RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10817
(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 = 63.8 bits (156), Expect = 2e-13
Identities = 18/56 (32%), Positives = 29/56 (51%)
Query: 1 MSSLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAK 56
++L+A+ S ++ L+ +I +L G ++ W P H GI GNE D AK
Sbjct: 69 QAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERADRLAK 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 = 43.8 bits (104), Expect = 4e-06
Identities = 17/54 (31%), Positives = 23/54 (42%), Gaps = 2/54 (3%)
Query: 4 LQAITSKSCNNALLSK-IYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAK 56
+ IT SK I + +L+ ++ W P H GI GNE D AK
Sbjct: 70 IGGIT-NGWPTKSESKPIKNEIWELLQKKHKVYIQWVPGHSGIPGNELADKLAK 122
>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 = 33.3 bits (77), Expect = 0.034
Identities = 13/31 (41%), Positives = 15/31 (48%)
Query: 26 DLVACGKEISFMWCPSHCGISGNEAVDVAAK 56
+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 = 32.1 bits (74), Expect = 0.073
Identities = 14/46 (30%), Positives = 21/46 (45%), Gaps = 1/46 (2%)
Query: 12 CNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKN 57
N +K Y ++D + +ISF+ +H G NE D AK
Sbjct: 87 ANKEG-TKEYKEFMDKIKKKIKISFVKVKAHSGDKYNELADKLAKK 131
>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 = 31.3 bits (72), Expect = 0.14
Identities = 10/32 (31%), Positives = 15/32 (46%)
Query: 25 LDLVACGKEISFMWCPSHCGISGNEAVDVAAK 56
LD + ++++ W H G GNE D A
Sbjct: 104 LDALLAKHQVTWHWVKGHAGHPGNERADELAN 135
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 30.0 bits (68), Expect = 0.40
Identities = 7/25 (28%), Positives = 11/25 (44%)
Query: 32 KEISFMWCPSHCGISGNEAVDVAAK 56
+ + + W H G NE D A+
Sbjct: 116 ELVFWEWVKGHAGHPENERADQLAR 140
>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 = 0.68
Identities = 8/29 (27%), Positives = 14/29 (48%)
Query: 78 KKIVQRNWQSSWNSVPNGNKLKSIKPNIE 106
+ R + + V +GNK SI P+ +
Sbjct: 2245 MLTLIRKLDADFPQVTSGNKRWSINPSAD 2273
>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 = 28.5 bits (64), Expect = 1.2
Identities = 14/58 (24%), Positives = 20/58 (34%), Gaps = 4/58 (6%)
Query: 1 MSSLQAITSKSCNNALLSKIYSTWLDLVACGKEISFMWCPSHCGISGNEAVDVAAKNP 58
+ I S S + + L L++ +I F P GNE D AK
Sbjct: 69 KYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPR----EGNEVADRLAKEA 122
>gnl|CDD|187697 cd09273, RNase_HI_RT_Bel, Bel/Pao family of RNase HI in long-term
repeat retroelements. 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 eukaryote. RNase HI has
also been observed as adjunct domains to the reverse
transcriptase gene in retroviruses, in 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.
Phylogenetic patterns of RNase HI of LTR retroelements
is classified into five major families, Ty3/Gypsy,
Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate
retroviruses. Bel/Pao family has been described only in
metazoan genomes. RNase H inhibitors have been explored
as an anti-HIV drug target because RNase H inactivation
inhibits reverse transcription.
Length = 135
Score = 28.4 bits (64), Expect = 1.2
Identities = 11/47 (23%), Positives = 18/47 (38%), Gaps = 8/47 (17%)
Query: 18 SKIYSTWLDL---VACGKEISFMWCPSHCG-----ISGNEAVDVAAK 56
+ S L L + K ++ + +H G GN D AA+
Sbjct: 86 IALASLILQLQKAIQRPKPVAVIHIRAHSGLPGPLALGNARADQAAR 132
>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 = 28.8 bits (65), Expect = 1.7
Identities = 19/52 (36%), Positives = 24/52 (46%), Gaps = 16/52 (30%)
Query: 88 SWNSVPNGNKLKSIKPNIEKWPSSNRKTRLEEVVLTRMRIGHTRLTHSYLFS 139
+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 = 28.9 bits (65), Expect = 2.0
Identities = 18/68 (26%), Positives = 27/68 (39%), Gaps = 18/68 (26%)
Query: 65 LKLCSASDYKPLIKKIVQRNWQSSWNSVPNGNKLKSIKPNIEKWPSSNRKTRLEEVVLTR 124
LKLC KP+I GN++ I +I+ P ++ R VVL +
Sbjct: 51 LKLCKGKGIKPII-----------------GNEMYVINGSIDD-PQPKKEKRYHLVVLAK 92
Query: 125 MRIGHTRL 132
G+ L
Sbjct: 93 NATGYKNL 100
>gnl|CDD|173592 PTZ00401, PTZ00401, aspartyl-tRNA synthetase; Provisional.
Length = 550
Score = 28.0 bits (62), Expect = 3.5
Identities = 14/38 (36%), Positives = 18/38 (47%), Gaps = 2/38 (5%)
Query: 108 WPSSNRKTRLEEVVLTRMRIGHTRLTHSYLFSRSPQPT 145
WP LE VV+ + + + RL LF R PQ T
Sbjct: 513 WPHGGFGVGLERVVMLYLGLSNVRLAS--LFPRDPQRT 548
>gnl|CDD|237002 PRK11857, PRK11857, dihydrolipoamide acetyltransferase; Reviewed.
Length = 306
Score = 26.7 bits (59), Expect = 8.8
Identities = 13/45 (28%), Positives = 22/45 (48%)
Query: 48 NEAVDVAAKNPSPSFPPLKLCSASDYKPLIKKIVQRNWQSSWNSV 92
+ AAK +P+ P KL + I+K + R +SW++V
Sbjct: 55 VSSAQQAAKTAAPAAAPPKLEGKREKVAPIRKAIARAMTNSWSNV 99
>gnl|CDD|180954 PRK07380, PRK07380, adenylosuccinate lyase; Provisional.
Length = 431
Score = 26.9 bits (60), Expect = 8.9
Identities = 11/42 (26%), Positives = 21/42 (50%), Gaps = 5/42 (11%)
Query: 79 KIVQRNWQSSWNSVPNGNKLKSIKPNIEKWPSSNRKTRLEEV 120
++VQ+N ++WN+ GN + N+E P + E+
Sbjct: 373 RLVQKNAHTAWNT-EGGN----FRANLEADPEVTQLLSAAEL 409
>gnl|CDD|227441 COG5110, RPN1, 26S proteasome regulatory complex component
[Posttranslational modification, protein turnover,
chaperones].
Length = 881
Score = 26.8 bits (59), Expect = 9.6
Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 9/50 (18%)
Query: 79 KIVQRNWQSSWNSVPNGNKLKSIKPN-------IEKWPSSNRKTRLEEVV 121
K V ++ SS +VP LK ++PN +KW N+K L +++
Sbjct: 72 KEVIKSSTSSMTAVPK--PLKFLRPNYLDLLEIYDKWLEGNKKRWLADIL 119
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
0.317 0.131 0.407
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: 9,701,598
Number of extensions: 849202
Number of successful extensions: 626
Number of sequences better than 10.0: 1
Number of HSP's gapped: 626
Number of HSP's successfully gapped: 17
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: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (25.6 bits)