RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7520
(402 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 = 108 bits (272), Expect = 1e-28
Identities = 44/123 (35%), Positives = 60/123 (48%), Gaps = 4/123 (3%)
Query: 139 CYTDGSKSVNGTSCAYSI--NNLIVLSTSLNQVVCVYSSELIAIHLCLEHLKFLPSSH-- 194
YTDGSK T ++I I S L V+ +EL+AI L+
Sbjct: 2 IYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRARK 61
Query: 195 FLIISDSKSALTALSNNTSDNPIVAKISVTWRKLKDYGKTVSFLWCPSHSGIAGNEFVDN 254
I SDS++AL AL + S +P+V +I R+L ++G V W P HSGI GNE D
Sbjct: 62 ITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERADR 121
Query: 255 AAR 257
A+
Sbjct: 122 LAK 124
>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 = 71.5 bits (176), Expect = 3e-15
Identities = 38/125 (30%), Positives = 52/125 (41%), Gaps = 14/125 (11%)
Query: 139 CYTDGSKSVN-GTSCA-YSINNLIVLSTSLNQVVCVYSSELIAIHLCLEHLKFLPSSHFL 196
YTDGS + N G A Y + S L +EL+A+ LE L
Sbjct: 6 VYTDGSCNGNPGPGGAGYVTDGGKQRSKPLPGT-TNQRAELLALIEALEAL---SGQKVN 61
Query: 197 IISDSKSALTALSNN----TSDNPIVAKISVTWRKLKDYGKTVSFLWCPSHSGIAGNEFV 252
I +DS+ + ++N + PI +I W L+ V W P HSGI GNE
Sbjct: 62 IYTDSQYVIGGITNGWPTKSESKPIKNEI---WELLQK-KHKVYIQWVPGHSGIPGNELA 117
Query: 253 DNAAR 257
D A+
Sbjct: 118 DKLAK 122
>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 = 51.2 bits (123), Expect = 4e-08
Identities = 26/130 (20%), Positives = 39/130 (30%), Gaps = 18/130 (13%)
Query: 140 YTDGSKSVNGTSCAYSINNLIVLSTSLNQVVCVYSS----------ELIAIHLCLEHLKF 189
TDGS N VL + S EL+A+ LE
Sbjct: 1 NTDGSCKGNPGPAGAGG----VLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALD 56
Query: 190 LPSSHFLIISDSKSALTALSNNTSDNPIVAKISVTWRKLKDYGKTVSFLWCPSHSGIAGN 249
L +I +DSK + +++ + + L + F P GN
Sbjct: 57 LGLKKLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPRE----GN 112
Query: 250 EFVDNAARNP 259
E D A+
Sbjct: 113 EVADRLAKEA 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 = 48.8 bits (117), Expect = 3e-07
Identities = 32/140 (22%), Positives = 49/140 (35%), Gaps = 30/140 (21%)
Query: 139 CYTDGSKSVNGTSCA-YSINNLIVLSTSLNQVVCVYSSELIAIHLCLEHLKFLPSSHFLI 197
+TDGS V A + + ++ +L +ELIA+ LE K P I
Sbjct: 2 VFTDGSSFVRKAGYAVVTGPD-VLEIATLPYGTSAQRAELIALIRALELAKGKP---VNI 57
Query: 198 ISDSKSALTAL--------------SNNTSDNPIVAKI-SVTWRKLKDYGKTVSFLWCPS 242
+DS A L + ++ ++ R K V+ + +
Sbjct: 58 YTDSAYAFGILHALETIWKERGFLTGKPIALASLILQLQKAIQRP-----KPVAVIHIRA 112
Query: 243 HSG-----IAGNEFVDNAAR 257
HSG GN D AAR
Sbjct: 113 HSGLPGPLALGNARADQAAR 132
>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 = 41.7 bits (99), Expect = 1e-04
Identities = 25/96 (26%), Positives = 41/96 (42%), Gaps = 19/96 (19%)
Query: 176 ELIAIHLCLEHLKFLP-SSHFLIISDSKSALTALS--------NN--TSDNPIVAKISVT 224
EL A +E L+ L L+ +DS+ + ++ N T+D V + +
Sbjct: 45 ELTA---VIEALEALKEPCPVLLYTDSQYVINGITKWIHGWKKNGWKTADGKPVKNVDL- 100
Query: 225 WRKLKDY---GKTVSFLWCPSHSGIAGNEFVDNAAR 257
W++L D V++ W H+G GNE D A
Sbjct: 101 WQEL-DALLAKHQVTWHWVKGHAGHPGNERADELAN 135
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 40.0 bits (94), Expect = 4e-04
