RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3301
(608 letters)
>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 = 213 bits (545), Expect = 3e-66
Identities = 92/170 (54%), Positives = 111/170 (65%), Gaps = 23/170 (13%)
Query: 9 RNVRILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPTHIVDYSEVD 68
++VRI+L+GD VGK+SLI+SLVSEEFPE VP EITIP DVTPE VPT IVD S
Sbjct: 1 KDVRIVLIGDEGVGKSSLIMSLVSEEFPENVPRVLPEITIPADVTPERVPTTIVDTSSRP 60
Query: 69 QTVDELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGNKVDLV 128
Q L EI+KA+VICLVYSV ++++R+ + WLP +R V PI+LVGNK DL
Sbjct: 61 QDRANLAAEIRKANVICLVYSVDRPSTLERIRTKWLPLIRRLGVKV--PIILVGNKSDLR 118
Query: 129 DYST---------------------VESSAKTLKNISEMFYYAQKAVLHP 157
D S+ VE SAKTL N+SE+FYYAQKAVLHP
Sbjct: 119 DGSSQAGLEEEMLPIMNEFREIETCVECSAKTLINVSEVFYYAQKAVLHP 168
>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 = 145 bits (369), Expect = 9e-41
Identities = 59/183 (32%), Positives = 85/183 (46%), Gaps = 30/183 (16%)
Query: 407 RNVYVCHVIGNRSTGKTALCQSIL-RKHHDSSKTSITSPVECDPPYTINTTTVYGQEKYL 465
RNV++C V+G + +GK+AL Q+ L R ++ + P Y +NT V GQEKYL
Sbjct: 2 RNVFLCFVLGAKGSGKSALLQAFLGRSFSQNAYSPTI-----KPRYAVNTVEVPGQEKYL 56
Query: 466 VLKEILVRDEQLP----VLLPVDVDC------------------DKYFSTSKIPVMLVAG 503
+L+E+ +E + L DV C KYF +IP + VA
Sbjct: 57 ILREVGEDEEAILLNDAELAACDVACLVYDSSDPNSFSYCAEVYKKYFMLGEIPCLFVAA 116
Query: 504 KSDMPRARQDYLMQPDIFCETHKLSPAHSFSAANND--REVFVKLATMAAFPRFHPAWML 561
K+D+ +Q +QPD FC L P FS+ D E+F KLAT A +P +
Sbjct: 117 KADLDEQQQRAEVQPDEFCRKLGLPPPLHFSSRLGDSSNELFTKLATAAQYPHLSIPELE 176
Query: 562 FYP 564
Sbjct: 177 SGK 179
Score = 31.4 bits (72), Expect = 0.70
Identities = 28/127 (22%), Positives = 46/127 (36%), Gaps = 16/127 (12%)
Query: 9 RNV-RILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPTHIVDY--- 64
RNV +LG + GK++L+ + + F + A TI P V +
Sbjct: 2 RNVFLCFVLGAKGSGKSALLQAFLGRSFSQ----NAYSPTIKPRYAVNTVEVPGQEKYLI 57
Query: 65 -SEVDQTVDELTEEIQK---AHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVL 120
EV + + + + V CLVY D S + + + +P +
Sbjct: 58 LREVGEDEEAILLNDAELAACDVACLVYDSSDPNSFSYCAE----VYKKYFMLGEIPCLF 113
Query: 121 VGNKVDL 127
V K DL
Sbjct: 114 VAAKADL 120
>gnl|CDD|192013 pfam08356, EF_assoc_2, EF hand associated. This region
predominantly appears near EF-hands (pfam00036) in
GTP-binding proteins. It is found in all three
eukaryotic kingdoms.
Length = 89
Score = 123 bits (312), Expect = 7e-34
Identities = 42/89 (47%), Positives = 59/89 (66%), Gaps = 1/89 (1%)
Query: 206 DAPLSRDSLEDVKIVIRKNINDGVSANNCITLNGFLFLHNLFMQRGRSHTTWTVLRKFGY 265
+ PL + LE +K V+++ I DGV +TL GFLFL+ LF++RGR TTWT+LRKFGY
Sbjct: 1 NKPLQPEDLEGIKRVVQEEIPDGV-NEKGLTLKGFLFLNKLFIERGRHETTWTILRKFGY 59
Query: 266 NEDLQISKEFLHPPLNIPATCTAELSDKG 294
+ L + +FLHP ++P + ELS G
Sbjct: 60 TDSLSLRDDFLHPKFDVPPDQSVELSPAG 88
>gnl|CDD|192012 pfam08355, EF_assoc_1, EF hand associated. This region typically
appears on the C-terminus of EF hands in GTP-binding
proteins such as Arht/Rhot (may be involved in
mitochondrial homeostasis and apoptosis). The EF hand
associated region is found in yeast, vertebrates and
plants.
Length = 75
Score = 102 bits (257), Expect = 1e-26
Identities = 35/75 (46%), Positives = 50/75 (66%)
Query: 331 PWTDREMRAMVATNSKGWITMQGFLCYWILTTLFNVNKTLEYLAYFGYPITDRENQTSGV 390
PW + TN G++T+QG+L W LTTL + TLEYLAY G+P+ ++E+QTS +
Sbjct: 1 PWLETNFPDSTVTNEDGYLTLQGWLAQWSLTTLLDYKTTLEYLAYLGFPVGEQESQTSAI 60
Query: 391 LVTREKQVDLLKKQT 405
VTRE+++D K QT
Sbjct: 61 TVTRERKLDRKKGQT 75
>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 = 74.1 bits (183), Expect = 2e-15
Identities = 50/181 (27%), Positives = 73/181 (40%), Gaps = 57/181 (31%)
Query: 12 RILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPTHIVDYSEVDQTV 71
+++L+GD VGK+SL++ +FPE E +PT VD+ V
Sbjct: 1 KLVLVGDGGVGKSSLLIRFTQNKFPE-----------------EYIPTIGVDFYTKTIEV 43
Query: 72 DELTEEIQ-------------------KAHVICLVYSVVDDASIDRLSSHWLP-FLRNCL 111
D T ++Q A LVY + S + + WL LR+
Sbjct: 44 DGKTVKLQIWDTAGQERFRALRPLYYRGAQGFLLVYDITSRDSFENVK-KWLEEILRHA- 101
Query: 112 VDTCLPIVLVGNKVDL-----VDYST------------VESSAKTLKNISEMFYYAQKAV 154
D +PIVLVGNK DL V +E+SAKT +N+ E F + +
Sbjct: 102 -DENVPIVLVGNKCDLEDQRVVSTEEGEALAKELGLPFMETSAKTNENVEEAFEELAREI 160
Query: 155 L 155
L
Sbjct: 161 L 161
>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 = 71.8 bits (177), Expect = 8e-15
Identities = 44/164 (26%), Positives = 66/164 (40%), Gaps = 35/164 (21%)
Query: 12 RILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITI------PPDVTPEMVPTHIVDYS 65
++++LG VGK++L + VS EF E + TI V E I+D +
Sbjct: 1 KLVVLGAGGVGKSALTIRFVSGEFVE-----EYDPTIEDSYRKQIVVDGETYTLDILDTA 55
Query: 66 EVDQTVDELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLV---DTCLPIVLVG 122
++ + I+ LVYS+ S + + + L +PIVLVG
Sbjct: 56 GQEEFSAMRDQYIRNGDGFILVYSITSRESFEEIKN----IREQILRVKDKEDVPIVLVG 111
Query: 123 NKVDLVDYSTV-----------------ESSAKTLKNISEMFYY 149
NK DL + V E+SAKT NI E+F
Sbjct: 112 NKCDLENERQVSTEEGEALAEEWGCPFLETSAKTNINIDELFNT 155
>gnl|CDD|206640 cd00154, Rab, Ras-related in brain (Rab) family of small guanosine
triphosphatases (GTPases). Rab GTPases form the largest
family within the Ras superfamily. There are at least 60
Rab genes in the human genome, and a number of Rab
GTPases are conserved from yeast to humans. Rab GTPases
are small, monomeric proteins that function as molecular
switches to regulate vesicle trafficking pathways. The
different Rab GTPases are localized to the cytosolic
face of specific intracellular membranes, where they
regulate distinct steps in membrane traffic pathways. In
the GTP-bound form, Rab GTPases recruit specific sets of
effector proteins onto membranes. Through their
effectors, Rab GTPases regulate vesicle formation,
actin- and tubulin-dependent vesicle movement, and
membrane fusion. GTPase activating proteins (GAPs)
interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which mask C-terminal lipid binding and promote
cytosolic localization. While most unicellular organisms
possess 5-20 Rab members, several have been found to
possess 60 or more Rabs; for many of these Rab isoforms,
homologous proteins are not found in other organisms.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Since crystal
structures often lack C-terminal residues, the lipid
modification site is not available for annotation in
many of the CDs in the hierarchy, but is included where
possible.
Length = 159
Score = 71.7 bits (177), Expect = 8e-15
Identities = 50/176 (28%), Positives = 65/176 (36%), Gaps = 55/176 (31%)
Query: 11 VRILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPTHIVDYSEVDQT 70
+I+L+GD VGKTSL+L V +F E T VD+
Sbjct: 1 FKIVLIGDSGVGKTSLLLRFVDNKFSE-----------------NYKSTIGVDFKSKTIE 43
Query: 71 VDELTEEIQ-------------------KAHVICLVYSVVDDASIDRLSSHWLPFLRNCL 111
VD ++Q AH LVY V + S + L WL L+
Sbjct: 44 VDGKKVKLQIWDTAGQERFRSITSSYYRGAHGAILVYDVTNRESFENLDK-WLNELKEYA 102
Query: 112 VDTCLPIVLVGNKVDLVDYSTV-----------------ESSAKTLKNISEMFYYA 150
PI+LVGNK DL D V E+SAKT +N+ E F
Sbjct: 103 PPNI-PIILVGNKSDLEDERQVSTEEAQQFAKENGLLFFETSAKTGENVDEAFESL 157
Score = 29.7 bits (68), Expect = 2.1
Identities = 19/65 (29%), Positives = 28/65 (43%), Gaps = 9/65 (13%)
Query: 489 KYFSTSKIPVMLVAGKSDMPRARQ---DYLMQPDIFCETHKLSPAHSFSAANND--REVF 543
K ++ IP++LV KSD+ RQ + Q F + + L SA + E F
Sbjct: 99 KEYAPPNIPIILVGNKSDLEDERQVSTEEAQQ---FAKENGL-LFFETSAKTGENVDEAF 154
Query: 544 VKLAT 548
LA
Sbjct: 155 ESLAR 159
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 73.5 bits (180), Expect = 9e-15
Identities = 62/223 (27%), Positives = 93/223 (41%), Gaps = 17/223 (7%)
Query: 9 RNVRILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPTHIVDYSEVD 68
+ +I++LGD VGKT+L+ LV +EFPE P + + P + +
Sbjct: 4 KEFKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAG 63
Query: 69 Q-TVDELTEE-IQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGNKVD 126
Q L E + A+ I +VY S D L+ WL LR L +PI+LVGNK+D
Sbjct: 64 QEEYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRE-LAPDDVPILLVGNKID 122
Query: 127 LVDYSTVESSAKTLKNISEMFYY---AQKAVLHP---MAPIYISDKQELTPECIKALTRI 180
L + SS + L ++ A KAVL A + S K LT + L
Sbjct: 123 L--FDEQSSSEEILNQLNREVVLLVLAPKAVLPEVANPALLETSAKS-LTGPNVNEL--- 176
Query: 181 FKVCDLDNDNLLSDKELNAFQRRCF--DAPLSRDSLEDVKIVI 221
FK + L R+ + P+ + +L V+
Sbjct: 177 FKELLRKLLEEIEKLVLKNELRQLDRLNNPIEQAALASFNCVL 219
>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 = 67.4 bits (165), Expect = 9e-14
Identities = 37/118 (31%), Positives = 62/118 (52%), Gaps = 8/118 (6%)
Query: 12 RILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPT---HIVDYSEVD 68
+++++GD+ GK+SL+ LV EFP P + + T+ D T +I D+ +
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPP-EPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGRE 59
Query: 69 QTVDELTEEIQKAHVICLVYSVVDDASIDRLSSH--WLPFLRNCLVDTCLPIVLVGNK 124
+ E ++ A I LVY + D S++ +S WLP LR + +P++LVGNK
Sbjct: 60 ELKFEHIIFMKWADAILLVYDLTDRESLNEVSRLIAWLPNLRK--LGGKIPVILVGNK 115
>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 = 67.9 bits (166), Expect = 3e-13
Identities = 41/167 (24%), Positives = 65/167 (38%), Gaps = 34/167 (20%)
Query: 14 LLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPT-----HIVD----- 63
+++G VGK+SL+ +L+ E E S T PDV + + +VD
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGE--VSDVPGTTRDPDVYVKELDKGKVKLVLVDTPGLD 58
Query: 64 YSEVDQTVDELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGN 123
+ ++ A +I LV D S + L LR + PI+LVGN
Sbjct: 59 EFGGLGREELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLRKEGI----PIILVGN 114
Query: 124 KVDLVD------------------YSTVESSAKTLKNISEMFYYAQK 152
K+DL++ E SAKT + + E+F +
Sbjct: 115 KIDLLEEREVEELLRLEELAKILGVPVFEVSAKTGEGVDELFEKLIE 161
Score = 39.7 bits (93), Expect = 0.001
Identities = 29/160 (18%), Positives = 51/160 (31%), Gaps = 25/160 (15%)
Query: 414 VIGNRSTGKTALCQSILRKH-------HDSSKTSITSPVECDPP-YTINTTTVYGQEKYL 465
V+G GK++L ++L +++ E D + G +++
Sbjct: 2 VVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPGLDEFG 61
Query: 466 VLKEILVRDEQLP----VLLPVDVDCDKYF-----------STSKIPVMLVAGKSDMPRA 510
L + L +LL VD + IP++LV K D+
Sbjct: 62 GLGREELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLRKEGIPIILVGNKIDLLEE 121
Query: 511 RQDYLMQPDIFCETHKLSPAHSFSAANND--REVFVKLAT 548
R+ + P SA + E+F KL
Sbjct: 122 REVEELLRLEELAKILGVPVFEVSAKTGEGVDELFEKLIE 161
>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 = 61.1 bits (149), Expect = 7e-11
Identities = 47/195 (24%), Positives = 72/195 (36%), Gaps = 71/195 (36%)
Query: 13 ILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPTHIVDYSEVDQTVD 72
++++GD VGKT L++ + FPE + VPT +YS D VD
Sbjct: 1 LVVVGDGAVGKTCLLIVYTTNAFPE-----------------DYVPTVFENYS-ADVEVD 42
