RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15732
(550 letters)
>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 = 137 bits (345), Expect = 5e-38
Identities = 59/95 (62%), Positives = 78/95 (82%)
Query: 456 DSADKERLPEALAELTKLIAEKELKDAALLLLANKQDIPGCETVESITEAFDLYKLCCGR 515
DS+ ++R+ EA +EL KL+ EKEL+DA LL+ ANKQD+ G +VE +TE L+KLCCGR
Sbjct: 75 DSSHRDRVSEAHSELAKLLTEKELRDALLLIFANKQDVAGALSVEEMTELLSLHKLCCGR 134
Query: 516 SWHIQACNAQSGEGLHEGLDWLSRQLIAAGVNDMS 550
SW+IQ C+A+SG GL+EGLDWLSRQL+AAGV D++
Sbjct: 135 SWYIQGCDARSGMGLYEGLDWLSRQLVAAGVLDVA 169
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 113 bits (286), Expect = 2e-29
Identities = 46/86 (53%), Positives = 59/86 (68%), Gaps = 1/86 (1%)
Query: 456 DSADKERLPEALAELTKLIAEKELKDAALLLLANKQDIPGCETVESITEAFDLYKLCCGR 515
DSAD++R+ EA EL L+ E+EL DA LL+LANKQD+PG + I E L++L R
Sbjct: 90 DSADRDRIEEAKEELHALLNEEELADAPLLILANKQDLPGAMSEAEIRELLGLHEL-KDR 148
Query: 516 SWHIQACNAQSGEGLHEGLDWLSRQL 541
W IQ C+A +GEGL EGLDWLS +
Sbjct: 149 PWEIQGCSAVTGEGLDEGLDWLSNYI 174
Score = 29.9 bits (68), Expect = 2.0
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 431 FTKDNRVHIGPKMEMRVVTLGLDSA 455
F G EMR++ LGLD+A
Sbjct: 1 FLSILAKLFGWNKEMRILILGLDNA 25
>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 = 111 bits (280), Expect = 1e-28
Identities = 47/85 (55%), Positives = 58/85 (68%), Gaps = 1/85 (1%)
Query: 456 DSADKERLPEALAELTKLIAEKELKDAALLLLANKQDIPGCETVESITEAFDLYKLCCGR 515
DS+D+ER+ EA EL KL+ E+ELK A LL+LANKQD+PG T + E L GR
Sbjct: 75 DSSDRERIEEAKNELHKLLNEEELKGAPLLILANKQDLPGALTESELIELLGLES-IKGR 133
Query: 516 SWHIQACNAQSGEGLHEGLDWLSRQ 540
WHIQ C+A +G+GL EGLDWL Q
Sbjct: 134 RWHIQPCSAVTGDGLDEGLDWLIEQ 158
>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 = 105 bits (265), Expect = 8e-27
Identities = 42/85 (49%), Positives = 58/85 (68%), Gaps = 1/85 (1%)
Query: 456 DSADKERLPEALAELTKLIAEKELKDAALLLLANKQDIPGCETVESITEAFDLYKLCCGR 515
DS D+ER+ EA EL +++ E EL+DA LL+ ANKQD+P + +T+ L+ L R
Sbjct: 76 DSNDRERIGEAREELQRMLNEDELRDAVLLVFANKQDLPNAMSAAEVTDKLGLHSL-RNR 134
Query: 516 SWHIQACNAQSGEGLHEGLDWLSRQ 540
+W+IQA A SG+GL+EGLDWLS
Sbjct: 135 NWYIQATCATSGDGLYEGLDWLSNN 159
>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 = 101 bits (253), Expect = 5e-25
Identities = 38/85 (44%), Positives = 58/85 (68%), Gaps = 1/85 (1%)
Query: 456 DSADKERLPEALAELTKLIAEKELKDAALLLLANKQDIPGCETVESITEAFDLYKLCCGR 515
DSAD++R EA EL +L+ E++L +L+ ANKQD+ E + EA +L+ + R
Sbjct: 91 DSADRKRFEEAGQELVELLEEEKLAGVPVLVFANKQDLLTAAPAEEVAEALNLHDI-RDR 149
Query: 516 SWHIQACNAQSGEGLHEGLDWLSRQ 540
SWHIQAC+A++GEGL EG++W+ +
Sbjct: 150 SWHIQACSAKTGEGLQEGMNWVCKN 174
>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 = 100 bits (250), Expect = 1e-24
Identities = 41/82 (50%), Positives = 55/82 (67%), Gaps = 1/82 (1%)
Query: 456 DSADKERLPEALAELTKLIAEKELKDAALLLLANKQDIPGCETVESITEAFDLYKLCCGR 515
DS D+ERLP EL K++A ++L+ A LL+LANKQD+ G T I+E+ L +
Sbjct: 91 DSTDRERLPLTKEELYKMLAHEDLRKAVLLVLANKQDLKGAMTPAEISESLGLTSI-RDH 149
Query: 516 SWHIQACNAQSGEGLHEGLDWL 537
+WHIQ C A +GEGL EGLDW+
Sbjct: 150 TWHIQGCCALTGEGLPEGLDWI 171
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 99 bits (249), Expect = 2e-24
Identities = 39/86 (45%), Positives = 59/86 (68%), Gaps = 1/86 (1%)
Query: 456 DSADKERLPEALAELTKLIAEKELKDAALLLLANKQDIPGCETVESITEAFDLYKLCCGR 515
DS D+ER+ +A EL ++++E EL+DA LL+ ANKQD+P + +TE L+ + R
Sbjct: 93 DSNDRERIGDAREELERMLSEDELRDAVLLVFANKQDLPNAMSTTEVTEKLGLHSV-RQR 151
