RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2646
(168 letters)
>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 = 226 bits (578), Expect = 6e-77
Identities = 91/112 (81%), Positives = 99/112 (88%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVNKLLVG 83
IWDTAGQERFRTITSSYYRGAHGII+VYD TDQE+FNN+KQWL+EIDRYA +NVNKLLVG
Sbjct: 55 IWDTAGQERFRTITSSYYRGAHGIIIVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVG 114
Query: 84 NKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEIKKR 135
NK D T KK VDY AKE+AD L IPFLETSAKN NVE+AF+TMA EIKKR
Sbjct: 115 NKCDLTDKKVVDYTEAKEFADELGIPFLETSAKNATNVEEAFMTMAREIKKR 166
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 184 bits (469), Expect = 2e-60
Identities = 65/127 (51%), Positives = 88/127 (69%), Gaps = 8/127 (6%)
Query: 17 RTRTLIV--------IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEE 68
+T+T+ V IWDTAGQERFR+ITSSYYRGA G ++VYD T++E+F NL+ WL+E
Sbjct: 38 KTKTIEVDGKRVKLQIWDTAGQERFRSITSSYYRGAVGALLVYDITNRESFENLENWLKE 97
Query: 69 IDRYACDNVNKLLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTM 128
+ YA NV +LVGNK+D ++ V + A+ +A+ +PF ETSAK NVE+AF +
Sbjct: 98 LREYASPNVVIMLVGNKSDLEEQRQVSREEAEAFAEEHGLPFFETSAKTNTNVEEAFEEL 157
Query: 129 ATEIKKR 135
A EI KR
Sbjct: 158 AREILKR 164
>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 = 183 bits (466), Expect = 6e-60
Identities = 63/112 (56%), Positives = 82/112 (73%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVNKLLVG 83
IWDTAGQERFRTIT+SYYRGA GII+VYD TD+++F N+K W+ ID +A ++V ++LVG
Sbjct: 56 IWDTAGQERFRTITTSYYRGAMGIILVYDITDEKSFENIKNWMRNIDEHASEDVERMLVG 115
Query: 84 NKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEIKKR 135
NK D K+ V + + A I FLETSAK NVE+AFLT+A +I K+
Sbjct: 116 NKCDMEEKRVVSKEEGEALAREYGIKFLETSAKANINVEEAFLTLAKDILKK 167
>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 = 177 bits (451), Expect = 1e-57
Identities = 58/107 (54%), Positives = 79/107 (73%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVNKLLVG 83
IWDTAGQERFR+ITSSYYRGAHG I+VYD T++E+F NL +WL E+ YA N+ +LVG
Sbjct: 53 IWDTAGQERFRSITSSYYRGAHGAILVYDVTNRESFENLDKWLNELKEYAPPNIPIILVG 112
Query: 84 NKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMAT 130
NK+D ++ V + A+++A + F ETSAK G NV++AF ++A
Sbjct: 113 NKSDLEDERQVSTEEAQQFAKENGLLFFETSAKTGENVDEAFESLAR 159
>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 = 172 bits (439), Expect = 7e-56
Identities = 58/111 (52%), Positives = 77/111 (69%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVNKLLVG 83
IWDTAGQERFR + YYRGA G ++VYD T +++F N+K+WLEEI R+A +NV +LVG
Sbjct: 52 IWDTAGQERFRALRPLYYRGAQGFLLVYDITSRDSFENVKKWLEEILRHADENVPIVLVG 111
Query: 84 NKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEIKK 134
NK D ++ V + + A L +PF+ETSAK NVE+AF +A EI K
Sbjct: 112 NKCDLEDQRVVSTEEGEALAKELGLPFMETSAKTNENVEEAFEELAREILK 162
>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 = 150 bits (382), Expect = 3e-47
Identities = 59/123 (47%), Positives = 84/123 (68%), Gaps = 8/123 (6%)
Query: 18 TRTLIV--------IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEI 69
TRT+ + IWDTAGQER+R ITS+YYRGA G ++VYD T + TF N+++WL+E+
Sbjct: 42 TRTIQIDGKTIKAQIWDTAGQERYRAITSAYYRGAVGALLVYDITKKSTFENVERWLKEL 101
Query: 70 DRYACDNVNKLLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMA 129
+A N+ +LVGNK+D +AV + AK +A+ + F+ETSA +G NVE+AF +
Sbjct: 102 RDHADSNIVIMLVGNKSDLRHLRAVPTEEAKAFAEKNGLSFIETSALDGTNVEEAFKQLL 161
Query: 130 TEI 132
TEI
Sbjct: 162 TEI 164
>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 = 143 bits (364), Expect = 1e-44
Identities = 55/116 (47%), Positives = 79/116 (68%), Gaps = 2/116 (1%)
Query: 18 TRTLIVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYAC-DN 76
+ + IWDTAGQERFRT+TSSYYRGA G+I+VYD T ++TF+NL WL E+D Y+ +
Sbjct: 47 KKVKLAIWDTAGQERFRTLTSSYYRGAQGVILVYDVTRRDTFDNLDTWLNELDTYSTNPD 106
Query: 77 VNKLLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEI 132
K+LVGNK D+ + + V + +++A + F+ETSAK V+QAF + +I
Sbjct: 107 AVKMLVGNKIDKEN-REVTREEGQKFARKHNMLFIETSAKTRIGVQQAFEELVEKI 161
>gnl|CDD|133310 cd04110, Rab35, Rab GTPase family 35 (Rab35). Rab35 is one of
several Rab proteins to be found to participate in the
regulation of osteoclast cells in rats. In addition,
Rab35 has been identified as a protein that interacts
with nucleophosmin-anaplastic lymphoma kinase (NPM-ALK)
in human cells. Overexpression of NPM-ALK is a key
oncogenic event in some anaplastic large-cell lymphomas;
since Rab35 interacts with N|PM-ALK, it may provide a
target for cancer treatments. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 199
Score = 143 bits (362), Expect = 7e-44
Identities = 68/142 (47%), Positives = 94/142 (66%), Gaps = 4/142 (2%)
Query: 19 RTLIVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVN 78
R + IWDTAGQERFRTITS+YYRG HG+IVVYD T+ E+F N+K+WL+EI++ CD+V
Sbjct: 54 RVKLQIWDTAGQERFRTITSTYYRGTHGVIVVYDVTNGESFVNVKRWLQEIEQ-NCDDVC 112
Query: 79 KLLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEI---KKR 135
K+LVGNKND +K V+ + A ++A + I ETSAK NVE+ F + + KK
Sbjct: 113 KVLVGNKNDDPERKVVETEDAYKFAGQMGISLFETSAKENINVEEMFNCITELVLRAKKD 172
Query: 136 VTKDEKPSSESDAKKLNLNSGK 157
++ ++D KL NS +
Sbjct: 173 NLAKQQQQQQNDVVKLPKNSKR 194
>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 = 140 bits (355), Expect = 3e-43
Identities = 58/110 (52%), Positives = 77/110 (70%), Gaps = 1/110 (0%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVNKLLVG 83
IWDTAGQERFRTIT SYYR A+G I+ YD T + +F ++ W+EE+++Y NV LL+G
Sbjct: 56 IWDTAGQERFRTITQSYYRSANGAIIAYDITRRSSFESVPHWIEEVEKYGASNVVLLLIG 115
Query: 84 NKNDQTSKKAVDYQVAKEYADHLKIPF-LETSAKNGANVEQAFLTMATEI 132
NK D ++ V ++ A A+H I LETSAK +NVE+AFL MATE+
Sbjct: 116 NKCDLEEQREVLFEEACTLAEHYGILAVLETSAKESSNVEEAFLLMATEL 165
>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 = 135 bits (341), Expect = 5e-41
Identities = 55/112 (49%), Positives = 78/112 (69%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVNKLLVG 83
IWDTAGQE FR+IT SYYRGA G ++VYD T +ETFN+L WLE+ +++ N+ +L+G
Sbjct: 57 IWDTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQHSNSNMTIMLIG 116
Query: 84 NKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEIKKR 135
NK D S++ V Y+ + +A + F+ETSAK +NVE+AF+ A EI +
Sbjct: 117 NKCDLESRREVSYEEGEAFAREHGLIFMETSAKTASNVEEAFINTAKEIYDK 168
>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 = 131 bits (332), Expect = 1e-39
Identities = 55/109 (50%), Positives = 76/109 (69%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVNKLLVG 83
IWDTAGQERFR+IT SYYR A+ +I+ YD T +E+F L +WL EI++YA + V +LVG
Sbjct: 60 IWDTAGQERFRSITQSYYRSANALILTYDITCEESFRCLPEWLREIEQYANNKVITILVG 119
Query: 84 NKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEI 132
NK D ++ V Q A+E++D + +LETSAK NVE+ FL +A +
Sbjct: 120 NKIDLAERREVSQQRAEEFSDAQDMYYLETSAKESDNVEKLFLDLACRL 168
>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 = 131 bits (331), Expect = 2e-39
Identities = 51/109 (46%), Positives = 70/109 (64%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVNKLLVG 83
IWDTAGQER+R++ YYRGA IVVYD T +E+F K W++E+ + N+ L G
Sbjct: 54 IWDTAGQERYRSLAPMYYRGAAAAIVVYDITSEESFEKAKSWVKELQEHGPPNIVIALAG 113
Query: 84 NKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEI 132
NK D SK+ V + A+EYAD + F+ETSAK G NV + F +A ++
Sbjct: 114 NKADLESKRQVSTEEAQEYADENGLLFMETSAKTGENVNELFTEIARKL 162
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 131 bits (330), Expect = 7e-39
Identities = 63/152 (41%), Positives = 90/152 (59%), Gaps = 7/152 (4%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVNKLLVG 83
IWDTAGQE FR+IT SYYRGA G ++VYD T +ETFN+L WLE+ ++A N+ +L+G
Sbjct: 59 IWDTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLASWLEDARQHANANMTIMLIG 118
Query: 84 NKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEIKKRVTKDE-KP 142
NK D ++AV + +++A + F+E SAK NVE+AF+ A +I K++
Sbjct: 119 NKCDLAHRRAVSTEEGEQFAKEHGLIFMEASAKTAQNVEEAFIKTAAKIYKKIQDGVFDV 178
Query: 143 SSESDAKKLNLNSGKPVDAPR------SGGCC 168
S+ES K+ + R GGCC
Sbjct: 179 SNESYGIKVGYGAIPGASGGRDGTSSQGGGCC 210
>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 = 126 bits (317), Expect = 6e-37
Identities = 58/164 (35%), Positives = 90/164 (54%), Gaps = 10/164 (6%)
Query: 15 EERTRTLIVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRY-A 73
E R + +WDTAGQERFR+IT SYYR + G+++V+D T++E+F ++ WLEE +
Sbjct: 47 EPGVRIKLQLWDTAGQERFRSITRSYYRNSVGVLLVFDITNRESFEHVHDWLEEARSHIQ 106
Query: 74 CDNVNKLLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEIK 133
+LVG+K D S++ V + A++ A L + ++ETSA+ G NVE+AF + EI
Sbjct: 107 PHRPVFILVGHKCDLESQRQVTREEAEKLAKDLGMKYIETSARTGDNVEEAFELLTQEIY 166
Query: 134 KRVTKDEKP---------SSESDAKKLNLNSGKPVDAPRSGGCC 168
+R+ + E S + +L P A CC
Sbjct: 167 ERIKRGELCALDGWDGVKSGFPAGRAFSLEERSPTFASPEKSCC 210
>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 = 124 bits (313), Expect = 8e-37
Identities = 55/109 (50%), Positives = 71/109 (65%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVNKLLVG 83
IWDTAGQERFR +T SYYRGA G ++VYD T + T+N+L WL + N L+G
Sbjct: 55 IWDTAGQERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTVIFLIG 114
Query: 84 NKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEI 132
NK D +++ V Y+ AK++AD + FLE SAK G NVE AFL A +I
Sbjct: 115 NKADLEAQRDVTYEEAKQFADENGLLFLECSAKTGENVEDAFLETAKKI 163
>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 = 123 bits (310), Expect = 2e-36
Identities = 45/111 (40%), Positives = 71/111 (63%)
Query: 22 IVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVNKLL 81
+ IWDTAGQER+ + YYR A G I+VYD TD ++F +K+W++E+ + +N++ ++
Sbjct: 51 LAIWDTAGQERYHALGPIYYRDADGAILVYDITDADSFQKVKKWIKELKQMRGNNISLVI 110
Query: 82 VGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEI 132
VGNK D ++ V A+EYA + ETSAK G +E+ FL++A +
Sbjct: 111 VGNKIDLERQRVVSKSEAEEYAKSVGAKHFETSAKTGKGIEELFLSLAKRM 161
>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 = 122 bits (307), Expect = 1e-35
Identities = 53/118 (44%), Positives = 80/118 (67%)
Query: 18 TRTLIVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNV 77
+ + IWDTAGQERFR++T +YYR AH ++++YD T++ +F+N++ WL EI YA +V
Sbjct: 48 VKVKLQIWDTAGQERFRSVTHAYYRDAHALLLLYDVTNKSSFDNIRAWLTEILEYAQSDV 107
Query: 78 NKLLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEIKKR 135
+L+GNK D + ++ V + + A +PF+ETSAK G NVE AF +A E+K R
Sbjct: 108 VIMLLGNKADMSGERVVKREDGERLAKEYGVPFMETSAKTGLNVELAFTAVAKELKHR 165
>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 = 120 bits (303), Expect = 3e-35
Identities = 43/109 (39%), Positives = 70/109 (64%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVNKLLVG 83
+WDTAGQERFR++ SY R + +VVYD T++++F+N +W++++ ++V +LVG
Sbjct: 53 LWDTAGQERFRSLIPSYIRDSSVAVVVYDITNRQSFDNTDKWIDDVRDERGNDVIIVLVG 112
Query: 84 NKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEI 132
NK D + K+ V + ++ A F+ETSAK G NV+Q F +A +
Sbjct: 113 NKTDLSDKRQVSTEEGEKKAKENNAMFIETSAKAGHNVKQLFKKIAQAL 161
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 122 bits (306), Expect = 3e-35
Identities = 70/153 (45%), Positives = 93/153 (60%), Gaps = 6/153 (3%)
Query: 19 RTLIVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQ-WLEEIDRYACD-N 76
R + IWDTAGQERFRT+TSSYYR A GII+VYD T +ETF NL W +E++ Y+ + +
Sbjct: 61 RLKLTIWDTAGQERFRTLTSSYYRNAQGIILVYDVTRRETFTNLSDVWGKEVELYSTNQD 120
Query: 77 VNKLLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEIKKRV 136
K+LVGNK D+ S++ V + A FLE SAK NVEQ F +A +I +
Sbjct: 121 CVKMLVGNKVDRESERDVSREEGMALAKEHGCLFLECSAKTRENVEQCFEELALKIMEVP 180
Query: 137 TKDEKPSSESDAKKLNLNSGKPVD-APRSGGCC 168
+ E+ S+ A K N+ KP P +GGCC
Sbjct: 181 SLLEEGST---AVKRNILKQKPEHQPPPNGGCC 210
>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 = 120 bits (302), Expect = 3e-35
