RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12794
(106 letters)
>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 = 184 bits (470), Expect = 1e-61
Identities = 73/101 (72%), Positives = 85/101 (84%)
Query: 1 PYWRCYYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMS 60
PYWRCYYSNTDAIIYVVDS+DRDR+GISK EL AML+EEEL+DA+L++ ANKQDM +S
Sbjct: 58 PYWRCYYSNTDAIIYVVDSTDRDRLGISKSELHAMLEEEELKDAVLLVFANKQDMPGALS 117
Query: 61 VAEVHRALGLENLKDRTFQIFKTSAKEGEGLNDSMDWLSNA 101
AEV LGL LKDRT+QIFKTSA +GEGL++ MDWL N
Sbjct: 118 EAEVAEKLGLSELKDRTWQIFKTSATKGEGLDEGMDWLVNT 158
>gnl|CDD|200938 pfam00025, Arf, ADP-ribosylation factor family. Pfam combines a
number of different Prosite families together.
Length = 174
Score = 162 bits (413), Expect = 8e-53
Identities = 61/100 (61%), Positives = 75/100 (75%)
Query: 1 PYWRCYYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMS 60
P WR Y+ NTDA+I+VVDS+DRDRI +KEEL A+L EEEL DA L+ILANKQD+ MS
Sbjct: 73 PLWRNYFPNTDAVIFVVDSADRDRIEEAKEELHALLNEEELADAPLLILANKQDLPGAMS 132
Query: 61 VAEVHRALGLENLKDRTFQIFKTSAKEGEGLNDSMDWLSN 100
AE+ LGL LKDR ++I SA GEGL++ +DWLSN
Sbjct: 133 EAEIRELLGLHELKDRPWEIQGCSAVTGEGLDEGLDWLSN 172
>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 = 143 bits (362), Expect = 3e-45
Identities = 50/100 (50%), Positives = 70/100 (70%)
Query: 1 PYWRCYYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMS 60
P W+ YY NTD +I+VVDSSDR+RI +K EL +L EEEL+ A L+ILANKQD+ ++
Sbjct: 58 PLWKHYYENTDGLIFVVDSSDRERIEEAKNELHKLLNEEELKGAPLLILANKQDLPGALT 117
Query: 61 VAEVHRALGLENLKDRTFQIFKTSAKEGEGLNDSMDWLSN 100
+E+ LGLE++K R + I SA G+GL++ +DWL
Sbjct: 118 ESELIELLGLESIKGRRWHIQPCSAVTGDGLDEGLDWLIE 157
>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 = 136 bits (344), Expect = 2e-42
Identities = 55/100 (55%), Positives = 74/100 (74%)
Query: 1 PYWRCYYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMS 60
P WR Y+ NT +I+VVDS+DR+RIG ++EEL ML E+ELRDA+L++ ANKQD+ N MS
Sbjct: 59 PLWRHYFQNTQGLIFVVDSNDRERIGEAREELQRMLNEDELRDAVLLVFANKQDLPNAMS 118
Query: 61 VAEVHRALGLENLKDRTFQIFKTSAKEGEGLNDSMDWLSN 100
AEV LGL +L++R + I T A G+GL + +DWLSN
Sbjct: 119 AAEVTDKLGLHSLRNRNWYIQATCATSGDGLYEGLDWLSN 158
>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 = 134 bits (339), Expect = 1e-41
Identities = 48/98 (48%), Positives = 73/98 (74%)
Query: 3 WRCYYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMSVA 62
W YY+NTDA+I V+DS+DR+R+ ++KEEL ML E+LR A+L++LANKQD+K M+ A
Sbjct: 76 WNTYYTNTDAVILVIDSTDRERLPLTKEELYKMLAHEDLRKAVLLVLANKQDLKGAMTPA 135
Query: 63 EVHRALGLENLKDRTFQIFKTSAKEGEGLNDSMDWLSN 100
E+ +LGL +++D T+ I A GEGL + +DW+++
Sbjct: 136 EISESLGLTSIRDHTWHIQGCCALTGEGLPEGLDWIAS 173
>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
Length = 182
Score = 128 bits (322), Expect = 5e-39
Identities = 52/104 (50%), Positives = 73/104 (70%)
Query: 1 PYWRCYYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMS 60
P WR YY NT+ +I+VVDS+DR+RIG ++EEL ML E+ELRDA+L++ ANKQD+ N MS
Sbjct: 76 PLWRHYYQNTNGLIFVVDSNDRERIGDAREELERMLSEDELRDAVLLVFANKQDLPNAMS 135
Query: 61 VAEVHRALGLENLKDRTFQIFKTSAKEGEGLNDSMDWLSNALQK 104
EV LGL +++ R + I A +GL + +DWLS ++K
Sbjct: 136 TTEVTEKLGLHSVRQRNWYIQGCCATTAQGLYEGLDWLSANIKK 179
>gnl|CDD|165788 PLN00223, PLN00223, ADP-ribosylation factor; Provisional.
Length = 181
Score = 120 bits (302), Expect = 5e-36
Identities = 52/104 (50%), Positives = 73/104 (70%)
Query: 1 PYWRCYYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMS 60
P WR Y+ NT +I+VVDS+DRDR+ +++EL ML E+ELRDA+L++ ANKQD+ N M+
Sbjct: 76 PLWRHYFQNTQGLIFVVDSNDRDRVVEARDELHRMLNEDELRDAVLLVFANKQDLPNAMN 135
Query: 61 VAEVHRALGLENLKDRTFQIFKTSAKEGEGLNDSMDWLSNALQK 104
AE+ LGL +L+ R + I T A GEGL + +DWLSN +
Sbjct: 136 AAEITDKLGLHSLRQRHWYIQSTCATSGEGLYEGLDWLSNNIAN 179
>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 = 119 bits (299), Expect = 1e-35
Identities = 52/103 (50%), Positives = 74/103 (71%)
Query: 1 PYWRCYYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMS 60
P WR YY+NT +I+VVDS+DRDRI ++EEL ML E+ELRDA++++ ANKQD+ + M
Sbjct: 72 PLWRHYYTNTQGLIFVVDSNDRDRIDEAREELHRMLNEDELRDAVILVFANKQDLPDAMK 131
Query: 61 VAEVHRALGLENLKDRTFQIFKTSAKEGEGLNDSMDWLSNALQ 103
AE+ LGL +++DR + I T A G+GL + + WLSN L+
Sbjct: 132 AAEITEKLGLHSIRDRNWYIQPTCATSGDGLYEGLTWLSNNLK 174
>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 = 116 bits (293), Expect = 1e-34
Identities = 44/98 (44%), Positives = 66/98 (67%)
Query: 1 PYWRCYYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMS 60
PYWR Y+ NTD +IYV+DS+DR R + +EL+ +L+EE+L +++ ANKQD+
Sbjct: 74 PYWRNYFENTDVLIYVIDSADRKRFEEAGQELVELLEEEKLAGVPVLVFANKQDLLTAAP 133
Query: 61 VAEVHRALGLENLKDRTFQIFKTSAKEGEGLNDSMDWL 98
EV AL L +++DR++ I SAK GEGL + M+W+
Sbjct: 134 AEEVAEALNLHDIRDRSWHIQACSAKTGEGLQEGMNWV 171
>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 = 115 bits (289), Expect = 5e-34
Identities = 47/100 (47%), Positives = 64/100 (64%)
Query: 1 PYWRCYYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMS 60
YWR Y+ +TDA+I+VVDSSDR R+ K EL +L EE L A L+I ANKQD+ +S
Sbjct: 73 SYWRNYFESTDALIWVVDSSDRARLEDCKRELQKLLVEERLAGATLLIFANKQDLPGALS 132
Query: 61 VAEVHRALGLENLKDRTFQIFKTSAKEGEGLNDSMDWLSN 100
E+ L L+++K ++IF SA GE L D +DWL +
Sbjct: 133 PEEIREVLELDSIKSHHWRIFGCSAVTGENLLDGIDWLVD 172
>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 = 112 bits (283), Expect = 3e-33
Identities = 42/100 (42%), Positives = 68/100 (68%)
Query: 1 PYWRCYYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMS 60
P WR YY+ T +I+VVDS+DRDRI +++EL ++ + E+RDA+L++ ANKQD+ + M
Sbjct: 68 PLWRHYYTGTQGLIFVVDSADRDRIDEARQELHRIINDREMRDALLLVFANKQDLPDAMK 127
Query: 61 VAEVHRALGLENLKDRTFQIFKTSAKEGEGLNDSMDWLSN 100
E+ LGL ++DR + + + A G+GL + + WLS+
Sbjct: 128 PHEIQEKLGLTRIRDRNWYVQPSCATSGDGLYEGLTWLSS 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 = 111 bits (279), Expect = 1e-32
Identities = 39/100 (39%), Positives = 64/100 (64%), Gaps = 2/100 (2%)
Query: 3 WRCYYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEEL--RDAILVILANKQDMKNCMS 60
W YY N II+V+DSSDR R+ ++K+EL +L ++ R ++ ANK D+ + ++
Sbjct: 62 WEHYYKNIQGIIFVIDSSDRLRMVVAKDELELLLNHPDIKHRRIPILFYANKMDLPDALT 121
Query: 61 VAEVHRALGLENLKDRTFQIFKTSAKEGEGLNDSMDWLSN 100
++ + L LEN+KD+ + IF +SA GEGL++ +DWL
Sbjct: 122 AVKITQLLCLENIKDKPWHIFASSALTGEGLDEGVDWLQA 161
>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 = 95.5 bits (238), Expect = 2e-26
Identities = 35/99 (35%), Positives = 56/99 (56%), Gaps = 2/99 (2%)
Query: 3 WRCYYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMSVA 62
W YY+ + +IYV+DS+DR+R SK ++ E L L++LANKQD+ + +SVA
Sbjct: 68 WDKYYAESHGVIYVIDSTDRERFNESKSAFEKVINNEALEGVPLLVLANKQDLPDALSVA 127
Query: 63 EVHRALG--LENLKDRTFQIFKTSAKEGEGLNDSMDWLS 99
E+ + + R + SA EGEG+ + ++WL
Sbjct: 128 EIKEVFDDCIALIGRRDCLVQPVSALEGEGVEEGIEWLV 166
>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 = 93.2 bits (231), Expect = 2e-25
Identities = 47/103 (45%), Positives = 66/103 (64%), Gaps = 1/103 (0%)
Query: 1 PYWRCYYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMS 60
P W+ YY NT A+++V+DSS RDR+ + EL +L E+ELRDA+L+I ANKQD+ +S
Sbjct: 58 PLWKHYYLNTQAVVFVIDSSHRDRVSEAHSELAKLLTEKELRDALLLIFANKQDVAGALS 117
Query: 61 VAEVHRALGLENL-KDRTFQIFKTSAKEGEGLNDSMDWLSNAL 102
V E+ L L L R++ I A+ G GL + +DWLS L
Sbjct: 118 VEEMTELLSLHKLCCGRSWYIQGCDARSGMGLYEGLDWLSRQL 160
>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 = 87.5 bits (217), Expect = 2e-23
Identities = 38/94 (40%), Positives = 57/94 (60%), Gaps = 1/94 (1%)
Query: 1 PYWRCYYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMS 60
W+CY NTD ++YVVDSSD R+ S++EL +LK E ++ +V+LANKQD+ ++
Sbjct: 59 TVWKCYLENTDGLVYVVDSSDEARLDESQKELKHILKNEHIKGVPVVLLANKQDLPGALT 118
Query: 61 VAEVHRALGLENL-KDRTFQIFKTSAKEGEGLND 93
