RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17235
(170 letters)
>gnl|CDD|153305 cd07621, BAR_SNX5_6, The Bin/Amphiphysin/Rvs (BAR) domain of
Sorting Nexins 5 and 6. BAR domains are dimerization,
lipid binding and curvature sensing modules found in
many different proteins with diverse functions. Sorting
nexins (SNXs) are Phox homology (PX) domain containing
proteins that are involved in regulating membrane
traffic and protein sorting in the endosomal system.
SNXs differ from each other in their lipid-binding
specificity, subcellular localization and specific
function in the endocytic pathway. A subset of SNXs also
contain BAR domains. The PX-BAR structural unit
determines the specific membrane targeting of SNXs.
Members of this subfamily include SNX5, SNX6, the
mammalian SNX32, and similar proteins. SNX5 and SNX6 may
be components of the retromer complex, a membrane coat
multimeric complex required for endosomal retrieval of
lysosomal hydrolase receptors to the Golgi, acting as a
mammalian equivalent of yeast Vsp17p. The function of
SNX32 is still unknown. BAR domains form dimers that
bind to membranes, induce membrane bending and
curvature, and may also be involved in protein-protein
interactions.
Length = 219
Score = 108 bits (272), Expect = 5e-30
Identities = 46/68 (67%), Positives = 56/68 (82%)
Query: 100 EVVEAEQVQQEACDKFEQMSDKAKEELNDFKERRVEAFKKNLMELAELEIKHAESQVNIL 159
+V AE QQEAC+KFE MS+ AK+EL DFK RRV AF+KNL+ELAELEIKHA++Q+ +L
Sbjct: 152 DVHAAEAAQQEACEKFESMSESAKQELLDFKTRRVAAFRKNLVELAELEIKHAKAQIQLL 211
Query: 160 KKCLAELK 167
K CLA LK
Sbjct: 212 KNCLAALK 219
>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 = 87.5 bits (218), Expect = 2e-22
Identities = 40/82 (48%), Positives = 50/82 (60%), Gaps = 2/82 (2%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYA-ENAKIFL 59
+Q+WDT G ER SITSSYY+ A AILV+ + N SF L + L E+ YA N I L
Sbjct: 51 LQIWDTAGQERFRSITSSYYRGAHGAILVYDVTNRESFENLDKWLNELKEYAPPNIPIIL 110
Query: 60 CGNKSDLEGTTPQVTEADMENF 81
GNKSDLE QV+ + + F
Sbjct: 111 VGNKSDLEDER-QVSTEEAQQF 131
>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 = 78.3 bits (194), Expect = 6e-19
Identities = 30/82 (36%), Positives = 46/82 (56%), Gaps = 2/82 (2%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYA-ENAKIFL 59
+Q+WDT G ER ++ YY+ A+ +LV+ + + SF + + L EI+ +A EN I L
Sbjct: 50 LQIWDTAGQERFRALRPLYYRGAQGFLLVYDITSRDSFENVKKWLEEILRHADENVPIVL 109
Query: 60 CGNKSDLEGTTPQVTEADMENF 81
GNK DLE V+ + E
Sbjct: 110 VGNKCDLEDQR-VVSTEEGEAL 130
>gnl|CDD|153346 cd07662, BAR_SNX6, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting
Nexin 6. BAR domains are dimerization, lipid binding
and curvature sensing modules found in many different
proteins with diverse functions. Sorting nexins (SNXs)
are Phox homology (PX) domain containing proteins that
are involved in regulating membrane traffic and protein
sorting in the endosomal system. SNXs differ from each
other in their lipid-binding specificity, subcellular
localization and specific function in the endocytic
pathway. A subset of SNXs also contain BAR domains. The
PX-BAR structural unit determines the specific membrane
targeting of SNXs. SNX6 forms a stable complex with SNX1
and may be a component of the retromer complex, a
membrane coat multimeric complex required for endosomal
retrieval of lysosomal hydrolase receptors to the Golgi,
acting as a mammalian equivalent of yeast Vsp17p. It
interacts with the receptor serine/threonine kinases
from the transforming growth factor-beta family. It also
plays roles in enhancing the degradation of EGFR and in
regulating the activity of Na,K-ATPase through its
interaction with Translationally Controlled Tumor
Protein (TCTP). BAR domains form dimers that bind to
membranes, induce membrane bending and curvature, and
may also be involved in protein-protein interactions.
Length = 218
Score = 78.9 bits (194), Expect = 1e-18
Identities = 39/69 (56%), Positives = 54/69 (78%)
Query: 99 QEVVEAEQVQQEACDKFEQMSDKAKEELNDFKERRVEAFKKNLMELAELEIKHAESQVNI 158
++V++AE QQ C KFE++S+ AK+EL DFK RRV AF+KNL+ELAELE+KHA+ + +
Sbjct: 150 KDVLQAETTQQLCCQKFEKISESAKQELIDFKTRRVAAFRKNLVELAELELKHAKGNLQL 209
Query: 159 LKKCLAELK 167
L+ CLA L
Sbjct: 210 LQSCLAVLN 218
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 76.8 bits (190), Expect = 2e-18
Identities = 36/68 (52%), Positives = 43/68 (63%), Gaps = 1/68 (1%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYA-ENAKIFL 59
+Q+WDT G ER SITSSYY+ A A+LV+ + N SF L L E+ YA N I L
Sbjct: 51 LQIWDTAGQERFRSITSSYYRGAVGALLVYDITNRESFENLENWLKELREYASPNVVIML 110
Query: 60 CGNKSDLE 67
GNKSDLE
Sbjct: 111 VGNKSDLE 118
>gnl|CDD|153347 cd07663, BAR_SNX5, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting
Nexin 5. BAR domains are dimerization, lipid binding
and curvature sensing modules found in many different
proteins with diverse functions. Sorting nexins (SNXs)
are Phox homology (PX) domain containing proteins that
are involved in regulating membrane traffic and protein
sorting in the endosomal system. SNXs differ from each
other in their lipid-binding specificity, subcellular
localization and specific function in the endocytic
pathway. A subset of SNXs also contain BAR domains. The
PX-BAR structural unit determines the specific membrane
targeting of SNXs. SNX5, abundantly expressed in
macrophages, regulates macropinocytosis, a process that
enables cells to internalize large amounts of external
solutes. It may also be a component of the retromer
complex, a membrane coat multimeric complex required for
endosomal retrieval of lysosomal hydrolase receptors to
the Golgi, acting as a mammalian equivalent of yeast
Vsp17p. It also binds the Fanconi anaemia
complementation group A protein (FANCA). SNX5 is
localized to a subdomain of early endosome and is
recruited to the plasma membrane following EGF
stimulation and elevation of PI(3,4)P2 levels. BAR
domains form dimers that bind to membranes, induce
membrane bending and curvature, and may also be involved
in protein-protein interactions.
Length = 218
Score = 76.9 bits (189), Expect = 8e-18
Identities = 37/69 (53%), Positives = 53/69 (76%)
Query: 99 QEVVEAEQVQQEACDKFEQMSDKAKEELNDFKERRVEAFKKNLMELAELEIKHAESQVNI 158
++V +AE QQE C KFE++S+ AK+EL FK RRV AF+KNL+E+ ELEIKHA++ V++
Sbjct: 150 KDVKQAEAHQQECCQKFEKLSESAKQELISFKRRRVAAFRKNLIEMTELEIKHAKNNVSL 209
Query: 159 LKKCLAELK 167
L+ C+ K
Sbjct: 210 LQSCIDLFK 218
>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 = 65.4 bits (160), Expect = 5e-14
Identities = 32/68 (47%), Positives = 42/68 (61%), Gaps = 1/68 (1%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYA-ENAKIFL 59
+Q+WDT G ER +ITSSYY+ A I+V+ + + SF+ + Q L EI YA EN L
Sbjct: 53 LQIWDTAGQERFRTITSSYYRGAHGIIIVYDVTDQESFNNVKQWLQEIDRYASENVNKLL 112
Query: 60 CGNKSDLE 67
GNK DL
Sbjct: 113 VGNKCDLT 120
>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 = 64.5 bits (158), Expect = 1e-13
Identities = 29/67 (43%), Positives = 43/67 (64%), Gaps = 1/67 (1%)
Query: 2 QLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAE-NAKIFLC 60
Q+WDT G ER +ITS+YY+ A A+LV+ + ++F + + L E+ +A+ N I L
Sbjct: 55 QIWDTAGQERYRAITSAYYRGAVGALLVYDITKKSTFENVERWLKELRDHADSNIVIMLV 114
Query: 61 GNKSDLE 67
GNKSDL
Sbjct: 115 GNKSDLR 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 = 63.6 bits (155), Expect = 3e-13
Identities = 28/68 (41%), Positives = 40/68 (58%), Gaps = 1/68 (1%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTY-AENAKIFL 59
+Q+WDT G ER +IT SYY+ A AI+ + + +SF + + E+ Y A N + L
Sbjct: 54 LQIWDTAGQERFRTITQSYYRSANGAIIAYDITRRSSFESVPHWIEEVEKYGASNVVLLL 113
Query: 60 CGNKSDLE 67
GNK DLE
Sbjct: 114 IGNKCDLE 121
>gnl|CDD|206696 cd04113, Rab4, Rab GTPase family 4 (Rab4). Rab4 subfamily. Rab4
has been implicated in numerous functions within the
cell. It helps regulate endocytosis through the sorting,
recycling, and degradation of early endosomes. Mammalian
Rab4 is involved in the regulation of many surface
proteins including G-protein-coupled receptors,
transferrin receptor, integrins, and surfactant protein
A. Experimental data implicate Rab4 in regulation of the
recycling of internalized receptors back to the plasma
membrane. It is also believed to influence
receptor-mediated antigen processing in B-lymphocytes,
in calcium-dependent exocytosis in platelets, in
alpha-amylase secretion in pancreatic cells, and in
insulin-induced translocation of Glut4 from internal
vesicles to the cell surface. Rab4 is known to share
effector proteins with Rab5 and Rab11. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 161
Score = 63.2 bits (154), Expect = 4e-13
Identities = 30/68 (44%), Positives = 42/68 (61%), Gaps = 1/68 (1%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAE-NAKIFL 59
+Q+WDT G ER S+T SYY+ A A+LV+ + + SF+ L+ L + T A + I L
Sbjct: 51 LQIWDTAGQERFRSVTRSYYRGAAGALLVYDITSRESFNALTNWLTDARTLASPDIVIIL 110
Query: 60 CGNKSDLE 67
GNK DLE
Sbjct: 111 VGNKKDLE 118
>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 = 63.9 bits (155), Expect = 5e-13
Identities = 36/91 (39%), Positives = 53/91 (58%), Gaps = 2/91 (2%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYA-ENAKIFL 59
+Q+WDT G ER SITS+YY+ A+ ILV+ + +F L + + I YA E+A++ L
Sbjct: 51 LQIWDTAGQERFNSITSAYYRSAKGIILVYDITKKETFDDLPKWMKMIDKYASEDAELLL 110
Query: 60 CGNKSDLEGTTPQVTEADMENFWSRRSSRRF 90
GNK D E T ++T E F + + RF
Sbjct: 111 VGNKLDCE-TDREITRQQGEKFAQQITGMRF 140
>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 = 62.7 bits (153), Expect = 5e-13
Identities = 28/70 (40%), Positives = 40/70 (57%), Gaps = 2/70 (2%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYA--ENAKIF 58
+ +WDT G ER ++TSSYY+ A+ ILV+ + +F L L E+ TY+ +A
Sbjct: 51 LAIWDTAGQERFRTLTSSYYRGAQGVILVYDVTRRDTFDNLDTWLNELDTYSTNPDAVKM 110
Query: 59 LCGNKSDLEG 68
L GNK D E
Sbjct: 111 LVGNKIDKEN 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 = 62.1 bits (151), Expect = 1e-12
Identities = 29/71 (40%), Positives = 43/71 (60%), Gaps = 6/71 (8%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASF----HVLSQHLLEIVTYAENAK 56
+QLWDT G ER S+T+++++ A +L+F L + SF + +SQ L+ Y EN
Sbjct: 65 LQLWDTAGQERFRSLTTAFFRDAMGFLLMFDLTSEQSFLNVRNWMSQ--LQAHAYCENPD 122
Query: 57 IFLCGNKSDLE 67
I L GNK+DL
Sbjct: 123 IVLIGNKADLP 133
>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 = 61.9 bits (151), Expect = 1e-12
Identities = 26/82 (31%), Positives = 46/82 (56%), Gaps = 2/82 (2%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYA-ENAKIFL 59
+ +WDT G ER ++ YY+ A+ AILV+ + +A SF + + + E+ N + +
Sbjct: 51 LAIWDTAGQERYHALGPIYYRDADGAILVYDITDADSFQKVKKWIKELKQMRGNNISLVI 110
Query: 60 CGNKSDLEGTTPQVTEADMENF 81
GNK DLE V++++ E +
Sbjct: 111 VGNKIDLE-RQRVVSKSEAEEY 131
>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 = 61.1 bits (148), Expect = 3e-12
Identities = 28/68 (41%), Positives = 45/68 (66%), Gaps = 1/68 (1%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYA-ENAKIFL 59
+Q+WDT G ER +IT++YY+ A IL++ + N SF+ + +I TY+ +NA++ L
Sbjct: 52 LQIWDTAGQERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSWDNAQVIL 111
Query: 60 CGNKSDLE 67
GNK D+E
Sbjct: 112 VGNKCDME 119
>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 = 60.7 bits (147), Expect = 4e-12
Identities = 33/67 (49%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAENAKI-FL 59
+Q+WDT G ER SIT SYY+ A A IL + + SF L + L EI YA N I L
Sbjct: 58 LQIWDTAGQERFRSITQSYYRSANALILTYDITCEESFRCLPEWLREIEQYANNKVITIL 117
Query: 60 CGNKSDL 66
GNK DL
Sbjct: 118 VGNKIDL 124
>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 = 60.4 bits (147), Expect = 5e-12
Identities = 27/68 (39%), Positives = 41/68 (60%), Gaps = 1/68 (1%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYA-ENAKIFL 59
+Q+WDT G ER +IT+SYY+ A ILV+ + + SF + + I +A E+ + L
Sbjct: 54 LQIWDTAGQERFRTITTSYYRGAMGIILVYDITDEKSFENIKNWMRNIDEHASEDVERML 113
Query: 60 CGNKSDLE 67
GNK D+E
Sbjct: 114 VGNKCDME 121
>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 = 60.1 bits (146), Expect = 6e-12
Identities = 28/68 (41%), Positives = 40/68 (58%), Gaps = 1/68 (1%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYA-ENAKIFL 59
+Q+WDT G E SIT SYY+ A A+LV+ + +F+ L+ L + ++ N I L
Sbjct: 55 LQIWDTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQHSNSNMTIML 114
Query: 60 CGNKSDLE 67
GNK DLE
Sbjct: 115 IGNKCDLE 122
>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 = 59.9 bits (146), Expect = 6e-12
Identities = 27/82 (32%), Positives = 42/82 (51%), Gaps = 2/82 (2%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAEN-AKIFL 59
+QLWDT G ER S+ SY + + A++V+ + N SF + + ++ N I L
Sbjct: 51 LQLWDTAGQERFRSLIPSYIRDSSVAVVVYDITNRQSFDNTDKWIDDVRDERGNDVIIVL 110
Query: 60 CGNKSDLEGTTPQVTEADMENF 81
GNK+DL QV+ + E
Sbjct: 111 VGNKTDLSDKR-QVSTEEGEKK 131
