RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16304
(537 letters)
>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 = 79.5 bits (197), Expect = 1e-17
Identities = 26/63 (41%), Positives = 43/63 (68%), Gaps = 1/63 (1%)
Query: 199 ILVLGLDNAGKSSIIKRILGEPIISLVPTVGFNRARVEYGNKYEVFLYDLGGSEDFRTIW 258
IL+LGLD AGK++I+ ++ +++ +PT+GFN VEY N + ++D+GG + R +W
Sbjct: 2 ILMLGLDGAGKTTILYKLKLGEVVTTIPTIGFNVETVEYKN-VKFTVWDVGGQDKIRPLW 60
Query: 259 KQY 261
K Y
Sbjct: 61 KHY 63
Score = 79.5 bits (197), Expect = 1e-17
Identities = 26/63 (41%), Positives = 43/63 (68%), Gaps = 1/63 (1%)
Query: 313 ILVLGLDNAGKSSIIKRILGEPIISLVPTVGFNRARVEYGNKYEVFLYDLGGSEDFRTIW 372
IL+LGLD AGK++I+ ++ +++ +PT+GFN VEY N + ++D+GG + R +W
Sbjct: 2 ILMLGLDGAGKTTILYKLKLGEVVTTIPTIGFNVETVEYKN-VKFTVWDVGGQDKIRPLW 60
Query: 373 KQY 375
K Y
Sbjct: 61 KHY 63
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 74.6 bits (184), Expect = 1e-15
Identities = 29/69 (42%), Positives = 46/69 (66%), Gaps = 3/69 (4%)
Query: 194 FRSVPILVLGLDNAGKSSIIKRILGEPIISLVPTVGFNRARVEYGN-KYEVFLYDLGGSE 252
+ + IL+LGLDNAGK++I+ ++ I++ +PT+GFN V Y N K+ V+ D+GG E
Sbjct: 12 NKEMRILILGLDNAGKTTILYKLKLGEIVTTIPTIGFNVETVTYKNVKFTVW--DVGGQE 69
Query: 253 DFRTIWKQY 261
R +W+ Y
Sbjct: 70 SLRPLWRNY 78
Score = 74.6 bits (184), Expect = 1e-15
Identities = 29/69 (42%), Positives = 46/69 (66%), Gaps = 3/69 (4%)
Query: 308 FRSVPILVLGLDNAGKSSIIKRILGEPIISLVPTVGFNRARVEYGN-KYEVFLYDLGGSE 366
+ + IL+LGLDNAGK++I+ ++ I++ +PT+GFN V Y N K+ V+ D+GG E
Sbjct: 12 NKEMRILILGLDNAGKTTILYKLKLGEIVTTIPTIGFNVETVTYKNVKFTVW--DVGGQE 69
Query: 367 DFRTIWKQY 375
R +W+ Y
Sbjct: 70 SLRPLWRNY 78
>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 = 74.3 bits (183), Expect = 1e-15
Identities = 31/67 (46%), Positives = 49/67 (73%), Gaps = 1/67 (1%)
Query: 195 RSVPILVLGLDNAGKSSIIKRILGEPIISLVPTVGFNRARVEYGNKYEVFLYDLGGSEDF 254
R + IL+LGLDNAGK++I+K+ GE I ++ PT+GFN +EY N Y++ ++D+GG +
Sbjct: 13 REMRILMLGLDNAGKTTILKKFNGEDISTISPTLGFNIKTLEY-NGYKLNIWDVGGQKSL 71
Query: 255 RTIWKQY 261
R+ W+ Y
Sbjct: 72 RSYWRNY 78
Score = 74.3 bits (183), Expect = 1e-15
Identities = 31/67 (46%), Positives = 49/67 (73%), Gaps = 1/67 (1%)
Query: 309 RSVPILVLGLDNAGKSSIIKRILGEPIISLVPTVGFNRARVEYGNKYEVFLYDLGGSEDF 368
R + IL+LGLDNAGK++I+K+ GE I ++ PT+GFN +EY N Y++ ++D+GG +
Sbjct: 13 REMRILMLGLDNAGKTTILKKFNGEDISTISPTLGFNIKTLEY-NGYKLNIWDVGGQKSL 71
Query: 369 RTIWKQY 375
R+ W+ Y
Sbjct: 72 RSYWRNY 78
>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 = 66.7 bits (163), Expect = 5e-13
Identities = 28/65 (43%), Positives = 42/65 (64%), Gaps = 2/65 (3%)
Query: 199 ILVLGLDNAGKSSIIKRILGEPII-SLVPTVGFNRARVEYGNKYEVFLYDLGGSEDFRTI 257
ILVLGLD AGK+S++ + E + S+VPT GFN + + + L ++GGS++ R
Sbjct: 2 ILVLGLDGAGKTSLLHSLSSERSLESVVPTTGFNSVAIPTQD-AIMELLEIGGSQNLRKY 60
Query: 258 WKQYL 262
WK+YL
Sbjct: 61 WKRYL 65
Score = 66.7 bits (163), Expect = 5e-13
Identities = 28/65 (43%), Positives = 42/65 (64%), Gaps = 2/65 (3%)
Query: 313 ILVLGLDNAGKSSIIKRILGEPII-SLVPTVGFNRARVEYGNKYEVFLYDLGGSEDFRTI 371
ILVLGLD AGK+S++ + E + S+VPT GFN + + + L ++GGS++ R
Sbjct: 2 ILVLGLDGAGKTSLLHSLSSERSLESVVPTTGFNSVAIPTQD-AIMELLEIGGSQNLRKY 60
Query: 372 WKQYL 376
WK+YL
Sbjct: 61 WKRYL 65
>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 = 66.3 bits (162), Expect = 6e-13
Identities = 30/65 (46%), Positives = 45/65 (69%), Gaps = 5/65 (7%)
Query: 199 ILVLGLDNAGKSSIIKRI-LGEPIISLVPTVGFNRARVEYGN-KYEVFLYDLGGSEDFRT 256
IL+LGLD AGK++I+ R+ +GE +++ +PT+GFN V Y N K++V +DLGG R
Sbjct: 2 ILILGLDGAGKTTILYRLQVGE-VVTTIPTIGFNVETVTYKNLKFQV--WDLGGQTSIRP 58
Query: 257 IWKQY 261
W+ Y
Sbjct: 59 YWRCY 63
Score = 66.3 bits (162), Expect = 6e-13
Identities = 30/65 (46%), Positives = 45/65 (69%), Gaps = 5/65 (7%)
Query: 313 ILVLGLDNAGKSSIIKRI-LGEPIISLVPTVGFNRARVEYGN-KYEVFLYDLGGSEDFRT 370
IL+LGLD AGK++I+ R+ +GE +++ +PT+GFN V Y N K++V +DLGG R
Sbjct: 2 ILILGLDGAGKTTILYRLQVGE-VVTTIPTIGFNVETVTYKNLKFQV--WDLGGQTSIRP 58
Query: 371 IWKQY 375
W+ Y
Sbjct: 59 YWRCY 63
>gnl|CDD|133361 cd04161, Arl2l1_Arl13_like, Arl2-like protein 1 (Arl2l1) and Arl13.
Arl2l1 (Arl2-like protein 1) and Arl13 form a subfamily
of the Arf family of small GTPases. Arl2l1 was
identified in human cells during a search for the
gene(s) responsible for Bardet-Biedl syndrome (BBS).
Like Arl6, the identified BBS gene, Arl2l1 is proposed
to have cilia-specific functions. Arl13 is found on the
X chromosome, but its expression has not been confirmed;
it may be a pseudogene.
Length = 167
Score = 66.3 bits (162), Expect = 7e-13
Identities = 28/65 (43%), Positives = 41/65 (63%), Gaps = 1/65 (1%)
Query: 199 ILVLGLDNAGKSSIIKRILGEPIISLVPTVGFNRARVEYGNKYEVFLYDLGGSEDFRTIW 258
+L +GLDNAGK++++ + GE + PTVGF ++ KYEV ++DLGG +FR IW
Sbjct: 2 LLTVGLDNAGKTTLVSALQGEIPKKVAPTVGFTPTKLRLD-KYEVCIFDLGGGANFRGIW 60
Query: 259 KQYLG 263
Y
Sbjct: 61 VNYYA 65
Score = 66.3 bits (162), Expect = 7e-13
Identities = 28/65 (43%), Positives = 41/65 (63%), Gaps = 1/65 (1%)
Query: 313 ILVLGLDNAGKSSIIKRILGEPIISLVPTVGFNRARVEYGNKYEVFLYDLGGSEDFRTIW 372
+L +GLDNAGK++++ + GE + PTVGF ++ KYEV ++DLGG +FR IW
Sbjct: 2 LLTVGLDNAGKTTLVSALQGEIPKKVAPTVGFTPTKLRLD-KYEVCIFDLGGGANFRGIW 60
Query: 373 KQYLG 377
Y
Sbjct: 61 VNYYA 65
>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 = 65.9 bits (161), Expect = 8e-13
Identities = 25/64 (39%), Positives = 44/64 (68%)
Query: 199 ILVLGLDNAGKSSIIKRILGEPIISLVPTVGFNRARVEYGNKYEVFLYDLGGSEDFRTIW 258
+L+LGLD+AGKS+++ ++ +++ +PTVGFN ++ + ++D+GG E RT+W
Sbjct: 2 VLLLGLDSAGKSTLLYKLKHAELVTTIPTVGFNVEMLQLEKHLSLTVWDVGGQEKMRTVW 61
Query: 259 KQYL 262
K YL
Sbjct: 62 KCYL 65
Score = 65.9 bits (161), Expect = 8e-13
Identities = 25/64 (39%), Positives = 44/64 (68%)
Query: 313 ILVLGLDNAGKSSIIKRILGEPIISLVPTVGFNRARVEYGNKYEVFLYDLGGSEDFRTIW 372
+L+LGLD+AGKS+++ ++ +++ +PTVGFN ++ + ++D+GG E RT+W
Sbjct: 2 VLLLGLDSAGKSTLLYKLKHAELVTTIPTVGFNVEMLQLEKHLSLTVWDVGGQEKMRTVW 61
Query: 373 KQYL 376
K YL
Sbjct: 62 KCYL 65
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 64.1 bits (156), Expect = 7e-12
Identities = 32/74 (43%), Positives = 52/74 (70%), Gaps = 5/74 (6%)
Query: 190 SLFDFRSVPILVLGLDNAGKSSIIKRI-LGEPIISLVPTVGFNRARVEYGN-KYEVFLYD 247
SLF + V IL++GLD AGK++I+ ++ LGE +++ +PT+GFN VEY N K+ + +D
Sbjct: 11 SLFGKKEVRILMVGLDAAGKTTILYKLKLGE-VVTTIPTIGFNVETVEYKNLKFTM--WD 67
Query: 248 LGGSEDFRTIWKQY 261
+GG + R +W+ Y
Sbjct: 68 VGGQDKLRPLWRHY 81
Score = 60.6 bits (147), Expect = 8e-11
Identities = 30/73 (41%), Positives = 50/73 (68%), Gaps = 5/73 (6%)
Query: 305 LVDFRSVPILVLGLDNAGKSSIIKRI-LGEPIISLVPTVGFNRARVEYGN-KYEVFLYDL 362
L + V IL++GLD AGK++I+ ++ LGE +++ +PT+GFN VEY N K+ + +D+
Sbjct: 12 LFGKKEVRILMVGLDAAGKTTILYKLKLGE-VVTTIPTIGFNVETVEYKNLKFTM--WDV 68
Query: 363 GGSEDFRTIWKQY 375
GG + R +W+ Y
Sbjct: 69 GGQDKLRPLWRHY 81
>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 = 63.6 bits (155), Expect = 7e-12
Identities = 29/72 (40%), Positives = 46/72 (63%), Gaps = 3/72 (4%)
Query: 191 LFDFRSVPILVLGLDNAGKSSIIKRILGEPIISLVPTVGFNRARVEYGN-KYEVFLYDLG 249
LF + + IL+LGLD AGK++I+ ++ ++ +PTVGFN V Y N K+ V +D+G
Sbjct: 4 LFGNKEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNV--WDVG 61
Query: 250 GSEDFRTIWKQY 261
G + R +W+ Y
Sbjct: 62 GQDKIRPLWRHY 73
Score = 61.3 bits (149), Expect = 4e-11
