RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6968
(93 letters)
>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 = 117 bits (296), Expect = 1e-35
Identities = 45/61 (73%), Positives = 55/61 (90%)
Query: 25 LRLGIVGSLASGKSALVHRFMTGAFLQEESPEGGRFKKEVVIDGHSHLLLIRDEGVPPEL 84
L+LGIVG+L SGKSALVHR++TG+++Q ESPEGGRFKKEV++DG SHLLLIRDEG P+
Sbjct: 1 LKLGIVGNLRSGKSALVHRYLTGSYVQLESPEGGRFKKEVLVDGQSHLLLIRDEGGAPDA 60
Query: 85 Q 85
Q
Sbjct: 61 Q 61
>gnl|CDD|219856 pfam08477, Miro, Miro-like protein. Mitochondrial Rho proteins
(Miro-1, and Miro-2), are atypical Rho GTPases. They
have a unique domain organisation, with tandem
GTP-binding domains and two EF hand domains
(pfam00036), that may bind calcium. They are also
larger than classical small GTPases. It has been
proposed that they are involved in mitochondrial
homeostasis and apoptosis.
Length = 116
Score = 48.6 bits (116), Expect = 6e-09
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 26 RLGIVGSLASGKSALVHRFMTGAFLQE--ESPEGGRFKKEVVIDGHSHLLLIRDEGVPPE 83
++ ++G SGKS+L+ + + G F E E + +DG + LL I D G E
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREE 60
Query: 84 LQ 85
L+
Sbjct: 61 LK 62
>gnl|CDD|133342 cd04142, RRP22, Ras-related protein on chromosome 22 (RRP22)
family. RRP22 (Ras-related protein on chromosome 22)
subfamily consists of proteins that inhibit cell growth
and promote caspase-independent cell death. Unlike most
Ras proteins, RRP22 is down-regulated in many human
tumor cells due to promoter methylation. RRP22
localizes to the nucleolus in a GTP-dependent manner,
suggesting a novel function in modulating transport of
nucleolar components. 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. Like most Ras family proteins, RRP22 is
farnesylated.
Length = 198
Score = 43.3 bits (102), Expect = 2e-06
Identities = 21/70 (30%), Positives = 37/70 (52%), Gaps = 5/70 (7%)
Query: 25 LRLGIVGSLASGKSALVHRFMTGAFLQEESPEGGR--FKKEVVIDGHSHLLLIRDEGVPP 82
+R+ ++G+ GK+A+V +F+ F +E P R ++ VV+ G + L I D VP
Sbjct: 1 VRVAVLGAPGVGKTAIVRQFLAQEFPEEYIPTEHRRLYRPAVVLSGRVYDLHILD--VPN 58
Query: 83 ELQPPNPSAP 92
+Q +A
Sbjct: 59 -MQRYPGTAG 67
>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 = 42.5 bits (101), Expect = 3e-06
Identities = 20/53 (37%), Positives = 35/53 (66%), Gaps = 1/53 (1%)
Query: 26 RLGIVGSLASGKSALVHRFMTGAFLQEESP-EGGRFKKEVVIDGHSHLLLIRD 77
+L ++G+ GKSAL RF++G F++E P ++K++V+DG ++ L I D
Sbjct: 1 KLVVLGAGGVGKSALTIRFVSGEFVEEYDPTIEDSYRKQIVVDGETYTLDILD 53
>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 = 38.6 bits (91), Expect = 6e-05
Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 2/51 (3%)
Query: 29 IVGSLASGKSALVHRFMTGAFLQE-ESPEGGRFK-KEVVIDGHSHLLLIRD 77
+VG GKS+L+ RF F +E G F K + +DG + L I D
Sbjct: 4 LVGDGGVGKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIWD 54
>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 = 37.5 bits (88), Expect = 2e-04
Identities = 21/57 (36%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 23 PDLRLGIVGSLASGKSALVHRFMTGAFLQEESP--EGGRFKKEVVIDGHSHLLLIRD 77
+ +L ++G GKSAL +F+ G F+ E P E ++K++ IDG LL I D
Sbjct: 1 REYKLVVLGGGGVGKSALTIQFVQGHFVDEYDPTIEDS-YRKQIEIDGEVCLLDILD 56
>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 = 37.5 bits (88), Expect = 2e-04
Identities = 21/54 (38%), Positives = 32/54 (59%), Gaps = 3/54 (5%)
Query: 26 RLGIVGSLASGKSALVHRFMTGAFLQEESP--EGGRFKKEVVIDGHSHLLLIRD 77
+L ++GS GKSAL +F+ G F+ + P E ++K++ IDG LL I D
Sbjct: 2 KLVVLGSGGVGKSALTIQFIQGHFVDDYDPTIEDS-YRKQIEIDGEVCLLDILD 54
>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 = 37.5 bits (87), Expect = 2e-04
Identities = 18/50 (36%), Positives = 30/50 (60%), Gaps = 1/50 (2%)
Query: 29 IVGSLASGKSALVHRFMTGAFLQEESPEGGRF-KKEVVIDGHSHLLLIRD 77
++GS GKSAL +F++G F+++ P F +KE+ +D +L I D
Sbjct: 6 VLGSGGVGKSALTVQFVSGTFIEKYDPTIEDFYRKEIEVDSSPSVLEILD 55
>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 = 37.3 bits (87), Expect = 2e-04
Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 27 LGIVGSLASGKSALVHRFMTGAFLQE-ESPEGGRFKKEVVIDGHSHLLLIRD 77
+ ++G+ GKSAL RF+T F+ E E + ++V IDG L I+D
Sbjct: 2 IAVLGASGVGKSALTVRFLTKRFIGEYEPNLESLYSRQVTIDGEQVSLEIQD 53
>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 = 36.7 bits (86), Expect = 3e-04
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 25 LRLGIVGSLASGKSALVHRFMTGAFLQEESPE-GGRFK-KEVVIDGHSHLLLIRD 77
++ ++G GK++L+ RF+ F + G FK K + +DG L I D
Sbjct: 1 FKIVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGVDFKSKTIEVDGKKVKLQIWD 55
>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 = 36.2 bits (84), Expect = 6e-04
Identities = 21/55 (38%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 24 DLRLGIVGSLASGKSALVHRFMTGAFLQEESPE-GGRFKKEVVIDGHSHLLLIRD 77
+ +L +VG+ GKSAL + + F+ E P ++K+VVIDG + LL I D
Sbjct: 1 EYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILD 55
>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 = 36.0 bits (83), Expect = 6e-04
Identities = 19/55 (34%), Positives = 33/55 (60%), Gaps = 1/55 (1%)
Query: 24 DLRLGIVGSLASGKSALVHRFMTGAFLQEESPE-GGRFKKEVVIDGHSHLLLIRD 77
+ +L ++GS GKSAL +F+ G F+++ P ++K+V +DG +L I D
Sbjct: 1 EYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDGQQCMLEILD 55
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins
[General function prediction only].
Length = 219
Score = 36.1 bits (83), Expect = 8e-04
Identities = 12/64 (18%), Positives = 25/64 (39%), Gaps = 2/64 (3%)
Query: 25 LRLGIVGSLASGKSALVHRFMTGAFLQEESPEGG-RF-KKEVVIDGHSHLLLIRDEGVPP 82
++ ++G GK+ L++R + F + P G K + + L + D
Sbjct: 6 FKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQE 65
Query: 83 ELQP 86
E +
Sbjct: 66 EYRS 69
>gnl|CDD|206711 cd04140, ARHI_like, A Ras homolog member I (ARHI). ARHI (A Ras
homolog member I) is a member of the Ras family with
several unique structural and functional properties.
