RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15725
(355 letters)
>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 = 281 bits (720), Expect = 1e-95
Identities = 131/216 (60%), Positives = 142/216 (65%), Gaps = 64/216 (29%)
Query: 14 FKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGIDF 73
KLVFLG+QSVGKTS+ITRFMYD+FDN YQATI GIDF
Sbjct: 1 HKLVFLGDQSVGKTSIITRFMYDTFDNQYQATI-----------------------GIDF 37
Query: 74 LSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDD 133
LSKTMY++D+TVRLQLWDTAGQERFRSLIPSYIRDS+VAVVVYDITN
Sbjct: 38 LSKTMYVDDKTVRLQLWDTAGQERFRSLIPSYIRDSSVAVVVYDITN------------- 84
Query: 134 VRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGNKTD 193
SF T KWIDDVR ERG+DVII+LVGNKTD
Sbjct: 85 ----------------------------RQSFDNTDKWIDDVRDERGNDVIIVLVGNKTD 116
Query: 194 LSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQ 229
LSDKRQVSTEEGE+KAKE N MFIETSAKAG+NVKQ
Sbjct: 117 LSDKRQVSTEEGEKKAKENNAMFIETSAKAGHNVKQ 152
Score = 229 bits (585), Expect = 3e-75
Identities = 97/118 (82%), Positives = 106/118 (89%)
Query: 225 YNVKQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERG 284
+ K VRLQLWDTAGQERFRSLIPSYIRDS+VAVVVYDITN SF T KWIDDVR ERG
Sbjct: 44 VDDKTVRLQLWDTAGQERFRSLIPSYIRDSSVAVVVYDITNRQSFDNTDKWIDDVRDERG 103
Query: 285 SDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVAAAL 342
+DVII+LVGNKTDLSDKRQVSTEEGE+KAKE N MFIETSAKAG+NVKQLF+++A AL
Sbjct: 104 NDVIIVLVGNKTDLSDKRQVSTEEGEKKAKENNAMFIETSAKAGHNVKQLFKKIAQAL 161
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 207 bits (529), Expect = 9e-67
Identities = 72/184 (39%), Positives = 103/184 (55%), Gaps = 41/184 (22%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
VGK+SL++RF F Y++TIG+DF +KT+ ++ + V+LQ+WDTAGQERFRS+ SY
Sbjct: 11 VGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIEVDGKRVKLQIWDTAGQERFRSITSSYY 70
Query: 107 RDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFH 166
R + A++VYDITN SF W+ ++R +A+
Sbjct: 71 RGAVGALLVYDITNRESFENLENWLKELRE------------------------YAS--- 103
Query: 167 QTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYN 226
+V+IMLVGNK+DL ++RQVS EE E A+E + F ETSAK N
Sbjct: 104 --------------PNVVIMLVGNKSDLEEQRQVSREEAEAFAEEHGLPFFETSAKTNTN 149
Query: 227 VKQV 230
V++
Sbjct: 150 VEEA 153
Score = 175 bits (446), Expect = 3e-54
Identities = 58/112 (51%), Positives = 78/112 (69%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDV 287
K+V+LQ+WDTAGQERFRS+ SY R + A++VYDITN SF W+ ++R +V
Sbjct: 47 KRVKLQIWDTAGQERFRSITSSYYRGAVGALLVYDITNRESFENLENWLKELREYASPNV 106
Query: 288 IIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVA 339
+IMLVGNK+DL ++RQVS EE E A+E + F ETSAK NV++ F +A
Sbjct: 107 VIMLVGNKSDLEEQRQVSREEAEAFAEEHGLPFFETSAKTNTNVEEAFEELA 158
>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 = 200 bits (510), Expect = 7e-64
Identities = 75/184 (40%), Positives = 103/184 (55%), Gaps = 41/184 (22%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
VGK+SL+ RF + F Y TIG+DF +KT+ ++ +TV+LQ+WDTAGQERFR+L P Y
Sbjct: 10 VGKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAGQERFRALRPLYY 69
Query: 107 RDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFH 166
R + ++VYDIT+ +SF KW++++ HA
Sbjct: 70 RGAQGFLLVYDITSRDSFENVKKWLEEIL------------------------RHA---- 101
Query: 167 QTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYN 226
+V I+LVGNK DL D+R VSTEEGE AKEL + F+ETSAK N
Sbjct: 102 -------------DENVPIVLVGNKCDLEDQRVVSTEEGEALAKELGLPFMETSAKTNEN 148
Query: 227 VKQV 230
V++
Sbjct: 149 VEEA 152
Score = 170 bits (434), Expect = 2e-52
Identities = 59/116 (50%), Positives = 80/116 (68%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDV 287
K V+LQ+WDTAGQERFR+L P Y R + ++VYDIT+ +SF KW++++ +V
Sbjct: 46 KTVKLQIWDTAGQERFRALRPLYYRGAQGFLLVYDITSRDSFENVKKWLEEILRHADENV 105
Query: 288 IIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVAAALP 343
I+LVGNK DL D+R VSTEEGE AKEL + F+ETSAK NV++ F +A +
Sbjct: 106 PIVLVGNKCDLEDQRVVSTEEGEALAKELGLPFMETSAKTNENVEEAFEELAREIL 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 = 199 bits (509), Expect = 9e-64
Identities = 79/221 (35%), Positives = 114/221 (51%), Gaps = 64/221 (28%)
Query: 14 FKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGIDF 73
FK+V +G+ VGKTSL+ RF+ + F Y++TI G+DF
Sbjct: 1 FKIVLIGDSGVGKTSLLLRFVDNKFSENYKSTI-----------------------GVDF 37
Query: 74 LSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDD 133
SKT+ ++ + V+LQ+WDTAGQERFRS+ SY R + A++VYD+TN SF KW+++
Sbjct: 38 KSKTIEVDGKKVKLQIWDTAGQERFRSITSSYYRGAHGAILVYDVTNRESFENLDKWLNE 97
Query: 134 VRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGNKTD 193
++ E ++ I+LVGNK+D
Sbjct: 98 LK-EYAPP----------------------------------------NIPIILVGNKSD 116
Query: 194 LSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQVRLQL 234
L D+RQVSTEE ++ AKE ++F ETSAK G NV + L
Sbjct: 117 LEDERQVSTEEAQQFAKENGLLFFETSAKTGENVDEAFESL 157
Score = 172 bits (439), Expect = 3e-53
Identities = 58/115 (50%), Positives = 83/115 (72%)
Query: 225 YNVKQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERG 284
+ K+V+LQ+WDTAGQERFRS+ SY R + A++VYD+TN SF KW+++++
Sbjct: 44 VDGKKVKLQIWDTAGQERFRSITSSYYRGAHGAILVYDVTNRESFENLDKWLNELKEYAP 103
Query: 285 SDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVA 339
++ I+LVGNK+DL D+RQVSTEE ++ AKE ++F ETSAK G NV + F +A
Sbjct: 104 PNIPIILVGNKSDLEDERQVSTEEAQQFAKENGLLFFETSAKTGENVDEAFESLA 158
>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 = 185 bits (472), Expect = 3e-58
Identities = 76/224 (33%), Positives = 111/224 (49%), Gaps = 64/224 (28%)
Query: 13 KFKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGID 72
+FKLV LG+ SVGK+S++ RF+ + F Q + TIG
Sbjct: 1 QFKLVLLGDSSVGKSSIVLRFVKNEFSE-NQES----------------------TIGAA 37
Query: 73 FLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWID 132
FL++T+ L+D TV+ ++WDTAGQER+RSL P Y R + A+VVYDIT+ SF + W+
Sbjct: 38 FLTQTVNLDDTTVKFEIWDTAGQERYRSLAPMYYRGAAAAIVVYDITSEESFEKAKSWVK 97
Query: 133 DVRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGNKT 192
+++ H +++I L GNK
Sbjct: 98 ELQ------------------------EHGP-----------------PNIVIALAGNKA 116
Query: 193 DLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQVRLQLWD 236
DL KRQVSTEE + A E ++F+ETSAK G NV ++ ++
Sbjct: 117 DLESKRQVSTEEAQEYADENGLLFMETSAKTGENVNELFTEIAR 160
Score = 163 bits (414), Expect = 2e-49
Identities = 56/115 (48%), Positives = 77/115 (66%)
Query: 229 QVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVI 288
V+ ++WDTAGQER+RSL P Y R + A+VVYDIT+ SF + W+ +++ +++
Sbjct: 49 TVKFEIWDTAGQERYRSLAPMYYRGAAAAIVVYDITSEESFEKAKSWVKELQEHGPPNIV 108
Query: 289 IMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVAAALP 343
I L GNK DL KRQVSTEE + A E ++F+ETSAK G NV +LF +A LP
Sbjct: 109 IALAGNKADLESKRQVSTEEAQEYADENGLLFMETSAKTGENVNELFTEIARKLP 163
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 174 bits (443), Expect = 7e-54
Identities = 96/172 (55%), Positives = 110/172 (63%), Gaps = 41/172 (23%)
Query: 57 MYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVY 116
MYD+FDN YQ+TIGIDFLSKT+YL++ VRLQLWDTAGQERFRSLIPSYIRDS A+VVY
Sbjct: 1 MYDTFDNNYQSTIGIDFLSKTLYLDEGPVRLQLWDTAGQERFRSLIPSYIRDSAAAIVVY 60
Query: 117 DITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVR 176
DITN SF T+KWI D+
Sbjct: 61 DITN-----------------------------------------RQSFENTTKWIQDIL 79
Query: 177 TERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVK 228
ERG DVII LVGNKTDL D R+V+ EEG +KA+E N MF ETSAKAG+N+K
Sbjct: 80 NERGKDVIIALVGNKTDLGDLRKVTYEEGMQKAQEYNTMFHETSAKAGHNIK 131
Score = 169 bits (428), Expect = 1e-51
Identities = 83/121 (68%), Positives = 99/121 (81%)
Query: 230 VRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVII 289
VRLQLWDTAGQERFRSLIPSYIRDS A+VVYDITN SF T+KWI D+ ERG DVII
Sbjct: 29 VRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDITNRQSFENTTKWIQDILNERGKDVII 88
Query: 290 MLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVAAALPGMDSTE 349
LVGNKTDL D R+V+ EEG +KA+E N MF ETSAKAG+N+K LF+++AA LP +D++
Sbjct: 89 ALVGNKTDLGDLRKVTYEEGMQKAQEYNTMFHETSAKAGHNIKVLFKKIAAKLPNLDNSN 148
Query: 350 N 350
+
Sbjct: 149 S 149
>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 = 152 bits (387), Expect = 1e-45
Identities = 70/221 (31%), Positives = 109/221 (49%), Gaps = 64/221 (28%)
Query: 14 FKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGIDF 73
FK+V LGE VGKTSL+ R++ + F+ +++T QA+ F
Sbjct: 1 FKVVLLGEGRVGKTSLVLRYVENKFNEKHESTT-------------------QAS----F 37
Query: 74 LSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDD 133
KT+ + + + L +WDTAGQER+ +L P Y RD+ A++VYDIT+A+SF +
Sbjct: 38 FQKTVNIGGKRIDLAIWDTAGQERYHALGPIYYRDADGAILVYDITDADSFQK------- 90
Query: 134 VRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGNKTD 193
V+ KWI +++ RG+++ +++VGNK D
Sbjct: 91 VK----------------------------------KWIKELKQMRGNNISLVIVGNKID 116
Query: 194 LSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQVRLQL 234
L +R VS E E AK + ETSAK G ++++ L L
Sbjct: 117 LERQRVVSKSEAEEYAKSVGAKHFETSAKTGKGIEELFLSL 157
Score = 135 bits (343), Expect = 5e-39
Identities = 51/115 (44%), Positives = 78/115 (67%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDV 287
K++ L +WDTAGQER+ +L P Y RD+ A++VYDIT+A+SF + KWI +++ RG+++
Sbjct: 47 KRIDLAIWDTAGQERYHALGPIYYRDADGAILVYDITDADSFQKVKKWIKELKQMRGNNI 106
Query: 288 IIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVAAAL 342
+++VGNK DL +R VS E E AK + ETSAK G +++LF +A +
Sbjct: 107 SLVIVGNKIDLERQRVVSKSEAEEYAKSVGAKHFETSAKTGKGIEELFLSLAKRM 161
>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 = 152 bits (386), Expect = 3e-45
Identities = 72/188 (38%), Positives = 102/188 (54%), Gaps = 41/188 (21%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
VGK+ L+ RF DSF+ ++ +TIGIDF +T+ L+ + ++LQ+WDTAGQERFR++ SY
Sbjct: 14 VGKSCLLLRFSEDSFNPSFISTIGIDFKIRTIELDGKKIKLQIWDTAGQERFRTITTSYY 73
Query: 107 RDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFH 166
R + ++VYDIT+ SF W+ ++ HA+
Sbjct: 74 RGAMGIILVYDITDEKSFENIKNWMRNI------------------------DEHAS--- 106
Query: 167 QTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYN 226
DV MLVGNK D+ +KR VS EEGE A+E + F+ETSAKA N
Sbjct: 107 --------------EDVERMLVGNKCDMEEKRVVSKEEGEALAREYGIKFLETSAKANIN 152
Query: 227 VKQVRLQL 234
V++ L L
Sbjct: 153 VEEAFLTL 160
Score = 130 bits (330), Expect = 5e-37
Identities = 54/112 (48%), Positives = 75/112 (66%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDV 287
K+++LQ+WDTAGQERFR++ SY R + ++VYDIT+ SF W+ ++ DV
Sbjct: 50 KKIKLQIWDTAGQERFRTITTSYYRGAMGIILVYDITDEKSFENIKNWMRNIDEHASEDV 109
Query: 288 IIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVA 339
MLVGNK D+ +KR VS EEGE A+E + F+ETSAKA NV++ F +A
Sbjct: 110 ERMLVGNKCDMEEKRVVSKEEGEALAREYGIKFLETSAKANINVEEAFLTLA 161
>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 = 147 bits (374), Expect = 2e-43
Identities = 69/221 (31%), Positives = 115/221 (52%), Gaps = 64/221 (28%)
Query: 14 FKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGIDF 73
FK+V +G+ VGK++L++RF + F+ DS ++TIG++F
Sbjct: 4 FKIVLIGDSGVGKSNLLSRFTRNEFN------------------LDS-----KSTIGVEF 40
Query: 74 LSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDD 133
++T+ ++ +T++ Q+WDTAGQER+R++ +Y R + A++VYDIT ++F +W+ +
Sbjct: 41 ATRTIQIDGKTIKAQIWDTAGQERYRAITSAYYRGAVGALLVYDITKKSTFENVERWLKE 100
Query: 134 VRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGNKTD 193
+R HA+ S+++IMLVGNK+D
Sbjct: 101 LRD------------------------HAD-----------------SNIVIMLVGNKSD 119
Query: 194 LSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQVRLQL 234
L R V TEE + A++ + FIETSA G NV++ QL
Sbjct: 120 LRHLRAVPTEEAKAFAEKNGLSFIETSALDGTNVEEAFKQL 160
Score = 131 bits (333), Expect = 2e-37
Identities = 48/111 (43%), Positives = 77/111 (69%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDV 287
K ++ Q+WDTAGQER+R++ +Y R + A++VYDIT ++F +W+ ++R S++
Sbjct: 50 KTIKAQIWDTAGQERYRAITSAYYRGAVGALLVYDITKKSTFENVERWLKELRDHADSNI 109
Query: 288 IIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRV 338
+IMLVGNK+DL R V TEE + A++ + FIETSA G NV++ F+++
Sbjct: 110 VIMLVGNKSDLRHLRAVPTEEAKAFAEKNGLSFIETSALDGTNVEEAFKQL 160
>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 = 145 bits (368), Expect = 1e-42
Identities = 64/184 (34%), Positives = 99/184 (53%), Gaps = 41/184 (22%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
VGK+SL+ RF D+FD +TIG+DF KT+ ++ + V+L +WDTAGQERFR+L SY
Sbjct: 11 VGKSSLLLRFTDDTFDEDLSSTIGVDFKVKTVTVDGKKVKLAIWDTAGQERFRTLTSSYY 70
Query: 107 RDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFH 166
R + ++VYD+T ++F W++++ T ++
Sbjct: 71 RGAQGVILVYDVTRRDTFDNLDTWLNELDT-----------------YS----------- 102
Query: 167 QTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYN 226
D + MLVGNK D + R+V+ EEG++ A++ N++FIETSAK
Sbjct: 103 ------------TNPDAVKMLVGNKIDKEN-REVTREEGQKFARKHNMLFIETSAKTRIG 149
Query: 227 VKQV 230
V+Q
Sbjct: 150 VQQA 153
Score = 127 bits (321), Expect = 8e-36
Identities = 49/113 (43%), Positives = 75/113 (66%), Gaps = 2/113 (1%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRT-ERGSD 286
K+V+L +WDTAGQERFR+L SY R + ++VYD+T ++F W++++ T D
Sbjct: 47 KKVKLAIWDTAGQERFRTLTSSYYRGAQGVILVYDVTRRDTFDNLDTWLNELDTYSTNPD 106
Query: 287 VIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVA 339
+ MLVGNK D + R+V+ EEG++ A++ N++FIETSAK V+Q F +
Sbjct: 107 AVKMLVGNKIDKEN-REVTREEGQKFARKHNMLFIETSAKTRIGVQQAFEELV 158
>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 = 139 bits (353), Expect = 2e-40
Identities = 63/183 (34%), Positives = 99/183 (54%), Gaps = 41/183 (22%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
VGK+ L+ RF D++ +Y +TIG+DF +T+ L+ +TV+LQ+WDTAGQERFR++ SY
Sbjct: 13 VGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTVKLQIWDTAGQERFRTITSSYY 72
Query: 107 RDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFH 166
R + ++VYD+T+ SF+ +W+ ++ +A+
Sbjct: 73 RGAHGIIIVYDVTDQESFNNVKQWLQEID------------------------RYAS--- 105
Query: 167 QTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYN 226
+V +LVGNK DL+DK+ V E + A EL + F+ETSAK N
Sbjct: 106 --------------ENVNKLLVGNKCDLTDKKVVDYTEAKEFADELGIPFLETSAKNATN 151
Query: 227 VKQ 229
V++
Sbjct: 152 VEE 154
Score = 125 bits (316), Expect = 4e-35
Identities = 49/115 (42%), Positives = 74/115 (64%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDV 287
K V+LQ+WDTAGQERFR++ SY R + ++VYD+T+ SF+ +W+ ++ +V
Sbjct: 49 KTVKLQIWDTAGQERFRTITSSYYRGAHGIIIVYDVTDQESFNNVKQWLQEIDRYASENV 108
Query: 288 IIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVAAAL 342
+LVGNK DL+DK+ V E + A EL + F+ETSAK NV++ F +A +
Sbjct: 109 NKLLVGNKCDLTDKKVVDYTEAKEFADELGIPFLETSAKNATNVEEAFMTMAREI 163
>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 = 136 bits (344), Expect = 4e-39
Identities = 55/115 (47%), Positives = 79/115 (68%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDV 287
KQ++LQ+WDTAGQE FRS+ SY R + A++VYDIT +F+ + W++D R S++
Sbjct: 51 KQIKLQIWDTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLTSWLEDARQHSNSNM 110
Query: 288 IIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVAAAL 342
IML+GNK DL +R+VS EEGE A+E ++F+ETSAK NV++ F A +
Sbjct: 111 TIMLIGNKCDLESRREVSYEEGEAFAREHGLIFMETSAKTASNVEEAFINTAKEI 165
Score = 134 bits (338), Expect = 3e-38
Identities = 64/189 (33%), Positives = 98/189 (51%), Gaps = 41/189 (21%)
Query: 45 TIVGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPS 104
T VGK+ L+ +F F + TIG++F ++ + ++ + ++LQ+WDTAGQE FRS+ S
Sbjct: 13 TGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQESFRSITRS 72
Query: 105 YIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANS 164
Y R + A++VYDIT F HL
Sbjct: 73 YYRGAAGALLVYDITR------------------------------RETFNHL------- 95
Query: 165 FHQTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAG 224
+ W++D R S++ IML+GNK DL +R+VS EEGE A+E ++F+ETSAK
Sbjct: 96 ----TSWLEDARQHSNSNMTIMLIGNKCDLESRREVSYEEGEAFAREHGLIFMETSAKTA 151
Query: 225 YNVKQVRLQ 233
NV++ +
Sbjct: 152 SNVEEAFIN 160
>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 = 132 bits (333), Expect = 1e-37
Identities = 65/187 (34%), Positives = 100/187 (53%), Gaps = 41/187 (21%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
GK+ L+ +F+ + F TIG++F S+ + + ++V+LQ+WDTAGQERFRS+ SY
Sbjct: 11 TGKSCLLHQFIENKFKQDSNHTIGVEFGSRVVNVGGKSVKLQIWDTAGQERFRSVTRSYY 70
Query: 107 RDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFH 166
R + A++VYDIT+ SF+ + W+ D RT + S
Sbjct: 71 RGAAGALLVYDITSRESFNALTNWLTDART----------LAS----------------- 103
Query: 167 QTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYN 226
D++I+LVGNK DL D R+V+ E R A+E ++F+ETSA G N
Sbjct: 104 --------------PDIVIILVGNKKDLEDDREVTFLEASRFAQENGLLFLETSALTGEN 149
Query: 227 VKQVRLQ 233
V++ L+
Sbjct: 150 VEEAFLK 156
Score = 129 bits (326), Expect = 2e-36
Identities = 56/112 (50%), Positives = 78/112 (69%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDV 287
K V+LQ+WDTAGQERFRS+ SY R + A++VYDIT+ SF+ + W+ D RT D+
Sbjct: 47 KSVKLQIWDTAGQERFRSVTRSYYRGAAGALLVYDITSRESFNALTNWLTDARTLASPDI 106
Query: 288 IIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVA 339
+I+LVGNK DL D R+V+ E R A+E ++F+ETSA G NV++ F + A
Sbjct: 107 VIILVGNKKDLEDDREVTFLEASRFAQENGLLFLETSALTGENVEEAFLKCA 158
>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 = 131 bits (332), Expect = 3e-37
Identities = 66/185 (35%), Positives = 94/185 (50%), Gaps = 38/185 (20%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
VGKTSL+ +++ F N Y+ATIG DFL+K + ++DR V LQ+WDTAGQERF+SL ++
Sbjct: 11 VGKTSLMNQYVNKKFSNQYKATIGADFLTKEVTVDDRLVTLQIWDTAGQERFQSLGVAFY 70
Query: 107 RDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFH 166
R + V+VYD+TN SF W D+ S +F
Sbjct: 71 RGADCCVLVYDVTNPKSFESLDSWRDEF-------------------LIQASPRDPENFP 111
Query: 167 QTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVM-FIETSAKAGY 225
+++GNK DL +KRQVST++ ++ K + + ETSAK
Sbjct: 112 ------------------FVVLGNKIDLEEKRQVSTKKAQQWCKSKGNIPYFETSAKEAI 153
Query: 226 NVKQV 230
NV Q
Sbjct: 154 NVDQA 158
Score = 100 bits (251), Expect = 2e-25
Identities = 48/120 (40%), Positives = 68/120 (56%), Gaps = 11/120 (9%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSD- 286
+ V LQ+WDTAGQERF+SL ++ R + V+VYD+TN SF W D+ +
Sbjct: 47 RLVTLQIWDTAGQERFQSLGVAFYRGADCCVLVYDVTNPKSFESLDSWRDEFLIQASPRD 106
Query: 287 ------VIIMLVGNKTDLSDKRQVSTEEGERKAKELNVM-FIETSAKAGYNVKQLFRRVA 339
V++ GNK DL +KRQVST++ ++ K + + ETSAK NV Q F +A
Sbjct: 107 PENFPFVVL---GNKIDLEEKRQVSTKKAQQWCKSKGNIPYFETSAKEAINVDQAFETIA 163
>gnl|CDD|206642 cd00876, Ras, Rat sarcoma (Ras) family of small guanosine
triphosphatases (GTPases). The Ras family of the Ras
superfamily includes classical N-Ras, H-Ras, and K-Ras,
as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG,
Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins.
