RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15004
(167 letters)
>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 = 144 bits (364), Expect = 7e-44
Identities = 58/165 (35%), Positives = 83/165 (50%), Gaps = 24/165 (14%)
Query: 10 TPHGFIIVYSTIDLASFHVAEQCLQALWKKDSIRSKAVILVANKTDLVRCRVVTDEDGKD 69
++IVYS D +SF A + L + +ILV NK+DLVR R V+ ++G+
Sbjct: 72 VGDAYVIVYSVTDRSSFEKASELRIQLRRARQAEDIPIILVGNKSDLVRSREVSVQEGRA 131
Query: 70 MATAYDCKFIETSVGINHNVDELLVGILTQIRLKLDNPPEPVLTREQFSCRRRRSKSPGG 129
A +DCKFIETS + HNVDEL GI+ Q+RL+ D+ + + R+RR
Sbjct: 132 CAVVFDCKFIETSAALQHNVDELFEGIVRQVRLRRDSKE---KNTRRMASRKRRESITK- 187
Query: 130 FRKLRGHRTSASLKVKGLLSKVWQRDS-------KSKSCQNLHVL 167
K K LSK+ +++ KSKSC +L VL
Sbjct: 188 -------------KAKRFLSKIVAKNNKGMAFKQKSKSCHDLSVL 219
>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 = 87.6 bits (218), Expect = 2e-22
Identities = 34/90 (37%), Positives = 48/90 (53%), Gaps = 2/90 (2%)
Query: 12 HGFIIVYSTIDLASFHVAEQCL-QALWKKDSIRSKAVILVANKTDLVRCRVVTDEDGKDM 70
GFI+VYS SF + Q L KD ++LV NK DL R V+ E+G+ +
Sbjct: 72 DGFILVYSITSRESFEEIKNIREQILRVKDK-EDVPIVLVGNKCDLENERQVSTEEGEAL 130
Query: 71 ATAYDCKFIETSVGINHNVDELLVGILTQI 100
A + C F+ETS N N+DEL ++ +I
Sbjct: 131 AEEWGCPFLETSAKTNINIDELFNTLVREI 160
>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 = 79.5 bits (197), Expect = 2e-19
Identities = 37/96 (38%), Positives = 51/96 (53%), Gaps = 8/96 (8%)
Query: 12 HGFIIVYSTIDLASFHVA----EQCLQALWKKDSIRSKAVILVANKTDLVRCRVVTDEDG 67
GF++VYS D SF EQ L+ KD ++LV NK DL RVV+ E+G
Sbjct: 75 EGFLLVYSITDRQSFEEIAKFREQILR---VKDR-DDVPIVLVGNKCDLENERVVSTEEG 130
Query: 68 KDMATAYDCKFIETSVGINHNVDELLVGILTQIRLK 103
K++A + C F+ETS NVDE ++ +IR
Sbjct: 131 KELARQWGCPFLETSAKERINVDEAFYDLVREIRKS 166
>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 = 78.8 bits (195), Expect = 4e-19
Identities = 37/93 (39%), Positives = 51/93 (54%), Gaps = 8/93 (8%)
Query: 13 GFIIVYSTIDLASFHVA----EQCLQALWKKDSIRSKAVILVANKTDLVRCRVVTDEDGK 68
GF++VYS D SF EQ L+ KD ++LV NK DL RVV+ E+GK
Sbjct: 74 GFLLVYSITDRQSFEEIKKFREQILRV---KDR-DDVPIVLVGNKCDLESERVVSTEEGK 129
Query: 69 DMATAYDCKFIETSVGINHNVDELLVGILTQIR 101
++A + C F+ETS NVDE ++ +IR
Sbjct: 130 ELARQWGCPFLETSAKERVNVDEAFYDLVREIR 162
>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 = 76.5 bits (189), Expect = 4e-18
Identities = 36/103 (34%), Positives = 59/103 (57%), Gaps = 9/103 (8%)
Query: 12 HGFIIVYSTIDLASFHVAEQCLQALWKK--DSIRSKAV--ILVANKTDLVRCRVVTDEDG 67
HG+I+VYS SF V + ++ K D + ++V +LV NK+DL R V+ E+G
Sbjct: 74 HGYILVYSVTSRKSFEVVK----VIYDKILDMLGKESVPIVLVGNKSDLHMERQVSAEEG 129
Query: 68 KDMATAYDCKFIETSVGINHNVDELLVGILTQIRLKLDNPPEP 110
K +A ++ F+E+S N NV+E ++ +I K++NP P
Sbjct: 130 KKLAESWGAAFLESSAKENENVEEAFELLIEEIE-KVENPLPP 171
>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 = 71.7 bits (177), Expect = 2e-16
Identities = 28/86 (32%), Positives = 40/86 (46%), Gaps = 11/86 (12%)
Query: 12 HGFIIVYSTIDLASFHVAEQCLQALWKKDSIRSKA-----VILVANKTDLVRCRVVTDED 66
HG I+VY + SF ++ W + ++ A +ILV NK+DL R V+ E+
Sbjct: 74 HGAILVYDVTNRESFENLDK-----WLNE-LKEYAPPNIPIILVGNKSDLEDERQVSTEE 127
Query: 67 GKDMATAYDCKFIETSVGINHNVDEL 92
+ A F ETS NVDE
Sbjct: 128 AQQFAKENGLLFFETSAKTGENVDEA 153
>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 = 70.6 bits (174), Expect = 5e-16
Identities = 30/98 (30%), Positives = 47/98 (47%), Gaps = 9/98 (9%)
Query: 8 YETPHGFIIVYSTIDLASFHVAEQCLQALWKKDSIRSK----AVILVANKTDLVRCRVVT 63
Y GF++VY SF ++ W ++ +R ++LV NK DL RVV+
Sbjct: 69 YRGAQGFLLVYDITSRDSFENVKK-----WLEEILRHADENVPIVLVGNKCDLEDQRVVS 123
Query: 64 DEDGKDMATAYDCKFIETSVGINHNVDELLVGILTQIR 101
E+G+ +A F+ETS N NV+E + +I
Sbjct: 124 TEEGEALAKELGLPFMETSAKTNENVEEAFEELAREIL 161
>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 = 69.1 bits (169), Expect = 3e-15
Identities = 33/95 (34%), Positives = 52/95 (54%)
Query: 13 GFIIVYSTIDLASFHVAEQCLQALWKKDSIRSKAVILVANKTDLVRCRVVTDEDGKDMAT 72
GFII YS D SF A + + + + ++LV NK DL + R VT E+G+++A
Sbjct: 76 GFIICYSVTDRHSFQEASEFKELITRVRLTEDIPLVLVGNKVDLEQQRQVTTEEGRNLAR 135
Query: 73 AYDCKFIETSVGINHNVDELLVGILTQIRLKLDNP 107
++C F ETS + +D+ G++ +IR K P
Sbjct: 136 EFNCPFFETSAALRFYIDDAFHGLVREIRRKESMP 170
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 66.4 bits (163), Expect = 2e-14
Identities = 28/95 (29%), Positives = 45/95 (47%), Gaps = 13/95 (13%)
Query: 12 HGFIIVYSTIDLASF-HVAEQCLQALWKKDSIRSKA-----VILVANKTDLVRCRVVTDE 65
G ++VY + SF ++ W K+ +R A ++LV NK+DL R V+ E
Sbjct: 74 VGALLVYDITNRESFENLEN------WLKE-LREYASPNVVIMLVGNKSDLEEQRQVSRE 126
Query: 66 DGKDMATAYDCKFIETSVGINHNVDELLVGILTQI 100
+ + A + F ETS N NV+E + +I
Sbjct: 127 EAEAFAEEHGLPFFETSAKTNTNVEEAFEELAREI 161
>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 = 65.0 bits (159), Expect = 8e-14
Identities = 32/79 (40%), Positives = 41/79 (51%), Gaps = 3/79 (3%)
Query: 12 HGFIIVYSTIDLASFHVAEQCLQ--ALWKKDSIRSKAVILVANKTDLVRCRVVTDEDGKD 69
GF++VYS D +SF V Q LQ KK VILV NK DL+ R V+ E+G+
Sbjct: 74 DGFVLVYSITDRSSFDVVSQLLQLIREIKKRDGEI-PVILVGNKADLLHSRQVSTEEGQK 132
Query: 70 MATAYDCKFIETSVGINHN 88
+A C F E S N+
Sbjct: 133 LALELGCLFFEVSAAENYL 151
>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 = 64.7 bits (158), Expect = 9e-14
Identities = 34/93 (36%), Positives = 48/93 (51%), Gaps = 2/93 (2%)
Query: 10 TPHGFIIVYSTIDLASF-HVAEQCLQALWKKDSIRSKAVILVANKTDLVRCRVVTDEDGK 68
T GF++V+S D SF V + Q L KD +ILV NK DL R V+ E+G+
Sbjct: 73 TGEGFLLVFSVTDRGSFEEVDKFHTQILRVKD-RDEFPMILVGNKADLEHQRQVSREEGQ 131
Query: 69 DMATAYDCKFIETSVGINHNVDELLVGILTQIR 101
++A +IETS NVD+ ++ IR
Sbjct: 132 ELARQLKIPYIETSAKDRVNVDKAFHDLVRVIR 164
>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 = 61.7 bits (150), Expect = 2e-12
Identities = 30/93 (32%), Positives = 45/93 (48%), Gaps = 3/93 (3%)
Query: 10 TPHGFIIVYSTIDLASFH-VAEQCLQALWKKDSIRSKAVILVANKTDLVRCRVVTDEDGK 68
T GF+ V++ SF + Q KDS ++LV NK DL R V+ G+
Sbjct: 72 TGEGFLCVFAINSRKSFEDIHTYREQIKRVKDS-DDVPMVLVGNKCDL-AARTVSTRQGQ 129
Query: 69 DMATAYDCKFIETSVGINHNVDELLVGILTQIR 101
D+A +Y +IETS V+E ++ +IR
Sbjct: 130 DLAKSYGIPYIETSAKTRQGVEEAFYTLVREIR 162
>gnl|CDD|206654 cd01861, Rab6, Rab GTPase family 6 (Rab6). Rab6 is involved in
microtubule-dependent transport pathways through the
Golgi and from endosomes to the Golgi. Rab6A of mammals
is implicated in retrograde transport through the Golgi
stack, and is also required for a slow,
COPI-independent, retrograde transport pathway from the
Golgi to the endoplasmic reticulum (ER). This pathway
may allow Golgi residents to be recycled through the ER
for scrutiny by ER quality-control systems. Yeast Ypt6p,
the homolog of the mammalian Rab6 GTPase, is not
essential for cell viability. Ypt6p acts in
endosome-to-Golgi, in intra-Golgi retrograde transport,
and possibly also in Golgi-to-ER trafficking. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 161
Score = 61.1 bits (149), Expect = 2e-12
Identities = 30/82 (36%), Positives = 40/82 (48%), Gaps = 9/82 (10%)
Query: 15 IIVYSTIDLASFHVAEQCLQALWKKD--SIRSKAVI--LVANKTDLVRCRVVTDEDGKDM 70
++VY + SF ++ W D R VI LV NKTDL R V+ E+G+
Sbjct: 77 VVVYDITNRQSFDNTDK-----WIDDVRDERGNDVIIVLVGNKTDLSDKRQVSTEEGEKK 131
Query: 71 ATAYDCKFIETSVGINHNVDEL 92
A + FIETS HNV +L
Sbjct: 132 AKENNAMFIETSAKAGHNVKQL 153
>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 = 60.6 bits (147), Expect = 4e-12
Identities = 34/92 (36%), Positives = 52/92 (56%), Gaps = 8/92 (8%)
Query: 13 GFIIVYSTIDLASFH----VAEQCLQALWKKDSIRSKAVILVANKTDLVRCRVVTDEDGK 68
GF++VYS ++F+ + EQ L+ KD+ +ILV NK DL RVV E G+
Sbjct: 75 GFVLVYSITAQSTFNDLQDLREQILRV---KDT-EDVPMILVGNKCDLEDERVVGKEQGQ 130
Query: 69 DMATAYDCKFIETSVGINHNVDELLVGILTQI 100
++A + C F+ETS NV+E+ ++ QI
Sbjct: 131 NLARQWGCAFLETSAKAKINVNEIFYDLVRQI 162
>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 = 60.6 bits (147), Expect = 4e-12
Identities = 29/87 (33%), Positives = 45/87 (51%), Gaps = 10/87 (11%)
Query: 12 HGFIIVYSTIDLASFHVAEQCLQALW------KKDSIRSKAVILVANKTDLVRCRVVTDE 65
H FI+VYS S + L+ ++ K +++ ++LV NK D R V+
Sbjct: 74 HAFILVYSITSKQSL----EELKPIYELICEIKGNNLEKIPIMLVGNKCDESPSREVSSS 129
Query: 66 DGKDMATAYDCKFIETSVGINHNVDEL 92
+G +A ++C F+ETS NHNV EL
Sbjct: 130 EGAALARTWNCAFMETSAKTNHNVQEL 156
>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 = 60.3 bits (146), Expect = 4e-12
Identities = 35/90 (38%), Positives = 52/90 (57%), Gaps = 3/90 (3%)
Query: 13 GFIIVYSTIDLASFH-VAEQCLQALWKKDSIRSKAVILVANKTDLVRCRVVTDEDGKDMA 71
GF +VYS SF+ + + Q L KD+ +ILV NK DL RVV+ E+G+++A
Sbjct: 75 GFALVYSITAQQSFNDLQDLREQILRVKDTEDV-PMILVGNKCDLEDERVVSKEEGQNLA 133
Query: 72 TAY-DCKFIETSVGINHNVDELLVGILTQI 100
+ +C F+ETS NVDE+ ++ QI
Sbjct: 134 RQWGNCPFLETSAKSKINVDEIFYDLVRQI 163