Identities = 32/89 (35%), Positives = 52/89 (58%), Gaps = 4/89 (4%)
Query: 309 RSVPILVLGLDNAGKSSIIKRILGEPIISLVPTVGFNRARVEYGN-KYEVFLYDLGGSED 367
+ + IL+LGLD AGK++I+ ++ ++ +PTVGFN V Y N K+ V +D+GG +
Sbjct: 8 KEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNV--WDVGGQDK 65
Query: 368 FRTIWKQYL-GTVSQTLLVSHSLSGRPDD 395
R +W+ Y GT +V + R D+
Sbjct: 66 IRPLWRHYYTGTQGLIFVVDSADRDRIDE 94
>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 = 62.4 bits (152), Expect = 2e-11
Identities = 26/71 (36%), Positives = 41/71 (57%), Gaps = 9/71 (12%)
Query: 199 ILVLGLDNAGKSSIIKRIL--------GEPIISLVPTVGFNRARVEYGNKYEVFLYDLGG 250
+L+LGLDNAGK++ +++ G + PTVG N +E G +F +DLGG
Sbjct: 2 VLILGLDNAGKTTFLEQTKTKFSKNYKGLNPSKITPTVGLNIGTIEVGKARLMF-WDLGG 60
Query: 251 SEDFRTIWKQY 261
E+ R++W +Y
Sbjct: 61 QEELRSLWDKY 71
Score = 62.4 bits (152), Expect = 2e-11
Identities = 26/71 (36%), Positives = 41/71 (57%), Gaps = 9/71 (12%)
Query: 313 ILVLGLDNAGKSSIIKRIL--------GEPIISLVPTVGFNRARVEYGNKYEVFLYDLGG 364
+L+LGLDNAGK++ +++ G + PTVG N +E G +F +DLGG
Sbjct: 2 VLILGLDNAGKTTFLEQTKTKFSKNYKGLNPSKITPTVGLNIGTIEVGKARLMF-WDLGG 60
Query: 365 SEDFRTIWKQY 375
E+ R++W +Y
Sbjct: 61 QEELRSLWDKY 71
>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 = 61.7 bits (150), Expect = 3e-11
Identities = 30/65 (46%), Positives = 45/65 (69%), Gaps = 5/65 (7%)
Query: 199 ILVLGLDNAGKSSII-KRILGEPIISLVPTVGFNRARVEYGN-KYEVFLYDLGGSEDFRT 256
IL++GLD AGK++I+ K LGE I++ +PT+GFN VEY N + V +D+GG + R
Sbjct: 3 ILMVGLDAAGKTTILYKLKLGE-IVTTIPTIGFNVETVEYKNISFTV--WDVGGQDKIRP 59
Query: 257 IWKQY 261
+W+ Y
Sbjct: 60 LWRHY 64
Score = 61.7 bits (150), Expect = 3e-11
Identities = 30/65 (46%), Positives = 45/65 (69%), Gaps = 5/65 (7%)
Query: 313 ILVLGLDNAGKSSII-KRILGEPIISLVPTVGFNRARVEYGN-KYEVFLYDLGGSEDFRT 370
IL++GLD AGK++I+ K LGE I++ +PT+GFN VEY N + V +D+GG + R
Sbjct: 3 ILMVGLDAAGKTTILYKLKLGE-IVTTIPTIGFNVETVEYKNISFTV--WDVGGQDKIRP 59
Query: 371 IWKQY 375
+W+ Y
Sbjct: 60 LWRHY 64
>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 = 61.9 bits (151), Expect = 3e-11
Identities = 37/126 (29%), Positives = 54/126 (42%), Gaps = 27/126 (21%)
Query: 199 ILVLGLDNAGKSSIIKRILGEPIISLVPTVGFNRARVEYGN-KYEVFLYDLGGSEDFRTI 257
I+ LGLDNAGK++++ + + + VPT+ + GN K+ F DLGG E R +
Sbjct: 22 IVFLGLDNAGKTTLLHMLKDDRLAQHVPTLHPTSEELTIGNVKFTTF--DLGGHEQARRV 79
Query: 258 WKQYLGTVSQTPLGRPDSRTCQVYLIMCGVHQVSGIP------DELTSATHLPLVDFRSV 311
WK Y V V+L+ D L + L +V
Sbjct: 80 WKDYFPEV-----------DGIVFLVDA--ADPERFQESKEELDSLLNDEELA-----NV 121
Query: 312 PILVLG 317
PIL+LG
Sbjct: 122 PILILG 127
Score = 61.5 bits (150), Expect = 6e-11
Identities = 26/68 (38%), Positives = 38/68 (55%), Gaps = 3/68 (4%)
Query: 313 ILVLGLDNAGKSSIIKRILGEPIISLVPTVGFNRARVEYGN-KYEVFLYDLGGSEDFRTI 371
I+ LGLDNAGK++++ + + + VPT+ + GN K+ F DLGG E R +
Sbjct: 22 IVFLGLDNAGKTTLLHMLKDDRLAQHVPTLHPTSEELTIGNVKFTTF--DLGGHEQARRV 79
Query: 372 WKQYLGTV 379
WK Y V
Sbjct: 80 WKDYFPEV 87
>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 = 61.3 bits (149), Expect = 5e-11
Identities = 27/67 (40%), Positives = 42/67 (62%), Gaps = 1/67 (1%)
Query: 195 RSVPILVLGLDNAGKSSIIKRILGEPIISLVPTVGFNRARVEYGNKYEVFLYDLGGSEDF 254
+ V IL+LGLDNAGK++I+K++ E I + PT GFN V+ ++ ++D+GG
Sbjct: 14 QEVRILLLGLDNAGKTTILKQLASEDISHITPTQGFNIKNVQADGF-KLNVWDIGGQRKI 72
Query: 255 RTIWKQY 261
R W+ Y
Sbjct: 73 RPYWRNY 79
Score = 61.3 bits (149), Expect = 5e-11
Identities = 27/67 (40%), Positives = 42/67 (62%), Gaps = 1/67 (1%)
Query: 309 RSVPILVLGLDNAGKSSIIKRILGEPIISLVPTVGFNRARVEYGNKYEVFLYDLGGSEDF 368
+ V IL+LGLDNAGK++I+K++ E I + PT GFN V+ ++ ++D+GG
Sbjct: 14 QEVRILLLGLDNAGKTTILKQLASEDISHITPTQGFNIKNVQADGF-KLNVWDIGGQRKI 72
Query: 369 RTIWKQY 375
R W+ Y
Sbjct: 73 RPYWRNY 79
>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 = 61.1 bits (148), Expect = 5e-11
Identities = 29/73 (39%), Positives = 48/73 (65%), Gaps = 5/73 (6%)
Query: 191 LFDFRSVPILVLGLDNAGKSSIIKRI-LGEPIISLVPTVGFNRARVEYGN-KYEVFLYDL 248
LF + + IL++GLD AGK++I+ ++ LGE ++ +PT+GFN V Y N + V +D+
Sbjct: 8 LFGNKEMRILMVGLDAAGKTTILYKLKLGE-SVTTIPTIGFNVETVTYKNISFTV--WDV 64
Query: 249 GGSEDFRTIWKQY 261
GG + R +W+ Y
Sbjct: 65 GGQDKIRPLWRHY 77
Score = 59.2 bits (143), Expect = 2e-10
Identities = 27/65 (41%), Positives = 44/65 (67%), Gaps = 5/65 (7%)
Query: 313 ILVLGLDNAGKSSIIKRI-LGEPIISLVPTVGFNRARVEYGN-KYEVFLYDLGGSEDFRT 370
IL++GLD AGK++I+ ++ LGE ++ +PT+GFN V Y N + V +D+GG + R
Sbjct: 16 ILMVGLDAAGKTTILYKLKLGE-SVTTIPTIGFNVETVTYKNISFTV--WDVGGQDKIRP 72
Query: 371 IWKQY 375
+W+ Y
Sbjct: 73 LWRHY 77
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 61.1 bits (148), Expect = 6e-11
Identities = 30/72 (41%), Positives = 49/72 (68%), Gaps = 3/72 (4%)
Query: 191 LFDFRSVPILVLGLDNAGKSSIIKRI-LGEPIISLVPTVGFNRARVEYGNKYEVFLYDLG 249
LF + + IL++GLD AGK++I+ ++ LGE I++ +PT+GFN VEY N ++D+G
Sbjct: 12 LFAKKEMRILMVGLDAAGKTTILYKLKLGE-IVTTIPTIGFNVETVEYKN-ISFTVWDVG 69
Query: 250 GSEDFRTIWKQY 261
G + R +W+ Y
Sbjct: 70 GQDKIRPLWRHY 81
Score = 59.2 bits (143), Expect = 3e-10
Identities = 30/81 (37%), Positives = 50/81 (61%), Gaps = 3/81 (3%)
Query: 309 RSVPILVLGLDNAGKSSIIKRI-LGEPIISLVPTVGFNRARVEYGNKYEVFLYDLGGSED 367
+ + IL++GLD AGK++I+ ++ LGE I++ +PT+GFN VEY N ++D+GG +
Sbjct: 16 KEMRILMVGLDAAGKTTILYKLKLGE-IVTTIPTIGFNVETVEYKN-ISFTVWDVGGQDK 73
Query: 368 FRTIWKQYLGTVSQTLLVSHS 388
R +W+ Y + V S
Sbjct: 74 IRPLWRHYFQNTQGLIFVVDS 94
>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 = 60.8 bits (148), Expect = 6e-11
Identities = 23/73 (31%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 190 SLFDFRSVPILVLGLDNAGKSSIIKRILGEPIISLVPTVGFNRARVEYGNKYEVFLYDLG 249
F + ++++GLDNAGK++I+ + L ++ PT+G N + Y N ++D+G
Sbjct: 9 LFFPRKEYKVIIVGLDNAGKTTILYQFLLGEVVHTSPTIGSNVEEIVYKN-IRFLMWDIG 67
Query: 250 GSEDFRTIWKQYL 262
G E R+ W Y
Sbjct: 68 GQESLRSSWNTYY 80
Score = 60.4 bits (147), Expect = 1e-10
Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 4/73 (5%)
Query: 313 ILVLGLDNAGKSSIIKRILGEPIISLVPTVGFNRARVEYGNKYEVFLYDLGGSEDFRTIW 372
++++GLDNAGK++I+ + L ++ PT+G N + Y N ++D+GG E R+ W
Sbjct: 18 VIIVGLDNAGKTTILYQFLLGEVVHTSPTIGSNVEEIVYKN-IRFLMWDIGGQESLRSSW 76
Query: 373 KQYLGTVSQTLLV 385
Y + T V
Sbjct: 77 NTYY---TNTDAV 86
>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 = 59.0 bits (143), Expect = 3e-10
Identities = 29/72 (40%), Positives = 46/72 (63%), Gaps = 4/72 (5%)
Query: 194 FRSVPILVLGLDNAGKSSIIKRILGEPIISLVPTVGFN--RARVEYGNKYEV--FLYDLG 249
F+S+ I++LGLD+AGK++++ R+ ++ VPT GFN + +V GN V +D+G
Sbjct: 1 FQSLHIVMLGLDSAGKTTVLYRLKFNEFVNTVPTKGFNTEKIKVSLGNAKGVTFHFWDVG 60
Query: 250 GSEDFRTIWKQY 261
G E R +WK Y
Sbjct: 61 GQEKLRPLWKSY 72
Score = 59.0 bits (143), Expect = 3e-10
Identities = 29/72 (40%), Positives = 46/72 (63%), Gaps = 4/72 (5%)
Query: 308 FRSVPILVLGLDNAGKSSIIKRILGEPIISLVPTVGFN--RARVEYGNKYEV--FLYDLG 363
F+S+ I++LGLD+AGK++++ R+ ++ VPT GFN + +V GN V +D+G
Sbjct: 1 FQSLHIVMLGLDSAGKTTVLYRLKFNEFVNTVPTKGFNTEKIKVSLGNAKGVTFHFWDVG 60
Query: 364 GSEDFRTIWKQY 375
G E R +WK Y
Sbjct: 61 GQEKLRPLWKSY 72
>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 = 58.2 bits (141), Expect = 4e-10
Identities = 28/66 (42%), Positives = 40/66 (60%), Gaps = 5/66 (7%)
Query: 199 ILVLGLDNAGKSSIIKRILGEPIIS--LVPTVGFNRARVEYGN-KYEVFLYDLGGSEDFR 255
ILVLGLDN+GK++II ++ S +VPTVGFN + GN + F D+ G +R
