RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4433
(211 letters)
>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 = 175 bits (445), Expect = 1e-55
Identities = 79/204 (38%), Positives = 122/204 (59%), Gaps = 6/204 (2%)
Query: 12 KVVLLSGLSLSGKTLLFARLVYSKYFESCTSLKENVGNFT---YEKKNIKIVDLPGEDRL 68
VLL G S SGKT LF +L K + TS++ NV +F + K + +VD+PG ++L
Sbjct: 1 PTVLLLGPSDSGKTALFTKLTTGKVRSTVTSIEPNVASFYSNSSKGKKLTLVDVPGHEKL 60
Query: 69 RNKFFDQYKSSAKGIVYVLDSSTVQKTLRDVAESLYVILADPQVQSSRVNILVCCNKQDQ 128
R+K + K+S K IV+V+DS+T QK +RDVAE LY IL D + +++ IL+ CNKQD
Sbjct: 61 RDKLLEYLKASLKAIVFVVDSATFQKNIRDVAEFLYDILTDLEKIKNKIPILIACNKQDL 120
Query: 129 TLAKSSSVVKTLLQKELNLVRRTKSNQLEDTNDVAANQTFLG-NPDKDFEFSDLYNQVSF 187
AK + +K LL+KE+N +R ++S LE + ++ LG KDFEF L +V F
Sbjct: 121 FTAKPAKKIKELLEKEINTLRESRSKSLESLDGDDGSKDTLGDKGGKDFEFDQLEGEVDF 180
Query: 188 CDTTGLDSASEYDVEQLQDWMVTL 211
+ + S+ ++ +++W+ L
Sbjct: 181 VEGSVKK--SKGGIDDIEEWIDEL 202
>gnl|CDD|204242 pfam09439, SRPRB, Signal recognition particle receptor beta
subunit. The beta subunit of the signal recognition
particle receptor (SRP) is a transmembrane GTPase which
anchors the alpha subunit to the endoplasmic reticulum
membrane.
Length = 181
Score = 137 bits (347), Expect = 4e-41
Identities = 63/184 (34%), Positives = 95/184 (51%), Gaps = 10/184 (5%)
Query: 9 SSQKVVLLSGLSLSGKTLLFARLVYSKYFESCTSLKENVGNFTYEKKNIK-----IVDLP 63
SSQ V+++GL SGKT LF L ++ TS E + Y+ K ++D P
Sbjct: 1 SSQPAVIIAGLCDSGKTSLFTLLTTGTVKKTVTSQ-EP--SAAYKYMLHKGFSFTLIDFP 57
Query: 64 GEDRLRNKFFDQ--YKSSAKGIVYVLDSSTVQKTLRDVAESLYVILADPQVQSSRVNILV 121
G +LR K + SS +GIV+V+DS+ K + D AE LY IL+ ++ + ++IL+
Sbjct: 58 GHVKLRQKLLETIKDSSSLRGIVFVVDSTAFPKEVTDTAEFLYEILSITELLKNGIDILI 117
Query: 122 CCNKQDQTLAKSSSVVKTLLQKELNLVRRTKSNQLEDTNDVAANQTFLGNPDKDFEFSDL 181
CNKQ+ A+ +K L+KE+N +R +S L + LG KDF+F L
Sbjct: 118 ACNKQESFTARPPKKIKQALEKEINTIRERRSKALSGLDGSDDLSAVLGKKGKDFKFDQL 177
Query: 182 YNQV 185
V
Sbjct: 178 EGNV 181
>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 = 55.8 bits (135), Expect = 4e-10
Identities = 37/145 (25%), Positives = 72/145 (49%), Gaps = 12/145 (8%)
Query: 14 VLLSGLSLSGKTLLFARL--VYSKYFES------CTSLKENVGNFTYEKKNIKIVDLPGE 65
VL+ GL +GKT + +SK ++ ++ N+G K + DL G+
Sbjct: 2 VLILGLDNAGKTTFLEQTKTKFSKNYKGLNPSKITPTVGLNIGTIEVGKARLMFWDLGGQ 61
Query: 66 DRLRNKFFDQYKSSAKGIVYVLDSSTVQKTLRDVAESLYVILADPQVQSSRVNILVCCNK 125
+ LR+ +D+Y + + G++YV+DS T ++ + + ++ + ++ V +LV NK
Sbjct: 62 EELRS-LWDKYYAESHGVIYVIDS-TDRERFNESKSAFEKVINNEALEG--VPLLVLANK 117
Query: 126 QDQTLAKSSSVVKTLLQKELNLVRR 150
QD A S + +K + + L+ R
Sbjct: 118 QDLPDALSVAEIKEVFDDCIALIGR 142
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 54.2 bits (131), Expect = 2e-09
Identities = 34/130 (26%), Positives = 67/130 (51%), Gaps = 8/130 (6%)
Query: 14 VLLSGLSLSGKTLLFARLVYSKYFESCTSLKENVGNFTYEKKNIKIV--DLPGEDRLRNK 71
+L+ GL +GKT + +L + + ++ NV TY KN+K D+ G++ LR
Sbjct: 17 ILILGLDNAGKTTILYKLKLGEIVTTIPTIGFNVETVTY--KNVKFTVWDVGGQESLR-P 73
Query: 72 FFDQYKSSAKGIVYVLDSSTVQKTLRDVAESLYVILADPQVQSSRVNILVCCNKQDQTLA 131
+ Y + +++V+DS+ + + + E L+ +L + ++ +L+ NKQD A
Sbjct: 74 LWRNYFPNTDAVIFVVDSADRDR-IEEAKEELHALLNEEELA--DAPLLILANKQDLPGA 130
Query: 132 KSSSVVKTLL 141
S + ++ LL
Sbjct: 131 MSEAEIRELL 140
>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 = 52.2 bits (126), Expect = 8e-09
Identities = 30/133 (22%), Positives = 62/133 (46%), Gaps = 12/133 (9%)
Query: 14 VLLSGLSLSGKTLLFARLVYSKYFESCTSLKENVG----NFTYEKKNIKIVDLPGEDRLR 69
+L+ GL +GKT + +L + +G Y+ + D+ G+D++R
Sbjct: 2 ILMLGLDGAGKTTILYKLK----LGEVVTTIPTIGFNVETVEYKNVKFTVWDVGGQDKIR 57
Query: 70 NKFFDQYKSSAKGIVYVLDSSTVQKTLRDVAESLYVILADPQVQSSRVNILVCCNKQDQT 129
+ Y + G+++V+DSS ++ + + L+ +L + ++ +L+ NKQD
