RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2970
(329 letters)
>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 = 229 bits (585), Expect = 1e-75
Identities = 100/166 (60%), Positives = 112/166 (67%), Gaps = 41/166 (24%)
Query: 22 ELTLVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRKITKGNVTIKVWDIGGQPRFRSM 81
E+TLVGLQ SGKTT VNVIASGQFS+D IPTVGFNMRK+TKGNVTIKVWD+GGQPRFRSM
Sbjct: 1 EITLVGLQNSGKTTLVNVIASGQFSEDTIPTVGFNMRKVTKGNVTIKVWDLGGQPRFRSM 60
Query: 82 WERYCRGVNAIVWTGGLYIVSKHIKRSAILYYEPVDLGVSGPMWLSLLFQLIKYMVDAAD 141
WERYCRGVNAIV Y+VDAAD
Sbjct: 61 WERYCRGVNAIV-----------------------------------------YVVDAAD 79
Query: 142 TDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDR 187
+KLE ++NELH L+EKP L GIP+LVLGNK DLP AL ELI++
Sbjct: 80 REKLEVAKNELHDLLEKPSLEGIPLLVLGNKNDLPGALSVDELIEQ 125
>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 = 141 bits (359), Expect = 1e-41
Identities = 49/164 (29%), Positives = 82/164 (50%), Gaps = 42/164 (25%)
Query: 23 LTLVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRKITKGNVTIKVWDIGGQPRFRSMW 82
+ ++GL +GKTT + + G+ IPT+GFN+ + NV VWD+GGQ + R +W
Sbjct: 2 ILMLGLDGAGKTTILYKLKLGEV-VTTIPTIGFNVETVEYKNVKFTVWDVGGQDKIRPLW 60
Query: 83 ERYCRGVNAIVWTGGLYIVSKHIKRSAILYYEPVDLGVSGPMWLSLLFQLIKYMVDAADT 142
+ Y + +++ +VD++D
Sbjct: 61 KHYYENTDGLIF-----------------------------------------VVDSSDR 79
Query: 143 DKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELID 186
+++E ++NELH L+ + +L G P+L+L NK+DLP AL E ELI+
Sbjct: 80 ERIEEAKNELHKLLNEEELKGAPLLILANKQDLPGALTESELIE 123
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 122 bits (308), Expect = 6e-34
Identities = 55/178 (30%), Positives = 86/178 (48%), Gaps = 43/178 (24%)
Query: 8 ILDWFKSLF-WKEEMELTLVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRKITKGNVT 66
L LF W +EM + ++GL +GKTT + + G+ IPT+GFN+ +T NV
Sbjct: 1 FLSILAKLFGWNKEMRILILGLDNAGKTTILYKLKLGEIVT-TIPTIGFNVETVTYKNVK 59
Query: 67 IKVWDIGGQPRFRSMWERYCRGVNAIVWTGGLYIVSKHIKRSAILYYEPVDLGVSGPMWL 126
VWD+GGQ R +W Y +A+++
Sbjct: 60 FTVWDVGGQESLRPLWRNYFPNTDAVIF-------------------------------- 87
Query: 127 SLLFQLIKYMVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKEL 184
+VD+AD D++E ++ ELHAL+ + +L P+L+L NK+DLP A+ E E+
Sbjct: 88 ---------VVDSADRDRIEEAKEELHALLNEEELADAPLLILANKQDLPGAMSEAEI 136
>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 = 111 bits (281), Expect = 8e-30
Identities = 52/193 (26%), Positives = 92/193 (47%), Gaps = 47/193 (24%)
Query: 8 ILDWFKSLF-----WKEEMELTLVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRKITK 62
I DWF ++ +K+E ++ +GL +GKTT ++++ + +Q +PT+ ++T
Sbjct: 2 IFDWFYNVLSSLGLYKKEAKIVFLGLDNAGKTTLLHMLKDDRLAQ-HVPTLHPTSEELTI 60
Query: 63 GNVTIKVWDIGGQPRFRSMWERYCRGVNAIVWTGGLYIVSKHIKRSAILYYEPVDLGVSG 122
GNV +D+GG + R +W+ Y V+ IV
Sbjct: 61 GNVKFTTFDLGGHEQARRVWKDYFPEVDGIV----------------------------- 91
Query: 123 PMWLSLLFQLIKYMVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEK 182
++VDAAD ++ + S+ EL +L+ +L +PIL+LGNK D P A+ E+
Sbjct: 92 ------------FLVDAADPERFQESKEELDSLLNDEELANVPILILGNKIDKPGAVSEE 139
Query: 183 ELIDRIMIDFWIT 195
EL + + + T
Sbjct: 140 ELREALGLYGTTT 152
>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 = 106 bits (267), Expect = 5e-28
Identities = 52/180 (28%), Positives = 85/180 (47%), Gaps = 42/180 (23%)
Query: 12 FKSLFWKEEMELTLVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRKITKGNVTIKVWD 71
LF +EM + ++GL +GKTT + + GQ S IPTVGFN+ +T NV VWD
Sbjct: 1 LSKLFGNKEMRILMLGLDAAGKTTILYKLKLGQ-SVTTIPTVGFNVETVTYKNVKFNVWD 59
Query: 72 IGGQPRFRSMWERYCRGVNAIVWTGGLYIVSKHIKRSAILYYEPVDLGVSGPMWLSLLFQ 131
+GGQ + R +W Y G ++
Sbjct: 60 VGGQDKIRPLWRHYYTGTQGLI-------------------------------------- 81
Query: 132 LIKYMVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRIMID 191
++VD+AD D+++ +R ELH +I ++ +LV NK+DLP+A+ E+ +++ +
Sbjct: 82 ---FVVDSADRDRIDEARQELHRIINDREMRDALLLVFANKQDLPDAMKPHEIQEKLGLT 138
>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 = 99.2 bits (247), Expect = 4e-25
Identities = 50/177 (28%), Positives = 85/177 (48%), Gaps = 42/177 (23%)
Query: 12 FKSLFWKEEMELTLVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRKITKGNVTIKVWD 71
F LF +EM + +VGL +GKTT + + G+ S IPT+GFN+ +T N++ VWD
Sbjct: 5 FSKLFGNKEMRILMVGLDAAGKTTILYKLKLGE-SVTTIPTIGFNVETVTYKNISFTVWD 63
Query: 72 IGGQPRFRSMWERYCRGVNAIVWTGGLYIVSKHIKRSAILYYEPVDLGVSGPMWLSLLFQ 131
+GGQ + R +W Y ++
Sbjct: 64 VGGQDKIRPLWRHYYTNTQGLI-------------------------------------- 85
Query: 132 LIKYMVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRI 188
++VD+ D D+++ +R ELH ++ + +L ILV NK+DLP+A+ E+ +++
Sbjct: 86 ---FVVDSNDRDRIDEAREELHRMLNEDELRDAVILVFANKQDLPDAMKAAEITEKL 139
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 95.0 bits (236), Expect = 2e-23
Identities = 50/177 (28%), Positives = 86/177 (48%), Gaps = 42/177 (23%)
Query: 12 FKSLFWKEEMELTLVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRKITKGNVTIKVWD 71
F LF K+EM + +VGL +GKTT + + G+ IPT+GFN+ + N++ VWD
Sbjct: 9 FSRLFAKKEMRILMVGLDAAGKTTILYKLKLGEIVT-TIPTIGFNVETVEYKNISFTVWD 67
Query: 72 IGGQPRFRSMWERYCRGVNAIVWTGGLYIVSKHIKRSAILYYEPVDLGVSGPMWLSLLFQ 131
+GGQ + R +W Y + ++
Sbjct: 68 VGGQDKIRPLWRHYFQNTQGLI-------------------------------------- 89
Query: 132 LIKYMVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRI 188
++VD+ D D++ +R+ELH ++ + +L +LV NK+DLPNA++ E+ D++
Sbjct: 90 ---FVVDSNDRDRVVEARDELHRMLNEDELRDAVLLVFANKQDLPNAMNAAEITDKL 143
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 93.4 bits (232), Expect = 6e-23
Identities = 48/177 (27%), Positives = 85/177 (48%), Gaps = 42/177 (23%)
Query: 12 FKSLFWKEEMELTLVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRKITKGNVTIKVWD 71
FKSLF K+E+ + +VGL +GKTT + + G+ IPT+GFN+ + N+ +WD
Sbjct: 9 FKSLFGKKEVRILMVGLDAAGKTTILYKLKLGEVVT-TIPTIGFNVETVEYKNLKFTMWD 67
Query: 72 IGGQPRFRSMWERYCRGVNAIVWTGGLYIVSKHIKRSAILYYEPVDLGVSGPMWLSLLFQ 131
+GGQ + R +W Y + N ++
Sbjct: 68 VGGQDKLRPLWRHYYQNTNGLI-------------------------------------- 89
Query: 132 LIKYMVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRI 188
++VD+ D +++ +R EL ++ + +L +LV NK+DLPNA+ E+ +++
Sbjct: 90 ---FVVDSNDRERIGDAREELERMLSEDELRDAVLLVFANKQDLPNAMSTTEVTEKL 143
>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 = 92.1 bits (229), Expect = 2e-22
Identities = 50/181 (27%), Positives = 83/181 (45%), Gaps = 44/181 (24%)
Query: 8 ILDWFKSL--FWKEEMELTLVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRKITKGNV 65
+L + L ++E+ + L+GL +GKTT + +AS S + PT GFN++ +
Sbjct: 1 LLSILRKLKPSSRQEVRILLLGLDNAGKTTILKQLASEDISH-ITPTQGFNIKNVQADGF 59
Query: 66 TIKVWDIGGQPRFRSMWERYCRGVNAIVWTGGLYIVSKHIKRSAILYYEPVDLGVSGPMW 125
+ VWDIGGQ + R W Y+E D
Sbjct: 60 KLNVWDIGGQRKIRPYWRN---------------------------YFENTD-------- 84
Query: 126 LSLLFQLIKYMVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELI 185
++ Y++D+AD + E + EL L+E+ +L G+P+LV NK+DL A +E+
Sbjct: 85 ------VLIYVIDSADRKRFEEAGQELVELLEEEKLAGVPVLVFANKQDLLTAAPAEEVA 138
Query: 186 D 186
+
Sbjct: 139 E 139
>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 = 91.0 bits (226), Expect = 3e-22
Identities = 45/164 (27%), Positives = 77/164 (46%), Gaps = 44/164 (26%)
Query: 26 VGLQCSGKTTFVNVIA-SGQFSQDMIPTVGFNMRKITKGNVTIKVWDIGGQPRFRSMWER 84
+GL SGKTT +N + S SQ+++PTVGFN+ KGN++ +D+ GQ ++R +WE
Sbjct: 5 LGLDNSGKTTIINQLKPSNAQSQNIVPTVGFNVESFKKGNLSFTAFDMSGQGKYRGLWEH 64
Query: 85 YCRGVNAIVWTGGLYIVSKHIKRSAILYYEPVDLGVSGPMWLSLLFQLIKYMVDAADTDK 144
Y + + I+ +++D++D +
Sbjct: 65 YYKNIQGII-----------------------------------------FVIDSSDRLR 83
Query: 145 LEASRNELHALIEKPQLI--GIPILVLGNKRDLPNALDEKELID 186
+ +++EL L+ P + IPIL NK DLP+AL ++
Sbjct: 84 MVVAKDELELLLNHPDIKHRRIPILFYANKMDLPDALTAVKITQ 127
>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 = 90.9 bits (226), Expect = 3e-22
Identities = 44/168 (26%), Positives = 75/168 (44%), Gaps = 50/168 (29%)
Query: 25 LVGLQCSGKTTFVNVIASGQFSQD--------MIPTVGFNMRKITKGNVTIKVWDIGGQP 76
++GL +GKTTF+ + +FS++ + PTVG N+ I G + WD+GGQ
Sbjct: 4 ILGLDNAGKTTFLEQTKT-KFSKNYKGLNPSKITPTVGLNIGTIEVGKARLMFWDLGGQE 62
Query: 77 RFRSMWERYCRGVNAIVWTGGLYIVSKHIKRSAILYYEPVDLGVSGPMWLSLLFQLIKYM 136
RS+W++Y + ++ Y+
Sbjct: 63 ELRSLWDKYYAESHGVI-----------------------------------------YV 81
Query: 137 VDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKEL 184
+D+ D ++ S++ +I L G+P+LVL NK+DLP+AL E+
Sbjct: 82 IDSTDRERFNESKSAFEKVINNEALEGVPLLVLANKQDLPDALSVAEI 129
>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 = 91.0 bits (226), Expect = 4e-22
Identities = 50/169 (29%), Positives = 81/169 (47%), Gaps = 47/169 (27%)
Query: 21 MELTLVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRKI--TKGN---VTIKVWDIGGQ 75