Query: 73 ELTEEIQ-------------------KAHVICLVYSVVDDASIDRLSSHWLPFLR-NCLV 112
E+ V + +SV AS + + W P ++ C
Sbjct: 43 GKPVELGLWDTAGQEDYDRLRPLSYPDTDVFLICFSVDSPASFENVKEKWYPEVKHFCP- 101
Query: 113 DTCLPIVLVGNKVDL-VDYSTV-----------------------------ESSAKTLKN 142
+PI+LVG K+DL D ST+ E SA T +
Sbjct: 102 --NVPIILVGTKLDLRNDKSTLEELSKKKQEPVTYEQGQALAKRIGAVKYLECSALTQEG 159
Query: 143 ISEMFYYAQKAVLHP 157
+ E+F A +A L+
Sbjct: 160 VREVFEEAIRAALNK 174
>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 = 60.3 bits (147), Expect = 1e-10
Identities = 42/155 (27%), Positives = 69/155 (44%), Gaps = 40/155 (25%)
Query: 11 VRILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPTHIVDYSEVDQT 70
++I+++GD VGKT L++S + +FP E VPT + D + T
Sbjct: 1 IKIVVVGDGAVGKTCLLISYTTNKFPT-----------------EYVPT-VFDNYSANVT 42
Query: 71 VD----ELT-------EEI--------QKAHVICLVYSVVDDASIDRLSSHWLPFLRNCL 111
VD L EE + V L +SV +S + + + W P +++
Sbjct: 43 VDGKQVNLGLWDTAGQEEYDRLRPLSYPQTDVFLLCFSVDSPSSFENVKTKWYPEIKHYC 102
Query: 112 VDTCLPIVLVGNKVDL-VDYSTVESSAKTLKNISE 145
+ PI+LVG K+DL D +T++ K K I+
Sbjct: 103 PNV--PIILVGTKIDLRDDGNTLKKLEKKQKPITP 135
>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 = 58.0 bits (141), Expect = 6e-10
Identities = 49/178 (27%), Positives = 68/178 (38%), Gaps = 59/178 (33%)
Query: 9 RNVRILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPTHIVD-YS-- 65
R ++++LG VGK++L + V F + E PT I D Y
Sbjct: 1 REYKLVVLGGGGVGKSALTIQFVQGHFVD-----------------EYDPT-IEDSYRKQ 42
Query: 66 -EVDQTVDEL-------TEE--------IQKAHVICLVYSVVDDASIDRLSSHWLPFLRN 109
E+D V L EE ++ LVYS+ D S + ++ LR
Sbjct: 43 IEIDGEVCLLDILDTAGQEEFSAMRDQYMRTGEGFLLVYSITDRQSFEEIAKFREQILR- 101
Query: 110 CLVDTC--LPIVLVGNKVDLVDYSTV-----------------ESSAKTLKNISEMFY 148
V +PIVLVGNK DL + V E+SAK N+ E FY
Sbjct: 102 --VKDRDDVPIVLVGNKCDLENERVVSTEEGKELARQWGCPFLETSAKERINVDEAFY 157
>gnl|CDD|133330 cd04130, Wrch_1, Wnt-1 responsive Cdc42 homolog (Wrch-1) is a Rho
family GTPase similar to Cdc42. Wrch-1 (Wnt-1
responsive Cdc42 homolog) is a Rho family GTPase that
shares significant sequence and functional similarity
with Cdc42. Wrch-1 was first identified in mouse mammary
epithelial cells, where its transcription is upregulated
in Wnt-1 transformation. Wrch-1 contains N- and
C-terminal extensions relative to cdc42, suggesting
potential differences in cellular localization and
function. The Wrch-1 N-terminal extension contains
putative SH3 domain-binding motifs and has been shown to
bind the SH3 domain-containing protein Grb2, which
increases the level of active Wrch-1 in cells. Unlike
Cdc42, which localizes to the cytosol and perinuclear
membranes, Wrch-1 localizes extensively with the plasma
membrane and endosomes. The membrane association,
localization, and biological activity of Wrch-1 indicate
an atypical model of regulation distinct from other Rho
family GTPases. Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 173
Score = 57.4 bits (139), Expect = 1e-09
Identities = 45/170 (26%), Positives = 70/170 (41%), Gaps = 37/170 (21%)
Query: 11 VRILLLGDRHVGKTSLILSLVSEEFP-ELVPSKAEEITIPPDVTPEMVPTHIVDYSEVDQ 69
++ +L+GD VGKTSLI+S + +P E VP+ + ++ V + P + Q
Sbjct: 1 LKCVLVGDGAVGKTSLIVSYTTNGYPTEYVPTAFDNFSV--VVLVDGKPVRLQLCDTAGQ 58
Query: 70 -TVDELTEEI-QKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGNKVDL 127
D+L V L +SVV+ +S +S W+P +R PI+LVG + DL
Sbjct: 59 DEFDKLRPLCYPDTDVFLLCFSVVNPSSFQNISEKWIPEIRKHNPKA--PIILVGTQADL 116
Query: 128 VD------------------------------YSTVESSAKTLKNISEMF 147
+E SA T KN+ E+F
Sbjct: 117 RTDVNVLIQLARYGEKPVSQSRAKALAEKIGACEYIECSALTQKNLKEVF 166
>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 = 56.8 bits (138), Expect = 1e-09
Identities = 43/183 (23%), Positives = 66/183 (36%), Gaps = 59/183 (32%)
Query: 11 VRILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPTHIVDYSEVDQT 70
+++LLG+ VGKTSL+L V +F + T S +T
Sbjct: 1 FKVVLLGEGRVGKTSLVLRYVENKF-----------------NEKHEST--TQASFFQKT 41
Query: 71 VDELTEEIQ---------------------KAHVICLVYSVVDDASIDRLSSHWLPFLRN 109
V+ + I A LVY + D S ++ W+ L+
Sbjct: 42 VNIGGKRIDLAIWDTAGQERYHALGPIYYRDADGAILVYDITDADSFQKVKK-WIKELKQ 100
Query: 110 CLVDTCLPIVLVGNKVDLVDYSTV-----------------ESSAKTLKNISEMFYYAQK 152
+ +V+VGNK+DL V E+SAKT K I E+F K
Sbjct: 101 MRGNNIS-LVIVGNKIDLERQRVVSKSEAEEYAKSVGAKHFETSAKTGKGIEELFLSLAK 159
Query: 153 AVL 155
++
Sbjct: 160 RMI 162
Score = 29.9 bits (68), Expect = 2.4
Identities = 25/104 (24%), Positives = 41/104 (39%), Gaps = 17/104 (16%)
Query: 460 GQEKYLVLKEILVRDEQLPVLLPVDV-DCD------------KYFSTSKIPVMLVAGKSD 506
GQE+Y L I RD +L D+ D D K + I +++V K D
Sbjct: 58 GQERYHALGPIYYRDAD-GAILVYDITDADSFQKVKKWIKELKQMRGNNISLVIVGNKID 116
Query: 507 MPRARQDYLMQPDIFCETHKLSPAHSFSAANND--REVFVKLAT 548
+ R R + + + ++ + SA E+F+ LA
Sbjct: 117 LERQRVVSKSEAEEYAKSVG-AKHFETSAKTGKGIEELFLSLAK 159
>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 = 56.8 bits (138), Expect = 2e-09
Identities = 44/177 (24%), Positives = 65/177 (36%), Gaps = 63/177 (35%)
Query: 12 RILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPTHIVD-YS---EV 67
++++LG VGK++L + + F + + PT I D Y E+
Sbjct: 2 KLVVLGSGGVGKSALTIQFIQGHFVD-----------------DYDPT-IEDSYRKQIEI 43
Query: 68 DQTVDEL-------TEE--------IQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLV 112
D V L EE ++ LVYS+ D S + + R ++
Sbjct: 44 DGEVCLLDILDTAGQEEFSAMRDQYMRTGEGFLLVYSITDRQSFEEIKK-----FREQIL 98
Query: 113 DT----CLPIVLVGNKVDLVDYSTV-----------------ESSAKTLKNISEMFY 148
+PIVLVGNK DL V E+SAK N+ E FY
Sbjct: 99 RVKDRDDVPIVLVGNKCDLESERVVSTEEGKELARQWGCPFLETSAKERVNVDEAFY 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 = 55.5 bits (134), Expect = 5e-09
Identities = 44/162 (27%), Positives = 72/162 (44%), Gaps = 31/162 (19%)
Query: 11 VRILLLGDRHVGKTSLILSLVSEEFPE-LVPSKAEEITIPPDVTPEMVPTHIVD------ 63
+++++G VGK++L L + +EF E P+KA+ + E V +I+D
Sbjct: 1 HKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEVQLNILDTAGQED 60
Query: 64 YSEVDQTVDELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGN 123
Y+ + E LV+S+ D S L+ LR D +P++LVGN
Sbjct: 61 YAAIRDNYFRSGEGF------LLVFSITDMESFTALAEFREQILRVKEDDN-VPLLLVGN 113
Query: 124 KVDLVDY-----------------STVESSAKTLKNISEMFY 148
K DL D + VE+SAKT N+ ++F+
Sbjct: 114 KCDLEDKRQVSVEEAANLAEQWGVNYVETSAKTRANVDKVFF 155
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 55.2 bits (134), Expect = 5e-09
Identities = 46/168 (27%), Positives = 67/168 (39%), Gaps = 45/168 (26%)
Query: 11 VRILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPTHIVDYSEVDQT 70
+I+L+GD VGK+SL+ +F E K+ TI D T ++ +
Sbjct: 1 FKIILIGDSGVGKSSLLSRFTDGKFSE--QYKS---TIGVDFK-----TKTIEVD--GKR 48
Query: 71 V-----DELTEE---------IQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCL 116
V D +E + A LVY + + S + L +WL LR +
Sbjct: 49 VKLQIWDTAGQERFRSITSSYYRGAVGALLVYDITNRESFENLE-NWLKELRE-YASPNV 106
Query: 117 PIVLVGNKVDLVDYSTV-----------------ESSAKTLKNISEMF 147
I+LVGNK DL + V E+SAKT N+ E F
Sbjct: 107 VIMLVGNKSDLEEQRQVSREEAEAFAEEHGLPFFETSAKTNTNVEEAF 154
Score = 33.3 bits (77), Expect = 0.15
Identities = 21/65 (32%), Positives = 31/65 (47%), Gaps = 4/65 (6%)
Query: 486 DCDKYFSTSKIPVMLVAGKSDMPRARQDYLMQPDIFCETHKLSPAHSFSAANND--REVF 543
+ +Y ++ + +MLV KSD+ RQ + + F E H L P SA N E F
Sbjct: 97 ELREY-ASPNVVIMLVGNKSDLEEQRQVSREEAEAFAEEHGL-PFFETSAKTNTNVEEAF 154
Query: 544 VKLAT 548
+LA
Sbjct: 155 EELAR 159
>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 = 54.5 bits (131), Expect = 1e-08
Identities = 41/159 (25%), Positives = 74/159 (46%), Gaps = 10/159 (6%)
Query: 12 RILLLGDRHVGKTSLILSLVSE--EFPE--LVPSKAEEI--TIPPDVTPEMVPTHIVDYS 65
+ ++GD VGK++L+ S+ F + + + + + T+P T + V I D +
Sbjct: 2 QCAVVGDPAVGKSALVQMFHSDGATFQKNYTMTTGCDLVVKTVPVPDTSDSVELFIFDSA 61
Query: 66 EVDQTVDELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGNKV 125
+ D + ++ V+C+VY V ++ S + S W+ +R P VLVGNK
Sbjct: 62 GQELFSDMVENVWEQPAVVCVVYDVTNEVSFNN-CSRWINRVRTHSHGLHTPGVLVGNKC 120
Query: 126 DLVDYSTV-ESSAKTLKNISEMFYY--AQKAVLHPMAPI 161
DL D V + A+ L + + +Y + K + AP
Sbjct: 121 DLTDRREVDAAQAQALAQANTLKFYETSAKEGVGYEAPF 159
Score = 29.8 bits (67), Expect = 2.9
Identities = 24/124 (19%), Positives = 46/124 (37%), Gaps = 32/124 (25%)
Query: 412 CHVIGNRSTGKTALCQSILRKHHDSSKTSITSPVECDPPYTINTTTVYGQEKYLVLKEIL 471
C V+G+ + GK+AL Q + + + + T CD LV+K +
Sbjct: 3 CAVVGDPAVGKSALVQ-MFHSDGATFQKNYTMTTGCD----------------LVVKTV- 44
Query: 472 VRDEQLPVLLPVDVDCDKYFSTSKIPVMLVAGKSDMPRARQDYLMQPDIFCETHKLSPAH 531
PV D + ++ + AG+ ++ QP + C + ++
Sbjct: 45 ----------PVPDTSD----SVELFIFDSAGQELFSDMVENVWEQPAVVCVVYDVTNEV 90
Query: 532 SFSA 535
SF+
Sbjct: 91 SFNN 94
>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 = 53.0 bits (128), Expect = 3e-08
Identities = 40/172 (23%), Positives = 65/172 (37%), Gaps = 55/172 (31%)
Query: 12 RILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPTHIVDYSEVDQTV 71
+++ LGD+ VGKTS+I + + F + T +D+ V
Sbjct: 2 KLVFLGDQSVGKTSIITRFMYDTF-----------------DNQYQATIGIDFLSKTMYV 44
Query: 72 DELTEEIQ-------------------KAHVICLVYSVVDDASIDRLSSHWLPFLRNCLV 112
D+ T +Q + V +VY + + S D W+ +R+
Sbjct: 45 DDKTVRLQLWDTAGQERFRSLIPSYIRDSSVAVVVYDITNRQSFDNTD-KWIDDVRDERG 103
Query: 113 DTCLPIVLVGNKVDLVDYSTV-----------------ESSAKTLKNISEMF 147
+ + IVLVGNK DL D V E+SAK N+ ++F
Sbjct: 104 NDVI-IVLVGNKTDLSDKRQVSTEEGEKKAKENNAMFIETSAKAGHNVKQLF 154
>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 = 53.0 bits (128), Expect = 4e-08
Identities = 48/169 (28%), Positives = 67/169 (39%), Gaps = 49/169 (28%)
Query: 12 RILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPTHIVDYSEVDQTV 71
+I +LG R VGK+SL + V F E + TI E + I+ Y + +
Sbjct: 3 KIAVLGSRSVGKSSLTVQFVEGHFVE-----SYYPTI------ENTFSKIITYKGQEYHL 51
Query: 72 --------DELTEEIQK----AHVICLVYSVVDDASIDRLSSHWLPFLRNCLVD----TC 115
DE + QK H LVYSV S + + + + ++D
Sbjct: 52 EIVDTAGQDEYSILPQKYSIGIHGYILVYSVTSRKSFEVV-----KVIYDKILDMLGKES 106
Query: 116 LPIVLVGNKVDLVDYSTV-----------------ESSAKTLKNISEMF 147
+PIVLVGNK DL V ESSAK +N+ E F
Sbjct: 107 VPIVLVGNKSDLHMERQVSAEEGKKLAESWGAAFLESSAKENENVEEAF 155
>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 = 50.5 bits (121), Expect = 2e-07
Identities = 43/174 (24%), Positives = 79/174 (45%), Gaps = 45/174 (25%)
Query: 11 VRILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPTHIVDYSEVD-- 68
++++++G+ +VGK+S+I V F +K + TI D + + S+ D
Sbjct: 1 IKVIVVGNGNVGKSSMIQRFVKGIF-----TKDYKKTIGVDF---LEKQIFLRQSDEDVR 52
Query: 69 ---------QTVDELTEEIQK-AHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTC--L 116
+ D +T+ + A LV+S D S + + S W + + C +
Sbjct: 53 LMLWDTAGQEEFDAITKAYYRGAQACILVFSTTDRESFEAIES-W----KEKVEAECGDI 107
Query: 117 PIVLVGNKVDLVDYSTV-----ESSAKTLK------------NISEMF-YYAQK 152
P+VLV K+DL+D + + E+ AK L+ N++E+F Y A+K
Sbjct: 108 PMVLVQTKIDLLDQAVITNEEAEALAKRLQLPLFRTSVKDDFNVTELFEYLAEK 161
