RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6566
(126 letters)
>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 = 238 bits (610), Expect = 2e-82
Identities = 91/126 (72%), Positives = 109/126 (86%)
Query: 1 MNEVVHTSPTIGSNVEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRE 60
+ EVVHTSPTIGSNVEE+++KNI F+MWD+GGQ+SLR++W+TYYTNT+ VILVIDSTDRE
Sbjct: 37 LGEVVHTSPTIGSNVEEIVYKNIRFLMWDIGGQESLRSSWNTYYTNTDAVILVIDSTDRE 96
Query: 61 RISLTKEELYKMLNHEDLSKAAVLIYANKQDIKNSMSPVEISNLLDLTSIKKQQWHIQSC 120
R+ LTKEELYKML HEDL KA +L+ ANKQD+K +M+P EIS L LTSI+ WHIQ C
Sbjct: 97 RLPLTKEELYKMLAHEDLRKAVLLVLANKQDLKGAMTPAEISESLGLTSIRDHTWHIQGC 156
Query: 121 CALTGE 126
CALTGE
Sbjct: 157 CALTGE 162
>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 = 181 bits (461), Expect = 5e-60
Identities = 66/125 (52%), Positives = 88/125 (70%)
Query: 2 NEVVHTSPTIGSNVEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRER 61
EVV T PTIG NVE V +KN+ F +WD+GGQ +R W YY NT+ +I V+DS+DRER
Sbjct: 22 GEVVTTIPTIGFNVETVEYKNVKFTVWDVGGQDKIRPLWKHYYENTDGLIFVVDSSDRER 81
Query: 62 ISLTKEELYKMLNHEDLSKAAVLIYANKQDIKNSMSPVEISNLLDLTSIKKQQWHIQSCC 121
I K EL+K+LN E+L A +LI ANKQD+ +++ E+ LL L SIK ++WHIQ C
Sbjct: 82 IEEAKNELHKLLNEEELKGAPLLILANKQDLPGALTESELIELLGLESIKGRRWHIQPCS 141
Query: 122 ALTGE 126
A+TG+
Sbjct: 142 AVTGD 146
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 178 bits (455), Expect = 8e-59
Identities = 67/126 (53%), Positives = 88/126 (69%)
Query: 1 MNEVVHTSPTIGSNVEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRE 60
+ E+V T PTIG NVE V +KN+ F +WD+GGQ+SLR W Y+ NT+ VI V+DS DR+
Sbjct: 36 LGEIVTTIPTIGFNVETVTYKNVKFTVWDVGGQESLRPLWRNYFPNTDAVIFVVDSADRD 95
Query: 61 RISLTKEELYKMLNHEDLSKAAVLIYANKQDIKNSMSPVEISNLLDLTSIKKQQWHIQSC 120
RI KEEL+ +LN E+L+ A +LI ANKQD+ +MS EI LL L +K + W IQ C
Sbjct: 96 RIEEAKEELHALLNEEELADAPLLILANKQDLPGAMSEAEIRELLGLHELKDRPWEIQGC 155
Query: 121 CALTGE 126
A+TGE
Sbjct: 156 SAVTGE 161
>gnl|CDD|206718 cd04151, Arl1, ADP ribosylation factor 1 (Arf1). Arl1 subfamily.
Arl1 (Arf-like 1) localizes to the Golgi complex, where
it is believed to recruit effector proteins to the
trans-Golgi network. Like most members of the Arf
family, Arl1 is myristoylated at its N-terminal helix
and mutation of the myristoylation site disrupts Golgi
targeting. In humans, the Golgi-localized proteins
golgin-97 and golgin-245 have been identified as Arl1
effectors. Golgins are large coiled-coil proteins found
in the Golgi, and these golgins contain a C-terminal
GRIP domain, which is the site of Arl1 binding.
Additional Arl1 effectors include the GARP
(Golgi-associated retrograde protein)/VFT (Vps53)
vesicle-tethering complex and Arfaptin 2. Arl1 is not
required for exocytosis, but appears necessary for
trafficking from the endosomes to the Golgi. In
Drosophila zygotes, mutation of Arl1 is lethal, and in
the host-bloodstream form of Trypanosoma brucei, Arl1 is
essential for viability.
Length = 158
Score = 162 bits (412), Expect = 1e-52
Identities = 60/126 (47%), Positives = 86/126 (68%)
Query: 1 MNEVVHTSPTIGSNVEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRE 60
+ EVV T PTIG NVE V +KN+ F +WDLGGQ S+R W YY+NT+ +I V+DSTDR+
Sbjct: 21 VGEVVTTIPTIGFNVETVTYKNLKFQVWDLGGQTSIRPYWRCYYSNTDAIIYVVDSTDRD 80
Query: 61 RISLTKEELYKMLNHEDLSKAAVLIYANKQDIKNSMSPVEISNLLDLTSIKKQQWHIQSC 120
R+ ++K EL+ ML E+L A +L++ANKQD+ ++S E++ L L+ +K + W I
Sbjct: 81 RLGISKSELHAMLEEEELKDAVLLVFANKQDMPGALSEAEVAEKLGLSELKDRTWQIFKT 140
Query: 121 CALTGE 126
A GE
Sbjct: 141 SATKGE 146
>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 = 161 bits (409), Expect = 3e-52
Identities = 61/124 (49%), Positives = 89/124 (71%)
Query: 3 EVVHTSPTIGSNVEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERI 62
E+V T PTIG NVE V +KNI F +WD+GGQ +R W Y+ NT+ +I V+DS DRERI
Sbjct: 24 EIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERI 83
Query: 63 SLTKEELYKMLNHEDLSKAAVLIYANKQDIKNSMSPVEISNLLDLTSIKKQQWHIQSCCA 122
+EEL +MLN ++L A +L++ANKQD+ N+MS E+++ L L S++ + W+IQ+ CA
Sbjct: 84 GEAREELQRMLNEDELRDAVLLVFANKQDLPNAMSAAEVTDKLGLHSLRNRNWYIQATCA 143
Query: 123 LTGE 126
+G+
Sbjct: 144 TSGD 147
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 158 bits (402), Expect = 9e-51
Identities = 64/126 (50%), Positives = 88/126 (69%)
Query: 1 MNEVVHTSPTIGSNVEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRE 60
+ EVV T PTIG NVE V +KN+ F MWD+GGQ LR W YY NT +I V+DS DRE
Sbjct: 39 LGEVVTTIPTIGFNVETVEYKNLKFTMWDVGGQDKLRPLWRHYYQNTNGLIFVVDSNDRE 98
Query: 61 RISLTKEELYKMLNHEDLSKAAVLIYANKQDIKNSMSPVEISNLLDLTSIKKQQWHIQSC 120
RI +EEL +ML+ ++L A +L++ANKQD+ N+MS E++ L L S++++ W+IQ C
Sbjct: 99 RIGDAREELERMLSEDELRDAVLLVFANKQDLPNAMSTTEVTEKLGLHSVRQRNWYIQGC 158
Query: 121 CALTGE 126
CA T +
Sbjct: 159 CATTAQ 164
>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 = 148 bits (375), Expect = 9e-47
Identities = 62/126 (49%), Positives = 88/126 (69%)
Query: 1 MNEVVHTSPTIGSNVEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRE 60
+ E V T PTIG NVE V +KNI F +WD+GGQ +R W YYTNT+ +I V+DS DR+
Sbjct: 35 LGESVTTIPTIGFNVETVTYKNISFTVWDVGGQDKIRPLWRHYYTNTQGLIFVVDSNDRD 94
Query: 61 RISLTKEELYKMLNHEDLSKAAVLIYANKQDIKNSMSPVEISNLLDLTSIKKQQWHIQSC 120
RI +EEL++MLN ++L A +L++ANKQD+ ++M EI+ L L SI+ + W+IQ
Sbjct: 95 RIDEAREELHRMLNEDELRDAVILVFANKQDLPDAMKAAEITEKLGLHSIRDRNWYIQPT 154
Query: 121 CALTGE 126
CA +G+
Sbjct: 155 CATSGD 160
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 148 bits (374), Expect = 2e-46
Identities = 60/126 (47%), Positives = 92/126 (73%)
Query: 1 MNEVVHTSPTIGSNVEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRE 60
+ E+V T PTIG NVE V +KNI F +WD+GGQ +R W Y+ NT+ +I V+DS DR+
Sbjct: 39 LGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRD 98
Query: 61 RISLTKEELYKMLNHEDLSKAAVLIYANKQDIKNSMSPVEISNLLDLTSIKKQQWHIQSC 120
R+ ++EL++MLN ++L A +L++ANKQD+ N+M+ EI++ L L S++++ W+IQS
Sbjct: 99 RVVEARDELHRMLNEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRQRHWYIQST 158
Query: 121 CALTGE 126
CA +GE
Sbjct: 159 CATSGE 164
>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 = 140 bits (354), Expect = 9e-44
Identities = 54/126 (42%), Positives = 86/126 (68%)
Query: 1 MNEVVHTSPTIGSNVEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRE 60
+ + V T PT+G NVE V +KN+ F +WD+GGQ +R W YYT T+ +I V+DS DR+
Sbjct: 31 LGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGQDKIRPLWRHYYTGTQGLIFVVDSADRD 90
Query: 61 RISLTKEELYKMLNHEDLSKAAVLIYANKQDIKNSMSPVEISNLLDLTSIKKQQWHIQSC 120
