RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17467
(730 letters)
>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 = 254 bits (649), Expect = 1e-80
Identities = 97/119 (81%), Positives = 110/119 (92%)
Query: 1 MEDYKFLFKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQI 60
MEDY FLFK+VL+GNAGVGKTCLVRRFTQG+FPPGQGATIGVDFMIKTVEI E+IKLQI
Sbjct: 1 MEDYDFLFKIVLIGNAGVGKTCLVRRFTQGLFPPGQGATIGVDFMIKTVEIKGEKIKLQI 60
Query: 61 WDTAGQERFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRVLVG 119
WDTAGQERFRSITQSYYRSA+ALIL YDI+C+ +F CL +WLREIE+YA+ KV+ +LVG
Sbjct: 61 WDTAGQERFRSITQSYYRSANALILTYDITCEESFRCLPEWLREIEQYANNKVITILVG 119
Score = 81.5 bits (201), Expect = 7e-18
Identities = 36/81 (44%), Positives = 50/81 (61%), Gaps = 11/81 (13%)
Query: 173 CIPKLARNEACFYLASLEGHSNN--IHCMARNKIDR-EDREIPTEVGEDFAKRHDMYYLE 229
C+P+ +L +E ++NN I + NKID E RE+ + E+F+ DMYYLE
Sbjct: 97 CLPE--------WLREIEQYANNKVITILVGNKIDLAERREVSQQRAEEFSDAQDMYYLE 148
Query: 230 TSAKASDNVEKLFMQIAAELM 250
TSAK SDNVEKLF+ +A L+
Sbjct: 149 TSAKESDNVEKLFLDLACRLI 169
>gnl|CDD|204301 pfam09735, Nckap1, Membrane-associated apoptosis protein.
Expression of this protein was found to be markedly
reduced in patients with Alzheimer's disease. It is
involved in the regulation of actin polymerisation in
the brain as part of a WAVE2 signalling complex.
Length = 1118
Score = 242 bits (620), Expect = 5e-68
Identities = 94/168 (55%), Positives = 118/168 (70%)
Query: 385 AQIASRRKKDKNNKKILNEIIKPGAESYRKTREELTTMDKLHMALTELCFAINYCTNIQV 444
+ +++ K KK E KPG ESYRK R +T +DKLH+ LTELC A+N+ I V
Sbjct: 634 SAARNKKSKKAKAKKGEPEREKPGHESYRKNRSSVTMLDKLHLRLTELCSALNHVEPICV 693
Query: 445 WDFTFAPREYLHQHLESRFSRALVGMVMFNPDTSEIAKPSELLASVRAYMNVLQTVENYV 504
W+ TFAPREYL HLE RF+RA+VGM +N T EIA+PSELL+ VRAYM VLQ++E YV
Sbjct: 694 WEHTFAPREYLSSHLEGRFTRAIVGMAQYNQATQEIARPSELLSLVRAYMTVLQSLEQYV 753
Query: 505 HIDMTRVFNNALLQQTQRMDSHGEKTVAALYIQWYSEVLLRRVSETQV 552
+D+TRV N LLQQTQ +DSHGE T+ ALY WY + LLR+VS +
Sbjct: 754 SMDITRVIRNVLLQQTQPLDSHGEGTITALYTNWYLDNLLRQVSGGGI 801
Score = 154 bits (391), Expect = 1e-38
Identities = 70/135 (51%), Positives = 87/135 (64%), Gaps = 15/135 (11%)
Query: 557 LLNFLRVY-----TVENYVHIDMTRVFNNALLQQTQRMDSHGEKTVAALYIQWYSEVLLR 611
LL+ +R Y ++E YV +D+TRV N LLQQTQ +DSHGE T+ ALY WY + LLR
Sbjct: 735 LLSLVRAYMTVLQSLEQYVSMDITRVIRNVLLQQTQPLDSHGEGTITALYTNWYLDNLLR 794
Query: 612 RVSAGNICFSLNQRAFVSLTAEGAIPFNAEEFSDVNELRALADLIGPYGMKLLNELSLKA 671
+VS G I FS +AFVS E + FNAEEFSD++ELRAL +L+GPYGMK L+E
Sbjct: 795 QVSGGGIVFSPAMKAFVSSPPEE-LGFNAEEFSDISELRALVELLGPYGMKFLSESL--- 850
Query: 672 FNAAHEMVHNQSDVN 686
M H S VN
Sbjct: 851 ------MWHIASQVN 859
Score = 141 bits (356), Expect = 2e-34
Identities = 66/95 (69%), Positives = 78/95 (82%), Gaps = 2/95 (2%)
Query: 252 KLAEKLTIMHDRGVGMLTRIYNIKKACGDAKSKPSFLSDKSLESCIKQIVKKFPNIDIKS 311
KLAEKLTI++DRGVGMLTRIYNIKKACGD KSKPSFLSDK LE IK IV+KFPN+D ++
Sbjct: 5 KLAEKLTILNDRGVGMLTRIYNIKKACGDPKSKPSFLSDKFLEPSIKFIVRKFPNVDTRT 64
Query: 312 VS--GISQIRSDIVKSLSLYYYTFVDLLHFKDCVY 344
+ + + +I+KSLSLYYYTFVDL+ FKD V
Sbjct: 65 QQLDAVQEEKEEILKSLSLYYYTFVDLMEFKDHVL 99
Score = 104 bits (261), Expect = 7e-23
Identities = 48/115 (41%), Positives = 69/115 (60%), Gaps = 9/115 (7%)
Query: 96 DCLTDWLREIEE------YASFKVLRVLVGGTSGLKI---VNEMASAAGLLCTVDPALAT 146
D + LR + E +S + L+ V + K+ + EMASAAG+ C VDPAL
Sbjct: 913 DLAQEALRAVLESHVPFLMSSIEDLKEHVPEVTDKKVILRIFEMASAAGVPCDVDPALVN 972
Query: 147 ALASDKTDLDEDEHVLACLLMVFVAVCIPKLARNEACFYLASLEGHSNNIHCMAR 201
AL + K + E+++ +CLL+VFVAV +P LA + FY +EGHSNNIHC+A+
Sbjct: 973 ALLAQKGENSEEDYKNSCLLLVFVAVSLPTLAMWDTSFYNPEIEGHSNNIHCLAK 1027
Score = 75.5 bits (186), Expect = 7e-14
Identities = 30/43 (69%), Positives = 36/43 (83%)
Query: 669 LKAFNAAHEMVHNQSDVNFPRLGQMIMDYEVPMKKLSEEFIPH 711
L +NAAHEM H QSD +FPRLGQMI+DY+ P+KKL EEF+PH
Sbjct: 148 LGLYNAAHEMQHGQSDCSFPRLGQMILDYDPPLKKLHEEFVPH 190
>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 = 189 bits (484), Expect = 1e-56
Identities = 62/112 (55%), Positives = 83/112 (74%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE 67
FK+VL+G++GVGKT L+ RF F +TIGVDF KT+E++ +++KLQIWDTAGQE
Sbjct: 1 FKIVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGVDFKSKTIEVDGKKVKLQIWDTAGQE 60
Query: 68 RFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRVLVG 119
RFRSIT SYYR AH ILVYD++ + +F+ L WL E++EYA + +LVG
Sbjct: 61 RFRSITSSYYRGAHGAILVYDVTNRESFENLDKWLNELKEYAPPNIPIILVG 112
Score = 62.5 bits (153), Expect = 2e-11
Identities = 18/46 (39%), Positives = 30/46 (65%), Gaps = 1/46 (2%)
Query: 202 NKID-REDREIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIA 246
NK D ++R++ TE + FAK + + + ETSAK +NV++ F +A
Sbjct: 113 NKSDLEDERQVSTEEAQQFAKENGLLFFETSAKTGENVDEAFESLA 158
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 183 bits (466), Expect = 5e-54
Identities = 64/112 (57%), Positives = 87/112 (77%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE 67
FK++L+G++GVGK+ L+ RFT G F +TIGVDF KT+E++ +R+KLQIWDTAGQE
Sbjct: 1 FKIILIGDSGVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIEVDGKRVKLQIWDTAGQE 60
Query: 68 RFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRVLVG 119
RFRSIT SYYR A +LVYDI+ + +F+ L +WL+E+ EYAS V+ +LVG
Sbjct: 61 RFRSITSSYYRGAVGALLVYDITNRESFENLENWLKELREYASPNVVIMLVG 112
Score = 64.1 bits (157), Expect = 6e-12
Identities = 21/52 (40%), Positives = 35/52 (67%), Gaps = 1/52 (1%)
Query: 202 NKIDRED-REIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIAAELMEK 252
NK D E+ R++ E E FA+ H + + ETSAK + NVE+ F ++A E++++
Sbjct: 113 NKSDLEEQRQVSREEAEAFAEEHGLPFFETSAKTNTNVEEAFEELAREILKR 164
>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 = 179 bits (455), Expect = 1e-52
Identities = 73/160 (45%), Positives = 108/160 (67%), Gaps = 13/160 (8%)
Query: 6 FLFKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAG 65
FLFK++L+G++ VGKTC+V+RF G F QG TIGVDF +KT+EI +R+KLQIWDTAG
Sbjct: 2 FLFKIILIGDSNVGKTCVVQRFKSGTFSERQGNTIGVDFTMKTLEIQGKRVKLQIWDTAG 61
Query: 66 QERFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRVLVGGTSGLK 125
QERFR+ITQSYYRSA+ I+ YDI+ + +F+ + W+ E+E+Y + V+ +L+G L+
Sbjct: 62 QERFRTITQSYYRSANGAIIAYDITRRSSFESVPHWIEEVEKYGASNVVLLLIGNKCDLE 121
Query: 126 IVNE--------MASAAGLLCTVDPALATALASDKTDLDE 157
E +A G+L L T+ A + ++++E
Sbjct: 122 EQREVLFEEACTLAEHYGILA----VLETS-AKESSNVEE 156
Score = 43.6 bits (103), Expect = 7e-05
Identities = 25/61 (40%), Positives = 35/61 (57%), Gaps = 2/61 (3%)
Query: 191 GHSNNIHCMARNKIDRED-REIPTEVGEDFAKRHDMYY-LETSAKASDNVEKLFMQIAAE 248
G SN + + NK D E+ RE+ E A+ + + LETSAK S NVE+ F+ +A E
Sbjct: 105 GASNVVLLLIGNKCDLEEQREVLFEEACTLAEHYGILAVLETSAKESSNVEEAFLLMATE 164
Query: 249 L 249
L
Sbjct: 165 L 165
>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 = 169 bits (431), Expect = 4e-49
Identities = 63/114 (55%), Positives = 93/114 (81%)
Query: 6 FLFKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAG 65
+LFK++L+G++GVGK+CL+ RF++ F P +TIG+DF I+T+E++ ++IKLQIWDTAG
Sbjct: 2 YLFKLLLIGDSGVGKSCLLLRFSEDSFNPSFISTIGIDFKIRTIELDGKKIKLQIWDTAG 61
Query: 66 QERFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRVLVG 119
QERFR+IT SYYR A +ILVYDI+ + +F+ + +W+R I+E+AS V R+LVG
Sbjct: 62 QERFRTITTSYYRGAMGIILVYDITDEKSFENIKNWMRNIDEHASEDVERMLVG 115
Score = 52.7 bits (127), Expect = 5e-08
Identities = 22/52 (42%), Positives = 36/52 (69%), Gaps = 1/52 (1%)
Query: 202 NKIDRED-REIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIAAELMEK 252
NK D E+ R + E GE A+ + + +LETSAKA+ NVE+ F+ +A ++++K
Sbjct: 116 NKCDMEEKRVVSKEEGEALAREYGIKFLETSAKANINVEEAFLTLAKDILKK 167
>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 = 167 bits (424), Expect = 3e-48
Identities = 62/120 (51%), Positives = 90/120 (75%)
Query: 6 FLFKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAG 65
+LFK++L+G++GVGK+CL+ RF + +TIGVDF I+T+E++ + +KLQIWDTAG
Sbjct: 1 YLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTVKLQIWDTAG 60
Query: 66 QERFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRVLVGGTSGLK 125
QERFR+IT SYYR AH +I+VYD++ Q +F+ + WL+EI+ YAS V ++LVG L
Sbjct: 61 QERFRTITSSYYRGAHGIIIVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLT 120
Score = 56.2 bits (136), Expect = 3e-09
Identities = 19/52 (36%), Positives = 31/52 (59%), Gaps = 1/52 (1%)
Query: 202 NKIDRED-REIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIAAELMEK 252
NK D D + + ++FA + +LETSAK + NVE+ FM +A E+ ++
Sbjct: 115 NKCDLTDKKVVDYTEAKEFADELGIPFLETSAKNATNVEEAFMTMAREIKKR 166
>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 = 163 bits (416), Expect = 4e-47
Identities = 59/111 (53%), Positives = 77/111 (69%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQER 68
K+VLVG+ GVGK+ L+ RFTQ FP TIGVDF KT+E++ + +KLQIWDTAGQER
Sbjct: 1 KLVLVGDGGVGKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAGQER 60
Query: 69 FRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRVLVG 119
FR++ YYR A +LVYDI+ + +F+ + WL EI +A V VLVG
Sbjct: 61 FRALRPLYYRGAQGFLLVYDITSRDSFENVKKWLEEILRHADENVPIVLVG 111
Score = 65.2 bits (160), Expect = 2e-12
Identities = 21/51 (41%), Positives = 34/51 (66%), Gaps = 1/51 (1%)
Query: 202 NKID-REDREIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIAAELME 251
NK D + R + TE GE AK + ++ETSAK ++NVE+ F ++A E+++
Sbjct: 112 NKCDLEDQRVVSTEEGEALAKELGLPFMETSAKTNENVEEAFEELAREILK 162
>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 = 160 bits (406), Expect = 1e-45
Identities = 66/242 (27%), Positives = 110/242 (45%), Gaps = 81/242 (33%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE 67
FK+VL+G++ VGK+ +V RF + F Q +TIG F+ +TV +++ +K +IWDTAGQE
Sbjct: 2 FKLVLLGDSSVGKSSIVLRFVKNEFSENQESTIGAAFLTQTVNLDDTTVKFEIWDTAGQE 61
Query: 68 RFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRVLVGGTSGLKIV 127
R+RS+ YYR A A I+VYDI+ + +F+ W++E++E+
Sbjct: 62 RYRSLAPMYYRGAAAAIVVYDITSEESFEKAKSWVKELQEHG------------------ 103
Query: 128 NEMASAAGLLCTVDPALATALASDKTDLDEDEHVLACLLMVFVAVCIPKLARNEACFYLA 187
P + ALA +K DL+
Sbjct: 104 -------------PPNIVIALAGNKADLESK----------------------------- 121
Query: 188 SLEGHSNNIHCMARNKIDREDREIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIAA 247
++ E+ +++A + + ++ETSAK +NV +LF +IA
Sbjct: 122 --------------RQVSTEE-------AQEYADENGLLFMETSAKTGENVNELFTEIAR 160
Query: 248 EL 249
+L
Sbjct: 161 KL 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 = 158 bits (403), Expect = 3e-45
Identities = 57/120 (47%), Positives = 88/120 (73%)
Query: 6 FLFKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAG 65
+LFK+VL+G++GVGK+ L+ RFT+ F +TIGV+F +T++I+ + IK QIWDTAG
Sbjct: 2 YLFKIVLIGDSGVGKSNLLSRFTRNEFNLDSKSTIGVEFATRTIQIDGKTIKAQIWDTAG 61
Query: 66 QERFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRVLVGGTSGLK 125
QER+R+IT +YYR A +LVYDI+ + TF+ + WL+E+ ++A ++ +LVG S L+
Sbjct: 62 QERYRAITSAYYRGAVGALLVYDITKKSTFENVERWLKELRDHADSNIVIMLVGNKSDLR 121
Score = 62.6 bits (153), Expect = 2e-11
Identities = 26/68 (38%), Positives = 40/68 (58%), Gaps = 3/68 (4%)
Query: 185 YLASLEGHS-NNIHCM-ARNKID-REDREIPTEVGEDFAKRHDMYYLETSAKASDNVEKL 241
+L L H+ +NI M NK D R R +PTE + FA+++ + ++ETSA NVE+
Sbjct: 97 WLKELRDHADSNIVIMLVGNKSDLRHLRAVPTEEAKAFAEKNGLSFIETSALDGTNVEEA 156
Query: 242 FMQIAAEL 249
F Q+ E+
Sbjct: 157 FKQLLTEI 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 = 155 bits (394), Expect = 4e-44
Identities = 56/113 (49%), Positives = 83/113 (73%), Gaps = 1/113 (0%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE 67
K++L+G++GVGK+ L+ RFT F +TIGVDF +KTV ++ +++KL IWDTAGQE
Sbjct: 1 LKILLIGDSGVGKSSLLLRFTDDTFDEDLSSTIGVDFKVKTVTVDGKKVKLAIWDTAGQE 60
Query: 68 RFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFK-VLRVLVG 119
RFR++T SYYR A +ILVYD++ + TFD L WL E++ Y++ +++LVG
Sbjct: 61 RFRTLTSSYYRGAQGVILVYDVTRRDTFDNLDTWLNELDTYSTNPDAVKMLVG 113
Score = 60.4 bits (147), Expect = 9e-11
Identities = 20/45 (44%), Positives = 33/45 (73%)
Query: 202 NKIDREDREIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIA 246
NKID+E+RE+ E G+ FA++H+M ++ETSAK V++ F ++
Sbjct: 114 NKIDKENREVTREEGQKFARKHNMLFIETSAKTRIGVQQAFEELV 158
>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 = 151 bits (383), Expect = 2e-42
Identities = 61/127 (48%), Positives = 88/127 (69%), Gaps = 2/127 (1%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE 67
FK++++G++ VGKTCL RF G FP ATIGVDF +TVEI+ ERIK+Q+WDTAGQE
Sbjct: 3 FKIIVIGDSNVGKTCLTYRFCAGRFPERTEATIGVDFRERTVEIDGERIKVQLWDTAGQE 62
Query: 68 RFR-SITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYA-SFKVLRVLVGGTSGLK 125
RFR S+ Q YYR+ HA++ VYD++ +F L W+ E E+++ +V R+LVG L+
Sbjct: 63 RFRKSMVQHYYRNVHAVVFVYDVTNMASFHSLPSWIEECEQHSLPNEVPRILVGNKCDLR 122
Query: 126 IVNEMAS 132
++ +
Sbjct: 123 EQIQVPT 129
Score = 45.5 bits (108), Expect = 1e-05
Identities = 23/52 (44%), Positives = 33/52 (63%), Gaps = 4/52 (7%)
Query: 202 NKID-REDREIPTEVGEDFAKRHDMYYLETSAKA---SDNVEKLFMQIAAEL 249
NK D RE ++PT++ + FA H M ETSAK +D+VE +FM +A +L
Sbjct: 117 NKCDLREQIQVPTDLAQRFADAHSMPLFETSAKDPSENDHVEAIFMTLAHKL 168
>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 = 144 bits (366), Expect = 3e-40
Identities = 57/121 (47%), Positives = 84/121 (69%)
Query: 4 YKFLFKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDT 63
Y +LFK +++G+ GVGK+CL+ +FT F P TIGV+F + + I+ ++IKLQIWDT