Query: 516 SWHIQACNAQSGEGLHEGLDWLSRQL 541
+W+IQ C A + +GL+EGLDWLS +
Sbjct: 152 NWYIQGCCATTAQGLYEGLDWLSANI 177
>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 = 95.6 bits (238), Expect = 5e-23
Identities = 38/83 (45%), Positives = 56/83 (67%), Gaps = 1/83 (1%)
Query: 456 DSADKERLPEALAELTKLIAEKELKDAALLLLANKQDIPGCETVESITEAFDLYKLCCGR 515
DSAD++R+ EA EL ++I ++E++DA LL+ ANKQD+P I E L ++ R
Sbjct: 85 DSADRDRIDEARQELHRIINDREMRDALLLVFANKQDLPDAMKPHEIQEKLGLTRI-RDR 143
Query: 516 SWHIQACNAQSGEGLHEGLDWLS 538
+W++Q A SG+GL+EGL WLS
Sbjct: 144 NWYVQPSCATSGDGLYEGLTWLS 166
>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 = 95.2 bits (237), Expect = 5e-23
Identities = 36/79 (45%), Positives = 50/79 (63%)
Query: 456 DSADKERLPEALAELTKLIAEKELKDAALLLLANKQDIPGCETVESITEAFDLYKLCCGR 515
DS+D+ RL E+ EL ++ + +K ++LLANKQD+PG T E IT F L K C R
Sbjct: 76 DSSDEARLDESQKELKHILKNEHIKGVPVVLLANKQDLPGALTAEEITRRFKLKKYCSDR 135
Query: 516 SWHIQACNAQSGEGLHEGL 534
W++Q C+A +GEGL E
Sbjct: 136 DWYVQPCSAVTGEGLAEAF 154
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 95.8 bits (238), Expect = 6e-23
Identities = 42/86 (48%), Positives = 57/86 (66%), Gaps = 1/86 (1%)
Query: 456 DSADKERLPEALAELTKLIAEKELKDAALLLLANKQDIPGCETVESITEAFDLYKLCCGR 515
DS D++R+ EA EL +++ E EL+DA LL+ ANKQD+P IT+ L+ L R
Sbjct: 93 DSNDRDRVVEARDELHRMLNEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSL-RQR 151
Query: 516 SWHIQACNAQSGEGLHEGLDWLSRQL 541
W+IQ+ A SGEGL+EGLDWLS +
Sbjct: 152 HWYIQSTCATSGEGLYEGLDWLSNNI 177
>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 = 94.6 bits (235), Expect = 2e-22
Identities = 40/86 (46%), Positives = 56/86 (65%), Gaps = 1/86 (1%)
Query: 456 DSADKERLPEALAELTKLIAEKELKDAALLLLANKQDIPGCETVESITEAFDLYKLCCGR 515
DS D++R+ EA EL +++ E EL+DA +L+ ANKQD+P ITE L+ + R
Sbjct: 89 DSNDRDRIDEAREELHRMLNEDELRDAVILVFANKQDLPDAMKAAEITEKLGLHSI-RDR 147
Query: 516 SWHIQACNAQSGEGLHEGLDWLSRQL 541
+W+IQ A SG+GL+EGL WLS L
Sbjct: 148 NWYIQPTCATSGDGLYEGLTWLSNNL 173
>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 = 94.0 bits (234), Expect = 2e-22
Identities = 38/85 (44%), Positives = 53/85 (62%), Gaps = 1/85 (1%)
Query: 456 DSADKERLPEALAELTKLIAEKELKDAALLLLANKQDIPGCETVESITEAFDLYKLCCGR 515
DS D++RL + +EL ++ E+ELKDA LL+ ANKQD+PG + + E L +L R
Sbjct: 75 DSTDRDRLGISKSELHAMLEEEELKDAVLLVFANKQDMPGALSEAEVAEKLGLSEL-KDR 133
Query: 516 SWHIQACNAQSGEGLHEGLDWLSRQ 540
+W I +A GEGL EG+DWL
Sbjct: 134 TWQIFKTSATKGEGLDEGMDWLVNT 158
>gnl|CDD|206720 cd04154, Arl2, Arf-like 2 (Arl2) GTPase. Arl2 (Arf-like 2) GTPases
are members of the Arf family that bind GDP and GTP with
very low affinity. Unlike most Arf family proteins, Arl2
is not myristoylated at its N-terminal helix. The
protein PDE-delta, first identified in photoreceptor rod
cells, binds specifically to Arl2 and is structurally
very similar to RhoGDI. Despite the high structural
similarity between Arl2 and Rho proteins and between
PDE-delta and RhoGDI, the interactions between the
GTPases and their effectors are very different. In its
GTP bound form, Arl2 interacts with the protein Binder
of Arl2 (BART), and the complex is believed to play a
role in mitochondrial adenine nucleotide transport. In
its GDP bound form, Arl2 interacts with tubulin- folding
Cofactor D; this interaction is believed to play a role
in regulation of microtubule dynamics that impact the
cytoskeleton, cell division, and cytokinesis.
