RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8318
(313 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 = 525 bits (1356), Expect = 0.0
Identities = 200/315 (63%), Positives = 238/315 (75%), Gaps = 23/315 (7%)
Query: 11 VKLLLLGAGESGKSTIVKQMKIIHETGYSKEECEQYRPVVYSNSIQSLMAIIRAMGQLKI 70
VKLLLLGAGESGKSTI+KQMKI+H G+S EE ++RPV+YSN +QS+ A++RAM L I
Sbjct: 1 VKLLLLGAGESGKSTILKQMKILHGNGFSDEERREFRPVIYSNILQSMKALLRAMETLNI 60
Query: 71 DFGDHKNADCARQFFTLASAAEEGDLTPDLVILMKRLWSDQGVQHCFHRSREYQLNDSAA 130
+GD +N A++ +LA AEEG L P+L +KRLW D G+Q C+ R EYQLNDSA
Sbjct: 61 PYGDPENEKDAKKILSLAPRAEEGPLPPELAEAIKRLWKDPGIQACYDRRNEYQLNDSAK 120
Query: 131 YYLNALDRISQPNYIPTQQDVLRTRVKTTGIIETHFTFKDLHFKMFDVGGQRSERKKWIH 190
Y+L+ LDRIS P+YIPT+QD+LR+RVKTTGIIET F+ K+L F+MFDVGGQRSERKKWIH
Sbjct: 121 YFLDNLDRISDPDYIPTEQDILRSRVKTTGIIETDFSIKNLKFRMFDVGGQRSERKKWIH 180
Query: 191 CFEGVTAIIFCVALSGYDSVLAEDEEMNRMIESMKLFDSICNSKWFMDTSIILFLNKNDL 250
CFE VTAIIF VALS YD VL EDE +NRM ES+KLFDSICNS+WF +TSIILFLNK DL
Sbjct: 181 CFEDVTAIIFVVALSEYDQVLVEDESVNRMQESLKLFDSICNSRWFANTSIILFLNKKDL 240
Query: 251 FQEKITKSPLTVCFPEYT-----------------------DQKEIYTHFTCATDTSNIQ 287
F+EKI KSPLT FP+YT KEIY HFTCATDT NI+
Sbjct: 241 FEEKIKKSPLTDYFPDYTGPPNDYEEAAKYIKKKFLDLNRNPNKEIYPHFTCATDTENIR 300
Query: 288 FVFDAVTDVIIKANL 302
FVFDAV D+I++ NL
Sbjct: 301 FVFDAVKDIILQNNL 315
>gnl|CDD|214595 smart00275, G_alpha, G protein alpha subunit. Subunit of G
proteins that contains the guanine nucleotide binding
site.
Length = 342
Score = 476 bits (1227), Expect = e-170
Identities = 180/326 (55%), Positives = 227/326 (69%), Gaps = 27/326 (8%)
Query: 7 QEREVKLLLLGAGESGKSTIVKQMKIIHETGYSKEECEQYRPVVYSNSIQSLMAIIRAMG 66
++REVKLLLLGAGESGKSTI+KQM+I+H G+S+EE +YRP++YSN ++S+ A++ AM
Sbjct: 18 KKREVKLLLLGAGESGKSTILKQMRILHGDGFSQEERREYRPLIYSNILESMKALVDAME 77
Query: 67 QLKIDFGD---HKNADCARQFFTLASAAEEGDLTPDLVILMKRLWSDQGVQHCFHRSREY 123
+L I F D + + F E L ++ +K LW D+G+Q C+ R E+
Sbjct: 78 ELNIPFEDPESILDIRIITEQFNKTDETENV-LPKEIAKAIKALWKDEGIQECYRRRNEF 136
Query: 124 QLNDSAAYYLNALDRISQPNYIPTQQDVLRTRVKTTGIIETHFTFKDLHFKMFDVGGQRS 183
QLNDSA+Y+L+ +DRI P+Y+PT+QD+LR+RV TTGI ET F K L F+MFDVGGQRS
Sbjct: 137 QLNDSASYFLDNIDRIGDPDYVPTEQDILRSRVPTTGIQETAFIVKKLFFRMFDVGGQRS 196
Query: 184 ERKKWIHCFEGVTAIIFCVALSGYDSVLAEDEEMNRMIESMKLFDSICNSKWFMDTSIIL 243
ERKKWIHCF+ VTAIIFCVALS YD VL EDE NRM ES+ LF+SICNS+WF +TSIIL
Sbjct: 197 ERKKWIHCFDNVTAIIFCVALSEYDQVLEEDESTNRMQESLNLFESICNSRWFANTSIIL 256
Query: 244 FLNKNDLFQEKITKSPLTVCFPEYT-----------------------DQKEIYTHFTCA 280
FLNK DLF+EKI K PL FP+Y +K IY HFTCA
Sbjct: 257 FLNKIDLFEEKIKKVPLVDYFPDYKGPNDYEAAAKFIKQKFLRLNRNSSRKSIYHHFTCA 316
Query: 281 TDTSNIQFVFDAVTDVIIKANLKDCG 306
TDT NI+ VFDAV D+I++ NLKD G
Sbjct: 317 TDTRNIRVVFDAVKDIILQRNLKDAG 342
>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 = 442 bits (1139), Expect = e-157
Identities = 176/329 (53%), Positives = 231/329 (70%), Gaps = 29/329 (8%)
Query: 9 REVKLLLLGAGESGKSTIVKQMKIIHETGYSKEECEQYRPVVYSNSIQSLMAIIRAMGQL 68
RE+KLLLLGAGESGKSTI+KQMKI+H G+S EE EQYR V+YSN I+SL ++ A+ L
Sbjct: 1 REIKLLLLGAGESGKSTILKQMKILHGGGFSDEEREQYRAVIYSNIIRSLKTLLEALENL 60
Query: 69 KIDFGDHK--NADCARQFFTLAS---AAEEGDLTPDLVILMKRLWSDQGVQHCFHRSREY 123
+I+ + K N + A++ ++ +E + +L +K LW+D G+Q ++RS E+
Sbjct: 61 EIESSNSKPENEEIAKKLKSILDSLLDVDETRFSEELAEDIKELWNDPGIQEVYNRSNEF 120