Sbjct: 1 YAYLFKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDT 60
Query: 64 AGQERFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRVLVGGTSG 123
AGQE FRSIT+SYYR A +LVYDI+ + TF+ LT WL + ++++ + +L+G
Sbjct: 61 AGQESFRSITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQHSNSNMTIMLIGNKCD 120
Query: 124 L 124
L
Sbjct: 121 L 121
Score = 58.2 bits (141), Expect = 7e-10
Identities = 24/52 (46%), Positives = 34/52 (65%), Gaps = 1/52 (1%)
Query: 202 NKIDRE-DREIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIAAELMEK 252
NK D E RE+ E GE FA+ H + ++ETSAK + NVE+ F+ A E+ +K
Sbjct: 117 NKCDLESRREVSYEEGEAFAREHGLIFMETSAKTASNVEEAFINTAKEIYDK 168
>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 = 141 bits (358), Expect = 4e-39
Identities = 46/112 (41%), Positives = 73/112 (65%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE 67
K+V +G+ VGKT ++ RF F ATIG+DF+ KT+ ++++ ++LQ+WDTAGQE
Sbjct: 1 HKLVFLGDQSVGKTSIITRFMYDTFDNQYQATIGIDFLSKTMYVDDKTVRLQLWDTAGQE 60
Query: 68 RFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRVLVG 119
RFRS+ SY R + ++VYDI+ + +FD W+ ++ + V+ VLVG
Sbjct: 61 RFRSLIPSYIRDSSVAVVVYDITNRQSFDNTDKWIDDVRDERGNDVIIVLVG 112
Score = 64.2 bits (157), Expect = 6e-12
Identities = 24/49 (48%), Positives = 33/49 (67%), Gaps = 1/49 (2%)
Query: 202 NKIDRED-REIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIAAEL 249
NK D D R++ TE GE AK ++ ++ETSAKA NV++LF +IA L
Sbjct: 113 NKTDLSDKRQVSTEEGEKKAKENNAMFIETSAKAGHNVKQLFKKIAQAL 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 = 141 bits (357), Expect = 1e-38
Identities = 62/116 (53%), Positives = 85/116 (73%), Gaps = 1/116 (0%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQ-GATIGVDFMIKTVEINNERIKLQIWDTAGQ 66
FKV+LVG++GVGKTCL+ RF G F G AT+G+ F K V ++ ++KLQIWDTAGQ
Sbjct: 1 FKVMLVGDSGVGKTCLLVRFKDGAFLAGSFIATVGIQFTNKVVTVDGVKVKLQIWDTAGQ 60
Query: 67 ERFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRVLVGGTS 122
ERFRS+T +YYR AHAL+L+YD++ + +FD + WL EI EYA V+ +L+G +
Sbjct: 61 ERFRSVTHAYYRDAHALLLLYDVTNKSSFDNIRAWLTEILEYAQSDVVIMLLGNKA 116
Score = 40.2 bits (94), Expect = 0.001
Identities = 21/49 (42%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 202 NKID-REDREIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIAAEL 249
NK D +R + E GE AK + + ++ETSAK NVE F +A EL
Sbjct: 114 NKADMSGERVVKREDGERLAKEYGVPFMETSAKTGLNVELAFTAVAKEL 162
>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 = 139 bits (353), Expect = 2e-38
Identities = 53/112 (47%), Positives = 78/112 (69%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE 67
FK +++G+AG GK+CL+ +F + F TIGV+F + V + + +KLQIWDTAGQE
Sbjct: 1 FKFLIIGSAGTGKSCLLHQFIENKFKQDSNHTIGVEFGSRVVNVGGKSVKLQIWDTAGQE 60
Query: 68 RFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRVLVG 119
RFRS+T+SYYR A +LVYDI+ + +F+ LT+WL + AS ++ +LVG
Sbjct: 61 RFRSVTRSYYRGAAGALLVYDITSRESFNALTNWLTDARTLASPDIVIILVG 112
Score = 37.8 bits (88), Expect = 0.006
Identities = 18/46 (39%), Positives = 28/46 (60%), Gaps = 1/46 (2%)
Query: 202 NKID-REDREIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIA 246
NK D +DRE+ FA+ + + +LETSA +NVE+ F++ A
Sbjct: 113 NKKDLEDDREVTFLEASRFAQENGLLFLETSALTGENVEEAFLKCA 158
>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 = 138 bits (350), Expect = 1e-37
Identities = 63/117 (53%), Positives = 84/117 (71%), Gaps = 1/117 (0%)
Query: 3 DYKFLFKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWD 62
DY LFK++++G++GVGK+ L+ RF F TIGVDF I+TVEIN ER+KLQIWD
Sbjct: 2 DYDHLFKLLIIGDSGVGKSSLLLRFADNTFSGSYITTIGVDFKIRTVEINGERVKLQIWD 61
Query: 63 TAGQERFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRVLVG 119
TAGQERFR+IT +YYR H +I+VYD++ +F + WL+EIE+ V +VLVG
Sbjct: 62 TAGQERFRTITSTYYRGTHGVIVVYDVTNGESFVNVKRWLQEIEQNCD-DVCKVLVG 117
Score = 34.1 bits (78), Expect = 0.15
Identities = 18/45 (40%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 202 NKIDREDRE-IPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQI 245
NK D +R+ + TE FA + + ETSAK + NVE++F I
Sbjct: 118 NKNDDPERKVVETEDAYKFAGQMGISLFETSAKENINVEEMFNCI 162
>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 = 138 bits (350), Expect = 2e-37
Identities = 53/119 (44%), Positives = 83/119 (69%), Gaps = 2/119 (1%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNE-RIKLQIWDTAGQ 66
F+++++G++ VGK+ L++RFT+G F T+GVDF + +EI RIKLQ+WDTAGQ
Sbjct: 3 FRLIVIGDSTVGKSSLLKRFTEGRFAEVSDPTVGVDFFSRLIEIEPGVRIKLQLWDTAGQ 62
Query: 67 ERFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYAS-FKVLRVLVGGTSGL 124
ERFRSIT+SYYR++ ++LV+DI+ + +F+ + DWL E + + + +LVG L
Sbjct: 63 ERFRSITRSYYRNSVGVLLVFDITNRESFEHVHDWLEEARSHIQPHRPVFILVGHKCDL 121
Score = 46.7 bits (111), Expect = 1e-05
Identities = 21/51 (41%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 203 KIDRED-REIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIAAELMEK 252
K D E R++ E E AK M Y+ETSA+ DNVE+ F + E+ E+
Sbjct: 118 KCDLESQRQVTREEAEKLAKDLGMKYIETSARTGDNVEEAFELLTQEIYER 168
>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 = 132 bits (333), Expect = 1e-35
Identities = 52/112 (46%), Positives = 84/112 (75%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE 67
F+++L+G++GVGKTCL+ RFT F +TIGVDF +KT+E++ ++++QIWDTAGQE
Sbjct: 1 FRLLLIGDSGVGKTCLLCRFTDNEFHSSHISTIGVDFKMKTIEVDGIKVRIQIWDTAGQE 60
Query: 68 RFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRVLVG 119
R+++IT+ YYR A + LVYDIS + ++ + W+ +++EYA V ++L+G
Sbjct: 61 RYQTITKQYYRRAQGIFLVYDISSERSYQHIMKWVSDVDEYAPEGVQKILIG 112
Score = 29.6 bits (66), Expect = 3.2
Identities = 16/46 (34%), Positives = 26/46 (56%), Gaps = 1/46 (2%)
Query: 202 NKIDRED-REIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIA 246
NK D E R++ E G AK + M + ETSA + N+++ F ++
Sbjct: 113 NKADEEQKRQVGDEQGNKLAKEYGMDFFETSACTNKNIKESFTRLT 158
>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 = 131 bits (331), Expect = 2e-35
Identities = 51/119 (42%), Positives = 82/119 (68%)
Query: 6 FLFKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAG 65
++FK +++G+ GVGK+CL+ +FT+ F TIGV+F + +E+N ++IKLQIWDTAG
Sbjct: 1 YIFKYIIIGDMGVGKSCLLHQFTEKKFMADCPHTIGVEFGTRIIEVNGQKIKLQIWDTAG 60
Query: 66 QERFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRVLVGGTSGL 124
QERFR++T+SYYR A ++VYDI+ + T++ L+ WL + + + L+G + L
Sbjct: 61 QERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTVIFLIGNKADL 119
Score = 43.3 bits (102), Expect = 9e-05
Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 202 NKIDRED-REIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIAAELMEK 252
NK D E R++ E + FA + + +LE SAK +NVE F++ A ++ +
Sbjct: 115 NKADLEAQRDVTYEEAKQFADENGLLFLECSAKTGENVEDAFLETAKKIYQN 166
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 132 bits (333), Expect = 3e-35
Identities = 58/121 (47%), Positives = 83/121 (68%)
Query: 4 YKFLFKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDT 63
Y +LFK +++G+ GVGK+CL+ +FT F P TIGV+F + + I+N+ IKLQIWDT
Sbjct: 3 YAYLFKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDNKPIKLQIWDT 62
Query: 64 AGQERFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRVLVGGTSG 123
AGQE FRSIT+SYYR A +LVYDI+ + TF+ L WL + ++A+ + +L+G
Sbjct: 63 AGQESFRSITRSYYRGAAGALLVYDITRRETFNHLASWLEDARQHANANMTIMLIGNKCD 122
Query: 124 L 124
L
Sbjct: 123 L 123
Score = 53.4 bits (128), Expect = 6e-08
Identities = 35/92 (38%), Positives = 54/92 (58%), Gaps = 7/92 (7%)
Query: 171 AVCIPKLARNEACFYLAS-LEG---HSN-NIHCM-ARNKID-REDREIPTEVGEDFAKRH 223
A+ + + R E +LAS LE H+N N+ M NK D R + TE GE FAK H
Sbjct: 82 ALLVYDITRRETFNHLASWLEDARQHANANMTIMLIGNKCDLAHRRAVSTEEGEQFAKEH 141
Query: 224 DMYYLETSAKASDNVEKLFMQIAAELMEKLAE 255
+ ++E SAK + NVE+ F++ AA++ +K+ +
Sbjct: 142 GLIFMEASAKTAQNVEEAFIKTAAKIYKKIQD 173
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 130 bits (328), Expect = 2e-34
Identities = 55/123 (44%), Positives = 87/123 (70%)
Query: 3 DYKFLFKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWD 62
+Y +LFK+VL+G++GVGK+ ++ RFT+ F +TIGV+F +T+++ + +K QIWD
Sbjct: 8 EYDYLFKIVLIGDSGVGKSNILSRFTRNEFCLESKSTIGVEFATRTLQVEGKTVKAQIWD 67
Query: 63 TAGQERFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRVLVGGTS 122
TAGQER+R+IT +YYR A +LVYDI+ + TFD + WLRE+ ++A ++ ++ G S
Sbjct: 68 TAGQERYRAITSAYYRGAVGALLVYDITKRQTFDNVQRWLRELRDHADSNIVIMMAGNKS 127
Query: 123 GLK 125
L
Sbjct: 128 DLN 130
Score = 43.4 bits (102), Expect = 2e-04
Identities = 27/75 (36%), Positives = 40/75 (53%), Gaps = 3/75 (4%)
Query: 185 YLASLEGH--SNNIHCMARNKIDRED-REIPTEVGEDFAKRHDMYYLETSAKASDNVEKL 241
+L L H SN + MA NK D R + E G+ A++ + +LETSA + NVEK
Sbjct: 106 WLRELRDHADSNIVIMMAGNKSDLNHLRSVAEEDGQALAEKEGLSFLETSALEATNVEKA 165
Query: 242 FMQIAAELMEKLAEK 256
F I E+ +++K
Sbjct: 166 FQTILLEIYHIISKK 180
>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 = 128 bits (324), Expect = 5e-34
Identities = 61/111 (54%), Positives = 82/111 (73%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQER 68
+V+++G+ GVGKT L+ RFT F +T+GVDF IKTVE+ ++I+LQIWDTAGQER
Sbjct: 2 QVIIIGSRGVGKTSLMERFTDDTFCEACKSTVGVDFKIKTVELRGKKIRLQIWDTAGQER 61
Query: 69 FRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRVLVG 119
F SIT +YYRSA +ILVYDI+ + TFD L W++ I++YAS +LVG
Sbjct: 62 FNSITSAYYRSAKGIILVYDITKKETFDDLPKWMKMIDKYASEDAELLLVG 112
Score = 40.4 bits (94), Expect = 0.001
Identities = 21/54 (38%), Positives = 38/54 (70%), Gaps = 2/54 (3%)
Query: 202 NKIDRE-DREIPTEVGEDFAKR-HDMYYLETSAKASDNVEKLFMQIAAELMEKL 253
NK+D E DREI + GE FA++ M + E SAK + NV+++F+++ ++++K+
Sbjct: 113 NKLDCETDREITRQQGEKFAQQITGMRFCEASAKDNFNVDEIFLKLVDDILKKM 166
>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 = 122 bits (308), Expect = 2e-32
Identities = 52/113 (46%), Positives = 79/113 (69%)
Query: 7 LFKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQ 66
+FK++++GN+ VGKT + R+ F +T+G+DF +KTV N++RIKLQIWDTAGQ
Sbjct: 1 MFKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVYRNDKRIKLQIWDTAGQ 60
Query: 67 ERFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRVLVG 119
ER+R+IT +YYR A IL+YDI+ + +F+ + DW +I+ Y+ +LVG
Sbjct: 61 ERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSWDNAQVILVG 113
Score = 33.0 bits (75), Expect = 0.29
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 202 NKIDRED-REIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIAAELMEK 252
NK D ED R + E G A + + E SAK + NV+++F ++ + +K
Sbjct: 114 NKCDMEDERVVSAERGRQLADQLGFEFFEASAKENINVKQVFERLVDIICDK 165
>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 = 120 bits (303), Expect = 2e-31
Identities = 44/105 (41%), Positives = 67/105 (63%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE 67
KV+++G++GVGKT L+ ++ F ATIG DF+ K V +++ + LQIWDTAGQE
Sbjct: 1 LKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGADFLTKEVTVDDRLVTLQIWDTAGQE 60
Query: 68 RFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFK 112
RF+S+ ++YR A +LVYD++ +F+ L W E AS +
Sbjct: 61 RFQSLGVAFYRGADCCVLVYDVTNPKSFESLDSWRDEFLIQASPR 105
Score = 45.7 bits (109), Expect = 2e-05
Identities = 21/56 (37%), Positives = 35/56 (62%), Gaps = 2/56 (3%)
Query: 202 NKIDRED-REIPTEVGEDFAK-RHDMYYLETSAKASDNVEKLFMQIAAELMEKLAE 255
NKID E+ R++ T+ + + K + ++ Y ETSAK + NV++ F IA +E+ E
Sbjct: 117 NKIDLEEKRQVSTKKAQQWCKSKGNIPYFETSAKEAINVDQAFETIARLALEQEKE 172
>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 = 118 bits (298), Expect = 2e-30
Identities = 50/169 (29%), Positives = 88/169 (52%), Gaps = 9/169 (5%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERI-KLQIWDTAGQ 66
FKV+++G+ GVGKT +++R+ GVF ATIGVDF +K +E + + +LQ+WD AGQ
Sbjct: 1 FKVLVIGDLGVGKTSIIKRYVHGVFSQHYKATIGVDFALKVIEWDPNTVVRLQLWDIAGQ 60
Query: 67 ERFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASF----KVLRVLVGGTS 122
ERF +T+ YY+ A I+V+D++ TF+ + W +++ + + +L+
Sbjct: 61 ERFGGMTRVYYKGAVGAIIVFDVTRPSTFEAVLKWKADLDSKVTLPNGEPIPALLLANKC 120
Query: 123 GLKIVNEMASA--AGLLCTVDPALATALASDKTDLDEDE--HVLACLLM 167
LK C + + S K +++ +E L ++
Sbjct: 121 DLKKERLAKDPEQMDQFCKENGFIGWFETSAKENINIEEAMRFLVKNIL 169
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 118 bits (298), Expect = 2e-30
Identities = 54/184 (29%), Positives = 81/184 (44%), Gaps = 7/184 (3%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE 67
FK+V++G+ GVGKT L+ R FP G TIG KT+E IKLQ+WDTAGQE
Sbjct: 6 FKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQE 65
Query: 68 RFRSITQSYYRSAHALILVYDISCQP-TFDCLTDWLREIEEYASFKVLRVLVGGTSGLKI 126
+RS+ YYR A+ +++VYD + + + + +WL E+ E A V +LVG KI
Sbjct: 66 EYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVGN----KI 121
Query: 127 VNEMASAAGLLCTVDPALATALASDKTDLDEDEHVLACLLMVFVAVCIPKLARNEACFYL 186
++ L +A ++ + F
Sbjct: 122 DLFDEQSSSEEILNQLNREVVLLVLAP--KAVLPEVANPALLETSAKSLTGPNVNELFKE 179
Query: 187 ASLE 190
+
Sbjct: 180 LLRK 183
>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 = 113 bits (285), Expect = 4e-29
Identities = 49/118 (41%), Positives = 68/118 (57%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE 67
FKVVL+G VGKT LV R+ + F +T F KTV I +RI L IWDTAGQE
Sbjct: 1 FKVVLLGEGRVGKTSLVLRYVENKFNEKHESTTQASFFQKTVNIGGKRIDLAIWDTAGQE 60
Query: 68 RFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRVLVGGTSGLK 125
R+ ++ YYR A ILVYDI+ +F + W++E+++ + V+VG L+
Sbjct: 61 RYHALGPIYYRDADGAILVYDITDADSFQKVKKWIKELKQMRGNNISLVIVGNKIDLE 118
Score = 53.4 bits (129), Expect = 3e-08
