RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11794
(325 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 = 93.5 bits (233), Expect = 1e-23
Identities = 29/89 (32%), Positives = 43/89 (48%), Gaps = 1/89 (1%)
Query: 107 TTIYLAELLALYLCLKEISEFHSS-SRIAIISDSLSVLSALGNICFSHPFISKIYQLWKL 165
+++ AELLA+ L+ +I I SDS + L AL + S P + +I + +
Sbjct: 35 CSVFDAELLAILEALQLALREGRRARKITIFSDSQAALKALRSPRSSSPLVLRIRKAIRE 94
Query: 166 IVTRGTDVVFLWCPSHCGIDGNEAVDSAA 194
+ G V W P H GI+GNE D A
Sbjct: 95 LANHGVKVRLHWVPGHSGIEGNERADRLA 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 = 65.0 bits (159), Expect = 4e-13
Identities = 29/92 (31%), Positives = 41/92 (44%), Gaps = 12/92 (13%)
Query: 107 TTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSV----LSALGNICFSHPFISKIYQL 162
TT AELLAL L+ +S ++ I +DS V + S P ++I++L
Sbjct: 38 TTNQRAELLALIEALEALS----GQKVNIYTDSQYVIGGITNGWPTKSESKPIKNEIWEL 93
Query: 163 WKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAA 194
+ + V W P H GI GNE D A
Sbjct: 94 ----LQKKHKVYIQWVPGHSGIPGNELADKLA 121
>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 = 3e-08
Identities = 23/108 (21%), Positives = 39/108 (36%), Gaps = 9/108 (8%)
Query: 89 SCCYLGTLVGPGPRYFNLTTIYLAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGN 148
+L P T AELLAL L+ + ++ I +DS V+ + +
Sbjct: 23 EGAWLFAGSLSIPAA----TNNEAELLALLEALELALD-LGLKKLIIETDSKYVVDLINS 77
Query: 149 ICFSHPFISKIYQLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAANH 196
+ + L++++ D+ F P GNE D A
Sbjct: 78 WSKGWKKNNLLLWDILLLLSKFIDIRFEHVPRE----GNEVADRLAKE 121
>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 = 34.4 bits (80), Expect = 0.027
Identities = 12/36 (33%), Positives = 16/36 (44%), Gaps = 2/36 (5%)
Query: 162 LWKLI--VTRGTDVVFLWCPSHCGIDGNEAVDSAAN 195
LW+ + + V + W H G GNE D AN
Sbjct: 100 LWQELDALLAKHQVTWHWVKGHAGHPGNERADELAN 135
>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 = 32.2 bits (74), Expect = 0.14
Identities = 27/108 (25%), Positives = 37/108 (34%), Gaps = 31/108 (28%)
Query: 112 AELLALYLCLKEISE-FHSSSRIAIISDSLSVLSAL----------------GNICFSHP 154
AEL A+ L+ I E +++ I +DS V++ + G
Sbjct: 46 AELRAVIHALRLIKEVGEGLTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPV---- 101
Query: 155 FISKIYQLWKLIVT-------RGTDVVFLWCPSHCGIDGNEAVDSAAN 195
L K + RG V F P H GI GNE D A
Sbjct: 102 ---ANKDLIKELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLAK 146
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 30.0 bits (68), Expect = 0.95
Identities = 21/97 (21%), Positives = 33/97 (34%), Gaps = 15/97 (15%)
Query: 112 AELLALYLCLKEISEFHSSSRIAIISDSLSVLSAL-----GNICFSHPFISKIY------ 160
AEL AL L+ + E + + + +DS V+ + K
Sbjct: 46 AELRALIEALEALKEL-GACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDL 104
Query: 161 --QLWKLIVTRGTDVVFLWCPSHCGIDGNEAVDSAAN 195
+L +L+ V + W H G NE D A
Sbjct: 105 WEELDELLKRHEL-VFWEWVKGHAGHPENERADQLAR 140
>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 = 28.7 bits (65), Expect = 0.97
Identities = 17/89 (19%), Positives = 33/89 (37%), Gaps = 5/89 (5%)
Query: 111 LAELLALYLCLKEISEFHSSSRIAIISDSLSVLSALGNICFSHPFISKIYQLWKLIVTRG 170
AE AL L+ E R+ + SDS V+ + + ++ + + + ++ +
Sbjct: 4 EAEAEALLEGLQLALE-LGIRRLIVESDSQLVVQQIQGEYEARSRLAALLREIRKLLKKF 62
Query: 171 TDVVFLWCPSHCGIDGNEAVDSAANHHTH 199
V P C N D+ A +
Sbjct: 63 DSVSVSHVPREC----NRVADALAKLASA 87
>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 = 28.2 bits (64), Expect = 2.7
Identities = 7/23 (30%), Positives = 10/23 (43%)
Query: 172 DVVFLWCPSHCGIDGNEAVDSAA 194
+ F+ +H G NE D A
Sbjct: 107 KISFVKVKAHSGDKYNELADKLA 129
>gnl|CDD|147720 pfam05718, Pox_int_trans, Poxvirus intermediate transcription
factor. This family consists of several highly related
Poxvirus sequences which are thought to be intermediate
transcription factors.
