RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1873
(157 letters)
>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 = 260 bits (667), Expect = 2e-90
Identities = 97/155 (62%), Positives = 120/155 (77%), Gaps = 13/155 (8%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYSIFP 60
+G RSVGKSSL++QFV+G FV+SY PTIENTF K Q+Y L++VDTAGQDEYSI P
Sbjct: 7 LGSRSVGKSSLTVQFVEGHFVESYYPTIENTFSKIITYKGQEYHLEIVDTAGQDEYSILP 66
Query: 61 AQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVG 120
+YS+ IHGY+LVYS+TS KSFEVV+++YDK+LDM GK SVPIVLVG
Sbjct: 67 QKYSIGIHGYILVYSVTSRKSFEVVKVIYDKILDMLGK-------------ESVPIVLVG 113
Query: 121 NKKDLHMERMISYDEGKRLAESWKAGFVEASAKQD 155
NK DLHMER +S +EGK+LAESW A F+E+SAK++
Sbjct: 114 NKSDLHMERQVSAEEGKKLAESWGAAFLESSAKEN 148
>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 = 187 bits (477), Expect = 8e-62
Identities = 67/154 (43%), Positives = 94/154 (61%), Gaps = 13/154 (8%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYSIFP 60
+G VGKS+L+IQFV G FVD YDPTIE+++ K ++ + L ++DTAGQ+E+S
Sbjct: 8 LGGGGVGKSALTIQFVQGHFVDEYDPTIEDSYRKQIEIDGEVCLLDILDTAGQEEFSAMR 67
Query: 61 AQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVG 120
QY G++LVYSIT +SFE + +++L + + VPIVLVG
Sbjct: 68 DQYMRTGEGFLLVYSITDRQSFEEIAKFREQILRVKDR-------------DDVPIVLVG 114
Query: 121 NKKDLHMERMISYDEGKRLAESWKAGFVEASAKQ 154
NK DL ER++S +EGK LA W F+E SAK+
Sbjct: 115 NKCDLENERVVSTEEGKELARQWGCPFLETSAKE 148
>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 = 186 bits (476), Expect = 1e-61
Identities = 66/154 (42%), Positives = 95/154 (61%), Gaps = 13/154 (8%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYSIFP 60
+G VGKS+L+IQF+ G FVD YDPTIE+++ K ++ + L ++DTAGQ+E+S
Sbjct: 6 LGSGGVGKSALTIQFIQGHFVDDYDPTIEDSYRKQIEIDGEVCLLDILDTAGQEEFSAMR 65
Query: 61 AQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVG 120
QY G++LVYSIT +SFE ++ +++L + + VPIVLVG
Sbjct: 66 DQYMRTGEGFLLVYSITDRQSFEEIKKFREQILRVKDR-------------DDVPIVLVG 112
Query: 121 NKKDLHMERMISYDEGKRLAESWKAGFVEASAKQ 154
NK DL ER++S +EGK LA W F+E SAK+
Sbjct: 113 NKCDLESERVVSTEEGKELARQWGCPFLETSAKE 146
>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 = 178 bits (455), Expect = 2e-58
Identities = 68/155 (43%), Positives = 100/155 (64%), Gaps = 13/155 (8%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYSIFP 60
+G VGKS+L+I+FV G+FV+ YDPTIE+++ K ++ + Y L ++DTAGQ+E+S
Sbjct: 5 LGAGGVGKSALTIRFVSGEFVEEYDPTIEDSYRKQIVVDGETYTLDILDTAGQEEFSAMR 64
Query: 61 AQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVG 120
QY + G++LVYSITS +SFE ++ + +++L + K VPIVLVG
Sbjct: 65 DQYIRNGDGFILVYSITSRESFEEIKNIREQILRVKDK-------------EDVPIVLVG 111
Query: 121 NKKDLHMERMISYDEGKRLAESWKAGFVEASAKQD 155
NK DL ER +S +EG+ LAE W F+E SAK +
Sbjct: 112 NKCDLENERQVSTEEGEALAEEWGCPFLETSAKTN 146
>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 = 152 bits (386), Expect = 5e-48
Identities = 57/157 (36%), Positives = 87/157 (55%), Gaps = 15/157 (9%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTI-ENTFVKTTRMNNQDYDLKLVDTAGQDEYSIF 59
+G VGKSSL I+F +F + Y PTI + + KT ++ + L++ DTAGQ+ +
Sbjct: 5 VGDGGVGKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAGQERFRAL 64
Query: 60 PAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLV 119
Y G++LVY ITS SFE V+ +++L + +VPIVLV
Sbjct: 65 RPLYYRGAQGFLLVYDITSRDSFENVKKWLEEILRHADE--------------NVPIVLV 110
Query: 120 GNKKDLHMERMISYDEGKRLAESWKAGFVEASAKQDD 156
GNK DL +R++S +EG+ LA+ F+E SAK ++
Sbjct: 111 GNKCDLEDQRVVSTEEGEALAKELGLPFMETSAKTNE 147
>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 = 124 bits (313), Expect = 8e-37
Identities = 60/148 (40%), Positives = 90/148 (60%), Gaps = 11/148 (7%)
Query: 6 VGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYSIFPAQYSM 65
VGK++L+IQ FV++YDPTIE+++ K ++ Q L+++DTAGQ+EY+ Q+
Sbjct: 10 VGKTALTIQLCLNHFVETYDPTIEDSYRKQVVVDGQPCMLEVLDTAGQEEYTALRDQWIR 69
Query: 66 DIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVGNKKDL 125
+ G++LVYSITS +FE V+ + Q VK ++ + VPI++VGNK D
Sbjct: 70 EGEGFILVYSITSRSTFERVERFRE---------QIQRVKDESA--ADVPIMIVGNKCDK 118
Query: 126 HMERMISYDEGKRLAESWKAGFVEASAK 153
ER +S +EG LA F+EASAK
Sbjct: 119 VYEREVSTEEGAALARRLGCEFIEASAK 146
>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 = 122 bits (310), Expect = 2e-36
Identities = 53/154 (34%), Positives = 84/154 (54%), Gaps = 17/154 (11%)
Query: 5 SVGKSSLSIQFVDGQFVDSYDPTIENTF-VKTTRMNNQDYDLKLVDTAGQDEY-SIFPAQ 62
VGK+SL ++FVD +F ++Y TI F KT ++ + L++ DTAGQ+ + SI +
Sbjct: 10 GVGKTSLLLRFVDNKFSENYKSTIGVDFKSKTIEVDGKKVKLQIWDTAGQERFRSITSSY 69
Query: 63 YSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVGNK 122
Y HG +LVY +T+ +SFE + ++L + ++PI+LVGNK
Sbjct: 70 YR-GAHGAILVYDVTNRESFENLDKWLNELKEY--------------APPNIPIILVGNK 114
Query: 123 KDLHMERMISYDEGKRLAESWKAGFVEASAKQDD 156
DL ER +S +E ++ A+ F E SAK +
Sbjct: 115 SDLEDERQVSTEEAQQFAKENGLLFFETSAKTGE 148
>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 = 123 bits (309), Expect = 2e-36
Identities = 60/153 (39%), Positives = 93/153 (60%), Gaps = 13/153 (8%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYSIFP 60
+G VGKS+L++QFV G FV+ YDPTIE+++ K ++ Q L+++DTAG ++++
Sbjct: 7 LGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDGQQCMLEILDTAGTEQFTAMR 66
Query: 61 AQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVG 120
Y + G+VLVYSIT+ +F +Q L +++L VK VP++LVG
Sbjct: 67 DLYMKNGQGFVLVYSITAQSTFNDLQDLREQIL---------RVKD----TEDVPMILVG 113
Query: 121 NKKDLHMERMISYDEGKRLAESWKAGFVEASAK 153
NK DL ER++ ++G+ LA W F+E SAK
Sbjct: 114 NKCDLEDERVVGKEQGQNLARQWGCAFLETSAK 146
>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 = 120 bits (304), Expect = 1e-35
Identities = 59/149 (39%), Positives = 86/149 (57%), Gaps = 13/149 (8%)
Query: 6 VGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYSIFPAQYSM 65
VGKS+L+IQF+ FV YDPTIE+++ K ++ Q L ++DTAGQ+E+S QY
Sbjct: 13 VGKSALTIQFIQSYFVTDYDPTIEDSYTKQCEIDGQWARLDILDTAGQEEFSAMREQYMR 72
Query: 66 DIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVGNKKDL 125
G++LV+S+T SFE V + ++L VK P++LVGNK DL
Sbjct: 73 TGEGFLLVFSVTDRGSFEEVDKFHTQIL---------RVKD----RDEFPMILVGNKADL 119
Query: 126 HMERMISYDEGKRLAESWKAGFVEASAKQ 154
+R +S +EG+ LA K ++E SAK
Sbjct: 120 EHQRQVSREEGQELARQLKIPYIETSAKD 148
>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 = 120 bits (302), Expect = 2e-35
Identities = 58/149 (38%), Positives = 86/149 (57%), Gaps = 14/149 (9%)
Query: 6 VGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYSIFPAQYSM 65
VGKS+L+IQ + FVD YDPTIE+++ K ++ + L ++DTAGQ+EYS QY
Sbjct: 12 VGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMR 71
Query: 66 DIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVGNKKDL 125
G++ V++I S KSFE + +++ VK VP+VLVGNK DL
Sbjct: 72 TGEGFLCVFAINSRKSFEDIHTYREQIK---------RVKD----SDDVPMVLVGNKCDL 118
Query: 126 HMERMISYDEGKRLAESWKAGFVEASAKQ 154
R +S +G+ LA+S+ ++E SAK
Sbjct: 119 A-ARTVSTRQGQDLAKSYGIPYIETSAKT 146
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 121 bits (304), Expect = 2e-35
Identities = 64/154 (41%), Positives = 92/154 (59%), Gaps = 13/154 (8%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYSIFP 60
+G VGKS+L+IQF+ F+D YDPTIE+++ K ++ + L ++DTAGQ+EYS
Sbjct: 11 VGGGGVGKSALTIQFIQNHFIDEYDPTIEDSYRKQCVIDEETCLLDILDTAGQEEYSAMR 70
Query: 61 AQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVG 120
QY G++ VYSITS SFE + +++L + K VP++LVG
Sbjct: 71 DQYMRTGQGFLCVYSITSRSSFEEIASFREQILRVKDK-------------DRVPMILVG 117
Query: 121 NKKDLHMERMISYDEGKRLAESWKAGFVEASAKQ 154
NK DL ER +S EG+ LA+S+ F+E SAKQ
Sbjct: 118 NKCDLDSERQVSTGEGQELAKSFGIPFLETSAKQ 151
>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 = 118 bits (296), Expect = 2e-34
Identities = 55/155 (35%), Positives = 93/155 (60%), Gaps = 13/155 (8%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYSIFP 60
+G VGKS+L++QFV G F++ YDPTIE+ + K +++ L+++DTAG ++++
Sbjct: 7 LGSGGVGKSALTVQFVSGTFIEKYDPTIEDFYRKEIEVDSSPSVLEILDTAGTEQFASMR 66
Query: 61 AQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVG 120
Y + G+++VYS+ + ++F+ ++ + D+++ + G VPI+LVG
Sbjct: 67 DLYIKNGQGFIVVYSLVNQQTFQDIKPMRDQIVRVKG-------------YEKVPIILVG 113
Query: 121 NKKDLHMERMISYDEGKRLAESWKAGFVEASAKQD 155
NK DL ER +S EG+ LAE W F+E SAK
Sbjct: 114 NKVDLESEREVSSAEGRALAEEWGCPFMETSAKSK 148
>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 = 115 bits (290), Expect = 1e-33
Identities = 61/154 (39%), Positives = 97/154 (62%), Gaps = 14/154 (9%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYSIFP 60
+G VGKS+L++QFV G FVD YDPTIE+++ K ++ Q L+++DTAG ++++
Sbjct: 7 LGSGGVGKSALTVQFVQGIFVDKYDPTIEDSYRKQIEVDCQQCMLEILDTAGTEQFTAMR 66
Query: 61 AQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVG 120
Y + G+ LVYSIT+ +SF +Q L +++L +++++ VP++LVG
Sbjct: 67 DLYIKNGQGFALVYSITAQQSFNDLQDLREQIL----RVKDT---------EDVPMILVG 113
Query: 121 NKKDLHMERMISYDEGKRLAESW-KAGFVEASAK 153
NK DL ER++S +EG+ LA W F+E SAK
Sbjct: 114 NKCDLEDERVVSKEEGQNLARQWGNCPFLETSAK 147
>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 = 112 bits (282), Expect = 3e-32
Identities = 56/154 (36%), Positives = 94/154 (61%), Gaps = 14/154 (9%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYSIFP 60
+G VGKS+L++QFV F++SYDPTIE+++ K ++ + DL+++DTAG ++++
Sbjct: 7 LGAGGVGKSALTVQFVQNVFIESYDPTIEDSYRKQVEIDGRQCDLEILDTAGTEQFTAMR 66
Query: 61 AQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVG 120
Y G++LVYS+TS S + L +++L +I++S +VP+VLVG
Sbjct: 67 ELYIKSGQGFLLVYSVTSEASLNELGELREQVL----RIKDS---------DNVPMVLVG 113
Query: 121 NKKDLHMERMISYDEGKRLAESW-KAGFVEASAK 153
NK DL +R +S ++G L++ W F E SA+
Sbjct: 114 NKADLEDDRQVSREDGVSLSQQWGNVPFYETSAR 147
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 108 bits (273), Expect = 7e-31
Identities = 55/154 (35%), Positives = 79/154 (51%), Gaps = 17/154 (11%)
Query: 2 GYRSVGKSSLSIQFVDGQFVDSYDPTIENTF-VKTTRMNNQDYDLKLVDTAGQDEY-SIF 59
G VGKSSL +F DG+F + Y TI F KT ++ + L++ DTAGQ+ + SI
Sbjct: 7 GDSGVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIEVDGKRVKLQIWDTAGQERFRSIT 66
Query: 60 PAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLV 119
+ Y G +LVY IT+ +SFE ++ +L + +V I+LV
Sbjct: 67 SS-YYRGAVGALLVYDITNRESFENLENWLKELREYAS--------------PNVVIMLV 111
Query: 120 GNKKDLHMERMISYDEGKRLAESWKAGFVEASAK 153
GNK DL +R +S +E + AE F E SAK
Sbjct: 112 GNKSDLEEQRQVSREEAEAFAEEHGLPFFETSAK 145
>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 = 104 bits (260), Expect = 5e-29
Identities = 51/148 (34%), Positives = 86/148 (58%), Gaps = 13/148 (8%)
Query: 6 VGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYSIFPAQYSM 65
VGKS+L++QF+ +FV+ Y+PT +++ K ++ ++ L ++DTAGQ++Y+ Y
Sbjct: 11 VGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEVQLNILDTAGQEDYAAIRDNYFR 70
Query: 66 DIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVGNKKDL 125
G++LV+SIT +SF + +++L + +VP++LVGNK DL
Sbjct: 71 SGEGFLLVFSITDMESFTALAEFREQILRVKED-------------DNVPLLLVGNKCDL 117
Query: 126 HMERMISYDEGKRLAESWKAGFVEASAK 153
+R +S +E LAE W +VE SAK
Sbjct: 118 EDKRQVSVEEAANLAEQWGVNYVETSAK 145
>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 = 101 bits (252), Expect = 7e-28
Identities = 58/158 (36%), Positives = 86/158 (54%), Gaps = 17/158 (10%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYSIFP 60
G VGKSSL ++FV G F +SY PTIE+T+ + + L++ DT G + FP
Sbjct: 7 FGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCSKSICTLQITDTTGSHQ---FP 63
Query: 61 AQYSMDI---HGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIV 117
A + I H ++LVYSITS +S E ++ +Y+ + ++ G + +PI+
Sbjct: 64 AMQRLSISKGHAFILVYSITSKQSLEELKPIYELICEIKGNN-----------LEKIPIM 112
Query: 118 LVGNKKDLHMERMISYDEGKRLAESWKAGFVEASAKQD 155
LVGNK D R +S EG LA +W F+E SAK +
Sbjct: 113 LVGNKCDESPSREVSSSEGAALARTWNCAFMETSAKTN 150
>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 = 98.8 bits (246), Expect = 6e-27
Identities = 50/152 (32%), Positives = 84/152 (55%), Gaps = 13/152 (8%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYSIFP 60
+G VGKS++++QF+ F D +DPTIE+ + R++N+ L ++DTAGQ E++
Sbjct: 8 LGAGGVGKSAVTMQFISHSFPDYHDPTIEDAYKTQARIDNEPALLDILDTAGQAEFTAMR 67
