RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7630
(160 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 = 58.0 bits (141), Expect = 1e-11
Identities = 27/72 (37%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 45 HIYTDGSLINPEDGAGAGIFCE-LFSFYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFE 103
IYTDGS + GAG I + S +LG + + FD E+ AI AL L +
Sbjct: 1 VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRAR 60
Query: 104 RAVILSDSKAAI 115
+ I SDS+AA+
Sbjct: 61 KITIFSDSQAAL 72
>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 = 47.2 bits (113), Expect = 2e-07
Identities = 24/77 (31%), Positives = 34/77 (44%), Gaps = 7/77 (9%)
Query: 46 IYTDGSLI-NPEDGAGAGI---FCE--LFSFYKRL-GTFTTNFDGEIAAIKIALLQILNR 98
+YTDG+ N GA AG F + +RL G TN E+ A+ AL I
Sbjct: 2 VYTDGACRGNGRSGARAGYGVYFGPGHPRNVSERLPGPPQTNQRAELRAVIHALRLIKEV 61
Query: 99 TNQFERAVILSDSKAAI 115
+ VI +DS+ +
Sbjct: 62 GEGLTKLVIATDSEYVV 78
>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 = 42.0 bits (99), Expect = 1e-05
Identities = 22/80 (27%), Positives = 36/80 (45%), Gaps = 9/80 (11%)
Query: 47 YTDGS-LINPEDGAGAGIFCE-----LFSFYKRLGTFTTNFDGEIAAIKIALLQILNRTN 100
TDGS NP G+ + LF+ + TN + E+ A+ AL L+
Sbjct: 1 NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPA-ATNNEAELLALLEALELALD--L 57
Query: 101 QFERAVILSDSKAAIHPMNS 120
++ +I +DSK + +NS
Sbjct: 58 GLKKLIIETDSKYVVDLINS 77
>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 = 39.9 bits (94), Expect = 8e-05
Identities = 21/76 (27%), Positives = 30/76 (39%), Gaps = 9/76 (11%)
Query: 46 IYTDGSLI--NPEDGAGAGIFCELFSFYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFE 103
+YTDGS GAG K L TTN E+ A+ AL + +
Sbjct: 6 VYTDGSCNGNPGPGGAGYVTD-GGKQRSKPLP-GTTNQRAELLALIEALEALSG-----Q 58
Query: 104 RAVILSDSKAAIHPMN 119
+ I +DS+ I +
Sbjct: 59 KVNIYTDSQYVIGGIT 74
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 35.8 bits (83), Expect = 0.003
Identities = 20/84 (23%), Positives = 31/84 (36%), Gaps = 15/84 (17%)
Query: 44 LHIYTDG-SLINPEDGAGAGIFCELFSFYKRLG-------TFTTNFDGEIAAIKIALLQI 95
+ I+TDG L NP G + Y TTN E+ A+ AL +
Sbjct: 4 VEIFTDGACLGNPGPGGWGAVL-----RYGDGEKELSGGEGRTTNNRAELRALIEAL-EA 57
Query: 96 LNRTNQFERAVILSDSKAAIHPMN 119
L + + +DSK + +
Sbjct: 58 L-KELGACEVTLYTDSKYVVEGIT 80
>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 = 31.7 bits (73), Expect = 0.083
Identities = 21/84 (25%), Positives = 35/84 (41%), Gaps = 15/84 (17%)
Query: 44 LHIYTDGS-LINPEDGA-GAGIFC-----ELFSFYKRLGTFTTNFDGEIAAIKIALLQIL 96
+ IYTDG+ L NP G A + EL TTN E+ A+++ L
Sbjct: 2 ITIYTDGACLGNPGPGGWAAILRYGDHEKELSGGEAG----TTNNRMEL----TAVIEAL 53
Query: 97 NRTNQFERAVILSDSKAAIHPMNS 120
+ ++ +DS+ I+ +
Sbjct: 54 EALKEPCPVLLYTDSQYVINGITK 77
>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 = 29.0 bits (66), Expect = 0.55
Identities = 13/57 (22%), Positives = 17/57 (29%), Gaps = 8/57 (14%)
Query: 44 LHIYTDGSLINPEDGAGAGIFC----ELFSFYKRLGT--FTT--NFDGEIAAIKIAL 92
+ Y DGS G G+ E F + N GEI A+
Sbjct: 1 VIAYVDGSYNKETKVYGYGVVILKNGEEIKFSGSGNDPELASMRNVAGEIKGAIKAM 57
>gnl|CDD|235409 PRK05325, PRK05325, hypothetical protein; Provisional.