Length = 173
Score = 84.7 bits (210), Expect = 4e-19
Identities = 36/82 (43%), Positives = 50/82 (60%), Gaps = 1/82 (1%)
Query: 456 DSADKERLPEALAELTKLIAEKELKDAALLLLANKQDIPGCETVESITEAFDLYKLCCGR 515
DS+D+ RL + EL KL+ E+ L A LL+ ANKQD+PG + E I E +L +
Sbjct: 90 DSSDRARLEDCKRELQKLLVEERLAGATLLIFANKQDLPGALSPEEIREVLELDSI-KSH 148
Query: 516 SWHIQACNAQSGEGLHEGLDWL 537
W I C+A +GE L +G+DWL
Sbjct: 149 HWRIFGCSAVTGENLLDGIDWL 170
>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 = 81.6 bits (202), Expect = 4e-18
Identities = 34/85 (40%), Positives = 48/85 (56%), Gaps = 1/85 (1%)
Query: 456 DSADKERLPEALAELTKLIAEKELKDAALLLLANKQDIPGCETVESITEAFDLYKLCCG- 514
DS D+ER E+ + K+I + L+ LL+LANKQD+P +V I E FD G
Sbjct: 83 DSTDRERFNESKSAFEKVINNEALEGVPLLVLANKQDLPDALSVAEIKEVFDDCIALIGR 142
Query: 515 RSWHIQACNAQSGEGLHEGLDWLSR 539
R +Q +A GEG+ EG++WL
Sbjct: 143 RDCLVQPVSALEGEGVEEGIEWLVD 167
>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 = 72.1 bits (177), Expect = 8e-15
Identities = 34/87 (39%), Positives = 48/87 (55%), Gaps = 3/87 (3%)
Query: 456 DSADKERLPEALAELTKLIAEKELK--DAALLLLANKQDIPGCETVESITEAFDLYKLCC 513
DS+D+ R+ A EL L+ ++K +L ANK D+P T IT+ L +
Sbjct: 77 DSSDRLRMVVAKDELELLLNHPDIKHRRIPILFYANKMDLPDALTAVKITQLLCL-ENIK 135
Query: 514 GRSWHIQACNAQSGEGLHEGLDWLSRQ 540
+ WHI A +A +GEGL EG+DWL Q
Sbjct: 136 DKPWHIFASSALTGEGLDEGVDWLQAQ 162
>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 = 69.4 bits (170), Expect = 1e-13
Identities = 34/87 (39%), Positives = 48/87 (55%)
Query: 456 DSADKERLPEALAELTKLIAEKELKDAALLLLANKQDIPGCETVESITEAFDLYKLCCGR 515
DS D ER+ EA EL K+ E + +L+LANKQD+P V + + L++L
Sbjct: 84 DSVDVERMEEAKTELHKITKFSENQGVPVLVLANKQDLPNALPVSEVEKLLALHELSSST 143
Query: 516 SWHIQACNAQSGEGLHEGLDWLSRQLI 542
WH+Q A GEGL EGL+ L ++
Sbjct: 144 PWHVQPACAIIGEGLQEGLEKLYEMIL 170
>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 = 2e-10
Identities = 33/97 (34%), Positives = 47/97 (48%), Gaps = 11/97 (11%)
Query: 456 DSADKERLPEALAELTKLIAEKELKDAALLLLANKQDIPGCETVESITEAFDLYKLCCG- 514
D+AD ER E+ EL L+ ++EL + +L+L NK D PG + E + EA LY G
Sbjct: 95 DAADPERFQESKEELDSLLNDEELANVPILILGNKIDKPGAVSEEELREALGLYGTTTGK 154
Query: 515 ----------RSWHIQACNAQSGEGLHEGLDWLSRQL 541
R + C+ +G EG WLS+ L
Sbjct: 155 GGVSLKVSNIRPVEVFMCSVVKRQGYGEGFRWLSQYL 191
>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 = 55.5 bits (134), Expect = 3e-09
Identities = 28/69 (40%), Positives = 40/69 (57%), Gaps = 2/69 (2%)
Query: 456 DSADKERLPEALAELTKLIAEKELKDAALLLLANKQDIPGCETVESITEAFDLYKLCCGR 515
DSAD ERLP A EL +L+ D L++LANKQD+P +V+ I + +L + GR
Sbjct: 76 DSADSERLPLARQELHQLLQHP--PDLPLVVLANKQDLPAARSVQEIHKELELEPIARGR 133
Query: 516 SWHIQACNA 524
W +Q +
Sbjct: 134 RWILQGTSL 142
>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 = 55.7 bits (134), Expect = 5e-09
Identities = 28/90 (31%), Positives = 41/90 (45%), Gaps = 6/90 (6%)
Query: 456 DSADKERLPEALAELTKLIAEKELKDAALLLLANKQDIPGCETVESITEAFDLYKLCCG- 514
D+ DKER E+ EL L++++EL L+L NK D P + + + A L G
Sbjct: 93 DAYDKERFAESKRELDALLSDEELATVPFLILGNKIDAPYAASEDELRYALGLTNTTTGK 152
Query: 515 -----RSWHIQACNAQSGEGLHEGLDWLSR 539
R + C+ G EG WLS+
Sbjct: 153 GKVGVRPVEVFMCSVVRRMGYGEGFKWLSQ 182
>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 = 52.7 bits (127), Expect = 3e-08
Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 1/84 (1%)
Query: 456 DSADKERLPEALAELTKLIAEKELKDAALLLLANKQDIPGCETVESITEAFDLYKLCCGR 515
D+AD+E+L A EL L+ + L+ LL+L NK D+PG +V+ + E +L + R
Sbjct: 76 DAADREKLEVAKNELHDLLEKPSLEGIPLLVLGNKNDLPGALSVDELIEQMNLKSI-TDR 134
Query: 516 SWHIQACNAQSGEGLHEGLDWLSR 539
+ +A+ + LDWL +
Sbjct: 135 EVSCYSISAKEKTNIDIVLDWLIK 158
>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 = 49.7 bits (119), Expect = 5e-07
Identities = 29/90 (32%), Positives = 41/90 (45%), Gaps = 8/90 (8%)
Query: 456 DSADKERLPEALAELTKLIAEKELKDAALLLLANKQDIPGCETVESITEAFDLYKLCCGR 515
DS+D +R+ E L +L+ + +L+LANKQD + E L KL
Sbjct: 75 DSSDDDRVQEVKEILRELLQHPRVSGKPILVLANKQDKKNALLGADVIEYLSLEKLVNEN 134
Query: 516 S--WHIQACNAQSGEG------LHEGLDWL 537
HI+ C+A G G + EGL WL
Sbjct: 135 KSLCHIEPCSAIEGLGKKIDPSIVEGLRWL 164
>gnl|CDD|214546 smart00184, RING, Ring finger. E3 ubiquitin-protein ligase
activity is intrinsic to the RING domain of c-Cbl and is
likely to be a general function of this domain; Various
RING fingers exhibit binding activity towards E2
ubiquitin-conjugating enzymes (Ubc' s).