+ + ++GL +GKTT + + +F + +PT GFN KI + GN VT WD+GGQ
Sbjct: 4 LHIVMLGLDSAGKTTVLYRLKFNEFV-NTVPTKGFNTEKIKVSLGNAKGVTFHFWDVGGQ 62
Query: 76 PRFRSMWERYCRGVNAIVWTGGLYIVSKHIKRSAILYYEPVDLGVSGPMWLSLLFQLIKY 135
+ R +W+ Y R + IV +
Sbjct: 63 EKLRPLWKSYTRCTDGIV-----------------------------------------F 81
Query: 136 MVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKEL 184
+VD+ D +++E ++ ELH + + + G+P+LVL NK+DLPNAL E+
Sbjct: 82 VVDSVDVERMEEAKTELHKITKFSENQGVPVLVLANKQDLPNALPVSEV 130
>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 = 89.4 bits (222), Expect = 1e-21
Identities = 49/164 (29%), Positives = 79/164 (48%), Gaps = 42/164 (25%)
Query: 25 LVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRKITKGNVTIKVWDIGGQPRFRSMWER 84
++GL +GKTT + + G+ IPT+GFN+ +T N+ +VWD+GGQ R W
Sbjct: 4 ILGLDGAGKTTILYRLQVGEVVT-TIPTIGFNVETVTYKNLKFQVWDLGGQTSIRPYWRC 62
Query: 85 YCRGVNAIVWTGGLYIVSKHIKRSAILYYEPVDLGVSGPMWLSLLFQLIKYMVDAADTDK 144
Y +AI+ Y+VD+ D D+
Sbjct: 63 YYSNTDAII-----------------------------------------YVVDSTDRDR 81
Query: 145 LEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRI 188
L S++ELHA++E+ +L +LV NK+D+P AL E E+ +++
Sbjct: 82 LGISKSELHAMLEEEELKDAVLLVFANKQDMPGALSEAEVAEKL 125
>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 = 88.6 bits (220), Expect = 2e-21
Identities = 43/168 (25%), Positives = 77/168 (45%), Gaps = 42/168 (25%)
Query: 21 MELTLVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRKITKGNVTIKVWDIGGQPRFRS 80
M + +VGL +GKTT + + G+ IPT+GFN+ + N++ VWD+GGQ + R
Sbjct: 1 MRILMVGLDAAGKTTILYKLKLGEIVT-TIPTIGFNVETVEYKNISFTVWDVGGQDKIRP 59
Query: 81 MWERYCRGVNAIVWTGGLYIVSKHIKRSAILYYEPVDLGVSGPMWLSLLFQLIKYMVDAA 140
+W Y + ++ ++VD+
Sbjct: 60 LWRHYFQNTQGLI-----------------------------------------FVVDSN 78
Query: 141 DTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRI 188
D +++ +R EL ++ + +L +LV NK+DLPNA+ E+ D++
Sbjct: 79 DRERIGEAREELQRMLNEDELRDAVLLVFANKQDLPNAMSAAEVTDKL 126
>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 = 88.6 bits (220), Expect = 2e-21
Identities = 43/168 (25%), Positives = 81/168 (48%), Gaps = 43/168 (25%)
Query: 25 LVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRKI-TKGNVTIKVWDIGGQPRFRSMWE 83
L+GL +GK+T + + + IPTVGFN+ + + ++++ VWD+GGQ + R++W+
Sbjct: 4 LLGLDSAGKSTLLYKLKHAELVT-TIPTVGFNVEMLQLEKHLSLTVWDVGGQEKMRTVWK 62
Query: 84 RYCRGVNAIVWTGGLYIVSKHIKRSAILYYEPVDLGVSGPMWLSLLFQLIKYMVDAADTD 143
Y + +V Y+VD++D
Sbjct: 63 CYLENTDGLV-----------------------------------------YVVDSSDEA 81
Query: 144 KLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRIMID 191
+L+ S+ EL +++ + G+P+++L NK+DLP AL +E+ R +
Sbjct: 82 RLDESQKELKHILKNEHIKGVPVVLLANKQDLPGALTAEEITRRFKLK 129
>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 = 84.3 bits (209), Expect = 1e-19
Identities = 44/165 (26%), Positives = 75/165 (45%), Gaps = 42/165 (25%)
Query: 20 EMELTLVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRKITKGNVTIKVWDIGGQPRFR 79
EM + ++GL +GKTT + +G+ + PT+GFN++ + + +WD+GGQ R
Sbjct: 14 EMRILMLGLDNAGKTTILKKF-NGEDISTISPTLGFNIKTLEYNGYKLNIWDVGGQKSLR 72
Query: 80 SMWERYCRGVNAIVWTGGLYIVSKHIKRSAILYYEPVDLGVSGPMWLSLLFQLIKYMVDA 139
S W Y +A++W +VD+
Sbjct: 73 SYWRNYFESTDALIW-----------------------------------------VVDS 91
Query: 140 ADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKEL 184
+D +LE + EL L+ + +L G +L+ NK+DLP AL +E+
Sbjct: 92 SDRARLEDCKRELQKLLVEERLAGATLLIFANKQDLPGALSPEEI 136
>gnl|CDD|133362 cd04162, Arl9_Arfrp2_like, Arf-like 9 (Arl9)/Arfrp2-like GTPase.
Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first
identified as part of the Human Cancer Genome Project.
It maps to chromosome 4q12 and is sometimes referred to
as Arfrp2 (Arf-related protein 2). This is a novel
subfamily identified in human cancers that is
uncharacterized to date.
Length = 164
Score = 82.9 bits (205), Expect = 3e-19
Identities = 41/163 (25%), Positives = 78/163 (47%), Gaps = 43/163 (26%)
Query: 22 ELTLVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRKITKGNVTIKVWDIGGQPRFRSM 81
++ ++GL +GKT+ ++ ++S + + ++PT GFN I + +++ +IGG R
Sbjct: 1 QILVLGLDGAGKTSLLHSLSSERSLESVVPTTGFNSVAIPTQDAIMELLEIGGSQNLRKY 60
Query: 82 WERYCRGVNAIVWTGGLYIVSKHIKRSAILYYEPVDLGVSGPMWLSLLFQLIKYMVDAAD 141
W+RY G ++ ++VD+AD
Sbjct: 61 WKRYLSGSQGLI-----------------------------------------FVVDSAD 79
Query: 142 TDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKEL 184
+++L +R ELH L++ P +P++VL NK+DLP A +E+
Sbjct: 80 SERLPLARQELHQLLQHPP--DLPLVVLANKQDLPAARSVQEI 120
>gnl|CDD|197556 smart00178, SAR, Sar1p-like members of the Ras-family of small
GTPases. Yeast SAR1 is an essential gene required for
transport of secretory proteins from the endoplasmic
reticulum to the Golgi apparatus.
Length = 184
Score = 80.4 bits (198), Expect = 4e-18
Identities = 48/181 (26%), Positives = 77/181 (42%), Gaps = 47/181 (25%)
Query: 9 LDWFKSLF-----WKEEMELTLVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRKITKG 63
DWF + W + ++ +GL +GKTT ++++ + + +Q PT ++ G
Sbjct: 1 FDWFYDILASLGLWNKHAKILFLGLDNAGKTTLLHMLKNDRLAQ-HQPTQHPTSEELAIG 59
Query: 64 NVTIKVWDIGGQPRFRSMWERYCRGVNAIVWTGGLYIVSKHIKRSAILYYEPVDLGVSGP 123
N+ +D+GG + R +W+ Y VN IV
Sbjct: 60 NIKFTTFDLGGHQQARRLWKDYFPEVNGIV------------------------------ 89
Query: 124 MWLSLLFQLIKYMVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKE 183
Y+VDA D ++ S+ EL AL+ +L +P L+LGNK D P A E E
Sbjct: 90 -----------YLVDAYDKERFAESKRELDALLSDEELATVPFLILGNKIDAPYAASEDE 138
Query: 184 L 184
L
Sbjct: 139 L 139
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 78.5 bits (193), Expect = 4e-17
Identities = 40/178 (22%), Positives = 68/178 (38%), Gaps = 45/178 (25%)
Query: 16 FWKEEMELTLVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRKIT----KGNVTIKVWD 71
+ +E ++ ++G GKTT +N + +F + PT+G T + N+ +++WD
Sbjct: 1 LFMKEFKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWD 60
Query: 72 IGGQPRFRSMWERYCRGVNAIVWTGGLYIVSKHIKRSAILYYEPVDLGVSGPMWLSLLFQ 131
GQ +RS+ Y RG N I L + ++ S+
Sbjct: 61 TAGQEEYRSLRPEYYRGANGI-----LIVYDSTLRESS---------------------- 93
Query: 132 LIKYMVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRIM 189
E + L L E +PIL++GNK DL + E I +
Sbjct: 94 -------------DELTEEWLEELRELA-PDDVPILLVGNKIDLFDEQSSSEEILNQL 137
>gnl|CDD|133361 cd04161, Arl2l1_Arl13_like, Arl2-like protein 1 (Arl2l1) and Arl13.
Arl2l1 (Arl2-like protein 1) and Arl13 form a subfamily
of the Arf family of small GTPases. Arl2l1 was
identified in human cells during a search for the
gene(s) responsible for Bardet-Biedl syndrome (BBS).
Like Arl6, the identified BBS gene, Arl2l1 is proposed
to have cilia-specific functions. Arl13 is found on the
X chromosome, but its expression has not been confirmed;
it may be a pseudogene.
Length = 167
Score = 76.7 bits (189), Expect = 7e-17
Identities = 44/167 (26%), Positives = 73/167 (43%), Gaps = 48/167 (28%)
Query: 23 LTLVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRKITKGNVTIKVWDIGGQPRFRSMW 82
L VGL +GKTT V+ + G+ + + PTVGF K+ + ++D+GG FR +W
Sbjct: 2 LLTVGLDNAGKTTLVSAL-QGEIPKKVAPTVGFTPTKLRLDKYEVCIFDLGGGANFRGIW 60
Query: 83 ERY---CRGVNAIVWTGGLYIVSKHIKRSAILYYEPVDLGVSGPMWLSLLFQLIKYMVDA 139
Y G + ++VD+
Sbjct: 61 VNYYAEAHG--------------------------------------------LVFVVDS 76
Query: 140 ADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELID 186
+D D+++ + L L++ P++ G PILVL NK+D NAL ++I+
Sbjct: 77 SDDDRVQEVKEILRELLQHPRVSGKPILVLANKQDKKNALLGADVIE 123
>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 = 68.1 bits (167), Expect = 8e-14
Identities = 44/176 (25%), Positives = 76/176 (43%), Gaps = 43/176 (24%)
Query: 12 FKSLFW-KEEMELTLVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRKITKGNVTIKVW 70
SLF+ ++E ++ +VGL +GKTT + G+ PT+G N+ +I N+ +W
Sbjct: 6 LWSLFFPRKEYKVIIVGLDNAGKTTILYQFLLGEVVHTS-PTIGSNVEEIVYKNIRFLMW 64
Query: 71 DIGGQPRFRSMWERYCRGVNAIVWTGGLYIVSKHIKRSAILYYEPVDLGVSGPMWLSLLF 130
DIGGQ RS W Y +A++
Sbjct: 65 DIGGQESLRSSWNTYYTNTDAVI------------------------------------- 87
Query: 131 QLIKYMVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELID 186
++D+ D ++L ++ EL+ ++ L +LVL NK+DL A+ E+ +
Sbjct: 88 ----LVIDSTDRERLPLTKEELYKMLAHEDLRKAVLLVLANKQDLKGAMTPAEISE 139
>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 = 63.2 bits (155), Expect = 3e-12
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 4/73 (5%)
Query: 25 LVGLQCSGKTTFVNVIASGQFSQDMIPTVG--FNMRKITKGNVTIK--VWDIGGQPRFRS 80
L+G GKT+ + +FS++ T+G F + I +K +WD GQ RFRS
Sbjct: 5 LIGDSGVGKTSLLLRFVDNKFSENYKSTIGVDFKSKTIEVDGKKVKLQIWDTAGQERFRS 64
Query: 81 MWERYCRGVNAIV 93
+ Y RG + +
Sbjct: 65 ITSSYYRGAHGAI 77
>gnl|CDD|206723 cd04158, ARD1, (ADP-ribosylation factor domain protein 1 (ARD1).