RI ++EL++++N ++ A +L++ANKQD+ ++M P EI L LT I+ + W++Q
Sbjct: 91 RIDEARQELHRIINDREMRDALLLVFANKQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPS 150
Query: 121 CALTGE 126
CA +G+
Sbjct: 151 CATSGD 156
>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 = 135 bits (343), Expect = 7e-42
Identities = 54/119 (45%), Positives = 80/119 (67%)
Query: 8 SPTIGSNVEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERISLTKE 67
SPT+G N++ + + +WD+GGQ+SLR+ W Y+ +T+ +I V+DS+DR R+ K
Sbjct: 43 SPTLGFNIKTLEYNGYKLNIWDVGGQKSLRSYWRNYFESTDALIWVVDSSDRARLEDCKR 102
Query: 68 ELYKMLNHEDLSKAAVLIYANKQDIKNSMSPVEISNLLDLTSIKKQQWHIQSCCALTGE 126
EL K+L E L+ A +LI+ANKQD+ ++SP EI +L+L SIK W I C A+TGE
Sbjct: 103 ELQKLLVEERLAGATLLIFANKQDLPGALSPEEIREVLELDSIKSHHWRIFGCSAVTGE 161
>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 = 133 bits (336), Expect = 8e-41
Identities = 49/124 (39%), Positives = 76/124 (61%)
Query: 3 EVVHTSPTIGSNVEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERI 62
++ H +PT G N++ V +WD+GGQ+ +R W Y+ NT+ +I VIDS DR+R
Sbjct: 39 DISHITPTQGFNIKNVQADGFKLNVWDIGGQRKIRPYWRNYFENTDVLIYVIDSADRKRF 98
Query: 63 SLTKEELYKMLNHEDLSKAAVLIYANKQDIKNSMSPVEISNLLDLTSIKKQQWHIQSCCA 122
+EL ++L E L+ VL++ANKQD+ + E++ L+L I+ + WHIQ+C A
Sbjct: 99 EEAGQELVELLEEEKLAGVPVLVFANKQDLLTAAPAEEVAEALNLHDIRDRSWHIQACSA 158
Query: 123 LTGE 126
TGE
Sbjct: 159 KTGE 162
>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 = 126 bits (319), Expect = 2e-38
Identities = 52/123 (42%), Positives = 76/123 (61%), Gaps = 2/123 (1%)
Query: 6 HTSPTIGSNVEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERISLT 65
+ PT+G NVE N+ F +D+ GQ R W YY N + +I VIDS+DR R+ +
Sbjct: 28 NIVPTVGFNVESFKKGNLSFTAFDMSGQGKYRGLWEHYYKNIQGIIFVIDSSDRLRMVVA 87
Query: 66 KEELYKMLNHEDLSKAAV--LIYANKQDIKNSMSPVEISNLLDLTSIKKQQWHIQSCCAL 123
K+EL +LNH D+ + L YANK D+ ++++ V+I+ LL L +IK + WHI + AL
Sbjct: 88 KDELELLLNHPDIKHRRIPILFYANKMDLPDALTAVKITQLLCLENIKDKPWHIFASSAL 147
Query: 124 TGE 126
TGE
Sbjct: 148 TGE 150
>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 = 120 bits (302), Expect = 8e-36
Identities = 45/126 (35%), Positives = 78/126 (61%), Gaps = 2/126 (1%)
Query: 3 EVVHTSPTIGSNVEEV-IWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRER 61
E+V T PT+G NVE + + K++ +WD+GGQ+ +R W Y NT+ ++ V+DS+D R
Sbjct: 23 ELVTTIPTVGFNVEMLQLEKHLSLTVWDVGGQEKMRTVWKCYLENTDGLVYVVDSSDEAR 82
Query: 62 ISLTKEELYKMLNHEDLSKAAVLIYANKQDIKNSMSPVEISNLLDLTSI-KKQQWHIQSC 120
+ +++EL +L +E + V++ ANKQD+ +++ EI+ L + W++Q C
Sbjct: 83 LDESQKELKHILKNEHIKGVPVVLLANKQDLPGALTAEEITRRFKLKKYCSDRDWYVQPC 142
Query: 121 CALTGE 126
A+TGE
Sbjct: 143 SAVTGE 148
>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 = 113 bits (283), Expect = 5e-33
Identities = 55/125 (44%), Positives = 81/125 (64%), Gaps = 1/125 (0%)
Query: 2 NEVVHTSPTIGSNVEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRER 61
+E + PTIG NVE V +KN+ F +WD+GG+ LR W YY NT+ V+ VIDS+ R+R
Sbjct: 22 DEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHYYLNTQAVVFVIDSSHRDR 81
Query: 62 ISLTKEELYKMLNHEDLSKAAVLIYANKQDIKNSMSPVEISNLLDLTSI-KKQQWHIQSC 120
+S EL K+L ++L A +LI+ANKQD+ ++S E++ LL L + + W+IQ C
Sbjct: 82 VSEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEMTELLSLHKLCCGRSWYIQGC 141
Query: 121 CALTG 125
A +G
Sbjct: 142 DARSG 146
>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 = 110 bits (278), Expect = 3e-32
Identities = 47/120 (39%), Positives = 70/120 (58%), Gaps = 2/120 (1%)
Query: 9 PTIGSNVEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERISLTKEE 68
PT+G N+ + + WDLGGQ+ LR+ W YY + VI VIDSTDRER + +K
Sbjct: 37 PTVGLNIGTIEVGKARLMFWDLGGQEELRSLWDKYYAESHGVIYVIDSTDRERFNESKSA 96
Query: 69 LYKMLNHEDLSKAAVLIYANKQDIKNSMSPVEISNLLD--LTSIKKQQWHIQSCCALTGE 126
K++N+E L +L+ ANKQD+ +++S EI + D + I ++ +Q AL GE
Sbjct: 97 FEKVINNEALEGVPLLVLANKQDLPDALSVAEIKEVFDDCIALIGRRDCLVQPVSALEGE 156
>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 = 107 bits (270), Expect = 7e-31
Identities = 50/132 (37%), Positives = 73/132 (55%), Gaps = 6/132 (4%)
Query: 1 MNEVVHTSPTIGSNVEEV-----IWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVID 55
NE V+T PT G N E++ K + F WD+GGQ+ LR W +Y T+ ++ V+D
Sbjct: 25 FNEFVNTVPTKGFNTEKIKVSLGNAKGVTFHFWDVGGQEKLRPLWKSYTRCTDGIVFVVD 84
Query: 56 STDRERISLTKEELYKMLNHEDLSKAAVLIYANKQDIKNSMSPVEISNLLDLTSIKKQQ- 114
S D ER+ K EL+K+ + VL+ ANKQD+ N++ E+ LL L +
Sbjct: 85 SVDVERMEEAKTELHKITKFSENQGVPVLVLANKQDLPNALPVSEVEKLLALHELSSSTP 144
Query: 115 WHIQSCCALTGE 126
WH+Q CA+ GE
Sbjct: 145 WHVQPACAIIGE 156
>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 = 86.2 bits (214), Expect = 3e-22
Identities = 34/106 (32%), Positives = 56/106 (52%)
Query: 2 NEVVHTSPTIGSNVEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRER 61
+ + PT+ EE+ N+ F +DLGG + R W Y+ + ++ ++D+ D ER
Sbjct: 42 DRLAQHVPTLHPTSEELTIGNVKFTTFDLGGHEQARRVWKDYFPEVDGIVFLVDAADPER 101
Query: 62 ISLTKEELYKMLNHEDLSKAAVLIYANKQDIKNSMSPVEISNLLDL 107
+KEEL +LN E+L+ +LI NK D ++S E+ L L
Sbjct: 102 FQESKEELDSLLNDEELANVPILILGNKIDKPGAVSEEELREALGL 147
>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 = 82.8 bits (205), Expect = 3e-21
Identities = 36/118 (30%), Positives = 61/118 (51%), Gaps = 4/118 (3%)
Query: 4 VVHTSPTIGSNVEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERIS 63
T PT+G N+ +V N+ +WDLGGQ R+ W Y ++ V+D+ DRE++
Sbjct: 25 SEDTIPTVGFNMRKVTKGNVTIKVWDLGGQPRFRSMWERYCRGVNAIVYVVDAADREKLE 84
Query: 64 LTKEELYKMLNHEDLSKAAVLIYANKQDIKNSMSPVEISNLLDLTSIKKQQWHIQSCC 121
+ K EL+ +L L +L+ NK D+ ++S E+ ++L SI ++ C
Sbjct: 85 VAKNELHDLLEKPSLEGIPLLVLGNKNDLPGALSVDELIEQMNLKSITDREV----SC 138
>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 = 77.0 bits (190), Expect = 5e-19
Identities = 37/122 (30%), Positives = 63/122 (51%), Gaps = 3/122 (2%)
Query: 7 TSPTIGSNVEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERISLTK 66
+PT+G ++ ++DLGG + R W YY ++ V+DS+D +R+ K
Sbjct: 27 VAPTVGFTPTKLRLDKYEVCIFDLGGGANFRGIWVNYYAEAHGLVFVVDSSDDDRVQEVK 86
Query: 67 EELYKMLNHEDLSKAAVLIYANKQDIKNSMSPVEISNLLDLTSIKKQQ---WHIQSCCAL 123
E L ++L H +S +L+ ANKQD KN++ ++ L L + + HI+ C A+
Sbjct: 87 EILRELLQHPRVSGKPILVLANKQDKKNALLGADVIEYLSLEKLVNENKSLCHIEPCSAI 146
Query: 124 TG 125
G
Sbjct: 147 EG 148
>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 = 76.7 bits (189), Expect = 7e-19
Identities = 38/116 (32%), Positives = 66/116 (56%), Gaps = 5/116 (4%)
Query: 7 TSPTIGSNVEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERISLTK 66
PT G N + ++ + ++GG Q+LR W Y + ++ +I V+DS D ER+ L +
