RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy216
(650 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 = 110 bits (276), Expect = 2e-28
Identities = 47/129 (36%), Positives = 62/129 (48%), Gaps = 8/129 (6%)
Query: 198 FCYTDGSKTAANSGCA---YITETESQVFKLYNENSVFSSELLAIFMLLSHICNTRSRPE 254
YTDGSK +G T S+ +KL SVF +ELLAI L R
Sbjct: 1 VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRAR 60
Query: 255 YIFRDSVFICTDSKSSLLALKNIMSPNHLVNNILVKINELKILNITVKFLWIPSHLGIAG 314
I I +DS+++L AL++ S + LV I I EL + V+ W+P H GI G
Sbjct: 61 KIT-----IFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEG 115
Query: 315 NVQVDELAK 323
N + D LAK
Sbjct: 116 NERADRLAK 124
Score = 98.1 bits (245), Expect = 3e-24
Identities = 43/121 (35%), Positives = 57/121 (47%), Gaps = 8/121 (6%)
Query: 514 FCYTDGSKTAANSGCA---YITETESQVFKLYNENSVFSSELLAIFMLLSHIYSTSSRTE 570
YTDGSK +G T S+ +KL SVF +ELLAI L R
Sbjct: 1 VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRR-- 58
Query: 571 YIFRDSIFICTDSKSSLLALKNIMSPNHLVNNILVKINELKILNITVKFLWIPSHLGIAG 630
I I +DS+++L AL++ S + LV I I EL + V+ W+P H GI G
Sbjct: 59 ---ARKITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEG 115
Query: 631 N 631
N
Sbjct: 116 N 116
>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 = 70.8 bits (174), Expect = 1e-14
Identities = 36/135 (26%), Positives = 48/135 (35%), Gaps = 20/135 (14%)
Query: 195 NSLFCYTDGS--KTAANSGCAYITETESQVFKLYNENSVFSSELLAIFMLLSHICNTRSR 252
++ YTDGS G Y+T+ Q K + +ELLA+ L +
Sbjct: 2 EAVTVYTDGSCNGNPGPGGAGYVTDGGKQRSKPLPGTTNQRAELLALIEALEA---LSGQ 58
Query: 253 PEYIFRDSVFICTDSKSS----LLALKNIMSPNHLVNNILVKINELKILNITVKFLWIPS 308
V I TDS+ + N I EL V W+P
Sbjct: 59 K-------VNIYTDSQYVIGGITNGWPTKSESKPIKNEIW----ELLQKKHKVYIQWVPG 107
Query: 309 HLGIAGNVQVDELAK 323
H GI GN D+LAK
Sbjct: 108 HSGIPGNELADKLAK 122
Score = 59.6 bits (145), Expect = 8e-11
Identities = 31/127 (24%), Positives = 43/127 (33%), Gaps = 20/127 (15%)
Query: 511 NSLFCYTDGS--KTAANSGCAYITETESQVFKLYNENSVFSSELLAIFMLLSHIYSTSSR 568
++ YTDGS G Y+T+ Q K + +ELLA+ L +
Sbjct: 2 EAVTVYTDGSCNGNPGPGGAGYVTDGGKQRSKPLPGTTNQRAELLALIEALEAL------ 55
Query: 569 TEYIFRDSIFICTDSKSS----LLALKNIMSPNHLVNNILVKINELKILNITVKFLWIPS 624
+ I TDS+ + N I EL V W+P
Sbjct: 56 ----SGQKVNIYTDSQYVIGGITNGWPTKSESKPIKNEIW----ELLQKKHKVYIQWVPG 107
Query: 625 HLGIAGN 631
H GI GN
Sbjct: 108 HSGIPGN 114
>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 = 42.2 bits (100), Expect = 1e-04
Identities = 34/160 (21%), Positives = 52/160 (32%), Gaps = 52/160 (32%)
Query: 200 YTDGS-----KTAANSGCAYITETESQVFKLYNENSVFS--------------SELLAIF 240
YTDG+ ++ A +G V+ + + +EL A+
Sbjct: 3 YTDGACRGNGRSGARAGYG--------VY--FGPGHPRNVSERLPGPPQTNQRAELRAVI 52
Query: 241 MLLSHICNTRSRPEYIFRDSVFICTDSKSSLLALKNIMSPNHLVNN-------------- 286
L I + I TDS+ + + P N
Sbjct: 53 HALRLIKEVGEGLTK-----LVIATDSEYVVNGV-TEWIPKWKKNGWKTSKGKPVANKDL 106
Query: 287 ---ILVKINELKILNITVKFLWIPSHLGIAGNVQVDELAK 323
+ + EL+ I VKF +P H GI GN + D LAK
Sbjct: 107 IKELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLAK 146
Score = 32.6 bits (75), Expect = 0.31
