RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3058
(244 letters)
>gnl|CDD|187700 cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI domain of reverse
transcriptases. Ribonuclease H (RNase H) is classified
into two families, type 1 (prokaryotic RNase HI,
eukaryotic RNase H1 and viral RNase H) and type 2
(prokaryotic RNase HII and HIII, and eukaryotic RNase
H2). Ribonuclease HI (RNase HI) is an endonuclease that
cleaves the RNA strand of an RNA/DNA hybrid in a
sequence non-specific manner. RNase H is widely present
in various organisms, including bacteria, archaea and
eukaryotes. RNase HI has also been observed as an
adjunct domain to the reverse transcriptase gene in
retroviruses, long-term repeat (LTR)-bearing
retrotransposons and non-LTR retrotransposons. RNase HI
in LTR retrotransposons perform degradation of the
original RNA template, generation of a polypurine tract
(the primer for plus-strand DNA synthesis), and final
removal of RNA primers from newly synthesized minus and
plus strands. The catalytic residues for RNase H
enzymatic activity, three aspartatic acids and one
glutamatic acid residue (DEDD), are unvaried across all
RNase H domains. The position of the RNase domain of
non-LTR and LTR transposons is at the carboxyl terminal
of the reverse transcriptase (RT) domain and their RNase
domains group together, indicating a common evolutionary
origin. Many non-LTR transposons have lost the RNase
domain because their activity is at the nucleus and
cellular RNase may suffice; however LTR retotransposons
always encode their own RNase domain because it requires
RNase activity in RNA-protein particles in the
cytoplasm. RNase H inhibitors have been explored as an
anti-HIV drug target because RNase H inactivation
inhibits reverse transcription.
Length = 128
Score = 86.9 bits (216), Expect = 9e-22
Identities = 29/96 (30%), Positives = 48/96 (50%), Gaps = 1/96 (1%)
Query: 3 TYRLNSLSSSFTAEAFAMEMCLDNLINRPI-PDNILIFTDSKSLISSMQQLFCKNILIHD 61
+Y+L S F AE A+ L + I IF+DS++ + +++ + L+
Sbjct: 28 SYKLGPYCSVFDAELLAILEALQLALREGRRARKITIFSDSQAALKALRSPRSSSPLVLR 87
Query: 62 IQVACHKLILKGNNVKIIWIPSHCGIAGNEEVDKAA 97
I+ A +L G V++ W+P H GI GNE D+ A
Sbjct: 88 IRKAIRELANHGVKVRLHWVPGHSGIEGNERADRLA 123
>gnl|CDD|215695 pfam00075, RNase_H, RNase H. RNase H digests the RNA strand of an
RNA/DNA hybrid. Important enzyme in retroviral
replication cycle, and often found as a domain
associated with reverse transcriptases. Structure is a
mixed alpha+beta fold with three a/b/a layers.
Length = 126
Score = 63.4 bits (155), Expect = 5e-13
Identities = 26/90 (28%), Positives = 44/90 (48%), Gaps = 4/90 (4%)
Query: 10 SSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCKNILIHDIQVACHKL 69
+++ AE A+ L+ L + + I+TDS+ +I + + I+ +L
Sbjct: 38 TTNQRAELLALIEALEALSGQKV----NIYTDSQYVIGGITNGWPTKSESKPIKNEIWEL 93
Query: 70 ILKGNNVKIIWIPSHCGIAGNEEVDKAAQS 99
+ K + V I W+P H GI GNE DK A+
Sbjct: 94 LQKKHKVYIQWVPGHSGIPGNELADKLAKQ 123
>gnl|CDD|187690 cd06222, RNase_H, RNase H is an endonuclease that cleaves the RNA
strand of an RNA/DNA hybrid in a sequence non-specific
manner. Ribonuclease H (RNase H) enzymes are divided
into two major families, Type 1 and Type 2, based on
amino acid sequence similarities and biochemical
properties. RNase H is an endonuclease that cleaves the
RNA strand of an RNA/DNA hybrid in a sequence
non-specific manner in the presence of divalent cations.
