RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy125
(385 letters)
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 443 bits (1142), Expect = e-158
Identities = 164/215 (76%), Positives = 184/215 (85%)
Query: 1 MAAEMDMPSFKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRF 60
M ++P FK +LVGDGG GKTTFVKRHLTGEFEKKY+ TLGVEVHPL F+TN G I F
Sbjct: 1 MQQMDEVPEFKLILVGDGGVGKTTFVKRHLTGEFEKKYIPTLGVEVHPLKFYTNCGPICF 60
Query: 61 NVWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVCENIPIVLCG 120
NVWDTAGQEKFGGLRDGYYI+GQCAIIMFDVTSRITYKNVPNWHRD+VRVCENIPIVL G
Sbjct: 61 NVWDTAGQEKFGGLRDGYYIKGQCAIIMFDVTSRITYKNVPNWHRDIVRVCENIPIVLVG 120
Query: 121 NKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPA 180
NKVD+KDR+VKA+ I FHRKKNLQYYDISAKSNYNFEKPFLWLAR+L DPNL FV PA
Sbjct: 121 NKVDVKDRQVKARQITFHRKKNLQYYDISAKSNYNFEKPFLWLARRLTNDPNLVFVGAPA 180
Query: 181 LLPPEVTMDPQWQSRIEQDLKEAQETALPDDDEDL 215
L P E+ +DP+ ++ E++L+ A LPDDD+DL
Sbjct: 181 LAPEEIQIDPELVAQAEKELQAAANVPLPDDDDDL 215
Score = 317 bits (814), Expect = e-109
Identities = 126/215 (58%), Positives = 142/215 (66%), Gaps = 45/215 (20%)
Query: 216 MAAEMDMPSFKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRF 275
M ++P FK +LVGDGG GKTTFVKRHLTGEFEKKY+ TLGVEVHPL F+TN G I F
Sbjct: 1 MQQMDEVPEFKLILVGDGGVGKTTFVKRHLTGEFEKKYIPTLGVEVHPLKFYTNCGPICF 60
Query: 276 NVWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKN--------------------- 314
NVWDTAGQEKFGGLRDGYYI+GQCAIIMFDVTSRITYKN
Sbjct: 61 NVWDTAGQEKFGGLRDGYYIKGQCAIIMFDVTSRITYKNVPNWHRDIVRVCENIPIVLVG 120
Query: 315 ------------------------YYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPA 350
YYDISAKSNYNFEKPFLWLAR+L DPNL FV PA
Sbjct: 121 NKVDVKDRQVKARQITFHRKKNLQYYDISAKSNYNFEKPFLWLARRLTNDPNLVFVGAPA 180
Query: 351 LLPPEVTMDPQWQSRIEQDLKEAQETALPDDDEDL 385
L P E+ +DP+ ++ E++L+ A LPDDD+DL
Sbjct: 181 LAPEEIQIDPELVAQAEKELQAAANVPLPDDDDDL 215
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 423 bits (1090), Expect = e-150
Identities = 162/211 (76%), Positives = 177/211 (83%)
Query: 5 MDMPSFKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWD 64
+D PSFK V+VGDGGTGKTTFVKRHLTGEFEKKY T+GVEVHPL F TN G IRF WD
Sbjct: 9 VDYPSFKLVIVGDGGTGKTTFVKRHLTGEFEKKYEPTIGVEVHPLDFFTNCGKIRFYCWD 68
Query: 65 TAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVCENIPIVLCGNKVD 124
TAGQEKFGGLRDGYYI GQCAIIMFDVT+R+TYKNVP WHRDL RVCENIPIVLCGNKVD
Sbjct: 69 TAGQEKFGGLRDGYYIHGQCAIIMFDVTARLTYKNVPTWHRDLCRVCENIPIVLCGNKVD 128
Query: 125 IKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALLPP 184
+K+R+VKAK + FHRKKNLQYY+ISAKSNYNFEKPFL+LARKL GDPNL FV PAL PP
Sbjct: 129 VKNRQVKAKQVTFHRKKNLQYYEISAKSNYNFEKPFLYLARKLAGDPNLHFVESPALAPP 188
Query: 185 EVTMDPQWQSRIEQDLKEAQETALPDDDEDL 215
EV +D Q + E +L A LPDDD+D
Sbjct: 189 EVQIDLAAQQQHEAELAAAAAQPLPDDDDDA 219
Score = 302 bits (775), Expect = e-102
Identities = 125/211 (59%), Positives = 136/211 (64%), Gaps = 45/211 (21%)
Query: 220 MDMPSFKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWD 279
+D PSFK V+VGDGGTGKTTFVKRHLTGEFEKKY T+GVEVHPL F TN G IRF WD
Sbjct: 9 VDYPSFKLVIVGDGGTGKTTFVKRHLTGEFEKKYEPTIGVEVHPLDFFTNCGKIRFYCWD 68
Query: 280 TAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKN------------------------- 314
TAGQEKFGGLRDGYYI GQCAIIMFDVT+R+TYKN
Sbjct: 69 TAGQEKFGGLRDGYYIHGQCAIIMFDVTARLTYKNVPTWHRDLCRVCENIPIVLCGNKVD 128
Query: 315 --------------------YYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALLPP 354
YY+ISAKSNYNFEKPFL+LARKL GDPNL FV PAL PP
Sbjct: 129 VKNRQVKAKQVTFHRKKNLQYYEISAKSNYNFEKPFLYLARKLAGDPNLHFVESPALAPP 188
Query: 355 EVTMDPQWQSRIEQDLKEAQETALPDDDEDL 385
EV +D Q + E +L A LPDDD+D
Sbjct: 189 EVQIDLAAQQQHEAELAAAAAQPLPDDDDDA 219
>gnl|CDD|128473 smart00176, RAN, Ran (Ras-related nuclear proteins) /TC4 subfamily
of small GTPases. Ran is involved in the active
transport of proteins through nuclear pores.
Length = 200
Score = 405 bits (1042), Expect = e-143
Identities = 180/200 (90%), Positives = 188/200 (94%)
Query: 15 VGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEKFGGL 74
VGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRG IRFNVWDTAGQEKFGGL
Sbjct: 1 VGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIRFNVWDTAGQEKFGGL 60
Query: 75 RDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKS 134
RDGYYIQGQCAIIMFDVT+R+TYKNVPNWHRDLVRVCENIPIVLCGNKVD+KDRKVKAKS
Sbjct: 61 RDGYYIQGQCAIIMFDVTARVTYKNVPNWHRDLVRVCENIPIVLCGNKVDVKDRKVKAKS 120
Query: 135 IVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALLPPEVTMDPQWQS 194
I FHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPAL PPEV MDP +
Sbjct: 121 ITFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAA 180
Query: 195 RIEQDLKEAQETALPDDDED 214
+ E DL+ A TALPD+D+D
Sbjct: 181 QYEHDLEVAATTALPDEDDD 200
Score = 286 bits (732), Expect = 1e-96
Identities = 137/200 (68%), Positives = 144/200 (72%), Gaps = 45/200 (22%)
Query: 230 VGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEKFGGL 289
VGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRG IRFNVWDTAGQEKFGGL
Sbjct: 1 VGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIRFNVWDTAGQEKFGGL 60
Query: 290 RDGYYIQGQCAIIMFDVTSRITYKN----------------------------------- 314
RDGYYIQGQCAIIMFDVT+R+TYKN
Sbjct: 61 RDGYYIQGQCAIIMFDVTARVTYKNVPNWHRDLVRVCENIPIVLCGNKVDVKDRKVKAKS 120
Query: 315 ----------YYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALLPPEVTMDPQWQS 364
YYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPAL PPEV MDP +
Sbjct: 121 ITFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAA 180
Query: 365 RIEQDLKEAQETALPDDDED 384
+ E DL+ A TALPD+D+D
Sbjct: 181 QYEHDLEVAATTALPDEDDD 200
>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 = 376 bits (967), Expect = e-132
Identities = 156/166 (93%), Positives = 160/166 (96%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
FK VLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPL FHTNRG IRFNVWDTAGQE
Sbjct: 1 FKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLDFHTNRGKIRFNVWDTAGQE 60
Query: 70 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRK 129
KFGGLRDGYYIQGQCAIIMFDVTSR+TYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRK
Sbjct: 61 KFGGLRDGYYIQGQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRK 120
Query: 130 VKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEF 175
VK K I FHRKKNLQYY+ISAKSNYNFEKPFLWLARKL+G+PNLEF
Sbjct: 121 VKPKQITFHRKKNLQYYEISAKSNYNFEKPFLWLARKLLGNPNLEF 166
Score = 259 bits (663), Expect = 2e-86
Identities = 114/166 (68%), Positives = 118/166 (71%), Gaps = 45/166 (27%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
FK VLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPL FHTNRG IRFNVWDTAGQE
Sbjct: 1 FKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLDFHTNRGKIRFNVWDTAGQE 60
Query: 285 KFGGLRDGYYIQGQCAIIMFDVTSRITYKN------------------------------ 314
KFGGLRDGYYIQGQCAIIMFDVTSR+TYKN
Sbjct: 61 KFGGLRDGYYIQGQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRK 120
Query: 315 ---------------YYDISAKSNYNFEKPFLWLARKLIGDPNLEF 345
YY+ISAKSNYNFEKPFLWLARKL+G+PNLEF
Sbjct: 121 VKPKQITFHRKKNLQYYEISAKSNYNFEKPFLWLARKLLGNPNLEF 166
>gnl|CDD|215692 pfam00071, Ras, Ras family. Includes sub-families Ras, Rab, Rac,
Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with
GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025,
pfam00063. As regards Rab GTPases, these are important
regulators of vesicle formation, motility and fusion.
They share a fold in common with all Ras GTPases: this
is a six-stranded beta-sheet surrounded by five
alpha-helices.
Length = 162
Score = 196 bits (500), Expect = 5e-62
Identities = 61/161 (37%), Positives = 100/161 (62%), Gaps = 3/161 (1%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 70
K VLVGDGG GK++ + R +F ++Y+ T+GV+ + + ++ +WDTAGQE+
Sbjct: 1 KLVLVGDGGVGKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAGQER 60
Query: 71 FGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVC-ENIPIVLCGNKVDIKD-R 128
F LR YY Q ++++D+TSR +++NV W +++R EN+PIVL GNK D++D R
Sbjct: 61 FRALRPLYYRGAQGFLLVYDITSRDSFENVKKWLEEILRHADENVPIVLVGNKCDLEDQR 120
Query: 129 KVKAKS-IVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLI 168
V + ++ L + + SAK+N N E+ F LAR+++
Sbjct: 121 VVSTEEGEALAKELGLPFMETSAKTNENVEEAFEELAREIL 161
Score = 126 bits (319), Expect = 4e-35
Identities = 44/161 (27%), Positives = 74/161 (45%), Gaps = 48/161 (29%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 285
K VLVGDGG GK++ + R +F ++Y+ T+GV+ + + ++ +WDTAGQE+
Sbjct: 1 KLVLVGDGGVGKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAGQER 60
Query: 286 FGGLRDGYYIQGQCAIIMFDVTSRITYKN------------------------------- 314
F LR YY Q ++++D+TSR +++N
Sbjct: 61 FRALRPLYYRGAQGFLLVYDITSRDSFENVKKWLEEILRHADENVPIVLVGNKCDLEDQR 120
Query: 315 -----------------YYDISAKSNYNFEKPFLWLARKLI 338
+ + SAK+N N E+ F LAR+++
Sbjct: 121 VVSTEEGEALAKELGLPFMETSAKTNENVEEAFEELAREIL 161
>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 = 160 bits (408), Expect = 2e-48
Identities = 55/159 (34%), Positives = 92/159 (57%), Gaps = 3/159 (1%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
FK VL+GD G GKT+ + R + +F + Y +T+GV+ + ++ +WDTAGQE
Sbjct: 1 FKIVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGVDFKSKTIEVDGKKVKLQIWDTAGQE 60
Query: 70 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVC-ENIPIVLCGNKVDIKDR 128
+F + YY AI+++DVT+R +++N+ W +L NIPI+L GNK D++D
Sbjct: 61 RFRSITSSYYRGAHGAILVYDVTNRESFENLDKWLNELKEYAPPNIPIILVGNKSDLEDE 120
Query: 129 KVKAKSIV--FHRKKNLQYYDISAKSNYNFEKPFLWLAR 165
+ + F ++ L +++ SAK+ N ++ F LAR
Sbjct: 121 RQVSTEEAQQFAKENGLLFFETSAKTGENVDEAFESLAR 159
Score = 106 bits (267), Expect = 1e-27
Identities = 41/159 (25%), Positives = 69/159 (43%), Gaps = 48/159 (30%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
FK VL+GD G GKT+ + R + +F + Y +T+GV+ + ++ +WDTAGQE
Sbjct: 1 FKIVLIGDSGVGKTSLLLRFVDNKFSENYKSTIGVDFKSKTIEVDGKKVKLQIWDTAGQE 60
Query: 285 KFGGLRDGYYIQGQCAIIMFDVTSRITYKN------------------------------ 314
+F + YY AI+++DVT+R +++N
Sbjct: 61 RFRSITSSYYRGAHGAILVYDVTNRESFENLDKWLNELKEYAPPNIPIILVGNKSDLEDE 120
Query: 315 ------------------YYDISAKSNYNFEKPFLWLAR 335
+++ SAK+ N ++ F LAR
Sbjct: 121 RQVSTEEAQQFAKENGLLFFETSAKTGENVDEAFESLAR 159
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 140 bits (354), Expect = 1e-39
Identities = 62/212 (29%), Positives = 94/212 (44%), Gaps = 22/212 (10%)
Query: 7 MPSFKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTA 66
M FK V++GDGG GKTT + R + EF + Y T+G R I+ +WDTA
Sbjct: 3 MKEFKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTA 62
Query: 67 GQEKFGGLRDGYYIQGQCAIIMFDVTSR-ITYKNVPNWHRDLVRVC-ENIPIVLCGNKVD 124
GQE++ LR YY +I++D T R + + W +L + +++PI+L GNK+D
Sbjct: 63 GQEEYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVGNKID 122
Query: 125 IKDR-----------------KVKAKSIVFHRKKNLQYYDISAKS--NYNFEKPFLWLAR 165
+ D V A V N + SAKS N + F L R
Sbjct: 123 LFDEQSSSEEILNQLNREVVLLVLAPKAVLPEVANPALLETSAKSLTGPNVNELFKELLR 182
Query: 166 KLIGDPNLEFVAMPALLPPEVTMDPQWQSRIE 197
KL+ + + L + +P Q+ +
Sbjct: 183 KLLEEIEKLVLKN-ELRQLDRLNNPIEQAALA 213
Score = 103 bits (258), Expect = 7e-26
Identities = 35/88 (39%), Positives = 48/88 (54%)
Query: 222 MPSFKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTA 281
M FK V++GDGG GKTT + R + EF + Y T+G R I+ +WDTA
Sbjct: 3 MKEFKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTA 62
Query: 282 GQEKFGGLRDGYYIQGQCAIIMFDVTSR 309
GQE++ LR YY +I++D T R
Sbjct: 63 GQEEYRSLRPEYYRGANGILIVYDSTLR 90
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 132 bits (334), Expect = 3e-37
Identities = 55/164 (33%), Positives = 101/164 (61%), Gaps = 7/164 (4%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
FK +L+GD G GK++ + R G+F ++Y +T+GV+ + ++ +WDTAGQE
Sbjct: 1 FKIILIGDSGVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIEVDGKRVKLQIWDTAGQE 60
Query: 70 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVC-ENIPIVLCGNKVDIKD- 127
+F + YY A++++D+T+R +++N+ NW ++L N+ I+L GNK D+++
Sbjct: 61 RFRSITSSYYRGAVGALLVYDITNRESFENLENWLKELREYASPNVVIMLVGNKSDLEEQ 120
Query: 128 RKVK---AKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLI 168
R+V A++ F + L +++ SAK+N N E+ F LAR+++
Sbjct: 121 RQVSREEAEA--FAEEHGLPFFETSAKTNTNVEEAFEELAREIL 162
Score = 85.3 bits (212), Expect = 8e-20
Identities = 30/90 (33%), Positives = 56/90 (62%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
FK +L+GD G GK++ + R G+F ++Y +T+GV+ + ++ +WDTAGQE
Sbjct: 1 FKIILIGDSGVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIEVDGKRVKLQIWDTAGQE 60
Query: 285 KFGGLRDGYYIQGQCAIIMFDVTSRITYKN 314
+F + YY A++++D+T+R +++N
Sbjct: 61 RFRSITSSYYRGAVGALLVYDITNRESFEN 90
>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 = 115 bits (290), Expect = 5e-31
Identities = 49/160 (30%), Positives = 87/160 (54%), Gaps = 4/160 (2%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVE-VHPLVFHTNRGA-IRFNVWDTAGQ 68
K ++VG+G GK++ ++R + G F K Y T+GV+ + +F +R +WDTAGQ
Sbjct: 2 KVIVVGNGNVGKSSMIQRFVKGIFTKDYKKTIGVDFLEKQIFLRQSDEDVRLMLWDTAGQ 61
Query: 69 EKFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDR 128
E+F + YY Q I++F T R +++ + +W + C +IP+VL K+D+ D+
Sbjct: 62 EEFDAITKAYYRGAQACILVFSTTDRESFEAIESWKEKVEAECGDIPMVLVQTKIDLLDQ 121
Query: 129 KV--KAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARK 166
V ++ ++ L + S K ++N + F +LA K
Sbjct: 122 AVITNEEAEALAKRLQLPLFRTSVKDDFNVTELFEYLAEK 161
Score = 75.2 bits (185), Expect = 3e-16
Identities = 31/86 (36%), Positives = 49/86 (56%), Gaps = 2/86 (2%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVE-VHPLVFHTNRGA-IRFNVWDTAGQ 283
K ++VG+G GK++ ++R + G F K Y T+GV+ + +F +R +WDTAGQ
Sbjct: 2 KVIVVGNGNVGKSSMIQRFVKGIFTKDYKKTIGVDFLEKQIFLRQSDEDVRLMLWDTAGQ 61
Query: 284 EKFGGLRDGYYIQGQCAIIMFDVTSR 309
E+F + YY Q I++F T R
Sbjct: 62 EEFDAITKAYYRGAQACILVFSTTDR 87
>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 = 111 bits (281), Expect = 9e-30
Identities = 51/162 (31%), Positives = 94/162 (58%), Gaps = 3/162 (1%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
FK VL+G+G GKT+ V R++ +F +K+ +T + I +WDTAGQE
Sbjct: 1 FKVVLLGEGRVGKTSLVLRYVENKFNEKHESTTQASFFQKTVNIGGKRIDLAIWDTAGQE 60
Query: 70 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVC-ENIPIVLCGNKVDIKDR 128
++ L YY AI+++D+T +++ V W ++L ++ NI +V+ GNK+D++ +
Sbjct: 61 RYHALGPIYYRDADGAILVYDITDADSFQKVKKWIKELKQMRGNNISLVIVGNKIDLERQ 120
Query: 129 KVKAKSIV--FHRKKNLQYYDISAKSNYNFEKPFLWLARKLI 168
+V +KS + + ++++ SAK+ E+ FL LA+++I
Sbjct: 121 RVVSKSEAEEYAKSVGAKHFETSAKTGKGIEELFLSLAKRMI 162
Score = 68.0 bits (167), Expect = 1e-13
Identities = 29/83 (34%), Positives = 46/83 (55%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
FK VL+G+G GKT+ V R++ +F +K+ +T + I +WDTAGQE
Sbjct: 1 FKVVLLGEGRVGKTSLVLRYVENKFNEKHESTTQASFFQKTVNIGGKRIDLAIWDTAGQE 60
Query: 285 KFGGLRDGYYIQGQCAIIMFDVT 307
++ L YY AI+++D+T
Sbjct: 61 RYHALGPIYYRDADGAILVYDIT 83
>gnl|CDD|206642 cd00876, Ras, Rat sarcoma (Ras) family of small guanosine
triphosphatases (GTPases). The Ras family of the Ras
superfamily includes classical N-Ras, H-Ras, and K-Ras,
as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG,
Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins.
Ras proteins regulate cell growth, proliferation and
differentiation. Ras is activated by guanine nucleotide
exchange factors (GEFs) that release GDP and allow GTP
binding. Many RasGEFs have been identified. These are
sequestered in the cytosol until activation by growth
factors triggers recruitment to the plasma membrane or
Golgi, where the GEF colocalizes with Ras. Active
GTP-bound Ras interacts with several effector proteins:
among the best characterized are the Raf kinases,
phosphatidylinositol 3-kinase (PI3K), RalGEFs and
NORE/MST1. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 160
Score = 109 bits (274), Expect = 1e-28
Identities = 51/172 (29%), Positives = 88/172 (51%), Gaps = 27/172 (15%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATL-----------GVEVHPLVFHTNRGAIR 59
K V++G GG GK+ R ++GEF ++Y T+ G
Sbjct: 1 KLVVLGAGGVGKSALTIRFVSGEFVEEYDPTIEDSYRKQIVVDGETYT------------ 48
Query: 60 FNVWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRV--CENIPIV 117
++ DTAGQE+F +RD Y G I+++ +TSR +++ + N ++RV E++PIV
Sbjct: 49 LDILDTAGQEEFSAMRDQYIRNGDGFILVYSITSRESFEEIKNIREQILRVKDKEDVPIV 108
Query: 118 LCGNKVDIKD-RKV-KAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKL 167
L GNK D+++ R+V + + + + SAK+N N ++ F L R++
Sbjct: 109 LVGNKCDLENERQVSTEEGEALAEEWGCPFLETSAKTNINIDELFNTLVREI 160
Score = 67.2 bits (165), Expect = 2e-13
Identities = 31/106 (29%), Positives = 50/106 (47%), Gaps = 26/106 (24%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATL-----------GVEVHPLVFHTNRGAIR 274
K V++G GG GK+ R ++GEF ++Y T+ G
Sbjct: 1 KLVVLGAGGVGKSALTIRFVSGEFVEEYDPTIEDSYRKQIVVDGETYT------------ 48
Query: 275 FNVWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITY---KNYYD 317
++ DTAGQE+F +RD Y G I+++ +TSR ++ KN +
Sbjct: 49 LDILDTAGQEEFSAMRDQYIRNGDGFILVYSITSRESFEEIKNIRE 94
>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 = 106 bits (266), Expect = 1e-27
Identities = 53/166 (31%), Positives = 92/166 (55%), Gaps = 12/166 (7%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
FK +L+GD GKT V+R +G F ++ T+GV+ ++ +WDTAGQE
Sbjct: 4 FKIILIGDSNVGKTCVVQRFKSGTFSERQGNTIGVDFTMKTLEIQGKRVKLQIWDTAGQE 63
Query: 70 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRV-CENIPIVLCGNKVDIKDR 128
+F + YY AII +D+T R ++++VP+W ++ + N+ ++L GNK D++++
Sbjct: 64 RFRTITQSYYRSANGAIIAYDITRRSSFESVPHWIEEVEKYGASNVVLLLIGNKCDLEEQ 123
Query: 129 KVKAKSIVFHRKKNL-QYYDI------SAKSNYNFEKPFLWLARKL 167
+ ++F L ++Y I SAK + N E+ FL +A +L
Sbjct: 124 ----REVLFEEACTLAEHYGILAVLETSAKESSNVEEAFLLMATEL 165
Score = 73.2 bits (180), Expect = 2e-15
Identities = 31/90 (34%), Positives = 50/90 (55%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
FK +L+GD GKT V+R +G F ++ T+GV+ ++ +WDTAGQE
Sbjct: 4 FKIILIGDSNVGKTCVVQRFKSGTFSERQGNTIGVDFTMKTLEIQGKRVKLQIWDTAGQE 63
Query: 285 KFGGLRDGYYIQGQCAIIMFDVTSRITYKN 314
+F + YY AII +D+T R ++++
Sbjct: 64 RFRTITQSYYRSANGAIIAYDITRRSSFES 93
>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 = 106 bits (266), Expect = 2e-27
Identities = 52/163 (31%), Positives = 87/163 (53%), Gaps = 3/163 (1%)
Query: 9 SFKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQ 68
FK VL+GD GK++ V R + EF + +T+G + + ++F +WDTAGQ
Sbjct: 1 QFKLVLLGDSSVGKSSIVLRFVKNEFSENQESTIGAAFLTQTVNLDDTTVKFEIWDTAGQ 60
Query: 69 EKFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVR-VCENIPIVLCGNKVDIKD 127
E++ L YY AI+++D+TS +++ +W ++L NI I L GNK D++
Sbjct: 61 ERYRSLAPMYYRGAAAAIVVYDITSEESFEKAKSWVKELQEHGPPNIVIALAGNKADLES 120
Query: 128 -RKVKAKSI-VFHRKKNLQYYDISAKSNYNFEKPFLWLARKLI 168
R+V + + + L + + SAK+ N + F +ARKL
Sbjct: 121 KRQVSTEEAQEYADENGLLFMETSAKTGENVNELFTEIARKLP 163
Score = 71.4 bits (176), Expect = 7e-15
Identities = 30/90 (33%), Positives = 51/90 (56%)
Query: 224 SFKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQ 283
FK VL+GD GK++ V R + EF + +T+G + + ++F +WDTAGQ
Sbjct: 1 QFKLVLLGDSSVGKSSIVLRFVKNEFSENQESTIGAAFLTQTVNLDDTTVKFEIWDTAGQ 60
Query: 284 EKFGGLRDGYYIQGQCAIIMFDVTSRITYK 313
E++ L YY AI+++D+TS +++
Sbjct: 61 ERYRSLAPMYYRGAAAAIVVYDITSEESFE 90
>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 = 106 bits (265), Expect = 2e-27
Identities = 52/150 (34%), Positives = 78/150 (52%), Gaps = 1/150 (0%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 70
K +L+GD GK+ V+R L +E + ++T + ++ I + WDTAGQE+
Sbjct: 2 KIILLGDSAVGKSKLVERFLMDGYEPQQLSTYALTLYKHNAKFEGKTILVDFWDTAGQER 61
Query: 71 FGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKV 130
F + YY + I++FDVT +ITYKN+ W+ +L IP ++ NK+D+ D V
Sbjct: 62 FQTMHASYYHKAHACILVFDVTRKITYKNLSKWYEELREYRPEIPCIVVANKIDL-DPSV 120
Query: 131 KAKSIVFHRKKNLQYYDISAKSNYNFEKPF 160
K F K NL Y +SA N K F
Sbjct: 121 TQKKFNFAEKHNLPLYYVSAADGTNVVKLF 150
Score = 74.1 bits (182), Expect = 6e-16
Identities = 39/119 (32%), Positives = 62/119 (52%), Gaps = 1/119 (0%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 285
K +L+GD GK+ V+R L +E + ++T + ++ I + WDTAGQE+
Sbjct: 2 KIILLGDSAVGKSKLVERFLMDGYEPQQLSTYALTLYKHNAKFEGKTILVDFWDTAGQER 61
Query: 286 FGGLRDGYYIQGQCAIIMFDVTSRITYKNYYD-ISAKSNYNFEKPFLWLARKLIGDPNL 343
F + YY + I++FDVT +ITYKN Y E P + +A K+ DP++
Sbjct: 62 FQTMHASYYHKAHACILVFDVTRKITYKNLSKWYEELREYRPEIPCIVVANKIDLDPSV 120
>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 = 104 bits (262), Expect = 6e-27
Identities = 50/161 (31%), Positives = 86/161 (53%), Gaps = 3/161 (1%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
K +L+GD G GK++ + R F++ +T+GV+ + ++ +WDTAGQE
Sbjct: 1 LKILLIGDSGVGKSSLLLRFTDDTFDEDLSSTIGVDFKVKTVTVDGKKVKLAIWDTAGQE 60
Query: 70 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVC--ENIPIVLCGNKVDIKD 127