Ras proteins regulate cell growth, proliferation and
differentiation. Ras is activated by guanine nucleotide
exchange factors (GEFs) that release GDP and allow GTP
binding. Many RasGEFs have been identified. These are
sequestered in the cytosol until activation by growth
factors triggers recruitment to the plasma membrane or
Golgi, where the GEF colocalizes with Ras. Active
GTP-bound Ras interacts with several effector proteins:
among the best characterized are the Raf kinases,
phosphatidylinositol 3-kinase (PI3K), RalGEFs and
NORE/MST1. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 160
Score = 131 bits (331), Expect = 3e-37
Identities = 64/216 (29%), Positives = 92/216 (42%), Gaps = 64/216 (29%)
Query: 15 KLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGIDFL 74
KLV LG VGK++L RF+ F Y TI +++Y+ I +D
Sbjct: 1 KLVVLGAGGVGKSALTIRFVSGEFVEEYDPTI---------------EDSYRKQIVVD-- 43
Query: 75 SKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDV 134
T L + DTAGQE F ++ YIR+ ++VY IT+ SF + + +
Sbjct: 44 -------GETYTLDILDTAGQEEFSAMRDQYIRNGDGFILVYSITSRESFEEIKNIREQI 96
Query: 135 RTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGNKTDL 194
+ + DV I+LVGNK DL
Sbjct: 97 LRVKDKE----------------------------------------DVPIVLVGNKCDL 116
Query: 195 SDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQV 230
++RQVSTEEGE A+E F+ETSAK N+ ++
Sbjct: 117 ENERQVSTEEGEALAEEWGCPFLETSAKTNINIDEL 152
Score = 113 bits (285), Expect = 2e-30
Identities = 45/113 (39%), Positives = 67/113 (59%), Gaps = 1/113 (0%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDV 287
+ L + DTAGQE F ++ YIR+ ++VY IT+ SF + + + + +
Sbjct: 45 ETYTLDILDTAGQEEFSAMRDQYIRNGDGFILVYSITSRESFEEIKNIREQILRVKDKED 104
Query: 288 I-IMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVA 339
+ I+LVGNK DL ++RQVSTEEGE A+E F+ETSAK N+ +LF +
Sbjct: 105 VPIVLVGNKCDLENERQVSTEEGEALAEEWGCPFLETSAKTNINIDELFNTLV 157
>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 = 126 bits (319), Expect = 2e-35
Identities = 61/189 (32%), Positives = 95/189 (50%), Gaps = 42/189 (22%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
VGKT ++ RF +F TIG+DF KT+ ++ + V+LQ+WDTAGQERFR++ SY
Sbjct: 14 VGKTCVVQRFKSGTFSERQGNTIGVDFTMKTLEIQGKRVKLQIWDTAGQERFRTITQSYY 73
Query: 107 RDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFH 166
R + A++ YDIT +SF WI++V +
Sbjct: 74 RSANGAIIAYDITRRSSFESVPHWIEEVE------------------------KYG---- 105
Query: 167 QTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMF-IETSAKAGY 225
S+V+++L+GNK DL ++R+V EE A+ ++ +ETSAK
Sbjct: 106 -------------ASNVVLLLIGNKCDLEEQREVLFEEACTLAEHYGILAVLETSAKESS 152
Query: 226 NVKQVRLQL 234
NV++ L +
Sbjct: 153 NVEEAFLLM 161
Score = 126 bits (317), Expect = 4e-35
Identities = 50/116 (43%), Positives = 76/116 (65%), Gaps = 1/116 (0%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDV 287
K+V+LQ+WDTAGQERFR++ SY R + A++ YDIT +SF WI++V S+V
Sbjct: 50 KRVKLQIWDTAGQERFRTITQSYYRSANGAIIAYDITRRSSFESVPHWIEEVEKYGASNV 109
Query: 288 IIMLVGNKTDLSDKRQVSTEEGERKAKELNVMF-IETSAKAGYNVKQLFRRVAAAL 342
+++L+GNK DL ++R+V EE A+ ++ +ETSAK NV++ F +A L
Sbjct: 110 VLLLIGNKCDLEEQREVLFEEACTLAEHYGILAVLETSAKESSNVEEAFLLMATEL 165
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 128 bits (322), Expect = 2e-35
Identities = 55/115 (47%), Positives = 81/115 (70%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDV 287
K ++LQ+WDTAGQE FRS+ SY R + A++VYDIT +F+ + W++D R +++
Sbjct: 53 KPIKLQIWDTAGQESFRSITRSYYRGAAGALLVYDITRRETFNHLASWLEDARQHANANM 112
Query: 288 IIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVAAAL 342
IML+GNK DL+ +R VSTEEGE+ AKE ++F+E SAK NV++ F + AA +
Sbjct: 113 TIMLIGNKCDLAHRRAVSTEEGEQFAKEHGLIFMEASAKTAQNVEEAFIKTAAKI 167
Score = 126 bits (319), Expect = 5e-35
Identities = 65/185 (35%), Positives = 102/185 (55%), Gaps = 41/185 (22%)
Query: 45 TIVGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPS 104
T VGK+ L+ +F F + TIG++F ++ + ++++ ++LQ+WDTAGQE FRS+ S
Sbjct: 15 TGVGKSCLLLQFTDKRFQPVHDLTIGVEFGARMITIDNKPIKLQIWDTAGQESFRSITRS 74
Query: 105 YIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANS 164
Y R + A++VYDIT +F+ + W++D R HAN
Sbjct: 75 YYRGAAGALLVYDITRRETFNHLASWLEDAR------------------------QHAN- 109
Query: 165 FHQTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAG 224
+++ IML+GNK DL+ +R VSTEEGE+ AKE ++F+E SAK
Sbjct: 110 ----------------ANMTIMLIGNKCDLAHRRAVSTEEGEQFAKEHGLIFMEASAKTA 153
Query: 225 YNVKQ 229
NV++
Sbjct: 154 QNVEE 158
>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 = 125 bits (316), Expect = 8e-35
Identities = 75/214 (35%), Positives = 108/214 (50%), Gaps = 63/214 (29%)
Query: 14 FKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGIDF 73
FK++ +G+ VGKT L+ RF +F L F+ AT+GI F
Sbjct: 1 FKVMLVGDSGVGKTCLLVRFKDGAF-------------LAGSFI---------ATVGIQF 38
Query: 74 LSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDD 133
+K + ++ V+LQ+WDTAGQERFRS+ +Y RD+ +++YD+TN +SF D+
Sbjct: 39 TNKVVTVDGVKVKLQIWDTAGQERFRSVTHAYYRDAHALLLLYDVTNKSSF-------DN 91
Query: 134 VRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGNKTD 193
+R W+ ++ SDV+IML+GNK D
Sbjct: 92 IRA----------------------------------WLTEILEYAQSDVVIMLLGNKAD 117
Query: 194 LSDKRQVSTEEGERKAKELNVMFIETSAKAGYNV 227
+S +R V E+GER AKE V F+ETSAK G NV
Sbjct: 118 MSGERVVKREDGERLAKEYGVPFMETSAKTGLNV 151
Score = 124 bits (314), Expect = 2e-34
Identities = 58/114 (50%), Positives = 79/114 (69%)
Query: 229 QVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVI 288
+V+LQ+WDTAGQERFRS+ +Y RD+ +++YD+TN +SF W+ ++ SDV+
Sbjct: 49 KVKLQIWDTAGQERFRSVTHAYYRDAHALLLLYDVTNKSSFDNIRAWLTEILEYAQSDVV 108
Query: 289 IMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVAAAL 342
IML+GNK D+S +R V E+GER AKE V F+ETSAK G NV+ F VA L
Sbjct: 109 IMLLGNKADMSGERVVKREDGERLAKEYGVPFMETSAKTGLNVELAFTAVAKEL 162
>gnl|CDD|133311 cd04111, Rab39, Rab GTPase family 39 (Rab39). Found in eukaryotes,
Rab39 is mainly found in epithelial cell lines, but is
distributed widely in various human tissues and cell
lines. It is believed to be a novel Rab protein involved
in regulating Golgi-associated vesicular transport
during cellular endocytosis. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 211
Score = 124 bits (314), Expect = 4e-34
Identities = 66/182 (36%), Positives = 95/182 (52%), Gaps = 41/182 (22%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRT-VRLQLWDTAGQERFRSLIPSY 105
VGK+SL+ RF F T+G+DF S+ + +E ++LQLWDTAGQERFRS+ SY
Sbjct: 13 VGKSSLLKRFTEGRFAEVSDPTVGVDFFSRLIEIEPGVRIKLQLWDTAGQERFRSITRSY 72
Query: 106 IRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSF 165
R+S ++V+DITN SF W+++ R +H+ H
Sbjct: 73 YRNSVGVLLVFDITNRESFEHVHDWLEEAR-------------------SHIQPHR---- 109
Query: 166 HQTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGY 225
+ +LVG+K DL +RQV+ EE E+ AK+L + +IETSA+ G
Sbjct: 110 -----------------PVFILVGHKCDLESQRQVTREEAEKLAKDLGMKYIETSARTGD 152
Query: 226 NV 227
NV
Sbjct: 153 NV 154
Score = 119 bits (300), Expect = 4e-32
Identities = 51/113 (45%), Positives = 77/113 (68%), Gaps = 1/113 (0%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTE-RGSD 286
+++LQLWDTAGQERFRS+ SY R+S ++V+DITN SF W+++ R+ +
Sbjct: 50 VRIKLQLWDTAGQERFRSITRSYYRNSVGVLLVFDITNRESFEHVHDWLEEARSHIQPHR 109
Query: 287 VIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVA 339
+ +LVG+K DL +RQV+ EE E+ AK+L + +IETSA+ G NV++ F +
Sbjct: 110 PVFILVGHKCDLESQRQVTREEAEKLAKDLGMKYIETSARTGDNVEEAFELLT 162
>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 = 123 bits (311), Expect = 7e-34
Identities = 58/184 (31%), Positives = 86/184 (46%), Gaps = 40/184 (21%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRT-VRLQLWDTAGQERFRSLIPSY 105
VGKTS+I R+++ F Y+ATIG+DF K + + T VRLQLWD AGQERF + Y
Sbjct: 11 VGKTSIIKRYVHGVFSQHYKATIGVDFALKVIEWDPNTVVRLQLWDIAGQERFGGMTRVY 70
Query: 106 IRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSF 165
+ + A++V+D+T ++F KW D+
Sbjct: 71 YKGAVGAIIVFDVTRPSTFEAVLKWKADL------------------------------- 99
Query: 166 HQTSKWIDDVRTERGSDVIIMLVGNKTDLSDKR-QVSTEEGERKAKELN-VMFIETSAKA 223
SK V G + +L+ NK DL +R E+ ++ KE + + ETSAK
Sbjct: 100 --DSK----VTLPNGEPIPALLLANKCDLKKERLAKDPEQMDQFCKENGFIGWFETSAKE 153
Query: 224 GYNV 227
N+
Sbjct: 154 NINI 157
Score = 94.7 bits (236), Expect = 5e-23
Identities = 40/118 (33%), Positives = 62/118 (52%), Gaps = 6/118 (5%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDD----VRTER 283
VRLQLWD AGQERF + Y + + A++V+D+T ++F KW D V
Sbjct: 48 TVVRLQLWDIAGQERFGGMTRVYYKGAVGAIIVFDVTRPSTFEAVLKWKADLDSKVTLPN 107
Query: 284 GSDVIIMLVGNKTDLSDKR-QVSTEEGERKAKELN-VMFIETSAKAGYNVKQLFRRVA 339
G + +L+ NK DL +R E+ ++ KE + + ETSAK N+++ R +
Sbjct: 108 GEPIPALLLANKCDLKKERLAKDPEQMDQFCKENGFIGWFETSAKENINIEEAMRFLV 165
>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 = 120 bits (301), Expect = 6e-33
Identities = 68/190 (35%), Positives = 99/190 (52%), Gaps = 41/190 (21%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
VGKTS + R+ DSF + + +T+GIDF KT+Y D+ ++LQ+WDTAGQER+R++ +Y
Sbjct: 12 VGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVYRNDKRIKLQIWDTAGQERYRTITTAYY 71
Query: 107 RDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFH 166
R + +++YDITN SF+ W ++T S+ +A
Sbjct: 72 RGAMGFILMYDITNEESFNAVQDWSTQIKT--------------------YSWDNAQ--- 108
Query: 167 QTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYN 226
++LVGNK D+ D+R VS E G + A +L F E SAK N
Sbjct: 109 ------------------VILVGNKCDMEDERVVSAERGRQLADQLGFEFFEASAKENIN 150
Query: 227 VKQVRLQLWD 236
VKQV +L D
Sbjct: 151 VKQVFERLVD 160
Score = 109 bits (273), Expect = 9e-29
Identities = 49/113 (43%), Positives = 73/113 (64%)
Query: 226 NVKQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGS 285
N K+++LQ+WDTAGQER+R++ +Y R + +++YDITN SF+ W ++T
Sbjct: 46 NDKRIKLQIWDTAGQERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSWD 105
Query: 286 DVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRV 338
+ ++LVGNK D+ D+R VS E G + A +L F E SAK NVKQ+F R+
Sbjct: 106 NAQVILVGNKCDMEDERVVSAERGRQLADQLGFEFFEASAKENINVKQVFERL 158
>gnl|CDD|133322 cd04122, Rab14, Rab GTPase family 14 (Rab14). Rab14 GTPases are
localized to biosynthetic compartments, including the
rough ER, the Golgi complex, and the trans-Golgi
network, and to endosomal compartments, including early
endosomal vacuoles and associated vesicles. Rab14 is
believed to function in both the biosynthetic and
recycling pathways between the Golgi and endosomal
compartments. Rab14 has also been identified on GLUT4
vesicles, and has been suggested to help regulate GLUT4
translocation. In addition, Rab14 is believed to play a
role in the regulation of phagocytosis. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 166
Score = 118 bits (297), Expect = 3e-32
Identities = 49/114 (42%), Positives = 75/114 (65%)
Query: 226 NVKQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGS 285
N ++++LQ+WDTAGQERFR++ SY R + A++VYDIT ++++ S W+ D R
Sbjct: 47 NGQKIKLQIWDTAGQERFRAVTRSYYRGAAGALMVYDITRRSTYNHLSSWLTDARNLTNP 106
Query: 286 DVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVA 339
+ +I L+GNK DL +R V+ EE ++ A E ++F+E SAK G NV+ F A
Sbjct: 107 NTVIFLIGNKADLEAQRDVTYEEAKQFADENGLLFLECSAKTGENVEDAFLETA 160
Score = 118 bits (296), Expect = 4e-32
Identities = 59/187 (31%), Positives = 92/187 (49%), Gaps = 41/187 (21%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
VGK+ L+ +F F TIG++F ++ + + + ++LQ+WDTAGQERFR++ SY
Sbjct: 13 VGKSCLLHQFTEKKFMADCPHTIGVEFGTRIIEVNGQKIKLQIWDTAGQERFRAVTRSYY 72
Query: 107 RDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFH 166
R + A++VYDIT + + HL
Sbjct: 73 RGAAGALMVYDITR------------------------------RSTYNHL--------- 93
Query: 167 QTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYN 226
S W+ D R + +I L+GNK DL +R V+ EE ++ A E ++F+E SAK G N
Sbjct: 94 --SSWLTDARNLTNPNTVIFLIGNKADLEAQRDVTYEEAKQFADENGLLFLECSAKTGEN 151
Query: 227 VKQVRLQ 233
V+ L+
Sbjct: 152 VEDAFLE 158
>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 = 116 bits (292), Expect = 1e-31
Identities = 63/188 (33%), Positives = 96/188 (51%), Gaps = 41/188 (21%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
VGKT L+ RF F ATIG+DF+ KT+ ++ ++LQ+WDTAGQERFRS+ SY
Sbjct: 18 VGKTCLVRRFTQGLFPPGQGATIGVDFMIKTVEIKGEKIKLQIWDTAGQERFRSITQSYY 77
Query: 107 RDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFH 166
R + ++ YDIT SF +W+ ++ +AN
Sbjct: 78 RSANALILTYDITCEESFRCLPEWLREIEQ------------------------YAN--- 110
Query: 167 QTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYN 226
+ VI +LVGNK DL+++R+VS + E + ++ ++ETSAK N
Sbjct: 111 --------------NKVITILVGNKIDLAERREVSQQRAEEFSDAQDMYYLETSAKESDN 156
Query: 227 VKQVRLQL 234
V+++ L L
Sbjct: 157 VEKLFLDL 164
Score = 111 bits (280), Expect = 8e-30
Identities = 47/114 (41%), Positives = 74/114 (64%)
Query: 229 QVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVI 288
+++LQ+WDTAGQERFRS+ SY R + ++ YDIT SF +W+ ++ + VI
Sbjct: 55 KIKLQIWDTAGQERFRSITQSYYRSANALILTYDITCEESFRCLPEWLREIEQYANNKVI 114
Query: 289 IMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVAAAL 342
+LVGNK DL+++R+VS + E + ++ ++ETSAK NV++LF +A L
Sbjct: 115 TILVGNKIDLAERREVSQQRAEEFSDAQDMYYLETSAKESDNVEKLFLDLACRL 168
>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 = 114 bits (287), Expect = 1e-30
Identities = 61/185 (32%), Positives = 86/185 (46%), Gaps = 41/185 (22%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFR-SLIPSY 105
VGKT L RF F +ATIG+DF +T+ ++ +++QLWDTAGQERFR S++ Y
Sbjct: 13 VGKTCLTYRFCAGRFPERTEATIGVDFRERTVEIDGERIKVQLWDTAGQERFRKSMVQHY 72
Query: 106 IRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSF 165
R+ V VYD+TN SFH WI++ H+
Sbjct: 73 YRNVHAVVFVYDVTNMASFHSLPSWIEECE------------------------QHS--- 105
Query: 166 HQTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGY 225
++V +LVGNK DL ++ QV T+ +R A ++ ETSAK
Sbjct: 106 -------------LPNEVPRILVGNKCDLREQIQVPTDLAQRFADAHSMPLFETSAKDPS 152
Query: 226 NVKQV 230
V
Sbjct: 153 ENDHV 157
Score = 99.0 bits (247), Expect = 6e-25
Identities = 48/119 (40%), Positives = 71/119 (59%), Gaps = 5/119 (4%)
Query: 229 QVRLQLWDTAGQERFR-SLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTER-GSD 286
++++QLWDTAGQERFR S++ Y R+ V VYD+TN SFH WI++ ++
Sbjct: 50 RIKVQLWDTAGQERFRKSMVQHYYRNVHAVVFVYDVTNMASFHSLPSWIEECEQHSLPNE 109
Query: 287 VIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGY---NVKQLFRRVAAAL 342
V +LVGNK DL ++ QV T+ +R A ++ ETSAK +V+ +F +A L
Sbjct: 110 VPRILVGNKCDLREQIQVPTDLAQRFADAHSMPLFETSAKDPSENDHVEAIFMTLAHKL 168
>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 = 114 bits (287), Expect = 1e-30
Identities = 64/219 (29%), Positives = 95/219 (43%), Gaps = 64/219 (29%)
Query: 12 RKFKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGI 71
R++KLV LG VGK++L +F+ F + Y TI +++Y+ I I
Sbjct: 1 REYKLVVLGGGGVGKSALTIQFVQGHFVDEYDPTI---------------EDSYRKQIEI 45
Query: 72 DFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWI 131
D L + DTAGQE F ++ Y+R ++VY IT+ SF + +K
Sbjct: 46 D---------GEVCLLDILDTAGQEEFSAMRDQYMRTGEGFLLVYSITDRQSFEEIAK-- 94
Query: 132 DDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGNK 191
F + +R + DV I+LVGNK
Sbjct: 95 ---------------------------------FREQI-----LRVKDRDDVPIVLVGNK 116
Query: 192 TDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQV 230
DL ++R VSTEEG+ A++ F+ETSAK NV +
Sbjct: 117 CDLENERVVSTEEGKELARQWGCPFLETSAKERINVDEA 155
Score = 108 bits (271), Expect = 2e-28
Identities = 45/112 (40%), Positives = 68/112 (60%), Gaps = 1/112 (0%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDV-RTERGSD 286
+ L + DTAGQE F ++ Y+R ++VY IT+ SF + +K+ + + R + D
Sbjct: 48 EVCLLDILDTAGQEEFSAMRDQYMRTGEGFLLVYSITDRQSFEEIAKFREQILRVKDRDD 107
Query: 287 VIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRV 338
V I+LVGNK DL ++R VSTEEG+ A++ F+ETSAK NV + F +
Sbjct: 108 VPIVLVGNKCDLENERVVSTEEGKELARQWGCPFLETSAKERINVDEAFYDL 159
>gnl|CDD|214541 smart00173, RAS, Ras subfamily of RAS small GTPases. Similar in
fold and function to the bacterial EF-Tu GTPase. p21Ras
couples receptor Tyr kinases and G protein receptors to
protein kinase cascades.
Length = 164
Score = 113 bits (285), Expect = 2e-30
Identities = 64/217 (29%), Positives = 92/217 (42%), Gaps = 64/217 (29%)
Query: 14 FKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGIDF 73
+KLV LG VGK++L +F+ F + Y TI +++Y+ I ID
Sbjct: 1 YKLVVLGSGGVGKSALTIQFIQGHFVDDYDPTI---------------EDSYRKQIEID- 44
Query: 74 LSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDD 133
L + DTAGQE F ++ Y+R ++VY IT+ SF + K
Sbjct: 45 --------GEVCLLDILDTAGQEEFSAMRDQYMRTGEGFLLVYSITDRQSFEEIKK---- 92
Query: 134 VRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGNKTD 193
F + I +R + DV I+LVGNK D
Sbjct: 93 -------------------------------FREQ---I--LRVKDRDDVPIVLVGNKCD 116
Query: 194 LSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQV 230
L +R VSTEEG+ A++ F+ETSAK NV +
Sbjct: 117 LESERVVSTEEGKELARQWGCPFLETSAKERVNVDEA 153
Score = 108 bits (272), Expect = 2e-28
Identities = 45/112 (40%), Positives = 66/112 (58%), Gaps = 1/112 (0%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDV-RTERGSD 286
+ L + DTAGQE F ++ Y+R ++VY IT+ SF + K+ + + R + D
Sbjct: 46 EVCLLDILDTAGQEEFSAMRDQYMRTGEGFLLVYSITDRQSFEEIKKFREQILRVKDRDD 105
Query: 287 VIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRV 338
V I+LVGNK DL +R VSTEEG+ A++ F+ETSAK NV + F +
Sbjct: 106 VPIVLVGNKCDLESERVVSTEEGKELARQWGCPFLETSAKERVNVDEAFYDL 157
>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 = 112 bits (282), Expect = 4e-30
Identities = 57/186 (30%), Positives = 81/186 (43%), Gaps = 44/186 (23%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDR--TVRLQLWDTAGQERFRSLIPS 104
VGK+S+I RF+ F Y+ TIG+DFL K ++L VRL LWDTAGQE F ++ +
Sbjct: 11 VGKSSMIQRFVKGIFTKDYKKTIGVDFLEKQIFLRQSDEDVRLMLWDTAGQEEFDAITKA 70
Query: 105 YIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANS 164
Y R + ++V+ T+ SF W + V E G I
Sbjct: 71 YYRGAQACILVFSTTDRESFEAIESWKEKVEAE---------CGDIPM------------ 109
Query: 165 FHQTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAG 224
+LV K DL D+ ++ EE E AK L + TS K
Sbjct: 110 ---------------------VLVQTKIDLLDQAVITNEEAEALAKRLQLPLFRTSVKDD 148
Query: 225 YNVKQV 230
+NV ++
Sbjct: 149 FNVTEL 154
Score = 100 bits (251), Expect = 1e-25
Identities = 47/131 (35%), Positives = 70/131 (53%), Gaps = 1/131 (0%)
Query: 210 KELNVMFIETSAKAGYNVKQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSF 269
K + V F+E + + VRL LWDTAGQE F ++ +Y R + ++V+ T+ SF
Sbjct: 31 KTIGVDFLEKQIFLRQSDEDVRLMLWDTAGQEEFDAITKAYYRGAQACILVFSTTDRESF 90
Query: 270 HQTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGY 329
W + V E G D+ ++LV K DL D+ ++ EE E AK L + TS K +
Sbjct: 91 EAIESWKEKVEAECG-DIPMVLVQTKIDLLDQAVITNEEAEALAKRLQLPLFRTSVKDDF 149
Query: 330 NVKQLFRRVAA 340
NV +LF +A
Sbjct: 150 NVTELFEYLAE 160
>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 = 112 bits (282), Expect = 1e-29
Identities = 62/183 (33%), Positives = 93/183 (50%), Gaps = 42/183 (22%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
VGK+SL+ RF ++F +Y TIG+DF +T+ + V+LQ+WDTAGQERFR++ +Y
Sbjct: 17 VGKSSLLLRFADNTFSGSYITTIGVDFKIRTVEINGERVKLQIWDTAGQERFRTITSTYY 76
Query: 107 RDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFH 166
R + +VVYD+TN SF +W+ + IE N
Sbjct: 77 RGTHGVIVVYDVTNGESFVNVKRWLQE----------------IEQN------------- 107
Query: 167 QTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYN 226
DDV +LVGNK D +++ V TE+ + A ++ + ETSAK N
Sbjct: 108 -----CDDVCK--------VLVGNKNDDPERKVVETEDAYKFAGQMGISLFETSAKENIN 154
Query: 227 VKQ 229
V++
Sbjct: 155 VEE 157
Score = 97.6 bits (243), Expect = 4e-24
Identities = 45/111 (40%), Positives = 73/111 (65%), Gaps = 3/111 (2%)
Query: 226 NVKQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGS 285
N ++V+LQ+WDTAGQERFR++ +Y R + +VVYD+TN SF +W+ ++ E+
Sbjct: 51 NGERVKLQIWDTAGQERFRTITSTYYRGTHGVIVVYDVTNGESFVNVKRWLQEI--EQNC 108
Query: 286 DVII-MLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLF 335
D + +LVGNK D +++ V TE+ + A ++ + ETSAK NV+++F
Sbjct: 109 DDVCKVLVGNKNDDPERKVVETEDAYKFAGQMGISLFETSAKENINVEEMF 159
>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 = 111 bits (279), Expect = 2e-29
Identities = 59/230 (25%), Positives = 95/230 (41%), Gaps = 81/230 (35%)
Query: 15 KLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGIDFL 74
K+V +G+ +VGKT L+ + + F Y T+ FDN Y A + +D
Sbjct: 2 KIVVVGDGAVGKTCLLISYTTNKFPTEYVPTV--------------FDN-YSANVTVD-- 44
Query: 75 SKTMYLEDRTVRLQLWDTAGQERFRSLIP-SYIRDSTVAVVVYDITNANSFHQ-TSKWID 132
+ V L LWDTAGQE + L P SY + V ++ + + + +SF +KW
Sbjct: 45 -------GKQVNLGLWDTAGQEEYDRLRPLSY-PQTDVFLLCFSVDSPSSFENVKTKWYP 96
Query: 133 DVRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGNKT 192
+++ H+ +V I+LVG K
Sbjct: 97 EIK------------------------HYC------------------PNVPIILVGTKI 114
Query: 193 DLSD-----------KRQVSTEEGERKAKELN-VMFIETSAKAGYNVKQV 230
DL D ++ ++ EEGE+ AKE+ V ++E SA +K+V
Sbjct: 115 DLRDDGNTLKKLEKKQKPITPEEGEKLAKEIGAVKYMECSALTQEGLKEV 164
Score = 98.4 bits (246), Expect = 1e-24
Identities = 46/135 (34%), Positives = 73/135 (54%), Gaps = 16/135 (11%)
Query: 215 MFIETSAKAGYNVKQVRLQLWDTAGQERFRSLIP-SYIRDSTVAVVVYDITNANSFHQ-T 272
+F SA + KQV L LWDTAGQE + L P SY + V ++ + + + +SF
Sbjct: 33 VFDNYSANVTVDGKQVNLGLWDTAGQEEYDRLRPLSY-PQTDVFLLCFSVDSPSSFENVK 91
Query: 273 SKWIDDVRTERGSDVIIMLVGNKTDLSD-----------KRQVSTEEGERKAKELN-VMF 320
+KW +++ +V I+LVG K DL D ++ ++ EEGE+ AKE+ V +
Sbjct: 92 TKWYPEIK-HYCPNVPIILVGTKIDLRDDGNTLKKLEKKQKPITPEEGEKLAKEIGAVKY 150
Query: 321 IETSAKAGYNVKQLF 335
+E SA +K++F
Sbjct: 151 MECSALTQEGLKEVF 165
>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 = 110 bits (276), Expect = 8e-29
Identities = 66/191 (34%), Positives = 99/191 (51%), Gaps = 42/191 (21%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
VGKTSL+ RF D+F ++T+G+DF KT+ L + +RLQ+WDTAGQERF S+ +Y
Sbjct: 11 VGKTSLMERFTDDTFCEACKSTVGVDFKIKTVELRGKKIRLQIWDTAGQERFNSITSAYY 70
Query: 107 RDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFH 166
R + ++VYDIT +F KW+
Sbjct: 71 RSAKGIILVYDITKKETFDDLPKWM----------------------------------- 95
Query: 167 QTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVM-FIETSAKAGY 225
K ID +E D ++LVGNK D R+++ ++GE+ A+++ M F E SAK +
Sbjct: 96 ---KMIDKYASE---DAELLLVGNKLDCETDREITRQQGEKFAQQITGMRFCEASAKDNF 149
Query: 226 NVKQVRLQLWD 236
NV ++ L+L D
Sbjct: 150 NVDEIFLKLVD 160
Score = 98.5 bits (245), Expect = 2e-24
Identities = 44/112 (39%), Positives = 71/112 (63%), Gaps = 1/112 (0%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDV 287
K++RLQ+WDTAGQERF S+ +Y R + ++VYDIT +F KW+ + D
Sbjct: 47 KKIRLQIWDTAGQERFNSITSAYYRSAKGIILVYDITKKETFDDLPKWMKMIDKYASEDA 106
Query: 288 IIMLVGNKTDLSDKRQVSTEEGERKAKELNVM-FIETSAKAGYNVKQLFRRV 338
++LVGNK D R+++ ++GE+ A+++ M F E SAK +NV ++F ++
Sbjct: 107 ELLLVGNKLDCETDREITRQQGEKFAQQITGMRFCEASAKDNFNVDEIFLKL 158
>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 = 107 bits (268), Expect = 7e-28
Identities = 56/193 (29%), Positives = 88/193 (45%), Gaps = 50/193 (25%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRT----------VRLQLWDTAGQE 96
VGKT+ + R+ + F+ + T+GIDF K + + V LQLWDTAGQE
Sbjct: 15 VGKTTFLYRYTDNKFNPKFITTVGIDFREKRVVYNSQGPDGTSGKAFRVHLQLWDTAGQE 74
Query: 97 RFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTH 156
RFRSL ++ RD+ ++++D+T+ SF W+ ++
Sbjct: 75 RFRSLTTAFFRDAMGFLLMFDLTSEQSFLNVRNWMSQLQA-------------------- 114
Query: 157 LSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMF 216
HA + I+L+GNK DL D+R+VS + A + + +
Sbjct: 115 ----HAYC----------------ENPDIVLIGNKADLPDQREVSERQARELADKYGIPY 154
Query: 217 IETSAKAGYNVKQ 229
ETSA G NV++
Sbjct: 155 FETSAATGQNVEK 167
Score = 102 bits (256), Expect = 4e-26
Identities = 42/106 (39%), Positives = 66/106 (62%), Gaps = 1/106 (0%)
Query: 229 QVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSD-V 287
+V LQLWDTAGQERFRSL ++ RD+ ++++D+T+ SF W+ ++ +
Sbjct: 62 RVHLQLWDTAGQERFRSLTTAFFRDAMGFLLMFDLTSEQSFLNVRNWMSQLQAHAYCENP 121
Query: 288 IIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQ 333
I+L+GNK DL D+R+VS + A + + + ETSA G NV++
Sbjct: 122 DIVLIGNKADLPDQREVSERQARELADKYGIPYFETSAATGQNVEK 167
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 108 bits (270), Expect = 9e-28
Identities = 57/183 (31%), Positives = 102/183 (55%), Gaps = 41/183 (22%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
VGK+++++RF + F ++TIG++F ++T+ +E +TV+ Q+WDTAGQER+R++ +Y
Sbjct: 23 VGKSNILSRFTRNEFCLESKSTIGVEFATRTLQVEGKTVKAQIWDTAGQERYRAITSAYY 82
Query: 107 RDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFH 166
R + A++VYDIT +F +W+ ++R HA+
Sbjct: 83 RGAVGALLVYDITKRQTFDNVQRWLRELRD------------------------HAD--- 115
Query: 167 QTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYN 226
S+++IM+ GNK+DL+ R V+ E+G+ A++ + F+ETSA N
Sbjct: 116 --------------SNIVIMMAGNKSDLNHLRSVAEEDGQALAEKEGLSFLETSALEATN 161
Query: 227 VKQ 229
V++
Sbjct: 162 VEK 164
Score = 100 bits (251), Expect = 4e-25
Identities = 44/111 (39%), Positives = 75/111 (67%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDV 287
K V+ Q+WDTAGQER+R++ +Y R + A++VYDIT +F +W+ ++R S++
Sbjct: 59 KTVKAQIWDTAGQERYRAITSAYYRGAVGALLVYDITKRQTFDNVQRWLRELRDHADSNI 118
Query: 288 IIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRV 338
+IM+ GNK+DL+ R V+ E+G+ A++ + F+ETSA NV++ F+ +
Sbjct: 119 VIMMAGNKSDLNHLRSVAEEDGQALAEKEGLSFLETSALEATNVEKAFQTI 169
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 105 bits (264), Expect = 5e-27
Identities = 64/205 (31%), Positives = 92/205 (44%), Gaps = 57/205 (27%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
VGKT+L+ R + D F Y TIG +KT+ R ++LQLWDTAGQE +RSL P Y
Sbjct: 16 VGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQEEYRSLRPEYY 75
Query: 107 RDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFH 166
R + ++VYD T S D++ E
Sbjct: 76 RGANGILIVYDSTLRESS-------DELTEE----------------------------- 99
Query: 167 QTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKEL-------------- 212
W++++R DV I+LVGNK DL D++ S E + +E+
Sbjct: 100 ----WLEELRELAPDDVPILLVGNKIDLFDEQSSSEEILNQLNREVVLLVLAPKAVLPEV 155
Query: 213 -NVMFIETSAKA--GYNVKQVRLQL 234
