RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6025
(89 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 = 38.8 bits (91), Expect = 5e-05
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 6/55 (10%)
Query: 1 MIINMFHENPLVKRVQE--EELSSTDSSIEFLLCPSHVGIAGNEE----AKQATN 49
+ + +PLV R+++ EL++ + P H GI GNE AK+A
Sbjct: 74 ALRSPRSSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERADRLAKEAAK 128
>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 = 27.6 bits (62), Expect = 0.62
Identities = 11/42 (26%), Positives = 16/42 (38%), Gaps = 2/42 (4%)
Query: 9 NPLVKRVQEEELSSTDSSIEFLLCPSHVGIAGNEEAKQATND 50
P+ + E I++ P H GI GNE A +
Sbjct: 84 KPIKNEIWELLQKKHKVYIQW--VPGHSGIPGNELADKLAKQ 123
>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 = 27.6 bits (62), Expect = 0.66
Identities = 14/35 (40%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 10 PLVKRVQEEELSSTDSSIEFLLCPSHVGIAGNEEA 44
L K ++E E ++F P H GI GNEEA
Sbjct: 109 ELDKLLEELEERGIR--VKFWHVPGHSGIYGNEEA 141
>gnl|CDD|183606 PRK12578, PRK12578, acetyl-CoA acetyltransferase; Provisional.
Length = 385
Score = 26.7 bits (59), Expect = 1.6
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 36 VGIAGNEEAKQATNDDVTHQELFFDEIKINIE 67
V + G +K DDV+ QEL ++ IK +
Sbjct: 3 VAVIGVGNSKFGRRDDVSVQELAWESIKEALN 34
>gnl|CDD|235589 PRK05749, PRK05749, 3-deoxy-D-manno-octulosonic-acid transferase;
Reviewed.
Length = 425
Score = 26.3 bits (59), Expect = 2.2
Identities = 12/51 (23%), Positives = 25/51 (49%), Gaps = 7/51 (13%)
Query: 10 PLVKRVQEEELSSTDSSIEFLLCPSHVGIAGNEEAKQATNDDVTHQELFFD 60
PL++ +++ + L+ + + G+E A+ DDV H+ L +D
Sbjct: 68 PLIRALRKRY-----PDLPILV--TTMTPTGSERAQALFGDDVEHRYLPYD 111
>gnl|CDD|187787 cd09656, Cmr3_III-B, CRISPR/Cas system-associated RAMP superfamily
protein Cmr3. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
RAMP superfamily protein; This protein is a subunit of
Cmr complex.
Length = 318
Score = 25.8 bits (57), Expect = 3.4
Identities = 14/67 (20%), Positives = 28/67 (41%), Gaps = 4/67 (5%)
Query: 19 ELSSTDSSIEFLLCPSHVGIAGNEEAKQATNDDVTHQELFF---DEIKINIEKKYLEEWN 75
EL + D E +GIA + E ++ + + + F D++ + + E +
Sbjct: 125 ELHTVDGEEEIFKKEERIGIALDRE-RKVVKEGALYSQRFLRFKDDVGFIVWVEDPEIKD 183
Query: 76 IQNGPIL 82
I G I+
Sbjct: 184 ISPGRIV 190
>gnl|CDD|235262 PRK04235, PRK04235, hypothetical protein; Provisional.
Length = 196
Score = 25.3 bits (56), Expect = 4.1
Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 54 HQELFFDEIKINIEKKYLEE-WNIQNGPILLVQTKT 88
H + +E+ ++KK + W I GPIL V +
Sbjct: 74 HHPVTPEEVLEALKKKQVGRLWLIVQGPILHVAARD 109
>gnl|CDD|178988 PRK00364, groES, co-chaperonin GroES; Reviewed.
Length = 95
Score = 23.9 bits (53), Expect = 8.2
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 1 MIINMFHENPLVKRVQEEE 19
M + + LVKR++EEE
Sbjct: 1 MNLKPLGDRVLVKRLEEEE 19
>gnl|CDD|189790 pfam00980, Rota_Capsid_VP6, Rotavirus major capsid protein VP6.
Rotaviruses consist of three concentric protein shells.
The intermediate (middle) protein layer consists 260
trimers of VP6. VP6 in the most abundant protein in the
virion. VP6 is also involved in virion assembly, and
possesses the ability to interact with VP2, VP4 and VP7.
Length = 396
Score = 24.5 bits (53), Expect = 9.3
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 59 FDEIKINIEKKYLEEWNIQN 78
F I N +Y+E WN+QN
Sbjct: 124 FKRINFNNSSEYIENWNLQN 143
>gnl|CDD|206641 cd00157, Rho, Ras homology family (Rho) of small guanosine
triphosphatases (GTPases). Members of the Rho (Ras
homology) family include RhoA, Cdc42, Rac, Rnd, Wrch1,
RhoBTB, and Rop. There are 22 human Rho family members
identified currently. These proteins are all involved in
the reorganization of the actin cytoskeleton in response
to external stimuli. They also have roles in cell
transformation by Ras in cytokinesis, in focal adhesion
formation and in the stimulation of stress-activated
kinase. These various functions are controlled through
distinct effector proteins and mediated through a
GTP-binding/GTPase cycle involving three classes of
regulating proteins: GAPs (GTPase-activating proteins),
GEFs (guanine nucleotide exchange factors), and GDIs
(guanine nucleotide dissociation inhibitors). Most Rho
proteins contain a lipid modification site at the
C-terminus, with a typical sequence motif CaaX, where a
= an aliphatic amino acid and X = any amino acid. Lipid
binding is essential for membrane attachment, a key
feature of most Rho proteins. Since crystal structures
often lack C-terminal residues, this feature is not
available for annotation in many of the CDs in the
hierarchy.
Length = 171
Score = 24.4 bits (54), Expect = 9.7
Identities = 10/27 (37%), Positives = 14/27 (51%), Gaps = 2/27 (7%)
Query: 64 INIEKKYLEEWN--IQNGPILLVQTKT 88
N++ K+ E N PI+LV TK
Sbjct: 88 ENVKTKWYPEIKHYCPNVPIILVGTKI 114
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
0.313 0.132 0.372
Gapped
Lambda K H
0.267 0.0702 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,416,602
Number of extensions: 351695
Number of successful extensions: 209
Number of sequences better than 10.0: 1
Number of HSP's gapped: 209
Number of HSP's successfully gapped: 18
Length of query: 89
Length of database: 10,937,602
Length adjustment: 57
Effective length of query: 32
Effective length of database: 8,409,424
Effective search space: 269101568
Effective search space used: 269101568
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.2 bits)