RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15595
(221 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 = 88.1 bits (219), Expect = 2e-22
Identities = 37/105 (35%), Positives = 53/105 (50%), Gaps = 3/105 (2%)
Query: 99 QVYTDGSKSDSSVGCAFVIPQLHIVKKQ-TLNPKSSIFHAELLAISDAVSTIKSQSIG-- 155
+YTDGSK + G F I + + + L P S+F AELLAI +A+ +
Sbjct: 1 VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRAR 60
Query: 156 EAVIISDSLSALQAISSMSHSNPLVQSIHEEISTGDLKNVSLNLH 200
+ I SDS +AL+A+ S S+PLV I + I V + LH
Sbjct: 61 KITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRLH 105
>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 = 45.3 bits (108), Expect = 2e-06
Identities = 26/95 (27%), Positives = 41/95 (43%), Gaps = 11/95 (11%)
Query: 100 VYTDGS--KSDSSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEA 157
VYTDGS + G +V K P ++ AELLA+ +A+ + Q +
Sbjct: 6 VYTDGSCNGNPGPGGAGYVTDGGKQRSKP--LPGTTNQRAELLALIEALEALSGQKV--- 60
Query: 158 VIISDSLSALQAISSM----SHSNPLVQSIHEEIS 188
I +DS + I++ S S P+ I E +
Sbjct: 61 NIYTDSQYVIGGITNGWPTKSESKPIKNEIWELLQ 95
>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 = 40.4 bits (95), Expect = 9e-05
Identities = 20/92 (21%), Positives = 36/92 (39%), Gaps = 5/92 (5%)
Query: 101 YTDGSKSDSS--VGCAFVIPQLH---IVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIG 155
TDGS + G V+ + P ++ AELLA+ +A+ +
Sbjct: 1 NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLGLK 60
Query: 156 EAVIISDSLSALQAISSMSHSNPLVQSIHEEI 187
+ +I +DS + I+S S + +I
Sbjct: 61 KLIIETDSKYVVDLINSWSKGWKKNNLLLWDI 92
>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 = 37.2 bits (87), Expect = 0.002
Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 4/71 (5%)
Query: 100 VYTDGSKSDSSVGCAFVIPQLHIVKKQTLNPKSSIFHAELLAISDAVSTIKSQSIGEAVI 159
V+TDGS G A V +++ TL +S AEL+A+ A+ K + + I
Sbjct: 2 VFTDGSSFVRKAGYAVVTGP-DVLEIATLPYGTSAQRAELIALIRALELAKGKPVN---I 57
Query: 160 ISDSLSALQAI 170
+DS A +
Sbjct: 58 YTDSAYAFGIL 68
>gnl|CDD|215887 pfam00383, dCMP_cyt_deam_1, Cytidine and deoxycytidylate deaminase
zinc-binding region.
Length = 104
Score = 30.7 bits (70), Expect = 0.15
Identities = 14/65 (21%), Positives = 21/65 (32%), Gaps = 9/65 (13%)
Query: 101 YTDGSKSDSSVGCAFVIPQLHIV-----KKQTLNPKSSIFHAELLAISDAVSTIKSQSIG 155
YT S VG V I+ + + HAE AI +A + +
Sbjct: 19 YTPYSNF--PVGAVIVKNDGGIIATGYNGENAGYDPTI--HAERNAIRNAGRLGEGIKLE 74
Query: 156 EAVII 160
A +
Sbjct: 75 GATLY 79
>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 = 30.6 bits (70), Expect = 0.17
Identities = 12/55 (21%), Positives = 22/55 (40%)
Query: 133 SIFHAELLAISDAVSTIKSQSIGEAVIISDSLSALQAISSMSHSNPLVQSIHEEI 187
S AE A+ + + I ++ SDS +Q I + + ++ EI
Sbjct: 1 SPLEAEAEALLEGLQLALELGIRRLIVESDSQLVVQQIQGEYEARSRLAALLREI 55
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 30.4 bits (69), Expect = 0.41
Identities = 18/90 (20%), Positives = 33/90 (36%), Gaps = 15/90 (16%)
Query: 98 VQVYTDGSKSD--SSVGCAFVI--PQLHIV-----KKQTLNPKSSIFHAELLAISDAVST 148
V+++TDG+ G V+ + T N AEL A+ +A+
Sbjct: 4 VEIFTDGACLGNPGPGGWGAVLRYGDGEKELSGGEGRTTNN------RAELRALIEALEA 57
Query: 149 IKSQSIGEAVIISDSLSALQAISSMSHSNP 178
+K E + +DS ++ I+
Sbjct: 58 LKELGACEVTLYTDSKYVVEGITRWIVKWK 87
>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 = 30.3 bits (69), Expect = 0.41
Identities = 26/140 (18%), Positives = 46/140 (32%), Gaps = 37/140 (26%)
Query: 100 VYTDGS-----KSDSSVGCAFVIPQLHI--------VKKQTLNPKSSIFHAELLAISDAV 146
VYTDG+ +S + G H QT AEL A+ A+
Sbjct: 2 VYTDGACRGNGRSGARAGYGVYFGPGHPRNVSERLPGPPQTNQ------RAELRAVIHAL 55
Query: 147 STIKSQSIG--EAVIISDSLSALQAISSMSHS-----------NP-----LVQSIHEEIS 188
IK G + VI +DS + ++ P L++ + + +
Sbjct: 56 RLIKEVGEGLTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVANKDLIKELDKLLE 115
Query: 189 TGDLKNVSLNLHEVERNRII 208
+ + + + V + I
Sbjct: 116 ELEERGIRVKFWHVPGHSGI 135
>gnl|CDD|236933 PRK11573, PRK11573, hypothetical protein; Provisional.