Sbjct: 2 ILVLGLDNSGKTTIINQLKPSNAQSQNIVPTVGFNVESFKKGNLSFTAF--DMSGQGKYR 59
Query: 256 TIWKQY 261
+W+ Y
Sbjct: 60 GLWEHY 65
Score = 58.2 bits (141), Expect = 4e-10
Identities = 28/66 (42%), Positives = 40/66 (60%), Gaps = 5/66 (7%)
Query: 313 ILVLGLDNAGKSSIIKRILGEPIIS--LVPTVGFNRARVEYGN-KYEVFLYDLGGSEDFR 369
ILVLGLDN+GK++II ++ S +VPTVGFN + GN + F D+ G +R
Sbjct: 2 ILVLGLDNSGKTTIINQLKPSNAQSQNIVPTVGFNVESFKKGNLSFTAF--DMSGQGKYR 59
Query: 370 TIWKQY 375
+W+ Y
Sbjct: 60 GLWEHY 65
>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 = 56.6 bits (136), Expect = 2e-09
Identities = 24/63 (38%), Positives = 40/63 (63%), Gaps = 1/63 (1%)
Query: 199 ILVLGLDNAGKSSIIKRILGEPIISLVPTVGFNRARVEYGNKYEVFLYDLGGSEDFRTIW 258
++ LGLD AGK++I+ ++ + + +PT+GFN VEY N + ++D+GG R +W
Sbjct: 2 VVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKN-LKFTIWDVGGKHKLRPLW 60
Query: 259 KQY 261
K Y
Sbjct: 61 KHY 63
Score = 56.6 bits (136), Expect = 2e-09
Identities = 24/63 (38%), Positives = 40/63 (63%), Gaps = 1/63 (1%)
Query: 313 ILVLGLDNAGKSSIIKRILGEPIISLVPTVGFNRARVEYGNKYEVFLYDLGGSEDFRTIW 372
++ LGLD AGK++I+ ++ + + +PT+GFN VEY N + ++D+GG R +W
Sbjct: 2 VVTLGLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKN-LKFTIWDVGGKHKLRPLW 60
Query: 373 KQY 375
K Y
Sbjct: 61 KHY 63
>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 = 55.4 bits (134), Expect = 4e-09
Identities = 25/66 (37%), Positives = 40/66 (60%), Gaps = 6/66 (9%)
Query: 199 ILVLGLDNAGKSSIIKRILGEP-IISLVPTVGFNRARVEYGNKYEVFL--YDLGGSEDFR 255
I ++GL N+GK++++ I +PTVGFN +V GN V + +DLGG FR
Sbjct: 2 ITLVGLQNSGKTTLVNVIASGQFSEDTIPTVGFNMRKVTKGN---VTIKVWDLGGQPRFR 58
Query: 256 TIWKQY 261
++W++Y
Sbjct: 59 SMWERY 64
Score = 55.4 bits (134), Expect = 4e-09
Identities = 25/66 (37%), Positives = 40/66 (60%), Gaps = 6/66 (9%)
Query: 313 ILVLGLDNAGKSSIIKRILGEP-IISLVPTVGFNRARVEYGNKYEVFL--YDLGGSEDFR 369
I ++GL N+GK++++ I +PTVGFN +V GN V + +DLGG FR
Sbjct: 2 ITLVGLQNSGKTTLVNVIASGQFSEDTIPTVGFNMRKVTKGN---VTIKVWDLGGQPRFR 58
Query: 370 TIWKQY 375
++W++Y
Sbjct: 59 SMWERY 64
>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 = 52.0 bits (125), Expect = 7e-08
Identities = 25/78 (32%), Positives = 37/78 (47%), Gaps = 5/78 (6%)
Query: 313 ILVLGLDNAGKSSIIKRILGEPII--SLVPTVGFNRA--RVEY-GNKYEVFLYDLGGSED 367
I+++G N GKS+++ R+LG I P N +E G Y+ L D G ED
Sbjct: 4 IVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAGQED 63
Query: 368 FRTIWKQYLGTVSQTLLV 385
+ I + Y V +L V
Sbjct: 64 YDAIRRLYYRAVESSLRV 81
Score = 50.1 bits (120), Expect = 3e-07
Identities = 23/73 (31%), Positives = 34/73 (46%), Gaps = 5/73 (6%)
Query: 199 ILVLGLDNAGKSSIIKRILGEPII--SLVPTVGFNRA--RVEY-GNKYEVFLYDLGGSED 253
I+++G N GKS+++ R+LG I P N +E G Y+ L D G ED
Sbjct: 4 IVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAGQED 63
Query: 254 FRTIWKQYLGTVS 266
+ I + Y V
Sbjct: 64 YDAIRRLYYRAVE 76
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 51.1 bits (122), Expect = 3e-07
Identities = 31/125 (24%), Positives = 52/125 (41%), Gaps = 20/125 (16%)
Query: 199 ILVLGLDNAGKSSIIKRIL-GEPIISLVPTVGFN---RARVEYGNKYEVFLYDLGGSEDF 254
I+VLG GK++++ R++ E PT+G + Y ++ L+D G E++
Sbjct: 8 IVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQEEY 67
Query: 255 RTIWKQYLGTVSQTPLGRPDSRTCQVYLIMCGVHQVSGIPDELTSATHLPLVDFRS--VP 312
R++ +Y R LI+ DELT L + VP
Sbjct: 68 RSLRPEYY-------------RGANGILIVYDSTLRESS-DELTEEWLEELRELAPDDVP 113
Query: 313 ILVLG 317
IL++G
Sbjct: 114 ILLVG 118
Score = 50.7 bits (121), Expect = 3e-07
Identities = 18/67 (26%), Positives = 35/67 (52%), Gaps = 4/67 (5%)
Query: 313 ILVLGLDNAGKSSIIKRIL-GEPIISLVPTVGFN---RARVEYGNKYEVFLYDLGGSEDF 368
I+VLG GK++++ R++ E PT+G + Y ++ L+D G E++
Sbjct: 8 IVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQEEY 67
Query: 369 RTIWKQY 375
R++ +Y
Sbjct: 68 RSLRPEY 74
>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 = 47.6 bits (113), Expect = 3e-06
Identities = 36/121 (29%), Positives = 55/121 (45%), Gaps = 17/121 (14%)
Query: 199 ILVLGLDNAGKSSIIKRILGEPIISLVPTVGFNRARVEYGN-KYEVFLYDLGGSEDFRTI 257
IL LGLDNAGK++++ + + + PT + GN K+ F DLGG + R +
Sbjct: 20 ILFLGLDNAGKTTLLHMLKNDRLAQHQPTQHPTSEELAIGNIKFTTF--DLGGHQQARRL 77
Query: 258 WKQYLGTVSQTPLGRPDSRTCQVYLI-MCGVHQVSGIPDELTSATHLPLVDFRSVPILVL 316
WK Y V+ VYL+ + + EL + L + +VP L+L
Sbjct: 78 WKDYFPEVNGI-----------VYLVDAYDKERFAESKRELDAL--LSDEELATVPFLIL 124
Query: 317 G 317
G
Sbjct: 125 G 125
Score = 46.5 bits (110), Expect = 8e-06
Identities = 25/69 (36%), Positives = 37/69 (53%), Gaps = 3/69 (4%)
Query: 313 ILVLGLDNAGKSSIIKRILGEPIISLVPTVGFNRARVEYGN-KYEVFLYDLGGSEDFRTI 371
IL LGLDNAGK++++ + + + PT + GN K+ F DLGG + R +
Sbjct: 20 ILFLGLDNAGKTTLLHMLKNDRLAQHQPTQHPTSEELAIGNIKFTTF--DLGGHQQARRL 77
Query: 372 WKQYLGTVS 380
WK Y V+
Sbjct: 78 WKDYFPEVN 86
>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 = 44.8 bits (106), Expect = 2e-05
Identities = 15/64 (23%), Positives = 27/64 (42%), Gaps = 5/64 (7%)
Query: 200 LVLGLDNAGKSSIIKRILGEPI----ISLVPTVGFNRARVEY-GNKYEVFLYDLGGSEDF 254
+V+G GKSS++ +LG + T + E K ++ L D G ++F
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPGLDEF 60
Query: 255 RTIW 258
+
Sbjct: 61 GGLG 64
Score = 44.8 bits (106), Expect = 2e-05
Identities = 15/64 (23%), Positives = 27/64 (42%), Gaps = 5/64 (7%)
Query: 314 LVLGLDNAGKSSIIKRILGEPI----ISLVPTVGFNRARVEY-GNKYEVFLYDLGGSEDF 368
+V+G GKSS++ +LG + T + E K ++ L D G ++F
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPGLDEF 60
Query: 369 RTIW 372
+
Sbjct: 61 GGLG 64
>gnl|CDD|133311 cd04111, Rab39, Rab GTPase family 39 (Rab39). Found in eukaryotes,
Rab39 is mainly found in epithelial cell lines, but is
distributed widely in various human tissues and cell
lines. It is believed to be a novel Rab protein involved
in regulating Golgi-associated vesicular transport
during cellular endocytosis. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 211
Score = 40.1 bits (94), Expect = 0.001
Identities = 28/76 (36%), Positives = 43/76 (56%), Gaps = 10/76 (13%)
Query: 192 FDFRSVPILVLGLDNAGKSSIIKRILGEPIISLV--PTVG---FNRA-RVEYGNKYEVFL 245
+ FR ++V+G GKSS++KR E + V PTVG F+R +E G + ++ L
Sbjct: 1 YQFR---LIVIGDSTVGKSSLLKRFT-EGRFAEVSDPTVGVDFFSRLIEIEPGVRIKLQL 56
Query: 246 YDLGGSEDFRTIWKQY 261
+D G E FR+I + Y
Sbjct: 57 WDTAGQERFRSITRSY 72
Score = 39.7 bits (93), Expect = 0.002
Identities = 28/74 (37%), Positives = 42/74 (56%), Gaps = 10/74 (13%)
Query: 308 FRSVPILVLGLDNAGKSSIIKRILGEPIISLV--PTVG---FNRA-RVEYGNKYEVFLYD 361
FR ++V+G GKSS++KR E + V PTVG F+R +E G + ++ L+D
Sbjct: 3 FR---LIVIGDSTVGKSSLLKRFT-EGRFAEVSDPTVGVDFFSRLIEIEPGVRIKLQLWD 58
Query: 362 LGGSEDFRTIWKQY 375
G E FR+I + Y
Sbjct: 59 TAGQERFRSITRSY 72
>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 = 37.1 bits (87), Expect = 0.008
Identities = 18/67 (26%), Positives = 34/67 (50%), Gaps = 4/67 (5%)
Query: 199 ILVLGLDNAGKSSIIKR-ILGEPIISLVPTVG--FNRARVEYGNK-YEVFLYDLGGSEDF 254
I+++G GK+S++ R + + + T+G F +E K ++ ++D G E F
Sbjct: 3 IVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGVDFKSKTIEVDGKKVKLQIWDTAGQERF 62
Query: 255 RTIWKQY 261
R+I Y
Sbjct: 63 RSITSSY 69
Score = 37.1 bits (87), Expect = 0.008
Identities = 18/67 (26%), Positives = 34/67 (50%), Gaps = 4/67 (5%)
Query: 313 ILVLGLDNAGKSSIIKR-ILGEPIISLVPTVG--FNRARVEYGNK-YEVFLYDLGGSEDF 368
I+++G GK+S++ R + + + T+G F +E K ++ ++D G E F
