query: 68 TTHDLGGHVQARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILI 127
TT DLGGH QARR+W+DYFP V+ IV+++DA D+ RF ESK ELD LL+D+ L VP LI
Sbjct: 64 TTFDLGGHQQARRLWKDYFPEVNGIVYLVDAYDKERFAESKRELDALLSDEELATVPFLI 123
Query: 128 LGNKIDIFDAASEDEVRHFFGLYGLTTGKEFTPREILQMRPMELFMCSVLKRQGFGNGFR 187
LGNKID AASEDE+R+ GL TTGK + +RP+E+FMCSV++R G+G GF+
Sbjct: 124 LGNKIDAPYAASEDELRYALGLTNTTTGK-----GKVGVRPVEVFMCSVVRRMGYGEGFK 178
Query: 188 WLANYI 193
WL+ YI
Sbjct: 179 WLSQYI 184
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 233 bits (597), Expect = 3e-79
Identities = 74/186 (39%), Positives = 105/186 (56%), Gaps = 12/186 (6%)
Query: 8 FREVLLRLGLWKKSGKLLFLGLDNAGKTFLLQMLKNDRTAQHMPTLHPTSEELSMGDIVF 67
F +L +L W K ++L LGLDNAGKT +L LK +PT+ E ++ ++ F
Sbjct: 1 FLSILAKLFGWNKEMRILILGLDNAGKTTILYKLKLGEIVTTIPTIGFNVETVTYKNVKF 60
Query: 68 TTHDLGGHVQARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILI 127
T D+GG R +WR+YFP DA++F++D++DR R E+K EL LL ++ L D P+LI
Sbjct: 61 TVWDVGGQESLRPLWRNYFPNTDAVIFVVDSADRDRIEEAKEELHALLNEEELADAPLLI 120
Query: 128 LGNKIDIFDAASEDEVRHFFGLYGLTTGKEFTPREILQMRPMELFMCSVLKRQGFGNGFR 187
L NK D+ A SE E+R GL+ L RP E+ CS + +G G
Sbjct: 121 LANKQDLPGAMSEAEIRELLGLHELKD------------RPWEIQGCSAVTGEGLDEGLD 168
Query: 188 WLANYI 193
WL+NYI
Sbjct: 169 WLSNYI 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 = 146 bits (372), Expect = 2e-45
Identities = 56/169 (33%), Positives = 84/169 (49%), Gaps = 12/169 (7%)
Query: 23 KLLFLGLDNAGKTFLLQMLKNDRTAQHMPTLHPTSEELSMGDIVFTTHDLGGHVQARRVW 82
++L LGLD AGKT +L LK +PT+ E + ++ FT D+GG + R +W
Sbjct: 1 RILMLGLDGAGKTTILYKLKLGEVVTTIPTIGFNVETVEYKNVKFTVWDVGGQDKIRPLW 60
Query: 83 RDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKIDIFDAASEDE 142
+ Y+ D ++F++D+SDR R E+K EL LL ++ L P+LIL NK D+ A +E E
Sbjct: 61 KHYYENTDGLIFVVDSSDRERIEEAKNELHKLLNEEELKGAPLLILANKQDLPGALTESE 120
Query: 143 VRHFFGLYGLTTGKEFTPREILQMRPMELFMCSVLKRQGFGNGFRWLAN 191
+ GL + R + CS + G G WL
Sbjct: 121 LIELLGLESIKG------------RRWHIQPCSAVTGDGLDEGLDWLIE 157
>gnl|CDD|206718 cd04151, Arl1, ADP ribosylation factor 1 (Arf1). Arl1 subfamily.
Arl1 (Arf-like 1) localizes to the Golgi complex, where
it is believed to recruit effector proteins to the
trans-Golgi network. Like most members of the Arf
family, Arl1 is myristoylated at its N-terminal helix
and mutation of the myristoylation site disrupts Golgi
targeting. In humans, the Golgi-localized proteins
golgin-97 and golgin-245 have been identified as Arl1
effectors. Golgins are large coiled-coil proteins found
in the Golgi, and these golgins contain a C-terminal
GRIP domain, which is the site of Arl1 binding.
Additional Arl1 effectors include the GARP
(Golgi-associated retrograde protein)/VFT (Vps53)
vesicle-tethering complex and Arfaptin 2. Arl1 is not
required for exocytosis, but appears necessary for
trafficking from the endosomes to the Golgi. In
Drosophila zygotes, mutation of Arl1 is lethal, and in
the host-bloodstream form of Trypanosoma brucei, Arl1 is
essential for viability.
Length = 158
Score = 120 bits (302), Expect = 7e-35
Identities = 58/169 (34%), Positives = 84/169 (49%), Gaps = 12/169 (7%)
Query: 23 KLLFLGLDNAGKTFLLQMLKNDRTAQHMPTLHPTSEELSMGDIVFTTHDLGGHVQARRVW 82
++L LGLD AGKT +L L+ +PT+ E ++ ++ F DLGG R W
Sbjct: 1 RILILGLDGAGKTTILYRLQVGEVVTTIPTIGFNVETVTYKNLKFQVWDLGGQTSIRPYW 60
Query: 83 RDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKIDIFDAASEDE 142
R Y+ DAI++++D++DR R SK EL +L ++ L D +L+ NK D+ A SE E
Sbjct: 61 RCYYSNTDAIIYVVDSTDRDRLGISKSELHAMLEEEELKDAVLLVFANKQDMPGALSEAE 120
Query: 143 VRHFFGLYGLTTGKEFTPREILQMRPMELFMCSVLKRQGFGNGFRWLAN 191
V GL L R ++F S K +G G WL N
Sbjct: 121 VAEKLGLSELKD------------RTWQIFKTSATKGEGLDEGMDWLVN 157
>gnl|CDD|133353 cd04153, Arl5_Arl8, Arf-like 5 (Arl5) and 8 (Arl8) GTPases.
Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like
Arl4 and Arl7, are localized to the nucleus and
nucleolus. Arl5 is developmentally regulated during
embryogenesis in mice. Human Arl5 interacts with the
heterochromatin protein 1-alpha (HP1alpha), a nonhistone
chromosomal protein that is associated with
heterochromatin and telomeres, and prevents telomere
fusion. Arl5 may also play a role in embryonic nuclear
dynamics and/or signaling cascades. Arl8 was identified
from a fetal cartilage cDNA library. It is found in
brain, heart, lung, cartilage, and kidney. No function
has been assigned for Arl8 to date.
Length = 174
Score = 115 bits (290), Expect = 8e-33
Identities = 53/170 (31%), Positives = 81/170 (47%), Gaps = 14/170 (8%)
Query: 23 KLLFLGLDNAGKTFLL-QMLKNDRTAQHMPTLHPTSEELSMGDIVFTTHDLGGHVQARRV 81
K++ +GLDNAGKT +L Q L + PT+ EE+ +I F D+GG R
Sbjct: 17 KVIIVGLDNAGKTTILYQFLLGEVVHTS-PTIGSNVEEIVYKNIRFLMWDIGGQESLRSS 75
Query: 82 WRDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKIDIFDAASED 141
W Y+ DA++ +ID++DR R P +K EL +LA + L +L+L NK D+ A +
Sbjct: 76 WNTYYTNTDAVILVIDSTDRERLPLTKEELYKMLAHEDLRKAVLLVLANKQDLKGAMTPA 135
Query: 142 EVRHFFGLYGLTTGKEFTPREILQMRPMELFMCSVLKRQGFGNGFRWLAN 191
E+ GL + + C L +G G W+A+
Sbjct: 136 EISESLGLTSIRD------------HTWHIQGCCALTGEGLPEGLDWIAS 173
>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 = 111 bits (279), Expect = 3e-31
Identities = 52/172 (30%), Positives = 84/172 (48%), Gaps = 12/172 (6%)
Query: 19 KKSGKLLFLGLDNAGKTFLLQMLKNDRTAQHMPTLHPTSEELSMGDIVFTTHDLGGHVQA 78
++ ++L LGLDNAGKT +L+ L ++ + PT + + D+GG +
Sbjct: 13 RQEVRILLLGLDNAGKTTILKQLASEDISHITPTQGFNIKNVQADGFKLNVWDIGGQRKI 72
Query: 79 RRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKIDIFDAA 138
R WR+YF D ++++ID++DR RF E+ EL LL ++ L VP+L+ NK D+ AA
Sbjct: 73 RPYWRNYFENTDVLIYVIDSADRKRFEEAGQELVELLEEEKLAGVPVLVFANKQDLLTAA 132
Query: 139 SEDEVRHFFGLYGLTTGKEFTPREILQMRPMELFMCSVLKRQGFGNGFRWLA 190
+EV L ++ R + CS +G G W+
Sbjct: 133 PAEEVAEALNL------------HDIRDRSWHIQACSAKTGEGLQEGMNWVC 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 = 105 bits (263), Expect = 5e-29
Identities = 53/169 (31%), Positives = 89/169 (52%), Gaps = 12/169 (7%)
Query: 23 KLLFLGLDNAGKTFLLQMLKNDRTAQHMPTLHPTSEELSM-GDIVFTTHDLGGHVQARRV 81
++L LGLD+AGK+ LL LK+ +PT+ E L + + T D+GG + R V
Sbjct: 1 QVLLLGLDSAGKSTLLYKLKHAELVTTIPTVGFNVEMLQLEKHLSLTVWDVGGQEKMRTV 60
Query: 82 WRDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKIDIFDAASED 141
W+ Y D +V+++D+SD +R ES+ EL ++L ++ + VP+++L NK D+ A + +
Sbjct: 61 WKCYLENTDGLVYVVDSSDEARLDESQKELKHILKNEHIKGVPVVLLANKQDLPGALTAE 120
Query: 142 EVRHFFGLYGLTTGKEFTPREILQMRPMELFMCSVLKRQGFGNGFRWLA 190
E+ F L ++ R + CS + +G FR LA
Sbjct: 121 EITRRFKL-----------KKYCSDRDWYVQPCSAVTGEGLAEAFRKLA 158
>gnl|CDD|206722 cd04157, Arl6, Arf-like 6 (Arl6) GTPase. Arl6 (Arf-like 6) forms a
subfamily of the Arf family of small GTPases. Arl6
expression is limited to the brain and kidney in adult
mice, but it is expressed in the neural plate and
somites during embryogenesis, suggesting a possible role
for Arl6 in early development. Arl6 is also believed to
have a role in cilia or flagella function. Several
proteins have been identified that bind Arl6, including
Arl6 interacting protein (Arl6ip), and SEC61beta, a
subunit of the heterotrimeric conducting channel SEC61p.
Based on Arl6 binding to these effectors, Arl6 is also
proposed to play a role in protein transport, membrane
trafficking, or cell signaling during hematopoietic
maturation. At least three specific homozygous Arl6
mutations in humans have been found to cause
Bardet-Biedl syndrome, a disorder characterized by
obesity, retinopathy, polydactyly, renal and cardiac
malformations, learning disabilities, and
hypogenitalism. Older literature suggests that Arl6 is a
part of the Arl4/Arl7 subfamily, but analyses based on
more recent sequence data place Arl6 in its own
subfamily.
