RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9737
(368 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 = 49.2 bits (118), Expect = 2e-07
Identities = 15/44 (34%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 158 NPLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKATS 201
+ K I+E +++ + + W P H GI GN++AD AK+A
Sbjct: 86 LRIRKAIRELANH-GVKVRLHWVPGHSGIEGNERADRLAKEAAK 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 = 44.2 bits (105), Expect = 1e-05
Identities = 15/43 (34%), Positives = 18/43 (41%), Gaps = 1/43 (2%)
Query: 157 PNPLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKA 199
P+ EI E W P H GI GN+ AD AK+
Sbjct: 83 SKPIKNEIWELLQKKH-KVYIQWVPGHSGIPGNELADKLAKQG 124
>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 = 41.0 bits (97), Expect = 2e-04
Identities = 19/56 (33%), Positives = 26/56 (46%), Gaps = 1/56 (1%)
Query: 146 SSFQAISNLYHPNPLVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKATS 201
S + ++N L K ++E I KF P H GI GN++AD AKK
Sbjct: 96 SKGKPVANKDLIKELDKLLEELE-ERGIRVKFWHVPGHSGIYGNEEADRLAKKGAD 150
>gnl|CDD|237961 PRK15408, PRK15408, autoinducer 2-binding protein lsrB;
Provisional.
Length = 336
Score = 35.9 bits (83), Expect = 0.026
Identities = 28/74 (37%), Positives = 38/74 (51%), Gaps = 16/74 (21%)
Query: 31 YQPRETLLNFGIWDLVGDEVRG-VEYEVGNE-VRGGKYEVGDEVRGVEYEVGDEVRG-GK 87
Y R T+ FG+WD+V +G + V NE ++ GK VGD + +V G GK
Sbjct: 250 YVKRGTVKEFGLWDVV---QQGKISVYVANELLKKGKLNVGDSL---------DVPGIGK 297
Query: 88 YEVG-NEVRGGKYE 100
EV N V+G YE
Sbjct: 298 VEVSPNSVQGYDYE 311
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 34.3 bits (79), Expect = 0.038
Identities = 11/45 (24%), Positives = 21/45 (46%), Gaps = 3/45 (6%)
Query: 160 LVKEIQE-RSSNSQISFKFLWCPSHVGISGNDQADAEAKKATSEP 203
L +E+ E + + ++ W H G N++AD A++A
Sbjct: 104 LWEELDELLKRHELVFWE--WVKGHAGHPENERADQLAREAARAA 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 = 34.0 bits (79), Expect = 0.043
Identities = 12/40 (30%), Positives = 20/40 (50%), Gaps = 2/40 (5%)
Query: 160 LVKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKA 199
L +E+ + Q+++ W H G GN++AD A A
Sbjct: 100 LWQELDALLAKHQVTWH--WVKGHAGHPGNERADELANAA 137
>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 = 32.5 bits (75), Expect = 0.11
Identities = 12/40 (30%), Positives = 18/40 (45%), Gaps = 2/40 (5%)
Query: 161 VKEIQERSSNSQISFKFLWCPSHVGISGNDQADAEAKKAT 200
+ + + +ISF +H G N+ AD AKKA
Sbjct: 96 KEFMDKIKKKIKISFV--KVKAHSGDKYNELADKLAKKAL 133
>gnl|CDD|129775 TIGR00692, tdh, L-threonine 3-dehydrogenase. This protein is a
tetrameric, zinc-binding, NAD-dependent enzyme of
threonine catabolism. Closely related proteins include
sorbitol dehydrogenase, xylitol dehydrogenase, and
benzyl alcohol dehydrogenase. Eukaryotic examples of
this enzyme have been demonstrated experimentally but do
not appear in database search results.E. coli His-90
modulates substrate specificity and is believed part of
the active site [Energy metabolism, Amino acids and
amines].