Sbjct: 3 IVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGVDFKSKTIEVDGKKVKLQIWDTAGQERF 62
Query: 369 RTIWKQY 375
R+I Y
Sbjct: 63 RSITSSY 69
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 37.1 bits (86), Expect = 0.011
Identities = 25/123 (20%), Positives = 47/123 (38%), Gaps = 21/123 (17%)
Query: 309 RSVPILVLGLDNAGKSSIIKRILGEPIISLVP-------------TVGFNRARVEYGNKY 355
I+V+G AGK++ ++ + +P++ TV + +E
Sbjct: 9 IETKIVVIGPVGAGKTTFVRALSDKPLVITEADASSVSGKGKRPTTVAMDFGSIELDEDT 68
Query: 356 EVFLYDLGGSEDFRTIWKQYL-GTVSQTLLVSHSLSGRPDDRCQVYLM----SCNCQVYL 410
V L+ G E F+ +W+ G V +LV S RP ++ S N +
Sbjct: 69 GVHLFGTPGQERFKFMWEILSRGAVGAIVLV---DSSRPITFHAEEIIDFLTSRNPIPVV 125
Query: 411 ISA 413
++
Sbjct: 126 VAI 128
Score = 33.2 bits (76), Expect = 0.21
Identities = 16/81 (19%), Positives = 32/81 (39%), Gaps = 13/81 (16%)
Query: 195 RSVPILVLGLDNAGKSSIIKRILGEPIISLVP-------------TVGFNRARVEYGNKY 241
I+V+G AGK++ ++ + +P++ TV + +E
Sbjct: 9 IETKIVVIGPVGAGKTTFVRALSDKPLVITEADASSVSGKGKRPTTVAMDFGSIELDEDT 68
Query: 242 EVFLYDLGGSEDFRTIWKQYL 262
V L+ G E F+ +W+
Sbjct: 69 GVHLFGTPGQERFKFMWEILS 89
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 37.0 bits (85), Expect = 0.012
Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 3/79 (3%)
Query: 310 SVPILVLGLDNAGKSSIIKRILGEPIISLVPTVG--FNRARVEYGNK-YEVFLYDLGGSE 366
S IL++G GKSS++ + + L PT+G F ++ G K ++ ++D G E
Sbjct: 14 SFKILLIGDSGVGKSSLLVSFISSSVEDLAPTIGVDFKIKQLTVGGKRLKLTIWDTAGQE 73
Query: 367 DFRTIWKQYLGTVSQTLLV 385
FRT+ Y +LV
Sbjct: 74 RFRTLTSSYYRNAQGIILV 92
Score = 36.6 bits (84), Expect = 0.020
Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 3/69 (4%)
Query: 196 SVPILVLGLDNAGKSSIIKRILGEPIISLVPTVG--FNRARVEYGNK-YEVFLYDLGGSE 252
S IL++G GKSS++ + + L PT+G F ++ G K ++ ++D G E
Sbjct: 14 SFKILLIGDSGVGKSSLLVSFISSSVEDLAPTIGVDFKIKQLTVGGKRLKLTIWDTAGQE 73
Query: 253 DFRTIWKQY 261
FRT+ Y
Sbjct: 74 RFRTLTSSY 82
>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 = 35.4 bits (82), Expect = 0.027
Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 5/61 (8%)
Query: 199 ILVLGLDNAGKSSIIKRILGEPIISLVP-TVGFN----RARVEYGNKYEVFLYDLGGSED 253
++++G GK+S+ K+++GE T G N + K + ++D GG E
Sbjct: 4 LMLVGQGGVGKTSLCKQLIGEKFDGDESSTHGINVQDWKIPAPERKKIRLNVWDFGGQEI 63
Query: 254 F 254
+
Sbjct: 64 Y 64
Score = 35.4 bits (82), Expect = 0.027
Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 5/61 (8%)
Query: 313 ILVLGLDNAGKSSIIKRILGEPIISLVP-TVGFN----RARVEYGNKYEVFLYDLGGSED 367
++++G GK+S+ K+++GE T G N + K + ++D GG E
Sbjct: 4 LMLVGQGGVGKTSLCKQLIGEKFDGDESSTHGINVQDWKIPAPERKKIRLNVWDFGGQEI 63
Query: 368 F 368
+
Sbjct: 64 Y 64
>gnl|CDD|206656 cd01863, Rab18, Rab GTPase family 18 (Rab18). Rab18 subfamily.
Mammalian Rab18 is implicated in endocytic transport and
is expressed most highly in polarized epithelial cells.
However, trypanosomal Rab, TbRAB18, is upregulated in
the BSF (Blood Stream Form) stage and localized
predominantly to elements of the Golgi complex. In human
and mouse cells, Rab18 has been identified in lipid
droplets, organelles that store neutral lipids. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 161
Score = 35.0 bits (81), Expect = 0.037
Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 6/68 (8%)
Query: 199 ILVLGLDNAGKSSIIKR-ILGEPIISLVPTVGFNRARVEY----GNKYEVFLYDLGGSED 253
IL++G GKSS++ R L T+G + +V+ G K ++ ++D G E
Sbjct: 3 ILLIGDSGVGKSSLLLRFTDDTFDEDLSSTIGVD-FKVKTVTVDGKKVKLAIWDTAGQER 61
Query: 254 FRTIWKQY 261
FRT+ Y
Sbjct: 62 FRTLTSSY 69
Score = 35.0 bits (81), Expect = 0.037
Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 6/68 (8%)
Query: 313 ILVLGLDNAGKSSIIKR-ILGEPIISLVPTVGFNRARVEY----GNKYEVFLYDLGGSED 367
IL++G GKSS++ R L T+G + +V+ G K ++ ++D G E
Sbjct: 3 ILLIGDSGVGKSSLLLRFTDDTFDEDLSSTIGVD-FKVKTVTVDGKKVKLAIWDTAGQER 61
Query: 368 FRTIWKQY 375
FRT+ Y
Sbjct: 62 FRTLTSSY 69
>gnl|CDD|206746 cd01849, YlqF_related_GTPase, Circularly permuted YlqF-related
GTPases. These proteins are found in bacteria,
eukaryotes, and archaea. They all exhibit a circular
permutation of the GTPase signature motifs so that the
order of the conserved G box motifs is G4-G5-G1-G2-G3,
with G4 and G5 being permuted from the C-terminal region
of proteins in the Ras superfamily to the N-terminus of
YlqF-related GTPases.
Length = 146
Score = 33.9 bits (78), Expect = 0.080
Identities = 16/53 (30%), Positives = 27/53 (50%)
Query: 199 ILVLGLDNAGKSSIIKRILGEPIISLVPTVGFNRARVEYGNKYEVFLYDLGGS 251
+ V+GL N GKSS I +L + + + G + + + E++LYD G
Sbjct: 94 VGVVGLPNVGKSSFINALLNKFKLKVGSIPGTTKLQQDVKLDKEIYLYDTPGI 146
Score = 33.9 bits (78), Expect = 0.080
Identities = 16/53 (30%), Positives = 27/53 (50%)
Query: 313 ILVLGLDNAGKSSIIKRILGEPIISLVPTVGFNRARVEYGNKYEVFLYDLGGS 365
+ V+GL N GKSS I +L + + + G + + + E++LYD G
Sbjct: 94 VGVVGLPNVGKSSFINALLNKFKLKVGSIPGTTKLQQDVKLDKEIYLYDTPGI 146
>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 = 33.6 bits (78), Expect = 0.10
Identities = 18/67 (26%), Positives = 33/67 (49%), Gaps = 4/67 (5%)
Query: 199 ILVLGLDNAGKSSIIKR-ILGEPIISLVPTVG--FNRARVEYGNK-YEVFLYDLGGSEDF 254
++++G GKSS++ R + +PT+G F +E K ++ ++D G E F
Sbjct: 2 LVLVGDGGVGKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAGQERF 61
Query: 255 RTIWKQY 261
R + Y
Sbjct: 62 RALRPLY 68
Score = 33.6 bits (78), Expect = 0.10
Identities = 18/67 (26%), Positives = 33/67 (49%), Gaps = 4/67 (5%)
Query: 313 ILVLGLDNAGKSSIIKR-ILGEPIISLVPTVG--FNRARVEYGNK-YEVFLYDLGGSEDF 368
++++G GKSS++ R + +PT+G F +E K ++ ++D G E F
Sbjct: 2 LVLVGDGGVGKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAGQERF 61
Query: 369 RTIWKQY 375
R + Y
Sbjct: 62 RALRPLY 68
>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 = 33.4 bits (77), Expect = 0.12
Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 4/54 (7%)
Query: 201 VLGLDNAGKSSIIKRILGEP--IISLVP--TVGFNRARVEYGNKYEVFLYDLGG 250
+ G N GKSS++ +LG+ I+S +P T R E V L D G
Sbjct: 2 IFGRPNVGKSSLLNALLGQNVGIVSPIPGTTRDPVRKEWELLPLGPVVLIDTPG 55
Score = 33.4 bits (77), Expect = 0.12
Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 4/54 (7%)
Query: 315 VLGLDNAGKSSIIKRILGEP--IISLVP--TVGFNRARVEYGNKYEVFLYDLGG 364
+ G N GKSS++ +LG+ I+S +P T R E V L D G
Sbjct: 2 IFGRPNVGKSSLLNALLGQNVGIVSPIPGTTRDPVRKEWELLPLGPVVLIDTPG 55
>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 = 33.3 bits (77), Expect = 0.13
Identities = 28/128 (21%), Positives = 56/128 (43%), Gaps = 27/128 (21%)
Query: 199 ILVLGLDNAGKSSIIKR-ILGEPIISLVPTVG--FNRARVEYGNKYEVFLYDLGGSEDFR 255
++VLG GKS++ R + GE + PT+ + + V G Y + + D G E+F
Sbjct: 2 LVVLGAGGVGKSALTIRFVSGEFVEEYDPTIEDSYRKQIVVDGETYTLDILDTAGQEEFS 61
Query: 256 TIWKQYLGTVSQTPLGRPDSRTCQVYLIMCGV------HQVSGIPDELTSATHLPLVDFR 309
+ QY+ R ++++ + ++ I +++ L + D
Sbjct: 62 AMRDQYI-------------RNGDGFILVYSITSRESFEEIKNIREQI-----LRVKDKE 103
Query: 310 SVPILVLG 317
VPI+++G
Sbjct: 104 DVPIVLVG 111
Score = 31.7 bits (73), Expect = 0.40
Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 3/67 (4%)
Query: 313 ILVLGLDNAGKSSIIKR-ILGEPIISLVPTVG--FNRARVEYGNKYEVFLYDLGGSEDFR 369
++VLG GKS++ R + GE + PT+ + + V G Y + + D G E+F
Sbjct: 2 LVVLGAGGVGKSALTIRFVSGEFVEEYDPTIEDSYRKQIVVDGETYTLDILDTAGQEEFS 61
Query: 370 TIWKQYL 376
+ QY+
Sbjct: 62 AMRDQYI 68
>gnl|CDD|185391 PRK15494, era, GTPase Era; Provisional.