+F L YY Q I+++DVT R T+ N+ W +L + +L GNK+D ++
Sbjct: 61 RFRTLTSSYYRGAQGVILVYDVTRRDTFDNLDTWLNELDTYSTNPDAVKMLVGNKIDKEN 120
Query: 128 RKV-KAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKL 167
R+V + + F RK N+ + + SAK+ ++ F L K+
Sbjct: 121 REVTREEGQKFARKHNMLFIETSAKTRIGVQQAFEELVEKI 161
Score = 72.0 bits (177), Expect = 4e-15
Identities = 31/90 (34%), Positives = 50/90 (55%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
K +L+GD G GK++ + R F++ +T+GV+ + ++ +WDTAGQE
Sbjct: 1 LKILLIGDSGVGKSSLLLRFTDDTFDEDLSSTIGVDFKVKTVTVDGKKVKLAIWDTAGQE 60
Query: 285 KFGGLRDGYYIQGQCAIIMFDVTSRITYKN 314
+F L YY Q I+++DVT R T+ N
Sbjct: 61 RFRTLTSSYYRGAQGVILVYDVTRRDTFDN 90
>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 = 105 bits (265), Expect = 6e-27
Identities = 64/192 (33%), Positives = 100/192 (52%), Gaps = 19/192 (9%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVE--VHPLVFHTNRGAIRFNVWDTAG 67
FK +++GD G GKT+ +KR++ G F + Y AT+GV+ + + + N +R +WD AG
Sbjct: 1 FKVLVIGDLGVGKTSIIKRYVHGVFSQHYKATIGVDFALKVIEWDPNT-VVRLQLWDIAG 59
Query: 68 QEKFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDL---VRVC--ENIPIVLCGNK 122
QE+FGG+ YY AII+FDVT T++ V W DL V + E IP +L NK
Sbjct: 60 QERFGGMTRVYYKGAVGAIIVFDVTRPSTFEAVLKWKADLDSKVTLPNGEPIPALLLANK 119
Query: 123 VDIKDRKVKAKSIVFHR--KKN--LQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAM 178
D+K ++ + K+N + +++ SAK N N E+ +L + ++
Sbjct: 120 CDLKKERLAKDPEQMDQFCKENGFIGWFETSAKENINIEEAMRFLVKNIL-------KND 172
Query: 179 PALLPPEVTMDP 190
L PE D
Sbjct: 173 KGLQSPEPDEDN 184
Score = 83.1 bits (206), Expect = 1e-18
Identities = 45/120 (37%), Positives = 68/120 (56%), Gaps = 9/120 (7%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVE--VHPLVFHTNRGAIRFNVWDTAG 282
FK +++GD G GKT+ +KR++ G F + Y AT+GV+ + + + N +R +WD AG
Sbjct: 1 FKVLVIGDLGVGKTSIIKRYVHGVFSQHYKATIGVDFALKVIEWDPNT-VVRLQLWDIAG 59
Query: 283 QEKFGGLRDGYYIQGQCAIIMFDVTSRITYKNYY----DISAKSNYNFEKPF--LWLARK 336
QE+FGG+ YY AII+FDVT T++ D+ +K +P L LA K
Sbjct: 60 QERFGGMTRVYYKGAVGAIIVFDVTRPSTFEAVLKWKADLDSKVTLPNGEPIPALLLANK 119
>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 = 103 bits (260), Expect = 1e-26
Identities = 53/164 (32%), Positives = 92/164 (56%), Gaps = 7/164 (4%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
FK +L+GD G GK+ + R + + Y++T+GV+ + ++ +WDTAGQE
Sbjct: 3 FKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTVKLQIWDTAGQE 62
Query: 70 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVR-VCENIPIVLCGNKVDIKDR 128
+F + YY II++DVT + ++ NV W +++ R EN+ +L GNK D+ D+
Sbjct: 63 RFRTITSSYYRGAHGIIIVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTDK 122
Query: 129 KV----KAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLI 168
KV +AK F + + + + SAK+ N E+ F+ +AR++
Sbjct: 123 KVVDYTEAKE--FADELGIPFLETSAKNATNVEEAFMTMAREIK 164
Score = 65.8 bits (161), Expect = 8e-13
Identities = 29/90 (32%), Positives = 50/90 (55%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
FK +L+GD G GK+ + R + + Y++T+GV+ + ++ +WDTAGQE
Sbjct: 3 FKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTVKLQIWDTAGQE 62
Query: 285 KFGGLRDGYYIQGQCAIIMFDVTSRITYKN 314
+F + YY II++DVT + ++ N
Sbjct: 63 RFRTITSSYYRGAHGIIIVYDVTDQESFNN 92
>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 = 103 bits (258), Expect = 2e-26
Identities = 47/156 (30%), Positives = 81/156 (51%), Gaps = 7/156 (4%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
K V +GD GKT+ + R + F+ +Y AT+G++ + + +R +WDTAGQE
Sbjct: 1 HKLVFLGDQSVGKTSIITRFMYDTFDNQYQATIGIDFLSKTMYVDDKTVRLQLWDTAGQE 60
Query: 70 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVCENIP-IVLCGNKVDIKDR 128
+F L Y A++++D+T+R ++ N W D+ N IVL GNK D+ D+
Sbjct: 61 RFRSLIPSYIRDSSVAVVVYDITNRQSFDNTDKWIDDVRDERGNDVIIVLVGNKTDLSDK 120
Query: 129 KVKAKSIV----FHRKKNLQYYDISAKSNYNFEKPF 160
+ S ++ N + + SAK+ +N ++ F
Sbjct: 121 RQ--VSTEEGEKKAKENNAMFIETSAKAGHNVKQLF 154
Score = 72.3 bits (178), Expect = 4e-15
Identities = 29/90 (32%), Positives = 51/90 (56%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
K V +GD GKT+ + R + F+ +Y AT+G++ + + +R +WDTAGQE
Sbjct: 1 HKLVFLGDQSVGKTSIITRFMYDTFDNQYQATIGIDFLSKTMYVDDKTVRLQLWDTAGQE 60
Query: 285 KFGGLRDGYYIQGQCAIIMFDVTSRITYKN 314
+F L Y A++++D+T+R ++ N
Sbjct: 61 RFRSLIPSYIRDSSVAVVVYDITNRQSFDN 90
>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 = 101 bits (254), Expect = 8e-26
Identities = 52/162 (32%), Positives = 92/162 (56%), Gaps = 5/162 (3%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
FK +++G GTGK+ + + + +F++ T+GVE V + +++ +WDTAGQE
Sbjct: 1 FKFLIIGSAGTGKSCLLHQFIENKFKQDSNHTIGVEFGSRVVNVGGKSVKLQIWDTAGQE 60
Query: 70 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVR--VCENIPIVLCGNKVDIK- 126
+F + YY A++++D+TSR ++ + NW D R +I I+L GNK D++
Sbjct: 61 RFRSVTRSYYRGAAGALLVYDITSRESFNALTNWLTD-ARTLASPDIVIILVGNKKDLED 119
Query: 127 DRKVK-AKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKL 167
DR+V ++ F ++ L + + SA + N E+ FL AR +
Sbjct: 120 DREVTFLEASRFAQENGLLFLETSALTGENVEEAFLKCARSI 161
Score = 69.8 bits (171), Expect = 2e-14
Identities = 28/90 (31%), Positives = 53/90 (58%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
FK +++G GTGK+ + + + +F++ T+GVE V + +++ +WDTAGQE
Sbjct: 1 FKFLIIGSAGTGKSCLLHQFIENKFKQDSNHTIGVEFGSRVVNVGGKSVKLQIWDTAGQE 60
Query: 285 KFGGLRDGYYIQGQCAIIMFDVTSRITYKN 314
+F + YY A++++D+TSR ++
Sbjct: 61 RFRSVTRSYYRGAAGALLVYDITSRESFNA 90
>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 = 101 bits (253), Expect = 1e-25
Identities = 53/159 (33%), Positives = 80/159 (50%), Gaps = 13/159 (8%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
FK VL+GD G GK+ + R EF +T+GVE + I+ +WDTAGQE
Sbjct: 4 FKIVLIGDSGVGKSNLLSRFTRNEFNLDSKSTIGVEFATRTIQIDGKTIKAQIWDTAGQE 63
Query: 70 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNW------HRDLVRVCENIPIVLCGNKV 123
++ + YY A++++D+T + T++NV W H D NI I+L GNK
Sbjct: 64 RYRAITSAYYRGAVGALLVYDITKKSTFENVERWLKELRDHAD-----SNIVIMLVGNKS 118
Query: 124 DIK-DRKV-KAKSIVFHRKKNLQYYDISAKSNYNFEKPF 160
D++ R V ++ F K L + + SA N E+ F
Sbjct: 119 DLRHLRAVPTEEAKAFAEKNGLSFIETSALDGTNVEEAF 157
Score = 73.4 bits (181), Expect = 2e-15
Identities = 31/90 (34%), Positives = 50/90 (55%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
FK VL+GD G GK+ + R EF +T+GVE + I+ +WDTAGQE
Sbjct: 4 FKIVLIGDSGVGKSNLLSRFTRNEFNLDSKSTIGVEFATRTIQIDGKTIKAQIWDTAGQE 63
Query: 285 KFGGLRDGYYIQGQCAIIMFDVTSRITYKN 314
++ + YY A++++D+T + T++N
Sbjct: 64 RYRAITSAYYRGAVGALLVYDITKKSTFEN 93
>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 = 101 bits (253), Expect = 2e-25
Identities = 48/172 (27%), Positives = 94/172 (54%), Gaps = 18/172 (10%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHT-----NRGAIRFNVWD 64
K +++GD G GKT+ + +++ +F +Y AT+G + F T + + +WD
Sbjct: 1 LKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGAD-----FLTKEVTVDDRLVTLQIWD 55
Query: 65 TAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRD-LVRVC----ENIPIVLC 119
TAGQE+F L +Y C ++++DVT+ +++++ +W + L++ EN P V+
Sbjct: 56 TAGQERFQSLGVAFYRGADCCVLVYDVTNPKSFESLDSWRDEFLIQASPRDPENFPFVVL 115
Query: 120 GNKVDIKDRKVKAKSIVFH---RKKNLQYYDISAKSNYNFEKPFLWLARKLI 168
GNK+D+++++ + K N+ Y++ SAK N ++ F +AR +
Sbjct: 116 GNKIDLEEKRQVSTKKAQQWCKSKGNIPYFETSAKEAINVDQAFETIARLAL 167
Score = 62.7 bits (153), Expect = 1e-11
Identities = 28/95 (29%), Positives = 54/95 (56%), Gaps = 10/95 (10%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHT-----NRGAIRFNVWD 279
K +++GD G GKT+ + +++ +F +Y AT+G + F T + + +WD
Sbjct: 1 LKVIILGDSGVGKTSLMNQYVNKKFSNQYKATIGAD-----FLTKEVTVDDRLVTLQIWD 55
Query: 280 TAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKN 314
TAGQE+F L +Y C ++++DVT+ ++++
Sbjct: 56 TAGQERFQSLGVAFYRGADCCVLVYDVTNPKSFES 90
>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 = 99.6 bits (248), Expect = 6e-25
Identities = 55/162 (33%), Positives = 88/162 (54%), Gaps = 3/162 (1%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
FK VL+G+ G GKT V+R G F AT+GV+ I+ +WDTAGQE
Sbjct: 8 FKIVLIGNAGVGKTCLVRRFTQGLFPPGQGATIGVDFMIKTVEIKGEKIKLQIWDTAGQE 67
Query: 70 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVCEN-IPIVLCGNKVDIKDR 128
+F + YY I+ +D+T +++ +P W R++ + N + +L GNK+D+ +R
Sbjct: 68 RFRSITQSYYRSANALILTYDITCEESFRCLPEWLREIEQYANNKVITILVGNKIDLAER 127
Query: 129 KVKAKSIV--FHRKKNLQYYDISAKSNYNFEKPFLWLARKLI 168
+ ++ F +++ Y + SAK + N EK FL LA +LI
Sbjct: 128 REVSQQRAEEFSDAQDMYYLETSAKESDNVEKLFLDLACRLI 169
Score = 67.2 bits (164), Expect = 2e-13
Identities = 31/89 (34%), Positives = 46/89 (51%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
FK VL+G+ G GKT V+R G F AT+GV+ I+ +WDTAGQE
Sbjct: 8 FKIVLIGNAGVGKTCLVRRFTQGLFPPGQGATIGVDFMIKTVEIKGEKIKLQIWDTAGQE 67
Query: 285 KFGGLRDGYYIQGQCAIIMFDVTSRITYK 313
+F + YY I+ +D+T +++
Sbjct: 68 RFRSITQSYYRSANALILTYDITCEESFR 96
>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 = 96.0 bits (239), Expect = 9e-24
Identities = 36/164 (21%), Positives = 66/164 (40%), Gaps = 14/164 (8%)
Query: 13 VLVGDGGTGKTTFVKRHLTGEF---EKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
V+VG GG GK++ + L GE T +V+ + + DT G +
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVL--VDTPGLD 58
Query: 70 KFGGLRDG-----YYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVCENIPIVLCGNKVD 124
+FGGL +++ D T R + ++ E IPI+L GNK+D
Sbjct: 59 EFGGLGREELARLLLRGADLILLVVDSTDRESEEDAKL-LILRRLRKEGIPIILVGNKID 117
Query: 125 IKDRKVKAK---SIVFHRKKNLQYYDISAKSNYNFEKPFLWLAR 165
+ + + + + + +++SAK+ ++ F L
Sbjct: 118 LLEEREVEELLRLEELAKILGVPVFEVSAKTGEGVDELFEKLIE 161
Score = 65.2 bits (159), Expect = 1e-12
Identities = 24/117 (20%), Positives = 44/117 (37%), Gaps = 10/117 (8%)
Query: 228 VLVGDGGTGKTTFVKRHLTGEF---EKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
V+VG GG GK++ + L GE T +V+ + + DT G +
Sbjct: 1 VVVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVL--VDTPGLD 58
Query: 285 KFGGLRDG-----YYIQGQCAIIMFDVTSRITYKNYYDISAKSNYNFEKPFLWLARK 336
+FGGL +++ D T R + ++ + + P + + K
Sbjct: 59 EFGGLGREELARLLLRGADLILLVVDSTDRESEEDAKLLILRRLRKEGIPIILVGNK 115
>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 = 95.8 bits (239), Expect = 1e-23
Identities = 49/159 (30%), Positives = 91/159 (57%), Gaps = 3/159 (1%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
FK +L+GD G GK+ + R F +++T+G++ + I+ +WDTAGQE
Sbjct: 4 FKLLLIGDSGVGKSCLLLRFSEDSFNPSFISTIGIDFKIRTIELDGKKIKLQIWDTAGQE 63
Query: 70 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVR-VCENIPIVLCGNKVDIKDR 128
+F + YY I+++D+T +++N+ NW R++ E++ +L GNK D++++
Sbjct: 64 RFRTITTSYYRGAMGIILVYDITDEKSFENIKNWMRNIDEHASEDVERMLVGNKCDMEEK 123
Query: 129 KV--KAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLAR 165
+V K + R+ +++ + SAK+N N E+ FL LA+
Sbjct: 124 RVVSKEEGEALAREYGIKFLETSAKANINVEEAFLTLAK 162
Score = 62.3 bits (152), Expect = 1e-11
Identities = 27/90 (30%), Positives = 49/90 (54%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
FK +L+GD G GK+ + R F +++T+G++ + I+ +WDTAGQE
Sbjct: 4 FKLLLIGDSGVGKSCLLLRFSEDSFNPSFISTIGIDFKIRTIELDGKKIKLQIWDTAGQE 63
Query: 285 KFGGLRDGYYIQGQCAIIMFDVTSRITYKN 314
+F + YY I+++D+T +++N
Sbjct: 64 RFRTITTSYYRGAMGIILVYDITDEKSFEN 93
>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 = 95.6 bits (238), Expect = 2e-23
Identities = 49/162 (30%), Positives = 87/162 (53%), Gaps = 5/162 (3%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
FK +++GD G GK+ + + F+ + T+GVE + + I+ +WDTAGQE
Sbjct: 5 FKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQE 64
Query: 70 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVR--VCENIPIVLCGNKVDIKD 127
F + YY A++++D+T R T+ ++ +W D R N+ I+L GNK D++
Sbjct: 65 SFRSITRSYYRGAAGALLVYDITRRETFNHLTSWLED-ARQHSNSNMTIMLIGNKCDLES 123
Query: 128 RKV--KAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKL 167
R+ + F R+ L + + SAK+ N E+ F+ A+++
Sbjct: 124 RREVSYEEGEAFAREHGLIFMETSAKTASNVEEAFINTAKEI 165
Score = 60.9 bits (148), Expect = 4e-11
Identities = 28/88 (31%), Positives = 48/88 (54%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
FK +++GD G GK+ + + F+ + T+GVE + + I+ +WDTAGQE
Sbjct: 5 FKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQE 64
Query: 285 KFGGLRDGYYIQGQCAIIMFDVTSRITY 312
F + YY A++++D+T R T+
Sbjct: 65 SFRSITRSYYRGAAGALLVYDITRRETF 92
>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 = 95.6 bits (238), Expect = 2e-23
Identities = 52/162 (32%), Positives = 81/162 (50%), Gaps = 14/162 (8%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVH----------PLVFHTNRGAIRF 60
K + +GD G GKTTF+ R+ +F K++ T+G++ P +
Sbjct: 6 KLLALGDSGVGKTTFLYRYTDNKFNPKFITTVGIDFREKRVVYNSQGPDGTSGKAFRVHL 65
Query: 61 NVWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVR--VCENIPIVL 118
+WDTAGQE+F L ++ ++MFD+TS ++ NV NW L CEN IVL
Sbjct: 66 QLWDTAGQERFRSLTTAFFRDAMGFLLMFDLTSEQSFLNVRNWMSQLQAHAYCENPDIVL 125
Query: 119 CGNKVDIKDRKVKAKSIV--FHRKKNLQYYDISAKSNYNFEK 158
GNK D+ D++ ++ K + Y++ SA + N EK
Sbjct: 126 IGNKADLPDQREVSERQARELADKYGIPYFETSAATGQNVEK 167
Score = 60.2 bits (146), Expect = 8e-11
Identities = 30/99 (30%), Positives = 50/99 (50%), Gaps = 10/99 (10%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVH----------PLVFHTNRGAIRF 275
K + +GD G GKTTF+ R+ +F K++ T+G++ P +
Sbjct: 6 KLLALGDSGVGKTTFLYRYTDNKFNPKFITTVGIDFREKRVVYNSQGPDGTSGKAFRVHL 65
Query: 276 NVWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKN 314
+WDTAGQE+F L ++ ++MFD+TS ++ N
Sbjct: 66 QLWDTAGQERFRSLTTAFFRDAMGFLLMFDLTSEQSFLN 104
>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 = 94.9 bits (236), Expect = 2e-23
Identities = 49/158 (31%), Positives = 83/158 (52%), Gaps = 7/158 (4%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
K +L+GDGG GK++ + R++T +F+ + T+GVE + + +WDTAGQE
Sbjct: 6 LKVILLGDGGVGKSSLMNRYVTNKFDTQLFHTIGVEFLNKDLEVDGHFVTLQIWDTAGQE 65
Query: 70 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDL-----VRVCENIPIVLCGNKVD 124
+F LR +Y C ++ F V +++N+ NW ++ V+ E+ P V+ GNK+D
Sbjct: 66 RFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVILGNKID 125
Query: 125 IKDRKVKAKSIV--FHRKKNLQYYDISAKSNYNFEKPF 160
I +R+V + + Y++ SAK N F
Sbjct: 126 IPERQVSTEEAQAWCRDNGDYPYFETSAKDATNVAAAF 163
Score = 67.6 bits (165), Expect = 2e-13
Identities = 30/90 (33%), Positives = 51/90 (56%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
K +L+GDGG GK++ + R++T +F+ + T+GVE + + +WDTAGQE
Sbjct: 6 LKVILLGDGGVGKSSLMNRYVTNKFDTQLFHTIGVEFLNKDLEVDGHFVTLQIWDTAGQE 65
Query: 285 KFGGLRDGYYIQGQCAIIMFDVTSRITYKN 314
+F LR +Y C ++ F V +++N
Sbjct: 66 RFRSLRTPFYRGSDCCLLTFSVDDSQSFQN 95
>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 = 94.5 bits (235), Expect = 4e-23
Identities = 55/165 (33%), Positives = 88/165 (53%), Gaps = 11/165 (6%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVA----TLGVEVHPLVFHTNRGAIRFNVWDT 65
FK +++GD G GK+ + + EKK++A T+GVE + N I+ +WDT
Sbjct: 3 FKYIIIGDMGVGKSCLLHQFT----EKKFMADCPHTIGVEFGTRIIEVNGQKIKLQIWDT 58
Query: 66 AGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVCE-NIPIVLCGNKVD 124
AGQE+F + YY A++++D+T R TY ++ +W D + N I L GNK D
Sbjct: 59 AGQERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDARNLTNPNTVIFLIGNKAD 118
Query: 125 IKD-RKVK-AKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKL 167
++ R V ++ F + L + + SAK+ N E FL A+K+
Sbjct: 119 LEAQRDVTYEEAKQFADENGLLFLECSAKTGENVEDAFLETAKKI 163
Score = 67.2 bits (164), Expect = 2e-13
Identities = 33/92 (35%), Positives = 52/92 (56%), Gaps = 8/92 (8%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVA----TLGVEVHPLVFHTNRGAIRFNVWDT 280
FK +++GD G GK+ + + EKK++A T+GVE + N I+ +WDT
Sbjct: 3 FKYIIIGDMGVGKSCLLHQFT----EKKFMADCPHTIGVEFGTRIIEVNGQKIKLQIWDT 58
Query: 281 AGQEKFGGLRDGYYIQGQCAIIMFDVTSRITY 312
AGQE+F + YY A++++D+T R TY
Sbjct: 59 AGQERFRAVTRSYYRGAAGALMVYDITRRSTY 90
>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 = 95.3 bits (237), Expect = 4e-23
Identities = 49/161 (30%), Positives = 86/161 (53%), Gaps = 2/161 (1%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
FK +++GD G GK++ + R F Y+ T+GV+ N ++ +WDTAGQE
Sbjct: 7 FKLLIIGDSGVGKSSLLLRFADNTFSGSYITTIGVDFKIRTVEINGERVKLQIWDTAGQE 66
Query: 70 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRK 129
+F + YY I+++DVT+ ++ NV W +++ + C+++ VL GNK D +RK
Sbjct: 67 RFRTITSTYYRGTHGVIVVYDVTNGESFVNVKRWLQEIEQNCDDVCKVLVGNKNDDPERK 126
Query: 130 V--KAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLI 168
V + F + + ++ SAK N N E+ F + ++
Sbjct: 127 VVETEDAYKFAGQMGISLFETSAKENINVEEMFNCITELVL 167
Score = 62.9 bits (153), Expect = 1e-11
Identities = 29/90 (32%), Positives = 49/90 (54%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
FK +++GD G GK++ + R F Y+ T+GV+ N ++ +WDTAGQE
Sbjct: 7 FKLLIIGDSGVGKSSLLLRFADNTFSGSYITTIGVDFKIRTVEINGERVKLQIWDTAGQE 66
Query: 285 KFGGLRDGYYIQGQCAIIMFDVTSRITYKN 314
+F + YY I+++DVT+ ++ N
Sbjct: 67 RFRTITSTYYRGTHGVIVVYDVTNGESFVN 96
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 94.6 bits (235), Expect = 1e-22
Identities = 52/154 (33%), Positives = 79/154 (51%), Gaps = 3/154 (1%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
FK VL+GD G GK+ + R EF + +T+GVE ++ +WDTAGQE
Sbjct: 13 FKIVLIGDSGVGKSNILSRFTRNEFCLESKSTIGVEFATRTLQVEGKTVKAQIWDTAGQE 72
Query: 70 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVCE-NIPIVLCGNKVDIKD- 127
++ + YY A++++D+T R T+ NV W R+L + NI I++ GNK D+
Sbjct: 73 RYRAITSAYYRGAVGALLVYDITKRQTFDNVQRWLRELRDHADSNIVIMMAGNKSDLNHL 132
Query: 128 RKVKAK-SIVFHRKKNLQYYDISAKSNYNFEKPF 160
R V + K+ L + + SA N EK F
Sbjct: 133 RSVAEEDGQALAEKEGLSFLETSALEATNVEKAF 166
Score = 70.0 bits (171), Expect = 7e-14
Identities = 31/90 (34%), Positives = 49/90 (54%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
FK VL+GD G GK+ + R EF + +T+GVE ++ +WDTAGQE
Sbjct: 13 FKIVLIGDSGVGKSNILSRFTRNEFCLESKSTIGVEFATRTLQVEGKTVKAQIWDTAGQE 72
Query: 285 KFGGLRDGYYIQGQCAIIMFDVTSRITYKN 314
++ + YY A++++D+T R T+ N
Sbjct: 73 RYRAITSAYYRGAVGALLVYDITKRQTFDN 102
>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 = 93.0 bits (232), Expect = 1e-22
Identities = 40/118 (33%), Positives = 66/118 (55%), Gaps = 2/118 (1%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 70
K V+VGDG GKT + + T +F +YV T+ + + + + +WDTAGQE+
Sbjct: 2 KIVVVGDGAVGKTCLLISYTTNKFPTEYVPTV-FDNYSANVTVDGKQVNLGLWDTAGQEE 60
Query: 71 FGGLRDGYYIQGQCAIIMFDVTSRITYKNVPN-WHRDLVRVCENIPIVLCGNKVDIKD 127
+ LR Y Q ++ F V S +++NV W+ ++ C N+PI+L G K+D++D
Sbjct: 61 YDRLRPLSYPQTDVFLLCFSVDSPSSFENVKTKWYPEIKHYCPNVPIILVGTKIDLRD 118
Score = 64.9 bits (159), Expect = 2e-12
Identities = 29/89 (32%), Positives = 47/89 (52%), Gaps = 1/89 (1%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 285
K V+VGDG GKT + + T +F +YV T+ + + + + +WDTAGQE+
Sbjct: 2 KIVVVGDGAVGKTCLLISYTTNKFPTEYVPTV-FDNYSANVTVDGKQVNLGLWDTAGQEE 60
Query: 286 FGGLRDGYYIQGQCAIIMFDVTSRITYKN 314
+ LR Y Q ++ F V S +++N
Sbjct: 61 YDRLRPLSYPQTDVFLLCFSVDSPSSFEN 89
>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 = 91.8 bits (229), Expect = 3e-22
Identities = 47/168 (27%), Positives = 85/168 (50%), Gaps = 21/168 (12%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLG------VEVHPLVFHTNRGAIRFNVW 63
+K V++G GG GK+ + + G F Y T+ +E+ V ++
Sbjct: 1 YKLVVLGSGGVGKSALTIQFIQGHFVDDYDPTIEDSYRKQIEIDGEVCL-------LDIL 53
Query: 64 DTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRV--CENIPIVLCGN 121
DTAGQE+F +RD Y G+ ++++ +T R +++ + + ++RV +++PIVL GN
Sbjct: 54 DTAGQEEFSAMRDQYMRTGEGFLLVYSITDRQSFEEIKKFREQILRVKDRDDVPIVLVGN 113
Query: 122 KVDIKD-RKV---KAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLAR 165
K D++ R V + K + R+ + + SAK N ++ F L R
Sbjct: 114 KCDLESERVVSTEEGKELA--RQWGCPFLETSAKERVNVDEAFYDLVR 159
Score = 49.5 bits (119), Expect = 3e-07
Identities = 26/91 (28%), Positives = 45/91 (49%), Gaps = 13/91 (14%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLG------VEVHPLVFHTNRGAIRFNVW 278
+K V++G GG GK+ + + G F Y T+ +E+ V ++
Sbjct: 1 YKLVVLGSGGVGKSALTIQFIQGHFVDDYDPTIEDSYRKQIEIDGEVCL-------LDIL 53
Query: 279 DTAGQEKFGGLRDGYYIQGQCAIIMFDVTSR 309
DTAGQE+F +RD Y G+ ++++ +T R
Sbjct: 54 DTAGQEEFSAMRDQYMRTGEGFLLVYSITDR 84
>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 = 90.5 bits (225), Expect = 8e-22
Identities = 41/156 (26%), Positives = 75/156 (48%), Gaps = 5/156 (3%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGE-FEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQ 68
K V+VGD GK+T + R L + +Y V + +FN+ DTAGQ
Sbjct: 2 IKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAGQ 61
Query: 69 EKFGGLRDGYYIQGQCAIIMFDVTSRI--TYKNVPNWHRDLVRVCE-NIPIVLCGNKVDI 125
E + +R YY + ++ +FD+ + + + ++++ E +PI+L GNK+D+
Sbjct: 62 EDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAESGVPIILVGNKIDL 121
Query: 126 KDRKVKAKSI-VFHRKKNLQYYDISAKSNYNFEKPF 160
+D K+K +F + +SA++ N + F
Sbjct: 122 RDAKLKTHVAFLFAKLNGEPIIPLSAETGKNIDSAF 157
Score = 59.3 bits (144), Expect = 1e-10