Query: 124 QLNDSAAYYLNALDRISQPNYIPTQQDVLRTRVKTTGIIETHFTFKDLHFKMFDVGGQRS 183
QL+DSA Y+L+ LDRI+ P+Y+PT QD+LR RVKTTGIIET F FK L F++FDVGGQRS
Sbjct: 121 QLSDSAKYFLDNLDRIASPDYVPTDQDILRARVKTTGIIETKFDFKGLKFRLFDVGGQRS 180
Query: 184 ERKKWIHCFEGVTAIIFCVALSGYDSVLAEDEEMNRMIESMKLFDSICNSKWFMDTSIIL 243
ERKKWIHCFE VTAIIF V+LS YD VL ED+ NR+ ES+ LF+ ICNS WF +T IIL
Sbjct: 181 ERKKWIHCFEDVTAIIFVVSLSEYDQVLYEDDSTNRLEESLNLFEEICNSPWFKNTPIIL 240
Query: 244 FLNKNDLFQEKITKSPLTVCFPEYT------------------------DQKEIYTHFTC 279
FLNK DLF+EK+ K PL+ FPEY +++IYTHFT
Sbjct: 241 FLNKKDLFEEKLKKGPLSDYFPEYEGDPNDYESASKYIRNKFLELNKNNSERKIYTHFTN 300
Query: 280 ATDTSNIQFVFDAVTDVIIKANLKDCGIR 308
ATDT N++FVF+AV D+I++ NLK+ G+
Sbjct: 301 ATDTENVRFVFEAVKDIILQNNLKESGLL 329
>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 = 61.4 bits (150), Expect = 1e-11
Identities = 26/89 (29%), Positives = 41/89 (46%), Gaps = 11/89 (12%)
Query: 162 IETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSGYDSVLAEDEEMNRMI 221
+ET +K++ F ++DVGGQ R W H +E +IF V DS E R+
Sbjct: 35 VET-VEYKNVKFTVWDVGGQDKIRPLWKHYYENTDGLIFVV-----DSSDRE-----RIE 83
Query: 222 ESMKLFDSICNSKWFMDTSIILFLNKNDL 250
E+ + N + +++ NK DL
Sbjct: 84 EAKNELHKLLNEEELKGAPLLILANKQDL 112
Score = 27.9 bits (63), Expect = 3.9
Identities = 8/20 (40%), Positives = 16/20 (80%)
Query: 12 KLLLLGAGESGKSTIVKQMK 31
++L+LG +GK+TI+ ++K
Sbjct: 1 RILMLGLDGAGKTTILYKLK 20
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 57.2 bits (139), Expect = 5e-10
Identities = 28/89 (31%), Positives = 46/89 (51%), Gaps = 11/89 (12%)
Query: 162 IETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSGYDSVLAEDEEMNRMI 221
+ET T+K++ F ++DVGGQ S R W + F A+IF V DS + R+
Sbjct: 50 VET-VTYKNVKFTVWDVGGQESLRPLWRNYFPNTDAVIFVV-----DSADRD-----RIE 98
Query: 222 ESMKLFDSICNSKWFMDTSIILFLNKNDL 250
E+ + ++ N + D +++ NK DL
Sbjct: 99 EAKEELHALLNEEELADAPLLILANKQDL 127
Score = 29.9 bits (68), Expect = 1.0
Identities = 9/24 (37%), Positives = 19/24 (79%)
Query: 8 EREVKLLLLGAGESGKSTIVKQMK 31
+E+++L+LG +GK+TI+ ++K
Sbjct: 12 NKEMRILILGLDNAGKTTILYKLK 35
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 55.0 bits (132), Expect = 4e-09
Identities = 39/136 (28%), Positives = 61/136 (44%), Gaps = 26/136 (19%)
Query: 154 TRVKTTGIIETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSGYDSVLAE 213
T + T G +K++ F ++DVGGQ R W H F+ +IF V + D V+
Sbjct: 44 TTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRDRVVEA 103
Query: 214 DEEMNRMIESMKLFDSICNSKWFMDTSIILFLNKNDLFQEKITKSPLTVCFPEYTD---- 269
+E++RM+ +L D++ +++F NK DL P + E TD
Sbjct: 104 RDELHRMLNEDELRDAV----------LLVFANKQDL--------PNAMNAAEITDKLGL 145
Query: 270 ----QKEIYTHFTCAT 281
Q+ Y TCAT
Sbjct: 146 HSLRQRHWYIQSTCAT 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 = 54.4 bits (131), Expect = 4e-09
Identities = 32/98 (32%), Positives = 50/98 (51%), Gaps = 12/98 (12%)
Query: 154 TRVKTTGI-IETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSGYDSVLA 212
T + T G +ET T+K++ F ++DVGGQ R W H + G +IF V DS
Sbjct: 36 TTIPTVGFNVET-VTYKNVKFNVWDVGGQDKIRPLWRHYYTGTQGLIFVV-----DS--- 86
Query: 213 EDEEMNRMIESMKLFDSICNSKWFMDTSIILFLNKNDL 250
+ +R+ E+ + I N + D +++F NK DL
Sbjct: 87 --ADRDRIDEARQELHRIINDREMRDALLLVFANKQDL 122
Score = 27.4 bits (61), Expect = 7.4
Identities = 9/24 (37%), Positives = 20/24 (83%)
Query: 9 REVKLLLLGAGESGKSTIVKQMKI 32
+E+++L+LG +GK+TI+ ++K+
Sbjct: 8 KEMRILMLGLDAAGKTTILYKLKL 31