Sbjct: 28 VVPTTGFNSVAIPTQDAIMELLEIGGSQNLRKYWKRYLSGSQGLIFVVDSADSERLPLAR 87
Query: 67 EELYKMLNHE-DLSKAAVLIYANKQDIKNSMSPVEISNLLDLTSI-KKQQWHIQSC 120
+EL+++L H DL +++ ANKQD+ + S EI L+L I + ++W +Q
Sbjct: 88 QELHQLLQHPPDLP---LVVLANKQDLPAARSVQEIHKELELEPIARGRRWILQGT 140
>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 = 71.5 bits (175), Expect = 1e-16
Identities = 35/106 (33%), Positives = 54/106 (50%)
Query: 9 PTIGSNVEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERISLTKEE 68
PT EE+ NI F +DLGG Q R W Y+ ++ ++D+ D+ER + +K E
Sbjct: 47 PTQHPTSEELAIGNIKFTTFDLGGHQQARRLWKDYFPEVNGIVYLVDAYDKERFAESKRE 106
Query: 69 LYKMLNHEDLSKAAVLIYANKQDIKNSMSPVEISNLLDLTSIKKQQ 114
L +L+ E+L+ LI NK D + S E+ L LT+ +
Sbjct: 107 LDALLSDEELATVPFLILGNKIDAPYAASEDELRYALGLTNTTTGK 152
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 66.1 bits (161), Expect = 2e-14
Identities = 29/98 (29%), Positives = 42/98 (42%), Gaps = 4/98 (4%)
Query: 8 SPTIGSNV----EEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERIS 63
PTIG+ E +NI +WD GQ+ R+ YY +++V DST RE
Sbjct: 35 PPTIGNLDPAKTIEPYRRNIKLQLWDTAGQEEYRSLRPEYYRGANGILIVYDSTLRESSD 94
Query: 64 LTKEELYKMLNHEDLSKAAVLIYANKQDIKNSMSPVEI 101
EE + L +L+ NK D+ + S E
Sbjct: 95 ELTEEWLEELRELAPDDVPILLVGNKIDLFDEQSSSEE 132
>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 = 46.6 bits (111), Expect = 2e-07
Identities = 23/110 (20%), Positives = 36/110 (32%), Gaps = 6/110 (5%)
Query: 4 VVHTSPTIGSN----VEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDR 59
+ P N V E K F + D GQ+ A YY E + V D
Sbjct: 28 ITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAGQEDYDAIRRLYYRAVESSLRVFDIVIL 87
Query: 60 -ERISLTKEELYKMLNHEDLSKAAVLIYANKQDIK-NSMSPVEISNLLDL 107
+ E+ K + H S +++ NK D++ + L
Sbjct: 88 VLDVEEILEKQTKEIIHHAESGVPIILVGNKIDLRDAKLKTHVAFLFAKL 137
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 44.4 bits (105), Expect = 2e-06
Identities = 19/81 (23%), Positives = 37/81 (45%), Gaps = 4/81 (4%)
Query: 27 MWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERISLTKEELYKMLNHEDLSKAAVLIY 86
++ GQ+ + W I+++DS+ I+ EE+ L + V++
Sbjct: 72 LFGTPGQERFKFMWEILSRGAVGAIVLVDSSRP--ITFHAEEIIDFLTSRN--PIPVVVA 127
Query: 87 ANKQDIKNSMSPVEISNLLDL 107
NKQD+ +++ P +I L L
Sbjct: 128 INKQDLFDALPPEKIREALKL 148
>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 = 44.0 bits (104), Expect = 2e-06
Identities = 24/128 (18%), Positives = 42/128 (32%), Gaps = 12/128 (9%)
Query: 6 HTSPTIGSNVEEVIW--KNIHFIMWDLGGQQSLRAAWST-----YYTNTEFVILVIDSTD 58
T +V + ++ D G + ++LV+DSTD
Sbjct: 28 VPGTTRDPDVYVKELDKGKVKLVLVDTPGLDEFGGLGREELARLLLRGADLILLVVDSTD 87
Query: 59 RERISLTKEELYKMLNHEDLSKAAVLIYANKQDIKNSMSPVEISNLLDLTSIKKQQWHIQ 118
RE ++ +L +++ NK D+ E+ L +L K +
Sbjct: 88 RESE---EDAKLLILRRLRKEGIPIILVGNKIDLLEEREVEELLRLEEL--AKILGVPVF 142
Query: 119 SCCALTGE 126
A TGE
Sbjct: 143 EVSAKTGE 150
>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 = 43.7 bits (103), Expect = 3e-06
Identities = 34/123 (27%), Positives = 56/123 (45%), Gaps = 9/123 (7%)
Query: 10 TIGSNVE----EVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERISLT 65
TIG + E EV+ +WD GQ+ + STYY + +I+V D TD + T
Sbjct: 32 TIGVDFEMERFEVLGVPFSLQLWDTAGQERFKCIASTYYRGAQAIIIVFDLTDVASLEHT 91
Query: 66 KEELYKMLNHEDLSKAAVLIYANKQDIKN--SMSPVEISNLLDLTSIKKQQWHIQSCCAL 123
++ L L D S + + K+D+ + + +E + +K + W + AL
Sbjct: 92 RQWLEDALKENDPSSVLLFLVGTKKDLSSPAQYALMEQDAIKLAREMKAEYW---AVSAL 148
Query: 124 TGE 126
TGE
Sbjct: 149 TGE 151
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 42.7 bits (100), Expect = 7e-06
Identities = 28/88 (31%), Positives = 41/88 (46%), Gaps = 14/88 (15%)
Query: 8 SPTIGSNVE----EVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERIS 63
+PTIG + + V K + +WD GQ+ R S+YY N + +ILV D T RE +
Sbjct: 43 APTIGVDFKIKQLTVGGKRLKLTIWDTAGQERFRTLTSSYYRNAQGIILVYDVTRRETFT 102
Query: 64 LTKEELYKMLNHEDLSKAAVLIYANKQD 91
N D+ V +Y+ QD
Sbjct: 103 ----------NLSDVWGKEVELYSTNQD 120
>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 = 41.5 bits (98), Expect = 1e-05
Identities = 30/93 (32%), Positives = 39/93 (41%), Gaps = 12/93 (12%)
Query: 7 TSPTIG----SNVEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERI 62
S TIG V K + +WD GQ+ R S+YY + VILV D T R+
Sbjct: 29 LSSTIGVDFKVKTVTVDGKKVKLAIWDTAGQERFRTLTSSYYRGAQGVILVYDVTRRD-- 86
Query: 63 SLTKEELYKMLNHEDL----SKAAVLIYANKQD 91
T + L LN D A ++ NK D
Sbjct: 87 --TFDNLDTWLNELDTYSTNPDAVKMLVGNKID 117
>gnl|CDD|215955 pfam00503, G-alpha, G-protein alpha subunit. G proteins couple
receptors of extracellular signals to intracellular
signaling pathways. The G protein alpha subunit binds
guanyl nucleotide and is a weak GTPase. A set of
residues that are unique to G-alpha as compared to its
ancestor the Arf-like family form a ring of residues
centered on the nucleotide binding site. A Ggamma is
found fused to an inactive Galpha in the Dictyostelium
protein gbqA.
Length = 329
Score = 41.9 bits (99), Expect = 2e-05
Identities = 24/97 (24%), Positives = 45/97 (46%), Gaps = 16/97 (16%)
Query: 9 PTIGSNVEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVI------------DS 56
T G + +K + F ++D+GGQ+S R W + + +I V+ DS
Sbjct: 154 KTTGIIETKFDFKGLKFRLFDVGGQRSERKKWIHCFEDVTAIIFVVSLSEYDQVLYEDDS 213
Query: 57 TDRERISLTKEELYK-MLNHEDLSKAAVLIYANKQDI 92
T+R SL L++ + N ++++ NK+D+
Sbjct: 214 TNRLEESL---NLFEEICNSPWFKNTPIILFLNKKDL 247
>gnl|CDD|206691 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta), together with SR-alpha, forms the
heterodimeric signal recognition particle (SRP). Signal
recognition particle receptor, beta subunit (SR-beta).
SR-beta and SR-alpha form the heterodimeric signal
recognition particle (SRP or SR) receptor that binds SRP
to regulate protein translocation across the ER
membrane. Nascent polypeptide chains are synthesized
with an N-terminal hydrophobic signal sequence that
binds SRP54, a component of the SRP. SRP directs
targeting of the ribosome-nascent chain complex (RNC) to
the ER membrane via interaction with the SR, which is
localized to the ER membrane. The RNC is then
transferred to the protein-conducting channel, or
translocon, which facilitates polypeptide translation
across the ER membrane or integration into the ER
membrane. SR-beta is found only in eukaryotes; it is
believed to control the release of the signal sequence
from SRP54 upon binding of the ribosome to the
translocon. High expression of SR-beta has been observed
in human colon cancer, suggesting it may play a role in
the development of this type of cancer.
