RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13868
(128 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 = 85.8 bits (213), Expect = 1e-22
Identities = 38/93 (40%), Positives = 53/93 (56%), Gaps = 1/93 (1%)
Query: 35 VWYTDGSKTEAGSGAGIHCVKPRV-NISLPLGTYTGVYQAEVLAIRNCAEENINMGLSKR 93
V YTDGSK E +GAG V+ + S LG Y V+ AE+LAI + + G R
Sbjct: 1 VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRAR 60
Query: 94 EIYIFSDSQAALRAIGNFQTKSKITWESTQAIC 126
+I IFSDSQAAL+A+ + ++ S + +AI
Sbjct: 61 KITIFSDSQAALKALRSPRSSSPLVLRIRKAIR 93
>gnl|CDD|139967 PRK13907, rnhA, ribonuclease H; Provisional.
Length = 128
Score = 41.6 bits (97), Expect = 1e-05
Identities = 34/88 (38%), Positives = 46/88 (52%), Gaps = 13/88 (14%)
Query: 37 YTDG-SKTEAG-SGAG--IHCVKPRVNISLPLGT---YTGVYQAEVLAIRNCAEENINMG 89
Y DG SK G SGAG I V+P V +SLPLGT + Y A + A++ C E N N+
Sbjct: 5 YIDGASKGNPGPSGAGVFIKGVQPAVQLSLPLGTMSNHEAEYHALLAALKYCTEHNYNI- 63
Query: 90 LSKREIYIFSDSQAALRAIGNFQTKSKI 117
+ +DSQ RA+ K+K+
Sbjct: 64 -----VSFRTDSQLVERAVEKEYAKNKM 86
>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 = 39.2 bits (92), Expect = 8e-05
Identities = 24/83 (28%), Positives = 33/83 (39%), Gaps = 15/83 (18%)
Query: 31 KGAVVWYTDGS--KTEAGSGAGIHCVKPRVNISLPLGTYTGVYQAEVLAIRNCAEENINM 88
AV YTDGS GAG S PL T +AE+LA+
Sbjct: 1 PEAVTVYTDGSCNGNPGPGGAGY-VTDGGKQRSKPLP-GTTNQRAELLALI--------E 50
Query: 89 GLSK---REIYIFSDSQAALRAI 108
L +++ I++DSQ + I
Sbjct: 51 ALEALSGQKVNIYTDSQYVIGGI 73
>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 = 34.3 bits (79), Expect = 0.004
Identities = 20/78 (25%), Positives = 34/78 (43%), Gaps = 9/78 (11%)
Query: 37 YTDGSKTEAGSGAGI-----HCVKPRV-NISLPLGTYTGVYQAEVLAIRNCAEENINMGL 90
TDGS AG + SL + T +AE+LA+ E +++GL
Sbjct: 1 NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPAAT-NNEAELLALLEALELALDLGL 59
Query: 91 SKREIYIFSDSQAALRAI 108
+++ I +DS+ + I
Sbjct: 60 --KKLIIETDSKYVVDLI 75
>gnl|CDD|220823 pfam10605, 3HBOH, 3HB-oligomer hydrolase (3HBOH).
D-(-)-3-hydroxybutyrate oligomer hydrolase (also known
as 3HB-oligomer hydrolase) functions in the degradation
of poly-3-hydroxybutyrate (PHB). It catalyzes the
hydrolysis of D(-)-3-hydroxybutyrate oligomers
(3HB-oligomers) into 3HB-monomers.
Length = 689
Score = 35.1 bits (81), Expect = 0.005
Identities = 18/38 (47%), Positives = 20/38 (52%), Gaps = 11/38 (28%)
Query: 15 IETAGNWGVKETQLLKKGAVVWYTDGSKTEAGSGAGIH 52
I TAG WG LK+G V YTD G+GAG H
Sbjct: 160 IGTAGEWG------LKRGCAVAYTD-----KGTGAGPH 186
>gnl|CDD|187703 cd09279, RNase_HI_archaeal_like, RNAse HI family that includes
Archaeal RNase HI. 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. Most archaeal genomes contain
only type 2 RNase H (RNase HII); however, a few contain
RNase HI as well. Although archaeal RNase HI sequences
conserve the DEDD active-site motif, they lack other
common features important for catalytic function, such
as the basic protrusion region. Archaeal RNase HI
homologs are more closely related to retroviral RNase HI
than bacterial and eukaryotic type I RNase H in
enzymatic properties.
