RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7230
(306 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 = 114 bits (287), Expect = 1e-31
Identities = 41/124 (33%), Positives = 64/124 (51%), Gaps = 5/124 (4%)
Query: 71 ICYTDGSKTPTTTGCAYSV---GNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSG-- 125
+ YTDGSK TG +++ G + RS L P S+F AEL+AI L+ L
Sbjct: 1 VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRAR 60
Query: 126 EFLVVTDSRSSLAALSNVRFTNPLITKVYSTWNYLKLCKKDITFMWCPSHCGIKGNEIVD 185
+ + +DS+++L AL + R ++PL+ ++ L + W P H GI+GNE D
Sbjct: 61 KITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERAD 120
Query: 186 VAAR 189
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 = 76.9 bits (190), Expect = 2e-17
Identities = 35/126 (27%), Positives = 49/126 (38%), Gaps = 9/126 (7%)
Query: 68 NHTICYTDGS--KTPTTTGCAYSV-GNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPS 124
YTDGS P G Y G RS L P + AEL+A+ +EA+
Sbjct: 2 EAVTVYTDGSCNGNPGPGGAGYVTDGGKQRSKPL-PGTTNQRAELLAL---IEALEALSG 57
Query: 125 GEFLVVTDSRSSL-AALSNVRFTNPLITKVYSTWNYLKLCKKDITFMWCPSHCGIKGNEI 183
+ + TDS+ + + + W L K + W P H GI GNE+
Sbjct: 58 QKVNIYTDSQYVIGGITNGWPTKSESKPIKNEIWE-LLQKKHKVYIQWVPGHSGIPGNEL 116
Query: 184 VDVAAR 189
D A+
Sbjct: 117 ADKLAK 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 = 54.3 bits (131), Expect = 2e-09
Identities = 30/128 (23%), Positives = 47/128 (36%), Gaps = 15/128 (11%)
Query: 73 YTDGSKTPTTTGCAYSVGNVVR---------STLLNPVNSIFSAELIAIFLCLEAILDSP 123
TDGS G V+R +L P + AEL+A+ LE LD
Sbjct: 1 NTDGSCKGN--PGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLG 58
Query: 124 SGEFLVVTDSRSSLAALSNVRFTNPLITKVYSTWNYLKLCKKDITFMWCPSHCGIKGNEI 183
+ ++ TDS+ + +++ + L DI F P +GNE+
Sbjct: 59 LKKLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPR----EGNEV 114
Query: 184 VDVAARNP 191
D A+
Sbjct: 115 ADRLAKEA 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 = 49.6 bits (119), Expect = 1e-07
Identities = 30/134 (22%), Positives = 45/134 (33%), Gaps = 19/134 (14%)
Query: 72 CYTDGSKTPTTTGCA-YSVGNVVRSTLLNPVNSIFSAELIAIFLCLEAILDSPSGEFLVV 130
+TDGS G A + +V+ L S AELIA+ + A+ + +
Sbjct: 2 VFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIAL---IRALELAKGKPVNIY 58
Query: 131 TDSR-------SSLAALSNVRFTNPLITKVYSTWNYLK---LCKKDITFMWCPSHCG--- 177
TDS + F + S L+ K + + +H G
Sbjct: 59 TDSAYAFGILHALETIWKERGFLTGKPIALASLILQLQKAIQRPKPVAVIHIRAHSGLPG 118
Query: 178 --IKGNEIVDVAAR 189
GN D AAR
Sbjct: 119 PLALGNARADQAAR 132
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 40.0 bits (94), Expect = 4e-04
Identities = 23/95 (24%), Positives = 34/95 (35%), Gaps = 12/95 (12%)
Query: 107 AELIAIFLCLEAILDSPSGEFLVVTDSRSSLAALSNVRFTNPLI---------TKVYSTW 157
AEL A+ LEA+ + + E + TDS+ + ++ K W
Sbjct: 46 AELRALIEALEALKELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPVKNKDLW 105
Query: 158 NYLKLCKKD---ITFMWCPSHCGIKGNEIVDVAAR 189
L K + + W H G NE D AR
Sbjct: 106 EELDELLKRHELVFWEWVKGHAGHPENERADQLAR 140
