RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16673
(373 letters)
>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 = 97.2 bits (243), Expect = 3e-24
Identities = 33/80 (41%), Positives = 47/80 (58%), Gaps = 2/80 (2%)
Query: 145 VDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPI 204
+DILDT G +F AMR I F+LVYS T ESF+ +K E+I + +++PI
Sbjct: 49 LDILDTAGQEEFSAMRDQYIRNGDGFILVYSITSRESFEEIKNIREQILRVKDK-EDVPI 107
Query: 205 VVAGNKSDMTSHHRAVHLED 224
V+ GNK D+ + R V E+
Sbjct: 108 VLVGNKCDL-ENERQVSTEE 126
Score = 88.0 bits (219), Expect = 7e-21
Identities = 40/134 (29%), Positives = 53/134 (39%), Gaps = 34/134 (25%)
Query: 225 VDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQFPAM 284
+DILDT G +F AMR I F+LVYS T ESF+ +K E+I + P +
Sbjct: 49 LDILDTAGQEEFSAMRDQYIRNGDGFILVYSITSRESFEEIKNIREQILRVKDKEDVPIV 108
Query: 285 -----------RRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQLLECSAKD 333
R++S A + C F LE SAK
Sbjct: 109 LVGNKCDLENERQVSTEEGEAL-----------AEEWGCPF------------LETSAKT 145
Query: 334 NYNIKEVFRTFLTL 347
N NI E+F T +
Sbjct: 146 NINIDELFNTLVRE 159
Score = 65.6 bits (161), Expect = 6e-13
Identities = 37/134 (27%), Positives = 60/134 (44%), Gaps = 15/134 (11%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHVGAVTIK-EIPIVVAGNK- 69
+LV+LG GVGKS + RF+ + + Y T+ED Y + V T +I + AG +
Sbjct: 1 KLVVLGAGGVGKSALTIRFVSGEFVEEYDPTIEDSYRKQIVVDGETYTLDI-LDTAGQEE 59
Query: 70 -SDMTSHH-RAVH-------LEDVSEWLYCELPKLRYVIQSSSFGDEIPIVVAGNKSDMT 120
S M + R + + E+ +R I +++PIV+ GNK D+
Sbjct: 60 FSAMRDQYIRNGDGFILVYSITSRESFE--EIKNIREQILRVKDKEDVPIVLVGNKCDL- 116
Query: 121 SHHRAVHLEDVSEW 134
+ R V E+
Sbjct: 117 ENERQVSTEEGEAL 130
>gnl|CDD|206714 cd04147, Ras_dva, Ras - dorsal-ventral anterior localization
(Ras-dva) family. Ras-dva subfamily. Ras-dva (Ras -
dorsal-ventral anterior localization) subfamily consists
of a set of proteins characterized only in Xenopus
leavis, to date. In Xenopus Ras-dva expression is
activated by the transcription factor Otx2 and begins
during gastrulation throughout the anterior ectoderm.
Ras-dva expression is inhibited in the anterior neural
plate by factor Xanf1. Downregulation of Ras-dva results
in head development abnormalities through the inhibition
of several regulators of the anterior neural plate and
folds patterning, including Otx2, BF-1, Xag2, Pax6,
Slug, and Sox9. Downregulation of Ras-dva also
interferes with the FGF-8a signaling within the anterior
ectoderm. Most Ras proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins.
Length = 197
Score = 78.3 bits (193), Expect = 4e-17
Identities = 42/86 (48%), Positives = 52/86 (60%), Gaps = 4/86 (4%)
Query: 145 VDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPI 204
+DILDT G FPAMR+LSI AF LVYS ESF+ VK EEI E ++D + +PI
Sbjct: 49 IDILDTSGSYSFPAMRKLSIQNGDAFALVYSVDDPESFEEVKRLREEILEVKED-KFVPI 107
Query: 205 VVAGNKSDMTSHHRAVHLEDVDILDT 230
VV GNK D + + +E D L T
Sbjct: 108 VVVGNKIDSLAERQ---VEAADALST 130
Score = 72.6 bits (178), Expect = 5e-15
Identities = 47/132 (35%), Positives = 60/132 (45%), Gaps = 33/132 (25%)
Query: 225 VDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQFP-- 282
+DILDT G FPAMR+LSI AF LVYS ESF+ VK EEI E ++D P
Sbjct: 49 IDILDTSGSYSFPAMRKLSIQNGDAFALVYSVDDPESFEEVKRLREEILEVKEDKFVPIV 108
Query: 283 ---------AMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQLLECSAKD 333
A R++ A A + + E + +E SAKD
Sbjct: 109 VVGNKIDSLAERQVEAADALSTV----------------------ELDWNNGFVEASAKD 146
Query: 334 NYNIKEVFRTFL 345
N N+ EVF+ L
Sbjct: 147 NENVTEVFKELL 158
Score = 64.1 bits (156), Expect = 5e-12
Identities = 37/129 (28%), Positives = 66/129 (51%), Gaps = 8/129 (6%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHVGAVTIKEIPIVVAGNKSD 71
RLV +G GVGK+ +++RFL++T+ ++R TVE+L+S+++ V V + + +G+ S
Sbjct: 1 RLVFMGAAGVGKTALIQRFLYDTFEPKHRRTVEELHSKEYEVAGVKVTIDILDTSGSYSF 60
Query: 72 MTSHHRAVHLEDVSEWLYC--------ELPKLRYVIQSSSFGDEIPIVVAGNKSDMTSHH 123
++ D +Y E+ +LR I +PIVV GNK D +
Sbjct: 61 PAMRKLSIQNGDAFALVYSVDDPESFEEVKRLREEILEVKEDKFVPIVVVGNKIDSLAER 120
Query: 124 RAVHLEDVS 132
+ + +S
Sbjct: 121 QVEAADALS 129
>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 = 75.2 bits (185), Expect = 3e-16
Identities = 36/79 (45%), Positives = 50/79 (63%), Gaps = 2/79 (2%)
Query: 147 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQR-QDFQEIPIV 205
I DT G QFPAM+RLSI+ HAF+LVYS T +S + +K +E I E + + ++IPI+
Sbjct: 53 ITDTTGSHQFPAMQRLSISKGHAFILVYSITSKQSLEELKPIYELICEIKGNNLEKIPIM 112
Query: 206 VAGNKSDMTSHHRAVHLED 224
+ GNK D S R V +
Sbjct: 113 LVGNKCD-ESPSREVSSSE 130
Score = 65.2 bits (159), Expect = 1e-12
Identities = 43/136 (31%), Positives = 63/136 (46%), Gaps = 36/136 (26%)
Query: 227 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDF--QFPAM 284
I DT G QFPAM+RLSI+ HAF+LVYS T +S + +K +E I E + + + P M
Sbjct: 53 ITDTTGSHQFPAMQRLSISKGHAFILVYSITSKQSLEELKPIYELICEIKGNNLEKIPIM 112
Query: 285 -----------RRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQLLECSAKD 333
R +S + A + C F +E SAK
Sbjct: 113 LVGNKCDESPSREVSSSEGAALARTW-----------NCAF------------METSAKT 149
Query: 334 NYNIKEVFRTFLTLSQ 349
N+N++E+F+ L L +
Sbjct: 150 NHNVQELFQELLNLEK 165
Score = 40.6 bits (95), Expect = 4e-04
Identities = 38/146 (26%), Positives = 58/146 (39%), Gaps = 45/146 (30%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLY----SRDFHVGAVTIKEIPIVVAG 67
R+V+ G GVGKS ++ RF+ T+ + Y T+ED Y S + + I
Sbjct: 3 RVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIEDTYRQVISCSKSICTLQI--------- 53
Query: 68 NKSDMTSHHRAVHLEDVSEWLYCELPK-----LRYVIQSSSFGDE--------------- 107
+D T H+ ++ +S + K L Y I S +E
Sbjct: 54 --TDTTGSHQFPAMQRLS------ISKGHAFILVYSITSKQSLEELKPIYELICEIKGNN 105
Query: 108 ---IPIVVAGNKSDMTSHHRAVHLED 130
IPI++ GNK D S R V +
Sbjct: 106 LEKIPIMLVGNKCD-ESPSREVSSSE 130
>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 = 76.3 bits (188), Expect = 6e-16
Identities = 38/91 (41%), Positives = 54/91 (59%), Gaps = 8/91 (8%)
Query: 145 VDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQR-------Q 197
+DILDT G+ FPAMRRLSI T F+LV+S ESF+ V E+I E + +
Sbjct: 50 LDILDTSGNHPFPAMRRLSILTGDVFILVFSLDNRESFEEVCRLREQILETKSCLKNKTK 109
Query: 198 DFQEIPIVVAGNKSDMTSHHRAVHLEDVDIL 228
+ +IP+V+ GNK+D R V ++V+ L
Sbjct: 110 ENVKIPMVICGNKADRDF-PREVQRDEVEQL 139
Score = 70.9 bits (174), Expect = 5e-14
Identities = 43/137 (31%), Positives = 66/137 (48%), Gaps = 25/137 (18%)
Query: 225 VDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQFPAM 284
+DILDT G+ FPAMRRLSI T F+LV+S ESF+ V E+I E + +
Sbjct: 50 LDILDTSGNHPFPAMRRLSILTGDVFILVFSLDNRESFEEVCRLREQILETKS-----CL 104
Query: 285 RRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQD--FQLL---------ECSAKD 333
+ + +++ K + RE ++D QL+ E SAK
Sbjct: 105 KNKTKENVKIPMVICGN---------KADRDFPREVQRDEVEQLVGGDENCAYFEVSAKK 155
Query: 334 NYNIKEVFRTFLTLSQI 350
N N+ E+FR +L+++
Sbjct: 156 NSNLDEMFRALFSLAKL 172
Score = 47.4 bits (113), Expect = 3e-06
Identities = 37/147 (25%), Positives = 61/147 (41%), Gaps = 31/147 (21%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHV-GAV-------TIKEIPI 63
R+V+LG VGK+ I+ RFL + ++Y T+ED + + + + G V T P
Sbjct: 2 RMVVLGASKVGKTAIVSRFLGGRFEEQYTPTIEDFHRKLYSIRGEVYQLDILDTSGNHPF 61
Query: 64 VVAGNKSDMT--------------SHHRAVHL-EDVSEWLYCELPKLRYVIQSSSFGDEI 108
S +T S L E + E C K + ++ I
Sbjct: 62 PAMRRLSILTGDVFILVFSLDNRESFEEVCRLREQILETKSCLKNKTKENVK-------I 114
Query: 109 PIVVAGNKSDMTSHHRAVHLEDVSEWL 135
P+V+ GNK+D R V ++V + +
Sbjct: 115 PMVICGNKADRDF-PREVQRDEVEQLV 140
Score = 29.7 bits (67), Expect = 1.9
Identities = 29/119 (24%), Positives = 46/119 (38%), Gaps = 20/119 (16%)
Query: 60 EIPIVVAGNKSDMTSHHRAVHLEDVSEWLYCELPKLRYVIQSSSFGDEIP------IVVA 113
+IP+V+ GNK+D R V ++V + L Y S+ + +A
Sbjct: 113 KIPMVICGNKADRDF-PREVQRDEVEQ-LVGGDENCAYFEVSAKKNSNLDEMFRALFSLA 170
Query: 114 GNKSDMT-SHHRAVHLEDVSEWLYCELPK-----LRYVDILDTCGDLQFPAMRRLSIAT 166
++M+ S HR +S L K R D CG + P RR S+ +
Sbjct: 171 KLPNEMSPSLHR-----KISVQYGDALHKKSRGGSRKRKEGDACGAVA-PFARRPSVHS 223
>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 = 73.7 bits (182), Expect = 9e-16
Identities = 40/129 (31%), Positives = 57/129 (44%), Gaps = 19/129 (14%)
Query: 217 HRAVHLEDVDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQR 276
L DILDT G +F AMR + T FLLVYS T +SF+ + + E+I +
Sbjct: 47 GEVCLL---DILDTAGQEEFSAMRDQYMRTGEGFLLVYSITDRQSFEEIAKFREQILRVK 103
Query: 277 QDFQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDF--QLLECSAKDN 334
P +LV + LE+ + V EE +E + + LE SAK+
Sbjct: 104 DRDDVP------------IVLVGNKCDLENERVVS--TEEGKELARQWGCPFLETSAKER 149
Query: 335 YNIKEVFRT 343
N+ E F
Sbjct: 150 INVDEAFYD 158
Score = 72.2 bits (178), Expect = 4e-15
Identities = 33/79 (41%), Positives = 47/79 (59%), Gaps = 2/79 (2%)
Query: 146 DILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIV 205
DILDT G +F AMR + T FLLVYS T +SF+ + + E+I + D ++PIV
Sbjct: 53 DILDTAGQEEFSAMRDQYMRTGEGFLLVYSITDRQSFEEIAKFREQILRVK-DRDDVPIV 111
Query: 206 VAGNKSDMTSHHRAVHLED 224
+ GNK D+ + R V E+
Sbjct: 112 LVGNKCDL-ENERVVSTEE 129
Score = 46.0 bits (110), Expect = 4e-06
Identities = 17/38 (44%), Positives = 25/38 (65%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSR 49
+LV+LGG GVGKS + +F+ + D Y T+ED Y +
Sbjct: 4 KLVVLGGGGVGKSALTIQFVQGHFVDEYDPTIEDSYRK 41
>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 = 72.5 bits (179), Expect = 2e-15
Identities = 42/145 (28%), Positives = 60/145 (41%), Gaps = 21/145 (14%)
Query: 202 IPIVVAGNKS-DMTSHHRAVHLEDVDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLE 260
IP + + + + V L I DT G +F A+R L A FLLVY T +
Sbjct: 29 IPTIGVDFYTKTIEVDGKTVKL---QIWDTAGQERFRALRPLYYRGAQGFLLVYDITSRD 85
Query: 261 SFQSVKCYFEEIREQRQDFQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIRE- 319
SF++VK + EEI + P +LV + LE + V EE
Sbjct: 86 SFENVKKWLEEILRHADE-NVP------------IVLVGNKCDLEDQRVVS--TEEGEAL 130
Query: 320 -QRQDFQLLECSAKDNYNIKEVFRT 343
+ +E SAK N N++E F
Sbjct: 131 AKELGLPFMETSAKTNENVEEAFEE 155
Score = 68.7 bits (169), Expect = 6e-14
Identities = 32/79 (40%), Positives = 43/79 (54%), Gaps = 3/79 (3%)
Query: 146 DILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIV 205
I DT G +F A+R L A FLLVY T +SF++VK + EEI + +PIV
Sbjct: 51 QIWDTAGQERFRALRPLYYRGAQGFLLVYDITSRDSFENVKKWLEEILRHADE--NVPIV 108
Query: 206 VAGNKSDMTSHHRAVHLED 224
+ GNK D+ R V E+
Sbjct: 109 LVGNKCDL-EDQRVVSTEE 126
Score = 60.6 bits (148), Expect = 4e-11
Identities = 37/147 (25%), Positives = 60/147 (40%), Gaps = 41/147 (27%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRSTV-EDLYSRDFHVGAVTIK----------- 59
+LV++G GVGKS +L RF N + + Y T+ D Y++ V T+K
Sbjct: 1 KLVLVGDGGVGKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAGQER 60
Query: 60 ------------EIPIVVAGNKSDMTSHHRAVHLEDVSEWLYCELPKLRYVIQSSSFGDE 107
+ ++V D+TS E+V +W L ++ +
Sbjct: 61 FRALRPLYYRGAQGFLLV----YDITSR---DSFENVKKW----LEEILRH-----ADEN 104
Query: 108 IPIVVAGNKSDMTSHHRAVHLEDVSEW 134
+PIV+ GNK D+ R V E+
Sbjct: 105 VPIVLVGNKCDL-EDQRVVSTEEGEAL 130
>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 = 71.8 bits (177), Expect = 4e-15
Identities = 42/129 (32%), Positives = 58/129 (44%), Gaps = 19/129 (14%)
Query: 217 HRAVHLEDVDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQR 276
L DILDT G +F AMR + T FLLVYS T +SF+ +K + E+I +
Sbjct: 45 GEVCLL---DILDTAGQEEFSAMRDQYMRTGEGFLLVYSITDRQSFEEIKKFREQILRVK 101
Query: 277 QDFQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDF--QLLECSAKDN 334
P +LV + LES + V EE +E + + LE SAK+
Sbjct: 102 DRDDVP------------IVLVGNKCDLESERVVS--TEEGKELARQWGCPFLETSAKER 147
Query: 335 YNIKEVFRT 343
N+ E F
Sbjct: 148 VNVDEAFYD 156
Score = 70.3 bits (173), Expect = 2e-14
Identities = 34/79 (43%), Positives = 47/79 (59%), Gaps = 2/79 (2%)
Query: 146 DILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIV 205
DILDT G +F AMR + T FLLVYS T +SF+ +K + E+I + D ++PIV
Sbjct: 51 DILDTAGQEEFSAMRDQYMRTGEGFLLVYSITDRQSFEEIKKFREQILRVK-DRDDVPIV 109
Query: 206 VAGNKSDMTSHHRAVHLED 224
+ GNK D+ R V E+
Sbjct: 110 LVGNKCDL-ESERVVSTEE 127
Score = 45.6 bits (109), Expect = 6e-06
Identities = 38/136 (27%), Positives = 59/136 (43%), Gaps = 27/136 (19%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHVGAVTIKEIPIVV-----A 66
+LV+LG GVGKS + +F+ + D Y T+ED Y + + I ++ A
Sbjct: 2 KLVVLGSGGVGKSALTIQFIQGHFVDDYDPTIEDSYRKQ-----IEIDGEVCLLDILDTA 56
Query: 67 GNK--SDMTSHHRAVHLEDVSEWLYC----------ELPKLRYVIQSSSFGDEIPIVVAG 114
G + S M R ++ +L E+ K R I D++PIV+ G
Sbjct: 57 GQEEFSAM----RDQYMRTGEGFLLVYSITDRQSFEEIKKFREQILRVKDRDDVPIVLVG 112
Query: 115 NKSDMTSHHRAVHLED 130
NK D+ R V E+
Sbjct: 113 NKCDL-ESERVVSTEE 127
>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 = 62.8 bits (153), Expect = 6e-12
Identities = 25/70 (35%), Positives = 42/70 (60%), Gaps = 1/70 (1%)
Query: 146 DILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIV 205
DILDT G ++ AMR + T FL V++ +SF+ + Y E+I+ + D ++P+V
Sbjct: 52 DILDTAGQEEYSAMRDQYMRTGEGFLCVFAINSRKSFEDIHTYREQIKRVK-DSDDVPMV 110
Query: 206 VAGNKSDMTS 215
+ GNK D+ +
Sbjct: 111 LVGNKCDLAA 120
Score = 48.6 bits (116), Expect = 6e-07
Identities = 30/120 (25%), Positives = 55/120 (45%), Gaps = 17/120 (14%)
Query: 226 DILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQFPAMR 285
DILDT G ++ AMR + T FL V++ +SF+ + Y E+I+ + P
Sbjct: 52 DILDTAGQEEYSAMRDQYMRTGEGFLCVFAINSRKSFEDIHTYREQIKRVKDSDDVP--- 108
Query: 286 RLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQL--LECSAKDNYNIKEVFRT 343
+LV + L + ++V + ++ + + + +E SAK ++E F T
Sbjct: 109 ---------MVLVGNKCDLAA-RTVS--TRQGQDLAKSYGIPYIETSAKTRQGVEEAFYT 156
Score = 41.3 bits (97), Expect = 2e-04
Identities = 34/139 (24%), Positives = 59/139 (42%), Gaps = 28/139 (20%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHV-GAVTIKEIPIVVAGNK- 69
+LV++G GVGKS + + + N + D Y T+ED Y + + G + +I + AG +
Sbjct: 3 KLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDI-LDTAGQEE 61
Query: 70 -SDMTSHH--------------RAVHLEDVSEWLYCELPKLRYVIQSSSFGDEIPIVVAG 114
S M + ED+ + R I+ D++P+V+ G
Sbjct: 62 YSAMRDQYMRTGEGFLCVFAINSRKSFEDIHTY--------REQIKRVKDSDDVPMVLVG 113
Query: 115 NKSDMTSHHRAVHLEDVSE 133
NK D+ + R V +
Sbjct: 114 NKCDLAA--RTVSTRQGQD 130
>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 = 62.1 bits (152), Expect = 1e-11
Identities = 40/154 (25%), Positives = 72/154 (46%), Gaps = 39/154 (25%)
Query: 11 IRLVILGGQGVGKSCILKRFLFNTYSDRYRSTV-EDLYSRDFHVGAVTIKEIPIVV---A 66
++V++G GVGK+ +L RF+ N +S+ Y+ST+ D S+ V +K + + A
Sbjct: 1 FKIVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGVDFKSKTIEVDGKKVK---LQIWDTA 57
Query: 67 GN---KSDMTSHHRAVH-------------LEDVSEWLYCELPKLRYVIQSSSFGDEIPI 110
G +S +S++R H E++ +W L + + + IPI
Sbjct: 58 GQERFRSITSSYYRGAHGAILVYDVTNRESFENLDKW-------LNELKEYAP--PNIPI 108
Query: 111 VVAGNKSDMTSHHRAVHLEDVSEW------LYCE 138
++ GNKSD+ R V E+ ++ L+ E
Sbjct: 109 ILVGNKSDLED-ERQVSTEEAQQFAKENGLLFFE 141
Score = 60.2 bits (147), Expect = 6e-11
Identities = 27/79 (34%), Positives = 41/79 (51%), Gaps = 3/79 (3%)
Query: 147 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIVV 206
I DT G +F ++ AH +LVY T ESF+++ + E++E IPI++
Sbjct: 53 IWDTAGQERFRSITSSYYRGAHGAILVYDVTNRESFENLDKWLNELKEYAPP--NIPIIL 110
Query: 207 AGNKSDMTSHHRAVHLEDV 225
GNKSD+ R V E+
Sbjct: 111 VGNKSDLED-ERQVSTEEA 128
Score = 55.2 bits (134), Expect = 3e-09
Identities = 31/119 (26%), Positives = 50/119 (42%), Gaps = 17/119 (14%)
Query: 227 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQFPAMRR 286
I DT G +F ++ AH +LVY T ESF+++ + E++E P
Sbjct: 53 IWDTAGQERFRSITSSYYRGAHGAILVYDVTNRESFENLDKWLNELKEY-APPNIP---- 107
Query: 287 LSIATAHAFLLVYSTTCLESFQSVKCYFEEIRE--QRQDFQLLECSAKDNYNIKEVFRT 343
+LV + + LE + V EE ++ + E SAK N+ E F +
Sbjct: 108 --------IILVGNKSDLEDERQVS--TEEAQQFAKENGLLFFETSAKTGENVDEAFES 156
>gnl|CDD|206708 cd04136, Rap_like, Rap-like family consists of Rap1, Rap2 and RSR1.