RNase H is widely present in various organisms,
including bacteria, archaea and eukaryotes. Most
prokaryotic and eukaryotic genomes contain multiple
RNase H genes. Despite the lack of amino acid sequence
homology, Type 1 and type 2 RNase H share a main-chain
fold and steric configurations of the four acidic
active-site residues and have the same catalytic
mechanism and functions in cells. RNase H is involved in
DNA replication, repair and transcription. One of the
important functions of RNase H is to remove Okazaki
fragments during DNA replication. RNase H inhibitors
have been explored as an anti-HIV drug target because
RNase H inactivation inhibits reverse transcription.
Length = 123
Score = 46.6 bits (111), Expect = 7e-07
Identities = 19/95 (20%), Positives = 39/95 (41%), Gaps = 13/95 (13%)
Query: 7 NSLSSSFTAEA----FAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQLFCKNILIHDI 62
+++ AE A+E+ LD + + ++I TDSK ++ + + +
Sbjct: 34 IPAATNNEAELLALLEALELALDLGLKK-----LIIETDSKYVVDLINSWSKGWKKNNLL 88
Query: 63 QVACHKLILKGNNVKIIWIPSHCGIAGNEEVDKAA 97
L+ K +++ +P GNE D+ A
Sbjct: 89 LWDILLLLSKFIDIRFEHVPRE----GNEVADRLA 119
>gnl|CDD|187704 cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase H is longer and
more complex than their prokaryotic counterparts and
unlike prokaryote, RNase H are essential in higher
eukaryote. Ribonuclease H (RNase H) is classified into
two families, type 1 (prokaryotic RNase HI, eukaryotic
RNase H1 and viral RNase H) and type 2 (prokaryotic
RNase HII and HIII, and eukaryotic RNase H2). RNase H is
an endonuclease that cleaves the RNA strand of an
RNA/DNA hybrid in a sequence non-specific manner. RNase
H is involved in DNA replication, repair and
transcription. One of the important functions of RNase H
is to remove Okazaki fragments during DNA replication.
RNase H is widely present in various organisms,
including bacteria, archaea and eukaryote and most
prokaryotic and eukaryotic genomes contain multiple
RNase H genes. Despite the lack of amino acid sequence
homology, Type 1 and type 2 RNase H share a main-chain
fold and steric configurations of the four acidic
active-site (DEDD) residues and have the same catalytic
mechanism and functions in cells. Eukaryotic RNase H is
longer and more complex than in prokaryotes. Almost all
eukaryotic RNase HI have highly conserved regions at the
N-terminal called hybrid binding domain (HBD). It is
speculated that the HBD contributes to binding the
RNA/DNA hybrid. Prokaryotes and some single-cell
eukaryotes do not require RNase H for viability, but
RNase H is essential in higher eukaryotes. RNase H
knockout mice lack mitochondrial DNA replication and die
as embryos.
Length = 150
Score = 44.5 bits (106), Expect = 7e-06
Identities = 25/100 (25%), Positives = 41/100 (41%), Gaps = 17/100 (17%)
Query: 15 AEAFAMEMCLDNLINRPIP-DNILIFTDSKSLISSMQQLF---------------CKNI- 57
AE A+ L + ++I TDS+ +++ + + N
Sbjct: 46 AELRAVIHALRLIKEVGEGLTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVANKD 105
Query: 58 LIHDIQVACHKLILKGNNVKIIWIPSHCGIAGNEEVDKAA 97
LI ++ +L +G VK +P H GI GNEE D+ A
Sbjct: 106 LIKELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLA 145
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 34.3 bits (79), Expect = 0.022
Identities = 15/77 (19%), Positives = 28/77 (36%), Gaps = 12/77 (15%)
Query: 33 PDNILIFTDSKSLISSMQQLFCKNILI------------HDIQVACHKLILKGNNVKIIW 80
+ ++TDSK ++ + + K D+ +L+ + V W
Sbjct: 63 ACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEW 122
Query: 81 IPSHCGIAGNEEVDKAA 97
+ H G NE D+ A
Sbjct: 123 VKGHAGHPENERADQLA 139
>gnl|CDD|187702 cd09278, RNase_HI_prokaryote_like, RNase HI family found mainly in
prokaryotes. Ribonuclease H (RNase H) is classified
into two evolutionarily unrelated families, type 1
(prokaryotic RNase HI, eukaryotic RNase H1 and viral
RNase H) and type 2 (prokaryotic RNase HII and HIII, and
eukaryotic RNase H2). RNase H is an endonuclease that
cleaves the RNA strand of an RNA/DNA hybrid in a
sequence non-specific manner. RNase H is involved in DNA
replication, repair and transcription. RNase H is widely
present in various organisms, including bacteria,
archaea and eukaryotes and most prokaryotic and
eukaryotic genomes contain multiple RNase H genes.