Length = 383
Score = 28.4 bits (64), Expect = 5.4
Identities = 12/27 (44%), Positives = 19/27 (70%), Gaps = 5/27 (18%)
Query: 207 STDDLKPWIKAIVKK---DIVDMWNSI 230
+D+ KPWIK+I K+ DI++ N+I
Sbjct: 168 RSDESKPWIKSISKRLRVDIIN--NAI 192
>gnl|CDD|224928 COG2017, GalM, Galactose mutarotase and related enzymes
[Carbohydrate transport and metabolism].
Length = 308
Score = 28.1 bits (63), Expect = 5.5
Identities = 12/47 (25%), Positives = 20/47 (42%)
Query: 61 TLHLQSVMQLFIFHIDTDTAYRLQENRYSCCYLGTLVGPGPRYFNLT 107
+L L+ + +++ Y L E+ + Y T G P FNL
Sbjct: 118 SLVLRDGEDGYPGNLEATVTYTLNEDGLTVTYEVTNDGDEPTPFNLG 164
>gnl|CDD|131322 TIGR02269, TIGR02269, Myxococcus xanthus paralogous lipoprotein
family TIGR02269. This family consists of at least 9
paralogs in Myxococcus xanthus, a member of the
Deltaproteobacteria. One appears truncated toward the
N-terminus; the others are predicted lipoproteins. The
function is unknown.
Length = 211
Score = 27.9 bits (62), Expect = 6.6
Identities = 11/31 (35%), Positives = 15/31 (48%)
Query: 250 FRNNRYEEVVLTRLRIGHTRVTHNHLFKKLP 280
+RN E RL +G R +HLF + P
Sbjct: 104 WRNAPPSEHRAPRLPLGPGRWVRHHLFPQAP 134
>gnl|CDD|183139 PRK11445, PRK11445, putative oxidoreductase; Provisional.
Length = 351
Score = 28.1 bits (63), Expect = 7.1
Identities = 14/75 (18%), Positives = 29/75 (38%), Gaps = 14/75 (18%)
Query: 214 WIKAIVKKDIVDMWNSIPPSNKLKRIKPTVDSWTSSFRNNRYEEVVLTRLRIG------H 267
W+K+++ + NS+ ++I D + FR + +E+ + R +G
Sbjct: 104 WLKSLIPASVEVYHNSL-----CRKIWREDDGYHVIFRADGWEQHITARYLVGADGANSM 158
Query: 268 TRVTHNHLFKKLPPP 282
R HL+
Sbjct: 159 VR---RHLYPDHQIR 170
>gnl|CDD|215222 PLN02397, PLN02397, aspartate transaminase.
Length = 423
Score = 27.6 bits (62), Expect = 9.2
Identities = 10/37 (27%), Positives = 16/37 (43%), Gaps = 4/37 (10%)
Query: 189 AVDSAANHHTHPRHVNLC----STDDLKPWIKAIVKK 221
V A P +NL T++ KP + +V+K
Sbjct: 37 GVTEAFLADPSPVKLNLGVGAYRTEEGKPVVLNVVRK 73
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
0.324 0.138 0.443
Gapped
Lambda K H
0.267 0.0797 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,413,588
Number of extensions: 1547066
Number of successful extensions: 1426
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1423
Number of HSP's successfully gapped: 18
Length of query: 325
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 228
Effective length of database: 6,635,264
Effective search space: 1512840192
Effective search space used: 1512840192
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 59 (26.4 bits)