ARHI is expressed in normal human ovarian and breast
tissue, but its expression is decreased or eliminated
in breast and ovarian cancer. ARHI contains an
N-terminal extension of 34 residues (human) that is
required to retain its tumor suppressive activity.
Unlike most other Ras family members, ARHI is
maintained in the constitutively active (GTP-bound)
state in resting cells and has modest GTPase activity.
ARHI inhibits STAT3 (signal transducers and activators
of transcription 3), a latent transcription factor
whose abnormal activation plays a critical role in
oncogenesis. 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 = 165
Score = 35.2 bits (81), Expect = 0.002
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 24 DLRLGIVGSLASGKSALVHRFMTGAFLQEESP 55
D R+ + G+ GKS+LV RF+ G F + P
Sbjct: 1 DYRVVVFGAGGVGKSSLVLRFVKGTFRESYIP 32
>gnl|CDD|206653 cd01860, Rab5_related, Rab-related GTPase family includes Rab5
and Rab22; regulates early endosome fusion. The
Rab5-related subfamily includes Rab5 and Rab22 of
mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of
plants. The members of this subfamily are involved in
endocytosis and endocytic-sorting pathways. In mammals,
Rab5 GTPases localize to early endosomes and regulate
fusion of clathrin-coated vesicles to early endosomes
and fusion between early endosomes. In yeast, Ypt51p
family members similarly regulate membrane trafficking
through prevacuolar compartments. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 163
Score = 33.7 bits (78), Expect = 0.004
Identities = 13/51 (25%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 29 IVGSLASGKSALVHRFMTGAFLQEESPEGGR--FKKEVVIDGHSHLLLIRD 77
++G + GKS++V RF+ F + + G + V +D + I D
Sbjct: 6 LLGDSSVGKSSIVLRFVKNEFSENQESTIGAAFLTQTVNLDDTTVKFEIWD 56
>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 = 33.7 bits (77), Expect = 0.005
Identities = 17/55 (30%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 24 DLRLGIVGSLASGKSALVHRFMTGAFLQEESPE-GGRFKKEVVIDGHSHLLLIRD 77
+ +L ++GS GKSAL +F+ G F+ + P ++K++ +D +L I D
Sbjct: 1 EYKLVVLGSGGVGKSALTVQFVQGIFVDKYDPTIEDSYRKQIEVDCQQCMLEILD 55
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 32.5 bits (74), Expect = 0.014
Identities = 20/53 (37%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 26 RLGIVGSLASGKSALVHRFMTGAFLQEESPE-GGRFKKEVVIDGHSHLLLIRD 77
+L +VG GKSAL +F+ F+ E P ++K+ VID + LL I D
Sbjct: 7 KLVVVGGGGVGKSALTIQFIQNHFIDEYDPTIEDSYRKQCVIDEETCLLDILD 59
>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 = 32.4 bits (74), Expect = 0.014
Identities = 20/50 (40%), Positives = 30/50 (60%), Gaps = 1/50 (2%)
Query: 29 IVGSLASGKSALVHRFMTGAFLQEESP-EGGRFKKEVVIDGHSHLLLIRD 77
+VGS GKSAL +FM F+++ P + ++K+VV+DG L I D
Sbjct: 5 MVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEVQLNILD 54
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 31.7 bits (73), Expect = 0.021
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 25 LRLGIVGSLASGKSALVHRFMTGAFLQEESPEGG-RFK-KEVVIDGH 69
++ ++G GKS+L+ RF G F ++ G FK K + +DG
Sbjct: 1 FKIILIGDSGVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIEVDGK 47
>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 = 31.4 bits (71), Expect = 0.033
Identities = 13/36 (36%), Positives = 22/36 (61%)
Query: 25 LRLGIVGSLASGKSALVHRFMTGAFLQEESPEGGRF 60
L++ ++G + GK++L+HR+M F S GG F
Sbjct: 1 LKVVLLGDMNVGKTSLLHRYMERRFKDTVSTVGGAF 36
>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 = 31.3 bits (71), Expect = 0.041
Identities = 20/51 (39%), Positives = 28/51 (54%), Gaps = 2/51 (3%)
Query: 29 IVGSLASGKSALVHRFMTGAFLQEESPE-GGRFKKEVV-IDGHSHLLLIRD 77
I+GS +GKS L+H+F+ F Q+ + G F VV + G S L I D
Sbjct: 5 IIGSAGTGKSCLLHQFIENKFKQDSNHTIGVEFGSRVVNVGGKSVKLQIWD 55
>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 = 31.1 bits (71), Expect = 0.046
Identities = 20/55 (36%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 25 LRLGIVGSLASGKSALVHRFMTGAFLQEESPE-GGRFK-KEVVIDGHSHLLLIRD 77
L++ ++G GKS+L+ RF F ++ S G FK K V +DG L I D
Sbjct: 1 LKILLIGDSGVGKSSLLLRFTDDTFDEDLSSTIGVDFKVKTVTVDGKKVKLAIWD 55
>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 = 31.0 bits (70), Expect = 0.056
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 8/57 (14%)
Query: 29 IVGSLASGKSALVHRFMTGAFLQEESPEGGRFKKEVVIDGHSHLLLIRDEGVPPELQ 85
+VG GK+ L+ RF GAFL G F V I + ++ + +GV +LQ
Sbjct: 5 LVGDSGVGKTCLLVRFKDGAFL------AGSFIATVGIQFTNKVVTV--DGVKVKLQ 53
>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 = 30.5 bits (69), Expect = 0.078
Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 24 DLRLGIVGSLASGKSALVHRFMTGAFLQEESPE-GGRFKKEVVIDGHSHLLLIRD 77
D ++ ++G+ GKSAL +F+ F++ P ++K+V IDG L I D
Sbjct: 1 DYKIVVLGAGGVGKSALTVQFVQNVFIESYDPTIEDSYRKQVEIDGRQCDLEILD 55
>gnl|CDD|213219 cd03252, ABCC_Hemolysin, ATP-binding cassette domain of hemolysin
B, subfamily C. The ABC-transporter hemolysin B is a
central component of the secretion machinery that
translocates the toxin, hemolysin A, in a
Sec-independent fashion across both membranes of E.
coli. The hemolysin A (HlyA) transport machinery is
composed of the ATP-binding cassette (ABC) transporter
HlyB located in the inner membrane, hemolysin D (HlyD),
also anchored in the inner membrane, and TolC, which
resides in the outer membrane. HlyD apparently forms a
continuous channel that bridges the entire periplasm,
interacting with TolC and HlyB. This arrangement
prevents the appearance of periplasmic intermediates of
HlyA during substrate transport. Little is known about
the molecular details of HlyA transport, but it is
evident that ATP-hydrolysis by the ABC-transporter HlyB
is a necessary source of energy.
Length = 237
Score = 30.5 bits (69), Expect = 0.079
Identities = 17/43 (39%), Positives = 24/43 (55%), Gaps = 9/43 (20%)
Query: 27 LGIVGSLASGKSALVHRFMTGAFLQEESPEGGRFKKEVVIDGH 69
+GIVG SGKS L + + ++ PE GR V++DGH
Sbjct: 31 VGIVGRSGSGKSTLT-KLIQRFYV----PENGR----VLVDGH 64
>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 = 30.2 bits (68), Expect = 0.087
Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 2/55 (3%)
Query: 25 LRLGIVGSLASGKSALVHRFMTGAF-LQEESPEGGRF-KKEVVIDGHSHLLLIRD 77
L++ ++G GKS+L++R++T F Q G F K++ +DGH L I D
Sbjct: 6 LKVILLGDGGVGKSSLMNRYVTNKFDTQLFHTIGVEFLNKDLEVDGHFVTLQIWD 60
>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 = 30.5 bits (69), Expect = 0.091
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 8/53 (15%)
Query: 26 RLGIVGSLASGKSALVHRFMTGAFLQEESPEGGRFKKEVVIDGHSHLLLIRDE 78
R+ ++G+ GK+A+V RF+ G F ++ +P + D H L IR E
Sbjct: 2 RMVVLGASKVGKTAIVSRFLGGRFEEQYTP--------TIEDFHRKLYSIRGE 46
>gnl|CDD|240253 PTZ00068, PTZ00068, 60S ribosomal protein L13a; Provisional.