Length = 40
Score = 40.2 bits (94), Expect = 5e-05
Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 5/44 (11%)
Query: 68 CRVCEDIFLTQGDKVPRLLHCGHTVCLACLLRLPIKDDTITCPF 111
C +C + +L K P +L CGHT C +C+ + ++ TCP
Sbjct: 1 CPICLEEYL----KDPVILPCGHTFCRSCIRKW-LESGNNTCPI 39
>gnl|CDD|216039 pfam00643, zf-B_box, B-box zinc finger.
Length = 42
Score = 39.8 bits (93), Expect = 8e-05
Identities = 16/43 (37%), Positives = 19/43 (44%), Gaps = 5/43 (11%)
Query: 170 KCDEDESHIAVLYCTVCASHLCEQCASDSHATRTLQKHRRIPL 212
C E E LYC C LCE+CA H + H +PL
Sbjct: 5 LCPEHEEKPLELYCEDCQQLLCEECALSGH-----KGHTVVPL 42
Score = 26.3 bits (58), Expect = 5.5
Identities = 11/51 (21%), Positives = 16/51 (31%), Gaps = 9/51 (17%)
Query: 217 REKPFCSSHPTNIAEFICLEEHCQTSAQYPPLMCFICKDYGRHKTHKHALV 267
++ C H E C + L+C C G HK H +
Sbjct: 1 SKERLCPEHEEKPLELYCEDCQQ--------LLCEECALSG-HKGHTVVPL 42
>gnl|CDD|233043 TIGR00599, rad18, DNA repair protein rad18. All proteins in this
family for which functions are known are involved in
nucleotide excision repair.This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 397
Score = 43.8 bits (103), Expect = 2e-04
Identities = 28/96 (29%), Positives = 42/96 (43%), Gaps = 14/96 (14%)
Query: 43 LDTTRYSVLLGTRTTRILILELALECRVCEDIFLTQGDKVPRLLHCGHTVCLACLLR-LP 101
LD T S L T + L+ +L C +C+D F VP L C HT C C+ R L
Sbjct: 4 LDITDSSDWLTTPIPSLYPLDTSLRCHICKDFF-----DVPVLTSCSHTFCSLCIRRCLS 58
Query: 102 IKDDTITCPFDRQPTPVGYSGVWGLKKNFALLELIE 137
+ C + Q + L+ N+ + E++E
Sbjct: 59 NQPKCPLCRAEDQESK--------LRSNWLVSEIVE 86
>gnl|CDD|222135 pfam13445, zf-RING_LisH, RING-type zinc-finger, LisH dimerisation
motif. This zinc-finger is the dimerisation motif for
LisH proteins, and is also a typical RING-type of plant
ubiquitin ligases.
Length = 55
Score = 38.1 bits (89), Expect = 4e-04
Identities = 10/45 (22%), Positives = 18/45 (40%), Gaps = 1/45 (2%)
Query: 66 LECRVCEDIFLTQGDKVPRLLHCGHTVCLACLLRLPIKDDTITCP 110
C + +++ + + P +L CGH L +L CP
Sbjct: 11 FVCPISKEVMTDEENP-PVMLPCGHVYSRKALEKLAKNGGKFKCP 54
>gnl|CDD|237988 cd00021, BBOX, B-Box-type zinc finger; zinc binding domain
(CHC3H2); often present in combination with other
motifs, like RING zinc finger, NHL motif, coiled-coil or
RFP domain in functionally unrelated proteins, most
likely mediating protein-protein interaction.