E+ R L+ DR + + SA GEGL +
Sbjct: 119 AEEITRRFKLKKYCSDRDWYVQPCSAVTGEGLAE 152
>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 = 83.9 bits (208), Expect = 5e-22
Identities = 33/98 (33%), Positives = 58/98 (59%)
Query: 1 PYWRCYYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMS 60
W Y +AI+YVVD++DR+++ ++K EL +L++ L L++L NK D+ +S
Sbjct: 59 SMWERYCRGVNAIVYVVDAADREKLEVAKNELHDLLEKPSLEGIPLLVLGNKNDLPGALS 118
Query: 61 VAEVHRALGLENLKDRTFQIFKTSAKEGEGLNDSMDWL 98
V E+ + L+++ DR + SAKE ++ +DWL
Sbjct: 119 VDELIEQMNLKSITDREVSCYSISAKEKTNIDIVLDWL 156
>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 = 81.9 bits (203), Expect = 7e-21
Identities = 35/109 (32%), Positives = 56/109 (51%), Gaps = 12/109 (11%)
Query: 3 WRCYYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMSVA 62
W+ Y+ D I+++VD++D +R SKEEL ++L +EEL + ++IL NK D +S
Sbjct: 80 WKDYFPEVDGIVFLVDAADPERFQESKEELDSLLNDEELANVPILILGNKIDKPGAVSEE 139
Query: 63 EVHRALGLENL------------KDRTFQIFKTSAKEGEGLNDSMDWLS 99
E+ ALGL R ++F S + +G + WLS
Sbjct: 140 ELREALGLYGTTTGKGGVSLKVSNIRPVEVFMCSVVKRQGYGEGFRWLS 188
>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 = 75.6 bits (186), Expect = 1e-18
Identities = 38/105 (36%), Positives = 59/105 (56%), Gaps = 1/105 (0%)
Query: 1 PYWRCYYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMS 60
P W+ Y TD I++VVDS D +R+ +K EL + K E + +++LANKQD+ N +
Sbjct: 67 PLWKSYTRCTDGIVFVVDSVDVERMEEAKTELHKITKFSENQGVPVLVLANKQDLPNALP 126
Query: 61 VAEVHRALGLENLKDRT-FQIFKTSAKEGEGLNDSMDWLSNALQK 104
V+EV + L L L T + + A GEGL + ++ L + K
Sbjct: 127 VSEVEKLLALHELSSSTPWHVQPACAIIGEGLQEGLEKLYEMILK 171
>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 = 73.3 bits (180), Expect = 9e-18
Identities = 33/85 (38%), Positives = 54/85 (63%), Gaps = 3/85 (3%)
Query: 2 YWRCYYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMSV 61
YW+ Y S + +I+VVDS+D +R+ ++++EL +L+ D LV+LANKQD+ SV
Sbjct: 60 YWKRYLSGSQGLIFVVDSADSERLPLARQELHQLLQHPP--DLPLVVLANKQDLPAARSV 117
Query: 62 AEVHRALGLENL-KDRTFQIFKTSA 85
E+H+ L LE + + R + + TS
Sbjct: 118 QEIHKELELEPIARGRRWILQGTSL 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 = 70.3 bits (172), Expect = 2e-16
Identities = 36/104 (34%), Positives = 51/104 (49%), Gaps = 7/104 (6%)
Query: 3 WRCYYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMSVA 62
W+ Y+ + I+Y+VD+ D++R SK EL A+L +EEL +IL NK D S
Sbjct: 78 WKDYFPEVNGIVYLVDAYDKERFAESKRELDALLSDEELATVPFLILGNKIDAPYAASED 137
Query: 63 EVHRALGLENLKD-------RTFQIFKTSAKEGEGLNDSMDWLS 99
E+ ALGL N R ++F S G + WLS
Sbjct: 138 ELRYALGLTNTTTGKGKVGVRPVEVFMCSVVRRMGYGEGFKWLS 181
>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 = 64.0 bits (156), Expect = 3e-14
Identities = 38/108 (35%), Positives = 55/108 (50%), Gaps = 9/108 (8%)
Query: 3 WRCYYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMSVA 62
W YY+ +++VVDSSD DR+ KE L +L+ + +++LANKQD KN + A
Sbjct: 60 WVNYYAEAHGLVFVVDSSDDDRVQEVKEILRELLQHPRVSGKPILVLANKQDKKNALLGA 119
Query: 63 EVHRALGLENLKDRT---FQIFKTSAKEGEG------LNDSMDWLSNA 101
+V L LE L + I SA EG G + + + WL A
Sbjct: 120 DVIEYLSLEKLVNENKSLCHIEPCSAIEGLGKKIDPSIVEGLRWLLAA 167
>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 = 52.8 bits (127), Expect = 6e-10
Identities = 25/93 (26%), Positives = 45/93 (48%), Gaps = 5/93 (5%)
Query: 6 YYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMSVAEVH 65
D I+ VVDS+DR+ ++ L +L+ ++++ NK D+ V E+
Sbjct: 72 LLRGADLILLVVDSTDRESE---EDAKLLILRRLRKEGIPIILVGNKIDLLEEREVEELL 128
Query: 66 RALGLENLKDRTFQIFKTSAKEGEGLNDSMDWL 98
R L + +F+ SAK GEG+++ + L
Sbjct: 129 RLEELAKILG--VPVFEVSAKTGEGVDELFEKL 159
>gnl|CDD|225138 COG2229, COG2229, Predicted GTPase [General function prediction
only].
Length = 187
Score = 52.1 bits (125), Expect = 1e-09
Identities = 25/97 (25%), Positives = 39/97 (40%), Gaps = 7/97 (7%)
Query: 3 WRCYYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMSVA 62
W I +VDSS I+ + +V+ NKQD+ + +
Sbjct: 85 WEILSRGAVGAIVLVDSSR----PITFHAEEIIDFLTSRNPIPVVVAINKQDLFDALPPE 140
Query: 63 EVHRALGLENLKDRTFQIFKTSAKEGEGLNDSMDWLS 99
++ AL LE L + + + A EGEG D +D L
Sbjct: 141 KIREALKLELL---SVPVIEIDATEGEGARDQLDVLL 174
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
function prediction only].
Length = 219
Score = 48.4 bits (115), Expect = 5e-08
Identities = 16/57 (28%), Positives = 27/57 (47%)
Query: 1 PYWRCYYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKN 57
YY + I+ V DS+ R+ EE L L+E D ++++ NK D+ +
Sbjct: 69 SLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVGNKIDLFD 125
>gnl|CDD|133323 cd04123, Rab21, Rab GTPase family 21 (Rab21). The localization and
function of Rab21 are not clearly defined, with
conflicting data reported. Rab21 has been reported to
localize in the ER in human intestinal epithelial cells,
with partial colocalization with alpha-glucosidase, a
late endosomal/lysosomal marker. More recently, Rab21
was shown to colocalize with and affect the morphology
of early endosomes. In Dictyostelium, GTP-bound Rab21,
together with two novel LIM domain proteins, LimF and
ChLim, has been shown to regulate phagocytosis. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 162
Score = 44.1 bits (105), Expect = 8e-07
Identities = 28/101 (27%), Positives = 47/101 (46%), Gaps = 10/101 (9%)
Query: 6 YYSNTDAIIYVVDSSDRD---RIGISKEELLAMLKEEELRDAILVILANKQDMKNCMSVA 62
YY + D I V D +D D ++ +EL M + LVI+ NK D++ V+
Sbjct: 69 YYRDADGAILVYDITDADSFQKVKKWIKELKQMRGN----NISLVIVGNKIDLERQRVVS 124
Query: 63 EVHRALGLENLKDRTFQIFKTSAKEGEGLNDSMDWLSNALQ 103
+ + E K + F+TSAK G+G+ + L+ +
Sbjct: 125 K---SEAEEYAKSVGAKHFETSAKTGKGIEELFLSLAKRMI 162
>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 = 44.0 bits (105), Expect = 1e-06
Identities = 24/93 (25%), Positives = 45/93 (48%), Gaps = 9/93 (9%)
Query: 11 DAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMSVAEVHRALGL 70
D +++VVD+S+ G E +L +LK+ + ILV+ NK D+
Sbjct: 84 DLVLFVVDASEWIGEGD--EFILELLKKSKTP-VILVL--NKIDLVKDKEDLLPLLE--- 135
Query: 71 ENLKDRTFQ-IFKTSAKEGEGLNDSMDWLSNAL 102
+ + F IF SA +GE +++ ++++ L
Sbjct: 136 KLKELHPFAEIFPISALKGENVDELLEYIVEYL 168
>gnl|CDD|206684 cd01897, NOG, Nucleolar GTP-binding protein (NOG). NOG1 is a
nucleolar GTP-binding protein present in eukaryotes
ranging from trypanosomes to humans. NOG1 is
functionally linked to ribosome biogenesis and found in
association with the nuclear pore complexes and
identified in many preribosomal complexes. Thus, defects
in NOG1 can lead to defects in 60S biogenesis. The S.
cerevisiae NOG1 gene is essential for cell viability,
and mutations in the predicted G motifs abrogate
function. It is a member of the ODN family of
GTP-binding proteins that also includes the bacterial
Obg and DRG proteins.
Length = 167
Score = 40.6 bits (96), Expect = 2e-05
Identities = 21/93 (22%), Positives = 44/93 (47%), Gaps = 8/93 (8%)
Query: 11 DAIIYVVDSSDRDRIGISKEELLAMLKE-EELRDAILVILANKQDMKNCMSVAEVHRALG 69
A+++ +D S+ G S EE L++ KE + L + ++++ NK D+ E +
Sbjct: 81 AAVLFFIDPSET--CGYSIEEQLSLFKEIKPLFNKPVIVVLNKIDLLT-----EEDLSEI 133
Query: 70 LENLKDRTFQIFKTSAKEGEGLNDSMDWLSNAL 102
+ L+ ++ K S EG+++ + L
Sbjct: 134 EKELEKEGEEVIKISTLTEEGVDELKNKACELL 166
>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 = 40.5 bits (96), Expect = 2e-05
Identities = 25/91 (27%), Positives = 43/91 (47%), Gaps = 10/91 (10%)
Query: 6 YYSNTDAIIYVVDSSDRDRIGISKEEL---LAMLKEEELRDAILVILANKQDMKNCMSVA 62
YY I V D ++R+ S E L L LKE + ++++ NK D+++
Sbjct: 69 YYRGAHGAILVYDVTNRE----SFENLDKWLNELKEYAPPNIPIILVGNKSDLEDER--- 121
Query: 63 EVHRALGLENLKDRTFQIFKTSAKEGEGLND 93
+V + K+ F+TSAK GE +++
Sbjct: 122 QVSTEEAQQFAKENGLLFFETSAKTGENVDE 152
>gnl|CDD|224082 COG1160, COG1160, Predicted GTPases [General function prediction
only].
