RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13568
(485 letters)
>gnl|CDD|206744 cd11384, RagA_like, Rag GTPase, subfamily of Ras-related GTPases,
includes Ras-related GTP-binding proteins A and B. RagA
and RagB are closely related Rag GTPases (ras-related
GTP-binding protein A and B) that constitute a unique
subgroup of the Ras superfamily, and are functional
homologs of Saccharomyces cerevisiae Gtr1. These domains
function by forming heterodimers with RagC or RagD, and
similarly, Gtr1 dimerizes with Gtr2, through the
carboxy-terminal segments. They play an essential role
in regulating amino acid-induced target of rapamycin
complex 1 (TORC1) kinase signaling, exocytic cargo
sorting at endosomes, and epigenetic control of gene
expression. In response to amino acids, the Rag GTPases
guide the TORC1 complex to activate the platform
containing Rheb proto-oncogene by driving the
relocalization of mTORC1 from discrete locations in the
cytoplasm to a late endosomal and/or lysosomal
compartment that is Rheb-enriched and contains Rab-7.
Length = 286
Score = 302 bits (777), Expect = e-100
Identities = 128/202 (63%), Positives = 148/202 (73%), Gaps = 34/202 (16%)
Query: 31 LEVEHSHVRFLGNLVLNLWDCGGQEAFMENYFTSQRDNIFRNVAVLIYVFDVESRELDRD 90
++VEHSHVRFLGNLVLNLWDCGGQ+AFMENYFTSQRD+IFRNV VLIYVFDVESREL++D
Sbjct: 35 IDVEHSHVRFLGNLVLNLWDCGGQDAFMENYFTSQRDHIFRNVEVLIYVFDVESRELEKD 94
Query: 91 LHYYQSCLEAMLHNSPDSKVFCLIHKIDLVHENQRDV----------------------- 127
L Y++SCLEA+ NSPD+KVF LIHK+DLV E++R+
Sbjct: 95 LTYFRSCLEALRQNSPDAKVFVLIHKMDLVQEDEREAVFERKEKELRRLSEPLEVTCFPT 154
Query: 128 ---------AWSSIVYQLIPNVKELEQSLHLFATLMDGDEVLLFERATFLVISHCQRKE- 177
AWSSIVY LIPN++ LE +L FA + + DEV+LFERATFLVISH RKE
Sbjct: 155 SIWDETLYKAWSSIVYSLIPNIQVLESNLKKFADICEADEVVLFERATFLVISHSSRKEA 214
Query: 178 -HRDIHRFEKISNIIKQFKLSC 198
D HRFEKISNIIKQFKLSC
Sbjct: 215 SALDPHRFEKISNIIKQFKLSC 236
Score = 59.9 bits (146), Expect = 5e-10
Identities = 24/30 (80%), Positives = 29/30 (96%)
Query: 1 MEVRNSQFAAFIDEFTSNTFVMVVISDPNI 30
MEVRNS F+AFIDEFTSNT++MVV+SDP+I
Sbjct: 246 MEVRNSNFSAFIDEFTSNTYIMVVMSDPSI 275
>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 = 209 bits (534), Expect = 5e-65
Identities = 90/195 (46%), Positives = 112/195 (57%), Gaps = 35/195 (17%)
Query: 32 EVEHSHVRFLGNLVLNLWDCGGQEAFMENYFTSQRDNIFRNVAVLIYVFDVESRELDRDL 91
+VE SHVRFLGNL LNLWDC GQ+ FMENY T Q+++IF NV VLIYVFDVESRE + DL
Sbjct: 36 DVEQSHVRFLGNLTLNLWDCPGQDDFMENYLTRQKEHIFSNVGVLIYVFDVESREYEEDL 95
Query: 92 HYYQSCLEAMLHNSPDSKVFCLIHKIDLVHENQRDV------------------------ 127
+EA+ SP++KVF LIHK+DL+ E++R
Sbjct: 96 ATLVKIIEALYQYSPNAKVFVLIHKMDLLSEDERKEIFEDRKEEIIEEIEDFGIEDLTFF 155
Query: 128 -----------AWSSIVYQLIPNVKELEQSLHLFATLMDGDEVLLFERATFLVISHCQRK 176
AWS IV +LIPN+ LE L + + +EV LFER+TFLVI+ R
Sbjct: 156 LTSIWDHSLYKAWSKIVQKLIPNLSTLENLLKKLGSSSNAEEVFLFERSTFLVIATDSRS 215
Query: 177 EHRDIHRFEKISNII 191
R+EK SNII
Sbjct: 216 PVDIPQRYEKCSNII 230
>gnl|CDD|206742 cd09915, Rag, Rag GTPase subfamily of Ras-related GTPases. Rag
GTPases (ras-related GTP-binding proteins) constitute a
unique subgroup of the Ras superfamily, playing an
essential role in regulating amino acid-induced target
of rapamycin complex 1 (TORC1) kinase signaling,
exocytic cargo sorting at endosomes, and epigenetic
control of gene expression. This subfamily consists of
RagA and RagB as well as RagC and RagD that are closely
related. Saccharomyces cerevisiae encodes single
orthologs of metazoan RagA/B and RagC/D, Gtr1 and Gtr2,
respectively. Dimer formation is important for their
cellular function; these domains form heterodimers, as
RagA or RagB dimerizes with RagC or RagD, and similarly,
Gtr1 dimerizes with Gtr2. In response to amino acids,
the Rag GTPases guide the TORC1 complex to activate the
platform containing Rheb proto-oncogene by driving the
relocalization of mTORC1 from discrete locations in the
cytoplasm to a late endosomal and/or lysosomal
compartment that is Rheb-enriched and contains Rab-7.