Length = 202
Score = 41.2 bits (97), Expect = 3e-05
Identities = 24/89 (26%), Positives = 40/89 (44%), Gaps = 6/89 (6%)
Query: 21 KNIHFIMWDLGGQQSLRAAWSTYYTNTEF-VILVIDSTDRER-ISLTKEELYKMLNHEDL 78
K + + D+ G + LR Y + ++ V+DS ++ I E LY +L +
Sbjct: 47 KKLTLV--DVPGHEKLRDKLLEYLKASLKAIVFVVDSATFQKNIRDVAEFLYDILTDLEK 104
Query: 79 SKAA--VLIYANKQDIKNSMSPVEISNLL 105
K +LI NKQD+ + +I LL
Sbjct: 105 IKNKIPILIACNKQDLFTAKPAKKIKELL 133
>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 = 40.5 bits (96), Expect = 4e-05
Identities = 26/94 (27%), Positives = 43/94 (45%), Gaps = 7/94 (7%)
Query: 6 HTSPTIGSNVE----EVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRER 61
+ TIG + + EV K + +WD GQ+ R+ S+YY ILV D T+RE
Sbjct: 28 NYKSTIGVDFKSKTIEVDGKKVKLQIWDTAGQERFRSITSSYYRGAHGAILVYDVTNRE- 86
Query: 62 ISLTK-EELYKMLNHEDLSKAAVLIYANKQDIKN 94
S ++ L +++ NK D+++
Sbjct: 87 -SFENLDKWLNELKEYAPPNIPIILVGNKSDLED 119
>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 = 39.7 bits (93), Expect = 4e-05
Identities = 20/87 (22%), Positives = 34/87 (39%), Gaps = 5/87 (5%)
Query: 7 TSPTIGSNVEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDR---ERIS 63
T+ + EV +WD GG++ L+ + + ++LV D TDR +S
Sbjct: 32 QGDTLAVDTLEVDGDTGLLNIWDFGGREELKFEHIIFMKWADAILLVYDLTDRESLNEVS 91
Query: 64 LTKEELYKMLNHEDLSKAAVLIYANKQ 90
L + K V++ NK
Sbjct: 92 RLIAWLPNLRKLG--GKIPVILVGNKL 116
>gnl|CDD|133323 cd04123, Rab21, Rab GTPase family 21 (Rab21). The localization and
function of Rab21 are not clearly defined, with
conflicting data reported. Rab21 has been reported to
localize in the ER in human intestinal epithelial cells,
with partial colocalization with alpha-glucosidase, a
late endosomal/lysosomal marker. More recently, Rab21
was shown to colocalize with and affect the morphology
of early endosomes. In Dictyostelium, GTP-bound Rab21,
together with two novel LIM domain proteins, LimF and
ChLim, has been shown to regulate 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 = 162
Score = 39.5 bits (93), Expect = 7e-05
Identities = 24/81 (29%), Positives = 37/81 (45%), Gaps = 11/81 (13%)
Query: 21 KNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERISLTK-----EELYKMLNH 75
K I +WD GQ+ A YY + + ILV D TD + S K +EL +M
Sbjct: 47 KRIDLAIWDTAGQERYHALGPIYYRDADGAILVYDITDAD--SFQKVKKWIKELKQMRG- 103
Query: 76 EDLSKAAVLIYANKQDIKNSM 96
+ +++I NK D++
Sbjct: 104 ---NNISLVIVGNKIDLERQR 121
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 38.8 bits (90), Expect = 2e-04
Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 21 KNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERISLTKEELYKMLNHEDLSK 80
K + +WD GQ+ RA S YY +LV D T R+ + L ++ +H D S
Sbjct: 59 KTVKAQIWDTAGQERYRAITSAYYRGAVGALLVYDITKRQTFDNVQRWLRELRDHAD-SN 117
Query: 81 AAVLIYANKQDIKN 94
+++ NK D+ +
Sbjct: 118 IVIMMAGNKSDLNH 131
>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 = 38.5 bits (89), Expect = 3e-04
Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 7/78 (8%)
Query: 17 EVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERISLTKEEL---YKML 73
E+ K I +WD GQ+ + S YY + + +ILV D T +E T ++L KM+
Sbjct: 43 ELRGKKIRLQIWDTAGQERFNSITSAYYRSAKGIILVYDITKKE----TFDDLPKWMKMI 98
Query: 74 NHEDLSKAAVLIYANKQD 91
+ A +L+ NK D
Sbjct: 99 DKYASEDAELLLVGNKLD 116
>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 = 38.3 bits (89), Expect = 3e-04
Identities = 24/65 (36%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 27 MWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERISLTKEELYKMLNHEDLSKAAVLIY 86
+WD GQ+ R STYY T VI+V D T+ E K L ++ + D VL+
Sbjct: 59 IWDTAGQERFRTITSTYYRGTHGVIVVYDVTNGESFVNVKRWLQEIEQNCDDVC-KVLV- 116
Query: 87 ANKQD 91
NK D
Sbjct: 117 GNKND 121
>gnl|CDD|206710 cd04139, RalA_RalB, Ral (Ras-like) family containing highly
homologous RalA and RalB. The Ral (Ras-like) subfamily
consists of the highly homologous RalA and RalB. Ral
proteins are believed to play a crucial role in
tumorigenesis, metastasis, endocytosis, and actin
cytoskeleton dynamics. Despite their high sequence
similarity (>80% sequence identity), nonoverlapping and
opposing functions have been assigned to RalA and RalBs
in tumor migration. In human bladder and prostate cancer
cells, RalB promotes migration while RalA inhibits it. A
Ral-specific set of GEFs has been identified that are
activated by Ras binding. This RalGEF activity is
enhanced by Ras binding to another of its target
proteins, phosphatidylinositol 3-kinase (PI3K). Ral
effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and
the exocyst (Sec6/8) complex, a heterooctomeric protein
complex that is involved in tethering vesicles to
specific sites on the plasma membrane prior to
exocytosis. In rat kidney cells, RalB is required for
functional assembly of the exocyst and for localizing
the exocyst to the leading edge of migrating cells. In
human cancer cells, RalA is required to support
anchorage-independent proliferation and RalB is required
to suppress apoptosis. RalA has been shown to localize
to the plasma membrane while RalB is localized to the
intracellular vesicles. Most Ras proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Ras proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 163
Score = 38.2 bits (89), Expect = 3e-04
Identities = 17/64 (26%), Positives = 29/64 (45%)
Query: 29 DLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERISLTKEELYKMLNHEDLSKAAVLIYAN 88
D GQ+ A Y+ + E +LV TD E + E ++L ++ +L+ N
Sbjct: 54 DTAGQEDYAAIRDNYFRSGEGFLLVFSITDMESFTALAEFREQILRVKEDDNVPLLLVGN 113
Query: 89 KQDI 92
K D+
Sbjct: 114 KCDL 117
>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 = 37.8 bits (88), Expect = 4e-04
Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 5/57 (8%)
Query: 9 PTIGSN-----VEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRE 60
PT+G + +E I +WD GQ+ R+ +YY N+ V+LV D T+RE
Sbjct: 33 PTVGVDFFSRLIEIEPGVRIKLQLWDTAGQERFRSITRSYYRNSVGVLLVFDITNRE 89
>gnl|CDD|206661 cd01869, Rab1_Ypt1, Rab GTPase family 1 includes the yeast homolog
Ypt1. Rab1/Ypt1 subfamily. Rab1 is found in every
eukaryote and is a key regulatory component for the
transport of vesicles from the ER to the Golgi
apparatus. Studies on mutations of Ypt1, the yeast
homolog of Rab1, showed that this protein is necessary
for the budding of vesicles of the ER as well as for
their transport to, and fusion with, the Golgi
apparatus. 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 = 36.5 bits (85), Expect = 0.001
Identities = 23/77 (29%), Positives = 41/77 (53%), Gaps = 5/77 (6%)
Query: 21 KNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERISLTKEELYKMLNH--EDL 78
K + +WD GQ+ R S+YY +I+V D TD+E + K+ L ++ + E++
Sbjct: 49 KTVKLQIWDTAGQERFRTITSSYYRGAHGIIIVYDVTDQESFNNVKQWLQEIDRYASENV 108
Query: 79 SKAAVLIYANKQDIKNS 95
+K L+ NK D+ +
Sbjct: 109 NK---LLVGNKCDLTDK 122
>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 = 36.2 bits (84), Expect = 0.001
Identities = 29/93 (31%), Positives = 47/93 (50%), Gaps = 12/93 (12%)
Query: 9 PTIGSN--VEEVIWKN----IHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERI 62
PTIG + V++V +N ++F +DL G + +Y +T+ V+LV D TDR+
Sbjct: 31 PTIGIDYGVKKVSVRNKEVRVNF--FDLSGHPEYLEVRNEFYKDTQGVLLVYDVTDRQSF 88
Query: 63 ----SLTKEELYKMLNHEDLSKAAVLIYANKQD 91
S KE + H ++ V++ ANK D
Sbjct: 89 EALDSWLKEMKQEGGPHGNMENIVVVVCANKID 121
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 36.5 bits (84), Expect = 0.002
Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 1/72 (1%)
Query: 21 KNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERISLTKEELYKMLNHEDLSK 80
K I +WD GQ+S R+ +YY +LV D T RE + L H + +
Sbjct: 53 KPIKLQIWDTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLASWLEDARQHAN-AN 111
Query: 81 AAVLIYANKQDI 92
+++ NK D+
Sbjct: 112 MTIMLIGNKCDL 123
>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 = 36.0 bits (83), Expect = 0.002
Identities = 26/96 (27%), Positives = 40/96 (41%), Gaps = 2/96 (2%)
Query: 1 MNEVVHT-SPTIGSNVEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDR 59
M + HT G+ + EV + I +WD GQ+ RA +YY ++V D T R
Sbjct: 28 MADCPHTIGVEFGTRIIEVNGQKIKLQIWDTAGQERFRAVTRSYYRGAAGALMVYDITRR 87
Query: 60 ERISLTKEELYKMLNHEDLSKAAVLIYANKQDIKNS 95
+ L N + + LI NK D++
Sbjct: 88 STYNHLSSWLTDARNLTNPNTVIFLI-GNKADLEAQ 122
>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 = 35.9 bits (83), Expect = 0.002
Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 4/58 (6%)
Query: 7 TSPTIG----SNVEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRE 60
++ TIG S V V K++ +WD GQ+ R+ +YY +LV D T RE
Sbjct: 29 SNHTIGVEFGSRVVNVGGKSVKLQIWDTAGQERFRSVTRSYYRGAAGALLVYDITSRE 86
>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 = 35.4 bits (81), Expect = 0.003
Identities = 25/96 (26%), Positives = 42/96 (43%), Gaps = 18/96 (18%)
Query: 9 PTIGSNVEEVIWKN----IHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERISL 64
T+G V +++ I F +WD GQ+ YY + I++ D T R +
Sbjct: 26 ATLGVEVHPLVFHTNRGPIRFNVWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTAR----V 81
Query: 65 TKEELYKMLN--HEDLSKAA----VLIYANKQDIKN 94
T YK + H DL + +++ NK D+K+
Sbjct: 82 T----YKNVPNWHRDLVRVCENIPIVLCGNKVDVKD 113
>gnl|CDD|204242 pfam09439, SRPRB, Signal recognition particle receptor beta
subunit. The beta subunit of the signal recognition
particle receptor (SRP) is a transmembrane GTPase which
anchors the alpha subunit to the endoplasmic reticulum
membrane.