Length = 444
Score = 39.5 bits (93), Expect = 1e-04
Identities = 27/96 (28%), Positives = 42/96 (43%), Gaps = 16/96 (16%)
Query: 10 TDAIIYVVDSSDRDRIGISK--EELLAMLKEEELRDAILVILANKQDMKNCMSVAEVHRA 67
D I++VVD R GI+ EE+ +L+ + + ILV NK D +A +
Sbjct: 84 ADVILFVVDG----REGITPADEEIAKILRRSK-KPVILV--VNKIDNLKAEELAYEFYS 136
Query: 68 LGLENLKDRTFQIFKTSAKEGEGLNDSMDWLSNALQ 103
LG + SA+ G G+ D +D + L
Sbjct: 137 LGFG-------EPVPISAEHGRGIGDLLDAVLELLP 165
Score = 26.4 bits (59), Expect = 2.9
Identities = 26/94 (27%), Positives = 44/94 (46%), Gaps = 17/94 (18%)
Query: 11 DAIIYVVDSSDRDRIGISKEEL-LAMLKEEELRDAILVILANKQDMKNCMSVAEVHRALG 69
D ++ V+D+++ GIS+++L +A L EE R +VI+ NK D+ + E
Sbjct: 262 DVVLLVIDATE----GISEQDLRIAGLIEEAGRG--IVIVVNKWDL---VEEDEATMEEF 312
Query: 70 LENLKDRTFQ------IFKTSAKEGEGLNDSMDW 97
+ L R I SA G+GL+ +
Sbjct: 313 KKKL-RRKLPFLDFAPIVFISALTGQGLDKLFEA 345
>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 = 38.9 bits (91), Expect = 1e-04
Identities = 27/100 (27%), Positives = 47/100 (47%), Gaps = 13/100 (13%)
Query: 6 YYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEE-----ELRDAILVILANKQD--MKNC 58
+Y +T ++ V D +DR + + L +K+E + + ++V+ ANK D
Sbjct: 69 FYKDTQGVLLVYDVTDRQSFE-ALDSWLKEMKQEGGPHGNMENIVVVVCANKIDLTKHRA 127
Query: 59 MSVAEVHRALGLENLKDRTFQIFKTSAKEGEGLNDSMDWL 98
+S E R + F+ F+TSA GEG+N+ L
Sbjct: 128 VSEDE-GRLWAES----KGFKYFETSACTGEGVNEMFQTL 162
>gnl|CDD|234274 TIGR03594, GTPase_EngA, ribosome-associated GTPase EngA. EngA
(YfgK, Der) is a ribosome-associated essential GTPase
with a duplication of its GTP-binding domain. It is
broadly to universally distributed among bacteria. It
appears to function in ribosome biogenesis or stability
[Protein synthesis, Other].
Length = 429
Score = 38.2 bits (90), Expect = 3e-04
Identities = 29/95 (30%), Positives = 43/95 (45%), Gaps = 18/95 (18%)
Query: 11 DAIIYVVDSSDRDRIGISK--EELLAMLKEEELRDAILVILANKQD-MKNCMSVAEVHRA 67
D I++VVD R G++ EE+ L++ + ILV ANK D K AE +
Sbjct: 80 DVILFVVDG----REGLTPEDEEIAKWLRKSG-KPVILV--ANKIDGKKEDAVAAEFYS- 131
Query: 68 LGLENLKDRTFQIFKTSAKEGEGLNDSMDWLSNAL 102
LG + SA+ G G+ D +D + L
Sbjct: 132 LGFG-------EPIPISAEHGRGIGDLLDAILELL 159
Score = 28.6 bits (65), Expect = 0.51
Identities = 28/122 (22%), Positives = 51/122 (41%), Gaps = 38/122 (31%)
Query: 11 DAIIYVVDSSDRDRIGISKEEL-LAMLKEEELRDAILVILANKQD-MKNCMSVAEVHRAL 68
D ++ V+D+++ GI++++L +A L E + LVI+ NK D +K+ E R
Sbjct: 256 DVVLLVLDATE----GITEQDLRIAGLALEAGKA--LVIVVNKWDLVKD-----EKTREE 304
Query: 69 GLENLKDRTFQ-----IFKTSAKEGEGLNDSMD--------------------WLSNALQ 103
+ L+ + I SA G+G++ +D L A+
Sbjct: 305 FKKELRRKLPFLDFAPIVFISALTGQGVDKLLDAIDEVYENANRRISTSKLNRVLEEAVA 364
Query: 104 KH 105
H
Sbjct: 365 AH 366
>gnl|CDD|206681 cd01894, EngA1, EngA1 GTPase contains the first domain of EngA.
This EngA1 subfamily CD represents the first GTPase
domain of EngA and its orthologs, which are composed of
two adjacent GTPase domains. Since the sequences of the
two domains are more similar to each other than to other
GTPases, it is likely that an ancient gene duplication,
rather than a fusion of evolutionarily distinct GTPases,
gave rise to this family. Although the exact function of
these proteins has not been elucidated, studies have
revealed that the E. coli EngA homolog, Der, and
Neisseria gonorrhoeae EngA are essential for cell
viability. A recent report suggests that E. coli Der
functions in ribosome assembly and stability.
Length = 157
Score = 37.0 bits (87), Expect = 4e-04
Identities = 28/95 (29%), Positives = 43/95 (45%), Gaps = 18/95 (18%)
Query: 11 DAIIYVVDSSDRDRIGISK--EELLAMLKEEELRDAILVILANKQD-MKNCMSVAEVHRA 67
D I++VVD R G++ EE+ L++ + + ILV NK D +K AE +
Sbjct: 78 DVILFVVDG----REGLTPADEEIAKYLRKSK-KPVILV--VNKIDNIKEEEEAAEFYS- 129
Query: 68 LGLENLKDRTFQIFKTSAKEGEGLNDSMDWLSNAL 102
LG SA+ G G+ D +D + L
Sbjct: 130 LGFGE-------PIPISAEHGRGIGDLLDAILELL 157
>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 = 36.8 bits (86), Expect = 5e-04
Identities = 21/86 (24%), Positives = 34/86 (39%), Gaps = 12/86 (13%)
Query: 10 TDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMSVAEVHRALG 69
D ++ VVDS + +EE L E + +LV+ NK D+ L
Sbjct: 77 ADLVLLVVDSD----LTPVEEEAKLGLLRERGKPVLLVL--NKIDLVP----ESEEEELL 126
Query: 70 LENLKDRTFQ--IFKTSAKEGEGLND 93
E + + SA GEG+++
Sbjct: 127 RERKLELLPDLPVIAVSALPGEGIDE 152
>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 = 36.7 bits (86), Expect = 8e-04
Identities = 27/92 (29%), Positives = 42/92 (45%), Gaps = 9/92 (9%)
Query: 11 DAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMSVAEVHRALGL 70
D +++VVD+SD DR E + +LKE D ++++ NK D+ + E
Sbjct: 122 DLLLHVVDASDPDREEQ-IETVEEVLKELGADDIPIILVLNKIDLLD----DEELEERLR 176
Query: 71 ENLKDRTFQIFKTSAKEGEGLNDSMDWLSNAL 102
D F SAK GEGL+ + + L
Sbjct: 177 AGRPDAVF----ISAKTGEGLDLLKEAIEELL 204
>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
Length = 424
Score = 35.5 bits (83), Expect = 0.002
Identities = 28/101 (27%), Positives = 52/101 (51%), Gaps = 21/101 (20%)
Query: 13 IIYVVD---SSDRDRIGISKEELLAMLKEEELRDAIL-----VILANKQDMKNCMSVAEV 64
I++V+D S RD I E+ + KE +L + L +++ANK D+ AE
Sbjct: 240 IVHVIDMSGSEGRDPI----EDYEKINKELKLYNPRLLERPQIVVANKMDLPE----AEE 291
Query: 65 HRALGLENLKDRTF-QIFKTSAKEGEGLNDSMDWLSNALQK 104
+ LE K++ ++F SA G+GL++ + ++ L++
Sbjct: 292 N----LEEFKEKLGPKVFPISALTGQGLDELLYAVAELLEE 328
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 34.3 bits (80), Expect = 0.005
Identities = 25/98 (25%), Positives = 46/98 (46%), Gaps = 13/98 (13%)
Query: 11 DAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMSVAEVHRALGL 70
D +++VVD+ ++ IG E +L LK+ + ILV+ NK D+ V + L L
Sbjct: 86 DLVLFVVDADEK--IGPGDEFILEKLKKVKTP-VILVL--NKIDL-----VKDKEELLPL 135
Query: 71 ENLKDRTFQ---IFKTSAKEGEGLNDSMDWLSNALQKH 105
I SA +G+ +++ +D ++ L +
Sbjct: 136 LEELSELMDFAEIVPISALKGDNVDELLDVIAKYLPEG 173
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 33.9 bits (79), Expect = 0.009
Identities = 27/97 (27%), Positives = 44/97 (45%), Gaps = 18/97 (18%)
Query: 11 DAIIYVVDSSDRDRIGISK--EELLAMLKEEELRDAILVILANKQD-MKNCMSVAEVHRA 67
D I++VVD R G++ EE+ +L++ + ILV NK D E + +
Sbjct: 82 DVILFVVDG----RAGLTPADEEIAKILRKSN-KPVILV--VNKVDGPDEEADAYEFY-S 133
Query: 68 LGLENLKDRTFQIFKTSAKEGEGLNDSMDWLSNALQK 104
LGL + SA+ G G+ D +D + L +
Sbjct: 134 LGLGE-------PYPISAEHGRGIGDLLDAILEELPE 163
>gnl|CDD|235392 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed.
Length = 449
Score = 33.5 bits (78), Expect = 0.012
Identities = 21/96 (21%), Positives = 47/96 (48%), Gaps = 22/96 (22%)
Query: 11 DAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMSVAEVHRALGL 70
D ++ V+D+S+ +++E+ + EEL+D ++++ NK D+ +
Sbjct: 296 DLVLLVLDASE----PLTEEDDEIL---EELKDKPVIVVLNKADLTGE-----------I 337
Query: 71 ENLKDRTFQIFKTSAKEGEGLNDSMDWLSNALQKHL 106
+ ++ + + SAK GEG+ D L A+++
Sbjct: 338 DLEEENGKPVIRISAKTGEGI----DELREAIKELA 369
>gnl|CDD|223561 COG0486, ThdF, Predicted GTPase [General function prediction only].
Length = 454
Score = 33.3 bits (77), Expect = 0.012
Identities = 24/96 (25%), Positives = 44/96 (45%), Gaps = 18/96 (18%)
Query: 11 DAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMSVAEVHRALGL 70
D +++V+D+S + KE+L + + + I+V+ NK D+ + + + A G
Sbjct: 298 DLVLFVLDASQ----PLDKEDLALIELLPKKKPIIVVL--NKADLVSKIELESEKLANGD 351
Query: 71 ENLKDRTFQIFKTSAKEGEGLNDSMDWLSNALQKHL 106
I SAK GEGL+ L A+++
Sbjct: 352 --------AIISISAKTGEGLDA----LREAIKQLF 375
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 33.3 bits (77), Expect = 0.013
Identities = 25/106 (23%), Positives = 43/106 (40%), Gaps = 23/106 (21%)
Query: 7 YSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMSVAEVHR 66
+ D I++VVD+ + G E +L LK+ + ILV+ NK D V
Sbjct: 83 LKDVDLILFVVDADEG--WGPGDEFILEQLKKTKTPV-ILVV--NKIDK--------VKP 129
Query: 67 ALGLENLKDRTFQ------IFKTSAKEGEGLNDSMDWLSNALQKHL 106
L L + I SA +G+ ++ L ++++L
Sbjct: 130 KTVLLKLIAFLKKLLPFKEIVPISALKGDNVDT----LLEIIKEYL 171
>gnl|CDD|206656 cd01863, Rab18, Rab GTPase family 18 (Rab18). Rab18 subfamily.
Mammalian Rab18 is implicated in endocytic transport and
is expressed most highly in polarized epithelial cells.
