RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2977
(92 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 = 151 bits (383), Expect = 9e-49
Identities = 57/86 (66%), Positives = 68/86 (79%)
Query: 1 MVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRMNLCAIQD 60
+VDAAD +KLE ++NELH L+EKP L GIP+LVLGNK DLP AL ELI++MNL +I D
Sbjct: 74 VVDAADREKLEVAKNELHDLLEKPSLEGIPLLVLGNKNDLPGALSVDELIEQMNLKSITD 133
Query: 61 REICCYSISCKERDNIDITLQWLIAH 86
RE+ CYSIS KE+ NIDI L WLI H
Sbjct: 134 REVSCYSISAKEKTNIDIVLDWLIKH 159
>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 = 94.6 bits (236), Expect = 2e-26
Identities = 35/84 (41%), Positives = 54/84 (64%)
Query: 1 MVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRMNLCAIQD 60
+VD++D +++E ++NELH L+ + +L G P+L+L NK+DLP AL E ELI+ + L +I+
Sbjct: 73 VVDSSDRERIEEAKNELHKLLNEEELKGAPLLILANKQDLPGALTESELIELLGLESIKG 132
Query: 61 REICCYSISCKERDNIDITLQWLI 84
R S D +D L WLI
Sbjct: 133 RRWHIQPCSAVTGDGLDEGLDWLI 156
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 73.0 bits (180), Expect = 8e-18
Identities = 31/83 (37%), Positives = 50/83 (60%)
Query: 2 VDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRMNLCAIQDR 61
VD+AD D++E ++ ELHAL+ + +L P+L+L NK+DLP A+ E E+ + + L ++DR
Sbjct: 89 VDSADRDRIEEAKEELHALLNEEELADAPLLILANKQDLPGAMSEAEIRELLGLHELKDR 148
Query: 62 EICCYSISCKERDNIDITLQWLI 84
S + +D L WL
Sbjct: 149 PWEIQGCSAVTGEGLDEGLDWLS 171
>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 = 70.1 bits (172), Expect = 7e-17
Identities = 29/83 (34%), Positives = 52/83 (62%)
Query: 2 VDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRMNLCAIQDR 61
VD+ D D+L S++ELHA++E+ +L +LV NK+D+P AL E E+ +++ L ++DR
Sbjct: 74 VDSTDRDRLGISKSELHAMLEEEELKDAVLLVFANKQDMPGALSEAEVAEKLGLSELKDR 133
Query: 62 EICCYSISCKERDNIDITLQWLI 84
+ S + + +D + WL+
Sbjct: 134 TWQIFKTSATKGEGLDEGMDWLV 156
>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 = 62.1 bits (151), Expect = 9e-14
Identities = 27/86 (31%), Positives = 48/86 (55%)
Query: 1 MVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRMNLCAIQD 60
+VD+AD D+++ +R ELH +I ++ +LV NK+DLP+A+ E+ +++ L I+D
Sbjct: 83 VVDSADRDRIDEARQELHRIINDREMRDALLLVFANKQDLPDAMKPHEIQEKLGLTRIRD 142
Query: 61 REICCYSISCKERDNIDITLQWLIAH 86
R D + L WL ++
Sbjct: 143 RNWYVQPSCATSGDGLYEGLTWLSSN 168
>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 = 61.6 bits (150), Expect = 2e-13
Identities = 25/83 (30%), Positives = 46/83 (55%)
Query: 2 VDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRMNLCAIQDR 61
VD++D +LE + EL L+ + +L G +L+ NK+DLP AL +E+ + + L +I+
Sbjct: 89 VDSSDRARLEDCKRELQKLLVEERLAGATLLIFANKQDLPGALSPEEIREVLELDSIKSH 148
Query: 62 EICCYSISCKERDNIDITLQWLI 84
+ S +N+ + WL+
Sbjct: 149 HWRIFGCSAVTGENLLDGIDWLV 171
>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 = 61.6 bits (150), Expect = 2e-13
Identities = 27/83 (32%), Positives = 47/83 (56%)
Query: 2 VDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRMNLCAIQDR 61
+D+AD + E + EL L+E+ +L G+P+LV NK+DL A +E+ + +NL I+DR
Sbjct: 90 IDSADRKRFEEAGQELVELLEEEKLAGVPVLVFANKQDLLTAAPAEEVAEALNLHDIRDR 149
Query: 62 EICCYSISCKERDNIDITLQWLI 84
+ S K + + + W+
Sbjct: 150 SWHIQACSAKTGEGLQEGMNWVC 172
>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 = 60.0 bits (146), Expect = 9e-13
Identities = 24/55 (43%), Positives = 38/55 (69%)
Query: 1 MVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRMNL 55
+VDAAD ++ + S+ EL +L+ +L +PIL+LGNK D P A+ E+EL + + L
Sbjct: 93 LVDAADPERFQESKEELDSLLNDEELANVPILILGNKIDKPGAVSEEELREALGL 147
>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 = 55.1 bits (133), Expect = 4e-11
Identities = 24/82 (29%), Positives = 45/82 (54%)
Query: 2 VDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRMNLCAIQDR 61
VD+ D +++ +R EL ++ + +L +LV NK+DLPNA+ E+ D++ L ++++R
Sbjct: 75 VDSNDRERIGEAREELQRMLNEDELRDAVLLVFANKQDLPNAMSAAEVTDKLGLHSLRNR 134
Query: 62 EICCYSISCKERDNIDITLQWL 83
+ D + L WL
Sbjct: 135 NWYIQATCATSGDGLYEGLDWL 156
>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 = 54.0 bits (130), Expect = 1e-10
Identities = 25/86 (29%), Positives = 46/86 (53%), Gaps = 2/86 (2%)
Query: 2 VDAADTDKLEASRNELHALIEKPQLI--GIPILVLGNKRDLPNALDEKELIDRMNLCAIQ 59
+D++D ++ +++EL L+ P + IPIL NK DLP+AL ++ + L I+
Sbjct: 76 IDSSDRLRMVVAKDELELLLNHPDIKHRRIPILFYANKMDLPDALTAVKITQLLCLENIK 135
Query: 60 DREICCYSISCKERDNIDITLQWLIA 85
D+ ++ S + +D + WL A
Sbjct: 136 DKPWHIFASSALTGEGLDEGVDWLQA 161
>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 = 54.2 bits (130), Expect = 1e-10
Identities = 28/89 (31%), Positives = 50/89 (56%)
Query: 1 MVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRMNLCAIQD 60
+VD+ D D+++ +R ELH ++ + +L ILV NK+DLP+A+ E+ +++ L +I+D
Sbjct: 87 VVDSNDRDRIDEAREELHRMLNEDELRDAVILVFANKQDLPDAMKAAEITEKLGLHSIRD 146
Query: 61 REICCYSISCKERDNIDITLQWLIAHSKS 89
R D + L WL + K+
Sbjct: 147 RNWYIQPTCATSGDGLYEGLTWLSNNLKN 175
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 54.2 bits (130), Expect = 2e-10
Identities = 26/83 (31%), Positives = 48/83 (57%)
Query: 1 MVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRMNLCAIQD 60
+VD+ D D++ +R+ELH ++ + +L +LV NK+DLPNA++ E+ D++ L +++
Sbjct: 91 VVDSNDRDRVVEARDELHRMLNEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRQ 150
Query: 61 REICCYSISCKERDNIDITLQWL 83