Sbjct: 58 P-LWKHYYENTDGLIFVVDSSDRER-IEEAKNELHKLLNEEEL--KGAPLLILANKQDLP 113
Query: 130 LAKSSSVVKTLLQ 142
A + S + LL
Sbjct: 114 GALTESELIELLG 126
>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 = 50.5 bits (121), Expect = 4e-08
Identities = 38/136 (27%), Positives = 65/136 (47%), Gaps = 8/136 (5%)
Query: 14 VLLSGLSLSGKTLLFARLVYSKYFES--CTSLKENVGNFTYEKKNIKIVDLPGEDRLRNK 71
+L+ GL SGKT + +L S ++ NV +F + D+ G+ + R
Sbjct: 2 ILVLGLDNSGKTTIINQLKPSNAQSQNIVPTVGFNVESFKKGNLSFTAFDMSGQGKYRG- 60
Query: 72 FFDQYKSSAKGIVYVLDSSTVQKTLRDVA--ESLYVILADPQVQSSRVNILVCCNKQDQT 129
++ Y + +GI++V+DSS LR V + L ++L P ++ R+ IL NK D
Sbjct: 61 LWEHYYKNIQGIIFVIDSS---DRLRMVVAKDELELLLNHPDIKHRRIPILFYANKMDLP 117
Query: 130 LAKSSSVVKTLLQKEL 145
A ++ + LL E
Sbjct: 118 DALTAVKITQLLCLEN 133
>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 = 50.1 bits (120), Expect = 5e-08
Identities = 33/115 (28%), Positives = 63/115 (54%), Gaps = 5/115 (4%)
Query: 14 VLLSGLSLSGKTLLFARLVYSKYFESCTSLKENVGNFTYEKK-NIKIVDLPGEDRLRNKF 72
VLL GL +GK+ L +L +++ + ++ NV EK ++ + D+ G++++R
Sbjct: 2 VLLLGLDSAGKSTLLYKLKHAELVTTIPTVGFNVEMLQLEKHLSLTVWDVGGQEKMR-TV 60
Query: 73 FDQYKSSAKGIVYVLDSSTVQKTLRDVAESLYVILADPQVQSSRVNILVCCNKQD 127
+ Y + G+VYV+DSS + L + + L IL + ++ V +++ NKQD
Sbjct: 61 WKCYLENTDGLVYVVDSSD-EARLDESQKELKHILKNEHIKG--VPVVLLANKQD 112
>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 = 49.4 bits (118), Expect = 1e-07
Identities = 33/127 (25%), Positives = 68/127 (53%), Gaps = 8/127 (6%)
Query: 3 FFKFRKSSQKVVLLSGLSLSGKTLLFARLVYSKYFESCTSLKENVGNFTYEKKNIK--IV 60
K + + +L+ GL +GKT + +L + + ++ NV TY KN+K +
Sbjct: 1 LSKLFGNKEMRILMLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTY--KNVKFNVW 58
Query: 61 DLPGEDRLRNKFFDQYKSSAKGIVYVLDSSTVQKTLRDVAESLYVILADPQVQSSRVNIL 120
D+ G+D++R + Y + +G+++V+DS+ + + + + L+ I+ D +++ +L
Sbjct: 59 DVGGQDKIR-PLWRHYYTGTQGLIFVVDSADRDR-IDEARQELHRIINDREMRD--ALLL 114
Query: 121 VCCNKQD 127
V NKQD
Sbjct: 115 VFANKQD 121
>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 = 48.5 bits (116), Expect = 2e-07
Identities = 42/142 (29%), Positives = 66/142 (46%), Gaps = 17/142 (11%)
Query: 18 GLSLSGKTLL---FARLVYSKYFES--CTSLKENVGNFTYEKKNIKIVDLPGEDRLRNKF 72
GL +GKT L + K + T K + + + I DL G R +
Sbjct: 6 GLDNAGKTTLVSALQGEIPKKVAPTVGFTPTKLRLDKY-----EVCIFDLGGGANFRGIW 60
Query: 73 FDQYKSSAKGIVYVLDSSTVQKTLRDVAESLYVILADPQVQSSRVNILVCCNKQDQTLAK 132
+ Y + A G+V+V+DSS + +++V E L +L P+V ILV NKQD+ A
Sbjct: 61 VNYY-AEAHGLVFVVDSSDDDR-VQEVKEILRELLQHPRVSGK--PILVLANKQDKKNAL 116
Query: 133 S-SSVVKTLLQKELNLVRRTKS 153
+ V++ L ++ LV KS
Sbjct: 117 LGADVIEYLSLEK--LVNENKS 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 = 48.4 bits (116), Expect = 3e-07
Identities = 35/160 (21%), Positives = 62/160 (38%), Gaps = 5/160 (3%)
Query: 1 FLFFKFRKSSQKVVLLSGLSLSGKTLLFARLVYSKYFESCTSLKENVGNFTYEKKNIKIV 60
K K+V L GL +GKT L L + + +L T
Sbjct: 10 LSSLGLYKKEAKIVFL-GLDNAGKTTLLHMLKDDRLAQHVPTLHPTSEELTIGNVKFTTF 68
Query: 61 DLPGEDRLRNKFFDQYKSSAKGIVYVLDSSTVQKTLRDVAESLYVILADPQVQSSRVNIL 120
DL G ++ R + + Y GIV+++D++ ++ ++ E L +L D + + V IL
Sbjct: 69 DLGGHEQAR-RVWKDYFPEVDGIVFLVDAADPER-FQESKEELDSLLNDE--ELANVPIL 124
Query: 121 VCCNKQDQTLAKSSSVVKTLLQKELNLVRRTKSNQLEDTN 160
+ NK D+ A S ++ L + +
Sbjct: 125 ILGNKIDKPGAVSEEELREALGLYGTTTGKGGVSLKVSNI 164
>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 = 47.7 bits (114), Expect = 4e-07
Identities = 33/118 (27%), Positives = 65/118 (55%), Gaps = 9/118 (7%)
Query: 12 KVVLLSGLSLSGKTLLFARLVYSKYFESCTSLKENVGNFTYEKKNIKIV--DLPGEDRLR 69
KV+++ GL +GKT + + + + + ++ NV Y KNI+ + D+ G++ LR
Sbjct: 17 KVIIV-GLDNAGKTTILYQFLLGEVVHTSPTIGSNVEEIVY--KNIRFLMWDIGGQESLR 73
Query: 70 NKFFDQYKSSAKGIVYVLDSSTVQKTLRDVAESLYVILADPQVQSSRVNILVCCNKQD 127