ARD1 (ADP-ribosylation factor domain protein 1) is an
unusual member of the Arf family. In addition to the
C-terminal Arf domain, ARD1 has an additional 46-kDa
N-terminal domain that contains a RING finger domain,
two predicted B-Boxes, and a coiled-coil protein
interaction motif. This domain belongs to the TRIM
(tripartite motif) or RBCC (RING, B-Box, coiled-coil)
family. Like most Arfs, the ARD1 Arf domain lacks
detectable GTPase activity. However, unlike most Arfs,
the full-length ARD1 protein has significant GTPase
activity due to the GAP (GTPase-activating protein)
activity exhibited by the 46-kDa N-terminal domain. The
GAP domain of ARD1 is specific for its own Arf domain
and does not bind other Arfs. The rate of GDP
dissociation from the ARD1 Arf domain is slowed by the
adjacent 15 amino acids, which act as a GDI
(GDP-dissociation inhibitor) domain. ARD1 is
ubiquitously expressed in cells and localizes to the
Golgi and to the lysosomal membrane. Two Tyr-based
motifs in the Arf domain are responsible for Golgi
localization, while the GAP domain controls lysosomal
localization.
Length = 169
Score = 62.0 bits (150), Expect = 1e-11
Identities = 37/161 (22%), Positives = 72/161 (44%), Gaps = 42/161 (26%)
Query: 26 VGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRKITKGNVTIKVWDIGGQPRFRSMWERY 85
+GL +GKTT + + +F Q IPT+GFN+ + N+ +WD+GG+ + R +W+ Y
Sbjct: 5 LGLDGAGKTTILFKLKQDEFMQP-IPTIGFNVETVEYKNLKFTIWDVGGKHKLRPLWKHY 63
Query: 86 CRGVNAIVWTGGLYIVSKHIKRSAILYYEPVDLGVSGPMWLSLLFQLIKYMVDAADTDKL 145
A+V +++D++ D++
Sbjct: 64 YLNTQAVV-----------------------------------------FVIDSSHRDRV 82
Query: 146 EASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELID 186
+ +EL L+ + +L +L+ NK+D+ AL +E+ +
Sbjct: 83 SEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEMTE 123
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 56.7 bits (138), Expect = 6e-10
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 4/73 (5%)
Query: 25 LVGLQCSGKTTFVNVIASGQFSQDMIPTVG--FNMRKITKGNVTIK--VWDIGGQPRFRS 80
L+G GK++ ++ G+FS+ T+G F + I +K +WD GQ RFRS
Sbjct: 5 LIGDSGVGKSSLLSRFTDGKFSEQYKSTIGVDFKTKTIEVDGKRVKLQIWDTAGQERFRS 64
Query: 81 MWERYCRGVNAIV 93
+ Y RG +
Sbjct: 65 ITSSYYRGAVGAL 77
>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 = 56.7 bits (138), Expect = 6e-10
Identities = 25/75 (33%), Positives = 38/75 (50%), Gaps = 4/75 (5%)
Query: 23 LTLVGLQCSGKTTFVNVIASGQFSQDMIPTVG--FNMRKITKGNVTIK--VWDIGGQPRF 78
L LVG GK++ + +F ++ IPT+G F + I T+K +WD GQ RF
Sbjct: 2 LVLVGDGGVGKSSLLIRFTQNKFPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAGQERF 61
Query: 79 RSMWERYCRGVNAIV 93
R++ Y RG +
Sbjct: 62 RALRPLYYRGAQGFL 76
>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 = 56.3 bits (136), Expect = 1e-09
Identities = 35/170 (20%), Positives = 59/170 (34%), Gaps = 44/170 (25%)
Query: 25 LVGLQCSGKTTFVNVIASGQF---SQDMIPTVGFNMRKIT--KGNVTIKVWDIGGQPRFR 79
+VG GK++ +N + G+ S T ++ KG V + + D G F
Sbjct: 2 VVGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPGLDEFG 61
Query: 80 SMWERYCRGVNAIVWTGGLYIVSKHIKRSAILYYEPVDLGVSGPMWLSLLFQLIKYMVDA 139
+ A L DL I +VD+
Sbjct: 62 GLGRE----------------------ELARLLLRGADL--------------ILLVVDS 85
Query: 140 ADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRIM 189
D + E ++ + + K GIPI+++GNK DL + +EL+
Sbjct: 86 TDRESEEDAKLLILRRLRKE---GIPIILVGNKIDLLEEREVEELLRLEE 132
>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 = 52.3 bits (126), Expect = 3e-08
Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 4/75 (5%)
Query: 23 LTLVGLQCSGKTTFVNVIASGQFSQDMIPTVG--FNMRKITKGNVTIKV--WDIGGQPRF 78
+ L+G GK++ + F +D+ T+G F ++ +T +K+ WD GQ RF
Sbjct: 3 ILLIGDSGVGKSSLLLRFTDDTFDEDLSSTIGVDFKVKTVTVDGKKVKLAIWDTAGQERF 62
Query: 79 RSMWERYCRGVNAIV 93
R++ Y RG ++
Sbjct: 63 RTLTSSYYRGAQGVI 77
>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 = 51.4 bits (124), Expect = 5e-08
Identities = 26/76 (34%), Positives = 40/76 (52%), Gaps = 5/76 (6%)
Query: 23 LTLVGLQCSGKTTFVNVIASGQFSQDMIPTVG--FNMRKITKGNVTIK--VWDIGGQPRF 78
L L+G GK++ V +FS++ T+G F + + + T+K +WD GQ R+
Sbjct: 4 LVLLGDSSVGKSSIVLRFVKNEFSENQESTIGAAFLTQTVNLDDTTVKFEIWDTAGQERY 63
Query: 79 RSMWERYCRGVN-AIV 93
RS+ Y RG AIV
Sbjct: 64 RSLAPMYYRGAAAAIV 79
>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 = 49.0 bits (117), Expect = 4e-07
Identities = 26/76 (34%), Positives = 40/76 (52%), Gaps = 4/76 (5%)
Query: 22 ELTLVGLQCSGKTTFVNVIASGQFSQDMIPTVG--FNMR--KITKGNVTIKVWDIGGQPR 77
++ L+G GKT V SG FS+ T+G F M+ +I V +++WD GQ R
Sbjct: 5 KIILIGDSNVGKTCVVQRFKSGTFSERQGNTIGVDFTMKTLEIQGKRVKLQIWDTAGQER 64
Query: 78 FRSMWERYCRGVNAIV 93
FR++ + Y R N +
Sbjct: 65 FRTITQSYYRSANGAI 80
>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 = 48.7 bits (116), Expect = 5e-07
Identities = 28/88 (31%), Positives = 41/88 (46%), Gaps = 9/88 (10%)
Query: 12 FKSLFWKEEMELTLVGLQCSGKTTFVNVIASGQFSQDMIPTVG--FNMRKITKGNVTIK- 68
+ LF ++ L+G GKT V G F T+G F ++ + IK
Sbjct: 4 YDFLF-----KIVLIGNAGVGKTCLVRRFTQGLFPPGQGATIGVDFMIKTVEIKGEKIKL 58
Query: 69 -VWDIGGQPRFRSMWERYCRGVNAIVWT 95
+WD GQ RFRS+ + Y R NA++ T
Sbjct: 59 QIWDTAGQERFRSITQSYYRSANALILT 86
>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 = 48.7 bits (117), Expect = 5e-07
Identities = 40/149 (26%), Positives = 62/149 (41%), Gaps = 48/149 (32%)
Query: 32 GKTTFVNVIASGQFSQDMIPTVG--FNMRKITKGNVTIK--VWDIGGQPRFRSMWERYCR 87
GK+ ++ +F+ D T+G F R I TIK +WD GQ R+R++ Y R
Sbjct: 15 GKSNLLSRFTRNEFNLDSKSTIGVEFATRTIQIDGKTIKAQIWDTAGQERYRAITSAYYR 74
Query: 88 G-VNAIVWTGGLYIVSKHIKRSAILYYEPVDLGVSGPMWLSLLFQLIKYMVDAADTDKLE 146
G V A++ +Y ++K +E V+ WL L D AD++
Sbjct: 75 GAVGALL----VYDITKKST------FENVER------WLKEL-------RDHADSN--- 108
Query: 147 ASRNELHALIEKPQLIGIPILVLGNKRDL 175
I I+++GNK DL
Sbjct: 109 -----------------IVIMLVGNKSDL 120
>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 = 48.4 bits (116), Expect = 5e-07
Identities = 25/77 (32%), Positives = 37/77 (48%), Gaps = 4/77 (5%)
Query: 21 MELTLVGLQCSGKTTFVNVIASGQFSQDMIPTVG--FNMRKITKGNVTIK--VWDIGGQP 76
+L L+G GK+ + + F+ I T+G F +R I IK +WD GQ
Sbjct: 4 FKLLLIGDSGVGKSCLLLRFSEDSFNPSFISTIGIDFKIRTIELDGKKIKLQIWDTAGQE 63
Query: 77 RFRSMWERYCRGVNAIV 93
RFR++ Y RG I+
Sbjct: 64 RFRTITTSYYRGAMGII 80
>gnl|CDD|240284 PTZ00132, PTZ00132, GTP-binding nuclear protein Ran; Provisional.