Despite the lack of amino acid sequence homology, Type 1
and type 2 RNase H share a main-chain fold and steric
configurations of the four acidic active-site (DEDD),
residues and have the same catalytic mechanism and
functions in cells. One of the important functions of
RNase H is to remove Okazaki fragments during DNA
replication. Prokaryotic RNase H varies greatly in
domain structures and substrate specificities.
Prokaryotes and some single-cell eukaryotes do not
require RNase H for viability.
Length = 139
Score = 33.6 bits (78), Expect = 0.027
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 70 ILKGNNVKIIWIPSHCGIAGNEEVDKAAQ 98
+L + V W+ H G GNE D+ A
Sbjct: 107 LLAKHQVTWHWVKGHAGHPGNERADELAN 135
>gnl|CDD|205634 pfam13456, RVT_3, Reverse transcriptase-like. This domain is
found in plants and appears to be part of a
retrotransposon.
Length = 88
Score = 32.5 bits (75), Expect = 0.033
Identities = 22/96 (22%), Positives = 45/96 (46%), Gaps = 21/96 (21%)
Query: 11 SSFTAEAFA----MEMCLDNLINRPIPDNILIFTDSKSLISSMQQL-FCKNI---LIHDI 62
S AEA A +++ L+ I R +++ +DS+ ++ +Q ++ L+ +I
Sbjct: 1 SPLEAEAEALLEGLQLALELGIRR-----LIVESDSQLVVQQIQGEYEARSRLAALLREI 55
Query: 63 QVACHKLILKGNNVKIIWIPSHCGIAGNEEVDKAAQ 98
+ KL+ K ++V + +P C N D A+
Sbjct: 56 R----KLLKKFDSVSVSHVPREC----NRVADALAK 83
>gnl|CDD|187703 cd09279, RNase_HI_archaeal_like, RNAse HI family that includes
Archaeal RNase HI. Ribonuclease H (RNase H) is
classified into two evolutionarily unrelated families,
type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and
viral RNase H) and type 2 (prokaryotic RNase HII and
HIII, and eukaryotic RNase H2). RNase H is an
endonuclease that cleaves the RNA strand of an RNA/DNA
hybrid in a sequence non-specific manner. RNase H is
involved in DNA replication, repair and transcription.
RNase H is widely present in various organisms,
including bacteria, archaea and eukaryotes and most
prokaryotic and eukaryotic genomes contain multiple
RNase H genes. Despite the lack of amino acid sequence
homology, Type 1 and type 2 RNase H share a main-chain
fold and steric configurations of the four acidic
active-site (DEDD) residues and have the same catalytic
mechanism and functions in cells. One of the important
functions of RNase H is to remove Okazaki fragments
during DNA replication. Most archaeal genomes contain
only type 2 RNase H (RNase HII); however, a few contain
RNase HI as well. Although archaeal RNase HI sequences
conserve the DEDD active-site motif, they lack other
common features important for catalytic function, such
as the basic protrusion region. Archaeal RNase HI
homologs are more closely related to retroviral RNase HI
than bacterial and eukaryotic type I RNase H in
enzymatic properties.