Length = 181
Score = 34.7 bits (80), Expect = 0.005
Identities = 26/100 (26%), Positives = 48/100 (48%), Gaps = 8/100 (8%)
Query: 21 KNIHFIMWDLGGQQSLRAAWSTYY---TNTEFVILVIDST-DRERISLTKEELYKMLNHE 76
K F + D G LR ++ ++ V+DST + ++ T E LY++L+
Sbjct: 47 KGFSFTLIDFPGHVKLRQKLLETIKDSSSLRGIVFVVDSTAFPKEVTDTAEFLYEILSIT 106
Query: 77 DLSKAAV--LIYANKQDIKNSMSPVEISNLL--DLTSIKK 112
+L K + LI NKQ+ + P +I L ++ +I++
Sbjct: 107 ELLKNGIDILIACNKQESFTARPPKKIKQALEKEINTIRE 146
>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 = 33.9 bits (78), Expect = 0.009
Identities = 17/49 (34%), Positives = 25/49 (51%)
Query: 12 GSNVEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRE 60
G+ + + K I +WD GQ+S R+ +YY +LV D T RE
Sbjct: 42 GARMITIDGKQIKLQIWDTAGQESFRSITRSYYRGAAGALLVYDITRRE 90
>gnl|CDD|206643 cd00877, Ran, Ras-related nuclear proteins (Ran)/TC4 family of
small GTPases. Ran GTPase is involved in diverse
biological functions, such as nuclear transport,
spindle formation during mitosis, DNA replication, and
cell division. Among the Ras superfamily, Ran is a
unique small G protein. It does not have a lipid
modification motif at the C-terminus to bind to the
membrane, which is often observed within the Ras
superfamily. Ran may therefore interact with a wide
range of proteins in various intracellular locations.
Like other GTPases, Ran exists in GTP- and GDP-bound
conformations that interact differently with effectors.
Conversion between these forms and the assembly or
disassembly of effector complexes requires the
interaction of regulator proteins. The intrinsic GTPase
activity of Ran is very low, but it is greatly
stimulated by a GTPase-activating protein (RanGAP1)
located in the cytoplasm. By contrast, RCC1, a guanine
nucleotide exchange factor that generates RanGTP, is
bound to chromatin and confined to the nucleus. Ran
itself is mobile and is actively imported into the
nucleus by a mechanism involving NTF-2. Together with
the compartmentalization of its regulators, this is
thought to produce a relatively high concentration of
RanGTP in the nucleus.
Length = 166
Score = 33.4 bits (77), Expect = 0.013
Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 4/56 (7%)
Query: 9 PTIGSNVEEVIWKN----IHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRE 60
T+G V + + I F +WD GQ+ YY + I++ D T R
Sbjct: 31 ATLGVEVHPLDFHTNRGKIRFNVWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRV 86
>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 = 32.9 bits (76), Expect = 0.022
Identities = 20/56 (35%), Positives = 27/56 (48%), Gaps = 4/56 (7%)
Query: 9 PTIG----SNVEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRE 60
PTIG + EV K + +WD GQ+ RA YY + +LV D T R+
Sbjct: 30 PTIGVDFYTKTIEVDGKTVKLQIWDTAGQERFRALRPLYYRGAQGFLLVYDITSRD 85
>gnl|CDD|206659 cd01867, Rab8_Rab10_Rab13_like, Rab GTPase families 8, 10, 13
(Rab8, Rab10, Rab13). Rab8/Sec4/Ypt2 are known or
suspected to be involved in post-Golgi transport to the
plasma membrane. It is likely that these Rabs have
functions that are specific to the mammalian lineage
and have no orthologs in plants. Rab8 modulates
polarized membrane transport through reorganization of
actin and microtubules, induces the formation of new
surface extensions, and has an important role in
directed membrane transport to cell surfaces. The Ypt2
gene of the fission yeast Schizosaccharomyces pombe
encodes a member of the Ypt/Rab family of small
GTP-binding proteins, related in sequence to Sec4p of
Saccharomyces cerevisiae but closer to mammalian Rab8.
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 = 167
Score = 32.6 bits (75), Expect = 0.027
Identities = 15/40 (37%), Positives = 21/40 (52%)
Query: 21 KNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRE 60
K I +WD GQ+ R ++YY +ILV D TD +
Sbjct: 50 KKIKLQIWDTAGQERFRTITTSYYRGAMGIILVYDITDEK 89
>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 = 32.6 bits (75), Expect = 0.027
Identities = 21/96 (21%), Positives = 41/96 (42%), Gaps = 5/96 (5%)
Query: 6 HTSPTIG----SNVEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRER 61
TIG S V K + +WD GQ+ R+ +Y ++ ++V D T+R+
Sbjct: 28 QYQATIGIDFLSKTMYVDDKTVRLQLWDTAGQERFRSLIPSYIRDSSVAVVVYDITNRQS 87
Query: 62 ISLTKEELYKMLNHEDLSKAAVLIYANKQDIKNSMS 97
T ++ + E + +++ NK D+ +
Sbjct: 88 FDNT-DKWIDDVRDERGNDVIIVLVGNKTDLSDKRQ 122
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 32.4 bits (73), Expect = 0.036
Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 1/66 (1%)
Query: 27 MWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERISLTKEELYKMLNHEDLSKAAVLIY 86
+WD GQ+ R+ +Y ++ I+V D T+R+ T + + +LN E + +
Sbjct: 33 LWDTAGQERFRSLIPSYIRDSAAAIVVYDITNRQSFENTTKWIQDILN-ERGKDVIIALV 91
Query: 87 ANKQDI 92
NK D+
Sbjct: 92 GNKTDL 97
>gnl|CDD|206639 cd00066, G-alpha, Alpha subunit of G proteins (guanine nucleotide
binding). The alpha subunit of G proteins contains the
guanine nucleotide binding site. The heterotrimeric
GNP-binding proteins are signal transducers that
communicate signals from many hormones,
neurotransmitters, chemokines, and autocrine and
paracrine factors. Extracellular signals are received by
receptors, which activate the G proteins, which in turn
route the signals to several distinct intracellular
signaling pathways. The alpha subunit of G proteins is a
weak GTPase. In the resting state, heterotrimeric G
proteins are associated at the cytosolic face of the
plasma membrane and the alpha subunit binds to GDP. Upon
activation by a receptor GDP is replaced with GTP, and
the G-alpha/GTP complex dissociates from the beta and
gamma subunits. This results in activation of downstream
signaling pathways, such as cAMP synthesis by adenylyl
cyclase, which is terminated when GTP is hydrolized and
the heterotrimers reconstitute.
