RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9524
(81 letters)
>gnl|CDD|206745 cd11385, RagC_like, Rag GTPase, subfamily of Ras-related GTPases,
includes Ras-related GTP-binding proteins C and D.
RagC and RagD are closely related Rag GTPases
(ras-related GTP-binding protein C and D) that
constitute a unique subgroup of the Ras superfamily,
and are functional homologs of Saccharomyces cerevisiae
Gtr2. These domains form heterodimers with RagA or
RagB, and similarly, Gtr2 dimerizes with Gtr1 in order
to function. They play an essential role in regulating
amino acid-induced target of rapamycin complex 1
(TORC1) kinase signaling, exocytic cargo sorting at
endosomes, and epigenetic control of gene expression.
In response to amino acids, the Rag GTPases guide the
TORC1 complex to activate the platform containing Rheb
proto-oncogene by driving the relocalization of mTORC1
from discrete locations in the cytoplasm to a late
endosomal and/or lysosomal compartment that is
Rheb-enriched and contains Rab-7.
Length = 175
Score = 143 bits (362), Expect = 1e-45
Identities = 57/79 (72%), Positives = 68/79 (86%), Gaps = 2/79 (2%)
Query: 1 MGLRRSGKTSIQKVVFQKMSPNETLFLEGTNKMTKEDIANSSFLQYQLWDCPGQMDFQD- 59
MGLRRSGK+SIQKVVF KMSPNETLFLE TNK+TK+DI+NSSF+ +Q+WD PGQ+D D
Sbjct: 5 MGLRRSGKSSIQKVVFHKMSPNETLFLESTNKITKDDISNSSFVNFQIWDFPGQLDPFDP 64
Query: 60 -FDAELIFARCGALIFVID 77
D E+IF+ CGAL+FVID
Sbjct: 65 TLDPEMIFSGCGALVFVID 83
>gnl|CDD|206742 cd09915, Rag, Rag GTPase subfamily of Ras-related GTPases. Rag
GTPases (ras-related GTP-binding proteins) constitute a
unique subgroup of the Ras superfamily, playing an
essential role in regulating amino acid-induced target
of rapamycin complex 1 (TORC1) kinase signaling,
exocytic cargo sorting at endosomes, and epigenetic
control of gene expression. This subfamily consists of
RagA and RagB as well as RagC and RagD that are closely
related. Saccharomyces cerevisiae encodes single
orthologs of metazoan RagA/B and RagC/D, Gtr1 and Gtr2,
respectively. Dimer formation is important for their
cellular function; these domains form heterodimers, as
RagA or RagB dimerizes with RagC or RagD, and
similarly, Gtr1 dimerizes with Gtr2. In response to
amino acids, the Rag GTPases guide the TORC1 complex to
activate the platform containing Rheb proto-oncogene by
driving the relocalization of mTORC1 from discrete
locations in the cytoplasm to a late endosomal and/or
lysosomal compartment that is Rheb-enriched and
contains Rab-7.
Length = 175
Score = 108 bits (271), Expect = 8e-32
Identities = 38/80 (47%), Positives = 46/80 (57%), Gaps = 2/80 (2%)
Query: 1 MGLRRSGKTSIQKVVFQKMSPNETLFLEGTNKMTKEDIANSSFLQYQLWDCPGQMDFQD- 59
G RRSGK+SI+KVVF SP +TL LE T + ++ LWDCPGQ F +
Sbjct: 5 XGRRRSGKSSIRKVVFHNYSPFDTLRLESTIDVEHSHLSFLGNXTLNLWDCPGQDVFFEP 64
Query: 60 -FDAELIFARCGALIFVIDT 78
D E IF GALI+VID
Sbjct: 65 TKDKEHIFQXVGALIYVIDV 84
>gnl|CDD|218203 pfam04670, Gtr1_RagA, Gtr1/RagA G protein conserved region. GTR1
was first identified in S. cerevisiae as a suppressor
of a mutation in RCC1. Biochemical analysis revealed
that Gtr1 is in fact a G protein of the Ras family. The
RagA/B proteins are the human homologues of Gtr1.
