RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16693
(196 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 = 74.2 bits (183), Expect = 2e-17
Identities = 28/79 (35%), Positives = 42/79 (53%), Gaps = 4/79 (5%)
Query: 18 LTGTAEKSECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDK-NKHVFSLHFTWVPS 76
L + ++ D S +AL+++++ SS+P+ IR + + H + WVP
Sbjct: 53 LREGRRARKITIFS--D-SQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPG 109
Query: 77 HVGIAGNEEADRLAKEALS 95
H GI GNE ADRLAKEA
Sbjct: 110 HSGIEGNERADRLAKEAAK 128
>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 = 62.7 bits (153), Expect = 6e-13
Identities = 25/58 (43%), Positives = 28/58 (48%), Gaps = 3/58 (5%)
Query: 38 SALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEALS 95
S S PI EI LL K V+ WVP H GI GNE AD+LAK+ S
Sbjct: 72 GITNGWPTKSESKPIKNEIWELLQKKHKVY---IQWVPGHSGIPGNELADKLAKQGAS 126
>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 = 52.5 bits (127), Expect = 4e-09
Identities = 17/45 (37%), Positives = 24/45 (53%)
Query: 50 NPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEAL 94
+E + +DK K + F V +H G NE AD+LAK+AL
Sbjct: 89 KEGTKEYKEFMDKIKKKIKISFVKVKAHSGDKYNELADKLAKKAL 133
>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 = 51.1 bits (123), Expect = 2e-08
Identities = 19/42 (45%), Positives = 25/42 (59%), Gaps = 1/42 (2%)
Query: 55 EIRNLLDK-NKHVFSLHFTWVPSHVGIAGNEEADRLAKEALS 95
E+ LL++ + + F VP H GI GNEEADRLAK+
Sbjct: 109 ELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLAKKGAD 150
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 43.1 bits (102), Expect = 1e-05
Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 3/44 (6%)
Query: 54 REIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEALSSN 97
E+ LL +++ VF + WV H G NE AD+LA+EA +
Sbjct: 106 EELDELLKRHELVF---WEWVKGHAGHPENERADQLAREAARAA 146
>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 = 42.5 bits (101), Expect = 2e-05
Identities = 16/40 (40%), Positives = 22/40 (55%), Gaps = 4/40 (10%)
Query: 54 REIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEA 93
+E+ LL K++ + + WV H G GNE AD LA A
Sbjct: 102 QELDALLAKHQ----VTWHWVKGHAGHPGNERADELANAA 137
>gnl|CDD|187703 cd09279, RNase_HI_archaeal_like, RNAse HI family that includes
Archaeal RNase HI. 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. Most archaeal genomes contain
only type 2 RNase H (RNase HII); however, a few contain
RNase HI as well. Although archaeal RNase HI sequences
conserve the DEDD active-site motif, they lack other
common features important for catalytic function, such
as the basic protrusion region. Archaeal RNase HI
homologs are more closely related to retroviral RNase HI
than bacterial and eukaryotic type I RNase H in
enzymatic properties.
Length = 128
Score = 39.0 bits (92), Expect = 3e-04
Identities = 17/46 (36%), Positives = 21/46 (45%), Gaps = 7/46 (15%)
Query: 50 NPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEALS 95
P E R LL K + V W+P N+EAD LA +AL
Sbjct: 90 APYLEEARELLKKFEEVE---IKWIPRE----ENKEADALANQALD 128
>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 = 36.9 bits (86), Expect = 0.001
Identities = 18/60 (30%), Positives = 21/60 (35%), Gaps = 6/60 (10%)
Query: 35 NSLSALQSIQNVSSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEAL 94
+ + S N + LL F VP GNE ADRLAKEA
Sbjct: 70 YVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIR--FEHVPRE----GNEVADRLAKEAA 123
>gnl|CDD|178927 PRK00203, rnhA, ribonuclease H; Reviewed.
Length = 150
Score = 34.0 bits (79), Expect = 0.017
Identities = 9/29 (31%), Positives = 12/29 (41%)
Query: 70 HFTWVPSHVGIAGNEEADRLAKEALSSNS 98
+ WV H G NE D LA+ +
Sbjct: 116 KWHWVKGHAGHPENERCDELARAGAEEAT 144
>gnl|CDD|205634 pfam13456, RVT_3, Reverse transcriptase-like. This domain is
found in plants and appears to be part of a
retrotransposon.