Query: 61 AQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVG 120
QY G+++ YS+T SF+ + +L+ ++ +P+VLVG
Sbjct: 68 DQYMRCGEGFIICYSVTDRHSFQEAS-EFKELITRVRLTED------------IPLVLVG 114
Query: 121 NKKDLHMERMISYDEGKRLAESWKAGFVEASA 152
NK DL +R ++ +EG+ LA + F E SA
Sbjct: 115 NKVDLEQQRQVTTEEGRNLAREFNCPFFETSA 146
>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 = 97.3 bits (243), Expect = 2e-26
Identities = 56/154 (36%), Positives = 85/154 (55%), Gaps = 17/154 (11%)
Query: 2 GYRSVGKSSLSIQFVDGQFVDSYDPTIENTFV-KTTRMNNQDYDLKLVDTAGQDEY-SIF 59
G +SVGK+S+ +F+ F + Y TI F+ KT ++++ L+L DTAGQ+ + S+
Sbjct: 7 GDQSVGKTSIITRFMYDTFDNQYQATIGIDFLSKTMYVDDKTVRLQLWDTAGQERFRSLI 66
Query: 60 PAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLV 119
P+ Y D V+VY IT+ +SF+ D + D G + V IVLV
Sbjct: 67 PS-YIRDSSVAVVVYDITNRQSFDNTDKWIDDVRDERG--------------NDVIIVLV 111
Query: 120 GNKKDLHMERMISYDEGKRLAESWKAGFVEASAK 153
GNK DL +R +S +EG++ A+ A F+E SAK
Sbjct: 112 GNKTDLSDKRQVSTEEGEKKAKENNAMFIETSAK 145
>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 = 97.3 bits (243), Expect = 2e-26
Identities = 50/152 (32%), Positives = 78/152 (51%), Gaps = 15/152 (9%)
Query: 6 VGKSSLSIQFVDGQFVDSYDPTIENTFV-KTTRMNNQDYDLKLVDTAGQDEYSIFPAQYS 64
VGK+SL +++V+ +F + ++ T + +F KT + + DL + DTAGQ+ Y Y
Sbjct: 11 VGKTSLVLRYVENKFNEKHESTTQASFFQKTVNIGGKRIDLAIWDTAGQERYHALGPIYY 70
Query: 65 MDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVGNKKD 124
D G +LVY IT SF+ V+ +L M G ++ +V+VGNK D
Sbjct: 71 RDADGAILVYDITDADSFQKVKKWIKELKQMRGN--------------NISLVIVGNKID 116
Query: 125 LHMERMISYDEGKRLAESWKAGFVEASAKQDD 156
L +R++S E + A+S A E SAK
Sbjct: 117 LERQRVVSKSEAEEYAKSVGAKHFETSAKTGK 148
>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 = 93.9 bits (234), Expect = 4e-25
Identities = 48/156 (30%), Positives = 80/156 (51%), Gaps = 14/156 (8%)
Query: 2 GYRSVGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQD-EYSIFP 60
G VGKS+L+++F+ +F+ Y+P +E+ + + ++ + L++ DT GQ
Sbjct: 6 GASGVGKSALTVRFLTKRFIGEYEPNLESLYSRQVTIDGEQVSLEIQDTPGQQQNEDPES 65
Query: 61 AQYSMD-IHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLV 119
+ S+ G+VLVYSIT SF+VV L ++ +P++LV
Sbjct: 66 LERSLRWADGFVLVYSITDRSSFDVVSQLLQL------------IREIKKRDGEIPVILV 113
Query: 120 GNKKDLHMERMISYDEGKRLAESWKAGFVEASAKQD 155
GNK DL R +S +EG++LA F E SA ++
Sbjct: 114 GNKADLLHSRQVSTEEGQKLALELGCLFFEVSAAEN 149
>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 = 93.0 bits (232), Expect = 8e-25
Identities = 53/155 (34%), Positives = 77/155 (49%), Gaps = 19/155 (12%)
Query: 2 GYRSVGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLV--DTAGQDEY-SI 58
G SVGKSS+ ++FV +F ++ + TI F+ T +N D +K DTAGQ+ Y S+
Sbjct: 8 GDSSVGKSSIVLRFVKNEFSENQESTIGAAFL-TQTVNLDDTTVKFEIWDTAGQERYRSL 66
Query: 59 FPAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVL 118
P Y ++VY ITS +SFE + +L P + V I L
Sbjct: 67 APMYYR-GAAAAIVVYDITSEESFEKAKSWVKEL----------QEHGPPNIV----IAL 111
Query: 119 VGNKKDLHMERMISYDEGKRLAESWKAGFVEASAK 153
GNK DL +R +S +E + A+ F+E SAK
Sbjct: 112 AGNKADLESKRQVSTEEAQEYADENGLLFMETSAK 146
>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 = 91.9 bits (229), Expect = 3e-24
Identities = 48/151 (31%), Positives = 76/151 (50%), Gaps = 15/151 (9%)
Query: 6 VGKSSLSIQFVDGQFVDSYDPTIENTF-VKTTRMNNQDYDLKLVDTAGQDEYSIFPAQYS 64
VGKS L ++F + F S+ TI F ++T ++ + L++ DTAGQ+ + Y
Sbjct: 14 VGKSCLLLRFSEDSFNPSFISTIGIDFKIRTIELDGKKIKLQIWDTAGQERFRTITTSYY 73
Query: 65 MDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVGNKKD 124
G +LVY IT KSFE ++ ++ S V +LVGNK D
Sbjct: 74 RGAMGIILVYDITDEKSFENIKNWM------------RNIDEHAS--EDVERMLVGNKCD 119
Query: 125 LHMERMISYDEGKRLAESWKAGFVEASAKQD 155
+ +R++S +EG+ LA + F+E SAK +
Sbjct: 120 MEEKRVVSKEEGEALAREYGIKFLETSAKAN 150
>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 = 88.8 bits (221), Expect = 4e-23
Identities = 49/168 (29%), Positives = 80/168 (47%), Gaps = 34/168 (20%)
Query: 2 GYRSVGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEY-SIFP 60
G +VGK+ L I + +F Y PT+ + + ++ + +L L DTAGQ+EY + P
Sbjct: 7 GDGAVGKTCLLISYTTNKFPTEYVPTVFDNYSANVTVDGKQVNLGLWDTAGQEEYDRLRP 66
Query: 61 AQYSM-DIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVK--SPTSCVSSVPIV 117
Y D+ ++L +S+ S SFE V+ + +K P VPI+
Sbjct: 67 LSYPQTDV--FLLCFSVDSPSSFENVKTKW-----------YPEIKHYCPN-----VPII 108
Query: 118 LVGNKKDL-----------HMERMISYDEGKRLAESWKA-GFVEASAK 153
LVG K DL ++ I+ +EG++LA+ A ++E SA
Sbjct: 109 LVGTKIDLRDDGNTLKKLEKKQKPITPEEGEKLAKEIGAVKYMECSAL 156
>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 = 84.7 bits (210), Expect = 2e-21
Identities = 47/154 (30%), Positives = 77/154 (50%), Gaps = 15/154 (9%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTF-VKTTRMNNQDYDLKLVDTAGQDEYSIF 59
+G VGKS L ++F D + +SY TI F ++T ++ + L++ DTAGQ+ +
Sbjct: 8 IGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTVKLQIWDTAGQERFRTI 67
Query: 60 PAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLV 119
+ Y HG ++VY +T +SF V + L + + +V +LV
Sbjct: 68 TSSYYRGAHGIIIVYDVTDQESFNNV----KQWLQEIDRYASENVNK----------LLV 113
Query: 120 GNKKDLHMERMISYDEGKRLAESWKAGFVEASAK 153
GNK DL ++++ Y E K A+ F+E SAK
Sbjct: 114 GNKCDLTDKKVVDYTEAKEFADELGIPFLETSAK 147
>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 = 83.0 bits (205), Expect = 8e-21
Identities = 52/156 (33%), Positives = 84/156 (53%), Gaps = 15/156 (9%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTF-VKTTRMNNQDYDLKLVDTAGQDEYSIF 59
+G SVGK+S ++ D F ++ T+ F VKT N++ L++ DTAGQ+ Y
Sbjct: 7 IGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVYRNDKRIKLQIWDTAGQERYRTI 66
Query: 60 PAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLV 119
Y G++L+Y IT+ +SF VQ D + +I+ S + ++LV
Sbjct: 67 TTAYYRGAMGFILMYDITNEESFNAVQ-------DWSTQIKTYSWDNAQ-------VILV 112
Query: 120 GNKKDLHMERMISYDEGKRLAESWKAGFVEASAKQD 155
GNK D+ ER++S + G++LA+ F EASAK++
Sbjct: 113 GNKCDMEDERVVSAERGRQLADQLGFEFFEASAKEN 148
>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 = 82.7 bits (205), Expect = 8e-21
Identities = 46/157 (29%), Positives = 71/157 (45%), Gaps = 15/157 (9%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTF-VKTTRMNNQDYDLKLVDTAGQDEYSIF 59
+G VGKSSL ++F D F + TI F VKT ++ + L + DTAGQ+ +
Sbjct: 6 IGDSGVGKSSLLLRFTDDTFDEDLSSTIGVDFKVKTVTVDGKKVKLAIWDTAGQERFRTL 65
Query: 60 PAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLV 119
+ Y G +LVY +T +F+ + ++L S +LV
Sbjct: 66 TSSYYRGAQGVILVYDVTRRDTFDNLDTWLNEL-------------DTYSTNPDAVKMLV 112
Query: 120 GNKKDLHMERMISYDEGKRLAESWKAGFVEASAKQDD 156
GNK D R ++ +EG++ A F+E SAK
Sbjct: 113 GNKIDKE-NREVTREEGQKFARKHNMLFIETSAKTRI 148
>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 = 84.4 bits (209), Expect = 1e-20
Identities = 47/158 (29%), Positives = 83/158 (52%), Gaps = 12/158 (7%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYSIFP 60
+G VGK+++ +F+ G+F + Y PTIE+ K + + Y L ++DT+G FP
Sbjct: 6 LGASKVGKTAIVSRFLGGRFEEQYTPTIEDFHRKLYSIRGEVYQLDILDTSG---NHPFP 62
Query: 61 AQYSMDIHG---YVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIV 117
A + I ++LV+S+ + +SFE V L +++L+ ++N + K +P+V
Sbjct: 63 AMRRLSILTGDVFILVFSLDNRESFEEVCRLREQILETKSCLKNKT-KEN----VKIPMV 117
Query: 118 LVGNKKDLHMERMISYDEGKRL-AESWKAGFVEASAKQ 154
+ GNK D R + DE ++L + E SAK+
Sbjct: 118 ICGNKADRDFPREVQRDEVEQLVGGDENCAYFEVSAKK 155
>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 = 82.2 bits (203), Expect = 3e-20
Identities = 53/159 (33%), Positives = 77/159 (48%), Gaps = 20/159 (12%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYSIFP 60
MG VGK++L +F+ F + T+E K + + ++DT+G YS FP
Sbjct: 5 MGAAGVGKTALIQRFLYDTFEPKHRRTVEELHSKEYEVAGVKVTIDILDTSGS--YS-FP 61
Query: 61 AQYSMDIH---GYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIV 117
A + I + LVYS+ +SFE V+ L +++L+ VK VPIV
Sbjct: 62 AMRKLSIQNGDAFALVYSVDDPESFEEVKRLREEILE---------VKEDKF----VPIV 108
Query: 118 LVGNKKDLHMERMISYDEGKRLAE-SWKAGFVEASAKQD 155
+VGNK D ER + + E W GFVEASAK +
Sbjct: 109 VVGNKIDSLAERQVEAADALSTVELDWNNGFVEASAKDN 147
>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 = 82.1 bits (203), Expect = 5e-20
Identities = 42/155 (27%), Positives = 68/155 (43%), Gaps = 18/155 (11%)
Query: 1 MGYRSVGKSSLSIQFVDG-QFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYSIF 59
+G VGKSSL+ F G +Y+ + ++T+ +T ++ ++ L + D Q++
Sbjct: 6 LGDSGVGKSSLANIFTAGVYEDSAYEASGDDTYERTVSVDGEEATLVVYDHWEQEDGMWL 65
Query: 60 PAQYSMDIHGYVLVYSITSHKSFEVVQ--ILYDKLLDMTGKIQNSSVKSPTSCVSSVPIV 117
YV+VYS+T SFE + + +PI+
Sbjct: 66 EDSCMQVGDAYVIVYSVTDRSSFEKASELRIQLRRARQA---------------EDIPII 110
Query: 118 LVGNKKDLHMERMISYDEGKRLAESWKAGFVEASA 152
LVGNK DL R +S EG+ A + F+E SA
Sbjct: 111 LVGNKSDLVRSREVSVQEGRACAVVFDCKFIETSA 145
>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 = 80.7 bits (199), Expect = 1e-19
Identities = 46/163 (28%), Positives = 72/163 (44%), Gaps = 21/163 (12%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTI-ENTFVKTTRMNNQDYDLKLVDTAGQDEYSIF 59
+G VGK+++ QF+ +F + Y PT + ++ + YDL ++D Y
Sbjct: 6 LGAPGVGKTAIVRQFLAQEFPEEYIPTEHRRLYRPAVVLSGRVYDLHILDVPNMQRYPGT 65
Query: 60 PAQYSMD--------IHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCV 111
Q MD ++LVY I S SF V++L ++L+ +
Sbjct: 66 AGQEWMDPRFRGLRNSRAFILVYDICSPDSFHYVKLLRQQILETR-----------PAGN 114
Query: 112 SSVPIVLVGNKKDLHMERMISYDEGKRLA-ESWKAGFVEASAK 153
PIV+VGNK+D R L +SWK G++E SAK
Sbjct: 115 KEPPIVVVGNKRDQQRHRFAPRHVLSVLVRKSWKCGYLECSAK 157
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 81.2 bits (200), Expect = 1e-19
Identities = 49/170 (28%), Positives = 72/170 (42%), Gaps = 31/170 (18%)
Query: 2 GYRSVGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRM-NNQDYDLKLVDTAGQDEY-SIF 59
G VGK++L + V +F + Y PTI N T ++ L+L DTAGQ+EY S+
Sbjct: 12 GDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQEEYRSLR 71
Query: 60 PAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLV 119
P Y +G ++VY T +S + + + + L VPI+LV
Sbjct: 72 PEYYRGA-NGILIVYDSTLRESSDELTEEWLEELREL-------------APDDVPILLV 117
Query: 120 GNKKDLHMERMISYDEGKRLA---------------ESWKAGFVEASAKQ 154
GNK DL E+ S + +L E +E SAK
Sbjct: 118 GNKIDLFDEQSSSEEILNQLNREVVLLVLAPKAVLPEVANPALLETSAKS 167
>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 = 77.2 bits (191), Expect = 1e-18
Identities = 52/153 (33%), Positives = 68/153 (44%), Gaps = 25/153 (16%)
Query: 6 VGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLV-----DTAGQDEY-SIF 59
VGKS+L +F +F TI F TR D K + DTAGQ+ Y +I
Sbjct: 14 VGKSNLLSRFTRNEFNLDSKSTIGVEF--ATR--TIQIDGKTIKAQIWDTAGQERYRAIT 69
Query: 60 PAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLV 119
A Y G +LVY IT +FE V+ +L D S++ I+LV
Sbjct: 70 SAYYR-GAVGALLVYDITKKSTFENVERWLKELRDHAD--------------SNIVIMLV 114
Query: 120 GNKKDLHMERMISYDEGKRLAESWKAGFVEASA 152
GNK DL R + +E K AE F+E SA
Sbjct: 115 GNKSDLRHLRAVPTEEAKAFAEKNGLSFIETSA 147
>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 = 76.9 bits (190), Expect = 2e-18
Identities = 44/164 (26%), Positives = 80/164 (48%), Gaps = 29/164 (17%)
Query: 5 SVGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEY-SIFPAQY 63
+VGK+ L I + F + Y PT+ + ++ + +L L DTAGQ++Y + P Y
Sbjct: 8 AVGKTCLLIVYTTNAFPEDYVPTVFENYSADVEVDGKPVELGLWDTAGQEDYDRLRPLSY 67
Query: 64 SMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVGNKK 123
D +++ +S+ S SFE V+ +K ++++ +VPI+LVG K
Sbjct: 68 P-DTDVFLICFSVDSPASFENVK---EK---WYPEVKHFC--------PNVPIILVGTKL 112
Query: 124 DLH--------MERM----ISYDEGKRLAESWKA-GFVEASAKQ 154
DL + + ++Y++G+ LA+ A ++E SA
Sbjct: 113 DLRNDKSTLEELSKKKQEPVTYEQGQALAKRIGAVKYLECSALT 156
>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 = 76.7 bits (189), Expect = 2e-18
Identities = 49/154 (31%), Positives = 76/154 (49%), Gaps = 15/154 (9%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTF-VKTTRMNNQDYDLKLVDTAGQDEYSIF 59
+G VGKS L +QF D +F +D TI F + ++ + L++ DTAGQ+ +
Sbjct: 10 IGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQESFRSI 69
Query: 60 PAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLV 119
Y G +LVY IT ++F + + Q+S+ S++ I+L+
Sbjct: 70 TRSYYRGAAGALLVYDITRRETFNHLTSWLEDAR------QHSN--------SNMTIMLI 115
Query: 120 GNKKDLHMERMISYDEGKRLAESWKAGFVEASAK 153