Included in this family is the human Rag C, a novel
protein that has been shown to interact with RagA/B.
Length = 230
Score = 108 bits (273), Expect = 2e-31
Identities = 33/81 (40%), Positives = 45/81 (55%), Gaps = 4/81 (4%)
Query: 1 MGLRRSGKTSIQKVVFQKMSPNETLFLEGTNKMTKEDIANSSFLQYQLWDCPGQMDFQD- 59
MGLR SGK+S++ ++F SP +TL L T + + + L LWDCPGQ DF +
Sbjct: 5 MGLRGSGKSSMRSIIFSNYSPRDTLRLGATIDVEQSHVRFLGNLTLNLWDCPGQDDFMEN 64
Query: 60 ---FDAELIFARCGALIFVID 77
E IF+ G LI+V D
Sbjct: 65 YLTRQKEHIFSNVGVLIYVFD 85
>gnl|CDD|206744 cd11384, RagA_like, Rag GTPase, subfamily of Ras-related GTPases,
includes Ras-related GTP-binding proteins A and B.
RagA and RagB are closely related Rag GTPases
(ras-related GTP-binding protein A and B) that
constitute a unique subgroup of the Ras superfamily,
and are functional homologs of Saccharomyces cerevisiae
Gtr1. These domains function by forming heterodimers
with RagC or RagD, and similarly, Gtr1 dimerizes with
Gtr2, through the carboxy-terminal segments. They play
an essential role in regulating amino acid-induced
target of rapamycin complex 1 (TORC1) kinase signaling,
exocytic cargo sorting at endosomes, and epigenetic
control of gene expression. In response to amino acids,
the Rag GTPases guide the TORC1 complex to activate the
platform containing Rheb proto-oncogene by driving the
relocalization of mTORC1 from discrete locations in the
cytoplasm to a late endosomal and/or lysosomal
compartment that is Rheb-enriched and contains Rab-7.
Length = 286
Score = 44.5 bits (106), Expect = 6e-07
Identities = 27/86 (31%), Positives = 37/86 (43%), Gaps = 14/86 (16%)
Query: 1 MGLRRSGKTSIQKVVFQKMSPNETLFLEGTNKMTKEDIANSSF-----LQYQLWDCPGQM 55
MG SGKTS++ ++F +T L T D+ +S L LWDC GQ
Sbjct: 5 MGKSGSGKTSMRSIIFANYLARDTRRLGATI-----DVEHSHVRFLGNLVLNLWDCGGQD 59
Query: 56 DFQD----FDAELIFARCGALIFVID 77
F + + IF LI+V D
Sbjct: 60 AFMENYFTSQRDHIFRNVEVLIYVFD 85
>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 = 42.8 bits (101), Expect = 2e-06
Identities = 14/84 (16%), Positives = 27/84 (32%), Gaps = 5/84 (5%)
Query: 1 MGLRRSGKTSIQKVVFQKMSPNETLFLEGTNKMTKEDIANSSFL-QYQLWDCPGQMDFQD 59
+G GK+S+ + + T + L D PG +F
Sbjct: 3 VGRGGVGKSSLLNALLGGEVGEVSDVPGTTRDPDVYVKELDKGKVKLVLVDTPGLDEFGG 62
Query: 60 FD----AELIFARCGALIFVIDTS 79
A L+ ++ V+D++
Sbjct: 63 LGREELARLLLRGADLILLVVDST 86
>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 = 31.6 bits (72), Expect = 0.021
Identities = 22/79 (27%), Positives = 36/79 (45%), Gaps = 4/79 (5%)
Query: 1 MGLRRSGKTSIQKVVFQKMSPNETLFLEGTNKMTKEDIANSSFLQYQLWDCPGQMDFQDF 60
+GL SGKT+I + K S ++ + T E + L + +D GQ ++
Sbjct: 5 LGLDNSGKTTI--INQLKPSNAQSQNIVPTVGFNVESFKKGN-LSFTAFDMSGQGKYRGL 61
Query: 61 DAELIFARCGALIFVIDTS 79
E + +IFVID+S
Sbjct: 62 -WEHYYKNIQGIIFVIDSS 79
>gnl|CDD|224025 COG1100, COG1100, GTPase SAR1 and related small G proteins
[General function prediction only].