Length = 175
Score = 81.1 bits (200), Expect = 6e-18
Identities = 38/94 (40%), Positives = 57/94 (60%), Gaps = 3/94 (3%)
Query: 32 EVEHSHVRFLGNLVLNLWDCGGQEAFMENYFTSQRDNIFRNVAVLIYVFDVESRELDRDL 91
+VEHSH+ FLGN LNLWDC GQ+ F E T +++IF+ V LIYV DV+ E + +
Sbjct: 36 DVEHSHLSFLGNXTLNLWDCPGQDVFFE--PTKDKEHIFQXVGALIYVIDVQD-EYLKAI 92
Query: 92 HYYQSCLEAMLHNSPDSKVFCLIHKIDLVHENQR 125
L+ +PD+ + LIHK+D + +++
Sbjct: 93 TILAKALKQAYKVNPDANIEVLIHKVDGLSLDKK 126
>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 = 40.9 bits (96), Expect = 6e-04
Identities = 41/114 (35%), Positives = 53/114 (46%), Gaps = 27/114 (23%)
Query: 25 ISDPNILEVEHSHVRFLGNLV---------LNLWDCGGQEAFMENYFTSQRDNIFRN-VA 74
+SDP + V F L+ L LWD GQE F S + +RN V
Sbjct: 30 VSDPTV------GVDFFSRLIEIEPGVRIKLQLWDTAGQER-----FRSITRSYYRNSVG 78
Query: 75 VLIYVFDVESRELDRDLHYYQSCLEAMLHNSPDSKVFCLI-HKIDLVHENQRDV 127
VL+ VFD+ +RE +H + EA H P VF L+ HK DL E+QR V
Sbjct: 79 VLL-VFDITNRESFEHVHDWLE--EARSHIQPHRPVFILVGHKCDL--ESQRQV 127
>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 = 39.0 bits (92), Expect = 0.001
Identities = 33/122 (27%), Positives = 52/122 (42%), Gaps = 27/122 (22%)
Query: 15 FTSNTFVMVVISDPNI--------LEVEHSHVRFLGNLVLNLWDCGGQEAFMENYFTSQR 66
FT N F P I +EV+ V+ L +WD GQE F + R
Sbjct: 19 FTQNKFPEE--YIPTIGVDFYTKTIEVDGKTVK------LQIWDTAGQERF-----RALR 65
Query: 67 DNIFRNVAVLIYVFDVESRELDRDLHYYQSCLEAMLHNSPDSKVFCLI-HKIDLVHENQR 125
+R + V+D+ SR+ + LE +L ++ ++ L+ +K DL E+QR
Sbjct: 66 PLYYRGAQGFLLVYDITSRD---SFENVKKWLEEILRHADENVPIVLVGNKCDL--EDQR 120
Query: 126 DV 127
V
Sbjct: 121 VV 122
>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 = 38.9 bits (91), Expect = 0.002
Identities = 28/97 (28%), Positives = 38/97 (39%), Gaps = 22/97 (22%)
Query: 29 NILEVEHSHVRFLGNLVLNLWDCGGQEA---FMENYFTSQRDNIFRNVAVLIYVFDVESR 85
NI V+ + LN+WD GGQ + NY F N VLIYV D R
Sbjct: 50 NIKNVQADGFK------LNVWDIGGQRKIRPYWRNY--------FENTDVLIYVIDSADR 95
Query: 86 ELDRDLHYYQSCLEAMLHNSPDSKVFCLI--HKIDLV 120
+ L +L + V L+ +K DL+
Sbjct: 96 ---KRFEEAGQELVELLEEEKLAGVPVLVFANKQDLL 129
>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 = 38.5 bits (90), Expect = 0.003
Identities = 19/81 (23%), Positives = 36/81 (44%), Gaps = 8/81 (9%)
Query: 44 LVLNLWDCGGQEAFMENYFTSQRDNIFRNVAVLIYVFDVESRELDRDLHYYQSCLEAMLH 103
+ LN+WD GGQE + + T Q + ++ + VFD+ + + + Y+ ++A
Sbjct: 51 IRLNVWDFGGQEIY---HATHQ--FFLTSRSLYLLVFDLRTGDEVSRVPYWLRQIKA--- 102
Query: 104 NSPDSKVFCLIHKIDLVHENQ 124
S V + ID +
Sbjct: 103 FGGVSPVILVGTHIDESCDED 123
>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 = 36.8 bits (86), Expect = 0.008
Identities = 28/130 (21%), Positives = 47/130 (36%), Gaps = 41/130 (31%)
Query: 29 NILEVEHSHVRFLGNLVLNLWDCGGQEAFM---ENYFTSQRDNIFRNVAVLIYVFDVESR 85
N+ VE+ +V+F +WD GGQ+ ++Y + N LI+V D R
Sbjct: 34 NVETVEYKNVKF------TVWDVGGQDKIRPLWKHY--------YENTDGLIFVVDSSDR 79
Query: 86 ELDRDLHYYQSC--LEAMLHNSP--DSKVFCLIHKIDLVHENQRDVAWSSIVYQLIPNVK 141
E ++ L +L+ + + L +K DL
Sbjct: 80 E-----RIEEAKNELHKLLNEEELKGAPLLILANKQDLPGAL---------------TES 119
Query: 142 ELEQSLHLFA 151
EL + L L +
Sbjct: 120 ELIELLGLES 129
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 36.4 bits (85), Expect = 0.014
Identities = 18/62 (29%), Positives = 25/62 (40%), Gaps = 17/62 (27%)
Query: 28 PNILEVEHSHVRFLGNLVLNLWDCGGQEAFMENYFTSQR---DNIFRNVAVLIYVFDVES 84
N+ V + N+ +WD GGQE S R N F N +I+V D
Sbjct: 48 FNVETVTY------KNVKFTVWDVGGQE--------SLRPLWRNYFPNTDAVIFVVDSAD 93
Query: 85 RE 86
R+
Sbjct: 94 RD 95
>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 = 35.5 bits (83), Expect = 0.021