Identities = 25/87 (28%), Positives = 41/87 (47%), Gaps = 1/87 (1%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGE-FEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQ 283
K V+VGD GK+T + R L + +Y V + +FN+ DTAGQ
Sbjct: 2 IKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAGQ 61
Query: 284 EKFGGLRDGYYIQGQCAIIMFDVTSRI 310
E + +R YY + ++ +FD+ +
Sbjct: 62 EDYDAIRRLYYRAVESSLRVFDIVILV 88
>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 = 90.3 bits (225), Expect = 1e-21
Identities = 47/170 (27%), Positives = 87/170 (51%), Gaps = 21/170 (12%)
Query: 8 PSFKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLG------VEVHPLVFHTNRGAIRFN 61
+K V++G GG GK+ + + G F +Y T+ +E+ V +
Sbjct: 1 REYKLVVLGGGGVGKSALTIQFVQGHFVDEYDPTIEDSYRKQIEIDGEVCL-------LD 53
Query: 62 VWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRV--CENIPIVLC 119
+ DTAGQE+F +RD Y G+ ++++ +T R +++ + + ++RV +++PIVL
Sbjct: 54 ILDTAGQEEFSAMRDQYMRTGEGFLLVYSITDRQSFEEIAKFREQILRVKDRDDVPIVLV 113
Query: 120 GNKVDIKD-RKV---KAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLAR 165
GNK D+++ R V + K + R+ + + SAK N ++ F L R
Sbjct: 114 GNKCDLENERVVSTEEGKELA--RQWGCPFLETSAKERINVDEAFYDLVR 161
Score = 49.1 bits (118), Expect = 4e-07
Identities = 26/93 (27%), Positives = 46/93 (49%), Gaps = 13/93 (13%)
Query: 223 PSFKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLG------VEVHPLVFHTNRGAIRFN 276
+K V++G GG GK+ + + G F +Y T+ +E+ V +
Sbjct: 1 REYKLVVLGGGGVGKSALTIQFVQGHFVDEYDPTIEDSYRKQIEIDGEVCL-------LD 53
Query: 277 VWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTSR 309
+ DTAGQE+F +RD Y G+ ++++ +T R
Sbjct: 54 ILDTAGQEEFSAMRDQYMRTGEGFLLVYSITDR 86
>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 = 91.1 bits (226), Expect = 1e-21
Identities = 47/162 (29%), Positives = 87/162 (53%), Gaps = 4/162 (2%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEF-EKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQ 68
FK +LVGD G GKT + R G F ++AT+G++ V + ++ +WDTAGQ
Sbjct: 1 FKVMLVGDSGVGKTCLLVRFKDGAFLAGSFIATVGIQFTNKVVTVDGVKVKLQIWDTAGQ 60
Query: 69 EKFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVC-ENIPIVLCGNKVDIKD 127
E+F + YY ++++DVT++ ++ N+ W +++ ++ I+L GNK D+
Sbjct: 61 ERFRSVTHAYYRDAHALLLLYDVTNKSSFDNIRAWLTEILEYAQSDVVIMLLGNKADMSG 120
Query: 128 RKV--KAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKL 167
+V + ++ + + + SAK+ N E F +A++L
Sbjct: 121 ERVVKREDGERLAKEYGVPFMETSAKTGLNVELAFTAVAKEL 162
Score = 71.4 bits (175), Expect = 1e-14
Identities = 31/91 (34%), Positives = 52/91 (57%), Gaps = 1/91 (1%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEF-EKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQ 283
FK +LVGD G GKT + R G F ++AT+G++ V + ++ +WDTAGQ
Sbjct: 1 FKVMLVGDSGVGKTCLLVRFKDGAFLAGSFIATVGIQFTNKVVTVDGVKVKLQIWDTAGQ 60
Query: 284 EKFGGLRDGYYIQGQCAIIMFDVTSRITYKN 314
E+F + YY ++++DVT++ ++ N
Sbjct: 61 ERFRSVTHAYYRDAHALLLLYDVTNKSSFDN 91
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 90.1 bits (223), Expect = 4e-21
Identities = 52/170 (30%), Positives = 88/170 (51%), Gaps = 6/170 (3%)
Query: 9 SFKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQ 68
SFK +L+GD G GK++ + ++ E T+GV+ ++ +WDTAGQ
Sbjct: 14 SFKILLIGDSGVGKSSLLVSFISSSVED-LAPTIGVDFKIKQLTVGGKRLKLTIWDTAGQ 72
Query: 69 EKFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPN-WHRDLVRVCENIPIV--LCGNKVDI 125
E+F L YY Q I+++DVT R T+ N+ + W +++ N V L GNKVD
Sbjct: 73 ERFRTLTSSYYRNAQGIILVYDVTRRETFTNLSDVWGKEVELYSTNQDCVKMLVGNKVDR 132
Query: 126 KDRKV--KAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNL 173
+ + + + + ++ + + SAK+ N E+ F LA K++ P+L
Sbjct: 133 ESERDVSREEGMALAKEHGCLFLECSAKTRENVEQCFEELALKIMEVPSL 182
Score = 68.5 bits (167), Expect = 2e-13
Identities = 34/98 (34%), Positives = 52/98 (53%), Gaps = 1/98 (1%)
Query: 224 SFKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQ 283
SFK +L+GD G GK++ + ++ E T+GV+ ++ +WDTAGQ
Sbjct: 14 SFKILLIGDSGVGKSSLLVSFISSSVED-LAPTIGVDFKIKQLTVGGKRLKLTIWDTAGQ 72
Query: 284 EKFGGLRDGYYIQGQCAIIMFDVTSRITYKNYYDISAK 321
E+F L YY Q I+++DVT R T+ N D+ K
Sbjct: 73 ERFRTLTSSYYRNAQGIILVYDVTRRETFTNLSDVWGK 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 = 87.8 bits (218), Expect = 9e-21
Identities = 49/170 (28%), Positives = 87/170 (51%), Gaps = 21/170 (12%)
Query: 8 PSFKCVLVGDGGTGKTT----FVKRHLTGEF----EKKYVATLGVEVHPLVFHTNRGAIR 59
P++K V+VG GG GK+ F++ + ++ E Y ++ R
Sbjct: 1 PTYKLVVVGGGGVGKSALTIQFIQSYFVTDYDPTIEDSYTKQCEIDGQW---------AR 51
Query: 60 FNVWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRV--CENIPIV 117
++ DTAGQE+F +R+ Y G+ +++F VT R +++ V +H ++RV + P++
Sbjct: 52 LDILDTAGQEEFSAMREQYMRTGEGFLLVFSVTDRGSFEEVDKFHTQILRVKDRDEFPMI 111
Query: 118 LCGNKVDIKD-RKV-KAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLAR 165
L GNK D++ R+V + + R+ + Y + SAK N +K F L R
Sbjct: 112 LVGNKADLEHQRQVSREEGQELARQLKIPYIETSAKDRVNVDKAFHDLVR 161
Score = 50.5 bits (121), Expect = 1e-07
Identities = 27/98 (27%), Positives = 49/98 (50%), Gaps = 17/98 (17%)
Query: 223 PSFKCVLVGDGGTGKTT----FVKRHLTGEF----EKKYVATLGVEVHPLVFHTNRGAIR 274
P++K V+VG GG GK+ F++ + ++ E Y ++ R
Sbjct: 1 PTYKLVVVGGGGVGKSALTIQFIQSYFVTDYDPTIEDSYTKQCEIDGQW---------AR 51
Query: 275 FNVWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITY 312
++ DTAGQE+F +R+ Y G+ +++F VT R ++
Sbjct: 52 LDILDTAGQEEFSAMREQYMRTGEGFLLVFSVTDRGSF 89
>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 = 88.1 bits (218), Expect = 2e-20
Identities = 46/124 (37%), Positives = 70/124 (56%), Gaps = 2/124 (1%)
Query: 7 MPSFKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTA 66
M S KCV+VGDG GKT + + T F K+Y+ T+ + + + + N+WDTA
Sbjct: 1 MQSIKCVVVGDGAVGKTCLLICYTTNAFPKEYIPTV-FDNYSAQTAVDGRTVSLNLWDTA 59
Query: 67 GQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPN-WHRDLVRVCENIPIVLCGNKVDI 125
GQE++ LR Y Q II F + S +Y+NV + WH ++ C N+PI+L G K D+
Sbjct: 60 GQEEYDRLRTLSYPQTNVFIICFSIASPSSYENVRHKWHPEVCHHCPNVPILLVGTKKDL 119
Query: 126 KDRK 129
++
Sbjct: 120 RNDA 123
Score = 66.2 bits (161), Expect = 8e-13
Identities = 35/93 (37%), Positives = 51/93 (54%), Gaps = 1/93 (1%)
Query: 222 MPSFKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTA 281
M S KCV+VGDG GKT + + T F K+Y+ T+ + + + + N+WDTA
Sbjct: 1 MQSIKCVVVGDGAVGKTCLLICYTTNAFPKEYIPTV-FDNYSAQTAVDGRTVSLNLWDTA 59
Query: 282 GQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKN 314
GQE++ LR Y Q II F + S +Y+N
Sbjct: 60 GQEEYDRLRTLSYPQTNVFIICFSIASPSSYEN 92
>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 = 87.8 bits (218), Expect = 2e-20
Identities = 49/169 (28%), Positives = 77/169 (45%), Gaps = 16/169 (9%)
Query: 8 PSFKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAG 67
K V+VGDGG GKT + + G F ++YV T+ + N I +WDTAG
Sbjct: 2 LKVKIVVVGDGGCGKTCLLMVYAQGSFPEEYVPTVFENYVTTLQVPNGKIIELALWDTAG 61
Query: 68 QEKFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPN-WHRDLVRVCENIPIVLCGNKVDI- 125
QE + LR Y +I + V + + NV + W+ ++ C PIVL G K D+
Sbjct: 62 QEDYDRLRPLSYPDVDVILICYSVDNPTSLDNVEDKWYPEVNHFCPGTPIVLVGLKTDLR 121
Query: 126 KDRKVKAKS-------IVFHRKKNL-------QYYDISAKSNYNFEKPF 160
KD+ +K + + +++ Y + SAK N ++ F
Sbjct: 122 KDKNSVSKLRAQGLEPVTPEQGESVAKSIGAVAYIECSAKLMENVDEVF 170
Score = 64.3 bits (157), Expect = 4e-12
Identities = 30/92 (32%), Positives = 43/92 (46%)
Query: 223 PSFKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAG 282
K V+VGDGG GKT + + G F ++YV T+ + N I +WDTAG
Sbjct: 2 LKVKIVVVGDGGCGKTCLLMVYAQGSFPEEYVPTVFENYVTTLQVPNGKIIELALWDTAG 61
Query: 283 QEKFGGLRDGYYIQGQCAIIMFDVTSRITYKN 314
QE + LR Y +I + V + + N
Sbjct: 62 QEDYDRLRPLSYPDVDVILICYSVDNPTSLDN 93
>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 = 86.6 bits (214), Expect = 3e-20
Identities = 44/158 (27%), Positives = 84/158 (53%), Gaps = 3/158 (1%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
F+ +L+GD G GKT + R EF +++T+GV+ + +R +WDTAGQE
Sbjct: 1 FRLLLIGDSGVGKTCLLCRFTDNEFHSSHISTIGVDFKMKTIEVDGIKVRIQIWDTAGQE 60
Query: 70 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVC-ENIPIVLCGNKVDI-KD 127
++ + YY + Q +++D++S +Y+++ W D+ E + +L GNK D +
Sbjct: 61 RYQTITKQYYRRAQGIFLVYDISSERSYQHIMKWVSDVDEYAPEGVQKILIGNKADEEQK 120
Query: 128 RKV-KAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLA 164
R+V + ++ + +++ SA +N N ++ F L
Sbjct: 121 RQVGDEQGNKLAKEYGMDFFETSACTNKNIKESFTRLT 158
Score = 66.5 bits (162), Expect = 4e-13
Identities = 28/90 (31%), Positives = 52/90 (57%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
F+ +L+GD G GKT + R EF +++T+GV+ + +R +WDTAGQE
Sbjct: 1 FRLLLIGDSGVGKTCLLCRFTDNEFHSSHISTIGVDFKMKTIEVDGIKVRIQIWDTAGQE 60
Query: 285 KFGGLRDGYYIQGQCAIIMFDVTSRITYKN 314
++ + YY + Q +++D++S +Y++
Sbjct: 61 RYQTITKQYYRRAQGIFLVYDISSERSYQH 90
>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 = 86.5 bits (214), Expect = 3e-20
Identities = 45/158 (28%), Positives = 85/158 (53%), Gaps = 11/158 (6%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
FK +++G+ GKT+F+ R+ F +V+T+G++ + N I+ +WDTAGQE
Sbjct: 2 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVYRNDKRIKLQIWDTAGQE 61
Query: 70 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVC-ENIPIVLCGNKVDIKDR 128
++ + YY I+M+D+T+ ++ V +W + +N ++L GNK D++D
Sbjct: 62 RYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSWDNAQVILVGNKCDMEDE 121
Query: 129 KVKAKSIVFHRKKNL------QYYDISAKSNYNFEKPF 160
+V + R + L ++++ SAK N N ++ F
Sbjct: 122 RV----VSAERGRQLADQLGFEFFEASAKENINVKQVF 155
Score = 61.9 bits (150), Expect = 2e-11
Identities = 28/93 (30%), Positives = 52/93 (55%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
FK +++G+ GKT+F+ R+ F +V+T+G++ + N I+ +WDTAGQE
Sbjct: 2 FKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVYRNDKRIKLQIWDTAGQE 61
Query: 285 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNYYD 317
++ + YY I+M+D+T+ ++ D
Sbjct: 62 RYRTITTAYYRGAMGFILMYDITNEESFNAVQD 94
>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 = 85.3 bits (211), Expect = 8e-20
Identities = 46/163 (28%), Positives = 87/163 (53%), Gaps = 5/163 (3%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
+K V++G GG GK+ + + G F +KY T+ V + + + DTAG E
Sbjct: 2 YKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDGQQCM-LEILDTAGTE 60
Query: 70 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRV--CENIPIVLCGNKVDIKD 127
+F +RD Y GQ ++++ +T++ T+ ++ + ++RV E++P++L GNK D++D
Sbjct: 61 QFTAMRDLYMKNGQGFVLVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLED 120
Query: 128 RKV--KAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLI 168
+V K + R+ + + SAK+ N + F L R++
Sbjct: 121 ERVVGKEQGQNLARQWGCAFLETSAKAKINVNEIFYDLVRQIN 163
Score = 48.3 bits (115), Expect = 7e-07
Identities = 27/94 (28%), Positives = 50/94 (53%), Gaps = 1/94 (1%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
+K V++G GG GK+ + + G F +KY T+ V + + + DTAG E
Sbjct: 2 YKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDGQQCM-LEILDTAGTE 60
Query: 285 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNYYDI 318
+F +RD Y GQ ++++ +T++ T+ + D+
Sbjct: 61 QFTAMRDLYMKNGQGFVLVYSITAQSTFNDLQDL 94
>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 = 85.0 bits (211), Expect = 1e-19
Identities = 40/119 (33%), Positives = 63/119 (52%), Gaps = 2/119 (1%)
Query: 12 CVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEKF 71
V+VGDG GKT + + T F + YV T+ E + + + +WDTAGQE +
Sbjct: 1 LVVVGDGAVGKTCLLIVYTTNAFPEDYVPTV-FENYSADVEVDGKPVELGLWDTAGQEDY 59
Query: 72 GGLRDGYYIQGQCAIIMFDVTSRITYKNVPN-WHRDLVRVCENIPIVLCGNKVDIKDRK 129
LR Y +I F V S +++NV W+ ++ C N+PI+L G K+D+++ K
Sbjct: 60 DRLRPLSYPDTDVFLICFSVDSPASFENVKEKWYPEVKHFCPNVPIILVGTKLDLRNDK 118
Score = 61.9 bits (151), Expect = 2e-11
Identities = 30/95 (31%), Positives = 45/95 (47%), Gaps = 4/95 (4%)
Query: 227 CVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEKF 286
V+VGDG GKT + + T F + YV T+ E + + + +WDTAGQE +
Sbjct: 1 LVVVGDGAVGKTCLLIVYTTNAFPEDYVPTV-FENYSADVEVDGKPVELGLWDTAGQEDY 59
Query: 287 GGLRDGYYIQGQCAIIMFDVTSRITYKNYYDISAK 321
LR Y +I F V S +++N + K
Sbjct: 60 DRLRPLSYPDTDVFLICFSVDSPASFEN---VKEK 91
>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 = 84.1 bits (208), Expect = 2e-19
Identities = 49/170 (28%), Positives = 87/170 (51%), Gaps = 21/170 (12%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLG--------VEVHPLVFHTNRGAIRFN 61
+K V++G GG GK+ + ++G F +KY T+ V+ P V
Sbjct: 2 YKVVVLGSGGVGKSALTVQFVSGTFIEKYDPTIEDFYRKEIEVDSSPSVLE--------- 52
Query: 62 VWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRV--CENIPIVLC 119
+ DTAG E+F +RD Y GQ I+++ + ++ T++++ +VRV E +PI+L
Sbjct: 53 ILDTAGTEQFASMRDLYIKNGQGFIVVYSLVNQQTFQDIKPMRDQIVRVKGYEKVPIILV 112
Query: 120 GNKVDIK-DRKVK-AKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKL 167
GNKVD++ +R+V A+ + + + SAKS + F + R++
Sbjct: 113 GNKVDLESEREVSSAEGRALAEEWGCPFMETSAKSKTMVNELFAEIVRQM 162
Score = 55.2 bits (133), Expect = 3e-09
Identities = 28/98 (28%), Positives = 50/98 (51%), Gaps = 17/98 (17%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLG--------VEVHPLVFHTNRGAIRFN 276
+K V++G GG GK+ + ++G F +KY T+ V+ P V
Sbjct: 2 YKVVVLGSGGVGKSALTVQFVSGTFIEKYDPTIEDFYRKEIEVDSSPSVLE--------- 52
Query: 277 VWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKN 314
+ DTAG E+F +RD Y GQ I+++ + ++ T+++
Sbjct: 53 ILDTAGTEQFASMRDLYIKNGQGFIVVYSLVNQQTFQD 90
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 85.4 bits (211), Expect = 2e-19
Identities = 48/161 (29%), Positives = 85/161 (52%), Gaps = 3/161 (1%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
FK +++GD G GK+ + + F+ + T+GVE + + I+ +WDTAGQE
Sbjct: 7 FKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDNKPIKLQIWDTAGQE 66
Query: 70 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVR-VCENIPIVLCGNKVDIKDR 128
F + YY A++++D+T R T+ ++ +W D + N+ I+L GNK D+ R
Sbjct: 67 SFRSITRSYYRGAAGALLVYDITRRETFNHLASWLEDARQHANANMTIMLIGNKCDLAHR 126
Query: 129 KV--KAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKL 167
+ + F ++ L + + SAK+ N E+ F+ A K+
Sbjct: 127 RAVSTEEGEQFAKEHGLIFMEASAKTAQNVEEAFIKTAAKI 167
Score = 60.3 bits (146), Expect = 1e-10
Identities = 28/88 (31%), Positives = 48/88 (54%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
FK +++GD G GK+ + + F+ + T+GVE + + I+ +WDTAGQE
Sbjct: 7 FKYIIIGDTGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDNKPIKLQIWDTAGQE 66
Query: 285 KFGGLRDGYYIQGQCAIIMFDVTSRITY 312
F + YY A++++D+T R T+
Sbjct: 67 SFRSITRSYYRGAAGALLVYDITRRETF 94
>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 = 83.9 bits (208), Expect = 3e-19
Identities = 39/153 (25%), Positives = 85/153 (55%), Gaps = 14/153 (9%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVE--VHPLVFHTNRG-AIRFNVWDTAG 67
K + +G+ G GK+ +KR+ G F KY+ T+G++ V + + R +R N +D +G
Sbjct: 2 KVISMGNSGVGKSCIIKRYCEGRFVSKYLPTIGIDYGVKKV---SVRNKEVRVNFFDLSG 58
Query: 68 QEKFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVC------ENIPIVLCGN 121
++ +R+ +Y Q ++++DVT R +++ + +W +++ + ENI +V+C N
Sbjct: 59 HPEYLEVRNEFYKDTQGVLLVYDVTDRQSFEALDSWLKEMKQEGGPHGNMENIVVVVCAN 118
Query: 122 KVDIKDRKVKAKS--IVFHRKKNLQYYDISAKS 152
K+D+ + ++ ++ K +Y++ SA +
Sbjct: 119 KIDLTKHRAVSEDEGRLWAESKGFKYFETSACT 151
Score = 57.8 bits (140), Expect = 5e-10
Identities = 26/87 (29%), Positives = 50/87 (57%), Gaps = 6/87 (6%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVE--VHPLVFHTNRG-AIRFNVWDTAG 282
K + +G+ G GK+ +KR+ G F KY+ T+G++ V + + R +R N +D +G
Sbjct: 2 KVISMGNSGVGKSCIIKRYCEGRFVSKYLPTIGIDYGVKKV---SVRNKEVRVNFFDLSG 58
Query: 283 QEKFGGLRDGYYIQGQCAIIMFDVTSR 309
++ +R+ +Y Q ++++DVT R
Sbjct: 59 HPEYLEVRNEFYKDTQGVLLVYDVTDR 85
>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 = 82.2 bits (203), Expect = 1e-18
Identities = 51/164 (31%), Positives = 84/164 (51%), Gaps = 10/164 (6%)
Query: 11 KCVLVGDGGTGKTTFVKR-HLTG-EFEKKYVATLGVE--VHPLVFHTNRGAIRFNVWDTA 66
+C +VGD GK+ V+ H G F+K Y T G + V + ++ ++D+A
Sbjct: 2 QCAVVGDPAVGKSALVQMFHSDGATFQKNYTMTTGCDLVVKTVPVPDTSDSVELFIFDSA 61
Query: 67 GQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVR---VCENIPIVLCGNKV 123
GQE F + + + Q +++DVT+ +++ N W + VR + P VL GNK
Sbjct: 62 GQELFSDMVENVWEQPAVVCVVYDVTNEVSFNNCSRW-INRVRTHSHGLHTPGVLVGNKC 120
Query: 124 DIKDRK--VKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLAR 165
D+ DR+ A++ + L++Y+ SAK +E PFL LAR
Sbjct: 121 DLTDRREVDAAQAQALAQANTLKFYETSAKEGVGYEAPFLSLAR 164
Score = 53.7 bits (129), Expect = 1e-08
Identities = 26/93 (27%), Positives = 48/93 (51%), Gaps = 4/93 (4%)
Query: 226 KCVLVGDGGTGKTTFVKR-HLTG-EFEKKYVATLGVE--VHPLVFHTNRGAIRFNVWDTA 281
+C +VGD GK+ V+ H G F+K Y T G + V + ++ ++D+A
Sbjct: 2 QCAVVGDPAVGKSALVQMFHSDGATFQKNYTMTTGCDLVVKTVPVPDTSDSVELFIFDSA 61
Query: 282 GQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKN 314
GQE F + + + Q +++DVT+ +++ N
Sbjct: 62 GQELFSDMVENVWEQPAVVCVVYDVTNEVSFNN 94
>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 = 82.1 bits (203), Expect = 1e-18
Identities = 50/170 (29%), Positives = 85/170 (50%), Gaps = 16/170 (9%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
FK +++GD GKT R G F ++ AT+GV+ + I+ +WDTAGQE
Sbjct: 3 FKIIVIGDSNVGKTCLTYRFCAGRFPERTEATIGVDFRERTVEIDGERIKVQLWDTAGQE 62
Query: 70 KF-GGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVCEN------IPIVLCGNK 122
+F + YY + ++DVT+ ++ ++P+W + CE +P +L GNK
Sbjct: 63 RFRKSMVQHYYRNVHAVVFVYDVTNMASFHSLPSW----IEECEQHSLPNEVPRILVGNK 118
Query: 123 VDIKD-RKVKA-KSIVFHRKKNLQYYDISAK---SNYNFEKPFLWLARKL 167
D+++ +V + F ++ ++ SAK N + E F+ LA KL
Sbjct: 119 CDLREQIQVPTDLAQRFADAHSMPLFETSAKDPSENDHVEAIFMTLAHKL 168
Score = 61.3 bits (149), Expect = 2e-11
Identities = 28/91 (30%), Positives = 47/91 (51%), Gaps = 1/91 (1%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
FK +++GD GKT R G F ++ AT+GV+ + I+ +WDTAGQE
Sbjct: 3 FKIIVIGDSNVGKTCLTYRFCAGRFPERTEATIGVDFRERTVEIDGERIKVQLWDTAGQE 62
Query: 285 KF-GGLRDGYYIQGQCAIIMFDVTSRITYKN 314
+F + YY + ++DVT+ ++ +
Sbjct: 63 RFRKSMVQHYYRNVHAVVFVYDVTNMASFHS 93
>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 = 81.7 bits (202), Expect = 2e-18
Identities = 44/161 (27%), Positives = 81/161 (50%), Gaps = 4/161 (2%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
+K V+VG GG GK+ + + F +Y T+ V + ++ DTAGQE
Sbjct: 2 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCL-LDILDTAGQE 60
Query: 70 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRV--CENIPIVLCGNKVDIKD 127
++ +RD Y G+ + +F + SR +++++ + + RV +++P+VL GNK D+
Sbjct: 61 EYSAMRDQYMRTGEGFLCVFAINSRKSFEDIHTYREQIKRVKDSDDVPMVLVGNKCDLAA 120
Query: 128 RKVKAKSIV-FHRKKNLQYYDISAKSNYNFEKPFLWLARKL 167
R V + + + Y + SAK+ E+ F L R++
Sbjct: 121 RTVSTRQGQDLAKSYGIPYIETSAKTRQGVEEAFYTLVREI 161
Score = 46.6 bits (111), Expect = 3e-06
Identities = 28/95 (29%), Positives = 47/95 (49%), Gaps = 4/95 (4%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
+K V+VG GG GK+ + + F +Y T+ V + ++ DTAGQE
Sbjct: 2 YKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCL-LDILDTAGQE 60
Query: 285 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNYYDIS 319
++ +RD Y G+ + +F + SR K++ DI
Sbjct: 61 EYSAMRDQYMRTGEGFLCVFAINSR---KSFEDIH 92
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 81.7 bits (201), Expect = 2e-18
Identities = 46/144 (31%), Positives = 83/144 (57%), Gaps = 6/144 (4%)
Query: 34 FEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTS 93
F+ Y +T+G++ + + G +R +WDTAGQE+F L Y AI+++D+T+
Sbjct: 5 FDNNYQSTIGIDFLSKTLYLDEGPVRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDITN 64
Query: 94 RITYKNVPNWHRDLV-RVCENIPIVLCGNKVDIKD-RKVK-AKSIVFHRKKNLQYYDISA 150
R +++N W +D++ +++ I L GNK D+ D RKV + + ++ N +++ SA
Sbjct: 65 RQSFENTTKWIQDILNERGKDVIIALVGNKTDLGDLRKVTYEEGMQKAQEYNTMFHETSA 124
Query: 151 KSNYNFEKPFLWLARKLIGDPNLE 174
K+ +N + F +A KL PNL+
Sbjct: 125 KAGHNIKVLFKKIAAKL---PNLD 145
Score = 55.5 bits (133), Expect = 3e-09
Identities = 22/66 (33%), Positives = 40/66 (60%)
Query: 249 FEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTS 308
F+ Y +T+G++ + + G +R +WDTAGQE+F L Y AI+++D+T+
Sbjct: 5 FDNNYQSTIGIDFLSKTLYLDEGPVRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDITN 64
Query: 309 RITYKN 314
R +++N
Sbjct: 65 RQSFEN 70
>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 = 82.1 bits (203), Expect = 3e-18
Identities = 46/168 (27%), Positives = 85/168 (50%), Gaps = 19/168 (11%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGV-------EVHPLVFHTNRGAIRFNV 62
F+ +++GD GK++ +KR G F + T+GV E+ P V I+ +
Sbjct: 3 FRLIVIGDSTVGKSSLLKRFTEGRFAEVSDPTVGVDFFSRLIEIEPGVR------IKLQL 56
Query: 63 WDTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRV---CENIPIVLC 119
WDTAGQE+F + YY +++FD+T+R ++++V +W + R +L
Sbjct: 57 WDTAGQERFRSITRSYYRNSVGVLLVFDITNRESFEHVHDWLEE-ARSHIQPHRPVFILV 115
Query: 120 GNKVD-IKDRKV-KAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLAR 165
G+K D R+V + ++ + ++Y + SA++ N E+ F L +
Sbjct: 116 GHKCDLESQRQVTREEAEKLAKDLGMKYIETSARTGDNVEEAFELLTQ 163
Score = 57.1 bits (138), Expect = 1e-09
