RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16468
(463 letters)
>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 = 387 bits (997), Expect = e-133
Identities = 128/245 (52%), Positives = 166/245 (67%), Gaps = 23/245 (9%)
Query: 20 GTGESGKSTFIKQMRIIHGSGYSDEDKRGFIKLVYQNIFMAMQSMIRAMDLLKIQYADPT 79
G GESGKST +KQM+I+HG+G+SDE++R F ++Y NI +M++++RAM+ L I Y DP
Sbjct: 7 GAGESGKSTILKQMKILHGNGFSDEERREFRPVIYSNILQSMKALLRAMETLNIPYGDPE 66
Query: 80 CEEKAELIRSVDFE-TVTTFESPYVEAIKELWADPGIQECYDRRREYQLTDSAKYYLMEI 138
E+ A+ I S+ EAIK LW DPGIQ CYDRR EYQL DSAKY+L +
Sbjct: 67 NEKDAKKILSLAPRAEEGPLPPELAEAIKRLWKDPGIQACYDRRNEYQLNDSAKYFLDNL 126
Query: 139 DRVAAPNYLPTEQDILRVRVPTTGIIEYPFDLEEIRFRMVDVGGQRSERRKWIHCFENVT 198
DR++ P+Y+PTEQDILR RV TTGIIE F ++ ++FRM DVGGQRSER+K
Sbjct: 127 DRISDPDYIPTEQDILRSRVKTTGIIETDFSIKNLKFRMFDVGGQRSERKK--------- 177
Query: 199 MVDVGGQRSERRKWIHCFENVTSIIFLVALSEYDQILFESENENRMEESKALFKTIITYP 258
WIHCFE+VT+IIF+VALSEYDQ+L E E+ NRM+ES LF +I
Sbjct: 178 -------------WIHCFEDVTAIIFVVALSEYDQVLVEDESVNRMQESLKLFDSICNSR 224
Query: 259 WFQHS 263
WF ++
Sbjct: 225 WFANT 229
Score = 153 bits (388), Expect = 1e-42
Identities = 54/137 (39%), Positives = 66/137 (48%), Gaps = 46/137 (33%)
Query: 366 YLGDLARIEDPGYMPTEQDILRARQPTTGIIEYPFDLDGI-------------------- 405
+L +L RI DP Y+PTEQDILR+R TTGIIE F + +
Sbjct: 122 FLDNLDRISDPDYIPTEQDILRSRVKTTGIIETDFSIKNLKFRMFDVGGQRSERKKWIHC 181
Query: 406 --------------------------NRMEESKALFKTIITYPWFQHSSVILFLNKKDLL 439
NRM+ES LF +I WF ++S+ILFLNKKDL
Sbjct: 182 FEDVTAIIFVVALSEYDQVLVEDESVNRMQESLKLFDSICNSRWFANTSIILFLNKKDLF 241
Query: 440 EEKIMYSHLVDYFPEYD 456
EEKI S L DYFP+Y
Sbjct: 242 EEKIKKSPLTDYFPDYT 258
Score = 68.3 bits (168), Expect = 9e-13
Identities = 25/40 (62%), Positives = 30/40 (75%), Gaps = 6/40 (15%)
Query: 264 MVDVGGQRSERRKWIHCFENVT---FCNSVQLFSQYNVIL 300
M DVGGQRSER+KWIHCFE+VT F V L S+Y+ +L
Sbjct: 165 MFDVGGQRSERKKWIHCFEDVTAIIFV--VAL-SEYDQVL 201
>gnl|CDD|214595 smart00275, G_alpha, G protein alpha subunit. Subunit of G
proteins that contains the guanine nucleotide binding
site.