Identities = 21/59 (35%), Positives = 32/59 (54%), Gaps = 2/59 (3%)
Query: 194 NNIH-CMARNKIDRED-REIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIAAELM 250
NNI + NKID E R + E++AK + ETSAK +E+LF+ +A ++
Sbjct: 104 NNISLVIVGNKIDLERQRVVSKSEAEEYAKSVGAKHFETSAKTGKGIEELFLSLAKRMI 162
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 113 bits (285), Expect = 1e-28
Identities = 55/118 (46%), Positives = 82/118 (69%), Gaps = 3/118 (2%)
Query: 4 YKFLFKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDT 63
Y FK++L+G++GVGK+ L+ F TIGVDF IK + + +R+KL IWDT
Sbjct: 11 YDLSFKILLIGDSGVGKSSLLVSFISSSVE-DLAPTIGVDFKIKQLTVGGKRLKLTIWDT 69
Query: 64 AGQERFRSITQSYYRSAHALILVYDISCQPTFDCLTD-WLREIEEYASFK-VLRVLVG 119
AGQERFR++T SYYR+A +ILVYD++ + TF L+D W +E+E Y++ + +++LVG
Sbjct: 70 AGQERFRTLTSSYYRNAQGIILVYDVTRRETFTNLSDVWGKEVELYSTNQDCVKMLVG 127
Score = 48.1 bits (114), Expect = 4e-06
Identities = 27/67 (40%), Positives = 41/67 (61%), Gaps = 4/67 (5%)
Query: 189 LEGHSNNIHC---MARNKIDRE-DREIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQ 244
+E +S N C + NK+DRE +R++ E G AK H +LE SAK +NVE+ F +
Sbjct: 112 VELYSTNQDCVKMLVGNKVDRESERDVSREEGMALAKEHGCLFLECSAKTRENVEQCFEE 171
Query: 245 IAAELME 251
+A ++ME
Sbjct: 172 LALKIME 178
>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 = 111 bits (280), Expect = 2e-28
Identities = 42/101 (41%), Positives = 68/101 (67%), Gaps = 2/101 (1%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEIN--NERIKLQIWDTAGQ 66
KV++VGN VGK+ +++RF +G+F TIGVDF+ K + + +E ++L +WDTAGQ
Sbjct: 2 KVIVVGNGNVGKSSMIQRFVKGIFTKDYKKTIGVDFLEKQIFLRQSDEDVRLMLWDTAGQ 61
Query: 67 ERFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEE 107
E F +IT++YYR A A ILV+ + + +F+ + W ++E
Sbjct: 62 EEFDAITKAYYRGAQACILVFSTTDRESFEAIESWKEKVEA 102
>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 = 103 bits (257), Expect = 2e-25
Identities = 50/112 (44%), Positives = 71/112 (63%), Gaps = 1/112 (0%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQER 68
KV++VG+ VGKTCL+ RF + VF ATIGVDF ++ E+ LQ+WDTAGQER
Sbjct: 2 KVIVVGDLSVGKTCLINRFCKDVFDKNYKATIGVDFEMERFEVLGVPFSLQLWDTAGQER 61
Query: 69 FRSITQSYYRSAHALILVYDISCQPTFDCLTDWLRE-IEEYASFKVLRVLVG 119
F+ I +YYR A A+I+V+D++ + + WL + ++E VL LVG
Sbjct: 62 FKCIASTYYRGAQAIIIVFDLTDVASLEHTRQWLEDALKENDPSSVLLFLVG 113
>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 = 102 bits (256), Expect = 4e-25
Identities = 42/116 (36%), Positives = 73/116 (62%), Gaps = 10/116 (8%)
Query: 4 YKFLFKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINN---------- 53
Y +L K++ +G++GVGKT + R+T F P T+G+DF K V N+
Sbjct: 1 YDYLIKLLALGDSGVGKTTFLYRYTDNKFNPKFITTVGIDFREKRVVYNSQGPDGTSGKA 60
Query: 54 ERIKLQIWDTAGQERFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYA 109
R+ LQ+WDTAGQERFRS+T +++R A +L++D++ + +F + +W+ +++ +A
Sbjct: 61 FRVHLQLWDTAGQERFRSLTTAFFRDAMGFLLMFDLTSEQSFLNVRNWMSQLQAHA 116
Score = 33.2 bits (76), Expect = 0.25
Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 202 NKIDRED-REIPTEVGEDFAKRHDMYYLETSAKASDNVEK 240
NK D D RE+ + A ++ + Y ETSA NVEK
Sbjct: 128 NKADLPDQREVSERQARELADKYGIPYFETSAATGQNVEK 167
>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 = 102 bits (256), Expect = 4e-25
Identities = 47/118 (39%), Positives = 76/118 (64%), Gaps = 1/118 (0%)
Query: 2 EDYKFLFKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIW 61
+ Y +L K +LVG++ VGK ++ G G +G+D+ T+ ++ R+KLQ+W
Sbjct: 1 KAYDYLLKFLLVGDSDVGKGEILASLQDGSTESPYGYNMGIDYKTTTILLDGRRVKLQLW 60
Query: 62 DTAGQERFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRVLVG 119
DT+GQ RF +I +SY R A +ILVYDI+ + +FD + W++EI+E+A V ++LVG
Sbjct: 61 DTSGQGRFCTIFRSYSRGAQGIILVYDITNRWSFDGIDRWIKEIDEHAP-GVPKILVG 117
Score = 28.7 bits (64), Expect = 6.9
Identities = 11/38 (28%), Positives = 23/38 (60%)
Query: 209 REIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIA 246
R++ TE + +A+R+ M + E S + N+ + F ++A
Sbjct: 126 RQVATEQAQAYAERNGMTFFEVSPLCNFNITESFTELA 163
>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 = 100 bits (252), Expect = 9e-25
Identities = 35/97 (36%), Positives = 52/97 (53%), Gaps = 1/97 (1%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQER 68
K+V++G GVGK+ L RF G F TI D K + ++ E L I DTAGQE
Sbjct: 1 KLVVLGAGGVGKSALTIRFVSGEFVEEYDPTIE-DSYRKQIVVDGETYTLDILDTAGQEE 59
Query: 69 FRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREI 105
F ++ Y R+ ILVY I+ + +F+ + + +I
Sbjct: 60 FSAMRDQYIRNGDGFILVYSITSRESFEEIKNIREQI 96
Score = 47.9 bits (115), Expect = 2e-06
Identities = 19/42 (45%), Positives = 28/42 (66%), Gaps = 1/42 (2%)
Query: 202 NKIDRED-REIPTEVGEDFAKRHDMYYLETSAKASDNVEKLF 242
NK D E+ R++ TE GE A+ +LETSAK + N+++LF
Sbjct: 112 NKCDLENERQVSTEEGEALAEEWGCPFLETSAKTNINIDELF 153
>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 = 99 bits (249), Expect = 3e-24
Identities = 43/106 (40%), Positives = 65/106 (61%)
Query: 7 LFKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQ 66
L KV+L+G+ GVGK+ L+ R+ F TIGV+F+ K +E++ + LQIWDTAGQ
Sbjct: 5 LLKVILLGDGGVGKSSLMNRYVTNKFDTQLFHTIGVEFLNKDLEVDGHFVTLQIWDTAGQ 64
Query: 67 ERFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFK 112
ERFRS+ +YR + +L + + +F L++W +E YA K
Sbjct: 65 ERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVK 110
Score = 33.7 bits (77), Expect = 0.16
Identities = 17/42 (40%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 202 NKIDREDREIPTEVGEDFAKRHDMY-YLETSAKASDNVEKLF 242
NKID +R++ TE + + + + Y Y ETSAK + NV F
Sbjct: 122 NKIDIPERQVSTEEAQAWCRDNGDYPYFETSAKDATNVAAAF 163
>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 = 96.3 bits (240), Expect = 5e-23
Identities = 31/100 (31%), Positives = 65/100 (65%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQER 68
KV+ +GN+GVGK+C+++R+ +G F TIG+D+ +K V + N+ +++ +D +G
Sbjct: 2 KVISMGNSGVGKSCIIKRYCEGRFVSKYLPTIGIDYGVKKVSVRNKEVRVNFFDLSGHPE 61
Query: 69 FRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEY 108
+ + +Y+ ++LVYD++ + +F+ L WL+E+++
Sbjct: 62 YLEVRNEFYKDTQGVLLVYDVTDRQSFEALDSWLKEMKQE 101
Score = 34.6 bits (80), Expect = 0.083
Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 1/42 (2%)
Query: 202 NKIDRED-REIPTEVGEDFAKRHDMYYLETSAKASDNVEKLF 242
NKID R + + G +A+ Y ETSA + V ++F
Sbjct: 118 NKIDLTKHRAVSEDEGRLWAESKGFKYFETSACTGEGVNEMF 159
>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 = 89.9 bits (223), Expect = 5e-21
Identities = 39/100 (39%), Positives = 61/100 (61%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQER 68
K++L+G++ VGK+ LV RF + P Q +T + + + I + WDTAGQER
Sbjct: 2 KIILLGDSAVGKSKLVERFLMDGYEPQQLSTYALTLYKHNAKFEGKTILVDFWDTAGQER 61
Query: 69 FRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEY 108
F+++ SYY AHA ILV+D++ + T+ L+ W E+ EY
Sbjct: 62 FQTMHASYYHKAHACILVFDVTRKITYKNLSKWYEELREY 101
Score = 28.3 bits (63), Expect = 8.2
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 3/59 (5%)
Query: 185 YLASLEGHSNNIHCM-ARNKIDREDREIPTEVGEDFAKRHDMYYLETSAKASDNVEKLF 242
+ L + I C+ NKID + T+ +FA++H++ SA NV KLF
Sbjct: 94 WYEELREYRPEIPCIVVANKIDLDPS--VTQKKFNFAEKHNLPLYYVSAADGTNVVKLF 150
>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 = 90.7 bits (225), Expect = 7e-21
Identities = 39/101 (38%), Positives = 60/101 (59%), Gaps = 3/101 (2%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVF--PPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQ 66
KVV++G VGKT LV R+ F P Q TIG F+ K + + + L IWDTAG
Sbjct: 2 KVVMLGKESVGKTSLVERYVHHRFLVGPYQN-TIGAAFVAKRMVVGERVVTLGIWDTAGS 60
Query: 67 ERFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEE 107
ER+ ++++ YYR A A I+ YD++ +F+ W++E++
Sbjct: 61 ERYEAMSRIYYRGAKAAIVCYDLTDSSSFERAKFWVKELQN 101
Score = 36.8 bits (85), Expect = 0.021
Identities = 17/68 (25%), Positives = 32/68 (47%)
Query: 205 DREDREIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIAAELMEKLAEKLTIMHDRG 264
DR R++ +DFA + ETS+K NV++LF ++A + + + ++
Sbjct: 121 DRSLRQVDFHDVQDFADEIKAQHFETSSKTGQNVDELFQKVAEDFVSRANNQMNTEKGVD 180
Query: 265 VGMLTRIY 272
+G Y
Sbjct: 181 LGQKKNSY 188
>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 = 88.4 bits (220), Expect = 3e-20
Identities = 50/238 (21%), Positives = 90/238 (37%), Gaps = 79/238 (33%)
Query: 10 VVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE-- 67
+V+VG+ VGKTCL+ +T FP T+ + VE++ + ++L +WDTAGQE
Sbjct: 1 LVVVGDGAVGKTCLLIVYTTNAFPEDYVPTV-FENYSADVEVDGKPVELGLWDTAGQEDY 59
Query: 68 -RFRSITQSYYRSAHALILVYDISCQPTFDCLTD-WLREIEEYASFKVLRVLVGGTSGLK 125
R R ++ Y ++ + + +F+ + + W E++ + V +LVG
Sbjct: 60 DRLRPLS---YPDTDVFLICFSVDSPASFENVKEKWYPEVKHFCP-NVPIILVG------ 109
Query: 126 IVNEMASAAGLLCTVDPALATALASDKTDLDEDEHVLACLLMVFVAVCIPKLARNEACFY 185
K DL D+ + +L++
Sbjct: 110 -------------------------TKLDLRNDKS------------TLEELSK------ 126
Query: 186 LASLEGHSNNIHCMARNKIDREDREIPTEVGEDFAKR-HDMYYLETSAKASDNVEKLF 242
++ + E G+ AKR + YLE SA + V ++F
Sbjct: 127 --------------------KKQEPVTYEQGQALAKRIGAVKYLECSALTQEGVREVF 164
>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 = 88.7 bits (220), Expect = 5e-20
Identities = 42/116 (36%), Positives = 64/116 (55%), Gaps = 4/116 (3%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEI-NNERIKLQIWDTAGQ 66
K+V++G+ GKT L+RRF Q F TIG+DF + + + + + LQ+WD GQ
Sbjct: 1 IKIVVLGDGASGKTSLIRRFAQEGFGKSYKQTIGLDFFSRRITLPGSLNVTLQVWDIGGQ 60
Query: 67 ERFRSITQSYYRSAHALILVYDISCQPTFDCLTDWL---REIEEYASFKVLRVLVG 119
+ + Y A A+ LVYDI+ +F+ L DWL +++ E + K VLVG
Sbjct: 61 QIGGKMLDKYIYGAQAVCLVYDITNSQSFENLEDWLSVVKKVNEESETKPKMVLVG 116
Score = 37.9 bits (88), Expect = 0.011
Identities = 21/50 (42%), Positives = 28/50 (56%), Gaps = 1/50 (2%)
Query: 202 NKIDRED-REIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIAAELM 250
NK D E R++ E FA+ +DM + SAK D V F +IAAEL+
Sbjct: 117 NKTDLEHNRQVTAEKHARFAQENDMESIFVSAKTGDRVFLCFQRIAAELL 166
>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 = 86.7 bits (215), Expect = 9e-20
Identities = 32/115 (27%), Positives = 56/115 (48%), Gaps = 3/115 (2%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQG-VFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQ 66
K+V+VG+ VGK+ L+ R + +++ +E + + K + DTAGQ
Sbjct: 2 IKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAGQ 61
Query: 67 ERFRSITQSYYRSAHALILVYDIS--CQPTFDCLTDWLREIEEYASFKVLRVLVG 119
E + +I + YYR+ + + V+DI + L +EI +A V +LVG
Sbjct: 62 EDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAESGVPIILVG 116
Score = 35.4 bits (82), Expect = 0.033
Identities = 14/41 (34%), Positives = 21/41 (51%)
Query: 202 NKIDREDREIPTEVGEDFAKRHDMYYLETSAKASDNVEKLF 242
NKID D ++ T V FAK + + SA+ N++ F
Sbjct: 117 NKIDLRDAKLKTHVAFLFAKLNGEPIIPLSAETGKNIDSAF 157
>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 = 85.7 bits (213), Expect = 2e-19
Identities = 54/240 (22%), Positives = 87/240 (36%), Gaps = 74/240 (30%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQER 68
K+V+VG+ VGKTCL+ +T FP T+ D V ++ +++ L +WDTAGQE
Sbjct: 2 KIVVVGDGAVGKTCLLISYTTNKFPTEYVPTV-FDNYSANVTVDGKQVNLGLWDTAGQEE 60
Query: 69 FRSITQSYYRSAHALILVYDISCQPTFD-CLTDWLREIEEYASFKVLRVLVGGTSGLKIV 127
+ + Y +L + + +F+ T W EI+ Y V +LV GT
Sbjct: 61 YDRLRPLSYPQTDVFLLCFSVDSPSSFENVKTKWYPEIKHYC-PNVPIILV-GT------ 112
Query: 128 NEMASAAGLLCTVDPALATALASDKTDLDEDEHVLACLLMVFVAVCIPKLARNEACFYLA 187
K DL +D + + KL + +
Sbjct: 113 ------------------------KIDLRDDGNT------------LKKLEKKQKP---- 132
Query: 188 SLEGHSNNIHCMARNKIDREDREIPTEVGEDFAKRHDMY-YLETSAKASDNVEKLFMQIA 246
I E GE AK Y+E SA + ++++F +
Sbjct: 133 -----------------------ITPEEGEKLAKEIGAVKYMECSALTQEGLKEVFDEAI 169
>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 = 80.7 bits (200), Expect = 1e-17
Identities = 40/109 (36%), Positives = 59/109 (54%), Gaps = 9/109 (8%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE 67
+K+V++G GVGK+ L +F QG F TI D K +EI+ E L I DTAGQE
Sbjct: 3 YKLVVLGGGGVGKSALTIQFVQGHFVDEYDPTIE-DSYRKQIEIDGEVCLLDILDTAGQE 61
Query: 68 RFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRV 116
F ++ Y R+ +LVY I+ + +F+ + RE ++LRV
Sbjct: 62 EFSAMRDQYMRTGEGFLLVYSITDRQSFEEIAK-FRE-------QILRV 102
Score = 49.9 bits (120), Expect = 5e-07
Identities = 19/50 (38%), Positives = 30/50 (60%), Gaps = 1/50 (2%)
Query: 202 NKIDRED-REIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIAAELM 250
NK D E+ R + TE G++ A++ +LETSAK NV++ F + E+
Sbjct: 115 NKCDLENERVVSTEEGKELARQWGCPFLETSAKERINVDEAFYDLVREIR 164
>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 = 80.3 bits (199), Expect = 2e-17
Identities = 40/109 (36%), Positives = 60/109 (55%), Gaps = 9/109 (8%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE 67
+K+V++G+ GVGK+ L +F QG F TI D K +EI+ E L I DTAGQE
Sbjct: 1 YKLVVLGSGGVGKSALTIQFIQGHFVDDYDPTIE-DSYRKQIEIDGEVCLLDILDTAGQE 59
Query: 68 RFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRV 116
F ++ Y R+ +LVY I+ + +F+ + RE ++LRV
Sbjct: 60 EFSAMRDQYMRTGEGFLLVYSITDRQSFEEIKK-FRE-------QILRV 100
Score = 50.2 bits (121), Expect = 3e-07
Identities = 20/52 (38%), Positives = 31/52 (59%), Gaps = 1/52 (1%)
Query: 202 NKIDRED-REIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIAAELMEK 252
NK D E R + TE G++ A++ +LETSAK NV++ F + E+ +K
Sbjct: 113 NKCDLESERVVSTEEGKELARQWGCPFLETSAKERVNVDEAFYDLVREIRKK 164
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 81.7 bits (202), Expect = 2e-17