Length = 39
Score = 36.5 bits (85), Expect = 0.001
Identities = 14/44 (31%), Positives = 17/44 (38%), Gaps = 5/44 (11%)
Query: 169 IKCDEDESHIAVLYCTVCASHLCEQCASDSHATRTLQKHRRIPL 212
CDE L+C + LC C H HRR+PL
Sbjct: 1 RLCDEHGEEPLSLFCETDRALLCVDCDLSVH-----SGHRRVPL 39
>gnl|CDD|238093 cd00162, RING, RING-finger (Really Interesting New Gene) domain, a
specialized type of Zn-finger of 40 to 60 residues that
binds two atoms of zinc; defined by the 'cross-brace'
motif C-X2-C-X(9-39)-C-X(1-3)-
H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved
in mediating protein-protein interactions; identified in
a proteins with a wide range of functions such as viral
replication, signal transduction, and development; has
two variants, the C3HC4-type and a C3H2C3-type (RING-H2
finger), which have different cysteine/histidine
pattern; a subset of RINGs are associated with B-Boxes
(C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
Length = 45
Score = 36.3 bits (84), Expect = 0.002
Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 5/50 (10%)
Query: 67 ECRVCEDIFLTQGDKVPRLLHCGHTVCLACLLRLPIKDDTITCPFDRQPT 116
EC +C + F + LL CGH C +C+ + +K TCP R P
Sbjct: 1 ECPICLEEF----REPVVLLPCGHVFCRSCIDKW-LKSGKNTCPLCRTPI 45
>gnl|CDD|217232 pfam02789, Peptidase_M17_N, Cytosol aminopeptidase family,
N-terminal domain.
Length = 126
Score = 35.9 bits (83), Expect = 0.013
Identities = 16/78 (20%), Positives = 26/78 (33%), Gaps = 5/78 (6%)
Query: 438 HIGPKMEMRVVTLGLDSADSADKERLPEALAELTKLIAEKELKDAALLL--LANKQDIPG 495
+ RV+ +GL + E L +A + + ++K A+ L L
Sbjct: 46 SLPGVKAKRVLLVGLGKEEELSAEALRKAAGAAARALKGLKVKTVAVDLPTLNIDAAEVA 105
Query: 496 CETVESITEA---FDLYK 510
E FD YK
Sbjct: 106 RAAAEGALLGAYRFDRYK 123
>gnl|CDD|197662 smart00336, BBOX, B-Box-type zinc finger.
Length = 42
Score = 33.1 bits (76), Expect = 0.019
Identities = 12/43 (27%), Positives = 16/43 (37%), Gaps = 5/43 (11%)
Query: 170 KCDEDESHIAVLYCTVCASHLCEQCASDSHATRTLQKHRRIPL 212
KCD A +C C + LC C H + H + L
Sbjct: 5 KCDSHGDEPAEFFCEECGALLCRTCDEAEH-----RGHTVVLL 42
Score = 28.5 bits (64), Expect = 0.93
Identities = 16/51 (31%), Positives = 21/51 (41%), Gaps = 9/51 (17%)
Query: 217 REKPFCSSHPTNIAEFICLEEHCQTSAQYPPLMCFICKDYGRHKTHKHALV 267
+ P C SH AEF C E C L+C C + H+ H L+
Sbjct: 1 QRAPKCDSHGDEPAEFFCEE--CGA------LLCRTCDEA-EHRGHTVVLL 42
>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain.
Length = 46
Score = 31.6 bits (72), Expect = 0.075
Identities = 16/49 (32%), Positives = 22/49 (44%), Gaps = 4/49 (8%)
Query: 67 ECRVCEDIFLTQGDKVPRLLHCGHTVCLACLLRLPIKDDTITCPFDRQP 115
EC +C D F + + +L CGH CL + + TCP R P
Sbjct: 2 ECPICLDEF--EPGEEVVVLPCGHVFHKECLDKW--LRSSNTCPLCRAP 46
>gnl|CDD|183093 PRK11346, PRK11346, hypothetical protein; Provisional.
Length = 285
Score = 34.9 bits (80), Expect = 0.090
Identities = 10/31 (32%), Positives = 15/31 (48%)
Query: 397 REIKEAIETIEKYDTLFNELTPEQIHPDPCI 427
R I+ IE I+K ++ N L P Q+
Sbjct: 83 RYIRSRIEKIQKDESFTNRLEPRQLKNPEYW 113
>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger).
Length = 45
Score = 31.3 bits (71), Expect = 0.094
Identities = 16/49 (32%), Positives = 19/49 (38%), Gaps = 6/49 (12%)
Query: 66 LECRVCEDIFLTQGDKVPRLLHCGHTVCLACLLRLPIKDDTITCPFDRQ 114
LEC +C D+ L CGH C C+LR CP R
Sbjct: 3 LECPICLDLL----RDPVVLTPCGHVFCRECILR--YLKKKSKCPICRT 45
>gnl|CDD|222454 pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RING finger).
Length = 49
Score = 31.2 bits (71), Expect = 0.12
Identities = 16/50 (32%), Positives = 19/50 (38%), Gaps = 9/50 (18%)
Query: 67 ECRVCEDIFLTQGDKVPRLLHCGHTV-CLACLLRLPIKDDTITCPFDRQP 115
C +C + + L CGH C C RL K CP RQP
Sbjct: 4 LCVICLE-----RPRNVVFLPCGHLCLCEECAKRLRSKK---KCPICRQP 45
>gnl|CDD|238247 cd00433, Peptidase_M17, Cytosol aminopeptidase family, N-terminal
and catalytic domains. Family M17 contains zinc- and
manganese-dependent exopeptidases ( EC 3.4.11.1),
including leucine aminopeptidase. They catalyze removal
of amino acids from the N-terminus of a protein and play
a key role in protein degradation and in the metabolism
of biologically active peptides. They do not contain
HEXXH motif (which is used as one of the signature
patterns to group the peptidase families) in the
metal-binding site. The two associated zinc ions and the
active site are entirely enclosed within the C-terminal
catalytic domain in leucine aminopeptidase. The enzyme
is a hexamer, with the catalytic domains clustered
around the three-fold axis, and the two trimers related
to one another by a two-fold rotation. The N-terminal
domain is structurally similar to the ADP-ribose binding
Macro domain. This family includes proteins from
bacteria, archaea, animals and plants.
