RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10246
(287 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 = 46.9 bits (112), Expect = 8e-07
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 228 INIKFLWIPSHCGIVENERVDQAAK 252
+ ++ W+P H GI NER D+ AK
Sbjct: 100 VKVRLHWVPGHSGIEGNERADRLAK 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 = 40.3 bits (95), Expect = 2e-04
Identities = 11/50 (22%), Positives = 17/50 (34%)
Query: 207 KKVIFSPWSVRNVRAMKFARDINIKFLWIPSHCGIVENERVDQAAKNSIY 256
++N + + W+P H GI NE D+ AK
Sbjct: 77 WPTKSESKPIKNEIWELLQKKHKVYIQWVPGHSGIPGNELADKLAKQGAS 126
>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 = 37.9 bits (89), Expect = 0.001
Identities = 11/33 (33%), Positives = 18/33 (54%)
Query: 223 KFARDINIKFLWIPSHCGIVENERVDQAAKNSI 255
K + I I F+ + +H G NE D+ AK ++
Sbjct: 101 KIKKKIKISFVKVKAHSGDKYNELADKLAKKAL 133
>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 = 35.2 bits (82), Expect = 0.010
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 229 NIKFLWIPSHCGIVENERVDQAAK 252
+ + W+ H G NER D+ A
Sbjct: 112 QVTWHWVKGHAGHPGNERADELAN 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 = 34.5 bits (80), Expect = 0.026
Identities = 13/36 (36%), Positives = 17/36 (47%)
Query: 217 RNVRAMKFARDINIKFLWIPSHCGIVENERVDQAAK 252
+ R I +KF +P H GI NE D+ AK
Sbjct: 111 DKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLAK 146
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 33.5 bits (77), Expect = 0.057
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 219 VRAMKFA-RDINIKFLWIPSHCGIVENERVDQAAK 252
+ R + + W+ H G ENER DQ A+
Sbjct: 106 EELDELLKRHELVFWEWVKGHAGHPENERADQLAR 140
>gnl|CDD|178927 PRK00203, rnhA, ribonuclease H; Reviewed.
Length = 150
Score = 32.9 bits (76), Expect = 0.088
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 229 NIKFLWIPSHCGIVENERVDQAAKNSI 255
IK+ W+ H G ENER D+ A+
Sbjct: 114 QIKWHWVKGHAGHPENERCDELARAGA 140
>gnl|CDD|216648 pfam01690, PLRV_ORF5, Potato leaf roll virus readthrough protein.
This family consists mainly of the potato leaf roll
virus readthrough protein. This is generated via a
readthrough of open reading frame 3 a coat protein
allowing transcription of open reading frame 5 to give
an extended coat protein with a large c-terminal
addition or read through domain. The readthrough protein
is thought to play a role in the circulative aphid
transmission of potato leaf roll virus. Also in the
family is open reading frame 6 from beet western yellows
virus and potato leaf roll virus both luteovirus and an
unknown protein from cucurbit aphid-borne yellows virus
a closterovirus.
Length = 460
Score = 29.3 bits (66), Expect = 2.2
Identities = 12/39 (30%), Positives = 20/39 (51%), Gaps = 6/39 (15%)
Query: 48 CQFQNNEILEKDSPVSAHRILFLLLNPDCNDPSFFLPDP 86
C+F + +++E+D +S H + D SFFL P
Sbjct: 168 CKFDDGQVVERDGIISFH------VEATGKDASFFLVAP 200
>gnl|CDD|150536 pfam09876, DUF2103, Predicted metal-binding protein (DUF2103).
This domain, found in various putative metal binding
prokaryotic proteins, has no known function.
Length = 103
Score = 27.8 bits (62), Expect = 2.9
Identities = 11/27 (40%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 194 KWLEISVLGSPDVKKVIFSPWSVRNVR 220
K LE ++ P+VKKVI S + R
Sbjct: 24 KLLE-TIAQHPEVKKVIPGVISAKGSR 49
>gnl|CDD|225498 COG2947, COG2947, Uncharacterized conserved protein [Function
unknown].
Length = 156
Score = 27.8 bits (62), Expect = 4.4
Identities = 21/57 (36%), Positives = 26/57 (45%), Gaps = 9/57 (15%)
Query: 195 WL---EISVLGSPDVKKVIFSPWS-VRNVRAMKFARDINI--KFLWIPSHC---GIV 242
WL E V +K V PW VRN +A F RD+ I + S+C GIV
Sbjct: 5 WLMKSEPDVFSIEMLKAVGEEPWDGVRNYQARNFMRDMKIGDLGFFYHSNCKPPGIV 61
>gnl|CDD|140320 PTZ00299, PTZ00299, homoserine kinase; Provisional.
Length = 336
Score = 27.9 bits (62), Expect = 6.3
Identities = 14/26 (53%), Positives = 18/26 (69%), Gaps = 2/26 (7%)
Query: 2 ATRKPKKVGI-LKATT-NITPAYDSL 25
+ PKKV + + ATT NI PAYD+L
Sbjct: 1 MSPLPKKVVLRVPATTANIGPAYDTL 26
>gnl|CDD|178608 PLN03046, PLN03046, D-glycerate 3-kinase; Provisional.
Length = 460
Score = 28.0 bits (62), Expect = 7.2
Identities = 19/81 (23%), Positives = 23/81 (28%), Gaps = 7/81 (8%)
Query: 32 ASAFSWPRLAGHSRSACQFQNNEILEKDSPVSAHRILFLLLNPDCNDPSF----FLPDPG 87
A A S L S Q N I D P+ NP N + + P
Sbjct: 2 AVASSLSSLIS---SNLQHYMNPIHAADYPIPCASAAAFNFNPISNPFNLKRRPYSPSSH 58
Query: 88 SFEKDNDNISSVYLVSRSESI 108
F S Y S+ S
Sbjct: 59 KFNDRVAASCSSYPSSKLSSR 79
>gnl|CDD|237544 PRK13887, PRK13887, conjugal transfer protein TrbF; Provisional.
Length = 250
Score = 27.4 bits (61), Expect = 7.7
Identities = 10/25 (40%), Positives = 15/25 (60%), Gaps = 4/25 (16%)
Query: 262 SVVVKDVIIQSKKTILNEWKTDWLE 286
SV +K V+ Q+ T W+ DW+E
Sbjct: 176 SVEIKSVLPQTPDT----WQVDWVE 196
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 0.133 0.402
Gapped
Lambda K H
0.267 0.0678 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,232,009
Number of extensions: 1308067
Number of successful extensions: 855
Number of sequences better than 10.0: 1
Number of HSP's gapped: 855
Number of HSP's successfully gapped: 15
Length of query: 287
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 191
Effective length of database: 6,679,618
Effective search space: 1275807038
Effective search space used: 1275807038
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 (26.2 bits)