Length = 413
Score = 30.9 bits (70), Expect = 0.44
Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 3/70 (4%)
Query: 154 IGEAVIISDSLSA--LQAISSMSHSNPLVQSIHEEISTGDLKNVSLNLHEVERNRII-CH 210
I +++S +LS L+ I S S ++ +S DL+ V+++ V RN I+
Sbjct: 144 IKTDIVVSGALSKEELRTIVHESRSQISRRNQDMLLSVLDLEKVTVDDIMVPRNEIVGID 203
Query: 211 IFGSWLSIIR 220
I W SI+R
Sbjct: 204 INDDWKSILR 213
>gnl|CDD|182265 PRK10144, PRK10144, formate-dependent nitrite reductase complex
subunit NrfF; Provisional.
Length = 126
Score = 28.3 bits (63), Expect = 1.5
Identities = 12/31 (38%), Positives = 15/31 (48%), Gaps = 8/31 (25%)
Query: 77 MPHQVF--------QQEFQRNMNENYGDFVQ 99
M HQV+ + E M E YGDFV+
Sbjct: 62 MRHQVYSMVAEGKSEVEIIGWMTERYGDFVR 92
>gnl|CDD|238612 cd01285, nucleoside_deaminase, Nucleoside deaminases include
adenosine, guanine and cytosine deaminases. These
enzymes are Zn dependent and catalyze the deamination of
nucleosides. The zinc ion in the active site plays a
central role in the proposed catalytic mechanism,
activating a water molecule to form a hydroxide ion that
performs a nucleophilic attack on the substrate. The
functional enzyme is a homodimer. Cytosine deaminase
catalyzes the deamination of cytosine to uracil and
ammonia and is a member of the pyrimidine salvage
pathway. Cytosine deaminase is found in bacteria and
fungi but is not present in mammals; for this reason,
the enzyme is currently of interest for antimicrobial
drug design and gene therapy applications against
tumors. Some members of this family are tRNA-specific
adenosine deaminases that generate inosine at the first
position of their anticodon (position 34) of specific
tRNAs; this modification is thought to enlarge the codon
recognition capacity during protein synthesis. Other
members of the family are guanine deaminases which
deaminate guanine to xanthine as part of the utilization
of guanine as a nitrogen source.
Length = 109
Score = 28.0 bits (63), Expect = 1.6
Identities = 8/38 (21%), Positives = 15/38 (39%), Gaps = 3/38 (7%)
Query: 111 VGCAFVIPQLHIVKK---QTLNPKSSIFHAELLAISDA 145
G V ++ + + HAE++AI +A
Sbjct: 19 FGAVIVDDDGKVIARGHNRVEQDGDPTAHAEIVAIRNA 56
>gnl|CDD|235052 PRK02597, rpoC2, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1331
Score = 29.2 bits (66), Expect = 2.2
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 133 SIFHAELLAISDAVSTIKSQSIGE 156
S+ H L+ + +AV I +QSIGE
Sbjct: 301 SLAHNHLVDLGEAVGIIAAQSIGE 324
>gnl|CDD|225463 COG2911, COG2911, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 1278
Score = 28.9 bits (65), Expect = 2.3
Identities = 14/65 (21%), Positives = 29/65 (44%), Gaps = 1/65 (1%)
Query: 129 NPKSSIFHAELLAISDAVS-TIKSQSIGEAVIISDSLSALQAISSMSHSNPLVQSIHEEI 187
+P+ + F + +A+S + +S+ + I+ +A A++ S LV + E
Sbjct: 1146 SPRITFFSEPAMPQDEALSYLLFGRSLSSSGEIAQLAAAAAALAGGGGSGSLVGKLGEAF 1205
Query: 188 STGDL 192
DL
Sbjct: 1206 GVDDL 1210
>gnl|CDD|233841 TIGR02388, rpoC2_cyan, DNA-directed RNA polymerase, beta'' subunit.
The family consists of the product of the rpoC2 gene, a
subunit of DNA-directed RNA polymerase of cyanobacteria
and chloroplasts. RpoC2 corresponds largely to the
C-terminal region of the RpoC (the beta' subunit) of
other bacteria. Members of this family are designated
beta'' in chloroplasts/plastids, and beta' (confusingly)
in Cyanobacteria, where RpoC1 is called beta' in
chloroplasts/plastids and gamma in Cyanobacteria. We
prefer to name this family beta'', after its organellar
members, to emphasize that this RpoC1 and RpoC2 together
replace RpoC in other bacteria [Transcription,
DNA-dependent RNA polymerase].
Length = 1227
Score = 27.9 bits (62), Expect = 5.0
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 133 SIFHAELLAISDAVSTIKSQSIGE 156
S+ HA L+ + +AV I +QSIGE
Sbjct: 299 SLAHAHLVDLGEAVGIIAAQSIGE 322
>gnl|CDD|236309 PRK08599, PRK08599, coproporphyrinogen III oxidase; Provisional.
Length = 377
Score = 26.8 bits (60), Expect = 9.2
Identities = 9/31 (29%), Positives = 19/31 (61%)
Query: 69 LTLYKKDGMPHQVFQQEFQRNMNENYGDFVQ 99
L L KK G+ F+++F ++ + +G+ +Q
Sbjct: 311 LGLRKKSGVSKARFEEKFGQSFEDVFGETIQ 341
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
0.317 0.131 0.380
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: 10,785,353
Number of extensions: 953493
Number of successful extensions: 713
Number of sequences better than 10.0: 1
Number of HSP's gapped: 709
Number of HSP's successfully gapped: 22
Length of query: 221
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 128
Effective length of database: 6,812,680
Effective search space: 872023040
Effective search space used: 872023040
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: 57 (25.6 bits)