Length = 202
Score = 30.0 bits (68), Expect = 0.093
Identities = 9/14 (64%), Positives = 10/14 (71%)
Query: 60 FKKEVVIDGHSHLL 73
FKK +VID HLL
Sbjct: 2 FKKVIVIDCKGHLL 15
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 30.1 bits (68), Expect = 0.093
Identities = 15/38 (39%), Positives = 21/38 (55%)
Query: 21 DVPDLRLGIVGSLASGKSALVHRFMTGAFLQEESPEGG 58
D P +L IVG +GK+ V R +TG F ++ P G
Sbjct: 10 DYPSFKLVIVGDGGTGKTTFVKRHLTGEFEKKYEPTIG 47
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 30.0 bits (68), Expect = 0.094
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 19 ARDVPDLRLGIVGSLASGKSALVHRFMTGAF 49
+VP+ +L +VG GK+ V R +TG F
Sbjct: 4 MDEVPEFKLILVGDGGVGKTTFVKRHLTGEF 34
>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 = 29.6 bits (67), Expect = 0.14
Identities = 8/23 (34%), Positives = 16/23 (69%)
Query: 29 IVGSLASGKSALVHRFMTGAFLQ 51
++G L GK++++ R++ G F Q
Sbjct: 5 VIGDLGVGKTSIIKRYVHGVFSQ 27
>gnl|CDD|150276 pfam09547, Spore_IV_A, Stage IV sporulation protein A
(spore_IV_A). SpoIVA is designated stage IV
sporulation protein A. It acts in the mother cell
compartment and plays a role in spore coat
morphogenesis. A comparative genome analysis of all
sequenced genomes of Firmicutes shows that the proteins
are strictly conserved among the sub-set of
endospore-forming species.
Length = 492
Score = 29.5 bits (67), Expect = 0.20
Identities = 10/22 (45%), Positives = 16/22 (72%)
Query: 24 DLRLGIVGSLASGKSALVHRFM 45
D+ +G+VG + +GKS + RFM
Sbjct: 17 DIYIGVVGPVRTGKSTFIKRFM 38
>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 = 29.2 bits (66), Expect = 0.21
Identities = 13/47 (27%), Positives = 27/47 (57%), Gaps = 2/47 (4%)
Query: 25 LRLGIVGSLASGKSALVHRFMTGAFLQE-ESPEGGRF-KKEVVIDGH 69
L++ I+G GK++L+++++ F + ++ G F KEV +D
Sbjct: 1 LKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVTVDDR 47
>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 = 29.3 bits (66), Expect = 0.22
Identities = 21/60 (35%), Positives = 29/60 (48%), Gaps = 8/60 (13%)
Query: 26 RLGIVGSLASGKSALVHRFMTGAFLQEESPEGGRFKKEVVIDGHSHLLLIRDEGVPPELQ 85
RL ++G GKS+L+ RF G F + P G +D S L+ I GV +LQ
Sbjct: 4 RLIVIGDSTVGKSSLLKRFTEGRFAEVSDPTVG-------VDFFSRLIEIEP-GVRIKLQ 55
>gnl|CDD|233596 TIGR01846, type_I_sec_HlyB, type I secretion system ABC
transporter, HlyB family. Type I protein secretion is a
system in some Gram-negative bacteria to export proteins
(often proteases) across both inner and outer membranes
to the extracellular medium. This is one of three
proteins of the type I secretion apparatus. Targeted
proteins are not cleaved at the N-terminus, but rather
carry signals located toward the extreme C-terminus to
direct type I secretion [Protein fate, Protein and
peptide secretion and trafficking].
Length = 694
Score = 29.3 bits (66), Expect = 0.22
Identities = 16/46 (34%), Positives = 22/46 (47%), Gaps = 15/46 (32%)
Query: 27 LGIVGSLASGKSA---LVHRFMTGAFLQEESPEGGRFKKEVVIDGH 69
+GIVG SGKS L+ R T P+ G+ V++DG
Sbjct: 486 IGIVGPSGSGKSTLTKLLQRLYT--------PQHGQ----VLVDGV 519
>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 = 28.9 bits (65), Expect = 0.26
Identities = 12/39 (30%), Positives = 23/39 (58%), Gaps = 7/39 (17%)
Query: 29 IVGSLASGKSALVHRFMTGAFLQEESPEGGRFKKEVVID 67
+VG+ GKS+++ RF+ G F ++ +KK + +D
Sbjct: 5 VVGNGNVGKSSMIQRFVKGIFTKD-------YKKTIGVD 36
>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 = 28.6 bits (64), Expect = 0.34
Identities = 15/42 (35%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 29 IVGSLASGKSALVHRFMTGAFLQE-ESPEGGRFK-KEVVIDG 68
++G GK+ L +RF G F + E+ G F+ + V IDG
Sbjct: 7 VIGDSNVGKTCLTYRFCAGRFPERTEATIGVDFRERTVEIDG 48
>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 = 28.6 bits (64), Expect = 0.35
Identities = 11/53 (20%), Positives = 20/53 (37%), Gaps = 3/53 (5%)
Query: 28 GIVGSLASGKSALVHRFMTGAFLQEESPEG---GRFKKEVVIDGHSHLLLIRD 77
+VG GKS+L++ + G + G +D L++ D
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVLVD 53
>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 = 28.4 bits (64), Expect = 0.40
Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 3/51 (5%)
Query: 29 IVGSLASGKSALVHRFMTGAFLQEESP--EGGRFKKEVVIDGHSHLLLIRD 77
++GS + GKS+L +F+ G F++ P E F K + G + L I D
Sbjct: 6 VLGSRSVGKSSLTVQFVEGHFVESYYPTIE-NTFSKIITYKGQEYHLEIVD 55
>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 = 28.3 bits (63), Expect = 0.47
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 26 RLGIVGSLASGKSALVHRFMTGAFLQEESPE-GGRFKKEVVIDGHSHLLLIRD 77
++ ++G+ GKSA+ +F++ +F P +K + ID LL I D
Sbjct: 4 KIVMLGAGGVGKSAVTMQFISHSFPDYHDPTIEDAYKTQARIDNEPALLDILD 56
>gnl|CDD|131883 TIGR02836, spore_IV_A, stage IV sporulation protein A. A
comparative genome analysis of all sequenced genomes of
shows a number of proteins conserved strictly among the
endospore-forming subset of the Firmicutes. This
protein, a member of this panel, is designated stage IV
sporulation protein A. It acts in the mother cell
compartment and plays a role in spore coat
morphogenesis [Cellular processes, Sporulation and
germination].
Length = 492
Score = 28.2 bits (63), Expect = 0.49
Identities = 9/22 (40%), Positives = 16/22 (72%)
Query: 24 DLRLGIVGSLASGKSALVHRFM 45
D+ +G+VG + +GKS + +FM
Sbjct: 17 DIYIGVVGPVRTGKSTFIKKFM 38
>gnl|CDD|200134 TIGR01842, type_I_sec_PrtD, type I secretion system ABC
transporter, PrtD family. Type I protein secretion is a
system in some Gram-negative bacteria to export proteins
(often proteases) across both inner and outer membranes
to the extracellular medium. This is one of three
proteins of the type I secretion apparatus. Targeted
proteins are not cleaved at the N-terminus, but rather
carry signals located toward the extreme C-terminus to
direct type I secretion [Protein fate, Protein and
peptide secretion and trafficking].