>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 = 53.2 bits (128), Expect = 9e-09
Identities = 39/137 (28%), Positives = 61/137 (44%), Gaps = 28/137 (20%)
Query: 154 TRVKTTGI-IETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSGYDSVLA 212
T + T G +ET +K++ F ++DVGGQ R W H F+ +IF V + + +
Sbjct: 27 TTIPTIGFNVET-VEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERIGE 85
Query: 213 EDEEMNRMIESMKLFDSICNSKWFMDTSIILFLNKNDLFQEKITKSPLTVCFPEYTD--- 269
EE+ RM+ +L D++ +++F NK DL P + E TD
Sbjct: 86 AREELQRMLNEDELRDAV----------LLVFANKQDL--------PNAMSAAEVTDKLG 127
Query: 270 -----QKEIYTHFTCAT 281
+ Y TCAT
Sbjct: 128 LHSLRNRNWYIQATCAT 144
>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 = 53.4 bits (128), Expect = 1e-08
Identities = 30/97 (30%), Positives = 48/97 (49%), Gaps = 10/97 (10%)
Query: 154 TRVKTTGIIETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSGYDSVLAE 213
T + T G T+K++ F ++DVGGQ R W H + +IF V + D +
Sbjct: 40 TTIPTIGFNVETVTYKNISFTVWDVGGQDKIRPLWRHYYTNTQGLIFVVDSNDRDRIDEA 99
Query: 214 DEEMNRMIESMKLFDSICNSKWFMDTSIILFLNKNDL 250
EE++RM+ +L D++ I++F NK DL
Sbjct: 100 REELHRMLNEDELRDAV----------ILVFANKQDL 126
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 50.6 bits (121), Expect = 1e-07
Identities = 39/137 (28%), Positives = 61/137 (44%), Gaps = 28/137 (20%)
Query: 154 TRVKTTGI-IETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSGYDSVLA 212
T + T G +ET +K+L F M+DVGGQ R W H ++ +IF V + + +
Sbjct: 44 TTIPTIGFNVET-VEYKNLKFTMWDVGGQDKLRPLWRHYYQNTNGLIFVVDSNDRERIGD 102
Query: 213 EDEEMNRMIESMKLFDSICNSKWFMDTSIILFLNKNDLFQEKITKSPLTVCFPEYTD--- 269
EE+ RM+ +L D++ +++F NK DL P + E T+
Sbjct: 103 AREELERMLSEDELRDAV----------LLVFANKQDL--------PNAMSTTEVTEKLG 144
Query: 270 -----QKEIYTHFTCAT 281
Q+ Y CAT
Sbjct: 145 LHSVRQRNWYIQGCCAT 161
>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 = 47.0 bits (112), Expect = 1e-06
Identities = 30/98 (30%), Positives = 52/98 (53%), Gaps = 12/98 (12%)
Query: 154 TRVKTTGI-IETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSGYDSVLA 212
T + T G +ET T+K+L F+++D+GGQ S R W + AII+ V + D +
Sbjct: 26 TTIPTIGFNVET-VTYKNLKFQVWDLGGQTSIRPYWRCYYSNTDAIIYVVDSTDRDRLGI 84
Query: 213 EDEEMNRMIESMKLFDSICNSKWFMDTSIILFLNKNDL 250
E++ M+E +L D++ +++F NK D+
Sbjct: 85 SKSELHAMLEEEELKDAV----------LLVFANKQDM 112
>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 = 45.8 bits (108), Expect = 4e-06
Identities = 26/103 (25%), Positives = 48/103 (46%), Gaps = 10/103 (9%)
Query: 148 QQDVLRTRVKTTGIIETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSGY 207
+QD + T G +K+L F ++DVGG+ R W H + A++F + S
Sbjct: 20 KQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVIDSSHR 79
Query: 208 DSVLAEDEEMNRMIESMKLFDSICNSKWFMDTSIILFLNKNDL 250
D V E+ +++ +L D++ +++F NK D+
Sbjct: 80 DRVSEAHSELAKLLTEKELRDAL----------LLIFANKQDV 112
>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 = 44.6 bits (106), Expect = 9e-06
Identities = 21/77 (27%), Positives = 37/77 (48%), Gaps = 10/77 (12%)
Query: 174 KMFDVGGQRSERKKWIHCFEGVTAIIFCVALSGYDSVLAEDEEMNRMIESMKLFDSICNS 233
K++D+GGQ R W GV AI++ V + + + E++ ++E L + I
Sbjct: 47 KVWDLGGQPRFRSMWERYCRGVNAIVYVVDAADREKLEVAKNELHDLLEKPSL-EGI--- 102
Query: 234 KWFMDTSIILFLNKNDL 250
+++ NKNDL
Sbjct: 103 ------PLLVLGNKNDL 113
>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 = 42.4 bits (100), Expect = 5e-05
