RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10399
(442 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 = 53.0 bits (128), Expect = 1e-08
Identities = 13/35 (37%), Positives = 16/35 (45%)
Query: 269 HTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAK 303
+L G ++ W P H GI GNE D AK
Sbjct: 90 KAIRELANHGVKVRLHWVPGHSGIEGNERADRLAK 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 = 43.0 bits (102), Expect = 3e-05
Identities = 12/30 (40%), Positives = 15/30 (50%)
Query: 274 LVACGKEISFMWCPSHCGISGNEAVDVAAK 303
L+ ++ W P H GI GNE D AK
Sbjct: 93 LLQKKHKVYIQWVPGHSGIPGNELADKLAK 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 = 35.2 bits (82), Expect = 0.021
Identities = 17/64 (26%), Positives = 27/64 (42%), Gaps = 5/64 (7%)
Query: 245 IDAMSDRLLEMKK---FTNNDKMQLNQHTW--LDLVACGKEISFMWCPSHCGISGNEAVD 299
I+ ++ + KK T + K N W LD + ++++ W H G GNE D
Sbjct: 72 INGITKWIHGWKKNGWKTADGKPVKNVDLWQELDALLAKHQVTWHWVKGHAGHPGNERAD 131
Query: 300 VAAK 303
A
Sbjct: 132 ELAN 135
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 33.5 bits (77), Expect = 0.10
Identities = 15/65 (23%), Positives = 28/65 (43%), Gaps = 6/65 (9%)
Query: 245 IDAMSDRLLEMKKF---TNNDKMQLNQHTWLDLVACGK---EISFMWCPSHCGISGNEAV 298
++ ++ +++ KK T + K N+ W +L K + + W H G NE
Sbjct: 76 VEGITRWIVKWKKNGWKTADKKPVKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERA 135
Query: 299 DVAAK 303
D A+
Sbjct: 136 DQLAR 140
>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 = 33.0 bits (76), Expect = 0.14
Identities = 13/31 (41%), Positives = 15/31 (48%)
Query: 273 DLVACGKEISFMWCPSHCGISGNEAVDVAAK 303
+L G + F P H GI GNE D AK
Sbjct: 116 ELEERGIRVKFWHVPGHSGIYGNEEADRLAK 146
>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 = 30.9 bits (71), Expect = 0.44
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 280 EISFMWCPSHCGISGNEAVDVAAKN 304
+ISF+ +H G NE D AK
Sbjct: 107 KISFVKVKAHSGDKYNELADKLAKK 131
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 30.7 bits (69), Expect = 2.0
Identities = 12/37 (32%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 39 SPPNNLKAELTKWTLESRISKNHVSSLLRSLRPYHPQ 75
+PP + A L++W LE S+ +L P HP+
Sbjct: 656 TPPAEVYARLSEWLLER--SRAGPDTLFAPATPTHPE 690
>gnl|CDD|234493 TIGR04189, surface_SprA, cell surface protein SprA. SprA is a cell
surface protein widely distributed in the Bacteroidetes
lineage. In Flavobacterium johnsoniae, a species that
shows gliding motility, mutation disrupts gliding.
Length = 2315
Score = 30.4 bits (69), Expect = 2.7
Identities = 8/29 (27%), Positives = 14/29 (48%)
Query: 325 KKIVQRNWQSSWNSVPNGNKLKSIKPNIE 353
+ R + + V +GNK SI P+ +
Sbjct: 2245 MLTLIRKLDADFPQVTSGNKRWSINPSAD 2273
>gnl|CDD|221127 pfam11523, DUF3223, Protein of unknown function (DUF3223). This
family of proteins has no known function.
Length = 76
Score = 27.2 bits (61), Expect = 3.5
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 44 LKAELTKWTLESRISKNHVSSLLRSLRPYHP 74
KA L ++ R+S +LL +L YHP
Sbjct: 1 FKAILHRYDDGDRLSDEDEKTLLEALLEYHP 31
>gnl|CDD|234010 TIGR02781, VirB9, P-type conjugative transfer protein VirB9. The
VirB9 protein is found in the vir locus of Agrobacterium
Ti plasmids where it is involved in a type IV secretion
system. VirB9 is a homolog of the F-type conjugative
transfer system TraK protein (which is believed to be an
outer membrane pore-forming secretin, TIGR02756) as well
as the Ti system TrbG protein [Cellular processes,
Conjugation].
Length = 243
Score = 28.1 bits (63), Expect = 8.6
Identities = 19/52 (36%), Positives = 24/52 (46%), Gaps = 16/52 (30%)
Query: 335 SWNSVPNGNKLKSIKPNIEKWPSSNRKTRLEEVVLTRMRIGHTRLTHSYLFS 386
+W PNGNKL IKP + W KT + V+T R SY+F
Sbjct: 71 AWEVTPNGNKL-FIKPTEKDW-----KTNM--TVVTNKR--------SYVFD 106
>gnl|CDD|168927 PRK07374, dnaE, DNA polymerase III subunit alpha; Validated.
Length = 1170
Score = 28.5 bits (64), Expect = 8.9
Identities = 18/68 (26%), Positives = 27/68 (39%), Gaps = 18/68 (26%)
Query: 312 LKLCSASDYKPLIKKIVQRNWQSSWNSVPNGNKLKSIKPNIEKWPSSNRKTRLEEVVLTR 371
LKLC KP+I GN++ I +I+ P ++ R VVL +
Sbjct: 51 LKLCKGKGIKPII-----------------GNEMYVINGSIDD-PQPKKEKRYHLVVLAK 92
Query: 372 MRIGHTRL 379
G+ L
Sbjct: 93 NATGYKNL 100
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 0.134 0.413
Gapped
Lambda K H
0.267 0.0617 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,206,006
Number of extensions: 2089351
Number of successful extensions: 1422
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1422
Number of HSP's successfully gapped: 12
Length of query: 442
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 342
Effective length of database: 6,502,202
Effective search space: 2223753084
Effective search space used: 2223753084
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: 61 (27.5 bits)