R S + + L WL
Sbjct: 151 RHWYIQSTCATSGEGLYEGLDWL 173
>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 = 53.8 bits (129), Expect = 2e-10
Identities = 22/49 (44%), Positives = 30/49 (61%)
Query: 1 MVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKEL 49
+VDA D ++ S+ EL AL+ +L +P L+LGNK D P A E EL
Sbjct: 91 LVDAYDKERFAESKRELDALLSDEELATVPFLILGNKIDAPYAASEDEL 139
>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 = 52.8 bits (127), Expect = 3e-10
Identities = 23/69 (33%), Positives = 42/69 (60%), Gaps = 5/69 (7%)
Query: 2 VDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRMNL---CAI 58
VD++D +L+ S+ EL +++ + G+P+++L NK+DLP AL +E+ R L C+
Sbjct: 75 VDSSDEARLDESQKELKHILKNEHIKGVPVVLLANKQDLPGALTAEEITRRFKLKKYCSD 134
Query: 59 QDREI--CC 65
+D + C
Sbjct: 135 RDWYVQPCS 143
>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 = 52.9 bits (127), Expect = 5e-10
Identities = 21/49 (42%), Positives = 35/49 (71%)
Query: 1 MVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKEL 49
+VD+ D +++E ++ ELH + + + G+P+LVL NK+DLPNAL E+
Sbjct: 82 VVDSVDVERMEEAKTELHKITKFSENQGVPVLVLANKQDLPNALPVSEV 130
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 52.5 bits (126), Expect = 6e-10
Identities = 24/89 (26%), Positives = 46/89 (51%)
Query: 1 MVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRMNLCAIQD 60
+VD+ D +++ +R EL ++ + +L +LV NK+DLPNA+ E+ +++ L +++
Sbjct: 91 VVDSNDRERIGDAREELERMLSEDELRDAVLLVFANKQDLPNAMSTTEVTEKLGLHSVRQ 150
Query: 61 REICCYSISCKERDNIDITLQWLIAHSKS 89
R + L WL A+ K
Sbjct: 151 RNWYIQGCCATTAQGLYEGLDWLSANIKK 179
>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 = 51.6 bits (124), Expect = 1e-09
Identities = 27/93 (29%), Positives = 48/93 (51%), Gaps = 9/93 (9%)
Query: 2 VDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRMNLCAIQDR 61
VD++D D+++ + L L++ P++ G PILVL NK+D NAL ++I+ ++L + +
Sbjct: 74 VDSSDDDRVQEVKEILRELLQHPRVSGKPILVLANKQDKKNALLGADVIEYLSLEKLVNE 133
Query: 62 EICCYSI--SCKERD-------NIDITLQWLIA 85
I +I L+WL+A
Sbjct: 134 NKSLCHIEPCSAIEGLGKKIDPSIVEGLRWLLA 166
>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 = 51.2 bits (123), Expect = 1e-09
Identities = 20/68 (29%), Positives = 37/68 (54%), Gaps = 4/68 (5%)
Query: 2 VDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRMNLCAIQDR 61
+D+ D ++L ++ EL+ ++ L +LVL NK+DL A+ E+ + + L +I+D
Sbjct: 90 IDSTDRERLPLTKEELYKMLAHEDLRKAVLLVLANKQDLKGAMTPAEISESLGLTSIRDH 149
Query: 62 EI----CC 65
CC
Sbjct: 150 TWHIQGCC 157
>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 = 50.8 bits (122), Expect = 2e-09
Identities = 25/85 (29%), Positives = 47/85 (55%), Gaps = 2/85 (2%)
Query: 2 VDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRMNLCA--IQ 59
+D+ D ++ S++ +I L G+P+LVL NK+DLP+AL E+ + + C I
Sbjct: 82 IDSTDRERFNESKSAFEKVINNEALEGVPLLVLANKQDLPDALSVAEIKEVFDDCIALIG 141
Query: 60 DREICCYSISCKERDNIDITLQWLI 84
R+ +S E + ++ ++WL+
Sbjct: 142 RRDCLVQPVSALEGEGVEEGIEWLV 166
>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 = 49.0 bits (117), Expect = 1e-08
Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 6/72 (8%)
Query: 2 VDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRMNLCAI-QD 60
VD+AD+++L +R ELH L++ P +P++VL NK+DLP A +E+ + L I +
Sbjct: 75 VDSADSERLPLARQELHQLLQHPP--DLPLVVLANKQDLPAARSVQEIHKELELEPIARG 132
Query: 61 RE---ICCYSIS 69
R
Sbjct: 133 RRWILQGTSLDD 144
>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 = 46.3 bits (110), Expect = 1e-07
Identities = 23/84 (27%), Positives = 42/84 (50%), Gaps = 5/84 (5%)
Query: 1 MVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRMNLCAIQD 60
+VD+ D + E ++ + + K GIPI+++GNK DL + +EL+ L I
Sbjct: 82 VVDSTDRESEEDAKLLILRRLRKE---GIPIILVGNKIDLLEEREVEELLRLEELAKILG 138
Query: 61 REICCYSISCKERDNIDITLQWLI 84
+ + +S K + +D + LI
Sbjct: 139 --VPVFEVSAKTGEGVDELFEKLI 160
>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 = 38.0 bits (89), Expect = 1e-04
Identities = 20/73 (27%), Positives = 33/73 (45%), Gaps = 3/73 (4%)
Query: 14 RNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRMNLCAIQDREICCYSISCKER 73
E A + + G P+L++ NK DL +E+EL+ L + D + +S
Sbjct: 90 PVEEEAKLGLLRERGKPVLLVLNKIDLVPESEEEELLRERKLELLPDLPVIA--VSALPG 147
Query: 74 DNIDITLQWLIAH 86
+ ID L+ IA
Sbjct: 148 EGID-ELRKKIAE 159
>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 = 36.3 bits (85), Expect = 6e-04
Identities = 25/91 (27%), Positives = 39/91 (42%), Gaps = 20/91 (21%)
Query: 1 MVDAADTDK------LEASRNEL----HALIEKPQLIGIPILVLGNKRDLPNALDEKELI 50
++D + D E RNEL L EKP+ I+VL NK DL + + +EL+
Sbjct: 242 LIDISPEDGSDPIEDYEIIRNELKKYSPELAEKPR-----IVVL-NKIDLLDEEELEELL 295
Query: 51 DRMNLCAIQDREICCYSISCKERDNIDITLQ 81
L + + + IS + +D L
Sbjct: 296 KE--LKEALGKPV--FPISALTGEGLDELLY 322
>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 = 35.0 bits (80), Expect = 0.002
Identities = 22/89 (24%), Positives = 46/89 (51%), Gaps = 11/89 (12%)
Query: 1 MVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRMNLCAIQD 60
++D++ D++ + +EL L+ + +L +L+ NK+D+ AL +E+ + ++L
Sbjct: 73 VIDSSHRDRVSEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEMTELLSL----- 127
Query: 61 REICC----YSISCKERDNIDI--TLQWL 83
++CC Y C R + + L WL
Sbjct: 128 HKLCCGRSWYIQGCDARSGMGLYEGLDWL 156
>gnl|CDD|184037 PRK13409, PRK13409, putative ATPase RIL; Provisional.