Length = 128
Score = 32.5 bits (75), Expect = 0.066
Identities = 23/97 (23%), Positives = 43/97 (44%), Gaps = 6/97 (6%)
Query: 3 TYRLNSLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQ-QLFCKNILIHD 61
+ L +++ AE A+ L+ + I + I+ DS+ +++ +Q + KN +
Sbjct: 33 SIPLGFPATNNEAEYEALIAGLELALELGI-KKLEIYGDSQLVVNQIQGEYEVKNERLAP 91
Query: 62 IQVACHKLILKGNNVKIIWIPSHCGIAGNEEVDKAAQ 98
+L+ K V+I WIP N+E D A
Sbjct: 92 YLEEARELLKKFEEVEIKWIPREE----NKEADALAN 124
>gnl|CDD|237371 PRK13381, PRK13381, peptidase T; Provisional.
Length = 404
Score = 31.8 bits (73), Expect = 0.25
Identities = 12/48 (25%), Positives = 21/48 (43%), Gaps = 9/48 (18%)
Query: 205 QIRLKYNLNNLQ---------IKDILGDNPRTIDLLFRFLKDSNLLPK 243
+I KY + I + + D+ R +DL F +K+ + PK
Sbjct: 299 KINAKYPTARVSLTLTDQYSNISNSIKDDRRAVDLAFDAMKELGIEPK 346
>gnl|CDD|213406 cd12213, ABD, Alpha-Mannosidase Binding Domain of Atg19/34.
These proteins are related to the Alpha-mannosidase
(Ams1) Binding Domain of Atg19/Atg34, a key component
in the targeting pathway that directs alpha-mannosidase
and aminopeptidase I to the vacuole, either through
cytoplasm-to-vacuole trafficking or via autophagy in
starvation conditions. Autophagy in a eukaryotic
mechanism in which cytoplasm is enclosed in
double-membraned autophagosomes which fuse with a
vacuole for transport into the lumen. In Saccharomyces
cerevisiae, alpha-mannosidase is selectively directed
to the vacuole via the direct interaction with Atg19
(and paralog Atg34) in the Cvt pathway. Ams1 binding
domains (ABD) Atg19/34 have a immunoglobulin fold with
eight beta-strands. The ABD is responsible for Ams1
recognition, but its deletion does not affect the
fusion of Atg19 with prApe1, and the transport of
prApe1 to the vacuole. The Atg19 N-terminal region is a
distinct coiled-coil domain.
Length = 112
Score = 29.6 bits (67), Expect = 0.53
Identities = 16/74 (21%), Positives = 25/74 (33%), Gaps = 8/74 (10%)
Query: 24 LDNLINRPIPDNILIFTDSKSLISSMQQLFCKNILIHDIQVACHKLILKGNNVKIIWIPS 83
L N + +P N L+ Q N + I + H+L G+ K++ P
Sbjct: 19 LYNRGDSALPGN-------LKLVFQYQADDTANPVTVSIYMGPHELQPNGSK-KLLNFPY 70
Query: 84 HCGIAGNEEVDKAA 97
I E K
Sbjct: 71 FGSIILLEGPCKID 84
>gnl|CDD|187701 cd09277, RNase_HI_bacteria_HBD, Bacterial RNase HI containing a
hybrid binding domain (HBD) at the N-terminus.
Ribonuclease H (RNase H) enzymes are divided into two
major families, Type 1 and Type 2, based on amino acid
sequence similarities and biochemical properties. RNase
H is an endonuclease that cleaves the RNA strand of an
RNA/DNA hybrid in a sequence non-specific manner in the
presence of divalent cations. RNase H is involved in
DNA replication, repair and transcription. RNase H is
widely present in various organisms, including bacteria,
archaea and eukaryotes and most prokaryotic and
eukaryotic genomes contain multiple RNase H genes.
Despite the lack of amino acid sequence homology, Type 1
and type 2 RNase H share a main-chain fold and steric
configurations of the four acidic active-site (DEDD)
residues and have the same catalytic mechanism and
functions in cells. One of the important functions of
RNase H is to remove Okazaki fragments during DNA
replication. Prokaryotic RNase H varies greatly in
domain structures and substrate specificities.