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 9/82 (10%)
Query: 46 LNLWDCGGQEAFMENYFTSQRDNIFRNVAVLIYVFDVESRELDRDLHYYQSCLEAMLHNS 105
L +WD GQE F S + +R I V+DV +RE +L + + E +
Sbjct: 51 LQIWDTAGQERFR-----SITSSYYRGAHGAILVYDVTNRESFENLDKWLN--ELKEYAP 103
Query: 106 PDSKVFCLIHKIDLVHENQRDV 127
P+ + + +K DL E++R V
Sbjct: 104 PNIPIILVGNKSDL--EDERQV 123
>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 = 35.1 bits (81), Expect = 0.029
Identities = 22/115 (19%), Positives = 37/115 (32%), Gaps = 8/115 (6%)
Query: 27 DPNILEVEHSHVRFLGNLVLNLWDCGGQEAFMENYFTSQRDNIFRNVAVLIYVFDVESRE 86
DP++ E + L L D G + F + R +++ V D RE
Sbjct: 34 DPDVYVKELDKGKVK----LVLVDTPGLDEFGGLGREELARLLLRGADLILLVVDSTDRE 89
Query: 87 LDRDLHYYQSCLEAMLHNSPDSKVFCLIHKIDLVHENQRDVAWSSIVYQLIPNVK 141
+ D L + + +KIDL+ E + + I V
Sbjct: 90 SEEDAKL----LILRRLRKEGIPIILVGNKIDLLEEREVEELLRLEELAKILGVP 140
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 35.7 bits (82), Expect = 0.031
Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 9/77 (11%)
Query: 46 LNLWDCGGQEAFMENYFTSQRDNIFRNVAVLIYVFDVESRELDRDLHYYQSCLE-AMLHN 104
L +WD GQE+ F S + +R A + V+D+ RE ++ S LE A H
Sbjct: 57 LQIWDTAGQES-----FRSITRSYYRGAAGALLVYDITRRE---TFNHLASWLEDARQHA 108
Query: 105 SPDSKVFCLIHKIDLVH 121
+ + + + +K DL H
Sbjct: 109 NANMTIMLIGNKCDLAH 125
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 34.9 bits (80), Expect = 0.062
Identities = 38/152 (25%), Positives = 54/152 (35%), Gaps = 18/152 (11%)
Query: 13 DEFTSNTFVMVVISDPNILEVEHSHVRFLGNLVLNLWDCGGQEAFMENYFTSQRDNIFRN 72
DEF + DP + N+ L LWD GQE + S R +R
Sbjct: 28 DEFPEGYPPTIGNLDPAKTIEPYR-----RNIKLQLWDTAGQEEYR-----SLRPEYYRG 77
Query: 73 VAVLIYVFDVESRELDRDLHYYQSCLEAMLHNSPDSKVFCLI-HKIDLVHENQRDVAWSS 131
++ V+D RE + LE + +PD L+ +KIDL E SS
Sbjct: 78 ANGILIVYDSTLRE--SSDELTEEWLEELRELAPDDVPILLVGNKIDLFDE-----QSSS 130
Query: 132 IVYQLIPNVKELEQSLHLFATLMDGDEVLLFE 163
N + + L A L + L E
Sbjct: 131 EEILNQLNREVVLLVLAPKAVLPEVANPALLE 162
>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 = 33.9 bits (78), Expect = 0.085
Identities = 20/63 (31%), Positives = 28/63 (44%), Gaps = 8/63 (12%)
Query: 42 GNLVLNLWDCGGQEAFMENYFTSQRDNIFRNVAVLIYVFDVESRELDRDLHYYQSCLEAM 101
+L L +WD GGQE + N L+YV V+S + R L Q L+ +
Sbjct: 42 KHLSLTVWDVGGQEKMRTVW-----KCYLENTDGLVYV--VDSSDEAR-LDESQKELKHI 93
Query: 102 LHN 104
L N
Sbjct: 94 LKN 96
>gnl|CDD|206699 cd04120, Rab12, Rab GTPase family 12 (Rab12). Rab12 was first
identified in canine cells, where it was localized to
the Golgi complex. The specific function of Rab12
remains unknown, and inconsistent results about its
cellular localization have been reported. More recent
studies have identified Rab12 associated with post-Golgi
vesicles, or with other small vesicle-like structures
but not with the Golgi complex. 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. 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 = 202
Score = 33.8 bits (77), Expect = 0.13
Identities = 23/83 (27%), Positives = 42/83 (50%), Gaps = 9/83 (10%)
Query: 46 LNLWDCGGQEAFMENYFTSQRDNIFRNVAVLIYVFDVESRELDRDLHYYQSCLEAMLHNS 105
L +WD GQE F N TS +R+ +I V+D+ +E DL + ++ + S
Sbjct: 51 LQIWDTAGQERF--NSITSA---YYRSAKGIILVYDITKKETFDDLPKWMKMIDK--YAS 103
Query: 106 PDSKVFCLIHKIDLVHENQRDVA 128
D+++ + +K+D E R++
Sbjct: 104 EDAELLLVGNKLDC--ETDREIT 124
>gnl|CDD|206654 cd01861, Rab6, Rab GTPase family 6 (Rab6). Rab6 is involved in
microtubule-dependent transport pathways through the
Golgi and from endosomes to the Golgi. Rab6A of mammals
is implicated in retrograde transport through the Golgi
stack, and is also required for a slow,