Identities = 25/82 (30%), Positives = 35/82 (42%), Gaps = 10/82 (12%)
Query: 169 KDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSGYDSVLAEDEEMNRMIESMKLFD 228
K L ++DVGGQ R W E +++ V DS DE R+ ES K
Sbjct: 42 KHLSLTVWDVGGQEKMRTVWKCYLENTDGLVYVV-----DS---SDEA--RLDESQKELK 91
Query: 229 SICNSKWFMDTSIILFLNKNDL 250
I ++ ++L NK DL
Sbjct: 92 HILKNEHIKGVPVVLLANKQDL 113
>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 = 42.3 bits (100), Expect = 8e-05
Identities = 20/85 (23%), Positives = 39/85 (45%), Gaps = 10/85 (11%)
Query: 166 FTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSGYDSVLAEDEEMNRMIESMK 225
+K++ F M+D+GGQ S R W + A+I + + + + EE+ +M+
Sbjct: 54 IVYKNIRFLMWDIGGQESLRSSWNTYYTNTDAVILVIDSTDRERLPLTKEELYKMLAHED 113
Query: 226 LFDSICNSKWFMDTSIILFLNKNDL 250
L ++ +++ NK DL
Sbjct: 114 LRKAV----------LLVLANKQDL 128
>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 = 40.8 bits (96), Expect = 2e-04
Identities = 23/89 (25%), Positives = 41/89 (46%), Gaps = 11/89 (12%)
Query: 162 IETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSGYDSVLAEDEEMNRMI 221
I+T + ++DVGGQ+S R W + FE A+I+ V DS + R+
Sbjct: 50 IKT-LEYNGYKLNIWDVGGQKSLRSYWRNYFESTDALIWVV-----DSS-----DRARLE 98
Query: 222 ESMKLFDSICNSKWFMDTSIILFLNKNDL 250
+ + + + ++++F NK DL
Sbjct: 99 DCKRELQKLLVEERLAGATLLIFANKQDL 127
Score = 31.9 bits (73), Expect = 0.21
Identities = 11/22 (50%), Positives = 19/22 (86%)
Query: 7 QEREVKLLLLGAGESGKSTIVK 28
+ERE+++L+LG +GK+TI+K
Sbjct: 11 KEREMRILMLGLDNAGKTTILK 32
>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 = 38.1 bits (89), Expect = 0.002
Identities = 22/80 (27%), Positives = 35/80 (43%), Gaps = 12/80 (15%)
Query: 171 LHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSGYDSVLAEDEEMNRMIESMKLFDSI 230
L F +D+GGQ R W + +I+ + DS D E R ES F+ +
Sbjct: 53 LMF--WDLGGQEELRSLWDKYYAESHGVIYVI-----DST---DRE--RFNESKSAFEKV 100
Query: 231 CNSKWFMDTSIILFLNKNDL 250
N++ +++ NK DL
Sbjct: 101 INNEALEGVPLLVLANKQDL 120
>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 = 37.8 bits (88), Expect = 0.002
Identities = 22/145 (15%), Positives = 38/145 (26%), Gaps = 22/145 (15%)
Query: 154 TRVKTTGIIETHFTFKDLHFKMFDVGGQRSERKKWI-----HCFEGVTAIIFCVALSGYD 208
TR + E L D G G I+ V + +
Sbjct: 32 TRDPDVYVKELDKGKVKLVL--VDTPGLDEFGGLGREELARLLLRGADLILLVVDSTDRE 89
Query: 209 SVLAEDEEMNRMIESMKLFDSICNSKWFMDTSIILFLNKNDLFQEKITKSPLTVCFPEYT 268
S + R + + IIL NK DL +E+ + L +
Sbjct: 90 SEEDAKLLILRRLRKEGI-------------PIILVGNKIDLLEEREVEELLRLEELAK- 135
Query: 269 DQKEIYTHFTCATDTSNIQFVFDAV 293
+ A + +F+ +
Sbjct: 136 -ILGVPVFEVSAKTGEGVDELFEKL 159
>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 = 37.3 bits (87), Expect = 0.004
Identities = 31/114 (27%), Positives = 47/114 (41%), Gaps = 23/114 (20%)
Query: 137 DRISQPNYIPTQQDVLRTRVKTTGIIETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVT 196
DR++Q ++PT T ++ F FD+GG R+ W F V
Sbjct: 42 DRLAQ--HVPTLHPT-----------SEELTIGNVKFTTFDLGGHEQARRVWKDYFPEVD 88
Query: 197 AIIFCVALSGYDSVLAEDEEMNRMIESMKLFDSICNSKWFMDTSIILFLNKNDL 250
I+F V D+ D E R ES + DS+ N + + I++ NK D
Sbjct: 89 GIVFLV-----DAA---DPE--RFQESKEELDSLLNDEELANVPILILGNKIDK 132
>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 = 37.0 bits (86), Expect = 0.005
Identities = 19/81 (23%), Positives = 34/81 (41%), Gaps = 10/81 (12%)