Length = 342
Score = 336 bits (864), Expect = e-113
Identities = 132/313 (42%), Positives = 177/313 (56%), Gaps = 47/313 (15%)
Query: 20 GTGESGKSTFIKQMRIIHGSGYSDEDKRGFIKLVYQNIFMAMQSMIRAMDLLKIQYADPT 79
G GESGKST +KQMRI+HG G+S E++R + L+Y NI +M++++ AM+ L I + DP
Sbjct: 28 GAGESGKSTILKQMRILHGDGFSQEERREYRPLIYSNILESMKALVDAMEELNIPFEDPE 87
Query: 80 CEEKAELIRSVDFET---VTTFESPYVEAIKELWADPGIQECYDRRREYQLTDSAKYYLM 136
+I +T +AIK LW D GIQECY RR E+QL DSA Y+L
Sbjct: 88 SILDIRIITEQFNKTDETENVLPKEIAKAIKALWKDEGIQECYRRRNEFQLNDSASYFLD 147
Query: 137 EIDRVAAPNYLPTEQDILRVRVPTTGIIEYPFDLEEIRFRMVDVGGQRSERRKWIHCFEN 196
IDR+ P+Y+PTEQDILR RVPTTGI E F ++++ FRM DVGGQRSER+K
Sbjct: 148 NIDRIGDPDYVPTEQDILRSRVPTTGIQETAFIVKKLFFRMFDVGGQRSERKK------- 200
Query: 197 VTMVDVGGQRSERRKWIHCFENVTSIIFLVALSEYDQILFESENENRMEESKALFKTIIT 256
WIHCF+NVT+IIF VALSEYDQ+L E E+ NRM+ES LF++I
Sbjct: 201 ---------------WIHCFDNVTAIIFCVALSEYDQVLEEDESTNRMQESLNLFESICN 245
Query: 257 YPWFQHSMVDVGGQRSERRKWIHCFENVTFCNSVQLFSQYNVILNCMNYTIVPPLHTGPQ 316
WF ++ + + F N + LF + + + P + GP
Sbjct: 246 SRWFANTSI------------------ILFLNKIDLFEE---KIKKVPLVDYFPDYKGPN 284
Query: 317 RDAIAAREFILRM 329
AA +FI +
Sbjct: 285 DYE-AAAKFIKQK 296
Score = 127 bits (322), Expect = 4e-33
Identities = 52/137 (37%), Positives = 66/137 (48%), Gaps = 46/137 (33%)
Query: 366 YLGDLARIEDPGYMPTEQDILRARQPTTGIIEYPFDLDGI-------------------- 405
+L ++ RI DP Y+PTEQDILR+R PTTGI E F + +
Sbjct: 145 FLDNIDRIGDPDYVPTEQDILRSRVPTTGIQETAFIVKKLFFRMFDVGGQRSERKKWIHC 204
Query: 406 --------------------------NRMEESKALFKTIITYPWFQHSSVILFLNKKDLL 439
NRM+ES LF++I WF ++S+ILFLNK DL
Sbjct: 205 FDNVTAIIFCVALSEYDQVLEEDESTNRMQESLNLFESICNSRWFANTSIILFLNKIDLF 264
Query: 440 EEKIMYSHLVDYFPEYD 456
EEKI LVDYFP+Y
Sbjct: 265 EEKIKKVPLVDYFPDYK 281
>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 = 319 bits (821), Expect = e-107
Identities = 119/252 (47%), Positives = 174/252 (69%), Gaps = 28/252 (11%)
Query: 18 FVGTGESGKSTFIKQMRIIHGSGYSDEDKRGFIKLVYQNIFMAMQSMIRAMDLLKIQYAD 77
+G GESGKST +KQM+I+HG G+SDE++ + ++Y NI ++++++ A++ L+I+ ++
Sbjct: 7 LLGAGESGKSTILKQMKILHGGGFSDEEREQYRAVIYSNIIRSLKTLLEALENLEIESSN 66
Query: 78 --PTCEEKAELIRSVDFETV----TTFESPYVEAIKELWADPGIQECYDRRREYQLTDSA 131
P EE A+ ++S+ + T F E IKELW DPGIQE Y+R E+QL+DSA
Sbjct: 67 SKPENEEIAKKLKSILDSLLDVDETRFSEELAEDIKELWNDPGIQEVYNRSNEFQLSDSA 126
Query: 132 KYYLMEIDRVAAPNYLPTEQDILRVRVPTTGIIEYPFDLEEIRFRMVDVGGQRSERRKWI 191
KY+L +DR+A+P+Y+PT+QDILR RV TTGIIE FD + ++FR+ DVGGQRSER+K
Sbjct: 127 KYFLDNLDRIASPDYVPTDQDILRARVKTTGIIETKFDFKGLKFRLFDVGGQRSERKK-- 184
Query: 192 HCFENVTMVDVGGQRSERRKWIHCFENVTSIIFLVALSEYDQILFESENENRMEESKALF 251
WIHCFE+VT+IIF+V+LSEYDQ+L+E ++ NR+EES LF
Sbjct: 185 --------------------WIHCFEDVTAIIFVVSLSEYDQVLYEDDSTNRLEESLNLF 224
Query: 252 KTIITYPWFQHS 263
+ I PWF+++
Sbjct: 225 EEICNSPWFKNT 236
Score = 130 bits (329), Expect = 3e-34
Identities = 54/137 (39%), Positives = 67/137 (48%), Gaps = 46/137 (33%)