COPI-independent, retrograde transport pathway from the
Golgi to the endoplasmic reticulum (ER). This pathway
may allow Golgi residents to be recycled through the ER
for scrutiny by ER quality-control systems. Yeast
Ypt6p, the homolog of the mammalian Rab6 GTPase, is not
essential for cell viability. Ypt6p acts in
endosome-to-Golgi, in intra-Golgi retrograde transport,
and possibly also in Golgi-to-ER trafficking. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 161
Score = 33.4 bits (77), Expect = 0.13
Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 11/44 (25%)
Query: 46 LNLWDCGGQEAF---MENYFTSQRDNIFRNVAVLIYVFDVESRE 86
L LWD GQE F + +Y R+ +V + V+D+ +R+
Sbjct: 51 LQLWDTAGQERFRSLIPSY--------IRDSSVAVVVYDITNRQ 86
>gnl|CDD|206653 cd01860, Rab5_related, Rab-related GTPase family includes Rab5 and
Rab22; regulates early endosome fusion. The
Rab5-related subfamily includes Rab5 and Rab22 of
mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of plants.
The members of this subfamily are involved in
endocytosis and endocytic-sorting pathways. In mammals,
Rab5 GTPases localize to early endosomes and regulate
fusion of clathrin-coated vesicles to early endosomes
and fusion between early endosomes. In yeast, Ypt51p
family members similarly regulate membrane trafficking
through prevacuolar compartments. 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 = 163
Score = 33.3 bits (77), Expect = 0.14
Identities = 22/83 (26%), Positives = 36/83 (43%), Gaps = 21/83 (25%)
Query: 49 WDCGGQEAF-----MENYFTSQRDNIFRNVAVLIYVFDVESRE-LDRDLHYYQSCLEAML 102
WD GQE + M Y+ R A I V+D+ S E ++ +S ++ +
Sbjct: 55 WDTAGQERYRSLAPM--YY--------RGAAAAIVVYDITSEESFEK----AKSWVKELQ 100
Query: 103 HNSPDSKVFCLI-HKIDLVHENQ 124
+ P + V L +K DL + Q
Sbjct: 101 EHGPPNIVIALAGNKADLESKRQ 123
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 33.5 bits (76), Expect = 0.17
Identities = 18/43 (41%), Positives = 23/43 (53%), Gaps = 5/43 (11%)
Query: 44 LVLNLWDCGGQEAFMENYFTSQRDNIFRNVAVLIYVFDVESRE 86
L L +WD GQE F TS + +RN +I V+DV RE
Sbjct: 62 LKLTIWDTAGQERF--RTLTS---SYYRNAQGIILVYDVTRRE 99
>gnl|CDD|133315 cd04115, Rab33B_Rab33A, Rab GTPase family 33 includes Rab33A and
Rab33B. Rab33B/Rab33A subfamily. Rab33B is
ubiquitously expressed in mouse tissues and cells,
where it is localized to the medial Golgi cisternae. It
colocalizes with alpha-mannose II. Together with the
other cisternal Rabs, Rab6A and Rab6A', it is believed
to regulate the Golgi response to stress and is likely
a molecular target in stress-activated signaling
pathways. Rab33A (previously known as S10) is expressed
primarily in the brain and immune system cells. In
humans, it is located on the X chromosome at Xq26 and
its expression is down-regulated in tuberculosis
patients. Experimental evidence suggests that Rab33A is
a novel CD8+ T cell factor that likely plays a role in
tuberculosis disease processes. 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 = 170
Score = 32.8 bits (75), Expect = 0.19
Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 4/49 (8%)
Query: 43 NLVLNLWDCGGQEAFMENYFTSQRDNIFRNVAVLIYVFDVESRELDRDL 91
+ + LWD GQE F + S + +RNV +++V+DV + L
Sbjct: 50 RIKVQLWDTAGQERFRK----SMVQHYYRNVHAVVFVYDVTNMASFHSL 94
>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 = 32.8 bits (75), Expect = 0.21
Identities = 22/77 (28%), Positives = 31/77 (40%), Gaps = 8/77 (10%)
Query: 46 LNLWDCGGQEAFMENYFTSQRDNIFRNVAVLIYVFDVESRELDRDLHYYQSCLEAMLHNS 105
L LWD GQE F + +R I VF RE + ++ +EA +
Sbjct: 53 LMLWDTAGQEE-----FDAITKAYYRGAQACILVFSTTDRESFEAIESWKEKVEAECGDI 107