Identities = 31/100 (31%), Positives = 55/100 (55%), Gaps = 13/100 (13%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGV-------EVHPLVFHTNRGAIRFNV 277
F+ +++GD GK++ +KR G F + T+GV E+ P V I+ +
Sbjct: 3 FRLIVIGDSTVGKSSLLKRFTEGRFAEVSDPTVGVDFFSRLIEIEPGVR------IKLQL 56
Query: 278 WDTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKNYYD 317
WDTAGQE+F + YY +++FD+T+R ++++ +D
Sbjct: 57 WDTAGQERFRSITRSYYRNSVGVLLVFDITNRESFEHVHD 96
>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 = 79.4 bits (196), Expect = 1e-17
Identities = 43/162 (26%), Positives = 85/162 (52%), Gaps = 5/162 (3%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
K ++VG GG GK+ + + EF + Y T + + + ++ N+ DTAGQE
Sbjct: 1 HKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKA-DSYRKKVVLDGEEVQLNILDTAGQE 59
Query: 70 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRV--CENIPIVLCGNKVDIKD 127
+ +RD Y+ G+ +++F +T ++ + + ++RV +N+P++L GNK D++D
Sbjct: 60 DYAAIRDNYFRSGEGFLLVFSITDMESFTALAEFREQILRVKEDDNVPLLLVGNKCDLED 119
Query: 128 RKVKAKSIV--FHRKKNLQYYDISAKSNYNFEKPFLWLARKL 167
++ + + + Y + SAK+ N +K F L R++
Sbjct: 120 KRQVSVEEAANLAEQWGVNYVETSAKTRANVDKVFFDLVREI 161
Score = 44.3 bits (105), Expect = 2e-05
Identities = 24/88 (27%), Positives = 46/88 (52%), Gaps = 1/88 (1%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
K ++VG GG GK+ + + EF + Y T + + + ++ N+ DTAGQE
Sbjct: 1 HKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKA-DSYRKKVVLDGEEVQLNILDTAGQE 59
Query: 285 KFGGLRDGYYIQGQCAIIMFDVTSRITY 312
+ +RD Y+ G+ +++F +T ++
Sbjct: 60 DYAAIRDNYFRSGEGFLLVFSITDMESF 87
>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 = 79.9 bits (197), Expect = 1e-17
Identities = 47/167 (28%), Positives = 76/167 (45%), Gaps = 13/167 (7%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 70
K V++GDG GKT+ + G F + Y T+ E + + A+ ++WDTAGQE+
Sbjct: 2 KVVVLGDGACGKTSLLNVFTRGYFPQVYEPTV-FENYIHDIFVDGLAVELSLWDTAGQEE 60
Query: 71 FGGLRDGYYIQGQCAIIMFDVTSRITYKNVPN-WHRDLVRVCENIPIVLCGNKVDIKD-- 127
F LR Y ++ F V + + +NV + W ++ C + +VL K D+++
Sbjct: 61 FDRLRSLSYADTHVIMLCFSVDNPDSLENVESKWLAEIRHHCPGVKLVLVALKCDLREPR 120
Query: 128 --RKVKAKSI-------VFHRKKNLQYYDISAKSNYNFEKPFLWLAR 165
R +I V R +Y + SAK N + F AR
Sbjct: 121 NERDRGTHTISYEEGLAVAKRINACRYLECSAKLNRGVNEAFTEAAR 167
Score = 61.0 bits (148), Expect = 4e-11
Identities = 28/89 (31%), Positives = 45/89 (50%), Gaps = 1/89 (1%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 285
K V++GDG GKT+ + G F + Y T+ E + + A+ ++WDTAGQE+
Sbjct: 2 KVVVLGDGACGKTSLLNVFTRGYFPQVYEPTV-FENYIHDIFVDGLAVELSLWDTAGQEE 60
Query: 286 FGGLRDGYYIQGQCAIIMFDVTSRITYKN 314
F LR Y ++ F V + + +N
Sbjct: 61 FDRLRSLSYADTHVIMLCFSVDNPDSLEN 89
>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 = 78.5 bits (193), Expect = 5e-17
Identities = 46/162 (28%), Positives = 88/162 (54%), Gaps = 8/162 (4%)
Query: 13 VLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEKFG 72
+++G G GKT+ ++R F + +T+GV+ IR +WDTAGQE+F
Sbjct: 4 IIIGSRGVGKTSLMERFTDDTFCEACKSTVGVDFKIKTVELRGKKIRLQIWDTAGQERFN 63
Query: 73 GLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVR-VCENIPIVLCGNKVDIK-DRKV 130
+ YY + I+++D+T + T+ ++P W + + + E+ ++L GNK+D + DR++
Sbjct: 64 SITSAYYRSAKGIILVYDITKKETFDDLPKWMKMIDKYASEDAELLLVGNKLDCETDREI 123
Query: 131 KAKSI--VFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGD 170
+ + +++ + SAK N+N ++ FL KL+ D
Sbjct: 124 TRQQGEKFAQQITGMRFCEASAKDNFNVDEIFL----KLVDD 161
Score = 53.1 bits (127), Expect = 3e-08
Identities = 26/87 (29%), Positives = 47/87 (54%)
Query: 228 VLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEKFG 287
+++G G GKT+ ++R F + +T+GV+ IR +WDTAGQE+F
Sbjct: 4 IIIGSRGVGKTSLMERFTDDTFCEACKSTVGVDFKIKTVELRGKKIRLQIWDTAGQERFN 63
Query: 288 GLRDGYYIQGQCAIIMFDVTSRITYKN 314
+ YY + I+++D+T + T+ +
Sbjct: 64 SITSAYYRSAKGIILVYDITKKETFDD 90
>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 = 77.6 bits (191), Expect = 5e-17
Identities = 49/162 (30%), Positives = 76/162 (46%), Gaps = 10/162 (6%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 70
K ++VGD GKT + R F+K Y AT+GV+ F +WDTAGQE+
Sbjct: 2 KVIVVGDLSVGKTCLINRFCKDVFDKNYKATIGVDFEMERFEVLGVPFSLQLWDTAGQER 61
Query: 71 FGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVCENIP----IVLCGNKVDIK 126
F + YY Q II+FD+T + ++ W D ++ EN P + L G K D+
Sbjct: 62 FKCIASTYYRGAQAIIIVFDLTDVASLEHTRQWLEDALK--ENDPSSVLLFLVGTKKDLS 119
Query: 127 D----RKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLA 164
++ +I R+ +Y+ +SA + N F +A
Sbjct: 120 SPAQYALMEQDAIKLAREMKAEYWAVSALTGENVRDFFFRVA 161
Score = 63.7 bits (155), Expect = 4e-12
Identities = 32/83 (38%), Positives = 43/83 (51%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 285
K ++VGD GKT + R F+K Y AT+GV+ F +WDTAGQE+
Sbjct: 2 KVIVVGDLSVGKTCLINRFCKDVFDKNYKATIGVDFEMERFEVLGVPFSLQLWDTAGQER 61
Query: 286 FGGLRDGYYIQGQCAIIMFDVTS 308
F + YY Q II+FD+T
Sbjct: 62 FKCIASTYYRGAQAIIIVFDLTD 84
>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 = 77.5 bits (191), Expect = 6e-17
Identities = 42/122 (34%), Positives = 65/122 (53%), Gaps = 2/122 (1%)
Query: 9 SFKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQ 68
+ KCV+VGDG GKT + + T F +Y+ T+ V + + +WDTAGQ
Sbjct: 1 AIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGK-PVNLGLWDTAGQ 59
Query: 69 EKFGGLRDGYYIQGQCAIIMFDVTSRITYKNV-PNWHRDLVRVCENIPIVLCGNKVDIKD 127
E + LR Y Q +I F + S +++NV W+ ++ C N PI+L G K+D++D
Sbjct: 60 EDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRD 119
Query: 128 RK 129
K
Sbjct: 120 DK 121
Score = 55.2 bits (133), Expect = 3e-09
Identities = 32/98 (32%), Positives = 49/98 (50%), Gaps = 4/98 (4%)
Query: 224 SFKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQ 283
+ KCV+VGDG GKT + + T F +Y+ T+ V + + +WDTAGQ
Sbjct: 1 AIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGK-PVNLGLWDTAGQ 59
Query: 284 EKFGGLRDGYYIQGQCAIIMFDVTSRITYKNYYDISAK 321
E + LR Y Q +I F + S +++N + AK
Sbjct: 60 EDYDRLRPLSYPQTDVFLICFSLVSPASFEN---VRAK 94
>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 = 75.7 bits (186), Expect = 2e-16
Identities = 48/170 (28%), Positives = 87/170 (51%), Gaps = 18/170 (10%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATL------GVEVHPLVFHTNRGAIRFNVW 63
+K V++G GG GK+ + + G F KY T+ +EV +
Sbjct: 2 YKLVVLGSGGVGKSALTVQFVQGIFVDKYDPTIEDSYRKQIEVDCQQCM-------LEIL 54
Query: 64 DTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRV--CENIPIVLCGN 121
DTAG E+F +RD Y GQ +++ +T++ ++ ++ + ++RV E++P++L GN
Sbjct: 55 DTAGTEQFTAMRDLYIKNGQGFALVYSITAQQSFNDLQDLREQILRVKDTEDVPMILVGN 114
Query: 122 KVDIKDRKVKAKS--IVFHRK-KNLQYYDISAKSNYNFEKPFLWLARKLI 168
K D++D +V +K R+ N + + SAKS N ++ F L R++
Sbjct: 115 KCDLEDERVVSKEEGQNLARQWGNCPFLETSAKSKINVDEIFYDLVRQIN 164
Score = 46.4 bits (110), Expect = 4e-06
Identities = 27/100 (27%), Positives = 48/100 (48%), Gaps = 13/100 (13%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATL------GVEVHPLVFHTNRGAIRFNVW 278
+K V++G GG GK+ + + G F KY T+ +EV +
Sbjct: 2 YKLVVLGSGGVGKSALTVQFVQGIFVDKYDPTIEDSYRKQIEVDCQQCM-------LEIL 54
Query: 279 DTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKNYYDI 318
DTAG E+F +RD Y GQ +++ +T++ ++ + D+
Sbjct: 55 DTAGTEQFTAMRDLYIKNGQGFALVYSITAQQSFNDLQDL 94
>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 = 75.1 bits (185), Expect = 4e-16
Identities = 35/118 (29%), Positives = 61/118 (51%), Gaps = 2/118 (1%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 70
KCVLVGDG GKT+ + + T + +YV T + +V + +R + DTAGQ++
Sbjct: 2 KCVLVGDGAVGKTSLIVSYTTNGYPTEYVPT-AFDNFSVVVLVDGKPVRLQLCDTAGQDE 60
Query: 71 FGGLRDGYYIQGQCAIIMFDVTSRITYKNVPN-WHRDLVRVCENIPIVLCGNKVDIKD 127
F LR Y ++ F V + +++N+ W ++ + PI+L G + D++
Sbjct: 61 FDKLRPLCYPDTDVFLLCFSVVNPSSFQNISEKWIPEIRKHNPKAPIILVGTQADLRT 118
Score = 63.2 bits (154), Expect = 7e-12
Identities = 29/89 (32%), Positives = 47/89 (52%), Gaps = 1/89 (1%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 285
KCVLVGDG GKT+ + + T + +YV T + +V + +R + DTAGQ++
Sbjct: 2 KCVLVGDGAVGKTSLIVSYTTNGYPTEYVPT-AFDNFSVVVLVDGKPVRLQLCDTAGQDE 60
Query: 286 FGGLRDGYYIQGQCAIIMFDVTSRITYKN 314
F LR Y ++ F V + +++N
Sbjct: 61 FDKLRPLCYPDTDVFLLCFSVVNPSSFQN 89
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 74.9 bits (184), Expect = 6e-16
Identities = 43/167 (25%), Positives = 84/167 (50%), Gaps = 5/167 (2%)
Query: 5 MDMPSFKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWD 64
M +K V+VG GG GK+ + + F +Y T+ + ++ D
Sbjct: 1 MASTEYKLVVVGGGGVGKSALTIQFIQNHFIDEYDPTIEDSYRKQCVIDEETCL-LDILD 59
Query: 65 TAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVCEN--IPIVLCGNK 122
TAGQE++ +RD Y GQ + ++ +TSR +++ + ++ ++RV + +P++L GNK
Sbjct: 60 TAGQEEYSAMRDQYMRTGQGFLCVYSITSRSSFEEIASFREQILRVKDKDRVPMILVGNK 119
Query: 123 VDIK-DRKVK-AKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKL 167
D+ +R+V + + + + + SAK N ++ F L R++
Sbjct: 120 CDLDSERQVSTGEGQELAKSFGIPFLETSAKQRVNVDEAFYELVREI 166
Score = 48.3 bits (115), Expect = 1e-06
Identities = 26/93 (27%), Positives = 45/93 (48%), Gaps = 1/93 (1%)
Query: 220 MDMPSFKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWD 279
M +K V+VG GG GK+ + + F +Y T+ + ++ D
Sbjct: 1 MASTEYKLVVVGGGGVGKSALTIQFIQNHFIDEYDPTIEDSYRKQCVIDEETCL-LDILD 59
Query: 280 TAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITY 312
TAGQE++ +RD Y GQ + ++ +TSR ++
Sbjct: 60 TAGQEEYSAMRDQYMRTGQGFLCVYSITSRSSF 92
>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 = 74.5 bits (183), Expect = 1e-15
Identities = 51/163 (31%), Positives = 85/163 (52%), Gaps = 7/163 (4%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 70
K V++GDGG GKT + F + Y T+ V + + V DTAGQE+
Sbjct: 1 KLVVLGDGGVGKTALTIQLCLNHFVETYDPTIEDSYRKQVVVDGQPCM-LEVLDTAGQEE 59
Query: 71 FGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVCEN----IPIVLCGNKVD-I 125
+ LRD + +G+ I+++ +TSR T++ V + + RV + +PI++ GNK D +
Sbjct: 60 YTALRDQWIREGEGFILVYSITSRSTFERVERFREQIQRVKDESAADVPIMIVGNKCDKV 119
Query: 126 KDRKV-KAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKL 167
+R+V + R+ ++ + SAK+N N E+ F L R L
Sbjct: 120 YEREVSTEEGAALARRLGCEFIEASAKTNVNVERAFYTLVRAL 162
Score = 46.0 bits (109), Expect = 6e-06
Identities = 29/87 (33%), Positives = 46/87 (52%), Gaps = 1/87 (1%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 285
K V++GDGG GKT + F + Y T+ V + + V DTAGQE+
Sbjct: 1 KLVVLGDGGVGKTALTIQLCLNHFVETYDPTIEDSYRKQVVVDGQPCM-LEVLDTAGQEE 59
Query: 286 FGGLRDGYYIQGQCAIIMFDVTSRITY 312
+ LRD + +G+ I+++ +TSR T+
Sbjct: 60 YTALRDQWIREGEGFILVYSITSRSTF 86
>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 = 73.7 bits (181), Expect = 3e-15
Identities = 49/172 (28%), Positives = 88/172 (51%), Gaps = 17/172 (9%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNR------GAIRFNVW 63
K V++GDG +GKT+ ++R F K Y T+G++ F + R + VW
Sbjct: 1 IKIVVLGDGASGKTSLIRRFAQEGFGKSYKQTIGLD-----FFSRRITLPGSLNVTLQVW 55
Query: 64 DTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVCEN----IPIVLC 119
D GQ+ G + D Y Q +++D+T+ +++N+ +W + +V E +VL
Sbjct: 56 DIGGQQIGGKMLDKYIYGAQAVCLVYDITNSQSFENLEDWLSVVKKVNEESETKPKMVLV 115
Query: 120 GNKVDIKD-RKVKA-KSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIG 169
GNK D++ R+V A K F ++ +++ +SAK+ F +A +L+G
Sbjct: 116 GNKTDLEHNRQVTAEKHARFAQENDMESIFVSAKTGDRVFLCFQRIAAELLG 167
Score = 53.3 bits (128), Expect = 3e-08
Identities = 29/99 (29%), Positives = 50/99 (50%), Gaps = 11/99 (11%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNR------GAIRFNVW 278
K V++GDG +GKT+ ++R F K Y T+G++ F + R + VW
Sbjct: 1 IKIVVLGDGASGKTSLIRRFAQEGFGKSYKQTIGLD-----FFSRRITLPGSLNVTLQVW 55
Query: 279 DTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKNYYD 317
D GQ+ G + D Y Q +++D+T+ +++N D
Sbjct: 56 DIGGQQIGGKMLDKYIYGAQAVCLVYDITNSQSFENLED 94
>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 = 72.5 bits (178), Expect = 3e-15
Identities = 44/164 (26%), Positives = 84/164 (51%), Gaps = 6/164 (3%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
+K V++G GG GK+ + + F + Y T+ V R + DTAG E
Sbjct: 2 YKIVVLGAGGVGKSALTVQFVQNVFIESYDPTIEDSYRKQVEIDGRQCD-LEILDTAGTE 60
Query: 70 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRV--CENIPIVLCGNKVDIKD 127
+F +R+ Y GQ ++++ VTS + + ++R+ +N+P+VL GNK D++D
Sbjct: 61 QFTAMRELYIKSGQGFLLVYSVTSEASLNELGELREQVLRIKDSDNVPMVLVGNKADLED 120
Query: 128 RKV--KAKSIVFHRK-KNLQYYDISAKSNYNFEKPFLWLARKLI 168
+ + + ++ N+ +Y+ SA+ N ++ F+ L R++I
Sbjct: 121 DRQVSREDGVSLSQQWGNVPFYETSARKRTNVDEVFIDLVRQII 164
Score = 43.2 bits (102), Expect = 5e-05
Identities = 25/85 (29%), Positives = 41/85 (48%), Gaps = 1/85 (1%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
+K V++G GG GK+ + + F + Y T+ V R + DTAG E
Sbjct: 2 YKIVVLGAGGVGKSALTVQFVQNVFIESYDPTIEDSYRKQVEIDGRQCD-LEILDTAGTE 60
Query: 285 KFGGLRDGYYIQGQCAIIMFDVTSR 309
+F +R+ Y GQ ++++ VTS
Sbjct: 61 QFTAMRELYIKSGQGFLLVYSVTSE 85
>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 = 70.9 bits (174), Expect = 4e-15
Identities = 28/115 (24%), Positives = 55/115 (47%), Gaps = 3/115 (2%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 70
K V++GD G+GK++ + + + GEF + + G + + N+WD G+E+
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREE 60
Query: 71 FGGLRDGYYIQGQCAIIMFDVTSRITYKNVPN---WHRDLVRVCENIPIVLCGNK 122
+ ++++D+T R + V W +L ++ IP++L GNK
Sbjct: 61 LKFEHIIFMKWADAILLVYDLTDRESLNEVSRLIAWLPNLRKLGGKIPVILVGNK 115
Score = 56.6 bits (137), Expect = 3e-10
Identities = 24/114 (21%), Positives = 48/114 (42%), Gaps = 1/114 (0%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 285
K V++GD G+GK++ + + + GEF + + G + + N+WD G+E+
Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREE 60
Query: 286 FGGLRDGYYIQGQCAIIMFDVTSRITYKNYYDISAKSNYNFEKPFLWLARKLIG 339
+ ++++D+T R + N N K + L+G
Sbjct: 61 LKFEHIIFMKWADAILLVYDLTDRESL-NEVSRLIAWLPNLRKLGGKIPVILVG 113
>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 = 72.6 bits (178), Expect = 4e-15
Identities = 42/127 (33%), Positives = 60/127 (47%), Gaps = 16/127 (12%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHT-------NRGAIRFNVW 63
KCV VGDG GKT + + + F YV P VF + + +W
Sbjct: 3 KCVTVGDGAVGKTCMLISYTSNTFPTDYV--------PTVFDNFSANVVVDGNTVNLGLW 54
Query: 64 DTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKNV-PNWHRDLVRVCENIPIVLCGNK 122
DTAGQE + LR Y ++ F + S+ +Y+NV W +L +PIVL G K
Sbjct: 55 DTAGQEDYNRLRPLSYRGADVFLLAFSLISKASYENVLKKWIPELRHYAPGVPIVLVGTK 114
Query: 123 VDIKDRK 129
+D++D K
Sbjct: 115 LDLRDDK 121
Score = 49.5 bits (118), Expect = 3e-07
Identities = 30/96 (31%), Positives = 43/96 (44%), Gaps = 15/96 (15%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHT-------NRGAIRFNVW 278
KCV VGDG GKT + + + F YV P VF + + +W
Sbjct: 3 KCVTVGDGAVGKTCMLISYTSNTFPTDYV--------PTVFDNFSANVVVDGNTVNLGLW 54
Query: 279 DTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKN 314
DTAGQE + LR Y ++ F + S+ +Y+N
Sbjct: 55 DTAGQEDYNRLRPLSYRGADVFLLAFSLISKASYEN 90
>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 = 70.7 bits (173), Expect = 2e-14
Identities = 48/163 (29%), Positives = 85/163 (52%), Gaps = 7/163 (4%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
+K V++G GG GK+ + ++ F + T+ N A+ ++ DTAGQ
Sbjct: 3 YKIVMLGAGGVGKSAVTMQFISHSFPDYHDPTIEDAYKTQARIDNEPAL-LDILDTAGQA 61
Query: 70 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDL---VRVCENIPIVLCGNKVDIK 126
+F +RD Y G+ II + VT R +++ + ++L VR+ E+IP+VL GNKVD++
Sbjct: 62 EFTAMRDQYMRCGEGFIICYSVTDRHSFQEASEF-KELITRVRLTEDIPLVLVGNKVDLE 120
Query: 127 D-RKV-KAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKL 167
R+V + R+ N +++ SA + + F L R++
Sbjct: 121 QQRQVTTEEGRNLAREFNCPFFETSAALRFYIDDAFHGLVREI 163
Score = 43.3 bits (102), Expect = 4e-05
Identities = 26/89 (29%), Positives = 45/89 (50%), Gaps = 1/89 (1%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
+K V++G GG GK+ + ++ F + T+ N A+ ++ DTAGQ
Sbjct: 3 YKIVMLGAGGVGKSAVTMQFISHSFPDYHDPTIEDAYKTQARIDNEPAL-LDILDTAGQA 61
Query: 285 KFGGLRDGYYIQGQCAIIMFDVTSRITYK 313
+F +RD Y G+ II + VT R +++
Sbjct: 62 EFTAMRDQYMRCGEGFIICYSVTDRHSFQ 90
>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 = 70.7 bits (173), Expect = 2e-14
Identities = 40/157 (25%), Positives = 77/157 (49%), Gaps = 7/157 (4%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEF-EKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
K V++G GKT+ V+R++ F Y T+G + +WDTAG E
Sbjct: 2 KVVMLGKESVGKTSLVERYVHHRFLVGPYQNTIGAAFVAKRMVVGERVVTLGIWDTAGSE 61
Query: 70 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRK 129
++ + YY + AI+ +D+T +++ W ++L + E+ I LCG K D+ ++
Sbjct: 62 RYEAMSRIYYRGAKAAIVCYDLTDSSSFERAKFWVKELQNLEEHCKIYLCGTKSDLIEQD 121
Query: 130 VKAKSIVFHRKKNL------QYYDISAKSNYNFEKPF 160
+ + FH ++ Q+++ S+K+ N ++ F
Sbjct: 122 RSLRQVDFHDVQDFADEIKAQHFETSSKTGQNVDELF 158
Score = 48.7 bits (116), Expect = 9e-07
Identities = 24/85 (28%), Positives = 40/85 (47%), Gaps = 1/85 (1%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEF-EKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
K V++G GKT+ V+R++ F Y T+G + +WDTAG E
Sbjct: 2 KVVMLGKESVGKTSLVERYVHHRFLVGPYQNTIGAAFVAKRMVVGERVVTLGIWDTAGSE 61
Query: 285 KFGGLRDGYYIQGQCAIIMFDVTSR 309
++ + YY + AI+ +D+T
Sbjct: 62 RYEAMSRIYYRGAKAAIVCYDLTDS 86
>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 = 70.2 bits (172), Expect = 3e-14
Identities = 42/128 (32%), Positives = 64/128 (50%), Gaps = 16/128 (12%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFN-------VW 63
K V+VGDG GKT+ + GEF ++Y HP VF R + +W
Sbjct: 3 KLVIVGDGACGKTSLLYVFTLGEFPEEY--------HPTVFENYVTDCRVDGKPVQLALW 54
Query: 64 DTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKNV-PNWHRDLVRVCENIPIVLCGNK 122
DTAGQE++ LR Y + +I F + + + +NV W ++ R C N+P++L G K
Sbjct: 55 DTAGQEEYERLRPLSYSKAHVILIGFAIDTPDSLENVRTKWIEEVRRYCPNVPVILVGLK 114
Query: 123 VDIKDRKV 130
D++ V
Sbjct: 115 KDLRQEAV 122
Score = 50.6 bits (121), Expect = 2e-07
Identities = 30/90 (33%), Positives = 43/90 (47%), Gaps = 15/90 (16%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFN-------VW 278
K V+VGDG GKT+ + GEF ++Y HP VF R + +W
Sbjct: 3 KLVIVGDGACGKTSLLYVFTLGEFPEEY--------HPTVFENYVTDCRVDGKPVQLALW 54
Query: 279 DTAGQEKFGGLRDGYYIQGQCAIIMFDVTS 308
DTAGQE++ LR Y + +I F + +
Sbjct: 55 DTAGQEEYERLRPLSYSKAHVILIGFAIDT 84
>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 = 70.3 bits (172), Expect = 3e-14
Identities = 50/192 (26%), Positives = 87/192 (45%), Gaps = 16/192 (8%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 70
+ V +G G GKT ++R L FE K+ T+ E+H + + ++ DT+G
Sbjct: 1 RLVFMGAAGVGKTALIQRFLYDTFEPKHRRTVE-ELHSKEYEVAGVKVTIDILDTSGSYS 59
Query: 71 FGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVCEN--IPIVLCGNKVD-IKD 127
F +R G +++ V +++ V +++ V E+ +PIV+ GNK+D + +
Sbjct: 60 FPAMRKLSIQNGDAFALVYSVDDPESFEEVKRLREEILEVKEDKFVPIVVVGNKIDSLAE 119
Query: 128 RKVKAKSI--VFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPAL---- 181
R+V+A N + + SAK N N + F ++L+ NL PAL
Sbjct: 120 RQVEAADALSTVELDWNNGFVEASAKDNENVTEVF----KELLQQANLPSWLSPALRRRR 175
Query: 182 --LPPEVTMDPQ 191
P E+ P
Sbjct: 176 ESAPSEIQRRPP 187
Score = 44.1 bits (104), Expect = 4e-05
Identities = 21/82 (25%), Positives = 37/82 (45%), Gaps = 1/82 (1%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 285
+ V +G G GKT ++R L FE K+ T+ E+H + + ++ DT+G
Sbjct: 1 RLVFMGAAGVGKTALIQRFLYDTFEPKHRRTVE-ELHSKEYEVAGVKVTIDILDTSGSYS 59
Query: 286 FGGLRDGYYIQGQCAIIMFDVT 307
F +R G +++ V
Sbjct: 60 FPAMRKLSIQNGDAFALVYSVD 81
>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 = 69.1 bits (169), Expect = 6e-14
Identities = 37/120 (30%), Positives = 62/120 (51%), Gaps = 2/120 (1%)
Query: 9 SFKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQ 68
+ KCV+VGDG GKT + + T +F +YV T+ + + + ++DTAGQ
Sbjct: 1 TIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTV-FDNYAVTVMIGGEPYTLGLFDTAGQ 59
Query: 69 EKFGGLRDGYYIQGQCAIIMFDVTSRITYKNV-PNWHRDLVRVCENIPIVLCGNKVDIKD 127
E + LR Y Q ++ F V S +++NV W ++ C P +L G ++D++D
Sbjct: 60 EDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQIDLRD 119
Score = 52.6 bits (126), Expect = 3e-08
Identities = 29/91 (31%), Positives = 47/91 (51%), Gaps = 1/91 (1%)
Query: 224 SFKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQ 283
+ KCV+VGDG GKT + + T +F +YV T+ + + + ++DTAGQ
Sbjct: 1 TIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTV-FDNYAVTVMIGGEPYTLGLFDTAGQ 59
Query: 284 EKFGGLRDGYYIQGQCAIIMFDVTSRITYKN 314
E + LR Y Q ++ F V S +++N
Sbjct: 60 EDYDRLRPLSYPQTDVFLVCFSVVSPSSFEN 90
>gnl|CDD|133321 cd04121, Rab40, Rab GTPase family 40 (Rab40) contains Rab40a,
Rab40b and Rab40c. The Rab40 subfamily contains Rab40a,
Rab40b, and Rab40c, which are all highly homologous. In
rat, Rab40c is localized to the perinuclear recycling
compartment (PRC), and is distributed in a
tissue-specific manor, with high expression in brain,
heart, kidney, and testis, low expression in lung and
liver, and no expression in spleen and skeletal muscle.