N +ETSAK+ G NV ++ +L
Sbjct: 156 ANPALLETSAKSLTGPNVNELFKEL 180
Score = 83.5 bits (206), Expect = 9e-19
Identities = 50/131 (38%), Positives = 73/131 (55%), Gaps = 18/131 (13%)
Query: 230 VRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQ-TSKWIDDVRTERGSDVI 288
++LQLWDTAGQE +RSL P Y R + ++VYD T S + T +W++++R DV
Sbjct: 54 IKLQLWDTAGQEEYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDDVP 113
Query: 289 IMLVGNKTDLSDKRQVSTEEGERKAKEL---------------NVMFIETSAKA--GYNV 331
I+LVGNK DL D++ S E + +E+ N +ETSAK+ G NV
Sbjct: 114 ILLVGNKIDLFDEQSSSEEILNQLNREVVLLVLAPKAVLPEVANPALLETSAKSLTGPNV 173
Query: 332 KQLFRRVAAAL 342
+LF+ + L
Sbjct: 174 NELFKELLRKL 184
>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 = 101 bits (252), Expect = 9e-26
Identities = 62/188 (32%), Positives = 93/188 (49%), Gaps = 41/188 (21%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
VGKT L+ RF + F +++ +TIG+DF KT+ ++ VR+Q+WDTAGQER++++ Y
Sbjct: 11 VGKTCLLCRFTDNEFHSSHISTIGVDFKMKTIEVDGIKVRIQIWDTAGQERYQTITKQYY 70
Query: 107 RDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFH 166
R + +VYDI++ S+ KW+ DV
Sbjct: 71 RRAQGIFLVYDISSERSYQHIMKWVSDV-------------------------------- 98
Query: 167 QTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYN 226
D+ E V +L+GNK D KRQV E+G + AKE + F ETSA N
Sbjct: 99 ------DEYAPEG---VQKILIGNKADEEQKRQVGDEQGNKLAKEYGMDFFETSACTNKN 149
Query: 227 VKQVRLQL 234
+K+ +L
Sbjct: 150 IKESFTRL 157
Score = 93.1 bits (231), Expect = 7e-23
Identities = 46/111 (41%), Positives = 67/111 (60%)
Query: 229 QVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVI 288
+VR+Q+WDTAGQER++++ Y R + +VYDI++ S+ KW+ DV V
Sbjct: 48 KVRIQIWDTAGQERYQTITKQYYRRAQGIFLVYDISSERSYQHIMKWVSDVDEYAPEGVQ 107
Query: 289 IMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVA 339
+L+GNK D KRQV E+G + AKE + F ETSA N+K+ F R+
Sbjct: 108 KILIGNKADEEQKRQVGDEQGNKLAKEYGMDFFETSACTNKNIKESFTRLT 158
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 101 bits (252), Expect = 2e-25
Identities = 71/228 (31%), Positives = 99/228 (43%), Gaps = 63/228 (27%)
Query: 2 SSSGDFGNPLRKFKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSF 61
SSSG FK++ +G+ VGK+SL+ F+ S ++
Sbjct: 3 SSSGQSSGYDLSFKILLIGDSGVGKSSLLVSFISSSVEDL-------------------- 42
Query: 62 DNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNA 121
TIG+DF K + + + ++L +WDTAGQERFR+L SY R++ ++VYD+T
Sbjct: 43 ----APTIGVDFKIKQLTVGGKRLKLTIWDTAGQERFRTLTSSYYRNAQGIILVYDVTRR 98
Query: 122 NSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGS 181
+F SDV V TN
Sbjct: 99 ETFTNL------------SDVWGKEVELYSTN---------------------------Q 119
Query: 182 DVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQ 229
D + MLVGNK D +R VS EEG AKE +F+E SAK NV+Q
Sbjct: 120 DCVKMLVGNKVDRESERDVSREEGMALAKEHGCLFLECSAKTRENVEQ 167
Score = 97.0 bits (241), Expect = 9e-24
Identities = 51/114 (44%), Positives = 69/114 (60%), Gaps = 2/114 (1%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSK-WIDDVRT-ERGS 285
K+++L +WDTAGQERFR+L SY R++ ++VYD+T +F S W +V
Sbjct: 60 KRLKLTIWDTAGQERFRTLTSSYYRNAQGIILVYDVTRRETFTNLSDVWGKEVELYSTNQ 119
Query: 286 DVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVA 339
D + MLVGNK D +R VS EEG AKE +F+E SAK NV+Q F +A
Sbjct: 120 DCVKMLVGNKVDRESERDVSREEGMALAKEHGCLFLECSAKTRENVEQCFEELA 173
>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 = 100 bits (250), Expect = 3e-25
Identities = 60/220 (27%), Positives = 93/220 (42%), Gaps = 68/220 (30%)
Query: 15 KLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGIDFL 74
K+V LG++SVGKTSL+ R+++ F YQ TIG F+
Sbjct: 2 KVVMLGKESVGKTSLVERYVHHRF----------------------LVGPYQNTIGAAFV 39
Query: 75 SKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDV 134
+K M + +R V L +WDTAG ER+ ++ Y R + A+V YD+T+++SF + W+ ++
Sbjct: 40 AKRMVVGERVVTLGIWDTAGSERYEAMSRIYYRGAKAAIVCYDLTDSSSFERAKFWVKEL 99
Query: 135 RTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGNKTDL 194
+ H I L G K+DL
Sbjct: 100 Q----------------NLEEHCK--------------------------IYLCGTKSDL 117
Query: 195 ----SDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQV 230
RQV + + A E+ ETS+K G NV ++
Sbjct: 118 IEQDRSLRQVDFHDVQDFADEIKAQHFETSSKTGQNVDEL 157
Score = 82.6 bits (204), Expect = 1e-18
Identities = 41/116 (35%), Positives = 65/116 (56%), Gaps = 5/116 (4%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDV 287
+ V L +WDTAG ER+ ++ Y R + A+V YD+T+++SF + W+ +++
Sbjct: 48 RVVTLGIWDTAGSERYEAMSRIYYRGAKAAIVCYDLTDSSSFERAKFWVKELQNLE-EHC 106
Query: 288 IIMLVGNKTDL----SDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVA 339
I L G K+DL RQV + + A E+ ETS+K G NV +LF++VA
Sbjct: 107 KIYLCGTKSDLIEQDRSLRQVDFHDVQDFADEIKAQHFETSSKTGQNVDELFQKVA 162
>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 = 99.9 bits (249), Expect = 9e-25
Identities = 59/182 (32%), Positives = 81/182 (44%), Gaps = 39/182 (21%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLE-DRTVRLQLWDTAGQERFRSLIPSY 105
GKTSLI RF + F +Y+ TIG+DF S+ + L V LQ+WD GQ+ ++ Y
Sbjct: 11 SGKTSLIRRFAQEGFGKSYKQTIGLDFFSRRITLPGSLNVTLQVWDIGGQQIGGKMLDKY 70
Query: 106 IRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSF 165
I + +VYDITN+ SF W+ V
Sbjct: 71 IYGAQAVCLVYDITNSQSFENLEDWLSVV------------------------------- 99
Query: 166 HQTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGY 225
V E + ++LVGNKTDL RQV+ E+ R A+E ++ I SAK G
Sbjct: 100 -------KKVNEESETKPKMVLVGNKTDLEHNRQVTAEKHARFAQENDMESIFVSAKTGD 152
Query: 226 NV 227
V
Sbjct: 153 RV 154
Score = 92.2 bits (229), Expect = 6e-22
Identities = 47/121 (38%), Positives = 66/121 (54%), Gaps = 3/121 (2%)
Query: 229 QVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKW---IDDVRTERGS 285
V LQ+WD GQ+ ++ YI + +VYDITN+ SF W + V E +
Sbjct: 49 NVTLQVWDIGGQQIGGKMLDKYIYGAQAVCLVYDITNSQSFENLEDWLSVVKKVNEESET 108
Query: 286 DVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVAAALPGM 345
++LVGNKTDL RQV+ E+ R A+E ++ I SAK G V F+R+AA L G+
Sbjct: 109 KPKMVLVGNKTDLEHNRQVTAEKHARFAQENDMESIFVSAKTGDRVFLCFQRIAAELLGV 168
Query: 346 D 346
Sbjct: 169 K 169
>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 = 97.7 bits (244), Expect = 2e-24
Identities = 60/230 (26%), Positives = 92/230 (40%), Gaps = 82/230 (35%)
Query: 16 LVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGIDFLS 75
LV +G+ +VGKT L+ + ++F Y T+ F+N Y A + +D
Sbjct: 1 LVVVGDGAVGKTCLLIVYTTNAFPEDYVPTV--------------FEN-YSADVEVD--- 42
Query: 76 KTMYLEDRTVRLQLWDTAGQERFRSLIP-SYIRDSTVAVVVYDITNANSFHQ-TSKWIDD 133
+ V L LWDTAGQE + L P SY D+ V ++ + + + SF KW +
Sbjct: 43 ------GKPVELGLWDTAGQEDYDRLRPLSY-PDTDVFLICFSVDSPASFENVKEKWYPE 95
Query: 134 VRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGNKTD 193
V+ H +V I+LVG K D
Sbjct: 96 VK------------------------HFCP------------------NVPIILVGTKLD 113
Query: 194 L----------SDKRQ--VSTEEGERKAKELN-VMFIETSAKAGYNVKQV 230
L S K+Q V+ E+G+ AK + V ++E SA V++V
Sbjct: 114 LRNDKSTLEELSKKKQEPVTYEQGQALAKRIGAVKYLECSALTQEGVREV 163
Score = 93.8 bits (234), Expect = 5e-23
Identities = 46/131 (35%), Positives = 68/131 (51%), Gaps = 17/131 (12%)
Query: 220 SAKAGYNVKQVRLQLWDTAGQERFRSLIP-SYIRDSTVAVVVYDITNANSFHQ-TSKWID 277
SA + K V L LWDTAGQE + L P SY D+ V ++ + + + SF KW
Sbjct: 36 SADVEVDGKPVELGLWDTAGQEDYDRLRPLSY-PDTDVFLICFSVDSPASFENVKEKWYP 94
Query: 278 DVRTERGSDVIIMLVGNKTDL----------SDKRQ--VSTEEGERKAKELN-VMFIETS 324
+V+ +V I+LVG K DL S K+Q V+ E+G+ AK + V ++E S
Sbjct: 95 EVK-HFCPNVPIILVGTKLDLRNDKSTLEELSKKKQEPVTYEQGQALAKRIGAVKYLECS 153
Query: 325 AKAGYNVKQLF 335
A V+++F
Sbjct: 154 ALTQEGVREVF 164
>gnl|CDD|206693 cd04108, Rab36_Rab34, Rab GTPase families 34 (Rab34) and 36
(Rab36). Rab34/Rab36 subfamily. Rab34, found primarily
in the Golgi, interacts with its effector,
Rab-interacting lysosomal protein (RILP). This enables
its participation in microtubular
dynenin-dynactin-mediated repositioning of lysosomes
from the cell periphery to the Golgi. A Rab34 (Rah)
isoform that lacks the consensus GTP-binding region has
been identified in mice. This isoform is associated with
membrane ruffles and promotes macropinosome formation.
Rab36 has been mapped to human chromosome 22q11.2, a
region that is homozygously deleted in malignant
rhabdoid tumors (MRTs). However, experimental
assessments do not implicate Rab36 as a tumor suppressor
that would enable tumor formation through a
loss-of-function mechanism. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 170
Score = 96.9 bits (241), Expect = 4e-24
Identities = 58/185 (31%), Positives = 83/185 (44%), Gaps = 42/185 (22%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
VGKT LI RF D FD Y+ATIG+DF + + LQLWDTAGQERF+ + +Y
Sbjct: 11 VGKTCLINRFCKDVFDKNYKATIGVDFEMERFEVLGVPFSLQLWDTAGQERFKCIASTYY 70
Query: 107 RDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFH 166
R + ++V+D+T+ S T +W++D E
Sbjct: 71 RGAQAIIIVFDLTDVASLEHTRQWLEDALKENDP-------------------------- 104
Query: 167 QTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGE--RKAKELNVMFIETSAKAG 224
S V++ LVG K DLS Q + E + + A+E+ + SA G
Sbjct: 105 --------------SSVLLFLVGTKKDLSSPAQYALMEQDAIKLAREMKAEYWAVSALTG 150
Query: 225 YNVKQ 229
NV+
Sbjct: 151 ENVRD 155
Score = 91.5 bits (227), Expect = 4e-22
Identities = 44/112 (39%), Positives = 66/112 (58%), Gaps = 3/112 (2%)
Query: 232 LQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTER-GSDVIIM 290
LQLWDTAGQERF+ + +Y R + ++V+D+T+ S T +W++D E S V++
Sbjct: 51 LQLWDTAGQERFKCIASTYYRGAQAIIIVFDLTDVASLEHTRQWLEDALKENDPSSVLLF 110
Query: 291 LVGNKTDLSDKRQVSTEEGE--RKAKELNVMFIETSAKAGYNVKQLFRRVAA 340
LVG K DLS Q + E + + A+E+ + SA G NV+ F RVA+
Sbjct: 111 LVGTKKDLSSPAQYALMEQDAIKLAREMKAEYWAVSALTGENVRDFFFRVAS 162
>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 = 94.6 bits (236), Expect = 3e-23
Identities = 62/220 (28%), Positives = 95/220 (43%), Gaps = 72/220 (32%)
Query: 15 KLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATI---GI 71
K+ LG +SVGK+SL +F+ F +Y TI +NT+ I G
Sbjct: 3 KIAVLGSRSVGKSSLTVQFVEGHFVESYYPTI---------------ENTFSKIITYKGQ 47
Query: 72 DFLSKTMYLEDRTVRLQLWDTAGQERFRSLIP-SYIRDSTVAVVVYDITNANSFHQTSKW 130
++ L++ DTAGQ+ + S++P Y ++VY +T+ SF + K
Sbjct: 48 EY------------HLEIVDTAGQDEY-SILPQKYSIGIHGYILVYSVTSRKSF-EVVKV 93
Query: 131 IDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGN 190
I D K +D + E V I+LVGN
Sbjct: 94 IYD------------------------------------KILDMLGKES---VPIVLVGN 114
Query: 191 KTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQV 230
K+DL +RQVS EEG++ A+ F+E+SAK NV++
Sbjct: 115 KSDLHMERQVSAEEGKKLAESWGAAFLESSAKENENVEEA 154
Score = 91.5 bits (228), Expect = 5e-22
Identities = 43/126 (34%), Positives = 70/126 (55%), Gaps = 6/126 (4%)
Query: 232 LQLWDTAGQERFRSLIP-SYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVI-I 289
L++ DTAGQ+ + S++P Y ++VY +T+ SF D + G + + I
Sbjct: 51 LEIVDTAGQDEY-SILPQKYSIGIHGYILVYSVTSRKSFEVVKVIYDKILDMLGKESVPI 109
Query: 290 MLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVAAALPGMDSTE 349
+LVGNK+DL +RQVS EEG++ A+ F+E+SAK NV++ F + + ++ E
Sbjct: 110 VLVGNKSDLHMERQVSAEEGKKLAESWGAAFLESSAKENENVEEAFELL---IEEIEKVE 166
Query: 350 NKPPED 355
N P
Sbjct: 167 NPLPPG 172
>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 = 93.0 bits (231), Expect = 1e-22
Identities = 60/182 (32%), Positives = 85/182 (46%), Gaps = 39/182 (21%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
VGKT+L + + F TY TI D K + ++ + L++ DTAGQE + +L +I
Sbjct: 10 VGKTALTIQLCLNHFVETYDPTIE-DSYRKQVVVDGQPCMLEVLDTAGQEEYTALRDQWI 68
Query: 107 RDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFH 166
R+ ++VY IT+ ++F R ER F
Sbjct: 69 REGEGFILVYSITSRSTFE---------RVER--------------------FREQ---- 95
Query: 167 QTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYN 226
I V+ E +DV IM+VGNK D +R+VSTEEG A+ L FIE SAK N
Sbjct: 96 -----IQRVKDESAADVPIMIVGNKCDKVYEREVSTEEGAALARRLGCEFIEASAKTNVN 150
Query: 227 VK 228
V+
Sbjct: 151 VE 152
Score = 90.3 bits (224), Expect = 2e-21
Identities = 47/114 (41%), Positives = 70/114 (61%), Gaps = 3/114 (2%)
Query: 232 LQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKW---IDDVRTERGSDVI 288
L++ DTAGQE + +L +IR+ ++VY IT+ ++F + ++ I V+ E +DV
Sbjct: 49 LEVLDTAGQEEYTALRDQWIREGEGFILVYSITSRSTFERVERFREQIQRVKDESAADVP 108
Query: 289 IMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVAAAL 342
IM+VGNK D +R+VSTEEG A+ L FIE SAK NV++ F + AL
Sbjct: 109 IMIVGNKCDKVYEREVSTEEGAALARRLGCEFIEASAKTNVNVERAFYTLVRAL 162
>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 = 91.9 bits (228), Expect = 4e-22
Identities = 44/112 (39%), Positives = 68/112 (60%), Gaps = 1/112 (0%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDV 287
++V+LQLWDT+GQ RF ++ SY R + ++VYDITN SF +WI ++ E V
Sbjct: 53 RRVKLQLWDTSGQGRFCTIFRSYSRGAQGIILVYDITNRWSFDGIDRWIKEI-DEHAPGV 111
Query: 288 IIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVA 339
+LVGN+ L+ KRQV+TE+ + A+ + F E S +N+ + F +A
Sbjct: 112 PKILVGNRLHLAFKRQVATEQAQAYAERNGMTFFEVSPLCNFNITESFTELA 163
Score = 90.0 bits (223), Expect = 2e-21
Identities = 56/183 (30%), Positives = 84/183 (45%), Gaps = 42/183 (22%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
VGK ++ S ++ Y +GID+ + T+ L+ R V+LQLWDT+GQ RF ++ SY
Sbjct: 17 VGKGEILASLQDGSTESPYGYNMGIDYKTTTILLDGRRVKLQLWDTSGQGRFCTIFRSYS 76
Query: 107 RDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFH 166
R + ++VYDITN SF +WI
Sbjct: 77 RGAQGIILVYDITNRWSFDGIDRWI----------------------------------- 101
Query: 167 QTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYN 226
K ID E V +LVGN+ L+ KRQV+TE+ + A+ + F E S +N
Sbjct: 102 ---KEID----EHAPGVPKILVGNRLHLAFKRQVATEQAQAYAERNGMTFFEVSPLCNFN 154
Query: 227 VKQ 229
+ +
Sbjct: 155 ITE 157
>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 = 91.3 bits (227), Expect = 4e-22
Identities = 45/184 (24%), Positives = 82/184 (44%), Gaps = 36/184 (19%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
VGK+ +I R+ F + Y TIGID+ K + + ++ VR+ +D +G + + +
Sbjct: 11 VGKSCIIKRYCEGRFVSKYLPTIGIDYGVKKVSVRNKEVRVNFFDLSGHPEYLEVRNEFY 70
Query: 107 RDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFH 166
+D+ ++VYD+T+ SF W+ +++ E G H N
Sbjct: 71 KDTQGVLLVYDVTDRQSFEALDSWLKEMKQEGGP--------------------HGNM-- 108
Query: 167 QTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYN 226
++++++ NK DL+ R VS +EG A+ + ETSA G
Sbjct: 109 --------------ENIVVVVCANKIDLTKHRAVSEDEGRLWAESKGFKYFETSACTGEG 154
Query: 227 VKQV 230
V ++
Sbjct: 155 VNEM 158
Score = 75.5 bits (186), Expect = 2e-16
Identities = 32/113 (28%), Positives = 61/113 (53%), Gaps = 5/113 (4%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGS-- 285
K+VR+ +D +G + + + +D+ ++VYD+T+ SF W+ +++ E G
Sbjct: 47 KEVRVNFFDLSGHPEYLEVRNEFYKDTQGVLLVYDVTDRQSFEALDSWLKEMKQEGGPHG 106
Query: 286 ---DVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLF 335
++++++ NK DL+ R VS +EG A+ + ETSA G V ++F
Sbjct: 107 NMENIVVVVCANKIDLTKHRAVSEDEGRLWAESKGFKYFETSACTGEGVNEMF 159
>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 = 91.6 bits (228), Expect = 6e-22
Identities = 45/124 (36%), Positives = 59/124 (47%), Gaps = 17/124 (13%)
Query: 228 KQVRLQLWDTAGQERFRSLIP-SYIRDSTVAVVVYDITNANSFHQ-TSKWIDDVRTERGS 285
K + L LWDTAGQE + L P SY D V ++ Y + N S KW +V
Sbjct: 50 KIIELALWDTAGQEDYDRLRPLSY-PDVDVILICYSVDNPTSLDNVEDKWYPEV-NHFCP 107
Query: 286 DVIIMLVGNKTDLSDKRQ------------VSTEEGERKAKELN-VMFIETSAKAGYNVK 332
I+LVG KTDL + V+ E+GE AK + V +IE SAK NV
Sbjct: 108 GTPIVLVGLKTDLRKDKNSVSKLRAQGLEPVTPEQGESVAKSIGAVAYIECSAKLMENVD 167
Query: 333 QLFR 336
++F
Sbjct: 168 EVFD 171
Score = 89.7 bits (223), Expect = 3e-21
Identities = 61/234 (26%), Positives = 84/234 (35%), Gaps = 81/234 (34%)
Query: 12 RKFKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGI 71
K K+V +G+ GKT L+ + SF Y T+ F+N Y T+ +
Sbjct: 2 LKVKIVVVGDGGCGKTCLLMVYAQGSFPEEYVPTV--------------FEN-YVTTLQV 46
Query: 72 DFLSKTMYLEDRTVRLQLWDTAGQERFRSLIP-SYIRDSTVAVVVYDITNANSFHQ-TSK 129
+ + L LWDTAGQE + L P SY D V ++ Y + N S K
Sbjct: 47 P--------NGKIIELALWDTAGQEDYDRLRPLSY-PDVDVILICYSVDNPTSLDNVEDK 97
Query: 130 WIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVG 189
W +V H I+LVG
Sbjct: 98 WYPEV--------------------NHFC----------------------PGTPIVLVG 115
Query: 190 NKTDLSDKRQ------------VSTEEGERKAKELN-VMFIETSAKAGYNVKQV 230
KTDL + V+ E+GE AK + V +IE SAK NV +V
Sbjct: 116 LKTDLRKDKNSVSKLRAQGLEPVTPEQGESVAKSIGAVAYIECSAKLMENVDEV 169
>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 = 89.2 bits (221), Expect = 3e-21
Identities = 57/182 (31%), Positives = 88/182 (48%), Gaps = 39/182 (21%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
VGK+SL+ R++ + FD TIG++FL+K + ++ V LQ+WDTAGQERFRSL +
Sbjct: 16 VGKSSLMNRYVTNKFDTQLFHTIGVEFLNKDLEVDGHFVTLQIWDTAGQERFRSLRTPFY 75
Query: 107 RDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFH 166
R S ++ + + ++ SF S W + F + +
Sbjct: 76 RGSDCCLLTFSVDDSQSFQNLSNW--------------------KKEFIYYA-------- 107
Query: 167 QTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVM-FIETSAKAGY 225
DV+ +I +GNK D+ +RQVSTEE + ++ + ETSAK
Sbjct: 108 -------DVKEPESFPFVI--LGNKIDIP-ERQVSTEEAQAWCRDNGDYPYFETSAKDAT 157
Query: 226 NV 227
NV
Sbjct: 158 NV 159
Score = 70.7 bits (173), Expect = 1e-14
Identities = 43/113 (38%), Positives = 60/113 (53%), Gaps = 10/113 (8%)
Query: 230 VRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKW------IDDVRTER 283
V LQ+WDTAGQERFRSL + R S ++ + + ++ SF S W DV+
Sbjct: 54 VTLQIWDTAGQERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPE 113
Query: 284 GSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVM-FIETSAKAGYNVKQLF 335
+I +GNK D+ +RQVSTEE + ++ + ETSAK NV F
Sbjct: 114 SFPFVI--LGNKIDIP-ERQVSTEEAQAWCRDNGDYPYFETSAKDATNVAAAF 163
>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 = 88.4 bits (219), Expect = 6e-21
Identities = 56/187 (29%), Positives = 83/187 (44%), Gaps = 44/187 (23%)
Query: 47 VGKTSLITRFMYD--SFDNTYQATIGIDFLSKTMYLED--RTVRLQLWDTAGQERFRSLI 102
VGK++L+ F D +F Y T G D + KT+ + D +V L ++D+AGQE F ++
Sbjct: 11 VGKSALVQMFHSDGATFQKNYTMTTGCDLVVKTVPVPDTSDSVELFIFDSAGQELFSDMV 70
Query: 103 PSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHA 162
+ V VVYD+TN SF+ S+WI+ VRT
Sbjct: 71 ENVWEQPAVVCVVYDVTNEVSFNNCSRWINRVRTH------------------------- 105
Query: 163 NSFHQTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAK 222
G +LVGNK DL+D+R+V + + A+ + F ETSAK
Sbjct: 106 ---------------SHGLHTPGVLVGNKCDLTDRREVDAAQAQALAQANTLKFYETSAK 150
Query: 223 AGYNVKQ 229
G +
Sbjct: 151 EGVGYEA 157
Score = 87.2 bits (216), Expect = 1e-20
Identities = 45/113 (39%), Positives = 65/113 (57%), Gaps = 1/113 (0%)
Query: 230 VRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTE-RGSDVI 288
V L ++D+AGQE F ++ + V VVYD+TN SF+ S+WI+ VRT G
Sbjct: 53 VELFIFDSAGQELFSDMVENVWEQPAVVCVVYDVTNEVSFNNCSRWINRVRTHSHGLHTP 112
Query: 289 IMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVAAA 341
+LVGNK DL+D+R+V + + A+ + F ETSAK G + F +A A
Sbjct: 113 GVLVGNKCDLTDRREVDAAQAQALAQANTLKFYETSAKEGVGYEAPFLSLARA 165
>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 = 86.6 bits (215), Expect = 2e-20
Identities = 56/217 (25%), Positives = 87/217 (40%), Gaps = 71/217 (32%)
Query: 15 KLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFM--YDS-FDNTYQATIGI 71
K+ LG VGK++L RF L RF+ Y+ ++ Y
Sbjct: 1 KIAVLGASGVGKSALTVRF------------------LTKRFIGEYEPNLESLY------ 36
Query: 72 DFLSKTMYLEDRTVRLQLWDTAGQERF--RSLIPSYIRDSTVAVVVYDITNANSFHQTSK 129
S+ + ++ V L++ DT GQ++ + +R + V+VY IT+ +SF
Sbjct: 37 ---SRQVTIDGEQVSLEIQDTPGQQQNEDPESLERSLRWADGFVLVYSITDRSSF----- 88
Query: 130 WIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVG 189
DV+ L+ + R ++ ++LVG
Sbjct: 89 -----------DVVSQLL------------QLIREIKK-----------RDGEIPVILVG 114
Query: 190 NKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYN 226
NK DL RQVSTEEG++ A EL +F E SA Y
Sbjct: 115 NKADLLHSRQVSTEEGQKLALELGCLFFEVSAAENYL 151
Score = 78.5 bits (194), Expect = 2e-17
Identities = 43/116 (37%), Positives = 68/116 (58%), Gaps = 5/116 (4%)
Query: 228 KQVRLQLWDTAGQERF--RSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVR--TER 283
+QV L++ DT GQ++ + +R + V+VY IT+ +SF S+ + +R +R
Sbjct: 45 EQVSLEIQDTPGQQQNEDPESLERSLRWADGFVLVYSITDRSSFDVVSQLLQLIREIKKR 104
Query: 284 GSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYN-VKQLFRRV 338
++ ++LVGNK DL RQVSTEEG++ A EL +F E SA Y V+ +F +
Sbjct: 105 DGEIPVILVGNKADLLHSRQVSTEEGQKLALELGCLFFEVSAAENYLEVQNVFHEL 160
>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 = 86.0 bits (213), Expect = 3e-20
Identities = 43/108 (39%), Positives = 62/108 (57%), Gaps = 1/108 (0%)
Query: 232 LQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDD-VRTERGSDVIIM 290
L++ DTAG E+F S+ YI++ +VVY + N +F D VR + V I+
Sbjct: 51 LEILDTAGTEQFASMRDLYIKNGQGFIVVYSLVNQQTFQDIKPMRDQIVRVKGYEKVPII 110
Query: 291 LVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRV 338
LVGNK DL +R+VS+ EG A+E F+ETSAK+ V +LF +
Sbjct: 111 LVGNKVDLESEREVSSAEGRALAEEWGCPFMETSAKSKTMVNELFAEI 158
Score = 85.7 bits (212), Expect = 4e-20
Identities = 60/222 (27%), Positives = 94/222 (42%), Gaps = 64/222 (28%)
Query: 13 KFKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGID 72
++K+V LG VGK++L +F+ +F Y TI D
Sbjct: 1 EYKVVVLGSGGVGKSALTVQFVSGTFIEKYDPTIE------------------------D 36
Query: 73 FLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWID 132
F K + ++ L++ DTAG E+F S+ YI++ +VVY + N +F
Sbjct: 37 FYRKEIEVDSSPSVLEILDTAGTEQFASMRDLYIKNGQGFIVVYSLVNQQTFQ------- 89
Query: 133 DVRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGNKT 192
D++ R D I VR + V I+LVGNK
Sbjct: 90 DIKPMR--DQI-------------------------------VRVKGYEKVPIILVGNKV 116
Query: 193 DLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQVRLQL 234
DL +R+VS+ EG A+E F+ETSAK+ V ++ ++
Sbjct: 117 DLESEREVSSAEGRALAEEWGCPFMETSAKSKTMVNELFAEI 158
>gnl|CDD|206710 cd04139, RalA_RalB, Ral (Ras-like) family containing highly
homologous RalA and RalB. The Ral (Ras-like) subfamily
consists of the highly homologous RalA and RalB. Ral
proteins are believed to play a crucial role in
tumorigenesis, metastasis, endocytosis, and actin
cytoskeleton dynamics. Despite their high sequence
similarity (>80% sequence identity), nonoverlapping and
opposing functions have been assigned to RalA and RalBs
in tumor migration. In human bladder and prostate cancer
cells, RalB promotes migration while RalA inhibits it. A
Ral-specific set of GEFs has been identified that are
activated by Ras binding. This RalGEF activity is
enhanced by Ras binding to another of its target
proteins, phosphatidylinositol 3-kinase (PI3K). Ral
effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and
the exocyst (Sec6/8) complex, a heterooctomeric protein
complex that is involved in tethering vesicles to
specific sites on the plasma membrane prior to
exocytosis. In rat kidney cells, RalB is required for
functional assembly of the exocyst and for localizing
the exocyst to the leading edge of migrating cells. In
human cancer cells, RalA is required to support
anchorage-independent proliferation and RalB is required
to suppress apoptosis. RalA has been shown to localize
to the plasma membrane while RalB is localized to the
intracellular vesicles. Most Ras proteins contain a
lipid modification site at the C-terminus, with a
typical sequence motif CaaX, where a = an aliphatic
amino acid and X = any amino acid. Lipid binding is
essential for membrane attachment, a key feature of most
Ras proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 163
Score = 85.6 bits (212), Expect = 4e-20
Identities = 57/188 (30%), Positives = 88/188 (46%), Gaps = 41/188 (21%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
VGK++L +FMYD F Y+ T D K + L+ V+L + DTAGQE + ++ +Y
Sbjct: 11 VGKSALTLQFMYDEFVEDYEPTKA-DSYRKKVVLDGEEVQLNILDTAGQEDYAAIRDNYF 69
Query: 107 RDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFH 166
R ++V+ IT+ SF +++ + +
Sbjct: 70 RSGEGFLLVFSITDMESFTALAEFREQI-------------------------------- 97
Query: 167 QTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYN 226
+R + +V ++LVGNK DL DKRQVS EE A++ V ++ETSAK N
Sbjct: 98 --------LRVKEDDNVPLLLVGNKCDLEDKRQVSVEEAANLAEQWGVNYVETSAKTRAN 149
Query: 227 VKQVRLQL 234
V +V L
Sbjct: 150 VDKVFFDL 157
Score = 79.8 bits (197), Expect = 5e-18
Identities = 42/108 (38%), Positives = 68/108 (62%), Gaps = 1/108 (0%)
Query: 229 QVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDV-RTERGSDV 287
+V+L + DTAGQE + ++ +Y R ++V+ IT+ SF +++ + + R + +V
Sbjct: 47 EVQLNILDTAGQEDYAAIRDNYFRSGEGFLLVFSITDMESFTALAEFREQILRVKEDDNV 106
Query: 288 IIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLF 335
++LVGNK DL DKRQVS EE A++ V ++ETSAK NV ++F
Sbjct: 107 PLLLVGNKCDLEDKRQVSVEEAANLAEQWGVNYVETSAKTRANVDKVF 154
>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 = 84.8 bits (210), Expect = 1e-19
Identities = 42/109 (38%), Positives = 66/109 (60%), Gaps = 1/109 (0%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDV-RTERGSD 286
+ RL + DTAGQE F ++ Y+R ++V+ +T+ SF + K+ + R + +
Sbjct: 48 QWARLDILDTAGQEEFSAMREQYMRTGEGFLLVFSVTDRGSFEEVDKFHTQILRVKDRDE 107
Query: 287 VIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLF 335
++LVGNK DL +RQVS EEG+ A++L + +IETSAK NV + F
Sbjct: 108 FPMILVGNKADLEHQRQVSREEGQELARQLKIPYIETSAKDRVNVDKAF 156
Score = 80.9 bits (200), Expect = 2e-18
Identities = 61/218 (27%), Positives = 92/218 (42%), Gaps = 64/218 (29%)
Query: 12 RKFKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGI 71
+KLV +G VGK++L +F+ F Y TI DS+ T Q I
Sbjct: 1 PTYKLVVVGGGGVGKSALTIQFIQSYFVTDYDPTI-----------EDSY--TKQCEI-- 45
Query: 72 DFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWI 131
+ + RL + DTAGQE F ++ Y+R ++V+ +T+ SF + K
Sbjct: 46 ---------DGQWARLDILDTAGQEEFSAMREQYMRTGEGFLLVFSVTDRGSFEEVDK-- 94
Query: 132 DDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGNK 191
FH +R + + ++LVGNK
Sbjct: 95 ---------------------------------FHTQI-----LRVKDRDEFPMILVGNK 116
Query: 192 TDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQ 229
DL +RQVS EEG+ A++L + +IETSAK NV +
Sbjct: 117 ADLEHQRQVSREEGQELARQLKIPYIETSAKDRVNVDK 154
>gnl|CDD|240385 PTZ00369, PTZ00369, Ras-like protein; Provisional.