Prokaryotes and some single-cell eukaryotes do not
require RNase H for viability. Some bacteria
distinguished from other bacterial RNase HI in the
presence of a hybrid binding domain (HBD) at the
N-terminus which is commonly present at the N-termini of
eukaryotic RNase HI. It has been reported that this
domain is required for dimerization and processivity of
RNase HI upon binding to RNA-DNA hybrids.
Length = 133
Score = 29.0 bits (66), Expect = 1.2
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 70 ILKGNNVKIIWIPSHCGIAGNEEVDKAA 97
I K + + + +H G NE DK A
Sbjct: 102 IKKKIKISFVKVKAHSGDKYNELADKLA 129
>gnl|CDD|222678 pfam14321, DUF4382, Domain of unknown function (DUF4382). This
family is found in bacteria and archaea, and is
typically between 142 and 161 amino acids in length.
Length = 138
Score = 28.7 bits (65), Expect = 1.5
Identities = 13/53 (24%), Positives = 21/53 (39%), Gaps = 12/53 (22%)
Query: 179 TDPPQCEVCNVTITVKHILCHCTKYTQIRLKYNLNNLQIKDILGDNPRTIDLL 231
TD P V +T+ + + + Y+ ++ L P TIDLL
Sbjct: 10 TDAPVDGAEKVVVTI----------SSVEVHYSNDDEG--SWLTITPETIDLL 50
>gnl|CDD|119338 cd06570, GH20_chitobiase-like_1, A functionally uncharacterized
subgroup of the Glycosyl hydrolase family 20 (GH20)
catalytic domain found in proteins similar to the
chitobiase of Serratia marcescens, a
beta-N-1,4-acetylhexosaminidase that hydrolyzes the
beta-1,4-glycosidic linkages in oligomers derived from
chitin. Chitin is degraded by a two step process: i) a
chitinase hydrolyzes the chitin to oligosaccharides and
disaccharides such as di-N-acetyl-D-glucosamine and
chitobiose, ii) chitobiase then further degrades these
oligomers into monomers. This subgroup lacks the
C-terminal PKD (polycystic kidney disease I)-like domain
found in the chitobiases. The GH20 hexosaminidases are
thought to act via a catalytic mechanism in which the
catalytic nucleophile is not provided by solvent or the
enzyme, but by the substrate itself.
Length = 311
Score = 28.1 bits (63), Expect = 4.6
Identities = 18/74 (24%), Positives = 29/74 (39%), Gaps = 15/74 (20%)
Query: 87 IAGNEEVDK------AAQSFINAQNYSLITHVDLKAFLKNEFKK------KWQIWWDNIQ 134
I G+E K Q+F+ L L+A+ +K K I WD +
Sbjct: 153 IGGDEVDPKQWNENPRIQAFMKEHG--LKDAAALQAYFNQRVEKILSKHGKKMIGWDEVL 210
Query: 135 PPNKIKDTVKE-WQ 147
P+ K+ V + W+
Sbjct: 211 HPDLPKNVVIQSWR 224
>gnl|CDD|212527 cd10003, HDAC6-dom2, Histone deacetylase 6, domain 2. Histone
deacetylase 6 is a class IIb Zn-dependent enzyme that
catalyzes hydrolysis of N(6)-acetyl-lysine residue of a
histone to yield a deacetylated histone (EC 3.5.1.98).
Histone acetylation/deacetylation process is important
for mediation of transcriptional regulation of many
genes. HDACs usually act via association with DNA
binding proteins to target specific chromatin regions.
HDAC6 is the only histone deacetylase with internal
duplication of two catalytic domains which appear to
function independently of each other, and also has a
C-terminal ubiquitin-binding domain. It is located in
the cytoplasm and associates with microtubule motor
complex, functioning as the tubulin deacetylase and
regulating microtubule-dependent cell motility. Known
interaction partners of HDAC6 are alpha tubulin and
ubiquitin-like modifier FAT10 (also known as Ubiquitin D
or UBD).