Rab40c is highly expressed in differentiated
oligodendrocytes but minimally expressed in
oligodendrocyte progenitors, suggesting a role in the
vesicular transport of myelin components. Unlike most
other Ras-superfamily proteins, Rab40c was shown to have
a much lower affinity for GTP, and an affinity for GDP
that is lower than for GTP. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 189
Score = 67.7 bits (165), Expect = 3e-13
Identities = 37/158 (23%), Positives = 76/158 (48%), Gaps = 2/158 (1%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
K +LVGD GK + G E Y +G++ + ++ +WDT+GQ
Sbjct: 7 LKFLLVGDSDVGKGEILASLQDGSTESPYGYNMGIDYKTTTILLDGRRVKLQLWDTSGQG 66
Query: 70 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVCENIPIVLCGNKVDIK-DR 128
+F + Y Q I+++D+T+R ++ + W +++ +P +L GN++ + R
Sbjct: 67 RFCTIFRSYSRGAQGIILVYDITNRWSFDGIDRWIKEIDEHAPGVPKILVGNRLHLAFKR 126
Query: 129 KVKAKSI-VFHRKKNLQYYDISAKSNYNFEKPFLWLAR 165
+V + + + + ++++S N+N + F LAR
Sbjct: 127 QVATEQAQAYAERNGMTFFEVSPLCNFNITESFTELAR 164
Score = 41.8 bits (98), Expect = 2e-04
Identities = 23/88 (26%), Positives = 42/88 (47%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
K +LVGD GK + G E Y +G++ + ++ +WDT+GQ
Sbjct: 7 LKFLLVGDSDVGKGEILASLQDGSTESPYGYNMGIDYKTTTILLDGRRVKLQLWDTSGQG 66
Query: 285 KFGGLRDGYYIQGQCAIIMFDVTSRITY 312
+F + Y Q I+++D+T+R ++
Sbjct: 67 RFCTIFRSYSRGAQGIILVYDITNRWSF 94
>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 = 68.2 bits (167), Expect = 4e-13
Identities = 46/168 (27%), Positives = 83/168 (49%), Gaps = 14/168 (8%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
++ V++G GKT V R L G FE++Y T+ + H ++ + ++ DT+G
Sbjct: 1 YRMVVLGASKVGKTAIVSRFLGGRFEEQYTPTIE-DFHRKLYSIRGEVYQLDILDTSGNH 59
Query: 70 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDL--VRVC------EN--IPIVLC 119
F +R + G I++F + +R +++ V + + C EN IP+V+C
Sbjct: 60 PFPAMRRLSILTGDVFILVFSLDNRESFEEVCRLREQILETKSCLKNKTKENVKIPMVIC 119
Query: 120 GNKVDIKD-RKVKAKSI--VFHRKKNLQYYDISAKSNYNFEKPFLWLA 164
GNK D R+V+ + + +N Y+++SAK N N ++ F L
Sbjct: 120 GNKADRDFPREVQRDEVEQLVGGDENCAYFEVSAKKNSNLDEMFRALF 167
Score = 42.4 bits (100), Expect = 1e-04
Identities = 23/85 (27%), Positives = 43/85 (50%), Gaps = 1/85 (1%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
++ V++G GKT V R L G FE++Y T+ + H ++ + ++ DT+G
Sbjct: 1 YRMVVLGASKVGKTAIVSRFLGGRFEEQYTPTIE-DFHRKLYSIRGEVYQLDILDTSGNH 59
Query: 285 KFGGLRDGYYIQGQCAIIMFDVTSR 309
F +R + G I++F + +R
Sbjct: 60 PFPAMRRLSILTGDVFILVFSLDNR 84
>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 = 66.0 bits (161), Expect = 5e-13
Identities = 42/159 (26%), Positives = 81/159 (50%), Gaps = 11/159 (6%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
++ V+ G GG GK++ V R + G F + Y+ T+ + + V ++ + DT G
Sbjct: 2 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIE-DTYRQVISCSKSICTLQITDTTGSH 60
Query: 70 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNV-PNWHRDLVR-----VCENIPIVLCGNKV 123
+F ++ +G I+++ +TS+ + + + P + +L+ E IPI+L GNK
Sbjct: 61 QFPAMQRLSISKGHAFILVYSITSKQSLEELKPIY--ELICEIKGNNLEKIPIMLVGNKC 118
Query: 124 D-IKDRKV-KAKSIVFHRKKNLQYYDISAKSNYNFEKPF 160
D R+V ++ R N + + SAK+N+N ++ F
Sbjct: 119 DESPSREVSSSEGAALARTWNCAFMETSAKTNHNVQELF 157
Score = 46.0 bits (109), Expect = 4e-06
Identities = 25/116 (21%), Positives = 53/116 (45%), Gaps = 13/116 (11%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
++ V+ G GG GK++ V R + G F + Y+ T+ + + V ++ + DT G
Sbjct: 2 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTIE-DTYRQVISCSKSICTLQITDTTGSH 60
Query: 285 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNYYDISAKSNYNFEKPFLWLARKLIGD 340
+F ++ +G I+++ +TS+ + + KP L ++ G+
Sbjct: 61 QFPAMQRLSISKGHAFILVYSITSKQSLEEL------------KPIYELICEIKGN 104
>gnl|CDD|206701 cd04128, Spg1, Septum-promoting GTPase (Spg1). Spg1p. Spg1p
(septum-promoting GTPase) was first identified in the
fission yeast S. pombe, where it regulates septum
formation in the septation initiation network (SIN)
through the cdc7 protein kinase. Spg1p is an essential
gene that localizes to the spindle pole bodies. When
GTP-bound, it binds cdc7 and causes it to translocate to
spindle poles. Sid4p (septation initiation defective) is
required for localization of Spg1p to the spindle pole
body, and the ability of Spg1p to promote septum
formation from any point in the cell cycle depends on
Sid4p. Spg1p is negatively regulated by Byr4 and cdc16,
which form a two-component GTPase activating protein
(GAP) for Spg1p. The existence of a SIN-related pathway
in plants has been proposed. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization.
Length = 182
Score = 65.9 bits (161), Expect = 8e-13
Identities = 39/119 (32%), Positives = 61/119 (51%), Gaps = 10/119 (8%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 70
K L+GD GKT+ + +++ GEF+++Y+ TLGV I F++WD GQ +
Sbjct: 2 KIGLLGDAQIGKTSLMVKYVEGEFDEEYIQTLGVNFMEKTISIRGTEITFSIWDLGGQRE 61
Query: 71 FGGLRDGYYI--QGQCAII-MFDVTSRITYKNVPNWHRDLVRVCEN--IPIVLCGNKVD 124
F + + + AI+ MFD+T + T ++ W+R R IPI L G K D
Sbjct: 62 F---INMLPLVCKDAVAILFMFDLTRKSTLNSIKEWYRQ-ARGFNKTAIPI-LVGTKYD 115
Score = 58.6 bits (142), Expect = 3e-10
Identities = 42/156 (26%), Positives = 68/156 (43%), Gaps = 27/156 (17%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 285
K L+GD GKT+ + +++ GEF+++Y+ TLGV I F++WD GQ +
Sbjct: 2 KIGLLGDAQIGKTSLMVKYVEGEFDEEYIQTLGVNFMEKTISIRGTEITFSIWDLGGQRE 61
Query: 286 FGGLRDGYYI--QGQCAII-MFDVTSRITY---KNYYDISAKSNYNFEKPFLWLARKLIG 339
F + + + AI+ MFD+T + T K +Y + N P L+G
Sbjct: 62 F---INMLPLVCKDAVAILFMFDLTRKSTLNSIKEWYRQARGFN-KTAIPI------LVG 111
Query: 340 DPNLEFVAMPALLPPEVTMDPQWQSRI-EQDLKEAQ 374
F + P+ Q I +Q K A+
Sbjct: 112 TKYDLF----------ADLPPEEQEEITKQARKYAK 137
>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 = 65.1 bits (159), Expect = 1e-12
Identities = 35/117 (29%), Positives = 57/117 (48%), Gaps = 2/117 (1%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 70
K VLVGD GKT ++ F + YV T+ E + F ++ I ++WDT+G
Sbjct: 3 KIVLVGDSQCGKTALLQVFAKDSFPENYVPTV-FENYTASFEVDKQRIELSLWDTSGSPY 61
Query: 71 FGGLRDGYYIQGQCAIIMFDVTSRITYKNV-PNWHRDLVRVCENIPIVLCGNKVDIK 126
+ +R Y +I FD++ T +V W ++ C N P++L G K D++
Sbjct: 62 YDNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEVREFCPNTPVLLVGCKSDLR 118
Score = 46.3 bits (110), Expect = 4e-06
Identities = 25/82 (30%), Positives = 40/82 (48%), Gaps = 1/82 (1%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 285
K VLVGD GKT ++ F + YV T+ E + F ++ I ++WDT+G
Sbjct: 3 KIVLVGDSQCGKTALLQVFAKDSFPENYVPTV-FENYTASFEVDKQRIELSLWDTSGSPY 61
Query: 286 FGGLRDGYYIQGQCAIIMFDVT 307
+ +R Y +I FD++
Sbjct: 62 YDNVRPLSYPDSDAVLICFDIS 83
>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 = 64.7 bits (157), Expect = 2e-12
Identities = 36/119 (30%), Positives = 60/119 (50%), Gaps = 2/119 (1%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
KCV+VGDG GKT + + F ++YV T+ + + + ++DTAGQE
Sbjct: 1 LKCVVVGDGAVGKTCLLMSYANDAFPEEYVPTV-FDHYAVSVTVGGKQYLLGLYDTAGQE 59
Query: 70 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNV-PNWHRDLVRVCENIPIVLCGNKVDIKD 127
+ LR Y +I F V + +++NV W +L N+P +L G ++D++D
Sbjct: 60 DYDRLRPLSYPMTDVFLICFSVVNPASFQNVKEEWVPELKEYAPNVPYLLIGTQIDLRD 118
Score = 48.1 bits (114), Expect = 1e-06
Identities = 27/90 (30%), Positives = 44/90 (48%), Gaps = 1/90 (1%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
KCV+VGDG GKT + + F ++YV T+ + + + ++DTAGQE
Sbjct: 1 LKCVVVGDGAVGKTCLLMSYANDAFPEEYVPTV-FDHYAVSVTVGGKQYLLGLYDTAGQE 59
Query: 285 KFGGLRDGYYIQGQCAIIMFDVTSRITYKN 314
+ LR Y +I F V + +++N
Sbjct: 60 DYDRLRPLSYPMTDVFLICFSVVNPASFQN 89
>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 = 64.4 bits (157), Expect = 3e-12
Identities = 39/125 (31%), Positives = 60/125 (48%), Gaps = 16/125 (12%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHT-------NRGAIRFNVW 63
K V+VGDG GKT + +F + YV P VF + + +W
Sbjct: 3 KLVIVGDGACGKTCLLIVFSKDQFPEVYV--------PTVFENYVADIEVDGKQVELALW 54
Query: 64 DTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPN-WHRDLVRVCENIPIVLCGNK 122
DTAGQE + LR Y ++ F + S + +N+P W ++ C N+PI+L GNK
Sbjct: 55 DTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNK 114
Query: 123 VDIKD 127
D+++
Sbjct: 115 KDLRN 119
Score = 40.1 bits (94), Expect = 6e-04
Identities = 28/96 (29%), Positives = 41/96 (42%), Gaps = 15/96 (15%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHT-------NRGAIRFNVW 278
K V+VGDG GKT + +F + YV P VF + + +W
Sbjct: 3 KLVIVGDGACGKTCLLIVFSKDQFPEVYV--------PTVFENYVADIEVDGKQVELALW 54
Query: 279 DTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKN 314
DTAGQE + LR Y ++ F + S + +N
Sbjct: 55 DTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLEN 90
>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 = 61.6 bits (150), Expect = 2e-11
Identities = 39/154 (25%), Positives = 64/154 (41%), Gaps = 9/154 (5%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGA-IRFNVWDTAGQE 69
K +LVG GG GKT+ K+ + +F+ +T G+ V IR NVWD GQE
Sbjct: 3 KLMLVGQGGVGKTSLCKQLIGEKFDGDESSTHGINVQDWKIPAPERKKIRLNVWDFGGQE 62
Query: 70 KFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVCENIPIVLCGNKVDI-KDR 128
+ + +++FD+ + VP W R + P++L G +D D
Sbjct: 63 IYHATHQFFLTSRSLYLLVFDLRTGDEVSRVPYWLRQIKAFGGVSPVILVGTHIDESCDE 122
Query: 129 KVKAKSIVFHRKKNLQ----YYDISAKSNYNFEK 158
+ K+ KK + +S K+ +
Sbjct: 123 DILKKA---LNKKFPAIINDIHFVSCKNGKGIAE 153
Score = 51.2 bits (123), Expect = 7e-08
Identities = 23/62 (37%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGA-IRFNVWDTAGQE 284
K +LVG GG GKT+ K+ + +F+ +T G+ V IR NVWD GQE
Sbjct: 3 KLMLVGQGGVGKTSLCKQLIGEKFDGDESSTHGINVQDWKIPAPERKKIRLNVWDFGGQE 62
Query: 285 KF 286
+
Sbjct: 63 IY 64
>gnl|CDD|206644 cd00878, Arf_Arl, ADP-ribosylation factor(Arf)/Arf-like (Arl) small
GTPases. Arf (ADP-ribosylation factor)/Arl (Arf-like)
small GTPases. Arf proteins are activators of
phospholipase D isoforms. Unlike Ras proteins they lack
cysteine residues at their C-termini and therefore are
unlikely to be prenylated. Arfs are N-terminally
myristoylated. Members of the Arf family are regulators
of vesicle formation in intracellular traffic that
interact reversibly with membranes of the secretory and
endocytic compartments in a GTP-dependent manner. They
depart from other small GTP-binding proteins by a unique
structural device, interswitch toggle, that implements
front-back communication from N-terminus to the
nucleotide binding site. Arf-like (Arl) proteins are
close relatives of the Arf, but only Arl1 has been shown
to function in membrane traffic like the Arf proteins.
Arl2 has an unrelated function in the folding of native
tubulin, and Arl4 may function in the nucleus. Most
other Arf family proteins are so far relatively poorly
characterized. Thus, despite their significant sequence
homologies, Arf family proteins may regulate unrelated
functions.
Length = 158
Score = 58.4 bits (142), Expect = 2e-10
Identities = 33/163 (20%), Positives = 66/163 (40%), Gaps = 18/163 (11%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 70
+ +++G G GKTT + + GE + T+G V + + ++F VWD GQ+K
Sbjct: 1 RILMLGLDGAGKTTILYKLKLGEVVTT-IPTIGFNVETVEYKN----VKFTVWDVGGQDK 55
Query: 71 FGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVCE-----NIPIVLCGNKVDI 125
L YY I + D + R + + +L ++ P+++ NK D+
Sbjct: 56 IRPLWKHYYENTDGLIFVVDSSDR---ERIEEAKNELHKLLNEEELKGAPLLILANKQDL 112
Query: 126 KDRKVKAK-----SIVFHRKKNLQYYDISAKSNYNFEKPFLWL 163
+++ + + + SA + ++ WL
Sbjct: 113 PGALTESELIELLGLESIKGRRWHIQPCSAVTGDGLDEGLDWL 155
Score = 54.1 bits (131), Expect = 7e-09
Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 5/84 (5%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 285
+ +++G G GKTT + + GE + T+G V + + ++F VWD GQ+K
Sbjct: 1 RILMLGLDGAGKTTILYKLKLGEVVTT-IPTIGFNVETVEYKN----VKFTVWDVGGQDK 55
Query: 286 FGGLRDGYYIQGQCAIIMFDVTSR 309
L YY I + D + R
Sbjct: 56 IRPLWKHYYENTDGLIFVVDSSDR 79
>gnl|CDD|133326 cd04126, Rab20, Rab GTPase family 20 (Rab20). Rab20 is one of
several Rab proteins that appear to be restricted in
expression to the apical domain of murine polarized
epithelial cells. It is expressed on the apical side of
polarized kidney tubule and intestinal epithelial cells,
and in non-polarized cells. It also localizes to
vesico-tubular structures below the apical brush border
of renal proximal tubule cells and in the apical region
of duodenal epithelial cells. Rab20 has also been shown
to colocalize with vacuolar H+-ATPases (V-ATPases) in
mouse kidney cells, suggesting a role in the regulation
of V-ATPase traffic in specific portions of the nephron.
It was also shown to be one of several proteins whose
expression is upregulated in human myelodysplastic
syndrome (MDS) patients. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 220
Score = 59.2 bits (143), Expect = 3e-10
Identities = 35/126 (27%), Positives = 60/126 (47%), Gaps = 6/126 (4%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 70
K VL+GD GKT+ + R++ F K V+T+G + G ++WDTAG+E+
Sbjct: 2 KVVLLGDMNVGKTSLLHRYMERRF-KDTVSTVGGAF----YLKQWGPYNISIWDTAGREQ 56
Query: 71 FGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVC-ENIPIVLCGNKVDIKDRK 129
F GL Y I+ +DV++ + + + + L E+ + GNK+D+ +
Sbjct: 57 FHGLGSMYCRGAAAVILTYDVSNVQSLEELEDRFLGLTDTANEDCLFAVVGNKLDLTEEG 116
Query: 130 VKAKSI 135
A
Sbjct: 117 ALAGQE 122
Score = 57.2 bits (138), Expect = 2e-09
Identities = 29/92 (31%), Positives = 47/92 (51%), Gaps = 5/92 (5%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 285
K VL+GD GKT+ + R++ F K V+T+G + G ++WDTAG+E+
Sbjct: 2 KVVLLGDMNVGKTSLLHRYMERRF-KDTVSTVGGAF----YLKQWGPYNISIWDTAGREQ 56
Query: 286 FGGLRDGYYIQGQCAIIMFDVTSRITYKNYYD 317
F GL Y I+ +DV++ + + D
Sbjct: 57 FHGLGSMYCRGAAAVILTYDVSNVQSLEELED 88
>gnl|CDD|206724 cd04159, Arl10_like, Arf-like 9 (Arl9) and 10 (Arl10) GTPases.
Arl10-like subfamily. Arl9/Arl10 was identified from a
human cancer-derived EST dataset. No functional
information about the subfamily is available at the
current time, but crystal structures of human Arl10b and
Arl10c have been solved.
Length = 159
Score = 58.1 bits (141), Expect = 3e-10
Identities = 42/157 (26%), Positives = 67/157 (42%), Gaps = 11/157 (7%)
Query: 14 LVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEKFGG 73
LVG +GKTT V +G+F + + T+G + + +G + VWD GQ +F
Sbjct: 4 LVGLQNSGKTTLVNVIASGQFSEDTIPTVGFNMRKV----TKGNVTIKVWDLGGQPRFRS 59
Query: 74 LRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRV--CENIPIVLCGNKVDIKDRKVK 131
+ + Y + + D R + N DL+ E IP+++ GNK D+
Sbjct: 60 MWERYCRGVNAIVYVVDAADREKLEVAKNELHDLLEKPSLEGIPLLVLGNKNDLPGALSV 119
Query: 132 AKSIVFHRKKNLQ-----YYDISAKSNYNFEKPFLWL 163
+ I K++ Y ISAK N + WL
Sbjct: 120 DELIEQMNLKSITDREVSCYSISAKEKTNIDIVLDWL 156
Score = 40.8 bits (96), Expect = 3e-04
Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 4/77 (5%)
Query: 229 LVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEKFGG 288
LVG +GKTT V +G+F + + T+G + + +G + VWD GQ +F
Sbjct: 4 LVGLQNSGKTTLVNVIASGQFSEDTIPTVGFNMRKV----TKGNVTIKVWDLGGQPRFRS 59
Query: 289 LRDGYYIQGQCAIIMFD 305
+ + Y + + D
Sbjct: 60 MWERYCRGVNAIVYVVD 76
>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 = 56.5 bits (137), Expect = 1e-09
Identities = 36/159 (22%), Positives = 67/159 (42%), Gaps = 22/159 (13%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 70
K ++G G GK+ R LT F +Y L V + + + DT GQ++
Sbjct: 1 KIAVLGASGVGKSALTVRFLTKRFIGEYEPNLESLYSRQV-TIDGEQVSLEIQDTPGQQQ 59
Query: 71 FGG-------LR--DGYYIQGQCAIIMFDVTSRITYKNVPNWHR--DLVRVCE-NIPIVL 118
LR DG+ ++++ +T R ++ V + ++ + IP++L
Sbjct: 60 NEDPESLERSLRWADGF-------VLVYSITDRSSFDVVSQLLQLIREIKKRDGEIPVIL 112
Query: 119 CGNKVDI-KDRKV-KAKSIVFHRKKNLQYYDISAKSNYN 155
GNK D+ R+V + + ++++SA NY
Sbjct: 113 VGNKADLLHSRQVSTEEGQKLALELGCLFFEVSAAENYL 151
Score = 37.3 bits (87), Expect = 0.004
Identities = 26/121 (21%), Positives = 46/121 (38%), Gaps = 29/121 (23%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 285
K ++G G GK+ R LT F +Y L V + + + DT GQ++
Sbjct: 1 KIAVLGASGVGKSALTVRFLTKRFIGEYEPNLESLYSRQV-TIDGEQVSLEIQDTPGQQQ 59
Query: 286 FGG-------LR--DGYYIQGQCAIIMFDVTSRITYKNYYDISAKSNYNFEKPFLWLARK 336
LR DG+ ++++ +T R S+++ L L R+
Sbjct: 60 NEDPESLERSLRWADGF-------VLVYSITDR------------SSFDVVSQLLQLIRE 100
Query: 337 L 337
+
Sbjct: 101 I 101
>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 = 56.9 bits (138), Expect = 1e-09
Identities = 43/161 (26%), Positives = 76/161 (47%), Gaps = 19/161 (11%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFN-------VW 63
K ++G GK++ + + G F + Y +P + +T I + +
Sbjct: 3 KIAVLGSRSVGKSSLTVQFVEGHFVESY--------YPTIENTFSKIITYKGQEYHLEIV 54
Query: 64 DTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVC--ENIPIVLCGN 121
DTAGQ+++ L Y I I+++ VTSR +++ V + ++ + E++PIVL GN
Sbjct: 55 DTAGQDEYSILPQKYSIGIHGYILVYSVTSRKSFEVVKVIYDKILDMLGKESVPIVLVGN 114
Query: 122 KVDIKD-RKVKAKS-IVFHRKKNLQYYDISAKSNYNFEKPF 160
K D+ R+V A+ + + SAK N N E+ F
Sbjct: 115 KSDLHMERQVSAEEGKKLAESWGAAFLESSAKENENVEEAF 155
Score = 28.0 bits (63), Expect = 5.5
Identities = 23/91 (25%), Positives = 41/91 (45%), Gaps = 15/91 (16%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFN-------VW 278
K ++G GK++ + + G F + Y +P + +T I + +
Sbjct: 3 KIAVLGSRSVGKSSLTVQFVEGHFVESY--------YPTIENTFSKIITYKGQEYHLEIV 54
Query: 279 DTAGQEKFGGLRDGYYIQGQCAIIMFDVTSR 309
DTAGQ+++ L Y I I+++ VTSR
Sbjct: 55 DTAGQDEYSILPQKYSIGIHGYILVYSVTSR 85
>gnl|CDD|206735 cd04172, Rnd3_RhoE_Rho8, Rnd3/RhoE/Rho8 GTPases. Rnd3/RhoE/Rho8
subfamily. Rnd3/RhoE/Rho8 is a member of the novel Rho
subfamily Rnd, together with Rnd1/Rho6 and Rnd2/Rho7.
Rnd3/RhoE is known to bind the serine-threonine kinase
ROCK I. Unphosphorylated Rnd3/RhoE associates primarily
with membranes, but ROCK I-phosphorylated Rnd3/RhoE
localizes in the cytosol. Phosphorylation of Rnd3/RhoE
correlates with its activity in disrupting RhoA-induced
stress fibers and inhibiting Ras-induced fibroblast
transformation. In cells that lack stress fibers, such
as macrophages and monocytes, Rnd3/RhoE induces a
redistribution of actin, causing morphological changes
in the cell. In addition, Rnd3/RhoE has been shown to
inhibit cell cycle progression in G1 phase at a point
upstream of the pRb family pocket protein checkpoint.
Rnd3/RhoE has also been shown to inhibit Ras- and
Raf-induced fibroblast transformation. In mammary
epithelial tumor cells, Rnd3/RhoE regulates the assembly
of the apical junction complex and tight junction
formation. Rnd3/RhoE is underexpressed in prostate
cancer cells both in vitro and in vivo; re-expression of
Rnd3/RhoE suppresses cell cycle progression and
increases apoptosis, suggesting it may play a role in
tumor suppression. Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 182
Score = 56.2 bits (135), Expect = 2e-09
Identities = 37/140 (26%), Positives = 62/140 (44%), Gaps = 4/140 (2%)
Query: 9 SFKC--VLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTA 66
+ KC V+VGD GKT + F + YV T+ E + F + I ++WDT+
Sbjct: 3 NVKCKIVVVGDSQCGKTALLHVFAKDCFPENYVPTV-FENYTASFEIDTQRIELSLWDTS 61
Query: 67 GQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKNV-PNWHRDLVRVCENIPIVLCGNKVDI 125
G + +R Y +I FD++ T +V W ++ C N ++L G K D+
Sbjct: 62 GSPYYDNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEIQEFCPNTKMLLVGCKSDL 121
Query: 126 KDRKVKAKSIVFHRKKNLQY 145
+ + HR+ + Y
Sbjct: 122 RTDVSTLVELSNHRQTPVSY 141
Score = 42.7 bits (100), Expect = 8e-05
Identities = 26/93 (27%), Positives = 42/93 (45%), Gaps = 3/93 (3%)
Query: 224 SFKC--VLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTA 281
+ KC V+VGD GKT + F + YV T+ E + F + I ++WDT+
Sbjct: 3 NVKCKIVVVGDSQCGKTALLHVFAKDCFPENYVPTV-FENYTASFEIDTQRIELSLWDTS 61
Query: 282 GQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKN 314
G + +R Y +I FD++ T +
Sbjct: 62 GSPYYDNVRPLSYPDSDAVLICFDISRPETLDS 94
>gnl|CDD|206736 cd04173, Rnd2_Rho7, Rnd2/Rho7 GTPases. Rnd2/Rho7 is a member of
the novel Rho subfamily Rnd, together with Rnd1/Rho6 and
Rnd3/RhoE/Rho8. Rnd2/Rho7 is transiently expressed in
radially migrating cells in the brain while they are
within the subventricular zone of the hippocampus and
cerebral cortex. These migrating cells typically develop
into pyramidal neurons. Cells that exogenously expressed
Rnd2/Rho7 failed to migrate to upper layers of the
brain, suggesting that Rnd2/Rho7 plays a role in the
radial migration and morphological changes of developing
pyramidal neurons, and that Rnd2/Rho7 degradation is
necessary for proper cellular migration. The Rnd2/Rho7
GEF Rapostlin is found primarily in the brain and
together with Rnd2/Rho7 induces dendrite branching.
Unlike Rnd1/Rho6 and Rnd3/RhoE/Rho8, which are RhoA
antagonists, Rnd2/Rho7 binds the GEF Pragmin and
significantly stimulates RhoA activity and Rho-A
mediated cell contraction. Rnd2/Rho7 is also found to be
expressed in spermatocytes and early spermatids, with
male-germ-cell Rac GTPase-activating protein
(MgcRacGAP), where it localizes to the Golgi-derived
pro-acrosomal vesicle. Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Length = 221
Score = 55.4 bits (133), Expect = 7e-09
Identities = 34/117 (29%), Positives = 55/117 (47%), Gaps = 2/117 (1%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 70
K V+VGD GKT + + + YV T+ E + F ++ I N+WDT+G
Sbjct: 3 KIVVVGDTQCGKTALLHVFAKDNYPESYVPTV-FENYTASFEIDKHRIELNMWDTSGSSY 61
Query: 71 FGGLRDGYYIQGQCAIIMFDVTSRITYKNV-PNWHRDLVRVCENIPIVLCGNKVDIK 126
+ +R Y +I FD++ T +V W + C N +VL G K+D++
Sbjct: 62 YDNVRPLAYPDSDAVLICFDISRPETLDSVLKKWQGETQEFCPNAKLVLVGCKLDMR 118
Score = 42.3 bits (99), Expect = 1e-04
Identities = 24/82 (29%), Positives = 39/82 (47%), Gaps = 1/82 (1%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 285
K V+VGD GKT + + + YV T+ E + F ++ I N+WDT+G
Sbjct: 3 KIVVVGDTQCGKTALLHVFAKDNYPESYVPTV-FENYTASFEIDKHRIELNMWDTSGSSY 61
Query: 286 FGGLRDGYYIQGQCAIIMFDVT 307
+ +R Y +I FD++
Sbjct: 62 YDNVRPLAYPDSDAVLICFDIS 83
>gnl|CDD|206737 cd04174, Rnd1_Rho6, Rnd1/Rho6 GTPases. Rnd1/Rho6 is a member of
the novel Rho subfamily Rnd, together with Rnd2/Rho7 and
Rnd3/RhoE/Rho8. Rnd1/Rho6 binds GTP but does not
hydrolyze it to GDP, indicating that it is
constitutively active. In rat, Rnd1/Rho6 is highly
expressed in the cerebral cortex and hippocampus during
synapse formation, and plays a role in spine formation.