Length = 189
Score = 80.3 bits (198), Expect = 7e-18
Identities = 60/217 (27%), Positives = 93/217 (42%), Gaps = 64/217 (29%)
Query: 13 KFKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGID 72
++KLV +G VGK++L +F+ + F + Y TI +++Y+ ID
Sbjct: 5 EYKLVVVGGGGVGKSALTIQFIQNHFIDEYDPTI---------------EDSYRKQCVID 49
Query: 73 FLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWID 132
+ T L + DTAGQE + ++ Y+R + VY IT+ +SF +
Sbjct: 50 ---------EETCLLDILDTAGQEEYSAMRDQYMRTGQGFLCVYSITSRSSFEEI----- 95
Query: 133 DVRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGNKT 192
SF + +R + V ++LVGNK
Sbjct: 96 ------------------------------ASFREQI-----LRVKDKDRVPMILVGNKC 120
Query: 193 DLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQ 229
DL +RQVST EG+ AK + F+ETSAK NV +
Sbjct: 121 DLDSERQVSTGEGQELAKSFGIPFLETSAKQRVNVDE 157
Score = 79.1 bits (195), Expect = 2e-17
Identities = 42/105 (40%), Positives = 63/105 (60%), Gaps = 1/105 (0%)
Query: 232 LQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDV-RTERGSDVIIM 290
L + DTAGQE + ++ Y+R + VY IT+ +SF + + + + + R + V ++
Sbjct: 55 LDILDTAGQEEYSAMRDQYMRTGQGFLCVYSITSRSSFEEIASFREQILRVKDKDRVPMI 114
Query: 291 LVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLF 335
LVGNK DL +RQVST EG+ AK + F+ETSAK NV + F
Sbjct: 115 LVGNKCDLDSERQVSTGEGQELAKSFGIPFLETSAKQRVNVDEAF 159
>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 = 79.0 bits (195), Expect = 2e-17
Identities = 62/226 (27%), Positives = 98/226 (43%), Gaps = 60/226 (26%)
Query: 15 KLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGIDFL 74
K V +G+ +VGKTSLI + + + Y T +FDN + + +D
Sbjct: 2 KCVLVGDGAVGKTSLIVSYTTNGYPTEYVPT--------------AFDN-FSVVVLVD-- 44
Query: 75 SKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQ-TSKWIDD 133
+ VRLQL DTAGQ+ F L P D+ V ++ + + N +SF + KWI +
Sbjct: 45 -------GKPVRLQLCDTAGQDEFDKLRPLCYPDTDVFLLCFSVVNPSSFQNISEKWIPE 97
Query: 134 VRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGNKTD 193
+R I+LVG+ Q D+RT+ +V+I L
Sbjct: 98 IRK-HNPKAPIILVGT-----------------QA-----DLRTD--VNVLIQLARYGE- 131
Query: 194 LSDKRQVSTEEGERKAKELN-VMFIETSAKAGYNVKQVRLQLWDTA 238
+ VS + A+++ +IE SA N+K+V +DTA
Sbjct: 132 ----KPVSQSRAKALAEKIGACEYIECSALTQKNLKEV----FDTA 169
Score = 68.6 bits (168), Expect = 7e-14
Identities = 40/130 (30%), Positives = 63/130 (48%), Gaps = 15/130 (11%)
Query: 220 SAKAGYNVKQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQ-TSKWIDD 278
S + K VRLQL DTAGQ+ F L P D+ V ++ + + N +SF + KWI +
Sbjct: 38 SVVVLVDGKPVRLQLCDTAGQDEFDKLRPLCYPDTDVFLLCFSVVNPSSFQNISEKWIPE 97
Query: 279 VRTERGSDVIIMLVGNKTDLSD------------KRQVSTEEGERKAKELN-VMFIETSA 325
+R I+LVG + DL ++ VS + A+++ +IE SA
Sbjct: 98 IRK-HNPKAPIILVGTQADLRTDVNVLIQLARYGEKPVSQSRAKALAEKIGACEYIECSA 156
Query: 326 KAGYNVKQLF 335
N+K++F
Sbjct: 157 LTQKNLKEVF 166
>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 = 77.9 bits (192), Expect = 2e-17
Identities = 41/109 (37%), Positives = 67/109 (61%), Gaps = 1/109 (0%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDV-RTERGSD 286
+Q L++ DTAG E+F ++ Y+++ V+VY IT ++F+ + + R + D
Sbjct: 47 QQCMLEILDTAGTEQFTAMRDLYMKNGQGFVLVYSITAQSTFNDLQDLREQILRVKDTED 106
Query: 287 VIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLF 335
V ++LVGNK DL D+R V E+G+ A++ F+ETSAKA NV ++F
Sbjct: 107 VPMILVGNKCDLEDERVVGKEQGQNLARQWGCAFLETSAKAKINVNEIF 155
Score = 77.2 bits (190), Expect = 4e-17
Identities = 57/218 (26%), Positives = 98/218 (44%), Gaps = 64/218 (29%)
Query: 13 KFKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGID 72
++KLV LG VGK++L +F+ F Y TI +++Y+
Sbjct: 1 EYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTI---------------EDSYR------ 39
Query: 73 FLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWID 132
K + ++ + L++ DTAG E+F ++ Y+++ V+VY IT ++F+ +
Sbjct: 40 ---KQVEVDGQQCMLEILDTAGTEQFTAMRDLYMKNGQGFVLVYSITAQSTFND----LQ 92
Query: 133 DVRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGNKT 192
D+R + +R + DV ++LVGNK
Sbjct: 93 DLREQI------------------------------------LRVKDTEDVPMILVGNKC 116
Query: 193 DLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQV 230
DL D+R V E+G+ A++ F+ETSAKA NV ++
Sbjct: 117 DLEDERVVGKEQGQNLARQWGCAFLETSAKAKINVNEI 154
>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 = 77.8 bits (192), Expect = 3e-17
Identities = 38/105 (36%), Positives = 59/105 (56%), Gaps = 2/105 (1%)
Query: 232 LQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDV-RTERGSDVIIM 290
L + DTAGQE + ++ Y+R + V+ I + SF + + + R + DV ++
Sbjct: 51 LDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINSRKSFEDIHTYREQIKRVKDSDDVPMV 110
Query: 291 LVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLF 335
LVGNK DL+ R VST +G+ AK + +IETSAK V++ F
Sbjct: 111 LVGNKCDLAA-RTVSTRQGQDLAKSYGIPYIETSAKTRQGVEEAF 154
Score = 77.5 bits (191), Expect = 4e-17
Identities = 56/215 (26%), Positives = 90/215 (41%), Gaps = 65/215 (30%)
Query: 13 KFKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGID 72
++KLV +G VGK++L + + + F + Y TI +++Y+ + ID
Sbjct: 1 EYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTI---------------EDSYRKQVVID 45
Query: 73 FLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWID 132
T L + DTAGQE + ++ Y+R + V+ I + SF +
Sbjct: 46 ---------GETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINSRKSF-------E 89
Query: 133 DVRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGNKT 192
D+ T + + K + D DV ++LVGNK
Sbjct: 90 DIHT----------------------------YREQIKRVKDS-----DDVPMVLVGNKC 116
Query: 193 DLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNV 227
DL+ R VST +G+ AK + +IETSAK V
Sbjct: 117 DLAA-RTVSTRQGQDLAKSYGIPYIETSAKTRQGV 150
>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 = 76.8 bits (189), Expect = 5e-17
Identities = 34/121 (28%), Positives = 62/121 (51%), Gaps = 2/121 (1%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
VGK+ L+ RF+ D ++ +T + E +T+ + WDTAGQERF+++ SY
Sbjct: 11 VGKSKLVERFLMDGYEPQQLSTYALTLYKHNAKFEGKTILVDFWDTAGQERFQTMHASYY 70
Query: 107 RDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIET--NFTHLSFHHANS 164
+ ++V+D+T ++ SKW +++R R I++ I+ + T F+ A
Sbjct: 71 HKAHACILVFDVTRKITYKNLSKWYEELREYRPEIPCIVVANKIDLDPSVTQKKFNFAEK 130
Query: 165 F 165
Sbjct: 131 H 131
Score = 69.1 bits (169), Expect = 3e-14
Identities = 35/109 (32%), Positives = 61/109 (55%), Gaps = 4/109 (3%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDV 287
K + + WDTAGQERF+++ SY + ++V+D+T ++ SKW +++R R ++
Sbjct: 47 KTILVDFWDTAGQERFQTMHASYYHKAHACILVFDVTRKITYKNLSKWYEELREYR-PEI 105
Query: 288 IIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFR 336
++V NK DL T++ A++ N+ SA G NV +LF+
Sbjct: 106 PCIVVANKIDLDPS---VTQKKFNFAEKHNLPLYYVSAADGTNVVKLFQ 151
>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 = 78.2 bits (193), Expect = 7e-17
Identities = 63/228 (27%), Positives = 97/228 (42%), Gaps = 73/228 (32%)
Query: 14 FKLVFLGEQSVGKTSLITRFMYDSFDN-TYQATIVGKTSLITRFMYDSFDNTYQATIGID 72
+++V LG+ VGK+SL F +++ Y+A S D+TY+ T+ +D
Sbjct: 1 YRVVLLGDSGVGKSSLANIFTAGVYEDSAYEA---------------SGDDTYERTVSVD 45
Query: 73 FLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWID 132
E+ T L ++D QE L S ++ V+VY +T+ +SF
Sbjct: 46 -------GEEAT--LVVYDHWEQEDGMWLEDSCMQVGDAYVIVYSVTDRSSF-------- 88
Query: 133 DVRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGNKT 192
E+ S++ I L R + D+ I+LVGNK+
Sbjct: 89 ----EKASELRIQLR----------------------------RARQAEDIPIILVGNKS 116
Query: 193 DLSDKRQVSTEEGERKAKELNVMFIETSAKAGYN--------VKQVRL 232
DL R+VS +EG A + FIETSA +N V+QVRL
Sbjct: 117 DLVRSREVSVQEGRACAVVFDCKFIETSAALQHNVDELFEGIVRQVRL 164
Score = 77.8 bits (192), Expect = 8e-17
Identities = 40/106 (37%), Positives = 60/106 (56%), Gaps = 1/106 (0%)
Query: 232 LQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGS-DVIIM 290
L ++D QE L S ++ V+VY +T+ +SF + S+ +R R + D+ I+
Sbjct: 51 LVVYDHWEQEDGMWLEDSCMQVGDAYVIVYSVTDRSSFEKASELRIQLRRARQAEDIPII 110
Query: 291 LVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFR 336
LVGNK+DL R+VS +EG A + FIETSA +NV +LF
Sbjct: 111 LVGNKSDLVRSREVSVQEGRACAVVFDCKFIETSAALQHNVDELFE 156
>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 = 76.8 bits (189), Expect = 8e-17
Identities = 56/219 (25%), Positives = 91/219 (41%), Gaps = 64/219 (29%)
Query: 12 RKFKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGI 71
R++K+V LG VGK+++ +F+ SF + + TI ++ Y+ I
Sbjct: 1 REYKIVMLGAGGVGKSAVTMQFISHSFPDYHDPTI---------------EDAYKTQARI 45
Query: 72 DFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWI 131
D + L + DTAGQ F ++ Y+R ++ Y +T+ +SF + S++
Sbjct: 46 D---------NEPALLDILDTAGQAEFTAMRDQYMRCGEGFIICYSVTDRHSFQEASEF- 95
Query: 132 DDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGNK 191
+ I VR D+ ++LVGNK
Sbjct: 96 -------------------------------------KELITRVR--LTEDIPLVLVGNK 116
Query: 192 TDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQV 230
DL +RQV+TEEG A+E N F ETSA + +
Sbjct: 117 VDLEQQRQVTTEEGRNLAREFNCPFFETSAALRFYIDDA 155
Score = 75.7 bits (186), Expect = 2e-16
Identities = 39/106 (36%), Positives = 61/106 (57%), Gaps = 1/106 (0%)
Query: 232 LQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDV-RTERGSDVIIM 290
L + DTAGQ F ++ Y+R ++ Y +T+ +SF + S++ + + R D+ ++
Sbjct: 52 LDILDTAGQAEFTAMRDQYMRCGEGFIICYSVTDRHSFQEASEFKELITRVRLTEDIPLV 111
Query: 291 LVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFR 336
LVGNK DL +RQV+TEEG A+E N F ETSA + + F
Sbjct: 112 LVGNKVDLEQQRQVTTEEGRNLAREFNCPFFETSAALRFYIDDAFH 157
>gnl|CDD|206708 cd04136, Rap_like, Rap-like family consists of Rap1, Rap2 and RSR1.
The Rap subfamily consists of the Rap1, Rap2, and RSR1.
Rap subfamily proteins perform different cellular
functions, depending on the isoform and its subcellular
localization. For example, in rat salivary gland,
neutrophils, and platelets, Rap1 localizes to secretory
granules and is believed to regulate exocytosis or the
formation of secretory granules. Rap1 has also been
shown to localize in the Golgi of rat fibroblasts,
zymogen granules, plasma membrane, and microsomal
membrane of the pancreatic acini, as well as in the
endocytic compartment of skeletal muscle cells and
fibroblasts. Rap1 localizes in the nucleus of human
oropharyngeal squamous cell carcinomas (SCCs) and cell
lines. Rap1 plays a role in phagocytosis by controlling
the binding of adhesion receptors (typically integrins)
to their ligands. In yeast, Rap1 has been implicated in
multiple functions, including activation and silencing
of transcription and maintenance of telomeres. Rap2 is
involved in multiple functions, including activation of
c-Jun N-terminal kinase (JNK) to regulate the actin
cytoskeleton and activation of the Wnt/beta-catenin
signaling pathway in embryonic Xenopus. A number of
effector proteins for Rap2 have been identified,
including isoform 3 of the human mitogen-activated
protein kinase kinase kinase kinase 4 (MAP4K4) and
Traf2- and Nck-interacting kinase (TNIK), and the
RalGEFs RalGDS, RGL, and Rlf, which also interact with
Rap1 and Ras. RSR1 is the fungal homolog of Rap1 and
Rap2. In budding yeasts, it is involved in selecting a
site for bud growth, which directs the establishment of
cell polarization. The Rho family GTPase Cdc42 and its
GEF, Cdc24, then establish an axis of polarized growth.
It is believed that Cdc42 interacts directly with RSR1
in vivo. In filamentous fungi such as Ashbya gossypii,
RSR1 is a key regulator of polar growth in the hypha.
Most Ras proteins contain a lipid modification site at
the C-terminus, with a typical sequence motif CaaX,
where a = an aliphatic amino acid and X = any amino
acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins. Due to
the presence of truncated sequences in this CD, the
lipid modification site is not available for annotation.
Length = 164
Score = 76.1 bits (187), Expect = 1e-16
Identities = 44/110 (40%), Positives = 67/110 (60%), Gaps = 2/110 (1%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDV-RTERGSD 286
+Q L++ DTAG E+F ++ YI++ +VY IT SF+ + + R + D
Sbjct: 47 QQCMLEILDTAGTEQFTAMRDLYIKNGQGFALVYSITAQQSFNDLQDLREQILRVKDTED 106
Query: 287 VIIMLVGNKTDLSDKRQVSTEEGERKAKEL-NVMFIETSAKAGYNVKQLF 335
V ++LVGNK DL D+R VS EEG+ A++ N F+ETSAK+ NV ++F
Sbjct: 107 VPMILVGNKCDLEDERVVSKEEGQNLARQWGNCPFLETSAKSKINVDEIF 156
Score = 74.5 bits (183), Expect = 5e-16
Identities = 53/185 (28%), Positives = 85/185 (45%), Gaps = 42/185 (22%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
VGK++L +F+ F + Y TI D K + ++ + L++ DTAG E+F ++ YI
Sbjct: 12 VGKSALTVQFVQGIFVDKYDPTIE-DSYRKQIEVDCQQCMLEILDTAGTEQFTAMRDLYI 70
Query: 107 RDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFH 166
++ +VY IT SF+ + +
Sbjct: 71 KNGQGFALVYSITAQQSFNDLQDLREQI-------------------------------- 98
Query: 167 QTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKEL-NVMFIETSAKAGY 225
+R + DV ++LVGNK DL D+R VS EEG+ A++ N F+ETSAK+
Sbjct: 99 --------LRVKDTEDVPMILVGNKCDLEDERVVSKEEGQNLARQWGNCPFLETSAKSKI 150
Query: 226 NVKQV 230
NV ++
Sbjct: 151 NVDEI 155
>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 = 76.0 bits (187), Expect = 1e-16
Identities = 45/197 (22%), Positives = 70/197 (35%), Gaps = 54/197 (27%)
Query: 47 VGKTSLITRFMYDSF---DNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERF----- 98
VGK+SL+ + + T D L+ V+L L DT G + F
Sbjct: 8 VGKSSLLNALLGGEVGEVSDVPGTTRDPDV--YVKELDKGKVKLVLVDTPGLDEFGGLGR 65
Query: 99 RSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLS 158
L +R + + ++V D T+ S +D +
Sbjct: 66 EELARLLLRGADLILLVVDSTDRESE-------EDAKLLI-------------------- 98
Query: 159 FHHANSFHQTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERK-AKELNVMFI 217
+R R + I+LVGNK DL ++R+V + AK L V
Sbjct: 99 ----------------LRRLRKEGIPIILVGNKIDLLEEREVEELLRLEELAKILGVPVF 142
Query: 218 ETSAKAGYNVKQVRLQL 234
E SAK G V ++ +L
Sbjct: 143 EVSAKTGEGVDELFEKL 159
Score = 74.4 bits (183), Expect = 4e-16
Identities = 38/128 (29%), Positives = 57/128 (44%), Gaps = 8/128 (6%)
Query: 218 ETSAKAGYNVKQVRLQLWDTAGQERF-----RSLIPSYIRDSTVAVVVYDITNANSFHQT 272
+ +V+L L DT G + F L +R + + ++V D T+ S
Sbjct: 35 PDVYVKELDKGKVKLVLVDTPGLDEFGGLGREELARLLLRGADLILLVVDSTDRESEEDA 94
Query: 273 SKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERK-AKELNVMFIETSAKAGYNV 331
I R R + I+LVGNK DL ++R+V + AK L V E SAK G V
Sbjct: 95 KLLIL--RRLRKEGIPIILVGNKIDLLEEREVEELLRLEELAKILGVPVFEVSAKTGEGV 152
Query: 332 KQLFRRVA 339
+LF ++
Sbjct: 153 DELFEKLI 160
>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 = 74.9 bits (184), Expect = 4e-16
Identities = 39/108 (36%), Positives = 61/108 (56%), Gaps = 3/108 (2%)
Query: 232 LQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSD---VI 288
LQ+ DT G +F ++ I ++VY IT+ S + + + +G++ +
Sbjct: 51 LQITDTTGSHQFPAMQRLSISKGHAFILVYSITSKQSLEELKPIYELICEIKGNNLEKIP 110
Query: 289 IMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFR 336
IMLVGNK D S R+VS+ EG A+ N F+ETSAK +NV++LF+
Sbjct: 111 IMLVGNKCDESPSREVSSSEGAALARTWNCAFMETSAKTNHNVQELFQ 158
Score = 73.3 bits (180), Expect = 1e-15
Identities = 53/217 (24%), Positives = 87/217 (40%), Gaps = 62/217 (28%)
Query: 14 FKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGIDF 73
+++V G VGK+SL+ RF+ +F +Y TI ++TY+ I
Sbjct: 2 YRVVVFGAGGVGKSSLVLRFVKGTFRESYIPTI---------------EDTYRQVISCS- 45
Query: 74 LSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDD 133
LQ+ DT G +F ++ I ++VY IT+ S + +
Sbjct: 46 --------KSICTLQITDTTGSHQFPAMQRLSISKGHAFILVYSITSKQSLEELKPIYEL 97
Query: 134 VRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGNKTD 193
+ +G+++ + IMLVGNK D
Sbjct: 98 ICEIKGNNL--------------------------------------EKIPIMLVGNKCD 119
Query: 194 LSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQV 230
S R+VS+ EG A+ N F+ETSAK +NV+++
Sbjct: 120 ESPSREVSSSEGAALARTWNCAFMETSAKTNHNVQEL 156
>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 = 71.7 bits (176), Expect = 6e-15
Identities = 41/122 (33%), Positives = 62/122 (50%), Gaps = 15/122 (12%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQT-SKWIDDVRTERGSD 286
KQV L LWDTAGQE + L P D+ V ++ + I + +S KW +V+ +
Sbjct: 47 KQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVK-HFCPN 105
Query: 287 VIIMLVGNKTDLSD------------KRQVSTEEGERKAKELNVM-FIETSAKAGYNVKQ 333
V I+LVGNK DL + + V EEG A+++ ++E SAK V++
Sbjct: 106 VPIILVGNKKDLRNDEHTIRELAKMKQEPVKPEEGRAMAEKIGAFGYLECSAKTKEGVRE 165
Query: 334 LF 335
+F
Sbjct: 166 VF 167
Score = 69.8 bits (171), Expect = 3e-14
Identities = 60/232 (25%), Positives = 91/232 (39%), Gaps = 79/232 (34%)
Query: 12 RKFKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGI 71
RK KLV +G+ + GKT L+ F D F Y T+ F+N Y A I +
Sbjct: 1 RK-KLVIVGDGACGKTCLLIVFSKDQFPEVYVPTV--------------FEN-YVADIEV 44
Query: 72 DFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWI 131
D + V L LWDTAGQE + L P D+ V ++ + I + +S
Sbjct: 45 D---------GKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSL------- 88
Query: 132 DDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGNK 191
+++ KW +V+ +V I+LVGNK
Sbjct: 89 ENIP---------------------------------EKWTPEVK-HFCPNVPIILVGNK 114
Query: 192 TDLSD------------KRQVSTEEGERKAKELNVM-FIETSAKAGYNVKQV 230
DL + + V EEG A+++ ++E SAK V++V
Sbjct: 115 KDLRNDEHTIRELAKMKQEPVKPEEGRAMAEKIGAFGYLECSAKTKEGVREV 166
>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 = 72.6 bits (178), Expect = 6e-15
Identities = 52/199 (26%), Positives = 82/199 (41%), Gaps = 43/199 (21%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLED-RTVRLQLWDTAGQERFRSLIPSY 105
VGKTSL+ R+M F +T +T+G F YL+ + +WDTAG+E+F L Y
Sbjct: 11 VGKTSLLHRYMERRFKDT-VSTVGGAF-----YLKQWGPYNISIWDTAGREQFHGLGSMY 64
Query: 106 IRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSF 165
R + ++ YD++N S + + D + +VG+
Sbjct: 65 CRGAAAVILTYDVSNVQSLEELEDRFLGLTDTANEDCLFAVVGNKL-------------- 110
Query: 166 HQTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELN------------ 213
D+ E G++ D+RQV+ E+ + K +N
Sbjct: 111 --------DLTEEGALAGQEKDAGDRVSPEDQRQVTLEDAKAFYKRINKYKMLDEDLSPA 162
Query: 214 --VMFIETSAKAGYNVKQV 230
M ETSAK GYNV ++
Sbjct: 163 AEKMCFETSAKTGYNVDEL 181
Score = 68.4 bits (167), Expect = 2e-13
Identities = 45/158 (28%), Positives = 69/158 (43%), Gaps = 38/158 (24%)
Query: 216 FIETSAKAG--YNVKQVR---LQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFH 270
F +T + G + +KQ + +WDTAG+E+F L Y R + ++ YD++N S
Sbjct: 25 FKDTVSTVGGAFYLKQWGPYNISIWDTAGREQFHGLGSMYCRGAAAVILTYDVSNVQSLE 84
Query: 271 QTSKWIDDVRTERGSDVIIMLVGNKTDLS-------------------DKRQVSTEEGER 311
+ + D + +VGNK DL+ D+RQV+ E+ +
Sbjct: 85 ELEDRFLGLTDTANEDCLFAVVGNKLDLTEEGALAGQEKDAGDRVSPEDQRQVTLEDAKA 144
Query: 312 KAKELN--------------VMFIETSAKAGYNVKQLF 335
K +N M ETSAK GYNV +LF
Sbjct: 145 FYKRINKYKMLDEDLSPAAEKMCFETSAKTGYNVDELF 182
>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 = 69.4 bits (170), Expect = 1e-14
Identities = 25/106 (23%), Positives = 54/106 (50%), Gaps = 4/106 (3%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
GK+SL+++ + F G T+ ++ T L +WD G+E + ++
Sbjct: 10 SGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREELKFEHIIFM 69
Query: 107 RDSTVAVVVYDITNANSFHQTS---KWIDDVRTERGSDVIIMLVGS 149
+ + ++VYD+T+ S ++ S W+ ++R + G + ++LVG+
Sbjct: 70 KWADAILLVYDLTDRESLNEVSRLIAWLPNLR-KLGGKIPVILVGN 114
Score = 48.6 bits (116), Expect = 2e-07
Identities = 26/126 (20%), Positives = 57/126 (45%), Gaps = 25/126 (19%)
Query: 185 IMLVGN----KTDL-----SDKRQVSTEE--GERKAKELNVMFIETSAKAGYNVKQVRLQ 233
++++G+ K+ L + E G+ A + + +T L
Sbjct: 2 VVVIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGL----------LN 51
Query: 234 LWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTS---KWIDDVRTERGSDVIIM 290
+WD G+E + +++ + ++VYD+T+ S ++ S W+ ++R + G + ++
Sbjct: 52 IWDFGGREELKFEHIIFMKWADAILLVYDLTDRESLNEVSRLIAWLPNLR-KLGGKIPVI 110
Query: 291 LVGNKT 296
LVGNK
Sbjct: 111 LVGNKL 116
>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 = 69.8 bits (171), Expect = 2e-14
Identities = 56/218 (25%), Positives = 94/218 (43%), Gaps = 65/218 (29%)
Query: 14 FKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGIDF 73
+K+V LG VGK++L +F+ + F +Y TI +++Y+ + ID
Sbjct: 2 YKIVVLGAGGVGKSALTVQFVQNVFIESYDPTI---------------EDSYRKQVEID- 45
Query: 74 LSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDD 133
R L++ DTAG E+F ++ YI+ ++VY +T+ S ++ + +
Sbjct: 46 --------GRQCDLEILDTAGTEQFTAMRELYIKSGQGFLLVYSVTSEASLNELGELREQ 97
Query: 134 VRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGNKTD 193
V +R + +V ++LVGNK D
Sbjct: 98 V----------------------------------------LRIKDSDNVPMVLVGNKAD 117
Query: 194 LSDKRQVSTEEGERKAKELN-VMFIETSAKAGYNVKQV 230
L D RQVS E+G +++ V F ETSA+ NV +V
Sbjct: 118 LEDDRQVSREDGVSLSQQWGNVPFYETSARKRTNVDEV 155
Score = 67.1 bits (164), Expect = 2e-13
Identities = 43/123 (34%), Positives = 71/123 (57%), Gaps = 4/123 (3%)
Query: 217 IETSAKAGYNV--KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSK 274
IE S + + +Q L++ DTAG E+F ++ YI+ ++VY +T+ S ++ +
Sbjct: 34 IEDSYRKQVEIDGRQCDLEILDTAGTEQFTAMRELYIKSGQGFLLVYSVTSEASLNELGE 93
Query: 275 WIDDV-RTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELN-VMFIETSAKAGYNVK 332
+ V R + +V ++LVGNK DL D RQVS E+G +++ V F ETSA+ NV
Sbjct: 94 LREQVLRIKDSDNVPMVLVGNKADLEDDRQVSREDGVSLSQQWGNVPFYETSARKRTNVD 153
Query: 333 QLF 335
++F
Sbjct: 154 EVF 156
>gnl|CDD|206714 cd04147, Ras_dva, Ras - dorsal-ventral anterior localization
(Ras-dva) family. Ras-dva subfamily. Ras-dva (Ras -
dorsal-ventral anterior localization) subfamily consists
of a set of proteins characterized only in Xenopus
leavis, to date. In Xenopus Ras-dva expression is
activated by the transcription factor Otx2 and begins
during gastrulation throughout the anterior ectoderm.
