RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy663
(275 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 = 80.8 bits (200), Expect = 3e-19
Identities = 38/100 (38%), Positives = 52/100 (52%), Gaps = 5/100 (5%)
Query: 181 ICYTDGSKSPDVTGCAFSI---GDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSD-- 235
+ YTDGSK TG F+I G + RS L P S+F AEL+AI L+ L
Sbjct: 1 VIYTDGSKLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRRAR 60
Query: 236 QFLIVSDSRSALAALANVKFSNPLVTKVFSTWRYLKLCNK 275
+ I SDS++AL AL + + S+PLV ++ R L
Sbjct: 61 KITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGV 100
>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 = 39.6 bits (93), Expect = 2e-04
Identities = 20/79 (25%), Positives = 35/79 (44%), Gaps = 11/79 (13%)
Query: 183 YTDGSKSPDVTGCAFSIGDMVR---------STLLNPINSIFSAELIAIFLCLEAILENP 233
TDGS + G A G ++R +L P + AEL+A+ LE L+
Sbjct: 1 NTDGSCKGNP-GPA-GAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDLG 58
Query: 234 SDQFLIVSDSRSALAALAN 252
+ +I +DS+ + + +
Sbjct: 59 LKKLIIETDSKYVVDLINS 77
>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 = 22/84 (26%), Positives = 32/84 (38%), Gaps = 7/84 (8%)
Query: 182 CYTDGSKSPDVTGCA-FSIGDMVRSTLLNPINSIFSAELIAIFLCLEAILENPSDQFLIV 240
+TDGS G A + D++ L S AELIA+ + A+ I
Sbjct: 2 VFTDGSSFVRKAGYAVVTGPDVLEIATLPYGTSAQRAELIAL---IRALELAKGKPVNIY 58
Query: 241 SDSR---SALAALANVKFSNPLVT 261
+DS L AL + +T
Sbjct: 59 TDSAYAFGILHALETIWKERGFLT 82
>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 = 33.0 bits (76), Expect = 0.044
Identities = 21/73 (28%), Positives = 32/73 (43%), Gaps = 7/73 (9%)
Query: 178 NHTICYTDGS--KSPDVTGCAFSI-GDMVRSTLLNPINSIFSAELIAIFLCLEAILENPS 234
YTDGS +P G + G RS L P + AEL+A+ +EA+
Sbjct: 2 EAVTVYTDGSCNGNPGPGGAGYVTDGGKQRSKPL-PGTTNQRAELLAL---IEALEALSG 57
Query: 235 DQFLIVSDSRSAL 247
+ I +DS+ +
Sbjct: 58 QKVNIYTDSQYVI 70
>gnl|CDD|237936 PRK15295, PRK15295, fimbrial assembly chaperone SthB; Provisional.
Length = 226
Score = 30.3 bits (68), Expect = 0.78
Identities = 24/78 (30%), Positives = 37/78 (47%), Gaps = 8/78 (10%)
Query: 70 RSKLMLNYVAKISASPFNPAQKLLYHQDMSGIIFTVNKPKPLYIRFREVANFNNVLESSE 129
+ KL+ A ++P + +Q+L + G + TVN P P Y+ F V L S E
Sbjct: 128 QIKLIYRPPALTKSTPDSQSQQLKWQTA--GDVITVNNPTPYYMNFASVT-----LNSHE 180
Query: 130 VAPYVRFVPPWSNCAPPV 147
V FVPP S+ + +
Sbjct: 181 VKS-ATFVPPKSSASFKL 197
>gnl|CDD|227564 COG5239, CCR4, mRNA deadenylase, exonuclease subunit and related
nucleases [RNA processing and modification].
Length = 378
Score = 30.1 bits (68), Expect = 1.1
Identities = 13/108 (12%), Positives = 37/108 (34%), Gaps = 7/108 (6%)
Query: 68 LRRSKLMLNYVAKISASPFNPAQKLLYHQDMSGIIFTVNKPKPLYIRFREVANFNNVLES 127
R++ ++LN + + + L++++ + N P ++R+V
Sbjct: 158 FRQTYILLNRIGEKDNIAWVCLFVGLFNKEPGDTPYVANTHLPWDPKYRDVKLI------ 211
Query: 128 SEVAPYVRFVPPWSNCAPPVDQCLGEEKKSDVAPVVFQQKFSEAINTK 175
+ + R + D+ G+ K ++ F+ +
Sbjct: 212 -QCSLLYRELKKVLKEELNDDKEEGDIKSYPEVDILITGDFNSLRASL 258
>gnl|CDD|179567 PRK03355, PRK03355, glycerol-3-phosphate acyltransferase;
Validated.
Length = 783
Score = 27.8 bits (62), Expect = 7.2
Identities = 17/65 (26%), Positives = 27/65 (41%), Gaps = 14/65 (21%)
Query: 47 GALRSSPVVSL-----YVDSGVPPLTLRRSKLMLNYV---AKISASPFNPAQKLLYHQDM 98
L P V L Y+D V P+ ++ ++L +V +S P P +
Sbjct: 262 ALLEEHPAVLLFSHRSYIDGLVVPVAMQENRLPPVHVFGGINLSFGPMGPIMR------R 315
Query: 99 SGIIF 103
SG+IF
Sbjct: 316 SGMIF 320
>gnl|CDD|239476 cd03381, PAP2_glucose_6_phosphatase, PAP2_like proteins,
glucose-6-phosphatase subfamily. Glucose-6-phosphatase
converts glucose-6-phosphate into free glucose and is
active in the lumen of the endoplasmic reticulum, where
it is bound to the membrane. The generation of free
glucose is an important control point in metabolism, and
stands at the end of gluconeogenesis and the release of
glucose from glycogen. Deficiency of
glucose-6-phosphatase leads to von Gierke's disease.
Length = 235
Score = 27.3 bits (61), Expect = 8.5
Identities = 11/39 (28%), Positives = 16/39 (41%), Gaps = 5/39 (12%)
Query: 196 AFSIGDMVRSTLLNPINSIFSAEL-----IAIFLCLEAI 229
A I + + + I I+SA L I FL A+
Sbjct: 138 AGVISGIAVAETFSHIRYIYSASLKRYVLITFFLFGFAL 176
>gnl|CDD|236115 PRK07854, PRK07854, enoyl-CoA hydratase; Provisional.
Length = 243
Score = 27.3 bits (61), Expect = 8.5
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 62 GVPPLTLRRSKLMLNYVAKISASPFNPAQKLLYHQ 96
G+ PL L+ +K +LN I + PA K L+ +
Sbjct: 186 GLAPLALQHAKRVLNDDGAIEEAW--PAHKELFDK 218
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 0.400
Gapped
Lambda K H
0.267 0.0775 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,741,905
Number of extensions: 1274912
Number of successful extensions: 929
Number of sequences better than 10.0: 1
Number of HSP's gapped: 926
Number of HSP's successfully gapped: 14
Length of query: 275
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 179
Effective length of database: 6,679,618
Effective search space: 1195651622
Effective search space used: 1195651622
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: 58 (26.0 bits)