The Rap subfamily consists of the Rap1, Rap2, and RSR1.
Rap subfamily proteins perform different cellular
functions, depending on the isoform and its subcellular
localization. For example, in rat salivary gland,
neutrophils, and platelets, Rap1 localizes to secretory
granules and is believed to regulate exocytosis or the
formation of secretory granules. Rap1 has also been
shown to localize in the Golgi of rat fibroblasts,
zymogen granules, plasma membrane, and microsomal
membrane of the pancreatic acini, as well as in the
endocytic compartment of skeletal muscle cells and
fibroblasts. Rap1 localizes in the nucleus of human
oropharyngeal squamous cell carcinomas (SCCs) and cell
lines. Rap1 plays a role in phagocytosis by controlling
the binding of adhesion receptors (typically integrins)
to their ligands. In yeast, Rap1 has been implicated in
multiple functions, including activation and silencing
of transcription and maintenance of telomeres. Rap2 is
involved in multiple functions, including activation of
c-Jun N-terminal kinase (JNK) to regulate the actin
cytoskeleton and activation of the Wnt/beta-catenin
signaling pathway in embryonic Xenopus. A number of
effector proteins for Rap2 have been identified,
including isoform 3 of the human mitogen-activated
protein kinase kinase kinase kinase 4 (MAP4K4) and
Traf2- and Nck-interacting kinase (TNIK), and the
RalGEFs RalGDS, RGL, and Rlf, which also interact with
Rap1 and Ras. RSR1 is the fungal homolog of Rap1 and
Rap2. In budding yeasts, it is involved in selecting a
site for bud growth, which directs the establishment of
cell polarization. The Rho family GTPase Cdc42 and its
GEF, Cdc24, then establish an axis of polarized growth.
It is believed that Cdc42 interacts directly with RSR1
in vivo. In filamentous fungi such as Ashbya gossypii,
RSR1 is a key regulator of polar growth in the hypha.
Most Ras proteins contain a lipid modification site at
the C-terminus, with a typical sequence motif CaaX,
where a = an aliphatic amino acid and X = any amino
acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 164
Score = 61.0 bits (148), Expect = 3e-11
Identities = 29/74 (39%), Positives = 44/74 (59%), Gaps = 7/74 (9%)
Query: 145 VDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQ---RQDFQE 201
++ILDT G QF AMR L I F LVYS T +SF ++ ++REQ +D ++
Sbjct: 51 LEILDTAGTEQFTAMRDLYIKNGQGFALVYSITAQQSFNDLQ----DLREQILRVKDTED 106
Query: 202 IPIVVAGNKSDMTS 215
+P+++ GNK D+
Sbjct: 107 VPMILVGNKCDLED 120
Score = 52.6 bits (126), Expect = 3e-08
Identities = 39/119 (32%), Positives = 56/119 (47%), Gaps = 13/119 (10%)
Query: 224 DVDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQFPA 283
++ILDT G QF AMR L I F LVYS T +SF ++ ++REQ
Sbjct: 50 MLEILDTAGTEQFTAMRDLYIKNGQGFALVYSITAQQSFNDLQ----DLREQ-------- 97
Query: 284 MRRLSIATAHAFLLVYSTTCLESFQSV-KCYFEEIREQRQDFQLLECSAKDNYNIKEVF 341
+ R+ +LV + LE + V K + + Q + LE SAK N+ E+F
Sbjct: 98 ILRVKDTEDVPMILVGNKCDLEDERVVSKEEGQNLARQWGNCPFLETSAKSKINVDEIF 156
Score = 47.9 bits (114), Expect = 1e-06
Identities = 36/141 (25%), Positives = 68/141 (48%), Gaps = 19/141 (13%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHV-GAVTIKEIPIVVAGNKS 70
+LV+LG GVGKS + +F+ + D+Y T+ED Y + V + EI + AG +
Sbjct: 3 KLVVLGSGGVGKSALTVQFVQGIFVDKYDPTIEDSYRKQIEVDCQQCMLEI-LDTAG--T 59
Query: 71 DMTSHHRAVHLED----------VSEWLYCELPKLRYVIQSSSFGDEIPIVVAGNKSDMT 120
+ + R +++++ ++ + +L LR I +++P+++ GNK D+
Sbjct: 60 EQFTAMRDLYIKNGQGFALVYSITAQQSFNDLQDLREQILRVKDTEDVPMILVGNKCDLE 119
Query: 121 SHHRAVHLED----VSEWLYC 137
R V E+ +W C
Sbjct: 120 D-ERVVSKEEGQNLARQWGNC 139
>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 = 60.6 bits (147), Expect = 4e-11
Identities = 28/77 (36%), Positives = 46/77 (59%), Gaps = 4/77 (5%)
Query: 145 VDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEI-REQRQDFQEIP 203
++ILDT G QF +MR L I F++VYS ++FQ +K ++I R + ++++P
Sbjct: 51 LEILDTAGTEQFASMRDLYIKNGQGFIVVYSLVNQQTFQDIKPMRDQIVRVKG--YEKVP 108
Query: 204 IVVAGNKSDMTSHHRAV 220
I++ GNK D+ R V
Sbjct: 109 IILVGNKVDL-ESEREV 124
Score = 55.6 bits (134), Expect = 3e-09
Identities = 32/117 (27%), Positives = 51/117 (43%), Gaps = 12/117 (10%)
Query: 225 VDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQFPAM 284
++ILDT G QF +MR L I F++VYS ++FQ +K ++I + + P
Sbjct: 51 LEILDTAGTEQFASMRDLYIKNGQGFIVVYSLVNQQTFQDIKPMRDQIVRVKGYEKVP-- 108
Query: 285 RRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQLLECSAKDNYNIKEVF 341
+LV + LES + V + +E SAK + E+F
Sbjct: 109 ----------IILVGNKVDLESEREVSSAEGRALAEEWGCPFMETSAKSKTMVNELF 155
Score = 47.5 bits (113), Expect = 1e-06
Identities = 32/126 (25%), Positives = 68/126 (53%), Gaps = 15/126 (11%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHV-GAVTIKEIPIVVAGNKS 70
++V+LG GVGKS + +F+ T+ ++Y T+ED Y ++ V + ++ EI + AG +
Sbjct: 3 KVVVLGSGGVGKSALTVQFVSGTFIEKYDPTIEDFYRKEIEVDSSPSVLEI-LDTAG--T 59
Query: 71 DMTSHHRAVHLED----------VSEWLYCELPKLRYVIQSSSFGDEIPIVVAGNKSDMT 120
+ + R +++++ V++ + ++ +R I +++PI++ GNK D+
Sbjct: 60 EQFASMRDLYIKNGQGFIVVYSLVNQQTFQDIKPMRDQIVRVKGYEKVPIILVGNKVDL- 118
Query: 121 SHHRAV 126
R V
Sbjct: 119 ESEREV 124
>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 = 60.6 bits (147), Expect = 4e-11
Identities = 35/83 (42%), Positives = 46/83 (55%), Gaps = 8/83 (9%)
Query: 145 VDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQR---QDFQE 201
++ILDT G QF AMR L I + FLLVYS T S + E+REQ +D
Sbjct: 51 LEILDTAGTEQFTAMRELYIKSGQGFLLVYSVTSEASLNEL----GELREQVLRIKDSDN 106
Query: 202 IPIVVAGNKSDMTSHHRAVHLED 224
+P+V+ GNK+D+ R V ED
Sbjct: 107 VPMVLVGNKADLED-DRQVSRED 128
Score = 50.6 bits (121), Expect = 1e-07
Identities = 38/130 (29%), Positives = 64/130 (49%), Gaps = 15/130 (11%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHV-GAVTIKEIPIVVAGNKS 70
++V+LG GVGKS + +F+ N + + Y T+ED Y + + G EI + AG +
Sbjct: 3 KIVVLGAGGVGKSALTVQFVQNVFIESYDPTIEDSYRKQVEIDGRQCDLEI-LDTAG--T 59
Query: 71 DMTSHHRAVHLED----------VSEWLYCELPKLRYVIQSSSFGDEIPIVVAGNKSDMT 120
+ + R ++++ SE EL +LR + D +P+V+ GNK+D+
Sbjct: 60 EQFTAMRELYIKSGQGFLLVYSVTSEASLNELGELREQVLRIKDSDNVPMVLVGNKADLE 119
Query: 121 SHHRAVHLED 130
R V ED
Sbjct: 120 D-DRQVSRED 128
Score = 47.5 bits (113), Expect = 2e-06
Identities = 25/52 (48%), Positives = 30/52 (57%), Gaps = 4/52 (7%)
Query: 224 DVDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQ 275
D++ILDT G QF AMR L I + FLLVYS T S + E+REQ
Sbjct: 50 DLEILDTAGTEQFTAMRELYIKSGQGFLLVYSVTSEASLNEL----GELREQ 97
Score = 37.1 bits (86), Expect = 0.006
Identities = 23/61 (37%), Positives = 28/61 (45%), Gaps = 11/61 (18%)
Query: 280 QFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQLLECSAKDNYNIKE 339
QF AMR L I + FLLVYS T S + E+REQ KD+ N+
Sbjct: 61 QFTAMRELYIKSGQGFLLVYSVTSEASLNEL----GELREQV-------LRIKDSDNVPM 109
Query: 340 V 340
V
Sbjct: 110 V 110
>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 = 60.5 bits (147), Expect = 5e-11
Identities = 32/79 (40%), Positives = 46/79 (58%), Gaps = 2/79 (2%)
Query: 146 DILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIV 205
DILDT G +F AMR + T FLLV+S T SF+ V + +I + +D E P++
Sbjct: 53 DILDTAGQEEFSAMREQYMRTGEGFLLVFSVTDRGSFEEVDKFHTQIL-RVKDRDEFPMI 111
Query: 206 VAGNKSDMTSHHRAVHLED 224
+ GNK+D+ H R V E+
Sbjct: 112 LVGNKADL-EHQRQVSREE 129
Score = 54.0 bits (130), Expect = 9e-09
Identities = 38/118 (32%), Positives = 56/118 (47%), Gaps = 16/118 (13%)
Query: 226 DILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQFPAMR 285
DILDT G +F AMR + T FLLV+S T SF+ V + +I + +FP
Sbjct: 53 DILDTAGQEEFSAMREQYMRTGEGFLLVFSVTDRGSFEEVDKFHTQILRVKDRDEFP--- 109
Query: 286 RLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQL--LECSAKDNYNIKEVF 341
+LV + LE + V EE +E + ++ +E SAKD N+ + F
Sbjct: 110 ---------MILVGNKADLEHQRQVS--REEGQELARQLKIPYIETSAKDRVNVDKAF 156
Score = 41.6 bits (98), Expect = 1e-04
Identities = 38/136 (27%), Positives = 63/136 (46%), Gaps = 15/136 (11%)
Query: 9 ERIRLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHV-GAVTIKEIPIVVAG 67
+LV++GG GVGKS + +F+ + + Y T+ED Y++ + G +I + AG
Sbjct: 1 PTYKLVVVGGGGVGKSALTIQFIQSYFVTDYDPTIEDSYTKQCEIDGQWARLDI-LDTAG 59
Query: 68 NK--SDMTSHH-RAVH-------LEDVSEWLYCELPKLRYVIQSSSFGDEIPIVVAGNKS 117
+ S M + R + D + E+ K I DE P+++ GNK+
Sbjct: 60 QEEFSAMREQYMRTGEGFLLVFSVTDRGS--FEEVDKFHTQILRVKDRDEFPMILVGNKA 117
Query: 118 DMTSHHRAVHLEDVSE 133
D+ H R V E+ E
Sbjct: 118 DL-EHQRQVSREEGQE 132
>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 = 60.0 bits (146), Expect = 6e-11
Identities = 31/82 (37%), Positives = 44/82 (53%), Gaps = 3/82 (3%)
Query: 145 VDILDTCGDLQFPAMRRL--SIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEI 202
++I DT G Q L S+ A F+LVYS T SF V + IRE ++ EI
Sbjct: 49 LEIQDTPGQQQNEDPESLERSLRWADGFVLVYSITDRSSFDVVSQLLQLIREIKKRDGEI 108
Query: 203 PIVVAGNKSDMTSHHRAVHLED 224
P+++ GNK+D+ H R V E+
Sbjct: 109 PVILVGNKADL-LHSRQVSTEE 129
Score = 41.9 bits (99), Expect = 1e-04
Identities = 35/135 (25%), Positives = 58/135 (42%), Gaps = 24/135 (17%)
Query: 13 LVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHVGAVTI--KEIPIVVAGNKS 70
+ +LG GVGKS + RFL + Y +E LYSR VTI +++ + + +
Sbjct: 2 IAVLGASGVGKSALTVRFLTKRFIGEYEPNLESLYSRQ-----VTIDGEQVSLEIQ-DTP 55
Query: 71 DMTSHHRAVHLEDVSEW------LY--CE-------LPKLRYVIQSSSFGDEIPIVVAGN 115
+ LE W +Y + L+ + + EIP+++ GN
Sbjct: 56 GQQQNEDPESLERSLRWADGFVLVYSITDRSSFDVVSQLLQLIREIKKRDGEIPVILVGN 115
Query: 116 KSDMTSHHRAVHLED 130
K+D+ H R V E+
Sbjct: 116 KADL-LHSRQVSTEE 129
Score = 40.0 bits (94), Expect = 5e-04
Identities = 24/70 (34%), Positives = 30/70 (42%), Gaps = 5/70 (7%)
Query: 210 KSDMTSHHRAVHLEDVDILDTCGDLQFPAMRRL--SIATAHAFLLVYSTTCLESFQSVKC 267
+T V LE I DT G Q L S+ A F+LVYS T SF V
Sbjct: 37 SRQVTIDGEQVSLE---IQDTPGQQQNEDPESLERSLRWADGFVLVYSITDRSSFDVVSQ 93
Query: 268 YFEEIREQRQ 277
+ IRE ++
Sbjct: 94 LLQLIREIKK 103
Score = 31.5 bits (72), Expect = 0.39
Identities = 13/31 (41%), Positives = 17/31 (54%)
Query: 292 AHAFLLVYSTTCLESFQSVKCYFEEIREQRQ 322
A F+LVYS T SF V + IRE ++
Sbjct: 73 ADGFVLVYSITDRSSFDVVSQLLQLIREIKK 103
>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 = 57.5 bits (139), Expect = 8e-10
Identities = 39/139 (28%), Positives = 66/139 (47%), Gaps = 16/139 (11%)
Query: 145 VDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEI-REQRQDFQEIP 203
+++LDT G ++ A+R I F+LVYS T +F+ V+ + E+I R + + ++P
Sbjct: 49 LEVLDTAGQEEYTALRDQWIREGEGFILVYSITSRSTFERVERFREQIQRVKDESAADVP 108
Query: 204 IVVAGNKSDMTSHHRAVHLEDVDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQ 263
I++ GNK D + R V E+ L RRL F+ + T + +
Sbjct: 109 IMIVGNKCDKV-YEREVSTEEGAAL----------ARRLGC----EFIEASAKTNVNVER 153
Query: 264 SVKCYFEEIREQRQDFQFP 282
+ +R+QRQ Q P
Sbjct: 154 AFYTLVRALRQQRQGGQGP 172
Score = 40.6 bits (95), Expect = 4e-04
Identities = 29/121 (23%), Positives = 53/121 (43%), Gaps = 14/121 (11%)
Query: 225 VDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQFPAM 284
+++LDT G ++ A+R I F+LVYS T +F+ V+ + E+I+
Sbjct: 49 LEVLDTAGQEEYTALRDQWIREGEGFILVYSITSRSTFERVERFREQIQ----------- 97
Query: 285 RRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDF--QLLECSAKDNYNIKEVFR 342
R+ +A ++ + + EE + + +E SAK N N++ F
Sbjct: 98 -RVKDESAADVPIMIVGNKCDKVYEREVSTEEGAALARRLGCEFIEASAKTNVNVERAFY 156
Query: 343 T 343
T
Sbjct: 157 T 157
Score = 34.8 bits (80), Expect = 0.032
Identities = 32/138 (23%), Positives = 55/138 (39%), Gaps = 29/138 (21%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHVGAVTIKEIPIVVAGNKSD 71
+LV+LG GVGK+ + + N + + Y T+ED Y + V + P ++ D
Sbjct: 1 KLVVLGDGGVGKTALTIQLCLNHFVETYDPTIEDSYRKQ-----VVVDGQPCML--EVLD 53
Query: 72 MTSHHRAVHLEDVSEWL-----------------YCELPKLRYVIQ--SSSFGDEIPIVV 112
L D +W+ + + + R IQ ++PI++
Sbjct: 54 TAGQEEYTALRD--QWIREGEGFILVYSITSRSTFERVERFREQIQRVKDESAADVPIMI 111
Query: 113 AGNKSDMTSHHRAVHLED 130
GNK D + R V E+
Sbjct: 112 VGNKCDKV-YEREVSTEE 128
Score = 30.6 bits (69), Expect = 0.96
Identities = 16/57 (28%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 267 CYFEEIREQRQDFQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQD 323
C E + Q+ ++ A+R I F+LVYS T +F+ V+ + E+I+ + +
Sbjct: 47 CMLEVLDTAGQE-EYTALRDQWIREGEGFILVYSITSRSTFERVERFREQIQRVKDE 102
>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 = 56.8 bits (137), Expect = 9e-10
Identities = 29/80 (36%), Positives = 45/80 (56%), Gaps = 2/80 (2%)
Query: 145 VDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPI 204
++ILDT G QF AMR L + F+LVYS T +F ++ E+I + D +++P+
Sbjct: 51 LEILDTAGTEQFTAMRDLYMKNGQGFVLVYSITAQSTFNDLQDLREQILRVK-DTEDVPM 109
Query: 205 VVAGNKSDMTSHHRAVHLED 224
++ GNK D+ R V E
Sbjct: 110 ILVGNKCDLED-ERVVGKEQ 128
Score = 51.4 bits (123), Expect = 7e-08
Identities = 36/131 (27%), Positives = 57/131 (43%), Gaps = 16/131 (12%)
Query: 215 SHHRAVHLED----VDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFE 270
S+ + V ++ ++ILDT G QF AMR L + F+LVYS T +F ++ E
Sbjct: 37 SYRKQVEVDGQQCMLEILDTAGTEQFTAMRDLYMKNGQGFVLVYSITAQSTFNDLQDLRE 96
Query: 271 EIREQRQDFQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQLLECS 330
+I + P +LV + LE + V + ++ LE S
Sbjct: 97 QILRVKDTEDVP------------MILVGNKCDLEDERVVGKEQGQNLARQWGCAFLETS 144
Query: 331 AKDNYNIKEVF 341
AK N+ E+F
Sbjct: 145 AKAKINVNEIF 155
Score = 43.3 bits (102), Expect = 4e-05
Identities = 34/130 (26%), Positives = 65/130 (50%), Gaps = 15/130 (11%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHV-GAVTIKEIPIVVAGNKS 70
+LV+LG GVGKS + +F+ + ++Y T+ED Y + V G + EI + AG +
Sbjct: 3 KLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDGQQCMLEI-LDTAG--T 59
Query: 71 DMTSHHRAVHLED----------VSEWLYCELPKLRYVIQSSSFGDEIPIVVAGNKSDMT 120
+ + R +++++ ++ + +L LR I +++P+++ GNK D+
Sbjct: 60 EQFTAMRDLYMKNGQGFVLVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLE 119
Query: 121 SHHRAVHLED 130
R V E
Sbjct: 120 D-ERVVGKEQ 128
>gnl|CDD|206712 cd04141, Rit_Rin_Ric, Ras-like protein in all tissues (Rit),
Ras-like protein in neurons (Rin) and Ras-related
protein which interacts with calmodulin (Ric). Rit
(Ras-like protein in all tissues), Rin (Ras-like protein
in neurons) and Ric (Ras-related protein which interacts
with calmodulin) form a subfamily with several unique
structural and functional characteristics. These
proteins all lack a the C-terminal CaaX lipid-binding
motif typical of Ras family proteins, and Rin and Ric
contain calmodulin-binding domains. Rin, which is
expressed only in neurons, induces neurite outgrowth in
rat pheochromocytoma cells through its association with
calmodulin and its activation of endogenous Rac/cdc42.
