RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11456
(574 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 = 122 bits (308), Expect = 4e-33
Identities = 47/124 (37%), Positives = 65/124 (52%), Gaps = 5/124 (4%)
Query: 314 ICFTDGSKSPDVTGCAFSI---GDMVQSTLLNPINSIFSAELIAIFLCLEAII--DSPSN 368
+ +TDGSK TG F+I G + +S L P S+F AEL+AI L+ + +
Sbjct: 1 VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRAR 60
Query: 369 QFLIVSDSRSALAALANVRFSNPLVTKVFSTWSYLKLCDKEVSFIWCPSHCGIRGNEIVD 428
+ I SDS++AL AL + R S+PLV ++ L +V W P H GI GNE D
Sbjct: 61 KITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERAD 120
Query: 429 VAAK 432
AK
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 = 66.5 bits (163), Expect = 3e-13
Identities = 33/126 (26%), Positives = 47/126 (37%), Gaps = 7/126 (5%)
Query: 310 PNHTICFTDGS--KSPDVTGCAFSIGDMVQSTLLNPINSIFSAELIAIFLCLEAIIDSPS 367
P +TDGS +P G + Q + P + AEL+A+ LEA+
Sbjct: 1 PEAVTVYTDGSCNGNPGPGGAGYVTDGGKQRSKPLPGTTNQRAELLALIEALEALSGQK- 59
Query: 368 NQFLIVSDSRSAL-AALANVRFSNPLVTKVFSTWSYLKLCDKEVSFIWCPSHCGIRGNEI 426
I +DS+ + + W L +V W P H GI GNE+
Sbjct: 60 --VNIYTDSQYVIGGITNGWPTKSESKPIKNEIW-ELLQKKHKVYIQWVPGHSGIPGNEL 116
Query: 427 VDVAAK 432
D AK
Sbjct: 117 ADKLAK 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 = 59.2 bits (144), Expect = 1e-10
Identities = 36/135 (26%), Positives = 48/135 (35%), Gaps = 21/135 (15%)
Query: 315 CFTDGSKSPDVTGCA-FSIGDMVQSTLLNPINSIFSAELIAIFLCLEAIIDSPSNQFLIV 373
FTDGS G A + D+++ L S AELIA+ LE P N I
Sbjct: 2 VFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIALIRALELAKGKPVN---IY 58
Query: 374 SDSR---SALAALANVRFSNPLVTKVFSTWSYLKLCD--------KEVSFIWCPSHCG-- 420
+DS L AL + +T + K V+ I +H G
Sbjct: 59 TDSAYAFGILHALETIWKERGFLTGK-PIALASLILQLQKAIQRPKPVAVIHIRAHSGLP 117
Query: 421 ---IRGNEIVDVAAK 432
GN D AA+
Sbjct: 118 GPLALGNARADQAAR 132
>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 = 42.7 bits (101), Expect = 5e-05
Identities = 26/126 (20%), Positives = 44/126 (34%), Gaps = 11/126 (8%)
Query: 316 FTDGSKSPDVT----GCAFSIGDMVQ---STLLNPINSIFSAELIAIFLCLEAIIDSPSN 368
TDGS + G + +L P + AEL+A+ LE +D
Sbjct: 1 NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLGLK 60
Query: 369 QFLIVSDSRSALAALANVRFSNPLVTKVFSTWSYLKLCDKEVSFIWCPSHCGIRGNEIVD 428
+ +I +DS+ + + + + L ++ F P GNE+ D
Sbjct: 61 KLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPRE----GNEVAD 116
Query: 429 VAAKNP 434
AK
Sbjct: 117 RLAKEA 122
>gnl|CDD|238827 cd01650, RT_nLTR_like, RT_nLTR: Non-LTR (long terminal repeat)
retrotransposon and non-LTR retrovirus reverse
transcriptase (RT). This subfamily contains both non-LTR
retrotransposons and non-LTR retrovirus RTs. RTs
catalyze the conversion of single-stranded RNA into
double-stranded DNA for integration into host
chromosomes. RT is a multifunctional enzyme with
RNA-directed DNA polymerase, DNA directed DNA polymerase
and ribonuclease hybrid (RNase H) activities.