Identities = 35/98 (35%), Positives = 54/98 (55%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE 67
FK++LVG+ GVGKT V+R G F T+GV+ N I +WDTAGQE
Sbjct: 10 FKLILVGDGGVGKTTFVKRHLTGEFEKKYIPTLGVEVHPLKFYTNCGPICFNVWDTAGQE 69
Query: 68 RFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREI 105
+F + YY I+++D++ + T+ + +W R+I
Sbjct: 70 KFGGLRDGYYIKGQCAIIMFDVTSRITYKNVPNWHRDI 107
Score = 31.2 bits (71), Expect = 1.4
Identities = 16/48 (33%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 202 NKIDREDREIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIAAEL 249
NK+D +DR++ F ++ ++ Y + SAK++ N EK F+ +A L
Sbjct: 121 NKVDVKDRQVKARQIT-FHRKKNLQYYDISAKSNYNFEKPFLWLARRL 167
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 80.6 bits (198), Expect = 2e-17
Identities = 39/99 (39%), Positives = 64/99 (64%)
Query: 38 ATIGVDFMIKTVEINNERIKLQIWDTAGQERFRSITQSYYRSAHALILVYDISCQPTFDC 97
+TIG+DF+ KT+ ++ ++LQ+WDTAGQERFRS+ SY R + A I+VYDI+ + +F+
Sbjct: 11 STIGIDFLSKTLYLDEGPVRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDITNRQSFEN 70
Query: 98 LTDWLREIEEYASFKVLRVLVGGTSGLKIVNEMASAAGL 136
T W+++I V+ LVG + L + ++ G+
Sbjct: 71 TTKWIQDILNERGKDVIIALVGNKTDLGDLRKVTYEEGM 109
Score = 35.9 bits (82), Expect = 0.031
Identities = 21/49 (42%), Positives = 31/49 (63%), Gaps = 1/49 (2%)
Query: 202 NKIDRED-REIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIAAEL 249
NK D D R++ E G A+ ++ + ETSAKA N++ LF +IAA+L
Sbjct: 93 NKTDLGDLRKVTYEEGMQKAQEYNTMFHETSAKAGHNIKVLFKKIAAKL 141
>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 = 78.8 bits (194), Expect = 5e-17
Identities = 43/130 (33%), Positives = 71/130 (54%), Gaps = 4/130 (3%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE 67
+K+V++G+ GVGK+ L +F QG+F TI D K +E++ ++ L+I DTAG E
Sbjct: 2 YKLVVLGSGGVGKSALTVQFVQGIFVDKYDPTIE-DSYRKQIEVDCQQCMLEILDTAGTE 60
Query: 68 RFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLRE--IEEYASFKVLRVLVGGTSGLK 125
+F ++ Y ++ LVY I+ Q +F+ L D LRE + + V +LVG L+
Sbjct: 61 QFTAMRDLYIKNGQGFALVYSITAQQSFNDLQD-LREQILRVKDTEDVPMILVGNKCDLE 119
Query: 126 IVNEMASAAG 135
++ G
Sbjct: 120 DERVVSKEEG 129
Score = 31.8 bits (72), Expect = 0.77
Identities = 18/50 (36%), Positives = 32/50 (64%), Gaps = 2/50 (4%)
Query: 202 NKIDRED-REIPTEVGEDFAKR-HDMYYLETSAKASDNVEKLFMQIAAEL 249
NK D ED R + E G++ A++ + +LETSAK+ NV+++F + ++
Sbjct: 114 NKCDLEDERVVSKEEGQNLARQWGNCPFLETSAKSKINVDEIFYDLVRQI 163
>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 = 77.3 bits (191), Expect = 1e-16
Identities = 35/98 (35%), Positives = 56/98 (57%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE 67
FK+VLVG+ G GKT V+R G F AT+GV+ N +I+ +WDTAGQE
Sbjct: 1 FKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLDFHTNRGKIRFNVWDTAGQE 60
Query: 68 RFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREI 105
+F + YY I+++D++ + T+ + +W R++
Sbjct: 61 KFGGLRDGYYIQGQCAIIMFDVTSRVTYKNVPNWHRDL 98
Score = 36.5 bits (85), Expect = 0.020
Identities = 17/48 (35%), Positives = 31/48 (64%), Gaps = 1/48 (2%)
Query: 202 NKIDREDREIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIAAEL 249
NK+D +DR++ + F ++ ++ Y E SAK++ N EK F+ +A +L
Sbjct: 112 NKVDIKDRKVKPKQIT-FHRKKNLQYYEISAKSNYNFEKPFLWLARKL 158
>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 = 77.2 bits (190), Expect = 2e-16
Identities = 41/160 (25%), Positives = 74/160 (46%), Gaps = 9/160 (5%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQ--GVFPPGQGATIGVDFMIKTVEI--NNERIKLQIWDTA 64
+ +VG+ VGK+ LV+ F F T G D ++KTV + ++ ++L I+D+A
Sbjct: 2 QCAVVGDPAVGKSALVQMFHSDGATFQKNYTMTTGCDLVVKTVPVPDTSDSVELFIFDSA 61
Query: 65 GQERFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVL-RVLVGGTSG 123
GQE F + ++ + + +VYD++ + +F+ + W+ + ++ VLVG
Sbjct: 62 GQELFSDMVENVWEQPAVVCVVYDVTNEVSFNNCSRWINRVRTHSHGLHTPGVLVGNKCD 121
Query: 124 LKIVNEMASAAGLLCTVDPALATALASDKTDLDEDEHVLA 163
L E+ +A A A L +T E A
Sbjct: 122 LTDRREVDAAQA----QALAQANTLKFYETSAKEGVGYEA 157
Score = 35.2 bits (81), Expect = 0.046
Identities = 23/86 (26%), Positives = 38/86 (44%), Gaps = 9/86 (10%)
Query: 171 AVCIPKLARNEACF-----YLASLEGHSNNIHC---MARNKIDREDR-EIPTEVGEDFAK 221
VC+ NE F ++ + HS+ +H + NK D DR E+ + A+
Sbjct: 79 VVCVVYDVTNEVSFNNCSRWINRVRTHSHGLHTPGVLVGNKCDLTDRREVDAAQAQALAQ 138
Query: 222 RHDMYYLETSAKASDNVEKLFMQIAA 247
+ + + ETSAK E F+ +A
Sbjct: 139 ANTLKFYETSAKEGVGYEAPFLSLAR 164
>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 = 77.4 bits (191), Expect = 3e-16
Identities = 37/116 (31%), Positives = 59/116 (50%), Gaps = 8/116 (6%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE 67
K+V+VG+ G GKTCL+ + QG FP T+ +++ N + I+L +WDTAGQE
Sbjct: 4 VKIVVVGDGGCGKTCLLMVYAQGSFPEEYVPTVFENYVTTLQVPNGKIIELALWDTAGQE 63
Query: 68 ---RFRSITQSYYRSAHALILVYDISCQPTFDCLTD-WLREIEEYASFKVLRVLVG 119
R R ++ Y +++ Y + + D + D W E+ + VLVG
Sbjct: 64 DYDRLRPLS---YPDVDVILICYSVDNPTSLDNVEDKWYPEVNHFCP-GTPIVLVG 115
Score = 28.5 bits (64), Expect = 9.3
Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 211 IPTEVGEDFAKRHDMY-YLETSAKASDNVEKLF 242
+ E GE AK Y+E SAK +NV+++F
Sbjct: 138 VTPEQGESVAKSIGAVAYIECSAKLMENVDEVF 170
>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 = 74.0 bits (182), Expect = 7e-16
Identities = 34/114 (29%), Positives = 59/114 (51%), Gaps = 4/114 (3%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQER 68
KVV++G+ G GK+ L+ + G FPP G + T+E++ + L IWD G+E
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREE 60
Query: 69 FRSITQSYYRSAHALILVYDISCQPTF---DCLTDWLREIEEYASFKVLRVLVG 119
+ + + A A++LVYD++ + + L WL + + K+ +LVG
Sbjct: 61 LKFEHIIFMKWADAILLVYDLTDRESLNEVSRLIAWLPNLRKLGG-KIPVILVG 113
>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 = 73.7 bits (181), Expect = 3e-15
Identities = 42/109 (38%), Positives = 65/109 (59%), Gaps = 9/109 (8%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE 67
+K+V++G+ GVGK+ L +F QG+F TI D K VE++ ++ L+I DTAG E
Sbjct: 2 YKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIE-DSYRKQVEVDGQQCMLEILDTAGTE 60
Query: 68 RFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRV 116
+F ++ Y ++ +LVY I+ Q TF+ L D LRE ++LRV
Sbjct: 61 QFTAMRDLYMKNGQGFVLVYSITAQSTFNDLQD-LRE-------QILRV 101
Score = 40.2 bits (94), Expect = 0.001
Identities = 19/42 (45%), Positives = 27/42 (64%), Gaps = 1/42 (2%)
Query: 202 NKIDRED-REIPTEVGEDFAKRHDMYYLETSAKASDNVEKLF 242
NK D ED R + E G++ A++ +LETSAKA NV ++F
Sbjct: 114 NKCDLEDERVVGKEQGQNLARQWGCAFLETSAKAKINVNEIF 155
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 74.0 bits (182), Expect = 7e-15
Identities = 34/100 (34%), Positives = 53/100 (53%)
Query: 6 FLFKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAG 65
FK+V+VG+ G GKT V+R G F TIGV+ N +I+ WDTAG
Sbjct: 12 PSFKLVIVGDGGTGKTTFVKRHLTGEFEKKYEPTIGVEVHPLDFFTNCGKIRFYCWDTAG 71
Query: 66 QERFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREI 105
QE+F + YY I+++D++ + T+ + W R++
Sbjct: 72 QEKFGGLRDGYYIHGQCAIIMFDVTARLTYKNVPTWHRDL 111
Score = 31.6 bits (72), Expect = 1.1
Identities = 17/49 (34%), Positives = 32/49 (65%), Gaps = 3/49 (6%)
Query: 202 NKIDREDREI-PTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIAAEL 249
NK+D ++R++ +V F ++ ++ Y E SAK++ N EK F+ +A +L
Sbjct: 125 NKVDVKNRQVKAKQV--TFHRKKNLQYYEISAKSNYNFEKPFLYLARKL 171
>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 = 73.4 bits (180), Expect = 1e-14
Identities = 40/111 (36%), Positives = 60/111 (54%), Gaps = 5/111 (4%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQER 68
KVVL+G+ VGKT L+ R+ + F +T+G F +K N + IWDTAG+E+
Sbjct: 2 KVVLLGDMNVGKTSLLHRYMERRFKD-TVSTVGGAFYLKQWGPYN----ISIWDTAGREQ 56
Query: 69 FRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRVLVG 119
F + Y R A A+IL YD+S + + L D + + A+ L +VG
Sbjct: 57 FHGLGSMYCRGAAAVILTYDVSNVQSLEELEDRFLGLTDTANEDCLFAVVG 107
>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 = 71.7 bits (176), Expect = 2e-14
Identities = 31/96 (32%), Positives = 56/96 (58%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQER 68
K+ L+G+A +GKT L+ ++ +G F T+GV+FM KT+ I I IWD GQ
Sbjct: 2 KIGLLGDAQIGKTSLMVKYVEGEFDEEYIQTLGVNFMEKTISIRGTEITFSIWDLGGQRE 61
Query: 69 FRSITQSYYRSAHALILVYDISCQPTFDCLTDWLRE 104
F ++ + A A++ ++D++ + T + + +W R+
Sbjct: 62 FINMLPLVCKDAVAILFMFDLTRKSTLNSIKEWYRQ 97
>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 = 71.0 bits (174), Expect = 3e-14
Identities = 51/154 (33%), Positives = 80/154 (51%), Gaps = 6/154 (3%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE 67
+KVV++G+ GVGK+ L +F G F TI DF K +E+++ L+I DTAG E
Sbjct: 2 YKVVVLGSGGVGKSALTVQFVSGTFIEKYDPTIE-DFYRKEIEVDSSPSVLEILDTAGTE 60
Query: 68 RFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASF-KVLRVLVGGTSGLKI 126
+F S+ Y ++ I+VY + Q TF + +I + KV +LVG L+
Sbjct: 61 QFASMRDLYIKNGQGFIVVYSLVNQQTFQDIKPMRDQIVRVKGYEKVPIILVGNKVDLES 120
Query: 127 VNEMASAAGLLCTVD---PALATALASDKTDLDE 157
E++SA G + P + T+ A KT ++E
Sbjct: 121 EREVSSAEGRALAEEWGCPFMETS-AKSKTMVNE 153
Score = 36.4 bits (84), Expect = 0.019
Identities = 17/49 (34%), Positives = 29/49 (59%), Gaps = 1/49 (2%)
Query: 202 NKIDRE-DREIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIAAEL 249
NK+D E +RE+ + G A+ ++ETSAK+ V +LF +I ++
Sbjct: 114 NKVDLESEREVSSAEGRALAEEWGCPFMETSAKSKTMVNELFAEIVRQM 162
>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 = 69.3 bits (170), Expect = 8e-14
Identities = 29/103 (28%), Positives = 52/103 (50%), Gaps = 1/103 (0%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEIN-NERIKLQIWDTAGQE 67
K++LVG GVGKT L ++ F + +T G++ + ++I+L +WD GQE
Sbjct: 3 KLMLVGQGGVGKTSLCKQLIGEKFDGDESSTHGINVQDWKIPAPERKKIRLNVWDFGGQE 62
Query: 68 RFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYAS 110
+ + Q + S +LV+D+ + WLR+I+ +
Sbjct: 63 IYHATHQFFLTSRSLYLLVFDLRTGDEVSRVPYWLRQIKAFGG 105
>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 = 70.0 bits (171), Expect = 1e-13
Identities = 31/93 (33%), Positives = 50/93 (53%)
Query: 13 VGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQERFRSI 72
VG+ G GKT V+R G F AT+GV+ N I+ +WDTAGQE+F +
Sbjct: 1 VGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIRFNVWDTAGQEKFGGL 60
Query: 73 TQSYYRSAHALILVYDISCQPTFDCLTDWLREI 105
YY I+++D++ + T+ + +W R++
Sbjct: 61 RDGYYIQGQCAIIMFDVTARVTYKNVPNWHRDL 93
Score = 33.4 bits (76), Expect = 0.23
Identities = 16/49 (32%), Positives = 32/49 (65%), Gaps = 1/49 (2%)
Query: 202 NKIDREDREIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIAAELM 250
NK+D +DR++ + F ++ ++ Y + SAK++ N EK F+ +A +L+
Sbjct: 107 NKVDVKDRKVKAK-SITFHRKKNLQYYDISAKSNYNFEKPFLWLARKLI 154
>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 = 67.9 bits (166), Expect = 3e-13
Identities = 45/146 (30%), Positives = 73/146 (50%), Gaps = 14/146 (9%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE 67
+K+V++G GVGK+ L +F Q VF TI D K VEI+ + L+I DTAG E
Sbjct: 2 YKIVVLGAGGVGKSALTVQFVQNVFIESYDPTIE-DSYRKQVEIDGRQCDLEILDTAGTE 60
Query: 68 RFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLRE--IEEYASFKVLRVLVGGTSGLK 125
+F ++ + Y +S +LVY ++ + + + L + LRE + S V VLVG + L+
Sbjct: 61 QFTAMRELYIKSGQGFLLVYSVTSEASLNELGE-LREQVLRIKDSDNVPMVLVGNKADLE 119
Query: 126 IVNEMASAAGLLCTVDPALATALASD 151
++ V +L+
Sbjct: 120 --DDRQ--------VSREDGVSLSQQ 135
Score = 29.0 bits (65), Expect = 5.4
Identities = 14/54 (25%), Positives = 33/54 (61%), Gaps = 2/54 (3%)
Query: 199 MARNKID-REDREIPTEVGEDFAKR-HDMYYLETSAKASDNVEKLFMQIAAELM 250
+ NK D +DR++ E G +++ ++ + ETSA+ NV+++F+ + +++
Sbjct: 111 LVGNKADLEDDRQVSREDGVSLSQQWGNVPFYETSARKRTNVDEVFIDLVRQII 164
>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 = 66.7 bits (163), Expect = 7e-13
Identities = 58/238 (24%), Positives = 95/238 (39%), Gaps = 81/238 (34%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE 67
+K+V+VG GVGK+ L +F Q F TI D K EI+ + +L I DTAGQE
Sbjct: 3 YKLVVVGGGGVGKSALTIQFIQSYFVTDYDPTIE-DSYTKQCEIDGQWARLDILDTAGQE 61
Query: 68 RFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRVLVGGTSGLKIV 127
F ++ + Y R+ +LV+ ++ + +F+ E++++ + ++LRV K
Sbjct: 62 EFSAMREQYMRTGEGFLLVFSVTDRGSFE-------EVDKFHT-QILRV--------KDR 105
Query: 128 NEMASAAGLLCTVDPALATALASDKTDLDEDEHVLACLLMVFVAVCIPKLARNEACFYLA 187
+E P + L +K DL+ V +R E
Sbjct: 106 DEF-----------PMI---LVGNKADLEHQRQV----------------SREEG----- 130
Query: 188 SLEGHSNNIHCMARNKIDREDREIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQI 245
+AR + + Y+ETSAK NV+K F +
Sbjct: 131 ---------QELAR--------------------QLKIPYIETSAKDRVNVDKAFHDL 159
>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 = 66.4 bits (163), Expect = 8e-13
Identities = 27/82 (32%), Positives = 44/82 (53%), Gaps = 5/82 (6%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQER 68
+++++G G GKT ++ + G TIG F ++TVE N +K +WD GQ++
Sbjct: 1 RILMLGLDGAGKTTILYKLKLGEVVTTI-PTIG--FNVETVEYKN--VKFTVWDVGGQDK 55
Query: 69 FRSITQSYYRSAHALILVYDIS 90
R + + YY + LI V D S
Sbjct: 56 IRPLWKHYYENTDGLIFVVDSS 77
>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 = 65.6 bits (160), Expect = 2e-12
Identities = 27/119 (22%), Positives = 49/119 (41%), Gaps = 13/119 (10%)
Query: 11 VLVGNAGVGKTCLVRRFTQGVFPPG---QGATIGVDFMIKTVEINNERIKLQIWDTAGQE 67
V+VG GVGK+ L+ G G T D E++ ++KL + DT G +
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDV--YVKELDKGKVKLVLVDTPGLD 58
Query: 68 RF-----RSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRVLVGGT 121
