RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16807
(220 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 = 41.1 bits (97), Expect = 6e-05
Identities = 16/53 (30%), Positives = 22/53 (41%), Gaps = 2/53 (3%)
Query: 6 ALIRLAMASPTELKCLNCFRYLLSDSYWTVVSFLWIPSHVGIRENNLVDEAAR 58
AL +SP L+ R L++ V W+P H GI N D A+
Sbjct: 74 ALRSPRSSSPLVLRIRKAIR-ELANHGVKV-RLHWVPGHSGIEGNERADRLAK 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 = 33.4 bits (77), Expect = 0.024
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 36 VSFLWIPSHVGIRENNLVDEAAR 58
V W+P H GI N L D+ A+
Sbjct: 100 VYIQWVPGHSGIPGNELADKLAK 122
>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 = 32.9 bits (76), Expect = 0.053
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 36 VSFLWIPSHVGIRENNLVDEAAR 58
V++ W+ H G N DE A
Sbjct: 113 VTWHWVKGHAGHPGNERADELAN 135
>gnl|CDD|218305 pfam04877, Hairpins, HrpZ. HrpZ from the plant pathogen
Pseudomonas syringae binds to lipid bilayers and forms a
cation-conducting pore in vivo. This pore-forming
activity may allow nutrient release or delivery of
virulence factors during bacterial colonisation of host
plants. The family of hairpinN proteins, Harpin, has
been merged into this family. HrpN is a virulence
determinant which elicits lesion formation in
Arabidopsis and tobacco and triggers systemic resistance
in Arabidopsis.
Length = 277
Score = 33.7 bits (77), Expect = 0.058
Identities = 14/34 (41%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 84 EVWAFADDYRAVFKKVQLEVWAKPWRE-NQLTGQ 116
E+ F DDY F K WA +E N LTG
Sbjct: 169 EIAQFMDDYPEQFGKPDSGSWANELKEDNGLTGA 202
>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 = 29.8 bits (68), Expect = 0.47
Identities = 8/25 (32%), Positives = 16/25 (64%)
Query: 36 VSFLWIPSHVGIRENNLVDEAARNS 60
+SF+ + +H G + N L D+ A+ +
Sbjct: 108 ISFVKVKAHSGDKYNELADKLAKKA 132
>gnl|CDD|178927 PRK00203, rnhA, ribonuclease H; Reviewed.
Length = 150
Score = 29.4 bits (67), Expect = 0.90
Identities = 10/35 (28%), Positives = 13/35 (37%)
Query: 36 VSFLWIPSHVGIRENNLVDEAARNSNEAPLSTICT 70
+ + W+ H G EN DE AR E
Sbjct: 115 IKWHWVKGHAGHPENERCDELARAGAEEATLEDTG 149
>gnl|CDD|238035 cd00081, Hint, Hedgehog/Intein domain, found in Hedgehog proteins
as well as proteins which contain inteins and undergo
protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In
protein splicing an intervening polypeptide sequence -
the intein - is excised from a protein, and the flanking
polypeptide sequences - the exteins - are joined by a
peptide bond. In addition to the autocatalytic splicing
domain, many inteins contain an inserted endonuclease
domain, which plays a role in spreading inteins.
Hedgehog proteins are a major class of intercellular
signaling molecules, which control inductive
interactions during animal development. The mature
signaling forms of hedgehog proteins are the N-terminal
fragments, which are covalently linked to cholesterol at
their C-termini. This modification is the result of an
autoprocessing step catalyzed by the C-terminal
fragments, which are aligned here.
Length = 136
Score = 28.4 bits (64), Expect = 1.5
Identities = 13/83 (15%), Positives = 30/83 (36%), Gaps = 5/83 (6%)
Query: 77 VFKKLQLEVWAFADDYRAVFKKVQLEVWAKPWREN--QLTGQKLKKIKCDTRKWKSSTRD 134
+ +K +V A + + VF KV V + + + ++ + ++I T +
Sbjct: 21 LVEKKGDKVLALDETGKLVFSKVLK-VLRRDYEKKFYKIKTESGREITL-TPDHLLFVLE 78
Query: 135 VRAEEIVVCR-LRIGHCLATHQY 156
+ V L+ G +
Sbjct: 79 DGELKWVFASDLKPGDYVLVPVL 101
>gnl|CDD|222478 pfam13966, zf-RVT, zinc-binding in reverse transcriptase. This
domain would appear to be a zinc-binding region of a
putative reverse transcriptase.
Length = 86
Score = 27.6 bits (62), Expect = 1.8
Identities = 8/24 (33%), Positives = 9/24 (37%)
Query: 161 QNPPACHLCNEVPITIKHWLLECP 184
Q P C LC + T H C
Sbjct: 57 QLPNRCVLCGQEEETRDHLFFHCS 80
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 27.3 bits (61), Expect = 4.2
Identities = 9/23 (39%), Positives = 12/23 (52%)
Query: 36 VSFLWIPSHVGIRENNLVDEAAR 58
V + W+ H G EN D+ AR
Sbjct: 118 VFWEWVKGHAGHPENERADQLAR 140
>gnl|CDD|234506 TIGR04221, SecA2_Mycobac, accessory Sec system translocase SecA2,
Actinobacterial type. Members of this family are the
SecA2 subunit of the Mycobacterial type of accessory
secretory system. This family is quite different SecA2
of the Staph/Strep type (TIGR03714).
Length = 762
Score = 27.1 bits (60), Expect = 8.0
Identities = 21/71 (29%), Positives = 31/71 (43%), Gaps = 6/71 (8%)
Query: 70 TADDYRAVFKKLQLEVWAFADDYRAVFKKVQLEVWAKPWRENQLTGQKLKKIKCDTRKWK 129
A+D R ++Q F D + V + LE+ A WR NQL Q+ I D R+
Sbjct: 562 PAEDGRIESPRVQ----DFVDHAQRVAEGQLLEIHANTWRYNQLIAQQRDII--DERRET 615
Query: 130 SSTRDVRAEEI 140
D +E+
Sbjct: 616 LLDTDTAWQEL 626
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
0.325 0.136 0.444
Gapped
Lambda K H
0.267 0.0780 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,215,706
Number of extensions: 1018314
Number of successful extensions: 875
Number of sequences better than 10.0: 1
Number of HSP's gapped: 875
Number of HSP's successfully gapped: 14
Length of query: 220
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 127
Effective length of database: 6,812,680
Effective search space: 865210360
Effective search space used: 865210360
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: 57 (25.6 bits)