Query: 170 DLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSGYDSVLAEDEEMNRMIESMKLFDS 229
++D+GGQR R W + FE +I+ + DS + R E+ +
Sbjct: 58 GFKLNVWDIGGQRKIRPYWRNYFENTDVLIYVI-----DS-----ADRKRFEEAGQELVE 107
Query: 230 ICNSKWFMDTSIILFLNKNDL 250
+ + +++F NK DL
Sbjct: 108 LLEEEKLAGVPVLVFANKQDL 128
Score = 31.2 bits (71), Expect = 0.38
Identities = 12/24 (50%), Positives = 19/24 (79%)
Query: 7 QEREVKLLLLGAGESGKSTIVKQM 30
+EV++LLLG +GK+TI+KQ+
Sbjct: 12 SRQEVRILLLGLDNAGKTTILKQL 35
>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 = 36.3 bits (84), Expect = 0.006
Identities = 29/101 (28%), Positives = 42/101 (41%), Gaps = 20/101 (19%)
Query: 156 VKTTGIIETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSGYDS------ 209
V T G F +L F FD+ GQ R W H ++ + IIF + DS
Sbjct: 30 VPTVGFNVESFKKGNLSFTAFDMSGQGKYRGLWEHYYKNIQGIIFVI-----DSSDRLRM 84
Query: 210 VLAEDEEMNRMIESMKLFDSICNSKWFMDTSIILFLNKNDL 250
V+A+DE +E + I + I+ + NK DL
Sbjct: 85 VVAKDE-----LELLLNHPDIKHR----RIPILFYANKMDL 116
>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 = 34.7 bits (80), Expect = 0.026
Identities = 15/87 (17%), Positives = 25/87 (28%), Gaps = 19/87 (21%)
Query: 173 FKMFDVGGQRSERKKWIHCFEGVTAIIFCVAL-----SGYDSVLAEDEEMNRMIESMKLF 227
F + D GQ + V + + + + + + +E+ E
Sbjct: 53 FNLLDTAGQEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAE----- 107
Query: 228 DSICNSKWFMDTSIILFLNKNDLFQEK 254
IIL NK DL K
Sbjct: 108 ---------SGVPIILVGNKIDLRDAK 125
>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 = 34.5 bits (79), Expect = 0.033
Identities = 28/115 (24%), Positives = 47/115 (40%), Gaps = 27/115 (23%)
Query: 137 DRIS--QPNYIPTQQDVLRTRVKTTGIIETHFTFKDLHFKMFDVGGQRSERKKWIHCFEG 194
DR++ QP PT +++ +K F FD+GG + R+ W F
Sbjct: 40 DRLAQHQPTQHPTSEELAIGNIK---------------FTTFDLGGHQQARRLWKDYFPE 84
Query: 195 VTAIIFCVALSGYDSVLAEDEEMNRMIESMKLFDSICNSKWFMDTSIILFLNKND 249
V I++ V A D+E R ES + D++ + + ++ NK D
Sbjct: 85 VNGIVYLVD--------AYDKE--RFAESKRELDALLSDEELATVPFLILGNKID 129
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 34.6 bits (79), Expect = 0.043
Identities = 22/111 (19%), Positives = 37/111 (33%), Gaps = 14/111 (12%)
Query: 147 TQQDVLRTRVKTTGIIETHFTFKDLH----FKMFDVGGQRSERKKWIHCFEGVTAIIFCV 202
+ T G ++ T + +++D GQ R + G I+
Sbjct: 26 VGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQEEYRSLRPEYYRGANGILIVY 85
Query: 203 ALSGYDSVLAEDEEMNRMIESMKLFDSICNSKWFMDTSIILFLNKNDLFQE 253
+ +S DE +E ++ D I+L NK DLF E
Sbjct: 86 DSTLRESS---DELTEEWLEELRELAPD-------DVPILLVGNKIDLFDE 126
Score = 29.5 bits (66), Expect = 2.0
Identities = 8/24 (33%), Positives = 17/24 (70%)
Query: 8 EREVKLLLLGAGESGKSTIVKQMK 31
+E K+++LG G GK+T++ ++
Sbjct: 3 MKEFKIVVLGDGGVGKTTLLNRLV 26
>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 = 31.6 bits (72), Expect = 0.27
Identities = 25/95 (26%), Positives = 39/95 (41%), Gaps = 12/95 (12%)
Query: 156 VKTTGIIETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSGYDSVLAEDE 215
V TTG +D ++ ++GG ++ RK W G +IF V DS +E
Sbjct: 29 VPTTGFNSVAIPTQDAIMELLEIGGSQNLRKYWKRYLSGSQGLIFVV-----DSADSERL 83
Query: 216 EMNRMIESMKLFDSICNSKWFMDTSIILFLNKNDL 250
+ R E +L D +++ NK DL
Sbjct: 84 PLARQ-ELHQLLQHPP------DLPLVVLANKQDL 111
>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 = 31.7 bits (72), Expect = 0.28
Identities = 33/141 (23%), Positives = 52/141 (36%), Gaps = 29/141 (20%)