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 60.6 bits (147), Expect = 5e-12
Identities = 39/106 (36%), Positives = 55/106 (51%), Gaps = 10/106 (9%)
Query: 10 TPHGFIIVYSTIDLASFH----VAEQCLQALWKKDSIRSKAVILVANKTDLVRCRVVTDE 65
T GF+ VYS +SF EQ L+ KD R +ILV NK DL R V+
Sbjct: 76 TGQGFLCVYSITSRSSFEEIASFREQILRV---KDKDRV-PMILVGNKCDLDSERQVSTG 131
Query: 66 DGKDMATAYDCKFIETSVGINHNVDELLVGILTQIR--LKLDNPPE 109
+G+++A ++ F+ETS NVDE ++ +IR LK D P +
Sbjct: 132 EGQELAKSFGIPFLETSAKQRVNVDEAFYELVREIRKYLKEDMPSQ 177
>gnl|CDD|206661 cd01869, Rab1_Ypt1, Rab GTPase family 1 includes the yeast homolog
Ypt1. Rab1/Ypt1 subfamily. Rab1 is found in every
eukaryote and is a key regulatory component for the
transport of vesicles from the ER to the Golgi
apparatus. Studies on mutations of Ypt1, the yeast
homolog of Rab1, showed that this protein is necessary
for the budding of vesicles of the ER as well as for
their transport to, and fusion with, the Golgi
apparatus. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation of
the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 166
Score = 60.0 bits (146), Expect = 5e-12
Identities = 34/96 (35%), Positives = 48/96 (50%), Gaps = 5/96 (5%)
Query: 8 YETPHGFIIVYSTIDLASFHVAEQCLQALWKKDSIRSKAV--ILVANKTDLVRCRVVTDE 65
Y HG IIVY D SF+ +Q LQ + D S+ V +LV NK DL +VV
Sbjct: 72 YRGAHGIIIVYDVTDQESFNNVKQWLQEI---DRYASENVNKLLVGNKCDLTDKKVVDYT 128
Query: 66 DGKDMATAYDCKFIETSVGINHNVDELLVGILTQIR 101
+ K+ A F+ETS NV+E + + +I+
Sbjct: 129 EAKEFADELGIPFLETSAKNATNVEEAFMTMAREIK 164
>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 = 58.7 bits (142), Expect = 2e-11
Identities = 28/89 (31%), Positives = 45/89 (50%)
Query: 12 HGFIIVYSTIDLASFHVAEQCLQALWKKDSIRSKAVILVANKTDLVRCRVVTDEDGKDMA 71
GFI+VYS ++ +F + + + +ILV NK DL R V+ +G+ +A
Sbjct: 74 QGFIVVYSLVNQQTFQDIKPMRDQIVRVKGYEKVPIILVGNKVDLESEREVSSAEGRALA 133
Query: 72 TAYDCKFIETSVGINHNVDELLVGILTQI 100
+ C F+ETS V+EL I+ Q+
Sbjct: 134 EEWGCPFMETSAKSKTMVNELFAEIVRQM 162
>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 = 57.6 bits (140), Expect = 4e-11
Identities = 25/90 (27%), Positives = 48/90 (53%), Gaps = 5/90 (5%)
Query: 13 GFIIVYSTIDLASFHVAEQCLQALWK--KDSIRSKAVILVANKTDLVRCRVVTDEDGKDM 70
G I+VY D SF ++ ++ L + ++I ++++V NK DL R RVV+ + ++
Sbjct: 75 GAILVYDITDADSFQKVKKWIKELKQMRGNNI---SLVIVGNKIDLERQRVVSKSEAEEY 131
Query: 71 ATAYDCKFIETSVGINHNVDELLVGILTQI 100
A + K ETS ++EL + + ++
Sbjct: 132 AKSVGAKHFETSAKTGKGIEELFLSLAKRM 161
>gnl|CDD|206660 cd01868, Rab11_like, Rab GTPase family 11 (Rab11)-like includes
Rab11a, Rab11b, and Rab25. Rab11a, Rab11b, and Rab25
are closely related, evolutionary conserved Rab proteins
that are differentially expressed. Rab11a is
ubiquitously synthesized, Rab11b is enriched in brain
and heart and Rab25 is only found in epithelia. Rab11/25
proteins seem to regulate recycling pathways from
endosomes to the plasma membrane and to the trans-Golgi
network. Furthermore, Rab11a is thought to function in
the histamine-induced fusion of tubulovesicles
containing H+, K+ ATPase with the plasma membrane in
gastric parietal cells and in insulin-stimulated
insertion of GLUT4 in the plasma membrane of
cardiomyocytes. Overexpression of Rab25 has recently
been observed in ovarian cancer and breast cancer, and
has been correlated with worsened outcomes in both
diseases. In addition, Rab25 overexpression has also
been observed in prostate cancer, transitional cell
carcinoma of the bladder, and invasive breast tumor
cells. GTPase activating proteins (GAPs) interact with
GTP-bound Rab and accelerate the hydrolysis of GTP to
GDP. Guanine nucleotide exchange factors (GEFs) interact
with GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 165
Score = 56.8 bits (138), Expect = 9e-11
Identities = 35/96 (36%), Positives = 47/96 (48%), Gaps = 3/96 (3%)
Query: 6 ANYETPHGFIIVYSTIDLASFHVAEQCLQALWKKDSIRSKAVI-LVANKTDLVRCRVVTD 64
A Y G ++VY ++F E+ L+ L +D S VI LV NK+DL R V
Sbjct: 71 AYYRGAVGALLVYDITKKSTFENVERWLKEL--RDHADSNIVIMLVGNKSDLRHLRAVPT 128
Query: 65 EDGKDMATAYDCKFIETSVGINHNVDELLVGILTQI 100
E+ K A FIETS NV+E +LT+I
Sbjct: 129 EEAKAFAEKNGLSFIETSALDGTNVEEAFKQLLTEI 164
>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 = 56.8 bits (137), Expect = 1e-10
Identities = 29/91 (31%), Positives = 47/91 (51%), Gaps = 2/91 (2%)
Query: 13 GFIIVYSTIDLASFHVAEQCLQALW--KKDSIRSKAVILVANKTDLVRCRVVTDEDGKDM 70
GFI+VYS ++F E+ + + K +S +++V NK D V R V+ E+G +
Sbjct: 73 GFILVYSITSRSTFERVERFREQIQRVKDESAADVPIMIVGNKCDKVYEREVSTEEGAAL 132
Query: 71 ATAYDCKFIETSVGINHNVDELLVGILTQIR 101
A C+FIE S N NV+ ++ +R
Sbjct: 133 ARRLGCEFIEASAKTNVNVERAFYTLVRALR 163
>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 = 55.6 bits (135), Expect = 3e-10
Identities = 25/82 (30%), Positives = 39/82 (47%), Gaps = 1/82 (1%)
Query: 15 IIVYSTIDLASFHVAEQCLQALWKKDSIRSKAVILVANKTDLVRCRVVTDEDGKDMATAY 74
I+VY SF A+ ++ L ++ + + L NK DL R V+ E+ ++ A
Sbjct: 78 IVVYDITSEESFEKAKSWVKEL-QEHGPPNIVIALAGNKADLESKRQVSTEEAQEYADEN 136
Query: 75 DCKFIETSVGINHNVDELLVGI 96
F+ETS NV+EL I
Sbjct: 137 GLLFMETSAKTGENVNELFTEI 158
>gnl|CDD|206659 cd01867, Rab8_Rab10_Rab13_like, Rab GTPase families 8, 10, 13
(Rab8, Rab10, Rab13). Rab8/Sec4/Ypt2 are known or
suspected to be involved in post-Golgi transport to the
plasma membrane. It is likely that these Rabs have
functions that are specific to the mammalian lineage and
have no orthologs in plants. Rab8 modulates polarized
membrane transport through reorganization of actin and
microtubules, induces the formation of new surface
extensions, and has an important role in directed
membrane transport to cell surfaces. The Ypt2 gene of
the fission yeast Schizosaccharomyces pombe encodes a
member of the Ypt/Rab family of small GTP-binding
proteins, related in sequence to Sec4p of Saccharomyces
cerevisiae but closer to mammalian Rab8. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 167
Score = 55.0 bits (133), Expect = 4e-10
Identities = 34/100 (34%), Positives = 51/100 (51%), Gaps = 5/100 (5%)
Query: 6 ANYETPHGFIIVYSTIDLASFHVAEQCLQALWKKDSIRSKAV--ILVANKTDLVRCRVVT 63
+ Y G I+VY D SF + ++ + D S+ V +LV NK D+ RVV+
Sbjct: 71 SYYRGAMGIILVYDITDEKSFENIKNWMRNI---DEHASEDVERMLVGNKCDMEEKRVVS 127
Query: 64 DEDGKDMATAYDCKFIETSVGINHNVDELLVGILTQIRLK 103
E+G+ +A Y KF+ETS N NV+E + + I K
Sbjct: 128 KEEGEALAREYGIKFLETSAKANINVEEAFLTLAKDILKK 167
>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 = 50.9 bits (122), Expect = 2e-08
Identities = 35/91 (38%), Positives = 47/91 (51%), Gaps = 3/91 (3%)
Query: 13 GFIIVYSTIDLASF-HVAEQCLQALWKKDSIRSKAVILVANKTDLVRCRVVTDEDGKDMA 71
GF++VYS AS + E Q L KDS V LV NK DL R V+ EDG ++
Sbjct: 75 GFLLVYSVTSEASLNELGELREQVLRIKDSDNVPMV-LVGNKADLEDDRQVSREDGVSLS 133
Query: 72 TAY-DCKFIETSVGINHNVDELLVGILTQIR 101
+ + F ETS NVDE+ + ++ QI
Sbjct: 134 QQWGNVPFYETSARKRTNVDEVFIDLVRQII 164
>gnl|CDD|206657 cd01865, Rab3, Rab GTPase family 3 contains Rab3A, Rab3B, Rab3C and
Rab3D. The Rab3 subfamily contains Rab3A, Rab3B, Rab3C,
and Rab3D. All four isoforms were found in mouse brain
and endocrine tissues, with varying levels of
expression. Rab3A, Rab3B, and Rab3C localized to
synaptic and secretory vesicles; Rab3D was expressed at
high levels only in adipose tissue, exocrine glands, and
the endocrine pituitary, where it is localized to
cytoplasmic secretory granules. Rab3 appears to control
Ca2+-regulated exocytosis. The appropriate GDP/GTP
exchange cycle of Rab3A is required for Ca2+-regulated
exocytosis to occur, and interaction of the GTP-bound
form of Rab3A with effector molecule(s) is widely
believed to be essential for this process. Functionally,
most studies point toward a role for Rab3 in the
secretion of hormones and neurotransmitters. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 165
Score = 49.5 bits (118), Expect = 4e-08
Identities = 35/96 (36%), Positives = 47/96 (48%), Gaps = 6/96 (6%)
Query: 6 ANYETPHGFIIVYSTIDLASFH-VAEQCLQALWKKDSIRSKAVILVANKTDLVRCRVVTD 64
A Y GFI++Y + SF+ V + Q K S + VILV NK D+ RVV+
Sbjct: 69 AYYRGAMGFILMYDITNEESFNAVQDWSTQI--KTYSWDNAQVILVGNKCDMEDERVVSA 126
Query: 65 EDGKDMATAYDCKFIETSVGINHNVD---ELLVGIL 97
E G+ +A +F E S N NV E LV I+
Sbjct: 127 ERGRQLADQLGFEFFEASAKENINVKQVFERLVDII 162
>gnl|CDD|206688 cd04101, RabL4, Rab GTPase-like family 4 (Rab-like4). RabL4
(Rab-like4) subfamily. RabL4s are novel proteins that
have high sequence similarity with Rab family members,
but display features that are distinct from Rabs, and
have been termed Rab-like. As in other Rab-like
proteins, RabL4 lacks a prenylation site at the
C-terminus. The specific function of RabL4 remains
unknown.