>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 = 38.6 bits (91), Expect = 7e-04
Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 2/46 (4%)
Query: 146 TNPLITKVYSTWNYLKLCKK-DITFMWCPSHCGIKGNEIVDVAARN 190
N TK Y + K+ KK I+F+ +H G K NE+ D A+
Sbjct: 87 ANKEGTKEYKEF-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 = 34.4 bits (80), Expect = 0.026
Identities = 11/32 (34%), Positives = 13/32 (40%), Gaps = 1/32 (3%)
Query: 159 YLKLCKK-DITFMWCPSHCGIKGNEIVDVAAR 189
L K +T+ W H G GNE D A
Sbjct: 104 LDALLAKHQVTWHWVKGHAGHPGNERADELAN 135
>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 = 33.3 bits (77), Expect = 0.068
Identities = 25/111 (22%), Positives = 37/111 (33%), Gaps = 38/111 (34%)
Query: 107 AELIAIFLCLEAILDSPSG--EFLVVTDSRSSLAALSNVRFTNPLITKVYSTW------- 157
AEL A+ L I + G + ++ TDS + +T+ W
Sbjct: 46 AELRAVIHALRLIKEVGEGLTKLVIATDSE----------YVVNGVTEWIPKWKKNGWKT 95
Query: 158 -------NY------LKLCKK------DITFMWCPSHCGIKGNEIVDVAAR 189
N KL ++ + F P H GI GNE D A+
Sbjct: 96 SKGKPVANKDLIKELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLAK 146
>gnl|CDD|225537 COG2990, VirK, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 300
Score = 33.4 bits (77), Expect = 0.13
Identities = 21/72 (29%), Positives = 30/72 (41%), Gaps = 12/72 (16%)
Query: 225 IPNTNKLKNIRPSIKAWKTSDQDKRFQELAGNRRER----PYHKSVKAPN---SKKRASI 277
+ N + +R K +D D +QE G + R P H + K SKKR+
Sbjct: 221 VSNKGHVYRLRYRDKKRIHADYDAFWQESGGRKIGRYWHLPLHIARKDLADIASKKRSMY 280
Query: 278 ASNRKKARYRIL 289
RK RY +L
Sbjct: 281 ---RK--RYAML 287
>gnl|CDD|204616 pfam11240, DUF3042, Protein of unknown function (DUF3042). This
family of proteins with unknown function appears to be
restricted to Firmicutes.
Length = 54
Score = 28.1 bits (63), Expect = 0.93
Identities = 12/28 (42%), Positives = 15/28 (53%), Gaps = 1/28 (3%)
Query: 262 YHKSVKAPNSKKRASIASNRKKA-RYRI 288
+ K V P +K I NRKKA R R+
Sbjct: 26 FKKKVIEPIEEKEEFIEENRKKAARKRV 53
>gnl|CDD|237339 PRK13299, PRK13299, tRNA CCA-pyrophosphorylase; Provisional.
Length = 394
Score = 29.0 bits (66), Expect = 3.3
Identities = 8/20 (40%), Positives = 15/20 (75%)
Query: 230 KLKNIRPSIKAWKTSDQDKR 249
K++NI+ +KAWK S++ +
Sbjct: 261 KIENIKSFLKAWKLSNKFIK 280
>gnl|CDD|184271 PRK13717, PRK13717, conjugal transfer protein TrbI; Provisional.
Length = 128
Score = 27.8 bits (61), Expect = 4.2
Identities = 14/37 (37%), Positives = 21/37 (56%)
Query: 270 NSKKRASIASNRKKARYRILCSPSFVSGTPPTDREIK 306
N+ AS+ + ++K IL SP+ V G P REI+
Sbjct: 81 NTALEASLQAWQQKHHAVILVSPAVVQGAPDITREIQ 117
>gnl|CDD|204870 pfam12282, H_kinase_N, Signal transduction histidine kinase. This
domain is found in bacteria. This domain is about 150
amino acids in length. This domain is found associated
with pfam07568, pfam08448, pfam02518. This domain has a
single completely conserved residue P that may be
functionally important. This family is mostly annotated
as a histidine kinase involved in signal transduction
but there is little published evidence to support this.