Length = 339
Score = 34.3 bits (78), Expect = 0.14
Identities = 24/76 (31%), Positives = 40/76 (52%), Gaps = 10/76 (13%)
Query: 299 SATHLPL-VDF------RSVPILVLGLDNAGKSSIIKRILGEPIISLVPTVGFNRARVE- 350
S + LPL V F ++V + ++G N+GKS+++ RI+GE + + P V R+ +
Sbjct: 34 STSKLPLEVKFGKMSNQKTVSVCIIGRPNSGKSTLLNRIIGEKLSIVTPKVQTTRSIITG 93
Query: 351 --YGNKYEVFLYDLGG 364
+V LYD G
Sbjct: 94 IITLKDTQVILYDTPG 109
Score = 33.9 bits (77), Expect = 0.21
Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 195 RSVPILVLGLDNAGKSSIIKRILGEPIISLVPTVGFNRARVE---YGNKYEVFLYDLGG 250
++V + ++G N+GKS+++ RI+GE + + P V R+ + +V LYD G
Sbjct: 51 KTVSVCIIGRPNSGKSTLLNRIIGEKLSIVTPKVQTTRSIITGIITLKDTQVILYDTPG 109
>gnl|CDD|226124 COG3596, COG3596, Predicted GTPase [General function prediction
only].
Length = 296
Score = 34.0 bits (78), Expect = 0.14
Identities = 28/97 (28%), Positives = 40/97 (41%), Gaps = 12/97 (12%)
Query: 168 SDDPAPTFENFLDLRVLLPTH-------LSLFDFRSVPILVLGLDNAGKSSIIKRILGEP 220
SD + L L LL L L + V +L++G AGKSS+I +
Sbjct: 4 SDSLNNVLKGLLGLPSLLSERILEQLRMLQLTEKEPVNVLLMGATGAGKSSLINALFQGE 63
Query: 221 I--ISLVP--TVGFNRARVEYGNKYEVFLYDLGGSED 253
+ +S V T R R+ Y + V L+D G D
Sbjct: 64 VKEVSKVGVGTDITTRLRLSYDGENLV-LWDTPGLGD 99
Score = 29.0 bits (65), Expect = 6.3
Identities = 23/85 (27%), Positives = 37/85 (43%), Gaps = 5/85 (5%)
Query: 303 LPLVDFRSVPILVLGLDNAGKSSIIKRILGEPI--ISLVP--TVGFNRARVEYGNKYEVF 358
L L + V +L++G AGKSS+I + + +S V T R R+ Y + V
Sbjct: 32 LQLTEKEPVNVLLMGATGAGKSSLINALFQGEVKEVSKVGVGTDITTRLRLSYDGENLV- 90
Query: 359 LYDLGGSEDFRTIWKQYLGTVSQTL 383
L+D G D + ++ L
Sbjct: 91 LWDTPGLGDGKDKDAEHRQLYRDYL 115
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 34.2 bits (79), Expect = 0.16
Identities = 24/62 (38%), Positives = 34/62 (54%), Gaps = 8/62 (12%)
Query: 197 VPIL-VLGLDNAGKSSIIKRILG--EPIISLVPTVGFNRARVEYG---NKYEVFLYDLGG 250
+P++ V+G N GKS+++ RILG E ++ VP G R RV Y N + D GG
Sbjct: 38 LPVVAVVGRPNVGKSTLVNRILGRREAVVEDVP--GVTRDRVSYDAEWNGRRFTVVDTGG 95
Query: 251 SE 252
E
Sbjct: 96 WE 97
Score = 34.2 bits (79), Expect = 0.16
Identities = 24/62 (38%), Positives = 34/62 (54%), Gaps = 8/62 (12%)
Query: 311 VPIL-VLGLDNAGKSSIIKRILG--EPIISLVPTVGFNRARVEYG---NKYEVFLYDLGG 364
+P++ V+G N GKS+++ RILG E ++ VP G R RV Y N + D GG
Sbjct: 38 LPVVAVVGRPNVGKSTLVNRILGRREAVVEDVP--GVTRDRVSYDAEWNGRRFTVVDTGG 95
Query: 365 SE 366
E
Sbjct: 96 WE 97
>gnl|CDD|215565 PLN03083, PLN03083, E3 UFM1-protein ligase 1 homolog; Provisional.
Length = 803
Score = 34.4 bits (79), Expect = 0.18
Identities = 20/80 (25%), Positives = 31/80 (38%), Gaps = 15/80 (18%)
Query: 416 LSNGFKKS--ERDETNISNFQIKNSSE--------NLQDNNTSDNHDSKKKQPRKRK--- 462
LSNGF K ++ E + F I+ SS +L N +S + K +K+K
Sbjct: 368 LSNGFIKGIYDQIEKEMDAFSIQASSAGLIGSSEKSLGSNESSPAASNSDKGSKKKKGKS 427
Query: 463 --KKVAPLNTDDETELSLPP 480
K + + E P
Sbjct: 428 TSTKGGTAESIPDDEEDAPK 447
>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 = 32.3 bits (74), Expect = 0.19
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 6/56 (10%)
Query: 199 ILVLGLDNAGKSSIIKRILGE--PIISLVP--TVGFNRARVEYGNKYEVFLYDLGG 250
+ ++G N GKS++I + G I+S P T + G ++ L D G
Sbjct: 2 VALVGRPNVGKSTLINALTGAKVAIVSDYPGTTR--DPILGVLGLGRQIILVDTPG 55
Score = 32.3 bits (74), Expect = 0.19
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 6/56 (10%)
Query: 313 ILVLGLDNAGKSSIIKRILGE--PIISLVP--TVGFNRARVEYGNKYEVFLYDLGG 364
+ ++G N GKS++I + G I+S P T + G ++ L D G
Sbjct: 2 VALVGRPNVGKSTLINALTGAKVAIVSDYPGTTR--DPILGVLGLGRQIILVDTPG 55
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 33.5 bits (77), Expect = 0.26
Identities = 13/49 (26%), Positives = 23/49 (46%)
Query: 199 ILVLGLDNAGKSSIIKRILGEPIISLVPTVGFNRARVEYGNKYEVFLYD 247
+ V+G N GKS++I R+LG+ + G + ++L D
Sbjct: 135 VGVVGYPNVGKSTLINRLLGKKVAKTSNRPGTTKGIQWIKLDDGIYLLD 183
Score = 33.5 bits (77), Expect = 0.26
Identities = 13/49 (26%), Positives = 23/49 (46%)
Query: 313 ILVLGLDNAGKSSIIKRILGEPIISLVPTVGFNRARVEYGNKYEVFLYD 361
+ V+G N GKS++I R+LG+ + G + ++L D
Sbjct: 135 VGVVGYPNVGKSTLINRLLGKKVAKTSNRPGTTKGIQWIKLDDGIYLLD 183
>gnl|CDD|206652 cd01853, Toc34_like, Translocon at the Outer-envelope membrane of
Chloroplasts 34-like (Toc34-like). The Toc34-like
(Translocon at the Outer-envelope membrane of
Chloroplasts) family contains several Toc proteins,
including Toc34, Toc33, Toc120, Toc159, Toc86, Toc125,
and Toc90. The Toc complex at the outer envelope
membrane of chloroplasts is a molecular machine of ~500
kDa that contains a single Toc159 protein, four Toc75
molecules, and four or five copies of Toc34. Toc64 and
Toc12 are associated with the translocon, but do not
appear to be part of the core complex. The Toc
translocon initiates the import of nuclear-encoded
preproteins from the cytosol into the organelle. Toc34
and Toc159 are both GTPases, while Toc75 is a
beta-barrel integral membrane protein. Toc159 is equally
distributed between a soluble cytoplasmic form and a
membrane-inserted form, suggesting that assembly of the
Toc complex is dynamic. Toc34 and Toc75 act sequentially
to mediate docking and insertion of Toc159 resulting in
assembly of the functional translocon.