Length = 167
Score = 48.7 bits (116), Expect = 1e-07
Identities = 22/83 (26%), Positives = 33/83 (39%), Gaps = 1/83 (1%)
Query: 2 EECIANY-ETPHGFIIVYSTIDLASFHVAEQCLQALWKKDSIRSKAVILVANKTDLVRCR 60
+ + N E P +VY + SF+ + + + +LV NK DL R
Sbjct: 67 SDMVENVWEQPAVVCVVYDVTNEVSFNNCSRWINRVRTHSHGLHTPGVLVGNKCDLTDRR 126
Query: 61 VVTDEDGKDMATAYDCKFIETSV 83
V + +A A KF ETS
Sbjct: 127 EVDAAQAQALAQANTLKFYETSA 149
>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 = 47.7 bits (114), Expect = 2e-07
Identities = 31/94 (32%), Positives = 43/94 (45%), Gaps = 7/94 (7%)
Query: 8 YETPHGFIIVYSTIDLASFHVAEQCLQALWKKDSIRSKAV-ILVANKTDLVRCRVVTDED 66
Y G I+VY +F + L L S AV +LV NK D R VT E+
Sbjct: 70 YRGAQGVILVYDVTRRDTFDNLDTWLNEL-DTYSTNPDAVKMLVGNKIDKEN-REVTREE 127
Query: 67 GKDMATAYDCKFIETS----VGINHNVDELLVGI 96
G+ A ++ FIETS +G+ +EL+ I
Sbjct: 128 GQKFARKHNMLFIETSAKTRIGVQQAFEELVEKI 161
>gnl|CDD|133310 cd04110, Rab35, Rab GTPase family 35 (Rab35). Rab35 is one of
several Rab proteins to be found to participate in the
regulation of osteoclast cells in rats. In addition,
Rab35 has been identified as a protein that interacts
with nucleophosmin-anaplastic lymphoma kinase (NPM-ALK)
in human cells. Overexpression of NPM-ALK is a key
oncogenic event in some anaplastic large-cell lymphomas;
since Rab35 interacts with N|PM-ALK, it may provide a
target for cancer treatments. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 199
Score = 47.5 bits (113), Expect = 4e-07
Identities = 36/126 (28%), Positives = 52/126 (41%), Gaps = 8/126 (6%)
Query: 8 YETPHGFIIVYSTIDLASFHVAEQCLQALWKKDSIRSKAVILVANKTDLVRCRVVTDEDG 67
Y HG I+VY + SF ++ LQ + + K +LV NK D +VV ED
Sbjct: 76 YRGTHGVIVVYDVTNGESFVNVKRWLQEIEQNCDDVCK--VLVGNKNDDPERKVVETEDA 133
Query: 68 KDMATAYDCKFIETSVGINHNVDELLVGILT-QIRLKLDNPPEPVLTREQFSCRRRRSKS 126
A ETS N NV+E+ I +R K DN ++Q + K
Sbjct: 134 YKFAGQMGISLFETSAKENINVEEMFNCITELVLRAKKDNLA-----KQQQQQQNDVVKL 188
Query: 127 PGGFRK 132
P ++
Sbjct: 189 PKNSKR 194
>gnl|CDD|206694 cd04109, Rab28, Rab GTPase family 28 (Rab28). Rab28 subfamily.
First identified in maize, Rab28 has been shown to be a
late embryogenesis-abundant (Lea) protein that is
regulated by the plant hormone abcisic acid (ABA). In
Arabidopsis, Rab28 is expressed during embryo
development and is generally restricted to provascular
tissues in mature embryos. Unlike maize Rab28, it is not
ABA-inducible. Characterization of the human Rab28
homolog revealed two isoforms, which differ by a 95-base
pair insertion, producing an alternative sequence for
the 30 amino acids at the C-terminus. The two human
isoforms are presumably the result of alternative
splicing. Since they differ at the C-terminus but not in
the GTP-binding region, they are predicted to be
targeted to different cellular locations. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins.
Length = 213
Score = 46.7 bits (111), Expect = 7e-07
Identities = 22/76 (28%), Positives = 31/76 (40%), Gaps = 3/76 (3%)
Query: 3 ECIANYET-PHGFIIVYSTIDLASFHVAEQCLQALWK--KDSIRSKAVILVANKTDLVRC 59
+ + Y +VY + SF E L + K ++S ++LV NKTDL
Sbjct: 65 KMLDKYIYGAQAVCLVYDITNSQSFENLEDWLSVVKKVNEESETKPKMVLVGNKTDLEHN 124
Query: 60 RVVTDEDGKDMATAYD 75
R VT E A D
Sbjct: 125 RQVTAEKHARFAQEND 140
>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 = 45.5 bits (108), Expect = 1e-06
Identities = 28/94 (29%), Positives = 49/94 (52%), Gaps = 10/94 (10%)
Query: 13 GFIIVYSTIDLASFHVAEQCLQALWKKDSIRSKA-----VILVANKTDLVRCRVVTDEDG 67
GF++V+S D+ SF L ++ +R K ++LV NK DL R V+ E+
Sbjct: 74 GFLLVFSITDMESF----TALAEFREQ-ILRVKEDDNVPLLLVGNKCDLEDKRQVSVEEA 128
Query: 68 KDMATAYDCKFIETSVGINHNVDELLVGILTQIR 101
++A + ++ETS NVD++ ++ +IR
Sbjct: 129 ANLAEQWGVNYVETSAKTRANVDKVFFDLVREIR 162
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 45.5 bits (107), Expect = 1e-06
Identities = 35/94 (37%), Positives = 46/94 (48%), Gaps = 6/94 (6%)
Query: 15 IIVYSTIDLASFHVAEQCLQALWKKDSIRSKAVI--LVANKTDLVRCRVVTDEDGKDMAT 72
I+VY + SF + +Q + + R K VI LV NKTDL R VT E+G A
Sbjct: 57 IVVYDITNRQSFENTTKWIQDILNE---RGKDVIIALVGNKTDLGDLRKVTYEEGMQKAQ 113
Query: 73 AYDCKFIETSVGINHNVDELLVGILTQIRLKLDN 106
Y+ F ETS HN+ L I ++ LDN
Sbjct: 114 EYNTMFHETSAKAGHNIKVLFKKIAAKLP-NLDN 146
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 45.7 bits (108), Expect = 2e-06
Identities = 32/96 (33%), Positives = 49/96 (51%), Gaps = 3/96 (3%)
Query: 6 ANYETPHGFIIVYSTIDLASFHVAEQCLQALWKKDSIRSKAVILVA-NKTDLVRCRVVTD 64
A Y G ++VY +F ++ L+ L +D S VI++A NK+DL R V +
Sbjct: 80 AYYRGAVGALLVYDITKRQTFDNVQRWLREL--RDHADSNIVIMMAGNKSDLNHLRSVAE 137
Query: 65 EDGKDMATAYDCKFIETSVGINHNVDELLVGILTQI 100
EDG+ +A F+ETS NV++ IL +I
Sbjct: 138 EDGQALAEKEGLSFLETSALEATNVEKAFQTILLEI 173
>gnl|CDD|206658 cd01866, Rab2, Rab GTPase family 2 (Rab2). Rab2 is localized on
cis-Golgi membranes and interacts with Golgi matrix
proteins. Rab2 is also implicated in the maturation of
vesicular tubular clusters (VTCs), which are
microtubule-associated intermediates in transport
between the ER and Golgi apparatus. In plants, Rab2
regulates vesicle trafficking between the ER and the
Golgi bodies and is important to pollen tube growth.
GTPase activating proteins (GAPs) interact with
GTP-bound Rab and accelerate the hydrolysis of GTP to
GDP. Guanine nucleotide exchange factors (GEFs) interact
with GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 168
Score = 44.7 bits (106), Expect = 3e-06
Identities = 18/55 (32%), Positives = 29/55 (52%)
Query: 46 AVILVANKTDLVRCRVVTDEDGKDMATAYDCKFIETSVGINHNVDELLVGILTQI 100
++L+ NK DL R V+ E+G+ A + F+ETS NV+E + +I
Sbjct: 111 TIMLIGNKCDLESRREVSYEEGEAFAREHGLIFMETSAKTASNVEEAFINTAKEI 165
>gnl|CDD|133319 cd04119, RJL, Rab GTPase family J-like (RabJ-like). RJLs are found
in many protists and as chimeras with C-terminal DNAJ
domains in deuterostome metazoa. They are not found in
plants, fungi, and protostome metazoa, suggesting a
horizontal gene transfer between protists and
deuterostome metazoa. RJLs lack any known membrane
targeting signal and contain a degenerate
phosphate/magnesium-binding 3 (PM3) motif, suggesting an
impaired ability to hydrolyze GTP. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization.
Length = 168
Score = 44.7 bits (106), Expect = 3e-06
Identities = 26/101 (25%), Positives = 48/101 (47%), Gaps = 12/101 (11%)
Query: 8 YETPHGFIIVYSTIDLASFHVAEQCLQALWK--------KDSIRSKAVILVANKTDLVRC 59
Y+ G ++VY D SF + L + K ++ + V++ ANK DL +
Sbjct: 70 YKDTQGVLLVYDVTDRQSF----EALDSWLKEMKQEGGPHGNMENIVVVVCANKIDLTKH 125
Query: 60 RVVTDEDGKDMATAYDCKFIETSVGINHNVDELLVGILTQI 100
R V++++G+ A + K+ ETS V+E+ + + I
Sbjct: 126 RAVSEDEGRLWAESKGFKYFETSACTGEGVNEMFQTLFSSI 166
>gnl|CDD|206714 cd04147, Ras_dva, Ras - dorsal-ventral anterior localization
(Ras-dva) family. Ras-dva subfamily. Ras-dva (Ras -
dorsal-ventral anterior localization) subfamily consists
of a set of proteins characterized only in Xenopus
leavis, to date. In Xenopus Ras-dva expression is
activated by the transcription factor Otx2 and begins
during gastrulation throughout the anterior ectoderm.
Ras-dva expression is inhibited in the anterior neural
plate by factor Xanf1. Downregulation of Ras-dva results
in head development abnormalities through the inhibition
of several regulators of the anterior neural plate and
folds patterning, including Otx2, BF-1, Xag2, Pax6,
Slug, and Sox9. Downregulation of Ras-dva also
interferes with the FGF-8a signaling within the anterior
ectoderm. Most Ras proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins.
