RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10247
(315 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 = 109 bits (275), Expect = 8e-30
Identities = 42/128 (32%), Positives = 70/128 (54%), Gaps = 7/128 (5%)
Query: 48 FIFTDGTKTATNTGFAYV---SGDLCQTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDN 104
I+TDG+K TG + G + ++Y+L P S+F AE LAIL+ L+ + +
Sbjct: 1 VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLA----LREG 56
Query: 105 FNFRSVIICSDSRSSLEALRTQFTLNEISFNILCTVHQLKARDINIKFLWIPSHCGIVEN 164
R + I SDS+++L+ALR+ + + + I + +L + ++ W+P H GI N
Sbjct: 57 RRARKITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGN 116
Query: 165 ERVDQAAK 172
ER D+ AK
Sbjct: 117 ERADRLAK 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 = 63.0 bits (154), Expect = 2e-12
Identities = 31/137 (22%), Positives = 54/137 (39%), Gaps = 17/137 (12%)
Query: 45 DSLFIFTDG--TKTATNTGFAYVSGDLCQTYRLNPLSSIFTAESLAI---LKCLEYIMSL 99
+++ ++TDG G YV+ Q + P ++ AE LA+ L+ L
Sbjct: 2 EAVTVYTDGSCNGNPGPGGAGYVTDGGKQRSKPLPGTTNQRAELLALIEALEALSG---- 57
Query: 100 VIVDNFNFRSVIICSDSRSSLEALRTQFTLNEISFNILCTVHQLKARDINIKFLWIPSHC 159
+ V I +DS+ + + + S I + +L + + W+P H
Sbjct: 58 --------QKVNIYTDSQYVIGGITNGWPTKSESKPIKNEIWELLQKKHKVYIQWVPGHS 109
Query: 160 GIVENERVDQAAKNSIY 176
GI NE D+ AK
Sbjct: 110 GIPGNELADKLAKQGAS 126
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 42.0 bits (99), Expect = 7e-05
Identities = 23/102 (22%), Positives = 43/102 (42%), Gaps = 20/102 (19%)
Query: 84 AESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSSLEALRTQFTLNEISF--------- 134
AE A+++ LE + L V + +DS+ +E + T++ +
Sbjct: 46 AELRALIEALEALKEL------GACEVTLYTDSKYVVEGI-TRWIVKWKKNGWKTADKKP 98
Query: 135 ----NILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAK 172
++ + +L R + + W+ H G ENER DQ A+
Sbjct: 99 VKNKDLWEELDELLKRHELVFWEWVKGHAGHPENERADQLAR 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 = 41.2 bits (97), Expect = 9e-05
Identities = 24/100 (24%), Positives = 48/100 (48%), Gaps = 10/100 (10%)
Query: 76 NPLSSIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSSLEALRTQFTLNEISFN 135
P ++ AE LA+L+ LE + L + +II +DS+ ++ + + + +
Sbjct: 34 IPAATNNEAELLALLEALELALDL------GLKKLIIETDSKYVVDLINSWSKGWKKNNL 87
Query: 136 ILCTVHQLKARDINIKFLWIPSHCGIVENERVDQAAKNSI 175
+L + L ++ I+I+F +P NE D+ AK +
Sbjct: 88 LLWDILLLLSKFIDIRFEHVPREG----NEVADRLAKEAA 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 = 37.6 bits (88), Expect = 0.002
Identities = 24/114 (21%), Positives = 38/114 (33%), Gaps = 38/114 (33%)
Query: 84 AESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSSLEALRTQFTLNEISFN-------- 135
AE A++ L I ++I +DS ++ +N ++
Sbjct: 46 AELRAVIHALRLIKE----VGEGLTKLVIATDS---------EYVVNGVTEWIPKWKKNG 92
Query: 136 --------------ILCTVHQLK---ARDINIKFLWIPSHCGIVENERVDQAAK 172
I L+ R I +KF +P H GI NE D+ AK
Sbjct: 93 WKTSKGKPVANKDLIKELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLAK 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 = 35.9 bits (84), Expect = 0.007
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 147 DINIKFLWIPSHCGIVENERVDQAAKNSI 175
I I F+ + +H G NE D+ AK ++
Sbjct: 105 KIKISFVKVKAHSGDKYNELADKLAKKAL 133
>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 = 35.7 bits (83), Expect = 0.007
Identities = 35/140 (25%), Positives = 60/140 (42%), Gaps = 25/140 (17%)
Query: 49 IFTDGTKTATNTGFAYVSG-DLCQTYRLNPLSSIFTAESLAILKCLEYIMSLVIVDNFNF 107
+FTDG+ G+A V+G D+ + L +S AE +A+++ LE
Sbjct: 2 VFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIALIRALE---------LAKG 52
Query: 108 RSVIICSDSR------SSLEAL---RTQFTLNEI-SFNILCTVHQLKARDINIKFLWIPS 157
+ V I +DS +LE + R T I +++ + + R + + I +
Sbjct: 53 KPVNIYTDSAYAFGILHALETIWKERGFLTGKPIALASLILQLQKAIQRPKPVAVIHIRA 112
Query: 158 HCG----IVE-NERVDQAAK 172
H G + N R DQAA+
Sbjct: 113 HSGLPGPLALGNARADQAAR 132
>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 = 35.6 bits (83), Expect = 0.010
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 149 NIKFLWIPSHCGIVENERVDQAAK 172
+ + W+ H G NER D+ A
Sbjct: 112 QVTWHWVKGHAGHPGNERADELAN 135
>gnl|CDD|178927 PRK00203, rnhA, ribonuclease H; Reviewed.