Length = 468
Score = 34.1 bits (79), Expect = 0.20
Identities = 24/109 (22%), Positives = 39/109 (35%), Gaps = 15/109 (13%)
Query: 446 RVVTLGLDSADSADKERLPEALAELTKLIAEKELKDAALLLLANKQDIPGCETVESITEA 505
RV +GL + D E L +A + + + K A+ L E E+ E
Sbjct: 58 RVALVGLGKEEDLDVENLRKAAGAAARALKKLGSKSVAVDL------PTLAEDAEAAAEG 111
Query: 506 -------FDLYKLCCGRSWHIQACNAQSGEGLHEGLDWLSRQLIAAGVN 547
FD YK ++ + + + L+ + IA GVN
Sbjct: 112 ALLGAYRFDRYKSKKKKTPLLVVLELGNDKAAEAALERG--EAIAEGVN 158
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 32.8 bits (75), Expect = 0.23
Identities = 23/99 (23%), Positives = 37/99 (37%), Gaps = 11/99 (11%)
Query: 452 LDSADSADKERLPEALAELTKLIAEKELKDAALLLLANKQDIPGCETVESITEAFDLYKL 511
+DS+ E + LT +++ NKQD+ E I EA L
Sbjct: 99 VDSSRPITFHAE-EIIDFLT------SRNPIPVVVAINKQDLFDALPPEKIREALKL--- 148
Query: 512 CCGRSWHIQACNAQSGEGLHEGLDWLSRQLIAAGVNDMS 550
S + +A GEG + LD L + + N+ +
Sbjct: 149 -ELLSVPVIEIDATEGEGARDQLDVLLLKDLLGSANEEA 186
>gnl|CDD|215715 pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING finger). The
C3HC4 type zinc-finger (RING finger) is a cysteine-rich
domain of 40 to 60 residues that coordinates two zinc
ions, and has the consensus sequence:
C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C
where X is any amino acid. Many proteins containing a
RING finger play a key role in the ubiquitination
pathway.
Length = 40
Score = 29.4 bits (66), Expect = 0.42
Identities = 12/44 (27%), Positives = 19/44 (43%), Gaps = 5/44 (11%)
Query: 68 CRVCEDIFLTQGDKVPRLLHCGHTVCLACLLRLPIKDDTITCPF 111
C +C + +L CGH C C+L ++ +TCP
Sbjct: 1 CPICLEEPKDP----VTILPCGHLFCSKCILSW-LESGNVTCPL 39
>gnl|CDD|227505 COG5178, PRP8, U5 snRNP spliceosome subunit [RNA processing and
modification].
Length = 2365
Score = 33.4 bits (76), Expect = 0.44
Identities = 32/153 (20%), Positives = 53/153 (34%), Gaps = 19/153 (12%)
Query: 328 HAYFNHLRESLLVQEAAATSAVDMFVRERL--GCLVQLHDDMGFWLQEVAKLYLKCEQMI 385
A + + +A ++ F RER+ G V L + +L++K EQ
Sbjct: 760 PAPILEVIRRYIKSKADLWTSSAHFNRERISRGAGVG-KTKEKKNLGRLTRLWVKLEQER 818
Query: 386 LQDDARVLTSGREIKEAIETIEKYDTLFNELTPEQIHPDPCIPITFTKDNRVHIGPKMEM 445
D A+V G + E L P P P+ K +
Sbjct: 819 QVDSAKV---GPKST-KEEAKRIGKITVLWLESRMFEPIPFPPLR----------YKEDT 864
Query: 446 RVVTLGLDSADS--ADKERLPEALAELTKLIAE 476
+++ L L+ S K RL E+ E L+ +
Sbjct: 865 KILVLALEYLKSKYTGKIRLNESTREELALLEK 897
>gnl|CDD|227719 COG5432, RAD18, RING-finger-containing E3 ubiquitin ligase [Signal
transduction mechanisms].
Length = 391
Score = 32.8 bits (74), Expect = 0.49
Identities = 24/96 (25%), Positives = 36/96 (37%), Gaps = 14/96 (14%)
Query: 43 LDTTRYSVLLGTRTTRILILELALECRVCEDIFLTQGDKVPRLLHCGHTVCLACLLR-LP 101
LD T S T+ + L+ L CR+C+ +P CGHT C C+ R L
Sbjct: 3 LDATDPSDWNQTKIPSLKGLDSMLRCRICDCRI-----SIPCETTCGHTFCSLCIRRHLG 57
Query: 102 IKDDTITCPFDRQPTPVGYSGVWGLKKNFALLELIE 137
+ C D + L+ + E+ E
Sbjct: 58 TQPFCPVCREDPCESR--------LRGSSGSREINE 85
>gnl|CDD|238453 cd00890, Prefoldin, Prefoldin is a hexameric molecular chaperone
complex, found in both eukaryotes and archaea, that
binds and stabilizes newly synthesized polypeptides
allowing them to fold correctly. The complex contains
two alpha and four beta subunits, the two subunits being
evolutionarily related. In archaea, there is usually
only one gene for each subunit while in eukaryotes there
two or more paralogous genes encoding each subunit
adding heterogeneity to the structure of the hexamer.