>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 = 51.6 bits (124), Expect = 2e-07
Identities = 38/120 (31%), Positives = 58/120 (48%), Gaps = 5/120 (4%)
Query: 12 RILLLGDRHVGKTSLILSLVSEEFPELVPSKAE-EITIPPDVTPEMVPTHIVDYSEVDQT 70
R++LLGD VGK+SL + + E +A + T V+ + +V Y +Q
Sbjct: 2 RVVLLGDSGVGKSSLANIFTAGVY-EDSAYEASGDDTYERTVSVDGEEATLVVYDHWEQE 60
Query: 71 VDELTEE--IQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGNKVDLV 128
E+ +Q +VYSV D +S ++ +S LR +PI+LVGNK DLV
Sbjct: 61 DGMWLEDSCMQVGDAYVIVYSVTDRSSFEK-ASELRIQLRRARQAEDIPIILVGNKSDLV 119
>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 = 49.2 bits (117), Expect = 7e-07
Identities = 37/140 (26%), Positives = 72/140 (51%), Gaps = 15/140 (10%)
Query: 11 VRILLLGDRHVGKTSLILSLVSEEFPE-LVPSKAEEITIPPDVTPEMVPTHIVDYS---E 66
++ +++GD VGKT L++S ++ FPE VP+ + + V + + D + +
Sbjct: 1 LKCVVVGDGAVGKTCLLMSYANDAFPEEYVPTVFDHYAVSVTVGGKQYLLGLYDTAGQED 60
Query: 67 VDQTVDELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGNKVD 126
D+ + L+ + +IC +SVV+ AS + W+P L+ + +P +L+G ++D
Sbjct: 61 YDR-LRPLSYPMTDVFLIC--FSVVNPASFQNVKEEWVPELKEYAPN--VPYLLIGTQID 115
Query: 127 LVDYSTVESSAKTLKNISEM 146
L D KTL +++M
Sbjct: 116 LRD------DPKTLARLNDM 129
>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 = 48.8 bits (117), Expect = 9e-07
Identities = 44/169 (26%), Positives = 65/169 (38%), Gaps = 47/169 (27%)
Query: 11 VRILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPTHIVDYSEVDQT 70
++ILL+GD VGK+SL+L + F E + S TI D V VD
Sbjct: 1 LKILLIGDSGVGKSSLLLRFTDDTFDEDLSS-----TIGVDFK--------VKTVTVDGK 47
Query: 71 VDELT------EE---------IQKAHVICLVYSVVDDASIDRLSSHWLPFLRN-CLVDT 114
+L +E + A + LVY V + D L + WL L
Sbjct: 48 KVKLAIWDTAGQERFRTLTSSYYRGAQGVILVYDVTRRDTFDNLDT-WLNELDTYSTNPD 106
Query: 115 CLPIVLVGNKVDLVDYST----------------VESSAKTLKNISEMF 147
+ +LVGNK+D + +E+SAKT + + F
Sbjct: 107 AV-KMLVGNKIDKENREVTREEGQKFARKHNMLFIETSAKTRIGVQQAF 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 = 48.6 bits (116), Expect = 1e-06
Identities = 42/159 (26%), Positives = 67/159 (42%), Gaps = 28/159 (17%)
Query: 12 RILLLGDRHVGKTSLILSLVSEEFPELV-PSKAEEITIPPDVTPEMVPTHIVDYSEVDQT 70
+I++LG VGK++L + V F E P+ + ++ I+D + +Q
Sbjct: 3 KIVVLGAGGVGKSALTVQFVQNVFIESYDPTIEDSYRKQVEIDGRQCDLEILDTAGTEQF 62
Query: 71 VDELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLV----DTCLPIVLVGNKVD 126
I+ LVYSV +AS++ L LR ++ +P+VLVGNK D
Sbjct: 63 TAMRELYIKSGQGFLLVYSVTSEASLNELGE-----LREQVLRIKDSDNVPMVLVGNKAD 117
Query: 127 LVDYSTV------------------ESSAKTLKNISEMF 147
L D V E+SA+ N+ E+F
Sbjct: 118 LEDDRQVSREDGVSLSQQWGNVPFYETSARKRTNVDEVF 156
>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 = 48.7 bits (117), Expect = 1e-06
Identities = 48/175 (27%), Positives = 71/175 (40%), Gaps = 46/175 (26%)
Query: 10 NVRILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPTHIVDYSEVDQ 69
+++LLGD VGK+S++L V EF E E TI T V+ D
Sbjct: 1 QFKLVLLGDSSVGKSSIVLRFVKNEFSENQ-----ESTIGAAFL-----TQTVNLD--DT 48
Query: 70 TV-----DELTEEIQK---------AHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTC 115
TV D +E + A +VY + + S ++ S W+ L+
Sbjct: 49 TVKFEIWDTAGQERYRSLAPMYYRGAAAAIVVYDITSEESFEKAKS-WVKELQEHGPPNI 107
Query: 116 LPIVLVGNKVDLVDYSTV-----------------ESSAKTLKNISEMFYY-AQK 152
+ I L GNK DL V E+SAKT +N++E+F A+K
Sbjct: 108 V-IALAGNKADLESKRQVSTEEAQEYADENGLLFMETSAKTGENVNELFTEIARK 161
>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 = 48.1 bits (115), Expect = 2e-06
Identities = 47/185 (25%), Positives = 70/185 (37%), Gaps = 44/185 (23%)
Query: 8 RRNVRILLLGDRHVGKTSLILSLVSEEFPE-LVPSKAEE-ITIPPDVTPEMVPTHIVDYS 65
V+I+++GD GKT L++ FPE VP+ E +T +++ + D +
Sbjct: 1 DLKVKIVVVGDGGCGKTCLLMVYAQGSFPEEYVPTVFENYVTTLQVPNGKIIELALWDTA 60
Query: 66 EVDQTVDELTE-EIQKAHVICLVYSVVDDASIDRLSSHWLP----FLRNCLVDTCLPIVL 120
+ D L VI + YSV + S+D + W P F PIVL
Sbjct: 61 GQED-YDRLRPLSYPDVDVILICYSVDNPTSLDNVEDKWYPEVNHFCPG------TPIVL 113
Query: 121 VGNKVDL-----------------VDYST-------------VESSAKTLKNISEMFYYA 150
VG K DL V +E SAK ++N+ E+F A
Sbjct: 114 VGLKTDLRKDKNSVSKLRAQGLEPVTPEQGESVAKSIGAVAYIECSAKLMENVDEVFDAA 173
Query: 151 QKAVL 155
L
Sbjct: 174 INVAL 178
>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 = 47.9 bits (114), Expect = 3e-06
Identities = 45/159 (28%), Positives = 69/159 (43%), Gaps = 28/159 (17%)
Query: 12 RILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEI-TIPPDVTPEMVPTHIVDYSEVDQT 70
R++ +G VGKT+LI + + F EE+ + +V V I+D S
Sbjct: 1 RLVFMGAAGVGKTALIQRFLYDTFEPKHRRTVEELHSKEYEVAGVKVTIDILDTSGSYSF 60
Query: 71 VDELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLV----DTCLPIVLVGNKVD 126
IQ LVYSV D S + + LR ++ D +PIV+VGNK+D
Sbjct: 61 PAMRKLSIQNGDAFALVYSVDDPESFEEVKR-----LREEILEVKEDKFVPIVVVGNKID 115
Query: 127 L-----VDYST-------------VESSAKTLKNISEMF 147
V+ + VE+SAK +N++E+F
Sbjct: 116 SLAERQVEAADALSTVELDWNNGFVEASAKDNENVTEVF 154
>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 = 47.0 bits (112), Expect = 5e-06
Identities = 42/176 (23%), Positives = 77/176 (43%), Gaps = 35/176 (19%)
Query: 12 RILLLGDRHVGKTSLILSLVSEEFPEL-VPSKAEEITIPPDVTPEMVPTHIVDYSEVDQT 70
+++++GD GKT L++ ++FPE+ VP+ E +V + V + D + +
Sbjct: 3 KLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWD-TAGQED 61
Query: 71 VDEL-TEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGNKVDLVD 129
D L VI + +S+ S++ + W P +++ + +PI+LVGNK DL +
Sbjct: 62 YDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPN--VPIILVGNKKDLRN 119
Query: 130 ------------------------------YSTVESSAKTLKNISEMFYYAQKAVL 155
+ +E SAKT + + E+F A +A L
Sbjct: 120 DEHTIRELAKMKQEPVKPEEGRAMAEKIGAFGYLECSAKTKEGVREVFEMATRAAL 175
>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 = 46.1 bits (110), Expect = 7e-06
Identities = 52/176 (29%), Positives = 72/176 (40%), Gaps = 42/176 (23%)
Query: 12 RILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPD-VTPEMVPTHIVDYSEVD-Q 69
++++LGD VGKTSL+ V+++F KA TI D +T E+ VD V Q
Sbjct: 2 KVIILGDSGVGKTSLMNQYVNKKFSNQY--KA---TIGADFLTKEVT----VDDRLVTLQ 52
Query: 70 TVDEL-TEEIQK--------AHVICLVYSVVDDASIDRLSSHWL-PFLRN-CLVDTC-LP 117
D E Q A LVY V + S + L S W FL D P
Sbjct: 53 IWDTAGQERFQSLGVAFYRGADCCVLVYDVTNPKSFESLDS-WRDEFLIQASPRDPENFP 111
Query: 118 IVLVGNKVDLVDYSTV------------------ESSAKTLKNISEMFYYAQKAVL 155
V++GNK+DL + V E+SAK N+ + F + L
Sbjct: 112 FVVLGNKIDLEEKRQVSTKKAQQWCKSKGNIPYFETSAKEAINVDQAFETIARLAL 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 = 46.0 bits (109), Expect = 8e-06
Identities = 41/156 (26%), Positives = 65/156 (41%), Gaps = 21/156 (13%)
Query: 12 RILLLGDRHVGKTSLILSLVSEEFPE-LVPSKAEEITIPPDVTPEMVPTHIVDYSEVDQT 70
R+++ G VGK+SL+L V F E +P+ + + + I D + Q
Sbjct: 3 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCSKSICTLQITDTTGSHQF 62
Query: 71 VDELTEEIQKAHVICLVYSVVDDASIDRLSSHW--LPFLRNCLVDTCLPIVLVGNKVDLV 128
I K H LVYS+ S++ L + + ++ ++ PI+LVGNK D
Sbjct: 63 PAMQRLSISKGHAFILVYSITSKQSLEELKPIYELICEIKGNNLEKI-PIMLVGNKCDES 121
Query: 129 DYSTV-----------------ESSAKTLKNISEMF 147
V E+SAKT N+ E+F
Sbjct: 122 PSREVSSSEGAALARTWNCAFMETSAKTNHNVQELF 157
>gnl|CDD|206708 cd04136, Rap_like, Rap-like family consists of Rap1, Rap2 and RSR1.
The Rap subfamily consists of the Rap1, Rap2, and RSR1.
Rap subfamily proteins perform different cellular
functions, depending on the isoform and its subcellular
localization. For example, in rat salivary gland,
neutrophils, and platelets, Rap1 localizes to secretory
granules and is believed to regulate exocytosis or the
formation of secretory granules. Rap1 has also been
shown to localize in the Golgi of rat fibroblasts,
zymogen granules, plasma membrane, and microsomal
membrane of the pancreatic acini, as well as in the
endocytic compartment of skeletal muscle cells and
fibroblasts. Rap1 localizes in the nucleus of human
oropharyngeal squamous cell carcinomas (SCCs) and cell
lines. Rap1 plays a role in phagocytosis by controlling
the binding of adhesion receptors (typically integrins)
to their ligands. In yeast, Rap1 has been implicated in
multiple functions, including activation and silencing
of transcription and maintenance of telomeres. Rap2 is
involved in multiple functions, including activation of
c-Jun N-terminal kinase (JNK) to regulate the actin
cytoskeleton and activation of the Wnt/beta-catenin
signaling pathway in embryonic Xenopus. A number of
effector proteins for Rap2 have been identified,
including isoform 3 of the human mitogen-activated
protein kinase kinase kinase kinase 4 (MAP4K4) and
Traf2- and Nck-interacting kinase (TNIK), and the
RalGEFs RalGDS, RGL, and Rlf, which also interact with
Rap1 and Ras. RSR1 is the fungal homolog of Rap1 and
Rap2. In budding yeasts, it is involved in selecting a
site for bud growth, which directs the establishment of
cell polarization. The Rho family GTPase Cdc42 and its
GEF, Cdc24, then establish an axis of polarized growth.
It is believed that Cdc42 interacts directly with RSR1
in vivo. In filamentous fungi such as Ashbya gossypii,
RSR1 is a key regulator of polar growth in the hypha.
Most Ras proteins contain a lipid modification site at
the C-terminus, with a typical sequence motif CaaX,
where a = an aliphatic amino acid and X = any amino
acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 164
Score = 46.0 bits (109), Expect = 9e-06
Identities = 42/158 (26%), Positives = 66/158 (41%), Gaps = 24/158 (15%)
Query: 12 RILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEI---TIPPDVTPEMVPTHIVDYSEVD 68
++++LG VGK++L + V F + E+ I D M+ I+D + +
Sbjct: 3 KLVVLGSGGVGKSALTVQFVQGIFVDKYDPTIEDSYRKQIEVDCQQCML--EILDTAGTE 60
Query: 69 QTVDELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGNKVDLV 128
Q I+ LVYS+ S + L LR + +P++LVGNK DL
Sbjct: 61 QFTAMRDLYIKNGQGFALVYSITAQQSFNDLQDLREQILRVKDTED-VPMILVGNKCDLE 119
Query: 129 DYSTV------------------ESSAKTLKNISEMFY 148
D V E+SAK+ N+ E+FY
Sbjct: 120 DERVVSKEEGQNLARQWGNCPFLETSAKSKINVDEIFY 157
>gnl|CDD|206694 cd04109, Rab28, Rab GTPase family 28 (Rab28). Rab28 subfamily.
First identified in maize, Rab28 has been shown to be a
late embryogenesis-abundant (Lea) protein that is
regulated by the plant hormone abcisic acid (ABA). In
Arabidopsis, Rab28 is expressed during embryo
development and is generally restricted to provascular
tissues in mature embryos. Unlike maize Rab28, it is not
ABA-inducible. Characterization of the human Rab28
homolog revealed two isoforms, which differ by a 95-base
pair insertion, producing an alternative sequence for
the 30 amino acids at the C-terminus. The two human
isoforms are presumably the result of alternative
splicing. Since they differ at the C-terminus but not in
the GTP-binding region, they are predicted to be
targeted to different cellular locations. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins.