Ras-dva expression is inhibited in the anterior neural
plate by factor Xanf1. Downregulation of Ras-dva results
in head development abnormalities through the inhibition
of several regulators of the anterior neural plate and
folds patterning, including Otx2, BF-1, Xag2, Pax6,
Slug, and Sox9. Downregulation of Ras-dva also
interferes with the FGF-8a signaling within the anterior
ectoderm. Most Ras proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins.
Length = 197
Score = 69.5 bits (170), Expect = 5e-14
Identities = 56/244 (22%), Positives = 92/244 (37%), Gaps = 73/244 (29%)
Query: 15 KLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGIDFL 74
+LVF+G VGKT+LI RF+YD+F+ ++ T+ +
Sbjct: 1 RLVFMGAAGVGKTALIQRFLYDTFEPKHRRTVE------------------------ELH 36
Query: 75 SKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDV 134
SK + V + + DT+G F ++ I++ +VY + + SF ++V
Sbjct: 37 SKEYEVAGVKVTIDILDTSGSYSFPAMRKLSIQNGDAFALVYSVDDPESF-------EEV 89
Query: 135 RTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGNKTDL 194
+ R + I+ + V I++VGNK D
Sbjct: 90 KRLR--EEIL-------------------------------EVKEDKFVPIVVVGNKIDS 116
Query: 195 SDKRQVSTEEGERKAK-ELNVMFIETSAKAGYNV--------KQVRLQLWDTAGQERFRS 245
+RQV + + + N F+E SAK NV +Q L W + R R
Sbjct: 117 LAERQVEAADALSTVELDWNNGFVEASAKDNENVTEVFKELLQQANLPSWLSPALRRRRE 176
Query: 246 LIPS 249
PS
Sbjct: 177 SAPS 180
Score = 60.6 bits (147), Expect = 7e-11
Identities = 29/110 (26%), Positives = 56/110 (50%), Gaps = 2/110 (1%)
Query: 229 QVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDV-RTERGSDV 287
+V + + DT+G F ++ I++ +VY + + SF + + +++ + V
Sbjct: 46 KVTIDILDTSGSYSFPAMRKLSIQNGDAFALVYSVDDPESFEEVKRLREEILEVKEDKFV 105
Query: 288 IIMLVGNKTDLSDKRQVSTEEGERKAK-ELNVMFIETSAKAGYNVKQLFR 336
I++VGNK D +RQV + + + N F+E SAK NV ++F+
Sbjct: 106 PIVVVGNKIDSLAERQVEAADALSTVELDWNNGFVEASAKDNENVTEVFK 155
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 69.0 bits (169), Expect = 1e-13
Identities = 44/186 (23%), Positives = 74/186 (39%), Gaps = 56/186 (30%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
VGKT+ + R + F+ Y T+G++ Y + +WDTAGQE+F L Y
Sbjct: 20 VGKTTFVKRHLTGEFEKKYIPTLGVEVHPLKFYTNCGPICFNVWDTAGQEKFGGLRDGYY 79
Query: 107 RDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFH 166
A++++D+T+ ++ W D+
Sbjct: 80 IKGQCAIIMFDVTSRITYKNVPNWHRDI-------------------------------- 107
Query: 167 QTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKEL------NVMFIETS 220
++ I+LVGNK D+ D RQV KA+++ N+ + + S
Sbjct: 108 ----------VRVCENIPIVLVGNKVDVKD-RQV-------KARQITFHRKKNLQYYDIS 149
Query: 221 AKAGYN 226
AK+ YN
Sbjct: 150 AKSNYN 155
Score = 64.3 bits (157), Expect = 5e-12
Identities = 38/125 (30%), Positives = 64/125 (51%), Gaps = 15/125 (12%)
Query: 226 NVKQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGS 285
N + +WDTAGQE+F L Y A++++D+T+ ++ W D+
Sbjct: 54 NCGPICFNVWDTAGQEKFGGLRDGYYIKGQCAIIMFDVTSRITYKNVPNWHRDI-VRVCE 112
Query: 286 DVIIMLVGNKTDLSDKRQVSTEEGERKAKEL------NVMFIETSAKAGYNVKQLFRRVA 339
++ I+LVGNK D+ D RQV KA+++ N+ + + SAK+ YN ++ F +A
Sbjct: 113 NIPIVLVGNKVDVKD-RQV-------KARQITFHRKKNLQYYDISAKSNYNFEKPFLWLA 164
Query: 340 AALPG 344
L
Sbjct: 165 RRLTN 169
>gnl|CDD|232886 TIGR00231, small_GTP, small GTP-binding protein domain. Proteins
with a small GTP-binding domain recognized by this model
include Ras, RhoA, Rab11, translation elongation factor
G, translation initiation factor IF-2, tetratcycline
resistance protein TetM, CDC42, Era, ADP-ribosylation
factors, tdhF, and many others. In some proteins the
domain occurs more than once.This model recognizes a
large number of small GTP-binding proteins and related
domains in larger proteins. Note that the alpha chains
of heterotrimeric G proteins are larger proteins in
which the NKXD motif is separated from the GxxxxGK[ST]
motif (P-loop) by a long insert and are not easily
detected by this model [Unknown function, General].
Length = 162
Score = 67.4 bits (165), Expect = 1e-13
Identities = 34/113 (30%), Positives = 50/113 (44%), Gaps = 3/113 (2%)
Query: 225 YNVKQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNA-NSFHQT-SKWIDDVRTE 282
+ K + L DTAGQE + ++ Y R ++ V+DI + K ++
Sbjct: 46 EDGKTYKFNLLDTAGQEDYDAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHH 105
Query: 283 RGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLF 335
S V I+LVGNK DL D ++ T AK I SA+ G N+ F
Sbjct: 106 AESGVPIILVGNKIDLRD-AKLKTHVAFLFAKLNGEPIIPLSAETGKNIDSAF 157
Score = 65.9 bits (161), Expect = 5e-13
Identities = 43/182 (23%), Positives = 71/182 (39%), Gaps = 41/182 (22%)
Query: 47 VGKTSLITRFMYDSFDNT-YQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSY 105
VGK++L+ R + + T Y+ ++++ + + +T + L DTAGQE + ++ Y
Sbjct: 12 VGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAGQEDYDAIRRLY 71
Query: 106 IRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSF 165
R ++ V+DI LV +E
Sbjct: 72 YRAVESSLRVFDIVI-------------------------LVLDVEEILE---------- 96
Query: 166 HQTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGY 225
K ++ S V I+LVGNK DL D ++ T AK I SA+ G
Sbjct: 97 ----KQTKEIIHHAESGVPIILVGNKIDLRD-AKLKTHVAFLFAKLNGEPIIPLSAETGK 151
Query: 226 NV 227
N+
Sbjct: 152 NI 153
>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 = 67.4 bits (165), Expect = 2e-13
Identities = 24/89 (26%), Positives = 50/89 (56%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
+GKTSL+ +++ FD Y T+G++F+ KT+ + + +WD GQ F +++P
Sbjct: 11 IGKTSLMVKYVEGEFDEEYIQTLGVNFMEKTISIRGTEITFSIWDLGGQREFINMLPLVC 70
Query: 107 RDSTVAVVVYDITNANSFHQTSKWIDDVR 135
+D+ + ++D+T ++ + +W R
Sbjct: 71 KDAVAILFMFDLTRKSTLNSIKEWYRQAR 99
Score = 49.7 bits (119), Expect = 3e-07
Identities = 44/170 (25%), Positives = 80/170 (47%), Gaps = 19/170 (11%)
Query: 185 IMLVGN----KTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQVRLQLWDTAGQ 240
I L+G+ KT L K V E E + L V F+E + ++ +WD GQ
Sbjct: 3 IGLLGDAQIGKTSLMVK-YVEGEFDEEYIQTLGVNFMEKTISIRGT--EITFSIWDLGGQ 59
Query: 241 ERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSD--VIIMLVGNKTDL 298
F +++P +D+ + ++D+T ++ + +W R RG + I +LVG K DL
Sbjct: 60 REFINMLPLVCKDAVAILFMFDLTRKSTLNSIKEW---YRQARGFNKTAIPILVGTKYDL 116
Query: 299 ------SDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVAAAL 342
++ ++ T++ + AK + I S NV+++F+ V A +
Sbjct: 117 FADLPPEEQEEI-TKQARKYAKAMKAPLIFCSTSHSINVQKIFKFVLAKV 165
>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 = 66.6 bits (163), Expect = 3e-13
Identities = 38/130 (29%), Positives = 66/130 (50%), Gaps = 15/130 (11%)
Query: 226 NVKQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGS 285
N ++R +WDTAGQE+F L Y A++++D+T+ ++ W D+
Sbjct: 45 NRGKIRFNVWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTSRVTYKNVPNWHRDLVRVCE- 103
Query: 286 DVIIMLVGNKTDLSDKRQVSTEEGERKAKEL------NVMFIETSAKAGYNVKQLFRRVA 339
++ I+L GNK D+ D++ K K++ N+ + E SAK+ YN ++ F +A
Sbjct: 104 NIPIVLCGNKVDIKDRK--------VKPKQITFHRKKNLQYYEISAKSNYNFEKPFLWLA 155
Query: 340 AALPGMDSTE 349
L G + E
Sbjct: 156 RKLLGNPNLE 165
Score = 59.6 bits (145), Expect = 8e-11
Identities = 41/189 (21%), Positives = 74/189 (39%), Gaps = 56/189 (29%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
GKT+ + R + F+ Y AT+G++ + +R +WDTAGQE+F L Y
Sbjct: 11 TGKTTFVKRHLTGEFEKKYVATLGVEVHPLDFHTNRGKIRFNVWDTAGQEKFGGLRDGYY 70
Query: 107 RDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFH 166
A++++D+T+ ++ W D+
Sbjct: 71 IQGQCAIIMFDVTSRVTYKNVPNWHRDLVRVCE--------------------------- 103
Query: 167 QTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKEL------NVMFIETS 220
++ I+L GNK D+ D++ K K++ N+ + E S
Sbjct: 104 ---------------NIPIVLCGNKVDIKDRK--------VKPKQITFHRKKNLQYYEIS 140
Query: 221 AKAGYNVKQ 229
AK+ YN ++
Sbjct: 141 AKSNYNFEK 149
>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 = 66.4 bits (162), Expect = 4e-13
Identities = 55/229 (24%), Positives = 87/229 (37%), Gaps = 78/229 (34%)
Query: 15 KLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGIDFL 74
K V +G+ +VGKT L+ + ++F Y T+ FDN Y A + +D
Sbjct: 3 KCVVVGDGAVGKTCLLISYTTNAFPGEYIPTV--------------FDN-YSANVMVD-- 45
Query: 75 SKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDV 134
+ V L LWDTAGQE + L P + V ++ + + + SF ++V
Sbjct: 46 -------GKPVNLGLWDTAGQEDYDRLRPLSYPQTDVFLICFSLVSPASF-------ENV 91
Query: 135 RTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGNKTDL 194
R + +V HH + I+LVG K DL
Sbjct: 92 RAKWYPEV----------------RHHC------------------PNTPIILVGTKLDL 117
Query: 195 SDKRQ------------VSTEEGERKAKELN-VMFIETSAKAGYNVKQV 230
D + ++ +G AKE+ V ++E SA +K V
Sbjct: 118 RDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTV 166
Score = 62.1 bits (151), Expect = 1e-11
Identities = 41/135 (30%), Positives = 62/135 (45%), Gaps = 15/135 (11%)
Query: 215 MFIETSAKAGYNVKQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTS- 273
+F SA + K V L LWDTAGQE + L P + V ++ + + + SF
Sbjct: 34 VFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRA 93
Query: 274 KWIDDVRTERGSDVIIMLVGNKTDLSDKRQ------------VSTEEGERKAKELN-VMF 320
KW +VR + I+LVG K DL D + ++ +G AKE+ V +
Sbjct: 94 KWYPEVR-HHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKY 152
Query: 321 IETSAKAGYNVKQLF 335
+E SA +K +F
Sbjct: 153 LECSALTQRGLKTVF 167
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 65.9 bits (161), Expect = 2e-12
Identities = 46/142 (32%), Positives = 72/142 (50%), Gaps = 23/142 (16%)
Query: 226 NVKQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGS 285
N ++R WDTAGQE+F L Y A++++D+T ++ W D+ R
Sbjct: 58 NCGKIRFYCWDTAGQEKFGGLRDGYYIHGQCAIIMFDVTARLTYKNVPTWHRDLC--RVC 115
Query: 286 DVI-IMLVGNKTDLSDKRQVSTEEGERKAKEL------NVMFIETSAKAGYNVKQLF--- 335
+ I I+L GNK D+ + RQV KAK++ N+ + E SAK+ YN ++ F
Sbjct: 116 ENIPIVLCGNKVDVKN-RQV-------KAKQVTFHRKKNLQYYEISAKSNYNFEKPFLYL 167
Query: 336 -RRVA--AALPGMDSTENKPPE 354
R++A L ++S PPE
Sbjct: 168 ARKLAGDPNLHFVESPALAPPE 189
Score = 59.4 bits (144), Expect = 2e-10
Identities = 45/186 (24%), Positives = 74/186 (39%), Gaps = 56/186 (30%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
GKT+ + R + F+ Y+ TIG++ + +R WDTAGQE+F L Y
Sbjct: 24 TGKTTFVKRHLTGEFEKKYEPTIGVEVHPLDFFTNCGKIRFYCWDTAGQEKFGGLRDGYY 83
Query: 107 RDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFH 166
A++++D+T ++ W D+ R +
Sbjct: 84 IHGQCAIIMFDVTARLTYKNVPTWHRDLC--RVCE------------------------- 116
Query: 167 QTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKEL------NVMFIETS 220
++ I+L GNK D+ + RQV KAK++ N+ + E S
Sbjct: 117 ---------------NIPIVLCGNKVDVKN-RQV-------KAKQVTFHRKKNLQYYEIS 153
Query: 221 AKAGYN 226
AK+ YN
Sbjct: 154 AKSNYN 159
>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 = 64.6 bits (157), Expect = 3e-12
Identities = 37/119 (31%), Positives = 62/119 (52%), Gaps = 3/119 (2%)
Query: 226 NVKQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGS 285
N +R +WDTAGQE+F L Y A++++D+T ++ W D+
Sbjct: 40 NRGPIRFNVWDTAGQEKFGGLRDGYYIQGQCAIIMFDVTARVTYKNVPNWHRDL-VRVCE 98
Query: 286 DVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVAAALPG 344
++ I+L GNK D+ D R+V + K+ N+ + + SAK+ YN ++ F +A L G
Sbjct: 99 NIPIVLCGNKVDVKD-RKVKAKSITFHRKK-NLQYYDISAKSNYNFEKPFLWLARKLIG 155
Score = 61.2 bits (148), Expect = 5e-11
Identities = 46/187 (24%), Positives = 77/187 (41%), Gaps = 44/187 (23%)
Query: 48 GKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIR 107
GKT+ + R + F+ Y AT+G++ + +R +WDTAGQE+F L Y
Sbjct: 7 GKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIRFNVWDTAGQEKFGGLRDGYYI 66
Query: 108 DSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQ 167
A++++D+T ++ W D LV E
Sbjct: 67 QGQCAIIMFDVTARVTYKNVPNWHRD------------LVRVCE---------------- 98
Query: 168 TSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNV 227
++ I+L GNK D+ D R+V + K+ N+ + + SAK+ YN
Sbjct: 99 --------------NIPIVLCGNKVDVKD-RKVKAKSITFHRKK-NLQYYDISAKSNYNF 142
Query: 228 KQVRLQL 234
++ L L
Sbjct: 143 EKPFLWL 149
>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 = 64.1 bits (156), Expect = 3e-12
Identities = 45/126 (35%), Positives = 61/126 (48%), Gaps = 17/126 (13%)
Query: 228 KQVRLQLWDTAGQERF---RSLIPSYIRDSTVAVVVYDITNANSFHQT-SKWIDDVRTER 283
V L LWDTAGQE F RSL SY D+ V ++ + + N +S SKW+ ++R
Sbjct: 46 LAVELSLWDTAGQEEFDRLRSL--SY-ADTHVIMLCFSVDNPDSLENVESKWLAEIR-HH 101
Query: 284 GSDVIIMLVGNKTDLSDKRQV--------STEEGERKAKELN-VMFIETSAKAGYNVKQL 334
V ++LV K DL + R S EEG AK +N ++E SAK V +
Sbjct: 102 CPGVKLVLVALKCDLREPRNERDRGTHTISYEEGLAVAKRINACRYLECSAKLNRGVNEA 161
Query: 335 FRRVAA 340
F A
Sbjct: 162 FTEAAR 167
Score = 61.0 bits (148), Expect = 4e-11
Identities = 60/233 (25%), Positives = 88/233 (37%), Gaps = 82/233 (35%)
Query: 15 KLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGIDFL 74
K+V LG+ + GKTSL+ F F Y+ T+ F+N
Sbjct: 2 KVVVLGDGACGKTSLLNVFTRGYFPQVYEPTV--------------FEN----------Y 37
Query: 75 SKTMYLEDRTVRLQLWDTAGQERF---RSLIPSYIRDSTVAVVVYDITNANSFHQT-SKW 130
++++ V L LWDTAGQE F RSL SY D+ V ++ + + N +S SKW
Sbjct: 38 IHDIFVDGLAVELSLWDTAGQEEFDRLRSL--SY-ADTHVIMLCFSVDNPDSLENVESKW 94
Query: 131 IDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGN 190
+ ++R HH V ++LV
Sbjct: 95 LAEIR------------------------HHCPG------------------VKLVLVAL 112
Query: 191 KTDLSDKRQV--------STEEGERKAKELN-VMFIETSAKAGYNVKQVRLQL 234
K DL + R S EEG AK +N ++E SAK V + +
Sbjct: 113 KCDLREPRNERDRGTHTISYEEGLAVAKRINACRYLECSAKLNRGVNEAFTEA 165
>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 = 64.1 bits (156), Expect = 4e-12
Identities = 55/227 (24%), Positives = 86/227 (37%), Gaps = 76/227 (33%)
Query: 15 KLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGIDFL 74
KLV +G+ + GKTSL+ F F Y T+ F+N Y +D
Sbjct: 3 KLVIVGDGACGKTSLLYVFTLGEFPEEYHPTV--------------FEN-YVTDCRVD-- 45
Query: 75 SKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDV 134
+ V+L LWDTAGQE + L P + V ++ + I +S +++V
Sbjct: 46 -------GKPVQLALWDTAGQEEYERLRPLSYSKAHVILIGFAIDTPDS-------LENV 91
Query: 135 RTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGNKTDL 194
RT KWI++VR +V ++LVG K DL
Sbjct: 92 RT---------------------------------KWIEEVRRYCP-NVPVILVGLKKDL 117
Query: 195 SDK----------RQVSTEEGERKAKELNVM-FIETSAKAGYNVKQV 230
+ V ++ + A+ + ++E SA G V V
Sbjct: 118 RQEAVAKGNYATDEFVPIQQAKLVARAIGAKKYMECSALTGEGVDDV 164
Score = 63.3 bits (154), Expect = 8e-12
Identities = 36/120 (30%), Positives = 58/120 (48%), Gaps = 13/120 (10%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQ-TSKWIDDVRTERGSD 286
K V+L LWDTAGQE + L P + V ++ + I +S +KWI++VR +
Sbjct: 47 KPVQLALWDTAGQEEYERLRPLSYSKAHVILIGFAIDTPDSLENVRTKWIEEVRRYCP-N 105
Query: 287 VIIMLVGNKTDLSDK----------RQVSTEEGERKAKELNVM-FIETSAKAGYNVKQLF 335
V ++LVG K DL + V ++ + A+ + ++E SA G V +F
Sbjct: 106 VPVILVGLKKDLRQEAVAKGNYATDEFVPIQQAKLVARAIGAKKYMECSALTGEGVDDVF 165
>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 = 63.2 bits (154), Expect = 5e-12
Identities = 56/214 (26%), Positives = 91/214 (42%), Gaps = 60/214 (28%)
Query: 13 KFKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGID 72
+ K+V +G+ GKT+L+ F DSF Y T+ F+N Y A+ +D
Sbjct: 1 RCKIVLVGDSQCGKTALLQVFAKDSFPENYVPTV--------------FEN-YTASFEVD 45
Query: 73 FLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQT-SKWI 131
+ + L LWDT+G + ++ P DS ++ +DI+ + KW
Sbjct: 46 ---------KQRIELSLWDTSGSPYYDNVRPLSYPDSDAVLICFDISRPETLDSVLKKWK 96
Query: 132 DDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGNK 191
+VR E + ++LVG D+RT+ +
Sbjct: 97 GEVR-EFCPNTPVLLVGCKS----------------------DLRTD---------LSTL 124
Query: 192 TDLSDKRQ--VSTEEGERKAKELN-VMFIETSAK 222
T+LS+KRQ VS E+G AK++ ++E SAK
Sbjct: 125 TELSNKRQIPVSHEQGRNLAKQIGAAAYVECSAK 158
Score = 55.1 bits (133), Expect = 3e-09
Identities = 42/134 (31%), Positives = 67/134 (50%), Gaps = 18/134 (13%)
Query: 220 SAKAGYNVKQVR--LQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQT-SKWI 276
+ A + V + R L LWDT+G + ++ P DS ++ +DI+ + KW
Sbjct: 37 NYTASFEVDKQRIELSLWDTSGSPYYDNVRPLSYPDSDAVLICFDISRPETLDSVLKKWK 96
Query: 277 DDVRTERGSDVIIMLVGNKTD----------LSDKRQ--VSTEEGERKAKELN-VMFIET 323
+VR E + ++LVG K+D LS+KRQ VS E+G AK++ ++E
Sbjct: 97 GEVR-EFCPNTPVLLVGCKSDLRTDLSTLTELSNKRQIPVSHEQGRNLAKQIGAAAYVEC 155
Query: 324 SAKAGYN-VKQLFR 336
SAK N V+ +F
Sbjct: 156 SAKTSENSVRDVFE 169
>gnl|CDD|206705 cd04133, Rop_like, Rho-related protein from plants (Rop)-like. The
Rop (Rho-related protein from plants) subfamily plays a
role in diverse cellular processes, including
cytoskeletal organization, pollen and vegetative cell
growth, hormone responses, stress responses, and
pathogen resistance. Rops are able to regulate several
downstream pathways to amplify a specific signal by
acting as master switches early in the signaling
cascade. They transmit a variety of extracellular and
intracellular signals. Rops are involved in establishing
cell polarity in root-hair development, root-hair
elongation, pollen-tube growth, cell-shape formation,
responses to hormones such as abscisic acid (ABA) and
auxin, responses to abiotic stresses such as oxygen
deprivation, and disease resistance and disease
susceptibility. An individual Rop can have a unique
function or an overlapping function shared with other
Rop proteins; in addition, a given Rop-regulated
function can be controlled by one or multiple Rop
proteins. For example, Rop1, Rop3, and Rop5 are all
involved in pollen-tube growth; Rop2 plays a role in
response to low-oxygen environments, cell-morphology,
and root-hair development; root-hair development is also
regulated by Rop4 and Rop6; Rop6 is also responsible for
ABA response, and ABA response is also regulated by
Rop10. Plants retain some of the regulatory mechanisms
that are shared by other members of the Rho family, but
have also developed a number of unique modes for
regulating Rops. Unique RhoGEFs have been identified
that are exclusively active toward Rop proteins, such as
those containing the domain PRONE (plant-specific Rop
nucleotide exchanger). Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 173
Score = 61.8 bits (150), Expect = 1e-11
Identities = 43/128 (33%), Positives = 64/128 (50%), Gaps = 13/128 (10%)
Query: 220 SAKAGYNVKQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTS-KWIDD 278
SA + V L LWDTAGQE + L P R + V ++ + + + S+ KWI +
Sbjct: 39 SANVVVDGNTVNLGLWDTAGQEDYNRLRPLSYRGADVFLLAFSLISKASYENVLKKWIPE 98
Query: 279 VRTERGSDVIIMLVGNKTDLSDKRQ----------VSTEEGERKAKELNV-MFIETSAKA 327
+R V I+LVG K DL D +Q ++T +GE K++ +IE S+K
Sbjct: 99 LR-HYAPGVPIVLVGTKLDLRDDKQFFADHPGAVPITTAQGEELRKQIGAAAYIECSSKT 157
Query: 328 GYNVKQLF 335
NVK +F
Sbjct: 158 QQNVKAVF 165
Score = 58.3 bits (141), Expect = 3e-10
Identities = 52/195 (26%), Positives = 80/195 (41%), Gaps = 53/195 (27%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
VGKT ++ + ++F Y T+ D S + ++ TV L LWDTAGQE + L P
Sbjct: 12 VGKTCMLISYTSNTFPTDYVPTV-FDNFSANVVVDGNTVNLGLWDTAGQEDYNRLRPLSY 70
Query: 107 RDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFH 166
R + V ++ + + + S+ K
Sbjct: 71 RGADVFLLAFSLISKASYENVLK------------------------------------- 93
Query: 167 QTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQ----------VSTEEGERKAKELNV-M 215
KWI ++R V I+LVG K DL D +Q ++T +GE K++
Sbjct: 94 ---KWIPELR-HYAPGVPIVLVGTKLDLRDDKQFFADHPGAVPITTAQGEELRKQIGAAA 149
Query: 216 FIETSAKAGYNVKQV 230
+IE S+K NVK V
Sbjct: 150 YIECSSKTQQNVKAV 164
>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 = 60.0 bits (146), Expect = 5e-11
Identities = 34/187 (18%), Positives = 67/187 (35%), Gaps = 45/187 (24%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDR-TVRLQLWDTAGQERFRSLIPSY 105
VGKTSL + + + FD +T GI+ + +R +RL +WD GQE + + +
Sbjct: 12 VGKTSLCKQLIGEKFDGDESSTHGINVQDWKIPAPERKKIRLNVWDFGGQEIYHATHQFF 71
Query: 106 IRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSF 165
+ ++ ++V+D+ + + W+ +F
Sbjct: 72 LTSRSLYLLVFDLRTGDEVSRVPYWL----------------------------RQIKAF 103
Query: 166 HQTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFI-ETSAKAG 224
G ++LVG D S + ++ K + I S K G
Sbjct: 104 --------------GGVSPVILVGTHIDESCDEDI-LKKALNKKFPAIINDIHFVSCKNG 148
Query: 225 YNVKQVR 231
+ +++
Sbjct: 149 KGIAELK 155
Score = 55.8 bits (135), Expect = 2e-09
Identities = 24/113 (21%), Positives = 52/113 (46%), Gaps = 3/113 (2%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDV 287
K++RL +WD GQE + + ++ ++ ++V+D+ + + W+ ++ G
Sbjct: 49 KKIRLNVWDFGGQEIYHATHQFFLTSRSLYLLVFDLRTGDEVSRVPYWLRQIKA-FGGVS 107
Query: 288 IIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFI-ETSAKAGYNVKQLFRRVA 339
++LVG D S + ++ K + I S K G + +L + +A
Sbjct: 108 PVILVGTHIDESCDEDI-LKKALNKKFPAIINDIHFVSCKNGKGIAELKKAIA 159
>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 = 61.3 bits (149), Expect = 8e-11
Identities = 51/232 (21%), Positives = 92/232 (39%), Gaps = 38/232 (16%)
Query: 44 ATIVGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIP 103
A+ VGKT++++RF+ F+ Y TI DF K + +L + DT+G F ++
Sbjct: 8 ASKVGKTAIVSRFLGGRFEEQYTPTIE-DFHRKLYSIRGEVYQLDILDTSGNHPFPAMRR 66
Query: 104 SYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHHAN 163
I V ++V+ + N SF + + + +
Sbjct: 67 LSILTGDVFILVFSLDNRESFEEVCRLREQIL---------------------------- 98
Query: 164 SFHQTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGER-KAKELNVMFIETSAK 222
+K +T+ + +++ GNK D R+V +E E+ + N + E SAK
Sbjct: 99 ----ETKSCLKNKTKENVKIPMVICGNKADRDFPREVQRDEVEQLVGGDENCAYFEVSAK 154
Query: 223 AGYNVKQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSK 274
N+ ++ L+ A S PS R ++V D + S + K
Sbjct: 155 KNSNLDEMFRALFSLAKLPNEMS--PSLHRK--ISVQYGDALHKKSRGGSRK 202
Score = 54.4 bits (131), Expect = 1e-08
Identities = 34/133 (25%), Positives = 61/133 (45%), Gaps = 14/133 (10%)
Query: 225 YNVKQVRLQL--WDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQ---------TS 273
Y+++ QL DT+G F ++ I V ++V+ + N SF + +
Sbjct: 41 YSIRGEVYQLDILDTSGNHPFPAMRRLSILTGDVFILVFSLDNRESFEEVCRLREQILET 100
Query: 274 KWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGER-KAKELNVMFIETSAKAGYNVK 332
K +T+ + +++ GNK D R+V +E E+ + N + E SAK N+
Sbjct: 101 KSCLKNKTKENVKIPMVICGNKADRDFPREVQRDEVEQLVGGDENCAYFEVSAKKNSNLD 160
Query: 333 QLFRRVA--AALP 343
++FR + A LP
Sbjct: 161 EMFRALFSLAKLP 173
>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 = 56.9 bits (137), Expect = 1e-09
Identities = 45/143 (31%), Positives = 69/143 (48%), Gaps = 32/143 (22%)
Query: 11 LRKFKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIG 70
++ K V +G+ +VGKT L+ + ++F Y T+ FDN Y A
Sbjct: 1 MQSIKCVVVGDGAVGKTCLLICYTTNAFPKEYIPTV--------------FDN-YSAQTA 45
Query: 71 IDFLSKTMYLEDRTVRLQLWDTAGQE---RFRSLIPSYIRDSTVAVVVYDITNANSFHQT 127
+D RTV L LWDTAGQE R R+L SY + + V ++ + I + +S+
Sbjct: 46 VD---------GRTVSLNLWDTAGQEEYDRLRTL--SYPQ-TNVFIICFSIASPSSYENV 93
Query: 128 S-KWIDDVRTERGSDVIIMLVGS 149
KW +V +V I+LVG+
Sbjct: 94 RHKWHPEV-CHHCPNVPILLVGT 115
Score = 50.8 bits (121), Expect = 1e-07
Identities = 45/145 (31%), Positives = 74/145 (51%), Gaps = 21/145 (14%)
Query: 215 MFIETSAKAGYNVKQVRLQLWDTAGQE---RFRSLIPSYIRDSTVAVVVYDITNANSFHQ 271
+F SA+ + + V L LWDTAGQE R R+L SY + + V ++ + I + +S+
Sbjct: 36 VFDNYSAQTAVDGRTVSLNLWDTAGQEEYDRLRTL--SYPQ-TNVFIICFSIASPSSYEN 92
Query: 272 TS-KWIDDVRTERGSDVIIMLVGNKTDLSD--------KRQ----VSTEEGERKAKELN- 317
KW +V +V I+LVG K DL + K Q ++ ++G AK+++
Sbjct: 93 VRHKWHPEV-CHHCPNVPILLVGTKKDLRNDADTLKKLKEQGQAPITPQQGGALAKQIHA 151
Query: 318 VMFIETSAKAGYNVKQLFRRVAAAL 342
V ++E SA VK++F A+
Sbjct: 152 VKYLECSALNQDGVKEVFAEAVRAV 176
>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 = 55.7 bits (135), Expect = 2e-09
Identities = 25/121 (20%), Positives = 44/121 (36%), Gaps = 9/121 (7%)
Query: 224 GYNV-----KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDD 278
G+NV K V+ +WD GQ++ R L Y ++ + V D ++ + +
Sbjct: 32 GFNVETVEYKNVKFTVWDVGGQDKIRPLWKHYYENTDGLIFVVDSSDRERIEEAKNELHK 91
Query: 279 V-RTERGSDVIIMLVGNKTDLSDKRQVST---EEGERKAKELNVMFIETSAKAGYNVKQL 334
+ E ++++ NK DL S G K SA G + +
Sbjct: 92 LLNEEELKGAPLLILANKQDLPGALTESELIELLGLESIKGRRWHIQPCSAVTGDGLDEG 151
Query: 335 F 335
Sbjct: 152 L 152
Score = 46.4 bits (111), Expect = 3e-06
Identities = 20/87 (22%), Positives = 39/87 (44%), Gaps = 5/87 (5%)
Query: 48 GKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIR 107
GKT+++ + T TIG F +T +E + V+ +WD GQ++ R L Y
Sbjct: 11 GKTTILYKLKLGEVVTT-IPTIG--FNVET--VEYKNVKFTVWDVGGQDKIRPLWKHYYE 65
Query: 108 DSTVAVVVYDITNANSFHQTSKWIDDV 134
++ + V D ++ + + +
Sbjct: 66 NTDGLIFVVDSSDRERIEEAKNELHKL 92
>gnl|CDD|206664 cd01874, Cdc42, cell division cycle 42 (Cdc42) is a small GTPase of
the Rho family. Cdc42 is an essential GTPase that
belongs to the Rho family of Ras-like GTPases. These
proteins act as molecular switches by responding to
exogenous and/or endogenous signals and relaying those
signals to activate downstream components of a
biological pathway. Cdc42 transduces signals to the
actin cytoskeleton to initiate and maintain polarized
growth and to mitogen-activated protein morphogenesis.