Length = 162
Score = 104 bits (262), Expect = 7e-29
Identities = 55/172 (31%), Positives = 86/172 (50%), Gaps = 16/172 (9%)
Query: 24 LLFLGLDNAGKTFLLQMLK--NDRTAQHMPTLHPTSEELSMGDIVFTTHDLGGHVQARRV 81
+L LGLDN+GKT ++ LK N ++ +PT+ E G++ FT D+ G + R +
Sbjct: 2 ILVLGLDNSGKTTIINQLKPSNAQSQNIVPTVGFNVESFKKGNLSFTAFDMSGQGKYRGL 61
Query: 82 WRDYFPAVDAIVFIIDASDRSRFPESKYELDNLL--ADDALTDVPILILGNKIDIFDAAS 139
W Y+ + I+F+ID+SDR R +K EL+ LL D +PIL NK+D+ DA +
Sbjct: 62 WEHYYKNIQGIIFVIDSSDRLRMVVAKDELELLLNHPDIKHRRIPILFYANKMDLPDALT 121
Query: 140 EDEVRHFFGLYGLTTGKEFTPREILQMRPMELFMCSVLKRQGFGNGFRWLAN 191
++ L E ++ +P +F S L +G G WL
Sbjct: 122 AVKITQLLCL------------ENIKDKPWHIFASSALTGEGLDEGVDWLQA 161
>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 = 101 bits (254), Expect = 1e-27
Identities = 48/173 (27%), Positives = 84/173 (48%), Gaps = 12/173 (6%)
Query: 19 KKSGKLLFLGLDNAGKTFLLQMLKNDRTAQHMPTLHPTSEELSMGDIVFTTHDLGGHVQA 78
K ++L LGLD AGKT +L LK ++ +PT+ E ++ ++ F D+GG +
Sbjct: 7 NKEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGQDKI 66
Query: 79 RRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKIDIFDAA 138
R +WR Y+ ++F++D++DR R E++ EL ++ D + D +L+ NK D+ DA
Sbjct: 67 RPLWRHYYTGTQGLIFVVDSADRDRIDEARQELHRIINDREMRDALLLVFANKQDLPDAM 126
Query: 139 SEDEVRHFFGLYGLTTGKEFTPREILQMRPMELFMCSVLKRQGFGNGFRWLAN 191
E++ GL ++ R + G G WL++
Sbjct: 127 KPHEIQEKLGL------------TRIRDRNWYVQPSCATSGDGLYEGLTWLSS 167
>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 = 100 bits (251), Expect = 3e-27
Identities = 47/138 (34%), Positives = 79/138 (57%), Gaps = 7/138 (5%)
Query: 27 LGLDNAGKTFLLQMLKNDRTAQHM-PTLHPTSEELSMGDIVFTTHDLGGHVQARRVWRDY 85
+GL N+GKT L+ ++ + + ++ PT+ +++ G++ DLGG + R +W Y
Sbjct: 5 VGLQNSGKTTLVNVIASGQFSEDTIPTVGFNMRKVTKGNVTIKVWDLGGQPRFRSMWERY 64
Query: 86 FPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKIDIFDAASEDEVRH 145
V+AIV+++DA+DR + +K EL +LL +L +P+L+LGNK D+ A S DE+
Sbjct: 65 CRGVNAIVYVVDAADREKLEVAKNELHDLLEKPSLEGIPLLVLGNKNDLPGALSVDELIE 124
Query: 146 FFGLYGLTTGKEFTPREI 163
L K T RE+
Sbjct: 125 QMNL------KSITDREV 136
>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 = 100 bits (251), Expect = 6e-27
Identities = 52/169 (30%), Positives = 84/169 (49%), Gaps = 12/169 (7%)
Query: 23 KLLFLGLDNAGKTFLLQMLKNDRTAQHMPTLHPTSEELSMGDIVFTTHDLGGHVQARRVW 82
++L LGLDNAGKT +L+ + + PTL + L D+GG R W
Sbjct: 16 RILMLGLDNAGKTTILKKFNGEDISTISPTLGFNIKTLEYNGYKLNIWDVGGQKSLRSYW 75
Query: 83 RDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKIDIFDAASEDE 142
R+YF + DA+++++D+SDR+R + K EL LL ++ L +LI NK D+ A S +E
Sbjct: 76 RNYFESTDALIWVVDSSDRARLEDCKRELQKLLVEERLAGATLLIFANKQDLPGALSPEE 135
Query: 143 VRHFFGLYGLTTGKEFTPREILQMRPMELFMCSVLKRQGFGNGFRWLAN 191
+R L + ++ +F CS + + +G WL +
Sbjct: 136 IREVLEL------------DSIKSHHWRIFGCSAVTGENLLDGIDWLVD 172
>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 = 98.2 bits (245), Expect = 4e-26
Identities = 52/173 (30%), Positives = 82/173 (47%), Gaps = 18/173 (10%)
Query: 25 LFLGLDNAGKTFLLQMLKNDRTAQH--------MPTLHPTSEELSMGDIVFTTHDLGGHV 76
L LGLDNAGKT L+ K + + PT+ + +G DLGG
Sbjct: 3 LILGLDNAGKTTFLEQTKTKFSKNYKGLNPSKITPTVGLNIGTIEVGKARLMFWDLGGQE 62
Query: 77 QARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKIDIFD 136
+ R +W Y+ ++++ID++DR RF ESK + ++ ++AL VP+L+L NK D+ D
Sbjct: 63 ELRSLWDKYYAESHGVIYVIDSTDRERFNESKSAFEKVINNEALEGVPLLVLANKQDLPD 122
Query: 137 AASEDEVRHFFGLYGLTTGKEFTPREILQMRPMELFMCSVLKRQGFGNGFRWL 189
A S E++ F ++ R + S L+ +G G WL
Sbjct: 123 ALSVAEIKEVFDDCI----------ALIGRRDCLVQPVSALEGEGVEEGIEWL 165
>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 = 96.5 bits (240), Expect = 2e-25
Identities = 47/134 (35%), Positives = 76/134 (56%)
Query: 19 KKSGKLLFLGLDNAGKTFLLQMLKNDRTAQHMPTLHPTSEELSMGDIVFTTHDLGGHVQA 78
K ++L +GLD AGKT +L LK + +PT+ E ++ +I FT D+GG +
Sbjct: 11 NKEMRILMVGLDAAGKTTILYKLKLGESVTTIPTIGFNVETVTYKNISFTVWDVGGQDKI 70
Query: 79 RRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKIDIFDAA 138
R +WR Y+ ++F++D++DR R E++ EL +L +D L D IL+ NK D+ DA
Sbjct: 71 RPLWRHYYTNTQGLIFVVDSNDRDRIDEAREELHRMLNEDELRDAVILVFANKQDLPDAM 130
Query: 139 SEDEVRHFFGLYGL 152
E+ GL+ +
Sbjct: 131 KAAEITEKLGLHSI 144
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 96.2 bits (239), Expect = 2e-25
Identities = 56/184 (30%), Positives = 88/184 (47%), Gaps = 16/184 (8%)
Query: 12 LLRLGLWKKSGKLLFLGLDNAGKTFLLQMLKNDRTAQHMPTLHPTSEELSMGDIVFTTHD 71
L KK ++L +GLD AGKT +L LK +PT+ E + +I FT D
Sbjct: 8 LFSRLFAKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWD 67
Query: 72 LGGHVQARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNK 131
+GG + R +WR YF ++F++D++DR R E++ EL +L +D L D +L+ NK
Sbjct: 68 VGGQDKIRPLWRHYFQNTQGLIFVVDSNDRDRVVEARDELHRMLNEDELRDAVLLVFANK 127
Query: 132 IDIFDAASEDEVRHFFGLYGLTTGKEFTPREILQMRPMELFM--CSVLKRQGFGNGFRWL 189
D+ +A + E+ GL+ L R ++ +G G WL
Sbjct: 128 QDLPNAMNAAEITDKLGLHSL--------------RQRHWYIQSTCATSGEGLYEGLDWL 173
Query: 190 ANYI 193
+N I
Sbjct: 174 SNNI 177
>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 = 95.2 bits (237), Expect = 4e-25
Identities = 54/170 (31%), Positives = 83/170 (48%), Gaps = 12/170 (7%)
Query: 23 KLLFLGLDNAGKTFLLQMLKNDRTAQHMPTLHPTSEELSMGDIVFTTHDLGGHVQARRVW 82
++L +GLD AGKT +L LK +PT+ E + +I FT D+GG + R +W
Sbjct: 2 RILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLW 61
Query: 83 RDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKIDIFDAASEDE 142
R YF ++F++D++DR R E++ EL +L +D L D +L+ NK D+ +A S E
Sbjct: 62 RHYFQNTQGLIFVVDSNDRERIGEAREELQRMLNEDELRDAVLLVFANKQDLPNAMSAAE 121
Query: 143 VRHFFGLYGLTTGKEFTPREILQMRPMELFMCSVLKRQGFGNGFRWLANY 192
V GL+ L+ R + G G WL+N
Sbjct: 122 VTDKLGLHS------------LRNRNWYIQATCATSGDGLYEGLDWLSNN 159
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 95.7 bits (238), Expect = 5e-25
Identities = 54/175 (30%), Positives = 90/175 (51%), Gaps = 12/175 (6%)
Query: 19 KKSGKLLFLGLDNAGKTFLLQMLKNDRTAQHMPTLHPTSEELSMGDIVFTTHDLGGHVQA 78
KK ++L +GLD AGKT +L LK +PT+ E + ++ FT D+GG +
Sbjct: 15 KKEVRILMVGLDAAGKTTILYKLKLGEVVTTIPTIGFNVETVEYKNLKFTMWDVGGQDKL 74
Query: 79 RRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKIDIFDAA 138
R +WR Y+ + ++F++D++DR R +++ EL+ +L++D L D +L+ NK D+ +A
Sbjct: 75 RPLWRHYYQNTNGLIFVVDSNDRERIGDAREELERMLSEDELRDAVLLVFANKQDLPNAM 134
Query: 139 SEDEVRHFFGLYGLTTGKEFTPREILQMRPMELFMCSVLKRQGFGNGFRWLANYI 193
S EV GL+ ++ R + C QG G WL+ I
Sbjct: 135 STTEVTEKLGLHS------------VRQRNWYIQGCCATTAQGLYEGLDWLSANI 177
>gnl|CDD|206723 cd04158, ARD1, (ADP-ribosylation factor domain protein 1 (ARD1).
ARD1 (ADP-ribosylation factor domain protein 1) is an
unusual member of the Arf family. In addition to the
C-terminal Arf domain, ARD1 has an additional 46-kDa
N-terminal domain that contains a RING finger domain,
two predicted B-Boxes, and a coiled-coil protein
interaction motif. This domain belongs to the TRIM
(tripartite motif) or RBCC (RING, B-Box, coiled-coil)
family. Like most Arfs, the ARD1 Arf domain lacks
detectable GTPase activity. However, unlike most Arfs,
the full-length ARD1 protein has significant GTPase
activity due to the GAP (GTPase-activating protein)
activity exhibited by the 46-kDa N-terminal domain. The
GAP domain of ARD1 is specific for its own Arf domain
and does not bind other Arfs. The rate of GDP
dissociation from the ARD1 Arf domain is slowed by the
adjacent 15 amino acids, which act as a GDI
(GDP-dissociation inhibitor) domain. ARD1 is
ubiquitously expressed in cells and localizes to the
Golgi and to the lysosomal membrane. Two Tyr-based
motifs in the Arf domain are responsible for Golgi
localization, while the GAP domain controls lysosomal
localization.
Length = 169
Score = 90.9 bits (225), Expect = 2e-23
Identities = 56/168 (33%), Positives = 82/168 (48%), Gaps = 11/168 (6%)
Query: 23 KLLFLGLDNAGKTFLLQMLKNDRTAQHMPTLHPTSEELSMGDIVFTTHDLGGHVQARRVW 82
+++ LGLD AGKT +L LK D Q +PT+ E + ++ FT D+GG + R +W
Sbjct: 1 RVVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLW 60
Query: 83 RDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKIDIFDAASEDE 142
+ Y+ A+VF+ID+S R R E+ EL LL + L D +LI NK D+ A S +E
Sbjct: 61 KHYYLNTQAVVFVIDSSHRDRVSEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEE 120
Query: 143 VRHFFGLYGLTTGKEFTPREILQMRPMELFMCSVLKRQGFGNGFRWLA 190
+ L+ L G R + C G G WL+
Sbjct: 121 MTELLSLHKLCCG-----------RSWYIQGCDARSGMGLYEGLDWLS 157
>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 = 85.6 bits (212), Expect = 2e-21
Identities = 42/137 (30%), Positives = 71/137 (51%), Gaps = 3/137 (2%)
Query: 24 LLFLGLDNAGKTFLLQMLKNDRTAQ-HMPTLHPTSEELSMGDIVFTTHDLGGHVQARRVW 82
+L LGLD AGKT LL L ++R+ + +PT S + D + ++GG R+ W
Sbjct: 2 ILVLGLDGAGKTSLLHSLSSERSLESVVPTTGFNSVAIPTQDAIMELLEIGGSQNLRKYW 61
Query: 83 RDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKIDIFDAASEDE 142
+ Y ++F++D++D R P ++ EL LL D+P+++L NK D+ A S E
Sbjct: 62 KRYLSGSQGLIFVVDSADSERLPLARQELHQLLQHPP--DLPLVVLANKQDLPAARSVQE 119
Query: 143 VRHFFGLYGLTTGKEFT 159
+ L + G+ +
Sbjct: 120 IHKELELEPIARGRRWI 136
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 85.4 bits (211), Expect = 9e-21
Identities = 40/132 (30%), Positives = 59/132 (44%), Gaps = 5/132 (3%)
Query: 17 LWKKSGKLLFLGLDNAGKTFLLQMLKNDRTAQHMPTL-----HPTSEELSMGDIVFTTHD 71
L+ K K++ LG GKT LL L D + P + E +I D
Sbjct: 1 LFMKEFKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWD 60
Query: 72 LGGHVQARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNK 131
G + R + +Y+ + I+ + D++ R E E L + A DVPIL++GNK
Sbjct: 61 TAGQEEYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVGNK 120
Query: 132 IDIFDAASEDEV 143
ID+FD S E
Sbjct: 121 IDLFDEQSSSEE 132
>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 = 83.2 bits (206), Expect = 2e-20
Identities = 43/120 (35%), Positives = 63/120 (52%)
Query: 24 LLFLGLDNAGKTFLLQMLKNDRTAQHMPTLHPTSEELSMGDIVFTTHDLGGHVQARRVWR 83