Length = 88
Score = 32.2 bits (74), Expect = 0.031
Identities = 18/46 (39%), Positives = 21/46 (45%), Gaps = 7/46 (15%)
Query: 51 PIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEALSS 96
+ REIR LL K S+ HV N AD LAK A +S
Sbjct: 50 ALLREIRKLLKKF-DSVSVS------HVPRECNRVADALAKLASAS 88
>gnl|CDD|236334 PRK08719, PRK08719, ribonuclease H; Reviewed.
Length = 147
Score = 32.5 bits (74), Expect = 0.066
Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 7/51 (13%)
Query: 47 SSSNPIA-REIRNLLD---KNKHVFSLHFTWVPSHVGIAGNEEADRLAKEA 93
S P+A R++ +D K+V V +H GI GNE AD LA+ A
Sbjct: 97 SDKKPVANRDLWQQVDELRARKYVEVEK---VTAHSGIEGNEAADMLAQAA 144
>gnl|CDD|180903 PRK07238, PRK07238, bifunctional RNase H/acid phosphatase;
Provisional.
Length = 372
Score = 33.0 bits (76), Expect = 0.077
Identities = 17/44 (38%), Positives = 23/44 (52%), Gaps = 7/44 (15%)
Query: 51 PIAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEAL 94
P+A + R L + V +TW+P A N ADRLA EA+
Sbjct: 94 PLAAQARELASQFGRV---TYTWIPR----ARNAHADRLANEAM 130
>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 = 29.9 bits (68), Expect = 0.47
Identities = 11/53 (20%), Positives = 24/53 (45%), Gaps = 8/53 (15%)
Query: 47 SSSNPIAREIRNLLDKNKHVFSLHFTWVPSHVG-----IAGNEEADRLAKEAL 94
+ + +++ + + K V +H + +H G GN AD+ A++A
Sbjct: 86 IALASLILQLQKAIQRPKPVAVIH---IRAHSGLPGPLALGNARADQAARQAA 135
>gnl|CDD|221997 pfam13233, Complex1_LYR_2, Complex1_LYR-like. This is a family of
proteins carrying the LYR motif of family Complex1_LYR,
pfam05347, likely to be involved in Fe-S cluster
biogenesis in mitochondria.
Length = 97
Score = 28.2 bits (63), Expect = 1.1
Identities = 11/37 (29%), Positives = 14/37 (37%), Gaps = 2/37 (5%)
Query: 124 EWANLAD--NKLRQIKEENRPWNPPFSMSRKEQVSIT 158
E N R E +NP MS +E+V T
Sbjct: 54 EAENYLAYLKAQRHYLELLERYNPGLDMSEEEKVRQT 90
>gnl|CDD|75628 PRK06548, PRK06548, ribonuclease H; Provisional.
Length = 161
Score = 29.0 bits (64), Expect = 1.1
Identities = 18/54 (33%), Positives = 30/54 (55%), Gaps = 4/54 (7%)
Query: 52 IAREIRNLLDKNKHVFSLHFTWVPSHVGIAGNEEADRLAKEALSSNSPPVNTIP 105
I +EI +L++ ++ +WV +H G NE AD LA++A ++ S IP
Sbjct: 102 IIQEIDSLMENR----NIRMSWVNAHTGHPLNEAADSLARQAANNFSTRSAHIP 151
>gnl|CDD|184807 PRK14730, coaE, dephospho-CoA kinase; Provisional.
Length = 195
Score = 29.1 bits (66), Expect = 1.2
Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 11/61 (18%)
Query: 86 ADRLAKEALSSNSPPVNTIPINDFKRFFKSKILTTWNTEWANLADNKLRQI---KEENRP 142
AD A+EAL+ SP + I +R + +KI+ +E L L +I E R
Sbjct: 32 ADIYAREALAPGSPILKAI----LQR-YGNKIIDPDGSE---LNRKALGEIIFNDPEERR 83
Query: 143 W 143
W
Sbjct: 84 W 84
>gnl|CDD|223457 COG0380, OtsA, Trehalose-6-phosphate synthase [Carbohydrate
transport and metabolism].