Length = 590
Score = 33.2 bits (77), Expect = 0.010
Identities = 17/46 (36%), Positives = 27/46 (58%), Gaps = 5/46 (10%)
Query: 23 KPQLIG-IPILVLGNKRDLPNALDEK----ELIDRMNLCAIQDREI 63
KPQ + IP + G R+L +DE+ E+++R+ L I DR+I
Sbjct: 165 KPQYVDLIPKVFKGKVRELLKKVDERGKLDEVVERLGLENILDRDI 210
>gnl|CDD|224166 COG1245, COG1245, Predicted ATPase, RNase L inhibitor (RLI) homolog
[General function prediction only].
Length = 591
Score = 32.7 bits (75), Expect = 0.013
Identities = 18/54 (33%), Positives = 31/54 (57%), Gaps = 6/54 (11%)
Query: 15 NELHALIEKPQLIG-IPILVLGNKRDLPNALDEK----ELIDRMNLCAIQDREI 63
EL A+ KPQ + IP +V G +L +DE+ E+++R+ L + DR++
Sbjct: 159 GELRAVH-KPQYVDLIPKVVKGKVGELLKKVDERGKFDEVVERLGLENVLDRDV 211
>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
Length = 369
Score = 32.1 bits (74), Expect = 0.024
Identities = 27/90 (30%), Positives = 39/90 (43%), Gaps = 24/90 (26%)
Query: 1 MVDAADTDK------LEASRNELHA----LIEKPQLIGIPILVLGNKRDLPNALDE-KEL 49
++D + D + RNEL L EKP+ I+VL NK DLP +E +EL
Sbjct: 244 VIDLSPIDGRDPIEDYQTIRNELEKYSPKLAEKPR-----IVVL-NKIDLPLDEEELEEL 297
Query: 50 IDRMNLCAIQDREICC--YSISCKERDNID 77
A+ + Y IS R+ +D
Sbjct: 298 KK-----ALAEALGWEVFYLISALTREGLD 322
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 31.3 bits (71), Expect = 0.037
Identities = 15/63 (23%), Positives = 28/63 (44%), Gaps = 4/63 (6%)
Query: 1 MVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRMNLCAIQD 60
+VD++ A P IP++V NK+DL +AL +++ + + L +
Sbjct: 98 LVDSSRPITFHAEEIIDFLTSRNP----IPVVVAINKQDLFDALPPEKIREALKLELLSV 153
Query: 61 REI 63
I
Sbjct: 154 PVI 156
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 31.5 bits (72), Expect = 0.038
Identities = 22/88 (25%), Positives = 39/88 (44%), Gaps = 15/88 (17%)
Query: 2 VDAADTD---KLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRMNLCAI 58
VDA+D + KLEA + L + IPI+++ NK DL + ++R + +
Sbjct: 279 VDASDPEILEKLEAVEDVLAEIGAD----EIPIILVLNKIDLLEDEEILAELERGSPNPV 334
Query: 59 QDREICCYSISCKERDNIDITLQWLIAH 86
IS K + +D+ + +I
Sbjct: 335 F--------ISAKTGEGLDLLRERIIEL 354
>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 = 30.4 bits (69), Expect = 0.068
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 10/54 (18%)
Query: 28 GIPILVLGNKRDLPNAL---DEKELIDRMNLCAIQDREICCYSISCKERDNIDI 78
G+PI+++GNK DL +A L ++N I +S + NID
Sbjct: 109 GVPIILVGNKIDLRDAKLKTHVAFLFAKLNGEPI-------IPLSAETGKNIDS 155
>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 = 30.5 bits (70), Expect = 0.069
Identities = 13/51 (25%), Positives = 25/51 (49%), Gaps = 7/51 (13%)
Query: 29 IPILVLGNKRDLPN--ALDEKELIDRMNLCAIQDREICCYSISCKERDNID 77
IPI+++GNK DL + + +E ++ + + S K +N+D
Sbjct: 106 IPIILVGNKSDLEDERQVSTEEA---QQFA--KENGLLFFETSAKTGENVD 151
>gnl|CDD|213203 cd03236, ABC_RNaseL_inhibitor_domain1, The ATP-binding cassette
domain 1 of RNase L inhibitor. The ABC ATPase, RNase L
inhibitor (RLI), is a key enzyme in ribosomal
biogenesis, formation of translation preinitiation
complexes, and assembly of HIV capsids. RLI s are not
transport proteins and thus cluster with a group of
soluble proteins that lack the transmembrane components
commonly found in other members of the family.
Structurally, RLIs have an N-terminal Fe-S domain and
two nucleotide binding domains which are arranged to
form two composite active sites in their interface
cleft. RLI is one of the most conserved enzymes between
archaea and eukaryotes with a sequence identity more
than 48%. The high degree of evolutionary conservation
suggests that RLI performs a central role in archaeal
and eukaryotic physiology.