>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 = 58.7 bits (143), Expect = 1e-11
Identities = 25/79 (31%), Positives = 38/79 (48%), Gaps = 3/79 (3%)
Query: 5 DTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEI--VTYAENAKIFLCGN 62
DT G E +++ Y + + ILV+S+ + SF + +I V E+ I L GN
Sbjct: 53 DTAGQEEFSAMRDQYIRNGDGFILVYSITSRESFEEIKNIREQILRVKDKEDVPIVLVGN 112
Query: 63 KSDLEGTTPQVTEADMENF 81
K DLE QV+ + E
Sbjct: 113 KCDLENER-QVSTEEGEAL 130
>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 = 59.8 bits (145), Expect = 2e-11
Identities = 32/91 (35%), Positives = 45/91 (49%), Gaps = 3/91 (3%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAENAKI--F 58
+QLWDT G ER SIT SYY+ + +LVF + N SF + L E ++ + +
Sbjct: 54 LQLWDTAGQERFRSITRSYYRNSVGVLLVFDITNRESFEHVHDWLEEARSHIQPHRPVFI 113
Query: 59 LCGNKSDLEGTTPQVTEADMENFWSRRSSRR 89
L G+K DLE QVT + E +
Sbjct: 114 LVGHKCDLESQR-QVTREEAEKLAKDLGMKY 143
>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 = 58.7 bits (142), Expect = 3e-11
Identities = 32/80 (40%), Positives = 47/80 (58%), Gaps = 2/80 (2%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYA-ENAKIFL 59
+Q+WDT G ER S+T +YY+ A A +L++ + N +SF + L EI+ YA + I L
Sbjct: 52 LQIWDTAGQERFRSVTHAYYRDAHALLLLYDVTNKSSFDNIRAWLTEILEYAQSDVVIML 111
Query: 60 CGNKSDLEGTTPQVTEADME 79
GNK+D+ G V D E
Sbjct: 112 LGNKADMSGER-VVKREDGE 130
>gnl|CDD|133318 cd04118, Rab24, Rab GTPase family 24 (Rab24). Rab24 is distinct
from other Rabs in several ways. It exists primarily in
the GTP-bound state, having a low intrinsic GTPase
activity; it is not efficiently geranyl-geranylated at
the C-terminus; it does not form a detectable complex
with Rab GDP-dissociation inhibitors (GDIs); and it has
recently been shown to undergo tyrosine phosphorylation
when overexpressed in vitro. The specific function of
Rab24 still remains unknown. It is found in a transport
route between ER-cis-Golgi and late endocytic
compartments. It is putatively involved in an autophagic
pathway, possibly directing misfolded proteins in the ER
to degradative pathways. 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 = 193
Score = 58.7 bits (142), Expect = 3e-11
Identities = 37/136 (27%), Positives = 63/136 (46%), Gaps = 15/136 (11%)
Query: 3 LWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAENAKIFLCGN 62
+WDT G ER +++ YY+ A+AAI+ + L +++SF + E+ E+ KI+LCG
Sbjct: 54 IWDTAGSERYEAMSRIYYRGAKAAIVCYDLTDSSSFERAKFWVKELQNLEEHCKIYLCGT 113
Query: 63 KSDL---EGTTPQVTEADMENFWSRRSSRRFKP------------QEVVEPQEVVEAEQV 107
KSDL + + QV D+++F ++ F+ Q+V E Q+
Sbjct: 114 KSDLIEQDRSLRQVDFHDVQDFADEIKAQHFETSSKTGQNVDELFQKVAEDFVSRANNQM 173
Query: 108 QQEACDKFEQMSDKAK 123
E Q +
Sbjct: 174 NTEKGVDLGQKKNSYF 189
>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 = 57.2 bits (138), Expect = 9e-11
Identities = 27/70 (38%), Positives = 42/70 (60%), Gaps = 1/70 (1%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAE-NAKIFL 59
+Q+WDT G ER ++T SYY+ A A++V+ + ++++ LS L + N IFL
Sbjct: 53 LQIWDTAGQERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTVIFL 112
Query: 60 CGNKSDLEGT 69
GNK+DLE
Sbjct: 113 IGNKADLEAQ 122
>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 = 56.4 bits (136), Expect = 2e-10
Identities = 29/93 (31%), Positives = 45/93 (48%), Gaps = 1/93 (1%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAENAKIFLC 60
+Q+WDT G ER +ITS+YY+ I+V+ + N SF + + L EI ++ L
Sbjct: 57 LQIWDTAGQERFRTITSTYYRGTHGVIVVYDVTNGESFVNVKRWLQEIEQNCDDVCKVLV 116
Query: 61 GNKSDLEGTTPQVTEADMENFWSRRSSRRFKPQ 93
GNK+D + V D F + F+
Sbjct: 117 GNKND-DPERKVVETEDAYKFAGQMGISLFETS 148
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 55.7 bits (134), Expect = 6e-10
Identities = 24/77 (31%), Positives = 35/77 (45%), Gaps = 2/77 (2%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTY--AENAKIF 58
+QLWDT G E S+ YY+ A ++V+ S L++ LE + ++ I
Sbjct: 56 LQLWDTAGQEEYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPIL 115
Query: 59 LCGNKSDLEGTTPQVTE 75
L GNK DL E
Sbjct: 116 LVGNKIDLFDEQSSSEE 132
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 54.9 bits (132), Expect = 9e-10
Identities = 28/66 (42%), Positives = 42/66 (63%), Gaps = 1/66 (1%)
Query: 2 QLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAE-NAKIFLC 60
Q+WDT G ER +ITS+YY+ A A+LV+ + +F + + L E+ +A+ N I +
Sbjct: 64 QIWDTAGQERYRAITSAYYRGAVGALLVYDITKRQTFDNVQRWLRELRDHADSNIVIMMA 123
Query: 61 GNKSDL 66
GNKSDL
Sbjct: 124 GNKSDL 129
>gnl|CDD|206641 cd00157, Rho, Ras homology family (Rho) of small guanosine
triphosphatases (GTPases). Members of the Rho (Ras
homology) family include RhoA, Cdc42, Rac, Rnd, Wrch1,
RhoBTB, and Rop. There are 22 human Rho family members
identified currently. These proteins are all involved in
the reorganization of the actin cytoskeleton in response
to external stimuli. They also have roles in cell
transformation by Ras in cytokinesis, in focal adhesion
formation and in the stimulation of stress-activated
kinase. These various functions are controlled through
distinct effector proteins and mediated through a
GTP-binding/GTPase cycle involving three classes of
regulating proteins: GAPs (GTPase-activating proteins),
GEFs (guanine nucleotide exchange factors), and GDIs
(guanine nucleotide dissociation inhibitors). Most Rho
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. Since crystal structures
often lack C-terminal residues, this feature is not
available for annotation in many of the CDs in the
hierarchy.
Length = 171
Score = 54.5 bits (132), Expect = 9e-10
Identities = 38/134 (28%), Positives = 59/134 (44%), Gaps = 19/134 (14%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASF-HVLSQHLLEIVTYAENAKIFL 59
+ LWDT G E + Y + +L FS+D+ +SF +V ++ EI Y N I L
Sbjct: 50 LGLWDTAGQEEYDRLRPLSYPQTDVFLLCFSVDSPSSFENVKTKWYPEIKHYCPNVPIIL 109
Query: 60 CGNKSDLEGTTPQVTEADMENFWSRRSSRRFKPQEVVEPQEVVEAEQVQQE-ACDKFEQM 118
G K DL D N + K Q+ + P+ E E++ +E K+ +
Sbjct: 110 VGTKIDLR---------DDGNT----LKKLEKKQKPITPE---EGEKLAKEIGAVKYMEC 153
Query: 119 SDKAKEELND-FKE 131
S +E L + F E
Sbjct: 154 SALTQEGLKEVFDE 167
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 54.9 bits (132), Expect = 1e-09
Identities = 28/67 (41%), Positives = 39/67 (58%), Gaps = 1/67 (1%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAE-NAKIFL 59
+Q+WDT G E SIT SYY+ A A+LV+ + +F+ L+ L + +A N I L
Sbjct: 57 LQIWDTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLASWLEDARQHANANMTIML 116
Query: 60 CGNKSDL 66
GNK DL
Sbjct: 117 IGNKCDL 123
>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 = 52.9 bits (128), Expect = 2e-09
Identities = 28/79 (35%), Positives = 42/79 (53%), Gaps = 2/79 (2%)
Query: 4 WDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYA-ENAKIFLCGN 62
WDT G ER S+ YY+ A AAI+V+ + + SF + E+ + N I L GN
Sbjct: 55 WDTAGQERYRSLAPMYYRGAAAAIVVYDITSEESFEKAKSWVKELQEHGPPNIVIALAGN 114
Query: 63 KSDLEGTTPQVTEADMENF 81
K+DLE QV+ + + +
Sbjct: 115 KADLESKR-QVSTEEAQEY 132
>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 = 53.1 bits (128), Expect = 4e-09
Identities = 28/86 (32%), Positives = 37/86 (43%), Gaps = 5/86 (5%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLS---QHLLEIVTYAENAKI 57
+QLWD G ER +T YYK A AI+VF + ++F + L VT I
Sbjct: 52 LQLWDIAGQERFGGMTRVYYKGAVGAIIVFDVTRPSTFEAVLKWKADLDSKVTLPNGEPI 111
Query: 58 --FLCGNKSDLEGTTPQVTEADMENF 81
L NK DL+ M+ F
Sbjct: 112 PALLLANKCDLKKERLAKDPEQMDQF 137
>gnl|CDD|206655 cd01862, Rab7, Rab GTPase family 7 (Rab7). Rab7 subfamily. Rab7 is
a small Rab GTPase that regulates vesicular traffic from
early to late endosomal stages of the endocytic pathway.
The yeast Ypt7 and mammalian Rab7 are both involved in
transport to the vacuole/lysosome, whereas Ypt7 is also
required for homotypic vacuole fusion. Mammalian Rab7 is
an essential participant in the autophagic pathway for
sequestration and targeting of cytoplasmic components to
the lytic compartment. Mammalian Rab7 is also proposed
to function as a tumor suppressor. 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 = 172
Score = 51.5 bits (124), Expect = 1e-08
Identities = 28/86 (32%), Positives = 43/86 (50%), Gaps = 6/86 (6%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYA-----ENA 55
+Q+WDT G ER S+ ++Y+ A+ +LV+ + N SF L E + A EN
Sbjct: 51 LQIWDTAGQERFQSLGVAFYRGADCCVLVYDVTNPKSFESLDSWRDEFLIQASPRDPENF 110
Query: 56 KIFLCGNKSDLEGTTPQVTEADMENF 81
+ GNK DLE QV+ + +
Sbjct: 111 PFVVLGNKIDLEE-KRQVSTKKAQQW 135
>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 = 51.3 bits (123), Expect = 1e-08
Identities = 23/64 (35%), Positives = 33/64 (51%)
Query: 3 LWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAENAKIFLCGN 62
LWDT G E +IT +YY+ A+A ILVFS + SF + ++ + + L
Sbjct: 55 LWDTAGQEEFDAITKAYYRGAQACILVFSTTDRESFEAIESWKEKVEAECGDIPMVLVQT 114
Query: 63 KSDL 66
K DL
Sbjct: 115 KIDL 118
>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 = 51.0 bits (122), Expect = 1e-08
Identities = 28/68 (41%), Positives = 39/68 (57%), Gaps = 2/68 (2%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAE--NAKIF 58
+QLWDT G ER I S+YY+ A+A I+VF L + AS Q L + + + + +F
Sbjct: 51 LQLWDTAGQERFKCIASTYYRGAQAIIIVFDLTDVASLEHTRQWLEDALKENDPSSVLLF 110
Query: 59 LCGNKSDL 66
L G K DL
Sbjct: 111 LVGTKKDL 118
>gnl|CDD|206713 cd04146, RERG_RasL11_like, Ras-related and Estrogen-Regulated
Growth inhibitor (RERG) and Ras-like 11 (RasL11)-like
families. RERG (Ras-related and Estrogen- Regulated
Growth inhibitor) and Ras-like 11 are members of a novel
subfamily of Ras that were identified based on their
behavior in breast and prostate tumors, respectively.
RERG expression was decreased or lost in a significant
fraction of primary human breast tumors that lack
estrogen receptor and are correlated with poor clinical
prognosis. Elevated RERG expression correlated with
favorable patient outcome in a breast tumor subtype that
is positive for estrogen receptor expression. In
contrast to most Ras proteins, RERG overexpression
inhibited the growth of breast tumor cells in vitro and
in vivo. RasL11 was found to be ubiquitously expressed
in human tissue, but down-regulated in prostate tumors.
Both RERG and RasL11 lack the C-terminal CaaX
prenylation motif, where a = an aliphatic amino acid and
X = any amino acid, and are localized primarily in the
cytoplasm. Both are believed to have tumor suppressor
activity.
Length = 166
Score = 49.6 bits (119), Expect = 4e-08
Identities = 22/82 (26%), Positives = 42/82 (51%), Gaps = 6/82 (7%)
Query: 1 MQLWDTGGMERVAS--ITSSYYKFAEAAILVFSLDNAASFHVLS---QHLLEIVTYAENA 55
+++ DT G ++ ++A+ +LV+S+ + +SF V+S Q + EI
Sbjct: 49 LEIQDTPGQQQNEDPESLERSLRWADGFVLVYSITDRSSFDVVSQLLQLIREIKKRDGEI 108
Query: 56 KIFLCGNKSDLEGTTPQVTEAD 77
+ L GNK+DL + QV+ +
Sbjct: 109 PVILVGNKADLLHSR-QVSTEE 129
>gnl|CDD|153314 cd07630, BAR_SNX_like, The Bin/Amphiphysin/Rvs (BAR) domain of
uncharacterized Sorting Nexins. BAR domains are
dimerization, lipid binding and curvature sensing
modules found in many different proteins with diverse
functions. This subfamily is composed of uncharacterized
proteins with similarity to sorting nexins (SNXs), which
are Phox homology (PX) domain containing proteins that
are involved in regulating membrane traffic and protein
sorting in the endosomal system. SNXs differ from each
other in their lipid-binding specificity, subcellular
localization and specific function in the endocytic
pathway. A subset of SNXs also contain BAR domains. The
PX-BAR structural unit determines the specific membrane
targeting of SNXs. BAR domains form dimers that bind to
membranes, induce membrane bending and curvature, and
may also be involved in protein-protein interactions.
Length = 198
Score = 50.2 bits (120), Expect = 5e-08
Identities = 26/73 (35%), Positives = 44/73 (60%)
Query: 91 KPQEVVEPQEVVEAEQVQQEACDKFEQMSDKAKEELNDFKERRVEAFKKNLMELAELEIK 150
K E +PQ+ +AE+ +++A +FE++S AK+EL F +RV + L+ AE +IK
Sbjct: 124 KALEKAKPQKKEQAEEAKKKAETEFEEISSLAKKELERFHRQRVLELQSALVCYAESQIK 183
Query: 151 HAESQVNILKKCL 163
+A+ +L K L
Sbjct: 184 NAKEAAAVLTKTL 196
>gnl|CDD|153280 cd07596, BAR_SNX, The Bin/Amphiphysin/Rvs (BAR) domain of Sorting
Nexins. BAR domains are dimerization, lipid binding and
curvature sensing modules found in many different
proteins with diverse functions. Sorting nexins (SNXs)
are Phox homology (PX) domain containing proteins that
are involved in regulating membrane traffic and protein
sorting in the endosomal system. SNXs differ from each
other in their lipid-binding specificity, subcellular
localization and specific function in the endocytic
pathway. A subset of SNXs also contain BAR domains. The
PX-BAR structural unit determines the specific membrane
targeting of SNXs. BAR domains form dimers that bind to
membranes, induce membrane bending and curvature, and
may also be involved in protein-protein interactions.