GNK DL R +SY+EG+ A F+E SAK
Sbjct: 116 GNKCDLESRREVSYEEGEAFAREHGLIFMETSAK 149
>gnl|CDD|206662 cd01870, RhoA_like, Ras homology family A (RhoA)-like includes
RhoA, RhoB and RhoC. The RhoA subfamily consists of
RhoA, RhoB, and RhoC. RhoA promotes the formation of
stress fibers and focal adhesions, regulating cell
shape, attachment, and motility. RhoA can bind to
multiple effector proteins, thereby triggering different
downstream responses. In many cell types, RhoA mediates
local assembly of the contractile ring, which is
necessary for cytokinesis. RhoA is vital for muscle
contraction; in vascular smooth muscle cells, RhoA plays
a key role in cell contraction, differentiation,
migration, and proliferation. RhoA activities appear to
be elaborately regulated in a time- and space-dependent
manner to control cytoskeletal changes. Most Rho
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. RhoA and RhoC are observed
only in geranylgeranylated forms; however, RhoB can be
present in palmitoylated, farnesylated, and
geranylgeranylated forms. RhoA and RhoC are highly
relevant for tumor progression and invasiveness;
however, RhoB has recently been suggested to be a tumor
suppressor. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 175
Score = 76.7 bits (189), Expect = 2e-18
Identities = 52/164 (31%), Positives = 83/164 (50%), Gaps = 29/164 (17%)
Query: 7 GKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYS-IFPAQYSM 65
GK+ L I F QF + Y PT+ +V ++ + +L L DTAGQ++Y + P Y
Sbjct: 13 GKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLRPLSYP- 71
Query: 66 DIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVGNKKDL 125
D ++ +SI S S E + +K T ++++ C +VPI+LVGNKKDL
Sbjct: 72 DTDVILMCFSIDSPDSLENIP---EK---WTPEVKH-------FC-PNVPIILVGNKKDL 117
Query: 126 H--------MERM----ISYDEGKRLAESWKA-GFVEASAKQDD 156
+ +M + +EG+ +AE A G++E SAK +
Sbjct: 118 RNDEHTIRELAKMKQEPVKPEEGRAMAEKIGAFGYLECSAKTKE 161
>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 = 77.1 bits (190), Expect = 4e-18
Identities = 51/158 (32%), Positives = 82/158 (51%), Gaps = 15/158 (9%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIE-NTFVKTTRMN-NQDYDLKLVDTAGQDEYSI 58
+G +VGKSSL +F +G+F + DPT+ + F + + L+L DTAGQ+ +
Sbjct: 8 IGDSTVGKSSLLKRFTEGRFAEVSDPTVGVDFFSRLIEIEPGVRIKLQLWDTAGQERFRS 67
Query: 59 FPAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVL 118
Y + G +LV+ IT+ +SFE V D L + IQ P V +L
Sbjct: 68 ITRSYYRNSVGVLLVFDITNRESFEHVH---DWLEEARSHIQ------PHRPV----FIL 114
Query: 119 VGNKKDLHMERMISYDEGKRLAESWKAGFVEASAKQDD 156
VG+K DL +R ++ +E ++LA+ ++E SA+ D
Sbjct: 115 VGHKCDLESQRQVTREEAEKLAKDLGMKYIETSARTGD 152
>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 = 72.9 bits (179), Expect = 7e-17
Identities = 48/155 (30%), Positives = 73/155 (47%), Gaps = 17/155 (10%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTF-VKTTRMNNQDYDLKLVDTAGQDEYSIF 59
+G GKS L QF++ +F + TI F + + + L++ DTAGQ+ +
Sbjct: 6 IGSAGTGKSCLLHQFIENKFKQDSNHTIGVEFGSRVVNVGGKSVKLQIWDTAGQERFRSV 65
Query: 60 PAQYSMDIHGYVLVYSITSHKSFE-VVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVL 118
Y G +LVY ITS +SF + L D ++ SP + I+L
Sbjct: 66 TRSYYRGAAGALLVYDITSRESFNALTNWLTDA----------RTLASP-----DIVIIL 110
Query: 119 VGNKKDLHMERMISYDEGKRLAESWKAGFVEASAK 153
VGNKKDL +R +++ E R A+ F+E SA
Sbjct: 111 VGNKKDLEDDREVTFLEASRFAQENGLLFLETSAL 145
>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 = 72.5 bits (178), Expect = 8e-17
Identities = 49/158 (31%), Positives = 75/158 (47%), Gaps = 18/158 (11%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTFVKTT---RMNNQDYDLKLVDTAGQDEYS 57
+G +VGKSS+ +FV G F Y TI F++ R +++D L L DTAGQ+E+
Sbjct: 6 VGNGNVGKSSMIQRFVKGIFTKDYKKTIGVDFLEKQIFLRQSDEDVRLMLWDTAGQEEFD 65
Query: 58 IFPAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIV 117
Y +LV+S T +SFE ++ +K+ G I P+V
Sbjct: 66 AITKAYYRGAQACILVFSTTDRESFEAIESWKEKVEAECGDI---------------PMV 110
Query: 118 LVGNKKDLHMERMISYDEGKRLAESWKAGFVEASAKQD 155
LV K DL + +I+ +E + LA+ + S K D
Sbjct: 111 LVQTKIDLLDQAVITNEEAEALAKRLQLPLFRTSVKDD 148
>gnl|CDD|206704 cd04132, Rho4_like, Ras homology family 4 (Rho4) of small guanosine
triphosphatases (GTPases)-like. Rho4 is a GTPase that
controls septum degradation by regulating secretion of
Eng1 or Agn1 during cytokinesis. Rho4 also plays a role
in cell morphogenesis. Rho4 regulates septation and cell
morphology by controlling the actin cytoskeleton and
cytoplasmic microtubules. The localization of Rho4 is
modulated by Rdi1, which may function as a GDI, and by
Rga9, which is believed to function as a GAP. In S.
pombe, both Rho4 deletion and Rho4 overexpression result
in a defective cell wall, suggesting a role for Rho4 in
maintaining cell wall integrity. Most Rho proteins
contain a lipid modification site at the C-terminus,
with a typical sequence motif CaaX, where a = an
aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins.
Length = 197
Score = 72.8 bits (179), Expect = 1e-16
Identities = 44/166 (26%), Positives = 72/166 (43%), Gaps = 34/166 (20%)
Query: 6 VGKSSLSIQFVDGQFVDSYDPTI-ENTFVKTTRMNNQDYDLKLVDTAGQDEYS-IFPAQY 63
GK+ L + + G F + Y PT+ EN N + +L L DTAGQ++Y + P Y
Sbjct: 14 CGKTCLLMVYAQGSFPEEYVPTVFENYVTTLQVPNGKIIELALWDTAGQEDYDRLRPLSY 73
Query: 64 SMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSP--TSCVSSVPIVLVGN 121
D+ ++ YS+ + S + V+ + P PIVLVG
Sbjct: 74 P-DVDVILICYSVDNPTSLDNVEDKW----------------YPEVNHFCPGTPIVLVGL 116
Query: 122 KKDL--HMERM----------ISYDEGKRLAESWKA-GFVEASAKQ 154
K DL + ++ ++G+ +A+S A ++E SAK
Sbjct: 117 KTDLRKDKNSVSKLRAQGLEPVTPEQGESVAKSIGAVAYIECSAKL 162
>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 = 72.2 bits (177), Expect = 2e-16
Identities = 47/156 (30%), Positives = 77/156 (49%), Gaps = 16/156 (10%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTF-VKTTRMNNQDYDLKLVDTAGQDEYSIF 59
+G VGKSSL ++F D F SY TI F ++T +N + L++ DTAGQ+ +
Sbjct: 12 IGDSGVGKSSLLLRFADNTFSGSYITTIGVDFKIRTVEINGERVKLQIWDTAGQERFRTI 71
Query: 60 PAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLV 119
+ Y HG ++VY +T+ +SF V+ + L +I+ + V VLV
Sbjct: 72 TSTYYRGTHGVIVVYDVTNGESFVNVK----RWLQ---EIEQN--------CDDVCKVLV 116
Query: 120 GNKKDLHMERMISYDEGKRLAESWKAGFVEASAKQD 155
GNK D +++ ++ + A E SAK++
Sbjct: 117 GNKNDDPERKVVETEDAYKFAGQMGISLFETSAKEN 152
>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 = 70.2 bits (172), Expect = 6e-16
Identities = 43/162 (26%), Positives = 59/162 (36%), Gaps = 26/162 (16%)
Query: 1 MGYRSVGKSSLSIQFVDGQFV---DSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYS 57
+G VGKSSL + G+ D T + ++ L LVDT G DE+
Sbjct: 3 VGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDV-YVKELDKGKVKLVLVDTPGLDEFG 61
Query: 58 IFP-----AQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVS 112
+LV T +S E ++L + L G
Sbjct: 62 GLGREELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLRKEGI-------------- 107
Query: 113 SVPIVLVGNKKDLHMERMISYDE-GKRLAESWKAGFVEASAK 153
PI+LVGNK DL ER + + LA+ E SAK
Sbjct: 108 --PIILVGNKIDLLEEREVEELLRLEELAKILGVPVFEVSAK 147
>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 = 70.2 bits (172), Expect = 7e-16
Identities = 45/156 (28%), Positives = 74/156 (47%), Gaps = 16/156 (10%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTF-VKTTRMNNQDYDLKLVDTAGQDEYSIF 59
+G +VGK+ + +F G F + TI F +KT + + L++ DTAGQ+ +
Sbjct: 9 IGDSNVGKTCVVQRFKSGTFSERQGNTIGVDFTMKTLEIQGKRVKLQIWDTAGQERFRTI 68
Query: 60 PAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLV 119
Y +G ++ Y IT SFE V +++ S+V ++L+
Sbjct: 69 TQSYYRSANGAIIAYDITRRSSFESVPHWIEEVEKYGA--------------SNVVLLLI 114
Query: 120 GNKKDLHMERMISYDEGKRLAESWKAGFV-EASAKQ 154
GNK DL +R + ++E LAE + V E SAK+
Sbjct: 115 GNKCDLEEQREVLFEEACTLAEHYGILAVLETSAKE 150
>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 = 69.6 bits (171), Expect = 1e-15
Identities = 51/163 (31%), Positives = 82/163 (50%), Gaps = 22/163 (13%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTFV-KTTRMNNQDYDLKLVDTAGQDEY-SI 58
+G VGK+SL Q+V+ +F + Y TI F+ K ++++ L++ DTAGQ+ + S+
Sbjct: 6 LGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVTVDDRLVTLQIWDTAGQERFQSL 65
Query: 59 FPAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVL 118
A Y VLVY +T+ KSFE + D+ L +S + P + P V+
Sbjct: 66 GVAFYR-GADCCVLVYDVTNPKSFESLDSWRDEFL------IQASPRDP----ENFPFVV 114
Query: 119 VGNKKDLHMERMISYDEGKRLAESWKAG-----FVEASAKQDD 156
+GNK DL +R +S + A+ W + E SAK+
Sbjct: 115 LGNKIDLEEKRQVS----TKKAQQWCKSKGNIPYFETSAKEAI 153
>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 = 69.9 bits (171), Expect = 1e-15
Identities = 46/155 (29%), Positives = 80/155 (51%), Gaps = 16/155 (10%)
Query: 1 MGYRSVGKSSLSIQFVDGQFV-DSYDPTIENTFV-KTTRMNNQDYDLKLVDTAGQDEYSI 58
+G VGK+ L ++F DG F+ S+ T+ F K ++ L++ DTAGQ+ +
Sbjct: 6 VGDSGVGKTCLLVRFKDGAFLAGSFIATVGIQFTNKVVTVDGVKVKLQIWDTAGQERFRS 65
Query: 59 FPAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVL 118
Y D H +L+Y +T+ SF+ ++ ++L+ V I+L
Sbjct: 66 VTHAYYRDAHALLLLYDVTNKSSFDNIRAWLTEILEYAQS--------------DVVIML 111
Query: 119 VGNKKDLHMERMISYDEGKRLAESWKAGFVEASAK 153
+GNK D+ ER++ ++G+RLA+ + F+E SAK
Sbjct: 112 LGNKADMSGERVVKREDGERLAKEYGVPFMETSAK 146
>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 = 69.1 bits (169), Expect = 2e-15
Identities = 46/157 (29%), Positives = 72/157 (45%), Gaps = 15/157 (9%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTF-VKTTRMNNQDYDLKLVDTAGQDEYSIF 59
+G VGKS L QF + +F+ TI F + +N Q L++ DTAGQ+ +
Sbjct: 8 IGDMGVGKSCLLHQFTEKKFMADCPHTIGVEFGTRIIEVNGQKIKLQIWDTAGQERFRAV 67
Query: 60 PAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLV 119
Y G ++VY IT ++ + L D ++V I L+
Sbjct: 68 TRSYYRGAAGALMVYDITRRSTYNHLSSW---LTDARNLTNPNTV-----------IFLI 113
Query: 120 GNKKDLHMERMISYDEGKRLAESWKAGFVEASAKQDD 156
GNK DL +R ++Y+E K+ A+ F+E SAK +
Sbjct: 114 GNKADLEAQRDVTYEEAKQFADENGLLFLECSAKTGE 150
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 70.1 bits (171), Expect = 2e-15
Identities = 49/154 (31%), Positives = 77/154 (50%), Gaps = 14/154 (9%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTF-VKTTRMNNQDYDLKLVDTAGQDEYSIF 59
+G VGKSSL + F+ V+ PTI F +K + + L + DTAGQ+ +
Sbjct: 20 IGDSGVGKSSLLVSFISSS-VEDLAPTIGVDFKIKQLTVGGKRLKLTIWDTAGQERFRTL 78
Query: 60 PAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLV 119
+ Y + G +LVY +T ++F + ++ K +++ Q+ CV +LV
Sbjct: 79 TSSYYRNAQGIILVYDVTRRETFTNLSDVWGKEVELYSTNQD--------CVK----MLV 126
Query: 120 GNKKDLHMERMISYDEGKRLAESWKAGFVEASAK 153
GNK D ER +S +EG LA+ F+E SAK
Sbjct: 127 GNKVDRESERDVSREEGMALAKEHGCLFLECSAK 160
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 69.2 bits (169), Expect = 4e-15
Identities = 51/154 (33%), Positives = 80/154 (51%), Gaps = 15/154 (9%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTF-VKTTRMNNQDYDLKLVDTAGQDEYSIF 59
+G VGKS L +QF D +F +D TI F + ++N+ L++ DTAGQ+ +
Sbjct: 12 IGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDNKPIKLQIWDTAGQESFRSI 71
Query: 60 PAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLV 119
Y G +LVY IT ++F L L D Q+++ +++ I+L+
Sbjct: 72 TRSYYRGAAGALLVYDITRRETF---NHLASWLEDAR---QHAN--------ANMTIMLI 117
Query: 120 GNKKDLHMERMISYDEGKRLAESWKAGFVEASAK 153
GNK DL R +S +EG++ A+ F+EASAK
Sbjct: 118 GNKCDLAHRRAVSTEEGEQFAKEHGLIFMEASAK 151
>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 = 67.8 bits (166), Expect = 4e-15
Identities = 39/155 (25%), Positives = 65/155 (41%), Gaps = 15/155 (9%)
Query: 1 MGYRSVGKSSLSIQFVDGQ-FVDSYDPTIENTFVKTT-RMNNQDYDLKLVDTAGQDEYSI 58
+G +VGKS+L + + + + Y P +V T + + Y L+DTAGQ++Y
Sbjct: 7 VGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAGQEDYDA 66
Query: 59 FPAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVL 118
Y + + V+ I V + + L T +I + S VPI+L
Sbjct: 67 IRRLYYRAVESSLRVFDIVIL-----VLDVEEILEKQTKEIIH-------HAESGVPIIL 114
Query: 119 VGNKKDLHMERMISYDEGKRLAESWKAGFVEASAK 153
VGNK DL ++ A+ + SA+
Sbjct: 115 VGNKIDLRDAKL-KTHVAFLFAKLNGEPIIPLSAE 148
>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 = 67.1 bits (164), Expect = 1e-14