Length = 315
Score = 32.5 bits (75), Expect = 0.041
Identities = 22/85 (25%), Positives = 44/85 (51%), Gaps = 16/85 (18%)
Query: 21 KNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVI------------DSTDRERISLTKEE 68
KN+ F M+D+GGQ+S R W + + +I V+ +S +R + SL +
Sbjct: 159 KNLKFRMFDVGGQRSERKKWIHCFEDVTAIIFVVALSEYDQVLVEDESVNRMQESL---K 215
Query: 69 LYK-MLNHEDLSKAAVLIYANKQDI 92
L+ + N + +++++ NK+D+
Sbjct: 216 LFDSICNSRWFANTSIILFLNKKDL 240
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 31.7 bits (73), Expect = 0.047
Identities = 26/99 (26%), Positives = 43/99 (43%), Gaps = 15/99 (15%)
Query: 6 HTSPTIGSNVE------EVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDR 59
TIG V+ EV K + +WD GQ+ R+ S+YY +LV D T+R
Sbjct: 28 QYKSTIG--VDFKTKTIEVDGKRVKLQIWDTAGQERFRSITSSYYRGAVGALLVYDITNR 85
Query: 60 ---ERISLTKEELYKMLNHEDLSKAAVLIYANKQDIKNS 95
E + +EL + + +++ NK D++
Sbjct: 86 ESFENLENWLKELREYAS----PNVVIMLVGNKSDLEEQ 120
>gnl|CDD|206700 cd04127, Rab27A, Rab GTPase family 27a (Rab27a). The Rab27a
subfamily consists of Rab27a and its highly homologous
isoform, Rab27b. Unlike most Rab proteins whose
functions remain poorly defined, Rab27a has many known
functions. Rab27a has multiple effector proteins, and
depending on which effector it binds, Rab27a has
different functions as well as tissue distribution
and/or cellular localization. Putative functions have
been assigned to Rab27a when associated with the
effector proteins Slp1, Slp2, Slp3, Slp4, Slp5, DmSlp,
rabphilin, Dm/Ce-rabphilin, Slac2-a, Slac2-b, Slac2-c,
Noc2, JFC1, and Munc13-4. Rab27a has been associated
with several human diseases, including hemophagocytic
syndrome (Griscelli syndrome or GS), Hermansky-Pudlak
syndrome, and choroidermia. In the case of GS, a rare,
autosomal recessive disease, a Rab27a mutation is
directly responsible for the disorder. When Rab27a is
localized to the secretory granules of pancreatic beta
cells, it is believed to mediate glucose-stimulated
insulin secretion, making it a potential target for
diabetes therapy. When bound to JFC1 in prostate cells,
Rab27a is believed to regulate the exocytosis of
prostate- specific markers. 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 = 180
Score = 31.7 bits (72), Expect = 0.050
Identities = 13/72 (18%), Positives = 33/72 (45%)
Query: 23 IHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERISLTKEELYKMLNHEDLSKAA 82
+H +WD GQ+ R+ + ++ + +L+ D T + + + ++ H
Sbjct: 63 VHLQLWDTAGQERFRSLTTAFFRDAMGFLLMFDLTSEQSFLNVRNWMSQLQAHAYCENPD 122
Query: 83 VLIYANKQDIKN 94
+++ NK D+ +
Sbjct: 123 IVLIGNKADLPD 134
>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 = 31.6 bits (72), Expect = 0.051
Identities = 14/38 (36%), Positives = 20/38 (52%)
Query: 23 IHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRE 60
+ ++WD GQ+ A YY + ILV +TDRE
Sbjct: 51 VRLMLWDTAGQEEFDAITKAYYRGAQACILVFSTTDRE 88
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 32.0 bits (73), Expect = 0.052
Identities = 29/96 (30%), Positives = 42/96 (43%), Gaps = 18/96 (18%)
Query: 9 PTIGSNVEEVIWKN----IHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERISL 64
PTIG V + + I F WD GQ+ YY + + I++ D T R L
Sbjct: 44 PTIGVEVHPLDFFTNCGKIRFYCWDTAGQEKFGGLRDGYYIHGQCAIIMFDVTAR----L 99
Query: 65 TKEELYKMLN--HEDLSKAA----VLIYANKQDIKN 94
T YK + H DL + +++ NK D+KN
Sbjct: 100 T----YKNVPTWHRDLCRVCENIPIVLCGNKVDVKN 131
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 31.2 bits (71), Expect = 0.095
Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 4/55 (7%)
Query: 9 PTIGSNVEEVIWKN----IHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDR 59
PT+G V + + I F +WD GQ+ YY + I++ D T R
Sbjct: 40 PTLGVEVHPLKFYTNCGPICFNVWDTAGQEKFGGLRDGYYIKGQCAIIMFDVTSR 94
>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 = 31.0 bits (71), Expect = 0.10
Identities = 19/98 (19%), Positives = 31/98 (31%), Gaps = 16/98 (16%)
Query: 2 NEVVHTSPTIGSNVEEVIW-KNIHFIMWDLGGQQSLRAAWSTY-----YTNTEFVILVID 55
+ + TI V + N+ +WD GQ + T ++N +I V D
Sbjct: 26 RDTLRLGATIDVEQSHVRFLGNLTLNLWDCPGQDDFMENYLTRQKEHIFSNVGVLIYVFD 85
Query: 56 STDRERISLTKEELYKMLNHEDLSKAAVLIYANKQDIK 93
RE + L K +Y + K
Sbjct: 86 VESREYEE----------DLATLVKIIEALYQYSPNAK 113
>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 = 30.9 bits (70), Expect = 0.11
Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 5/60 (8%)
Query: 6 HTSPTIGSNVEE----VIWKNIHFIMWDLGGQQSLRAAW-STYYTNTEFVILVIDSTDRE 60
T TIG + E + + I +WD GQ+ R + YY N V+ V D T+
Sbjct: 30 RTEATIGVDFRERTVEIDGERIKVQLWDTAGQERFRKSMVQHYYRNVHAVVFVYDVTNMA 89
>gnl|CDD|214595 smart00275, G_alpha, G protein alpha subunit. Subunit of G
proteins that contains the guanine nucleotide binding
site.
Length = 342
Score = 30.6 bits (70), Expect = 0.19
Identities = 25/97 (25%), Positives = 46/97 (47%), Gaps = 16/97 (16%)
Query: 9 PTIGSNVEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVI------------DS 56
PT G I K + F M+D+GGQ+S R W + N +I + +S
Sbjct: 170 PTTGIQETAFIVKKLFFRMFDVGGQRSERKKWIHCFDNVTAIIFCVALSEYDQVLEEDES 229
Query: 57 TDRERISLTKEELYKMLNHED-LSKAAVLIYANKQDI 92
T+R + SL L++ + + + +++++ NK D+
Sbjct: 230 TNRMQESL---NLFESICNSRWFANTSIILFLNKIDL 263
>gnl|CDD|206657 cd01865, Rab3, Rab GTPase family 3 contains Rab3A, Rab3B, Rab3C and
Rab3D. The Rab3 subfamily contains Rab3A, Rab3B, Rab3C,
and Rab3D. All four isoforms were found in mouse brain
and endocrine tissues, with varying levels of
expression. Rab3A, Rab3B, and Rab3C localized to
synaptic and secretory vesicles; Rab3D was expressed at
high levels only in adipose tissue, exocrine glands, and
the endocrine pituitary, where it is localized to
cytoplasmic secretory granules. Rab3 appears to control
Ca2+-regulated exocytosis. The appropriate GDP/GTP
exchange cycle of Rab3A is required for Ca2+-regulated
exocytosis to occur, and interaction of the GTP-bound
form of Rab3A with effector molecule(s) is widely
believed to be essential for this process. Functionally,
most studies point toward a role for Rab3 in the
secretion of hormones and neurotransmitters. 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 = 165
Score = 29.9 bits (67), Expect = 0.20
Identities = 19/74 (25%), Positives = 35/74 (47%), Gaps = 1/74 (1%)
Query: 21 KNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERISLTKEELYKMLNHEDLSK 80
K I +WD GQ+ R + YY IL+ D T+ E + ++ ++ +
Sbjct: 48 KRIKLQIWDTAGQERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYS-WDN 106
Query: 81 AAVLIYANKQDIKN 94
A V++ NK D+++
Sbjct: 107 AQVILVGNKCDMED 120
>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 = 0.21
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 1/75 (1%)
Query: 17 EVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERISLTKEELYKMLNHE 76
E+ + I +WD GQ+ R+ +YY + +IL D T E E L ++ +
Sbjct: 50 EIKGEKIKLQIWDTAGQERFRSITQSYYRSANALILTYDITCEESFRCLPEWLREIEQYA 109
Query: 77 DLSKAAVLIYANKQD 91
+ +K ++ NK D
Sbjct: 110 N-NKVITILVGNKID 123
>gnl|CDD|206660 cd01868, Rab11_like, Rab GTPase family 11 (Rab11)-like includes
Rab11a, Rab11b, and Rab25. Rab11a, Rab11b, and Rab25
are closely related, evolutionary conserved Rab proteins
that are differentially expressed. Rab11a is
ubiquitously synthesized, Rab11b is enriched in brain
and heart and Rab25 is only found in epithelia. Rab11/25
proteins seem to regulate recycling pathways from
endosomes to the plasma membrane and to the trans-Golgi
network. Furthermore, Rab11a is thought to function in
the histamine-induced fusion of tubulovesicles
containing H+, K+ ATPase with the plasma membrane in
gastric parietal cells and in insulin-stimulated
insertion of GLUT4 in the plasma membrane of
cardiomyocytes. Overexpression of Rab25 has recently
been observed in ovarian cancer and breast cancer, and
has been correlated with worsened outcomes in both
diseases. In addition, Rab25 overexpression has also
been observed in prostate cancer, transitional cell
carcinoma of the bladder, and invasive breast tumor
cells. 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 = 165
Score = 29.1 bits (66), Expect = 0.42
Identities = 29/95 (30%), Positives = 42/95 (44%), Gaps = 17/95 (17%)
Query: 9 PTIGSNVE------EVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERI 62
TIG VE ++ K I +WD GQ+ RA S YY +LV D T +
Sbjct: 34 STIG--VEFATRTIQIDGKTIKAQIWDTAGQERYRAITSAYYRGAVGALLVYDITKK--- 88
Query: 63 SLTKEELYKMLN----HEDLSKAAVLIYANKQDIK 93
T E + + L H D S +++ NK D++
Sbjct: 89 -STFENVERWLKELRDHAD-SNIVIMLVGNKSDLR 121
>gnl|CDD|133267 cd01864, Rab19, Rab GTPase family 19 (Rab19). Rab19 subfamily.
Rab19 proteins are associated with Golgi stacks.