Length = 218
Score = 50.0 bits (120), Expect = 5e-08
Identities = 24/66 (36%), Positives = 37/66 (56%)
Query: 100 EVVEAEQVQQEACDKFEQMSDKAKEELNDFKERRVEAFKKNLMELAELEIKHAESQVNIL 159
E+ EAE +EA ++E++S++ KEEL F E R K L E A L++++AE
Sbjct: 153 ELEEAESALEEARKRYEEISERLKEELKRFHEERARDLKAALKEFARLQVQYAEKIAEAW 212
Query: 160 KKCLAE 165
+ L E
Sbjct: 213 ESLLPE 218
>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 = 48.7 bits (116), Expect = 8e-08
Identities = 26/73 (35%), Positives = 37/73 (50%), Gaps = 3/73 (4%)
Query: 3 LWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAENAKIFLCGN 62
WDT G ER ++ +SYY A A ILVF + ++ LS+ E+ Y + N
Sbjct: 53 FWDTAGQERFQTMHASYYHKAHACILVFDVTRKITYKNLSKWYEELREYRPEIPCIVVAN 112
Query: 63 KSDLEGTTPQVTE 75
K DL+ P VT+
Sbjct: 113 KIDLD---PSVTQ 122
>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 = 48.7 bits (116), Expect = 9e-08
Identities = 27/81 (33%), Positives = 44/81 (54%), Gaps = 5/81 (6%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAE--NAKIF 58
+Q+WDT G ER S+ + +Y+ ++ +L FS+D++ SF LS E + YA+ + F
Sbjct: 56 LQIWDTAGQERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPESF 115
Query: 59 ---LCGNKSDLEGTTPQVTEA 76
+ GNK D+ EA
Sbjct: 116 PFVILGNKIDIPERQVSTEEA 136
>gnl|CDD|206698 cd04117, Rab15, Rab GTPase family 15 (Rab15). Rab15 colocalizes
with the transferrin receptor in early endosome
compartments, but not with late endosomal markers. It
codistributes with Rab4 and Rab5 on early/sorting
endosomes, and with Rab11 on pericentriolar recycling
endosomes. It is believed to function as an inhibitory
GTPase that regulates distinct steps in early endocytic
trafficking. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation of
the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 164
Score = 48.8 bits (116), Expect = 1e-07
Identities = 27/72 (37%), Positives = 42/72 (58%), Gaps = 9/72 (12%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVT----YA-ENA 55
+Q+WDT G ER +IT YY+ A+ LV+ + + S+ QH+++ V+ YA E
Sbjct: 51 IQIWDTAGQERYQTITKQYYRRAQGIFLVYDISSERSY----QHIMKWVSDVDEYAPEGV 106
Query: 56 KIFLCGNKSDLE 67
+ L GNK+D E
Sbjct: 107 QKILIGNKADEE 118
>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 = 48.6 bits (116), Expect = 1e-07
Identities = 31/95 (32%), Positives = 44/95 (46%), Gaps = 4/95 (4%)
Query: 1 MQLWDTGGMERV-ASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAENAKI-- 57
+QLWDT G ER S+ YY+ A + V+ + N ASFH L + E ++ ++
Sbjct: 53 VQLWDTAGQERFRKSMVQHYYRNVHAVVFVYDVTNMASFHSLPSWIEECEQHSLPNEVPR 112
Query: 58 FLCGNKSDLEGTTPQVTEADMENFWSRRSSRRFKP 92
L GNK DL QV + F S F+
Sbjct: 113 ILVGNKCDLREQI-QVPTDLAQRFADAHSMPLFET 146
>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 = 48.2 bits (115), Expect = 1e-07
Identities = 21/101 (20%), Positives = 34/101 (33%), Gaps = 12/101 (11%)
Query: 2 QLWDTGGMERV-----ASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAENAK 56
L DT G++ + + A+ +LV + S +L + E
Sbjct: 50 VLVDTPGLDEFGGLGREELARLLLRGADLILLVVDSTDRESEEDAKLLILRRL-RKEGIP 108
Query: 57 IFLCGNKSDLEGTTPQVTEADMENFWSRRSSRRFKPQEVVE 97
I L GNK DL + E ++E + V E
Sbjct: 109 IILVGNKIDL------LEEREVEELLRLEELAKILGVPVFE 143
>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 = 48.4 bits (115), Expect = 2e-07
Identities = 27/84 (32%), Positives = 40/84 (47%), Gaps = 1/84 (1%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAENAKIFLC 60
+QLWDT G R +I SY + A+ ILV+ + N SF + + + EI +A L
Sbjct: 57 LQLWDTSGQGRFCTIFRSYSRGAQGIILVYDITNRWSFDGIDRWIKEIDEHAPGVPKILV 116
Query: 61 GNKSDLEGTTPQVTEADMENFWSR 84
GN+ L QV + + R
Sbjct: 117 GNRLHL-AFKRQVATEQAQAYAER 139
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 47.8 bits (113), Expect = 3e-07
Identities = 26/67 (38%), Positives = 41/67 (61%), Gaps = 1/67 (1%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVT-YAENAKIFL 59
+QLWDT G ER S+ SY + + AAI+V+ + N SF ++ + +I+ ++ I L
Sbjct: 31 LQLWDTAGQERFRSLIPSYIRDSAAAIVVYDITNRQSFENTTKWIQDILNERGKDVIIAL 90
Query: 60 CGNKSDL 66
GNK+DL
Sbjct: 91 VGNKTDL 97
>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 = 47.4 bits (113), Expect = 3e-07
Identities = 24/74 (32%), Positives = 33/74 (44%), Gaps = 11/74 (14%)
Query: 2 QLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLS------QHLLEIVTYAE-N 54
L DT G E +I YY+ E+++ VF + VL + EI+ +AE
Sbjct: 54 NLLDTAGQEDYDAIRRLYYRAVESSLRVFDI----VILVLDVEEILEKQTKEIIHHAESG 109
Query: 55 AKIFLCGNKSDLEG 68
I L GNK DL
Sbjct: 110 VPIILVGNKIDLRD 123
>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 = 47.4 bits (113), Expect = 3e-07
Identities = 24/94 (25%), Positives = 39/94 (41%), Gaps = 10/94 (10%)
Query: 4 WDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTY------AENAKI 57
+D G + + +YK + +LV+ + + SF L L E+ EN +
Sbjct: 54 FDLSGHPEYLEVRNEFYKDTQGVLLVYDVTDRQSFEALDSWLKEMKQEGGPHGNMENIVV 113
Query: 58 FLCGNKSDLEGTTPQVTEADMENFWSRRSSRRFK 91
+C NK DL T + D W+ S+ FK
Sbjct: 114 VVCANKIDL--TKHRAVSEDEGRLWA--ESKGFK 143
>gnl|CDD|206705 cd04133, Rop_like, Rho-related protein from plants (Rop)-like. The
Rop (Rho-related protein from plants) subfamily plays a
role in diverse cellular processes, including
cytoskeletal organization, pollen and vegetative cell
growth, hormone responses, stress responses, and
pathogen resistance. Rops are able to regulate several
downstream pathways to amplify a specific signal by
acting as master switches early in the signaling
cascade. They transmit a variety of extracellular and
intracellular signals. Rops are involved in establishing
cell polarity in root-hair development, root-hair
elongation, pollen-tube growth, cell-shape formation,
responses to hormones such as abscisic acid (ABA) and
auxin, responses to abiotic stresses such as oxygen
deprivation, and disease resistance and disease
susceptibility. An individual Rop can have a unique
function or an overlapping function shared with other
Rop proteins; in addition, a given Rop-regulated
function can be controlled by one or multiple Rop
proteins. For example, Rop1, Rop3, and Rop5 are all
involved in pollen-tube growth; Rop2 plays a role in
response to low-oxygen environments, cell-morphology,
and root-hair development; root-hair development is also
regulated by Rop4 and Rop6; Rop6 is also responsible for
ABA response, and ABA response is also regulated by
Rop10. Plants retain some of the regulatory mechanisms
that are shared by other members of the Rho family, but
have also developed a number of unique modes for
regulating Rops. Unique RhoGEFs have been identified
that are exclusively active toward Rop proteins, such as
those containing the domain PRONE (plant-specific Rop
nucleotide exchanger). Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 173
Score = 44.8 bits (106), Expect = 2e-06
Identities = 25/65 (38%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 3 LWDTGGMERVASITSSYYKFAEAAILVFSLDNAASF-HVLSQHLLEIVTYAENAKIFLCG 61
LWDT G E + Y+ A+ +L FSL + AS+ +VL + + E+ YA I L G
Sbjct: 53 LWDTAGQEDYNRLRPLSYRGADVFLLAFSLISKASYENVLKKWIPELRHYAPGVPIVLVG 112
Query: 62 NKSDL 66
K DL
Sbjct: 113 TKLDL 117
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 44.7 bits (105), Expect = 4e-06
Identities = 27/70 (38%), Positives = 38/70 (54%), Gaps = 3/70 (4%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLL-EIVTYAENAKI-- 57
+ +WDT G ER ++TSSYY+ A+ ILV+ + +F LS E+ Y+ N
Sbjct: 64 LTIWDTAGQERFRTLTSSYYRNAQGIILVYDVTRRETFTNLSDVWGKEVELYSTNQDCVK 123
Query: 58 FLCGNKSDLE 67
L GNK D E
Sbjct: 124 MLVGNKVDRE 133
>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 = 44.6 bits (105), Expect = 5e-06
Identities = 20/65 (30%), Positives = 34/65 (52%)
Query: 3 LWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAENAKIFLCGN 62
+WDT G E+ + YY + AI++F + ++ + ++V EN I LCGN
Sbjct: 48 VWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTARVTYKNVPNWHRDLVRVCENIPIVLCGN 107
Query: 63 KSDLE 67
K D++
Sbjct: 108 KVDVK 112
>gnl|CDD|133326 cd04126, Rab20, Rab GTPase family 20 (Rab20). Rab20 is one of
several Rab proteins that appear to be restricted in
expression to the apical domain of murine polarized
epithelial cells. It is expressed on the apical side of
polarized kidney tubule and intestinal epithelial cells,
and in non-polarized cells. It also localizes to
vesico-tubular structures below the apical brush border
of renal proximal tubule cells and in the apical region
of duodenal epithelial cells. Rab20 has also been shown
to colocalize with vacuolar H+-ATPases (V-ATPases) in
mouse kidney cells, suggesting a role in the regulation
of V-ATPase traffic in specific portions of the nephron.
It was also shown to be one of several proteins whose
expression is upregulated in human myelodysplastic
syndrome (MDS) patients. 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 = 220
Score = 44.5 bits (105), Expect = 5e-06
Identities = 27/101 (26%), Positives = 40/101 (39%), Gaps = 6/101 (5%)
Query: 3 LWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAENAKIF-LCG 61
+WDT G E+ + S Y + A A IL + + N S L L + A +F + G
Sbjct: 48 IWDTAGREQFHGLGSMYCRGAAAVILTYDVSNVQSLEELEDRFLGLTDTANEDCLFAVVG 107
Query: 62 NKSDLEGTTPQVTEADMENFWSRRSSRRFKPQEVVEPQEVV 102
NK DL T ++ R S Q V ++
Sbjct: 108 NKLDL--TEEGALAGQEKDAGDRVSPE---DQRQVTLEDAK 143
>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 = 43.2 bits (102), Expect = 8e-06
Identities = 28/79 (35%), Positives = 42/79 (53%), Gaps = 3/79 (3%)
Query: 5 DTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEI--VTYAENAKIFLCGN 62
DT G E A+I +Y++ E +LVFS+ + SF L++ +I V +N + L GN
Sbjct: 54 DTAGQEDYAAIRDNYFRSGEGFLLVFSITDMESFTALAEFREQILRVKEDDNVPLLLVGN 113
Query: 63 KSDLEGTTPQVTEADMENF 81
K DLE QV+ + N
Sbjct: 114 KCDLEDKR-QVSVEEAANL 131
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 42.8 bits (101), Expect = 2e-05
Identities = 20/62 (32%), Positives = 31/62 (50%)
Query: 4 WDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAENAKIFLCGNK 63
WDT G E+ + YY + AI++F + + ++ + +IV EN I L GNK
Sbjct: 63 WDTAGQEKFGGLRDGYYIKGQCAIIMFDVTSRITYKNVPNWHRDIVRVCENIPIVLVGNK 122
Query: 64 SD 65
D
Sbjct: 123 VD 124
>gnl|CDD|133376 cd04176, Rap2, Rap2 family GTPase consists of Rap2a, Rap2b, and
Rap2c. The Rap2 subgroup is part of the Rap subfamily
of the Ras family. It consists of Rap2a, Rap2b, and
Rap2c. Both isoform 3 of the human mitogen-activated
protein kinase kinase kinase kinase 4 (MAP4K4) and
Traf2- and Nck-interacting kinase (TNIK) are putative
effectors of Rap2 in mediating the activation of c-Jun
N-terminal kinase (JNK) to regulate the actin
cytoskeleton. In human platelets, Rap2 was shown to
interact with the cytoskeleton by binding the actin
filaments. In embryonic Xenopus development, Rap2 is
necessary for the Wnt/beta-catenin signaling pathway.
The Rap2 interacting protein 9 (RPIP9) is highly
expressed in human breast carcinomas and correlates with
a poor prognosis, suggesting a role for Rap2 in breast
cancer oncogenesis. Rap2b, but not Rap2a, Rap2c, Rap1a,
or Rap1b, is expressed in human red blood cells, where
it is believed to be involved in vesiculation. A number
of additional effector proteins for Rap2 have been
identified, including the RalGEFs RalGDS, RGL, and Rlf,
which also interact with Rap1 and Ras. 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 = 41.7 bits (98), Expect = 3e-05
Identities = 25/69 (36%), Positives = 36/69 (52%), Gaps = 2/69 (2%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEI--VTYAENAKIF 58
+++ DT G E+ AS+ Y K + I+V+SL N +F + +I V E I
Sbjct: 51 LEILDTAGTEQFASMRDLYIKNGQGFIVVYSLVNQQTFQDIKPMRDQIVRVKGYEKVPII 110
Query: 59 LCGNKSDLE 67
L GNK DLE
Sbjct: 111 LVGNKVDLE 119
>gnl|CDD|197466 smart00010, small_GTPase, Small GTPase of the Ras superfamily;
ill-defined subfamily. SMART predicts Ras-like small
GTPases of the ARF, RAB, RAN, RAS, and SAR subfamilies.
Others that could not be classified in this way are
predicted to be members of the small GTPase superfamily
without predictions of the subfamily.
Length = 166
Score = 41.4 bits (98), Expect = 4e-05
Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 4/70 (5%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASF---HVLSQHLLEIVTYAENAKI 57
+ + DT G E +++ Y + E +LV+S+ + SF + +L + ++ I
Sbjct: 52 LDILDTAGQEEFSAMRDQYMRTGEGFLLVYSITDRQSFEEIAKFREQILRVKDR-DDVPI 110
Query: 58 FLCGNKSDLE 67
L GNK DLE
Sbjct: 111 VLVGNKCDLE 120
>gnl|CDD|197554 smart00174, RHO, Rho (Ras homology) subfamily of Ras-like small
GTPases. Members of this subfamily of Ras-like small
GTPases include Cdc42 and Rac, as well as Rho isoforms.
Length = 174
Score = 41.4 bits (98), Expect = 4e-05
Identities = 24/69 (34%), Positives = 35/69 (50%), Gaps = 7/69 (10%)
Query: 2 QLWDTGGME---RVASITSSYYKFAEAAILVFSLDNAASF-HVLSQHLLEIVTYAENAKI 57
LWDT G E R+ + SY + ++ FS+D+ ASF +V + E+ + N I
Sbjct: 49 GLWDTAGQEDYDRLRPL--SYPD-TDVFLICFSVDSPASFENVKEKWYPEVKHFCPNVPI 105
Query: 58 FLCGNKSDL 66
L G K DL
Sbjct: 106 ILVGTKLDL 114
>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 = 41.1 bits (97), Expect = 5e-05
Identities = 20/62 (32%), Positives = 32/62 (51%)
Query: 4 WDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAENAKIFLCGNK 63
WDT G E+ + YY + AI++F + + ++ + ++V EN I LCGNK
Sbjct: 54 WDTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNK 113
Query: 64 SD 65
D
Sbjct: 114 VD 115
>gnl|CDD|206706 cd04134, Rho3, Ras homology family 3 (Rho3) of small guanosine
triphosphatases (GTPases). Rho3 is a member of the Rho
family found only in fungi. Rho3 is believed to regulate
cell polarity by interacting with the diaphanous/formin
family protein For3 to control both the actin
cytoskeleton and microtubules. Rho3 is also believed to
have a direct role in exocytosis that is independent of
its role in regulating actin polarity. The function in
exocytosis may be two-pronged: first, in the transport
of post-Golgi vesicles from the mother cell to the bud,
mediated by myosin (Myo2); second, in the docking and
fusion of vesicles to the plasma membrane, mediated by
an exocyst (Exo70) protein. Most Rho proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Rho proteins.
Length = 185
Score = 41.4 bits (97), Expect = 6e-05
Identities = 24/69 (34%), Positives = 32/69 (46%), Gaps = 1/69 (1%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASF-HVLSQHLLEIVTYAENAKIFL 59
+ LWDT G E + S Y +L FS+DN S +V S+ L EI + K+ L
Sbjct: 50 LSLWDTAGQEEFDRLRSLSYADTHVIMLCFSVDNPDSLENVESKWLAEIRHHCPGVKLVL 109
Query: 60 CGNKSDLEG 68
K DL
Sbjct: 110 VALKCDLRE 118
>gnl|CDD|133330 cd04130, Wrch_1, Wnt-1 responsive Cdc42 homolog (Wrch-1) is a Rho
family GTPase similar to Cdc42. Wrch-1 (Wnt-1
responsive Cdc42 homolog) is a Rho family GTPase that
shares significant sequence and functional similarity
with Cdc42. Wrch-1 was first identified in mouse mammary
epithelial cells, where its transcription is upregulated
in Wnt-1 transformation. Wrch-1 contains N- and
C-terminal extensions relative to cdc42, suggesting
potential differences in cellular localization and
function. The Wrch-1 N-terminal extension contains
putative SH3 domain-binding motifs and has been shown to
bind the SH3 domain-containing protein Grb2, which
increases the level of active Wrch-1 in cells. Unlike
Cdc42, which localizes to the cytosol and perinuclear
membranes, Wrch-1 localizes extensively with the plasma
membrane and endosomes. The membrane association,
localization, and biological activity of Wrch-1 indicate
an atypical model of regulation distinct from other Rho
family GTPases. Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 173
Score = 40.8 bits (96), Expect = 7e-05
Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 1/67 (1%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLL-EIVTYAENAKIFL 59
+QL DT G + + Y + +L FS+ N +SF +S+ + EI + A I L
Sbjct: 50 LQLCDTAGQDEFDKLRPLCYPDTDVFLLCFSVVNPSSFQNISEKWIPEIRKHNPKAPIIL 109
Query: 60 CGNKSDL 66
G ++DL
Sbjct: 110 VGTQADL 116
>gnl|CDD|214541 smart00173, RAS, Ras subfamily of RAS small GTPases. Similar in
fold and function to the bacterial EF-Tu GTPase. p21Ras
couples receptor Tyr kinases and G protein receptors to
protein kinase cascades.