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 603 ILVKINELKILNITVKFLWIPSHLGIAGNVQ 633
+ + EL+ I VKF +P H GI GN +
Sbjct: 110 LDKLLEELEERGIRVKFWHVPGHSGIYGNEE 140
>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 = 39.3 bits (92), Expect = 0.001
Identities = 29/134 (21%), Positives = 44/134 (32%), Gaps = 18/134 (13%)
Query: 200 YTDGSKTA--ANSGCAYITETESQV----FKLYNEN-SVFSSELLAIFMLLSHICNTRSR 252
TDGS +G + L + +ELLA+ L + +
Sbjct: 1 NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLGLK 60
Query: 253 PEYIFRDSVFICTDSKSSLLALKNIMSPNHLVNNILVKINELKILNITVKFLWIPSHLGI 312
I TDSK + + + N +L I L I ++F +P
Sbjct: 61 KLIIE-------TDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPRE--- 110
Query: 313 AGNVQVDELAKNSQ 326
GN D LAK +
Sbjct: 111 -GNEVADRLAKEAA 123
Score = 32.3 bits (74), Expect = 0.23
Identities = 23/115 (20%), Positives = 36/115 (31%), Gaps = 14/115 (12%)
Query: 516 YTDGSKTA--ANSGCAYITETESQV----FKLYNEN-SVFSSELLAIFMLLSHIYSTSSR 568
TDGS +G + L + +ELLA+ L +
Sbjct: 1 NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLGLK 60
Query: 569 TEYIFRDSIFICTDSKSSLLALKNIMSPNHLVNNILVKINELKILNITVKFLWIP 623
I TDSK + + + N +L I L I ++F +P
Sbjct: 61 KLIIE-------TDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVP 108
>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 = 36.1 bits (84), Expect = 0.015
Identities = 31/141 (21%), Positives = 49/141 (34%), Gaps = 26/141 (18%)
Query: 199 CYTDGSKTAANSGCAYITETESQV-FKLYNENSVFSSELLAIFMLLSHICNTRSRPEYIF 257
+TDGS +G A +T + L S +EL+A+ L
Sbjct: 2 VFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIALIRALELAKGKP------- 54
Query: 258 RDSVFICTDSK---SSLLALKNIMSPNHLVNNILVKINEL--KILNI-----TVKFLWIP 307
V I TDS L AL+ I + + + L ++ V + I
Sbjct: 55 ---VNIYTDSAYAFGILHALETIWKERGFLTGKPIALASLILQLQKAIQRPKPVAVIHIR 111
Query: 308 SHLG-----IAGNVQVDELAK 323
+H G GN + D+ A+
Sbjct: 112 AHSGLPGPLALGNARADQAAR 132
Score = 30.7 bits (70), Expect = 1.0
Identities = 25/122 (20%), Positives = 41/122 (33%), Gaps = 21/122 (17%)
Query: 515 CYTDGSKTAANSGCAYITETESQV-FKLYNENSVFSSELLAIFMLLSHIYSTSSRTEYIF 573
+TDGS +G A +T + L S +EL+A+ L
Sbjct: 2 VFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIALIRALELAKGK-------- 53
Query: 574 RDSIFICTDSK---SSLLALKNIMSPNHLVNNILVKINEL--KILNI-----TVKFLWIP 623
+ I TDS L AL+ I + + + L ++ V + I
Sbjct: 54 --PVNIYTDSAYAFGILHALETIWKERGFLTGKPIALASLILQLQKAIQRPKPVAVIHIR 111
Query: 624 SH 625
+H
Sbjct: 112 AH 113
>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 = 34.4 bits (80), Expect = 0.062
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 300 TVKFLWIPSHLGIAGNVQVDELAK 323
V + W+ H G GN + DELA
Sbjct: 112 QVTWHWVKGHAGHPGNERADELAN 135
>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 = 32.9 bits (76), Expect = 0.18
Identities = 9/28 (32%), Positives = 15/28 (53%)
Query: 298 NITVKFLWIPSHLGIAGNVQVDELAKNS 325
I + F+ + +H G N D+LAK +
Sbjct: 105 KIKISFVKVKAHSGDKYNELADKLAKKA 132
>gnl|CDD|118907 pfam10386, DUF2441, Protein of unknown function (DUF2441). This is
a family of highly conserved, predicted, proteins from
Bacillus species. The structure forms a homo-dimer. The
function is unknown.