Length = 340
Score = 31.0 bits (70), Expect = 0.98
Identities = 19/62 (30%), Positives = 26/62 (41%), Gaps = 5/62 (8%)
Query: 43 WDLVGDEVRGVEYEVGNEVRGGKYEVGDEVRGVEYEVGDEVRGGKYEVGNE---VRGGKY 99
WD VG+EV G +G V G+ +VGD V + V + R G+Y
Sbjct: 45 WDEWAQSRIKPPQVVGHEVAGEVVGIGPGVEGI--KVGDYVSVETHIVCGKCYACRRGQY 102
Query: 100 EV 101
V
Sbjct: 103 HV 104
>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 = 2.7
Identities = 10/47 (21%), Positives = 20/47 (42%), Gaps = 6/47 (12%)
Query: 158 NPLVKEIQERSSNSQISFKFLWCPSHVG-----ISGNDQADAEAKKA 199
L+ ++Q+ + + +H G GN +AD A++A
Sbjct: 89 ASLILQLQKAIQRPK-PVAVIHIRAHSGLPGPLALGNARADQAARQA 134
>gnl|CDD|176197 cd08235, iditol_2_DH_like, L-iditol 2-dehydrogenase. Putative
L-iditol 2-dehydrogenase based on annotation of some
members in this subgroup. L-iditol 2-dehydrogenase
catalyzes the NAD+-dependent conversion of L-iditol to
L-sorbose in fructose and mannose metabolism. This
enzyme is related to sorbitol dehydrogenase, alcohol
dehydrogenase, and other medium chain
dehydrogenase/reductases. The zinc-dependent alcohol
dehydrogenase (ADH-Zn)-like family of proteins is a
diverse group of proteins related to the first
identified member, class I mammalian ADH. This group is
also called the medium chain dehydrogenases/reductase
family (MDR) to highlight its broad range of activities
and to distinguish from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal GroES-like catalytic
domain. The MDR group contains a host of activities,
including the founding alcohol dehydrogenase (ADH),
quinone reductase, sorbitol dehydrogenase, formaldehyde
dehydrogenase, butanediol DH, ketose reductase, cinnamyl
reductase, and numerous others. The zinc-dependent
alcohol dehydrogenases (ADHs) catalyze the
NAD(P)(H)-dependent interconversion of alcohols to
aldehydes or ketones. Active site zinc has a catalytic
role, while structural zinc aids in stability. ADH-like
proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
generally have 2 tightly bound zinc atoms per subunit.
The active site zinc is coordinated by a histidine, two
cysteines, and a water molecule. The second zinc seems
to play a structural role, affects subunit interactions,
and is typically coordinated by 4 cysteines.
Length = 343
Score = 28.3 bits (64), Expect = 5.7
Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 17/61 (27%)
Query: 110 RTVGNEVRGGKYEVGDEVRGGKYEVGDEV--------------RGGKYD-CSSFQAISNL 154
R +G+E+ G EVGD V G ++VGD V G + C +++ NL
Sbjct: 55 RILGHEIAGEIVEVGDGVTG--FKVGDRVFVAPHVPCGECHYCLRGNENMCPNYKKFGNL 112
Query: 155 Y 155
Y
Sbjct: 113 Y 113
>gnl|CDD|166155 PLN02514, PLN02514, cinnamyl-alcohol dehydrogenase.
Length = 357
Score = 28.2 bits (63), Expect = 7.3
Identities = 13/26 (50%), Positives = 16/26 (61%), Gaps = 2/26 (7%)
Query: 113 GNEVRGGKYEVGDEVRGGKYEVGDEV 138
G+EV G EVG +V K+ VGD V
Sbjct: 68 GHEVVGEVVEVGSDVS--KFTVGDIV 91
>gnl|CDD|219567 pfam07775, PaRep2b, PaRep2b protein. This is a family of proteins,
expressed in the crenarchaeon Pyrobaculum aerophilum,
whose members are variable in length and level of
conservation. The presence of numerous frameshifts and
internal stop codons in multiple alignments are thought
to indicate that most family members are no longer
functional.