Length = 150
Score = 32.5 bits (75), Expect = 0.11
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 149 NIKFLWIPSHCGIVENERVDQAAKNSI 175
IK+ W+ H G ENER D+ A+
Sbjct: 114 QIKWHWVKGHAGHPENERCDELARAGA 140
>gnl|CDD|185323 PRK15425, gapA, glyceraldehyde-3-phosphate dehydrogenase A;
Provisional.
Length = 331
Score = 28.9 bits (64), Expect = 4.0
Identities = 18/72 (25%), Positives = 31/72 (43%), Gaps = 2/72 (2%)
Query: 10 IIASPTIIYLLNENKKSLIPQQARNSFLEFKSQNLDSLFIFTDGTKTATNTGFAYVSGDL 69
++A T ++L +E + I A+ + S+ D+ +F G G VS
Sbjct: 92 VVAEATGLFLTDETARKHITAGAKKVVMTGPSK--DNTPMFVKGANFDKYAGQDIVSNAS 149
Query: 70 CQTYRLNPLSSI 81
C T L PL+ +
Sbjct: 150 CTTNCLAPLAKV 161
>gnl|CDD|237544 PRK13887, PRK13887, conjugal transfer protein TrbF; Provisional.
Length = 250
Score = 28.2 bits (63), Expect = 6.0
Identities = 10/25 (40%), Positives = 15/25 (60%), Gaps = 4/25 (16%)
Query: 182 SVVVKDVIIQSKKTILNEWKTDWLE 206
SV +K V+ Q+ T W+ DW+E
Sbjct: 176 SVEIKSVLPQTPDT----WQVDWVE 196
>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 = 26.4 bits (59), Expect = 6.2
Identities = 21/93 (22%), Positives = 42/93 (45%), Gaps = 10/93 (10%)
Query: 80 SIFTAESLAILKCLEYIMSLVIVDNFNFRSVIICSDSRSSLEALRTQFTLNEISFNILCT 139
S AE+ A+L+ L+ + L I R +I+ SDS+ ++ ++ ++ +L
Sbjct: 1 SPLEAEAEALLEGLQLALELGI------RRLIVESDSQLVVQQIQGEYEARSRLAALLRE 54
Query: 140 VHQLKARDINIKFLWIPSHCGIVENERVDQAAK 172
+ +L + ++ +P C N D AK
Sbjct: 55 IRKLLKKFDSVSVSHVPREC----NRVADALAK 83
>gnl|CDD|149008 pfam07711, RabGGT_insert, Rab geranylgeranyl transferase
alpha-subunit, insert domain. Rab geranylgeranyl
transferase (RabGGT) catalyzes the addition of two
geranylgeranyl groups to the C-terminal cysteine
residues of Rab proteins, which is crucial for membrane
association and function of these proteins in
intracellular vesicular trafficking. This domain is
inserted between pfam01239 repeats. This domain adopts
an Ig-like fold and is thought to be involved in
protein-protein interactions and might be involved in
the recognition and binding of REP.
Length = 102
Score = 26.4 bits (58), Expect = 8.8
Identities = 14/76 (18%), Positives = 20/76 (26%), Gaps = 24/76 (31%)
Query: 225 WKTVHWRNRRDEIAVCRLRIGHTKLTQEYLFKKDAPPEC-------RTCGVVLTIKHILT 277
W+T H R R + +C D P V T
Sbjct: 43 WRTAHPRLRHSPVWLC-----------------DLPAGSINDQLNQHNFTVHWTDGDAQK 85
Query: 278 QCKAYAALRRKWKLES 293
+C Y + W +S
Sbjct: 86 ECALYTGRQEGWCRDS 101
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
0.322 0.135 0.408
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: 15,675,133
Number of extensions: 1458233
Number of successful extensions: 1208
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1204
Number of HSP's successfully gapped: 23
Length of query: 315
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 218
Effective length of database: 6,635,264
Effective search space: 1446487552
Effective search space used: 1446487552
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 (22.0 bits)
S2: 59 (26.4 bits)