Length = 197
Score = 44.4 bits (105), Expect = 4e-06
Identities = 32/131 (24%), Positives = 49/131 (37%), Gaps = 10/131 (7%)
Query: 14 FIIVYSTIDLASFHVAEQCLQALWKKDSIRSKAVILVANKTDLVRCRVVTDEDGKDMATA 73
F +VYS D SF ++ + + + + +++V NK D + R V D
Sbjct: 74 FALVYSVDDPESFEEVKRLREEILEVKEDKFVPIVVVGNKIDSLAERQVEAADALSTVEL 133
Query: 74 -YDCKFIETSVGINHNVDELLVGILTQIRLKLDNPPEPVLTREQFSCRRRRSKSP-GGFR 131
++ F+E S N NV E+ +L Q L P RRR S R
Sbjct: 134 DWNNGFVEASAKDNENVTEVFKELLQQANLPSWLSPA--------LRRRRESAPSEIQRR 185
Query: 132 KLRGHRTSASL 142
S S+
Sbjct: 186 PPMNKTNSCSV 196
>gnl|CDD|206648 cd00882, Ras_like_GTPase, Rat sarcoma (Ras)-like superfamily of
small guanosine triphosphatases (GTPases). Ras-like
GTPase superfamily. The Ras-like superfamily of small
GTPases consists of several families with an extremely
high degree of structural and functional similarity. The
Ras superfamily is divided into at least four families
in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families.
This superfamily also includes proteins like the GTP
translation factors, Era-like GTPases, and G-alpha chain
of the heterotrimeric G proteins. Members of the Ras
superfamily regulate a wide variety of cellular
functions: the Ras family regulates gene expression, the
Rho family regulates cytoskeletal reorganization and
gene expression, the Rab and Sar1/Arf families regulate
vesicle trafficking, and the Ran family regulates
nucleocytoplasmic transport and microtubule
organization. The GTP translation factor family
regulates initiation, elongation, termination, and
release in translation, and the Era-like GTPase family
regulates cell division, sporulation, and DNA
replication. Members of the Ras superfamily are
identified by the GTP binding site, which is made up of
five characteristic sequence motifs, and the switch I
and switch II regions.
Length = 161
Score = 44.0 bits (104), Expect = 4e-06
Identities = 19/87 (21%), Positives = 31/87 (35%), Gaps = 4/87 (4%)
Query: 8 YETPHGFIIVYSTIDLASFHVAEQCLQALWKKDSIRSKAVILVANKTDLV-RCRVVTDED 66
++V + D S A+ + ++ +ILV NK DL+ V
Sbjct: 73 LRGADLILLVVDSTDRESEEDAKLLI---LRRLRKEGIPIILVGNKIDLLEEREVEELLR 129
Query: 67 GKDMATAYDCKFIETSVGINHNVDELL 93
+++A E S VDEL
Sbjct: 130 LEELAKILGVPVFEVSAKTGEGVDELF 156
>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 = 43.7 bits (103), Expect = 8e-06
Identities = 28/106 (26%), Positives = 50/106 (47%), Gaps = 2/106 (1%)
Query: 6 ANYETPHGFIIVYSTIDLASFHVAEQCLQALWKKDSIRSKAVILVANKTDLVRCRVVTDE 65
A Y H +++Y + +SF L + + ++L+ NK D+ RVV E
Sbjct: 69 AYYRDAHALLLLYDVTNKSSFDNIRAWLTEILEYAQ-SDVVIMLLGNKADMSGERVVKRE 127
Query: 66 DGKDMATAYDCKFIETSVGINHNVDELLVGILTQIRLK-LDNPPEP 110
DG+ +A Y F+ETS NV+ + +++ + ++ P EP
Sbjct: 128 DGERLAKEYGVPFMETSAKTGLNVELAFTAVAKELKHRSVEQPDEP 173
>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 = 43.2 bits (102), Expect = 9e-06
Identities = 25/89 (28%), Positives = 39/89 (43%), Gaps = 10/89 (11%)
Query: 8 YETPHGFIIVYSTIDLASFHVAEQCLQALWKKDSIRSKA----VILVANKTDLVRCRVVT 63
Y + +G II Y +SF W ++ + A ++L+ NK DL R V
Sbjct: 73 YRSANGAIIAYDITRRSSFESVPH-----WIEEVEKYGASNVVLLLIGNKCDLEEQREVL 127
Query: 64 DEDGKDMATAYDCKF-IETSVGINHNVDE 91
E+ +A Y +ETS + NV+E
Sbjct: 128 FEEACTLAEHYGILAVLETSAKESSNVEE 156
>gnl|CDD|206700 cd04127, Rab27A, Rab GTPase family 27a (Rab27a). The Rab27a
subfamily consists of Rab27a and its highly homologous
isoform, Rab27b. Unlike most Rab proteins whose
functions remain poorly defined, Rab27a has many known
functions. Rab27a has multiple effector proteins, and
depending on which effector it binds, Rab27a has
different functions as well as tissue distribution
and/or cellular localization. Putative functions have
been assigned to Rab27a when associated with the
effector proteins Slp1, Slp2, Slp3, Slp4, Slp5, DmSlp,
rabphilin, Dm/Ce-rabphilin, Slac2-a, Slac2-b, Slac2-c,
Noc2, JFC1, and Munc13-4. Rab27a has been associated
with several human diseases, including hemophagocytic
syndrome (Griscelli syndrome or GS), Hermansky-Pudlak
syndrome, and choroidermia. In the case of GS, a rare,
autosomal recessive disease, a Rab27a mutation is
directly responsible for the disorder. When Rab27a is
localized to the secretory granules of pancreatic beta
cells, it is believed to mediate glucose-stimulated
insulin secretion, making it a potential target for
diabetes therapy. When bound to JFC1 in prostate cells,
Rab27a is believed to regulate the exocytosis of
prostate- specific markers. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 180
Score = 42.9 bits (101), Expect = 1e-05
Identities = 22/99 (22%), Positives = 43/99 (43%), Gaps = 3/99 (3%)
Query: 4 CIANYETPHGFIIVYSTIDLASFHVAEQCLQALWKKDSIRSKAVILVANKTDLVRCRVVT 63
A + GF++++ SF + L + ++L+ NK DL R V+
Sbjct: 80 TTAFFRDAMGFLLMFDLTSEQSFLNVRNWMSQLQAHAYCENPDIVLIGNKADLPDQREVS 139
Query: 64 DEDGKDMATAYDCKFIETSVGINHNVD---ELLVGILTQ 99
+ +++A Y + ETS NV+ E L+ ++ +
Sbjct: 140 ERQARELADKYGIPYFETSAATGQNVEKAVETLLDLIMK 178
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 42.2 bits (99), Expect = 3e-05
Identities = 29/105 (27%), Positives = 48/105 (45%), Gaps = 13/105 (12%)
Query: 8 YETPHGFIIVYSTIDLASF-HVAEQCLQALWKKDSIRSKA-----VILVANKTDLVRCRV 61
Y G ++VY +F H+A W +D+ R A ++L+ NK DL R
Sbjct: 76 YRGAAGALLVYDITRRETFNHLAS------WLEDA-RQHANANMTIMLIGNKCDLAHRRA 128
Query: 62 VTDEDGKDMATAYDCKFIETSVGINHNVDELLVGILTQIRLKLDN 106
V+ E+G+ A + F+E S NV+E + +I K+ +
Sbjct: 129 VSTEEGEQFAKEHGLIFMEASAKTAQNVEEAFIKTAAKIYKKIQD 173
>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 = 42.1 bits (99), Expect = 3e-05
Identities = 30/111 (27%), Positives = 49/111 (44%), Gaps = 12/111 (10%)
Query: 8 YETPHGFIIVYSTIDLASF-HVAEQCLQALWKKDSIR----SKAV-ILVANKTDLVRCRV 61
Y G ++V+ + SF HV + W +++ + V ILV +K DL R
Sbjct: 73 YRNSVGVLLVFDITNRESFEHVHD------WLEEARSHIQPHRPVFILVGHKCDLESQRQ 126
Query: 62 VTDEDGKDMATAYDCKFIETSVGINHNVDELLVGILTQIRLKLDNPPEPVL 112
VT E+ + +A K+IETS NV+E + +I ++ L
Sbjct: 127 VTREEAEKLAKDLGMKYIETSARTGDNVEEAFELLTQEIYERIKRGELCAL 177
>gnl|CDD|133314 cd04114, Rab30, Rab GTPase family 30 (Rab30). Rab30 subfamily.