However, trypanosomal Rab, TbRAB18, is upregulated in
the BSF (Blood Stream Form) stage and localized
predominantly to elements of the Golgi complex. In human
and mouse cells, Rab18 has been identified in lipid
droplets, organelles that store neutral lipids. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 161
Score = 33.1 bits (76), Expect = 0.013
Identities = 26/97 (26%), Positives = 42/97 (43%), Gaps = 12/97 (12%)
Query: 6 YYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEEL----RDAILVILANKQDMKNCMSV 61
YY +I V D + RD + + L L E + DA+ +++ NK D +N
Sbjct: 69 YYRGAQGVILVYDVTRRD----TFDNLDTWLNELDTYSTNPDAVKMLVGNKIDKEN---- 120
Query: 62 AEVHRALGLENLKDRTFQIFKTSAKEGEGLNDSMDWL 98
EV R G + + +TSAK G+ + + L
Sbjct: 121 REVTREEGQKFARKHNMLFIETSAKTRIGVQQAFEEL 157
>gnl|CDD|206653 cd01860, Rab5_related, Rab-related GTPase family includes Rab5 and
Rab22; regulates early endosome fusion. The
Rab5-related subfamily includes Rab5 and Rab22 of
mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of plants.
The members of this subfamily are involved in
endocytosis and endocytic-sorting pathways. In mammals,
Rab5 GTPases localize to early endosomes and regulate
fusion of clathrin-coated vesicles to early endosomes
and fusion between early endosomes. In yeast, Ypt51p
family members similarly regulate membrane trafficking
through prevacuolar compartments. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 163
Score = 32.9 bits (76), Expect = 0.014
Identities = 27/98 (27%), Positives = 39/98 (39%), Gaps = 24/98 (24%)
Query: 6 YYSNTDAIIYVVDSSDRDRIGISKEELLAMLKE--EELR-----DAILVILANKQDM--K 56
YY A I V D I+ EE K +EL+ + ++ + NK D+ K
Sbjct: 70 YYRGAAAAIVVYD--------ITSEESFEKAKSWVKELQEHGPPNIVIALAGNKADLESK 121
Query: 57 NCMSVAEVHRALGLENLKDRTFQIFK-TSAKEGEGLND 93
+S E L +F TSAK GE +N+
Sbjct: 122 RQVSTEEAQEYADENGL------LFMETSAKTGENVNE 153
>gnl|CDD|206668 cd01881, Obg_like, Obg-like family of GTPases consist of five
subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1. The
Obg-like subfamily consists of five well-delimited,
ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210,
and NOG1. Four of these groups (Obg, DRG, YyaF/YchF, and
Ygr210) are characterized by a distinct glycine-rich
motif immediately following the Walker B motif (G3 box).
Obg/CgtA is an essential gene that is involved in the
initiation of sporulation and DNA replication in the
bacteria Caulobacter and Bacillus, but its exact
molecular role is unknown. Furthermore, several OBG
family members possess a C-terminal RNA-binding domain,
the TGS domain, which is also present in threonyl-tRNA
synthetase and in bacterial guanosine polyphosphatase
SpoT. Nog1 is a nucleolar protein that might function in
ribosome assembly. The DRG and Nog1 subfamilies are
ubiquitous in archaea and eukaryotes, the Ygr210
subfamily is present in archaea and fungi, and the Obg
and YyaF/YchF subfamilies are ubiquitous in bacteria and
eukaryotes. The Obg/Nog1 and DRG subfamilies appear to
form one major branch of the Obg family and the Ygr210
and YchF subfamilies form another branch. No GEFs, GAPs,
or GDIs for Obg have been identified.
Length = 167
Score = 32.8 bits (75), Expect = 0.017
Identities = 24/89 (26%), Positives = 40/89 (44%), Gaps = 11/89 (12%)
Query: 10 TDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAIL-----VILANKQDMKNCMSVAEV 64
+D I++V+D+S+ E+ + +E L +I+ANK DM +
Sbjct: 76 SDLILHVIDASEDCVGDPL-EDQKTLNEEVSGSFLFLKNKPEMIVANKIDMAS----ENN 130
Query: 65 HRALGLENLKDRTFQIFKTSAKEGEGLND 93
+ L L+ LK R + TSA GL+
Sbjct: 131 LKRLKLDKLK-RGIPVVPTSALTRLGLDR 158
>gnl|CDD|236546 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der;
Reviewed.
Length = 712
Score = 32.8 bits (75), Expect = 0.018
Identities = 24/97 (24%), Positives = 43/97 (44%), Gaps = 16/97 (16%)
Query: 11 DAIIYVVDSSDRDRIGI--SKEELLAMLKEEELRDAILVILANKQDMKNCMSVAEVHRAL 68
DA+++VVD ++G+ + E ++ ML+ +V+ NK D + A L
Sbjct: 356 DAVVFVVDG----QVGLTSTDERIVRMLRRA---GKPVVLAVNKIDDQASEYDAAEFWKL 408
Query: 69 GLENLKDRTFQIFKTSAKEGEGLNDSMDWLSNALQKH 105
GL + SA G G+ D +D ++L+
Sbjct: 409 GLGE-------PYPISAMHGRGVGDLLDEALDSLKVA 438
>gnl|CDD|129567 TIGR00475, selB, selenocysteine-specific elongation factor SelB.
In prokaryotes, the incorporation of selenocysteine as
the 21st amino acid, encoded by TGA, requires several
elements: SelC is the tRNA itself, SelD acts as a donor
of reduced selenium, SelA modifies a serine residue on
SelC into selenocysteine, and SelB is a
selenocysteine-specific translation elongation factor.
3-prime or 5-prime non-coding elements of mRNA have been
found as probable structures for directing
selenocysteine incorporation. This model describes the
elongation factor SelB, a close homolog rf EF-Tu. It may
function by replacing EF-Tu. A C-terminal domain not
found in EF-Tu is in all SelB sequences in the seed
alignment except that from Methanococcus jannaschii.
This model does not find an equivalent protein for
eukaryotes [Protein synthesis, Translation factors].
Length = 581
Score = 32.9 bits (75), Expect = 0.019
Identities = 29/97 (29%), Positives = 44/97 (45%), Gaps = 9/97 (9%)
Query: 11 DAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMSVAEVHRALGL 70
DA + VVD+ + + E LA+L + I+VI K D N + +
Sbjct: 75 DAALLVVDA--DEGVMTQTGEHLAVLDLLGIPHTIVVI--TKADRVNEEEIKRTEMFM-K 129
Query: 71 ENLKDRTF----QIFKTSAKEGEGLNDSMDWLSNALQ 103
+ L F +IFKTSAK G+G+ + L N L+
Sbjct: 130 QILNSYIFLKNAKIFKTSAKTGQGIGELKKELKNLLE 166
>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 = 32.1 bits (74), Expect = 0.024
Identities = 23/96 (23%), Positives = 40/96 (41%), Gaps = 10/96 (10%)
Query: 6 YYSNTDAIIYVVDSSDRD---RIGISKEELLAMLKEEELRDAILVILANKQDMKNCMSVA 62
YY + V D + RD + EE+L E + +V++ NK D+++
Sbjct: 68 YYRGAQGFLLVYDITSRDSFENVKKWLEEILRHADE----NVPIVLVGNKCDLED---QR 120
Query: 63 EVHRALGLENLKDRTFQIFKTSAKEGEGLNDSMDWL 98
V G K+ +TSAK E + ++ + L
Sbjct: 121 VVSTEEGEALAKELGLPFMETSAKTNENVEEAFEEL 156
>gnl|CDD|234125 TIGR03156, GTP_HflX, GTP-binding protein HflX. This protein family
is one of a number of homologous small, well-conserved
GTP-binding proteins with pleiotropic effects. Bacterial
members are designated HflX, following the naming
convention in Escherichia coli where HflX is encoded
immediately downstream of the RNA chaperone Hfq, and
immediately upstream of HflKC, a membrane-associated
protease pair with an important housekeeping function.
Over large numbers of other bacterial genomes, the
pairing with hfq is more significant than with hflK and
hlfC. The gene from Homo sapiens in this family has been
named PGPL (pseudoautosomal GTP-binding protein-like)
[Unknown function, General].
Length = 351
Score = 32.1 bits (74), Expect = 0.031
Identities = 27/93 (29%), Positives = 44/93 (47%), Gaps = 12/93 (12%)
Query: 11 DAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILA-NKQDMKNCMSVAEVHRALG 69
D +++VVD+SD DR E + +L+E + I +L NK D+ + E
Sbjct: 270 DLLLHVVDASDPDREE-QIEAVEKVLEELGA-EDIPQLLVYNKIDL-----LDEPRIERL 322
Query: 70 LENLKDRTFQIFKTSAKEGEGLNDSMDWLSNAL 102
E + F SAK GEGL+ ++ ++ L
Sbjct: 323 EEGYPEAVF----VSAKTGEGLDLLLEAIAERL 351
>gnl|CDD|206674 cd01887, IF2_eIF5B, Initiation Factor 2 (IF2)/ eukaryotic
Initiation Factor 5B (eIF5B) family. IF2/eIF5B
contribute to ribosomal subunit joining and function as
GTPases that are maximally activated by the presence of
both ribosomal subunits. As seen in other GTPases,
IF2/IF5B undergoes conformational changes between its
GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess
three characteristic segments, including a divergent
N-terminal region followed by conserved central and
C-terminal segments. This core region is conserved among
all known eukaryotic and archaeal IF2/eIF5Bs and
eubacterial IF2s.
Length = 169
Score = 31.3 bits (72), Expect = 0.042
Identities = 25/93 (26%), Positives = 35/93 (37%), Gaps = 17/93 (18%)
Query: 10 TDAIIYVVDSSDRDRIGISK--EELLAMLKEEELRDAILVILANKQD-----MKNCMSVA 62
TD I VV + D G+ E + K + +++ NK D + V
Sbjct: 73 TDIAILVVAADD----GVMPQTIEAINHAKA---ANVPIIVAINKIDKPYGTEADPERVK 125
Query: 63 EVHRALGL--ENLKDRTFQIFKTSAKEGEGLND 93
LGL E I SAK GEG++D
Sbjct: 126 NELSELGLVGEEWG-GDVSIVPISAKTGEGIDD 157
>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 = 31.3 bits (72), Expect = 0.045
Identities = 25/96 (26%), Positives = 44/96 (45%), Gaps = 21/96 (21%)
Query: 11 DAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMSVAEVHRALGL 70
D ++ VVD+S+ G+ +E+L E ++++ NK D+ + A G+
Sbjct: 84 DLVLLVVDASE----GLDEEDLE---ILELPAKKPVIVVLNKSDLLS--------DAEGI 128
Query: 71 ENLKDRTFQIFKTSAKEGEGLNDSMDWLSNALQKHL 106
L + I SAK GEG+++ L AL +
Sbjct: 129 SELNGKP--IIAISAKTGEGIDE----LKEALLELA 158
>gnl|CDD|216791 pfam01926, MMR_HSR1, 50S ribosome-binding GTPase. The full-length
GTPase protein is required for the complete activity of
the protein of interacting with the 50S ribosome and
binding of both adenine and guanine nucleotides, with a
preference for guanine nucleotide.
Length = 117
Score = 31.1 bits (71), Expect = 0.046
Identities = 15/44 (34%), Positives = 24/44 (54%), Gaps = 4/44 (9%)
Query: 9 NTDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANK 52
D I+ VVD+S + + EE+L L++ + ILV+ NK
Sbjct: 78 EADLILLVVDAS--EGLTEDDEEILEELEKLPKKPIILVL--NK 117
>gnl|CDD|225171 COG2262, HflX, GTPases [General function prediction only].