F + + R A ++LV D + + + + D I + + +++ G
Sbjct: 59 EFGGLGREELARLLLRGADLILLVVDSTDRESEE---DAKLLILRRLRKEGIPIILVGN 114
Score = 37.4 bits (87), Expect = 0.008
Identities = 21/86 (24%), Positives = 36/86 (41%), Gaps = 3/86 (3%)
Query: 163 ACLLMVFVAVCIPKLARNEACFYLASLEGHSNNIHCMARNKIDREDREIPTEV--GEDFA 220
A L+++ V + + L L I + NKID + E+ E+ A
Sbjct: 76 ADLILLVVDSTDRESEEDAKLLILRRLRKEGIPIILVG-NKIDLLEEREVEELLRLEELA 134
Query: 221 KRHDMYYLETSAKASDNVEKLFMQIA 246
K + E SAK + V++LF ++
Sbjct: 135 KILGVPVFEVSAKTGEGVDELFEKLI 160
>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 = 64.0 bits (156), Expect = 7e-12
Identities = 40/146 (27%), Positives = 71/146 (48%), Gaps = 9/146 (6%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQER 68
K VLVG+ VGKT L+ +T +P T +F + V ++ + ++LQ+ DTAGQ+
Sbjct: 2 KCVLVGDGAVGKTSLIVSYTTNGYPTEYVPTAFDNFSVV-VLVDGKPVRLQLCDTAGQDE 60
Query: 69 FRSITQSYYRSAHALILVYDISCQPTFDCLTD-WLREIEEYASFKVLRVLVGGTSGL--- 124
F + Y +L + + +F +++ W+ EI ++ K +LVG + L
Sbjct: 61 FDKLRPLCYPDTDVFLLCFSVVNPSSFQNISEKWIPEIRKHNP-KAPIILVGTQADLRTD 119
Query: 125 -KIVNEMASAAGLLCTVDPALATALA 149
++ ++A V + A ALA
Sbjct: 120 VNVLIQLARYGEK--PVSQSRAKALA 143
>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 = 64.2 bits (157), Expect = 8e-12
Identities = 35/117 (29%), Positives = 57/117 (48%), Gaps = 2/117 (1%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQER 68
K+ ++G+ VGK+ L +F +G F TI F K + + L+I DTAGQ+
Sbjct: 3 KIAVLGSRSVGKSSLTVQFVEGHFVESYYPTIENTF-SKIITYKGQEYHLEIVDTAGQDE 61
Query: 69 FRSITQSYYRSAHALILVYDISCQPTFD-CLTDWLREIEEYASFKVLRVLVGGTSGL 124
+ + Q Y H ILVY ++ + +F+ + + ++ V VLVG S L
Sbjct: 62 YSILPQKYSIGIHGYILVYSVTSRKSFEVVKVIYDKILDMLGKESVPIVLVGNKSDL 118
Score = 42.6 bits (101), Expect = 2e-04
Identities = 19/52 (36%), Positives = 31/52 (59%), Gaps = 2/52 (3%)
Query: 202 NKID-REDREIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIAAELMEK 252
NK D +R++ E G+ A+ +LE+SAK ++NVE+ F + E +EK
Sbjct: 114 NKSDLHMERQVSAEEGKKLAESWGAAFLESSAKENENVEEAFELLIEE-IEK 164
>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 = 64.0 bits (156), Expect = 9e-12
Identities = 40/130 (30%), Positives = 70/130 (53%), Gaps = 9/130 (6%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQER 68
K+VLVG++ GKT L++ F + FP T+ + + E++ +RI+L +WDT+G
Sbjct: 3 KIVLVGDSQCGKTALLQVFAKDSFPENYVPTV-FENYTASFEVDKQRIELSLWDTSGSPY 61
Query: 69 FRSITQSYYRSAHALILVYDISCQPTFD-CLTDWLREIEEYA-SFKVLRVLVGGTSGL-- 124
+ ++ Y + A+++ +DIS T D L W E+ E+ + VL LVG S L
Sbjct: 62 YDNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEVREFCPNTPVL--LVGCKSDLRT 119
Query: 125 --KIVNEMAS 132
+ E+++
Sbjct: 120 DLSTLTELSN 129
>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 = 63.6 bits (155), Expect = 9e-12
Identities = 39/118 (33%), Positives = 59/118 (50%), Gaps = 2/118 (1%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE 67
+K+V+VG GVGK+ L + Q F TI D K V I+ E L I DTAGQE
Sbjct: 2 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIE-DSYRKQVVIDGETCLLDILDTAGQE 60
Query: 68 RFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYA-SFKVLRVLVGGTSGL 124
+ ++ Y R+ + V+ I+ + +F+ + + +I+ S V VLVG L
Sbjct: 61 EYSAMRDQYMRTGEGFLCVFAINSRKSFEDIHTYREQIKRVKDSDDVPMVLVGNKCDL 118
Score = 44.3 bits (105), Expect = 4e-05
Identities = 19/48 (39%), Positives = 27/48 (56%)
Query: 202 NKIDREDREIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIAAEL 249
NK D R + T G+D AK + + Y+ETSAK VE+ F + E+
Sbjct: 114 NKCDLAARTVSTRQGQDLAKSYGIPYIETSAKTRQGVEEAFYTLVREI 161
>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 = 63.9 bits (155), Expect = 1e-11
Identities = 40/119 (33%), Positives = 68/119 (57%), Gaps = 5/119 (4%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQER 68
K+V+VG++ GKT L+ F + FP T+ ++ + EI+ +RI+L +WDT+G
Sbjct: 7 KIVVVGDSQCGKTALLHVFAKDCFPENYVPTVFENYT-ASFEIDTQRIELSLWDTSGSPY 65
Query: 69 FRSITQSYYRSAHALILVYDISCQPTFD-CLTDWLREIEEYA-SFKVLRVLVGGTSGLK 125
+ ++ Y + A+++ +DIS T D L W EI+E+ + K+L LVG S L+
Sbjct: 66 YDNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEIQEFCPNTKML--LVGCKSDLR 122
>gnl|CDD|206662 cd01870, RhoA_like, Ras homology family A (RhoA)-like includes
RhoA, RhoB and RhoC. The RhoA subfamily consists of
RhoA, RhoB, and RhoC. RhoA promotes the formation of
stress fibers and focal adhesions, regulating cell
shape, attachment, and motility. RhoA can bind to
multiple effector proteins, thereby triggering different
downstream responses. In many cell types, RhoA mediates
local assembly of the contractile ring, which is
necessary for cytokinesis. RhoA is vital for muscle
contraction; in vascular smooth muscle cells, RhoA plays
a key role in cell contraction, differentiation,
migration, and proliferation. RhoA activities appear to
be elaborately regulated in a time- and space-dependent
manner to control cytoskeletal changes. Most Rho
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. RhoA and RhoC are observed
only in geranylgeranylated forms; however, RhoB can be
present in palmitoylated, farnesylated, and
geranylgeranylated forms. RhoA and RhoC are highly
relevant for tumor progression and invasiveness;
however, RhoB has recently been suggested to be a tumor
suppressor. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 175
Score = 63.2 bits (154), Expect = 1e-11
Identities = 49/236 (20%), Positives = 92/236 (38%), Gaps = 73/236 (30%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQER 68
K+V+VG+ GKTCL+ F++ FP T+ ++ + +E++ ++++L +WDTAGQE
Sbjct: 3 KLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENY-VADIEVDGKQVELALWDTAGQED 61
Query: 69 FRSITQSYYRSAHALILVYDISCQPTFDCLTD-WLREIEEYASFKVLRVLVGGTSGLKIV 127
+ + Y +++ + I + + + + W E++ +
Sbjct: 62 YDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHF------------------- 102
Query: 128 NEMASAAGLLCTVDPALATALASDKTDLDEDEHVLACLLMVFVAVCIPKLARNEACFYLA 187
C P + L +K DL DEH I +LA+
Sbjct: 103 ----------C---PNVPIILVGNKKDLRNDEHT------------IRELAK-------- 129
Query: 188 SLEGHSNNIHCMARNKIDREDREIPTEVGEDFAKRHDMY-YLETSAKASDNVEKLF 242
+ + E G A++ + YLE SAK + V ++F
Sbjct: 130 ------------------MKQEPVKPEEGRAMAEKIGAFGYLECSAKTKEGVREVF 167
>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 = 62.2 bits (151), Expect = 3e-11
Identities = 45/155 (29%), Positives = 71/155 (45%), Gaps = 4/155 (2%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE 67
++VV+ G GVGK+ LV RF +G F TI D + + + LQI DT G
Sbjct: 2 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIE-DTYRQVISCSKSICTLQITDTTGSH 60
Query: 68 RFRSITQSYYRSAHALILVYDISCQPTFDCLT---DWLREIEEYASFKVLRVLVGGTSGL 124
+F ++ + HA ILVY I+ + + + L + + EI+ K+ +LVG
Sbjct: 61 QFPAMQRLSISKGHAFILVYSITSKQSLEELKPIYELICEIKGNNLEKIPIMLVGNKCDE 120
Query: 125 KIVNEMASAAGLLCTVDPALATALASDKTDLDEDE 159
E++S+ G A S KT+ + E
Sbjct: 121 SPSREVSSSEGAALARTWNCAFMETSAKTNHNVQE 155
Score = 32.5 bits (74), Expect = 0.41
Identities = 16/45 (35%), Positives = 27/45 (60%), Gaps = 1/45 (2%)
Query: 202 NKIDR-EDREIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQI 245
NK D RE+ + G A+ + ++ETSAK + NV++LF ++
Sbjct: 116 NKCDESPSREVSSSEGAALARTWNCAFMETSAKTNHNVQELFQEL 160
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 61.4 bits (149), Expect = 8e-11
Identities = 44/140 (31%), Positives = 65/140 (46%), Gaps = 22/140 (15%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE 67
+K+V+VG GVGK+ L +F Q F TI D K I+ E L I DTAGQE
Sbjct: 6 YKLVVVGGGGVGKSALTIQFIQNHFIDEYDPTIE-DSYRKQCVIDEETCLLDILDTAGQE 64
Query: 68 RFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFK--VLRV--------- 116
+ ++ Y R+ + VY I+ + +F+ E ASF+ +LRV
Sbjct: 65 EYSAMRDQYMRTGQGFLCVYSITSRSSFE----------EIASFREQILRVKDKDRVPMI 114
Query: 117 LVGGTSGLKIVNEMASAAGL 136
LVG L ++++ G
Sbjct: 115 LVGNKCDLDSERQVSTGEGQ 134
Score = 38.3 bits (89), Expect = 0.006
Identities = 20/55 (36%), Positives = 34/55 (61%), Gaps = 1/55 (1%)
Query: 202 NKIDRE-DREIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIAAELMEKLAE 255
NK D + +R++ T G++ AK + +LETSAK NV++ F ++ E+ + L E
Sbjct: 118 NKCDLDSERQVSTGEGQELAKSFGIPFLETSAKQRVNVDEAFYELVREIRKYLKE 172
>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 = 60.2 bits (146), Expect = 2e-10
Identities = 37/112 (33%), Positives = 58/112 (51%), Gaps = 3/112 (2%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQER 68
K V VG+ VGKTC++ +T FP T+ +F V ++ + L +WDTAGQE
Sbjct: 3 KCVTVGDGAVGKTCMLISYTSNTFPTDYVPTVFDNFS-ANVVVDGNTVNLGLWDTAGQED 61
Query: 69 FRSITQSYYRSAHALILVYDISCQPTFD-CLTDWLREIEEYASFKVLRVLVG 119
+ + YR A +L + + + +++ L W+ E+ YA V VLVG
Sbjct: 62 YNRLRPLSYRGADVFLLAFSLISKASYENVLKKWIPELRHYAP-GVPIVLVG 112
>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 = 59.6 bits (145), Expect = 2e-10
Identities = 36/112 (32%), Positives = 55/112 (49%), Gaps = 4/112 (3%)
Query: 10 VVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQERF 69
+ LVG GKT LV G F T+G F ++ V N IK +WD GQ RF
Sbjct: 2 ITLVGLQNSGKTTLVNVIASGQFSEDTIPTVG--FNMRKVTKGNVTIK--VWDLGGQPRF 57
Query: 70 RSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRVLVGGT 121
RS+ + Y R +A++ V D + + + + L ++ E S + + +LV G
Sbjct: 58 RSMWERYCRGVNAIVYVVDAADREKLEVAKNELHDLLEKPSLEGIPLLVLGN 109
>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 = 59.9 bits (145), Expect = 3e-10
Identities = 33/117 (28%), Positives = 61/117 (52%), Gaps = 4/117 (3%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQER 68
K+V++G+ GVGKT L + F TI D K V ++ + L++ DTAGQE
Sbjct: 1 KLVVLGDGGVGKTALTIQLCLNHFVETYDPTIE-DSYRKQVVVDGQPCMLEVLDTAGQEE 59
Query: 69 FRSITQSYYRSAHALILVYDISCQPTFDCLTDW---LREIEEYASFKVLRVLVGGTS 122
+ ++ + R ILVY I+ + TF+ + + ++ +++ ++ V ++VG
Sbjct: 60 YTALRDQWIREGEGFILVYSITSRSTFERVERFREQIQRVKDESAADVPIMIVGNKC 116
Score = 37.5 bits (87), Expect = 0.010
Identities = 18/42 (42%), Positives = 26/42 (61%), Gaps = 1/42 (2%)
Query: 202 NKIDR-EDREIPTEVGEDFAKRHDMYYLETSAKASDNVEKLF 242
NK D+ +RE+ TE G A+R ++E SAK + NVE+ F
Sbjct: 114 NKCDKVYEREVSTEEGAALARRLGCEFIEASAKTNVNVERAF 155
>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 = 58.2 bits (141), Expect = 6e-10
Identities = 35/100 (35%), Positives = 53/100 (53%), Gaps = 5/100 (5%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE 67
KV++VG+ GVGK+ L +F F T D K V ++ E ++L I DTAGQE
Sbjct: 1 HKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKA-DSYRKKVVLDGEEVQLNILDTAGQE 59
Query: 68 RFRSITQSYYRSAHALILVYDISCQPTFDCLTD----WLR 103
+ +I +Y+RS +LV+ I+ +F L + LR
Sbjct: 60 DYAAIRDNYFRSGEGFLLVFSITDMESFTALAEFREQILR 99
Score = 42.0 bits (99), Expect = 3e-04
Identities = 19/49 (38%), Positives = 30/49 (61%), Gaps = 1/49 (2%)
Query: 202 NKIDRED-REIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIAAEL 249
NK D ED R++ E + A++ + Y+ETSAK NV+K+F + E+
Sbjct: 113 NKCDLEDKRQVSVEEAANLAEQWGVNYVETSAKTRANVDKVFFDLVREI 161
>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 = 58.7 bits (142), Expect = 7e-10
Identities = 37/115 (32%), Positives = 59/115 (51%), Gaps = 9/115 (7%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQER 68
K+V+VG+ GKT L+ FT G FP T+ + + ++ + ++L +WDTAGQE
Sbjct: 3 KLVIVGDGACGKTSLLYVFTLGEFPEEYHPTV-FENYVTDCRVDGKPVQLALWDTAGQEE 61
Query: 69 FRSITQSYYRSAHALILVYDISCQPTFDCL----TDWLREIEEYASFKVLRVLVG 119
+ + Y AH +++ + I T D L T W+ E+ Y V +LVG
Sbjct: 62 YERLRPLSYSKAHVILIGFAID---TPDSLENVRTKWIEEVRRYCP-NVPVILVG 112
>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 = 59.3 bits (143), Expect = 8e-10
Identities = 35/112 (31%), Positives = 60/112 (53%), Gaps = 3/112 (2%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQER 68
K+V+VG+ GKT L+ F + +P T+ ++ + EI+ RI+L +WDT+G
Sbjct: 3 KIVVVGDTQCGKTALLHVFAKDNYPESYVPTVFENYT-ASFEIDKHRIELNMWDTSGSSY 61
Query: 69 FRSITQSYYRSAHALILVYDISCQPTFDCLT-DWLREIEEYASFKVLRVLVG 119
+ ++ Y + A+++ +DIS T D + W E +E+ L VLVG
Sbjct: 62 YDNVRPLAYPDSDAVLICFDISRPETLDSVLKKWQGETQEFCPNAKL-VLVG 112
>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 = 58.6 bits (142), Expect = 1e-09
Identities = 39/136 (28%), Positives = 65/136 (47%), Gaps = 5/136 (3%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE 67
++VVL+G++GVGK+ L FT GV+ G D +TV ++ E L ++D QE
Sbjct: 1 YRVVLLGDSGVGKSSLANIFTAGVYEDSAYEASGDDTYERTVSVDGEEATLVVYDHWEQE 60
Query: 68 RFRSITQSYYRSAHALILVYDISCQPTFDC---LTDWLREIEEYASFKVLRVLVGGTSGL 124
+ S + A ++VY ++ + +F+ L LR + + +LVG S L
Sbjct: 61 DGMWLEDSCMQVGDAYVIVYSVTDRSSFEKASELRIQLRRARQAEDIPI--ILVGNKSDL 118
Query: 125 KIVNEMASAAGLLCTV 140
E++ G C V
Sbjct: 119 VRSREVSVQEGRACAV 134
>gnl|CDD|206706 cd04134, Rho3, Ras homology family 3 (Rho3) of small guanosine
triphosphatases (GTPases). Rho3 is a member of the Rho
family found only in fungi. Rho3 is believed to regulate
cell polarity by interacting with the diaphanous/formin
family protein For3 to control both the actin
cytoskeleton and microtubules. Rho3 is also believed to
have a direct role in exocytosis that is independent of
its role in regulating actin polarity. The function in
exocytosis may be two-pronged: first, in the transport
of post-Golgi vesicles from the mother cell to the bud,
mediated by myosin (Myo2); second, in the docking and
fusion of vesicles to the plasma membrane, mediated by
an exocyst (Exo70) protein. Most Rho proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Rho proteins.