Query: 169 KDLHFKMFDVGGQRSERKKW---IHCFEGVTAIIFCVALSGYDSVLAEDEEMNRMIESMK 225
K + F +DVGGQ R W C +G I+F V DSV ++ RM E+
Sbjct: 50 KGVTFHFWDVGGQEKLRPLWKSYTRCTDG---IVFVV-----DSV-----DVERMEEAKT 96
Query: 226 LFDSICNSKWFMDTSIILFLNKNDLFQEKITKSPLTV-------CFPEYTDQKEIYTHFT 278
I +++ NK DL + L V E + +
Sbjct: 97 ELHKITKFSENQGVPVLVLANKQDL------PNALPVSEVEKLLALHELSSSTPWHVQPA 150
Query: 279 CATDTSNIQFVFDAVTDVIIK 299
CA +Q + + ++I+K
Sbjct: 151 CAIIGEGLQEGLEKLYEMILK 171
>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 = 30.0 bits (68), Expect = 0.89
Identities = 10/22 (45%), Positives = 16/22 (72%)
Query: 10 EVKLLLLGAGESGKSTIVKQMK 31
E KL+L+G G GK+++ KQ+
Sbjct: 1 EAKLMLVGQGGVGKTSLCKQLI 22
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 30.6 bits (70), Expect = 1.0
Identities = 31/160 (19%), Positives = 55/160 (34%), Gaps = 38/160 (23%)
Query: 162 IETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGV---------TAI----IFCVALSGYD 208
I+ F + + D G R RK I E V AI + + + +
Sbjct: 217 IDIEFERDGRKYVLIDTAGIR--RKGKIT--ESVEKYSVARTLKAIERADVVLLVIDATE 272
Query: 209 SVLAEDEEMNRMIESMKLFDSICNSKWFMDTSIILFLNKNDLFQE-----KITKSPLTVC 263
+ +D + +IE I++ +NK DL +E + K L
Sbjct: 273 GISEQDLRIAGLIEEAGR-------------GIVIVVNKWDLVEEDEATMEEFKKKLRRK 319
Query: 264 FPEYTDQKEIYTHFTCATDTSNIQFVFDAVTDVIIKANLK 303
P + D I F A + +F+A+ ++ A +
Sbjct: 320 LP-FLDFAPI--VFISALTGQGLDKLFEAIKEIYECATRR 356
>gnl|CDD|177808 PLN00415, PLN00415, 3-ketoacyl-CoA synthase.
Length = 466
Score = 30.4 bits (68), Expect = 1.3
Identities = 40/157 (25%), Positives = 63/157 (40%), Gaps = 29/157 (18%)
Query: 123 YQLNDSAAYYLNALDRISQPNYIPTQ--QDVLRTRVKTTGIIETHFTFKDLHFKMFDVGG 180
Y+ ND + N L R+ + + QD +R++ + T I+ TH D H+ +
Sbjct: 231 YRGNDRSMLVPNCLFRVGGAAVMLSNRSQDRVRSKYELTHIVRTHKGSSDKHYTCAE--- 287
Query: 181 QRSERKKWIHCFEGVTAIIFCVALSGYDSVLAEDEEMNRMIESMKLFDSICNSKWFMDTS 240
Q+ + K I VALS +V+A D + L + F
Sbjct: 288 QKEDSKG-----------IVGVALSKELTVVAGDTLKTNLTALGPLVLPLSEKLRF---- 332
Query: 241 IILFLNKNDLFQEKITKSPLTVCFPEYTDQKEIYTHF 277
ILFL K+ LF+ K++ P D K + HF
Sbjct: 333 -ILFLVKSKLFRLKVS--------PYVPDFKLCFKHF 360
>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 = 29.3 bits (66), Expect = 1.6
Identities = 20/93 (21%), Positives = 37/93 (39%), Gaps = 10/93 (10%)
Query: 158 TTGIIETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSGYDSVLAEDEEM 217
T G T +FD+GG + R W++ + ++F V DS ++D+
Sbjct: 30 TVGFTPTKLRLDKYEVCIFDLGGGANFRGIWVNYYAEAHGLVFVV-----DS--SDDD-- 80
Query: 218 NRMIESMKLFDSICNSKWFMDTSIILFLNKNDL 250
R+ E ++ + I++ NK D
Sbjct: 81 -RVQEVKEILRELLQHPRVSGKPILVLANKQDK 112
>gnl|CDD|233120 TIGR00764, lon_rel, lon-related putative ATP-dependent protease.
This model represents a set of proteins with extensive
C-terminal homology to the ATP-dependent protease La,
product of the lon gene of E. coli. The model is based
on a seed alignment containing only archaeal members,
but several bacterial proteins match the model well.
Because several species, including Thermotoga maritima
and Treponema pallidum, contain both a close homolog of
the lon protease and nearly full-length homolog of the
members of this family, we suggest there may also be a
functional division between the two families. Members of
this family from Pyrococcus horikoshii and Pyrococcus
abyssi each contain a predicted intein [Protein fate,
Degradation of proteins, peptides, and glycopeptides].
