RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12035
(251 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 = 53.4 bits (129), Expect = 3e-09
Identities = 15/55 (27%), Positives = 28/55 (50%)
Query: 53 SAILPLSVRRRLLFSNIIAKQEYYFASTNGSQISFMWIPSHSNIALNDKADQLAK 107
+A+ L R + ++ + +G ++ W+P HS I N++AD+LAK
Sbjct: 70 AALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERADRLAK 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 = 49.6 bits (119), Expect = 8e-08
Identities = 20/80 (25%), Positives = 29/80 (36%), Gaps = 7/80 (8%)
Query: 32 MGIRLISRALKSSPVN----SLYAESAILPLSVRRRLLFSNIIAKQEYYFASTNGSQISF 87
+ + AL VN S Y I + K E + ++
Sbjct: 46 LALIEALEALSGQKVNIYTDSQYVIGGIT---NGWPTKSESKPIKNEIWELLQKKHKVYI 102
Query: 88 MWIPSHSNIALNDKADQLAK 107
W+P HS I N+ AD+LAK
Sbjct: 103 QWVPGHSGIPGNELADKLAK 122
>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 = 41.3 bits (98), Expect = 7e-05
Identities = 11/27 (40%), Positives = 19/27 (70%)
Query: 84 QISFMWIPSHSNIALNDKADQLAKNSI 110
+ISF+ + +HS N+ AD+LAK ++
Sbjct: 107 KISFVKVKAHSGDKYNELADKLAKKAL 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 = 36.8 bits (86), Expect = 0.003
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 82 GSQISFMWIPSHSNIALNDKADQLAK 107
G ++ F +P HS I N++AD+LAK
Sbjct: 121 GIRVKFWHVPGHSGIYGNEEADRLAK 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 = 35.2 bits (82), Expect = 0.009
Identities = 8/24 (33%), Positives = 16/24 (66%)
Query: 84 QISFMWIPSHSNIALNDKADQLAK 107
Q+++ W+ H+ N++AD+LA
Sbjct: 112 QVTWHWVKGHAGHPGNERADELAN 135
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 33.9 bits (78), Expect = 0.031
Identities = 8/24 (33%), Positives = 15/24 (62%)
Query: 84 QISFMWIPSHSNIALNDKADQLAK 107
+ + W+ H+ N++ADQLA+
Sbjct: 117 LVFWEWVKGHAGHPENERADQLAR 140
>gnl|CDD|129679 TIGR00591, phr2, photolyase PhrII. All proteins in this family for
which functions are known are DNA-photolyases used for
the direct repair of UV irradiation induced DNA damage.
Some repair 6-4 photoproducts while others repair
cyclobutane pyrimidine dimers. This family is based on
the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 454
Score = 31.7 bits (72), Expect = 0.35
Identities = 17/63 (26%), Positives = 20/63 (31%), Gaps = 3/63 (4%)
Query: 17 NANKKYLSHLDTIHHMGIRLISRALKSS-PVNSLYAES--AILPLSVRRRLLFSNIIAKQ 73
+ N LS L H G RA ++ ES V RR L N
Sbjct: 250 DPNNDALSMLSPWLHFGQLSAQRAARAVERARGNAGESVEFFEEELVVRRELADNFCFYN 309
Query: 74 EYY 76
YY
Sbjct: 310 PYY 312
>gnl|CDD|178927 PRK00203, rnhA, ribonuclease H; Reviewed.
Length = 150
Score = 30.6 bits (70), Expect = 0.39
Identities = 9/32 (28%), Positives = 16/32 (50%)
Query: 84 QISFMWIPSHSNIALNDKADQLAKNSINSKLL 115
QI + W+ H+ N++ D+LA+ L
Sbjct: 114 QIKWHWVKGHAGHPENERCDELARAGAEEATL 145
>gnl|CDD|152929 pfam12495, Vip3A_N, Vegetative insecticide protein 3A N terminal.
This family of proteins is found in bacteria. Proteins
in this family are typically between 170 and 789 amino
acids in length. The family is found in association with
pfam02018. Vip3A represents a novel class of proteins
insecticidal to lepidopteran insect larvae.
Length = 177
Score = 29.6 bits (66), Expect = 0.99
Identities = 27/69 (39%), Positives = 36/69 (52%), Gaps = 7/69 (10%)
Query: 98 LNDKADQLAKNSINSKLLDFYIQDDLKNHLRKNIVKLYNDQ--WTNIQNNKLRTIKDNTT 155
LND + +L + +N L D Q +L L K I+K+ N+Q N NNKL I NT
Sbjct: 47 LNDISGKL--DGVNGSLNDLIAQGNLNTELSKEILKIANEQNQVLNDVNNKLDAI--NTM 102
Query: 156 LWKTSLRKI 164
L + L KI
Sbjct: 103 L-RVYLPKI 110
>gnl|CDD|225921 COG3386, COG3386, Gluconolactonase [Carbohydrate transport and
metabolism].