Identities = 54/111 (48%), Positives = 70/111 (63%)
Query: 22 IVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVNKLL 81
+ IWDTAGQERFR++T SYYRGA G ++VYD T +E+FN L WL + A ++ +L
Sbjct: 51 LQIWDTAGQERFRSVTRSYYRGAAGALLVYDITSRESFNALTNWLTDARTLASPDIVIIL 110
Query: 82 VGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEI 132
VGNK D + V + A +A + FLETSA G NVE+AFL A I
Sbjct: 111 VGNKKDLEDDREVTFLEASRFAQENGLLFLETSALTGENVEEAFLKCARSI 161
>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 = 118 bits (296), Expect = 3e-34
Identities = 51/107 (47%), Positives = 71/107 (66%)
Query: 19 RTLIVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVN 78
R + IWDTAGQER+RTIT++YYRGA G I++YD T++E+FN ++ W +I Y+ DN
Sbjct: 49 RIKLQIWDTAGQERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSWDNAQ 108
Query: 79 KLLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAF 125
+LVGNK D ++ V + ++ AD L F E SAK NV+Q F
Sbjct: 109 VILVGNKCDMEDERVVSAERGRQLADQLGFEFFEASAKENINVKQVF 155
>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 = 117 bits (293), Expect = 2e-33
Identities = 54/117 (46%), Positives = 81/117 (69%), Gaps = 1/117 (0%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVNKLLVG 83
IWDTAGQERF +ITS+YYR A GII+VYD T +ETF++L +W++ ID+YA ++ LLVG
Sbjct: 53 IWDTAGQERFNSITSAYYRSAKGIILVYDITKKETFDDLPKWMKMIDKYASEDAELLLVG 112
Query: 84 NKNDQTSKKAVDYQVAKEYADHLK-IPFLETSAKNGANVEQAFLTMATEIKKRVTKD 139
NK D + + + Q +++A + + F E SAK+ NV++ FL + +I K++ D
Sbjct: 113 NKLDCETDREITRQQGEKFAQQITGMRFCEASAKDNFNVDEIFLKLVDDILKKMPLD 169
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 117 bits (294), Expect = 2e-33
Identities = 64/152 (42%), Positives = 92/152 (60%), Gaps = 13/152 (8%)
Query: 15 EERTRTLIV--------IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWL 66
E TRTL V IWDTAGQER+R ITS+YYRGA G ++VYD T ++TF+N+++WL
Sbjct: 48 EFATRTLQVEGKTVKAQIWDTAGQERYRAITSAYYRGAVGALLVYDITKRQTFDNVQRWL 107
Query: 67 EEIDRYACDNVNKLLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFL 126
E+ +A N+ ++ GNK+D ++V + + A+ + FLETSA NVE+AF
Sbjct: 108 RELRDHADSNIVIMMAGNKSDLNHLRSVAEEDGQALAEKEGLSFLETSALEATNVEKAFQ 167
Query: 127 TMATEIKKRVTKDEKPSSESDAKKLNLNSGKP 158
T+ EI ++K + E+ A NSG P
Sbjct: 168 TILLEIYHIISKKALAAQEAAA-----NSGLP 194
>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 = 113 bits (284), Expect = 3e-32
Identities = 48/121 (39%), Positives = 81/121 (66%), Gaps = 1/121 (0%)
Query: 17 RTRTLIVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYA-CD 75
R + +WDTAGQERFR++T++++R A G ++++D T +++F N++ W+ ++ +A C+
Sbjct: 60 AFRVHLQLWDTAGQERFRSLTTAFFRDAMGFLLMFDLTSEQSFLNVRNWMSQLQAHAYCE 119
Query: 76 NVNKLLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEIKKR 135
N + +L+GNK D ++ V + A+E AD IP+ ETSA G NVE+A T+ I KR
Sbjct: 120 NPDIVLIGNKADLPDQREVSERQARELADKYGIPYFETSAATGQNVEKAVETLLDLIMKR 179
Query: 136 V 136
+
Sbjct: 180 M 180
>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 = 109 bits (275), Expect = 5e-31
Identities = 45/112 (40%), Positives = 69/112 (61%), Gaps = 5/112 (4%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYAC----DNVNK 79
IWDTAGQERF+++ ++YRGA ++VYD T+ ++F +L W +E A +N
Sbjct: 53 IWDTAGQERFQSLGVAFYRGADCCVLVYDVTNPKSFESLDSWRDEFLIQASPRDPENFPF 112
Query: 80 LLVGNKNDQTSKKAVDYQVAKEY-ADHLKIPFLETSAKNGANVEQAFLTMAT 130
+++GNK D K+ V + A+++ IP+ ETSAK NV+QAF T+A
Sbjct: 113 VVLGNKIDLEEKRQVSTKKAQQWCKSKGNIPYFETSAKEAINVDQAFETIAR 164
>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 = 109 bits (274), Expect = 6e-31
Identities = 43/110 (39%), Positives = 62/110 (56%), Gaps = 1/110 (0%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRY-ACDNVNKLLV 82
I DTAGQE F + Y R G I+VY T +E+F +K E+I R ++V +LV
Sbjct: 51 ILDTAGQEEFSAMRDQYIRNGDGFILVYSITSRESFEEIKNIREQILRVKDKEDVPIVLV 110
Query: 83 GNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEI 132
GNK D +++ V + + A+ PFLETSAK N+++ F T+ EI
Sbjct: 111 GNKCDLENERQVSTEEGEALAEEWGCPFLETSAKTNINIDELFNTLVREI 160
>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 = 104 bits (261), Expect = 7e-29
Identities = 50/130 (38%), Positives = 80/130 (61%), Gaps = 13/130 (10%)
Query: 17 RTRTLIV--------IWDTAGQERFR-TITSSYYRGAHGIIVVYDCTDQETFNNLKQWLE 67
R RT+ + +WDTAGQERFR ++ YYR H ++ VYD T+ +F++L W+E
Sbjct: 40 RERTVEIDGERIKVQLWDTAGQERFRKSMVQHYYRNVHAVVFVYDVTNMASFHSLPSWIE 99
Query: 68 EIDRYACDN-VNKLLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGA---NVEQ 123
E ++++ N V ++LVGNK D + V +A+ +AD +P ETSAK+ + +VE
Sbjct: 100 ECEQHSLPNEVPRILVGNKCDLREQIQVPTDLAQRFADAHSMPLFETSAKDPSENDHVEA 159
Query: 124 AFLTMATEIK 133
F+T+A ++K
Sbjct: 160 IFMTLAHKLK 169
>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 = 100 bits (249), Expect = 3e-27
Identities = 43/108 (39%), Positives = 69/108 (63%)
Query: 22 IVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVNKLL 81
I IWDTAGQER++TIT YYR A GI +VYD + + ++ ++ +W+ ++D YA + V K+L
Sbjct: 51 IQIWDTAGQERYQTITKQYYRRAQGIFLVYDISSERSYQHIMKWVSDVDEYAPEGVQKIL 110
Query: 82 VGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMA 129
+GNK D+ K+ V + + A + F ETSA N++++F +
Sbjct: 111 IGNKADEEQKRQVGDEQGNKLAKEYGMDFFETSACTNKNIKESFTRLT 158
>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 = 92.2 bits (230), Expect = 2e-24
Identities = 48/113 (42%), Positives = 68/113 (60%), Gaps = 1/113 (0%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDR-YACDNVNKLLV 82
I DTAGQE F + Y R G ++VY TD+++F +K++ E+I R D+V +LV
Sbjct: 52 ILDTAGQEEFSAMRDQYMRTGEGFLLVYSITDRQSFEEIKKFREQILRVKDRDDVPIVLV 111
Query: 83 GNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEIKKR 135
GNK D S++ V + KE A PFLETSAK NV++AF + EI+K+
Sbjct: 112 GNKCDLESERVVSTEEGKELARQWGCPFLETSAKERVNVDEAFYDLVREIRKK 164
>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 = 91.5 bits (228), Expect = 5e-24
Identities = 46/113 (40%), Positives = 66/113 (58%), Gaps = 1/113 (0%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDR-YACDNVNKLLV 82
I DTAGQE F + Y R G ++VY TD+++F + ++ E+I R D+V +LV
Sbjct: 54 ILDTAGQEEFSAMRDQYMRTGEGFLLVYSITDRQSFEEIAKFREQILRVKDRDDVPIVLV 113
Query: 83 GNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEIKKR 135
GNK D +++ V + KE A PFLETSAK NV++AF + EI+K
Sbjct: 114 GNKCDLENERVVSTEEGKELARQWGCPFLETSAKERINVDEAFYDLVREIRKS 166
>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 = 91.5 bits (227), Expect = 1e-23
Identities = 52/159 (32%), Positives = 73/159 (45%), Gaps = 16/159 (10%)
Query: 15 EERTRTLIVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYAC 74
ER TL IWDTAG ER+ ++ YYRGA IV YD TD +F K W++E+
Sbjct: 46 GERVVTL-GIWDTAGSERYEAMSRIYYRGAKAAIVCYDLTDSSSFERAKFWVKELQN--L 102
Query: 75 DNVNKL-LVGNKND----QTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMA 129
+ K+ L G K+D S + VD+ +++AD +K ETS+K G NV++ F +A
Sbjct: 103 EEHCKIYLCGTKSDLIEQDRSLRQVDFHDVQDFADEIKAQHFETSSKTGQNVDELFQKVA 162
Query: 130 TEIKKRVTKDEKPSSESDAKKLNLNSGKPVDAPRSGGCC 168
+ R D L CC
Sbjct: 163 EDFVSRANNQMNTEKGVD---LGQKKN-----SYFYSCC 193
>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 = 90.1 bits (224), Expect = 4e-23
Identities = 47/154 (30%), Positives = 67/154 (43%), Gaps = 15/154 (9%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVNK---- 79
+WD AGQERF +T YY+GA G I+V+D T TF + +W ++D +
Sbjct: 54 LWDIAGQERFGGMTRVYYKGAVGAIIVFDVTRPSTFEAVLKWKADLDSKVTLPNGEPIPA 113
Query: 80 LLVGNKNDQTSKKAVDYQVAKEYAD-----HLKIPFLETSAKNGANVEQAFLTMATEIKK 134
LL+ NK D K E D + I + ETSAK N+E+A + I K
Sbjct: 114 LLLANKCDL---KKERLAKDPEQMDQFCKENGFIGWFETSAKENINIEEAMRFLVKNILK 170
Query: 135 RVTKDEKPSSESDAKKLNLNSGKPVDAPRSGGCC 168
S E D + + + +S CC
Sbjct: 171 N--DKGLQSPEPDEDNVIDLKQETTTS-KSKSCC 201
>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 = 89.6 bits (222), Expect = 5e-23
Identities = 45/111 (40%), Positives = 69/111 (62%), Gaps = 1/111 (0%)
Query: 19 RTLIVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVN 78
R + +WDT+GQ RF TI SY RGA GII+VYD T++ +F+ + +W++EID +A V
Sbjct: 54 RVKLQLWDTSGQGRFCTIFRSYSRGAQGIILVYDITNRWSFDGIDRWIKEIDEHA-PGVP 112
Query: 79 KLLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMA 129
K+LVGN+ K+ V + A+ YA+ + F E S N+ ++F +A
Sbjct: 113 KILVGNRLHLAFKRQVATEQAQAYAERNGMTFFEVSPLCNFNITESFTELA 163
>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 = 89.0 bits (221), Expect = 5e-23
Identities = 39/117 (33%), Positives = 66/117 (56%), Gaps = 1/117 (0%)
Query: 14 KEERTRTLIVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYA 73
++ +++WDTAGQE F IT +YYRGA I+V+ TD+E+F ++ W E+++
Sbjct: 45 RQSDEDVRLMLWDTAGQEEFDAITKAYYRGAQACILVFSTTDRESFEAIESWKEKVEA-E 103
Query: 74 CDNVNKLLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMAT 130
C ++ +LV K D + + + A+ A L++P TS K+ NV + F +A
Sbjct: 104 CGDIPMVLVQTKIDLLDQAVITNEEAEALAKRLQLPLFRTSVKDDFNVTELFEYLAE 160
>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 = 89.0 bits (221), Expect = 5e-23
Identities = 45/115 (39%), Positives = 67/115 (58%), Gaps = 1/115 (0%)
Query: 21 LIVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRY-ACDNVNK 79
+ I DTAGQE + I +Y+R G ++V+ TD E+F L ++ E+I R DNV
Sbjct: 49 QLNILDTAGQEDYAAIRDNYFRSGEGFLLVFSITDMESFTALAEFREQILRVKEDDNVPL 108
Query: 80 LLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEIKK 134
LLVGNK D K+ V + A A+ + ++ETSAK ANV++ F + EI++
Sbjct: 109 LLVGNKCDLEDKRQVSVEEAANLAEQWGVNYVETSAKTRANVDKVFFDLVREIRQ 163
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 90.0 bits (223), Expect = 7e-23
Identities = 51/162 (31%), Positives = 79/162 (48%), Gaps = 18/162 (11%)
Query: 11 QNKKEERTRTLIVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQE-TFNNLKQWLEEI 69
+ + R + +WDTAGQE +R++ YYRGA+GI++VYD T +E + ++WLEE+
Sbjct: 45 KTIEPYRRNIKLQLWDTAGQEEYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEEL 104
Query: 70 DRYACDNVNKLLVGNKND------------QTSKKAVDYQVAKEYADHLKIP---FLETS 114
A D+V LLVGNK D + V V A ++ LETS
Sbjct: 105 RELAPDDVPILLVGNKIDLFDEQSSSEEILNQLNREVVLLVLAPKAVLPEVANPALLETS 164
Query: 115 AKN--GANVEQAFLTMATEIKKRVTKDEKPSSESDAKKLNLN 154
AK+ G NV + F + ++ + + K + +LN
Sbjct: 165 AKSLTGPNVNELFKELLRKLLEEIEKLVLKNELRQLDRLNNP 206
>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 = 87.5 bits (217), Expect = 2e-22
Identities = 40/114 (35%), Positives = 64/114 (56%), Gaps = 2/114 (1%)
Query: 21 LIVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYA-CDNVNK 79
L+ I DTAGQE + + Y R G + V+ +++F ++ + E+I R D+V
Sbjct: 50 LLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINSRKSFEDIHTYREQIKRVKDSDDVPM 109
Query: 80 LLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEIK 133
+LVGNK D ++ V + ++ A IP++ETSAK VE+AF T+ EI+
Sbjct: 110 VLVGNKCDLAART-VSTRQGQDLAKSYGIPYIETSAKTRQGVEEAFYTLVREIR 162
>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 = 87.5 bits (217), Expect = 2e-22
Identities = 40/103 (38%), Positives = 60/103 (58%), Gaps = 1/103 (0%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYA-CDNVNKLLV 82
I DTAGQE F + Y R G ++V+ TD+ +F + ++ +I R D +LV
Sbjct: 54 ILDTAGQEEFSAMREQYMRTGEGFLLVFSVTDRGSFEEVDKFHTQILRVKDRDEFPMILV 113
Query: 83 GNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAF 125
GNK D ++ V + +E A LKIP++ETSAK+ NV++AF
Sbjct: 114 GNKADLEHQRQVSREEGQELARQLKIPYIETSAKDRVNVDKAF 156
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 86.1 bits (213), Expect = 1e-21
Identities = 49/134 (36%), Positives = 69/134 (51%), Gaps = 1/134 (0%)
Query: 21 LIVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYA-CDNVNK 79
L+ I DTAGQE + + Y R G + VY T + +F + + E+I R D V
Sbjct: 54 LLDILDTAGQEEYSAMRDQYMRTGQGFLCVYSITSRSSFEEIASFREQILRVKDKDRVPM 113
Query: 80 LLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEIKKRVTKD 139
+LVGNK D S++ V +E A IPFLETSAK NV++AF + EI+K + +D