In the budding yeast Saccharomyces cerevisiae, Cdc42
plays an important role in multiple actin-dependent
morphogenetic events such as bud emergence,
mating-projection formation, and pseudohyphal growth. In
mammalian cells, Cdc42 regulates a variety of
actin-dependent events and induces the JNK/SAPK protein
kinase cascade, which leads to the activation of
transcription factors within the nucleus. Cdc42 mediates
these processes through interactions with a myriad of
downstream effectors, whose number and regulation we are
just starting to understand. In addition, Cdc42 has been
implicated in a number of human diseases through
interactions with its regulators and downstream
effectors. Most Rho proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Rho proteins.
Due to the presence of truncated sequences in this CD,
the lipid modification site is not available for
annotation.
Length = 175
Score = 54.5 bits (131), Expect = 6e-09
Identities = 37/126 (29%), Positives = 62/126 (49%), Gaps = 16/126 (12%)
Query: 232 LQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQT-SKWIDDVRTERGSDVIIM 290
L L+DTAGQE + L P + V +V + + + +SF KW+ ++ T +
Sbjct: 51 LGLFDTAGQEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEI-THHCPKTPFL 109
Query: 291 LVGNKTDLSD------------KRQVSTEEGERKAKELN-VMFIETSAKAGYNVKQLF-R 336
LVG + DL D ++ ++ E GE+ A++L V ++E SA +K +F
Sbjct: 110 LVGTQIDLRDDPSTIEKLAKNKQKPITPETGEKLARDLKAVKYVECSALTQKGLKNVFDE 169
Query: 337 RVAAAL 342
+ AAL
Sbjct: 170 AILAAL 175
Score = 53.3 bits (128), Expect = 2e-08
Identities = 52/230 (22%), Positives = 84/230 (36%), Gaps = 80/230 (34%)
Query: 15 KLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGIDFL 74
K V +G+ +VGKT L+ + + F + Y T+ FDN Y T+ I
Sbjct: 3 KCVVVGDGAVGKTCLLISYTTNKFPSEYVPTV--------------FDN-YAVTVMIG-- 45
Query: 75 SKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQT-SKWIDD 133
L L+DTAGQE + L P + V +V + + + +SF KW+ +
Sbjct: 46 -------GEPYTLGLFDTAGQEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPE 98
Query: 134 VRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGNKTD 193
+ HH +LVG + D
Sbjct: 99 IT------------------------HHC------------------PKTPFLLVGTQID 116
Query: 194 LSD------------KRQVSTEEGERKAKELN-VMFIETSAKAGYNVKQV 230
L D ++ ++ E GE+ A++L V ++E SA +K V
Sbjct: 117 LRDDPSTIEKLAKNKQKPITPETGEKLARDLKAVKYVECSALTQKGLKNV 166
>gnl|CDD|206707 cd04135, Tc10, Rho GTPase TC10 (Tc10). TC10 is a Rho family
protein that has been shown to induce microspike
formation and neurite outgrowth in vitro. Its expression
changes dramatically after peripheral nerve injury,
suggesting an important role in promoting axonal
outgrowth and regeneration. TC10 regulates translocation
of insulin-stimulated GLUT4 in adipocytes and has also
been shown to bind directly to Golgi COPI coat proteins.
GTP-bound TC10 in vitro can bind numerous potential
effectors. Depending on its subcellular localization and
distinct functional domains, TC10 can differentially
regulate two types of filamentous actin in adipocytes.
TC10 mRNAs are highly expressed in three types of mouse
muscle tissues: leg skeletal muscle, cardiac muscle, and
uterus; they were also present in brain, with higher
levels in adults than in newborns. TC10 has also been
shown to play a role in regulating the expression of
cystic fibrosis transmembrane conductance regulator
(CFTR) through interactions with CFTR-associated ligand
(CAL). The GTP-bound form of TC10 directs the
trafficking of CFTR from the juxtanuclear region to the
secretory pathway toward the plasma membrane, away from
CAL-mediated DFTR degradation in the lysosome. Most Rho
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 174
Score = 51.6 bits (123), Expect = 6e-08
Identities = 34/122 (27%), Positives = 62/122 (50%), Gaps = 15/122 (12%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQT-SKWIDDVRTERGSD 286
KQ L L+DTAGQE + L P + V ++ + + N SF +W+ +++ E +
Sbjct: 46 KQYLLGLYDTAGQEDYDRLRPLSYPMTDVFLICFSVVNPASFQNVKEEWVPELK-EYAPN 104
Query: 287 VIIMLVGNKTDLSD------------KRQVSTEEGERKAKELNVM-FIETSAKAGYNVKQ 333
V +L+G + DL D ++ ++ E+G++ AKE+ ++E SA +K
Sbjct: 105 VPYLLIGTQIDLRDDPKTLARLNDMKEKPITVEQGQKLAKEIGACCYVECSALTQKGLKT 164
Query: 334 LF 335
+F
Sbjct: 165 VF 166
Score = 48.5 bits (115), Expect = 8e-07
Identities = 29/104 (27%), Positives = 54/104 (51%), Gaps = 3/104 (2%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
VGKT L+ + D+F Y T+ D + ++ + + L L+DTAGQE + L P
Sbjct: 11 VGKTCLLMSYANDAFPEEYVPTV-FDHYAVSVTVGGKQYLLGLYDTAGQEDYDRLRPLSY 69
Query: 107 RDSTVAVVVYDITNANSFHQT-SKWIDDVRTERGSDVIIMLVGS 149
+ V ++ + + N SF +W+ +++ E +V +L+G+
Sbjct: 70 PMTDVFLICFSVVNPASFQNVKEEWVPELK-EYAPNVPYLLIGT 112
>gnl|CDD|206680 cd01893, Miro1, Mitochondrial Rho family 1 (Miro1), N-terminal.
Miro1 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the N-terminal
GTPase domain of Miro proteins. These atypical Rho
GTPases have roles in mitochondrial homeostasis and
apoptosis. Most Rho proteins contain a lipid
modification site at the C-terminus; however, Miro is
one of few Rho subfamilies that lack this feature.
Length = 168
Score = 51.2 bits (123), Expect = 7e-08
Identities = 42/164 (25%), Positives = 78/164 (47%), Gaps = 17/164 (10%)
Query: 182 DVIIMLVGN----KTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQVRLQLWDT 237
DV I+L+G+ K+ L + + E + + + E + A ++V + DT
Sbjct: 2 DVRIVLIGDEGVGKSSL-----IMSLVSEEFPENVPRVLPEITIPADVTPERVPTTIVDT 56
Query: 238 AGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQ-TSKWIDDVRTERGSDVIIMLVGNKT 296
+ + + R+ + + IR + V +VY + ++ + +KW+ +R II LVGNK+
Sbjct: 57 SSRPQDRANLAAEIRKANVICLVYSVDRPSTLERIRTKWLPLIRRLGVKVPII-LVGNKS 115
Query: 297 DLSDKRQVSTEEGE-----RKAKELNVMFIETSAKAGYNVKQLF 335
DL D + E E + +E+ +E SAK NV ++F
Sbjct: 116 DLRDGSSQAGLEEEMLPIMNEFREIET-CVECSAKTLINVSEVF 158
Score = 44.6 bits (106), Expect = 1e-05
Identities = 45/194 (23%), Positives = 72/194 (37%), Gaps = 59/194 (30%)
Query: 47 VGKTSLITRFMYDSF-DNTY----QATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSL 101
VGK+SLI + + F +N + TI D E + DT+ + + R+
Sbjct: 13 VGKSSLIMSLVSEEFPENVPRVLPEITIPADVTP-----ERVPTTIV--DTSSRPQDRAN 65
Query: 102 IPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGSIETNFTHLSFHH 161
+ + IR + V +VY + ++ +RT
Sbjct: 66 LAAEIRKANVICLVYSVD-------RPSTLERIRT------------------------- 93
Query: 162 ANSFHQTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGE-----RKAKELNVMF 216
KW+ +R II LVGNK+DL D + E E + +E+
Sbjct: 94 --------KWLPLIRRLGVKVPII-LVGNKSDLRDGSSQAGLEEEMLPIMNEFREIET-C 143
Query: 217 IETSAKAGYNVKQV 230
+E SAK NV +V
Sbjct: 144 VECSAKTLINVSEV 157
>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 = 49.1 bits (117), Expect = 6e-07
Identities = 35/119 (29%), Positives = 53/119 (44%), Gaps = 21/119 (17%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWD---------TAGQE- 96
VGKT+++ +F+ F Y T + L R L + D TAGQE
Sbjct: 11 VGKTAIVRQFLAQEFPEEYIPTEHRRLYRPAVVLSGRVYDLHILDVPNMQRYPGTAGQEW 70
Query: 97 ---RFRSLIPSYIRDSTVAVVVYDITNANSFHQTS---KWIDDVRTERGSDVIIMLVGS 149
RFR L R+S ++VYDI + +SFH + I + R + I++VG+
Sbjct: 71 MDPRFRGL-----RNSRAFILVYDICSPDSFHYVKLLRQQILETRPAGNKEPPIVVVGN 124
Score = 45.6 bits (108), Expect = 1e-05
Identities = 35/113 (30%), Positives = 51/113 (45%), Gaps = 23/113 (20%)
Query: 237 TAGQE----RFRSLIPSYIRDSTVAVVVYDITNANSFHQTS---KWIDDVRTERGSDVII 289
TAGQE RFR L R+S ++VYDI + +SFH + I + R + I
Sbjct: 65 TAGQEWMDPRFRGL-----RNSRAFILVYDICSPDSFHYVKLLRQQILETRPAGNKEPPI 119
Query: 290 MLVGNKTDLSDKRQVSTEEGERKA------KELNVMFIETSAKAGYNVKQLFR 336
++VGNK D R R K ++E SAK +++ LF+
Sbjct: 120 VVVGNKRDQQRHRF-----APRHVLSVLVRKSWKCGYLECSAKYNWHILLLFK 167
>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 = 48.9 bits (116), Expect = 6e-07
Identities = 54/218 (24%), Positives = 88/218 (40%), Gaps = 60/218 (27%)
Query: 13 KFKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGID 72
K K+V +G+ GKT+L+ F D F Y T+ F+N Y A+ ID
Sbjct: 5 KCKIVVVGDSQCGKTALLHVFAKDCFPENYVPTV--------------FEN-YTASFEID 49
Query: 73 FLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQT-SKWI 131
+ L LWDT+G + ++ P DS ++ +DI+ + KW
Sbjct: 50 TQR---------IELSLWDTSGSPYYDNVRPLSYPDSDAVLICFDISRPETLDSVLKKWK 100
Query: 132 DDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGNK 191
+++ E + ++LVG D+RT+ + V
Sbjct: 101 GEIQ-EFCPNTKMLLVGCKS----------------------DLRTDVSTLV-------- 129
Query: 192 TDLSDKRQ--VSTEEGERKAKELNVM-FIETSAKAGYN 226
+LS+ RQ VS ++G AK++ +IE SA N
Sbjct: 130 -ELSNHRQTPVSYDQGANMAKQIGAATYIECSALQSEN 166
Score = 43.9 bits (103), Expect = 2e-05
Identities = 37/136 (27%), Positives = 67/136 (49%), Gaps = 16/136 (11%)
Query: 215 MFIETSAKAGYNVKQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQT-S 273
+F +A + +++ L LWDT+G + ++ P DS ++ +DI+ +
Sbjct: 38 VFENYTASFEIDTQRIELSLWDTSGSPYYDNVRPLSYPDSDAVLICFDISRPETLDSVLK 97
Query: 274 KWIDDVRTERGSDVIIMLVGNKTD----------LSDKRQ--VSTEEGERKAKELNVM-F 320
KW +++ E + ++LVG K+D LS+ RQ VS ++G AK++ +
Sbjct: 98 KWKGEIQ-EFCPNTKMLLVGCKSDLRTDVSTLVELSNHRQTPVSYDQGANMAKQIGAATY 156
Query: 321 IETSAKAGYN-VKQLF 335
IE SA N V+ +F
Sbjct: 157 IECSALQSENSVRDIF 172
>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 = 48.6 bits (116), Expect = 6e-07
Identities = 31/135 (22%), Positives = 62/135 (45%), Gaps = 11/135 (8%)
Query: 216 FIETSAKAGYNV------KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSF 269
+ T G+NV K + L +WD GQE+ R++ Y+ ++ V V D ++
Sbjct: 24 LVTTIPTVGFNVEMLQLEKHLSLTVWDVGGQEKMRTVWKCYLENTDGLVYVVDSSDEARL 83
Query: 270 HQTSKWIDDV-RTERGSDVIIMLVGNKTDLSDK---RQVSTEEGERKAKELNVMFIE-TS 324
++ K + + + E V ++L+ NK DL +++ +K +++ S
Sbjct: 84 DESQKELKHILKNEHIKGVPVVLLANKQDLPGALTAEEITRRFKLKKYCSDRDWYVQPCS 143
Query: 325 AKAGYNVKQLFRRVA 339
A G + + FR++A
Sbjct: 144 AVTGEGLAEAFRKLA 158
Score = 36.2 bits (84), Expect = 0.009
Identities = 20/73 (27%), Positives = 39/73 (53%), Gaps = 4/73 (5%)
Query: 48 GKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIR 107
GK++L+ + + T T+G F + + LE + + L +WD GQE+ R++ Y+
Sbjct: 11 GKSTLLYKLKHAELVTTI-PTVG--FNVEMLQLE-KHLSLTVWDVGGQEKMRTVWKCYLE 66
Query: 108 DSTVAVVVYDITN 120
++ V V D ++
Sbjct: 67 NTDGLVYVVDSSD 79
>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 = 47.7 bits (113), Expect = 3e-06
Identities = 48/211 (22%), Positives = 87/211 (41%), Gaps = 60/211 (28%)
Query: 15 KLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGIDFL 74
KLV +G+ GKT+++ D + TY T+ F+N Y A
Sbjct: 15 KLVLVGDVQCGKTAMLQVLAKDCYPETYVPTV--------------FEN-YTAC------ 53
Query: 75 SKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQT-SKWIDD 133
+ E++ V L LWDT+G + ++ P DS ++ +DI+ F KW +
Sbjct: 54 ---LETEEQRVELSLWDTSGSPYYDNVRPLCYSDSDAVLLCFDISRPEIFDSALKKWRAE 110
Query: 134 VRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIMLVGNKTD 193
+ + I+L+G +T+ +D+ ++ +
Sbjct: 111 I-LDYCPSTRILLIG--------------------------CKTDLRTDLSTLM-----E 138
Query: 194 LSDKRQ--VSTEEGERKAKELNV-MFIETSA 221
LS+++Q +S E+G AK+L ++E SA
Sbjct: 139 LSNQKQAPISYEQGCAMAKQLGAEAYLECSA 169
Score = 47.4 bits (112), Expect = 3e-06
Identities = 35/129 (27%), Positives = 63/129 (48%), Gaps = 16/129 (12%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQT-SKWIDDVRTERGSD 286
++V L LWDT+G + ++ P DS ++ +DI+ F KW ++ +
Sbjct: 59 QRVELSLWDTSGSPYYDNVRPLCYSDSDAVLLCFDISRPEIFDSALKKWRAEI-LDYCPS 117
Query: 287 VIIMLVGNKTD----------LSDKRQ--VSTEEGERKAKELNV-MFIETSA-KAGYNVK 332
I+L+G KTD LS+++Q +S E+G AK+L ++E SA + ++
Sbjct: 118 TRILLIGCKTDLRTDLSTLMELSNQKQAPISYEQGCAMAKQLGAEAYLECSAFTSEKSIH 177
Query: 333 QLFRRVAAA 341
+FR +
Sbjct: 178 SIFRTASLL 186
>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 = 46.2 bits (110), Expect = 3e-06
Identities = 25/84 (29%), Positives = 39/84 (46%), Gaps = 6/84 (7%)
Query: 224 GYNVKQVR-----LQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDD 278
G+N+++V +++WD GQ RFRS+ Y R V V D + + D
Sbjct: 33 GFNMRKVTKGNVTIKVWDLGGQPRFRSMWERYCRGVNAIVYVVDAADREKLEVAKNELHD 92
Query: 279 VRTERGSDVIIMLV-GNKTDLSDK 301
+ + + I +LV GNK DL
Sbjct: 93 LLEKPSLEGIPLLVLGNKNDLPGA 116
Score = 36.1 bits (84), Expect = 0.010
Identities = 23/75 (30%), Positives = 33/75 (44%), Gaps = 14/75 (18%)
Query: 48 GKTSLIT-----RFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLI 102
GKT+L+ +F D+ T+G + T V +++WD GQ RFRS+
Sbjct: 11 GKTTLVNVIASGQFSEDTI-----PTVGFNMRKVTK----GNVTIKVWDLGGQPRFRSMW 61
Query: 103 PSYIRDSTVAVVVYD 117
Y R V V D
Sbjct: 62 ERYCRGVNAIVYVVD 76
>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 = 45.3 bits (107), Expect = 1e-05
Identities = 56/223 (25%), Positives = 87/223 (39%), Gaps = 44/223 (19%)
Query: 14 FKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGIDF 73
K V +G+ +VGKT LI + YQ T + T + D Q + +
Sbjct: 3 IKCVVVGDNAVGKTRLICARACNKTLTQYQLL---ATHVPTVWAID------QYRVCQEV 53
Query: 74 LSKTMYLEDR-TVRLQLWDTAG----QERFRSLIPSYIRDSTVAVVVYDITNANSFHQTS 128
L ++ + D +V L+LWDT G RF +Y R S V ++ + I + NS
Sbjct: 54 LERSRDVVDGVSVSLRLWDTFGDHDKDRRF-----AYGR-SDVVLLCFSIASPNSLRNVK 107
Query: 129 K-WIDDVRTERGSDVIIMLVGSIETNFTHLSFHHANSFHQTSKWIDDVRTERGSDVIIML 187
W ++R V ++LVG L +A+ +D+V R +
Sbjct: 108 TMWYPEIR-HFCPRVPVILVG------CKLDLRYAD--------LDEVNRARRPLARPIK 152
Query: 188 VGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQV 230
+ R V AKEL + + ETS + VK V
Sbjct: 153 NADILPPETGRAV--------AKELGIPYYETSVVTQFGVKDV 187
Score = 43.4 bits (102), Expect = 5e-05
Identities = 37/130 (28%), Positives = 53/130 (40%), Gaps = 31/130 (23%)
Query: 230 VRLQLWDTAG----QERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSK-WIDDVRTERG 284
V L+LWDT G RF +Y R S V ++ + I + NS W ++R
Sbjct: 66 VSLRLWDTFGDHDKDRRF-----AYGR-SDVVLLCFSIASPNSLRNVKTMWYPEIR-HFC 118
Query: 285 SDVIIMLVGNKTDL-------------------SDKRQVSTEEGERKAKELNVMFIETSA 325
V ++LVG K DL + + E G AKEL + + ETS
Sbjct: 119 PRVPVILVGCKLDLRYADLDEVNRARRPLARPIKNADILPPETGRAVAKELGIPYYETSV 178
Query: 326 KAGYNVKQLF 335
+ VK +F
Sbjct: 179 VTQFGVKDVF 188
>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 = 43.9 bits (104), Expect = 2e-05
Identities = 30/113 (26%), Positives = 49/113 (43%), Gaps = 6/113 (5%)
Query: 227 VKQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDV-RTERGS 285
V + RL WD GQE RSL Y +S + V D T+ F+++ + V E
Sbjct: 48 VGKARLMFWDLGGQEELRSLWDKYYAESHGVIYVIDSTDRERFNESKSAFEKVINNEALE 107
Query: 286 DVIIMLVGNKTDLSDKRQVST-----EEGERKAKELNVMFIETSAKAGYNVKQ 333
V ++++ NK DL D V+ ++ + + SA G V++
Sbjct: 108 GVPLLVLANKQDLPDALSVAEIKEVFDDCIALIGRRDCLVQPVSALEGEGVEE 160
Score = 30.8 bits (70), Expect = 0.69
Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 1/63 (1%)
Query: 85 VRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDV-RTERGSDVI 143
RL WD GQE RSL Y +S + V D T+ F+++ + V E V
Sbjct: 51 ARLMFWDLGGQEELRSLWDKYYAESHGVIYVIDSTDRERFNESKSAFEKVINNEALEGVP 110
Query: 144 IML 146
+++
Sbjct: 111 LLV 113
>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 = 42.5 bits (100), Expect = 9e-05
Identities = 25/72 (34%), Positives = 36/72 (50%), Gaps = 8/72 (11%)
Query: 48 GKTSLITRFMYDSFDNTYQATIGIDFLSKTMYL---EDRTVRLQLWDTAGQERFRSLIPS 104
GKT+++ R ++ F NT T G F ++ + + + V WD GQE+ R L S
Sbjct: 15 GKTTVLYRLKFNEFVNTV-PTKG--FNTEKIKVSLGNAKGVTFHFWDVGGQEKLRPLWKS 71
Query: 105 YIR--DSTVAVV 114
Y R D V VV
Sbjct: 72 YTRCTDGIVFVV 83
Score = 41.3 bits (97), Expect = 2e-04
Identities = 25/104 (24%), Positives = 44/104 (42%), Gaps = 11/104 (10%)
Query: 216 FIETSAKAGYNVKQVRL----------QLWDTAGQERFRSLIPSYIRDSTVAVVVYDITN 265
F+ T G+N +++++ WD GQE+ R L SY R + V V D +
Sbjct: 28 FVNTVPTKGFNTEKIKVSLGNAKGVTFHFWDVGGQEKLRPLWKSYTRCTDGIVFVVDSVD 87
Query: 266 ANSFHQTSKWIDDV-RTERGSDVIIMLVGNKTDLSDKRQVSTEE 308
+ + + + V ++++ NK DL + VS E
Sbjct: 88 VERMEEAKTELHKITKFSENQGVPVLVLANKQDLPNALPVSEVE 131
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 42.2 bits (100), Expect = 1e-04
Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 5/70 (7%)
Query: 48 GKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIR 107
GKT+++ + T TIG F +T + + V+ +WD GQE R L +Y
Sbjct: 26 GKTTILYKLKLGEIVTT-IPTIG--FNVET--VTYKNVKFTVWDVGGQESLRPLWRNYFP 80
Query: 108 DSTVAVVVYD 117
++ + V D
Sbjct: 81 NTDAVIFVVD 90
Score = 39.1 bits (92), Expect = 0.001
Identities = 21/91 (23%), Positives = 41/91 (45%), Gaps = 6/91 (6%)
Query: 216 FIETSAKAGYNVKQV-----RLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFH 270
+ T G+NV+ V + +WD GQE R L +Y ++ + V D + +
Sbjct: 39 IVTTIPTIGFNVETVTYKNVKFTVWDVGGQESLRPLWRNYFPNTDAVIFVVDSADRDRIE 98
Query: 271 QTSKWIDDV-RTERGSDVIIMLVGNKTDLSD 300
+ + + + E +D ++++ NK DL
Sbjct: 99 EAKEELHALLNEEELADAPLLILANKQDLPG 129
>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 = 42.3 bits (99), Expect = 2e-04
Identities = 29/117 (24%), Positives = 51/117 (43%), Gaps = 25/117 (21%)
Query: 15 KLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGIDFL 74
K+V +G+ GKT+L+ F D++ +Y T+ F+N Y A+ ID
Sbjct: 3 KIVVVGDTQCGKTALLHVFAKDNYPESYVPTV--------------FEN-YTASFEID-- 45
Query: 75 SKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQ-TSKW 130
+ L +WDT+G + ++ P DS ++ +DI+ + KW
Sbjct: 46 -------KHRIELNMWDTSGSSYYDNVRPLAYPDSDAVLICFDISRPETLDSVLKKW 95
Score = 40.0 bits (93), Expect = 9e-04
Identities = 33/123 (26%), Positives = 61/123 (49%), Gaps = 16/123 (13%)
Query: 228 KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQ-TSKWIDDVRTERGSD 286
++ L +WDT+G + ++ P DS ++ +DI+ + KW + + E +
Sbjct: 47 HRIELNMWDTSGSSYYDNVRPLAYPDSDAVLICFDISRPETLDSVLKKWQGETQ-EFCPN 105
Query: 287 VIIMLVGNK----TDLSDKRQVST--------EEGERKAKELN-VMFIETSAKAGYN-VK 332
++LVG K TDLS R++S E+G A++L V ++E S++ N V+
Sbjct: 106 AKLVLVGCKLDMRTDLSTLRELSKQRLIPVTHEQGSLLARQLGAVAYVECSSRMSENSVR 165
Query: 333 QLF 335
+F
Sbjct: 166 DVF 168
>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 = 4e-04
Identities = 21/84 (25%), Positives = 41/84 (48%), Gaps = 6/84 (7%)
Query: 223 AGYNVKQV-----RLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWID 277
G+N+K V +L +WD GQ + R +Y ++ V + V D + F + + +
Sbjct: 47 QGFNIKNVQADGFKLNVWDIGGQRKIRPYWRNYFENTDVLIYVIDSADRKRFEEAGQELV 106
Query: 278 DV-RTERGSDVIIMLVGNKTDLSD 300
++ E+ + V +++ NK DL
Sbjct: 107 ELLEEEKLAGVPVLVFANKQDLLT 130
Score = 30.4 bits (69), Expect = 0.81
Identities = 14/62 (22%), Positives = 29/62 (46%)
Query: 86 RLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIM 145
+L +WD GQ + R +Y ++ V + V D + F + + + ++ E + +
Sbjct: 60 KLNVWDIGGQRKIRPYWRNYFENTDVLIYVIDSADRKRFEEAGQELVELLEEEKLAGVPV 119
Query: 146 LV 147
LV
Sbjct: 120 LV 121
>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 = 39.0 bits (91), Expect = 0.001
Identities = 21/83 (25%), Positives = 39/83 (46%), Gaps = 6/83 (7%)
Query: 224 GYNV-----KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDD 278
G+NV K V+ +WD GQ++ R L Y + + V D + + + + +
Sbjct: 42 GFNVETVTYKNVKFNVWDVGGQDKIRPLWRHYYTGTQGLIFVVDSADRDRIDEARQELHR 101
Query: 279 VRTERG-SDVIIMLVGNKTDLSD 300
+ +R D ++++ NK DL D
Sbjct: 102 IINDREMRDALLLVFANKQDLPD 124
Score = 29.0 bits (65), Expect = 2.8
Identities = 14/55 (25%), Positives = 24/55 (43%), Gaps = 7/55 (12%)
Query: 83 RTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTE 137
+ V+ +WD GQ++ R L Y + + V D + + ID+ R E
Sbjct: 51 KNVKFNVWDVGGQDKIRPLWRHYYTGTQGLIFVVDSADRDR-------IDEARQE 98
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 39.0 bits (91), Expect = 0.001
Identities = 29/119 (24%), Positives = 50/119 (42%), Gaps = 18/119 (15%)
Query: 9 NPLRKFKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMY--DSFDNTYQ 66
N + + K+V +G GKT+ + + K +IT S
Sbjct: 6 NKMIETKIVVIGPVGAGKTTFV-------------RALSDKPLVITEADASSVSGKGKRP 52
Query: 67 ATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFH 125
T+ +DF S + + T + L+ T GQERF+ + R + A+V+ D + +FH
Sbjct: 53 TTVAMDFGSIELD--EDTG-VHLFGTPGQERFKFMWEILSRGAVGAIVLVDSSRPITFH 108
Score = 33.6 bits (77), Expect = 0.090
Identities = 29/105 (27%), Positives = 44/105 (41%), Gaps = 6/105 (5%)
Query: 232 LQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIML 291
+ L+ T GQERF+ + R + A+V+ D +S T + + + I ++
Sbjct: 70 VHLFGTPGQERFKFMWEILSRGAVGAIVLVD----SSRPITFHAEEIIDFLTSRNPIPVV 125
Query: 292 VG-NKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAG-YNVKQL 334
V NK DL D K + L+V IE A G QL
Sbjct: 126 VAINKQDLFDALPPEKIREALKLELLSVPVIEIDATEGEGARDQL 170
>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 = 38.4 bits (89), Expect = 0.002
Identities = 22/90 (24%), Positives = 40/90 (44%), Gaps = 6/90 (6%)
Query: 217 IETSAKAGYNV-----KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQ 271
+ T G+NV K + +WD GQ++ R L Y ++ + V D + + +
Sbjct: 39 VTTIPTIGFNVETVTYKNISFTVWDVGGQDKIRPLWRHYYTNTQGLIFVVDSNDRDRIDE 98
Query: 272 TSKWIDDVRTERG-SDVIIMLVGNKTDLSD 300
+ + + E D +I++ NK DL D
Sbjct: 99 AREELHRMLNEDELRDAVILVFANKQDLPD 128
Score = 28.0 bits (62), Expect = 5.6
Identities = 9/38 (23%), Positives = 18/38 (47%)
Query: 80 LEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYD 117
+ + + +WD GQ++ R L Y ++ + V D
Sbjct: 52 VTYKNISFTVWDVGGQDKIRPLWRHYYTNTQGLIFVVD 89
>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 = 37.7 bits (88), Expect = 0.003
Identities = 26/99 (26%), Positives = 44/99 (44%), Gaps = 11/99 (11%)
Query: 28 SLITRFMYDSFDNT-YQATIVG-----KTSLITRFMYDSFDNTYQATIGIDFLSKTMYLE 81
L + F Y+ IVG KT+++ +F+ +T TIG S +
Sbjct: 1 LLFSSLWSLFFPRKEYKVIIVGLDNAGKTTILYQFLLGEVVHT-SPTIG----SNVEEIV 55
Query: 82 DRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITN 120
+ +R +WD GQE RS +Y ++ ++V D T+
Sbjct: 56 YKNIRFLMWDIGGQESLRSSWNTYYTNTDAVILVIDSTD 94
Score = 35.4 bits (82), Expect = 0.020
Identities = 23/90 (25%), Positives = 42/90 (46%), Gaps = 6/90 (6%)
Query: 217 IETSAKAGYNVKQV-----RLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQ 271
+ TS G NV+++ R +WD GQE RS +Y ++ ++V D T+
Sbjct: 41 VHTSPTIGSNVEEIVYKNIRFLMWDIGGQESLRSSWNTYYTNTDAVILVIDSTDRERLPL 100
Query: 272 TSKWIDD-VRTERGSDVIIMLVGNKTDLSD 300
T + + + E +++++ NK DL
Sbjct: 101 TKEELYKMLAHEDLRKAVLLVLANKQDLKG 130
>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 = 36.9 bits (86), Expect = 0.007
Identities = 21/80 (26%), Positives = 38/80 (47%), Gaps = 3/80 (3%)
Query: 230 VRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDV-RTERGSDVI 288
V+ +D G E+ R + Y + V + D + F ++ + +D + E ++V
Sbjct: 63 VKFTTFDLGGHEQARRVWKDYFPEVDGIVFLVDAADPERFQESKEELDSLLNDEELANVP 122
Query: 289 IMLVGNKTDLSDKRQVSTEE 308
I+++GNK D VS EE
Sbjct: 123 ILILGNKIDK--PGAVSEEE 140
Score = 29.9 bits (68), Expect = 1.5
Identities = 24/120 (20%), Positives = 44/120 (36%), Gaps = 28/120 (23%)
Query: 15 KLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGIDFL 74
K+VFLG + GKT+L+ D + T+ + + TIG
Sbjct: 21 KIVFLGLDNAGKTTLLHMLKDDRLA-QHVPTL--------------HPTSEELTIG---- 61
Query: 75 SKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDV 134
V+ +D G E+ R + Y + V + D + F ++ + +D +
Sbjct: 62 ---------NVKFTTFDLGGHEQARRVWKDYFPEVDGIVFLVDAADPERFQESKEELDSL 112
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes. TrmE
contains a GTPase domain that forms a canonical Ras-like
fold. It functions a molecular switch GTPase, and
apparently uses a conformational change associated with
GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 36.3 bits (85), Expect = 0.008
Identities = 25/117 (21%), Positives = 44/117 (37%), Gaps = 29/117 (24%)
Query: 230 VRLQLWDTAG------------QERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWID 277
+ ++L DTAG ER R I ++ + ++V D + D
Sbjct: 51 IPVRLIDTAGLRETEDEIEKIGIERAREAI----EEADLVLLVVDASEGLDEE------D 100
Query: 278 DVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQL 334
E + +++V NK+DL + +E + I SAK G + +L
Sbjct: 101 LEILELPAKKPVIVVLNKSDLLSDAEGISELNGKP-------IIAISAKTGEGIDEL 150
Score = 31.3 bits (72), Expect = 0.37
Identities = 16/67 (23%), Positives = 29/67 (43%), Gaps = 7/67 (10%)
Query: 173 DDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQVRL 232
D E + +++V NK+DL + +E + I SAK G + +++
Sbjct: 100 DLEILELPAKKPVIVVLNKSDLLSDAEGISELNGKP-------IIAISAKTGEGIDELKE 152
Query: 233 QLWDTAG 239
L + AG
Sbjct: 153 ALLELAG 159
>gnl|CDD|133303 cd04103, Centaurin_gamma, Centaurin gamma (CENTG) GTPase. The
centaurins (alpha, beta, gamma, and delta) are large,
multi-domain proteins that all contain an ArfGAP domain
and ankyrin repeats, and in some cases, numerous
additional domains. Centaurin gamma contains an
additional GTPase domain near its N-terminus. The
specific function of this GTPase domain has not been
well characterized, but centaurin gamma 2 (CENTG2) may
play a role in the development of autism. Centaurin
gamma 1 is also called PIKE (phosphatidyl inositol (PI)
3-kinase enhancer) and centaurin gamma 2 is also known
as AGAP (ArfGAP protein with a GTPase-like domain,
ankyrin repeats and a Pleckstrin homology domain) or
GGAP. Three isoforms of PIKE have been identified.