Length = 164
Score = 39.8 bits (94), Expect = 2e-04
Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 4/70 (5%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLS---QHLLEIVTYAENAKI 57
+ + DT G E +++ Y + E +LV+S+ + SF + + +L + ++ I
Sbjct: 50 LDILDTAGQEEFSAMRDQYMRTGEGFLLVYSITDRQSFEEIKKFREQILRVKDR-DDVPI 108
Query: 58 FLCGNKSDLE 67
L GNK DLE
Sbjct: 109 VLVGNKCDLE 118
>gnl|CDD|133353 cd04153, Arl5_Arl8, Arf-like 5 (Arl5) and 8 (Arl8) GTPases.
Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like
Arl4 and Arl7, are localized to the nucleus and
nucleolus. Arl5 is developmentally regulated during
embryogenesis in mice. Human Arl5 interacts with the
heterochromatin protein 1-alpha (HP1alpha), a nonhistone
chromosomal protein that is associated with
heterochromatin and telomeres, and prevents telomere
fusion. Arl5 may also play a role in embryonic nuclear
dynamics and/or signaling cascades. Arl8 was identified
from a fetal cartilage cDNA library. It is found in
brain, heart, lung, cartilage, and kidney. No function
has been assigned for Arl8 to date.
Length = 174
Score = 39.6 bits (93), Expect = 2e-04
Identities = 21/78 (26%), Positives = 41/78 (52%), Gaps = 4/78 (5%)
Query: 3 LWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAE--NAKIFLC 60
+WD GG E + S ++YY +A ILV + + + L +++ + + A + +
Sbjct: 63 MWDIGGQESLRSSWNTYYTNTDAVILVIDSTDRERLPLTKEELYKMLAHEDLRKAVLLVL 122
Query: 61 GNKSDLEG--TTPQVTEA 76
NK DL+G T +++E+
Sbjct: 123 ANKQDLKGAMTPAEISES 140
>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 = 37.8 bits (88), Expect = 4e-04
Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 3/64 (4%)
Query: 3 LWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIV---TYAENAKIFL 59
+WD GG E + + K+A+A +LV+ L + S + +S+ + + + L
Sbjct: 52 IWDFGGREELKFEHIIFMKWADAILLVYDLTDRESLNEVSRLIAWLPNLRKLGGKIPVIL 111
Query: 60 CGNK 63
GNK
Sbjct: 112 VGNK 115
>gnl|CDD|133338 cd04138, H_N_K_Ras_like, Ras GTPase family containing H-Ras,N-Ras
and K-Ras4A/4B. H-Ras/N-Ras/K-Ras subfamily. H-Ras,
N-Ras, and K-Ras4A/4B are the prototypical members of
the Ras family. These isoforms generate distinct signal
outputs despite interacting with a common set of
activators and effectors, and are strongly associated
with oncogenic progression in tumor initiation. Mutated
versions of Ras that are insensitive to GAP stimulation
(and are therefore constitutively active) are found in a
significant fraction of human cancers. Many Ras guanine
nucleotide exchange factors (GEFs) have been identified.
They 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 that stimulate a variety of diverse cytoplasmic
signaling activities. Some are known to positively
mediate the oncogenic properties of Ras, including Raf,
phosphatidylinositol 3-kinase (PI3K), RalGEFs, and
Tiam1. Others are proposed to play negative regulatory
roles in oncogenesis, including RASSF 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 = 162
Score = 38.2 bits (89), Expect = 5e-04
Identities = 19/68 (27%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 5 DTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEI--VTYAENAKIFLCGN 62
DT G E +++ Y + E + VF++++ SF + + +I V +++ + L GN
Sbjct: 55 DTAGQEEYSAMRDQYMRTGEGFLCVFAINSRKSFEDIHTYREQIKRVKDSDDVPMVLVGN 114
Query: 63 KSDLEGTT 70
K DL T
Sbjct: 115 KCDLAART 122
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 38.6 bits (90), Expect = 5e-04
Identities = 19/63 (30%), Positives = 31/63 (49%)
Query: 4 WDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAENAKIFLCGNK 63
WDT G E+ + YY + AI++F + ++ + ++ EN I LCGNK
Sbjct: 67 WDTAGQEKFGGLRDGYYIHGQCAIIMFDVTARLTYKNVPTWHRDLCRVCENIPIVLCGNK 126
Query: 64 SDL 66
D+
Sbjct: 127 VDV 129
>gnl|CDD|133343 cd04143, Rhes_like, Ras homolog enriched in striatum (Rhes) and
activator of G-protein signaling 1 (Dexras1/AGS1). This
subfamily includes Rhes (Ras homolog enriched in
striatum) and Dexras1/AGS1 (activator of G-protein
signaling 1). These proteins are homologous, but exhibit
significant differences in tissue distribution and
subcellular localization. Rhes is found primarily in the
striatum of the brain, but is also expressed in other
areas of the brain, such as the cerebral cortex,
hippocampus, inferior colliculus, and cerebellum. Rhes
expression is controlled by thyroid hormones. In rat
PC12 cells, Rhes is farnesylated and localizes to the
plasma membrane. Rhes binds and activates PI3K, and
plays a role in coupling serpentine membrane receptors
with heterotrimeric G-protein signaling. Rhes has
recently been shown to be reduced under conditions of
dopamine supersensitivity and may play a role in
determining dopamine receptor sensitivity. Dexras1/AGS1
is a dexamethasone-induced Ras protein that is expressed
primarily in the brain, with low expression levels in
other tissues. Dexras1 localizes primarily to the
cytoplasm, and is a critical regulator of the circadian
master clock to photic and nonphotic input. 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.
Length = 247
Score = 38.2 bits (89), Expect = 0.001
Identities = 24/62 (38%), Positives = 30/62 (48%), Gaps = 11/62 (17%)
Query: 27 ILVFSLDNAASFH---VLSQHLLEIVTYA-----ENAKI--FLCGNKSDL-EGTTPQVTE 75
ILVFSLDN SF L + +LE + EN KI +CGNK+D Q E
Sbjct: 76 ILVFSLDNRESFEEVCRLREQILETKSCLKNKTKENVKIPMVICGNKADRDFPREVQRDE 135
Query: 76 AD 77
+
Sbjct: 136 VE 137
>gnl|CDD|133377 cd04177, RSR1, RSR1/Bud1p family GTPase. RSR1/Bud1p is a member of
the Rap subfamily of the Ras family that is found in
fungi. In budding yeasts, RSR1 is involved in selecting
a site for bud growth on the cell cortex, which directs
the establishment of cell polarization. The Rho family
GTPase cdc42 and its GEF, cdc24, then establish an axis
of polarized growth by organizing the actin cytoskeleton
and secretory apparatus at the bud site. It is believed
that cdc42 interacts directly with RSR1 in vivo. In
filamentous fungi, polar growth occurs at the tips of
hypha and at novel growth sites along the extending
hypha. In Ashbya gossypii, RSR1 is a key regulator of
hyphal growth, localizing at the tip region and
regulating in apical polarization of the actin
cytoskeleton. 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.
Length = 168
Score = 37.5 bits (87), Expect = 0.001
Identities = 20/69 (28%), Positives = 40/69 (57%), Gaps = 2/69 (2%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTY--AENAKIF 58
+++ DT G E+ ++ Y K + +LV+S+ + AS + L + +++ ++N +
Sbjct: 51 LEILDTAGTEQFTAMRELYIKSGQGFLLVYSVTSEASLNELGELREQVLRIKDSDNVPMV 110
Query: 59 LCGNKSDLE 67
L GNK+DLE
Sbjct: 111 LVGNKADLE 119
>gnl|CDD|220180 pfam09325, Vps5, Vps5 C terminal like. Vps5 is a sorting nexin
that functions in membrane trafficking. This is the C
terminal dimerisation domain.
Length = 236
Score = 37.6 bits (88), Expect = 0.001
Identities = 21/55 (38%), Positives = 32/55 (58%)
Query: 99 QEVVEAEQVQQEACDKFEQMSDKAKEELNDFKERRVEAFKKNLMELAELEIKHAE 153
+EV EAE+ Q+A +FE +S+ K+EL F+ RV+ FK L E I+ +
Sbjct: 170 KEVDEAERKVQQAKKEFEDISETIKKELERFETERVDDFKNVLEIYLESAIESQK 224
>gnl|CDD|206708 cd04136, Rap_like, Rap-like family consists of Rap1, Rap2 and RSR1.
The Rap subfamily consists of the Rap1, Rap2, and RSR1.
Rap subfamily proteins perform different cellular
functions, depending on the isoform and its subcellular
localization. For example, in rat salivary gland,
neutrophils, and platelets, Rap1 localizes to secretory
granules and is believed to regulate exocytosis or the
formation of secretory granules. Rap1 has also been
shown to localize in the Golgi of rat fibroblasts,
zymogen granules, plasma membrane, and microsomal
membrane of the pancreatic acini, as well as in the
endocytic compartment of skeletal muscle cells and
fibroblasts. Rap1 localizes in the nucleus of human
oropharyngeal squamous cell carcinomas (SCCs) and cell
lines. Rap1 plays a role in phagocytosis by controlling
the binding of adhesion receptors (typically integrins)
to their ligands. In yeast, Rap1 has been implicated in
multiple functions, including activation and silencing
of transcription and maintenance of telomeres. Rap2 is
involved in multiple functions, including activation of
c-Jun N-terminal kinase (JNK) to regulate the actin
cytoskeleton and activation of the Wnt/beta-catenin
signaling pathway in embryonic Xenopus. A number of
effector proteins for Rap2 have been identified,
including isoform 3 of the human mitogen-activated
protein kinase kinase kinase kinase 4 (MAP4K4) and
Traf2- and Nck-interacting kinase (TNIK), and the
RalGEFs RalGDS, RGL, and Rlf, which also interact with
Rap1 and Ras. RSR1 is the fungal homolog of Rap1 and
Rap2. In budding yeasts, it is involved in selecting a
site for bud growth, which directs the establishment of
cell polarization. The Rho family GTPase Cdc42 and its
GEF, Cdc24, then establish an axis of polarized growth.
It is believed that Cdc42 interacts directly with RSR1
in vivo. In filamentous fungi such as Ashbya gossypii,
RSR1 is a key regulator of polar growth in the hypha.
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 = 164
Score = 36.4 bits (84), Expect = 0.002
Identities = 22/69 (31%), Positives = 35/69 (50%), Gaps = 2/69 (2%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEI--VTYAENAKIF 58
+++ DT G E+ ++ Y K + LV+S+ SF+ L +I V E+ +
Sbjct: 51 LEILDTAGTEQFTAMRDLYIKNGQGFALVYSITAQQSFNDLQDLREQILRVKDTEDVPMI 110
Query: 59 LCGNKSDLE 67
L GNK DLE
Sbjct: 111 LVGNKCDLE 119
>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 = 36.7 bits (85), Expect = 0.002
Identities = 24/71 (33%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAENA----K 56
+Q+WD GG + + Y A+A LV+ + N+ SF L L + E + K
Sbjct: 52 LQVWDIGGQQIGGKMLDKYIYGAQAVCLVYDITNSQSFENLEDWLSVVKKVNEESETKPK 111
Query: 57 IFLCGNKSDLE 67
+ L GNK+DLE
Sbjct: 112 MVLVGNKTDLE 122
>gnl|CDD|153307 cd07623, BAR_SNX1_2, The Bin/Amphiphysin/Rvs (BAR) domain of
Sorting Nexins 1 and 2. BAR domains are dimerization,
lipid binding and curvature sensing modules found in
many different proteins with diverse functions. Sorting
nexins (SNXs) are Phox homology (PX) domain containing
proteins that are involved in regulating membrane
traffic and protein sorting in the endosomal system.
SNXs differ from each other in their lipid-binding
specificity, subcellular localization and specific
function in the endocytic pathway. A subset of SNXs also
contain BAR domains. The PX-BAR structural unit
determines the specific membrane targeting of SNXs. This
subfamily consists of SNX1, SNX2, and similar proteins.
SNX1 and SNX2 are components of the retromer complex, a
membrane coat multimeric complex required for endosomal
retrieval of lysosomal hydrolase receptors to the Golgi.
The retromer consists of a cargo-recognition subcomplex
and a subcomplex formed by a dimer of sorting nexins
(SNX1 and/or SNX2), which ensures efficient cargo
sorting by facilitating proper membrane localization of
the cargo-recognition subcomplex. BAR domains form
dimers that bind to membranes, induce membrane bending
and curvature, and may also be involved in
protein-protein interactions.
Length = 224
Score = 36.5 bits (85), Expect = 0.003
Identities = 15/53 (28%), Positives = 28/53 (52%)
Query: 99 QEVVEAEQVQQEACDKFEQMSDKAKEELNDFKERRVEAFKKNLMELAELEIKH 151
QE+ E E +FE++S K+E+ F++ RV+ FK +++ E +
Sbjct: 156 QEIKEWEAKVDRGQKEFEEISKTIKKEIERFEKNRVKDFKDIIIKYLESLLNT 208
>gnl|CDD|206715 cd04148, RGK, Rem, Rem2, Rad, Gem/Kir (RGK) subfamily of Ras
GTPases. RGK subfamily. The RGK (Rem, Rem2, Rad,
Gem/Kir) subfamily of Ras GTPases are expressed in a
tissue-specific manner and are dynamically regulated by
transcriptional and posttranscriptional mechanisms in
response to environmental cues. RGK proteins bind to the
beta subunit of L-type calcium channels, causing
functional down-regulation of these voltage-dependent
calcium channels, and either termination of
calcium-dependent secretion or modulation of electrical
conduction and contractile function. Inhibition of
L-type calcium channels by Rem2 may provide a mechanism
for modulating calcium-triggered exocytosis in
hormone-secreting cells, and has been proposed to
influence the secretion of insulin in pancreatic beta
cells. RGK proteins also interact with and inhibit the
Rho/Rho kinase pathway to modulate remodeling of the
cytoskeleton. Two characteristics of RGK proteins cited
in the literature are N-terminal and C-terminal
extensions beyond the GTPase domain typical of Ras
superfamily members. The N-terminal extension is not
conserved among family members; the C-terminal extension
is reported to be conserved among the family and lack
the CaaX prenylation motif typical of
membrane-associated Ras proteins. However, a putative
CaaX motif has been identified in the alignment of the
C-terminal residues of this CD.
Length = 219
Score = 36.2 bits (84), Expect = 0.003
Identities = 19/68 (27%), Positives = 36/68 (52%), Gaps = 2/68 (2%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEI--VTYAENAKIF 58
+ ++D E + S + +A ++V+S+ + +SF S+ +++ AE+ I
Sbjct: 51 LVVYDHWEQEDGMWLEDSCMQVGDAYVIVYSVTDRSSFEKASELRIQLRRARQAEDIPII 110
Query: 59 LCGNKSDL 66
L GNKSDL
Sbjct: 111 LVGNKSDL 118
>gnl|CDD|206704 cd04132, Rho4_like, Ras homology family 4 (Rho4) of small guanosine
triphosphatases (GTPases)-like. Rho4 is a GTPase that
controls septum degradation by regulating secretion of
Eng1 or Agn1 during cytokinesis. Rho4 also plays a role
in cell morphogenesis. Rho4 regulates septation and cell
morphology by controlling the actin cytoskeleton and
cytoplasmic microtubules. The localization of Rho4 is
modulated by Rdi1, which may function as a GDI, and by
Rga9, which is believed to function as a GAP. In S.
pombe, both Rho4 deletion and Rho4 overexpression result
in a defective cell wall, suggesting a role for Rho4 in
maintaining cell wall integrity. Most Rho proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins.