Sbjct: 114 ILVGNKCDLDSERQVSTGEGQELAKSFGIPFLETSAKQRVNVDEAFYELVREIRKYLKED 173
Query: 140 EKPSSESDAKKLNL 153
+ L L
Sbjct: 174 MPSQKQKKKGGLCL 187
>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 = 85.5 bits (212), Expect = 1e-21
Identities = 31/114 (27%), Positives = 58/114 (50%), Gaps = 5/114 (4%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVNK---- 79
+D +G + + + +Y+ G+++VYD TD+++F L WL+E+ + + N
Sbjct: 53 FFDLSGHPEYLEVRNEFYKDTQGVLLVYDVTDRQSFEALDSWLKEMKQEGGPHGNMENIV 112
Query: 80 -LLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEI 132
++ NK D T +AV + +A+ + ETSA G V + F T+ + I
Sbjct: 113 VVVCANKIDLTKHRAVSEDEGRLWAESKGFKYFETSACTGEGVNEMFQTLFSSI 166
>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 = 85.4 bits (212), Expect = 2e-21
Identities = 42/112 (37%), Positives = 65/112 (58%), Gaps = 1/112 (0%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEI-DRYACDNVNKLLV 82
I DTAGQ+ + + Y G HG I+VY T +++F +K ++I D ++V +LV
Sbjct: 53 IVDTAGQDEYSILPQKYSIGIHGYILVYSVTSRKSFEVVKVIYDKILDMLGKESVPIVLV 112
Query: 83 GNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEIKK 134
GNK+D ++ V + K+ A+ FLE+SAK NVE+AF + EI+K
Sbjct: 113 GNKSDLHMERQVSAEEGKKLAESWGAAFLESSAKENENVEEAFELLIEEIEK 164
>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 = 83.8 bits (207), Expect = 5e-21
Identities = 42/111 (37%), Positives = 61/111 (54%), Gaps = 5/111 (4%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEE-IDRYACDNVNKLLV 82
+WDTAGQERF+ I S+YYRGA II+V+D TD + + +QWLE+ + +V LV
Sbjct: 53 LWDTAGQERFKCIASTYYRGAQAIIIVFDLTDVASLEHTRQWLEDALKENDPSSVLLFLV 112
Query: 83 GNKNDQTSKKAVDYQVAKE---YADHLKIPFLETSAKNGANVEQAFLTMAT 130
G K D +S + ++ A +K + SA G NV F +A+
Sbjct: 113 GTKKDLSSPAQY-ALMEQDAIKLAREMKAEYWAVSALTGENVRDFFFRVAS 162
>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 = 83.4 bits (206), Expect = 8e-21
Identities = 40/105 (38%), Positives = 58/105 (55%), Gaps = 4/105 (3%)
Query: 21 LIVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVNKL 80
L+ WDTAGQERF+T+ +SYY AH I+V+D T + T+ NL +W EE+ Y + +
Sbjct: 50 LVDFWDTAGQERFQTMHASYYHKAHACILVFDVTRKITYKNLSKWYEELREY-RPEIPCI 108
Query: 81 LVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAF 125
+V NK D Q +A+ +P SA +G NV + F
Sbjct: 109 VVANKIDLDPSVT---QKKFNFAEKHNLPLYYVSAADGTNVVKLF 150
>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 = 81.0 bits (200), Expect = 6e-20
Identities = 38/109 (34%), Positives = 61/109 (55%), Gaps = 1/109 (0%)
Query: 22 IVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACD-NVNKL 80
+ I+D+AGQE F + + + + VVYD T++ +FNN +W+ + ++ + +
Sbjct: 55 LFIFDSAGQELFSDMVENVWEQPAVVCVVYDVTNEVSFNNCSRWINRVRTHSHGLHTPGV 114
Query: 81 LVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMA 129
LVGNK D T ++ VD A+ A + F ETSAK G E FL++A
Sbjct: 115 LVGNKCDLTDRREVDAAQAQALAQANTLKFYETSAKEGVGYEAPFLSLA 163
>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 = 80.3 bits (198), Expect = 1e-19
Identities = 40/112 (35%), Positives = 59/112 (52%), Gaps = 1/112 (0%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYA-CDNVNKLLV 82
I DTAG E+F + Y + G ++VY T Q TFN+L+ E+I R ++V +LV
Sbjct: 53 ILDTAGTEQFTAMRDLYMKNGQGFVLVYSITAQSTFNDLQDLREQILRVKDTEDVPMILV 112
Query: 83 GNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEIKK 134
GNK D ++ V + + A FLETSAK NV + F + +I +
Sbjct: 113 GNKCDLEDERVVGKEQGQNLARQWGCAFLETSAKAKINVNEIFYDLVRQINR 164
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 80.6 bits (198), Expect = 1e-19
Identities = 43/109 (39%), Positives = 64/109 (58%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVNKLLVG 83
+WDTAGQERFR++ SY R + IVVYD T++++F N +W+++I +V LVG
Sbjct: 33 LWDTAGQERFRSLIPSYIRDSAAAIVVYDITNRQSFENTTKWIQDILNERGKDVIIALVG 92
Query: 84 NKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEI 132
NK D + V Y+ + A F ETSAK G N++ F +A ++
Sbjct: 93 NKTDLGDLRKVTYEEGMQKAQEYNTMFHETSAKAGHNIKVLFKKIAAKL 141
>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 = 79.9 bits (197), Expect = 2e-19
Identities = 38/110 (34%), Positives = 60/110 (54%), Gaps = 1/110 (0%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRY-ACDNVNKLLV 82
I DTAG E+F ++ Y + G IVVY +Q+TF ++K ++I R + V +LV
Sbjct: 53 ILDTAGTEQFASMRDLYIKNGQGFIVVYSLVNQQTFQDIKPMRDQIVRVKGYEKVPIILV 112
Query: 83 GNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEI 132
GNK D S++ V + A+ PF+ETSAK+ V + F + ++
Sbjct: 113 GNKVDLESEREVSSAEGRALAEEWGCPFMETSAKSKTMVNELFAEIVRQM 162
>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 = 78.8 bits (194), Expect = 5e-19
Identities = 37/106 (34%), Positives = 57/106 (53%), Gaps = 4/106 (3%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYA-CDNVNK--- 79
IWDTAGQERFR++ + +YRG+ ++ + D ++F NL W +E YA
Sbjct: 58 IWDTAGQERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPESFPF 117
Query: 80 LLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAF 125
+++GNK D ++ + D+ P+ ETSAK+ NV AF
Sbjct: 118 VILGNKIDIPERQVSTEEAQAWCRDNGDYPYFETSAKDATNVAAAF 163
>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 = 78.7 bits (194), Expect = 5e-19
Identities = 35/115 (30%), Positives = 57/115 (49%), Gaps = 8/115 (6%)
Query: 22 IVIWDTAGQERF-----RTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDN 76
+V+ DT G + F + RGA I++V D TD+E+ + K L + R +
Sbjct: 49 LVLVDTPGLDEFGGLGREELARLLLRGADLILLVVDSTDRESEEDAK--LLILRRLRKEG 106
Query: 77 VNKLLVGNKNDQTSKKAVDYQV-AKEYADHLKIPFLETSAKNGANVEQAFLTMAT 130
+ +LVGNK D ++ V+ + +E A L +P E SAK G V++ F +
Sbjct: 107 IPIILVGNKIDLLEEREVEELLRLEELAKILGVPVFEVSAKTGEGVDELFEKLIE 161
>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 = 76.2 bits (188), Expect = 5e-18
Identities = 35/110 (31%), Positives = 56/110 (50%), Gaps = 11/110 (10%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVNKLLVG 83
+WDTAGQE+F + YY I+++D T + T+ N+ W ++ R C+N+ +L G
Sbjct: 53 VWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRVTYKNVPNWHRDLVR-VCENIPIVLCG 111
Query: 84 NKND----QTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMA 129
NK D + K + + K + E SAK+ N E+ FL +A
Sbjct: 112 NKVDIKDRKVKPKQITFHRKKNLQ------YYEISAKSNYNFEKPFLWLA 155
>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 = 74.1 bits (183), Expect = 3e-17
Identities = 29/119 (24%), Positives = 51/119 (42%), Gaps = 14/119 (11%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQ-WLEEIDRYACDNVNKLLV 82
+WDTAGQE + + Y ++ + +F N+K W EI Y C NV +LV
Sbjct: 52 LWDTAGQEEYDRLRPLSYPQTDVFLLCFSVDSPSSFENVKTKWYPEIKHY-CPNVPIILV 110
Query: 83 GNKND-----------QTSKKAVDYQVAKEYADHLK-IPFLETSAKNGANVEQAFLTMA 129
G K D + +K + + ++ A + + ++E SA +++ F
Sbjct: 111 GTKIDLRDDGNTLKKLEKKQKPITPEEGEKLAKEIGAVKYMECSALTQEGLKEVFDEAI 169
>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 = 72.4 bits (178), Expect = 1e-16
Identities = 34/108 (31%), Positives = 50/108 (46%), Gaps = 3/108 (2%)
Query: 20 TLIVIWDTAGQERFRTITSSYYRGAHGIIVVYDCT--DQETFNNLKQWLEEIDRYACDNV 77
+ DTAGQE + I YYR + V+D + L++ +EI +A V
Sbjct: 51 YKFNLLDTAGQEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAESGV 110
Query: 78 NKLLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAF 125
+LVGNK D K + VA +A P + SA+ G N++ AF
Sbjct: 111 PIILVGNKIDLRDAK-LKTHVAFLFAKLNGEPIIPLSAETGKNIDSAF 157
>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 = 70.7 bits (173), Expect = 5e-16
Identities = 40/111 (36%), Positives = 61/111 (54%), Gaps = 2/111 (1%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYA-CDNVNKLLV 82
I DTAG E+F + Y + G +VY T Q++FN+L+ E+I R ++V +LV
Sbjct: 53 ILDTAGTEQFTAMRDLYIKNGQGFALVYSITAQQSFNDLQDLREQILRVKDTEDVPMILV 112
Query: 83 GNKNDQTSKKAVDYQVAKEYADHL-KIPFLETSAKNGANVEQAFLTMATEI 132
GNK D ++ V + + A PFLETSAK+ NV++ F + +I
Sbjct: 113 GNKCDLEDERVVSKEEGQNLARQWGNCPFLETSAKSKINVDEIFYDLVRQI 163
>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 = 69.9 bits (171), Expect = 2e-15
Identities = 40/133 (30%), Positives = 69/133 (51%), Gaps = 3/133 (2%)
Query: 21 LIVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDN---V 77
++ + DTAGQE + + + R G I+VY T + TF ++++ E+I R ++ V
Sbjct: 48 MLEVLDTAGQEEYTALRDQWIREGEGFILVYSITSRSTFERVERFREQIQRVKDESAADV 107
Query: 78 NKLLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEIKKRVT 137
++VGNK D+ ++ V + A L F+E SAK NVE+AF T+ ++++
Sbjct: 108 PIMIVGNKCDKVYEREVSTEEGAALARRLGCEFIEASAKTNVNVERAFYTLVRALRQQRQ 167
Query: 138 KDEKPSSESDAKK 150
+ P KK
Sbjct: 168 GGQGPKGGPTKKK 180
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 70.1 bits (172), Expect = 3e-15
Identities = 40/109 (36%), Positives = 61/109 (55%), Gaps = 9/109 (8%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVNKLLVG 83
+WDTAGQE+F + YY I+++D T + T+ N+ W +I R C+N+ +LVG
Sbjct: 62 VWDTAGQEKFGGLRDGYYIKGQCAIIMFDVTSRITYKNVPNWHRDIVR-VCENIPIVLVG 120
Query: 84 NKNDQTSKKAVDYQV-AKEYADHLK--IPFLETSAKNGANVEQAFLTMA 129
NK D D QV A++ H K + + + SAK+ N E+ FL +A
Sbjct: 121 NKVD-----VKDRQVKARQITFHRKKNLQYYDISAKSNYNFEKPFLWLA 164
>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 = 67.5 bits (165), Expect = 9e-15
Identities = 36/111 (32%), Positives = 57/111 (51%), Gaps = 2/111 (1%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYA-CDNVNKLLV 82
I DTAG E+F + Y + G ++VY T + + N L + E++ R DNV +LV
Sbjct: 53 ILDTAGTEQFTAMRELYIKSGQGFLLVYSVTSEASLNELGELREQVLRIKDSDNVPMVLV 112
Query: 83 GNKNDQTSKKAVDYQVAKEYADHL-KIPFLETSAKNGANVEQAFLTMATEI 132
GNK D + V + + +PF ETSA+ NV++ F+ + +I
Sbjct: 113 GNKADLEDDRQVSREDGVSLSQQWGNVPFYETSARKRTNVDEVFIDLVRQI 163
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 68.2 bits (167), Expect = 1e-14
Identities = 38/120 (31%), Positives = 63/120 (52%), Gaps = 11/120 (9%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVNKLLVG 83
WDTAGQE+F + YY I+++D T + T+ N+ W ++ R C+N+ +L G
Sbjct: 66 CWDTAGQEKFGGLRDGYYIHGQCAIIMFDVTARLTYKNVPTWHRDLCR-VCENIPIVLCG 124
Query: 84 NKNDQTSKKAVDYQVAKEYADHLK--IPFLETSAKNGANVEQAFLTMATEIKKRVTKDEK 141
NK D +++ AK+ H K + + E SAK+ N E+ FL +A +++ D
Sbjct: 125 NKVDVKNRQV----KAKQVTFHRKKNLQYYEISAKSNYNFEKPFLYLA----RKLAGDPN 176
>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 = 66.1 bits (162), Expect = 3e-14
Identities = 31/123 (25%), Positives = 51/123 (41%), Gaps = 16/123 (13%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLK-QWLEEIDRYACDNVNKLLV 82
+WDTAGQE + + Y ++ + +F N+K +W E+ + C NV +LV
Sbjct: 50 LWDTAGQEDYDRLRPLSYPDTDVFLICFSVDSPASFENVKEKWYPEVKHF-CPNVPIILV 108
Query: 83 GNKNDQ------------TSKKAVDYQVAKEYADHLK-IPFLETSAKNGANVEQAFLTMA 129
G K D ++ V Y+ + A + + +LE SA V + F A
Sbjct: 109 GTKLDLRNDKSTLEELSKKKQEPVTYEQGQALAKRIGAVKYLECSALTQEGVREVF-EEA 167
Query: 130 TEI 132
Sbjct: 168 IRA 170
>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 = 65.6 bits (160), Expect = 6e-14
Identities = 36/116 (31%), Positives = 57/116 (49%), Gaps = 1/116 (0%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYA-CDNVNKLLV 82
I DTAGQ F + Y R G I+ Y TD+ +F ++ E I R +++ +LV
Sbjct: 54 ILDTAGQAEFTAMRDQYMRCGEGFIICYSVTDRHSFQEASEFKELITRVRLTEDIPLVLV 113
Query: 83 GNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEIKKRVTK 138
GNK D ++ V + + A PF ETSA ++ AF + EI+++ +
Sbjct: 114 GNKVDLEQQRQVTTEEGRNLAREFNCPFFETSAALRFYIDDAFHGLVREIRRKESM 169
>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 = 65.8 bits (160), Expect = 9e-14
Identities = 34/109 (31%), Positives = 59/109 (54%), Gaps = 3/109 (2%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVNKLLVG 83
+WDTAGQE+F + YY I+++D T + T+ N+ W ++ R C+N+ +L G
Sbjct: 48 VWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTARVTYKNVPNWHRDLVR-VCENIPIVLCG 106
Query: 84 NKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEI 132
NK D +K + +L+ + + SAK+ N E+ FL +A ++
Sbjct: 107 NKVDVKDRKVKAKSITFHRKKNLQ--YYDISAKSNYNFEKPFLWLARKL 153