Query: 366 YLGDLARIEDPGYMPTEQDILRARQPTTGIIEYPFDLDGI-------------------- 405
+L +L RI P Y+PT+QDILRAR TTGIIE FD G+
Sbjct: 129 FLDNLDRIASPDYVPTDQDILRARVKTTGIIETKFDFKGLKFRLFDVGGQRSERKKWIHC 188
Query: 406 --------------------------NRMEESKALFKTIITYPWFQHSSVILFLNKKDLL 439
NR+EES LF+ I PWF+++ +ILFLNKKDL
Sbjct: 189 FEDVTAIIFVVSLSEYDQVLYEDDSTNRLEESLNLFEEICNSPWFKNTPIILFLNKKDLF 248
Query: 440 EEKIMYSHLVDYFPEYD 456
EEK+ L DYFPEY+
Sbjct: 249 EEKLKKGPLSDYFPEYE 265
Score = 59.6 bits (145), Expect = 9e-10
Identities = 18/24 (75%), Positives = 21/24 (87%)
Query: 264 MVDVGGQRSERRKWIHCFENVTFC 287
+ DVGGQRSER+KWIHCFE+VT
Sbjct: 172 LFDVGGQRSERKKWIHCFEDVTAI 195
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 44.9 bits (107), Expect = 1e-05
Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 10/59 (16%)
Query: 198 TMVDVGGQRSERRKWIHCFENVTSIIFLVALSEYDQILFESENENRMEESKALFKTIIT 256
T+ DVGGQ S R W + F N ++IF+V +S + +R+EE+K ++
Sbjct: 61 TVWDVGGQESLRPLWRNYFPNTDAVIFVV----------DSADRDRIEEAKEELHALLN 109
Score = 29.9 bits (68), Expect = 1.6
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 255 ITYPWFQHSMVDVGGQRSERRKWIHCFENV 284
+TY + ++ DVGGQ S R W + F N
Sbjct: 53 VTYKNVKFTVWDVGGQESLRPLWRNYFPNT 82
>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 = 40.6 bits (96), Expect = 4e-04
Identities = 19/60 (31%), Positives = 29/60 (48%), Gaps = 10/60 (16%)
Query: 196 NVTMVDVGGQRSERRKWIHCFENVTSIIFLVALSEYDQILFESENENRMEESKALFKTII 255
T+ DVGGQ R W H +EN +IF+V +S + R+EE+K ++
Sbjct: 44 KFTVWDVGGQDKIRPLWKHYYENTDGLIFVV----------DSSDRERIEEAKNELHKLL 93
Score = 29.1 bits (66), Expect = 2.6
Identities = 13/51 (25%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 392 TTGIIEYPFDLDGIN--RMEESKALFKTIITYPWFQHSSVILFLNKKDLLE 440
T G+I F +D + R+EE+K ++ + + +++ NK+DL
Sbjct: 67 TDGLI---FVVDSSDRERIEEAKNELHKLLNEEELKGAPLLILANKQDLPG 114
>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 = 40.1 bits (94), Expect = 7e-04
Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 10/58 (17%)
Query: 198 TMVDVGGQRSERRKWIHCFENVTSIIFLVALSEYDQILFESENENRMEESKALFKTII 255
T+ DVGGQ R W EN ++++V +S +E R++ES+ K I+
Sbjct: 47 TVWDVGGQEKMRTVWKCYLENTDGLVYVV----------DSSDEARLDESQKELKHIL 94
Score = 28.2 bits (63), Expect = 5.7
Identities = 14/41 (34%), Positives = 18/41 (43%), Gaps = 1/41 (2%)
Query: 158 VPTTGIIEYPFDLEE-IRFRMVDVGGQRSERRKWIHCFENV 197
+PT G LE+ + + DVGGQ R W EN
Sbjct: 28 IPTVGFNVEMLQLEKHLSLTVWDVGGQEKMRTVWKCYLENT 68
>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 = 36.6 bits (85), Expect = 0.009
Identities = 24/87 (27%), Positives = 39/87 (44%), Gaps = 22/87 (25%)
Query: 158 VPTTGIIEYPFDLEEIRFRMVDVGGQRSERRKWIHCFENVTMVDVGGQRSERRKWIHCFE 217
+PT G F++E + ++ + F T+ DVGGQ R W H F+
Sbjct: 29 IPTIG-----FNVETVEYKNI--------------SF---TVWDVGGQDKIRPLWRHYFQ 66
Query: 218 NVTSIIFLVALSEYDQILFESENENRM 244
N +IF+V ++ ++I E RM
Sbjct: 67 NTQGLIFVVDSNDRERIGEAREELQRM 93
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 36.9 bits (85), Expect = 0.010