Length = 197
Score = 35.8 bits (83), Expect = 0.005
Identities = 19/65 (29%), Positives = 29/65 (44%), Gaps = 1/65 (1%)
Query: 3 LWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFH-VLSQHLLEIVTYAENAKIFLCG 61
LWDT G E + Y + ++ +S+DN S V + E+ + I L G
Sbjct: 56 LWDTAGQEDYDRLRPLSYPDVDVILICYSVDNPTSLDNVEDKWYPEVNHFCPGTPIVLVG 115
Query: 62 NKSDL 66
K+DL
Sbjct: 116 LKTDL 120
>gnl|CDD|206663 cd01871, Rac1_like, Ras-related C3 botulinum toxin substrate 1 (rho
family, small GTP binding protein Rac1)-like consists of
Rac1, Rac2 and Rac3. The Rac1-like subfamily consists
of Rac1, Rac2, and Rac3 proteins, plus the splice
variant Rac1b that contains a 19-residue insertion near
switch II relative to Rac1. While Rac1 is ubiquitously
expressed, Rac2 and Rac3 are largely restricted to
hematopoietic and neural tissues respectively. Rac1
stimulates the formation of actin lamellipodia and
membrane ruffles. It also plays a role in cell-matrix
adhesion and cell anoikis. In intestinal epithelial
cells, Rac1 is an important regulator of migration and
mediates apoptosis. Rac1 is also essential for
RhoA-regulated actin stress fiber and focal adhesion
complex formation. In leukocytes, Rac1 and Rac2 have
distinct roles in regulating cell morphology, migration,
and invasion, but are not essential for macrophage
migration or chemotaxis. Rac3 has biochemical properties
that are closely related to Rac1, such as effector
interaction, nucleotide binding, and hydrolysis; Rac2
has a slower nucleotide association and is more
efficiently activated by the RacGEF Tiam1. Both Rac1 and
Rac3 have been implicated in the regulation of cell
migration and invasion in human metastatic breast
cancer. Most Rho proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Rho proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 174
Score = 35.2 bits (81), Expect = 0.006
Identities = 22/65 (33%), Positives = 32/65 (49%), Gaps = 1/65 (1%)
Query: 3 LWDTGGMERVASITSSYYKFAEAAILVFSLDNAASF-HVLSQHLLEIVTYAENAKIFLCG 61
LWDT G E + Y + ++ FSL + ASF +V ++ E+ + N I L G
Sbjct: 53 LWDTAGQEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVG 112
Query: 62 NKSDL 66
K DL
Sbjct: 113 TKLDL 117
>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 = 34.6 bits (80), Expect = 0.009
Identities = 22/73 (30%), Positives = 33/73 (45%), Gaps = 8/73 (10%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQ-----HLLEIVTYAENA 55
+++WD GG R S+ Y + A +V+ +D AA L H L E
Sbjct: 46 IKVWDLGGQPRFRSMWERYCRGVNA--IVYVVD-AADREKLEVAKNELHDLLEKPSLEGI 102
Query: 56 KIFLCGNKSDLEG 68
+ + GNK+DL G
Sbjct: 103 PLLVLGNKNDLPG 115
>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 = 34.1 bits (79), Expect = 0.014
Identities = 18/83 (21%), Positives = 35/83 (42%), Gaps = 5/83 (6%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAE--NAKIF 58
+WD GG +++ + YY+ + I V + L +++ E A +
Sbjct: 45 FTVWDVGGQDKIRPLWKHYYENTDGLIFVVDSSDRERIEEAKNELHKLLNEEELKGAPLL 104
Query: 59 LCGNKSDLEGTTPQVTEADMENF 81
+ NK DL G +TE+++
Sbjct: 105 ILANKQDLPG---ALTESELIEL 124
>gnl|CDD|133375 cd04175, Rap1, Rap1 family GTPase consists of Rap1a and Rap1b
isoforms. The Rap1 subgroup is part of the Rap
subfamily of the Ras family. It can be further divided
into the Rap1a and Rap1b isoforms. In humans, Rap1a and
Rap1b share 95% sequence homology, but are products of
two different genes located on chromosomes 1 and 12,
respectively. Rap1a is sometimes called smg p21 or Krev1
in the older literature. Rap1 proteins are believed to
perform different cellular functions, depending on the
isoform, its subcellular localization, and the effector
proteins it binds. For example, in rat salivary gland,
neutrophils, and platelets, Rap1 localizes to secretory
granules and is believed to regulate exocytosis or the
formation of secretory granules. Rap1 has also been
shown to localize in the Golgi of rat fibroblasts,
zymogen granules, plasma membrane, and the microsomal
membrane of pancreatic acini, as well as in the
endocytic compartment of skeletal muscle cells and
fibroblasts. High expression of Rap1 has been observed
in the nucleus of human oropharyngeal squamous cell
carcinomas (SCCs) and cell lines; interestingly, in the
SCCs, the active GTP-bound form localized to the
nucleus, while the inactive GDP-bound form localized to
the cytoplasm. Rap1 plays a role in phagocytosis by
controlling the binding of adhesion receptors (typically
integrins) to their ligands. In yeast, Rap1 has been
implicated in multiple functions, including activation
and silencing of transcription and maintenance of
telomeres. Rap1a, which is stimulated by T-cell receptor
(TCR) activation, is a positive regulator of T cells by
directing integrin activation and augmenting lymphocyte
responses. In murine hippocampal neurons, Rap1b
determines which neurite will become the axon and
directs the recruitment of Cdc42, which is required for
formation of dendrites and axons. In murine platelets,
Rap1b is required for normal homeostasis in vivo and is
involved in integrin activation. 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 = 164
Score = 34.0 bits (78), Expect = 0.014
Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 2/69 (2%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEI--VTYAENAKIF 58
+++ DT G E+ ++ Y K + +LV+S+ ++F+ L +I V E+ +
Sbjct: 51 LEILDTAGTEQFTAMRDLYMKNGQGFVLVYSITAQSTFNDLQDLREQILRVKDTEDVPMI 110
Query: 59 LCGNKSDLE 67
L GNK DLE
Sbjct: 111 LVGNKCDLE 119
>gnl|CDD|206735 cd04172, Rnd3_RhoE_Rho8, Rnd3/RhoE/Rho8 GTPases. Rnd3/RhoE/Rho8
subfamily. Rnd3/RhoE/Rho8 is a member of the novel Rho
subfamily Rnd, together with Rnd1/Rho6 and Rnd2/Rho7.
Rnd3/RhoE is known to bind the serine-threonine kinase
ROCK I. Unphosphorylated Rnd3/RhoE associates primarily
with membranes, but ROCK I-phosphorylated Rnd3/RhoE
localizes in the cytosol. Phosphorylation of Rnd3/RhoE
correlates with its activity in disrupting RhoA-induced
stress fibers and inhibiting Ras-induced fibroblast
transformation. In cells that lack stress fibers, such
as macrophages and monocytes, Rnd3/RhoE induces a
redistribution of actin, causing morphological changes
in the cell. In addition, Rnd3/RhoE has been shown to
inhibit cell cycle progression in G1 phase at a point
upstream of the pRb family pocket protein checkpoint.
Rnd3/RhoE has also been shown to inhibit Ras- and
Raf-induced fibroblast transformation. In mammary
epithelial tumor cells, Rnd3/RhoE regulates the assembly
of the apical junction complex and tight junction
formation. Rnd3/RhoE is underexpressed in prostate
cancer cells both in vitro and in vivo; re-expression of
Rnd3/RhoE suppresses cell cycle progression and
increases apoptosis, suggesting it may play a role in
tumor suppression. Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 182
Score = 34.3 bits (78), Expect = 0.015
Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASF-HVLSQHLLEIVTYAENAKIFL 59
+ LWDT G ++ Y ++A ++ F + + VL + EI + N K+ L
Sbjct: 55 LSLWDTSGSPYYDNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEIQEFCPNTKMLL 114
Query: 60 CGNKSDL 66
G KSDL
Sbjct: 115 VGCKSDL 121
>gnl|CDD|201191 pfam00378, ECH, Enoyl-CoA hydratase/isomerase family. This family
contains a diverse set of enzymes including: Enoyl-CoA
hydratase. Napthoate synthase. Carnitate racemase.
3-hydoxybutyryl-CoA dehydratase. Dodecanoyl-CoA
delta-isomerase.
Length = 245
Score = 34.6 bits (80), Expect = 0.016
Identities = 17/72 (23%), Positives = 34/72 (47%), Gaps = 3/72 (4%)
Query: 86 SSRRFKPQEVVE---PQEVVEAEQVQQEACDKFEQMSDKAKEELNDFKERRVEAFKKNLM 142
+ RR + QE ++ +VV EQ+ +EA + ++++DK L K A + L
Sbjct: 157 TGRRIRAQEALKMGLVDKVVPEEQLVEEAIELAQRLADKPPLALAALKAAMRAALEDALP 216
Query: 143 ELAELEIKHAES 154
E+ ++ +
Sbjct: 217 EVRAQALRLYPA 228
>gnl|CDD|133345 cd04145, M_R_Ras_like, R-Ras2/TC21, M-Ras/R-Ras3. The
M-Ras/R-Ras-like subfamily contains R-Ras2/TC21,
M-Ras/R-Ras3, and related members of the Ras family.
M-Ras is expressed in lympho-hematopoetic cells. It
interacts with some of the known Ras effectors, but
appears to also have its own effectors. Expression of
mutated M-Ras leads to transformation of several types
of cell lines, including hematopoietic cells, mammary
epithelial cells, and fibroblasts. Overexpression of
M-Ras is observed in carcinomas from breast, uterus,
thyroid, stomach, colon, kidney, lung, and rectum. In
addition, expression of a constitutively active M-Ras
mutant in murine bone marrow induces a malignant mast
cell leukemia that is distinct from the monocytic
leukemia induced by H-Ras. TC21, along with H-Ras, has
been shown to regulate the branching morphogenesis of
ureteric bud cell branching in mice. 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 = 164
Score = 33.9 bits (78), Expect = 0.016
Identities = 23/84 (27%), Positives = 39/84 (46%), Gaps = 5/84 (5%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASF---HVLSQHLLEIVTYAENAKI 57
+ + DT G E +++ Y + E +LVFS+ + SF +L V + +
Sbjct: 52 LDILDTAGQEEFSAMREQYMRTGEGFLLVFSVTDRGSFEEVDKFHTQILR-VKDRDEFPM 110
Query: 58 FLCGNKSDLEGTTPQVTEADMENF 81
L GNK+DLE QV+ + +
Sbjct: 111 ILVGNKADLEHQR-QVSREEGQEL 133
>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 = 33.7 bits (77), Expect = 0.024
Identities = 17/83 (20%), Positives = 37/83 (44%), Gaps = 3/83 (3%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAENAKI--F 58
+ ++D+ G E + + + ++ +V+ + N SF+ S+ + + T++
Sbjct: 55 LFIFDSAGQELFSDMVENVWEQPAVVCVVYDVTNEVSFNNCSRWINRVRTHSHGLHTPGV 114
Query: 59 LCGNKSDLEGTTPQVTEADMENF 81
L GNK DL +V A +
Sbjct: 115 LVGNKCDLTDRR-EVDAAQAQAL 136
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes. TrmE
contains a GTPase domain that forms a canonical Ras-like
fold. It functions a molecular switch GTPase, and
apparently uses a conformational change associated with
GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 33.2 bits (77), Expect = 0.028
Identities = 16/74 (21%), Positives = 31/74 (41%), Gaps = 9/74 (12%)
Query: 8 GMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAENAKIFLCGNKSDLE 67
G+ER + EA +++ +D + L + LEI+ + + NKSDL
Sbjct: 72 GIER------AREAIEEADLVLLVVDASEG---LDEEDLEILELPAKKPVIVVLNKSDLL 122
Query: 68 GTTPQVTEADMENF 81
++E + +
Sbjct: 123 SDAEGISELNGKPI 136
>gnl|CDD|153311 cd07627, BAR_Vps5p, The Bin/Amphiphysin/Rvs (BAR) domain of yeast
Sorting Nexin Vps5p. BAR domains are dimerization,
lipid binding and curvature sensing modules found in
many different proteins with diverse functions. Sorting
nexins (SNXs) are Phox homology (PX) domain containing
proteins that are involved in regulating membrane
traffic and protein sorting in the endosomal system.
SNXs differ from each other in their lipid-binding
specificity, subcellular localization and specific
function in the endocytic pathway. A subset of SNXs also
contain BAR domains. The PX-BAR structural unit
determines the specific membrane targeting of SNXs.
Vsp5p is the yeast counterpart of human SNX1 and is part
of the retromer complex, which functions in the
endosome-to-Golgi retrieval of vacuolar protein sorting
receptor Vps10p, the Golgi-resident membrane protein
A-ALP, and endopeptidase Kex2. BAR domains form dimers
that bind to membranes, induce membrane bending and
curvature, and may also be involved in protein-protein
interactions.
Length = 216
Score = 33.4 bits (77), Expect = 0.031
Identities = 16/43 (37%), Positives = 26/43 (60%)
Query: 99 QEVVEAEQVQQEACDKFEQMSDKAKEELNDFKERRVEAFKKNL 141
E+ EAE+ E +FE++S+ K EL F+ RVE F+ ++
Sbjct: 150 SELEEAERRASELKKEFEEVSELIKSELERFERERVEDFRNSV 192
>gnl|CDD|206712 cd04141, Rit_Rin_Ric, Ras-like protein in all tissues (Rit),
Ras-like protein in neurons (Rin) and Ras-related
protein which interacts with calmodulin (Ric). Rit
(Ras-like protein in all tissues), Rin (Ras-like protein
in neurons) and Ric (Ras-related protein which interacts
with calmodulin) form a subfamily with several unique
structural and functional characteristics. These
proteins all lack a the C-terminal CaaX lipid-binding
motif typical of Ras family proteins, and Rin and Ric
contain calmodulin-binding domains. Rin, which is
expressed only in neurons, induces neurite outgrowth in
rat pheochromocytoma cells through its association with
calmodulin and its activation of endogenous Rac/cdc42.
Rit, which is ubiquitously expressed in mammals,
inhibits growth-factor withdrawl-mediated apoptosis and
induces neurite extension in pheochromocytoma cells. Rit
and Rin are both able to form a ternary complex with
PAR6, a cell polarity-regulating protein, and Rac/cdc42.
This ternary complex is proposed to have physiological
function in processes such as tumorigenesis. Activated
Ric is likely to signal in parallel with the Ras pathway
or stimulate the Ras pathway at some upstream point, and
binding of calmodulin to Ric may negatively regulate Ric
activity.
Length = 172
Score = 33.3 bits (76), Expect = 0.032
Identities = 26/88 (29%), Positives = 40/88 (45%), Gaps = 4/88 (4%)
Query: 5 DTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQH--LLEIVTYAENAKIFLCGN 62
DT G ++ Y + E I+ +S+ + SF S+ L+ V E+ + L GN
Sbjct: 56 DTAGQAEFTAMRDQYMRCGEGFIICYSVTDRHSFQEASEFKELITRVRLTEDIPLVLVGN 115
Query: 63 KSDLEGTTPQVTEADMENFWSRRSSRRF 90
K DLE QVT + N +R + F
Sbjct: 116 KVDLE-QQRQVTTEEGRNL-AREFNCPF 141
>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 = 32.7 bits (75), Expect = 0.040
Identities = 19/68 (27%), Positives = 27/68 (39%), Gaps = 4/68 (5%)
Query: 4 WDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAE---NAKIFLC 60
WD GG E + S+ YY + I V + F+ S+ E V E + +
Sbjct: 56 WDLGGQEELRSLWDKYYAESHGVIYVIDSTDRERFNE-SKSAFEKVINNEALEGVPLLVL 114
Query: 61 GNKSDLEG 68
NK DL
Sbjct: 115 ANKQDLPD 122
>gnl|CDD|206662 cd01870, RhoA_like, Ras homology family A (RhoA)-like includes
RhoA, RhoB and RhoC. The RhoA subfamily consists of
RhoA, RhoB, and RhoC. RhoA promotes the formation of
stress fibers and focal adhesions, regulating cell
shape, attachment, and motility. RhoA can bind to
multiple effector proteins, thereby triggering different
downstream responses. In many cell types, RhoA mediates
local assembly of the contractile ring, which is
necessary for cytokinesis. RhoA is vital for muscle
contraction; in vascular smooth muscle cells, RhoA plays
a key role in cell contraction, differentiation,
migration, and proliferation. RhoA activities appear to
be elaborately regulated in a time- and space-dependent
manner to control cytoskeletal changes. Most Rho
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. RhoA and RhoC are observed
only in geranylgeranylated forms; however, RhoB can be
present in palmitoylated, farnesylated, and
geranylgeranylated forms. RhoA and RhoC are highly
relevant for tumor progression and invasiveness;
however, RhoB has recently been suggested to be a tumor
suppressor. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 175
Score = 32.8 bits (75), Expect = 0.042
Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 3 LWDTGGMERVASITSSYYKFAEAAILVFSLDNAASF-HVLSQHLLEIVTYAENAKIFLCG 61
LWDT G E + Y + ++ FS+D+ S ++ + E+ + N I L G
Sbjct: 53 LWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVG 112
Query: 62 NKSDL 66
NK DL
Sbjct: 113 NKKDL 117
>gnl|CDD|206702 cd04129, Rho2, Ras homology family 2 (Rho2) of small guanosine
triphosphatases (GTPases). Rho2 is a fungal GTPase that
plays a role in cell morphogenesis, control of cell wall
integrity, control of growth polarity, and maintenance
of growth direction. Rho2 activates the protein kinase C
homolog Pck2, and Pck2 controls Mok1, the major (1-3)
alpha-D-glucan synthase. Together with Rho1 (RhoA), Rho2
regulates the construction of the cell wall. Unlike
Rho1, Rho2 is not an essential protein, but its
overexpression is lethal. Most Rho proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for proper intracellular localization via
membrane attachment. As with other Rho family GTPases,
the GDP/GTP cycling is regulated by GEFs (guanine
nucleotide exchange factors), GAPs (GTPase-activating
proteins) and GDIs (guanine nucleotide dissociation
inhibitors).