>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 = 65.4 bits (160), Expect = 1e-13
Identities = 29/116 (25%), Positives = 52/116 (44%), Gaps = 15/116 (12%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLK-QWLEEIDRYACDNVNKLLV 82
+WDTAGQE + + Y I++ Y + + +N++ +W E++ + C +LV
Sbjct: 56 LWDTAGQEDYDRLRPLSYPDVDVILICYSVDNPTSLDNVEDKWYPEVNHF-CPGTPIVLV 114
Query: 83 GNKNDQTSKKA------------VDYQVAKEYADHLK-IPFLETSAKNGANVEQAF 125
G K D K V + + A + + ++E SAK NV++ F
Sbjct: 115 GLKTDLRKDKNSVSKLRAQGLEPVTPEQGESVAKSIGAVAYIECSAKLMENVDEVF 170
>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 = 64.1 bits (156), Expect = 2e-13
Identities = 33/105 (31%), Positives = 48/105 (45%), Gaps = 3/105 (2%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVNK---L 80
I DT G +F + H I+VY T +++ LK E I +N+ K +
Sbjct: 53 ITDTTGSHQFPAMQRLSISKGHAFILVYSITSKQSLEELKPIYELICEIKGNNLEKIPIM 112
Query: 81 LVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAF 125
LVGNK D++ + V A F+ETSAK NV++ F
Sbjct: 113 LVGNKCDESPSREVSSSEGAALARTWNCAFMETSAKTNHNVQELF 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 = 63.7 bits (155), Expect = 6e-13
Identities = 33/112 (29%), Positives = 54/112 (48%), Gaps = 3/112 (2%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVNK---L 80
+WD GQ+ + Y GA + +VYD T+ ++F NL+ WL + + ++ K +
Sbjct: 54 VWDIGGQQIGGKMLDKYIYGAQAVCLVYDITNSQSFENLEDWLSVVKKVNEESETKPKMV 113
Query: 81 LVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEI 132
LVGNK D + V + +A + + SAK G V F +A E+
Sbjct: 114 LVGNKTDLEHNRQVTAEKHARFAQENDMESIFVSAKTGDRVFLCFQRIAAEL 165
>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 = 61.1 bits (148), Expect = 6e-12
Identities = 44/181 (24%), Positives = 72/181 (39%), Gaps = 40/181 (22%)
Query: 22 IVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVNKLL 81
I IWDTAG+E+F + S Y RGA +I+ YD ++ ++ L+ + A ++ +
Sbjct: 46 ISIWDTAGREQFHGLGSMYCRGAAAVILTYDVSNVQSLEELEDRFLGLTDTANEDCLFAV 105
Query: 82 VGNKNDQTSKKAVDYQV-----------------------AKEYADHLKI---------- 108
VGNK D T + A+ Q K + +
Sbjct: 106 VGNKLDLTEEGALAGQEKDAGDRVSPEDQRQVTLEDAKAFYKRINKYKMLDEDLSPAAEK 165
Query: 109 PFLETSAKNGANVEQAFLTMATEIKKRVTKDEKPSSESDAKKLNLNSGKPVDAPRS-GGC 167
ETSAK G NV++ F + + + ++ + +NL + K RS C
Sbjct: 166 MCFETSAKTGYNVDELFEYLFNLVLPLILA-QRAEANRTQGTVNLPNPK-----RSKSKC 219
Query: 168 C 168
C
Sbjct: 220 C 220
>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 = 59.2 bits (144), Expect = 1e-11
Identities = 33/116 (28%), Positives = 53/116 (45%), Gaps = 5/116 (4%)
Query: 24 IWDTAGQERFRT--ITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYA-CD-NVNK 79
I DT GQ++ R A G ++VY TD+ +F+ + Q L+ I D +
Sbjct: 51 IQDTPGQQQNEDPESLERSLRWADGFVLVYSITDRSSFDVVSQLLQLIREIKKRDGEIPV 110
Query: 80 LLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGAN-VEQAFLTMATEIKK 134
+LVGNK D + V + ++ A L F E SA V+ F + E+++
Sbjct: 111 ILVGNKADLLHSRQVSTEEGQKLALELGCLFFEVSAAENYLEVQNVFHELCREVRR 166
>gnl|CDD|206725 cd04160, Arfrp1, Arf-related protein 1 (Arfrp1). Arfrp1
(Arf-related protein 1), formerly known as ARP, is a
membrane-associated Arf family member that lacks the
N-terminal myristoylation motif. Arfrp1 is mainly
associated with the trans-Golgi compartment and the
trans-Golgi network, where it regulates the targeting of
Arl1 and the GRIP domain-containing proteins, golgin-97
and golgin-245, onto Golgi membranes. It is also
involved in the anterograde transport of the vesicular
stomatitis virus G protein from the Golgi to the plasma
membrane, and in the retrograde transport of TGN38 and
Shiga toxin from endosomes to the trans-Golgi network.
Arfrp1 also inhibits Arf/Sec7-dependent activation of
phospholipase D. Deletion of Arfrp1 in mice causes
embryonic lethality at the gastrulation stage and
apoptosis of mesodermal cells, indicating its importance
in development.
Length = 168
Score = 57.4 bits (139), Expect = 6e-11
Identities = 36/113 (31%), Positives = 50/113 (44%), Gaps = 10/113 (8%)
Query: 20 TLIVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEE-IDRYACDNVN 78
++ WD GQE R++ YY +HG+I V D TD+E FN K E+ I+ A + V
Sbjct: 51 ARLMFWDLGGQEELRSLWDKYYAESHGVIYVIDSTDRERFNESKSAFEKVINNEALEGVP 110
Query: 79 KLLVGNKNDQTSKKAVDYQVAKEYADHLKIP-------FLETSAKNGANVEQA 124
L++ NK D +V KE D SA G VE+
Sbjct: 111 LLVLANKQDLPDALSVAE--IKEVFDDCIALIGRRDCLVQPVSALEGEGVEEG 161
>gnl|CDD|206644 cd00878, Arf_Arl, ADP-ribosylation factor(Arf)/Arf-like (Arl) small
GTPases. Arf (ADP-ribosylation factor)/Arl (Arf-like)
small GTPases. Arf proteins are activators of
phospholipase D isoforms. Unlike Ras proteins they lack
cysteine residues at their C-termini and therefore are
unlikely to be prenylated. Arfs are N-terminally
myristoylated. Members of the Arf family are regulators
of vesicle formation in intracellular traffic that
interact reversibly with membranes of the secretory and
endocytic compartments in a GTP-dependent manner. They
depart from other small GTP-binding proteins by a unique
structural device, interswitch toggle, that implements
front-back communication from N-terminus to the
nucleotide binding site. Arf-like (Arl) proteins are
close relatives of the Arf, but only Arl1 has been shown
to function in membrane traffic like the Arf proteins.
Arl2 has an unrelated function in the folding of native
tubulin, and Arl4 may function in the nucleus. Most
other Arf family proteins are so far relatively poorly
characterized. Thus, despite their significant sequence
homologies, Arf family proteins may regulate unrelated
functions.
Length = 158
Score = 57.2 bits (139), Expect = 6e-11
Identities = 25/112 (22%), Positives = 41/112 (36%), Gaps = 12/112 (10%)
Query: 22 IVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEI---DRYACDNVN 78
+WD GQ++ R + YY G+I V D +D+E K L ++ +
Sbjct: 45 FTVWDVGGQDKIRPLWKHYYENTDGLIFVVDSSDRERIEEAKNELHKLLNEEEL--KGAP 102
Query: 79 KLLVGNKNDQTSKKAVDYQVAKEYADHLKIP-----FLETSAKNGANVEQAF 125
L++ NK D A+ E I SA G +++
Sbjct: 103 LLILANKQDL--PGALTESELIELLGLESIKGRRWHIQPCSAVTGDGLDEGL 152
>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 = 56.8 bits (137), Expect = 1e-10
Identities = 36/116 (31%), Positives = 56/116 (48%), Gaps = 13/116 (11%)
Query: 22 IVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQ-WLEEIDRYACDNVNKL 80
+ +WDTAGQE + + Y AH I++ + ++ N++ W+EE+ RY C NV +
Sbjct: 51 LALWDTAGQEEYERLRPLSYSKAHVILIGFAIDTPDSLENVRTKWIEEVRRY-CPNVPVI 109
Query: 81 LVGNKNDQTSK----------KAVDYQVAKEYADHLKI-PFLETSAKNGANVEQAF 125
LVG K D + + V Q AK A + ++E SA G V+ F
Sbjct: 110 LVGLKKDLRQEAVAKGNYATDEFVPIQQAKLVARAIGAKKYMECSALTGEGVDDVF 165
>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 = 56.6 bits (137), Expect = 2e-10
Identities = 31/113 (27%), Positives = 51/113 (45%), Gaps = 6/113 (5%)
Query: 18 TRTLIVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNV 77
T IWD GQ F + + A I+ ++D T + T N++K+W + R
Sbjct: 47 TEITFSIWDLGGQREFINMLPLVCKDAVAILFMFDLTRKSTLNSIKEWYRQA-RGFNKTA 105
Query: 78 NKLLVGNKNDQTSKKAVDYQ-----VAKEYADHLKIPFLETSAKNGANVEQAF 125
+LVG K D + + Q A++YA +K P + S + NV++ F
Sbjct: 106 IPILVGTKYDLFADLPPEEQEEITKQARKYAKAMKAPLIFCSTSHSINVQKIF 158
>gnl|CDD|206724 cd04159, Arl10_like, Arf-like 9 (Arl9) and 10 (Arl10) GTPases.
Arl10-like subfamily. Arl9/Arl10 was identified from a
human cancer-derived EST dataset. No functional
information about the subfamily is available at the
current time, but crystal structures of human Arl10b and
Arl10c have been solved.
Length = 159
Score = 55.0 bits (133), Expect = 4e-10
Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 1/84 (1%)
Query: 13 KKEERTRTLIVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEE-IDR 71
+K + I +WD GQ RFR++ Y RG + I+ V D D+E K L + +++
Sbjct: 37 RKVTKGNVTIKVWDLGGQPRFRSMWERYCRGVNAIVYVVDAADREKLEVAKNELHDLLEK 96
Query: 72 YACDNVNKLLVGNKNDQTSKKAVD 95
+ + + L++GNKND +VD
Sbjct: 97 PSLEGIPLLVLGNKNDLPGALSVD 120
>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 = 52.0 bits (125), Expect = 7e-09
Identities = 26/118 (22%), Positives = 51/118 (43%), Gaps = 15/118 (12%)
Query: 22 IVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLK-QWLEEIDRYACDNVNKL 80
+ + DTAGQ+ F + Y ++ + + +F N+ +W+ EI ++ +
Sbjct: 50 LQLCDTAGQDEFDKLRPLCYPDTDVFLLCFSVVNPSSFQNISEKWIPEIRKH-NPKAPII 108
Query: 81 LVGNKND------------QTSKKAVDYQVAKEYADHLK-IPFLETSAKNGANVEQAF 125
LVG + D + +K V AK A+ + ++E SA N+++ F
Sbjct: 109 LVGTQADLRTDVNVLIQLARYGEKPVSQSRAKALAEKIGACEYIECSALTQKNLKEVF 166
>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 = 50.0 bits (120), Expect = 3e-08
Identities = 26/132 (19%), Positives = 55/132 (41%), Gaps = 11/132 (8%)
Query: 8 QTLQNKKEERTRTLIVIWDTAGQERFRTITSSYYRGAHGI-IVVYDCTDQETFNNLKQWL 66
Q + ER + + +WD GQE + T ++ + + ++V+D + + + WL
Sbjct: 39 QDWKIPAPERKKIRLNVWDFGGQEIYHA-THQFFLTSRSLYLLVFDLRTGDEVSRVPYWL 97
Query: 67 EEIDRYACDNVNKLLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFL 126
+I + + +LVG D++ + + + + + S KNG +
Sbjct: 98 RQIKAFGGVSP-VILVGTHIDESCDEDILKKALNKKFPAIINDIHFVSCKNGKGIA---- 152
Query: 127 TMATEIKKRVTK 138
E+KK + K
Sbjct: 153 ----ELKKAIAK 160
>gnl|CDD|219856 pfam08477, Miro, Miro-like protein. Mitochondrial Rho proteins
(Miro-1, and Miro-2), are atypical Rho GTPases. They
have a unique domain organisation, with tandem
GTP-binding domains and two EF hand domains (pfam00036),
that may bind calcium. They are also larger than
classical small GTPases. It has been proposed that they
are involved in mitochondrial homeostasis and apoptosis.
Length = 116
Score = 48.9 bits (117), Expect = 3e-08
Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 4/70 (5%)
Query: 19 RTLIVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFN---NLKQWLEEIDRYACD 75
L+ IWD G+E + + + A I++VYD TD+E+ N L WL + +
Sbjct: 47 TGLLNIWDFGGREELKFEHIIFMKWADAILLVYDLTDRESLNEVSRLIAWLPNLRKLG-G 105
Query: 76 NVNKLLVGNK 85
+ +LVGNK
Sbjct: 106 KIPVILVGNK 115
>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 = 50.1 bits (120), Expect = 4e-08
Identities = 32/121 (26%), Positives = 55/121 (45%), Gaps = 21/121 (17%)
Query: 24 IWDTAGQE---RFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQ-WLEEIDRYACDNVNK 79
+WDTAGQE R R ++ Y I++ + ++ N+ + W E+ ++ C NV
Sbjct: 53 LWDTAGQEDYDRLRPLS---YPDTDVILMCFSIDSPDSLENIPEKWTPEV-KHFCPNVPI 108
Query: 80 LLVGNKND------------QTSKKAVDYQVAKEYADHLK-IPFLETSAKNGANVEQAFL 126
+LVGNK D + ++ V + + A+ + +LE SAK V + F
Sbjct: 109 ILVGNKKDLRNDEHTIRELAKMKQEPVKPEEGRAMAEKIGAFGYLECSAKTKEGVREVFE 168
Query: 127 T 127
Sbjct: 169 M 169
>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 = 49.5 bits (118), Expect = 5e-08
Identities = 34/116 (29%), Positives = 54/116 (46%), Gaps = 13/116 (11%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNN-LKQWLEEIDRYACDNVNKLLV 82
+WDTAGQE + + YRGA ++ + + ++ N LK+W+ E+ YA V +LV
Sbjct: 53 LWDTAGQEDYNRLRPLSYRGADVFLLAFSLISKASYENVLKKWIPELRHYA-PGVPIVLV 111
Query: 83 GNKNDQTSKKA--VDYQVA--------KEYADHLKIP-FLETSAKNGANVEQAFLT 127
G K D K D+ A +E + ++E S+K NV+ F
Sbjct: 112 GTKLDLRDDKQFFADHPGAVPITTAQGEELRKQIGAAAYIECSSKTQQNVKAVFDA 167
>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 = 49.1 bits (117), Expect = 9e-08
Identities = 38/135 (28%), Positives = 57/135 (42%), Gaps = 15/135 (11%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLK-QWLEEIDRYACDNVNKLLV 82
+WDTAGQE F + S Y H I++ + + ++ N++ +WL EI + C V +LV
Sbjct: 52 LWDTAGQEEFDRLRSLSYADTHVIMLCFSVDNPDSLENVESKWLAEIRHH-CPGVKLVLV 110
Query: 83 GNKND--------QTSKKAVDYQVAKEYADHLK-IPFLETSAKNGANVEQAFLTMATEIK 133
K D + Y+ A + +LE SAK V +AF TE
Sbjct: 111 ALKCDLREPRNERDRGTHTISYEEGLAVAKRINACRYLECSAKLNRGVNEAF----TEAA 166
Query: 134 KRVTKDEKPSSESDA 148
+ P S A
Sbjct: 167 RVALNARPPHPHSRA 181
>gnl|CDD|133353 cd04153, Arl5_Arl8, Arf-like 5 (Arl5) and 8 (Arl8) GTPases.
Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like
Arl4 and Arl7, are localized to the nucleus and
nucleolus. Arl5 is developmentally regulated during
embryogenesis in mice. Human Arl5 interacts with the
heterochromatin protein 1-alpha (HP1alpha), a nonhistone
chromosomal protein that is associated with
heterochromatin and telomeres, and prevents telomere
fusion. Arl5 may also play a role in embryonic nuclear
dynamics and/or signaling cascades. Arl8 was identified
from a fetal cartilage cDNA library. It is found in
brain, heart, lung, cartilage, and kidney. No function
has been assigned for Arl8 to date.
Length = 174
Score = 47.7 bits (114), Expect = 2e-07
Identities = 22/68 (32%), Positives = 38/68 (55%), Gaps = 5/68 (7%)
Query: 23 VIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVNK--- 79
++WD GQE R+ ++YY +I+V D TD+E K+ L ++ A +++ K
Sbjct: 62 LMWDIGGQESLRSSWNTYYTNTDAVILVIDSTDRERLPLTKEELYKM--LAHEDLRKAVL 119
Query: 80 LLVGNKND 87
L++ NK D
Sbjct: 120 LVLANKQD 127
>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 = 47.0 bits (112), Expect = 6e-07
Identities = 33/115 (28%), Positives = 53/115 (46%), Gaps = 8/115 (6%)
Query: 14 KEERTRTLIVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETF---NNLKQWLEEID 70
EE T + W+ QE + S + ++VY TD+ +F + L+ L
Sbjct: 46 GEEATLVVYDHWE---QEDGMWLEDSCMQVGDAYVIVYSVTDRSSFEKASELRIQLRRA- 101
Query: 71 RYACDNVNKLLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAF 125
R A +++ +LVGNK+D + V Q + A F+ETSA NV++ F
Sbjct: 102 RQA-EDIPIILVGNKSDLVRSREVSVQEGRACAVVFDCKFIETSAALQHNVDELF 155
>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 = 45.8 bits (109), Expect = 1e-06
Identities = 34/121 (28%), Positives = 50/121 (41%), Gaps = 20/121 (16%)
Query: 16 ERTRTLIVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLK-QWLEEIDRYAC 74
ER T IV DT+ + + R ++ R A+ I +VY T ++ +WL I R
Sbjct: 47 ERVPTTIV--DTSSRPQDRANLAAEIRKANVICLVYSVDRPSTLERIRTKWLPLI-RRLG 103
Query: 75 DNVNKLLVGNKNDQTSKKAVDYQVAKEYADHLKIPF----------LETSAKNGANVEQA 124
V +LVGNK+D A + +P +E SAK NV +
Sbjct: 104 VKVPIILVGNKSDLRD----GSSQAG--LEEEMLPIMNEFREIETCVECSAKTLINVSEV 157
Query: 125 F 125
F
Sbjct: 158 F 158
>gnl|CDD|128474 smart00177, ARF, ARF-like small GTPases; ARF, ADP-ribosylation
factor. Ras homologues involved in vesicular transport.
Activator of phospholipase D isoforms. Unlike Ras
proteins they lack cysteine residues at their C-termini
and therefore are unlikely to be prenylated. ARFs are
N-terminally myristoylated. Contains ATP/GTP-binding
motif (P-loop).
Length = 175
Score = 46.1 bits (109), Expect = 1e-06
Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 3/66 (4%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEI--DRYACDNVNKLL 81
+WD GQ++ R + YY G+I V D D++ + ++ L + + D V L+
Sbjct: 61 VWDVGGQDKIRPLWRHYYTNTQGLIFVVDSNDRDRIDEAREELHRMLNEDELRDAV-ILV 119
Query: 82 VGNKND 87
NK D
Sbjct: 120 FANKQD 125
>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 = 45.4 bits (107), Expect = 2e-06
Identities = 30/109 (27%), Positives = 53/109 (48%), Gaps = 9/109 (8%)
Query: 16 ERTRTLIVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNN-LKQWLEEIDRYAC 74
+ R + +WDT+G + + Y + +++ +D + ET ++ LK+W EI + C
Sbjct: 49 DTQRIELSLWDTSGSPYYDNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEIQEF-C 107
Query: 75 DNVNKLLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQ 123
N LLVG K+D + D E ++H + P S GAN+ +
Sbjct: 108 PNTKMLLVGCKSDLRT----DVSTLVELSNHRQTP---VSYDQGANMAK 149
>gnl|CDD|206719 cd04152, Arl4_Arl7, Arf-like 4 (Arl4) and 7 (Arl7) GTPases. Arl4
(Arf-like 4) is highly expressed in testicular germ
cells, and is found in the nucleus and nucleolus. In
mice, Arl4 is developmentally expressed during
embryogenesis, and a role in somite formation and
central nervous system differentiation has been
proposed. Arl7 has been identified as the only Arf/Arl
protein to be induced by agonists of liver X-receptor
and retinoid X-receptor and by cholesterol loading in
human macrophages. Arl7 is proposed to play a role in
transport between a perinuclear compartment and the
plasma membrane, apparently linked to the ABCA1-mediated
cholesterol secretion pathway. Older literature suggests
that Arl6 is a part of the Arl4/Arl7 subfamily, but
analyses based on more recent sequence data place Arl6
in its own subfamily.
Length = 183
Score = 45.2 bits (107), Expect = 2e-06
Identities = 24/66 (36%), Positives = 34/66 (51%), Gaps = 3/66 (4%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDN--VNKLL 81
WD GQE+ R + SY R GI+ V D D E K L +I +++ +N V L+
Sbjct: 56 FWDVGGQEKLRPLWKSYTRCTDGIVFVVDSVDVERMEEAKTELHKITKFS-ENQGVPVLV 114
Query: 82 VGNKND 87
+ NK D
Sbjct: 115 LANKQD 120
>gnl|CDD|177661 PLN00023, PLN00023, GTP-binding protein; Provisional.
Length = 334
Score = 45.6 bits (108), Expect = 3e-06
Identities = 15/46 (32%), Positives = 29/46 (63%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEI 69
+WD +G ER++ S +Y +G+I V+D + + T +L++W E+
Sbjct: 87 LWDVSGHERYKDCRSLFYSQINGVIFVHDLSQRRTKTSLQKWASEV 132
>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 = 44.3 bits (105), Expect = 4e-06
Identities = 33/129 (25%), Positives = 60/129 (46%), Gaps = 15/129 (11%)
Query: 16 ERTRTLIVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNN-LKQWLEEIDRYAC 74
++ R + +WDT+G + + Y + +++ +D + ET ++ LK+W E+ + C
Sbjct: 45 DKQRIELSLWDTSGSPYYDNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEVREF-C 103
Query: 75 DNVNKLLVGNKND---------QTSKK---AVDYQVAKEYADHL-KIPFLETSAKNGANV 121
N LLVG K+D + S K V ++ + A + ++E SAK N
Sbjct: 104 PNTPVLLVGCKSDLRTDLSTLTELSNKRQIPVSHEQGRNLAKQIGAAAYVECSAKTSENS 163
Query: 122 EQAFLTMAT 130
+ MAT
Sbjct: 164 VRDVFEMAT 172
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 44.1 bits (105), Expect = 5e-06
Identities = 18/69 (26%), Positives = 31/69 (44%), Gaps = 5/69 (7%)
Query: 22 IVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEI---DRYACDNVN 78
+WD GQE R + +Y+ +I V D D++ K+ L + + A +
Sbjct: 60 FTVWDVGGQESLRPLWRNYFPNTDAVIFVVDSADRDRIEEAKEELHALLNEEELA--DAP 117
Query: 79 KLLVGNKND 87
L++ NK D
Sbjct: 118 LLILANKQD 126
>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 = 44.0 bits (104), Expect = 5e-06
Identities = 26/114 (22%), Positives = 44/114 (38%), Gaps = 14/114 (12%)
Query: 22 IVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETF----NNLKQWLEEIDRYACDNV 77
+D +GQ ++R + YY+ GII V D +D+ + L+ L D +
Sbjct: 47 FTAFDMSGQGKYRGLWEHYYKNIQGIIFVIDSSDRLRMVVAKDELELLLNHPDIKHRR-I 105
Query: 78 NKLLVGNKND----QTSKKAVDYQVAKEYADHLKIPF--LETSAKNGANVEQAF 125
L NK D T+ K + D P+ +SA G +++
Sbjct: 106 PILFYANKMDLPDALTAVKITQLLCLENIKDK---PWHIFASSALTGEGLDEGV 156
>gnl|CDD|206714 cd04147, Ras_dva, Ras - dorsal-ventral anterior localization
(Ras-dva) family. Ras-dva subfamily. Ras-dva (Ras -
dorsal-ventral anterior localization) subfamily consists
of a set of proteins characterized only in Xenopus
leavis, to date. In Xenopus Ras-dva expression is
activated by the transcription factor Otx2 and begins
during gastrulation throughout the anterior ectoderm.
Ras-dva expression is inhibited in the anterior neural
plate by factor Xanf1. Downregulation of Ras-dva results
in head development abnormalities through the inhibition
of several regulators of the anterior neural plate and
folds patterning, including Otx2, BF-1, Xag2, Pax6,
Slug, and Sox9. Downregulation of Ras-dva also
interferes with the FGF-8a signaling within the anterior
ectoderm. Most Ras proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins.
Length = 197
Score = 44.1 bits (104), Expect = 6e-06
Identities = 32/106 (30%), Positives = 49/106 (46%), Gaps = 2/106 (1%)
Query: 22 IVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDN-VNKL 80
I I DT+G F + + +VY D E+F +K+ EEI D V +
Sbjct: 49 IDILDTSGSYSFPAMRKLSIQNGDAFALVYSVDDPESFEEVKRLREEILEVKEDKFVPIV 108
Query: 81 LVGNKNDQTSKKAVDYQVAKEYAD-HLKIPFLETSAKNGANVEQAF 125
+VGNK D +++ V+ A + F+E SAK+ NV + F
Sbjct: 109 VVGNKIDSLAERQVEAADALSTVELDWNNGFVEASAKDNENVTEVF 154
>gnl|CDD|206716 cd04149, Arf6, ADP ribosylation factor 6 (Arf6). Arf6 subfamily.
Arf6 (ADP ribosylation factor 6) proteins localize to
the plasma membrane, where they perform a wide variety
of functions. In its active, GTP-bound form, Arf6 is
involved in cell spreading, Rac-induced formation of
plasma membrane ruffles, cell migration, wound healing,
and Fc-mediated phagocytosis. Arf6 appears to change the
actin structure at the plasma membrane by activating
Rac, a Rho family protein involved in membrane ruffling.
Arf6 is required for and enhances Rac formation of
ruffles. Arf6 can regulate dendritic branching in
hippocampal neurons, and in yeast it localizes to the
growing bud, where it plays a role in polarized growth
and bud site selection. In leukocytes, Arf6 is required
for chemokine-stimulated migration across endothelial
cells. Arf6 also plays a role in down-regulation of
beta2-adrenergic receptors and luteinizing hormone
receptors by facilitating the release of sequestered
arrestin to allow endocytosis. Arf6 is believed to
function at multiple sites on the plasma membrane
through interaction with a specific set of GEFs, GAPs,
and effectors. Arf6 has been implicated in breast cancer
and melanoma cell invasion, and in actin remodelling at
the invasion site of Chlamydia infection.
Length = 168
Score = 42.5 bits (100), Expect = 2e-05
Identities = 25/67 (37%), Positives = 35/67 (52%), Gaps = 5/67 (7%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEI--DRYACDNVNKLL 81
+WD GQ++ R + YY G G+I V D D++ + +Q L I DR D + LL
Sbjct: 57 VWDVGGQDKIRPLWRHYYTGTQGLIFVVDSADRDRIDEARQELHRIINDREMRDAL--LL 114
Query: 82 V-GNKND 87
V NK D
Sbjct: 115 VFANKQD 121
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 42.1 bits (99), Expect = 2e-05
Identities = 15/46 (32%), Positives = 27/46 (58%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEI 69
+WD GQ++ R + YY+ +G+I V D D+E + ++ LE +
Sbjct: 65 MWDVGGQDKLRPLWRHYYQNTNGLIFVVDSNDRERIGDAREELERM 110
>gnl|CDD|206717 cd04150, Arf1_5_like, ADP-ribosylation factor-1 (Arf1) and
ADP-ribosylation factor-5 (Arf5). The Arf1-Arf5-like
subfamily contains Arf1, Arf2, Arf3, Arf4, Arf5, and
related proteins. Arfs1-5 are soluble proteins that are
crucial for assembling coat proteins during vesicle
formation. Each contains an N-terminal myristoylated
amphipathic helix that is folded into the protein in
the GDP-bound state. GDP/GTP exchange exposes the
helix, which anchors to the membrane. Following GTP
hydrolysis, the helix dissociates from the membrane and
folds back into the protein. A general feature of
Arf1-5 signaling may be the cooperation of two Arfs at
the same site. Arfs1-5 are generally considered to be
interchangeable in function and location, but some
specific functions have been assigned. Arf1 localizes
to the early/cis-Golgi, where it is activated by GBF1
and recruits the coat protein COPI. It also localizes
to the trans-Golgi network (TGN), where it is activated
by BIG1/BIG2 and recruits the AP1, AP3, AP4, and GGA
proteins. Humans, but not rodents and other lower
eukaryotes, lack Arf2. Human Arf3 shares 96% sequence
identity with Arf1 and is believed to generally
function interchangeably with Arf1. Human Arf4 in the
activated (GTP-bound) state has been shown to interact
with the cytoplasmic domain of epidermal growth factor
receptor (EGFR) and mediate the EGF-dependent
activation of phospholipase D2 (PLD2), leading to
activation of the activator protein 1 (AP-1)
transcription factor. Arf4 has also been shown to
recognize the C-terminal sorting signal of rhodopsin
and regulate its incorporation into specialized
post-Golgi rhodopsin transport carriers (RTCs). There
is some evidence that Arf5 functions at the early-Golgi
and the trans-Golgi to affect Golgi-associated
alpha-adaptin homology Arf-binding proteins (GGAs).