+ ++ Y ++ ++ V+DS+ ++ L E LY +LA ++ + +LV NKQD
Sbjct: 74 SS-WNTYYTNTDAVILVIDSTDRER-LPLTKEELYKMLAHEDLRKAV--LLVLANKQD 127
>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 = 47.0 bits (112), Expect = 8e-07
Identities = 36/150 (24%), Positives = 72/150 (48%), Gaps = 8/150 (5%)
Query: 2 LFFKFRKSSQKV--VLLSGLSLSGKTLLFARLVYSKYFESCTSLKENVGNFTYEKKNIKI 59
+ K + SS++ +LL GL +GKT + +L + N+ N + + +
Sbjct: 4 ILRKLKPSSRQEVRILLLGLDNAGKTTILKQLASEDISHITPTQGFNIKNVQADGFKLNV 63
Query: 60 VDLPGEDRLRNKFFDQYKSSAKGIVYVLDSSTVQKTLRDVAESLYVILADPQVQSSRVNI 119
D+ G+ ++R ++ Y + ++YV+DS+ +K + + L +L + ++ + V +
Sbjct: 64 WDIGGQRKIR-PYWRNYFENTDVLIYVIDSAD-RKRFEEAGQELVELLEEEKL--AGVPV 119
Query: 120 LVCCNKQDQTLAKSSSVVKTLLQKELNLVR 149
LV NKQD A + V L L+ +R
Sbjct: 120 LVFANKQDLLTAAPAEEVAEAL--NLHDIR 147
>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 = 46.1 bits (109), Expect = 2e-06
Identities = 33/126 (26%), Positives = 70/126 (55%), Gaps = 4/126 (3%)
Query: 2 LFFKFRKSSQKVVLLSGLSLSGKTLLFARLVYSKYFESCTSLKENVGNFTYEKKNIKIVD 61
LF K + + +L+ GL +GKT + +L + + ++ NV TY+ + + D
Sbjct: 4 LFSKLFGNKEMRILMVGLDAAGKTTILYKLKLGESVTTIPTIGFNVETVTYKNISFTVWD 63
Query: 62 LPGEDRLRNKFFDQYKSSAKGIVYVLDSSTVQKTLRDVAESLYVILADPQVQSSRVNILV 121
+ G+D++R + Y ++ +G+++V+DS+ + + + E L+ +L + +++ + ILV
Sbjct: 64 VGGQDKIR-PLWRHYYTNTQGLIFVVDSNDRDR-IDEAREELHRMLNEDELRDAV--ILV 119
Query: 122 CCNKQD 127
NKQD
Sbjct: 120 FANKQD 125
>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 = 45.9 bits (109), Expect = 2e-06
Identities = 35/124 (28%), Positives = 64/124 (51%), Gaps = 4/124 (3%)
Query: 14 VLLSGLSLSGKTLLFARLVYSKYFESCTSLKENVGNFTYEKKNIKIVDLPGEDRLRNKFF 73
+L+ GL +GKT + RL + + ++ NV TY+ ++ DL G+ +R ++
Sbjct: 2 ILILGLDGAGKTTILYRLQVGEVVTTIPTIGFNVETVTYKNLKFQVWDLGGQTSIR-PYW 60
Query: 74 DQYKSSAKGIVYVLDSSTVQKTLRDVAESLYVILADPQVQSSRVNILVCCNKQDQTLAKS 133
Y S+ I+YV+DS+ + L L+ +L + +++ + +LV NKQD A S
Sbjct: 61 RCYYSNTDAIIYVVDSTDRDR-LGISKSELHAMLEEEELKDAV--LLVFANKQDMPGALS 117
Query: 134 SSVV 137
+ V
Sbjct: 118 EAEV 121
>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 = 45.5 bits (108), Expect = 2e-06
Identities = 35/126 (27%), Positives = 69/126 (54%), Gaps = 8/126 (6%)
Query: 14 VLLSGLSLSGKTLLFARLVYSKYFESCTSLKENVGNFTYEKKNIKIV--DLPGEDRLRNK 71
+L+ GL +GKT + +L + + ++ NV T E KNI D+ G+D++R
Sbjct: 3 ILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVE--TVEYKNISFTVWDVGGQDKIR-P 59
Query: 72 FFDQYKSSAKGIVYVLDSSTVQKTLRDVAESLYVILADPQVQSSRVNILVCCNKQDQTLA 131
+ Y + +G+++V+DS+ ++ + + E L +L + +++ + +LV NKQD A
Sbjct: 60 LWRHYFQNTQGLIFVVDSNDRER-IGEAREELQRMLNEDELRDAV--LLVFANKQDLPNA 116
Query: 132 KSSSVV 137
S++ V
Sbjct: 117 MSAAEV 122
>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 = 45.0 bits (107), Expect = 3e-06
Identities = 35/114 (30%), Positives = 58/114 (50%), Gaps = 7/114 (6%)
Query: 16 LSGLSLSGKTLLFARLVYSKYFE-SCTSLKENVGNFTYEKKNIKIVDLPGEDRLRNKFFD 74
L GL SGKT L + ++ E + ++ N+ T IK+ DL G+ R R ++
Sbjct: 4 LVGLQNSGKTTLVNVIASGQFSEDTIPTVGFNMRKVTKGNVTIKVWDLGGQPRFR-SMWE 62
Query: 75 QYKSSAKGIVYVLDSSTVQKTLRDVA-ESLYVILADPQVQSSRVNILVCCNKQD 127
+Y IVYV+D++ +K +VA L+ +L P ++ + +LV NK D
Sbjct: 63 RYCRGVNAIVYVVDAADREKL--EVAKNELHDLLEKPSLEG--IPLLVLGNKND 112
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 44.6 bits (105), Expect = 1e-05
Identities = 39/131 (29%), Positives = 60/131 (45%), Gaps = 10/131 (7%)
Query: 12 KVVLLSGLSLSGKTLLFARLVYSKYFESCTSLKEN-VGNFTYE--KKNIK--IVDLPGED 66
K+V+L G GKT L RLV ++ E N T E ++NIK + D G++
Sbjct: 7 KIVVL-GDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQE 65
Query: 67 RLRNKFFDQYKSSAKGIVYVLDSSTVQKTLRDVAESLYVILADPQVQSSRVNILVCCNKQ 126
R+ +Y A GI+ V DS+ + + ++ E L + + V IL+ NK
Sbjct: 66 EYRS-LRPEYYRGANGILIVYDSTLRESSD-ELTEEWLEELRE--LAPDDVPILLVGNKI 121