Length = 248
Score = 32.7 bits (75), Expect = 0.33
Identities = 15/28 (53%), Positives = 17/28 (60%)
Query: 196 SVPILVLGLDNAGKSSIIKRILGEPIIS 223
S+ ILVLG GKSS I I GE +S
Sbjct: 31 SLTILVLGKTGVGKSSTINSIFGERKVS 58
Score = 32.7 bits (75), Expect = 0.33
Identities = 15/28 (53%), Positives = 17/28 (60%)
Query: 310 SVPILVLGLDNAGKSSIIKRILGEPIIS 337
S+ ILVLG GKSS I I GE +S
Sbjct: 31 SLTILVLGKTGVGKSSTINSIFGERKVS 58
>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 = 32.5 bits (75), Expect = 0.34
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 7/70 (10%)
Query: 199 ILVLGLDNAGKSSIIKRILGEPI--ISLVPTVGFNRARVEYGNKYEVFLYD---LGGSED 253
+ V+G +AGKS+++ +LGE + + PT + YG V L D L + +
Sbjct: 3 LAVVGEFSAGKSTLLNALLGEEVLPTGVTPTTA-VITVLRYGLLKGVVLVDTPGLNSTIE 61
Query: 254 FRTIW-KQYL 262
T + +L
Sbjct: 62 HHTEITESFL 71
Score = 32.5 bits (75), Expect = 0.34
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 7/70 (10%)
Query: 313 ILVLGLDNAGKSSIIKRILGEPI--ISLVPTVGFNRARVEYGNKYEVFLYD---LGGSED 367
+ V+G +AGKS+++ +LGE + + PT + YG V L D L + +
Sbjct: 3 LAVVGEFSAGKSTLLNALLGEEVLPTGVTPTTA-VITVLRYGLLKGVVLVDTPGLNSTIE 61
Query: 368 FRTIW-KQYL 376
T + +L
Sbjct: 62 HHTEITESFL 71
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 32.1 bits (74), Expect = 0.64
Identities = 10/27 (37%), Positives = 20/27 (74%)
Query: 195 RSVPILVLGLDNAGKSSIIKRILGEPI 221
R++ +++G+ N GKS++I R+ G+ I
Sbjct: 120 RAIRAMIIGIPNVGKSTLINRLAGKKI 146
Score = 32.1 bits (74), Expect = 0.64
Identities = 10/27 (37%), Positives = 20/27 (74%)
Query: 309 RSVPILVLGLDNAGKSSIIKRILGEPI 335
R++ +++G+ N GKS++I R+ G+ I
Sbjct: 120 RAIRAMIIGIPNVGKSTLINRLAGKKI 146
>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 = 31.0 bits (71), Expect = 1.0
Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 3/59 (5%)
Query: 199 ILVLGLDNAGKSSI-IKRILGEPIISLVPTVGFNR-ARVEYGNK-YEVFLYDLGGSEDF 254
I+V+G GK+ + I + VPTV N A V K + L+D G E++
Sbjct: 3 IVVVGDGAVGKTCLLISYTTNKFPTEYVPTVFDNYSANVTVDGKQVNLGLWDTAGQEEY 61
Score = 31.0 bits (71), Expect = 1.0
Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 3/59 (5%)
Query: 313 ILVLGLDNAGKSSI-IKRILGEPIISLVPTVGFNR-ARVEYGNK-YEVFLYDLGGSEDF 368
I+V+G GK+ + I + VPTV N A V K + L+D G E++
Sbjct: 3 IVVVGDGAVGKTCLLISYTTNKFPTEYVPTVFDNYSANVTVDGKQVNLGLWDTAGQEEY 61
>gnl|CDD|215874 pfam00350, Dynamin_N, Dynamin family.
Length = 168
Score = 30.7 bits (70), Expect = 1.1
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 199 ILVLGLDNAGKSSIIKRILGEPI 221
I V+G +AGKSS++ +LG I
Sbjct: 1 IAVVGDQSAGKSSVLNALLGRDI 23
Score = 30.7 bits (70), Expect = 1.1
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 313 ILVLGLDNAGKSSIIKRILGEPI 335
I V+G +AGKSS++ +LG I
Sbjct: 1 IAVVGDQSAGKSSVLNALLGRDI 23
>gnl|CDD|130064 TIGR00991, 3a0901s02IAP34, GTP-binding protein (Chloroplast
Envelope Protein Translocase). [Transport and binding
proteins, Nucleosides, purines and pyrimidines].
Length = 313
Score = 31.4 bits (71), Expect = 1.2
Identities = 14/34 (41%), Positives = 20/34 (58%)
Query: 193 DFRSVPILVLGLDNAGKSSIIKRILGEPIISLVP 226
D S+ ILV+G GKSS + I+GE I ++
Sbjct: 35 DVSSLTILVMGKGGVGKSSTVNSIIGERIATVSA 68
Score = 31.4 bits (71), Expect = 1.2
Identities = 14/34 (41%), Positives = 20/34 (58%)
Query: 307 DFRSVPILVLGLDNAGKSSIIKRILGEPIISLVP 340
D S+ ILV+G GKSS + I+GE I ++
Sbjct: 35 DVSSLTILVMGKGGVGKSSTVNSIIGERIATVSA 68
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 31.7 bits (72), Expect = 1.3
Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 3/57 (5%)
Query: 199 ILVLGLDNAGKSSIIKRILGEPIISLVPTVGFNRARVEYGNKY---EVFLYDLGGSE 252
+ ++G N GKS+++ RILG + T G R RV Y ++ + L D GG E
Sbjct: 278 VAIVGRPNVGKSTLVNRILGRREAVVEDTPGVTRDRVSYDAEWAGTDFKLVDTGGWE 334
Score = 31.7 bits (72), Expect = 1.3
Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 3/57 (5%)
Query: 313 ILVLGLDNAGKSSIIKRILGEPIISLVPTVGFNRARVEYGNKY---EVFLYDLGGSE 366
+ ++G N GKS+++ RILG + T G R RV Y ++ + L D GG E
Sbjct: 278 VAIVGRPNVGKSTLVNRILGRREAVVEDTPGVTRDRVSYDAEWAGTDFKLVDTGGWE 334
>gnl|CDD|206748 cd01855, YqeH, Circularly permuted YqeH GTPase. YqeH is an
essential GTP-binding protein. Depletion of YqeH induces
an excess initiation of DNA replication, suggesting that
it negatively controls initiation of chromosome
replication. The YqeH subfamily is common in eukaryotes
and sporadically present in bacteria with probable
acquisition by plants from chloroplasts. Proteins of the
YqeH family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases.
Length = 191
Score = 30.7 bits (70), Expect = 1.4
Identities = 16/67 (23%), Positives = 26/67 (38%), Gaps = 19/67 (28%)
Query: 199 ILVLGLDNAGKSSIIKRILGE-------------PIISLVP--TVGFNRARVEYGNKYEV 243
+ V+G N GKS++I +L +S +P T+G ++
Sbjct: 128 VYVVGATNVGKSTLINALLKSNGGKVQAQALVQRLTVSPIPGTTLGL----IKIPLGEGK 183
Query: 244 FLYDLGG 250
LYD G
Sbjct: 184 KLYDTPG 190
Score = 30.7 bits (70), Expect = 1.4
Identities = 16/67 (23%), Positives = 26/67 (38%), Gaps = 19/67 (28%)
Query: 313 ILVLGLDNAGKSSIIKRILGE-------------PIISLVP--TVGFNRARVEYGNKYEV 357
+ V+G N GKS++I +L +S +P T+G ++
Sbjct: 128 VYVVGATNVGKSTLINALLKSNGGKVQAQALVQRLTVSPIPGTTLGL----IKIPLGEGK 183
Query: 358 FLYDLGG 364
LYD G
Sbjct: 184 KLYDTPG 190
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 31.2 bits (72), Expect = 1.6
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 206 NAGKSSIIKRILGE 219
N GKSS+I +LGE
Sbjct: 183 NVGKSSLINALLGE 196
Score = 31.2 bits (72), Expect = 1.6
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 320 NAGKSSIIKRILGE 333
N GKSS+I +LGE
Sbjct: 183 NVGKSSLINALLGE 196
>gnl|CDD|177947 PLN02313, PLN02313, Pectinesterase/pectinesterase inhibitor.
Length = 587
Score = 31.2 bits (70), Expect = 1.7
Identities = 29/105 (27%), Positives = 50/105 (47%), Gaps = 22/105 (20%)
Query: 427 ETNISNFQIKNSSENLQDNNTSDNHDSKKKQPRKRKKKVAPLNTDD-ETELSLPPLRLLG 485
ET+I+NF++++ S + +NN RK K+ L+++ T LS+ RLL
Sbjct: 221 ETDIANFELRDKSSSFTNNNN-----------RKLKEVTGDLDSEGWPTWLSVGDRRLLQ 269
Query: 486 RNVTHTDSNQEQRCLNLSSDPLGTGAFNVLHAIATDAARRNPNQR 530
+ D+ +++D G+G F + A A AA N+R
Sbjct: 270 GSTIKADA-------TVAAD--GSGDFTTV-AAAVAAAPEKSNKR 304
>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 = 30.6 bits (70), Expect = 1.8
Identities = 16/60 (26%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 199 ILVLGLDNAGKSSIIKRI----LGEPIISLVPTVGFNRARVEYGNKYEVFLYDLGGSEDF 254
+L++GL +GKSS+ I + L T+ ++ V + + L+D G +DF
Sbjct: 2 VLLMGLRGSGKSSMRSIIFSNYSPRDTLRLGATIDVEQSHVRFLGNLTLNLWDCPGQDDF 61
Score = 30.6 bits (70), Expect = 1.8
Identities = 16/60 (26%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 313 ILVLGLDNAGKSSIIKRI----LGEPIISLVPTVGFNRARVEYGNKYEVFLYDLGGSEDF 368
+L++GL +GKSS+ I + L T+ ++ V + + L+D G +DF
Sbjct: 2 VLLMGLRGSGKSSMRSIIFSNYSPRDTLRLGATIDVEQSHVRFLGNLTLNLWDCPGQDDF 61
>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 = 29.9 bits (67), Expect = 2.4
Identities = 22/89 (24%), Positives = 43/89 (48%), Gaps = 5/89 (5%)
Query: 313 ILVLGLDNAGKSSIIKRI---LGEPIISLVPTVGFNRARVEYGN-KYEVFLYDLGGSEDF 368
I+++G GK+ +++R L P V F VE K ++ ++D G E F
Sbjct: 10 IVLIGNAGVGKTCLVRRFTQGLFPPGQGATIGVDFMIKTVEIKGEKIKLQIWDTAGQERF 69
Query: 369 RTIWKQYLGTVSQTLLVSHSLSGRPDDRC 397
R+I + Y + + L++++ ++ RC
Sbjct: 70 RSITQSYYRS-ANALILTYDITCEESFRC 97
>gnl|CDD|215521 PLN02967, PLN02967, kinase.
Length = 581
Score = 30.4 bits (68), Expect = 2.5
Identities = 17/87 (19%), Positives = 35/87 (40%), Gaps = 3/87 (3%)
Query: 411 ISAKNLSNGFKKSERDETNISNFQIKNSSENLQDNNTSDNHDSKKKQPRKRKKKVAPLNT 470
+S K + K++ + + ++ SE + N + KK PR+ ++K A ++
Sbjct: 68 VSKKKPTRSVKRATKKTVVEISEPLEEGSELVV-NEDAALDKESKKTPRRTRRKAAAASS 126
Query: 471 DDETELSLPPLRLLGRNVTHTDSNQEQ 497
D E E + +R R +
Sbjct: 127 DVEEEKTEKKVR--KRRKVKKMDEDVE 151
>gnl|CDD|178164 PLN02549, PLN02549, asparagine synthase (glutamine-hydrolyzing).