Rit, which is ubiquitously expressed in mammals,
inhibits growth-factor withdrawl-mediated apoptosis and
induces neurite extension in pheochromocytoma cells. Rit
and Rin are both able to form a ternary complex with
PAR6, a cell polarity-regulating protein, and Rac/cdc42.
This ternary complex is proposed to have physiological
function in processes such as tumorigenesis. Activated
Ric is likely to signal in parallel with the Ras pathway
or stimulate the Ras pathway at some upstream point, and
binding of calmodulin to Ric may negatively regulate Ric
activity.
Length = 172
Score = 56.4 bits (136), Expect = 1e-09
Identities = 27/75 (36%), Positives = 39/75 (52%), Gaps = 1/75 (1%)
Query: 144 YVDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIP 203
+DILDT G +F AMR + F++ YS T SFQ + E I R ++IP
Sbjct: 51 LLDILDTAGQAEFTAMRDQYMRCGEGFIICYSVTDRHSFQEASEFKELITRVRLT-EDIP 109
Query: 204 IVVAGNKSDMTSHHR 218
+V+ GNK D+ +
Sbjct: 110 LVLVGNKVDLEQQRQ 124
Score = 45.6 bits (108), Expect = 6e-06
Identities = 35/121 (28%), Positives = 48/121 (39%), Gaps = 16/121 (13%)
Query: 225 VDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQFPAM 284
+DILDT G +F AMR + F++ YS T SFQ + E I R P
Sbjct: 52 LDILDTAGQAEFTAMRDQYMRCGEGFIICYSVTDRHSFQEASEFKELITRVRLTEDIP-- 109
Query: 285 RRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQ--LLECSAKDNYNIKEVFR 342
+LV + LE + V EE R ++F E SA + I + F
Sbjct: 110 ----------LVLVGNKVDLEQQRQVTT--EEGRNLAREFNCPFFETSAALRFYIDDAFH 157
Query: 343 T 343
Sbjct: 158 G 158
Score = 40.6 bits (95), Expect = 3e-04
Identities = 29/127 (22%), Positives = 58/127 (45%), Gaps = 20/127 (15%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHVGAVTIKEIP----IVVAG 67
++V+LG GVGKS + +F+ +++ D + T+ED Y I P I+
Sbjct: 4 KIVMLGAGGVGKSAVTMQFISHSFPDYHDPTIEDAYKTQ-----ARIDNEPALLDILDTA 58
Query: 68 NKSDMTSHHRAVHLEDVSEWLYC----------ELPKLRYVIQSSSFGDEIPIVVAGNKS 117
+++ T+ R ++ ++ C E + + +I ++IP+V+ GNK
Sbjct: 59 GQAEFTA-MRDQYMRCGEGFIICYSVTDRHSFQEASEFKELITRVRLTEDIPLVLVGNKV 117
Query: 118 DMTSHHR 124
D+ +
Sbjct: 118 DLEQQRQ 124
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 56.0 bits (135), Expect = 3e-09
Identities = 27/71 (38%), Positives = 41/71 (57%), Gaps = 1/71 (1%)
Query: 145 VDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPI 204
+DILDT G ++ AMR + T FL VYS T SF+ + + E+I + D +P+
Sbjct: 55 LDILDTAGQEEYSAMRDQYMRTGQGFLCVYSITSRSSFEEIASFREQILRVK-DKDRVPM 113
Query: 205 VVAGNKSDMTS 215
++ GNK D+ S
Sbjct: 114 ILVGNKCDLDS 124
Score = 47.2 bits (112), Expect = 2e-06
Identities = 38/133 (28%), Positives = 60/133 (45%), Gaps = 20/133 (15%)
Query: 215 SHHRAVHLED----VDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFE 270
S+ + +++ +DILDT G ++ AMR + T FL VYS T SF+ + + E
Sbjct: 41 SYRKQCVIDEETCLLDILDTAGQEEYSAMRDQYMRTGQGFLCVYSITSRSSFEEIASFRE 100
Query: 271 EIREQRQDFQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDF--QLLE 328
+I + + P +LV + L+S + V E +E + F LE
Sbjct: 101 QILRVKDKDRVP------------MILVGNKCDLDSERQVST--GEGQELAKSFGIPFLE 146
Query: 329 CSAKDNYNIKEVF 341
SAK N+ E F
Sbjct: 147 TSAKQRVNVDEAF 159
Score = 44.1 bits (104), Expect = 3e-05
Identities = 33/120 (27%), Positives = 55/120 (45%), Gaps = 12/120 (10%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHVGAVTIKEIPIVVAGNKSD 71
+LV++GG GVGKS + +F+ N + D Y T+ED Y + + T + AG +
Sbjct: 7 KLVVVGGGGVGKSALTIQFIQNHFIDEYDPTIEDSYRKQCVIDEETCLLDILDTAGQ--E 64
Query: 72 MTSHHRAVHLEDVSEWL----------YCELPKLRYVIQSSSFGDEIPIVVAGNKSDMTS 121
S R ++ +L + E+ R I D +P+++ GNK D+ S
Sbjct: 65 EYSAMRDQYMRTGQGFLCVYSITSRSSFEEIASFREQILRVKDKDRVPMILVGNKCDLDS 124
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 54.8 bits (133), Expect = 4e-09
Identities = 37/142 (26%), Positives = 66/142 (46%), Gaps = 29/142 (20%)
Query: 11 IRLVILGGQGVGKSCILKRFLFNTYSDRYRSTVE-DLYSRDFHVGAVTIKEIPIV-VAGN 68
+++++G GVGKS +L RF +S++Y+ST+ D ++ V +K + I AG
Sbjct: 1 FKIILIGDSGVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIEVDGKRVK-LQIWDTAGQ 59
Query: 69 ---KSDMTSHHRAVH-------------LEDVSEWLYCELPKLRYVIQSSSFGDEIPIVV 112
+S +S++R E++ W L +LR +S + I++
Sbjct: 60 ERFRSITSSYYRGAVGALLVYDITNRESFENLENW----LKELR--EYASP---NVVIML 110
Query: 113 AGNKSDMTSHHRAVHLEDVSEW 134
GNKSD+ R V E+ +
Sbjct: 111 VGNKSDL-EEQRQVSREEAEAF 131
Score = 53.3 bits (129), Expect = 1e-08
Identities = 26/78 (33%), Positives = 41/78 (52%), Gaps = 3/78 (3%)
Query: 147 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIVV 206
I DT G +F ++ A LLVY T ESF++++ + +E+RE + I++
Sbjct: 53 IWDTAGQERFRSITSSYYRGAVGALLVYDITNRESFENLENWLKELREYAS--PNVVIML 110
Query: 207 AGNKSDMTSHHRAVHLED 224
GNKSD+ R V E+
Sbjct: 111 VGNKSDL-EEQRQVSREE 127
Score = 46.7 bits (112), Expect = 3e-06
Identities = 32/122 (26%), Positives = 49/122 (40%), Gaps = 17/122 (13%)
Query: 227 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQFPAMRR 286
I DT G +F ++ A LLVY T ESF++++ + +E+RE
Sbjct: 53 IWDTAGQERFRSITSSYYRGAVGALLVYDITNRESFENLENWLKELREYASP-NVV---- 107
Query: 287 LSIATAHAFLLVYSTTCLESFQSVKCYFEEIRE--QRQDFQLLECSAKDNYNIKEVFRTF 344
+LV + + LE + V EE + E SAK N N++E F
Sbjct: 108 --------IMLVGNKSDLEEQRQVS--REEAEAFAEEHGLPFFETSAKTNTNVEEAFEEL 157
Query: 345 LT 346
Sbjct: 158 AR 159
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 53.4 bits (128), Expect = 3e-08
Identities = 29/133 (21%), Positives = 56/133 (42%), Gaps = 25/133 (18%)
Query: 8 NERIRLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLY-SRDFHVGAVTIKEIPIVVA 66
+ ++V+LG GVGK+ +L R + + + + Y T+ +L ++ IK A
Sbjct: 3 MKEFKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTA 62
Query: 67 GN---KSDMTSHHR-------------AVHLEDVSEWLYCELPKLRYVIQSSSFGDEIPI 110
G +S ++R ++++E EL +L D++PI
Sbjct: 63 GQEEYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELA--------PDDVPI 114
Query: 111 VVAGNKSDMTSHH 123
++ GNK D+
Sbjct: 115 LLVGNKIDLFDEQ 127
Score = 40.7 bits (95), Expect = 5e-04
Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 147 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLES-FQSVKCYFEEIREQRQDFQEIPIV 205
+ DT G ++ ++R A+ L+VY +T ES + + + EE+RE D ++PI+
Sbjct: 58 LWDTAGQEEYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPD--DVPIL 115
Query: 206 VAGNKSDMTSHH 217
+ GNK D+
Sbjct: 116 LVGNKIDLFDEQ 127
Score = 28.0 bits (62), Expect = 7.6
Identities = 32/149 (21%), Positives = 54/149 (36%), Gaps = 20/149 (13%)
Query: 224 DVDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLES-FQSVKCYFEEIREQRQDFQFP 282
+ + DT G ++ ++R A+ L+VY +T ES + + + EE+RE D P
Sbjct: 55 KLQLWDTAGQEEYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPD-DVP 113
Query: 283 --------AMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQLLECSAK-- 332
+ ++ + L E LLE SAK
Sbjct: 114 ILLVGNKIDLFDEQSSSEEILNQLNREVVLLVLAPKAVLPEVAN-----PALLETSAKSL 168
Query: 333 DNYNIKEVFRTFLTLSQILTTNGDENSLK 361
N+ E+ F L + L ++ LK
Sbjct: 169 TGPNVNEL---FKELLRKLLEEIEKLVLK 194
>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 = 52.2 bits (126), Expect = 3e-08
Identities = 25/80 (31%), Positives = 42/80 (52%), Gaps = 3/80 (3%)
Query: 147 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIVV 206
I DT G ++ A+ + A +LVY T +SFQ VK + +E+++ R + I +V+
Sbjct: 53 IWDTAGQERYHALGPIYYRDADGAILVYDITDADSFQKVKKWIKELKQMRGN--NISLVI 110
Query: 207 AGNKSDMTSHHRAVHLEDVD 226
GNK D+ R V + +
Sbjct: 111 VGNKIDLER-QRVVSKSEAE 129
Score = 46.1 bits (110), Expect = 4e-06
Identities = 32/147 (21%), Positives = 65/147 (44%), Gaps = 39/147 (26%)
Query: 11 IRLVILGGQGVGKSCILKRFLFNTYSDRYRSTVED-LYSRDFHVGAVTIK-EI------- 61
++V+LG VGK+ ++ R++ N +++++ ST + + + ++G I I
Sbjct: 1 FKVVLLGEGRVGKTSLVLRYVENKFNEKHESTTQASFFQKTVNIGGKRIDLAIWDTAGQE 60
Query: 62 ------PI--------VVAGNKSDMTSHHRAVHLEDVSEWLYCELPKLRYVIQSSSFGDE 107
PI ++ + +D S + V +W+ EL ++R G+
Sbjct: 61 RYHALGPIYYRDADGAILVYDITDADS------FQKVKKWIK-ELKQMR--------GNN 105
Query: 108 IPIVVAGNKSDMTSHHRAVHLEDVSEW 134
I +V+ GNK D+ R V + E+
Sbjct: 106 ISLVIVGNKIDLER-QRVVSKSEAEEY 131
Score = 34.5 bits (80), Expect = 0.039
Identities = 33/119 (27%), Positives = 56/119 (47%), Gaps = 15/119 (12%)
Query: 224 DVDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQFPA 283
D+ I DT G ++ A+ + A +LVY T +SFQ VK + +E+++ R +
Sbjct: 50 DLAIWDTAGQERYHALGPIYYRDADGAILVYDITDADSFQKVKKWIKELKQMRGN----- 104
Query: 284 MRRLSIATAHAFLLVYSTTCLESFQSV-KCYFEEIREQRQDFQLLECSAKDNYNIKEVF 341
+I + ++V + LE + V K EE + + E SAK I+E+F
Sbjct: 105 ----NI----SLVIVGNKIDLERQRVVSKSEAEEYAKS-VGAKHFETSAKTGKGIEELF 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 = 52.2 bits (126), Expect = 4e-08
Identities = 26/80 (32%), Positives = 46/80 (57%), Gaps = 2/80 (2%)
Query: 145 VDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPI 204
++I+DT G ++ + + H ++LVYS T +SF+ VK +++I + + +PI
Sbjct: 51 LEIVDTAGQDEYSILPQKYSIGIHGYILVYSVTSRKSFEVVKVIYDKILDMLGK-ESVPI 109
Query: 205 VVAGNKSDMTSHHRAVHLED 224
V+ GNKSD+ R V E+
Sbjct: 110 VLVGNKSDLHM-ERQVSAEE 128
Score = 51.9 bits (125), Expect = 5e-08
Identities = 31/137 (22%), Positives = 59/137 (43%), Gaps = 16/137 (11%)
Query: 224 DVDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQFPA 283
++I+DT G ++ + + H ++LVYS T +SF+ VK +++I + P
Sbjct: 50 HLEIVDTAGQDEYSILPQKYSIGIHGYILVYSVTSRKSFEVVKVIYDKILDMLGKESVPI 109
Query: 284 MRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIRE--QRQDFQLLECSAKDNYNIKEVF 341
+ LV + + L + V EE ++ + LE SAK+N N++E F
Sbjct: 110 V------------LVGNKSDLHMERQVSA--EEGKKLAESWGAAFLESSAKENENVEEAF 155
Query: 342 RTFLTLSQILTTNGDEN 358
+ + +
Sbjct: 156 ELLIEEIEKVENPLPPG 172
Score = 41.5 bits (98), Expect = 2e-04
Identities = 34/142 (23%), Positives = 61/142 (42%), Gaps = 39/142 (27%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSR-------DFHVGAVTIKEIPIV 64
++ +LG + VGKS + +F+ + + Y T+E+ +S+ ++H+ EI +
Sbjct: 3 KIAVLGSRSVGKSSLTVQFVEGHFVESYYPTIENTFSKIITYKGQEYHL------EI-VD 55
Query: 65 VAGNKSDMTSHHRAVHLEDVSEWLYCELPKLRYVIQS-SSF---------------GDEI 108
AG D S + + ++ L Y + S SF + +
Sbjct: 56 TAGQ--DEYSILPQKYSIGIHGYI------LVYSVTSRKSFEVVKVIYDKILDMLGKESV 107
Query: 109 PIVVAGNKSDMTSHHRAVHLED 130
PIV+ GNKSD+ R V E+
Sbjct: 108 PIVLVGNKSDLHM-ERQVSAEE 128
>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 = 50.9 bits (122), Expect = 4e-08
Identities = 22/96 (22%), Positives = 36/96 (37%), Gaps = 7/96 (7%)
Query: 115 NKSDMTSHHRAVHLEDVSEWLYCELPKLRYVDILDTCGDLQFPAMRRLSIATAHAFLLVY 174
++ AV L + ++I D G + + + A A LLVY
Sbjct: 27 EPLEIQGDTLAVDT------LEVDGDT-GLLNIWDFGGREELKFEHIIFMKWADAILLVY 79
Query: 175 STTCLESFQSVKCYFEEIREQRQDFQEIPIVVAGNK 210
T ES V + R+ +IP+++ GNK
Sbjct: 80 DLTDRESLNEVSRLIAWLPNLRKLGGKIPVILVGNK 115
Score = 37.0 bits (86), Expect = 0.002
Identities = 18/75 (24%), Positives = 25/75 (33%), Gaps = 7/75 (9%)
Query: 209 NKSDMTSHHRAVHLEDVD-------ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLES 261
++ AV +VD I D G + + + A A LLVY T ES
Sbjct: 27 EPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREELKFEHIIFMKWADAILLVYDLTDRES 86
Query: 262 FQSVKCYFEEIREQR 276
V + R
Sbjct: 87 LNEVSRLIAWLPNLR 101
Score = 36.6 bits (85), Expect = 0.003
Identities = 27/122 (22%), Positives = 43/122 (35%), Gaps = 24/122 (19%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRSTVED-LYSRDFHVGAVTIKEIPIVVAG--- 67
++V++G +G GKS +L + + + D L V T G
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREE 60
Query: 68 ---------NKSD----MTSHHRAVHLEDVSEWLYCELPKLRYVIQSSSFGDEIPIVVAG 114
+D + L +VS L LP LR G +IP+++ G
Sbjct: 61 LKFEHIIFMKWADAILLVYDLTDRESLNEVSR-LIAWLPNLR------KLGGKIPVILVG 113
Query: 115 NK 116
NK
Sbjct: 114 NK 115
Score = 32.0 bits (73), Expect = 0.15
Identities = 12/52 (23%), Positives = 17/52 (32%)
Query: 270 EEIREQRQDFQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQR 321
I + + + + A A LLVY T ES V + R
Sbjct: 50 LNIWDFGGREELKFEHIIFMKWADAILLVYDLTDRESLNEVSRLIAWLPNLR 101
>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 = 51.7 bits (124), Expect = 5e-08
Identities = 21/78 (26%), Positives = 32/78 (41%), Gaps = 9/78 (11%)
Query: 141 KLRYVDILDTCG-----DLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQ 195
+ ++DT G L + RL + A LLV +T ES + K +
Sbjct: 45 GKVKLVLVDTPGLDEFGGLGREELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLRK 104
Query: 196 RQDFQEIPIVVAGNKSDM 213
IPI++ GNK D+
Sbjct: 105 E----GIPIILVGNKIDL 118
Score = 48.2 bits (115), Expect = 8e-07
Identities = 25/129 (19%), Positives = 41/129 (31%), Gaps = 21/129 (16%)
Query: 221 HLEDVDILDTCG-----DLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQ 275
+ ++DT G L + RL + A LLV +T ES + K +
Sbjct: 45 GKVKLVLVDTPGLDEFGGLGREELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLRK 104
Query: 276 RQDFQFPAMRRLSIATAHAFLLVYSTT-CLESFQSVKCYFEEIREQRQDFQLLECSAKDN 334
+LV + LE + + E + + E SAK
Sbjct: 105 EG---------------IPIILVGNKIDLLEEREVEELLRLEELAKILGVPVFEVSAKTG 149
Query: 335 YNIKEVFRT 343
+ E+F
Sbjct: 150 EGVDELFEK 158
Score = 38.6 bits (90), Expect = 0.002
Identities = 32/157 (20%), Positives = 55/157 (35%), Gaps = 24/157 (15%)
Query: 14 VILGGQGVGKSCILKRFL---FNTYSDRYRSTVEDLYSRDFHVGAVTIKEIPIV---VAG 67
V++G GVGKS +L L SD +T + D +V + ++ +V G
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRD----PDVYVKELDKGKVKLVLVDTPG 56
Query: 68 --NKSDMTSHHRA----------VHLEDVSEWLYCELPKLRYVIQSSSFGDEIPIVVAGN 115
+ A + + D ++ E KL + + + IPI++ GN
Sbjct: 57 LDEFGGLGREELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLR--KEGIPIILVGN 114
Query: 116 KSDMTSHHRAVHLEDVSEWLYCELPKLRYVDILDTCG 152
K D+ L + E + V G
Sbjct: 115 KIDLLEEREVEELLRLEELAKILGVPVFEVSAKTGEG 151
>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 = 5e-07
Identities = 43/148 (29%), Positives = 63/148 (42%), Gaps = 41/148 (27%)
Query: 10 RIRLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLY-SRDFHVGAVTIK-EI------ 61
+ +LV+LG VGKS I+ RF+ N +S+ ST+ + ++ ++ T+K EI
Sbjct: 1 QFKLVLLGDSSVGKSSIVLRFVKNEFSENQESTIGAAFLTQTVNLDDTTVKFEIWDTAGQ 60
Query: 62 -------P---------IVVAGNKSDMTSHHRAVHLEDVSEWLYCELPKLRYVIQSSSFG 105
P IVV D+TS E W+ EL Q
Sbjct: 61 ERYRSLAPMYYRGAAAAIVVY----DITSEES---FEKAKSWVK-EL-------QEHG-P 104
Query: 106 DEIPIVVAGNKSDMTSHHRAVHLEDVSE 133
I I +AGNK+D+ S R V E+ E
Sbjct: 105 PNIVIALAGNKADLES-KRQVSTEEAQE 131
Score = 41.8 bits (99), Expect = 1e-04
Identities = 26/80 (32%), Positives = 43/80 (53%), Gaps = 3/80 (3%)
Query: 146 DILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIV 205
+I DT G ++ ++ + A A ++VY T ESF+ K + +E++E I I
Sbjct: 53 EIWDTAGQERYRSLAPMYYRGAAAAIVVYDITSEESFEKAKSWVKELQEHGP--PNIVIA 110
Query: 206 VAGNKSDMTSHHRAVHLEDV 225
+AGNK+D+ S R V E+
Sbjct: 111 LAGNKADLES-KRQVSTEEA 129
Score = 37.5 bits (88), Expect = 0.004
Identities = 37/128 (28%), Positives = 59/128 (46%), Gaps = 21/128 (16%)
Query: 220 VHLEDV----DILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQ 275
V+L+D +I DT G ++ ++ + A A ++VY T ESF+ K + +E++E
Sbjct: 43 VNLDDTTVKFEIWDTAGQERYRSLAPMYYRGAAAAIVVYDITSEESFEKAKSWVKELQEH 102
Query: 276 RQDFQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQLL--ECSAKD 333
+I A L + LES + V EE +E + LL E SAK
Sbjct: 103 GPP---------NIVIA----LAGNKADLESKRQVS--TEEAQEYADENGLLFMETSAKT 147
Query: 334 NYNIKEVF 341
N+ E+F
Sbjct: 148 GENVNELF 155
>gnl|CDD|206680 cd01893, Miro1, Mitochondrial Rho family 1 (Miro1), N-terminal.