LL +GLDNAGKT L+ L+ + + PT+ T +L + DLGG R +W
Sbjct: 2 LLTVGLDNAGKTTLVSALQGEIPKKVAPTVGFTPTKLRLDKYEVCIFDLGGGANFRGIWV 61
Query: 84 DYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKIDIFDAASEDEV 143
+Y+ +VF++D+SD R E K L LL ++ PIL+L NK D +A +V
Sbjct: 62 NYYAEAHGLVFVVDSSDDDRVQEVKEILRELLQHPRVSGKPILVLANKQDKKNALLGADV 121
>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 = 72.9 bits (179), Expect = 2e-16
Identities = 46/131 (35%), Positives = 70/131 (53%), Gaps = 5/131 (3%)
Query: 27 LGLDNAGKTFLLQMLKNDRTAQHMPTLHPTSE--ELSMGD---IVFTTHDLGGHVQARRV 81
LGLD+AGKT +L LK + +PT +E ++S+G+ + F D+GG + R +
Sbjct: 9 LGLDSAGKTTVLYRLKFNEFVNTVPTKGFNTEKIKVSLGNAKGVTFHFWDVGGQEKLRPL 68
Query: 82 WRDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKIDIFDAASED 141
W+ Y D IVF++D+ D R E+K EL + VP+L+L NK D+ +A
Sbjct: 69 WKSYTRCTDGIVFVVDSVDVERMEEAKTELHKITKFSENQGVPVLVLANKQDLPNALPVS 128
Query: 142 EVRHFFGLYGL 152
EV L+ L
Sbjct: 129 EVEKLLALHEL 139
>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 = 67.5 bits (165), Expect = 2e-14
Identities = 33/178 (18%), Positives = 64/178 (35%), Gaps = 28/178 (15%)
Query: 25 LFLGLDNAGKTFLLQMLKNDRTAQHMPTLHPTSEE------LSMGDIVFTTHDLGGHVQA 78
+ +G GK+ LL L + T + L G + D G +
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPGLDEF 60
Query: 79 RRVW-----RDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKID 133
+ R D I+ ++D++DR ++K + L + +PI+++GNKID
Sbjct: 61 GGLGREELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLRKE---GIPIILVGNKID 117
Query: 134 IFDAASEDEVRHFFGLYGLTTGKEFTPREILQMRPMELFMCSVLKRQGFGNGFRWLAN 191
+ + +E+ E+ ++ + +F S +G F L
Sbjct: 118 LLEEREVEELLRL--------------EELAKILGVPVFEVSAKTGEGVDELFEKLIE 161
>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 = 57.8 bits (140), Expect = 7e-11
Identities = 34/133 (25%), Positives = 56/133 (42%), Gaps = 7/133 (5%)
Query: 22 GKLLFLGLDNAGKTFLL-QMLKNDR---TAQHMPTLH--PTSEELSMGDIVFTTHDLGGH 75
K++ +G N GK+ LL ++L N + T + T E F D G
Sbjct: 2 IKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAGQ 61
Query: 76 VQARRVWRDYFPAVDAIVFIID-ASDRSRFPESKYELDNLLADDALTDVPILILGNKIDI 134
+ R Y+ AV++ + + D E + + A + VPI+++GNKID+
Sbjct: 62 EDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAESGVPIILVGNKIDL 121
Query: 135 FDAASEDEVRHFF 147
DA + V F
Sbjct: 122 RDAKLKTHVAFLF 134
>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 = 56.9 bits (138), Expect = 3e-10
Identities = 34/132 (25%), Positives = 59/132 (44%), Gaps = 15/132 (11%)
Query: 25 LFLGLDNAGKTFLLQMLKNDRTAQHMPTLHP---TSEELSMGDIVFTTHDLGGHVQAR-R 80
L LG ++GKT L L + + ++ P + S T D+ GH + R +
Sbjct: 4 LLLGPSDSGKTALFTKLTTGKVRSTVTSIEPNVASFYSNSSKGKKLTLVDVPGHEKLRDK 63
Query: 81 VWRDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTD-------VPILILGNKID 133
+ ++ AIVF++D++ + + + L D LTD +PILI NK D
Sbjct: 64 LLEYLKASLKAIVFVVDSATFQK--NIRDVAEFLY--DILTDLEKIKNKIPILIACNKQD 119
Query: 134 IFDAASEDEVRH 145
+F A +++
Sbjct: 120 LFTAKPAKKIKE 131
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 47.1 bits (112), Expect = 8e-07
Identities = 25/140 (17%), Positives = 55/140 (39%), Gaps = 18/140 (12%)
Query: 19 KKSGKLLFLGLDNAGKTFLLQML--------KNDRTAQHMPTLHPTSEELSMGDI----- 65
K++ +G AGKT ++ L + D ++ PT+ + G I
Sbjct: 8 MIETKIVVIGPVGAGKTTFVRALSDKPLVITEADASSVSGKGKRPTTVAMDFGSIELDED 67
Query: 66 -VFTTHDLGGHVQARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVP 124
G + + +W + ++D+S P + + + + + +P
Sbjct: 68 TGVHLFGTPGQERFKFMWEILSRGAVGAIVLVDSSR----PITFHAEEIIDFLTSRNPIP 123
Query: 125 ILILGNKIDIFDAASEDEVR 144
+++ NK D+FDA +++R
Sbjct: 124 VVVAINKQDLFDALPPEKIR 143
>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 = 43.4 bits (103), Expect = 2e-05
Identities = 21/87 (24%), Positives = 36/87 (41%), Gaps = 10/87 (11%)
Query: 59 ELSMGDIVFTTHDLGGHVQARRVWRDYFPAVDAIVFIIDASD----------RSRFPESK 108
+ + F D+GG R+ W F V AI+F++ S+ +R ES
Sbjct: 162 KFDFKGLKFRLFDVGGQRSERKKWIHCFEDVTAIIFVVSLSEYDQVLYEDDSTNRLEESL 221
Query: 109 YELDNLLADDALTDVPILILGNKIDIF 135
+ + + PI++ NK D+F
Sbjct: 222 NLFEEICNSPWFKNTPIILFLNKKDLF 248
>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 = 40.1 bits (94), Expect = 9e-05
Identities = 24/118 (20%), Positives = 49/118 (41%), Gaps = 10/118 (8%)
Query: 23 KLLFLGLDNAGKT-FLLQMLKNDRTAQHMPTLHPT----SEELSMGDIVFTTHDLGGHVQ 77
K++ +G +GK+ L Q++ + + + T + E+ + D GG +
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREE 60
Query: 78 ARRVWRDYFPAVDAIVFIIDASDRSRF---PESKYELDNLLADDALTDVPILILGNKI 132
+ + DAI+ + D +DR L NL +P++++GNK+
Sbjct: 61 LKFEHIIFMKWADAILLVYDLTDRESLNEVSRLIAWLPNL--RKLGGKIPVILVGNKL 116
>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 = 40.9 bits (96), Expect = 1e-04
Identities = 31/137 (22%), Positives = 55/137 (40%), Gaps = 14/137 (10%)
Query: 19 KKSGKLLFLGLDNAGKTFLLQMLKNDRTAQHMPTLHPTSEELSMG--DIVFTTHDLGGHV 76
++ GL ++GKT L +L + + + P++ M FT D GHV
Sbjct: 1 SSQPAVIIAGLCDSGKTSLFTLLTTGTVKKTVTSQEPSAAYKYMLHKGFSFTLIDFPGHV 60
Query: 77 QARRVWRDYFPAVD---AIVFIIDASDRSR----FPESKYE--LDNLLADDALTDVPILI 127
+ R+ + IVF++D++ + E YE L + + ILI
Sbjct: 61 KLRQKLLETIKDSSSLRGIVFVVDSTAFPKEVTDTAEFLYEILSITELLKNG---IDILI 117
Query: 128 LGNKIDIFDAASEDEVR 144
NK + F A +++
Sbjct: 118 ACNKQESFTARPPKKIK 134
>gnl|CDD|206714 cd04147, Ras_dva, Ras - dorsal-ventral anterior localization
(Ras-dva) family. Ras-dva subfamily. Ras-dva (Ras -
dorsal-ventral anterior localization) subfamily consists
of a set of proteins characterized only in Xenopus
leavis, to date. In Xenopus Ras-dva expression is
activated by the transcription factor Otx2 and begins
during gastrulation throughout the anterior ectoderm.
Ras-dva expression is inhibited in the anterior neural
plate by factor Xanf1. Downregulation of Ras-dva results
in head development abnormalities through the inhibition
of several regulators of the anterior neural plate and
folds patterning, including Otx2, BF-1, Xag2, Pax6,
Slug, and Sox9. Downregulation of Ras-dva also
interferes with the FGF-8a signaling within the anterior
ectoderm. Most Ras proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins.
Length = 197
Score = 40.6 bits (95), Expect = 1e-04
Identities = 33/129 (25%), Positives = 50/129 (38%), Gaps = 28/129 (21%)
Query: 23 KLLFLGLDNAGKTFLLQMLKND-------RTAQHMPTLHPTSEELSMG-DIVFTTHDLGG 74
+L+F+G GKT L+Q D RT + + + + + DI+ D G
Sbjct: 1 RLVFMGAAGVGKTALIQRFLYDTFEPKHRRTVEELHSKEYEVAGVKVTIDIL----DTSG 56
Query: 75 HVQARRVWRDYFPAV--------DAIVFIIDASDRSRFPESKYELDNLLADDALTDVPIL 126
FPA+ DA + D F E K + +L VPI+
Sbjct: 57 SYS--------FPAMRKLSIQNGDAFALVYSVDDPESFEEVKRLREEILEVKEDKFVPIV 108
Query: 127 ILGNKIDIF 135
++GNKID
Sbjct: 109 VVGNKIDSL 117
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 39.2 bits (92), Expect = 6e-04
Identities = 38/137 (27%), Positives = 64/137 (46%), Gaps = 26/137 (18%)
Query: 28 GLDNAGKTFLLQMLKNDRT--AQHMP-TLHPTSEELSMGD---IVFT-T--------HDL 72
G NAGK+ L L A + TL PT+ + +GD ++ T T H L
Sbjct: 199 GYTNAGKSTLFNALTGADVYVADQLFATLDPTTRRIELGDGRKVLLTDTVGFIRDLPHPL 258
Query: 73 GGHVQARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELD---NLLADDALTDVPILILG 129
V+A + + D ++ ++DASD PE +L+ ++LA+ ++PI+++
Sbjct: 259 ---VEAFKSTLEEVKEADLLLHVVDASD----PEILEKLEAVEDVLAEIGADEIPIILVL 311
Query: 130 NKID-IFDAASEDEVRH 145
NKID + D E+
Sbjct: 312 NKIDLLEDEEILAELER 328
>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 = 37.6 bits (88), Expect = 0.001
Identities = 33/172 (19%), Positives = 58/172 (33%), Gaps = 38/172 (22%)
Query: 26 FLGLDNAGKTFLLQMLKNDRTAQ--HMP--TLHPTS---EELSMGDIVFTTHDLGG---- 74
G N GK+ LL L +P T P E L +G +V D G
Sbjct: 2 IFGRPNVGKSSLLNALLGQNVGIVSPIPGTTRDPVRKEWELLPLGPVVLI--DTPGLDEE 59
Query: 75 ----HVQARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGN 130
+ + A D ++ ++D+ + E + L P+L++ N
Sbjct: 60 GGLGRERVEEARQVADRA-DLVLLVVDSD------LTPVEEEAKLGLLRERGKPVLLVLN 112
Query: 131 KIDIFDAASEDEVRHFFGLYGLTTGKEFTPREILQMRPMELFMCSVLKRQGF 182
KID+ + E+E R++ + + + S L +G
Sbjct: 113 KIDLVPESEEEE--------------LLRERKLELLPDLPVIAVSALPGEGI 150
>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 = 35.9 bits (84), Expect = 0.004
Identities = 29/118 (24%), Positives = 56/118 (47%), Gaps = 10/118 (8%)
Query: 23 KLLFLGLDNAGKT-FLLQMLKNDRTAQHMPTL----HPTSEELSMGDIVFTTHDLGGHVQ 77
KL+ +G GK+ L++ +N +++PT+ + + E+ + D G +
Sbjct: 1 KLVLVGDGGVGKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAGQER 60
Query: 78 ARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDNLL--ADDALTDVPILILGNKID 133
R + Y+ + + D + R F K L+ +L AD+ +VPI+++GNK D
Sbjct: 61 FRALRPLYYRGAQGFLLVYDITSRDSFENVKKWLEEILRHADE---NVPIVLVGNKCD 115
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 36.0 bits (84), Expect = 0.008
Identities = 38/161 (23%), Positives = 56/161 (34%), Gaps = 46/161 (28%)
Query: 9 REVLLRLGLWKKSGKLL----FLGLDNAGKTFLLQMLKNDRT---AQHMPTLHPT----- 56
R++ L L KLL +GL NAGK+ LL + + TL P
Sbjct: 150 RDLRLEL-------KLLADVGLVGLPNAGKSTLLSAVSAAKPKIADYPFTTLVPNLGVVR 202
Query: 57 ---SEELSMGDI----------VFTTHDLGGHVQARRVWRDYFPAVDAIVFIIDAS-DRS 102
E + DI V H++ RV + +ID S
Sbjct: 203 VDGGESFVVADIPGLIEGASEGVGLGLRFLRHIERTRVL----------LHVIDLSPIDG 252
Query: 103 RFPESKYEL--DNLLA-DDALTDVPILILGNKIDIFDAASE 140
R P Y+ + L L + P +++ NKID+ E
Sbjct: 253 RDPIEDYQTIRNELEKYSPKLAEKPRIVVLNKIDLPLDEEE 293
>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 = 35.1 bits (82), Expect = 0.009
Identities = 23/106 (21%), Positives = 41/106 (38%), Gaps = 25/106 (23%)
Query: 77 QARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKID-IF 135
A +D VD ++F++DAS+ ++ L+ L + P++++ NKID +
Sbjct: 75 AAWSALKD----VDLVLFVVDASEWIG-EGDEFILELL----KKSKTPVILVLNKIDLVK 125
Query: 136 DAASEDEVRHFFGLYGLTTGKEFTPREILQMRPMELFMCSVLKRQG 181
D + L F E+F S LK +
Sbjct: 126 DKEDLLPLLEK-----LKELHPFA----------EIFPISALKGEN 156
>gnl|CDD|182934 PRK11058, PRK11058, GTPase HflX; Provisional.