Length = 608
Score = 29.8 bits (67), Expect = 1.9
Identities = 22/75 (29%), Positives = 31/75 (41%), Gaps = 10/75 (13%)
Query: 7 QEREVKLLLLGAGESGKSTIVKQMKIIHETGYSKEECEQYRPVVYSNSIQSLMAIIRAM- 65
Q+R V LL+G GKS + K M + EE E +VY N M I +
Sbjct: 36 QKRNV--LLIGEPGVGKSMLAKAMAEL----LPDEELEDI--LVYPNPEDPNMPRIVEVP 87
Query: 66 -GQLKIDFGDHKNAD 79
G+ + D+K
Sbjct: 88 AGEGREIVEDYKKKA 102
>gnl|CDD|188619 cd09899, H3TH_T4-like, H3TH domain of bacteriophage T3, T4 RNase H,
T5-5' nucleases, and homologs. H3TH
(helix-3-turn-helix) domains of bacteriophage
T5-5'nuclease (5'-3' exonuclease or T5FEN),
bacteriophage T4 RNase H (T4FEN), bacteriophage T3 (T3
phage exodeoxyribonuclease) and other similar 5'
nucleases are included in this family. The T5-5'nuclease
is a 5'-3' exodeoxyribonuclease that also exhibits
endonucleolytic activity on flap structures (branched
duplex DNA containing a free single-stranded 5'end). T4
RNase H, which removes the RNA primers that initiate
lagging strand fragments, has 5'- 3' exonuclease
activity on DNA/DNA and RNA/DNA duplexes and has
endonuclease activity on flap or forked DNA structures.
Bacteriophage T3 is believed to function in the removal
of DNA-linked RNA primers and is essential for phage DNA
replication and also necessary for host DNA degradation
and phage genetic recombination. These nucleases are
members of the structure-specific, 5' nuclease family
that catalyzes hydrolysis of DNA duplex-containing
nucleic acid structures during DNA replication, repair,
and recombination. They contain a PIN (PilT N terminus)
domain with a helical arch/clamp region/I domain (not
included here) and inserted within the PIN domain is an
atypical helix-hairpin-helix-2 (HhH2)-like region. This
atypical HhH2 region, the H3TH domain, has an extended
loop with at least three turns between the first two
helices, and only three of the four helices appear to be
conserved. Both the H3TH domain and the helical
arch/clamp region are involved in DNA binding. Studies
suggest that a glycine-rich loop in the H3TH domain
contacts the phosphate backbone of the template strand
in the downstream DNA duplex. The nucleases within this
family have a carboxylate rich active site that is
involved in binding essential divalent metal ion
cofactors required for nuclease activity. The first
metal binding site (MBS-1) is composed entirely of
Asp/Glu residues from the PIN domain, whereas, the
second metal binding site (MBS-2) is composed generally
of two Asp residues from the PIN domain and two Asp
residues from the H3TH domain. In the T5-5'nuclease,
structure-specific endonuclease activity requires
binding of a single metal ion in the high-affinity,
MBS-1, whereas exonuclease activity requires both, the
high-affinity, MBS-1 and the low-affinity, MBS-2 to be
occupied by a divalent cofactor. The T5-5'nuclease is
reported to be able to bind several metal ions
including, Mg2+, Mn2+, Zn2+ and Co2+, as co-factors.
Together with the helical arch and network of amino
acids interacting with metal binding ions, the H3TH
region defines a positively charged active-site
DNA-binding groove in structure-specific 5' nucleases.
Length = 74
Score = 27.5 bits (61), Expect = 2.2
Identities = 13/51 (25%), Positives = 19/51 (37%), Gaps = 1/51 (1%)
Query: 179 GGQRSERKKWIHCFEGVTAIIFCVALSG-YDSVLAEDEEMNRMIESMKLFD 228
G K + V II + G + LA +E R E++ L D
Sbjct: 24 GIGTGRATKLLEEIGDVADIIDALLTPGKVKNSLALEEAYERFKENLILID 74
>gnl|CDD|225884 COG3347, COG3347, Uncharacterized conserved protein [Function
unknown].