Length = 411
Score = 31.5 bits (72), Expect = 0.048
Identities = 25/97 (25%), Positives = 44/97 (45%), Gaps = 15/97 (15%)
Query: 11 DAIIYVVDSSDRDRIGISKEE-LLAMLKEEELRDAILVILANKQDMKNCMSVAEVHRALG 69
D +++VVD+SD + + K E + +L E + ++++ NK D+ +
Sbjct: 273 DLLLHVVDASDPEI--LEKLEAVEDVLAEIGADEIPIILVLNKIDL--------LEDEEI 322
Query: 70 LENLKDRTFQIFKTSAKEGEGLNDSMDWLSNALQKHL 106
L L+ + SAK GEGL D L + + L
Sbjct: 323 LAELERGSPNPVFISAKTGEGL----DLLRERIIELL 355
>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 = 31.2 bits (72), Expect = 0.058
Identities = 26/103 (25%), Positives = 46/103 (44%), Gaps = 16/103 (15%)
Query: 10 TDAIIYVVDSSDRDRIGISKEELLAMLKE-----EELRDAILVILANKQDMKNCMSVAEV 64
T +++++D S D E+ + E EL + +++ NK D+ + E
Sbjct: 236 TRVLLHLIDISPEDGSDP-IEDYEIIRNELKKYSPELAEKPRIVVLNKIDL-----LDEE 289
Query: 65 HRALGLENLKDRTFQ-IFKTSAKEGEGLNDSMDWLSNALQKHL 106
L+ LK+ + +F SA GEGL++ L AL + L
Sbjct: 290 ELEELLKELKEALGKPVFPISALTGEGLDE----LLYALAELL 328
>gnl|CDD|206685 cd01898, Obg, Obg GTPase. The Obg nucleotide binding protein
subfamily has been implicated in stress response,
chromosome partitioning, replication initiation,
mycelium development, and sporulation. Obg proteins are
among a large group of GTP binding proteins conserved
from bacteria to humans. The E. coli homolog, ObgE is
believed to function in ribosomal biogenesis. Members of
the subfamily contain two equally and highly conserved
domains, a C-terminal GTP binding domain and an
N-terminal glycine-rich domain.
Length = 170
Score = 30.5 bits (70), Expect = 0.083
Identities = 28/102 (27%), Positives = 47/102 (46%), Gaps = 15/102 (14%)
Query: 10 TDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAIL-----VILANKQDMKNCMSVAEV 64
T +++V+D S D E+ + E E + L +++ NK D+ + E
Sbjct: 79 TRVLLHVIDLSGEDDP---VEDYETIRNELEAYNPGLAEKPRIVVLNKIDLLDAEERFEK 135
Query: 65 HRALGLENLKDRTFQIFKTSAKEGEGLNDSMDWLSNALQKHL 106
+ L L+ LK + ++F SA GEGL++ L L K L
Sbjct: 136 LKEL-LKELKGK--KVFPISALTGEGLDE----LLKKLAKLL 170
>gnl|CDD|197555 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are
implicated in vesicle trafficking.
Length = 164
Score = 30.6 bits (70), Expect = 0.084
Identities = 21/92 (22%), Positives = 41/92 (44%), Gaps = 10/92 (10%)
Query: 6 YYSNTDAIIYVVDSSDRDRIGISKEEL---LAMLKEEELRDAILVILANKQDMKNCMSVA 62
YY + V D ++R+ S E L L L+E + +++++ NK D++
Sbjct: 69 YYRGAVGALLVYDITNRE----SFENLENWLKELREYASPNVVIMLVGNKSDLEEQ---R 121
Query: 63 EVHRALGLENLKDRTFQIFKTSAKEGEGLNDS 94
+V R ++ F+TSAK + ++
Sbjct: 122 QVSREEAEAFAEEHGLPFFETSAKTNTNVEEA 153
>gnl|CDD|129528 TIGR00436, era, GTP-binding protein Era. Era is an essential
GTPase in Escherichia coli and many other bacteria. It
plays a role in ribosome biogenesis. Few bacteria lack
this protein [Protein synthesis, Other].
Length = 270
Score = 30.4 bits (69), Expect = 0.10
Identities = 26/100 (26%), Positives = 44/100 (44%), Gaps = 15/100 (15%)
Query: 8 SNTDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKN-CMSVAEVHR 66
D I++VVDS + G E +L L+ L+ +++ NK D K + + +
Sbjct: 78 GGVDLILFVVDSDQWNGDG---EFVLTKLQ--NLKRPVVLTR-NKLDNKFKDKLLPLIDK 131
Query: 67 ALGLENLKDRTFQIFKTSAKEGEGLNDSMDWLSNALQKHL 106
LE+ KD I SA G+ +L+ ++ HL
Sbjct: 132 YAILEDFKD----IVPISALTGDNT----SFLAAFIEVHL 163
>gnl|CDD|206688 cd04101, RabL4, Rab GTPase-like family 4 (Rab-like4). RabL4
(Rab-like4) subfamily. RabL4s are novel proteins that
have high sequence similarity with Rab family members,
but display features that are distinct from Rabs, and
have been termed Rab-like. As in other Rab-like
proteins, RabL4 lacks a prenylation site at the
C-terminus. The specific function of RabL4 remains
unknown.
Length = 167
Score = 30.2 bits (68), Expect = 0.11
Identities = 19/96 (19%), Positives = 33/96 (34%), Gaps = 3/96 (3%)
Query: 6 YYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMSVAEVH 65
+ + V D ++ + + V++ NK D+ EV
Sbjct: 73 VWEQPAVVCVVYDVTNEVSFNNCSRWINRVRTHSHGLHTPGVLVGNKCDL---TDRREVD 129
Query: 66 RALGLENLKDRTFQIFKTSAKEGEGLNDSMDWLSNA 101
A + T + ++TSAKEG G L+ A
Sbjct: 130 AAQAQALAQANTLKFYETSAKEGVGYEAPFLSLARA 165
>gnl|CDD|206734 cd04171, SelB, SelB, the dedicated elongation factor for delivery
of selenocysteinyl-tRNA to the ribosome. SelB is an
elongation factor needed for the co-translational
incorporation of selenocysteine. Selenocysteine is coded
by a UGA stop codon in combination with a specific
downstream mRNA hairpin. In bacteria, the C-terminal
part of SelB recognizes this hairpin, while the
N-terminal part binds GTP and tRNA in analogy with
elongation factor Tu (EF-Tu). It specifically recognizes
the selenocysteine charged tRNAsec, which has a UCA
anticodon, in an EF-Tu like manner. This allows
insertion of selenocysteine at in-frame UGA stop codons.
In E. coli SelB binds GTP, selenocysteyl-tRNAsec, and a
stem-loop structure immediately downstream of the UGA
codon (the SECIS sequence). The absence of active SelB
prevents the participation of selenocysteyl-tRNAsec in
translation. Archaeal and animal mechanisms of
selenocysteine incorporation are more complex. Although
the SECIS elements have different secondary structures
and conserved elements between archaea and eukaryotes,
they do share a common feature. Unlike in E. coli, these
SECIS elements are located in the 3' UTRs. This group
contains bacterial SelBs, as well as, one from archaea.
Length = 170
Score = 29.9 bits (68), Expect = 0.15
Identities = 19/90 (21%), Positives = 40/90 (44%), Gaps = 16/90 (17%)
Query: 11 DAIIYVVDSSDRDRIGI--SKEELLAMLKEEELRDAILVI----LANKQDMKNCMS-VAE 63
DA++ VV + + GI E L +L+ ++ ++V+ L ++ ++ + E
Sbjct: 75 DAVLLVVAADE----GIMPQTREHLEILELLGIKKGLVVLTKADLVDEDRLELVEEEILE 130
Query: 64 VHRALGLENLKDRTFQIFKTSAKEGEGLND 93
+ L + IF S+ GEG+ +
Sbjct: 131 LLAGTFLADAP-----IFPVSSVTGEGIEE 155
>gnl|CDD|133315 cd04115, Rab33B_Rab33A, Rab GTPase family 33 includes Rab33A and
Rab33B. Rab33B/Rab33A subfamily. Rab33B is ubiquitously
expressed in mouse tissues and cells, where it is
localized to the medial Golgi cisternae. It colocalizes
with alpha-mannose II. Together with the other cisternal
Rabs, Rab6A and Rab6A', it is believed to regulate the
Golgi response to stress and is likely a molecular
target in stress-activated signaling pathways. Rab33A
(previously known as S10) is expressed primarily in the
brain and immune system cells. In humans, it is located
on the X chromosome at Xq26 and its expression is
down-regulated in tuberculosis patients. Experimental
evidence suggests that Rab33A is a novel CD8+ T cell
factor that likely plays a role in tuberculosis disease
processes. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation of
the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization. Most Rab
GTPases contain a lipid modification site at the
C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
binding is essential for membrane attachment, a key
feature of most Rab proteins. Due to the presence of
truncated sequences in this CD, the lipid modification
site is not available for annotation.
Length = 170
Score = 30.1 bits (68), Expect = 0.15
Identities = 23/85 (27%), Positives = 39/85 (45%), Gaps = 11/85 (12%)
Query: 6 YYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEE---LRDAILVILA-NKQDMKNCMSV 61
YY N A+++V D ++ S L + ++E E L + + IL NK D++
Sbjct: 72 YYRNVHAVVFVYDVTNMA----SFHSLPSWIEECEQHSLPNEVPRILVGNKCDLREQ--- 124
Query: 62 AEVHRALGLENLKDRTFQIFKTSAK 86
+V L + +F+TSAK
Sbjct: 125 IQVPTDLAQRFADAHSMPLFETSAK 149
>gnl|CDD|206654 cd01861, Rab6, Rab GTPase family 6 (Rab6). Rab6 is involved in
microtubule-dependent transport pathways through the
Golgi and from endosomes to the Golgi. Rab6A of mammals
is implicated in retrograde transport through the Golgi
stack, and is also required for a slow,
COPI-independent, retrograde transport pathway from the
Golgi to the endoplasmic reticulum (ER). This pathway
may allow Golgi residents to be recycled through the ER
for scrutiny by ER quality-control systems. Yeast Ypt6p,
the homolog of the mammalian Rab6 GTPase, is not
essential for cell viability. Ypt6p acts in
endosome-to-Golgi, in intra-Golgi retrograde transport,
and possibly also in Golgi-to-ER trafficking. GTPase
activating proteins (GAPs) interact with GTP-bound Rab
and accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the GTP-bound
state. Rabs are further regulated by guanine nucleotide
dissociation inhibitors (GDIs), which facilitate Rab
recycling by masking C-terminal lipid binding and
promoting cytosolic localization. Most Rab GTPases
contain a lipid modification site at the C-terminus,
with sequence motifs CC, CXC, or CCX. Lipid binding is
essential for membrane attachment, a key feature of most
Rab proteins. Due to the presence of truncated sequences
in this CD, the lipid modification site is not available
for annotation.
Length = 161
Score = 29.9 bits (68), Expect = 0.16
Identities = 21/98 (21%), Positives = 44/98 (44%), Gaps = 6/98 (6%)
Query: 6 YYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMSVAEVH 65
Y ++ + V D ++R + ++ + +++E D I+V++ NK D+ + V+
Sbjct: 69 YIRDSSVAVVVYDITNRQSF-DNTDKWIDDVRDERGNDVIIVLVGNKTDLSDKRQVSTEE 127
Query: 66 RALGLENLKDRTFQIF-KTSAKEGEGLNDSMDWLSNAL 102
E +F +TSAK G + ++ AL
Sbjct: 128 G----EKKAKENNAMFIETSAKAGHNVKQLFKKIAQAL 161
>gnl|CDD|206665 cd01876, YihA_EngB, YihA (EngB) GTPase family. The YihA (EngB)
subfamily of GTPases is typified by the E. coli YihA, an
essential protein involved in cell division control.