Length = 401
Score = 29.8 bits (68), Expect = 0.59
Identities = 12/26 (46%), Positives = 16/26 (61%), Gaps = 5/26 (19%)
Query: 29 MALETINTRYPSDDWLHIY----TDG 50
+ALE I RYP +W +IY +DG
Sbjct: 297 LALEIIEERYPPAEW-NIYAFQASDG 321
>gnl|CDD|193549 cd05674, M20_yscS, M20 Peptidase, carboxypeptidase yscS.
Peptidase M20 family, yscS (GlyX-carboxypeptidase,
CPS1, carboxypeptidase S, carboxypeptidase a,
carboxypeptidase yscS, glycine carboxypeptidase)-like
subfamily. This group mostly contains proteins that
have been uncharacterized to date, but also includes
vacuolar proteins involved in nitrogen metabolism which
are essential for use of certain peptides that are sole
nitrogen sources. YscS releases a C-terminal amino acid
from a peptide that has glycine as the penultimate
residue. It is synthesized as one polypeptide chain
precursor which yields two active precursor molecules
after carbohydrate modification in the secretory
pathway. The proteolytically unprocessed forms are
associated with the membrane, whereas the mature forms
of the enzyme are soluble. Enzymes in this subfamily
may also cleave intracellularly generated peptides in
order to recycle amino acids for protein synthesis.
Length = 441
Score = 27.9 bits (63), Expect = 2.9
Identities = 10/26 (38%), Positives = 16/26 (61%), Gaps = 6/26 (23%)
Query: 11 FLEETFRKQDVAPLIAKTMALETINT 36
+LE+T+ PL+ K + LE +NT
Sbjct: 34 YLEKTY------PLVHKALKLEVVNT 53
>gnl|CDD|225477 COG2925, SbcB, Exonuclease I [DNA replication, recombination, and
repair].
Length = 475
Score = 27.8 bits (62), Expect = 3.1
Identities = 11/38 (28%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 98 RTNQFERAVILSDSKAAIHPMNSVHLNSCPALEASNDI 135
R + R L + + A+ P+ VH+N CP L + +
Sbjct: 280 RERLYTRKADLGEGELAV-PVKLVHINKCPILAPAKTL 316
>gnl|CDD|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA
selenocysteine-associated protein 1 (SECp43) and
similar proteins. This subfamily corresponds to the
RRM2 in tRNA selenocysteine-associated protein 1
(SECp43), yeast negative growth regulatory protein NGR1
(RBP1), yeast protein NAM8, and similar proteins.
SECp43 is an RNA-binding protein associated
specifically with eukaryotic selenocysteine tRNA
[tRNA(Sec)]. It may play an adaptor role in the
mechanism of selenocysteine insertion. SECp43 is
located primarily in the nucleus and contains two
N-terminal RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a C-terminal polar/acidic region. Yeast
proteins, NGR1 and NAM8, show high sequence similarity
with SECp43. NGR1 is a putative glucose-repressible
protein that binds both RNA and single-stranded DNA
(ssDNA). It may function in regulating cell growth in
early log phase, possibly through its participation in
RNA metabolism. NGR1 contains three RRMs, two of which
are followed by a glutamine-rich stretch that may be
involved in transcriptional activity. In addition, NGR1
has an asparagine-rich region near the C-terminus which
also harbors a methionine-rich region. NAM8 is a
putative RNA-binding protein that acts as a suppressor
of mitochondrial splicing deficiencies when
overexpressed in yeast. It may be a non-essential
component of the mitochondrial splicing machinery. NAM8
also contains three RRMs. .