Length = 159
Score = 41.6 bits (98), Expect = 3e-05
Identities = 13/46 (28%), Positives = 25/46 (54%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEI 69
+WD GQ++ R + Y++ G+I V D D+E ++ L+ +
Sbjct: 48 VWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERIGEAREELQRM 93
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 41.7 bits (98), Expect = 4e-05
Identities = 23/105 (21%), Positives = 43/105 (40%), Gaps = 5/105 (4%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVNKLLVG 83
++ T GQERF+ + RGA G IV+ D + TF+ + ++ + + ++
Sbjct: 72 LFGTPGQERFKFMWEILSRGAVGAIVLVDSSRPITFHAEEI-IDFLTSRNP--IPVVVAI 128
Query: 84 NKNDQTSKKAVDYQVAKEYADHLK-IPFLETSAKNGANVEQAFLT 127
NK D + ++ + L +P +E A G
Sbjct: 129 NKQDLFDALPPE-KIREALKLELLSVPVIEIDATEGEGARDQLDV 172
>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 = 41.7 bits (98), Expect = 6e-05
Identities = 20/93 (21%), Positives = 40/93 (43%), Gaps = 10/93 (10%)
Query: 48 IVVYDCTDQETFNNLKQWLEEIDRYACDNVNKL---------LVGNKNDQTSKKAVD-YQ 97
I+V+ ++E+F + + E+I NK + GNK D+ + V +
Sbjct: 76 ILVFSLDNRESFEEVCRLREQILETKSCLKNKTKENVKIPMVICGNKADRDFPREVQRDE 135
Query: 98 VAKEYADHLKIPFLETSAKNGANVEQAFLTMAT 130
V + + E SAK +N+++ F + +
Sbjct: 136 VEQLVGGDENCAYFEVSAKKNSNLDEMFRALFS 168
>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 = 40.8 bits (95), Expect = 8e-05
Identities = 21/65 (32%), Positives = 35/65 (53%), Gaps = 2/65 (3%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLK-QWLEEIDRYACDNVNKLLV 82
+WDTAGQE + + + Y + I+ + ++ N++ +W E+ + C NV LLV
Sbjct: 55 LWDTAGQEEYDRLRTLSYPQTNVFIICFSIASPSSYENVRHKWHPEVCHH-CPNVPILLV 113
Query: 83 GNKND 87
G K D
Sbjct: 114 GTKKD 118
>gnl|CDD|206721 cd04155, Arl3, Arf-like 3 (Arl3) GTPase. Arl3 (Arf-like 3) is an
Arf family protein that differs from most Arf family
members in the N-terminal extension. In is inactive,
GDP-bound form, the N-terminal extension forms an
elongated loop that is hydrophobically anchored into the
membrane surface; however, it has been proposed that
this region might form a helix in the GTP-bound form.
The delta subunit of the rod-specific cyclic GMP
phosphodiesterase type 6 (PDEdelta) is an Arl3 effector.
Arl3 binds microtubules in a regulated manner to alter
specific aspects of cytokinesis via interactions with
retinitis pigmentosa 2 (RP2). It has been proposed that
RP2 functions in concert with Arl3 to link the cell
membrane and the cytoskeleton in photoreceptors as part
of the cell signaling or vesicular transport machinery.
In mice, the absence of Arl3 is associated with abnormal
epithelial cell proliferation and cyst formation.
Length = 174
Score = 40.5 bits (95), Expect = 9e-05
Identities = 22/83 (26%), Positives = 34/83 (40%), Gaps = 1/83 (1%)
Query: 6 PYQTLQNKKEERTRTLIVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQW 65
P Q K + + +WD GQ + R +Y+ +I V D D++ F Q
Sbjct: 45 PTQGFNIKNVQADGFKLNVWDIGGQRKIRPYWRNYFENTDVLIYVIDSADRKRFEEAGQE 104
Query: 66 LEEI-DRYACDNVNKLLVGNKND 87
L E+ + V L+ NK D
Sbjct: 105 LVELLEEEKLAGVPVLVFANKQD 127
>gnl|CDD|206689 cd04102, RabL3, Rab GTPase-like family 3 (Rab-like3). RabL3
(Rab-like3) subfamily. RabL3s are novel proteins that
have high sequence similarity with Rab family members,
but display features that are distinct from Rabs, and
have been termed Rab-like. As in other Rab-like
proteins, RabL3 lacks a prenylation site at the
C-terminus. The specific function of RabL3 remains
unknown.
Length = 204
Score = 40.7 bits (95), Expect = 9e-05
Identities = 33/149 (22%), Positives = 62/149 (41%), Gaps = 26/149 (17%)
Query: 15 EERTRTLIVIWDTAGQ----ERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQW-LEEI 69
EE+T + +WD G E ++ + +Y +GII V+D T++++ NL +W LE +
Sbjct: 50 EEKT-FYVELWDVGGSVGSAESVKSTRAVFYNQINGIIFVHDLTNKKSSQNLYRWSLEAL 108
Query: 70 DRYACDNVNKLLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMA 129
+R D L+ D S++ +P L K ++Q
Sbjct: 109 NR---DTFPAGLLVTNGDYDSEQFAG----------NPVPLLVIGTK----LDQIPEAKR 151
Query: 130 TEIKKRVTKDEKPSSESDAKKLNLNSGKP 158
+ R S + +A+++NL+
Sbjct: 152 NWVLTRTA---FLSEDFNAEEINLDCTNG 177
>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 = 40.1 bits (94), Expect = 1e-04
Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYA-CDNVNKLLV 82
+WD GQE+ RT+ Y G++ V D +D+ + ++ L+ I + V +L+
Sbjct: 48 VWDVGGQEKMRTVWKCYLENTDGLVYVVDSSDEARLDESQKELKHILKNEHIKGVPVVLL 107
Query: 83 GNKND 87
NK D
Sbjct: 108 ANKQD 112
>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 = 40.4 bits (94), Expect = 1e-04
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 2/73 (2%)
Query: 16 ERTRTLIVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNN-LKQWLEEIDRYAC 74
E R + +WDT+G + + Y + +++ +D + E F++ LK+W EI Y C
Sbjct: 57 EEQRVELSLWDTSGSPYYDNVRPLCYSDSDAVLLCFDISRPEIFDSALKKWRAEILDY-C 115
Query: 75 DNVNKLLVGNKND 87
+ LL+G K D
Sbjct: 116 PSTRILLIGCKTD 128
>gnl|CDD|206645 cd00879, Sar1, Sar1 is an essential component of COPII vesicle
coats. Sar1 is an essential component of COPII vesicle
coats involved in export of cargo from the ER. The
GTPase activity of Sar1 functions as a molecular switch
to control protein-protein and protein-lipid
interactions that direct vesicle budding from the ER.
Activation of the GDP to the GTP-bound form of Sar1
involves the membrane-associated guanine nucleotide
exchange factor (GEF) Sec12. Sar1 is unlike all Ras
superfamily GTPases that use either myristoyl or prenyl
groups to direct membrane association and function, in
that Sar1 lacks such modification. Instead, Sar1
contains a unique nine-amino-acid N-terminal extension.
This extension contains an evolutionarily conserved
cluster of bulky hydrophobic amino acids, referred to as
the Sar1-N-terminal activation recruitment (STAR) motif.
The STAR motif mediates the recruitment of Sar1 to ER
membranes and facilitates its interaction with mammalian
Sec12 GEF leading to activation.
Length = 191
Score = 38.0 bits (89), Expect = 7e-04
Identities = 23/67 (34%), Positives = 32/67 (47%), Gaps = 7/67 (10%)
Query: 25 WDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACD----NVNKL 80
+D G E+ R + Y+ GI+ + D D E F K EE+D D NV L
Sbjct: 68 FDLGGHEQARRVWKDYFPEVDGIVFLVDAADPERFQESK---EELDSLLNDEELANVPIL 124
Query: 81 LVGNKND 87
++GNK D
Sbjct: 125 ILGNKID 131
>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 = 37.3 bits (86), Expect = 0.001
Identities = 21/87 (24%), Positives = 45/87 (51%), Gaps = 2/87 (2%)
Query: 16 ERTRTLIVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNN-LKQWLEEIDRYAC 74
++ R + +WDT+G + + Y + +++ +D + ET ++ LK+W E + C
Sbjct: 45 DKHRIELNMWDTSGSSYYDNVRPLAYPDSDAVLICFDISRPETLDSVLKKWQGETQEF-C 103
Query: 75 DNVNKLLVGNKNDQTSKKAVDYQVAKE 101
N +LVG K D + + +++K+
Sbjct: 104 PNAKLVLVGCKLDMRTDLSTLRELSKQ 130
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 37.4 bits (88), Expect = 0.002
Identities = 27/140 (19%), Positives = 50/140 (35%), Gaps = 36/140 (25%)
Query: 21 LIVIWDTAG------------QER-FRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLE 67
+ + DTAG ER I A +++V D ++ T + + E
Sbjct: 264 PLRLIDTAGIRETDDEVEKIGIERSREAI-----EEADLVLLVLDASEPLTEEDDEILEE 318
Query: 68 EIDRYACDNVNKLLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLT 127
D+ ++V NK D T + ++ + K P + SAK G +++
Sbjct: 319 LKDK------PVIVVLNKADLTGEIDLEEENGK--------PVIRISAKTGEGIDE---- 360
Query: 128 MATEIKKRVTKDEKPSSESD 147
+ IK+ + E
Sbjct: 361 LREAIKELAFGGFGGNQEGV 380
>gnl|CDD|206726 cd04163, Era, E. coli Ras-like protein (Era) is a multifunctional
GTPase. Era (E. coli Ras-like protein) is a
multifunctional GTPase found in all bacteria except some
eubacteria. It binds to the 16S ribosomal RNA (rRNA) of
the 30S subunit and appears to play a role in the
assembly of the 30S subunit, possibly by chaperoning the
16S rRNA. It also contacts several assembly elements of
the 30S subunit. Era couples cell growth with
cytokinesis and plays a role in cell division and energy
metabolism. Homologs have also been found in eukaryotes.
Era contains two domains: the N-terminal GTPase domain
and a C-terminal domain KH domain that is critical for
RNA binding. Both domains are important for Era
function. Era is functionally able to compensate for
deletion of RbfA, a cold-shock adaptation protein that
is required for efficient processing of the 16S rRNA.
Length = 168
Score = 35.9 bits (84), Expect = 0.004
Identities = 17/67 (25%), Positives = 27/67 (40%), Gaps = 10/67 (14%)
Query: 64 QWLEEIDRYACD-----NVNKLLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLET---SA 115
+W+ E D + + +LV NK D K + ++ + PF E SA
Sbjct: 94 EWIGEGDEFILELLKKSKTPVILVLNKIDLVKDKEDLLPLLEKLKE--LHPFAEIFPISA 151
Query: 116 KNGANVE 122
G NV+
Sbjct: 152 LKGENVD 158
>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 = 34.8 bits (80), Expect = 0.008
Identities = 22/79 (27%), Positives = 37/79 (46%), Gaps = 2/79 (2%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQ-WLEEIDRYACDNVNKLLV 82
++DTAGQE + + Y +V + +F N+K+ W+ EI + C LLV
Sbjct: 53 LFDTAGQEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEI-THHCPKTPFLLV 111
Query: 83 GNKNDQTSKKAVDYQVAKE 101
G + D + ++AK
Sbjct: 112 GTQIDLRDDPSTIEKLAKN 130
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 34.6 bits (79), Expect = 0.010
Identities = 11/34 (32%), Positives = 20/34 (58%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQE 57
+WD GQ++ R + Y++ G+I V D D++
Sbjct: 65 VWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRD 98
>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 = 34.3 bits (79), Expect = 0.011
Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 7/72 (9%)
Query: 21 LIVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTD----QETFNNLKQWLEEIDRYACDN 76
+ I+D G FR I +YY AHG++ V D +D QE L++ L+ R +
Sbjct: 44 EVCIFDLGGGANFRGIWVNYYAEAHGLVFVVDSSDDDRVQEVKEILRELLQH-PRVSGKP 102
Query: 77 VNKLLVGNKNDQ 88
+ L++ NK D+
Sbjct: 103 I--LVLANKQDK 112
>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 = 34.4 bits (79), Expect = 0.014
Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 2/65 (3%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLK-QWLEEIDRYACDNVNKLLV 82
+WDTAGQE + + Y ++ + +F N++ +W E+ R+ C N +LV
Sbjct: 53 LWDTAGQEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEV-RHHCPNTPIILV 111
Query: 83 GNKND 87
G K D
Sbjct: 112 GTKLD 116
>gnl|CDD|206720 cd04154, Arl2, Arf-like 2 (Arl2) GTPase. Arl2 (Arf-like 2) GTPases
are members of the Arf family that bind GDP and GTP with
very low affinity. Unlike most Arf family proteins, Arl2
is not myristoylated at its N-terminal helix. The
protein PDE-delta, first identified in photoreceptor rod
cells, binds specifically to Arl2 and is structurally
very similar to RhoGDI. Despite the high structural
similarity between Arl2 and Rho proteins and between
PDE-delta and RhoGDI, the interactions between the
GTPases and their effectors are very different. In its
GTP bound form, Arl2 interacts with the protein Binder
of Arl2 (BART), and the complex is believed to play a
role in mitochondrial adenine nucleotide transport. In
its GDP bound form, Arl2 interacts with tubulin- folding
Cofactor D; this interaction is believed to play a role
in regulation of microtubule dynamics that impact the
cytoskeleton, cell division, and cytokinesis.
Length = 173
Score = 34.2 bits (79), Expect = 0.015
Identities = 27/112 (24%), Positives = 48/112 (42%), Gaps = 16/112 (14%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEI---DRYACDNVNKL 80
IWD GQ+ R+ +Y+ +I V D +D+ + K+ L+++ +R A + L
Sbjct: 62 IWDVGGQKSLRSYWRNYFESTDALIWVVDSSDRARLEDCKRELQKLLVEERLAGATL--L 119
Query: 81 LVGNKNDQTSKKAVDYQVAKEYAD-------HLKIPFLETSAKNGANVEQAF 125
+ NK D A+ + +E + H +I SA G N+
Sbjct: 120 IFANKQDL--PGALSPEEIREVLELDSIKSHHWRI--FGCSAVTGENLLDGI 167
>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 = 33.8 bits (77), Expect = 0.021
Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 2/68 (2%)
Query: 21 LIVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLK-QWLEEIDRYACDNVNK 79
L+ ++DTAGQE + + Y ++ + + +F N+K +W+ E+ YA NV
Sbjct: 49 LLGLYDTAGQEDYDRLRPLSYPMTDVFLICFSVVNPASFQNVKEEWVPELKEYA-PNVPY 107
Query: 80 LLVGNKND 87
LL+G + D
Sbjct: 108 LLIGTQID 115
>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 = 32.8 bits (75), Expect = 0.047
Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 1/61 (1%)
Query: 29 GQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVNKLLVGNKNDQ 88
G + R Y G+ G+I V D D E +Q L ++ ++ D + +++ NK D
Sbjct: 53 GSQNLRKYWKRYLSGSQGLIFVVDSADSERLPLARQELHQLLQHPPD-LPLVVLANKQDL 111
Query: 89 T 89
Sbjct: 112 P 112
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 32.7 bits (76), Expect = 0.062
Identities = 17/71 (23%), Positives = 26/71 (36%), Gaps = 15/71 (21%)
Query: 55 DQETFNNLKQWLEEIDRYACDNVNKLLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLET- 113
D+ LK+ +LV NK D K + +E ++ + F E
Sbjct: 102 DEFILEKLKKV----------KTPVILVLNKIDLVKDKEELLPLLEELSE--LMDFAEIV 149
Query: 114 --SAKNGANVE 122
SA G NV+
Sbjct: 150 PISALKGDNVD 160
>gnl|CDD|237039 PRK12288, PRK12288, GTPase RsgA; Reviewed.