Rnd1/Rho6 is also expressed in the liver and in
endothelial cells, and is upregulated in uterine
myometrial cells during pregnancy. Like Rnd3/RhoE/Rho8,
Rnd1/Rho6 is believed to function as an antagonist to
RhoA. Most Rho proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Rho proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 232
Score = 47.4 bits (112), Expect = 4e-06
Identities = 29/117 (24%), Positives = 55/117 (47%), Gaps = 2/117 (1%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 70
K VLVGD GKT ++ + + YV T+ E + T + ++WDT+G
Sbjct: 15 KLVLVGDVQCGKTAMLQVLAKDCYPETYVPTV-FENYTACLETEEQRVELSLWDTSGSPY 73
Query: 71 FGGLRDGYYIQGQCAIIMFDVTSRITYKN-VPNWHRDLVRVCENIPIVLCGNKVDIK 126
+ +R Y ++ FD++ + + + W +++ C + I+L G K D++
Sbjct: 74 YDNVRPLCYSDSDAVLLCFDISRPEIFDSALKKWRAEILDYCPSTRILLIGCKTDLR 130
Score = 36.2 bits (83), Expect = 0.016
Identities = 22/82 (26%), Positives = 38/82 (46%), Gaps = 1/82 (1%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 285
K VLVGD GKT ++ + + YV T+ E + T + ++WDT+G
Sbjct: 15 KLVLVGDVQCGKTAMLQVLAKDCYPETYVPTV-FENYTACLETEEQRVELSLWDTSGSPY 73
Query: 286 FGGLRDGYYIQGQCAIIMFDVT 307
+ +R Y ++ FD++
Sbjct: 74 YDNVRPLCYSDSDAVLLCFDIS 95
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 45.7 bits (109), Expect = 8e-06
Identities = 27/124 (21%), Positives = 49/124 (39%), Gaps = 13/124 (10%)
Query: 9 SFKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQ 68
+ +++G GKTT + + GE + T+G V + + ++F VWD GQ
Sbjct: 14 EMRILILGLDNAGKTTILYKLKLGEI-VTTIPTIGFNVETVTY----KNVKFTVWDVGGQ 68
Query: 69 EKFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVCE-----NIPIVLCGNKV 123
E L Y+ I + D R + +L + + P+++ NK
Sbjct: 69 ESLRPLWRNYFPNTDAVIFVVDSADR---DRIEEAKEELHALLNEEELADAPLLILANKQ 125
Query: 124 DIKD 127
D+
Sbjct: 126 DLPG 129
Score = 44.1 bits (105), Expect = 3e-05
Identities = 22/86 (25%), Positives = 36/86 (41%), Gaps = 5/86 (5%)
Query: 224 SFKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQ 283
+ +++G GKTT + + GE + T+G V + + ++F VWD GQ
Sbjct: 14 EMRILILGLDNAGKTTILYKLKLGEI-VTTIPTIGFNVETVTY----KNVKFTVWDVGGQ 68
Query: 284 EKFGGLRDGYYIQGQCAIIMFDVTSR 309
E L Y+ I + D R
Sbjct: 69 ESLRPLWRNYFPNTDAVIFVVDSADR 94
>gnl|CDD|206722 cd04157, Arl6, Arf-like 6 (Arl6) GTPase. Arl6 (Arf-like 6) forms a
subfamily of the Arf family of small GTPases. Arl6
expression is limited to the brain and kidney in adult
mice, but it is expressed in the neural plate and
somites during embryogenesis, suggesting a possible role
for Arl6 in early development. Arl6 is also believed to
have a role in cilia or flagella function. Several
proteins have been identified that bind Arl6, including
Arl6 interacting protein (Arl6ip), and SEC61beta, a
subunit of the heterotrimeric conducting channel SEC61p.
Based on Arl6 binding to these effectors, Arl6 is also
proposed to play a role in protein transport, membrane
trafficking, or cell signaling during hematopoietic
maturation. At least three specific homozygous Arl6
mutations in humans have been found to cause
Bardet-Biedl syndrome, a disorder characterized by
obesity, retinopathy, polydactyly, renal and cardiac
malformations, learning disabilities, and
hypogenitalism. Older literature suggests that Arl6 is a
part of the Arl4/Arl7 subfamily, but analyses based on
more recent sequence data place Arl6 in its own
subfamily.
Length = 162
Score = 44.7 bits (106), Expect = 1e-05
Identities = 37/140 (26%), Positives = 60/140 (42%), Gaps = 17/140 (12%)
Query: 13 VLVGDGGTGKTTFVKRHLTGEFEKKY--VATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 70
+++G +GKTT + L + V T+G V F G + F +D +GQ K
Sbjct: 3 LVLGLDNSGKTTIIN-QLKPSNAQSQNIVPTVGFNVE--SFKK--GNLSFTAFDMSGQGK 57
Query: 71 FGGLRDGYYIQGQCAIIMFDVTSRITY-------KNVPNWHRDLVRVCENIPIVLCGNKV 123
+ GL + YY Q I + D + R+ + + N H D+ IPI+ NK+
Sbjct: 58 YRGLWEHYYKNIQGIIFVIDSSDRLRMVVAKDELELLLN-HPDIKH--RRIPILFYANKM 114
Query: 124 DIKDRKVKAKSIVFHRKKNL 143
D+ D K +N+
Sbjct: 115 DLPDALTAVKITQLLCLENI 134
Score = 35.9 bits (83), Expect = 0.014
Identities = 32/122 (26%), Positives = 51/122 (41%), Gaps = 22/122 (18%)
Query: 228 VLVGDGGTGKTTFVKRHLTGEFEKKY--VATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 285
+++G +GKTT + L + V T+G V F G + F +D +GQ K
Sbjct: 3 LVLGLDNSGKTTIIN-QLKPSNAQSQNIVPTVGFNVE--SFKK--GNLSFTAFDMSGQGK 57
Query: 286 FGGLRDGYYIQGQCAIIMFDVTSRI----------TYKNYYDISAKSNYNFEKPFLWLAR 335
+ GL + YY Q I + D + R+ N+ DI + P L+ A
Sbjct: 58 YRGLWEHYYKNIQGIIFVIDSSDRLRMVVAKDELELLLNHPDIKHR-----RIPILFYAN 112
Query: 336 KL 337
K+
Sbjct: 113 KM 114
>gnl|CDD|133353 cd04153, Arl5_Arl8, Arf-like 5 (Arl5) and 8 (Arl8) GTPases.
Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like
Arl4 and Arl7, are localized to the nucleus and
nucleolus. Arl5 is developmentally regulated during
embryogenesis in mice. Human Arl5 interacts with the
heterochromatin protein 1-alpha (HP1alpha), a nonhistone
chromosomal protein that is associated with
heterochromatin and telomeres, and prevents telomere
fusion. Arl5 may also play a role in embryonic nuclear
dynamics and/or signaling cascades. Arl8 was identified
from a fetal cartilage cDNA library. It is found in
brain, heart, lung, cartilage, and kidney. No function
has been assigned for Arl8 to date.
Length = 174
Score = 44.6 bits (106), Expect = 2e-05
Identities = 40/133 (30%), Positives = 57/133 (42%), Gaps = 31/133 (23%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVA---TLGVEVHPLVFHTNRGAIRFNVWDTA 66
+K ++VG GKTT + + L GE V T+G V +V+ IRF +WD
Sbjct: 16 YKVIIVGLDNAGKTTILYQFLLGE----VVHTSPTIGSNVEEIVYKN----IRFLMWDIG 67
Query: 67 GQEKFGGLRDG---YYIQGQCAIIMFDVT--SRIT------YKNVPNWHRDLVRVCENIP 115
GQE LR YY I++ D T R+ YK + H DL
Sbjct: 68 GQES---LRSSWNTYYTNTDAVILVIDSTDRERLPLTKEELYKMLA--HEDL----RKAV 118
Query: 116 IVLCGNKVDIKDR 128
+++ NK D+K
Sbjct: 119 LLVLANKQDLKGA 131
Score = 42.3 bits (100), Expect = 1e-04
Identities = 31/91 (34%), Positives = 42/91 (46%), Gaps = 17/91 (18%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVA---TLGVEVHPLVFHTNRGAIRFNVWDTA 281
+K ++VG GKTT + + L GE V T+G V +V+ IRF +WD
Sbjct: 16 YKVIIVGLDNAGKTTILYQFLLGE----VVHTSPTIGSNVEEIVYKN----IRFLMWDIG 67
Query: 282 GQEKFGGLRDG---YYIQGQCAIIMFDVTSR 309
GQE LR YY I++ D T R
Sbjct: 68 GQES---LRSSWNTYYTNTDAVILVIDSTDR 95
>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 = 44.3 bits (105), Expect = 4e-05
Identities = 35/129 (27%), Positives = 55/129 (42%), Gaps = 24/129 (18%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKK---------YVATLGVEVHP--LVFHTNRGAI 58
++ VL+GD G GK++ G +E Y T+ V+ LV
Sbjct: 1 YRVVLLGDSGVGKSSLANIFTAGVYEDSAYEASGDDTYERTVSVDGEEATLVV------- 53
Query: 59 RFNVWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDL--VRVCENIPI 116
++ W+ QE L D G +I++ VT R +++ L R E+IPI
Sbjct: 54 -YDHWE---QEDGMWLEDSCMQVGDAYVIVYSVTDRSSFEKASELRIQLRRARQAEDIPI 109
Query: 117 VLCGNKVDI 125
+L GNK D+
Sbjct: 110 ILVGNKSDL 118
Score = 31.6 bits (72), Expect = 0.48
Identities = 24/99 (24%), Positives = 40/99 (40%), Gaps = 22/99 (22%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKK---------YVATLGVEVHP--LVFHTNRGAI 273
++ VL+GD G GK++ G +E Y T+ V+ LV
Sbjct: 1 YRVVLLGDSGVGKSSLANIFTAGVYEDSAYEASGDDTYERTVSVDGEEATLVV------- 53
Query: 274 RFNVWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITY 312
++ W+ QE L D G +I++ VT R ++
Sbjct: 54 -YDHWE---QEDGMWLEDSCMQVGDAYVIVYSVTDRSSF 88
>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 = 42.7 bits (101), Expect = 6e-05
Identities = 43/173 (24%), Positives = 71/173 (41%), Gaps = 23/173 (13%)
Query: 12 CVL-VGDGGTGKTTFVKRHLTGEFEKKY--------VATLGVEVHPLVFHTNRGAIRFNV 62
CVL +G GKTTF+++ T +F K Y T+G+ + + G R
Sbjct: 1 CVLILGLDNAGKTTFLEQTKT-KFSKNYKGLNPSKITPTVGLNIGTIEV----GKARLMF 55
Query: 63 WDTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVR--VCENIPIVLCG 120
WD GQE+ L D YY + I + D T R + + ++ E +P+++
Sbjct: 56 WDLGGQEELRSLWDKYYAESHGVIYVIDSTDRERFNESKSAFEKVINNEALEGVPLLVLA 115
Query: 121 NKVDIKD-------RKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARK 166
NK D+ D ++V I +++ +SA E+ WL
Sbjct: 116 NKQDLPDALSVAEIKEVFDDCIALIGRRDCLVQPVSALEGEGVEEGIEWLVDC 168
Score = 33.1 bits (76), Expect = 0.12
Identities = 30/92 (32%), Positives = 42/92 (45%), Gaps = 14/92 (15%)
Query: 227 CVL-VGDGGTGKTTFVKRHLTGEFEKKY--------VATLGVEVHPLVFHTNRGAIRFNV 277
CVL +G GKTTF+++ T +F K Y T+G+ + + G R
Sbjct: 1 CVLILGLDNAGKTTFLEQTKT-KFSKNYKGLNPSKITPTVGLNIGTIEV----GKARLMF 55
Query: 278 WDTAGQEKFGGLRDGYYIQGQCAIIMFDVTSR 309
WD GQE+ L D YY + I + D T R
Sbjct: 56 WDLGGQEELRSLWDKYYAESHGVIYVIDSTDR 87
>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 = 42.5 bits (100), Expect = 1e-04
Identities = 42/168 (25%), Positives = 76/168 (45%), Gaps = 29/168 (17%)
Query: 10 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVH-PLVFHTNR----------GAI 58
+ ++G G GKT V++ L EF ++Y+ T ++ P V + R
Sbjct: 1 VRVAVLGAPGVGKTAIVRQFLAQEFPEEYIPTEHRRLYRPAVVLSGRVYDLHILDVPNMQ 60
Query: 59 RFNVWDTAGQE----KFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLV--RVCE 112
R+ TAGQE +F GLR+ + I+++D+ S ++ V + ++ R
Sbjct: 61 RYPG--TAGQEWMDPRFRGLRN-----SRAFILVYDICSPDSFHYVKLLRQQILETRPAG 113
Query: 113 N--IPIVLCGNKVDIKDRKVKAKSIVFH---RKKNLQYYDISAKSNYN 155
N PIV+ GNK D + + + ++ + Y + SAK N++
Sbjct: 114 NKEPPIVVVGNKRDQQRHRFAPRHVLSVLVRKSWKCGYLECSAKYNWH 161
Score = 31.4 bits (71), Expect = 0.57
Identities = 11/38 (28%), Positives = 21/38 (55%)
Query: 225 FKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVH 262
+ ++G G GKT V++ L EF ++Y+ T ++
Sbjct: 1 VRVAVLGAPGVGKTAIVRQFLAQEFPEEYIPTEHRRLY 38
>gnl|CDD|177661 PLN00023, PLN00023, GTP-binding protein; Provisional.
Length = 334
Score = 42.9 bits (101), Expect = 2e-04
Identities = 34/144 (23%), Positives = 55/144 (38%), Gaps = 36/144 (25%)
Query: 13 VLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRG--AIRFN--------- 61
++VGD G GK++ V + G + T+G V V H G N
Sbjct: 25 LVVGDSGVGKSSLVHLIVKGSSIARPPQTIGCTVG--VKHITYGSPGSSSNSIKGDSERD 82
Query: 62 ----VWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVCEN---- 113
+WD +G E++ R +Y Q I + D++ R T ++ W + V
Sbjct: 83 FFVELWDVSGHERYKDCRSLFYSQINGVIFVHDLSQRRTKTSLQKWASE---VAATGTFS 139
Query: 114 ------------IPIVLCGNKVDI 125
+P ++ GNK DI
Sbjct: 140 APLGSGGPGGLPVPYIVIGNKADI 163
Score = 34.8 bits (80), Expect = 0.059
Identities = 26/102 (25%), Positives = 42/102 (41%), Gaps = 17/102 (16%)
Query: 228 VLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRG--AIRFN--------- 276
++VGD G GK++ V + G + T+G V V H G N
Sbjct: 25 LVVGDSGVGKSSLVHLIVKGSSIARPPQTIGCTVG--VKHITYGSPGSSSNSIKGDSERD 82
Query: 277 ----VWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRITYKN 314
+WD +G E++ R +Y Q I + D++ R T +
Sbjct: 83 FFVELWDVSGHERYKDCRSLFYSQINGVIFVHDLSQRRTKTS 124
>gnl|CDD|133356 cd04156, ARLTS1, Arf-like tumor suppressor gene 1 (ARLTS1 or
Arl11). ARLTS1 (Arf-like tumor suppressor gene 1), also
known as Arl11, is a member of the Arf family of small
GTPases that is believed to play a major role in
apoptotic signaling. ARLTS1 is widely expressed and
functions as a tumor suppressor gene in several human
cancers. ARLTS1 is a low-penetrance suppressor that
accounts for a small percentage of familial melanoma or
familial chronic lymphocytic leukemia (CLL). ARLTS1
inactivation seems to occur most frequently through
biallelic down-regulation by hypermethylation of the
promoter. In breast cancer, ARLTS1 alterations were
typically a combination of a hypomorphic polymorphism
plus loss of heterozygosity. In a case of thyroid
adenoma, ARLTS1 alterations were polymorphism plus
promoter hypermethylation. The nonsense polymorphism
Trp149Stop occurs with significantly greater frequency
in familial cancer cases than in sporadic cancer cases,
and the Cys148Arg polymorphism is associated with an
increase in high-risk familial breast cancer.
Length = 160
Score = 40.9 bits (96), Expect = 2e-04
Identities = 29/122 (23%), Positives = 52/122 (42%), Gaps = 16/122 (13%)
Query: 13 VLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEKFG 72
+L+G GK+T + + E + T+G V L + + VWD GQEK
Sbjct: 3 LLLGLDSAGKSTLLYKLKHAELVTT-IPTVGFNVEML--QLEK-HLSLTVWDVGGQEK-- 56
Query: 73 GLRD--GYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVCEN-----IPIVLCGNKVDI 125
+R Y++ +++ V S + ++L + +N +P+VL NK D+
Sbjct: 57 -MRTVWKCYLEN-TDGLVYVVDSS-DEARLDESQKELKHILKNEHIKGVPVVLLANKQDL 113
Query: 126 KD 127
Sbjct: 114 PG 115
Score = 32.0 bits (73), Expect = 0.24
Identities = 21/83 (25%), Positives = 36/83 (43%), Gaps = 10/83 (12%)
Query: 228 VLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEKFG 287
+L+G GK+T + + E + T+G V L + + VWD GQEK
Sbjct: 3 LLLGLDSAGKSTLLYKLKHAELVTT-IPTVGFNVEML--QLEK-HLSLTVWDVGGQEK-- 56
Query: 288 GLRD--GYYIQGQCAIIMFDVTS 308
+R Y++ +++ V S
Sbjct: 57 -MRTVWKCYLEN-TDGLVYVVDS 77
>gnl|CDD|206721 cd04155, Arl3, Arf-like 3 (Arl3) GTPase. Arl3 (Arf-like 3) is an
Arf family protein that differs from most Arf family
members in the N-terminal extension. In is inactive,
GDP-bound form, the N-terminal extension forms an
elongated loop that is hydrophobically anchored into the
membrane surface; however, it has been proposed that
this region might form a helix in the GTP-bound form.
The delta subunit of the rod-specific cyclic GMP
phosphodiesterase type 6 (PDEdelta) is an Arl3 effector.
Arl3 binds microtubules in a regulated manner to alter
specific aspects of cytokinesis via interactions with
retinitis pigmentosa 2 (RP2). It has been proposed that
RP2 functions in concert with Arl3 to link the cell
membrane and the cytoskeleton in photoreceptors as part
of the cell signaling or vesicular transport machinery.
In mice, the absence of Arl3 is associated with abnormal
epithelial cell proliferation and cyst formation.
Length = 174
Score = 40.5 bits (95), Expect = 5e-04
Identities = 30/117 (25%), Positives = 46/117 (39%), Gaps = 13/117 (11%)
Query: 14 LVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEKFGG 73
L+G GKTT +K+ L E T G + + + NVWD GQ K
Sbjct: 20 LLGLDNAGKTTILKQ-LASEDISHITPTQGFNIKNV----QADGFKLNVWDIGGQRKIRP 74
Query: 74 LRDGYYIQGQCAIIMFDVTSRITYKNVPNWHRDLVRVCE-----NIPIVLCGNKVDI 125
Y+ I + D R K ++LV + E +P+++ NK D+
Sbjct: 75 YWRNYFENTDVLIYVIDSADR---KRFEEAGQELVELLEEEKLAGVPVLVFANKQDL 128
Score = 33.9 bits (78), Expect = 0.074
Identities = 22/81 (27%), Positives = 30/81 (37%), Gaps = 5/81 (6%)
Query: 229 LVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEKFGG 288
L+G GKTT +K+ L E T G + + + NVWD GQ K
Sbjct: 20 LLGLDNAGKTTILKQ-LASEDISHITPTQGFNIKNV----QADGFKLNVWDIGGQRKIRP 74
Query: 289 LRDGYYIQGQCAIIMFDVTSR 309
Y+ I + D R
Sbjct: 75 YWRNYFENTDVLIYVIDSADR 95
>gnl|CDD|206723 cd04158, ARD1, (ADP-ribosylation factor domain protein 1 (ARD1).
ARD1 (ADP-ribosylation factor domain protein 1) is an
unusual member of the Arf family. In addition to the
C-terminal Arf domain, ARD1 has an additional 46-kDa
N-terminal domain that contains a RING finger domain,
two predicted B-Boxes, and a coiled-coil protein
interaction motif. This domain belongs to the TRIM
(tripartite motif) or RBCC (RING, B-Box, coiled-coil)
family. Like most Arfs, the ARD1 Arf domain lacks
detectable GTPase activity. However, unlike most Arfs,
the full-length ARD1 protein has significant GTPase
activity due to the GAP (GTPase-activating protein)
activity exhibited by the 46-kDa N-terminal domain. The
GAP domain of ARD1 is specific for its own Arf domain
and does not bind other Arfs. The rate of GDP
dissociation from the ARD1 Arf domain is slowed by the
adjacent 15 amino acids, which act as a GDI
(GDP-dissociation inhibitor) domain. ARD1 is
ubiquitously expressed in cells and localizes to the
Golgi and to the lysosomal membrane. Two Tyr-based
motifs in the Arf domain are responsible for Golgi
localization, while the GAP domain controls lysosomal
localization.
Length = 169
Score = 40.0 bits (93), Expect = 5e-04
Identities = 23/84 (27%), Positives = 40/84 (47%), Gaps = 5/84 (5%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 70
+ V +G G GKTT + + EF + + T+G V + + ++F +WD G+ K
Sbjct: 1 RVVTLGLDGAGKTTILFKLKQDEFMQP-IPTIGFNVETVEYKN----LKFTIWDVGGKHK 55
Query: 71 FGGLRDGYYIQGQCAIIMFDVTSR 94
L YY+ Q + + D + R
Sbjct: 56 LRPLWKHYYLNTQAVVFVIDSSHR 79
Score = 40.0 bits (93), Expect = 5e-04
Identities = 23/84 (27%), Positives = 40/84 (47%), Gaps = 5/84 (5%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 285
+ V +G G GKTT + + EF + + T+G V + + ++F +WD G+ K
Sbjct: 1 RVVTLGLDGAGKTTILFKLKQDEFMQP-IPTIGFNVETVEYKN----LKFTIWDVGGKHK 55
Query: 286 FGGLRDGYYIQGQCAIIMFDVTSR 309
L YY+ Q + + D + R
Sbjct: 56 LRPLWKHYYLNTQAVVFVIDSSHR 79
>gnl|CDD|128474 smart00177, ARF, ARF-like small GTPases; ARF, ADP-ribosylation
factor. Ras homologues involved in vesicular
transport. Activator of phospholipase D isoforms.
Unlike Ras proteins they lack cysteine residues at
their C-termini and therefore are unlikely to be
prenylated. ARFs are N-terminally myristoylated.
Contains ATP/GTP-binding motif (P-loop).
Length = 175
Score = 39.5 bits (92), Expect = 0.001
Identities = 26/84 (30%), Positives = 37/84 (44%), Gaps = 5/84 (5%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 70
+ ++VG GKTT + + GE + T+G V + + I F VWD GQ+K
Sbjct: 15 RILMVGLDAAGKTTILYKLKLGESVTT-IPTIGFNVETVTYKN----ISFTVWDVGGQDK 69
Query: 71 FGGLRDGYYIQGQCAIIMFDVTSR 94
L YY Q I + D R
Sbjct: 70 IRPLWRHYYTNTQGLIFVVDSNDR 93
Score = 39.5 bits (92), Expect = 0.001
Identities = 26/84 (30%), Positives = 37/84 (44%), Gaps = 5/84 (5%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 285
+ ++VG GKTT + + GE + T+G V + + I F VWD GQ+K
Sbjct: 15 RILMVGLDAAGKTTILYKLKLGESVTT-IPTIGFNVETVTYKN----ISFTVWDVGGQDK 69
Query: 286 FGGLRDGYYIQGQCAIIMFDVTSR 309
L YY Q I + D R
Sbjct: 70 IRPLWRHYYTNTQGLIFVVDSNDR 93
>gnl|CDD|133275 cd01873, RhoBTB, RhoBTB protein is an atypical member of the Rho
family of small GTPases. Members of the RhoBTB
subfamily of Rho GTPases are present in vertebrates,
Drosophila, and Dictyostelium. RhoBTB proteins are
characterized by a modular organization, consisting of a
GTPase domain, a proline rich region, a tandem of two
BTB (Broad-Complex, Tramtrack, and Bric a brac) domains,
and a C-terminal region of unknown function. RhoBTB
proteins may act as docking points for multiple
components participating in signal transduction
cascades. RhoBTB genes appeared upregulated in some
cancer cell lines, suggesting a participation of RhoBTB
proteins in the pathogenesis of particular tumors. Note
that the Dictyostelium RacA GTPase domain is more
closely related to Rac proteins than to RhoBTB proteins,
where RacA actually belongs. Thus, the Dictyostelium
RacA is not included here. Most Rho proteins contain a
lipid modification site at the C-terminus; however,
RhoBTB is one of few Rho subfamilies that lack this
feature.
Length = 195
Score = 38.0 bits (88), Expect = 0.003
Identities = 33/138 (23%), Positives = 61/138 (44%), Gaps = 28/138 (20%)
Query: 10 FKCVLVGDGGTGKTTFV-----KRHLTGEFEKKYVATLGVEVHPL--------VFHTNRG 56
KCV+VGD GKT + + LT + + +AT V + V +R
Sbjct: 3 IKCVVVGDNAVGKTRLICARACNKTLT---QYQLLATHVPTVWAIDQYRVCQEVLERSRD 59
Query: 57 AIR-----FNVWDTAGQEKFGGLRDGYYIQGQCAIIM--FDVTSRITYKNVPN-WHRDLV 108
+ +WDT G +D + G+ +++ F + S + +NV W+ ++
Sbjct: 60 VVDGVSVSLRLWDTFGDHD----KDRRFAYGRSDVVLLCFSIASPNSLRNVKTMWYPEIR 115
Query: 109 RVCENIPIVLCGNKVDIK 126
C +P++L G K+D++
Sbjct: 116 HFCPRVPVILVGCKLDLR 133
Score = 27.6 bits (61), Expect = 9.9
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 225 FKCVLVGDGGTGKTTFV 241
KCV+VGD GKT +
Sbjct: 3 IKCVVVGDNAVGKTRLI 19
>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 = 36.9 bits (86), Expect = 0.006
Identities = 35/134 (26%), Positives = 58/134 (43%), Gaps = 29/134 (21%)
Query: 13 VLVGDGGTGKTTFVKRHLTGEF--EKKYVA---TLGVEVHPLVFHTNRGAIRFNVWDTAG 67
VL+GD G GK++ + ++ EF V T+ +V P T + DT+
Sbjct: 6 VLIGDEGVGKSSLIMSLVSEEFPENVPRVLPEITIPADVTPERVPTT-------IVDTSS 58
Query: 68 QEKFGGLRDGYY--IQGQCAI-IMFDVTS-----RITYKNVPNWHRDLVRV-CENIPIVL 118
+ + R I+ I +++ V RI K +P L+R +PI+L
Sbjct: 59 RPQ---DRANLAAEIRKANVICLVYSVDRPSTLERIRTKWLP-----LIRRLGVKVPIIL 110
Query: 119 CGNKVDIKDRKVKA 132
GNK D++D +A
Sbjct: 111 VGNKSDLRDGSSQA 124
Score = 28.5 bits (64), Expect = 4.7
Identities = 9/22 (40%), Positives = 15/22 (68%)
Query: 228 VLVGDGGTGKTTFVKRHLTGEF 249
VL+GD G GK++ + ++ EF
Sbjct: 6 VLIGDEGVGKSSLIMSLVSEEF 27
>gnl|CDD|206645 cd00879, Sar1, Sar1 is an essential component of COPII vesicle
coats. Sar1 is an essential component of COPII vesicle
coats involved in export of cargo from the ER. The
GTPase activity of Sar1 functions as a molecular switch
to control protein-protein and protein-lipid
interactions that direct vesicle budding from the ER.
Activation of the GDP to the GTP-bound form of Sar1
involves the membrane-associated guanine nucleotide
exchange factor (GEF) Sec12. Sar1 is unlike all Ras
superfamily GTPases that use either myristoyl or prenyl
groups to direct membrane association and function, in
that Sar1 lacks such modification. Instead, Sar1
contains a unique nine-amino-acid N-terminal extension.
This extension contains an evolutionarily conserved
cluster of bulky hydrophobic amino acids, referred to as
the Sar1-N-terminal activation recruitment (STAR) motif.
The STAR motif mediates the recruitment of Sar1 to ER
membranes and facilitates its interaction with mammalian
Sec12 GEF leading to activation.
Length = 191
Score = 36.5 bits (85), Expect = 0.009
Identities = 31/126 (24%), Positives = 50/126 (39%), Gaps = 21/126 (16%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 70
K V +G GKTT + ++V TL HP G ++F +D G E+
Sbjct: 21 KIVFLGLDNAGKTTLLHMLKDDRL-AQHVPTL----HPTSEELTIGNVKFTTFDLGGHEQ 75
Query: 71 FGGL-RDGYYIQGQCAII-MFDVT-------SRITYKNVPNWHRDLVRVCENIPIVLCGN 121
+ +D Y I+ + D S+ ++ N D N+PI++ GN
Sbjct: 76 ARRVWKD--YFPEVDGIVFLVDAADPERFQESKEELDSLLN---DEELA--NVPILILGN 128
Query: 122 KVDIKD 127
K+D
Sbjct: 129 KIDKPG 134
Score = 29.9 bits (68), Expect = 1.6
Identities = 17/61 (27%), Positives = 25/61 (40%), Gaps = 5/61 (8%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 285
K V +G GKTT + ++V TL HP G ++F +D G E+
Sbjct: 21 KIVFLGLDNAGKTTLLHMLKDDRL-AQHVPTL----HPTSEELTIGNVKFTTFDLGGHEQ 75
Query: 286 F 286
Sbjct: 76 A 76
>gnl|CDD|206716 cd04149, Arf6, ADP ribosylation factor 6 (Arf6). Arf6 subfamily.