Identities = 45/158 (28%), Positives = 75/158 (47%), Gaps = 17/158 (10%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTF-VKTTRMNNQDYDLKLVDTAGQDEY--S 57
+G +VGK+ L+ +F G+F + + TI F +T ++ + ++L DTAGQ+ + S
Sbjct: 8 IGDSNVGKTCLTYRFCAGRFPERTEATIGVDFRERTVEIDGERIKVQLWDTAGQERFRKS 67
Query: 58 IFPAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIV 117
+ Y ++H V VY +T+ SF + I+ S + VP +
Sbjct: 68 MVQ-HYYRNVHAVVFVYDVTNMASFH----------SLPSWIEECE---QHSLPNEVPRI 113
Query: 118 LVGNKKDLHMERMISYDEGKRLAESWKAGFVEASAKQD 155
LVGNK DL + + D +R A++ E SAK
Sbjct: 114 LVGNKCDLREQIQVPTDLAQRFADAHSMPLFETSAKDP 151
>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 = 66.8 bits (163), Expect = 2e-14
Identities = 43/157 (27%), Positives = 70/157 (44%), Gaps = 15/157 (9%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTF-VKTTRMNNQDYDLKLVDTAGQDEYSIF 59
+G VGK+ L +F G F TI F +KT + + L++ DTAGQ+ +
Sbjct: 13 IGNAGVGKTCLVRRFTQGLFPPGQGATIGVDFMIKTVEIKGEKIKLQIWDTAGQERFRSI 72
Query: 60 PAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLV 119
Y + +L Y IT +SF L + +I+ + + V +LV
Sbjct: 73 TQSYYRSANALILTYDITCEESF-------RCLPEWLREIEQYA-------NNKVITILV 118
Query: 120 GNKKDLHMERMISYDEGKRLAESWKAGFVEASAKQDD 156
GNK DL R +S + +++ ++E SAK+ D
Sbjct: 119 GNKIDLAERREVSQQRAEEFSDAQDMYYLETSAKESD 155
>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 = 66.2 bits (162), Expect = 2e-14
Identities = 47/153 (30%), Positives = 73/153 (47%), Gaps = 10/153 (6%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTF-VKTTRMNNQDYDLKLVDTAGQDEYSIF 59
MG VGKS + ++ +G+FV Y PTI + VK + N++ + D +G EY
Sbjct: 6 MGNSGVGKSCIIKRYCEGRFVSKYLPTIGIDYGVKKVSVRNKEVRVNFFDLSGHPEYLEV 65
Query: 60 PAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLV 119
++ D G +LVY +T +SFE + ++ G N ++ +V+
Sbjct: 66 RNEFYKDTQGVLLVYDVTDRQSFEALDSWLKEMKQEGGPHGNME---------NIVVVVC 116
Query: 120 GNKKDLHMERMISYDEGKRLAESWKAGFVEASA 152
NK DL R +S DEG+ AES + E SA
Sbjct: 117 ANKIDLTKHRAVSEDEGRLWAESKGFKYFETSA 149
>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 = 65.8 bits (160), Expect = 5e-14
Identities = 47/157 (29%), Positives = 79/157 (50%), Gaps = 16/157 (10%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTF-VKTTRMNNQDYDLKLVDTAGQDEYSIF 59
+G R VGK+SL +F D F ++ T+ F +KT + + L++ DTAGQ+ ++
Sbjct: 6 IGSRGVGKTSLMERFTDDTFCEACKSTVGVDFKIKTVELRGKKIRLQIWDTAGQERFNSI 65
Query: 60 PAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLV 119
+ Y G +LVY IT ++F+ + K + M K + + ++LV
Sbjct: 66 TSAYYRSAKGIILVYDITKKETFDDLP----KWMKMIDKYASEDAE----------LLLV 111
Query: 120 GNKKDLHMERMISYDEGKRLAESWKA-GFVEASAKQD 155
GNK D +R I+ +G++ A+ F EASAK +
Sbjct: 112 GNKLDCETDREITRQQGEKFAQQITGMRFCEASAKDN 148
>gnl|CDD|206702 cd04129, Rho2, Ras homology family 2 (Rho2) of small guanosine
triphosphatases (GTPases). Rho2 is a fungal GTPase that
plays a role in cell morphogenesis, control of cell wall
integrity, control of growth polarity, and maintenance
of growth direction. Rho2 activates the protein kinase C
homolog Pck2, and Pck2 controls Mok1, the major (1-3)
alpha-D-glucan synthase. Together with Rho1 (RhoA), Rho2
regulates the construction of the cell wall. Unlike
Rho1, Rho2 is not an essential protein, but its
overexpression is lethal. Most Rho proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for proper intracellular localization via
membrane attachment. As with other Rho family GTPases,
the GDP/GTP cycling is regulated by GEFs (guanine
nucleotide exchange factors), GAPs (GTPase-activating
proteins) and GDIs (guanine nucleotide dissociation
inhibitors).
Length = 190
Score = 63.7 bits (155), Expect = 3e-13
Identities = 45/162 (27%), Positives = 74/162 (45%), Gaps = 27/162 (16%)
Query: 7 GKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYS-IFPAQYSM 65
GK+SL F G+F + Y PT+ +V R++ + L L DTAGQ+EY + P YS
Sbjct: 13 GKTSLLYVFTLGEFPEEYHPTVFENYVTDCRVDGKPVQLALWDTAGQEEYERLRPLSYS- 71
Query: 66 DIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVGNKKDL 125
H ++ ++I + S E V+ + ++ +VP++LVG KKDL
Sbjct: 72 KAHVILIGFAIDTPDSLENVRTKW--------------IEEVRRYCPNVPVILVGLKKDL 117
Query: 126 HME----------RMISYDEGKRLAESWKA-GFVEASAKQDD 156
E + + K +A + A ++E SA +
Sbjct: 118 RQEAVAKGNYATDEFVPIQQAKLVARAIGAKKYMECSALTGE 159
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 63.8 bits (155), Expect = 5e-13
Identities = 45/153 (29%), Positives = 74/153 (48%), Gaps = 15/153 (9%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTF-VKTTRMNNQDYDLKLVDTAGQDEYSIF 59
+G VGKS++ +F +F TI F +T ++ + ++ DTAGQ+ Y
Sbjct: 18 IGDSGVGKSNILSRFTRNEFCLESKSTIGVEFATRTLQVEGKTVKAQIWDTAGQERYRAI 77
Query: 60 PAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLV 119
+ Y G +LVY IT ++F+ VQ +L D S++ I++
Sbjct: 78 TSAYYRGAVGALLVYDITKRQTFDNVQRWLRELRDHAD--------------SNIVIMMA 123
Query: 120 GNKKDLHMERMISYDEGKRLAESWKAGFVEASA 152
GNK DL+ R ++ ++G+ LAE F+E SA
Sbjct: 124 GNKSDLNHLRSVAEEDGQALAEKEGLSFLETSA 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 = 61.0 bits (148), Expect = 3e-12
Identities = 40/163 (24%), Positives = 73/163 (44%), Gaps = 24/163 (14%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTI-----------ENTFVKTTRMNNQDYDLKLVD 49
+G VGK++ ++ D +F + T+ + T L+L D
Sbjct: 10 LGDSGVGKTTFLYRYTDNKFNPKFITTVGIDFREKRVVYNSQGPDGTSGKAFRVHLQLWD 69
Query: 50 TAGQDEYSIFPAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTS 109
TAGQ+ + + D G++L++ +TS +SF V+ +L ++ ++P
Sbjct: 70 TAGQERFRSLTTAFFRDAMGFLLMFDLTSEQSFLNVRNWMSQLQ------AHAYCENPD- 122
Query: 110 CVSSVPIVLVGNKKDLHMERMISYDEGKRLAESWKAGFVEASA 152
IVL+GNK DL +R +S + + LA+ + + E SA
Sbjct: 123 ------IVLIGNKADLPDQREVSERQARELADKYGIPYFETSA 159
>gnl|CDD|206664 cd01874, Cdc42, cell division cycle 42 (Cdc42) is a small GTPase of
the Rho family. Cdc42 is an essential GTPase that
belongs to the Rho family of Ras-like GTPases. These
proteins act as molecular switches by responding to
exogenous and/or endogenous signals and relaying those
signals to activate downstream components of a
biological pathway. Cdc42 transduces signals to the
actin cytoskeleton to initiate and maintain polarized
growth and to mitogen-activated protein morphogenesis.
In the budding yeast Saccharomyces cerevisiae, Cdc42
plays an important role in multiple actin-dependent
morphogenetic events such as bud emergence,
mating-projection formation, and pseudohyphal growth. In
mammalian cells, Cdc42 regulates a variety of
actin-dependent events and induces the JNK/SAPK protein
kinase cascade, which leads to the activation of
transcription factors within the nucleus. Cdc42 mediates
these processes through interactions with a myriad of
downstream effectors, whose number and regulation we are
just starting to understand. In addition, Cdc42 has been
implicated in a number of human diseases through
interactions with its regulators and downstream
effectors. Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 175
Score = 60.7 bits (147), Expect = 3e-12
Identities = 46/167 (27%), Positives = 77/167 (46%), Gaps = 31/167 (18%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYS-IF 59
+G +VGK+ L I + +F Y PT+ + + T + + Y L L DTAGQ++Y +
Sbjct: 7 VGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTLGLFDTAGQEDYDRLR 66
Query: 60 PAQY-SMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVL 118
P Y D+ +++ +S+ S SFE ++ V T P +L
Sbjct: 67 PLSYPQTDV--FLVCFSVVSPSSFE--------------NVKEKWVPEITHHCPKTPFLL 110
Query: 119 VGNKKDL------------HMERMISYDEGKRLAESWKA-GFVEASA 152
VG + DL + ++ I+ + G++LA KA +VE SA
Sbjct: 111 VGTQIDLRDDPSTIEKLAKNKQKPITPETGEKLARDLKAVKYVECSA 157
>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 = 60.6 bits (147), Expect = 6e-12
Identities = 45/158 (28%), Positives = 68/158 (43%), Gaps = 13/158 (8%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTFV--KTTRMNNQDYDLKLVDTAGQDEYSI 58
+G + GK+SL +F F SY TI F + T + + L++ D GQ
Sbjct: 6 LGDGASGKTSLIRRFAQEGFGKSYKQTIGLDFFSRRITLPGSLNVTLQVWDIGGQQIGGK 65
Query: 59 FPAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVL 118
+Y LVY IT+ +SFE ++ L + K+ S P +VL
Sbjct: 66 MLDKYIYGAQAVCLVYDITNSQSFENLE----DWLSVVKKVNEESETKPK-------MVL 114
Query: 119 VGNKKDLHMERMISYDEGKRLAESWKAGFVEASAKQDD 156
VGNK DL R ++ ++ R A+ + SAK D
Sbjct: 115 VGNKTDLEHNRQVTAEKHARFAQENDMESIFVSAKTGD 152
>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 = 58.8 bits (142), Expect = 1e-11
Identities = 44/153 (28%), Positives = 72/153 (47%), Gaps = 15/153 (9%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTF-VKTTRMNNQDYDLKLVDTAGQDEYSIF 59
+G VGK+ L +F D +F S+ TI F +KT ++ +++ DTAGQ+ Y
Sbjct: 6 IGDSGVGKTCLLCRFTDNEFHSSHISTIGVDFKMKTIEVDGIKVRIQIWDTAGQERYQTI 65
Query: 60 PAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLV 119
QY G LVY I+S +S++ + K + + V+ L+
Sbjct: 66 TKQYYRRAQGIFLVYDISSERSYQHIM----KWVSDVDEYAPEGVQKI----------LI 111
Query: 120 GNKKDLHMERMISYDEGKRLAESWKAGFVEASA 152
GNK D +R + ++G +LA+ + F E SA
Sbjct: 112 GNKADEEQKRQVGDEQGNKLAKEYGMDFFETSA 144
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 59.0 bits (142), Expect = 1e-11
Identities = 45/135 (33%), Positives = 65/135 (48%), Gaps = 15/135 (11%)
Query: 20 FVDSYDPTIENTFV-KTTRMNNQDYDLKLVDTAGQDEYSIFPAQYSMDIHGYVLVYSITS 78
F ++Y TI F+ KT ++ L+L DTAGQ+ + Y D ++VY IT+
Sbjct: 5 FDNNYQSTIGIDFLSKTLYLDEGPVRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDITN 64
Query: 79 HKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVGNKKDLHMERMISYDEGKR 138
+SFE +L+ GK V I LVGNK DL R ++Y+EG +
Sbjct: 65 RQSFENTTKWIQDILNERGK--------------DVIIALVGNKTDLGDLRKVTYEEGMQ 110
Query: 139 LAESWKAGFVEASAK 153
A+ + F E SAK
Sbjct: 111 KAQEYNTMFHETSAK 125
>gnl|CDD|133330 cd04130, Wrch_1, Wnt-1 responsive Cdc42 homolog (Wrch-1) is a Rho
family GTPase similar to Cdc42. Wrch-1 (Wnt-1
responsive Cdc42 homolog) is a Rho family GTPase that
shares significant sequence and functional similarity
with Cdc42. Wrch-1 was first identified in mouse mammary
epithelial cells, where its transcription is upregulated
in Wnt-1 transformation. Wrch-1 contains N- and
C-terminal extensions relative to cdc42, suggesting
potential differences in cellular localization and
function. The Wrch-1 N-terminal extension contains
putative SH3 domain-binding motifs and has been shown to
bind the SH3 domain-containing protein Grb2, which
increases the level of active Wrch-1 in cells. Unlike
Cdc42, which localizes to the cytosol and perinuclear
membranes, Wrch-1 localizes extensively with the plasma
membrane and endosomes. The membrane association,
localization, and biological activity of Wrch-1 indicate
an atypical model of regulation distinct from other Rho
family GTPases. Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 173
Score = 57.4 bits (139), Expect = 4e-11
Identities = 41/161 (25%), Positives = 66/161 (40%), Gaps = 27/161 (16%)
Query: 5 SVGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYSIFPAQYS 64
+VGK+SL + + + Y PT + F ++ + L+L DTAGQDE+
Sbjct: 10 AVGKTSLIVSYTTNGYPTEYVPTAFDNFSVVVLVDGKPVRLQLCDTAGQDEFDKLRPLCY 69
Query: 65 MDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVGNKKD 124
D ++L +S+ + SF+ I + PI+LVG + D
Sbjct: 70 PDTDVFLLCFSVVNPSSFQ--------------NISEKWIPEIRKHNPKAPIILVGTQAD 115
Query: 125 L------------HMERMISYDEGKRLAESWKAG-FVEASA 152
L + E+ +S K LAE A ++E SA
Sbjct: 116 LRTDVNVLIQLARYGEKPVSQSRAKALAEKIGACEYIECSA 156
>gnl|CDD|206706 cd04134, Rho3, Ras homology family 3 (Rho3) of small guanosine
triphosphatases (GTPases). Rho3 is a member of the Rho
family found only in fungi. Rho3 is believed to regulate
cell polarity by interacting with the diaphanous/formin
family protein For3 to control both the actin
cytoskeleton and microtubules. Rho3 is also believed to
have a direct role in exocytosis that is independent of
its role in regulating actin polarity. The function in
exocytosis may be two-pronged: first, in the transport
of post-Golgi vesicles from the mother cell to the bud,
mediated by myosin (Myo2); second, in the docking and
fusion of vesicles to the plasma membrane, mediated by
an exocyst (Exo70) protein. Most Rho proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Rho proteins.