Length = 80
Score = 26.1 bits (58), Expect = 3.9
Identities = 13/33 (39%), Positives = 17/33 (51%), Gaps = 6/33 (18%)
Query: 8 HSLFLEETFRKQDVAPLIAKTMALETINTRYPS 40
HS+F+ D+AP + M ET RYPS
Sbjct: 2 HSIFV------GDLAPDVTDYMLQETFRARYPS 28
>gnl|CDD|236979 PRK11779, sbcB, exonuclease I; Provisional.
Length = 476
Score = 27.1 bits (61), Expect = 4.6
Identities = 11/32 (34%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 98 RTNQFERAVILSDSKAAIHPMNSVHLNSCPAL 129
R + R L++ + + P+ VHLN CP L
Sbjct: 277 RERLYTRRADLAEGELPV-PLKLVHLNKCPVL 307
>gnl|CDD|235774 PRK06292, PRK06292, dihydrolipoamide dehydrogenase; Validated.
Length = 460
Score = 26.3 bits (59), Expect = 8.8
Identities = 12/47 (25%), Positives = 15/47 (31%), Gaps = 11/47 (23%)
Query: 58 GAGAGIFCELFSFYKRLGTFTT----------NFDGEIAAIKIALLQ 94
G G I EL RLG T D E++ +L
Sbjct: 176 GGGV-IGLELGQALSRLGVKVTVFERGDRILPLEDPEVSKQAQKILS 221
>gnl|CDD|224056 COG1133, SbmA, ABC-type long-chain fatty acid transport system,
fused permease and ATPase components [Lipid metabolism].
Length = 405
Score = 26.3 bits (58), Expect = 9.8
Identities = 10/19 (52%), Positives = 11/19 (57%)
Query: 66 ELFSFYKRLGTFTTNFDGE 84
EL S YKRL F DG+
Sbjct: 377 ELLSIYKRLRAFEAALDGK 395
>gnl|CDD|234046 TIGR02877, spore_yhbH, sporulation protein YhbH. This protein
family, typified by YhbH in Bacillus subtilis, is found
in nearly every endospore-forming bacterium and in no
other genome (but note that the trusted cutoff score is
set high to exclude a single high-scoring sequence from
Nitrosococcus oceani ATCC 19707, which is classified in
the Gammaproteobacteria). The gene in Bacillus subtilis
was shown to be in the regulon of the sporulation sigma
factor, sigma-E, and its mutation was shown to create a
sporulation defect [Cellular processes, Sporulation and
germination].
Length = 371
Score = 26.2 bits (58), Expect = 10.0
Identities = 20/84 (23%), Positives = 29/84 (34%), Gaps = 16/84 (19%)
Query: 30 ALETINTRYPSDDWLHIYT----DGSLINPEDG---AGAGIFCE---LFSF-----YKRL 74
ALE I+ RY + +IY DG + ++ E LF + Y
Sbjct: 278 ALEIIDERYNPARY-NIYAFHFSDGDNLTSDNERAVKLVRKLLEVCNLFGYGEIMPYGYS 336
Query: 75 GTFTTNFDGEIAAIKIALLQILNR 98
T F EI L I ++
Sbjct: 337 NTLKNKFKNEIKDPNFVPLIIRDK 360
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 0.395
Gapped
Lambda K H
0.267 0.0720 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,987,660
Number of extensions: 724859
Number of successful extensions: 500
Number of sequences better than 10.0: 1
Number of HSP's gapped: 496
Number of HSP's successfully gapped: 19
Length of query: 160
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 71
Effective length of database: 6,990,096
Effective search space: 496296816
Effective search space used: 496296816
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: 55 (25.0 bits)