Length = 255
Score = 30.4 bits (69), Expect = 0.071
Identities = 18/61 (29%), Positives = 27/61 (44%), Gaps = 5/61 (8%)
Query: 8 DKLEASRNELHALIEKPQLIG-IPILVLGNKRDLPNALDEK----ELIDRMNLCAIQDRE 62
+ +I KPQ + IP V G +L DE+ EL+D++ L + DR
Sbjct: 77 NYFTKLLEGDVKVIVKPQYVDLIPKAVKGKVGELLKKKDERGKLDELVDQLELRHVLDRN 136
Query: 63 I 63
I
Sbjct: 137 I 137
>gnl|CDD|234395 TIGR03918, GTP_HydF, [FeFe] hydrogenase H-cluster maturation GTPase
HydF. This model describes the family of the [Fe]
hydrogenase maturation protein HypF as characterized in
Chlamydomonas reinhardtii and found, in an operon with
radical SAM proteins HydE and HydG, in numerous
bacteria. It has GTPase activity, can bind an 4Fe-4S
cluster, and is essential for hydrogenase activity
[Protein fate, Protein modification and repair].
Length = 391
Score = 29.8 bits (68), Expect = 0.13
Identities = 15/58 (25%), Positives = 24/58 (41%), Gaps = 7/58 (12%)
Query: 20 LIEKPQLIGIPILVLGNKRDLPNALDEKELIDRMNLCAIQDREICCYSISCKERDNID 77
LIE+ + IP +V+ NK DL E E + + + +S + ID
Sbjct: 106 LIEELKERKIPYIVVINKIDLGEESAELEKL-------EKKFGLPPIFVSALTGEGID 156
>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 = 29.3 bits (67), Expect = 0.16
Identities = 26/89 (29%), Positives = 43/89 (48%), Gaps = 17/89 (19%)
Query: 1 MVDAADTDK----LEASRNELHA----LIEKPQLIGIPILVLGNKRDLPNALDEKELIDR 52
++D + D E RNEL A L EKP+ I+VL NK DL +A +E+ +
Sbjct: 85 VIDLSGEDDPVEDYETIRNELEAYNPGLAEKPR-----IVVL-NKIDLLDA-EERFEKLK 137
Query: 53 MNLCAIQDREICCYSISCKERDNIDITLQ 81
L ++ +++ IS + +D L+
Sbjct: 138 ELLKELKGKKVFP--ISALTGEGLDELLK 164
>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 = 29.4 bits (67), Expect = 0.17
Identities = 20/85 (23%), Positives = 36/85 (42%), Gaps = 17/85 (20%)
Query: 1 MVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRMNLCAIQD 60
+VDA ++ L+ E+ L K P++V+ NK DL + + ++ + A
Sbjct: 89 VVDA--SEGLDEEDLEILELPAK-----KPVIVVLNKSDLLSDAEGISELNGKPIIA--- 138
Query: 61 REICCYSISCKERDNIDITLQWLIA 85
IS K + ID + L+
Sbjct: 139 -------ISAKTGEGIDELKEALLE 156
>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 = 29.2 bits (66), Expect = 0.17
Identities = 10/29 (34%), Positives = 18/29 (62%), Gaps = 2/29 (6%)
Query: 17 LHALIEKPQLI--GIPILVLGNKRDLPNA 43
L LI + + IP++++GNK DL ++
Sbjct: 94 LLQLIREIKKRDGEIPVILVGNKADLLHS 122
>gnl|CDD|133342 cd04142, RRP22, Ras-related protein on chromosome 22 (RRP22)
family. RRP22 (Ras-related protein on chromosome 22)
subfamily consists of proteins that inhibit cell growth
and promote caspase-independent cell death. Unlike most
Ras proteins, RRP22 is down-regulated in many human
tumor cells due to promoter methylation. RRP22 localizes
to the nucleolus in a GTP-dependent manner, suggesting a
novel function in modulating transport of nucleolar
components. Most Ras proteins contain a lipid
modification site at the C-terminus, with a typical
sequence motif CaaX, where a = an aliphatic amino acid
and X = any amino acid. Lipid binding is essential for
membrane attachment, a key feature of most Ras proteins.
Like most Ras family proteins, RRP22 is farnesylated.
Length = 198
Score = 29.5 bits (66), Expect = 0.19
Identities = 15/51 (29%), Positives = 21/51 (41%), Gaps = 4/51 (7%)
Query: 30 PILVLGNKRDLPNALDEKELIDRMNLCAIQDREICCYSISCKERDNIDITL 80
PI+V+GNKRD R L + + C + C + N I L
Sbjct: 118 PIVVVGNKRD----QQRHRFAPRHVLSVLVRKSWKCGYLECSAKYNWHILL 164
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 29.3 bits (67), Expect = 0.22
Identities = 17/77 (22%), Positives = 31/77 (40%), Gaps = 18/77 (23%)
Query: 1 MVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRMNLCAIQD 60
++DA++ E ++E+ P++V+ NK DL +D +E +
Sbjct: 301 VLDASEPLT-----EEDDEILEEL--KDKPVIVVLNKADLTGEIDLEEENGK-------- 345
Query: 61 REICCYSISCKERDNID 77
IS K + ID
Sbjct: 346 ---PVIRISAKTGEGID 359
>gnl|CDD|179177 PRK00945, PRK00945, acetyl-CoA decarbonylase/synthase complex
subunit epsilon; Provisional.
Length = 171
Score = 28.8 bits (65), Expect = 0.25
Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 12/59 (20%)
Query: 1 MVDAADTDKLEASRNELHALIEKPQLIGI-------PILVLGNKRDLPNALDEKELIDR 52
MVD + A HA I P++ + P+LV+G LD++EL+DR
Sbjct: 1 MVDRTKPYQPTAISGPKHAKIVSPKIAAMMIKKAKRPLLVVG-----SLLLDDEELLDR 54
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 28.8 bits (64), Expect = 0.30
Identities = 14/49 (28%), Positives = 20/49 (40%), Gaps = 1/49 (2%)
Query: 10 LEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRMNLCAI 58
E + L L E +PIL++GNK DL + E I +
Sbjct: 94 DELTEEWLEELRELA-PDDVPILLVGNKIDLFDEQSSSEEILNQLNREV 141
>gnl|CDD|206666 cd01878, HflX, HflX GTPase family. HflX subfamily. A distinct
conserved domain with a glycine-rich segment N-terminal
of the GTPase domain characterizes the HflX subfamily.
The E. coli HflX has been implicated in the control of
the lambda cII repressor proteolysis, but the actual
biological functions of these GTPases remain unclear.
HflX is widespread, but not universally represented in
all three superkingdoms.