Query: 127 DQTLAKSSSVV 137
D +SSS
Sbjct: 122 DLFDEQSSSEE 132
>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 = 43.6 bits (103), Expect = 1e-05
Identities = 29/140 (20%), Positives = 50/140 (35%), Gaps = 16/140 (11%)
Query: 18 GLSLSGKTLLFARLVYSKYFES----CTSLKENVGNFTYEKKNIK--IVDLPG----EDR 67
G GK+ L L+ + E T+ +V +K +K +VD PG
Sbjct: 4 GRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPGLDEFGGL 63
Query: 68 LRNKFFDQYKSSAKGIVYVLDSSTVQKTLRDVAESLYVILADPQVQSSRVNILVCCNKQD 127
R + A I+ V+D ST +++ D + L + I++ NK D
Sbjct: 64 GREELARLLLRGADLILLVVD-STDRESEEDAKLLILRRLRKEG-----IPIILVGNKID 117
Query: 128 QTLAKSSSVVKTLLQKELNL 147
+ + L + L
Sbjct: 118 LLEEREVEELLRLEELAKIL 137
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 42.4 bits (100), Expect = 4e-05
Identities = 21/94 (22%), Positives = 41/94 (43%), Gaps = 8/94 (8%)
Query: 52 YEKKNIKIVDLPGEDRLRNKFFDQYKSSAKGIVYVLDSSTVQKTLRDVAESLYVILADPQ 111
E + + PG++R + + + A G + ++DSS + + AE + L
Sbjct: 65 DEDTGVHLFGTPGQERFKFMW-EILSRGAVGAIVLVDSS---RPITFHAEEIIDFLT--- 117
Query: 112 VQSSRVNILVCCNKQDQTLAKSSSVVKTLLQKEL 145
+ + ++V NKQD A ++ L+ EL
Sbjct: 118 -SRNPIPVVVAINKQDLFDALPPEKIREALKLEL 150
>gnl|CDD|206719 cd04152, Arl4_Arl7, Arf-like 4 (Arl4) and 7 (Arl7) GTPases. Arl4
(Arf-like 4) is highly expressed in testicular germ
cells, and is found in the nucleus and nucleolus. In
mice, Arl4 is developmentally expressed during
embryogenesis, and a role in somite formation and
central nervous system differentiation has been
proposed. Arl7 has been identified as the only Arf/Arl
protein to be induced by agonists of liver X-receptor
and retinoid X-receptor and by cholesterol loading in
human macrophages. Arl7 is proposed to play a role in
transport between a perinuclear compartment and the
plasma membrane, apparently linked to the ABCA1-mediated
cholesterol secretion pathway. Older literature suggests
that Arl6 is a part of the Arl4/Arl7 subfamily, but
analyses based on more recent sequence data place Arl6
in its own subfamily.
Length = 183
Score = 42.1 bits (99), Expect = 4e-05
Identities = 40/138 (28%), Positives = 68/138 (49%), Gaps = 18/138 (13%)
Query: 13 VVLLSGLSLSGKTLLFARLVYSKYFES-------CTSLKENVGNFTYEKKNI--KIVDLP 63
+V+L GL +GKT + RL ++++ + +K ++GN K + D+
Sbjct: 6 IVML-GLDSAGKTTVLYRLKFNEFVNTVPTKGFNTEKIKVSLGN----AKGVTFHFWDVG 60
Query: 64 GEDRLRNKFFDQYKSSAKGIVYVLDSSTVQKTLRDVAESLYVILADPQVQSSRVNILVCC 123
G+++LR + Y GIV+V+DS V++ + + L+ I + Q V +LV
Sbjct: 61 GQEKLR-PLWKSYTRCTDGIVFVVDSVDVER-MEEAKTELHKITKFSENQG--VPVLVLA 116
Query: 124 NKQDQTLAKSSSVVKTLL 141
NKQD A S V+ LL
Sbjct: 117 NKQDLPNALPVSEVEKLL 134
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 41.9 bits (98), Expect = 5e-05
Identities = 28/122 (22%), Positives = 67/122 (54%), Gaps = 4/122 (3%)
Query: 14 VLLSGLSLSGKTLLFARLVYSKYFESCTSLKENVGNFTYEKKNIKIVDLPGEDRLRNKFF 73
+L+ GL +GKT + +L + + ++ NV Y+ + + D+ G+D++R +
Sbjct: 20 ILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIR-PLW 78
Query: 74 DQYKSSAKGIVYVLDSSTVQKTLRDVAESLYVILADPQVQSSRVNILVCCNKQDQTLAKS 133
Y + +G+++V+DS+ + + + + L+ +L + +++ + +LV NKQD A +
Sbjct: 79 RHYFQNTQGLIFVVDSNDRDRVV-EARDELHRMLNEDELRDA--VLLVFANKQDLPNAMN 135
Query: 134 SS 135
++
Sbjct: 136 AA 137
>gnl|CDD|206667 cd01879, FeoB, Ferrous iron transport protein B (FeoB) family.
Ferrous iron transport protein B (FeoB) subfamily. E.
coli has an iron(II) transport system, known as feo,
which may make an important contribution to the iron
supply of the cell under anaerobic conditions. FeoB has
been identified as part of this transport system. FeoB
is a large 700-800 amino acid integral membrane protein.
The N terminus contains a P-loop motif suggesting that
iron transport may be ATP dependent.
