RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17738
(316 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 = 91.6 bits (228), Expect = 6e-23
Identities = 35/105 (33%), Positives = 48/105 (45%), Gaps = 11/105 (10%)
Query: 202 RIYTDGSKDEENAGCAFVIPDRN-ITKMFSLDPKSSIFACELYAIYAALEYL---HHPNN 257
IYTDGSK E G F I + I++ + L P S+F EL AI AL+
Sbjct: 1 VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRAR 60
Query: 258 NTVENYVIISDSQAALQAISNI---YTIQNQLITNIQTLNQGGFK 299
I SDSQAAL+A+ + + ++ I+ L G K
Sbjct: 61 ----KITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVK 101
>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 = 43.1 bits (102), Expect = 2e-05
Identities = 25/107 (23%), Positives = 39/107 (36%), Gaps = 11/107 (10%)
Query: 204 YTDGSKDEE--NAGCAFVIPDRNI--TKMFSLD-PKSSIFACELYAIYAALEYLHHPNNN 258
TDGS AG V+ D SL P ++ EL A+ ALE
Sbjct: 1 NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLGLK 60
Query: 259 TVENYVIISDSQAALQAISN---IYTIQNQLITNIQTLNQGGFKCEI 302
+ +I +DS+ + I++ + N L+ +I L
Sbjct: 61 KL---IIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRF 104
>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 = 42.6 bits (101), Expect = 3e-05
Identities = 26/99 (26%), Positives = 39/99 (39%), Gaps = 17/99 (17%)
Query: 198 ETHVRIYTDGS--KDEENAGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALEYLHHP 255
V +YTDGS + G +V D + L ++ A EL A+ ALE L
Sbjct: 1 PEAVTVYTDGSCNGNPGPGGAGYVT-DGGKQRSKPLPGTTNQRA-ELLALIEALEALSG- 57
Query: 256 NNNTVENYVIISDSQAALQAI-------SNIYTIQNQLI 287
+ I +DSQ + I S I+N++
Sbjct: 58 -----QKVNIYTDSQYVIGGITNGWPTKSESKPIKNEIW 91
>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 = 43.0 bits (102), Expect = 4e-05
Identities = 24/127 (18%), Positives = 46/127 (36%), Gaps = 29/127 (22%)
Query: 203 IYTDGS-----KDEENAGCAFVI---PDRNITKMFSLDPKSSIFACELYAIYAALEYLHH 254
+YTDG+ + AG RN+++ P+++ A EL A+ AL +
Sbjct: 2 VYTDGACRGNGRSGARAGYGVYFGPGHPRNVSERLPGPPQTNQRA-ELRAVIHALRLIKE 60
Query: 255 PNNNTVENYVIISDSQAALQAI--------------SNIYTIQNQ-----LITNIQTLNQ 295
VI +DS+ + + S + N+ L ++ L +
Sbjct: 61 VGEGLT-KLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVANKDLIKELDKLLEELEE 119
Query: 296 GGFKCEI 302
G + +
Sbjct: 120 RGIRVKF 126
>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 = 38.0 bits (89), Expect = 0.001
Identities = 24/81 (29%), Positives = 37/81 (45%), Gaps = 9/81 (11%)
Query: 203 IYTDGSKDEENAGCAFVIPDRNITKMFSLDPKSSIFACELYAIYAALEYLHH-PNNNTVE 261
++TDGS AG A V+ ++ ++ +L +S EL A+ ALE P N
Sbjct: 2 VFTDGSSFVRKAGYA-VVTGPDVLEIATLPYGTSAQRAELIALIRALELAKGKPVN---- 56
Query: 262 NYVIISDSQAALQAISNIYTI 282
I +DS A + + TI
Sbjct: 57 ---IYTDSAYAFGILHALETI 74
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 37.3 bits (87), Expect = 0.003
Identities = 18/89 (20%), Positives = 30/89 (33%), Gaps = 22/89 (24%)
Query: 200 HVRIYTDGSKDEEN--AGCAFVIPDRNITKMFSLDPKSSIFAC---------ELYAIYAA 248
V I+TDG+ G V+ D + + EL A+ A
Sbjct: 3 KVEIFTDGACLGNPGPGGWGAVL--------RYGDGEKELSGGEGRTTNNRAELRALIEA 54
Query: 249 LEYLHHPNNNTVENYVIISDSQAALQAIS 277
LE L + +DS+ ++ I+
Sbjct: 55 LEALKELG---ACEVTLYTDSKYVVEGIT 80
>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 = 33.6 bits (78), Expect = 0.040
Identities = 21/85 (24%), Positives = 32/85 (37%), Gaps = 16/85 (18%)
Query: 201 VRIYTDGSKDEEN--AGCAFVIPDRNITKMFSLDPKSSIFAC-----ELYAIYAALEYLH 253
+ IYTDG+ G A ++ + K S EL A+ ALE L
Sbjct: 2 ITIYTDGACLGNPGPGGWAAILRYGDHEKELS----GGEAGTTNNRMELTAVIEALEALK 57
Query: 254 HPNNNTVENYVIISDSQAALQAISN 278
P ++ +DSQ + I+
Sbjct: 58 EP-----CPVLLYTDSQYVINGITK 77
>gnl|CDD|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional.