Length = 426
Score = 35.8 bits (83), Expect = 0.010
Identities = 32/125 (25%), Positives = 56/125 (44%), Gaps = 19/125 (15%)
Query: 27 LGLDNAGKTFLL-QMLKNDRTA--QHMPTLHPTSEELSMGDIVFTT------------HD 71
+G NAGK+ L ++ + A Q TL PT + + D+ T HD
Sbjct: 203 VGYTNAGKSTLFNRITEARVYAADQLFATLDPTLRRIDVADVGETVLADTVGFIRHLPHD 262
Query: 72 LGGHVQARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNK 131
L V A + ++ ++DA+D R E+ ++ +L + ++P L++ NK
Sbjct: 263 L---VAAFKATLQETRQATLLLHVVDAAD-VRVQENIEAVNTVLEEIDAHEIPTLLVMNK 318
Query: 132 IDIFD 136
ID+ D
Sbjct: 319 IDMLD 323
>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 = 34.0 bits (79), Expect = 0.021
Identities = 30/140 (21%), Positives = 57/140 (40%), Gaps = 30/140 (21%)
Query: 23 KLLFLGLDNAGKTFLLQMLKNDR-TAQHMPTLHPTSEELSMGDIVFTTHDLGGHVQARRV 81
K++ +G GKT LL +++ + + T+ D T ++ G ++
Sbjct: 2 KIVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGV--------DFKSKTIEVDGKKVKLQI 53
Query: 82 W------------RDYFPAVDAIVFIIDASDRSRFPESKYELDNLLAD---DALTDVPIL 126
W Y+ + + D ++R ES LD L + A ++PI+
Sbjct: 54 WDTAGQERFRSITSSYYRGAHGAILVYDVTNR----ESFENLDKWLNELKEYAPPNIPII 109
Query: 127 ILGNKIDIFD--AASEDEVR 144
++GNK D+ D S +E +
Sbjct: 110 LVGNKSDLEDERQVSTEEAQ 129
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 33.8 bits (78), Expect = 0.035
Identities = 19/79 (24%), Positives = 32/79 (40%), Gaps = 7/79 (8%)
Query: 90 DAIVFIIDASDRSRFP-ESKYELDNLLADDALTDVPILILGNKIDIFDAASEDEVRHFFG 148
I+F+ D S+ + E + L + + L PI+++ NKIDI D +E+
Sbjct: 249 GVILFLFDPSETCGYSLEEQISLLEEIKE--LFKAPIVVVINKIDIADEEKLEEIEASV- 305
Query: 149 LYGLTTGKEFTPREILQMR 167
L G E +
Sbjct: 306 ---LEEGGEEPLKISATKG 321
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 33.9 bits (79), Expect = 0.036
Identities = 39/167 (23%), Positives = 62/167 (37%), Gaps = 57/167 (34%)
Query: 9 REVLLRLGLWKKSGKLL----FLGLDNAGKTFLLQMLKNDRTAQHMP--------TLHP- 55
R + L L KLL +GL NAGK+ L+ + + P TLHP
Sbjct: 149 RWLRLEL-------KLLADVGLVGLPNAGKSTLISAVSAAK-----PKIADYPFTTLHPN 196
Query: 56 -------TSEELSMGDI---VFTTHD---LG----GHVQARRVWRDYFPAVDAIVFIIDA 98
+ + DI + + LG H++ R+ ++ ++D
Sbjct: 197 LGVVRVDDYKSFVIADIPGLIEGASEGAGLGHRFLKHIERTRL----------LLHLVDI 246
Query: 99 SDRSRFPESKYE-LDNLLA--DDALTDVPILILGNKIDIFDAASEDE 142
P Y+ + N L L D P +++ NKID+ D E E
Sbjct: 247 EAVD--PVEDYKTIRNELEKYSPELADKPRILVLNKIDLLDEEEERE 291
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 33.7 bits (78), Expect = 0.039
Identities = 31/135 (22%), Positives = 54/135 (40%), Gaps = 19/135 (14%)
Query: 19 KKSGKLLFLGLDNAGKTFLLQMLKNDRTA--QHMP--TLHPTSEELSMGD--IVFT---- 68
KSG + +G N GK+ LL L + + P T + ++ + I+F
Sbjct: 4 FKSGFVAIIGRPNVGKSTLLNALVGQKISIVSPKPQTTRNRIRGIVTTDNAQIIFVDTPG 63
Query: 69 ---THDLGGHVQARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPI 125
G + + VD I+F++DA D P ++ L+ L T P+
Sbjct: 64 IHKPKHALGELMNKAARSAL-KDVDLILFVVDA-DEGWGPGDEFILEQL----KKTKTPV 117
Query: 126 LILGNKIDIFDAASE 140
+++ NKID +
Sbjct: 118 ILVVNKIDKVKPKTV 132
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 33.5 bits (78), Expect = 0.046
Identities = 13/45 (28%), Positives = 26/45 (57%), Gaps = 5/45 (11%)
Query: 89 VDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKID 133
VD ++F++DA ++ P ++ L+ L P++++ NKID
Sbjct: 85 VDLVLFVVDADEKIG-PGDEFILEKL----KKVKTPVILVLNKID 124
>gnl|CDD|214595 smart00275, G_alpha, G protein alpha subunit. Subunit of G
proteins that contains the guanine nucleotide binding
site.
Length = 342
Score = 33.3 bits (77), Expect = 0.050
Identities = 25/95 (26%), Positives = 38/95 (40%), Gaps = 10/95 (10%)
Query: 51 PTLHPTSEELSMGDIVFTTHDLGGHVQARRVWRDYFPAVDAIVFIIDAS--------DRS 102
PT + + F D+GG R+ W F V AI+F + S D S
Sbjct: 170 PTTGIQETAFIVKKLFFRMFDVGGQRSERKKWIHCFDNVTAIIFCVALSEYDQVLEEDES 229
Query: 103 --RFPESKYELDNLLADDALTDVPILILGNKIDIF 135
R ES +++ + I++ NKID+F
Sbjct: 230 TNRMQESLNLFESICNSRWFANTSIILFLNKIDLF 264
>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 = 32.7 bits (75), Expect = 0.063
Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 6/80 (7%)
Query: 71 DLGGHVQARRVWRDYFPAVDAIVFIIDASDRSRFPE-SKYEL---DNLLADDALTDVPIL 126
DL GH + V +++ ++ + D +DR F + + ++ ++
Sbjct: 55 DLSGHPEYLEVRNEFYKDTQGVLLVYDVTDRQSFEALDSWLKEMKQEGGPHGNMENIVVV 114
Query: 127 ILGNKIDIFD--AASEDEVR 144
+ NKID+ A SEDE R
Sbjct: 115 VCANKIDLTKHRAVSEDEGR 134
>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 = 32.4 bits (74), Expect = 0.070
Identities = 36/133 (27%), Positives = 54/133 (40%), Gaps = 20/133 (15%)
Query: 26 FLGLDNAGKTFLLQML---KNDRTAQHMPTLHPTSEELSMGDIV-FTTHDLGGHVQ---- 77
+GL N GK+ LL L K + + TL P GD V DL G +
Sbjct: 2 LVGLPNVGKSTLLSALTSAKVEIASYPFTTLEPNVGVFEFGDGVDIQIIDLPGLLDGASE 61
Query: 78 ----ARRVWRDYFPAVDAIVFIIDASDRS-RFPESKYELDN---LLADDALTDVPILILG 129
++ + + D I+ +IDAS+ P + N + L + P +I+
Sbjct: 62 GRGLGEQILAHLYRS-DLILHVIDASEDCVGDPLEDQKTLNEEVSGSFLFLKNKPEMIVA 120
Query: 130 NKIDIFDAASEDE 142
NKI D ASE+
Sbjct: 121 NKI---DMASENN 130
>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 = 32.9 bits (76), Expect = 0.070
Identities = 17/93 (18%), Positives = 39/93 (41%), Gaps = 18/93 (19%)
Query: 23 KLLFLGLDNAGKTFLLQMLKNDRTAQHMPTLHPTSE-ELS----MGDIVFTTHDLGG--- 74
K+L +GL +GK+ + ++ ++ + + L T + E S +G++ D G
Sbjct: 1 KVLLMGLRGSGKSSMRSIIFSNYSPRDTLRLGATIDVEQSHVRFLGNLTLNLWDCPGQDD 60
Query: 75 ------HVQARRVWRDYFPAVDAIVFIIDASDR 101
Q ++ + V ++++ D R
Sbjct: 61 FMENYLTRQKEHIFSN----VGVLIYVFDVESR 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 = 31.9 bits (73), Expect = 0.080
Identities = 27/122 (22%), Positives = 44/122 (36%), Gaps = 24/122 (19%)
Query: 26 FLGLDNAGKTFLLQMLKNDRTAQ--HMP--TLHPTSEELSMGDIV------------FTT 69
+G N GK+ L+ L + A P T P L +G +
Sbjct: 4 LVGRPNVGKSTLINALTGAKVAIVSDYPGTTRDPILGVLGLGRQIILVDTPGLIEGASEG 63
Query: 70 HDLGGHVQARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILG 129
+ G + R+ D I+ ++DAS+ E E+ L L PI+++
Sbjct: 64 KGVEGFNRFLEAIRE----ADLILLVVDASE--GLTEDDEEILEELEK--LPKKPIILVL 115
Query: 130 NK 131
NK
Sbjct: 116 NK 117
>gnl|CDD|206703 cd04131, Rnd, Rho family GTPase subfamily Rnd includes Rnd1/Rho6,
Rnd2/Rho7, and Rnd3/RhoE/Rho8. The Rnd subfamily
contains Rnd1/Rho6, Rnd2/Rho7, and Rnd3/RhoE/Rho8. These
novel Rho family proteins have substantial structural
differences compared to other Rho members, including N-
and C-terminal extensions relative to other Rhos.
Rnd3/RhoE is farnesylated at the C-terminal prenylation
site, unlike most other Rho proteins that are
geranylgeranylated. In addition, Rnd members are unable
to hydrolyze GTP and are resistant to GAP activity. They
are believed to exist only in the GTP-bound
conformation, and are antagonists of RhoA activity. Most
Rho proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 176
Score = 32.4 bits (74), Expect = 0.080
Identities = 32/122 (26%), Positives = 55/122 (45%), Gaps = 17/122 (13%)
Query: 23 KLLFLGLDNAGKTFLLQML-KNDRTAQHMPTL---HPTSEELSMGDIVFTTHDLGGHVQA 78
K++ +G GKT LLQ+ K+ ++PT+ + S E+ I + D G
Sbjct: 3 KIVLVGDSQCGKTALLQVFAKDSFPENYVPTVFENYTASFEVDKQRIELSLWDTSGSPYY 62
Query: 79 RRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDNLL------ADDALTDVPILILGNKI 132
V +P DA++ D S PE+ LD++L + + P+L++G K
Sbjct: 63 DNVRPLSYPDSDAVLICFDISR----PET---LDSVLKKWKGEVREFCPNTPVLLVGCKS 115
Query: 133 DI 134
D+
Sbjct: 116 DL 117
>gnl|CDD|206684 cd01897, NOG, Nucleolar GTP-binding protein (NOG). NOG1 is a
nucleolar GTP-binding protein present in eukaryotes
ranging from trypanosomes to humans. NOG1 is
functionally linked to ribosome biogenesis and found in
association with the nuclear pore complexes and
identified in many preribosomal complexes. Thus, defects
in NOG1 can lead to defects in 60S biogenesis. The S.
cerevisiae NOG1 gene is essential for cell viability,
and mutations in the predicted G motifs abrogate
function. It is a member of the ODN family of
GTP-binding proteins that also includes the bacterial
Obg and DRG proteins.
Length = 167
Score = 32.1 bits (74), Expect = 0.080
Identities = 14/56 (25%), Positives = 27/56 (48%), Gaps = 5/56 (8%)
Query: 90 DAIVFIIDASDRSRFP-ESKYEL-DNLLADDALTDVPILILGNKIDIFDAASEDEV 143
A++F ID S+ + E + L + L + P++++ NKID+ E+
Sbjct: 81 AAVLFFIDPSETCGYSIEEQLSLFKEIKP---LFNKPVIVVLNKIDLLTEEDLSEI 133
>gnl|CDD|223597 COG0523, COG0523, Putative GTPases (G3E family) [General function
prediction only].
Length = 323
Score = 32.7 bits (75), Expect = 0.100
Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 6/69 (8%)
Query: 77 QARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKIDIFD 136
D +D +V ++DA+ F E + L A+D L +++L NK D+ D
Sbjct: 106 LTDPELADGV-RLDGVVTVVDAA---HFLEGLDAIAEL-AEDQLAFADVIVL-NKTDLVD 159
Query: 137 AASEDEVRH 145
A + +
Sbjct: 160 AEELEALEA 168
>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 = 32.2 bits (73), Expect = 0.11
Identities = 30/141 (21%), Positives = 50/141 (35%), Gaps = 2/141 (1%)
Query: 23 KLLFLGLDNAGKTFLLQMLKNDRTAQHMPTLHPTSEELSMGDIVFTTHDLGGHVQARRVW 82
K++ LG N GKT LL R + T+ G + D G Q +
Sbjct: 2 KVVLLGDMNVGKTSLLHRYMERRFKDTVSTVGGAFYLKQWGPYNISIWDTAGREQFHGLG 61
Query: 83 RDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKIDIFD-AASED 141
Y A++ D S+ E + L D A D ++GNK+D+ + A
Sbjct: 62 SMYCRGAAAVILTYDVSNVQSLEELEDRFLGLT-DTANEDCLFAVVGNKLDLTEEGALAG 120
Query: 142 EVRHFFGLYGLTTGKEFTPRE 162
+ + ++ T +
Sbjct: 121 QEKDAGDRVSPEDQRQVTLED 141
>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 = 31.3 bits (72), Expect = 0.23
Identities = 36/138 (26%), Positives = 60/138 (43%), Gaps = 34/138 (24%)
Query: 31 NAGKTFLLQML-KNDRTAQHMP--TLHPTSEELSMGD---IVFT-T--------HDLGGH 75
NAGK+ L L D A+ TL PT+ + + ++ T T H L
Sbjct: 51 NAGKSTLFNALTGADVLAEDQLFATLDPTTRRIKLPGGREVLLTDTVGFIRDLPHQL--- 107
Query: 76 VQARRVWRDYFPA-------VDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILIL 128
V+A F + D ++ ++DASD E ++ +L + D+PI+++
Sbjct: 108 VEA-------FRSTLEEVAEADLLLHVVDASD-PDREEQIETVEEVLKELGADDIPIILV 159
Query: 129 GNKID-IFDAASEDEVRH 145
NKID + D E+ +R
Sbjct: 160 LNKIDLLDDEELEERLRA 177
>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 = 31.3 bits (72), Expect = 0.25
Identities = 36/125 (28%), Positives = 53/125 (42%), Gaps = 33/125 (26%)
Query: 31 NAGKTFLLQMLKNDRT-AQHMP--TLHPTSEEL---SMGDIVFT-T--------HDLGGH 75
NAGK+ L L A TL PT+ L G+++ T T H+L
Sbjct: 199 NAGKSTLFNALTGADVYAADQLFATLDPTTRRLDLPDGGEVLLTDTVGFIRDLPHEL--- 255
Query: 76 VQARRVWRDYFPA-------VDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILIL 128
V A F A D ++ ++DASD R E ++ +L + D+P L++
Sbjct: 256 VAA-------FRATLEEVREADLLLHVVDASDPDRE-EQIEAVEKVLEELGAEDIPQLLV 307
Query: 129 GNKID 133
NKID
Sbjct: 308 YNKID 312
>gnl|CDD|179843 PRK04390, rnpA, ribonuclease P; Reviewed.
Length = 120
Score = 30.1 bits (68), Expect = 0.29
Identities = 14/45 (31%), Positives = 23/45 (51%), Gaps = 7/45 (15%)
Query: 79 RRVWRDYF-------PAVDAIVFIIDASDRSRFPESKYELDNLLA 116
+RV R++F P VD +V + DR+ ++ EL L+A
Sbjct: 65 KRVIREWFRLNQHRLPPVDFVVRVQRKFDRATAKQAVAELAQLMA 109
>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 = 30.6 bits (70), Expect = 0.32
Identities = 27/115 (23%), Positives = 52/115 (45%), Gaps = 4/115 (3%)
Query: 23 KLLFLGLDNAGKTFL-LQMLKNDRTAQHMPTLHPT-SEELSMGDIVFTTH--DLGGHVQA 78
KL+ LG GK+ L ++ + + ++ PT+ + +++ + +T D G +
Sbjct: 1 KLVVLGAGGVGKSALTIRFVSGEFVEEYDPTIEDSYRKQIVVDGETYTLDILDTAGQEEF 60
Query: 79 RRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKID 133
+ Y D + + + R F E K + +L DVPI+++GNK D
Sbjct: 61 SAMRDQYIRNGDGFILVYSITSRESFEEIKNIREQILRVKDKEDVPIVLVGNKCD 115
>gnl|CDD|206689 cd04102, RabL3, Rab GTPase-like family 3 (Rab-like3). RabL3
(Rab-like3) subfamily. RabL3s are novel proteins that
have high sequence similarity with Rab family members,
but display features that are distinct from Rabs, and
have been termed Rab-like. As in other Rab-like
proteins, RabL3 lacks a prenylation site at the
C-terminus. The specific function of RabL3 remains
unknown.