Length = 510
Score = 28.3 bits (63), Expect = 8.3
Identities = 24/97 (24%), Positives = 36/97 (37%), Gaps = 8/97 (8%)
Query: 49 EVRGVEYEVGNEVRGGKYEVGDEVRG---VEYEVGDEVRGGKYE---VGNEVRGGKYEVG 102
V ++YE + G++ R VEYE G E + K+E + + GK V
Sbjct: 392 RVVDLKYEFVENGQPVSQCAGEDCRLRVIVEYEAGGERKQFKFEWYWAKKQKKKGKTTVT 451
Query: 103 DKVRGRRRTVGNEVRGG--KYEVGDEVRGGKYEVGDE 137
TV N+V K G RG + +
Sbjct: 452 YYYEIAAPTVKNDVEAAVLKALTGKAKRGRVQLLAKQ 488
>gnl|CDD|176221 cd08260, Zn_ADH6, Alcohol dehydrogenases of the MDR family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. This group has the
characteristic catalytic and structural zinc sites of
the zinc-dependent alcohol dehydrogenases. Alcohol
dehydrogenase in the liver converts ethanol and NAD+ to
acetaldehyde and NADH, while in yeast and some other
microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. A GxGxxG motif
after the first mononucleotide contact half allows the
close contact of the coenzyme with the ADH backbone.
The N-terminal catalytic domain has a distant homology
to GroES. These proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and have 2 tightly bound zinc atoms per
subunit, a catalytic zinc at the active site and a
structural zinc in a lobe of the catalytic domain.
NAD(H)-binding occurs in the cleft between the
catalytic and coenzyme-binding domains at the active
site, and coenzyme binding induces a conformational
closing of this cleft. Coenzyme binding typically
precedes and contributes to substrate binding. In human
ADH catalysis, the zinc ion helps coordinate the
alcohol, followed by deprotonation of a histidine, the
ribose of NAD, a serine, then the alcohol, which allows
the transfer of a hydride to NAD+, creating NADH and a
zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 345
Score = 28.0 bits (63), Expect = 9.8
Identities = 14/38 (36%), Positives = 16/38 (42%), Gaps = 8/38 (21%)
Query: 41 GIWDLV------GDEVRGVEYEVGNEVRGGKYEVGDEV 72
G V G E GV EVG +V + VGD V
Sbjct: 47 GHDPDVTLPHVPGHEFAGVVVEVGEDVSR--WRVGDRV 82
>gnl|CDD|176245 cd08285, NADP_ADH, NADP(H)-dependent alcohol dehydrogenases. This
group is predominated by atypical alcohol
dehydrogenases; they exist as tetramers and exhibit
specificity for NADP(H) as a cofactor in the
interconversion of alcohols and aldehydes, or ketones.
Like other zinc-dependent alcohol dehydrogenases (ADH)
of the medium chain alcohol dehydrogenase/reductase
family (MDR), tetrameric ADHs have a catalytic zinc that
resides between the catalytic and NAD(H)binding domains;
however, they do not have and a structural zinc in a
lobe of the catalytic domain. The medium chain alcohol
dehydrogenase family (MDR) has a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit.
Length = 351
Score = 27.6 bits (62), Expect = 10.0
Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 2/29 (6%)
Query: 110 RTVGNEVRGGKYEVGDEVRGGKYEVGDEV 138
+G+E G EVG EV+ ++ GD V
Sbjct: 55 MILGHEAVGVVEEVGSEVKD--FKPGDRV 81
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
0.314 0.134 0.403
Gapped
Lambda K H
0.267 0.0616 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 18,473,852
Number of extensions: 1758769
Number of successful extensions: 1132
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1128
Number of HSP's successfully gapped: 26
Length of query: 368
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 270
Effective length of database: 6,590,910
Effective search space: 1779545700
Effective search space used: 1779545700
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: 42 (22.0 bits)
S2: 60 (27.1 bits)