Length = 307
Score = 29.7 bits (67), Expect = 1.5
Identities = 11/46 (23%), Positives = 19/46 (41%)
Query: 61 RRRLLFSNIIAKQEYYFASTNGSQISFMWIPSHSNIALNDKADQLA 106
R LL+ +I+ + + G + F S+ AL D +L
Sbjct: 36 RGALLWVDILGGRIHRLDPETGKKRVFPSPGGFSSGALIDAGGRLI 81
>gnl|CDD|234405 TIGR03936, sam_1_link_chp, radical SAM-linked protein. This
model describes an uncharacterized protein encoded
adjacent to, or as a fusion protein with, an
uncharacterized radical SAM protein.
Length = 209
Score = 29.1 bits (66), Expect = 1.7
Identities = 10/22 (45%), Positives = 14/22 (63%), Gaps = 5/22 (22%)
Query: 21 KYLSHLDTIHHMGIRLISRALK 42
++LSHLD +RL RAL+
Sbjct: 13 RFLSHLDL-----MRLFERALR 29
>gnl|CDD|216687 pfam01763, Herpes_UL6, Herpesvirus UL6 like. This family consists
of various proteins from the herpesviridae that are
similar to herpes simplex virus type I UL6 virion
protein. UL6 is essential for cleavage and packaging of
the viral genome.
Length = 556
Score = 29.1 bits (66), Expect = 2.4
Identities = 16/66 (24%), Positives = 27/66 (40%), Gaps = 4/66 (6%)
Query: 119 IQDDLKNHLRKNIVKLYNDQWTNIQNNKLRTIKDNTTLWKTSLRKIRNEEILLTRLRIGH 178
+ + + ++ K Q I N + TI+D + L+K+R E L+RLR
Sbjct: 351 TRQAFRKSVSNSVNKCLEGQ---I-NEQFDTIEDLKEENEDLLKKLRELESELSRLREEA 406
Query: 179 TRITHS 184
S
Sbjct: 407 RASRGS 412
>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 = 28.0 bits (63), Expect = 2.4
Identities = 10/29 (34%), Positives = 17/29 (58%), Gaps = 5/29 (17%)
Query: 84 QISFMWIPSHSN----IAL-NDKADQLAK 107
++ + I +HS +AL N +ADQ A+
Sbjct: 104 PVAVIHIRAHSGLPGPLALGNARADQAAR 132
>gnl|CDD|220573 pfam10105, DUF2344, Uncharacterized protein conserved in bacteria
(DUF2344). This domain, found in various hypothetical
bacterial proteins and Radical Sam domain proteins, has
no known function.
Length = 186
Score = 28.3 bits (64), Expect = 2.7
Identities = 10/22 (45%), Positives = 14/22 (63%), Gaps = 5/22 (22%)
Query: 21 KYLSHLDTIHHMGIRLISRALK 42
++LSHLD +RL RAL+
Sbjct: 13 RFLSHLDL-----MRLFERALR 29
>gnl|CDD|227868 COG5581, COG5581, c-di-GMP-binding protein [Signal transduction
mechanisms].
Length = 233
Score = 27.8 bits (62), Expect = 5.7
Identities = 6/26 (23%), Positives = 11/26 (42%)
Query: 203 VKHIFECNKYKKFREKLSLPSIEIAL 228
K+ F ++ +E L LP+
Sbjct: 76 AKYEFTSEVLEQVKEYLQLPAFSTPP 101
>gnl|CDD|223618 COG0544, Tig, FKBP-type peptidyl-prolyl cis-trans isomerase
(trigger factor) [Posttranslational modification,
protein turnover, chaperones].
Length = 441
Score = 27.6 bits (62), Expect = 6.1
Identities = 12/48 (25%), Positives = 19/48 (39%), Gaps = 9/48 (18%)
Query: 103 DQLAKNSINSKLLDFYIQDDLKNHLRKNIVKLYNDQWTNIQNNKLRTI 150
D+ AK KL + ++LK LRKN+ + K +
Sbjct: 250 DEFAK-----KLGEEDTLEELKEKLRKNLERELK----EATLEKRKEQ 288
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
0.321 0.134 0.394
Gapped
Lambda K H
0.267 0.0709 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,496,152
Number of extensions: 1155243
Number of successful extensions: 1032
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1032
Number of HSP's successfully gapped: 29
Length of query: 251
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 156
Effective length of database: 6,723,972
Effective search space: 1048939632
Effective search space used: 1048939632
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 (21.9 bits)
S2: 58 (26.2 bits)