Length = 215
Score = 49.3 bits (118), Expect = 5e-07
Identities = 24/64 (37%), Positives = 33/64 (51%), Gaps = 4/64 (6%)
Query: 19 EEMELTLVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRKI----TKGNVTIKVWDIGG 74
E +L LVG GKTTFV +G+F + IPT+G + + G + VWD G
Sbjct: 8 PEFKLILVGDGGVGKTTFVKRHLTGEFEKKYIPTLGVEVHPLKFYTNCGPICFNVWDTAG 67
Query: 75 QPRF 78
Q +F
Sbjct: 68 QEKF 71
>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 = 47.4 bits (113), Expect = 1e-06
Identities = 23/68 (33%), Positives = 36/68 (52%), Gaps = 4/68 (5%)
Query: 25 LVGLQCSGKTTFVNVIASGQFSQDMIPTVG--FNMRKITKGNVTIK--VWDIGGQPRFRS 80
++G +GK+ ++ +F QD T+G F R + G ++K +WD GQ RFRS
Sbjct: 5 IIGSAGTGKSCLLHQFIENKFKQDSNHTIGVEFGSRVVNVGGKSVKLQIWDTAGQERFRS 64
Query: 81 MWERYCRG 88
+ Y RG
Sbjct: 65 VTRSYYRG 72
>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 = 46.9 bits (112), Expect = 2e-06
Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 4/67 (5%)
Query: 23 LTLVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRKI----TKGNVTIKVWDIGGQPRF 78
L LVG +GKTTFV +G+F + + T+G + + +G + VWD GQ +F
Sbjct: 3 LVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLDFHTNRGKIRFNVWDTAGQEKF 62
Query: 79 RSMWERY 85
+ + Y
Sbjct: 63 GGLRDGY 69
>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 = 46.6 bits (111), Expect = 3e-06
Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 4/74 (5%)
Query: 25 LVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNM--RKITKGNVTI--KVWDIGGQPRFRS 80
L+G GKT+ + G+F ++ I T+G N + I+ I +WD+GGQ F +
Sbjct: 5 LLGDAQIGKTSLMVKYVEGEFDEEYIQTLGVNFMEKTISIRGTEITFSIWDLGGQREFIN 64
Query: 81 MWERYCRGVNAIVW 94
M C+ AI++
Sbjct: 65 MLPLVCKDAVAILF 78
>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 = 46.3 bits (110), Expect = 4e-06
Identities = 23/69 (33%), Positives = 37/69 (53%), Gaps = 5/69 (7%)
Query: 32 GKTTFVNVIASGQFSQDMIPTVGFNMRK----ITKGNVTIKVWDIGGQPRFR-SMWERYC 86
GKT +G+F + T+G + R+ I + +++WD GQ RFR SM + Y
Sbjct: 14 GKTCLTYRFCAGRFPERTEATIGVDFRERTVEIDGERIKVQLWDTAGQERFRKSMVQHYY 73
Query: 87 RGVNAIVWT 95
R V+A+V+
Sbjct: 74 RNVHAVVFV 82
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 46.3 bits (110), Expect = 4e-06
Identities = 37/178 (20%), Positives = 55/178 (30%), Gaps = 68/178 (38%)
Query: 20 EMELTLVGLQCSGKTTFVNVIASGQFSQDMIPTV--------GFNMRKITK----GNVTI 67
E ++ ++G +GKTTFV S + G R T G++ +
Sbjct: 10 ETKIVVIGPVGAGKTTFV-----RALSDKPLVITEADASSVSGKGKRPTTVAMDFGSIEL 64
Query: 68 ----KVWDIG--GQPRFRSMWERYCRGVNAIVWTGGLYIVSKHIKRSAILYYEPVDLGVS 121
V G GQ RF+ MWE RG +
Sbjct: 65 DEDTGVHLFGTPGQERFKFMWEILSRGAVGAI---------------------------- 96
Query: 122 GPMWLSLLFQLIKYMVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNAL 179
+VD++ A P IP++V NK+DL +AL
Sbjct: 97 -------------VLVDSSRPITFHAEEIIDFLTSRNP----IPVVVAINKQDLFDAL 137
>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 = 45.8 bits (109), Expect = 4e-06
Identities = 37/170 (21%), Positives = 61/170 (35%), Gaps = 46/170 (27%)
Query: 20 EMELTLVGLQCSGKTTFVNVIASGQFSQD-MIPTVGFN--MRKITKGNVTIKV--WDIGG 74
E+++ +VG GK+T +N + + S P N I + T K D G
Sbjct: 1 EIKIVIVGDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAG 60
Query: 75 QPRFRSMWERYCRGVNAIVWTGGLYIVSKHIKRSAILYYEPVDLGVSGPMWLSLLFQLIK 134
Q + ++ Y R V + L V F ++
Sbjct: 61 QEDYDAIRRLYYRAVESS-------------------------LRV---------FDIVI 86
Query: 135 YMVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNA-LDEKE 183
++D + LE E+ E G+PI+++GNK DL +A L
Sbjct: 87 LVLDVEEI--LEKQTKEIIHHAES----GVPIILVGNKIDLRDAKLKTHV 130
>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 = 45.7 bits (109), Expect = 5e-06
Identities = 32/159 (20%), Positives = 54/159 (33%), Gaps = 50/159 (31%)
Query: 25 LVGLQCSGKTTFVNVIASGQFSQDMIPTV--GFNMRKIT--KGNVTIKVWDIGGQPRFRS 80
L+G GKT+ V +F++ T F + + + + +WD GQ R+ +
Sbjct: 5 LLGEGRVGKTSLVLRYVENKFNEKHESTTQASFFQKTVNIGGKRIDLAIWDTAGQERYHA 64
Query: 81 MWERYCRGVNAIVWTGGLYIVSKHIKRSAILYYEPVDLGVSGPMWLSLLFQLIKYMVDAA 140
+ Y R + AIL Y D
Sbjct: 65 LGPIYYRDADG-----------------AILVY------------------------DIT 83
Query: 141 DTDKLEASRNELHALIEKPQLIG--IPILVLGNKRDLPN 177
D D + + + L Q+ G I ++++GNK DL
Sbjct: 84 DADSFQKVKKWIKELK---QMRGNNISLVIVGNKIDLER 119
>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 = 45.3 bits (108), Expect = 6e-06
Identities = 22/75 (29%), Positives = 34/75 (45%), Gaps = 4/75 (5%)
Query: 23 LTLVGLQCSGKTTFVNVIASGQFSQDMIPTVG--FNMRKITKGNVTIK--VWDIGGQPRF 78
L +G Q GKT+ + F T+G F + + + T++ +WD GQ RF
Sbjct: 3 LVFLGDQSVGKTSIITRFMYDTFDNQYQATIGIDFLSKTMYVDDKTVRLQLWDTAGQERF 62
Query: 79 RSMWERYCRGVNAIV 93
RS+ Y R + V
Sbjct: 63 RSLIPSYIRDSSVAV 77
>gnl|CDD|215587 PLN03118, PLN03118, Rab family protein; Provisional.
Length = 211
Score = 45.8 bits (108), Expect = 8e-06
Identities = 25/77 (32%), Positives = 44/77 (57%), Gaps = 7/77 (9%)
Query: 22 ELTLVGLQCSGKTTF-VNVIASGQFSQDMIPTVG--FNMRKITKGNVTIK--VWDIGGQP 76
++ L+G GK++ V+ I+S +D+ PT+G F ++++T G +K +WD GQ
Sbjct: 16 KILLIGDSGVGKSSLLVSFISSS--VEDLAPTIGVDFKIKQLTVGGKRLKLTIWDTAGQE 73
Query: 77 RFRSMWERYCRGVNAIV 93
RFR++ Y R I+
Sbjct: 74 RFRTLTSSYYRNAQGII 90
>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 = 45.6 bits (108), Expect = 9e-06
Identities = 27/73 (36%), Positives = 39/73 (53%), Gaps = 5/73 (6%)
Query: 25 LVGLQCSGKTTFVNVIASGQFSQDMIPTVG--FNMRKIT---KGNVTIKVWDIGGQPRFR 79
++G SGKT+ + A F + T+G F R+IT NVT++VWDIGGQ
Sbjct: 5 VLGDGASGKTSLIRRFAQEGFGKSYKQTIGLDFFSRRITLPGSLNVTLQVWDIGGQQIGG 64
Query: 80 SMWERYCRGVNAI 92
M ++Y G A+
Sbjct: 65 KMLDKYIYGAQAV 77
>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 = 44.6 bits (106), Expect = 1e-05
Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 4/75 (5%)
Query: 23 LTLVGLQCSGKTTFVNVIASGQFSQDMIPTVG--FNMRKITKGNVTIK--VWDIGGQPRF 78
L L+G GK+ + A +++ I T+G F +R I T+K +WD GQ RF
Sbjct: 5 LLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTVKLQIWDTAGQERF 64
Query: 79 RSMWERYCRGVNAIV 93
R++ Y RG + I+
Sbjct: 65 RTITSSYYRGAHGII 79
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 45.1 bits (107), Expect = 2e-05
Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 4/60 (6%)
Query: 23 LTLVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRKI----TKGNVTIKVWDIGGQPRF 78
L +VG +GKTTFV +G+F + PT+G + + G + WD GQ +F
Sbjct: 16 LVIVGDGGTGKTTFVKRHLTGEFEKKYEPTIGVEVHPLDFFTNCGKIRFYCWDTAGQEKF 75
>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 = 44.1 bits (104), Expect = 2e-05
Identities = 23/72 (31%), Positives = 35/72 (48%), Gaps = 4/72 (5%)
Query: 26 VGLQCSGKTTFVNVIASGQFSQDMIPTVG--FNMRKITKGNV--TIKVWDIGGQPRFRSM 81
VG GKT +N F ++ T+G F M + V ++++WD GQ RF+ +
Sbjct: 6 VGDLSVGKTCLINRFCKDVFDKNYKATIGVDFEMERFEVLGVPFSLQLWDTAGQERFKCI 65
Query: 82 WERYCRGVNAIV 93
Y RG AI+
Sbjct: 66 ASTYYRGAQAII 77
>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 = 43.4 bits (102), Expect = 3e-05
Identities = 21/71 (29%), Positives = 40/71 (56%), Gaps = 4/71 (5%)
Query: 22 ELTLVGLQCSGKTTFVNVIASGQFSQDMIPTVG--FNMRKITKGN--VTIKVWDIGGQPR 77
+L ++G GKT+F+ A F+ + TVG F ++ + + + + +++WD GQ R
Sbjct: 3 KLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVYRNDKRIKLQIWDTAGQER 62
Query: 78 FRSMWERYCRG 88
+R++ Y RG
Sbjct: 63 YRTITTAYYRG 73
>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 = 43.7 bits (103), Expect = 3e-05
Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 4/76 (5%)
Query: 22 ELTLVGLQCSGKTTFVNVIASGQFSQDMIPTVG--FNMR--KITKGNVTIKVWDIGGQPR 77
+L ++G GK++ + A FS I T+G F +R +I V +++WD GQ R
Sbjct: 8 KLLIIGDSGVGKSSLLLRFADNTFSGSYITTIGVDFKIRTVEINGERVKLQIWDTAGQER 67
Query: 78 FRSMWERYCRGVNAIV 93
FR++ Y RG + ++
Sbjct: 68 FRTITSTYYRGTHGVI 83
>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 = 42.7 bits (101), Expect = 7e-05
Identities = 25/69 (36%), Positives = 35/69 (50%), Gaps = 6/69 (8%)
Query: 31 SGKTTFVNVIASGQFSQDMIPTVG--FNMRKIT---KGNVTIKVWDIGGQPRFRSMWERY 85
GKT+ + G FSQ T+G F ++ I V +++WDI GQ RF M Y
Sbjct: 11 VGKTSIIKRYVHGVFSQHYKATIGVDFALKVIEWDPNTVVRLQLWDIAGQERFGGMTRVY 70
Query: 86 CRG-VNAIV 93
+G V AI+
Sbjct: 71 YKGAVGAII 79
>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 = 41.5 bits (97), Expect = 2e-04
Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 4/64 (6%)
Query: 26 VGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRKI----TKGNVTIKVWDIGGQPRFRSM 81
VG +GKTTFV +G+F + + T+G + + +G + VWD GQ +F +
Sbjct: 1 VGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIRFNVWDTAGQEKFGGL 60
Query: 82 WERY 85
+ Y
Sbjct: 61 RDGY 64
>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 = 41.4 bits (97), Expect = 2e-04
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 5/73 (6%)
Query: 32 GKTTFVNVIASGQFSQDMIPTVG--FNMRKITKGNVTIKVWDIGGQPRFRSMWERYCRGV 89
GKT+ ++ +F +D + TVG F +++ G I +WD G+ +F + YCRG
Sbjct: 12 GKTSLLHRYMERRF-KDTVSTVGGAFYLKQW--GPYNISIWDTAGREQFHGLGSMYCRGA 68
Query: 90 NAIVWTGGLYIVS 102
A++ T + V
Sbjct: 69 AAVILTYDVSNVQ 81
>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 = 40.8 bits (96), Expect = 3e-04