Rab30 appears to be associated with the Golgi stack. It
is expressed in a wide variety of tissue types and in
humans maps to chromosome 11. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 169
Score = 41.4 bits (97), Expect = 5e-05
Identities = 23/93 (24%), Positives = 45/93 (48%), Gaps = 1/93 (1%)
Query: 8 YETPHGFIIVYSTIDLASFHVAEQCLQALWKKDSIRSKAVILVANKTDLVRCRVVTDEDG 67
Y + + I+ Y SF + L+ + + + ILV NK DL R V+ +
Sbjct: 77 YRSANALILTYDITCEESFRCLPEWLREIEQYAN-NKVITILVGNKIDLAERREVSQQRA 135
Query: 68 KDMATAYDCKFIETSVGINHNVDELLVGILTQI 100
++ + A D ++ETS + NV++L + + ++
Sbjct: 136 EEFSDAQDMYYLETSAKESDNVEKLFLDLACRL 168
>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 = 40.1 bits (94), Expect = 1e-04
Identities = 26/81 (32%), Positives = 38/81 (46%), Gaps = 8/81 (9%)
Query: 15 IIVYSTIDLASFHVAEQCLQALWKKDSIR---SKAVILVANKTDLVRCRVVTDEDGKDMA 71
I+V+ST D SF E WK+ ++LV K DL+ V+T+E+ + +A
Sbjct: 79 ILVFSTTDRESFEAIES-----WKEKVEAECGDIPMVLVQTKIDLLDQAVITNEEAEALA 133
Query: 72 TAYDCKFIETSVGINHNVDEL 92
TSV + NV EL
Sbjct: 134 KRLQLPLFRTSVKDDFNVTEL 154
>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 = 38.8 bits (91), Expect = 5e-04
Identities = 30/121 (24%), Positives = 45/121 (37%), Gaps = 29/121 (23%)
Query: 8 YETPHGFIIVY-----STIDLASFHVAEQCLQALWKKDSIRSKA---------VILVANK 53
Y+ G IIV+ ST + WK D + SK +L+ANK
Sbjct: 71 YKGAVGAIIVFDVTRPSTFEAVL----------KWKAD-LDSKVTLPNGEPIPALLLANK 119
Query: 54 TDLVRCRVVTDEDGKDMATAYDCKFI---ETSVGINHNVDELLVGILTQIRLKLDNPPEP 110
DL + R+ D + + FI ETS N N++E + ++ I P
Sbjct: 120 CDLKKERLAKD-PEQMDQFCKENGFIGWFETSAKENINIEEAMRFLVKNILKNDKGLQSP 178
Query: 111 V 111
Sbjct: 179 E 179
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 38.1 bits (88), Expect = 7e-04
Identities = 27/89 (30%), Positives = 39/89 (43%), Gaps = 9/89 (10%)
Query: 8 YETPHGFIIVYSTIDLASFHVAEQCLQALWKKD----SIRSKAV-ILVANKTDLVRCRVV 62
Y G I+VY +F L +W K+ S V +LV NK D R V
Sbjct: 83 YRNAQGIILVYDVTRRETF----TNLSDVWGKEVELYSTNQDCVKMLVGNKVDRESERDV 138
Query: 63 TDEDGKDMATAYDCKFIETSVGINHNVDE 91
+ E+G +A + C F+E S NV++
Sbjct: 139 SREEGMALAKEHGCLFLECSAKTRENVEQ 167
>gnl|CDD|206698 cd04117, Rab15, Rab GTPase family 15 (Rab15). Rab15 colocalizes
with the transferrin receptor in early endosome
compartments, but not with late endosomal markers. It
codistributes with Rab4 and Rab5 on early/sorting
endosomes, and with Rab11 on pericentriolar recycling
endosomes. It is believed to function as an inhibitory
GTPase that regulates distinct steps in early endocytic
trafficking. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation of
the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 164
Score = 37.6 bits (87), Expect = 8e-04
Identities = 30/98 (30%), Positives = 45/98 (45%), Gaps = 6/98 (6%)
Query: 8 YETPHGFIIVYSTIDLASFHVAEQCLQALWKKDSIRSKAV--ILVANKTDLVRCRVVTDE 65
Y G +VY D++S + ++ + D + V IL+ NK D + R V DE
Sbjct: 70 YRRAQGIFLVY---DISSERSYQHIMKWVSDVDEYAPEGVQKILIGNKADEEQKRQVGDE 126
Query: 66 DGKDMATAYDCKFIETSVGINHNVDELLVGILTQIRLK 103
G +A Y F ETS N N+ E LT++ L+
Sbjct: 127 QGNKLAKEYGMDFFETSACTNKNIKESFTR-LTELVLQ 163
>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 = 36.7 bits (85), Expect = 0.003
Identities = 26/104 (25%), Positives = 44/104 (42%), Gaps = 9/104 (8%)
Query: 14 FIIVYSTIDLASFH----VAEQCLQALW----KKDSIRSKAVILVANKTDLVRCRVV-TD 64
FI+V+S + SF + EQ L+ K +++ NK D R V D
Sbjct: 75 FILVFSLDNRESFEEVCRLREQILETKSCLKNKTKENVKIPMVICGNKADRDFPREVQRD 134
Query: 65 EDGKDMATAYDCKFIETSVGINHNVDELLVGILTQIRLKLDNPP 108
E + + +C + E S N N+DE+ + + +L + P
Sbjct: 135 EVEQLVGGDENCAYFEVSAKKNSNLDEMFRALFSLAKLPNEMSP 178
>gnl|CDD|206696 cd04113, Rab4, Rab GTPase family 4 (Rab4). Rab4 subfamily. Rab4
has been implicated in numerous functions within the
cell. It helps regulate endocytosis through the sorting,
recycling, and degradation of early endosomes. Mammalian
Rab4 is involved in the regulation of many surface
proteins including G-protein-coupled receptors,
transferrin receptor, integrins, and surfactant protein
A. Experimental data implicate Rab4 in regulation of the
recycling of internalized receptors back to the plasma
membrane. It is also believed to influence
receptor-mediated antigen processing in B-lymphocytes,
in calcium-dependent exocytosis in platelets, in
alpha-amylase secretion in pancreatic cells, and in
insulin-induced translocation of Glut4 from internal
vesicles to the cell surface. Rab4 is known to share
effector proteins with Rab5 and Rab11. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 161
Score = 35.5 bits (82), Expect = 0.005
Identities = 28/89 (31%), Positives = 37/89 (41%), Gaps = 11/89 (12%)
Query: 8 YETPHGFIIVYSTIDLASFHVAEQCLQALWKKDSIRSKA-----VILVANKTDLVRCRVV 62
Y G ++VY SF+ W D+ R+ A +ILV NK DL R V
Sbjct: 70 YRGAAGALLVYDITSRESFNALTN-----WLTDA-RTLASPDIVIILVGNKKDLEDDREV 123
Query: 63 TDEDGKDMATAYDCKFIETSVGINHNVDE 91
T + A F+ETS NV+E
Sbjct: 124 TFLEASRFAQENGLLFLETSALTGENVEE 152
>gnl|CDD|206699 cd04120, Rab12, Rab GTPase family 12 (Rab12). Rab12 was first
identified in canine cells, where it was localized to
the Golgi complex. The specific function of Rab12
remains unknown, and inconsistent results about its
cellular localization have been reported. More recent
studies have identified Rab12 associated with post-Golgi
vesicles, or with other small vesicle-like structures
but not with the Golgi complex. Most Rab GTPases contain
a lipid modification site at the C-terminus, with
sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation of
the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins.
Length = 202
Score = 35.0 bits (80), Expect = 0.009
Identities = 31/111 (27%), Positives = 50/111 (45%), Gaps = 5/111 (4%)
Query: 6 ANYETPHGFIIVYSTIDLASFHVAEQCLQALWKKDSIRSKAVILVANKTDLVRCRVVTDE 65
A Y + G I+VY +F + ++ + K S ++LV NK D R +T +
Sbjct: 68 AYYRSAKGIILVYDITKKETFDDLPKWMKMIDKYAS-EDAELLLVGNKLDCETDREITRQ 126
Query: 66 DGKDMATAYD-CKFIETSVGINHNVDELLVGILTQIRLKLDNPPEPVLTRE 115
G+ A +F E S N NVDE+ + ++ I K+ P +L E
Sbjct: 127 QGEKFAQQITGMRFCEASAKDNFNVDEIFLKLVDDILKKM---PLDILRNE 174
>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 = 34.0 bits (78), Expect = 0.017
Identities = 17/57 (29%), Positives = 26/57 (45%)
Query: 44 SKAVILVANKTDLVRCRVVTDEDGKDMATAYDCKFIETSVGINHNVDELLVGILTQI 100
+ + L+ NK DL R VT E+ K A F+E S NV++ + +I
Sbjct: 107 NTVIFLIGNKADLEAQRDVTYEEAKQFADENGLLFLECSAKTGENVEDAFLETAKKI 163
>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 = 32.5 bits (75), Expect = 0.046
Identities = 20/95 (21%), Positives = 39/95 (41%), Gaps = 21/95 (22%)
Query: 14 FIIVYSTIDLASFHVAEQCLQALWKKDSIR----SKAVILVANKTDL-----------VR 58
F++ +S +SF + W + I+ + +ILV K DL +
Sbjct: 75 FLLCFSVDSPSSFENVKT----KWYPE-IKHYCPNVPIILVGTKIDLRDDGNTLKKLEKK 129
Query: 59 CRVVTDEDGKDMATAYDC-KFIETSVGINHNVDEL 92
+ +T E+G+ +A K++E S + E+
Sbjct: 130 QKPITPEEGEKLAKEIGAVKYMECSALTQEGLKEV 164
>gnl|CDD|133315 cd04115, Rab33B_Rab33A, Rab GTPase family 33 includes Rab33A and
Rab33B. Rab33B/Rab33A subfamily. Rab33B is ubiquitously
expressed in mouse tissues and cells, where it is
localized to the medial Golgi cisternae. It colocalizes
with alpha-mannose II. Together with the other cisternal
Rabs, Rab6A and Rab6A', it is believed to regulate the
Golgi response to stress and is likely a molecular
target in stress-activated signaling pathways. Rab33A
(previously known as S10) is expressed primarily in the
brain and immune system cells. In humans, it is located
on the X chromosome at Xq26 and its expression is
down-regulated in tuberculosis patients. Experimental
evidence suggests that Rab33A is a novel CD8+ T cell
factor that likely plays a role in tuberculosis disease
processes. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation of
the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 170
Score = 32.4 bits (74), Expect = 0.055
Identities = 25/79 (31%), Positives = 33/79 (41%), Gaps = 8/79 (10%)
Query: 8 YETPHGFIIVYSTIDLASFHV----AEQCLQALWKKDSIRSKAVILVANKTDLVRCRVVT 63
Y H + VY ++ASFH E+C Q + R ILV NK DL V
Sbjct: 73 YRNVHAVVFVYDVTNMASFHSLPSWIEECEQHSLPNEVPR----ILVGNKCDLREQIQVP 128
Query: 64 DEDGKDMATAYDCKFIETS 82
+ + A A+ ETS
Sbjct: 129 TDLAQRFADAHSMPLFETS 147
>gnl|CDD|206717 cd04150, Arf1_5_like, ADP-ribosylation factor-1 (Arf1) and
ADP-ribosylation factor-5 (Arf5). The Arf1-Arf5-like
subfamily contains Arf1, Arf2, Arf3, Arf4, Arf5, and
related proteins. Arfs1-5 are soluble proteins that are
crucial for assembling coat proteins during vesicle
formation. Each contains an N-terminal myristoylated
amphipathic helix that is folded into the protein in the
GDP-bound state. GDP/GTP exchange exposes the helix,
which anchors to the membrane. Following GTP hydrolysis,
the helix dissociates from the membrane and folds back
into the protein. A general feature of Arf1-5 signaling
may be the cooperation of two Arfs at the same site.
Arfs1-5 are generally considered to be interchangeable
in function and location, but some specific functions
have been assigned. Arf1 localizes to the
early/cis-Golgi, where it is activated by GBF1 and
recruits the coat protein COPI. It also localizes to the
trans-Golgi network (TGN), where it is activated by
BIG1/BIG2 and recruits the AP1, AP3, AP4, and GGA
proteins. Humans, but not rodents and other lower
eukaryotes, lack Arf2. Human Arf3 shares 96% sequence
identity with Arf1 and is believed to generally function
interchangeably with Arf1. Human Arf4 in the activated
(GTP-bound) state has been shown to interact with the
cytoplasmic domain of epidermal growth factor receptor
(EGFR) and mediate the EGF-dependent activation of
phospholipase D2 (PLD2), leading to activation of the
activator protein 1 (AP-1) transcription factor. Arf4
has also been shown to recognize the C-terminal sorting
signal of rhodopsin and regulate its incorporation into
specialized post-Golgi rhodopsin transport carriers
(RTCs). There is some evidence that Arf5 functions at
the early-Golgi and the trans-Golgi to affect
Golgi-associated alpha-adaptin homology Arf-binding
proteins (GGAs).
Length = 159
Score = 31.6 bits (72), Expect = 0.11
Identities = 14/49 (28%), Positives = 24/49 (48%)
Query: 8 YETPHGFIIVYSTIDLASFHVAEQCLQALWKKDSIRSKAVILVANKTDL 56
++ G I V + D A + LQ + +D +R +++ ANK DL
Sbjct: 65 FQNTQGLIFVVDSNDRERIGEAREELQRMLNEDELRDAVLLVFANKQDL 113
>gnl|CDD|225434 COG2879, COG2879, Uncharacterized small protein [Function unknown].