Length = 544
Score = 28.1 bits (63), Expect = 0.58
Identities = 10/24 (41%), Positives = 13/24 (54%), Gaps = 1/24 (4%)
Query: 27 LGIVGSLASGKSALVHRFMTGAFL 50
L I+G SGKS L R + G +
Sbjct: 347 LAIIGPSGSGKSTLA-RLIVGIWP 369
>gnl|CDD|226969 COG4618, ArpD, ABC-type protease/lipase transport system, ATPase
and permease components [General function prediction
only].
Length = 580
Score = 28.0 bits (63), Expect = 0.58
Identities = 16/42 (38%), Positives = 20/42 (47%), Gaps = 9/42 (21%)
Query: 27 LGIVGSLASGKSALVHRFMTGAFLQEESPEGGRFKKEVVIDG 68
LGI+G SGKS L R + G + P G V +DG
Sbjct: 365 LGIIGPSGSGKSTLA-RLLVGIWP----PTSG----SVRLDG 397
>gnl|CDD|240327 PTZ00243, PTZ00243, ABC transporter; Provisional.
Length = 1560
Score = 28.2 bits (63), Expect = 0.63
Identities = 13/26 (50%), Positives = 16/26 (61%)
Query: 20 RDVPDLRLGIVGSLASGKSALVHRFM 45
R P ++GIVG SGKS L+ FM
Sbjct: 1332 RIAPREKVGIVGRTGSGKSTLLLTFM 1357
>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 = 27.9 bits (62), Expect = 0.66
Identities = 15/53 (28%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 26 RLGIVGSLASGKSALVHRFMTGAFLQEESPE-GGRFKKEVVIDGHSHLLLIRD 77
+L ++G GK+AL + F++ P ++K+VV+DG +L + D
Sbjct: 1 KLVVLGDGGVGKTALTIQLCLNHFVETYDPTIEDSYRKQVVVDGQPCMLEVLD 53
>gnl|CDD|188098 TIGR00957, MRP_assoc_pro, multi drug resistance-associated protein
(MRP). This model describes multi drug
resistance-associated protein (MRP) in eukaryotes. The
multidrug resistance-associated protein is an integral
membrane protein that causes multidrug resistance when
overexpressed in mammalian cells. It belongs to ABC
transporter superfamily. The protein topology and
function was experimentally demonstrated by epitope
tagging and immunofluorescence. Insertion of tags in the
critical regions associated with drug efflux, abrogated
its function. The C-terminal domain seem to highly
conserved [Transport and binding proteins, Other].
Length = 1522
Score = 28.0 bits (62), Expect = 0.66
Identities = 18/43 (41%), Positives = 24/43 (55%), Gaps = 9/43 (20%)
Query: 26 RLGIVGSLASGKSALVHRFMTGAFLQEESPEGGRFKKEVVIDG 68
++GIVG +GKS+L G F ES EG E++IDG
Sbjct: 1314 KVGIVGRTGAGKSSLT----LGLFRINESAEG-----EIIIDG 1347
>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 = 27.4 bits (61), Expect = 0.80
Identities = 13/42 (30%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 29 IVGSLASGKSALVHRFMTGAFLQ-EESPEGGRFK-KEVVIDG 68
++G GK+ +V RF +G F + + + G F K + I G
Sbjct: 8 LIGDSNVGKTCVVQRFKSGTFSERQGNTIGVDFTMKTLEIQG 49
>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 = 27.3 bits (61), Expect = 0.85
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 26 RLGIVGSLASGKSALVHRFMTGAF 49
+L +VG +GK+ V R +TG F
Sbjct: 2 KLVLVGDGGTGKTTFVKRHLTGEF 25
>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 = 27.4 bits (61), Expect = 0.90
Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 6/57 (10%)
Query: 25 LRLGIVGSLASGKSALVHRFMTGAFLQEESP---EGGRF-KKEVVIDGHSHLLLIRD 77
R+ ++G GKS+L + F G + E+S G ++ V +DG L++ D
Sbjct: 1 YRVVLLGDSGVGKSSLANIFTAG--VYEDSAYEASGDDTYERTVSVDGEEATLVVYD 55
>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 = 27.2 bits (61), Expect = 0.90
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 2/44 (4%)
Query: 36 GKSALVHRFMTGAFL--QEESPEGGRFKKEVVIDGHSHLLLIRD 77
GK++LV R++ F E + + F+K V I G L I D
Sbjct: 12 GKTSLVLRYVENKFNEKHESTTQASFFQKTVNIGGKRIDLAIWD 55
>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 = 27.4 bits (61), Expect = 0.92
Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 1/56 (1%)
Query: 23 PDLRLGIVGSLASGKSALVHRFMTGAFLQEESPE-GGRFKKEVVIDGHSHLLLIRD 77
P +L +VG GKSAL +F+ F+ + P + K+ IDG L I D
Sbjct: 1 PTYKLVVVGGGGVGKSALTIQFIQSYFVTDYDPTIEDSYTKQCEIDGQWARLDILD 56
>gnl|CDD|213213 cd03246, ABCC_Protease_Secretion, ATP-binding cassette domain of
PrtD, subfamily C. This family represents the ABC
component of the protease secretion system PrtD, a
60-kDa integral membrane protein sharing 37% identity
with HlyB, the ABC component of the alpha-hemolysin
secretion pathway, in the C-terminal domain. They
export degradative enzymes by using a type I protein
secretion system and lack an N-terminal signal peptide,
but contain a C-terminal secretion signal. The Type I
secretion apparatus is made up of three components, an
ABC transporter, a membrane fusion protein (MFP), and
an outer membrane protein (OMP). For the HlyA
transporter complex, HlyB (ABC transporter) and HlyD
(MFP) reside in the inner membrane of E. coli. The OMP
component is TolC, which is thought to interact with
the MFP to form a continuous channel across the
periplasm from the cytoplasm to the exterior. HlyB
belongs to the family of ABC transporters, which are
ubiquitous, ATP-dependent transmembrane pumps or
channels. The spectrum of transport substrates ranges
from inorganic ions, nutrients such as amino acids,
sugars, or peptides, hydrophobic drugs, to large
polypeptides, such as HlyA.
Length = 173
Score = 27.2 bits (61), Expect = 0.93
Identities = 16/42 (38%), Positives = 19/42 (45%), Gaps = 9/42 (21%)
Query: 27 LGIVGSLASGKSALVHRFMTGAFLQEESPEGGRFKKEVVIDG 68
L I+G SGKS L R + G P GR V +DG
Sbjct: 31 LAIIGPSGSGKSTLA-RLILGLLR----PTSGR----VRLDG 63
>gnl|CDD|226647 COG4181, COG4181, Predicted ABC-type transport system involved in
lysophospholipase L1 biosynthesis, ATPase component
[Secondary metabolites biosynthesis, transport, and
catabolism].
Length = 228
Score = 27.4 bits (61), Expect = 0.99
Identities = 15/45 (33%), Positives = 19/45 (42%), Gaps = 9/45 (20%)
Query: 26 RLGIVGSLASGKSALVHRFMTGAFLQEESPEGGRFKKEVVIDGHS 70
+ IVG SGKS L+ A L + P G EV + G
Sbjct: 38 TVAIVGPSGSGKSTLL---AVLAGL--DDPSSG----EVRLLGQP 73
>gnl|CDD|183244 PRK11629, lolD, lipoprotein transporter ATP-binding subunit;
Provisional.