Miro1 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the N-terminal
GTPase domain of Miro proteins. These atypical Rho
GTPases have roles in mitochondrial homeostasis and
apoptosis. Most Rho proteins contain a lipid
modification site at the C-terminus; however, Miro is
one of few Rho subfamilies that lack this feature.
Length = 168
Score = 48.5 bits (116), Expect = 8e-07
Identities = 21/79 (26%), Positives = 36/79 (45%), Gaps = 2/79 (2%)
Query: 147 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIVV 206
I+DT Q A I A+ LVYS + + ++ + + R+ ++PI++
Sbjct: 53 IVDTSSRPQDRANLAAEIRKANVICLVYSVDRPSTLERIRTKW--LPLIRRLGVKVPIIL 110
Query: 207 AGNKSDMTSHHRAVHLEDV 225
GNKSD+ LE+
Sbjct: 111 VGNKSDLRDGSSQAGLEEE 129
Score = 37.7 bits (88), Expect = 0.003
Identities = 32/156 (20%), Positives = 58/156 (37%), Gaps = 46/156 (29%)
Query: 11 IRLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHVGAVTIKEIPIVVAGNKS 70
+R+V++G +GVGKS ++ + + + + + +TI +
Sbjct: 3 VRIVLIGDEGVGKSSLIMSLVSEEFPENVPRVLPE----------ITIP----------A 42
Query: 71 DMTSHHRAVHLEDVS------EWLYCELPK-----LRY-VIQSSSF-------------- 104
D+T + D S L E+ K L Y V + S+
Sbjct: 43 DVTPERVPTTIVDTSSRPQDRANLAAEIRKANVICLVYSVDRPSTLERIRTKWLPLIRRL 102
Query: 105 GDEIPIVVAGNKSDMTSHHRAVHLEDVSEWLYCELP 140
G ++PI++ GNKSD+ LE+ + E
Sbjct: 103 GVKVPIILVGNKSDLRDGSSQAGLEEEMLPIMNEFR 138
Score = 37.7 bits (88), Expect = 0.003
Identities = 23/108 (21%), Positives = 39/108 (36%), Gaps = 28/108 (25%)
Query: 33 NTYSDRYRSTVEDLYSR---DFHVGAVTIKEIPIVVAGNKSDMTSHHRAVHLEDVSEWLY 89
YS ST+E + ++ V ++PI++ GNKSD+ LE+ +
Sbjct: 78 LVYSVDRPSTLERIRTKWLPLIRRLGV---KVPIILVGNKSDLRDGSSQAGLEEEMLPIM 134
Query: 90 CELPKLRYVIQSSSFGDEIPIVVAGNKSDMTSHHRAVHLEDVSEWLYC 137
E ++ ++ S A L +VSE Y
Sbjct: 135 NEFREIETCVECS----------------------AKTLINVSEVFYY 160
Score = 33.8 bits (78), Expect = 0.067
Identities = 31/119 (26%), Positives = 47/119 (39%), Gaps = 17/119 (14%)
Query: 227 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQFPAMRR 286
I+DT Q A I A+ LVYS + + ++ + P +RR
Sbjct: 53 IVDTSSRPQDRANLAAEIRKANVICLVYSVDRPSTLERIRTKW-----------LPLIRR 101
Query: 287 LSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDF----QLLECSAKDNYNIKEVF 341
L + +LV + + L S EE+ +F +ECSAK N+ EVF
Sbjct: 102 LGVKVP--IILVGNKSDLRDGSSQAGLEEEMLPIMNEFREIETCVECSAKTLINVSEVF 158
>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 = 47.4 bits (113), Expect = 1e-06
Identities = 28/81 (34%), Positives = 47/81 (58%), Gaps = 4/81 (4%)
Query: 145 VDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEI-REQRQDFQEIP 203
++ILDT G + A+R + FLLV+S T +ESF ++ + E+I R + D +P
Sbjct: 50 LNILDTAGQEDYAAIRDNYFRSGEGFLLVFSITDMESFTALAEFREQILRVKEDD--NVP 107
Query: 204 IVVAGNKSDMTSHHRAVHLED 224
+++ GNK D+ R V +E+
Sbjct: 108 LLLVGNKCDLE-DKRQVSVEE 127
Score = 41.3 bits (97), Expect = 2e-04
Identities = 33/117 (28%), Positives = 53/117 (45%), Gaps = 12/117 (10%)
Query: 225 VDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQFPAM 284
++ILDT G + A+R + FLLV+S T +ESF ++ + E+I ++D P
Sbjct: 50 LNILDTAGQEDYAAIRDNYFRSGEGFLLVFSITDMESFTALAEFREQILRVKEDDNVP-- 107
Query: 285 RRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQLLECSAKDNYNIKEVF 341
LLV + LE + V ++ +E SAK N+ +VF
Sbjct: 108 ----------LLLVGNKCDLEDKRQVSVEEAANLAEQWGVNYVETSAKTRANVDKVF 154
Score = 37.8 bits (88), Expect = 0.003
Identities = 27/134 (20%), Positives = 58/134 (43%), Gaps = 23/134 (17%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHVGAVTIKEIPIVVAGNKSD 71
+++++G GVGKS + +F+++ + + Y T D Y + + ++ + AG +
Sbjct: 2 KVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEVQLNILDTAGQE-- 59
Query: 72 MTSHHRAV---------------HLEDVSEWLYCELPKLRYVIQSSSFGDEIPIVVAGNK 116
+ A+ + D+ + L + R I D +P+++ GNK
Sbjct: 60 ---DYAAIRDNYFRSGEGFLLVFSITDMES--FTALAEFREQILRVKEDDNVPLLLVGNK 114
Query: 117 SDMTSHHRAVHLED 130
D+ R V +E+
Sbjct: 115 CDLE-DKRQVSVEE 127
>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 = 46.0 bits (110), Expect = 5e-06
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 149 DTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIVVAG 208
DT G ++ +R LS FLL +S SF++VK + E + +PI++ G
Sbjct: 54 DTAGQEEYDRLRPLSYPQTDVFLLCFSVDSPSSFENVKTKW--YPEIKHYCPNVPIILVG 111
Query: 209 NKSDM 213
K D+
Sbjct: 112 TKIDL 116
Score = 43.3 bits (103), Expect = 5e-05
Identities = 34/153 (22%), Positives = 60/153 (39%), Gaps = 30/153 (19%)
Query: 202 IPIVVAGNKSDMTSHHRAVHLEDVDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLES 261
+P V +++T + V+L + DT G ++ +R LS FLL +S S
Sbjct: 30 VPTVFDNYSANVTVDGKQVNLG---LWDTAGQEEYDRLRPLSYPQTDVFLLCFSVDSPSS 86
Query: 262 FQSVK-CYFEEIREQRQDFQFPAMRRLSIATAHAFLLV---------YSTTCLESFQSVK 311
F++VK ++ EI+ + +LV +T +
Sbjct: 87 FENVKTKWYPEIKHYCPNVP--------------IILVGTKIDLRDDGNTLKKLEKKQKP 132
Query: 312 CYFEEIREQRQD---FQLLECSAKDNYNIKEVF 341
EE + ++ + +ECSA +KEVF
Sbjct: 133 ITPEEGEKLAKEIGAVKYMECSALTQEGLKEVF 165
Score = 37.9 bits (89), Expect = 0.003
Identities = 35/139 (25%), Positives = 52/139 (37%), Gaps = 53/139 (38%)
Query: 11 IRLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHVGAVTIKEIPIVV----- 65
I++V++G VGK+C+L + N + Y TV D YS + VT+ + +
Sbjct: 1 IKIVVVGDGAVGKTCLLISYTTNKFPTEYVPTVFDNYSAN-----VTVDGKQVNLGLWDT 55
Query: 66 AGNKSDMTSHHRAVHLEDVSEWLYCELPKLRY-----------VIQSSSFGD-------E 107
AG E+ Y L L Y V SSF + E
Sbjct: 56 AGQ-------------EE-----YDRLRPLSYPQTDVFLLCFSVDSPSSFENVKTKWYPE 97
Query: 108 I-------PIVVAGNKSDM 119
I PI++ G K D+
Sbjct: 98 IKHYCPNVPIILVGTKIDL 116
>gnl|CDD|206695 cd04112, Rab26, Rab GTPase family 26 (Rab26). Rab26 subfamily.
First identified in rat pancreatic acinar cells, Rab26
is believed to play a role in recruiting mature granules
to the plasma membrane upon beta-adrenergic stimulation.
Rab26 belongs to the Rab functional group III, which are
considered key regulators of intracellular vesicle
transport during exocytosis. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 191
Score = 45.6 bits (108), Expect = 8e-06
Identities = 28/78 (35%), Positives = 42/78 (53%), Gaps = 3/78 (3%)
Query: 147 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIVV 206
I DT G +F ++ AHA LL+Y T SF +++ + EI E Q ++ I++
Sbjct: 54 IWDTAGQERFRSVTHAYYRDAHALLLLYDVTNKSSFDNIRAWLTEILEYAQ--SDVVIML 111
Query: 207 AGNKSDMTSHHRAVHLED 224
GNK+DM+ R V ED
Sbjct: 112 LGNKADMSG-ERVVKRED 128
Score = 32.1 bits (73), Expect = 0.25
Identities = 18/51 (35%), Positives = 26/51 (50%)
Query: 227 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQ 277
I DT G +F ++ AHA LL+Y T SF +++ + EI E Q
Sbjct: 54 IWDTAGQERFRSVTHAYYRDAHALLLLYDVTNKSSFDNIRAWLTEILEYAQ 104
Score = 28.7 bits (64), Expect = 4.4
Identities = 13/36 (36%), Positives = 20/36 (55%)
Query: 292 AHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQLL 327
AHA LL+Y T SF +++ + EI E Q ++
Sbjct: 74 AHALLLLYDVTNKSSFDNIRAWLTEILEYAQSDVVI 109
>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 = 9e-06
Identities = 33/131 (25%), Positives = 53/131 (40%), Gaps = 19/131 (14%)
Query: 11 IRLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSR-----DFHVGAVTIKEIPIVV 65
+R+ +LG GVGK+ I+++FL + + Y T R V + I ++P +
Sbjct: 1 VRVAVLGAPGVGKTAIVRQFLAQEFPEEYIPTEHRRLYRPAVVLSGRVYDLHILDVPNMQ 60
Query: 66 A--GNKSDMTSHHRAVHLEDVSEWLY----CELPKLRYV-------IQSSSFGD-EIPIV 111
G R L + ++ C YV +++ G+ E PIV
Sbjct: 61 RYPGTAGQEWMDPRFRGLRNSRAFILVYDICSPDSFHYVKLLRQQILETRPAGNKEPPIV 120
Query: 112 VAGNKSDMTSH 122
V GNK D H
Sbjct: 121 VVGNKRDQQRH 131
Score = 44.9 bits (106), Expect = 2e-05
Identities = 23/63 (36%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 155 QFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDF-QEIPIVVAGNKSDM 213
++ R + + AF+LVY +SF VK ++I E R +E PIVV GNK D
Sbjct: 69 EWMDPRFRGLRNSRAFILVYDICSPDSFHYVKLLRQQILETRPAGNKEPPIVVVGNKRDQ 128
Query: 214 TSH 216
H
Sbjct: 129 QRH 131
Score = 36.0 bits (83), Expect = 0.018
Identities = 33/143 (23%), Positives = 52/143 (36%), Gaps = 37/143 (25%)
Query: 221 HLEDVDILD--------TCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEI 272
+ D+ ILD ++ R + + AF+LVY +SF VK ++I
Sbjct: 47 RVYDLHILDVPNMQRYPGTAGQEWMDPRFRGLRNSRAFILVYDICSPDSFHYVKLLRQQI 106
Query: 273 REQRQDFQFPA----------MRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQ 322
E R +R A H ++ +S KC +
Sbjct: 107 LETRPAGNKEPPIVVVGNKRDQQRHRFAPRHVLSVLVR-------KSWKCGY-------- 151
Query: 323 DFQLLECSAKDNYNIKEVFRTFL 345
LECSAK N++I +F+ L
Sbjct: 152 ----LECSAKYNWHILLLFKELL 170
>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 = 44.2 bits (105), Expect = 2e-05
Identities = 33/148 (22%), Positives = 64/148 (43%), Gaps = 39/148 (26%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHVGAVTIKEIPIVV-----A 66
+++ILG GVGK+ ++ +++ +S++Y++T+ DF VT+ + + + A
Sbjct: 2 KVIILGDSGVGKTSLMNQYVNKKFSNQYKATI----GADFLTKEVTVDDRLVTLQIWDTA 57
Query: 67 GNKS-------------------DMTSHHRAVHLEDVSEWLYCELPKLRYVIQSS-SFGD 106
G + D+T+ E + W + ++IQ+S +
Sbjct: 58 GQERFQSLGVAFYRGADCCVLVYDVTN---PKSFESLDSW------RDEFLIQASPRDPE 108
Query: 107 EIPIVVAGNKSDMTSHHRAVHLEDVSEW 134
P VV GNK D+ R V + +W
Sbjct: 109 NFPFVVLGNKIDLEE-KRQVSTKKAQQW 135
Score = 35.3 bits (82), Expect = 0.019
Identities = 27/85 (31%), Positives = 39/85 (45%), Gaps = 9/85 (10%)
Query: 147 ILDTCGDLQFPAMRRLSIA---TAHAFLLVYSTTCLESFQSVKCYFEEIREQRQ--DFQE 201
I DT G +F + L +A A +LVY T +SF+S+ + +E Q D +
Sbjct: 53 IWDTAGQERF---QSLGVAFYRGADCCVLVYDVTNPKSFESLDSWRDEFLIQASPRDPEN 109
Query: 202 IPIVVAGNKSDMTSHHRAVHLEDVD 226
P VV GNK D+ R V +
Sbjct: 110 FPFVVLGNKIDLEE-KRQVSTKKAQ 133
>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 = 43.9 bits (104), Expect = 2e-05
Identities = 20/49 (40%), Positives = 31/49 (63%), Gaps = 1/49 (2%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRSTVE-DLYSRDFHVGAVTIK 59
+L+++G GVGKSC+L RF +TY++ Y ST+ D R + T+K
Sbjct: 4 KLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTVK 52
Score = 40.0 bits (94), Expect = 6e-04
Identities = 36/132 (27%), Positives = 57/132 (43%), Gaps = 21/132 (15%)
Query: 218 RAVHLED----VDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIR 273
R + L+ + I DT G +F + AH ++VY T ESF +VK + +EI
Sbjct: 42 RTIELDGKTVKLQIWDTAGQERFRTITSSYYRGAHGIIIVYDVTDQESFNNVKQWLQEI- 100
Query: 274 EQRQDFQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQL--LECSA 331
R + + LLV + L + V + E +E + + LE SA
Sbjct: 101 -----------DRYASENVNK-LLVGNKCDLTDKKVVD--YTEAKEFADELGIPFLETSA 146
Query: 332 KDNYNIKEVFRT 343
K+ N++E F T
Sbjct: 147 KNATNVEEAFMT 158
Score = 39.6 bits (93), Expect = 7e-04
Identities = 24/74 (32%), Positives = 37/74 (50%), Gaps = 3/74 (4%)
Query: 147 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIVV 206
I DT G +F + AH ++VY T ESF +VK + +EI R + + ++
Sbjct: 55 IWDTAGQERFRTITSSYYRGAHGIIIVYDVTDQESFNNVKQWLQEI--DRYASENVNKLL 112
Query: 207 AGNKSDMTSHHRAV 220
GNK D+T + V
Sbjct: 113 VGNKCDLTD-KKVV 125
>gnl|CDD|133324 cd04124, RabL2, Rab GTPase-like family 2 (Rab-like2). RabL2
(Rab-like2) subfamily. RabL2s are novel Rab proteins
identified recently which display features that are
distinct from other Rabs, and have been termed Rab-like.
RabL2 contains RabL2a and RabL2b, two very similar Rab
proteins that share > 98% sequence identity in humans.
RabL2b maps to the subtelomeric region of chromosome
22q13.3 and RabL2a maps to 2q13, a region that suggests
it is also a subtelomeric gene. Both genes are believed
to be expressed ubiquitously, suggesting that RabL2s are
the first example of duplicated genes in human proximal
subtelomeric regions that are both expressed actively.
Like other Rab-like proteins, RabL2s lack a prenylation
site at the C-terminus. The specific functions of RabL2a
and RabL2b remain unknown. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization.