Length = 213
Score = 46.3 bits (110), Expect = 1e-05
Identities = 39/135 (28%), Positives = 60/135 (44%), Gaps = 20/135 (14%)
Query: 11 VRILLLGDRHVGKTSLILSLVSEEFPEL------VPSKAEEITIP--PDVTPEMVPTHIV 62
++I++LGD GKTSLI E F + + + IT+P +VT +
Sbjct: 1 IKIVVLGDGASGKTSLIRRFAQEGFGKSYKQTIGLDFFSRRITLPGSLNVT-----LQVW 55
Query: 63 DYSEVDQTV--DELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLP--I 118
D Q + L + I A +CLVY + + S + L WL ++ ++ +
Sbjct: 56 DIG--GQQIGGKMLDKYIYGAQAVCLVYDITNSQSFENLED-WLSVVKKVNEESETKPKM 112
Query: 119 VLVGNKVDLVDYSTV 133
VLVGNK DL V
Sbjct: 113 VLVGNKTDLEHNRQV 127
>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 = 45.6 bits (108), Expect = 2e-05
Identities = 39/133 (29%), Positives = 64/133 (48%), Gaps = 21/133 (15%)
Query: 11 VRILLLGDRHVGKTSLILSLVSEEFPEL-VPSKAEEITIPPDVTPEMV-PTHIVDYSEV- 67
VR+ +LG VGKT+++ +++EFPE +P++ + P V V HI+D +
Sbjct: 1 VRVAVLGAPGVGKTAIVRQFLAQEFPEEYIPTEHRRLYRPAVVLSGRVYDLHILDVPNMQ 60
Query: 68 -------DQTVDELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCL---- 116
+ +D ++ + LVY D S D S H++ LR +++T
Sbjct: 61 RYPGTAGQEWMDPRFRGLRNSRAFILVY---DICSPD--SFHYVKLLRQQILETRPAGNK 115
Query: 117 --PIVLVGNKVDL 127
PIV+VGNK D
Sbjct: 116 EPPIVVVGNKRDQ 128
>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 = 43.4 bits (103), Expect = 7e-05
Identities = 41/168 (24%), Positives = 68/168 (40%), Gaps = 27/168 (16%)
Query: 13 ILLLGDRHVGKTSLILSLVSEEF-PELVPSKAEEITIPPDVTPEMVPTHIVDYSEVDQTV 71
I +LG VGK++L + +++ F E P+ E VT + + Q
Sbjct: 2 IAVLGASGVGKSALTVRFLTKRFIGEYEPN--LESLYSRQVTIDGEQVSLEIQDTPGQQQ 59
Query: 72 DE----LTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLR-NCLVDTCLPIVLVGNKVD 126
+E L ++ A LVYS+ D +S D + S L +R D +P++LVGNK D
Sbjct: 60 NEDPESLERSLRWADGFVLVYSITDRSSFD-VVSQLLQLIREIKKRDGEIPVILVGNKAD 118
Query: 127 LVDYSTVE------------------SSAKTLKNISEMFYYAQKAVLH 156
L+ V S+A+ + +F+ + V
Sbjct: 119 LLHSRQVSTEEGQKLALELGCLFFEVSAAENYLEVQNVFHELCREVRR 166
Score = 30.7 bits (70), Expect = 1.2
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 493 TSKIPVMLVAGKSDMPRARQ 512
+IPV+LV K+D+ +RQ
Sbjct: 105 DGEIPVILVGNKADLLHSRQ 124
>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 = 43.7 bits (103), Expect = 7e-05
Identities = 41/166 (24%), Positives = 73/166 (43%), Gaps = 27/166 (16%)
Query: 12 RILLLGDRHVGKTSLILSLVSEEF-----PELVPSKAEEITIPPDVTPEMVPTHIVDYSE 66
++++LGD VGKT+L + L F P + S +++ + D P M+ ++D +
Sbjct: 1 KLVVLGDGGVGKTALTIQLCLNHFVETYDPTIEDSYRKQVVV--DGQPCML--EVLDTAG 56
Query: 67 VDQTVDELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLR-NCLVDTCLPIVLVGNKV 125
++ + I++ LVYS+ ++ +R+ R +PI++VGNK
Sbjct: 57 QEEYTALRDQWIREGEGFILVYSITSRSTFERVERFREQIQRVKDESAADVPIMIVGNKC 116
Query: 126 DLVDYSTV-----------------ESSAKTLKNISEMFYYAQKAV 154
D V V E+SAKT N+ FY +A+
Sbjct: 117 DKVYEREVSTEEGAALARRLGCEFIEASAKTNVNVERAFYTLVRAL 162
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 43.5 bits (102), Expect = 1e-04
Identities = 43/155 (27%), Positives = 66/155 (42%), Gaps = 20/155 (12%)
Query: 12 RILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPP-DVTPEMVPTHIVDYSEVDQT 70
+ILL+GD VGK+SL++S +S +L P+ + I V + + I D + ++
Sbjct: 16 KILLIGDSGVGKSSLLVSFISSSVEDLAPTIGVDFKIKQLTVGGKRLKLTIWDTAGQERF 75
Query: 71 VDELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLR-NCLVDTCLPIVLVGNKVDLVD 129
+ + A I LVY V + LS W + C+ + LVGNKVD
Sbjct: 76 RTLTSSYYRNAQGIILVYDVTRRETFTNLSDVWGKEVELYSTNQDCVKM-LVGNKVDRES 134
Query: 130 YSTV-----------------ESSAKTLKNISEMF 147
V E SAKT +N+ + F
Sbjct: 135 ERDVSREEGMALAKEHGCLFLECSAKTRENVEQCF 169
>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 = 43.3 bits (102), Expect = 1e-04
Identities = 45/163 (27%), Positives = 70/163 (42%), Gaps = 31/163 (19%)
Query: 11 VRILLLGDRHVGKTSLILSLVSEEF---PELVPSKAEEITIPPDVTPEMVPTHIVDY--S 65
V++++LG VGKTSL+ V F P A + V +V I D S
Sbjct: 1 VKVVMLGKESVGKTSLVERYVHHRFLVGPYQNTIGAAFVAKRMVVGERVVTLGIWDTAGS 60
Query: 66 EVDQTVDELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGNKV 125
E + + + KA ++C Y + D +S +R + W+ L+N + I L G K
Sbjct: 61 ERYEAMSRIYYRGAKAAIVC--YDLTDSSSFER-AKFWVKELQNL--EEHCKIYLCGTKS 115
Query: 126 DL---------VDYSTV------------ESSAKTLKNISEMF 147
DL VD+ V E+S+KT +N+ E+F
Sbjct: 116 DLIEQDRSLRQVDFHDVQDFADEIKAQHFETSSKTGQNVDELF 158
>gnl|CDD|206659 cd01867, Rab8_Rab10_Rab13_like, Rab GTPase families 8, 10, 13
(Rab8, Rab10, Rab13). Rab8/Sec4/Ypt2 are known or
suspected to be involved in post-Golgi transport to the
plasma membrane. It is likely that these Rabs have
functions that are specific to the mammalian lineage and
have no orthologs in plants. Rab8 modulates polarized
membrane transport through reorganization of actin and
microtubules, induces the formation of new surface
extensions, and has an important role in directed
membrane transport to cell surfaces. The Ypt2 gene of
the fission yeast Schizosaccharomyces pombe encodes a
member of the Ypt/Rab family of small GTP-binding
proteins, related in sequence to Sec4p of Saccharomyces
cerevisiae but closer to mammalian Rab8. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 167
Score = 42.6 bits (101), Expect = 1e-04
Identities = 43/182 (23%), Positives = 69/182 (37%), Gaps = 57/182 (31%)
Query: 12 RILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPTHIVDYS----EV 67
++LL+GD VGK+ L+L + F P + T +D+ E+
Sbjct: 5 KLLLIGDSGVGKSCLLLRFSEDSF-----------------NPSFISTIGIDFKIRTIEL 47
Query: 68 D------QTVDELTEE---------IQKAHVICLVYSVVDDASIDRLSSHWLPFL-RNCL 111
D Q D +E + A I LVY + D+ S + + +W+ + +
Sbjct: 48 DGKKIKLQIWDTAGQERFRTITTSYYRGAMGIILVYDITDEKSFENIK-NWMRNIDEHAS 106
Query: 112 VDTCLPIVLVGNKVDLVDYSTV-----------------ESSAKTLKNISEMFYYAQKAV 154
D +LVGNK D+ + V E+SAK N+ E F K +
Sbjct: 107 EDVER--MLVGNKCDMEEKRVVSKEEGEALAREYGIKFLETSAKANINVEEAFLTLAKDI 164
Query: 155 LH 156
L
Sbjct: 165 LK 166
>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 = 42.5 bits (100), Expect = 1e-04
Identities = 35/126 (27%), Positives = 63/126 (50%), Gaps = 13/126 (10%)
Query: 10 NVRILLLGDRHVGKTSLILSLVSEEFP-ELVPSKAEEITIPPDVTPEMVPTHIVDYSEVD 68
++ +++GD VGKT L++S + FP E +P+ + + MV V+ D
Sbjct: 1 AIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYS-----ANVMVDGKPVNLGLWD 55
Query: 69 QTVDELTEEIQ-----KAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGN 123
E + ++ + V + +S+V AS + + + W P +R+ +T PI+LVG
Sbjct: 56 TAGQEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNT--PIILVGT 113
Query: 124 KVDLVD 129
K+DL D
Sbjct: 114 KLDLRD 119
>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 = 42.0 bits (99), Expect = 2e-04
Identities = 22/79 (27%), Positives = 35/79 (44%), Gaps = 17/79 (21%)
Query: 86 LVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGNKVDL----VDYST--------- 132
V+++ S + + ++ R D +P+VLVGNK DL V
Sbjct: 78 CVFAINSRKSFEDIHTYREQIKRVKDSDD-VPMVLVGNKCDLAARTVSTRQGQDLAKSYG 136
Query: 133 ---VESSAKTLKNISEMFY 148
+E+SAKT + + E FY
Sbjct: 137 IPYIETSAKTRQGVEEAFY 155
>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 = 42.3 bits (100), Expect = 2e-04
Identities = 38/139 (27%), Positives = 61/139 (43%), Gaps = 14/139 (10%)
Query: 13 ILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPTHIVDYSEVDQTVD 72
+LLLG GKT+L L + + V S + + + +VD ++ D
Sbjct: 3 VLLLGPSDSGKTALFTKLTTGKVRSTVTSIEPNVASFYSNSSKGKKLTLVDVPGHEKLRD 62
Query: 73 ELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTC-----LPIVLVGNKVDL 127
+L E + KA + +V+ VVD A+ + FL + L D +PI++ NK DL
Sbjct: 63 KLLEYL-KASLKAIVF-VVDSATFQKNIRDVAEFLYDILTDLEKIKNKIPILIACNKQDL 120
Query: 128 VDYSTVESSAKTLKNISEM 146
+AK K I E+
Sbjct: 121 -------FTAKPAKKIKEL 132
>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 = 41.3 bits (97), Expect = 4e-04
Identities = 47/191 (24%), Positives = 73/191 (38%), Gaps = 53/191 (27%)
Query: 9 RNVRILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPTHIVDYSEVD 68
R +I+++GD +VGKT L + FPE E TI VD+ E
Sbjct: 1 RIFKIIVIGDSNVGKTCLTYRFCAGRFPERT-----EATIG------------VDFRE-- 41
Query: 69 QTVDELTEEIQ----------------------KAHVICLVYSVVDDASIDRLSSHWLPF 106
+TV+ E I+ H + VY V + AS L S W+
Sbjct: 42 RTVEIDGERIKVQLWDTAGQERFRKSMVQHYYRNVHAVVFVYDVTNMASFHSLPS-WIEE 100
Query: 107 LRNCLVDTCLPIVLVGNKVDLVDYSTVESSAKTLKNISEMFYYAQKAVLHPMAPIYISDK 166
+ +P +LVGNK DL + V + ++++ F A H M S K
Sbjct: 101 CEQHSLPNEVPRILVGNKCDLREQIQVPT------DLAQRF-----ADAHSMPLFETSAK 149
Query: 167 QELTPECIKAL 177
+ ++A+
Sbjct: 150 DPSENDHVEAI 160
>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 = 41.2 bits (97), Expect = 4e-04
Identities = 48/162 (29%), Positives = 71/162 (43%), Gaps = 35/162 (21%)
Query: 12 RILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDV---TPEM----VPTHIVDY 64
++LL+GD VGK+ L+L + + E S TI D T E+ V I D
Sbjct: 4 KLLLIGDSGVGKSCLLLRFADDTYTESYIS-----TIGVDFKIRTIELDGKTVKLQIWDT 58
Query: 65 S--EVDQTVDELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVG 122
+ E +T+ + + AH I +VY V D S + + WL + + + LVG
Sbjct: 59 AGQERFRTIT--SSYYRGAHGIIIVYDVTDQESFNNVKQ-WLQEIDRYASENVNKL-LVG 114
Query: 123 NKVDL-----VDYST------------VESSAKTLKNISEMF 147
NK DL VDY+ +E+SAK N+ E F
Sbjct: 115 NKCDLTDKKVVDYTEAKEFADELGIPFLETSAKNATNVEEAF 156
>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 = 41.0 bits (96), Expect = 4e-04
Identities = 35/115 (30%), Positives = 56/115 (48%), Gaps = 3/115 (2%)
Query: 16 LGDRHVGKTSLILSLVSEEFP-ELVPSKAEEITIPPDVTPEMVPTHIVDYSEVDQTVDEL 74
+GD VGKT +++S S FP + VP+ + + V V + D + +
Sbjct: 7 VGDGAVGKTCMLISYTSNTFPTDYVPTVFDNFSANVVVDGNTVNLGLWDTAGQEDYNRLR 66
Query: 75 TEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGNKVDLVD 129
+ A V L +S++ AS + + W+P LR+ +PIVLVG K+DL D
Sbjct: 67 PLSYRGADVFLLAFSLISKASYENVLKKWIPELRHYAPG--VPIVLVGTKLDLRD 119
>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 = 40.9 bits (96), Expect = 5e-04
Identities = 34/155 (21%), Positives = 65/155 (41%), Gaps = 19/155 (12%)
Query: 12 RILLLGDRHVGKTSLILSLVSEEF-PELVPSKAEEITIPPDVTPEMVPTHIVDYSEVDQT 70
+++++G VGK++L + + F + P+ + T ++ + I+D + ++
Sbjct: 4 KLVVVGGGGVGKSALTIQFIQSYFVTDYDPTIEDSYTKQCEIDGQWARLDILDTAGQEEF 63
Query: 71 VDELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGNKVDLVDY 130
+ ++ LV+SV D S + + LR D P++LVGNK DL
Sbjct: 64 SAMREQYMRTGEGFLLVFSVTDRGSFEEVDKFHTQILRVKDRDE-FPMILVGNKADLEHQ 122
Query: 131 STV-----------------ESSAKTLKNISEMFY 148
V E+SAK N+ + F+
Sbjct: 123 RQVSREEGQELARQLKIPYIETSAKDRVNVDKAFH 157
>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 = 40.2 bits (94), Expect = 8e-04
Identities = 39/155 (25%), Positives = 67/155 (43%), Gaps = 19/155 (12%)
Query: 12 RILLLGDRHVGKTSLILSLVSEEFPELV-PSKAEEITIPPDVTPEMVPTHIVDYSEVDQT 70
++++LG VGK++L + V F E P+ + +V + I+D + +Q
Sbjct: 3 KLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDGQQCMLEILDTAGTEQF 62
Query: 71 VDELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGNKVDLVDY 130
++ LVYS+ ++ + L LR + +P++LVGNK DL D
Sbjct: 63 TAMRDLYMKNGQGFVLVYSITAQSTFNDLQDLREQILRVKDTED-VPMILVGNKCDLEDE 121
Query: 131 STV-----------------ESSAKTLKNISEMFY 148
V E+SAK N++E+FY
Sbjct: 122 RVVGKEQGQNLARQWGCAFLETSAKAKINVNEIFY 156
>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 = 40.0 bits (94), Expect = 8e-04
Identities = 35/162 (21%), Positives = 59/162 (36%), Gaps = 28/162 (17%)
Query: 11 VRILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPTHIVDYSEVDQT 70
++++ +G+ VGK+ +I F V I I V V V + D +
Sbjct: 1 IKVISMGNSGVGKSCIIKRYCEGRF---VSKYLPTIGIDYGVKKVSVRNKEVRVNFFDLS 57
Query: 71 VDELTEEIQK-----AHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCL---PIVLVG 122
E++ + LVY V D S + L S + + +V+
Sbjct: 58 GHPEYLEVRNEFYKDTQGVLLVYDVTDRQSFEALDSWLKEMKQEGGPHGNMENIVVVVCA 117
Query: 123 NKVDLVDYSTV-----------------ESSAKTLKNISEMF 147
NK+DL + V E+SA T + ++EMF
Sbjct: 118 NKIDLTKHRAVSEDEGRLWAESKGFKYFETSACTGEGVNEMF 159
>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 = 40.1 bits (94), Expect = 0.001
Identities = 38/128 (29%), Positives = 60/128 (46%), Gaps = 8/128 (6%)
Query: 10 NVRILLLGDRHVGKTSLILSLVSEEFPE-LVPSKAEEITIPPDVTPEMVPTHIVDYS--E 66
+I+L+GD GKT+L+ + FPE VP+ E T +V + + + D S
Sbjct: 1 RCKIVLVGDSQCGKTALLQVFAKDSFPENYVPTVFENYTASFEVDKQRIELSLWDTSGSP 60
Query: 67 VDQTVDELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGNKVD 126
V L+ A +IC S + ++D + W +R +T P++LVG K D
Sbjct: 61 YYDNVRPLSYPDSDAVLICFDISRPE--TLDSVLKKWKGEVREFCPNT--PVLLVGCKSD 116
Query: 127 L-VDYSTV 133
L D ST+
Sbjct: 117 LRTDLSTL 124
>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 = 39.4 bits (92), Expect = 0.001
Identities = 41/160 (25%), Positives = 71/160 (44%), Gaps = 31/160 (19%)
Query: 12 RILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEI---TIPPDVTPEMVPTHIVDYSEVD 68
++++LG VGK++L + VS F E E+ I D +P ++ I+D + +
Sbjct: 3 KVVVLGSGGVGKSALTVQFVSGTFIEKYDPTIEDFYRKEIEVDSSPSVL--EILDTAGTE 60
Query: 69 QTVDELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDT----CLPIVLVGNK 124
Q I+ +VYS+V+ + + +R+ +V +PI+LVGNK
Sbjct: 61 QFASMRDLYIKNGQGFIVVYSLVNQQTFQDIKP-----MRDQIVRVKGYEKVPIILVGNK 115
Query: 125 VDLVDYSTV-----------------ESSAKTLKNISEMF 147
VDL V E+SAK+ ++E+F
Sbjct: 116 VDLESEREVSSAEGRALAEEWGCPFMETSAKSKTMVNELF 155