Length = 238
Score = 30.1 bits (68), Expect = 1.4
Identities = 29/121 (23%), Positives = 48/121 (39%), Gaps = 24/121 (19%)
Query: 117 YKLLMFPKYV-----QNYKNKKINTINVFLEEKF---PLFKKIHTLTHPPPPPWTLDTPD 168
KLL KYV + Y K ++ IN + ++ P KI+ + + D
Sbjct: 89 PKLL---KYVLNWISEEYCAKVLSIINEYNQKILKNKPSNDKINYI-------YMRKEED 138
Query: 169 LNFQLHIFTKKITSSPIIKSNFLAILQNYETHVRIYTDGSKDEENAGCAFVIPDRNITKM 228
+ + I KK + ++L YE + SKD+E A C + D+ I M
Sbjct: 139 MFYA--IINKKGKNYKKFLKTIPSVLSEYEK----LYNRSKDKECAICMEKVYDKEIKNM 192
Query: 229 F 229
+
Sbjct: 193 Y 193
>gnl|CDD|225467 COG2915, COG2915, Uncharacterized protein involved in purine
metabolism [General function prediction only].
Length = 207
Score = 28.5 bits (64), Expect = 4.2
Identities = 8/42 (19%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 2 RSAIDYTSMYRQINQIPRRNAYTWCSAEQVMELFGDLYLHTI 43
+ A+D ++ +I+Q+ R+ + +E ++ +Y+ I
Sbjct: 101 KDALD--TLGNRISQLERQLEHFDLQSETMLSTLASIYVDVI 140
>gnl|CDD|233251 TIGR01054, rgy, reverse gyrase. This model describes reverse
gyrase, found in both archaeal and bacterial
thermophiles. This enzyme, a fusion of a type I
topoisomerase domain and a helicase domain, introduces
positive supercoiling to increase the melting
temperature of DNA double strands. Generally, these
gyrases are encoded as a single polypeptide. An
exception was found in Methanopyrus kandleri, where
enzyme is split within the topoisomerase domain,
yielding a heterodimer of gene products designated RgyB
and RgyA [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1171
Score = 28.3 bits (63), Expect = 7.8
Identities = 10/26 (38%), Positives = 14/26 (53%), Gaps = 2/26 (7%)
Query: 157 PPPPPWTLDT--PDLNFQLHIFTKKI 180
P PP+T DT D N +L + K+
Sbjct: 880 NPLPPYTTDTMLEDANRKLGLSVKET 905
>gnl|CDD|177843 PLN02191, PLN02191, L-ascorbate oxidase.
Length = 574
Score = 28.1 bits (62), Expect = 8.5
Identities = 17/53 (32%), Positives = 22/53 (41%), Gaps = 2/53 (3%)
Query: 155 THPPP--PPWTLDTPDLNFQLHIFTKKITSSPIIKSNFLAILQNYETHVRIYT 205
+ PPP P W NF IF+ + SP K IL N + + YT
Sbjct: 330 SSPPPVTPRWDDFERSKNFSKKIFSAMGSPSPPKKYRKRLILLNTQNLIDGYT 382
>gnl|CDD|223593 COG0519, GuaA, GMP synthase, PP-ATPase domain/subunit [Nucleotide
transport and metabolism].
Length = 315
Score = 27.5 bits (62), Expect = 8.9
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 5/34 (14%)
Query: 28 AEQVMELFGDLYLHTIDIIKVLNPDASENNLKIL 61
AEQV+E+F + +++I V DA + L L
Sbjct: 64 AEQVVEMFREHL--GLNLIVV---DAKDRFLSAL 92
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
0.321 0.135 0.405
Gapped
Lambda K H
0.267 0.0703 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,948,053
Number of extensions: 1507815
Number of successful extensions: 1304
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1296
Number of HSP's successfully gapped: 29
Length of query: 316
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 219
Effective length of database: 6,635,264
Effective search space: 1453122816
Effective search space used: 1453122816
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 (21.9 bits)
S2: 59 (26.6 bits)