Length = 161
Score = 42.9 bits (101), Expect = 4e-05
Identities = 25/69 (36%), Positives = 38/69 (55%), Gaps = 3/69 (4%)
Query: 145 VDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPI 204
VD DT G +F M AHA +LV+ T +++++ ++EE+RE R EIP
Sbjct: 51 VDFWDTAGQERFQTMHASYYHKAHACILVFDVTRKITYKNLSKWYEELREYR---PEIPC 107
Query: 205 VVAGNKSDM 213
+V NK D+
Sbjct: 108 IVVANKIDL 116
Score = 36.0 bits (83), Expect = 0.010
Identities = 34/126 (26%), Positives = 54/126 (42%), Gaps = 27/126 (21%)
Query: 11 IRLVILGGQGVGKSCILKRFLFNTYSDRYRSTVE-DLYSRDFHVGAVTIKEIPIVVAGNK 69
+++++LG VGKS +++RFL + Y + ST LY + TI AG +
Sbjct: 1 VKIILLGDSAVGKSKLVERFLMDGYEPQQLSTYALTLYKHNAKFEGKTILVDFWDTAGQE 60
Query: 70 SDMTSH----------------HRAVHLEDVSEWLYCELPKLRYVIQSSSFGDEIPIVVA 113
T H R + +++S+W Y EL + R EIP +V
Sbjct: 61 RFQTMHASYYHKAHACILVFDVTRKITYKNLSKW-YEELREYR---------PEIPCIVV 110
Query: 114 GNKSDM 119
NK D+
Sbjct: 111 ANKIDL 116
Score = 34.8 bits (80), Expect = 0.030
Identities = 18/53 (33%), Positives = 29/53 (54%)
Query: 224 DVDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQR 276
VD DT G +F M AHA +LV+ T +++++ ++EE+RE R
Sbjct: 50 LVDFWDTAGQERFQTMHASYYHKAHACILVFDVTRKITYKNLSKWYEELREYR 102
>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 = 43.1 bits (102), Expect = 5e-05
Identities = 30/125 (24%), Positives = 50/125 (40%), Gaps = 21/125 (16%)
Query: 10 RIRLVILGGQGVGKSCILKRFLFNTYS-DRYRSTVEDLY-SRDFHVGAVTIKEIPIVVAG 67
I++VI+G VGKS +L R L N S Y+ Y + T K + AG
Sbjct: 1 EIKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAG 60
Query: 68 --NKSDMTSHHR------------AVHLEDVSEWLYCELPKLRYVIQSSSFGDEIPIVVA 113
+ + + + + DV E L + ++ + +S +PI++
Sbjct: 61 QEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAES-----GVPIILV 115
Query: 114 GNKSD 118
GNK D
Sbjct: 116 GNKID 120
Score = 42.4 bits (100), Expect = 8e-05
Identities = 19/70 (27%), Positives = 32/70 (45%), Gaps = 4/70 (5%)
Query: 145 VDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCL-ESFQSVKC-YFEEIREQRQDFQEI 202
++LDT G + A+RRL + L V+ L + + +EI + +
Sbjct: 53 FNLLDTAGQEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAE--SGV 110
Query: 203 PIVVAGNKSD 212
PI++ GNK D
Sbjct: 111 PIILVGNKID 120
Score = 28.5 bits (64), Expect = 3.3
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 225 VDILDTCGDLQFPAMRRLSIATAHAFLLVYS 255
++LDT G + A+RRL + L V+
Sbjct: 53 FNLLDTAGQEDYDAIRRLYYRAVESSLRVFD 83
>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 = 43.0 bits (102), Expect = 5e-05
Identities = 30/128 (23%), Positives = 61/128 (47%), Gaps = 34/128 (26%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHVGAVTIKEIPIVV-----A 66
+LV LG Q VGK+ I+ RF+++T+ ++Y++T+ DF + + + + + A
Sbjct: 2 KLVFLGDQSVGKTSIITRFMYDTFDNQYQATI----GIDFLSKTMYVDDKTVRLQLWDTA 57
Query: 67 GN---KSDMTSHHRAVHL-------------EDVSEWLYCELPKLRYVIQSSSFGDEIPI 110
G +S + S+ R + ++ +W ++ R G+++ I
Sbjct: 58 GQERFRSLIPSYIRDSSVAVVVYDITNRQSFDNTDKW-IDDVRDER--------GNDVII 108
Query: 111 VVAGNKSD 118
V+ GNK+D
Sbjct: 109 VLVGNKTD 116
Score = 41.1 bits (97), Expect = 2e-04
Identities = 18/66 (27%), Positives = 38/66 (57%), Gaps = 2/66 (3%)
Query: 147 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIVV 206
+ DT G +F ++ I + ++VY T +SF + + +++R++R + ++ IV+
Sbjct: 53 LWDTAGQERFRSLIPSYIRDSSVAVVVYDITNRQSFDNTDKWIDDVRDERGN--DVIIVL 110
Query: 207 AGNKSD 212
GNK+D
Sbjct: 111 VGNKTD 116
Score = 38.0 bits (89), Expect = 0.002
Identities = 26/118 (22%), Positives = 54/118 (45%), Gaps = 17/118 (14%)
Query: 227 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQFPAMRR 286
+ DT G +F ++ I + ++VY T +SF + + +++R++R +
Sbjct: 53 LWDTAGQERFRSLIPSYIRDSSVAVVVYDITNRQSFDNTDKWIDDVRDERGN-------- 104
Query: 287 LSIATAHAFLLVYSTTCLESFQSVKCYFEEIRE--QRQDFQLLECSAKDNYNIKEVFR 342
+LV + T L + V EE + + + +E SAK +N+K++F+
Sbjct: 105 -----DVIIVLVGNKTDLSDKRQVS--TEEGEKKAKENNAMFIETSAKAGHNVKQLFK 155
>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 = 42.8 bits (101), Expect = 6e-05
Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 3/78 (3%)
Query: 147 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIVV 206
I DT G F ++ R A LLVY T E+F + + E+ R+ + I++
Sbjct: 57 IWDTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQHSNS--NMTIML 114
Query: 207 AGNKSDMTSHHRAVHLED 224
GNK D+ R V E+
Sbjct: 115 IGNKCDL-ESRREVSYEE 131
Score = 38.6 bits (90), Expect = 0.001
Identities = 30/115 (26%), Positives = 45/115 (39%), Gaps = 13/115 (11%)
Query: 227 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQFPAMRR 286
I DT G F ++ R A LLVY T E+F + + E+ R+ M
Sbjct: 57 IWDTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQHSN----SNM-- 110
Query: 287 LSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQLLECSAKDNYNIKEVF 341
+L+ + LES + V E + +E SAK N++E F
Sbjct: 111 -------TIMLIGNKCDLESRREVSYEEGEAFAREHGLIFMETSAKTASNVEEAF 158
Score = 31.6 bits (72), Expect = 0.33
Identities = 39/135 (28%), Positives = 62/135 (45%), Gaps = 29/135 (21%)
Query: 14 VILGGQGVGKSCILKRFLFNTYSDRYRSTVEDL-YSRDFHVGAVTIKEIPIVV-----AG 67
+I+G GVGKSC+L +F +D+ V DL +F +TI I + AG
Sbjct: 8 IIIGDTGVGKSCLLLQF-----TDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAG 62
Query: 68 NKS--DMT-SHHR----AVHLEDVS-----EWLYCELPKLRYVIQSSSFGDEIPIVVAGN 115
+S +T S++R A+ + D++ L L R Q S+ + I++ GN
Sbjct: 63 QESFRSITRSYYRGAAGALLVYDITRRETFNHLTSWLEDAR---QHSN--SNMTIMLIGN 117
Query: 116 KSDMTSHHRAVHLED 130
K D+ R V E+
Sbjct: 118 KCDL-ESRREVSYEE 131
>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 = 42.8 bits (101), Expect = 6e-05
Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 10/74 (13%)
Query: 145 VDILDTCGDLQFPAMRRLSIA-----TAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDF 199
V + DT G +F R S+ HA + VY T + SF S+ + EE EQ
Sbjct: 53 VQLWDTAGQERF----RKSMVQHYYRNVHAVVFVYDVTNMASFHSLPSWIEEC-EQHSLP 107
Query: 200 QEIPIVVAGNKSDM 213
E+P ++ GNK D+
Sbjct: 108 NEVPRILVGNKCDL 121
Score = 33.6 bits (77), Expect = 0.081
Identities = 24/88 (27%), Positives = 30/88 (34%), Gaps = 33/88 (37%)
Query: 293 HAFLLVYSTTCLESFQSVKCYFEE--------------------IREQRQ---------- 322
HA + VY T + SF S+ + EE +REQ Q
Sbjct: 77 HAVVFVYDVTNMASFHSLPSWIEECEQHSLPNEVPRILVGNKCDLREQIQVPTDLAQRFA 136
Query: 323 ---DFQLLECSAKDNYNIKEVFRTFLTL 347
L E SAKD V F+TL
Sbjct: 137 DAHSMPLFETSAKDPSENDHVEAIFMTL 164
Score = 32.8 bits (75), Expect = 0.14
Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 9/54 (16%)
Query: 225 VDILDTCGDLQFPAMRRLSIA-----TAHAFLLVYSTTCLESFQSVKCYFEEIR 273
V + DT G +F R S+ HA + VY T + SF S+ + EE
Sbjct: 53 VQLWDTAGQERF----RKSMVQHYYRNVHAVVFVYDVTNMASFHSLPSWIEECE 102
Score = 31.6 bits (72), Expect = 0.34
Identities = 30/127 (23%), Positives = 52/127 (40%), Gaps = 28/127 (22%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRSTVE-DLYSRDFHVGAVTIKEIPIVVAGN-- 68
+++++G VGK+C+ RF + +R +T+ D R + IK AG
Sbjct: 4 KIIVIGDSNVGKTCLTYRFCAGRFPERTEATIGVDFRERTVEIDGERIKVQLWDTAGQER 63
Query: 69 --KSDMTSHHRAVH-------------LEDVSEWLY-CELPKLRYVIQSSSFGDEIPIVV 112
KS + ++R VH + W+ CE S +E+P ++
Sbjct: 64 FRKSMVQHYYRNVHAVVFVYDVTNMASFHSLPSWIEECE---------QHSLPNEVPRIL 114
Query: 113 AGNKSDM 119
GNK D+
Sbjct: 115 VGNKCDL 121
>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 = 43.1 bits (102), Expect = 7e-05
Identities = 26/135 (19%), Positives = 44/135 (32%), Gaps = 32/135 (23%)
Query: 225 VDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVK-CYFEEIR---------- 273
+ + DT G + +R LS L+ YS S +V+ ++ E+
Sbjct: 54 LALWDTAGQEDYDRLRPLSYPDVDVILICYSVDNPTSLDNVEDKWYPEVNHFCPGTPIVL 113
Query: 274 -----EQRQDFQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQLLE 328
+ R+D + R + Q E + + +E
Sbjct: 114 VGLKTDLRKDKNSVSKLRAQ-----------GLEPVTPEQG-----ESVAKSIGAVAYIE 157
Query: 329 CSAKDNYNIKEVFRT 343
CSAK N+ EVF
Sbjct: 158 CSAKLMENVDEVFDA 172
Score = 41.6 bits (98), Expect = 2e-04
Identities = 20/80 (25%), Positives = 34/80 (42%), Gaps = 6/80 (7%)
Query: 145 VDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVK-CYFEEIREQRQDFQE-I 202
+ + DT G + +R LS L+ YS S +V+ ++ E+ F
Sbjct: 54 LALWDTAGQEDYDRLRPLSYPDVDVILICYSVDNPTSLDNVEDKWYPEVNH----FCPGT 109
Query: 203 PIVVAGNKSDMTSHHRAVHL 222
PIV+ G K+D+ +V
Sbjct: 110 PIVLVGLKTDLRKDKNSVSK 129
Score = 30.4 bits (69), Expect = 0.95
Identities = 12/44 (27%), Positives = 24/44 (54%)
Query: 11 IRLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHVG 54
+++V++G G GK+C+L + ++ + Y TV + Y V
Sbjct: 4 VKIVVVGDGGCGKTCLLMVYAQGSFPEEYVPTVFENYVTTLQVP 47
>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 = 42.4 bits (100), Expect = 8e-05
Identities = 31/122 (25%), Positives = 54/122 (44%), Gaps = 20/122 (16%)
Query: 225 VDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQFPAM 284
+ I DT G +F + + +A+ ++ Y T SF+SV + EE+ +
Sbjct: 54 LQIWDTAGQERFRTITQSYYRSANGAIIAYDITRRSSFESVPHWIEEVEK---------- 103
Query: 285 RRLSIATAHAFLLVYSTTC-LESFQSVKCYFEEIREQRQDFQLL---ECSAKDNYNIKEV 340
++ LL+ C LE + V FEE + + +L E SAK++ N++E
Sbjct: 104 ----YGASNVVLLLIGNKCDLEEQREVL--FEEACTLAEHYGILAVLETSAKESSNVEEA 157
Query: 341 FR 342
F
Sbjct: 158 FL 159
Score = 41.7 bits (98), Expect = 2e-04
Identities = 23/89 (25%), Positives = 41/89 (46%), Gaps = 3/89 (3%)
Query: 140 PKLRYVDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDF 199
K + I DT G +F + + +A+ ++ Y T SF+SV + EE+ +
Sbjct: 49 GKRVKLQIWDTAGQERFRTITQSYYRSANGAIIAYDITRRSSFESVPHWIEEVE--KYGA 106
Query: 200 QEIPIVVAGNKSDMTSHHRAVHLEDVDIL 228
+ +++ GNK D+ R V E+ L
Sbjct: 107 SNVVLLLIGNKCDL-EEQREVLFEEACTL 134
Score = 40.5 bits (95), Expect = 4e-04
Identities = 32/140 (22%), Positives = 63/140 (45%), Gaps = 35/140 (25%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHVGAVTI--KEIPIVV---A 66
+++++G VGK+C+++RF T+S+R +T+ DF + + I K + + + A
Sbjct: 5 KIILIGDSNVGKTCVVQRFKSGTFSERQGNTI----GVDFTMKTLEIQGKRVKLQIWDTA 60
Query: 67 GNKSDMT---SHHRAVH-------------LEDVSEWLYCELPKLRYVIQSSSFGDEIPI 110
G + T S++R+ + E V W+ E+ K + +
Sbjct: 61 GQERFRTITQSYYRSANGAIIAYDITRRSSFESVPHWIE-EVEKYG--------ASNVVL 111
Query: 111 VVAGNKSDMTSHHRAVHLED 130
++ GNK D+ R V E+
Sbjct: 112 LLIGNKCDL-EEQREVLFEE 130
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 43.0 bits (101), Expect = 9e-05
Identities = 31/90 (34%), Positives = 46/90 (51%), Gaps = 3/90 (3%)
Query: 147 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIVV 206
I DT G ++ A+ A LLVY T ++F +V+ + E+R+ I I++
Sbjct: 65 IWDTAGQERYRAITSAYYRGAVGALLVYDITKRQTFDNVQRWLRELRDHAD--SNIVIMM 122
Query: 207 AGNKSDMTSHHRAVHLEDVDILDTCGDLQF 236
AGNKSD+ +H R+V ED L L F
Sbjct: 123 AGNKSDL-NHLRSVAEEDGQALAEKEGLSF 151
Score = 41.8 bits (98), Expect = 2e-04
Identities = 40/136 (29%), Positives = 65/136 (47%), Gaps = 27/136 (19%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRSTVE-DLYSRDFHVGAVTIKEIPIVVAGN-- 68
++V++G GVGKS IL RF N + +ST+ + +R V T+K AG
Sbjct: 14 KIVLIGDSGVGKSNILSRFTRNEFCLESKSTIGVEFATRTLQVEGKTVKAQIWDTAGQER 73
Query: 69 -KSDMTSHHRAV-------------HLEDVSEWLYCELPKLRYVIQSSSFGDEIPIVVAG 114
++ ++++R ++V WL +LR S+ I I++AG
Sbjct: 74 YRAITSAYYRGAVGALLVYDITKRQTFDNVQRWLR----ELRDHADSN-----IVIMMAG 124
Query: 115 NKSDMTSHHRAVHLED 130
NKSD+ +H R+V ED
Sbjct: 125 NKSDL-NHLRSVAEED 139
Score = 31.1 bits (70), Expect = 0.76
Identities = 28/120 (23%), Positives = 53/120 (44%), Gaps = 13/120 (10%)
Query: 227 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQFPAMRR 286
I DT G ++ A+ A LLVY T ++F +V+ + E+R+ A
Sbjct: 65 IWDTAGQERYRAITSAYYRGAVGALLVYDITKRQTFDNVQRWLRELRDH-------ADSN 117
Query: 287 LSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQLLECSAKDNYNIKEVFRTFLT 346
+ I ++ + + L +SV + +++ LE SA + N+++ F+T L
Sbjct: 118 IVI------MMAGNKSDLNHLRSVAEEDGQALAEKEGLSFLETSALEATNVEKAFQTILL 171
>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 = 41.4 bits (98), Expect = 2e-04
Identities = 22/58 (37%), Positives = 34/58 (58%), Gaps = 3/58 (5%)
Query: 167 AHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIVVAGNKSDMTSHHRAVHLED 224
A LLVY T +F++V+ + +E+R+ I I++ GNKSD+ H RAV E+
Sbjct: 76 AVGALLVYDITKKSTFENVERWLKELRDHAD--SNIVIMLVGNKSDL-RHLRAVPTEE 130
Score = 38.7 bits (91), Expect = 0.001
Identities = 44/155 (28%), Positives = 64/155 (41%), Gaps = 39/155 (25%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRST--VEDLYSRDFHVGAVTIKEIPIVVAGNK 69
++V++G GVGKS +L RF N ++ +ST VE +R + TIK AG +
Sbjct: 5 KIVLIGDSGVGKSNLLSRFTRNEFNLDSKSTIGVE-FATRTIQIDGKTIKAQIWDTAGQE 63
Query: 70 S-------------------DMTSHHRAVHLEDVSEWLYCELPKLRYVIQSSSFGD-EIP 109
D+T E+V W L +LR D I
Sbjct: 64 RYRAITSAYYRGAVGALLVYDITKK---STFENVERW----LKELR------DHADSNIV 110
Query: 110 IVVAGNKSDMTSHHRAVHLEDVSEWLYCELPKLRY 144
I++ GNKSD+ H RAV E+ + E L +
Sbjct: 111 IMLVGNKSDL-RHLRAVPTEEAKA--FAEKNGLSF 142
Score = 30.2 bits (69), Expect = 1.1
Identities = 19/87 (21%), Positives = 33/87 (37%), Gaps = 32/87 (36%)
Query: 292 AHAFLLVYSTTCLESFQSVKCYFEEIRE-------------------------------- 319
A LLVY T +F++V+ + +E+R+
Sbjct: 76 AVGALLVYDITKKSTFENVERWLKELRDHADSNIVIMLVGNKSDLRHLRAVPTEEAKAFA 135
Query: 320 QRQDFQLLECSAKDNYNIKEVFRTFLT 346
++ +E SA D N++E F+ LT
Sbjct: 136 EKNGLSFIETSALDGTNVEEAFKQLLT 162
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 41.5 bits (97), Expect = 2e-04
Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 3/78 (3%)
Query: 147 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIVV 206
I DT G F ++ R A LLVY T E+F + + E+ R+ + I++
Sbjct: 59 IWDTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLASWLEDARQHAN--ANMTIML 116
Query: 207 AGNKSDMTSHHRAVHLED 224
GNK D+ +H RAV E+
Sbjct: 117 IGNKCDL-AHRRAVSTEE 133
Score = 33.0 bits (75), Expect = 0.16
Identities = 36/133 (27%), Positives = 62/133 (46%), Gaps = 21/133 (15%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDL-YSRDFHVGAVTIKEIPIVV----- 65
+ +I+G GVGKSC+L +F +D+ V DL +F +TI PI +
Sbjct: 8 KYIIIGDTGVGKSCLLLQF-----TDKRFQPVHDLTIGVEFGARMITIDNKPIKLQIWDT 62
Query: 66 AGNKSDMTSHHRAVHLEDVSEWLYCELPKLRYVIQSSSFGDE--------IPIVVAGNKS 117
AG +S S R+ + L ++ + +S+ ++ + I++ GNK
Sbjct: 63 AGQES-FRSITRSYYRGAAGALLVYDITRRETFNHLASWLEDARQHANANMTIMLIGNKC 121
Query: 118 DMTSHHRAVHLED 130
D+ +H RAV E+
Sbjct: 122 DL-AHRRAVSTEE 133
Score = 30.3 bits (68), Expect = 1.3
Identities = 28/116 (24%), Positives = 45/116 (38%), Gaps = 15/116 (12%)
Query: 227 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQFPAMRR 286
I DT G F ++ R A LLVY T E+F + + E+ R+
Sbjct: 59 IWDTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLASWLEDARQH----------- 107
Query: 287 LSIATAHAFLLVYSTTCLESFQSVKCYFE-EIREQRQDFQLLECSAKDNYNIKEVF 341
A A+ +++ C + + E E + +E SAK N++E F
Sbjct: 108 ---ANANMTIMLIGNKCDLAHRRAVSTEEGEQFAKEHGLIFMEASAKTAQNVEEAF 160
>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 = 40.3 bits (94), Expect = 4e-04
Identities = 32/115 (27%), Positives = 54/115 (46%), Gaps = 13/115 (11%)
Query: 227 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQFPAMRR 286
I DT G +F ++ + +A+A +L Y TC ESF+ + + EI Q+ +
Sbjct: 60 IWDTAGQERFRSITQSYYRSANALILTYDITCEESFRCLPEWLREIE------QYANNKV 113
Query: 287 LSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQLLECSAKDNYNIKEVF 341
++I LV + L + V E QD LE SAK++ N++++F
Sbjct: 114 ITI-------LVGNKIDLAERREVSQQRAEEFSDAQDMYYLETSAKESDNVEKLF 161
Score = 40.3 bits (94), Expect = 5e-04
Identities = 25/67 (37%), Positives = 39/67 (58%), Gaps = 2/67 (2%)
Query: 147 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIVV 206
I DT G +F ++ + +A+A +L Y TC ESF+ + + EI EQ + + I I+V
Sbjct: 60 IWDTAGQERFRSITQSYYRSANALILTYDITCEESFRCLPEWLREI-EQYANNKVITILV 118
Query: 207 AGNKSDM 213
GNK D+
Sbjct: 119 -GNKIDL 124
Score = 32.9 bits (75), Expect = 0.14
Identities = 36/141 (25%), Positives = 63/141 (44%), Gaps = 15/141 (10%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRSTVE-DLYSRDFHVGAVTIKEIPIVVAGN-- 68
++V++G GVGK+C+++RF + +T+ D + + IK AG
Sbjct: 9 KIVLIGNAGVGKTCLVRRFTQGLFPPGQGATIGVDFMIKTVEIKGEKIKLQIWDTAGQER 68
Query: 69 -KSDMTSHHRAVHLEDVSEWLYCE-----LPKLRYVIQSSSFGDEIPIVVAGNKSDM--- 119
+S S++R+ + ++ + CE LP+ I+ + I I+V GNK D+
Sbjct: 69 FRSITQSYYRSANALILTYDITCEESFRCLPEWLREIEQYANNKVITILV-GNKIDLAER 127
Query: 120 --TSHHRAVHLEDVSEWLYCE 138
S RA D + Y E
Sbjct: 128 REVSQQRAEEFSDAQDMYYLE 148
>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 = 39.8 bits (93), Expect = 7e-04
Identities = 24/82 (29%), Positives = 37/82 (45%), Gaps = 6/82 (7%)
Query: 147 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIVV 206
I DT G ++ AM R+ A A ++ Y T SF+ K + +E+ + + I +
Sbjct: 54 IWDTAGSERYEAMSRIYYRGAKAAIVCYDLTDSSSFERAKFWVKEL---QNLEEHCKIYL 110
Query: 207 AGNKSDMTSHH---RAVHLEDV 225
G KSD+ R V DV
Sbjct: 111 CGTKSDLIEQDRSLRQVDFHDV 132
Score = 34.1 bits (78), Expect = 0.062
Identities = 33/147 (22%), Positives = 58/147 (39%), Gaps = 16/147 (10%)
Query: 227 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQFPAMRR 286
I DT G ++ AM R+ A A ++ Y T SF+ K + +E++ +
Sbjct: 54 IWDTAGSERYEAMSRIYYRGAKAAIVCYDLTDSSSFERAKFWVKELQNLE-----EHCKI 108
Query: 287 LSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQLLECSAKDNYNIKEVFRTF-- 344
T + + F V+ + +EI+ Q E S+K N+ E+F+
Sbjct: 109 YLCGTKSDLIEQDRSLRQVDFHDVQDFADEIKA-----QHFETSSKTGQNVDELFQKVAE 163
Query: 345 ----LTLSQILTTNGDENSLKRRSSAY 367
+Q+ T G + K+ S Y
Sbjct: 164 DFVSRANNQMNTEKGVDLGQKKNSYFY 190
>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 = 39.5 bits (93), Expect = 8e-04
Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 4/66 (6%)
Query: 149 DTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKC-YFEEIREQRQDFQEIPIVVA 207
DT G + +R LS FL+ +S SF++VK ++ E+ + +PI++
Sbjct: 52 DTAGQEDYDRLRPLSYPDTDVFLICFSVDSPASFENVKEKWYPEV---KHFCPNVPIILV 108
Query: 208 GNKSDM 213
G K D+
Sbjct: 109 GTKLDL 114
Score = 36.8 bits (86), Expect = 0.007