Query: 106 PDSKVFCLIHKIDLVHE 122
P V KIDL+ +
Sbjct: 108 P--MVLVQ-TKIDLLDQ 121
>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 = 32.4 bits (74), Expect = 0.27
Identities = 26/85 (30%), Positives = 42/85 (49%), Gaps = 9/85 (10%)
Query: 43 NLVLNLWDCGGQEAFMENYFTSQRDNIFRNVAVLIYVFDVESRELDRDLHYYQSCLEAML 102
++ L +WD GQE F S + +R A + V+D+ SRE L + + +A
Sbjct: 48 SVKLQIWDTAGQER-----FRSVTRSYYRGAAGALLVYDITSRESFNALTNWLT--DART 100
Query: 103 HNSPDSKVFCLIHKIDLVHENQRDV 127
SPD + + +K DL E+ R+V
Sbjct: 101 LASPDIVIILVGNKKDL--EDDREV 123
>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 = 31.9 bits (73), Expect = 0.31
Identities = 16/46 (34%), Positives = 22/46 (47%), Gaps = 5/46 (10%)
Query: 41 LGNLVLNLWDCGGQEAFMENYFTSQRDNIFRNVAVLIYVFDVESRE 86
GN+ + +WD GGQ F S + R V ++YV D RE
Sbjct: 41 KGNVTIKVWDLGGQPR-----FRSMWERYCRGVNAIVYVVDAADRE 81
>gnl|CDD|133322 cd04122, Rab14, Rab GTPase family 14 (Rab14). Rab14 GTPases are
localized to biosynthetic compartments, including the
rough ER, the Golgi complex, and the trans-Golgi
network, and to endosomal compartments, including early
endosomal vacuoles and associated vesicles. Rab14 is
believed to function in both the biosynthetic and
recycling pathways between the Golgi and endosomal
compartments. Rab14 has also been identified on GLUT4
vesicles, and has been suggested to help regulate GLUT4
translocation. In addition, Rab14 is believed to play a
role in the regulation of phagocytosis. 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 = 166
Score = 31.3 bits (71), Expect = 0.51
Identities = 24/84 (28%), Positives = 41/84 (48%), Gaps = 9/84 (10%)
Query: 46 LNLWDCGGQEAFMENYFTSQRDNIFRNVAVLIYVFDVESRELDRDLHYYQSCLEAMLHNS 105
L +WD GQE F + + +R A + V+D+ R L + + +A +
Sbjct: 53 LQIWDTAGQER-----FRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLT--DARNLTN 105
Query: 106 PDSKVFCLIHKIDLVHENQRDVAW 129
P++ +F + +K DL E QRDV +
Sbjct: 106 PNTVIFLIGNKADL--EAQRDVTY 127
>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 = 31.3 bits (71), Expect = 0.59
Identities = 20/71 (28%), Positives = 32/71 (45%), Gaps = 21/71 (29%)
Query: 29 NILEVEHSHVRFLGNLVLNLWDCGGQE---AFMENYFTSQRDNIFRNVAVLIYVFDVESR 85
N+ V + +V+F N+WD GGQ+ +Y+T + LI+V D R
Sbjct: 44 NVETVTYKNVKF------NVWDVGGQDKIRPLWRHYYTGTQ--------GLIFVVDSADR 89
Query: 86 ----ELDRDLH 92
E ++LH
Sbjct: 90 DRIDEARQELH 100
>gnl|CDD|226407 COG3890, ERG8, Phosphomevalonate kinase [Lipid metabolism].
Length = 337
Score = 31.8 bits (72), Expect = 0.74
Identities = 32/197 (16%), Positives = 59/197 (29%), Gaps = 39/197 (19%)
Query: 56 AFMENYFTSQRDNIFRNVAVLIYVFDVESRELDRDLHY---------------YQSCLEA 100
F+ YF N F+N+ V + D L
Sbjct: 69 DFVFKYFAYLSQNCFQNLEVFADDAYYDQSNFFFDDGTKTGLGSSAAVATSLTCGLFLSH 128
Query: 101 MLHNSPDSKVFCLIHKIDLVHENQR--------DVA---WSSIVYQ-----LIPNVKELE 144
+ D K IHK+ + D+A + SI+Y+ LIP ++++
Sbjct: 129 ANATNVDEKG--EIHKLAQIAHCYAQGGIGSGFDIAAAIFGSIIYRRFEPGLIPKLRQIG 186
Query: 145 QSLHLFATLMDGDEVLLFERATFLVISHCQRKEHRDIHRFEKISNIIKQFKLSCRLVYSL 204
LM GD+ + V C+ + R+ E++ + L+
Sbjct: 187 AVNFGDYYLMMGDQ----AIGSETVGLVCKVNKWRNSILPEELKCNDEMNSRVLNLIKLS 242
Query: 205 FN--RDHFRLVYSLFNR 219
+ + + R
Sbjct: 243 LDESNSKSKAIRRSLRR 259
>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 = 30.1 bits (68), Expect = 0.81
Identities = 11/41 (26%), Positives = 19/41 (46%), Gaps = 5/41 (12%)
Query: 46 LNLWDCGGQEAFMENYFTSQRDNIFRNVAVLIYVFDVESRE 86
LN+WD GG+E + + ++ V+D+ RE
Sbjct: 50 LNIWDFGGRE-----ELKFEHIIFMKWADAILLVYDLTDRE 85
>gnl|CDD|206694 cd04109, Rab28, Rab GTPase family 28 (Rab28). Rab28 subfamily.