Identities = 32/139 (23%), Positives = 50/139 (35%), Gaps = 26/139 (18%)
Query: 140 YTDGSKSVNGTSCAYSINNLIVLSTSLNQVVCVY-------SSELIAIHLCLEHLKFLPS 192
+TDG+ N + ++ + + +EL A+ LE LK L +
Sbjct: 7 FTDGACLGNPGPGGWGA---VLRYGDGEKELSGGEGRTTNNRAELRALIEALEALKELGA 63
Query: 193 SHFLIISDSK---SALTALSNN-------TSDNPIVAKISVTWRKL----KDYGKTVSFL 238
+ +DSK +T T+D V K W +L K + V +
Sbjct: 64 CEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPV-KNKDLWEELDELLKRHEL-VFWE 121
Query: 239 WCPSHSGIAGNEFVDNAAR 257
W H+G NE D AR
Sbjct: 122 WVKGHAGHPENERADQLAR 140
>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 = 33.6 bits (78), Expect = 0.051
Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 226 RKLKDYGKTVSFLWCPSHSGIAGNEFVDNAARNPV 260
K+K K +SF+ +HSG NE D A+ +
Sbjct: 100 DKIKKKIK-ISFVKVKAHSGDKYNELADKLAKKAL 133
>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 = 31.0 bits (71), Expect = 0.53
Identities = 39/149 (26%), Positives = 58/149 (38%), Gaps = 36/149 (24%)
Query: 140 YTDGSKSVNGTSCA---YSI--NNLIVLSTSL--------NQVVCVYSSELIAIHLCLEH 186
YTDG+ NG S A Y + + S NQ +EL A+ L
Sbjct: 3 YTDGACRGNGRSGARAGYGVYFGPGHPRNVSERLPGPPQTNQR-----AELRAVIHALRL 57
Query: 187 LKFL--PSSHFLIISDSK---SALTALSNN-------TSDNPIVA------KISVTWRKL 228
+K + + +I +DS+ + +T TS VA ++ +L
Sbjct: 58 IKEVGEGLTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVANKDLIKELDKLLEEL 117
Query: 229 KDYGKTVSFLWCPSHSGIAGNEFVDNAAR 257
++ G V F P HSGI GNE D A+
Sbjct: 118 EERGIRVKFWHVPGHSGIYGNEEADRLAK 146
>gnl|CDD|226533 COG4047, COG4047, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 243
Score = 30.2 bits (68), Expect = 1.4
Identities = 16/79 (20%), Positives = 25/79 (31%), Gaps = 14/79 (17%)
Query: 173 YSSELIAIHLCLEHLKFLPSSHFLII------SDSKSALTALSNNTSDNP--IVAKISVT 224
Y + + +FLP+S F + A + L T +N +S+
Sbjct: 69 YFRGREVRDIYRAYKEFLPNSRFNRRLIEQKLRRIRRAESFLETLTEENIEVYYEDMSLL 128
Query: 225 WRKL------KDYGKTVSF 237
L KTV F
Sbjct: 129 LEALARALGADRESKTVVF 147
>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 = 29.8 bits (67), Expect = 1.8
Identities = 20/67 (29%), Positives = 28/67 (41%), Gaps = 5/67 (7%)
Query: 256 ARNPVNPHLPLKLCS--PLDLKPFAAKLTKTKWQALWDTLPIPNKLKRVKPVIEDWGSSN 313
N NPH L + + PLD F K K+++ + I K R K EDWGS
Sbjct: 109 RDNDENPHAHL-MLTLRPLDPDGFGGKKKKSEYILDENGNKIRTK--RGKIKTEDWGSKE 165
Query: 314 RDNRYEE 320
+ +
Sbjct: 166 LVEEWRK 172
>gnl|CDD|114709 pfam06003, SMN, Survival motor neuron protein (SMN). This family
consists of several eukaryotic survival motor neuron
(SMN) proteins. The Survival of Motor Neurons (SMN)
protein, the product of the spinal muscular
atrophy-determining gene, is part of a large
macromolecular complex (SMN complex) that functions in
the assembly of spliceosomal small nuclear
ribonucleoproteins (snRNPs). The SMN complex functions
as a specificity factor essential for the efficient
assembly of Sm proteins on U snRNAs and likely protects
cells from illicit, and potentially deleterious,
non-specific binding of Sm proteins to RNAs.