Identities = 18/53 (33%), Positives = 32/53 (60%), Gaps = 2/53 (3%)
Query: 194 FENV--TMVDVGGQRSERRKWIHCFENVTSIIFLVALSEYDQILFESENENRM 244
++N+ T+ DVGGQ R W H F+N +IF+V ++ D+++ + +RM
Sbjct: 58 YKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRDRVVEARDELHRM 110
Score = 30.7 bits (69), Expect = 1.0
Identities = 15/39 (38%), Positives = 20/39 (51%)
Query: 158 VPTTGIIEYPFDLEEIRFRMVDVGGQRSERRKWIHCFEN 196
+PT G + + I F + DVGGQ R W H F+N
Sbjct: 46 IPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQN 84
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 36.0 bits (83), Expect = 0.018
Identities = 18/47 (38%), Positives = 26/47 (55%)
Query: 198 TMVDVGGQRSERRKWIHCFENVTSIIFLVALSEYDQILFESENENRM 244
TM DVGGQ R W H ++N +IF+V ++ ++I E RM
Sbjct: 64 TMWDVGGQDKLRPLWRHYYQNTNGLIFVVDSNDRERIGDAREELERM 110
Score = 31.0 bits (70), Expect = 0.79
Identities = 14/39 (35%), Positives = 21/39 (53%)
Query: 158 VPTTGIIEYPFDLEEIRFRMVDVGGQRSERRKWIHCFEN 196
+PT G + + ++F M DVGGQ R W H ++N
Sbjct: 46 IPTIGFNVETVEYKNLKFTMWDVGGQDKLRPLWRHYYQN 84
>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 = 35.5 bits (82), Expect = 0.020
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 10/55 (18%)
Query: 201 DVGGQRSERRKWIHCFENVTSIIFLVALSEYDQILFESENENRMEESKALFKTII 255
DVGGQ R W H + +IF+V +S + +R++E++ II
Sbjct: 59 DVGGQDKIRPLWRHYYTGTQGLIFVV----------DSADRDRIDEARQELHRII 103
>gnl|CDD|206675 cd01888, eIF2_gamma, Gamma subunit of initiation factor 2 (eIF2
gamma). eIF2 is a heterotrimeric translation
initiation factor that consists of alpha, beta, and
gamma subunits. The GTP-bound gamma subunit also binds
initiator methionyl-tRNA and delivers it to the 40S
ribosomal subunit. Following hydrolysis of GTP to GDP,
eIF2:GDP is released from the ribosome. The gamma
subunit has no intrinsic GTPase activity, but is
stimulated by the GTPase activating protein (GAP) eIF5,
and GDP/GTP exchange is stimulated by the guanine
nucleotide exchange factor (GEF) eIF2B. eIF2B is a
heteropentamer, and the epsilon chain binds eIF2. Both
eIF5 and eIF2B-epsilon are known to bind strongly to
eIF2-beta, but have also been shown to bind directly to
eIF2-gamma. It is possible that eIF2-beta serves simply
as a high-affinity docking site for eIF5 and
eIF2B-epsilon, or that eIF2-beta serves a regulatory
role. eIF2-gamma is found only in eukaryotes and
archaea. It is closely related to SelB, the
selenocysteine-specific elongation factor from
eubacteria. The translational factor components of the
ternary complex, IF2 in eubacteria and eIF2 in
eukaryotes are not the same protein (despite their
unfortunately similar names). Both factors are GTPases;
however, eubacterial IF-2 is a single polypeptide,
while eIF2 is heterotrimeric. eIF2-gamma is a member of
the same family as eubacterial IF2, but the two
proteins are only distantly related. This family
includes translation initiation, elongation, and
release factors.