Length = 185
Score = 57.2 bits (138), Expect = 7e-11
Identities = 44/156 (28%), Positives = 68/156 (43%), Gaps = 23/156 (14%)
Query: 7 GKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYSIFPAQYSMD 66
GK+SL F G F Y+PT+ ++ ++ +L L DTAGQ+E+ + D
Sbjct: 12 GKTSLLNVFTRGYFPQVYEPTVFENYIHDIFVDGLAVELSLWDTAGQEEFDRLRSLSYAD 71
Query: 67 IHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVGNKKDLH 126
H +L +S+ + S E V ++ + V +VLV K DL
Sbjct: 72 THVIMLCFSVDNPDSLENV--------------ESKWLAEIRHHCPGVKLVLVALKCDLR 117
Query: 127 MER--------MISYDEGKRLAESWKAG-FVEASAK 153
R ISY+EG +A+ A ++E SAK
Sbjct: 118 EPRNERDRGTHTISYEEGLAVAKRINACRYLECSAK 153
>gnl|CDD|219856 pfam08477, Miro, Miro-like protein. Mitochondrial Rho proteins
(Miro-1, and Miro-2), are atypical Rho GTPases. They
have a unique domain organisation, with tandem
GTP-binding domains and two EF hand domains (pfam00036),
that may bind calcium. They are also larger than
classical small GTPases. It has been proposed that they
are involved in mitochondrial homeostasis and apoptosis.
Length = 116
Score = 55.5 bits (134), Expect = 1e-10
Identities = 30/118 (25%), Positives = 46/118 (38%), Gaps = 13/118 (11%)
Query: 6 VGKSSLSIQFVDGQFVDSYDPTIENT-FVKTTRMNNQDYDLKLVDTAGQDEYSIFPAQYS 64
GKSSL Q V G+F +T V T ++ L + D G++E +
Sbjct: 10 SGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREELKFEHIIFM 69
Query: 65 MDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVGNK 122
+LVY +T +S V L L ++ +P++LVGNK
Sbjct: 70 KWADAILLVYDLTDRESLNEVSRLIAWLPNLRKL------------GGKIPVILVGNK 115
>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 = 56.9 bits (138), Expect = 1e-10
Identities = 44/153 (28%), Positives = 65/153 (42%), Gaps = 14/153 (9%)
Query: 5 SVGKSSLSIQFVDGQFVDSYDPTIENTF-VKTTRM-NNQDYDLKLVDTAGQDEYSIFPAQ 62
VGK+S+ ++V G F Y TI F +K N L+L D AGQ+ +
Sbjct: 10 GVGKTSIIKRYVHGVFSQHYKATIGVDFALKVIEWDPNTVVRLQLWDIAGQERFGGMTRV 69
Query: 63 YSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVGNK 122
Y G ++V+ +T +FE V L +S V P +P +L+ NK
Sbjct: 70 YYKGAVGAIIVFDVTRPSTFEAVLKWKADL--------DSKVTLPNG--EPIPALLLANK 119
Query: 123 KDLHMERMI--SYDEGKRLAESWKAGFVEASAK 153
DL ER+ + E+ G+ E SAK
Sbjct: 120 CDLKKERLAKDPEQMDQFCKENGFIGWFETSAK 152
>gnl|CDD|133277 cd01875, RhoG, Ras homolog family, member G (RhoG) of small
guanosine triphosphatases (GTPases). RhoG is a GTPase
with high sequence similarity to members of the Rac
subfamily, including the regions involved in effector
recognition and binding. However, RhoG does not bind to
known Rac1 and Cdc42 effectors, including proteins
containing a Cdc42/Rac interacting binding (CRIB) motif.
Instead, RhoG interacts directly with Elmo, an upstream
regulator of Rac1, in a GTP-dependent manner and forms a
ternary complex with Dock180 to induce activation of
Rac1. The RhoG-Elmo-Dock180 pathway is required for
activation of Rac1 and cell spreading mediated by
integrin, as well as for neurite outgrowth induced by
nerve growth factor. Thus RhoG activates Rac1 through
Elmo and Dock180 to control cell morphology. RhoG has
also been shown to play a role in caveolar trafficking
and has a novel role in signaling the neutrophil
respiratory burst stimulated by G protein-coupled
receptor (GPCR) agonists. Most Rho proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Rho proteins.
Length = 191
Score = 56.6 bits (136), Expect = 1e-10
Identities = 47/171 (27%), Positives = 77/171 (45%), Gaps = 31/171 (18%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYSIFP 60
+G +VGK+ L I + F Y PT+ + + T ++ + L L DTAGQ+EY
Sbjct: 9 VGDGAVGKTCLLICYTTNAFPKEYIPTVFDNYSAQTAVDGRTVSLNLWDTAGQEEYDRLR 68
Query: 61 AQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSC--VSSVPIVL 118
+ +++ +SI S S+E V+ + P C +VPI+L
Sbjct: 69 TLSYPQTNVFIICFSIASPSSYENVRHKW----------------HPEVCHHCPNVPILL 112
Query: 119 VGNKKDLH-----MERM-------ISYDEGKRLAESWKA-GFVEASAKQDD 156
VG KKDL ++++ I+ +G LA+ A ++E SA D
Sbjct: 113 VGTKKDLRNDADTLKKLKEQGQAPITPQQGGALAKQIHAVKYLECSALNQD 163
>gnl|CDD|206707 cd04135, Tc10, Rho GTPase TC10 (Tc10). TC10 is a Rho family
protein that has been shown to induce microspike
formation and neurite outgrowth in vitro. Its expression
changes dramatically after peripheral nerve injury,
suggesting an important role in promoting axonal
outgrowth and regeneration. TC10 regulates translocation
of insulin-stimulated GLUT4 in adipocytes and has also
been shown to bind directly to Golgi COPI coat proteins.
GTP-bound TC10 in vitro can bind numerous potential
effectors. Depending on its subcellular localization and
distinct functional domains, TC10 can differentially
regulate two types of filamentous actin in adipocytes.
TC10 mRNAs are highly expressed in three types of mouse
muscle tissues: leg skeletal muscle, cardiac muscle, and
uterus; they were also present in brain, with higher
levels in adults than in newborns. TC10 has also been
shown to play a role in regulating the expression of
cystic fibrosis transmembrane conductance regulator
(CFTR) through interactions with CFTR-associated ligand
(CAL). The GTP-bound form of TC10 directs the
trafficking of CFTR from the juxtanuclear region to the
secretory pathway toward the plasma membrane, away from
CAL-mediated DFTR degradation in the lysosome. Most Rho
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 174
Score = 55.8 bits (134), Expect = 2e-10
Identities = 43/167 (25%), Positives = 81/167 (48%), Gaps = 31/167 (18%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYS-IF 59
+G +VGK+ L + + + F + Y PT+ + + + + + Y L L DTAGQ++Y +
Sbjct: 6 VGDGAVGKTCLLMSYANDAFPEEYVPTVFDHYAVSVTVGGKQYLLGLYDTAGQEDYDRLR 65
Query: 60 PAQYSM-DIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVL 118
P Y M D+ +++ +S+ + SF+ ++ V +VP +L
Sbjct: 66 PLSYPMTDV--FLICFSVVNPASFQ--------------NVKEEWVPELKEYAPNVPYLL 109
Query: 119 VGNKKDL-----------HM-ERMISYDEGKRLAESWKAG-FVEASA 152
+G + DL M E+ I+ ++G++LA+ A +VE SA
Sbjct: 110 IGTQIDLRDDPKTLARLNDMKEKPITVEQGQKLAKEIGACCYVECSA 156
>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 = 55.3 bits (133), Expect = 4e-10
Identities = 42/159 (26%), Positives = 64/159 (40%), Gaps = 21/159 (13%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDS-YDPTIENTFV-KTTRMNNQDYDLKLVDTAGQDEYSI 58
+G SVGK+SL ++V +F+ Y TI FV K + + L + DTAG + Y
Sbjct: 6 LGKESVGKTSLVERYVHHRFLVGPYQNTIGAAFVAKRMVVGERVVTLGIWDTAGSERYEA 65
Query: 59 FPAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVL 118
Y ++ Y +T SFE + VK + I L
Sbjct: 66 MSRIYYRGAKAAIVCYDLTDSSSFERAKFW---------------VKELQNLEEHCKIYL 110
Query: 119 VGNKKDLHME----RMISYDEGKRLAESWKAGFVEASAK 153
G K DL + R + + + + A+ KA E S+K
Sbjct: 111 CGTKSDLIEQDRSLRQVDFHDVQDFADEIKAQHFETSSK 149
>gnl|CDD|206703 cd04131, Rnd, Rho family GTPase subfamily Rnd includes Rnd1/Rho6,
Rnd2/Rho7, and Rnd3/RhoE/Rho8. The Rnd subfamily
contains Rnd1/Rho6, Rnd2/Rho7, and Rnd3/RhoE/Rho8. These
novel Rho family proteins have substantial structural
differences compared to other Rho members, including N-
and C-terminal extensions relative to other Rhos.
Rnd3/RhoE is farnesylated at the C-terminal prenylation
site, unlike most other Rho proteins that are
geranylgeranylated. In addition, Rnd members are unable
to hydrolyze GTP and are resistant to GAP activity. They
are believed to exist only in the GTP-bound
conformation, and are antagonists of RhoA activity. Most
Rho proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 176
Score = 52.8 bits (127), Expect = 3e-09
Identities = 39/164 (23%), Positives = 74/164 (45%), Gaps = 29/164 (17%)
Query: 7 GKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEY-SIFPAQYSM 65
GK++L F F ++Y PT+ + + ++ Q +L L DT+G Y ++ P Y
Sbjct: 13 GKTALLQVFAKDSFPENYVPTVFENYTASFEVDKQRIELSLWDTSGSPYYDNVRPLSYP- 71
Query: 66 DIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVGNKKDL 125
D ++ + I+ ++ + V L G+++ + P++LVG K DL
Sbjct: 72 DSDAVLICFDISRPETLDSV------LKKWKGEVRE--------FCPNTPVLLVGCKSDL 117
Query: 126 ------------HMERMISYDEGKRLAESWKA-GFVEASAKQDD 156
+ +S+++G+ LA+ A +VE SAK +
Sbjct: 118 RTDLSTLTELSNKRQIPVSHEQGRNLAKQIGAAAYVECSAKTSE 161
>gnl|CDD|206663 cd01871, Rac1_like, Ras-related C3 botulinum toxin substrate 1 (rho
family, small GTP binding protein Rac1)-like consists of
Rac1, Rac2 and Rac3. The Rac1-like subfamily consists
of Rac1, Rac2, and Rac3 proteins, plus the splice
variant Rac1b that contains a 19-residue insertion near
switch II relative to Rac1. While Rac1 is ubiquitously
expressed, Rac2 and Rac3 are largely restricted to
hematopoietic and neural tissues respectively. Rac1
stimulates the formation of actin lamellipodia and
membrane ruffles. It also plays a role in cell-matrix
adhesion and cell anoikis. In intestinal epithelial
cells, Rac1 is an important regulator of migration and
mediates apoptosis. Rac1 is also essential for
RhoA-regulated actin stress fiber and focal adhesion
complex formation. In leukocytes, Rac1 and Rac2 have
distinct roles in regulating cell morphology, migration,
and invasion, but are not essential for macrophage
migration or chemotaxis. Rac3 has biochemical properties
that are closely related to Rac1, such as effector
interaction, nucleotide binding, and hydrolysis; Rac2
has a slower nucleotide association and is more
efficiently activated by the RacGEF Tiam1. Both Rac1 and
Rac3 have been implicated in the regulation of cell
migration and invasion in human metastatic breast
cancer. Most Rho proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Rho proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 174
Score = 50.6 bits (121), Expect = 2e-08
Identities = 44/164 (26%), Positives = 73/164 (44%), Gaps = 33/164 (20%)
Query: 5 SVGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYSIF-PAQY 63
+VGK+ L I + F Y PT+ + + ++ + +L L DTAGQ++Y P Y
Sbjct: 11 AVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSY 70
Query: 64 -SMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQ-NSSVKSPTSCVSSVPIVLVGN 121
D+ +++ +S+ S SFE V+ K P + PI+LVG
Sbjct: 71 PQTDV--FLICFSLVSPASFENVR----------AKWYPEVRHHCP-----NTPIILVGT 113
Query: 122 KKDLHMERM------------ISYDEGKRLAESWKA-GFVEASA 152
K DL ++ I+Y +G +A+ A ++E SA
Sbjct: 114 KLDLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSA 157
>gnl|CDD|133321 cd04121, Rab40, Rab GTPase family 40 (Rab40) contains Rab40a,
Rab40b and Rab40c. The Rab40 subfamily contains Rab40a,
Rab40b, and Rab40c, which are all highly homologous. In
rat, Rab40c is localized to the perinuclear recycling
compartment (PRC), and is distributed in a
tissue-specific manor, with high expression in brain,
heart, kidney, and testis, low expression in lung and
liver, and no expression in spleen and skeletal muscle.