Length = 159
Score = 40.5 bits (96), Expect = 1e-04
Identities = 35/132 (26%), Positives = 52/132 (39%), Gaps = 52/132 (39%)
Query: 22 SGKTLLFARLVYSKYFESCTSLKENVGNF---TYEKK---------NIKIVDLPG----- 64
GKT LF L T ++ VGN+ T EKK I+IVDLPG
Sbjct: 8 VGKTTLFNAL---------TGARQKVGNWPGVTVEKKEGEFKLGGKEIEIVDLPGTYSLT 58
Query: 65 ---------EDRLRNKFFDQYKSSAKGIVYVLDSSTVQKTLRDVAESLYVILADPQVQSS 115
D L + D IV V+D++ +++ +LY+ L Q+
Sbjct: 59 PYSEDEKVARDFLLGEEPD-------LIVNVVDATNLER-------NLYLTL---QLLEL 101
Query: 116 RVNILVCCNKQD 127
+ ++V N D
Sbjct: 102 GLPVVVALNMID 113
>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 = 40.0 bits (94), Expect = 3e-04
Identities = 36/139 (25%), Positives = 65/139 (46%), Gaps = 8/139 (5%)
Query: 7 RKSSQKV----VLLSGLSLSGKTLLFARLVYSKYFESCTSLKENVGNFTYEKKNIKIVDL 62
RK+ QK +L+ GL +GKT + + +L N+ Y + I D+
Sbjct: 6 RKTKQKEREMRILMLGLDNAGKTTILKKFNGEDISTISPTLGFNIKTLEYNGYKLNIWDV 65
Query: 63 PGEDRLRNKFFDQYKSSAKGIVYVLDSSTVQKTLRDVAESLYVILADPQVQSSRVNILVC 122
G+ LR+ ++ Y S +++V+DSS + L D L +L + ++ + +L+
Sbjct: 66 GGQKSLRS-YWRNYFESTDALIWVVDSSDRAR-LEDCKRELQKLLVEERLAGA--TLLIF 121
Query: 123 CNKQDQTLAKSSSVVKTLL 141
NKQD A S ++ +L
Sbjct: 122 ANKQDLPGALSPEEIREVL 140
>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 = 39.2 bits (91), Expect = 4e-04
Identities = 34/130 (26%), Positives = 65/130 (50%), Gaps = 5/130 (3%)
Query: 12 KVVLLSGLSLSGKTLLFARLVYSKYFESCTSLKENVGNFTYEKKNIKIVDLPGEDRLRNK 71
+VV L GL +GKT + +L ++ + ++ NV Y+ I D+ G+ +LR
Sbjct: 1 RVVTL-GLDGAGKTTILFKLKQDEFMQPIPTIGFNVETVEYKNLKFTIWDVGGKHKLR-P 58
Query: 72 FFDQYKSSAKGIVYVLDSSTVQKTLRDVAESLYVILADPQVQSSRVNILVCCNKQDQTLA 131
+ Y + + +V+V+DSS + + + L +L + +++ + +L+ NKQD A
Sbjct: 59 LWKHYYLNTQAVVFVIDSSHRDR-VSEAHSELAKLLTEKELRDAL--LLIFANKQDVAGA 115
Query: 132 KSSSVVKTLL 141
S + LL
Sbjct: 116 LSVEEMTELL 125
>gnl|CDD|223447 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
transport and metabolism].
Length = 653
Score = 38.4 bits (90), Expect = 0.002
Identities = 44/179 (24%), Positives = 74/179 (41%), Gaps = 49/179 (27%)
Query: 9 SSQKVVLLSGLSLSGKTLLFARLVYSKYFESCTSLKENVGNF---TYEKK---------N 56
+ V L G GKT LF L T + VGN+ T EKK
Sbjct: 1 MKKLTVALVGNPNVGKTTLFNAL---------TGANQKVGNWPGVTVEKKEGKLKYKGHE 51
Query: 57 IKIVDLPG---------EDRLRNKFFDQYKSSAKGIVYVLDSSTVQKTLRDVAESLYVIL 107
I+IVDLPG ++++ F + K IV V+D++ +++ +LY+ L
Sbjct: 52 IEIVDLPGTYSLTAYSEDEKVARDFLLEGK--PDLIVNVVDATNLER-------NLYLTL 102
Query: 108 ADPQVQSSRVNILVCCNKQDQTLAKSSSV---VKTLLQKELNL-VRRTKSNQLEDTNDV 162
Q+ + +++ N D AK + ++ L K L + V T + + E ++
Sbjct: 103 ---QLLELGIPMILALNMID--EAKKRGIRIDIE-KLSKLLGVPVVPTVAKRGEGLEEL 155
>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 = 37.0 bits (86), Expect = 0.002
Identities = 29/138 (21%), Positives = 52/138 (37%), Gaps = 10/138 (7%)
Query: 12 KVVLLSGLSLSGKTLLFARLVYSKYFE----SCTSLKENVGNFTYEKKNIK--IVDLPGE 65
K+V++ G GK+ L RL+ +K T+ + K K ++D G+
Sbjct: 3 KIVIV-GDPNVGKSTLLNRLLGNKISITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAGQ 61
Query: 66 DRLRNKFFDQYKSSAKGIVYVLDSSTVQKTLRDVAESLYVILADPQVQSSRVNILVCCNK 125
+ Y + + + V D + + ++ E + S V I++ NK
Sbjct: 62 EDYD-AIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIH--HAESGVPIILVGNK 118
Query: 126 QDQTLAKSSSVVKTLLQK 143
D AK + V L K
Sbjct: 119 IDLRDAKLKTHVAFLFAK 136
>gnl|CDD|217025 pfam02421, FeoB_N, Ferrous iron transport protein B. Escherichia
coli has an iron(II) transport system (feo) which may
make an important contribution to the iron supply of
the cell under anaerobic conditions. FeoB has been
identified as part of this transport system. FeoB is a
large 700-800 amino acid integral membrane protein. The
N terminus contains a P-loop motif suggesting that iron
transport may be ATP dependent.
Length = 190
Score = 36.7 bits (86), Expect = 0.003
Identities = 21/55 (38%), Positives = 26/55 (47%), Gaps = 21/55 (38%)
Query: 22 SGKTLLFARLVYSKYFESCTSLKENVGNF---TYEKK---------NIKIVDLPG 64
GKT LF L T +++VGN+ T EKK I+IVDLPG
Sbjct: 11 VGKTTLFNAL---------TGARQHVGNWPGVTVEKKEGTFKYKGYEIEIVDLPG 56
>gnl|CDD|216791 pfam01926, MMR_HSR1, 50S ribosome-binding GTPase. The full-length
GTPase protein is required for the complete activity of
the protein of interacting with the 50S ribosome and
binding of both adenine and guanine nucleotides, with a
preference for guanine nucleotide.