First identified in maize, Rab28 has been shown to be a
late embryogenesis-abundant (Lea) protein that is
regulated by the plant hormone abcisic acid (ABA). In
Arabidopsis, Rab28 is expressed during embryo
development and is generally restricted to provascular
tissues in mature embryos. Unlike maize Rab28, it is not
ABA-inducible. Characterization of the human Rab28
homolog revealed two isoforms, which differ by a 95-base
pair insertion, producing an alternative sequence for
the 30 amino acids at the C-terminus. The two human
isoforms are presumably the result of alternative
splicing. Since they differ at the C-terminus but not in
the GTP-binding region, they are predicted to be
targeted to different cellular locations. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins.
Length = 213
Score = 31.3 bits (71), Expect = 0.83
Identities = 21/86 (24%), Positives = 39/86 (45%), Gaps = 12/86 (13%)
Query: 43 NLVLNLWDCGGQE---AFMENYFTSQRDNIFRNVAVLIYVFDVESRELDRDLHYYQSCLE 99
N+ L +WD GGQ+ ++ Y + AV + V+D+ + + +L + S ++
Sbjct: 49 NVTLQVWDIGGQQIGGKMLDKYIYGAQ-------AVCL-VYDITNSQSFENLEDWLSVVK 100
Query: 100 AMLHNSPDSKVFCLI-HKIDLVHENQ 124
+ S L+ +K DL H Q
Sbjct: 101 KVNEESETKPKMVLVGNKTDLEHNRQ 126
>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 = 30.8 bits (70), Expect = 0.90
Identities = 21/84 (25%), Positives = 29/84 (34%), Gaps = 15/84 (17%)
Query: 45 VLNLWDCGGQEAFMENYFTSQRDNIFRNVAVLIYVFDVESRELDRDLHYYQSCLEAML-- 102
NL D GQE + R +R V + VFD+ LD + LE
Sbjct: 52 KFNLLDTAGQEDYDA-----IRRLYYRAVESSLRVFDIVILVLD-----VEEILEKQTKE 101
Query: 103 ---HNSPDSKVFCLIHKIDLVHEN 123
H + + +KIDL
Sbjct: 102 IIHHAESGVPIILVGNKIDLRDAK 125
>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 = 29.6 bits (67), Expect = 2.1
Identities = 11/22 (50%), Positives = 15/22 (68%), Gaps = 3/22 (13%)
Query: 46 LNLWDCGGQEA---FMENYFTS 64
LN+WD GGQ++ + NYF S
Sbjct: 60 LNIWDVGGQKSLRSYWRNYFES 81
>gnl|CDD|128473 smart00176, RAN, Ran (Ras-related nuclear proteins) /TC4 subfamily
of small GTPases. Ran is involved in the active
transport of proteins through nuclear pores.
Length = 200
Score = 30.0 bits (67), Expect = 2.2
Identities = 28/105 (26%), Positives = 45/105 (42%), Gaps = 11/105 (10%)
Query: 42 GNLVLNLWDCGGQEAFMENYFTSQRDNIFRNVAVLIYVFDVESRELDRDLHYYQSCLEAM 101
G + N+WD GQE F RD + I +FDV +R +++ + L +
Sbjct: 42 GPIRFNVWDTAGQEK-----FGGLRDGYYIQGQCAIIMFDVTARVTYKNVPNWHRDLVRV 96
Query: 102 LHNSPDSKVFCLIHKIDLVHENQRDVAWSSIVYQLIPNVKELEQS 146
N P V C +K+D+ R V SI + N++ + S
Sbjct: 97 CENIP--IVLCG-NKVDV---KDRKVKAKSITFHRKKNLQYYDIS 135
>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 = 29.0 bits (66), Expect = 3.6
Identities = 30/118 (25%), Positives = 44/118 (37%), Gaps = 23/118 (19%)
Query: 15 FTSNTFVMVVISDPNILEVEHSHVRFLGN--LVLNLWDCGGQEAFMENYFTSQRDNIFRN 72
F S FV DP I E + + L++ D GQE F ++ RD RN
Sbjct: 19 FVSGEFV--EEYDPTI-EDSYRKQIVVDGETYTLDILDTAGQEEF-----SAMRDQYIRN 70
Query: 73 VAVLIYVFDVESR----ELDRDLHYYQSCLEAMLHNSPDSKVFCLI--HKIDLVHENQ 124
I V+ + SR E+ + L V ++ +K DL +E Q
Sbjct: 71 GDGFILVYSITSRESFEEIKN---IREQILRV----KDKEDVPIVLVGNKCDLENERQ 121
>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 = 3.7
Identities = 27/87 (31%), Positives = 39/87 (44%), Gaps = 19/87 (21%)
Query: 46 LNLWDCGGQEAFMENYFTSQRDNIFRNVAVLIYVFDVESRE----LDRDLHYYQSCLEAM 101
L +WD GQE F S + +R + V+D+ +RE L+ L E
Sbjct: 51 LQIWDTAGQER-----FRSITSSYYRGAVGALLVYDITNRESFENLENWLK------ELR 99
