RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15277
(269 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 = 116 bits (292), Expect = 1e-32
Identities = 42/124 (33%), Positives = 62/124 (50%), Gaps = 5/124 (4%)
Query: 10 VCFSDGSKTPNSTSCAYSI---DKQIHSFNLNKVNSVFSAELMAILLCIKNLKFL--PHN 64
V ++DGSK T ++I S+ L SVF AEL+AIL ++
Sbjct: 1 VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRAR 60
Query: 65 KFIIISDSMSALQAISNLNSNNSLVPKIYSHWLDLKSCGKNLCFLWCPSHCGIKGNESVD 124
K I SDS +AL+A+ + S++ LV +I +L + G + W P H GI+GNE D
Sbjct: 61 KITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERAD 120
Query: 125 NAAR 128
A+
Sbjct: 121 RLAK 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 = 66.9 bits (164), Expect = 5e-14
Identities = 33/124 (26%), Positives = 49/124 (39%), Gaps = 5/124 (4%)
Query: 7 DSVVCFSDGS--KTPNSTSCAYSIDKQIHSFNLNKVNSVFSAELMAILLCIKNLKFLPHN 64
++V ++DGS P Y D + AEL+A+ I+ L+ L
Sbjct: 2 EAVTVYTDGSCNGNPGPGGAGYVTDGGKQRSKPLPGTTNQRAELLAL---IEALEALSGQ 58
Query: 65 KFIIISDSMSALQAISNLNSNNSLVPKIYSHWLDLKSCGKNLCFLWCPSHCGIKGNESVD 124
K I +DS + I+N S I + +L + W P H GI GNE D
Sbjct: 59 KVNIYTDSQYVIGGITNGWPTKSESKPIKNEIWELLQKKHKVYIQWVPGHSGIPGNELAD 118
Query: 125 NAAR 128
A+
Sbjct: 119 KLAK 122
>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 = 55.4 bits (134), Expect = 6e-10
Identities = 28/126 (22%), Positives = 48/126 (38%), Gaps = 11/126 (8%)
Query: 12 FSDGSKTPNSTSCAYSI---DKQIH---SFNLNKVN-SVFSAELMAILLCIKNLKFLPHN 64
+DGS N D + + +L+ + AEL+A+L ++ L
Sbjct: 1 NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLGLK 60
Query: 65 KFIIISDSMSALQAISNLNSNNSLVPKIYSHWLDLKSCGKNLCFLWCPSHCGIKGNESVD 124
K II +DS + I++ + + L L S ++ F P +GNE D
Sbjct: 61 KLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPR----EGNEVAD 116
Query: 125 NAARNP 130
A+
Sbjct: 117 RLAKEA 122
>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 = 41.1 bits (97), Expect = 9e-05
Identities = 31/135 (22%), Positives = 46/135 (34%), Gaps = 19/135 (14%)
Query: 10 VCFSDGSKTPNSTSCA-YSIDKQIHSFNLNKVNSVFSAELMAILLCIKNLKFLPHNKFII 68
F+DGS A + + L S AEL+A++ ++ K P N I
Sbjct: 1 TVFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIALIRALELAKGKPVN---I 57
Query: 69 ISDSMSALQAISNL-------NSNNSLVPKIYSHWLDLK---SCGKNLCFLWCPSHCG-- 116
+DS A + L + S L L+ K + + +H G
Sbjct: 58 YTDSAYAFGILHALETIWKERGFLTGKPIALASLILQLQKAIQRPKPVAVIHIRAHSGLP 117
Query: 117 ---IKGNESVDNAAR 128
GN D AAR
Sbjct: 118 GPLALGNARADQAAR 132
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 39.3 bits (92), Expect = 5e-04
Identities = 22/95 (23%), Positives = 34/95 (35%), Gaps = 12/95 (12%)
Query: 46 AELMAILLCIKNLKFLPHNKFIIISDSMSALQAISNLNSNN--------SLVPKIYSH-W 96
AEL A++ ++ LK L + + +DS ++ I+ P W
Sbjct: 46 AELRALIEALEALKELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLW 105
Query: 97 LDLKSCGKNLC---FLWCPSHCGIKGNESVDNAAR 128
+L K + W H G NE D AR
Sbjct: 106 EELDELLKRHELVFWEWVKGHAGHPENERADQLAR 140
>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 = 35.6 bits (83), Expect = 0.009
Identities = 22/108 (20%), Positives = 37/108 (34%), Gaps = 32/108 (29%)
Query: 46 AELMAILLCIKNLKFL--PHNKFIIISDSMSALQAISNL----------NSNN------- 86
AEL A++ ++ +K + K +I +DS + ++ S
Sbjct: 46 AELRAVIHALRLIKEVGEGLTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVANKD 105
Query: 87 ---SLVPKIYS---HWLDLKSCGKNLCFLWCPSHCGIKGNESVDNAAR 128
L + + +K F P H GI GNE D A+
Sbjct: 106 LIKELDKLLEELEERGIRVK-------FWHVPGHSGIYGNEEADRLAK 146
>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 = 29.8 bits (68), Expect = 0.37
Identities = 19/90 (21%), Positives = 28/90 (31%), Gaps = 10/90 (11%)