Length = 117
Score = 34.2 bits (79), Expect = 0.011
Identities = 27/128 (21%), Positives = 48/128 (37%), Gaps = 25/128 (19%)
Query: 12 KVVLLSGLSLSGKTLLFARLVYSKYFES-----CTSLKENVGNFTYEKKNIKIVDLPG-- 64
+V L+ G GK+ L L +K T ++ + + I +VD PG
Sbjct: 1 RVALV-GRPNVGKSTLINALTGAKVAIVSDYPGTT--RDPILGVLGLGRQIILVDTPGLI 57
Query: 65 EDRLRNKFFDQYKSS------AKGIVYVLDSS-TVQKTLRDVAESLYVILADPQVQSSRV 117
E K + + A I+ V+D+S + + ++ E L + P
Sbjct: 58 EGASEGKGVEGFNRFLEAIREADLILLVVDASEGLTEDDEEILEELEKLPKKP------- 110
Query: 118 NILVCCNK 125
I++ NK
Sbjct: 111 -IILVLNK 117
>gnl|CDD|232975 TIGR00437, feoB, ferrous iron transporter FeoB. FeoB (773 amino
acids in E. coli), a cytoplasmic membrane protein
required for iron(II) update, is encoded in an operon
with FeoA (75 amino acids), which is also required, and
is regulated by Fur. There appear to be two copies in
Archaeoglobus fulgidus and Clostridium acetobutylicum
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 591
Score = 35.1 bits (81), Expect = 0.021
Identities = 38/165 (23%), Positives = 67/165 (40%), Gaps = 46/165 (27%)
Query: 22 SGKTLLFARLVYSKYFESCTSLKENVGNF---TYEKK---------NIKIVDLPG----- 64
GK+ LF L T + VGN+ T EKK +I+IVDLPG
Sbjct: 5 VGKSTLFNAL---------TGANQTVGNWPGVTVEKKEGKLGFQGEDIEIVDLPGIYSLT 55
Query: 65 ----EDRLRNKFFDQYKSSAKGIVYVLDSSTVQKTLRDVAESLYVILADPQVQSSRVNIL 120
E+ + + K +V V+D+S +++ +LY+ L Q+ + ++
Sbjct: 56 TFSLEEEVARDYLLNEK--PDLVVNVVDASNLER-------NLYLTL---QLLELGIPMI 103
Query: 121 VCCNKQDQTLAKSSSVVKTLLQKELNL----VRRTKSNQLEDTND 161
+ N D+ K + + L++ L + T+ +E D
Sbjct: 104 LALNLVDEAEKKGIRIDEEKLEERLGVPVVPTSATEGRGIERLKD 148
>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 = 33.6 bits (77), Expect = 0.037
Identities = 32/121 (26%), Positives = 62/121 (51%), Gaps = 7/121 (5%)
Query: 14 VLLSGLSLSGKTLLFARLVYSKYFESCTSLKE-NVGNFTYEKKNIKIVDLPGEDRLRNKF 72
+L+ GL +GKT L L + ES N + ++++++ G LR K+
Sbjct: 2 ILVLGLDGAGKTSLLHSLSSERSLESVVPTTGFNSVAIPTQDAIMELLEIGGSQNLR-KY 60
Query: 73 FDQYKSSAKGIVYVLDSSTVQKTLRDVAESLYVILADPQVQSSRVNILVCCNKQDQTLAK 132
+ +Y S ++G+++V+DS+ ++ L + L+ +L P + ++V NKQD A+
Sbjct: 61 WKRYLSGSQGLIFVVDSADSER-LPLARQELHQLLQHP----PDLPLVVLANKQDLPAAR 115
Query: 133 S 133
S
Sbjct: 116 S 116
>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 = 31.9 bits (72), Expect = 0.17
Identities = 34/119 (28%), Positives = 53/119 (44%), Gaps = 10/119 (8%)
Query: 14 VLLSGLSLSGKTLLFARLVYSKYFESCTS-----LKENVGNFTYEKKNIKIVDLPGEDRL 68
V++ G GKT L R + E+C S K +K ++I D G++R
Sbjct: 3 VIIIGSRGVGKTSLMERFTDDTFCEACKSTVGVDFKIKTVELRGKKIRLQIWDTAGQERF 62
Query: 69 RNKFFDQYKSSAKGIVYVLDSSTVQKTLRDVAESLYVILADPQVQSSRVNILVCCNKQD 127
N Y SAKGI+ V D T ++T D+ + + +I + S +L+ NK D
Sbjct: 63 -NSITSAYYRSAKGIILVYD-ITKKETFDDLPKWMKMI---DKYASEDAELLLVGNKLD 116
>gnl|CDD|130492 TIGR01425, SRP54_euk, signal recognition particle protein SRP54.
This model represents examples from the eukaryotic
cytosol of the signal recognition particle protein
component, SRP54. This GTP-binding protein is a
component of the eukaryotic signal recognition particle,
along with several other protein subunits and a 7S RNA.
Some species, including Arabidopsis, have several
closely related forms. The extreme C-terminal region is
glycine-rich and lower in complexity, poorly conserved
between species, and excluded from this model.
Length = 429
Score = 31.3 bits (71), Expect = 0.32
Identities = 24/78 (30%), Positives = 32/78 (41%), Gaps = 18/78 (23%)
Query: 4 FKFRKSSQKVVLLSGLSLSGKTLLFARLVYSKYFESCTSLKENVGNFTYEKKNIKIVDLP 63
F +K Q V++ GL SGKT +CT L + Y++K K L
Sbjct: 93 FTPKKGKQNVIMFVGLQGSGKT------------TTCTKLA-----YYYQRKGFK-PCLV 134
Query: 64 GEDRLRNKFFDQYKSSAK 81
D R FDQ K +A
Sbjct: 135 CADTFRAGAFDQLKQNAT 152
>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1. Members
of this family are necessary for accurate chromosome
transmission during cell division.
Length = 804
Score = 30.9 bits (70), Expect = 0.49
Identities = 12/36 (33%), Positives = 21/36 (58%), Gaps = 2/36 (5%)
Query: 154 NQLEDTNDVAANQTFLGNPD--KDFEFSDLYNQVSF 187
+QL++ +D ++TF G D KDF+F ++S
Sbjct: 38 DQLDEEDDALNDETFGGVADVGKDFDFGGETAKLSA 73
>gnl|CDD|233336 TIGR01272, gluP, glucose/galactose transporter. This model
describes the glucose/galactose transporter in bacteria.
This belongs to the larger facilitator superfamily.
Disruption of the loci leads to the total loss of
glucose or galactose uptake in E.coli. Putative
transporters in other bacterial species were isolated by
functional complementation, which restored it functional
activity [Transport and binding proteins, Carbohydrates,
organic alcohols, and acids].
Length = 310
Score = 30.6 bits (69), Expect = 0.51
Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 4/51 (7%)
Query: 82 GIVYVLDSSTVQKTLRDVAESLYV-ILADPQVQSSRVNILVCCNKQDQTLA 131
G ++VL S T+ VA + YV IL + +SR+ + NK T+A
Sbjct: 15 GALFVLASGL---TILQVAANPYVSILGPIETAASRLALTQAFNKLGTTVA 62
>gnl|CDD|234813 PRK00696, sucC, succinyl-CoA synthetase subunit beta; Provisional.