Length = 197
Score = 35.3 bits (82), Expect = 0.036
Identities = 18/70 (25%), Positives = 29/70 (41%), Gaps = 2/70 (2%)
Query: 25 GKSTFIKQMRIIHGSGYSDEDKRGF-IKLVYQNI-FMAMQSMIRAMDLLKIQYADPTCEE 82
GK+T +K + + + +E KR IKL Y N + + P C
Sbjct: 12 GKTTLVKALSGVWTVRHKEELKRNITIKLGYANAKIYKCPNCGCPRPYDTPECECPGCGG 71
Query: 83 KAELIRSVDF 92
+ +L+R V F
Sbjct: 72 ETKLVRHVSF 81
>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 = 34.3 bits (79), Expect = 0.060
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 201 DVGGQRSERRKWIHCFENVTSIIFLVALSEYDQILFESENEN 242
D+GGQR R W + FEN +I+++ + D+ FE +
Sbjct: 65 DIGGQRKIRPYWRNYFENTDVLIYVIDSA--DRKRFEEAGQE 104
Score = 32.4 bits (74), Expect = 0.30
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 171 EEIRFRMVDVGGQRSERRKWIHCFEN 196
+ + + D+GGQR R W + FEN
Sbjct: 57 DGFKLNVWDIGGQRKIRPYWRNYFEN 82
Score = 28.9 bits (65), Expect = 4.1
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 266 DVGGQRSERRKWIHCFEN 283
D+GGQR R W + FEN
Sbjct: 65 DIGGQRKIRPYWRNYFEN 82
>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 = 33.9 bits (78), Expect = 0.075
Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 10/58 (17%)
Query: 201 DVGGQRSERRKWIHCFENVTSIIFLVALSEYDQILFESENENRMEESKALFKTIITYP 258
D+GGQ R W + +I+++ +S + R ESK+ F+ +I
Sbjct: 57 DLGGQEELRSLWDKYYAESHGVIYVI----------DSTDRERFNESKSAFEKVINNE 104
>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 = 33.4 bits (76), Expect = 0.14
Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 2/64 (3%)
Query: 194 FENV--TMVDVGGQRSERRKWIHCFENVTSIIFLVALSEYDQILFESENENRMEESKALF 251
++N+ T+ DVGGQ R W H + N +IF+V ++ D+I E +RM L
Sbjct: 54 YKNISFTVWDVGGQDKIRPLWRHYYTNTQGLIFVVDSNDRDRIDEAREELHRMLNEDELR 113
Query: 252 KTII 255
+I
Sbjct: 114 DAVI 117
Score = 29.1 bits (65), Expect = 3.2
Identities = 14/39 (35%), Positives = 18/39 (46%)
Query: 158 VPTTGIIEYPFDLEEIRFRMVDVGGQRSERRKWIHCFEN 196
+PT G + I F + DVGGQ R W H + N
Sbjct: 42 IPTIGFNVETVTYKNISFTVWDVGGQDKIRPLWRHYYTN 80
>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 = 32.8 bits (75), Expect = 0.19
Identities = 17/67 (25%), Positives = 32/67 (47%), Gaps = 10/67 (14%)
Query: 196 NVTMVDVGGQRSERRKWIHCFENVTSIIFLVALSEYDQILFESENENRMEESKALFKTII 255
+ T D+ GQ R W H ++N+ IIF++ +S + RM +K + ++
Sbjct: 46 SFTAFDMSGQGKYRGLWEHYYKNIQGIIFVI----------DSSDRLRMVVAKDELELLL 95
Query: 256 TYPWFQH 262
+P +H
Sbjct: 96 NHPDIKH 102
>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 = 33.0 bits (76), Expect = 0.19
Identities = 16/56 (28%), Positives = 24/56 (42%), Gaps = 10/56 (17%)
Query: 201 DVGGQRSERRKWIHCFENVTSIIFLVALSEYDQILFESENENRMEESKALFKTIIT 256
D+GG RR W F V I+FLV ++ R +ESK +++
Sbjct: 69 DLGGHEQARRVWKDYFPEVDGIVFLVDAADP----------ERFQESKEELDSLLN 114
Score = 28.4 bits (64), Expect = 6.9
Identities = 16/55 (29%), Positives = 21/55 (38%), Gaps = 4/55 (7%)
Query: 152 DILRVRVPTTGIIEYPFDLEEIRFRMVDVGGQRSERRKWIHCFENVT----MVDV 202
D L VPT + ++F D+GG RR W F V +VD
Sbjct: 42 DRLAQHVPTLHPTSEELTIGNVKFTTFDLGGHEQARRVWKDYFPEVDGIVFLVDA 96
>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 = 32.4 bits (74), Expect = 0.25
Identities = 13/63 (20%), Positives = 33/63 (52%), Gaps = 10/63 (15%)
Query: 196 NVTMVDVGGQRSERRKWIHCFENVTSIIFLVALSEYDQILFESENENRMEESKALFKTII 255
V + D+GG + R W++ + ++F+V +S +++R++E K + + ++
Sbjct: 44 EVCIFDLGGGANFRGIWVNYYAEAHGLVFVV----------DSSDDDRVQEVKEILRELL 93
Query: 256 TYP 258
+P
Sbjct: 94 QHP 96
>gnl|CDD|211860 TIGR03680, eif2g_arch, translation initiation factor 2 subunit
gamma. This model represents the archaeal translation
initiation factor 2 subunit gamma and is found in all
known archaea. eIF-2 functions in the early steps of
protein synthesis by forming a ternary complex with GTP
and initiator tRNA.
