RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5156
(389 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 = 81.5 bits (202), Expect = 7e-19
Identities = 44/194 (22%), Positives = 69/194 (35%), Gaps = 68/194 (35%)
Query: 20 IYTDGSKDETGVGCALIIPQLNVTKR-FTLNKYSSIFHAELFSILQSLKNAKLLNIKKVL 78
IYTDGSK E G I + R + L Y S+F AEL +IL++L+ A
Sbjct: 2 IYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGR---- 57
Query: 79 IISDSLSSFQAISNLYHPNPLVKEIPHAELFSILQSLKNAELLNIKKVLIISDSLSSFQA 138
+K+ I SDS ++ +A
Sbjct: 58 -------------------------------------------RARKITIFSDSQAALKA 74
Query: 139 ISNLYHPNPLVKEIQETYSSAQISIKFLWCPSHPCWYFWKRSSSQISIKFLWCPSHVGIS 198
+ + +PLV I++ ++ + ++ W P H GI
Sbjct: 75 LRSPRSSSPLVLRIRKAIRE--------------------LANHGVKVRLHWVPGHSGIE 114
Query: 199 GNDQADTEAKKATS 212
GN++AD AK+A
Sbjct: 115 GNERADRLAKEAAK 128
>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 = 46.9 bits (112), Expect = 1e-06
Identities = 27/105 (25%), Positives = 41/105 (39%), Gaps = 23/105 (21%)
Query: 106 AELFSILQSLKNAELLNIKKVLIISDSLSSFQAISNLYHPNPLVKEIQETYSSAQISIKF 165
AEL +++++L+ +KV I +DS I+N P S IK
Sbjct: 43 AELLALIEALEALSG---QKVNIYTDSQYVIGGITN---GWPT--------KSESKPIKN 88
Query: 166 LWCPSHPCWYFWKRSSSQISIKFLWCPSHVGISGNDQADTEAKKA 210
W+ + + W P H GI GN+ AD AK+
Sbjct: 89 E---------IWELLQKKHKVYIQWVPGHSGIPGNELADKLAKQG 124
>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 = 45.4 bits (108), Expect = 3e-06
Identities = 19/89 (21%), Positives = 35/89 (39%), Gaps = 6/89 (6%)
Query: 21 YTDGSKDETG--VGCALIIPQLNVTKRFTL---NKYSSIFHAELFSILQSLKNAKLLNIK 75
TDGS G ++ F ++ AEL ++L++L+ A L +K
Sbjct: 1 NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLGLK 60
Query: 76 KVLIISDSLSSFQAISN-LYHPNPLVKEI 103
K++I +DS I++ +
Sbjct: 61 KLIIETDSKYVVDLINSWSKGWKKNNLLL 89
Score = 42.0 bits (99), Expect = 5e-05
Identities = 26/107 (24%), Positives = 41/107 (38%), Gaps = 26/107 (24%)
Query: 105 HAELFSILQSLKNAELLNIKKVLIISDSLSSFQAISN-LYHPNPLVKEIQETYSSAQISI 163
AEL ++L++L+ A L +KK++I +DS I++ +
Sbjct: 41 EAELLALLEALELALDLGLKKLIIETDSKYVVDLINSWSKGWKKNNLLL----------- 89
Query: 164 KFLWCPSHPCWYFWKRSSSQISIKFLWCPSHVGISGNDQADTEAKKA 210
W S I I+F P GN+ AD AK+A
Sbjct: 90 ----------WDILLLLSKFIDIRFEHVPR----EGNEVADRLAKEA 122
>gnl|CDD|187697 cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase HI in long-term
repeat retroelements. 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 eukaryote. RNase HI has
also been observed as adjunct domains to the reverse
transcriptase gene in retroviruses, in 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.
Phylogenetic patterns of RNase HI of LTR retroelements
is classified into five major families, Ty3/Gypsy,
Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate
retroviruses. Bel/Pao family has been described only in
metazoan genomes. RNase H inhibitors have been explored
as an anti-HIV drug target because RNase H inactivation
inhibits reverse transcription.