Identities = 37/180 (20%), Positives = 60/180 (33%), Gaps = 58/180 (32%)
Query: 25 LVGLQCSGKTTFVNVIASGQFSQ---DMIPTVGFNMRKITKGNVTIKVWDIGGQPRFRSM 81
L+G SGKT + +G+ + P V +KG + + D+ G + R
Sbjct: 5 LLGPSDSGKTALFTKLTTGKVRSTVTSIEPNVASFYSNSSKGKK-LTLVDVPGHEKLRDK 63
Query: 82 -WERYCRGVNAIVWTGGLYIVSKHIKRSAILYYEPVDLGVSGPMWLSLLFQLIKYMVDAA 140
E + AIV ++VD+A
Sbjct: 64 LLEYLKASLKAIV-----------------------------------------FVVDSA 82
Query: 141 DTDK-LEASRNELHALIEKPQLI--GIPILVLGNKRDLPNALD--------EKELIDRIM 189
K + L+ ++ + I IPIL+ NK+DL A EKE I+ +
Sbjct: 83 TFQKNIRDVAEFLYDILTDLEKIKNKIPILIACNKQDLFTAKPAKKIKELLEKE-INTLR 141
>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 = 39.2 bits (92), Expect = 7e-04
Identities = 19/66 (28%), Positives = 29/66 (43%), Gaps = 5/66 (7%)
Query: 20 EMELTLVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRKITKGN-----VTIKVWDIGG 74
E +L LVG GKT+ + +F D T G N++ + + VWD GG
Sbjct: 1 EAKLMLVGQGGVGKTSLCKQLIGEKFDGDESSTHGINVQDWKIPAPERKKIRLNVWDFGG 60
Query: 75 QPRFRS 80
Q + +
Sbjct: 61 QEIYHA 66
>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 = 39.5 bits (92), Expect = 0.001
Identities = 27/74 (36%), Positives = 37/74 (50%), Gaps = 5/74 (6%)
Query: 25 LVGLQCSGKTTFVNVIASGQF-SQDMIPTVG--FNMRKITKGNVTIK--VWDIGGQPRFR 79
LVG GKT + G F + I TVG F + +T V +K +WD GQ RFR
Sbjct: 5 LVGDSGVGKTCLLVRFKDGAFLAGSFIATVGIQFTNKVVTVDGVKVKLQIWDTAGQERFR 64
Query: 80 SMWERYCRGVNAIV 93
S+ Y R +A++
Sbjct: 65 SVTHAYYRDAHALL 78
>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 = 39.0 bits (91), Expect = 0.001
Identities = 26/70 (37%), Positives = 37/70 (52%), Gaps = 5/70 (7%)
Query: 23 LTLVGLQCSGKTTFVNVIASGQFSQDMIPTVG--FNMRKI-TKGNVTIK--VWDIGGQPR 77
L ++G GK++ + G+F++ PTVG F R I + V IK +WD GQ R
Sbjct: 5 LIVIGDSTVGKSSLLKRFTEGRFAEVSDPTVGVDFFSRLIEIEPGVRIKLQLWDTAGQER 64
Query: 78 FRSMWERYCR 87
FRS+ Y R
Sbjct: 65 FRSITRSYYR 74
>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 = 38.4 bits (89), Expect = 0.002
Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 4/74 (5%)
Query: 23 LTLVGLQCSGKTTFVNVIASGQFSQDMIPTVG--FNMRKITKG--NVTIKVWDIGGQPRF 78
L L+G GKT + +F I T+G F M+ I V I++WD GQ R+
Sbjct: 3 LLLIGDSGVGKTCLLCRFTDNEFHSSHISTIGVDFKMKTIEVDGIKVRIQIWDTAGQERY 62
Query: 79 RSMWERYCRGVNAI 92
+++ ++Y R I
Sbjct: 63 QTITKQYYRRAQGI 76
>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 = 37.0 bits (86), Expect = 0.002
Identities = 15/73 (20%), Positives = 34/73 (46%), Gaps = 4/73 (5%)
Query: 25 LVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRKITK--GNVTIK--VWDIGGQPRFRS 80
++G + SGK++ ++ + G+F + + G + T T +WD GG+ +
Sbjct: 4 VIGDKGSGKSSLLSQLVGGEFPPEPLEIQGDTLAVDTLEVDGDTGLLNIWDFGGREELKF 63
Query: 81 MWERYCRGVNAIV 93
+ + +AI+
Sbjct: 64 EHIIFMKWADAIL 76
>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 = 36.8 bits (85), Expect = 0.005
Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 4/72 (5%)
Query: 21 MELTLVGLQCSGKTTFVNVIASGQFSQDMIPTVG---FNMRKITKGN-VTIKVWDIGGQP 76
+++ L+G GK++ +N + +F + T+G N G+ VT+++WD GQ
Sbjct: 6 LKVILLGDGGVGKSSLMNRYVTNKFDTQLFHTIGVEFLNKDLEVDGHFVTLQIWDTAGQE 65
Query: 77 RFRSMWERYCRG 88
RFRS+ + RG
Sbjct: 66 RFRSLRTPFYRG 77
>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 = 36.7 bits (85), Expect = 0.006
Identities = 21/61 (34%), Positives = 29/61 (47%), Gaps = 4/61 (6%)
Query: 32 GKTTFVNVIASGQFSQDMIPTVG--FNMRKITKGNVTIK--VWDIGGQPRFRSMWERYCR 87
GK+ ++ +F D T+G F R I IK +WD GQ RFR++ Y R
Sbjct: 14 GKSCLLHQFTEKKFMADCPHTIGVEFGTRIIEVNGQKIKLQIWDTAGQERFRAVTRSYYR 73
Query: 88 G 88
G
Sbjct: 74 G 74
>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 = 36.7 bits (85), Expect = 0.008
Identities = 22/64 (34%), Positives = 31/64 (48%), Gaps = 14/64 (21%)
Query: 32 GKTTFVNVIASGQFSQDMIPTVGFNMRK-----------ITKG---NVTIKVWDIGGQPR 77
GKTTF+ +F+ I TVG + R+ T G V +++WD GQ R
Sbjct: 16 GKTTFLYRYTDNKFNPKFITTVGIDFREKRVVYNSQGPDGTSGKAFRVHLQLWDTAGQER 75
Query: 78 FRSM 81
FRS+
Sbjct: 76 FRSL 79
>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 = 36.6 bits (85), Expect = 0.008
Identities = 18/60 (30%), Positives = 32/60 (53%), Gaps = 4/60 (6%)
Query: 20 EMELTLVGLQCSGKTTFVNVIASGQFSQDMIPTVGFN-MRKITKGN---VTIKVWDIGGQ 75
++++ +VG GKT + V A G F ++ +PTV N + + N + + +WD GQ
Sbjct: 3 KVKIVVVGDGGCGKTCLLMVYAQGSFPEEYVPTVFENYVTTLQVPNGKIIELALWDTAGQ 62
>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 = 36.2 bits (83), Expect = 0.011
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 3/60 (5%)
Query: 22 ELTLVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMR---KITKGNVTIKVWDIGGQPRF 78
++ +VG GKT ++V A F ++ +PTV N +I + + +WD G P +
Sbjct: 7 KIVVVGDSQCGKTALLHVFAKDCFPENYVPTVFENYTASFEIDTQRIELSLWDTSGSPYY 66
>gnl|CDD|206702 cd04129, Rho2, Ras homology family 2 (Rho2) of small guanosine
triphosphatases (GTPases). Rho2 is a fungal GTPase
that plays a role in cell morphogenesis, control of
cell wall integrity, control of growth polarity, and
maintenance of growth direction. Rho2 activates the
protein kinase C homolog Pck2, and Pck2 controls Mok1,
the major (1-3) alpha-D-glucan synthase. Together with
Rho1 (RhoA), Rho2 regulates the construction of the
cell wall. Unlike Rho1, Rho2 is not an essential
protein, but its overexpression is lethal. Most Rho
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for proper intracellular
localization via membrane attachment. As with other Rho
family GTPases, the GDP/GTP cycling is regulated by
GEFs (guanine nucleotide exchange factors), GAPs
(GTPase-activating proteins) and GDIs (guanine
nucleotide dissociation inhibitors).
Length = 190
Score = 36.0 bits (83), Expect = 0.011
Identities = 20/66 (30%), Positives = 32/66 (48%), Gaps = 6/66 (9%)
Query: 22 ELTLVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMR---KITKGNVTIKVWDIGGQ--- 75
+L +VG GKT+ + V G+F ++ PTV N ++ V + +WD GQ
Sbjct: 3 KLVIVGDGACGKTSLLYVFTLGEFPEEYHPTVFENYVTDCRVDGKPVQLALWDTAGQEEY 62
Query: 76 PRFRSM 81
R R +
Sbjct: 63 ERLRPL 68
>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 = 35.5 bits (82), Expect = 0.015
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 6/79 (7%)
Query: 21 MELTLVGLQCSGKTTFVNVIASGQFSQDMIPTVG--FNMRKI----TKGNVTIKVWDIGG 74
+++ +VG GK++ + G F++D T+G F ++I + +V + +WD G
Sbjct: 1 IKVIVVGNGNVGKSSMIQRFVKGIFTKDYKKTIGVDFLEKQIFLRQSDEDVRLMLWDTAG 60
Query: 75 QPRFRSMWERYCRGVNAIV 93
Q F ++ + Y RG A +
Sbjct: 61 QEEFDAITKAYYRGAQACI 79
>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 = 35.6 bits (82), Expect = 0.017
Identities = 19/51 (37%), Positives = 23/51 (45%), Gaps = 3/51 (5%)
Query: 31 SGKTTFVNVIASGQFSQDMIPTVGFNMRKI--TKGN-VTIKVWDIGGQPRF 78
GKT+ +NV G F Q PTV N G V + +WD GQ F
Sbjct: 11 CGKTSLLNVFTRGYFPQVYEPTVFENYIHDIFVDGLAVELSLWDTAGQEEF 61
>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 = 35.1 bits (81), Expect = 0.018
Identities = 18/43 (41%), Positives = 21/43 (48%), Gaps = 2/43 (4%)
Query: 48 DMIPTVGFNMRKITKGNVTIK--VWDIGGQPRFRSMWERYCRG 88
D+ V F R IT IK +WD GQ FRS+ Y RG
Sbjct: 34 DLTIGVEFGARMITIDGKQIKLQIWDTAGQESFRSITRSYYRG 76
>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 = 35.6 bits (82), Expect = 0.019
Identities = 21/79 (26%), Positives = 38/79 (48%), Gaps = 7/79 (8%)
Query: 21 MELTLVGLQCSGKTTFVNVIASGQF----SQDMIPTVGFNMRKITKGN--VTIKVWDIGG 74
+++ ++G + GKT+ V +F Q+ I F +++ G VT+ +WD G
Sbjct: 1 VKVVMLGKESVGKTSLVERYVHHRFLVGPYQNTI-GAAFVAKRMVVGERVVTLGIWDTAG 59
Query: 75 QPRFRSMWERYCRGVNAIV 93
R+ +M Y RG A +
Sbjct: 60 SERYEAMSRIYYRGAKAAI 78
>gnl|CDD|178655 PLN03108, PLN03108, Rab family protein; Provisional.
Length = 210
Score = 35.7 bits (82), Expect = 0.021
Identities = 20/47 (42%), Positives = 23/47 (48%), Gaps = 2/47 (4%)
Query: 44 QFSQDMIPTVGFNMRKITKGNVTIK--VWDIGGQPRFRSMWERYCRG 88
Q D+ V F R IT N IK +WD GQ FRS+ Y RG
Sbjct: 32 QPVHDLTIGVEFGARMITIDNKPIKLQIWDTAGQESFRSITRSYYRG 78
>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 = 34.9 bits (81), Expect = 0.021
Identities = 21/61 (34%), Positives = 36/61 (59%), Gaps = 4/61 (6%)
Query: 32 GKTTFVNVIASGQFSQDMIPTVG--FNMRKITKGN--VTIKVWDIGGQPRFRSMWERYCR 87
GKT+ +N + +FS T+G F +++T + VT+++WD GQ RF+S+ + R
Sbjct: 12 GKTSLMNQYVNKKFSNQYKATIGADFLTKEVTVDDRLVTLQIWDTAGQERFQSLGVAFYR 71
Query: 88 G 88
G
Sbjct: 72 G 72
>gnl|CDD|233986 TIGR02729, Obg_CgtA, Obg family GTPase CgtA. This model describes
a univeral, mostly one-gene-per-genome GTP-binding
protein that associates with ribosomal subunits and
appears to play a role in ribosomal RNA maturation. This
GTPase, related to the nucleolar protein Obg, is
designated CgtA in bacteria. Mutations in this gene are
pleiotropic, but it appears that effects on cellular
functions such as chromosome partition may be secondary
to the effect on ribosome structure. Recent work done in
Vibrio cholerae shows an essential role in the stringent
response, in which RelA-dependent ability to synthesize
the alarmone ppGpp is required for deletion of this
GTPase to be lethal [Protein synthesis, Other].