YihA and its orthologs are small proteins that typically
contain less than 200 amino acid residues and consists
of the GTPase domain only (some of the eukaryotic
homologs contain an N-terminal extension of about 120
residues that might be involved in organellar
targeting). Homologs of yihA are found in most
Gram-positive and Gram-negative pathogenic bacteria,
with the exception of Mycobacterium tuberculosis. The
broad-spectrum nature of YihA and its essentiality for
cell viability in bacteria make it an attractive
antibacterial target.
Length = 170
Score = 29.8 bits (68), Expect = 0.16
Identities = 18/94 (19%), Positives = 41/94 (43%), Gaps = 10/94 (10%)
Query: 12 AIIYVVDSSDRDRIGISKE--ELLAMLKEEELRDAILVILANKQD-MKNCMSVAEVHRAL 68
++ ++D+ R G + E+L L+E + +I+ K D +K + +
Sbjct: 84 GVVLLIDA----RHGPTPIDLEMLEFLEELGIP---FLIVLTKADKLKKSELAKVLKKIK 136
Query: 69 GLENLKDRTFQIFKTSAKEGEGLNDSMDWLSNAL 102
NL + + S+K+G G+++ ++ L
Sbjct: 137 EELNLFNILPPVILFSSKKGTGIDELRALIAEWL 170
>gnl|CDD|206693 cd04108, Rab36_Rab34, Rab GTPase families 34 (Rab34) and 36
(Rab36). Rab34/Rab36 subfamily. Rab34, found primarily
in the Golgi, interacts with its effector,
Rab-interacting lysosomal protein (RILP). This enables
its participation in microtubular
dynenin-dynactin-mediated repositioning of lysosomes
from the cell periphery to the Golgi. A Rab34 (Rah)
isoform that lacks the consensus GTP-binding region has
been identified in mice. This isoform is associated with
membrane ruffles and promotes macropinosome formation.
Rab36 has been mapped to human chromosome 22q11.2, a
region that is homozygously deleted in malignant
rhabdoid tumors (MRTs). However, experimental
assessments do not implicate Rab36 as a tumor suppressor
that would enable tumor formation through a
loss-of-function mechanism. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 170
Score = 29.5 bits (66), Expect = 0.23
Identities = 21/88 (23%), Positives = 42/88 (47%), Gaps = 1/88 (1%)
Query: 6 YYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMSVAEVH 65
YY AII V D +D + +++ L LKE + +L ++ K+D+ + A +
Sbjct: 69 YYRGAQAIIIVFDLTDVASLEHTRQWLEDALKENDPSSVLLFLVGTKKDLSSPAQYALME 128
Query: 66 RALGLENLKDRTFQIFKTSAKEGEGLND 93
+ ++ ++ + + SA GE + D
Sbjct: 129 QD-AIKLAREMKAEYWAVSALTGENVRD 155
>gnl|CDD|206739 cd09912, DLP_2, Dynamin-like protein including dynamins,
mitofusins, and guanylate-binding proteins. The dynamin
family of large mechanochemical GTPases includes the
classical dynamins and dynamin-like proteins (DLPs) that
are found throughout the Eukarya. This family also
includes bacterial DLPs. These proteins catalyze
membrane fission during clathrin-mediated endocytosis.
Dynamin consists of five domains; an N-terminal G domain
that binds and hydrolyzes GTP, a middle domain (MD)
involved in self-assembly and oligomerization, a
pleckstrin homology (PH) domain responsible for
interactions with the plasma membrane, GED, which is
also involved in self-assembly, and a proline arginine
rich domain (PRD) that interacts with SH3 domains on
accessory proteins. To date, three vertebrate dynamin
genes have been identified; dynamin 1, which is brain
specific, mediates uptake of synaptic vesicles in
presynaptic terminals; dynamin-2 is expressed
ubiquitously and similarly participates in membrane
fission; mutations in the MD, PH and GED domains of
dynamin 2 have been linked to human diseases such as
Charcot-Marie-Tooth peripheral neuropathy and rare forms
of centronuclear myopathy. Dynamin 3 participates in
megakaryocyte progenitor amplification, and is also
involved in cytoplasmic enlargement and the formation of
the demarcation membrane system. This family also
includes mitofusins (MFN1 and MFN2 in mammals) that are
involved in mitochondrial fusion. Dynamin oligomerizes
into helical structures around the neck of budding
vesicles in a GTP hydrolysis-dependent manner.
Length = 180
Score = 29.4 bits (67), Expect = 0.26
Identities = 21/87 (24%), Positives = 38/87 (43%), Gaps = 10/87 (11%)
Query: 6 YYSNTDAIIYVVDSSDRDR-IGISKEELLAMLKEEELRDAILVILANKQDMKN----CMS 60
+ DA+I+V+ + D+ + S+ E L + + + V+ NK D+ +
Sbjct: 70 FLPRADAVIFVLSA---DQPLTESEREFLKEILKWSGKKIFFVL--NKIDLLSEEELEEV 124
Query: 61 VAEVHRALGLENLKDRTFQIFKTSAKE 87
+ LG+ L +IF SAKE
Sbjct: 125 LEYSREELGVLELGGGEPRIFPVSAKE 151
>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 = 28.8 bits (65), Expect = 0.36
Identities = 16/47 (34%), Positives = 27/47 (57%), Gaps = 5/47 (10%)
Query: 12 AIIYVVDSSDRDRIGISKE-ELL--AMLKEEELRDAI-LVILANKQD 54
AI++VVDS+ + I E L + E++++ I ++I NKQD
Sbjct: 74 AIVFVVDSATFQK-NIRDVAEFLYDILTDLEKIKNKIPILIACNKQD 119
>gnl|CDD|204242 pfam09439, SRPRB, Signal recognition particle receptor beta
subunit. The beta subunit of the signal recognition
particle receptor (SRP) is a transmembrane GTPase which
anchors the alpha subunit to the endoplasmic reticulum
membrane.
Length = 181
Score = 28.9 bits (65), Expect = 0.37
Identities = 26/102 (25%), Positives = 47/102 (46%), Gaps = 8/102 (7%)
Query: 6 YYSNTDAIIYVVDSS-DRDRIGISKEELLAMLKE-EELRDAILVILA-NKQDMKNCMSVA 62
S+ I++VVDS+ + + E L +L E L++ I +++A NKQ+
Sbjct: 72 DSSSLRGIVFVVDSTAFPKEVTDTAEFLYEILSITELLKNGIDILIACNKQESFTARPPK 131
Query: 63 EVHRALGLENLKDRTFQIFKTSAKEGEGLNDSMDWLSNALQK 104
++ +AL E I + +K GL+ S D + +K
Sbjct: 132 KIKQALEKE-----INTIRERRSKALSGLDGSDDLSAVLGKK 168
>gnl|CDD|165407 PHA03135, PHA03135, thymidine kinase; Provisional.
Length = 343
Score = 29.1 bits (65), Expect = 0.40
Identities = 12/25 (48%), Positives = 17/25 (68%), Gaps = 2/25 (8%)
Query: 2 YWRCYYSNTDAIIYVVDSSDRDRIG 26
YWRCY+ TD ++ V D+ +R R G
Sbjct: 49 YWRCYF--TDLVVAVNDTPERRRRG 71
>gnl|CDD|133343 cd04143, Rhes_like, Ras homolog enriched in striatum (Rhes) and
activator of G-protein signaling 1 (Dexras1/AGS1). This
subfamily includes Rhes (Ras homolog enriched in
striatum) and Dexras1/AGS1 (activator of G-protein
signaling 1). These proteins are homologous, but exhibit
significant differences in tissue distribution and
subcellular localization. Rhes is found primarily in the
striatum of the brain, but is also expressed in other
areas of the brain, such as the cerebral cortex,
hippocampus, inferior colliculus, and cerebellum. Rhes
expression is controlled by thyroid hormones. In rat
PC12 cells, Rhes is farnesylated and localizes to the
plasma membrane. Rhes binds and activates PI3K, and
plays a role in coupling serpentine membrane receptors
with heterotrimeric G-protein signaling. Rhes has
recently been shown to be reduced under conditions of
dopamine supersensitivity and may play a role in
determining dopamine receptor sensitivity. Dexras1/AGS1
is a dexamethasone-induced Ras protein that is expressed
primarily in the brain, with low expression levels in
other tissues. Dexras1 localizes primarily to the
cytoplasm, and is a critical regulator of the circadian
master clock to photic and nonphotic input. Most Ras
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Ras proteins.
Length = 247
Score = 28.6 bits (64), Expect = 0.45
Identities = 17/59 (28%), Positives = 25/59 (42%), Gaps = 6/59 (10%)
Query: 37 KEEELRDAILVILANKQDMKNCMSV--AEVHRALGLENLKDRTFQIFKTSAKEGEGLND 93
K +E +VI NK D V EV + +G D F+ SAK+ L++
Sbjct: 107 KTKENVKIPMVICGNKADRDFPREVQRDEVEQLVG----GDENCAYFEVSAKKNSNLDE 161
>gnl|CDD|237045 PRK12296, obgE, GTPase CgtA; Reviewed.
Length = 500
Score = 28.7 bits (65), Expect = 0.55
Identities = 24/108 (22%), Positives = 46/108 (42%), Gaps = 18/108 (16%)
Query: 12 AIIYVVD----SSDRDRIG----ISKE------ELLAMLKEEELRDAILVILANKQDMKN 57
+++VVD RD + + E L L +L + +++ NK D+ +
Sbjct: 239 VLVHVVDCATLEPGRDPLSDIDALEAELAAYAPALDGDLGLGDLAERPRLVVLNKIDVPD 298
Query: 58 CMSVAEVHRALGLENLKDRTFQIFKTSAKEGEGLNDSMDWLSNALQKH 105
+AE R L+ R + +F+ SA EGL + L+ +++
Sbjct: 299 ARELAEFVR----PELEARGWPVFEVSAASREGLRELSFALAELVEEA 342
>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 = 28.5 bits (65), Expect = 0.55
Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 5/54 (9%)
Query: 47 VILANKQDMKNCMSVAEVHRALGLENLKDRTFQIFKTSAKEGEGLNDSMDWLSN 100
VI+ NK D+ + + E+ LE + + + SAK GEGL++ + L
Sbjct: 37 VIVLNKADLVDDEELEEL-----LEIYEKLGYPVLAVSAKTGEGLDELRELLKG 85
>gnl|CDD|225815 COG3276, SelB, Selenocysteine-specific translation elongation
factor [Translation, ribosomal structure and
biogenesis].
Length = 447
Score = 28.5 bits (64), Expect = 0.64
Identities = 22/85 (25%), Positives = 42/85 (49%), Gaps = 9/85 (10%)
Query: 11 DAIIYVVDSSDRDRIGISKE--ELLAMLKEEELRDAILVILANKQDMKNCMSVAEVHRAL 68
D + VV + + G+ + E L +L +++ I+V+ K D + + + + +
Sbjct: 75 DYALLVVAADE----GLMAQTGEHLLILDLLGIKNGIIVL--TKADRVDEARIEQKIKQI 128
Query: 69 GLENLKDRTFQIFKTSAKEGEGLND 93
L +L +IFKTSAK G G+ +
Sbjct: 129 -LADLSLANAKIFKTSAKTGRGIEE 152
>gnl|CDD|224617 COG1703, ArgK, Putative periplasmic protein kinase ArgK and related
GTPases of G3E family [Amino acid transport and
metabolism].