Length = 264
Score = 30.0 bits (67), Expect = 2.1
Identities = 21/54 (38%), Positives = 23/54 (42%), Gaps = 11/54 (20%)
Query: 59 KGGLPQGHPDSLLG--PPFLLASPLFLKTIFLPYIKPLPPWSFDVPTFDNSLGS 110
G P G P L G PPF L P+ I P PP S D D +LGS
Sbjct: 186 HGEKPSGWPPFLSGWPPPFPLGPPM---------IPPPPPMSPDFGEDDEALGS 230
>gnl|CDD|178927 PRK00203, rnhA, ribonuclease H; Reviewed.
Length = 150
Score = 28.6 bits (65), Expect = 3.4
Identities = 11/36 (30%), Positives = 16/36 (44%), Gaps = 2/36 (5%)
Query: 225 WRKLKDYGK--TVSFLWCPSHSGIAGNEFVDNAARN 258
W++L K + + W H+G NE D AR
Sbjct: 103 WQRLDAALKRHQIKWHWVKGHAGHPENERCDELARA 138
>gnl|CDD|178322 PLN02720, PLN02720, complex II.
Length = 140
Score = 28.2 bits (63), Expect = 4.8
Identities = 14/30 (46%), Positives = 14/30 (46%), Gaps = 1/30 (3%)
Query: 79 SPLFLKTIFLPYIKPLPPWS-FDVPTFDNS 107
S L F KPLPPWS DV F S
Sbjct: 22 SFLENYARFSKRDKPLPPWSDSDVDEFIAS 51
>gnl|CDD|187696 cd09272, RNase_HI_RT_Ty1, Ty1/Copia 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 eukaryotes. RNase HI
has also been observed as adjunct domains to the reverse
transcriptase gene in retroviruses, in long-term repeat
(LTR)-bearing 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. Ty1/Copia family is widely distributed
among the genomes of plants, fungi and animals. RNase H
inhibitors have been explored as an anti-HIV drug target
because RNase H inactivation inhibits reverse
transcription.
Length = 142
Score = 27.4 bits (62), Expect = 7.4
Identities = 21/96 (21%), Positives = 33/96 (34%), Gaps = 28/96 (29%)
Query: 139 CYTDGS--------KSVNGTSCAYSI---NNLIVLSTSLNQVVCVYS--SELIAIHLC-- 183
Y+D +S +G Y I + V + S +E IA+
Sbjct: 2 GYSDADWAGDLDDRRSTSG----YVFFLGGGPISWKSKKQTTVALSSTEAEYIALAEAAK 57
Query: 184 --------LEHLKFLPSSHFLIISDSKSALTALSNN 211
L+ L S I D++SA+ AL+ N
Sbjct: 58 EALWLRRLLKELGIPLSGPITIYCDNQSAI-ALAKN 92
>gnl|CDD|224691 COG1777, COG1777, Predicted transcriptional regulators
[Transcription].
Length = 217
Score = 27.8 bits (62), Expect = 8.2
Identities = 10/35 (28%), Positives = 20/35 (57%)
Query: 10 LWNILLLVEHEYKKMSKAKGDLSLDLDQLDCACKN 44
L + LL + E +++S+A+ +L L++L K
Sbjct: 123 LISRLLEINREIEELSRAQTELQKQLNELMDRIKE 157
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
0.321 0.137 0.434
Gapped
Lambda K H
0.267 0.0563 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 20,350,830
Number of extensions: 1922233
Number of successful extensions: 1375
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1369
Number of HSP's successfully gapped: 17
Length of query: 402
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 303
Effective length of database: 6,546,556
Effective search space: 1983606468
Effective search space used: 1983606468
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 (21.9 bits)
S2: 60 (27.3 bits)