Length = 204
Score = 30.6 bits (69), Expect = 0.36
Identities = 33/176 (18%), Positives = 64/176 (36%), Gaps = 42/176 (23%)
Query: 23 KLLFLGLDNAGKTFLLQMLKNDRT-------------AQHMPTLHPTSEELSMGDIVFTT 69
K+L LG GK+ L+ +L ++ +H T EE
Sbjct: 2 KVLVLGDSGVGKSSLVHLLCKNQVLGNPSWTVGCSVDVRHHTYGEGTPEE---KTFYVEL 58
Query: 70 HDLGGHVQARRVWRD----YFPAVDAIVFIIDASDR-SRFPESKYELDNLLADDALT--- 121
D+GG V + + ++ ++ I+F+ D +++ S ++ L+ L D
Sbjct: 59 WDVGGSVGSAESVKSTRAVFYNQINGIIFVHDLTNKKSSQNLYRWSLEALNRDTFPAGLL 118
Query: 122 --------------DVPILILGNKIDIFDAASEDEVRHFFGLYGLTTGKEFTPREI 163
VP+L++G K+D + R++ ++F EI
Sbjct: 119 VTNGDYDSEQFAGNPVPLLVIGTKLDQ----IPEAKRNWVLTRTAFLSEDFNAEEI 170
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 30.8 bits (71), Expect = 0.40
Identities = 51/205 (24%), Positives = 75/205 (36%), Gaps = 71/205 (34%)
Query: 9 REVLLRLGLWKKSGKLL----FLGLDNAGKTFLLQMLKNDR---TAQHMPTLHPTSEELS 61
RE+ L L KLL +G N GK+ LL ++ N + H TL P L
Sbjct: 149 RELRLEL-------KLLADVGLVGFPNVGKSTLLSVVSNAKPKIANYHFTTLVP---NLG 198
Query: 62 M----GDIVFTTHDLGG-----------------HVQARRVWRDYFPAVDAIVFIIDAS- 99
+ F D+ G H++ RV IV +ID S
Sbjct: 199 VVETDDGRSFVMADIPGLIEGASEGVGLGHQFLRHIERTRV----------IVHVIDMSG 248
Query: 100 DRSRFPESKYELDN--L-LADDALTDVPILILGNKIDIFDAASEDEVRHFFGLYGLTTGK 156
R P YE N L L + L + P +++ NK+D+ +A E+ + F K
Sbjct: 249 SEGRDPIEDYEKINKELKLYNPRLLERPQIVVANKMDLPEA--EENLEEF---------K 297
Query: 157 EFTPREILQMRPMELFMCSVLKRQG 181
E ++ + S L QG
Sbjct: 298 EKLGPKVFPI--------SALTGQG 314
>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 = 29.6 bits (67), Expect = 0.55
Identities = 25/128 (19%), Positives = 40/128 (31%), Gaps = 30/128 (23%)
Query: 23 KLLFLGLDNAGKTFLLQMLKNDRTAQHMPTLH--------PTSEELSMGDIVFTTHDLGG 74
KL+ +G GKT L + L ++ + H + E I D GG
Sbjct: 3 KLMLVGQGGVGKTSLCKQLIGEKFDGDESSTHGINVQDWKIPAPERK--KIRLNVWDFGG 60
Query: 75 ---------HVQARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPI 125
R ++ +VF D Y L + A P+
Sbjct: 61 QEIYHATHQFFLTSR-------SLYLLVF--DLRTGDEVSRVPYWLRQIKA--FGGVSPV 109
Query: 126 LILGNKID 133
+++G ID
Sbjct: 110 ILVGTHID 117
>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 = 29.9 bits (68), Expect = 0.57
Identities = 12/46 (26%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 90 DAIVFIIDASDRSRFPESK--YELDNLLADDALTDVPILILGNKID 133
D V + +DRS F +L + ++P++++GNK D
Sbjct: 74 DGFVLVYSITDRSSFDVVSQLLQLIREIKKRDG-EIPVILVGNKAD 118
>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 = 30.1 bits (69), Expect = 0.67
Identities = 38/168 (22%), Positives = 58/168 (34%), Gaps = 46/168 (27%)
Query: 9 REVLLRLGLWKKSGKLL----FLGLDNAGKTFLLQMLKNDRT---AQHMPTLHP------ 55
R + L L KLL +GL NAGK+ L+ + + TL P
Sbjct: 148 RWLRLEL-------KLLADVGLVGLPNAGKSTLISAVSAAKPKIADYPFTTLVPNLGVVR 200
Query: 56 --TSEELSMGDI----------VFTTHDLGGHVQARRVWRDYFPAVDAIVFIIDASD-RS 102
+ DI H H++ RV ++ +ID S
Sbjct: 201 VDDGRSFVIADIPGLIEGASEGAGLGHRFLKHIERTRV----------LLHLIDISPEDG 250
Query: 103 RFPESKYE-LDNLLA--DDALTDVPILILGNKIDIFDAASEDEVRHFF 147
P YE + N L L + P +++ NKID+ D +E+
Sbjct: 251 SDPIEDYEIIRNELKKYSPELAEKPRIVVLNKIDLLDEEELEELLKEL 298
>gnl|CDD|206743 cd11383, YfjP, YfjP GTPase. The Era (E. coli Ras-like
protein)-like YfjP subfamily includes several
uncharacterized bacterial GTPases that are similar to
Era. They generally show sequence conservation in the
region between the Walker A and B motifs (G1 and G3 box
motifs), to the exclusion of other GTPases. Era is
characterized by a distinct derivative of the KH domain
(the pseudo-KH domain) which is located C-terminal to
the GTPase domain.
Length = 140
Score = 29.2 bits (66), Expect = 0.70
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 11/70 (15%)
Query: 71 DLGGHVQARR-------VWRDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDV 123
DL G + R ++R P D +++++DA DR+ + + L L DA
Sbjct: 51 DLPGVGERGRRDREYEELYRRLLPEADLVLWLLDADDRALAADHDFYLLPLAGHDA---- 106
Query: 124 PILILGNKID 133
P+L + N++D
Sbjct: 107 PLLFVLNQVD 116
>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 = 29.5 bits (67), Expect = 0.77
Identities = 13/56 (23%), Positives = 28/56 (50%), Gaps = 8/56 (14%)
Query: 92 IVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKID-IFDAASEDEVRHF 146
+V ++D D FP S + L + + P++++GNKID + + ++ +
Sbjct: 37 VVHVVDIFD---FPGSL--IPGLA--ELIGAKPVILVGNKIDLLPKDVKPNRLKQW 85
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes. TrmE
contains a GTPase domain that forms a canonical Ras-like
fold. It functions a molecular switch GTPase, and
apparently uses a conformational change associated with
GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 29.4 bits (67), Expect = 0.81
Identities = 9/45 (20%), Positives = 23/45 (51%), Gaps = 7/45 (15%)
Query: 90 DAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKIDI 134
D ++ ++DAS+ + ++L + P++++ NK D+
Sbjct: 84 DLVLLVVDASE-------GLDEEDLEILELPAKKPVIVVLNKSDL 121
>gnl|CDD|206749 cd01856, YlqF, Circularly permuted YlqF GTPase. Proteins of the
YlqF family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases. The YlqF subfamily is represented in all
eukaryotes as well as a phylogenetically diverse array
of bacteria (including gram-positive bacteria,
proteobacteria, Synechocystis, Borrelia, and
Thermotoga).
Length = 171
Score = 29.4 bits (67), Expect = 0.81
Identities = 23/75 (30%), Positives = 34/75 (45%), Gaps = 8/75 (10%)
Query: 74 GHVQ-ARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKI 132
GH+ A R ++ VD ++ + DA R P S N D L + P LI+ NK
Sbjct: 4 GHMAKALRQIKEKLKLVDVVIEVRDA----RIPLSSR---NPDLDKILGNKPRLIVLNKA 56
Query: 133 DIFDAASEDEVRHFF 147
D+ D A + +F
Sbjct: 57 DLADPAKTKKWLKYF 71
>gnl|CDD|206739 cd09912, DLP_2, Dynamin-like protein including dynamins,
mitofusins, and guanylate-binding proteins. The dynamin
family of large mechanochemical GTPases includes the
classical dynamins and dynamin-like proteins (DLPs) that
are found throughout the Eukarya. This family also
includes bacterial DLPs. These proteins catalyze
membrane fission during clathrin-mediated endocytosis.
Dynamin consists of five domains; an N-terminal G domain
that binds and hydrolyzes GTP, a middle domain (MD)
involved in self-assembly and oligomerization, a
pleckstrin homology (PH) domain responsible for
interactions with the plasma membrane, GED, which is
also involved in self-assembly, and a proline arginine
rich domain (PRD) that interacts with SH3 domains on
accessory proteins. To date, three vertebrate dynamin
genes have been identified; dynamin 1, which is brain
specific, mediates uptake of synaptic vesicles in
presynaptic terminals; dynamin-2 is expressed
ubiquitously and similarly participates in membrane
fission; mutations in the MD, PH and GED domains of
dynamin 2 have been linked to human diseases such as
Charcot-Marie-Tooth peripheral neuropathy and rare forms
of centronuclear myopathy. Dynamin 3 participates in
megakaryocyte progenitor amplification, and is also
involved in cytoplasmic enlargement and the formation of
the demarcation membrane system. This family also
includes mitofusins (MFN1 and MFN2 in mammals) that are
involved in mitochondrial fusion. Dynamin oligomerizes
into helical structures around the neck of budding
vesicles in a GTP hydrolysis-dependent manner.
Length = 180
Score = 29.4 bits (67), Expect = 0.84
Identities = 17/66 (25%), Positives = 29/66 (43%), Gaps = 6/66 (9%)
Query: 83 RDYFPAVDAIVFIIDASDRSRFPES-KYELDNLLADDALTDVPILILGNKIDIFDAASED 141
+ P DA++F++ A D+ ES + L +L I + NKID+ +
Sbjct: 68 ESFLPRADAVIFVLSA-DQP-LTESEREFLKEILKWSGK---KIFFVLNKIDLLSEEELE 122
Query: 142 EVRHFF 147
EV +
Sbjct: 123 EVLEYS 128
>gnl|CDD|206712 cd04141, Rit_Rin_Ric, Ras-like protein in all tissues (Rit),
Ras-like protein in neurons (Rin) and Ras-related
protein which interacts with calmodulin (Ric). Rit
(Ras-like protein in all tissues), Rin (Ras-like protein
in neurons) and Ric (Ras-related protein which interacts
with calmodulin) form a subfamily with several unique
structural and functional characteristics. These
proteins all lack a the C-terminal CaaX lipid-binding
motif typical of Ras family proteins, and Rin and Ric
contain calmodulin-binding domains. Rin, which is
expressed only in neurons, induces neurite outgrowth in
rat pheochromocytoma cells through its association with
calmodulin and its activation of endogenous Rac/cdc42.
Rit, which is ubiquitously expressed in mammals,
inhibits growth-factor withdrawl-mediated apoptosis and
induces neurite extension in pheochromocytoma cells. Rit
and Rin are both able to form a ternary complex with
PAR6, a cell polarity-regulating protein, and Rac/cdc42.
This ternary complex is proposed to have physiological
function in processes such as tumorigenesis. Activated
Ric is likely to signal in parallel with the Ras pathway
or stimulate the Ras pathway at some upstream point, and
binding of calmodulin to Ric may negatively regulate Ric
activity.
Length = 172
Score = 29.4 bits (66), Expect = 0.90
Identities = 29/121 (23%), Positives = 54/121 (44%), Gaps = 14/121 (11%)
Query: 23 KLLFLGLDNAGKTFL-LQMLKNDRTAQHMPTLHPT-------SEELSMGDIVFTTHDLGG 74
K++ LG GK+ + +Q + + H PT+ E ++ DI+ D G
Sbjct: 4 KIVMLGAGGVGKSAVTMQFISHSFPDYHDPTIEDAYKTQARIDNEPALLDIL----DTAG 59
Query: 75 HVQARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALT-DVPILILGNKID 133
+ + Y + + +DR F E+ E L+ LT D+P++++GNK+D
Sbjct: 60 QAEFTAMRDQYMRCGEGFIICYSVTDRHSFQEAS-EFKELITRVRLTEDIPLVLVGNKVD 118
Query: 134 I 134
+
Sbjct: 119 L 119
>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 = 29.4 bits (67), Expect = 0.93
Identities = 24/86 (27%), Positives = 38/86 (44%), Gaps = 12/86 (13%)
Query: 61 SMGDIVFTTHDLGGHVQARRVWRDYFPAVDAIVFIIDASDR----------SRFPESKYE 110
S+ ++ F D+GG R+ W F V AI+F++ S+ +R ES
Sbjct: 157 SIKNLKFRMFDVGGQRSERKKWIHCFEDVTAIIFVVALSEYDQVLVEDESVNRMQESLKL 216
Query: 111 LDNLLADDALTDVP-ILILGNKIDIF 135
D++ + IL L NK D+F
Sbjct: 217 FDSICNSRWFANTSIILFL-NKKDLF 241
>gnl|CDD|153105 cd01046, Rubrerythrin_like, rubrerythrin-like, diiron-binding
domain. Rubrerythrin-like domain, similar to
rubrerythrin, a nonheme iron binding domain found in
many air-sensitive bacteria and archaea, and member of a
broad superfamily of ferritin-like diiron-carboxylate
proteins. Rubrerythrin is thought to reduce hydrogen
peroxide as part of an oxidative stress protection
system. The rubrerythrin protein has two domains, a
binuclear metal center located within a four-helix
bundle of the rubrerythrin domain, and a rubredoxin
domain. The Rubrerythrin-like domains in this CD are
singular domains (no C-terminus rubredoxin domain) and
are phylogenetically distinct from rubrerythrin domains
of rubrerythrin-rubredoxin proteins.