Length = 185
Score = 57.6 bits (139), Expect = 2e-09
Identities = 31/101 (30%), Positives = 54/101 (53%), Gaps = 2/101 (1%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQER 68
KVV++G+ GKT L+ FT+G FP T+ ++ I + ++ ++L +WDTAGQE
Sbjct: 2 KVVVLGDGACGKTSLLNVFTRGYFPQVYEPTVFENY-IHDIFVDGLAVELSLWDTAGQEE 60
Query: 69 FRSITQSYYRSAHALILVYDISCQPTF-DCLTDWLREIEEY 108
F + Y H ++L + + + + + WL EI +
Sbjct: 61 FDRLRSLSYADTHVIMLCFSVDNPDSLENVESKWLAEIRHH 101
>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 = 56.0 bits (135), Expect = 4e-09
Identities = 37/137 (27%), Positives = 61/137 (44%), Gaps = 16/137 (11%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE 67
+K+V++G GVGK+ + +F FP TI + + I+NE L I DTAGQ
Sbjct: 3 YKIVMLGAGGVGKSAVTMQFISHSFPDYHDPTIEDAYKTQAR-IDNEPALLDILDTAGQA 61
Query: 68 RFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYAS--FKVLR------VLVG 119
F ++ Y R I+ Y ++ + +F +E E+ +V VLVG
Sbjct: 62 EFTAMRDQYMRCGEGFIICYSVTDRHSF-------QEASEFKELITRVRLTEDIPLVLVG 114
Query: 120 GTSGLKIVNEMASAAGL 136
L+ ++ + G
Sbjct: 115 NKVDLEQQRQVTTEEGR 131
>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 = 55.8 bits (134), Expect = 6e-09
Identities = 26/88 (29%), Positives = 47/88 (53%), Gaps = 1/88 (1%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQER 68
K V+VG+ VGKTCL+ +T FP T+ ++ +T ++ + L +WDTAGQE
Sbjct: 5 KCVVVGDGAVGKTCLLICYTTNAFPKEYIPTVFDNYSAQTA-VDGRTVSLNLWDTAGQEE 63
Query: 69 FRSITQSYYRSAHALILVYDISCQPTFD 96
+ + Y + I+ + I+ +++
Sbjct: 64 YDRLRTLSYPQTNVFIICFSIASPSSYE 91
>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 = 55.2 bits (133), Expect = 7e-09
Identities = 33/115 (28%), Positives = 55/115 (47%), Gaps = 9/115 (7%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE- 67
K V+VG+ VGKTCL+ +T F PG+ D V ++ + + L +WDTAGQE
Sbjct: 3 KCVVVGDGAVGKTCLLISYTTNAF-PGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQED 61
Query: 68 --RFRSITQSYYRSAHALILVYDISCQPTFDCL-TDWLREIEEYASFKVLRVLVG 119
R R ++ Y ++ + + +F+ + W E+ + +LVG
Sbjct: 62 YDRLRPLS---YPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCP-NTPIILVG 112
>gnl|CDD|177661 PLN00023, PLN00023, GTP-binding protein; Provisional.
Length = 334
Score = 56.8 bits (137), Expect = 1e-08
Identities = 33/116 (28%), Positives = 62/116 (53%), Gaps = 13/116 (11%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQG--VFPPGQ--GATIGVDFMI--------KTVEINNER- 55
+V++VG++GVGK+ LV +G + P Q G T+GV + +++ ++ER
Sbjct: 23 RVLVVGDSGVGKSSLVHLIVKGSSIARPPQTIGCTVGVKHITYGSPGSSSNSIKGDSERD 82
Query: 56 IKLQIWDTAGQERFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASF 111
+++WD +G ER++ +Y + +I V+D+S + T L W E+ +F
Sbjct: 83 FFVELWDVSGHERYKDCRSLFYSQINGVIFVHDLSQRRTKTSLQKWASEVAATGTF 138
>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 = 54.9 bits (132), Expect = 2e-08
Identities = 34/102 (33%), Positives = 45/102 (44%), Gaps = 18/102 (17%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWD----- 62
+V ++G GVGKT +VR+F FP T V ++ L I D
Sbjct: 1 VRVAVLGAPGVGKTAIVRQFLAQEFPEEYIPTEHRRLYRPAVVLSGRVYDLHILDVPNMQ 60
Query: 63 ----TAGQE----RFRSITQSYYRSAHALILVYDISCQPTFD 96
TAGQE RFR + R++ A ILVYDI +F
Sbjct: 61 RYPGTAGQEWMDPRFRGL-----RNSRAFILVYDICSPDSFH 97
>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 = 54.3 bits (131), Expect = 2e-08
Identities = 27/94 (28%), Positives = 47/94 (50%), Gaps = 11/94 (11%)
Query: 10 VVLVGNAGVGKTCLVRR----FTQ--GVFPPGQ-GATIGVDFMIKTVEINNERIKLQIWD 62
V+++G GKT + + F++ P + T+G++ I T+E+ +L WD
Sbjct: 2 VLILGLDNAGKTTFLEQTKTKFSKNYKGLNPSKITPTVGLN--IGTIEVGK--ARLMFWD 57
Query: 63 TAGQERFRSITQSYYRSAHALILVYDISCQPTFD 96
GQE RS+ YY +H +I V D + + F+
Sbjct: 58 LGGQEELRSLWDKYYAESHGVIYVIDSTDRERFN 91
>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 = 53.8 bits (130), Expect = 2e-08
Identities = 35/119 (29%), Positives = 61/119 (51%), Gaps = 13/119 (10%)
Query: 9 KVVLVGNAGVGKTCLVRRF-TQ---GVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTA 64
K+ ++G +GVGK+ L RF T+ G + P + + V I+ E++ L+I DT
Sbjct: 1 KIAVLGASGVGKSALTVRFLTKRFIGEYEPNLESLYS-----RQVTIDGEQVSLEIQDTP 55
Query: 65 GQERF--RSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASF--KVLRVLVG 119
GQ++ + R A +LVY I+ + +FD ++ L+ I E ++ +LVG
Sbjct: 56 GQQQNEDPESLERSLRWADGFVLVYSITDRSSFDVVSQLLQLIREIKKRDGEIPVILVG 114
>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 = 55.4 bits (133), Expect = 2e-08
Identities = 35/119 (29%), Positives = 64/119 (53%), Gaps = 5/119 (4%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQER 68
K+VLVG+ GKT +++ + +P T+ ++ +E +R++L +WDT+G
Sbjct: 15 KLVLVGDVQCGKTAMLQVLAKDCYPETYVPTVFENYT-ACLETEEQRVELSLWDTSGSPY 73
Query: 69 FRSITQSYYRSAHALILVYDISCQPTFDC-LTDWLREIEEYA-SFKVLRVLVGGTSGLK 125
+ ++ Y + A++L +DIS FD L W EI +Y S ++L L+G + L+
Sbjct: 74 YDNVRPLCYSDSDAVLLCFDISRPEIFDSALKKWRAEILDYCPSTRIL--LIGCKTDLR 130
>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 = 54.5 bits (131), Expect = 2e-08
Identities = 32/112 (28%), Positives = 56/112 (50%), Gaps = 1/112 (0%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQER 68
++V +G AGVGKT L++RF F P T+ + K E+ ++ + I DT+G
Sbjct: 1 RLVFMGAAGVGKTALIQRFLYDTFEPKHRRTVE-ELHSKEYEVAGVKVTIDILDTSGSYS 59
Query: 69 FRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRVLVGG 120
F ++ + ++ A LVY + +F+ + EI E K + ++V G
Sbjct: 60 FPAMRKLSIQNGDAFALVYSVDDPESFEEVKRLREEILEVKEDKFVPIVVVG 111
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 53.4 bits (129), Expect = 3e-08
Identities = 25/87 (28%), Positives = 44/87 (50%), Gaps = 13/87 (14%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVF----PPGQGATIGVDFMIKTVEINNERIKLQIWDT 63
+++++G GKT ++ + G P TIG F ++TV N +K +WD
Sbjct: 15 MRILILGLDNAGKTTILYKLKLGEIVTTIP-----TIG--FNVETVTYKN--VKFTVWDV 65
Query: 64 AGQERFRSITQSYYRSAHALILVYDIS 90
GQE R + ++Y+ + A+I V D +
Sbjct: 66 GGQESLRPLWRNYFPNTDAVIFVVDSA 92
>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 = 53.3 bits (128), Expect = 4e-08
Identities = 34/112 (30%), Positives = 57/112 (50%), Gaps = 3/112 (2%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQER 68
K V+VG+ VGKTCL+ +T FP T+ ++ + TV I E L ++DTAGQE
Sbjct: 3 KCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAV-TVMIGGEPYTLGLFDTAGQED 61
Query: 69 FRSITQSYYRSAHALILVYDISCQPTFDCLTD-WLREIEEYASFKVLRVLVG 119
+ + Y ++ + + +F+ + + W+ EI + K +LVG
Sbjct: 62 YDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCP-KTPFLLVG 112
>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 = 52.7 bits (127), Expect = 6e-08
Identities = 41/144 (28%), Positives = 64/144 (44%), Gaps = 17/144 (11%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFPPG-----QGATIGVDFMIKTVEINNERIKLQIWDT 63
++VL+G+ GVGK+ L+ FP TI D ER+ I DT
Sbjct: 4 RIVLIGDEGVGKSSLIMSLVSEEFPENVPRVLPEITIPADV-------TPERVPTTIVDT 56
Query: 64 AGQERFRSITQSYYRSAHALILVYDISCQPTFDCL-TDWLREIEEYASFKVLRVLVGGTS 122
+ + + R+ + R A+ + LVY + T + + T WL I KV +LVG S
Sbjct: 57 SSRPQDRANLAAEIRKANVICLVYSVDRPSTLERIRTKWLPLIRRLGV-KVPIILVGNKS 115
Query: 123 GLKIVNEMASAAGLLCTVDPALAT 146
L+ + +S AGL + P +
Sbjct: 116 DLR---DGSSQAGLEEEMLPIMNE 136
>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 = 51.6 bits (123), Expect = 2e-07
Identities = 32/113 (28%), Positives = 57/113 (50%), Gaps = 3/113 (2%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE 67
K V+VG+ VGKTCL+ + FP T+ D +V + ++ L ++DTAGQE
Sbjct: 1 LKCVVVGDGAVGKTCLLMSYANDAFPEEYVPTV-FDHYAVSVTVGGKQYLLGLYDTAGQE 59
Query: 68 RFRSITQSYYRSAHALILVYDISCQPTF-DCLTDWLREIEEYASFKVLRVLVG 119
+ + Y ++ + + +F + +W+ E++EYA V +L+G
Sbjct: 60 DYDRLRPLSYPMTDVFLICFSVVNPASFQNVKEEWVPELKEYAP-NVPYLLIG 111
>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 = 48.4 bits (115), Expect = 2e-06
Identities = 26/84 (30%), Positives = 41/84 (48%), Gaps = 13/84 (15%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQG----VFPPGQGATIGVDFMIKTVEINNERIKLQIWDTA 64
++++VG GKT ++ + G P TIG F ++TV N I +WD
Sbjct: 15 RILMVGLDAAGKTTILYKLKLGESVTTIP-----TIG--FNVETVTYKN--ISFTVWDVG 65
Query: 65 GQERFRSITQSYYRSAHALILVYD 88
GQ++ R + + YY + LI V D
Sbjct: 66 GQDKIRPLWRHYYTNTQGLIFVVD 89
>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 = 46.9 bits (112), Expect = 5e-06
Identities = 31/87 (35%), Positives = 47/87 (54%), Gaps = 13/87 (14%)
Query: 8 FKVVLVGNAGVGKTCLVRRF----TQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDT 63
+++++G GKT ++++F + P T+G F IKT+E N KL IWD
Sbjct: 15 MRILMLGLDNAGKTTILKKFNGEDISTISP-----TLG--FNIKTLEYNG--YKLNIWDV 65
Query: 64 AGQERFRSITQSYYRSAHALILVYDIS 90
GQ+ RS ++Y+ S ALI V D S
Sbjct: 66 GGQKSLRSYWRNYFESTDALIWVVDSS 92
>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 = 47.6 bits (113), Expect = 6e-06
Identities = 26/112 (23%), Positives = 49/112 (43%), Gaps = 9/112 (8%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQG---VFPPGQ-GATIGVDFMIKTVEINNER-IKLQIWDT 63
KV+++G++GVGK+ LV + P G ++ V E+ +++WD
Sbjct: 2 KVLVLGDSGVGKSSLVHLLCKNQVLGNPSWTVGCSVDVRHHTYGEGTPEEKTFYVELWDV 61
Query: 64 AGQ----ERFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASF 111
G E +S +Y + +I V+D++ + + L W E +F
Sbjct: 62 GGSVGSAESVKSTRAVFYNQINGIIFVHDLTNKKSSQNLYRWSLEALNRDTF 113
>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 = 46.6 bits (111), Expect = 7e-06
Identities = 28/81 (34%), Positives = 43/81 (53%), Gaps = 5/81 (6%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE 67
+KV++VG GKT ++ +F G TIG + ++ + N I+ +WD GQE
Sbjct: 16 YKVIIVGLDNAGKTTILYQFLLGEVVHTS-PTIGSN--VEEIVYKN--IRFLMWDIGGQE 70
Query: 68 RFRSITQSYYRSAHALILVYD 88
RS +YY + A+ILV D
Sbjct: 71 SLRSSWNTYYTNTDAVILVID 91
>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 = 46.6 bits (110), Expect = 8e-06
Identities = 34/107 (31%), Positives = 55/107 (51%), Gaps = 8/107 (7%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQER 68
+VV +G G GKT ++ + Q F TIG F ++TVE N +K IWD G+ +
Sbjct: 1 RVVTLGLDGAGKTTILFKLKQDEFMQPI-PTIG--FNVETVEYKN--LKFTIWDVGGKHK 55
Query: 69 FRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLR 115
R + + YY + A++ V D S D +++ E+ + + K LR
Sbjct: 56 LRPLWKHYYLNTQAVVFVID-SSHR--DRVSEAHSELAKLLTEKELR 99
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 46.4 bits (110), Expect = 1e-05
Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 13/84 (15%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQG----VFPPGQGATIGVDFMIKTVEINNERIKLQIWDTA 64
++++VG GKT ++ + G P TIG F ++TVE N +K +WD
Sbjct: 19 RILMVGLDAAGKTTILYKLKLGEVVTTIP-----TIG--FNVETVEYKN--LKFTMWDVG 69
Query: 65 GQERFRSITQSYYRSAHALILVYD 88
GQ++ R + + YY++ + LI V D
Sbjct: 70 GQDKLRPLWRHYYQNTNGLIFVVD 93
>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 = 45.9 bits (109), Expect = 1e-05
Identities = 26/84 (30%), Positives = 43/84 (51%), Gaps = 13/84 (15%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQG----VFPPGQGATIGVDFMIKTVEINNERIKLQIWDTA 64
++++VG GKT ++ + G P TIG F ++TVE N I +WD
Sbjct: 2 RILMVGLDAAGKTTILYKLKLGEIVTTIP-----TIG--FNVETVEYKN--ISFTVWDVG 52
Query: 65 GQERFRSITQSYYRSAHALILVYD 88
GQ++ R + + Y+++ LI V D
Sbjct: 53 GQDKIRPLWRHYFQNTQGLIFVVD 76
>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 = 46.7 bits (111), Expect = 2e-05
Identities = 31/103 (30%), Positives = 51/103 (49%), Gaps = 1/103 (0%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQE 67
+++V++G + VGKT +V RF G F TI DF K I E +L I DT+G
Sbjct: 1 YRMVVLGASKVGKTAIVSRFLGGRFEEQYTPTIE-DFHRKLYSIRGEVYQLDILDTSGNH 59
Query: 68 RFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYAS 110
F ++ + + ILV+ + + +F+ + +I E S
Sbjct: 60 PFPAMRRLSILTGDVFILVFSLDNRESFEEVCRLREQILETKS 102
Score = 33.2 bits (76), Expect = 0.38
Identities = 27/106 (25%), Positives = 46/106 (43%), Gaps = 19/106 (17%)
Query: 202 NKIDR-EDREIP-TEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIAAELMEKLAEKLTI 259
NK DR RE+ EV + + Y E SAK + N++++F + + + KL +++
Sbjct: 121 NKADRDFPREVQRDEVEQLVGGDENCAYFEVSAKKNSNLDEMFRALFS--LAKLPNEMSP 178
Query: 260 MHDRGVGMLT--------RIYNIKKACGDA-------KSKPSFLSD 290
R + + R + K+ GDA +PS SD
Sbjct: 179 SLHRKISVQYGDALHKKSRGGSRKRKEGDACGAVAPFARRPSVHSD 224
>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 = 45.1 bits (107), Expect = 2e-05
Identities = 24/113 (21%), Positives = 52/113 (46%), Gaps = 15/113 (13%)
Query: 10 VVLVGNAGVGKTCLVRRF------TQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDT 63
++++G GKT ++ + +Q + P T+G F +++ + N + +D
Sbjct: 2 ILVLGLDNSGKTTIINQLKPSNAQSQNIVP-----TVG--FNVESFKKGN--LSFTAFDM 52
Query: 64 AGQERFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRV 116
+GQ ++R + + YY++ +I V D S + D L + + K R+
Sbjct: 53 SGQGKYRGLWEHYYKNIQGIIFVIDSSDRLRMVVAKDELELLLNHPDIKHRRI 105
>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 = 44.5 bits (106), Expect = 7e-05
Identities = 23/108 (21%), Positives = 43/108 (39%), Gaps = 18/108 (16%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFP---PGQGATIGVDFMIKTVEINNERIKLQIWDTAG 65
KV+L+G G GK+ + P GATI V+ ++ + L +WD G
Sbjct: 1 KVLLMGLRGSGKSSMRSIIFSNYSPRDTLRLGATIDVE---QSHVRFLGNLTLNLWDCPG 57
Query: 66 QERFRSITQSY-----YRSAHALILVYDISCQPTFDCLTDWLREIEEY 108
Q+ F + + + LI V+D+ + ++ ++
Sbjct: 58 QDDFMENYLTRQKEHIFSNVGVLIYVFDVESR-------EYEEDLATL 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 = 43.5 bits (103), Expect = 8e-05
Identities = 34/112 (30%), Positives = 50/112 (44%), Gaps = 11/112 (9%)
Query: 10 VVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQERF 69
++ VG GKT LV QG P T+G T ++ ++ ++ I+D G F
Sbjct: 2 LLTVGLDNAGKTTLVSAL-QGEIPKKVAPTVG---FTPT-KLRLDKYEVCIFDLGGGANF 56
Query: 70 RSITQSYYRSAHALILVYDIS----CQPTFDCLTDWLREIEEYASFKVLRVL 117
R I +YY AH L+ V D S Q + L + L+ S K + VL
Sbjct: 57 RGIWVNYYAEAHGLVFVVDSSDDDRVQEVKEILRELLQ--HPRVSGKPILVL 106
>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 = 43.2 bits (102), Expect = 1e-04
Identities = 31/113 (27%), Positives = 51/113 (45%), Gaps = 11/113 (9%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVFP---PGQGATIGVDFMIKTVEINNERIKLQIWDTAG 65
+++L+G GKT ++++ P QG F IK V + KL +WD G
Sbjct: 17 RILLLGLDNAGKTTILKQLASEDISHITPTQG------FNIKNV--QADGFKLNVWDIGG 68
Query: 66 QERFRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKVLRVLV 118
Q + R ++Y+ + LI V D + + F+ L E+ E + VLV
Sbjct: 69 QRKIRPYWRNYFENTDVLIYVIDSADRKRFEEAGQELVELLEEEKLAGVPVLV 121
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 43.0 bits (101), Expect = 1e-04
Identities = 26/84 (30%), Positives = 43/84 (51%), Gaps = 13/84 (15%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQG----VFPPGQGATIGVDFMIKTVEINNERIKLQIWDTA 64
++++VG GKT ++ + G P TIG F ++TVE N I +WD
Sbjct: 19 RILMVGLDAAGKTTILYKLKLGEIVTTIP-----TIG--FNVETVEYKN--ISFTVWDVG 69
Query: 65 GQERFRSITQSYYRSAHALILVYD 88
GQ++ R + + Y+++ LI V D
Sbjct: 70 GQDKIRPLWRHYFQNTQGLIFVVD 93
>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 = 42.8 bits (101), Expect = 1e-04
Identities = 17/49 (34%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 42 VDFMIKTVEINNERIKLQIWDTAGQERFRSITQSYYRSAHALILVYDIS 90
V F ++TV N +K +WD GQ++ R + + YY LI V D +
Sbjct: 41 VGFNVETVTYKN--VKFNVWDVGGQDKIRPLWRHYYTGTQGLIFVVDSA 87
>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 = 42.4 bits (100), Expect = 2e-04
Identities = 28/84 (33%), Positives = 42/84 (50%), Gaps = 13/84 (15%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQG----VFPPGQGATIGVDFMIKTVEINNERIKLQIWDTA 64
+++++G G GKT ++ R G P TIG F ++TV N +K Q+WD
Sbjct: 1 RILILGLDGAGKTTILYRLQVGEVVTTIP-----TIG--FNVETVTYKN--LKFQVWDLG 51
Query: 65 GQERFRSITQSYYRSAHALILVYD 88
GQ R + YY + A+I V D
Sbjct: 52 GQTSIRPYWRCYYSNTDAIIYVVD 75
>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 = 39.4 bits (92), Expect = 0.002
Identities = 23/88 (26%), Positives = 41/88 (46%), Gaps = 14/88 (15%)
Query: 8 FKVVLVGNAGVGKTCLVRR--FTQGV--FPPGQGATIGVDFMIKTVEINN---ERIKLQI 60
+V++G GKT ++ R F + V P T G F + ++++ + +
Sbjct: 4 LHIVMLGLDSAGKTTVLYRLKFNEFVNTVP-----TKG--FNTEKIKVSLGNAKGVTFHF 56
Query: 61 WDTAGQERFRSITQSYYRSAHALILVYD 88
WD GQE+ R + +SY R ++ V D
Sbjct: 57 WDVGGQEKLRPLWKSYTRCTDGIVFVVD 84
>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 = 38.9 bits (91), Expect = 0.003
Identities = 22/86 (25%), Positives = 43/86 (50%), Gaps = 12/86 (13%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQGVF----PPGQGATIGVDFMIKTVEINNERIKLQIWDTA 64
+V+L+G GK+ L+ + P T+G F ++ +++ + + L +WD
Sbjct: 1 QVLLLGLDSAGKSTLLYKLKHAELVTTIP-----TVG--FNVEMLQLE-KHLSLTVWDVG 52
Query: 65 GQERFRSITQSYYRSAHALILVYDIS 90
GQE+ R++ + Y + L+ V D S
Sbjct: 53 GQEKMRTVWKCYLENTDGLVYVVDSS 78
>gnl|CDD|216791 pfam01926, MMR_HSR1, 50S ribosome-binding GTPase. The full-length
GTPase protein is required for the complete activity of
the protein of interacting with the 50S ribosome and
binding of both adenine and guanine nucleotides, with a
preference for guanine nucleotide.