Length = 135
Score = 45.0 bits (107), Expect = 7e-06
Identities = 29/101 (28%), Positives = 47/101 (46%), Gaps = 9/101 (8%)
Query: 20 IYTDGSKDETGVGCALIIPQLNVTKRFTLNKYSSIFHAELFSILQSLKNAKLLNIKKVLI 79
++TDGS G A++ +V + TL +S AEL +++++L+ AK K V I
Sbjct: 2 VFTDGSSFVRKAGYAVVTGP-DVLEIATLPYGTSAQRAELIALIRALELAKG---KPVNI 57
Query: 80 ISDSLSSFQAISNL---YHPNPLV--KEIPHAELFSILQSL 115
+DS +F + L + + K I A L LQ
Sbjct: 58 YTDSAYAFGILHALETIWKERGFLTGKPIALASLILQLQKA 98
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 43.5 bits (103), Expect = 3e-05
Identities = 22/109 (20%), Positives = 43/109 (39%), Gaps = 8/109 (7%)
Query: 106 AELFSILQSLKNAELLNIKKVLIISDSLSSFQAISNLYHPNPLVKEIQETYSSAQISIKF 165
AEL +++++L+ + L +V + +DS + I+ K +T + K
Sbjct: 46 AELRALIEALEALKELGACEVTLYTDSKYVVEGITRWIVKWK--KNGWKTADKKPVKNKD 103
Query: 166 LWCPSHPCWYFWKRSSSQISIKFLWCPSHVGISGNDQADTEAKKATSEP 214
LW + + + W H G N++AD A++A
Sbjct: 104 LWEE------LDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAA 146
Score = 28.5 bits (64), Expect = 3.4
Identities = 18/89 (20%), Positives = 36/89 (40%), Gaps = 13/89 (14%)
Query: 18 LKIYTDG-SKDETGVGCALIIPQLNVTKR-------FTLNKYSSIFHAELFSILQSLKNA 69
++I+TDG G G + + ++ T N AEL +++++L+
Sbjct: 4 VEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEGRTTNNR-----AELRALIEALEAL 58
Query: 70 KLLNIKKVLIISDSLSSFQAISNLYHPNP 98
K L +V + +DS + I+
Sbjct: 59 KELGACEVTLYTDSKYVVEGITRWIVKWK 87
>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 = 41.4 bits (98), Expect = 1e-04
Identities = 26/129 (20%), Positives = 44/129 (34%), Gaps = 46/129 (35%)
Query: 106 AELFSILQSLKNA--ELLNIKKVLIISDS--------------------LSSFQAISNLY 143
AEL +++ +L+ + K++I +DS S + ++N
Sbjct: 46 AELRAVIHALRLIKEVGEGLTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVANKD 105
Query: 144 HPNPLVKEIQETYSSAQISIKFLWCPSHPCWYFWKRSSSQISIKFLWCPSHVGISGNDQA 203
L K ++ + I +KF P H GI GN++A
Sbjct: 106 LIKELDKLLE------------------------ELEERGIRVKFWHVPGHSGIYGNEEA 141
Query: 204 DTEAKKATS 212
D AKK
Sbjct: 142 DRLAKKGAD 150
>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 = 36.4 bits (85), Expect = 0.003
Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 4/55 (7%)
Query: 53 SIFHAELFSILQSLKNAKLLNIKKVLIISDSLSSFQAISNLYHPN----PLVKEI 103
S AE ++L+ L+ A L I+++++ SDS Q I Y L++EI
Sbjct: 1 SPLEAEAEALLEGLQLALELGIRRLIVESDSQLVVQQIQGEYEARSRLAALLREI 55
Score = 36.0 bits (84), Expect = 0.003
Identities = 18/69 (26%), Positives = 32/69 (46%), Gaps = 5/69 (7%)
Query: 105 HAELFSILQSLKNAELLNIKKVLIISDSLSSFQAISNLYHPN----PLVKEIQETYSSAQ 160
AE ++L+ L+ A L I+++++ SDS Q I Y L++EI++
Sbjct: 4 EAEAEALLEGLQLALELGIRRLIVESDSQLVVQQIQGEYEARSRLAALLREIRKL-LKKF 62
Query: 161 ISIKFLWCP 169
S+ P
Sbjct: 63 DSVSVSHVP 71
>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 = 34.8 bits (81), Expect = 0.024
Identities = 13/36 (36%), Positives = 18/36 (50%)
Query: 176 FWKRSSSQISIKFLWCPSHVGISGNDQADTEAKKAT 211
F + +I I F+ +H G N+ AD AKKA
Sbjct: 98 FMDKIKKKIKISFVKVKAHSGDKYNELADKLAKKAL 133
Score = 28.6 bits (65), Expect = 3.1
Identities = 17/73 (23%), Positives = 31/73 (42%), Gaps = 8/73 (10%)
Query: 18 LKIYTDGS-KDETGV-GCALIIPQLNVTKRFTLNKYSSIFH------AELFSILQSLKNA 69
+ Y DGS ET V G ++I + +F+ + E+ +++++ A
Sbjct: 1 VIAYVDGSYNKETKVYGYGVVILKNGEEIKFSGSGNDPELASMRNVAGEIKGAIKAMEYA 60