Length = 65
Score = 28.9 bits (65), Expect = 0.25
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 10/48 (20%)
Query: 92 LLVGI------LTQIRLKLDNPPEPVLTREQF--SCRRRRSKSPGGFR 131
L+VG+ + +R K +P +P +T E+F C+ R GG R
Sbjct: 18 LMVGVPDYDNYVEHMRKK--HPDKPPMTYEEFFRECQDARYGGGGGGR 63
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes. TrmE
contains a GTPase domain that forms a canonical Ras-like
fold. It functions a molecular switch GTPase, and
apparently uses a conformational change associated with
GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 30.2 bits (69), Expect = 0.29
Identities = 15/58 (25%), Positives = 24/58 (41%), Gaps = 7/58 (12%)
Query: 40 DSIRSKAVILVANKTDLVRCRVVTDEDGKDMATAYDCKFIETSVGINHNVDELLVGIL 97
+ K VI+V NK+DL+ D + ++ I S +DEL +L
Sbjct: 105 ELPAKKPVIVVLNKSDLL-------SDAEGISELNGKPIIAISAKTGEGIDELKEALL 155
>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 = 30.3 bits (69), Expect = 0.30
Identities = 24/106 (22%), Positives = 37/106 (34%), Gaps = 42/106 (39%)
Query: 14 FIIVYSTIDLASFHVAEQCLQALWKKDSIRSK------------AVILVANKTDL----- 56
F+I +S ASF ++++ K +ILV K DL
Sbjct: 73 FLICFSVDSPASF-------------ENVKEKWYPEVKHFCPNVPIILVGTKLDLRNDKS 119
Query: 57 -------VRCRVVTDEDGKDMAT---AYDCKFIETSVGINHNVDEL 92
+ VT E G+ +A A K++E S V E+
Sbjct: 120 TLEELSKKKQEPVTYEQGQALAKRIGA--VKYLECSALTQEGVREV 163
>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 = 30.6 bits (69), Expect = 0.31
Identities = 30/130 (23%), Positives = 49/130 (37%), Gaps = 13/130 (10%)
Query: 1 PEECIANYETPHGFIIVYSTIDLASFHVAEQCLQALWKKDSIRSKA--VILVANKTDLVR 58
+ FI+VY SFH + Q + + +K +++V NK D R
Sbjct: 71 MDPRFRGLRNSRAFILVYDICSPDSFHYVKLLRQQILETRPAGNKEPPIVVVGNKRDQQR 130
Query: 59 CRVVTDEDGKDMA-TAYDCKFIETSVGINHNV----DELLVGILTQIRLKLDNPPEPVLT 113
R + ++ C ++E S N ++ ELL+ T+ R P L
Sbjct: 131 HRFAPRHVLSVLVRKSWKCGYLECSAKYNWHILLLFKELLISATTRGR-----STHPAL- 184
Query: 114 REQFSCRRRR 123
R Q + R R
Sbjct: 185 RLQGALHRER 194
>gnl|CDD|133318 cd04118, Rab24, Rab GTPase family 24 (Rab24). Rab24 is distinct
from other Rabs in several ways. It exists primarily in
the GTP-bound state, having a low intrinsic GTPase
activity; it is not efficiently geranyl-geranylated at
the C-terminus; it does not form a detectable complex
with Rab GDP-dissociation inhibitors (GDIs); and it has
recently been shown to undergo tyrosine phosphorylation
when overexpressed in vitro. The specific function of
Rab24 still remains unknown. It is found in a transport
route between ER-cis-Golgi and late endocytic
compartments. It is putatively involved in an autophagic
pathway, possibly directing misfolded proteins in the ER
to degradative pathways. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 193
Score = 30.2 bits (68), Expect = 0.34
Identities = 25/85 (29%), Positives = 35/85 (41%), Gaps = 12/85 (14%)
Query: 15 IIVYSTIDLASFHVAEQCLQALWKKDSIRSKA---VILVANKTDLV----RCRVVTDEDG 67
I+ Y D +SF A+ W K+ + + L K+DL+ R V D
Sbjct: 78 IVCYDLTDSSSFERAK-----FWVKELQNLEEHCKIYLCGTKSDLIEQDRSLRQVDFHDV 132
Query: 68 KDMATAYDCKFIETSVGINHNVDEL 92
+D A + ETS NVDEL
Sbjct: 133 QDFADEIKAQHFETSSKTGQNVDEL 157
>gnl|CDD|232886 TIGR00231, small_GTP, small GTP-binding protein domain. Proteins
with a small GTP-binding domain recognized by this model
include Ras, RhoA, Rab11, translation elongation factor
G, translation initiation factor IF-2, tetratcycline
resistance protein TetM, CDC42, Era, ADP-ribosylation
factors, tdhF, and many others. In some proteins the
domain occurs more than once.This model recognizes a
large number of small GTP-binding proteins and related
domains in larger proteins. Note that the alpha chains
of heterotrimeric G proteins are larger proteins in
which the NKXD motif is separated from the GxxxxGK[ST]
motif (P-loop) by a long insert and are not easily
detected by this model [Unknown function, General].
Length = 162
Score = 30.0 bits (68), Expect = 0.36
Identities = 13/46 (28%), Positives = 17/46 (36%), Gaps = 1/46 (2%)
Query: 47 VILVANKTDLVRCRVVTDEDGKDMATAYDCKFIETSVGINHNVDEL 92
+ILV NK DL ++ T A I S N+D
Sbjct: 112 IILVGNKIDLRDAKLKTHV-AFLFAKLNGEPIIPLSAETGKNIDSA 156
>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 = 29.9 bits (68), Expect = 0.41
Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 1/45 (2%)
Query: 48 ILVANKTDLVRCRVVTDEDGKDMATAYDC-KFIETSVGINHNVDE 91
+++ NK DL R V+ + + + + ETS NVD+
Sbjct: 113 VVLGNKIDLEEKRQVSTKKAQQWCKSKGNIPYFETSAKEAINVDQ 157
>gnl|CDD|206684 cd01897, NOG, Nucleolar GTP-binding protein (NOG). NOG1 is a
nucleolar GTP-binding protein present in eukaryotes
ranging from trypanosomes to humans. NOG1 is
functionally linked to ribosome biogenesis and found in
association with the nuclear pore complexes and
identified in many preribosomal complexes. Thus, defects
in NOG1 can lead to defects in 60S biogenesis. The S.
cerevisiae NOG1 gene is essential for cell viability,
and mutations in the predicted G motifs abrogate
function. It is a member of the ODN family of
GTP-binding proteins that also includes the bacterial
Obg and DRG proteins.
Length = 167
Score = 29.5 bits (67), Expect = 0.52
Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 9/68 (13%)
Query: 28 VAEQCLQALWKKDSIRS---KAVILVANKTDLVRCRVVTDEDGKDMATAYDCKFIETSVG 84
+ EQ +L+K I+ K VI+V NK DL+ + + + + I+ S
Sbjct: 97 IEEQL--SLFK--EIKPLFNKPVIVVLNKIDLLTEEDL--SEIEKELEKEGEEVIKISTL 150
Query: 85 INHNVDEL 92
VDEL
Sbjct: 151 TEEGVDEL 158
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 30.1 bits (69), Expect = 0.52
Identities = 18/77 (23%), Positives = 24/77 (31%), Gaps = 9/77 (11%)
Query: 40 DSIRSKAVILVANKTDLVRCRVVTDEDGKDMATAYDCKFIETSVGINHNVDELLVGILTQ 99
+ ++ K VI+V NK DL D+ I S +DEL I
Sbjct: 317 EELKDKPVIVVLNKADL--------TGEIDLEEENGKPVIRISAKTGEGIDELREAIKEL 368
Query: 100 IRLKLDNPPE-PVLTRE 115
E LT
Sbjct: 369 AFGGFGGNQEGVFLTNA 385
>gnl|CDD|234221 TIGR03467, HpnE, squalene-associated FAD-dependent desaturase. The
sequences in this family are members of the pfam01593
superfamily of flavin-containing amine oxidases which
include the phytoene desaturases. These sequences also
include a FAD-dependent oxidoreductase domain,
pfam01266. The genes of the family modeled here are
generally in the same locus with genes involved in the
biosynthesis and elaboration of squalene, the
condensation product of the polyisoprenoid farnesyl
pyrophosphate. This gene and its association with hopene
biosynthesis in Zymomonas mobilis has been noted in the
literature where the gene symbol hpnE was assigned. This
gene is also found in contexts where the downstream
conversion of squalene to hopenes is not evidence. The
precise nature of the reaction catalyzed by this enzyme
is unknown at this time.
Length = 411
Score = 30.0 bits (68), Expect = 0.53
Identities = 25/106 (23%), Positives = 37/106 (34%), Gaps = 11/106 (10%)
Query: 58 RCRVVTDEDGKDMATAYDCKFIETSVGINHNVDELLVGILTQIRLKLDNPPEPVLTREQF 117
R R EDG T + + + +G N+ LL I + RL+ P P
Sbjct: 17 RARSF--EDGGLGQTIDNGQHV--LLGAYTNLLALLRRIGAEPRLQGPRLPLPFYDPGGR 72
Query: 118 SCRRRRSKSPGGFRKLRGHRTSASLK-------VKGLLSKVWQRDS 156
R R S+ P RG + L + LL+ +R
Sbjct: 73 LSRLRLSRLPAPLHLARGLLRAPGLSWADKLALARALLALRRERFR 118
>gnl|CDD|206693 cd04108, Rab36_Rab34, Rab GTPase families 34 (Rab34) and 36
(Rab36). Rab34/Rab36 subfamily. Rab34, found primarily
in the Golgi, interacts with its effector,
Rab-interacting lysosomal protein (RILP). This enables
its participation in microtubular
dynenin-dynactin-mediated repositioning of lysosomes
from the cell periphery to the Golgi. A Rab34 (Rah)
isoform that lacks the consensus GTP-binding region has
been identified in mice. This isoform is associated with
membrane ruffles and promotes macropinosome formation.
Rab36 has been mapped to human chromosome 22q11.2, a
region that is homozygously deleted in malignant
rhabdoid tumors (MRTs). However, experimental
assessments do not implicate Rab36 as a tumor suppressor
that would enable tumor formation through a
loss-of-function mechanism. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 170
Score = 29.5 bits (66), Expect = 0.59
Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 2/56 (3%)
Query: 3 ECIAN--YETPHGFIIVYSTIDLASFHVAEQCLQALWKKDSIRSKAVILVANKTDL 56
+CIA+ Y IIV+ D+AS Q L+ K++ S + LV K DL
Sbjct: 63 KCIASTYYRGAQAIIIVFDLTDVASLEHTRQWLEDALKENDPSSVLLFLVGTKKDL 118
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 29.5 bits (66), Expect = 0.65
Identities = 26/101 (25%), Positives = 43/101 (42%), Gaps = 19/101 (18%)
Query: 11 PHGFIIVY-STIDLASFHVAEQCLQALWKKDSIRSKAVILVANKTDL------------- 56
+G +IVY ST+ +S + E+ L+ L ++ + ++LV NK DL
Sbjct: 78 ANGILIVYDSTLRESSDELTEEWLEEL-RELAPDDVPILLVGNKIDLFDEQSSSEEILNQ 136
Query: 57 -VRCRVVTDEDGK-DMATAYDCKFIETSV--GINHNVDELL 93
R V+ K + + +ETS NV+EL
Sbjct: 137 LNREVVLLVLAPKAVLPEVANPALLETSAKSLTGPNVNELF 177
>gnl|CDD|198352 cd07774, FGGY_1, uncharacterized subgroup; belongs to the FGGY
family of carbohydrate kinases. This subfamily is
composed of uncharacterized carbohydrate kinases. They
are sequence homologous to bacterial glycerol kinase and
have been classified as members of the FGGY family of
carbohydrate kinases. The monomers of FGGY proteins
contain two large domains, which are separated by a deep
cleft that forms the active site. This model includes
both the N-terminal domain, which adopts a ribonuclease
H-like fold, and the structurally related C-terminal
domain.
Length = 430
Score = 29.3 bits (66), Expect = 0.97
Identities = 15/54 (27%), Positives = 22/54 (40%), Gaps = 1/54 (1%)
Query: 61 VVTDEDGKDMATA-YDCKFIETSVGINHNVDELLVGILTQIRLKLDNPPEPVLT 113
VV D+DG +A + + G + DEL I I L P+P+
Sbjct: 15 VVFDDDGTIIAIRKFKTPKNVSDGGPYFDPDELWRAIEKVICQALAAAPDPIAA 68
>gnl|CDD|128474 smart00177, ARF, ARF-like small GTPases; ARF, ADP-ribosylation
factor. Ras homologues involved in vesicular transport.
Activator of phospholipase D isoforms. Unlike Ras
proteins they lack cysteine residues at their C-termini
and therefore are unlikely to be prenylated. ARFs are
N-terminally myristoylated. Contains ATP/GTP-binding
motif (P-loop).
Length = 175
Score = 28.7 bits (64), Expect = 1.2
Identities = 14/49 (28%), Positives = 22/49 (44%)
Query: 8 YETPHGFIIVYSTIDLASFHVAEQCLQALWKKDSIRSKAVILVANKTDL 56
Y G I V + D A + L + +D +R +++ ANK DL
Sbjct: 78 YTNTQGLIFVVDSNDRDRIDEAREELHRMLNEDELRDAVILVFANKQDL 126
>gnl|CDD|133353 cd04153, Arl5_Arl8, Arf-like 5 (Arl5) and 8 (Arl8) GTPases.
Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like
Arl4 and Arl7, are localized to the nucleus and
nucleolus. Arl5 is developmentally regulated during
embryogenesis in mice. Human Arl5 interacts with the
heterochromatin protein 1-alpha (HP1alpha), a nonhistone
chromosomal protein that is associated with
heterochromatin and telomeres, and prevents telomere
fusion. Arl5 may also play a role in embryonic nuclear
dynamics and/or signaling cascades. Arl8 was identified
from a fetal cartilage cDNA library. It is found in
brain, heart, lung, cartilage, and kidney. No function
has been assigned for Arl8 to date.
Length = 174
Score = 28.5 bits (64), Expect = 1.5
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 2/50 (4%)
Query: 8 YETPHGFIIVYSTIDLASFHVAEQCLQALWKKDSIRSKAVILV-ANKTDL 56
Y I+V + D + ++ L + + +R KAV+LV ANK DL
Sbjct: 80 YTNTDAVILVIDSTDRERLPLTKEELYKMLAHEDLR-KAVLLVLANKQDL 128
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 28.7 bits (65), Expect = 1.5
Identities = 22/101 (21%), Positives = 36/101 (35%), Gaps = 8/101 (7%)
Query: 16 IVYSTIDLASFHVAEQCLQALWKKDSIRSKAVILVANKTDLVRCRVVTDEDGKDMATAYD 75
+V +D AS + ++ L + K +I+V NK DL V+ + + A
Sbjct: 299 LVLFVLD-ASQPLDKEDLALIELLPK--KKPIIVVLNKADL-----VSKIELESEKLANG 350
Query: 76 CKFIETSVGINHNVDELLVGILTQIRLKLDNPPEPVLTREQ 116
I S +D L I L N L+ +
Sbjct: 351 DAIISISAKTGEGLDALREAIKQLFGKGLGNQEGLFLSNLR 391
>gnl|CDD|206685 cd01898, Obg, Obg GTPase. The Obg nucleotide binding protein
subfamily has been implicated in stress response,
chromosome partitioning, replication initiation,
mycelium development, and sporulation. Obg proteins are
among a large group of GTP binding proteins conserved
from bacteria to humans. The E. coli homolog, ObgE is
believed to function in ribosomal biogenesis. Members of
the subfamily contain two equally and highly conserved
domains, a C-terminal GTP binding domain and an
N-terminal glycine-rich domain.
Length = 170
Score = 27.8 bits (63), Expect = 2.0
Identities = 17/90 (18%), Positives = 29/90 (32%), Gaps = 15/90 (16%)
Query: 21 IDLASFHVAEQCLQALWK-----KDSIRSKAVILVANKTDLVRCRVVTDEDGKDMATAY- 74
IDL+ + + + + K I+V NK DL + E+ +
Sbjct: 86 IDLSGEDDPVEDYETIRNELEAYNPGLAEKPRIVVLNKIDL-----LDAEERFEKLKELL 140
Query: 75 ----DCKFIETSVGINHNVDELLVGILTQI 100
K S +DELL + +
Sbjct: 141 KELKGKKVFPISALTGEGLDELLKKLAKLL 170
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 27.9 bits (62), Expect = 2.0
Identities = 15/57 (26%), Positives = 27/57 (47%)
Query: 8 YETPHGFIIVYSTIDLASFHVAEQCLQALWKKDSIRSKAVILVANKTDLVRCRVVTD 64
Y+ +G I V + D A + L+ + +D +R +++ ANK DL T+
Sbjct: 82 YQNTNGLIFVVDSNDRERIGDAREELERMLSEDELRDAVLLVFANKQDLPNAMSTTE 138
>gnl|CDD|132735 cd06937, NR_LBD_RAR, The ligand binding domain (LBD) of retinoic
acid receptor (RAR), a members of the nuclear receptor
superfamily. The ligand binding domain (LBD) of
retinoic acid receptor (RAR): Retinoic acid receptors
are members of the nuclear receptor (NR) superfamily of
ligand-regulated transcription factors. RARs mediate the
biological effect of retinoids, including both naturally
dietary vitamin A (retinol) metabolites and active
synthetic analogs. Retinoids play key roles in a wide
variety of essential biological processes, such as
vertebrate embryonic morphogenesis and organogenesis,
differentiation and apoptosis, and homeostasis. RARs
function as heterodimers with retinoic X receptors by
binding to specific RAR response elements (RAREs) found
in the promoter regions of retinoid target genes. In the
absence of ligand, the RAR-RXR heterodimer recruits the
corepressor proteins NCoR or AMRT, and associated
factors such as histone deacetylases or
DNA-methyltransferases, leading to an inactive condensed
chromatin structure, preventing transcription. Upon
ligand binding, the corepressors are released, and
coactivator complexes such as histone acetyltransferase
or histone arginine methyltransferases are recruited to
activate transcription. There are three RAR subtypes
(alpha, beta, gamma), originating from three distinct
genes. For each subtype, several isoforms exist that
differ in their N-terminal region, allowing retinoids to
exert their pleiotropic effects. Like other members of
the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, retinoic acid
receptors have a central well conserved DNA binding
domain (DBD), a variable N-terminal domain, a
non-conserved hinge and a C-terminal ligand binding
domain (LBD).
Length = 231
Score = 27.9 bits (62), Expect = 2.5
Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 12/58 (20%)
Query: 88 NVDELLVGILTQI------RLKLDNPP------EPVLTREQFSCRRRRSKSPGGFRKL 133
+D+ +G+L+ I R L+ P EP+L + R+RR P F K+
Sbjct: 135 EMDDTEIGLLSAICLICGDRQDLEEPDRVEKLQEPLLEALKIYARKRRPDKPHMFPKM 192
>gnl|CDD|218029 pfam04328, DUF466, Protein of unknown function (DUF466). Small
bacterial protein of unknown function. Structural
modelling suggests this domain may bind nucleic acids.
Length = 64
Score = 26.1 bits (58), Expect = 3.1
Identities = 9/26 (34%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 106 NPPEPVLTREQFSCRR--RRSKSPGG 129
+P +PV++ +F R R +PGG
Sbjct: 36 HPDKPVMSEREFFRERQDARYGNPGG 61
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 27.5 bits (62), Expect = 3.5
Identities = 9/28 (32%), Positives = 14/28 (50%)
Query: 43 RSKAVILVANKTDLVRCRVVTDEDGKDM 70
+ +++V NK DLV T E+ K
Sbjct: 288 AGRGIVIVVNKWDLVEEDEATMEEFKKK 315
>gnl|CDD|206747 cd01854, YjeQ_EngC, Ribosomal interacting GTPase YjeQ/EngC, a
circularly permuted subfamily of the Ras GTPases. YjeQ
(YloQ in Bacillus subtilis) is a ribosomal small
subunit-dependent GTPase; hence also known as RsgA.
YjeQ is a late-stage ribosomal biogenesis factor
involved in the 30S subunit maturation, and it
represents a protein family whose members are broadly
conserved in bacteria and have been shown to be
essential to the growth of E. coli and B. subtilis.
Proteins of the YjeQ family contain all sequence motifs
typical of the vast class of P-loop-containing GTPases,
but show a circular permutation, with a G4-G1-G3
pattern of motifs as opposed to the regular G1-G3-G4
pattern seen in most GTPases. All YjeQ family proteins
display a unique domain architecture, which includes an
N-terminal OB-fold RNA-binding domain, the central
permuted GTPase domain, and a zinc knuckle-like
C-terminal cysteine domain.
Length = 211
Score = 27.4 bits (62), Expect = 3.7
Identities = 13/49 (26%), Positives = 21/49 (42%), Gaps = 8/49 (16%)
Query: 47 VILVANKTDLVRCRVVTDEDGKDMATAY---DCKFIETSVGINHNVDEL 92
++V NK DL V DE+ +++ Y + S +DEL
Sbjct: 36 PVIVLNKADL-----VDDEELEELLEIYEKLGYPVLAVSAKTGEGLDEL 79
>gnl|CDD|100093 cd05800, PGM_like2, This PGM-like (phosphoglucomutase-like) protein
of unknown function belongs to the
alpha-D-phosphohexomutase superfamily and is found in
both archaea and bacteria. The
alpha-D-phosphohexomutases include several related
enzymes that catalyze a reversible intramolecular
phosphoryl transfer on their sugar substrates. Other
members of this superfamily include phosphoglucosamine
mutase (PNGM), phosphoacetylglucosamine mutase (PAGM),
the bacterial phosphomannomutase ManB, the bacterial
phosphoglucosamine mutase GlmM, and the bifunctional
phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of
these enzymes has four structural domains (subdomains)
with a centrally located active site formed by four
loops, one from each subdomain. All four subdomains are
included in this alignment model.
Length = 461
Score = 27.1 bits (61), Expect = 4.9
Identities = 12/60 (20%), Positives = 22/60 (36%), Gaps = 11/60 (18%)
Query: 36 LWKKDSIRSKAVILVANKTDLVRCRVVTDEDGKDMATAYDCKFIETSVGINHNVDELLVG 95
L + +R V V+ T L+ +A + ET VG + +++L
Sbjct: 271 LLENKGLRGPVVKTVST-THLID----------RIAEKHGLPVYETPVGFKYIAEKMLEE 319
>gnl|CDD|128635 smart00341, HRDC, Helicase and RNase D C-terminal. Hypothetical
role in nucleic acid binding. Mutations in the HRDC
domain cause human disease.
Length = 81
Score = 25.7 bits (57), Expect = 5.5
Identities = 10/44 (22%), Positives = 18/44 (40%), Gaps = 7/44 (15%)
Query: 28 VAEQCLQALWKKDSIRSKAVILVANKTDLVRCRVVTDEDGKDMA 71
+ L+ L + R + +A + D+ V+ DE MA
Sbjct: 3 RQLRLLRRLRQ---WRDE----IARREDVPPYFVLPDETLIKMA 39
>gnl|CDD|131014 TIGR01959, nuoF_fam, NADH-quinone oxidoreductase, F subunit. This
model describes the F chain of complexes that resemble
NADH-quinone oxidoreductases. The electron acceptor is a
quinone, ubiquinone, in mitochondria and most bacteria,
including Escherichia coli, where the recommended gene
symbol is nuoF. This family does not have any members in
chloroplast or cyanobacteria, where the quinone may be
plastoquinone and NADH may be replaced by NADPH, nor in
Methanosarcina, where NADH is replaced by F420H2 [Energy
metabolism, Electron transport].
Length = 411
Score = 26.9 bits (60), Expect = 5.5
Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 7/37 (18%)
Query: 29 AEQCLQALWKKDSIR-------SKAVILVANKTDLVR 58
AEQ L A DS+ + AVI++ T +V+
Sbjct: 290 AEQHLDAPMDYDSLAAAGSMLGTGAVIVMDESTCMVK 326
>gnl|CDD|233986 TIGR02729, Obg_CgtA, Obg family GTPase CgtA. This model describes
a univeral, mostly one-gene-per-genome GTP-binding
protein that associates with ribosomal subunits and
appears to play a role in ribosomal RNA maturation. This
GTPase, related to the nucleolar protein Obg, is
designated CgtA in bacteria. Mutations in this gene are
pleiotropic, but it appears that effects on cellular
functions such as chromosome partition may be secondary
to the effect on ribosome structure. Recent work done in
Vibrio cholerae shows an essential role in the stringent
response, in which RelA-dependent ability to synthesize
the alarmone ppGpp is required for deletion of this
GTPase to be lethal [Protein synthesis, Other].
Length = 329
Score = 27.0 bits (61), Expect = 5.7
Identities = 15/57 (26%), Positives = 24/57 (42%), Gaps = 1/57 (1%)
Query: 45 KAVILVANKTDLVRCRVVTDEDGKDMATAYDCKFIETSVGINHNVDELLVGILTQIR 101
K I+V NK DL+ + +E K++ A S +DELL + +
Sbjct: 274 KPRIVVLNKIDLLDEEEL-EELLKELKEALGKPVFPISALTGEGLDELLYALAELLE 329
>gnl|CDD|237546 PRK13889, PRK13889, conjugal transfer relaxase TraA; Provisional.