Length = 117
Score = 35.3 bits (82), Expect = 0.023
Identities = 28/124 (22%), Positives = 44/124 (35%), Gaps = 24/124 (19%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQ------GVFPPGQGATIGVDFMIKTVEINNERIKLQIWD 62
+V LVG VGK+ L+ T +P G T + + ++ + D
Sbjct: 1 RVALVGRPNVGKSTLINALTGAKVAIVSDYP---GTTRDP-----ILGVLGLGRQIILVD 52
Query: 63 TAGQER---------FRSITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASFKV 113
T G + R A ++LV D S T D L E+E+ +
Sbjct: 53 TPGLIEGASEGKGVEGFNRFLEAIREADLILLVVDASEGLTEDDEE-ILEELEKLPKKPI 111
Query: 114 LRVL 117
+ VL
Sbjct: 112 ILVL 115
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 36.3 bits (84), Expect = 0.027
Identities = 26/99 (26%), Positives = 43/99 (43%), Gaps = 15/99 (15%)
Query: 9 KVVLVGNAGVGKTCLVR----RFTQGVFPPG--------QGATIGVDFMIKTVEINNERI 56
K+V++G G GKT VR + + T+ +DF + +E
Sbjct: 12 KIVVIGPVGAGKTTFVRALSDKPLVITEADASSVSGKGKRPTTVAMDFGSIEL---DEDT 68
Query: 57 KLQIWDTAGQERFRSITQSYYRSAHALILVYDISCQPTF 95
+ ++ T GQERF+ + + R A I++ D S TF
Sbjct: 69 GVHLFGTPGQERFKFMWEILSRGAVGAIVLVDSSRPITF 107
>gnl|CDD|206744 cd11384, RagA_like, Rag GTPase, subfamily of Ras-related GTPases,
includes Ras-related GTP-binding proteins A and B. RagA
and RagB are closely related Rag GTPases (ras-related
GTP-binding protein A and B) that constitute a unique
subgroup of the Ras superfamily, and are functional
homologs of Saccharomyces cerevisiae Gtr1. These domains
function by forming heterodimers with RagC or RagD, and
similarly, Gtr1 dimerizes with Gtr2, through the
carboxy-terminal segments. They play an essential role
in regulating amino acid-induced target of rapamycin
complex 1 (TORC1) kinase signaling, exocytic cargo
sorting at endosomes, and epigenetic control of gene
expression. In response to amino acids, the Rag GTPases
guide the TORC1 complex to activate the platform
containing Rheb proto-oncogene by driving the
relocalization of mTORC1 from discrete locations in the
cytoplasm to a late endosomal and/or lysosomal
compartment that is Rheb-enriched and contains Rab-7.
Length = 286
Score = 36.0 bits (84), Expect = 0.048
Identities = 30/127 (23%), Positives = 51/127 (40%), Gaps = 52/127 (40%)
Query: 9 KVVLVGNAGVGKTCL------------VRRFTQGVFPPGQGATIGVD-----FMIKTVEI 51
KV+L+G +G GKT + RR GATI V+ F+
Sbjct: 1 KVLLMGKSGSGKTSMRSIIFANYLARDTRRL---------GATIDVEHSHVRFL------ 45
Query: 52 NNERIKLQIWDTAGQERFRSITQSY--------YRSAHALILVYDISCQPTFDCLTDWLR 103
N + L +WD GQ+ F ++Y +R+ LI V+D+ + + +
Sbjct: 46 GN--LVLNLWDCGGQDAF---MENYFTSQRDHIFRNVEVLIYVFDVESR-------ELEK 93
Query: 104 EIEEYAS 110
++ + S
Sbjct: 94 DLTYFRS 100
>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 = 34.2 bits (79), Expect = 0.14
Identities = 17/83 (20%), Positives = 31/83 (37%), Gaps = 11/83 (13%)
Query: 9 KVVLVGNAGVGKTCLVRRFTQG---VFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAG 65
K+V +G GKT L+ P T + E+ +K +D G
Sbjct: 21 KIVFLGLDNAGKTTLLHMLKDDRLAQHVPTLHPT--------SEELTIGNVKFTTFDLGG 72
Query: 66 QERFRSITQSYYRSAHALILVYD 88
E+ R + + Y+ ++ + D
Sbjct: 73 HEQARRVWKDYFPEVDGIVFLVD 95
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the
AAA superfamily.
Length = 154
Score = 32.6 bits (74), Expect = 0.29
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 10 VVLVGNAGVGKTCLVRRFTQGV 31
V+L G +G GKT L+R +G+
Sbjct: 27 VLLTGPSGTGKTSLLRELLEGL 48
>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 = 0.31
Identities = 17/79 (21%), Positives = 33/79 (41%), Gaps = 4/79 (5%)
Query: 10 VVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIWDTAGQERF 69
++++G G GKT L+ + T G + +V I + +++ + G +
Sbjct: 2 ILVLGLDGAGKTSLLHSLSSERSLESVVPTTGFN----SVAIPTQDAIMELLEIGGSQNL 57
Query: 70 RSITQSYYRSAHALILVYD 88
R + Y + LI V D
Sbjct: 58 RKYWKRYLSGSQGLIFVVD 76
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 33.3 bits (77), Expect = 0.40
Identities = 22/82 (26%), Positives = 33/82 (40%), Gaps = 23/82 (28%)
Query: 186 LASLEGHSNNIHCM-ARNKIDREDREIPTEVGEDFAKRHDMY------YLETSAKASDNV 238
L E +N I + NKID D E+ + +Y LE SAK + +
Sbjct: 104 LVLAE--ANGIKPIIVLNKIDLLDDL------EEARELLALYRAIGYDVLELSAKEGEGL 155
Query: 239 EKLFMQIAAELMEKLAEKLTIM 260
+ EL LA K+T++
Sbjct: 156 D--------ELKPLLAGKVTVL 169
>gnl|CDD|235444 PRK05399, PRK05399, DNA mismatch repair protein MutS; Provisional.
Length = 854
Score = 33.5 bits (78), Expect = 0.49
Identities = 24/105 (22%), Positives = 44/105 (41%), Gaps = 12/105 (11%)
Query: 478 SEIAK--PSELLASVRAYMNVLQTVENYVHIDMTRVFN-----NALLQQ--TQRMDSHGE 528
+E+A+ P+E+L + L + + F+ LL+Q +D G
Sbjct: 165 AELARLNPAEILVPEDFSEDELLLLRRGLRRRPPWEFDLDTAEKRLLEQFGVASLDGFGV 224
Query: 529 KTVAALYIQWYSEVLLRRVSETQVKSLNLLNFLRVYTVENYVHID 573
A+ + LL+ + ETQ +SL L + Y +Y+ +D
Sbjct: 225 DLPLAIRA---AGALLQYLKETQKRSLPHLRSPKRYEESDYLILD 266
>gnl|CDD|177799 PLN00210, PLN00210, 40S ribosomal protein S16; Provisional.
Length = 141
Score = 31.6 bits (72), Expect = 0.68
Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 7/59 (11%)
Query: 284 KPSFLSDKSLESCIKQIVKKFPNIDIK-------SVSGISQIRSDIVKSLSLYYYTFVD 335
+P L K+ E + +F +D++ S I IR I K+L YY +VD
Sbjct: 38 QPEILRFKAFEPILLLGRHRFAGVDMRIRVKGGGHTSQIYAIRQSIAKALVAYYQKYVD 96
>gnl|CDD|220925 pfam10987, DUF2806, Protein of unknown function (DUF2806). This
bacterial family of proteins has no known function.
Length = 223
Score = 31.9 bits (73), Expect = 0.98
Identities = 19/65 (29%), Positives = 26/65 (40%), Gaps = 15/65 (23%)
Query: 365 KIL-NEIIKPGAESYRK-------TREEAQI-------ASRRKKDKNNKKILNEIIKPGA 409
KIL EI PG S R T+ EAQ+ A + D + K +L + G
Sbjct: 65 KILAGEITNPGTFSLRTLQTLKSLTKREAQLFQKACSLAVKVGGDSSLKLLLGYYKQGGL 124
Query: 410 ESYRK 414
S +
Sbjct: 125 FSLFR 129
>gnl|CDD|204242 pfam09439, SRPRB, Signal recognition particle receptor beta
subunit. The beta subunit of the signal recognition
particle receptor (SRP) is a transmembrane GTPase which
anchors the alpha subunit to the endoplasmic reticulum
membrane.
Length = 181
Score = 31.2 bits (71), Expect = 1.0
Identities = 24/126 (19%), Positives = 44/126 (34%), Gaps = 23/126 (18%)
Query: 10 VVLVGNAGVGKTCLVRRFTQGVFPP---GQGATIGVDFMIKTVEINNERIKLQIWDTAGQ 66
V++ G GKT L T G Q + +M ++ + D G
Sbjct: 6 VIIAGLCDSGKTSLFTLLTTGTVKKTVTSQEPSAAYKYM------LHKGFSFTLIDFPGH 59
Query: 67 ERFRS---ITQSYYRSAHALILVYDISCQPTFDCLTDWLREIEEYASF--KVLRVLVGGT 121
+ R T S ++ V D + P +E+ + A F ++L +
Sbjct: 60 VKLRQKLLETIKDSSSLRGIVFVVDSTAFP---------KEVTDTAEFLYEILSITELLK 110
Query: 122 SGLKIV 127
+G+ I+
Sbjct: 111 NGIDIL 116
>gnl|CDD|236964 PRK11727, PRK11727, 23S rRNA mA1618 methyltransferase; Provisional.
Length = 321
Score = 32.1 bits (74), Expect = 1.0
Identities = 20/66 (30%), Positives = 27/66 (40%), Gaps = 17/66 (25%)
Query: 351 AQIASRRKKDKNNKKILNEIIKPGAESYRKT---------REEAQIASRRK-----KDKN 396
I R +KD K I II E + T EA+ S+RK +K+
Sbjct: 166 GAIRLRLQKDS--KAIFKGIIHKN-ERFDATLCNPPFHASAAEARAGSQRKLRNLGLNKD 222
Query: 397 NKKILN 402
KK+LN
Sbjct: 223 KKKVLN 228
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 30.7 bits (70), Expect = 1.1
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 10 VVLVGNAGVGKTCLVRRFTQ 29
VL G +G GKT L+RR +
Sbjct: 7 GVLTGESGSGKTTLLRRLAR 26
>gnl|CDD|201420 pfam00735, Septin, Septin. Members of this family include CDC3,
CDC10, CDC11 and CDC12/Septin. Members of this family
bind GTP. As regards the septins, these are
polypeptides of 30-65kDa with three characteristic
GTPase motifs (G-1, G-3 and G-4) that are similar to
those of the Ras family. The G-4 motif is strictly
conserved with a unique septin consensus of AKAD. Most
septins are thought to have at least one coiled-coil
region, which in some cases is necessary for
intermolecular interactions that allow septins to
polymerise to form rod-shaped complexes. In turn, these
are arranged into tandem arrays to form filaments. They
are multifunctional proteins, with roles in
cytokinesis, sporulation, germ cell development,
exocytosis and apoptosis.
Length = 280
Score = 31.5 bits (72), Expect = 1.4
Identities = 20/69 (28%), Positives = 34/69 (49%), Gaps = 9/69 (13%)
Query: 6 FLFKVVLVGNAGVGKTCLVRRF-------TQGVFPPGQGATIGVDFMIKTVEI--NNERI 56
F F +++VG +G+GKT L+ +G+ P + V+ TVEI + ++
Sbjct: 3 FDFTLMVVGESGLGKTTLINTLFLTDLIPERGIPGPSEKIKKTVEIKATTVEIEEDGVKL 62
Query: 57 KLQIWDTAG 65
L + DT G
Sbjct: 63 NLTVIDTPG 71
>gnl|CDD|206649 cd01850, CDC_Septin, CDC/Septin GTPase family. Septins are a
conserved family of GTP-binding proteins associated
with diverse processes in dividing and non-dividing
cells. They were first discovered in the budding yeast
S. cerevisiae as a set of genes (CDC3, CDC10, CDC11 and
CDC12) required for normal bud morphology. Septins are
also present in metazoan cells, where they are required
for cytokinesis in some systems, and implicated in a
variety of other processes involving organization of
the cell cortex and exocytosis. In humans, 12 septin
genes generate dozens of polypeptides, many of which
comprise heterooligomeric complexes. Since septin
mutants are commonly defective in cytokinesis and
formation of the neck formation of the neck
filaments/septin rings, septins have been considered to
be the primary constituents of the neck filaments.
Septins belong to the GTPase superfamily for their
conserved GTPase motifs and enzymatic activities.
Length = 275
Score = 31.4 bits (72), Expect = 1.6
Identities = 19/69 (27%), Positives = 34/69 (49%), Gaps = 9/69 (13%)
Query: 6 FLFKVVLVGNAGVGKTCLVRRF-------TQGVFPPGQGATIGVDFMIKTVEI--NNERI 56
F F +++VG +G+GK+ + ++ PG+ T V+ I E+ N ++
Sbjct: 3 FQFNIMVVGESGLGKSTFINTLFGTKLYPSKYPPAPGEHITKTVEIKISKAELEENGVKL 62
Query: 57 KLQIWDTAG 65
KL + DT G
Sbjct: 63 KLTVIDTPG 71
>gnl|CDD|185336 PRK15439, PRK15439, autoinducer 2 ABC transporter ATP-binding
protein LsrA; Provisional.
