RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18013
(563 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 = 128 bits (324), Expect = 2e-35
Identities = 50/124 (40%), Positives = 65/124 (52%), Gaps = 5/124 (4%)
Query: 181 ICYTDGSKSPDVTGCAFSI---GDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSD-- 235
+ YTDGSK TG F+I G + RS L P S+F AEL+AI L+ L
Sbjct: 1 VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRAR 60
Query: 236 QFLIVSDSRSALAALANVKFSNPLVTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVD 295
+ I SDS++AL AL + + S+PLV ++ R L +V W P H GI GNE D
Sbjct: 61 KITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERAD 120
Query: 296 DAAK 299
AK
Sbjct: 121 RLAK 124
Score = 61.9 bits (151), Expect = 1e-11
Identities = 24/56 (42%), Positives = 29/56 (51%), Gaps = 3/56 (5%)
Query: 411 CYTDGSKSPDVTGCAFSI---GDMVRSTLLNPISSIFSAELIAIFLCLEAILENPS 463
YTDGSK TG F+I G + RS L P S+F AEL+AI L+ L
Sbjct: 2 IYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGR 57
>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 = 65.0 bits (159), Expect = 9e-13
Identities = 35/126 (27%), Positives = 49/126 (38%), Gaps = 9/126 (7%)
Query: 178 NHTICYTDGS--KSPDVTGCAFSI-GDMVRSTLLNPINSIFSAELIAIFLCLEAILENPS 234
YTDGS +P G + G RS L P + AEL+A+ +EA+
Sbjct: 2 EAVTVYTDGSCNGNPGPGGAGYVTDGGKQRSKPL-PGTTNQRAELLAL---IEALEALSG 57
Query: 235 DQFLIVSDSRSAL-AALANVKFSNPLVTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEI 293
+ I +DS+ + + W L +V W P H GI GNE+
Sbjct: 58 QKVNIYTDSQYVIGGITNGWPTKSESKPIKNEIWE-LLQKKHKVYIQWVPGHSGIPGNEL 116
Query: 294 VDDAAK 299
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 = 51.9 bits (125), Expect = 3e-08
Identities = 33/134 (24%), Positives = 48/134 (35%), Gaps = 19/134 (14%)
Query: 182 CYTDGSKSPDVTGCA-FSIGDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIV 240
+TDGS G A + D++ L S AELIA+ + A+ I
Sbjct: 2 VFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIAL---IRALELAKGKPVNIY 58
Query: 241 SDSR---SALAALANVKFSNPLVT----KVFSTWRYLK---LCNKEVTFMWCPSHCG--- 287
+DS L AL + +T + S L+ K V + +H G
Sbjct: 59 TDSAYAFGILHALETIWKERGFLTGKPIALASLILQLQKAIQRPKPVAVIHIRAHSGLPG 118
Query: 288 --IRGNEIVDDAAK 299
GN D AA+
Sbjct: 119 PLALGNARADQAAR 132
Score = 33.0 bits (76), Expect = 0.15
Identities = 16/48 (33%), Positives = 22/48 (45%), Gaps = 1/48 (2%)
Query: 410 NCYTDGSKSPDVTGCA-FSIGDMVRSTLLNPISSIFSAELIAIFLCLE 456
+TDGS G A + D++ L +S AELIA+ LE
Sbjct: 1 TVFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIALIRALE 48
>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 = 47.3 bits (113), Expect = 1e-06
Identities = 29/128 (22%), Positives = 48/128 (37%), Gaps = 15/128 (11%)
Query: 183 YTDGSKSPDVTGCAFSIGDMVR---------STLLNPINSIFSAELIAIFLCLEAILENP 233
TDGS + G A G ++R +L P + AEL+A+ LE L+
Sbjct: 1 NTDGSCKGNP-GPA-GAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLG 58
Query: 234 SDQFLIVSDSRSALAALANVKFSNPLVTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEI 293
+ +I +DS+ + + + + L ++ F P GNE+