Length = 329
Score = 35.5 bits (83), Expect = 0.031
Identities = 25/96 (26%), Positives = 39/96 (40%), Gaps = 38/96 (39%)
Query: 103 KHIKRSAILYYEPVDLGVSGPMWLSLLFQLIKYMVDAADTDK------LEASRNEL---- 152
KHI+R+ +L + ++D + D E RNEL
Sbjct: 231 KHIERTRVLLH----------------------LIDISPEDGSDPIEDYEIIRNELKKYS 268
Query: 153 HALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRI 188
L EKP+ I+VL NK DL + + +EL+ +
Sbjct: 269 PELAEKPR-----IVVL-NKIDLLDEEELEELLKEL 298
>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 = 33.9 bits (78), Expect = 0.050
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 23 LTLVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMR---KITKGNVTIKVWDIGGQPRF 78
+ LVG GKT + V A F ++ +PTV N ++ K + + +WD G P +
Sbjct: 4 IVLVGDSQCGKTALLQVFAKDSFPENYVPTVFENYTASFEVDKQRIELSLWDTSGSPYY 62
>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
Length = 216
Score = 34.5 bits (79), Expect = 0.050
Identities = 20/71 (28%), Positives = 35/71 (49%), Gaps = 4/71 (5%)
Query: 22 ELTLVGLQCSGKTTFVNVIASGQFSQDMIPTVG--FNMRKITKGNVTIK--VWDIGGQPR 77
++ L+G GK+ ++ +F + T+G F R + T+K +WD GQ R
Sbjct: 14 KIVLIGDSGVGKSNILSRFTRNEFCLESKSTIGVEFATRTLQVEGKTVKAQIWDTAGQER 73
Query: 78 FRSMWERYCRG 88
+R++ Y RG
Sbjct: 74 YRAITSAYYRG 84
>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 = 34.2 bits (78), Expect = 0.057
Identities = 18/77 (23%), Positives = 37/77 (48%), Gaps = 4/77 (5%)
Query: 21 MELTLVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMR----KITKGNVTIKVWDIGGQP 76
+++ ++G + GKT+ + F + TVG + + ++ + +++WD GQ
Sbjct: 1 LQVIIIGSRGVGKTSLMERFTDDTFCEACKSTVGVDFKIKTVELRGKKIRLQIWDTAGQE 60
Query: 77 RFRSMWERYCRGVNAIV 93
RF S+ Y R I+
Sbjct: 61 RFNSITSAYYRSAKGII 77
>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 = 33.7 bits (78), Expect = 0.064
Identities = 36/178 (20%), Positives = 65/178 (36%), Gaps = 49/178 (27%)
Query: 23 LTLVGLQCSGKTTFVNVIASGQFSQDMIPTVG--FNMR-KITKGNVTIKVWDIGGQPRFR 79
L ++G GK+ SG+F ++ PT+ + + + T+ + D GQ F
Sbjct: 2 LVVLGAGGVGKSALTIRFVSGEFVEEYDPTIEDSYRKQIVVDGETYTLDILDTAGQEEFS 61
Query: 80 SMWERYCRGVNAIVWTGGLYIVSKHIKRSAILYYEPVDLGVSGPMWLSLLFQLIKYMVDA 139
+M ++Y R + IL Y S F+ IK +
Sbjct: 62 AMRDQYIRNGDGF-----------------ILVYSITSRE-S--------FEEIKNI--- 92
Query: 140 ADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPN-----ALDEKELIDRIMIDF 192
R ++ + +K +PI+++GNK DL N + + L + F
Sbjct: 93 ---------REQILRVKDKED---VPIVLVGNKCDLENERQVSTEEGEALAEEWGCPF 138
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 34.5 bits (80), Expect = 0.070
Identities = 49/178 (27%), Positives = 75/178 (42%), Gaps = 65/178 (36%)
Query: 25 LVGLQCSGKTTFVNV-------IASGQFSQDMIPTVGFNMRKITKGNVTIKVWDIGGQPR 77
LVGL +GK+T ++ IA F+ ++P +G + ++ G + V DI G
Sbjct: 164 LVGLPNAGKSTLLSAVSAAKPKIADYPFTT-LVPNLG--VVRVDGGESFV-VADIPG--- 216
Query: 78 FRSMWERYCRGVNAIVWTGGLYIVS-KHIKRSAILYYEPVDLGVSGPMWLSLLFQLIKYM 136
+ E GV GL + +HI+R+ +L + +
Sbjct: 217 ---LIEGASEGV-------GLGLRFLRHIERTRVLLH----------------------V 244
Query: 137 VDAADTDK------LEASRNELHA----LIEKPQLIGIPILVLGNKRDLPNALDEKEL 184
+D + D + RNEL L EKP+ I+VL NK DLP LDE+EL
Sbjct: 245 IDLSPIDGRDPIEDYQTIRNELEKYSPKLAEKPR-----IVVL-NKIDLP--LDEEEL 294
>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 = 33.2 bits (77), Expect = 0.086
Identities = 25/94 (26%), Positives = 39/94 (41%), Gaps = 36/94 (38%)
Query: 103 KHIKRSAILYYEPVDLGVSGPMWLSLLFQLIKYMVDAADTDK----LEASRNELHA---- 154
+HI+R+ +L + ++D + D E RNEL A
Sbjct: 74 RHIERTRVLLH----------------------VIDLSGEDDPVEDYETIRNELEAYNPG 111
Query: 155 LIEKPQLIGIPILVLGNKRDLPNALDEKELIDRI 188
L EKP+ I+VL NK DL +A + E + +
Sbjct: 112 LAEKPR-----IVVL-NKIDLLDAEERFEKLKEL 139
>gnl|CDD|185444 PTZ00099, PTZ00099, rab6; Provisional.
Length = 176
Score = 33.2 bits (75), Expect = 0.10
Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 4/53 (7%)
Query: 45 FSQDMIPTVGFNMRKIT----KGNVTIKVWDIGGQPRFRSMWERYCRGVNAIV 93
F + T+G + T +G V +++WD GQ RFRS+ Y R A +
Sbjct: 5 FDNNYQSTIGIDFLSKTLYLDEGPVRLQLWDTAGQERFRSLIPSYIRDSAAAI 57
>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 = 33.3 bits (77), Expect = 0.11
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 14/63 (22%)
Query: 25 LVGLQCSGKTTFVNVIASGQFSQDMI---PTVGFNMRKITK------GNVTIKVWDIGGQ 75
L+GL+ SGK++ ++I S +D + T+ + + GN+T+ +WD GQ
Sbjct: 4 LMGLRGSGKSSMRSIIFSNYSPRDTLRLGATI-----DVEQSHVRFLGNLTLNLWDCPGQ 58
Query: 76 PRF 78
F
Sbjct: 59 DDF 61
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 33.5 bits (78), Expect = 0.13
Identities = 14/59 (23%), Positives = 29/59 (49%), Gaps = 7/59 (11%)
Query: 132 LIKYMVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRIMI 190
L+ ++DA++ E ++E+ P++V+ NK DL +D +E + +I
Sbjct: 297 LVLLVLDASEPLT-----EEDDEILEEL--KDKPVIVVLNKADLTGEIDLEEENGKPVI 348
>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 = 32.5 bits (75), Expect = 0.13
Identities = 13/54 (24%), Positives = 24/54 (44%), Gaps = 5/54 (9%)
Query: 32 GKTTFVNVIASGQFSQDMIPTVGFN--MRKITKGNVTIKV--WDIGGQPRFRSM 81
GKT + + +F + +PTV F+ +T + + WD GQ + +
Sbjct: 12 GKTCLLISYTTNKFPTEYVPTV-FDNYSANVTVDGKQVNLGLWDTAGQEEYDRL 64
>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 = 32.3 bits (73), Expect = 0.24
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 5/61 (8%)
Query: 22 ELTLVG-LQCSGKTTFVNVIASGQFSQDMIPTVGFNMR---KITKGNVTIKVWDIGGQPR 77
+L LVG +QC GKT + V+A + + +PTV N + + V + +WD G P
Sbjct: 15 KLVLVGDVQC-GKTAMLQVLAKDCYPETYVPTVFENYTACLETEEQRVELSLWDTSGSPY 73
Query: 78 F 78
+
Sbjct: 74 Y 74
>gnl|CDD|215955 pfam00503, G-alpha, G-protein alpha subunit. G proteins couple
receptors of extracellular signals to intracellular
signaling pathways. The G protein alpha subunit binds
guanyl nucleotide and is a weak GTPase. A set of
residues that are unique to G-alpha as compared to its
ancestor the Arf-like family form a ring of residues
centered on the nucleotide binding site. A Ggamma is
found fused to an inactive Galpha in the Dictyostelium
protein gbqA.
Length = 329
Score = 32.2 bits (74), Expect = 0.31
Identities = 31/133 (23%), Positives = 49/133 (36%), Gaps = 34/133 (25%)
Query: 50 IPTVGFNMRKITKGNVTIKVWDIGGQPRFRSMWERYCRGVNAIVWTGGLYIVSKHIKRSA 109
+ T G K + +++D+GGQ R W V AI +++VS
Sbjct: 153 VKTTGIIETKFDFKGLKFRLFDVGGQRSERKKWIHCFEDVTAI-----IFVVS------- 200
Query: 110 ILYYEPVDLGVSGPMWLSLLFQLIKYMVDAADTDKLEASRNELHALIEKPQLIGIPILVL 169
LS Q + + T++LE S N + P PI++
Sbjct: 201 ----------------LSEYDQ---VLYEDDSTNRLEESLNLFEEICNSPWFKNTPIILF 241
Query: 170 GNKRDLPNALDEK 182
NK+DL +EK
Sbjct: 242 LNKKDL---FEEK 251
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 32.2 bits (74), Expect = 0.33
Identities = 19/60 (31%), Positives = 35/60 (58%), Gaps = 10/60 (16%)
Query: 132 LIKYMVDAADTD---KLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRI 188
L+ ++VDA+D + KLEA + L + IPI+++ NK DL L+++E++ +
Sbjct: 274 LLLHVVDASDPEILEKLEAVEDVLAEIGAD----EIPIILVLNKIDL---LEDEEILAEL 326
>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 = 31.6 bits (72), Expect = 0.34
Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 3/57 (5%)
Query: 22 ELTLVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRK---ITKGNVTIKVWDIGGQ 75
+L +VG GKT + V + QF + +PTV N + V + +WD GQ
Sbjct: 3 KLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQ 59
>gnl|CDD|206646 cd00880, Era_like, E. coli Ras-like protein (Era)-like GTPase. The
Era (E. coli Ras-like protein)-like family includes
several distinct subfamilies (TrmE/ThdF, FeoB, YihA
(EngB), Era, and EngA/YfgK) that generally show sequence
conservation in the region between the Walker A and B
motifs (G1 and G3 box motifs), to the exclusion of other
GTPases. TrmE is ubiquitous in bacteria and is a
widespread mitochondrial protein in eukaryotes, but is
absent from archaea. The yeast member of TrmE family,
MSS1, is involved in mitochondrial translation;
bacterial members are often present in
translation-related operons. FeoB represents an unusual
adaptation of GTPases for high-affinity iron (II)
transport. YihA (EngB) family of GTPases is typified by
the E. coli YihA, which is an essential protein involved
in cell division control. Era is characterized by a
distinct derivative of the KH domain (the pseudo-KH
domain) which is located C-terminal to the GTPase
domain. EngA and its orthologs are composed of two
GTPase domains and, since the sequences of the two
domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family.
Length = 161
Score = 31.4 bits (72), Expect = 0.35
Identities = 16/57 (28%), Positives = 27/57 (47%), Gaps = 6/57 (10%)
Query: 132 LIKYMVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRI 188
L+ +VD+ T E A + + G P+L++ NK DL +E+EL+
Sbjct: 79 LVLLVVDSDLT------PVEEEAKLGLLRERGKPVLLVLNKIDLVPESEEEELLRER 129
>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 = 31.4 bits (72), Expect = 0.40
Identities = 19/65 (29%), Positives = 29/65 (44%), Gaps = 6/65 (9%)
Query: 23 LTLVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNM-RKITKGNVTIKV--WDIGGQP--- 76
L +VG GKT + V + F +D +PTV N + +++ WD GQ
Sbjct: 1 LVVVGDGAVGKTCLLIVYTTNAFPEDYVPTVFENYSADVEVDGKPVELGLWDTAGQEDYD 60
Query: 77 RFRSM 81
R R +
Sbjct: 61 RLRPL 65
>gnl|CDD|218528 pfam05272, VirE, Virulence-associated protein E. This family
contains several bacterial virulence-associated protein
E like proteins. These proteins contain a P-loop motif.