Query: 42 SVFSAELMAILL---CIKNLKFLPHNKFIIISDSMSALQAISNLNSNNSLVPKIYSHWLD 98
S AE A+L L + I+ SDS +Q I S + +
Sbjct: 1 SPLEAEAEALLEGLQLALELGI---RRLIVESDSQLVVQQIQGEYEARSRLAALLREIRK 57
Query: 99 LKSCGKNLCFLWCPSHCGIKGNESVDNAAR 128
L ++ P C N D A+
Sbjct: 58 LLKKFDSVSVSHVPREC----NRVADALAK 83
>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 = 30.6 bits (70), Expect = 0.43
Identities = 21/95 (22%), Positives = 33/95 (34%), Gaps = 17/95 (17%)
Query: 47 ELMAILLCIKNLKFLPHN-KFIIISDSMSALQAISN----------LNSNNSLVPKIYSH 95
EL A I+ L+ L ++ +DS + I+ ++ V +
Sbjct: 45 ELTA---VIEALEALKEPCPVLLYTDSQYVINGITKWIHGWKKNGWKTADGKPVKNV-DL 100
Query: 96 W--LDLKSCGKNLCFLWCPSHCGIKGNESVDNAAR 128
W LD + + W H G GNE D A
Sbjct: 101 WQELDALLAKHQVTWHWVKGHAGHPGNERADELAN 135
>gnl|CDD|179877 PRK04778, PRK04778, septation ring formation regulator EzrA;
Provisional.
Length = 569
Score = 30.2 bits (69), Expect = 1.3
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 156 WQTSWDNITNNKLKNIKPKIEE 177
W+ WD I N L +I+ ++ E
Sbjct: 69 WRQKWDEIVTNSLPDIEEQLFE 90
>gnl|CDD|224779 COG1866, PckA, Phosphoenolpyruvate carboxykinase (ATP) [Energy
production and conversion].
Length = 529
Score = 30.0 bits (68), Expect = 1.6
Identities = 11/23 (47%), Positives = 12/23 (52%), Gaps = 1/23 (4%)
Query: 7 DSVVCFSDGSKTPNSTSCAYSID 29
D F DGS T N T AY I+
Sbjct: 304 DGTPDFDDGSLTEN-TRAAYPIE 325
>gnl|CDD|233835 TIGR02361, dak_ATP, dihydroxyacetone kinase, ATP-dependent. This
family consists of examples of the form of
dihydroxyacetone kinase (also called glycerone kinase)
that uses ATP (2.7.1.29) as the phosphate donor, rather
than a phosphoprotein as in E. coli. This form is
composed of a single chain with separable domains
homologous to the K and L subunits of the E. coli
enzyme, and is found in yeasts and other eukaryotes and
in some bacteria, including Citrobacter freundii. The
member from tomato has been shown to phosphorylate
dihydroxyacetone, 3,4-dihydroxy-2-butanone, and some
other aldoses and ketoses (PMID:11985845).
Length = 574
Score = 29.3 bits (66), Expect = 2.2
Identities = 6/35 (17%), Positives = 11/35 (31%)
Query: 38 NKVNSVFSAELMAILLCIKNLKFLPHNKFIIISDS 72
N + L ++ L+ L K + D
Sbjct: 5 NDPEHLVDDALKGLVAANPGLQLLESRKVVYRRDL 39
>gnl|CDD|114855 pfam06160, EzrA, Septation ring formation regulator, EzrA. During
the bacterial cell cycle, the tubulin-like cell-division
protein FtsZ polymerises into a ring structure that
establishes the location of the nascent division site.
EzrA modulates the frequency and position of FtsZ ring
formation.
Length = 559
Score = 28.7 bits (65), Expect = 3.4
Identities = 10/22 (45%), Positives = 12/22 (54%), Gaps = 4/22 (18%)
Query: 156 WQTSWDNITNNKLKNIKPKIEE 177
W+ WD+I N L P IEE
Sbjct: 65 WRQKWDDIVTNSL----PDIEE 82
>gnl|CDD|114219 pfam05483, SCP-1, Synaptonemal complex protein 1 (SCP-1).
Synaptonemal complex protein 1 (SCP-1) is the major
component of the transverse filaments of the
synaptonemal complex. Synaptonemal complexes are
structures that are formed between homologous
chromosomes during meiotic prophase.
Length = 787
Score = 28.9 bits (64), Expect = 3.6
Identities = 20/65 (30%), Positives = 33/65 (50%), Gaps = 3/65 (4%)
Query: 126 AARNPNYNTTLRKCTSDDFR-PIISTIIMKNWQTSWDNITNNKLKNIKPKIEEWVSSNRD 184
A + N+ + KCT DDF P + + KN + + KL N P +E+ V+++ D
Sbjct: 1 AGGDSNFFKSFNKCTEDDFEFPFAKSNLSKNGENIDSDPAFQKL-NFLPMLEQ-VANSGD 58
Query: 185 SRYEE 189
Y+E
Sbjct: 59 CHYQE 63
>gnl|CDD|149916 pfam09002, DUF1887, Domain of unknown function (DUF1887). This
domain is found in a set of hypothetical bacterial
proteins.