Sbjct: 59 LKKLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPRE----GNEV 114
Query: 294 VDDAAKNP 301
D AK
Sbjct: 115 ADRLAKEA 122
Score = 32.3 bits (74), Expect = 0.20
Identities = 18/68 (26%), Positives = 30/68 (44%), Gaps = 11/68 (16%)
Query: 412 YTDGSKSPDVTGCAFSIGDMVR---------STLLNPISSIFSAELIAIFLCLEAILENP 462
TDGS + G A G ++R +L P ++ AEL+A+ LE L+
Sbjct: 1 NTDGSCKGNP-GPA-GAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLG 58
Query: 463 SDQFLIVS 470
+ +I +
Sbjct: 59 LKKLIIET 66
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 38.1 bits (89), Expect = 0.004
Identities = 27/105 (25%), Positives = 37/105 (35%), Gaps = 16/105 (15%)
Query: 217 AELIAIFLCLEAILENPSDQFLIVSDS---RSALAALANVKFSNPLVT------KVFSTW 267
AEL A+ LEA+ E + + + +DS + N T K W
Sbjct: 46 AELRALIEALEALKELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLW 105
Query: 268 RYLKLCNK---EVTFMWCPSHCGIRGNEIVD----DAAKNPNVSA 305
L K V + W H G NE D +AA+ SA
Sbjct: 106 EELDELLKRHELVFWEWVKGHAGHPENERADQLAREAARAAKKSA 150
>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 = 0.064
Identities = 13/35 (37%), Positives = 16/35 (45%), Gaps = 2/35 (5%)
Query: 267 W-RYLKLCNK-EVTFMWCPSHCGIRGNEIVDDAAK 299
W L K +VT+ W H G GNE D+ A
Sbjct: 101 WQELDALLAKHQVTWHWVKGHAGHPGNERADELAN 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 = 32.9 bits (76), Expect = 0.13
Identities = 10/33 (30%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 269 YLKLCNK-EVTFMWCPSHCGIRGNEIVDDAAKN 300
K+ K +++F+ +H G + NE+ D AK
Sbjct: 99 MDKIKKKIKISFVKVKAHSGDKYNELADKLAKK 131
>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 = 33.0 bits (76), Expect = 0.15
Identities = 26/107 (24%), Positives = 33/107 (30%), Gaps = 30/107 (28%)
Query: 217 AELIAIFLCLEAILE--NPSDQFLIVSDSRSA-----------------LAALANVKFSN 257
AEL A+ L I E + +I +DS + V N
Sbjct: 46 AELRAVIHALRLIKEVGEGLTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVA--N 103
Query: 258 -----PLVTKVFSTWRYLKLCNKEVTFMWCPSHCGIRGNEIVDDAAK 299
L + L+ V F P H GI GNE D AK
Sbjct: 104 KDLIKELDKLL----EELEERGIRVKFWHVPGHSGIYGNEEADRLAK 146
>gnl|CDD|215776 pfam00185, OTCace, Aspartate/ornithine carbamoyltransferase,
Asp/Orn binding domain.
Length = 156
Score = 30.6 bits (70), Expect = 1.0
Identities = 12/35 (34%), Positives = 13/35 (37%), Gaps = 6/35 (17%)
Query: 270 LKLCNKEVTFMWCPSHCG--IRGNEIVDDAAKNPN 302
LK + FM H RG EI DD P
Sbjct: 105 LKKAKPDAIFM----HPLPAHRGEEITDDVDDGPR 135
>gnl|CDD|237936 PRK15295, PRK15295, fimbrial assembly chaperone SthB; Provisional.
Length = 226
Score = 31.1 bits (70), Expect = 1.4
Identities = 24/78 (30%), Positives = 37/78 (47%), Gaps = 8/78 (10%)
Query: 70 RSKLMLNYVAKISASPFNPAQKLLYHQDMSGIIFTVNKPKPLYIRFREVANFNNVLESSE 129
+ KL+ A ++P + +Q+L + G + TVN P P Y+ F V L S E
Sbjct: 128 QIKLIYRPPALTKSTPDSQSQQLKWQTA--GDVITVNNPTPYYMNFASVT-----LNSHE 180
Query: 130 VAPYVRFVPPWSNCAPPV 147
V FVPP S+ + +
Sbjct: 181 VKS-ATFVPPKSSASFKL 197
>gnl|CDD|217751 pfam03830, PTSIIB_sorb, PTS system sorbose subfamily IIB component.