Length = 988
Score = 27.0 bits (60), Expect = 6.0
Identities = 21/93 (22%), Positives = 33/93 (35%), Gaps = 16/93 (17%)
Query: 50 VANKTDLVRCRVVTDEDGKDMATAYD-------------CKFIETSVGINHN-VDELLVG 95
A++ LVR ++ + KDMA+ Y+ F E I V E L G
Sbjct: 706 FADRDRLVR--TLSRDRAKDMASDYERADPAQSYAERRGITFRERVAEIVRKIVPEKLRG 763
Query: 96 ILTQIRLKLDNPPEPVLTREQFSCRRRRSKSPG 128
+ +RL P R + + +P
Sbjct: 764 MFDGLRLPDPVPGPEAGRRPERESAAATTDAPA 796
>gnl|CDD|206718 cd04151, Arl1, ADP ribosylation factor 1 (Arf1). Arl1 subfamily.
Arl1 (Arf-like 1) localizes to the Golgi complex, where
it is believed to recruit effector proteins to the
trans-Golgi network. Like most members of the Arf
family, Arl1 is myristoylated at its N-terminal helix
and mutation of the myristoylation site disrupts Golgi
targeting. In humans, the Golgi-localized proteins
golgin-97 and golgin-245 have been identified as Arl1
effectors. Golgins are large coiled-coil proteins found
in the Golgi, and these golgins contain a C-terminal
GRIP domain, which is the site of Arl1 binding.
Additional Arl1 effectors include the GARP
(Golgi-associated retrograde protein)/VFT (Vps53)
vesicle-tethering complex and Arfaptin 2. Arl1 is not
required for exocytosis, but appears necessary for
trafficking from the endosomes to the Golgi. In
Drosophila zygotes, mutation of Arl1 is lethal, and in
the host-bloodstream form of Trypanosoma brucei, Arl1 is
essential for viability.
Length = 158
Score = 26.2 bits (58), Expect = 6.1
Identities = 10/49 (20%), Positives = 24/49 (48%)
Query: 8 YETPHGFIIVYSTIDLASFHVAEQCLQALWKKDSIRSKAVILVANKTDL 56
Y I V + D +++ L A+ +++ ++ +++ ANK D+
Sbjct: 64 YSNTDAIIYVVDSTDRDRLGISKSELHAMLEEEELKDAVLLVFANKQDM 112
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 26.6 bits (60), Expect = 6.3
Identities = 14/57 (24%), Positives = 20/57 (35%)
Query: 45 KAVILVANKTDLVRCRVVTDEDGKDMATAYDCKFIETSVGINHNVDELLVGILTQIR 101
K ILV NK DL+ ++ A S +DELL + +
Sbjct: 272 KPRILVLNKIDLLDEEEEREKRAALELAALGGPVFLISAVTGEGLDELLRALWELLE 328
>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 = 26.4 bits (59), Expect = 6.5
Identities = 20/62 (32%), Positives = 27/62 (43%), Gaps = 6/62 (9%)
Query: 45 KAVILVANKTDLV----RCRVVTDEDGKDMATAYDCKFIETSVGINHNVDELLVGILTQI 100
KA +LV NKTDL V D K++ + I T++ +DE L I Q
Sbjct: 143 KADLLVINKTDLAPYVGADLEVMARDAKEVNP--EAPIIFTNLKTGEGLDEWLRFIEPQA 200
Query: 101 RL 102
L
Sbjct: 201 LL 202
>gnl|CDD|220781 pfam10493, Rod_C, Rough deal protein C-terminal region. Rod, the
Rough deal protein, displays a dynamic intracellular
staining pattern, localising first to kinetochores in
pro-metaphase, but moving to kinetochore microtubules at
metaphase. Early in anaphase the protein is once again
restricted to the kinetochores, where it persists until
the end of telophase. This behaviour is in all respects
similar to that described for ZW10, and indeed the two
proteins function together, localisation of each
depending upon the other. These two proteins are found
at the kinetochore in complex with a third, Zwilch, in
both flies and humans. The C-terminus is the most
conserved part of the protein. During pro-metaphase, the
ZW10-Rod complex, dynein/dynactin, and Mad2 all
accumulate on unattached kinetochores; microtubule
capture leads to Mad2 depletion as it is carried off by
dynein/dynactin; ZW10-Rod complex accumulation
continues, replenishing kinetochore dynein. The
continuing recruitment of the ZW10-Rod complex during
metaphase may serve to maintain adequate dynein/dynactin
complex on kinetochores for assisting chromatid movement
during anaphase. The ZW10-Rod complex acts as a bridge
whose association with Zwint-1 links Mad1 and Mad2,
components that are directly responsible for generating
the diffusible 'wait anaphase' signal, to a structural,
inner kinetochore complex containing Mis12 and
KNL-1AF15q14, the last of which has been proved to be
essential for kinetochore assembly in C. elegans.
Removal of ZW10 or Rod inactivates the mitotic
checkpoint.
Length = 555
Score = 26.7 bits (59), Expect = 6.9
Identities = 9/37 (24%), Positives = 17/37 (45%), Gaps = 2/37 (5%)
Query: 18 YSTIDLASFHVAEQ--CLQALWKKDSIRSKAVILVAN 52
+ I + F + L+ LW+ + KA+ +VA
Sbjct: 356 FLNITVEKFESTPKEGLLKGLWQNHAHEPKALEVVAE 392
>gnl|CDD|211710 TIGR02035, D_Ser_am_lyase, D-serine ammonia-lyase. This family
consists of D-serine ammonia-lyase (EC 4.3.1.18), a
pyridoxal-phosphate enzyme that converts D-serine to
pyruvate and NH3. This enzyme is also called D-serine
dehydratase and D-serine deaminase and was previously
designated EC 4.2.1.14. It is homologous to an enzyme
that acts on threonine and may itself act weakly on
threonine [Energy metabolism, Amino acids and amines].
Length = 431
Score = 26.7 bits (59), Expect = 7.1
Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 3/44 (6%)
Query: 37 WKKDSIRSKAVILVANKTDLVRCRVVTDEDGKDMATAYDCKFIE 80
WKKD +RS V +V ++D V +E K + +C FI+
Sbjct: 189 WKKDKLRSHGVTVVEYESDY---GVAVEEGRKAAQSDPNCYFID 229
>gnl|CDD|100092 cd05799, PGM2, This CD includes PGM2 (phosphoglucomutase 2) and
PGM2L1 (phosphoglucomutase 2-like 1). The mammalian PGM2
is thought to be a phosphopentomutase that catalyzes the
conversion of the nucleoside breakdown products,
ribose-1-phosphate and deoxyribose-1-phosphate to the
corresponding 5-phosphopentoses. PGM2L1 is thought to
catalyze the 1,3-bisphosphoglycerate-dependent synthesis
of glucose 1,6-bisphosphate and other
aldose-bisphosphates that serve as cofactors for several
sugar phosphomutases and possibly also as regulators of
glycolytic enzymes. PGM2 and PGM2L1 belong to the
alpha-D-phosphohexomutase superfamily which includes
several related enzymes that catalyze a reversible
intramolecular phosphoryl transfer on their sugar
substrates. Other members of this superfamily include
phosphoglucosamine mutase (PNGM),
phosphoacetylglucosamine mutase (PAGM), the bacterial
phosphomannomutase ManB, the bacterial
phosphoglucosamine mutase GlmM, and the bifunctional
phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of
these enzymes has four domains with a centrally located
active site formed by four loops, one from each domain.
All four domains are included in this alignment model.
Length = 487
Score = 26.7 bits (60), Expect = 7.2
Identities = 15/56 (26%), Positives = 24/56 (42%), Gaps = 9/56 (16%)
Query: 29 AEQCLQALWKKDSIRSKAVILVANKTDLVRCRVVTDEDGKDMATAYDCKFIETSVG 84
A+ L+ +K + VI+ KT +V+ E + +A Y K ET G
Sbjct: 290 ADYLLEQRKEKGKLPKNPVIV---KT------IVSSELLRKIAKKYGVKVEETLTG 336
>gnl|CDD|224122 COG1201, Lhr, Lhr-like helicases [General function prediction
only].
Length = 814
Score = 26.8 bits (60), Expect = 7.4
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 43 RSKAVILVANKTDLVRCRVVTD 64
SK +I+ ++ DL+ C V+ D
Sbjct: 352 VSKGIIIAEDRDDLLECLVLAD 373
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase. The
Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that generally show sequence
conservation in the region between the Walker A and B
motifs (G1 and G3 box motifs), to the exclusion of other
GTPases. TrmE is ubiquitous in bacteria and is a
widespread mitochondrial protein in eukaryotes, but is
absent from archaea. The yeast member of TrmE family,
MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family.
Length = 161
Score = 26.1 bits (58), Expect = 8.4
Identities = 17/57 (29%), Positives = 20/57 (35%), Gaps = 3/57 (5%)
Query: 45 KAVILVANKTDLV--RCRVVTDEDGKDMATAYDCKFIETSVGINHNVDELLVGILTQ 99
K V+LV NK DLV + K D I S +DEL I
Sbjct: 105 KPVLLVLNKIDLVPESEEEELLRERKLELL-PDLPVIAVSALPGEGIDELRKKIAEL 160
>gnl|CDD|206674 cd01887, IF2_eIF5B, Initiation Factor 2 (IF2)/ eukaryotic
Initiation Factor 5B (eIF5B) family. IF2/eIF5B
contribute to ribosomal subunit joining and function as
GTPases that are maximally activated by the presence of
both ribosomal subunits. As seen in other GTPases,
IF2/IF5B undergoes conformational changes between its
GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess
three characteristic segments, including a divergent
N-terminal region followed by conserved central and
C-terminal segments. This core region is conserved among
all known eukaryotic and archaeal IF2/eIF5Bs and
eubacterial IF2s.
Length = 169
Score = 25.9 bits (58), Expect = 8.7
Identities = 13/62 (20%), Positives = 20/62 (32%), Gaps = 9/62 (14%)
Query: 47 VILVANKTDLVRCRVVTDEDGKDMATAY---------DCKFIETSVGINHNVDELLVGIL 97
+I+ NK D E K+ + D + S +D+LL IL
Sbjct: 104 IIVAINKIDKPYGTEADPERVKNELSELGLVGEEWGGDVSIVPISAKTGEGIDDLLEAIL 163
Query: 98 TQ 99
Sbjct: 164 LL 165
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 26.3 bits (59), Expect = 8.7
Identities = 14/48 (29%), Positives = 18/48 (37%), Gaps = 3/48 (6%)
Query: 47 VILVANKTDLVRCRVVTDEDGKDMATA-YDCKFIETSVGINHNVDELL 93
I+V NK DL+ E YD +E S +DEL
Sbjct: 114 PIIVLNKIDLLDDLEEARELLALYRAIGYDV--LELSAKEGEGLDELK 159
>gnl|CDD|235799 PRK06419, rpl15p, 50S ribosomal protein L15P; Reviewed.
Length = 148
Score = 25.9 bits (58), Expect = 9.1
Identities = 10/19 (52%), Positives = 12/19 (63%), Gaps = 4/19 (21%)
Query: 120 RRRRSKSPGGFRKLRGHRT 138
R++ KS RKLRG RT
Sbjct: 2 IRKKKKS----RKLRGSRT 16
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 26.0 bits (58), Expect = 9.7
Identities = 12/50 (24%), Positives = 23/50 (46%)
Query: 8 YETPHGFIIVYSTIDLASFHVAEQCLQALWKKDSIRSKAVILVANKTDLV 57
+ I V + D A++ L AL ++ + ++++ANK DL
Sbjct: 79 FPNTDAVIFVVDSADRDRIEEAKEELHALLNEEELADAPLLILANKQDLP 128
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.135 0.403
Gapped
Lambda K H
0.267 0.0736 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,168,437
Number of extensions: 717691
Number of successful extensions: 677
Number of sequences better than 10.0: 1
Number of HSP's gapped: 643
Number of HSP's successfully gapped: 110
Length of query: 167
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 77
Effective length of database: 6,945,742
Effective search space: 534822134
Effective search space used: 534822134
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.0 bits)