Identities = 22/104 (21%), Positives = 34/104 (32%), Gaps = 45/104 (43%)
Query: 285 RRLSIATAHAFLLVYSTTCLESFQSVK----------C-------------------YFE 315
R LS FL+ +S SF++VK C E
Sbjct: 63 RPLSYPDTDVFLICFSVDSPASFENVKEKWYPEVKHFCPNVPIILVGTKLDLRNDKSTLE 122
Query: 316 EIREQRQD----------------FQLLECSAKDNYNIKEVFRT 343
E+ +++Q+ + LECSA ++EVF
Sbjct: 123 ELSKKKQEPVTYEQGQALAKRIGAVKYLECSALTQEGVREVFEE 166
Score = 33.4 bits (77), Expect = 0.11
Identities = 16/47 (34%), Positives = 26/47 (55%)
Query: 13 LVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHVGAVTIK 59
LV++G VGK+C+L + N + + Y TV + YS D V ++
Sbjct: 1 LVVVGDGAVGKTCLLIVYTTNAFPEDYVPTVFENYSADVEVDGKPVE 47
>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 = 39.3 bits (92), Expect = 0.001
Identities = 39/143 (27%), Positives = 65/143 (45%), Gaps = 26/143 (18%)
Query: 11 IRLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHVGAVTIKEIPIVVAGNKS 70
I+++ +G GVGKSCI+KR+ + +Y T+ D+ V V+++ + V N
Sbjct: 1 IKVISMGNSGVGKSCIIKRYCEGRFVSKYLPTI----GIDYGVKKVSVRNKEVRV--NFF 54
Query: 71 DMTSH--HRAVHLE------------DVS-----EWLYCELPKLRYVIQSSSFGDEIPIV 111
D++ H + V E DV+ E L L +++ + I +V
Sbjct: 55 DLSGHPEYLEVRNEFYKDTQGVLLVYDVTDRQSFEALDSWLKEMKQEGGPHGNMENIVVV 114
Query: 112 VAGNKSDMTSHHRAVHLEDVSEW 134
V NK D+T HRAV ++ W
Sbjct: 115 VCANKIDLTK-HRAVSEDEGRLW 136
Score = 38.5 bits (90), Expect = 0.002
Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 4/79 (5%)
Query: 145 VDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDF---QE 201
V+ D G ++ +R LLVY T +SF+++ + +E++++ +
Sbjct: 51 VNFFDLSGHPEYLEVRNEFYKDTQGVLLVYDVTDRQSFEALDSWLKEMKQEGGPHGNMEN 110
Query: 202 IPIVVAGNKSDMTSHHRAV 220
I +VV NK D+T HRAV
Sbjct: 111 IVVVVCANKIDLTK-HRAV 128
>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 = 38.9 bits (91), Expect = 0.001
Identities = 23/83 (27%), Positives = 39/83 (46%), Gaps = 12/83 (14%)
Query: 147 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKC-YFEEIREQRQDFQEIPIV 205
+ DT G +F +R L FLL +S SFQ++ + EIR+ + PI+
Sbjct: 52 LCDTAGQDEFDKLRPLCYPDTDVFLLCFSVVNPSSFQNISEKWIPEIRKHN---PKAPII 108
Query: 206 VAGNKSDMTSHHRAVHLEDVDIL 228
+ G ++D+ DV++L
Sbjct: 109 LVGTQADLR--------TDVNVL 123
Score = 35.8 bits (83), Expect = 0.014
Identities = 36/145 (24%), Positives = 52/145 (35%), Gaps = 41/145 (28%)
Query: 218 RAVHLEDVDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKC-YFEEIRE-- 274
+ V L+ + DT G +F +R L FLL +S SFQ++ + EIR+
Sbjct: 46 KPVRLQ---LCDTAGQDEFDKLRPLCYPDTDVFLLCFSVVNPSSFQNISEKWIPEIRKHN 102
Query: 275 -------------QRQDFQFPAMRRLSIATAHAFLLVYSTTCLE---SFQSVKCYFEEIR 318
R D +L+ E S K E+I
Sbjct: 103 PKAPIILVGTQADLRTDVN---------------VLIQLARYGEKPVSQSRAKALAEKIG 147
Query: 319 EQRQDFQLLECSAKDNYNIKEVFRT 343
+ +ECSA N+KEVF T
Sbjct: 148 AC----EYIECSALTQKNLKEVFDT 168
Score = 32.8 bits (75), Expect = 0.18
Identities = 29/123 (23%), Positives = 49/123 (39%), Gaps = 21/123 (17%)
Query: 11 IRLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHVGAVTIKEIPIVVAGNKS 70
++ V++G VGK+ ++ + N Y Y T D +S V ++ AG
Sbjct: 1 LKCVLVGDGAVGKTSLIVSYTTNGYPTEYVPTAFDNFSVVVLVDGKPVRLQLCDTAGQ-- 58
Query: 71 DMTSHHRAVHLEDVSEWLYCELPKLRYVIQSSSFGD-------EI-------PIVVAGNK 116
D R + D +L C V+ SSF + EI PI++ G +
Sbjct: 59 DEFDKLRPLCYPDTDVFLLC-----FSVVNPSSFQNISEKWIPEIRKHNPKAPIILVGTQ 113
Query: 117 SDM 119
+D+
Sbjct: 114 ADL 116
>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 = 39.0 bits (91), Expect = 0.001
Identities = 10/33 (30%), Positives = 23/33 (69%)
Query: 11 IRLVILGGQGVGKSCILKRFLFNTYSDRYRSTV 43
I+++++G VGKS +++RF+ ++ Y+ T+
Sbjct: 1 IKVIVVGNGNVGKSSMIQRFVKGIFTKDYKKTI 33
Score = 35.9 bits (83), Expect = 0.013
Identities = 28/94 (29%), Positives = 48/94 (51%), Gaps = 6/94 (6%)
Query: 147 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIVV 206
+ DT G +F A+ + A A +LV+STT ESF++++ + E++ + D IP+V+
Sbjct: 55 LWDTAGQEEFDAITKAYYRGAQACILVFSTTDRESFEAIESWKEKVEAECGD---IPMVL 111
Query: 207 AGNKSDMTSHHRAVHLEDVDILDTCGDLQFPAMR 240
K D+ + E+ + L LQ P R
Sbjct: 112 VQTKIDL-LDQAVITNEEAEALAK--RLQLPLFR 142
Score = 31.6 bits (72), Expect = 0.31
Identities = 33/122 (27%), Positives = 55/122 (45%), Gaps = 16/122 (13%)
Query: 223 EDVDIL--DTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQ 280
EDV ++ DT G +F A+ + A A +LV+STT ESF++++ + E++ + D
Sbjct: 49 EDVRLMLWDTAGQEEFDAITKAYYRGAQACILVFSTTDRESFEAIESWKEKVEAECGD-- 106
Query: 281 FPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQLLECSAKDNYNIKEV 340
I LV + L + E +R L S KD++N+ E+
Sbjct: 107 --------IPMV----LVQTKIDLLDQAVITNEEAEALAKRLQLPLFRTSVKDDFNVTEL 154
Query: 341 FR 342
F
Sbjct: 155 FE 156
>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 = 38.1 bits (89), Expect = 0.002
Identities = 17/48 (35%), Positives = 29/48 (60%), Gaps = 4/48 (8%)
Query: 11 IRLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHVGAVTI 58
++++++G GVGKS +L RF +T+ + ST+ DF V VT+
Sbjct: 1 LKILLIGDSGVGKSSLLLRFTDDTFDEDLSSTI----GVDFKVKTVTV 44
Score = 32.7 bits (75), Expect = 0.15
Identities = 16/70 (22%), Positives = 30/70 (42%), Gaps = 1/70 (1%)
Query: 147 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIVV 206
I DT G +F + A +LVY T ++F ++ + E+ + + ++
Sbjct: 53 IWDTAGQERFRTLTSSYYRGAQGVILVYDVTRRDTFDNLDTWLNEL-DTYSTNPDAVKML 111
Query: 207 AGNKSDMTSH 216
GNK D +
Sbjct: 112 VGNKIDKENR 121
Score = 30.7 bits (70), Expect = 0.60
Identities = 16/82 (19%), Positives = 28/82 (34%), Gaps = 32/82 (39%)
Query: 292 AHAFLLVYSTTCLESFQSVKCYFEEI--------------------------REQRQDFQ 325
A +LVY T ++F ++ + E+ RE+ Q F
Sbjct: 73 AQGVILVYDVTRRDTFDNLDTWLNELDTYSTNPDAVKMLVGNKIDKENREVTREEGQKFA 132
Query: 326 ------LLECSAKDNYNIKEVF 341
+E SAK +++ F
Sbjct: 133 RKHNMLFIETSAKTRIGVQQAF 154
>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 = 38.5 bits (90), Expect = 0.003
Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 2/58 (3%)
Query: 166 TAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIVVAGNKSDMTSHHRAVHLE 223
A+++VYS T SF+ ++R RQ ++IPI++ GNKSD+ R V ++
Sbjct: 72 VGDAYVIVYSVTDRSSFEKASELRIQLRRARQA-EDIPIILVGNKSDLV-RSREVSVQ 127
Score = 28.5 bits (64), Expect = 5.4
Identities = 35/143 (24%), Positives = 55/143 (38%), Gaps = 42/143 (29%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTY-SDRYRSTVEDLYSRDFHVGAVTIKEIPIVVAGNKS 70
R+V+LG GVGKS + F Y Y ++ +D Y R + V G ++
Sbjct: 2 RVVLLGDSGVGKSSLANIFTAGVYEDSAYEASGDDTYERT------------VSVDGEEA 49
Query: 71 DMT--SHHRAVHLEDVSEWLY------CELPKLRY-VIQSSSF---------------GD 106
+ H + WL + + Y V SSF +
Sbjct: 50 TLVVYDHWEQ----EDGMWLEDSCMQVGDAYVIVYSVTDRSSFEKASELRIQLRRARQAE 105
Query: 107 EIPIVVAGNKSDMTSHHRAVHLE 129
+IPI++ GNKSD+ R V ++
Sbjct: 106 DIPIILVGNKSDLV-RSREVSVQ 127
>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 = 37.9 bits (88), Expect = 0.004
Identities = 20/47 (42%), Positives = 28/47 (59%), Gaps = 4/47 (8%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHVGAVTI 58
+L+I+G GVGKS +L RF NT+S Y +T+ DF + V I
Sbjct: 8 KLLIIGDSGVGKSSLLLRFADNTFSGSYITTI----GVDFKIRTVEI 50
Score = 36.0 bits (83), Expect = 0.017
Identities = 25/81 (30%), Positives = 38/81 (46%), Gaps = 12/81 (14%)
Query: 141 KLRYVDI---------LDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEE 191
K+R V+I DT G +F + H ++VY T ESF +VK + +E
Sbjct: 44 KIRTVEINGERVKLQIWDTAGQERFRTITSTYYRGTHGVIVVYDVTNGESFVNVKRWLQE 103
Query: 192 IREQRQDFQEIPIVVAGNKSD 212
I + D + V+ GNK+D
Sbjct: 104 IEQNCDDVCK---VLVGNKND 121
Score = 33.3 bits (76), Expect = 0.13
Identities = 28/117 (23%), Positives = 47/117 (40%), Gaps = 18/117 (15%)
Query: 227 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQFPAMRR 286
I DT G +F + H ++VY T ESF +VK + +EI + D
Sbjct: 59 IWDTAGQERFRTITSTYYRGTHGVIVVYDVTNGESFVNVKRWLQEIEQNCDDVC------ 112
Query: 287 LSIATAHAFLLVYSTTCLESFQSVKCYFEEIRE--QRQDFQLLECSAKDNYNIKEVF 341
++ + + V E+ + + L E SAK+N N++E+F
Sbjct: 113 ---------KVLVGNKNDDPERKV-VETEDAYKFAGQMGISLFETSAKENINVEEMF 159
>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 = 37.2 bits (87), Expect = 0.004
Identities = 13/33 (39%), Positives = 24/33 (72%)
Query: 11 IRLVILGGQGVGKSCILKRFLFNTYSDRYRSTV 43
+L+++G GVGKSC+L RF ++++ + ST+
Sbjct: 4 FKLLLIGDSGVGKSCLLLRFSEDSFNPSFISTI 36
Score = 35.3 bits (82), Expect = 0.019
Identities = 27/82 (32%), Positives = 37/82 (45%), Gaps = 13/82 (15%)
Query: 147 ILDTCGDLQFPAMRRLSIAT-----AHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQE 201
I DT G +F +I T A +LVY T +SF+++K + I E + E
Sbjct: 56 IWDTAGQERFR-----TITTSYYRGAMGIILVYDITDEKSFENIKNWMRNIDEHASEDVE 110
Query: 202 IPIVVAGNKSDMTSHHRAVHLE 223
+V GNK DM R V E
Sbjct: 111 RMLV--GNKCDME-EKRVVSKE 129
Score = 33.8 bits (78), Expect = 0.061
Identities = 33/125 (26%), Positives = 52/125 (41%), Gaps = 29/125 (23%)
Query: 227 ILDTCGDLQFPAMRRLSIAT-----AHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQF 281
I DT G +F +I T A +LVY T +SF+++K + I E
Sbjct: 56 IWDTAGQERFR-----TITTSYYRGAMGIILVYDITDEKSFENIKNWMRNIDEH------ 104
Query: 282 PAMRRLSIATAHAFLLVYSTTC-LESFQSVKCYFEEIREQRQDFQL--LECSAKDNYNIK 338
A+ ++ C +E + V EE +++ + LE SAK N N++
Sbjct: 105 --------ASEDVERMLVGNKCDMEEKRVVS--KEEGEALAREYGIKFLETSAKANINVE 154
Query: 339 EVFRT 343
E F T
Sbjct: 155 EAFLT 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 = 37.0 bits (86), Expect = 0.006
Identities = 24/77 (31%), Positives = 35/77 (45%), Gaps = 2/77 (2%)
Query: 147 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIVV 206
I DT G +F ++ R A LLVY T ESF ++ + + R +I I++
Sbjct: 53 IWDTAGQERFRSVTRSYYRGAAGALLVYDITSRESFNALTNWLTDARTLAS--PDIVIIL 110
Query: 207 AGNKSDMTSHHRAVHLE 223
GNK D+ LE
Sbjct: 111 VGNKKDLEDDREVTFLE 127
Score = 35.1 bits (81), Expect = 0.023
Identities = 16/49 (32%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRSTV-EDLYSRDFHVGAVTIK 59
+ +I+G G GKSC+L +F+ N + T+ + SR +VG ++K
Sbjct: 2 KFLIIGSAGTGKSCLLHQFIENKFKQDSNHTIGVEFGSRVVNVGGKSVK 50
Score = 30.9 bits (70), Expect = 0.55
Identities = 32/117 (27%), Positives = 48/117 (41%), Gaps = 17/117 (14%)
Query: 227 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQFPAMRR 286
I DT G +F ++ R A LLVY T ESF ++ + + R
Sbjct: 53 IWDTAGQERFRSVTRSYYRGAAGALLVYDITSRESFNALTNWLTDAR------------- 99
Query: 287 LSIATAH-AFLLVYSTTCLESFQSVKCYFEEIR-EQRQDFQLLECSAKDNYNIKEVF 341
++A+ +LV + LE + V + E R Q LE SA N++E F
Sbjct: 100 -TLASPDIVIILVGNKKDLEDDREVT-FLEASRFAQENGLLFLETSALTGENVEEAF 154
>gnl|CDD|206657 cd01865, Rab3, Rab GTPase family 3 contains Rab3A, Rab3B, Rab3C and
Rab3D. The Rab3 subfamily contains Rab3A, Rab3B, Rab3C,
and Rab3D. All four isoforms were found in mouse brain
and endocrine tissues, with varying levels of
expression. Rab3A, Rab3B, and Rab3C localized to
synaptic and secretory vesicles; Rab3D was expressed at
high levels only in adipose tissue, exocrine glands, and
the endocrine pituitary, where it is localized to
cytoplasmic secretory granules. Rab3 appears to control
Ca2+-regulated exocytosis. The appropriate GDP/GTP
exchange cycle of Rab3A is required for Ca2+-regulated
exocytosis to occur, and interaction of the GTP-bound
form of Rab3A with effector molecule(s) is widely
believed to be essential for this process. Functionally,
most studies point toward a role for Rab3 in the
secretion of hormones and neurotransmitters. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 165
Score = 36.8 bits (85), Expect = 0.006
Identities = 31/118 (26%), Positives = 52/118 (44%), Gaps = 19/118 (16%)
Query: 227 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQFPAMRR 286
I DT G ++ + A F+L+Y T ESF +V+ + +I+ D
Sbjct: 54 IWDTAGQERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSWD-------- 105
Query: 287 LSIATAHAFLLVYSTTC-LESFQSVKCYFEEIREQRQD--FQLLECSAKDNYNIKEVF 341
+A +++ C +E + V E R+ F+ E SAK+N N+K+VF
Sbjct: 106 ------NAQVILVGNKCDMEDERVVS--AERGRQLADQLGFEFFEASAKENINVKQVF 155
Score = 36.4 bits (84), Expect = 0.009
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 3/78 (3%)
Query: 147 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIVV 206
I DT G ++ + A F+L+Y T ESF +V+ + +I+ D + +++
Sbjct: 54 IWDTAGQERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSWDNAQ--VIL 111
Query: 207 AGNKSDMTSHHRAVHLED 224
GNK DM R V E
Sbjct: 112 VGNKCDMED-ERVVSAER 128
>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 = 0.015
Identities = 22/81 (27%), Positives = 38/81 (46%), Gaps = 4/81 (4%)
Query: 147 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEI--REQRQDFQEIPI 204
I DT G +F ++R + LL +S +SFQ++ + +E ++ + P
Sbjct: 58 IWDTAGQERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPESFPF 117
Query: 205 VVAGNKSDMTSHHRAVHLEDV 225
V+ GNK D+ R V E+
Sbjct: 118 VILGNKIDIPE--RQVSTEEA 136
Score = 32.9 bits (75), Expect = 0.15
Identities = 33/151 (21%), Positives = 56/151 (37%), Gaps = 44/151 (29%)
Query: 11 IRLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHVGAVTIKEIPIVVAGN-- 68
+++++LG GVGKS ++ R++ N + ++ FH V + V G+
Sbjct: 6 LKVILLGDGGVGKSSLMNRYVTNKFD-----------TQLFHTIGVEFLNKDLEVDGHFV 54
Query: 69 -------------KSDMTSHHR---------AVHLEDVSEWLYCELPKLRY---VIQSSS 103
+S T +R +V + L + Y V + S
Sbjct: 55 TLQIWDTAGQERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPES 114
Query: 104 FGDEIPIVVAGNKSDMTSHHRAVHLEDVSEW 134
F P V+ GNK D+ R V E+ W
Sbjct: 115 F----PFVILGNKIDIPE--RQVSTEEAQAW 139
>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 = 35.9 bits (83), Expect = 0.018
Identities = 16/39 (41%), Positives = 24/39 (61%), Gaps = 1/39 (2%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRSTVE-DLYSR 49
RL+++G VGKS +LKRF +++ TV D +SR
Sbjct: 4 RLIVIGDSTVGKSSLLKRFTEGRFAEVSDPTVGVDFFSR 42
Score = 35.9 bits (83), Expect = 0.019
Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 1/70 (1%)
Query: 147 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIVV 206
+ DT G +F ++ R + LLV+ T ESF+ V + EE R Q + + I+V
Sbjct: 56 LWDTAGQERFRSITRSYYRNSVGVLLVFDITNRESFEHVHDWLEEARSHIQPHRPVFILV 115
Query: 207 AGNKSDMTSH 216
G+K D+ S
Sbjct: 116 -GHKCDLESQ 124
Score = 32.8 bits (75), Expect = 0.21
Identities = 35/136 (25%), Positives = 53/136 (38%), Gaps = 17/136 (12%)
Query: 227 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQFPAMRR 286
+ DT G +F ++ R + LLV+ T ESF+ V + EE R Q
Sbjct: 56 LWDTAGQERFRSITRSYYRNSVGVLLVFDITNRESFEHVHDWLEEARSHIQPH------- 108
Query: 287 LSIATAHAFLLVYSTTCLESFQSVKCYFE-EIREQRQDFQLLECSAKDNYNIKEVFRTFL 345
F+LV LES + V E E + + +E SA+ N++E F
Sbjct: 109 -----RPVFILVGHKCDLESQRQV-TREEAEKLAKDLGMKYIETSARTGDNVEEAFE--- 159
Query: 346 TLSQILTTNGDENSLK 361
L+Q + L
Sbjct: 160 LLTQEIYERIKRGELC 175
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 35.1 bits (80), Expect = 0.025
Identities = 23/103 (22%), Positives = 55/103 (53%), Gaps = 3/103 (2%)
Query: 121 SHHRAVHLEDVSEWLYCELPKLRYVDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLE 180
++ + ++ +S+ LY + +R + + DT G +F ++ I + A ++VY T +
Sbjct: 8 NYQSTIGIDFLSKTLYLDEGPVR-LQLWDTAGQERFRSLIPSYIRDSAAAIVVYDITNRQ 66
Query: 181 SFQSVKCYFEEIREQRQDFQEIPIVVAGNKSDMTSHHRAVHLE 223
SF++ + ++I +R +++ I + GNK+D+ + + E
Sbjct: 67 SFENTTKWIQDILNERG--KDVIIALVGNKTDLGDLRKVTYEE 107
Score = 32.4 bits (73), Expect = 0.24
Identities = 31/120 (25%), Positives = 59/120 (49%), Gaps = 17/120 (14%)
Query: 225 VDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQFPAM 284
+ + DT G +F ++ I + A ++VY T +SF++ + ++I +R
Sbjct: 31 LQLWDTAGQERFRSLIPSYIRDSAAAIVVYDITNRQSFENTTKWIQDILNERG------- 83
Query: 285 RRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQLL--ECSAKDNYNIKEVFR 342
+ + IA LV + T L + V +EE ++ Q++ + E SAK +NIK +F+
Sbjct: 84 KDVIIA------LVGNKTDLGDLRKVT--YEEGMQKAQEYNTMFHETSAKAGHNIKVLFK 135
>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 = 35.4 bits (81), Expect = 0.026
Identities = 17/50 (34%), Positives = 26/50 (52%)
Query: 9 ERIRLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHVGAVTI 58
+ I+ V++G VGK+C+L + N + Y TV D YS V T+
Sbjct: 2 QSIKCVVVGDGAVGKTCLLICYTTNAFPKEYIPTVFDNYSAQTAVDGRTV 51
Score = 30.7 bits (69), Expect = 0.71
Identities = 16/65 (24%), Positives = 30/65 (46%), Gaps = 3/65 (4%)
Query: 202 IPIVVAGNKSDMTSHHRAVHLEDVDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLES 261
IP V + R V L ++ DT G ++ +R LS + F++ +S S
Sbjct: 33 IPTVFDNYSAQTAVDGRTVSL---NLWDTAGQEEYDRLRTLSYPQTNVFIICFSIASPSS 89
Query: 262 FQSVK 266
+++V+
Sbjct: 90 YENVR 94
Score = 30.7 bits (69), Expect = 0.89
Identities = 24/115 (20%), Positives = 48/115 (41%), Gaps = 22/115 (19%)
Query: 101 SSSFGDE-IPIVVAGNKSDMTSHHRAVHLEDVSEWLYCELPKLRYVDILDTCGDLQFPAM 159
+++F E IP V + R V L ++ DT G ++ +
Sbjct: 25 TNAFPKEYIPTVFDNYSAQTAVDGRTVSL-----------------NLWDTAGQEEYDRL 67
Query: 160 RRLSIATAHAFLLVYSTTCLESFQSVKC-YFEEIREQRQDFQEIPIVVAGNKSDM 213
R LS + F++ +S S+++V+ + E+ + +PI++ G K D+
Sbjct: 68 RTLSYPQTNVFIICFSIASPSSYENVRHKWHPEVCHHCPN---VPILLVGTKKDL 119
>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 = 35.0 bits (81), Expect = 0.031
Identities = 14/31 (45%), Positives = 22/31 (70%), Gaps = 1/31 (3%)
Query: 13 LVILGGQGVGKSCILKRFLFNTYSDRYRSTV 43
LVI G GVGK+ I+KR++ +S Y++T+
Sbjct: 4 LVI-GDLGVGKTSIIKRYVHGVFSQHYKATI 33
>gnl|CDD|206725 cd04160, Arfrp1, Arf-related protein 1 (Arfrp1). Arfrp1
(Arf-related protein 1), formerly known as ARP, is a
membrane-associated Arf family member that lacks the
N-terminal myristoylation motif. Arfrp1 is mainly
associated with the trans-Golgi compartment and the
trans-Golgi network, where it regulates the targeting of
Arl1 and the GRIP domain-containing proteins, golgin-97
and golgin-245, onto Golgi membranes. It is also
involved in the anterograde transport of the vesicular
stomatitis virus G protein from the Golgi to the plasma
membrane, and in the retrograde transport of TGN38 and
Shiga toxin from endosomes to the trans-Golgi network.