Length = 190
Score = 32.9 bits (75), Expect = 0.046
Identities = 20/65 (30%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 3 LWDTGGMERVASITSSYYKFAEAAILVFSLDNAASF-HVLSQHLLEIVTYAENAKIFLCG 61
LWDT G E + Y A ++ F++D S +V ++ + E+ Y N + L G
Sbjct: 53 LWDTAGQEEYERLRPLSYSKAHVILIGFAIDTPDSLENVRTKWIEEVRRYCPNVPVILVG 112
Query: 62 NKSDL 66
K DL
Sbjct: 113 LKKDL 117
>gnl|CDD|206737 cd04174, Rnd1_Rho6, Rnd1/Rho6 GTPases. Rnd1/Rho6 is a member of
the novel Rho subfamily Rnd, together with Rnd2/Rho7 and
Rnd3/RhoE/Rho8. Rnd1/Rho6 binds GTP but does not
hydrolyze it to GDP, indicating that it is
constitutively active. In rat, Rnd1/Rho6 is highly
expressed in the cerebral cortex and hippocampus during
synapse formation, and plays a role in spine formation.
Rnd1/Rho6 is also expressed in the liver and in
endothelial cells, and is upregulated in uterine
myometrial cells during pregnancy. Like Rnd3/RhoE/Rho8,
Rnd1/Rho6 is believed to function as an antagonist to
RhoA. Most Rho proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Rho proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 232
Score = 33.1 bits (75), Expect = 0.050
Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASF-HVLSQHLLEIVTYAENAKIFL 59
+ LWDT G ++ Y ++A +L F + F L + EI+ Y + +I L
Sbjct: 63 LSLWDTSGSPYYDNVRPLCYSDSDAVLLCFDISRPEIFDSALKKWRAEILDYCPSTRILL 122
Query: 60 CGNKSDL 66
G K+DL
Sbjct: 123 IGCKTDL 129
>gnl|CDD|133303 cd04103, Centaurin_gamma, Centaurin gamma (CENTG) GTPase. The
centaurins (alpha, beta, gamma, and delta) are large,
multi-domain proteins that all contain an ArfGAP domain
and ankyrin repeats, and in some cases, numerous
additional domains. Centaurin gamma contains an
additional GTPase domain near its N-terminus. The
specific function of this GTPase domain has not been
well characterized, but centaurin gamma 2 (CENTG2) may
play a role in the development of autism. Centaurin
gamma 1 is also called PIKE (phosphatidyl inositol (PI)
3-kinase enhancer) and centaurin gamma 2 is also known
as AGAP (ArfGAP protein with a GTPase-like domain,
ankyrin repeats and a Pleckstrin homology domain) or
GGAP. Three isoforms of PIKE have been identified.
PIKE-S (short) and PIKE-L (long) are brain-specific
isoforms, with PIKE-S restricted to the nucleus and
PIKE-L found in multiple cellular compartments. A third
isoform, PIKE-A was identified in human glioblastoma
brain cancers and has been found in various tissues.
GGAP has been shown to have high GTPase activity due to
a direct intramolecular interaction between the
N-terminal GTPase domain and the C-terminal ArfGAP
domain. In human tissue, AGAP mRNA was detected in
skeletal muscle, kidney, placenta, brain, heart, colon,
and lung. Reduced expression levels were also observed
in the spleen, liver, and small intestine.
Length = 158
Score = 32.5 bits (74), Expect = 0.057
Identities = 15/58 (25%), Positives = 31/58 (53%), Gaps = 2/58 (3%)
Query: 22 FAEAAILVFSLDNAASFHVLSQHLLEIVTYAENAKI--FLCGNKSDLEGTTPQVTEAD 77
+ +A I VFSL++ ASF + + ++ +Y ++I L G + + + P+V +
Sbjct: 65 WVDAVIFVFSLEDEASFQTVYRLYHQLSSYRNISEIPLILVGTQDAISASNPRVIDDA 122
>gnl|CDD|133277 cd01875, RhoG, Ras homolog family, member G (RhoG) of small
guanosine triphosphatases (GTPases). RhoG is a GTPase
with high sequence similarity to members of the Rac
subfamily, including the regions involved in effector
recognition and binding. However, RhoG does not bind to
known Rac1 and Cdc42 effectors, including proteins
containing a Cdc42/Rac interacting binding (CRIB) motif.
Instead, RhoG interacts directly with Elmo, an upstream
regulator of Rac1, in a GTP-dependent manner and forms a
ternary complex with Dock180 to induce activation of
Rac1. The RhoG-Elmo-Dock180 pathway is required for
activation of Rac1 and cell spreading mediated by
integrin, as well as for neurite outgrowth induced by
nerve growth factor. Thus RhoG activates Rac1 through
Elmo and Dock180 to control cell morphology. RhoG has
also been shown to play a role in caveolar trafficking
and has a novel role in signaling the neutrophil
respiratory burst stimulated by G protein-coupled
receptor (GPCR) agonists. Most Rho proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Rho proteins.
Length = 191
Score = 32.7 bits (74), Expect = 0.059
Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 1/69 (1%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASF-HVLSQHLLEIVTYAENAKIFL 59
+ LWDT G E + + Y I+ FS+ + +S+ +V + E+ + N I L
Sbjct: 53 LNLWDTAGQEEYDRLRTLSYPQTNVFIICFSIASPSSYENVRHKWHPEVCHHCPNVPILL 112
Query: 60 CGNKSDLEG 68
G K DL
Sbjct: 113 VGTKKDLRN 121
>gnl|CDD|206723 cd04158, ARD1, (ADP-ribosylation factor domain protein 1 (ARD1).
ARD1 (ADP-ribosylation factor domain protein 1) is an
unusual member of the Arf family. In addition to the
C-terminal Arf domain, ARD1 has an additional 46-kDa
N-terminal domain that contains a RING finger domain,
two predicted B-Boxes, and a coiled-coil protein
interaction motif. This domain belongs to the TRIM
(tripartite motif) or RBCC (RING, B-Box, coiled-coil)
family. Like most Arfs, the ARD1 Arf domain lacks
detectable GTPase activity. However, unlike most Arfs,
the full-length ARD1 protein has significant GTPase
activity due to the GAP (GTPase-activating protein)
activity exhibited by the 46-kDa N-terminal domain. The
GAP domain of ARD1 is specific for its own Arf domain
and does not bind other Arfs. The rate of GDP
dissociation from the ARD1 Arf domain is slowed by the
adjacent 15 amino acids, which act as a GDI
(GDP-dissociation inhibitor) domain. ARD1 is
ubiquitously expressed in cells and localizes to the
Golgi and to the lysosomal membrane. Two Tyr-based
motifs in the Arf domain are responsible for Golgi
localization, while the GAP domain controls lysosomal
localization.
Length = 169
Score = 31.9 bits (72), Expect = 0.084
Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 8/79 (10%)
Query: 3 LWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQH--LLEIVTYAE--NAKIF 58
+WD GG ++ + YY +A +VF +D++ V H L +++T E +A +
Sbjct: 47 IWDVGGKHKLRPLWKHYYLNTQA--VVFVIDSSHRDRVSEAHSELAKLLTEKELRDALLL 104
Query: 59 LCGNKSDLEGTTP--QVTE 75
+ NK D+ G ++TE
Sbjct: 105 IFANKQDVAGALSVEEMTE 123
>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 = 32.2 bits (73), Expect = 0.084
Identities = 16/66 (24%), Positives = 29/66 (43%), Gaps = 2/66 (3%)
Query: 3 LWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAE--NAKIFLC 60
+WD GG +++ + YY + I V ++ + L ++ E +A I +
Sbjct: 61 VWDVGGQDKIRPLWRHYYTNTQGLIFVVDSNDRDRIDEAREELHRMLNEDELRDAVILVF 120
Query: 61 GNKSDL 66
NK DL
Sbjct: 121 ANKQDL 126
>gnl|CDD|206703 cd04131, Rnd, Rho family GTPase subfamily Rnd includes Rnd1/Rho6,
Rnd2/Rho7, and Rnd3/RhoE/Rho8. The Rnd subfamily
contains Rnd1/Rho6, Rnd2/Rho7, and Rnd3/RhoE/Rho8. These
novel Rho family proteins have substantial structural
differences compared to other Rho members, including N-
and C-terminal extensions relative to other Rhos.
Rnd3/RhoE is farnesylated at the C-terminal prenylation
site, unlike most other Rho proteins that are
geranylgeranylated. In addition, Rnd members are unable
to hydrolyze GTP and are resistant to GAP activity. They
are believed to exist only in the GTP-bound
conformation, and are antagonists of RhoA activity. Most
Rho proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 176
Score = 32.0 bits (73), Expect = 0.087
Identities = 22/81 (27%), Positives = 36/81 (44%), Gaps = 11/81 (13%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVF------SLDNAASFHVLSQHLLEIVTYAEN 54
+ LWDT G ++ Y ++A ++ F +LD+ VL + E+ + N
Sbjct: 51 LSLWDTSGSPYYDNVRPLSYPDSDAVLICFDISRPETLDS-----VLKKWKGEVREFCPN 105
Query: 55 AKIFLCGNKSDLEGTTPQVTE 75
+ L G KSDL +TE
Sbjct: 106 TPVLLVGCKSDLRTDLSTLTE 126
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 31.8 bits (72), Expect = 0.10
Identities = 18/79 (22%), Positives = 41/79 (51%), Gaps = 3/79 (3%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAENAK--IF 58
+ + DT G E +++ Y + + + V+S+ + +SF ++ +I+ + + +
Sbjct: 55 LDILDTAGQEEYSAMRDQYMRTGQGFLCVYSITSRSSFEEIASFREQILRVKDKDRVPMI 114
Query: 59 LCGNKSDLEGTTPQVTEAD 77
L GNK DL+ + QV+ +
Sbjct: 115 LVGNKCDLD-SERQVSTGE 132
>gnl|CDD|145973 pfam03114, BAR, BAR domain. BAR domains are dimerisation, lipid
binding and curvature sensing modules found in many
different protein families. A BAR domain with an
additional N-terminal amphipathic helix (an N-BAR) can
drive membrane curvature. These N-BAR domains are found
in amphiphysin, endophilin, BRAP and Nadrin. BAR domains
are also frequently found alongside domains that
determine lipid specificity, like pfam00169 and
pfam00787 domains in beta centaurins and sorting nexins
respectively.
Length = 230
Score = 31.5 bits (72), Expect = 0.14
Identities = 18/81 (22%), Positives = 40/81 (49%)
Query: 87 SRRFKPQEVVEPQEVVEAEQVQQEACDKFEQMSDKAKEELNDFKERRVEAFKKNLMELAE 146
++R + ++ +E+ +AE+ ++A KFE+ +++ KEEL + VE L E
Sbjct: 149 AKRHRLKKAKSKKELSKAEEELRQAQQKFEESNEELKEELPNLLALEVEFVVNCLQAFVE 208
Query: 147 LEIKHAESQVNILKKCLAELK 167
++ +L++ +L
Sbjct: 209 AQLDFHRQSYQLLEQLQQQLF 229
>gnl|CDD|206707 cd04135, Tc10, Rho GTPase TC10 (Tc10). TC10 is a Rho family
protein that has been shown to induce microspike
formation and neurite outgrowth in vitro. Its expression
changes dramatically after peripheral nerve injury,
suggesting an important role in promoting axonal
outgrowth and regeneration. TC10 regulates translocation
of insulin-stimulated GLUT4 in adipocytes and has also
been shown to bind directly to Golgi COPI coat proteins.
GTP-bound TC10 in vitro can bind numerous potential
effectors. Depending on its subcellular localization and
distinct functional domains, TC10 can differentially
regulate two types of filamentous actin in adipocytes.
TC10 mRNAs are highly expressed in three types of mouse
muscle tissues: leg skeletal muscle, cardiac muscle, and
uterus; they were also present in brain, with higher
levels in adults than in newborns. TC10 has also been
shown to play a role in regulating the expression of
cystic fibrosis transmembrane conductance regulator
(CFTR) through interactions with CFTR-associated ligand
(CAL). The GTP-bound form of TC10 directs the
trafficking of CFTR from the juxtanuclear region to the
secretory pathway toward the plasma membrane, away from
CAL-mediated DFTR degradation in the lysosome. Most Rho
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 174
Score = 31.1 bits (70), Expect = 0.17
Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 1/65 (1%)
Query: 3 LWDTGGMERVASITSSYYKFAEAAILVFSLDNAASF-HVLSQHLLEIVTYAENAKIFLCG 61
L+DT G E + Y + ++ FS+ N ASF +V + + E+ YA N L G
Sbjct: 52 LYDTAGQEDYDRLRPLSYPMTDVFLICFSVVNPASFQNVKEEWVPELKEYAPNVPYLLIG 111
Query: 62 NKSDL 66
+ DL
Sbjct: 112 TQIDL 116
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 31.0 bits (70), Expect = 0.19
Identities = 19/77 (24%), Positives = 36/77 (46%), Gaps = 4/77 (5%)
Query: 3 LWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAE--NAKIFLC 60
+WD GG +++ + YY+ I V ++ + L +++ E +A + +
Sbjct: 65 MWDVGGQDKLRPLWRHYYQNTNGLIFVVDSNDRERIGDAREELERMLSEDELRDAVLLVF 124
Query: 61 GNKSDLEG--TTPQVTE 75
NK DL +T +VTE
Sbjct: 125 ANKQDLPNAMSTTEVTE 141
>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 = 30.9 bits (70), Expect = 0.20
Identities = 20/75 (26%), Positives = 34/75 (45%), Gaps = 7/75 (9%)
Query: 3 LWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHV--LSQHLLEIVTYAE--NAKIF 58
+WD GG +++ + YY + L+F +D+A + Q L I+ E +A +
Sbjct: 57 VWDVGGQDKIRPLWRHYYTGTQG--LIFVVDSADRDRIDEARQELHRIINDREMRDALLL 114
Query: 59 LCGNKSDLEGT-TPQ 72
+ NK DL P
Sbjct: 115 VFANKQDLPDAMKPH 129
>gnl|CDD|206680 cd01893, Miro1, Mitochondrial Rho family 1 (Miro1), N-terminal.
Miro1 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the N-terminal
GTPase domain of Miro proteins. These atypical Rho
GTPases have roles in mitochondrial homeostasis and
apoptosis. Most Rho proteins contain a lipid
modification site at the C-terminus; however, Miro is
one of few Rho subfamilies that lack this feature.
Length = 168
Score = 30.8 bits (70), Expect = 0.23
Identities = 15/45 (33%), Positives = 20/45 (44%), Gaps = 1/45 (2%)
Query: 23 AEAAILVFSLDNAASFHVLSQH-LLEIVTYAENAKIFLCGNKSDL 66
A LV+S+D ++ + L I I L GNKSDL
Sbjct: 73 ANVICLVYSVDRPSTLERIRTKWLPLIRRLGVKVPIILVGNKSDL 117
>gnl|CDD|214787 smart00721, BAR, BAR domain.
Length = 239
Score = 30.8 bits (70), Expect = 0.27
Identities = 17/74 (22%), Positives = 36/74 (48%)
Query: 94 EVVEPQEVVEAEQVQQEACDKFEQMSDKAKEELNDFKERRVEAFKKNLMELAELEIKHAE 153
E + +++ +AE+ ++A +FE+ + + EEL RV+ F L L E ++
Sbjct: 165 EKKKDEKLAKAEEELRKAKQEFEESNAQLVEELPQLVASRVDFFVNCLQALIEAQLNFHR 224
Query: 154 SQVNILKKCLAELK 167
+L++ +L
Sbjct: 225 ESYKLLQQLQQQLD 238
>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 = 30.1 bits (68), Expect = 0.35
Identities = 23/90 (25%), Positives = 42/90 (46%), Gaps = 9/90 (10%)
Query: 3 LWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHV-LSQHLLEIVTYAENAK---IF 58
+WD GG E++ ++ Y LV+ +D++ + SQ L+ + E+ K +
Sbjct: 48 VWDVGGQEKMRTVWKCY--LENTDGLVYVVDSSDEARLDESQKELKHILKNEHIKGVPVV 105
Query: 59 LCGNKSDLEGTTP--QVTEA-DMENFWSRR 85
L NK DL G ++T ++ + S R
Sbjct: 106 LLANKQDLPGALTAEEITRRFKLKKYCSDR 135
>gnl|CDD|206709 cd04137, RheB, Ras Homolog Enriched in Brain (RheB) is a small
GTPase. Rheb (Ras Homolog Enriched in Brain) subfamily.
Rheb was initially identified in rat brain, where its
expression is elevated by seizures or by long-term
potentiation. It is expressed ubiquitously, with
elevated levels in muscle and brain. Rheb functions as
an important mediator between the tuberous sclerosis
complex proteins, TSC1 and TSC2, and the mammalian
target of rapamycin (TOR) kinase to stimulate cell
growth. TOR kinase regulates cell growth by controlling
nutrient availability, growth factors, and the energy
status of the cell. TSC1 and TSC2 form a dimeric complex
that has tumor suppressor activity, and TSC2 is a GTPase
activating protein (GAP) for Rheb. The TSC1/TSC2 complex
inhibits the activation of TOR kinase through Rheb. Rheb
has also been shown to induce the formation of large
cytoplasmic vacuoles in a process that is dependent on
the GTPase cycle of Rheb, but independent of the TOR
kinase, suggesting Rheb plays a role in endocytic
trafficking that leads to cell growth and cell-cycle
progression. 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.
