RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7660
(250 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 = 96.9 bits (242), Expect = 2e-25
Identities = 37/120 (30%), Positives = 54/120 (45%), Gaps = 5/120 (4%)
Query: 1 GSKTLQNTSCAVYA---GGTTKSYILNNINSIFTAELLAIVFCLDSVKNRPD-VNTLIVC 56
GSK T G ++SY L S+F AELLAI+ L + +
Sbjct: 6 GSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRARKITIF 65
Query: 57 -DSMSALTSIANKNTTIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQ 115
DS +AL ++ + ++ PL+ I L + G V W P H+GI GNE DR ++
Sbjct: 66 SDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERADRLAKE 125
>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 = 61.9 bits (151), Expect = 3e-12
Identities = 33/105 (31%), Positives = 47/105 (44%), Gaps = 4/105 (3%)
Query: 11 AVYAGGTTKSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNT 70
V GG +S L + AELLA++ L+++ + VN I DS + I N
Sbjct: 23 YVTDGGKQRSKPLPG-TTNQRAELLALIEALEALSGQK-VN--IYTDSQYVIGGITNGWP 78
Query: 71 TIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDRATRQ 115
T I N + L V W P H+GI GNE+ D+ +Q
Sbjct: 79 TKSESKPIKNEIWELLQKKHKVYIQWVPGHSGIPGNELADKLAKQ 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 = 39.6 bits (93), Expect = 2e-04
Identities = 20/92 (21%), Positives = 35/92 (38%), Gaps = 4/92 (4%)
Query: 24 NNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNTTIPLIAHILNTWY 83
+ AELLA++ L+ + +I DS + I + + +L
Sbjct: 34 IPAATNNEAELLALLEALELALDLGLKKLIIETDSKYVVDLINSWSKGWKKNNLLLWDIL 93
Query: 84 SLKSCGKNVAFLWCPSHTGISGNEIVDRATRQ 115
L S ++ F P GNE+ DR ++
Sbjct: 94 LLLSKFIDIRFEHVPR----EGNEVADRLAKE 121
>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 = 35.6 bits (83), Expect = 0.007
Identities = 28/102 (27%), Positives = 37/102 (36%), Gaps = 26/102 (25%)
Query: 32 AELLAIVFCLDSVKNR--PDVNTLIVCDSM--------------------SALTSIANKN 69
AEL A++ L +K +I DS S +ANK+
Sbjct: 46 AELRAVIHALRLIKEVGEGLTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVANKD 105
Query: 70 TTIPLIAHILNTWYSLKSCGKNVAFLWCPSHTGISGNEIVDR 111
LI + L+ G V F P H+GI GNE DR
Sbjct: 106 ----LIKELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADR 143
>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 = 33.8 bits (78), Expect = 0.031
Identities = 37/133 (27%), Positives = 53/133 (39%), Gaps = 23/133 (17%)
Query: 1 GSKTLQNTSCAVYAG-GTTKSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSM 59
GS ++ AV G + L S AEL+A++ L+ K +P VN I DS
Sbjct: 6 GSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIALIRALELAKGKP-VN--IYTDS- 61
Query: 60 SALTSIANKNTTIPL---------IAH---ILNTWYSLKSCGKNVAFLWCPSHTG----- 102
+ I + TI IA IL ++ K VA + +H+G
Sbjct: 62 AYAFGILHALETIWKERGFLTGKPIALASLILQLQKAI-QRPKPVAVIHIRAHSGLPGPL 120
Query: 103 ISGNEIVDRATRQ 115
GN D+A RQ
Sbjct: 121 ALGNARADQAARQ 133
>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 = 31.7 bits (73), Expect = 0.15
Identities = 10/30 (33%), Positives = 11/30 (36%), Gaps = 1/30 (3%)
Query: 89 GKNVAFLWCPSHTGISGNEIVDR-ATRQLD 117
V + W H G GNE D A D
Sbjct: 110 KHQVTWHWVKGHAGHPGNERADELANAAAD 139
>gnl|CDD|179877 PRK04778, PRK04778, septation ring formation regulator EzrA;
Provisional.