Length = 220
Score = 42.3 bits (100), Expect = 2e-04
Identities = 24/91 (26%), Positives = 42/91 (46%), Gaps = 12/91 (13%)
Query: 9 KPPLKRVLFIDDLLIIGRGK--DLDLLIQRFQHTLDEIHLWAETNGTLFSTDPGKSVCID 66
P + + + DD+++ GK L L+QR Q W++ +G + P KS +
Sbjct: 139 GPGITHLAYADDIVLFSEGKSRKLQELLQRLQE-------WSKESGLKIN--PSKSKVML 189
Query: 67 FHRLRVARSPILSYNGTPLHFVTNNKFLGLL 97
+ R ++ NGTP+ V K+LG+
Sbjct: 190 IGNKKK-RLKDITLNGTPIEAVETFKYLGVT 219
>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 = 35.9 bits (84), Expect = 0.013
Identities = 11/33 (33%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 402 YLKLCDK-EVSFIWCPSHCGIRGNEIVDVAAKN 433
K+ K ++SF+ +H G + NE+ D AK
Sbjct: 99 MDKIKKKIKISFVKVKAHSGDKYNELADKLAKK 131
>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 = 0.062
Identities = 11/32 (34%), Positives = 14/32 (43%), Gaps = 1/32 (3%)
Query: 402 YLKLCDK-EVSFIWCPSHCGIRGNEIVDVAAK 432
L K +V++ W H G GNE D A
Sbjct: 104 LDALLAKHQVTWHWVKGHAGHPGNERADELAN 135
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 33.9 bits (78), Expect = 0.099
Identities = 22/95 (23%), Positives = 33/95 (34%), Gaps = 12/95 (12%)
Query: 350 AELIAIFLCLEAIIDSPSNQFLIVSDS---RSALAALANVRFSNPLVT------KVFSTW 400
AEL A+ LEA+ + + + + +DS + N T K W
Sbjct: 46 AELRALIEALEALKELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLW 105
Query: 401 SYLKLC---DKEVSFIWCPSHCGIRGNEIVDVAAK 432
L + V + W H G NE D A+
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 = 31.4 bits (72), Expect = 0.62
Identities = 26/105 (24%), Positives = 34/105 (32%), Gaps = 26/105 (24%)
Query: 350 AELIAIFLCLEAIIDS--PSNQFLIVSDS--------------------RSALAALANVR 387
AEL A+ L I + + +I +DS S +AN
Sbjct: 46 AELRAVIHALRLIKEVGEGLTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVANKD 105
Query: 388 FSNPLVTKVFSTWSYLKLCDKEVSFIWCPSHCGIRGNEIVDVAAK 432
L + L+ V F P H GI GNE D AK
Sbjct: 106 LIKELDKLL----EELEERGIRVKFWHVPGHSGIYGNEEADRLAK 146
>gnl|CDD|237936 PRK15295, PRK15295, fimbrial assembly chaperone SthB; Provisional.
Length = 226
Score = 29.9 bits (67), Expect = 2.8
Identities = 20/78 (25%), Positives = 38/78 (48%), Gaps = 8/78 (10%)
Query: 203 RSKLMLNYVSKISASPFNPAQKVLFHQDMSGTIFTVNKPKPLYVRFREIANFINVLDSSE 262
+ KL+ + ++P + +Q++ + G + TVN P P Y+ F + L+S E
Sbjct: 128 QIKLIYRPPALTKSTPDSQSQQLKWQTA--GDVITVNNPTPYYMNFASVT-----LNSHE 180
Query: 263 IAPYVRFVPPWSNCAPPV 280
+ FVPP S+ + +
Sbjct: 181 VKS-ATFVPPKSSASFKL 197
>gnl|CDD|181395 PRK08341, PRK08341, amidophosphoribosyltransferase; Provisional.
Length = 442
Score = 29.8 bits (67), Expect = 4.1
Identities = 17/46 (36%), Positives = 24/46 (52%), Gaps = 5/46 (10%)
Query: 154 YIYSSAKDSVLNKLNTVHHAGIRIATGALRSSP----VVSLYVDSG 195
YIY + DSV++ ++ V+ A R+ R SP VV DSG
Sbjct: 238 YIYFARPDSVIDGVS-VYSARYRMGVELARESPAEGDVVIAVPDSG 282
>gnl|CDD|190315 pfam02457, DisA_N, DisA bacterial checkpoint controller
nucleotide-binding. The DisA protein is a bacterial
checkpoint protein that dimerises into an octameric
complex. The protein consists of three distinct domains.
This domain is the first and is a globular,
nucleotide-binding region; the next 146-289 residues
constitute the DisA-linker family, pfam10635, that
consists of an elongated bundle of three alpha helices
(alpha-6, alpha-10, and alpha-11), one side of which
carries an additional three helices (alpha7-9), which
thus forms a spine like-linker between domains 1 and 3.
The C-terminal residues, of domain 3, are represented by
family HHH, pfam00633, the specific DNA-binding domain.
The octameric complex thus has structurally linked
nucleotide-binding and DNA-binding HhH domains and the
nucleotide-binding domains are bound to a cyclic
di-adenosine phosphate such that DisA is a specific
di-adenylate cyclase. The di-adenylate cyclase activity
is strongly suppressed by binding to branched DNA, but
not to duplex or single-stranded DNA, suggesting a role
for DisA as a monitor of the presence of stalled
replication forks or recombination intermediates via DNA
structure-modulated c-di-AMP synthesis.
Length = 122
Score = 28.2 bits (64), Expect = 5.8
Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 7/49 (14%)
Query: 152 GCYIYSSAKDSVLNKLNTVHHAGIRIA--TGAL-----RSSPVVSLYVD 193
GCY+ S S+ +L T H A + I+ T AL + V+SL
Sbjct: 70 GCYLPLSPDPSIPKELGTRHRAALGISEQTDALVIVVSEETGVISLAKG 118
>gnl|CDD|172739 PRK14251, PRK14251, phosphate ABC transporter ATP-binding protein;
Provisional.
Length = 251
Score = 28.8 bits (64), Expect = 7.6
Identities = 14/44 (31%), Positives = 22/44 (50%), Gaps = 6/44 (13%)
Query: 28 KDLDLLIQRFQHTLDEIHLWAET------NGTLFSTDPGKSVCI 65
KD +L+ QR + +L + +W ET N FS + +CI
Sbjct: 115 KDKELIDQRVEESLKQAAIWKETKDNLDRNAQAFSGGQQQRICI 158
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
0.323 0.138 0.429
Gapped
Lambda K H
0.267 0.0773 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 29,482,196
Number of extensions: 2840739
Number of successful extensions: 2232
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2223
Number of HSP's successfully gapped: 22
Length of query: 574
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 472
Effective length of database: 6,413,494
Effective search space: 3027169168
Effective search space used: 3027169168
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 62 (27.6 bits)