Query: 70 KLLNIKKVLIISD 82
IKK+ I D
Sbjct: 61 VENGIKKITIYYD 73
>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 = 32.9 bits (76), Expect = 0.077
Identities = 29/115 (25%), Positives = 44/115 (38%), Gaps = 10/115 (8%)
Query: 18 LKIYTDGSKD----ETGVGCALIIPQLNVTKR-FTLNKYSSIFHAELFSILQSLKNAKLL 72
+Y DG+ G G + P V ++ L ++ AE +++ L+ A L
Sbjct: 1 WTLYFDGASRGNPGPAGAGIVIKSPDGEVLEQSIPLGFPATNNEAEYEALIAGLELALEL 60
Query: 73 NIKKVLIISDSLSSFQAISNLYHPNPLVKEIPHAELFS-ILQSLKNAELLNIKKV 126
IKK+ I DS I Y VK A + LK E + IK +
Sbjct: 61 GIKKLEIYGDSQLVVNQIQGEYE----VKNERLAPYLEEARELLKKFEEVEIKWI 111
>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 = 31.3 bits (72), Expect = 0.33
Identities = 9/25 (36%), Positives = 13/25 (52%)
Query: 186 IKFLWCPSHVGISGNDQADTEAKKA 210
+ + W H G GN++AD A A
Sbjct: 113 VTWHWVKGHAGHPGNERADELANAA 137
>gnl|CDD|235005 PRK02122, PRK02122, glucosamine-6-phosphate deaminase-like protein;
Validated.
Length = 652
Score = 31.5 bits (72), Expect = 0.89
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 337 NPDSISSLMRFLKQNNFLKHIGDSTANAPVPNGAL 371
PDS+ S RF+K+ N H+ N +P+G +
Sbjct: 104 QPDSLQSYHRFMKE-NLFDHVDIPPENIHIPDGTI 137
>gnl|CDD|214944 smart00968, SMC_hinge, SMC proteins Flexible Hinge Domain. This
entry represents the hinge region of the SMC (Structural
Maintenance of Chromosomes) family of proteins. The
hinge region is responsible for formation of the DNA
interacting dimer. It is also possible that the precise
structure of it is an essential determinant of the
specificity of the DNA-protein interaction.
Length = 120
Score = 29.9 bits (68), Expect = 0.96
Identities = 8/27 (29%), Positives = 14/27 (51%)
Query: 326 LGNSLANILSDNPDSISSLMRFLKQNN 352
LG L ++ D ++ + FLK+N
Sbjct: 25 LGGRLQAVVVDTEETAKKAIEFLKKNR 51
>gnl|CDD|219044 pfam06470, SMC_hinge, SMC proteins Flexible Hinge Domain. This
family represents the hinge region of the SMC
(Structural Maintenance of Chromosomes) family of
proteins. The hinge region is responsible for formation
of the DNA interacting dimer. It is also possible that
the precise structure of it is an essential determinant
of the specificity of the DNA-protein interaction.
Length = 117
Score = 29.6 bits (67), Expect = 1.1
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 326 LGNSLANILSDNPDSISSLMRFLKQNN 352
LG L I+ D+ ++ + + FLK+NN
Sbjct: 26 LGGRLQAIVVDDEETAKAAIEFLKKNN 52
>gnl|CDD|235966 PRK07207, PRK07207, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 965
Score = 29.9 bits (68), Expect = 3.1
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 271 DEVCLMRMRIGHTKITHSYLFKREER 296
D+V L MR G K+ +Y+ RE+R
Sbjct: 105 DQVELALMRSGEHKVARAYVLYREKR 130
>gnl|CDD|237554 PRK13909, PRK13909, putative recombination protein RecB;
Provisional.
Length = 910
Score = 29.6 bits (67), Expect = 3.3
Identities = 22/82 (26%), Positives = 33/82 (40%), Gaps = 13/82 (15%)
Query: 14 YKDFLKIYTDGSKDETGVGCALIIPQLNVTKRFTLNKYSSIFHAELFSILQSLKNAKLLN 73
Y+ F K+Y + E + L KR+ K + +LF +LQ K AK
Sbjct: 240 YRYFKKLYNEELDAE----FEELKNAL---KRYYDAKENYKLS-KLFKLLQLYKEAKNEL 291
Query: 74 IKKVLIISDSLSSFQAISNLYH 95
KK ++L F IS +
Sbjct: 292 NKK----KNAL-DFDDISKKVY 308
>gnl|CDD|222063 pfam13350, Y_phosphatase3, Tyrosine phosphatase family. This
family is closely related to the pfam00102 and pfam00782
families.