Length = 233
Score = 27.5 bits (61), Expect = 1.0
Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 9/44 (20%)
Query: 27 LGIVGSLASGKSALVHRFMTGAFLQEESPEGGRFKKEVVIDGHS 70
+ IVGS SGKS L+H + G ++P G +V+ +G
Sbjct: 38 MAIVGSSGSGKSTLLH--LLGGL---DTPTSG----DVIFNGQP 72
>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 = 27.1 bits (60), Expect = 1.1
Identities = 13/30 (43%), Positives = 19/30 (63%)
Query: 26 RLGIVGSLASGKSALVHRFMTGAFLQEESP 55
+L IVG A GK++L++ F G F +E P
Sbjct: 3 KLVIVGDGACGKTSLLYVFTLGEFPEEYHP 32
>gnl|CDD|224057 COG1134, TagH, ABC-type polysaccharide/polyol phosphate transport
system, ATPase component [Carbohydrate transport and
metabolism / Cell envelope biogenesis, outer membrane].
Length = 249
Score = 27.2 bits (61), Expect = 1.2
Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 9/59 (15%)
Query: 26 RLGIVGSLASGKSALVHRFMTGAFLQEESPEGGRFKKEVVIDGHSHLLLIRDEGVPPEL 84
R+GI+G +GKS L+ + + G P G +V + G L+ G PEL
Sbjct: 55 RVGIIGHNGAGKSTLL-KLIAGI----YKPTSG----KVKVTGKVAPLIELGAGFDPEL 104
>gnl|CDD|213211 cd03244, ABCC_MRP_domain2, ATP-binding cassette domain 2 of
multidrug resistance-associated protein. The ABC
subfamily C is also known as MRP (multidrug
resistance-associated protein). Some of the MRP members
have five additional transmembrane segments in their
N-terminus, but the function of these additional
membrane-spanning domains is not clear. The MRP was
found in the multidrug-resistance lung cancer cell in
which p-glycoprotein was not overexpressed. MRP exports
glutathione by drug stimulation, as well as, certain
substrates in conjugated forms with anions, such as
glutathione, glucuronate, and sulfate.
Length = 221
Score = 27.1 bits (61), Expect = 1.2
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 9/44 (20%)
Query: 26 RLGIVGSLASGKSALVHRFMTGAFLQEESPEGGRFKKEVVIDGH 69
++GIVG SGKS+L+ A + G ++IDG
Sbjct: 32 KVGIVGRTGSGKSSLLL-----ALFRLVELSSG----SILIDGV 66
>gnl|CDD|163652 cd07409, MPP_CD73_N, CD73 ecto-5'-nucleotidase and related
proteins, N-terminal metallophosphatase domain. CD73 is
a mammalian ecto-5'-nucleotidase expressed in
endothelial cells and lymphocytes that catalyzes the
conversion of 5'-AMP to adenosine in the final step of a
pathway that generates adenosine from ATP. This pathway
also includes a CD39 nucleoside triphosphate
dephosphorylase that mediates the dephosphorylation of
ATP to ADP and then to 5'-AMP. These enzymes all have
an N-terminal metallophosphatase domain and a C-terminal
5'nucleotidase domain. The N-terminal
metallophosphatase domain belongs to a large superfamily
of distantly related metallophosphatases (MPPs) that
includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA
lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). MPPs are functionally
diverse, but all share a conserved domain with an active
site consisting of two metal ions (usually manganese,
iron, or zinc) coordinated with octahedral geometry by a
cage of histidine, aspartate, and asparagine residues.
The conserved domain is a double beta-sheet sandwich
with a di-metal active site made up of residues located
at the C-terminal side of the sheets. This domain is
thought to allow for productive metal coordination.
Length = 281
Score = 26.7 bits (60), Expect = 1.4
Identities = 12/30 (40%), Positives = 14/30 (46%), Gaps = 4/30 (13%)
Query: 64 VVIDGHSHLLLIRDEGVPPELQPPNPSAPY 93
V++ GHSH L G PP P PY
Sbjct: 209 VIVGGHSHTFLY--TGPPP--SGEKPVGPY 234
>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 = 26.7 bits (60), Expect = 1.5
Identities = 13/54 (24%), Positives = 24/54 (44%), Gaps = 8/54 (14%)
Query: 25 LRLGIVGSLASGKSALVHRFMTGAFLQEESPEGGRFKKEVVIDGHSHLLLIRDE 78
+++ +VG A GK+ L+ + T F E P V D +S + + +
Sbjct: 1 IKIVVVGDGAVGKTCLLISYTTNKFPTEYVP--------TVFDNYSANVTVDGK 46
>gnl|CDD|233335 TIGR01271, CFTR_protein, cystic fibrosis transmembrane conductor
regulator (CFTR). The model describes the cystis
fibrosis transmembrane conductor regulator (CFTR) in
eukaryotes. The principal role of this protein is
chloride ion conductance. The protein is predicted to
consist of 12 transmembrane domains. Mutations or lesions
in the genetic loci have been linked to the aetiology of
asthma, bronchiectasis, chronic obstructive pulmonary
disease etc. Disease-causing mutations have been studied
by 36Cl efflux assays in vitro cell cultures and
electrophysiology, all of which point to the impairment
of chloride channel stability and not the biosynthetic
processing per se [Transport and binding proteins,
Anions].
Length = 1490
Score = 26.8 bits (59), Expect = 1.7
Identities = 18/48 (37%), Positives = 24/48 (50%), Gaps = 10/48 (20%)
Query: 23 PDLRLGIVGSLASGKSALVHRFMTGAFLQEESPEGGRFKKEVVIDGHS 70
R+G++G SGKS L+ A L+ S EG E+ IDG S
Sbjct: 1244 GGQRVGLLGRTGSGKSTLL-----SALLRLLSTEG-----EIQIDGVS 1281
>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 = 26.7 bits (59), Expect = 1.7
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 29 IVGSLASGKSALVHRFMTGAFL 50
I+G + GKS L+H+F F+
Sbjct: 7 IIGDMGVGKSCLLHQFTEKKFM 28
>gnl|CDD|223315 COG0237, CoaE, Dephospho-CoA kinase [Coenzyme metabolism].
Length = 201
Score = 26.5 bits (59), Expect = 1.9
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 25 LRLGIVGSLASGKSALVHRF 44
L +G+ G + SGKS +
Sbjct: 3 LIIGLTGGIGSGKSTVAKIL 22
>gnl|CDD|218447 pfam05123, S_layer_N, S-layer like family, N-terminal region.
Length = 279
Score = 26.6 bits (59), Expect = 1.9
Identities = 11/39 (28%), Positives = 21/39 (53%)
Query: 30 VGSLASGKSALVHRFMTGAFLQEESPEGGRFKKEVVIDG 68
+G++A G + + +GAF E+ + +F + V DG
Sbjct: 3 IGAIAVGGAMVASALASGAFAAEKVGDVDKFMDDFVKDG 41
>gnl|CDD|213256 cd03289, ABCC_CFTR2, ATP-binding cassette domain 2 of
CFTR,subfamily C. The cystic fibrosis transmembrane
regulator (CFTR), the product of the gene mutated in
patients with cystic fibrosis, has adapted the ABC
transporter structural motif to form a tightly
regulated anion channel at the apical surface of many
epithelia. Use of the term assembly of a functional ion
channel implies the coming together of subunits or at
least smaller not-yet functional components of the
active whole. In fact, on the basis of current
knowledge only the CFTR polypeptide itself is required
to form an ATP- and protein kinase A-dependent
low-conductance chloride channel of the type present in
the apical membrane of many epithelial cells. CFTR
displays the typical organization (IM-ABC)2 and carries
a characteristic hydrophilic R-domain that separates
IM1-ABC1 from IM2-ABC2.