Length = 379
Score = 28.6 bits (64), Expect = 3.8
Identities = 11/35 (31%), Positives = 18/35 (51%)
Query: 144 FRPIISTIIMKNWQTSWDNITNNKLKNIKPKIEEW 178
FRP+ IM+ I ++L ++K +EEW
Sbjct: 341 FRPLRHNDIMRAEDLGLAIIGPDELGDLKEHLEEW 375
>gnl|CDD|187698 cd09274, RNase_HI_RT_Ty3, Ty3/Gypsy 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 eukaryotes.
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. Ty3/Gypsy family widely
distributed among the genomes of plants, fungi and
animals. RNase H inhibitors have been explored as an
anti-HIV drug target because RNase H inactivation
inhibits reverse transcription.
Length = 121
Score = 27.4 bits (62), Expect = 3.9
Identities = 17/61 (27%), Positives = 31/61 (50%), Gaps = 10/61 (16%)
Query: 42 SVFSAELMAILLCIKNLKFLPH---NKFIIISDSMSALQAISNLNSNNSLVPKIYSHWLD 98
S + EL+AI+ +K KF + KF + +D +++ L + L P++ + WL
Sbjct: 41 STYEKELLAIVFALK--KFRHYLLGRKFTVYTDH----KSLKYLLTKKDLNPRL-ARWLL 93
Query: 99 L 99
L
Sbjct: 94 L 94
>gnl|CDD|238270 cd00484, PEPCK_ATP, Phosphoenolpyruvate carboxykinase (PEPCK), a
critical gluconeogenic enzyme, catalyzes the first
committed step in the diversion of tricarboxylic acid
cycle intermediates toward gluconeogenesis. It catalyzes
the reversible decarboxylation and phosphorylation of
oxaloacetate to yield phosphoenolpyruvate and carbon
dioxide, using a nucleotide molecule (ATP) for the
phosphoryl transfer, and has a strict requirement for
divalent metal ions for activity. PEPCK's separate into
two phylogenetic groups based on their nucleotide
substrate specificity, this model describes the
ATP-dependent groups.
Length = 508
Score = 28.0 bits (63), Expect = 5.9
Identities = 9/23 (39%), Positives = 11/23 (47%), Gaps = 1/23 (4%)
Query: 7 DSVVCFSDGSKTPNSTSCAYSID 29
V + D S T N T AY I+
Sbjct: 287 TREVDYDDDSITEN-TRAAYPIE 308
>gnl|CDD|161774 TIGR00224, pckA, phosphoenolpyruvate carboxykinase (ATP). Involved
in the gluconeogenesis pathway. It converts oxaloacetic
acid to phosphoenolpyruvate using ATP. Enzyme is a
monomer. The reaction is also catalysed by
phosphoenolpyruvate carboxykinase (GTP) (EC 4.1.1.32)
using GTP instead of ATP, described in PROSITE:PDOC00421
[Energy metabolism, Glycolysis/gluconeogenesis].
Length = 532
Score = 27.9 bits (62), Expect = 7.3
Identities = 12/23 (52%), Positives = 13/23 (56%), Gaps = 1/23 (4%)
Query: 7 DSVVCFSDGSKTPNSTSCAYSID 29
D V F DGSKT N T +Y I
Sbjct: 310 DGTVDFDDGSKTEN-TRVSYPIY 331
>gnl|CDD|224009 COG1084, COG1084, Predicted GTPase [General function prediction
only].
Length = 346
Score = 27.3 bits (61), Expect = 8.2
Identities = 12/50 (24%), Positives = 26/50 (52%), Gaps = 8/50 (16%)
Query: 4 KYLDSVVCF-SDGSKTPNSTSCAYSIDKQIHSFNLNKVNSVFSAELMAIL 52
++L V+ F D S +C YS+++QI ++ +F A ++ ++
Sbjct: 245 RHLAGVILFLFDPS-----ETCGYSLEEQISLL--EEIKELFKAPIVVVI 287
>gnl|CDD|179746 PRK04136, rpl40e, 50S ribosomal protein L40e; Provisional.
Length = 48
Score = 24.9 bits (55), Expect = 8.2
Identities = 10/20 (50%), Positives = 11/20 (55%)
Query: 127 ARNPNYNTTLRKCTSDDFRP 146
ARNP T RKC + RP
Sbjct: 22 ARNPWRATKCRKCGYKNLRP 41
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 0.132 0.409
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: 13,069,734
Number of extensions: 1170529
Number of successful extensions: 930
Number of sequences better than 10.0: 1
Number of HSP's gapped: 926
Number of HSP's successfully gapped: 29
Length of query: 269
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 174
Effective length of database: 6,723,972
Effective search space: 1169971128
Effective search space used: 1169971128
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: 58 (26.0 bits)