Length = 204
Score = 28.6 bits (65), Expect = 0.32
Identities = 21/88 (23%), Positives = 37/88 (42%), Gaps = 15/88 (17%)
Query: 2 VDAADTD---KLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRMNLCAI 58
VDA+D D ++E L L IPI+++ NK DL + + +E + A+
Sbjct: 128 VDASDPDREEQIETVEEVLKELGAD----DIPIILVLNKIDLLDDEELEERLRAGRPDAV 183
Query: 59 QDREICCYSISCKERDNIDITLQWLIAH 86
IS K + +D+ + +
Sbjct: 184 F--------ISAKTGEGLDLLKEAIEEL 203
>gnl|CDD|206691 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta), together with SR-alpha, forms the
heterodimeric signal recognition particle (SRP). Signal
recognition particle receptor, beta subunit (SR-beta).
SR-beta and SR-alpha form the heterodimeric signal
recognition particle (SRP or SR) receptor that binds SRP
to regulate protein translocation across the ER
membrane. Nascent polypeptide chains are synthesized
with an N-terminal hydrophobic signal sequence that
binds SRP54, a component of the SRP. SRP directs
targeting of the ribosome-nascent chain complex (RNC) to
the ER membrane via interaction with the SR, which is
localized to the ER membrane. The RNC is then
transferred to the protein-conducting channel, or
translocon, which facilitates polypeptide translation
across the ER membrane or integration into the ER
membrane. SR-beta is found only in eukaryotes; it is
believed to control the release of the signal sequence
from SRP54 upon binding of the ribosome to the
translocon. High expression of SR-beta has been observed
in human colon cancer, suggesting it may play a role in
the development of this type of cancer.
Length = 202
Score = 28.4 bits (64), Expect = 0.34
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 28 GIPILVLGNKRDLPNALDEK 47
IPIL+ NK+DL A K
Sbjct: 108 KIPILIACNKQDLFTAKPAK 127
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 28.5 bits (65), Expect = 0.38
Identities = 20/90 (22%), Positives = 37/90 (41%), Gaps = 29/90 (32%)
Query: 1 MVDAADTD------KLEASRNELHA----LIEKPQLIGIPILVLGNKRDLPNALDEKELI 50
++D + ++ E EL L+E+PQ++ V NK DLP A +
Sbjct: 243 VIDMSGSEGRDPIEDYEKINKELKLYNPRLLERPQIV-----VA-NKMDLPEAEE----- 291
Query: 51 DRMNLCAIQDR---EICCYSISCKERDNID 77
NL +++ ++ + IS +D
Sbjct: 292 ---NLEEFKEKLGPKV--FPISALTGQGLD 316
>gnl|CDD|206714 cd04147, Ras_dva, Ras - dorsal-ventral anterior localization
(Ras-dva) family. Ras-dva subfamily. Ras-dva (Ras -
dorsal-ventral anterior localization) subfamily consists
of a set of proteins characterized only in Xenopus
leavis, to date. In Xenopus Ras-dva expression is
activated by the transcription factor Otx2 and begins
during gastrulation throughout the anterior ectoderm.
Ras-dva expression is inhibited in the anterior neural
plate by factor Xanf1. Downregulation of Ras-dva results
in head development abnormalities through the inhibition
of several regulators of the anterior neural plate and
folds patterning, including Otx2, BF-1, Xag2, Pax6,
Slug, and Sox9. Downregulation of Ras-dva also
interferes with the FGF-8a signaling within the anterior
ectoderm. Most Ras proteins contain a lipid modification
site at the C-terminus, with a typical sequence motif
CaaX, where a = an aliphatic amino acid and X = any
amino acid. Lipid binding is essential for membrane
attachment, a key feature of most Ras proteins.
Length = 197
Score = 28.3 bits (63), Expect = 0.40
Identities = 18/91 (19%), Positives = 38/91 (41%), Gaps = 4/91 (4%)
Query: 3 DAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRMNLCAIQ-DR 61
D + E + ++E + +PI+V+GNK D L E+++ L ++ D
Sbjct: 79 SVDDPESFEEVKRLREEILEVKEDKFVPIVVVGNKIDS---LAERQVEAADALSTVELDW 135
Query: 62 EICCYSISCKERDNIDITLQWLIAHSKSHTR 92
S K+ +N+ + L+ + +
Sbjct: 136 NNGFVEASAKDNENVTEVFKELLQQANLPSW 166
>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 = 27.1 bits (61), Expect = 0.88
Identities = 18/71 (25%), Positives = 28/71 (39%), Gaps = 20/71 (28%)
Query: 14 RNELHALIEKPQLIGIPILVLGNKRDLPN-----ALDEKELIDRMNLCAIQDREICC--Y 66
R ++ + +K +PI+++GNK DL N + + L E C
Sbjct: 93 REQILRVKDKED---VPIVLVGNKCDLENERQVSTEEGEALA----------EEWGCPFL 139
Query: 67 SISCKERDNID 77
S K NID
Sbjct: 140 ETSAKTNINID 150
>gnl|CDD|223606 COG0532, InfB, Translation initiation factor 2 (IF-2; GTPase)
[Translation, ribosomal structure and biogenesis].
Length = 509
Score = 27.5 bits (62), Expect = 0.95
Identities = 17/68 (25%), Positives = 26/68 (38%), Gaps = 14/68 (20%)
Query: 23 KPQLI---------GIPILVLGNKRDLPNALDEKELIDRMNLCAIQ----DREICCYSIS 69
PQ I G+PI+V NK D P A +K + + ++ +S
Sbjct: 93 MPQTIEAINHAKAAGVPIVVAINKIDKPEANPDKVKQELQEY-GLVPEEWGGDVIFVPVS 151
Query: 70 CKERDNID 77
K + ID
Sbjct: 152 AKTGEGID 159
>gnl|CDD|237045 PRK12296, obgE, GTPase CgtA; Reviewed.
Length = 500
Score = 27.1 bits (61), Expect = 1.1
Identities = 23/86 (26%), Positives = 37/86 (43%), Gaps = 26/86 (30%)
Query: 5 ADTDKLEASRNELHA-------------LIEKPQLIGIPILVLGNKRDLPNALDEKELID 51
+D D LEA EL A L E+P+L+ VL NK D+P+A + E +
Sbjct: 257 SDIDALEA---ELAAYAPALDGDLGLGDLAERPRLV-----VL-NKIDVPDARELAEFVR 307
Query: 52 RMNLCAIQDREICCYSISCKERDNID 77
++ R + +S R+ +
Sbjct: 308 PE----LEARGWPVFEVSAASREGLR 329
>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 = 27.1 bits (60), Expect = 1.1
Identities = 22/72 (30%), Positives = 37/72 (51%), Gaps = 8/72 (11%)
Query: 11 EASRNELHALIEKPQLI----GIPILVLGNKRDLPNALDEKELIDRMNLCAIQD-REICC 65
EAS NEL L E+ I +P++++GNK DL D++++ + Q +
Sbjct: 85 EASLNELGELREQVLRIKDSDNVPMVLVGNKADL---EDDRQVSREDGVSLSQQWGNVPF 141
Query: 66 YSISCKERDNID 77
Y S ++R N+D
Sbjct: 142 YETSARKRTNVD 153
>gnl|CDD|206747 cd01854, YjeQ_EngC, Ribosomal interacting GTPase YjeQ/EngC, a
circularly permuted subfamily of the Ras GTPases. YjeQ
(YloQ in Bacillus subtilis) is a ribosomal small
subunit-dependent GTPase; hence also known as RsgA.