Length = 275
Score = 26.7 bits (59), Expect = 2.0
Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 10/48 (20%)
Query: 23 PDLRLGIVGSLASGKSALVHRFMTGAFLQEESPEGGRFKKEVVIDGHS 70
P R+G++G SGKS L+ AFL+ + EG ++ IDG S
Sbjct: 29 PGQRVGLLGRTGSGKSTLLS-----AFLRLLNTEG-----DIQIDGVS 66
>gnl|CDD|153339 cd07655, F-BAR_PACSIN, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Protein kinase C and
Casein kinase Substrate in Neurons (PACSIN) proteins.
F-BAR domains are dimerization modules that bind and
bend membranes and are found in proteins involved in
membrane dynamics and actin reorganization. Protein
kinase C and Casein kinase Substrate in Neurons (PACSIN)
proteins, also called Synaptic dynamin-associated
proteins (Syndapins), act as regulators of cytoskeletal
and membrane dynamics. They bind both dynamin and
Wiskott-Aldrich syndrome protein (WASP), and may provide
direct links between the actin cytoskeletal machinery
through WASP and dynamin-dependent endocytosis.
Vetebrates harbor three isoforms with distinct
expression patterns and specific functions. PACSINs
contain an N-terminal F-BAR domain and a C-terminal SH3
domain. F-BAR domains form banana-shaped dimers with a
positively-charged concave surface that binds to
negatively-charged lipid membranes. They can induce
membrane deformation in the form of long tubules.
Length = 258
Score = 26.5 bits (59), Expect = 2.1
Identities = 11/42 (26%), Positives = 17/42 (40%), Gaps = 2/42 (4%)
Query: 45 MTGAFLQEESPEGGR--FKKEVVIDGHSHLLLIRDEGVPPEL 84
M F + + E R F KE+++ H HL L +
Sbjct: 209 MEQVFDKCQEFEEKRLDFFKEILLSYHRHLDLSTNPSFKAIY 250
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 26.4 bits (59), Expect = 2.3
Identities = 23/60 (38%), Positives = 33/60 (55%), Gaps = 11/60 (18%)
Query: 19 ARDVPDLRLGIVGSLASGKSALVHRFM--TGAF-------LQEESPEGGR--FKKEVVID 67
A++ P L L ++G + GKS LV R + TGA L+EE+ E G+ FK V+D
Sbjct: 1 AKEKPHLNLAVIGHVDHGKSTLVGRLLYETGAIDEHIIEELREEAKEKGKESFKFAWVMD 60
>gnl|CDD|213264 cd03297, ABC_ModC_molybdenum_transporter, ATP-binding cassette
domain of the molybdenum transport system. ModC is an
ABC-type transporter and the ATPase component of a
molybdate transport system that also includes the
periplasmic binding protein ModA and the membrane
protein ModB. ABC transporters are a large family of
proteins involved in the transport of a wide variety of
different compounds, like sugars, ions, peptides and
more complex organic molecules. The nucleotide binding
domain shows the highest similarity between all members
of the family. ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 214
Score = 26.1 bits (58), Expect = 2.4
Identities = 16/56 (28%), Positives = 27/56 (48%), Gaps = 9/56 (16%)
Query: 13 SHEFTLARDVPDLRLGIVGSLASGKSALVHRFMTGAFLQEESPEGGRFKKEVVIDG 68
+ D+ + GI G+ +GKS L+ R + G E P+GG +V++G
Sbjct: 12 DFTLKIDFDLNEEVTGIFGASGAGKSTLL-RCIAGL----EKPDGGT----IVLNG 58
>gnl|CDD|131266 TIGR02211, LolD_lipo_ex, lipoprotein releasing system,
ATP-binding protein. This model represents LolD, a
member of the ABC transporter family (pfam00005). LolD
is involved in localization of lipoproteins in some
bacteria. It works with a transmembrane protein LolC,
which in some species is a paralogous pair LolC and
LolE. Depending on whether the residue immediately
following the new, modified N-terminal Cys residue, the
nascent lipoprotein may be carried further by LolA and
LolB to the outer membrane, or remain at the inner
membrane. The top scoring proteins excluded by this
model include homologs from the archaeal genus
Methanosarcina [Protein fate, Protein and peptide
secretion and trafficking].
Length = 221
Score = 26.2 bits (58), Expect = 2.6
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 27 LGIVGSLASGKSALVH 42
+ IVGS SGKS L+H
Sbjct: 34 VAIVGSSGSGKSTLLH 49
>gnl|CDD|112137 pfam03308, ArgK, ArgK protein. The ArgK protein acts as an
ATPase enzyme and as a kinase, and phosphorylates
periplasmic binding proteins involved in the LAO
(lysine, arginine, ornithine)/AO transport systems.
Length = 267
Score = 26.2 bits (58), Expect = 3.0
Identities = 10/29 (34%), Positives = 14/29 (48%), Gaps = 2/29 (6%)
Query: 25 LRLGIVGSLASGKSALVHRFMTGAFLQEE 53
R+GI G +GKS L+ G L+
Sbjct: 30 HRVGITGVPGAGKSTLIEAL--GMELRRR 56
>gnl|CDD|220500 pfam09982, DUF2219, Uncharacterized protein conserved in bacteria
(DUF2219). This domain, found in various hypothetical
bacterial proteins, has no known function.
Length = 281
Score = 25.7 bits (57), Expect = 3.4
Identities = 14/53 (26%), Positives = 20/53 (37%), Gaps = 2/53 (3%)
Query: 8 DTFVTSHEFTLARDVPDLRLGIVGSLASGKSALVHRFMTGAFLQEESPEGGRF 60
+TF SH L V D+R G+ + + + F E EG F
Sbjct: 222 NTFRDSHSVDLEPFVGDVRAGVAWQYGRWSLSYSLVYRSKEF--EGQDEGQSF 272
>gnl|CDD|163651 cd07408, MPP_SA0022_N, Staphylococcus aureus SA0022 and related
proteins, N-terminal metallophosphatase domain. SA0022
is an uncharacterized Staphylococcus aureus UshA-like
protein with two putative domains, an N-terminal
metallophosphatase domain and a C-terminal nucleotidase
domain. SA0022 also contains a putative C-terminal cell
wall anchor domain. The N-terminal metallophosphatase
domain belongs to a large superfamily of distantly
related metallophosphatases (MPPs) that includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). MPPs are functionally
diverse, but all share a conserved domain with an active
site consisting of two metal ions (usually manganese,
iron, or zinc) coordinated with octahedral geometry by a
cage of histidine, aspartate, and asparagine residues.
The conserved domain is a double beta-sheet sandwich
with a di-metal active site made up of residues located
at the C-terminal side of the sheets. This domain is
thought to allow for productive metal coordination.
Length = 257
Score = 25.7 bits (57), Expect = 3.5
Identities = 6/8 (75%), Positives = 8/8 (100%)
Query: 64 VVIDGHSH 71
++IDGHSH
Sbjct: 204 LIIDGHSH 211
>gnl|CDD|179560 PRK03333, coaE, dephospho-CoA kinase/protein folding accessory
domain-containing protein; Provisional.
Length = 395
Score = 25.7 bits (57), Expect = 3.6
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 25 LRLGIVGSLASGKSALVHRF 44
LR+G+ G + +GKS + R
Sbjct: 2 LRIGLTGGIGAGKSTVAARL 21
>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 = 25.4 bits (56), Expect = 3.8
Identities = 8/21 (38%), Positives = 14/21 (66%)
Query: 24 DLRLGIVGSLASGKSALVHRF 44
++++ IVG GKS L++R
Sbjct: 1 EIKIVIVGDPNVGKSTLLNRL 21
>gnl|CDD|205447 pfam13267, DUF4058, Protein of unknown function (DUF4058). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are typically between 244 and 264 amino
acids in length.