Length = 347
Score = 32.5 bits (75), Expect = 0.078
Identities = 21/73 (28%), Positives = 32/73 (43%), Gaps = 11/73 (15%)
Query: 69 IDRY--ACDNVN--KLLVGNKND---QTSKKAVDYQVAKEYADHLKIPFLETSAKNGANV 121
IDRY AC+ + L+V NK D + V+ + Y ++ L S+ G +
Sbjct: 139 IDRYLVACETLGIEPLIVLNKIDLLDDEGRAFVN-EQLDIY-RNIGYRVLMVSSHTGEGL 196
Query: 122 E--QAFLTMATEI 132
E +A LT I
Sbjct: 197 EELEAALTGRISI 209
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 32.1 bits (74), Expect = 0.096
Identities = 23/113 (20%), Positives = 39/113 (34%), Gaps = 22/113 (19%)
Query: 21 LIVIWDTAGQ-------ERF---RTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEID 70
+ + DTAG ER R + A ++ V D + K+ L I+
Sbjct: 266 PVRLVDTAGIRETDDVVERIGIERAKKAI--EEADLVLFVLDASQPLD----KEDLALIE 319
Query: 71 RYACDNVNKLLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQ 123
++V NK D SK ++ + + SAK G ++
Sbjct: 320 LLPK-KKPIIVVLNKADLVSKIELESEKLAN-----GDAIISISAKTGEGLDA 366
>gnl|CDD|133275 cd01873, RhoBTB, RhoBTB protein is an atypical member of the Rho
family of small GTPases. Members of the RhoBTB
subfamily of Rho GTPases are present in vertebrates,
Drosophila, and Dictyostelium. RhoBTB proteins are
characterized by a modular organization, consisting of a
GTPase domain, a proline rich region, a tandem of two
BTB (Broad-Complex, Tramtrack, and Bric a brac) domains,
and a C-terminal region of unknown function. RhoBTB
proteins may act as docking points for multiple
components participating in signal transduction
cascades. RhoBTB genes appeared upregulated in some
cancer cell lines, suggesting a participation of RhoBTB
proteins in the pathogenesis of particular tumors. Note
that the Dictyostelium RacA GTPase domain is more
closely related to Rac proteins than to RhoBTB proteins,
where RacA actually belongs. Thus, the Dictyostelium
RacA is not included here. Most Rho proteins contain a
lipid modification site at the C-terminus; however,
RhoBTB is one of few Rho subfamilies that lack this
feature.
Length = 195
Score = 31.9 bits (72), Expect = 0.11
Identities = 30/126 (23%), Positives = 46/126 (36%), Gaps = 31/126 (24%)
Query: 24 IWDTAG----QERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQ-WLEEIDRYACDNVN 78
+WDT G RF Y + +++ + + N+K W EI + C V
Sbjct: 70 LWDTFGDHDKDRRFA------YGRSDVVLLCFSIASPNSLRNVKTMWYPEIRHF-CPRVP 122
Query: 79 KLLVGNKND-----------------QTSKKA--VDYQVAKEYADHLKIPFLETSAKNGA 119
+LVG K D + K A + + + A L IP+ ETS
Sbjct: 123 VILVGCKLDLRYADLDEVNRARRPLARPIKNADILPPETGRAVAKELGIPYYETSVVTQF 182
Query: 120 NVEQAF 125
V+ F
Sbjct: 183 GVKDVF 188
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 31.8 bits (73), Expect = 0.13
Identities = 15/51 (29%), Positives = 21/51 (41%), Gaps = 5/51 (9%)
Query: 76 NVNKLLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLET---SAKNGANVEQ 123
+LV NK D+ K V ++ +PF E SA G NV+
Sbjct: 114 KTPVILVVNKIDKVKPKTVLLKLIAFL--KKLLPFKEIVPISALKGDNVDT 162
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes. TrmE
contains a GTPase domain that forms a canonical Ras-like
fold. It functions a molecular switch GTPase, and
apparently uses a conformational change associated with
GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 30.9 bits (71), Expect = 0.16
Identities = 14/77 (18%), Positives = 33/77 (42%), Gaps = 13/77 (16%)
Query: 47 IIVVYDCTDQETFNNLKQWLEEIDRYACDNVNKLLVGNKNDQTSKKAVDYQVAKEYADHL 106
+++V D ++ ++ LE ++ ++V NK+D S ++ +
Sbjct: 86 VLLVVDASEGLD----EEDLEILEL--PAKKPVIVVLNKSDLLSDAEGISELNGK----- 134
Query: 107 KIPFLETSAKNGANVEQ 123
P + SAK G +++
Sbjct: 135 --PIIAISAKTGEGIDE 149
>gnl|CDD|197556 smart00178, SAR, Sar1p-like members of the Ras-family of small
GTPases. Yeast SAR1 is an essential gene required for
transport of secretory proteins from the endoplasmic
reticulum to the Golgi apparatus.
Length = 184
Score = 31.1 bits (70), Expect = 0.18
Identities = 18/64 (28%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 25 WDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEI-DRYACDNVNKLLVG 83
+D G ++ R + Y+ +GI+ + D D+E F K+ L+ + V L++G
Sbjct: 66 FDLGGHQQARRLWKDYFPEVNGIVYLVDAYDKERFAESKRELDALLSDEELATVPFLILG 125
Query: 84 NKND 87
NK D
Sbjct: 126 NKID 129
>gnl|CDD|133342 cd04142, RRP22, Ras-related protein on chromosome 22 (RRP22)
family. RRP22 (Ras-related protein on chromosome 22)
subfamily consists of proteins that inhibit cell growth
and promote caspase-independent cell death. Unlike most
Ras proteins, RRP22 is down-regulated in many human
tumor cells due to promoter methylation. RRP22 localizes
to the nucleolus in a GTP-dependent manner, suggesting a
novel function in modulating transport of nucleolar
components. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras proteins.
Like most Ras family proteins, RRP22 is farnesylated.
Length = 198
Score = 30.6 bits (69), Expect = 0.25
Identities = 31/102 (30%), Positives = 45/102 (44%), Gaps = 21/102 (20%)
Query: 27 TAGQE----RFRTITSSYYRGAHGIIVVYDCTDQETFNNLK---QWLEEIDRYACDNVNK 79
TAGQE RFR + R + I+VYD ++F+ +K Q + E
Sbjct: 65 TAGQEWMDPRFRGL-----RNSRAFILVYDICSPDSFHYVKLLRQQILETRPAGNKEPPI 119
Query: 80 LLVGNKNDQTS-----KKAVDYQVAKEYADHLKIPFLETSAK 116
++VGNK DQ + + V K + K +LE SAK
Sbjct: 120 VVVGNKRDQQRHRFAPRHVLSVLVRKSW----KCGYLECSAK 157
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 30.8 bits (70), Expect = 0.27
Identities = 20/77 (25%), Positives = 32/77 (41%), Gaps = 5/77 (6%)
Query: 65 WLEEIDRYACDNVNKLLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVE-- 122
E++R KLLV NK D K+ + K + I + SAK+ +
Sbjct: 51 RNPELERIV-KEKPKLLVLNKADLAPKEVTK-KWKKYFKKEEGIKPIFVSAKSRQGGKKI 108
Query: 123 -QAFLTMATEIKKRVTK 138
+A ++ E KR+ K
Sbjct: 109 RKALEKLSEEKIKRLKK 125
>gnl|CDD|181721 PRK09242, PRK09242, tropinone reductase; Provisional.
Length = 257
Score = 30.9 bits (70), Expect = 0.27
Identities = 25/113 (22%), Positives = 38/113 (33%), Gaps = 27/113 (23%)
Query: 21 LIVIWDTAGQERFRTITSSYYRG--AHGIIVVYDCTDQETFNNLKQWLEEIDRYACDNVN 78
LIV D + R + + HG+ D +D E + W+E D+ +
Sbjct: 37 LIVARDADALAQARDELAEEFPEREVHGLAA--DVSDDEDRRAILDWVE-------DHWD 87
Query: 79 KL--LVGNKNDQTSKKAVDYQVAKEYADHLKI-------------PFLETSAK 116
L LV N K A+DY E+ + P L+ A
Sbjct: 88 GLHILVNNAGGNIRKAAIDYT-EDEWRGIFETNLFSAFELSRYAHPLLKQHAS 139
>gnl|CDD|206666 cd01878, HflX, HflX GTPase family. HflX subfamily. A distinct
conserved domain with a glycine-rich segment N-terminal
of the GTPase domain characterizes the HflX subfamily.
The E. coli HflX has been implicated in the control of
the lambda cII repressor proteolysis, but the actual
biological functions of these GTPases remain unclear.
HflX is widespread, but not universally represented in
all three superkingdoms.
Length = 204
Score = 30.5 bits (70), Expect = 0.28
Identities = 17/79 (21%), Positives = 35/79 (44%), Gaps = 11/79 (13%)
Query: 47 IIVVYDCTDQETFNNLKQ---WLEEIDRYACDNVNKLLVGNKNDQTSKKAVDYQVAKEYA 103
++ V D +D + ++ L+E+ D++ +LV NK D +D + +E
Sbjct: 124 LLHVVDASDPDREEQIETVEEVLKELG---ADDIPIILVLNKIDL-----LDDEELEERL 175
Query: 104 DHLKIPFLETSAKNGANVE 122
+ + SAK G ++
Sbjct: 176 RAGRPDAVFISAKTGEGLD 194
>gnl|CDD|215653 pfam00009, GTP_EFTU, Elongation factor Tu GTP binding domain. This
domain contains a P-loop motif, also found in several
other families such as pfam00071, pfam00025 and
pfam00063. Elongation factor Tu consists of three
structural domains, this plus two C-terminal beta barrel
domains.
Length = 184
Score = 30.2 bits (69), Expect = 0.35
Identities = 27/131 (20%), Positives = 45/131 (34%), Gaps = 26/131 (19%)
Query: 15 EERTRTLIVIWDTAGQERFR--TITSSYYRGAHGIIVVYDCTD----QETFNNLKQWLEE 68
E + R + +I DT G F I + A G I+V D + Q T +L
Sbjct: 62 ETKKRLINII-DTPGHVDFTKEMIRGA--SQADGAILVVDAVEGVMPQ-TREHLLLAKTL 117
Query: 69 IDRYACDNVNKLLVGNKNDQTSKKAVDYQVAKEYADHLK--------IPFLETSAKNGAN 120
V ++ NK D+ ++ V + + L+ +P + SA G
Sbjct: 118 -------GVPIIVFINKIDRVDDAELEEVVEEISRELLEKYGFGGETVPVVPGSALTGEG 170
Query: 121 VEQAFLTMATE 131
+ L
Sbjct: 171 I-DELLEALDL 180
>gnl|CDD|206718 cd04151, Arl1, ADP ribosylation factor 1 (Arf1). Arl1 subfamily.
Arl1 (Arf-like 1) localizes to the Golgi complex, where
it is believed to recruit effector proteins to the
trans-Golgi network. Like most members of the Arf
family, Arl1 is myristoylated at its N-terminal helix
and mutation of the myristoylation site disrupts Golgi
targeting. In humans, the Golgi-localized proteins
golgin-97 and golgin-245 have been identified as Arl1
effectors. Golgins are large coiled-coil proteins found
in the Golgi, and these golgins contain a C-terminal
GRIP domain, which is the site of Arl1 binding.
Additional Arl1 effectors include the GARP
(Golgi-associated retrograde protein)/VFT (Vps53)
vesicle-tethering complex and Arfaptin 2. Arl1 is not
required for exocytosis, but appears necessary for
trafficking from the endosomes to the Golgi. In
Drosophila zygotes, mutation of Arl1 is lethal, and in
the host-bloodstream form of Trypanosoma brucei, Arl1
is essential for viability.
Length = 158
Score = 29.3 bits (66), Expect = 0.56
Identities = 13/34 (38%), Positives = 16/34 (47%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQE 57
+WD GQ R YY II V D TD++
Sbjct: 47 VWDLGGQTSIRPYWRCYYSNTDAIIYVVDSTDRD 80
>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 = 29.0 bits (65), Expect = 0.76
Identities = 21/90 (23%), Positives = 43/90 (47%), Gaps = 4/90 (4%)
Query: 47 IIVVYDCTDQETFNNLKQWLEEIDRY-ACDNVNKLLVGNKN--DQTSKKAVDYQVAKEYA 103
+I V+ D+ +F + + ++ Y + +LVG ++ ++ + +D A++
Sbjct: 69 VIFVFSLEDEASFQTVYRLYHQLSSYRNISEIPLILVGTQDAISASNPRVIDDARARQLC 128
Query: 104 DHLK-IPFLETSAKNGANVEQAFLTMATEI 132
+K + ET A G NVE+ F A +I
Sbjct: 129 ADMKRCSYYETCATYGLNVERVFQEAAQKI 158
>gnl|CDD|180982 PRK07452, PRK07452, DNA polymerase III subunit delta; Validated.
Length = 326
Score = 29.1 bits (66), Expect = 1.1
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 9 TLQNKKEERTRTLIVIWDTAGQERF 33
LQ EE+ +LI WDT G ++
Sbjct: 114 LLQKLAEEKEFSLIPPWDTEGLKQL 138
>gnl|CDD|225918 COG3383, COG3383, Uncharacterized anaerobic dehydrogenase [General
function prediction only].
Length = 978
Score = 28.9 bits (65), Expect = 1.5
Identities = 16/59 (27%), Positives = 24/59 (40%), Gaps = 11/59 (18%)
Query: 12 NKKEERTRTLI--------VIWDTAGQ---ERFRTITSSYYRGAHGIIVVYDCTDQETF 59
N ++ T+ LI V W+ A R R I Y + G I CT++E +
Sbjct: 314 NSRDRITKPLIREGDRFREVSWEEALDLVASRLREIKEKYGGDSIGFIASSKCTNEENY 372
>gnl|CDD|206723 cd04158, ARD1, (ADP-ribosylation factor domain protein 1 (ARD1).
ARD1 (ADP-ribosylation factor domain protein 1) is an
unusual member of the Arf family. In addition to the
C-terminal Arf domain, ARD1 has an additional 46-kDa
N-terminal domain that contains a RING finger domain,
two predicted B-Boxes, and a coiled-coil protein
interaction motif. This domain belongs to the TRIM
(tripartite motif) or RBCC (RING, B-Box, coiled-coil)
family. Like most Arfs, the ARD1 Arf domain lacks
detectable GTPase activity. However, unlike most Arfs,
the full-length ARD1 protein has significant GTPase
activity due to the GAP (GTPase-activating protein)
activity exhibited by the 46-kDa N-terminal domain. The
GAP domain of ARD1 is specific for its own Arf domain
and does not bind other Arfs. The rate of GDP
dissociation from the ARD1 Arf domain is slowed by the
adjacent 15 amino acids, which act as a GDI
(GDP-dissociation inhibitor) domain. ARD1 is
ubiquitously expressed in cells and localizes to the
Golgi and to the lysosomal membrane. Two Tyr-based
motifs in the Arf domain are responsible for Golgi
localization, while the GAP domain controls lysosomal
localization.
Length = 169
Score = 28.1 bits (62), Expect = 2.0
Identities = 9/34 (26%), Positives = 17/34 (50%)
Query: 24 IWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQE 57
IWD G+ + R + YY ++ V D + ++
Sbjct: 47 IWDVGGKHKLRPLWKHYYLNTQAVVFVIDSSHRD 80
>gnl|CDD|235638 PRK05896, PRK05896, DNA polymerase III subunits gamma and tau;
Validated.
Length = 605
Score = 28.3 bits (63), Expect = 2.1
Identities = 26/112 (23%), Positives = 39/112 (34%), Gaps = 9/112 (8%)
Query: 57 ETFNNLKQWL-----EEIDRYACDNVN-KLLVGNKNDQTSKKAVDYQVAKEYADHLKIPF 110
N LK + EI Y N N L K + + K + KI
Sbjct: 338 SLINRLKASVNQVFEFEIYLYKIINANPDKLENKKIEISIKPEKKTINNSQIITTKKINI 397
Query: 111 LETSAKNGANVEQAFLTMATEIKKRVTKDEKPSSESDAKKLNLNSGKPVDAP 162
+E S KN + + + T KK++ ++ K D KK L + V
Sbjct: 398 VEESNKNSVHFDTLYKTKIFYHKKKINQNNKE---QDIKKEELLEKEFVKKS 446
>gnl|CDD|239881 cd04434, LanC_like, LanC-like proteins. LanC is the cyclase enzyme
of the lanthionine synthetase. Lanthionine is a
lantibiotic, a unique class of peptide antibiotics. They
are ribosomally synthesized as a precursor peptide and
then post-translationally modified to contain thioether
cross-links called lanthionines (Lans) or
methyllanthionines (MeLans), in addition to
2,3-didehydroalanine (Dha) and (Z)-2,3-didehydrobutyrine
(Dhb). These unusual amino acids are introduced by the
dehydration of serine and threonine residues, followed
by thioether formation via addition of cysteine thiols,
catalysed by LanB and LanC or LanM. LanC, the cyclase
component, is a zinc metalloprotein, whose bound metal
has been proposed to activate the thiol substrate for
nucleophilic addition. A related domain is also present
in LanM and other pro- and eukaryotic proteins of
unknown function.