Length = 406
Score = 32.7 bits (75), Expect = 0.39
Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 1/76 (1%)
Query: 18 FVGTGESGKSTFIKQMRIIHGSGYSDEDKRGF-IKLVYQNIFMAMQSMIRAMDLLKIQYA 76
VG + GK+T K + + +S+E KRG I+L Y + + + +
Sbjct: 9 MVGHVDHGKTTLTKALTGVWTDTHSEELKRGISIRLGYADAEIYKCPECDGPECYTTEPV 68
Query: 77 DPTCEEKAELIRSVDF 92
P C + EL+R V F
Sbjct: 69 CPNCGSETELLRRVSF 84
>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 = 31.5 bits (72), Expect = 0.58
Identities = 16/51 (31%), Positives = 28/51 (54%), Gaps = 10/51 (19%)
Query: 198 TMVDVGGQRSERRKWIHCFENVTSIIFLVALSEYDQILFESENENRMEESK 248
+ DVGGQ+S R W + FE+ ++I++V +S + R+E+ K
Sbjct: 61 NIWDVGGQKSLRSYWRNYFESTDALIWVV----------DSSDRARLEDCK 101
Score = 30.0 bits (68), Expect = 1.6
Identities = 13/38 (34%), Positives = 19/38 (50%)
Query: 159 PTTGIIEYPFDLEEIRFRMVDVGGQRSERRKWIHCFEN 196
PT G + + + DVGGQ+S R W + FE+
Sbjct: 44 PTLGFNIKTLEYNGYKLNIWDVGGQKSLRSYWRNYFES 81
Score = 27.7 bits (62), Expect = 9.6
Identities = 13/32 (40%), Positives = 21/32 (65%), Gaps = 1/32 (3%)
Query: 252 KTIITYPWFQHSMVDVGGQRSERRKWIHCFEN 283
KT+ Y ++ ++ DVGGQ+S R W + FE+
Sbjct: 51 KTLE-YNGYKLNIWDVGGQKSLRSYWRNYFES 81
>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 = 31.2 bits (70), Expect = 0.65
Identities = 14/44 (31%), Positives = 26/44 (59%), Gaps = 1/44 (2%)
Query: 198 TMVDVGGQRSERRKWIHCFENVTSIIFLVALSEYDQILFESENE 241
T+ DVGG+ R W H + N +++F++ S D++ E+ +E
Sbjct: 46 TIWDVGGKHKLRPLWKHYYLNTQAVVFVIDSSHRDRVS-EAHSE 88
Score = 30.0 bits (67), Expect = 1.8
Identities = 15/51 (29%), Positives = 24/51 (47%)
Query: 150 EQDILRVRVPTTGIIEYPFDLEEIRFRMVDVGGQRSERRKWIHCFENVTMV 200
+QD +PT G + + ++F + DVGG+ R W H + N V
Sbjct: 20 KQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAV 70
>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 = 30.4 bits (69), Expect = 1.2
Identities = 12/41 (29%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 196 NVTMV--DVGGQRSERRKWIHCFENVTSIIFLVALSEYDQI 234
NVT+ D+GGQ R W V +I+++V ++ +++
Sbjct: 43 NVTIKVWDLGGQPRFRSMWERYCRGVNAIVYVVDAADREKL 83
>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 = 29.9 bits (67), Expect = 1.9
Identities = 16/48 (33%), Positives = 22/48 (45%), Gaps = 5/48 (10%)
Query: 198 TMVDVGGQRSERRKWIHCFENVTSIIFLVALSEYDQILFESENENRME 245
T D+GG + RR W F V I++LV D E E++ E
Sbjct: 64 TTFDLGGHQQARRLWKDYFPEVNGIVYLV-----DAYDKERFAESKRE 106
>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 = 29.6 bits (67), Expect = 2.0
Identities = 16/42 (38%), Positives = 19/42 (45%)
Query: 159 PTTGIIEYPFDLEEIRFRMVDVGGQRSERRKWIHCFENVTMV 200
PT G + IRF M D+GGQ S R W + N V
Sbjct: 45 PTIGSNVEEIVYKNIRFLMWDIGGQESLRSSWNTYYTNTDAV 86
Score = 28.5 bits (64), Expect = 5.3
Identities = 10/30 (33%), Positives = 16/30 (53%)
Query: 197 VTMVDVGGQRSERRKWIHCFENVTSIIFLV 226