The structure of the complex consists of a double beta
barrel assembly with six protruding coiled-coils.
Length = 129
Score = 30.0 bits (68), Expect = 1.3
Identities = 29/122 (23%), Positives = 46/122 (37%), Gaps = 21/122 (17%)
Query: 371 LQEVAKLYLKCEQMI--LQDD-ARVLTSGREIKEAIETIEKYDTLFNELTPEQIHPDPC- 426
LQE+A + +Q + LQ ++ E ++A ET+E E
Sbjct: 1 LQELAAQLQQLQQQLEALQQQLQKLEAQLTEYEKAKETLETLKKAEEEKELLVPLGAGLF 60
Query: 427 IPITFTKDNRVHIGPKMEMRVVTLGLD-----SADSADKERLPEALAELTKLIA--EKEL 479
+ D++V +V LG S + A E L + L L K I EK+L
Sbjct: 61 VKAEVKDDDKV---------LVDLGTGVYVEKSLEEA-IEFLKKRLETLEKQIEKLEKQL 110
Query: 480 KD 481
+
Sbjct: 111 EK 112
>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 = 30.5 bits (69), Expect = 1.3
Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 6/82 (7%)
Query: 456 DSADKERLPEALAELTKLIAEKELKDAALLLLANKQDIPGCETVESITEAFDLYKLCCGR 515
DS D+E +A ++ + ++L+ NK D+ VE + +L K+
Sbjct: 84 DSTDRESEEDAK---LLILRRLRKEGIPIILVGNKIDLLEEREVEELLRLEELAKI---L 137
Query: 516 SWHIQACNAQSGEGLHEGLDWL 537
+ +A++GEG+ E + L
Sbjct: 138 GVPVFEVSAKTGEGVDELFEKL 159
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 31.1 bits (70), Expect = 1.5
Identities = 41/214 (19%), Positives = 68/214 (31%), Gaps = 45/214 (21%)
Query: 68 CRVCEDIFLTQGDKVPRLLHCGHTVCLACLLRLPIKDDTITCPF-----------DRQPT 116
C++C CGH +C AC +RL CP P
Sbjct: 64 CQIC-----AGSTTYSARYPCGHQICHACAVRLRALYMQKGCPLCRTETEAVVFTASSPA 118
Query: 117 PVGYSGVWGLKKNFALLELIEKIQTNDEKATESIPLFS-----AELHIKCDF--SLQLHI 169
+ W ++ E + ++ E L S ++ H +C L+ H
Sbjct: 119 DITDRRQWKGRE-----EKVGIFYEGEDVRDEMEDLLSFKCPKSKCHRRCGSLKELKKHY 173
Query: 170 KCDEDESHIAVLYCTVCASHLCE-QCASDSHATRTLQKHRRIPLSEKP-REKP---FCSS 224
K + C+ C + + + TL+ H+ L E+ + P FC
Sbjct: 174 KAQHGF-----VLCSECIGNKKDFWNEIRLFRSSTLRDHKNGGLEEEGFKGHPLCIFCKI 228
Query: 225 HPTNIAEFICLEEHCQTSAQYPPLMCFICKDYGR 258
+ + E L HC+ + C IC G
Sbjct: 229 YFYDDDE---LRRHCRLRHE----ACHICDMVGP 255
>gnl|CDD|176190 cd05288, PGDH, Prostaglandin dehydrogenases. Prostaglandins and
related eicosanoids are metabolized by the oxidation of
the 15(S)-hydroxyl group of the NAD+-dependent (type I
15-PGDH) 15-prostaglandin dehydrogenase (15-PGDH)
followed by reduction by NADPH/NADH-dependent (type II
15-PGDH) delta-13 15-prostaglandin reductase (13-PGR) to
15-keto-13,14,-dihydroprostaglandins. 13-PGR is a
bifunctional enzyme, since it also has leukotriene B(4)
12-hydroxydehydrogenase activity. These 15-PGDH and
related enzymes are members of the medium chain
dehydrogenase/reductase family. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES.
Length = 329
Score = 30.1 bits (69), Expect = 2.6
Identities = 21/46 (45%), Positives = 26/46 (56%), Gaps = 7/46 (15%)
Query: 440 GPKMEMRVVTL-----GLDSADSADKERLPEALAELTKLIAEKELK 480
GPK ++T G +D AD R PEALAEL K +AE +LK
Sbjct: 256 GPKNLGNIITKRLTMQGFIVSDYAD--RFPEALAELAKWLAEGKLK 299
>gnl|CDD|234863 PRK00913, PRK00913, multifunctional aminopeptidase A; Provisional.
Length = 483
Score = 30.5 bits (70), Expect = 2.8
Identities = 16/72 (22%), Positives = 33/72 (45%), Gaps = 11/72 (15%)
Query: 446 RVVTLGLDSADSADKERLPEALAELTKLIAEKELKDAALLLLANKQDIPGCETVESITEA 505
RV+ +GL + D+E+L +A + + + + ++K+A + L ++ + E
Sbjct: 70 RVLLVGLGKEEELDEEQLRKAAGKAARALKKTKVKEAVIFLT----ELHTYWKARAAAEG 125
Query: 506 -------FDLYK 510
FD YK
Sbjct: 126 ALLGLYRFDKYK 137
>gnl|CDD|217282 pfam02911, Formyl_trans_C, Formyl transferase, C-terminal domain.