Arfrp1 also inhibits Arf/Sec7-dependent activation of
phospholipase D. Deletion of Arfrp1 in mice causes
embryonic lethality at the gastrulation stage and
apoptosis of mesodermal cells, indicating its importance
in development.
Length = 168
Score = 34.6 bits (80), Expect = 0.032
Identities = 15/62 (24%), Positives = 30/62 (48%), Gaps = 4/62 (6%)
Query: 165 ATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIVVAGNKSDMTSHHRAVHLED 224
A +H + V +T E F K FE++ + + +P++V NK D+ A+ + +
Sbjct: 73 AESHGVIYVIDSTDRERFNESKSAFEKVINN-EALEGVPLLVLANKQDLPD---ALSVAE 128
Query: 225 VD 226
+
Sbjct: 129 IK 130
Score = 28.1 bits (63), Expect = 5.5
Identities = 7/39 (17%), Positives = 19/39 (48%), Gaps = 3/39 (7%)
Query: 58 IKEIPIVVAGNKSDMTSHHRAVHLEDVSEWLYCELPKLR 96
++ +P++V NK D+ A+ + ++ E + +
Sbjct: 106 LEGVPLLVLANKQDLPD---ALSVAEIKEVFDDCIALIG 141
Score = 27.7 bits (62), Expect = 7.9
Identities = 9/41 (21%), Positives = 19/41 (46%), Gaps = 3/41 (7%)
Query: 108 IPIVVAGNKSDMTSHHRAVHLEDVSEWLYCELPKLRYVDIL 148
+P++V NK D+ A+ + ++ E + + D L
Sbjct: 109 VPLLVLANKQDLPD---ALSVAEIKEVFDDCIALIGRRDCL 146
>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 = 34.2 bits (78), Expect = 0.046
Identities = 14/32 (43%), Positives = 22/32 (68%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRSTV 43
RL+++G GVGK+C+L RF N + + ST+
Sbjct: 2 RLLLIGDSGVGKTCLLCRFTDNEFHSSHISTI 33
Score = 27.2 bits (60), Expect = 9.3
Identities = 17/72 (23%), Positives = 34/72 (47%), Gaps = 3/72 (4%)
Query: 141 KLRYVDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQ 200
K+R + I DT G ++ + + A LVY + S+Q + + ++ E +
Sbjct: 48 KVR-IQIWDTAGQERYQTITKQYYRRAQGIFLVYDISSERSYQHIMKWVSDVDEYAPEGV 106
Query: 201 EIPIVVAGNKSD 212
+ ++ GNK+D
Sbjct: 107 QKILI--GNKAD 116
>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 = 34.4 bits (79), Expect = 0.064
Identities = 35/137 (25%), Positives = 63/137 (45%), Gaps = 25/137 (18%)
Query: 11 IRLVILGGQGVGKSCILKRFLFNTYSDRYRSTVE-DLYSRDF---HVGAVTIKEIPI--- 63
I++V+LG GK+ +++RF + Y+ T+ D +SR VT++ I
Sbjct: 1 IKIVVLGDGASGKTSLIRRFAQEGFGKSYKQTIGLDFFSRRITLPGSLNVTLQVWDIGGQ 60
Query: 64 VVAGNKSDMTSH-HRAVHL----------EDVSEWLYCELPKLRYVIQSSSFGDEIPIVV 112
+ G D + +AV L E++ +WL ++ V + S + +V+
Sbjct: 61 QIGGKMLDKYIYGAQAVCLVYDITNSQSFENLEDWLSV----VKKVNEES--ETKPKMVL 114
Query: 113 AGNKSDMTSHHRAVHLE 129
GNK+D+ H+R V E
Sbjct: 115 VGNKTDL-EHNRQVTAE 130
Score = 33.6 bits (77), Expect = 0.11
Identities = 19/61 (31%), Positives = 36/61 (59%), Gaps = 2/61 (3%)
Query: 164 IATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIP-IVVAGNKSDMTSHHRAVHL 222
I A A LVY T +SF++++ + +++ ++ + P +V+ GNK+D+ H+R V
Sbjct: 71 IYGAQAVCLVYDITNSQSFENLEDWLSVVKKVNEESETKPKMVLVGNKTDL-EHNRQVTA 129
Query: 223 E 223
E
Sbjct: 130 E 130
>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 = 33.6 bits (77), Expect = 0.070
Identities = 16/48 (33%), Positives = 25/48 (52%)
Query: 11 IRLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHVGAVTI 58
I+ V++G VGK+C+L + N + Y TV D YS + V +
Sbjct: 2 IKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPV 49
Score = 32.1 bits (73), Expect = 0.30
Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 4/66 (6%)
Query: 149 DTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKC-YFEEIREQRQDFQEIPIVVA 207
DT G + +R LS FL+ +S SF++V+ ++ E+R + PI++
Sbjct: 55 DTAGQEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPN---TPIILV 111
Query: 208 GNKSDM 213
G K D+
Sbjct: 112 GTKLDL 117
>gnl|CDD|206700 cd04127, Rab27A, Rab GTPase family 27a (Rab27a). The Rab27a
subfamily consists of Rab27a and its highly homologous
isoform, Rab27b. Unlike most Rab proteins whose
functions remain poorly defined, Rab27a has many known
functions. Rab27a has multiple effector proteins, and
depending on which effector it binds, Rab27a has
different functions as well as tissue distribution
and/or cellular localization. Putative functions have
been assigned to Rab27a when associated with the
effector proteins Slp1, Slp2, Slp3, Slp4, Slp5, DmSlp,
rabphilin, Dm/Ce-rabphilin, Slac2-a, Slac2-b, Slac2-c,
Noc2, JFC1, and Munc13-4. Rab27a has been associated
with several human diseases, including hemophagocytic
syndrome (Griscelli syndrome or GS), Hermansky-Pudlak
syndrome, and choroidermia. In the case of GS, a rare,
autosomal recessive disease, a Rab27a mutation is
directly responsible for the disorder. When Rab27a is
localized to the secretory granules of pancreatic beta
cells, it is believed to mediate glucose-stimulated
insulin secretion, making it a potential target for
diabetes therapy. When bound to JFC1 in prostate cells,
Rab27a is believed to regulate the exocytosis of
prostate- specific markers. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab
proteins. Due to the presence of truncated sequences in
this CD, the lipid modification site is not available
for annotation.
Length = 180
Score = 33.6 bits (77), Expect = 0.077
Identities = 13/33 (39%), Positives = 22/33 (66%)
Query: 11 IRLVILGGQGVGKSCILKRFLFNTYSDRYRSTV 43
I+L+ LG GVGK+ L R+ N ++ ++ +TV
Sbjct: 5 IKLLALGDSGVGKTTFLYRYTDNKFNPKFITTV 37
Score = 33.2 bits (76), Expect = 0.11
Identities = 24/86 (27%), Positives = 42/86 (48%), Gaps = 4/86 (4%)
Query: 144 YVDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIP 203
++ + DT G +F ++ A FLL++ T +SF +V+ + ++ Q + E P
Sbjct: 64 HLQLWDTAGQERFRSLTTAFFRDAMGFLLMFDLTSEQSFLNVRNWMSQL--QAHAYCENP 121
Query: 204 -IVVAGNKSDMTSHHRAVHLEDVDIL 228
IV+ GNK+D+ R V L
Sbjct: 122 DIVLIGNKADLPD-QREVSERQAREL 146
Score = 28.6 bits (64), Expect = 4.0
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 4/77 (5%)
Query: 198 DFQEIPIVVAGNKSDMTSHHR-AVHLEDVDILDTCGDLQFPAMRRLSIATAHAFLLVYST 256
DF+E +V D TS VHL+ + DT G +F ++ A FLL++
Sbjct: 40 DFREKRVVYNSQGPDGTSGKAFRVHLQ---LWDTAGQERFRSLTTAFFRDAMGFLLMFDL 96
Query: 257 TCLESFQSVKCYFEEIR 273
T +SF +V+ + +++
Sbjct: 97 TSEQSFLNVRNWMSQLQ 113
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 33.6 bits (77), Expect = 0.098
Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 5 MCDNERIRLVILGGQGVGKSCILKRFLFNTYSDRYRSTVE-DLYSRDFH 52
D +LVI+G G GK+ +KR L + +Y T+ +++ DF
Sbjct: 8 TVDYPSFKLVIVGDGGTGKTTFVKRHLTGEFEKKYEPTIGVEVHPLDFF 56
>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 = 32.9 bits (75), Expect = 0.16
Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 4/69 (5%)
Query: 149 DTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSV-KCYFEEIREQRQDFQEIPIVVA 207
DT G + +R LS A FLL +S S+++V K + E+R +PIV+
Sbjct: 55 DTAGQEDYNRLRPLSYRGADVFLLAFSLISKASYENVLKKWIPELRHYAPG---VPIVLV 111
Query: 208 GNKSDMTSH 216
G K D+
Sbjct: 112 GTKLDLRDD 120
Score = 28.3 bits (63), Expect = 4.8
Identities = 34/129 (26%), Positives = 54/129 (41%), Gaps = 27/129 (20%)
Query: 11 IRLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHVGAVTIKEIPIVVAG--- 67
I+ V +G VGK+C+L + NT+ Y TV D +S + V T+ AG
Sbjct: 2 IKCVTVGDGAVGKTCMLISYTSNTFPTDYVPTVFDNFSANVVVDGNTVNLGLWDTAGQED 61
Query: 68 -NKSDMTSHHRA------------VHLEDVS-EWLYCELPKLRYVIQSSSFGDEIPIVVA 113
N+ S+ A E+V +W +P+LR+ + +PIV+
Sbjct: 62 YNRLRPLSYRGADVFLLAFSLISKASYENVLKKW----IPELRH------YAPGVPIVLV 111
Query: 114 GNKSDMTSH 122
G K D+
Sbjct: 112 GTKLDLRDD 120
>gnl|CDD|206741 cd09914, RocCOR, Ras of complex proteins (Roc) C-terminal of Roc
(COR) domain family. RocCOR (or Roco) protein family is
characterized by a superdomain containing a Ras-like
GTPase domain, called Roc (Ras of complex proteins), and
a characteristic second domain called COR (C-terminal of
Roc). A kinase domain and diverse regulatory domains are
also often found in Roco proteins. Their functions are
diverse; in Dictyostelium discoideum, which encodes 11
Roco proteins, they are involved in cell division,
chemotaxis and development, while in human, where 4 Roco
proteins (LRRK1, LRRK2, DAPK1, and MFHAS1) are encoded,
these proteins are involved in epilepsy and cancer.
Mutations in LRRK2 (leucine-rich repeat kinase 2) are
known to cause familial Parkinson's disease.
Length = 161
Score = 32.3 bits (74), Expect = 0.18
Identities = 27/133 (20%), Positives = 61/133 (45%), Gaps = 11/133 (8%)
Query: 10 RIRLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHVGAVTIKEIPIVV--AG 67
+L+++G GVGK+ + K+ + + D S+ + +D+ + A K+I + V G
Sbjct: 1 EAKLMLVGQGGVGKTSLCKQLIGEKF-DGDESSTHGINVQDWKIPAPERKKIRLNVWDFG 59
Query: 68 NKSDMTSHH------RAVHLEDVSEWLYCELPKLRY-VIQSSSFGDEIPIVVAGNKSDMT 120
+ + H R+++L E+ ++ Y + Q +FG P+++ G D
Sbjct: 60 GQEIYHATHQFFLTSRSLYLLVFDLRTGDEVSRVPYWLRQIKAFGGVSPVILVGTHID-E 118
Query: 121 SHHRAVHLEDVSE 133
S + + +++
Sbjct: 119 SCDEDILKKALNK 131
>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 = 32.3 bits (73), Expect = 0.19
Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 2/67 (2%)
Query: 147 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIVV 206
+ DT G + +R LS FL+ +S SFQ+VK E + E ++ +P ++
Sbjct: 52 LYDTAGQEDYDRLRPLSYPMTDVFLICFSVVNPASFQNVK--EEWVPELKEYAPNVPYLL 109
Query: 207 AGNKSDM 213
G + D+
Sbjct: 110 IGTQIDL 116
Score = 31.9 bits (72), Expect = 0.26
Identities = 14/45 (31%), Positives = 25/45 (55%)
Query: 11 IRLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHVGA 55
++ V++G VGK+C+L + + + + Y TV D Y+ VG
Sbjct: 1 LKCVVVGDGAVGKTCLLMSYANDAFPEEYVPTVFDHYAVSVTVGG 45
>gnl|CDD|206699 cd04120, Rab12, Rab GTPase family 12 (Rab12). Rab12 was first
identified in canine cells, where it was localized to
the Golgi complex. The specific function of Rab12
remains unknown, and inconsistent results about its
cellular localization have been reported. More recent
studies have identified Rab12 associated with post-Golgi
vesicles, or with other small vesicle-like structures
but not with the Golgi complex. Most Rab GTPases contain
a lipid modification site at the C-terminus, with
sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation of
the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins.
Length = 202
Score = 32.7 bits (74), Expect = 0.21
Identities = 27/117 (23%), Positives = 48/117 (41%), Gaps = 12/117 (10%)
Query: 225 VDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQFPAM 284
+ I DT G +F ++ +A +LVY T E+F + + + I + +
Sbjct: 51 LQIWDTAGQERFNSITSAYYRSAKGIILVYDITKKETFDDLPKWMKMIDKYASE------ 104
Query: 285 RRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQLLECSAKDNYNIKEVF 341
A L+ C + + E+ +Q + E SAKDN+N+ E+F
Sbjct: 105 ------DAELLLVGNKLDCETDREITRQQGEKFAQQITGMRFCEASAKDNFNVDEIF 155
>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 = 32.1 bits (73), Expect = 0.21
Identities = 27/120 (22%), Positives = 49/120 (40%), Gaps = 19/120 (15%)
Query: 225 VDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQFPAM 284
+ I DT G +F A+ R A L+VY T ++ + + + R
Sbjct: 53 LQIWDTAGQERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDAR----------- 101
Query: 285 RRLSIATAH-AFLLVYSTTCLESFQSVKCYFEEIRE--QRQDFQLLECSAKDNYNIKEVF 341
++ + L+ + LE+ + V +EE ++ LECSAK N+++ F
Sbjct: 102 ---NLTNPNTVIFLIGNKADLEAQRDVT--YEEAKQFADENGLLFLECSAKTGENVEDAF 156
Score = 29.4 bits (66), Expect = 1.7
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 12 RLVILGGQGVGKSCILKRF 30
+ +I+G GVGKSC+L +F
Sbjct: 4 KYIIIGDMGVGKSCLLHQF 22
Score = 28.3 bits (63), Expect = 4.6
Identities = 23/92 (25%), Positives = 37/92 (40%), Gaps = 3/92 (3%)
Query: 145 VDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPI 204
+ I DT G +F A+ R A L+VY T ++ + + + R I
Sbjct: 53 LQIWDTAGQERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDAR--NLTNPNTVI 110
Query: 205 VVAGNKSDMTSHHRAVHLEDVDILDTCGDLQF 236
+ GNK+D+ + R V E+ L F
Sbjct: 111 FLIGNKADLEA-QRDVTYEEAKQFADENGLLF 141
>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 = 32.1 bits (73), Expect = 0.26
Identities = 18/69 (26%), Positives = 25/69 (36%), Gaps = 1/69 (1%)
Query: 147 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIVV 206
I D+ G F M +VY T SF + + +R P V+
Sbjct: 57 IFDSAGQELFSDMVENVWEQPAVVCVVYDVTNEVSFNNCSRWINRVRTHSHG-LHTPGVL 115
Query: 207 AGNKSDMTS 215
GNK D+T
Sbjct: 116 VGNKCDLTD 124
>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 = 31.8 bits (72), Expect = 0.33
Identities = 41/170 (24%), Positives = 61/170 (35%), Gaps = 41/170 (24%)
Query: 185 VKCYFEEIREQRQDFQEIPIVVAGNKSDMTSHHRAVHLEDVDILDTCGDLQFPAMRRLSI 244
+ YF ++ E P V D+ AV L + DT G +F +R LS
Sbjct: 21 TRGYFPQVYE--------PTVFENYIHDIFVDGLAVELS---LWDTAGQEEFDRLRSLSY 69
Query: 245 ATAHAFLLVYSTTCLESFQSVKC-YFEEIREQRQDFQFPAMRRLSIA------------T 291
A H +L +S +S ++V+ + EIR P ++ + +A
Sbjct: 70 ADTHVIMLCFSVDNPDSLENVESKWLAEIRH-----HCPGVKLVLVALKCDLREPRNERD 124
Query: 292 AHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQLLECSAKDNYNIKEVF 341
+ Y E K I R LECSAK N + E F
Sbjct: 125 RGTHTISYE----EGLAVAK----RINACR----YLECSAKLNRGVNEAF 162
Score = 27.5 bits (61), Expect = 7.8
Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 149 DTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKC-YFEEIRE 194
DT G +F +R LS A H +L +S +S ++V+ + EIR
Sbjct: 54 DTAGQEEFDRLRSLSYADTHVIMLCFSVDNPDSLENVESKWLAEIRH 100
>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 = 31.8 bits (72), Expect = 0.35
Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 4/68 (5%)
Query: 147 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVK-CYFEEIREQRQDFQEIPIV 205
+ DT G + +R LS FL+ +S SF++VK + EI + P +
Sbjct: 53 LFDTAGQEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHH---CPKTPFL 109
Query: 206 VAGNKSDM 213
+ G + D+
Sbjct: 110 LVGTQIDL 117
Score = 31.4 bits (71), Expect = 0.51
Identities = 15/44 (34%), Positives = 24/44 (54%)
Query: 11 IRLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHVG 54
I+ V++G VGK+C+L + N + Y TV D Y+ +G
Sbjct: 2 IKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIG 45
Score = 29.5 bits (66), Expect = 1.9
Identities = 15/48 (31%), Positives = 23/48 (47%), Gaps = 1/48 (2%)
Query: 227 ILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVK-CYFEEIR 273
+ DT G + +R LS FL+ +S SF++VK + EI
Sbjct: 53 LFDTAGQEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEIT 100
>gnl|CDD|115510 pfam06858, NOG1, Nucleolar GTP-binding protein 1 (NOG1). This
family represents a conserved region of approximately 60
residues in length within nucleolar GTP-binding protein
1 (NOG1). In S. cerevisiae, the NOG1 gene has been shown
to be essential for cell viability, suggesting that NOG1
may play an important role in nucleolar functions.