Length = 123
Score = 28.8 bits (65), Expect = 0.95
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 132 IDIFDAASEDEVRHFFGLYGL 152
D F A++DE RH L GL
Sbjct: 98 HDFFHEAAKDEARHGKMLKGL 118
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 29.0 bits (66), Expect = 0.96
Identities = 28/135 (20%), Positives = 52/135 (38%), Gaps = 42/135 (31%)
Query: 23 KLLFLGLDNAGKTFLLQMLKNDR-TAQHMPTLHPTSEELSMGDIVFTTHDLGGHVQARRV 81
K++ +G GK+ LL + + + Q+ T+ + F T + V +RV
Sbjct: 2 KIILIGDSGVGKSSLLSRFTDGKFSEQYKSTI----------GVDFKTKTI--EVDGKRV 49
Query: 82 ----W------------RDYFPAVDAIVFIIDASDRSRFPESKYELDNL------LADDA 119
W Y+ + + D ++R F +NL L + A
Sbjct: 50 KLQIWDTAGQERFRSITSSYYRGAVGALLVYDITNRESF-------ENLENWLKELREYA 102
Query: 120 LTDVPILILGNKIDI 134
+V I+++GNK D+
Sbjct: 103 SPNVVIMLVGNKSDL 117
>gnl|CDD|213234 cd03267, ABC_NatA_like, ATP-binding cassette domain of an
uncharacterized transporter similar in sequence to NatA.
NatA is the ATPase component of a bacterial ABC-type
Na+ transport system called NatAB, which catalyzes
ATP-dependent electrogenic Na+ extrusion without
mechanically coupled to proton or K+ uptake. NatB
possess six putative membrane spanning regions at its
C-terminus. In B. subtilis, NatAB is inducible by agents
such as ethanol and protonophores, which lower the
proton-motive force across the membrane. The closest
sequence similarity to NatA is exhibited by DrrA of the
two-component daunorubicin- and doxorubicin-efflux
system. Hence, the functional NatAB is presumably
assembled with two copies of the single ATP-binding
protein and the single integral membrane protein.
Length = 236
Score = 29.2 bits (66), Expect = 1.2
Identities = 33/127 (25%), Positives = 57/127 (44%), Gaps = 25/127 (19%)
Query: 20 KSGKLL-FLGLDNAGKTFLLQMLKNDRTAQHMPTLHPTSEELSMGDIV-FTTHDLGGHV- 76
+ G+++ F+G + AGKT L++L L PTS E+ + +V + +
Sbjct: 45 EKGEIVGFIGPNGAGKTTTLKILSG--------LLQPTSGEVRVAGLVPWKRRK--KFLR 94
Query: 77 -------QARRVWRDYFPAVDAIVFI--IDASDRSRFPESKYELDNLLADDALTDVPI-- 125
Q ++W D P +D+ + I +RF + EL LL + L D P+
Sbjct: 95 RIGVVFGQKTQLWWD-LPVIDSFYLLAAIYDLPPARFKKRLDELSELLDLEELLDTPVRQ 153
Query: 126 LILGNKI 132
L LG ++
Sbjct: 154 LSLGQRM 160
>gnl|CDD|133090 cd06232, M14-like_5, Peptidase M14-like domain; uncharacterized
subfamily. Peptidase M14-like domain of a functionally
uncharacterized subgroup of the M14 family of
metallocarboxypeptidases (MCPs). The M14 family are
zinc-binding carboxypeptidases (CPs) which hydrolyze
single, C-terminal amino acids from polypeptide chains,
and have a recognition site for the free C-terminal
carboxyl group, which is a key determinant of
specificity. Two major subfamilies of the M14 family,
defined based on sequence and structural homology, are
the A/B and N/E subfamilies. Enzymes belonging to the
A/B subfamily are normally synthesized as inactive
precursors containing preceding signal peptide,
followed by an N-terminal pro-region linked to the
enzyme; these proenzymes are called
procarboxypeptidases. The A/B enzymes can be further
divided based on their substrate specificity;
Carboxypeptidase A-like (CPA-like) enzymes favor
hydrophobic residues while carboxypeptidase B-like
(CPB-like) enzymes only cleave the basic residues
lysine or arginine. The A forms have slightly different
specificities, with Carboxypeptidase A1 (CPA1)
preferring aliphatic and small aromatic residues, and
CPA2 preferring the bulky aromatic side chains. Enzymes
belonging to the N/E subfamily enzymes are not produced
as inactive precursors and instead rely on their
substrate specificity and subcellular
compartmentalization to prevent inappropriate
cleavages. They contain an extra C-terminal
transthyretin-like domain, thought to be involved in
folding or formation of oligomers. MCPs can also be
classified based on their involvement in specific
physiological processes; the pancreatic MCPs
participate only in alimentary digestion and include
carboxypeptidase A and B (A/B subfamily), while others,
namely regulatory MCPs or the N/E subfamily, are
involved in more selective reactions, mainly in
non-digestive tissues and fluids, acting on blood
coagulation/fibrinolysis, inflammation and local
anaphylaxis, pro-hormone and neuropeptide processing,
cellular response and others. Another MCP subfamily,
is that of succinylglutamate desuccinylase
/aspartoacylase, which hydrolyzes N-acetyl-L-aspartate
(NAA), and deficiency in which is the established cause
of Canavan disease. Another subfamily (referred to as
subfamily C) includes an exceptional type of activity
in the MCP family, that of dipeptidyl-peptidase
activity of gamma-glutamyl-(L)-meso-diaminopimelate
peptidase I which is involved in bacterial cell wall
metabolism.
Length = 240
Score = 28.5 bits (64), Expect = 1.7
Identities = 13/42 (30%), Positives = 15/42 (35%), Gaps = 6/42 (14%)
Query: 60 LSMGDIVFTTHDLGG------HVQARRVWRDYFPAVDAIVFI 95
LS G I + L G Q R V Y +D V I
Sbjct: 2 LSAGQIAYELAVLPGIEFAARSRQGRPVTGRYVAGLDHPVVI 43
>gnl|CDD|213833 TIGR03596, GTPase_YlqF, ribosome biogenesis GTP-binding protein
YlqF. Members of this protein family are GTP-binding
proteins involved in ribosome biogenesis, including the
essential YlqF protein of Bacillus subtilis, which is an
essential protein. They are related to Era, EngA, and
other GTPases of ribosome biogenesis, but are circularly
permuted. This family is not universal, and is not
present in Escherichia coli, and so is not as well
studied as some other GTPases. This model is built for
bacterial members [Protein synthesis, Other].
Length = 276
Score = 28.6 bits (65), Expect = 1.8
Identities = 23/75 (30%), Positives = 41/75 (54%), Gaps = 9/75 (12%)
Query: 74 GHV-QARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKI 132
GH+ +ARR ++ VD ++ ++DA R P S N + D+ + P LI+ NK
Sbjct: 6 GHMAKARREIKEKLKLVDVVIEVLDA----RIPLSSR---NPMIDEIRGNKPRLIVLNKA 58
Query: 133 DIFD-AASEDEVRHF 146
D+ D A ++ +++F
Sbjct: 59 DLADPAVTKQWLKYF 73
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 28.3 bits (63), Expect = 2.0
Identities = 28/120 (23%), Positives = 52/120 (43%), Gaps = 12/120 (10%)
Query: 23 KLLFLGLDNAGKTFL-LQMLKNDRTAQHMPTLHPT-------SEELSMGDIVFTTHDLGG 74
KL+ +G GK+ L +Q ++N ++ PT+ + EE + DI+ D G
Sbjct: 7 KLVVVGGGGVGKSALTIQFIQNHFIDEYDPTIEDSYRKQCVIDEETCLLDIL----DTAG 62
Query: 75 HVQARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKIDI 134
+ + Y + + + RS F E + +L VP++++GNK D+
Sbjct: 63 QEEYSAMRDQYMRTGQGFLCVYSITSRSSFEEIASFREQILRVKDKDRVPMILVGNKCDL 122
>gnl|CDD|176253 cd08293, PTGR2, Prostaglandin reductase. Prostaglandins and
related eicosanoids are metabolized by the oxidation of
the 15(S)-hydroxyl group of the NAD+-dependent (type I
15-PGDH) 15-prostaglandin dehydrogenase (15-PGDH)
followed by reduction by NADPH/NADH-dependent (type II
15-PGDH) delta-13 15-prostaglandin reductase (13-PGR) to
15-keto-13,14,-dihydroprostaglandins. 13-PGR is a
bifunctional enzyme, since it also has leukotriene B(4)
12-hydroxydehydrogenase activity. These 15-PGDH and
related enzymes are members of the medium chain
dehydrogenase/reductase family. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES.
Length = 345
Score = 28.5 bits (64), Expect = 2.2
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 5/39 (12%)
Query: 7 KFREVLLRLGLWKKSGKL-----LFLGLDNAGKTFLLQM 40
KF E + +L W K GKL ++ GL+NAG+ F M
Sbjct: 295 KFEEAIAQLSQWVKEGKLKVKETVYEGLENAGEAFQSMM 333
>gnl|CDD|206643 cd00877, Ran, Ras-related nuclear proteins (Ran)/TC4 family of
small GTPases. Ran GTPase is involved in diverse
biological functions, such as nuclear transport, spindle
formation during mitosis, DNA replication, and cell
division. Among the Ras superfamily, Ran is a unique
small G protein. It does not have a lipid modification
motif at the C-terminus to bind to the membrane, which
is often observed within the Ras superfamily. Ran may
therefore interact with a wide range of proteins in
various intracellular locations. Like other GTPases, Ran
exists in GTP- and GDP-bound conformations that interact
differently with effectors. Conversion between these
forms and the assembly or disassembly of effector
complexes requires the interaction of regulator
proteins. The intrinsic GTPase activity of Ran is very
low, but it is greatly stimulated by a GTPase-activating
protein (RanGAP1) located in the cytoplasm. By contrast,
RCC1, a guanine nucleotide exchange factor that
generates RanGTP, is bound to chromatin and confined to
the nucleus. Ran itself is mobile and is actively
imported into the nucleus by a mechanism involving
NTF-2. Together with the compartmentalization of its
regulators, this is thought to produce a relatively high
concentration of RanGTP in the nucleus.
Length = 166
Score = 28.0 bits (63), Expect = 2.2
Identities = 36/140 (25%), Positives = 57/140 (40%), Gaps = 17/140 (12%)
Query: 23 KLLFLGLDNAGKT-FLLQMLKNDRTAQHMPTL----HPTSEELSMGDIVFTTHDLGGHVQ 77
KL+ +G GKT F+ + L + +++ TL HP + G I F D G +
Sbjct: 2 KLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLDFHTNRGKIRFNVWDTAGQ-E 60
Query: 78 ARRVWRD-YFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDV----PILILGNKI 132
RD Y+ + + D + R + + N D L V PI++ GNK+
Sbjct: 61 KFGGLRDGYYIQGQCAIIMFDVTSR----VTYKNVPNWHRD--LVRVCENIPIVLCGNKV 114
Query: 133 DIFDAASEDEVRHFFGLYGL 152
DI D + + F L
Sbjct: 115 DIKDRKVKPKQITFHRKKNL 134
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 28.5 bits (65), Expect = 2.4
Identities = 11/54 (20%), Positives = 25/54 (46%), Gaps = 7/54 (12%)
Query: 90 DAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKIDIFDAASEDEV 143
D ++ ++DAS+ ++ + L D P++++ NK D+ +E
Sbjct: 296 DLVLLVLDASE-------PLTEEDDEILEELKDKPVIVVLNKADLTGEIDLEEE 342
>gnl|CDD|206654 cd01861, Rab6, Rab GTPase family 6 (Rab6). Rab6 is involved in
microtubule-dependent transport pathways through the
Golgi and from endosomes to the Golgi. Rab6A of mammals
is implicated in retrograde transport through the Golgi
stack, and is also required for a slow,
COPI-independent, retrograde transport pathway from the
Golgi to the endoplasmic reticulum (ER). This pathway
may allow Golgi residents to be recycled through the ER
for scrutiny by ER quality-control systems. Yeast Ypt6p,
the homolog of the mammalian Rab6 GTPase, is not
essential for cell viability. Ypt6p acts in
endosome-to-Golgi, in intra-Golgi retrograde transport,
and possibly also in Golgi-to-ER trafficking. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 161
Score = 28.0 bits (63), Expect = 2.5
Identities = 18/54 (33%), Positives = 31/54 (57%), Gaps = 5/54 (9%)
Query: 83 RDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKIDIFD 136
RD AV +V+ D ++R F + +D++ D+ DV I+++GNK D+ D
Sbjct: 71 RDSSVAV--VVY--DITNRQSFDNTDKWIDDVR-DERGNDVIIVLVGNKTDLSD 119
>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 = 27.9 bits (63), Expect = 2.9
Identities = 19/68 (27%), Positives = 32/68 (47%), Gaps = 19/68 (27%)
Query: 122 DVPILILGNKIDIFDAASEDEVRHFFGLYGLTTGKEF-TPREILQM-------RPMELFM 173
+VPI+++G KID+ D + L L ++ TP E ++ + ME
Sbjct: 104 NVPIILVGTKIDLRDDGNT--------LKKLEKKQKPITPEEGEKLAKEIGAVKYME--- 152
Query: 174 CSVLKRQG 181
CS L ++G
Sbjct: 153 CSALTQEG 160
>gnl|CDD|206667 cd01879, FeoB, Ferrous iron transport protein B (FeoB) family.
Ferrous iron transport protein B (FeoB) subfamily. E.
coli has an iron(II) transport system, known as feo,
which may make an important contribution to the iron
supply of the cell under anaerobic conditions. FeoB has
been identified as part of this transport system. FeoB
is a large 700-800 amino acid integral membrane protein.
The N terminus contains a P-loop motif suggesting that
iron transport may be ATP dependent.