>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 = 39.5 bits (92), Expect = 0.002
Identities = 37/153 (24%), Positives = 61/153 (39%), Gaps = 25/153 (16%)
Query: 12 RILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPTHIVDYSEVDQTV 71
++++LGD GKTSL+ FP+ P V + VD V+ ++
Sbjct: 2 KVVVLGDGACGKTSLLNVFTRGYFPQ---------VYEPTVFENYIHDIFVDGLAVELSL 52
Query: 72 DELT--EEIQK--------AHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTC--LPIV 119
+ EE + HVI L +SV + S++ + S WL +R C + +V
Sbjct: 53 WDTAGQEEFDRLRSLSYADTHVIMLCFSVDNPDSLENVESKWLAEIR----HHCPGVKLV 108
Query: 120 LVGNKVDLVDYSTVESSAKTLKNISEMFYYAQK 152
LV K DL + + E A++
Sbjct: 109 LVALKCDLREPRNERDRGTHTISYEEGLAVAKR 141
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 39.5 bits (92), Expect = 0.002
Identities = 36/159 (22%), Positives = 66/159 (41%), Gaps = 27/159 (16%)
Query: 12 RILLLGDRHVGKTSLILSLVSEEF-----PELVPSKAEEITIPPDVTPEMVPTHIVDYSE 66
+++++G VGK++L + + F P + S ++ I + I+D +
Sbjct: 7 KLVVVGGGGVGKSALTIQFIQNHFIDEYDPTIEDSYRKQCVIDEETCL----LDILDTAG 62
Query: 67 VDQTVDELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGNKVD 126
++ + ++ VYS+ +S + ++S LR D +P++LVGNK D
Sbjct: 63 QEEYSAMRDQYMRTGQGFLCVYSITSRSSFEEIASFREQILRVKDKDR-VPMILVGNKCD 121
Query: 127 LVDYSTV-----------------ESSAKTLKNISEMFY 148
L V E+SAK N+ E FY
Sbjct: 122 LDSERQVSTGEGQELAKSFGIPFLETSAKQRVNVDEAFY 160
>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 = 39.6 bits (92), Expect = 0.002
Identities = 33/138 (23%), Positives = 67/138 (48%), Gaps = 9/138 (6%)
Query: 9 RNVRILLLGDRHVGKTSLILSLVSEEFP-ELVPSKAEEITIPPDVTPEMVPTHIVDYSEV 67
++++ +++GD VGKT L++ + FP E +P+ + + V V ++ D +
Sbjct: 2 QSIKCVVVGDGAVGKTCLLICYTTNAFPKEYIPTVFDNYSAQTAVDGRTVSLNLWDTAGQ 61
Query: 68 DQTVDELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGNKVDL 127
++ T + +V + +S+ +S + + W P + + + +PI+LVG K DL
Sbjct: 62 EEYDRLRTLSYPQTNVFIICFSIASPSSYENVRHKWHPEVCHHCPN--VPILLVGTKKDL 119
Query: 128 VDYSTVESSAKTLKNISE 145
+ A TLK + E
Sbjct: 120 ------RNDADTLKKLKE 131
>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 = 39.1 bits (91), Expect = 0.002
Identities = 37/131 (28%), Positives = 66/131 (50%), Gaps = 6/131 (4%)
Query: 11 VRILLLGDRHVGKTSLILSLVSEEFP-ELVPSKAEEITIPPDVTPEMVPTHIVDYSEVDQ 69
++ +++GD VGKT L++S + +FP E VP+ + + + E + D + +
Sbjct: 2 IKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTLGLFDTAG-QE 60
Query: 70 TVDELTE-EIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGNKVDLV 128
D L + V + +SVV +S + + W+P + + T P +LVG ++DL
Sbjct: 61 DYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCPKT--PFLLVGTQIDLR 118
Query: 129 -DYSTVESSAK 138
D ST+E AK
Sbjct: 119 DDPSTIEKLAK 129
>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 = 38.5 bits (90), Expect = 0.003
Identities = 37/175 (21%), Positives = 64/175 (36%), Gaps = 45/175 (25%)
Query: 11 VRILLLGDRHVGKTSLILSLVSEEFPELVPS----KAEEITIPPDVTPEMVPTHIVDYSE 66
+++L+G VGKTSL L+ E+F S ++ IP ++ ++ D+
Sbjct: 2 AKLMLVGQGGVGKTSLCKQLIGEKFDGDESSTHGINVQDWKIPAPERKKIR-LNVWDFGG 60
Query: 67 VDQTVDELTEEIQKAHVICL----VYSVVDDASI----DRLSSHWLPFLRNCLVDTCLPI 118
E H L +Y +V D R+ +WL ++ + P+
Sbjct: 61 --------QEIYHATHQFFLTSRSLYLLVFDLRTGDEVSRV-PYWLRQIKAFGGVS--PV 109
Query: 119 VLVGNKVD-----------LVDYSTVES------SAKTLKNISEMFYYAQKAVLH 156
+LVG +D L S K K I+E+ +KA+
Sbjct: 110 ILVGTHIDESCDEDILKKALNKKFPAIINDIHFVSCKNGKGIAEL----KKAIAK 160
Score = 29.6 bits (67), Expect = 2.5
Identities = 15/60 (25%), Positives = 23/60 (38%), Gaps = 8/60 (13%)
Query: 413 HVIGNRSTGKTALCQSIL--RKHHDSSKT------SITSPVECDPPYTINTTTVYGQEKY 464
++G GKT+LC+ ++ + D S T P +N GQE Y
Sbjct: 5 MLVGQGGVGKTSLCKQLIGEKFDGDESSTHGINVQDWKIPAPERKKIRLNVWDFGGQEIY 64
>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 = 38.7 bits (90), Expect = 0.003
Identities = 35/124 (28%), Positives = 59/124 (47%), Gaps = 10/124 (8%)
Query: 9 RNVRILLLGDRHVGKTSLILSLVSEEFPELV-PSKAEEITIPPDVTPEMVPTHIVDYS-E 66
R +I++LG VGK+++ + +S FP+ P+ + + E I+D + +
Sbjct: 1 REYKIVMLGAGGVGKSAVTMQFISHSFPDYHDPTIEDAYKTQARIDNEPALLDILDTAGQ 60
Query: 67 VDQTVDELTEEIQKA---HVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGN 123
+ T + ++ + +IC YSV D S S R L + +P+VLVGN
Sbjct: 61 AEFTA--MRDQYMRCGEGFIIC--YSVTDRHSFQEASEFKELITRVRLTED-IPLVLVGN 115
Query: 124 KVDL 127
KVDL
Sbjct: 116 KVDL 119
>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 = 38.3 bits (89), Expect = 0.003
Identities = 37/159 (23%), Positives = 64/159 (40%), Gaps = 27/159 (16%)
Query: 12 RILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITI-----PPDVTPEMVPTHIVDYSE 66
+I+L+G+ VGKT L+ FP P + I + ++ E + I D +
Sbjct: 9 KIVLIGNAGVGKTCLVRRFTQGLFP---PGQGATIGVDFMIKTVEIKGEKIKLQIWDTAG 65
Query: 67 VDQTVDELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGNKVD 126
++ + A+ + L Y + + S L WL + + + I LVGNK+D
Sbjct: 66 QERFRSITQSYYRSANALILTYDITCEESFRCLPE-WLREIEQYANNKVITI-LVGNKID 123
Query: 127 LVDYSTV-----------------ESSAKTLKNISEMFY 148
L + V E+SAK N+ ++F
Sbjct: 124 LAERREVSQQRAEEFSDAQDMYYLETSAKESDNVEKLFL 162
>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 = 37.5 bits (87), Expect = 0.006
Identities = 41/160 (25%), Positives = 67/160 (41%), Gaps = 21/160 (13%)
Query: 14 LLLGDRHVGKTSLILSLVSEEFPELVPSK--AEEITIPPDVTPEMVPTHIVDYSEVDQTV 71
+++GD VGK+ L+ ++F P E T +V + + I D + ++
Sbjct: 6 IIIGDMGVGKSCLLHQFTEKKFMADCPHTIGVEFGTRIIEVNGQKIKLQIWDTAGQERFR 65
Query: 72 DELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGNKVDL---- 127
+ A +VY + ++ + LSS WL RN L + I L+GNK DL
Sbjct: 66 AVTRSYYRGAAGALMVYDITRRSTYNHLSS-WLTDARN-LTNPNTVIFLIGNKADLEAQR 123
Query: 128 -VDYST------------VESSAKTLKNISEMFYYAQKAV 154
V Y +E SAKT +N+ + F K +
Sbjct: 124 DVTYEEAKQFADENGLLFLECSAKTGENVEDAFLETAKKI 163
>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 = 37.2 bits (86), Expect = 0.012
Identities = 33/123 (26%), Positives = 59/123 (47%), Gaps = 13/123 (10%)
Query: 11 VRILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITI----PPDVTPEMVPTHIVDYSE 66
++++LLGD +VGKTSL+ + F + V + + P +++ I D +
Sbjct: 1 LKVVLLGDMNVGKTSLLHRYMERRFKDTVSTVGGAFYLKQWGPYNIS-------IWDTAG 53
Query: 67 VDQTVDELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGNKVD 126
+Q + + A + L Y V + S++ L +L L + + CL V VGNK+D
Sbjct: 54 REQFHGLGSMYCRGAAAVILTYDVSNVQSLEELEDRFLG-LTDTANEDCLFAV-VGNKLD 111
Query: 127 LVD 129
L +
Sbjct: 112 LTE 114
>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 = 36.7 bits (85), Expect = 0.014
Identities = 42/162 (25%), Positives = 65/162 (40%), Gaps = 43/162 (26%)
Query: 8 RRNVRILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPTHIVDY--- 64
RR +++++GD GKTSL+ EFPE E PT +Y
Sbjct: 1 RR--KLVIVGDGACGKTSLLYVFTLGEFPE-----------------EYHPTVFENYVTD 41
Query: 65 SEVDQTVDELT-------EEIQ--------KAHVICLVYSVVDDASIDRLSSHWLPFLRN 109
VD +L EE + KAHVI + +++ S++ + + W+ +R
Sbjct: 42 CRVDGKPVQLALWDTAGQEEYERLRPLSYSKAHVILIGFAIDTPDSLENVRTKWIEEVRR 101
Query: 110 CLVDTCLPIVLVGNKVDLVDYSTVESSAKTLKNISEMFYYAQ 151
+ P++LVG K DL E+ AK E Q
Sbjct: 102 YCPNV--PVILVGLKKDLRQ----EAVAKGNYATDEFVPIQQ 137
>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 = 36.4 bits (84), Expect = 0.019
Identities = 40/155 (25%), Positives = 64/155 (41%), Gaps = 22/155 (14%)
Query: 12 RILLLGDRHVGKTSLILSLVSEEFPE-LVPSKAEEITIPP-DVTPEMVPTHIVDYSEVDQ 69
++L++GD VGK+SL+L F + + + I ++ E V I D + ++
Sbjct: 8 KLLIIGDSGVGKSSLLLRFADNTFSGSYITTIGVDFKIRTVEINGERVKLQIWDTAGQER 67
Query: 70 TVDELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGNKVD--- 126
+ + H + +VY V + S + WL + D C VLVGNK D
Sbjct: 68 FRTITSTYYRGTHGVIVVYDVTNGESFVNVK-RWLQEIEQNCDDVCK--VLVGNKNDDPE 124
Query: 127 --------------LVDYSTVESSAKTLKNISEMF 147
+ S E+SAK N+ EMF
Sbjct: 125 RKVVETEDAYKFAGQMGISLFETSAKENINVEEMF 159
>gnl|CDD|206696 cd04113, Rab4, Rab GTPase family 4 (Rab4). Rab4 subfamily. Rab4
has been implicated in numerous functions within the
cell. It helps regulate endocytosis through the sorting,
recycling, and degradation of early endosomes. Mammalian
Rab4 is involved in the regulation of many surface
proteins including G-protein-coupled receptors,
transferrin receptor, integrins, and surfactant protein
A. Experimental data implicate Rab4 in regulation of the
recycling of internalized receptors back to the plasma
membrane. It is also believed to influence
receptor-mediated antigen processing in B-lymphocytes,
in calcium-dependent exocytosis in platelets, in
alpha-amylase secretion in pancreatic cells, and in
insulin-induced translocation of Glut4 from internal
vesicles to the cell surface. Rab4 is known to share
effector proteins with Rab5 and Rab11. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 161
Score = 35.9 bits (83), Expect = 0.020
Identities = 26/79 (32%), Positives = 35/79 (44%), Gaps = 19/79 (24%)
Query: 86 LVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGNKVDLVDYSTV------------ 133
LVY + S + L+ +WL R L + I+LVGNK DL D V
Sbjct: 78 LVYDITSRESFNALT-NWLTDART-LASPDIVIILVGNKKDLEDDREVTFLEASRFAQEN 135
Query: 134 -----ESSAKTLKNISEMF 147
E+SA T +N+ E F
Sbjct: 136 GLLFLETSALTGENVEEAF 154
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 36.5 bits (84), Expect = 0.024
Identities = 39/163 (23%), Positives = 66/163 (40%), Gaps = 37/163 (22%)
Query: 12 RILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPTHIVDYSEV---- 67
+ +++GD VGK+ L+L + F ++TI + M+ +D +
Sbjct: 8 KYIIIGDTGVGKSCLLLQFTDKRF-----QPVHDLTIGVEFGARMI---TIDNKPIKLQI 59
Query: 68 -DQTVDELTEEIQKAHV-----ICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLV 121
D E I +++ LVY + + + L+S WL R + + I+L+
Sbjct: 60 WDTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLAS-WLEDARQ-HANANMTIMLI 117
Query: 122 GNKVDLVDYSTV-----------------ESSAKTLKNISEMF 147
GNK DL V E+SAKT +N+ E F
Sbjct: 118 GNKCDLAHRRAVSTEEGEQFAKEHGLIFMEASAKTAQNVEEAF 160
>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 = 35.6 bits (82), Expect = 0.030
Identities = 41/165 (24%), Positives = 68/165 (41%), Gaps = 21/165 (12%)
Query: 11 VRILLLGDRHVGKTSLILSLVSEEFPE--LVPSKAEEITIPPDVTPEMVPTHIVDYSEVD 68
++++LLGD VGK+SL+ V+ +F E + +V V I D + +
Sbjct: 6 LKVILLGDGGVGKSSLMNRYVTNKFDTQLFHTIGVEFLNKDLEVDGHFVTLQIWDTAGQE 65
Query: 69 QTVDELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTC--LPIVLVGNKVD 126
+ T + + L +SV D S LS+ F+ V P V++GNK+D
Sbjct: 66 RFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVILGNKID 125
Query: 127 LVD-----------------YSTVESSAKTLKNISEMFYYAQKAV 154
+ + Y E+SAK N++ F A + V
Sbjct: 126 IPERQVSTEEAQAWCRDNGDYPYFETSAKDATNVAAAFEEAVRRV 170
>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 = 35.0 bits (81), Expect = 0.041
Identities = 19/63 (30%), Positives = 25/63 (39%), Gaps = 17/63 (26%)
Query: 102 HWLPFLRNCLVDTCLPIVLVGNKVDLVD---------------YSTVESSAKTLKNISEM 146
+W L V +PIVL GNKVD+ D E SAK+ N +
Sbjct: 93 NWHRDLVR--VCENIPIVLCGNKVDIKDRKVKPKQITFHRKKNLQYYEISAKSNYNFEKP 150
Query: 147 FYY 149
F +
Sbjct: 151 FLW 153
>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 = 35.1 bits (81), Expect = 0.044
Identities = 39/164 (23%), Positives = 65/164 (39%), Gaps = 38/164 (23%)
Query: 12 RILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPTHIVDYSEVD-QT 70
+I+L+GD +VGKT ++ S F E + TI D T + T + V Q
Sbjct: 5 KIILIGDSNVGKTCVVQRFKSGTFSE-----RQGNTIGVDFT---MKTLEIQGKRVKLQI 56
Query: 71 VDELTEE---------IQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLV 121
D +E + A+ + Y + +S + + HW+ + + ++L+
Sbjct: 57 WDTAGQERFRTITQSYYRSANGAIIAYDITRRSSFESV-PHWIEEVEKYGASNVV-LLLI 114
Query: 122 GNKVDLVDYSTV------------------ESSAKTLKNISEMF 147
GNK DL + V E+SAK N+ E F
Sbjct: 115 GNKCDLEEQREVLFEEACTLAEHYGILAVLETSAKESSNVEEAF 158
>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 = 35.0 bits (81), Expect = 0.045
Identities = 34/175 (19%), Positives = 58/175 (33%), Gaps = 53/175 (30%)
Query: 11 VRILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPTHIVDYSEVDQT 70
++I+++GD +VGK++L+ L+ + E P +Y
Sbjct: 2 IKIVIVGDPNVGKSTLLNRLLGNKISIT----------------EYKPGTTRNYVTTVIE 45
Query: 71 VDELTEEIQ-------------KAHVICLVYSVVDDASIDRLSS-------HWLPFLRNC 110
D T + + V S + I L + +
Sbjct: 46 EDGKTYKFNLLDTAGQEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIH- 104
Query: 111 LVDTCLPIVLVGNKVDLVDYST----------------VESSAKTLKNISEMFYY 149
++ +PI+LVGNK+DL D + SA+T KNI F
Sbjct: 105 HAESGVPIILVGNKIDLRDAKLKTHVAFLFAKLNGEPIIPLSAETGKNIDSAFKI 159
>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 = 34.7 bits (80), Expect = 0.067
Identities = 42/169 (24%), Positives = 72/169 (42%), Gaps = 37/169 (21%)
Query: 14 LLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPTHIVDYSEVD-QTVD 72
+++GD VGK+ L+L + F ++TI + M+ +D ++ Q D
Sbjct: 8 IIIGDTGVGKSCLLLQFTDKRFQP-----VHDLTIGVEFGARMIT---IDGKQIKLQIWD 59
Query: 73 ELTEE----IQKAHV-----ICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGN 123
+E I +++ LVY + + + L+S WL R ++ + I+L+GN
Sbjct: 60 TAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLTS-WLEDARQ-HSNSNMTIMLIGN 117
Query: 124 KVDL-----VDYST------------VESSAKTLKNISEMFYYAQKAVL 155
K DL V Y +E+SAKT N+ E F K +
Sbjct: 118 KCDLESRREVSYEEGEAFAREHGLIFMETSAKTASNVEEAFINTAKEIY 166
>gnl|CDD|205383 pfam13202, EF_hand_3, EF hand.