Length = 578
Score = 30.5 bits (69), Expect = 2.6
Identities = 24/74 (32%), Positives = 33/74 (44%), Gaps = 16/74 (21%)
Query: 197 VPILVL---GLDNAGKSSIIKRILGEPIISLVPTVGFNRARVEYGNKYEVFLYDLGGSED 253
VP VL GLD++ +SI R L E +A ++G + F L GS D
Sbjct: 226 VPFGVLLSGGLDSSLVASIAARHLAE-----------TKAARQWGQQLHSFCVGLEGSPD 274
Query: 254 FRTIWK--QYLGTV 265
+ + YLGTV
Sbjct: 275 LKAAREVADYLGTV 288
Score = 30.5 bits (69), Expect = 2.6
Identities = 24/74 (32%), Positives = 33/74 (44%), Gaps = 16/74 (21%)
Query: 311 VPILVL---GLDNAGKSSIIKRILGEPIISLVPTVGFNRARVEYGNKYEVFLYDLGGSED 367
VP VL GLD++ +SI R L E +A ++G + F L GS D
Sbjct: 226 VPFGVLLSGGLDSSLVASIAARHLAE-----------TKAARQWGQQLHSFCVGLEGSPD 274
Query: 368 FRTIWK--QYLGTV 379
+ + YLGTV
Sbjct: 275 LKAAREVADYLGTV 288
>gnl|CDD|133306 cd04106, Rab23_like, Rab GTPase family 23 (Rab23)-like. Rab23-like
subfamily. Rab23 is a member of the Rab family of small
GTPases. In mouse, Rab23 has been shown to function as a
negative regulator in the sonic hedgehog (Shh) signaling
pathway. Rab23 mediates the activity of Gli2 and Gli3,
transcription factors that regulate Shh signaling in the
spinal cord, primarily by preventing Gli2 activation in
the absence of Shh ligand. Rab23 also regulates a step
in the cytoplasmic signal transduction pathway that
mediates the effect of Smoothened (one of two integral
membrane proteins that are essential components of the
Shh signaling pathway in vertebrates). In humans, Rab23
is expressed in the retina. Mice contain an isoform that
shares 93% sequence identity with the human Rab23 and an
alternative splicing isoform that is specific to the
brain. This isoform causes the murine open brain
phenotype, indicating it may have a role in the
development of the central nervous system. 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 = 162
Score = 29.3 bits (66), Expect = 2.9
Identities = 23/81 (28%), Positives = 38/81 (46%), Gaps = 6/81 (7%)
Query: 311 VPILVLGLDNAGKSSIIKR-ILGEPIISLVPTVG--FNRARV---EYGNKYEVFLYDLGG 364
+ ++V+G N GKSS+I+R + G T+G F ++ + + L+D G
Sbjct: 1 IKVIVVGNGNVGKSSMIQRFVKGIFTKDYKKTIGVDFLEKQIFLRQSDEDVRLMLWDTAG 60
Query: 365 SEDFRTIWKQYLGTVSQTLLV 385
E+F I K Y +LV
Sbjct: 61 QEEFDAITKAYYRGAQACILV 81
Score = 29.3 bits (66), Expect = 3.1
Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 6/71 (8%)
Query: 197 VPILVLGLDNAGKSSIIKR-ILGEPIISLVPTVG--FNRARV---EYGNKYEVFLYDLGG 250
+ ++V+G N GKSS+I+R + G T+G F ++ + + L+D G
Sbjct: 1 IKVIVVGNGNVGKSSMIQRFVKGIFTKDYKKTIGVDFLEKQIFLRQSDEDVRLMLWDTAG 60
Query: 251 SEDFRTIWKQY 261
E+F I K Y
Sbjct: 61 QEEFDAITKAY 71
>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 = 30.2 bits (69), Expect = 3.0
Identities = 12/27 (44%), Positives = 18/27 (66%), Gaps = 1/27 (3%)
Query: 199 ILVLGLDNAGKSSIIKRILGEPIISLV 225
I + G NAGKSS+I + G+ I++V
Sbjct: 9 IGIFGRRNAGKSSLINALTGQD-IAIV 34
Score = 30.2 bits (69), Expect = 3.0
Identities = 12/27 (44%), Positives = 18/27 (66%), Gaps = 1/27 (3%)
Query: 313 ILVLGLDNAGKSSIIKRILGEPIISLV 339
I + G NAGKSS+I + G+ I++V
Sbjct: 9 IGIFGRRNAGKSSLINALTGQD-IAIV 34
>gnl|CDD|206682 cd01895, EngA2, EngA2 GTPase contains the second domain of EngA.
This EngA2 subfamily CD represents the second GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. 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. Although the exact function of
these proteins has not been elucidated, studies have
revealed that the E. coli EngA homolog, Der, and
Neisseria gonorrhoeae EngA are essential for cell
viability. A recent report suggests that E. coli Der
functions in ribosome assembly and stability.
Length = 174
Score = 29.3 bits (67), Expect = 3.1
Identities = 8/14 (57%), Positives = 11/14 (78%)
Query: 206 NAGKSSIIKRILGE 219
N GKSS++ +LGE
Sbjct: 12 NVGKSSLLNALLGE 25
Score = 29.3 bits (67), Expect = 3.1
Identities = 8/14 (57%), Positives = 11/14 (78%)
Query: 320 NAGKSSIIKRILGE 333
N GKSS++ +LGE
Sbjct: 12 NVGKSSLLNALLGE 25
>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 = 29.8 bits (68), Expect = 3.2
Identities = 9/24 (37%), Positives = 17/24 (70%)
Query: 195 RSVPILVLGLDNAGKSSIIKRILG 218
R + +++G+ N GKS++I R+ G
Sbjct: 117 RPIRAMIVGIPNVGKSTLINRLAG 140
Score = 29.8 bits (68), Expect = 3.2
Identities = 9/24 (37%), Positives = 17/24 (70%)
Query: 309 RSVPILVLGLDNAGKSSIIKRILG 332
R + +++G+ N GKS++I R+ G
Sbjct: 117 RPIRAMIVGIPNVGKSTLINRLAG 140
>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 = 3.3
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 195 RSVPILVLGLDNAGKSSIIKRILG 218
R + +V+G+ N GKS++I R+ G
Sbjct: 114 RPLRAMVVGIPNVGKSTLINRLRG 137
Score = 29.4 bits (67), Expect = 3.3
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 309 RSVPILVLGLDNAGKSSIIKRILG 332
R + +V+G+ N GKS++I R+ G
Sbjct: 114 RPLRAMVVGIPNVGKSTLINRLRG 137
>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 = 3.5
Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 4/67 (5%)
Query: 199 ILVLGLDNAGKSSIIKRIL-GEPIISLVPTVG--FNRARVEY-GNKYEVFLYDLGGSEDF 254
I+++G GKSS++ R G+ T+G F +E G + ++ ++D G E F
Sbjct: 3 IILIGDSGVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIEVDGKRVKLQIWDTAGQERF 62
Query: 255 RTIWKQY 261
R+I Y
Sbjct: 63 RSITSSY 69
Score = 29.0 bits (66), Expect = 3.5
Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 4/67 (5%)
Query: 313 ILVLGLDNAGKSSIIKRIL-GEPIISLVPTVG--FNRARVEY-GNKYEVFLYDLGGSEDF 368
I+++G GKSS++ R G+ T+G F +E G + ++ ++D G E F
Sbjct: 3 IILIGDSGVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIEVDGKRVKLQIWDTAGQERF 62
Query: 369 RTIWKQY 375
R+I Y
Sbjct: 63 RSITSSY 69
>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 = 29.2 bits (66), Expect = 3.7
Identities = 22/84 (26%), Positives = 37/84 (44%), Gaps = 14/84 (16%)
Query: 311 VPILVLGLDNAGKSSIIKRILGEPIIS-LVPTVGFNRARVEYGNK--------YEVFLYD 361
+ ++ +G GKS IIKR +S +PT+G ++YG K V +D
Sbjct: 1 IKVISMGNSGVGKSCIIKRYCEGRFVSKYLPTIG-----IDYGVKKVSVRNKEVRVNFFD 55
Query: 362 LGGSEDFRTIWKQYLGTVSQTLLV 385
L G ++ + ++ LLV
Sbjct: 56 LSGHPEYLEVRNEFYKDTQGVLLV 79
Score = 28.1 bits (63), Expect = 8.1
Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 14/70 (20%)
Query: 197 VPILVLGLDNAGKSSIIKRILGEPIIS-LVPTVGFNRARVEYGNK--------YEVFLYD 247
+ ++ +G GKS IIKR +S +PT+G ++YG K V +D
Sbjct: 1 IKVISMGNSGVGKSCIIKRYCEGRFVSKYLPTIG-----IDYGVKKVSVRNKEVRVNFFD 55
Query: 248 LGGSEDFRTI 257
L G ++ +
Sbjct: 56 LSGHPEYLEV 65
>gnl|CDD|233224 TIGR00993, 3a0901s04IAP86, chloroplast protein import component
Toc86/159, G and M domains. The long precursor of the
86K protein originally described is proposed to have
three domains. The N-terminal A-domain is acidic,
repetitive, weakly conserved, readily removed by
proteolysis during chloroplast isolation, and not
required for protein translocation. The other domains
are designated G (GTPase) and M (membrane anchor); this
family includes most of the G domain and all of M
[Transport and binding proteins, Amino acids, peptides
and amines].
Length = 763
Score = 29.9 bits (67), Expect = 4.1
Identities = 16/32 (50%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 192 FDFRSVPILVLGLDNAGKSSIIKRILGEPIIS 223
DF S+ ILVLG GKS+ I I GE S
Sbjct: 115 LDF-SLNILVLGKSGVGKSATINSIFGEVKFS 145
>gnl|CDD|227578 COG5253, MSS4, Phosphatidylinositol-4-phosphate 5-kinase [Signal
transduction mechanisms].
Length = 612
Score = 29.9 bits (67), Expect = 4.4
Identities = 14/87 (16%), Positives = 28/87 (32%), Gaps = 5/87 (5%)
Query: 421 KKSERDETNISNFQIKNSSENLQDNNTSDNHDSKKKQPRKRKKKVAPLNTDDETELSLPP 480
KS R N + +S L + ++ ++ +K + D LS
Sbjct: 19 DKSTR--PNDRSMSNDSSLCGLNQASDANGNEYSPNNKVSKKDTFSDQLHD---ALSKEF 73
Query: 481 LRLLGRNVTHTDSNQEQRCLNLSSDPL 507
R+ + + Q +S P+
Sbjct: 74 TLERERDRLQLNKRKYQAIRLQTSTPI 100
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 29.5 bits (67), Expect = 4.8
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 199 ILVLGLDNAGKSSIIKRILGE 219
I ++G N GKSS+I ILGE
Sbjct: 181 IAIIGRPNVGKSSLINAILGE 201
Score = 29.5 bits (67), Expect = 4.8
Identities = 12/21 (57%), Positives = 15/21 (71%)
Query: 313 ILVLGLDNAGKSSIIKRILGE 333
I ++G N GKSS+I ILGE
Sbjct: 181 IAIIGRPNVGKSSLINAILGE 201
>gnl|CDD|234274 TIGR03594, GTPase_EngA, ribosome-associated GTPase EngA. EngA
(YfgK, Der) is a ribosome-associated essential GTPase
with a duplication of its GTP-binding domain. It is
broadly to universally distributed among bacteria. It
appears to function in ribosome biogenesis or stability
[Protein synthesis, Other].