Length = 159
Score = 27.4 bits (62), Expect = 2.9
Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 13/70 (18%)
Query: 69 THDLGGHVQARRVWRDY--FPAVDAIVFIIDASDRSRFPESKYELDNL-LADDAL-TDVP 124
T+ L + + +V RD+ D IV ++DA++ R NL L L +P
Sbjct: 54 TYSLTPYSEDEKVARDFLLGEEPDLIVNVVDATNLER---------NLYLTLQLLELGLP 104
Query: 125 ILILGNKIDI 134
+++ N ID
Sbjct: 105 VVVALNMIDE 114
>gnl|CDD|181721 PRK09242, PRK09242, tropinone reductase; Provisional.
Length = 257
Score = 27.8 bits (62), Expect = 3.0
Identities = 25/95 (26%), Positives = 38/95 (40%), Gaps = 9/95 (9%)
Query: 57 SEELSMG-DIVFTTHDLGGHVQARRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDNLL 115
E L +G D++ D QAR + FP + D SD E + + + +
Sbjct: 27 REFLGLGADVLIVARDADALAQARDELAEEFPEREVHGLAADVSD----DEDRRAILDWV 82
Query: 116 ADDALTDVPILILGNKIDIFDAA---SEDEVRHFF 147
D + IL+ +I AA +EDE R F
Sbjct: 83 EDHW-DGLHILVNNAGGNIRKAAIDYTEDEWRGIF 116
>gnl|CDD|221746 pfam12739, TRAPPC-Trs85, ER-Golgi trafficking TRAPP I complex 85
kDa subunit. This family is one of the subunits of the
TRAPP Golgi trafficking complex. TRAPP subunits are
found in two different sized complexes, TRAPP I and
TRAPP II, and this Trs85 is in the smaller complex.
TRAPP I, but Not TRAPP II, functions in ER-Golgi
transport. Trs85p was reported to function in the
cytosol-to-vacuole targeting pathway, suggesting a role
for this subunit in autophagy as well as in secretion.
The overall architecture of TRAPP I shows the other
components to be Bet3p (TRAPPC3), Bet5p (TRAPPC1),
Trs20p (TRAPPC2), Trs23p (TRAPPC4), Trs31p (TRAPPC5),
Trs33p (TRAPPC6a and b) and Trs85p.
Length = 390
Score = 28.1 bits (63), Expect = 3.2
Identities = 7/38 (18%), Positives = 14/38 (36%)
Query: 4 IWTKFREVLLRLGLWKKSGKLLFLGLDNAGKTFLLQML 41
W+ E L + G L + A + F+ + +
Sbjct: 89 EWSSALEDLQEISSAGPEGVYLSVSDVEAIRAFVREFV 126
>gnl|CDD|183229 PRK11611, PRK11611, enhanced serine sensitivity protein SseB;
Provisional.
Length = 246
Score = 27.7 bits (62), Expect = 3.3
Identities = 10/12 (83%), Positives = 10/12 (83%)
Query: 152 LTTGKEFTPREI 163
L TGKEF PREI
Sbjct: 98 LPTGKEFMPREI 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 = 27.5 bits (61), Expect = 3.3
Identities = 27/117 (23%), Positives = 51/117 (43%), Gaps = 6/117 (5%)
Query: 23 KLLFLGLDNAGK-TFLLQMLKNDRTAQHMPTLHPTSEE-LSMGDIVFTTH--DLGGHVQA 78
+++ G GK + +L+ +K ++PT+ T + +S + T D G Q
Sbjct: 3 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCSKSICTLQITDTTGSHQF 62
Query: 79 RRVWRDYFPAVDAIVFIIDASDRSRFPESK--YELDNLLADDALTDVPILILGNKID 133
+ R A + + + + E K YEL + + L +PI+++GNK D
Sbjct: 63 PAMQRLSISKGHAFILVYSITSKQSLEELKPIYELICEIKGNNLEKIPIMLVGNKCD 119
>gnl|CDD|206715 cd04148, RGK, Rem, Rem2, Rad, Gem/Kir (RGK) subfamily of Ras
GTPases. RGK subfamily. The RGK (Rem, Rem2, Rad,
Gem/Kir) subfamily of Ras GTPases are expressed in a
tissue-specific manner and are dynamically regulated by
transcriptional and posttranscriptional mechanisms in
response to environmental cues. RGK proteins bind to the
beta subunit of L-type calcium channels, causing
functional down-regulation of these voltage-dependent
calcium channels, and either termination of
calcium-dependent secretion or modulation of electrical
conduction and contractile function. Inhibition of
L-type calcium channels by Rem2 may provide a mechanism
for modulating calcium-triggered exocytosis in
hormone-secreting cells, and has been proposed to
influence the secretion of insulin in pancreatic beta
cells. RGK proteins also interact with and inhibit the
Rho/Rho kinase pathway to modulate remodeling of the
cytoskeleton. Two characteristics of RGK proteins cited
in the literature are N-terminal and C-terminal
extensions beyond the GTPase domain typical of Ras
superfamily members. The N-terminal extension is not
conserved among family members; the C-terminal extension
is reported to be conserved among the family and lack
the CaaX prenylation motif typical of
membrane-associated Ras proteins. However, a putative
CaaX motif has been identified in the alignment of the
C-terminal residues of this CD.
Length = 219
Score = 27.8 bits (62), Expect = 3.3
Identities = 18/46 (39%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 90 DAIVFIIDASDRSRFPESKYELDNLL-ADDALTDVPILILGNKIDI 134
DA V + +DRS F E EL L D+PI+++GNK D+
Sbjct: 74 DAYVIVYSVTDRSSF-EKASELRIQLRRARQAEDIPIILVGNKSDL 118
>gnl|CDD|232995 TIGR00487, IF-2, translation initiation factor IF-2. This model
discriminates eubacterial (and mitochondrial)
translation initiation factor 2 (IF-2), encoded by the
infB gene in bacteria, from similar proteins in the
Archaea and Eukaryotes. In the bacteria and in
organelles, the initiator tRNA is charged with
N-formyl-Met instead of Met. This translation factor
acts in delivering the initator tRNA to the ribosome. It
is one of a number of GTP-binding translation factors
recognized by the pfam model GTP_EFTU [Protein
synthesis, Translation factors].
Length = 587
Score = 28.2 bits (63), Expect = 3.4
Identities = 38/128 (29%), Positives = 58/128 (45%), Gaps = 18/128 (14%)
Query: 33 GKTFLLQMLKNDRTA--------QHMPTLHPTSEELSMGDIVFTTHDLGGHVQARRVWRD 84
GKT LL ++ + A QH+ H +E+ M I F D GH +A R
Sbjct: 99 GKTSLLDSIRKTKVAQGEAGGITQHIGAYHVENEDGKM--ITFL--DTPGH-EAFTSMRA 153
Query: 85 YFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKIDIFDAASEDEVR 144
V IV ++ A+D P++ + + A +VPI++ NKID + A+ D V+
Sbjct: 154 RGAKVTDIVVLVVAADDGVMPQTIEAISHAKA----ANVPIIVAINKIDKPE-ANPDRVK 208
Query: 145 HFFGLYGL 152
YGL
Sbjct: 209 QELSEYGL 216
>gnl|CDD|225176 COG2267, PldB, Lysophospholipase [Lipid metabolism].
Length = 298
Score = 27.7 bits (62), Expect = 4.1
Identities = 14/62 (22%), Positives = 22/62 (35%), Gaps = 7/62 (11%)
Query: 49 HMPTLHPTSEELSMGDIVFTTHDLGGHVQARR-------VWRDYFPAVDAIVFIIDASDR 101
H +++L+ DL GH ++ R + DY +DA V I D
Sbjct: 46 HSGRYEELADDLAARGFDVYALDLRGHGRSPRGQRGHVDSFADYVDDLDAFVETIAEPDP 105
Query: 102 SR 103
Sbjct: 106 GL 107
>gnl|CDD|145415 pfam02251, PA28_alpha, Proteasome activator pa28 alpha subunit.
PA28 activator complex (also known as 11s regulator of
20S proteasome) is a ring shaped hexameric structure of
alternating alpha and beta subunits. This family
represents the alpha subunit. The activator complex
binds to the 20S proteasome ana simulates peptidase
activity in and ATP-independent manner.
Length = 64
Score = 25.7 bits (57), Expect = 4.1
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 104 FPESKYELDNLLADDAL 120
FPE ELD LL + L
Sbjct: 28 FPEKILELDALLKEPIL 44
>gnl|CDD|206710 cd04139, RalA_RalB, Ral (Ras-like) family containing highly
homologous RalA and RalB. The Ral (Ras-like) subfamily
consists of the highly homologous RalA and RalB. Ral
proteins are believed to play a crucial role in
tumorigenesis, metastasis, endocytosis, and actin
cytoskeleton dynamics. Despite their high sequence
similarity (>80% sequence identity), nonoverlapping and
opposing functions have been assigned to RalA and RalBs
in tumor migration. In human bladder and prostate cancer
cells, RalB promotes migration while RalA inhibits it. A
Ral-specific set of GEFs has been identified that are
activated by Ras binding. This RalGEF activity is
enhanced by Ras binding to another of its target
proteins, phosphatidylinositol 3-kinase (PI3K). Ral
effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and
the exocyst (Sec6/8) complex, a heterooctomeric protein
complex that is involved in tethering vesicles to
specific sites on the plasma membrane prior to
exocytosis. In rat kidney cells, RalB is required for
functional assembly of the exocyst and for localizing
the exocyst to the leading edge of migrating cells. In
human cancer cells, RalA is required to support
anchorage-independent proliferation and RalB is required
to suppress apoptosis. RalA has been shown to localize
to the plasma membrane while RalB is localized to the
intracellular vesicles. Most Ras proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Ras proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 163
Score = 27.4 bits (61), Expect = 4.1
Identities = 25/121 (20%), Positives = 51/121 (42%), Gaps = 4/121 (3%)
Query: 23 KLLFLGLDNAGKTFL-LQMLKNDRTAQHMPTLHPTSEE---LSMGDIVFTTHDLGGHVQA 78
K++ +G GK+ L LQ + ++ + PT + + L ++ D G
Sbjct: 2 KVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEVQLNILDTAGQEDY 61
Query: 79 RRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKIDIFDAA 138
+ +YF + + + + +D F + +L +VP+L++GNK D+ D
Sbjct: 62 AAIRDNYFRSGEGFLLVFSITDMESFTALAEFREQILRVKEDDNVPLLLVGNKCDLEDKR 121
Query: 139 S 139
Sbjct: 122 Q 122
>gnl|CDD|117515 pfam08948, DUF1859, Domain of unknown function (DUF1859). This
domain has no known function. It is predominantly found
in the N-terminus of bacteriophage spike proteins.
Length = 126
Score = 27.0 bits (59), Expect = 4.4
Identities = 7/48 (14%), Positives = 13/48 (27%), Gaps = 4/48 (8%)
Query: 62 MGDIVFTTHDLGGHVQARRVWRDYFP--AVDAIVFIIDAS--DRSRFP 105
G + G ++ + YFP F+ + P
Sbjct: 66 DGAFEIDVEETGQRIKCPAGKQGYFPLLVPGRAKFVARHLGSGKKSVP 113
>gnl|CDD|153428 cd08001, WGR_PARP1_like, WGR domain of poly(ADP-ribose) polymerase
1 and similar proteins. The WGR domain is found in a
variety of eukaryotic poly(ADP-ribose) polymerases
(PARPs). It has been called WGR after the most conserved
central motif of the domain. The domain typically occurs
together with a catalytic PARP domain, and is between 70
and 80 residues in length. It has been proposed to
function as a nucleic acid binding domain. PARPs
catalyze the NAD(+)-dependent synthesis of ADP-ribose
polymers and their addition to various nuclear proteins.
Higher eukaryotes contain several PARPs and and there
may be up to 17 human PARP-like proteins, with three of
them (PARP-1, PARP-2, and PARP-3) containing a WGR
domain. The synthesis of poly-ADP-ribose requires
multiple enzymatic activities for initiation,
trans-ADP-ribosylation, elongation, branching, and
release of the polymer from the enzyme. This subfamily
is composed of vertebrate PARP-1 and similar proteins,
including Arabidopsis thaliana PARP-1 and PARP-3. PARP-1
is the best-studied among the PARPs. It is a widely
expressed nuclear chromatin-associated enzyme that
possesses auto-mono-ADP-ribosylation (initiation),
elongation, and branching activities. PARP-1 is
implicated in DNA damage and cell death pathways and is
important in maintaining genomic stability and
regulating cell proliferation, differentiation, neuronal
function, inflammation, and aging.
Length = 104
Score = 26.4 bits (59), Expect = 4.4
Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 1/47 (2%)
Query: 126 LILGNKIDIFDAASEDEVRHFFGLYGLTTGKEFTPREILQMRPMELF 172
I GNK++ F + E+ F LY TG +F R+ + +P + +
Sbjct: 53 TIGGNKLEEFSS-LEEAKMAFEELYEEKTGNDFENRKNFKKKPGKFY 98
>gnl|CDD|128473 smart00176, RAN, Ran (Ras-related nuclear proteins) /TC4 subfamily
of small GTPases. Ran is involved in the active
transport of proteins through nuclear pores.
Length = 200
Score = 27.3 bits (60), Expect = 5.2
Identities = 23/106 (21%), Positives = 45/106 (42%), Gaps = 6/106 (5%)
Query: 35 TFLLQMLKNDRTAQHMPTL----HPTSEELSMGDIVFTTHDLGGHVQARRVWRDYFPAVD 90
TF+ + L + +++ TL HP + G I F D G + + Y+
Sbjct: 10 TFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIRFNVWDTAGQEKFGGLRDGYYIQGQ 69
Query: 91 AIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKIDIFD 136
+ + D + R + +L+ ++PI++ GNK+D+ D
Sbjct: 70 CAIIMFDVTARVTYKNVPNWHRDLVR--VCENIPIVLCGNKVDVKD 113
>gnl|CDD|130324 TIGR01257, rim_protein, retinal-specific rim ABC transporter. This
model describes the photoreceptor protein (rim protein)
in eukaryotes. It is the member of ABC transporter
superfamily. Rim protein is a membrane glycoprotein which
is localized in the photoreceptor outer segment discs.
Mutation/s in its genetic loci is implicated in the
recessive Stargardt's disease [Transport and binding
proteins, Other].