Length = 219
Score = 29.9 bits (67), Expect = 0.097
Identities = 15/76 (19%), Positives = 26/76 (34%), Gaps = 1/76 (1%)
Query: 2 GLRRSGKTSIQKVVFQKMSPNETLFLEGTNKMTKEDIANSSFLQYQLWDCPGQMDFQDFD 61
G GKT++ + P G K ++ QLWD GQ +++
Sbjct: 12 GDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAGQEEYRSL- 70
Query: 62 AELIFARCGALIFVID 77
+ ++ V D
Sbjct: 71 RPEYYRGANGILIVYD 86
>gnl|CDD|232886 TIGR00231, small_GTP, small GTP-binding protein domain. Proteins
with a small GTP-binding domain recognized by this
model include Ras, RhoA, Rab11, translation elongation
factor G, translation initiation factor IF-2,
tetratcycline resistance protein TetM, CDC42, Era,
ADP-ribosylation factors, tdhF, and many others. In
some proteins the domain occurs more than once.This
model recognizes a large number of small GTP-binding
proteins and related domains in larger proteins. Note
that the alpha chains of heterotrimeric G proteins are
larger proteins in which the NKXD motif is separated
from the GxxxxGK[ST] motif (P-loop) by a long insert
and are not easily detected by this model [Unknown
function, General].
Length = 162
Score = 28.9 bits (65), Expect = 0.17
Identities = 17/80 (21%), Positives = 34/80 (42%), Gaps = 6/80 (7%)
Query: 1 MGLRRSGKTSI-QKVVFQKMSPNETLFLEGTNKMTKEDI--ANSSFLQYQLWDCPGQMDF 57
+G GK+++ +++ K+S E GT + + + ++ L D GQ D+
Sbjct: 7 VGDPNVGKSTLLNRLLGNKISITEYK--PGTTRNYVTTVIEEDGKTYKFNLLDTAGQEDY 64
Query: 58 QDFDAELIFARCGALIFVID 77
D L + + + V D
Sbjct: 65 -DAIRRLYYRAVESSLRVFD 83
>gnl|CDD|236629 PRK09849, PRK09849, putative oxidoreductase; Provisional.
Length = 702
Score = 28.9 bits (65), Expect = 0.19
Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 6/40 (15%)
Query: 19 MSPNETLFLEGTNKMTKEDIANSSFLQYQL--WD----CP 52
P++ F EGT KM ++D+ + + Y+ WD CP
Sbjct: 638 KDPDKPPFTEGTIKMDRDDMQAALTMFYKEMGWDPQTGCP 677
>gnl|CDD|221955 pfam13173, AAA_14, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily.
Length = 127
Score = 27.1 bits (61), Expect = 0.60
Identities = 6/26 (23%), Positives = 14/26 (53%)
Query: 2 GLRRSGKTSIQKVVFQKMSPNETLFL 27
G R+ GKT++ +++ L++
Sbjct: 9 GPRQVGKTTLLLQFLKELLSENILYI 34
>gnl|CDD|206655 cd01862, Rab7, Rab GTPase family 7 (Rab7). Rab7 subfamily. Rab7
is a small Rab GTPase that regulates vesicular traffic
from early to late endosomal stages of the endocytic
pathway. The yeast Ypt7 and mammalian Rab7 are both
involved in transport to the vacuole/lysosome, whereas
Ypt7 is also required for homotypic vacuole fusion.
Mammalian Rab7 is an essential participant in the
autophagic pathway for sequestration and targeting of
cytoplasmic components to the lytic compartment.