Length = 569
Score = 32.1 bits (74), Expect = 0.23
Identities = 7/20 (35%), Positives = 12/20 (60%)
Query: 138 LLEKWQKSWTELINNKLKRI 157
E+W++ W E++ N L I
Sbjct: 65 KFEEWRQKWDEIVTNSLPDI 84
>gnl|CDD|224071 COG1149, COG1149, MinD superfamily P-loop ATPase containing an
inserted ferredoxin domain [Energy production and
conversion].
Length = 284
Score = 30.8 bits (70), Expect = 0.58
Identities = 15/49 (30%), Positives = 19/49 (38%), Gaps = 9/49 (18%)
Query: 211 CPVIAS--ACDSVLV-------SLSDFLVVLALSERTRVRVWTLDNLYN 250
CPVIAS D ++ L D L L E + + N YN
Sbjct: 177 CPVIASLKGADLAILVTEPTPFGLHDLKRALELVEHFGIPTGIVINRYN 225
>gnl|CDD|114855 pfam06160, EzrA, Septation ring formation regulator, EzrA. During
the bacterial cell cycle, the tubulin-like cell-division
protein FtsZ polymerises into a ring structure that
establishes the location of the nascent division site.
EzrA modulates the frequency and position of FtsZ ring
formation.
Length = 559
Score = 30.6 bits (70), Expect = 0.76
Identities = 7/36 (19%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 138 LLEKWQKSWTELINNKLKRIKPTIGPWNVSDCNSRY 173
E+W++ W +++ N L I+ + + N ++
Sbjct: 61 TFEEWRQKWDDIVTNSLPDIEELLF--EAEELNDKF 94
>gnl|CDD|225427 COG2872, COG2872, Predicted metal-dependent hydrolases related to
alanyl-tRNA synthetase HxxxH domain [General function
prediction only].
Length = 241
Score = 30.0 bits (68), Expect = 0.98
Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 7/54 (12%)
Query: 98 PSHTGI----SGNEIVDRATRQLDGAEIVNLSSPADLIPVGKKYLLE-KWQKSW 146
P TG G +V+ T+ DG EIV++ + + VG K L+ W++ +
Sbjct: 42 PGDTGTLIWAGGEYVVEDVTK--DGEEIVHVLAEHAKLKVGDKVKLKIDWERRY 93
>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 = 1.1
Identities = 6/21 (28%), Positives = 13/21 (61%)
Query: 91 NVAFLWCPSHTGISGNEIVDR 111
++F+ +H+G NE+ D+
Sbjct: 107 KISFVKVKAHSGDKYNELADK 127
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 29.2 bits (66), Expect = 1.2
Identities = 28/123 (22%), Positives = 42/123 (34%), Gaps = 32/123 (26%)
Query: 11 AVYAGGTTKSYILNNINSIFTAELLAIVFCLDSVKNRPDVNTLIVCDSMSALTSIANKNT 70
+ G TT NN AEL A++ L+++K + DS + I
Sbjct: 35 SGGEGRTT-----NN-----RAELRALIEALEALKELGACEVTLYTDSKYVVEGI----- 79
Query: 71 TIPLIAHILNTWY-SLKSCGKN----------------VAFLWCPSHTGISGNEIVDRAT 113
T ++ N W + K KN V + W H G NE D+
Sbjct: 80 TRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLA 139
Query: 114 RQL 116
R+
Sbjct: 140 REA 142
>gnl|CDD|188704 cd08750, RGS_GRK4, Regulator of G protein signaling domain (RGS)
found in G protein-coupled receptor kinase 4 (GRK4).