PIKE-S (short) and PIKE-L (long) are brain-specific
isoforms, with PIKE-S restricted to the nucleus and
PIKE-L found in multiple cellular compartments. A third
isoform, PIKE-A was identified in human glioblastoma
brain cancers and has been found in various tissues.
GGAP has been shown to have high GTPase activity due to
a direct intramolecular interaction between the
N-terminal GTPase domain and the C-terminal ArfGAP
domain. In human tissue, AGAP mRNA was detected in
skeletal muscle, kidney, placenta, brain, heart, colon,
and lung. Reduced expression levels were also observed
in the spleen, liver, and small intestine.
Length = 158
Score = 34.8 bits (80), Expect = 0.023
Identities = 20/86 (23%), Positives = 41/86 (47%), Gaps = 4/86 (4%)
Query: 258 VVVYDITNANSFHQTSKWIDDVRTERG-SDVIIMLVGNKTDLSDKR-QVSTEEGERK--A 313
+ V+ + + SF + + + R S++ ++LVG + +S +V + R+ A
Sbjct: 70 IFVFSLEDEASFQTVYRLYHQLSSYRNISEIPLILVGTQDAISASNPRVIDDARARQLCA 129
Query: 314 KELNVMFIETSAKAGYNVKQLFRRVA 339
+ ET A G NV+++F+ A
Sbjct: 130 DMKRCSYYETCATYGLNVERVFQEAA 155
>gnl|CDD|206691 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta), together with SR-alpha, forms the
heterodimeric signal recognition particle (SRP). Signal
recognition particle receptor, beta subunit (SR-beta).
SR-beta and SR-alpha form the heterodimeric signal
recognition particle (SRP or SR) receptor that binds SRP
to regulate protein translocation across the ER
membrane. Nascent polypeptide chains are synthesized
with an N-terminal hydrophobic signal sequence that
binds SRP54, a component of the SRP. SRP directs
targeting of the ribosome-nascent chain complex (RNC) to
the ER membrane via interaction with the SR, which is
localized to the ER membrane. The RNC is then
transferred to the protein-conducting channel, or
translocon, which facilitates polypeptide translation
across the ER membrane or integration into the ER
membrane. SR-beta is found only in eukaryotes; it is
believed to control the release of the signal sequence
from SRP54 upon binding of the ribosome to the
translocon. High expression of SR-beta has been observed
in human colon cancer, suggesting it may play a role in
the development of this type of cancer.
Length = 202
Score = 33.8 bits (78), Expect = 0.071
Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 5/74 (6%)
Query: 48 GKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLE-DRTVRLQLWDTAGQERFRSLIPSYI 106
GKT+L T+ +T + I+ + Y + +L L D G E+ R + Y+
Sbjct: 12 GKTALFTKLTTGKVRSTVTS---IEPNVASFYSNSSKGKKLTLVDVPGHEKLRDKLLEYL 68
Query: 107 RDSTVAVV-VYDIT 119
+ S A+V V D
Sbjct: 69 KASLKAIVFVVDSA 82
Score = 31.9 bits (73), Expect = 0.34
Identities = 27/100 (27%), Positives = 47/100 (47%), Gaps = 7/100 (7%)
Query: 214 VMFIETSAKAGY--NVKQVRLQLWDTAGQERFRSLIPSYIRDSTVAVV-VYDI-TNANSF 269
V IE + + Y + K +L L D G E+ R + Y++ S A+V V D T +
Sbjct: 29 VTSIEPNVASFYSNSSKGKKLTLVDVPGHEKLRDKLLEYLKASLKAIVFVVDSATFQKNI 88
Query: 270 HQTSKWIDDVRT--ERGSDVI-IMLVGNKTDLSDKRQVST 306
++++ D+ T E+ + I I++ NK DL +
Sbjct: 89 RDVAEFLYDILTDLEKIKNKIPILIACNKQDLFTAKPAKK 128
>gnl|CDD|206679 cd01892, Miro2, Mitochondrial Rho family 2 (Miro2), C-terminal.
Miro2 subfamily. Miro (mitochondrial Rho) proteins have
tandem GTP-binding domains separated by a linker region
containing putative calcium-binding EF hand motifs.
Genes encoding Miro-like proteins were found in several
eukaryotic organisms. This CD represents the putative
GTPase domain in the C terminus of Miro proteins. These
atypical Rho GTPases have roles in mitochondrial
homeostasis and apoptosis. Most Rho proteins contain a
lipid modification site at the C-terminus; however, Miro
is one of few Rho subfamilies that lack this feature.
Length = 180
Score = 33.4 bits (77), Expect = 0.080
Identities = 22/106 (20%), Positives = 48/106 (45%), Gaps = 15/106 (14%)
Query: 256 VAVVVYDITNANSFHQTSKWIDDVRT--ERGSDVIIMLVGNKTDLSDKRQVSTEEGERKA 313
VA +VYD ++ NSF + +V ++ + V K DL +++Q + + +
Sbjct: 80 VACLVYDSSDPNSF----SYCAEVYKKYFMLGEIPCLFVAAKADLDEQQQRAEVQPDEFC 135
Query: 314 KELNVMFIET----SAKAGYNVKQLFRRV--AAALPGMDSTENKPP 353
++ + + S++ G + +LF ++ AA P + E +
Sbjct: 136 RK---LGLPPPLHFSSRLGDSSNELFTKLATAAQYPHLSIPELESG 178
Score = 30.3 bits (69), Expect = 1.1
Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 1/79 (1%)
Query: 47 VGKTSLITRFMYDSF-DNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSY 105
GK++L+ F+ SF N Y TI + T+ + + L L + E L +
Sbjct: 15 SGKSALLQAFLGRSFSQNAYSPTIKPRYAVNTVEVPGQEKYLILREVGEDEEAILLNDAE 74
Query: 106 IRDSTVAVVVYDITNANSF 124
+ VA +VYD ++ NSF
Sbjct: 75 LAACDVACLVYDSSDPNSF 93
>gnl|CDD|206682 cd01895, EngA2, EngA2 GTPase contains the second domain of EngA.
This EngA2 subfamily CD represents the second GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. Since the sequences of the
two domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family. Although the exact function of
these proteins has not been elucidated, studies have
revealed that the E. coli EngA homolog, Der, and
Neisseria gonorrhoeae EngA are essential for cell
viability. A recent report suggests that E. coli Der
functions in ribosome assembly and stability.
Length = 174
Score = 33.6 bits (78), Expect = 0.081
Identities = 31/136 (22%), Positives = 53/136 (38%), Gaps = 26/136 (19%)
Query: 225 YNVKQVRLQLWDTAGQER---------FRSLIPSY--IRDSTVAVVVYDITNANSFHQTS 273
+ + L DTAG + S++ + I + V ++V D + +
Sbjct: 45 FEYDGQKYTLIDTAGIRKKGKVTEGIEKYSVLRTLKAIERADVVLLVLDASE--GITEQD 102
Query: 274 KWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMF--------IETSA 325
I + E G +II++ NK DL +K + + +E E KEL + SA
Sbjct: 103 LRIAGLILEEGKALIIVV--NKWDLVEKDEKTMKEFE---KELRRKLPFLDYAPIVFISA 157
Query: 326 KAGYNVKQLFRRVAAA 341
G V +LF +
Sbjct: 158 LTGQGVDKLFDAIKEV 173
>gnl|CDD|213833 TIGR03596, GTPase_YlqF, ribosome biogenesis GTP-binding protein
YlqF. Members of this protein family are GTP-binding
proteins involved in ribosome biogenesis, including the
essential YlqF protein of Bacillus subtilis, which is an
essential protein. They are related to Era, EngA, and
other GTPases of ribosome biogenesis, but are circularly
permuted. This family is not universal, and is not
present in Escherichia coli, and so is not as well
studied as some other GTPases. This model is built for
bacterial members [Protein synthesis, Other].
Length = 276
Score = 34.0 bits (79), Expect = 0.087
Identities = 17/81 (20%), Positives = 38/81 (46%), Gaps = 3/81 (3%)
Query: 185 IMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQVRLQLWDTAGQERFR 244
++V NK DL+D T++ + +E + + +AK G VK++ ++ +E+
Sbjct: 51 RLIVLNKADLADPAV--TKQWLKYFEEKGIKALAINAKKGKGVKKI-IKAAKKLLKEKNE 107
Query: 245 SLIPSYIRDSTVAVVVYDITN 265
L + + + ++ I N
Sbjct: 108 KLKAKGLLNRPIRAMIVGIPN 128
Score = 32.1 bits (74), Expect = 0.37
Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 289 IMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVAAALP 343
++V NK DL+D T++ + +E + + +AK G VK++ + L
Sbjct: 51 RLIVLNKADLADPAV--TKQWLKYFEEKGIKALAINAKKGKGVKKIIKAAKKLLK 103
>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 = 33.7 bits (78), Expect = 0.11
Identities = 28/132 (21%), Positives = 52/132 (39%), Gaps = 45/132 (34%)
Query: 15 KLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGID-- 72
K++ +G + GK+S+ + F N Y T + ATI ++
Sbjct: 1 KVLLMGLRGSGKSSMRSII----FSN-YSPRD-------TLRLG--------ATIDVEQS 40
Query: 73 ---FLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRD---STVAVVVY--DITNANSF 124
FL + L LWD GQ+ F + ++ S V V++Y D+
Sbjct: 41 HVRFLGN--------LTLNLWDCPGQDDFMENYLTRQKEHIFSNVGVLIYVFDV------ 86
Query: 125 HQTSKWIDDVRT 136
++ ++ +D+ T
Sbjct: 87 -ESREYEEDLAT 97
Score = 29.1 bits (66), Expect = 3.0
Identities = 24/121 (19%), Positives = 48/121 (39%), Gaps = 30/121 (24%)
Query: 232 LQLWDTAGQERFRSLIPSYIRD---STVAVVVY--DITNANSFHQTSKWIDDVRT----- 281
L LWD GQ+ F + ++ S V V++Y D+ ++ ++ +D+ T
Sbjct: 50 LNLWDCPGQDDFMENYLTRQKEHIFSNVGVLIYVFDV-------ESREYEEDLATLVKII 102
Query: 282 ----ERGSDVIIMLVGNKTDL--SDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLF 335
+ + + ++ +K DL D+R+ E+ + + IE G F
Sbjct: 103 EALYQYSPNAKVFVLIHKMDLLSEDERKEIFEDRKEEI-------IEEIEDFGIEDLTFF 155
Query: 336 R 336
Sbjct: 156 L 156
>gnl|CDD|223455 COG0378, HypB, Ni2+-binding GTPase involved in regulation of
expression and maturation of urease and hydrogenase
[Posttranslational modification, protein turnover,
chaperones / Transcription].
Length = 202
Score = 33.3 bits (77), Expect = 0.11
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 5/57 (8%)
Query: 285 SDVIIMLVGNKTDLSDKRQVSTEEGERKAKELN--VMFIETSAKAGYNVKQLFRRVA 339
+D++++ NKTDL+ E R AKE+N I T+ K G + + R +
Sbjct: 144 ADLLVI---NKTDLAPYVGADLEVMARDAKEVNPEAPIIFTNLKTGEGLDEWLRFIE 197
Score = 31.8 bits (73), Expect = 0.34
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 5/46 (10%)
Query: 181 SDVIIMLVGNKTDLSDKRQVSTEEGERKAKELN--VMFIETSAKAG 224
+D++++ NKTDL+ E R AKE+N I T+ K G
Sbjct: 144 ADLLVI---NKTDLAPYVGADLEVMARDAKEVNPEAPIIFTNLKTG 186
>gnl|CDD|234395 TIGR03918, GTP_HydF, [FeFe] hydrogenase H-cluster maturation GTPase
HydF. This model describes the family of the [Fe]
hydrogenase maturation protein HypF as characterized in
Chlamydomonas reinhardtii and found, in an operon with
radical SAM proteins HydE and HydG, in numerous
bacteria. It has GTPase activity, can bind an 4Fe-4S
cluster, and is essential for hydrogenase activity
[Protein fate, Protein modification and repair].
Length = 391
Score = 33.3 bits (77), Expect = 0.18
Identities = 21/88 (23%), Positives = 39/88 (44%), Gaps = 8/88 (9%)
Query: 256 VAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKE 315
+A++V D + I++++ ER I+++ NK DL + E E+ K+
Sbjct: 88 LALLVVDAGVGPG-EYELELIEELK-ERKIPYIVVI--NKIDLG----EESAELEKLEKK 139
Query: 316 LNVMFIETSAKAGYNVKQLFRRVAAALP 343
+ I SA G + +L + LP
Sbjct: 140 FGLPPIFVSALTGEGIDELKEAIIELLP 167
>gnl|CDD|236570 PRK09563, rbgA, GTPase YlqF; Reviewed.
Length = 287
Score = 32.5 bits (75), Expect = 0.26
Identities = 18/80 (22%), Positives = 36/80 (45%), Gaps = 3/80 (3%)
Query: 187 LVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQVRLQLWDTAGQERFRSL 246
L+ NK+DL+D T++ +E + + +AK G VK++ L+ +E+
Sbjct: 56 LILNKSDLADPEV--TKKWIEYFEEQGIKALAINAKKGQGVKKI-LKAAKKLLKEKNERR 112
Query: 247 IPSYIRDSTVAVVVYDITNA 266
+R + ++ I N
Sbjct: 113 KAKGMRPRAIRAMIIGIPNV 132
>gnl|CDD|206666 cd01878, HflX, HflX GTPase family. HflX subfamily. A distinct
conserved domain with a glycine-rich segment N-terminal
of the GTPase domain characterizes the HflX subfamily.
The E. coli HflX has been implicated in the control of
the lambda cII repressor proteolysis, but the actual
biological functions of these GTPases remain unclear.
HflX is widespread, but not universally represented in
all three superkingdoms.
Length = 204
Score = 32.0 bits (74), Expect = 0.29
Identities = 25/96 (26%), Positives = 42/96 (43%), Gaps = 13/96 (13%)
Query: 251 IRDSTVAVVVYDITNANSFHQTSKWIDDVRT---ERGSDVIIML-VGNKTDLSDKRQVST 306
+ ++ + + V D ++ + Q I+ V E G+D I ++ V NK DL D
Sbjct: 118 VAEADLLLHVVDASDPDREEQ----IETVEEVLKELGADDIPIILVLNKIDLLDD---EE 170
Query: 307 EEGERKAKELNVMFIETSAKAGYNVKQLFRRVAAAL 342
E +A + +FI SAK G + L + L
Sbjct: 171 LEERLRAGRPDAVFI--SAKTGEGLDLLKEAIEELL 204
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 32.8 bits (76), Expect = 0.30
Identities = 28/121 (23%), Positives = 47/121 (38%), Gaps = 30/121 (24%)
Query: 226 NVKQVRLQLWDTAG------------QERFRSLIPSYIRDSTVAVVVYDITNANSFHQTS 273
N+ + L+L DTAG ER R I ++ + ++V D + +
Sbjct: 259 NLDGIPLRLIDTAGIRETDDEVEKIGIERSREAI----EEADLVLLVLDASEPLTEEDDE 314
Query: 274 KWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQ 333
+ + VI+ V NK DL+ + + E G+ I SAK G + +
Sbjct: 315 ILEE----LKDKPVIV--VLNKADLTGEIDLEEENGKP--------VIRISAKTGEGIDE 360
Query: 334 L 334
L
Sbjct: 361 L 361
Score = 29.3 bits (67), Expect = 2.9
Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 8/62 (12%)
Query: 173 DDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQVRL 232
DD E D +++V NK DL+ + + E G+ I SAK G + ++R
Sbjct: 312 DDEILEELKDKPVIVVLNKADLTGEIDLEEENGKP--------VIRISAKTGEGIDELRE 363
Query: 233 QL 234
+
Sbjct: 364 AI 365
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 31.9 bits (74), Expect = 0.41
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 11/61 (18%)
Query: 289 IMLVGNKTDL-SDKRQVSTEEGERKAKELNVMF-----IETSAKAGYNVKQLFRRVAAAL 342
++LV NK DL DK ++ +EL+ + + SA G NV +L +A L
Sbjct: 116 VILVLNKIDLVKDKEEL-----LPLLEELSELMDFAEIVPISALKGDNVDELLDVIAKYL 170
Query: 343 P 343
P
Sbjct: 171 P 171
>gnl|CDD|237048 PRK12299, obgE, GTPase CgtA; Reviewed.
Length = 335
Score = 32.0 bits (74), Expect = 0.42
Identities = 15/60 (25%), Positives = 22/60 (36%)
Query: 291 LVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVAAALPGMDSTEN 350
LV NK DL D+ + + + L SA G + +L R + L E
Sbjct: 276 LVLNKIDLLDEEEEREKRAALELAALGGPVFLISAVTGEGLDELLRALWELLEEARREEE 335
Score = 30.4 bits (70), Expect = 1.2
Identities = 14/56 (25%), Positives = 23/56 (41%)
Query: 187 LVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQVRLQLWDTAGQER 242
LV NK DL D+ + + + L SA G + ++ LW+ + R
Sbjct: 276 LVLNKIDLLDEEEEREKRAALELAALGGPVFLISAVTGEGLDELLRALWELLEEAR 331
>gnl|CDD|232843 TIGR00133, gatB, aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase,
B subunit. The heterotrimer GatABC is responsible for
transferring the NH2 group that converts Glu to Gln, or
Asp to Asn after the Glu or Asp has been ligated to the
tRNA for Gln or Asn, respectively. In Lactobacillus,
GatABC is responsible only for tRNA(Gln). In the
Archaea, GatABC is responsible only for tRNA(Asn), while
GatDE is responsible for tRNA(Gln). In lineages that
include Thermus, Chlamydia, or Acidithiobacillus, the
GatABC complex catalyzes both [Protein synthesis, tRNA
aminoacylation].
Length = 478
Score = 32.0 bits (73), Expect = 0.52
Identities = 19/81 (23%), Positives = 31/81 (38%), Gaps = 3/81 (3%)
Query: 198 RQVSTEEGERKAKELNVMFIETSAKAGYNVKQVRLQLWDTAGQERFRSLIPSYIRDSTVA 257
R T R E ++ I VK+V +L + +R R + +
Sbjct: 264 RSKETSIDYRYFPEPDLPPINIDELL---VKEVAGKLPELPSAKRIRLKKEYGLSEQDAK 320
Query: 258 VVVYDITNANSFHQTSKWIDD 278
V+ D+T A+ F + K I D
Sbjct: 321 VLTSDLTLADYFEEVVKLIGD 341
>gnl|CDD|234274 TIGR03594, GTPase_EngA, ribosome-associated GTPase EngA. EngA
(YfgK, Der) is a ribosome-associated essential GTPase
with a duplication of its GTP-binding domain. It is
broadly to universally distributed among bacteria. It
appears to function in ribosome biogenesis or stability
[Protein synthesis, Other].
Length = 429
Score = 31.6 bits (73), Expect = 0.53
Identities = 34/136 (25%), Positives = 53/136 (38%), Gaps = 27/136 (19%)
Query: 225 YNVKQVRLQLWDTAG----------QERF---RSLIPSYIRDSTVAVVVYDITNANSFHQ 271
+ + L DTAG E++ R+L I + V ++V D T + Q
Sbjct: 215 FERNGKKYTLIDTAGIRRKGKVTEGVEKYSVLRTL--KAIERADVVLLVLDATEGIT-EQ 271
Query: 272 TSKWIDDVRTERGSDVIIMLVGNKTDL---SDKRQVSTEEGERKAKELN---VMFIETSA 325
+ E G ++I V NK DL R+ +E RK L+ ++FI SA
Sbjct: 272 DLRIAGLA-LEAGKALVI--VVNKWDLVKDEKTREEFKKELRRKLPFLDFAPIVFI--SA 326
Query: 326 KAGYNVKQLFRRVAAA 341
G V +L +
Sbjct: 327 LTGQGVDKLLDAIDEV 342
>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 = 31.4 bits (72), Expect = 0.70
Identities = 31/114 (27%), Positives = 51/114 (44%), Gaps = 14/114 (12%)
Query: 241 ERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDV-RTERGSDVIIMLVGNKTDL- 298
+ F +L+ S + + V V DI + I ++ R G+ V+ LVGNK DL
Sbjct: 51 DDFLNLLNSLGDSNALIVYVVDIFDFEG-----SLIPELKRFVGGNPVL--LVGNKIDLL 103
Query: 299 --SDKRQVSTEEGERKAKELNVMFIE---TSAKAGYNVKQLFRRVAAALPGMDS 347
S E +++AKEL + ++ SAK G + +L ++ A D
Sbjct: 104 PKSVNLSKIKEWMKKRAKELGLKPVDIILVSAKKGNGIDELLDKIKKARNKKDV 157
>gnl|CDD|217025 pfam02421, FeoB_N, Ferrous iron transport protein B. Escherichia
coli has an iron(II) transport system (feo) which may
make an important contribution to the iron supply of the
cell under anaerobic conditions. FeoB has been
identified as part of this transport system. FeoB is a
large 700-800 amino acid integral membrane protein. The
N terminus contains a P-loop motif suggesting that iron
transport may be ATP dependent.
Length = 190
Score = 30.5 bits (70), Expect = 0.79
Identities = 15/63 (23%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 282 ERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVAAA 341
E G V++ L N D ++K+ + + ++ ++ L V + TSA+ G + +L +
Sbjct: 103 ELGIPVVVAL--NMMDEAEKKGIKIDI-KKLSELLGVPVVPTSARKGEGIDELKDAIIEV 159
Query: 342 LPG 344
G
Sbjct: 160 AEG 162
Score = 28.2 bits (64), Expect = 4.4
Identities = 17/74 (22%), Positives = 38/74 (51%), Gaps = 4/74 (5%)
Query: 178 ERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQVRLQLWDT 237
E G V++ L N D ++K+ + + ++ ++ L V + TSA+ G + +++ + +
Sbjct: 103 ELGIPVVVAL--NMMDEAEKKGIKIDI-KKLSELLGVPVVPTSARKGEGIDELKDAIIEV 159
Query: 238 A-GQERFRSLIPSY 250
A G+ L +Y
Sbjct: 160 AEGKVPPAPLRINY 173
>gnl|CDD|206685 cd01898, Obg, Obg GTPase. The Obg nucleotide binding protein
subfamily has been implicated in stress response,
chromosome partitioning, replication initiation,
mycelium development, and sporulation. Obg proteins are
among a large group of GTP binding proteins conserved
from bacteria to humans. The E. coli homolog, ObgE is
believed to function in ribosomal biogenesis. Members of
the subfamily contain two equally and highly conserved
domains, a C-terminal GTP binding domain and an
N-terminal glycine-rich domain.