Length = 151
Score = 29.7 bits (68), Expect = 2.1
Identities = 12/49 (24%), Positives = 19/49 (38%), Gaps = 6/49 (12%)
Query: 277 VTFMWCPSHCGIRGNEIV---DDAAKNPNVSAPLKLCTPEDLKPFIASI 322
V W + N I+ D+ A + LK+ P +K I S+
Sbjct: 16 VATTWTKE---LGANRIIVVNDEVANDELRKTLLKMAAPAGVKVSIFSV 61
>gnl|CDD|227564 COG5239, CCR4, mRNA deadenylase, exonuclease subunit and related
nucleases [RNA processing and modification].
Length = 378
Score = 30.1 bits (68), Expect = 2.9
Identities = 13/108 (12%), Positives = 37/108 (34%), Gaps = 7/108 (6%)
Query: 68 LRRSKLMLNYVAKISASPFNPAQKLLYHQDMSGIIFTVNKPKPLYIRFREVANFNNVLES 127
R++ ++LN + + + L++++ + N P ++R+V
Sbjct: 158 FRQTYILLNRIGEKDNIAWVCLFVGLFNKEPGDTPYVANTHLPWDPKYRDVKLI------ 211
Query: 128 SEVAPYVRFVPPWSNCAPPVDQCLGEEKKSDVAPVVFQQKFSEAINTK 175
+ + R + D+ G+ K ++ F+ +
Sbjct: 212 -QCSLLYRELKKVLKEELNDDKEEGDIKSYPEVDILITGDFNSLRASL 258
>gnl|CDD|130624 TIGR01561, gde_arch, glycogen debranching enzyme, archaeal type,
putative. The seed for this model is composed of two
uncharacterized archaeal proteins from Methanosarcina
acetivorans and Sulfolobus solfataricus. Trusted cutoff
is set so that essentially only archaeal members hit the
model. The notable exceptions to archaeal membership are
the Gram positive Clostridium perfringens which scores
much better than some other archaea and the
Cyanobacterium Nostoc sp. which scores just above the
trusted cutoff. Noise cutoff is set to exclude the
characterized eukaryotic glycogen debranching enzyme in
S. cerevisiae. These cutoffs leave the prokaryotes
Porphyromonas gingivalis and Deinococcus radiodurans
below trusted but above noise. Multiple alignments
including these last two species exhibit sequence
divergence which may suggest a subtly different function
for these prokaryotic proteins [Energy metabolism,
Biosynthesis and degradation of polysaccharides].
Length = 575
Score = 30.0 bits (67), Expect = 3.9
Identities = 18/73 (24%), Positives = 25/73 (34%), Gaps = 10/73 (13%)
Query: 329 IQWNNVPNTNKLKSIRPN----IKQWNTSTQDRRTKEVILTRMR------IGHTRLTHNH 378
I + N K K+IRPN I D + IL + G L+ +
Sbjct: 480 IHQDEAGNQVKDKAIRPNQIFAISLPFPIIDDESIAKAILDLIEKDLLRPFGLKSLSRDD 539
Query: 379 LFTKGGQTGNRGS 391
KG G+ S
Sbjct: 540 PLYKGQYKGDALS 552
>gnl|CDD|178927 PRK00203, rnhA, ribonuclease H; Reviewed.
Length = 150
Score = 28.3 bits (64), Expect = 7.3
Identities = 9/36 (25%), Positives = 15/36 (41%), Gaps = 2/36 (5%)
Query: 267 W-RYLKLCNK-EVTFMWCPSHCGIRGNEIVDDAAKN 300
W R + ++ + W H G NE D+ A+
Sbjct: 103 WQRLDAALKRHQIKWHWVKGHAGHPENERCDELARA 138
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 0.405
Gapped
Lambda K H
0.267 0.0753 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 27,847,980
Number of extensions: 2645164
Number of successful extensions: 1839
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1833
Number of HSP's successfully gapped: 20
Length of query: 563
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 461
Effective length of database: 6,413,494
Effective search space: 2956620734
Effective search space used: 2956620734
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: 62 (27.6 bits)