Length = 429
Score = 29.3 bits (67), Expect = 4.9
Identities = 7/14 (50%), Positives = 11/14 (78%)
Query: 206 NAGKSSIIKRILGE 219
N GKS+++ +LGE
Sbjct: 182 NVGKSTLVNALLGE 195
Score = 29.3 bits (67), Expect = 4.9
Identities = 7/14 (50%), Positives = 11/14 (78%)
Query: 320 NAGKSSIIKRILGE 333
N GKS+++ +LGE
Sbjct: 182 NVGKSTLVNALLGE 195
>gnl|CDD|206696 cd04113, Rab4, Rab GTPase family 4 (Rab4). Rab4 subfamily. Rab4
has been implicated in numerous functions within the
cell. It helps regulate endocytosis through the sorting,
recycling, and degradation of early endosomes. Mammalian
Rab4 is involved in the regulation of many surface
proteins including G-protein-coupled receptors,
transferrin receptor, integrins, and surfactant protein
A. Experimental data implicate Rab4 in regulation of the
recycling of internalized receptors back to the plasma
membrane. It is also believed to influence
receptor-mediated antigen processing in B-lymphocytes,
in calcium-dependent exocytosis in platelets, in
alpha-amylase secretion in pancreatic cells, and in
insulin-induced translocation of Glut4 from internal
vesicles to the cell surface. Rab4 is known to share
effector proteins with Rab5 and Rab11. 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 = 28.6 bits (64), Expect = 5.6
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 4/76 (5%)
Query: 314 LVLGLDNAGKSSIIKRILGEPIISLVP-TVG--FNRARVEYGNKY-EVFLYDLGGSEDFR 369
L++G GKS ++ + + T+G F V G K ++ ++D G E FR
Sbjct: 4 LIIGSAGTGKSCLLHQFIENKFKQDSNHTIGVEFGSRVVNVGGKSVKLQIWDTAGQERFR 63
Query: 370 TIWKQYLGTVSQTLLV 385
++ + Y + LLV
Sbjct: 64 SVTRSYYRGAAGALLV 79
>gnl|CDD|133310 cd04110, Rab35, Rab GTPase family 35 (Rab35). Rab35 is one of
several Rab proteins to be found to participate in the
regulation of osteoclast cells in rats. In addition,
Rab35 has been identified as a protein that interacts
with nucleophosmin-anaplastic lymphoma kinase (NPM-ALK)
in human cells. Overexpression of NPM-ALK is a key
oncogenic event in some anaplastic large-cell lymphomas;
since Rab35 interacts with N|PM-ALK, it may provide a
target for cancer treatments. 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 = 199
Score = 28.7 bits (64), Expect = 5.6
Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 4/67 (5%)
Query: 199 ILVLGLDNAGKSSIIKRILGEPII-SLVPTVGFN---RARVEYGNKYEVFLYDLGGSEDF 254
+L++G GKSS++ R S + T+G + R G + ++ ++D G E F
Sbjct: 9 LLIIGDSGVGKSSLLLRFADNTFSGSYITTIGVDFKIRTVEINGERVKLQIWDTAGQERF 68
Query: 255 RTIWKQY 261
RTI Y
Sbjct: 69 RTITSTY 75
Score = 28.7 bits (64), Expect = 5.6
Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 4/67 (5%)
Query: 313 ILVLGLDNAGKSSIIKRILGEPII-SLVPTVGFN---RARVEYGNKYEVFLYDLGGSEDF 368
+L++G GKSS++ R S + T+G + R G + ++ ++D G E F
Sbjct: 9 LLIIGDSGVGKSSLLLRFADNTFSGSYITTIGVDFKIRTVEINGERVKLQIWDTAGQERF 68
Query: 369 RTIWKQY 375
RTI Y
Sbjct: 69 RTITSTY 75
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 28.7 bits (65), Expect = 7.2
Identities = 9/28 (32%), Positives = 19/28 (67%)
Query: 194 FRSVPILVLGLDNAGKSSIIKRILGEPI 221
F+S + ++G N GKS+++ ++G+ I
Sbjct: 4 FKSGFVAIIGRPNVGKSTLLNALVGQKI 31
Score = 28.7 bits (65), Expect = 7.2
Identities = 9/28 (32%), Positives = 19/28 (67%)
Query: 308 FRSVPILVLGLDNAGKSSIIKRILGEPI 335
F+S + ++G N GKS+++ ++G+ I
Sbjct: 4 FKSGFVAIIGRPNVGKSTLLNALVGQKI 31
>gnl|CDD|206685 cd01898, Obg, Obg GTPase. The Obg nucleotide binding protein
subfamily has been implicated in stress response,
chromosome partitioning, replication initiation,
mycelium development, and sporulation. Obg proteins are
among a large group of GTP binding proteins conserved
from bacteria to humans. The E. coli homolog, ObgE is
believed to function in ribosomal biogenesis. Members of
the subfamily contain two equally and highly conserved
domains, a C-terminal GTP binding domain and an
N-terminal glycine-rich domain.
Length = 170
Score = 28.2 bits (64), Expect = 7.6
Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 11/56 (19%)
Query: 202 LGLDNAGKSSIIKRILG-EPIIS------LVPTVGFNRARVEYGNKYEVFLYDLGG 250
+GL NAGKS+++ I +P I+ LVP +G V + + D+ G
Sbjct: 6 VGLPNAGKSTLLSAISNAKPKIADYPFTTLVPNLGV----VRVDDGRSFVIADIPG 57
Score = 28.2 bits (64), Expect = 7.6
Identities = 17/56 (30%), Positives = 27/56 (48%), Gaps = 11/56 (19%)
Query: 316 LGLDNAGKSSIIKRILG-EPIIS------LVPTVGFNRARVEYGNKYEVFLYDLGG 364
+GL NAGKS+++ I +P I+ LVP +G V + + D+ G
Sbjct: 6 VGLPNAGKSTLLSAISNAKPKIADYPFTTLVPNLGV----VRVDDGRSFVIADIPG 57
>gnl|CDD|206698 cd04117, Rab15, Rab GTPase family 15 (Rab15). Rab15 colocalizes
with the transferrin receptor in early endosome
compartments, but not with late endosomal markers. It
codistributes with Rab4 and Rab5 on early/sorting
endosomes, and with Rab11 on pericentriolar recycling
endosomes. It is believed to function as an inhibitory
GTPase that regulates distinct steps in early endocytic
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 = 164
Score = 28.0 bits (62), Expect = 7.7
Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 4/67 (5%)
Query: 199 ILVLGLDNAGKSSIIKRIL-GEPIISLVPTVG--FNRARVEY-GNKYEVFLYDLGGSEDF 254
+L++G GK+ ++ R E S + T+G F +E G K + ++D G E +
Sbjct: 3 LLLIGDSGVGKTCLLCRFTDNEFHSSHISTIGVDFKMKTIEVDGIKVRIQIWDTAGQERY 62
Query: 255 RTIWKQY 261
+TI KQY
Sbjct: 63 QTITKQY 69
Score = 28.0 bits (62), Expect = 7.7
Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 4/67 (5%)
Query: 313 ILVLGLDNAGKSSIIKRIL-GEPIISLVPTVG--FNRARVEY-GNKYEVFLYDLGGSEDF 368
+L++G GK+ ++ R E S + T+G F +E G K + ++D G E +
Sbjct: 3 LLLIGDSGVGKTCLLCRFTDNEFHSSHISTIGVDFKMKTIEVDGIKVRIQIWDTAGQERY 62
Query: 369 RTIWKQY 375
+TI KQY
Sbjct: 63 QTITKQY 69
>gnl|CDD|225748 COG3207, DIT1, Pyoverdine/dityrosine biosynthesis protein
[Secondary metabolites biosynthesis, transport, and
catabolism].
Length = 330
Score = 28.4 bits (63), Expect = 9.1
Identities = 14/48 (29%), Positives = 18/48 (37%), Gaps = 5/48 (10%)
Query: 36 LKMNLEKFGGISKN--SSICATSYKV---HIICRIRTFANSIEPIEMV 78
LK L +N S+ + RIR F + EPIE V
Sbjct: 14 LKELLLYRRFYPENRQSASENDEINRGEQVQLPRIRAFIEAGEPIEFV 61
>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 = 27.4 bits (61), Expect = 9.7
Identities = 18/77 (23%), Positives = 36/77 (46%), Gaps = 4/77 (5%)
Query: 313 ILVLGLDNAGKSSIIKRILG-EPIISLVPTVGFNRARVEY---GNKYEVFLYDLGGSEDF 368
++V+G +GKSS++ +++G E + G A G+ + ++D GG E+
Sbjct: 2 VVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREEL 61
Query: 369 RTIWKQYLGTVSQTLLV 385
+ ++ LLV
Sbjct: 62 KFEHIIFMKWADAILLV 78
>gnl|CDD|116198 pfam07579, DUF1548, Domain of Unknown Function (DUF1548). This
family appears to be found only in a small family of
Chlamydia proteins.
Length = 135
Score = 27.3 bits (61), Expect = 9.8
Identities = 11/58 (18%), Positives = 23/58 (39%), Gaps = 12/58 (20%)
Query: 102 LQKNIHNIACKDMNMQNVPNFQTSSVLSD-------DPAPTFEVCIVSLLVHLMRGIL 152
+ + N D+ N+P + + ++S+ + I LL L+ GI+
Sbjct: 83 QKAALRNYLLDDLTAINLPETEHADIVSELFYDDNYELNRE---GIAYLL--LIMGII 135
>gnl|CDD|206680 cd01893, Miro1, Mitochondrial Rho family 1 (Miro1), N-terminal.
Miro1 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the N-terminal
GTPase domain of Miro proteins. These atypical Rho
GTPases have roles in mitochondrial homeostasis and
apoptosis. Most Rho proteins contain a lipid
modification site at the C-terminus; however, Miro is
one of few Rho subfamilies that lack this feature.
Length = 168
Score = 27.7 bits (62), Expect = 9.8
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 195 RSVPILVLGLDNAGKSSIIKRILGEPIISLVPTV 228
+ V I+++G + GKSS+I ++ E VP V
Sbjct: 1 KDVRIVLIGDEGVGKSSLIMSLVSEEFPENVPRV 34
Score = 27.7 bits (62), Expect = 9.8
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 309 RSVPILVLGLDNAGKSSIIKRILGEPIISLVPTV 342
+ V I+++G + GKSS+I ++ E VP V
Sbjct: 1 KDVRIVLIGDEGVGKSSLIMSLVSEEFPENVPRV 34
>gnl|CDD|185405 PTZ00029, PTZ00029, 60S ribosomal protein L10a; Provisional.
Length = 216
Score = 28.2 bits (63), Expect = 9.9
Identities = 31/107 (28%), Positives = 46/107 (42%), Gaps = 15/107 (14%)
Query: 109 IACKDMNMQNVPNFQTSSVLSDDPAPTFEVCIVSLLVHLMR----GI-LMGIQNVPNFQT 163
I KD + Q F S L + P P +VC++ VH G+ M I+ + F
Sbjct: 35 IGLKDYDTQKDKRFSGSVKLPNVPKPNLKVCVLGDAVHCDEAKKLGLDFMDIEGLKKFNK 94
Query: 164 SSVLSDDPAPTFENFLDLRVLLPTHLSLFDFRSVPILV-LGLDNAGK 209
+ L A ++ FL + LLP +P L+ GL+ AGK
Sbjct: 95 NKKLVKKLAKKYDAFLASQSLLP---------QIPRLLGPGLNKAGK 132
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
0.320 0.137 0.406
Gapped
Lambda K H
0.267 0.0585 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 26,843,062
Number of extensions: 2595083
Number of successful extensions: 2533
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2459
Number of HSP's successfully gapped: 174
Length of query: 537
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 435
Effective length of database: 6,413,494
Effective search space: 2789869890
Effective search space used: 2789869890
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 (21.8 bits)
S2: 61 (27.6 bits)