Length = 254
Score = 25.7 bits (57), Expect = 3.9
Identities = 11/36 (30%), Positives = 19/36 (52%), Gaps = 4/36 (11%)
Query: 61 KKEVVIDGHSHLL---LIRDEGVPPELQPPNPSAPY 93
K++ V+ +HL+ L+R G P + P P + Y
Sbjct: 139 KRQEVLASLTHLVEIDLLR-GGEPMPVLGPLPQSDY 173
>gnl|CDD|213195 cd03228, ABCC_MRP_Like, ATP-binding cassette domain of multidrug
resistance protein-like transporters. The MRP
(Multidrug Resistance Protein)-like transporters are
involved in drug, peptide, and lipid export. They
belong to the subfamily C of the ATP-binding cassette
(ABC) superfamily of transport proteins. The ABCC
subfamily contains transporters with a diverse
functional spectrum that includes ion transport, cell
surface receptor, and toxin secretion activities. The
MRP-like family, similar to all ABC proteins, have a
common four-domain core structure constituted by two
membrane-spanning domains, each composed of six
transmembrane (TM) helices, and two nucleotide-binding
domains (NBD). ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 171
Score = 25.4 bits (57), Expect = 4.0
Identities = 15/48 (31%), Positives = 20/48 (41%), Gaps = 15/48 (31%)
Query: 26 RLGIVGSLASGKSALVH---RFMTGAFLQEESPEGGRFKKEVVIDGHS 70
++ IVG SGKS L+ R P G E++IDG
Sbjct: 30 KVAIVGPSGSGKSTLLKLLLRLY--------DPTSG----EILIDGVD 65
>gnl|CDD|224533 COG1618, COG1618, Predicted nucleotide kinase [Nucleotide
transport and metabolism].
Length = 179
Score = 25.4 bits (56), Expect = 4.2
Identities = 12/44 (27%), Positives = 20/44 (45%), Gaps = 9/44 (20%)
Query: 25 LRLGIVGSLASGKSALVHR---------FMTGAFLQEESPEGGR 59
+++ I G GK+ LV + + G F+ E EGG+
Sbjct: 6 MKIFITGRPGVGKTTLVLKIAEKLREKGYKVGGFITPEVREGGK 49
>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 = 25.6 bits (56), Expect = 4.4
Identities = 9/24 (37%), Positives = 16/24 (66%)
Query: 26 RLGIVGSLASGKSALVHRFMTGAF 49
++ +VG L+ GK+ L++RF F
Sbjct: 2 KVIVVGDLSVGKTCLINRFCKDVF 25
>gnl|CDD|185466 PTZ00130, PTZ00130, heat shock protein 90; Provisional.
Length = 814
Score = 25.8 bits (56), Expect = 4.6
Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 5/45 (11%)
Query: 44 FMTGAFLQEESPEGGRFKKEVVIDGHSHLLLIRDEGVPPELQPPN 88
F T QE+SP+G +F +E+ ID I+ + E N
Sbjct: 772 FETKKIEQEDSPDGQKFHEEINIDDE-----IQKQDNANESNDKN 811
>gnl|CDD|236151 PRK08099, PRK08099, bifunctional DNA-binding transcriptional
repressor/ NMN adenylyltransferase; Provisional.
Length = 399
Score = 25.4 bits (56), Expect = 4.9
Identities = 8/15 (53%), Positives = 12/15 (80%)
Query: 29 IVGSLASGKSALVHR 43
I+G +SGKS LV++
Sbjct: 224 ILGGESSGKSTLVNK 238
>gnl|CDD|224617 COG1703, ArgK, Putative periplasmic protein kinase ArgK and
related GTPases of G3E family [Amino acid transport and
metabolism].
Length = 323
Score = 25.4 bits (56), Expect = 5.2
Identities = 10/29 (34%), Positives = 14/29 (48%), Gaps = 2/29 (6%)
Query: 25 LRLGIVGSLASGKSALVHRFMTGAFLQEE 53
+GI G +GKS L+ G L+E
Sbjct: 52 HVIGITGVPGAGKSTLIEAL--GRELRER 78
>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 = 25.3 bits (56), Expect = 5.3
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 27 LGIVGSLASGKSALVHRFMTGAF 49
L +VG A GK+ L+ + T AF
Sbjct: 1 LVVVGDGAVGKTCLLIVYTTNAF 23
>gnl|CDD|223455 COG0378, HypB, Ni2+-binding GTPase involved in regulation of
expression and maturation of urease and hydrogenase
[Posttranslational modification, protein turnover,
chaperones / Transcription].
Length = 202
Score = 25.3 bits (56), Expect = 5.5
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 23 PDLRLGIVGSLASGKSALV 41
P LR+G+ G SGK+AL+
Sbjct: 12 PMLRIGVGGPPGSGKTALI 30
>gnl|CDD|216308 pfam01121, CoaE, Dephospho-CoA kinase. This family catalyzes the
phosphorylation of the 3'-hydroxyl group of
dephosphocoenzyme A to form Coenzyme A EC:2.7.1.24.
This enzyme uses ATP in its reaction.
Length = 179
Score = 24.9 bits (55), Expect = 5.7
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 25 LRLGIVGSLASGKSALVHRF 44
L +G+ G + SGKS + + F
Sbjct: 1 LIVGLTGGIGSGKSTVANLF 20
>gnl|CDD|225183 COG2274, SunT, ABC-type bacteriocin/lantibiotic exporters, contain
an N-terminal double-glycine peptidase domain [Defense
mechanisms].
Length = 709
Score = 25.3 bits (56), Expect = 5.9
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 9/48 (18%)
Query: 23 PDLRLGIVGSLASGKSALVHRFMTGAFLQEESPEGGRFKKEVVIDGHS 70
P ++ IVG SGKS L+ + + G + P+ GR +++DG
Sbjct: 498 PGEKVAIVGRSGSGKSTLL-KLLLG-LYK---PQQGR----ILLDGVD 536
>gnl|CDD|224052 COG1127, Ttg2A, ABC-type transport system involved in resistance
to organic solvents, ATPase component [Secondary
metabolites biosynthesis, transport, and catabolism].
Length = 263
Score = 25.2 bits (56), Expect = 5.9
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 9/52 (17%)
Query: 27 LGIVGSLASGKSALVHRFMTGAFLQEESPEGGRFKKEVVIDGHSHLLLIRDE 78
L I+G SGKS L+ R + G P+ G E++IDG L +E
Sbjct: 37 LAILGGSGSGKSTLL-RLILG----LLRPDKG----EILIDGEDIPQLSEEE 79
>gnl|CDD|213269 cd03369, ABCC_NFT1, ATP-binding cassette domain 2 of NFT1,
subfamily C. Domain 2 of NFT1 (New full-length
MRP-type transporter 1). NFT1 belongs to the MRP
(multidrug resistance-associated protein) family of ABC
transporters. Some of the MRP members have five
additional transmembrane segments in their N-terminus,
but the function of these additional membrane-spanning
domains is not clear. The MRP was found in the
multidrug-resisting lung cancer cell in which
p-glycoprotein was not overexpressed. MRP exports
glutathione by drug stimulation, as well as, certain
substrates in conjugated forms with anions such as
glutathione, glucuronate, and sulfate.
Length = 207
Score = 25.1 bits (55), Expect = 6.5
Identities = 14/43 (32%), Positives = 20/43 (46%), Gaps = 9/43 (20%)
Query: 26 RLGIVGSLASGKSALVHRFMTGAFLQEESPEGGRFKKEVVIDG 68
++GIVG +GKS L A + E G+ + IDG
Sbjct: 36 KIGIVGRTGAGKSTL-----ILALFRFLEAEEGKIE----IDG 69
>gnl|CDD|234620 PRK00081, coaE, dephospho-CoA kinase; Reviewed.