Length = 100
Score = 28.4 bits (64), Expect = 3.4
Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 7/56 (12%)
Query: 12 GARLSVLDTTRSSVLDTTRYSELPGTRYYPVLDTTRYSVLLGTRTTRILILELALE 67
G R+ +L V++ + + PGT ++ + +L+ +LILEL E
Sbjct: 37 GKRVKILKA---EVVEDSSGAASPGT----IVSVDKGGLLVACGDGALLILELQPE 85
>gnl|CDD|224541 COG1626, TreA, Neutral trehalase [Carbohydrate transport and
metabolism].
Length = 558
Score = 29.7 bits (67), Expect = 4.3
Identities = 11/69 (15%), Positives = 19/69 (27%), Gaps = 6/69 (8%)
Query: 374 VAKLYLKCEQ-MILQDDARVLTSGREIKEAIETIEKYDTLFNELTPEQIHPD-----PCI 427
+ Q I +V+ G + Y LF ++ ++ PD
Sbjct: 22 EREDTEANLQITIEDTGPKVVDVGTANSRDLRPTYFYGELFQDVQDAKLFPDHKTFLDEA 81
Query: 428 PITFTKDNR 436
P N
Sbjct: 82 PSNENPVNI 90
>gnl|CDD|225229 COG2354, COG2354, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 303
Score = 29.3 bits (66), Expect = 4.4
Identities = 12/53 (22%), Positives = 22/53 (41%), Gaps = 5/53 (9%)
Query: 327 VHAYFNHLRESLLVQEAAATSAVDM----FVRERLGCLVQLHDDMGFWLQEVA 375
+ + E L+ +A V + V + +V++ DD+G WL A
Sbjct: 151 MAIALAEVAEQPLLTQALVLVLVALLITVGVYGVVAVIVKM-DDLGLWLARSA 202
>gnl|CDD|224085 COG1163, DRG, Predicted GTPase [General function prediction only].
Length = 365
Score = 29.6 bits (67), Expect = 4.8
Identities = 8/37 (21%), Positives = 17/37 (45%)
Query: 485 LLLANKQDIPGCETVESITEAFDLYKLCCGRSWHIQA 521
L + NK D+PG E +E + + + + ++
Sbjct: 243 LYVVNKIDLPGLEELERLARKPNSVPISAKKGINLDE 279
>gnl|CDD|133319 cd04119, RJL, Rab GTPase family J-like (RabJ-like). RJLs are found
in many protists and as chimeras with C-terminal DNAJ
domains in deuterostome metazoa. They are not found in
plants, fungi, and protostome metazoa, suggesting a
horizontal gene transfer between protists and
deuterostome metazoa. RJLs lack any known membrane
targeting signal and contain a degenerate
phosphate/magnesium-binding 3 (PM3) motif, suggesting an
impaired ability to hydrolyze GTP. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization.
Length = 168
Score = 28.1 bits (63), Expect = 7.4
Identities = 22/103 (21%), Positives = 37/103 (35%), Gaps = 17/103 (16%)
Query: 448 VTLGLDSADSADKERLPEALAELTK-LIAEKELKDAALLLLANKQDIPGCETVESITEAF 506
V L D D E L L E+ + +++ +++ ANK D+ V
Sbjct: 76 VLLVYDVTDRQSFEALDSWLKEMKQEGGPHGNMENIVVVVCANKIDLTKHRAVSEDE--- 132
Query: 507 DLYKLCCGRSW------HIQACNAQSGEGLHEGLDWLSRQLIA 543
GR W +A +GEG++E L ++
Sbjct: 133 -------GRLWAESKGFKYFETSACTGEGVNEMFQTLFSSIVD 168
>gnl|CDD|188272 TIGR03036, trp_2_3_diox, tryptophan 2,3-dioxygenase. Members of
this family are tryptophan 2,3-dioxygenase, as confirmed
by several experimental characterizations, and by
conserved operon structure for many of the other
members. This enzyme represents the first of a two-step
degradation to L-kynurenine, and a three-step pathway
(via kynurenine) to anthranilate plus alanine [Energy
metabolism, Amino acids and amines].
Length = 264
Score = 28.8 bits (65), Expect = 7.5
Identities = 13/32 (40%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 464 PEALAELTKLIAEKELKDAALLLLANKQ-DIP 494
PE AEL + L D L LLA + IP
Sbjct: 135 PELHAELEAALHAPSLYDEVLRLLARRGFPIP 166
>gnl|CDD|182070 PRK09776, PRK09776, putative diguanylate cyclase; Provisional.
Length = 1092
Score = 28.9 bits (65), Expect = 10.0
Identities = 21/85 (24%), Positives = 36/85 (42%), Gaps = 8/85 (9%)
Query: 383 QMILQDD-ARVLTSGREIKEAIETIEKYDTLFNELTPEQI-HPDPCIPITFTKDNRVH-- 438
+ +D RV +EI++A++ + F + + + H KD V
Sbjct: 458 ACLHPEDRQRVE---KEIRDALQGRSPFKLEFRIVVKDGVRHIRALANRVLNKDGEVERL 514
Query: 439 IGPKMEMRVVTLGLDSADSADKERL 463
+G M+M V L+ A +KERL
Sbjct: 515 LGINMDMTEVR-QLNEALFQEKERL 538
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 0.135 0.409
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 27,372,146
Number of extensions: 2635782
Number of successful extensions: 2528
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2511
Number of HSP's successfully gapped: 65
Length of query: 550
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 448
Effective length of database: 6,413,494
Effective search space: 2873245312
Effective search space used: 2873245312
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: 61 (27.2 bits)