Length = 343
Score = 28.3 bits (63), Expect = 2.4
Identities = 17/117 (14%), Positives = 38/117 (32%), Gaps = 17/117 (14%)
Query: 7 YQTLQNKKEERTRTLIVIWDTAGQERFRTITSSYYRGAHGII----VVYDCT-DQETFNN 61
Y+ ++K + + + S + G GI + DQE
Sbjct: 15 YRVTPDEKYQDLAHKALEYIVKSLSSLPDTDISLFSGLAGIAYALAALSKGLGDQELLKE 74
Query: 62 LKQWLEEIDRYACDNVNK----LLVGN--------KNDQTSKKAVDYQVAKEYADHL 106
L + L + +++ LL G +T + + ++ ++ D+L
Sbjct: 75 LLELLLLLVELILEDLKDLNYDLLSGLAGLLLALLLLYKTFGEEIFLELIRKILDYL 131
>gnl|CDD|204135 pfam09104, BRCA-2_OB3, BRCA2,
oligonucleotide/oligosaccharide-binding, domain 3.
Members of this family assume an OB fold, which consists
of a highly curved five-stranded beta-sheet that closes
on itself to form a beta-barrel. OB3 has a pronounced
groove formed by one face of the curved sheet and is
demarcated by two loops, one between beta 1 and beta 2
and another between beta 4 and beta 5, which allows for
strong ssDNA binding.
Length = 143
Score = 27.5 bits (61), Expect = 2.7
Identities = 12/33 (36%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 56 QETFNNLKQWLEEIDRYACDNVNKLL-VGNKND 87
QE FN+L+ +E ID + + KL + N N
Sbjct: 109 QERFNSLRATIENIDTFYKEAEKKLAHLLNGNS 141
>gnl|CDD|223455 COG0378, HypB, Ni2+-binding GTPase involved in regulation of
expression and maturation of urease and hydrogenase
[Posttranslational modification, protein turnover,
chaperones / Transcription].
Length = 202
Score = 27.6 bits (62), Expect = 2.9
Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 2/46 (4%)
Query: 80 LLVGNKNDQTSKKAVDYQVAKEYADHL--KIPFLETSAKNGANVEQ 123
LLV NK D D +V A + + P + T+ K G +++
Sbjct: 146 LLVINKTDLAPYVGADLEVMARDAKEVNPEAPIIFTNLKTGEGLDE 191
>gnl|CDD|240982 cd12538, RRM_U2AF35, RNA recognition motif in U2 small nuclear
ribonucleoprotein auxiliary factor U2AF 35 kDa subunit
(U2AF35). This subgroup corresponds to the RRM of
U2AF35, also termed U2AF1, which is one of the small
subunits of U2 small nuclear ribonucleoprotein (snRNP)
auxiliary factor (U2AF). It has been implicated in the
recruitment of U2 snRNP to pre-mRNAs and is a highly
conserved heterodimer composed of large and small
subunits. U2AF35 directly binds to the 3' splice site
of the conserved AG dinucleotide and performs multiple
functions in the splicing process in a
substrate-specific manner. It promotes U2 snRNP binding
to the branch-point sequences of introns through
association with the large subunit of U2AF, U2AF65
(also termed U2AF2). U2AF35 contains two N-terminal
zinc fingers, a central RNA recognition motif (RRM),
also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal
arginine/serine (SR)-rich segment interrupted by
glycines. U2AF35 binds both U2AF65 and the pre-mRNA
through its RRM domain. .
Length = 104
Score = 26.5 bits (59), Expect = 3.1
Identities = 12/35 (34%), Positives = 22/35 (62%), Gaps = 7/35 (20%)
Query: 66 LEEIDRYACDNVNKLLVGN-----KNDQTSKKAVD 95
+EE++ CDN+ LVGN + ++ ++KAV+
Sbjct: 54 IEEMN--VCDNLGDHLVGNVYVKFRREEDAEKAVN 86
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 27.3 bits (62), Expect = 4.2
Identities = 23/113 (20%), Positives = 40/113 (35%), Gaps = 34/113 (30%)
Query: 16 ERTRTLIVIWDTAGQ---ERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEIDRY 72
ERTR L+ + D E ++TI E+++Y
Sbjct: 235 ERTRLLLHLVDIEAVDPVEDYKTI-----------------------------RNELEKY 265
Query: 73 ACDNVNK--LLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQ 123
+ + +K +LV NK D ++ + A L P SA G +++
Sbjct: 266 SPELADKPRILVLNKIDLLDEEEEREKRAALELAALGGPVFLISAVTGEGLDE 318
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 27.3 bits (61), Expect = 4.2
Identities = 12/47 (25%), Positives = 21/47 (44%), Gaps = 1/47 (2%)
Query: 76 NVNKLLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVE 122
+ +L N D+ K+ + + K L +P + T AK G +E
Sbjct: 108 GIPMILALNMIDEAKKRGIRIDIEKLSK-LLGVPVVPTVAKRGEGLE 153
>gnl|CDD|211860 TIGR03680, eif2g_arch, translation initiation factor 2 subunit
gamma. This model represents the archaeal translation
initiation factor 2 subunit gamma and is found in all
known archaea. eIF-2 functions in the early steps of
protein synthesis by forming a ternary complex with GTP
and initiator tRNA.
Length = 406
Score = 27.3 bits (61), Expect = 4.3
Identities = 25/90 (27%), Positives = 40/90 (44%), Gaps = 7/90 (7%)
Query: 78 NKLLVGNKNDQTSK-KAVD-YQVAKEYADHL---KIPFLETSAKNGANVEQAFLTMATEI 132
N ++V NK D SK KA++ Y+ KE+ P + SA + AN++ + I
Sbjct: 136 NIVIVQNKIDLVSKEKALENYEEIKEFVKGTIAENAPIIPVSALHNANIDALLEAIEKFI 195
Query: 133 KKRVTKDEKPSSESDAKKLNLNSGKPVDAP 162
+KP A+ ++N KP P
Sbjct: 196 PTPERDLDKPPLMYVARSFDVN--KPGTPP 223
>gnl|CDD|177773 PLN00178, PLN00178, sulfite reductase.
Length = 623
Score = 27.4 bits (61), Expect = 4.5
Identities = 10/30 (33%), Positives = 18/30 (60%), Gaps = 3/30 (10%)
Query: 12 NKKEERTRTLIVIWDTAGQERFRTITSSYY 41
++K+ R + L+ W G E+FR++ YY
Sbjct: 351 DRKQSRMKYLVHSW---GIEKFRSVVEQYY 377
>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 = 27.2 bits (61), Expect = 4.7
Identities = 10/56 (17%), Positives = 21/56 (37%), Gaps = 12/56 (21%)
Query: 22 IVIWDTAGQERFRTITSSY-----YRGAHGIIVVYDCTDQETFNNLKQWLEEIDRY 72
+ +WD GQ+ F + + +I V+D +E + E++
Sbjct: 50 LNLWDCPGQDDFMENYLTRQKEHIFSNVGVLIYVFDVESRE-------YEEDLATL 98
>gnl|CDD|182913 PRK11029, PRK11029, FtsH protease regulator HflC; Provisional.
Length = 334
Score = 26.6 bits (59), Expect = 6.6
Identities = 14/37 (37%), Positives = 21/37 (56%), Gaps = 4/37 (10%)
Query: 105 HLKIPFLETSAKNGANVEQAFLTMATEIKKRVTKDEK 141
H KIPF+ET A ++ TM + + VTK++K
Sbjct: 53 HFKIPFIETVKMLDARIQ----TMDNQADRFVTKEKK 85
>gnl|CDD|233905 TIGR02515, IV_pilus_PilQ, type IV pilus secretin (or competence
protein) PilQ. A number of proteins homologous to PilQ
are involved in type IV pilus formation, competence for
transformation, type III secretion, and type II
secretion (also called the main terminal branch of the
general secretion pathway). Members of this family
include PilQ itself, which is a component of the type IV
pilus structure, from a number of species. In
Haemophilus influenzae, the member of this family is
associated with competence for transformation with
exogenous DNA rather than with formation of a type IV
pilus; the surface structure required for competence may
be considered an unusual, incomplete type IV pilus
structure [Cell envelope, Surface structures].
Length = 418
Score = 26.9 bits (60), Expect = 6.9
Identities = 11/34 (32%), Positives = 21/34 (61%), Gaps = 4/34 (11%)
Query: 108 IPFLETSAKNGANVE--QAFLTMATEIKKRVTKD 139
IP+ +TS+ +VE +A L++ E+ ++T D
Sbjct: 291 IPYQQTSSSGATSVEFKEAVLSL--EVTPQITPD 322
>gnl|CDD|215300 PLN02545, PLN02545, 3-hydroxybutyryl-CoA dehydrogenase.
Length = 295
Score = 26.6 bits (59), Expect = 7.3
Identities = 12/53 (22%), Positives = 19/53 (35%), Gaps = 15/53 (28%)
Query: 42 RGAHGIIVVYDCTDQETFNNLKQWLEEIDRYACDN-------VNKLLVGNKND 87
RGA T E F+ K E + + VN++L+ N+
Sbjct: 156 RGAD--------TSDEVFDATKALAERFGKTVVCSQDYPGFIVNRILMPMINE 200
>gnl|CDD|227582 COG5257, GCD11, Translation initiation factor 2, gamma subunit
(eIF-2gamma; GTPase) [Translation, ribosomal structure
and biogenesis].
Length = 415
Score = 26.5 bits (59), Expect = 8.9
Identities = 23/96 (23%), Positives = 43/96 (44%), Gaps = 10/96 (10%)
Query: 78 NKLLVGNKNDQTSKKAV--DYQVAKEY-----ADHLKIPFLETSAKNGANVEQAFLTMAT 130
N ++V NK D S++ +Y+ KE+ A+ P + SA++ AN++ +
Sbjct: 142 NIIIVQNKIDLVSRERALENYEQIKEFVKGTVAE--NAPIIPISAQHKANIDALIEAIEK 199
Query: 131 EIKKRVTKDEKPSSESDAKKLNLNS-GKPVDAPRSG 165
I +KP A+ ++N G P + + G
Sbjct: 200 YIPTPERDLDKPPRMYVARSFDVNKPGTPPEELKGG 235
>gnl|CDD|197237 cd09139, PLDc_pPLD_like_1, Catalytic domain, repeat 1, of plant
phospholipase D and similar proteins. Catalytic domain,
repeat 1, of plant phospholipase D (PLD, EC 3.1.4.4) and
similar proteins. Plant PLDs have broad substrate
specificity and can hydrolyze the terminal
phosphodiester bond of several common membrane
phospholipids such as phosphatidylcholine (PC),
phosphatidylethanolamine (PE), phosphatidylglycerol
(PG), and phosphatidylserine (PS), with the formation of
phosphatidic acid and alcohols. Phosphatidic acid is an
essential compound involved in signal transduction. PLDs
also catalyze the transphosphatidylation of
phospholipids to acceptor alcohols, by which various
phospholipids can be synthesized. Most plant PLDs
possess a regulatory calcium-dependent
phospholipid-binding C2 domain in the N-terminus and
require calcium for activity, which is unique to plant
PLDs and is not present in animal or fungal PLDs. Like
other PLD enzymes, the monomer of plant PLDs consists of
two catalytic domains, each of which contains one copy
of the conserved HKD motif (H-x-K-x(4)-D, where x
represents any amino acid residue). Two HKD motifs from
two domains form a single active site. Plant PLDs may
utilize a common two-step ping-pong catalytic mechanism
involving an enzyme-substrate intermediate to cleave
phosphodiester bonds. The two histidine residues from
the two HKD motifs play key roles in the catalysis. Upon
substrate binding, a histidine residue from one HKD
motif could function as the nucleophile, attacking the
phosphodiester bond to create a covalent
phosphohistidine intermediate, while the other histidine
residue from the second HKD motif could serve as a
general acid, stabilizing the leaving group. This
subfamily includes two types of plant PLDs, alpha-type
and beta-type PLDs, which are derived from different
gene products and distinctly regulated. The zeta-type
PLD from Arabidopsis is not included in this subfamily.
Length = 176
Score = 25.8 bits (57), Expect = 9.2
Identities = 24/113 (21%), Positives = 36/113 (31%), Gaps = 22/113 (19%)
Query: 10 LQNKKEERTRTLIVIWDTAGQERFRTITSSYYRGAHGIIVVYDCTDQETFNNLKQWLEEI 69
L+ K EE L+++WD V D+ET N +
Sbjct: 58 LKRKAEEGVAVLLLLWD------------DKTVNGFKNDGVMATHDEETRNFFRN----- 100
Query: 70 DRYACDNVNKLLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVE 122
VN LL D + +V+ + H K ++ A NG E
Sbjct: 101 -----TKVNCLLCPRNGDAGNTYVEQIEVSTAFTHHQKTVIVDAPAPNGERRE 148
>gnl|CDD|237055 PRK12317, PRK12317, elongation factor 1-alpha; Reviewed.
Length = 425
Score = 26.4 bits (59), Expect = 9.3
Identities = 21/60 (35%), Positives = 29/60 (48%), Gaps = 20/60 (33%)
Query: 77 VNKLLVG-NKNDQTSKKAVDY------QVAKEYADHLK--------IPFLETSAKNGANV 121
+N+L+V NK D AV+Y +V +E + LK IPF+ SA G NV
Sbjct: 139 INQLIVAINKMD-----AVNYDEKRYEEVKEEVSKLLKMVGYKPDDIPFIPVSAFEGDNV 193
>gnl|CDD|217025 pfam02421, FeoB_N, Ferrous iron transport protein B. Escherichia
coli has an iron(II) transport system (feo) which may
make an important contribution to the iron supply of the
cell under anaerobic conditions. FeoB has been
identified as part of this transport system. FeoB is a
large 700-800 amino acid integral membrane protein. The
N terminus contains a P-loop motif suggesting that iron
transport may be ATP dependent.
Length = 190
Score = 25.9 bits (58), Expect = 9.6
Identities = 12/66 (18%), Positives = 29/66 (43%), Gaps = 1/66 (1%)
Query: 76 NVNKLLVGNKNDQTSKKAVDYQVAKEYADHLKIPFLETSAKNGANVEQAFLTMATEIKKR 135
+ ++ N D+ KK + + K ++ L +P + TSA+ G +++ + + +
Sbjct: 105 GIPVVVALNMMDEAEKKGIKIDIKK-LSELLGVPVVPTSARKGEGIDELKDAIIEVAEGK 163
Query: 136 VTKDEK 141
V
Sbjct: 164 VPPAPL 169
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.314 0.130 0.376
Gapped
Lambda K H
0.267 0.0585 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,175,518
Number of extensions: 712910
Number of successful extensions: 774
Number of sequences better than 10.0: 1
Number of HSP's gapped: 703
Number of HSP's successfully gapped: 158
Length of query: 168
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 78
Effective length of database: 6,945,742
Effective search space: 541767876
Effective search space used: 541767876
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 55 (25.3 bits)