Length = 198
Score = 30.8 bits (70), Expect = 0.76
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 18 KEEMELTLVGLQCSGKTTFVNVIASGQFSQDM 49
K + L L G Q SGK+TF+ + F+ +
Sbjct: 50 KFDHVLILQGAQGSGKSTFLKKLGGEWFTDSI 81
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 31.0 bits (71), Expect = 0.78
Identities = 25/96 (26%), Positives = 37/96 (38%), Gaps = 38/96 (39%)
Query: 103 KHIKRSAILYYEPVDLGVSGPMWLSLLFQLIKYMVDAA---DTDKLEASR---NELHA-- 154
KH++R +L L ++D A +D +E +R NEL
Sbjct: 233 KHLERCRVL-----------------LH-----LIDIAPIDGSDPVENARIIINELEKYS 270
Query: 155 --LIEKPQLIGIPILVLGNKRDLPNALDEKELIDRI 188
L EKP+ LV NK DL + + +E I
Sbjct: 271 PKLAEKPR-----WLVF-NKIDLLDEEEAEERAKAI 300
>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 = 30.3 bits (69), Expect = 0.91
Identities = 10/29 (34%), Positives = 18/29 (62%), Gaps = 2/29 (6%)
Query: 152 LHALIEKPQLI--GIPILVLGNKRDLPNA 178
L LI + + IP++++GNK DL ++
Sbjct: 94 LLQLIREIKKRDGEIPVILVGNKADLLHS 122
>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 = 30.2 bits (68), Expect = 0.98
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 3/53 (5%)
Query: 32 GKTTFVNVIASGQFSQDMIPTVGFNMRKI---TKGNVTIKVWDIGGQPRFRSM 81
GK++ V G F + IPT+ R++ +K T+++ D G +F +M
Sbjct: 13 GKSSLVLRFVKGTFRESYIPTIEDTYRQVISCSKSICTLQITDTTGSHQFPAM 65
>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 = 30.3 bits (68), Expect = 1.0
Identities = 11/29 (37%), Positives = 18/29 (62%)
Query: 65 VTIKVWDIGGQPRFRSMWERYCRGVNAIV 93
V +++WD GQ RF +++ Y RG I+
Sbjct: 55 VKLQLWDTSGQGRFCTIFRSYSRGAQGII 83
>gnl|CDD|167325 PRK02166, PRK02166, hypothetical protein; Reviewed.
Length = 184
Score = 30.1 bits (68), Expect = 1.1
Identities = 23/84 (27%), Positives = 37/84 (44%), Gaps = 22/84 (26%)
Query: 135 YMVDAADTDKLEASRNELHALIE-----KPQLIG--IPILVLGNKRDLPNALDEKELIDR 187
++ DAA+ + E N ALI K +L + +++L LP+ D+ L +R
Sbjct: 46 WLADAAELLEGEPGDNVRAALIGLQEMVKGELTADDVAVVLL-----LPD--DDAPLTER 98
Query: 188 IMIDFWITLTLLIRWCESFLHHFG 211
L +WC+ FL FG
Sbjct: 99 A--------AALGQWCQGFLAGFG 114
>gnl|CDD|129876 TIGR00794, kup, potassium uptake protein. Proteins of the KUP
family include the KUP (TrkD) protein of E. coli, a
partially sequenced ORF from Lactococcus lactis, high
affinity K+ uptake systems (Hak1) of the yeast
Debaryomyces occidentalis as well as the fungus,
Neurospora crassa, and several homologues in plants.
While the E. coli KUP protein is assumed to be a
secondary transporter, and uptake is blocked by
protonophores such as CCCP (but not arsenate), the
energy coupling mechanism has not been defined. However,
the N. crassa protein has been shown to be a K+:H+
symporter, establishing that the KUP family consists of
secondary carriers. The plant high affinity (20mM) K+
transporter can complement K+ uptake defects in E. coli
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 688
Score = 30.5 bits (69), Expect = 1.4
Identities = 17/80 (21%), Positives = 28/80 (35%), Gaps = 18/80 (22%)
Query: 194 ITLTLLIRWCESFLHHFGSHPNWAVKWHTLPKLLFLSLVDSYVSSGASDYTEEAGCTIS- 252
+T+ + I W W + + L L+FLS+ Y SS E +S
Sbjct: 408 MTVVMTIVW------------KWNIYFVALFLLVFLSVELIYFSSNLDKVPEGGWFPLSL 455
Query: 253 -----ILMLSWYSVTVRQHW 267
+M +W R+
Sbjct: 456 SGIFMSVMTTWRYGRFRKLR 475
>gnl|CDD|179177 PRK00945, PRK00945, acetyl-CoA decarbonylase/synthase complex
subunit epsilon; Provisional.
Length = 171
Score = 29.6 bits (67), Expect = 1.6
Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 12/60 (20%)
Query: 136 MVDAADTDKLEASRNELHALIEKPQLIGI-------PILVLGNKRDLPNALDEKELIDRI 188
MVD + A HA I P++ + P+LV+G LD++EL+DR
Sbjct: 1 MVDRTKPYQPTAISGPKHAKIVSPKIAAMMIKKAKRPLLVVG-----SLLLDDEELLDRA 55
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 30.1 bits (69), Expect = 1.6
Identities = 16/60 (26%), Positives = 28/60 (46%), Gaps = 16/60 (26%)
Query: 132 LIKYMVDAADTD------KLEASRNELHA----LIEKPQLIGIPILVLGNKRDLPNALDE 181
+I +++D + ++ E EL L+E+PQ++ V NK DLP A +
Sbjct: 239 VIVHVIDMSGSEGRDPIEDYEKINKELKLYNPRLLERPQIV-----VA-NKMDLPEAEEN 292
>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 = 29.0 bits (65), Expect = 1.9
Identities = 21/71 (29%), Positives = 31/71 (43%), Gaps = 3/71 (4%)
Query: 26 VGLQCSGKTTFVNVIASGQFSQDMIPTV--GFNMRKITKGN-VTIKVWDIGGQPRFRSMW 82
VG GKT + S F D +PTV F+ + GN V + +WD GQ + +
Sbjct: 7 VGDGAVGKTCMLISYTSNTFPTDYVPTVFDNFSANVVVDGNTVNLGLWDTAGQEDYNRLR 66
Query: 83 ERYCRGVNAIV 93
RG + +
Sbjct: 67 PLSYRGADVFL 77
>gnl|CDD|165096 PHA02728, PHA02728, uncharacterized protein; Provisional.
Length = 184
Score = 29.3 bits (65), Expect = 2.0
Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 6/53 (11%)
Query: 174 DLPNALDEKELIDRIMI-DFWITLTLLIRWCESFLHH---FGSHPNWAVKWHT 222
DLPN D+ +I FWIT+ + +WC F+ + SH N +++++
Sbjct: 51 DLPNPNDDTTSFVKIYFKKFWITV--MTKWCAPFIDTVSVYTSHDNLNIQFYS 101
>gnl|CDD|236780 PRK10867, PRK10867, signal recognition particle protein;
Provisional.
Length = 433
Score = 30.0 bits (69), Expect = 2.0
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 25 LVGLQCSGKTTFV 37
+VGLQ +GKTT
Sbjct: 105 MVGLQGAGKTTTA 117
>gnl|CDD|222307 pfam13671, AAA_33, AAA domain. This family of domains contain
only a P-loop motif, that is characteristic of the AAA
superfamily. Many of the proteins in this family are
just short fragments so there is no Walker B motif.
Length = 143
Score = 28.4 bits (64), Expect = 2.6
Identities = 10/30 (33%), Positives = 14/30 (46%), Gaps = 4/30 (13%)
Query: 25 LVGLQCSGKTTFVNVIASGQF----SQDMI 50
+VGL SGK+TF + S D +
Sbjct: 4 MVGLPGSGKSTFARRLLRELGAVVLSSDTL 33
>gnl|CDD|233210 TIGR00959, ffh, signal recognition particle protein. This model
represents Ffh (Fifty-Four Homolog), the protein
component that forms the bacterial (and organellar)
signal recognition particle together with a 4.5S RNA.
Ffh is a GTPase homologous to eukaryotic SRP54 and also
to the GTPase FtsY (TIGR00064) that is the receptor for
the signal recognition particle [Protein fate, Protein
and peptide secretion and trafficking].
Length = 428
Score = 29.6 bits (67), Expect = 2.8
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 25 LVGLQCSGKTTFVNVIA 41
+VGLQ SGKTT +A
Sbjct: 104 MVGLQGSGKTTTCGKLA 120
>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 = 28.8 bits (64), Expect = 2.9
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 4/49 (8%)
Query: 29 QCSGKTTFVNVIASGQFSQDMIPTVGFNMR---KITKGNVTIKVWDIGG 74
QC GKT ++V A + + +PTV N +I K + + +WD G
Sbjct: 11 QC-GKTALLHVFAKDNYPESYVPTVFENYTASFEIDKHRIELNMWDTSG 58
>gnl|CDD|206727 cd04164, trmE, trmE is a tRNA modification GTPase. TrmE (MnmE,
ThdF, MSS1) is a 3-domain protein found in bacteria and
eukaryotes. It controls modification of the uridine at
the wobble position (U34) of tRNAs that read codons
ending with A or G in the mixed codon family boxes. TrmE
contains a GTPase domain that forms a canonical Ras-like
fold. It functions a molecular switch GTPase, and
apparently uses a conformational change associated with
GTP hydrolysis to promote the tRNA modification
reaction, in which the conserved cysteine in the
C-terminal domain is thought to function as a catalytic
residue. In bacteria that are able to survive in
extremely low pH conditions, TrmE regulates
glutamate-dependent acid resistance.
Length = 159
Score = 28.6 bits (65), Expect = 3.1
Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 7/55 (12%)
Query: 132 LIKYMVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELID 186
L+ +VDA ++ L+ E+ L K P++V+ NK DL + + ++
Sbjct: 85 LVLLVVDA--SEGLDEEDLEILELPAK-----KPVIVVLNKSDLLSDAEGISELN 132
>gnl|CDD|206742 cd09915, Rag, Rag GTPase subfamily of Ras-related GTPases. Rag
GTPases (ras-related GTP-binding proteins) constitute a
unique subgroup of the Ras superfamily, playing an
essential role in regulating amino acid-induced target
of rapamycin complex 1 (TORC1) kinase signaling,
exocytic cargo sorting at endosomes, and epigenetic
control of gene expression. This subfamily consists of
RagA and RagB as well as RagC and RagD that are closely
related. Saccharomyces cerevisiae encodes single
orthologs of metazoan RagA/B and RagC/D, Gtr1 and Gtr2,
respectively. Dimer formation is important for their
cellular function; these domains form heterodimers, as
RagA or RagB dimerizes with RagC or RagD, and
similarly, Gtr1 dimerizes with Gtr2. In response to
amino acids, the Rag GTPases guide the TORC1 complex to
activate the platform containing Rheb proto-oncogene by
driving the relocalization of mTORC1 from discrete
locations in the cytoplasm to a late endosomal and/or
lysosomal compartment that is Rheb-enriched and
contains Rab-7.
Length = 175
Score = 28.7 bits (64), Expect = 3.2
Identities = 20/81 (24%), Positives = 33/81 (40%), Gaps = 11/81 (13%)
Query: 23 LTLVGLQCSGKTTFVNVIASGQFSQDMI---PTVGFNMRKI-TKGNVTIKVWDIGGQ--- 75
L L G + SGK++ V+ D + T+ + GN T+ +WD GQ
Sbjct: 2 LLLXGRRRSGKSSIRKVVFHNYSPFDTLRLESTIDVEHSHLSFLGNXTLNLWDCPGQDVF 61
Query: 76 --PRFRSMWERYCRGVNAIVW 94
P E + V A+++
Sbjct: 62 FEPTKDK--EHIFQXVGALIY 80
>gnl|CDD|221270 pfam11855, DUF3375, Protein of unknown function (DUF3375). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria. Proteins in this
family are typically between 479 to 499 amino acids in
length.