YjeQ is a late-stage ribosomal biogenesis factor
involved in the 30S subunit maturation, and it
represents a protein family whose members are broadly
conserved in bacteria and have been shown to be
essential to the growth of E. coli and B. subtilis.
Proteins of the YjeQ family contain all sequence motifs
typical of the vast class of P-loop-containing GTPases,
but show a circular permutation, with a G4-G1-G3
pattern of motifs as opposed to the regular G1-G3-G4
pattern seen in most GTPases. All YjeQ family proteins
display a unique domain architecture, which includes an
N-terminal OB-fold RNA-binding domain, the central
permuted GTPase domain, and a zinc knuckle-like
C-terminal cysteine domain.
Length = 211
Score = 27.0 bits (61), Expect = 1.3
Identities = 13/54 (24%), Positives = 26/54 (48%), Gaps = 6/54 (11%)
Query: 30 PILVLGNKRDLPNALDEKELIDRMNLCAIQDREICCYSISCKERDNIDITLQWL 83
P++VL NK DL + + +EL++ + ++S K + +D + L
Sbjct: 36 PVIVL-NKADLVDDEELEELLEI-----YEKLGYPVLAVSAKTGEGLDELRELL 83
>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 = 26.9 bits (59), Expect = 1.4
Identities = 10/35 (28%), Positives = 18/35 (51%)
Query: 28 GIPILVLGNKRDLPNALDEKELIDRMNLCAIQDRE 62
+PIL++G K+DL N D + + I ++
Sbjct: 107 NVPILLVGTKKDLRNDADTLKKLKEQGQAPITPQQ 141
>gnl|CDD|206726 cd04163, Era, E. coli Ras-like protein (Era) is a multifunctional
GTPase. Era (E. coli Ras-like protein) is a
multifunctional GTPase found in all bacteria except some
eubacteria. It binds to the 16S ribosomal RNA (rRNA) of
the 30S subunit and appears to play a role in the
assembly of the 30S subunit, possibly by chaperoning the
16S rRNA. It also contacts several assembly elements of
the 30S subunit. Era couples cell growth with
cytokinesis and plays a role in cell division and energy
metabolism. Homologs have also been found in eukaryotes.
Era contains two domains: the N-terminal GTPase domain
and a C-terminal domain KH domain that is critical for
RNA binding. Both domains are important for Era
function. Era is functionally able to compensate for
deletion of RbfA, a cold-shock adaptation protein that
is required for efficient processing of the 16S rRNA.
Length = 168
Score = 26.3 bits (59), Expect = 1.8
Identities = 18/87 (20%), Positives = 42/87 (48%), Gaps = 9/87 (10%)
Query: 1 MVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDL-PNALDEKELIDRMNLCAIQ 59
+VDA++ ++E + P++++ NK DL + D L++++
Sbjct: 89 VVDASEWIG-----EGDEFILELLKKSKTPVILVLNKIDLVKDKEDLLPLLEKLKE-LHP 142
Query: 60 DREICCYSISCKERDNIDITLQWLIAH 86
EI + IS + +N+D L++++ +
Sbjct: 143 FAEI--FPISALKGENVDELLEYIVEY 167
>gnl|CDD|221202 pfam11745, DUF3304, Protein of unknown function (DUF3304). This
is a family of bacterial proteins of unknown function.
Length = 119
Score = 26.1 bits (58), Expect = 2.2
Identities = 7/21 (33%), Positives = 13/21 (61%)
Query: 62 EICCYSISCKERDNIDITLQW 82
+CCYS+ K R + + ++W
Sbjct: 52 TVCCYSVPRKWRPGLTVKVEW 72
>gnl|CDD|216078 pfam00716, Peptidase_S21, Assemblin (Peptidase family S21).
Length = 326
Score = 26.2 bits (58), Expect = 2.5
Identities = 16/59 (27%), Positives = 23/59 (38%), Gaps = 12/59 (20%)
Query: 30 PILVLGNKRDLPNALDEKELIDRMNLCAIQDRE--ICCYSISCKERDNIDITLQWLIAH 86
P L L ++R PN + + LCA+ R + Y TL+W IA
Sbjct: 90 PSLSLSSRRLAPNEAPDTTFFAHVALCALGRRRGTVAVY----------GRTLEWAIAP 138
>gnl|CDD|183208 PRK11572, PRK11572, copper homeostasis protein CutC; Provisional.
Length = 248
Score = 26.1 bits (58), Expect = 2.7
Identities = 7/9 (77%), Positives = 8/9 (88%)
Query: 62 EICCYSISC 70
EICCYS+ C
Sbjct: 5 EICCYSMEC 13
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 26.1 bits (58), Expect = 2.9
Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 10/49 (20%)
Query: 29 IPILVLGNKRDLPNALDEKELIDRMNLCAIQDREICCYSISCKERDNID 77
P L + NK DLP E ++R+ R+ IS K+ N+D
Sbjct: 240 KPALYVVNKIDLP----GLEELERL------ARKPNSVPISAKKGINLD 278
>gnl|CDD|206688 cd04101, RabL4, Rab GTPase-like family 4 (Rab-like4). RabL4
(Rab-like4) subfamily. RabL4s are novel proteins that
have high sequence similarity with Rab family members,
but display features that are distinct from Rabs, and
have been termed Rab-like. As in other Rab-like
proteins, RabL4 lacks a prenylation site at the
C-terminus. The specific function of RabL4 remains
unknown.