Length = 180
Score = 30.3 bits (69), Expect = 0.37
Identities = 23/79 (29%), Positives = 38/79 (48%), Gaps = 5/79 (6%)
Query: 2 QLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLS---QHLLEIVTYAENAKIF 58
++ DT G + + + Y ILV+S+ + SF V+ +L+ + E+ I
Sbjct: 52 EIVDTAGQDEYSILPQKYSIGIHGYILVYSVTSRKSFEVVKVIYDKILD-MLGKESVPIV 110
Query: 59 LCGNKSDLEGTTPQVTEAD 77
L GNKSDL QV+ +
Sbjct: 111 LVGNKSDL-HMERQVSAEE 128
>gnl|CDD|234084 TIGR03007, pepcterm_ChnLen, polysaccharide chain length determinant
protein, PEP-CTERM locus subfamily. Members of this
protein family belong to the family of polysaccharide
chain length determinant proteins (pfam02706). All are
found in species that encode the PEP-CTERM/exosortase
system predicted to act in protein sorting in a number
of Gram-negative bacteria, and are found near the epsH
homolog that is the putative exosortase gene [Cell
envelope, Biosynthesis and degradation of surface
polysaccharides and lipopolysaccharides].
Length = 498
Score = 30.0 bits (68), Expect = 0.52
Identities = 19/91 (20%), Positives = 36/91 (39%), Gaps = 19/91 (20%)
Query: 90 FKPQEVVEPQEVVEAEQVQQEACDKFEQMSDKAKEELNDFKERRVE-------AFKKNLM 142
K Q+ Q ++ EQ++ +E+ + A+ L FK+ + +
Sbjct: 154 SKRQDSDSAQRFID-EQIKT-----YEKKLEAAENRLKAFKQENGGILPDQEGDYYSEIS 207
Query: 143 EL------AELEIKHAESQVNILKKCLAELK 167
E A LE+ A +Q + LK+ L +
Sbjct: 208 EAQEELEAARLELNEAIAQRDALKRQLGGEE 238
>gnl|CDD|223294 COG0216, PrfA, Protein chain release factor A [Translation,
ribosomal structure and biogenesis].
Length = 363
Score = 29.9 bits (68), Expect = 0.55
Identities = 18/46 (39%), Positives = 27/46 (58%)
Query: 121 KAKEELNDFKERRVEAFKKNLMELAELEIKHAESQVNILKKCLAEL 166
KA+E+L D KE E + E+AE EIK E+++ L++ L L
Sbjct: 57 KAQEDLEDAKEMLAEEKDPEMREMAEEEIKELEAKIEELEEELKIL 102
>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 = 29.7 bits (67), Expect = 0.56
Identities = 20/78 (25%), Positives = 34/78 (43%), Gaps = 4/78 (5%)
Query: 3 LWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAENAKI--FLC 60
+WD GG ++ +Y++ + I V + F Q L+E++ + A + +
Sbjct: 63 VWDIGGQRKIRPYWRNYFENTDVLIYVIDSADRKRFEEAGQELVELLEEEKLAGVPVLVF 122
Query: 61 GNKSDLEGTTPQ--VTEA 76
NK DL P V EA
Sbjct: 123 ANKQDLLTAAPAEEVAEA 140
>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 = 29.6 bits (67), Expect = 0.70
Identities = 26/98 (26%), Positives = 42/98 (42%), Gaps = 15/98 (15%)
Query: 2 QLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHV----LSQHLLEIVTYAENAK- 56
L D G E++ Y K + AI VF +D +A+F +++ L +I+T E K
Sbjct: 50 TLVDVPGHEKLRDKLLEYLKASLKAI-VFVVD-SATFQKNIRDVAEFLYDILTDLEKIKN 107
Query: 57 ---IFLCGNKSDL-----EGTTPQVTEADMENFWSRRS 86
I + NK DL ++ E ++ RS
Sbjct: 108 KIPILIACNKQDLFTAKPAKKIKELLEKEINTLRESRS 145
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 29.1 bits (66), Expect = 0.73
Identities = 17/71 (23%), Positives = 31/71 (43%), Gaps = 6/71 (8%)
Query: 2 QLWDTGGMERVASITSSYYKFAEAAILVFSLDNAAS--FHVLSQHLLEIVTYAENAK--I 57
+WD GG E + + +Y+ ++F +D+A + L ++ E A +
Sbjct: 61 TVWDVGGQESLRPLWRNYF--PNTDAVIFVVDSADRDRIEEAKEELHALLNEEELADAPL 118
Query: 58 FLCGNKSDLEG 68
+ NK DL G
Sbjct: 119 LILANKQDLPG 129
>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 = 28.9 bits (65), Expect = 0.92
Identities = 16/77 (20%), Positives = 35/77 (45%), Gaps = 4/77 (5%)
Query: 3 LWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAE--NAKIFLC 60
+WD GG +++ + Y++ + I V ++ + L ++ E +A + +
Sbjct: 48 VWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERIGEAREELQRMLNEDELRDAVLLVF 107
Query: 61 GNKSDLEG--TTPQVTE 75
NK DL + +VT+
Sbjct: 108 ANKQDLPNAMSAAEVTD 124
>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 = 28.5 bits (64), Expect = 1.0
Identities = 19/79 (24%), Positives = 32/79 (40%), Gaps = 4/79 (5%)
Query: 2 QLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAE--NAKIFL 59
Q+WD GG + YY +A I V + + L ++ E +A + +
Sbjct: 46 QVWDLGGQTSIRPYWRCYYSNTDAIIYVVDSTDRDRLGISKSELHAMLEEEELKDAVLLV 105
Query: 60 CGNKSDLEG--TTPQVTEA 76
NK D+ G + +V E
Sbjct: 106 FANKQDMPGALSEAEVAEK 124
>gnl|CDD|223220 COG0142, IspA, Geranylgeranyl pyrophosphate synthase [Coenzyme
metabolism].
Length = 322
Score = 29.3 bits (66), Expect = 1.1
Identities = 17/68 (25%), Positives = 27/68 (39%), Gaps = 3/68 (4%)
Query: 83 SRRSSRRFKPQEVVEPQEVVEAEQVQQEACDKFEQMSDKAKEELNDFKERRVEAFKKNLM 142
EV E E++ + A + + +KAKE L + K+ L+
Sbjct: 255 KLLRILLEGGGEVEEALELLRKSGAIEYAKNLAKTYVEKAKEALEKLPDSEA---KEALL 311
Query: 143 ELAELEIK 150
ELA+ IK
Sbjct: 312 ELADFIIK 319
>gnl|CDD|131952 TIGR02906, spore_CotS, spore coat protein, CotS family. Members of
this family include the spore coat proteins CotS and
YtaA from Bacillus subtilis and, from other
endospore-forming bacteria, homologs that are more
closely related to these two than to the spore coat
proteins YutH and YsxE. The CotS family is more broadly
distributed than YutH or YsxE, but still is not
universal among spore-formers [Cellular processes,
Sporulation and germination].
Length = 313
Score = 29.2 bits (66), Expect = 1.1
Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 2/50 (4%)
Query: 121 KAKEELNDFKERRVEAFKKNLMELAELEIKHAESQVNILKKCLAELKTSD 170
K +EL FK+ +E K+ E +L +K + + KK L L S
Sbjct: 128 KRLKELERFKKIALEKKYKD--EFDKLYLKEVDYFLERGKKALELLNKSK 175
>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 = 28.7 bits (65), Expect = 1.1
Identities = 17/74 (22%), Positives = 31/74 (41%), Gaps = 8/74 (10%)
Query: 1 MQLWDTGGMERVASITSSYYK---FAEAAILVFSLDN-----AASFHVLSQHLLEIVTYA 52
+ LWD G + + K F+ +L++ D L + + + Y+
Sbjct: 50 LNLWDCPGQDDFMENYLTRQKEHIFSNVGVLIYVFDVESREYEEDLATLVKIIEALYQYS 109
Query: 53 ENAKIFLCGNKSDL 66
NAK+F+ +K DL
Sbjct: 110 PNAKVFVLIHKMDL 123
>gnl|CDD|239057 cd02143, NADH_nitroreductase, Nitroreductase family. Members of
this family utilize FMN as a cofactor. This family is
involved in the reduction of flavin or nitroaromatic
compounds by using NAD(P)H as electron donor in a
obligatory two-electron transfer. Nitrogenase is
homodimer. Each subunit contains one FMN molecule.
Members of this family are also called NADH
dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or
dihydropteridine reductase.
Length = 147
Score = 28.4 bits (64), Expect = 1.1
Identities = 7/22 (31%), Positives = 11/22 (50%), Gaps = 1/22 (4%)
Query: 83 SRRSSRRFKPQEVVEPQEVVEA 104
RRS R ++P E V + +
Sbjct: 4 GRRSVRHYRP-EPVPRETIERL 24
>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 = 28.6 bits (64), Expect = 1.3
Identities = 30/134 (22%), Positives = 55/134 (41%), Gaps = 7/134 (5%)
Query: 2 QLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAEN--AKIFL 59
WD GG E++ + SY + + + V + L +I ++EN + +
Sbjct: 55 HFWDVGGQEKLRPLWKSYTRCTDGIVFVVDSVDVERMEEAKTELHKITKFSENQGVPVLV 114
Query: 60 CGNKSDLEGTTPQVTEADMENFWSRRSSRRFKPQEVVEPQEVVEAEQVQQEACDKFEQMS 119
NK DL P +++E + P V+P + E + QE +K +M
Sbjct: 115 LANKQDLPNALPV---SEVEKLLALHELSSSTPWH-VQPACAIIGEGL-QEGLEKLYEMI 169
Query: 120 DKAKEELNDFKERR 133
K ++ L K++R
Sbjct: 170 LKRRKMLRQQKKKR 183
>gnl|CDD|203332 pfam05831, GAGE, GAGE protein. This family consists of several
GAGE and XAGE proteins which are found exclusively in
humans. The function of this family is unknown although
they have been implicated in human cancers.
Length = 112
Score = 27.9 bits (62), Expect = 1.4
Identities = 11/36 (30%), Positives = 22/36 (61%)
Query: 82 WSRRSSRRFKPQEVVEPQEVVEAEQVQQEACDKFEQ 117
W RS+ R +P+ V+P E+V VQ+ + ++ ++
Sbjct: 3 WRGRSTYRPRPRRSVQPPELVGPMLVQEPSDEEPQE 38
>gnl|CDD|227911 COG5624, TAF61, Transcription initiation factor TFIID, subunit
TAF12 (also component of histone acetyltransferase SAGA)
[Transcription].
Length = 505
Score = 28.9 bits (64), Expect = 1.6
Identities = 11/65 (16%), Positives = 18/65 (27%), Gaps = 2/65 (3%)
Query: 71 PQVTEADMENFWSRRSSRRFKPQEVVEPQEVVEAEQVQQEACDKFEQMSDKAKEELNDFK 130
PQ+ + R RF P + P ++ F S A +
Sbjct: 122 PQLHMQGRVSGIVRH--GRFMPSSMYLPSMGMQLSVGWNWRPVNFRGQSRNANGLFGAWP 179
Query: 131 ERRVE 135
V+
Sbjct: 180 YLEVK 184
>gnl|CDD|216833 pfam01991, vATP-synt_E, ATP synthase (E/31 kDa) subunit. This
family includes the vacuolar ATP synthase E subunit, as
well as the archaebacterial ATP synthase E subunit.
Length = 195
Score = 28.1 bits (63), Expect = 1.7
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 4/55 (7%)
Query: 107 VQQEACDKFEQMSDKAKEELNDFKERRVEAFKKNLMELAELEIKHAESQVNILKK 161
++QEA +K E++ +A+EE K VE +K + E + E Q + K+
Sbjct: 2 IRQEAEEKAEEIRAEAEEEFEIEKAEAVEEAEKKIEE----IYEKKEKQAEMEKQ 52
>gnl|CDD|239051 cd02136, Nitroreductase, Nitroreductase family. Members of this
family utilize FMN as a cofactor and catalyze reduction
of a variety of nitroaromatic compounds, including
nitrofurans, nitrobenzens, nitrophenol, nitrobenzoate
and quinones by using either NADH or NADPH as a source
of reducing equivalents in an obligatory two-election
transfer mechanism. The enzyme is typically a
homodimer. Members of this family are also called NADH
dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or
dihydropteridine reductase.
Length = 178
Score = 27.9 bits (63), Expect = 1.9
Identities = 10/22 (45%), Positives = 12/22 (54%), Gaps = 2/22 (9%)
Query: 83 SRRSSRRFKPQEVVEPQEVVEA 104
SR S R F P V P+E +E
Sbjct: 7 SRHSVRAFLPDPV--PRETIEE 26
>gnl|CDD|227467 COG5138, COG5138, Uncharacterized conserved protein [Function
unknown].
Length = 168
Score = 27.9 bits (62), Expect = 2.0
Identities = 15/80 (18%), Positives = 27/80 (33%), Gaps = 8/80 (10%)
Query: 14 SITSSYYKFAEAAILVFSLDN--AASFHVLSQHLLEIVTYAENAKIFLCGNKSDLEGTTP 71
SI ++ AE ++ S + A L + + + + N K N +
Sbjct: 86 SICPHFFYLAEKYAMLLSEGSLVAGLPEFLYERAGDYSSASLNLKGTFSENSQFVWRLD- 144
Query: 72 QVTEADMENFWSRRSSRRFK 91
+E S RRF+
Sbjct: 145 -----MVEKSIVVGSHRRFQ 159
>gnl|CDD|215637 PLN03223, PLN03223, Polycystin cation channel protein; Provisional.
Length = 1634
Score = 28.8 bits (64), Expect = 2.0
Identities = 32/128 (25%), Positives = 54/128 (42%), Gaps = 15/128 (11%)
Query: 52 AENAKIFLCGNKS-DLEG----------TTPQVTEADMENFWSRRSSRRFKPQEVVEPQE 100
E K+F NK D G T Q T+ + R K ++
Sbjct: 1487 EEKEKVFTYLNKELDEAGLKRVLRRCVIETYQKTD-KSKVLLRLRVGNVGKGKKKETLAT 1545
Query: 101 VVEAEQVQQEACDKFEQM-SDKAKEELNDFKERRVEAFKKNLMELAELEIKHAESQVNIL 159
E +Q D+ Q+ D+ +E D E+ V+ +++L LAE++ + AE QV ++
Sbjct: 1546 ADEIDQAAHMLMDQVGQVPDDEDDDEDGDVLEKEVDQLQQSLERLAEVQRELAEGQVKVI 1605
Query: 160 --KKCLAE 165
+K +AE
Sbjct: 1606 EGQKQMAE 1613
>gnl|CDD|218769 pfam05833, FbpA, Fibronectin-binding protein A N-terminus (FbpA).
This family consists of the N-terminal region of the
prokaryotic fibronectin-binding protein. Fibronectin
binding is considered to be an important virulence
factor in streptococcal infections. Fibronectin is a
dimeric glycoprotein that is present in a soluble form
in plasma and extracellular fluids; it is also present
in a fibrillar form on cell surfaces. Both the soluble
and cellular forms of fibronectin may be incorporated
into the extracellular tissue matrix. While fibronectin
has critical roles in eukaryotic cellular processes,
such as adhesion, migration and differentiation, it is
also a substrate for the attachment of bacteria. The
binding of pathogenic Streptococcus pyogenes and
Staphylococcus aureus to epithelial cells via
fibronectin facilitates their internalisation and
systemic spread within the host.
Length = 447
Score = 28.4 bits (64), Expect = 2.0
Identities = 19/98 (19%), Positives = 40/98 (40%), Gaps = 9/98 (9%)
Query: 78 MENFWSRRSSRRFKPQEVVEPQEVVEAEQVQQEACDKFEQMSDKAKEELNDF-----KER 132
+ + F P E V+ + FE +S E L+++ +
Sbjct: 233 FKELLNDLEEGNFSPTITPEDFSVLPLSHLSGYEKRSFESLS----EALDEYYSKKAERD 288
Query: 133 RVEAFKKNLMELAELEIKHAESQVNILKKCLAELKTSD 170
RV+ + +L + E E++ E ++ L+K L E + ++
Sbjct: 289 RVKQKRSDLEKRVENELEKLEKKLEKLEKELEEAENAE 326
>gnl|CDD|216169 pfam00881, Nitroreductase, Nitroreductase family. The
nitroreductase family comprises a group of FMN- or
FAD-dependent and NAD(P)H-dependent enzymes able to
metabolize nitrosubstituted compounds.