Similarity analysis indicated that Rab41 is closely
related to Rab19. However, the function of these Rabs
is not yet characterized. 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 = 165
Score = 28.9 bits (65), Expect = 0.51
Identities = 13/43 (30%), Positives = 20/43 (46%)
Query: 17 EVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDR 59
E+ K + +WD GQ+ R +YY + I+ D T R
Sbjct: 46 EIQGKRVKLQIWDTAGQERFRTITQSYYRSANGAIIAYDITRR 88
>gnl|CDD|233812 TIGR02290, M3_fam_3, oligoendopeptidase, pepF/M3 family. The M3
family of metallopeptidases contains several distinct
clades. Oligoendopeptidase F as characterized in
Lactococcus, the functionally equivalent
oligoendopeptidase B of group B Streptococcus, and
closely related sequences are described by TIGR00181.
The present family is quite similar but forms a distinct
clade, and a number of species have one member of each.
A greater sequence difference separates members of
TIGR02289, probable oligoendopeptidases of the M3 family
that probably should not be designated PepF.
Length = 587
Score = 29.2 bits (66), Expect = 0.55
Identities = 14/43 (32%), Positives = 19/43 (44%), Gaps = 3/43 (6%)
Query: 37 RAAWSTYYTNT--EFVILVIDSTDRERISLTKEELYKMLNHED 77
RAAWS Y I +D D E +L+ E+ +L D
Sbjct: 159 RAAWSRLYDELTGTLRI-PVDGKDGEEETLSLEQALNLLRDPD 200
>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 = 28.6 bits (64), Expect = 0.81
Identities = 19/68 (27%), Positives = 33/68 (48%), Gaps = 2/68 (2%)
Query: 27 MWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERISLTKE--ELYKMLNHEDLSKAAVL 84
+WD+GGQQ Y + V LV D T+ + ++ + K +N E +K ++
Sbjct: 54 VWDIGGQQIGGKMLDKYIYGAQAVCLVYDITNSQSFENLEDWLSVVKKVNEESETKPKMV 113
Query: 85 IYANKQDI 92
+ NK D+
Sbjct: 114 LVGNKTDL 121
>gnl|CDD|206692 cd04107, Rab32_Rab38, Rab GTPase families 18 (Rab18) and 32
(Rab32). Rab38/Rab32 subfamily. Rab32 and Rab38 are
members of the Rab family of small GTPases. Human Rab32
was first identified in platelets but it is expressed in
a variety of cell types, where it functions as an
A-kinase anchoring protein (AKAP). Rab38 has been shown
to be melanocyte-specific. 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 = 201
Score = 28.0 bits (63), Expect = 1.1
Identities = 18/76 (23%), Positives = 28/76 (36%), Gaps = 3/76 (3%)
Query: 21 KNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERISLT---KEELYKMLNHED 77
+ +WD+ GQ+ YY I+V D T K +L + +
Sbjct: 48 TVVRLQLWDIAGQERFGGMTRVYYKGAVGAIIVFDVTRPSTFEAVLKWKADLDSKVTLPN 107
Query: 78 LSKAAVLIYANKQDIK 93
L+ ANK D+K
Sbjct: 108 GEPIPALLLANKCDLK 123
>gnl|CDD|206695 cd04112, Rab26, Rab GTPase family 26 (Rab26). Rab26 subfamily.
First identified in rat pancreatic acinar cells, Rab26
is believed to play a role in recruiting mature
granules to the plasma membrane upon beta-adrenergic
stimulation. Rab26 belongs to the Rab functional group
III, which are considered key regulators of
intracellular vesicle transport during exocytosis.
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 = 191
Score = 27.9 bits (62), Expect = 1.3
Identities = 10/33 (30%), Positives = 19/33 (57%)
Query: 27 MWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDR 59
+WD GQ+ R+ YY + ++L+ D T++
Sbjct: 54 IWDTAGQERFRSVTHAYYRDAHALLLLYDVTNK 86
>gnl|CDD|206697 cd04116, Rab9, Rab GTPase family 9 (Rab9). Rab9 is found in late
endosomes, together with mannose 6-phosphate receptors
(MPRs) and the tail-interacting protein of 47 kD
(TIP47). Rab9 is a key mediator of vesicular transport
from late endosomes to the trans-Golgi network (TGN) by
redirecting the MPRs. Rab9 has been identified as a key
component for the replication of several viruses,
including HIV1, Ebola, Marburg, and measles, making it a
potential target for inhibiting a variety of viruses.
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 = 27.5 bits (61), Expect = 1.4
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 3/69 (4%)
Query: 27 MWDLGGQQSLRAAWSTYYTNTEFVIL---VIDSTDRERISLTKEELYKMLNHEDLSKAAV 83
+WD GQ+ R+ + +Y ++ +L V DS + +S K+E + ++
Sbjct: 58 IWDTAGQERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPESFPF 117
Query: 84 LIYANKQDI 92
+I NK DI
Sbjct: 118 VILGNKIDI 126
>gnl|CDD|206688 cd04101, RabL4, Rab GTPase-like family 4 (Rab-like4). RabL4
(Rab-like4) subfamily. RabL4s are novel proteins that
have high sequence similarity with Rab family members,
but display features that are distinct from Rabs, and
have been termed Rab-like. As in other Rab-like
proteins, RabL4 lacks a prenylation site at the
C-terminus. The specific function of RabL4 remains
unknown.
Length = 167
Score = 27.1 bits (60), Expect = 2.1
Identities = 11/70 (15%), Positives = 25/70 (35%)
Query: 23 IHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDRERISLTKEELYKMLNHEDLSKAA 82
+ ++D GQ+ + V +V D T+ + + ++ H
Sbjct: 53 VELFIFDSAGQELFSDMVENVWEQPAVVCVVYDVTNEVSFNNCSRWINRVRTHSHGLHTP 112
Query: 83 VLIYANKQDI 92
++ NK D+
Sbjct: 113 GVLVGNKCDL 122
>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 = 27.1 bits (61), Expect = 2.2
Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 6/70 (8%)
Query: 29 DLGGQQSLRAAWSTYYTNTEFVILVIDSTDR---ERISLTKEELYKMLNHEDLSKAAVLI 85
D GQ+ A Y N + ILV T R E I +E++ ++ + ED+ +++
Sbjct: 53 DTAGQEEFSAMRDQYIRNGDGFILVYSITSRESFEEIKNIREQILRVKDKEDVP---IVL 109
Query: 86 YANKQDIKNS 95
NK D++N
Sbjct: 110 VGNKCDLENE 119
>gnl|CDD|151307 pfam10858, DUF2659, Protein of unknown function (DUF2659). This
bacterial family of proteins has no known function.
Length = 220
Score = 27.2 bits (60), Expect = 2.4
Identities = 24/83 (28%), Positives = 33/83 (39%), Gaps = 6/83 (7%)
Query: 41 STYYTNTEFVILVIDSTDRERISLTKEELYKMLNHEDLSK----AAVLIYANKQDIKNSM 96
+T Y + LVID + + KE+L K LN+ D A IY DIKN+M
Sbjct: 129 TTSYARINWCSLVIDDNNLDIDD--KEKLIKYLNYFDDESKPFWATASIYKAIWDIKNNM 186
Query: 97 SPVEISNLLDLTSIKKQQWHIQS 119
NL L ++
Sbjct: 187 DNKAEKNLEALIRSNNSSDLLKD 209
>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 = 26.7 bits (60), Expect = 2.6
Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 10/61 (16%)
Query: 7 TSPTIGS-------NVEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDR 59
TIG+ N+++ + F +WD GQ+ R+ YY I+V D T
Sbjct: 30 QESTIGAAFLTQTVNLDDT---TVKFEIWDTAGQERYRSLAPMYYRGAAAAIVVYDITSE 86
Query: 60 E 60
E
Sbjct: 87 E 87
>gnl|CDD|177661 PLN00023, PLN00023, GTP-binding protein; Provisional.
Length = 334
Score = 27.1 bits (60), Expect = 2.8
Identities = 19/65 (29%), Positives = 31/65 (47%), Gaps = 2/65 (3%)
Query: 4 VVHTSPTIGSNVEEVIWKNIHFI-MWDLGGQQSLRAAWSTYYTNTEFVILVID-STDRER 61
+ + SP SN + + F+ +WD+ G + + S +Y+ VI V D S R +
Sbjct: 63 ITYGSPGSSSNSIKGDSERDFFVELWDVSGHERYKDCRSLFYSQINGVIFVHDLSQRRTK 122
Query: 62 ISLTK 66
SL K
Sbjct: 123 TSLQK 127
>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 = 26.5 bits (59), Expect = 3.0
Identities = 19/65 (29%), Positives = 28/65 (43%), Gaps = 9/65 (13%)
Query: 6 HTSPTIGSNVEEVIWKN-------IHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTD 58
S T G NV++ WK I +WD GGQ+ A + T+ +LV D
Sbjct: 29 DESSTHGINVQD--WKIPAPERKKIRLNVWDFGGQEIYHATHQFFLTSRSLYLLVFDLRT 86
Query: 59 RERIS 63
+ +S
Sbjct: 87 GDEVS 91
>gnl|CDD|150838 pfam10226, DUF2216, Uncharacterized conserved proteins (DUF2216).
This is the conserved N-terminal half of a proteins
which are found from worms to humans. some annotation
suggests it might be PKR, the Hepatitis delta
antigen-interacting protein A, but this could not be
confirmed.