Length = 404
Score = 29.3 bits (66), Expect = 3.1
Identities = 24/114 (21%), Positives = 44/114 (38%), Gaps = 21/114 (18%)
Query: 11 VKLLLLG------AGESGKSTIVKQMKIIHETGYSKEECEQYRPVVYSNSIQ-------- 56
+ L+L G++ K + + I++E ++E + V + +
Sbjct: 183 AEGLVLENHGLFTFGDTAKEAYERMISIVNE---AEEYLARRGGKVAKSLARPVRLAIAA 239
Query: 57 SLMAIIR-AMGQLKIDFGDHKNADCARQFFT---LASAAEEGDLTPDLVILMKR 106
L +IR A+ + K ++D +F L A+ G TPD VI K
Sbjct: 240 DLAPVIRGAVSEKKKKIYRLDDSDAVLEFANSLDLRRIAQRGSATPDHVIRTKI 293
>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 = 28.6 bits (65), Expect = 3.2
Identities = 15/79 (18%), Positives = 28/79 (35%), Gaps = 13/79 (16%)
Query: 234 KWFMDTSIILFLNKNDLFQEKITKSPLTVCFPEYTDQKEIYTHFTCATDTSNIQFVFDAV 293
K + ++ LNK DL TK + +Y + F A + ++
Sbjct: 42 KILGNKPRLIVLNKADLADPAKTKK-----WLKYFKSQGEPVLFVNAKNGKGVK------ 90
Query: 294 TDVIIKANLKDCGIREEVK 312
++K K E++K
Sbjct: 91 --KLLKKAKKLLKENEKLK 107
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 28.5 bits (64), Expect = 3.9
Identities = 14/28 (50%), Positives = 18/28 (64%), Gaps = 4/28 (14%)
Query: 10 EVKLLLLGAGESGKSTIVKQMKIIHETG 37
E KL+L+G G GK+T VK+ H TG
Sbjct: 9 EFKLILVGDGGVGKTTFVKR----HLTG 32
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 28.2 bits (63), Expect = 4.3
Identities = 15/39 (38%), Positives = 24/39 (61%), Gaps = 7/39 (17%)
Query: 12 KLLLLGAGESGKSTIVKQMKIIHETGYSKEECEQYRPVV 50
KL+++G G +GK+T VK+ H TG E ++Y P +
Sbjct: 15 KLVIVGDGGTGKTTFVKR----HLTG---EFEKKYEPTI 46
>gnl|CDD|238423 cd00827, init_cond_enzymes, "initiating" condensing enzymes are a
subclass of decarboxylating condensing enzymes,
including beta-ketoacyl [ACP] synthase, type III and
polyketide synthases, type III, which include chalcone
synthase and related enzymes. They are characterized by
the utlization of CoA substrate primers, as well as the
nature of their active site residues.
Length = 324
Score = 28.2 bits (63), Expect = 5.7
Identities = 11/59 (18%), Positives = 16/59 (27%), Gaps = 1/59 (1%)
Query: 47 RPVVYSNSIQSLMAIIRAMGQLKIDFGDHK-NADCARQFFTLASAAEEGDLTPDLVILM 104
+ + L Q + N A LAS E G L +L+
Sbjct: 252 GKKILEAVAKKLGGPPEKASQTRWILLRRVGNMYAASILLGLASLLESGKLKAGDRVLL 310
>gnl|CDD|223637 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
transport and metabolism].
Length = 178
Score = 27.6 bits (62), Expect = 6.2
Identities = 11/32 (34%), Positives = 20/32 (62%), Gaps = 5/32 (15%)
Query: 12 KLLLLGAGESGKST----IVKQMKIIH-ETGY 38
++L+LG +GKST + K++ + H +TG
Sbjct: 2 RILILGPPGAGKSTLAKKLAKKLGLPHLDTGD 33
>gnl|CDD|213833 TIGR03596, GTPase_YlqF, ribosome biogenesis GTP-binding protein
YlqF. Members of this protein family are GTP-binding
proteins involved in ribosome biogenesis, including the
essential YlqF protein of Bacillus subtilis, which is an
essential protein. They are related to Era, EngA, and
other GTPases of ribosome biogenesis, but are circularly
permuted. This family is not universal, and is not
present in Escherichia coli, and so is not as well
studied as some other GTPases. This model is built for
bacterial members [Protein synthesis, Other].
Length = 276
Score = 27.9 bits (63), Expect = 6.9
Identities = 16/77 (20%), Positives = 30/77 (38%), Gaps = 7/77 (9%)
Query: 234 KWFMDTSIILFLNKNDLFQEKITKSPLTVCFPEYTDQKEIYTHFTCATDTSNIQFVFDAV 293
+ + ++ LNK DL +TK L +Y ++K I A ++ + A
Sbjct: 44 EIRGNKPRLIVLNKADLADPAVTKQWL-----KYFEEKGIKALAINAKKGKGVKKIIKAA 98
Query: 294 TDVI--IKANLKDCGIR 308
++ LK G+
Sbjct: 99 KKLLKEKNEKLKAKGLL 115
>gnl|CDD|181235 PRK08118, PRK08118, topology modulation protein; Reviewed.
Length = 167
Score = 27.3 bits (61), Expect = 7.0
Identities = 11/29 (37%), Positives = 19/29 (65%), Gaps = 6/29 (20%)
Query: 12 KLLLLGAGESGKSTIVKQM------KIIH 34
K++L+G+G SGKST+ +Q+ + H
Sbjct: 3 KIILIGSGGSGKSTLARQLGEKLNIPVHH 31
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 27.8 bits (63), Expect = 8.1
Identities = 17/79 (21%), Positives = 32/79 (40%), Gaps = 7/79 (8%)
Query: 234 KWFMDTSIILFLNKNDLFQEKITKSPLTVCFPEYTDQKEIYTHFTCATDTSNIQFVFDAV 293
K + +L LNK+DL ++TK + EY +++ I A ++ + A
Sbjct: 47 KIIGNKPRLLILNKSDLADPEVTKKWI-----EYFEEQGIKALAINAKKGQGVKKILKAA 101
Query: 294 TDVI--IKANLKDCGIREE 310
++ K G+R
Sbjct: 102 KKLLKEKNERRKAKGMRPR 120
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 0.136 0.406
Gapped
Lambda K H
0.267 0.0740 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,686,503
Number of extensions: 1466662
Number of successful extensions: 1444
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1428
Number of HSP's successfully gapped: 60
Length of query: 313
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 216
Effective length of database: 6,635,264
Effective search space: 1433217024
Effective search space used: 1433217024
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 (22.0 bits)
S2: 59 (26.5 bits)