Mammalian Rab7 is also proposed to function as a tumor
suppressor. GTPase activating proteins (GAPs) interact
with GTP-bound Rab and accelerate the hydrolysis of GTP
to GDP. Guanine nucleotide exchange factors (GEFs)
interact with GDP-bound Rabs to promote the formation
of the GTP-bound state. Rabs are further regulated by
guanine nucleotide dissociation inhibitors (GDIs),
which facilitate Rab recycling by masking C-terminal
lipid binding and promoting cytosolic localization.
Most Rab GTPases contain a lipid modification site at
the C-terminus, with sequence motifs CC, CXC, or CCX.
Lipid binding is essential for membrane attachment, a
key feature of most Rab proteins. Due to the presence
of truncated sequences in this CD, the lipid
modification site is not available for annotation.
Length = 172
Score = 27.2 bits (61), Expect = 0.70
Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 2/55 (3%)
Query: 7 GKTS-IQKVVFQKMSPNETLFLEGTNKMTKEDIANSSFLQYQLWDCPGQMDFQDF 60
GKTS + + V +K S N+ G + +TKE + + Q+WD GQ FQ
Sbjct: 12 GKTSLMNQYVNKKFS-NQYKATIGADFLTKEVTVDDRLVTLQIWDTAGQERFQSL 65
>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 = 26.6 bits (59), Expect = 1.1
Identities = 10/36 (27%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 44 LQYQLWDCPGQMDFQDFDAELIFARCGALIFVIDTS 79
L++Q+WD GQ + + ++ A+I+V+D++
Sbjct: 43 LKFQVWDLGGQTSIRPY-WRCYYSNTDAIIYVVDST 77
>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 = 26.5 bits (59), Expect = 1.2
Identities = 9/31 (29%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 49 WDCPGQMDFQDFDAELIFARCGALIFVIDTS 79
WD GQ + + + +A +I+VID++
Sbjct: 56 WDLGGQEELRSLWDKY-YAESHGVIYVIDST 85
>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 = 26.6 bits (59), Expect = 1.3
Identities = 18/78 (23%), Positives = 33/78 (42%), Gaps = 6/78 (7%)
Query: 2 GLRRSGKTSIQKVVFQKMSPNETLFLEGTNKMTKEDIANSSFLQYQLWDCPGQMDFQDFD 61
GL +GKT++ Q P + T T + + + ++D G +F+
Sbjct: 6 GLDNAGKTTLVSA-LQGEIPKKV---APTVGFTPTKLRLDKY-EVCIFDLGGGANFRGIW 60
Query: 62 AELIFARCGALIFVIDTS 79
+A L+FV+D+S
Sbjct: 61 VNY-YAEAHGLVFVVDSS 77
>gnl|CDD|223026 PHA03261, PHA03261, Capsid triplex subunit 1; Provisional.
Length = 469
Score = 26.2 bits (58), Expect = 1.8
Identities = 12/29 (41%), Positives = 14/29 (48%), Gaps = 4/29 (13%)
Query: 57 FQDFDAELIFARCGA----LIFVIDTSMG 81
F D DAELI G L+FV +G
Sbjct: 296 FLDLDAELILGDDGVKFLYLVFVYTQRLG 324
>gnl|CDD|206733 cd04170, EF-G_bact, Elongation factor G (EF-G) family.
Translocation is mediated by EF-G (also called
translocase). The structure of EF-G closely resembles
that of the complex between EF-Tu and tRNA. This is an
example of molecular mimicry; a protein domain evolved
so that it mimics the shape of a tRNA molecule. EF-G in
the GTP form binds to the ribosome, primarily through
the interaction of its EF-Tu-like domain with the 50S
subunit. The binding of EF-G to the ribosome in this
manner stimulates the GTPase activity of EF-G. On GTP
hydrolysis, EF-G undergoes a conformational change that
forces its arm deeper into the A site on the 30S
subunit. To accommodate this domain, the peptidyl-tRNA
in the A site moves to the P site, carrying the mRNA and
the deacylated tRNA with it. The ribosome may be
prepared for these rearrangements by the initial binding
of EF-G as well. The dissociation of EF-G leaves the
ribosome ready to accept the next aminoacyl-tRNA into
the A site. This group contains only bacterial members.