Length = 128
Score = 30.9 bits (71), Expect = 0.089
Identities = 27/86 (31%), Positives = 43/86 (50%), Gaps = 8/86 (9%)
Query: 37 YTDG-SKTEAG-SGAGIHCVKP---RVNISLPLGTYTGVYQAEVLAIRNCAEENINMGLS 91
Y DG S+ G +GAGI P + S+PLG +AE A+ E + +G+
Sbjct: 4 YFDGASRGNPGPAGAGIVIKSPDGEVLEQSIPLGFPATNNEAEYEALIAGLELALELGIK 63
Query: 92 KREIYIFSDSQAALRAI-GNFQTKSK 116
K + I+ DSQ + I G ++ K++
Sbjct: 64 K--LEIYGDSQLVVNQIQGEYEVKNE 87
>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 = 29.5 bits (67), Expect = 0.28
Identities = 19/78 (24%), Positives = 30/78 (38%), Gaps = 14/78 (17%)
Query: 35 VWYTDGSKTEAGSGAGIHCVKPRVNISLPLGTYTGVYQAEVLA-IRNC---AEENINMGL 90
+TDGS +G + P V L T +AE++A IR + +N
Sbjct: 1 TVFTDGSSFVRKAGYAV-VTGPDVLEIATLPYGTSAQRAELIALIRALELAKGKPVN--- 56
Query: 91 SKREIYIFSDSQAALRAI 108
I++DS A +
Sbjct: 57 ------IYTDSAYAFGIL 68
>gnl|CDD|212521 cd09996, HDAC_classII_1, Histone deacetylases and histone-like
deacetylases, classII. This subfamily includes
bacterial as well as eukaryotic Class II histone
deacetylase (HDAC) and related proteins. Deacetylases of
class II are Zn-dependent enzymes that catalyze
hydrolysis of N(6)-acetyl-lysine residues of histones
(EC 3.5.1.98) and possibly other proteins to yield
deacetylated histones/other proteins. Included in this
family is a bacterial HDAC-like amidohydrolase
(Bordetella/Alcaligenes species FB18817, denoted as
FB188 HDAH) shown to be most similar in sequence and
function to class II HDAC6 domain 3 or b (HDAC6b). FB188
HDAH is able to remove the acetyl moiety from acetylated
histones, and can be inhibited by common HDAC inhibitors
such as SAHA (suberoylanilide hydroxamic acid) as well
as class II-specific but not class I specific
inhibitors.
Length = 359
Score = 27.9 bits (63), Expect = 1.6
Identities = 13/34 (38%), Positives = 16/34 (47%), Gaps = 3/34 (8%)
Query: 40 GSKTEAGSGAGIHCVKPRVNISLPLGTYTGVYQA 73
G+ E G GAG +NI LP G+ G Y
Sbjct: 208 GAVEERGEGAGEGY---NLNIPLPPGSGDGAYLH 238
>gnl|CDD|200163 TIGR02186, alph_Pro_TM, conserved hypothetical protein. This
family consists of predicted transmembrane proteins of
about 270 amino acids. Members are found, so far, only
among the Alphaproteobacteria and only once in each
genome.
Length = 261
Score = 26.3 bits (58), Expect = 5.1
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 73 AEVLAIRNCAEENINMGLSKREIYIFSD 100
A V +N A E + +G+S EI I S+
Sbjct: 17 ATVAQAQNPAAERLEIGVSTEEIAITSN 44
>gnl|CDD|220310 pfam09608, Alph_Pro_TM, Putative transmembrane protein
(Alph_Pro_TM). This family consists of predicted
transmembrane proteins of about 270 amino acids. Members
are found, so far, only among the Alphaproteobacteria
and only once in each genome.
Length = 236
Score = 26.0 bits (58), Expect = 6.1
Identities = 7/24 (29%), Positives = 10/24 (41%)
Query: 57 RVNISLPLGTYTGVYQAEVLAIRN 80
R +I LP G Y + R+
Sbjct: 158 RASIRLPANVPVGTYTVRIYLFRD 181
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 25.8 bits (57), Expect = 6.6
Identities = 18/80 (22%), Positives = 29/80 (36%), Gaps = 25/80 (31%)
Query: 32 GAVVWYTDGSKTEAGSGAGIHCVKPRVNISLPLGTYTG---VYQAEVLAIRNCAEENINM 88
GAV+ Y DG K +S G T +A + A+ E
Sbjct: 22 GAVLRYGDGEKE----------------LSGGEGRTTNNRAELRALIEALEALKE----- 60
Query: 89 GLSKREIYIFSDSQAALRAI 108
L E+ +++DS+ + I
Sbjct: 61 -LGACEVTLYTDSKYVVEGI 79
>gnl|CDD|188569 TIGR04054, rSAM_NirJ1, putative heme d1 biosynthesis radical SAM
protein NirJ1. Members of this radical SAM protein
subfamily, designated NirJ1, occur in genomic contexts
with a paralog NirJ2 and with other nitrite reductase
operon genes associated with heme d1 biosynthesis, as in
Heliobacillus mobilis and Heliophilum fasciatum. NirJ1
is presumed by bioinformatics analysis (Xiong, et al.)
to be a heme d1 biosynthesis protein by context, perhaps
involved in conversions of acetate groups to methyl
groups in conversion from uroporphyrinogen III.
Length = 351
Score = 25.4 bits (56), Expect = 8.9
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 69 GVYQAEVLAIRNCAEENINMGL 90
G ++A + IRNC +GL
Sbjct: 121 GAFEAALEGIRNCVAVGQKVGL 142
>gnl|CDD|215173 PLN02304, PLN02304, probable pectinesterase.
Length = 379
Score = 25.6 bits (56), Expect = 9.9
Identities = 9/22 (40%), Positives = 14/22 (63%)
Query: 98 FSDSQAALRAIGNFQTKSKITW 119
F+ Q+A+ A+GNF K + W
Sbjct: 87 FTTVQSAVDAVGNFSQKRNVIW 108
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
0.314 0.131 0.387
Gapped
Lambda K H
0.267 0.0683 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,262,384
Number of extensions: 534428
Number of successful extensions: 271
Number of sequences better than 10.0: 1
Number of HSP's gapped: 267
Number of HSP's successfully gapped: 15
Length of query: 128
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 42
Effective length of database: 7,123,158
Effective search space: 299172636
Effective search space used: 299172636
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: 42 (22.0 bits)
S2: 53 (24.3 bits)