RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16114
(202 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 = 69.2 bits (170), Expect = 2e-15
Identities = 20/55 (36%), Positives = 30/55 (54%)
Query: 10 SALSALSNIKFTNPLVSKAYSCWDLLTSNNKDVRFMWCPSHCGIRGNEDVDQAAR 64
+AL AL + + ++PLV + L ++ VR W P H GI GNE D+ A+
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 = 48.4 bits (116), Expect = 1e-07
Identities = 15/55 (27%), Positives = 23/55 (41%), Gaps = 4/55 (7%)
Query: 10 SALSALSNIKFTNPLVSKAYSCWDLLTSNNKDVRFMWCPSHCGIRGNEDVDQAAR 64
+ + P+ ++ W+LL V W P H GI GNE D+ A+
Sbjct: 72 GITNGWPTKSESKPIKNE---IWELL-QKKHKVYIQWVPGHSGIPGNELADKLAK 122
>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 = 33.7 bits (78), Expect = 0.025
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 39 NKDVRFMWCPSHCGIRGNEDVDQAAR 64
V+F P H GI GNE+ D+ A+
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 = 32.5 bits (75), Expect = 0.059
Identities = 9/28 (32%), Positives = 11/28 (39%)
Query: 37 SNNKDVRFMWCPSHCGIRGNEDVDQAAR 64
V + W H G GNE D+ A
Sbjct: 108 LAKHQVTWHWVKGHAGHPGNERADELAN 135
>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 = 30.5 bits (70), Expect = 0.22
Identities = 7/25 (28%), Positives = 13/25 (52%)
Query: 41 DVRFMWCPSHCGIRGNEDVDQAARN 65
+ F+ +H G + NE D+ A+
Sbjct: 107 KISFVKVKAHSGDKYNELADKLAKK 131
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 30.0 bits (68), Expect = 0.44
Identities = 12/32 (37%), Positives = 15/32 (46%)
Query: 33 DLLTSNNKDVRFMWCPSHCGIRGNEDVDQAAR 64
D L ++ V + W H G NE DQ AR
Sbjct: 109 DELLKRHELVFWEWVKGHAGHPENERADQLAR 140
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 31.1 bits (70), Expect = 0.46
Identities = 21/101 (20%), Positives = 33/101 (32%), Gaps = 24/101 (23%)
Query: 48 PSHCGIRGNEDVDQAARNPTDLDQLKLCSPDDFKPLAASLVRK--------EWQDQW-NL 98
P C + + A N PDD P A L ++ EW+ +
Sbjct: 3085 PETCELAELYERYVAGLN-----------PDDNAPCAGELSKRESGDDDLSEWEKVASSE 3133
Query: 99 VPVTNKLKSIKPLITNW---DTSNQENRTK-EITLTRMRIG 135
V + N+ + I LI W + S N + E +
Sbjct: 3134 VSLRNEDQLITKLINLWRKIELSKWGNLYRGEFRKGKKLNM 3174
>gnl|CDD|184023 PRK13392, PRK13392, 5-aminolevulinate synthase; Provisional.
Length = 410
Score = 30.2 bits (68), Expect = 0.76
Identities = 17/54 (31%), Positives = 21/54 (38%), Gaps = 13/54 (24%)
Query: 142 GFIFTKTDPPNCPCGEHLSVRHILTC----HRHAQIRASL---------PHPPS 182
GFIFT PP G ++RH+ T H A+L P PS
Sbjct: 273 GFIFTTALPPAVAAGATAAIRHLKTSQTERDAHQDRVAALKAKLNANGIPVMPS 326
>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 = 28.5 bits (64), Expect = 1.4
Identities = 12/57 (21%), Positives = 20/57 (35%), Gaps = 4/57 (7%)
Query: 10 SALSALSNIKFTNPLVSKAYSCWDLLTSNNKDVRFMWCPSHCGIRGNEDVDQAARNP 66
+ +++ + LL S D+RF P GNE D+ A+
Sbjct: 70 YVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPRE----GNEVADRLAKEA 122
>gnl|CDD|215866 pfam00339, Arrestin_N, Arrestin (or S-antigen), N-terminal domain.
Ig-like beta-sandwich fold. Scop reports duplication
with C-terminal domain.