Length = 510
Score = 31.2 bits (71), Expect = 2.2
Identities = 19/51 (37%), Positives = 31/51 (60%), Gaps = 2/51 (3%)
Query: 212 PTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIAAELMEKLAEKLTIMHD 262
PT G D + R+D+Y L S A+ NV LF+ E +E++A+++ +MH
Sbjct: 430 PTR-GVDVSARNDIYQLIRSI-AAQNVAVLFISSDLEEIEQMADRVLVMHQ 478
>gnl|CDD|206647 cd00881, GTP_translation_factor, GTP translation factor family
primarily contains translation initiation, elongation
and release factors. The GTP translation factor family
consists primarily of translation initiation,
elongation, and release factors, which play specific
roles in protein translation. In addition, the family
includes Snu114p, a component of the U5 small nuclear
riboprotein particle which is a component of the
spliceosome and is involved in excision of introns,
TetM, a tetracycline resistance gene that protects the
ribosome from tetracycline binding, and the unusual
subfamily CysN/ATPS, which has an unrelated function
(ATP sulfurylase) acquired through lateral transfer of
the EF1-alpha gene and development of a new function.
Length = 183
Score = 30.3 bits (69), Expect = 2.3
Identities = 29/125 (23%), Positives = 42/125 (33%), Gaps = 23/125 (18%)
Query: 10 VVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFM------------IKT--VEINNER 55
V ++G+ GKT L + T F+ IKT VE +
Sbjct: 2 VGVIGHVDHGKTTLTGSLLYQTGAIDRRGTRKETFLDTLKEERERGITIKTGVVEFEWPK 61
Query: 56 IKLQIWDTAGQERFRSITQSYYRSAHALILVYDIS--CQPTFDCLTDWLREIEEYASFKV 113
++ DT G E F T A +LV D + +P RE A
Sbjct: 62 RRINFIDTPGHEDFSKETVRGLAQADGALLVVDANEGVEPQ-------TREHLNIALAGG 114
Query: 114 LRVLV 118
L ++V
Sbjct: 115 LPIIV 119
>gnl|CDD|218719 pfam05729, NACHT, NACHT domain. This NTPase domain is found in
apoptosis proteins as well as those involved in MHC
transcription activation. This family is closely
related to pfam00931.
Length = 165
Score = 30.0 bits (68), Expect = 2.5
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 10 VVLVGNAGVGKTCLVRRF 27
V+L G AG GKT L+++
Sbjct: 3 VILQGEAGSGKTTLLQKI 20
>gnl|CDD|132763 cd07349, NR_LBD_SHP, The ligand binding domain of DAX1 protein, a
nuclear receptor lacking DNA binding domain. The ligand
binding domain of the Small Heterodimer Partner (SHP):
SHP is a member of the nuclear receptor superfamily. SHP
has a ligand binding domain, but lacks the DNA binding
domain, typical to almost all of the nuclear receptors.
It functions as a transcriptional coregulator by
directly interacting with other nuclear receptors
through its AF-2 motif. The closest relative of SHP is
DAX1 and they can form heterodimer. SHP is an orphan
receptor, lacking an identified ligand.
Length = 222
Score = 30.2 bits (68), Expect = 3.0
Identities = 13/56 (23%), Positives = 21/56 (37%), Gaps = 10/56 (17%)
Query: 445 WDFTFAPREYLHQHLESRFSRALVGMVMFNPDTSEIAKPSELLASVRAYMNVLQTV 500
W +P+EY + L G ++FNPD + S + + L V
Sbjct: 125 WSLDLSPKEYAY----------LKGTILFNPDVPGLTASSHVGHLQQEAQWALCEV 170
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 30.9 bits (69), Expect = 3.5
Identities = 17/61 (27%), Positives = 26/61 (42%)
Query: 357 RKKDKNNKKILNEIIKPGAESYRKTREEAQIASRRKKDKNNKKILNEIIKPGAESYRKTR 416
+ + K+ E K AE +K E A KK + KK + ++ K AE +K
Sbjct: 1591 EARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEEKKKAE 1650
Query: 417 E 417
E
Sbjct: 1651 E 1651
>gnl|CDD|129465 TIGR00368, TIGR00368, Mg chelatase-related protein. The N-terminal
end matches very strongly a pfam Mg_chelatase domain
[Unknown function, General].
Length = 499
Score = 30.6 bits (69), Expect = 3.5
Identities = 23/74 (31%), Positives = 31/74 (41%), Gaps = 18/74 (24%)
Query: 10 VVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKL-QIWDTAGQER 68
++L G G GKT L R QG+ PP N E I+ +IW G+
Sbjct: 214 LLLFGPPGSGKTMLASRL-QGILPPLT---------------NEEAIETARIWSLVGKLI 257
Query: 69 -FRSITQSYYRSAH 81
+ I Q +RS H
Sbjct: 258 DRKQIKQRPFRSPH 271
>gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional.
Length = 201
Score = 29.9 bits (68), Expect = 3.8
Identities = 20/71 (28%), Positives = 28/71 (39%), Gaps = 18/71 (25%)
Query: 8 FKVVLVGNAGVGKTCLVRRFTQGVFPPGQ--GATI----------------GVDFMIKTV 49
++V VG + VGK+ LVR T G+ G T G FM
Sbjct: 10 PEIVFVGRSNVGKSTLVRELTGKKVRVGKRPGVTRKPNHYDWGDFILTDLPGFGFMSGVP 69
Query: 50 EINNERIKLQI 60
+ E+IK +I
Sbjct: 70 KEVQEKIKDEI 80
>gnl|CDD|219978 pfam08701, GN3L_Grn1, GNL3L/Grn1 putative GTPase. Grn1 (yeast) and
GNL3L (human) are putative GTPases which are required
for growth and play a role in processing of nucleolar
pre-rRNA. This family contains a potential nuclear
localisation signal.
Length = 80
Score = 28.0 bits (63), Expect = 4.3
Identities = 23/60 (38%), Positives = 30/60 (50%), Gaps = 15/60 (25%)
Query: 370 IIKPGAESYRKTREEA----QIASRRKKD---KNN----KKILNEIIKPGAESYRKTREE 418
I K AE +RK R+EA S++KKD N+ ++IL EI E RK EE
Sbjct: 6 IEKKVAEHHRKLRKEAKKNPTWKSKKKKDPGIPNSFPFKEEILEEI----EEKKRKQEEE 61
>gnl|CDD|146279 pfam03557, Bunya_G1, Bunyavirus glycoprotein G1. Bunyavirus has
three genomic segments: small (S), middle-sized (M), and
large (L). The S segment encodes the nucleocapsid and a
non-structural protein. The M segment codes for two
glycoproteins, G1 and G2, and another non-structural
protein (NSm). The L segment codes for an RNA
polymerase. This family contains the G1 glycoprotein
which is the viral attachment protein.
Length = 871
Score = 30.4 bits (69), Expect = 4.6
Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 11/43 (25%)
Query: 403 EIIKPGAESYRKTREELTTMDKLHMALTELCFAI---NYCTNI 442
+IIKP + YRK EE+ + ELC YCT +
Sbjct: 578 DIIKPELKVYRKATEEVVVL--------ELCITFPDKTYCTEL 612
>gnl|CDD|179251 PRK01216, PRK01216, DNA polymerase IV; Validated.
Length = 351
Score = 30.1 bits (68), Expect = 4.6
Identities = 34/157 (21%), Positives = 65/157 (41%), Gaps = 24/157 (15%)
Query: 224 DMYYLETSAKASDNVEK--LFMQIAAELMEKLAEKLTIMHDRGVGMLTRIYNIKKACGDA 281
D YL+ S K + + L ++I +++EK EK+T+ VG+
Sbjct: 105 DEAYLDISDKVKNYQDAYNLGLEIKNKILEK--EKITVT----VGI-----------SKN 147
Query: 282 KSKPSFLSDKSLESCIKQI----VKKF-PNIDIKSVSGISQIRSDIVKSLSLYYYTFVDL 336
K +D + + IK I VK+F +DI + GI I ++ +K L +
Sbjct: 148 KVFAKIAADMAKPNGIKVIDDEEVKRFINELDIADIPGIGDITAEKLKKLGVNKLVDTLR 207
Query: 337 LHFKDCVYLSGHFDAQIASRRKKDKNNKKILNEIIKP 373
+ F + + G A+ +++ N+ + + K
Sbjct: 208 IEFDELKGIIGEAKAKYLFSLARNEYNEPVRARVRKS 244
>gnl|CDD|219538 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This
Pfam entry includes some of the AAA proteins not
detected by the pfam00004 model.
Length = 135
Score = 28.8 bits (65), Expect = 4.6
Identities = 9/18 (50%), Positives = 11/18 (61%)
Query: 10 VVLVGNAGVGKTCLVRRF 27
V+LVG G GK+ L R
Sbjct: 2 VLLVGPPGTGKSELAERL 19
>gnl|CDD|234172 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family.
Members of this protein family are homologs of ClpB, an
ATPase associated with chaperone-related functions.
These ClpB homologs, designated ClpV1, are a key
component of the bacterial pathogenicity-associated type
VI secretion system [Protein fate, Protein and peptide
secretion and trafficking, Cellular processes,
Pathogenesis].
Length = 852
Score = 30.3 bits (69), Expect = 4.8
Identities = 13/28 (46%), Positives = 15/28 (53%), Gaps = 4/28 (14%)
Query: 11 VLVGNAGVGKTCLV----RRFTQGVFPP 34
+L G AGVGKT +V R G PP
Sbjct: 212 ILTGEAGVGKTAVVEGLALRIAAGDVPP 239
>gnl|CDD|206691 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta), together with SR-alpha, forms the
heterodimeric signal recognition particle (SRP). Signal
recognition particle receptor, beta subunit (SR-beta).
SR-beta and SR-alpha form the heterodimeric signal
recognition particle (SRP or SR) receptor that binds SRP
to regulate protein translocation across the ER
membrane. Nascent polypeptide chains are synthesized
with an N-terminal hydrophobic signal sequence that
binds SRP54, a component of the SRP. SRP directs
targeting of the ribosome-nascent chain complex (RNC) to
the ER membrane via interaction with the SR, which is
localized to the ER membrane. The RNC is then
transferred to the protein-conducting channel, or
translocon, which facilitates polypeptide translation
across the ER membrane or integration into the ER
membrane. SR-beta is found only in eukaryotes; it is
believed to control the release of the signal sequence
from SRP54 upon binding of the ribosome to the
translocon. High expression of SR-beta has been observed
in human colon cancer, suggesting it may play a role in
the development of this type of cancer.
Length = 202
Score = 29.2 bits (66), Expect = 5.9
Identities = 22/105 (20%), Positives = 37/105 (35%), Gaps = 16/105 (15%)
Query: 10 VVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIKLQIW--DTAGQE 67
V+L+G + GKT L + T G + +N ++ D G E
Sbjct: 3 VLLLGPSDSGKTALFTKLTTGKVRSTVTSIEPNV----ASFYSNSSKGKKLTLVDVPGHE 58
Query: 68 RFRSITQSYYR-SAHALILVYDISCQPTFDCLTDWLREIEEYASF 111
+ R Y + S A++ V D + + I + A F
Sbjct: 59 KLRDKLLEYLKASLKAIVFVVDSATFQ---------KNIRDVAEF 94
>gnl|CDD|233986 TIGR02729, Obg_CgtA, Obg family GTPase CgtA. This model describes
a univeral, mostly one-gene-per-genome GTP-binding
protein that associates with ribosomal subunits and
appears to play a role in ribosomal RNA maturation. This
GTPase, related to the nucleolar protein Obg, is
designated CgtA in bacteria. Mutations in this gene are
pleiotropic, but it appears that effects on cellular
functions such as chromosome partition may be secondary
to the effect on ribosome structure. Recent work done in
Vibrio cholerae shows an essential role in the stringent
response, in which RelA-dependent ability to synthesize
the alarmone ppGpp is required for deletion of this
GTPase to be lethal [Protein synthesis, Other].
Length = 329
Score = 29.3 bits (67), Expect = 6.8
Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 8/56 (14%)
Query: 202 NKIDREDREIPTEVGEDFAKRHDMYYLETSAKASDNVEKLFMQIAAELMEKLAEKL 257
NKID D E E+ ++ + SA + ++ EL+ LAE L
Sbjct: 281 NKIDLLDEEELEELLKELKEALGKPVFPISALTGEGLD--------ELLYALAELL 328
>gnl|CDD|206742 cd09915, Rag, Rag GTPase subfamily of Ras-related GTPases. Rag
GTPases (ras-related GTP-binding proteins) constitute a
unique subgroup of the Ras superfamily, playing an
essential role in regulating amino acid-induced target
of rapamycin complex 1 (TORC1) kinase signaling,
exocytic cargo sorting at endosomes, and epigenetic
control of gene expression. This subfamily consists of
RagA and RagB as well as RagC and RagD that are closely
related. Saccharomyces cerevisiae encodes single
orthologs of metazoan RagA/B and RagC/D, Gtr1 and Gtr2,
respectively. Dimer formation is important for their
cellular function; these domains form heterodimers, as
RagA or RagB dimerizes with RagC or RagD, and similarly,
Gtr1 dimerizes with Gtr2. In response to amino acids,
the Rag GTPases guide the TORC1 complex to activate the
platform containing Rheb proto-oncogene by driving the
relocalization of mTORC1 from discrete locations in the
cytoplasm to a late endosomal and/or lysosomal
compartment that is Rheb-enriched and contains Rab-7.
Length = 175
Score = 28.7 bits (64), Expect = 7.0
Identities = 15/57 (26%), Positives = 23/57 (40%), Gaps = 11/57 (19%)
Query: 56 IKLQIWDTAGQERFRSITQSY---YRSAHALILVYDISCQPTFDCLTDWLREIEEYA 109
L +WD GQ+ F T+ ++ ALI V D ++L+ I A
Sbjct: 48 XTLNLWDCPGQDVFFEPTKDKEHIFQXVGALIYV--------IDVQDEYLKAITILA 96
>gnl|CDD|227447 COG5117, NOC3, Protein involved in the nuclear export of
pre-ribosomes [Translation, ribosomal structure and
biogenesis / Intracellular trafficking and secretion].
Length = 657
Score = 29.6 bits (66), Expect = 7.0
Identities = 16/60 (26%), Positives = 28/60 (46%), Gaps = 9/60 (15%)
Query: 350 DAQIASRRKKD-----KNNKKILNEIIKPGAESYRKTREEAQIASRRKKDKNNKKILNEI 404
+ ++ R KKD K +KI E ++ +E R+ I +++KN +IL I
Sbjct: 353 NKPVSKREKKDIFHLSKKLRKIEKERLRIQSE----MRDAEDIEEAIEEEKNQSEILKII 408
>gnl|CDD|206679 cd01892, Miro2, Mitochondrial Rho family 2 (Miro2), C-terminal.
Miro2 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the putative
GTPase domain in the C terminus of Miro proteins. These
atypical Rho GTPases have roles in mitochondrial
homeostasis and apoptosis. Most Rho proteins contain a
lipid modification site at the C-terminus; however,
Miro is one of few Rho subfamilies that lack this
feature.
Length = 180
Score = 28.7 bits (65), Expect = 8.3
Identities = 20/85 (23%), Positives = 35/85 (41%), Gaps = 1/85 (1%)
Query: 7 LFKVVLVGNAGVGKTCLVRRFTQGVFPP-GQGATIGVDFMIKTVEINNERIKLQIWDTAG 65
+F ++G G GK+ L++ F F TI + + TVE+ + L + +
Sbjct: 4 VFLCFVLGAKGSGKSALLQAFLGRSFSQNAYSPTIKPRYAVNTVEVPGQEKYLILREVGE 63
Query: 66 QERFRSITQSYYRSAHALILVYDIS 90
E + + + LVYD S
Sbjct: 64 DEEAILLNDAELAACDVACLVYDSS 88
>gnl|CDD|184412 PRK13947, PRK13947, shikimate kinase; Provisional.
Length = 171
Score = 28.5 bits (64), Expect = 8.4
Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 15/70 (21%)
Query: 7 LFKVVLVGNAGVGKTCLVRRFTQGVFPPGQGATIGVDFMIKTVEINNERIK----LQIWD 62
+ +VL+G G GKT + +R T+ F+ EI E++ +I++
Sbjct: 1 MKNIVLIGFMGTGKTTVGKRV---------ATTLSFGFIDTDKEI--EKMTGMTVAEIFE 49
Query: 63 TAGQERFRSI 72
G+ RFRS
Sbjct: 50 KDGEVRFRSE 59
>gnl|CDD|188414 TIGR03899, TIGR03899, TIGR03899 family protein. Members of this
protein family are conserved hypothetical proteins with
a limited species distribution within the
Gammaproteobacteria. It is common in the genera Vibrio
and Shewanella, and in this resembles the C-terminal
domain and putative protein sorting motif TIGR03501.
This model, but design, does not extend to all
homologs,but rather represents a particular clade.
Length = 250
Score = 28.7 bits (65), Expect = 8.7
Identities = 21/65 (32%), Positives = 27/65 (41%), Gaps = 15/65 (23%)
Query: 365 KIL-NEIIKPGAESYRK-------TREEAQI-------ASRRKKDKNNKKILNEIIKPGA 409
KIL EI PG+ S R T+ EAQI A R D + K +L + G
Sbjct: 84 KILAREITNPGSFSLRTLKTLKQMTQREAQIFQKALSLACRFGNDTSLKLLLGYKKQGGL 143
Query: 410 ESYRK 414
S +
Sbjct: 144 FSLFR 148
>gnl|CDD|219124 pfam06658, DUF1168, Protein of unknown function (DUF1168). This
family consists of several hypothetical eukaryotic
proteins of unknown function.
Length = 142
Score = 28.1 bits (63), Expect = 8.9
Identities = 16/62 (25%), Positives = 24/62 (38%), Gaps = 15/62 (24%)
Query: 346 SGHFDAQIASRRKK-------DKNNKK-ILNEIIKPGAESYRKTREEAQIASRRKKDKNN 397
SG F A RR++ D+ KK +E +++ REE + K K
Sbjct: 35 SGEFHVYRALRRREYERLELMDEKWKKETEDEE-------FQQKREEKKRKDEEKTAKKR 87
Query: 398 KK 399
K
Sbjct: 88 AK 89
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
0.321 0.134 0.389
Gapped
Lambda K H
0.267 0.0735 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 36,800,322
Number of extensions: 3638786
Number of successful extensions: 4153
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4066
Number of HSP's successfully gapped: 235
Length of query: 730
Length of database: 10,937,602
Length adjustment: 104
Effective length of query: 626
Effective length of database: 6,324,786
Effective search space: 3959316036
Effective search space used: 3959316036
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 63 (28.0 bits)