Length = 195
Score = 26.7 bits (59), Expect = 3.1
Identities = 9/29 (31%), Positives = 17/29 (58%)
Query: 57 TDRERISLTKEELYKMLNHEDLSKAAVLI 85
+D E + +KEEL + L E+ K + ++
Sbjct: 10 SDEELLKWSKEELVRRLRREEAEKMSAIV 38
>gnl|CDD|235020 PRK02264, PRK02264, N(5),N(10)-methenyltetrahydromethanopterin
cyclohydrolase; Provisional.
Length = 317
Score = 26.7 bits (60), Expect = 3.9
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 66 KEELYKMLNHEDLSKAAVL 84
KEELY+ L + D + AVL
Sbjct: 118 KEELYEELGYRDDADFAVL 136
>gnl|CDD|238305 cd00545, MCH, Methenyltetrahydromethanopterin (methenyl-H4MPT)
cyclohydrolase (MCH). MCH is a cytoplasmic enzyme that
has been identified in methanogenic archaea, sulfate-
reducing archaea, and methylotrophic bacteria. It
catalyzes the reversible formation of N(5),
N(10)-methenyltetrahydromethanopterin (methenyl-H4MPT+)
from N(5)-formyltetrahydromethanopterin (formyl- H4MPT),
in the third step of the reaction to reduce CO2 to CH4.
The protein functions as a homodimer or homotrimer,
depending on the organism.
Length = 312
Score = 26.5 bits (59), Expect = 4.7
Identities = 9/24 (37%), Positives = 17/24 (70%)
Query: 62 ISLTKEELYKMLNHEDLSKAAVLI 85
++L EELY+ + + D ++ AVL+
Sbjct: 113 LALKPEELYEEIGYRDDAEVAVLV 136
>gnl|CDD|236284 PRK08541, PRK08541, flagellin; Validated.
Length = 211
Score = 26.0 bits (58), Expect = 5.4
Identities = 14/52 (26%), Positives = 22/52 (42%), Gaps = 9/52 (17%)
Query: 38 AAWSTYYTNTEFVILVI-DSTDRERISLTKEELYKMLNHEDLSKAAVLIYAN 88
WS T F I+V+ D+ SL+ Y +N D A+L+ +
Sbjct: 125 TVWSNLNGGTSFGIIVLQDADG----SLS--NSYPTINKGD--IVALLVNVS 168
>gnl|CDD|133321 cd04121, Rab40, Rab GTPase family 40 (Rab40) contains Rab40a,
Rab40b and Rab40c. The Rab40 subfamily contains
Rab40a, Rab40b, and Rab40c, which are all highly
homologous. In rat, Rab40c is localized to the
perinuclear recycling compartment (PRC), and is
distributed in a tissue-specific manor, with high
expression in brain, heart, kidney, and testis, low
expression in lung and liver, and no expression in
spleen and skeletal muscle. Rab40c is highly expressed
in differentiated oligodendrocytes but minimally
expressed in oligodendrocyte progenitors, suggesting a
role in the vesicular transport of myelin components.
Unlike most other Ras-superfamily proteins, Rab40c was
shown to have a much lower affinity for GTP, and an
affinity for GDP that is lower than for 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. 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 = 189
Score = 26.1 bits (57), Expect = 5.5
Identities = 11/39 (28%), Positives = 19/39 (48%)
Query: 21 KNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDSTDR 59
+ + +WD GQ + +Y + +ILV D T+R
Sbjct: 53 RRVKLQLWDTSGQGRFCTIFRSYSRGAQGIILVYDITNR 91
>gnl|CDD|221720 pfam12697, Abhydrolase_6, Alpha/beta hydrolase family. This
family contains alpha/beta hydrolase enzymes of diverse
specificity.
Length = 187
Score = 25.9 bits (57), Expect = 5.9
Identities = 6/25 (24%), Positives = 12/25 (48%)
Query: 15 VEEVIWKNIHFIMWDLGGQQSLRAA 39
++ + + + LGG +L AA
Sbjct: 59 LDALGLGPVVLVGHSLGGAVALAAA 83
>gnl|CDD|241476 cd13322, PH_PHLPP-like, PH domain leucine-rich repeat protein
phosphatase family Pleckstrin homology-like domain. The
PHLPP family has members PHLPP1 (also called
hSCOP/Suprachiasmatic nucleus circadian oscillatory
protein; PLEKHE1/Pleckstrin homology domain-containing
family E member 1) and PHLPP2 (PHLPP-like/PHLPPL). The
PHLPP family of novel Ser/Thr phosphatases serve as
important regulators of cell survival and apoptosis.
PHLPP isozymes catalyze the dephosphorylation of a
conserved regulatory motif, the hydrophobic motif, on
the AGC kinases Akt, PKC, and S6 kinase, as well as an
inhibitory site on the kinase Mst1, to inhibit cellular
proliferation and induce apoptosis and negatively
regulates ERK1/2 activation. Reductions in their
expression have been detected in several cancers and
linked to cancer progression. PHLPP1 and PHLPP2 both
contain an N-terminal PH domain, followed by 21 LRR
(leucine-rich) repeats, and a C-terminal PP2C-like
domain. PH domains have diverse functions, but in
general are involved in targeting proteins to the
appropriate cellular location or in the interaction with
a binding partner. They share little sequence
conservation, but all have a common fold, which is
electrostatically polarized. Less than 10% of PH domains
bind phosphoinositide phosphates (PIPs) with high
affinity and specificity. PH domains are distinguished
from other PIP-binding domains by their specific
high-affinity binding to PIPs with two vicinal phosphate
groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3
which results in targeting some PH domain proteins to
the plasma membrane. A few display strong specificity in
lipid binding. Any specificity is usually determined by
loop regions or insertions in the N-terminus of the
domain, which are not conserved across all PH domains.
PH domains are found in cellular signaling proteins such
as serine/threonine kinase, tyrosine kinases, regulators
of G-proteins, endocytotic GTPases, adaptors, as well as
cytoskeletal associated molecules and in lipid
associated enzymes.
Length = 194
Score = 25.6 bits (56), Expect = 7.9
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 6/44 (13%)
Query: 5 VHTSPTIGSNVEEVIWKNIHFIMWDLGGQQSLRAAWSTYYTNTE 48
+H P IG VEEV K+ H + + G QS TYY + +
Sbjct: 136 MHILPLIGGKVEEVK-KHQHCLAFSSAGPQS-----QTYYVSFD 173
>gnl|CDD|133324 cd04124, RabL2, Rab GTPase-like family 2 (Rab-like2). RabL2
(Rab-like2) subfamily. RabL2s are novel Rab proteins
identified recently which display features that are
distinct from other Rabs, and have been termed
Rab-like. RabL2 contains RabL2a and RabL2b, two very
similar Rab proteins that share > 98% sequence identity
in humans. RabL2b maps to the subtelomeric region of
chromosome 22q13.3 and RabL2a maps to 2q13, a region
that suggests it is also a subtelomeric gene. Both
genes are believed to be expressed ubiquitously,
suggesting that RabL2s are the first example of
duplicated genes in human proximal subtelomeric regions
that are both expressed actively. Like other Rab-like
proteins, RabL2s lack a prenylation site at the
C-terminus. The specific functions of RabL2a and RabL2b
remain unknown. 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 = 161
Score = 25.2 bits (55), Expect = 8.4
Identities = 13/37 (35%), Positives = 17/37 (45%)
Query: 21 KNIHFIMWDLGGQQSLRAAWSTYYTNTEFVILVIDST 57
K I WD GQ+ + ++YY ILV D T
Sbjct: 47 KTILVDFWDTAGQERFQTMHASYYHKAHACILVFDVT 83
>gnl|CDD|215277 PLN02501, PLN02501, digalactosyldiacylglycerol synthase.
Length = 794
Score = 25.7 bits (56), Expect = 8.9
Identities = 19/66 (28%), Positives = 28/66 (42%), Gaps = 13/66 (19%)
Query: 41 STYYTNTEFVILVIDSTDRERISLTKEELY---------KMLNHEDLSKAAVLIYANKQD 91
TY T+ +FV V ++ E LT E+ Y + + + DL K + N D
Sbjct: 663 LTYKTSEDFVAKVKEALANEPQPLTPEQRYNLSWEAATQRFMEYSDLDK----VLNNGDD 718
Query: 92 IKNSMS 97
K S S
Sbjct: 719 AKLSKS 724
>gnl|CDD|220691 pfam10323, 7TM_GPCR_Srv, Serpentine type 7TM GPCR chemoreceptor
Srv. Chemoreception is mediated in Caenorhabditis
elegans by members of the seven-transmembrane
G-protein-coupled receptor class (7TM GPCRs) of proteins
which are of the serpentine type. Srv is a member of the
Srg superfamily of chemoreceptors. Chemoperception is
one of the central senses of soil nematodes like C.
elegans which are otherwise 'blind' and 'deaf'.
Length = 283
Score = 25.3 bits (56), Expect = 9.5
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 3/49 (6%)
Query: 19 IWKNIHFIMWDLGGQQSLRAAWST--YYTNTEFVILVIDSTDRERISLT 65
+WK I I W G SL +T YY N E + +V D +R +L
Sbjct: 120 LWK-IILIYWLPGLLISLVVLKNTDIYYDNEENMPVVADKDVIQRFTLI 167
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
0.316 0.129 0.382
Gapped
Lambda K H
0.267 0.0791 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,190,794
Number of extensions: 518452
Number of successful extensions: 611
Number of sequences better than 10.0: 1
Number of HSP's gapped: 599
Number of HSP's successfully gapped: 106
Length of query: 126
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 41
Effective length of database: 7,167,512
Effective search space: 293867992
Effective search space used: 293867992
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.1 bits)