Length = 25
Score = 31.1 bits (72), Expect = 0.077
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 301 LFYRFDKDGDGALSPEE 317
LF +FD +GDG +S EE
Sbjct: 4 LFRQFDTNGDGKISKEE 20
>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 = 34.7 bits (80), Expect = 0.091
Identities = 36/161 (22%), Positives = 64/161 (39%), Gaps = 31/161 (19%)
Query: 12 RILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDV---TPEMVPTHIVDYSEVD 68
R++++GD VGK+SL+ F E+ + T+ D E+ P + D
Sbjct: 4 RLIVIGDSTVGKSSLLKRFTEGRFAEV-----SDPTVGVDFFSRLIEIEPGVRIKLQLWD 58
Query: 69 QTVDELTEEIQKAHV-----ICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGN 123
E I +++ + LV+ + + S + + WL R+ + +LVG+
Sbjct: 59 TAGQERFRSITRSYYRNSVGVLLVFDITNRESFEHVHD-WLEEARSHIQPHRPVFILVGH 117
Query: 124 KVDLVD-----------------YSTVESSAKTLKNISEMF 147
K DL +E+SA+T N+ E F
Sbjct: 118 KCDLESQRQVTREEAEKLAKDLGMKYIETSARTGDNVEEAF 158
>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 = 33.3 bits (77), Expect = 0.14
Identities = 33/139 (23%), Positives = 50/139 (35%), Gaps = 36/139 (25%)
Query: 12 RILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPTHIVDYSEVDQTV 71
RIL+LG GKT+++ L E +P TI +V V+Y V TV
Sbjct: 1 RILMLGLDGAGKTTILYKLKLGEVVTTIP------TIGFNV-------ETVEYKNVKFTV 47
Query: 72 -------------DELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDT---C 115
E L++ VVD + +R+ L L +
Sbjct: 48 WDVGGQDKIRPLWKHYYENTD-----GLIF-VVDSSDRERIEEA-KNELHKLLNEEELKG 100
Query: 116 LPIVLVGNKVDLVDYSTVE 134
P++++ NK DL T
Sbjct: 101 APLLILANKQDLPGALTES 119
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a wide
variety of presumed phage proteins.
Length = 201
Score = 33.8 bits (78), Expect = 0.15
Identities = 23/102 (22%), Positives = 43/102 (42%), Gaps = 23/102 (22%)
Query: 8 RRNVRILLLGDRHVGKTSLILSLVSEEFPELVPSKA-----EEITIPPDVTPEMVPTHIV 62
+N+++L+ G +GKTSL +L P K + T + V I
Sbjct: 1 TKNIKVLIYGPPGIGKTSLAKTL---------PPKTLFLDLDAGTTKVLSRGDNVD--IR 49
Query: 63 DYSEVDQTVDELTEEIQKAHVICLVYSVVDDASIDRLSSHWL 104
+ ++ +DEL E++ + + V+D +I +L L
Sbjct: 50 SWQDLRDFLDELAEDLAEYDTL-----VID--TITKLERLCL 84
>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 = 32.9 bits (76), Expect = 0.20
Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 7/66 (10%)
Query: 86 LVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGNKVDLVDY---STVESSAKTLKN 142
LVY + ++ + + WL LR+ D+ + I+LVGNK DL T E+ A KN
Sbjct: 81 LVYDITKKSTFENVE-RWLKELRD-HADSNIVIMLVGNKSDLRHLRAVPTEEAKAFAEKN 138
Query: 143 ISEMFY 148
+ +
Sbjct: 139 --GLSF 142
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase. The
Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that generally show sequence
conservation in the region between the Walker A and B
motifs (G1 and G3 box motifs), to the exclusion of other
GTPases. TrmE is ubiquitous in bacteria and is a
widespread mitochondrial protein in eukaryotes, but is
absent from archaea. The yeast member of TrmE family,
MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family.
Length = 161
Score = 32.6 bits (75), Expect = 0.24
Identities = 36/163 (22%), Positives = 59/163 (36%), Gaps = 44/163 (26%)
Query: 15 LLGDRHVGKTSLI-------LSLVSEEFPELVP-----SKAEEITIPPDVTPEMVPTHIV 62
+ G +VGK+SL+ + +VS +P +E + P ++ T +
Sbjct: 2 IFGRPNVGKSSLLNALLGQNVGIVSP-----IPGTTRDPVRKEWELLPLGPVVLIDTPGL 56
Query: 63 DYSEVDQT--VDELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVL 120
D V+E + +A ++ LV VD D L L + P++L
Sbjct: 57 DEEGGLGRERVEEARQVADRADLVLLV---VDS---DLTPVEEEAKLGL-LRERGKPVLL 109
Query: 121 VGNKVDLV------------------DYSTVESSAKTLKNISE 145
V NK+DLV D + SA + I E
Sbjct: 110 VLNKIDLVPESEEEELLRERKLELLPDLPVIAVSALPGEGIDE 152
>gnl|CDD|222177 pfam13499, EF_hand_5, EF-hand domain pair.
Length = 60
Score = 30.4 bits (69), Expect = 0.32
Identities = 16/63 (25%), Positives = 24/63 (38%), Gaps = 10/63 (15%)
Query: 303 YRFDKDGDGALSPEEQARLFSLCPPECPPWTDREMRAMVA-------TNSKGWITMQGFL 355
DKDGDG + EE +L TD E+ ++ + G I+ + FL
Sbjct: 1 KLLDKDGDGYIDVEELRKLLKAL---GLKLTDEEVEELIEADFNEIDKDGDGRISFEEFL 57
Query: 356 CYW 358
Sbjct: 58 EAM 60
Score = 28.1 bits (63), Expect = 2.2
Identities = 10/28 (35%), Positives = 14/28 (50%)
Query: 295 QQFLTTLFYRFDKDGDGALSPEEQARLF 322
++ + F DKDGDG +S EE
Sbjct: 33 EELIEADFNEIDKDGDGRISFEEFLEAM 60
>gnl|CDD|238008 cd00051, EFh, EF-hand, calcium binding motif; A diverse superfamily
of calcium sensors and calcium signal modulators; most
examples in this alignment model have 2 active canonical
EF hands. Ca2+ binding induces a conformational change
in the EF-hand motif, leading to the activation or
inactivation of target proteins. EF-hands tend to occur
in pairs or higher copy numbers.
Length = 63
Score = 30.2 bits (69), Expect = 0.35
Identities = 12/39 (30%), Positives = 17/39 (43%), Gaps = 3/39 (7%)
Query: 302 FYRFDKDGDGALSPEEQARLFSLCPPECPPWTDREMRAM 340
F FDKDGDG +S +E ++ E+ M
Sbjct: 6 FRLFDKDGDGTISADELKAALKSL---GEGLSEEEIDEM 41
Score = 28.7 bits (65), Expect = 1.3
Identities = 18/68 (26%), Positives = 28/68 (41%), Gaps = 7/68 (10%)
Query: 177 LTRIFKVCDLDNDNLLSDKELNAFQRRCFDAPLSRDSLEDVKIVIRKNINDGVSANNCIT 236
L F++ D D D +S EL + + S E++ +IR+ DG + I
Sbjct: 2 LREAFRLFDKDGDGTISADEL----KAALKSLGEGLSEEEIDEMIREVDKDG---DGKID 54
Query: 237 LNGFLFLH 244
FL L
Sbjct: 55 FEEFLELM 62
>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 = 31.5 bits (72), Expect = 0.47
Identities = 20/97 (20%), Positives = 34/97 (35%), Gaps = 14/97 (14%)
Query: 13 ILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPTHIVDYSEV-DQTV 71
+LL+G GK+ L L + L + + D T E + + V
Sbjct: 2 VLLVGPPGTGKSELAERLAA----ALSNRPVFYVQLTRDTTEEDL-KGRRNIDPGGASWV 56
Query: 72 D-ELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFL 107
D L ++ + L D+ I+R + L L
Sbjct: 57 DGPLVRAAREGEIAVL-----DE--INRANPDVLNSL 86
>gnl|CDD|222407 pfam13833, EF_hand_6, EF-hand domain pair.
Length = 53
Score = 29.4 bits (67), Expect = 0.52
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 298 LTTLFYRFDKDGDGALSPEE 317
+ LF FD DGDG +S EE
Sbjct: 26 VDILFREFDTDGDGKISFEE 45
>gnl|CDD|217424 pfam03205, MobB, Molybdopterin guanine dinucleotide synthesis
protein B. This protein contains a P-loop.
Length = 126
Score = 31.2 bits (71), Expect = 0.52
Identities = 16/76 (21%), Positives = 26/76 (34%), Gaps = 20/76 (26%)
Query: 413 HVIGNRSTGKTALCQSILR------------KHHDSSKTSITSPVECDPPYTINTTTVYG 460
V+G + +GKT L + +L KH D + I D P I +
Sbjct: 4 LVVGPKDSGKTTLIRKLLNYLKRRGYRVAVVKHLDHGQGEI------DKPGKI--AALSI 55
Query: 461 QEKYLVLKEILVRDEQ 476
+E + +E
Sbjct: 56 EEPADGPEGFHQEEEM 71
>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 = 32.0 bits (73), Expect = 0.59
Identities = 14/27 (51%), Positives = 19/27 (70%)
Query: 11 VRILLLGDRHVGKTSLILSLVSEEFPE 37
++I LLGD +GKTSL++ V EF E
Sbjct: 1 LKIGLLGDAQIGKTSLMVKYVEGEFDE 27
>gnl|CDD|133275 cd01873, RhoBTB, RhoBTB protein is an atypical member of the Rho
family of small GTPases. Members of the RhoBTB
subfamily of Rho GTPases are present in vertebrates,
Drosophila, and Dictyostelium. RhoBTB proteins are
characterized by a modular organization, consisting of a
GTPase domain, a proline rich region, a tandem of two
BTB (Broad-Complex, Tramtrack, and Bric a brac) domains,
and a C-terminal region of unknown function. RhoBTB
proteins may act as docking points for multiple
components participating in signal transduction
cascades. RhoBTB genes appeared upregulated in some
cancer cell lines, suggesting a participation of RhoBTB
proteins in the pathogenesis of particular tumors. Note
that the Dictyostelium RacA GTPase domain is more
closely related to Rac proteins than to RhoBTB proteins,
where RacA actually belongs. Thus, the Dictyostelium
RacA is not included here. Most Rho proteins contain a
lipid modification site at the C-terminus; however,
RhoBTB is one of few Rho subfamilies that lack this
feature.
Length = 195
Score = 31.9 bits (72), Expect = 0.64
Identities = 31/147 (21%), Positives = 60/147 (40%), Gaps = 47/147 (31%)
Query: 11 VRILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPTHI-----VDYS 65
++ +++GD VGKT LI + +A T+ +++ TH+ +D
Sbjct: 3 IKCVVVGDNAVGKTRLICA------------RACNKTL---TQYQLLATHVPTVWAIDQY 47
Query: 66 EVDQTVDELTEEIQ-------------------------KAHVICLVYSVVDDASIDRLS 100
V Q V E + ++ ++ V+ L +S+ S+ +
Sbjct: 48 RVCQEVLERSRDVVDGVSVSLRLWDTFGDHDKDRRFAYGRSDVVLLCFSIASPNSLRNVK 107
Query: 101 SHWLPFLRNCLVDTCLPIVLVGNKVDL 127
+ W P +R+ P++LVG K+DL
Sbjct: 108 TMWYPEIRHFCPRV--PVILVGCKLDL 132
>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 = 31.2 bits (71), Expect = 0.89
Identities = 15/35 (42%), Positives = 24/35 (68%)
Query: 8 RRNVRILLLGDRHVGKTSLILSLVSEEFPELVPSK 42
R+ VRILLLG + GKT+++ L SE+ + P++
Sbjct: 13 RQEVRILLLGLDNAGKTTILKQLASEDISHITPTQ 47
>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 = 31.0 bits (70), Expect = 0.99
Identities = 17/70 (24%), Positives = 29/70 (41%), Gaps = 6/70 (8%)
Query: 391 LVTREKQV----DLLKKQTTRNVYVCHVIGNRSTGKTALCQSILRKHHDSSKTSITSPVE 446
LV RE+++ D L++ + + G TGKT+L + +L E
Sbjct: 2 LVGREEELERLLDALRRARSGGPPSVLLTGPSGTGKTSLLRELLE--GLLVAAGKCDQAE 59
Query: 447 CDPPYTINTT 456
+PPY +
Sbjct: 60 RNPPYAFSQA 69
>gnl|CDD|206750 cd01857, HSR1_MMR1, A circularly permuted subfamily of the Ras
GTPases. Human HSR1 is localized to the human MHC class
I region and is highly homologous to a putative
GTP-binding protein, MMR1 from mouse. These proteins
represent a new subfamily of GTP-binding proteins that
has only eukaryote members. This subfamily shows a
circular permutation of the GTPase signature motifs so
that the C-terminal strands 5, 6, and 7 (strand 6
contains the G4 box with sequence NKXD) are relocated to
the N-terminus.