Length = 170
Score = 30.5 bits (70), Expect = 0.80
Identities = 14/54 (25%), Positives = 24/54 (44%), Gaps = 4/54 (7%)
Query: 185 IMLVGNKTDLSDKRQVST--EEGERKAKELNVMFIETSAKAGYNVKQVRLQLWD 236
++V NK DL D + +E ++ K V I SA G + ++ +L
Sbjct: 117 RIVVLNKIDLLDAEERFEKLKELLKELKGKKVFPI--SALTGEGLDELLKKLAK 168
Score = 29.3 bits (67), Expect = 1.8
Identities = 14/48 (29%), Positives = 22/48 (45%), Gaps = 4/48 (8%)
Query: 289 IMLVGNKTDLSDKRQVST--EEGERKAKELNVMFIETSAKAGYNVKQL 334
++V NK DL D + +E ++ K V I SA G + +L
Sbjct: 117 RIVVLNKIDLLDAEERFEKLKELLKELKGKKVFPI--SALTGEGLDEL 162
>gnl|CDD|177661 PLN00023, PLN00023, GTP-binding protein; Provisional.
Length = 334
Score = 31.0 bits (70), Expect = 0.82
Identities = 30/130 (23%), Positives = 55/130 (42%), Gaps = 16/130 (12%)
Query: 8 GNPLRKFKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQA 67
G P + +++ +G+ VGK+SL+ + +G T + Y S ++ +
Sbjct: 16 GPPCGQVRVLVVGDSGVGKSSLV-HLIVKGSSIARPPQTIGCTVGVKHITYGSPGSSSNS 74
Query: 68 TIGIDFLSKTMYLEDRTVRLQLWDTAGQERF---RSLIPSYIRDSTVAVVVYDITNANSF 124
G +R ++LWD +G ER+ RSL S I + V+D++ +
Sbjct: 75 IKGD---------SERDFFVELWDVSGHERYKDCRSLFYSQING---VIFVHDLSQRRTK 122
Query: 125 HQTSKWIDDV 134
KW +V
Sbjct: 123 TSLQKWASEV 132
Score = 29.1 bits (65), Expect = 3.8
Identities = 23/85 (27%), Positives = 38/85 (44%), Gaps = 18/85 (21%)
Query: 232 LQLWDTAGQERF---RSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTER----- 283
++LWD +G ER+ RSL S I + V+D++ + KW +V
Sbjct: 85 VELWDVSGHERYKDCRSLFYSQING---VIFVHDLSQRRTKTSLQKWASEVAATGTFSAP 141
Query: 284 -------GSDVIIMLVGNKTDLSDK 301
G V +++GNK D++ K
Sbjct: 142 LGSGGPGGLPVPYIVIGNKADIAPK 166
>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 = 30.1 bits (68), Expect = 0.94
Identities = 29/122 (23%), Positives = 52/122 (42%), Gaps = 11/122 (9%)
Query: 217 IETSAKAGYNV-----KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQ 271
+ T G+NV K ++ Q+WD GQ R Y ++ + V D T+ +
Sbjct: 25 VTTIPTIGFNVETVTYKNLKFQVWDLGGQTSIRPYWRCYYSNTDAIIYVVDSTDRDRL-G 83
Query: 272 TSK--WIDDVRTERGSDVIIMLVGNKTDLS---DKRQVSTEEGERKAKELNVMFIETSAK 326
SK + E D ++++ NK D+ + +V+ + G + K+ +TSA
Sbjct: 84 ISKSELHAMLEEEELKDAVLLVFANKQDMPGALSEAEVAEKLGLSELKDRTWQIFKTSAT 143
Query: 327 AG 328
G
Sbjct: 144 KG 145
>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 = 30.1 bits (68), Expect = 0.99
Identities = 23/88 (26%), Positives = 39/88 (44%), Gaps = 16/88 (18%)
Query: 224 GYNV-----KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYD------ITNANSFHQT 272
G+NV K + +WD GQ++ R L Y +++ + V D I A Q
Sbjct: 33 GFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERIGEAREELQR 92
Query: 273 SKWIDDVRTERGSDVIIMLVGNKTDLSD 300
D++R D ++++ NK DL +
Sbjct: 93 MLNEDELR-----DAVLLVFANKQDLPN 115
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 30.3 bits (68), Expect = 1.0
Identities = 20/95 (21%), Positives = 41/95 (43%), Gaps = 6/95 (6%)
Query: 217 IETSAKAGYNV-----KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQ 271
+ T G+NV K + +WD GQ++ R L Y +++ + V D + + +
Sbjct: 43 VTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRDRVVE 102
Query: 272 TSKWIDDVRTERG-SDVIIMLVGNKTDLSDKRQVS 305
+ + E D ++++ NK DL + +
Sbjct: 103 ARDELHRMLNEDELRDAVLLVFANKQDLPNAMNAA 137
>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 = 30.3 bits (69), Expect = 1.0
Identities = 27/100 (27%), Positives = 44/100 (44%), Gaps = 19/100 (19%)
Query: 249 SYIRDSTVAVVVY--DITNANSFHQTSKWIDDVRTERGSDVIIMLVGNKTDL-------- 298
S + + A+VV+ DI + F + I + G+ +I LVGNK DL
Sbjct: 28 STLLNDN-ALVVHVVDIFD---FPGS--LIPGLAELIGAKPVI-LVGNKIDLLPKDVKPN 80
Query: 299 SDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRV 338
K+ V K +V+ + SAK G+ V++L +
Sbjct: 81 RLKQWVKKRLKIGGLKIKDVILV--SAKKGWGVEELIEEI 118
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 30.2 bits (68), Expect = 1.1
Identities = 22/88 (25%), Positives = 37/88 (42%), Gaps = 20/88 (22%)
Query: 224 GYNV-----KQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDD 278
G+NV K ++ +WD GQ++ R L Y +++ + V D + I D
Sbjct: 50 GFNVETVEYKNLKFTMWDVGGQDKLRPLWRHYYQNTNGLIFVVDSNDRER-------IGD 102
Query: 279 VRTERGS--------DVIIMLVGNKTDL 298
R E D ++++ NK DL
Sbjct: 103 AREELERMLSEDELRDAVLLVFANKQDL 130
>gnl|CDD|206667 cd01879, FeoB, Ferrous iron transport protein B (FeoB) family.
Ferrous iron transport protein B (FeoB) subfamily. E.
coli has an iron(II) transport system, known as feo,
which may make an important contribution to the iron
supply of the cell under anaerobic conditions. FeoB has
been identified as part of this transport system. FeoB
is a large 700-800 amino acid integral membrane protein.
The N terminus contains a P-loop motif suggesting that
iron transport may be ATP dependent.
Length = 159
Score = 29.7 bits (68), Expect = 1.3
Identities = 16/63 (25%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 282 ERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVAAA 341
E G V++ L N D ++KR + + ++ ++ L V + TSA+ G + +L +A
Sbjct: 100 ELGLPVVVAL--NMIDEAEKRGIKIDL-DKLSELLGVPVVPTSARKGEGIDELLDAIAKL 156
Query: 342 LPG 344
Sbjct: 157 AES 159
>gnl|CDD|204242 pfam09439, SRPRB, Signal recognition particle receptor beta
subunit. The beta subunit of the signal recognition
particle receptor (SRP) is a transmembrane GTPase which
anchors the alpha subunit to the endoplasmic reticulum
membrane.
Length = 181
Score = 29.7 bits (67), Expect = 1.5
Identities = 33/153 (21%), Positives = 57/153 (37%), Gaps = 24/153 (15%)
Query: 208 KAKELNVMFIETSAKAGY-NVKQVRLQLWDTAGQERFRSLIPSYIRDSTVA---VVVYDI 263
+ V E SA Y K L D G + R + I+DS+ V V D
Sbjct: 26 GTVKKTVTSQEPSAAYKYMLHKGFSFTLIDFPGHVKLRQKLLETIKDSSSLRGIVFVVDS 85
Query: 264 T-NANSFHQTSKWIDDV--RTERGSDVI-IMLVGNKTDLSDKRQVSTEEGERKAKELNVM 319
T T++++ ++ TE + I I++ NK + R + + KE+N
Sbjct: 86 TAFPKEVTDTAEFLYEILSITELLKNGIDILIACNKQESFTARPPKKIKQALE-KEIN-- 142
Query: 320 FIETSAKAGYNVKQLFRRVAAALPGMDSTENKP 352
+ R + AL G+D +++
Sbjct: 143 -------------TIRERRSKALSGLDGSDDLS 162
Score = 27.4 bits (61), Expect = 9.0
Identities = 19/96 (19%), Positives = 27/96 (28%), Gaps = 26/96 (27%)
Query: 17 VFLGEQSVGKTSLITRFMYDSFDNTYQATIVGKTSLITRFMYDSFDNTYQATIGIDFLSK 76
+ G GKTSL T + T TS Y
Sbjct: 7 IIAGLCDSGKTSLFTLLTTGTVKKTV-------TSQEPSAAYK----------------- 42
Query: 77 TMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVA 112
Y+ + L D G + R + I+DS+
Sbjct: 43 --YMLHKGFSFTLIDFPGHVKLRQKLLETIKDSSSL 76
>gnl|CDD|206684 cd01897, NOG, Nucleolar GTP-binding protein (NOG). NOG1 is a
nucleolar GTP-binding protein present in eukaryotes
ranging from trypanosomes to humans. NOG1 is
functionally linked to ribosome biogenesis and found in
association with the nuclear pore complexes and
identified in many preribosomal complexes. Thus, defects
in NOG1 can lead to defects in 60S biogenesis. The S.
cerevisiae NOG1 gene is essential for cell viability,
and mutations in the predicted G motifs abrogate
function. It is a member of the ODN family of
GTP-binding proteins that also includes the bacterial
Obg and DRG proteins.
Length = 167
Score = 29.5 bits (67), Expect = 1.5
Identities = 11/50 (22%), Positives = 23/50 (46%), Gaps = 2/50 (4%)
Query: 182 DVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQVR 231
+ +++V NK DL + +S E E + + I+ S V +++
Sbjct: 112 NKPVIVVLNKIDLLTEEDLSEIEKELEKE--GEEVIKISTLTEEGVDELK 159
Score = 28.3 bits (64), Expect = 4.8
Identities = 12/49 (24%), Positives = 22/49 (44%), Gaps = 2/49 (4%)
Query: 286 DVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQL 334
+ +++V NK DL + +S E E + + I+ S V +L
Sbjct: 112 NKPVIVVLNKIDLLTEEDLSEIEKELEKE--GEEVIKISTLTEEGVDEL 158
>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 = 29.5 bits (66), Expect = 2.0
Identities = 22/95 (23%), Positives = 37/95 (38%), Gaps = 13/95 (13%)
Query: 47 VGKTSLITRFMYDSFDNTYQATIG-------IDFLSKTMYLEDRTVRLQLWDTAGQ---- 95
VGK+SL+ + T+G + T E++T ++LWD G
Sbjct: 11 VGKSSLVHLLCKNQVLGNPSWTVGCSVDVRHHTYGEGTP--EEKTFYVELWDVGGSVGSA 68
Query: 96 ERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSKW 130
E +S + + V+D+TN S +W
Sbjct: 69 ESVKSTRAVFYNQINGIIFVHDLTNKKSSQNLYRW 103
>gnl|CDD|180343 PRK05993, PRK05993, short chain dehydrogenase; Provisional.
Length = 277
Score = 29.6 bits (67), Expect = 2.0
Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 9/47 (19%)
Query: 130 WIDDVRTE-RGSDVIIMLV--GSIETNFTHLSFHHANSFHQTSKWID 173
+R E +GS + + L+ G IET F AN+ +WID
Sbjct: 158 LSLTLRMELQGSGIHVSLIEPGPIETRFR------ANALAAFKRWID 198
>gnl|CDD|206677 cd01890, LepA, LepA also known as Elongation Factor 4 (EF4). LepA
(also known as elongation factor 4, EF4) belongs to the
GTPase family and exhibits significant homology to the
translation factors EF-G and EF-Tu, indicating its
possible involvement in translation and association with
the ribosome. LepA is ubiquitous in bacteria and
eukaryota (e.g. yeast GUF1p), but is missing from
archaea. This pattern of phyletic distribution suggests
that LepA evolved through a duplication of the EF-G gene
in bacteria, followed by early transfer into the
eukaryotic lineage, most likely from the
promitochondrial endosymbiont. Yeast GUF1p is not
essential and mutant cells did not reveal any marked
phenotype.
Length = 179
Score = 29.0 bits (66), Expect = 2.4
Identities = 16/65 (24%), Positives = 27/65 (41%), Gaps = 13/65 (20%)
Query: 286 DVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMF-------IETSAKAGYNVKQLFRRV 338
++ I+ V NK DL + +R +E+ + I SAK G V+ L +
Sbjct: 119 NLEIIPVINKIDLP------AADPDRVKQEIEDVLGLDASEAILVSAKTGLGVEDLLEAI 172
Query: 339 AAALP 343
+P
Sbjct: 173 VERIP 177
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 29.6 bits (67), Expect = 2.5
Identities = 20/52 (38%), Positives = 29/52 (55%), Gaps = 7/52 (13%)
Query: 188 VGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQVRLQLWDTAG 239
V NK DL EE ER A++ N + I SAK G N+ +++ ++WD G
Sbjct: 245 VVNKIDL-----PGLEELERLARKPNSVPI--SAKKGINLDELKERIWDVLG 289
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 29.7 bits (68), Expect = 2.5
Identities = 16/64 (25%), Positives = 23/64 (35%), Gaps = 4/64 (6%)
Query: 292 VGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFRRVAAALPGMDSTENK 351
V NK DL + + E E ++L SA G + +L VA L +
Sbjct: 280 VANKMDLPE----AEENLEEFKEKLGPKVFPISALTGQGLDELLYAVAELLEETPEFPLE 335
Query: 352 PPED 355
E
Sbjct: 336 EEEV 339
>gnl|CDD|215633 PLN03210, PLN03210, Resistant to P. syringae 6; Provisional.
Length = 1153
Score = 29.5 bits (66), Expect = 3.2
Identities = 25/69 (36%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 58 YDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSY---IRDSTVAVV 114
YD F + + I FLS + DR + + D ER +SL P IRDS +AVV
Sbjct: 13 YDVFPSFSGEDVRITFLSHFLKELDRKLIIAFKDNE-IERSQSLDPELKQAIRDSRIAVV 71
Query: 115 VYDITNANS 123
V+ A+S
Sbjct: 72 VFSKNYASS 80
>gnl|CDD|237511 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 29.1 bits (66), Expect = 3.4
Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 6/52 (11%)
Query: 289 IMLVGNKTDL---SDKRQVSTEEGERKAKELN---VMFIETSAKAGYNVKQL 334
++LVGNK DL S K+ ++AKEL V + SA+ G+ + +L
Sbjct: 99 VLLVGNKADLLPKSVKKNKVKNWLRQEAKELGLRPVDVVLISAQKGHGIDEL 150
Score = 27.9 bits (63), Expect = 8.5
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 6/52 (11%)
Query: 185 IMLVGNKTDL---SDKRQVSTEEGERKAKELN---VMFIETSAKAGYNVKQV 230
++LVGNK DL S K+ ++AKEL V + SA+ G+ + ++
Sbjct: 99 VLLVGNKADLLPKSVKKNKVKNWLRQEAKELGLRPVDVVLISAQKGHGIDEL 150
>gnl|CDD|206668 cd01881, Obg_like, Obg-like family of GTPases consist of five
subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1. The
Obg-like subfamily consists of five well-delimited,
ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210,
and NOG1. Four of these groups (Obg, DRG, YyaF/YchF, and
Ygr210) are characterized by a distinct glycine-rich
motif immediately following the Walker B motif (G3 box).
Obg/CgtA is an essential gene that is involved in the
initiation of sporulation and DNA replication in the
bacteria Caulobacter and Bacillus, but its exact
molecular role is unknown. Furthermore, several OBG
family members possess a C-terminal RNA-binding domain,
the TGS domain, which is also present in threonyl-tRNA
synthetase and in bacterial guanosine polyphosphatase
SpoT. Nog1 is a nucleolar protein that might function in
ribosome assembly. The DRG and Nog1 subfamilies are
ubiquitous in archaea and eukaryotes, the Ygr210
subfamily is present in archaea and fungi, and the Obg
and YyaF/YchF subfamilies are ubiquitous in bacteria and
eukaryotes. The Obg/Nog1 and DRG subfamilies appear to
form one major branch of the Obg family and the Ygr210
and YchF subfamilies form another branch. No GEFs, GAPs,
or GDIs for Obg have been identified.
Length = 167
Score = 28.5 bits (64), Expect = 3.7
Identities = 21/126 (16%), Positives = 49/126 (38%), Gaps = 16/126 (12%)
Query: 230 VRLQLWDTAG------QERFR-SLIPSYIRDSTVAVVVYDITNANSFHQTSKWIDDVRTE 282
V +Q+ D G + R I +++ S + + V D + + + + E
Sbjct: 45 VDIQIIDLPGLLDGASEGRGLGEQILAHLYRSDLILHVIDASE-DCVGDPLEDQKTLNEE 103
Query: 283 ------RGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQLFR 336
+ M+V NK D++ + + + ++ + + V + TSA + ++ R
Sbjct: 104 VSGSFLFLKNKPEMIVANKIDMASENNLKRLKLDKLKRGIPV--VPTSALTRLGLDRVIR 161
Query: 337 RVAAAL 342
+ L
Sbjct: 162 TIRKLL 167
>gnl|CDD|217066 pfam02492, cobW, CobW/HypB/UreG, nucleotide-binding domain. This
domain is found in HypB, a hydrogenase expression /
formation protein, and UreG a urease accessory protein.
Both these proteins contain a P-loop nucleotide binding
motif. HypB has GTPase activity and is a guanine
nucleotide binding protein. It is not known whether UreG
binds GTP or some other nucleotide. Both enzymes are
involved in nickel binding. HypB can store nickel and is
required for nickel dependent hydrogenase expression.
UreG is required for functional incorporation of the
urease nickel metallocenter. GTP hydrolysis may required
by these proteins for nickel incorporation into other
nickel proteins. This family of domains also contains
P47K, a Pseudomonas chlororaphis protein needed for
nitrile hydratase expression, and the cobW gene product,
which may be involved in cobalamin biosynthesis in
Pseudomonas denitrificans.
Length = 178
Score = 28.4 bits (64), Expect = 4.1
Identities = 25/112 (22%), Positives = 40/112 (35%), Gaps = 18/112 (16%)
Query: 206 ERKAKELNVMFIETSAKAGYNVKQVRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITN 265
+ L+++FIET+ A V + D V VV D+
Sbjct: 78 LELKERLDLLFIETTGLA--CPAPVAQTFLSPELRSDLGL-------DGVVTVV--DVAE 126
Query: 266 ANSFHQTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELN 317
K D + +D+I++ NKTDL+ E+ E + LN
Sbjct: 127 TEGEDIPEKAPDQIAF---ADLIVI---NKTDLAPAVA-DLEKLEADLRRLN 171
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 28.9 bits (66), Expect = 4.1
Identities = 36/134 (26%), Positives = 57/134 (42%), Gaps = 36/134 (26%)
Query: 231 RLQLWDTAG----------QERF---RSLIPSYIRDSTVAVVVYDITNANSFHQTSKWID 277
+ L DTAG E++ R+L I + V ++V D T + Q
Sbjct: 222 KYTLIDTAGIRRKGKVTEGVEKYSVIRTL--KAIERADVVLLVIDATEGIT-EQ------ 272
Query: 278 DVR-----TERGSDVIIMLVGNKTDLSDKRQVS--TEEGERKAKELN---VMFIETSAKA 327
D+R E G ++I V NK DL D++ + +E R+ L+ ++FI SA
Sbjct: 273 DLRIAGLALEAGRALVI--VVNKWDLVDEKTMEEFKKELRRRLPFLDYAPIVFI--SALT 328
Query: 328 GYNVKQLFRRVAAA 341
G V +L + A
Sbjct: 329 GQGVDKLLEAIDEA 342
>gnl|CDD|206571 pfam14403, CP_ATPgrasp_2, Circularly permuted ATP-grasp type 2.
Circularly permuted ATP-grasp prototyped by Roseiflexus
RoseRS_2616 that is associated in gene neighborhoods
with a GCS2-like COOH-NH2 ligase, alpha/beta hydrolase
fold peptidase, GAT-II -like amidohydrolase, and M20
peptidase. Members of this family are predicted to be
involved in the biosynthesis of small peptides.
Length = 445
Score = 29.0 bits (65), Expect = 4.2
Identities = 12/54 (22%), Positives = 19/54 (35%)
Query: 52 LITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSY 105
L++R Y+ F + L +R +L T +ER P Y
Sbjct: 49 LLSRTQYELLRRGTDRLAQALFRACQARLATPALRARLGLTPLEERLIDEDPGY 102
>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 = 28.2 bits (63), Expect = 4.9
Identities = 17/89 (19%), Positives = 35/89 (39%), Gaps = 8/89 (8%)
Query: 220 SAKAGYNVKQ-----VRLQLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTSK 274
G+NV+ + +D +GQ ++R L Y ++ + V D ++
Sbjct: 30 VPTVGFNVESFKKGNLSFTAFDMSGQGKYRGLWEHYYKNIQGIIFVIDSSDRLRMVVAKD 89
Query: 275 WIDDVRTE---RGSDVIIMLVGNKTDLSD 300
++ + + + I+ NK DL D
Sbjct: 90 ELELLLNHPDIKHRRIPILFYANKMDLPD 118
Score = 27.4 bits (61), Expect = 8.0
Identities = 15/71 (21%), Positives = 31/71 (43%), Gaps = 5/71 (7%)
Query: 48 GKTSLITRFMYDSFDN-TYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYI 106
GKT++I + + + T+G + S + + +D +GQ ++R L Y
Sbjct: 11 GKTTIINQLKPSNAQSQNIVPTVGFNVES----FKKGNLSFTAFDMSGQGKYRGLWEHYY 66
Query: 107 RDSTVAVVVYD 117
++ + V D
Sbjct: 67 KNIQGIIFVID 77
>gnl|CDD|206746 cd01849, YlqF_related_GTPase, Circularly permuted YlqF-related
GTPases. These proteins are found in bacteria,
eukaryotes, and archaea. They all exhibit a circular
permutation of the GTPase signature motifs so that the
order of the conserved G box motifs is G4-G5-G1-G2-G3,
with G4 and G5 being permuted from the C-terminal region
of proteins in the Ras superfamily to the N-terminus of
YlqF-related GTPases.
Length = 146
Score = 27.7 bits (62), Expect = 5.2
Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 4/49 (8%)
Query: 256 VAVVVYDITNANSFHQTSKWIDDVRTERGSDVIIMLVGNKTDLSDKRQV 304
V V V D + S + I+ + E+ +I+ V NK DL K +
Sbjct: 2 VVVEVVDARDPLSS--RNPDIEVLINEKNKKLIM--VLNKADLVPKEVL 46
>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 = 28.1 bits (63), Expect = 5.3
Identities = 27/120 (22%), Positives = 50/120 (41%), Gaps = 11/120 (9%)
Query: 224 GYNVKQV-----RLQLWDTAGQERFRSLIPSYIRDSTVAVV-VYDITNANSFHQTSKWID 277
G+N+K + +L +WD GQ+ RS +Y +ST A++ V D ++ + +
Sbjct: 47 GFNIKTLEYNGYKLNIWDVGGQKSLRSYWRNYF-ESTDALIWVVDSSDRARLEDCKRELQ 105
Query: 278 DV-RTERGSDVIIMLVGNKTDLS---DKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQ 333
+ ER + +++ NK DL ++ K + SA G N+
Sbjct: 106 KLLVEERLAGATLLIFANKQDLPGALSPEEIREVLELDSIKSHHWRIFGCSAVTGENLLD 165
Score = 27.3 bits (61), Expect = 9.9
Identities = 23/67 (34%), Positives = 37/67 (55%), Gaps = 6/67 (8%)
Query: 48 GKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIR 107
GKT+++ +F + +T T+G F KT LE +L +WD GQ+ RS +Y
Sbjct: 26 GKTTILKKFNGEDI-STISPTLG--FNIKT--LEYNGYKLNIWDVGGQKSLRSYWRNYF- 79
Query: 108 DSTVAVV 114
+ST A++
Sbjct: 80 ESTDALI 86
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 28.7 bits (65), Expect = 5.5
Identities = 28/139 (20%), Positives = 47/139 (33%), Gaps = 26/139 (18%)
Query: 226 NVKQVRLQLWDTAGQ------------ERFRSLIPSYIRDSTVAVVVYDITNANSFHQTS 273
N+ + ++L DTAG ER + I ++ + + V D + +
Sbjct: 261 NLNGIPVRLVDTAGIRETDDVVERIGIERAKKAI----EEADLVLFVLDAS-QPLDKEDL 315
Query: 274 KWIDDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQ 333
I+ + +I +V NK DL VS E E + I SAK G +
Sbjct: 316 ALIELLPK--KKPII--VVLNKADL-----VSKIELESEKLANGDAIISISAKTGEGLDA 366
Query: 334 LFRRVAAALPGMDSTENKP 352
L + +
Sbjct: 367 LREAIKQLFGKGLGNQEGL 385
>gnl|CDD|206750 cd01857, HSR1_MMR1, A circularly permuted subfamily of the Ras
GTPases. Human HSR1 is localized to the human MHC class
I region and is highly homologous to a putative
GTP-binding protein, MMR1 from mouse. These proteins
represent a new subfamily of GTP-binding proteins that
has only eukaryote members. This subfamily shows a
circular permutation of the GTPase signature motifs so
that the C-terminal strands 5, 6, and 7 (strand 6
contains the G4 box with sequence NKXD) are relocated to
the N-terminus.
Length = 140
Score = 27.2 bits (61), Expect = 7.2
Identities = 23/101 (22%), Positives = 35/101 (34%), Gaps = 21/101 (20%)
Query: 233 QLWDTAGQERFRSLIPSYIRDSTVAVVVYDITNANSFHQTS--KWIDDVRTERGSDVIIM 290
QLW ER S V V + D N F K++ E +
Sbjct: 4 QLWRVI--ER-----------SDVVVQIVDARNPLFFRCPDLEKYV----KEVDPSKENV 46
Query: 291 LVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNV 331
L+ NK DL + Q + R K+ ++ + SA +
Sbjct: 47 LLLNKADLVTEEQR--KAWARYFKKEGIVVLFFSALNEATI 85
>gnl|CDD|223557 COG0481, LepA, Membrane GTPase LepA [Cell envelope biogenesis,
outer membrane].
Length = 603
Score = 28.3 bits (64), Expect = 7.2
Identities = 16/74 (21%), Positives = 32/74 (43%), Gaps = 13/74 (17%)
Query: 286 DVIIMLVGNKTDLSDKRQVSTEEGERKAKEL-NVMFIET------SAKAGYNVKQLFRRV 338
++ I+ V NK DL + ER +E+ +++ I+ SAK G ++ + +
Sbjct: 128 NLEIIPVLNKIDLP------AADPERVKQEIEDIIGIDASDAVLVSAKTGIGIEDVLEAI 181
Query: 339 AAALPGMDSTENKP 352
+P + P
Sbjct: 182 VEKIPPPKGDPDAP 195
>gnl|CDD|224084 COG1162, COG1162, Predicted GTPases [General function prediction
only].
Length = 301
Score = 28.0 bits (63), Expect = 8.0
Identities = 15/53 (28%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 282 ERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKELNVMFIETSAKAGYNVKQL 334
G + +I+L NK DL D + + +E R+ +++ + SAK G +++L
Sbjct: 108 AGGIEPVIVL--NKIDLLDDEEAAVKELLREYEDIGYPVLFVSAKNGDGLEEL 158
>gnl|CDD|233815 TIGR02294, nickel_nikA, nickel ABC transporter, nickel/metallophore
periplasmic binding protein. Members of this family are
periplasmic nickel-binding proteins of nickel ABC
transporters. Most appear to be lipoproteins. This
protein was previously (circa 2003) thought to mediate
binding to nickel through water molecules, but is now
thought to involve a chelating organic molecule, perhaps
butane-1,2,4-tricarboxylate, acting as a metallophore
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 500
Score = 27.8 bits (62), Expect = 8.8
Identities = 14/62 (22%), Positives = 25/62 (40%), Gaps = 4/62 (6%)
Query: 261 YDITNANSFHQTSKWI----DDVRTERGSDVIIMLVGNKTDLSDKRQVSTEEGERKAKEL 316
YD+ AN+ + W DVR + G + + L +KT K + E + +
Sbjct: 312 YDVKKANALLDEAGWKLGKGKDVREKDGKPLELELYYDKTSALQKSLAEYLQAEWRKIGI 371
Query: 317 NV 318
+
Sbjct: 372 KL 373
>gnl|CDD|224083 COG1161, COG1161, Predicted GTPases [General function prediction
only].
Length = 322
Score = 27.7 bits (62), Expect = 8.9
Identities = 19/80 (23%), Positives = 37/80 (46%), Gaps = 4/80 (5%)
Query: 187 LVGNKTDLSDKRQVS-TEEGERKAKELNVMFIETSAKAGYNVKQVRLQLWDTAGQERFRS 245
LV NK DL+ K ++ +K + + +F+ SAK+ K++R + + +E+ +
Sbjct: 66 LVLNKADLAPKEVTKKWKKYFKKEEGIKPIFV--SAKSRQGGKKIR-KALEKLSEEKIKR 122
Query: 246 LIPSYIRDSTVAVVVYDITN 265
L + + V V N
Sbjct: 123 LKKKGLLKRKIRVGVVGYPN 142
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the
AAA superfamily.
Length = 154
Score = 27.2 bits (60), Expect = 9.1
Identities = 6/19 (31%), Positives = 10/19 (52%)
Query: 16 LVFLGEQSVGKTSLITRFM 34
++ G GKTSL+ +
Sbjct: 27 VLLTGPSGTGKTSLLRELL 45
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
0.317 0.132 0.372
Gapped
Lambda K H
0.267 0.0591 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,432,936
Number of extensions: 1628071
Number of successful extensions: 2180
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1964
Number of HSP's successfully gapped: 373
Length of query: 355
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 257
Effective length of database: 6,590,910
Effective search space: 1693863870
Effective search space used: 1693863870
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 60 (27.2 bits)