Length = 388
Score = 30.4 bits (70), Expect = 0.64
Identities = 11/21 (52%), Positives = 16/21 (76%)
Query: 99 VAESLYVILADPQVQSSRVNI 119
VAE+ +IL+DP V++ VNI
Sbjct: 298 VAEAFKIILSDPNVKAILVNI 318
>gnl|CDD|191388 pfam05849, L-fibroin, Fibroin light chain (L-fibroin). This family
consists of several moth fibroin light chain (L-fibroin)
proteins. Fibroin of the silkworm, Bombyx mori, is
secreted into the lumen of posterior silk gland (PSG)
from the surrounding PSG cells as a molecular complex
consisting of a heavy (H)-chain of approximately 350
kDa, a light (L)-chain of 25 kDa and a P25 of about 27
kDa. The H- and L-chains are disulfide-linked but P25 is
associated with the H-L complex by non-covalent force.
Length = 245
Score = 29.9 bits (67), Expect = 0.95
Identities = 12/46 (26%), Positives = 21/46 (45%)
Query: 127 DQTLAKSSSVVKTLLQKELNLVRRTKSNQLEDTNDVAANQTFLGNP 172
D LA + V +L+ +E + +R + +N+V A T P
Sbjct: 159 DSVLAYADPVGSSLINEEYCIAKRLYNAFNSRSNNVGAAITARSLP 204
>gnl|CDD|222000 pfam13238, AAA_18, AAA domain.
Length = 128
Score = 28.9 bits (65), Expect = 1.0
Identities = 21/103 (20%), Positives = 40/103 (38%), Gaps = 4/103 (3%)
Query: 14 VLLSGLSLSGKTLL---FARLVYSKYFESCTSLKENVGNFTYEKKNIKIVDLPGEDRLRN 70
+L++G SGKT L A + + + K +D +L +
Sbjct: 1 ILITGTPGSGKTTLAKELAERLGDVLRDLAKENGLVLELDEEITDESKRLDEDKLAKLLD 60
Query: 71 KFFDQYKSSAKGIVYVLDSSTVQKTLRDVAESLYVIL-ADPQV 112
K + A+G ++D + L + ++V+L ADP+
Sbjct: 61 KLEKIIEELAEGENVIIDGHLAELELERFKDLVFVVLRADPEE 103
>gnl|CDD|236563 PRK09554, feoB, ferrous iron transport protein B; Reviewed.
Length = 772
Score = 29.7 bits (67), Expect = 1.2
Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 21/55 (38%)
Query: 22 SGKTLLFARLVYSKYFESCTSLKENVGNF---TYEKK---------NIKIVDLPG 64
SGKT LF +L T ++ VGN+ T E+K + +VDLPG
Sbjct: 14 SGKTTLFNQL---------TGARQRVGNWAGVTVERKEGQFSTTDHQVTLVDLPG 59
>gnl|CDD|173797 cd05561, Peptidases_S8_4, Peptidase S8 family domain,
uncharacterized subfamily 4. This family is a member of
the Peptidases S8 or Subtilases serine endo- and
exo-peptidase clan. They have an Asp/His/Ser catalytic
triad similar to that found in trypsin-like proteases,
but do not share their three-dimensional structure and
are not homologous to trypsin. The stability of
subtilases may be enhanced by calcium, some members have
been shown to bind up to 4 ions via binding sites with
different affinity. Some members of this clan contain
disulfide bonds. These enzymes can be intra- and
extracellular, some function at extreme temperatures and
pH values.
Length = 239
Score = 28.8 bits (65), Expect = 1.9
Identities = 9/30 (30%), Positives = 13/30 (43%)
Query: 180 DLYNQVSFCDTTGLDSASEYDVEQLQDWMV 209
DLY F G + AS + + DW+
Sbjct: 61 DLYGADVFGRAGGGEGASALALARALDWLA 90
>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 = 28.0 bits (63), Expect = 1.9
Identities = 8/20 (40%), Positives = 13/20 (65%)
Query: 13 VVLLSGLSLSGKTLLFARLV 32
++L+ GL SGK+ RL+
Sbjct: 1 LILMVGLPGSGKSTFARRLL 20
>gnl|CDD|145440 pfam02286, Dehydratase_LU, Dehydratase large subunit. This family
contains the large subunit of the trimeric diol
dehydratases and glycerol dehydratases. These enzymes
are produced by some enterobacteria in response to
growth substances.
Length = 554
Score = 28.9 bits (65), Expect = 2.1
Identities = 31/113 (27%), Positives = 48/113 (42%), Gaps = 17/113 (15%)
Query: 55 KNIKIVDLPGEDRLRNKFFDQYKSSAKGIV-YVLDSSTVQKTLRDVAESLYVILADPQVQ 113
+N K+V++ G+ R D++ I Y +D ++ + + L +L DP V
Sbjct: 44 ENGKVVEMDGKKREDFDLIDRF------IARYGIDLERAEEAMAMDSVKLARMLVDPNV- 96
Query: 114 SSRVNILVCCNKQDQTLAKSSSVVKTLLQKELNLV------RRTKSNQLEDTN 160
R I+ T AK + VV L E+ + RRT SNQ TN
Sbjct: 97 -PREEIVRLTTGM--TPAKLAEVVSQLNVVEMMMAMQKMRARRTPSNQAHVTN 146
>gnl|CDD|179250 PRK01215, PRK01215, competence damage-inducible protein A;
Provisional.
Length = 264
Score = 28.1 bits (63), Expect = 3.6
Identities = 19/73 (26%), Positives = 23/73 (31%), Gaps = 13/73 (17%)
Query: 38 ESCTSLKENVG---NFTYEKKNIKIVDLPG-----EDRLRNKFFDQYKSSAKGIVYVLDS 89
L+ VG E IV LPG E N F + + + Y DS
Sbjct: 125 PGAVPLENPVGTAPGILIEHGGKDIVALPGVPREMEAIFEN-FVEPLLKNRPPLKYYEDS 183
Query: 90 STVQKTLRDVAES 102
V V ES
Sbjct: 184 ILV----EGVMES 192
>gnl|CDD|219158 pfam06745, KaiC, KaiC. This family represents a conserved region
within bacterial and archaeal proteins, most of which
are hypothetical. More than one copy is sometimes found
in each protein. This family includes KaiC, which is
one of the Kai proteins among which direct
protein-protein association may be a critical process
in the generation of circadian rhythms in
cyanobacteria.