Arf6 (ADP ribosylation factor 6) proteins localize to
the plasma membrane, where they perform a wide variety
of functions. In its active, GTP-bound form, Arf6 is
involved in cell spreading, Rac-induced formation of
plasma membrane ruffles, cell migration, wound healing,
and Fc-mediated phagocytosis. Arf6 appears to change
the actin structure at the plasma membrane by
activating Rac, a Rho family protein involved in
membrane ruffling. Arf6 is required for and enhances
Rac formation of ruffles. Arf6 can regulate dendritic
branching in hippocampal neurons, and in yeast it
localizes to the growing bud, where it plays a role in
polarized growth and bud site selection. In leukocytes,
Arf6 is required for chemokine-stimulated migration
across endothelial cells. Arf6 also plays a role in
down-regulation of beta2-adrenergic receptors and
luteinizing hormone receptors by facilitating the
release of sequestered arrestin to allow endocytosis.
Arf6 is believed to function at multiple sites on the
plasma membrane through interaction with a specific set
of GEFs, GAPs, and effectors. Arf6 has been implicated
in breast cancer and melanoma cell invasion, and in
actin remodelling at the invasion site of Chlamydia
infection.
Length = 168
Score = 35.5 bits (82), Expect = 0.017
Identities = 26/84 (30%), Positives = 40/84 (47%), Gaps = 5/84 (5%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 70
+ +++G GKTT + + G+ + T+G V V + N ++FNVWD GQ+K
Sbjct: 11 RILMLGLDAAGKTTILYKLKLGQ-SVTTIPTVGFNVET-VTYKN---VKFNVWDVGGQDK 65
Query: 71 FGGLRDGYYIQGQCAIIMFDVTSR 94
L YY Q I + D R
Sbjct: 66 IRPLWRHYYTGTQGLIFVVDSADR 89
Score = 35.5 bits (82), Expect = 0.017
Identities = 26/84 (30%), Positives = 40/84 (47%), Gaps = 5/84 (5%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 285
+ +++G GKTT + + G+ + T+G V V + N ++FNVWD GQ+K
Sbjct: 11 RILMLGLDAAGKTTILYKLKLGQ-SVTTIPTVGFNVET-VTYKN---VKFNVWDVGGQDK 65
Query: 286 FGGLRDGYYIQGQCAIIMFDVTSR 309
L YY Q I + D R
Sbjct: 66 IRPLWRHYYTGTQGLIFVVDSADR 89
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 35.7 bits (82), Expect = 0.018
Identities = 25/84 (29%), Positives = 37/84 (44%), Gaps = 5/84 (5%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 70
+ ++VG GKTT + + GE + T+G V + + I F VWD GQ+K
Sbjct: 19 RILMVGLDAAGKTTILYKLKLGEIVTT-IPTIGFNVETVEYKN----ISFTVWDVGGQDK 73
Query: 71 FGGLRDGYYIQGQCAIIMFDVTSR 94
L Y+ Q I + D R
Sbjct: 74 IRPLWRHYFQNTQGLIFVVDSNDR 97
Score = 35.7 bits (82), Expect = 0.018
Identities = 25/84 (29%), Positives = 37/84 (44%), Gaps = 5/84 (5%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEK 285
+ ++VG GKTT + + GE + T+G V + + I F VWD GQ+K
Sbjct: 19 RILMVGLDAAGKTTILYKLKLGEIVTT-IPTIGFNVETVEYKN----ISFTVWDVGGQDK 73
Query: 286 FGGLRDGYYIQGQCAIIMFDVTSR 309
L Y+ Q I + D R
Sbjct: 74 IRPLWRHYFQNTQGLIFVVDSNDR 97
>gnl|CDD|206717 cd04150, Arf1_5_like, ADP-ribosylation factor-1 (Arf1) and
ADP-ribosylation factor-5 (Arf5). The Arf1-Arf5-like
subfamily contains Arf1, Arf2, Arf3, Arf4, Arf5, and
related proteins. Arfs1-5 are soluble proteins that are
crucial for assembling coat proteins during vesicle
formation. Each contains an N-terminal myristoylated
amphipathic helix that is folded into the protein in
the GDP-bound state. GDP/GTP exchange exposes the
helix, which anchors to the membrane. Following GTP
hydrolysis, the helix dissociates from the membrane and
folds back into the protein. A general feature of
Arf1-5 signaling may be the cooperation of two Arfs at
the same site. Arfs1-5 are generally considered to be
interchangeable in function and location, but some
specific functions have been assigned. Arf1 localizes
to the early/cis-Golgi, where it is activated by GBF1
and recruits the coat protein COPI. It also localizes
to the trans-Golgi network (TGN), where it is activated
by BIG1/BIG2 and recruits the AP1, AP3, AP4, and GGA
proteins. Humans, but not rodents and other lower
eukaryotes, lack Arf2. Human Arf3 shares 96% sequence
identity with Arf1 and is believed to generally
function interchangeably with Arf1. Human Arf4 in the
activated (GTP-bound) state has been shown to interact
with the cytoplasmic domain of epidermal growth factor
receptor (EGFR) and mediate the EGF-dependent
activation of phospholipase D2 (PLD2), leading to
activation of the activator protein 1 (AP-1)
transcription factor. Arf4 has also been shown to
recognize the C-terminal sorting signal of rhodopsin
and regulate its incorporation into specialized
post-Golgi rhodopsin transport carriers (RTCs). There
is some evidence that Arf5 functions at the early-Golgi
and the trans-Golgi to affect Golgi-associated
alpha-adaptin homology Arf-binding proteins (GGAs).
Length = 159
Score = 34.3 bits (79), Expect = 0.047
Identities = 25/82 (30%), Positives = 36/82 (43%), Gaps = 5/82 (6%)
Query: 13 VLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEKFG 72
++VG GKTT + + GE + T+G V + + I F VWD GQ+K
Sbjct: 4 LMVGLDAAGKTTILYKLKLGEIVTT-IPTIGFNVETVEYKN----ISFTVWDVGGQDKIR 58
Query: 73 GLRDGYYIQGQCAIIMFDVTSR 94
L Y+ Q I + D R
Sbjct: 59 PLWRHYFQNTQGLIFVVDSNDR 80
Score = 34.3 bits (79), Expect = 0.047
Identities = 25/82 (30%), Positives = 36/82 (43%), Gaps = 5/82 (6%)
Query: 228 VLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEKFG 287
++VG GKTT + + GE + T+G V + + I F VWD GQ+K
Sbjct: 4 LMVGLDAAGKTTILYKLKLGEIVTT-IPTIGFNVETVEYKN----ISFTVWDVGGQDKIR 58
Query: 288 GLRDGYYIQGQCAIIMFDVTSR 309
L Y+ Q I + D R
Sbjct: 59 PLWRHYFQNTQGLIFVVDSNDR 80
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 33.7 bits (77), Expect = 0.097
Identities = 23/82 (28%), Positives = 36/82 (43%), Gaps = 5/82 (6%)
Query: 13 VLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEKFG 72
++VG GKTT + + GE + T+G V + + ++F +WD GQ+K
Sbjct: 21 LMVGLDAAGKTTILYKLKLGEVVTT-IPTIGFNVETVEYKN----LKFTMWDVGGQDKLR 75
Query: 73 GLRDGYYIQGQCAIIMFDVTSR 94
L YY I + D R
Sbjct: 76 PLWRHYYQNTNGLIFVVDSNDR 97
Score = 33.7 bits (77), Expect = 0.097
Identities = 23/82 (28%), Positives = 36/82 (43%), Gaps = 5/82 (6%)
Query: 228 VLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEKFG 287
++VG GKTT + + GE + T+G V + + ++F +WD GQ+K
Sbjct: 21 LMVGLDAAGKTTILYKLKLGEVVTT-IPTIGFNVETVEYKN----LKFTMWDVGGQDKLR 75
Query: 288 GLRDGYYIQGQCAIIMFDVTSR 309
L YY I + D R
Sbjct: 76 PLWRHYYQNTNGLIFVVDSNDR 97
>gnl|CDD|240412 PTZ00420, PTZ00420, coronin; Provisional.
Length = 568
Score = 33.4 bits (76), Expect = 0.24
Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 6/75 (8%)
Query: 181 LLPPEVTMDPQ-----WQSRIEQDLKEAQETALPDDDEDLMAAEMDMP-SFKCVLVGDGG 234
L PP + DP+ W + +K L +DD + +P SF +++G+
Sbjct: 358 LYPPILMHDPERSSRNWIDGKDNKMKRINIKDLTEDDLRITKKYKFVPQSFNSIIIGENY 417
Query: 235 TGKTTFVKRHLTGEF 249
T K T + R T +F
Sbjct: 418 TSKRTSIIRQFTKKF 432
>gnl|CDD|213188 cd03221, ABCF_EF-3, ATP-binding cassette domain of elongation
factor 3, subfamily F. Elongation factor 3 (EF-3) is a
cytosolic protein required by fungal ribosomes for in
vitro protein synthesis and for in vivo growth. EF-3
stimulates the binding of the EF-1: GTP: aa-tRNA
ternary complex to the ribosomal A site by facilitated
release of the deacylated tRNA from the E site. The
reaction requires ATP hydrolysis. EF-3 contains two ATP
nucleotide binding sequence (NBS) motifs. NBSI is
sufficient for the intrinsic ATPase activity. NBSII is
essential for the ribosome-stimulated functions.
Length = 144
Score = 31.7 bits (73), Expect = 0.24
Identities = 11/25 (44%), Positives = 15/25 (60%), Gaps = 1/25 (4%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFE 35
+ LVG G GK+T +K + GE E
Sbjct: 28 RIGLVGRNGAGKSTLLK-LIAGELE 51
Score = 31.7 bits (73), Expect = 0.24
Identities = 11/25 (44%), Positives = 15/25 (60%), Gaps = 1/25 (4%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFE 250
+ LVG G GK+T +K + GE E
Sbjct: 28 RIGLVGRNGAGKSTLLK-LIAGELE 51
>gnl|CDD|206718 cd04151, Arl1, ADP ribosylation factor 1 (Arf1). Arl1 subfamily.
Arl1 (Arf-like 1) localizes to the Golgi complex, where
it is believed to recruit effector proteins to the
trans-Golgi network. Like most members of the Arf
family, Arl1 is myristoylated at its N-terminal helix
and mutation of the myristoylation site disrupts Golgi
targeting. In humans, the Golgi-localized proteins
golgin-97 and golgin-245 have been identified as Arl1
effectors. Golgins are large coiled-coil proteins found
in the Golgi, and these golgins contain a C-terminal
GRIP domain, which is the site of Arl1 binding.
Additional Arl1 effectors include the GARP
(Golgi-associated retrograde protein)/VFT (Vps53)
vesicle-tethering complex and Arfaptin 2. Arl1 is not
required for exocytosis, but appears necessary for
trafficking from the endosomes to the Golgi. In
Drosophila zygotes, mutation of Arl1 is lethal, and in
the host-bloodstream form of Trypanosoma brucei, Arl1
is essential for viability.
Length = 158
Score = 31.6 bits (72), Expect = 0.31
Identities = 24/81 (29%), Positives = 34/81 (41%), Gaps = 5/81 (6%)
Query: 14 LVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEKFGG 73
++G G GKTT + R GE + T+G V + + ++F VWD GQ
Sbjct: 4 ILGLDGAGKTTILYRLQVGEVVTT-IPTIGFNVETVTYKN----LKFQVWDLGGQTSIRP 58
Query: 74 LRDGYYIQGQCAIIMFDVTSR 94
YY I + D T R
Sbjct: 59 YWRCYYSNTDAIIYVVDSTDR 79
Score = 31.6 bits (72), Expect = 0.31
Identities = 24/81 (29%), Positives = 34/81 (41%), Gaps = 5/81 (6%)
Query: 229 LVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQEKFGG 288
++G G GKTT + R GE + T+G V + + ++F VWD GQ
Sbjct: 4 ILGLDGAGKTTILYRLQVGEVVTT-IPTIGFNVETVTYKN----LKFQVWDLGGQTSIRP 58
Query: 289 LRDGYYIQGQCAIIMFDVTSR 309
YY I + D T R
Sbjct: 59 YWRCYYSNTDAIIYVVDSTDR 79
>gnl|CDD|206719 cd04152, Arl4_Arl7, Arf-like 4 (Arl4) and 7 (Arl7) GTPases. Arl4
(Arf-like 4) is highly expressed in testicular germ
cells, and is found in the nucleus and nucleolus. In
mice, Arl4 is developmentally expressed during
embryogenesis, and a role in somite formation and
central nervous system differentiation has been
proposed. Arl7 has been identified as the only Arf/Arl
protein to be induced by agonists of liver X-receptor
and retinoid X-receptor and by cholesterol loading in
human macrophages. Arl7 is proposed to play a role in
transport between a perinuclear compartment and the
plasma membrane, apparently linked to the ABCA1-mediated
cholesterol secretion pathway. Older literature suggests
that Arl6 is a part of the Arl4/Arl7 subfamily, but
analyses based on more recent sequence data place Arl6
in its own subfamily.
Length = 183
Score = 31.7 bits (72), Expect = 0.37
Identities = 37/125 (29%), Positives = 54/125 (43%), Gaps = 14/125 (11%)
Query: 9 SFKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPL-VFHTNRGAIRFNVWDTAG 67
S V++G GKTT + R EF V T G + V N + F+ WD G
Sbjct: 3 SLHIVMLGLDSAGKTTVLYRLKFNEFVNT-VPTKGFNTEKIKVSLGNAKGVTFHFWDVGG 61
Query: 68 QEKFGGLRDGYYIQGQCAI-IMFDVTS----RITYKNVPNWHRDLVRVCEN--IPIVLCG 120
QEK L Y +C I+F V S R+ H+ + + EN +P+++
Sbjct: 62 QEKLRPLWKSY---TRCTDGIVFVVDSVDVERMEEAKT-ELHK-ITKFSENQGVPVLVLA 116
Query: 121 NKVDI 125
NK D+
Sbjct: 117 NKQDL 121
Score = 31.7 bits (72), Expect = 0.39
Identities = 24/71 (33%), Positives = 30/71 (42%), Gaps = 2/71 (2%)
Query: 224 SFKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPL-VFHTNRGAIRFNVWDTAG 282
S V++G GKTT + R EF V T G + V N + F+ WD G
Sbjct: 3 SLHIVMLGLDSAGKTTVLYRLKFNEFVNT-VPTKGFNTEKIKVSLGNAKGVTFHFWDVGG 61
Query: 283 QEKFGGLRDGY 293
QEK L Y
Sbjct: 62 QEKLRPLWKSY 72
>gnl|CDD|147512 pfam05363, Herpes_US12, Herpesvirus US12 family. US12 a key factor
in the evasion of cellular immune response against
HSV-infected cells. Specific inhibition of the
transporter associated with antigen processing (TAP) by
US12 prevents peptide transport into the endoplasmic
reticulum and subsequent loading of major
histocompatibility complex (MHC) class I molecules. US12
is comprised of three helices and is associated with
cellular membranes.
Length = 86
Score = 29.7 bits (66), Expect = 0.57
Identities = 18/63 (28%), Positives = 27/63 (42%), Gaps = 1/63 (1%)
Query: 303 MFDVTSRITYKNYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALLPPEVTMDPQW 362
MF R ++ Y D+ A+ + E+ AR + DP L + P LLP +P
Sbjct: 10 MFLDNMRCGHRTYADVCAEIHKR-EREDREAARTAVHDPELPLLCPPDLLPDIAPRNPTN 68
Query: 363 QSR 365
S
Sbjct: 69 ASL 71
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 31.6 bits (72), Expect = 0.61
Identities = 15/57 (26%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 103 WHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSI-VFHRKKNLQYYDISAKSNYNFEK 158
+ +L R+ + P +L NK D+ ++V K F +++ ++ +SAKS +K
Sbjct: 51 RNPELERIVKEKPKLLVLNKADLAPKEVTKKWKKYFKKEEGIKPIFVSAKSRQGGKK 107
>gnl|CDD|188437 TIGR03922, T7SS_EccA, type VII secretion AAA-ATPase EccA. This
model represents the AAA family ATPase, EccA, of the
actinobacterial flavor of type VII secretion systems.
Species such as Mycobacterium tuberculosis have several
instances of this system per genome, designated EccA1,
EccA2, etc [Protein fate, Protein and peptide secretion
and trafficking].
Length = 557
Score = 31.7 bits (72), Expect = 0.61
Identities = 21/60 (35%), Positives = 26/60 (43%), Gaps = 10/60 (16%)
Query: 215 LMAAEMDMP----SFKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNR 270
L AE +P S + G GTGKTT + R + K LGV PLV +R
Sbjct: 299 LARAERGLPVAQTSNHMLFAGPPGTGKTT-IARVVA-----KIYCGLGVLRKPLVREVSR 352
Score = 30.6 bits (69), Expect = 1.5
Identities = 20/59 (33%), Positives = 25/59 (42%), Gaps = 10/59 (16%)
Query: 1 MAAEMDMP----SFKCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNR 55
AE +P S + G GTGKTT + R + K LGV PLV +R
Sbjct: 300 ARAERGLPVAQTSNHMLFAGPPGTGKTT-IARVVA-----KIYCGLGVLRKPLVREVSR 352
>gnl|CDD|206689 cd04102, RabL3, Rab GTPase-like family 3 (Rab-like3). RabL3
(Rab-like3) subfamily. RabL3s are novel proteins that
have high sequence similarity with Rab family members,
but display features that are distinct from Rabs, and
have been termed Rab-like. As in other Rab-like
proteins, RabL3 lacks a prenylation site at the
C-terminus. The specific function of RabL3 remains
unknown.
Length = 204
Score = 31.0 bits (70), Expect = 0.79
Identities = 30/144 (20%), Positives = 52/144 (36%), Gaps = 29/144 (20%)
Query: 11 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGA-----IRFNVWDT 65
K +++GD G GK++ V + T+G V G +WD
Sbjct: 2 KVLVLGDSGVGKSSLVHLLCKNQVLGNPSWTVGCSVDVRHHTYGEGTPEEKTFYVELWDV 61
Query: 66 AGQ----EKFGGLRDGYYIQGQCAIIMFDVTSRITYKNVPNW-----HRDLVRV------ 110
G E R +Y Q I + D+T++ + +N+ W +RD
Sbjct: 62 GGSVGSAESVKSTRAVFYNQINGIIFVHDLTNKKSSQNLYRWSLEALNRDTFPAGLLVTN 121
Query: 111 --------CEN-IPIVLCGNKVDI 125
N +P+++ G K+D
Sbjct: 122 GDYDSEQFAGNPVPLLVIGTKLDQ 145
Score = 27.6 bits (61), Expect = 8.5
Identities = 23/100 (23%), Positives = 38/100 (38%), Gaps = 9/100 (9%)
Query: 226 KCVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGA-----IRFNVWDT 280
K +++GD G GK++ V + T+G V G +WD
Sbjct: 2 KVLVLGDSGVGKSSLVHLLCKNQVLGNPSWTVGCSVDVRHHTYGEGTPEEKTFYVELWDV 61
Query: 281 AGQ----EKFGGLRDGYYIQGQCAIIMFDVTSRITYKNYY 316
G E R +Y Q I + D+T++ + +N Y
Sbjct: 62 GGSVGSAESVKSTRAVFYNQINGIIFVHDLTNKKSSQNLY 101
>gnl|CDD|220219 pfam09392, MxiH, Type III secretion needle MxiH like. Type III
secretion systems are essential virulence determinants
for many gram-negative bacterial pathogens. MxiH is an
extracellular alpha helical needle that is required for
translocation of effector proteins into host cells. Once
inside, the effector proteins subvert normal cell
function to aid infection.
Length = 55
Score = 28.3 bits (64), Expect = 0.87
Identities = 9/29 (31%), Positives = 12/29 (41%)
Query: 194 SRIEQDLKEAQETALPDDDEDLMAAEMDM 222
Q L TA DD EDL+ + +
Sbjct: 2 DAFSQALGTGANTAASDDPEDLLELQRAL 30
>gnl|CDD|206720 cd04154, Arl2, Arf-like 2 (Arl2) GTPase. Arl2 (Arf-like 2)
GTPases are members of the Arf family that bind GDP and
GTP with very low affinity. Unlike most Arf family
proteins, Arl2 is not myristoylated at its N-terminal
helix. The protein PDE-delta, first identified in
photoreceptor rod cells, binds specifically to Arl2 and
is structurally very similar to RhoGDI. Despite the
high structural similarity between Arl2 and Rho
proteins and between PDE-delta and RhoGDI, the
interactions between the GTPases and their effectors
are very different. In its GTP bound form, Arl2
interacts with the protein Binder of Arl2 (BART), and
the complex is believed to play a role in mitochondrial
adenine nucleotide transport. In its GDP bound form,
Arl2 interacts with tubulin- folding Cofactor D; this
interaction is believed to play a role in regulation of
microtubule dynamics that impact the cytoskeleton, cell
division, and cytokinesis.
Length = 173
Score = 30.4 bits (69), Expect = 1.1
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 5/49 (10%)
Query: 21 GKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 69
GKTT +K+ GE TLG + L ++ + N+WD GQ+
Sbjct: 26 GKTTILKK-FNGEDISTISPTLGFNIKTLEYN----GYKLNIWDVGGQK 69
Score = 30.4 bits (69), Expect = 1.1
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 5/49 (10%)
Query: 236 GKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWDTAGQE 284
GKTT +K+ GE TLG + L ++ + N+WD GQ+
Sbjct: 26 GKTTILKK-FNGEDISTISPTLGFNIKTLEYN----GYKLNIWDVGGQK 69
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 30.2 bits (69), Expect = 1.6
Identities = 12/43 (27%), Positives = 19/43 (44%), Gaps = 3/43 (6%)
Query: 113 NIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYD---ISAKS 152
P++L NK+D K ++ KK L + + ISA
Sbjct: 114 KTPVILVVNKIDKVKPKTVLLKLIAFLKKLLPFKEIVPISALK 156
>gnl|CDD|201420 pfam00735, Septin, Septin. Members of this family include CDC3,
CDC10, CDC11 and CDC12/Septin. Members of this family
bind GTP. As regards the septins, these are
polypeptides of 30-65kDa with three characteristic
GTPase motifs (G-1, G-3 and G-4) that are similar to
those of the Ras family. The G-4 motif is strictly
conserved with a unique septin consensus of AKAD. Most
septins are thought to have at least one coiled-coil
region, which in some cases is necessary for
intermolecular interactions that allow septins to
polymerise to form rod-shaped complexes. In turn, these
are arranged into tandem arrays to form filaments. They
are multifunctional proteins, with roles in
cytokinesis, sporulation, germ cell development,
exocytosis and apoptosis.
Length = 280
Score = 30.0 bits (68), Expect = 1.7
Identities = 19/74 (25%), Positives = 30/74 (40%), Gaps = 14/74 (18%)
Query: 9 SFKCVLVGDGGTGKTTFVK----------RHLTGEFEKKYVATLGVEVHPLVFHTNRGAI 58
F ++VG+ G GKTT + R + G EK T+ ++ + + +
Sbjct: 4 DFTLMVVGESGLGKTTLINTLFLTDLIPERGIPGPSEKI-KKTVEIKATTVEIEEDGVKL 62
Query: 59 RFNVWDTAGQEKFG 72
V DT G FG
Sbjct: 63 NLTVIDTPG---FG 73
Score = 30.0 bits (68), Expect = 1.7
Identities = 19/74 (25%), Positives = 30/74 (40%), Gaps = 14/74 (18%)
Query: 224 SFKCVLVGDGGTGKTTFVK----------RHLTGEFEKKYVATLGVEVHPLVFHTNRGAI 273
F ++VG+ G GKTT + R + G EK T+ ++ + + +
Sbjct: 4 DFTLMVVGESGLGKTTLINTLFLTDLIPERGIPGPSEKI-KKTVEIKATTVEIEEDGVKL 62
Query: 274 RFNVWDTAGQEKFG 287
V DT G FG
Sbjct: 63 NLTVIDTPG---FG 73
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 30.2 bits (69), Expect = 1.7
Identities = 12/36 (33%), Positives = 18/36 (50%), Gaps = 4/36 (11%)
Query: 12 CVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVH 47
++ G GTGKTT VK+ + E E+ + V
Sbjct: 58 VLIYGPPGTGKTTTVKK-VFEELEE---IAVKVVYV 89
Score = 30.2 bits (69), Expect = 1.7
Identities = 12/36 (33%), Positives = 18/36 (50%), Gaps = 4/36 (11%)
Query: 227 CVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVH 262
++ G GTGKTT VK+ + E E+ + V
Sbjct: 58 VLIYGPPGTGKTTTVKK-VFEELEE---IAVKVVYV 89
>gnl|CDD|206726 cd04163, Era, E. coli Ras-like protein (Era) is a multifunctional
GTPase. Era (E. coli Ras-like protein) is a
multifunctional GTPase found in all bacteria except some
eubacteria. It binds to the 16S ribosomal RNA (rRNA) of
the 30S subunit and appears to play a role in the
assembly of the 30S subunit, possibly by chaperoning the
16S rRNA. It also contacts several assembly elements of
the 30S subunit. Era couples cell growth with
cytokinesis and plays a role in cell division and energy
metabolism. Homologs have also been found in eukaryotes.
Era contains two domains: the N-terminal GTPase domain
and a C-terminal domain KH domain that is critical for
RNA binding. Both domains are important for Era
function. Era is functionally able to compensate for
deletion of RbfA, a cold-shock adaptation protein that
is required for efficient processing of the 16S rRNA.
Length = 168
Score = 29.4 bits (67), Expect = 2.0
Identities = 11/49 (22%), Positives = 22/49 (44%), Gaps = 3/49 (6%)
Query: 113 NIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYD---ISAKSNYNFEK 158
P++L NK+D+ K ++ K+ + + ISA N ++
Sbjct: 111 KTPVILVLNKIDLVKDKEDLLPLLEKLKELHPFAEIFPISALKGENVDE 159
>gnl|CDD|234631 PRK00098, PRK00098, GTPase RsgA; Reviewed.
Length = 298
Score = 29.8 bits (68), Expect = 2.0
Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 7/57 (12%)
Query: 111 CE--NIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQY--YDISAKSNYNFE--KPFL 161
E I ++ NK+D+ D +A+ ++ + + Y ++SAK + KP L
Sbjct: 107 AEANGIKPIIVLNKIDLLDDLEEARELL-ALYRAIGYDVLELSAKEGEGLDELKPLL 162
>gnl|CDD|227352 COG5019, CDC3, Septin family protein [Cell division and
chromosome partitioning / Cytoskeleton].
Length = 373
Score = 30.0 bits (68), Expect = 2.4
Identities = 19/69 (27%), Positives = 28/69 (40%), Gaps = 13/69 (18%)
Query: 14 LVGDGGTGKTTFVK----RHLTGEFE------KKYVATLGVEVHPLVFHTNRGAIRFNVW 63
+VG+ G GKTTF+ L E E + TL +++ + + V
Sbjct: 28 VVGESGLGKTTFINTLFGTSLVDETEIDDIRAEGTSPTLEIKITKAELEEDGFHLNLTVI 87
Query: 64 DTAGQEKFG 72
DT G FG
Sbjct: 88 DTPG---FG 93
Score = 30.0 bits (68), Expect = 2.4
Identities = 19/69 (27%), Positives = 28/69 (40%), Gaps = 13/69 (18%)
Query: 229 LVGDGGTGKTTFVK----RHLTGEFE------KKYVATLGVEVHPLVFHTNRGAIRFNVW 278
+VG+ G GKTTF+ L E E + TL +++ + + V
Sbjct: 28 VVGESGLGKTTFINTLFGTSLVDETEIDDIRAEGTSPTLEIKITKAELEEDGFHLNLTVI 87
Query: 279 DTAGQEKFG 287
DT G FG
Sbjct: 88 DTPG---FG 93
>gnl|CDD|222165 pfam13481, AAA_25, AAA domain. This AAA domain is found in a wide
variety of presumed DNA repair proteins.
Length = 154
Score = 28.8 bits (65), Expect = 2.5
Identities = 10/50 (20%), Positives = 17/50 (34%), Gaps = 10/50 (20%)
Query: 202 EAQETALPDDDEDLMAAEMDMPSF----------KCVLVGDGGTGKTTFV 241
A+ + L + + A + +L G GTGK+T
Sbjct: 1 AAEPSELLPSSAEDLDAPPPPLRWLVKGLLPRGGLTLLAGAPGTGKSTLA 50
Score = 28.4 bits (64), Expect = 3.3
Identities = 7/19 (36%), Positives = 9/19 (47%)
Query: 8 PSFKCVLVGDGGTGKTTFV 26
+L G GTGK+T
Sbjct: 32 RGGLTLLAGAPGTGKSTLA 50
>gnl|CDD|222307 pfam13671, AAA_33, AAA domain. This family of domains contain
only a P-loop motif, that is characteristic of the AAA
superfamily. Many of the proteins in this family are
just short fragments so there is no Walker B motif.