Length = 268
Score = 26.0 bits (58), Expect = 2.1
Identities = 11/36 (30%), Positives = 15/36 (41%), Gaps = 5/36 (13%)
Query: 48 LWDCPGQMDFQDFDAELIFA--RCGALIFVIDTSMG 81
L D PG DF E + A A + V++ G
Sbjct: 68 LIDTPGYADFV---GETLSALRAVDAALIVVEAQSG 100
>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 = 26.0 bits (58), Expect = 2.2
Identities = 21/82 (25%), Positives = 31/82 (37%), Gaps = 14/82 (17%)
Query: 2 GLRRSGKTSI----QKVVFQKMSPNETLFLEGTNKMTKEDIANSSFLQYQLWDCPGQMDF 57
GL +GKT+I + P G N + + N F +WD GQ
Sbjct: 6 GLDGAGKTTILYKLKLGEVVTTIPTI-----GFN-VETVEYKNVKF---TVWDVGGQDKI 56
Query: 58 QDFDAELIFARCGALIFVIDTS 79
+ + LIFV+D+S
Sbjct: 57 RPLWKHY-YENTDGLIFVVDSS 77
>gnl|CDD|224586 COG1672, COG1672, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 359
Score = 25.5 bits (56), Expect = 3.5
Identities = 12/44 (27%), Positives = 17/44 (38%)
Query: 1 MGLRRSGKTSIQKVVFQKMSPNETLFLEGTNKMTKEDIANSSFL 44
G RR GKTS+ K ++ L N K + F+
Sbjct: 29 YGRRRVGKTSLLKEFIKEKLGIYILVDFYINLRNKRFSSYLDFI 72
>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 = 25.4 bits (56), Expect = 3.5
Identities = 20/83 (24%), Positives = 34/83 (40%), Gaps = 14/83 (16%)
Query: 1 MGLRRSGKTSIQKV----VFQKMSPNETLFLEGTNKMTKEDIANSSFLQYQLWDCPGQMD 56
+GL +GKT+I K ++P + G N + + +WD GQ
Sbjct: 21 LGLDNAGKTTILKQLASEDISHITPTQ-----GFNIKN----VQADGFKLNVWDIGGQRK 71
Query: 57 FQDFDAELIFARCGALIFVIDTS 79
+ + F LI+VID++
Sbjct: 72 IRPY-WRNYFENTDVLIYVIDSA 93
>gnl|CDD|107155 PHA02241, PHA02241, hypothetical protein.
Length = 182
Score = 25.1 bits (54), Expect = 3.9
Identities = 6/28 (21%), Positives = 12/28 (42%), Gaps = 1/28 (3%)
Query: 23 ETLFLEGTNKMTKED-IANSSFLQYQLW 49
+F+ +TKE I + +Y +
Sbjct: 52 NPIFINEYPYITKEKLIEEQRYFRYNSY 79
>gnl|CDD|233380 TIGR01370, TIGR01370, extracellular protein. Original assignment
of this protein family as cysteinyl-tRNA synthetase is
controversial, supported by PMID:11333988 but challenged
by PMID:14679218 and by subsequent discovery of the
actual mechanism for synthesizing Cys-tRNA in species
where a direct Cys--tRNA ligase was not found. Lingering
legacy annotations of members of this family probably
should be removed. Evidence against the role includes a
signal peptide. This family as been renamed
"extracellular protein" to facilitate correction.
Members of this family occur in Deinococcus radiodurans
(bacterial) and Methanococcus jannaschii (archaeal). A
number of homologous but more distantly related proteins
are annotated as alpha-1,4 polygalactosaminidases. The
function remains unknown [Unknown function, General].