Length = 163
Score = 28.6 bits (65), Expect = 3.4
Identities = 11/48 (22%), Positives = 22/48 (45%), Gaps = 12/48 (25%)
Query: 1 MLQNRFREILHEN--YKDFLKIYTDGS----------KDETGVGCALI 36
+ + +R+++ + Y+ L++ D KD TGV AL+
Sbjct: 97 FMADLYRDLVTDAAAYRALLELLADPDGPVLFHCTAGKDRTGVAAALL 144
>gnl|CDD|132963 cd06632, STKc_MEKK1_plant, Catalytic domain of the Protein
Serine/Threonine Kinase, Plant MAP/ERK kinase kinase 1.
Serine/threonine kinases (STKs), plant MAP/ERK kinase
kinase 1 (MEKK1)-like subfamily, catalytic (c) domain.
STKs catalyze the transfer of the gamma-phosphoryl group
from ATP to serine/threonine residues on protein
substrates. The plant MEKK1 subfamily is part of a
larger superfamily that includes the catalytic domains
of other protein STKs, protein tyrosine kinases, RIO
kinases, aminoglycoside phosphotransferase, choline
kinase, and phosphoinositide 3-kinase. This subfamily is
composed of plant mitogen-activated protein kinase
(MAPK) kinase kinases (MAPKKKs or MKKKs or MAP3Ks)
including Arabidopsis thaliana MEKK1 and MAPKKK3. MEKK1
is a MAPKKK that phosphorylates and activates MAPK
kinases (MAPKKs or MKKs or MAP2Ks), which in turn
phosphorylate and activate MAPKs during signaling
cascades that are important in mediating cellular
responses to extracellular signals. Arabidopsis thaliana
MEKK1 activates MPK4, a MAPK that regulates systemic
acquired resistance. MEKK1 also participates in the
regulation of temperature-sensitive and tissue-specific
cell death.
Length = 258
Score = 28.9 bits (65), Expect = 4.0
Identities = 14/63 (22%), Positives = 27/63 (42%), Gaps = 12/63 (19%)
Query: 114 SLKNAELLNIKKVLIISDSLSSFQAI----------SNLYHPNPLVKEIQETYSSAQISI 163
+L + + +K+V + D + +A+ S L HPN +V+ + + I
Sbjct: 21 NLDDGDFFAVKEVSLADDGQTGQEAVKQLEQEIALLSKLQHPN-IVQYLGTEREEDNLYI 79
Query: 164 KFL 166
FL
Sbjct: 80 -FL 81
Score = 28.5 bits (64), Expect = 6.1
Identities = 14/71 (19%), Positives = 31/71 (43%)
Query: 65 SLKNAKLLNIKKVLIISDSLSSFQAISNLYHPNPLVKEIPHAELFSILQSLKNAELLNIK 124
+L + +K+V + D + +A+ L L+ ++ H + L + + + L I
Sbjct: 21 NLDDGDFFAVKEVSLADDGQTGQEAVKQLEQEIALLSKLQHPNIVQYLGTEREEDNLYIF 80
Query: 125 KVLIISDSLSS 135
L+ SL+
Sbjct: 81 LELVPGGSLAK 91
>gnl|CDD|151642 pfam11200, DUF2981, Protein of unknown function (DUF2981). This
eukaryotic family of proteins has no known function.
Length = 319
Score = 28.3 bits (62), Expect = 8.4
Identities = 16/57 (28%), Positives = 23/57 (40%), Gaps = 7/57 (12%)
Query: 314 HCNKLRFRPPSF-LGNSLANILS--DNPDSISSLMRFLKQ----NNFLKHIGDSTAN 363
HCNKL + L+ +L D+ D + L LKQ N GD+ +
Sbjct: 128 HCNKLDSAIGDDRFDDDLSGVLDNFDDADDLKDLRNALKQRLGDKNSGDTTGDTNGD 184
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.133 0.408
Gapped
Lambda K H
0.267 0.0771 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,241,390
Number of extensions: 1785775
Number of successful extensions: 1823
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1812
Number of HSP's successfully gapped: 40
Length of query: 389
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 290
Effective length of database: 6,546,556
Effective search space: 1898501240
Effective search space used: 1898501240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 60 (26.8 bits)