Rab40c is highly expressed in differentiated
oligodendrocytes but minimally expressed in
oligodendrocyte progenitors, suggesting a role in the
vesicular transport of myelin components. Unlike most
other Ras-superfamily proteins, Rab40c was shown to have
a much lower affinity for GTP, and an affinity for GDP
that is lower than for GTP. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 189
Score = 48.0 bits (114), Expect = 2e-07
Identities = 39/152 (25%), Positives = 63/152 (41%), Gaps = 16/152 (10%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTFVKTT-RMNNQDYDLKLVDTAGQDEYSIF 59
+G VGK + DG Y + + TT ++ + L+L DT+GQ +
Sbjct: 12 VGDSDVGKGEILASLQDGSTESPYGYNMGIDYKTTTILLDGRRVKLQLWDTSGQGRFCTI 71
Query: 60 PAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLV 119
YS G +LVY IT+ SF+ + + +K VP +LV
Sbjct: 72 FRSYSRGAQGIILVYDITNRWSFDGI---------------DRWIKEIDEHAPGVPKILV 116
Query: 120 GNKKDLHMERMISYDEGKRLAESWKAGFVEAS 151
GN+ L +R ++ ++ + AE F E S
Sbjct: 117 GNRLHLAFKRQVATEQAQAYAERNGMTFFEVS 148
>gnl|CDD|206705 cd04133, Rop_like, Rho-related protein from plants (Rop)-like. The
Rop (Rho-related protein from plants) subfamily plays a
role in diverse cellular processes, including
cytoskeletal organization, pollen and vegetative cell
growth, hormone responses, stress responses, and
pathogen resistance. Rops are able to regulate several
downstream pathways to amplify a specific signal by
acting as master switches early in the signaling
cascade. They transmit a variety of extracellular and
intracellular signals. Rops are involved in establishing
cell polarity in root-hair development, root-hair
elongation, pollen-tube growth, cell-shape formation,
responses to hormones such as abscisic acid (ABA) and
auxin, responses to abiotic stresses such as oxygen
deprivation, and disease resistance and disease
susceptibility. An individual Rop can have a unique
function or an overlapping function shared with other
Rop proteins; in addition, a given Rop-regulated
function can be controlled by one or multiple Rop
proteins. For example, Rop1, Rop3, and Rop5 are all
involved in pollen-tube growth; Rop2 plays a role in
response to low-oxygen environments, cell-morphology,
and root-hair development; root-hair development is also
regulated by Rop4 and Rop6; Rop6 is also responsible for
ABA response, and ABA response is also regulated by
Rop10. Plants retain some of the regulatory mechanisms
that are shared by other members of the Rho family, but
have also developed a number of unique modes for
regulating Rops. Unique RhoGEFs have been identified
that are exclusively active toward Rop proteins, such as
those containing the domain PRONE (plant-specific Rop
nucleotide exchanger). Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 173
Score = 47.5 bits (113), Expect = 2e-07
Identities = 35/123 (28%), Positives = 56/123 (45%), Gaps = 18/123 (14%)
Query: 5 SVGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYS-IFPAQY 63
+VGK+ + I + F Y PT+ + F ++ +L L DTAGQ++Y+ + P Y
Sbjct: 11 AVGKTCMLISYTSNTFPTDYVPTVFDNFSANVVVDGNTVNLGLWDTAGQEDYNRLRPLSY 70
Query: 64 -SMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVGNK 122
D+ ++L +S+ S S+E + + VPIVLVG K
Sbjct: 71 RGADV--FLLAFSLISKASYE--------------NVLKKWIPELRHYAPGVPIVLVGTK 114
Query: 123 KDL 125
DL
Sbjct: 115 LDL 117
>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 = 46.0 bits (109), Expect = 8e-07
Identities = 44/158 (27%), Positives = 66/158 (41%), Gaps = 18/158 (11%)
Query: 2 GYRSVGKSSLSIQF-VDG-QFVDSYDPTIENTF-VKTTRMNNQDYDLKLV--DTAGQDEY 56
G +VGKS+L F DG F +Y T VKT + + ++L D+AGQ+ +
Sbjct: 7 GDPAVGKSALVQMFHSDGATFQKNYTMTTGCDLVVKTVPVPDTSDSVELFIFDSAGQELF 66
Query: 57 SIFPAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPI 116
S +VY +T+ SF +++ S P
Sbjct: 67 SDMVENVWEQPAVVCVVYDVTNEVSFNNCSRWINRV-------------RTHSHGLHTPG 113
Query: 117 VLVGNKKDLHMERMISYDEGKRLAESWKAGFVEASAKQ 154
VLVGNK DL R + + + LA++ F E SAK+
Sbjct: 114 VLVGNKCDLTDRREVDAAQAQALAQANTLKFYETSAKE 151
>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 = 44.9 bits (106), Expect = 2e-06
Identities = 43/156 (27%), Positives = 66/156 (42%), Gaps = 18/156 (11%)
Query: 5 SVGKSSLSIQFVDGQFVDSYDPTIENTF-VKTTRMNNQDYDLKLVDTAGQDEYSIFPAQY 63
SVGK+ L +F F +Y TI F ++ + + L+L DTAGQ+ + + Y
Sbjct: 10 SVGKTCLINRFCKDVFDKNYKATIGVDFEMERFEVLGVPFSLQLWDTAGQERFKCIASTY 69
Query: 64 SMDIHGYVLVYSITSHKSFE-VVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVGNK 122
++V+ +T S E Q L D L + P+S + + LVG K
Sbjct: 70 YRGAQAIIIVFDLTDVASLEHTRQWLEDALKE----------NDPSSVL----LFLVGTK 115
Query: 123 KDLHMERMISYDEGK--RLAESWKAGFVEASAKQDD 156
KDL + E +LA KA + SA +
Sbjct: 116 KDLSSPAQYALMEQDAIKLAREMKAEYWAVSALTGE 151
>gnl|CDD|206697 cd04116, Rab9, Rab GTPase family 9 (Rab9). Rab9 is found in late
endosomes, together with mannose 6-phosphate receptors
(MPRs) and the tail-interacting protein of 47 kD
(TIP47). Rab9 is a key mediator of vesicular transport
from late endosomes to the trans-Golgi network (TGN) by
redirecting the MPRs. Rab9 has been identified as a key
component for the replication of several viruses,
including HIV1, Ebola, Marburg, and measles, making it a
potential target for inhibiting a variety of viruses.
GTPase activating proteins (GAPs) interact with
GTP-bound Rab and accelerate the hydrolysis of GTP to
GDP. Guanine nucleotide exchange factors (GEFs) interact
with GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 170
Score = 44.1 bits (104), Expect = 4e-06
Identities = 41/157 (26%), Positives = 71/157 (45%), Gaps = 13/157 (8%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTFV-KTTRMNNQDYDLKLVDTAGQDEYSIF 59
+G VGKSSL ++V +F TI F+ K ++ L++ DTAGQ+ +
Sbjct: 11 LGDGGVGKSSLMNRYVTNKFDTQLFHTIGVEFLNKDLEVDGHFVTLQIWDTAGQERFRSL 70
Query: 60 PAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLV 119
+ +L +S+ +SF+ + + + + VK P S P V++
Sbjct: 71 RTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYY------ADVKEP----ESFPFVIL 120
Query: 120 GNKKDLHMERMISYDEGKR-LAESWKAGFVEASAKQD 155
GNK D+ ER +S +E + ++ + E SAK
Sbjct: 121 GNKIDIP-ERQVSTEEAQAWCRDNGDYPYFETSAKDA 156
>gnl|CDD|206735 cd04172, Rnd3_RhoE_Rho8, Rnd3/RhoE/Rho8 GTPases. Rnd3/RhoE/Rho8
subfamily. Rnd3/RhoE/Rho8 is a member of the novel Rho
subfamily Rnd, together with Rnd1/Rho6 and Rnd2/Rho7.
Rnd3/RhoE is known to bind the serine-threonine kinase
ROCK I. Unphosphorylated Rnd3/RhoE associates primarily
with membranes, but ROCK I-phosphorylated Rnd3/RhoE
localizes in the cytosol. Phosphorylation of Rnd3/RhoE
correlates with its activity in disrupting RhoA-induced
stress fibers and inhibiting Ras-induced fibroblast
transformation. In cells that lack stress fibers, such
as macrophages and monocytes, Rnd3/RhoE induces a
redistribution of actin, causing morphological changes
in the cell. In addition, Rnd3/RhoE has been shown to
inhibit cell cycle progression in G1 phase at a point
upstream of the pRb family pocket protein checkpoint.
Rnd3/RhoE has also been shown to inhibit Ras- and
Raf-induced fibroblast transformation. In mammary
epithelial tumor cells, Rnd3/RhoE regulates the assembly
of the apical junction complex and tight junction
formation. Rnd3/RhoE is underexpressed in prostate
cancer cells both in vitro and in vivo; re-expression of
Rnd3/RhoE suppresses cell cycle progression and
increases apoptosis, suggesting it may play a role in
tumor suppression. Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 182
Score = 43.5 bits (102), Expect = 8e-06
Identities = 42/170 (24%), Positives = 75/170 (44%), Gaps = 29/170 (17%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEY-SIF 59
+G GK++L F F ++Y PT+ + + ++ Q +L L DT+G Y ++
Sbjct: 11 VGDSQCGKTALLHVFAKDCFPENYVPTVFENYTASFEIDTQRIELSLWDTSGSPYYDNVR 70
Query: 60 PAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLV 119
P Y D ++ + I+ ++ + V L G+IQ + ++LV
Sbjct: 71 PLSYP-DSDAVLICFDISRPETLDSV------LKKWKGEIQ--------EFCPNTKMLLV 115
Query: 120 GNKKDL------------HMERMISYDEGKRLAESWKAG-FVEASAKQDD 156
G K DL H + +SYD+G +A+ A ++E SA Q +
Sbjct: 116 GCKSDLRTDVSTLVELSNHRQTPVSYDQGANMAKQIGAATYIECSALQSE 165
>gnl|CDD|133324 cd04124, RabL2, Rab GTPase-like family 2 (Rab-like2). RabL2
(Rab-like2) subfamily. RabL2s are novel Rab proteins
identified recently which display features that are
distinct from other Rabs, and have been termed Rab-like.
RabL2 contains RabL2a and RabL2b, two very similar Rab
proteins that share > 98% sequence identity in humans.
RabL2b maps to the subtelomeric region of chromosome
22q13.3 and RabL2a maps to 2q13, a region that suggests
it is also a subtelomeric gene. Both genes are believed
to be expressed ubiquitously, suggesting that RabL2s are
the first example of duplicated genes in human proximal
subtelomeric regions that are both expressed actively.
Like other Rab-like proteins, RabL2s lack a prenylation
site at the C-terminus. The specific functions of RabL2a
and RabL2b remain unknown. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization.
Length = 161
Score = 40.2 bits (94), Expect = 8e-05
Identities = 32/130 (24%), Positives = 58/130 (44%), Gaps = 24/130 (18%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTFVKT-----TRMNNQDYDLKLVDTAGQDE 55
+G +VGKS L +F+ +D Y+P +T+ T + + + DTAGQ+
Sbjct: 6 LGDSAVGKSKLVERFL----MDGYEPQQLSTYALTLYKHNAKFEGKTILVDFWDTAGQER 61
Query: 56 YSIFPAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVP 115
+ A Y H +LV+ +T +++ + Y++L + +I P
Sbjct: 62 FQTMHASYYHKAHACILVFDVTRKITYKNLSKWYEELREYRPEI---------------P 106
Query: 116 IVLVGNKKDL 125
++V NK DL
Sbjct: 107 CIVVANKIDL 116
>gnl|CDD|133303 cd04103, Centaurin_gamma, Centaurin gamma (CENTG) GTPase. The
centaurins (alpha, beta, gamma, and delta) are large,
multi-domain proteins that all contain an ArfGAP domain
and ankyrin repeats, and in some cases, numerous
additional domains. Centaurin gamma contains an
additional GTPase domain near its N-terminus. The
specific function of this GTPase domain has not been
well characterized, but centaurin gamma 2 (CENTG2) may
play a role in the development of autism. Centaurin
gamma 1 is also called PIKE (phosphatidyl inositol (PI)
3-kinase enhancer) and centaurin gamma 2 is also known
as AGAP (ArfGAP protein with a GTPase-like domain,
ankyrin repeats and a Pleckstrin homology domain) or
GGAP. Three isoforms of PIKE have been identified.
PIKE-S (short) and PIKE-L (long) are brain-specific
isoforms, with PIKE-S restricted to the nucleus and
PIKE-L found in multiple cellular compartments. A third
isoform, PIKE-A was identified in human glioblastoma
brain cancers and has been found in various tissues.
GGAP has been shown to have high GTPase activity due to
a direct intramolecular interaction between the
N-terminal GTPase domain and the C-terminal ArfGAP
domain. In human tissue, AGAP mRNA was detected in
skeletal muscle, kidney, placenta, brain, heart, colon,
and lung. Reduced expression levels were also observed
in the spleen, liver, and small intestine.
Length = 158
Score = 39.8 bits (93), Expect = 1e-04
Identities = 35/146 (23%), Positives = 65/146 (44%), Gaps = 21/146 (14%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYSIFP 60
+G GKS+L +++ G +V P F K ++ Q + L + D G +
Sbjct: 6 VGNLRSGKSALVHRYLTGSYVQLESPEGGR-FKKEVLVDGQSHLLLIRDEGGAPD----- 59
Query: 61 AQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVG 120
AQ++ + + V+S+ SF+ V LY +L SS ++ +S +P++LVG
Sbjct: 60 AQFAGWVDAVIFVFSLEDEASFQTVYRLYHQL---------SSYRN----ISEIPLILVG 106
Query: 121 NKKDLHME--RMISYDEGKRLAESWK 144
+ + R+I ++L K
Sbjct: 107 TQDAISASNPRVIDDARARQLCADMK 132
>gnl|CDD|206680 cd01893, Miro1, Mitochondrial Rho family 1 (Miro1), N-terminal.
Miro1 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the N-terminal
GTPase domain of Miro proteins. These atypical Rho
GTPases have roles in mitochondrial homeostasis and
apoptosis. Most Rho proteins contain a lipid
modification site at the C-terminus; however, Miro is
one of few Rho subfamilies that lack this feature.
Length = 168
Score = 40.0 bits (94), Expect = 1e-04
Identities = 41/159 (25%), Positives = 62/159 (38%), Gaps = 33/159 (20%)
Query: 6 VGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAG---QDEYSIFPAQ 62
VGKSSL + V +F ++ + + + + +VDT+ +
Sbjct: 13 VGKSSLIMSLVSEEFPENVPRVLPEITIPAD-VTPERVPTTIVDTSSRPQDRANLAAEIR 71
Query: 63 YSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVGNK 122
+ I LVYS+ + E ++ K L + I+ VK VPI+LVGNK
Sbjct: 72 KANVI---CLVYSVDRPSTLERIRT---KWLPL---IRRLGVK--------VPIILVGNK 114
Query: 123 KDL--------HMERMISYDEGKRLAESWKAGFVEASAK 153
DL E M+ R E+ VE SAK
Sbjct: 115 SDLRDGSSQAGLEEEMLPIMNEFREIETC----VECSAK 149
>gnl|CDD|133326 cd04126, Rab20, Rab GTPase family 20 (Rab20). Rab20 is one of
several Rab proteins that appear to be restricted in
expression to the apical domain of murine polarized
epithelial cells. It is expressed on the apical side of
polarized kidney tubule and intestinal epithelial cells,
and in non-polarized cells. It also localizes to
vesico-tubular structures below the apical brush border
of renal proximal tubule cells and in the apical region
of duodenal epithelial cells. Rab20 has also been shown
to colocalize with vacuolar H+-ATPases (V-ATPases) in
mouse kidney cells, suggesting a role in the regulation
of V-ATPase traffic in specific portions of the nephron.
It was also shown to be one of several proteins whose
expression is upregulated in human myelodysplastic
syndrome (MDS) patients. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 220
Score = 35.7 bits (82), Expect = 0.005
Identities = 31/126 (24%), Positives = 61/126 (48%), Gaps = 20/126 (15%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTF-VKTTRMNNQDYDLKLVDTAGQDEYSIF 59
+G +VGK+SL ++++ +F D+ T+ F +K Y++ + DTAG++++
Sbjct: 6 LGDMNVGKTSLLHRYMERRFKDT-VSTVGGAFYLKQWG----PYNISIWDTAGREQFHGL 60
Query: 60 PAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLV 119
+ Y +L Y +++ +S E ++ + L D + C+ +V V
Sbjct: 61 GSMYCRGAAAVILTYDVSNVQSLEELEDRFLGLTDTANE----------DCLFAV----V 106
Query: 120 GNKKDL 125
GNK DL
Sbjct: 107 GNKLDL 112
>gnl|CDD|206679 cd01892, Miro2, Mitochondrial Rho family 2 (Miro2), C-terminal.