Length = 140
Score = 30.7 bits (70), Expect = 1.0
Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 112 VDTCLPIVLVGNKVDLVDYSTVESSAKTLK--NISEMFYYAQKA 153
VD VL+ NK DLV ++ A+ K I +F+ A
Sbjct: 39 VDPSKENVLLLNKADLVTEEQRKAWARYFKKEGIVVLFFSALNE 82
>gnl|CDD|205583 pfam13405, EF_hand_4, EF-hand domain.
Length = 30
Score = 27.9 bits (63), Expect = 1.0
Identities = 11/17 (64%), Positives = 12/17 (70%)
Query: 301 LFYRFDKDGDGALSPEE 317
F FDKDGDG +S EE
Sbjct: 5 AFKLFDKDGDGYISAEE 21
>gnl|CDD|227455 COG5126, FRQ1, Ca2+-binding protein (EF-Hand superfamily) [Signal
transduction mechanisms / Cytoskeleton / Cell division
and chromosome partitioning / General function
prediction only].
Length = 160
Score = 30.7 bits (70), Expect = 1.1
Identities = 40/161 (24%), Positives = 66/161 (40%), Gaps = 23/161 (14%)
Query: 168 ELTPECIKALTRIFKVCDLDNDNLLSDKELNAFQRRC-FDAPLSRDSLEDVKIVIRKNIN 226
+LT E I+ L F++ D D+D L+ EL R F+ + I K
Sbjct: 13 QLTEEQIQELKEAFQLFDRDSDGLIDRNELGKILRSLGFNPSEA---------EINKLFE 63
Query: 227 DGVSANNCITLNGFLFLHNLFMQRGRSHTTWTVLRK----FGYNEDLQISKEFLHPPLNI 282
+ + N + FL + ++ ++RG LR+ F + D IS L +
Sbjct: 64 EIDAGNETVDFPEFLTVMSVKLKRGDKEEE---LREAFKLFDKDHDGYISIGEL---RRV 117
Query: 283 PATCTAELSDKGQQFLTTLFYRFDKDGDGALSPEEQARLFS 323
+ LSD+ + L +D+DGDG + EE +L
Sbjct: 118 LKSLGERLSDEEVE---KLLKEYDEDGDGEIDYEEFKKLIK 155
>gnl|CDD|200946 pfam00036, efhand, EF hand. The EF-hands can be divided into two
classes: signaling proteins and buffering/transport
proteins. The first group is the largest and includes
the most well-known members of the family such as
calmodulin, troponin C and S100B. These proteins
typically undergo a calcium-dependent conformational
change which opens a target binding site. The latter
group is represented by calbindin D9k and do not undergo
calcium dependent conformational changes.
Length = 29
Score = 27.8 bits (63), Expect = 1.1
Identities = 11/17 (64%), Positives = 12/17 (70%)
Query: 301 LFYRFDKDGDGALSPEE 317
F FDKDGDG +S EE
Sbjct: 5 AFKEFDKDGDGKISFEE 21
>gnl|CDD|204523 pfam10591, SPARC_Ca_bdg, Secreted protein acidic and rich in
cysteine Ca binding region. The SPARC_Ca_bdg domain of
Secreted Protein Acidic and Rich in Cysteine is
responsible for the anti-spreading activity of human
urothelial cells. It is rich in alpha-helices. This
extracellular calcium-binding domain contains two
EF-hands that each coordinates one Ca2+ ion, forming a
helix-loop-helix structure that not only drives the
conformation of the protein but is also necessary for
biological activity. The anti-spreading activity was
dependent on the coordination of Ca2+ by a Glu residue
at the Z position of EF-hand 2.
Length = 112
Score = 30.0 bits (68), Expect = 1.2
Identities = 15/41 (36%), Positives = 18/41 (43%), Gaps = 12/41 (29%)
Query: 165 DKQELTP---------ECIKALTRIFKVCDLDNDNLLSDKE 196
+ EL P CIK FK CD D D L+S +E
Sbjct: 71 SRSELAPLRAPLVPMEHCIKPF---FKSCDADKDGLISLRE 108
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 30.8 bits (70), Expect = 1.5
Identities = 13/21 (61%), Positives = 16/21 (76%), Gaps = 2/21 (9%)
Query: 111 LVDTC--LPIVLVGNKVDLVD 129
+V C +PIVLVGNKVD+ D
Sbjct: 107 IVRVCENIPIVLVGNKVDVKD 127
>gnl|CDD|238155 cd00252, SPARC_EC, SPARC_EC; extracellular Ca2+ binding domain
(containing 2 EF-hand motifs) of SPARC and related
proteins (QR1, SC1/hevin, testican and tsc-36/FRP).
SPARC (BM-40) is a multifunctional glycoprotein, a
matricellular protein, that functions to regulate
cell-matrix interactions; binds to such proteins as
collagen and vitronectin and binds to endothelial cells
thus inhibiting cellular proliferation. The EC domain
interacts with a follistatin-like (FS) domain which
appears to stabilize Ca2+ binding. The two EF-hands
interact canonically but their conserved disulfide bonds
confer a tight association between the EF-hand pair and
an acid/amphiphilic N-terminal helix. Proposed active
form involves a Ca2+ dependent symmetric
homodimerization of EC-FS modules.
Length = 116
Score = 29.7 bits (67), Expect = 1.5
Identities = 17/41 (41%), Positives = 21/41 (51%), Gaps = 7/41 (17%)
Query: 156 HPMAPIYISDKQELTPECIKALTRIFKVCDLDNDNLLSDKE 196
H +API + D E CIK F+ CDLD D +S E
Sbjct: 68 HELAPIRL-DPNE---HCIK---PFFESCDLDKDGSISLDE 101
>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 = 30.3 bits (68), Expect = 1.8
Identities = 50/168 (29%), Positives = 70/168 (41%), Gaps = 47/168 (27%)
Query: 12 RILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEI-------TIPPDVTPEMVPTHIVDY 64
R+LL+GD VGKT L+ EF S I TI +V V I D
Sbjct: 2 RLLLIGDSGVGKTCLLCRFTDNEFH---SSHISTIGVDFKMKTI--EVDGIKVRIQIWDT 56
Query: 65 S--EVDQTVDELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLP----I 118
+ E QT+ + + ++A I LVY D S +R H + ++ + VD P
Sbjct: 57 AGQERYQTITK--QYYRRAQGIFLVY----DISSERSYQHIMKWVSD--VDEYAPEGVQK 108
Query: 119 VLVGNKVD-------------------LVDYSTVESSAKTLKNISEMF 147
+L+GNK D +D+ E+SA T KNI E F
Sbjct: 109 ILIGNKADEEQKRQVGDEQGNKLAKEYGMDF--FETSACTNKNIKESF 154
>gnl|CDD|221955 pfam13173, AAA_14, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily.
Length = 127
Score = 29.4 bits (67), Expect = 2.1
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 13 ILLLGDRHVGKTSLILSLVSEEFPE 37
I++ G R VGKT+L+L + E E
Sbjct: 5 IVITGPRQVGKTTLLLQFLKELLSE 29
>gnl|CDD|234743 PRK00390, leuS, leucyl-tRNA synthetase; Validated.
Length = 805
Score = 31.2 bits (72), Expect = 2.1
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 470 ILVRDEQLPVLLPVDVD 486
+ V +E LPV+LP DV
Sbjct: 441 VPVPEEDLPVVLPEDVV 457
>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 = 30.0 bits (67), Expect = 2.1
Identities = 30/119 (25%), Positives = 55/119 (46%), Gaps = 7/119 (5%)
Query: 12 RILLLGDRHVGKTSLILSLVSEEFPE-LVPSKAEEITIPPDVTPEMVPTHIVDYSEVD-- 68
+I+++GD GKT+L+ + FPE VP+ E T ++ + + + D S
Sbjct: 7 KIVVVGDSQCGKTALLHVFAKDCFPENYVPTVFENYTASFEIDTQRIELSLWDTSGSPYY 66
Query: 69 QTVDELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGNKVDL 127
V L+ A +IC + + ++D + W ++ +T ++LVG K DL
Sbjct: 67 DNVRPLSYPDSDAVLIC--FDISRPETLDSVLKKWKGEIQEFCPNT--KMLLVGCKSDL 121
>gnl|CDD|240051 cd04695, Nudix_Hydrolase_36, Members of the Nudix hydrolase
superfamily catalyze the hydrolysis of NUcleoside
DIphosphates linked to other moieties, X. Enzymes
belonging to this superfamily require a divalent cation,
such as Mg2+ or Mn2+, for their activity and contain a
highly conserved 23-residue nudix motif
(GX5EX7REUXEEXGU, where U = I, L or V), which functions
as a metal binding and catalytic site. Substrates of
nudix hydrolases include intact and oxidatively damaged
nucleoside triphosphates, dinucleoside polyphosphates,
nucleotide-sugars and dinucleotide enzymes. These
substrates are metabolites or cell signaling molecules
that require regulation during different stages of the
cell cycle or during periods of stress. In general, the
role of the nudix hydrolase is to sanitize the
nucleotide pools and to maintain cell viability, thereby
serving as surveillance & "house-cleaning" enzymes.
Substrate specificity is used to define families within
the superfamily. Differences in substrate specificity
are determined by the N-terminal extension or by
residues in variable loop regions. Mechanistically,
substrate hydrolysis occurs by a nucleophilic
substitution reaction, with variation in the numbers and
roles of divalent cations required.
Length = 131
Score = 29.3 bits (66), Expect = 2.3
Identities = 25/80 (31%), Positives = 37/80 (46%), Gaps = 11/80 (13%)
Query: 388 SGVLVTR---EKQVDLLKKQTTRNVYVCHVIGNRSTGKTALCQSILRKHHDSSKTSITSP 444
SGVL+ E +V LLK+ T + CHV G G+TA Q+ LR+ + +T I+ P
Sbjct: 3 SGVLLRSLDKETKVLLLKRVKTLGGFWCHVAGGVEAGETAW-QAALRELKE--ETGISLP 59
Query: 445 V-----ECDPPYTINTTTVY 459
+ Y N +
Sbjct: 60 ELYNADYLEQFYEANDNRIL 79
>gnl|CDD|133343 cd04143, Rhes_like, Ras homolog enriched in striatum (Rhes) and
activator of G-protein signaling 1 (Dexras1/AGS1). This
subfamily includes Rhes (Ras homolog enriched in
striatum) and Dexras1/AGS1 (activator of G-protein
signaling 1). These proteins are homologous, but exhibit
significant differences in tissue distribution and
subcellular localization. Rhes is found primarily in the
striatum of the brain, but is also expressed in other
areas of the brain, such as the cerebral cortex,
hippocampus, inferior colliculus, and cerebellum. Rhes
expression is controlled by thyroid hormones. In rat
PC12 cells, Rhes is farnesylated and localizes to the
plasma membrane. Rhes binds and activates PI3K, and
plays a role in coupling serpentine membrane receptors
with heterotrimeric G-protein signaling. Rhes has
recently been shown to be reduced under conditions of
dopamine supersensitivity and may play a role in
determining dopamine receptor sensitivity. Dexras1/AGS1
is a dexamethasone-induced Ras protein that is expressed
primarily in the brain, with low expression levels in
other tissues. Dexras1 localizes primarily to the
cytoplasm, and is a critical regulator of the circadian
master clock to photic and nonphotic input. Most Ras
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins.
Length = 247
Score = 30.5 bits (69), Expect = 2.4
Identities = 15/51 (29%), Positives = 19/51 (37%), Gaps = 18/51 (35%)
Query: 116 LPIVLVGNKVDLVDYSTV------------------ESSAKTLKNISEMFY 148
+P+V+ GNK D V E SAK N+ EMF
Sbjct: 114 IPMVICGNKADRDFPREVQRDEVEQLVGGDENCAYFEVSAKKNSNLDEMFR 164
>gnl|CDD|215874 pfam00350, Dynamin_N, Dynamin family.
Length = 168
Score = 29.9 bits (68), Expect = 2.4
Identities = 19/78 (24%), Positives = 31/78 (39%), Gaps = 12/78 (15%)
Query: 13 ILLLGDRHVGKTSLILSLVSEEFPELVPSKAEEIT-IP--------PDVTPEMVPTHIVD 63
I ++GD+ GK+S++ +L+ + P T P P P V D
Sbjct: 1 IAVVGDQSAGKSSVLNALLGRDIL---PRGPGPTTRRPLVLRLGEEPGAIPGAVKVEYKD 57
Query: 64 YSEVDQTVDELTEEIQKA 81
+ + EL EEI+
Sbjct: 58 GLKKFEDFSELREEIEDE 75
>gnl|CDD|133362 cd04162, Arl9_Arfrp2_like, Arf-like 9 (Arl9)/Arfrp2-like GTPase.
Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first
identified as part of the Human Cancer Genome Project.
It maps to chromosome 4q12 and is sometimes referred to
as Arfrp2 (Arf-related protein 2). This is a novel
subfamily identified in human cancers that is
uncharacterized to date.
Length = 164
Score = 29.7 bits (67), Expect = 2.5
Identities = 37/126 (29%), Positives = 53/126 (42%), Gaps = 27/126 (21%)
Query: 13 ILLLGDRHVGKTSLILSLVSEEFPE-LVPSKAEEITIPPDVTPEMVPTH--IVDYSEV-- 67
IL+LG GKTSL+ SL SE E +VP+ +PT I++ E+
Sbjct: 2 ILVLGLDGAGKTSLLHSLSSERSLESVVPTTGFNSV--------AIPTQDAIMELLEIGG 53
Query: 68 -DQTVDELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCL-----VDTCLPIVLV 121
+ + L++ VVD A +R LP R L LP+V++
Sbjct: 54 SQNLRKYWKRYLSGSQG--LIF-VVDSADSER-----LPLARQELHQLLQHPPDLPLVVL 105
Query: 122 GNKVDL 127
NK DL
Sbjct: 106 ANKQDL 111
>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 = 30.0 bits (67), Expect = 2.8
Identities = 35/128 (27%), Positives = 56/128 (43%), Gaps = 12/128 (9%)
Query: 12 RILLLGDRHVGKTSLILSLVSEEFPE-LVPSKAEEITIPPDVTPEMVPTHIVDYSEVD-- 68
+++L+GD GKT+++ L + +PE VP+ E T + + V + D S
Sbjct: 15 KLVLVGDVQCGKTAMLQVLAKDCYPETYVPTVFENYTACLETEEQRVELSLWDTSGSPYY 74
Query: 69 QTVDELTEEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTC--LPIVLVGNKVD 126
V L A ++C S + D W R ++D C I+L+G K D
Sbjct: 75 DNVRPLCYSDSDAVLLCFDISRPE--IFDSALKKW----RAEILDYCPSTRILLIGCKTD 128
Query: 127 L-VDYSTV 133
L D ST+
Sbjct: 129 LRTDLSTL 136
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 30.5 bits (70), Expect = 3.0
Identities = 20/79 (25%), Positives = 29/79 (36%), Gaps = 17/79 (21%)
Query: 76 EEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGNKVDLV------- 128
E I++A ++ LV DAS P+++V NK DL
Sbjct: 290 EAIEEADLVLLVL----DASEPLTEEDDEILEELKDK----PVIVVLNKADLTGEIDLEE 341
Query: 129 --DYSTVESSAKTLKNISE 145
+ SAKT + I E
Sbjct: 342 ENGKPVIRISAKTGEGIDE 360
>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 = 29.6 bits (67), Expect = 3.4
Identities = 8/30 (26%), Positives = 15/30 (50%)
Query: 114 TCLPIVLVGNKVDLVDYSTVESSAKTLKNI 143
LPI++ NK+D V + + +K +
Sbjct: 113 GGLPIIVAVNKIDRVGEEDFDEVLREIKEL 142
>gnl|CDD|238844 cd01709, RT_like_1, RT_like_1: A subfamily of reverse
transcriptases (RTs). An RT gene is usually indicative
of a mobile element such as a retrotransposon or
retrovirus. RTs occur in a variety of mobile elements,
including retrotransposons, retroviruses, group II
introns, bacterial msDNAs, hepadnaviruses, and
caulimoviruses. These elements can be divided into two
major groups. One group contains retroviruses and DNA
viruses whose propagation involves an RNA intermediate.