Length = 486
Score = 27.7 bits (62), Expect = 4.3
Identities = 7/28 (25%), Positives = 12/28 (42%)
Query: 51 PIAREIRNLLDKNKHVFSLHFTWVPSHV 78
+ + +R + K F LH + S V
Sbjct: 160 LVPQMLRERIPDAKIGFFLHIPFPSSEV 187
>gnl|CDD|224875 COG1964, COG1964, Predicted Fe-S oxidoreductases [General function
prediction only].
Length = 475
Score = 27.7 bits (62), Expect = 4.4
Identities = 7/26 (26%), Positives = 12/26 (46%)
Query: 46 VSSSNPIAREIRNLLDKNKHVFSLHF 71
V + PI+R + L K+ + H
Sbjct: 281 VPIAVPISRFVEALTGDPKYELTSHP 306
>gnl|CDD|237488 PRK13739, PRK13739, conjugal transfer protein TraP; Provisional.
Length = 198
Score = 27.1 bits (60), Expect = 5.1
Identities = 18/63 (28%), Positives = 24/63 (38%), Gaps = 21/63 (33%)
Query: 6 DTCDEHI--YYQVDLTGTAEKSECQVYLTPDNSLSALQSIQNVSSSNPIAREIRNLLDKN 63
T DEH+ Y D + + +C VY PD+ R RN DKN
Sbjct: 155 VTADEHLKEVYTEDASLPGKIRKCPVYF-PDD------------------RTNRNNGDKN 195
Query: 64 KHV 66
+H
Sbjct: 196 EHA 198
>gnl|CDD|225930 COG3395, COG3395, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 413
Score = 27.4 bits (61), Expect = 6.4
Identities = 8/19 (42%), Positives = 10/19 (52%)
Query: 153 EQVSITRLRIGPCISHGSP 171
Q+ T RIG I+ G P
Sbjct: 363 GQLGATGFRIGGEIAPGVP 381
>gnl|CDD|215643 PLN03241, PLN03241, magnesium chelatase subunit H; Provisional.
Length = 1315
Score = 27.1 bits (60), Expect = 7.1
Identities = 17/54 (31%), Positives = 23/54 (42%), Gaps = 6/54 (11%)
Query: 32 TPDNSLSALQSIQNVSSS-NPIAREIRNLLDKNKHVFS-----LHFTWVPSHVG 79
T + S L + +SS A EIR+LL +N S L +VP G
Sbjct: 841 TDEQLGSYLAAYNCPTSSQTQEAVEIRDLLSRNTEELSGVLKALGGEYVPPAPG 894
>gnl|CDD|218689 pfam05681, Fumerase, Fumarate hydratase (Fumerase). This family
consists of several bacterial fumarate hydratase
proteins FumA and FumB. Fumarase, or fumarate hydratase
(EC 4.2.1.2), is a component of the citric acid cycle.
In facultative anaerobes such as Escherichia coli,
fumarase also engages in the reductive pathway from
oxaloacetate to succinate during anaerobic growth. Three
fumarases, FumA, FumB, and FumC, have been reported in
E. coli. fumA and fumB genes are homologous and encode
products of identical sizes which form thermolabile
dimers of Mr 120,000. FumA and FumB are class I enzymes
and are members of the iron-dependent hydrolases, which
include aconitase and malate hydratase. The active FumA
contains a 4Fe-4S centre, and it can be inactivated upon
oxidation to give a 3Fe-4S centre.
Length = 271
Score = 26.3 bits (59), Expect = 9.8
Identities = 11/18 (61%), Positives = 13/18 (72%), Gaps = 1/18 (5%)
Query: 78 VGIAGN-EEADRLAKEAL 94
VGI G E+A LAK+AL
Sbjct: 181 VGIGGTSEKAALLAKKAL 198
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
0.316 0.131 0.400
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: 9,851,303
Number of extensions: 865586
Number of successful extensions: 858
Number of sequences better than 10.0: 1
Number of HSP's gapped: 856
Number of HSP's successfully gapped: 28
Length of query: 196
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 104
Effective length of database: 6,857,034
Effective search space: 713131536
Effective search space used: 713131536
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 (21.6 bits)
S2: 56 (25.2 bits)