RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1455
(221 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 = 51.9 bits (125), Expect = 8e-09
Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 1/50 (2%)
Query: 42 IQNMALRIATGAFKSSRIENLQVDAGNNVKIIWIPSHCGIAGNEEVDKAA 91
+++ I L + G V++ W+P H GI GNE D+ A
Sbjct: 75 LRSPRSSSPLVLRIRKAIRELA-NHGVKVRLHWVPGHSGIEGNERADRLA 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 = 42.6 bits (101), Expect = 2e-05
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 3/44 (6%)
Query: 53 AFKSSRIENL---QVDAGNNVKIIWIPSHCGIAGNEEVDKAAQS 93
+S I+N + + V I W+P H GI GNE DK A+
Sbjct: 80 KSESKPIKNEIWELLQKKHKVYIQWVPGHSGIPGNELADKLAKQ 123
>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 = 34.1 bits (79), Expect = 0.022
Identities = 13/25 (52%), Positives = 15/25 (60%)
Query: 67 GNNVKIIWIPSHCGIAGNEEVDKAA 91
G VK +P H GI GNEE D+ A
Sbjct: 121 GIRVKFWHVPGHSGIYGNEEADRLA 145
>gnl|CDD|237371 PRK13381, PRK13381, peptidase T; Provisional.
Length = 404
Score = 33.4 bits (77), Expect = 0.083
Identities = 11/47 (23%), Positives = 22/47 (46%), Gaps = 2/47 (4%)
Query: 174 ERTDPPQCEIRLKYNLNNLQIKDILGDNPRTIDLLFKFLKDSNLLPK 220
+ + + L +N I + + D+ R +DL F +K+ + PK
Sbjct: 302 AKYPTARVSLTLTDQYSN--ISNSIKDDRRAVDLAFDAMKELGIEPK 346
>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 = 32.1 bits (74), Expect = 0.086
Identities = 10/27 (37%), Positives = 13/27 (48%)
Query: 66 AGNNVKIIWIPSHCGIAGNEEVDKAAQ 92
A + V W+ H G GNE D+ A
Sbjct: 109 AKHQVTWHWVKGHAGHPGNERADELAN 135
>gnl|CDD|131685 TIGR02637, RhaS, rhamnose ABC transporter, rhamnose-binding
protein. This sugar-binding component of ABC
transporter complexes is found in rhamnose catabolism
operon contexts. Mutation of this gene in Rhizobium
leguminosarum abolishes rhamnose transport and prevents
growth on rhamnose as a carbon source.
Length = 302
Score = 29.8 bits (67), Expect = 0.90
Identities = 13/55 (23%), Positives = 25/55 (45%)
Query: 69 NVKIIWIPSHCGIAGNEEVDKAAQSFTNAQIYSLITPVDLKAFLKNEFKKKWQIW 123
N+K I P+ GI + A+ ++ L P ++ ++KN K + +W
Sbjct: 185 NLKGIIAPTTVGIKAAAQAVSDAKLIGKVKLTGLGLPSEMAKYVKNGTVKAFALW 239
>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 = 27.9 bits (63), Expect = 2.5
Identities = 7/23 (30%), Positives = 11/23 (47%)
Query: 69 NVKIIWIPSHCGIAGNEEVDKAA 91
+ + + +H G NE DK A
Sbjct: 107 KISFVKVKAHSGDKYNELADKLA 129
>gnl|CDD|218509 pfam05223, MecA_N, NTF2-like N-terminal transpeptidase domain. The
structure of this domain from MecA is known, and is
found to be similar to that found in NTF2 pfam02136.
This domain seems unlikely to have an enzymatic
function, and its role remains unknown.
Length = 118
Score = 27.8 bits (62), Expect = 2.5
Identities = 13/65 (20%), Positives = 27/65 (41%), Gaps = 8/65 (12%)
Query: 85 EEVDKAAQSFTNA-------QIYSLITPVDLKAFLKNEFKKKWQIWWDNIQPPNKIKEIK 137
+KAA++F +A SL + K + E +++Q +D + ++
Sbjct: 1 ASPEKAAETFLDAWAKGDFKTAASLTSEASKKDISEKEATERYQAIYDGLG-AKDLEITA 59
Query: 138 DTVKE 142
VK+
Sbjct: 60 LKVKK 64
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 26.9 bits (60), Expect = 6.8
Identities = 8/23 (34%), Positives = 10/23 (43%)
Query: 69 NVKIIWIPSHCGIAGNEEVDKAA 91
V W+ H G NE D+ A
Sbjct: 117 LVFWEWVKGHAGHPENERADQLA 139
>gnl|CDD|236334 PRK08719, PRK08719, ribonuclease H; Reviewed.
Length = 147
Score = 26.7 bits (59), Expect = 7.2
Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 3/33 (9%)
Query: 63 QVD---AGNNVKIIWIPSHCGIAGNEEVDKAAQ 92
QVD A V++ + +H GI GNE D AQ
Sbjct: 110 QVDELRARKYVEVEKVTAHSGIEGNEAADMLAQ 142
>gnl|CDD|183090 PRK11339, abgT, putative aminobenzoyl-glutamate transporter;
Provisional.
Length = 508
Score = 27.1 bits (60), Expect = 9.1
Identities = 11/31 (35%), Positives = 15/31 (48%)
Query: 20 IIEYGAPIYGSASEKQLSRLEPIQNMALRIA 50
IIE + S+++L L Q LRIA
Sbjct: 235 IIEPRLGQWQGNSDEKLQTLTESQRFGLRIA 265
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
0.320 0.137 0.426
Gapped
Lambda K H
0.267 0.0794 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,427,863
Number of extensions: 1069635
Number of successful extensions: 1013
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1012
Number of HSP's successfully gapped: 28
Length of query: 221
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 128
Effective length of database: 6,812,680
Effective search space: 872023040
Effective search space used: 872023040
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 (21.8 bits)
S2: 57 (25.6 bits)