Length = 141
Score = 30.0 bits (67), Expect = 2.0
Identities = 18/41 (43%), Positives = 23/41 (56%), Gaps = 1/41 (2%)
Query: 369 EDTLLWKSSFDKDRRKEIVICRLR-IGHSHLTHNFLLKRED 408
ED L WK+ FD R+ + I +LR IG S LL +ED
Sbjct: 84 EDALKWKALFDSYNREVLQIVKLRVIGSSFEGDGNLLPKED 124
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 30.0 bits (68), Expect = 2.2
Identities = 10/38 (26%), Positives = 21/38 (55%)
Query: 286 NILVKINELKILNITVKFLWIPSHLGIAGNVQVDELAK 323
++ +++EL + V + W+ H G N + D+LA+
Sbjct: 103 DLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAR 140
>gnl|CDD|130298 TIGR01231, lacC, tagatose-6-phosphate kinase. This enzyme is part
of the tagatose-6-phosphate pathway of lactose
degradation [Energy metabolism, Biosynthesis and
degradation of polysaccharides].
Length = 309
Score = 30.6 bits (69), Expect = 2.7
Identities = 16/63 (25%), Positives = 30/63 (47%)
Query: 177 LSSVAVKNAFFQFKGENQNSLFCYTDGSKTAANSGCAYITETESQVFKLYNENSVFSSEL 236
L +K+AF++ GE +N + +G +T I+ E+ F + E + E+
Sbjct: 70 LDHSDIKHAFYKISGETRNCIAILHEGQQTEILEQGPEISNQEAAGFLKHFEQLLEKVEV 129
Query: 237 LAI 239
+AI
Sbjct: 130 VAI 132
Score = 30.6 bits (69), Expect = 2.7
Identities = 16/63 (25%), Positives = 30/63 (47%)
Query: 493 LSSVAVKNAFFQFKGENQNSLFCYTDGSKTAANSGCAYITETESQVFKLYNENSVFSSEL 552
L +K+AF++ GE +N + +G +T I+ E+ F + E + E+
Sbjct: 70 LDHSDIKHAFYKISGETRNCIAILHEGQQTEILEQGPEISNQEAAGFLKHFEQLLEKVEV 129
Query: 553 LAI 555
+AI
Sbjct: 130 VAI 132
>gnl|CDD|178927 PRK00203, rnhA, ribonuclease H; Reviewed.
Length = 150
Score = 28.3 bits (64), Expect = 6.6
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 300 TVKFLWIPSHLGIAGNVQVDELAKN 324
+K+ W+ H G N + DELA+
Sbjct: 114 QIKWHWVKGHAGHPENERCDELARA 138
>gnl|CDD|237369 PRK13376, pyrB, bifunctional aspartate carbamoyltransferase
catalytic subunit/aspartate carbamoyltransferase
regulatory subunit; Provisional.
Length = 525
Score = 29.3 bits (66), Expect = 7.6
Identities = 16/47 (34%), Positives = 26/47 (55%), Gaps = 8/47 (17%)
Query: 130 RTVKSRLEDLQIFDRISAQVIKRDEYIAPWELSVPEIIYLTSEKKEN 176
RTV S++ L+IF + + IAP EL++PE + + K+N
Sbjct: 187 RTVHSKVNGLKIFKNVKVDL------IAPEELAMPE--HYVEKMKKN 225
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 0.392
Gapped
Lambda K H
0.267 0.0797 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 31,699,817
Number of extensions: 3053380
Number of successful extensions: 2308
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2301
Number of HSP's successfully gapped: 25
Length of query: 650
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 547
Effective length of database: 6,369,140
Effective search space: 3483919580
Effective search space used: 3483919580
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: 62 (27.5 bits)