Length = 167
Score = 26.0 bits (57), Expect = 2.9
Identities = 15/86 (17%), Positives = 28/86 (32%), Gaps = 3/86 (3%)
Query: 1 MVDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRMNLCAIQD 60
+ D + ++ + + P +++GNK DL D +E+ Q
Sbjct: 83 VYDVTNEVSFNNCSRWINRVRTHSHGLHTPGVLVGNKCDL---TDRREVDAAQAQALAQA 139
Query: 61 REICCYSISCKERDNIDITLQWLIAH 86
+ Y S KE + L
Sbjct: 140 NTLKFYETSAKEGVGYEAPFLSLARA 165
>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 = 25.5 bits (57), Expect = 4.1
Identities = 13/62 (20%), Positives = 27/62 (43%), Gaps = 13/62 (20%)
Query: 28 GIPILVLGNKRDLPN-----ALDEKELIDRMNLCAIQDREICCYSISCKERDNIDITLQW 82
+PI+++GNK DL + + + L + L ++ S K +N++ +
Sbjct: 104 NVPIVLVGNKCDLEDQRVVSTEEGEALAKELGLPFME--------TSAKTNENVEEAFEE 155
Query: 83 LI 84
L
Sbjct: 156 LA 157
>gnl|CDD|214541 smart00173, RAS, Ras subfamily of RAS small GTPases. Similar in
fold and function to the bacterial EF-Tu GTPase. p21Ras
couples receptor Tyr kinases and G protein receptors to
protein kinase cascades.
Length = 164
Score = 25.2 bits (56), Expect = 5.1
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 13/54 (24%)
Query: 29 IPILVLGNKRDLPN----ALDE-KELIDRMNLCAIQDREICCYSISCKERDNID 77
+PI+++GNK DL + + +E KEL + C S KER N+D
Sbjct: 106 VPIVLVGNKCDLESERVVSTEEGKELARQWG-CPF-------LETSAKERVNVD 151
>gnl|CDD|235117 PRK03343, PRK03343, transaldolase; Validated.
Length = 368
Score = 25.2 bits (56), Expect = 6.0
Identities = 11/28 (39%), Positives = 15/28 (53%), Gaps = 1/28 (3%)
Query: 4 AADTDKLEASRNELHALIEKPQL-IGIP 30
A DT+ A L A +++P L I IP
Sbjct: 115 AHDTEATIAEARRLWAAVDRPNLMIKIP 142
>gnl|CDD|184290 PRK13738, PRK13738, conjugal transfer pilus assembly protein TraW;
Provisional.
Length = 209
Score = 25.1 bits (55), Expect = 6.1
Identities = 11/51 (21%), Positives = 22/51 (43%), Gaps = 5/51 (9%)
Query: 2 VDAADTDKLEASRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDR 52
++ D ++ + + P L ILV G+ ++ ALD + D+
Sbjct: 126 INGDDPAQVAWMKRQT-----PPTLESKIILVQGSIPEMSKALDSRIYFDQ 171
>gnl|CDD|206686 cd01899, Ygr210, Ygr210 GTPase. Ygr210 is a member of Obg-like
family and present in archaea and fungi. They are
characterized by a distinct glycine-rich motif
immediately following the Walker B motif. The Ygr210 and
YyaF/YchF subfamilies appear to form one major branch of
the Obg-like family. Among eukaryotes, the Ygr210
subfamily is represented only in fungi. These fungal
proteins form a tight cluster with their archaeal
orthologs, which suggests the possibility of horizontal
transfer from archaea to fungi.
Length = 318
Score = 24.9 bits (55), Expect = 6.6
Identities = 8/41 (19%), Positives = 18/41 (43%)
Query: 13 SRNELHALIEKPQLIGIPILVLGNKRDLPNALDEKELIDRM 53
+L L + + P+++ NK D+P+A + +
Sbjct: 199 DDEDLLRLARELRKRRKPMVIAANKADIPDAEENISKLRLK 239
>gnl|CDD|232962 TIGR00409, proS_fam_II, prolyl-tRNA synthetase, family II.
Prolyl-tRNA synthetase is a class II tRNA synthetase and
is recognized by pfam model tRNA-synt_2b, which
recognizes tRNA synthetases for Gly, His, Ser, and Pro.
The prolyl-tRNA synthetases are divided into two widely
divergent groups. This group includes enzymes from
Escherichia coli, Bacillus subtilis, Aquifex aeolicus,
the spirochete Treponema pallidum, Synechocystis
PCC6803, and one of the two prolyL-tRNA synthetases of
Saccharomyces cerevisiae. The other group includes the
Pro-specific domain of a human multifunctional tRNA
ligase and the prolyl-tRNA synthetases from the Archaea,
the Mycoplasmas, and the spirochete Borrelia burgdorferi
[Protein synthesis, tRNA aminoacylation].
Length = 568
Score = 25.2 bits (55), Expect = 6.6
Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 2/31 (6%)
Query: 25 QLIGIPILVLGNKRDLPNALDEKELIDRMNL 55
+LIGIP+ V+ K++L N E E+ R N
Sbjct: 523 ELIGIPLRVVVGKKNLDN--GEIEVKKRRNG 551
>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 = 24.7 bits (54), Expect = 6.8
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 28 GIPILVLGNKRDLPNALDEKELIDRMN 54
+PI+++GNK+DL N + +M
Sbjct: 105 NVPIILVGNKKDLRNDEHTIRELAKMK 131
>gnl|CDD|223882 COG0812, MurB, UDP-N-acetylmuramate dehydrogenase [Cell envelope
biogenesis, outer membrane].
Length = 291
Score = 24.9 bits (55), Expect = 7.0
Identities = 7/27 (25%), Positives = 13/27 (48%)
Query: 10 LEASRNELHALIEKPQLIGIPILVLGN 36
EL A ++ + +P+L+LG
Sbjct: 26 EPRDIEELKAALKYAKAEDLPVLILGG 52
>gnl|CDD|178620 PLN03071, PLN03071, GTP-binding nuclear protein Ran; Provisional.
Length = 219
Score = 24.7 bits (54), Expect = 7.0
Identities = 8/14 (57%), Positives = 11/14 (78%)
Query: 29 IPILVLGNKRDLPN 42
IPI++ GNK D+ N
Sbjct: 118 IPIVLCGNKVDVKN 131
>gnl|CDD|213834 TIGR03597, GTPase_YqeH, ribosome biogenesis GTPase YqeH. This
family describes YqeH, a member of a larger family of
GTPases involved in ribosome biogenesis. Like YqlF, it
shows a cyclical permutation relative to GTPases EngA
(in which the GTPase domain is duplicated), Era, and
others. Members of this protein family are found in a
relatively small number of bacterial species, including
Bacillus subtilis but not Escherichia coli [Protein
synthesis, Other].