Length = 315
Score = 25.3 bits (55), Expect = 4.2
Identities = 8/31 (25%), Positives = 12/31 (38%)
Query: 20 SPNETLFLEGTNKMTKEDIANSSFLQYQLWD 50
E LF N+ T+ + Y+LW
Sbjct: 232 WAVEELFYYAANRPTEAERQRRLLALYRLWQ 262
>gnl|CDD|173837 cd00868, Terpene_cyclase_C1, Terpene cyclases, Class 1. Terpene
cyclases, Class 1 (C1) of the class 1 family of
isoprenoid biosynthesis enzymes, which share the
'isoprenoid synthase fold' and convert linear,
all-trans, isoprenoids, geranyl (C10)-, farnesyl
(C15)-, or geranylgeranyl (C20)-diphosphate into
numerous cyclic forms of monoterpenes, diterpenes, and
sesquiterpenes. Also included in this CD are the
cis-trans terpene cyclases such as trichodiene
synthase. The class I terpene cyclization reactions
proceed via electrophilic alkylations in which a new
carbon-carbon single bond is generated through
interaction between a highly reactive
electron-deficient allylic carbocation and an
electron-rich carbon-carbon double bond. The catalytic
site consists of a large central cavity formed by
mostly antiparallel alpha helices with two
aspartate-rich regions located on opposite walls. These
residues mediate binding of prenyl phosphates via
bridging Mg2+ ions, inducing proposed conformational
changes that close the active site to solvent,
stabilizing reactive carbocation intermediates.
Mechanistically and structurally distinct, class II
terpene cyclases and cis-IPPS are not included in this
CD. Taxonomic distribution includes bacteria, fungi and
plants.
Length = 284
Score = 24.6 bits (54), Expect = 6.9
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 58 QDFDAELIFARCGALIFVID 77
Q +A + A+ AL+ VID
Sbjct: 44 QYSEARIALAKTIALLTVID 63
>gnl|CDD|237498 PRK13768, PRK13768, GTPase; Provisional.
Length = 253
Score = 24.4 bits (54), Expect = 8.2
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 8/53 (15%)
Query: 35 KEDIANSSFLQYQLWDCPGQMD---FQDFDAELIFARCG----ALIFVIDTSM 80
KE+I + Y L D PGQM+ F++ +L+ G ++F+ID +
Sbjct: 89 KEEIESLD-ADYVLVDTPGQMELFAFRESGRKLVERLSGSSKSVVVFLIDAVL 140
>gnl|CDD|238982 cd02024, NRK1, Nicotinamide riboside kinase (NRK) is an enzyme
involved in the metabolism of nicotinamide adenine
dinucleotide (NAD+). This enzyme catalyzes the
phosphorylation of nicotinamide riboside (NR) to form
nicotinamide mononucleotide (NMN). It defines the NR
salvage pathway of NAD+ biosynthesis in addition to the
pathways through nicotinic acid mononucleotide (NaMN).
This enzyme can also phosphorylate the anticancer drug
tiazofurin, which is an analog of nicotinamide
riboside.
Length = 187
Score = 24.2 bits (53), Expect = 8.6
Identities = 4/20 (20%), Positives = 9/20 (45%)
Query: 45 QYQLWDCPGQMDFQDFDAEL 64
++ WD +D + + L
Sbjct: 47 GFKQWDVLEALDMEAMMSTL 66
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
0.323 0.137 0.407
Gapped
Lambda K H
0.267 0.0802 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,960,625
Number of extensions: 293461
Number of successful extensions: 297
Number of sequences better than 10.0: 1
Number of HSP's gapped: 288
Number of HSP's successfully gapped: 30
Length of query: 81
Length of database: 10,937,602
Length adjustment: 50
Effective length of query: 31
Effective length of database: 8,719,902
Effective search space: 270316962
Effective search space used: 270316962
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.1 bits)