Length = 350
Score = 28.1 bits (63), Expect = 4.9
Identities = 14/48 (29%), Positives = 18/48 (37%), Gaps = 7/48 (14%)
Query: 4 YRLNSLSSSFTAEAFAMEMCLDNLINRPIPDNILIFTDSKSLISSMQQ 51
Y L S+S S M MC L+ P P L S + S+
Sbjct: 297 YNLTSISES-------MSMCTKTLLGDPPPVLDLPRPPCSSALKSINN 337
>gnl|CDD|171444 PRK12371, PRK12371, ribonuclease III; Reviewed.
Length = 235
Score = 27.7 bits (62), Expect = 5.3
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 5 RLNSLSSSFTAEAFAMEMCLDNLI 28
RLN L ++ T A A E+ L +LI
Sbjct: 80 RLNQLVNAETCAAIADEIGLHDLI 103
>gnl|CDD|223683 COG0610, COG0610, Type I site-specific restriction-modification
system, R (restriction) subunit and related helicases
[Defense mechanisms].
Length = 962
Score = 28.1 bits (63), Expect = 5.4
Identities = 10/43 (23%), Positives = 14/43 (32%), Gaps = 3/43 (6%)
Query: 118 LKNEFKKKWQIWWDNIQPPNKIKDTVKEWQTSNRNSRKEEIIL 160
L F K + I+ +KEW R +K L
Sbjct: 821 LLQTFNDKNGAYESLK---ELIERIIKEWIEDLRQKKKLIERL 860
>gnl|CDD|236334 PRK08719, PRK08719, ribonuclease H; Reviewed.
Length = 147
Score = 26.7 bits (59), Expect = 7.0
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 76 VKIIWIPSHCGIAGNEEVDKAAQ 98
V++ + +H GI GNE D AQ
Sbjct: 120 VEVEKVTAHSGIEGNEAADMLAQ 142
>gnl|CDD|238212 cd00352, Gn_AT_II, Glutamine amidotransferases class-II (GATase).
The glutaminase domain catalyzes an amide nitrogen
transfer from glutamine to the appropriate substrate. In
this process, glutamine is hydrolyzed to glutamic acid
and ammonia. This domain is related to members of the
Ntn (N-terminal nucleophile) hydrolase superfamily and
is found at the N-terminus of enzymes such as
glucosamine-fructose 6-phosphate synthase (GLMS or
GFAT), glutamine phosphoribosylpyrophosphate (Prpp)
amidotransferase (GPATase), asparagine synthetase B
(AsnB), beta lactam synthetase (beta-LS) and glutamate
synthase (GltS). GLMS catalyzes the formation of
glucosamine 6-phosphate from fructose 6-phosphate and
glutamine in amino sugar synthesis. GPATase catalyzes
the first step in purine biosynthesis, an amide transfer
from glutamine to PRPP, resulting in
phosphoribosylamine, pyrophosphate and glutamate.
Asparagine synthetase B synthesizes asparagine from
aspartate and glutamine. Beta-LS catalyzes the formation
of the beta-lactam ring in the beta-lactamase inhibitor
clavulanic acid. GltS synthesizes L-glutamate from
2-oxoglutarate and L-glutamine. These enzymes are
generally dimers, but GPATase also exists as a
homotetramer.
Length = 220
Score = 27.0 bits (60), Expect = 8.1
Identities = 10/50 (20%), Positives = 17/50 (34%), Gaps = 3/50 (6%)
Query: 126 WQIWWDNIQPPNKIKDTVKEWQTSNRNSRKEEIILSRLRIGHTRL-THGF 174
I + K + +E + S + +GH RL T+G
Sbjct: 35 AGIAVYDGDGLFVEKRAGPVSDVALDL--LDEPLKSGVALGHVRLATNGL 82
>gnl|CDD|132949 cd06618, PKc_MKK7, Catalytic domain of the dual-specificity Protein
Kinase, MAP kinase kinase 7. Protein kinases (PKs), MAP
kinase kinase 7 (MKK7) subfamily, catalytic (c) domain.