The RGS domain is an essential part of the GRK4 (G
protein-coupled receptor kinase4) proteins, which are
membrane-associated serine/threonine protein kinases
that phosphorylate G protein-coupled receptors (GPCRs)
upon agonist stimulation. This phosphorylation initiates
beta-arrestin-mediated receptor desensitization,
internalization, and signaling events. GRK4 is a member
of the GRK kinase family which includes three major
subfamilies: the GRK4 subfamily (GRK4, GRK5 and GRK6),
the rhodopsin kinase or visual GRK subfamily (GRK1 and
GRK7), and the beta-adrenergic receptor kinases
subfamily (GRK2/GRK3). The RGS domain of the GRKs has
very little sequence similarity with the canonical RGS
domain of the RGS proteins and therefore is often
refered to as the RH (RGS Homology) domain. GRK4 plays a
key role in regulating dopaminergic-mediated natriuresis
and is associated with essential hypertension and/or
salt-sensitive hypertension. GRK4 exists in four splice
variants involved in hyperphosphorylation,
desensitization, and internalization of two dopamine
receptors (D1R and D3R). GRK4 also increases the
expression of a key receptor of the renin-angiotensin
system, the AT1R (angiotensin type 1 receptor). RGS
proteins regulate many aspects of embryonic development
such as glial differentiation, embryonic axis formation,
skeletal and muscle development, cell migration during
early embryogenesis, as well as apoptosis, cell
proliferation, and modulation of cardiac development.
Length = 132
Score = 28.7 bits (64), Expect = 1.5
Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 5/57 (8%)
Query: 151 NNKLKRIKPTIGPWNVSDCNSRYEESISWSGNKCFID--HYSHPYLKVLPFNMFKQS 205
NN P I V++C + EE+ S + F + H YL PF +++S
Sbjct: 60 NNGSAAHLPEIPQDVVTECRLKLEENPS---KELFEECTRVVHEYLSGEPFEAYQES 113
>gnl|CDD|226297 COG3774, OCH1, Mannosyltransferase OCH1 and related enzymes [Cell
envelope biogenesis, outer membrane].
Length = 347
Score = 27.8 bits (62), Expect = 6.5
Identities = 16/75 (21%), Positives = 22/75 (29%), Gaps = 6/75 (8%)
Query: 96 WCPSHTGISGNEIVDR--ATRQLDGAEIVNLSSPADLIPVGKKYLLEKWQKSWTELINNK 153
+S EI + VNLS PA +Y L SWT N
Sbjct: 229 ASTGPLILS--EIHSAYTVQTPPASFDAVNLSDPAFTNKRNNQYFLHTGGSSWTHTNNKD 286
Query: 154 LKRIKPTIGPWNVSD 168
+ + + D
Sbjct: 287 VLKSA--YRHLDWFD 299
>gnl|CDD|217529 pfam03389, MobA_MobL, MobA/MobL family. This family includes of
the MobA protein from the E. coli plasmid RSF1010, and
the MobL protein from the Thiobacillus ferrooxidans
plasmid PTF1. These sequences are mobilisation proteins,
which are essential for specific plasmid transfer.
Length = 219
Score = 27.1 bits (60), Expect = 9.3
Identities = 13/55 (23%), Positives = 22/55 (40%)
Query: 102 GISGNEIVDRATRQLDGAEIVNLSSPADLIPVGKKYLLEKWQKSWTELINNKLKR 156
G G + +G +I G K L+E+W+K+W + N L+
Sbjct: 130 GFGGKKKKSEYILDENGNKIRTKRGKIKTEDWGSKELVEEWRKAWADHANAHLEL 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 0.414
Gapped
Lambda K H
0.267 0.0801 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,259,405
Number of extensions: 1104266
Number of successful extensions: 973
Number of sequences better than 10.0: 1
Number of HSP's gapped: 971
Number of HSP's successfully gapped: 24
Length of query: 250
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 155
Effective length of database: 6,723,972
Effective search space: 1042215660
Effective search space used: 1042215660
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: 58 (26.0 bits)