Miro2 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the putative
GTPase domain in the C terminus of Miro proteins. These
atypical Rho GTPases have roles in mitochondrial
homeostasis and apoptosis. Most Rho proteins contain a
lipid modification site at the C-terminus; however, Miro
is one of few Rho subfamilies that lack this feature.
Length = 180
Score = 34.1 bits (79), Expect = 0.014
Identities = 36/130 (27%), Positives = 51/130 (39%), Gaps = 24/130 (18%)
Query: 2 GYRSVGKSSLSIQFVDGQFVDS-YDPTI-ENTFVKTTRMNNQDYDLKLVDTAGQDEYSIF 59
G + GKS+L F+ F + Y PTI V T + Q+ L L + G+DE +I
Sbjct: 11 GAKGSGKSALLQAFLGRSFSQNAYSPTIKPRYAVNTVEVPGQEKYLILREV-GEDEEAIL 69
Query: 60 PAQYSM---DIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPI 116
+ D+ LVY + SF +Y K M G+I P
Sbjct: 70 LNDAELAACDV--ACLVYDSSDPNSFSYCAEVYKKY-FMLGEI---------------PC 111
Query: 117 VLVGNKKDLH 126
+ V K DL
Sbjct: 112 LFVAAKADLD 121
>gnl|CDD|206643 cd00877, Ran, Ras-related nuclear proteins (Ran)/TC4 family of
small GTPases. Ran GTPase is involved in diverse
biological functions, such as nuclear transport, spindle
formation during mitosis, DNA replication, and cell
division. Among the Ras superfamily, Ran is a unique
small G protein. It does not have a lipid modification
motif at the C-terminus to bind to the membrane, which
is often observed within the Ras superfamily. Ran may
therefore interact with a wide range of proteins in
various intracellular locations. Like other GTPases, Ran
exists in GTP- and GDP-bound conformations that interact
differently with effectors. Conversion between these
forms and the assembly or disassembly of effector
complexes requires the interaction of regulator
proteins. The intrinsic GTPase activity of Ran is very
low, but it is greatly stimulated by a GTPase-activating
protein (RanGAP1) located in the cytoplasm. By contrast,
RCC1, a guanine nucleotide exchange factor that
generates RanGTP, is bound to chromatin and confined to
the nucleus. Ran itself is mobile and is actively
imported into the nucleus by a mechanism involving
NTF-2. Together with the compartmentalization of its
regulators, this is thought to produce a relatively high
concentration of RanGTP in the nucleus.
Length = 166
Score = 33.8 bits (78), Expect = 0.014
Identities = 35/156 (22%), Positives = 65/156 (41%), Gaps = 32/156 (20%)
Query: 6 VGKSSLSIQFVDGQFVDSYDPTI--ENTFVK-TTRMNNQDYDLKLVDTAGQDEYSIFPAQ 62
GK++ + + G+F Y T+ E + T +++ DTAGQ+++
Sbjct: 11 TGKTTFVKRHLTGEFEKKYVATLGVEVHPLDFHTNRGKIRFNV--WDTAGQEKFGGLRDG 68
Query: 63 YSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVGNK 122
Y + ++++ +TS +++ V + L+ + I PIVL GNK
Sbjct: 69 YYIQGQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENI---------------PIVLCGNK 113
Query: 123 KDLHMER-----MISYDEGKRLAESWKAGFVEASAK 153
D+ +R I++ K L + E SAK
Sbjct: 114 VDI-KDRKVKPKQITFHRKKNL------QYYEISAK 142
>gnl|CDD|206691 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta), together with SR-alpha, forms the
heterodimeric signal recognition particle (SRP). Signal
recognition particle receptor, beta subunit (SR-beta).
SR-beta and SR-alpha form the heterodimeric signal
recognition particle (SRP or SR) receptor that binds SRP
to regulate protein translocation across the ER
membrane. Nascent polypeptide chains are synthesized
with an N-terminal hydrophobic signal sequence that
binds SRP54, a component of the SRP. SRP directs
targeting of the ribosome-nascent chain complex (RNC) to
the ER membrane via interaction with the SR, which is
localized to the ER membrane. The RNC is then
transferred to the protein-conducting channel, or
translocon, which facilitates polypeptide translation
across the ER membrane or integration into the ER
membrane. SR-beta is found only in eukaryotes; it is
believed to control the release of the signal sequence
from SRP54 upon binding of the ribosome to the
translocon. High expression of SR-beta has been observed
in human colon cancer, suggesting it may play a role in
the development of this type of cancer.
Length = 202
Score = 31.9 bits (73), Expect = 0.077
Identities = 29/122 (23%), Positives = 50/122 (40%), Gaps = 16/122 (13%)
Query: 7 GKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEY-SIFPAQYSM 65
GK++L + G+ + +IE +++ L LVD G ++
Sbjct: 12 GKTALFTKLTTGKVRSTV-TSIEPNVASFYSNSSKGKKLTLVDVPGHEKLRDKLLEYLKA 70
Query: 66 DIHGYVLVYSITS-HKSF-EVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVGNKK 123
+ V V + K+ +V + LYD L D KI+N +PI++ NK+
Sbjct: 71 SLKAIVFVVDSATFQKNIRDVAEFLYDILTD-LEKIKNK-----------IPILIACNKQ 118
Query: 124 DL 125
DL
Sbjct: 119 DL 120
>gnl|CDD|206741 cd09914, RocCOR, Ras of complex proteins (Roc) C-terminal of Roc
(COR) domain family. RocCOR (or Roco) protein family is
characterized by a superdomain containing a Ras-like
GTPase domain, called Roc (Ras of complex proteins), and
a characteristic second domain called COR (C-terminal of
Roc). A kinase domain and diverse regulatory domains are
also often found in Roco proteins. Their functions are
diverse; in Dictyostelium discoideum, which encodes 11
Roco proteins, they are involved in cell division,
chemotaxis and development, while in human, where 4 Roco
proteins (LRRK1, LRRK2, DAPK1, and MFHAS1) are encoded,
these proteins are involved in epilepsy and cancer.
Mutations in LRRK2 (leucine-rich repeat kinase 2) are
known to cause familial Parkinson's disease.
Length = 161
Score = 31.2 bits (71), Expect = 0.12
Identities = 32/161 (19%), Positives = 50/161 (31%), Gaps = 25/161 (15%)
Query: 2 GYRSVGKSSLSIQFVDGQFVDSYDPT--IENTFVKTTRMNNQDYDLKLVDTAGQDEYSIF 59
G VGK+SL Q + +F T I K + L + D GQ+ Y
Sbjct: 8 GQGGVGKTSLCKQLIGEKFDGDESSTHGINVQDWKIPAPERKKIRLNVWDFGGQEIY--- 64
Query: 60 PAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCV----SSVP 115
H +H+ F + LY + D+ + S V + P
Sbjct: 65 --------HA--------THQFFLTSRSLYLLVFDLRTGDEVSRVPYWLRQIKAFGGVSP 108
Query: 116 IVLVGNKKDLHMERMISYDEGKRLAESWKAGFVEASAKQDD 156
++LVG D + I + + S K
Sbjct: 109 VILVGTHIDESCDEDILKKALNKKFPAIINDIHFVSCKNGK 149
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 31.4 bits (72), Expect = 0.15
Identities = 25/113 (22%), Positives = 46/113 (40%), Gaps = 24/113 (21%)
Query: 45 LKLVDTAGQDEYSIFPAQYSMDIHGYVLVYSITSHKSFEVVQ----ILYDKLLDMTGKIQ 100
++LVDTAG E + D+ V I ++ + ++ +L+ +LD + +
Sbjct: 267 VRLVDTAGIRE--------TDDV-----VERIGIERAKKAIEEADLVLF--VLDASQPLD 311
Query: 101 NSSVKSPTSCVSSVPIVLVGNKKDLHMERMISYDEGKRLAESWKAGFVEASAK 153
+ PI++V NK DL +S E + + + SAK
Sbjct: 312 KEDLALIELLPKKKPIIVVLNKADL-----VSKIELESEKLANGDAIISISAK 359
>gnl|CDD|133356 cd04156, ARLTS1, Arf-like tumor suppressor gene 1 (ARLTS1 or
Arl11). ARLTS1 (Arf-like tumor suppressor gene 1), also
known as Arl11, is a member of the Arf family of small
GTPases that is believed to play a major role in
apoptotic signaling. ARLTS1 is widely expressed and
functions as a tumor suppressor gene in several human
cancers. ARLTS1 is a low-penetrance suppressor that
accounts for a small percentage of familial melanoma or
familial chronic lymphocytic leukemia (CLL). ARLTS1
inactivation seems to occur most frequently through
biallelic down-regulation by hypermethylation of the
promoter. In breast cancer, ARLTS1 alterations were
typically a combination of a hypomorphic polymorphism
plus loss of heterozygosity. In a case of thyroid
adenoma, ARLTS1 alterations were polymorphism plus
promoter hypermethylation. The nonsense polymorphism
Trp149Stop occurs with significantly greater frequency
in familial cancer cases than in sporadic cancer cases,
and the Cys148Arg polymorphism is associated with an
increase in high-risk familial breast cancer.
Length = 160
Score = 30.5 bits (69), Expect = 0.22
Identities = 30/125 (24%), Positives = 49/125 (39%), Gaps = 16/125 (12%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYSIFP 60
+G S GKS+L + + V + PT+ F + L + D GQ++
Sbjct: 5 LGLDSAGKSTLLYKLKHAELVTTI-PTV--GFNVEMLQLEKHLSLTVWDVGGQEKMRTVW 61
Query: 61 AQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVG 120
Y + G V V + + Q +L +N +K VP+VL+
Sbjct: 62 KCYLENTDGLVYVVDSSDEARLDESQKELKHIL------KNEHIKG-------VPVVLLA 108
Query: 121 NKKDL 125
NK+DL
Sbjct: 109 NKQDL 113
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 30.5 bits (69), Expect = 0.25
Identities = 30/124 (24%), Positives = 53/124 (42%), Gaps = 22/124 (17%)
Query: 6 VGKSSLSIQFVDGQFVDSYDPTI--ENTFVKTTRMNNQDYDLKLVDTAGQDEYSIFPAQY 63
GK++ + + G+F Y+PTI E + N DTAGQ+++ Y
Sbjct: 24 TGKTTFVKRHLTGEFEKKYEPTIGVEVHPLDFF-TNCGKIRFYCWDTAGQEKFGGLRDGY 82
Query: 64 SMDIHGY--VLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVGN 121
IHG ++++ +T+ +++ V + L ++PIVL GN
Sbjct: 83 Y--IHGQCAIIMFDVTARLTYKNVPTWHRDL---------------CRVCENIPIVLCGN 125
Query: 122 KKDL 125
K D+
Sbjct: 126 KVDV 129
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 30.0 bits (68), Expect = 0.33
Identities = 32/148 (21%), Positives = 59/148 (39%), Gaps = 42/148 (28%)
Query: 6 VGKSSLSIQFVDGQFVDSYDPTIE--------NTFVKTTRMNNQDYDLKLVDTAGQDEYS 57
VGK++ + + G+F Y PT+ T N + DTAGQ+++
Sbjct: 20 VGKTTFVKRHLTGEFEKKYIPTLGVEVHPLKFYTNCGPICFN-------VWDTAGQEKFG 72
Query: 58 IFPAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIV 117
Y + ++++ +TS +++ V + D+ +N +PIV
Sbjct: 73 GLRDGYYIKGQCAIIMFDVTSRITYKNVPNWHR---DIVRVCEN------------IPIV 117
Query: 118 LVGNKKDL------------HMERMISY 133
LVGNK D+ H ++ + Y
Sbjct: 118 LVGNKVDVKDRQVKARQITFHRKKNLQY 145
>gnl|CDD|133362 cd04162, Arl9_Arfrp2_like, Arf-like 9 (Arl9)/Arfrp2-like GTPase.
Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first
identified as part of the Human Cancer Genome Project.
It maps to chromosome 4q12 and is sometimes referred to
as Arfrp2 (Arf-related protein 2). This is a novel
subfamily identified in human cancers that is
uncharacterized to date.
Length = 164
Score = 29.3 bits (66), Expect = 0.62
Identities = 24/119 (20%), Positives = 46/119 (38%), Gaps = 18/119 (15%)
Query: 7 GKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYSIFPAQYSMD 66
GK+SL + ++S PT T + + QD ++L++ G + +Y
Sbjct: 11 GKTSLLHSLSSERSLESVVPT---TGFNSVAIPTQDAIMELLEIGGSQNLRKYWKRYLSG 67
Query: 67 IHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVGNKKDL 125
G + V + + + +LL P +P+V++ NK+DL
Sbjct: 68 SQGLIFVVDSADSERLPLARQELHQLLQ----------HPPD-----LPLVVLANKQDL 111
>gnl|CDD|206701 cd04128, Spg1, Septum-promoting GTPase (Spg1). Spg1p. Spg1p
(septum-promoting GTPase) was first identified in the
fission yeast S. pombe, where it regulates septum
formation in the septation initiation network (SIN)
through the cdc7 protein kinase. Spg1p is an essential
gene that localizes to the spindle pole bodies. When
GTP-bound, it binds cdc7 and causes it to translocate to
spindle poles. Sid4p (septation initiation defective) is
required for localization of Spg1p to the spindle pole
body, and the ability of Spg1p to promote septum
formation from any point in the cell cycle depends on
Sid4p. Spg1p is negatively regulated by Byr4 and cdc16,
which form a two-component GTPase activating protein
(GAP) for Spg1p. The existence of a SIN-related pathway
in plants has been proposed. 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 = 182
Score = 29.3 bits (66), Expect = 0.63
Identities = 39/166 (23%), Positives = 71/166 (42%), Gaps = 33/166 (19%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTFV-KTTRMNNQDYDLKLVDTAGQDEYS-I 58
+G +GK+SL +++V+G+F + Y T+ F+ KT + + + D GQ E+ +
Sbjct: 6 LGDAQIGKTSLMVKYVEGEFDEEYIQTLGVNFMEKTISIRGTEITFSIWDLGGQREFINM 65
Query: 59 FPAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCV-----SS 113
P + + V IL+ + D+T K +S+K ++
Sbjct: 66 LP---------------LVCKDA---VAILF--MFDLTRKSTLNSIKEWYRQARGFNKTA 105
Query: 114 VPIVLVGNKKDLHMERMISYDE-----GKRLAESWKAGFVEASAKQ 154
+PI LVG K DL + E ++ A++ KA + S
Sbjct: 106 IPI-LVGTKYDLFADLPPEEQEEITKQARKYAKAMKAPLIFCSTSH 150
>gnl|CDD|133361 cd04161, Arl2l1_Arl13_like, Arl2-like protein 1 (Arl2l1) and Arl13.
Arl2l1 (Arl2-like protein 1) and Arl13 form a subfamily
of the Arf family of small GTPases. Arl2l1 was
identified in human cells during a search for the
gene(s) responsible for Bardet-Biedl syndrome (BBS).
Like Arl6, the identified BBS gene, Arl2l1 is proposed
to have cilia-specific functions. Arl13 is found on the
X chromosome, but its expression has not been confirmed;
it may be a pseudogene.
