RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy556
(435 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 = 58.0 bits (141), Expect = 2e-10
Identities = 15/34 (44%), Positives = 19/34 (55%)
Query: 267 WRNLTSNNIKLTFIWCPSHCGIEGNEEVDRAANR 300
R L ++ +K+ W P H GIEGNE DR A
Sbjct: 92 IRELANHGVKVRLHWVPGHSGIEGNERADRLAKE 125
>gnl|CDD|238827 cd01650, RT_nLTR_like, RT_nLTR: Non-LTR (long terminal repeat)
retrotransposon and non-LTR retrovirus reverse
transcriptase (RT). This subfamily contains both non-LTR
retrotransposons and non-LTR retrovirus RTs. RTs
catalyze the conversion of single-stranded RNA into
double-stranded DNA for integration into host
chromosomes. RT is a multifunctional enzyme with
RNA-directed DNA polymerase, DNA directed DNA polymerase
and ribonuclease hybrid (RNase H) activities.
Length = 220
Score = 46.1 bits (110), Expect = 1e-05
Identities = 28/114 (24%), Positives = 45/114 (39%), Gaps = 36/114 (31%)
Query: 22 GLVQGSSLSTLLFAVFMNDIFHVINLPTRG---------LLFVDDLLLTIRGK---ILEQ 69
G+ QG LS LLF + ++D+ ++N L + DD++L GK + E
Sbjct: 106 GVRQGDPLSPLLFNLALDDLLRLLNKEEEIKLGGPGITHLAYADDIVLFSEGKSRKLQEL 165
Query: 70 L------------------------GSRNPTLPLIMLNGNQLKFDNTAKFLGLI 99
L G++ L I LNG ++ T K+LG+
Sbjct: 166 LQRLQEWSKESGLKINPSKSKVMLIGNKKKRLKDITLNGTPIEAVETFKYLGVT 219
>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 = 43.4 bits (103), Expect = 2e-05
Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 265 DLWRNLTSNNIKLTFIWCPSHCGIEGNEEVDRAA 298
++W L K+ W P H GI GNE D+ A
Sbjct: 89 EIWELL-QKKHKVYIQWVPGHSGIPGNELADKLA 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 = 40.6 bits (96), Expect = 2e-04
Identities = 14/39 (35%), Positives = 19/39 (48%), Gaps = 2/39 (5%)
Query: 264 IDLWRNL--TSNNIKLTFIWCPSHCGIEGNEEVDRAANR 300
+DLW+ L ++T+ W H G GNE D AN
Sbjct: 98 VDLWQELDALLAKHQVTWHWVKGHAGHPGNERADELANA 136
>gnl|CDD|215698 pfam00078, RVT_1, Reverse transcriptase (RNA-dependent DNA
polymerase). A reverse transcriptase gene is usually
indicative of a mobile element such as a retrotransposon
or retrovirus. Reverse transcriptases occur in a variety
of mobile elements, including retrotransposons,
retroviruses, group II introns, bacterial msDNAs,
hepadnaviruses, and caulimoviruses.
Length = 194
Score = 41.6 bits (98), Expect = 3e-04
Identities = 21/66 (31%), Positives = 30/66 (45%), Gaps = 4/66 (6%)
Query: 3 RRIAVKCNNLISNFKGLENGLVQGSSLSTLLFAVFMNDIFHVINLPTRG---LLFVDDLL 59
R +V N GL QGS LS LLF +FMN++ + G L + DD+L
Sbjct: 89 RTFSVLVNGNPGGRY-EWRGLPQGSVLSPLLFNLFMNELLRPLRKRFPGLTYLRYADDIL 147
Query: 60 LTIRGK 65
+ +
Sbjct: 148 IFSKSP 153
>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 = 38.0 bits (89), Expect = 0.003
Identities = 17/43 (39%), Positives = 22/43 (51%)
Query: 258 DDMSEVIDLWRNLTSNNIKLTFIWCPSHCGIEGNEEVDRAANR 300
D + E+ L L I++ F P H GI GNEE DR A +
Sbjct: 105 DLIKELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLAKK 147
>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 = 36.3 bits (85), Expect = 0.007
Identities = 9/27 (33%), Positives = 15/27 (55%)
Query: 272 SNNIKLTFIWCPSHCGIEGNEEVDRAA 298
IK++F+ +H G + NE D+ A
Sbjct: 103 KKKIKISFVKVKAHSGDKYNELADKLA 129
>gnl|CDD|238826 cd01648, TERT, TERT: Telomerase reverse transcriptase (TERT).
Telomerase is a ribonucleoprotein (RNP) that
synthesizes telomeric DNA repeats. The telomerase RNA
subunit provides the template for synthesis of these
repeats. The catalytic subunit of RNP is known as
telomerase reverse transcriptase (TERT). The reverse
transcriptase (RT) domain is located in the C-terminal
region of the TERT polypeptide. Single amino acid
substitutions in this region lead to telomere
shortening and senescence. Telomerase is an enzyme
that, in certain cells, maintains the physical ends of
chromosomes (telomeres) during replication. In somatic
cells, replication of the lagging strand requires the
continual presence of an RNA primer approximately 200
nucleotides upstream, which is complementary to the
template strand. Since there is a region of DNA less
than 200 base pairs from the end of the chromosome
where this is not possible, the chromosome is
continually shortened. However, a surplus of repetitive
DNA at the chromosome ends protects against the erosion
of gene-encoding DNA. Telomerase is not normally
expressed in somatic cells. It has been suggested that
exogenous TERT may extend the lifespan of, or even
immortalize, the cell. However, recent studies have
shown that telomerase activity can be induced by a
number of oncogenes. Conversely, the oncogene c-myc can
be activated in human TERT immortalized cells. Sequence
comparisons place the telomerase proteins in the RT
family but reveal hallmarks that distinguish them from
retroviral and retrotransposon relatives.