Length = 146
Score = 27.9 bits (63), Expect = 4.4
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 3/31 (9%)
Query: 169 FMWCPSHCGIKGNEIVDVAARNPTTGTTPSK 199
F+W P+ G+ V VA P+TG T K
Sbjct: 39 FLWVPTK---DGDSAVVVAQARPSTGPTLYK 66
>gnl|CDD|222451 pfam13910, DUF4209, Domain of unknown function (DUF4209). This
short domain is found in bacteria and eukaryotes,
though not in yeasts or Archaea. It carries a highly
conserved RNxxxHG sequence motif.
Length = 97
Score = 26.9 bits (60), Expect = 5.3
Identities = 9/33 (27%), Positives = 14/33 (42%)
Query: 37 VDLSLCDGKKCDSAPVVFQSLFRDVINSKYTNH 69
VDL L G K + SL +++ S+
Sbjct: 13 VDLLLSSGLKSNKNAPKLPSLLSELLASEELKT 45
>gnl|CDD|152066 pfam11630, DUF3254, Protein of unknown function (DUF3254). This
family of proteins is most likely a family of
anti-lipopolysaccharide factor proteins however this
cannot be confirmed.
Length = 97
Score = 26.6 bits (59), Expect = 6.2
Identities = 12/49 (24%), Positives = 20/49 (40%), Gaps = 7/49 (14%)
Query: 170 MWCPSHCGIKGN-------EIVDVAARNPTTGTTPSKLCTPEDFKPFVA 211
MWCP I G +V+ A R+ + L T E+ +++
Sbjct: 49 MWCPGWTPITGESRTRSRSGVVEHAVRDFVQKALQAGLITEEEANAWLS 97
>gnl|CDD|220247 pfam09451, ATG27, Autophagy-related protein 27.
Length = 265
Score = 27.4 bits (61), Expect = 9.4
Identities = 21/73 (28%), Positives = 31/73 (42%), Gaps = 8/73 (10%)
Query: 110 IAIFLCLE---AILDSPSGEFLVVTD--SRSSLAALSNVRFTNPLITKVYSTWNYLKLCK 164
IA+ L L + D + E L+ D S + ++S V T P T TW YL +C
Sbjct: 1 IALLLALATAASAFDCSNIEVLINYDLSSLGGVHSVSTVEDTPPSETNT--TW-YLNICL 57
Query: 165 KDITFMWCPSHCG 177
+ + P C
Sbjct: 58 EKDASIPVPDQCP 70
>gnl|CDD|218763 pfam05817, Ribophorin_II, Oligosaccharyltransferase subunit
Ribophorin II. This family contains eukaryotic
Ribophorin II (RPN2) proteins. The mammalian
oligosaccharyltransferase (OST) is a protein complex
that effects the cotranslational N-glycosylation of
newly synthesised polypeptides, and is composed of the
following proteins: ribophorins I and II (RI and RII),
OST48, and Dadl, N33/IAP, OST4, STT3. The family also
includes the SWP1 protein from yeast. In yeast the
oligosaccharyltransferase complex is composed 7 or 8
subunits, SWP1, being one of them.
Length = 636
Score = 27.8 bits (62), Expect = 9.6
Identities = 9/39 (23%), Positives = 17/39 (43%), Gaps = 4/39 (10%)
Query: 118 AILDSPSGEFLVVTDSRSSLAALSNVRFTNPLITKVYST 156
+ S F ++ +LA LSN +F P++ +
Sbjct: 249 KSVQSAKDAFSLL----EALAVLSNNKFHVPVVVSLPGP 283
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
0.318 0.131 0.406
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: 15,175,093
Number of extensions: 1360201
Number of successful extensions: 1064
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1058
Number of HSP's successfully gapped: 23
Length of query: 306
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 209
Effective length of database: 6,635,264
Effective search space: 1386770176
Effective search space used: 1386770176
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (26.5 bits)