PKs catalyze the transfer of the gamma-phosphoryl group
from ATP to serine/threonine or tyrosine residues on
protein substrates. The MKK7 subfamily is part of a
larger superfamily that includes the catalytic domains
of other protein serine/threonine kinases, protein
tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. The mitogen-activated protein (MAP) kinase
signaling pathways are important mediators of cellular
responses to extracellular signals. The pathways involve
a triple kinase core cascade comprising the MAP kinase
(MAPK), which is phosphorylated and activated by a MAPK
kinase (MAPKK or MKK), which itself is phosphorylated
and activated by a MAPK kinase kinase (MAPKKK or MKKK).
MKK7 is a dual-specificity PK that phosphorylates and
activates its downstream target, c-Jun N-terminal kinase
(JNK), on specific threonine and tyrosine residues.
Although MKK7 is capable of dual phosphorylation, it
prefers to phosphorylate the threonine residue of JNK.
Thus, optimal activation of JNK requires both MKK4 (not
included in this subfamily) and MKK7. MKK7 is primarily
activated by cytokines. MKK7 is essential for liver
formation during embryogenesis. It plays roles in G2/M
cell cycle arrest and cell growth. In addition, it is
involved in the control of programmed cell death, which
is crucial in oncogenesis, cancer chemoresistance, and
antagonism to TNFalpha-induced killing, through its
inhibition by Gadd45beta and the subsequent suppression
of the JNK cascade.
Length = 296
Score = 27.0 bits (60), Expect = 8.5
Identities = 11/21 (52%), Positives = 13/21 (61%), Gaps = 3/21 (14%)
Query: 20 MEMCLDNL---INRPIPDNIL 37
M CLD L I PIP++IL
Sbjct: 96 MSTCLDKLLKRIQGPIPEDIL 116
>gnl|CDD|99734 cd00609, AAT_like, Aspartate aminotransferase family. This family
belongs to pyridoxal phosphate (PLP)-dependent aspartate
aminotransferase superfamily (fold I). Pyridoxal
phosphate combines with an alpha-amino acid to form a
compound called a Schiff base or aldimine intermediate,
which depending on the reaction, is the substrate in
four kinds of reactions (1) transamination (movement of
amino groups), (2) racemization (redistribution of
enantiomers), (3) decarboxylation (removing COOH
groups), and (4) various side-chain reactions depending
on the enzyme involved. Pyridoxal phosphate (PLP)
dependent enzymes were previously classified into alpha,
beta and gamma classes, based on the chemical
characteristics (carbon atom involved) of the reaction
they catalyzed. The availability of several structures
allowed a comprehensive analysis of the evolutionary
classification of PLP dependent enzymes, and it was
found that the functional classification did not always
agree with the evolutionary history of these enzymes.
The major groups in this CD corresponds to Aspartate
aminotransferase a, b and c, Tyrosine, Alanine,
Aromatic-amino-acid, Glutamine phenylpyruvate,
1-Aminocyclopropane-1-carboxylate synthase,
Histidinol-phosphate, gene products of malY and cobC,
Valine-pyruvate aminotransferase and Rhizopine
catabolism regulatory protein.
Length = 350
Score = 27.3 bits (61), Expect = 8.7
Identities = 6/53 (11%), Positives = 23/53 (43%), Gaps = 3/53 (5%)
Query: 33 PDNILIFTDSKSLISSMQQLFCK---NILIHDIQVACHKLILKGNNVKIIWIP 82
P+ I++ ++ +S + + +L+ D ++ + +++ +P
Sbjct: 59 PEEIVVTNGAQEALSLLLRALLNPGDEVLVPDPTYPGYEAAARLAGAEVVPVP 111
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 0.136 0.421
Gapped
Lambda K H
0.267 0.0794 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,154,432
Number of extensions: 1117058
Number of successful extensions: 1046
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1042
Number of HSP's successfully gapped: 32
Length of query: 244
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 150
Effective length of database: 6,768,326
Effective search space: 1015248900
Effective search space used: 1015248900
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: 58 (26.0 bits)