Length = 119
Score = 35.3 bits (82), Expect = 0.013
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 9/47 (19%)
Query: 22 GLVQGSSLSTLLFAVFMNDI------FHVINLPTRGLL--FVDDLLL 60
G+ QGS LS+LL +++ D+ F + LL VDD LL
Sbjct: 19 GIPQGSPLSSLLCSLYYADLENKYLSFLDVIDK-DSLLLRLVDDFLL 64
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 33.5 bits (77), Expect = 0.090
Identities = 11/39 (28%), Positives = 15/39 (38%), Gaps = 3/39 (7%)
Query: 265 DLWRN---LTSNNIKLTFIWCPSHCGIEGNEEVDRAANR 300
DLW L + + + W H G NE D+ A
Sbjct: 103 DLWEELDELLKRHELVFWEWVKGHAGHPENERADQLARE 141
>gnl|CDD|178927 PRK00203, rnhA, ribonuclease H; Reviewed.
Length = 150
Score = 30.6 bits (70), Expect = 0.86
Identities = 11/39 (28%), Positives = 16/39 (41%), Gaps = 2/39 (5%)
Query: 264 IDLWRNL--TSNNIKLTFIWCPSHCGIEGNEEVDRAANR 300
+DLW+ L ++ + W H G NE D A
Sbjct: 100 VDLWQRLDAALKRHQIKWHWVKGHAGHPENERCDELARA 138
>gnl|CDD|238185 cd00304, RT_like, RT_like: Reverse transcriptase (RT, RNA-dependent
DNA polymerase)_like family. An RT gene is usually
indicative of a mobile element such as a retrotransposon
or retrovirus. RTs occur in a variety of mobile
elements, including retrotransposons, retroviruses,
group II introns, bacterial msDNAs, hepadnaviruses, and
caulimoviruses. These elements can be divided into two
major groups. One group contains retroviruses and DNA
viruses whose propagation involves an RNA intermediate.
They are grouped together with transposable elements
containing long terminal repeats (LTRs). The other
group, also called poly(A)-type retrotransposons,
contain fungal mitochondrial introns and transposable
elements that lack LTRs.
Length = 98
Score = 28.1 bits (63), Expect = 3.4
Identities = 19/89 (21%), Positives = 32/89 (35%), Gaps = 17/89 (19%)
Query: 25 QGSSLSTLLFAVFMNDI---FHVINLPTRGLLFVDDLLLTIRGKILEQLGSR-------- 73
QGS LS L ++M + L + +VDDL++ + +
Sbjct: 14 QGSPLSPALANLYMEKLEAPILKQLLDITLIRYVDDLVVIAKSEQQAVKKRELEEFLARL 73
Query: 74 --NPTLPLIMLNGNQLKFDNTAKFLGLIW 100
N + + KF KFLG++
Sbjct: 74 GLNLSDEKTQFTEKEKKF----KFLGILV 98
>gnl|CDD|225119 COG2209, NqrE, Na+-transporting NADH:ubiquinone oxidoreductase,
subunit NqrE [Energy production and conversion].
Length = 198
Score = 28.2 bits (63), Expect = 7.3
Identities = 13/34 (38%), Positives = 17/34 (50%)
Query: 5 IAVKCNNLISNFKGLENGLVQGSSLSTLLFAVFM 38
I V NNL+ F + L +G LS L F F+
Sbjct: 51 ITVPVNNLVYTFILKDGALAEGVDLSFLNFITFI 84
>gnl|CDD|84141 PRK12456, PRK12456, Na(+)-translocating NADH-quinone reductase
subunit E; Provisional.
Length = 199
Score = 28.0 bits (62), Expect = 7.8
Identities = 15/34 (44%), Positives = 18/34 (52%)
Query: 5 IAVKCNNLISNFKGLENGLVQGSSLSTLLFAVFM 38
IA NNLI + EN L+ G LS L F F+
Sbjct: 52 IATPLNNLIYTYILRENALIDGVDLSFLDFITFI 85
>gnl|CDD|166421 PLN02780, PLN02780, ketoreductase/ oxidoreductase.
Length = 320
Score = 27.9 bits (62), Expect = 9.7
Identities = 18/71 (25%), Positives = 31/71 (43%), Gaps = 7/71 (9%)
Query: 187 LLNYVTKISACPSNPVYNILFPTSLRRRLGIY-------EFTRTPKPLFVRFRAIEAYVQ 239
LL + K++ + V + P L+R+ G PL+ + A +AY+
Sbjct: 157 LLKNLIKVNVEGTTKVTQAVLPGMLKRKKGAIINIGSGAAIVIPSDPLYAVYAATKAYID 216
Query: 240 ELDRCDMMEYK 250
+ RC +EYK
Sbjct: 217 QFSRCLYVEYK 227
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 0.419
Gapped
Lambda K H
0.267 0.0712 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,203,466
Number of extensions: 2165338
Number of successful extensions: 1563
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1560
Number of HSP's successfully gapped: 24
Length of query: 435
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 335
Effective length of database: 6,502,202
Effective search space: 2178237670
Effective search space used: 2178237670
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 (26.9 bits)