Family members include eukaryotic, bacterial and
archaeal proteins.
Length = 58
Score = 29.1 bits (66), Expect = 0.50
Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 3/49 (6%)
Query: 164 IATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIVVAGNKSD 212
+ A F+ S C S + F+EI+ F+ P++V NK D
Sbjct: 13 LRAAVLFVFDPSEQCGYSLEEQLHLFKEIKPL---FKNKPVIVVLNKID 58
>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 = 31.3 bits (71), Expect = 0.57
Identities = 18/65 (27%), Positives = 36/65 (55%), Gaps = 2/65 (3%)
Query: 149 DTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIVVAG 208
DT G ++ +R LS + AH L+ ++ +S ++V+ + I E R+ +P+++ G
Sbjct: 55 DTAGQEEYERLRPLSYSKAHVILIGFAIDTPDSLENVRTKW--IEEVRRYCPNVPVILVG 112
Query: 209 NKSDM 213
K D+
Sbjct: 113 LKKDL 117
>gnl|CDD|217326 pfam03029, ATP_bind_1, Conserved hypothetical ATP binding protein.
Members of this family are found in a range of archaea
and eukaryotes and have hypothesised ATP binding
activity.
Length = 235
Score = 31.2 bits (71), Expect = 0.70
Identities = 18/64 (28%), Positives = 24/64 (37%), Gaps = 3/64 (4%)
Query: 201 EIPIVVAGNKSDMTSHHRAV-HLEDVDILDTCGDLQFPAMRRLSIATAHA-FLLVYSTTC 258
+P VVA NK D+ S A+ D D L +L + +I A F LV
Sbjct: 155 GLPFVVALNKFDLLSLEFALKWFTDPDDLQLLLELDPSKLNE-AIREALDLFYLVPRFLP 213
Query: 259 LESF 262
Sbjct: 214 DARE 217
>gnl|CDD|133303 cd04103, Centaurin_gamma, Centaurin gamma (CENTG) GTPase. The
centaurins (alpha, beta, gamma, and delta) are large,
multi-domain proteins that all contain an ArfGAP domain
and ankyrin repeats, and in some cases, numerous
additional domains. Centaurin gamma contains an
additional GTPase domain near its N-terminus. The
specific function of this GTPase domain has not been
well characterized, but centaurin gamma 2 (CENTG2) may
play a role in the development of autism. Centaurin
gamma 1 is also called PIKE (phosphatidyl inositol (PI)
3-kinase enhancer) and centaurin gamma 2 is also known
as AGAP (ArfGAP protein with a GTPase-like domain,
ankyrin repeats and a Pleckstrin homology domain) or
GGAP. Three isoforms of PIKE have been identified.
PIKE-S (short) and PIKE-L (long) are brain-specific
isoforms, with PIKE-S restricted to the nucleus and
PIKE-L found in multiple cellular compartments. A third
isoform, PIKE-A was identified in human glioblastoma
brain cancers and has been found in various tissues.
GGAP has been shown to have high GTPase activity due to
a direct intramolecular interaction between the
N-terminal GTPase domain and the C-terminal ArfGAP
domain. In human tissue, AGAP mRNA was detected in
skeletal muscle, kidney, placenta, brain, heart, colon,
and lung. Reduced expression levels were also observed
in the spleen, liver, and small intestine.
Length = 158
Score = 30.5 bits (69), Expect = 0.77
Identities = 17/67 (25%), Positives = 32/67 (47%), Gaps = 2/67 (2%)
Query: 169 AFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIVVAGNKSDMTSHHRAVHLEDVDIL 228
A + V+S SFQ+V + ++ R + EIP+++ G + D S ++D
Sbjct: 68 AVIFVFSLEDEASFQTVYRLYHQLSSYR-NISEIPLILVGTQ-DAISASNPRVIDDARAR 125
Query: 229 DTCGDLQ 235
C D++
Sbjct: 126 QLCADMK 132
>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 = 30.1 bits (68), Expect = 1.2
Identities = 16/44 (36%), Positives = 24/44 (54%)
Query: 10 RIRLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHV 53
R +LVI+G GK+C+L F + + + Y TV + Y D V
Sbjct: 1 RKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEV 44
Score = 30.1 bits (68), Expect = 1.2
Identities = 16/65 (24%), Positives = 30/65 (46%), Gaps = 2/65 (3%)
Query: 149 DTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIVVAG 208
DT G + +R LS L+ +S +S +++ + E + +PI++ G
Sbjct: 55 DTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIP--EKWTPEVKHFCPNVPIILVG 112
Query: 209 NKSDM 213
NK D+
Sbjct: 113 NKKDL 117
Score = 28.5 bits (64), Expect = 3.9
Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 3/33 (9%)
Query: 314 FEEIREQRQD---FQLLECSAKDNYNIKEVFRT 343
EE R + F LECSAK ++EVF
Sbjct: 137 PEEGRAMAEKIGAFGYLECSAKTKEGVREVFEM 169
>gnl|CDD|163622 cd07379, MPP_239FB, Homo sapiens 239FB and related proteins,
metallophosphatase domain. 239FB (Fetal brain protein
239) is thought to play a role in central nervous system
development, but its specific role in unknown. 239FB is
expressed predominantly in human fetal brain from a gene
located in the chromosome 11p13 region associated with
the mental retardation component of the WAGR (Wilms
tumor, Aniridia, Genitourinary anomalies, Mental
retardation) syndrome. Orthologous brp-like (brain
protein 239-like) proteins have been identified in the
invertebrate amphioxus group and in vertebrates. 239FB
belongs to the metallophosphatase (MPP) superfamily.
MPPs are functionally diverse, but all share a conserved
domain with an active site consisting of two metal ions
(usually manganese, iron, or zinc) coordinated with
octahedral geometry by a cage of histidine, aspartate,
and asparagine residues. The MPP superfamily includes:
Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat
debranching enzymes, YfcE-like phosphodiesterases,
purple acid phosphatases (PAPs), YbbF-like
UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). The conserved domain is a
double beta-sheet sandwich with a di-metal active site
made up of residues located at the C-terminal side of
the sheets. This domain is thought to allow for
productive metal coordination.
Length = 135
Score = 29.5 bits (67), Expect = 1.4
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 211 SDMTSHHRAVHLEDVDILDTCGDLQ 235
SD S HR + + D D+L GDL
Sbjct: 6 SDTHSRHRTISIPDGDVLIHAGDLT 30
>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 = 29.7 bits (67), Expect = 1.7
Identities = 13/44 (29%), Positives = 26/44 (59%)
Query: 10 RIRLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHV 53
R ++V++G GK+ +L+ F +++ + Y TV + Y+ F V
Sbjct: 1 RCKIVLVGDSQCGKTALLQVFAKDSFPENYVPTVFENYTASFEV 44
>gnl|CDD|215295 PLN02538, PLN02538, 2,3-bisphosphoglycerate-independent
phosphoglycerate mutase.
Length = 558
Score = 30.4 bits (69), Expect = 1.8
Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 111 VVAGN-KSD-MTSHHRAVHLEDVSEWLYCELPKLRYVDILDTCGDLQFPA 158
VV N ++D M +A+ ED ++ +PK+RY +L G+L+ P+
Sbjct: 282 VVTFNFRADRMVMIAKALEYEDFDKFDRVRVPKIRYAGMLQYDGELKLPS 331
>gnl|CDD|218199 pfam04665, Pox_A32, Poxvirus A32 protein. The A32 protein is
thought to be involved in viral DNA packaging.
Length = 241
Score = 29.7 bits (67), Expect = 2.1
Identities = 10/29 (34%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYR 40
R+ I+GG G GK+ L L T +++
Sbjct: 15 RMAIVGGSGSGKTTYLL-SLLRTLVRKFK 42
>gnl|CDD|224533 COG1618, COG1618, Predicted nucleotide kinase [Nucleotide
transport and metabolism].
Length = 179
Score = 28.4 bits (64), Expect = 4.0
Identities = 11/56 (19%), Positives = 21/56 (37%), Gaps = 12/56 (21%)
Query: 6 CDNERIRLVILGGQGVGKSCILKRFLFNTYSDRYRSTVEDLYSRDFHVGAVTIKEI 61
+++ I G GVGK+ ++ + E L + + VG E+
Sbjct: 1 MIKMAMKIFITGRPGVGKTTLVLK------------IAEKLREKGYKVGGFITPEV 44
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 28.6 bits (64), Expect = 4.2
Identities = 22/110 (20%), Positives = 46/110 (41%), Gaps = 10/110 (9%)
Query: 106 DEIPIVVAGNKSDMTSHHRAVHLEDVS-EWLYCELPKLRYVDILDTCGDLQFPAMRRLSI 164
D+ ++ + S ++ + V+ ++ EL + V + T G +F M +
Sbjct: 32 DKPLVITEADASSVSG--KGKRPTTVAMDFGSIELDEDTGVHLFGTPGQERFKFMWEILS 89
Query: 165 ATAHAFLLVYSTTCLESFQSVKCY-FEEIREQRQDFQEIPIVVAGNKSDM 213
A +++ ++ +F + + F R IP+VVA NK D+
Sbjct: 90 RGAVGAIVLVDSSRPITFHAEEIIDFLTSRNP------IPVVVAINKQDL 133
>gnl|CDD|222735 pfam14398, ATPgrasp_YheCD, YheC/D like ATP-grasp. A member of the
ATP-grasp fold predicted to be involved in the
modification/biosynthesis of spore-wall and capsular
proteins.
Length = 262
Score = 28.4 bits (64), Expect = 5.0
Identities = 8/45 (17%), Positives = 16/45 (35%)
Query: 56 VTIKEIPIVVAGNKSDMTSHHRAVHLEDVSEWLYCELPKLRYVIQ 100
+T E +V L ++ W+ L +Y++Q
Sbjct: 74 LTKLEGRYIVRYRDDGKNQTRTFSSLASLASWILKHLSTRKYIVQ 118
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 28.5 bits (64), Expect = 5.2
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 9 ERIRLVILGGQGVGKSCILKRFLFNTYSDRYRSTV 43
+L+++G GVGK+ +KR L + +Y T+
Sbjct: 8 PEFKLILVGDGGVGKTTFVKRHLTGEFEKKYIPTL 42
>gnl|CDD|216457 pfam01366, PRTP, Herpesvirus processing and transport protein. The
members of this family are associate with capsid
intermediates during packaging of the virus.
Length = 635
Score = 28.8 bits (65), Expect = 5.9
Identities = 16/90 (17%), Positives = 30/90 (33%), Gaps = 7/90 (7%)
Query: 82 EDVSEWLYCELPKLRYVIQSSSFGDEIPIVVAGNKSDMTSHHRAVHLEDVSEWLYCELPK 141
++ +Y EL +L Y SSS + N S + + + + + L
Sbjct: 281 SEIPPRIY-ELSELTYWSSSSSRAETAIDAFCSNLSQLNAREA--LMHLLRAAVELALFG 337
Query: 142 LRYVDILDTCGDLQFPAMRRL---SIATAH 168
R D + + RL I ++
Sbjct: 338 RRPEHFFDLFAP-ELAPIERLFVGGIFSSP 366
>gnl|CDD|188365 TIGR03675, arCOG00543, arCOG00543 universal archaeal
KH-domain/beta-lactamase-domain protein. This family of
proteins is universal in the archaea and consistsof an
N-terminal type-1 KH-domain (pfam00013) a central
beta-lactamase-domain (pfam00753) with a C-terminal
motif associated with RNA metabolism (pfam07521).
KH-domains are associated with RNA-binding, so taken
together, this protein is a likely metal-dependent
RNAase. This family was defined in as arCOG01782.
Length = 630
Score = 28.7 bits (65), Expect = 6.1
Identities = 8/26 (30%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 3 PVMCDNERIRLVILGG-QGVGKSCIL 27
+ + +R+ LGG + VG+S +L
Sbjct: 167 DPIFKDRWVRVTALGGFREVGRSALL 192
>gnl|CDD|131096 TIGR02041, CysI, sulfite reductase (NADPH) hemoprotein,
beta-component. Sulfite reductase (NADPH) catalyzes a
six electron reduction of sulfite to sulfide in
prokaryotic organisms. It is a complex oligomeric enzyme
composed of two different peptides with a subunit
composition of alpha(8)-beta(4). The alpha component,
encoded by cysJ, is a flavoprotein containing both FMN
and FAD, while the beta component, encoded by cysI, is a
siroheme, iron-sulfur protein. In Salmonella typhimurium
and Escherichia coli, both the alpha and beta subunits
of sulfite reductase are located in a unidirectional
gene cluster along with phosphoadenosine phosphosulfate
reductase, which catalyzes a two step reduction of PAPS
to give free sulfite. In cyanobacteria and plant
species, sulfite reductase ferredoxin (EC 1.8.7.1)
catalyzes the reduction of sulfite to sulfide [Central
intermediary metabolism, Sulfur metabolism].
Length = 541
Score = 28.6 bits (64), Expect = 7.4
Identities = 14/39 (35%), Positives = 23/39 (58%), Gaps = 4/39 (10%)
Query: 196 RQDFQEIPIVVAGNKSDMTSHHRAVHLEDVDILDTCGDL 234
RQ FQ I+ K ++ + H+A+H +D + TCGD+
Sbjct: 98 RQTFQFHGIL----KRNLKAVHQAIHSAGLDSIATCGDV 132
>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 = 27.7 bits (62), Expect = 7.7
Identities = 18/72 (25%), Positives = 36/72 (50%), Gaps = 4/72 (5%)
Query: 141 KLRYVDILDTCGDLQFPAMRRLSIATAHAFLLVYSTTCLESFQSVKCYFEEIREQRQDFQ 200
K+R+ ++ DT G +F +R ++++ T ++++V + ++ R
Sbjct: 48 KIRF-NVWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRVTYKNVPNWHRDL--VRVCE- 103
Query: 201 EIPIVVAGNKSD 212
IPIV+ GNK D
Sbjct: 104 NIPIVLCGNKVD 115
>gnl|CDD|225176 COG2267, PldB, Lysophospholipase [Lipid metabolism].
Length = 298
Score = 28.1 bits (63), Expect = 7.9
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 32 FNTYSDRYRSTVEDLYSRDFHV 53
+S RY +DL +R F V
Sbjct: 43 LGEHSGRYEELADDLAARGFDV 64
>gnl|CDD|218528 pfam05272, VirE, Virulence-associated protein E. This family
contains several bacterial virulence-associated protein
E like proteins. These proteins contain a P-loop motif.
Length = 198
Score = 27.7 bits (62), Expect = 8.1
Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 4/63 (6%)
Query: 13 LVILGGQGVGKSCILKRFLFNTYSDRYRST-VEDLYSRDFHVGAVTIKEIPIVVAGNKSD 71
L++ G QG GKS LK+ ++D RS +D Y + V I EI + +K++
Sbjct: 55 LILQGAQGSGKSTFLKKLGGEWFTDSIRSFEGKDAYE---KLQGVWIVEIAELDGFSKAE 111
Query: 72 MTS 74
+ +
Sbjct: 112 VEA 114
>gnl|CDD|206693 cd04108, Rab36_Rab34, Rab GTPase families 34 (Rab34) and 36
(Rab36). Rab34/Rab36 subfamily. Rab34, found primarily
in the Golgi, interacts with its effector,
Rab-interacting lysosomal protein (RILP). This enables
its participation in microtubular
dynenin-dynactin-mediated repositioning of lysosomes
from the cell periphery to the Golgi. A Rab34 (Rah)
isoform that lacks the consensus GTP-binding region has
been identified in mice. This isoform is associated
with membrane ruffles and promotes macropinosome
formation. Rab36 has been mapped to human chromosome
22q11.2, a region that is homozygously deleted in
malignant rhabdoid tumors (MRTs). However, experimental
assessments do not implicate Rab36 as a tumor
suppressor that would enable tumor formation through a
loss-of-function mechanism. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab
proteins.
Length = 170
Score = 27.5 bits (61), Expect = 8.2
Identities = 9/32 (28%), Positives = 22/32 (68%)
Query: 12 RLVILGGQGVGKSCILKRFLFNTYSDRYRSTV 43
+++++G VGK+C++ RF + + Y++T+
Sbjct: 2 KVIVVGDLSVGKTCLINRFCKDVFDKNYKATI 33
>gnl|CDD|213228 cd03261, ABC_Org_Solvent_Resistant, ATP-binding cassette
transport system involved in resistant to organic
solvents. ABC transporters are a large family of
proteins involved in the transport of a wide variety of
different compounds, like sugars, ions, peptides, and
more complex organic molecules. The nucleotide binding
domain shows the highest similarity between all members
of the family. ABC transporters are a subset of
nucleotide hydrolases that contain a signature motif,
Q-loop, and H-loop/switch region, in addition to, the
Walker A motif/P-loop and Walker B motif commonly found
in a number of ATP- and GTP-binding and hydrolyzing
proteins.
Length = 235
Score = 27.9 bits (63), Expect = 8.3
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 13 LVILGGQGVGKSCILK 28
L I+G G GKS +L+
Sbjct: 29 LAIIGPSGSGKSTLLR 44
>gnl|CDD|183615 PRK12597, PRK12597, F0F1 ATP synthase subunit beta; Provisional.
Length = 461
Score = 28.3 bits (64), Expect = 8.4
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 15 ILGGQGVGKSCILKRFLFNT 34
+ GG GVGK+ ++ +FN
Sbjct: 148 LFGGAGVGKTVLMMELIFNI 167
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 27.6 bits (62), Expect = 9.2
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 8 NERIRLVILGGQGVGKSCILKRFLFN 33
N+ +R++ILG GK+ IL +
Sbjct: 12 NKEMRILILGLDNAGKTTILYKLKLG 37
>gnl|CDD|239136 cd02671, Peptidase_C19O, A subfamily of Peptidase C19. Peptidase
C19 contains ubiquitinyl hydrolases. They are
intracellular peptidases that remove ubiquitin molecules
from polyubiquinated peptides by cleavage of isopeptide
bonds. They hydrolyze bonds involving the carboxyl group
of the C-terminal Gly residue of ubiquitin. The purpose
of the de-ubiquitination is thought to be editing of the
ubiquitin conjugates, which could rescue them from
degradation, as well as recycling of the ubiquitin. The
ubiquitin/proteasome system is responsible for most
protein turnover in the mammalian cell, and with over 50
members, family C19 is one of the largest families of
peptidases in the human genome.
Length = 332
Score = 27.9 bits (62), Expect = 9.4
Identities = 15/36 (41%), Positives = 19/36 (52%), Gaps = 8/36 (22%)
Query: 172 LVYSTTCLESFQSVKCYFEEIREQRQDFQEIPIVVA 207
LV T CLE C E E+R+DFQ+I + V
Sbjct: 131 LVLRTRCLE------C--ETFTERREDFQDISVPVQ 158
>gnl|CDD|99915 cd05532, POLBc_alpha, DNA polymerase type-B alpha subfamily
catalytic domain. Three DNA-dependent DNA polymerases
type B (alpha, delta, and epsilon) have been identified
as essential for nuclear DNA replication in eukaryotes.
DNA polymerase (Pol) alpha is almost exclusively
required for the initiation of DNA replication and the
priming of Okazaki fragments during elongation. In most
organisms no specific repair role, other than check
point control, has been assigned to this enzyme. Pol
alpha contains both polymerase and exonuclease domains,
but lacks exonuclease activity suggesting that the
exonuclease domain may be for structural purposes only.
Length = 400
Score = 27.9 bits (63), Expect = 9.8
Identities = 9/27 (33%), Positives = 15/27 (55%)
Query: 105 GDEIPIVVAGNKSDMTSHHRAVHLEDV 131
GD IP ++ + S + RA H ++V
Sbjct: 330 GDTIPYIICKDGSSKSLADRAYHPDEV 356
>gnl|CDD|237196 PRK12768, PRK12768, CysZ-like protein; Reviewed.
Length = 240
Score = 27.6 bits (62), Expect = 10.0
Identities = 13/27 (48%), Positives = 17/27 (62%)
Query: 276 RQDFQFPAMRRLSIATAHAFLLVYSTT 302
R+ F+F AMR S A A AF ++TT
Sbjct: 165 REFFEFAAMRFRSEAEAKAFRRKHATT 191
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
0.324 0.136 0.405
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: 18,884,494
Number of extensions: 1785678
Number of successful extensions: 2791
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2664
Number of HSP's successfully gapped: 305
Length of query: 373
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 275
Effective length of database: 6,590,910
Effective search space: 1812500250
Effective search space used: 1812500250
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 60 (26.7 bits)