Length = 143
Score = 28.8 bits (65), Expect = 2.7
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 13 VLVGDGGTGKTTFVKRHL 30
++VG G+GK+TF +R L
Sbjct: 3 LMVGLPGSGKSTFARRLL 20
Score = 28.8 bits (65), Expect = 2.7
Identities = 9/18 (50%), Positives = 14/18 (77%)
Query: 228 VLVGDGGTGKTTFVKRHL 245
++VG G+GK+TF +R L
Sbjct: 3 LMVGLPGSGKSTFARRLL 20
>gnl|CDD|234457 TIGR04075, bacter_Pnkp, polynucleotide kinase-phosphatase.
Members of this protein family are the bacterial
polynucleotide kinase-phosphatase (Pnkp) whose genes
occur paired with genes for the 3' terminal RNA ribose
2'-O-methyltransferase Hen1. All members of the seed
alignment belong to a cassette with the Hen1. The pair
acts in bacterial RNA repair. This enzyme performs
end-healing reactions on broken RNA, preparing from the
RNA ligase to close the break. The working hypothesis
is that the combination of Pnkp (RNA repair) and Hen1
(RNA modification) serves to first repair RNA damage
from ribotoxins and then perform a modification that
prevents the damage from recurring [Transcription, RNA
processing].
Length = 851
Score = 30.0 bits (68), Expect = 2.9
Identities = 10/17 (58%), Positives = 14/17 (82%)
Query: 13 VLVGDGGTGKTTFVKRH 29
VLVG G+GK+TF ++H
Sbjct: 12 VLVGASGSGKSTFARKH 28
Score = 30.0 bits (68), Expect = 2.9
Identities = 10/17 (58%), Positives = 14/17 (82%)
Query: 228 VLVGDGGTGKTTFVKRH 244
VLVG G+GK+TF ++H
Sbjct: 12 VLVGASGSGKSTFARKH 28
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 28.9 bits (64), Expect = 3.0
Identities = 16/134 (11%), Positives = 40/134 (29%), Gaps = 12/134 (8%)
Query: 8 PSFKCVLVGDGGTGKTTFVK---RHLTGEFEKKYVATLGVEVHPLVFHTNRGAIRFNVWD 64
P ++VG G+GKTT + R L + ++ +
Sbjct: 1 PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60
Query: 65 TAGQEKFGGLRDGYYIQGQCAIIMFD--------VTSRITYKNVPNWHRDLVRVCENIPI 116
+G+ + + + +++ D + L++ +N+ +
Sbjct: 61 GSGELRLRLALALAR-KLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLTV 119
Query: 117 VLCGNKVDIKDRKV 130
+L N +
Sbjct: 120 ILTTNDEKDLGPAL 133
>gnl|CDD|224071 COG1149, COG1149, MinD superfamily P-loop ATPase containing an
inserted ferredoxin domain [Energy production and
conversion].
Length = 284
Score = 29.2 bits (66), Expect = 3.6
Identities = 13/31 (41%), Positives = 14/31 (45%), Gaps = 1/31 (3%)
Query: 12 CVLVGDGGTGKTTFVKRHLTGEFEKKYVATL 42
V G GGTGKTT +L KY L
Sbjct: 5 AVASGKGGTGKTTVAA-NLAVLLGDKYKLVL 34
Score = 29.2 bits (66), Expect = 3.6
Identities = 13/31 (41%), Positives = 14/31 (45%), Gaps = 1/31 (3%)
Query: 227 CVLVGDGGTGKTTFVKRHLTGEFEKKYVATL 257
V G GGTGKTT +L KY L
Sbjct: 5 AVASGKGGTGKTTVAA-NLAVLLGDKYKLVL 34
>gnl|CDD|223645 COG0572, Udk, Uridine kinase [Nucleotide transport and
metabolism].
Length = 218
Score = 28.8 bits (65), Expect = 3.6
Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 4/39 (10%)
Query: 5 MDMPSFKCVLV---GDGGTGKTTFVKRHLTGEFEKKYVA 40
M K +++ G G+GKTT K L+ + + V
Sbjct: 1 MMKKPEKVIIIGIAGGSGSGKTTVAKE-LSEQLGVEKVV 38
Score = 28.8 bits (65), Expect = 3.6
Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 4/39 (10%)
Query: 220 MDMPSFKCVLV---GDGGTGKTTFVKRHLTGEFEKKYVA 255
M K +++ G G+GKTT K L+ + + V
Sbjct: 1 MMKKPEKVIIIGIAGGSGSGKTTVAKE-LSEQLGVEKVV 38
>gnl|CDD|239386 cd03112, CobW_like, The function of this protein family is
unkown. The amino acid sequence of YjiA protein in E.
coli contains several conserved motifs that
characterizes it as a P-loop GTPase. YijA gene is among
the genes significantly induced in response to
DNA-damage caused by mitomycin. YijA gene is a
homologue of the CobW gene which encodes the cobalamin
synthesis protein/P47K.
Length = 158
Score = 28.4 bits (64), Expect = 3.7
Identities = 11/26 (42%), Positives = 14/26 (53%)
Query: 13 VLVGDGGTGKTTFVKRHLTGEFEKKY 38
VL G G GKTT + LT + +K
Sbjct: 4 VLTGFLGAGKTTLLNHILTEQHGRKI 29
Score = 28.4 bits (64), Expect = 3.7
Identities = 11/26 (42%), Positives = 14/26 (53%)
Query: 228 VLVGDGGTGKTTFVKRHLTGEFEKKY 253
VL G G GKTT + LT + +K
Sbjct: 4 VLTGFLGAGKTTLLNHILTEQHGRKI 29
>gnl|CDD|206691 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta), together with SR-alpha, forms the
heterodimeric signal recognition particle (SRP). Signal
recognition particle receptor, beta subunit (SR-beta).
SR-beta and SR-alpha form the heterodimeric signal
recognition particle (SRP or SR) receptor that binds SRP
to regulate protein translocation across the ER
membrane. Nascent polypeptide chains are synthesized
with an N-terminal hydrophobic signal sequence that
binds SRP54, a component of the SRP. SRP directs
targeting of the ribosome-nascent chain complex (RNC) to
the ER membrane via interaction with the SR, which is
localized to the ER membrane. The RNC is then
transferred to the protein-conducting channel, or
translocon, which facilitates polypeptide translation
across the ER membrane or integration into the ER
membrane. SR-beta is found only in eukaryotes; it is
believed to control the release of the signal sequence
from SRP54 upon binding of the ribosome to the
translocon. High expression of SR-beta has been observed
in human colon cancer, suggesting it may play a role in
the development of this type of cancer.
Length = 202
Score = 28.8 bits (65), Expect = 3.8
Identities = 31/123 (25%), Positives = 51/123 (41%), Gaps = 16/123 (13%)
Query: 13 VLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGAIR-FNVWDTAGQEKF 71
+L+G +GKT + TG+ + F++N + + D G EK
Sbjct: 4 LLLGPSDSGKTALFTKLTTGKVRSTVTSIEPNVA---SFYSNSSKGKKLTLVDVPGHEK- 59
Query: 72 GGLRDGY--YIQGQCAIIMFDVTSRITYKNV-------PNWHRDLVRVCENIPIVLCGNK 122
LRD Y++ I+F V S KN+ + DL ++ IPI++ NK
Sbjct: 60 --LRDKLLEYLKASLKAIVFVVDSATFQKNIRDVAEFLYDILTDLEKIKNKIPILIACNK 117
Query: 123 VDI 125
D+
Sbjct: 118 QDL 120
>gnl|CDD|238977 cd02019, NK, Nucleoside/nucleotide kinase (NK) is a protein
superfamily consisting of multiple families of enzymes
that share structural similarity and are functionally
related to the catalysis of the reversible phosphate
group transfer from nucleoside triphosphates to
nucleosides/nucleotides, nucleoside monophosphates, or
sugars. Members of this family play a wide variety of
essential roles in nucleotide metabolism, the
biosynthesis of coenzymes and aromatic compounds, as
well as the metabolism of sugar and sulfate.
Length = 69
Score = 26.9 bits (60), Expect = 3.8
Identities = 10/41 (24%), Positives = 17/41 (41%), Gaps = 3/41 (7%)
Query: 13 VLVGDGGTGKTTFVKRHLTGEFEKK--YVATLGVEVHPLVF 51
+ G G+GK+T K+ L + + V V + L
Sbjct: 3 AITGGSGSGKSTVAKK-LAEQLGGRSVVVLDEIVILEGLYA 42
Score = 26.9 bits (60), Expect = 3.8
Identities = 10/41 (24%), Positives = 17/41 (41%), Gaps = 3/41 (7%)
Query: 228 VLVGDGGTGKTTFVKRHLTGEFEKK--YVATLGVEVHPLVF 266
+ G G+GK+T K+ L + + V V + L
Sbjct: 3 AITGGSGSGKSTVAKK-LAEQLGGRSVVVLDEIVILEGLYA 42
>gnl|CDD|213204 cd03237, ABC_RNaseL_inhibitor_domain2, The ATP-binding cassette
domain 2 of RNase L inhibitor. The ABC ATPase, RNase L
inhibitor (RLI), is a key enzyme in ribosomal
biogenesis, formation of translation preinitiation
complexes, and assembly of HIV capsids. RLI's are not
transport proteins and thus cluster with a group of
soluble proteins that lack the transmembrane components
commonly found in other members of the family.
Structurally, RLI's have an N-terminal Fe-S domain and
two nucleotide-binding domains which are arranged to
form two composite active sites in their interface
cleft. RLI is one of the most conserved enzymes between
archaea and eukaryotes with a sequence identity of more
than 48%. The high degree of evolutionary conservation
suggests that RLI performs a central role in archaeal
and eukaryotic physiology.
Length = 246
Score = 28.9 bits (65), Expect = 3.9
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 13 VLVGDGGTGKTTFVK 27
++G G GKTTF+K
Sbjct: 29 GILGPNGIGKTTFIK 43
Score = 28.9 bits (65), Expect = 3.9
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 228 VLVGDGGTGKTTFVK 242
++G G GKTTF+K
Sbjct: 29 GILGPNGIGKTTFIK 43
>gnl|CDD|226929 COG4559, COG4559, ABC-type hemin transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 259
Score = 28.9 bits (65), Expect = 4.4
Identities = 9/23 (39%), Positives = 14/23 (60%), Gaps = 1/23 (4%)
Query: 13 VLVGDGGTGKTTFVKRHLTGEFE 35
++G G GK+T +K L+GE
Sbjct: 31 AILGPNGAGKSTLLK-ALSGELS 52
Score = 28.9 bits (65), Expect = 4.4
Identities = 9/23 (39%), Positives = 14/23 (60%), Gaps = 1/23 (4%)
Query: 228 VLVGDGGTGKTTFVKRHLTGEFE 250
++G G GK+T +K L+GE
Sbjct: 31 AILGPNGAGKSTLLK-ALSGELS 52
>gnl|CDD|223873 COG0802, COG0802, Predicted ATPase or kinase [General function
prediction only].
Length = 149
Score = 28.0 bits (63), Expect = 4.4
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 13 VLVGDGGTGKTTFVK 27
+L GD G GKTT V+
Sbjct: 29 LLSGDLGAGKTTLVR 43
Score = 28.0 bits (63), Expect = 4.4
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 228 VLVGDGGTGKTTFVK 242
+L GD G GKTT V+
Sbjct: 29 LLSGDLGAGKTTLVR 43
>gnl|CDD|216999 pfam02367, UPF0079, Uncharacterized P-loop hydrolase UPF0079.
This uncharacterized family contains a P-loop.
Length = 123
Score = 27.6 bits (62), Expect = 4.9
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 13 VLVGDGGTGKTTFVK 27
+L GD G GKTTFV+
Sbjct: 19 LLSGDLGAGKTTFVR 33
Score = 27.6 bits (62), Expect = 4.9
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 228 VLVGDGGTGKTTFVK 242
+L GD G GKTTFV+
Sbjct: 19 LLSGDLGAGKTTFVR 33
>gnl|CDD|218719 pfam05729, NACHT, NACHT domain. This NTPase domain is found in
apoptosis proteins as well as those involved in MHC
transcription activation. This family is closely
related to pfam00931.
Length = 165
Score = 28.0 bits (63), Expect = 5.1
Identities = 7/17 (41%), Positives = 13/17 (76%)
Query: 12 CVLVGDGGTGKTTFVKR 28
+L G+ G+GKTT +++
Sbjct: 3 VILQGEAGSGKTTLLQK 19
Score = 28.0 bits (63), Expect = 5.1
Identities = 7/17 (41%), Positives = 13/17 (76%)
Query: 227 CVLVGDGGTGKTTFVKR 243
+L G+ G+GKTT +++
Sbjct: 3 VILQGEAGSGKTTLLQK 19
>gnl|CDD|237612 PRK14108, PRK14108, bifunctional glutamine-synthetase
adenylyltransferase/deadenyltransferase; Provisional.
Length = 986
Score = 28.8 bits (65), Expect = 5.3
Identities = 25/77 (32%), Positives = 32/77 (41%), Gaps = 13/77 (16%)
Query: 195 RIEQDLKEAQETALPDDDEDLMA-AEM----DMPSFKCVLVGDGGTGKTTFVKRHLTGEF 249
RI Q + + Q LP+DDE L A M D SF L+ V+ H F
Sbjct: 415 RI-QMVADEQTHLLPEDDEALERFARMMGYEDRASFAEDLLAVLKV-----VEGHYAALF 468
Query: 250 EKKYVATLGVEVHPLVF 266
E+ L E+ LVF
Sbjct: 469 EQ--EPELSAELGNLVF 483
>gnl|CDD|184037 PRK13409, PRK13409, putative ATPase RIL; Provisional.
Length = 590
Score = 28.6 bits (65), Expect = 5.9
Identities = 11/21 (52%), Positives = 12/21 (57%), Gaps = 1/21 (4%)
Query: 15 VGDGGTGKTTFVKRHLTGEFE 35
VG G GKTTF K L G +
Sbjct: 371 VGPNGIGKTTFAKL-LAGVLK 390
Score = 28.6 bits (65), Expect = 5.9
Identities = 11/21 (52%), Positives = 12/21 (57%), Gaps = 1/21 (4%)
Query: 230 VGDGGTGKTTFVKRHLTGEFE 250
VG G GKTTF K L G +
Sbjct: 371 VGPNGIGKTTFAKL-LAGVLK 390
>gnl|CDD|206744 cd11384, RagA_like, Rag GTPase, subfamily of Ras-related GTPases,
includes Ras-related GTP-binding proteins A and B. RagA
and RagB are closely related Rag GTPases (ras-related
GTP-binding protein A and B) that constitute a unique
subgroup of the Ras superfamily, and are functional
homologs of Saccharomyces cerevisiae Gtr1. These domains
function by forming heterodimers with RagC or RagD, and
similarly, Gtr1 dimerizes with Gtr2, through the
carboxy-terminal segments. They play an essential role
in regulating amino acid-induced target of rapamycin
complex 1 (TORC1) kinase signaling, exocytic cargo
sorting at endosomes, and epigenetic control of gene
expression. In response to amino acids, the Rag GTPases
guide the TORC1 complex to activate the platform
containing Rheb proto-oncogene by driving the
relocalization of mTORC1 from discrete locations in the
cytoplasm to a late endosomal and/or lysosomal
compartment that is Rheb-enriched and contains Rab-7.
Length = 286
Score = 28.3 bits (64), Expect = 6.0
Identities = 23/79 (29%), Positives = 33/79 (41%), Gaps = 27/79 (34%)
Query: 40 ATLGVEVHPLVFHTNRGAIRF------NVWDTAGQEKF-----GGLRDGYYIQGQCAIIM 88
AT+ VE H++ +RF N+WD GQ+ F RD + + I +
Sbjct: 33 ATIDVE------HSH---VRFLGNLVLNLWDCGGQDAFMENYFTSQRDHIFRNVEVLIYV 83
Query: 89 FDVTSRITYKNVPNWHRDL 107
FDV SR +DL
Sbjct: 84 FDVESR-------ELEKDL 95
Score = 27.9 bits (63), Expect = 8.1
Identities = 21/66 (31%), Positives = 30/66 (45%), Gaps = 20/66 (30%)
Query: 255 ATLGVEVHPLVFHTNRGAIRF------NVWDTAGQEKF-----GGLRDGYYIQGQCAIIM 303
AT+ VE H++ +RF N+WD GQ+ F RD + + I +
Sbjct: 33 ATIDVE------HSH---VRFLGNLVLNLWDCGGQDAFMENYFTSQRDHIFRNVEVLIYV 83
Query: 304 FDVTSR 309
FDV SR
Sbjct: 84 FDVESR 89
>gnl|CDD|239384 cd03110, Fer4_NifH_child, This protein family's function is
unkown. It contains nucleotide binding site. It uses
NTP as energy source to transfer electron or ion.
Length = 179
Score = 28.0 bits (63), Expect = 6.0
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 12 CVLVGDGGTGKTTFV 26
V+ G GGTGKTT
Sbjct: 3 AVISGKGGTGKTTVT 17
Score = 28.0 bits (63), Expect = 6.0
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 227 CVLVGDGGTGKTTFV 241
V+ G GGTGKTT
Sbjct: 3 AVISGKGGTGKTTVT 17
>gnl|CDD|100014 cd00286, Tubulin_FtsZ, Tubulin/FtsZ: Family includes tubulin
alpha-, beta-, gamma-, delta-, and epsilon-tubulins as
well as FtsZ, all of which are involved in polymer
formation. Tubulin is the major component of
microtubules, but also exists as a heterodimer and as a
curved oligomer. Microtubules exist in all eukaryotic
cells and are responsible for many functions, including
cellular transport, cell motility, and mitosis. FtsZ
forms a ring-shaped septum at the site of bacterial cell
division, which is required for constriction of cell
membrane and cell envelope to yield two daughter cells.
FtsZ can polymerize into tubes, sheets, and rings in
vitro and is ubiquitous in eubacteria, archaea, and
chloroplasts.
Length = 328
Score = 28.5 bits (64), Expect = 6.5
Identities = 8/33 (24%), Positives = 13/33 (39%)
Query: 12 CVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGV 44
L G G+G + L E+ K+ T +
Sbjct: 96 HSLGGGTGSGLGPVLAERLKDEYPKRLKITFSI 128
Score = 28.5 bits (64), Expect = 6.5
Identities = 8/33 (24%), Positives = 13/33 (39%)
Query: 227 CVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGV 259
L G G+G + L E+ K+ T +
Sbjct: 96 HSLGGGTGSGLGPVLAERLKDEYPKRLKITFSI 128
>gnl|CDD|222290 pfam13654, AAA_32, AAA domain. This family includes a wide
variety of AAA domains including some that have lost
essential nucleotide binding residues in the P-loop.
Length = 509
Score = 28.6 bits (65), Expect = 6.6
Identities = 10/30 (33%), Positives = 18/30 (60%)
Query: 1 MAAEMDMPSFKCVLVGDGGTGKTTFVKRHL 30
+ P + ++G+ GTG+TT V+R+L
Sbjct: 22 FGLGIRHPGYNIFVLGEPGTGRTTLVRRYL 51
Score = 28.6 bits (65), Expect = 6.6
Identities = 10/30 (33%), Positives = 18/30 (60%)
Query: 216 MAAEMDMPSFKCVLVGDGGTGKTTFVKRHL 245
+ P + ++G+ GTG+TT V+R+L
Sbjct: 22 FGLGIRHPGYNIFVLGEPGTGRTTLVRRYL 51
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 27.2 bits (61), Expect = 6.8
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 12 CVLVGDGGTGKTTFVKRHL 30
VL G+ G+GKTT ++R
Sbjct: 7 GVLTGESGSGKTTLLRRLA 25
Score = 27.2 bits (61), Expect = 6.8
Identities = 9/19 (47%), Positives = 13/19 (68%)
Query: 227 CVLVGDGGTGKTTFVKRHL 245
VL G+ G+GKTT ++R
Sbjct: 7 GVLTGESGSGKTTLLRRLA 25
>gnl|CDD|218203 pfam04670, Gtr1_RagA, Gtr1/RagA G protein conserved region. GTR1
was first identified in S. cerevisiae as a suppressor of
a mutation in RCC1. Biochemical analysis revealed that
Gtr1 is in fact a G protein of the Ras family. The
RagA/B proteins are the human homologues of Gtr1.
Included in this family is the human Rag C, a novel
protein that has been shown to interact with RagA/B.
Length = 230
Score = 27.9 bits (63), Expect = 7.0
Identities = 30/117 (25%), Positives = 46/117 (39%), Gaps = 25/117 (21%)
Query: 226 KCVLVGDGGTGKTTFVKR--HLTGEFEKKYV-ATLGVE---VHPLVFHTNRGAIRFNVWD 279
K +L+G G+GK++ + + AT+ VE V L G + N+WD
Sbjct: 1 KVLLMGLRGSGKSSMRSIIFSNYSPRDTLRLGATIDVEQSHVRFL------GNLTLNLWD 54
Query: 280 TAGQEKF---GGLRDGYYIQGQCAIIM--FDVTSR------ITYKNYYDISAKSNYN 325
GQ+ F R +I +++ FDV SR T I A Y+
Sbjct: 55 CPGQDDFMENYLTRQKEHIFSNVGVLIYVFDVESREYEEDLATLVKI--IEALYQYS 109
Score = 27.9 bits (63), Expect = 8.3
Identities = 28/110 (25%), Positives = 44/110 (40%), Gaps = 24/110 (21%)
Query: 11 KCVLVGDGGTGKTTFVKR--HLTGEFEKKYV-ATLGVE---VHPLVFHTNRGAIRFNVWD 64
K +L+G G+GK++ + + AT+ VE V L G + N+WD
Sbjct: 1 KVLLMGLRGSGKSSMRSIIFSNYSPRDTLRLGATIDVEQSHVRFL------GNLTLNLWD 54
Query: 65 TAGQEKF---GGLRDGYYIQGQCAIIM--FDVTSRITYKNVPNWHRDLVR 109
GQ+ F R +I +++ FDV SR + DL
Sbjct: 55 CPGQDDFMENYLTRQKEHIFSNVGVLIYVFDVESR-------EYEEDLAT 97
>gnl|CDD|218745 pfam05783, DLIC, Dynein light intermediate chain (DLIC). This
family consists of several eukaryotic dynein light
intermediate chain proteins. The light intermediate
chains (LICs) of cytoplasmic dynein consist of multiple
isoforms, which undergo post-translational modification
to produce a large number of species. DLIC1 is known to
be involved in assembly, organisation, and function of
centrosomes and mitotic spindles when bound to
pericentrin. DLIC2 is a subunit of cytoplasmic dynein 2
that may play a role in maintaining Golgi organisation
by binding cytoplasmic dynein 2 to its Golgi-associated
cargo.
Length = 490
Score = 28.3 bits (63), Expect = 7.5
Identities = 15/32 (46%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 7 MPSFKCVLV-GDGGTGKTTFVKRHLTGEFEKK 37
+PS K VLV G+ G+GKTT + + E KK
Sbjct: 42 LPSGKNVLVLGEDGSGKTTLIAKLQGVEHPKK 73
Score = 28.3 bits (63), Expect = 7.5
Identities = 15/32 (46%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 222 MPSFKCVLV-GDGGTGKTTFVKRHLTGEFEKK 252
+PS K VLV G+ G+GKTT + + E KK
Sbjct: 42 LPSGKNVLVLGEDGSGKTTLIAKLQGVEHPKK 73
>gnl|CDD|206748 cd01855, YqeH, Circularly permuted YqeH GTPase. YqeH is an
essential GTP-binding protein. Depletion of YqeH induces
an excess initiation of DNA replication, suggesting that
it negatively controls initiation of chromosome
replication. The YqeH subfamily is common in eukaryotes
and sporadically present in bacteria with probable
acquisition by plants from chloroplasts. Proteins of the
YqeH family contain all sequence motifs typical of the
vast class of P-loop-containing GTPases, but show a
circular permutation, with a G4-G1-G3 pattern of motifs
as opposed to the regular G1-G3-G4 pattern seen in most
GTPases.
Length = 191
Score = 27.6 bits (62), Expect = 7.6
Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 8/52 (15%)
Query: 115 PIVLCGNKVDI--KDRKV-KAKSIVFHRKKNLQYYD-----ISAKSNYNFEK 158
P++L GNK+D+ KD K + K V R K +SAK + E+
Sbjct: 62 PVILVGNKIDLLPKDVKPNRLKQWVKKRLKIGGLKIKDVILVSAKKGWGVEE 113
>gnl|CDD|213189 cd03222, ABC_RNaseL_inhibitor, ATP-binding cassette domain of
RNase L inhibitor. The ABC ATPase RNase L inhibitor
(RLI) is a key enzyme in ribosomal biogenesis,
formation of translation preinitiation complexes, and
assembly of HIV capsids. RLI's are not transport
proteins, and thus cluster with a group of soluble
proteins that lack the transmembrane components
commonly found in other members of the family.
Structurally, RLI's have an N-terminal Fe-S domain and
two nucleotide-binding domains, which are arranged to
form two composite active sites in their interface
cleft. RLI is one of the most conserved enzymes between
archaea and eukaryotes with a sequence identity more
than 48%. The high degree of evolutionary conservation
suggests that RLI performs a central role in archaeal
and eukaryotic physiology.
Length = 177
Score = 27.5 bits (61), Expect = 8.9
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 13 VLVGDGGTGKTTFVK 27
+VG GTGKTT VK
Sbjct: 29 GIVGPNGTGKTTAVK 43
Score = 27.5 bits (61), Expect = 8.9
Identities = 10/15 (66%), Positives = 11/15 (73%)
Query: 228 VLVGDGGTGKTTFVK 242
+VG GTGKTT VK
Sbjct: 29 GIVGPNGTGKTTAVK 43
>gnl|CDD|213834 TIGR03597, GTPase_YqeH, ribosome biogenesis GTPase YqeH. This
family describes YqeH, a member of a larger family of
GTPases involved in ribosome biogenesis. Like YqlF, it
shows a cyclical permutation relative to GTPases EngA
(in which the GTPase domain is duplicated), Era, and
others. Members of this protein family are found in a
relatively small number of bacterial species, including
Bacillus subtilis but not Escherichia coli [Protein
synthesis, Other].
Length = 360
Score = 28.0 bits (63), Expect = 9.0
Identities = 14/60 (23%), Positives = 25/60 (41%), Gaps = 8/60 (13%)
Query: 115 PIVLCGNKVDIKDRKVKAKSI---VFHRKKNLQYYD-----ISAKSNYNFEKPFLWLARK 166
P++L GNK+D+ + V I + R K L +SAK ++ + +
Sbjct: 92 PVLLVGNKIDLLPKSVNLSKIKEWMKKRAKELGLKPVDIILVSAKKGNGIDELLDKIKKA 151
>gnl|CDD|226984 COG4637, COG4637, Predicted ATPase [General function prediction
only].
Length = 373
Score = 27.8 bits (62), Expect = 9.1
Identities = 6/22 (27%), Positives = 13/22 (59%), Gaps = 1/22 (4%)
Query: 4 EMDMPSFKCVLVGDGGTGKTTF 25
++++ V++G G GK+ F
Sbjct: 18 DLEIRRV-NVIIGANGAGKSNF 38
Score = 27.8 bits (62), Expect = 9.1
Identities = 6/22 (27%), Positives = 13/22 (59%), Gaps = 1/22 (4%)
Query: 219 EMDMPSFKCVLVGDGGTGKTTF 240
++++ V++G G GK+ F
Sbjct: 18 DLEIRRV-NVIIGANGAGKSNF 38
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 27.7 bits (63), Expect = 9.6
Identities = 14/50 (28%), Positives = 20/50 (40%), Gaps = 11/50 (22%)
Query: 113 NIPIVLCGNKVDIKDRKVKAKSIVFHRKKNL-QYYD------ISAKSNYN 155
P++L NK+D VK K + + L + D ISA N
Sbjct: 113 KTPVILVLNKID----LVKDKEELLPLLEELSELMDFAEIVPISALKGDN 158
>gnl|CDD|163592 TIGR03880, KaiC_arch_3, KaiC domain protein, AF_0351 family.
This model represents a rather narrowly distributed
archaeal protein family in which members have a single
copy of the KaiC domain. This stands in contrast to the
circadian clock protein KaiC itself, with two copies of
the domain. Members are expected to have weak ATPase
activity, by homology to the
autokinase/autophosphorylase KaiC itself.
Length = 224
Score = 27.7 bits (62), Expect = 9.8
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 12 CVLVGDGGTGKTTF 25
V++G+ GTGKTTF
Sbjct: 19 IVVIGEYGTGKTTF 32
Score = 27.7 bits (62), Expect = 9.8
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 227 CVLVGDGGTGKTTF 240
V++G+ GTGKTTF
Sbjct: 19 IVVIGEYGTGKTTF 32
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.321 0.138 0.428
Gapped
Lambda K H
0.267 0.0534 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,652,848
Number of extensions: 2050156
Number of successful extensions: 3327
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3060
Number of HSP's successfully gapped: 318
Length of query: 385
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 286
Effective length of database: 6,546,556
Effective search space: 1872315016
Effective search space used: 1872315016
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 60 (27.3 bits)