Length = 148
Score = 28.4 bits (64), Expect = 1.5
Identities = 17/73 (23%), Positives = 28/73 (38%), Gaps = 6/73 (8%)
Query: 102 TNKLKSIKPLITNWDTSNQENRTKEITLTRMRIGHTRL---THGFIFTKTDPPNCPC--- 155
L K + + S + + L + + G L TH F F+ PPNCP
Sbjct: 52 VMGLTFRKQIYPTVNYSKETYLDTQERLWKKKDGSNELPAGTHAFPFSFELPPNCPPSFE 111
Query: 156 GEHLSVRHILTCH 168
G+ +R+ +
Sbjct: 112 GQPGGIRYEVKVE 124
>gnl|CDD|184024 PRK13393, PRK13393, 5-aminolevulinate synthase; Provisional.
Length = 406
Score = 28.9 bits (65), Expect = 1.7
Identities = 12/23 (52%), Positives = 14/23 (60%)
Query: 142 GFIFTKTDPPNCPCGEHLSVRHI 164
GFIFT + PP G SVRH+
Sbjct: 272 GFIFTTSLPPAVAAGALASVRHL 294
>gnl|CDD|236370 PRK09064, PRK09064, 5-aminolevulinate synthase; Validated.
Length = 407
Score = 29.1 bits (66), Expect = 1.8
Identities = 10/23 (43%), Positives = 13/23 (56%)
Query: 142 GFIFTKTDPPNCPCGEHLSVRHI 164
GFIFT + PP S+RH+
Sbjct: 273 GFIFTTSLPPAIAAAALASIRHL 295
>gnl|CDD|233587 TIGR01821, 5aminolev_synth, 5-aminolevulinic acid synthase. This
model represents 5-aminolevulinic acid synthase, an
enzyme for one of two routes to the heme precursor
5-aminolevulinate. The protein is a pyridoxal
phosphate-dependent enzyme related to
2-amino-3-ketobutyrate CoA tranferase and
8-amino-7-oxononanoate synthase. This enzyme appears
restricted to the alpha Proteobacteria and mitochondrial
derivatives [Biosynthesis of cofactors, prosthetic
groups, and carriers, Heme, porphyrin, and cobalamin].
Length = 402
Score = 27.8 bits (62), Expect = 4.1
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 142 GFIFTKTDPPNCPCGEHLSVRHILTCHRHAQIR 174
GFIFT + PP G S+RH L + +
Sbjct: 272 GFIFTTSLPPAIAAGATASIRH-LKESQDLRRA 303
>gnl|CDD|235539 PRK05638, PRK05638, threonine synthase; Validated.
Length = 442
Score = 27.1 bits (60), Expect = 6.6
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 142 GFIFTKTDPPNCPCGEHLSVRH 163
G + PP C CGE L + +
Sbjct: 8 GREYNSYIPPFCICGELLEIIY 29
>gnl|CDD|227495 COG5166, COG5166, Uncharacterized conserved protein [Function
unknown].
Length = 657
Score = 27.3 bits (60), Expect = 7.2
Identities = 22/101 (21%), Positives = 39/101 (38%), Gaps = 22/101 (21%)
Query: 116 DTSNQENRTKEITLTRMRIGHTRLTH---------GFIFTKTDPPNCPCGEHLSVRHILT 166
DT ++ EIT ++ I H + H GF + + S RH +
Sbjct: 126 DTMKHLDKITEITGAKIYIMHRSMCHDIDFQLTDSGFSNGLNEQQSFYQRHLESTRHEFS 185
Query: 167 CHRHAQIR---------ASLPHPPS----LADDVEGVKSLF 194
C ++A++ S+ H S L D++ G+ +F
Sbjct: 186 CQKNAEMSFFIVIYGAFCSVEHARSRVLALMDEIRGLSVIF 226
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
0.319 0.134 0.433
Gapped
Lambda K H
0.267 0.0749 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,875,502
Number of extensions: 856163
Number of successful extensions: 614
Number of sequences better than 10.0: 1
Number of HSP's gapped: 614
Number of HSP's successfully gapped: 19
Length of query: 202
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 110
Effective length of database: 6,857,034
Effective search space: 754273740
Effective search space used: 754273740
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 (21.8 bits)
S2: 56 (25.3 bits)