They are grouped together with transposable elements
containing long terminal repeats (LTRs). The other
group, also called poly(A)-type retrotransposons,
contain fungal mitochondrial introns and transposable
elements that lack LTRs.
Length = 346
Score = 30.0 bits (68), Expect = 3.9
Identities = 13/31 (41%), Positives = 16/31 (51%), Gaps = 2/31 (6%)
Query: 253 SHTT-WTVLRKFGYNED-LQISKEFLHPPLN 281
H+T VL+ FG E L K+FL PL
Sbjct: 37 PHSTILAVLKFFGVPEKWLDFFKKFLEAPLR 67
>gnl|CDD|238649 cd01328, FSL_SPARC, Follistatin-like SPARC (secreted protein,
acidic, and rich in cysteines) domain;
SPARC/BM-40/osteonectin is a multifunctional
glycoprotein which modulates cellular interaction with
the extracellular matrix by its binding to structural
matrix proteins such as collagen and vitronectin. The
protein it composed of an N-terminal acidic region, a
follistatin (FS) domain and an EF-hand calcium binding
domain. The FS domain consists of an N-terminal beta
hairpin (FOLN/EGF-like domain) and a small hydrophobic
core of alpha/beta structure (Kazal domain) and has five
disulfide bonds and a conserved N-glycosylation site.
The FSL_SPARC domain is a member of the superfamily of
kazal-like proteinase inhibitors and follistatin-like
proteins.
Length = 86
Score = 27.8 bits (62), Expect = 4.7
Identities = 12/35 (34%), Positives = 17/35 (48%), Gaps = 2/35 (5%)
Query: 171 PECIKALTRIFKVCDLDNDNLLSDKELNAFQRRCF 205
C + + KVC DN+ SD EL ++ RC
Sbjct: 27 DPCPEEVDDRRKVCTNDNETFDSDCEL--YRTRCL 59
>gnl|CDD|139913 PRK13853, PRK13853, type IV secretion system protein VirB4;
Provisional.
Length = 789
Score = 29.8 bits (67), Expect = 5.0
Identities = 13/35 (37%), Positives = 19/35 (54%), Gaps = 3/35 (8%)
Query: 287 TAELSDKGQQFLTTLFYRFDKDGDGALSPEEQARL 321
TA D ++++ L + DG G +SPEE RL
Sbjct: 501 TAASRDFLREWIVALI---ESDGRGGISPEENRRL 532
>gnl|CDD|180820 PRK07064, PRK07064, hypothetical protein; Provisional.
Length = 544
Score = 29.6 bits (67), Expect = 5.0
Identities = 14/44 (31%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 31 VSEEFPELVPSKAEEITIPPDVTPEMVPTHIVDYSEVDQTVDEL 74
VS E P + +A EI +P D+ P V D + V + + L
Sbjct: 159 VSVEIP--IDIQAAEIELPDDLAPVHVAVPEPDAAAVAELAERL 200
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes. TrmE
contains a GTPase domain that forms a canonical Ras-like
fold. It functions a molecular switch GTPase, and
apparently uses a conformational change associated with
GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 28.6 bits (65), Expect = 5.2
Identities = 21/89 (23%), Positives = 32/89 (35%), Gaps = 25/89 (28%)
Query: 76 EEIQKAHVICLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGNKVDLV------- 128
E I++A ++ LV DAS P+++V NK DL+
Sbjct: 78 EAIEEADLVLLVV----DASEGLDEEDLEILELPAKK----PVIVVLNKSDLLSDAEGIS 129
Query: 129 ---DYSTVESSAKT------LKN-ISEMF 147
+ SAKT LK + E+
Sbjct: 130 ELNGKPIIAISAKTGEGIDELKEALLELA 158
>gnl|CDD|233849 TIGR02401, trehalose_TreY, malto-oligosyltrehalose synthase. This
enzyme, formally named (1->4)-alpha-D-glucan
1-alpha-D-glucosylmutase, is the TreY enzyme of the
TreYZ pathway of trehalose biosynthesis, an alternative
to the OtsAB pathway. Trehalose may be incorporated into
more complex compounds but is best known as compatible
solute. It is one of the most effective osmoprotectants,
and unlike the various betaines does not require
nitrogen for its synthesis [Energy metabolism,
Biosynthesis and degradation of polysaccharides].
Length = 825
Score = 29.7 bits (67), Expect = 5.6
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 460 GQEKYLVLKEILVRDEQLPVLLPVD 484
G +YLV+++IL E LP PVD
Sbjct: 274 GPARYLVVEKILAPGEHLPADWPVD 298
>gnl|CDD|107273 cd06278, PBP1_LacI_like_2, Ligand-binding domain of uncharacterized
DNA-binding regulatory proteins that are members of the
LacI-GalR family of bacterial transcription repressors.
This group includes the ligand-binding domain of
uncharacterized DNA-binding regulatory proteins that are
members of the LacI-GalR family of bacterial
transcription repressors. The LacI-GalR family
repressors are composed of two functional domains: an
N-terminal HTH (helix-turn-helix) domain, which is
responsible for the DNA-binding specificity, and a
C-terminal ligand-binding domain, which is homologous to
the sugar-binding domain of ABC-type transport systems
that contain the type I periplasmic binding protein-like
fold. As also observed in the periplasmic binding
proteins, the C-terminal domain of the bacterial
transcription repressor undergoes a conformational
change upon ligand binding which in turn changes the DNA
binding affinity of the repressor.
Length = 266
Score = 29.1 bits (66), Expect = 5.8
Identities = 19/89 (21%), Positives = 31/89 (34%), Gaps = 26/89 (29%)
Query: 64 YSEVDQTVDELTEEIQKAHVICLVYSVVDDASIDR---------------LSSHWLPFLR 108
YSE+ ++ L+ +Q L+ + DD +D S L
Sbjct: 14 YSEL---LEALSRALQARGYQPLLINTDDDEDLDAALRQLLQYRVDGVIVTSGT----LS 66
Query: 109 NCLVDTCL----PIVLVGNKVDLVDYSTV 133
+ L + C P+VL+ VD V
Sbjct: 67 SELAEECRRNGIPVVLINRYVDGPGVDAV 95
>gnl|CDD|206748 cd01855, YqeH, Circularly permuted YqeH GTPase. YqeH is an
essential GTP-binding protein. Depletion of YqeH induces
an excess initiation of DNA replication, suggesting that
it negatively controls initiation of chromosome
replication. The YqeH subfamily is common in eukaryotes
and sporadically present in bacteria with probable
acquisition by plants from chloroplasts. Proteins of the
YqeH family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases.
Length = 191
Score = 28.8 bits (65), Expect = 6.4
Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 7/73 (9%)
Query: 85 CLVYSVVDDASIDRLSSHWLPFLRNCLVDTCLPIVLVGNKVDLVDYSTVESS-AKTLKN- 142
LV VVD D +P L L+ P++LVGNK+DL+ + + +K
Sbjct: 35 ALVVHVVD--IFD-FPGSLIPGLAE-LIGA-KPVILVGNKIDLLPKDVKPNRLKQWVKKR 89
Query: 143 ISEMFYYAQKAVL 155
+ + +L
Sbjct: 90 LKIGGLKIKDVIL 102
>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 = 28.7 bits (64), Expect = 6.6
Identities = 10/17 (58%), Positives = 15/17 (88%)
Query: 11 VRILLLGDRHVGKTSLI 27
V++L+LGD VGK+SL+
Sbjct: 1 VKVLVLGDSGVGKSSLV 17
>gnl|CDD|181028 PRK07559, PRK07559, 2'-deoxycytidine 5'-triphosphate deaminase;
Provisional.
Length = 365
Score = 29.1 bits (66), Expect = 6.8
Identities = 16/37 (43%), Positives = 19/37 (51%), Gaps = 4/37 (10%)
Query: 22 GKTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVP 58
G LIL EF L S+ E + +PPD EMVP
Sbjct: 244 GDGELILD--PGEFYILA-SR-EAVHVPPDYAAEMVP 276
>gnl|CDD|206676 cd01889, SelB_euk, SelB, the dedicated elongation factor for
delivery of selenocysteinyl-tRNA to the ribosome. SelB
is an elongation factor needed for the co-translational
incorporation of selenocysteine. Selenocysteine is coded
by a UGA stop codon in combination with a specific
downstream mRNA hairpin. In bacteria, the C-terminal
part of SelB recognizes this hairpin, while the
N-terminal part binds GTP and tRNA in analogy with
elongation factor Tu (EF-Tu). It specifically recognizes
the selenocysteine charged tRNAsec, which has a UCA
anticodon, in an EF-Tu like manner. This allows
insertion of selenocysteine at in-frame UGA stop codons.
In E. coli SelB binds GTP, selenocysteyl-tRNAsec and a
stem-loop structure immediately downstream of the UGA
codon (the SECIS sequence). The absence of active SelB
prevents the participation of selenocysteyl-tRNAsec in
translation. Archaeal and animal mechanisms of
selenocysteine incorporation are more complex. Although
the SECIS elements have different secondary structures
and conserved elements between archaea and eukaryotes,
they do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains eukaryotic SelBs and some from archaea.
Length = 192
Score = 28.5 bits (64), Expect = 6.9
Identities = 11/37 (29%), Positives = 19/37 (51%), Gaps = 3/37 (8%)
Query: 110 CLV---DTCLPIVLVGNKVDLVDYSTVESSAKTLKNI 143
CLV C P+++V NK+DL+ + + +K
Sbjct: 112 CLVIGELLCKPLIVVLNKIDLIPEEERKRKIEKMKKR 148
>gnl|CDD|236137 PRK07956, ligA, NAD-dependent DNA ligase LigA; Validated.
Length = 665
Score = 29.3 bits (67), Expect = 7.1
Identities = 19/66 (28%), Positives = 29/66 (43%), Gaps = 5/66 (7%)
Query: 16 LGDRHVG-KTSLILSLVSEEFPELVPSKAEEITIPPDVTPEMVPTHIVDYSEVD---QTV 71
LG RHVG K + L+ L + EE+ V + IV++ V+ + +
Sbjct: 514 LGIRHVGEKAAKALARHFGSLEALRAASEEELAAVEGVGEVVA-QSIVEFFAVEENRELI 572
Query: 72 DELTEE 77
DEL E
Sbjct: 573 DELLEA 578
>gnl|CDD|227254 COG4917, EutP, Ethanolamine utilization protein [Amino acid
transport and metabolism].
Length = 148
Score = 28.3 bits (63), Expect = 7.3
Identities = 20/102 (19%), Positives = 37/102 (36%), Gaps = 11/102 (10%)
Query: 414 VIGNRSTGKTALCQSILRKHHDSSKTSITSPVECDPPYTINTTTVYGQEKYLVLKEILVR 473
+G GKT L QS+ + + + T VE + I+T Y + ++
Sbjct: 6 FVGQVGCGKTTLFQSL---YGNDTLYKKTQAVEFNDKGDIDTPGEYFEHPRW-YHALITT 61
Query: 474 DEQLPVLLPVDVDCDK-------YFSTSKIPVMLVAGKSDMP 508
+ V++ V D + V+ V K+D+
Sbjct: 62 LQDADVIIYVHAANDPESRFPPGFLDIGVKKVIGVVTKADLA 103
>gnl|CDD|177661 PLN00023, PLN00023, GTP-binding protein; Provisional.
Length = 334
Score = 29.1 bits (65), Expect = 7.8
Identities = 10/17 (58%), Positives = 15/17 (88%)
Query: 11 VRILLLGDRHVGKTSLI 27
VR+L++GD VGK+SL+
Sbjct: 22 VRVLVVGDSGVGKSSLV 38
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 28.6 bits (64), Expect = 7.9
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 116 LPIVLVGNKVDLVD 129
+PIVL GNKVD+ +
Sbjct: 118 IPIVLCGNKVDVKN 131
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 28.3 bits (64), Expect = 8.0
Identities = 13/43 (30%), Positives = 23/43 (53%), Gaps = 3/43 (6%)
Query: 9 RNVRILLLGDRHVGKTSLILSLVSEEFPELVPSK---AEEITI 48
+ +RIL+LG + GKT+++ L E +P+ E +T
Sbjct: 13 KEMRILILGLDNAGKTTILYKLKLGEIVTTIPTIGFNVETVTY 55
>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 = 28.4 bits (64), Expect = 8.0
Identities = 15/61 (24%), Positives = 23/61 (37%), Gaps = 9/61 (14%)
Query: 494 SKIPVMLVAGKSDMPRAR----QDYLMQPDIFCETHKLSPAHSFSAAN--NDREVFVKLA 547
IP +L+A K D+ + R + + Q FC+ + SA N E L
Sbjct: 109 EPIPALLLANKCDLKKERLAKDPEQMDQ---FCKENGFIGWFETSAKENINIEEAMRFLV 165
Query: 548 T 548
Sbjct: 166 K 166
>gnl|CDD|217324 pfam03024, Folate_rec, Folate receptor family. This family
includes the folate receptor which binds to folate and
reduced folic acid derivatives and mediates delivery of
5-methyltetrahydrofolate to the interior of cells. These
proteins are attached to the membrane by a GPI-anchor.
The proteins contain 16 conserved cysteines that form
eight disulphide bridges.
Length = 166
Score = 28.2 bits (63), Expect = 8.4
Identities = 19/52 (36%), Positives = 25/52 (48%), Gaps = 5/52 (9%)
Query: 286 CTAELSDKGQQFLTTLFYRFDKDGDGALSPE-----EQARLFSLCPPECPPW 332
CTA S++ + + L Y F+ + G LSPE EQ F C P PW
Sbjct: 31 CTANTSEEAHRDPSILLYNFNWNHCGTLSPECERFFEQLECFYECSPNLGPW 82
>gnl|CDD|235476 PRK05454, PRK05454, glucosyltransferase MdoH; Provisional.
Length = 605
Score = 29.1 bits (66), Expect = 8.6
Identities = 19/87 (21%), Positives = 32/87 (36%), Gaps = 13/87 (14%)
Query: 527 LSPAHSFSAANNDREVFVKLATMAAFPRFHPAW----------MLFYPDLTSHFYM-FNL 575
L A + AA + E F +P++ P +LF P L + +
Sbjct: 415 LGTALALQAALTEPEYFQPRQLFPVWPQWDPELAIALFAATMVLLFLPKLLGLLLVLLDP 474
Query: 576 HDNKAY--LWKTGLSVAVITLLGIIFA 600
+A+ + LSV + TL + A
Sbjct: 475 KRRRAFGGALRLLLSVLLETLFSALLA 501
>gnl|CDD|217042 pfam02449, Glyco_hydro_42, Beta-galactosidase. This group of
beta-galactosidase enzymes belong to the glycosyl
hydrolase 42 family. The enzyme catalyzes the hydrolysis
of terminal, non-reducing terminal beta-D-galactosidase
residues.
Length = 376
Score = 28.8 bits (65), Expect = 9.3
Identities = 10/39 (25%), Positives = 15/39 (38%), Gaps = 2/39 (5%)
Query: 44 EEITIPPDVTPEMVPTHIVDYSE--VDQTVDELTEEIQK 80
+EI P P I+DY DQ ++ E +
Sbjct: 185 DEIEPPRPAPTTPNPGQILDYRRFSSDQLLEFYRAEREI 223
>gnl|CDD|218946 pfam06226, DUF1007, Protein of unknown function (DUF1007). Family
of conserved bacterial proteins with unknown function.
Length = 212
Score = 28.4 bits (64), Expect = 9.6
Identities = 11/25 (44%), Positives = 12/25 (48%)
Query: 297 FLTTLFYRFDKDGDGALSPEEQARL 321
F DK+ DG L PEE A L
Sbjct: 52 FSAYALQGLDKNKDGKLDPEELAEL 76
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
0.322 0.137 0.416
Gapped
Lambda K H
0.267 0.0830 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 30,956,949
Number of extensions: 3008178
Number of successful extensions: 3589
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3486
Number of HSP's successfully gapped: 173
Length of query: 608
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 505
Effective length of database: 6,369,140
Effective search space: 3216415700
Effective search space used: 3216415700
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: 62 (27.5 bits)