Length = 163
Score = 27.4 bits (61), Expect = 3.0
Identities = 9/22 (40%), Positives = 12/22 (54%), Gaps = 2/22 (9%)
Query: 83 SRRSSRRFKPQEVVEPQEVVEA 104
RRS R+F + V P E +E
Sbjct: 3 KRRSIRKFDDEPV--PDEDLEK 22
>gnl|CDD|206739 cd09912, DLP_2, Dynamin-like protein including dynamins,
mitofusins, and guanylate-binding proteins. The dynamin
family of large mechanochemical GTPases includes the
classical dynamins and dynamin-like proteins (DLPs) that
are found throughout the Eukarya. This family also
includes bacterial DLPs. These proteins catalyze
membrane fission during clathrin-mediated endocytosis.
Dynamin consists of five domains; an N-terminal G domain
that binds and hydrolyzes GTP, a middle domain (MD)
involved in self-assembly and oligomerization, a
pleckstrin homology (PH) domain responsible for
interactions with the plasma membrane, GED, which is
also involved in self-assembly, and a proline arginine
rich domain (PRD) that interacts with SH3 domains on
accessory proteins. To date, three vertebrate dynamin
genes have been identified; dynamin 1, which is brain
specific, mediates uptake of synaptic vesicles in
presynaptic terminals; dynamin-2 is expressed
ubiquitously and similarly participates in membrane
fission; mutations in the MD, PH and GED domains of
dynamin 2 have been linked to human diseases such as
Charcot-Marie-Tooth peripheral neuropathy and rare forms
of centronuclear myopathy. Dynamin 3 participates in
megakaryocyte progenitor amplification, and is also
involved in cytoplasmic enlargement and the formation of
the demarcation membrane system. This family also
includes mitofusins (MFN1 and MFN2 in mammals) that are
involved in mitochondrial fusion. Dynamin oligomerizes
into helical structures around the neck of budding
vesicles in a GTP hydrolysis-dependent manner.
Length = 180
Score = 27.1 bits (61), Expect = 3.2
Identities = 25/137 (18%), Positives = 46/137 (33%), Gaps = 26/137 (18%)
Query: 13 ASITSSYYKFAEAAILVFSLDNAAS---FHVLSQHLLEIVTYAENAKIFLCGNKSDLEGT 69
IT S+ A+A I V S D + L + L KIF NK DL
Sbjct: 64 TEITESFLPRADAVIFVLSADQPLTESEREFLKEILKW-----SGKKIFFVLNKIDL--- 115
Query: 70 TPQVTEADMENFWSRRSSRRFKPQEVVEPQEV--VEAEQVQQEACDKFEQMSDKAKEELN 127
++E ++E + + V A++ + + + +
Sbjct: 116 ---LSEEELEEVLEYSREELGVLELGGGEPRIFPVSAKEALE----------ARLQGDEE 162
Query: 128 DFKERRVEAFKKNLMEL 144
++ E +++L E
Sbjct: 163 LLEQSGFEELEEHLEEF 179
>gnl|CDD|206689 cd04102, RabL3, Rab GTPase-like family 3 (Rab-like3). RabL3
(Rab-like3) subfamily. RabL3s 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, RabL3 lacks a prenylation site at the
C-terminus. The specific function of RabL3 remains
unknown.
Length = 204
Score = 27.2 bits (60), Expect = 3.6
Identities = 17/52 (32%), Positives = 22/52 (42%), Gaps = 4/52 (7%)
Query: 1 MQLWDTGG----MERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEI 48
++LWD GG E V S + +Y I V L N S L + LE
Sbjct: 56 VELWDVGGSVGSAESVKSTRAVFYNQINGIIFVHDLTNKKSSQNLYRWSLEA 107
>gnl|CDD|234847 PRK00847, thyX, FAD-dependent thymidylate synthase; Reviewed.
Length = 217
Score = 27.1 bits (61), Expect = 3.9
Identities = 12/55 (21%), Positives = 24/55 (43%), Gaps = 7/55 (12%)
Query: 87 SRRF---KPQEVVEPQEVVEAEQV----QQEACDKFEQMSDKAKEELNDFKERRV 134
S+R+ E P + + Q Q+E + FE+ ++ A E + E+ +
Sbjct: 91 SQRYVLLDEFEFYIPPSIRKDNQSNSNSQEELLELFEEAAEAAYEAYEELLEKGI 145
>gnl|CDD|239015 cd02062, Nitro_FMN_reductase, Proteins of this family catalyze the
reduction of flavin or nitrocompounds using NAD(P)H as
electron donor in a obligatory two-electron transfer,
utilizing FMN or FAD as cofactor. They are often found
to be homodimers. Enzymes of this family are described
as NAD(P)H:FMN oxidoreductases, oxygen-insensitive
nitroreductase, flavin reductase P, dihydropteridine
reductase, NADH oxidase or NADH dehydrogenase.
Length = 122
Score = 26.8 bits (60), Expect = 3.9
Identities = 10/21 (47%), Positives = 14/21 (66%), Gaps = 2/21 (9%)
Query: 83 SRRSSRRFKPQEVVEPQEVVE 103
RRS R+F + V P+EV+E
Sbjct: 3 KRRSVRKFTDEPV--PEEVLE 21
>gnl|CDD|221740 pfam12732, YtxH, YtxH-like protein. This family of proteins is
found in bacteria. Proteins in this family are typically
between 100 and 143 amino acids in length. The
N-terminal region is the most conserved. Proteins is
this family are functionally uncharacterized.
Length = 66
Score = 25.7 bits (57), Expect = 3.9
Identities = 13/42 (30%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 105 EQVQQEACDKFEQMSDKAKEELNDFKERRVEAFKKNLMELAE 146
++ +++ DK + + +KAKE D KE + E K+ E+A+
Sbjct: 25 KETRKKLKDKAKDLKEKAKELAEDLKE-KAEEAKEKAKEVAD 65
>gnl|CDD|220497 pfam09973, DUF2208, Predicted membrane protein (DUF2208). This
domain, found in various hypothetical archaeal proteins,
has no known function.
Length = 232
Score = 26.9 bits (60), Expect = 4.4
Identities = 10/60 (16%), Positives = 23/60 (38%), Gaps = 6/60 (10%)
Query: 85 RSSRRFKPQEVVEPQEVVEAEQVQQEACDKFEQMSDKAKEELNDFKERRVEAFKKNLMEL 144
+ R E QE+ + +E + ++ +K +E + K + K ++ L
Sbjct: 42 VMTLRSNRSERKSLQEISSGRTLYEE--KEANKLVEKDEELTKELKAQ----AKASMSPL 95
>gnl|CDD|235582 PRK05729, valS, valyl-tRNA synthetase; Reviewed.
Length = 874
Score = 27.4 bits (62), Expect = 4.7
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 3/34 (8%)
Query: 98 PQEVVEAEQVQQEACDKFEQMSDKAKEELNDFKE 131
P+EVVE E+ + ++E+ K KE L K
Sbjct: 844 PEEVVEKEREKLA---EYEEKLAKLKERLARLKA 874
>gnl|CDD|132364 TIGR03321, alt_F1F0_F0_B, alternate F1F0 ATPase, F0 subunit B. A
small number of taxonomically diverse prokaryotic
species, including Methanosarcina barkeri, have what
appears to be a second ATP synthase, in addition to the
normal F1F0 ATPase in bacteria and A1A0 ATPase in
archaea. These enzymes use ion gradients to synthesize
ATP, CC and in principle may run in either direction.
This model represents the F0 subunit B of this apparent
second ATP synthase.
Length = 246
Score = 26.9 bits (60), Expect = 5.1
Identities = 22/99 (22%), Positives = 54/99 (54%), Gaps = 2/99 (2%)
Query: 74 TEADMENFWSRRSSRRFKPQ-EVVEPQEVVEAEQVQQEACDKFEQMSDKAKEELNDFKER 132
+AD + + + R ++ + E ++ Q V + ++EA + +++ D+A+EE ++ +E+
Sbjct: 46 ADADTKKREAEQERREYEEKNEELDQQREVLLTKAKEEAQAERQRLLDEAREEADEIREK 105
Query: 133 RVEAFKKNLMELAELEIKHAESQV-NILKKCLAELKTSD 170
EA ++ L++ + ++V I +K L +L +D
Sbjct: 106 WQEALRREQAALSDELRRRTGAEVFAIARKVLTDLADTD 144
>gnl|CDD|133344 cd04144, Ras2, Rat sarcoma (Ras) family 2 of small guanosine
triphosphatases (GTPases). The Ras2 subfamily, found
exclusively in fungi, was first identified in Ustilago
maydis. In U. maydis, Ras2 is regulated by Sql2, a
protein that is homologous to GEFs (guanine nucleotide
exchange factors) of the CDC25 family. Ras2 has been
shown to induce filamentous growth, but the signaling
cascade through which Ras2 and Sql2 regulate cell
morphology is not known. 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.
Length = 190
Score = 26.7 bits (59), Expect = 5.6
Identities = 17/69 (24%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIV----TYAENAK 56
+++ DT G E ++ + + E ILV+S+ + ++F + + +I A +
Sbjct: 49 LEVLDTAGQEEYTALRDQWIREGEGFILVYSITSRSTFERVERFREQIQRVKDESAADVP 108
Query: 57 IFLCGNKSD 65
I + GNK D
Sbjct: 109 IMIVGNKCD 117
>gnl|CDD|148805 pfam07406, NICE-3, NICE-3 protein. This family consists of several
eukaryotic NICE-3 and related proteins. The gene coding
for NICE-3 is part of the epidermal differentiation
complex (EDC) which comprises a large number of genes
that are of crucial importance for the maturation of the
human epidermis. The function of NICE-3 is unknown.
Length = 186
Score = 26.6 bits (59), Expect = 5.6
Identities = 15/72 (20%), Positives = 30/72 (41%)
Query: 76 ADMENFWSRRSSRRFKPQEVVEPQEVVEAEQVQQEACDKFEQMSDKAKEELNDFKERRVE 135
A M ++R + + + + V + Q D+ M + A+ N+F E
Sbjct: 115 ASMSGSYTRHTGQSLRSYLLDLRTLHVPLKGDGQRLIDQLLDMYEHARHGPNEFGEAEYL 174
Query: 136 AFKKNLMELAEL 147
+++ L ELA+
Sbjct: 175 KYQQLLTELADA 186
>gnl|CDD|223957 COG1026, COG1026, Predicted Zn-dependent peptidases,
insulinase-like [General function prediction only].
Length = 978
Score = 27.3 bits (61), Expect = 5.7
Identities = 14/63 (22%), Positives = 23/63 (36%), Gaps = 2/63 (3%)
Query: 53 ENAKIFLCGNKSDLEGTTPQVTEADMENFWSRRSSRRFKPQEVV-EPQEVVEAEQVQQEA 111
N KIF+ GN E + E + F R Q+ +P+ V + +
Sbjct: 214 SNCKIFVYGN-IPTERLLDFIEEKVLRPFGKRELDVPIPDQKAFKKPRRKVLEYPISFDE 272
Query: 112 CDK 114
D+
Sbjct: 273 EDE 275
>gnl|CDD|223446 COG0369, CysJ, Sulfite reductase, alpha subunit (flavoprotein)
[Inorganic ion transport and metabolism].
Length = 587
Score = 27.0 bits (60), Expect = 5.8
Identities = 10/39 (25%), Positives = 17/39 (43%), Gaps = 4/39 (10%)
Query: 39 HVLSQHLLEIVTYAEN-AKIFLCGNKSDLEGTTPQVTEA 76
L + E+ + E A I++CG+ + V EA
Sbjct: 518 DRLREQADELWEWLEEGAHIYVCGDAKGMA---KDVEEA 553
>gnl|CDD|234980 PRK01759, glnD, PII uridylyl-transferase; Provisional.
Length = 854
Score = 27.0 bits (60), Expect = 5.9
Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 3/40 (7%)
Query: 58 FLCGNKSDLEGTTPQVTEADMENFWSRRSSRRFKPQEVVE 97
FL GN+ + + +AD FWS+ + + K QE +E
Sbjct: 137 FLTGNEKLFDALVELLQQAD---FWSKEAFFQAKIQEKIE 173
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 26.7 bits (59), Expect = 6.2
Identities = 15/79 (18%), Positives = 32/79 (40%), Gaps = 2/79 (2%)
Query: 3 LWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAENAKIFLCGN 62
L+ T G ER + + A AI++ +D++ ++ +++ +T + + N
Sbjct: 72 LFGTPGQERFKFMWEILSRGAVGAIVL--VDSSRPITFHAEEIIDFLTSRNPIPVVVAIN 129
Query: 63 KSDLEGTTPQVTEADMENF 81
K DL P +
Sbjct: 130 KQDLFDALPPEKIREALKL 148
>gnl|CDD|206714 cd04147, Ras_dva, Ras - dorsal-ventral anterior localization
(Ras-dva) family. Ras-dva subfamily. Ras-dva (Ras -
dorsal-ventral anterior localization) subfamily consists
of a set of proteins characterized only in Xenopus
leavis, to date. In Xenopus Ras-dva expression is
activated by the transcription factor Otx2 and begins
during gastrulation throughout the anterior ectoderm.
Ras-dva expression is inhibited in the anterior neural
plate by factor Xanf1. Downregulation of Ras-dva results
in head development abnormalities through the inhibition
of several regulators of the anterior neural plate and
folds patterning, including Otx2, BF-1, Xag2, Pax6,
Slug, and Sox9. Downregulation of Ras-dva also
interferes with the FGF-8a signaling within the anterior
ectoderm. 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.
Length = 197
Score = 26.7 bits (59), Expect = 6.3
Identities = 22/81 (27%), Positives = 36/81 (44%), Gaps = 3/81 (3%)
Query: 1 MQLWDTGGMERVASITSSYYKFAEAAILVFSLDNAASFHVLSQHLLEIVTYAENA--KIF 58
+ + DT G ++ + +A LV+S+D+ SF + + EI+ E+ I
Sbjct: 49 IDILDTSGSYSFPAMRKLSIQNGDAFALVYSVDDPESFEEVKRLREEILEVKEDKFVPIV 108
Query: 59 LCGNKSDLEGTTPQVTEADME 79
+ GNK D QV AD
Sbjct: 109 VVGNKIDSLAER-QVEAADAL 128
>gnl|CDD|236265 PRK08439, PRK08439, 3-oxoacyl-(acyl carrier protein) synthase II;
Reviewed.
Length = 406
Score = 26.6 bits (59), Expect = 7.3
Identities = 15/40 (37%), Positives = 23/40 (57%), Gaps = 9/40 (22%)
Query: 90 FKPQEVVEPQEVVEAEQVQQEACDKFEQMSDKA-KEELND 128
F P EV++P+EV +A D+F Q+ KA +E + D
Sbjct: 55 FDPTEVMDPKEVKKA--------DRFIQLGLKAAREAMKD 86
>gnl|CDD|226654 COG4191, COG4191, Signal transduction histidine kinase regulating
C4-dicarboxylate transport system [Signal transduction
mechanisms].
Length = 603
Score = 26.5 bits (59), Expect = 8.0
Identities = 19/80 (23%), Positives = 36/80 (45%), Gaps = 14/80 (17%)
Query: 35 AASFHVLSQHLLEIVTYAENAKIFLCGNKSD-LEGTTPQVTE---------ADMENFWSR 84
A H L+Q L I TYA+NA++ L +++ +++ A +++F +R
Sbjct: 389 AGIAHELNQPLAAIRTYADNARLLLERGRTEEARENLERISALTERMAAITAHLKSF-AR 447
Query: 85 RSSRRFKPQEVVEPQEVVEA 104
+S V +E +E
Sbjct: 448 KSRDA---AGPVSLREAIEG 464
>gnl|CDD|227570 COG5245, DYN1, Dynein, heavy chain [Cytoskeleton].
Length = 3164
Score = 26.5 bits (58), Expect = 9.0
Identities = 16/85 (18%), Positives = 29/85 (34%), Gaps = 7/85 (8%)
Query: 82 WSRRSSRRFKPQEVVEP--QEV--VEAEQVQQEACDKFEQMSDKAKEELNDFKERRVEAF 137
W R R K EV P +E ++ E E + +L FK RR +
Sbjct: 2292 WLVRECNRSKVLEVKIPLREEEKRIDGEAFLVEDR---LTLGKGLSSDLMTFKLRRRSYY 2348
Query: 138 KKNLMELAELEIKHAESQVNILKKC 162
+++ + ++L+
Sbjct: 2349 SLDILRVHGKIADMDTVHKDVLRSI 2373
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
0.314 0.127 0.350
Gapped
Lambda K H
0.267 0.0693 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,310,074
Number of extensions: 745673
Number of successful extensions: 1440
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1362
Number of HSP's successfully gapped: 261
Length of query: 170
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 80
Effective length of database: 6,945,742
Effective search space: 555659360
Effective search space used: 555659360
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 55 (25.0 bits)