Length = 323
Score = 28.1 bits (63), Expect = 0.70
Identities = 22/72 (30%), Positives = 34/72 (47%), Gaps = 12/72 (16%)
Query: 40 ELRDAILVILANKQDMKNC-MSVAEVHRALGLENLKDRTF----QIFKTSAKEGEGLNDS 94
E+ D I++ NK D K + E+ AL L R + TSA EGEG+++
Sbjct: 189 EIADIIVI---NKADRKGAEKAARELRSALDLLREVWRENGWRPPVVTTSALEGEGIDE- 244
Query: 95 MDWLSNALQKHL 106
L +A++ H
Sbjct: 245 ---LWDAIEDHR 253
>gnl|CDD|206647 cd00881, GTP_translation_factor, GTP translation factor family
primarily contains translation initiation, elongation
and release factors. The GTP translation factor family
consists primarily of translation initiation,
elongation, and release factors, which play specific
roles in protein translation. In addition, the family
includes Snu114p, a component of the U5 small nuclear
riboprotein particle which is a component of the
spliceosome and is involved in excision of introns,
TetM, a tetracycline resistance gene that protects the
ribosome from tetracycline binding, and the unusual
subfamily CysN/ATPS, which has an unrelated function
(ATP sulfurylase) acquired through lateral transfer of
the EF1-alpha gene and development of a new function.
Length = 183
Score = 28.0 bits (63), Expect = 0.70
Identities = 21/89 (23%), Positives = 36/89 (40%), Gaps = 16/89 (17%)
Query: 11 DAIIYVVDSSDRDRIGISK--EELLAMLKEEELRDAILVILANKQDM-------KNCMSV 61
D + VVD+++ G+ E L + L +++ NK D + +
Sbjct: 87 DGALLVVDANE----GVEPQTREHLNIALAGGLP---IIVAVNKIDRVGEEDFDEVLREI 139
Query: 62 AEVHRALGLENLKDRTFQIFKTSAKEGEG 90
E+ + +G LK + I SA GEG
Sbjct: 140 KELLKLIGFTFLKGKDVPIIPISALTGEG 168
>gnl|CDD|224496 COG1580, FliL, Flagellar basal body-associated protein [Cell
motility and secretion].
Length = 159
Score = 27.7 bits (62), Expect = 0.82
Identities = 13/39 (33%), Positives = 22/39 (56%), Gaps = 7/39 (17%)
Query: 37 KEEELRDAILVILANKQDMKNCMSVAEVHRALGLENLKD 75
K+ E+RDA+L++ ++K + AE+ G E LK
Sbjct: 101 KKPEVRDALLMLFSSK-------TAAELSTPEGKEKLKA 132
>gnl|CDD|223091 COG0012, COG0012, Predicted GTPase, probable translation factor
[Translation, ribosomal structure and biogenesis].
Length = 372
Score = 27.5 bits (62), Expect = 1.1
Identities = 20/107 (18%), Positives = 34/107 (31%), Gaps = 21/107 (19%)
Query: 9 NTDAIIYVVDSSDRDRI-----GISKEELLAMLKEEELRDAILVILANK----------- 52
DAII+VV I + E + ++ EL L L +
Sbjct: 97 EVDAIIHVVRCFGDTDIEHVEGKVDPVEDIEII-NTELILWDLESLEKRWERLEKRAKAG 155
Query: 53 ----QDMKNCMSVAEVHRALGLENLKDRTFQIFKTSAKEGEGLNDSM 95
+++K +S+ E R + K S ++ E L
Sbjct: 156 KKLDKELKEELSLLGKLEEHLEEGKPARGLDLSKWSEEDLEALASLN 202
>gnl|CDD|182479 PRK10463, PRK10463, hydrogenase nickel incorporation protein HypB;
Provisional.
Length = 290
Score = 27.5 bits (61), Expect = 1.3
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 79 QIFKTSAKEGEGLNDSMDWLSN 100
+I SA GEG++ ++WL
Sbjct: 265 EIILISATSGEGMDQWLNWLET 286
>gnl|CDD|220015 pfam08784, RPA_C, Replication protein A C terminal. This domain
corresponds to the C terminal of the single stranded DNA
binding protein RPA (replication protein A). RPA is
involved in many DNA metabolic pathways including DNA
replication, DNA repair, recombination, cell cycle and
DNA damage checkpoints.
Length = 103
Score = 26.9 bits (60), Expect = 1.3
Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 2/36 (5%)
Query: 69 GLENLKDRTFQIFKTSAKEGEGLNDSMDWLSNALQK 104
GL L+D+ + K S EG+ +D L+ L
Sbjct: 44 GLTPLQDQVLNLIKQSCPGEEGV--HVDELAAQLNG 77
>gnl|CDD|215653 pfam00009, GTP_EFTU, Elongation factor Tu GTP binding domain. This
domain contains a P-loop motif, also found in several
other families such as pfam00071, pfam00025 and
pfam00063. Elongation factor Tu consists of three
structural domains, this plus two C-terminal beta barrel
domains.
Length = 184
Score = 27.1 bits (61), Expect = 1.5
Identities = 21/92 (22%), Positives = 38/92 (41%), Gaps = 10/92 (10%)
Query: 10 TDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNC----MSVAEVH 65
D I VVD+ + + E L + K + +++ NK D + V E+
Sbjct: 90 ADGAILVVDA--VEGVMPQTREHLLLAKTLGVP---IIVFINKIDRVDDAELEEVVEEIS 144
Query: 66 RALGLE-NLKDRTFQIFKTSAKEGEGLNDSMD 96
R L + T + SA GEG+++ ++
Sbjct: 145 RELLEKYGFGGETVPVVPGSALTGEGIDELLE 176
>gnl|CDD|232811 TIGR00073, hypB, hydrogenase accessory protein HypB. A GTP
hydrolase for assembly of nickel metallocenter of
hydrogenase. A similar protein, ureG, is an accessory
protein for urease, which also uses nickel. hits scoring
75 and above are safe as orthologs. [SS 1/05/04 I
changed the role_ID and process GO from protein folding
to to protein modification, since a protein folding role
has not been established, but HypB is implicated in
insertion of nickel into the large subunit of NiFe
hydrogenases.] [Protein fate, Protein modification and
repair].
Length = 208
Score = 27.0 bits (60), Expect = 1.5
Identities = 8/20 (40%), Positives = 14/20 (70%)
Query: 79 QIFKTSAKEGEGLNDSMDWL 98
+I S K GEGL++ +++L
Sbjct: 183 EIILMSLKTGEGLDEWLEFL 202
>gnl|CDD|237436 PRK13581, PRK13581, D-3-phosphoglycerate dehydrogenase;
Provisional.
Length = 526
Score = 26.6 bits (60), Expect = 2.7
Identities = 9/26 (34%), Positives = 16/26 (61%), Gaps = 3/26 (11%)
Query: 22 RDRIGISKEELLAMLKEEELRDAILV 47
+ G+ KEELL ++ + DA++V
Sbjct: 26 DVKTGLDKEELLEIIGD---YDALIV 48
>gnl|CDD|237039 PRK12288, PRK12288, GTPase RsgA; Reviewed.
Length = 347
Score = 26.4 bits (59), Expect = 3.0
Identities = 12/47 (25%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 47 VILANKQDMKNCMSVAEVHRALGLENLKDRTFQIFKTSAKEGEGLND 93
+I+ NK D+ + A V+ L + ++ +++ S+ GEGL +
Sbjct: 154 LIVLNKIDLLDDEGRAFVNEQL--DIYRNIGYRVLMVSSHTGEGLEE 198
>gnl|CDD|107381 cd06386, PBP1_NPR_C_like, Ligand-binding domain of type C
natriuretic peptide receptor. Ligand-binding domain of
type C natriuretic peptide receptor (NPR-C). NPR-C is
found in atrial, mesentery, placenta, lung, kidney,
venous tissue, aortic smooth muscle, and aortic
endothelial cells. The affinity of NPR-C for natriuretic
peptides is ANP>CNP>BNP. The extracellular domain of
NPR-C is about 30% identical to NPR-A and NPR-B.
However, unlike the cyclase-linked receptors, it
contains only 37 intracellular amino acids and no
guanylyl cyclase activity. Major function of NPR-C is to
clear natriuretic peptides from the circulation or
extracellular surroundings through constitutive
receptor-mediated internalization and degradation.
Length = 387
Score = 26.3 bits (58), Expect = 3.2
Identities = 15/63 (23%), Positives = 26/63 (41%), Gaps = 2/63 (3%)
Query: 30 EELLAMLKEEELRDAILVILANKQDMKNCMSVAE-VHRALGLENLKDRTFQIFKTSAKEG 88
E A+ + R A+LV +KQ+ +NC E VH E + +T +
Sbjct: 126 ETFSALFERFHWRSALLVYEDDKQE-RNCYFTLEGVHHVFQEEGYHMSIYPFDETKDLDL 184
Query: 89 EGL 91
+ +
Sbjct: 185 DEI 187
>gnl|CDD|240655 cd12178, 2-Hacid_dh_13, Putative D-isomer specific 2-hydroxyacid
dehydrogenases, NAD-binding and catalytic domains.
2-Hydroxyacid dehydrogenases catalyze the conversion of
a wide variety of D-2-hydroxy acids to their
corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate/glycerate and related dehydrogenases of the
D-specific 2-hydroxyacid dehydrogenase superfamily
include groups such as formate dehydrogenase, glycerate
dehydrogenase, L-alanine dehydrogenase, and
S-adenosylhomocysteine hydrolase. Despite often low
sequence identity, these proteins typically have a
characteristic arrangement of 2 similar subdomains of
the alpha/beta Rossmann fold NAD+ binding form. The
NAD+ binding domain is inserted within the linear
sequence of the mostly N-terminal catalytic domain,
which has a similar domain structure to the internal
NAD binding domain. Structurally, these domains are
connected by extended alpha helices and create a cleft
in which NAD is bound, primarily to the C-terminal
portion of the 2nd (internal) domain. Some related
proteins have similar structural subdomain but with a
tandem arrangement of the catalytic and NAD-binding
subdomains in the linear sequence. While many members
of this family are dimeric, alanine DH is hexameric and
phosphoglycerate DH is tetrameric.
Length = 317
Score = 26.0 bits (58), Expect = 3.5
Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 4/40 (10%)
Query: 15 YVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQD 54
+ V D + ISKEELL + + DA++ L+ D
Sbjct: 21 FEVTYYDGLGL-ISKEELLERIAD---YDALITPLSTPVD 56
>gnl|CDD|216102 pfam00756, Esterase, Putative esterase. This family contains
Esterase D. However it is not clear if all members of
the family have the same function. This family is
related to the pfam00135 family.
Length = 245
Score = 25.9 bits (57), Expect = 3.8
Identities = 9/36 (25%), Positives = 19/36 (52%)
Query: 14 IYVVDSSDRDRIGISKEELLAMLKEEELRDAILVIL 49
+Y++D + + G +KE L + E+ I+V +
Sbjct: 26 LYLLDGTGWFQNGPAKEGLDRLAASGEIPPVIIVGV 61
>gnl|CDD|234770 PRK00454, engB, GTP-binding protein YsxC; Reviewed.