Length = 167
Score = 28.9 bits (65), Expect = 0.86
Identities = 30/126 (23%), Positives = 52/126 (41%), Gaps = 21/126 (16%)
Query: 7 GKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEY-SIFPAQYSM 65
GK++L + + G+ PT+ F T + Y++ + D G + I+ Y+
Sbjct: 11 GKTTL-VSALQGEIPKKVAPTVG--FTPTK-LRLDKYEVCIFDLGGGANFRGIWVNYYA- 65
Query: 66 DIHGYVLVY-SITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVGNKKD 124
+ HG V V S + EV +IL + L VS PI+++ NK+D
Sbjct: 66 EAHGLVFVVDSSDDDRVQEVKEILRELLQHPR--------------VSGKPILVLANKQD 111
Query: 125 LHMERM 130
+
Sbjct: 112 KKNALL 117
>gnl|CDD|206736 cd04173, Rnd2_Rho7, Rnd2/Rho7 GTPases. Rnd2/Rho7 is a member of
the novel Rho subfamily Rnd, together with Rnd1/Rho6 and
Rnd3/RhoE/Rho8. Rnd2/Rho7 is transiently expressed in
radially migrating cells in the brain while they are
within the subventricular zone of the hippocampus and
cerebral cortex. These migrating cells typically develop
into pyramidal neurons. Cells that exogenously expressed
Rnd2/Rho7 failed to migrate to upper layers of the
brain, suggesting that Rnd2/Rho7 plays a role in the
radial migration and morphological changes of developing
pyramidal neurons, and that Rnd2/Rho7 degradation is
necessary for proper cellular migration. The Rnd2/Rho7
GEF Rapostlin is found primarily in the brain and
together with Rnd2/Rho7 induces dendrite branching.
Unlike Rnd1/Rho6 and Rnd3/RhoE/Rho8, which are RhoA
antagonists, Rnd2/Rho7 binds the GEF Pragmin and
significantly stimulates RhoA activity and Rho-A
mediated cell contraction. Rnd2/Rho7 is also found to be
expressed in spermatocytes and early spermatids, with
male-germ-cell Rac GTPase-activating protein
(MgcRacGAP), where it localizes to the Golgi-derived
pro-acrosomal vesicle. Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Length = 221
Score = 28.8 bits (64), Expect = 0.91
Identities = 38/167 (22%), Positives = 73/167 (43%), Gaps = 29/167 (17%)
Query: 1 MGYRSVGKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEY-SIF 59
+G GK++L F + +SY PT+ + + ++ +L + DT+G Y ++
Sbjct: 7 VGDTQCGKTALLHVFAKDNYPESYVPTVFENYTASFEIDKHRIELNMWDTSGSSYYDNVR 66
Query: 60 PAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLV 119
P Y D ++ + I+ ++ + V K Q ++ C + +VLV
Sbjct: 67 PLAYP-DSDAVLICFDISRPETLDSV----------LKKWQ---GETQEFC-PNAKLVLV 111
Query: 120 GNKKD----------LHMERMI--SYDEGKRLAESWKA-GFVEASAK 153
G K D L +R+I ++++G LA A +VE S++
Sbjct: 112 GCKLDMRTDLSTLRELSKQRLIPVTHEQGSLLARQLGAVAYVECSSR 158
>gnl|CDD|206737 cd04174, Rnd1_Rho6, Rnd1/Rho6 GTPases. Rnd1/Rho6 is a member of
the novel Rho subfamily Rnd, together with Rnd2/Rho7 and
Rnd3/RhoE/Rho8. Rnd1/Rho6 binds GTP but does not
hydrolyze it to GDP, indicating that it is
constitutively active. In rat, Rnd1/Rho6 is highly
expressed in the cerebral cortex and hippocampus during
synapse formation, and plays a role in spine formation.
Rnd1/Rho6 is also expressed in the liver and in
endothelial cells, and is upregulated in uterine
myometrial cells during pregnancy. Like Rnd3/RhoE/Rho8,
Rnd1/Rho6 is believed to function as an antagonist to
RhoA. Most Rho proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Rho proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 232
Score = 28.5 bits (63), Expect = 1.2
Identities = 39/160 (24%), Positives = 65/160 (40%), Gaps = 29/160 (18%)
Query: 7 GKSSLSIQFVDGQFVDSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEY-SIFPAQYSM 65
GK+++ + ++Y PT+ + Q +L L DT+G Y ++ P YS
Sbjct: 25 GKTAMLQVLAKDCYPETYVPTVFENYTACLETEEQRVELSLWDTSGSPYYDNVRPLCYS- 83
Query: 66 DIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVGNKKDL 125
D +L + I+ + F D K + + S I+L+G K DL
Sbjct: 84 DSDAVLLCFDISRPEIF-----------DSALKKWRAEI---LDYCPSTRILLIGCKTDL 129
Query: 126 H------MERM------ISYDEGKRLAESWKA-GFVEASA 152
ME ISY++G +A+ A ++E SA
Sbjct: 130 RTDLSTLMELSNQKQAPISYEQGCAMAKQLGAEAYLECSA 169
>gnl|CDD|218203 pfam04670, Gtr1_RagA, Gtr1/RagA G protein conserved region. GTR1
was first identified in S. cerevisiae as a suppressor
of a mutation in RCC1. Biochemical analysis revealed
that Gtr1 is in fact a G protein of the Ras family. The
RagA/B proteins are the human homologues of Gtr1.
Included in this family is the human Rag C, a novel
protein that has been shown to interact with RagA/B.
Length = 230
Score = 28.7 bits (65), Expect = 1.2
Identities = 19/59 (32%), Positives = 28/59 (47%), Gaps = 5/59 (8%)
Query: 1 MGYRSVGKSSL-SIQFVDGQFVDSYD--PTIENTFVKTTRMNNQDYDLKLVDTAGQDEY 56
MG R GKSS+ SI F + D+ TI+ ++ + L L D GQD++
Sbjct: 5 MGLRGSGKSSMRSIIFSNYSPRDTLRLGATIDVE--QSHVRFLGNLTLNLWDCPGQDDF 61
>gnl|CDD|128473 smart00176, RAN, Ran (Ras-related nuclear proteins) /TC4 subfamily
of small GTPases. Ran is involved in the active
transport of proteins through nuclear pores.
Length = 200
Score = 28.4 bits (63), Expect = 1.2
Identities = 26/122 (21%), Positives = 53/122 (43%), Gaps = 20/122 (16%)
Query: 7 GKSSLSIQFVDGQFVDSYDPTIE---NTFVKTTRMNNQDYDLKLVDTAGQDEYSIFPAQY 63
GK++ + + G+F Y T+ + V T N + DTAGQ+++ Y
Sbjct: 7 GKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHT--NRGPIRFNVWDTAGQEKFGGLRDGY 64
Query: 64 SMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPTSCVSSVPIVLVGNKK 123
+ ++++ +T+ +++ V + L+ + ++PIVL GNK
Sbjct: 65 YIQGQCAIIMFDVTARVTYKNVPNWHRDLVRV---------------CENIPIVLCGNKV 109
Query: 124 DL 125
D+
Sbjct: 110 DV 111
>gnl|CDD|131709 TIGR02661, MauD, methylamine dehydrogenase accessory protein MauD.
This protein, MauD, appears critical to proper formation
of the small subunit of methylamine dehydrogenase, which
has both an unusual tryptophan tryptophylquinone
cofactor and multiple disulfide bonds. MauD shares
sequence similarity, including a CPxC motif, with a
number of thiol:disulfide interchange proteins. In MauD
mutants, the small subunit apparently does not form
properly and is rapidly degraded [Protein fate, Protein
folding and stabilization, Energy metabolism, Amino
acids and amines].
Length = 189
Score = 27.5 bits (61), Expect = 2.5
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 41 QDYDLKLVDTAGQDEYSIFPAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKI 99
++ D+ ++ E+ F + + YV+ S +F+V +I Y LLD GKI
Sbjct: 103 EETDVVMISDGTPAEHRRFLKDHELGGERYVV--SAEIGMAFQVGKIPYGVLLDQDGKI 159
>gnl|CDD|226075 COG3545, COG3545, Predicted esterase of the alpha/beta hydrolase
fold [General function prediction only].
Length = 181
Score = 27.3 bits (61), Expect = 3.0
Identities = 10/36 (27%), Positives = 20/36 (55%), Gaps = 4/36 (11%)
Query: 115 PIVLVGNKKDLHMERMISYDEGKRLAESWKAGFVEA 150
P V+V ++ D ++ SY+ + LA +W + V+
Sbjct: 119 PSVVVASRNDPYV----SYEHAEDLANAWGSALVDV 150
>gnl|CDD|234980 PRK01759, glnD, PII uridylyl-transferase; Provisional.
Length = 854
Score = 27.8 bits (62), Expect = 3.3
Identities = 13/28 (46%), Positives = 15/28 (53%)
Query: 45 LKLVDTAGQDEYSIFPAQYSMDIHGYVL 72
LK+V T G + SI AQ GYVL
Sbjct: 692 LKVVSTIGAKKLSIHDAQIITSQDGYVL 719
>gnl|CDD|237511 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 27.5 bits (62), Expect = 3.5
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 111 VSSVPIVLVGNKKDL 125
V + P++LVGNK DL
Sbjct: 94 VGNNPVLLVGNKADL 108
>gnl|CDD|173954 cd08195, DHQS, Dehydroquinate synthase (DHQS) catalyzes the
conversion of DAHP to DHQ in shikimate pathway for
aromatic compounds synthesis. Dehydroquinate synthase
(DHQS) catalyzes the conversion of
3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to
dehydroquinate (DHQ) in the second step of the
shikimate pathway. This pathway, which involves seven
sequential enzymatic steps in the conversion of
erythrose 4-phosphate and phosphoenolpyruvate into
chorismate for subsequent synthesis of aromatic
compounds, is found in bacteria, microbial eukaryotes,
and plants, but not in mammals. Therefore, enzymes of
this pathway are attractive targets for the development
of non-toxic antimicrobial compounds, herbicides and
anti-parasitic agents. The activity of DHQS requires
nicotinamide adenine dinucleotide (NAD) as cofactor. A
single active site in DHQS catalyzes five sequential
reactions involving alcohol oxidation, phosphate
elimination, carbonyl reduction, ring opening, and
intramolecular aldol condensation. The binding of
substrates and ligands induces domain conformational
changes. In some fungi and protozoa, this domain is
fused with the other four domains in shikimate pathway
and forms a penta-domain AROM protein, which catalyzes
steps 2-6 in the shikimate pathway.
Length = 345
Score = 27.0 bits (61), Expect = 4.1
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 78 SHKSFEVVQILYDKLLDM 95
+ KS E ++ LYD LL+
Sbjct: 64 ASKSLETLEKLYDALLEA 81
>gnl|CDD|236617 PRK09723, PRK09723, putative fimbrial-like adhesin protein;
Provisional.
Length = 421
Score = 27.1 bits (60), Expect = 4.4
Identities = 11/46 (23%), Positives = 16/46 (34%), Gaps = 5/46 (10%)
Query: 22 DSYDPTIENTFVKTTRMNNQDYDLKLVDTAGQDEYSIFPAQYSMDI 67
+++PT V + N Y K AG I Y + I
Sbjct: 207 TNFNPT-GAQQVSLSLSKNYLYSFK-AYGAG---SGINEHSYFLKI 247
>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 = 26.4 bits (59), Expect = 5.6
Identities = 17/56 (30%), Positives = 22/56 (39%), Gaps = 3/56 (5%)
Query: 2 GYRSVGKSSLSIQFVDGQFVDSYDPTI-ENTFVKTTRMNNQDY-DLKLVDTAGQDE 55
G +VGKSSL + + GQ V P + L+DT G DE
Sbjct: 4 GRPNVGKSSL-LNALLGQNVGIVSPIPGTTRDPVRKEWELLPLGPVVLIDTPGLDE 58
>gnl|CDD|239265 cd02967, mauD, Methylamine utilization (mau) D family; mauD protein
is the translation product of the mauD gene found in
methylotrophic bacteria, which are able to use
methylamine as a sole carbon source and a nitrogen
source. mauD is an essential accessory protein for the
biosynthesis of methylamine dehydrogenase (MADH), the
enzyme that catalyzes the oxidation of methylamine and
other primary amines. MADH possesses an alpha2beta2
subunit structure; the alpha subunit is also referred to
as the large subunit. Each beta (small) subunit contains
a tryptophan tryptophylquinone (TTQ) prosthetic group.
Accessory proteins are essential for the proper
transport of MADH to the periplasm, TTQ synthesis and
the formation of several structural disulfide bonds.
Bacterial mutants containing an insertion on the mauD
gene were unable to grow on methylamine as a sole carbon
source, were found to lack the MADH small subunit and
had decreased amounts of the MADH large subunit.
Length = 114
Score = 25.8 bits (57), Expect = 6.3
Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 2/47 (4%)
Query: 53 QDEYSIFPAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKI 99
+ E+ F ++ ++ YVL S +++V ++ Y LLD G I
Sbjct: 64 KAEHQRFLKKHGLEAFPYVL--SAELGMAYQVSKLPYAVLLDEAGVI 108
>gnl|CDD|206722 cd04157, Arl6, Arf-like 6 (Arl6) GTPase. Arl6 (Arf-like 6) forms a
subfamily of the Arf family of small GTPases. Arl6
expression is limited to the brain and kidney in adult
mice, but it is expressed in the neural plate and
somites during embryogenesis, suggesting a possible role
for Arl6 in early development. Arl6 is also believed to
have a role in cilia or flagella function. Several
proteins have been identified that bind Arl6, including
Arl6 interacting protein (Arl6ip), and SEC61beta, a
subunit of the heterotrimeric conducting channel SEC61p.
Based on Arl6 binding to these effectors, Arl6 is also
proposed to play a role in protein transport, membrane
trafficking, or cell signaling during hematopoietic
maturation. At least three specific homozygous Arl6
mutations in humans have been found to cause
Bardet-Biedl syndrome, a disorder characterized by
obesity, retinopathy, polydactyly, renal and cardiac
malformations, learning disabilities, and
hypogenitalism. Older literature suggests that Arl6 is a
part of the Arl4/Arl7 subfamily, but analyses based on
more recent sequence data place Arl6 in its own
subfamily.
Length = 162
Score = 26.2 bits (58), Expect = 6.4
Identities = 18/77 (23%), Positives = 28/77 (36%), Gaps = 11/77 (14%)
Query: 49 DTAGQDEYSIFPAQYSMDIHGYVLVYSITSHKSFEVVQILYDKLLDMTGKIQNSSVKSPT 108
D +GQ +Y Y +I G + V + V + + LL+ P
Sbjct: 51 DMSGQGKYRGLWEHYYKNIQGIIFVIDSSDRLRMVVAKDELELLLN-----------HPD 99
Query: 109 SCVSSVPIVLVGNKKDL 125
+PI+ NK DL
Sbjct: 100 IKHRRIPILFYANKMDL 116
>gnl|CDD|187541 cd05230, UGD_SDR_e, UDP-glucuronate decarboxylase (UGD) and related
proteins, extended (e) SDRs. UGD catalyzes the
formation of UDP-xylose from UDP-glucuronate; it is an
extended-SDR, and has the characteristic glycine-rich
NAD-binding pattern, TGXXGXXG, and active site tetrad.
Extended SDRs are distinct from classical SDRs. In
addition to the Rossmann fold (alpha/beta folding
pattern with a central beta-sheet) core region typical
of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 305
Score = 26.4 bits (59), Expect = 7.2
Identities = 8/10 (80%), Positives = 10/10 (100%)
Query: 133 YDEGKRLAES 142
YDEGKR+AE+
Sbjct: 143 YDEGKRVAET 152
>gnl|CDD|234565 PRK00002, aroB, 3-dehydroquinate synthase; Reviewed.
Length = 358
Score = 25.9 bits (58), Expect = 10.0
Identities = 7/18 (38%), Positives = 12/18 (66%)
Query: 78 SHKSFEVVQILYDKLLDM 95
+KS E ++ +YD LL+
Sbjct: 71 QYKSLETLEKIYDALLEA 88
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
0.315 0.131 0.370
Gapped
Lambda K H
0.267 0.0889 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,597,937
Number of extensions: 645019
Number of successful extensions: 809
Number of sequences better than 10.0: 1
Number of HSP's gapped: 671
Number of HSP's successfully gapped: 119
Length of query: 157
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 68
Effective length of database: 6,990,096
Effective search space: 475326528
Effective search space used: 475326528
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (24.7 bits)