RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7535
(199 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 = 75.0 bits (185), Expect = 1e-17
Identities = 36/113 (31%), Positives = 53/113 (46%), Gaps = 13/113 (11%)
Query: 16 QIFTDASKNEHSVSSAFCCEE---TKFSVKLDPRISICNAELISIQYAISFIISTTPLQV 72
I+TD SK E + F S KL P S+ +AEL++I A+ +
Sbjct: 1 VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALRE---GR 57
Query: 73 PTPKFVLYSDSLSALQSLQNIISSSPIALEI---INLLHKIQCQVR----PSH 118
K ++SDS +AL++L++ SSSP+ L I I L +VR P H
Sbjct: 58 RARKITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGH 110
>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 = 41.9 bits (99), Expect = 2e-05
Identities = 24/104 (23%), Positives = 37/104 (35%), Gaps = 14/104 (13%)
Query: 12 PNYKQIFTDAS--KNEHSVSSAFCCEETKFSVKLDPRISICNAELISIQYAISFIISTTP 69
P ++TD S N + + + K K P + AEL+++ A+
Sbjct: 1 PEAVTVYTDGSCNGNPGPGGAGYVTDGGKQRSKPLPGTTNQRAELLALIEALE------- 53
Query: 70 LQVPTPKFVLYSDSL----SALQSLQNIISSSPIALEIINLLHK 109
+ K +Y+DS S PI EI LL K
Sbjct: 54 -ALSGQKVNIYTDSQYVIGGITNGWPTKSESKPIKNEIWELLQK 96
>gnl|CDD|220251 pfam09462, Mus7, Mus7/MMS22 family. This family includes a
conserved region from the Mus7 protein. Mus7 is involved
in the repair of replication-associated DNA damage in
the fission yeast Schizosaccharomyces pombe. Mus7
functions in the same pathway as Mus81, a subunit of the
Mus81-Eme1 structure-specific endonuclease, which has
been implicated in the repair of the
replication-associated DNA damage. The MMS22 proteins
are involved in repairing double-stranded DNA breaks
created by the cleavage reaction of topoisomerase II.
Length = 603
Score = 30.6 bits (69), Expect = 0.60
Identities = 18/75 (24%), Positives = 29/75 (38%)
Query: 39 FSVKLDPRISICNAELISIQYAISFIISTTPLQVPTPKFVLYSDSLSALQSLQNIISSSP 98
FS L + + + SF+ + V K + S AL+SLQ++I +P
Sbjct: 250 FSQLLKQYVLARSEIEAQNEVWKSFLKNLADQLVEQNKRTIESLLKFALRSLQDMIQQAP 309
Query: 99 IALEIINLLHKIQCQ 113
LL K +
Sbjct: 310 TLEHANVLLSKSPLK 324
>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 = 27.7 bits (62), Expect = 2.4
Identities = 15/110 (13%), Positives = 34/110 (30%), Gaps = 19/110 (17%)
Query: 18 FTDASKNEHSVSSAF--------CCEETKFSVKLDPRISICNAELISIQYAISFIISTTP 69
TD S + + S+ + P + AEL+++ A+
Sbjct: 1 NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSI-PAATNNEAELLALLEALELA----- 54
Query: 70 LQVPTPKFVLYSDSLSALQSLQNIISSSPIALEIIN-----LLHKIQCQV 114
L + K ++ +DS + + + ++ L I +
Sbjct: 55 LDLGLKKLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRF 104
>gnl|CDD|222672 pfam14314, Methyltrans_Mon, Virus-capping methyltransferase. This
is the methyltransferase region of the Mononegavirales
single-stranded RNA viral RNA polymerase enzymes. This
region is involved in the mRNA-capping of the virion
particles.
Length = 674
Score = 27.3 bits (61), Expect = 7.1
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 82 DSLSALQSLQNIISSSPIALEIINLLHKI 110
D +SA N++ PI EI ++ HKI
Sbjct: 99 DKISASPPFLNLLRDGPIRDEIESIPHKI 127
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 0.136 0.408
Gapped
Lambda K H
0.267 0.0716 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,488,376
Number of extensions: 827673
Number of successful extensions: 754
Number of sequences better than 10.0: 1
Number of HSP's gapped: 751
Number of HSP's successfully gapped: 11
Length of query: 199
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 107
Effective length of database: 6,857,034
Effective search space: 733702638
Effective search space used: 733702638
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 (21.6 bits)
S2: 56 (25.4 bits)