Length = 2272
Score = 27.7 bits (61), Expect = 5.2
Identities = 9/22 (40%), Positives = 19/22 (86%)
Query: 25 LFLGLDNAGKTFLLQMLKNDRT 46
LF+G++++ TF+L++ +N+RT
Sbjct: 1800 LFIGINSSAITFVLELFENNRT 1821
>gnl|CDD|206707 cd04135, Tc10, Rho GTPase TC10 (Tc10). TC10 is a Rho family
protein that has been shown to induce microspike
formation and neurite outgrowth in vitro. Its expression
changes dramatically after peripheral nerve injury,
suggesting an important role in promoting axonal
outgrowth and regeneration. TC10 regulates translocation
of insulin-stimulated GLUT4 in adipocytes and has also
been shown to bind directly to Golgi COPI coat proteins.
GTP-bound TC10 in vitro can bind numerous potential
effectors. Depending on its subcellular localization and
distinct functional domains, TC10 can differentially
regulate two types of filamentous actin in adipocytes.
TC10 mRNAs are highly expressed in three types of mouse
muscle tissues: leg skeletal muscle, cardiac muscle, and
uterus; they were also present in brain, with higher
levels in adults than in newborns. TC10 has also been
shown to play a role in regulating the expression of
cystic fibrosis transmembrane conductance regulator
(CFTR) through interactions with CFTR-associated ligand
(CAL). The GTP-bound form of TC10 directs the
trafficking of CFTR from the juxtanuclear region to the
secretory pathway toward the plasma membrane, away from
CAL-mediated DFTR degradation in the lysosome. Most Rho
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 174
Score = 26.9 bits (59), Expect = 5.4
Identities = 28/118 (23%), Positives = 49/118 (41%), Gaps = 5/118 (4%)
Query: 23 KLLFLGLDNAGKTFLLQMLKNDR-TAQHMPTL---HPTSEELSMGDIVFTTHDLGGHVQA 78
K + +G GKT LL ND +++PT+ + S + + +D G
Sbjct: 2 KCVVVGDGAVGKTCLLMSYANDAFPEEYVPTVFDHYAVSVTVGGKQYLLGLYDTAGQEDY 61
Query: 79 RRVWRDYFPAVDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKIDIFD 136
R+ +P D + + + F K E L + +VP L++G +ID+ D
Sbjct: 62 DRLRPLSYPMTDVFLICFSVVNPASFQNVKEEWVPELKE-YAPNVPYLLIGTQIDLRD 118
>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 = 5.4
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 92 IVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKID 133
+V+ I DR F E + +L DVPI+++GNK D
Sbjct: 79 LVYSIT--DRQSFEEIAKFREQILRVKDRDDVPIVLVGNKCD 118
>gnl|CDD|206694 cd04109, Rab28, Rab GTPase family 28 (Rab28). Rab28 subfamily.
First identified in maize, Rab28 has been shown to be a
late embryogenesis-abundant (Lea) protein that is
regulated by the plant hormone abcisic acid (ABA). In
Arabidopsis, Rab28 is expressed during embryo
development and is generally restricted to provascular
tissues in mature embryos. Unlike maize Rab28, it is not
ABA-inducible. Characterization of the human Rab28
homolog revealed two isoforms, which differ by a 95-base
pair insertion, producing an alternative sequence for
the 30 amino acids at the C-terminus. The two human
isoforms are presumably the result of alternative
splicing. Since they differ at the C-terminus but not in
the GTP-binding region, they are predicted to be
targeted to different cellular locations. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins.
Length = 213
Score = 27.1 bits (60), Expect = 5.5
Identities = 13/66 (19%), Positives = 30/66 (45%), Gaps = 2/66 (3%)
Query: 71 DLGGHVQARRVWRDYFPAVDAIVFIIDASDRSRFP--ESKYELDNLLADDALTDVPILIL 128
D+GG ++ Y A+ + D ++ F E + + +++ T ++++
Sbjct: 56 DIGGQQIGGKMLDKYIYGAQAVCLVYDITNSQSFENLEDWLSVVKKVNEESETKPKMVLV 115
Query: 129 GNKIDI 134
GNK D+
Sbjct: 116 GNKTDL 121
>gnl|CDD|169396 PRK08349, PRK08349, hypothetical protein; Validated.
Length = 198
Score = 26.6 bits (59), Expect = 7.2
Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 13/58 (22%)
Query: 111 LDNLLADDALTDVPI---LILGNKIDIFDAASEDEVRHFFGLYGLTTGKE----FTPR 161
LDNL+ TD+P+ LI +K +I A E G + ++ E F P+
Sbjct: 123 LDNLMVISTATDLPVLRPLIGLDKEEIVKIAKE------IGTFEISIEPEPPCPFVPK 174
>gnl|CDD|226952 COG4586, COG4586, ABC-type uncharacterized transport system,
ATPase component [General function prediction only].
Length = 325
Score = 27.0 bits (60), Expect = 7.5
Identities = 12/29 (41%), Positives = 17/29 (58%), Gaps = 4/29 (13%)
Query: 24 LLFLGLDNAGKTFLLQMLKNDRTAQHMPT 52
+ FLG + AGK+ L+ML T +PT
Sbjct: 53 VGFLGANGAGKSTTLKML----TGLLLPT 77
>gnl|CDD|133376 cd04176, Rap2, Rap2 family GTPase consists of Rap2a, Rap2b, and
Rap2c. The Rap2 subgroup is part of the Rap subfamily
of the Ras family. It consists of Rap2a, Rap2b, and
Rap2c. Both isoform 3 of the human mitogen-activated
protein kinase kinase kinase kinase 4 (MAP4K4) and
Traf2- and Nck-interacting kinase (TNIK) are putative
effectors of Rap2 in mediating the activation of c-Jun
N-terminal kinase (JNK) to regulate the actin
cytoskeleton. In human platelets, Rap2 was shown to
interact with the cytoskeleton by binding the actin
filaments. In embryonic Xenopus development, Rap2 is
necessary for the Wnt/beta-catenin signaling pathway.
The Rap2 interacting protein 9 (RPIP9) is highly
expressed in human breast carcinomas and correlates with
a poor prognosis, suggesting a role for Rap2 in breast
cancer oncogenesis. Rap2b, but not Rap2a, Rap2c, Rap1a,
or Rap1b, is expressed in human red blood cells, where
it is believed to be involved in vesiculation. A number
of additional effector proteins for Rap2 have been
identified, including the RalGEFs RalGDS, RGL, and Rlf,
which also interact with Rap1 and Ras. Most Ras proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 163
Score = 26.3 bits (58), Expect = 7.6
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 3/46 (6%)
Query: 99 SDRSRFPESKYELDNLLADDALTDVPILILGNKIDIFDAASEDEVR 144
++ F + K D ++ VPI+++GNK+D+ SE EV
Sbjct: 83 VNQQTFQDIKPMRDQIVRVKGYEKVPIILVGNKVDL---ESEREVS 125
>gnl|CDD|234395 TIGR03918, GTP_HydF, [FeFe] hydrogenase H-cluster maturation GTPase
HydF. This model describes the family of the [Fe]
hydrogenase maturation protein HypF as characterized in
Chlamydomonas reinhardtii and found, in an operon with
radical SAM proteins HydE and HydG, in numerous
bacteria. It has GTPase activity, can bind an 4Fe-4S
cluster, and is essential for hydrogenase activity
[Protein fate, Protein modification and repair].
Length = 391
Score = 26.7 bits (60), Expect = 7.7
Identities = 14/59 (23%), Positives = 29/59 (49%), Gaps = 5/59 (8%)
Query: 89 VDAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKIDIFDAASEDEVRHFF 147
D + ++DA +YEL+ L+ + +P +++ NKID+ + ++E E
Sbjct: 86 TDLALLVVDA----GVGPGEYELE-LIEELKERKIPYIVVINKIDLGEESAELEKLEKK 139
>gnl|CDD|238402 cd00779, ProRS_core_prok, Prolyl-tRNA synthetase (ProRS) class II
core catalytic domain. ProRS is a homodimer. It is
responsible for the attachment of proline to the 3' OH
group of ribose of the appropriate tRNA. This domain is
primarily responsible for ATP-dependent formation of
the enzyme bound aminoacyl-adenylate. Class II
assignment is based upon its structure and the presence
of three characteristic sequence motifs in the core
domain. This subfamily contains the core domain of
ProRS from prokaryotes and from the mitochondria of
eukaryotes.
Length = 255
Score = 26.8 bits (60), Expect = 8.1
Identities = 17/43 (39%), Positives = 20/43 (46%), Gaps = 9/43 (20%)
Query: 17 LWKKSGKLLFLGLDNAGKTFLLQMLKNDRTAQHMPTLHPTSEE 59
LWK+SG+ D G L LK DR + L PT EE
Sbjct: 63 LWKESGR-----WDAYGPELL--RLK-DRHGKEF-LLGPTHEE 96
>gnl|CDD|115510 pfam06858, NOG1, Nucleolar GTP-binding protein 1 (NOG1). This
family represents a conserved region of approximately 60
residues in length within nucleolar GTP-binding protein
1 (NOG1). In S. cerevisiae, the NOG1 gene has been shown
to be essential for cell viability, suggesting that NOG1
may play an important role in nucleolar functions.
Family members include eukaryotic, bacterial and
archaeal proteins.
Length = 58
Score = 24.9 bits (55), Expect = 8.4
Identities = 11/45 (24%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 90 DAIVFIIDASDRSRFP-ESKYELDNLLADDALTDVPILILGNKID 133
A++F+ D S++ + E + L + + P++++ NKID
Sbjct: 15 AAVLFVFDPSEQCGYSLEEQLHLFKEIK-PLFKNKPVIVVLNKID 58
>gnl|CDD|133314 cd04114, Rab30, Rab GTPase family 30 (Rab30). Rab30 subfamily.
Rab30 appears to be associated with the Golgi stack. It
is expressed in a wide variety of tissue types and in
humans maps to chromosome 11. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 169
Score = 26.4 bits (58), Expect = 8.6
Identities = 16/69 (23%), Positives = 34/69 (49%), Gaps = 7/69 (10%)
Query: 71 DLGGHVQARRVWRDYFPAVDAIVFIIDASDRSRF---PESKYELDNLLADDALTDVPILI 127
D G + R + + Y+ + +A++ D + F PE E++ + +T ++
Sbjct: 62 DTAGQERFRSITQSYYRSANALILTYDITCEESFRCLPEWLREIEQYANNKVIT----IL 117
Query: 128 LGNKIDIFD 136
+GNKID+ +
Sbjct: 118 VGNKIDLAE 126
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 26.8 bits (60), Expect = 8.7
Identities = 14/55 (25%), Positives = 25/55 (45%), Gaps = 6/55 (10%)
Query: 90 DAIVFIIDASDRSRFPESKYELDNLLADDALTDVPILILGNKIDIFDAASEDEVR 144
D ++F++DAS P K D L + PI+++ NK D+ + +
Sbjct: 298 DLVLFVLDASQ----PLDK--EDLALIELLPKKKPIIVVLNKADLVSKIELESEK 346
>gnl|CDD|206647 cd00881, GTP_translation_factor, GTP translation factor family
primarily contains translation initiation, elongation
and release factors. The GTP translation factor family
consists primarily of translation initiation,
elongation, and release factors, which play specific
roles in protein translation. In addition, the family
includes Snu114p, a component of the U5 small nuclear
riboprotein particle which is a component of the
spliceosome and is involved in excision of introns,
TetM, a tetracycline resistance gene that protects the
ribosome from tetracycline binding, and the unusual
subfamily CysN/ATPS, which has an unrelated function
(ATP sulfurylase) acquired through lateral transfer of
the EF1-alpha gene and development of a new function.
Length = 183
Score = 26.1 bits (58), Expect = 9.2
Identities = 30/151 (19%), Positives = 46/151 (30%), Gaps = 30/151 (19%)
Query: 31 NAGKTFLLQML------KNDRTAQHMPTLHPTSEELSMG-------------DIVFTTHD 71
+ GKT L L + R + L EE G D
Sbjct: 9 DHGKTTLTGSLLYQTGAIDRRGTRKETFLDTLKEERERGITIKTGVVEFEWPKRRINFID 68
Query: 72 LGGHVQARRVWRDYFPAVDAIVFIIDASDRSRFPESK-YELDNLLADDALTDVPILILGN 130
GH + D + ++DA++ E + E N+ +PI++ N
Sbjct: 69 TPGHEDFSKETVRGLAQADGALLVVDANE---GVEPQTREHLNIAL---AGGLPIIVAVN 122
Query: 131 KIDIFDAA----SEDEVRHFFGLYGLTTGKE 157
KID E++ L G T K
Sbjct: 123 KIDRVGEEDFDEVLREIKELLKLIGFTFLKG 153
>gnl|CDD|212509 cd11723, YabN_N, N-terminal S-AdoMet dependent methylase domain
of Bacillus subtilis YabN and related proteins. This
family contains proteins similar to Bacillus subtilis
YabN, which is a fusion of an N-terminal TP-methylase
and a C-terminal MazG-type nucleotide
pyrophosphohydrolase domain. MazG-like NTP-PPases have
been implicated in house-cleaning functions such as
degrading abnormal (d)NTPs. TP-methylases use S-AdoMet
(S-adenosyl-L-methionine or SAM) in the methylation of
diverse substrates. Most members catalyze various
methylation steps in cobalamin (vitamin B12)
biosynthesis, other members like Diphthine synthase and
Ribosomal RNA small subunit methyltransferase I (RsmI)
act on other substrates. The specific function of
YabN's TP-methylase domain is not known.
Length = 220
Score = 26.4 bits (59), Expect = 9.2
Identities = 18/59 (30%), Positives = 22/59 (37%), Gaps = 20/59 (33%)
Query: 13 LRLGLWKKSGKLLFLGLDNAGKTFLLQMLKNDRTAQHMPTLHPTSEELSMGDIVFTTHD 71
L LG+++ L A K FL RTA H P EL I F + D
Sbjct: 15 LTLGVYRA--------LKAADKIFL-------RTAIH-----PVVAELEEEGISFESFD 53
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
0.326 0.143 0.440
Gapped
Lambda K H
0.267 0.0791 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,505,889
Number of extensions: 1009723
Number of successful extensions: 1515
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1465
Number of HSP's successfully gapped: 129
Length of query: 194
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 102
Effective length of database: 6,857,034
Effective search space: 699417468
Effective search space used: 699417468
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 56 (25.2 bits)