Query: 102 LHNSPDSKVFCLI-HKIDLVHENQRDV 127
+ SP+ V L+ +K DL E QR V
Sbjct: 100 EYASPNV-VIMLVGNKSDL--EEQRQV 123
>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 = 28.8 bits (65), Expect = 4.1
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 5/41 (12%)
Query: 46 LNLWDCGGQEAFMENYFTSQRDNIFRNVAVLIYVFDVESRE 86
L +WD GQE F TS + +R +I V+DV R+
Sbjct: 51 LAIWDTAGQERF--RTLTS---SYYRGAQGVILVYDVTRRD 86
>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 = 29.2 bits (66), Expect = 4.1
Identities = 23/90 (25%), Positives = 37/90 (41%), Gaps = 28/90 (31%)
Query: 41 LGNLVLNLWDCGGQEAFM---ENYFTSQRDNIFRNVAVLIYVFDV-------ESR-ELDR 89
+GN+ +D GG E ++YF V ++++ D ES+ ELD
Sbjct: 60 IGNVKFTTFDLGGHEQARRVWKDYFP--------EVDGIVFLVDAADPERFQESKEELDS 111
Query: 90 DLHYYQSCLEAMLHNSPDSKVFCLIHKIDL 119
L+ + L N P + L +KID
Sbjct: 112 LLN------DEELANVP---ILILGNKIDK 132
>gnl|CDD|206693 cd04108, Rab36_Rab34, Rab GTPase families 34 (Rab34) and 36
(Rab36). Rab34/Rab36 subfamily. Rab34, found primarily
in the Golgi, interacts with its effector,
Rab-interacting lysosomal protein (RILP). This enables
its participation in microtubular
dynenin-dynactin-mediated repositioning of lysosomes
from the cell periphery to the Golgi. A Rab34 (Rah)
isoform that lacks the consensus GTP-binding region has
been identified in mice. This isoform is associated with
membrane ruffles and promotes macropinosome formation.
Rab36 has been mapped to human chromosome 22q11.2, a
region that is homozygously deleted in malignant
rhabdoid tumors (MRTs). However, experimental
assessments do not implicate Rab36 as a tumor suppressor
that would enable tumor formation through a
loss-of-function mechanism. 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 = 170
Score = 28.7 bits (64), Expect = 4.2
Identities = 26/78 (33%), Positives = 32/78 (41%), Gaps = 14/78 (17%)
Query: 46 LNLWDCGGQEAFMENYFTSQRDNIFRNVAVLIYVFD---VESRELDRDLHYYQSCLEAML 102
L LWD GQE F +R +I VFD V S E H Q +A+
Sbjct: 51 LQLWDTAGQER-----FKCIASTYYRGAQAIIIVFDLTDVASLE-----HTRQWLEDALK 100
Query: 103 HNSPDSKVFCLI-HKIDL 119
N P S + L+ K DL
Sbjct: 101 ENDPSSVLLFLVGTKKDL 118
>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 = 28.9 bits (65), Expect = 4.3
Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 15/68 (22%)
Query: 23 VVISDP----NILEVEHSHVRFLGNLVLNLWDCGGQEAFMENYFTSQRDNIFRNVAVLIY 78
VV + P N+ E+ + ++RFL +WD GGQE+ ++ T + N +I
Sbjct: 40 VVHTSPTIGSNVEEIVYKNIRFL------MWDIGGQESLRSSWNT-----YYTNTDAVIL 88
Query: 79 VFDVESRE 86
V D RE
Sbjct: 89 VIDSTDRE 96
>gnl|CDD|206726 cd04163, Era, E. coli Ras-like protein (Era) is a multifunctional
GTPase. Era (E. coli Ras-like protein) is a
multifunctional GTPase found in all bacteria except some
eubacteria. It binds to the 16S ribosomal RNA (rRNA) of
the 30S subunit and appears to play a role in the
assembly of the 30S subunit, possibly by chaperoning the
16S rRNA. It also contacts several assembly elements of
the 30S subunit. Era couples cell growth with
cytokinesis and plays a role in cell division and energy
metabolism. Homologs have also been found in eukaryotes.
Era contains two domains: the N-terminal GTPase domain
and a C-terminal domain KH domain that is critical for
RNA binding. Both domains are important for Era
function. Era is functionally able to compensate for
deletion of RbfA, a cold-shock adaptation protein that
is required for efficient processing of the 16S rRNA.