Length = 194
Score = 25.1 bits (56), Expect = 6.6
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 25 LRLGIVGSLASGKSA 39
L +G+ G + SGKS
Sbjct: 3 LIIGLTGGIGSGKST 17
>gnl|CDD|233322 TIGR01227, hutG, formimidoylglutamase. Formiminoglutamase, the
fourth enzyme of histidine degradation, is similar to
arginases and agmatinases. It is often encoded near
other enzymes of the histidine degredation pathway:
histidine ammonia-lyase, urocanate hydratase, and
imidazolonepropionase [Energy metabolism, Amino acids
and amines].
Length = 307
Score = 25.1 bits (55), Expect = 6.6
Identities = 21/96 (21%), Positives = 30/96 (31%), Gaps = 9/96 (9%)
Query: 4 SSNSDTFVTSHEFTLARDVPDLRLGIVGSLASGKSALVH-------RFMTGAFLQEESPE 56
++ F + D LGI S AL R++T L+
Sbjct: 160 PTSGTPFRQILDECQIEDFHYAVLGI--RRFSNTQALFDYAKKLGVRYVTDDALRPGLLP 217
Query: 57 GGRFKKEVVIDGHSHLLLIRDEGVPPELQPPNPSAP 92
+ V +D H+ L D V P SAP
Sbjct: 218 TIKDILPVFLDKVDHIYLTVDMDVLDAAHAPGVSAP 253
>gnl|CDD|221803 pfam12846, AAA_10, AAA-like domain. This family of domains
contain a P-loop motif that is characteristic of the
AAA superfamily. Many of the proteins in this family
are conjugative transfer proteins.
Length = 316
Score = 25.1 bits (55), Expect = 6.8
Identities = 14/39 (35%), Positives = 17/39 (43%), Gaps = 8/39 (20%)
Query: 29 IVGSLASGKSALVHRFMTGAFLQEESPEGGRFKKEVVID 67
IVG SGKS L+ + GGR +VID
Sbjct: 6 IVGPSGSGKSTLLKLLALRLLAR-----GGRV---IVID 36
>gnl|CDD|185067 PRK15112, PRK15112, antimicrobial peptide ABC system ATP-binding
protein SapF; Provisional.
Length = 267
Score = 25.1 bits (55), Expect = 6.9
Identities = 19/59 (32%), Positives = 24/59 (40%), Gaps = 12/59 (20%)
Query: 11 VTSHEFTLARDVPDLRLGIVGSLASGKSALVHRFMTGAFLQEESPEGGRFKKEVVIDGH 69
V FTL L I+G SGKS L + + G P G E++ID H
Sbjct: 29 VKPLSFTLR---EGQTLAIIGENGSGKSTLA-KMLAGMI----EPTSG----ELLIDDH 75
>gnl|CDD|215595 PLN03130, PLN03130, ABC transporter C family member; Provisional.
Length = 1622
Score = 25.1 bits (55), Expect = 7.2
Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 9/46 (19%)
Query: 23 PDLRLGIVGSLASGKSALVHRFMTGAFLQEESPEGGRFKKEVVIDG 68
P ++GIVG +GKS+ M A + E GR ++IDG
Sbjct: 1264 PSEKVGIVGRTGAGKSS-----MLNALFRIVELERGR----ILIDG 1300
>gnl|CDD|234041 TIGR02868, CydC, thiol reductant ABC exporter, CydC subunit. The
gene pair cydCD encodes an ABC-family transporter in
which each gene contains an N-terminal membrane-spanning
domain (pfam00664) and a C-terminal ATP-binding domain
(pfam00005). In E. coli these genes were discovered as
mutants which caused the terminal heme-copper oxidase
complex cytochrome bd to fail to assemble. Recent work
has shown that the transporter is involved in export of
redox-active thiol compounds such as cysteine and
glutathione. The linkage to assembly of the cytochrome
bd complex is further supported by the conserved operon
structure found outside the gammaproteobacteria
(cydABCD) containing both the transporter and oxidase
genes components. The genes used as the seed members for
this model are all either found in the
gammproteobacterial context or the CydABCD context. All
members of this family scoring above trusted at the time
of its creation were from genomes which encode a
cytochrome bd complex.
Length = 530
Score = 25.0 bits (55), Expect = 7.4
Identities = 18/53 (33%), Positives = 24/53 (45%), Gaps = 9/53 (16%)
Query: 26 RLGIVGSLASGKSALVHRFMTGAFLQEESPEGGRFKKEVVIDGHSHLLLIRDE 78
R+ I+G SGKS L+ + G P G EV +DG L +DE
Sbjct: 363 RVAILGPSGSGKSTLLA-TLAGLL----DPLQG----EVTLDGVPVSSLDQDE 406
>gnl|CDD|180935 PRK07333, PRK07333, 2-octaprenyl-6-methoxyphenyl hydroxylase;
Provisional.
Length = 403
Score = 24.9 bits (55), Expect = 7.4
Identities = 13/41 (31%), Positives = 23/41 (56%)
Query: 1 MKMSSNSDTFVTSHEFTLARDVPDLRLGIVGSLASGKSALV 41
M ++++ + S++ TL R V D+ LG+V L KS +
Sbjct: 344 MGVTTDVLNRLFSNDSTLLRSVRDIGLGLVDRLPKLKSFFI 384
>gnl|CDD|213217 cd03250, ABCC_MRP_domain1, ATP-binding cassette domain 1 of
multidrug resistance-associated protein, subfamily C.
This subfamily is also known as MRP (multidrug
resistance-associated protein). Some of the MRP members
have five additional transmembrane segments in their
N-terminus, but the function of these additional
membrane-spanning domains is not clear. The MRP was
found in the multidrug-resisting lung cancer cell in
which p-glycoprotein was not overexpressed. MRP exports
glutathione by drug stimulation, as well as, certain
substrates in conjugated forms with anions, such as
glutathione, glucuronate, and sulfate.
Length = 204
Score = 24.7 bits (55), Expect = 7.8
Identities = 8/14 (57%), Positives = 11/14 (78%)
Query: 27 LGIVGSLASGKSAL 40
+ IVG + SGKS+L
Sbjct: 34 VAIVGPVGSGKSSL 47
>gnl|CDD|217066 pfam02492, cobW, CobW/HypB/UreG, nucleotide-binding domain. This
domain is found in HypB, a hydrogenase expression /
formation protein, and UreG a urease accessory protein.
Both these proteins contain a P-loop nucleotide binding
motif. HypB has GTPase activity and is a guanine
nucleotide binding protein. It is not known whether
UreG binds GTP or some other nucleotide. Both enzymes
are involved in nickel binding. HypB can store nickel
and is required for nickel dependent hydrogenase
expression. UreG is required for functional
incorporation of the urease nickel metallocenter. GTP
hydrolysis may required by these proteins for nickel
incorporation into other nickel proteins. This family
of domains also contains P47K, a Pseudomonas
chlororaphis protein needed for nitrile hydratase
expression, and the cobW gene product, which may be
involved in cobalamin biosynthesis in Pseudomonas
denitrificans.
Length = 178
Score = 24.5 bits (54), Expect = 9.6
Identities = 6/17 (35%), Positives = 9/17 (52%)
Query: 25 LRLGIVGSLASGKSALV 41
+ G L SGK+ L+
Sbjct: 1 PVTVLTGFLGSGKTTLL 17
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.316 0.135 0.392
Gapped
Lambda K H
0.267 0.0830 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,917,776
Number of extensions: 419596
Number of successful extensions: 679
Number of sequences better than 10.0: 1
Number of HSP's gapped: 676
Number of HSP's successfully gapped: 123
Length of query: 93
Length of database: 10,937,602
Length adjustment: 60
Effective length of query: 33
Effective length of database: 8,276,362
Effective search space: 273119946
Effective search space used: 273119946
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.0 bits)