Length = 196
Score = 25.8 bits (58), Expect = 4.1
Identities = 16/100 (16%), Positives = 43/100 (43%), Gaps = 24/100 (24%)
Query: 12 AIIYVVDSSDRDRIGISK--EELLAMLKEEELRDAILVILANKQD-------MKNCMSVA 62
++ ++DS R + + +++ LKE + ++I+ K D K +
Sbjct: 109 GVVLLIDS----RHPLKELDLQMIEWLKEYGIP---VLIVLTKADKLKKGERKKQ---LK 158
Query: 63 EVHRALGLENLKDRTFQIFKTSAKEGEGLNDSMDWLSNAL 102
+V +AL + ++ S+ + +G+++ ++ L
Sbjct: 159 KVRKALKFGD-----DEVILFSSLKKQGIDELRAAIAKWL 193
>gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol
utilisation. Members of this family function in
ethanolamine and propanediol degradation pathways,
however the exact roles of these proteins is poorly
understood.
Length = 143
Score = 25.7 bits (57), Expect = 4.1
Identities = 7/22 (31%), Positives = 13/22 (59%)
Query: 79 QIFKTSAKEGEGLNDSMDWLSN 100
+IF+ SA EG+++ +L
Sbjct: 122 KIFEVSAVTNEGIDELFAYLEE 143
>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 = 26.0 bits (58), Expect = 4.2
Identities = 27/99 (27%), Positives = 41/99 (41%), Gaps = 18/99 (18%)
Query: 13 IIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMSVAEVHRALGLEN 72
I+YVVD D + G EL + +LV NK D+ V+ + E
Sbjct: 67 IVYVVDIFDFE--GSLIPELKRFVGG---NPVLLVG--NKIDLLP----KSVNLSKIKEW 115
Query: 73 LKDR-------TFQIFKTSAKEGEGLNDSMDWLSNALQK 104
+K R I SAK+G G+++ +D + A K
Sbjct: 116 MKKRAKELGLKPVDIILVSAKKGNGIDELLDKIKKARNK 154
>gnl|CDD|233245 TIGR01042, V-ATPase_V1_A, V-type (H+)-ATPase V1, A subunit. This
models eukaryotic vacuolar (H+)-ATPase that is
responsible for acidifying cellular compartments. This
enzyme shares extensive sequence similarity with
archaeal ATP synthase [Transport and binding proteins,
Cations and iron carrying compounds].
Length = 591
Score = 25.9 bits (57), Expect = 4.9
Identities = 8/10 (80%), Positives = 10/10 (100%)
Query: 7 YSNTDAIIYV 16
YSN+DAI+YV
Sbjct: 249 YSNSDAIVYV 258
>gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed.
Length = 472
Score = 25.7 bits (57), Expect = 5.8
Identities = 28/95 (29%), Positives = 45/95 (47%), Gaps = 18/95 (18%)
Query: 11 DAIIYVVDSSDRDRIGISK--EELLAMLKEEELRDAILVIL-ANKQDMKNCMSVAEVHRA 67
DA+++VVD++ +G + E + +L+ R VIL ANK D + + A +
Sbjct: 119 DAVLFVVDAT----VGATATDEAVARVLR----RSGKPVILAANKVDDERGEADAAALWS 170
Query: 68 LGLENLKDRTFQIFKTSAKEGEGLNDSMDWLSNAL 102
LGL + SA G G+ D +D + AL
Sbjct: 171 LGLG-------EPHPVSALHGRGVGDLLDAVLAAL 198
>gnl|CDD|225256 COG2382, Fes, Enterochelin esterase and related enzymes [Inorganic
ion transport and metabolism].
Length = 299
Score = 25.4 bits (56), Expect = 6.1
Identities = 14/55 (25%), Positives = 23/55 (41%), Gaps = 3/55 (5%)
Query: 13 IIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMSVAEVHRA 67
++Y+ D D R G L +++ E+ AILV + K E+H
Sbjct: 100 VLYLQDGQDWFRSGRIPRILDSLIAAGEIPPAILVGIDYIDVKKR---REELHCN 151
>gnl|CDD|183263 PRK11658, PRK11658, UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate
aminotransferase; Provisional.
Length = 379
Score = 25.4 bits (56), Expect = 6.2
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 21 DRDRIGISKEELLAMLKE 38
D +R GIS++ L+ LKE
Sbjct: 298 DEERCGISRDALMEALKE 315
>gnl|CDD|224732 COG1819, COG1819, Glycosyl transferases, related to
UDP-glucuronosyltransferase [Carbohydrate transport and
metabolism / Signal transduction mechanisms].
Length = 406
Score = 25.5 bits (56), Expect = 6.3
Identities = 14/54 (25%), Positives = 21/54 (38%), Gaps = 14/54 (25%)
Query: 25 IGISKEELLAMLKEEELRDAILVILAN----------KQDMKNCMSVAEVHRAL 68
I + EEL EE LR A+ +LA+ ++ K A+ L
Sbjct: 346 IALPFEEL----TEERLRAAVNEVLADDSYRRAAERLAEEFKEEDGPAKAADLL 395
>gnl|CDD|236259 PRK08401, PRK08401, L-aspartate oxidase; Provisional.
Length = 466
Score = 25.5 bits (56), Expect = 6.4
Identities = 11/30 (36%), Positives = 17/30 (56%), Gaps = 2/30 (6%)
Query: 67 ALGLENLKDRTFQIFKTSAKEGEGLNDSMD 96
A G+E+ K R QI+ + EG++ S D
Sbjct: 271 ATGIEDFKRRFPQIY--AFLRKEGIDPSRD 298
>gnl|CDD|223455 COG0378, HypB, Ni2+-binding GTPase involved in regulation of
expression and maturation of urease and hydrogenase
[Posttranslational modification, protein turnover,
chaperones / Transcription].
Length = 202
Score = 25.3 bits (56), Expect = 6.7
Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 11/58 (18%)
Query: 45 ILVILANKQDMKNCMSVAEVHRALGLENLK----DRTFQIFKTSAKEGEGLNDSMDWL 98
+LVI NK D+ + + K + I T+ K GEGL++ + ++
Sbjct: 146 LLVI--NKTDL---APYVGADLEVMARDAKEVNPEA--PIIFTNLKTGEGLDEWLRFI 196
>gnl|CDD|215955 pfam00503, G-alpha, G-protein alpha subunit. G proteins couple
receptors of extracellular signals to intracellular
signaling pathways. The G protein alpha subunit binds
guanyl nucleotide and is a weak GTPase. A set of
residues that are unique to G-alpha as compared to its
ancestor the Arf-like family form a ring of residues
centered on the nucleotide binding site. A Ggamma is
found fused to an inactive Galpha in the Dictyostelium
protein gbqA.
Length = 329
Score = 25.3 bits (56), Expect = 7.4
Identities = 14/63 (22%), Positives = 30/63 (47%), Gaps = 10/63 (15%)
Query: 3 WRCYYSNTDAIIYVVDSSDRDRIGISKE------ELLAMLKE----EELRDAILVILANK 52
W + + AII+VV S+ D++ + E L + +E ++ +++ NK
Sbjct: 185 WIHCFEDVTAIIFVVSLSEYDQVLYEDDSTNRLEESLNLFEEICNSPWFKNTPIILFLNK 244
Query: 53 QDM 55
+D+
Sbjct: 245 KDL 247
>gnl|CDD|233311 TIGR01208, rmlA_long, glucose-1-phosphate thymidylylransferase,
long form. The family of known and putative
glucose-1-phosphate thymidyltransferase (also called
dTDP-glucose synthase) shows a deep split into a short
form (see TIGR01207) and a long form described by this
model. The homotetrameric short form is found in
numerous bacterial species that incorporate
dTDP-L-rhamnose, which it helps synthesize, into the
cell wall. It is subject to feedback inhibition. This
form, in contrast, is found in many species for which it
serves as a sugar-activating enzyme for antibiotic
biosynthesis and or other, unknown pathways, and in
which dTDP-L-rhamnose is not necessarily produced.
Alternate name: dTDP-D-glucose synthase.
Length = 353
Score = 25.4 bits (56), Expect = 7.5
Identities = 14/65 (21%), Positives = 29/65 (44%), Gaps = 1/65 (1%)
Query: 1 PYWRCYYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILAN-KQDMKNCM 59
P WR TDAI ++++ + K E+L DA +IL +++++
Sbjct: 187 PSWRGELEITDAIQWLIEKGYKVGGSKVTGWWKDTGKPEDLLDANRLILDEVEREVQGVD 246
Query: 60 SVAEV 64
+++
Sbjct: 247 DESKI 251
>gnl|CDD|240349 PTZ00295, PTZ00295, glucosamine-fructose-6-phosphate
aminotransferase; Provisional.
Length = 640
Score = 25.4 bits (56), Expect = 7.7
Identities = 10/35 (28%), Positives = 19/35 (54%), Gaps = 4/35 (11%)
Query: 33 LAMLKEEELRDAILVILA--NKQDMKNCMSVAEVH 65
A++ +E+ IL+IL +K+ M N + +V
Sbjct: 539 FALIDKEKNTPVILIILDDEHKELMIN--AAEQVK 571
>gnl|CDD|215812 pfam00239, Resolvase, Resolvase, N terminal domain. The N-terminal
domain of the resolvase family (this family) contains
the active site and the dimer interface. The extended
arm at the C-terminus of this domain connects to the
C-terminal helix-turn-helix domain of resolvase - see
pfam02796.
Length = 139
Score = 24.9 bits (55), Expect = 7.9
Identities = 18/76 (23%), Positives = 30/76 (39%), Gaps = 13/76 (17%)
Query: 23 DRIGISKEELLAMLKEEELRDAILVILANKQDMKNCM---------SVAEVHRALGLENL 73
DR+G S +LL +++E + LV L D ++AE R L +
Sbjct: 67 DRLGRSLRDLLELVEELREKGVRLVSLDEGIDTSTPAGRLLLTILAALAEFEREL----I 122
Query: 74 KDRTFQIFKTSAKEGE 89
+RT + G+
Sbjct: 123 SERTKAGLAAAKARGK 138
>gnl|CDD|232848 TIGR00157, TIGR00157, ribosome small subunit-dependent GTPase A.
Members of this protein were designated YjeQ and are now
designated RsgA (ribosome small subunit-dependent GTPase
A). The strongest motif in the alignment of these
proteins is GXSGVGKS[ST], a classic P-loop for
nucleotide binding. This protein has been shown to
cleave GTP and remain bound to GDP. A role as a
regulator of translation has been suggested. The Aquifex
aeolicus ortholog is split into consecutive open reading
frames. Consequently, this model was build in fragment
mode (-f option) [Protein synthesis, Translation
factors].
Length = 245
Score = 25.1 bits (55), Expect = 9.8
Identities = 22/98 (22%), Positives = 46/98 (46%), Gaps = 7/98 (7%)
Query: 3 WRCYYSNTDAIIYVVDSSDRDRIGISKEELLAMLKEEELRDAILVILANKQDMKNCMSVA 62
R +N D I+ V + + +S +L L E ++ +I+ NK D+ + +
Sbjct: 30 TRPIVANIDQIVIVSSAVLPE---LSLNQLDRFLVVAEAQNIEPIIVLNKIDLLDDEDME 86
Query: 63 EVHRALGLENLKDRTFQIFKTSAKEGEGLNDSMDWLSN 100
+ L+ ++ +Q+ TS+K +GL + ++ L N
Sbjct: 87 KEQ----LDIYRNIGYQVLMTSSKNQDGLKELIEALQN 120
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
0.318 0.133 0.383
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: 5,333,325
Number of extensions: 458422
Number of successful extensions: 741
Number of sequences better than 10.0: 1
Number of HSP's gapped: 709
Number of HSP's successfully gapped: 135
Length of query: 106
Length of database: 10,937,602
Length adjustment: 71
Effective length of query: 35
Effective length of database: 7,788,468
Effective search space: 272596380
Effective search space used: 272596380
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.5 bits)