Length = 360
Score = 24.9 bits (55), Expect = 7.2
Identities = 9/26 (34%), Positives = 18/26 (69%), Gaps = 1/26 (3%)
Query: 30 PILVLGNKRD-LPNALDEKELIDRMN 54
P+L++GNK D LP +++ ++ + M
Sbjct: 92 PVLLVGNKIDLLPKSVNLSKIKEWMK 117
>gnl|CDD|227698 COG5411, COG5411, Phosphatidylinositol 5-phosphate phosphatase
[Signal transduction mechanisms].
Length = 460
Score = 24.7 bits (54), Expect = 7.5
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 11 EASRNELHALIEKPQLIGIPILVLGNKRDLPN 42
A +E ++L+ PQL GI + V +LP
Sbjct: 102 GAQSDEKYSLLRSPQLGGILLRVFSLATNLPV 133
>gnl|CDD|224568 COG1654, BirA, Biotin operon repressor [Transcription].
Length = 79
Score = 24.2 bits (53), Expect = 7.6
Identities = 7/31 (22%), Positives = 15/31 (48%)
Query: 7 TDKLEASRNELHALIEKPQLIGIPILVLGNK 37
++L SR + I++ + G+ I + K
Sbjct: 26 AEELGISRTAVWKHIQQLREEGVDIESVRGK 56
>gnl|CDD|236584 PRK09602, PRK09602, translation-associated GTPase; Reviewed.
Length = 396
Score = 24.8 bits (55), Expect = 7.9
Identities = 10/24 (41%), Positives = 16/24 (66%), Gaps = 3/24 (12%)
Query: 30 PILVLGNKRDLPNALDEKELIDRM 53
P+++ NK DLP A +E I+R+
Sbjct: 219 PMVIAANKADLPPA---EENIERL 239
>gnl|CDD|173825 cd00691, ascorbate_peroxidase, Ascorbate peroxidases and
cytochrome C peroxidases. Ascorbate peroxidases are a
subgroup of heme-dependent peroxidases of the plant
superfamily that share a heme prosthetic group and
catalyze a multistep oxidative reaction involving
hydrogen peroxide as the electron acceptor. Along with
related catalase-peroxidases, ascorbate peroxidases
belong to class I of the plant superfamily. Ascorbate
peroxidases are found in the chloroplasts and/or
cytosol of algae and plants, where they have been shown
to control the concentration of lethal hydrogen
peroxide molecules. The yeast cytochrome c peroxidase
is a divergent member of the family; it forms a complex
with cytochrome c to catalyze the reduction of hydrogen
peroxide to water.
Length = 253
Score = 24.9 bits (55), Expect = 8.2
Identities = 15/33 (45%), Positives = 19/33 (57%), Gaps = 3/33 (9%)
Query: 2 VDAADTDK-LEASRNELHALIEKPQLIGIPILV 33
V AA K LEA+RN++ LI+ PILV
Sbjct: 4 VSAAYAAKDLEAARNDIAKLIDDKNC--APILV 34
>gnl|CDD|197466 smart00010, small_GTPase, Small GTPase of the Ras superfamily;
ill-defined subfamily. SMART predicts Ras-like small
GTPases of the ARF, RAB, RAN, RAS, and SAR subfamilies.
Others that could not be classified in this way are
predicted to be members of the small GTPase superfamily
without predictions of the subfamily.
Length = 166
Score = 24.4 bits (54), Expect = 8.4
Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 13/54 (24%)
Query: 29 IPILVLGNKRDLPN----ALDE-KELIDRMNLCAIQDREICCYSISCKERDNID 77
+PI+++GNK DL N + +E KEL + C S KER N+D
Sbjct: 108 VPIVLVGNKCDLENERVVSTEEGKELARQWG-CPF-------LETSAKERINVD 153
>gnl|CDD|239275 cd02977, ArsC_family, Arsenate Reductase (ArsC) family; composed of
TRX-fold arsenic reductases and similar proteins
including the transcriptional regulator, Spx. ArsC
catalyzes the reduction of arsenate [As(V)] to arsenite
[As(III)], using reducing equivalents derived from
glutathione (GSH) via glutaredoxin (GRX), through a
single catalytic cysteine. This family of predominantly
bacterial enzymes is unrelated to two other families of
arsenate reductases which show similarity to
low-molecular-weight acid phosphatases and
phosphotyrosyl phosphatases. Spx is a general regulator
that exerts negative and positive control over
transcription initiation by binding to the C-terminal
domain of the alpha subunit of RNA polymerase.
Length = 105
Score = 24.0 bits (53), Expect = 8.8
Identities = 14/36 (38%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 6 DTDKLEASRNE-LHALIEKPQLIGIPILVLGNKRDL 40
DK E S E L + E P+LI PI+V G++ +
Sbjct: 68 LADKDELSDEEALELMAEHPKLIKRPIVVDGDRLLV 103
>gnl|CDD|105955 PRK12820, PRK12820, bifunctional aspartyl-tRNA
synthetase/aspartyl/glutamyl-tRNA amidotransferase
subunit C; Provisional.
Length = 706
Score = 24.9 bits (54), Expect = 8.8
Identities = 10/34 (29%), Positives = 21/34 (61%)
Query: 21 IEKPQLIGIPILVLGNKRDLPNALDEKELIDRMN 54
+ + QL + +L LG+ LP ++++LID ++
Sbjct: 588 VAQEQLAELGLLDLGDADQLPGDAEKEDLIDHLS 621
>gnl|CDD|182646 PRK10683, PRK10683, putrescine transporter subunit: membrane
component of ABC superfamily; Provisional.
Length = 317
Score = 24.7 bits (54), Expect = 9.4
Identities = 8/13 (61%), Positives = 9/13 (69%)
Query: 80 LQWLIAHSKSHTR 92
L W +AHSK TR
Sbjct: 120 LAWAVAHSKPSTR 132
>gnl|CDD|223721 COG0648, Nfo, Endonuclease IV [DNA replication, recombination, and
repair].
Length = 280
Score = 24.5 bits (54), Expect = 9.7
Identities = 8/31 (25%), Positives = 17/31 (54%)
Query: 4 AADTDKLEASRNELHALIEKPQLIGIPILVL 34
+ + +K+E S L I++ + +G +LV
Sbjct: 76 SPEKEKVEKSIERLIDEIDRCEQLGAKLLVF 106
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
0.320 0.136 0.404
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: 4,610,061
Number of extensions: 380281
Number of successful extensions: 448
Number of sequences better than 10.0: 1
Number of HSP's gapped: 442
Number of HSP's successfully gapped: 95
Length of query: 92
Length of database: 10,937,602
Length adjustment: 59
Effective length of query: 33
Effective length of database: 8,320,716
Effective search space: 274583628
Effective search space used: 274583628
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.5 bits)