M D+GGQ S R W + N ++I ++
Sbjct: 61 FLMWDIGGQESLRSSWNTYYTNTDAVILVI 90
>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 = 29.3 bits (66), Expect = 2.4
Identities = 12/34 (35%), Positives = 21/34 (61%)
Query: 201 DVGGQRSERRKWIHCFENVTSIIFLVALSEYDQI 234
D+GGQ S R W + N +II++V ++ D++
Sbjct: 49 DLGGQTSIRPYWRCYYSNTDAIIYVVDSTDRDRL 82
>gnl|CDD|227582 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 30.0 bits (68), Expect = 2.6
Identities = 23/79 (29%), Positives = 33/79 (41%), Gaps = 9/79 (11%)
Query: 19 VGTGESGKSTFIKQMRIIHGSGYSDEDKRGF-IKLVYQNI-FMAMQSMIRAMDLLKIQYA 76
VG + GK+T K + + +S+E KRG IKL Y + R
Sbjct: 16 VGHVDHGKTTLTKALSGVWTDRHSEELKRGITIKLGYADAKIYKCPECYRPEC----YTT 71
Query: 77 DPTCEE---KAELIRSVDF 92
+P C + EL+R V F
Sbjct: 72 EPKCPNCGAETELVRRVSF 90
>gnl|CDD|217509 pfam03353, Lin-8, Ras-mediated vulval-induction antagonist. LIN-8
is a nuclear protein, present at the sites of
transcriptional repressor complexes, which interacts
with LIN-35 Rb.Lin35 Rb is a product of the class B
synMuv gene lin-35 which silences genes required for
vulval specification through chromatin modification and
remodelling. The biological role of the interaction has
not yet been determined however predictions have been
made. The interaction shows that class A synMuv genes
control vulval induction through the transcriptional
regulation of gene expression. LIN-8 normally functions
as part of a protein complex however when the complex is
absent, other family members can partially replace LIN-8
activity.
Length = 316
Score = 29.7 bits (67), Expect = 3.5
Identities = 13/42 (30%), Positives = 21/42 (50%)
Query: 82 EKAELIRSVDFETVTTFESPYVEAIKELWADPGIQECYDRRR 123
E+++LIR F+TV + P +++ D QE RR
Sbjct: 274 ERSKLIRKALFKTVLALDDPEYSNAGDVFEDLAAQENVKRRS 315
>gnl|CDD|191270 pfam05411, Peptidase_C32, Equine arteritis virus putative
proteinase. These proteins are characterized by a
region that has been proposed to have peptidase activity
involved in viral polyprotein processing in replication.
Length = 127
Score = 27.5 bits (61), Expect = 8.5
Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 353 GENHLLALHVRHSYLGDLARIEDPGYMPTEQDILRAR 389
G + A V S++ L ++P P D+LR R
Sbjct: 68 GPIIVQAFSVPESWIRHLKLADEPVP-PGFVDLLRFR 103
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.322 0.138 0.415
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: 24,277,748
Number of extensions: 2410510
Number of successful extensions: 2044
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2031
Number of HSP's successfully gapped: 57
Length of query: 463
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 363
Effective length of database: 6,502,202
Effective search space: 2360299326
Effective search space used: 2360299326
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 61 (27.2 bits)