Length = 471
Score = 29.3 bits (66), Expect = 3.3
Identities = 14/69 (20%), Positives = 29/69 (42%), Gaps = 18/69 (26%)
Query: 126 LSLLFQLIKYMVDAADTDK------LEASRNELHALIEKPQLIGIPILVLGNKRDLPNAL 179
L +F+L++ + + + D LE +EL A I++ + L L
Sbjct: 121 LLTVFELLRQLAEGTEPDPEARLAELEREIDELDAEIDR---------LEAGDVPL---L 168
Query: 180 DEKELIDRI 188
D+ ++ +R
Sbjct: 169 DDTQVRERF 177
>gnl|CDD|223615 COG0541, Ffh, Signal recognition particle GTPase [Intracellular
trafficking and secretion].
Length = 451
Score = 29.0 bits (66), Expect = 3.6
Identities = 9/13 (69%), Positives = 10/13 (76%)
Query: 25 LVGLQCSGKTTFV 37
+VGLQ SGKTT
Sbjct: 105 MVGLQGSGKTTTA 117
>gnl|CDD|215634 PLN03211, PLN03211, ABC transporter G-25; Provisional.
Length = 659
Score = 28.7 bits (64), Expect = 4.6
Identities = 14/40 (35%), Positives = 21/40 (52%)
Query: 23 LTLVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRKITK 62
L ++G SGK+T +N +A + T+ N RK TK
Sbjct: 97 LAVLGPSGSGKSTLLNALAGRIQGNNFTGTILANNRKPTK 136
>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 = 27.9 bits (62), Expect = 4.8
Identities = 17/77 (22%), Positives = 32/77 (41%), Gaps = 4/77 (5%)
Query: 21 MELTLVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRK---ITKGN-VTIKVWDIGGQP 76
+++ L+G GK+ V + + T + K +G + + WD GQ
Sbjct: 1 VKIILLGDSAVGKSKLVERFLMDGYEPQQLSTYALTLYKHNAKFEGKTILVDFWDTAGQE 60
Query: 77 RFRSMWERYCRGVNAIV 93
RF++M Y +A +
Sbjct: 61 RFQTMHASYYHKAHACI 77
>gnl|CDD|201420 pfam00735, Septin, Septin. Members of this family include CDC3,
CDC10, CDC11 and CDC12/Septin. Members of this family
bind GTP. As regards the septins, these are
polypeptides of 30-65kDa with three characteristic
GTPase motifs (G-1, G-3 and G-4) that are similar to
those of the Ras family. The G-4 motif is strictly
conserved with a unique septin consensus of AKAD. Most
septins are thought to have at least one coiled-coil
region, which in some cases is necessary for
intermolecular interactions that allow septins to
polymerise to form rod-shaped complexes. In turn, these
are arranged into tandem arrays to form filaments. They
are multifunctional proteins, with roles in
cytokinesis, sporulation, germ cell development,
exocytosis and apoptosis.
Length = 280
Score = 28.4 bits (64), Expect = 5.0
Identities = 17/48 (35%), Positives = 21/48 (43%), Gaps = 5/48 (10%)
Query: 23 LTLVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRK-ITKGNVTIKV 69
L +VG GKTT +N + F D+IP G K V IK
Sbjct: 7 LMVVGESGLGKTTLINTL----FLTDLIPERGIPGPSEKIKKTVEIKA 50
>gnl|CDD|184290 PRK13738, PRK13738, conjugal transfer pilus assembly protein TraW;
Provisional.
Length = 209
Score = 28.2 bits (63), Expect = 5.1
Identities = 14/57 (24%), Positives = 23/57 (40%), Gaps = 10/57 (17%)
Query: 135 YMVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRIMID 191
Y ++ D ++ + + P L ILV G+ ++ ALD RI D
Sbjct: 124 YFINGDDPAQVAWMKRQT-----PPTLESKIILVQGSIPEMSKALDS-----RIYFD 170
>gnl|CDD|223488 COG0411, LivG, ABC-type branched-chain amino acid transport
systems, ATPase component [Amino acid transport and
metabolism].
Length = 250
Score = 28.3 bits (64), Expect = 5.6
Identities = 16/52 (30%), Positives = 23/52 (44%), Gaps = 14/52 (26%)
Query: 25 LVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRKITKGNVTIKVWDIGGQP 76
L+G +GKTT N+I +G + K + G V + DI G P
Sbjct: 35 LIGPNGAGKTTLFNLI-TGFY-------------KPSSGTVIFRGRDITGLP 72
>gnl|CDD|179118 PRK00771, PRK00771, signal recognition particle protein Srp54;
Provisional.
Length = 437
Score = 28.2 bits (64), Expect = 6.2
Identities = 10/11 (90%), Positives = 10/11 (90%)
Query: 25 LVGLQCSGKTT 35
LVGLQ SGKTT
Sbjct: 100 LVGLQGSGKTT 110
>gnl|CDD|237247 PRK12886, ubiA, prenyltransferase; Reviewed.
Length = 291
Score = 28.1 bits (63), Expect = 7.0
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 107 RSAILYYEPVDLGVSGPMWLSLLFQLI 133
R L+ P LGV+G +W++ +F L+
Sbjct: 191 RKEGLHSIPAKLGVNGSLWIARVFHLL 217
>gnl|CDD|184130 PRK13545, tagH, teichoic acids export protein ATP-binding
subunit; Provisional.
Length = 549
Score = 27.9 bits (62), Expect = 7.7
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 18/56 (32%)
Query: 4 LLNRILDWFKSLFWKEE------------MELT------LVGLQCSGKTTFVNVIA 41
+ N+ D K LF++ + E+ ++GL SGK+T N+IA
Sbjct: 16 MYNKPFDKLKDLFFRSKDGEYHYALNNISFEVPEGEIVGIIGLNGSGKSTLSNLIA 71
>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 = 27.7 bits (61), Expect = 8.1
Identities = 16/63 (25%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 19 EEMELTLVGLQCSGKTTFVNVIASGQFSQDMIPTV--GFNMRKITKG-NVTIKVWDIGGQ 75
+ ++ +VG GKT + + F ++ IPTV ++ + G V++ +WD GQ
Sbjct: 2 QSIKCVVVGDGAVGKTCLLICYTTNAFPKEYIPTVFDNYSAQTAVDGRTVSLNLWDTAGQ 61
Query: 76 PRF 78
+
Sbjct: 62 EEY 64
>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 = 27.4 bits (61), Expect = 8.4
Identities = 15/36 (41%), Positives = 22/36 (61%), Gaps = 4/36 (11%)
Query: 146 EASRNELHALIEKPQLI----GIPILVLGNKRDLPN 177
EAS NEL L E+ I +P++++GNK DL +
Sbjct: 85 EASLNELGELREQVLRIKDSDNVPMVLVGNKADLED 120
>gnl|CDD|213186 cd03219, ABC_Mj1267_LivG_branched, ATP-binding cassette component
of branched chain amino acids transport system. The
Mj1267/LivG ABC transporter subfamily is involved in
the transport of the hydrophobic amino acids leucine,
isoleucine and valine. MJ1267 is a branched-chain amino
acid transporter with 29% similarity to both the LivF
and LivG components of the E. coli branched-chain amino
acid transporter. MJ1267 contains an insertion from
residues 114 to 123 characteristic of LivG
(Leucine-Isoleucine-Valine) homologs. The
branched-chain amino acid transporter from E. coli
comprises a heterodimer of ABCs (LivF and LivG), a
heterodimer of six-helix TM domains (LivM and LivH),
and one of two alternative soluble periplasmic
substrate binding proteins (LivK or LivJ).
Length = 236
Score = 27.4 bits (62), Expect = 8.7
Identities = 14/34 (41%), Positives = 17/34 (50%), Gaps = 8/34 (23%)
Query: 31 SGKTTFVNVIASGQFSQDMIPTVG---FNMRKIT 61
+GKTT N+I SG PT G F+ IT
Sbjct: 37 AGKTTLFNLI-SGFLR----PTSGSVLFDGEDIT 65
>gnl|CDD|223510 COG0433, COG0433, HerA helicase [Replication, recombination, and
repair].
Length = 520
Score = 28.0 bits (62), Expect = 9.0
Identities = 22/173 (12%), Positives = 51/173 (29%), Gaps = 15/173 (8%)
Query: 31 SGKTTFVNVIASGQFSQDMIPTVGFNM---------RKITKGNVTIKVWDIGGQPRFRSM 81
SGK+ V+ +D V F+ + I++ + GG
Sbjct: 179 SGKSNLAKVLLEELLGKDGATVVIFDPHGEYDLLRLDRADGEGYRIRILEAGG--LVPEG 236
Query: 82 WERYCRGVNAIVWTGGLYIVSKHIKRSAILYYEPVDLGVSGPMWLSLLFQLIKYMVDAAD 141
+ Y + + L + + + V L + + +L +++
Sbjct: 237 PKPY-EIADLLGVLRELIESLAEVLDLGLYPKDVVALAEARLLLFALAPKILLLDKLEEL 295
Query: 142 TDKLEASRNELHALIEKPQL-IGIPILVLGNKRDLPN--ALDEKELIDRIMID 191
+ E L +I + P+ L L + + + L + +
Sbjct: 296 VLEDEIRLKSLKGVIFVSIEDLERPLERLDVSLQLGSRVSPAIRALTEPGRLA 348
>gnl|CDD|178152 PLN02537, PLN02537, diaminopimelate decarboxylase.
Length = 410
Score = 27.8 bits (62), Expect = 9.1
Identities = 21/75 (28%), Positives = 30/75 (40%), Gaps = 8/75 (10%)
Query: 2 FVLLNRILDWFKSLFWKEEMELTLVGLQCS-GKT-TFVNVIASGQFSQDMIPTVGFNMRK 59
F + N L WF EL LVG C G T T V++ F + V + + +
Sbjct: 161 FGIRNEKLQWFLDAVKAHPNELKLVGAHCHLGSTITKVDI-----FRDAAVLMVNY-VDE 214
Query: 60 ITKGNVTIKVWDIGG 74
I + +IGG
Sbjct: 215 IRAQGFELSYLNIGG 229
>gnl|CDD|177351 PHA02117, PHA02117, glutathionylspermidine synthase
domain-containing protein.
Length = 397
Score = 27.5 bits (61), Expect = 9.8
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 122 GPMWLSLLFQLIKYMVDAADTDKLEASRNELHAL 155
GP W+ + + Y A+ D+LE + NELHA+
Sbjct: 29 GPYWIEAMARPPYYSFTQAEQDELEGAANELHAM 62
>gnl|CDD|226927 COG4555, NatA, ABC-type Na+ transport system, ATPase component
[Energy production and conversion / Inorganic ion
transport and metabolism].
Length = 245
Score = 27.4 bits (61), Expect = 9.9
Identities = 27/101 (26%), Positives = 39/101 (38%), Gaps = 24/101 (23%)
Query: 16 FWKEEMELT-LVGLQCSGKTTFVNVIASGQFSQDMIPTVGFNMRKITKGNVTIKVWDIGG 74
F EE E+T L+G +GKTT + +IA+ + G VTI D
Sbjct: 23 FEAEEGEITGLLGENGAGKTTLLRMIAT--------------LLIPDSGKVTIDGVDTVR 68
Query: 75 QPRFRSMWERYCRGVNAIVWTGGLY---IVSKHIKRSAILY 112
P F R + + GLY +++K A L
Sbjct: 69 DPSF------VRRKIGVLFGERGLYARLTARENLKYFARLN 103
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
0.325 0.138 0.446
Gapped
Lambda K H
0.267 0.0585 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,821,412
Number of extensions: 1602844
Number of successful extensions: 2256
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2201
Number of HSP's successfully gapped: 161
Length of query: 329
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 232
Effective length of database: 6,635,264
Effective search space: 1539381248
Effective search space used: 1539381248
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 59 (26.8 bits)