Length = 231
Score = 27.6 bits (62), Expect = 4.8
Identities = 17/69 (24%), Positives = 31/69 (44%), Gaps = 18/69 (26%)
Query: 12 KVVLLSGLSLSGKTLLFARLVY---SKYFESC---------TSLKENVGNF-----TYEK 54
+VVL++G +GKT+ + +Y +Y E L+EN +F E+
Sbjct: 20 RVVLITGGPGTGKTIFGLQFLYNGALEYGEPGVYVTLEEPPEDLRENAKSFGWDLEKLEE 79
Query: 55 KN-IKIVDL 62
+ + I+D
Sbjct: 80 EGKLAIIDA 88
>gnl|CDD|140232 PTZ00205, PTZ00205, DNA polymerase kappa; Provisional.
Length = 571
Score = 27.7 bits (61), Expect = 5.0
Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 7/66 (10%)
Query: 87 LDSSTVQKTLRDVAESLYVILADPQVQSSRVNILVCCNKQDQTLAKSSSVVKTLLQKELN 146
+D V+ +R+V+E ++ + ++ R KQ Q L + SS+ LL E N
Sbjct: 56 VDKERVEAIIRNVSEGSSFLMNEQRLAEGR-------EKQLQELKRKSSLFTQLLGGERN 108
Query: 147 LVRRTK 152
+R +
Sbjct: 109 AAQRKQ 114
>gnl|CDD|238985 cd02027, APSK, Adenosine 5'-phosphosulfate kinase (APSK)
catalyzes the phosphorylation of adenosine
5'-phosphosulfate to form 3'-phosphoadenosine
5'-phosphosulfate (PAPS). The end-product PAPS is a
biologically "activated" sulfate form important for the
assimilation of inorganic sulfate.
Length = 149
Score = 27.1 bits (61), Expect = 5.0
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 4/34 (11%)
Query: 13 VVLLSGLSLSGKTLLFARLVYSKYFE---SCTSL 43
V+ L+GLS SGK+ + AR + K F+ L
Sbjct: 1 VIWLTGLSGSGKSTI-ARALEEKLFQRGRPVYVL 33
>gnl|CDD|215773 pfam00180, Iso_dh, Isocitrate/isopropylmalate dehydrogenase.
Length = 349
Score = 27.2 bits (61), Expect = 6.1
Identities = 11/64 (17%), Positives = 24/64 (37%), Gaps = 3/64 (4%)
Query: 44 KENVGNFTYEKKNIKIVDLPGEDRLRNKFFDQYKSSAKGIVYVLDSSTVQKT---LRDVA 100
+ GN + K+ +R+ F+ + + V +D + V K+ R +
Sbjct: 143 IKGSGNGEEGAVDTKLYSRDEIERIARVAFELARKRGRKKVTSVDKANVLKSSRLWRKIV 202
Query: 101 ESLY 104
E +
Sbjct: 203 EEVA 206
>gnl|CDD|223603 COG0529, CysC, Adenylylsulfate kinase and related kinases
[Inorganic ion transport and metabolism].
Length = 197
Score = 26.9 bits (60), Expect = 6.1
Identities = 10/35 (28%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 4 FKFRKSSQKVVLLSGLSLSGKTLLFARLVYSKYFE 38
+ V+ +GLS SGK+ + A + K F
Sbjct: 16 EALKGQKGAVIWFTGLSGSGKSTI-ANALEEKLFA 49
>gnl|CDD|218203 pfam04670, Gtr1_RagA, Gtr1/RagA G protein conserved region. GTR1
was first identified in S. cerevisiae as a suppressor of
a mutation in RCC1. Biochemical analysis revealed that
Gtr1 is in fact a G protein of the Ras family. The
RagA/B proteins are the human homologues of Gtr1.
Included in this family is the human Rag C, a novel
protein that has been shown to interact with RagA/B.
Length = 230
Score = 27.2 bits (61), Expect = 6.7
Identities = 27/114 (23%), Positives = 48/114 (42%), Gaps = 32/114 (28%)
Query: 14 VLLSGLSLSGKT----LLFARLV--YSKYFESCTSLKENV----GNFTYEKKNIKIVDLP 63
VLL GL SGK+ ++F+ + + ++++ GN T + + D P
Sbjct: 2 VLLMGLRGSGKSSMRSIIFSNYSPRDTLRLGATIDVEQSHVRFLGNLT-----LNLWDCP 56
Query: 64 GEDRLRNKFFDQYKSSAKG--------IVYVLDSSTVQ-----KTLRDVAESLY 104
G+D F + Y + K ++YV D + + TL + E+LY
Sbjct: 57 GQDD----FMENYLTRQKEHIFSNVGVLIYVFDVESREYEEDLATLVKIIEALY 106
>gnl|CDD|233207 TIGR00955, 3a01204, The Eye Pigment Precursor Transporter (EPP)
Family protein. [Transport and binding proteins,
Other].
Length = 617
Score = 27.3 bits (61), Expect = 7.3
Identities = 11/20 (55%), Positives = 13/20 (65%), Gaps = 2/20 (10%)
Query: 187 FCD--TTGLDSASEYDVEQL 204
FCD T+GLDS Y V Q+
Sbjct: 189 FCDEPTSGLDSFMAYSVVQV 208
>gnl|CDD|205181 pfam12997, DUF3881, Domain of unknown function, E. rectale Gene
description (DUF3881). Based on Eubacterium rectale
gene EUBREC_3695. As seen in gene expression experiments
(http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14
737), it appears to be upregulated in the presence of
Bacteroides thetaiotaomicron vs when isolated in
culture.
Length = 283
Score = 26.7 bits (60), Expect = 8.7
Identities = 12/23 (52%), Positives = 13/23 (56%)
Query: 5 KFRKSSQKVVLLSGLSLSGKTLL 27
K V LSGLS+SGK LL
Sbjct: 126 GKDSIKAKSVTLSGLSVSGKILL 148
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.317 0.132 0.364
Gapped
Lambda K H
0.267 0.0591 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,962,419
Number of extensions: 878915
Number of successful extensions: 913
Number of sequences better than 10.0: 1
Number of HSP's gapped: 888
Number of HSP's successfully gapped: 65
Length of query: 211
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 118
Effective length of database: 6,812,680
Effective search space: 803896240
Effective search space used: 803896240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (26.0 bits)