Length = 168
Score = 28.6 bits (65), Expect = 5.5
Identities = 18/91 (19%), Positives = 39/91 (42%), Gaps = 19/91 (20%)
Query: 70 FRNVAVLIYVFDVESRELDRDLHYYQSCLEAMLHNSPDSKVFCLIHKIDLVHENQRDVAW 129
++V ++++V D S + + + +L S + V +++KIDLV + + +
Sbjct: 80 LKDVDLVLFVVDA-SEWIGEGDEF----ILELLKKS-KTPVILVLNKIDLVKDKEDLLPL 133
Query: 130 SSIVYQLIP-------------NVKELEQSL 147
+ +L P NV EL + +
Sbjct: 134 LEKLKELHPFAEIFPISALKGENVDELLEYI 164
>gnl|CDD|206658 cd01866, Rab2, Rab GTPase family 2 (Rab2). Rab2 is localized on
cis-Golgi membranes and interacts with Golgi matrix
proteins. Rab2 is also implicated in the maturation of
vesicular tubular clusters (VTCs), which are
microtubule-associated intermediates in transport
between the ER and Golgi apparatus. In plants, Rab2
regulates vesicle trafficking between the ER and the
Golgi bodies and is important to pollen tube growth.
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 = 168
Score = 28.2 bits (63), Expect = 5.9
Identities = 26/86 (30%), Positives = 42/86 (48%), Gaps = 11/86 (12%)
Query: 43 NLVLNLWDCGGQEAFMENYFTSQRDNIFRNVAVLIYVFDVESRELDRDLHYYQSCLEAML 102
+ L +WD GQE+ F S + +R A + V+D+ RE ++ S LE
Sbjct: 52 QIKLQIWDTAGQES-----FRSITRSYYRGAAGALLVYDITRRE---TFNHLTSWLEDAR 103
Query: 103 HNSPDSKVFCLI-HKIDLVHENQRDV 127
+S + LI +K DL E++R+V
Sbjct: 104 QHSNSNMTIMLIGNKCDL--ESRREV 127
>gnl|CDD|206706 cd04134, Rho3, Ras homology family 3 (Rho3) of small guanosine
triphosphatases (GTPases). Rho3 is a member of the Rho
family found only in fungi. Rho3 is believed to regulate
cell polarity by interacting with the diaphanous/formin
family protein For3 to control both the actin
cytoskeleton and microtubules. Rho3 is also believed to
have a direct role in exocytosis that is independent of
its role in regulating actin polarity. The function in
exocytosis may be two-pronged: first, in the transport
of post-Golgi vesicles from the mother cell to the bud,
mediated by myosin (Myo2); second, in the docking and
fusion of vesicles to the plasma membrane, mediated by
an exocyst (Exo70) protein. 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.
Length = 185
Score = 28.3 bits (63), Expect = 6.1
Identities = 36/125 (28%), Positives = 56/125 (44%), Gaps = 15/125 (12%)
Query: 15 FTSNTFVMVVISDPNILEVEHSHVRFL-GNLV-LNLWDCGGQEAFMENYFTSQRDNIFRN 72
FT F V +P + E + H F+ G V L+LWD GQE F R + +
Sbjct: 20 FTRGYFPQVY--EPTVFE-NYIHDIFVDGLAVELSLWDTAGQEE-----FDRLRSLSYAD 71
Query: 73 VAVLIYVFDVESRELDRDLHYYQS-CLEAMLHNSPDSKVFCLIHKIDLVH-ENQRDVAWS 130
V++ F V++ + L +S L + H+ P K+ + K DL N+RD
Sbjct: 72 THVIMLCFSVDNPD---SLENVESKWLAEIRHHCPGVKLVLVALKCDLREPRNERDRGTH 128
Query: 131 SIVYQ 135
+I Y+
Sbjct: 129 TISYE 133
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 27.8 bits (61), Expect = 8.5
Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 5/45 (11%)
Query: 42 GNLVLNLWDCGGQEAFMENYFTSQRDNIFRNVAVLIYVFDVESRE 86
G + L LWD GQE F S + R+ A I V+D+ +R+
Sbjct: 27 GPVRLQLWDTAGQER-----FRSLIPSYIRDSAAAIVVYDITNRQ 66
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 28.2 bits (63), Expect = 9.5
Identities = 14/44 (31%), Positives = 19/44 (43%), Gaps = 5/44 (11%)
Query: 42 GNLVLNLWDCGGQEAFMENYFTSQRDNIFRNVAVLIYVFDVESR 85
G + WD GQE F RD + + I +FDV +R
Sbjct: 60 GKIRFYCWDTAGQEK-----FGGLRDGYYIHGQCAIIMFDVTAR 98
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 28.1 bits (63), Expect = 9.9
Identities = 16/44 (36%), Positives = 20/44 (45%), Gaps = 5/44 (11%)
Query: 42 GNLVLNLWDCGGQEAFMENYFTSQRDNIFRNVAVLIYVFDVESR 85
G + N+WD GQE F RD + I +FDV SR
Sbjct: 56 GPICFNVWDTAGQEK-----FGGLRDGYYIKGQCAIIMFDVTSR 94
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
0.336 0.147 0.463
Gapped
Lambda K H
0.267 0.0591 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 25,957,543
Number of extensions: 2668936
Number of successful extensions: 4410
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4389
Number of HSP's successfully gapped: 153
Length of query: 485
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 384
Effective length of database: 6,457,848
Effective search space: 2479813632
Effective search space used: 2479813632
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.7 bits)
S2: 61 (27.6 bits)